diff --git a/.gitignore b/.gitignore new file mode 100644 index 0000000000000000000000000000000000000000..0c9e2900afda92428aa5ce1bb99737415051619d --- /dev/null +++ b/.gitignore @@ -0,0 +1,263 @@ +# ============================================================================= +# Python +# ============================================================================= + +# Byte-compiled / optimized / DLL files +__pycache__/ +*.py[cod] +*$py.class +# Distribution / packaging +.Python +build/ +develop-eggs/ +dist/ +downloads/ +eggs/ +.eggs/ +lib/ +lib64/ +parts/ +sdist/ +var/ +wheels/ +pip-wheel-metadata/ +share/python-wheels/ +*.egg-info/ +.installed.cfg +*.egg +MANIFEST + +# PyInstaller +*.manifest +*.spec + +# Installer logs +pip-log.txt +pip-delete-this-directory.txt + +# Unit test / coverage reports +htmlcov/ +.tox/ +.nox/ +.coverage +.coverage.* +.cache +nosetests.xml +coverage.xml +*.cover +*.py,cover +.hypothesis/ +.pytest_cache/ + +# Translations +*.mo +*.pot + +# Sphinx documentation +docs/_build/ + +# PyBuilder +target/ + +# IPython / Jupyter Notebook +.ipynb_checkpoints +*.ipynb_checkpoints/ +profile_default/ +ipython_config.py + +# pyenv +.python-version + +# pipenv +Pipfile.lock + +# poetry +poetry.lock + +# PEP 582 +__pypackages__/ + +# Celery +celerybeat-schedule +celerybeat.pid + +# SageMath parsed files +*.sage.py + +# Environments +.env +.venv +env/ +venv/ +ENV/ +env.bak/ +venv.bak/ +.conda/ +conda-env/ + +# Spyder project settings +.spyderproject.db +.spyproject + +# Rope project settings +.ropeproject + +# mkdocs documentation +/site + +# mypy +.mypy_cache/ +.dmypy.json +dmypy.json + +# Pyre type checker +.pyre/ + +# pytype +.pytype/ + +# Cython debug symbols +cython_debug/ + + +# ============================================================================= +# PyTorch / Deep Learning +# ============================================================================= + +# Model checkpoints & weights +*.pt +*.pth +*.ckpt +*.bin +*.safetensors +checkpoints/ +saved_models/ +weights/ +pretrained/ + +# TensorBoard logs +runs/ +logs/ +tb_logs/ +tensorboard_logs/ +lightning_logs/ + +# MLflow +mlruns/ +mlflow/ + +# Weights & Biases +wandb/ + +# Hydra outputs +outputs/ +multirun/ +.hydra/ + +# ONNX models +*.onnx + +# TorchScript +*.torchscript + +# CUDA profiling +*.nvvp +*.nvprof +*.qdrep + +# Data directories (customize as needed) +data/raw/ +data/processed/ +data/interim/ +datasets/ + +# Large result files +results/ +predictions/ +evaluations/ + +# Experiment configs with secrets +secrets.yaml +secrets.yml +.secrets + + +# ============================================================================= +# IDE / Editor +# ============================================================================= + +# VSCode +.vscode/ +*.code-workspace + +# PyCharm / JetBrains +.idea/ +*.iml +*.iws +*.ipr + +# Vim +*.swp +*.swo +*~ + +# Emacs +\#*\# +.\#* + +# Sublime Text +*.sublime-project +*.sublime-workspace + + +# ============================================================================= +# OS +# ============================================================================= + +# macOS +.DS_Store +.AppleDouble +.LSOverride +._* +.Spotlight-V100 +.Trashes + +# Windows +Thumbs.db +ehthumbs.db +Desktop.ini +$RECYCLE.BIN/ +*.lnk + +# Linux +*~ + + +# ============================================================================= +# Misc +# ============================================================================= + +# Compressed files +*.zip +*.tar.gz +*.tar.bz2 +*.rar +*.7z + +# Temporary files +*.tmp +*.temp +*.bak +*.orig + +# Secrets & credentials +.env.local +.env.*.local +*.pem +*.key +config/secrets.* + +# ============================================================================= +# Project specific +# ============================================================================= +csp_results/ \ No newline at end of file diff --git a/config.sh b/config.sh new file mode 100755 index 0000000000000000000000000000000000000000..c3076ab82182cdacb4e13c95f4b37ea638c07123 --- /dev/null +++ b/config.sh @@ -0,0 +1,70 @@ +#!/bin/bash +# ============================================================================= +# BOMLIP-CSP Configuration File +# ============================================================================= +# This file contains all configurable parameters for the crystal structure +# search and generation pipeline. Modify the values below to customize +# your run. +# ============================================================================= + +# ----------------------------------------------------------------------------- +# [Molecular Parameters] +# SMILES string of the input molecule(s). +# Use '.' (dot) to separate multiple molecules for co-crystal generation. +# Example single molecule: "C1CC2=COC=C12" +# Example co-crystal: "C1CC2=COC=C12.CCO" +SMILES="C1CC2=COC=C12" + +# Number of conformers to generate during the conformer search step. +# Higher values explore more conformational space but take longer. +# Set to 0 to skip generation and only load existing conformers. +GENERATE_CONFORMERS=10 + +# Number of conformers to actually use for crystal structure generation. +# Must be <= the number of generated conformers. +# Set to 0 to skip structure generation. +USE_CONFORMERS=4 + +# Number of molecules in the unit cell (Z'). +# Use comma-separated values for multiple molecule types (co-crystal), +# e.g. "1,1" means 1 copy of each molecule in the asymmetric unit. +# Use space-separated values for multiple packings, e.g. "1 2". +MOLECULE_NUM_IN_CELL=1 + +# ----------------------------------------------------------------------------- +# [Crystal Structure Parameters] +# Space group numbers for structure generation. +# Use comma-separated values within a packing, and space-separated +# values for multiple packings. +# Example: "14,61" means search space groups P21/c and Pbca in one packing. +# Example: "14 61" means P21/c in packing 1, Pbca in packing 2. +SPACE_GROUP_LIST="14,61" + +# Prefix name added to the output CIF files. +# Use space-separated values for multiple packings. +ADD_NAME="XULDUD" + +# Number of crystal structures to generate per (space group, conformer) combination. +# Use space-separated values for multiple packings. +NUM_GENERATION=100 + +# ----------------------------------------------------------------------------- +# [Compute Parameters] +# Maximum number of parallel workers for structure generation. +# Should not exceed the number of available CPU cores. +MAX_WORKERS=16 + +# ----------------------------------------------------------------------------- +# [Run Mode] +# Execution mode controlling which steps are performed. +# Available options: +# all - Run conformer search followed by structure generation (default) +# conformer_only - Only perform conformer search +# structure_only - Skip conformer search, use existing conformers to generate structures +MODE="all" + +# ----------------------------------------------------------------------------- +# [Path Parameters] +# Directory for storing intermediate conformers and output CIF structures. +# Relative to the project root directory. +OUTPUT_DIR="csp_results" diff --git a/mace-bench/3rdparty/SevenNet/CHANGELOG.md b/mace-bench/3rdparty/SevenNet/CHANGELOG.md deleted file mode 100644 index 83bbe2d29deea02fe9679d1e44f4c7e1100edd03..0000000000000000000000000000000000000000 --- a/mace-bench/3rdparty/SevenNet/CHANGELOG.md +++ /dev/null @@ -1,154 +0,0 @@ -# Changelog -All notable changes to this project will be documented in this file. - - -## [0.11.1] -From here, the version of 'main' branch has 'devX' after it diverges from the latest stable version - -CLI interface changed in backward-compatible manner. Now `sevenn` has subcommands for -inference, train, etc - -### Added -- subcommand with some aliases -- strict e3nn version requirement from __init__.py - -### Changed -- pre-commit uses python3.11 -- cuequivaraiance optional libraries -- some gitignores - -### Fixed -- Circular import in sevenn.checkpoint (dev0) -- Fix typing issues - - -## [0.11.0] - -Multi-fidelity learning implemented & New pretrained-models - -### Added -- Build multi-fidelity model, SevenNet-MF, based on given modality in the yaml -- Modality support for sevenn_inference, sevenn_get_modal, and SevenNetCalculator -- sevenn_cp tool for checkpoint summary, input generation, multi-modal routines -- Modality append / assign using sevenn_cp -- Loss weighting for energy, force and stress for corresponding data label -- Ignore unlabelled data when calculating loss. (e.g. stress data for non-pbc structure) -- Dict style dataset input for multi-modal and data-weight -- (experimental) cuEquivariance support -- Downloading large checkpoints from url (7net-MF-ompa, 7net-omat) -- D3 wB97M param - -### Changed -- Sort instructions of tensor product in convolution (+ fix flipped w3j coeff of old model) -- Lazy initialization for `IrrepsLinear` and `SelfConnection*` -- Checkpoint things using `sevenn/checkpoint.py` -- e3nn >= 0.5.0, to ensure changed CG coeff later on -- pandas as dependency -- old v1 presets are removed, liquid electrolyte fine-tune yaml is added - -### Fixed -- More refactor for shift scale things + few bug fixes -- Correctly shuffle training set when distributed training is enabled -- D3 calculator system swap memory error fixed -- D3 compile uses $HOME/.cache if package directory is not writable - - -## [0.10.4] -### Added -- feats: D3 calculator -### Fixed -- bug: info dict sharing (therefore energy stress) when structure_list used -- torch >= 2.5.0 works -- numpy >= 2.0 works (need more testing) -### Changed -- sevennet_calculator.py => calculator -- fine tunine preset to use original loss function (Huber) and loss weights - - -## [0.10.3] -### Added -- SevenNet-l3i5, checkpoint, preset. (keywords: 7net-l3i5, sevennet-l3i5) -- SevenNet-l3i5 test -### Changed -- Now --help do not load unnecessary imports (fast!) -- README - - -## [0.10.2] -### Added -- Accelerated graph build routine if matscipy is installed @hexagonerose -- matscipy vs. ase neighborlist unit test -- If valid set is not given but data_divide_ratio is given, validaset is created using random split. (shift, scale, and conv_denoiminator uses original whole statistics) -### Changed -- matscipy is included as dependency -- data_divide_ration defaults to 0.0 (not used) -### Fixed -- For torch version >= 2.4.0, Loading graph dataset no more raises warnings. -- Raise error when unknown element is found (SevenNetCalculator) - -## [0.10.1] -### Added -- experimental `SevenNetAtomsDataset` which is memory efficient, can be enabled with `dataset_type='atoms'` -- Save meta data & statistics when the `SevenNetGraphDataset` saves its data. -### Changed -- Save checkpoint_0.pth (model before any training) -- `SevenNetGraphDataset._file_to_graph_list` -> `SevenNetGraphDataset.file_to_graph_list` -- Refactoring `SevenNetGraphDataset`, skips computing statistics if it is loaded, more detailed logging -- Prefer use .get when accessing config dict -### Fixed -- Fix error when loading `SevenNetGraphDataset` with other types of data (ex: extxyz) in one dataset - - -## [0.10.0] -SevenNet now have CI workflows using pytest and its coverage is 78%! -Substantial changes in cli apps and some outputs. - -### Added -- [train_v2]: train_v2, with lots of refactoring + support `load_testset_path`. Original routine is accessible: `sevenn -m train_v1`. -- [train_v2]: `SevenNetGraphDataset` replaces old `AtomGrpahDataset`, which extends `InMemoryDataset` of PyG. -- [train_v2]: `sevenn_graph_build` for SevenNetGraphDataset. Previous .sevenn_data is accessible with --legacy option -- [train_v2]: Any number of additional datasets will be evaluated and recorded if it is given as 'load_{NAME}set_path' key (input.yaml). -- 'Univ' keyword for 'chemical_species' -- energy_key, force_key, stress_key options for `sevenn_graph_build`, @thangckt -- OpenMPI distributed training @thangckt -### Changed -- Read EFS of atoms from y_* keys of .info or .arrays dict, instead of caclculator results -- Now `type_map` and requires_grad is hidden inside `AtomGraphSequential`, and don't need to care about it. -- `log.sevenn` and `lc.csv` automatically find a safe filename (log0.sevenn, log1.sevenn, ...) to avoid overwriting. -- [train_v2]: train_v2 loads its training set via `load_trainset_path`, rather than previous `load_dataset_path`. -- [train_v2]: log.csv -> lc.csv, and columns have no units, (easier to postprocess with it) but still on `log.sevenn`. -### Fixed -- [e3gnn_serial]: can continue simulation even when atom tag becomes not consecutive (removing atom dynamically), @gasplant64 -- [e3gnn_parallel]: undefined behavior when there is no atoms to send/recv (for non pbc system) -- [e3gnn_parallel]: incorrect force/stress in some edge cases (too small simulation cell & 2 process) -- [e3gnn_parallel]: revert commit 14851ef, now e3gnn_parallel is sane. -- [e3gnn_*]: += instead of = when saving virial stress and forces @gasplant64 -- Now Logger correctly closes a file. -- ... and lots of small bugs I found during writing `pytest`. - -## [0.9.5] -### Note -This version is not stable, but I tag it as v0.9.5 before making further changes. -LAMMPS `pair_e3gnn_parallel.*` should be re-compiled for the below changes regarding LAMMPS parallel. -This is the first changelog and may not reflect all the changes. -### Added -- Stress compute for LAMMPS sevennet parallel -- `sevenn_inference` now takes .extxyz input -- `sevenn_inference` gives MAE error -- Experimental `sevenn_inference` on the fly graph build option -### Changed -- **[Breaking]** Parallel LAMMPS model changed, old deployed parallel models will not work -- **[Breaking]** Parallel LAMMPS takes the directory of potentials as input. Accordingly, `sevenn_get_model -p` creates a folder with potentials. -- **[Breaking]** Except for serial LAMMPS models, force and stress are computed from gradients of edge vectors, not positions. -- Separate interaction block from model build -- Add typing for most of functions -- Remove clang pre-commit hook as it breaks lammps pair files -- `torch.load` with `weights_only=False` -- Line length limit 80 -> 85 -- Refactor -### Fixed -- Correct batch size for SevenNet-0(11July2024) - -## [0.9.4] - 2024-08-26 -### Added -- D3 correction (contributed from dambi3613) for LAMMPS serial diff --git a/mace-bench/3rdparty/SevenNet/LICENSE b/mace-bench/3rdparty/SevenNet/LICENSE deleted file mode 100644 index 3877ae0a7ff6f94ac222fd704e112723db776114..0000000000000000000000000000000000000000 --- a/mace-bench/3rdparty/SevenNet/LICENSE +++ /dev/null @@ -1,674 +0,0 @@ - GNU GENERAL PUBLIC LICENSE - Version 3, 29 June 2007 - - Copyright (C) 2007 Free Software Foundation, Inc. - Everyone is permitted to copy and distribute verbatim copies - of this license document, but changing it is not allowed. - - Preamble - - The GNU General Public License is a free, copyleft license for -software and other kinds of works. - - The licenses for most software and other practical works are designed -to take away your freedom to share and change the works. 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If your program is a subroutine library, you -may consider it more useful to permit linking proprietary applications with -the library. If this is what you want to do, use the GNU Lesser General -Public License instead of this License. But first, please read -. diff --git a/mace-bench/3rdparty/SevenNet/README.md b/mace-bench/3rdparty/SevenNet/README.md deleted file mode 100644 index 9678f7f27cf3e5346a05a5debd8bf2036e34c861..0000000000000000000000000000000000000000 --- a/mace-bench/3rdparty/SevenNet/README.md +++ /dev/null @@ -1,387 +0,0 @@ - -Alt text - -# SevenNet - -SevenNet (Scalable EquiVariance-Enabled Neural Network) is a graph neural network (GNN)-based interatomic potential package that supports parallel molecular dynamics simulations using [`LAMMPS`](https://lammps.org). Its core model is based on [`NequIP`](https://github.com/mir-group/nequip). - -> [!NOTE] -> We will soon release a CUDA-accelerated version of SevenNet, which will significantly increase the speed of our pretrained models on [Matbench Discovery](https://matbench-discovery.materialsproject.org/). - -## Features - - Pretrained GNN interatomic potential and fine-tuning interface - - Support for the Python [Atomic Simulation Environment (ASE)](https://wiki.fysik.dtu.dk/ase/) calculator - - GPU-parallelized molecular dynamics with LAMMPS - - CUDA-accelerated D3 (van der Waals) dispersion - - Multi-fidelity training for combining multiple databases with different calculation settings ([Usage](https://github.com/MDIL-SNU/SevenNet/blob/main/sevenn/pretrained_potentials/SevenNet_MF_0/README.md)) - -## Pretrained models -So far, we have released multiple pretrained SevenNet models. Each model has various hyperparameters and training sets, leading to different levels of accuracy and speed. Please read the descriptions below carefully and choose the model that best suits your purpose. -We provide the F1 score, and RMSD for the WBM dataset, along with $\kappa_{\mathrm{SRME}}$ from phononDB and CPS (Combined Performance Score). For details on these metrics and performance comparisons with other pretrained models, please visit [Matbench Discovery](https://matbench-discovery.materialsproject.org/). - -These models can be used as interatomic potentials in LAMMPS and loaded through the ASE calculator using each model’s keywords. Please refer to the [ASE calculator](#ase_calculator) section for instructions on loading a model via the ASE calculator. -Additionally, `keywords` can be used in other parts of SevenNet, such as `sevenn_inference`, `sevenn_get_model`, and the `checkpoint` section in `input.yaml` for fine-tuning. - -**Acknowledgments**: The models trained on [`MPtrj`](https://figshare.com/articles/dataset/Materials_Project_Trjectory_MPtrj_Dataset/23713842) were supported by the Neural Processing Research Center program at Samsung Advanced Institute of Technology, part of Samsung Electronics Co., Ltd. The computations for training models were carried out using the Samsung SSC-21 cluster. - ---- - -### **SevenNet-MF-ompa (17Mar2025)** -> Model keywords: `7net-mf-ompa` | `SevenNet-mf-ompa` - -**This is our recommended pretrained model** - -This model leverages [multi-fidelity learning](https://pubs.acs.org/doi/10.1021/jacs.4c14455) to train simultaneously on the [MPtrj](https://figshare.com/articles/dataset/Materials_Project_Trjectory_MPtrj_Dataset/23713842), [sAlex](https://huggingface.co/datasets/fairchem/OMAT24), and [OMat24](https://huggingface.co/datasets/fairchem/OMAT24) datasets. This model is the best among our pretrained models and achieves a high ranking on the [Matbench Discovery]((https://matbench-discovery.materialsproject.org/)) leaderboard. Our evaluations show that it outperforms other models on most tasks, except for the isolated molecule energy task, where it performs slightly worse than `SevenNet-l3i5`. - -```python -from sevenn.calculator import SevenNetCalculator -# "mpa" refers to the MPtrj + sAlex modal, used for evaluating Matbench Discovery. -calc = SevenNetCalculator('7net-mf-ompa', modal='mpa') # Use modal='omat24' for OMat24-trained modal weights. -``` -> [!NOTE] -> Each modal is expected to produce results that are more consistent with the DFT settings in the training datasets (e.g., `mpa`, trained on the combined [MPtrj](https://figshare.com/articles/dataset/Materials_Project_Trjectory_MPtrj_Dataset/23713842) and [sAlex](https://huggingface.co/datasets/fairchem/OMAT24) datasets; `omat24`, trained on the [OMat24](https://huggingface.co/datasets/fairchem/OMAT24) dataset). For detailed DFT settings, please refer to their papers. - -When using the command-line interface of SevenNet, include the `--modal mpa` or `--modal omat24` option to select the desired modality. - - -#### **Matbench Discovery** -| CPS | F1 | $\kappa_{\mathrm{SRME}}$ | RMSD | -|:---:|:---:|:---:|:---:| -|**0.883**|**0.901**|0.317| **0.0115** | - -[Detailed instructions for multi-fidelity learning](https://github.com/MDIL-SNU/SevenNet/blob/main/sevenn/pretrained_potentials/SevenNet_MF_0/README.md) - -[Download link for fully detailed checkpoint](https://figshare.com/articles/software/7net_MF_ompa/28590722?file=53029859) - ---- -### **SevenNet-omat (17Mar2025)** -> Model keywords: `7net-omat` | `SevenNet-omat` - - This model was trained exclusively on the [OMat24](https://huggingface.co/datasets/fairchem/OMAT24) dataset. It achieves high performance in $\kappa_{\mathrm{SRME}}$ on [Matbench Discovery](https://matbench-discovery.materialsproject.org/), but its F1 score is unavailable due to a difference in the POTCAR version. Like `SevenNet-MF-ompa`, this model outperforms `SevenNet-l3i5` on most tasks, except for the isolated molecule energy. - -[Download link for fully detailed checkpoint](https://figshare.com/articles/software/SevenNet_omat/28593938). - -#### **Matbench Discovery** -* $\kappa_{\mathrm{SRME}}$: **0.221** ---- -### **SevenNet-l3i5 (12Dec2024)** -> Model keywords: `7net-l3i5` | `SevenNet-l3i5` - -This model increases the maximum spherical harmonic degree ($l_{\mathrm{max}}$) to 3, compared to `SevenNet-0`, which has an $l_{\mathrm{max}}$ of 2. While **l3i5** offers improved accuracy for various systems, it is approximately four times slower than `SevenNet-0`. - -#### **Matbench Discovery** -| CPS | F1 | $\kappa_{\mathrm{SRME}}$ | RMSD | -|:---:|:---:|:---:|:---:| -|0.764 |0.76|0.55|0.0182| - ---- - -### **SevenNet-0 (11Jul2024)** -> Model keywords:: `7net-0` | `SevenNet-0` | `7net-0_11Jul2024` | `SevenNet-0_11Jul2024` - -This model is one of our earliest pretrained models. Although we recommend using newer and more accurate models, it can still be useful in certain cases due to its shortest inference time. The model was trained on the [MPtrj](https://figshare.com/articles/dataset/Materials_Project_Trjectory_MPtrj_Dataset/23713842) and is loaded as the default pretrained model in the ASE calculator. -For more information, click [here](sevenn/pretrained_potentials/SevenNet_0__11Jul2024). - -#### **Matbench Discovery** -| F1 | $\kappa_{\mathrm{SRME}}$ | -|:---:|:---:| -|0.67|0.767| - ---- - -You can find our legacy models in [pretrained_potentials](./sevenn/pretrained_potentials). - -## Contents -- [Installation](#installation) -- [Usage](#usage) - - [ASE calculator](#ase-calculator) - - [Training & inference](#training-and-inference) - - [Notebook tutorials](#notebook-tutorial) - - [MD simulation with LAMMPS](#md-simulation-with-lammps) - - [Installation](#installation) - - [Single-GPU MD](#single-gpu-md) - - [Multi-GPU MD](#multi-gpu-md) - - [Application of SevenNet-0](#application-of-sevennet-0) -- [Citation](#citation) - -## Installation -### Requirements -- Python >= 3.8 -- PyTorch >= 2.0.0, PyTorch =< 2.5.2 - -For CUDA version, refer to PyTorch's compatibility matrix: https://github.com/pytorch/pytorch/blob/main/RELEASE.md#release-compatibility-matrix - -> [!IMPORTANT] -> Please install PyTorch manually based on your hardware before installing SevenNet. - -Once PyTorch is successfully installed, please run the following command: -```bash -pip install sevenn -pip install git+https://github.com/MDIL-SNU/SevenNet.git # for the latest main branch -``` -We strongly recommend checking `CHANGELOG.md` for new features and changes, as SevenNet is under active development. - -## Usage -### ASE calculator - -SevenNet provides an ASE interface via the ASE calculator. Models can be loaded using the following Python code: -```python -from sevenn.calculator import SevenNetCalculator -# The 'modal' argument is required if the model is trained with multi-fidelity learning enabled. -calc_mf_ompa = SevenNetCalculator(model='7net-mf-ompa', modal='mpa') -``` -SevenNet also supports CUDA-accelerated D3 calculations. -```python -from sevenn.calculator import SevenNetD3Calculator -calc = SevenNetD3Calculator(model='7net-0', device='cuda') -``` -If you encounter the error `CUDA is not installed or nvcc is not available`, please ensure the `nvcc` compiler is available. Currently, CPU + D3 is not supported. - -Various pretrained SevenNet models can be accessed by setting the model variable to predefined keywords like `7net-mf-ompa`, `7net-omat`, `7net-l3i5`, and `7net-0`. - -Additionally, user-trained models can be applied with the ASE calculator. In this case, the `model` parameter should be set to the checkpoint path from training. - -> [!TIP] -> When 'auto' is passed to the `device` parameter (the default setting), SevenNet utilizes GPU acceleration if available. - -### Training and inference - -SevenNet provides five commands for preprocessing, training, and deployment: `sevenn_preset`, `sevenn_graph_build`, `sevenn`, `sevenn_inference`, and `sevenn_get_model`. - -#### 1. Input generation - -With the `sevenn_preset` command, the input file setting the training parameters is generated automatically. -```bash -sevenn_preset {preset keyword} > input.yaml -``` - -Available preset keywords are: `base`, `fine_tune`, `multi_modal`, `sevennet-0`, and `sevennet-l3i5`. -Check comments in the preset YAML files for explanations. For fine-tuning, be aware that most model hyperparameters cannot be modified unless explicitly indicated. -To reuse a preprocessed training set, you can specify `sevenn_data/${dataset_name}.pt` for the `load_trainset_path:` in the `input.yaml`. - -#### 2. Preprocess (optional) - -To obtain the preprocessed data, `sevenn_data/graph.pt`, `sevenn_graph_build` command can be used. -The output files can be used for training (`sevenn`) or inference (`sevenn_inference`) to skip the graph build stage. - -```bash -sevenn_graph_build {dataset path} {cutoff radius} -``` - -The output `sevenn_data/graph.yaml` contains statistics and meta information about the dataset. -These files must be located in the `sevenn_data` directory. If you move the dataset, move the entire `sevenn_data` directory without changing the contents. - -See `sevenn_graph_build --help` for more information. - -#### 3. Training - -Given that `input.yaml` and `sevenn_data/graph.pt` are prepared, SevenNet can be trained by the following command: - -```bash -sevenn input.yaml -s -``` - -We support multi-GPU training using PyTorch DDP (distributed data parallel) with a single process (or a CPU core) per GPU. - -```bash -torchrun --standalone --nnodes {number of nodes} --nproc_per_node {number of GPUs} --no_python sevenn input.yaml -d -``` - -Please note that `batch_size` in `input.yaml` refers to the per-GPU batch size. - -#### 4. Inference - -Using the checkpoint after training, the properties such as energy, force, and stress can be inferred directly. - -```bash -sevenn_inference checkpoint_best.pth path_to_my_structures/* -``` - -This will create the `sevenn_infer_result` directory, where CSV files contain predicted energy, force, stress, and their references (if available). -See `sevenn_inference --help` for more information. - -#### 5. Deployment - -The checkpoint can be deployed as LAMMPS potentials. The argument is either the path to the checkpoint or the name of a pretrained potential. - -```bash -sevenn_get_model 7net-0 -sevenn_get_model {checkpoint path} -``` - -This will create `deployed_serial.pt`, which can be used as a LAMMPS potential with the `e3gnn` pair_style in LAMMPS. - -The potential for parallel MD simulation can be obtained similarly. - -```bash -sevenn_get_model 7net-0 -p -sevenn_get_model {checkpoint path} -p -``` - -This will create a directory with several `deployed_parallel_*.pt` files. The directory path itself is an argument for the LAMMPS script. Please do not modify or remove files in the directory. -These models can be used as LAMMPS potentials to run parallel MD simulations with a GNN potential across multiple GPUs. - -### Notebook tutorials - -If you want to learn how to use the `sevenn` Python library instead of the CLI command, please check out the notebook tutorials below. - -| Notebooks | Google Colab | Descriptions | -|-----------|-------------------|--------------| -|[From scratch](https://github.com/MDIL-SNU/sevennet_tutorial/blob/main/notebooks/SevenNet_python_tutorial.ipynb)|[![Open in Google Colab]](https://colab.research.google.com/github/MDIL-SNU/sevennet_tutorial/blob/main/notebooks/SevenNet_python_tutorial.ipynb)|We can learn how to train the SevenNet from scratch, predict energy, forces, and stress using the trained model, perform structure relaxation, and draw EOS curves.| -|[Fine-tuning](https://github.com/MDIL-SNU/sevennet_tutorial/blob/main/notebooks/SevenNet_finetune_tutorial.ipynb)|[![Open in Google Colab]](https://colab.research.google.com/github/MDIL-SNU/sevennet_tutorial/blob/main/notebooks/SevenNet_finetune_tutorial.ipynb)|We can learn how to fine-tune the SevenNet and compare the results of the pretrained model with the fine-tuned model.| - -[Open in Google Colab]: https://colab.research.google.com/assets/colab-badge.svg - -Sometimes, the Colab environment may crash due to memory issues. If you have sufficient GPU resources in your local environment, we recommend downloading the tutorials from GitHub and running them on your machine. -```bash -git clone https://github.com/MDIL-SNU/sevennet_tutorial.git -``` - -### MD simulation with LAMMPS - -#### Installation - -##### Requirements -- PyTorch (it is recommended to use the same version as used during training) -- LAMMPS version of `stable_2Aug2023_update3` -- MKL library -- [`CUDA-aware OpenMPI`](https://www.open-mpi.org/faq/?category=buildcuda) for parallel MD (optional) - -If your cluster supports the Intel MKL module (often included with Intel OneAPI, Intel Compiler, and other Intel-related modules), load that module. - -CUDA-aware OpenMPI is optional but recommended for parallel MD. If it is not available, GPUs will communicate via the CPU when running in parallel mode. It is still faster than using only one GPU, but its efficiency is lower. - -> [!IMPORTANT] -> CUDA-aware OpenMPI does not support NVIDIA gaming GPUs. Since the software is closely tied to hardware specifications, please consult your server administrator if CUDA-aware OpenMPI is unavailable. - -###### 1. Build LAMMPS with cmake. - -Ensure the LAMMPS version is `stable_2Aug2023_update3`. You can easily switch the version using Git. After switching the version, run `sevenn_patch_lammps` with the LAMMPS directory path as an argument. - -```bash -git clone https://github.com/lammps/lammps.git lammps_sevenn --branch stable_2Aug2023_update3 --depth=1 -sevenn_patch_lammps ./lammps_sevenn {--d3} -``` -You can refer to `sevenn/pair_e3gnn/patch_lammps.sh` for details of the patch process. - -> [!TIP] -> Add `--d3` option to install GPU-accelerated [Grimme's D3 method](https://doi.org/10.1063/1.3382344) pair style. For its usage and details, click [here](sevenn/pair_e3gnn). - -```bash -cd ./lammps_sevenn -mkdir build -cd build -cmake ../cmake -DCMAKE_PREFIX_PATH=`python -c 'import torch;print(torch.utils.cmake_prefix_path)'` -make -j4 -``` - -If the error `MKL_INCLUDE_DIR NOT-FOUND` occurs, please check the environment variable or read the `Possible solutions` section below. -If compilation completes without any errors, please skip this. - -
-Possible solutions - -###### 2. Install mkl-include via conda - -```bash -conda install -c intel mkl-include -conda install mkl-include # if the above failed -``` - -###### 3. Append `DMKL_INCLUDE_DIR` to the cmake command and repeat step 1 - -```bash -cmake ../cmake -DCMAKE_PREFIX_PATH=`python -c 'import torch;print(torch.utils.cmake_prefix_path)'` -DMKL_INCLUDE_DIR=$CONDA_PREFIX/include -``` - -If the `undefined reference to XXX` error with `libtorch_cpu.so` occurs, check the `$LD_LIBRARY_PATH`. -If PyTorch is installed using Conda, `libmkl_*.so` files can be found in `$CONDA_PREFIX/lib`. -Ensure that `$LD_LIBRARY_PATH` includes `$CONDA_PREFIX/lib`. - -For other error cases, solution can be found in the [`pair-nequip`](https://github.com/mir-group/pair_nequip) repository, as we share the same architecture. - -
- -If the compilation is successful, the executable `lmp` can be found at `{path_to_lammps_dir}/build`. -To use this binary easily, create a soft link to your bin directory, which should be included in your `$PATH`. - -```bash -ln -s {absolute_path_to_lammps_directory}/build/lmp $HOME/.local/bin/lmp -``` - -This allows you to run the binary using `lmp -in my_lammps_script.lmp`. - -#### Single-GPU MD - -For single-GPU MD simulations, the `e3gnn` pair_style should be used. A minimal input script is provided below: -```txt -units metal -atom_style atomic -pair_style e3gnn -pair_coeff * * {path to serial model} {space separated chemical species} -``` - -#### Multi-GPU MD - -For multi-GPU MD simulations, the `e3gnn/parallel` pair_style should be used. A minimal input script is provided below: -```txt -units metal -atom_style atomic -pair_style e3gnn/parallel -pair_coeff * * {number of message-passing layers} {directory of parallel model} {space separated chemical species} -``` - -For example, - -```txt -pair_style e3gnn/parallel -pair_coeff * * 4 ./deployed_parallel Hf O -``` -The number of message-passing layers corresponds to the number of `*.pt` files in the `./deployed_parallel` directory. - -To deploy LAMMPS models from checkpoints for both serial and parallel execution, use [`sevenn_get_model`](#deployment). - -It is expected that there is one GPU per MPI process. If the number of available GPUs is less than the number of MPI processes, the simulation may run inefficiently. - -> [!CAUTION] -> Currently, the parallel version encounters an error when one of the subdomain cells contains no atoms. This issue can be addressed using the `processors` command and, more effectively, the `fix balance` command in LAMMPS. A patch for this issue will be released in a future update. - -### Application of SevenNet-0 -If you are interested in practical applications of SevenNet, please refer to [this paper](https://arxiv.org/abs/2501.05211) (data available on [Zenodo](https://doi.org/10.5281/zenodo.15205477)). -This study utilized SevenNet-0 for simulating liquid electrolytes. - -The fine-tuning procedure and associated input files are accessible through the links above, specifically within the `Fine-tuning.tar.xz` archive on Zenodo. - -The YAML file used for fine-tuning can be obtained using the following command: -```bash -sevenn_preset fine_tune_le > input.yaml -``` - -## Citation - -If you use this code, please cite our paper: -```txt -@article{park_scalable_2024, - title = {Scalable Parallel Algorithm for Graph Neural Network Interatomic Potentials in Molecular Dynamics Simulations}, - volume = {20}, - doi = {10.1021/acs.jctc.4c00190}, - number = {11}, - journal = {J. Chem. Theory Comput.}, - author = {Park, Yutack and Kim, Jaesun and Hwang, Seungwoo and Han, Seungwu}, - year = {2024}, - pages = {4857--4868}, -} -``` - -If you utilize the multi-fidelity feature of this code or the pretrained model SevenNet-MF-ompa, please cite the following paper: -```txt -@article{kim_sevennet_mf_2024, - title = {Data-Efficient Multifidelity Training for High-Fidelity Machine Learning Interatomic Potentials}, - volume = {147}, - doi = {10.1021/jacs.4c14455}, - number = {1}, - journal = {J. Am. Chem. Soc.}, - author = {Kim, Jaesun and Kim, Jisu and Kim, Jaehoon and Lee, Jiho and Park, Yutack and Kang, Youngho and Han, Seungwu}, - year = {2024}, - pages = {1042--1054}, -``` diff --git a/mace-bench/3rdparty/SevenNet/SevenNet_logo.png b/mace-bench/3rdparty/SevenNet/SevenNet_logo.png deleted file mode 100644 index 435ac0a8d318af80dc34fffef7a6ed0e58b31934..0000000000000000000000000000000000000000 Binary files a/mace-bench/3rdparty/SevenNet/SevenNet_logo.png and /dev/null differ diff --git a/mace-bench/3rdparty/SevenNet/example_inputs/data/label_1/OUTCAR_1 b/mace-bench/3rdparty/SevenNet/example_inputs/data/label_1/OUTCAR_1 deleted file mode 100644 index 4f85af303c70524a252f56cb5fb693b2eaad53b0..0000000000000000000000000000000000000000 --- a/mace-bench/3rdparty/SevenNet/example_inputs/data/label_1/OUTCAR_1 +++ /dev/null @@ -1,3614 +0,0 @@ - vasp.6.3.2 27Jun22 (build Aug 12 2022 00:53:59) complex - - executed on tv2STD date 2022.09.21 10:45:26 - running 32 mpi-ranks, with 1 threads/rank - distrk: each k-point on 16 cores, 2 groups - distr: one band on NCORE= 4 cores, 4 groups - - --------------------------------------------------------------------------------------------------------- - - - INCAR: - SYSTEM = HfO2_p21c - NWRITE = 2 write-flag - ISTART = 0 job : 0-new, 1-cont, 2-samecut - ICHARG = 2 charge: 0-wave, 1-file, 2-atom, >10-const - INIWAV = 1 electr: 0-lowe 1-rand 2-diag - ENCUT = 500 - PREC = Accurate normal | accurate - ADDGRID = True - NELM = 100 - LREAL = Auto real-space projection (.FALSE., .TRUE., On, Auto) - ALGO = Fast Normal, Fast, Very_Fast - LWAVE = .F. - LCHARG = .F. - NSW = 0 - IBRION = 2 ionic relax: 0-MD, 1-quasi-Newton, 2-CG, 3-Damped MD - EDIFFG = -0.002 - ISIF = 3 (1:force\=y stress\=trace only ions\=y shape\=n volume\=n) - ISYM = 1 (1-use symmetry, 0-no symmetry) - ISMEAR = 0 (-1-Fermi, 1-Methfessel/Paxton) - SIGMA = 0.05 broadening in eV - NPAR = 4 - KPAR = 2 - METAGGA = SCAN - - POTCAR: PAW_PBE Hf 20Jan2003 - POTCAR: PAW_PBE O 08Apr2002 - POTCAR: PAW_PBE Hf 20Jan2003 - SHA256 = 0bb2207f9a10894133f750b65504b92b8afef976ae770762e0497daaaad8168a Hf/POTCAR - COPYR = (c) Copyright 20Jan2003 Georg Kresse - COPYR = This file is part of the software VASP. Any use, copying, and all other rights are regul - COPYR = If you do not have a valid VASP license, you may not use, copy or distribute this file. - VRHFIN =Hf: 6s5d - LEXCH = PE - EATOM = 75.9011 eV, 5.5786 Ry - - TITEL = PAW_PBE Hf 20Jan2003 - LULTRA = F use ultrasoft PP ? - IUNSCR = 1 unscreen: 0-lin 1-nonlin 2-no - RPACOR = 2.500 partial core radius - POMASS = 178.490; ZVAL = 4.000 mass and valenz - RCORE = 3.000 outmost cutoff radius - RWIGS = 3.050; RWIGS = 1.614 wigner-seitz radius (au A) - ENMAX = 220.334; ENMIN = 165.250 eV - RCLOC = 2.212 cutoff for local pot - LCOR = T correct aug charges - LPAW = T paw PP - EAUG = 335.116 - DEXC = 0.000 - RMAX = 3.077 core radius for proj-oper - RAUG = 1.300 factor for augmentation sphere - RDEP = 3.047 radius for radial grids - RDEPT = 2.344 core radius for aug-charge - - Atomic configuration - 16 entries - n l j E occ. - 1 0 0.50 -65259.4397 2.0000 - 2 0 0.50 -11157.9882 2.0000 - 2 1 1.50 -9795.2113 6.0000 - 3 0 0.50 -2541.4058 2.0000 - 3 1 1.50 -2134.4770 6.0000 - 3 2 2.50 -1653.5418 10.0000 - 4 0 0.50 -510.9575 2.0000 - 4 1 1.50 -377.5023 6.0000 - 4 2 2.50 -205.2085 10.0000 - 4 3 3.50 -15.4905 14.0000 - 5 0 0.50 -65.6020 2.0000 - 5 1 1.50 -34.2798 6.0000 - 5 2 2.50 -1.9877 3.0000 - 6 0 0.50 -4.7357 1.0000 - 6 1 1.50 -1.3606 0.0000 - 5 3 2.50 -1.3606 0.0000 - Description - l E TYP RCUT TYP RCUT - 2 -1.9876627 23 2.500 - 2 0.0744703 23 2.500 - 0 -4.7356889 23 2.600 - 0 3.2364747 23 2.600 - 1 -1.3605826 23 3.000 - 1 27.2116520 23 3.000 - local pseudopotential read in - partial core-charges read in - partial kinetic energy density read in - atomic valenz-charges read in - non local Contribution for L= 2 read in - real space projection operators read in - non local Contribution for L= 2 read in - real space projection operators read in - non local Contribution for L= 0 read in - real space projection operators read in - non local Contribution for L= 0 read in - real space projection operators read in - non local Contribution for L= 1 read in - real space projection operators read in - non local Contribution for L= 1 read in - real space projection operators read in - PAW grid and wavefunctions read in - - number of l-projection operators is LMAX = 6 - number of lm-projection operators is LMMAX = 18 - - POTCAR: PAW_PBE O 08Apr2002 - SHA256 = 818f92134a0a090dccd8ba1447fa70422a3b330e708bb4f08108d8ae51209ddf O/POTCAR - COPYR = (c) Copyright 08Apr2002 Georg Kresse - COPYR = This file is part of the software VASP. Any use, copying, and all other rights are regul - COPYR = If you do not have a valid VASP license, you may not use, copy or distribute this file. - VRHFIN =O: s2p4 - LEXCH = PE - EATOM = 432.3788 eV, 31.7789 Ry - - TITEL = PAW_PBE O 08Apr2002 - LULTRA = F use ultrasoft PP ? - IUNSCR = 1 unscreen: 0-lin 1-nonlin 2-no - RPACOR = 1.200 partial core radius - POMASS = 16.000; ZVAL = 6.000 mass and valenz - RCORE = 1.520 outmost cutoff radius - RWIGS = 1.550; RWIGS = 0.820 wigner-seitz radius (au A) - ENMAX = 400.000; ENMIN = 300.000 eV - ICORE = 2 local potential - LCOR = T correct aug charges - LPAW = T paw PP - EAUG = 605.392 - DEXC = 0.000 - RMAX = 1.553 core radius for proj-oper - RAUG = 1.300 factor for augmentation sphere - RDEP = 1.550 radius for radial grids - RDEPT = 1.329 core radius for aug-charge - - Atomic configuration - 4 entries - n l j E occ. - 1 0 0.50 -514.6923 2.0000 - 2 0 0.50 -23.9615 2.0000 - 2 1 0.50 -9.0305 4.0000 - 3 2 1.50 -9.5241 0.0000 - Description - l E TYP RCUT TYP RCUT - 0 -23.9615318 23 1.200 - 0 -9.5240782 23 1.200 - 1 -9.0304911 23 1.520 - 1 8.1634956 23 1.520 - 2 -9.5240782 7 1.500 - local pseudopotential read in - partial core-charges read in - partial kinetic energy density read in - kinetic energy density of atom read in - atomic valenz-charges read in - non local Contribution for L= 0 read in - real space projection operators read in - non local Contribution for L= 0 read in - real space projection operators read in - non local Contribution for L= 1 read in - real space projection operators read in - non local Contribution for L= 1 read in - real space projection operators read in - PAW grid and wavefunctions read in - - number of l-projection operators is LMAX = 4 - number of lm-projection operators is LMMAX = 8 - - Optimization of the real space projectors (new method) - - maximal supplied QI-value = 12.47 - optimisation between [QCUT,QGAM] = [ 11.35, 22.82] = [ 36.07,145.88] Ry - Optimized for a Real-space Cutoff 1.66 Angstroem - - l n(q) QCUT max X(q) W(low)/X(q) W(high)/X(q) e(spline) - 2 10 11.350 48.111 0.20E-03 0.11E-03 0.41E-06 - 2 10 11.350 40.545 0.19E-03 0.10E-03 0.39E-06 - 0 11 11.350 121.658 0.22E-04 0.19E-04 0.24E-06 - 0 11 11.350 71.177 0.17E-04 0.17E-04 0.23E-06 - 1 11 11.350 14.183 0.25E-03 0.43E-03 0.12E-05 - 1 11 11.350 8.257 0.17E-03 0.29E-03 0.81E-06 - Optimization of the real space projectors (new method) - - maximal supplied QI-value = 24.76 - optimisation between [QCUT,QGAM] = [ 11.39, 22.77] = [ 36.31,145.25] Ry - Optimized for a Real-space Cutoff 1.10 Angstroem - - l n(q) QCUT max X(q) W(low)/X(q) W(high)/X(q) e(spline) - 0 7 11.387 20.381 0.22E-03 0.48E-03 0.18E-06 - 0 7 11.387 15.268 0.22E-03 0.52E-03 0.19E-06 - 1 7 11.387 5.964 0.22E-03 0.73E-03 0.24E-06 - 1 7 11.387 5.382 0.19E-03 0.60E-03 0.21E-06 - PAW_PBE Hf 20Jan2003 : - energy of atom 1 EATOM= -75.9011 - kinetic energy error for atom= 0.0007 (will be added to EATOM!!) - PAW_PBE O 08Apr2002 : - energy of atom 2 EATOM= -432.3788 - kinetic energy error for atom= 0.0224 (will be added to EATOM!!) - - - POSCAR: name - positions in direct lattice - No initial velocities read in - WARNING: For meta-GGA calculations it is strongly recommended to include - aspherical contributions to the potential inside the PAW spheres (set - LASPH = .TRUE.) - - - METAGGA = SCAN LMAXTAU = 0 LMIXTAU = F - - exchange correlation table for LEXCH = 8 - RHO(1)= 0.500 N(1) = 2000 - RHO(2)= 100.500 N(2) = 4000 - - - --------------------------------------------------------------------------------------------------------- - - - ion position nearest neighbor table - 1 0.877 0.878 0.740- 34 1.99 89 2.01 35 2.05 76 2.09 68 2.23 64 2.34 87 2.35 77 2.70 - 7 3.19 14 3.24 32 3.42 6 3.44 26 3.46 30 3.63 3 3.63 5 3.65 - 2 0.854 0.362 0.260- 80 1.89 37 1.99 74 2.01 38 2.07 78 2.13 39 2.45 81 2.54 28 3.33 - 10 3.33 27 3.37 25 3.39 29 3.46 6 3.64 3 3.74 21 3.86 9 3.86 - 3 0.870 0.130 0.983- 95 1.98 81 2.19 76 2.19 64 2.28 82 2.28 38 2.30 65 2.32 42 2.51 - 25 3.37 20 3.43 32 3.48 18 3.56 1 3.63 29 3.63 4 3.69 31 3.70 - 4 0.879 0.896 0.252- 40 1.84 42 1.93 75 1.93 82 2.13 36 2.30 85 2.36 41 2.66 47 2.86 - 29 3.14 21 3.30 26 3.44 12 3.51 20 3.55 24 3.57 3 3.69 6 3.71 - 5 0.897 0.631 0.993- 36 1.92 77 1.98 57 2.01 68 2.15 39 2.28 93 2.33 78 2.69 85 2.72 - 17 3.11 21 3.17 14 3.35 30 3.37 24 3.50 1 3.65 20 3.76 25 3.81 - 6 0.866 0.130 0.524- 94 2.01 87 2.06 33 2.07 37 2.10 47 2.14 35 2.14 40 2.29 31 3.25 - 1 3.44 32 3.47 26 3.49 29 3.53 12 3.57 28 3.63 2 3.64 18 3.67 - 7 0.878 0.636 0.552- 34 1.89 41 1.98 43 1.98 71 2.02 90 2.13 89 2.16 80 2.72 9 3.14 - 1 3.19 31 3.29 30 3.45 26 3.51 27 3.53 14 3.54 21 3.79 - 8 0.342 0.349 0.250- 70 2.00 72 2.06 45 2.12 84 2.13 46 2.16 44 2.19 52 2.40 10 3.42 - 17 3.43 29 3.51 21 3.51 22 3.52 23 3.60 19 3.61 9 3.61 28 3.64 - 9 0.115 0.403 0.524- 43 1.91 60 1.99 74 2.11 71 2.11 44 2.11 54 2.45 45 2.83 33 2.85 - 7 3.14 31 3.35 15 3.49 16 3.51 8 3.61 19 3.65 21 3.65 18 3.70 - 10 0.123 0.134 0.244- 38 1.87 72 2.07 47 2.08 45 2.14 73 2.15 74 2.45 42 2.58 48 2.84 - 2 3.33 8 3.42 19 3.55 23 3.55 20 3.64 12 3.65 11 3.69 3 3.72 - 11 0.381 0.842 0.254- 86 1.95 48 1.97 51 1.99 50 2.29 49 2.31 73 2.33 69 2.47 27 3.16 - 12 3.36 22 3.39 20 3.57 24 3.67 10 3.69 19 3.76 26 3.77 15 3.78 - 12 0.139 0.873 0.481- 49 1.99 75 2.01 53 2.04 48 2.17 35 2.19 47 2.24 61 2.37 34 2.82 - 15 3.27 11 3.36 13 3.40 4 3.51 6 3.57 19 3.60 10 3.65 21 3.74 - 13 0.378 0.839 0.717- 56 1.91 58 1.96 92 2.03 53 2.05 55 2.20 61 2.44 67 2.77 30 3.00 - 15 3.15 14 3.38 12 3.40 19 3.57 18 3.64 26 3.69 - 14 0.139 0.657 0.777- 54 1.90 55 2.09 34 2.11 68 2.13 53 2.14 59 2.28 57 2.30 1 3.24 - 20 3.28 15 3.34 5 3.35 13 3.38 22 3.54 7 3.54 16 3.56 17 3.58 - 15 0.353 0.608 0.528- 49 1.91 56 2.06 54 2.09 44 2.11 53 2.18 79 2.19 66 2.20 28 3.09 - 13 3.15 12 3.27 14 3.34 16 3.46 9 3.49 11 3.78 - 16 0.371 0.365 0.758- 96 1.85 66 2.06 60 2.13 62 2.18 54 2.23 59 2.23 63 2.34 32 3.21 - 17 3.45 15 3.46 9 3.51 14 3.56 18 3.65 23 3.67 19 3.78 25 3.79 - 17 0.124 0.392 0.992- 57 1.88 72 2.06 65 2.08 39 2.13 59 2.18 62 2.23 70 2.52 5 3.11 - 8 3.43 16 3.45 21 3.47 14 3.58 23 3.60 18 3.61 22 3.65 10 3.76 - 18 0.138 0.134 0.759- 61 1.99 67 2.00 33 2.05 60 2.22 64 2.32 62 2.35 65 2.36 35 2.87 - 23 3.41 19 3.44 31 3.49 3 3.56 17 3.61 13 3.64 16 3.65 6 3.67 - 19 0.359 0.108 0.502- 45 1.95 63 2.01 83 2.09 48 2.09 61 2.13 58 2.41 60 2.66 26 3.23 - 18 3.44 10 3.55 13 3.57 12 3.60 8 3.61 9 3.65 32 3.70 11 3.76 - 20 0.129 0.875 0.007- 69 2.01 42 2.01 55 2.15 68 2.16 64 2.17 73 2.19 67 2.35 36 2.61 - 14 3.28 3 3.43 22 3.48 4 3.55 11 3.57 10 3.64 21 3.70 18 3.74 - 21 0.085 0.618 0.242- 36 1.93 39 2.02 71 2.04 70 2.05 75 2.21 69 2.29 5 3.17 4 3.30 - 17 3.47 8 3.51 22 3.60 9 3.65 20 3.70 12 3.74 7 3.79 2 3.86 - 22 0.373 0.603 0.034- 50 1.96 52 1.99 91 2.06 59 2.13 70 2.17 69 2.19 55 2.49 25 3.18 - 11 3.39 20 3.48 8 3.52 14 3.54 21 3.60 17 3.65 30 3.78 16 3.79 - 23 0.374 0.107 0.999- 88 1.94 62 2.01 46 2.05 67 2.10 73 2.33 51 2.34 72 2.68 24 3.17 - 18 3.41 32 3.54 10 3.55 17 3.60 8 3.60 16 3.67 20 3.75 11 3.81 - 24 0.630 0.889 0.007- 51 2.00 92 2.03 77 2.06 85 2.13 88 2.23 82 2.33 76 2.39 23 3.17 - 30 3.25 5 3.50 4 3.57 32 3.60 29 3.66 11 3.67 1 3.69 3 3.79 - 25 0.643 0.401 0.001- 52 1.91 81 2.03 78 2.12 96 2.23 93 2.29 91 2.41 95 2.45 22 3.18 - 3 3.37 2 3.39 30 3.52 31 3.60 16 3.79 5 3.81 29 3.86 32 3.86 - 26 0.641 0.913 0.494- 58 1.90 87 1.98 83 2.04 86 2.13 41 2.20 40 2.22 89 2.26 19 3.23 - 29 3.35 4 3.44 1 3.46 27 3.47 6 3.49 32 3.50 7 3.51 13 3.69 - 27 0.653 0.650 0.287- 86 1.95 85 2.05 50 2.07 79 2.09 41 2.16 80 2.18 78 2.23 11 3.16 - 28 3.31 2 3.37 26 3.47 7 3.53 4 3.74 24 3.80 - 28 0.604 0.405 0.475- 66 1.90 84 1.93 79 2.00 94 2.09 80 2.19 37 2.50 90 2.58 15 3.09 - 27 3.31 2 3.33 31 3.58 29 3.60 6 3.63 8 3.64 16 3.81 - 29 0.644 0.133 0.258- 83 1.97 82 2.04 40 2.14 81 2.15 37 2.15 46 2.16 84 2.23 4 3.14 - 26 3.35 2 3.46 8 3.51 6 3.53 28 3.60 3 3.63 24 3.66 25 3.86 - 30 0.634 0.665 0.788- 77 1.93 91 1.95 56 2.06 90 2.20 93 2.22 89 2.28 92 2.34 13 3.00 - 24 3.25 5 3.37 7 3.45 25 3.52 31 3.57 1 3.63 22 3.78 - 31 0.858 0.374 0.721- 43 1.87 33 1.97 93 2.13 94 2.21 90 2.23 95 2.28 65 2.55 57 2.92 - 6 3.25 7 3.29 9 3.35 18 3.49 30 3.57 28 3.58 25 3.60 3 3.70 - 32 0.616 0.129 0.755- 88 1.88 63 1.92 87 2.15 76 2.16 96 2.22 95 2.27 94 2.68 16 3.21 - 1 3.42 6 3.47 3 3.48 26 3.50 23 3.54 24 3.60 19 3.70 31 3.86 - 33 0.979 0.222 0.651- 31 1.97 18 2.05 6 2.07 9 2.85 - 34 0.989 0.734 0.644- 7 1.89 1 1.99 14 2.11 12 2.82 - 35 0.989 0.970 0.617- 1 2.05 6 2.14 12 2.19 18 2.87 - 36 0.976 0.730 0.120- 5 1.92 21 1.93 4 2.30 20 2.61 - 37 0.773 0.238 0.367- 2 1.99 6 2.10 29 2.15 28 2.50 - 38 0.967 0.211 0.160- 10 1.87 2 2.07 3 2.30 - 39 0.000 0.487 0.142- 21 2.02 17 2.13 5 2.28 2 2.45 - 40 0.783 0.003 0.373- 4 1.84 29 2.14 26 2.22 6 2.29 - 41 0.775 0.743 0.416- 7 1.98 27 2.16 26 2.20 4 2.66 - 42 0.997 0.968 0.136- 4 1.93 20 2.01 3 2.51 10 2.58 - 43 0.968 0.473 0.632- 31 1.87 9 1.91 7 1.98 - 44 0.278 0.462 0.425- 15 2.11 9 2.11 8 2.19 - 45 0.263 0.212 0.364- 19 1.95 8 2.12 10 2.14 9 2.83 - 46 0.461 0.190 0.150- 23 2.05 8 2.16 29 2.16 - 47 0.028 0.056 0.398- 10 2.08 6 2.14 12 2.24 4 2.86 - 48 0.302 0.956 0.396- 11 1.97 19 2.09 12 2.17 10 2.84 - 49 0.273 0.733 0.404- 15 1.91 12 1.99 11 2.31 - 50 0.500 0.666 0.152- 22 1.96 27 2.07 11 2.29 - 51 0.480 0.941 0.133- 11 1.99 24 2.00 23 2.34 - 52 0.468 0.426 0.077- 25 1.91 22 1.99 8 2.40 - 53 0.226 0.763 0.632- 12 2.04 13 2.05 14 2.14 15 2.18 - 54 0.237 0.531 0.666- 14 1.90 15 2.09 16 2.23 9 2.45 - 55 0.265 0.764 0.874- 14 2.09 20 2.15 13 2.20 22 2.49 - 56 0.480 0.682 0.654- 13 1.91 30 2.06 15 2.06 - 57 0.025 0.514 0.880- 17 1.88 5 2.01 14 2.30 31 2.92 - 58 0.495 0.929 0.612- 26 1.90 13 1.96 19 2.41 - 59 0.264 0.503 0.902- 22 2.13 17 2.18 16 2.23 14 2.28 - 60 0.221 0.288 0.653- 9 1.99 16 2.13 18 2.22 19 2.66 - 61 0.227 0.018 0.620- 18 1.99 19 2.13 12 2.37 13 2.44 - 62 0.271 0.247 0.887- 23 2.01 16 2.18 17 2.23 18 2.35 - 63 0.451 0.166 0.660- 32 1.92 19 2.01 16 2.34 - 64 0.016 0.993 0.858- 20 2.17 3 2.28 18 2.32 1 2.34 - 65 0.006 0.272 0.906- 17 2.08 3 2.32 18 2.36 31 2.55 - 66 0.476 0.435 0.610- 28 1.90 16 2.06 15 2.20 - 67 0.242 0.016 0.889- 18 2.00 23 2.10 20 2.35 13 2.77 - 68 0.997 0.772 0.901- 14 2.13 5 2.15 20 2.16 1 2.23 - 69 0.217 0.739 0.131- 20 2.01 22 2.19 21 2.29 11 2.47 - 70 0.247 0.505 0.158- 8 2.00 21 2.05 22 2.17 17 2.52 - 71 0.026 0.571 0.424- 7 2.02 21 2.04 9 2.11 - 72 0.203 0.272 0.141- 17 2.06 8 2.06 10 2.07 23 2.68 - 73 0.244 0.991 0.125- 10 2.15 20 2.19 23 2.33 11 2.33 - 74 0.027 0.331 0.360- 2 2.01 9 2.11 10 2.45 - 75 0.023 0.799 0.352- 4 1.93 12 2.01 21 2.21 - 76 0.762 0.003 0.870- 1 2.09 32 2.16 3 2.19 24 2.39 - 77 0.746 0.742 0.905- 30 1.93 5 1.98 24 2.06 1 2.70 - 78 0.739 0.505 0.139- 25 2.12 2 2.13 27 2.23 5 2.69 - 79 0.510 0.561 0.381- 28 2.00 27 2.09 15 2.19 - 80 0.770 0.483 0.382- 2 1.89 27 2.18 28 2.19 7 2.72 - 81 0.719 0.243 0.107- 25 2.03 29 2.15 3 2.19 2 2.54 - 82 0.754 0.020 0.122- 29 2.04 4 2.13 3 2.28 24 2.33 - 83 0.543 0.075 0.404- 29 1.97 26 2.04 19 2.09 - 84 0.542 0.327 0.322- 28 1.93 8 2.13 29 2.23 - 85 0.726 0.774 0.162- 27 2.05 24 2.13 4 2.36 5 2.72 - 86 0.547 0.808 0.354- 11 1.95 27 1.95 26 2.13 - 87 0.736 0.022 0.606- 26 1.98 6 2.06 32 2.15 1 2.35 - 88 0.546 0.075 0.911- 32 1.88 23 1.94 24 2.23 - 89 0.744 0.784 0.653- 1 2.01 7 2.16 26 2.26 30 2.28 - 90 0.726 0.540 0.630- 7 2.13 30 2.20 31 2.23 28 2.58 - 91 0.510 0.575 0.883- 30 1.95 22 2.06 25 2.41 - 92 0.494 0.842 0.879- 24 2.03 13 2.03 30 2.34 - 93 0.776 0.502 0.871- 31 2.13 30 2.22 25 2.29 5 2.33 - 94 0.731 0.277 0.592- 6 2.01 28 2.09 31 2.21 32 2.68 - 95 0.762 0.240 0.852- 3 1.98 32 2.27 31 2.28 25 2.45 - 96 0.531 0.316 0.845- 16 1.85 32 2.22 25 2.23 - - LATTYP: Found a simple monoclinic cell. - ALAT = 10.1297860000 - B/A-ratio = 1.0131648388 - C/A-ratio = 1.0379762742 - COS(beta) = -0.1645688048 - - Lattice vectors: - - A1 = ( 10.1297860000, 0.0000000000, 0.0000000000) - A2 = ( 0.0000000000, 10.2631430000, 0.0000000000) - A3 = ( -1.7303550000, 0.0000000000, 10.3711190000) - - -Analysis of symmetry for initial positions (statically): -===================================================================== - Subroutine PRICEL returns: - Original cell was already a primitive cell. - - - Routine SETGRP: Setting up the symmetry group for a - simple monoclinic supercell. - - - Subroutine GETGRP returns: Found 1 space group operations - (whereof 1 operations were pure point group operations) - out of a pool of 4 trial point group operations. - - -The static configuration has the point symmetry C_1 . - - -Analysis of symmetry for dynamics (positions and initial velocities): -===================================================================== - Subroutine PRICEL returns: - Original cell was already a primitive cell. - - - Routine SETGRP: Setting up the symmetry group for a - simple monoclinic supercell. - - - Subroutine GETGRP returns: Found 1 space group operations - (whereof 1 operations were pure point group operations) - out of a pool of 4 trial point group operations. - - -The dynamic configuration has the point symmetry C_1 . - - -Analysis of constrained symmetry for selective dynamics: -===================================================================== - Subroutine PRICEL returns: - Original cell was already a primitive cell. - - - Routine SETGRP: Setting up the symmetry group for a - simple monoclinic supercell. - - - Subroutine GETGRP returns: Found 1 space group operations - (whereof 1 operations were pure point group operations) - out of a pool of 4 trial point group operations. - - -The constrained configuration has the point symmetry C_1 . - - - Subroutine INISYM returns: Found 1 space group operations - (whereof 1 operations are pure point group operations), - and found 1 'primitive' translations - - ----------------------------------------------------------------------------------------- - - Primitive cell - - volume of cell : 1078.2172 - - direct lattice vectors reciprocal lattice vectors - 10.129786000 0.000000000 0.000000000 0.098718769 0.000000000 0.016470596 - 1.730355000 0.000000000-10.371119000 0.000000000 0.000000000 -0.096421611 - 0.000000000 10.263143000 0.000000000 0.000000000 0.097436039 0.000000000 - - length of vectors - 10.129786000 10.514477530 10.263143000 0.100083344 0.096421611 0.097436039 - - position of ions in fractional coordinates (direct lattice) - 0.877038300 0.877511130 0.740022880 - 0.853598140 0.362049080 0.259879770 - 0.870294400 0.129546970 0.982552250 - 0.878836250 0.896241730 0.252126230 - 0.896904840 0.630954560 0.993380550 - 0.865586680 0.129905610 0.524284040 - 0.878366350 0.635887240 0.551647880 - 0.341644340 0.349240400 0.249736230 - 0.115167680 0.403394100 0.523513770 - 0.123329520 0.133735080 0.244293950 - 0.380961210 0.842177610 0.253836850 - 0.139199220 0.872867240 0.481300610 - 0.378418830 0.838839180 0.716807280 - 0.138622670 0.657370100 0.776989050 - 0.353385470 0.608346810 0.528026380 - 0.370805370 0.364635780 0.757517110 - 0.123817230 0.392478380 0.991983630 - 0.138463890 0.133617760 0.758584520 - 0.359463740 0.108021800 0.501934870 - 0.129068830 0.875056580 0.007267130 - 0.084880800 0.618337390 0.241957640 - 0.373476190 0.602561140 0.034196820 - 0.373830300 0.106865780 0.998814220 - 0.630442940 0.888983200 0.006750480 - 0.642643440 0.401047430 0.001369610 - 0.641098230 0.912774070 0.493595630 - 0.653122040 0.649996630 0.287230320 - 0.604170310 0.405494680 0.474583590 - 0.644481760 0.132823770 0.257967300 - 0.633658050 0.664718230 0.788000810 - 0.858339580 0.373582390 0.720567810 - 0.615607210 0.128814850 0.754923220 - 0.978568850 0.221924280 0.650862970 - 0.988512780 0.734078570 0.643588250 - 0.988779350 0.970016020 0.617016910 - 0.976410740 0.730037390 0.119673120 - 0.772732160 0.237601690 0.367353250 - 0.966567990 0.211327950 0.160044330 - 0.000300680 0.486859310 0.142433340 - 0.782990750 0.003081220 0.372990460 - 0.775335200 0.743348070 0.416377220 - 0.997124100 0.968342470 0.135749010 - 0.967628210 0.472761100 0.632248210 - 0.277714990 0.462448530 0.424703350 - 0.263328690 0.211520520 0.364153840 - 0.460929810 0.189552190 0.150360140 - 0.027797050 0.056234890 0.397882210 - 0.301992160 0.956198500 0.395997640 - 0.272552570 0.732867240 0.404012000 - 0.500165840 0.665944700 0.151551720 - 0.480309040 0.940786310 0.133014300 - 0.468437520 0.426334870 0.077251670 - 0.226079670 0.762667960 0.631606260 - 0.237310870 0.530610530 0.666461420 - 0.265055950 0.763911170 0.873738550 - 0.480385080 0.681755840 0.654211970 - 0.024867140 0.513812250 0.879841990 - 0.494612480 0.929438140 0.611695520 - 0.263635590 0.503369660 0.902296560 - 0.220561440 0.287919180 0.652651950 - 0.227495020 0.018360360 0.619527480 - 0.271136930 0.246896760 0.887464570 - 0.450968590 0.165974610 0.659941240 - 0.016212320 0.992579480 0.858359510 - 0.005900240 0.271625780 0.906491370 - 0.475805310 0.435233460 0.610355990 - 0.241669830 0.015888150 0.889374730 - 0.996871460 0.771889910 0.900676150 - 0.217254450 0.738898000 0.131108100 - 0.247110050 0.505434900 0.157910580 - 0.026182510 0.571079930 0.423673630 - 0.202544370 0.272388150 0.140963170 - 0.243917310 0.991418850 0.125112770 - 0.026628050 0.331040500 0.359755730 - 0.022951080 0.798794270 0.352135040 - 0.762043160 0.003376580 0.869586190 - 0.745672220 0.742141820 0.905460860 - 0.739040010 0.504674010 0.139162880 - 0.509950670 0.560761100 0.380506730 - 0.769518020 0.482851320 0.382441790 - 0.719410190 0.242765620 0.106703550 - 0.753890100 0.020275280 0.121797770 - 0.542803180 0.074893310 0.404289500 - 0.541627610 0.327025520 0.321883960 - 0.725833420 0.774023640 0.161924770 - 0.546504370 0.808394530 0.353513290 - 0.735625040 0.021601200 0.606393480 - 0.545520540 0.074954500 0.911064170 - 0.743878090 0.783666160 0.652524780 - 0.726363870 0.540120900 0.629727010 - 0.510044400 0.575286910 0.883354290 - 0.494026520 0.841889570 0.878545590 - 0.776433480 0.502291950 0.871391730 - 0.730900220 0.276816250 0.591765470 - 0.762261180 0.240420480 0.852307290 - 0.530522950 0.316340570 0.845076210 - - ion indices of the primitive-cell ions - primitive index ion index - 1 1 - 2 2 - 3 3 - 4 4 - 5 5 - 6 6 - 7 7 - 8 8 - 9 9 - 10 10 - 11 11 - 12 12 - 13 13 - 14 14 - 15 15 - 16 16 - 17 17 - 18 18 - 19 19 - 20 20 - 21 21 - 22 22 - 23 23 - 24 24 - 25 25 - 26 26 - 27 27 - 28 28 - 29 29 - 30 30 - 31 31 - 32 32 - 33 33 - 34 34 - 35 35 - 36 36 - 37 37 - 38 38 - 39 39 - 40 40 - 41 41 - 42 42 - 43 43 - 44 44 - 45 45 - 46 46 - 47 47 - 48 48 - 49 49 - 50 50 - 51 51 - 52 52 - 53 53 - 54 54 - 55 55 - 56 56 - 57 57 - 58 58 - 59 59 - 60 60 - 61 61 - 62 62 - 63 63 - 64 64 - 65 65 - 66 66 - 67 67 - 68 68 - 69 69 - 70 70 - 71 71 - 72 72 - 73 73 - 74 74 - 75 75 - 76 76 - 77 77 - 78 78 - 79 79 - 80 80 - 81 81 - 82 82 - 83 83 - 84 84 - 85 85 - 86 86 - 87 87 - 88 88 - 89 89 - 90 90 - 91 91 - 92 92 - 93 93 - 94 94 - 95 95 - 96 96 - ----------------------------------------------------------------------------------------- - - - - KPOINTS: Auto k-point - -Automatic generation of k-mesh. - Grid dimensions read from file: - generate k-points for: 2 2 2 - - Generating k-lattice: - - Cartesian coordinates Fractional coordinates (reciprocal lattice) - 0.049359384 0.000000000 0.008235298 0.500000000 0.000000000 0.000000000 - 0.000000000 0.000000000 -0.048210805 0.000000000 0.500000000 0.000000000 - 0.000000000 0.048718019 0.000000000 0.000000000 0.000000000 0.500000000 - - Length of vectors - 0.050041672 0.048210805 0.048718019 - - Shift w.r.t. Gamma in fractional coordinates (k-lattice) - 0.500000000 0.500000000 0.500000000 - - - Subroutine IBZKPT returns following result: - =========================================== - - Found 4 irreducible k-points: - - Following reciprocal coordinates: - Coordinates Weight - 0.250000 0.250000 0.250000 2.000000 - -0.250000 -0.250000 0.250000 2.000000 - -0.250000 0.250000 0.250000 2.000000 - 0.250000 -0.250000 0.250000 2.000000 - - Following cartesian coordinates: - Coordinates Weight - 0.024680 0.024359 -0.019988 2.000000 - -0.024680 0.024359 0.019988 2.000000 - -0.024680 0.024359 -0.028223 2.000000 - 0.024680 0.024359 0.028223 2.000000 - - - --------------------------------------------------------------------------------------------------------- - - - - - Dimension of arrays: - k-points NKPTS = 4 k-points in BZ NKDIM = 4 number of bands NBANDS= 308 - number of dos NEDOS = 301 number of ions NIONS = 96 - non local maximal LDIM = 6 non local SUM 2l+1 LMDIM = 18 - total plane-waves NPLWV = 512000 - max r-space proj IRMAX = 9139 max aug-charges IRDMAX= 255251 - dimension x,y,z NGX = 80 NGY = 80 NGZ = 80 - dimension x,y,z NGXF= 160 NGYF= 160 NGZF= 160 - support grid NGXF= 320 NGYF= 320 NGZF= 320 - ions per type = 32 64 - NGX,Y,Z is equivalent to a cutoff of 13.13, 12.65, 12.96 a.u. - NGXF,Y,Z is equivalent to a cutoff of 26.26, 25.30, 25.92 a.u. - - SYSTEM = HfO2_p21c - POSCAR = name - - Startparameter for this run: - NWRITE = 2 write-flag & timer - PREC = accura normal or accurate (medium, high low for compatibility) - ISTART = 0 job : 0-new 1-cont 2-samecut - ICHARG = 2 charge: 1-file 2-atom 10-const - ISPIN = 1 spin polarized calculation? - LNONCOLLINEAR = F non collinear calculations - LSORBIT = F spin-orbit coupling - INIWAV = 1 electr: 0-lowe 1-rand 2-diag - LASPH = F aspherical Exc in radial PAW - Electronic Relaxation 1 - ENCUT = 500.0 eV 36.75 Ry 6.06 a.u. 18.47 19.17 18.71*2*pi/ulx,y,z - ENINI = 500.0 initial cutoff - ENAUG = 605.4 eV augmentation charge cutoff - NELM = 100; NELMIN= 2; NELMDL= -5 # of ELM steps - EDIFF = 0.1E-03 stopping-criterion for ELM - LREAL = T real-space projection - NLSPLINE = F spline interpolate recip. space projectors - LCOMPAT= F compatible to vasp.4.4 - GGA_COMPAT = T GGA compatible to vasp.4.4-vasp.4.6 - LMAXPAW = -100 max onsite density - LMAXMIX = 2 max onsite mixed and CHGCAR - VOSKOWN= 0 Vosko Wilk Nusair interpolation - ROPT = -0.00025 -0.00025 - Ionic relaxation - EDIFFG = -.2E-02 stopping-criterion for IOM - NSW = 0 number of steps for IOM - NBLOCK = 1; KBLOCK = 1 inner block; outer block - IBRION = -1 ionic relax: 0-MD 1-quasi-New 2-CG - NFREE = 1 steps in history (QN), initial steepest desc. (CG) - ISIF = 3 stress and relaxation - IWAVPR = 10 prediction: 0-non 1-charg 2-wave 3-comb - ISYM = 1 0-nonsym 1-usesym 2-fastsym - LCORR = T Harris-Foulkes like correction to forces - - POTIM = 0.5000 time-step for ionic-motion - TEIN = 0.0 initial temperature - TEBEG = 0.0; TEEND = 0.0 temperature during run - SMASS = -3.00 Nose mass-parameter (am) - estimated Nose-frequenzy (Omega) = 0.10E-29 period in steps = 0.13E+47 mass= -0.234E-26a.u. - SCALEE = 1.0000 scale energy and forces - NPACO = 256; APACO = 10.0 distance and # of slots for P.C. - PSTRESS= 0.0 pullay stress - - Mass of Ions in am - POMASS = 178.49 16.00 - Ionic Valenz - ZVAL = 4.00 6.00 - Atomic Wigner-Seitz radii - RWIGS = -1.00 -1.00 - virtual crystal weights - VCA = 1.00 1.00 - NELECT = 512.0000 total number of electrons - NUPDOWN= -1.0000 fix difference up-down - - DOS related values: - EMIN = 10.00; EMAX =-10.00 energy-range for DOS - EFERMI = 0.00 - ISMEAR = 0; SIGMA = 0.05 broadening in eV -4-tet -1-fermi 0-gaus - - Electronic relaxation 2 (details) - IALGO = 68 algorithm - LDIAG = T sub-space diagonalisation (order eigenvalues) - LSUBROT= F optimize rotation matrix (better conditioning) - TURBO = 0 0=normal 1=particle mesh - IRESTART = 0 0=no restart 2=restart with 2 vectors - NREBOOT = 0 no. of reboots - NMIN = 0 reboot dimension - EREF = 0.00 reference energy to select bands - IMIX = 4 mixing-type and parameters - AMIX = 0.40; BMIX = 1.00 - AMIX_MAG = 1.60; BMIX_MAG = 1.00 - AMIN = 0.10 - WC = 100.; INIMIX= 1; MIXPRE= 1; MAXMIX= -45 - - Intra band minimization: - WEIMIN = 0.0000 energy-eigenvalue tresh-hold - EBREAK = 0.81E-07 absolut break condition - DEPER = 0.30 relativ break condition - - TIME = 0.40 timestep for ELM - - volume/ion in A,a.u. = 11.23 75.79 - Fermi-wavevector in a.u.,A,eV,Ry = 1.277211 2.413579 22.194756 1.631269 - Thomas-Fermi vector in A = 2.409824 - - Write flags - LWAVE = F write WAVECAR - LDOWNSAMPLE = F k-point downsampling of WAVECAR - LCHARG = F write CHGCAR - LVTOT = F write LOCPOT, total local potential - LVHAR = F write LOCPOT, Hartree potential only - LELF = F write electronic localiz. function (ELF) - LORBIT = 0 0 simple, 1 ext, 2 COOP (PROOUT), +10 PAW based schemes - - - Dipole corrections - LMONO = F monopole corrections only (constant potential shift) - LDIPOL = F correct potential (dipole corrections) - IDIPOL = 0 1-x, 2-y, 3-z, 4-all directions - EPSILON= 1.0000000 bulk dielectric constant - - Exchange correlation treatment: - GGA = -- GGA type - LEXCH = 8 internal setting for exchange type - LIBXC = F Libxc - VOSKOWN = 0 Vosko Wilk Nusair interpolation - LHFCALC = F Hartree Fock is set to - LHFONE = F Hartree Fock one center treatment - AEXX = 0.0000 exact exchange contribution - - Linear response parameters - LEPSILON= F determine dielectric tensor - LRPA = F only Hartree local field effects (RPA) - LNABLA = F use nabla operator in PAW spheres - LVEL = F velocity operator in full k-point grid - CSHIFT =0.1000 complex shift for real part using Kramers Kronig - OMEGAMAX= -1.0 maximum frequency - DEG_THRESHOLD= 0.2000000E-02 threshold for treating states as degnerate - RTIME = -0.100 relaxation time in fs - (WPLASMAI= 0.000 imaginary part of plasma frequency in eV, 0.658/RTIME) - DFIELD = 0.0000000 0.0000000 0.0000000 field for delta impulse in time - - Optional k-point grid parameters - LKPOINTS_OPT = F use optional k-point grid - KPOINTS_OPT_MODE= 1 mode for optional k-point grid - - Orbital magnetization related: - ORBITALMAG= F switch on orbital magnetization - LCHIMAG = F perturbation theory with respect to B field - DQ = 0.001000 dq finite difference perturbation B field - LLRAUG = F two centre corrections for induced B field - - - --------------------------------------------------------------------------------------------------------- - - - Static calculation - charge density and potential will be updated during run - non-spin polarized calculation - RMM-DIIS sequential band-by-band and - variant of blocked Davidson during initial phase - perform sub-space diagonalisation - before iterative eigenvector-optimisation - modified Broyden-mixing scheme, WC = 100.0 - initial mixing is a Kerker type mixing with AMIX = 0.4000 and BMIX = 1.0000 - Hartree-type preconditioning will be used - using additional bands 52 - real space projection scheme for non local part - use partial core corrections - calculate Harris-corrections to forces - (improved forces if not selfconsistent) - use gradient corrections - use of overlap-Matrix (Vanderbilt PP) - Gauss-broadening in eV SIGMA = 0.05 - - --------------------------------------------------------------------------------------------------------- - - - energy-cutoff : 500.00 - volume of cell : 1078.22 - direct lattice vectors reciprocal lattice vectors - 10.129786000 0.000000000 0.000000000 0.098718769 0.000000000 0.016470596 - 1.730355000 0.000000000-10.371119000 0.000000000 0.000000000 -0.096421611 - 0.000000000 10.263143000 0.000000000 0.000000000 0.097436039 0.000000000 - - length of vectors - 10.129786000 10.514477530 10.263143000 0.100083344 0.096421611 0.097436039 - - - - k-points in units of 2pi/SCALE and weight: Auto k-point - 0.02467969 0.02435901 -0.01998775 0.250 - -0.02467969 0.02435901 0.01998775 0.250 - -0.02467969 0.02435901 -0.02822305 0.250 - 0.02467969 0.02435901 0.02822305 0.250 - - k-points in reciprocal lattice and weights: Auto k-point - 0.25000000 0.25000000 0.25000000 0.250 - -0.25000000 -0.25000000 0.25000000 0.250 - -0.25000000 0.25000000 0.25000000 0.250 - 0.25000000 -0.25000000 0.25000000 0.250 - - position of ions in fractional coordinates (direct lattice) - 0.87703830 0.87751113 0.74002288 - 0.85359814 0.36204908 0.25987977 - 0.87029440 0.12954697 0.98255225 - 0.87883625 0.89624173 0.25212623 - 0.89690484 0.63095456 0.99338055 - 0.86558668 0.12990561 0.52428404 - 0.87836635 0.63588724 0.55164788 - 0.34164434 0.34924040 0.24973623 - 0.11516768 0.40339410 0.52351377 - 0.12332952 0.13373508 0.24429395 - 0.38096121 0.84217761 0.25383685 - 0.13919922 0.87286724 0.48130061 - 0.37841883 0.83883918 0.71680728 - 0.13862267 0.65737010 0.77698905 - 0.35338547 0.60834681 0.52802638 - 0.37080537 0.36463578 0.75751711 - 0.12381723 0.39247838 0.99198363 - 0.13846389 0.13361776 0.75858452 - 0.35946374 0.10802180 0.50193487 - 0.12906883 0.87505658 0.00726713 - 0.08488080 0.61833739 0.24195764 - 0.37347619 0.60256114 0.03419682 - 0.37383030 0.10686578 0.99881422 - 0.63044294 0.88898320 0.00675048 - 0.64264344 0.40104743 0.00136961 - 0.64109823 0.91277407 0.49359563 - 0.65312204 0.64999663 0.28723032 - 0.60417031 0.40549468 0.47458359 - 0.64448176 0.13282377 0.25796730 - 0.63365805 0.66471823 0.78800081 - 0.85833958 0.37358239 0.72056781 - 0.61560721 0.12881485 0.75492322 - 0.97856885 0.22192428 0.65086297 - 0.98851278 0.73407857 0.64358825 - 0.98877935 0.97001602 0.61701691 - 0.97641074 0.73003739 0.11967312 - 0.77273216 0.23760169 0.36735325 - 0.96656799 0.21132795 0.16004433 - 0.00030068 0.48685931 0.14243334 - 0.78299075 0.00308122 0.37299046 - 0.77533520 0.74334807 0.41637722 - 0.99712410 0.96834247 0.13574901 - 0.96762821 0.47276110 0.63224821 - 0.27771499 0.46244853 0.42470335 - 0.26332869 0.21152052 0.36415384 - 0.46092981 0.18955219 0.15036014 - 0.02779705 0.05623489 0.39788221 - 0.30199216 0.95619850 0.39599764 - 0.27255257 0.73286724 0.40401200 - 0.50016584 0.66594470 0.15155172 - 0.48030904 0.94078631 0.13301430 - 0.46843752 0.42633487 0.07725167 - 0.22607967 0.76266796 0.63160626 - 0.23731087 0.53061053 0.66646142 - 0.26505595 0.76391117 0.87373855 - 0.48038508 0.68175584 0.65421197 - 0.02486714 0.51381225 0.87984199 - 0.49461248 0.92943814 0.61169552 - 0.26363559 0.50336966 0.90229656 - 0.22056144 0.28791918 0.65265195 - 0.22749502 0.01836036 0.61952748 - 0.27113693 0.24689676 0.88746457 - 0.45096859 0.16597461 0.65994124 - 0.01621232 0.99257948 0.85835951 - 0.00590024 0.27162578 0.90649137 - 0.47580531 0.43523346 0.61035599 - 0.24166983 0.01588815 0.88937473 - 0.99687146 0.77188991 0.90067615 - 0.21725445 0.73889800 0.13110810 - 0.24711005 0.50543490 0.15791058 - 0.02618251 0.57107993 0.42367363 - 0.20254437 0.27238815 0.14096317 - 0.24391731 0.99141885 0.12511277 - 0.02662805 0.33104050 0.35975573 - 0.02295108 0.79879427 0.35213504 - 0.76204316 0.00337658 0.86958619 - 0.74567222 0.74214182 0.90546086 - 0.73904001 0.50467401 0.13916288 - 0.50995067 0.56076110 0.38050673 - 0.76951802 0.48285132 0.38244179 - 0.71941019 0.24276562 0.10670355 - 0.75389010 0.02027528 0.12179777 - 0.54280318 0.07489331 0.40428950 - 0.54162761 0.32702552 0.32188396 - 0.72583342 0.77402364 0.16192477 - 0.54650437 0.80839453 0.35351329 - 0.73562504 0.02160120 0.60639348 - 0.54552054 0.07495450 0.91106417 - 0.74387809 0.78366616 0.65252478 - 0.72636387 0.54012090 0.62972701 - 0.51004440 0.57528691 0.88335429 - 0.49402652 0.84188957 0.87854559 - 0.77643348 0.50229195 0.87139173 - 0.73090022 0.27681625 0.59176547 - 0.76226118 0.24042048 0.85230729 - 0.53052295 0.31634057 0.84507621 - - position of ions in cartesian coordinates (Angst): - 10.40261606 7.59496064 -9.10077235 - 9.27323992 2.66718324 -3.75485409 - 9.04005828 10.08407425 -1.34354704 - 10.45323950 2.58760755 -9.29502963 - 10.17722947 10.19520664 -6.54370483 - 8.99299065 5.38080208 -1.34726654 - 9.99797382 5.66164108 -6.59486224 - 4.06509392 2.56307864 -3.62201375 - 1.86463895 5.37289668 -4.18364821 - 1.48071081 2.50722374 -1.38698243 - 5.31632177 2.60516389 -8.73432421 - 2.92042850 4.93965699 -9.05261002 - 5.28479134 7.35669562 -8.69970096 - 2.54170162 7.97434973 -6.81766353 - 4.63237513 5.41921025 -6.30923716 - 4.38712839 7.77450642 -3.78168107 - 1.93336897 10.18086985 -4.07043998 - 1.63381573 7.78546141 -1.38576569 - 3.82820682 5.15142935 -1.12030694 - 2.82159816 0.07458359 -9.07531592 - 1.92976753 2.48324586 -6.41285065 - 4.82587856 0.35096685 -6.24923329 - 3.97173668 10.25097317 -1.10831772 - 7.92450859 0.06928114 -9.21975056 - 7.20379495 0.01405650 -4.15931062 - 8.07361105 5.06584253 -9.46648850 - 7.74071142 2.94788585 -6.74119240 - 6.82176569 4.87071925 -4.20543358 - 6.75829458 2.64755529 -1.37753112 - 7.56901896 8.08736500 -6.89387186 - 9.34122642 7.39529048 -3.87446742 - 6.45886472 7.74788496 -1.33595414 - 10.29670082 6.67989973 -2.30160312 - 11.28363944 6.60523824 -7.61321620 - 11.69459529 6.33253278-10.06015158 - 11.15405569 1.22822234 -7.57130465 - 8.23874669 3.77019894 -2.46419540 - 10.15679927 1.64255785 -2.19170732 - 0.84548527 1.46181374 -5.04927584 - 7.93686034 3.82805443 -0.03195570 - 9.14023570 4.27333895 -7.70935129 - 11.77622998 1.39321150-10.04279499 - 10.61991123 6.48885379 -4.90306163 - 3.61339354 4.35879121 -4.79610874 - 3.03346887 3.73736293 -2.19370448 - 4.99711292 1.54316762 -1.96586832 - 0.37888449 4.08352202 -0.58321874 - 4.71367881 4.06418041 -9.91684843 - 4.02901970 4.14643293 -7.60065336 - 6.21889367 1.55539697 -6.90659173 - 6.49332208 1.36514478 -9.75700677 - 5.48288251 0.79284494 -4.42156967 - 3.60982499 6.48226537 -7.90972017 - 3.32205291 6.83998886 -5.50302495 - 4.00679756 8.96730368 -7.92261365 - 6.04587768 6.71427100 -7.07057095 - 1.14097640 9.02994416 -5.32880799 - 6.61857651 6.27791859 -9.63931355 - 3.54158032 9.26039862 -5.22050664 - 2.73244258 6.69826029 -2.98604408 - 2.33624581 6.35829912 -0.19041748 - 3.17377812 9.10817579 -2.56059568 - 4.85541031 6.77307132 -1.72134243 - 1.88174220 8.80946640-10.29415990 - 0.52977720 9.30345056 -2.81706329 - 5.57291436 6.26417081 -4.51385801 - 2.47555580 9.12778003 -0.16477789 - 11.43373812 9.24376812 -8.00536211 - 3.47929693 1.34558118 -7.66319909 - 3.37775373 1.62065886 -5.24192549 - 1.25339424 4.34822305 -5.92273791 - 2.52305932 1.44672517 -2.82496992 - 4.18633672 1.28405025-10.28212287 - 0.84255403 3.69222450 -3.43326042 - 1.61468719 3.61401227 -8.28439043 - 7.72517682 8.92468742 -0.03501891 - 8.83766882 9.29287429 -7.69684113 - 8.35958234 1.42824854 -5.23403421 - 6.13600693 3.90519498 -5.81572010 - 8.63055706 3.92505478 -5.00770850 - 7.70754198 1.09511379 -2.51775113 - 7.67182881 1.25002793 -0.21027734 - 5.62807207 4.14928095 -0.77672743 - 6.05244202 3.30354111 -3.39162058 - 8.69187289 1.66185707 -8.02749128 - 6.93478183 3.62815745 -8.38395587 - 7.48910198 6.22350300 -0.22402862 - 5.65570422 9.35038186 -0.77736204 - 8.89134652 6.69695513 -8.12749500 - 8.29251146 6.46297835 -5.60165813 - 6.16209120 9.06599140 -5.96636900 - 6.46115075 9.01663902 -8.73133692 - 8.73424838 8.94321793 -5.20932959 - 7.88285320 6.07337364 -2.87089427 - 8.13755541 8.74735160 -2.49342941 - 5.92146544 8.67313799 -3.28080570 - - - --------------------------------------------------------------------------------------------------------- - - - k-point 1 : 0.2500 0.2500 0.2500 plane waves: 27363 - k-point 2 : -0.2500-0.2500 0.2500 plane waves: 27363 - k-point 3 : -0.2500 0.2500 0.2500 plane waves: 27374 - k-point 4 : 0.2500-0.2500 0.2500 plane waves: 27374 - - maximum and minimum number of plane-waves per node : 6889 6813 - - maximum number of plane-waves: 27374 - maximum index in each direction: - IXMAX= 18 IYMAX= 19 IZMAX= 18 - IXMIN= -18 IYMIN= -19 IZMIN= -18 - - - real space projection operators: - total allocation : 49879.22 KBytes - max/ min on nodes : 12476.88 12461.69 - - - parallel 3D FFT for wavefunctions: - minimum data exchange during FFTs selected (reduces bandwidth) - parallel 3D FFT for charge: - minimum data exchange during FFTs selected (reduces bandwidth) - - - total amount of memory used by VASP MPI-rank0 162829. kBytes -======================================================================= - - base : 30000. kBytes - nonlr-proj: 30278. kBytes - fftplans : 41293. kBytes - grid : 25778. kBytes - one-center: 373. kBytes - wavefun : 35107. kBytes - - INWAV: cpu time 0.0000: real time 0.0004 - Broyden mixing: mesh for mixing (old mesh) - NGX = 37 NGY = 39 NGZ = 37 - (NGX =160 NGY =160 NGZ =160) - gives a total of 53391 points - - initial charge density was supplied: - charge density of overlapping atoms calculated - number of electron 512.0000000 magnetization - keeping initial charge density in first step - - --------------------------------------------------------------------------------------------------------- - - - Maximum index for non-local projection operator 2220 - Maximum index for augmentation-charges 15756 (set IRDMAX) - - --------------------------------------------------------------------------------------------------------- - - - First call to EWALD: gamma= 0.173 - Maximum number of real-space cells 3x 3x 3 - Maximum number of reciprocal cells 3x 3x 3 - - FEWALD: cpu time 0.0043: real time 0.0043 - - ---------------------------------------- Iteration 1( 1) --------------------------------------- - - - POTLOK: cpu time 0.4295: real time 0.4322 - SETDIJ: cpu time 0.3784: real time 0.3810 - EDDAV: cpu time 15.9341: real time 16.0792 - DOS: cpu time 0.0009: real time 0.0010 - -------------------------------------------- - LOOP: cpu time 16.7430: real time 16.8934 - - eigenvalue-minimisations : 2464 - total energy-change (2. order) : 0.1349628E+04 (-0.2724720E+05) - number of electron 512.0000000 magnetization - augmentation part 512.0000000 magnetization - - Free energy of the ion-electron system (eV) - --------------------------------------------------- - alpha Z PSCENC = 1957.98898647 - Ewald energy TEWEN = -24751.75528992 - -Hartree energ DENC = -7477.36693752 - -exchange EXHF = 0.00000000 - -V(xc)+E(xc) XCENC = 592.98155804 - PAW double counting = 25569.98736858 -25757.03612884 - entropy T*S EENTRO = -0.03132919 - eigenvalues EBANDS = 1115.23688544 - atomic energy EATOM = 30099.62314931 - Solvation Ediel_sol = 0.00000000 - --------------------------------------------------- - free energy TOTEN = 1349.62826237 eV - - energy without entropy = 1349.65959156 energy(sigma->0) = 1349.64392696 - - --------------------------------------------------------------------------------------------------------- - - - - ---------------------------------------- Iteration 1( 2) --------------------------------------- - - - EDDAV: cpu time 18.6996: real time 18.9839 - DOS: cpu time 0.0004: real time 0.0004 - -------------------------------------------- - LOOP: cpu time 18.7000: real time 18.9844 - - eigenvalue-minimisations : 3048 - total energy-change (2. order) :-0.4093752E+04 (-0.3974096E+04) - number of electron 512.0000000 magnetization - augmentation part 512.0000000 magnetization - - Free energy of the ion-electron system (eV) - --------------------------------------------------- - alpha Z PSCENC = 1957.98898647 - Ewald energy TEWEN = -24751.75528992 - -Hartree energ DENC = -7477.36693752 - -exchange EXHF = 0.00000000 - -V(xc)+E(xc) XCENC = 592.98155804 - PAW double counting = 25569.98736858 -25757.03612884 - entropy T*S EENTRO = -0.00000000 - eigenvalues EBANDS = -2978.54664612 - atomic energy EATOM = 30099.62314931 - Solvation Ediel_sol = 0.00000000 - --------------------------------------------------- - free energy TOTEN = -2744.12394000 eV - - energy without entropy = -2744.12394000 energy(sigma->0) = -2744.12394000 - - --------------------------------------------------------------------------------------------------------- - - - - ---------------------------------------- Iteration 1( 3) --------------------------------------- - - - EDDAV: cpu time 18.3514: real time 18.7060 - DOS: cpu time 0.0006: real time 0.0006 - -------------------------------------------- - LOOP: cpu time 18.3520: real time 18.7066 - - eigenvalue-minimisations : 2880 - total energy-change (2. order) :-0.2909814E+03 (-0.2892632E+03) - number of electron 512.0000000 magnetization - augmentation part 512.0000000 magnetization - - Free energy of the ion-electron system (eV) - --------------------------------------------------- - alpha Z PSCENC = 1957.98898647 - Ewald energy TEWEN = -24751.75528992 - -Hartree energ DENC = -7477.36693752 - -exchange EXHF = 0.00000000 - -V(xc)+E(xc) XCENC = 592.98155804 - PAW double counting = 25569.98736858 -25757.03612884 - entropy T*S EENTRO = -0.00000000 - eigenvalues EBANDS = -3269.52807870 - atomic energy EATOM = 30099.62314931 - Solvation Ediel_sol = 0.00000000 - --------------------------------------------------- - free energy TOTEN = -3035.10537258 eV - - energy without entropy = -3035.10537258 energy(sigma->0) = -3035.10537258 - - --------------------------------------------------------------------------------------------------------- - - - - ---------------------------------------- Iteration 1( 4) --------------------------------------- - - - EDDAV: cpu time 19.2417: real time 19.4551 - DOS: cpu time 0.0007: real time 0.0007 - -------------------------------------------- - LOOP: cpu time 19.2423: real time 19.4558 - - eigenvalue-minimisations : 2992 - total energy-change (2. order) :-0.6579059E+01 (-0.6556606E+01) - number of electron 512.0000000 magnetization - augmentation part 512.0000000 magnetization - - Free energy of the ion-electron system (eV) - --------------------------------------------------- - alpha Z PSCENC = 1957.98898647 - Ewald energy TEWEN = -24751.75528992 - -Hartree energ DENC = -7477.36693752 - -exchange EXHF = 0.00000000 - -V(xc)+E(xc) XCENC = 592.98155804 - PAW double counting = 25569.98736858 -25757.03612884 - entropy T*S EENTRO = -0.00000000 - eigenvalues EBANDS = -3276.10713750 - atomic energy EATOM = 30099.62314931 - Solvation Ediel_sol = 0.00000000 - --------------------------------------------------- - free energy TOTEN = -3041.68443138 eV - - energy without entropy = -3041.68443138 energy(sigma->0) = -3041.68443138 - - --------------------------------------------------------------------------------------------------------- - - - - ---------------------------------------- Iteration 1( 5) --------------------------------------- - - - EDDAV: cpu time 18.5895: real time 18.8333 - DOS: cpu time 0.0004: real time 0.0004 - CHARGE: cpu time 1.6324: real time 1.6473 - MIXING: cpu time 0.0080: real time 0.0080 - -------------------------------------------- - LOOP: cpu time 20.2303: real time 20.4891 - - eigenvalue-minimisations : 2880 - total energy-change (2. order) :-0.1578873E+00 (-0.1575926E+00) - number of electron 512.0000004 magnetization - augmentation part 53.5698785 magnetization - - Broyden mixing: - rms(total) = 0.15301E+02 rms(broyden)= 0.15300E+02 - rms(prec ) = 0.16575E+02 - weight for this iteration 100.00 - - Free energy of the ion-electron system (eV) - --------------------------------------------------- - alpha Z PSCENC = 1957.98898647 - Ewald energy TEWEN = -24751.75528992 - -Hartree energ DENC = -7477.36693752 - -exchange EXHF = 0.00000000 - -V(xc)+E(xc) XCENC = 592.98155804 - PAW double counting = 25569.98736858 -25757.03612884 - entropy T*S EENTRO = -0.00000000 - eigenvalues EBANDS = -3276.26502483 - atomic energy EATOM = 30099.62314931 - Solvation Ediel_sol = 0.00000000 - --------------------------------------------------- - free energy TOTEN = -3041.84231871 eV - - energy without entropy = -3041.84231871 energy(sigma->0) = -3041.84231871 - - --------------------------------------------------------------------------------------------------------- - - - - ---------------------------------------- Iteration 1( 6) --------------------------------------- - - - POTLOK: cpu time 0.4290: real time 0.4367 - SETDIJ: cpu time 0.3636: real time 0.3659 - EDDIAG: cpu time 3.4456: real time 3.5943 - RMM-DIIS: cpu time 20.3821: real time 20.7521 - ORTHCH: cpu time 0.1059: real time 0.1066 - DOS: cpu time 0.0009: real time 0.0009 - CHARGE: cpu time 1.6523: real time 1.7151 - MIXING: cpu time 0.9122: real time 0.9207 - -------------------------------------------- - LOOP: cpu time 27.2916: real time 27.8923 - - eigenvalue-minimisations : 2525 - total energy-change (2. order) : 0.3009434E+03 (-0.5397773E+02) - number of electron 512.0000003 magnetization - augmentation part 47.8666179 magnetization - - Broyden mixing: - rms(total) = 0.84266E+01 rms(broyden)= 0.84264E+01 - rms(prec ) = 0.86134E+01 - weight for this iteration 100.00 - - eigenvalues of (default mixing * dielectric matrix) - average eigenvalue GAMMA= 1.7467 - 1.7467 - - Free energy of the ion-electron system (eV) - --------------------------------------------------- - alpha Z PSCENC = 1957.98898647 - Ewald energy TEWEN = -24751.75528992 - -Hartree energ DENC = -8827.02427479 - -exchange EXHF = 0.00000000 - -V(xc)+E(xc) XCENC = 785.04531975 - PAW double counting = 36385.53466306 -36590.85078659 - entropy T*S EENTRO = -0.00000000 - eigenvalues EBANDS = -1799.46070877 - atomic energy EATOM = 30099.62314931 - Solvation Ediel_sol = 0.00000000 - --------------------------------------------------- - free energy TOTEN = -2740.89894149 eV - - energy without entropy = -2740.89894149 energy(sigma->0) = -2740.89894149 - - --------------------------------------------------------------------------------------------------------- - - - - ---------------------------------------- Iteration 1( 7) --------------------------------------- - - - POTLOK: cpu time 0.4226: real time 0.4267 - SETDIJ: cpu time 0.3664: real time 0.3687 - EDDIAG: cpu time 3.2856: real time 3.3126 - RMM-DIIS: cpu time 21.0417: real time 21.6921 - ORTHCH: cpu time 0.1155: real time 0.1162 - DOS: cpu time 0.0033: real time 0.0033 - CHARGE: cpu time 1.6947: real time 1.7100 - MIXING: cpu time 0.0066: real time 0.0195 - -------------------------------------------- - LOOP: cpu time 26.9363: real time 27.6491 - - eigenvalue-minimisations : 2764 - total energy-change (2. order) :-0.2438432E+02 (-0.2613955E+02) - number of electron 512.0000003 magnetization - augmentation part 44.2579405 magnetization - - Broyden mixing: - rms(total) = 0.27475E+01 rms(broyden)= 0.27465E+01 - rms(prec ) = 0.30813E+01 - weight for this iteration 100.00 - - eigenvalues of (default mixing * dielectric matrix) - average eigenvalue GAMMA= 1.6731 - 1.6731 1.6731 - - Free energy of the ion-electron system (eV) - --------------------------------------------------- - alpha Z PSCENC = 1957.98898647 - Ewald energy TEWEN = -24751.75528992 - -Hartree energ DENC = -9257.28558305 - -exchange EXHF = 0.00000000 - -V(xc)+E(xc) XCENC = 806.32740451 - PAW double counting = 50668.51092546 -50882.10358149 - entropy T*S EENTRO = -0.00000000 - eigenvalues EBANDS = -1406.58927120 - atomic energy EATOM = 30099.62314931 - Solvation Ediel_sol = 0.00000000 - --------------------------------------------------- - free energy TOTEN = -2765.28325991 eV - - energy without entropy = -2765.28325991 energy(sigma->0) = -2765.28325991 - - --------------------------------------------------------------------------------------------------------- - - - - ---------------------------------------- Iteration 1( 8) --------------------------------------- - - - POTLOK: cpu time 0.4109: real time 0.4140 - SETDIJ: cpu time 0.3645: real time 0.3668 - EDDIAG: cpu time 3.3217: real time 3.3495 - RMM-DIIS: cpu time 20.5928: real time 20.9749 - ORTHCH: cpu time 0.1004: real time 0.1011 - DOS: cpu time 0.0008: real time 0.0008 - CHARGE: cpu time 1.7089: real time 1.7239 - MIXING: cpu time 0.0075: real time 0.0075 - -------------------------------------------- - LOOP: cpu time 26.5074: real time 26.9384 - - eigenvalue-minimisations : 2634 - total energy-change (2. order) : 0.2411168E+01 (-0.1154514E+02) - number of electron 512.0000003 magnetization - augmentation part 47.1340963 magnetization - - Broyden mixing: - rms(total) = 0.14689E+01 rms(broyden)= 0.14684E+01 - rms(prec ) = 0.17164E+01 - weight for this iteration 100.00 - - eigenvalues of (default mixing * dielectric matrix) - average eigenvalue GAMMA= 1.4797 - 2.2125 1.1132 1.1132 - - Free energy of the ion-electron system (eV) - --------------------------------------------------- - alpha Z PSCENC = 1957.98898647 - Ewald energy TEWEN = -24751.75528992 - -Hartree energ DENC = -8699.29973372 - -exchange EXHF = 0.00000000 - -V(xc)+E(xc) XCENC = 755.25552905 - PAW double counting = 53503.81923924 -53714.12705792 - entropy T*S EENTRO = -0.00000000 - eigenvalues EBANDS = -1914.37691445 - atomic energy EATOM = 30099.62314931 - Solvation Ediel_sol = 0.00000000 - --------------------------------------------------- - free energy TOTEN = -2762.87209194 eV - - energy without entropy = -2762.87209194 energy(sigma->0) = -2762.87209194 - - --------------------------------------------------------------------------------------------------------- - - - - ---------------------------------------- Iteration 1( 9) --------------------------------------- - - - POTLOK: cpu time 0.4133: real time 0.4206 - SETDIJ: cpu time 0.3647: real time 0.3671 - EDDIAG: cpu time 3.3212: real time 3.3489 - RMM-DIIS: cpu time 21.6956: real time 21.8869 - ORTHCH: cpu time 0.0995: real time 0.1001 - DOS: cpu time 0.0013: real time 0.0013 - CHARGE: cpu time 1.6398: real time 1.6555 - MIXING: cpu time 0.0076: real time 0.0077 - -------------------------------------------- - LOOP: cpu time 27.5430: real time 27.7881 - - eigenvalue-minimisations : 2880 - total energy-change (2. order) : 0.3894405E+01 (-0.1027614E+01) - number of electron 512.0000003 magnetization - augmentation part 46.5812523 magnetization - - Broyden mixing: - rms(total) = 0.33367E+00 rms(broyden)= 0.33366E+00 - rms(prec ) = 0.40808E+00 - weight for this iteration 100.00 - - eigenvalues of (default mixing * dielectric matrix) - average eigenvalue GAMMA= 1.5076 - 2.3808 1.0720 1.2887 1.2887 - - Free energy of the ion-electron system (eV) - --------------------------------------------------- - alpha Z PSCENC = 1957.98898647 - Ewald energy TEWEN = -24751.75528992 - -Hartree energ DENC = -8928.94658189 - -exchange EXHF = 0.00000000 - -V(xc)+E(xc) XCENC = 792.30329227 - PAW double counting = 57156.08047285 -57370.57713046 - entropy T*S EENTRO = -0.00000000 - eigenvalues EBANDS = -1713.69458545 - atomic energy EATOM = 30099.62314931 - Solvation Ediel_sol = 0.00000000 - --------------------------------------------------- - free energy TOTEN = -2758.97768684 eV - - energy without entropy = -2758.97768684 energy(sigma->0) = -2758.97768684 - - --------------------------------------------------------------------------------------------------------- - - - - ---------------------------------------- Iteration 1( 10) --------------------------------------- - - - POTLOK: cpu time 0.4133: real time 0.4172 - SETDIJ: cpu time 0.3667: real time 0.3693 - EDDIAG: cpu time 3.3094: real time 3.3381 - RMM-DIIS: cpu time 21.6227: real time 21.8113 - ORTHCH: cpu time 0.0980: real time 0.0987 - DOS: cpu time 0.0019: real time 0.0019 - CHARGE: cpu time 1.6856: real time 1.7015 - MIXING: cpu time 0.0075: real time 0.0076 - -------------------------------------------- - LOOP: cpu time 27.5052: real time 27.7455 - - eigenvalue-minimisations : 2883 - total energy-change (2. order) :-0.5080966E+00 (-0.1013374E+01) - number of electron 512.0000003 magnetization - augmentation part 45.7646133 magnetization - - Broyden mixing: - rms(total) = 0.42647E+00 rms(broyden)= 0.42623E+00 - rms(prec ) = 0.52113E+00 - weight for this iteration 100.00 - - eigenvalues of (default mixing * dielectric matrix) - average eigenvalue GAMMA= 1.5435 - 2.6289 2.0293 1.0150 1.0223 1.0223 - - Free energy of the ion-electron system (eV) - --------------------------------------------------- - alpha Z PSCENC = 1957.98898647 - Ewald energy TEWEN = -24751.75528992 - -Hartree energ DENC = -9031.47944137 - -exchange EXHF = 0.00000000 - -V(xc)+E(xc) XCENC = 796.96872218 - PAW double counting = 57911.48144667 -58128.19461827 - entropy T*S EENTRO = -0.00000000 - eigenvalues EBANDS = -1614.11873853 - atomic energy EATOM = 30099.62314931 - Solvation Ediel_sol = 0.00000000 - --------------------------------------------------- - free energy TOTEN = -2759.48578346 eV - - energy without entropy = -2759.48578346 energy(sigma->0) = -2759.48578346 - - --------------------------------------------------------------------------------------------------------- - - - - ---------------------------------------- Iteration 1( 11) --------------------------------------- - - - POTLOK: cpu time 0.4073: real time 0.4096 - SETDIJ: cpu time 0.3628: real time 0.3653 - EDDIAG: cpu time 3.2834: real time 3.3121 - RMM-DIIS: cpu time 21.5717: real time 21.7601 - ORTHCH: cpu time 0.0973: real time 0.0980 - DOS: cpu time 0.0004: real time 0.0004 - CHARGE: cpu time 1.6928: real time 1.7091 - MIXING: cpu time 0.0073: real time 0.0073 - -------------------------------------------- - LOOP: cpu time 27.4230: real time 27.6619 - - eigenvalue-minimisations : 2879 - total energy-change (2. order) : 0.3752853E+00 (-0.1685581E+00) - number of electron 512.0000003 magnetization - augmentation part 46.0018998 magnetization - - Broyden mixing: - rms(total) = 0.13858E+00 rms(broyden)= 0.13857E+00 - rms(prec ) = 0.16031E+00 - weight for this iteration 100.00 - - eigenvalues of (default mixing * dielectric matrix) - average eigenvalue GAMMA= 1.6169 - 2.7001 2.7001 1.2304 1.0384 1.0161 1.0161 - - Free energy of the ion-electron system (eV) - --------------------------------------------------- - alpha Z PSCENC = 1957.98898647 - Ewald energy TEWEN = -24751.75528992 - -Hartree energ DENC = -8964.08048258 - -exchange EXHF = 0.00000000 - -V(xc)+E(xc) XCENC = 788.18030299 - PAW double counting = 57853.25143493 -58069.90488221 - entropy T*S EENTRO = -0.00000000 - eigenvalues EBANDS = -1672.41371720 - atomic energy EATOM = 30099.62314931 - Solvation Ediel_sol = 0.00000000 - --------------------------------------------------- - free energy TOTEN = -2759.11049821 eV - - energy without entropy = -2759.11049821 energy(sigma->0) = -2759.11049821 - - --------------------------------------------------------------------------------------------------------- - - - - ---------------------------------------- Iteration 1( 12) --------------------------------------- - - - POTLOK: cpu time 0.4046: real time 0.4118 - SETDIJ: cpu time 0.3654: real time 0.3680 - EDDIAG: cpu time 3.3413: real time 3.3708 - RMM-DIIS: cpu time 21.9551: real time 22.1466 - ORTHCH: cpu time 0.0937: real time 0.0944 - DOS: cpu time 0.0020: real time 0.0020 - CHARGE: cpu time 1.6967: real time 1.7123 - MIXING: cpu time 0.0071: real time 0.0072 - -------------------------------------------- - LOOP: cpu time 27.8658: real time 28.1130 - - eigenvalue-minimisations : 2945 - total energy-change (2. order) : 0.1313648E-02 (-0.4962148E-01) - number of electron 512.0000003 magnetization - augmentation part 46.1215366 magnetization - - Broyden mixing: - rms(total) = 0.58639E-01 rms(broyden)= 0.58573E-01 - rms(prec ) = 0.61842E-01 - weight for this iteration 100.00 - - eigenvalues of (default mixing * dielectric matrix) - average eigenvalue GAMMA= 1.7373 - 3.7182 2.4394 2.0823 1.0036 1.0036 1.0026 0.9112 - - Free energy of the ion-electron system (eV) - --------------------------------------------------- - alpha Z PSCENC = 1957.98898647 - Ewald energy TEWEN = -24751.75528992 - -Hartree energ DENC = -8946.84370197 - -exchange EXHF = 0.00000000 - -V(xc)+E(xc) XCENC = 788.22771961 - PAW double counting = 57704.32412612 -57921.02260020 - entropy T*S EENTRO = -0.00000000 - eigenvalues EBANDS = -1689.65157398 - atomic energy EATOM = 30099.62314931 - Solvation Ediel_sol = 0.00000000 - --------------------------------------------------- - free energy TOTEN = -2759.10918456 eV - - energy without entropy = -2759.10918456 energy(sigma->0) = -2759.10918456 - - --------------------------------------------------------------------------------------------------------- - - - - ---------------------------------------- Iteration 1( 13) --------------------------------------- - - - POTLOK: cpu time 0.4126: real time 0.4160 - SETDIJ: cpu time 0.3653: real time 0.3677 - EDDIAG: cpu time 3.2938: real time 3.3225 - RMM-DIIS: cpu time 23.3467: real time 23.5502 - ORTHCH: cpu time 0.0941: real time 0.0948 - DOS: cpu time 0.0003: real time 0.0003 - CHARGE: cpu time 1.6335: real time 1.6494 - MIXING: cpu time 0.0073: real time 0.0073 - -------------------------------------------- - LOOP: cpu time 29.1536: real time 29.4083 - - eigenvalue-minimisations : 3194 - total energy-change (2. order) :-0.6144415E-02 (-0.8297819E-02) - number of electron 512.0000003 magnetization - augmentation part 46.1210150 magnetization - - Broyden mixing: - rms(total) = 0.45494E-01 rms(broyden)= 0.45490E-01 - rms(prec ) = 0.48510E-01 - weight for this iteration 100.00 - - eigenvalues of (default mixing * dielectric matrix) - average eigenvalue GAMMA= 1.7080 - 4.2708 2.4696 2.1409 0.9849 0.9849 1.1030 0.8551 0.8551 - - Free energy of the ion-electron system (eV) - --------------------------------------------------- - alpha Z PSCENC = 1957.98898647 - Ewald energy TEWEN = -24751.75528992 - -Hartree energ DENC = -8950.31787048 - -exchange EXHF = 0.00000000 - -V(xc)+E(xc) XCENC = 789.20331883 - PAW double counting = 57859.42296026 -58076.06211343 - entropy T*S EENTRO = -0.00000000 - eigenvalues EBANDS = -1687.21847001 - atomic energy EATOM = 30099.62314931 - Solvation Ediel_sol = 0.00000000 - --------------------------------------------------- - free energy TOTEN = -2759.11532897 eV - - energy without entropy = -2759.11532897 energy(sigma->0) = -2759.11532897 - - --------------------------------------------------------------------------------------------------------- - - - - ---------------------------------------- Iteration 1( 14) --------------------------------------- - - - POTLOK: cpu time 0.4112: real time 0.4136 - SETDIJ: cpu time 0.3672: real time 0.3697 - EDDIAG: cpu time 3.3056: real time 3.3346 - RMM-DIIS: cpu time 21.6327: real time 22.0145 - ORTHCH: cpu time 0.1479: real time 0.1493 - DOS: cpu time 0.0261: real time 0.0263 - CHARGE: cpu time 1.6860: real time 1.7022 - MIXING: cpu time 0.0079: real time 0.0080 - -------------------------------------------- - LOOP: cpu time 27.5846: real time 28.0182 - - eigenvalue-minimisations : 2902 - total energy-change (2. order) :-0.3419217E-02 (-0.2171307E-02) - number of electron 512.0000003 magnetization - augmentation part 46.1416185 magnetization - - Broyden mixing: - rms(total) = 0.54125E-01 rms(broyden)= 0.54122E-01 - rms(prec ) = 0.62931E-01 - weight for this iteration 100.00 - - eigenvalues of (default mixing * dielectric matrix) - average eigenvalue GAMMA= 1.7176 - 4.4075 2.4318 2.4318 1.0392 1.0392 1.1512 1.1512 0.9030 0.9030 - - Free energy of the ion-electron system (eV) - --------------------------------------------------- - alpha Z PSCENC = 1957.98898647 - Ewald energy TEWEN = -24751.75528992 - -Hartree energ DENC = -8947.55990098 - -exchange EXHF = 0.00000000 - -V(xc)+E(xc) XCENC = 789.02999286 - PAW double counting = 57933.67689589 -58150.24438012 - entropy T*S EENTRO = -0.00000000 - eigenvalues EBANDS = -1689.87820170 - atomic energy EATOM = 30099.62314931 - Solvation Ediel_sol = 0.00000000 - --------------------------------------------------- - free energy TOTEN = -2759.11874819 eV - - energy without entropy = -2759.11874819 energy(sigma->0) = -2759.11874819 - - --------------------------------------------------------------------------------------------------------- - - - - ---------------------------------------- Iteration 1( 15) --------------------------------------- - - - POTLOK: cpu time 0.4108: real time 0.4186 - SETDIJ: cpu time 0.3629: real time 0.3655 - EDDIAG: cpu time 3.6095: real time 3.7206 - RMM-DIIS: cpu time 21.9396: real time 22.2882 - ORTHCH: cpu time 0.0954: real time 0.0960 - DOS: cpu time 0.0004: real time 0.0004 - CHARGE: cpu time 1.6900: real time 1.7052 - MIXING: cpu time 0.0080: real time 0.0080 - -------------------------------------------- - LOOP: cpu time 28.1166: real time 28.6026 - - eigenvalue-minimisations : 2942 - total energy-change (2. order) : 0.3193716E-02 (-0.8621474E-03) - number of electron 512.0000003 magnetization - augmentation part 46.1245960 magnetization - - Broyden mixing: - rms(total) = 0.23275E-01 rms(broyden)= 0.23274E-01 - rms(prec ) = 0.27923E-01 - weight for this iteration 100.00 - - eigenvalues of (default mixing * dielectric matrix) - average eigenvalue GAMMA= 1.8061 - 5.2937 2.6429 1.9963 1.9963 1.0188 1.0188 1.3848 0.9439 0.9439 0.8213 - - Free energy of the ion-electron system (eV) - --------------------------------------------------- - alpha Z PSCENC = 1957.98898647 - Ewald energy TEWEN = -24751.75528992 - -Hartree energ DENC = -8951.94619746 - -exchange EXHF = 0.00000000 - -V(xc)+E(xc) XCENC = 789.53317108 - PAW double counting = 58026.99858120 -58243.54374183 - entropy T*S EENTRO = -0.00000000 - eigenvalues EBANDS = -1686.01421332 - atomic energy EATOM = 30099.62314931 - Solvation Ediel_sol = 0.00000000 - --------------------------------------------------- - free energy TOTEN = -2759.11555448 eV - - energy without entropy = -2759.11555448 energy(sigma->0) = -2759.11555448 - - --------------------------------------------------------------------------------------------------------- - - - - ---------------------------------------- Iteration 1( 16) --------------------------------------- - - - POTLOK: cpu time 0.4158: real time 0.4198 - SETDIJ: cpu time 0.3567: real time 0.3590 - EDDIAG: cpu time 3.2878: real time 3.3148 - RMM-DIIS: cpu time 21.8763: real time 22.4051 - ORTHCH: cpu time 0.0958: real time 0.0964 - DOS: cpu time 0.0003: real time 0.0003 - CHARGE: cpu time 1.6878: real time 1.7025 - MIXING: cpu time 0.0080: real time 0.0080 - -------------------------------------------- - LOOP: cpu time 27.7285: real time 28.3059 - - eigenvalue-minimisations : 2945 - total energy-change (2. order) : 0.1698033E-03 (-0.9790279E-03) - number of electron 512.0000003 magnetization - augmentation part 46.0993536 magnetization - - Broyden mixing: - rms(total) = 0.38962E-02 rms(broyden)= 0.38712E-02 - rms(prec ) = 0.42356E-02 - weight for this iteration 100.00 - - eigenvalues of (default mixing * dielectric matrix) - average eigenvalue GAMMA= 1.7123 - 4.3736 2.7805 2.2159 2.2159 1.0197 1.0197 1.4127 1.2143 0.8693 0.8566 - 0.8566 - - Free energy of the ion-electron system (eV) - --------------------------------------------------- - alpha Z PSCENC = 1957.98898647 - Ewald energy TEWEN = -24751.75528992 - -Hartree energ DENC = -8954.90543163 - -exchange EXHF = 0.00000000 - -V(xc)+E(xc) XCENC = 789.62532579 - PAW double counting = 58075.68906198 -58292.24360349 - entropy T*S EENTRO = -0.00000000 - eigenvalues EBANDS = -1683.13758317 - atomic energy EATOM = 30099.62314931 - Solvation Ediel_sol = 0.00000000 - --------------------------------------------------- - free energy TOTEN = -2759.11538467 eV - - energy without entropy = -2759.11538467 energy(sigma->0) = -2759.11538467 - - --------------------------------------------------------------------------------------------------------- - - - - ---------------------------------------- Iteration 1( 17) --------------------------------------- - - - POTLOK: cpu time 0.4244: real time 0.4267 - SETDIJ: cpu time 1.3504: real time 1.3618 - EDDIAG: cpu time 3.2722: real time 3.2992 - RMM-DIIS: cpu time 22.4619: real time 22.9794 - ORTHCH: cpu time 0.0938: real time 0.0945 - DOS: cpu time 0.0014: real time 0.0014 - CHARGE: cpu time 1.6252: real time 1.6404 - MIXING: cpu time 0.0079: real time 0.0080 - -------------------------------------------- - LOOP: cpu time 29.2371: real time 29.8113 - - eigenvalue-minimisations : 3026 - total energy-change (2. order) :-0.1502959E-03 (-0.1896731E-03) - number of electron 512.0000003 magnetization - augmentation part 46.0965200 magnetization - - Broyden mixing: - rms(total) = 0.95770E-02 rms(broyden)= 0.95764E-02 - rms(prec ) = 0.97739E-02 - weight for this iteration 100.00 - - eigenvalues of (default mixing * dielectric matrix) - average eigenvalue GAMMA= 1.5847 - 4.4880 2.7763 2.2227 2.2227 1.0199 1.0199 1.4212 1.2107 0.8709 0.8556 - 0.8556 0.0534 - - Free energy of the ion-electron system (eV) - --------------------------------------------------- - alpha Z PSCENC = 1957.98898647 - Ewald energy TEWEN = -24751.75528992 - -Hartree energ DENC = -8954.58320176 - -exchange EXHF = 0.00000000 - -V(xc)+E(xc) XCENC = 789.46481450 - PAW double counting = 58051.33020625 -58267.90955645 - entropy T*S EENTRO = -0.00000000 - eigenvalues EBANDS = -1683.27464336 - atomic energy EATOM = 30099.62314931 - Solvation Ediel_sol = 0.00000000 - --------------------------------------------------- - free energy TOTEN = -2759.11553497 eV - - energy without entropy = -2759.11553497 energy(sigma->0) = -2759.11553497 - - --------------------------------------------------------------------------------------------------------- - - - - ---------------------------------------- Iteration 1( 18) --------------------------------------- - - - POTLOK: cpu time 0.4134: real time 0.4201 - SETDIJ: cpu time 0.3676: real time 0.3700 - EDDIAG: cpu time 3.5712: real time 3.7130 - RMM-DIIS: cpu time 16.3810: real time 16.7032 - ORTHCH: cpu time 0.0940: real time 0.0947 - DOS: cpu time 0.0004: real time 0.0004 - -------------------------------------------- - LOOP: cpu time 20.8275: real time 21.3013 - - eigenvalue-minimisations : 1909 - total energy-change (2. order) :-0.1972319E-04 (-0.1930657E-04) - number of electron 512.0000003 magnetization - augmentation part 46.0965200 magnetization - - Free energy of the ion-electron system (eV) - --------------------------------------------------- - alpha Z PSCENC = 1957.98898647 - Ewald energy TEWEN = -24751.75528992 - -Hartree energ DENC = -8954.61914649 - -exchange EXHF = 0.00000000 - -V(xc)+E(xc) XCENC = 789.45866930 - PAW double counting = 58055.02981690 -58271.61022103 - entropy T*S EENTRO = -0.00000000 - eigenvalues EBANDS = -1683.23151923 - atomic energy EATOM = 30099.62314931 - Solvation Ediel_sol = 0.00000000 - --------------------------------------------------- - free energy TOTEN = -2759.11555469 eV - - energy without entropy = -2759.11555469 energy(sigma->0) = -2759.11555469 - - --------------------------------------------------------------------------------------------------------- - - - - - average (electrostatic) potential at core - the test charge radii are 1.2481 0.7215 - (the norm of the test charge is 1.0000) - 1 -40.2476 2 -39.1528 3 -40.6207 4 -39.3786 5 -40.4739 - 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10.17723 10.19521 -6.54370 -1.912133 0.645921 1.299418 - 8.99299 5.38080 -1.34727 1.465509 -1.682114 1.508357 - 9.99797 5.66164 -6.59486 -4.060154 -2.745413 0.113744 - 4.06509 2.56308 -3.62201 2.161022 -0.404899 0.700634 - 1.86464 5.37290 -4.18365 1.898365 -4.811950 1.164616 - 1.48071 2.50722 -1.38698 -0.159761 0.654446 0.800545 - 5.31632 2.60516 -8.73432 -1.065002 -2.143604 0.385304 - 2.92043 4.93966 -9.05261 -1.038381 -0.273822 -3.492497 - 5.28479 7.35670 -8.69970 -1.826752 2.877095 -2.967491 - 2.54170 7.97435 -6.81766 1.329406 2.052918 0.078364 - 4.63238 5.41921 -6.30924 0.389829 -0.886029 2.737784 - 4.38713 7.77451 -3.78168 -1.410449 -0.334228 -1.229259 - 1.93337 10.18087 -4.07044 1.966737 0.918636 2.853180 - 1.63382 7.78546 -1.38577 0.224611 2.427942 0.301103 - 3.82821 5.15143 -1.12031 -0.548901 0.455424 1.269835 - 2.82160 0.07458 -9.07532 1.049343 -0.645265 -2.679311 - 1.92977 2.48325 -6.41285 2.351453 1.396510 -0.220755 - 4.82588 0.35097 -6.24923 -0.406801 -0.552217 0.282794 - 3.97174 10.25097 -1.10832 -1.747035 2.923356 0.134789 - 7.92451 0.06928 -9.21975 1.048177 1.571376 -1.578620 - 7.20379 0.01406 -4.15931 0.240223 -1.297658 0.343224 - 8.07361 5.06584 -9.46649 1.248680 -1.742931 3.123376 - 7.74071 2.94789 -6.74119 0.990235 -0.977882 2.005332 - 6.82177 4.87072 -4.20543 3.017913 -1.393136 0.027461 - 6.75829 2.64756 -1.37753 -0.419061 -1.734583 -3.612490 - 7.56902 8.08736 -6.89387 -0.028730 -1.524328 4.227224 - 9.34123 7.39529 -3.87447 -5.039369 3.137424 0.201434 - 6.45886 7.74788 -1.33595 3.203996 1.382863 -2.925098 - 10.29670 6.67990 -2.30160 0.055208 -1.231968 0.498367 - 11.28364 6.60524 -7.61322 2.288975 1.294560 1.171365 - 11.69460 6.33253 -10.06015 -1.449368 -0.123786 0.887939 - 11.15406 1.22822 -7.57130 -0.273106 1.339776 -0.148285 - 8.23875 3.77020 -2.46420 0.011999 -0.705991 0.885661 - 10.15680 1.64256 -2.19171 -0.842790 -2.125336 0.515394 - 0.84549 1.46181 -5.04928 -0.751256 -1.167158 -0.318719 - 7.93686 3.82805 -0.03196 -1.545977 1.874825 -0.860864 - 9.14024 4.27334 -7.70935 -0.046227 -1.146502 -0.678592 - 11.77623 1.39321 -10.04279 1.153054 -0.982092 -0.840093 - 10.61991 6.48885 -4.90306 2.100481 0.816389 0.097845 - 3.61339 4.35879 -4.79611 -0.565449 -0.594190 0.776575 - 3.03347 3.73736 -2.19370 0.986706 1.264216 -0.308223 - 4.99711 1.54317 -1.96587 -0.423417 0.365482 0.443933 - 0.37888 4.08352 -0.58322 0.816300 -0.464864 0.017809 - 4.71368 4.06418 -9.91685 -0.584270 -0.054221 -0.740849 - 4.02902 4.14643 -7.60065 0.214116 -2.501498 0.140141 - 6.21889 1.55540 -6.90659 -0.873618 0.403321 -1.859245 - 6.49332 1.36514 -9.75701 1.541818 -1.162581 0.250063 - 5.48288 0.79284 -4.42157 0.144945 0.843444 -0.066509 - 3.60982 6.48227 -7.90972 0.122916 0.451563 -0.121447 - 3.32205 6.83999 -5.50302 -0.520289 -1.811122 1.324500 - 4.00680 8.96730 -7.92261 -1.114987 0.039102 1.615578 - 6.04588 6.71427 -7.07057 -0.292217 -0.588797 -1.002194 - 1.14098 9.02994 -5.32881 -1.095054 -1.567429 -3.584275 - 6.61858 6.27792 -9.63931 -0.570733 -0.184688 -0.820547 - 3.54158 9.26040 -5.22051 -0.336706 -0.308601 0.679455 - 2.73244 6.69826 -2.98604 -0.549235 -0.737014 1.491923 - 2.33625 6.35830 -0.19042 1.224715 0.130796 0.107808 - 3.17378 9.10818 -2.56060 0.168396 -0.272836 -0.647745 - 4.85541 6.77307 -1.72134 -0.057901 0.012705 -1.467349 - 1.88174 8.80947 -10.29416 -0.908719 0.674762 -2.375021 - 0.52978 9.30345 -2.81706 0.003518 -0.541019 0.490965 - 5.57291 6.26417 -4.51386 -1.085061 0.345516 0.161456 - 2.47556 9.12778 -0.16478 1.353321 -0.443555 0.720877 - 11.43374 9.24377 -8.00536 -0.816749 -1.576021 1.284195 - 3.47930 1.34558 -7.66320 1.581078 0.624272 -0.077461 - 3.37775 1.62066 -5.24193 -0.629132 0.185197 -0.389502 - 1.25339 4.34822 -5.92274 0.115520 -0.055237 -0.086609 - 2.52306 1.44673 -2.82497 0.716669 -0.646724 0.766923 - 4.18634 1.28405 -10.28212 -0.558642 1.261340 -0.773964 - 0.84255 3.69222 -3.43326 0.177565 1.778082 0.307744 - 1.61469 3.61401 -8.28439 1.436486 1.056627 0.133399 - 7.72518 8.92469 -0.03502 0.537936 -0.233715 1.980664 - 8.83767 9.29287 -7.69684 1.078716 0.836110 -1.548030 - 8.35958 1.42825 -5.23403 -0.338921 -1.139686 0.310316 - 6.13601 3.90519 -5.81572 -0.361181 2.138605 -1.322023 - 8.63056 3.92505 -5.00771 -0.670356 1.984947 -2.225434 - 7.70754 1.09511 -2.51775 0.533649 -0.726997 -2.607798 - 7.67183 1.25003 -0.21028 -1.309313 -0.691626 1.185883 - 5.62807 4.14928 -0.77673 -2.202666 1.487480 0.456936 - 6.05244 3.30354 -3.39162 -1.804077 0.048683 1.381577 - 8.69187 1.66186 -8.02749 0.864298 -1.095826 -0.975893 - 6.93478 3.62816 -8.38396 -1.455618 1.126670 -1.776035 - 7.48910 6.22350 -0.22403 0.327175 2.328293 -1.246791 - 5.65570 9.35038 -0.77736 -2.560923 1.529491 0.923532 - 8.89135 6.69696 -8.12750 -1.069675 0.744436 -0.405608 - 8.29251 6.46298 -5.60166 -0.076631 0.821207 0.348408 - 6.16209 9.06599 -5.96637 0.542740 1.224802 0.237832 - 6.46115 9.01664 -8.73134 1.326101 -1.293391 1.229530 - 8.73425 8.94322 -5.20933 -0.661850 0.533967 0.151013 - 7.88285 6.07337 -2.87089 0.417031 2.721110 -0.449228 - 8.13756 8.74735 -2.49343 0.845868 -0.012559 0.076684 - 5.92147 8.67314 -3.28081 0.696122 0.272814 0.946084 - ----------------------------------------------------------------------------------- - total drift: -0.027614 0.070888 -0.101921 - - --------------------------------------------------------------------------------------------------------- - - - - FREE ENERGIE OF THE ION-ELECTRON SYSTEM (eV) - --------------------------------------------------- - free energy TOTEN = -2759.11555469 eV - - energy without entropy= -2759.11555469 energy(sigma->0) = -2759.11555469 - - - --------------------------------------------------------------------------------------------------------- - - - POTLOK: cpu time 0.7738: real time 0.7785 - - --------------------------------------------------------------------------------------------------------- - - - LOOP+: cpu time 485.2378: real time 492.8859 - 4ORBIT: cpu time 0.0000: real time 0.0000 - - total amount of memory used by VASP MPI-rank0 162829. kBytes -======================================================================= - - base : 30000. kBytes - nonlr-proj: 30278. kBytes - fftplans : 41293. kBytes - grid : 25778. kBytes - one-center: 373. kBytes - wavefun : 35107. kBytes - - - - General timing and accounting informations for this job: - ======================================================== - - Total CPU time used (sec): 490.672 - User time (sec): 473.085 - System time (sec): 17.587 - Elapsed time (sec): 499.227 - - Maximum memory used (kb): 411168. - Average memory used (kb): N/A - - Minor page faults: 755328 - Major page faults: 4157 - Voluntary context switches: 7256 diff --git a/mace-bench/3rdparty/SevenNet/example_inputs/data/label_1/OUTCAR_2 b/mace-bench/3rdparty/SevenNet/example_inputs/data/label_1/OUTCAR_2 deleted file mode 100644 index 1b17e235293cb0c31a045cb6524c910d46831862..0000000000000000000000000000000000000000 --- a/mace-bench/3rdparty/SevenNet/example_inputs/data/label_1/OUTCAR_2 +++ /dev/null @@ -1,3614 +0,0 @@ - vasp.6.3.2 27Jun22 (build Aug 12 2022 00:53:59) complex - - executed on tv2STD date 2022.09.21 12:09:47 - running 32 mpi-ranks, with 1 threads/rank - distrk: each k-point on 16 cores, 2 groups - distr: one band on NCORE= 4 cores, 4 groups - - --------------------------------------------------------------------------------------------------------- - - - INCAR: - SYSTEM = HfO2_p21c - NWRITE = 2 write-flag - ISTART = 0 job : 0-new, 1-cont, 2-samecut - ICHARG = 2 charge: 0-wave, 1-file, 2-atom, >10-const - INIWAV = 1 electr: 0-lowe 1-rand 2-diag - ENCUT = 500 - PREC = Accurate normal | accurate - ADDGRID = True - NELM = 100 - LREAL = Auto real-space projection (.FALSE., .TRUE., On, Auto) - ALGO = Fast Normal, Fast, Very_Fast - LWAVE = .F. - LCHARG = .F. - NSW = 0 - IBRION = 2 ionic relax: 0-MD, 1-quasi-Newton, 2-CG, 3-Damped MD - EDIFFG = -0.002 - ISIF = 3 (1:force\=y stress\=trace only ions\=y shape\=n volume\=n) - ISYM = 1 (1-use symmetry, 0-no symmetry) - ISMEAR = 0 (-1-Fermi, 1-Methfessel/Paxton) - SIGMA = 0.05 broadening in eV - NPAR = 4 - KPAR = 2 - METAGGA = SCAN - - POTCAR: PAW_PBE Hf 20Jan2003 - POTCAR: PAW_PBE O 08Apr2002 - POTCAR: PAW_PBE Hf 20Jan2003 - SHA256 = 0bb2207f9a10894133f750b65504b92b8afef976ae770762e0497daaaad8168a Hf/POTCAR - COPYR = (c) Copyright 20Jan2003 Georg Kresse - COPYR = This file is part of the software VASP. Any use, copying, and all other rights are regul - COPYR = If you do not have a valid VASP license, you may not use, copy or distribute this file. - VRHFIN =Hf: 6s5d - LEXCH = PE - EATOM = 75.9011 eV, 5.5786 Ry - - TITEL = PAW_PBE Hf 20Jan2003 - LULTRA = F use ultrasoft PP ? - IUNSCR = 1 unscreen: 0-lin 1-nonlin 2-no - RPACOR = 2.500 partial core radius - POMASS = 178.490; ZVAL = 4.000 mass and valenz - RCORE = 3.000 outmost cutoff radius - RWIGS = 3.050; RWIGS = 1.614 wigner-seitz radius (au A) - ENMAX = 220.334; ENMIN = 165.250 eV - RCLOC = 2.212 cutoff for local pot - LCOR = T correct aug charges - LPAW = T paw PP - EAUG = 335.116 - DEXC = 0.000 - RMAX = 3.077 core radius for proj-oper - RAUG = 1.300 factor for augmentation sphere - RDEP = 3.047 radius for radial grids - RDEPT = 2.344 core radius for aug-charge - - Atomic configuration - 16 entries - n l j E occ. - 1 0 0.50 -65259.4397 2.0000 - 2 0 0.50 -11157.9882 2.0000 - 2 1 1.50 -9795.2113 6.0000 - 3 0 0.50 -2541.4058 2.0000 - 3 1 1.50 -2134.4770 6.0000 - 3 2 2.50 -1653.5418 10.0000 - 4 0 0.50 -510.9575 2.0000 - 4 1 1.50 -377.5023 6.0000 - 4 2 2.50 -205.2085 10.0000 - 4 3 3.50 -15.4905 14.0000 - 5 0 0.50 -65.6020 2.0000 - 5 1 1.50 -34.2798 6.0000 - 5 2 2.50 -1.9877 3.0000 - 6 0 0.50 -4.7357 1.0000 - 6 1 1.50 -1.3606 0.0000 - 5 3 2.50 -1.3606 0.0000 - Description - l E TYP RCUT TYP RCUT - 2 -1.9876627 23 2.500 - 2 0.0744703 23 2.500 - 0 -4.7356889 23 2.600 - 0 3.2364747 23 2.600 - 1 -1.3605826 23 3.000 - 1 27.2116520 23 3.000 - local pseudopotential read in - partial core-charges read in - partial kinetic energy density read in - atomic valenz-charges read in - non local Contribution for L= 2 read in - real space projection operators read in - non local Contribution for L= 2 read in - real space projection operators read in - non local Contribution for L= 0 read in - real space projection operators read in - non local Contribution for L= 0 read in - real space projection operators read in - non local Contribution for L= 1 read in - real space projection operators read in - non local Contribution for L= 1 read in - real space projection operators read in - PAW grid and wavefunctions read in - - number of l-projection operators is LMAX = 6 - number of lm-projection operators is LMMAX = 18 - - POTCAR: PAW_PBE O 08Apr2002 - SHA256 = 818f92134a0a090dccd8ba1447fa70422a3b330e708bb4f08108d8ae51209ddf O/POTCAR - COPYR = (c) Copyright 08Apr2002 Georg Kresse - COPYR = This file is part of the software VASP. Any use, copying, and all other rights are regul - COPYR = If you do not have a valid VASP license, you may not use, copy or distribute this file. - VRHFIN =O: s2p4 - LEXCH = PE - EATOM = 432.3788 eV, 31.7789 Ry - - TITEL = PAW_PBE O 08Apr2002 - LULTRA = F use ultrasoft PP ? - IUNSCR = 1 unscreen: 0-lin 1-nonlin 2-no - RPACOR = 1.200 partial core radius - POMASS = 16.000; ZVAL = 6.000 mass and valenz - RCORE = 1.520 outmost cutoff radius - RWIGS = 1.550; RWIGS = 0.820 wigner-seitz radius (au A) - ENMAX = 400.000; ENMIN = 300.000 eV - ICORE = 2 local potential - LCOR = T correct aug charges - LPAW = T paw PP - EAUG = 605.392 - DEXC = 0.000 - RMAX = 1.553 core radius for proj-oper - RAUG = 1.300 factor for augmentation sphere - RDEP = 1.550 radius for radial grids - RDEPT = 1.329 core radius for aug-charge - - Atomic configuration - 4 entries - n l j E occ. - 1 0 0.50 -514.6923 2.0000 - 2 0 0.50 -23.9615 2.0000 - 2 1 0.50 -9.0305 4.0000 - 3 2 1.50 -9.5241 0.0000 - Description - l E TYP RCUT TYP RCUT - 0 -23.9615318 23 1.200 - 0 -9.5240782 23 1.200 - 1 -9.0304911 23 1.520 - 1 8.1634956 23 1.520 - 2 -9.5240782 7 1.500 - local pseudopotential read in - partial core-charges read in - partial kinetic energy density read in - kinetic energy density of atom read in - atomic valenz-charges read in - non local Contribution for L= 0 read in - real space projection operators read in - non local Contribution for L= 0 read in - real space projection operators read in - non local Contribution for L= 1 read in - real space projection operators read in - non local Contribution for L= 1 read in - real space projection operators read in - PAW grid and wavefunctions read in - - number of l-projection operators is LMAX = 4 - number of lm-projection operators is LMMAX = 8 - - Optimization of the real space projectors (new method) - - maximal supplied QI-value = 12.47 - optimisation between [QCUT,QGAM] = [ 11.35, 22.82] = [ 36.07,145.88] Ry - Optimized for a Real-space Cutoff 1.66 Angstroem - - l n(q) QCUT max X(q) W(low)/X(q) W(high)/X(q) e(spline) - 2 10 11.350 48.111 0.20E-03 0.11E-03 0.41E-06 - 2 10 11.350 40.545 0.19E-03 0.10E-03 0.39E-06 - 0 11 11.350 121.658 0.22E-04 0.19E-04 0.24E-06 - 0 11 11.350 71.177 0.17E-04 0.17E-04 0.23E-06 - 1 11 11.350 14.183 0.25E-03 0.43E-03 0.12E-05 - 1 11 11.350 8.257 0.17E-03 0.29E-03 0.81E-06 - Optimization of the real space projectors (new method) - - maximal supplied QI-value = 24.76 - optimisation between [QCUT,QGAM] = [ 11.39, 22.77] = [ 36.31,145.25] Ry - Optimized for a Real-space Cutoff 1.10 Angstroem - - l n(q) QCUT max X(q) W(low)/X(q) W(high)/X(q) e(spline) - 0 7 11.387 20.381 0.22E-03 0.48E-03 0.18E-06 - 0 7 11.387 15.268 0.22E-03 0.52E-03 0.19E-06 - 1 7 11.387 5.964 0.22E-03 0.73E-03 0.24E-06 - 1 7 11.387 5.382 0.19E-03 0.60E-03 0.21E-06 - PAW_PBE Hf 20Jan2003 : - energy of atom 1 EATOM= -75.9011 - kinetic energy error for atom= 0.0007 (will be added to EATOM!!) - PAW_PBE O 08Apr2002 : - energy of atom 2 EATOM= -432.3788 - kinetic energy error for atom= 0.0224 (will be added to EATOM!!) - - - POSCAR: name - positions in direct lattice - No initial velocities read in - WARNING: For meta-GGA calculations it is strongly recommended to include - aspherical contributions to the potential inside the PAW spheres (set - LASPH = .TRUE.) - - - METAGGA = SCAN LMAXTAU = 0 LMIXTAU = F - - exchange correlation table for LEXCH = 8 - RHO(1)= 0.500 N(1) = 2000 - RHO(2)= 100.500 N(2) = 4000 - - - --------------------------------------------------------------------------------------------------------- - - - ion position nearest neighbor table - 1 0.862 0.831 0.716- 35 1.85 77 1.99 89 2.06 34 2.15 68 2.17 76 2.35 87 2.57 30 3.21 - 7 3.26 26 3.29 14 3.31 12 3.33 24 3.34 6 3.56 5 3.66 32 3.87 - 2 0.877 0.392 0.230- 38 1.99 39 2.06 81 2.08 80 2.12 78 2.12 74 2.49 71 2.58 37 2.89 - 3 3.26 5 3.38 9 3.40 27 3.47 28 3.53 7 3.55 17 3.70 10 3.75 - 3 0.871 0.148 0.035- 81 1.91 64 1.95 82 1.99 95 2.10 38 2.11 76 2.76 42 2.90 2 3.26 - 20 3.38 24 3.49 25 3.59 18 3.61 29 3.66 32 3.66 10 3.81 31 3.84 - 4 0.892 0.837 0.247- 75 1.89 36 1.99 42 2.00 85 2.07 40 2.32 41 2.41 82 2.83 21 2.95 - 5 3.28 20 3.44 26 3.64 12 3.65 24 3.66 29 3.68 7 3.69 27 3.80 - 5 0.871 0.632 0.010- 85 1.93 39 2.03 78 2.06 36 2.08 57 2.21 77 2.27 93 2.35 68 2.63 - 4 3.28 17 3.31 2 3.38 30 3.39 24 3.42 25 3.62 14 3.66 1 3.66 - 6 0.846 0.117 0.528- 37 1.84 87 2.04 47 2.12 94 2.15 33 2.21 40 2.33 35 2.43 74 2.63 - 28 3.15 29 3.33 32 3.36 10 3.48 26 3.49 1 3.56 12 3.56 31 3.64 - 7 0.864 0.599 0.505- 71 1.96 41 2.03 80 2.05 43 2.13 90 2.15 34 2.22 89 2.36 75 2.42 - 9 3.25 1 3.26 31 3.37 28 3.44 27 3.47 2 3.55 26 3.60 21 3.68 - 8 0.379 0.381 0.231- 44 1.95 46 1.99 84 2.02 72 2.09 52 2.14 70 2.48 79 2.78 45 2.88 - 17 3.33 23 3.39 21 3.43 29 3.46 22 3.46 9 3.66 28 3.78 25 3.83 - 9 0.113 0.364 0.469- 74 1.82 71 2.01 43 2.04 45 2.06 60 2.20 44 2.25 54 2.50 10 3.22 - 7 3.25 19 3.34 2 3.40 16 3.42 21 3.57 8 3.66 31 3.68 - 10 0.118 0.095 0.318- 47 1.85 73 2.00 45 2.15 74 2.18 38 2.28 48 2.29 42 2.38 11 3.06 - 19 3.18 9 3.22 12 3.26 6 3.48 2 3.75 3 3.81 20 3.84 - 11 0.372 0.911 0.239- 51 1.97 73 2.05 86 2.13 69 2.22 48 2.24 50 2.25 83 2.47 10 3.06 - 23 3.32 27 3.43 22 3.53 20 3.54 19 3.59 29 3.64 26 3.65 - 12 0.118 0.856 0.520- 35 1.99 53 2.02 49 2.07 47 2.07 48 2.18 75 2.37 34 2.48 61 2.55 - 10 3.26 21 3.28 1 3.33 15 3.50 13 3.51 14 3.51 6 3.56 4 3.65 - 13 0.354 0.863 0.770- 92 1.94 55 1.98 61 2.07 58 2.11 53 2.14 56 2.14 67 2.26 30 3.16 - 18 3.32 20 3.42 14 3.50 22 3.50 12 3.51 15 3.54 19 3.56 - 14 0.143 0.631 0.776- 57 1.95 59 2.06 54 2.07 34 2.10 53 2.16 55 2.16 68 2.44 17 3.18 - 1 3.31 16 3.33 22 3.43 13 3.50 12 3.51 15 3.52 20 3.60 5 3.66 - 15 0.396 0.611 0.538- 56 1.95 66 1.98 79 1.99 49 2.18 53 2.30 54 2.50 44 2.81 28 3.27 - 16 3.40 12 3.50 27 3.50 14 3.52 13 3.54 30 3.54 21 3.70 - 16 0.342 0.352 0.716- 66 1.93 60 1.94 63 2.09 96 2.12 54 2.15 59 2.18 62 2.40 19 3.21 - 32 3.30 14 3.33 15 3.40 9 3.42 17 3.49 18 3.51 23 3.79 - 17 0.149 0.418 0.997- 39 1.94 72 1.97 70 2.01 59 2.06 57 2.18 65 2.30 62 2.34 14 3.18 - 23 3.25 5 3.31 8 3.33 22 3.48 16 3.49 2 3.70 18 3.73 21 3.77 - 18 0.129 0.130 0.790- 61 1.89 33 2.01 64 2.05 65 2.09 62 2.13 60 2.39 67 2.51 23 3.24 - 13 3.32 31 3.34 20 3.41 19 3.45 16 3.51 3 3.61 17 3.73 - 19 0.346 0.107 0.528- 45 1.93 58 2.06 60 2.09 63 2.09 83 2.11 48 2.14 61 2.38 10 3.18 - 16 3.21 9 3.34 26 3.34 18 3.45 13 3.56 11 3.59 29 3.75 12 3.78 - 20 0.117 0.889 0.009- 67 2.05 69 2.07 42 2.08 64 2.10 68 2.13 55 2.31 73 2.79 36 2.91 - 22 3.23 3 3.38 18 3.41 13 3.42 4 3.44 11 3.54 14 3.60 21 3.78 - 21 0.136 0.645 0.282- 36 1.97 75 2.05 49 2.08 70 2.18 44 2.25 71 2.28 69 2.33 4 2.95 - 12 3.28 22 3.43 8 3.43 9 3.57 7 3.68 15 3.70 17 3.77 20 3.78 - 22 0.359 0.648 0.030- 50 1.97 70 2.03 91 2.03 55 2.04 52 2.06 69 2.24 59 2.57 20 3.23 - 25 3.36 14 3.43 21 3.43 8 3.46 17 3.48 13 3.50 11 3.53 27 3.57 - 23 0.349 0.143 0.017- 62 1.76 72 2.02 88 2.10 73 2.15 67 2.16 51 2.35 46 2.37 18 3.24 - 17 3.25 11 3.32 8 3.39 24 3.66 32 3.76 16 3.79 20 3.83 - 24 0.664 0.921 0.972- 76 1.89 77 1.98 85 2.02 92 2.13 82 2.15 51 2.28 88 2.30 32 3.15 - 1 3.34 30 3.37 5 3.42 3 3.49 23 3.66 4 3.66 29 3.83 - 25 0.625 0.424 0.958- 93 2.04 91 2.06 96 2.07 52 2.24 81 2.29 95 2.35 78 2.54 30 3.16 - 22 3.36 31 3.36 32 3.41 3 3.59 5 3.62 2 3.75 8 3.83 - 26 0.628 0.895 0.492- 89 1.90 87 2.08 86 2.09 40 2.10 58 2.20 83 2.22 41 2.55 29 3.13 - 1 3.29 19 3.34 6 3.49 27 3.50 7 3.60 4 3.64 11 3.65 30 3.80 - 27 0.610 0.641 0.275- 79 1.92 41 1.98 86 2.06 50 2.16 78 2.27 80 2.53 52 2.60 11 3.43 - 7 3.47 2 3.47 28 3.49 26 3.50 15 3.50 22 3.57 5 3.79 4 3.80 - 28 0.648 0.378 0.487- 80 1.97 94 2.06 84 2.10 90 2.15 37 2.15 79 2.36 66 2.36 6 3.15 - 15 3.27 7 3.44 29 3.46 27 3.49 2 3.53 31 3.59 8 3.78 32 3.81 - 29 0.624 0.117 0.288- 83 1.93 40 2.00 37 2.15 84 2.16 46 2.24 82 2.25 51 2.70 26 3.13 - 6 3.33 8 3.46 28 3.46 11 3.64 3 3.66 4 3.68 19 3.75 24 3.83 - 30 0.627 0.669 0.781- 56 1.93 91 1.94 77 2.11 93 2.15 92 2.17 89 2.30 90 2.36 13 3.16 - 25 3.16 1 3.21 24 3.37 5 3.39 15 3.54 31 3.67 7 3.70 22 3.77 - 31 0.884 0.380 0.748- 43 1.87 65 1.92 93 2.06 33 2.14 94 2.31 95 2.33 57 2.60 90 2.71 - 18 3.34 25 3.36 7 3.37 28 3.59 6 3.64 30 3.67 9 3.68 5 3.76 - 32 0.625 0.154 0.774- 88 1.83 63 2.01 96 2.06 76 2.12 95 2.20 87 2.22 94 2.26 24 3.15 - 16 3.30 6 3.36 25 3.41 3 3.66 23 3.76 28 3.81 31 3.83 1 3.87 - 33 0.967 0.191 0.680- 18 2.01 31 2.14 6 2.21 - 34 0.008 0.688 0.623- 14 2.10 1 2.15 7 2.22 12 2.48 - 35 0.972 0.933 0.640- 1 1.85 12 1.99 6 2.43 - 36 0.998 0.694 0.148- 21 1.97 4 1.99 5 2.08 20 2.91 - 37 0.763 0.213 0.392- 6 1.84 29 2.15 28 2.15 2 2.89 - 38 0.987 0.226 0.176- 2 1.99 3 2.11 10 2.28 - 39 0.983 0.472 0.089- 17 1.94 5 2.03 2 2.06 - 40 0.758 0.986 0.379- 29 2.00 26 2.10 4 2.32 6 2.33 - 41 0.758 0.707 0.364- 27 1.98 7 2.03 4 2.41 26 2.55 - 42 0.027 0.944 0.188- 4 2.00 20 2.08 10 2.38 3 2.90 - 43 0.969 0.433 0.601- 31 1.87 9 2.04 7 2.13 - 44 0.261 0.468 0.366- 8 1.95 21 2.25 9 2.25 15 2.81 - 45 0.251 0.215 0.396- 19 1.93 9 2.06 10 2.15 8 2.88 - 46 0.501 0.242 0.141- 8 1.99 29 2.24 23 2.37 - 47 0.011 0.014 0.426- 10 1.85 12 2.07 6 2.12 - 48 0.271 0.952 0.432- 19 2.14 12 2.18 11 2.24 10 2.29 - 49 0.254 0.730 0.411- 12 2.07 21 2.08 15 2.18 - 50 0.480 0.741 0.128- 22 1.97 27 2.16 11 2.25 - 51 0.498 0.979 0.121- 11 1.97 24 2.28 23 2.35 29 2.70 - 52 0.487 0.503 0.121- 22 2.06 8 2.14 25 2.24 27 2.60 - 53 0.241 0.753 0.651- 12 2.02 13 2.14 14 2.16 15 2.30 - 54 0.210 0.507 0.624- 14 2.07 16 2.15 15 2.50 9 2.50 - 55 0.262 0.750 0.880- 13 1.98 22 2.04 14 2.16 20 2.31 - 56 0.478 0.713 0.664- 30 1.93 15 1.95 13 2.14 - 57 0.016 0.540 0.864- 14 1.95 17 2.18 5 2.21 31 2.60 - 58 0.453 0.948 0.620- 19 2.06 13 2.11 26 2.20 - 59 0.276 0.490 0.869- 14 2.06 17 2.06 16 2.18 22 2.57 - 60 0.223 0.253 0.628- 16 1.94 19 2.09 9 2.20 18 2.39 - 61 0.219 0.003 0.677- 18 1.89 13 2.07 19 2.38 12 2.55 - 62 0.262 0.234 0.891- 23 1.76 18 2.13 17 2.34 16 2.40 - 63 0.475 0.194 0.645- 32 2.01 16 2.09 19 2.09 - 64 0.012 0.057 0.924- 3 1.95 18 2.05 20 2.10 - 65 0.029 0.307 0.859- 31 1.92 18 2.09 17 2.30 - 66 0.463 0.445 0.626- 16 1.93 15 1.98 28 2.36 - 67 0.269 0.979 0.944- 20 2.05 23 2.16 13 2.26 18 2.51 - 68 0.990 0.800 0.886- 20 2.13 1 2.17 14 2.44 5 2.63 - 69 0.232 0.792 0.157- 20 2.07 11 2.22 22 2.24 21 2.33 - 70 0.224 0.546 0.108- 17 2.01 22 2.03 21 2.18 8 2.48 - 71 0.006 0.521 0.386- 7 1.96 9 2.01 21 2.28 2 2.58 - 72 0.248 0.292 0.119- 17 1.97 23 2.02 8 2.09 - 73 0.237 0.058 0.162- 10 2.00 11 2.05 23 2.15 20 2.79 - 74 0.997 0.262 0.410- 9 1.82 10 2.18 2 2.49 6 2.63 - 75 0.982 0.745 0.388- 4 1.89 21 2.05 12 2.37 7 2.42 - 76 0.766 0.001 0.852- 24 1.89 32 2.12 1 2.35 3 2.76 - 77 0.762 0.777 0.868- 24 1.98 1 1.99 30 2.11 5 2.27 - 78 0.751 0.537 0.124- 5 2.06 2 2.12 27 2.27 25 2.54 - 79 0.504 0.547 0.382- 27 1.92 15 1.99 28 2.36 8 2.78 - 80 0.773 0.474 0.397- 28 1.97 7 2.05 2 2.12 27 2.53 - 81 0.763 0.299 0.103- 3 1.91 2 2.08 25 2.29 - 82 0.741 0.045 0.110- 3 1.99 24 2.15 29 2.25 4 2.83 - 83 0.491 0.044 0.383- 29 1.93 19 2.11 26 2.22 11 2.47 - 84 0.521 0.301 0.358- 8 2.02 28 2.10 29 2.16 - 85 0.790 0.796 0.082- 5 1.93 24 2.02 4 2.07 - 86 0.510 0.801 0.370- 27 2.06 26 2.09 11 2.13 - 87 0.707 0.023 0.613- 6 2.04 26 2.08 32 2.22 1 2.57 - 88 0.533 0.114 0.918- 32 1.83 23 2.10 24 2.30 - 89 0.715 0.766 0.607- 26 1.90 1 2.06 30 2.30 7 2.36 - 90 0.700 0.534 0.602- 7 2.15 28 2.15 30 2.36 31 2.71 - 91 0.516 0.599 0.906- 30 1.94 22 2.03 25 2.06 - 92 0.514 0.836 0.877- 13 1.94 24 2.13 30 2.17 - 93 0.763 0.511 0.864- 25 2.04 31 2.06 30 2.15 5 2.35 - 94 0.736 0.271 0.641- 28 2.06 6 2.15 32 2.26 31 2.31 - 95 0.774 0.247 0.876- 3 2.10 32 2.20 31 2.33 25 2.35 - 96 0.514 0.324 0.838- 32 2.06 25 2.07 16 2.12 - - LATTYP: Found a simple monoclinic cell. - ALAT = 10.1297860000 - B/A-ratio = 1.0131648388 - C/A-ratio = 1.0379762742 - COS(beta) = -0.1645688048 - - Lattice vectors: - - A1 = ( 10.1297860000, 0.0000000000, 0.0000000000) - A2 = ( 0.0000000000, 10.2631430000, 0.0000000000) - A3 = ( -1.7303550000, 0.0000000000, 10.3711190000) - - -Analysis of symmetry for initial positions (statically): -===================================================================== - Subroutine PRICEL returns: - Original cell was already a primitive cell. - - - Routine SETGRP: Setting up the symmetry group for a - simple monoclinic supercell. - - - Subroutine GETGRP returns: Found 1 space group operations - (whereof 1 operations were pure point group operations) - out of a pool of 4 trial point group operations. - - -The static configuration has the point symmetry C_1 . - - -Analysis of symmetry for dynamics (positions and initial velocities): -===================================================================== - Subroutine PRICEL returns: - Original cell was already a primitive cell. - - - Routine SETGRP: Setting up the symmetry group for a - simple monoclinic supercell. - - - Subroutine GETGRP returns: Found 1 space group operations - (whereof 1 operations were pure point group operations) - out of a pool of 4 trial point group operations. - - -The dynamic configuration has the point symmetry C_1 . - - -Analysis of constrained symmetry for selective dynamics: -===================================================================== - Subroutine PRICEL returns: - Original cell was already a primitive cell. - - - Routine SETGRP: Setting up the symmetry group for a - simple monoclinic supercell. - - - Subroutine GETGRP returns: Found 1 space group operations - (whereof 1 operations were pure point group operations) - out of a pool of 4 trial point group operations. - - -The constrained configuration has the point symmetry C_1 . - - - Subroutine INISYM returns: Found 1 space group operations - (whereof 1 operations are pure point group operations), - and found 1 'primitive' translations - - ----------------------------------------------------------------------------------------- - - Primitive cell - - volume of cell : 1078.2172 - - direct lattice vectors reciprocal lattice vectors - 10.129786000 0.000000000 0.000000000 0.098718769 0.000000000 0.016470596 - 1.730355000 0.000000000-10.371119000 0.000000000 0.000000000 -0.096421611 - 0.000000000 10.263143000 0.000000000 0.000000000 0.097436039 0.000000000 - - length of vectors - 10.129786000 10.514477530 10.263143000 0.100083344 0.096421611 0.097436039 - - position of ions in fractional coordinates (direct lattice) - 0.861948460 0.830598790 0.716147450 - 0.876829950 0.392203120 0.230136450 - 0.871457950 0.147657010 0.035427150 - 0.891822010 0.837396670 0.247028630 - 0.871254260 0.632019790 0.010209840 - 0.845617420 0.117131820 0.527744430 - 0.863965970 0.598751850 0.505284860 - 0.378984990 0.381321240 0.231423920 - 0.113028530 0.364059470 0.468875900 - 0.117901040 0.095069070 0.318011420 - 0.372333300 0.911181260 0.239323540 - 0.118363930 0.855758220 0.520271040 - 0.354154750 0.863147670 0.769512740 - 0.143288120 0.631054670 0.775618550 - 0.396432640 0.610708770 0.537967770 - 0.342261730 0.351745810 0.715537920 - 0.149366770 0.417919960 0.996688930 - 0.129436060 0.130457660 0.789802850 - 0.346167270 0.106731450 0.527768730 - 0.117089310 0.889177050 0.009482670 - 0.136152950 0.645341660 0.281719680 - 0.358576530 0.647594110 0.030138800 - 0.348993960 0.142900250 0.017167270 - 0.664201570 0.921284840 0.971716710 - 0.625327580 0.423548360 0.958481800 - 0.628428160 0.894555540 0.492040440 - 0.609880400 0.641304150 0.275236080 - 0.648017010 0.378290830 0.487072200 - 0.624115580 0.117197720 0.288488190 - 0.627411330 0.668790630 0.780528200 - 0.883671490 0.380253330 0.748327420 - 0.624668600 0.153598210 0.773947810 - 0.967056810 0.191356500 0.680237340 - 0.007718580 0.687667090 0.623416940 - 0.972024870 0.932654390 0.639519920 - 0.998172250 0.693758470 0.147580370 - 0.763140820 0.213491970 0.392477970 - 0.986693200 0.226426610 0.176403640 - 0.982935840 0.472423080 0.089149400 - 0.758081020 0.986023610 0.378577240 - 0.758176660 0.706629130 0.364382890 - 0.026636240 0.943521660 0.187675810 - 0.969078150 0.432927770 0.601145770 - 0.261406770 0.467516590 0.366485270 - 0.251053390 0.215376520 0.395516370 - 0.501185750 0.241703040 0.141182550 - 0.011240360 0.014281990 0.426097780 - 0.270991210 0.952239140 0.432092480 - 0.253521580 0.730302790 0.411448930 - 0.479814270 0.741165140 0.127920450 - 0.498208730 0.978906890 0.121335770 - 0.487354660 0.502632790 0.120624550 - 0.241115990 0.752657550 0.651278650 - 0.209791550 0.506962580 0.624122930 - 0.262100680 0.750313790 0.879897110 - 0.477843680 0.713410520 0.663771120 - 0.016338710 0.540130920 0.863607520 - 0.453036140 0.948256820 0.619537670 - 0.275649990 0.490468620 0.868968650 - 0.222746030 0.253123840 0.627734980 - 0.218581290 0.002693090 0.676775510 - 0.261592300 0.234490090 0.890870750 - 0.474914460 0.193609520 0.644880710 - 0.012181820 0.057223320 0.923670670 - 0.029491490 0.307499160 0.859313500 - 0.463472250 0.445289570 0.625905710 - 0.269431420 0.978803550 0.944229790 - 0.990479920 0.800392980 0.886029990 - 0.231622110 0.791731950 0.157042640 - 0.224330650 0.545579790 0.108164200 - 0.005501960 0.520884340 0.386360320 - 0.248041750 0.292291920 0.119009520 - 0.236962250 0.058031150 0.162119630 - 0.996714490 0.262128710 0.409793040 - 0.982020610 0.745002380 0.388057840 - 0.765756040 0.000607730 0.851606540 - 0.762036770 0.777175590 0.867788290 - 0.751373200 0.537109910 0.124482110 - 0.504183790 0.546776540 0.381848240 - 0.772712750 0.474092050 0.396603890 - 0.763419930 0.299469610 0.102815280 - 0.741000860 0.045090600 0.109568980 - 0.490570620 0.043505540 0.382966280 - 0.521036760 0.300626310 0.358099350 - 0.789777120 0.795507750 0.082112710 - 0.509800930 0.801339670 0.370292590 - 0.707065050 0.022890570 0.612855790 - 0.533090500 0.114307290 0.918046860 - 0.715172840 0.765759000 0.607488010 - 0.699726170 0.533887030 0.602456120 - 0.515596430 0.598513240 0.906354260 - 0.513599650 0.836043280 0.876716680 - 0.763232610 0.511478390 0.863866660 - 0.736223800 0.270908050 0.641105760 - 0.774135800 0.246673780 0.875907290 - 0.513684980 0.324270370 0.837810360 - - ion indices of the primitive-cell ions - primitive index ion index - 1 1 - 2 2 - 3 3 - 4 4 - 5 5 - 6 6 - 7 7 - 8 8 - 9 9 - 10 10 - 11 11 - 12 12 - 13 13 - 14 14 - 15 15 - 16 16 - 17 17 - 18 18 - 19 19 - 20 20 - 21 21 - 22 22 - 23 23 - 24 24 - 25 25 - 26 26 - 27 27 - 28 28 - 29 29 - 30 30 - 31 31 - 32 32 - 33 33 - 34 34 - 35 35 - 36 36 - 37 37 - 38 38 - 39 39 - 40 40 - 41 41 - 42 42 - 43 43 - 44 44 - 45 45 - 46 46 - 47 47 - 48 48 - 49 49 - 50 50 - 51 51 - 52 52 - 53 53 - 54 54 - 55 55 - 56 56 - 57 57 - 58 58 - 59 59 - 60 60 - 61 61 - 62 62 - 63 63 - 64 64 - 65 65 - 66 66 - 67 67 - 68 68 - 69 69 - 70 70 - 71 71 - 72 72 - 73 73 - 74 74 - 75 75 - 76 76 - 77 77 - 78 78 - 79 79 - 80 80 - 81 81 - 82 82 - 83 83 - 84 84 - 85 85 - 86 86 - 87 87 - 88 88 - 89 89 - 90 90 - 91 91 - 92 92 - 93 93 - 94 94 - 95 95 - 96 96 - ----------------------------------------------------------------------------------------- - - - - KPOINTS: Auto k-point - -Automatic generation of k-mesh. - Grid dimensions read from file: - generate k-points for: 2 2 2 - - Generating k-lattice: - - Cartesian coordinates Fractional coordinates (reciprocal lattice) - 0.049359384 0.000000000 0.008235298 0.500000000 0.000000000 0.000000000 - 0.000000000 0.000000000 -0.048210805 0.000000000 0.500000000 0.000000000 - 0.000000000 0.048718019 0.000000000 0.000000000 0.000000000 0.500000000 - - Length of vectors - 0.050041672 0.048210805 0.048718019 - - Shift w.r.t. Gamma in fractional coordinates (k-lattice) - 0.500000000 0.500000000 0.500000000 - - - Subroutine IBZKPT returns following result: - =========================================== - - Found 4 irreducible k-points: - - Following reciprocal coordinates: - Coordinates Weight - 0.250000 0.250000 0.250000 2.000000 - -0.250000 -0.250000 0.250000 2.000000 - -0.250000 0.250000 0.250000 2.000000 - 0.250000 -0.250000 0.250000 2.000000 - - Following cartesian coordinates: - Coordinates Weight - 0.024680 0.024359 -0.019988 2.000000 - -0.024680 0.024359 0.019988 2.000000 - -0.024680 0.024359 -0.028223 2.000000 - 0.024680 0.024359 0.028223 2.000000 - - - --------------------------------------------------------------------------------------------------------- - - - - - Dimension of arrays: - k-points NKPTS = 4 k-points in BZ NKDIM = 4 number of bands NBANDS= 308 - number of dos NEDOS = 301 number of ions NIONS = 96 - non local maximal LDIM = 6 non local SUM 2l+1 LMDIM = 18 - total plane-waves NPLWV = 512000 - max r-space proj IRMAX = 9139 max aug-charges IRDMAX= 255251 - dimension x,y,z NGX = 80 NGY = 80 NGZ = 80 - dimension x,y,z NGXF= 160 NGYF= 160 NGZF= 160 - support grid NGXF= 320 NGYF= 320 NGZF= 320 - ions per type = 32 64 - NGX,Y,Z is equivalent to a cutoff of 13.13, 12.65, 12.96 a.u. - NGXF,Y,Z is equivalent to a cutoff of 26.26, 25.30, 25.92 a.u. - - SYSTEM = HfO2_p21c - POSCAR = name - - Startparameter for this run: - NWRITE = 2 write-flag & timer - PREC = accura normal or accurate (medium, high low for compatibility) - ISTART = 0 job : 0-new 1-cont 2-samecut - ICHARG = 2 charge: 1-file 2-atom 10-const - ISPIN = 1 spin polarized calculation? - LNONCOLLINEAR = F non collinear calculations - LSORBIT = F spin-orbit coupling - INIWAV = 1 electr: 0-lowe 1-rand 2-diag - LASPH = F aspherical Exc in radial PAW - Electronic Relaxation 1 - ENCUT = 500.0 eV 36.75 Ry 6.06 a.u. 18.47 19.17 18.71*2*pi/ulx,y,z - ENINI = 500.0 initial cutoff - ENAUG = 605.4 eV augmentation charge cutoff - NELM = 100; NELMIN= 2; NELMDL= -5 # of ELM steps - EDIFF = 0.1E-03 stopping-criterion for ELM - LREAL = T real-space projection - NLSPLINE = F spline interpolate recip. space projectors - LCOMPAT= F compatible to vasp.4.4 - GGA_COMPAT = T GGA compatible to vasp.4.4-vasp.4.6 - LMAXPAW = -100 max onsite density - LMAXMIX = 2 max onsite mixed and CHGCAR - VOSKOWN= 0 Vosko Wilk Nusair interpolation - ROPT = -0.00025 -0.00025 - Ionic relaxation - EDIFFG = -.2E-02 stopping-criterion for IOM - NSW = 0 number of steps for IOM - NBLOCK = 1; KBLOCK = 1 inner block; outer block - IBRION = -1 ionic relax: 0-MD 1-quasi-New 2-CG - NFREE = 1 steps in history (QN), initial steepest desc. (CG) - ISIF = 3 stress and relaxation - IWAVPR = 10 prediction: 0-non 1-charg 2-wave 3-comb - ISYM = 1 0-nonsym 1-usesym 2-fastsym - LCORR = T Harris-Foulkes like correction to forces - - POTIM = 0.5000 time-step for ionic-motion - TEIN = 0.0 initial temperature - TEBEG = 0.0; TEEND = 0.0 temperature during run - SMASS = -3.00 Nose mass-parameter (am) - estimated Nose-frequenzy (Omega) = 0.10E-29 period in steps = 0.13E+47 mass= -0.234E-26a.u. - SCALEE = 1.0000 scale energy and forces - NPACO = 256; APACO = 10.0 distance and # of slots for P.C. - PSTRESS= 0.0 pullay stress - - Mass of Ions in am - POMASS = 178.49 16.00 - Ionic Valenz - ZVAL = 4.00 6.00 - Atomic Wigner-Seitz radii - RWIGS = -1.00 -1.00 - virtual crystal weights - VCA = 1.00 1.00 - NELECT = 512.0000 total number of electrons - NUPDOWN= -1.0000 fix difference up-down - - DOS related values: - EMIN = 10.00; EMAX =-10.00 energy-range for DOS - EFERMI = 0.00 - ISMEAR = 0; SIGMA = 0.05 broadening in eV -4-tet -1-fermi 0-gaus - - Electronic relaxation 2 (details) - IALGO = 68 algorithm - LDIAG = T sub-space diagonalisation (order eigenvalues) - LSUBROT= F optimize rotation matrix (better conditioning) - TURBO = 0 0=normal 1=particle mesh - IRESTART = 0 0=no restart 2=restart with 2 vectors - NREBOOT = 0 no. of reboots - NMIN = 0 reboot dimension - EREF = 0.00 reference energy to select bands - IMIX = 4 mixing-type and parameters - AMIX = 0.40; BMIX = 1.00 - AMIX_MAG = 1.60; BMIX_MAG = 1.00 - AMIN = 0.10 - WC = 100.; INIMIX= 1; MIXPRE= 1; MAXMIX= -45 - - Intra band minimization: - WEIMIN = 0.0000 energy-eigenvalue tresh-hold - EBREAK = 0.81E-07 absolut break condition - DEPER = 0.30 relativ break condition - - TIME = 0.40 timestep for ELM - - volume/ion in A,a.u. = 11.23 75.79 - Fermi-wavevector in a.u.,A,eV,Ry = 1.277211 2.413579 22.194756 1.631269 - Thomas-Fermi vector in A = 2.409824 - - Write flags - LWAVE = F write WAVECAR - LDOWNSAMPLE = F k-point downsampling of WAVECAR - LCHARG = F write CHGCAR - LVTOT = F write LOCPOT, total local potential - LVHAR = F write LOCPOT, Hartree potential only - LELF = F write electronic localiz. function (ELF) - LORBIT = 0 0 simple, 1 ext, 2 COOP (PROOUT), +10 PAW based schemes - - - Dipole corrections - LMONO = F monopole corrections only (constant potential shift) - LDIPOL = F correct potential (dipole corrections) - IDIPOL = 0 1-x, 2-y, 3-z, 4-all directions - EPSILON= 1.0000000 bulk dielectric constant - - Exchange correlation treatment: - GGA = -- GGA type - LEXCH = 8 internal setting for exchange type - LIBXC = F Libxc - VOSKOWN = 0 Vosko Wilk Nusair interpolation - LHFCALC = F Hartree Fock is set to - LHFONE = F Hartree Fock one center treatment - AEXX = 0.0000 exact exchange contribution - - Linear response parameters - LEPSILON= F determine dielectric tensor - LRPA = F only Hartree local field effects (RPA) - LNABLA = F use nabla operator in PAW spheres - LVEL = F velocity operator in full k-point grid - CSHIFT =0.1000 complex shift for real part using Kramers Kronig - OMEGAMAX= -1.0 maximum frequency - DEG_THRESHOLD= 0.2000000E-02 threshold for treating states as degnerate - RTIME = -0.100 relaxation time in fs - (WPLASMAI= 0.000 imaginary part of plasma frequency in eV, 0.658/RTIME) - DFIELD = 0.0000000 0.0000000 0.0000000 field for delta impulse in time - - Optional k-point grid parameters - LKPOINTS_OPT = F use optional k-point grid - KPOINTS_OPT_MODE= 1 mode for optional k-point grid - - Orbital magnetization related: - ORBITALMAG= F switch on orbital magnetization - LCHIMAG = F perturbation theory with respect to B field - DQ = 0.001000 dq finite difference perturbation B field - LLRAUG = F two centre corrections for induced B field - - - --------------------------------------------------------------------------------------------------------- - - - Static calculation - charge density and potential will be updated during run - non-spin polarized calculation - RMM-DIIS sequential band-by-band and - variant of blocked Davidson during initial phase - perform sub-space diagonalisation - before iterative eigenvector-optimisation - modified Broyden-mixing scheme, WC = 100.0 - initial mixing is a Kerker type mixing with AMIX = 0.4000 and BMIX = 1.0000 - Hartree-type preconditioning will be used - using additional bands 52 - real space projection scheme for non local part - use partial core corrections - calculate Harris-corrections to forces - (improved forces if not selfconsistent) - use gradient corrections - use of overlap-Matrix (Vanderbilt PP) - Gauss-broadening in eV SIGMA = 0.05 - - --------------------------------------------------------------------------------------------------------- - - - energy-cutoff : 500.00 - volume of cell : 1078.22 - direct lattice vectors reciprocal lattice vectors - 10.129786000 0.000000000 0.000000000 0.098718769 0.000000000 0.016470596 - 1.730355000 0.000000000-10.371119000 0.000000000 0.000000000 -0.096421611 - 0.000000000 10.263143000 0.000000000 0.000000000 0.097436039 0.000000000 - - length of vectors - 10.129786000 10.514477530 10.263143000 0.100083344 0.096421611 0.097436039 - - - - k-points in units of 2pi/SCALE and weight: Auto k-point - 0.02467969 0.02435901 -0.01998775 0.250 - -0.02467969 0.02435901 0.01998775 0.250 - -0.02467969 0.02435901 -0.02822305 0.250 - 0.02467969 0.02435901 0.02822305 0.250 - - k-points in reciprocal lattice and weights: Auto k-point - 0.25000000 0.25000000 0.25000000 0.250 - -0.25000000 -0.25000000 0.25000000 0.250 - -0.25000000 0.25000000 0.25000000 0.250 - 0.25000000 -0.25000000 0.25000000 0.250 - - position of ions in fractional coordinates (direct lattice) - 0.86194846 0.83059879 0.71614745 - 0.87682995 0.39220312 0.23013645 - 0.87145795 0.14765701 0.03542715 - 0.89182201 0.83739667 0.24702863 - 0.87125426 0.63201979 0.01020984 - 0.84561742 0.11713182 0.52774443 - 0.86396597 0.59875185 0.50528486 - 0.37898499 0.38132124 0.23142392 - 0.11302853 0.36405947 0.46887590 - 0.11790104 0.09506907 0.31801142 - 0.37233330 0.91118126 0.23932354 - 0.11836393 0.85575822 0.52027104 - 0.35415475 0.86314767 0.76951274 - 0.14328812 0.63105467 0.77561855 - 0.39643264 0.61070877 0.53796777 - 0.34226173 0.35174581 0.71553792 - 0.14936677 0.41791996 0.99668893 - 0.12943606 0.13045766 0.78980285 - 0.34616727 0.10673145 0.52776873 - 0.11708931 0.88917705 0.00948267 - 0.13615295 0.64534166 0.28171968 - 0.35857653 0.64759411 0.03013880 - 0.34899396 0.14290025 0.01716727 - 0.66420157 0.92128484 0.97171671 - 0.62532758 0.42354836 0.95848180 - 0.62842816 0.89455554 0.49204044 - 0.60988040 0.64130415 0.27523608 - 0.64801701 0.37829083 0.48707220 - 0.62411558 0.11719772 0.28848819 - 0.62741133 0.66879063 0.78052820 - 0.88367149 0.38025333 0.74832742 - 0.62466860 0.15359821 0.77394781 - 0.96705681 0.19135650 0.68023734 - 0.00771858 0.68766709 0.62341694 - 0.97202487 0.93265439 0.63951992 - 0.99817225 0.69375847 0.14758037 - 0.76314082 0.21349197 0.39247797 - 0.98669320 0.22642661 0.17640364 - 0.98293584 0.47242308 0.08914940 - 0.75808102 0.98602361 0.37857724 - 0.75817666 0.70662913 0.36438289 - 0.02663624 0.94352166 0.18767581 - 0.96907815 0.43292777 0.60114577 - 0.26140677 0.46751659 0.36648527 - 0.25105339 0.21537652 0.39551637 - 0.50118575 0.24170304 0.14118255 - 0.01124036 0.01428199 0.42609778 - 0.27099121 0.95223914 0.43209248 - 0.25352158 0.73030279 0.41144893 - 0.47981427 0.74116514 0.12792045 - 0.49820873 0.97890689 0.12133577 - 0.48735466 0.50263279 0.12062455 - 0.24111599 0.75265755 0.65127865 - 0.20979155 0.50696258 0.62412293 - 0.26210068 0.75031379 0.87989711 - 0.47784368 0.71341052 0.66377112 - 0.01633871 0.54013092 0.86360752 - 0.45303614 0.94825682 0.61953767 - 0.27564999 0.49046862 0.86896865 - 0.22274603 0.25312384 0.62773498 - 0.21858129 0.00269309 0.67677551 - 0.26159230 0.23449009 0.89087075 - 0.47491446 0.19360952 0.64488071 - 0.01218182 0.05722332 0.92367067 - 0.02949149 0.30749916 0.85931350 - 0.46347225 0.44528957 0.62590571 - 0.26943142 0.97880355 0.94422979 - 0.99047992 0.80039298 0.88602999 - 0.23162211 0.79173195 0.15704264 - 0.22433065 0.54557979 0.10816420 - 0.00550196 0.52088434 0.38636032 - 0.24804175 0.29229192 0.11900952 - 0.23696225 0.05803115 0.16211963 - 0.99671449 0.26212871 0.40979304 - 0.98202061 0.74500238 0.38805784 - 0.76575604 0.00060773 0.85160654 - 0.76203677 0.77717559 0.86778829 - 0.75137320 0.53710991 0.12448211 - 0.50418379 0.54677654 0.38184824 - 0.77271275 0.47409205 0.39660389 - 0.76341993 0.29946961 0.10281528 - 0.74100086 0.04509060 0.10956898 - 0.49057062 0.04350554 0.38296628 - 0.52103676 0.30062631 0.35809935 - 0.78977712 0.79550775 0.08211271 - 0.50980093 0.80133967 0.37029259 - 0.70706505 0.02289057 0.61285579 - 0.53309050 0.11430729 0.91804686 - 0.71517284 0.76575900 0.60748801 - 0.69972617 0.53388703 0.60245612 - 0.51559643 0.59851324 0.90635426 - 0.51359965 0.83604328 0.87671668 - 0.76323261 0.51147839 0.86386666 - 0.73622380 0.27090805 0.64110576 - 0.77413580 0.24667378 0.87590729 - 0.51368498 0.32427037 0.83781036 - - position of ions in cartesian coordinates (Angst): - 10.16858421 7.34992369 -8.61423889 - 9.56075038 2.36192330 -4.06758523 - 9.08318159 0.36359391 -1.53136842 - 10.48295963 2.53529015 -8.68474051 - 9.91923781 0.10478505 -6.55475245 - 8.76860313 5.41631655 -1.21478804 - 9.78784364 5.18581077 -6.20972669 - 4.49885796 2.37513678 -3.95472796 - 1.77490695 4.81214041 -3.77570409 - 1.35881554 3.26379668 -0.98597264 - 5.34832370 2.45621171 -9.44996928 - 2.67976680 5.33961608 -8.87517033 - 5.08106371 7.89761929 -8.95180720 - 2.54342660 7.96028409 -6.54474308 - 5.07252078 5.52124015 -6.33373333 - 4.07568320 7.34366799 -3.64799765 - 2.23620331 10.22916102 -4.33429764 - 1.53689765 8.10585959 -1.35299192 - 3.69128366 5.41656595 -1.10692457 - 2.72468161 0.09732200 -9.22176100 - 2.49587041 2.89132936 -6.69291515 - 4.75287122 0.30931881 -6.71627558 - 3.78250229 0.17619015 -1.48203550 - 8.32236959 9.97286755 -9.55475471 - 7.06732359 9.83703578 -4.39267044 - 7.91374143 5.04988140 -9.27754196 - 7.28764178 2.82478725 -6.65104165 - 7.21885106 4.99889164 -3.92329921 - 6.52495093 2.96079555 -1.21547150 - 7.51278772 8.01067253 -6.93610721 - 9.60937634 7.68019132 -3.94365254 - 6.59353867 7.94313705 -1.59298531 - 10.12719321 6.98137309 -1.98458103 - 1.26809575 6.39821720 -7.13187722 - 11.46022711 6.56348439 -9.67266966 - 11.31171972 1.51463844 -7.19505165 - 8.09987009 4.02805753 -2.21415063 - 10.38678938 1.81045578 -2.34829732 - 10.77438935 0.91495304 -4.89955598 - 9.38536939 3.88539235-10.22616820 - 8.90288656 3.73971371 -7.32853480 - 1.90244683 1.92614368 -9.78537541 - 10.56567301 6.16964500 -4.48994542 - 3.45696431 3.76129073 -4.84867019 - 2.91579495 4.05924106 -2.23369552 - 5.49513646 1.44897670 -2.50673099 - 0.13857535 4.37310245 -0.14812022 - 4.39279472 4.43462691 -9.87578544 - 3.83180244 4.22275921 -7.57405714 - 6.14289468 1.31286587 -7.68671187 - 6.74060425 1.24528636-10.15235985 - 5.80653157 1.23798701 -5.21286448 - 3.74481813 6.68416592 -7.80590102 - 3.00236874 6.40546288 -5.25776925 - 3.95333302 9.03050987 -7.78159360 - 6.07490768 6.81237792 -7.39886540 - 1.10012587 8.86332747 -5.60176205 - 6.22998008 6.35840370 -9.83448432 - 3.64096024 8.91834952 -5.08670842 - 2.69436372 6.44253387 -2.62517747 - 2.21884169 6.94584384 -0.02793036 - 3.05562512 9.14313390 -2.43192463 - 5.14579505 6.61850294 -2.00794737 - 0.22241589 9.47976417 -0.59346986 - 0.83082519 8.81925733 -3.18911038 - 5.46538374 6.42375981 -4.61815112 - 4.42296024 9.69076536-10.15128809 - 11.41831362 9.09345249 -8.30097084 - 3.71625975 1.61175107 -8.21114627 - 3.21646820 1.11010465 -5.65827293 - 0.95704850 3.96527121 -5.40215348 - 3.01837863 1.22141172 -3.03139429 - 2.50079137 1.66385695 -0.60184796 - 10.55008021 4.20576457 -2.71856804 - 11.23677722 3.98269310 -7.72650834 - 7.75799640 8.74015970 -0.00630284 - 9.06405907 8.90623531 -8.06018053 - 8.54064054 1.27757770 -5.57043079 - 6.05339142 3.91896309 -5.67068456 - 8.64776235 4.07040244 -4.91686507 - 8.25146926 1.05520792 -3.10583496 - 7.58420288 1.12452211 -0.46763998 - 5.04465543 3.93043770 -0.45120113 - 5.79818112 3.67522484 -3.11783124 - 9.37678403 0.84273448 -8.25030554 - 6.55077643 3.80036580 -8.31078908 - 7.20202646 6.28982661 -0.23740083 - 5.59788487 9.42204620 -1.18549451 - 8.56958274 6.23473632 -7.94177771 - 8.01189045 6.18309331 -5.53700592 - 6.25852188 9.30204338 -6.20725204 - 6.64930621 8.99786866 -8.67070435 - 8.61642220 8.86598706 -5.30460325 - 7.92655664 6.57976009 -2.80961962 - 8.26866320 8.98956177 -2.55828313 - 5.76462177 8.59856753 -3.36304660 - - - --------------------------------------------------------------------------------------------------------- - - - k-point 1 : 0.2500 0.2500 0.2500 plane waves: 27363 - k-point 2 : -0.2500-0.2500 0.2500 plane waves: 27363 - k-point 3 : -0.2500 0.2500 0.2500 plane waves: 27374 - k-point 4 : 0.2500-0.2500 0.2500 plane waves: 27374 - - maximum and minimum number of plane-waves per node : 6889 6813 - - maximum number of plane-waves: 27374 - maximum index in each direction: - IXMAX= 18 IYMAX= 19 IZMAX= 18 - IXMIN= -18 IYMIN= -19 IZMIN= -18 - - - real space projection operators: - total allocation : 49873.72 KBytes - max/ min on nodes : 12473.44 12461.62 - - - parallel 3D FFT for wavefunctions: - minimum data exchange during FFTs selected (reduces bandwidth) - parallel 3D FFT for charge: - minimum data exchange during FFTs selected (reduces bandwidth) - - - total amount of memory used by VASP MPI-rank0 162804. kBytes -======================================================================= - - base : 30000. kBytes - nonlr-proj: 30253. kBytes - fftplans : 41293. kBytes - grid : 25778. kBytes - one-center: 373. kBytes - wavefun : 35107. kBytes - - INWAV: cpu time 0.0000: real time 0.0004 - Broyden mixing: mesh for mixing (old mesh) - NGX = 37 NGY = 39 NGZ = 37 - (NGX =160 NGY =160 NGZ =160) - gives a total of 53391 points - - initial charge density was supplied: - charge density of overlapping atoms calculated - number of electron 512.0000000 magnetization - keeping initial charge density in first step - - --------------------------------------------------------------------------------------------------------- - - - Maximum index for non-local projection operator 2225 - Maximum index for augmentation-charges 15777 (set IRDMAX) - - --------------------------------------------------------------------------------------------------------- - - - First call to EWALD: gamma= 0.173 - Maximum number of real-space cells 3x 3x 3 - Maximum number of reciprocal cells 3x 3x 3 - - FEWALD: cpu time 0.0053: real time 0.0053 - - ---------------------------------------- Iteration 1( 1) --------------------------------------- - - - POTLOK: cpu time 0.4235: real time 0.4268 - SETDIJ: cpu time 0.3537: real time 0.3869 - EDDAV: cpu time 16.0594: real time 16.2217 - DOS: cpu time 0.0010: real time 0.0010 - -------------------------------------------- - LOOP: cpu time 16.8376: real time 17.0364 - - eigenvalue-minimisations : 2464 - total energy-change (2. order) : 0.1367982E+04 (-0.2723673E+05) - number of electron 512.0000000 magnetization - augmentation part 512.0000000 magnetization - - Free energy of the ion-electron system (eV) - --------------------------------------------------- - alpha Z PSCENC = 1957.98898647 - Ewald energy TEWEN = -24665.75652663 - -Hartree energ DENC = -7545.40278343 - -exchange EXHF = 0.00000000 - -V(xc)+E(xc) XCENC = 592.98352221 - PAW double counting = 25569.98736858 -25757.03612884 - entropy T*S EENTRO = -0.02238617 - eigenvalues EBANDS = 1115.61677700 - atomic energy EATOM = 30099.62314931 - Solvation Ediel_sol = 0.00000000 - --------------------------------------------------- - free energy TOTEN = 1367.98197850 eV - - energy without entropy = 1368.00436467 energy(sigma->0) = 1367.99317159 - - --------------------------------------------------------------------------------------------------------- - - - - ---------------------------------------- Iteration 1( 2) --------------------------------------- - - - EDDAV: cpu time 20.1750: real time 20.5136 - DOS: cpu time 0.0249: real time 0.0250 - -------------------------------------------- - LOOP: cpu time 20.1999: real time 20.5386 - - eigenvalue-minimisations : 3040 - total energy-change (2. order) :-0.4107170E+04 (-0.3985199E+04) - number of electron 512.0000000 magnetization - augmentation part 512.0000000 magnetization - - Free energy of the ion-electron system (eV) - --------------------------------------------------- - alpha Z PSCENC = 1957.98898647 - Ewald energy TEWEN = -24665.75652663 - -Hartree energ DENC = -7545.40278343 - -exchange EXHF = 0.00000000 - -V(xc)+E(xc) XCENC = 592.98352221 - PAW double counting = 25569.98736858 -25757.03612884 - entropy T*S EENTRO = -0.00000000 - eigenvalues EBANDS = -2991.57516848 - atomic energy EATOM = 30099.62314931 - Solvation Ediel_sol = 0.00000000 - --------------------------------------------------- - free energy TOTEN = -2739.18758081 eV - - energy without entropy = -2739.18758081 energy(sigma->0) = -2739.18758081 - - --------------------------------------------------------------------------------------------------------- - - - - ---------------------------------------- Iteration 1( 3) --------------------------------------- - - - EDDAV: cpu time 17.9508: real time 18.1319 - DOS: cpu time 0.0004: real time 0.0004 - -------------------------------------------- - LOOP: cpu time 17.9512: real time 18.1323 - - eigenvalue-minimisations : 2880 - total energy-change (2. order) :-0.2921653E+03 (-0.2903742E+03) - number of electron 512.0000000 magnetization - augmentation part 512.0000000 magnetization - - Free energy of the ion-electron system (eV) - --------------------------------------------------- - alpha Z PSCENC = 1957.98898647 - Ewald energy TEWEN = -24665.75652663 - -Hartree energ DENC = -7545.40278343 - -exchange EXHF = 0.00000000 - -V(xc)+E(xc) XCENC = 592.98352221 - PAW double counting = 25569.98736858 -25757.03612884 - entropy T*S EENTRO = -0.00000000 - eigenvalues EBANDS = -3283.74044098 - atomic energy EATOM = 30099.62314931 - Solvation Ediel_sol = 0.00000000 - --------------------------------------------------- - free energy TOTEN = -3031.35285332 eV - - energy without entropy = -3031.35285332 energy(sigma->0) = -3031.35285332 - - --------------------------------------------------------------------------------------------------------- - - - - ---------------------------------------- Iteration 1( 4) --------------------------------------- - - - EDDAV: cpu time 18.2021: real time 18.4801 - DOS: cpu time 0.0009: real time 0.0009 - -------------------------------------------- - LOOP: cpu time 18.2029: real time 18.4810 - - eigenvalue-minimisations : 2968 - total energy-change (2. order) :-0.6552566E+01 (-0.6528248E+01) - number of electron 512.0000000 magnetization - augmentation part 512.0000000 magnetization - - Free energy of the ion-electron system (eV) - --------------------------------------------------- - alpha Z PSCENC = 1957.98898647 - Ewald energy TEWEN = -24665.75652663 - -Hartree energ DENC = -7545.40278343 - -exchange EXHF = 0.00000000 - -V(xc)+E(xc) XCENC = 592.98352221 - PAW double counting = 25569.98736858 -25757.03612884 - entropy T*S EENTRO = -0.00000000 - eigenvalues EBANDS = -3290.29300669 - atomic energy EATOM = 30099.62314931 - Solvation Ediel_sol = 0.00000000 - --------------------------------------------------- - free energy TOTEN = -3037.90541903 eV - - energy without entropy = -3037.90541903 energy(sigma->0) = -3037.90541903 - - --------------------------------------------------------------------------------------------------------- - - - - ---------------------------------------- Iteration 1( 5) --------------------------------------- - - - EDDAV: cpu time 18.3166: real time 18.5362 - DOS: cpu time 0.0007: real time 0.0007 - CHARGE: cpu time 1.6597: real time 1.6761 - MIXING: cpu time 0.0082: real time 0.0082 - -------------------------------------------- - LOOP: cpu time 19.9852: real time 20.2212 - - eigenvalue-minimisations : 2872 - total energy-change (2. order) :-0.1726818E+00 (-0.1723535E+00) - number of electron 512.0000002 magnetization - augmentation part 53.6019692 magnetization - - Broyden mixing: - rms(total) = 0.15587E+02 rms(broyden)= 0.15587E+02 - rms(prec ) = 0.16847E+02 - weight for this iteration 100.00 - - Free energy of the ion-electron system (eV) - --------------------------------------------------- - alpha Z PSCENC = 1957.98898647 - Ewald energy TEWEN = -24665.75652663 - -Hartree energ DENC = -7545.40278343 - -exchange EXHF = 0.00000000 - -V(xc)+E(xc) XCENC = 592.98352221 - PAW double counting = 25569.98736858 -25757.03612884 - entropy T*S EENTRO = -0.00000000 - eigenvalues EBANDS = -3290.46568846 - atomic energy EATOM = 30099.62314931 - Solvation Ediel_sol = 0.00000000 - --------------------------------------------------- - free energy TOTEN = -3038.07810079 eV - - energy without entropy = -3038.07810079 energy(sigma->0) = -3038.07810079 - - --------------------------------------------------------------------------------------------------------- - - - - ---------------------------------------- Iteration 1( 6) --------------------------------------- - - - POTLOK: cpu time 0.4186: real time 0.4272 - SETDIJ: cpu time 0.3658: real time 0.3684 - EDDIAG: cpu time 3.3090: real time 3.3391 - RMM-DIIS: cpu time 19.4446: real time 19.6858 - ORTHCH: cpu time 0.1065: real time 0.1072 - DOS: cpu time 0.0031: real time 0.0032 - CHARGE: cpu time 1.6482: real time 1.6649 - MIXING: cpu time 0.0079: real time 0.0080 - -------------------------------------------- - LOOP: cpu time 25.3038: real time 25.6039 - - eigenvalue-minimisations : 2514 - total energy-change (2. order) : 0.3010565E+03 (-0.5395306E+02) - number of electron 512.0000002 magnetization - augmentation part 47.8584060 magnetization - - Broyden mixing: - rms(total) = 0.85807E+01 rms(broyden)= 0.85804E+01 - rms(prec ) = 0.87622E+01 - weight for this iteration 100.00 - - eigenvalues of (default mixing * dielectric matrix) - average eigenvalue GAMMA= 1.7544 - 1.7544 - - Free energy of the ion-electron system (eV) - --------------------------------------------------- - alpha Z PSCENC = 1957.98898647 - Ewald energy TEWEN = -24665.75652663 - -Hartree energ DENC = -8897.88534450 - -exchange EXHF = 0.00000000 - -V(xc)+E(xc) XCENC = 785.43674131 - PAW double counting = 36598.32101723 -36803.84188345 - entropy T*S EENTRO = -0.00000000 - eigenvalues EBANDS = -1810.90774454 - atomic energy EATOM = 30099.62314931 - Solvation Ediel_sol = 0.00000000 - --------------------------------------------------- - free energy TOTEN = -2737.02160481 eV - - energy without entropy = -2737.02160481 energy(sigma->0) = -2737.02160481 - - --------------------------------------------------------------------------------------------------------- - - - - ---------------------------------------- Iteration 1( 7) --------------------------------------- - - - POTLOK: cpu time 0.4097: real time 0.4142 - SETDIJ: cpu time 0.3584: real time 0.3610 - EDDIAG: cpu time 3.2813: real time 3.3165 - RMM-DIIS: cpu time 21.2132: real time 21.4285 - ORTHCH: cpu time 0.1011: real time 0.1016 - DOS: cpu time 0.0027: real time 0.0027 - CHARGE: cpu time 1.5663: real time 1.7515 - MIXING: cpu time 0.0089: real time 0.0089 - -------------------------------------------- - LOOP: cpu time 26.9414: real time 27.3850 - - eigenvalue-minimisations : 2779 - total energy-change (2. order) :-0.2467362E+02 (-0.2595849E+02) - number of electron 512.0000002 magnetization - augmentation part 44.3005693 magnetization - - Broyden mixing: - rms(total) = 0.27650E+01 rms(broyden)= 0.27640E+01 - rms(prec ) = 0.30997E+01 - weight for this iteration 100.00 - - eigenvalues of (default mixing * dielectric matrix) - average eigenvalue GAMMA= 1.6751 - 1.6751 1.6751 - - Free energy of the ion-electron system (eV) - --------------------------------------------------- - alpha Z PSCENC = 1957.98898647 - Ewald energy TEWEN = -24665.75652663 - -Hartree energ DENC = -9323.11694113 - -exchange EXHF = 0.00000000 - -V(xc)+E(xc) XCENC = 805.73286176 - PAW double counting = 51364.95005734 -51579.02957694 - entropy T*S EENTRO = -0.00000000 - eigenvalues EBANDS = -1422.08723258 - atomic energy EATOM = 30099.62314931 - Solvation Ediel_sol = 0.00000000 - --------------------------------------------------- - free energy TOTEN = -2761.69522241 eV - - energy without entropy = -2761.69522241 energy(sigma->0) = -2761.69522241 - - --------------------------------------------------------------------------------------------------------- - - - - ---------------------------------------- Iteration 1( 8) --------------------------------------- - - - POTLOK: cpu time 0.5745: real time 0.5803 - SETDIJ: cpu time 0.3782: real time 0.3809 - EDDIAG: cpu time 3.2791: real time 3.3135 - RMM-DIIS: cpu time 20.2863: real time 20.4853 - ORTHCH: cpu time 0.0998: real time 0.1005 - DOS: cpu time 0.0025: real time 0.0025 - CHARGE: cpu time 1.6533: real time 1.6688 - MIXING: cpu time 0.0070: real time 0.0071 - -------------------------------------------- - LOOP: cpu time 26.2809: real time 26.5391 - - eigenvalue-minimisations : 2645 - total energy-change (2. order) : 0.2515737E+01 (-0.1134339E+02) - number of electron 512.0000002 magnetization - augmentation part 47.1661299 magnetization - - Broyden mixing: - rms(total) = 0.14791E+01 rms(broyden)= 0.14786E+01 - rms(prec ) = 0.17276E+01 - weight for this iteration 100.00 - - eigenvalues of (default mixing * dielectric matrix) - average eigenvalue GAMMA= 1.4635 - 2.1914 1.0996 1.0996 - - Free energy of the ion-electron system (eV) - --------------------------------------------------- - alpha Z PSCENC = 1957.98898647 - Ewald energy TEWEN = -24665.75652663 - -Hartree energ DENC = -8769.13137550 - -exchange EXHF = 0.00000000 - -V(xc)+E(xc) XCENC = 755.12125378 - PAW double counting = 54450.95078808 -54662.04651474 - entropy T*S EENTRO = -0.00000000 - eigenvalues EBANDS = -1925.92924619 - atomic energy EATOM = 30099.62314931 - Solvation Ediel_sol = 0.00000000 - --------------------------------------------------- - free energy TOTEN = -2759.17948542 eV - - energy without entropy = -2759.17948542 energy(sigma->0) = -2759.17948542 - - --------------------------------------------------------------------------------------------------------- - - - - ---------------------------------------- Iteration 1( 9) --------------------------------------- - - - POTLOK: cpu time 0.4127: real time 0.4211 - SETDIJ: cpu time 0.3662: real time 0.3688 - EDDIAG: cpu time 3.3061: real time 3.3360 - RMM-DIIS: cpu time 21.4238: real time 21.7416 - ORTHCH: cpu time 0.1037: real time 0.1044 - DOS: cpu time 0.0005: real time 0.0005 - CHARGE: cpu time 1.6366: real time 1.6541 - MIXING: cpu time 0.0073: real time 0.0074 - -------------------------------------------- - LOOP: cpu time 27.2568: real time 27.6338 - - eigenvalue-minimisations : 2879 - total energy-change (2. order) : 0.3829458E+01 (-0.9281334E+00) - number of electron 512.0000002 magnetization - augmentation part 46.6526570 magnetization - - Broyden mixing: - rms(total) = 0.38380E+00 rms(broyden)= 0.38380E+00 - rms(prec ) = 0.46844E+00 - weight for this iteration 100.00 - - eigenvalues of (default mixing * dielectric matrix) - average eigenvalue GAMMA= 1.4992 - 2.4005 1.0258 1.2852 1.2852 - - Free energy of the ion-electron system (eV) - --------------------------------------------------- - alpha Z PSCENC = 1957.98898647 - Ewald energy TEWEN = -24665.75652663 - -Hartree energ DENC = -8987.61887355 - -exchange EXHF = 0.00000000 - -V(xc)+E(xc) XCENC = 790.97929009 - PAW double counting = 58038.44282685 -58253.55874273 - entropy T*S EENTRO = -0.00000000 - eigenvalues EBANDS = -1735.45013738 - atomic energy EATOM = 30099.62314931 - Solvation Ediel_sol = 0.00000000 - --------------------------------------------------- - free energy TOTEN = -2755.35002758 eV - - energy without entropy = -2755.35002758 energy(sigma->0) = -2755.35002758 - - --------------------------------------------------------------------------------------------------------- - - - - ---------------------------------------- Iteration 1( 10) --------------------------------------- - - - POTLOK: cpu time 0.4102: real time 0.4146 - SETDIJ: cpu time 0.3631: real time 0.3662 - EDDIAG: cpu time 3.2760: real time 3.3101 - RMM-DIIS: cpu time 21.4564: real time 21.6867 - ORTHCH: cpu time 0.0955: real time 0.0962 - DOS: cpu time 0.0023: real time 0.0023 - CHARGE: cpu time 1.6263: real time 1.6434 - MIXING: cpu time 0.0075: real time 0.0075 - -------------------------------------------- - LOOP: cpu time 27.2373: real time 27.5270 - - eigenvalue-minimisations : 2884 - total energy-change (2. order) :-0.4545210E+00 (-0.1079998E+01) - number of electron 512.0000002 magnetization - augmentation part 45.8041316 magnetization - - Broyden mixing: - rms(total) = 0.43121E+00 rms(broyden)= 0.43096E+00 - rms(prec ) = 0.52794E+00 - weight for this iteration 100.00 - - eigenvalues of (default mixing * dielectric matrix) - average eigenvalue GAMMA= 1.5390 - 2.6317 2.0024 1.0322 1.0143 1.0143 - - Free energy of the ion-electron system (eV) - --------------------------------------------------- - alpha Z PSCENC = 1957.98898647 - Ewald energy TEWEN = -24665.75652663 - -Hartree energ DENC = -9099.66076799 - -exchange EXHF = 0.00000000 - -V(xc)+E(xc) XCENC = 796.67465656 - PAW double counting = 58968.07299783 -59185.48856551 - entropy T*S EENTRO = -0.00000000 - eigenvalues EBANDS = -1627.25847861 - atomic energy EATOM = 30099.62314931 - Solvation Ediel_sol = 0.00000000 - --------------------------------------------------- - free energy TOTEN = -2755.80454857 eV - - energy without entropy = -2755.80454857 energy(sigma->0) = -2755.80454857 - - --------------------------------------------------------------------------------------------------------- - - - - ---------------------------------------- Iteration 1( 11) --------------------------------------- - - - POTLOK: cpu time 0.4100: real time 0.4126 - SETDIJ: cpu time 0.3648: real time 0.3682 - EDDIAG: cpu time 3.2751: real time 3.3098 - RMM-DIIS: cpu time 21.3377: real time 21.5585 - ORTHCH: cpu time 0.0971: real time 0.0979 - DOS: cpu time 0.0005: real time 0.0005 - CHARGE: cpu time 1.6808: real time 1.6992 - MIXING: cpu time 0.0079: real time 0.0079 - -------------------------------------------- - LOOP: cpu time 27.1739: real time 27.4546 - - eigenvalue-minimisations : 2866 - total energy-change (2. order) : 0.3915144E+00 (-0.1827567E+00) - number of electron 512.0000002 magnetization - augmentation part 46.0585328 magnetization - - Broyden mixing: - rms(total) = 0.12749E+00 rms(broyden)= 0.12747E+00 - rms(prec ) = 0.14417E+00 - weight for this iteration 100.00 - - eigenvalues of (default mixing * dielectric matrix) - average eigenvalue GAMMA= 1.6036 - 2.7427 2.6247 1.1665 1.0943 0.9968 0.9968 - - Free energy of the ion-electron system (eV) - --------------------------------------------------- - alpha Z PSCENC = 1957.98898647 - Ewald energy TEWEN = -24665.75652663 - -Hartree energ DENC = -9028.31999313 - -exchange EXHF = 0.00000000 - -V(xc)+E(xc) XCENC = 787.40846685 - PAW double counting = 58913.33096832 -59130.67174805 - entropy T*S EENTRO = -0.00000000 - eigenvalues EBANDS = -1689.01633730 - atomic energy EATOM = 30099.62314931 - Solvation Ediel_sol = 0.00000000 - --------------------------------------------------- - free energy TOTEN = -2755.41303415 eV - - energy without entropy = -2755.41303415 energy(sigma->0) = -2755.41303415 - - --------------------------------------------------------------------------------------------------------- - - - - ---------------------------------------- Iteration 1( 12) --------------------------------------- - - - POTLOK: cpu time 0.4133: real time 0.4198 - SETDIJ: cpu time 0.3646: real time 0.3670 - EDDIAG: cpu time 3.2778: real time 3.3070 - RMM-DIIS: cpu time 21.9102: real time 22.1068 - ORTHCH: cpu time 0.0941: real time 0.0948 - DOS: cpu time 0.0041: real time 0.0041 - CHARGE: cpu time 1.6720: real time 1.6875 - MIXING: cpu time 0.0068: real time 0.0069 - -------------------------------------------- - LOOP: cpu time 27.7430: real time 27.9939 - - eigenvalue-minimisations : 2978 - total energy-change (2. order) :-0.8611452E-02 (-0.4280425E-01) - number of electron 512.0000002 magnetization - augmentation part 46.1552143 magnetization - - Broyden mixing: - rms(total) = 0.56278E-01 rms(broyden)= 0.56225E-01 - rms(prec ) = 0.58622E-01 - weight for this iteration 100.00 - - eigenvalues of (default mixing * dielectric matrix) - average eigenvalue GAMMA= 1.7467 - 3.8617 2.5105 1.9373 0.9867 0.9867 1.0375 0.9063 - - Free energy of the ion-electron system (eV) - --------------------------------------------------- - alpha Z PSCENC = 1957.98898647 - Ewald energy TEWEN = -24665.75652663 - -Hartree energ DENC = -9016.41644857 - -exchange EXHF = 0.00000000 - -V(xc)+E(xc) XCENC = 787.96759057 - PAW double counting = 58785.89799504 -59003.30399755 - entropy T*S EENTRO = -0.00000000 - eigenvalues EBANDS = -1701.42239424 - atomic energy EATOM = 30099.62314931 - Solvation Ediel_sol = 0.00000000 - --------------------------------------------------- - free energy TOTEN = -2755.42164561 eV - - energy without entropy = -2755.42164561 energy(sigma->0) = -2755.42164561 - - --------------------------------------------------------------------------------------------------------- - - - - ---------------------------------------- Iteration 1( 13) --------------------------------------- - - - POTLOK: cpu time 0.4109: real time 0.4151 - SETDIJ: cpu time 0.3609: real time 0.3637 - EDDIAG: cpu time 3.2832: real time 3.3128 - RMM-DIIS: cpu time 23.3465: real time 23.5598 - ORTHCH: cpu time 0.0966: real time 0.0973 - DOS: cpu time 0.0007: real time 0.0007 - CHARGE: cpu time 1.6359: real time 1.6517 - MIXING: cpu time 0.0079: real time 0.0080 - -------------------------------------------- - LOOP: cpu time 29.1427: real time 29.4091 - - eigenvalue-minimisations : 3238 - total energy-change (2. order) :-0.6692038E-02 (-0.7984662E-02) - number of electron 512.0000002 magnetization - augmentation part 46.1577758 magnetization - - Broyden mixing: - rms(total) = 0.50062E-01 rms(broyden)= 0.50057E-01 - rms(prec ) = 0.53175E-01 - weight for this iteration 100.00 - - eigenvalues of (default mixing * dielectric matrix) - average eigenvalue GAMMA= 1.7309 - 4.3708 2.4270 2.1325 0.9734 0.9734 1.1097 0.9301 0.9301 - - Free energy of the ion-electron system (eV) - --------------------------------------------------- - alpha Z PSCENC = 1957.98898647 - Ewald energy TEWEN = -24665.75652663 - -Hartree energ DENC = -9018.34149267 - -exchange EXHF = 0.00000000 - -V(xc)+E(xc) XCENC = 788.64622749 - PAW double counting = 58930.30054124 -59147.65218838 - entropy T*S EENTRO = -0.00000000 - eigenvalues EBANDS = -1700.23703448 - atomic energy EATOM = 30099.62314931 - Solvation Ediel_sol = 0.00000000 - --------------------------------------------------- - free energy TOTEN = -2755.42833764 eV - - energy without entropy = -2755.42833764 energy(sigma->0) = -2755.42833764 - - --------------------------------------------------------------------------------------------------------- - - - - ---------------------------------------- Iteration 1( 14) --------------------------------------- - - - POTLOK: cpu time 0.4100: real time 0.4124 - SETDIJ: cpu time 0.3623: real time 0.3647 - EDDIAG: cpu time 3.2689: real time 3.2997 - RMM-DIIS: cpu time 22.1505: real time 22.4718 - ORTHCH: cpu time 0.0987: real time 0.0994 - DOS: cpu time 0.0003: real time 0.0003 - CHARGE: cpu time 1.6405: real time 1.6560 - MIXING: cpu time 0.0074: real time 0.0075 - -------------------------------------------- - LOOP: cpu time 27.9387: real time 28.3117 - - eigenvalue-minimisations : 3004 - total energy-change (2. order) :-0.3168388E-02 (-0.2126612E-02) - number of electron 512.0000002 magnetization - augmentation part 46.1784040 magnetization - - Broyden mixing: - rms(total) = 0.52379E-01 rms(broyden)= 0.52376E-01 - rms(prec ) = 0.61217E-01 - weight for this iteration 100.00 - - eigenvalues of (default mixing * dielectric matrix) - average eigenvalue GAMMA= 1.7694 - 5.0425 2.4270 2.4270 1.0170 1.0170 0.9810 0.9810 1.0161 1.0161 - - Free energy of the ion-electron system (eV) - --------------------------------------------------- - alpha Z PSCENC = 1957.98898647 - Ewald energy TEWEN = -24665.75652663 - -Hartree energ DENC = -9015.73526581 - -exchange EXHF = 0.00000000 - -V(xc)+E(xc) XCENC = 788.55715954 - PAW double counting = 59029.62506761 -59246.90989431 - entropy T*S EENTRO = -0.00000000 - eigenvalues EBANDS = -1702.82418221 - atomic energy EATOM = 30099.62314931 - Solvation Ediel_sol = 0.00000000 - --------------------------------------------------- - free energy TOTEN = -2755.43150603 eV - - energy without entropy = -2755.43150603 energy(sigma->0) = -2755.43150603 - - --------------------------------------------------------------------------------------------------------- - - - - ---------------------------------------- Iteration 1( 15) --------------------------------------- - - - POTLOK: cpu time 0.4069: real time 0.4143 - SETDIJ: cpu time 0.3644: real time 0.3670 - EDDIAG: cpu time 3.4889: real time 3.5641 - RMM-DIIS: cpu time 21.9112: real time 22.3164 - ORTHCH: cpu time 0.0957: real time 0.0964 - DOS: cpu time 0.0004: real time 0.0665 - CHARGE: cpu time 1.6823: real time 1.6995 - MIXING: cpu time 0.0078: real time 0.0078 - -------------------------------------------- - LOOP: cpu time 27.9576: real time 28.5319 - - eigenvalue-minimisations : 2948 - total energy-change (2. order) : 0.2727759E-02 (-0.6141372E-03) - number of electron 512.0000002 magnetization - augmentation part 46.1639398 magnetization - - Broyden mixing: - rms(total) = 0.25235E-01 rms(broyden)= 0.25234E-01 - rms(prec ) = 0.31275E-01 - weight for this iteration 100.00 - - eigenvalues of (default mixing * dielectric matrix) - average eigenvalue GAMMA= 1.6875 - 4.0477 2.6803 2.0628 2.0628 0.9964 0.9964 1.0514 0.9430 1.0169 1.0169 - - Free energy of the ion-electron system (eV) - --------------------------------------------------- - alpha Z PSCENC = 1957.98898647 - Ewald energy TEWEN = -24665.75652663 - -Hartree energ DENC = -9019.38574590 - -exchange EXHF = 0.00000000 - -V(xc)+E(xc) XCENC = 788.97575230 - PAW double counting = 59136.73620313 -59353.98521553 - entropy T*S EENTRO = -0.00000000 - eigenvalues EBANDS = -1699.62538142 - atomic energy EATOM = 30099.62314931 - Solvation Ediel_sol = 0.00000000 - --------------------------------------------------- - free energy TOTEN = -2755.42877827 eV - - energy without entropy = -2755.42877827 energy(sigma->0) = -2755.42877827 - - --------------------------------------------------------------------------------------------------------- - - - - ---------------------------------------- Iteration 1( 16) --------------------------------------- - - - POTLOK: cpu time 0.4081: real time 0.4136 - SETDIJ: cpu time 0.3628: real time 0.3661 - EDDIAG: cpu time 3.2970: real time 3.3296 - RMM-DIIS: cpu time 21.8434: real time 22.1799 - ORTHCH: cpu time 0.0946: real time 0.0953 - DOS: cpu time 0.0008: real time 0.0008 - CHARGE: cpu time 1.6649: real time 1.6815 - MIXING: cpu time 0.0078: real time 0.0079 - -------------------------------------------- - LOOP: cpu time 27.6794: real time 28.0748 - - eigenvalue-minimisations : 2947 - total energy-change (2. order) : 0.5837641E-03 (-0.8020765E-03) - number of electron 512.0000002 magnetization - augmentation part 46.1420489 magnetization - - Broyden mixing: - rms(total) = 0.12220E-01 rms(broyden)= 0.12214E-01 - rms(prec ) = 0.12580E-01 - weight for this iteration 100.00 - - eigenvalues of (default mixing * dielectric matrix) - average eigenvalue GAMMA= 1.5313 - 3.9764 2.6755 2.0568 2.0568 0.9967 0.9967 1.0541 0.9425 1.0151 1.0151 - 0.0582 - - Free energy of the ion-electron system (eV) - --------------------------------------------------- - alpha Z PSCENC = 1957.98898647 - Ewald energy TEWEN = -24665.75652663 - -Hartree energ DENC = -9022.11417397 - -exchange EXHF = 0.00000000 - -V(xc)+E(xc) XCENC = 789.08363071 - PAW double counting = 59127.95202031 -59345.23341684 - entropy T*S EENTRO = -0.00000000 - eigenvalues EBANDS = -1696.97186386 - atomic energy EATOM = 30099.62314931 - Solvation Ediel_sol = 0.00000000 - --------------------------------------------------- - free energy TOTEN = -2755.42819451 eV - - energy without entropy = -2755.42819451 energy(sigma->0) = -2755.42819451 - - --------------------------------------------------------------------------------------------------------- - - - - ---------------------------------------- Iteration 1( 17) --------------------------------------- - - - POTLOK: cpu time 0.4091: real time 0.4116 - SETDIJ: cpu time 0.3656: real time 0.3683 - EDDIAG: cpu time 3.2902: real time 3.3224 - RMM-DIIS: cpu time 22.5907: real time 22.8621 - ORTHCH: cpu time 0.0947: real time 0.0953 - DOS: cpu time 0.0011: real time 0.0011 - CHARGE: cpu time 1.6400: real time 1.6552 - MIXING: cpu time 0.0079: real time 0.0080 - -------------------------------------------- - LOOP: cpu time 28.3992: real time 28.7241 - - eigenvalue-minimisations : 3074 - total energy-change (2. order) :-0.1228343E-03 (-0.1861092E-03) - number of electron 512.0000002 magnetization - augmentation part 46.1353917 magnetization - - Broyden mixing: - rms(total) = 0.12955E-01 rms(broyden)= 0.12954E-01 - rms(prec ) = 0.13004E-01 - weight for this iteration 100.00 - - eigenvalues of (default mixing * dielectric matrix) - average eigenvalue GAMMA= 1.4605 - 3.8481 2.6709 2.0973 2.0973 0.9951 0.9951 1.0080 0.9607 1.0175 1.0175 - 0.4975 0.3215 - - Free energy of the ion-electron system (eV) - --------------------------------------------------- - alpha Z PSCENC = 1957.98898647 - Ewald energy TEWEN = -24665.75652663 - -Hartree energ DENC = -9022.32744545 - -exchange EXHF = 0.00000000 - -V(xc)+E(xc) XCENC = 788.97334872 - PAW double counting = 59140.00231383 -59357.28602438 - entropy T*S EENTRO = -0.00000000 - eigenvalues EBANDS = -1696.64611920 - atomic energy EATOM = 30099.62314931 - Solvation Ediel_sol = 0.00000000 - --------------------------------------------------- - free energy TOTEN = -2755.42831734 eV - - energy without entropy = -2755.42831734 energy(sigma->0) = -2755.42831734 - - --------------------------------------------------------------------------------------------------------- - - - - ---------------------------------------- Iteration 1( 18) --------------------------------------- - - - POTLOK: cpu time 0.4108: real time 0.4195 - SETDIJ: cpu time 0.3593: real time 0.3620 - EDDIAG: cpu time 3.2793: real time 3.3110 - RMM-DIIS: cpu time 16.0500: real time 16.1979 - ORTHCH: cpu time 0.0946: real time 0.0953 - DOS: cpu time 0.0006: real time 0.0006 - -------------------------------------------- - LOOP: cpu time 20.1945: real time 20.3863 - - eigenvalue-minimisations : 1878 - total energy-change (2. order) :-0.1571118E-04 (-0.1503376E-04) - number of electron 512.0000002 magnetization - 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0.460E+01 0.430E+01 -.478E+01 0.250E+01 -.372E+01 0.299E+01 -.784E+01 0.120E+00 0.773E+00 -.373E-02 0.570E-02 0.195E-02 - 0.362E+02 0.616E+01 0.237E+02 -.358E+02 0.467E+01 -.242E+02 -.964E+00 -.131E+02 -.474E+00 -.139E-02 0.560E-03 -.108E-02 - -.143E+00 -.255E+02 0.636E+01 0.313E+01 0.202E+02 -.533E+01 -.366E+01 0.589E+01 -.209E+01 -.420E-02 0.169E-02 -.974E-03 - -.130E+01 -.454E+02 0.490E+02 -.336E+01 0.478E+02 -.506E+02 0.612E+01 -.656E+00 -.116E+01 0.247E-02 0.346E-02 -.478E-02 - ----------------------------------------------------------------------------------------------- - 0.218E+02 -.520E+01 -.456E+01 0.306E-12 0.426E-13 0.568E-13 -.218E+02 0.521E+01 0.452E+01 -.181E-02 0.419E-02 -.174E-02 - - - POSITION TOTAL-FORCE (eV/Angst) - ----------------------------------------------------------------------------------- - 10.16858 7.34992 -8.61424 1.580909 1.743569 -2.274193 - 9.56075 2.36192 -4.06759 0.082770 -1.714994 1.576682 - 9.08318 0.36359 -1.53137 -1.590152 -0.292693 -0.780380 - 10.48296 2.53529 -8.68474 -2.785418 -1.079558 -3.311421 - 9.91924 0.10479 -6.55475 0.832840 -1.339498 1.166484 - 8.76860 5.41632 -1.21479 2.863292 4.222905 1.664225 - 9.78784 5.18581 -6.20973 -0.324293 1.126582 -0.277481 - 4.49886 2.37514 -3.95473 2.713567 -1.953741 0.742687 - 1.77491 4.81214 -3.77570 3.461567 2.619996 -2.356652 - 1.35882 3.26380 -0.98597 -0.433422 -2.559668 -4.006829 - 5.34832 2.45621 -9.44997 2.576183 -1.048731 2.553559 - 2.67977 5.33962 -8.87517 1.268597 0.434576 0.760837 - 5.08106 7.89762 -8.95181 0.870661 -2.665735 -1.476307 - 2.54343 7.96028 -6.54474 0.384666 -2.065252 -0.295599 - 5.07252 5.52124 -6.33373 -3.339572 0.283930 -0.265899 - 4.07568 7.34367 -3.64800 1.568222 2.245414 -1.719557 - 2.23620 10.22916 -4.33430 -1.097121 -2.603108 2.379267 - 1.53690 8.10586 -1.35299 -3.335830 0.744379 -2.826941 - 3.69128 5.41657 -1.10692 1.605429 3.080642 2.366244 - 2.72468 0.09732 -9.22176 -0.518960 -1.127958 -0.754444 - 2.49587 2.89133 -6.69292 2.642565 1.998095 2.834524 - 4.75287 0.30932 -6.71628 2.077281 1.326968 0.323342 - 3.78250 0.17619 -1.48204 5.292232 5.836548 3.741637 - 8.32237 9.97287 -9.55475 -3.143426 2.373314 -2.470842 - 7.06732 9.83704 -4.39267 -0.992349 1.951153 3.290303 - 7.91374 5.04988 -9.27754 -3.009336 -0.202389 -1.083436 - 7.28764 2.82479 -6.65104 -1.226686 -2.442486 -0.734020 - 7.21885 4.99889 -3.92330 -1.721146 1.617177 -0.230095 - 6.52495 2.96080 -1.21547 -1.199484 -4.482583 -4.026121 - 7.51279 8.01067 -6.93611 0.089857 -0.923084 -0.119643 - 9.60938 7.68019 -3.94365 -0.783543 0.888490 4.183444 - 6.59354 7.94314 -1.59299 3.005103 -0.895005 -1.283395 - 10.12719 6.98137 -1.98458 0.334636 -1.360953 1.399730 - 1.26810 6.39822 -7.13188 -2.640333 0.845992 -0.870145 - 11.46023 6.56348 -9.67267 0.492685 -0.440421 -1.699194 - 11.31172 1.51464 -7.19505 0.384035 -0.207446 -0.543495 - 8.09987 4.02806 -2.21415 -1.982881 -2.221429 -2.322843 - 10.38679 1.81046 -2.34830 0.562807 -0.219025 1.788916 - 10.77439 0.91495 -4.89956 -0.248029 2.019560 1.150579 - 9.38537 3.88539 -10.22617 0.132855 -0.468154 2.740702 - 8.90289 3.73971 -7.32853 -0.230879 -1.074762 -1.957028 - 1.90245 1.92614 -9.78538 -1.352183 -0.734879 -0.756375 - 10.56567 6.16965 -4.48995 -0.092671 -0.579726 -1.269733 - 3.45696 3.76129 -4.84867 -1.816639 0.257829 -1.236630 - 2.91579 4.05924 -2.23370 -0.803786 -2.717697 0.320799 - 5.49514 1.44898 -2.50673 -0.901990 -0.675533 1.833214 - 0.13858 4.37310 -0.14812 -1.458060 0.955240 1.037554 - 4.39279 4.43463 -9.87579 -1.773241 -2.116988 -2.369116 - 3.83180 4.22276 -7.57406 -1.450490 -1.361584 2.143579 - 6.14289 1.31287 -7.68671 0.508066 1.907163 -0.073107 - 6.74060 1.24529 -10.15236 -0.331872 1.376228 -0.150667 - 5.80653 1.23799 -5.21286 -0.193614 0.282229 1.867514 - 3.74482 6.68417 -7.80590 -0.145720 -0.266780 -0.506027 - 3.00237 6.40546 -5.25777 1.208241 0.488375 0.174676 - 3.95333 9.03051 -7.78159 -2.030359 2.533156 1.042504 - 6.07491 6.81238 -7.39887 -0.129123 -0.400258 0.839057 - 1.10013 8.86333 -5.60176 -1.068703 0.412450 -1.483275 - 6.22998 6.35840 -9.83448 2.261015 -0.754642 0.645466 - 3.64096 8.91835 -5.08671 0.105041 0.346060 -0.337467 - 2.69436 6.44253 -2.62518 -1.799170 0.009736 0.995890 - 2.21884 6.94584 -0.02793 0.088284 -1.608053 0.483554 - 3.05563 9.14313 -2.43192 -0.990533 -4.914405 -2.235406 - 5.14580 6.61850 -2.00795 -1.503271 -1.468584 -0.064625 - 0.22242 9.47976 -0.59347 2.056466 -0.162484 1.620088 - 0.83083 8.81926 -3.18911 0.593090 1.881042 -0.886060 - 5.46538 6.42376 -4.61815 1.678619 -2.711113 -1.094144 - 4.42296 9.69077 -10.15129 -0.261744 -2.358766 -0.301686 - 11.41831 9.09345 -8.30097 2.290896 0.149894 0.781978 - 3.71626 1.61175 -8.21115 0.551390 -0.603132 1.088908 - 3.21647 1.11010 -5.65827 0.216763 1.703785 -0.328377 - 0.95705 3.96527 -5.40215 0.928105 -3.363280 0.553794 - 3.01838 1.22141 -3.03139 0.138804 1.332278 -1.323304 - 2.50079 1.66386 -0.60185 0.508906 1.307199 1.216329 - 10.55008 4.20576 -2.71857 -1.326271 -1.194678 1.270231 - 11.23678 3.98269 -7.72651 2.712553 1.409570 -1.904224 - 7.75800 8.74016 -0.00630 0.780616 -1.078433 -0.072023 - 9.06406 8.90624 -8.06018 -2.007027 -1.346025 4.957937 - 8.54064 1.27758 -5.57043 -1.094579 0.916799 -1.867861 - 6.05339 3.91896 -5.67068 0.531987 1.013495 0.451164 - 8.64776 4.07040 -4.91687 -0.700674 -3.088293 1.611188 - 8.25147 1.05521 -3.10583 -1.324284 1.929429 -3.640607 - 7.58420 1.12452 -0.46764 0.610696 1.590037 0.265549 - 5.04466 3.93044 -0.45120 0.077934 0.203681 -0.172546 - 5.79818 3.67522 -3.11783 0.809625 2.016564 0.268915 - 9.37678 0.84273 -8.25031 -1.338378 3.142603 -1.039176 - 6.55078 3.80037 -8.31079 0.541589 -0.073200 0.604591 - 7.20203 6.28983 -0.23740 0.243344 -0.183611 0.341524 - 5.59788 9.42205 -1.18549 -2.213394 1.398985 3.139973 - 8.56958 6.23474 -7.94178 2.178742 1.596364 1.157702 - 8.01189 6.18309 -5.53701 0.600382 1.909811 -0.287413 - 6.25852 9.30204 -6.20725 0.549183 -0.725245 1.556118 - 6.64931 8.99787 -8.67070 1.653858 -0.289005 0.130305 - 8.61642 8.86599 -5.30460 -0.747865 0.704751 -1.017049 - 7.92656 6.57976 -2.80962 -0.572431 -2.290357 -1.054984 - 8.26866 8.98956 -2.55828 -0.669840 0.591845 -1.059312 - 5.76462 8.59857 -3.36305 1.453818 1.729537 -2.846110 - ----------------------------------------------------------------------------------- - total drift: 0.009830 0.016753 -0.043235 - - --------------------------------------------------------------------------------------------------------- - - - - FREE ENERGIE OF THE ION-ELECTRON SYSTEM (eV) - --------------------------------------------------- - free energy TOTEN = -2755.42833306 eV - - energy without entropy= -2755.42833306 energy(sigma->0) = -2755.42833306 - - - --------------------------------------------------------------------------------------------------------- - - - POTLOK: cpu time 0.7643: real time 0.7690 - - --------------------------------------------------------------------------------------------------------- - - - LOOP+: cpu time 480.6909: real time 487.3090 - 4ORBIT: cpu time 0.0000: real time 0.0000 - - total amount of memory used by VASP MPI-rank0 162804. kBytes -======================================================================= - - base : 30000. kBytes - nonlr-proj: 30253. kBytes - fftplans : 41293. kBytes - grid : 25778. kBytes - one-center: 373. kBytes - wavefun : 35107. kBytes - - - - General timing and accounting informations for this job: - ======================================================== - - Total CPU time used (sec): 486.118 - User time (sec): 466.843 - System time (sec): 19.274 - Elapsed time (sec): 494.001 - - Maximum memory used (kb): 410144. - Average memory used (kb): N/A - - Minor page faults: 572434 - Major page faults: 4183 - Voluntary context switches: 7026 diff --git a/mace-bench/3rdparty/SevenNet/example_inputs/data/label_1/OUTCAR_3 b/mace-bench/3rdparty/SevenNet/example_inputs/data/label_1/OUTCAR_3 deleted file mode 100644 index d26b7a97737926b23a63f2fed830e5b401b8e57b..0000000000000000000000000000000000000000 --- a/mace-bench/3rdparty/SevenNet/example_inputs/data/label_1/OUTCAR_3 +++ /dev/null @@ -1,3562 +0,0 @@ - vasp.6.3.2 27Jun22 (build Aug 12 2022 00:53:59) complex - - executed on tv2STD date 2022.09.21 13:32:32 - running 32 mpi-ranks, with 1 threads/rank - distrk: each k-point on 16 cores, 2 groups - distr: one band on NCORE= 4 cores, 4 groups - - --------------------------------------------------------------------------------------------------------- - - - INCAR: - SYSTEM = HfO2_p21c - NWRITE = 2 write-flag - ISTART = 0 job : 0-new, 1-cont, 2-samecut - ICHARG = 2 charge: 0-wave, 1-file, 2-atom, >10-const - INIWAV = 1 electr: 0-lowe 1-rand 2-diag - ENCUT = 500 - PREC = Accurate normal | accurate - ADDGRID = True - NELM = 100 - LREAL = Auto real-space projection (.FALSE., .TRUE., On, Auto) - ALGO = Fast Normal, Fast, Very_Fast - LWAVE = .F. - LCHARG = .F. - NSW = 0 - IBRION = 2 ionic relax: 0-MD, 1-quasi-Newton, 2-CG, 3-Damped MD - EDIFFG = -0.002 - ISIF = 3 (1:force\=y stress\=trace only ions\=y shape\=n volume\=n) - ISYM = 1 (1-use symmetry, 0-no symmetry) - ISMEAR = 0 (-1-Fermi, 1-Methfessel/Paxton) - SIGMA = 0.05 broadening in eV - NPAR = 4 - KPAR = 2 - METAGGA = SCAN - - POTCAR: PAW_PBE Hf 20Jan2003 - POTCAR: PAW_PBE O 08Apr2002 - POTCAR: PAW_PBE Hf 20Jan2003 - SHA256 = 0bb2207f9a10894133f750b65504b92b8afef976ae770762e0497daaaad8168a Hf/POTCAR - COPYR = (c) Copyright 20Jan2003 Georg Kresse - COPYR = This file is part of the software VASP. Any use, copying, and all other rights are regul - COPYR = If you do not have a valid VASP license, you may not use, copy or distribute this file. - VRHFIN =Hf: 6s5d - LEXCH = PE - EATOM = 75.9011 eV, 5.5786 Ry - - TITEL = PAW_PBE Hf 20Jan2003 - LULTRA = F use ultrasoft PP ? - IUNSCR = 1 unscreen: 0-lin 1-nonlin 2-no - RPACOR = 2.500 partial core radius - POMASS = 178.490; ZVAL = 4.000 mass and valenz - RCORE = 3.000 outmost cutoff radius - RWIGS = 3.050; RWIGS = 1.614 wigner-seitz radius (au A) - ENMAX = 220.334; ENMIN = 165.250 eV - RCLOC = 2.212 cutoff for local pot - LCOR = T correct aug charges - LPAW = T paw PP - EAUG = 335.116 - DEXC = 0.000 - RMAX = 3.077 core radius for proj-oper - RAUG = 1.300 factor for augmentation sphere - RDEP = 3.047 radius for radial grids - RDEPT = 2.344 core radius for aug-charge - - Atomic configuration - 16 entries - n l j E occ. - 1 0 0.50 -65259.4397 2.0000 - 2 0 0.50 -11157.9882 2.0000 - 2 1 1.50 -9795.2113 6.0000 - 3 0 0.50 -2541.4058 2.0000 - 3 1 1.50 -2134.4770 6.0000 - 3 2 2.50 -1653.5418 10.0000 - 4 0 0.50 -510.9575 2.0000 - 4 1 1.50 -377.5023 6.0000 - 4 2 2.50 -205.2085 10.0000 - 4 3 3.50 -15.4905 14.0000 - 5 0 0.50 -65.6020 2.0000 - 5 1 1.50 -34.2798 6.0000 - 5 2 2.50 -1.9877 3.0000 - 6 0 0.50 -4.7357 1.0000 - 6 1 1.50 -1.3606 0.0000 - 5 3 2.50 -1.3606 0.0000 - Description - l E TYP RCUT TYP RCUT - 2 -1.9876627 23 2.500 - 2 0.0744703 23 2.500 - 0 -4.7356889 23 2.600 - 0 3.2364747 23 2.600 - 1 -1.3605826 23 3.000 - 1 27.2116520 23 3.000 - local pseudopotential read in - partial core-charges read in - partial kinetic energy density read in - atomic valenz-charges read in - non local Contribution for L= 2 read in - real space projection operators read in - non local Contribution for L= 2 read in - real space projection operators read in - non local Contribution for L= 0 read in - real space projection operators read in - non local Contribution for L= 0 read in - real space projection operators read in - non local Contribution for L= 1 read in - real space projection operators read in - non local Contribution for L= 1 read in - real space projection operators read in - PAW grid and wavefunctions read in - - number of l-projection operators is LMAX = 6 - number of lm-projection operators is LMMAX = 18 - - POTCAR: PAW_PBE O 08Apr2002 - SHA256 = 818f92134a0a090dccd8ba1447fa70422a3b330e708bb4f08108d8ae51209ddf O/POTCAR - COPYR = (c) Copyright 08Apr2002 Georg Kresse - COPYR = This file is part of the software VASP. Any use, copying, and all other rights are regul - COPYR = If you do not have a valid VASP license, you may not use, copy or distribute this file. - VRHFIN =O: s2p4 - LEXCH = PE - EATOM = 432.3788 eV, 31.7789 Ry - - TITEL = PAW_PBE O 08Apr2002 - LULTRA = F use ultrasoft PP ? - IUNSCR = 1 unscreen: 0-lin 1-nonlin 2-no - RPACOR = 1.200 partial core radius - POMASS = 16.000; ZVAL = 6.000 mass and valenz - RCORE = 1.520 outmost cutoff radius - RWIGS = 1.550; RWIGS = 0.820 wigner-seitz radius (au A) - ENMAX = 400.000; ENMIN = 300.000 eV - ICORE = 2 local potential - LCOR = T correct aug charges - LPAW = T paw PP - EAUG = 605.392 - DEXC = 0.000 - RMAX = 1.553 core radius for proj-oper - RAUG = 1.300 factor for augmentation sphere - RDEP = 1.550 radius for radial grids - RDEPT = 1.329 core radius for aug-charge - - Atomic configuration - 4 entries - n l j E occ. - 1 0 0.50 -514.6923 2.0000 - 2 0 0.50 -23.9615 2.0000 - 2 1 0.50 -9.0305 4.0000 - 3 2 1.50 -9.5241 0.0000 - Description - l E TYP RCUT TYP RCUT - 0 -23.9615318 23 1.200 - 0 -9.5240782 23 1.200 - 1 -9.0304911 23 1.520 - 1 8.1634956 23 1.520 - 2 -9.5240782 7 1.500 - local pseudopotential read in - partial core-charges read in - partial kinetic energy density read in - kinetic energy density of atom read in - atomic valenz-charges read in - non local Contribution for L= 0 read in - real space projection operators read in - non local Contribution for L= 0 read in - real space projection operators read in - non local Contribution for L= 1 read in - real space projection operators read in - non local Contribution for L= 1 read in - real space projection operators read in - PAW grid and wavefunctions read in - - number of l-projection operators is LMAX = 4 - number of lm-projection operators is LMMAX = 8 - - Optimization of the real space projectors (new method) - - maximal supplied QI-value = 12.47 - optimisation between [QCUT,QGAM] = [ 11.35, 22.82] = [ 36.07,145.88] Ry - Optimized for a Real-space Cutoff 1.66 Angstroem - - l n(q) QCUT max X(q) W(low)/X(q) W(high)/X(q) e(spline) - 2 10 11.350 48.111 0.20E-03 0.11E-03 0.41E-06 - 2 10 11.350 40.545 0.19E-03 0.10E-03 0.39E-06 - 0 11 11.350 121.658 0.22E-04 0.19E-04 0.24E-06 - 0 11 11.350 71.177 0.17E-04 0.17E-04 0.23E-06 - 1 11 11.350 14.183 0.25E-03 0.43E-03 0.12E-05 - 1 11 11.350 8.257 0.17E-03 0.29E-03 0.81E-06 - Optimization of the real space projectors (new method) - - maximal supplied QI-value = 24.76 - optimisation between [QCUT,QGAM] = [ 11.39, 22.77] = [ 36.31,145.25] Ry - Optimized for a Real-space Cutoff 1.10 Angstroem - - l n(q) QCUT max X(q) W(low)/X(q) W(high)/X(q) e(spline) - 0 7 11.387 20.381 0.22E-03 0.48E-03 0.18E-06 - 0 7 11.387 15.268 0.22E-03 0.52E-03 0.19E-06 - 1 7 11.387 5.964 0.22E-03 0.73E-03 0.24E-06 - 1 7 11.387 5.382 0.19E-03 0.60E-03 0.21E-06 - PAW_PBE Hf 20Jan2003 : - energy of atom 1 EATOM= -75.9011 - kinetic energy error for atom= 0.0007 (will be added to EATOM!!) - PAW_PBE O 08Apr2002 : - energy of atom 2 EATOM= -432.3788 - kinetic energy error for atom= 0.0224 (will be added to EATOM!!) - - - POSCAR: name - positions in direct lattice - No initial velocities read in - WARNING: For meta-GGA calculations it is strongly recommended to include - aspherical contributions to the potential inside the PAW spheres (set - LASPH = .TRUE.) - - - METAGGA = SCAN LMAXTAU = 0 LMIXTAU = F - - exchange correlation table for LEXCH = 8 - RHO(1)= 0.500 N(1) = 2000 - RHO(2)= 100.500 N(2) = 4000 - - - --------------------------------------------------------------------------------------------------------- - - - ion position nearest neighbor table - 1 0.864 0.870 0.753- 76 1.91 68 1.98 34 2.04 77 2.06 35 2.08 87 2.09 89 2.14 14 3.28 - 6 3.35 32 3.36 7 3.42 26 3.44 5 3.55 3 3.74 20 3.76 30 3.78 - 2 0.887 0.406 0.263- 80 1.90 74 1.97 81 2.00 78 2.23 71 2.25 39 2.36 38 2.45 37 2.85 - 10 3.21 27 3.24 9 3.43 17 3.51 5 3.60 7 3.61 25 3.63 21 3.65 - 3 0.878 0.119 0.011- 76 2.03 82 2.04 64 2.08 95 2.15 42 2.27 38 2.32 81 2.47 4 3.09 - 20 3.33 25 3.34 32 3.42 18 3.61 10 3.66 31 3.69 1 3.74 - 4 0.889 0.906 0.221- 82 1.96 42 1.99 40 2.02 85 2.08 75 2.12 47 2.44 36 2.49 3 3.09 - 21 3.19 12 3.35 5 3.38 29 3.41 20 3.51 - 5 0.872 0.655 0.020- 57 2.04 93 2.06 77 2.08 78 2.10 85 2.16 36 2.18 39 2.30 21 3.22 - 17 3.30 4 3.38 24 3.43 30 3.50 27 3.51 1 3.55 2 3.60 14 3.73 - 6 0.874 0.110 0.540- 33 1.84 35 2.01 87 2.07 47 2.13 37 2.22 94 2.31 40 2.49 12 3.03 - 1 3.35 31 3.43 29 3.46 32 3.48 28 3.48 18 3.75 26 3.84 - 7 0.883 0.619 0.539- 43 1.95 89 1.97 34 2.00 71 2.06 41 2.25 90 2.61 75 2.82 80 2.87 - 54 2.89 9 3.07 26 3.23 1 3.42 14 3.47 31 3.53 2 3.61 30 3.64 - 8 0.355 0.399 0.251- 70 1.99 44 1.99 84 2.08 72 2.09 52 2.21 46 2.38 45 2.50 79 2.86 - 21 3.33 9 3.45 15 3.46 22 3.50 17 3.59 25 3.59 29 3.62 10 3.65 - 9 0.126 0.405 0.500- 44 1.95 54 2.00 60 2.03 74 2.25 43 2.27 71 2.28 45 2.53 7 3.07 - 2 3.43 8 3.45 15 3.54 10 3.54 19 3.56 16 3.59 21 3.72 14 3.74 - 10 0.127 0.164 0.258- 73 2.00 45 2.03 74 2.10 38 2.21 72 2.22 47 2.33 42 2.56 48 2.81 - 2 3.21 23 3.29 12 3.46 9 3.54 19 3.60 17 3.62 8 3.65 3 3.66 - 11 0.354 0.854 0.274- 86 1.76 69 2.05 49 2.10 48 2.16 73 2.23 51 2.25 50 2.51 12 3.13 - 27 3.33 15 3.36 24 3.44 23 3.48 22 3.60 20 3.61 21 3.61 10 3.68 - 12 0.109 0.907 0.464- 48 1.90 47 2.04 75 2.05 35 2.06 49 2.12 53 2.39 6 3.03 11 3.13 - 4 3.35 10 3.46 21 3.60 15 3.62 19 3.65 13 3.67 - 13 0.348 0.871 0.736- 53 1.89 67 2.01 61 2.04 58 2.12 56 2.25 92 2.27 55 2.68 20 3.29 - 19 3.36 14 3.45 30 3.49 18 3.54 15 3.57 24 3.58 12 3.67 22 3.77 - 14 0.133 0.650 0.763- 34 1.85 55 2.00 54 2.00 57 2.14 53 2.19 68 2.19 59 2.48 1 3.28 - 20 3.44 13 3.45 7 3.47 15 3.52 22 3.54 16 3.59 17 3.61 5 3.73 - 15 0.359 0.621 0.499- 79 1.91 49 2.06 44 2.18 56 2.22 66 2.25 54 2.32 53 2.69 11 3.36 - 28 3.40 8 3.46 14 3.52 9 3.54 13 3.57 12 3.62 27 3.71 21 3.71 - 16 0.376 0.360 0.751- 66 1.95 59 1.97 96 2.04 60 2.08 63 2.29 62 2.57 32 3.21 18 3.43 - 19 3.50 9 3.59 14 3.59 28 3.59 17 3.69 15 3.75 25 3.83 22 3.87 - 17 0.109 0.400 0.999- 39 1.89 65 1.94 57 1.98 38 2.17 59 2.23 62 2.43 70 2.44 72 2.51 - 18 3.26 5 3.30 2 3.51 21 3.56 8 3.59 14 3.61 10 3.62 16 3.69 - 18 0.135 0.170 0.782- 61 1.95 64 1.99 62 2.07 65 2.14 33 2.23 60 2.24 67 2.89 17 3.26 - 31 3.33 16 3.43 19 3.47 13 3.54 20 3.61 3 3.61 6 3.75 23 3.78 - 19 0.360 0.113 0.525- 63 2.00 61 2.02 83 2.03 48 2.07 45 2.09 58 2.37 60 2.51 84 2.91 - 13 3.36 18 3.47 29 3.48 16 3.50 9 3.56 26 3.60 10 3.60 12 3.65 - 20 0.145 0.890 0.988- 67 1.91 68 1.97 64 2.03 69 2.07 42 2.10 55 2.13 36 2.33 73 2.66 - 13 3.29 3 3.33 22 3.34 14 3.44 4 3.51 11 3.61 18 3.61 23 3.64 - 21 0.105 0.649 0.236- 36 1.79 39 2.06 71 2.24 70 2.27 49 2.33 69 2.33 75 2.33 44 2.64 - 4 3.19 5 3.22 8 3.33 17 3.56 12 3.60 11 3.61 22 3.63 2 3.65 - 22 0.381 0.628 0.008- 55 1.89 91 1.99 70 2.15 50 2.18 92 2.20 52 2.31 69 2.35 59 2.54 - 24 3.25 20 3.34 30 3.35 25 3.38 8 3.50 14 3.54 11 3.60 21 3.63 - 23 0.384 0.104 0.059- 73 2.01 88 2.05 46 2.06 72 2.07 62 2.14 51 2.14 67 2.49 24 3.01 - 10 3.29 11 3.48 29 3.57 20 3.64 8 3.65 18 3.78 32 3.84 17 3.87 - 24 0.567 0.852 0.012- 92 1.93 51 1.99 50 2.05 88 2.05 85 2.33 77 2.38 23 3.01 22 3.25 - 30 3.26 5 3.43 27 3.44 11 3.44 13 3.58 - 25 0.629 0.370 0.026- 81 1.92 52 2.07 91 2.15 95 2.19 96 2.21 46 2.55 78 2.62 3 3.34 - 22 3.38 32 3.51 31 3.53 8 3.59 2 3.63 30 3.67 27 3.80 16 3.83 - 26 0.642 0.858 0.501- 58 1.90 89 2.08 41 2.12 86 2.16 83 2.26 40 2.30 87 2.39 7 3.23 - 27 3.29 1 3.44 29 3.46 19 3.60 11 3.73 30 3.81 13 3.82 6 3.84 - 27 0.637 0.642 0.269- 41 1.80 50 1.91 78 2.08 79 2.09 86 2.18 80 2.34 52 2.51 85 2.52 - 2 3.24 26 3.29 11 3.33 24 3.44 5 3.51 28 3.70 7 3.71 15 3.71 - 28 0.621 0.374 0.500- 84 2.02 66 2.04 80 2.06 94 2.07 37 2.12 79 2.38 90 2.39 29 3.20 - 15 3.40 31 3.42 6 3.48 16 3.59 2 3.69 8 3.69 27 3.70 32 3.81 - 29 0.622 0.131 0.310- 83 1.82 37 1.97 46 2.20 82 2.20 84 2.21 40 2.34 51 2.78 28 3.20 - 4 3.41 26 3.46 6 3.46 19 3.48 23 3.57 8 3.62 25 3.86 - 30 0.624 0.631 0.787- 91 1.91 90 1.97 92 2.05 56 2.07 93 2.12 77 2.45 89 2.50 24 3.26 - 31 3.28 22 3.35 13 3.49 5 3.50 7 3.64 25 3.67 1 3.78 26 3.81 - 31 0.842 0.366 0.753- 43 1.96 65 2.00 90 2.06 94 2.13 95 2.14 93 2.26 33 2.39 30 3.28 - 18 3.33 28 3.42 6 3.43 32 3.49 7 3.53 25 3.53 3 3.69 17 3.76 - 32 0.631 0.136 0.782- 96 1.99 63 2.00 95 2.11 94 2.18 76 2.22 88 2.25 87 2.30 16 3.21 - 1 3.36 3 3.42 6 3.48 31 3.49 25 3.51 28 3.81 23 3.84 19 3.84 - 33 0.983 0.209 0.624- 6 1.84 18 2.23 31 2.39 - 34 0.972 0.706 0.680- 14 1.85 7 2.00 1 2.04 - 35 0.981 0.951 0.619- 6 2.01 12 2.06 1 2.08 - 36 0.039 0.739 0.095- 21 1.79 5 2.18 20 2.33 4 2.49 - 37 0.748 0.229 0.394- 29 1.97 28 2.12 6 2.22 2 2.85 - 38 0.006 0.262 0.098- 17 2.17 10 2.21 3 2.32 2 2.45 - 39 0.027 0.510 0.131- 17 1.89 21 2.06 5 2.30 2 2.36 - 40 0.785 0.964 0.384- 4 2.02 26 2.30 29 2.34 6 2.49 - 41 0.744 0.709 0.381- 27 1.80 26 2.12 7 2.25 - 42 0.029 0.990 0.136- 4 1.99 20 2.10 3 2.27 10 2.56 - 43 0.941 0.456 0.628- 7 1.95 31 1.96 9 2.27 - 44 0.249 0.489 0.399- 9 1.95 8 1.99 15 2.18 21 2.64 - 45 0.266 0.226 0.373- 10 2.03 19 2.09 8 2.50 9 2.53 - 46 0.497 0.223 0.151- 23 2.06 29 2.20 8 2.38 25 2.55 - 47 0.984 0.049 0.369- 12 2.04 6 2.13 10 2.33 4 2.44 - 48 0.266 0.980 0.429- 12 1.90 19 2.07 11 2.16 10 2.81 - 49 0.234 0.746 0.380- 15 2.06 11 2.10 12 2.12 21 2.33 - 50 0.518 0.712 0.133- 27 1.91 24 2.05 22 2.18 11 2.51 - 51 0.503 0.955 0.170- 24 1.99 23 2.14 11 2.25 29 2.78 - 52 0.509 0.491 0.153- 25 2.07 8 2.21 22 2.31 27 2.51 - 53 0.212 0.798 0.652- 13 1.89 14 2.19 12 2.39 15 2.69 - 54 0.168 0.563 0.590- 9 2.00 14 2.00 15 2.32 7 2.89 - 55 0.245 0.716 0.901- 22 1.89 14 2.00 20 2.13 13 2.68 - 56 0.480 0.699 0.651- 30 2.07 15 2.22 13 2.25 - 57 0.046 0.575 0.931- 17 1.98 5 2.04 14 2.14 - 58 0.493 0.924 0.608- 26 1.90 13 2.12 19 2.37 - 59 0.269 0.468 0.881- 16 1.97 17 2.23 14 2.48 22 2.54 - 60 0.224 0.297 0.646- 9 2.03 16 2.08 18 2.24 19 2.51 - 61 0.262 0.052 0.679- 18 1.95 19 2.02 13 2.04 - 62 0.271 0.222 0.915- 18 2.07 23 2.14 17 2.43 16 2.57 - 63 0.484 0.178 0.650- 19 2.00 32 2.00 16 2.29 - 64 0.063 0.067 0.921- 18 1.99 20 2.03 3 2.08 - 65 0.014 0.343 0.852- 17 1.94 31 2.00 18 2.14 - 66 0.451 0.440 0.603- 16 1.95 28 2.04 15 2.25 - 67 0.294 0.951 0.910- 20 1.91 13 2.01 23 2.49 18 2.89 - 68 0.041 0.837 0.841- 20 1.97 1 1.98 14 2.19 - 69 0.242 0.778 0.137- 11 2.05 20 2.07 21 2.33 22 2.35 - 70 0.259 0.517 0.117- 8 1.99 22 2.15 21 2.27 17 2.44 - 71 0.987 0.548 0.375- 7 2.06 21 2.24 2 2.25 9 2.28 - 72 0.269 0.262 0.148- 23 2.07 8 2.09 10 2.22 17 2.51 - 73 0.251 0.027 0.166- 10 2.00 23 2.01 11 2.23 20 2.66 - 74 0.001 0.289 0.383- 2 1.97 10 2.10 9 2.25 - 75 0.985 0.797 0.378- 12 2.05 4 2.12 21 2.33 7 2.82 - 76 0.816 0.018 0.861- 1 1.91 3 2.03 32 2.22 - 77 0.761 0.777 0.886- 1 2.06 5 2.08 24 2.38 30 2.45 - 78 0.760 0.541 0.129- 27 2.08 5 2.10 2 2.23 25 2.62 - 79 0.508 0.560 0.391- 15 1.91 27 2.09 28 2.38 8 2.86 - 80 0.744 0.459 0.380- 2 1.90 28 2.06 27 2.34 7 2.87 - 81 0.796 0.328 0.117- 25 1.92 2 2.00 3 2.47 - 82 0.767 0.058 0.157- 4 1.96 3 2.04 29 2.20 - 83 0.529 0.046 0.423- 29 1.82 19 2.03 26 2.26 - 84 0.487 0.302 0.386- 28 2.02 8 2.08 29 2.21 19 2.91 - 85 0.755 0.797 0.145- 4 2.08 5 2.16 24 2.33 27 2.52 - 86 0.505 0.802 0.360- 11 1.76 26 2.16 27 2.18 - 87 0.748 0.001 0.630- 6 2.07 1 2.09 32 2.30 26 2.39 - 88 0.518 0.026 0.919- 23 2.05 24 2.05 32 2.25 - 89 0.760 0.748 0.639- 7 1.97 26 2.08 1 2.14 30 2.50 - 90 0.708 0.504 0.659- 30 1.97 31 2.06 28 2.39 7 2.61 - 91 0.543 0.538 0.916- 30 1.91 22 1.99 25 2.15 - 92 0.482 0.755 0.887- 24 1.93 30 2.05 22 2.20 13 2.27 - 93 0.799 0.540 0.885- 5 2.06 30 2.12 31 2.26 - 94 0.717 0.259 0.646- 28 2.07 31 2.13 32 2.18 6 2.31 - 95 0.751 0.248 0.884- 32 2.11 31 2.14 3 2.15 25 2.19 - 96 0.517 0.276 0.881- 32 1.99 16 2.04 25 2.21 - - LATTYP: Found a simple monoclinic cell. - ALAT = 10.1297860000 - B/A-ratio = 1.0131648388 - C/A-ratio = 1.0379762742 - COS(beta) = -0.1645688048 - - Lattice vectors: - - A1 = ( 10.1297860000, 0.0000000000, 0.0000000000) - A2 = ( 0.0000000000, 10.2631430000, 0.0000000000) - A3 = ( -1.7303550000, 0.0000000000, 10.3711190000) - - -Analysis of symmetry for initial positions (statically): -===================================================================== - Subroutine PRICEL returns: - Original cell was already a primitive cell. - - - Routine SETGRP: Setting up the symmetry group for a - simple monoclinic supercell. - - - Subroutine GETGRP returns: Found 1 space group operations - (whereof 1 operations were pure point group operations) - out of a pool of 4 trial point group operations. - - -The static configuration has the point symmetry C_1 . - - -Analysis of symmetry for dynamics (positions and initial velocities): -===================================================================== - Subroutine PRICEL returns: - Original cell was already a primitive cell. - - - Routine SETGRP: Setting up the symmetry group for a - simple monoclinic supercell. - - - Subroutine GETGRP returns: Found 1 space group operations - (whereof 1 operations were pure point group operations) - out of a pool of 4 trial point group operations. - - -The dynamic configuration has the point symmetry C_1 . - - -Analysis of constrained symmetry for selective dynamics: -===================================================================== - Subroutine PRICEL returns: - Original cell was already a primitive cell. - - - Routine SETGRP: Setting up the symmetry group for a - simple monoclinic supercell. - - - Subroutine GETGRP returns: Found 1 space group operations - (whereof 1 operations were pure point group operations) - out of a pool of 4 trial point group operations. - - -The constrained configuration has the point symmetry C_1 . - - - Subroutine INISYM returns: Found 1 space group operations - (whereof 1 operations are pure point group operations), - and found 1 'primitive' translations - - ----------------------------------------------------------------------------------------- - - Primitive cell - - volume of cell : 1078.2172 - - direct lattice vectors reciprocal lattice vectors - 10.129786000 0.000000000 0.000000000 0.098718769 0.000000000 0.016470596 - 1.730355000 0.000000000-10.371119000 0.000000000 0.000000000 -0.096421611 - 0.000000000 10.263143000 0.000000000 0.000000000 0.097436039 0.000000000 - - length of vectors - 10.129786000 10.514477530 10.263143000 0.100083344 0.096421611 0.097436039 - - position of ions in fractional coordinates (direct lattice) - 0.863886590 0.870249460 0.753164810 - 0.887247170 0.405810630 0.263149520 - 0.877779700 0.118731220 0.011492980 - 0.889117110 0.906193740 0.221042320 - 0.871835780 0.654737310 0.020464330 - 0.874022500 0.110222620 0.540162250 - 0.883136670 0.618972220 0.539209830 - 0.354584820 0.399436190 0.251148730 - 0.125830810 0.404925910 0.500448810 - 0.127001550 0.164422130 0.258457300 - 0.354415510 0.854048540 0.274201060 - 0.109350960 0.907431470 0.464079870 - 0.348284690 0.871276320 0.736126800 - 0.132955470 0.649703910 0.763006880 - 0.358859250 0.621254450 0.499384500 - 0.376487490 0.360229980 0.750869800 - 0.108910110 0.399622120 0.999243930 - 0.134533870 0.169718740 0.782428760 - 0.359813480 0.113212790 0.525375540 - 0.145320230 0.889634940 0.987866080 - 0.104511960 0.648570360 0.235703800 - 0.381366340 0.627768940 0.008288790 - 0.383868610 0.103926800 0.058694010 - 0.566910020 0.851747380 0.012244320 - 0.629451780 0.370358510 0.026120260 - 0.642096040 0.857766160 0.500884470 - 0.637027340 0.641702250 0.269492790 - 0.620717720 0.373612100 0.499698590 - 0.621735680 0.131246130 0.310144440 - 0.624463990 0.631271610 0.787335180 - 0.842207330 0.365558520 0.752766360 - 0.630544780 0.136187260 0.781757430 - 0.982624600 0.208800280 0.624176140 - 0.972230940 0.705633180 0.679741860 - 0.980721730 0.950764630 0.619349830 - 0.039356770 0.738659640 0.095163620 - 0.748045360 0.229329480 0.393919660 - 0.005640630 0.262192590 0.097577130 - 0.027158920 0.510391260 0.131261570 - 0.785120140 0.963527390 0.384118800 - 0.744432360 0.709226940 0.381178200 - 0.029126350 0.989716960 0.135962890 - 0.941423220 0.455678280 0.628269290 - 0.249382580 0.488595930 0.398664800 - 0.266256850 0.226039560 0.373396050 - 0.496517660 0.223446630 0.150777810 - 0.984008080 0.048531290 0.368647700 - 0.265839500 0.980031310 0.428516860 - 0.234436140 0.746220150 0.380295870 - 0.518337260 0.711565920 0.132947760 - 0.502690170 0.954556030 0.169810900 - 0.508642420 0.491070120 0.153458710 - 0.212055800 0.798347310 0.651868560 - 0.167541570 0.562581000 0.589797050 - 0.244534270 0.715545730 0.900795730 - 0.480297820 0.698784020 0.650569170 - 0.045862780 0.575445610 0.931073150 - 0.493382700 0.924426090 0.607800030 - 0.268515390 0.467989090 0.881439850 - 0.224319650 0.297359590 0.645832660 - 0.261811200 0.051891330 0.678979410 - 0.270522180 0.222245300 0.914788240 - 0.484483090 0.178036300 0.650138570 - 0.062892350 0.066861960 0.920786660 - 0.014172260 0.342838360 0.851977650 - 0.450986280 0.439598300 0.602503300 - 0.293574980 0.951444170 0.910260550 - 0.040554290 0.837193340 0.841242850 - 0.241695520 0.778453820 0.137335950 - 0.259481630 0.516935540 0.117182430 - 0.986524560 0.547734530 0.375332780 - 0.269377360 0.261857670 0.147761190 - 0.251435370 0.026747510 0.166197600 - 0.001122760 0.289145120 0.382820890 - 0.984668560 0.797316720 0.378462450 - 0.815660790 0.018295010 0.860849740 - 0.761210720 0.777362640 0.886139720 - 0.759524330 0.541190900 0.128893170 - 0.508326300 0.560030760 0.390548050 - 0.743996870 0.459357380 0.380428390 - 0.795815140 0.328016870 0.117481010 - 0.766798470 0.057527920 0.157019550 - 0.528511440 0.045504340 0.422957630 - 0.487096250 0.302239500 0.386420340 - 0.754747140 0.796565820 0.144838170 - 0.504731730 0.801885210 0.359602750 - 0.747789060 0.001314150 0.629869920 - 0.517962040 0.025941640 0.918873020 - 0.759995870 0.748012700 0.639459000 - 0.708213900 0.504074230 0.658809390 - 0.543048910 0.537504280 0.916004830 - 0.482104640 0.755231190 0.886744210 - 0.799462080 0.539875480 0.884906720 - 0.717078630 0.258751270 0.646020680 - 0.751130000 0.247720080 0.883919400 - 0.516712220 0.275538000 0.880630080 - - ion indices of the primitive-cell ions - primitive index ion index - 1 1 - 2 2 - 3 3 - 4 4 - 5 5 - 6 6 - 7 7 - 8 8 - 9 9 - 10 10 - 11 11 - 12 12 - 13 13 - 14 14 - 15 15 - 16 16 - 17 17 - 18 18 - 19 19 - 20 20 - 21 21 - 22 22 - 23 23 - 24 24 - 25 25 - 26 26 - 27 27 - 28 28 - 29 29 - 30 30 - 31 31 - 32 32 - 33 33 - 34 34 - 35 35 - 36 36 - 37 37 - 38 38 - 39 39 - 40 40 - 41 41 - 42 42 - 43 43 - 44 44 - 45 45 - 46 46 - 47 47 - 48 48 - 49 49 - 50 50 - 51 51 - 52 52 - 53 53 - 54 54 - 55 55 - 56 56 - 57 57 - 58 58 - 59 59 - 60 60 - 61 61 - 62 62 - 63 63 - 64 64 - 65 65 - 66 66 - 67 67 - 68 68 - 69 69 - 70 70 - 71 71 - 72 72 - 73 73 - 74 74 - 75 75 - 76 76 - 77 77 - 78 78 - 79 79 - 80 80 - 81 81 - 82 82 - 83 83 - 84 84 - 85 85 - 86 86 - 87 87 - 88 88 - 89 89 - 90 90 - 91 91 - 92 92 - 93 93 - 94 94 - 95 95 - 96 96 - ----------------------------------------------------------------------------------------- - - - - KPOINTS: Auto k-point - -Automatic generation of k-mesh. - Grid dimensions read from file: - generate k-points for: 2 2 2 - - Generating k-lattice: - - Cartesian coordinates Fractional coordinates (reciprocal lattice) - 0.049359384 0.000000000 0.008235298 0.500000000 0.000000000 0.000000000 - 0.000000000 0.000000000 -0.048210805 0.000000000 0.500000000 0.000000000 - 0.000000000 0.048718019 0.000000000 0.000000000 0.000000000 0.500000000 - - Length of vectors - 0.050041672 0.048210805 0.048718019 - - Shift w.r.t. Gamma in fractional coordinates (k-lattice) - 0.500000000 0.500000000 0.500000000 - - - Subroutine IBZKPT returns following result: - =========================================== - - Found 4 irreducible k-points: - - Following reciprocal coordinates: - Coordinates Weight - 0.250000 0.250000 0.250000 2.000000 - -0.250000 -0.250000 0.250000 2.000000 - -0.250000 0.250000 0.250000 2.000000 - 0.250000 -0.250000 0.250000 2.000000 - - Following cartesian coordinates: - Coordinates Weight - 0.024680 0.024359 -0.019988 2.000000 - -0.024680 0.024359 0.019988 2.000000 - -0.024680 0.024359 -0.028223 2.000000 - 0.024680 0.024359 0.028223 2.000000 - - - --------------------------------------------------------------------------------------------------------- - - - - - Dimension of arrays: - k-points NKPTS = 4 k-points in BZ NKDIM = 4 number of bands NBANDS= 308 - number of dos NEDOS = 301 number of ions NIONS = 96 - non local maximal LDIM = 6 non local SUM 2l+1 LMDIM = 18 - total plane-waves NPLWV = 512000 - max r-space proj IRMAX = 9139 max aug-charges IRDMAX= 255251 - dimension x,y,z NGX = 80 NGY = 80 NGZ = 80 - dimension x,y,z NGXF= 160 NGYF= 160 NGZF= 160 - support grid NGXF= 320 NGYF= 320 NGZF= 320 - ions per type = 32 64 - NGX,Y,Z is equivalent to a cutoff of 13.13, 12.65, 12.96 a.u. - NGXF,Y,Z is equivalent to a cutoff of 26.26, 25.30, 25.92 a.u. - - SYSTEM = HfO2_p21c - POSCAR = name - - Startparameter for this run: - NWRITE = 2 write-flag & timer - PREC = accura normal or accurate (medium, high low for compatibility) - ISTART = 0 job : 0-new 1-cont 2-samecut - ICHARG = 2 charge: 1-file 2-atom 10-const - ISPIN = 1 spin polarized calculation? - LNONCOLLINEAR = F non collinear calculations - LSORBIT = F spin-orbit coupling - INIWAV = 1 electr: 0-lowe 1-rand 2-diag - LASPH = F aspherical Exc in radial PAW - Electronic Relaxation 1 - ENCUT = 500.0 eV 36.75 Ry 6.06 a.u. 18.47 19.17 18.71*2*pi/ulx,y,z - ENINI = 500.0 initial cutoff - ENAUG = 605.4 eV augmentation charge cutoff - NELM = 100; NELMIN= 2; NELMDL= -5 # of ELM steps - EDIFF = 0.1E-03 stopping-criterion for ELM - LREAL = T real-space projection - NLSPLINE = F spline interpolate recip. space projectors - LCOMPAT= F compatible to vasp.4.4 - GGA_COMPAT = T GGA compatible to vasp.4.4-vasp.4.6 - LMAXPAW = -100 max onsite density - LMAXMIX = 2 max onsite mixed and CHGCAR - VOSKOWN= 0 Vosko Wilk Nusair interpolation - ROPT = -0.00025 -0.00025 - Ionic relaxation - EDIFFG = -.2E-02 stopping-criterion for IOM - NSW = 0 number of steps for IOM - NBLOCK = 1; KBLOCK = 1 inner block; outer block - IBRION = -1 ionic relax: 0-MD 1-quasi-New 2-CG - NFREE = 1 steps in history (QN), initial steepest desc. (CG) - ISIF = 3 stress and relaxation - IWAVPR = 10 prediction: 0-non 1-charg 2-wave 3-comb - ISYM = 1 0-nonsym 1-usesym 2-fastsym - LCORR = T Harris-Foulkes like correction to forces - - POTIM = 0.5000 time-step for ionic-motion - TEIN = 0.0 initial temperature - TEBEG = 0.0; TEEND = 0.0 temperature during run - SMASS = -3.00 Nose mass-parameter (am) - estimated Nose-frequenzy (Omega) = 0.10E-29 period in steps = 0.13E+47 mass= -0.234E-26a.u. - SCALEE = 1.0000 scale energy and forces - NPACO = 256; APACO = 10.0 distance and # of slots for P.C. - PSTRESS= 0.0 pullay stress - - Mass of Ions in am - POMASS = 178.49 16.00 - Ionic Valenz - ZVAL = 4.00 6.00 - Atomic Wigner-Seitz radii - RWIGS = -1.00 -1.00 - virtual crystal weights - VCA = 1.00 1.00 - NELECT = 512.0000 total number of electrons - NUPDOWN= -1.0000 fix difference up-down - - DOS related values: - EMIN = 10.00; EMAX =-10.00 energy-range for DOS - EFERMI = 0.00 - ISMEAR = 0; SIGMA = 0.05 broadening in eV -4-tet -1-fermi 0-gaus - - Electronic relaxation 2 (details) - IALGO = 68 algorithm - LDIAG = T sub-space diagonalisation (order eigenvalues) - LSUBROT= F optimize rotation matrix (better conditioning) - TURBO = 0 0=normal 1=particle mesh - IRESTART = 0 0=no restart 2=restart with 2 vectors - NREBOOT = 0 no. of reboots - NMIN = 0 reboot dimension - EREF = 0.00 reference energy to select bands - IMIX = 4 mixing-type and parameters - AMIX = 0.40; BMIX = 1.00 - AMIX_MAG = 1.60; BMIX_MAG = 1.00 - AMIN = 0.10 - WC = 100.; INIMIX= 1; MIXPRE= 1; MAXMIX= -45 - - Intra band minimization: - WEIMIN = 0.0000 energy-eigenvalue tresh-hold - EBREAK = 0.81E-07 absolut break condition - DEPER = 0.30 relativ break condition - - TIME = 0.40 timestep for ELM - - volume/ion in A,a.u. = 11.23 75.79 - Fermi-wavevector in a.u.,A,eV,Ry = 1.277211 2.413579 22.194756 1.631269 - Thomas-Fermi vector in A = 2.409824 - - Write flags - LWAVE = F write WAVECAR - LDOWNSAMPLE = F k-point downsampling of WAVECAR - LCHARG = F write CHGCAR - LVTOT = F write LOCPOT, total local potential - LVHAR = F write LOCPOT, Hartree potential only - LELF = F write electronic localiz. function (ELF) - LORBIT = 0 0 simple, 1 ext, 2 COOP (PROOUT), +10 PAW based schemes - - - Dipole corrections - LMONO = F monopole corrections only (constant potential shift) - LDIPOL = F correct potential (dipole corrections) - IDIPOL = 0 1-x, 2-y, 3-z, 4-all directions - EPSILON= 1.0000000 bulk dielectric constant - - Exchange correlation treatment: - GGA = -- GGA type - LEXCH = 8 internal setting for exchange type - LIBXC = F Libxc - VOSKOWN = 0 Vosko Wilk Nusair interpolation - LHFCALC = F Hartree Fock is set to - LHFONE = F Hartree Fock one center treatment - AEXX = 0.0000 exact exchange contribution - - Linear response parameters - LEPSILON= F determine dielectric tensor - LRPA = F only Hartree local field effects (RPA) - LNABLA = F use nabla operator in PAW spheres - LVEL = F velocity operator in full k-point grid - CSHIFT =0.1000 complex shift for real part using Kramers Kronig - OMEGAMAX= -1.0 maximum frequency - DEG_THRESHOLD= 0.2000000E-02 threshold for treating states as degnerate - RTIME = -0.100 relaxation time in fs - (WPLASMAI= 0.000 imaginary part of plasma frequency in eV, 0.658/RTIME) - DFIELD = 0.0000000 0.0000000 0.0000000 field for delta impulse in time - - Optional k-point grid parameters - LKPOINTS_OPT = F use optional k-point grid - KPOINTS_OPT_MODE= 1 mode for optional k-point grid - - Orbital magnetization related: - ORBITALMAG= F switch on orbital magnetization - LCHIMAG = F perturbation theory with respect to B field - DQ = 0.001000 dq finite difference perturbation B field - LLRAUG = F two centre corrections for induced B field - - - --------------------------------------------------------------------------------------------------------- - - - Static calculation - charge density and potential will be updated during run - non-spin polarized calculation - RMM-DIIS sequential band-by-band and - variant of blocked Davidson during initial phase - perform sub-space diagonalisation - before iterative eigenvector-optimisation - modified Broyden-mixing scheme, WC = 100.0 - initial mixing is a Kerker type mixing with AMIX = 0.4000 and BMIX = 1.0000 - Hartree-type preconditioning will be used - using additional bands 52 - real space projection scheme for non local part - use partial core corrections - calculate Harris-corrections to forces - (improved forces if not selfconsistent) - use gradient corrections - use of overlap-Matrix (Vanderbilt PP) - Gauss-broadening in eV SIGMA = 0.05 - - --------------------------------------------------------------------------------------------------------- - - - energy-cutoff : 500.00 - volume of cell : 1078.22 - direct lattice vectors reciprocal lattice vectors - 10.129786000 0.000000000 0.000000000 0.098718769 0.000000000 0.016470596 - 1.730355000 0.000000000-10.371119000 0.000000000 0.000000000 -0.096421611 - 0.000000000 10.263143000 0.000000000 0.000000000 0.097436039 0.000000000 - - length of vectors - 10.129786000 10.514477530 10.263143000 0.100083344 0.096421611 0.097436039 - - - - k-points in units of 2pi/SCALE and weight: Auto k-point - 0.02467969 0.02435901 -0.01998775 0.250 - -0.02467969 0.02435901 0.01998775 0.250 - -0.02467969 0.02435901 -0.02822305 0.250 - 0.02467969 0.02435901 0.02822305 0.250 - - k-points in reciprocal lattice and weights: Auto k-point - 0.25000000 0.25000000 0.25000000 0.250 - -0.25000000 -0.25000000 0.25000000 0.250 - -0.25000000 0.25000000 0.25000000 0.250 - 0.25000000 -0.25000000 0.25000000 0.250 - - position of ions in fractional coordinates (direct lattice) - 0.86388659 0.87024946 0.75316481 - 0.88724717 0.40581063 0.26314952 - 0.87777970 0.11873122 0.01149298 - 0.88911711 0.90619374 0.22104232 - 0.87183578 0.65473731 0.02046433 - 0.87402250 0.11022262 0.54016225 - 0.88313667 0.61897222 0.53920983 - 0.35458482 0.39943619 0.25114873 - 0.12583081 0.40492591 0.50044881 - 0.12700155 0.16442213 0.25845730 - 0.35441551 0.85404854 0.27420106 - 0.10935096 0.90743147 0.46407987 - 0.34828469 0.87127632 0.73612680 - 0.13295547 0.64970391 0.76300688 - 0.35885925 0.62125445 0.49938450 - 0.37648749 0.36022998 0.75086980 - 0.10891011 0.39962212 0.99924393 - 0.13453387 0.16971874 0.78242876 - 0.35981348 0.11321279 0.52537554 - 0.14532023 0.88963494 0.98786608 - 0.10451196 0.64857036 0.23570380 - 0.38136634 0.62776894 0.00828879 - 0.38386861 0.10392680 0.05869401 - 0.56691002 0.85174738 0.01224432 - 0.62945178 0.37035851 0.02612026 - 0.64209604 0.85776616 0.50088447 - 0.63702734 0.64170225 0.26949279 - 0.62071772 0.37361210 0.49969859 - 0.62173568 0.13124613 0.31014444 - 0.62446399 0.63127161 0.78733518 - 0.84220733 0.36555852 0.75276636 - 0.63054478 0.13618726 0.78175743 - 0.98262460 0.20880028 0.62417614 - 0.97223094 0.70563318 0.67974186 - 0.98072173 0.95076463 0.61934983 - 0.03935677 0.73865964 0.09516362 - 0.74804536 0.22932948 0.39391966 - 0.00564063 0.26219259 0.09757713 - 0.02715892 0.51039126 0.13126157 - 0.78512014 0.96352739 0.38411880 - 0.74443236 0.70922694 0.38117820 - 0.02912635 0.98971696 0.13596289 - 0.94142322 0.45567828 0.62826929 - 0.24938258 0.48859593 0.39866480 - 0.26625685 0.22603956 0.37339605 - 0.49651766 0.22344663 0.15077781 - 0.98400808 0.04853129 0.36864770 - 0.26583950 0.98003131 0.42851686 - 0.23443614 0.74622015 0.38029587 - 0.51833726 0.71156592 0.13294776 - 0.50269017 0.95455603 0.16981090 - 0.50864242 0.49107012 0.15345871 - 0.21205580 0.79834731 0.65186856 - 0.16754157 0.56258100 0.58979705 - 0.24453427 0.71554573 0.90079573 - 0.48029782 0.69878402 0.65056917 - 0.04586278 0.57544561 0.93107315 - 0.49338270 0.92442609 0.60780003 - 0.26851539 0.46798909 0.88143985 - 0.22431965 0.29735959 0.64583266 - 0.26181120 0.05189133 0.67897941 - 0.27052218 0.22224530 0.91478824 - 0.48448309 0.17803630 0.65013857 - 0.06289235 0.06686196 0.92078666 - 0.01417226 0.34283836 0.85197765 - 0.45098628 0.43959830 0.60250330 - 0.29357498 0.95144417 0.91026055 - 0.04055429 0.83719334 0.84124285 - 0.24169552 0.77845382 0.13733595 - 0.25948163 0.51693554 0.11718243 - 0.98652456 0.54773453 0.37533278 - 0.26937736 0.26185767 0.14776119 - 0.25143537 0.02674751 0.16619760 - 0.00112276 0.28914512 0.38282089 - 0.98466856 0.79731672 0.37846245 - 0.81566079 0.01829501 0.86084974 - 0.76121072 0.77736264 0.88613972 - 0.75952433 0.54119090 0.12889317 - 0.50832630 0.56003076 0.39054805 - 0.74399687 0.45935738 0.38042839 - 0.79581514 0.32801687 0.11748101 - 0.76679847 0.05752792 0.15701955 - 0.52851144 0.04550434 0.42295763 - 0.48709625 0.30223950 0.38642034 - 0.75474714 0.79656582 0.14483817 - 0.50473173 0.80188521 0.35960275 - 0.74778906 0.00131415 0.62986992 - 0.51796204 0.02594164 0.91887302 - 0.75999587 0.74801270 0.63945900 - 0.70821390 0.50407423 0.65880939 - 0.54304891 0.53750428 0.91600483 - 0.48210464 0.75523119 0.88674421 - 0.79946208 0.53987548 0.88490672 - 0.71707863 0.25875127 0.64602068 - 0.75113000 0.24772008 0.88391940 - 0.51671222 0.27553800 0.88063008 - - position of ions in cartesian coordinates (Angst): - 10.25682679 7.72983815 -9.02546071 - 9.68982041 2.70074115 -4.20871034 - 9.09716768 0.11795410 -1.23137561 - 10.57460292 2.26858894 -9.39824311 - 9.96443786 0.21002835 -6.79035856 - 9.04438515 5.54376241 -1.14313191 - 10.01702715 5.53398759 -6.41943455 - 4.28303475 2.57757533 -4.14260026 - 1.97530475 5.13617770 -4.19953480 - 1.57100718 2.65258423 -1.70524148 - 5.06796043 2.81416469 -8.85743904 - 2.67788040 4.76291807 -9.41107976 - 5.03566671 7.55497461 -9.03611040 - 2.47102887 7.83084872 -6.73815657 - 4.71015815 5.12525454 -6.44310383 - 4.43706345 7.70628413 -3.73598799 - 1.79472424 10.25538335 -4.14452856 - 1.65647298 8.03017825 -1.76017325 - 3.84073187 5.39200430 -1.17414332 - 3.01144710 10.13861084 -9.22650983 - 2.18094075 2.41906181 -6.72640038 - 4.94942254 0.08506904 -6.51066638 - 4.06833713 0.60238502 -1.07783721 - 7.21650252 0.12566521 -8.83357344 - 7.01706353 0.26807596 -3.84103218 - 7.98853544 5.14064894 -8.89599492 - 7.56332333 2.76584304 -6.65517040 - 6.93421924 5.12847809 -3.87477555 - 6.52515178 3.18305674 -1.36116923 - 7.41801057 8.08053354 -6.54699299 - 9.16392603 7.72574880 -3.79125091 - 6.62293599 8.02328830 -1.41241428 - 10.31507552 6.40600898 -2.16549255 - 11.06948727 6.97628791 -7.31820568 - 11.57966158 6.35647587 -9.86049312 - 1.67681906 0.97667784 -7.66072703 - 7.97436083 4.04285380 -2.37840333 - 0.51082463 1.00144804 -2.71923055 - 1.15827212 1.34715626 -5.29332849 - 9.62034344 3.94226617 -9.99285722 - 8.76815488 3.91208638 -7.35547699 - 2.00760538 1.39540658-10.26447237 - 10.32490094 6.44801757 -4.72589367 - 3.37163658 4.09155385 -5.06728653 - 3.08825359 3.83221706 -2.34428318 - 5.41625963 1.54745423 -2.31739159 - 10.05176763 3.78348406 -0.50332378 - 4.38869932 4.39792981-10.16402134 - 3.66601370 3.90303090 -7.73913798 - 6.48190717 1.36446187 -7.37973483 - 6.74386465 1.74279355 -9.89981418 - 6.00216450 1.57496869 -5.09294665 - 3.52950413 6.69022025 -8.27975496 - 2.67062510 6.05317147 -5.83459450 - 3.71522796 9.24499539 -7.42100992 - 6.07445856 6.67688442 -7.24717223 - 1.46030534 9.55573688 -5.96801490 - 6.59744647 6.23793862 -9.58733299 - 3.52979070 9.04634323 -4.85357054 - 2.78684770 6.62827294 -3.08395169 - 2.74188185 6.96846278 -0.53817116 - 3.12489506 9.38860252 -2.30493245 - 5.21577602 6.67246511 -1.84643565 - 0.75278097 9.45016516 -0.69343334 - 0.73679403 8.74396845 -3.55561743 - 5.32905562 6.18357753 -4.55912628 - 4.62018790 9.34213419 -9.86754071 - 1.85944796 8.63379567 -8.68263176 - 3.79532535 1.40949849 -8.07343720 - 3.52297538 1.20266004 -5.36120000 - 10.94105786 3.85209399 -5.68061999 - 3.18184174 1.51649422 -2.71575706 - 2.59326918 1.70570974 -0.27740161 - 0.51169702 3.92894554 -2.99875845 - 11.35412277 3.88421424 -8.26906658 - 8.29412611 8.83502398 -0.18973973 - 9.05601503 9.09457866 -8.06212045 - 8.63027130 1.32284904 -5.61275523 - 6.11828866 4.00825049 -5.80814566 - 8.33138042 3.90439097 -4.76405005 - 8.62902269 1.20572441 -3.40190199 - 7.86704813 1.61151410 -0.59662890 - 5.43244645 4.34087464 -0.47193093 - 5.45716240 3.96588721 -3.13456182 - 9.02376866 1.48649485 -8.26127891 - 6.50037049 3.69065445 -8.31644694 - 7.57721710 6.46444506 -0.01362921 - 5.29173287 9.43052520 -0.26904384 - 8.99292304 6.56285916 -7.75772873 - 8.04628261 6.76145498 -5.22781382 - 6.43104246 9.40108856 -5.57452085 - 6.19043490 9.10078263 -7.83259254 - 9.03255602 9.08192421 -5.59911285 - 7.71158462 6.63020262 -2.68354021 - 8.03742984 9.07179120 -2.56913443 - 5.71096277 9.03803244 -2.85763739 - - - --------------------------------------------------------------------------------------------------------- - - - k-point 1 : 0.2500 0.2500 0.2500 plane waves: 27363 - k-point 2 : -0.2500-0.2500 0.2500 plane waves: 27363 - k-point 3 : -0.2500 0.2500 0.2500 plane waves: 27374 - k-point 4 : 0.2500-0.2500 0.2500 plane waves: 27374 - - maximum and minimum number of plane-waves per node : 6889 6813 - - maximum number of plane-waves: 27374 - maximum index in each direction: - IXMAX= 18 IYMAX= 19 IZMAX= 18 - IXMIN= -18 IYMIN= -19 IZMIN= -18 - - - real space projection operators: - total allocation : 49876.00 KBytes - max/ min on nodes : 12473.34 12463.27 - - - parallel 3D FFT for wavefunctions: - minimum data exchange during FFTs selected (reduces bandwidth) - parallel 3D FFT for charge: - minimum data exchange during FFTs selected (reduces bandwidth) - - - total amount of memory used by VASP MPI-rank0 162781. kBytes -======================================================================= - - base : 30000. kBytes - nonlr-proj: 30230. kBytes - fftplans : 41293. kBytes - grid : 25778. kBytes - one-center: 373. kBytes - wavefun : 35107. kBytes - - INWAV: cpu time 0.0000: real time 0.0002 - Broyden mixing: mesh for mixing (old mesh) - NGX = 37 NGY = 39 NGZ = 37 - (NGX =160 NGY =160 NGZ =160) - gives a total of 53391 points - - initial charge density was supplied: - charge density of overlapping atoms calculated - number of electron 512.0000000 magnetization - keeping initial charge density in first step - - --------------------------------------------------------------------------------------------------------- - - - Maximum index for non-local projection operator 2220 - Maximum index for augmentation-charges 15778 (set IRDMAX) - - --------------------------------------------------------------------------------------------------------- - - - First call to EWALD: gamma= 0.173 - Maximum number of real-space cells 3x 3x 3 - Maximum number of reciprocal cells 3x 3x 3 - - FEWALD: cpu time 0.0053: real time 0.0053 - - ---------------------------------------- Iteration 1( 1) --------------------------------------- - - - POTLOK: cpu time 0.4241: real time 0.4266 - SETDIJ: cpu time 0.3765: real time 0.3789 - EDDAV: cpu time 15.8292: real time 15.9693 - DOS: cpu time 0.0014: real time 0.0014 - -------------------------------------------- - LOOP: cpu time 16.6312: real time 16.7763 - - eigenvalue-minimisations : 2464 - total energy-change (2. order) : 0.1369016E+04 (-0.2723344E+05) - number of electron 512.0000000 magnetization - augmentation part 512.0000000 magnetization - - Free energy of the ion-electron system (eV) - --------------------------------------------------- - alpha Z PSCENC = 1957.98898647 - Ewald energy TEWEN = -24596.82224917 - -Hartree energ DENC = -7629.84757714 - -exchange EXHF = 0.00000000 - -V(xc)+E(xc) XCENC = 592.84660713 - PAW double counting = 25569.98736858 -25757.03612884 - entropy T*S EENTRO = -0.03409210 - eigenvalues EBANDS = 1132.31022915 - atomic energy EATOM = 30099.62314931 - Solvation Ediel_sol = 0.00000000 - --------------------------------------------------- - free energy TOTEN = 1369.01629340 eV - - energy without entropy = 1369.05038550 energy(sigma->0) = 1369.03333945 - - --------------------------------------------------------------------------------------------------------- - - - - ---------------------------------------- Iteration 1( 2) --------------------------------------- - - - EDDAV: cpu time 19.1868: real time 19.5887 - DOS: cpu time 0.0021: real time 0.0021 - -------------------------------------------- - LOOP: cpu time 19.1889: real time 19.5908 - - eigenvalue-minimisations : 3048 - total energy-change (2. order) :-0.4103089E+04 (-0.3985645E+04) - number of electron 512.0000000 magnetization - augmentation part 512.0000000 magnetization - - Free energy of the ion-electron system (eV) - --------------------------------------------------- - alpha Z PSCENC = 1957.98898647 - Ewald energy TEWEN = -24596.82224917 - -Hartree energ DENC = -7629.84757714 - -exchange EXHF = 0.00000000 - -V(xc)+E(xc) XCENC = 592.84660713 - PAW double counting = 25569.98736858 -25757.03612884 - entropy T*S EENTRO = -0.00000000 - eigenvalues EBANDS = -2970.81334564 - atomic energy EATOM = 30099.62314931 - Solvation Ediel_sol = 0.00000000 - --------------------------------------------------- - free energy TOTEN = -2734.07318929 eV - - energy without entropy = -2734.07318929 energy(sigma->0) = -2734.07318929 - - --------------------------------------------------------------------------------------------------------- - - - - ---------------------------------------- Iteration 1( 3) --------------------------------------- - - - EDDAV: cpu time 17.9710: real time 18.1405 - DOS: cpu time 0.0021: real time 0.0021 - -------------------------------------------- - LOOP: cpu time 17.9731: real time 18.1427 - - eigenvalue-minimisations : 2880 - total energy-change (2. order) :-0.2946291E+03 (-0.2927052E+03) - number of electron 512.0000000 magnetization - augmentation part 512.0000000 magnetization - - Free energy of the ion-electron system (eV) - --------------------------------------------------- - alpha Z PSCENC = 1957.98898647 - Ewald energy TEWEN = -24596.82224917 - -Hartree energ DENC = -7629.84757714 - -exchange EXHF = 0.00000000 - -V(xc)+E(xc) XCENC = 592.84660713 - PAW double counting = 25569.98736858 -25757.03612884 - entropy T*S EENTRO = -0.00000000 - eigenvalues EBANDS = -3265.44241028 - atomic energy EATOM = 30099.62314931 - Solvation Ediel_sol = 0.00000000 - --------------------------------------------------- - free energy TOTEN = -3028.70225393 eV - - energy without entropy = -3028.70225393 energy(sigma->0) = -3028.70225393 - - --------------------------------------------------------------------------------------------------------- - - - - ---------------------------------------- Iteration 1( 4) --------------------------------------- - - - EDDAV: cpu time 18.8961: real time 19.0951 - DOS: cpu time 0.0007: real time 0.0007 - -------------------------------------------- - LOOP: cpu time 18.8968: real time 19.0958 - - eigenvalue-minimisations : 2952 - total energy-change (2. order) :-0.6735371E+01 (-0.6709904E+01) - number of electron 512.0000000 magnetization - augmentation part 512.0000000 magnetization - - Free energy of the ion-electron system (eV) - --------------------------------------------------- - alpha Z PSCENC = 1957.98898647 - Ewald energy TEWEN = -24596.82224917 - -Hartree energ DENC = -7629.84757714 - -exchange EXHF = 0.00000000 - -V(xc)+E(xc) XCENC = 592.84660713 - PAW double counting = 25569.98736858 -25757.03612884 - entropy T*S EENTRO = -0.00000000 - eigenvalues EBANDS = -3272.17778176 - atomic energy EATOM = 30099.62314931 - Solvation Ediel_sol = 0.00000000 - --------------------------------------------------- - free energy TOTEN = -3035.43762541 eV - - energy without entropy = -3035.43762541 energy(sigma->0) = -3035.43762541 - - --------------------------------------------------------------------------------------------------------- - - - - ---------------------------------------- Iteration 1( 5) --------------------------------------- - - - EDDAV: cpu time 18.8615: real time 19.8589 - DOS: cpu time 0.0007: real time 0.0007 - CHARGE: cpu time 1.7750: real time 1.7950 - MIXING: cpu time 0.7968: real time 0.8105 - -------------------------------------------- - LOOP: cpu time 21.4339: real time 22.4651 - - eigenvalue-minimisations : 2880 - total energy-change (2. order) :-0.1728229E+00 (-0.1724674E+00) - number of electron 512.0000002 magnetization - augmentation part 53.6248728 magnetization - - Broyden mixing: - rms(total) = 0.15496E+02 rms(broyden)= 0.15496E+02 - rms(prec ) = 0.16783E+02 - weight for this iteration 100.00 - - Free energy of the ion-electron system (eV) - --------------------------------------------------- - alpha Z PSCENC = 1957.98898647 - Ewald energy TEWEN = -24596.82224917 - -Hartree energ DENC = -7629.84757714 - -exchange EXHF = 0.00000000 - -V(xc)+E(xc) XCENC = 592.84660713 - PAW double counting = 25569.98736858 -25757.03612884 - entropy T*S EENTRO = -0.00000000 - eigenvalues EBANDS = -3272.35060462 - atomic energy EATOM = 30099.62314931 - Solvation Ediel_sol = 0.00000000 - --------------------------------------------------- - free energy TOTEN = -3035.61044827 eV - - energy without entropy = -3035.61044827 energy(sigma->0) = -3035.61044827 - - --------------------------------------------------------------------------------------------------------- - - - - ---------------------------------------- Iteration 1( 6) --------------------------------------- - - - POTLOK: cpu time 0.4068: real time 0.4086 - SETDIJ: cpu time 1.1116: real time 1.1586 - EDDIAG: cpu time 3.6465: real time 3.6738 - RMM-DIIS: cpu time 21.0290: real time 21.2585 - ORTHCH: cpu time 0.1002: real time 0.1008 - DOS: cpu time 0.0033: real time 0.0033 - CHARGE: cpu time 1.6693: real time 1.6850 - MIXING: cpu time 0.0093: real time 0.0094 - -------------------------------------------- - LOOP: cpu time 27.9760: real time 28.2979 - - eigenvalue-minimisations : 2516 - total energy-change (2. order) : 0.3040951E+03 (-0.5470828E+02) - number of electron 512.0000002 magnetization - augmentation part 47.7833755 magnetization - - Broyden mixing: - rms(total) = 0.85054E+01 rms(broyden)= 0.85052E+01 - rms(prec ) = 0.86879E+01 - weight for this iteration 100.00 - - eigenvalues of (default mixing * dielectric matrix) - average eigenvalue GAMMA= 1.7388 - 1.7388 - - Free energy of the ion-electron system (eV) - --------------------------------------------------- - alpha Z PSCENC = 1957.98898647 - Ewald energy TEWEN = -24596.82224917 - -Hartree energ DENC = -8998.13818490 - -exchange EXHF = 0.00000000 - -V(xc)+E(xc) XCENC = 785.68052528 - PAW double counting = 36506.96046976 -36712.40456191 - entropy T*S EENTRO = -0.00000000 - eigenvalues EBANDS = -1774.40347083 - atomic energy EATOM = 30099.62314931 - Solvation Ediel_sol = 0.00000000 - --------------------------------------------------- - free energy TOTEN = -2731.51533599 eV - - energy without entropy = -2731.51533599 energy(sigma->0) = -2731.51533599 - - --------------------------------------------------------------------------------------------------------- - - - - ---------------------------------------- Iteration 1( 7) --------------------------------------- - - - POTLOK: cpu time 1.8653: real time 1.8984 - SETDIJ: cpu time 0.6305: real time 0.6328 - EDDIAG: cpu time 3.3967: real time 3.4255 - RMM-DIIS: cpu time 22.1372: real time 23.0633 - ORTHCH: cpu time 0.1125: real time 0.1130 - DOS: cpu time 0.0025: real time 0.0025 - CHARGE: cpu time 1.7809: real time 1.7962 - MIXING: cpu time 0.0068: real time 0.0069 - -------------------------------------------- - LOOP: cpu time 29.9324: real time 30.9385 - - eigenvalue-minimisations : 2816 - total energy-change (2. order) :-0.2489927E+02 (-0.2590078E+02) - number of electron 512.0000002 magnetization - augmentation part 44.2592727 magnetization - - Broyden mixing: - rms(total) = 0.27597E+01 rms(broyden)= 0.27587E+01 - rms(prec ) = 0.30909E+01 - weight for this iteration 100.00 - - eigenvalues of (default mixing * dielectric matrix) - average eigenvalue GAMMA= 1.6655 - 1.6655 1.6655 - - Free energy of the ion-electron system (eV) - --------------------------------------------------- - alpha Z PSCENC = 1957.98898647 - Ewald energy TEWEN = -24596.82224917 - -Hartree energ DENC = -9418.03492709 - -exchange EXHF = 0.00000000 - -V(xc)+E(xc) XCENC = 804.55143126 - PAW double counting = 50897.03275267 -51110.73153324 - entropy T*S EENTRO = -0.00000000 - eigenvalues EBANDS = -1390.02221382 - atomic energy EATOM = 30099.62314931 - Solvation Ediel_sol = 0.00000000 - --------------------------------------------------- - free energy TOTEN = -2756.41460362 eV - - energy without entropy = -2756.41460362 energy(sigma->0) = -2756.41460362 - - --------------------------------------------------------------------------------------------------------- - - - - ---------------------------------------- Iteration 1( 8) --------------------------------------- - - - POTLOK: cpu time 0.4812: real time 0.4840 - SETDIJ: cpu time 0.3498: real time 0.3519 - EDDIAG: cpu time 3.3339: real time 3.3635 - RMM-DIIS: cpu time 20.2383: real time 20.9023 - ORTHCH: cpu time 0.0957: real time 0.0963 - DOS: cpu time 0.0027: real time 0.0027 - CHARGE: cpu time 1.8197: real time 1.8358 - MIXING: cpu time 0.0071: real time 0.0071 - -------------------------------------------- - LOOP: cpu time 26.3283: real time 27.0436 - - eigenvalue-minimisations : 2655 - total energy-change (2. order) : 0.2409229E+01 (-0.1100597E+02) - number of electron 512.0000002 magnetization - augmentation part 47.1064216 magnetization - - Broyden mixing: - rms(total) = 0.14714E+01 rms(broyden)= 0.14709E+01 - rms(prec ) = 0.17198E+01 - weight for this iteration 100.00 - - eigenvalues of (default mixing * dielectric matrix) - average eigenvalue GAMMA= 1.4754 - 2.2161 1.1051 1.1051 - - Free energy of the ion-electron system (eV) - --------------------------------------------------- - alpha Z PSCENC = 1957.98898647 - Ewald energy TEWEN = -24596.82224917 - -Hartree energ DENC = -8867.71070686 - -exchange EXHF = 0.00000000 - -V(xc)+E(xc) XCENC = 754.70379180 - PAW double counting = 53988.14842013 -54198.85539334 - entropy T*S EENTRO = -0.00000000 - eigenvalues EBANDS = -1891.08137292 - atomic energy EATOM = 30099.62314931 - Solvation Ediel_sol = 0.00000000 - --------------------------------------------------- - free energy TOTEN = -2754.00537457 eV - - energy without entropy = -2754.00537457 energy(sigma->0) = -2754.00537457 - - --------------------------------------------------------------------------------------------------------- - - - - ---------------------------------------- Iteration 1( 9) --------------------------------------- - - - POTLOK: cpu time 0.4658: real time 0.4760 - SETDIJ: cpu time 0.9435: real time 0.9575 - EDDIAG: cpu time 3.4968: real time 3.5245 - RMM-DIIS: cpu time 21.8120: real time 22.6747 - ORTHCH: cpu time 0.0949: real time 0.0955 - DOS: cpu time 0.0027: real time 0.0027 - CHARGE: cpu time 1.6594: real time 1.6750 - MIXING: cpu time 0.0070: real time 0.0070 - -------------------------------------------- - LOOP: cpu time 28.4821: real time 29.4129 - - eigenvalue-minimisations : 2880 - total energy-change (2. order) : 0.3798683E+01 (-0.9577773E+00) - number of electron 512.0000002 magnetization - augmentation part 46.5680858 magnetization - - Broyden mixing: - rms(total) = 0.35142E+00 rms(broyden)= 0.35141E+00 - rms(prec ) = 0.42811E+00 - weight for this iteration 100.00 - - eigenvalues of (default mixing * dielectric matrix) - average eigenvalue GAMMA= 1.4899 - 2.3955 1.2736 1.2736 1.0168 - - Free energy of the ion-electron system (eV) - --------------------------------------------------- - alpha Z PSCENC = 1957.98898647 - Ewald energy TEWEN = -24596.82224917 - -Hartree energ DENC = -9090.79151510 - -exchange EXHF = 0.00000000 - -V(xc)+E(xc) XCENC = 790.67585054 - PAW double counting = 57615.02570266 -57829.79145409 - entropy T*S EENTRO = -0.00000000 - eigenvalues EBANDS = -1696.11516245 - atomic energy EATOM = 30099.62314931 - Solvation Ediel_sol = 0.00000000 - --------------------------------------------------- - free energy TOTEN = -2750.20669183 eV - - energy without entropy = -2750.20669183 energy(sigma->0) = -2750.20669183 - - --------------------------------------------------------------------------------------------------------- - - - - ---------------------------------------- Iteration 1( 10) --------------------------------------- - - - POTLOK: cpu time 0.4148: real time 0.4234 - SETDIJ: cpu time 0.3657: real time 0.3681 - EDDIAG: cpu time 3.2924: real time 3.3218 - RMM-DIIS: cpu time 21.3591: real time 21.5465 - ORTHCH: cpu time 0.0929: real time 0.0935 - DOS: cpu time 0.0024: real time 0.0024 - CHARGE: cpu time 1.6375: real time 1.6531 - MIXING: cpu time 0.0072: real time 0.0072 - -------------------------------------------- - LOOP: cpu time 27.1720: real time 27.4161 - - eigenvalue-minimisations : 2889 - total energy-change (2. order) :-0.4551328E+00 (-0.9742186E+00) - number of electron 512.0000002 magnetization - augmentation part 45.7701551 magnetization - - Broyden mixing: - rms(total) = 0.40616E+00 rms(broyden)= 0.40592E+00 - rms(prec ) = 0.49790E+00 - weight for this iteration 100.00 - - eigenvalues of (default mixing * dielectric matrix) - average eigenvalue GAMMA= 1.5009 - 2.5673 1.9019 1.0406 0.9975 0.9975 - - Free energy of the ion-electron system (eV) - --------------------------------------------------- - alpha Z PSCENC = 1957.98898647 - Ewald energy TEWEN = -24596.82224917 - -Hartree energ DENC = -9191.71972722 - -exchange EXHF = 0.00000000 - -V(xc)+E(xc) XCENC = 795.35124348 - PAW double counting = 58436.41726179 -58653.29523249 - entropy T*S EENTRO = -0.00000000 - eigenvalues EBANDS = -1598.20525682 - atomic energy EATOM = 30099.62314931 - Solvation Ediel_sol = 0.00000000 - --------------------------------------------------- - free energy TOTEN = -2750.66182466 eV - - energy without entropy = -2750.66182466 energy(sigma->0) = -2750.66182466 - - --------------------------------------------------------------------------------------------------------- - - - - ---------------------------------------- Iteration 1( 11) --------------------------------------- - - - POTLOK: cpu time 0.4081: real time 0.4103 - SETDIJ: cpu time 0.3640: real time 0.3664 - EDDIAG: cpu time 3.2851: real time 3.3142 - RMM-DIIS: cpu time 21.2610: real time 21.4479 - ORTHCH: cpu time 0.0905: real time 0.0910 - DOS: cpu time 0.0031: real time 0.0031 - CHARGE: cpu time 1.7030: real time 1.7190 - MIXING: cpu time 0.0070: real time 0.0071 - -------------------------------------------- - LOOP: cpu time 27.1219: real time 27.3590 - - eigenvalue-minimisations : 2874 - total energy-change (2. order) : 0.3391557E+00 (-0.1562258E+00) - number of electron 512.0000002 magnetization - augmentation part 46.0011353 magnetization - - Broyden mixing: - rms(total) = 0.13194E+00 rms(broyden)= 0.13193E+00 - rms(prec ) = 0.15026E+00 - weight for this iteration 100.00 - - eigenvalues of (default mixing * dielectric matrix) - average eigenvalue GAMMA= 1.5735 - 2.5964 2.5964 1.1944 1.0766 0.9886 0.9886 - - Free energy of the ion-electron system (eV) - --------------------------------------------------- - alpha Z PSCENC = 1957.98898647 - Ewald energy TEWEN = -24596.82224917 - -Hartree energ DENC = -9126.84814929 - -exchange EXHF = 0.00000000 - -V(xc)+E(xc) XCENC = 786.88120159 - PAW double counting = 58391.50383802 -58608.34144070 - entropy T*S EENTRO = -0.00000000 - eigenvalues EBANDS = -1654.30800522 - atomic energy EATOM = 30099.62314931 - Solvation Ediel_sol = 0.00000000 - --------------------------------------------------- - free energy TOTEN = -2750.32266900 eV - - energy without entropy = -2750.32266900 energy(sigma->0) = -2750.32266900 - - --------------------------------------------------------------------------------------------------------- - - - - ---------------------------------------- Iteration 1( 12) --------------------------------------- - - - POTLOK: cpu time 0.4114: real time 0.4136 - SETDIJ: cpu time 0.3658: real time 0.3683 - EDDIAG: cpu time 3.3039: real time 3.3334 - RMM-DIIS: cpu time 21.9467: real time 22.1397 - ORTHCH: cpu time 0.0886: real time 0.0892 - DOS: cpu time 0.0056: real time 0.0056 - CHARGE: cpu time 1.6815: real time 1.6977 - MIXING: cpu time 0.0078: real time 0.0079 - -------------------------------------------- - LOOP: cpu time 27.8113: real time 28.0553 - - eigenvalue-minimisations : 2997 - total energy-change (2. order) :-0.5290319E-02 (-0.4202061E-01) - number of electron 512.0000002 magnetization - augmentation part 46.0998154 magnetization - - Broyden mixing: - rms(total) = 0.55153E-01 rms(broyden)= 0.55102E-01 - rms(prec ) = 0.56813E-01 - weight for this iteration 100.00 - - eigenvalues of (default mixing * dielectric matrix) - average eigenvalue GAMMA= 1.7159 - 3.7029 2.4706 1.9170 0.9815 0.9815 1.0541 0.9035 - - Free energy of the ion-electron system (eV) - --------------------------------------------------- - alpha Z PSCENC = 1957.98898647 - Ewald energy TEWEN = -24596.82224917 - -Hartree energ DENC = -9113.77377491 - -exchange EXHF = 0.00000000 - -V(xc)+E(xc) XCENC = 787.23222601 - PAW double counting = 58253.32754115 -58470.24589414 - entropy T*S EENTRO = -0.00000000 - eigenvalues EBANDS = -1667.65794404 - atomic energy EATOM = 30099.62314931 - Solvation Ediel_sol = 0.00000000 - --------------------------------------------------- - free energy TOTEN = -2750.32795931 eV - - energy without entropy = -2750.32795931 energy(sigma->0) = -2750.32795931 - - --------------------------------------------------------------------------------------------------------- - - - - ---------------------------------------- Iteration 1( 13) --------------------------------------- - - - POTLOK: cpu time 0.4128: real time 0.4218 - SETDIJ: cpu time 0.3637: real time 0.3661 - EDDIAG: cpu time 3.2684: real time 3.2976 - RMM-DIIS: cpu time 23.2615: real time 23.4685 - ORTHCH: cpu time 0.0949: real time 0.0956 - DOS: cpu time 0.0026: real time 0.0026 - CHARGE: cpu time 1.6574: real time 1.6727 - MIXING: cpu time 0.0075: real time 0.0075 - -------------------------------------------- - LOOP: cpu time 29.0688: real time 29.3325 - - eigenvalue-minimisations : 3238 - total energy-change (2. order) :-0.6443907E-02 (-0.7530119E-02) - number of electron 512.0000002 magnetization - augmentation part 46.1000749 magnetization - - Broyden mixing: - rms(total) = 0.45728E-01 rms(broyden)= 0.45724E-01 - rms(prec ) = 0.47852E-01 - weight for this iteration 100.00 - - eigenvalues of (default mixing * dielectric matrix) - average eigenvalue GAMMA= 1.7029 - 3.9844 2.3709 2.2507 0.9729 0.9729 1.0995 0.9861 0.9861 - - Free energy of the ion-electron system (eV) - --------------------------------------------------- - alpha Z PSCENC = 1957.98898647 - Ewald energy TEWEN = -24596.82224917 - -Hartree energ DENC = -9115.55291607 - -exchange EXHF = 0.00000000 - -V(xc)+E(xc) XCENC = 787.94969578 - PAW double counting = 58394.18488959 -58611.08075824 - entropy T*S EENTRO = -0.00000000 - eigenvalues EBANDS = -1666.62520090 - atomic energy EATOM = 30099.62314931 - Solvation Ediel_sol = 0.00000000 - --------------------------------------------------- - free energy TOTEN = -2750.33440322 eV - - energy without entropy = -2750.33440322 energy(sigma->0) = -2750.33440322 - - --------------------------------------------------------------------------------------------------------- - - - - ---------------------------------------- Iteration 1( 14) --------------------------------------- - - - POTLOK: cpu time 0.4073: real time 0.4096 - SETDIJ: cpu time 0.3638: real time 0.3663 - EDDIAG: cpu time 3.4690: real time 3.5190 - RMM-DIIS: cpu time 22.5399: real time 22.7771 - ORTHCH: cpu time 0.0946: real time 0.0952 - DOS: cpu time 0.0028: real time 0.0028 - CHARGE: cpu time 1.6474: real time 1.6631 - MIXING: cpu time 0.0075: real time 0.0076 - -------------------------------------------- - LOOP: cpu time 28.5323: real time 28.8407 - - eigenvalue-minimisations : 3078 - total energy-change (2. order) :-0.2070072E-02 (-0.1702151E-02) - number of electron 512.0000002 magnetization - augmentation part 46.1155720 magnetization - - Broyden mixing: - rms(total) = 0.41988E-01 rms(broyden)= 0.41986E-01 - rms(prec ) = 0.48586E-01 - weight for this iteration 100.00 - - eigenvalues of (default mixing * dielectric matrix) - average eigenvalue GAMMA= 1.7841 - 4.9965 2.4918 2.3911 1.0057 1.0057 1.1675 1.1675 0.9155 0.9155 - - Free energy of the ion-electron system (eV) - --------------------------------------------------- - alpha Z PSCENC = 1957.98898647 - Ewald energy TEWEN = -24596.82224917 - -Hartree energ DENC = -9113.64067377 - -exchange EXHF = 0.00000000 - -V(xc)+E(xc) XCENC = 787.89086831 - PAW double counting = 58493.82096831 -58710.63896065 - entropy T*S EENTRO = -0.00000000 - eigenvalues EBANDS = -1668.55856210 - atomic energy EATOM = 30099.62314931 - Solvation Ediel_sol = 0.00000000 - --------------------------------------------------- - free energy TOTEN = -2750.33647329 eV - - energy without entropy = -2750.33647329 energy(sigma->0) = -2750.33647329 - - --------------------------------------------------------------------------------------------------------- - - - - ---------------------------------------- Iteration 1( 15) --------------------------------------- - - - POTLOK: cpu time 0.4120: real time 0.4141 - SETDIJ: cpu time 0.3613: real time 0.3637 - EDDIAG: cpu time 3.2603: real time 3.2891 - RMM-DIIS: cpu time 22.2289: real time 22.4600 - ORTHCH: cpu time 0.0924: real time 0.0930 - DOS: cpu time 0.0032: real time 0.0032 - CHARGE: cpu time 1.7019: real time 1.7180 - MIXING: cpu time 0.0078: real time 0.0079 - -------------------------------------------- - LOOP: cpu time 28.0679: real time 28.3489 - - eigenvalue-minimisations : 3012 - total energy-change (2. order) : 0.1342293E-02 (-0.4039142E-03) - number of electron 512.0000002 magnetization - augmentation part 46.1047755 magnetization - - Broyden mixing: - rms(total) = 0.20619E-01 rms(broyden)= 0.20619E-01 - rms(prec ) = 0.25884E-01 - weight for this iteration 100.00 - - eigenvalues of (default mixing * dielectric matrix) - average eigenvalue GAMMA= 1.6536 - 3.5674 2.7689 2.0937 2.0937 0.9884 0.9884 0.9546 1.0257 1.0274 1.0274 - - Free energy of the ion-electron system (eV) - --------------------------------------------------- - alpha Z PSCENC = 1957.98898647 - Ewald energy TEWEN = -24596.82224917 - -Hartree energ DENC = -9116.08096548 - -exchange EXHF = 0.00000000 - -V(xc)+E(xc) XCENC = 788.17497732 - PAW double counting = 58594.88511796 -58811.65461356 - entropy T*S EENTRO = -0.00000000 - eigenvalues EBANDS = -1666.44953385 - atomic energy EATOM = 30099.62314931 - Solvation Ediel_sol = 0.00000000 - --------------------------------------------------- - free energy TOTEN = -2750.33513100 eV - - energy without entropy = -2750.33513100 energy(sigma->0) = -2750.33513100 - - --------------------------------------------------------------------------------------------------------- - - - - ---------------------------------------- Iteration 1( 16) --------------------------------------- - - - POTLOK: cpu time 0.4126: real time 0.4224 - SETDIJ: cpu time 0.3674: real time 0.3699 - EDDIAG: cpu time 3.3106: real time 3.3401 - RMM-DIIS: cpu time 22.0267: real time 22.2399 - ORTHCH: cpu time 0.0917: real time 0.0923 - DOS: cpu time 0.0031: real time 0.0032 - CHARGE: cpu time 1.6766: real time 1.6937 - MIXING: cpu time 0.0079: real time 0.0079 - -------------------------------------------- - LOOP: cpu time 27.8966: real time 28.1694 - - eigenvalue-minimisations : 2989 - total energy-change (2. order) : 0.4430918E-03 (-0.4879831E-03) - number of electron 512.0000002 magnetization - augmentation part 46.0877418 magnetization - - Broyden mixing: - rms(total) = 0.12838E-01 rms(broyden)= 0.12834E-01 - rms(prec ) = 0.13185E-01 - weight for this iteration 100.00 - - eigenvalues of (default mixing * dielectric matrix) - average eigenvalue GAMMA= 1.4962 - 3.1504 2.7526 2.2235 1.9219 0.9897 0.9897 1.0757 0.9502 0.9984 0.9984 - 0.4081 - - Free energy of the ion-electron system (eV) - --------------------------------------------------- - alpha Z PSCENC = 1957.98898647 - Ewald energy TEWEN = -24596.82224917 - -Hartree energ DENC = -9118.48376448 - -exchange EXHF = 0.00000000 - -V(xc)+E(xc) XCENC = 788.28801458 - PAW double counting = 58573.88220565 -58790.68956650 - entropy T*S EENTRO = -0.00000000 - eigenvalues EBANDS = -1664.12146377 - atomic energy EATOM = 30099.62314931 - Solvation Ediel_sol = 0.00000000 - --------------------------------------------------- - free energy TOTEN = -2750.33468791 eV - - energy without entropy = -2750.33468791 energy(sigma->0) = -2750.33468791 - - --------------------------------------------------------------------------------------------------------- - - - - ---------------------------------------- Iteration 1( 17) --------------------------------------- - - - POTLOK: cpu time 0.4067: real time 0.4091 - SETDIJ: cpu time 0.3641: real time 0.3670 - EDDIAG: cpu time 3.5945: real time 3.6416 - RMM-DIIS: cpu time 20.2367: real time 20.4405 - ORTHCH: cpu time 0.0928: real time 0.0934 - DOS: cpu time 0.0027: real time 0.0027 - 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-.345E+02 0.462E+02 0.400E+02 0.255E+02 -.520E+02 -.392E+02 0.831E+01 0.556E+01 -.263E+01 0.441E-02 0.278E-02 -.561E-02 - 0.139E+02 0.110E+02 -.379E+02 -.962E+01 -.988E+01 0.414E+02 -.509E+01 -.238E+01 -.139E+01 0.449E-02 0.378E-02 -.196E-04 - 0.148E+02 0.313E+00 0.525E+01 -.174E+02 0.713E-01 -.278E+01 0.292E+01 -.525E+00 -.204E+01 -.178E-03 -.249E-02 0.190E-02 - -.739E+01 -.252E+02 0.442E+01 0.774E+01 0.239E+02 -.544E+01 0.108E+01 0.256E+01 0.549E+00 0.251E-02 0.779E-02 0.406E-02 - 0.115E+02 -.278E+02 0.183E+02 -.166E+02 0.386E+02 -.185E+02 0.486E+01 -.110E+02 -.130E+01 0.150E-02 0.669E-02 0.304E-02 - ----------------------------------------------------------------------------------------------- - 0.126E+01 -.323E+01 -.619E+02 -.355E-13 -.597E-12 -.149E-12 -.122E+01 0.326E+01 0.619E+02 -.396E-02 0.103E-01 -.471E-02 - - - POSITION TOTAL-FORCE (eV/Angst) - ----------------------------------------------------------------------------------- - 10.25683 7.72984 -9.02546 0.071344 -1.923090 0.620328 - 9.68982 2.70074 -4.20871 0.395911 -2.210425 -0.343474 - 9.09717 0.11795 -1.23138 1.715722 1.042319 -2.161289 - 10.57460 2.26859 -9.39824 -1.477098 3.454308 0.566415 - 9.96444 0.21003 -6.79036 -1.193355 -0.894456 2.199932 - 9.04439 5.54376 -1.14313 -3.514681 -2.851436 1.048731 - 10.01703 5.53399 -6.41943 -0.783776 -0.488496 -0.065946 - 4.28303 2.57758 -4.14260 2.653659 -2.067070 4.126965 - 1.97530 5.13618 -4.19953 -1.625959 0.319805 1.743295 - 1.57101 2.65258 -1.70524 -0.478894 -1.867706 -0.403045 - 5.06796 2.81416 -8.85744 -1.771832 -3.565913 -3.800677 - 2.67788 4.76292 -9.41108 -4.268559 3.140157 2.261395 - 5.03567 7.55497 -9.03611 2.713165 -0.038441 0.989679 - 2.47103 7.83085 -6.73816 0.258499 2.985319 0.401264 - 4.71016 5.12525 -6.44310 0.549046 2.691505 0.489616 - 4.43706 7.70628 -3.73599 -0.816424 1.670134 2.118021 - 1.79472 10.25538 -4.14453 4.172503 -0.483423 1.650521 - 1.65647 8.03018 -1.76017 0.364830 1.806759 -0.634313 - 3.84073 5.39200 -1.17414 2.048842 -0.081901 -0.567937 - 3.01145 10.13861 -9.22651 -1.080043 0.937320 0.437455 - 2.18094 2.41906 -6.72640 2.006101 2.322595 1.648867 - 4.94942 0.08507 -6.51067 -0.494725 2.776391 1.740706 - 4.06834 0.60239 -1.07784 -0.570590 -0.565284 -2.787001 - 7.21650 0.12567 -8.83357 4.967801 1.454466 -1.190387 - 7.01706 0.26808 -3.84103 -1.364023 1.556790 -1.484142 - 7.98854 5.14065 -8.89599 1.732740 -1.209855 -2.695615 - 7.56332 2.76584 -6.65517 -0.852574 -0.832946 4.199286 - 6.93422 5.12848 -3.87478 0.711439 -1.524054 -0.754486 - 6.52515 3.18306 -1.36117 1.600870 -3.076540 -0.876439 - 7.41801 8.08053 -6.54699 3.416039 -1.558670 -1.209773 - 9.16393 7.72575 -3.79125 0.048153 -0.218862 -1.759024 - 6.62294 8.02329 -1.41241 0.142083 -0.283775 1.186457 - 10.31508 6.40601 -2.16549 1.716655 3.455734 -1.057177 - 11.06949 6.97629 -7.31821 -0.457299 -1.988664 1.266692 - 11.57966 6.35648 -9.86049 2.365099 -2.078659 -0.689192 - 1.67682 0.97668 -7.66073 -4.553458 -0.477074 -2.751063 - 7.97436 4.04285 -2.37840 -0.637033 1.056752 0.821207 - 0.51082 1.00145 -2.71923 2.845090 2.124348 1.623678 - 1.15827 1.34716 -5.29333 -3.538805 5.095164 -0.111132 - 9.62034 3.94227 -9.99286 -3.516173 0.392659 -0.485412 - 8.76815 3.91209 -7.35548 2.683820 4.304817 -1.085279 - 2.00761 1.39541 -10.26447 -2.189875 -0.769130 -0.407237 - 10.32490 6.44802 -4.72589 2.739806 -2.352104 -0.331267 - 3.37164 4.09155 -5.06729 1.401336 -2.708478 -0.197978 - 3.08825 3.83222 -2.34428 -1.308203 2.306062 -0.557061 - 5.41626 1.54745 -2.31739 2.933649 -0.396144 0.063357 - 10.05177 3.78348 -0.50332 3.200582 0.728261 0.011823 - 4.38870 4.39793 -10.16402 1.268163 -1.519690 -0.120855 - 3.66601 3.90303 -7.73914 1.257931 0.156882 0.905175 - 6.48191 1.36446 -7.37973 -3.226088 -3.009059 -2.736868 - 6.74386 1.74279 -9.89981 -1.066594 -1.196411 -0.745385 - 6.00216 1.57497 -5.09295 -0.887702 -0.154023 2.828766 - 3.52950 6.69022 -8.27975 0.305115 -1.921822 0.822771 - 2.67063 6.05317 -5.83459 1.199300 0.997510 0.425288 - 3.71523 9.24500 -7.42101 1.427772 -0.772679 -0.721777 - 6.07446 6.67688 -7.24717 -1.637791 -1.064934 1.181558 - 1.46031 9.55574 -5.96801 -0.744889 -3.474453 -1.138557 - 6.59745 6.23794 -9.58733 -2.450856 2.062326 -0.626368 - 3.52979 9.04634 -4.85357 1.372308 -2.218484 -0.491526 - 2.78685 6.62827 -3.08395 0.497326 -0.407367 0.044870 - 2.74188 6.96846 -0.53817 -0.335227 -0.877439 0.942416 - 3.12490 9.38860 -2.30493 -1.545343 -2.431313 0.283751 - 5.21578 6.67247 -1.84644 -0.281439 0.991795 -1.050956 - 0.75278 9.45017 -0.69343 -1.550432 -1.450552 -2.030482 - 0.73679 8.74397 -3.55562 -0.410750 -1.104497 1.791207 - 5.32906 6.18358 -4.55913 -0.884852 0.738952 -1.607368 - 4.62019 9.34213 -9.86754 1.544035 0.272287 -0.334043 - 1.85945 8.63380 -8.68263 -0.675403 1.082557 0.223831 - 3.79533 1.40950 -8.07344 3.066723 1.022635 1.514315 - 3.52298 1.20266 -5.36120 -0.167698 1.258976 -1.755902 - 10.94106 3.85209 -5.68062 0.669989 0.093488 0.726057 - 3.18184 1.51649 -2.71576 -2.722124 0.677473 -2.382832 - 2.59327 1.70571 -0.27740 0.778298 0.488026 0.946604 - 0.51170 3.92895 -2.99876 1.608252 -0.309296 -0.893909 - 11.35412 3.88421 -8.26907 1.579624 -1.817241 1.349507 - 8.29413 8.83502 -0.18974 -0.811287 2.975792 -2.324214 - 9.05602 9.09458 -8.06212 -2.457373 1.408797 -0.014466 - 8.63027 1.32285 -5.61276 0.972585 0.900228 -2.662680 - 6.11829 4.00825 -5.80815 -1.506299 1.094397 0.151255 - 8.33138 3.90439 -4.76405 -0.314792 0.696789 -1.314971 - 8.62902 1.20572 -3.40190 -3.978192 -0.509404 2.939308 - 7.86705 1.61151 -0.59663 -0.056311 -1.853025 -1.231923 - 5.43245 4.34087 -0.47193 -1.421713 0.774914 0.860578 - 5.45716 3.96589 -3.13456 2.035457 0.641549 0.382759 - 9.02377 1.48649 -8.26128 0.345986 -1.209544 0.195194 - 6.50037 3.69065 -8.31645 2.809999 3.570924 1.568345 - 7.57722 6.46445 -0.01363 -2.707975 0.565701 -0.633300 - 5.29173 9.43053 -0.26904 1.912187 -0.834836 0.659797 - 8.99292 6.56286 -7.75773 -4.088714 -1.154148 -1.392575 - 8.04628 6.76145 -5.22781 -1.409338 -1.419777 0.732797 - 6.43104 9.40109 -5.57452 -0.405320 -0.391538 3.259107 - 6.19043 9.10078 -7.83259 -0.698559 -0.268708 -1.853866 - 9.03256 9.08192 -5.59911 -0.817626 -1.202417 2.060243 - 7.71158 6.63020 -2.68354 0.373144 -0.143171 0.439661 - 8.03743 9.07179 -2.56913 1.430852 1.295267 -0.463352 - 5.71096 9.03803 -2.85764 -0.155767 -0.160504 -1.516326 - ----------------------------------------------------------------------------------- - total drift: 0.029568 0.033281 -0.031150 - - --------------------------------------------------------------------------------------------------------- - - - - FREE ENERGIE OF THE ION-ELECTRON SYSTEM (eV) - --------------------------------------------------- - free energy TOTEN = -2750.33473322 eV - - energy without entropy= -2750.33473322 energy(sigma->0) = -2750.33473322 - - - --------------------------------------------------------------------------------------------------------- - - - POTLOK: cpu time 0.7709: real time 0.7756 - - --------------------------------------------------------------------------------------------------------- - - - LOOP+: cpu time 465.9882: real time 473.5297 - 4ORBIT: cpu time 0.0000: real time 0.0000 - - total amount of memory used by VASP MPI-rank0 162781. kBytes -======================================================================= - - base : 30000. kBytes - nonlr-proj: 30230. kBytes - fftplans : 41293. kBytes - grid : 25778. kBytes - one-center: 373. kBytes - wavefun : 35107. kBytes - - - - General timing and accounting informations for this job: - ======================================================== - - Total CPU time used (sec): 471.381 - User time (sec): 450.145 - System time (sec): 21.235 - Elapsed time (sec): 479.789 - - Maximum memory used (kb): 411652. - Average memory used (kb): N/A - - Minor page faults: 669297 - Major page faults: 4204 - Voluntary context switches: 6830 diff --git a/mace-bench/3rdparty/SevenNet/example_inputs/data/label_1/OUTCAR_4 b/mace-bench/3rdparty/SevenNet/example_inputs/data/label_1/OUTCAR_4 deleted file mode 100644 index 40ba5e209fcbf98f3c1303a61b0e6b1afb46d16d..0000000000000000000000000000000000000000 --- a/mace-bench/3rdparty/SevenNet/example_inputs/data/label_1/OUTCAR_4 +++ /dev/null @@ -1,3614 +0,0 @@ - vasp.6.3.2 27Jun22 (build Aug 12 2022 00:53:59) complex - - executed on tv2STD date 2022.09.21 16:21:24 - running 32 mpi-ranks, with 1 threads/rank - distrk: each k-point on 16 cores, 2 groups - distr: one band on NCORE= 4 cores, 4 groups - - --------------------------------------------------------------------------------------------------------- - - - INCAR: - SYSTEM = HfO2_p21c - NWRITE = 2 write-flag - ISTART = 0 job : 0-new, 1-cont, 2-samecut - ICHARG = 2 charge: 0-wave, 1-file, 2-atom, >10-const - INIWAV = 1 electr: 0-lowe 1-rand 2-diag - ENCUT = 500 - PREC = Accurate normal | accurate - ADDGRID = True - NELM = 100 - LREAL = Auto real-space projection (.FALSE., .TRUE., On, Auto) - ALGO = Fast Normal, Fast, Very_Fast - LWAVE = .F. - LCHARG = .F. - NSW = 0 - IBRION = 2 ionic relax: 0-MD, 1-quasi-Newton, 2-CG, 3-Damped MD - EDIFFG = -0.002 - ISIF = 3 (1:force\=y stress\=trace only ions\=y shape\=n volume\=n) - ISYM = 1 (1-use symmetry, 0-no symmetry) - ISMEAR = 0 (-1-Fermi, 1-Methfessel/Paxton) - SIGMA = 0.05 broadening in eV - NPAR = 4 - KPAR = 2 - METAGGA = SCAN - - POTCAR: PAW_PBE Hf 20Jan2003 - POTCAR: PAW_PBE O 08Apr2002 - POTCAR: PAW_PBE Hf 20Jan2003 - SHA256 = 0bb2207f9a10894133f750b65504b92b8afef976ae770762e0497daaaad8168a Hf/POTCAR - COPYR = (c) Copyright 20Jan2003 Georg Kresse - COPYR = This file is part of the software VASP. Any use, copying, and all other rights are regul - COPYR = If you do not have a valid VASP license, you may not use, copy or distribute this file. - VRHFIN =Hf: 6s5d - LEXCH = PE - EATOM = 75.9011 eV, 5.5786 Ry - - TITEL = PAW_PBE Hf 20Jan2003 - LULTRA = F use ultrasoft PP ? - IUNSCR = 1 unscreen: 0-lin 1-nonlin 2-no - RPACOR = 2.500 partial core radius - POMASS = 178.490; ZVAL = 4.000 mass and valenz - RCORE = 3.000 outmost cutoff radius - RWIGS = 3.050; RWIGS = 1.614 wigner-seitz radius (au A) - ENMAX = 220.334; ENMIN = 165.250 eV - RCLOC = 2.212 cutoff for local pot - LCOR = T correct aug charges - LPAW = T paw PP - EAUG = 335.116 - DEXC = 0.000 - RMAX = 3.077 core radius for proj-oper - RAUG = 1.300 factor for augmentation sphere - RDEP = 3.047 radius for radial grids - RDEPT = 2.344 core radius for aug-charge - - Atomic configuration - 16 entries - n l j E occ. - 1 0 0.50 -65259.4397 2.0000 - 2 0 0.50 -11157.9882 2.0000 - 2 1 1.50 -9795.2113 6.0000 - 3 0 0.50 -2541.4058 2.0000 - 3 1 1.50 -2134.4770 6.0000 - 3 2 2.50 -1653.5418 10.0000 - 4 0 0.50 -510.9575 2.0000 - 4 1 1.50 -377.5023 6.0000 - 4 2 2.50 -205.2085 10.0000 - 4 3 3.50 -15.4905 14.0000 - 5 0 0.50 -65.6020 2.0000 - 5 1 1.50 -34.2798 6.0000 - 5 2 2.50 -1.9877 3.0000 - 6 0 0.50 -4.7357 1.0000 - 6 1 1.50 -1.3606 0.0000 - 5 3 2.50 -1.3606 0.0000 - Description - l E TYP RCUT TYP RCUT - 2 -1.9876627 23 2.500 - 2 0.0744703 23 2.500 - 0 -4.7356889 23 2.600 - 0 3.2364747 23 2.600 - 1 -1.3605826 23 3.000 - 1 27.2116520 23 3.000 - local pseudopotential read in - partial core-charges read in - partial kinetic energy density read in - atomic valenz-charges read in - non local Contribution for L= 2 read in - real space projection operators read in - non local Contribution for L= 2 read in - real space projection operators read in - non local Contribution for L= 0 read in - real space projection operators read in - non local Contribution for L= 0 read in - real space projection operators read in - non local Contribution for L= 1 read in - real space projection operators read in - non local Contribution for L= 1 read in - real space projection operators read in - PAW grid and wavefunctions read in - - number of l-projection operators is LMAX = 6 - number of lm-projection operators is LMMAX = 18 - - POTCAR: PAW_PBE O 08Apr2002 - SHA256 = 818f92134a0a090dccd8ba1447fa70422a3b330e708bb4f08108d8ae51209ddf O/POTCAR - COPYR = (c) Copyright 08Apr2002 Georg Kresse - COPYR = This file is part of the software VASP. Any use, copying, and all other rights are regul - COPYR = If you do not have a valid VASP license, you may not use, copy or distribute this file. - VRHFIN =O: s2p4 - LEXCH = PE - EATOM = 432.3788 eV, 31.7789 Ry - - TITEL = PAW_PBE O 08Apr2002 - LULTRA = F use ultrasoft PP ? - IUNSCR = 1 unscreen: 0-lin 1-nonlin 2-no - RPACOR = 1.200 partial core radius - POMASS = 16.000; ZVAL = 6.000 mass and valenz - RCORE = 1.520 outmost cutoff radius - RWIGS = 1.550; RWIGS = 0.820 wigner-seitz radius (au A) - ENMAX = 400.000; ENMIN = 300.000 eV - ICORE = 2 local potential - LCOR = T correct aug charges - LPAW = T paw PP - EAUG = 605.392 - DEXC = 0.000 - RMAX = 1.553 core radius for proj-oper - RAUG = 1.300 factor for augmentation sphere - RDEP = 1.550 radius for radial grids - RDEPT = 1.329 core radius for aug-charge - - Atomic configuration - 4 entries - n l j E occ. - 1 0 0.50 -514.6923 2.0000 - 2 0 0.50 -23.9615 2.0000 - 2 1 0.50 -9.0305 4.0000 - 3 2 1.50 -9.5241 0.0000 - Description - l E TYP RCUT TYP RCUT - 0 -23.9615318 23 1.200 - 0 -9.5240782 23 1.200 - 1 -9.0304911 23 1.520 - 1 8.1634956 23 1.520 - 2 -9.5240782 7 1.500 - local pseudopotential read in - partial core-charges read in - partial kinetic energy density read in - kinetic energy density of atom read in - atomic valenz-charges read in - non local Contribution for L= 0 read in - real space projection operators read in - non local Contribution for L= 0 read in - real space projection operators read in - non local Contribution for L= 1 read in - real space projection operators read in - non local Contribution for L= 1 read in - real space projection operators read in - PAW grid and wavefunctions read in - - number of l-projection operators is LMAX = 4 - number of lm-projection operators is LMMAX = 8 - - Optimization of the real space projectors (new method) - - maximal supplied QI-value = 12.47 - optimisation between [QCUT,QGAM] = [ 11.35, 22.82] = [ 36.07,145.88] Ry - Optimized for a Real-space Cutoff 1.66 Angstroem - - l n(q) QCUT max X(q) W(low)/X(q) W(high)/X(q) e(spline) - 2 10 11.350 48.111 0.20E-03 0.11E-03 0.41E-06 - 2 10 11.350 40.545 0.19E-03 0.10E-03 0.39E-06 - 0 11 11.350 121.658 0.22E-04 0.19E-04 0.24E-06 - 0 11 11.350 71.177 0.17E-04 0.17E-04 0.23E-06 - 1 11 11.350 14.183 0.25E-03 0.43E-03 0.12E-05 - 1 11 11.350 8.257 0.17E-03 0.29E-03 0.81E-06 - Optimization of the real space projectors (new method) - - maximal supplied QI-value = 24.76 - optimisation between [QCUT,QGAM] = [ 11.39, 22.77] = [ 36.31,145.25] Ry - Optimized for a Real-space Cutoff 1.10 Angstroem - - l n(q) QCUT max X(q) W(low)/X(q) W(high)/X(q) e(spline) - 0 7 11.387 20.381 0.22E-03 0.48E-03 0.18E-06 - 0 7 11.387 15.268 0.22E-03 0.52E-03 0.19E-06 - 1 7 11.387 5.964 0.22E-03 0.73E-03 0.24E-06 - 1 7 11.387 5.382 0.19E-03 0.60E-03 0.21E-06 - PAW_PBE Hf 20Jan2003 : - energy of atom 1 EATOM= -75.9011 - kinetic energy error for atom= 0.0007 (will be added to EATOM!!) - PAW_PBE O 08Apr2002 : - energy of atom 2 EATOM= -432.3788 - kinetic energy error for atom= 0.0224 (will be added to EATOM!!) - - - POSCAR: name - positions in direct lattice - No initial velocities read in - WARNING: For meta-GGA calculations it is strongly recommended to include - aspherical contributions to the potential inside the PAW spheres (set - LASPH = .TRUE.) - - - METAGGA = SCAN LMAXTAU = 0 LMIXTAU = F - - exchange correlation table for LEXCH = 8 - RHO(1)= 0.500 N(1) = 2000 - RHO(2)= 100.500 N(2) = 4000 - - - --------------------------------------------------------------------------------------------------------- - - - ion position nearest neighbor table - 1 0.868 0.863 0.747- 35 1.92 68 1.93 89 2.07 87 2.08 76 2.12 34 2.19 77 2.32 14 3.18 - 6 3.31 26 3.34 32 3.35 7 3.41 30 3.54 24 3.60 5 3.81 12 3.86 - 2 0.860 0.373 0.242- 39 1.92 80 2.00 38 2.09 74 2.09 81 2.24 78 2.25 37 2.49 10 3.36 - 3 3.40 27 3.40 25 3.43 5 3.47 29 3.50 28 3.50 17 3.61 9 3.73 - 3 0.863 0.121 0.034- 95 1.74 64 2.02 38 2.09 42 2.21 76 2.21 82 2.41 81 2.52 20 3.21 - 32 3.32 2 3.40 4 3.45 29 3.50 25 3.58 24 3.68 18 3.72 31 3.81 - 4 0.858 0.877 0.257- 42 1.96 82 2.01 40 2.04 75 2.06 41 2.12 85 2.44 36 2.61 21 3.14 - 26 3.32 3 3.45 27 3.53 24 3.53 5 3.58 29 3.58 20 3.73 12 3.74 - 5 0.843 0.627 0.023- 57 1.93 77 1.97 93 2.03 36 2.08 85 2.15 78 2.18 39 2.22 24 3.33 - 17 3.33 30 3.35 25 3.38 2 3.47 27 3.55 4 3.58 1 3.81 14 3.83 - 6 0.865 0.126 0.570- 33 1.99 35 2.05 47 2.08 87 2.08 94 2.11 40 2.24 37 2.46 31 3.04 - 32 3.29 1 3.31 12 3.36 26 3.49 28 3.64 18 3.77 10 3.83 29 3.84 - 7 0.848 0.609 0.546- 34 1.88 43 2.01 90 2.09 71 2.24 41 2.24 80 2.29 89 2.41 27 3.17 - 9 3.24 30 3.25 31 3.38 1 3.41 26 3.54 28 3.67 - 8 0.365 0.363 0.236- 52 1.96 84 1.98 72 2.07 44 2.09 46 2.16 70 2.17 45 2.34 29 3.05 - 17 3.18 22 3.31 23 3.35 28 3.52 9 3.55 10 3.60 25 3.74 21 3.78 - 9 0.123 0.411 0.488- 43 1.90 74 1.96 71 2.12 60 2.12 54 2.15 44 2.25 45 2.56 7 3.24 - 10 3.30 15 3.43 21 3.45 8 3.55 19 3.68 16 3.73 2 3.73 - 10 0.130 0.150 0.307- 47 1.95 74 1.97 38 2.17 72 2.23 45 2.24 73 2.28 48 2.34 12 3.15 - 9 3.30 2 3.36 19 3.44 23 3.57 8 3.60 6 3.83 - 11 0.380 0.839 0.227- 50 1.80 51 1.86 86 2.03 69 2.06 73 2.33 49 2.34 48 2.52 27 3.18 - 22 3.19 20 3.34 23 3.44 21 3.48 24 3.49 12 3.67 - 12 0.134 0.909 0.490- 48 1.89 75 2.00 53 2.08 47 2.15 35 2.20 49 2.24 61 2.38 10 3.15 - 13 3.33 21 3.35 6 3.36 15 3.61 19 3.65 11 3.67 4 3.74 1 3.86 - 13 0.346 0.868 0.740- 92 2.00 61 2.10 67 2.13 58 2.14 55 2.28 56 2.32 53 2.33 14 3.25 - 30 3.30 12 3.33 19 3.45 15 3.51 20 3.58 18 3.69 - 14 0.138 0.671 0.805- 68 2.01 55 2.01 57 2.08 59 2.17 54 2.28 53 2.28 34 2.30 1 3.18 - 22 3.23 13 3.25 20 3.28 17 3.50 15 3.63 5 3.83 16 3.85 - 15 0.359 0.607 0.525- 56 1.99 79 2.07 49 2.13 66 2.22 53 2.26 44 2.28 54 2.39 28 3.12 - 9 3.43 21 3.50 16 3.51 13 3.51 12 3.61 14 3.63 27 3.72 30 3.82 - 16 0.380 0.354 0.750- 63 1.89 96 1.91 66 1.99 59 2.04 62 2.20 60 2.28 54 2.65 19 3.26 - 32 3.28 18 3.38 15 3.51 25 3.68 28 3.69 9 3.73 17 3.80 14 3.85 - 17 0.130 0.422 0.028- 39 1.93 65 2.03 70 2.13 72 2.20 57 2.23 62 2.54 59 2.64 8 3.18 - 22 3.28 5 3.33 18 3.39 14 3.50 2 3.61 21 3.65 23 3.66 16 3.80 - 18 0.133 0.181 0.808- 65 1.99 33 2.03 64 2.17 67 2.21 62 2.23 60 2.28 61 2.35 23 3.26 - 31 3.29 16 3.38 17 3.39 20 3.61 13 3.69 19 3.70 3 3.72 6 3.77 - 19 0.379 0.123 0.539- 45 1.92 63 1.95 58 2.08 83 2.09 61 2.28 48 2.40 60 2.40 26 3.20 - 16 3.26 10 3.44 13 3.45 12 3.65 9 3.68 18 3.70 29 3.71 32 3.74 - 20 0.127 0.906 0.017- 69 1.89 42 1.95 68 2.13 64 2.21 67 2.32 73 2.34 55 2.53 3 3.21 - 14 3.28 11 3.34 23 3.42 13 3.58 18 3.61 22 3.62 21 3.69 4 3.73 - 21 0.117 0.669 0.280- 36 1.88 75 1.96 71 1.99 49 2.12 69 2.30 44 2.31 70 2.35 4 3.14 - 12 3.35 9 3.45 11 3.48 15 3.50 22 3.53 17 3.65 20 3.69 8 3.78 - 22 0.361 0.607 0.031- 70 1.82 55 1.98 52 2.06 91 2.11 50 2.21 59 2.26 69 2.35 25 3.14 - 11 3.19 14 3.23 17 3.28 8 3.31 21 3.53 20 3.62 30 3.85 - 23 0.355 0.111 0.038- 73 1.92 46 1.95 62 1.98 88 2.08 51 2.20 67 2.24 72 2.32 24 3.23 - 18 3.26 8 3.35 20 3.42 11 3.44 10 3.57 17 3.66 29 3.79 32 3.79 - 24 0.621 0.898 0.002- 51 1.89 85 2.05 92 2.09 88 2.13 76 2.22 77 2.42 82 2.43 32 3.20 - 23 3.23 5 3.33 30 3.41 11 3.49 4 3.53 1 3.60 3 3.68 - 25 0.629 0.413 0.995- 91 1.92 52 2.02 96 2.06 81 2.18 93 2.19 78 2.30 95 2.53 22 3.14 - 31 3.28 5 3.38 30 3.42 2 3.43 3 3.58 32 3.62 16 3.68 8 3.74 - 26 0.644 0.913 0.505- 83 2.00 58 2.02 89 2.07 86 2.17 40 2.18 87 2.21 41 2.32 19 3.20 - 4 3.32 1 3.34 27 3.42 6 3.49 7 3.54 29 3.54 32 3.75 - 27 0.644 0.648 0.310- 79 1.85 41 2.07 86 2.09 78 2.10 50 2.10 80 2.17 85 2.31 7 3.17 - 11 3.18 28 3.25 2 3.40 26 3.42 4 3.53 5 3.55 15 3.72 - 28 0.606 0.393 0.476- 84 1.71 66 1.88 79 2.03 37 2.07 80 2.26 94 2.40 90 2.72 29 3.07 - 15 3.12 27 3.25 2 3.50 8 3.52 6 3.64 31 3.65 7 3.67 16 3.69 - 29 0.622 0.171 0.280- 37 1.91 46 1.95 81 1.97 84 2.02 83 2.02 82 2.13 40 2.91 8 3.05 - 28 3.07 3 3.50 2 3.50 26 3.54 4 3.58 19 3.71 23 3.79 6 3.84 - 30 0.624 0.659 0.775- 77 1.97 56 1.97 90 2.00 91 2.04 89 2.15 92 2.24 93 2.72 7 3.25 - 13 3.30 5 3.35 24 3.41 25 3.42 1 3.54 31 3.55 15 3.82 22 3.85 - 31 0.839 0.358 0.750- 33 1.92 94 2.07 90 2.08 93 2.08 43 2.32 95 2.37 65 2.47 6 3.04 - 25 3.28 18 3.29 7 3.38 32 3.47 30 3.55 28 3.65 3 3.81 - 32 0.638 0.126 0.798- 88 1.97 87 2.04 63 2.15 95 2.17 96 2.18 94 2.28 76 2.32 24 3.20 - 16 3.28 6 3.29 3 3.32 1 3.35 31 3.47 25 3.62 19 3.74 26 3.75 - 33 0.950 0.193 0.724- 31 1.92 6 1.99 18 2.03 - 34 0.960 0.677 0.665- 7 1.88 1 2.19 14 2.30 - 35 0.969 0.954 0.632- 1 1.92 6 2.05 12 2.20 - 36 0.994 0.677 0.141- 21 1.88 5 2.08 4 2.61 - 37 0.739 0.246 0.391- 29 1.91 28 2.07 6 2.46 2 2.49 - 38 0.935 0.178 0.212- 3 2.09 2 2.09 10 2.17 - 39 0.960 0.455 0.117- 2 1.92 17 1.93 5 2.22 - 40 0.815 0.985 0.421- 4 2.04 26 2.18 6 2.24 29 2.91 - 41 0.781 0.752 0.389- 27 2.07 4 2.12 7 2.24 26 2.32 - 42 0.971 0.947 0.131- 20 1.95 4 1.96 3 2.21 - 43 0.965 0.441 0.592- 9 1.90 7 2.01 31 2.32 - 44 0.267 0.500 0.365- 8 2.09 9 2.25 15 2.28 21 2.31 - 45 0.300 0.230 0.398- 19 1.92 10 2.24 8 2.34 9 2.56 - 46 0.471 0.182 0.161- 29 1.95 23 1.95 8 2.16 - 47 0.045 0.108 0.468- 10 1.95 6 2.08 12 2.15 - 48 0.272 0.980 0.408- 12 1.89 10 2.34 19 2.40 11 2.52 - 49 0.264 0.746 0.389- 21 2.12 15 2.13 12 2.24 11 2.34 - 50 0.479 0.686 0.184- 11 1.80 27 2.10 22 2.21 - 51 0.470 0.930 0.112- 11 1.86 24 1.89 23 2.20 - 52 0.447 0.421 0.079- 8 1.96 25 2.02 22 2.06 - 53 0.204 0.760 0.618- 12 2.08 15 2.26 14 2.28 13 2.33 - 54 0.188 0.523 0.643- 9 2.15 14 2.28 15 2.39 16 2.65 - 55 0.288 0.735 0.898- 22 1.98 14 2.01 13 2.28 20 2.53 - 56 0.459 0.670 0.671- 30 1.97 15 1.99 13 2.32 - 57 0.017 0.603 0.943- 5 1.93 14 2.08 17 2.23 - 58 0.461 0.935 0.588- 26 2.02 19 2.08 13 2.14 - 59 0.288 0.508 0.856- 16 2.04 14 2.17 22 2.26 17 2.64 - 60 0.213 0.284 0.636- 9 2.12 16 2.28 18 2.28 19 2.40 - 61 0.228 0.028 0.652- 13 2.10 19 2.28 18 2.35 12 2.38 - 62 0.299 0.253 0.913- 23 1.98 16 2.20 18 2.23 17 2.54 - 63 0.451 0.183 0.699- 16 1.89 19 1.95 32 2.15 - 64 0.058 0.115 0.989- 3 2.02 18 2.17 20 2.21 - 65 0.056 0.361 0.861- 18 1.99 17 2.03 31 2.47 - 66 0.455 0.411 0.585- 28 1.88 16 1.99 15 2.22 - 67 0.263 0.006 0.882- 13 2.13 18 2.21 23 2.24 20 2.32 - 68 0.026 0.840 0.855- 1 1.93 14 2.01 20 2.13 - 69 0.221 0.782 0.130- 20 1.89 11 2.06 21 2.30 22 2.35 - 70 0.253 0.529 0.137- 22 1.82 17 2.13 8 2.17 21 2.35 - 71 0.010 0.574 0.396- 21 1.99 9 2.12 7 2.24 - 72 0.220 0.266 0.160- 8 2.07 17 2.20 10 2.23 23 2.32 - 73 0.247 0.026 0.151- 23 1.92 10 2.28 11 2.33 20 2.34 - 74 0.038 0.326 0.348- 9 1.96 10 1.97 2 2.09 - 75 0.020 0.817 0.376- 21 1.96 12 2.00 4 2.06 - 76 0.790 0.975 0.910- 1 2.12 3 2.21 24 2.22 32 2.32 - 77 0.760 0.732 0.876- 5 1.97 30 1.97 1 2.32 24 2.42 - 78 0.716 0.533 0.150- 27 2.10 5 2.18 2 2.25 25 2.30 - 79 0.547 0.584 0.440- 27 1.85 28 2.03 15 2.07 - 80 0.775 0.482 0.389- 2 2.00 27 2.17 28 2.26 7 2.29 - 81 0.696 0.282 0.155- 29 1.97 25 2.18 2 2.24 3 2.52 - 82 0.723 0.013 0.170- 4 2.01 29 2.13 3 2.41 24 2.43 - 83 0.565 0.090 0.445- 26 2.00 29 2.02 19 2.09 - 84 0.533 0.348 0.338- 28 1.71 8 1.98 29 2.02 - 85 0.706 0.763 0.135- 24 2.05 5 2.15 27 2.31 4 2.44 - 86 0.539 0.832 0.349- 11 2.03 27 2.09 26 2.17 - 87 0.740 0.013 0.658- 32 2.04 1 2.08 6 2.08 26 2.21 - 88 0.549 0.096 0.964- 32 1.97 23 2.08 24 2.13 - 89 0.715 0.788 0.655- 26 2.07 1 2.07 30 2.15 7 2.41 - 90 0.724 0.518 0.665- 30 2.00 31 2.08 7 2.09 28 2.72 - 91 0.545 0.579 0.932- 25 1.92 30 2.04 22 2.11 - 92 0.522 0.856 0.833- 13 2.00 24 2.09 30 2.24 - 93 0.801 0.483 0.908- 5 2.03 31 2.08 25 2.19 30 2.72 - 94 0.709 0.261 0.651- 31 2.07 6 2.11 32 2.28 28 2.40 - 95 0.780 0.215 0.910- 3 1.74 32 2.17 31 2.37 25 2.53 - 96 0.541 0.320 0.850- 16 1.91 25 2.06 32 2.18 - - LATTYP: Found a simple monoclinic cell. - ALAT = 10.1297860000 - B/A-ratio = 1.0131648388 - C/A-ratio = 1.0379762742 - COS(beta) = -0.1645688048 - - Lattice vectors: - - A1 = ( 10.1297860000, 0.0000000000, 0.0000000000) - A2 = ( 0.0000000000, 10.2631430000, 0.0000000000) - A3 = ( -1.7303550000, 0.0000000000, 10.3711190000) - - -Analysis of symmetry for initial positions (statically): -===================================================================== - Subroutine PRICEL returns: - Original cell was already a primitive cell. - - - Routine SETGRP: Setting up the symmetry group for a - simple monoclinic supercell. - - - Subroutine GETGRP returns: Found 1 space group operations - (whereof 1 operations were pure point group operations) - out of a pool of 4 trial point group operations. - - -The static configuration has the point symmetry C_1 . - - -Analysis of symmetry for dynamics (positions and initial velocities): -===================================================================== - Subroutine PRICEL returns: - Original cell was already a primitive cell. - - - Routine SETGRP: Setting up the symmetry group for a - simple monoclinic supercell. - - - Subroutine GETGRP returns: Found 1 space group operations - (whereof 1 operations were pure point group operations) - out of a pool of 4 trial point group operations. - - -The dynamic configuration has the point symmetry C_1 . - - -Analysis of constrained symmetry for selective dynamics: -===================================================================== - Subroutine PRICEL returns: - Original cell was already a primitive cell. - - - Routine SETGRP: Setting up the symmetry group for a - simple monoclinic supercell. - - - Subroutine GETGRP returns: Found 1 space group operations - (whereof 1 operations were pure point group operations) - out of a pool of 4 trial point group operations. - - -The constrained configuration has the point symmetry C_1 . - - - Subroutine INISYM returns: Found 1 space group operations - (whereof 1 operations are pure point group operations), - and found 1 'primitive' translations - - ----------------------------------------------------------------------------------------- - - Primitive cell - - volume of cell : 1078.2172 - - direct lattice vectors reciprocal lattice vectors - 10.129786000 0.000000000 0.000000000 0.098718769 0.000000000 0.016470596 - 1.730355000 0.000000000-10.371119000 0.000000000 0.000000000 -0.096421611 - 0.000000000 10.263143000 0.000000000 0.000000000 0.097436039 0.000000000 - - length of vectors - 10.129786000 10.514477530 10.263143000 0.100083344 0.096421611 0.097436039 - - position of ions in fractional coordinates (direct lattice) - 0.867867200 0.863268340 0.746650470 - 0.860472460 0.373142870 0.242001400 - 0.863346830 0.121138540 0.034024260 - 0.857593030 0.877209000 0.257085720 - 0.842583170 0.627480410 0.023404290 - 0.865307500 0.126459910 0.569626050 - 0.848363170 0.608678480 0.546174030 - 0.365485970 0.362534840 0.235813220 - 0.122930260 0.410539050 0.487937710 - 0.129521170 0.150168640 0.307294220 - 0.380289560 0.838557240 0.227094030 - 0.134013760 0.908995970 0.489986880 - 0.345667450 0.868168910 0.740412810 - 0.137782290 0.671440730 0.804947850 - 0.358548040 0.607140070 0.525104460 - 0.380266680 0.353836350 0.750288790 - 0.130406480 0.421569000 0.028399490 - 0.133251300 0.181337260 0.807838110 - 0.378846710 0.123127690 0.538634460 - 0.127017390 0.906480490 0.016731690 - 0.116912600 0.669141780 0.279516530 - 0.360680700 0.606821190 0.031429520 - 0.355472520 0.111200840 0.038239410 - 0.621047600 0.897865410 0.001587700 - 0.629027860 0.413494740 0.994880640 - 0.643819150 0.912628040 0.504997580 - 0.643981010 0.648334580 0.310374870 - 0.606427600 0.393489920 0.476283940 - 0.621846210 0.170609750 0.280124350 - 0.624285030 0.659234070 0.775395590 - 0.839452400 0.357827670 0.750326130 - 0.637587490 0.125757470 0.798411590 - 0.950224680 0.193483180 0.724342260 - 0.959545010 0.677299770 0.664955900 - 0.969285280 0.953708660 0.631674860 - 0.994308390 0.676723600 0.140847300 - 0.739343820 0.245956960 0.391090520 - 0.935435180 0.177642440 0.212329620 - 0.959638720 0.454648080 0.116660030 - 0.814801590 0.985082940 0.421383930 - 0.780646700 0.752498490 0.389094880 - 0.971453800 0.947331350 0.130671900 - 0.965499940 0.440775470 0.592154590 - 0.266686570 0.499743930 0.364996240 - 0.299565770 0.229853630 0.397547380 - 0.471056450 0.182192700 0.160743310 - 0.044850480 0.108114260 0.468429460 - 0.272133040 0.980450190 0.408326890 - 0.263736670 0.745559020 0.388707560 - 0.478640530 0.685558760 0.183814460 - 0.470302630 0.929911430 0.111777160 - 0.447284790 0.421167430 0.078506770 - 0.204262580 0.760406040 0.618252360 - 0.187868460 0.523208210 0.642997330 - 0.288269190 0.735305250 0.898365370 - 0.458886860 0.669813050 0.671482500 - 0.017253960 0.602735360 0.943072560 - 0.461088070 0.935201700 0.588249110 - 0.288275190 0.507834790 0.856027530 - 0.212874180 0.284269330 0.636299980 - 0.227873780 0.028242220 0.652493680 - 0.299008130 0.253215790 0.912589300 - 0.450688570 0.183350170 0.698829630 - 0.058389570 0.115352800 0.989174860 - 0.056011820 0.360570520 0.860637260 - 0.455454000 0.410704140 0.584929270 - 0.263148540 0.006236160 0.881938830 - 0.026209110 0.840086450 0.855089720 - 0.221310970 0.781598000 0.130225380 - 0.253383650 0.529145010 0.137239030 - 0.010444880 0.574299760 0.396004630 - 0.220447360 0.266316750 0.160060810 - 0.247188010 0.025682490 0.151435020 - 0.038392060 0.325520290 0.348040920 - 0.020073130 0.816698150 0.375998150 - 0.790166580 0.975492450 0.909732340 - 0.759979970 0.731960310 0.876310860 - 0.715718700 0.533418500 0.150447070 - 0.546569180 0.584492790 0.439855210 - 0.774735500 0.481703860 0.389123910 - 0.695723510 0.281947990 0.154508570 - 0.722995040 0.012879140 0.169739610 - 0.565163940 0.090481750 0.445465490 - 0.533300640 0.347547180 0.337793740 - 0.705675500 0.763449110 0.135304760 - 0.538792640 0.832170100 0.348837820 - 0.740428980 0.013257090 0.657733290 - 0.549162670 0.096098270 0.964426360 - 0.714651080 0.788464790 0.655461660 - 0.724310220 0.517926950 0.665419510 - 0.544972840 0.579076430 0.931548710 - 0.521542750 0.856222110 0.832892870 - 0.801237320 0.483108830 0.907632820 - 0.709197690 0.260907070 0.650646730 - 0.779714710 0.214605960 0.910128010 - 0.541005730 0.320131950 0.850058150 - - ion indices of the primitive-cell ions - primitive index ion index - 1 1 - 2 2 - 3 3 - 4 4 - 5 5 - 6 6 - 7 7 - 8 8 - 9 9 - 10 10 - 11 11 - 12 12 - 13 13 - 14 14 - 15 15 - 16 16 - 17 17 - 18 18 - 19 19 - 20 20 - 21 21 - 22 22 - 23 23 - 24 24 - 25 25 - 26 26 - 27 27 - 28 28 - 29 29 - 30 30 - 31 31 - 32 32 - 33 33 - 34 34 - 35 35 - 36 36 - 37 37 - 38 38 - 39 39 - 40 40 - 41 41 - 42 42 - 43 43 - 44 44 - 45 45 - 46 46 - 47 47 - 48 48 - 49 49 - 50 50 - 51 51 - 52 52 - 53 53 - 54 54 - 55 55 - 56 56 - 57 57 - 58 58 - 59 59 - 60 60 - 61 61 - 62 62 - 63 63 - 64 64 - 65 65 - 66 66 - 67 67 - 68 68 - 69 69 - 70 70 - 71 71 - 72 72 - 73 73 - 74 74 - 75 75 - 76 76 - 77 77 - 78 78 - 79 79 - 80 80 - 81 81 - 82 82 - 83 83 - 84 84 - 85 85 - 86 86 - 87 87 - 88 88 - 89 89 - 90 90 - 91 91 - 92 92 - 93 93 - 94 94 - 95 95 - 96 96 - ----------------------------------------------------------------------------------------- - - - - KPOINTS: Auto k-point - -Automatic generation of k-mesh. - Grid dimensions read from file: - generate k-points for: 2 2 2 - - Generating k-lattice: - - Cartesian coordinates Fractional coordinates (reciprocal lattice) - 0.049359384 0.000000000 0.008235298 0.500000000 0.000000000 0.000000000 - 0.000000000 0.000000000 -0.048210805 0.000000000 0.500000000 0.000000000 - 0.000000000 0.048718019 0.000000000 0.000000000 0.000000000 0.500000000 - - Length of vectors - 0.050041672 0.048210805 0.048718019 - - Shift w.r.t. Gamma in fractional coordinates (k-lattice) - 0.500000000 0.500000000 0.500000000 - - - Subroutine IBZKPT returns following result: - =========================================== - - Found 4 irreducible k-points: - - Following reciprocal coordinates: - Coordinates Weight - 0.250000 0.250000 0.250000 2.000000 - -0.250000 -0.250000 0.250000 2.000000 - -0.250000 0.250000 0.250000 2.000000 - 0.250000 -0.250000 0.250000 2.000000 - - Following cartesian coordinates: - Coordinates Weight - 0.024680 0.024359 -0.019988 2.000000 - -0.024680 0.024359 0.019988 2.000000 - -0.024680 0.024359 -0.028223 2.000000 - 0.024680 0.024359 0.028223 2.000000 - - - --------------------------------------------------------------------------------------------------------- - - - - - Dimension of arrays: - k-points NKPTS = 4 k-points in BZ NKDIM = 4 number of bands NBANDS= 308 - number of dos NEDOS = 301 number of ions NIONS = 96 - non local maximal LDIM = 6 non local SUM 2l+1 LMDIM = 18 - total plane-waves NPLWV = 512000 - max r-space proj IRMAX = 9139 max aug-charges IRDMAX= 255251 - dimension x,y,z NGX = 80 NGY = 80 NGZ = 80 - dimension x,y,z NGXF= 160 NGYF= 160 NGZF= 160 - support grid NGXF= 320 NGYF= 320 NGZF= 320 - ions per type = 32 64 - NGX,Y,Z is equivalent to a cutoff of 13.13, 12.65, 12.96 a.u. - NGXF,Y,Z is equivalent to a cutoff of 26.26, 25.30, 25.92 a.u. - - SYSTEM = HfO2_p21c - POSCAR = name - - Startparameter for this run: - NWRITE = 2 write-flag & timer - PREC = accura normal or accurate (medium, high low for compatibility) - ISTART = 0 job : 0-new 1-cont 2-samecut - ICHARG = 2 charge: 1-file 2-atom 10-const - ISPIN = 1 spin polarized calculation? - LNONCOLLINEAR = F non collinear calculations - LSORBIT = F spin-orbit coupling - INIWAV = 1 electr: 0-lowe 1-rand 2-diag - LASPH = F aspherical Exc in radial PAW - Electronic Relaxation 1 - ENCUT = 500.0 eV 36.75 Ry 6.06 a.u. 18.47 19.17 18.71*2*pi/ulx,y,z - ENINI = 500.0 initial cutoff - ENAUG = 605.4 eV augmentation charge cutoff - NELM = 100; NELMIN= 2; NELMDL= -5 # of ELM steps - EDIFF = 0.1E-03 stopping-criterion for ELM - LREAL = T real-space projection - NLSPLINE = F spline interpolate recip. space projectors - LCOMPAT= F compatible to vasp.4.4 - GGA_COMPAT = T GGA compatible to vasp.4.4-vasp.4.6 - LMAXPAW = -100 max onsite density - LMAXMIX = 2 max onsite mixed and CHGCAR - VOSKOWN= 0 Vosko Wilk Nusair interpolation - ROPT = -0.00025 -0.00025 - Ionic relaxation - EDIFFG = -.2E-02 stopping-criterion for IOM - NSW = 0 number of steps for IOM - NBLOCK = 1; KBLOCK = 1 inner block; outer block - IBRION = -1 ionic relax: 0-MD 1-quasi-New 2-CG - NFREE = 1 steps in history (QN), initial steepest desc. (CG) - ISIF = 3 stress and relaxation - IWAVPR = 10 prediction: 0-non 1-charg 2-wave 3-comb - ISYM = 1 0-nonsym 1-usesym 2-fastsym - LCORR = T Harris-Foulkes like correction to forces - - POTIM = 0.5000 time-step for ionic-motion - TEIN = 0.0 initial temperature - TEBEG = 0.0; TEEND = 0.0 temperature during run - SMASS = -3.00 Nose mass-parameter (am) - estimated Nose-frequenzy (Omega) = 0.10E-29 period in steps = 0.13E+47 mass= -0.234E-26a.u. - SCALEE = 1.0000 scale energy and forces - NPACO = 256; APACO = 10.0 distance and # of slots for P.C. - PSTRESS= 0.0 pullay stress - - Mass of Ions in am - POMASS = 178.49 16.00 - Ionic Valenz - ZVAL = 4.00 6.00 - Atomic Wigner-Seitz radii - RWIGS = -1.00 -1.00 - virtual crystal weights - VCA = 1.00 1.00 - NELECT = 512.0000 total number of electrons - NUPDOWN= -1.0000 fix difference up-down - - DOS related values: - EMIN = 10.00; EMAX =-10.00 energy-range for DOS - EFERMI = 0.00 - ISMEAR = 0; SIGMA = 0.05 broadening in eV -4-tet -1-fermi 0-gaus - - Electronic relaxation 2 (details) - IALGO = 68 algorithm - LDIAG = T sub-space diagonalisation (order eigenvalues) - LSUBROT= F optimize rotation matrix (better conditioning) - TURBO = 0 0=normal 1=particle mesh - IRESTART = 0 0=no restart 2=restart with 2 vectors - NREBOOT = 0 no. of reboots - NMIN = 0 reboot dimension - EREF = 0.00 reference energy to select bands - IMIX = 4 mixing-type and parameters - AMIX = 0.40; BMIX = 1.00 - AMIX_MAG = 1.60; BMIX_MAG = 1.00 - AMIN = 0.10 - WC = 100.; INIMIX= 1; MIXPRE= 1; MAXMIX= -45 - - Intra band minimization: - WEIMIN = 0.0000 energy-eigenvalue tresh-hold - EBREAK = 0.81E-07 absolut break condition - DEPER = 0.30 relativ break condition - - TIME = 0.40 timestep for ELM - - volume/ion in A,a.u. = 11.23 75.79 - Fermi-wavevector in a.u.,A,eV,Ry = 1.277211 2.413579 22.194756 1.631269 - Thomas-Fermi vector in A = 2.409824 - - Write flags - LWAVE = F write WAVECAR - LDOWNSAMPLE = F k-point downsampling of WAVECAR - LCHARG = F write CHGCAR - LVTOT = F write LOCPOT, total local potential - LVHAR = F write LOCPOT, Hartree potential only - LELF = F write electronic localiz. function (ELF) - LORBIT = 0 0 simple, 1 ext, 2 COOP (PROOUT), +10 PAW based schemes - - - Dipole corrections - LMONO = F monopole corrections only (constant potential shift) - LDIPOL = F correct potential (dipole corrections) - IDIPOL = 0 1-x, 2-y, 3-z, 4-all directions - EPSILON= 1.0000000 bulk dielectric constant - - Exchange correlation treatment: - GGA = -- GGA type - LEXCH = 8 internal setting for exchange type - LIBXC = F Libxc - VOSKOWN = 0 Vosko Wilk Nusair interpolation - LHFCALC = F Hartree Fock is set to - LHFONE = F Hartree Fock one center treatment - AEXX = 0.0000 exact exchange contribution - - Linear response parameters - LEPSILON= F determine dielectric tensor - LRPA = F only Hartree local field effects (RPA) - LNABLA = F use nabla operator in PAW spheres - LVEL = F velocity operator in full k-point grid - CSHIFT =0.1000 complex shift for real part using Kramers Kronig - OMEGAMAX= -1.0 maximum frequency - DEG_THRESHOLD= 0.2000000E-02 threshold for treating states as degnerate - RTIME = -0.100 relaxation time in fs - (WPLASMAI= 0.000 imaginary part of plasma frequency in eV, 0.658/RTIME) - DFIELD = 0.0000000 0.0000000 0.0000000 field for delta impulse in time - - Optional k-point grid parameters - LKPOINTS_OPT = F use optional k-point grid - KPOINTS_OPT_MODE= 1 mode for optional k-point grid - - Orbital magnetization related: - ORBITALMAG= F switch on orbital magnetization - LCHIMAG = F perturbation theory with respect to B field - DQ = 0.001000 dq finite difference perturbation B field - LLRAUG = F two centre corrections for induced B field - - - --------------------------------------------------------------------------------------------------------- - - - Static calculation - charge density and potential will be updated during run - non-spin polarized calculation - RMM-DIIS sequential band-by-band and - variant of blocked Davidson during initial phase - perform sub-space diagonalisation - before iterative eigenvector-optimisation - modified Broyden-mixing scheme, WC = 100.0 - initial mixing is a Kerker type mixing with AMIX = 0.4000 and BMIX = 1.0000 - Hartree-type preconditioning will be used - using additional bands 52 - real space projection scheme for non local part - use partial core corrections - calculate Harris-corrections to forces - (improved forces if not selfconsistent) - use gradient corrections - use of overlap-Matrix (Vanderbilt PP) - Gauss-broadening in eV SIGMA = 0.05 - - --------------------------------------------------------------------------------------------------------- - - - energy-cutoff : 500.00 - volume of cell : 1078.22 - direct lattice vectors reciprocal lattice vectors - 10.129786000 0.000000000 0.000000000 0.098718769 0.000000000 0.016470596 - 1.730355000 0.000000000-10.371119000 0.000000000 0.000000000 -0.096421611 - 0.000000000 10.263143000 0.000000000 0.000000000 0.097436039 0.000000000 - - length of vectors - 10.129786000 10.514477530 10.263143000 0.100083344 0.096421611 0.097436039 - - - - k-points in units of 2pi/SCALE and weight: Auto k-point - 0.02467969 0.02435901 -0.01998775 0.250 - -0.02467969 0.02435901 0.01998775 0.250 - -0.02467969 0.02435901 -0.02822305 0.250 - 0.02467969 0.02435901 0.02822305 0.250 - - k-points in reciprocal lattice and weights: Auto k-point - 0.25000000 0.25000000 0.25000000 0.250 - -0.25000000 -0.25000000 0.25000000 0.250 - -0.25000000 0.25000000 0.25000000 0.250 - 0.25000000 -0.25000000 0.25000000 0.250 - - position of ions in fractional coordinates (direct lattice) - 0.86786720 0.86326834 0.74665047 - 0.86047246 0.37314287 0.24200140 - 0.86334683 0.12113854 0.03402426 - 0.85759303 0.87720900 0.25708572 - 0.84258317 0.62748041 0.02340429 - 0.86530750 0.12645991 0.56962605 - 0.84836317 0.60867848 0.54617403 - 0.36548597 0.36253484 0.23581322 - 0.12293026 0.41053905 0.48793771 - 0.12952117 0.15016864 0.30729422 - 0.38028956 0.83855724 0.22709403 - 0.13401376 0.90899597 0.48998688 - 0.34566745 0.86816891 0.74041281 - 0.13778229 0.67144073 0.80494785 - 0.35854804 0.60714007 0.52510446 - 0.38026668 0.35383635 0.75028879 - 0.13040648 0.42156900 0.02839949 - 0.13325130 0.18133726 0.80783811 - 0.37884671 0.12312769 0.53863446 - 0.12701739 0.90648049 0.01673169 - 0.11691260 0.66914178 0.27951653 - 0.36068070 0.60682119 0.03142952 - 0.35547252 0.11120084 0.03823941 - 0.62104760 0.89786541 0.00158770 - 0.62902786 0.41349474 0.99488064 - 0.64381915 0.91262804 0.50499758 - 0.64398101 0.64833458 0.31037487 - 0.60642760 0.39348992 0.47628394 - 0.62184621 0.17060975 0.28012435 - 0.62428503 0.65923407 0.77539559 - 0.83945240 0.35782767 0.75032613 - 0.63758749 0.12575747 0.79841159 - 0.95022468 0.19348318 0.72434226 - 0.95954501 0.67729977 0.66495590 - 0.96928528 0.95370866 0.63167486 - 0.99430839 0.67672360 0.14084730 - 0.73934382 0.24595696 0.39109052 - 0.93543518 0.17764244 0.21232962 - 0.95963872 0.45464808 0.11666003 - 0.81480159 0.98508294 0.42138393 - 0.78064670 0.75249849 0.38909488 - 0.97145380 0.94733135 0.13067190 - 0.96549994 0.44077547 0.59215459 - 0.26668657 0.49974393 0.36499624 - 0.29956577 0.22985363 0.39754738 - 0.47105645 0.18219270 0.16074331 - 0.04485048 0.10811426 0.46842946 - 0.27213304 0.98045019 0.40832689 - 0.26373667 0.74555902 0.38870756 - 0.47864053 0.68555876 0.18381446 - 0.47030263 0.92991143 0.11177716 - 0.44728479 0.42116743 0.07850677 - 0.20426258 0.76040604 0.61825236 - 0.18786846 0.52320821 0.64299733 - 0.28826919 0.73530525 0.89836537 - 0.45888686 0.66981305 0.67148250 - 0.01725396 0.60273536 0.94307256 - 0.46108807 0.93520170 0.58824911 - 0.28827519 0.50783479 0.85602753 - 0.21287418 0.28426933 0.63629998 - 0.22787378 0.02824222 0.65249368 - 0.29900813 0.25321579 0.91258930 - 0.45068857 0.18335017 0.69882963 - 0.05838957 0.11535280 0.98917486 - 0.05601182 0.36057052 0.86063726 - 0.45545400 0.41070414 0.58492927 - 0.26314854 0.00623616 0.88193883 - 0.02620911 0.84008645 0.85508972 - 0.22131097 0.78159800 0.13022538 - 0.25338365 0.52914501 0.13723903 - 0.01044488 0.57429976 0.39600463 - 0.22044736 0.26631675 0.16006081 - 0.24718801 0.02568249 0.15143502 - 0.03839206 0.32552029 0.34804092 - 0.02007313 0.81669815 0.37599815 - 0.79016658 0.97549245 0.90973234 - 0.75997997 0.73196031 0.87631086 - 0.71571870 0.53341850 0.15044707 - 0.54656918 0.58449279 0.43985521 - 0.77473550 0.48170386 0.38912391 - 0.69572351 0.28194799 0.15450857 - 0.72299504 0.01287914 0.16973961 - 0.56516394 0.09048175 0.44546549 - 0.53330064 0.34754718 0.33779374 - 0.70567550 0.76344911 0.13530476 - 0.53879264 0.83217010 0.34883782 - 0.74042898 0.01325709 0.65773329 - 0.54916267 0.09609827 0.96442636 - 0.71465108 0.78846479 0.65546166 - 0.72431022 0.51792695 0.66541951 - 0.54497284 0.57907643 0.93154871 - 0.52154275 0.85622211 0.83289287 - 0.80123732 0.48310883 0.90763282 - 0.70919769 0.26090707 0.65064673 - 0.77971471 0.21460596 0.91012801 - 0.54100573 0.32013195 0.85005815 - - position of ions in cartesian coordinates (Angst): - 10.28506970 7.66298054 -8.95305868 - 9.36207151 2.48369497 -3.86990911 - 8.95513131 0.34919585 -1.25634221 - 10.20511685 2.63850751 -9.09763893 - 9.62095106 0.24020158 -6.50767400 - 8.98420034 5.84615361 -1.31153078 - 9.64696721 5.60546217 -6.31267695 - 4.32960864 2.42018480 -3.75989197 - 1.95563552 5.00777449 -4.25774934 - 1.57186679 3.15380452 -1.55741684 - 5.30325357 2.33069850 -8.69677692 - 2.93041643 5.02880542 -9.42730538 - 5.00377771 7.59896255 -9.00388308 - 2.55753594 8.26129489 -6.96359171 - 4.68258277 5.38922216 -6.29672192 - 4.46428259 7.70032114 -3.66967889 - 2.05045376 0.29146803 -4.37214227 - 1.66358499 8.29095804 -1.88067030 - 4.05069071 5.52808249 -1.27697193 - 2.85519203 0.17171973 -9.40121703 - 2.34215244 2.86871812 -6.93974903 - 4.70363439 0.32256566 -6.29341477 - 3.79327749 0.39245653 -1.15327714 - 7.84470519 0.01629479 -9.31186901 - 7.08741030 10.21060228 -4.28840315 - 8.10092070 5.18286238 -9.46497401 - 7.64523880 3.18542167 -6.72395508 - 6.82385906 4.88817018 -4.08093079 - 6.59438447 2.87495626 -1.76941402 - 7.46458273 7.95799582 -6.83699499 - 9.12264207 7.70070437 -3.71107335 - 6.67622990 8.19421232 -1.30424569 - 9.96036725 7.43402820 -2.00663708 - 10.89195465 6.82453749 -7.02435651 - 11.46890701 6.48296942 -9.89102600 - 11.24310327 1.44553598 -7.01838099 - 7.91498753 4.01381793 -2.55084890 - 9.78314267 2.17916925 -1.84235088 - 10.50763745 1.19729857 -4.71520934 - 9.95830893 4.32472353-10.21641240 - 9.20987354 3.99333639 -7.80425139 - 11.47983864 1.34110440 -9.82488616 - 10.54300581 6.07736724 -4.57133485 - 3.56621229 3.74600861 -5.18290377 - 3.43226552 4.08008561 -2.38383935 - 5.08695908 1.64973158 -1.88954217 - 0.64140181 4.80755853 -1.12126586 - 4.45317635 4.19071726-10.16836559 - 3.96167781 3.98936127 -7.73228132 - 6.03478617 1.88651409 -7.11001148 - 6.37314189 1.14718498 -9.64422210 - 5.25966837 0.80572621 -4.36797754 - 3.38490862 6.34521238 -7.88626153 - 2.80840324 6.59917355 -5.42625461 - 4.19244432 9.22005226 -7.62593825 - 5.80744005 6.89152092 -6.94671085 - 1.21772507 9.67888854 -6.25104014 - 6.28895441 6.03728474 -9.69908812 - 3.79890045 8.78553295 -5.26681504 - 2.64825674 6.53043769 -2.94819105 - 2.35718169 6.69663594 -0.29290342 - 3.46704158 9.36603449 -2.62613109 - 4.88263965 7.17218843 -1.90154643 - 0.79107514 10.15204304 -1.19633762 - 1.19130275 8.83284327 -3.73951977 - 5.32431552 6.00321274 -4.25946151 - 2.67642917 9.05146433 -0.06467596 - 1.71914046 8.77590807 -8.71263654 - 3.59427477 1.33652170 -8.10604587 - 3.48233086 1.40850379 -5.48782587 - 1.09954686 4.06425215 -5.95613115 - 2.69390710 1.64272698 -2.76200271 - 2.54840147 1.55419927 -0.26635616 - 0.95216901 3.57199373 -3.37600966 - 1.61651424 3.85892278 -8.47007370 - 9.69216660 9.33671310-10.11694828 - 8.96498564 8.99370367 -7.59124748 - 8.17308064 1.54405979 -5.53214674 - 6.54800885 4.51429692 -6.06184428 - 8.68142350 3.99363433 -4.99580805 - 7.53540039 1.58574355 -2.92411616 - 7.34607052 1.74206189 -0.13357109 - 5.88155532 4.57187603 -0.93839700 - 6.00360136 3.46682546 -3.60445316 - 8.46937979 1.38865210 -7.91782157 - 6.89780383 3.58017243 -8.63053514 - 7.52332659 6.75041081 -0.13749086 - 5.72918445 9.89804565 -0.99664659 - 8.60358650 6.72709675 -8.17726216 - 8.23330501 6.82929559 -5.37148203 - 6.52246604 9.56061762 -6.00567057 - 6.76468466 8.54809863 -8.87998139 - 8.95231237 9.31516542 -5.01037917 - 7.63548268 6.67768043 -2.70589827 - 8.26968765 9.34077391 -2.22570395 - 6.03421419 8.72426835 -3.32012655 - - - --------------------------------------------------------------------------------------------------------- - - - k-point 1 : 0.2500 0.2500 0.2500 plane waves: 27363 - k-point 2 : -0.2500-0.2500 0.2500 plane waves: 27363 - k-point 3 : -0.2500 0.2500 0.2500 plane waves: 27374 - k-point 4 : 0.2500-0.2500 0.2500 plane waves: 27374 - - maximum and minimum number of plane-waves per node : 6889 6813 - - maximum number of plane-waves: 27374 - maximum index in each direction: - IXMAX= 18 IYMAX= 19 IZMAX= 18 - IXMIN= -18 IYMIN= -19 IZMIN= -18 - - - real space projection operators: - total allocation : 49869.14 KBytes - max/ min on nodes : 12477.70 12458.86 - - - parallel 3D FFT for wavefunctions: - minimum data exchange during FFTs selected (reduces bandwidth) - parallel 3D FFT for charge: - minimum data exchange during FFTs selected (reduces bandwidth) - - - total amount of memory used by VASP MPI-rank0 162797. kBytes -======================================================================= - - base : 30000. kBytes - nonlr-proj: 30246. kBytes - fftplans : 41293. kBytes - grid : 25778. kBytes - one-center: 373. kBytes - wavefun : 35107. kBytes - - INWAV: cpu time 0.0000: real time 0.0002 - Broyden mixing: mesh for mixing (old mesh) - NGX = 37 NGY = 39 NGZ = 37 - (NGX =160 NGY =160 NGZ =160) - gives a total of 53391 points - - initial charge density was supplied: - charge density of overlapping atoms calculated - number of electron 512.0000000 magnetization - keeping initial charge density in first step - - --------------------------------------------------------------------------------------------------------- - - - Maximum index for non-local projection operator 2221 - Maximum index for augmentation-charges 15784 (set IRDMAX) - - --------------------------------------------------------------------------------------------------------- - - - First call to EWALD: gamma= 0.173 - Maximum number of real-space cells 3x 3x 3 - Maximum number of reciprocal cells 3x 3x 3 - - FEWALD: cpu time 0.0067: real time 0.0068 - - ---------------------------------------- Iteration 1( 1) --------------------------------------- - - - POTLOK: cpu time 0.4276: real time 0.4300 - SETDIJ: cpu time 0.3606: real time 0.3892 - EDDAV: cpu time 15.8575: real time 15.9888 - DOS: cpu time 0.0008: real time 0.0008 - -------------------------------------------- - LOOP: cpu time 16.6465: real time 16.8088 - - eigenvalue-minimisations : 2464 - total energy-change (2. order) : 0.1368751E+04 (-0.2725637E+05) - number of electron 512.0000000 magnetization - augmentation part 512.0000000 magnetization - - Free energy of the ion-electron system (eV) - --------------------------------------------------- - alpha Z PSCENC = 1957.98898647 - Ewald energy TEWEN = -24658.60879579 - -Hartree energ DENC = -7531.00015340 - -exchange EXHF = 0.00000000 - -V(xc)+E(xc) XCENC = 592.53701221 - PAW double counting = 25569.98736858 -25757.03612884 - entropy T*S EENTRO = -0.01041304 - eigenvalues EBANDS = 1095.26976032 - atomic energy EATOM = 30099.62314931 - Solvation Ediel_sol = 0.00000000 - --------------------------------------------------- - free energy TOTEN = 1368.75078584 eV - - energy without entropy = 1368.76119887 energy(sigma->0) = 1368.75599236 - - --------------------------------------------------------------------------------------------------------- - - - - ---------------------------------------- Iteration 1( 2) --------------------------------------- - - - EDDAV: cpu time 18.5539: real time 18.7183 - DOS: cpu time 0.0006: real time 0.0006 - -------------------------------------------- - LOOP: cpu time 18.5546: real time 18.7189 - - eigenvalue-minimisations : 3056 - total energy-change (2. order) :-0.4112179E+04 (-0.3993415E+04) - number of electron 512.0000000 magnetization - augmentation part 512.0000000 magnetization - - Free energy of the ion-electron system (eV) - --------------------------------------------------- - alpha Z PSCENC = 1957.98898647 - Ewald energy TEWEN = -24658.60879579 - -Hartree energ DENC = -7531.00015340 - -exchange EXHF = 0.00000000 - -V(xc)+E(xc) XCENC = 592.53701221 - PAW double counting = 25569.98736858 -25757.03612884 - entropy T*S EENTRO = -0.00000000 - eigenvalues EBANDS = -3016.91963070 - atomic energy EATOM = 30099.62314931 - Solvation Ediel_sol = 0.00000000 - --------------------------------------------------- - free energy TOTEN = -2743.42819215 eV - - energy without entropy = -2743.42819215 energy(sigma->0) = -2743.42819215 - - --------------------------------------------------------------------------------------------------------- - - - - ---------------------------------------- Iteration 1( 3) --------------------------------------- - - - EDDAV: cpu time 18.3470: real time 18.5563 - DOS: cpu time 0.0004: real time 0.0004 - -------------------------------------------- - LOOP: cpu time 18.3474: real time 18.5567 - - eigenvalue-minimisations : 2880 - total energy-change (2. order) :-0.2864011E+03 (-0.2846534E+03) - number of electron 512.0000000 magnetization - augmentation part 512.0000000 magnetization - - Free energy of the ion-electron system (eV) - --------------------------------------------------- - alpha Z PSCENC = 1957.98898647 - Ewald energy TEWEN = -24658.60879579 - -Hartree energ DENC = -7531.00015340 - -exchange EXHF = 0.00000000 - -V(xc)+E(xc) XCENC = 592.53701221 - PAW double counting = 25569.98736858 -25757.03612884 - entropy T*S EENTRO = -0.00000000 - eigenvalues EBANDS = -3303.32077166 - atomic energy EATOM = 30099.62314931 - Solvation Ediel_sol = 0.00000000 - --------------------------------------------------- - free energy TOTEN = -3029.82933311 eV - - energy without entropy = -3029.82933311 energy(sigma->0) = -3029.82933311 - - --------------------------------------------------------------------------------------------------------- - - - - ---------------------------------------- Iteration 1( 4) --------------------------------------- - - - EDDAV: cpu time 18.0822: real time 18.2769 - DOS: cpu time 0.0007: real time 0.0007 - -------------------------------------------- - LOOP: cpu time 18.0829: real time 18.2775 - - eigenvalue-minimisations : 2920 - total energy-change (2. order) :-0.6293194E+01 (-0.6268147E+01) - number of electron 512.0000000 magnetization - augmentation part 512.0000000 magnetization - - Free energy of the ion-electron system (eV) - --------------------------------------------------- - alpha Z PSCENC = 1957.98898647 - Ewald energy TEWEN = -24658.60879579 - -Hartree energ DENC = -7531.00015340 - -exchange EXHF = 0.00000000 - -V(xc)+E(xc) XCENC = 592.53701221 - PAW double counting = 25569.98736858 -25757.03612884 - entropy T*S EENTRO = -0.00000000 - eigenvalues EBANDS = -3309.61396604 - atomic energy EATOM = 30099.62314931 - Solvation Ediel_sol = 0.00000000 - --------------------------------------------------- - free energy TOTEN = -3036.12252749 eV - - energy without entropy = -3036.12252749 energy(sigma->0) = -3036.12252749 - - --------------------------------------------------------------------------------------------------------- - - - - ---------------------------------------- Iteration 1( 5) --------------------------------------- - - - EDDAV: cpu time 18.7268: real time 18.9823 - DOS: cpu time 0.0003: real time 0.0003 - CHARGE: cpu time 1.6394: real time 1.6549 - MIXING: cpu time 0.0076: real time 0.0077 - -------------------------------------------- - LOOP: cpu time 20.3742: real time 20.6452 - - eigenvalue-minimisations : 2880 - total energy-change (2. order) :-0.1817553E+00 (-0.1813730E+00) - number of electron 512.0000003 magnetization - augmentation part 53.6353135 magnetization - - Broyden mixing: - rms(total) = 0.15982E+02 rms(broyden)= 0.15982E+02 - rms(prec ) = 0.17206E+02 - weight for this iteration 100.00 - - Free energy of the ion-electron system (eV) - --------------------------------------------------- - alpha Z PSCENC = 1957.98898647 - Ewald energy TEWEN = -24658.60879579 - -Hartree energ DENC = -7531.00015340 - -exchange EXHF = 0.00000000 - -V(xc)+E(xc) XCENC = 592.53701221 - PAW double counting = 25569.98736858 -25757.03612884 - entropy T*S EENTRO = -0.00000000 - eigenvalues EBANDS = -3309.79572130 - atomic energy EATOM = 30099.62314931 - Solvation Ediel_sol = 0.00000000 - --------------------------------------------------- - free energy TOTEN = -3036.30428275 eV - - energy without entropy = -3036.30428275 energy(sigma->0) = -3036.30428275 - - --------------------------------------------------------------------------------------------------------- - - - - ---------------------------------------- Iteration 1( 6) --------------------------------------- - - - POTLOK: cpu time 0.4129: real time 0.4153 - SETDIJ: cpu time 0.3641: real time 0.3666 - EDDIAG: cpu time 3.4918: real time 3.6010 - RMM-DIIS: cpu time 19.9919: real time 20.2436 - ORTHCH: cpu time 0.1053: real time 0.1059 - DOS: cpu time 0.0023: real time 0.0024 - CHARGE: cpu time 1.6690: real time 1.6847 - MIXING: cpu time 0.0075: real time 0.0076 - -------------------------------------------- - LOOP: cpu time 26.0448: real time 26.4271 - - eigenvalue-minimisations : 2524 - total energy-change (2. order) : 0.2993461E+03 (-0.5363337E+02) - number of electron 512.0000003 magnetization - augmentation part 47.9103811 magnetization - - Broyden mixing: - rms(total) = 0.87795E+01 rms(broyden)= 0.87793E+01 - rms(prec ) = 0.89533E+01 - weight for this iteration 100.00 - - eigenvalues of (default mixing * dielectric matrix) - average eigenvalue GAMMA= 1.7694 - 1.7694 - - Free energy of the ion-electron system (eV) - --------------------------------------------------- - alpha Z PSCENC = 1957.98898647 - Ewald energy TEWEN = -24658.60879579 - -Hartree energ DENC = -8876.69621287 - -exchange EXHF = 0.00000000 - -V(xc)+E(xc) XCENC = 785.30561815 - PAW double counting = 36903.66483446 -37109.60683237 - entropy T*S EENTRO = -0.00000000 - eigenvalues EBANDS = -1838.62889962 - atomic energy EATOM = 30099.62314931 - Solvation Ediel_sol = 0.00000000 - --------------------------------------------------- - free energy TOTEN = -2736.95815226 eV - - energy without entropy = -2736.95815226 energy(sigma->0) = -2736.95815226 - - --------------------------------------------------------------------------------------------------------- - - - - ---------------------------------------- Iteration 1( 7) --------------------------------------- - - - POTLOK: cpu time 0.4136: real time 0.4228 - SETDIJ: cpu time 0.4723: real time 0.4781 - EDDIAG: cpu time 3.5795: real time 3.6128 - RMM-DIIS: cpu time 21.2446: real time 21.7260 - ORTHCH: cpu time 0.1018: real time 0.1024 - DOS: cpu time 0.0003: real time 0.0003 - CHARGE: cpu time 1.9776: real time 1.9929 - MIXING: cpu time 0.0200: real time 0.0200 - -------------------------------------------- - LOOP: cpu time 27.8097: real time 28.3554 - - eigenvalue-minimisations : 2779 - total energy-change (2. order) :-0.2410960E+02 (-0.2522132E+02) - number of electron 512.0000003 magnetization - augmentation part 44.3787508 magnetization - - Broyden mixing: - rms(total) = 0.27815E+01 rms(broyden)= 0.27805E+01 - rms(prec ) = 0.31106E+01 - weight for this iteration 100.00 - - eigenvalues of (default mixing * dielectric matrix) - average eigenvalue GAMMA= 1.6819 - 1.6819 1.6819 - - Free energy of the ion-electron system (eV) - --------------------------------------------------- - alpha Z PSCENC = 1957.98898647 - Ewald energy TEWEN = -24658.60879579 - -Hartree energ DENC = -9299.81486644 - -exchange EXHF = 0.00000000 - -V(xc)+E(xc) XCENC = 805.62114829 - PAW double counting = 52439.48661199 -52654.65553690 - entropy T*S EENTRO = -0.00000000 - eigenvalues EBANDS = -1450.70844905 - atomic energy EATOM = 30099.62314931 - Solvation Ediel_sol = 0.00000000 - --------------------------------------------------- - free energy TOTEN = -2761.06775212 eV - - energy without entropy = -2761.06775212 energy(sigma->0) = -2761.06775212 - - --------------------------------------------------------------------------------------------------------- - - - - ---------------------------------------- Iteration 1( 8) --------------------------------------- - - - POTLOK: cpu time 0.4420: real time 0.4437 - SETDIJ: cpu time 0.5468: real time 0.5491 - EDDIAG: cpu time 3.3217: real time 3.4699 - RMM-DIIS: cpu time 20.6911: real time 21.0342 - ORTHCH: cpu time 0.0972: real time 0.0977 - DOS: cpu time 0.0097: real time 0.0097 - CHARGE: cpu time 1.6480: real time 1.6628 - MIXING: cpu time 0.0069: real time 0.0070 - -------------------------------------------- - LOOP: cpu time 26.7635: real time 27.2742 - - eigenvalue-minimisations : 2665 - total energy-change (2. order) : 0.2594627E+01 (-0.1101197E+02) - number of electron 512.0000003 magnetization - augmentation part 47.2152993 magnetization - - Broyden mixing: - rms(total) = 0.14534E+01 rms(broyden)= 0.14529E+01 - rms(prec ) = 0.17016E+01 - weight for this iteration 100.00 - - eigenvalues of (default mixing * dielectric matrix) - average eigenvalue GAMMA= 1.4776 - 2.2244 1.1042 1.1042 - - Free energy of the ion-electron system (eV) - --------------------------------------------------- - alpha Z PSCENC = 1957.98898647 - Ewald energy TEWEN = -24658.60879579 - -Hartree energ DENC = -8753.12206963 - -exchange EXHF = 0.00000000 - -V(xc)+E(xc) XCENC = 755.76821866 - PAW double counting = 55916.14279821 -56128.69594047 - entropy T*S EENTRO = -0.00000000 - eigenvalues EBANDS = -1947.56947223 - atomic energy EATOM = 30099.62314931 - Solvation Ediel_sol = 0.00000000 - --------------------------------------------------- - free energy TOTEN = -2758.47312547 eV - - energy without entropy = -2758.47312547 energy(sigma->0) = -2758.47312547 - - --------------------------------------------------------------------------------------------------------- - - - - ---------------------------------------- Iteration 1( 9) --------------------------------------- - - - POTLOK: cpu time 0.4111: real time 0.4133 - SETDIJ: cpu time 0.3678: real time 0.3701 - EDDIAG: cpu time 3.7550: real time 3.7872 - RMM-DIIS: cpu time 22.8971: real time 23.1091 - ORTHCH: cpu time 0.1020: real time 0.1027 - DOS: cpu time 0.0029: real time 0.0029 - CHARGE: cpu time 1.6500: real time 1.6653 - MIXING: cpu time 0.0073: real time 0.0074 - -------------------------------------------- - LOOP: cpu time 29.1933: real time 29.4581 - - eigenvalue-minimisations : 2880 - total energy-change (2. order) : 0.3778792E+01 (-0.9359869E+00) - number of electron 512.0000003 magnetization - augmentation part 46.6822578 magnetization - - Broyden mixing: - rms(total) = 0.35797E+00 rms(broyden)= 0.35797E+00 - rms(prec ) = 0.43586E+00 - weight for this iteration 100.00 - - eigenvalues of (default mixing * dielectric matrix) - average eigenvalue GAMMA= 1.4966 - 2.4249 1.2922 1.2922 0.9771 - - Free energy of the ion-electron system (eV) - --------------------------------------------------- - alpha Z PSCENC = 1957.98898647 - Ewald energy TEWEN = -24658.60879579 - -Hartree energ DENC = -8971.69393476 - -exchange EXHF = 0.00000000 - -V(xc)+E(xc) XCENC = 791.26633003 - PAW double counting = 59472.85873661 -59689.44062763 - entropy T*S EENTRO = -0.00000000 - eigenvalues EBANDS = -1756.68817805 - atomic energy EATOM = 30099.62314931 - Solvation Ediel_sol = 0.00000000 - --------------------------------------------------- - free energy TOTEN = -2754.69433381 eV - - energy without entropy = -2754.69433381 energy(sigma->0) = -2754.69433381 - - --------------------------------------------------------------------------------------------------------- - - - - ---------------------------------------- Iteration 1( 10) --------------------------------------- - - - POTLOK: cpu time 0.4304: real time 0.4393 - SETDIJ: cpu time 0.3496: real time 0.3520 - EDDIAG: cpu time 3.2671: real time 3.2964 - RMM-DIIS: cpu time 21.4600: real time 21.6519 - ORTHCH: cpu time 0.0957: real time 0.0963 - DOS: cpu time 0.0015: real time 0.0015 - CHARGE: cpu time 1.6703: real time 1.6864 - MIXING: cpu time 0.0072: real time 0.0073 - -------------------------------------------- - LOOP: cpu time 27.2818: real time 27.5311 - - eigenvalue-minimisations : 2882 - total energy-change (2. order) :-0.4662152E+00 (-0.1002503E+01) - number of electron 512.0000003 magnetization - augmentation part 45.8662080 magnetization - - Broyden mixing: - rms(total) = 0.43037E+00 rms(broyden)= 0.43013E+00 - rms(prec ) = 0.52627E+00 - weight for this iteration 100.00 - - eigenvalues of (default mixing * dielectric matrix) - average eigenvalue GAMMA= 1.5340 - 2.5894 2.0135 1.0470 1.0101 1.0101 - - Free energy of the ion-electron system (eV) - --------------------------------------------------- - alpha Z PSCENC = 1957.98898647 - Ewald energy TEWEN = -24658.60879579 - -Hartree energ DENC = -9077.55941737 - -exchange EXHF = 0.00000000 - -V(xc)+E(xc) XCENC = 796.41412229 - PAW double counting = 60388.60794660 -60607.43049159 - entropy T*S EENTRO = -0.00000000 - eigenvalues EBANDS = -1654.19604894 - atomic energy EATOM = 30099.62314931 - Solvation Ediel_sol = 0.00000000 - --------------------------------------------------- - free energy TOTEN = -2755.16054902 eV - - energy without entropy = -2755.16054902 energy(sigma->0) = -2755.16054902 - - --------------------------------------------------------------------------------------------------------- - - - - ---------------------------------------- Iteration 1( 11) --------------------------------------- - - - POTLOK: cpu time 0.4125: real time 0.4149 - SETDIJ: cpu time 0.3678: real time 0.3704 - EDDIAG: cpu time 3.2824: real time 3.3121 - RMM-DIIS: cpu time 21.3548: real time 21.5462 - ORTHCH: cpu time 0.0932: real time 0.0938 - DOS: cpu time 0.0024: real time 0.0024 - CHARGE: cpu time 1.6870: real time 1.7035 - MIXING: cpu time 0.0072: real time 0.0072 - -------------------------------------------- - LOOP: cpu time 27.2072: real time 27.4505 - - eigenvalue-minimisations : 2873 - total energy-change (2. order) : 0.3915619E+00 (-0.1871883E+00) - number of electron 512.0000003 magnetization - augmentation part 46.1348344 magnetization - - Broyden mixing: - rms(total) = 0.11006E+00 rms(broyden)= 0.11004E+00 - rms(prec ) = 0.12157E+00 - weight for this iteration 100.00 - - eigenvalues of (default mixing * dielectric matrix) - average eigenvalue GAMMA= 1.5752 - 2.6438 2.6438 1.0902 1.0902 0.9917 0.9917 - - Free energy of the ion-electron system (eV) - --------------------------------------------------- - alpha Z PSCENC = 1957.98898647 - Ewald energy TEWEN = -24658.60879579 - -Hartree energ DENC = -9003.53562296 - -exchange EXHF = 0.00000000 - -V(xc)+E(xc) XCENC = 787.07763638 - PAW double counting = 60270.42874737 -60489.14104255 - entropy T*S EENTRO = -0.00000000 - eigenvalues EBANDS = -1718.60204530 - atomic energy EATOM = 30099.62314931 - Solvation Ediel_sol = 0.00000000 - --------------------------------------------------- - free energy TOTEN = -2754.76898708 eV - - energy without entropy = -2754.76898708 energy(sigma->0) = -2754.76898708 - - --------------------------------------------------------------------------------------------------------- - - - - ---------------------------------------- Iteration 1( 12) --------------------------------------- - - - POTLOK: cpu time 0.4070: real time 0.4094 - SETDIJ: cpu time 0.3646: real time 0.3678 - EDDIAG: cpu time 3.2880: real time 3.3175 - RMM-DIIS: cpu time 21.9511: real time 22.1466 - ORTHCH: cpu time 0.0951: real time 0.0957 - DOS: cpu time 0.0011: real time 0.0011 - CHARGE: cpu time 1.6583: real time 1.6741 - MIXING: cpu time 0.0074: real time 0.0074 - -------------------------------------------- - LOOP: cpu time 27.7726: real time 28.0197 - - eigenvalue-minimisations : 2978 - total energy-change (2. order) :-0.1605386E-01 (-0.3973957E-01) - number of electron 512.0000003 magnetization - augmentation part 46.2267933 magnetization - - Broyden mixing: - rms(total) = 0.58466E-01 rms(broyden)= 0.58417E-01 - rms(prec ) = 0.63044E-01 - weight for this iteration 100.00 - - eigenvalues of (default mixing * dielectric matrix) - average eigenvalue GAMMA= 1.7152 - 3.6906 2.4738 1.9294 0.9698 0.9698 1.0249 0.9479 - - Free energy of the ion-electron system (eV) - --------------------------------------------------- - alpha Z PSCENC = 1957.98898647 - Ewald energy TEWEN = -24658.60879579 - -Hartree energ DENC = -8993.81539252 - -exchange EXHF = 0.00000000 - -V(xc)+E(xc) XCENC = 787.95458027 - PAW double counting = 60151.73540925 -60370.53309132 - entropy T*S EENTRO = -0.00000000 - eigenvalues EBANDS = -1729.12988661 - atomic energy EATOM = 30099.62314931 - Solvation Ediel_sol = 0.00000000 - --------------------------------------------------- - free energy TOTEN = -2754.78504094 eV - - energy without entropy = -2754.78504094 energy(sigma->0) = -2754.78504094 - - --------------------------------------------------------------------------------------------------------- - - - - ---------------------------------------- Iteration 1( 13) --------------------------------------- - - - POTLOK: cpu time 0.4096: real time 0.4173 - SETDIJ: cpu time 0.3617: real time 0.3645 - EDDIAG: cpu time 3.2952: real time 3.3251 - RMM-DIIS: cpu time 22.9216: real time 23.1245 - ORTHCH: cpu time 0.0942: real time 0.0949 - DOS: cpu time 0.0007: real time 0.0007 - CHARGE: cpu time 1.6508: real time 1.6661 - MIXING: cpu time 0.0071: real time 0.0071 - -------------------------------------------- - LOOP: cpu time 28.7408: real time 29.0001 - - eigenvalue-minimisations : 3148 - total energy-change (2. order) :-0.4192773E-02 (-0.7070642E-02) - number of electron 512.0000003 magnetization - augmentation part 46.2108044 magnetization - - Broyden mixing: - rms(total) = 0.38849E-01 rms(broyden)= 0.38847E-01 - rms(prec ) = 0.40415E-01 - weight for this iteration 100.00 - - eigenvalues of (default mixing * dielectric matrix) - average eigenvalue GAMMA= 1.7132 - 4.2000 2.4647 2.1285 0.9623 0.9623 1.1174 0.9352 0.9352 - - Free energy of the ion-electron system (eV) - --------------------------------------------------- - alpha Z PSCENC = 1957.98898647 - Ewald energy TEWEN = -24658.60879579 - -Hartree energ DENC = -8999.55941007 - -exchange EXHF = 0.00000000 - -V(xc)+E(xc) XCENC = 788.86731291 - PAW double counting = 60288.33779569 -60507.11455904 - entropy T*S EENTRO = -0.00000000 - eigenvalues EBANDS = -1724.32371320 - atomic energy EATOM = 30099.62314931 - Solvation Ediel_sol = 0.00000000 - --------------------------------------------------- - free energy TOTEN = -2754.78923371 eV - - energy without entropy = -2754.78923371 energy(sigma->0) = -2754.78923371 - - --------------------------------------------------------------------------------------------------------- - - - - ---------------------------------------- Iteration 1( 14) --------------------------------------- - - - POTLOK: cpu time 0.4065: real time 0.4089 - SETDIJ: cpu time 0.3648: real time 0.3672 - EDDIAG: cpu time 3.2810: real time 3.3105 - RMM-DIIS: cpu time 21.8567: real time 22.0499 - ORTHCH: cpu time 0.0923: real time 0.0929 - DOS: cpu time 0.0014: real time 0.0014 - CHARGE: cpu time 1.6687: real time 1.6845 - MIXING: cpu time 0.0077: real time 0.0078 - -------------------------------------------- - LOOP: cpu time 27.6791: real time 27.9233 - - eigenvalue-minimisations : 2963 - total energy-change (2. order) :-0.2781083E-02 (-0.2056421E-02) - number of electron 512.0000003 magnetization - augmentation part 46.2313039 magnetization - - Broyden mixing: - rms(total) = 0.44803E-01 rms(broyden)= 0.44800E-01 - rms(prec ) = 0.51813E-01 - weight for this iteration 100.00 - - eigenvalues of (default mixing * dielectric matrix) - average eigenvalue GAMMA= 1.7617 - 4.8036 2.4469 2.4469 0.9910 0.9910 1.3290 1.0029 1.0029 0.8412 - - Free energy of the ion-electron system (eV) - --------------------------------------------------- - alpha Z PSCENC = 1957.98898647 - Ewald energy TEWEN = -24658.60879579 - -Hartree energ DENC = -8996.40756886 - -exchange EXHF = 0.00000000 - -V(xc)+E(xc) XCENC = 788.59399241 - PAW double counting = 60371.67343143 -60590.38198558 - entropy T*S EENTRO = -0.00000000 - eigenvalues EBANDS = -1727.27322419 - atomic energy EATOM = 30099.62314931 - Solvation Ediel_sol = 0.00000000 - --------------------------------------------------- - free energy TOTEN = -2754.79201480 eV - - energy without entropy = -2754.79201480 energy(sigma->0) = -2754.79201480 - - --------------------------------------------------------------------------------------------------------- - - - - ---------------------------------------- Iteration 1( 15) --------------------------------------- - - - POTLOK: cpu time 0.4071: real time 0.4095 - SETDIJ: cpu time 1.2220: real time 1.3294 - EDDIAG: cpu time 3.2805: real time 3.3099 - RMM-DIIS: cpu time 21.5834: real time 21.9257 - ORTHCH: cpu time 0.0934: real time 0.0940 - DOS: cpu time 0.0009: real time 0.0009 - CHARGE: cpu time 1.6889: real time 1.7052 - MIXING: cpu time 0.0079: real time 0.0079 - -------------------------------------------- - LOOP: cpu time 28.2841: real time 28.7825 - - eigenvalue-minimisations : 2898 - total energy-change (2. order) : 0.1845918E-02 (-0.5654369E-03) - number of electron 512.0000003 magnetization - augmentation part 46.2175005 magnetization - - Broyden mixing: - rms(total) = 0.18278E-01 rms(broyden)= 0.18277E-01 - rms(prec ) = 0.22821E-01 - weight for this iteration 100.00 - - eigenvalues of (default mixing * dielectric matrix) - average eigenvalue GAMMA= 1.6869 - 4.0046 2.7371 2.0671 2.0671 0.9769 0.9769 1.1320 0.8935 1.0070 1.0070 - - Free energy of the ion-electron system (eV) - --------------------------------------------------- - alpha Z PSCENC = 1957.98898647 - Ewald energy TEWEN = -24658.60879579 - -Hartree energ DENC = -8999.66193305 - -exchange EXHF = 0.00000000 - -V(xc)+E(xc) XCENC = 788.99444709 - PAW double counting = 60483.99269094 -60702.68233599 - entropy T*S EENTRO = -0.00000000 - eigenvalues EBANDS = -1724.43637786 - atomic energy EATOM = 30099.62314931 - Solvation Ediel_sol = 0.00000000 - --------------------------------------------------- - free energy TOTEN = -2754.79016888 eV - - energy without entropy = -2754.79016888 energy(sigma->0) = -2754.79016888 - - --------------------------------------------------------------------------------------------------------- - - - - ---------------------------------------- Iteration 1( 16) --------------------------------------- - - - POTLOK: cpu time 0.4125: real time 0.4213 - SETDIJ: cpu time 0.3654: real time 0.3679 - EDDIAG: cpu time 3.2880: real time 3.3173 - RMM-DIIS: cpu time 21.9163: real time 22.5605 - ORTHCH: cpu time 0.1657: real time 0.1671 - DOS: cpu time 0.0397: real time 0.0400 - CHARGE: cpu time 1.6412: real time 1.6568 - MIXING: cpu time 0.0077: real time 0.0078 - -------------------------------------------- - LOOP: cpu time 27.8365: real time 28.5387 - - eigenvalue-minimisations : 2944 - total energy-change (2. order) : 0.5229538E-04 (-0.6830801E-03) - number of electron 512.0000003 magnetization - augmentation part 46.1967397 magnetization - - Broyden mixing: - rms(total) = 0.97296E-02 rms(broyden)= 0.97227E-02 - rms(prec ) = 0.97763E-02 - weight for this iteration 100.00 - - eigenvalues of (default mixing * dielectric matrix) - average eigenvalue GAMMA= 1.5914 - 4.3404 2.7421 2.0881 2.0881 0.9771 0.9771 1.1580 1.0058 1.0058 0.8910 - 0.2323 - - Free energy of the ion-electron system (eV) - --------------------------------------------------- - alpha Z PSCENC = 1957.98898647 - Ewald energy TEWEN = -24658.60879579 - -Hartree energ DENC = -9001.90871915 - -exchange EXHF = 0.00000000 - -V(xc)+E(xc) XCENC = 789.05499636 - PAW double counting = 60466.86792880 -60685.58886857 - entropy T*S EENTRO = -0.00000000 - eigenvalues EBANDS = -1722.21879401 - atomic energy EATOM = 30099.62314931 - Solvation Ediel_sol = 0.00000000 - --------------------------------------------------- - free energy TOTEN = -2754.79011658 eV - - energy without entropy = -2754.79011658 energy(sigma->0) = -2754.79011658 - - --------------------------------------------------------------------------------------------------------- - - - - ---------------------------------------- Iteration 1( 17) --------------------------------------- - - - POTLOK: cpu time 0.4063: real time 0.4086 - SETDIJ: cpu time 0.3637: real time 0.3661 - EDDIAG: cpu time 3.4369: real time 3.4899 - RMM-DIIS: cpu time 22.5770: real time 22.8678 - ORTHCH: cpu time 0.0906: real time 0.0912 - DOS: cpu time 0.0015: real time 0.0015 - 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entropy T*S EENTRO = -0.00000000 - eigenvalues EBANDS = -1721.92343250 - atomic energy EATOM = 30099.62314931 - Solvation Ediel_sol = 0.00000000 - --------------------------------------------------- - free energy TOTEN = -2754.79026403 eV - - energy without entropy = -2754.79026403 energy(sigma->0) = -2754.79026403 - - --------------------------------------------------------------------------------------------------------- - - - - ---------------------------------------- Iteration 1( 18) --------------------------------------- - - - POTLOK: cpu time 0.4117: real time 0.4141 - SETDIJ: cpu time 0.3649: real time 0.3674 - EDDIAG: cpu time 3.5340: real time 3.6192 - RMM-DIIS: cpu time 16.1709: real time 16.3909 - ORTHCH: cpu time 0.0912: real time 0.0918 - DOS: cpu time 0.0022: real time 0.0022 - -------------------------------------------- - LOOP: cpu time 20.5748: real time 20.8856 - - eigenvalue-minimisations : 1856 - total energy-change (2. order) :-0.2179565E-04 (-0.1272347E-04) - number of electron 512.0000003 magnetization - 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0.522E+02 -.680E+01 0.441E+02 -.556E+02 -.564E+01 -.471E+02 -.182E+01 0.792E+01 0.264E+01 -.262E-03 -.512E-02 0.453E-02 - -.232E+02 0.919E+01 0.229E+02 0.173E+02 -.206E+01 -.204E+02 0.801E+01 -.779E+01 -.398E+01 -.716E-02 0.353E-02 0.544E-03 - 0.185E+02 -.467E+02 0.447E+02 -.181E+02 0.490E+02 -.521E+02 0.213E+00 -.643E+00 0.697E+01 -.231E-03 0.125E-02 -.615E-02 - 0.447E+02 -.124E+02 0.164E+02 -.476E+02 0.776E+01 -.137E+02 0.829E+00 0.525E+01 -.405E+01 -.646E-03 -.298E-02 -.819E-03 - 0.366E+01 0.367E+02 -.140E+02 -.208E+01 -.269E+02 0.382E+01 -.114E+01 -.123E+02 0.123E+02 -.782E-04 0.133E-02 -.967E-02 - 0.361E+02 0.419E+02 -.228E+02 -.397E+02 -.389E+02 0.221E+02 0.237E+01 -.550E+01 0.266E+01 -.411E-02 0.537E-02 0.878E-03 - 0.326E+02 0.797E+01 -.122E+02 -.386E+02 -.122E+02 0.173E+02 0.544E+01 0.325E+01 -.518E+01 0.365E-02 0.449E-02 0.705E-02 - 0.767E+01 0.343E+02 0.402E+02 -.100E+02 -.351E+02 -.487E+02 0.203E+01 0.343E+00 0.725E+01 -.216E-02 -.139E-02 0.203E-02 - 0.257E+02 -.108E+02 0.215E+02 -.219E+02 0.815E+01 -.261E+02 -.354E+01 0.393E+01 0.501E+01 0.316E-02 -.144E-02 -.156E-02 - -.112E+02 0.316E+02 -.387E+02 0.182E+02 -.323E+02 0.385E+02 -.924E+01 -.398E+00 0.224E+01 0.892E-02 -.577E-02 0.379E-02 - 0.120E+02 0.240E+02 0.356E+02 -.251E+02 -.272E+02 -.380E+02 0.140E+02 0.330E+01 0.163E+01 -.552E-02 0.423E-02 -.400E-02 - -.378E+02 0.140E+01 0.360E+02 0.349E+02 -.111E+02 -.455E+02 0.596E+00 0.425E+01 0.389E+01 -.656E-02 -.865E-02 -.799E-02 - -.251E+02 0.965E+01 0.454E+02 0.279E+02 -.577E+01 -.438E+02 0.128E+00 -.282E+01 -.245E+01 0.156E-02 0.538E-02 0.409E-02 - ----------------------------------------------------------------------------------------------- - 0.105E+02 0.443E+02 -.545E+02 0.448E-12 0.199E-12 0.142E-13 -.104E+02 -.443E+02 0.545E+02 0.901E-02 0.162E-01 -.925E-02 - - - POSITION TOTAL-FORCE (eV/Angst) - ----------------------------------------------------------------------------------- - 10.28507 7.66298 -8.95306 -1.148454 -0.334364 1.168775 - 9.36207 2.48369 -3.86991 -1.426211 1.681855 1.979050 - 8.95513 0.34920 -1.25634 1.655400 7.199611 4.420496 - 10.20512 2.63851 -9.09764 -1.758076 1.268364 0.525330 - 9.62095 0.24020 -6.50767 0.170638 2.751192 0.703281 - 8.98420 5.84615 -1.31153 -0.295137 -4.380701 2.783531 - 9.64697 5.60546 -6.31268 2.721147 -1.599442 -0.203352 - 4.32961 2.42018 -3.75989 -2.966186 0.327963 0.466216 - 1.95564 5.00777 -4.25775 2.956454 1.826496 -1.225826 - 1.57187 3.15380 -1.55742 1.018282 -1.776104 0.254518 - 5.30325 2.33070 -8.69678 -2.545516 6.515696 -4.339630 - 2.93042 5.02881 -9.42731 -0.009084 2.866319 0.897861 - 5.00378 7.59896 -9.00388 -0.094156 -1.536056 -1.900333 - 2.55754 8.26129 -6.96359 -1.535148 -4.274159 5.313560 - 4.68258 5.38922 -6.29672 -4.427706 0.680767 -1.314973 - 4.46428 7.70032 -3.66968 -4.902288 0.301765 -3.104019 - 2.05045 0.29147 -4.37214 -0.810929 -3.201018 0.546252 - 1.66358 8.29096 -1.88067 2.448653 -1.033765 0.650919 - 4.05069 5.52808 -1.27697 -3.448021 0.644054 2.677488 - 2.85519 0.17172 -9.40122 0.409165 -1.516506 -2.964748 - 2.34215 2.86872 -6.93975 1.050408 1.894601 2.623597 - 4.70363 0.32257 -6.29341 3.036083 -1.810601 -1.147419 - 3.79328 0.39246 -1.15328 0.207516 -0.314302 -0.968934 - 7.84471 0.01629 -9.31187 2.534099 -0.206170 -0.113470 - 7.08741 10.21060 -4.28840 0.611849 1.860489 2.561894 - 8.10092 5.18286 -9.46497 -0.080527 -1.937415 1.251815 - 7.64524 3.18542 -6.72396 2.237980 -4.870695 -2.436760 - 6.82386 4.88817 -4.08093 8.046220 5.237681 -0.383513 - 6.59438 2.87496 -1.76941 2.061175 -1.460177 5.244593 - 7.46458 7.95800 -6.83699 -0.375635 -0.015617 -0.713874 - 9.12264 7.70070 -3.71107 2.013594 1.301158 -3.278726 - 6.67623 8.19421 -1.30425 -0.817728 1.250442 -2.405447 - 9.96037 7.43403 -2.00664 1.146336 -0.715813 1.162292 - 10.89195 6.82454 -7.02436 0.401897 1.660084 -1.934650 - 11.46891 6.48297 -9.89103 1.396955 -0.787824 -0.221786 - 11.24310 1.44554 -7.01838 -2.080156 1.994794 -3.164180 - 7.91499 4.01382 -2.55085 3.849798 3.382723 -0.228066 - 9.78314 2.17917 -1.84235 1.044841 -0.458910 -0.863851 - 10.50764 1.19730 -4.71521 1.199544 -0.508534 1.542860 - 9.95831 4.32472 -10.21641 -0.962665 -0.743955 -0.361730 - 9.20987 3.99334 -7.80425 -1.091315 1.712488 1.503494 - 11.47984 1.34110 -9.82489 1.382284 -1.282256 0.992986 - 10.54301 6.07737 -4.57133 -3.452257 1.990566 1.619982 - 3.56621 3.74601 -5.18290 0.557590 1.545973 0.639696 - 3.43227 4.08009 -2.38384 -0.980815 -1.786188 -1.640890 - 5.08696 1.64973 -1.88954 -1.186075 2.236020 -1.806291 - 0.64140 4.80756 -1.12127 -1.245218 -0.210652 0.258035 - 4.45318 4.19072 -10.16837 0.783554 -2.365690 -1.784572 - 3.96168 3.98936 -7.73228 1.692546 -0.082641 0.830563 - 6.03479 1.88651 -7.11001 -0.774095 -2.342033 4.398962 - 6.37314 1.14718 -9.64422 1.101842 -2.435210 -0.942964 - 5.25967 0.80573 -4.36798 2.794813 -0.670147 0.076192 - 3.38491 6.34521 -7.88626 1.931892 2.457886 -1.133692 - 2.80840 6.59917 -5.42625 2.708742 -1.550689 -1.164881 - 4.19244 9.22005 -7.62594 -0.701300 -1.520804 -3.332251 - 5.80744 6.89152 -6.94671 -0.569079 0.146573 -0.974126 - 1.21773 9.67889 -6.25104 3.791126 -3.388710 1.168796 - 6.28895 6.03728 -9.69909 0.528587 1.176989 0.697101 - 3.79890 8.78553 -5.26682 -0.576300 3.844482 -1.097034 - 2.64826 6.53044 -2.94819 0.620218 0.910612 1.929086 - 2.35718 6.69664 -0.29290 0.200168 0.158253 0.428714 - 3.46704 9.36603 -2.62613 -1.770264 -0.892060 -0.570487 - 4.88264 7.17219 -1.90155 2.596680 0.139057 3.778733 - 0.79108 10.15204 -1.19634 -1.341095 -2.347464 -0.062667 - 1.19130 8.83284 -3.73952 -1.027222 0.532655 0.974711 - 5.32432 6.00321 -4.25946 -1.707780 0.371168 -1.274151 - 2.67643 9.05146 -0.06468 0.221631 1.276246 1.381319 - 1.71914 8.77591 -8.71264 2.611167 2.436693 -0.330554 - 3.59427 1.33652 -8.10605 0.526366 0.716774 1.960487 - 3.48233 1.40850 -5.48783 -5.193658 1.559103 1.029093 - 1.09955 4.06425 -5.95613 -0.185020 1.033379 0.211446 - 2.69391 1.64273 -2.76200 -0.422300 -1.489507 -1.993646 - 2.54840 1.55420 -0.26636 -3.096437 1.578668 1.820586 - 0.95217 3.57199 -3.37601 -0.741034 -0.463646 -0.361495 - 1.61651 3.85892 -8.47007 0.084205 -1.215327 -1.498893 - 9.69217 9.33671 -10.11695 -0.994334 -0.563502 -0.634703 - 8.96499 8.99370 -7.59125 0.631013 1.670655 -1.489280 - 8.17308 1.54406 -5.53215 -0.178901 -0.422027 2.000130 - 6.54801 4.51430 -6.06184 -3.090214 2.007020 0.604738 - 8.68142 3.99363 -4.99581 -0.558919 1.086944 -1.120859 - 7.53540 1.58574 -2.92412 2.561091 -3.298736 -1.668064 - 7.34607 1.74206 -0.13357 -0.353996 -0.818327 -0.778016 - 5.88156 4.57188 -0.93840 -1.930050 1.027267 -0.763554 - 6.00360 3.46683 -3.60445 -5.138663 -4.532804 -0.304035 - 8.46938 1.38865 -7.91782 2.112478 -0.648619 -1.469419 - 6.89780 3.58017 -8.63054 0.603884 1.602594 -0.379500 - 7.52333 6.75041 -0.13749 -2.066665 0.601212 -1.316102 - 5.72918 9.89805 -0.99665 0.437477 -2.465835 2.128643 - 8.60359 6.72710 -8.17726 -1.151311 -2.552679 1.932359 - 8.23331 6.82930 -5.37148 -0.583161 -1.016094 -0.050822 - 6.52247 9.56062 -6.00567 -0.328515 -0.479161 -1.252188 - 6.76468 8.54810 -8.87998 0.254294 1.293974 0.466398 - 8.95231 9.31517 -5.01038 -2.229924 -1.136084 2.044554 - 7.63548 6.67768 -2.70590 0.866408 0.073193 -0.746594 - 8.26969 9.34077 -2.22570 -2.379190 -5.448803 -5.600949 - 6.03421 8.72427 -3.32013 2.910649 1.075322 -0.833165 - ----------------------------------------------------------------------------------- - total drift: 0.021130 0.025813 -0.022256 - - --------------------------------------------------------------------------------------------------------- - - - - FREE ENERGIE OF THE ION-ELECTRON SYSTEM (eV) - --------------------------------------------------- - free energy TOTEN = -2754.79028583 eV - - energy without entropy= -2754.79028583 energy(sigma->0) = -2754.79028583 - - - --------------------------------------------------------------------------------------------------------- - - - POTLOK: cpu time 0.7662: real time 0.7708 - - --------------------------------------------------------------------------------------------------------- - - - LOOP+: cpu time 483.4503: real time 490.5531 - 4ORBIT: cpu time 0.0000: real time 0.0000 - - total amount of memory used by VASP MPI-rank0 162797. kBytes -======================================================================= - - base : 30000. kBytes - nonlr-proj: 30246. kBytes - fftplans : 41293. kBytes - grid : 25778. kBytes - one-center: 373. kBytes - wavefun : 35107. kBytes - - - - General timing and accounting informations for this job: - ======================================================== - - Total CPU time used (sec): 488.825 - User time (sec): 468.378 - System time (sec): 20.448 - Elapsed time (sec): 496.878 - - Maximum memory used (kb): 410032. - Average memory used (kb): N/A - - Minor page faults: 596382 - Major page faults: 4206 - Voluntary context switches: 7073 diff --git a/mace-bench/3rdparty/SevenNet/example_inputs/data/label_1/OUTCAR_5 b/mace-bench/3rdparty/SevenNet/example_inputs/data/label_1/OUTCAR_5 deleted file mode 100644 index f0898bf95313323a3f84c9ea3d746bea55e58769..0000000000000000000000000000000000000000 --- a/mace-bench/3rdparty/SevenNet/example_inputs/data/label_1/OUTCAR_5 +++ /dev/null @@ -1,2028 +0,0 @@ - vasp.5.4.4.18Apr17-6-g9f103f2a35 (build Sep 11 2017 17:27:03) complex - - executed on GRP7IFC17NORMAL date 2022.08.24 18:31:00 - running on 32 total cores - distrk: each k-point on 16 cores, 2 groups - distr: one band on NCORES_PER_BAND= 8 cores, 2 groups - - --------------------------------------------------------------------------------------------------------- - - - INCAR: - POTCAR: PAW_PBE Hf 20Jan2003 - POTCAR: PAW_PBE O 08Apr2002 - - ----------------------------------------------------------------------------- -| | -| W W AA RRRRR N N II N N GGGG !!! | -| W W A A R R NN N II NN N G G !!! | -| W W A A R R N N N II N N N G !!! | -| W WW W AAAAAA RRRRR N N N II N N N G GGG ! | -| WW WW A A R R N NN II N NN G G | -| W W A A R R N N II N N GGGG !!! | -| | -| You have enabled k-point parallelism (KPAR>1). | -| This developmental code was originally written by Paul Kent at ORNL, | -| and carefully double checked in Vienna. | -| GW as well as linear response parallelism added by Martijn Marsman | -| and Georg Kresse. | -| Carefully verify results versus KPAR=1. | -| Report problems to Paul Kent and Vienna. | -| | - ----------------------------------------------------------------------------- - - POTCAR: PAW_PBE Hf 20Jan2003 - SHA256 = 0bb2207f9a10894133f750b65504b92b8afef976ae770762e0497daaaad8168a Hf - COPYR = (c) Copyright 20Jan2003 Georg Kresse - COPYR = This file is part of the software VASP. Any use, copying, and all ot - COPYR = If you do not have a valid VASP license, you may not use, copy or di - VRHFIN =Hf: 6s5d - LEXCH = PE - EATOM = 75.9011 eV, 5.5786 Ry - - TITEL = PAW_PBE Hf 20Jan2003 - LULTRA = F use ultrasoft PP ? - IUNSCR = 1 unscreen: 0-lin 1-nonlin 2-no - RPACOR = 2.500 partial core radius - POMASS = 178.490; ZVAL = 4.000 mass and valenz - RCORE = 3.000 outmost cutoff radius - RWIGS = 3.050; RWIGS = 1.614 wigner-seitz radius (au A) - ENMAX = 220.334; ENMIN = 165.250 eV - RCLOC = 2.212 cutoff for local pot - LCOR = T correct aug charges - LPAW = T paw PP - EAUG = 335.116 - DEXC = 0.000 - RMAX = 3.077 core radius for proj-oper - RAUG = 1.300 factor for augmentation sphere - RDEP = 3.047 radius for radial grids - RDEPT = 2.344 core radius for aug-charge - - Atomic configuration - 16 entries - n l j E occ. - 1 0 0.50 -65259.4397 2.0000 - 2 0 0.50 -11157.9882 2.0000 - 2 1 1.50 -9795.2113 6.0000 - 3 0 0.50 -2541.4058 2.0000 - 3 1 1.50 -2134.4770 6.0000 - 3 2 2.50 -1653.5418 10.0000 - 4 0 0.50 -510.9575 2.0000 - 4 1 1.50 -377.5023 6.0000 - 4 2 2.50 -205.2085 10.0000 - 4 3 3.50 -15.4905 14.0000 - 5 0 0.50 -65.6020 2.0000 - 5 1 1.50 -34.2798 6.0000 - 5 2 2.50 -1.9877 3.0000 - 6 0 0.50 -4.7357 1.0000 - 6 1 1.50 -1.3606 0.0000 - 5 3 2.50 -1.3606 0.0000 - Description - l E TYP RCUT TYP RCUT - 2 -1.9876627 23 2.500 - 2 0.0744703 23 2.500 - 0 -4.7356889 23 2.600 - 0 3.2364747 23 2.600 - 1 -1.3605826 23 3.000 - 1 27.2116520 23 3.000 - local pseudopotential read in - partial core-charges read in - partial kinetic energy density read in - atomic valenz-charges read in - non local Contribution for L= 2 read in - real space projection operators read in - non local Contribution for L= 2 read in - real space projection operators read in - non local Contribution for L= 0 read in - real space projection operators read in - non local Contribution for L= 0 read in - real space projection operators read in - non local Contribution for L= 1 read in - real space projection operators read in - non local Contribution for L= 1 read in - real space projection operators read in - PAW grid and wavefunctions read in - - number of l-projection operators is LMAX = 6 - number of lm-projection operators is LMMAX = 18 - - POTCAR: PAW_PBE O 08Apr2002 - SHA256 = 818f92134a0a090dccd8ba1447fa70422a3b330e708bb4f08108d8ae51209ddf O/ - COPYR = (c) Copyright 08Apr2002 Georg Kresse - COPYR = This file is part of the software VASP. Any use, copying, and all ot - COPYR = If you do not have a valid VASP license, you may not use, copy or di - VRHFIN =O: s2p4 - LEXCH = PE - EATOM = 432.3788 eV, 31.7789 Ry - - TITEL = PAW_PBE O 08Apr2002 - LULTRA = F use ultrasoft PP ? - IUNSCR = 1 unscreen: 0-lin 1-nonlin 2-no - RPACOR = 1.200 partial core radius - POMASS = 16.000; ZVAL = 6.000 mass and valenz - RCORE = 1.520 outmost cutoff radius - RWIGS = 1.550; RWIGS = 0.820 wigner-seitz radius (au A) - ENMAX = 400.000; ENMIN = 300.000 eV - ICORE = 2 local potential - LCOR = T correct aug charges - LPAW = T paw PP - EAUG = 605.392 - DEXC = 0.000 - RMAX = 1.553 core radius for proj-oper - RAUG = 1.300 factor for augmentation sphere - RDEP = 1.550 radius for radial grids - RDEPT = 1.329 core radius for aug-charge - - Atomic configuration - 4 entries - n l j E occ. - 1 0 0.50 -514.6923 2.0000 - 2 0 0.50 -23.9615 2.0000 - 2 1 0.50 -9.0305 4.0000 - 3 2 1.50 -9.5241 0.0000 - Description - l E TYP RCUT TYP RCUT - 0 -23.9615318 23 1.200 - 0 -9.5240782 23 1.200 - 1 -9.0304911 23 1.520 - 1 8.1634956 23 1.520 - 2 -9.5240782 7 1.500 - local pseudopotential read in - partial core-charges read in - partial kinetic energy density read in - kinetic energy density of atom read in - atomic valenz-charges read in - non local Contribution for L= 0 read in - real space projection operators read in - non local Contribution for L= 0 read in - real space projection operators read in - non local Contribution for L= 1 read in - real space projection operators read in - non local Contribution for L= 1 read in - real space projection operators read in - PAW grid and wavefunctions read in - - number of l-projection operators is LMAX = 4 - number of lm-projection operators is LMMAX = 8 - - PAW_PBE Hf 20Jan2003 : - energy of atom 1 EATOM= -75.9011 - kinetic energy error for atom= 0.0007 (will be added to EATOM!!) - PAW_PBE O 08Apr2002 : - energy of atom 2 EATOM= -432.3788 - kinetic energy error for atom= 0.0224 (will be added to EATOM!!) - - - POSCAR: Primitive Cell - positions in direct lattice - No initial velocities read in - - METAGGA = SCAN LMAXTAU = 0 LMIXTAU = F - - exchange correlation table for LEXCH = 8 - RHO(1)= 0.500 N(1) = 2000 - RHO(2)= 100.500 N(2) = 4000 - - - --------------------------------------------------------------------------------------------------------- - - - ion position nearest neighbor table - 1 0.543 0.776 0.292- 7 1.98 8 1.99 10 2.08 6 2.08 5 2.10 12 2.18 11 2.18 4 3.22 - 3 3.31 3 3.31 2 3.34 2 3.34 4 3.36 4 3.46 2 3.79 2 3.79 - 2 0.043 0.224 0.208- 8 1.98 7 1.99 9 2.08 5 2.08 6 2.10 11 2.18 12 2.18 3 3.22 - 4 3.31 4 3.31 1 3.34 1 3.34 3 3.36 3 3.46 1 3.79 1 3.79 - 3 0.957 0.776 0.792- 10 1.98 9 1.99 7 2.08 12 2.08 11 2.10 6 2.18 5 2.18 2 3.22 - 1 3.31 1 3.31 4 3.34 4 3.34 2 3.36 2 3.46 4 3.79 4 3.79 - 4 0.457 0.224 0.708- 9 1.98 10 1.99 8 2.08 11 2.08 12 2.10 5 2.18 6 2.18 1 3.22 - 2 3.31 2 3.31 3 3.34 3 3.34 1 3.36 1 3.46 3 3.79 3 3.79 - 5 0.757 0.052 0.478- 2 2.08 1 2.10 4 2.18 3 2.18 - 6 0.257 0.948 0.022- 1 2.08 2 2.10 3 2.18 4 2.18 - 7 0.832 0.569 0.154- 1 1.98 2 1.99 3 2.08 - 8 0.332 0.431 0.346- 2 1.98 1 1.99 4 2.08 - 9 0.168 0.431 0.846- 4 1.98 3 1.99 2 2.08 - 10 0.668 0.569 0.654- 3 1.98 4 1.99 1 2.08 - 11 0.743 0.052 0.978- 4 2.08 3 2.10 2 2.18 1 2.18 - 12 0.243 0.948 0.522- 3 2.08 4 2.10 1 2.18 2 2.18 - - LATTYP: Found a simple monoclinic cell. - ALAT = 7.7179000670 - B/A-ratio = 0.6517496159 - C/A-ratio = 1.5432771295 - COS(beta) = -0.9616437168 - - Lattice vectors: - - A1 = ( 0.0000000000, -5.8098730802, -5.0804877952) - A2 = ( -5.0301384039, 0.0000000000, 0.0000000000) - A3 = ( 0.0000000000, 10.7730216579, 5.0804092757) - - -Analysis of symmetry for initial positions (statically): -===================================================================== - Subroutine PRICEL returns: - Original cell was already a primitive cell. - - - Routine SETGRP: Setting up the symmetry group for a - simple monoclinic supercell. - - - Subroutine GETGRP returns: Found 4 space group operations - (whereof 2 operations were pure point group operations) - out of a pool of 4 trial point group operations. - - -The static configuration has the point symmetry S_2 . - The point group associated with its full space group is C_2h. - - -Analysis of symmetry for dynamics (positions and initial velocities): -===================================================================== - Subroutine PRICEL returns: - Original cell was already a primitive cell. - - - Routine SETGRP: Setting up the symmetry group for a - simple monoclinic supercell. - - - Subroutine GETGRP returns: Found 4 space group operations - (whereof 2 operations were pure point group operations) - out of a pool of 4 trial point group operations. - - -The dynamic configuration has the point symmetry S_2 . - The point group associated with its full space group is C_2h. - - -Analysis of constrained symmetry for selective dynamics: -===================================================================== - Subroutine PRICEL returns: - Original cell was already a primitive cell. - - - Routine SETGRP: Setting up the symmetry group for a - simple monoclinic supercell. - - - Subroutine GETGRP returns: Found 4 space group operations - (whereof 2 operations were pure point group operations) - out of a pool of 4 trial point group operations. - - -The constrained configuration has the point symmetry S_2 . - The point group associated with its full space group is C_2h. - - - Subroutine INISYM returns: Found 4 space group operations - (whereof 2 operations are pure point group operations), - and found 1 'primitive' translations - - - - KPOINTS: Auto k-point - -Automatic generation of k-mesh. -Space group operators: - irot det(A) alpha n_x n_y n_z tau_x tau_y tau_z - 1 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 - 2 -1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 - 3 1.000000 180.000000 1.000000 0.000000 0.000000 -0.500000 1.000000 0.500000 - 4 -1.000000 180.000000 1.000000 0.000000 0.000000 -0.500000 1.000000 0.500000 - - Subroutine IBZKPT returns following result: - =========================================== - - Found 10 irreducible k-points: - - Following reciprocal coordinates: - Coordinates Weight - 0.000000 0.000000 0.000000 1.000000 - 0.333333 0.000000 0.000000 2.000000 - 0.000000 0.333333 -0.000000 2.000000 - 0.333333 0.333333 -0.000000 4.000000 - 0.000000 -0.000000 0.333333 2.000000 - 0.333333 -0.000000 0.333333 4.000000 - 0.000000 0.333333 0.333333 2.000000 - 0.333333 0.333333 0.333333 4.000000 - 0.000000 -0.333333 0.333333 2.000000 - 0.333333 -0.333333 0.333333 4.000000 - - Following cartesian coordinates: - Coordinates Weight - 0.000000 0.000000 0.000000 1.000000 - 0.066267 0.000000 0.000000 2.000000 - 0.000000 0.067161 -0.011193 2.000000 - 0.066267 0.067161 -0.011193 4.000000 - 0.000000 0.000001 0.065609 2.000000 - 0.066267 0.000001 0.065609 4.000000 - 0.000000 0.067163 0.054416 2.000000 - 0.066267 0.067163 0.054416 4.000000 - 0.000000 -0.067160 0.076802 2.000000 - 0.066267 -0.067160 0.076802 4.000000 - - - --------------------------------------------------------------------------------------------------------- - - - - - Dimension of arrays: - k-points NKPTS = 10 k-points in BZ NKDIM = 10 number of bands NBANDS= 40 - number of dos NEDOS = 301 number of ions NIONS = 12 - non local maximal LDIM = 6 non local SUM 2l+1 LMDIM = 18 - total plane-waves NPLWV = 57600 - max r-space proj IRMAX = 1 max aug-charges IRDMAX= 30689 - dimension x,y,z NGX = 40 NGY = 36 NGZ = 40 - dimension x,y,z NGXF= 80 NGYF= 72 NGZF= 80 - support grid NGXF= 80 NGYF= 72 NGZF= 80 - ions per type = 4 8 - NGX,Y,Z is equivalent to a cutoff of 13.22, 12.06, 12.91 a.u. - NGXF,Y,Z is equivalent to a cutoff of 26.44, 24.12, 25.82 a.u. - - SYSTEM = HfO2_p21c - POSCAR = Primitive Cell - - Startparameter for this run: - NWRITE = 2 write-flag & timer - PREC = accura normal or accurate (medium, high low for compatibility) - ISTART = 0 job : 0-new 1-cont 2-samecut - ICHARG = 2 charge: 1-file 2-atom 10-const - ISPIN = 1 spin polarized calculation? - LNONCOLLINEAR = F non collinear calculations - LSORBIT = F spin-orbit coupling - INIWAV = 1 electr: 0-lowe 1-rand 2-diag - LASPH = F aspherical Exc in radial PAW - METAGGA= F non-selfconsistent MetaGGA calc. - - Electronic Relaxation 1 - ENCUT = 500.0 eV 36.75 Ry 6.06 a.u. 9.17 9.05 9.39*2*pi/ulx,y,z - ENINI = 500.0 initial cutoff - ENAUG = 605.4 eV augmentation charge cutoff - NELM = 100; NELMIN= 2; NELMDL= -5 # of ELM steps - EDIFF = 0.1E-05 stopping-criterion for ELM - LREAL = F real-space projection - NLSPLINE = F spline interpolate recip. space projectors - LCOMPAT= F compatible to vasp.4.4 - GGA_COMPAT = T GGA compatible to vasp.4.4-vasp.4.6 - LMAXPAW = -100 max onsite density - LMAXMIX = 2 max onsite mixed and CHGCAR - VOSKOWN= 0 Vosko Wilk Nusair interpolation - ROPT = 0.00000 0.00000 - Ionic relaxation - EDIFFG = -.2E-02 stopping-criterion for IOM - NSW = 0 number of steps for IOM - NBLOCK = 1; KBLOCK = 1 inner block; outer block - IBRION = -1 ionic relax: 0-MD 1-quasi-New 2-CG - NFREE = 1 steps in history (QN), initial steepest desc. (CG) - ISIF = 3 stress and relaxation - IWAVPR = 10 prediction: 0-non 1-charg 2-wave 3-comb - ISYM = 1 0-nonsym 1-usesym 2-fastsym - LCORR = T Harris-Foulkes like correction to forces - - POTIM = 0.5000 time-step for ionic-motion - TEIN = 0.0 initial temperature - TEBEG = 0.0; TEEND = 0.0 temperature during run - SMASS = -3.00 Nose mass-parameter (am) - estimated Nose-frequenzy (Omega) = 0.10E-29 period in steps =****** mass= -0.578E-27a.u. - SCALEE = 1.0000 scale energy and forces - NPACO = 256; APACO = 16.0 distance and # of slots for P.C. - PSTRESS= 0.0 pullay stress - - Mass of Ions in am - POMASS = 178.49 16.00 - Ionic Valenz - ZVAL = 4.00 6.00 - Atomic Wigner-Seitz radii - RWIGS = -1.00 -1.00 - virtual crystal weights - VCA = 1.00 1.00 - NELECT = 64.0000 total number of electrons - NUPDOWN= -1.0000 fix difference up-down - - DOS related values: - EMIN = 10.00; EMAX =-10.00 energy-range for DOS - EFERMI = 0.00 - ISMEAR = 0; SIGMA = 0.05 broadening in eV -4-tet -1-fermi 0-gaus - - Electronic relaxation 2 (details) - IALGO = 38 algorithm - LDIAG = T sub-space diagonalisation (order eigenvalues) - LSUBROT= F optimize rotation matrix (better conditioning) - TURBO = 0 0=normal 1=particle mesh - IRESTART = 0 0=no restart 2=restart with 2 vectors - NREBOOT = 0 no. of reboots - NMIN = 0 reboot dimension - EREF = 0.00 reference energy to select bands - IMIX = 4 mixing-type and parameters - AMIX = 0.40; BMIX = 1.00 - AMIX_MAG = 1.60; BMIX_MAG = 1.00 - AMIN = 0.10 - WC = 100.; INIMIX= 1; MIXPRE= 1; MAXMIX= -45 - - Intra band minimization: - WEIMIN = 0.0000 energy-eigenvalue tresh-hold - EBREAK = 0.62E-08 absolut break condition - DEPER = 0.30 relativ break condition - - TIME = 0.40 timestep for ELM - - volume/ion in A,a.u. = 10.57 71.33 - Fermi-wavevector in a.u.,A,eV,Ry = 1.303321 2.462919 23.111470 1.698645 - Thomas-Fermi vector in A = 2.434331 - - Write flags - LWAVE = F write WAVECAR - LDOWNSAMPLE = F k-point downsampling of WAVECAR - LCHARG = F write CHGCAR - LVTOT = F write LOCPOT, total local potential - LVHAR = F write LOCPOT, Hartree potential only - LELF = F write electronic localiz. function (ELF) - LORBIT = 0 0 simple, 1 ext, 2 COOP (PROOUT), +10 PAW based schemes - - - Dipole corrections - LMONO = F monopole corrections only (constant potential shift) - LDIPOL = F correct potential (dipole corrections) - IDIPOL = 0 1-x, 2-y, 3-z, 4-all directions - EPSILON= 1.0000000 bulk dielectric constant - - Exchange correlation treatment: - GGA = -- GGA type - LEXCH = 8 internal setting for exchange type - VOSKOWN= 0 Vosko Wilk Nusair interpolation - LHFCALC = F Hartree Fock is set to - LHFONE = F Hartree Fock one center treatment - AEXX = 0.0000 exact exchange contribution - - Linear response parameters - LEPSILON= F determine dielectric tensor - LRPA = F only Hartree local field effects (RPA) - LNABLA = F use nabla operator in PAW spheres - LVEL = F velocity operator in full k-point grid - LINTERFAST= F fast interpolation - KINTER = 0 interpolate to denser k-point grid - CSHIFT =0.1000 complex shift for real part using Kramers Kronig - OMEGAMAX= -1.0 maximum frequency - DEG_THRESHOLD= 0.2000000E-02 threshold for treating states as degnerate - RTIME = -0.100 relaxation time in fs - (WPLASMAI= 0.000 imaginary part of plasma frequency in eV, 0.658/RTIME) - DFIELD = 0.0000000 0.0000000 0.0000000 field for delta impulse in time - - Orbital magnetization related: - ORBITALMAG= F switch on orbital magnetization - LCHIMAG = F perturbation theory with respect to B field - DQ = 0.001000 dq finite difference perturbation B field - LLRAUG = F two centre corrections for induced B field - - - --------------------------------------------------------------------------------------------------------- - - - Static calculation - charge density and potential will be updated during run - non-spin polarized calculation - Variant of blocked Davidson - Davidson routine will perform the subspace rotation - perform sub-space diagonalisation - after iterative eigenvector-optimisation - modified Broyden-mixing scheme, WC = 100.0 - initial mixing is a Kerker type mixing with AMIX = 0.4000 and BMIX = 1.0000 - Hartree-type preconditioning will be used - using additional bands 8 - reciprocal scheme for non local part - use partial core corrections - calculate Harris-corrections to forces - (improved forces if not selfconsistent) - use gradient corrections - use of overlap-Matrix (Vanderbilt PP) - Gauss-broadening in eV SIGMA = 0.05 - - --------------------------------------------------------------------------------------------------------- - - - energy-cutoff : 500.00 - volume of cell : 126.84 - direct lattice vectors reciprocal lattice vectors - 5.030138404 0.000000000 0.000000000 0.198801687 0.000000000 0.000000000 - 0.000000000 4.963148578 -0.000078519 0.000000000 0.201484471 -0.033579296 - 0.000000000 0.846724502 5.080566315 0.000000000 0.000003114 0.196827932 - - length of vectors - 5.030138404 4.963148578 5.150640393 0.198801687 0.204263460 0.196827932 - - - - k-points in units of 2pi/SCALE and weight: Auto k-point - 0.00000000 0.00000000 0.00000000 0.037 - 0.06626723 0.00000000 0.00000000 0.074 - 0.00000000 0.06716149 -0.01119310 0.074 - 0.06626723 0.06716149 -0.01119310 0.148 - 0.00000000 0.00000104 0.06560931 0.074 - 0.06626723 0.00000104 0.06560931 0.148 - 0.00000000 0.06716253 0.05441621 0.074 - 0.06626723 0.06716253 0.05441621 0.148 - 0.00000000 -0.06716045 0.07680241 0.074 - 0.06626723 -0.06716045 0.07680241 0.148 - - k-points in reciprocal lattice and weights: Auto k-point - 0.00000000 0.00000000 0.00000000 0.037 - 0.33333333 0.00000000 0.00000000 0.074 - 0.00000000 0.33333333 -0.00000000 0.074 - 0.33333333 0.33333333 -0.00000000 0.148 - 0.00000000 -0.00000000 0.33333333 0.074 - 0.33333333 -0.00000000 0.33333333 0.148 - 0.00000000 0.33333333 0.33333333 0.074 - 0.33333333 0.33333333 0.33333333 0.148 - 0.00000000 -0.33333333 0.33333333 0.074 - 0.33333333 -0.33333333 0.33333333 0.148 - - position of ions in fractional coordinates (direct lattice) - 0.54288322 0.77577220 0.29175508 - 0.04288322 0.22422780 0.20824492 - 0.95711678 0.77577220 0.79175508 - 0.45711678 0.22422780 0.70824492 - 0.75741482 0.05184460 0.47813308 - 0.25741482 0.94815540 0.02186692 - 0.83182355 0.56876319 0.15428653 - 0.33182355 0.43123681 0.34571347 - 0.16817645 0.43123681 0.84571347 - 0.66817645 0.56876319 0.65428653 - 0.74258518 0.05184460 0.97813308 - 0.24258518 0.94815540 0.52186692 - - position of ions in cartesian coordinates (Angst): - 2.73077773 4.09730885 1.48222010 - 0.21570852 1.28920198 1.05798454 - 4.81442988 4.52067110 4.02250325 - 2.29936068 1.71256424 3.59826770 - 3.80990139 0.66215946 2.42918275 - 1.29483219 4.72435137 0.11102189 - 4.18418758 2.95349440 0.78381831 - 1.66911838 2.43301643 1.75638632 - 0.84595083 2.85637868 4.29666948 - 3.36102003 3.37685665 3.32410147 - 3.73530621 1.08552171 4.96946591 - 1.22023701 5.14771362 2.65130504 - - - --------------------------------------------------------------------------------------------------------- - - - k-point 1 : 0.0000 0.0000 0.0000 plane waves: 3191 - k-point 2 : 0.3333 0.0000 0.0000 plane waves: 3218 - k-point 3 : 0.0000 0.3333-0.0000 plane waves: 3232 - k-point 4 : 0.3333 0.3333-0.0000 plane waves: 3229 - k-point 5 : 0.0000-0.0000 0.3333 plane waves: 3210 - k-point 6 : 0.3333-0.0000 0.3333 plane waves: 3214 - k-point 7 : 0.0000 0.3333 0.3333 plane waves: 3222 - k-point 8 : 0.3333 0.3333 0.3333 plane waves: 3219 - k-point 9 : 0.0000-0.3333 0.3333 plane waves: 3216 - k-point 10 : 0.3333-0.3333 0.3333 plane waves: 3226 - - maximum and minimum number of plane-waves per node : 425 386 - - maximum number of plane-waves: 3232 - maximum index in each direction: - IXMAX= 9 IYMAX= 9 IZMAX= 9 - IXMIN= -9 IYMIN= -9 IZMIN= -9 - - - parallel 3D FFT for wavefunctions: - minimum data exchange during FFTs selected (reduces bandwidth) - parallel 3D FFT for charge: - minimum data exchange during FFTs selected (reduces bandwidth) - - - total amount of memory used by VASP MPI-rank0 36296. kBytes -======================================================================= - - base : 30000. kBytes - nonl-proj : 1259. kBytes - fftplans : 1209. kBytes - grid : 2402. kBytes - one-center: 31. kBytes - wavefun : 1395. kBytes - - INWAV: cpu time 0.0000: real time 0.0002 - Broyden mixing: mesh for mixing (old mesh) - NGX = 19 NGY = 19 NGZ = 19 - (NGX = 80 NGY = 72 NGZ = 80) - gives a total of 6859 points - - initial charge density was supplied: - charge density of overlapping atoms calculated - number of electron 64.0000000 magnetization - keeping initial charge density in first step - - --------------------------------------------------------------------------------------------------------- - - - Maximum index for augmentation-charges 1800 (set IRDMAX) - - --------------------------------------------------------------------------------------------------------- - - - First call to EWALD: gamma= 0.353 - Maximum number of real-space cells 3x 3x 3 - Maximum number of reciprocal cells 3x 3x 3 - - FEWALD: cpu time 0.0013: real time 0.0013 - - ---------------------------------------- Iteration 1( 1) --------------------------------------- - - - POTLOK: cpu time 0.0438: real time 0.0914 - SETDIJ: cpu time 0.0026: real time 0.0026 - EDDAV: cpu time 0.2473: real time 0.2483 - DOS: cpu time 0.0004: real time 0.0004 - -------------------------------------------- - LOOP: cpu time 0.2941: real time 0.3426 - - eigenvalue-minimisations : 800 - total energy-change (2. order) : 0.1369543E+03 (-0.3459036E+04) - number of electron 64.0000000 magnetization - augmentation part 64.0000000 magnetization - - Free energy of the ion-electron system (eV) - --------------------------------------------------- - alpha Z PSCENC = 260.06748513 - Ewald energy TEWEN = -3165.74712649 - -Hartree energ DENC = -898.56887367 - -exchange EXHF = 0.00000000 - -V(xc)+E(xc) XCENC = 75.35632370 - PAW double counting = 3196.24842107 -3219.62951610 - entropy T*S EENTRO = -0.00418023 - eigenvalues EBANDS = 126.77891761 - atomic energy EATOM = 3762.45289366 - Solvation Ediel_sol = 0.00000000 - --------------------------------------------------- - free energy TOTEN = 136.95434468 eV - - energy without entropy = 136.95852491 energy(sigma->0) = 136.95643480 - - --------------------------------------------------------------------------------------------------------- - - - - ---------------------------------------- Iteration 1( 2) --------------------------------------- - - - EDDAV: cpu time 0.2911: real time 0.2945 - DOS: cpu time 0.0002: real time 0.0002 - -------------------------------------------- - LOOP: cpu time 0.2913: real time 0.2947 - - eigenvalue-minimisations : 1056 - total energy-change (2. order) :-0.4918140E+03 (-0.4768947E+03) - number of electron 64.0000000 magnetization - augmentation part 64.0000000 magnetization - - Free energy of the ion-electron system (eV) - --------------------------------------------------- - alpha Z PSCENC = 260.06748513 - Ewald energy TEWEN = -3165.74712649 - -Hartree energ DENC = -898.56887367 - -exchange EXHF = 0.00000000 - -V(xc)+E(xc) XCENC = 75.35632370 - PAW double counting = 3196.24842107 -3219.62951610 - entropy T*S EENTRO = -0.00000000 - eigenvalues EBANDS = -365.03924579 - atomic energy EATOM = 3762.45289366 - Solvation Ediel_sol = 0.00000000 - --------------------------------------------------- - free energy TOTEN = -354.85963848 eV - - energy without entropy = -354.85963848 energy(sigma->0) = -354.85963848 - - --------------------------------------------------------------------------------------------------------- - - - - ---------------------------------------- Iteration 1( 3) --------------------------------------- - - - EDDAV: cpu time 0.2744: real time 0.2753 - DOS: cpu time 0.0002: real time 0.0002 - -------------------------------------------- - LOOP: cpu time 0.2746: real time 0.2755 - - eigenvalue-minimisations : 960 - total energy-change (2. order) :-0.2606257E+02 (-0.2592087E+02) - number of electron 64.0000000 magnetization - augmentation part 64.0000000 magnetization - - Free energy of the ion-electron system (eV) - --------------------------------------------------- - alpha Z PSCENC = 260.06748513 - Ewald energy TEWEN = -3165.74712649 - -Hartree energ DENC = -898.56887367 - -exchange EXHF = 0.00000000 - -V(xc)+E(xc) XCENC = 75.35632370 - PAW double counting = 3196.24842107 -3219.62951610 - entropy T*S EENTRO = -0.00000000 - eigenvalues EBANDS = -391.10181650 - atomic energy EATOM = 3762.45289366 - Solvation Ediel_sol = 0.00000000 - --------------------------------------------------- - free energy TOTEN = -380.92220920 eV - - energy without entropy = -380.92220920 energy(sigma->0) = -380.92220920 - - --------------------------------------------------------------------------------------------------------- - - - - ---------------------------------------- Iteration 1( 4) --------------------------------------- - - - EDDAV: cpu time 0.2739: real time 0.2748 - DOS: cpu time 0.0002: real time 0.0002 - -------------------------------------------- - LOOP: cpu time 0.2741: real time 0.2750 - - eigenvalue-minimisations : 960 - total energy-change (2. order) :-0.3726745E+00 (-0.3714131E+00) - number of electron 64.0000000 magnetization - augmentation part 64.0000000 magnetization - - Free energy of the ion-electron system (eV) - --------------------------------------------------- - alpha Z PSCENC = 260.06748513 - Ewald energy TEWEN = -3165.74712649 - -Hartree energ DENC = -898.56887367 - -exchange EXHF = 0.00000000 - -V(xc)+E(xc) XCENC = 75.35632370 - PAW double counting = 3196.24842107 -3219.62951610 - entropy T*S EENTRO = -0.00000000 - eigenvalues EBANDS = -391.47449096 - atomic energy EATOM = 3762.45289366 - Solvation Ediel_sol = 0.00000000 - --------------------------------------------------- - free energy TOTEN = -381.29488366 eV - - energy without entropy = -381.29488366 energy(sigma->0) = -381.29488366 - - --------------------------------------------------------------------------------------------------------- - - - - ---------------------------------------- Iteration 1( 5) --------------------------------------- - - - EDDAV: cpu time 0.2716: real time 0.2765 - DOS: cpu time 0.0002: real time 0.0002 - CHARGE: cpu time 0.1095: real time 0.1098 - MIXING: cpu time 0.0011: real time 0.0011 - -------------------------------------------- - LOOP: cpu time 0.3825: real time 0.3877 - - eigenvalue-minimisations : 920 - total energy-change (2. order) :-0.8167890E-02 (-0.8164661E-02) - number of electron 63.9999995 magnetization - augmentation part 6.7471128 magnetization - - Broyden mixing: - rms(total) = 0.58632E+01 rms(broyden)= 0.58631E+01 - rms(prec ) = 0.73523E+01 - weight for this iteration 100.00 - - Free energy of the ion-electron system (eV) - --------------------------------------------------- - alpha Z PSCENC = 260.06748513 - Ewald energy TEWEN = -3165.74712649 - -Hartree energ DENC = -898.56887367 - -exchange EXHF = 0.00000000 - -V(xc)+E(xc) XCENC = 75.35632370 - PAW double counting = 3196.24842107 -3219.62951610 - entropy T*S EENTRO = -0.00000000 - eigenvalues EBANDS = -391.48265886 - atomic energy EATOM = 3762.45289366 - Solvation Ediel_sol = 0.00000000 - --------------------------------------------------- - free energy TOTEN = -381.30305155 eV - - energy without entropy = -381.30305155 energy(sigma->0) = -381.30305155 - - --------------------------------------------------------------------------------------------------------- - - - - ---------------------------------------- Iteration 1( 6) --------------------------------------- - - - POTLOK: cpu time 0.0405: real time 0.0408 - SETDIJ: cpu time 0.0190: real time 0.0190 - EDDAV: cpu time 0.2643: real time 0.2650 - DOS: cpu time 0.0002: real time 0.0002 - CHARGE: cpu time 0.1058: real time 0.1061 - MIXING: cpu time 0.0011: real time 0.0011 - -------------------------------------------- - LOOP: cpu time 0.4309: real time 0.4322 - - eigenvalue-minimisations : 920 - total energy-change (2. order) : 0.3494235E+02 (-0.6941192E+01) - number of electron 63.9999996 magnetization - augmentation part 5.9086957 magnetization - - Broyden mixing: - rms(total) = 0.29706E+01 rms(broyden)= 0.29704E+01 - rms(prec ) = 0.31169E+01 - weight for this iteration 100.00 - - eigenvalues of (default mixing * dielectric matrix) - average eigenvalue GAMMA= 1.6267 - 1.6267 - - Free energy of the ion-electron system (eV) - --------------------------------------------------- - alpha Z PSCENC = 260.06748513 - Ewald energy TEWEN = -3165.74712649 - -Hartree energ DENC = -1060.58774651 - -exchange EXHF = 0.00000000 - -V(xc)+E(xc) XCENC = 99.19760589 - PAW double counting = 4699.19513662 -4725.07809742 - entropy T*S EENTRO = -0.00000000 - eigenvalues EBANDS = -215.86085671 - atomic energy EATOM = 3762.45289366 - Solvation Ediel_sol = 0.00000000 - --------------------------------------------------- - free energy TOTEN = -346.36070584 eV - - energy without entropy = -346.36070584 energy(sigma->0) = -346.36070584 - - --------------------------------------------------------------------------------------------------------- - - - - ---------------------------------------- Iteration 1( 7) --------------------------------------- - - - POTLOK: cpu time 0.0400: real time 0.0404 - SETDIJ: cpu time 0.0194: real time 0.0194 - EDDAV: cpu time 0.2994: real time 0.3003 - DOS: cpu time 0.0002: real time 0.0002 - CHARGE: cpu time 0.1061: real time 0.1063 - MIXING: cpu time 0.0009: real time 0.0100 - -------------------------------------------- - LOOP: cpu time 0.4660: real time 0.4766 - - eigenvalue-minimisations : 1112 - total energy-change (2. order) :-0.1121869E+01 (-0.3614807E+00) - number of electron 63.9999996 magnetization - augmentation part 5.7927870 magnetization - - Broyden mixing: - rms(total) = 0.12901E+01 rms(broyden)= 0.12900E+01 - rms(prec ) = 0.13665E+01 - weight for this iteration 100.00 - - eigenvalues of (default mixing * dielectric matrix) - average eigenvalue GAMMA= 1.7420 - 1.1504 2.3336 - - Free energy of the ion-electron system (eV) - --------------------------------------------------- - alpha Z PSCENC = 260.06748513 - Ewald energy TEWEN = -3165.74712649 - -Hartree energ DENC = -1083.62197607 - -exchange EXHF = 0.00000000 - -V(xc)+E(xc) XCENC = 98.49415570 - PAW double counting = 6307.40934104 -6334.20939790 - entropy T*S EENTRO = -0.00000000 - eigenvalues EBANDS = -192.32795042 - atomic energy EATOM = 3762.45289366 - 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rms(prec ) = 0.24883E+00 - weight for this iteration 100.00 - - eigenvalues of (default mixing * dielectric matrix) - average eigenvalue GAMMA= 1.4824 - 2.4035 1.0218 1.0218 - - Free energy of the ion-electron system (eV) - --------------------------------------------------- - alpha Z PSCENC = 260.06748513 - Ewald energy TEWEN = -3165.74712649 - -Hartree energ DENC = -1074.87188722 - -exchange EXHF = 0.00000000 - -V(xc)+E(xc) XCENC = 99.24278197 - PAW double counting = 7916.23155313 -7943.86535727 - entropy T*S EENTRO = -0.00000000 - eigenvalues EBANDS = -200.95697750 - atomic energy EATOM = 3762.45289366 - Solvation Ediel_sol = 0.00000000 - --------------------------------------------------- - free energy TOTEN = -347.44663459 eV - - energy without entropy = -347.44663459 energy(sigma->0) = -347.44663459 - - --------------------------------------------------------------------------------------------------------- - - - - ---------------------------------------- Iteration 1( 9) --------------------------------------- - 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-exchange EXHF = 0.00000000 - -V(xc)+E(xc) XCENC = 100.41668234 - PAW double counting = 7994.36079688 -8022.12797242 - entropy T*S EENTRO = -0.00000000 - eigenvalues EBANDS = -194.84678569 - atomic energy EATOM = 3762.45289366 - Solvation Ediel_sol = 0.00000000 - --------------------------------------------------- - free energy TOTEN = -347.41061592 eV - - energy without entropy = -347.41061592 energy(sigma->0) = -347.41061592 - - --------------------------------------------------------------------------------------------------------- - - - - ---------------------------------------- Iteration 1( 10) --------------------------------------- - - - POTLOK: cpu time 0.0401: real time 0.0404 - SETDIJ: cpu time 0.0194: real time 0.0194 - EDDAV: cpu time 0.2741: real time 0.2747 - DOS: cpu time 0.0002: real time 0.0002 - CHARGE: cpu time 0.1058: real time 0.1060 - MIXING: cpu time 0.0010: real time 0.0010 - -------------------------------------------- - LOOP: cpu time 0.4405: real time 0.4418 - 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average eigenvalue GAMMA= 1.5076 - 2.5435 2.5435 0.9760 0.9760 1.0031 1.0031 - - Free energy of the ion-electron system (eV) - --------------------------------------------------- - alpha Z PSCENC = 260.06748513 - Ewald energy TEWEN = -3165.74712649 - -Hartree energ DENC = -1083.84937969 - -exchange EXHF = 0.00000000 - -V(xc)+E(xc) XCENC = 100.46306153 - PAW double counting = 8019.39373114 -8047.28156626 - entropy T*S EENTRO = -0.00000000 - eigenvalues EBANDS = -192.91184722 - atomic energy EATOM = 3762.45289366 - Solvation Ediel_sol = 0.00000000 - --------------------------------------------------- - free energy TOTEN = -347.41274820 eV - - energy without entropy = -347.41274820 energy(sigma->0) = -347.41274820 - - --------------------------------------------------------------------------------------------------------- - - - - ---------------------------------------- Iteration 1( 12) --------------------------------------- - - - POTLOK: cpu time 0.0399: real time 0.0403 - SETDIJ: cpu time 0.0194: real time 0.0194 - EDDAV: cpu time 0.2734: real time 0.2740 - DOS: cpu time 0.0002: real time 0.0002 - CHARGE: cpu time 0.1059: real time 0.1062 - MIXING: cpu time 0.0012: real time 0.0012 - -------------------------------------------- - LOOP: cpu time 0.4400: real time 0.4413 - - eigenvalue-minimisations : 952 - total energy-change (2. order) : 0.1250976E-02 (-0.7304998E-03) - number of electron 63.9999996 magnetization - augmentation part 5.8628316 magnetization - - Broyden mixing: - rms(total) = 0.35623E-02 rms(broyden)= 0.35419E-02 - rms(prec ) = 0.52636E-02 - weight for this iteration 100.00 - - eigenvalues of (default mixing * dielectric matrix) - average eigenvalue GAMMA= 1.4867 - 2.9309 2.4086 1.1612 0.9542 0.9542 0.9990 0.9990 - - Free energy of the ion-electron system (eV) - --------------------------------------------------- - alpha Z PSCENC = 260.06748513 - Ewald energy TEWEN = -3165.74712649 - -Hartree energ DENC = -1082.85710812 - -exchange EXHF = 0.00000000 - -V(xc)+E(xc) XCENC = 100.35872926 - PAW double counting = 8014.72198130 -8042.61658922 - entropy T*S EENTRO = -0.00000000 - eigenvalues EBANDS = -193.79176275 - atomic energy EATOM = 3762.45289366 - Solvation Ediel_sol = 0.00000000 - --------------------------------------------------- - free energy TOTEN = -347.41149722 eV - - energy without entropy = -347.41149722 energy(sigma->0) = -347.41149722 - - --------------------------------------------------------------------------------------------------------- - - - - ---------------------------------------- Iteration 1( 13) --------------------------------------- - - - POTLOK: cpu time 0.0400: real time 0.0404 - SETDIJ: cpu time 0.0194: real time 0.0195 - EDDAV: cpu time 0.2736: real time 0.2743 - DOS: cpu time 0.0002: real time 0.0002 - CHARGE: cpu time 0.1061: real time 0.1063 - MIXING: cpu time 0.0013: real time 0.0013 - -------------------------------------------- - LOOP: cpu time 0.4406: real time 0.4419 - - eigenvalue-minimisations : 960 - total energy-change (2. order) : 0.1216791E-04 (-0.3790577E-04) - number of electron 63.9999996 magnetization - augmentation part 5.8618349 magnetization - - Broyden mixing: - rms(total) = 0.31149E-02 rms(broyden)= 0.31147E-02 - rms(prec ) = 0.55417E-02 - weight for this iteration 100.00 - - eigenvalues of (default mixing * dielectric matrix) - average eigenvalue GAMMA= 1.4927 - 2.7641 2.4721 1.5806 1.0496 1.0496 1.0545 1.0545 0.9166 - - Free energy of the ion-electron system (eV) - --------------------------------------------------- - alpha Z PSCENC = 260.06748513 - Ewald energy TEWEN = -3165.74712649 - -Hartree energ DENC = -1082.92112837 - -exchange EXHF = 0.00000000 - -V(xc)+E(xc) XCENC = 100.41052929 - PAW double counting = 8019.35256048 -8047.25619907 - entropy T*S EENTRO = -0.00000000 - eigenvalues EBANDS = -193.77049969 - atomic energy EATOM = 3762.45289366 - Solvation Ediel_sol = 0.00000000 - --------------------------------------------------- - free energy TOTEN = -347.41148505 eV - - energy without entropy = -347.41148505 energy(sigma->0) = -347.41148505 - 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- Free energy of the ion-electron system (eV) - --------------------------------------------------- - alpha Z PSCENC = 260.06748513 - Ewald energy TEWEN = -3165.74712649 - -Hartree energ DENC = -1082.75057100 - -exchange EXHF = 0.00000000 - -V(xc)+E(xc) XCENC = 100.39144819 - PAW double counting = 8018.41337743 -8046.31400289 - entropy T*S EENTRO = -0.00000000 - eigenvalues EBANDS = -193.92495470 - atomic energy EATOM = 3762.45289366 - Solvation Ediel_sol = 0.00000000 - --------------------------------------------------- - free energy TOTEN = -347.41145067 eV - - energy without entropy = -347.41145067 energy(sigma->0) = -347.41145067 - - --------------------------------------------------------------------------------------------------------- - - - - ---------------------------------------- Iteration 1( 15) --------------------------------------- - - - POTLOK: cpu time 0.0400: real time 0.0403 - SETDIJ: cpu time 0.0194: real time 0.0194 - EDDAV: cpu time 0.2298: real time 0.2303 - DOS: cpu time 0.0002: real time 0.0002 - 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eigenvalues EBANDS = -193.93062538 - atomic energy EATOM = 3762.45289366 - Solvation Ediel_sol = 0.00000000 - --------------------------------------------------- - free energy TOTEN = -347.41144913 eV - - energy without entropy = -347.41144913 energy(sigma->0) = -347.41144913 - - --------------------------------------------------------------------------------------------------------- - - - - ---------------------------------------- Iteration 1( 16) --------------------------------------- - - - POTLOK: cpu time 0.0402: real time 0.0406 - SETDIJ: cpu time 0.0192: real time 0.0192 - EDDAV: cpu time 0.2461: real time 0.2469 - DOS: cpu time 0.0002: real time 0.0002 - CHARGE: cpu time 0.1058: real time 0.1060 - MIXING: cpu time 0.0012: real time 0.0012 - -------------------------------------------- - LOOP: cpu time 0.4128: real time 0.4142 - - eigenvalue-minimisations : 792 - total energy-change (2. order) : 0.1311465E-05 (-0.2731320E-06) - number of electron 63.9999996 magnetization - augmentation part 5.8627743 magnetization - 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- --------------------------------------------------------------------------------------------------------- - - - - FREE ENERGIE OF THE ION-ELECTRON SYSTEM (eV) - --------------------------------------------------- - free energy TOTEN = -347.41144759 eV - - energy without entropy= -347.41144759 energy(sigma->0) = -347.41144759 - - - --------------------------------------------------------------------------------------------------------- - - - POTLOK: cpu time 0.0601: real time 0.0602 - - --------------------------------------------------------------------------------------------------------- - - - LOOP+: cpu time 7.6645: real time 8.1858 - 4ORBIT: cpu time 0.0000: real time 0.0000 - - total amount of memory used by VASP MPI-rank0 36296. kBytes -======================================================================= - - base : 30000. kBytes - nonl-proj : 1259. kBytes - fftplans : 1209. kBytes - grid : 2402. kBytes - one-center: 31. kBytes - wavefun : 1395. kBytes - - - - General timing and accounting informations for this job: - ======================================================== - - Total CPU time used (sec): 8.294 - User time (sec): 8.256 - System time (sec): 0.038 - Elapsed time (sec): 9.405 - - Maximum memory used (kb): 50464. - Average memory used (kb): 0. - - Minor page faults: 13136 - Major page faults: 0 - Voluntary context switches: 287 diff --git a/mace-bench/3rdparty/SevenNet/example_inputs/data/label_2/OUTCAR_10 b/mace-bench/3rdparty/SevenNet/example_inputs/data/label_2/OUTCAR_10 deleted file mode 100644 index 59cd5a8ab1a82de3281547d2b51000cc01984f16..0000000000000000000000000000000000000000 --- a/mace-bench/3rdparty/SevenNet/example_inputs/data/label_2/OUTCAR_10 +++ /dev/null @@ -1,2837 +0,0 @@ - vasp.6.1.0 28Jan20 (build May 27 2020 11:20:12) complex - - executed on LinuxIFC date 2022.09.02 23:41:40 - running on 128 total cores - distrk: each k-point on 32 cores, 4 groups - distr: one band on NCORE= 8 cores, 4 groups - - --------------------------------------------------------------------------------------------------------- - - - INCAR: - POTCAR: PAW_PBE Hf 20Jan2003 - POTCAR: PAW_PBE O 08Apr2002 - POTCAR: PAW_PBE Hf 20Jan2003 - SHA256 = 0bb2207f9a10894133f750b65504b92b8afef976ae770762e0497daaaad8168a Hf/POTCAR - COPYR = (c) Copyright 20Jan2003 Georg Kresse - COPYR = This file is part of the software VASP. Any use, copying, and all other rights are regul - COPYR = If you do not have a valid VASP license, you may not use, copy or distribute this file. - VRHFIN =Hf: 6s5d - LEXCH = PE - EATOM = 75.9011 eV, 5.5786 Ry - - TITEL = PAW_PBE Hf 20Jan2003 - LULTRA = F use ultrasoft PP ? - IUNSCR = 1 unscreen: 0-lin 1-nonlin 2-no - RPACOR = 2.500 partial core radius - POMASS = 178.490; ZVAL = 4.000 mass and valenz - RCORE = 3.000 outmost cutoff radius - RWIGS = 3.050; RWIGS = 1.614 wigner-seitz radius (au A) - ENMAX = 220.334; ENMIN = 165.250 eV - RCLOC = 2.212 cutoff for local pot - LCOR = T correct aug charges - LPAW = T paw PP - EAUG = 335.116 - DEXC = 0.000 - RMAX = 3.077 core radius for proj-oper - RAUG = 1.300 factor for augmentation sphere - RDEP = 3.047 radius for radial grids - RDEPT = 2.344 core radius for aug-charge - - Atomic configuration - 16 entries - n l j E occ. - 1 0 0.50 -65259.4397 2.0000 - 2 0 0.50 -11157.9882 2.0000 - 2 1 1.50 -9795.2113 6.0000 - 3 0 0.50 -2541.4058 2.0000 - 3 1 1.50 -2134.4770 6.0000 - 3 2 2.50 -1653.5418 10.0000 - 4 0 0.50 -510.9575 2.0000 - 4 1 1.50 -377.5023 6.0000 - 4 2 2.50 -205.2085 10.0000 - 4 3 3.50 -15.4905 14.0000 - 5 0 0.50 -65.6020 2.0000 - 5 1 1.50 -34.2798 6.0000 - 5 2 2.50 -1.9877 3.0000 - 6 0 0.50 -4.7357 1.0000 - 6 1 1.50 -1.3606 0.0000 - 5 3 2.50 -1.3606 0.0000 - Description - l E TYP RCUT TYP RCUT - 2 -1.9876627 23 2.500 - 2 0.0744703 23 2.500 - 0 -4.7356889 23 2.600 - 0 3.2364747 23 2.600 - 1 -1.3605826 23 3.000 - 1 27.2116520 23 3.000 - local pseudopotential read in - partial core-charges read in - partial kinetic energy density read in - atomic valenz-charges read in - non local Contribution for L= 2 read in - real space projection operators read in - non local Contribution for L= 2 read in - real space projection operators read in - non local Contribution for L= 0 read in - real space projection operators read in - non local Contribution for L= 0 read in - real space projection operators read in - non local Contribution for L= 1 read in - real space projection operators read in - non local Contribution for L= 1 read in - real space projection operators read in - PAW grid and wavefunctions read in - - number of l-projection operators is LMAX = 6 - number of lm-projection operators is LMMAX = 18 - - POTCAR: PAW_PBE O 08Apr2002 - SHA256 = 818f92134a0a090dccd8ba1447fa70422a3b330e708bb4f08108d8ae51209ddf O/POTCAR - COPYR = (c) Copyright 08Apr2002 Georg Kresse - COPYR = This file is part of the software VASP. Any use, copying, and all other rights are regul - COPYR = If you do not have a valid VASP license, you may not use, copy or distribute this file. - VRHFIN =O: s2p4 - LEXCH = PE - EATOM = 432.3788 eV, 31.7789 Ry - - TITEL = PAW_PBE O 08Apr2002 - LULTRA = F use ultrasoft PP ? - IUNSCR = 1 unscreen: 0-lin 1-nonlin 2-no - RPACOR = 1.200 partial core radius - POMASS = 16.000; ZVAL = 6.000 mass and valenz - RCORE = 1.520 outmost cutoff radius - RWIGS = 1.550; RWIGS = 0.820 wigner-seitz radius (au A) - ENMAX = 400.000; ENMIN = 300.000 eV - ICORE = 2 local potential - LCOR = T correct aug charges - LPAW = T paw PP - EAUG = 605.392 - DEXC = 0.000 - RMAX = 1.553 core radius for proj-oper - RAUG = 1.300 factor for augmentation sphere - RDEP = 1.550 radius for radial grids - RDEPT = 1.329 core radius for aug-charge - - Atomic configuration - 4 entries - n l j E occ. - 1 0 0.50 -514.6923 2.0000 - 2 0 0.50 -23.9615 2.0000 - 2 1 0.50 -9.0305 4.0000 - 3 2 1.50 -9.5241 0.0000 - Description - l E TYP RCUT TYP RCUT - 0 -23.9615318 23 1.200 - 0 -9.5240782 23 1.200 - 1 -9.0304911 23 1.520 - 1 8.1634956 23 1.520 - 2 -9.5240782 7 1.500 - local pseudopotential read in - partial core-charges read in - partial kinetic energy density read in - kinetic energy density of atom read in - atomic valenz-charges read in - non local Contribution for L= 0 read in - real space projection operators read in - non local Contribution for L= 0 read in - real space projection operators read in - non local Contribution for L= 1 read in - real space projection operators read in - non local Contribution for L= 1 read in - real space projection operators read in - PAW grid and wavefunctions read in - - number of l-projection operators is LMAX = 4 - number of lm-projection operators is LMMAX = 8 - - Optimization of the real space projectors (new method) - - maximal supplied QI-value = 12.47 - optimisation between [QCUT,QGAM] = [ 11.35, 22.82] = [ 36.07,145.88] Ry - Optimized for a Real-space Cutoff 1.66 Angstroem - - l n(q) QCUT max X(q) W(low)/X(q) W(high)/X(q) e(spline) - 2 10 11.350 48.111 0.20E-03 0.11E-03 0.41E-06 - 2 10 11.350 40.545 0.19E-03 0.10E-03 0.39E-06 - 0 11 11.350 121.658 0.22E-04 0.19E-04 0.24E-06 - 0 11 11.350 71.177 0.17E-04 0.17E-04 0.23E-06 - 1 11 11.350 14.183 0.25E-03 0.43E-03 0.12E-05 - 1 11 11.350 8.257 0.17E-03 0.29E-03 0.81E-06 - Optimization of the real space projectors (new method) - - maximal supplied QI-value = 24.76 - optimisation between [QCUT,QGAM] = [ 11.39, 22.77] = [ 36.31,145.25] Ry - Optimized for a Real-space Cutoff 1.10 Angstroem - - l n(q) QCUT max X(q) W(low)/X(q) W(high)/X(q) e(spline) - 0 7 11.387 20.381 0.22E-03 0.48E-03 0.18E-06 - 0 7 11.387 15.268 0.22E-03 0.52E-03 0.19E-06 - 1 7 11.387 5.964 0.22E-03 0.73E-03 0.24E-06 - 1 7 11.387 5.382 0.19E-03 0.60E-03 0.21E-06 - PAW_PBE Hf 20Jan2003 : - energy of atom 1 EATOM= -75.9011 - kinetic energy error for atom= 0.0007 (will be added to EATOM!!) - PAW_PBE O 08Apr2002 : - energy of atom 2 EATOM= -432.3788 - kinetic energy error for atom= 0.0224 (will be added to EATOM!!) - - - POSCAR: name - positions in direct lattice - No initial velocities read in - - METAGGA = SCAN LMAXTAU = 0 LMIXTAU = F - - exchange correlation table for LEXCH = 8 - RHO(1)= 0.500 N(1) = 2000 - RHO(2)= 100.500 N(2) = 4000 - - - --------------------------------------------------------------------------------------------------------- - - - ion position nearest neighbor table - 1 0.675 0.468 0.210- 41 1.94 52 1.97 22 2.02 21 2.07 51 2.09 39 2.21 25 2.82 10 3.06 - 18 3.26 13 3.28 17 3.34 2 3.36 11 3.46 4 3.60 16 3.62 14 3.85 - 2 0.374 0.680 0.128- 59 1.87 28 2.01 27 2.12 29 2.15 57 2.16 51 2.27 21 2.31 20 3.14 - 6 3.30 1 3.36 19 3.38 7 3.46 4 3.48 17 3.65 3 3.72 - 3 0.492 0.895 0.820- 54 1.91 24 1.97 50 2.07 26 2.10 23 2.12 29 2.16 28 2.53 14 3.07 - 15 3.15 6 3.23 4 3.25 18 3.36 9 3.46 2 3.72 17 3.80 - 4 0.420 0.700 0.505- 21 1.97 55 1.99 24 2.10 25 2.10 26 2.18 33 2.20 59 2.26 16 3.22 - 3 3.25 20 3.26 9 3.32 2 3.48 14 3.51 1 3.60 19 3.79 - 5 0.264 0.273 0.410- 31 1.94 30 1.96 32 2.00 56 2.18 33 2.31 34 2.39 55 2.46 11 3.21 - 8 3.34 18 3.35 6 3.38 16 3.61 20 3.66 9 3.67 19 3.75 - 6 0.237 0.114 0.050- 32 1.88 23 1.90 42 2.08 40 2.11 27 2.30 29 2.39 9 3.13 3 3.23 - 18 3.29 2 3.30 5 3.38 10 3.48 19 3.74 7 3.75 11 3.76 - 7 0.076 0.634 0.031- 57 1.94 38 2.00 43 2.05 36 2.11 35 2.14 40 2.16 27 2.42 19 3.00 - 10 3.13 8 3.31 11 3.36 2 3.46 15 3.46 20 3.50 13 3.55 6 3.75 - 8 0.027 0.508 0.680- 31 1.97 36 1.99 48 2.02 34 2.07 37 2.08 38 2.11 47 2.82 19 3.23 - 11 3.29 7 3.31 5 3.34 15 3.44 14 3.46 9 3.46 10 3.51 12 3.82 - 9 0.181 0.037 0.717- 60 1.87 26 1.88 34 2.01 42 2.02 33 2.22 23 2.41 37 2.51 6 3.13 - 12 3.28 20 3.32 4 3.32 3 3.46 8 3.46 10 3.60 19 3.65 5 3.67 - 10 0.918 0.328 0.986- 41 2.06 49 2.07 40 2.08 38 2.11 42 2.14 22 2.14 37 2.35 1 3.06 - 7 3.13 11 3.26 17 3.44 12 3.45 6 3.48 8 3.51 9 3.60 13 3.70 - 11 0.977 0.461 0.326- 48 1.97 43 1.98 39 2.06 30 2.06 40 2.20 41 2.30 31 2.31 5 3.21 - 10 3.26 8 3.29 7 3.36 14 3.44 1 3.46 20 3.68 6 3.76 - 12 0.879 0.084 0.646- 37 1.92 47 1.99 44 2.13 46 2.16 60 2.16 45 2.17 49 2.32 17 3.21 - 9 3.28 14 3.29 16 3.43 10 3.45 20 3.50 15 3.51 13 3.74 8 3.82 - 13 0.828 0.023 0.242- 52 1.95 46 1.99 53 2.00 35 2.06 41 2.18 44 2.71 43 2.80 15 3.26 - 1 3.28 18 3.35 16 3.49 7 3.55 20 3.60 10 3.70 12 3.74 - 14 0.728 0.746 0.582- 47 1.88 24 2.00 48 2.03 44 2.15 54 2.20 39 2.30 25 2.38 3 3.07 - 15 3.09 12 3.29 11 3.44 8 3.46 4 3.51 16 3.81 1 3.85 - 15 0.777 0.837 0.912- 47 1.96 53 2.02 35 2.12 54 2.15 50 2.16 38 2.22 49 2.36 22 2.82 - 14 3.09 3 3.15 13 3.26 18 3.44 8 3.44 7 3.46 12 3.51 17 3.68 - 16 0.582 0.265 0.525- 25 1.96 58 2.03 44 2.04 56 2.08 52 2.17 45 2.26 55 2.50 17 3.08 - 4 3.22 12 3.43 13 3.49 18 3.53 19 3.60 5 3.61 1 3.62 14 3.81 - 17 0.623 0.335 0.858- 45 1.84 58 2.02 50 2.09 22 2.21 49 2.29 51 2.31 28 2.55 54 2.83 - 16 3.08 12 3.21 1 3.34 19 3.34 10 3.44 18 3.47 2 3.65 15 3.68 - 18 0.521 0.137 0.153- 56 1.94 51 1.98 53 1.98 32 2.12 29 2.16 50 2.32 52 2.38 1 3.26 - 6 3.29 5 3.35 13 3.35 3 3.36 15 3.44 17 3.47 16 3.53 - 19 0.308 0.453 0.805- 57 1.93 58 2.02 36 2.04 28 2.09 34 2.20 55 2.21 23 2.39 7 3.00 - 8 3.23 17 3.34 2 3.38 16 3.60 9 3.65 6 3.74 5 3.75 4 3.79 - 20 0.139 0.849 0.376- 59 1.85 27 2.18 43 2.21 33 2.24 60 2.26 46 2.39 30 2.57 31 2.88 - 2 3.14 4 3.26 9 3.32 7 3.50 12 3.50 13 3.60 5 3.66 11 3.68 - 21 0.514 0.688 0.311- 4 1.97 1 2.07 2 2.31 - 22 0.723 0.508 0.002- 1 2.02 10 2.14 17 2.21 15 2.82 - 23 0.329 0.142 0.874- 6 1.90 3 2.12 19 2.39 9 2.41 - 24 0.535 0.865 0.603- 3 1.97 14 2.00 4 2.10 - 25 0.606 0.522 0.519- 16 1.96 4 2.10 14 2.38 1 2.82 - 26 0.329 0.835 0.729- 9 1.88 3 2.10 4 2.18 - 27 0.182 0.865 0.142- 2 2.12 20 2.18 6 2.30 7 2.42 - 28 0.420 0.621 0.906- 2 2.01 19 2.09 3 2.53 17 2.55 - 29 0.450 0.902 0.055- 2 2.15 18 2.16 3 2.16 6 2.39 - 30 0.103 0.210 0.365- 5 1.96 11 2.06 20 2.57 - 31 0.126 0.505 0.490- 5 1.94 8 1.97 11 2.31 20 2.88 - 32 0.316 0.247 0.192- 6 1.88 5 2.00 18 2.12 - 33 0.283 0.980 0.489- 4 2.20 9 2.22 20 2.24 5 2.31 - 34 0.199 0.290 0.668- 9 2.01 8 2.07 19 2.20 5 2.39 - 35 0.927 0.898 0.035- 13 2.06 15 2.12 7 2.14 - 36 0.130 0.644 0.807- 8 1.99 19 2.04 7 2.11 - 37 0.961 0.275 0.725- 12 1.92 8 2.08 10 2.35 9 2.51 - 38 0.942 0.574 0.903- 7 2.00 10 2.11 8 2.11 15 2.22 - 39 0.790 0.636 0.333- 11 2.06 1 2.21 14 2.30 - 40 0.076 0.361 0.099- 10 2.08 6 2.11 7 2.16 11 2.20 - 41 0.850 0.299 0.195- 1 1.94 10 2.06 13 2.18 11 2.30 - 42 0.086 0.086 0.923- 9 2.02 6 2.08 10 2.14 - 43 0.022 0.682 0.256- 11 1.98 7 2.05 20 2.21 13 2.80 - 44 0.729 0.021 0.523- 16 2.04 12 2.13 14 2.15 13 2.71 - 45 0.718 0.345 0.686- 17 1.84 12 2.17 16 2.26 - 46 0.929 0.077 0.412- 13 1.99 12 2.16 20 2.39 - 47 0.829 0.859 0.708- 14 1.88 15 1.96 12 1.99 8 2.82 - 48 0.894 0.527 0.532- 11 1.97 8 2.02 14 2.03 - 49 0.817 0.138 0.901- 10 2.07 17 2.29 12 2.32 15 2.36 - 50 0.604 0.069 0.904- 3 2.07 17 2.09 15 2.16 18 2.32 - 51 0.526 0.390 0.100- 18 1.98 1 2.09 2 2.27 17 2.31 - 52 0.673 0.239 0.302- 13 1.95 1 1.97 16 2.17 18 2.38 - 53 0.694 0.945 0.123- 18 1.98 13 2.00 15 2.02 - 54 0.651 0.692 0.797- 3 1.91 15 2.15 14 2.20 17 2.83 - 55 0.357 0.490 0.574- 4 1.99 19 2.21 5 2.46 16 2.50 - 56 0.475 0.166 0.365- 18 1.94 16 2.08 5 2.18 - 57 0.261 0.509 0.017- 19 1.93 7 1.94 2 2.16 - 58 0.487 0.280 0.728- 17 2.02 19 2.02 16 2.03 - 59 0.297 0.667 0.314- 20 1.85 2 1.87 4 2.26 - 60 0.076 0.898 0.622- 9 1.87 12 2.16 20 2.26 - - LATTYP: Found a triclinic cell. - ALAT = 13.3740773175 - B/A-ratio = 0.8409539309 - C/A-ratio = 1.3935484075 - COS(alpha) = 0.0067163096 - COS(beta) = 0.6343190127 - COS(gamma) = 0.7387955733 - - Lattice vectors: - - A1 = ( 5.5939210000, -6.6389640000, -10.1734040000) - A2 = ( -1.2039270000, -9.9584460000, -5.0867020000) - A3 = ( 8.3908820000, 6.6389640000, -15.2601060000) - - -Analysis of symmetry for initial positions (statically): -===================================================================== - Subroutine PRICEL returns: - Original cell was already a primitive cell. - - - Routine SETGRP: Setting up the symmetry group for a - triclinic supercell. - - - Subroutine GETGRP returns: Found 1 space group operations - (whereof 1 operations were pure point group operations) - out of a pool of 2 trial point group operations. - - -The static configuration has the point symmetry C_1 . - - -Analysis of symmetry for dynamics (positions and initial velocities): -===================================================================== - Subroutine PRICEL returns: - Original cell was already a primitive cell. - - - Routine SETGRP: Setting up the symmetry group for a - triclinic supercell. - - - Subroutine GETGRP returns: Found 1 space group operations - (whereof 1 operations were pure point group operations) - out of a pool of 2 trial point group operations. - - -The dynamic configuration has the point symmetry C_1 . - - -Analysis of constrained symmetry for selective dynamics: -===================================================================== - Subroutine PRICEL returns: - Original cell was already a primitive cell. - - - Routine SETGRP: Setting up the symmetry group for a - triclinic supercell. - - - Subroutine GETGRP returns: Found 1 space group operations - (whereof 1 operations were pure point group operations) - out of a pool of 2 trial point group operations. - - -The constrained configuration has the point symmetry C_1 . - - - Subroutine INISYM returns: Found 1 space group operations - (whereof 1 operations are pure point group operations), - and found 1 'primitive' translations - - ----------------------------------------------------------------------------------------- - - Primitive cell - - volume of cell : 675.5585 - - direct lattice vectors reciprocal lattice vectors - 4.000887000 -9.958446000 0.000000000 0.024994456 -0.090375547 -0.025574821 - 5.204814000 0.000000000 5.086702000 0.074983367 0.030125180 0.119866570 - -6.797848000 -3.319482000 5.086702000 -0.074983367 -0.030125180 0.076724463 - - length of vectors - 10.732089429 7.277679988 9.116152446 0.097193281 0.144561497 0.111430135 - - position of ions in fractional coordinates (direct lattice) - 0.674552860 0.468004020 0.209761180 - 0.374398440 0.680423700 0.128229320 - 0.492375920 0.894932070 0.819586940 - 0.419592980 0.700424620 0.504709030 - 0.264197910 0.273040320 0.410072500 - 0.237187840 0.113551360 0.049571870 - 0.076127980 0.633674240 0.030556090 - 0.027134090 0.508047790 0.680308880 - 0.180726900 0.036988250 0.716678190 - 0.918437730 0.328202690 0.986206070 - 0.976583100 0.461207560 0.326014370 - 0.878873510 0.083991520 0.646231640 - 0.828145230 0.022919720 0.241936550 - 0.727681440 0.746102410 0.582342580 - 0.777055610 0.836782390 0.912219060 - 0.581571970 0.265442550 0.525224690 - 0.622688880 0.334790090 0.858083680 - 0.521387560 0.137162350 0.152773430 - 0.307637830 0.452870020 0.804868460 - 0.139469120 0.848745970 0.375886940 - 0.514296690 0.688125280 0.310643120 - 0.722523880 0.508198950 0.001510970 - 0.329215610 0.142404370 0.873576740 - 0.535269090 0.865020670 0.602883410 - 0.606159120 0.521764680 0.519344720 - 0.329114580 0.835369900 0.728590970 - 0.182357310 0.865039110 0.142200510 - 0.419681010 0.620858660 0.905738760 - 0.449531410 0.902112550 0.055159600 - 0.102715300 0.209832420 0.364586400 - 0.126143200 0.504951940 0.490326770 - 0.315899710 0.247311090 0.191626610 - 0.282971370 0.979696920 0.488803550 - 0.198958700 0.289644570 0.667732890 - 0.927234430 0.898304870 0.035127270 - 0.130136530 0.644350930 0.806635910 - 0.961341400 0.275114550 0.725425190 - 0.941971880 0.573764050 0.903326520 - 0.790406860 0.636276430 0.333011990 - 0.076299540 0.361412150 0.099093710 - 0.850035730 0.299301640 0.195087130 - 0.086104010 0.086134040 0.923154190 - 0.021533430 0.682457120 0.255697870 - 0.729149590 0.020562730 0.522513020 - 0.718000240 0.345431010 0.685814920 - 0.928619590 0.076823570 0.411853220 - 0.828925700 0.859389000 0.707680650 - 0.893874120 0.526661240 0.532251790 - 0.817480460 0.137815400 0.900799680 - 0.604147540 0.068941610 0.903790450 - 0.525746840 0.390214500 0.100074070 - 0.673467490 0.239323280 0.301685050 - 0.694352870 0.944678350 0.123236380 - 0.651208810 0.692387200 0.797017770 - 0.357174190 0.489850660 0.574434980 - 0.475029650 0.165552480 0.365025240 - 0.260967260 0.508909130 0.017030900 - 0.487008890 0.280358620 0.727917640 - 0.297231380 0.666806520 0.314437900 - 0.075690410 0.897785850 0.622319810 - - ion indices of the primitive-cell ions - primitive index ion index - 1 1 - 2 2 - 3 3 - 4 4 - 5 5 - 6 6 - 7 7 - 8 8 - 9 9 - 10 10 - 11 11 - 12 12 - 13 13 - 14 14 - 15 15 - 16 16 - 17 17 - 18 18 - 19 19 - 20 20 - 21 21 - 22 22 - 23 23 - 24 24 - 25 25 - 26 26 - 27 27 - 28 28 - 29 29 - 30 30 - 31 31 - 32 32 - 33 33 - 34 34 - 35 35 - 36 36 - 37 37 - 38 38 - 39 39 - 40 40 - 41 41 - 42 42 - 43 43 - 44 44 - 45 45 - 46 46 - 47 47 - 48 48 - 49 49 - 50 50 - 51 51 - 52 52 - 53 53 - 54 54 - 55 55 - 56 56 - 57 57 - 58 58 - 59 59 - 60 60 - ----------------------------------------------------------------------------------------- - - - - KPOINTS: Auto k-point - -Automatic generation of k-mesh. -Space group operators: - irot det(A) alpha n_x n_y n_z tau_x tau_y tau_z - 1 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 - - Subroutine IBZKPT returns following result: - =========================================== - - Found 4 irreducible k-points: - - Following reciprocal coordinates: - Coordinates Weight - 0.250000 0.250000 0.250000 2.000000 - -0.250000 0.250000 0.250000 2.000000 - 0.250000 -0.250000 0.250000 2.000000 - -0.250000 -0.250000 0.250000 2.000000 - - Following cartesian coordinates: - Coordinates Weight - 0.006249 -0.022594 0.042754 2.000000 - -0.006249 0.022594 0.055541 2.000000 - -0.031243 -0.037656 -0.017179 2.000000 - -0.043740 0.007531 -0.004392 2.000000 - - - --------------------------------------------------------------------------------------------------------- - - - - - Dimension of arrays: - k-points NKPTS = 4 k-points in BZ NKDIM = 4 number of bands NBANDS= 192 - number of dos NEDOS = 301 number of ions NIONS = 60 - non local maximal LDIM = 6 non local SUM 2l+1 LMDIM = 18 - total plane-waves NPLWV = 302400 - max r-space proj IRMAX = 8618 max aug-charges IRDMAX= 240626 - dimension x,y,z NGX = 80 NGY = 54 NGZ = 70 - dimension x,y,z NGXF= 160 NGYF= 108 NGZF= 140 - support grid NGXF= 320 NGYF= 216 NGZF= 280 - ions per type = 20 40 - NGX,Y,Z is equivalent to a cutoff of 12.39, 12.34, 12.77 a.u. - NGXF,Y,Z is equivalent to a cutoff of 24.78, 24.67, 25.53 a.u. - - SYSTEM = HfO2_p21c - POSCAR = name - - Startparameter for this run: - NWRITE = 2 write-flag & timer - PREC = accura normal or accurate (medium, high low for compatibility) - ISTART = 0 job : 0-new 1-cont 2-samecut - ICHARG = 2 charge: 1-file 2-atom 10-const - ISPIN = 1 spin polarized calculation? - LNONCOLLINEAR = F non collinear calculations - LSORBIT = F spin-orbit coupling - INIWAV = 1 electr: 0-lowe 1-rand 2-diag - LASPH = F aspherical Exc in radial PAW - METAGGA= F non-selfconsistent MetaGGA calc. - - Electronic Relaxation 1 - ENCUT = 500.0 eV 36.75 Ry 6.06 a.u. 19.57 13.27 16.62*2*pi/ulx,y,z - ENINI = 500.0 initial cutoff - ENAUG = 605.4 eV augmentation charge cutoff - NELM = 100; NELMIN= 2; NELMDL= -5 # of ELM steps - EDIFF = 0.1E-03 stopping-criterion for ELM - LREAL = T real-space projection - NLSPLINE = F spline interpolate recip. space projectors - LCOMPAT= F compatible to vasp.4.4 - GGA_COMPAT = T GGA compatible to vasp.4.4-vasp.4.6 - LMAXPAW = -100 max onsite density - LMAXMIX = 2 max onsite mixed and CHGCAR - VOSKOWN= 0 Vosko Wilk Nusair interpolation - ROPT = -0.00025 -0.00025 - Ionic relaxation - EDIFFG = -.2E-02 stopping-criterion for IOM - NSW = 0 number of steps for IOM - NBLOCK = 1; KBLOCK = 1 inner block; outer block - IBRION = -1 ionic relax: 0-MD 1-quasi-New 2-CG - NFREE = 1 steps in history (QN), initial steepest desc. (CG) - ISIF = 3 stress and relaxation - IWAVPR = 10 prediction: 0-non 1-charg 2-wave 3-comb - ISYM = 1 0-nonsym 1-usesym 2-fastsym - LCORR = T Harris-Foulkes like correction to forces - - POTIM = 0.5000 time-step for ionic-motion - TEIN = 0.0 initial temperature - TEBEG = 0.0; TEEND = 0.0 temperature during run - SMASS = -3.00 Nose mass-parameter (am) - estimated Nose-frequenzy (Omega) = 0.10E-29 period in steps = 0.13E+47 mass= -0.263E-26a.u. - SCALEE = 1.0000 scale energy and forces - NPACO = 256; APACO = 16.0 distance and # of slots for P.C. - PSTRESS= 0.0 pullay stress - - Mass of Ions in am - POMASS = 178.49 16.00 - Ionic Valenz - ZVAL = 4.00 6.00 - Atomic Wigner-Seitz radii - RWIGS = -1.00 -1.00 - virtual crystal weights - VCA = 1.00 1.00 - NELECT = 320.0000 total number of electrons - NUPDOWN= -1.0000 fix difference up-down - - DOS related values: - EMIN = 10.00; EMAX =-10.00 energy-range for DOS - EFERMI = 0.00 - ISMEAR = 0; SIGMA = 0.05 broadening in eV -4-tet -1-fermi 0-gaus - - Electronic relaxation 2 (details) - IALGO = 68 algorithm - LDIAG = T sub-space diagonalisation (order eigenvalues) - LSUBROT= F optimize rotation matrix (better conditioning) - TURBO = 0 0=normal 1=particle mesh - IRESTART = 0 0=no restart 2=restart with 2 vectors - NREBOOT = 0 no. of reboots - NMIN = 0 reboot dimension - EREF = 0.00 reference energy to select bands - IMIX = 4 mixing-type and parameters - AMIX = 0.40; BMIX = 1.00 - AMIX_MAG = 1.60; BMIX_MAG = 1.00 - AMIN = 0.10 - WC = 100.; INIMIX= 1; MIXPRE= 1; MAXMIX= -45 - - Intra band minimization: - WEIMIN = 0.0000 energy-eigenvalue tresh-hold - EBREAK = 0.13E-06 absolut break condition - DEPER = 0.30 relativ break condition - - TIME = 0.40 timestep for ELM - - volume/ion in A,a.u. = 11.26 75.98 - Fermi-wavevector in a.u.,A,eV,Ry = 1.276156 2.411586 22.158104 1.628575 - Thomas-Fermi vector in A = 2.408828 - - Write flags - LWAVE = F write WAVECAR - LDOWNSAMPLE = F k-point downsampling of WAVECAR - LCHARG = F write CHGCAR - LVTOT = F write LOCPOT, total local potential - LVHAR = F write LOCPOT, Hartree potential only - LELF = F write electronic localiz. function (ELF) - LORBIT = 0 0 simple, 1 ext, 2 COOP (PROOUT), +10 PAW based schemes - - - Dipole corrections - LMONO = F monopole corrections only (constant potential shift) - LDIPOL = F correct potential (dipole corrections) - IDIPOL = 0 1-x, 2-y, 3-z, 4-all directions - EPSILON= 1.0000000 bulk dielectric constant - - Exchange correlation treatment: - GGA = -- GGA type - LEXCH = 8 internal setting for exchange type - VOSKOWN= 0 Vosko Wilk Nusair interpolation - LHFCALC = F Hartree Fock is set to - LHFONE = F Hartree Fock one center treatment - AEXX = 0.0000 exact exchange contribution - - Linear response parameters - LEPSILON= F determine dielectric tensor - LRPA = F only Hartree local field effects (RPA) - LNABLA = F use nabla operator in PAW spheres - LVEL = F velocity operator in full k-point grid - LINTERFAST= F fast interpolation - KINTER = 0 interpolate to denser k-point grid - CSHIFT =0.1000 complex shift for real part using Kramers Kronig - OMEGAMAX= -1.0 maximum frequency - DEG_THRESHOLD= 0.2000000E-02 threshold for treating states as degnerate - RTIME = -0.100 relaxation time in fs - (WPLASMAI= 0.000 imaginary part of plasma frequency in eV, 0.658/RTIME) - DFIELD = 0.0000000 0.0000000 0.0000000 field for delta impulse in time - - Orbital magnetization related: - ORBITALMAG= F switch on orbital magnetization - LCHIMAG = F perturbation theory with respect to B field - DQ = 0.001000 dq finite difference perturbation B field - LLRAUG = F two centre corrections for induced B field - - - --------------------------------------------------------------------------------------------------------- - - - Static calculation - charge density and potential will be updated during run - non-spin polarized calculation - RMM-DIIS sequential band-by-band and - variant of blocked Davidson during initial phase - perform sub-space diagonalisation - before iterative eigenvector-optimisation - modified Broyden-mixing scheme, WC = 100.0 - initial mixing is a Kerker type mixing with AMIX = 0.4000 and BMIX = 1.0000 - Hartree-type preconditioning will be used - using additional bands 32 - real space projection scheme for non local part - use partial core corrections - calculate Harris-corrections to forces - (improved forces if not selfconsistent) - use gradient corrections - use of overlap-Matrix (Vanderbilt PP) - Gauss-broadening in eV SIGMA = 0.05 - - --------------------------------------------------------------------------------------------------------- - - - energy-cutoff : 500.00 - volume of cell : 675.56 - direct lattice vectors reciprocal lattice vectors - 4.000887000 -9.958446000 0.000000000 0.024994456 -0.090375547 -0.025574821 - 5.204814000 0.000000000 5.086702000 0.074983367 0.030125180 0.119866570 - -6.797848000 -3.319482000 5.086702000 -0.074983367 -0.030125180 0.076724463 - - length of vectors - 10.732089429 7.277679988 9.116152446 0.097193281 0.144561497 0.111430135 - - - - k-points in units of 2pi/SCALE and weight: Auto k-point - 0.00624861 -0.02259389 0.04275405 0.250 - -0.00624861 0.02259389 0.05554146 0.250 - -0.03124307 -0.03765648 -0.01717923 0.250 - -0.04374030 0.00753130 -0.00439182 0.250 - - k-points in reciprocal lattice and weights: Auto k-point - 0.25000000 0.25000000 0.25000000 0.250 - -0.25000000 0.25000000 0.25000000 0.250 - 0.25000000 -0.25000000 0.25000000 0.250 - -0.25000000 -0.25000000 0.25000000 0.250 - - position of ions in fractional coordinates (direct lattice) - 0.67455286 0.46800402 0.20976118 - 0.37439844 0.68042370 0.12822932 - 0.49237592 0.89493207 0.81958694 - 0.41959298 0.70042462 0.50470903 - 0.26419791 0.27304032 0.41007250 - 0.23718784 0.11355136 0.04957187 - 0.07612798 0.63367424 0.03055609 - 0.02713409 0.50804779 0.68030888 - 0.18072690 0.03698825 0.71667819 - 0.91843773 0.32820269 0.98620607 - 0.97658310 0.46120756 0.32601437 - 0.87887351 0.08399152 0.64623164 - 0.82814523 0.02291972 0.24193655 - 0.72768144 0.74610241 0.58234258 - 0.77705561 0.83678239 0.91221906 - 0.58157197 0.26544255 0.52522469 - 0.62268888 0.33479009 0.85808368 - 0.52138756 0.13716235 0.15277343 - 0.30763783 0.45287002 0.80486846 - 0.13946912 0.84874597 0.37588694 - 0.51429669 0.68812528 0.31064312 - 0.72252388 0.50819895 0.00151097 - 0.32921561 0.14240437 0.87357674 - 0.53526909 0.86502067 0.60288341 - 0.60615912 0.52176468 0.51934472 - 0.32911458 0.83536990 0.72859097 - 0.18235731 0.86503911 0.14220051 - 0.41968101 0.62085866 0.90573876 - 0.44953141 0.90211255 0.05515960 - 0.10271530 0.20983242 0.36458640 - 0.12614320 0.50495194 0.49032677 - 0.31589971 0.24731109 0.19162661 - 0.28297137 0.97969692 0.48880355 - 0.19895870 0.28964457 0.66773289 - 0.92723443 0.89830487 0.03512727 - 0.13013653 0.64435093 0.80663591 - 0.96134140 0.27511455 0.72542519 - 0.94197188 0.57376405 0.90332652 - 0.79040686 0.63627643 0.33301199 - 0.07629954 0.36141215 0.09909371 - 0.85003573 0.29930164 0.19508713 - 0.08610401 0.08613404 0.92315419 - 0.02153343 0.68245712 0.25569787 - 0.72914959 0.02056273 0.52251302 - 0.71800024 0.34543101 0.68581492 - 0.92861959 0.07682357 0.41185322 - 0.82892570 0.85938900 0.70768065 - 0.89387412 0.52666124 0.53225179 - 0.81748046 0.13781540 0.90079968 - 0.60414754 0.06894161 0.90379045 - 0.52574684 0.39021450 0.10007407 - 0.67346749 0.23932328 0.30168505 - 0.69435287 0.94467835 0.12323638 - 0.65120881 0.69238720 0.79701777 - 0.35717419 0.48985066 0.57443498 - 0.47502965 0.16555248 0.36502524 - 0.26096726 0.50890913 0.01703090 - 0.48700889 0.28035862 0.72791764 - 0.29723138 0.66680652 0.31443790 - 0.07569041 0.89778585 0.62231981 - - position of ions in cartesian coordinates (Angst): - 3.70875903 -7.41379669 3.44758960 - 4.16772122 -4.15408157 4.11337693 - 1.05646794 -7.62390311 8.72124728 - 1.89338870 -5.85386657 6.13015575 - -0.30946046 -3.99222890 3.47479135 - 1.20299342 -2.52657523 0.82975926 - 3.39502035 -0.85954677 3.37874175 - -1.87178168 -2.52848645 6.04481625 - -3.95628453 -4.17875943 3.83367659 - -1.32127943-12.41990584 6.68600567 - 4.09150206-10.80744890 4.00436337 - -0.43955062-10.89736869 3.71442761 - 1.78796047 -9.05014358 1.34724492 - 2.83601914 -9.17965204 6.75740379 - 1.26308187-10.76636108 8.89664917 - 0.13798523 -7.53502696 4.02188863 - -1.59929444 -9.04940692 6.06779339 - 1.76138667 -5.69933851 1.47481691 - -1.88344504 -5.73534108 6.39774084 - 2.42034281 -2.63664563 6.22934267 - 3.52750232 -6.15277006 5.08043722 - 5.52554606 -7.20023068 2.59274247 - -3.88009918 -6.17829814 5.16799314 - 2.54551305 -7.33170896 7.46679062 - 1.61043579 -7.76035831 5.29581327 - 0.71184453 -5.69601438 7.95540289 - 4.26530121 -2.28802746 5.12352779 - -1.24652428 -7.18595419 7.76534615 - 6.11888583 -4.65973557 4.86935816 - -0.97531190 -2.23312276 2.92189736 - -0.20030124 -2.88382113 5.06268620 - 1.24843870 -3.78197129 2.23274528 - 2.90846449 -4.44052969 7.46982428 - -2.23558930 -4.19784678 4.86989384 - 8.14648010 -9.35041834 4.74809113 - -1.60900002 -3.97357099 7.38073766 - 0.34680819-11.98150228 5.08944750 - 0.61438183-12.37915222 7.51351956 - 4.21026411 -8.97665134 4.93048134 - 1.51272488 -1.08876464 2.34245608 - 3.63253361 -9.11262313 2.51480835 - -5.48265779 -3.92185585 5.13394846 - 1.90001994 -1.06322398 4.77211486 - -0.52769379 -8.99566938 2.76246450 - 0.00847640 -9.42671690 5.24564073 - 1.31543885-10.61474739 2.48575321 - 2.97869246-10.60394500 7.97121632 - 2.69929638-10.66839739 5.38637503 - -2.13554883-11.13102334 5.28312540 - -3.36787581 -9.01648678 4.94799812 - 3.45415927 -5.56781559 2.49395185 - 1.88929137 -7.70812773 2.75194815 - 6.85716029 -7.32375651 5.43216399 - 0.79115380 -9.13071391 7.57615924 - 0.07367347 -5.46372646 5.41370389 - 0.28082372 -5.94225183 2.69889075 - 3.57710441 -2.65536213 2.67530020 - -1.54059147 -7.26616124 5.12880087 - 2.52229203 -4.00373360 4.99129795 - 0.74520166 -2.81953827 7.73232450 - - - --------------------------------------------------------------------------------------------------------- - - - k-point 1 : 0.2500 0.2500 0.2500 plane waves: 17150 - k-point 2 : -0.2500 0.2500 0.2500 plane waves: 17154 - k-point 3 : 0.2500-0.2500 0.2500 plane waves: 17136 - k-point 4 : -0.2500-0.2500 0.2500 plane waves: 17147 - - maximum and minimum number of plane-waves per node : 2169 2119 - - maximum number of plane-waves: 17154 - maximum index in each direction: - IXMAX= 19 IYMAX= 13 IZMAX= 16 - IXMIN= -19 IYMIN= -13 IZMIN= -16 - - - real space projection operators: - total allocation : 29382.80 KBytes - max/ min on nodes : 3686.08 3644.30 - - - parallel 3D FFT for wavefunctions: - minimum data exchange during FFTs selected (reduces bandwidth) - parallel 3D FFT for charge: - minimum data exchange during FFTs selected (reduces bandwidth) - - - total amount of memory used by VASP MPI-rank0 70248. kBytes -======================================================================= - - base : 30000. kBytes - nonlr-proj: 13317. kBytes - fftplans : 12220. kBytes - grid : 7620. kBytes - one-center: 124. kBytes - wavefun : 6967. kBytes - - INWAV: cpu time 0.0001: real time 0.0001 - Broyden mixing: mesh for mixing (old mesh) - NGX = 39 NGY = 27 NGZ = 33 - (NGX =160 NGY =108 NGZ =140) - gives a total of 34749 points - - initial charge density was supplied: - charge density of overlapping atoms calculated - number of electron 320.0000000 magnetization - keeping initial charge density in first step - - --------------------------------------------------------------------------------------------------------- - - - Maximum index for non-local projection operator 1078 - Maximum index for augmentation-charges 7423 (set IRDMAX) - - --------------------------------------------------------------------------------------------------------- - - - First call to EWALD: gamma= 0.202 - Maximum number of real-space cells 2x 3x 3 - Maximum number of reciprocal cells 3x 2x 3 - - FEWALD: cpu time 0.0086: real time 0.0086 - - ---------------------------------------- Iteration 1( 1) --------------------------------------- - - - POTLOK: cpu time 0.7425: real time 0.7462 - SETDIJ: cpu time 0.5238: real time 0.5250 - EDDAV: cpu time 3.7774: real time 3.7839 - DOS: cpu time 0.0047: real time 0.0047 - -------------------------------------------- - LOOP: cpu time 5.0485: real time 5.0600 - - eigenvalue-minimisations : 1536 - total energy-change (2. order) : 0.8611099E+03 (-0.1706359E+05) - number of electron 320.0000000 magnetization - augmentation part 320.0000000 magnetization - - Free energy of the ion-electron system (eV) - --------------------------------------------------- - alpha Z PSCENC = 1220.71312998 - Ewald energy TEWEN = -15275.91497308 - -Hartree energ DENC = -4817.34678545 - -exchange EXHF = 0.00000000 - -V(xc)+E(xc) XCENC = 370.93774932 - PAW double counting = 15981.24210537 -16098.14758052 - entropy T*S EENTRO = -0.02222157 - eigenvalues EBANDS = 667.38403424 - atomic energy EATOM = 18812.26446832 - Solvation Ediel_sol = 0.00000000 - --------------------------------------------------- - free energy TOTEN = 861.10992659 eV - - energy without entropy = 861.13214817 energy(sigma->0) = 861.12103738 - - --------------------------------------------------------------------------------------------------------- - - - - ---------------------------------------- Iteration 1( 2) --------------------------------------- - - - EDDAV: cpu time 4.2812: real time 4.3201 - DOS: cpu time 0.0015: real time 0.0015 - -------------------------------------------- - LOOP: cpu time 4.2827: real time 4.3216 - - eigenvalue-minimisations : 1920 - total energy-change (2. order) :-0.2574257E+04 (-0.2497538E+04) - number of electron 320.0000000 magnetization - augmentation part 320.0000000 magnetization - - Free energy of the ion-electron system (eV) - --------------------------------------------------- - alpha Z PSCENC = 1220.71312998 - Ewald energy TEWEN = -15275.91497308 - -Hartree energ DENC = -4817.34678545 - -exchange EXHF = 0.00000000 - -V(xc)+E(xc) XCENC = 370.93774932 - PAW double counting = 15981.24210537 -16098.14758052 - entropy T*S EENTRO = -0.00000000 - eigenvalues EBANDS = -1906.89491662 - atomic energy EATOM = 18812.26446832 - Solvation Ediel_sol = 0.00000000 - --------------------------------------------------- - free energy TOTEN = -1713.14680270 eV - - energy without entropy = -1713.14680270 energy(sigma->0) = -1713.14680270 - - --------------------------------------------------------------------------------------------------------- - - - - ---------------------------------------- Iteration 1( 3) --------------------------------------- - - - EDDAV: cpu time 4.1247: real time 4.1623 - DOS: cpu time 0.0018: real time 0.0018 - -------------------------------------------- - LOOP: cpu time 4.1266: real time 4.1641 - - eigenvalue-minimisations : 1792 - total energy-change (2. order) :-0.1771953E+03 (-0.1760921E+03) - number of electron 320.0000000 magnetization - augmentation part 320.0000000 magnetization - - Free energy of the ion-electron system (eV) - --------------------------------------------------- - alpha Z PSCENC = 1220.71312998 - Ewald energy TEWEN = -15275.91497308 - -Hartree energ DENC = -4817.34678545 - -exchange EXHF = 0.00000000 - -V(xc)+E(xc) XCENC = 370.93774932 - PAW double counting = 15981.24210537 -16098.14758052 - entropy T*S EENTRO = -0.00000000 - eigenvalues EBANDS = -2084.09025679 - atomic energy EATOM = 18812.26446832 - Solvation Ediel_sol = 0.00000000 - --------------------------------------------------- - free energy TOTEN = -1890.34214286 eV - - energy without entropy = -1890.34214286 energy(sigma->0) = -1890.34214286 - - --------------------------------------------------------------------------------------------------------- - - - - ---------------------------------------- Iteration 1( 4) --------------------------------------- - - - EDDAV: cpu time 4.2826: real time 4.3198 - DOS: cpu time 0.0019: real time 0.0019 - -------------------------------------------- - LOOP: cpu time 4.2845: real time 4.3217 - - eigenvalue-minimisations : 1872 - total energy-change (2. order) :-0.3944785E+01 (-0.3932303E+01) - number of electron 320.0000000 magnetization - augmentation part 320.0000000 magnetization - - Free energy of the ion-electron system (eV) - --------------------------------------------------- - alpha Z PSCENC = 1220.71312998 - Ewald energy TEWEN = -15275.91497308 - -Hartree energ DENC = -4817.34678545 - -exchange EXHF = 0.00000000 - -V(xc)+E(xc) XCENC = 370.93774932 - PAW double counting = 15981.24210537 -16098.14758052 - entropy T*S EENTRO = -0.00000000 - eigenvalues EBANDS = -2088.03504208 - atomic energy EATOM = 18812.26446832 - Solvation Ediel_sol = 0.00000000 - --------------------------------------------------- - free energy TOTEN = -1894.28692816 eV - - energy without entropy = -1894.28692816 energy(sigma->0) = -1894.28692816 - - --------------------------------------------------------------------------------------------------------- - - - - ---------------------------------------- Iteration 1( 5) --------------------------------------- - - - EDDAV: cpu time 4.1282: real time 4.1331 - DOS: cpu time 0.0017: real time 0.0017 - CHARGE: cpu time 0.9895: real time 0.9907 - MIXING: cpu time 0.0157: real time 0.0166 - -------------------------------------------- - LOOP: cpu time 5.1351: real time 5.1421 - - eigenvalue-minimisations : 1792 - total energy-change (2. order) :-0.9074758E-01 (-0.9059207E-01) - number of electron 320.0000001 magnetization - augmentation part 33.5426177 magnetization - - Broyden mixing: - rms(total) = 0.12597E+02 rms(broyden)= 0.12597E+02 - rms(prec ) = 0.13585E+02 - weight for this iteration 100.00 - - Free energy of the ion-electron system (eV) - --------------------------------------------------- - alpha Z PSCENC = 1220.71312998 - Ewald energy TEWEN = -15275.91497308 - -Hartree energ DENC = -4817.34678545 - -exchange EXHF = 0.00000000 - -V(xc)+E(xc) XCENC = 370.93774932 - PAW double counting = 15981.24210537 -16098.14758052 - entropy T*S EENTRO = -0.00000000 - eigenvalues EBANDS = -2088.12578966 - atomic energy EATOM = 18812.26446832 - Solvation Ediel_sol = 0.00000000 - --------------------------------------------------- - free energy TOTEN = -1894.37767574 eV - - energy without entropy = -1894.37767574 energy(sigma->0) = -1894.37767574 - - --------------------------------------------------------------------------------------------------------- - - - - ---------------------------------------- Iteration 1( 6) --------------------------------------- - - - POTLOK: cpu time 0.7205: real time 0.7490 - SETDIJ: cpu time 0.4749: real time 0.4750 - EDDIAG: cpu time 0.8769: real time 0.8781 - RMM-DIIS: cpu time 4.6265: real time 4.6323 - ORTHCH: cpu time 0.0242: real time 0.0242 - DOS: cpu time 0.0012: real time 0.0012 - CHARGE: cpu time 0.9743: real time 0.9753 - MIXING: cpu time 0.0120: real time 0.0120 - -------------------------------------------- - LOOP: cpu time 7.7105: real time 7.7470 - - eigenvalue-minimisations : 1569 - total energy-change (2. order) : 0.1877872E+03 (-0.3349325E+02) - number of electron 320.0000001 magnetization - augmentation part 29.9704023 magnetization - - Broyden mixing: - rms(total) = 0.69567E+01 rms(broyden)= 0.69565E+01 - rms(prec ) = 0.70962E+01 - weight for this iteration 100.00 - - eigenvalues of (default mixing * dielectric matrix) - average eigenvalue GAMMA= 1.7726 - 1.7726 - - Free energy of the ion-electron system (eV) - --------------------------------------------------- - alpha Z PSCENC = 1220.71312998 - Ewald energy TEWEN = -15275.91497308 - -Hartree energ DENC = -5660.50434172 - -exchange EXHF = 0.00000000 - -V(xc)+E(xc) XCENC = 491.69848413 - PAW double counting = 23059.85260496 -23188.54881947 - entropy T*S EENTRO = -0.00000000 - eigenvalues EBANDS = -1166.15099421 - atomic energy EATOM = 18812.26446832 - Solvation Ediel_sol = 0.00000000 - --------------------------------------------------- - free energy TOTEN = -1706.59044111 eV - - energy without entropy = -1706.59044111 energy(sigma->0) = -1706.59044111 - - --------------------------------------------------------------------------------------------------------- - - - - ---------------------------------------- Iteration 1( 7) --------------------------------------- - - - POTLOK: cpu time 0.7187: real time 0.7478 - SETDIJ: cpu time 0.4783: real time 0.4784 - EDDIAG: cpu time 0.8708: real time 0.8717 - RMM-DIIS: cpu time 4.8897: real time 4.8943 - ORTHCH: cpu time 0.0226: real time 0.0225 - DOS: cpu time 0.0064: real time 0.0064 - CHARGE: cpu time 0.9742: real time 0.9760 - MIXING: cpu time 0.0089: real time 0.0089 - -------------------------------------------- - LOOP: cpu time 7.9697: real time 8.0061 - - eigenvalue-minimisations : 1735 - total energy-change (2. order) :-0.1491250E+02 (-0.1577880E+02) - number of electron 320.0000001 magnetization - augmentation part 27.7745891 magnetization - - Broyden mixing: - rms(total) = 0.21858E+01 rms(broyden)= 0.21850E+01 - rms(prec ) = 0.24465E+01 - weight for this iteration 100.00 - - eigenvalues of (default mixing * dielectric matrix) - average eigenvalue GAMMA= 1.6811 - 1.6811 1.6811 - - Free energy of the ion-electron system (eV) - --------------------------------------------------- - alpha Z PSCENC = 1220.71312998 - Ewald energy TEWEN = -15275.91497308 - -Hartree energ DENC = -5929.29178537 - -exchange EXHF = 0.00000000 - -V(xc)+E(xc) XCENC = 504.39545662 - PAW double counting = 32779.52179590 -32914.03507740 - entropy T*S EENTRO = -0.00000000 - eigenvalues EBANDS = -919.15595140 - atomic energy EATOM = 18812.26446832 - Solvation Ediel_sol = 0.00000000 - --------------------------------------------------- - free energy TOTEN = -1721.50293644 eV - - energy without entropy = -1721.50293644 energy(sigma->0) = -1721.50293644 - - --------------------------------------------------------------------------------------------------------- - - - - ---------------------------------------- Iteration 1( 8) --------------------------------------- - - - POTLOK: cpu time 0.7451: real time 0.7457 - SETDIJ: cpu time 0.4759: real time 0.4775 - EDDIAG: cpu time 0.8631: real time 0.8640 - RMM-DIIS: cpu time 4.7916: real time 4.7964 - ORTHCH: cpu time 0.0228: real time 0.0228 - DOS: cpu time 0.0012: real time 0.0012 - CHARGE: cpu time 0.9721: real time 0.9730 - MIXING: cpu time 0.0090: real time 0.0090 - -------------------------------------------- - LOOP: cpu time 7.8807: real time 7.8894 - - eigenvalue-minimisations : 1653 - total energy-change (2. order) : 0.1636736E+01 (-0.6713393E+01) - number of electron 320.0000001 magnetization - augmentation part 29.5156632 magnetization - - Broyden mixing: - rms(total) = 0.11350E+01 rms(broyden)= 0.11346E+01 - rms(prec ) = 0.13271E+01 - weight for this iteration 100.00 - - eigenvalues of (default mixing * dielectric matrix) - average eigenvalue GAMMA= 1.4670 - 2.1991 1.1010 1.1010 - - Free energy of the ion-electron system (eV) - --------------------------------------------------- - alpha Z PSCENC = 1220.71312998 - Ewald energy TEWEN = -15275.91497308 - -Hartree energ DENC = -5593.42534511 - -exchange EXHF = 0.00000000 - -V(xc)+E(xc) XCENC = 473.61967395 - PAW double counting = 34918.69073875 -35051.59531128 - entropy T*S EENTRO = -0.00000000 - eigenvalues EBANDS = -1224.21858243 - atomic energy EATOM = 18812.26446832 - Solvation Ediel_sol = 0.00000000 - --------------------------------------------------- - free energy TOTEN = -1719.86620091 eV - - energy without entropy = -1719.86620091 energy(sigma->0) = -1719.86620091 - - --------------------------------------------------------------------------------------------------------- - - - - ---------------------------------------- Iteration 1( 9) --------------------------------------- - - - POTLOK: cpu time 0.7444: real time 0.7458 - SETDIJ: cpu time 0.4343: real time 0.4773 - EDDIAG: cpu time 0.8619: real time 0.8628 - RMM-DIIS: cpu time 5.0445: real time 5.0493 - ORTHCH: cpu time 0.0224: real time 0.0224 - DOS: cpu time 0.0015: real time 0.0015 - CHARGE: cpu time 0.9734: real time 0.9745 - MIXING: cpu time 0.0090: real time 0.0090 - -------------------------------------------- - LOOP: cpu time 8.0914: real time 8.1426 - - eigenvalue-minimisations : 1792 - total energy-change (2. order) : 0.2239133E+01 (-0.5476922E+00) - number of electron 320.0000001 magnetization - augmentation part 29.2053679 magnetization - - Broyden mixing: - rms(total) = 0.28863E+00 rms(broyden)= 0.28862E+00 - rms(prec ) = 0.35332E+00 - weight for this iteration 100.00 - - eigenvalues of (default mixing * dielectric matrix) - average eigenvalue GAMMA= 1.4909 - 2.3867 1.0168 1.2801 1.2801 - - Free energy of the ion-electron system (eV) - --------------------------------------------------- - alpha Z PSCENC = 1220.71312998 - Ewald energy TEWEN = -15275.91497308 - -Hartree energ DENC = -5725.97441928 - -exchange EXHF = 0.00000000 - -V(xc)+E(xc) XCENC = 495.38054459 - PAW double counting = 37136.77858502 -37272.17002481 - entropy T*S EENTRO = -0.00000000 - eigenvalues EBANDS = -1108.70437875 - atomic energy EATOM = 18812.26446832 - Solvation Ediel_sol = 0.00000000 - --------------------------------------------------- - free energy TOTEN = -1717.62706802 eV - - energy without entropy = -1717.62706802 energy(sigma->0) = -1717.62706802 - - --------------------------------------------------------------------------------------------------------- - - - - ---------------------------------------- Iteration 1( 10) --------------------------------------- - - - POTLOK: cpu time 0.7176: real time 0.7499 - SETDIJ: cpu time 0.4755: real time 0.4763 - EDDIAG: cpu time 0.8631: real time 0.8640 - RMM-DIIS: cpu time 5.0617: real time 5.0662 - ORTHCH: cpu time 0.0232: real time 0.0232 - DOS: cpu time 0.0012: real time 0.0012 - CHARGE: cpu time 0.9719: real time 0.9730 - MIXING: cpu time 0.0092: real time 0.0092 - -------------------------------------------- - LOOP: cpu time 8.1234: real time 8.1632 - - eigenvalue-minimisations : 1797 - total energy-change (2. order) :-0.2589605E+00 (-0.6115495E+00) - number of electron 320.0000001 magnetization - augmentation part 28.7069979 magnetization - - Broyden mixing: - rms(total) = 0.32198E+00 rms(broyden)= 0.32179E+00 - rms(prec ) = 0.39468E+00 - weight for this iteration 100.00 - - eigenvalues of (default mixing * dielectric matrix) - average eigenvalue GAMMA= 1.5227 - 2.5552 1.9796 1.0495 1.0145 1.0145 - - Free energy of the ion-electron system (eV) - --------------------------------------------------- - alpha Z PSCENC = 1220.71312998 - Ewald energy TEWEN = -15275.91497308 - -Hartree energ DENC = -5791.96838949 - -exchange EXHF = 0.00000000 - -V(xc)+E(xc) XCENC = 498.66737029 - PAW double counting = 37700.21643901 -37836.99027793 - entropy T*S EENTRO = -0.00000000 - eigenvalues EBANDS = -1044.87379561 - atomic energy EATOM = 18812.26446832 - Solvation Ediel_sol = 0.00000000 - --------------------------------------------------- - free energy TOTEN = -1717.88602852 eV - - energy without entropy = -1717.88602852 energy(sigma->0) = -1717.88602852 - - --------------------------------------------------------------------------------------------------------- - - - - ---------------------------------------- Iteration 1( 11) --------------------------------------- - - - POTLOK: cpu time 0.7452: real time 0.7468 - SETDIJ: cpu time 0.4706: real time 0.4716 - EDDIAG: cpu time 0.8700: real time 0.8720 - RMM-DIIS: cpu time 5.1469: real time 5.1522 - ORTHCH: cpu time 0.0227: real time 0.0227 - DOS: cpu time 0.0012: real time 0.0012 - CHARGE: cpu time 0.9818: real time 0.9837 - MIXING: cpu time 0.0091: real time 0.0091 - -------------------------------------------- - LOOP: cpu time 8.2476: real time 8.2591 - - eigenvalue-minimisations : 1783 - total energy-change (2. order) : 0.2172693E+00 (-0.1057677E+00) - number of electron 320.0000001 magnetization - augmentation part 28.8589130 magnetization - - Broyden mixing: - rms(total) = 0.89624E-01 rms(broyden)= 0.89607E-01 - rms(prec ) = 0.10010E+00 - weight for this iteration 100.00 - - eigenvalues of (default mixing * dielectric matrix) - average eigenvalue GAMMA= 1.5833 - 2.6212 2.6212 1.1967 1.0695 0.9956 0.9956 - - Free energy of the ion-electron system (eV) - --------------------------------------------------- - alpha Z PSCENC = 1220.71312998 - Ewald energy TEWEN = -15275.91497308 - -Hartree energ DENC = -5749.04685692 - -exchange EXHF = 0.00000000 - -V(xc)+E(xc) XCENC = 493.13098408 - PAW double counting = 37658.17885474 -37794.89870412 - entropy T*S EENTRO = -0.00000000 - eigenvalues EBANDS = -1082.09566220 - atomic energy EATOM = 18812.26446832 - Solvation Ediel_sol = 0.00000000 - --------------------------------------------------- - free energy TOTEN = -1717.66875920 eV - - energy without entropy = -1717.66875920 energy(sigma->0) = -1717.66875920 - - --------------------------------------------------------------------------------------------------------- - - - - ---------------------------------------- Iteration 1( 12) --------------------------------------- - - - POTLOK: cpu time 0.7186: real time 0.7454 - SETDIJ: cpu time 0.4735: real time 0.4746 - EDDIAG: cpu time 0.8638: real time 0.8646 - RMM-DIIS: cpu time 5.2557: real time 5.2613 - ORTHCH: cpu time 0.0228: real time 0.0228 - DOS: cpu time 0.0042: real time 0.0042 - CHARGE: cpu time 0.9726: real time 0.9817 - MIXING: cpu time 0.0094: real time 0.0094 - -------------------------------------------- - LOOP: cpu time 8.3204: real time 8.3639 - - eigenvalue-minimisations : 1878 - total energy-change (2. order) :-0.8432562E-02 (-0.2345520E-01) - number of electron 320.0000001 magnetization - augmentation part 28.9098139 magnetization - - Broyden mixing: - rms(total) = 0.40431E-01 rms(broyden)= 0.40395E-01 - rms(prec ) = 0.42039E-01 - weight for this iteration 100.00 - - eigenvalues of (default mixing * dielectric matrix) - average eigenvalue GAMMA= 1.7307 - 3.6901 2.5130 1.9299 0.9803 0.9803 1.0883 0.9332 - - Free energy of the ion-electron system (eV) - --------------------------------------------------- - alpha Z PSCENC = 1220.71312998 - Ewald energy TEWEN = -15275.91497308 - -Hartree energ DENC = -5743.54246777 - -exchange EXHF = 0.00000000 - -V(xc)+E(xc) XCENC = 493.62605298 - PAW double counting = 37591.10600874 -37727.89250435 - entropy T*S EENTRO = -0.00000000 - eigenvalues EBANDS = -1088.03690657 - atomic energy EATOM = 18812.26446832 - Solvation Ediel_sol = 0.00000000 - --------------------------------------------------- - free energy TOTEN = -1717.67719176 eV - - energy without entropy = -1717.67719176 energy(sigma->0) = -1717.67719176 - - --------------------------------------------------------------------------------------------------------- - - - - ---------------------------------------- Iteration 1( 13) --------------------------------------- - - - POTLOK: cpu time 0.7189: real time 0.7477 - SETDIJ: cpu time 0.4735: real time 0.4735 - EDDIAG: cpu time 0.8798: real time 0.8808 - RMM-DIIS: cpu time 5.6370: real time 5.6426 - ORTHCH: cpu time 0.0284: real time 0.0284 - DOS: cpu time 0.0011: real time 0.0012 - CHARGE: cpu time 0.9724: real time 0.9742 - MIXING: cpu time 0.0094: real time 0.0094 - -------------------------------------------- - LOOP: cpu time 8.7208: real time 8.7579 - - eigenvalue-minimisations : 2033 - total energy-change (2. order) :-0.3742004E-02 (-0.4339591E-02) - number of electron 320.0000001 magnetization - augmentation part 28.9092938 magnetization - - Broyden mixing: - rms(total) = 0.33858E-01 rms(broyden)= 0.33855E-01 - rms(prec ) = 0.35638E-01 - weight for this iteration 100.00 - - eigenvalues of (default mixing * dielectric matrix) - average eigenvalue GAMMA= 1.7220 - 4.2003 2.3656 2.1951 0.9742 0.9742 1.1209 0.9727 0.9727 - - Free energy of the ion-electron system (eV) - --------------------------------------------------- - alpha Z PSCENC = 1220.71312998 - Ewald energy TEWEN = -15275.91497308 - -Hartree energ DENC = -5744.73629565 - -exchange EXHF = 0.00000000 - -V(xc)+E(xc) XCENC = 493.98486134 - PAW double counting = 37667.69985117 -37804.46074764 - entropy T*S EENTRO = -0.00000000 - eigenvalues EBANDS = -1087.23122820 - atomic energy EATOM = 18812.26446832 - Solvation Ediel_sol = 0.00000000 - --------------------------------------------------- - free energy TOTEN = -1717.68093377 eV - - energy without entropy = -1717.68093377 energy(sigma->0) = -1717.68093377 - - --------------------------------------------------------------------------------------------------------- - - - - ---------------------------------------- Iteration 1( 14) --------------------------------------- - - - POTLOK: cpu time 0.7497: real time 0.7504 - SETDIJ: cpu time 0.4898: real time 0.4909 - EDDIAG: cpu time 0.8698: real time 0.8717 - RMM-DIIS: cpu time 5.1892: real time 5.1948 - ORTHCH: cpu time 0.0231: real time 0.0231 - DOS: cpu time 0.0039: real time 0.0039 - CHARGE: cpu time 0.9767: real time 0.9777 - MIXING: cpu time 0.0095: real time 0.0095 - -------------------------------------------- - LOOP: cpu time 8.3114: real time 8.3216 - - eigenvalue-minimisations : 1852 - total energy-change (2. order) :-0.1949165E-02 (-0.1266845E-02) - number of electron 320.0000001 magnetization - augmentation part 28.9230357 magnetization - - Broyden mixing: - rms(total) = 0.37526E-01 rms(broyden)= 0.37524E-01 - rms(prec ) = 0.44353E-01 - weight for this iteration 100.00 - - eigenvalues of (default mixing * dielectric matrix) - average eigenvalue GAMMA= 1.7518 - 4.8148 2.4261 2.4261 1.0105 1.0105 1.0346 1.0346 1.0044 1.0044 - - Free energy of the ion-electron system (eV) - --------------------------------------------------- - alpha Z PSCENC = 1220.71312998 - Ewald energy TEWEN = -15275.91497308 - -Hartree energ DENC = -5742.88633589 - -exchange EXHF = 0.00000000 - -V(xc)+E(xc) XCENC = 493.90190823 - PAW double counting = 37727.38579493 -37864.10722793 - entropy T*S EENTRO = -0.00000000 - eigenvalues EBANDS = -1089.03964749 - atomic energy EATOM = 18812.26446832 - Solvation Ediel_sol = 0.00000000 - --------------------------------------------------- - free energy TOTEN = -1717.68288293 eV - - energy without entropy = -1717.68288293 energy(sigma->0) = -1717.68288293 - - --------------------------------------------------------------------------------------------------------- - - - - ---------------------------------------- Iteration 1( 15) --------------------------------------- - - - POTLOK: cpu time 0.7188: real time 0.7486 - SETDIJ: cpu time 0.4723: real time 0.4723 - EDDIAG: cpu time 0.8655: real time 0.8665 - RMM-DIIS: cpu time 5.2209: real time 5.2266 - ORTHCH: cpu time 0.0226: real time 0.0226 - DOS: cpu time 0.0042: real time 0.0043 - CHARGE: cpu time 0.9757: real time 0.9766 - MIXING: cpu time 0.0098: real time 0.0099 - -------------------------------------------- - LOOP: cpu time 8.2899: real time 8.3273 - - eigenvalue-minimisations : 1845 - total energy-change (2. order) : 0.1509389E-02 (-0.3721887E-03) - number of electron 320.0000001 magnetization - augmentation part 28.9138323 magnetization - - Broyden mixing: - rms(total) = 0.17750E-01 rms(broyden)= 0.17750E-01 - rms(prec ) = 0.22061E-01 - weight for this iteration 100.00 - - eigenvalues of (default mixing * dielectric matrix) - average eigenvalue GAMMA= 1.7080 - 4.0642 2.6882 2.1318 2.1318 0.9886 0.9886 1.0788 1.0788 0.9646 0.9646 - - Free energy of the ion-electron system (eV) - --------------------------------------------------- - alpha Z PSCENC = 1220.71312998 - Ewald energy TEWEN = -15275.91497308 - -Hartree energ DENC = -5745.13394041 - -exchange EXHF = 0.00000000 - -V(xc)+E(xc) XCENC = 494.15733751 - PAW double counting = 37782.65715803 -37919.36051405 - entropy T*S EENTRO = -0.00000000 - eigenvalues EBANDS = -1087.06403984 - atomic energy EATOM = 18812.26446832 - Solvation Ediel_sol = 0.00000000 - --------------------------------------------------- - free energy TOTEN = -1717.68137354 eV - - energy without entropy = -1717.68137354 energy(sigma->0) = -1717.68137354 - - --------------------------------------------------------------------------------------------------------- - - - - ---------------------------------------- Iteration 1( 16) --------------------------------------- - - - POTLOK: cpu time 0.7187: real time 0.7468 - SETDIJ: cpu time 0.4656: real time 0.4656 - EDDIAG: cpu time 0.8736: real time 0.8747 - RMM-DIIS: cpu time 5.0694: real time 5.0747 - ORTHCH: cpu time 0.0226: real time 0.0226 - DOS: cpu time 0.0013: real time 0.0014 - CHARGE: cpu time 0.9754: real time 0.9764 - MIXING: cpu time 0.0096: real time 0.0096 - -------------------------------------------- - LOOP: cpu time 8.1361: real time 8.1717 - - eigenvalue-minimisations : 1845 - total energy-change (2. order) : 0.2436471E-03 (-0.4543779E-03) - number of electron 320.0000001 magnetization - augmentation part 28.9005741 magnetization - - Broyden mixing: - rms(total) = 0.74648E-02 rms(broyden)= 0.74589E-02 - rms(prec ) = 0.76088E-02 - weight for this iteration 100.00 - - eigenvalues of (default mixing * dielectric matrix) - average eigenvalue GAMMA= 1.5837 - 4.2232 2.7022 2.1480 2.1480 0.9885 0.9885 1.0895 1.0895 0.9568 0.9568 - 0.1301 - - Free energy of the ion-electron system (eV) - --------------------------------------------------- - alpha Z PSCENC = 1220.71312998 - Ewald energy TEWEN = -15275.91497308 - -Hartree energ DENC = -5746.73809417 - -exchange EXHF = 0.00000000 - -V(xc)+E(xc) XCENC = 494.21284152 - PAW double counting = 37779.69942358 -37916.42199576 - entropy T*S EENTRO = -0.00000000 - eigenvalues EBANDS = -1085.49593028 - atomic energy EATOM = 18812.26446832 - Solvation Ediel_sol = 0.00000000 - --------------------------------------------------- - free energy TOTEN = -1717.68112990 eV - - energy without entropy = -1717.68112990 energy(sigma->0) = -1717.68112990 - - --------------------------------------------------------------------------------------------------------- - - - - ---------------------------------------- Iteration 1( 17) --------------------------------------- - - - POTLOK: cpu time 0.7190: real time 0.7471 - SETDIJ: cpu time 0.4715: real time 0.4716 - EDDIAG: cpu time 0.8739: real time 0.8763 - RMM-DIIS: cpu time 4.9353: real time 4.9408 - ORTHCH: cpu time 0.0282: real time 0.0282 - DOS: cpu time 0.0011: real time 0.0011 - CHARGE: cpu time 0.9743: real time 0.9752 - MIXING: cpu time 0.0098: real time 0.0098 - -------------------------------------------- - LOOP: cpu time 8.0132: real time 8.0503 - - eigenvalue-minimisations : 1743 - total energy-change (2. order) :-0.9387703E-04 (-0.1114559E-03) - number of electron 320.0000001 magnetization - augmentation part 28.8963316 magnetization - - Broyden mixing: - rms(total) = 0.74063E-02 rms(broyden)= 0.74053E-02 - rms(prec ) = 0.75591E-02 - weight for this iteration 100.00 - - eigenvalues of (default mixing * dielectric matrix) - average eigenvalue GAMMA= 1.4522 - 4.2255 2.7023 2.1473 2.1473 0.9886 0.9886 1.0894 1.0894 0.9570 0.9570 - 0.0466 0.0877 - - Free energy of the ion-electron system (eV) - --------------------------------------------------- - alpha Z PSCENC = 1220.71312998 - Ewald energy TEWEN = -15275.91497308 - -Hartree energ DENC = -5746.94116431 - -exchange EXHF = 0.00000000 - -V(xc)+E(xc) XCENC = 494.15137857 - PAW double counting = 37787.76165950 -37924.48642649 - entropy T*S EENTRO = -0.00000000 - eigenvalues EBANDS = -1085.22929625 - atomic energy EATOM = 18812.26446832 - Solvation Ediel_sol = 0.00000000 - --------------------------------------------------- - free energy TOTEN = -1717.68122377 eV - - energy without entropy = -1717.68122377 energy(sigma->0) = -1717.68122377 - - --------------------------------------------------------------------------------------------------------- - - - - ---------------------------------------- Iteration 1( 18) --------------------------------------- - - - POTLOK: cpu time 0.7188: real time 0.7504 - SETDIJ: cpu time 0.4730: real time 0.4731 - EDDIAG: cpu time 0.8704: real time 0.8715 - RMM-DIIS: cpu time 3.8457: real time 3.8500 - ORTHCH: cpu time 0.0222: real time 0.0222 - DOS: cpu time 0.0059: real time 0.0059 - 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0.00848 -9.42672 5.24564 -1.114149 -0.823182 -2.520495 - 1.31544 -10.61475 2.48575 -1.569560 -0.702912 -0.966448 - 2.97869 -10.60395 7.97122 -1.562847 -3.189432 -0.276367 - 2.69930 -10.66840 5.38638 -1.652875 -0.574239 1.063289 - -2.13555 -11.13102 5.28313 0.999259 1.512967 0.068489 - -3.36788 -9.01649 4.94800 -0.343941 0.449275 -0.690470 - 3.45416 -5.56782 2.49395 0.415715 0.483514 0.262424 - 1.88929 -7.70813 2.75195 -0.910670 1.487496 -0.248461 - 6.85716 -7.32376 5.43216 -1.373891 0.274126 -1.104831 - 0.79115 -9.13071 7.57616 1.604575 -2.919377 0.419696 - 0.07367 -5.46373 5.41370 0.730152 0.034018 -1.501222 - 0.28082 -5.94225 2.69889 -1.470895 0.226000 0.781234 - 3.57710 -2.65536 2.67530 -1.861230 -0.512525 0.692791 - -1.54059 -7.26616 5.12880 -0.047612 -1.319955 -0.768206 - 2.52229 -4.00373 4.99130 -4.917939 -0.185760 0.044325 - 0.74520 -2.81954 7.73232 0.773564 3.197221 -2.421509 - ----------------------------------------------------------------------------------- - total drift: -0.017681 -0.009829 0.035063 - - --------------------------------------------------------------------------------------------------------- - - - - FREE ENERGIE OF THE ION-ELECTRON SYSTEM (eV) - --------------------------------------------------- - free energy TOTEN = -1717.68123322 eV - - energy without entropy= -1717.68123322 energy(sigma->0) = -1717.68123322 - - - --------------------------------------------------------------------------------------------------------- - - - POTLOK: cpu time 1.1630: real time 1.1651 - - --------------------------------------------------------------------------------------------------------- - - - LOOP+: cpu time 151.0311: real time 151.7021 - 4ORBIT: cpu time 0.0000: real time 0.0000 - - total amount of memory used by VASP MPI-rank0 70248. kBytes -======================================================================= - - base : 30000. kBytes - nonlr-proj: 13317. kBytes - fftplans : 12220. kBytes - grid : 7620. kBytes - one-center: 124. kBytes - wavefun : 6967. kBytes - - - - General timing and accounting informations for this job: - ======================================================== - - Total CPU time used (sec): 162.750 - User time (sec): 155.902 - System time (sec): 6.847 - Elapsed time (sec): 164.237 - - Maximum memory used (kb): 839448. - Average memory used (kb): 0. - - Minor page faults: 155034 - Major page faults: 0 - Voluntary context switches: 2423 diff --git a/mace-bench/3rdparty/SevenNet/example_inputs/data/label_2/OUTCAR_6 b/mace-bench/3rdparty/SevenNet/example_inputs/data/label_2/OUTCAR_6 deleted file mode 100644 index b66b44195050a9a39229688a79c9d7cf4ae07cb2..0000000000000000000000000000000000000000 --- a/mace-bench/3rdparty/SevenNet/example_inputs/data/label_2/OUTCAR_6 +++ /dev/null @@ -1,2028 +0,0 @@ - vasp.5.4.4.18Apr17-6-g9f103f2a35 (build Sep 11 2017 17:27:03) complex - - executed on GRP7IFC17NORMAL date 2022.08.24 18:31:10 - running on 32 total cores - distrk: each k-point on 16 cores, 2 groups - distr: one band on NCORES_PER_BAND= 8 cores, 2 groups - - --------------------------------------------------------------------------------------------------------- - - - INCAR: - POTCAR: PAW_PBE Hf 20Jan2003 - POTCAR: PAW_PBE O 08Apr2002 - - ----------------------------------------------------------------------------- -| | -| W W AA RRRRR N N II N N GGGG !!! | -| W W A A R R NN N II NN N G G !!! | -| W W A A R R N N N II N N N G !!! | -| W WW W AAAAAA RRRRR N N N II N N N G GGG ! | -| WW WW A A R R N NN II N NN G G | -| W W A A R R N N II N N GGGG !!! | -| | -| You have enabled k-point parallelism (KPAR>1). | -| This developmental code was originally written by Paul Kent at ORNL, | -| and carefully double checked in Vienna. | -| GW as well as linear response parallelism added by Martijn Marsman | -| and Georg Kresse. | -| Carefully verify results versus KPAR=1. | -| Report problems to Paul Kent and Vienna. | -| | - ----------------------------------------------------------------------------- - - POTCAR: PAW_PBE Hf 20Jan2003 - SHA256 = 0bb2207f9a10894133f750b65504b92b8afef976ae770762e0497daaaad8168a Hf - COPYR = (c) Copyright 20Jan2003 Georg Kresse - COPYR = This file is part of the software VASP. Any use, copying, and all ot - COPYR = If you do not have a valid VASP license, you may not use, copy or di - VRHFIN =Hf: 6s5d - LEXCH = PE - EATOM = 75.9011 eV, 5.5786 Ry - - TITEL = PAW_PBE Hf 20Jan2003 - LULTRA = F use ultrasoft PP ? - IUNSCR = 1 unscreen: 0-lin 1-nonlin 2-no - RPACOR = 2.500 partial core radius - POMASS = 178.490; ZVAL = 4.000 mass and valenz - RCORE = 3.000 outmost cutoff radius - RWIGS = 3.050; RWIGS = 1.614 wigner-seitz radius (au A) - ENMAX = 220.334; ENMIN = 165.250 eV - RCLOC = 2.212 cutoff for local pot - LCOR = T correct aug charges - LPAW = T paw PP - EAUG = 335.116 - DEXC = 0.000 - RMAX = 3.077 core radius for proj-oper - RAUG = 1.300 factor for augmentation sphere - RDEP = 3.047 radius for radial grids - RDEPT = 2.344 core radius for aug-charge - - Atomic configuration - 16 entries - n l j E occ. - 1 0 0.50 -65259.4397 2.0000 - 2 0 0.50 -11157.9882 2.0000 - 2 1 1.50 -9795.2113 6.0000 - 3 0 0.50 -2541.4058 2.0000 - 3 1 1.50 -2134.4770 6.0000 - 3 2 2.50 -1653.5418 10.0000 - 4 0 0.50 -510.9575 2.0000 - 4 1 1.50 -377.5023 6.0000 - 4 2 2.50 -205.2085 10.0000 - 4 3 3.50 -15.4905 14.0000 - 5 0 0.50 -65.6020 2.0000 - 5 1 1.50 -34.2798 6.0000 - 5 2 2.50 -1.9877 3.0000 - 6 0 0.50 -4.7357 1.0000 - 6 1 1.50 -1.3606 0.0000 - 5 3 2.50 -1.3606 0.0000 - Description - l E TYP RCUT TYP RCUT - 2 -1.9876627 23 2.500 - 2 0.0744703 23 2.500 - 0 -4.7356889 23 2.600 - 0 3.2364747 23 2.600 - 1 -1.3605826 23 3.000 - 1 27.2116520 23 3.000 - local pseudopotential read in - partial core-charges read in - partial kinetic energy density read in - atomic valenz-charges read in - non local Contribution for L= 2 read in - real space projection operators read in - non local Contribution for L= 2 read in - real space projection operators read in - non local Contribution for L= 0 read in - real space projection operators read in - non local Contribution for L= 0 read in - real space projection operators read in - non local Contribution for L= 1 read in - real space projection operators read in - non local Contribution for L= 1 read in - real space projection operators read in - PAW grid and wavefunctions read in - - number of l-projection operators is LMAX = 6 - number of lm-projection operators is LMMAX = 18 - - POTCAR: PAW_PBE O 08Apr2002 - SHA256 = 818f92134a0a090dccd8ba1447fa70422a3b330e708bb4f08108d8ae51209ddf O/ - COPYR = (c) Copyright 08Apr2002 Georg Kresse - COPYR = This file is part of the software VASP. Any use, copying, and all ot - COPYR = If you do not have a valid VASP license, you may not use, copy or di - VRHFIN =O: s2p4 - LEXCH = PE - EATOM = 432.3788 eV, 31.7789 Ry - - TITEL = PAW_PBE O 08Apr2002 - LULTRA = F use ultrasoft PP ? - IUNSCR = 1 unscreen: 0-lin 1-nonlin 2-no - RPACOR = 1.200 partial core radius - POMASS = 16.000; ZVAL = 6.000 mass and valenz - RCORE = 1.520 outmost cutoff radius - RWIGS = 1.550; RWIGS = 0.820 wigner-seitz radius (au A) - ENMAX = 400.000; ENMIN = 300.000 eV - ICORE = 2 local potential - LCOR = T correct aug charges - LPAW = T paw PP - EAUG = 605.392 - DEXC = 0.000 - RMAX = 1.553 core radius for proj-oper - RAUG = 1.300 factor for augmentation sphere - RDEP = 1.550 radius for radial grids - RDEPT = 1.329 core radius for aug-charge - - Atomic configuration - 4 entries - n l j E occ. - 1 0 0.50 -514.6923 2.0000 - 2 0 0.50 -23.9615 2.0000 - 2 1 0.50 -9.0305 4.0000 - 3 2 1.50 -9.5241 0.0000 - Description - l E TYP RCUT TYP RCUT - 0 -23.9615318 23 1.200 - 0 -9.5240782 23 1.200 - 1 -9.0304911 23 1.520 - 1 8.1634956 23 1.520 - 2 -9.5240782 7 1.500 - local pseudopotential read in - partial core-charges read in - partial kinetic energy density read in - kinetic energy density of atom read in - atomic valenz-charges read in - non local Contribution for L= 0 read in - real space projection operators read in - non local Contribution for L= 0 read in - real space projection operators read in - non local Contribution for L= 1 read in - real space projection operators read in - non local Contribution for L= 1 read in - real space projection operators read in - PAW grid and wavefunctions read in - - number of l-projection operators is LMAX = 4 - number of lm-projection operators is LMMAX = 8 - - PAW_PBE Hf 20Jan2003 : - energy of atom 1 EATOM= -75.9011 - kinetic energy error for atom= 0.0007 (will be added to EATOM!!) - PAW_PBE O 08Apr2002 : - energy of atom 2 EATOM= -432.3788 - kinetic energy error for atom= 0.0224 (will be added to EATOM!!) - - - POSCAR: Primitive Cell - positions in direct lattice - No initial velocities read in - - METAGGA = SCAN LMAXTAU = 0 LMIXTAU = F - - exchange correlation table for LEXCH = 8 - RHO(1)= 0.500 N(1) = 2000 - RHO(2)= 100.500 N(2) = 4000 - - - --------------------------------------------------------------------------------------------------------- - - - ion position nearest neighbor table - 1 0.543 0.776 0.292- 7 1.98 8 2.00 10 2.08 6 2.09 5 2.10 12 2.19 11 2.19 4 3.23 - 3 3.32 3 3.32 2 3.35 2 3.35 4 3.37 4 3.47 2 3.81 2 3.81 - 2 0.043 0.224 0.208- 8 1.98 7 2.00 9 2.08 5 2.09 6 2.10 11 2.19 12 2.19 3 3.23 - 4 3.32 4 3.32 1 3.35 1 3.35 3 3.37 3 3.47 1 3.81 1 3.81 - 3 0.957 0.776 0.792- 10 1.98 9 2.00 7 2.08 12 2.09 11 2.10 6 2.19 5 2.19 2 3.23 - 1 3.32 1 3.32 4 3.35 4 3.35 2 3.37 2 3.47 4 3.81 4 3.81 - 4 0.457 0.224 0.708- 9 1.98 10 2.00 8 2.08 11 2.09 12 2.10 5 2.19 6 2.19 1 3.23 - 2 3.32 2 3.32 3 3.35 3 3.35 1 3.37 1 3.47 3 3.81 3 3.81 - 5 0.757 0.052 0.478- 2 2.09 1 2.10 4 2.19 3 2.19 - 6 0.257 0.948 0.022- 1 2.09 2 2.10 3 2.19 4 2.19 - 7 0.832 0.569 0.154- 1 1.98 2 2.00 3 2.08 - 8 0.332 0.431 0.346- 2 1.98 1 2.00 4 2.08 - 9 0.168 0.431 0.846- 4 1.98 3 2.00 2 2.08 - 10 0.668 0.569 0.654- 3 1.98 4 2.00 1 2.08 - 11 0.743 0.052 0.978- 4 2.09 3 2.10 2 2.19 1 2.19 - 12 0.243 0.948 0.522- 3 2.09 4 2.10 1 2.19 2 2.19 - - LATTYP: Found a simple monoclinic cell. - ALAT = 7.7415262917 - B/A-ratio = 0.6517496159 - C/A-ratio = 1.5432771295 - COS(beta) = -0.9616437168 - - Lattice vectors: - - A1 = ( 0.0000000000, -5.8276584059, -5.0960403089) - A2 = ( -5.0455367868, 0.0000000000, 0.0000000000) - A3 = ( 0.0000000000, 10.8060002956, 5.0959615490) - - -Analysis of symmetry for initial positions (statically): -===================================================================== - Subroutine PRICEL returns: - Original cell was already a primitive cell. - - - Routine SETGRP: Setting up the symmetry group for a - simple monoclinic supercell. - - - Subroutine GETGRP returns: Found 4 space group operations - (whereof 2 operations were pure point group operations) - out of a pool of 4 trial point group operations. - - -The static configuration has the point symmetry S_2 . - The point group associated with its full space group is C_2h. - - -Analysis of symmetry for dynamics (positions and initial velocities): -===================================================================== - Subroutine PRICEL returns: - Original cell was already a primitive cell. - - - Routine SETGRP: Setting up the symmetry group for a - simple monoclinic supercell. - - - Subroutine GETGRP returns: Found 4 space group operations - (whereof 2 operations were pure point group operations) - out of a pool of 4 trial point group operations. - - -The dynamic configuration has the point symmetry S_2 . - The point group associated with its full space group is C_2h. - - -Analysis of constrained symmetry for selective dynamics: -===================================================================== - Subroutine PRICEL returns: - Original cell was already a primitive cell. - - - Routine SETGRP: Setting up the symmetry group for a - simple monoclinic supercell. - - - Subroutine GETGRP returns: Found 4 space group operations - (whereof 2 operations were pure point group operations) - out of a pool of 4 trial point group operations. - - -The constrained configuration has the point symmetry S_2 . - The point group associated with its full space group is C_2h. - - - Subroutine INISYM returns: Found 4 space group operations - (whereof 2 operations are pure point group operations), - and found 1 'primitive' translations - - - - KPOINTS: Auto k-point - -Automatic generation of k-mesh. -Space group operators: - irot det(A) alpha n_x n_y n_z tau_x tau_y tau_z - 1 1.000000 0.000001 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 - 2 -1.000000 0.000001 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 - 3 1.000000 179.999999 1.000000 0.000000 0.000000 -0.500000 1.000000 0.500000 - 4 -1.000000 179.999999 1.000000 0.000000 0.000000 -0.500000 1.000000 0.500000 - - Subroutine IBZKPT returns following result: - =========================================== - - Found 10 irreducible k-points: - - Following reciprocal coordinates: - Coordinates Weight - 0.000000 0.000000 0.000000 1.000000 - 0.333333 0.000000 0.000000 2.000000 - 0.000000 0.333333 0.000000 2.000000 - 0.333333 0.333333 0.000000 4.000000 - 0.000000 0.000000 0.333333 2.000000 - 0.333333 0.000000 0.333333 4.000000 - 0.000000 0.333333 0.333333 2.000000 - 0.333333 0.333333 0.333333 4.000000 - 0.000000 -0.333333 0.333333 2.000000 - 0.333333 -0.333333 0.333333 4.000000 - - Following cartesian coordinates: - Coordinates Weight - 0.000000 0.000000 0.000000 1.000000 - 0.066065 0.000000 0.000000 2.000000 - 0.000000 0.066957 -0.011159 2.000000 - 0.066065 0.066957 -0.011159 4.000000 - 0.000000 0.000001 0.065409 2.000000 - 0.066065 0.000001 0.065409 4.000000 - 0.000000 0.066958 0.054250 2.000000 - 0.066065 0.066958 0.054250 4.000000 - 0.000000 -0.066955 0.076568 2.000000 - 0.066065 -0.066955 0.076568 4.000000 - - - --------------------------------------------------------------------------------------------------------- - - - - - Dimension of arrays: - k-points NKPTS = 10 k-points in BZ NKDIM = 10 number of bands NBANDS= 40 - number of dos NEDOS = 301 number of ions NIONS = 12 - non local maximal LDIM = 6 non local SUM 2l+1 LMDIM = 18 - total plane-waves NPLWV = 57600 - max r-space proj IRMAX = 1 max aug-charges IRDMAX= 30410 - dimension x,y,z NGX = 40 NGY = 36 NGZ = 40 - dimension x,y,z NGXF= 80 NGYF= 72 NGZF= 80 - support grid NGXF= 80 NGYF= 72 NGZF= 80 - ions per type = 4 8 - NGX,Y,Z is equivalent to a cutoff of 13.18, 12.02, 12.87 a.u. - NGXF,Y,Z is equivalent to a cutoff of 26.36, 24.04, 25.74 a.u. - - SYSTEM = HfO2_p21c - POSCAR = Primitive Cell - - Startparameter for this run: - NWRITE = 2 write-flag & timer - PREC = accura normal or accurate (medium, high low for compatibility) - ISTART = 0 job : 0-new 1-cont 2-samecut - ICHARG = 2 charge: 1-file 2-atom 10-const - ISPIN = 1 spin polarized calculation? - LNONCOLLINEAR = F non collinear calculations - LSORBIT = F spin-orbit coupling - INIWAV = 1 electr: 0-lowe 1-rand 2-diag - LASPH = F aspherical Exc in radial PAW - METAGGA= F non-selfconsistent MetaGGA calc. - - Electronic Relaxation 1 - ENCUT = 500.0 eV 36.75 Ry 6.06 a.u. 9.20 9.08 9.42*2*pi/ulx,y,z - ENINI = 500.0 initial cutoff - ENAUG = 605.4 eV augmentation charge cutoff - NELM = 100; NELMIN= 2; NELMDL= -5 # of ELM steps - EDIFF = 0.1E-05 stopping-criterion for ELM - LREAL = F real-space projection - NLSPLINE = F spline interpolate recip. space projectors - LCOMPAT= F compatible to vasp.4.4 - GGA_COMPAT = T GGA compatible to vasp.4.4-vasp.4.6 - LMAXPAW = -100 max onsite density - LMAXMIX = 2 max onsite mixed and CHGCAR - VOSKOWN= 0 Vosko Wilk Nusair interpolation - ROPT = 0.00000 0.00000 - Ionic relaxation - EDIFFG = -.2E-02 stopping-criterion for IOM - NSW = 0 number of steps for IOM - NBLOCK = 1; KBLOCK = 1 inner block; outer block - IBRION = -1 ionic relax: 0-MD 1-quasi-New 2-CG - NFREE = 1 steps in history (QN), initial steepest desc. (CG) - ISIF = 3 stress and relaxation - IWAVPR = 10 prediction: 0-non 1-charg 2-wave 3-comb - ISYM = 1 0-nonsym 1-usesym 2-fastsym - LCORR = T Harris-Foulkes like correction to forces - - POTIM = 0.5000 time-step for ionic-motion - TEIN = 0.0 initial temperature - TEBEG = 0.0; TEEND = 0.0 temperature during run - SMASS = -3.00 Nose mass-parameter (am) - estimated Nose-frequenzy (Omega) = 0.10E-29 period in steps =****** mass= -0.582E-27a.u. - SCALEE = 1.0000 scale energy and forces - NPACO = 256; APACO = 16.0 distance and # of slots for P.C. - PSTRESS= 0.0 pullay stress - - Mass of Ions in am - POMASS = 178.49 16.00 - Ionic Valenz - ZVAL = 4.00 6.00 - Atomic Wigner-Seitz radii - RWIGS = -1.00 -1.00 - virtual crystal weights - VCA = 1.00 1.00 - NELECT = 64.0000 total number of electrons - NUPDOWN= -1.0000 fix difference up-down - - DOS related values: - EMIN = 10.00; EMAX =-10.00 energy-range for DOS - EFERMI = 0.00 - ISMEAR = 0; SIGMA = 0.05 broadening in eV -4-tet -1-fermi 0-gaus - - Electronic relaxation 2 (details) - IALGO = 38 algorithm - LDIAG = T sub-space diagonalisation (order eigenvalues) - LSUBROT= F optimize rotation matrix (better conditioning) - TURBO = 0 0=normal 1=particle mesh - IRESTART = 0 0=no restart 2=restart with 2 vectors - NREBOOT = 0 no. of reboots - NMIN = 0 reboot dimension - EREF = 0.00 reference energy to select bands - IMIX = 4 mixing-type and parameters - AMIX = 0.40; BMIX = 1.00 - AMIX_MAG = 1.60; BMIX_MAG = 1.00 - AMIN = 0.10 - WC = 100.; INIMIX= 1; MIXPRE= 1; MAXMIX= -45 - - Intra band minimization: - WEIMIN = 0.0000 energy-eigenvalue tresh-hold - EBREAK = 0.62E-08 absolut break condition - DEPER = 0.30 relativ break condition - - TIME = 0.40 timestep for ELM - - volume/ion in A,a.u. = 10.67 71.99 - Fermi-wavevector in a.u.,A,eV,Ry = 1.299343 2.455403 22.970618 1.688293 - Thomas-Fermi vector in A = 2.430613 - - Write flags - LWAVE = F write WAVECAR - LDOWNSAMPLE = F k-point downsampling of WAVECAR - LCHARG = F write CHGCAR - LVTOT = F write LOCPOT, total local potential - LVHAR = F write LOCPOT, Hartree potential only - LELF = F write electronic localiz. function (ELF) - LORBIT = 0 0 simple, 1 ext, 2 COOP (PROOUT), +10 PAW based schemes - - - Dipole corrections - LMONO = F monopole corrections only (constant potential shift) - LDIPOL = F correct potential (dipole corrections) - IDIPOL = 0 1-x, 2-y, 3-z, 4-all directions - EPSILON= 1.0000000 bulk dielectric constant - - Exchange correlation treatment: - GGA = -- GGA type - LEXCH = 8 internal setting for exchange type - VOSKOWN= 0 Vosko Wilk Nusair interpolation - LHFCALC = F Hartree Fock is set to - LHFONE = F Hartree Fock one center treatment - AEXX = 0.0000 exact exchange contribution - - Linear response parameters - LEPSILON= F determine dielectric tensor - LRPA = F only Hartree local field effects (RPA) - LNABLA = F use nabla operator in PAW spheres - LVEL = F velocity operator in full k-point grid - LINTERFAST= F fast interpolation - KINTER = 0 interpolate to denser k-point grid - CSHIFT =0.1000 complex shift for real part using Kramers Kronig - OMEGAMAX= -1.0 maximum frequency - DEG_THRESHOLD= 0.2000000E-02 threshold for treating states as degnerate - RTIME = -0.100 relaxation time in fs - (WPLASMAI= 0.000 imaginary part of plasma frequency in eV, 0.658/RTIME) - DFIELD = 0.0000000 0.0000000 0.0000000 field for delta impulse in time - - Orbital magnetization related: - ORBITALMAG= F switch on orbital magnetization - LCHIMAG = F perturbation theory with respect to B field - DQ = 0.001000 dq finite difference perturbation B field - LLRAUG = F two centre corrections for induced B field - - - --------------------------------------------------------------------------------------------------------- - - - Static calculation - charge density and potential will be updated during run - non-spin polarized calculation - Variant of blocked Davidson - Davidson routine will perform the subspace rotation - perform sub-space diagonalisation - after iterative eigenvector-optimisation - modified Broyden-mixing scheme, WC = 100.0 - initial mixing is a Kerker type mixing with AMIX = 0.4000 and BMIX = 1.0000 - Hartree-type preconditioning will be used - using additional bands 8 - reciprocal scheme for non local part - use partial core corrections - calculate Harris-corrections to forces - (improved forces if not selfconsistent) - use gradient corrections - use of overlap-Matrix (Vanderbilt PP) - Gauss-broadening in eV SIGMA = 0.05 - - --------------------------------------------------------------------------------------------------------- - - - energy-cutoff : 500.00 - volume of cell : 128.01 - direct lattice vectors reciprocal lattice vectors - 5.045536787 0.000000000 0.000000000 0.198194968 0.000000000 0.000000000 - 0.000000000 4.978341890 -0.000078760 0.000000000 0.200869564 -0.033476816 - 0.000000000 0.849316516 5.096119069 0.000000000 0.000003104 0.196227237 - - length of vectors - 5.045536787 4.978341890 5.166407660 0.198194968 0.203640072 0.196227237 - - - - k-points in units of 2pi/SCALE and weight: Auto k-point - 0.00000000 0.00000000 0.00000000 0.037 - 0.06606499 0.00000000 0.00000000 0.074 - 0.00000000 0.06695652 -0.01115894 0.074 - 0.06606499 0.06695652 -0.01115894 0.148 - 0.00000000 0.00000103 0.06540908 0.074 - 0.06606499 0.00000103 0.06540908 0.148 - 0.00000000 0.06695756 0.05425014 0.074 - 0.06606499 0.06695756 0.05425014 0.148 - 0.00000000 -0.06695549 0.07656802 0.074 - 0.06606499 -0.06695549 0.07656802 0.148 - - k-points in reciprocal lattice and weights: Auto k-point - 0.00000000 0.00000000 0.00000000 0.037 - 0.33333333 0.00000000 0.00000000 0.074 - 0.00000000 0.33333333 0.00000000 0.074 - 0.33333333 0.33333333 0.00000000 0.148 - 0.00000000 0.00000000 0.33333333 0.074 - 0.33333333 0.00000000 0.33333333 0.148 - 0.00000000 0.33333333 0.33333333 0.074 - 0.33333333 0.33333333 0.33333333 0.148 - 0.00000000 -0.33333333 0.33333333 0.074 - 0.33333333 -0.33333333 0.33333333 0.148 - - position of ions in fractional coordinates (direct lattice) - 0.54288322 0.77577220 0.29175508 - 0.04288322 0.22422780 0.20824492 - 0.95711678 0.77577220 0.79175508 - 0.45711678 0.22422780 0.70824492 - 0.75741482 0.05184460 0.47813308 - 0.25741482 0.94815540 0.02186692 - 0.83182355 0.56876319 0.15428653 - 0.33182355 0.43123681 0.34571347 - 0.16817645 0.43123681 0.84571347 - 0.66817645 0.56876319 0.65428653 - 0.74258518 0.05184460 0.97813308 - 0.24258518 0.94815540 0.52186692 - - position of ions in cartesian coordinates (Angst): - 2.73913725 4.10985163 1.48675750 - 0.21636886 1.29314852 1.06122327 - 4.82916793 4.53450989 4.03481704 - 2.30639954 1.71780678 3.60928280 - 3.82156436 0.66418648 2.43661903 - 1.29879596 4.73881367 0.11136175 - 4.19699631 2.96253571 0.78621776 - 1.67422792 2.44046444 1.76176302 - 0.84854047 2.86512270 4.30982255 - 3.37130887 3.38719397 3.33427729 - 3.74674082 1.08884473 4.98467856 - 1.22397243 5.16347193 2.65942128 - - - --------------------------------------------------------------------------------------------------------- - - - k-point 1 : 0.0000 0.0000 0.0000 plane waves: 3235 - k-point 2 : 0.3333 0.0000 0.0000 plane waves: 3246 - k-point 3 : 0.0000 0.3333 0.0000 plane waves: 3260 - k-point 4 : 0.3333 0.3333 0.0000 plane waves: 3264 - k-point 5 : 0.0000 0.0000 0.3333 plane waves: 3246 - k-point 6 : 0.3333 0.0000 0.3333 plane waves: 3248 - k-point 7 : 0.0000 0.3333 0.3333 plane waves: 3253 - k-point 8 : 0.3333 0.3333 0.3333 plane waves: 3254 - k-point 9 : 0.0000-0.3333 0.3333 plane waves: 3245 - k-point 10 : 0.3333-0.3333 0.3333 plane waves: 3251 - - maximum and minimum number of plane-waves per node : 433 382 - - maximum number of plane-waves: 3264 - maximum index in each direction: - IXMAX= 9 IYMAX= 9 IZMAX= 9 - IXMIN= -9 IYMIN= -9 IZMIN= -9 - - - parallel 3D FFT for wavefunctions: - minimum data exchange during FFTs selected (reduces bandwidth) - parallel 3D FFT for charge: - minimum data exchange during FFTs selected (reduces bandwidth) - - - total amount of memory used by VASP MPI-rank0 36333. kBytes -======================================================================= - - base : 30000. kBytes - nonl-proj : 1277. kBytes - fftplans : 1209. kBytes - grid : 2402. kBytes - one-center: 31. kBytes - wavefun : 1414. kBytes - - INWAV: cpu time 0.0000: real time 0.0000 - Broyden mixing: mesh for mixing (old mesh) - NGX = 19 NGY = 19 NGZ = 19 - (NGX = 80 NGY = 72 NGZ = 80) - gives a total of 6859 points - - initial charge density was supplied: - charge density of overlapping atoms calculated - number of electron 64.0000000 magnetization - keeping initial charge density in first step - - --------------------------------------------------------------------------------------------------------- - - - Maximum index for augmentation-charges 1791 (set IRDMAX) - - --------------------------------------------------------------------------------------------------------- - - - First call to EWALD: gamma= 0.352 - Maximum number of real-space cells 3x 3x 3 - Maximum number of reciprocal cells 3x 3x 3 - - FEWALD: cpu time 0.0014: real time 0.0014 - - ---------------------------------------- Iteration 1( 1) --------------------------------------- - - - POTLOK: cpu time 0.0436: real time 0.0913 - SETDIJ: cpu time 0.0025: real time 0.0025 - EDDAV: cpu time 0.2458: real time 0.2464 - DOS: cpu time 0.0004: real time 0.0004 - -------------------------------------------- - LOOP: cpu time 0.2923: real time 0.3406 - - eigenvalue-minimisations : 800 - total energy-change (2. order) : 0.1473633E+03 (-0.3436984E+04) - number of electron 64.0000000 magnetization - augmentation part 64.0000000 magnetization - - Free energy of the ion-electron system (eV) - --------------------------------------------------- - alpha Z PSCENC = 257.69365871 - Ewald energy TEWEN = -3156.08563984 - -Hartree energ DENC = -902.80395378 - -exchange EXHF = 0.00000000 - -V(xc)+E(xc) XCENC = 75.22532175 - PAW double counting = 3196.24842107 -3219.62951610 - entropy T*S EENTRO = -0.00142657 - eigenvalues EBANDS = 134.26357121 - atomic energy EATOM = 3762.45289366 - Solvation Ediel_sol = 0.00000000 - --------------------------------------------------- - free energy TOTEN = 147.36333012 eV - - energy without entropy = 147.36475669 energy(sigma->0) = 147.36404340 - - --------------------------------------------------------------------------------------------------------- - - - - ---------------------------------------- Iteration 1( 2) --------------------------------------- - - - EDDAV: cpu time 0.2955: real time 0.2992 - DOS: cpu time 0.0002: real time 0.0002 - -------------------------------------------- - LOOP: cpu time 0.2957: real time 0.2994 - - eigenvalue-minimisations : 1072 - total energy-change (2. order) :-0.5021166E+03 (-0.4850745E+03) - number of electron 64.0000000 magnetization - augmentation part 64.0000000 magnetization - - Free energy of the ion-electron system (eV) - --------------------------------------------------- - alpha Z PSCENC = 257.69365871 - Ewald energy TEWEN = -3156.08563984 - -Hartree energ DENC = -902.80395378 - -exchange EXHF = 0.00000000 - -V(xc)+E(xc) XCENC = 75.22532175 - PAW double counting = 3196.24842107 -3219.62951610 - entropy T*S EENTRO = -0.00000000 - eigenvalues EBANDS = -367.85441192 - atomic energy EATOM = 3762.45289366 - Solvation Ediel_sol = 0.00000000 - --------------------------------------------------- - free energy TOTEN = -354.75322645 eV - - energy without entropy = -354.75322645 energy(sigma->0) = -354.75322645 - - --------------------------------------------------------------------------------------------------------- - - - - ---------------------------------------- Iteration 1( 3) --------------------------------------- - - - EDDAV: cpu time 0.2730: real time 0.2739 - DOS: cpu time 0.0002: real time 0.0002 - -------------------------------------------- - LOOP: cpu time 0.2732: real time 0.2741 - - eigenvalue-minimisations : 960 - total energy-change (2. order) :-0.2638211E+02 (-0.2625204E+02) - number of electron 64.0000000 magnetization - augmentation part 64.0000000 magnetization - - Free energy of the ion-electron system (eV) - --------------------------------------------------- - alpha Z PSCENC = 257.69365871 - Ewald energy TEWEN = -3156.08563984 - -Hartree energ DENC = -902.80395378 - -exchange EXHF = 0.00000000 - -V(xc)+E(xc) XCENC = 75.22532175 - PAW double counting = 3196.24842107 -3219.62951610 - entropy T*S EENTRO = -0.00000000 - eigenvalues EBANDS = -394.23652007 - atomic energy EATOM = 3762.45289366 - Solvation Ediel_sol = 0.00000000 - --------------------------------------------------- - free energy TOTEN = -381.13533459 eV - - energy without entropy = -381.13533459 energy(sigma->0) = -381.13533459 - - --------------------------------------------------------------------------------------------------------- - - - - ---------------------------------------- Iteration 1( 4) --------------------------------------- - - - EDDAV: cpu time 0.2754: real time 0.2763 - DOS: cpu time 0.0002: real time 0.0002 - -------------------------------------------- - LOOP: cpu time 0.2756: real time 0.2765 - - eigenvalue-minimisations : 968 - total energy-change (2. order) :-0.3717037E+00 (-0.3705269E+00) - number of electron 64.0000000 magnetization - augmentation part 64.0000000 magnetization - - Free energy of the ion-electron system (eV) - --------------------------------------------------- - alpha Z PSCENC = 257.69365871 - Ewald energy TEWEN = -3156.08563984 - -Hartree energ DENC = -902.80395378 - -exchange EXHF = 0.00000000 - -V(xc)+E(xc) XCENC = 75.22532175 - PAW double counting = 3196.24842107 -3219.62951610 - entropy T*S EENTRO = -0.00000000 - eigenvalues EBANDS = -394.60822372 - atomic energy EATOM = 3762.45289366 - Solvation Ediel_sol = 0.00000000 - --------------------------------------------------- - free energy TOTEN = -381.50703825 eV - - energy without entropy = -381.50703825 energy(sigma->0) = -381.50703825 - - --------------------------------------------------------------------------------------------------------- - - - - ---------------------------------------- Iteration 1( 5) --------------------------------------- - - - EDDAV: cpu time 0.2665: real time 0.2675 - DOS: cpu time 0.0002: real time 0.0002 - CHARGE: cpu time 0.1095: real time 0.1097 - MIXING: cpu time 0.0013: real time 0.0014 - -------------------------------------------- - LOOP: cpu time 0.3775: real time 0.3788 - - eigenvalue-minimisations : 928 - total energy-change (2. order) :-0.7929114E-02 (-0.7925689E-02) - number of electron 63.9999989 magnetization - augmentation part 6.7358720 magnetization - - Broyden mixing: - rms(total) = 0.57406E+01 rms(broyden)= 0.57404E+01 - rms(prec ) = 0.72527E+01 - weight for this iteration 100.00 - - Free energy of the ion-electron system (eV) - --------------------------------------------------- - alpha Z PSCENC = 257.69365871 - Ewald energy TEWEN = -3156.08563984 - -Hartree energ DENC = -902.80395378 - -exchange EXHF = 0.00000000 - -V(xc)+E(xc) XCENC = 75.22532175 - PAW double counting = 3196.24842107 -3219.62951610 - entropy T*S EENTRO = -0.00000000 - eigenvalues EBANDS = -394.61615284 - atomic energy EATOM = 3762.45289366 - Solvation Ediel_sol = 0.00000000 - --------------------------------------------------- - free energy TOTEN = -381.51496736 eV - - energy without entropy = -381.51496736 energy(sigma->0) = -381.51496736 - - --------------------------------------------------------------------------------------------------------- - - - - ---------------------------------------- Iteration 1( 6) --------------------------------------- - - - POTLOK: cpu time 0.0404: real time 0.0407 - SETDIJ: cpu time 0.0194: real time 0.0194 - EDDAV: cpu time 0.2639: real time 0.2647 - DOS: cpu time 0.0002: real time 0.0002 - CHARGE: cpu time 0.1058: real time 0.1060 - MIXING: cpu time 0.0011: real time 0.0011 - -------------------------------------------- - LOOP: cpu time 0.4309: real time 0.4323 - - eigenvalue-minimisations : 920 - total energy-change (2. order) : 0.3504811E+02 (-0.6994518E+01) - number of electron 63.9999992 magnetization - augmentation part 5.8905898 magnetization - - Broyden mixing: - rms(total) = 0.28995E+01 rms(broyden)= 0.28994E+01 - rms(prec ) = 0.30489E+01 - weight for this iteration 100.00 - - eigenvalues of (default mixing * dielectric matrix) - average eigenvalue GAMMA= 1.6076 - 1.6076 - - Free energy of the ion-electron system (eV) - --------------------------------------------------- - alpha Z PSCENC = 257.69365871 - Ewald energy TEWEN = -3156.08563984 - -Hartree energ DENC = -1065.18746725 - -exchange EXHF = 0.00000000 - -V(xc)+E(xc) XCENC = 99.01751428 - PAW double counting = 4662.02176483 -4687.85751171 - entropy T*S EENTRO = -0.00000000 - eigenvalues EBANDS = -218.52207296 - atomic energy EATOM = 3762.45289366 - Solvation Ediel_sol = 0.00000000 - --------------------------------------------------- - free energy TOTEN = -346.46686028 eV - - energy without entropy = -346.46686028 energy(sigma->0) = -346.46686028 - - --------------------------------------------------------------------------------------------------------- - - - - ---------------------------------------- Iteration 1( 7) --------------------------------------- - - - POTLOK: cpu time 0.0404: real time 0.0407 - SETDIJ: cpu time 0.0193: real time 0.0194 - EDDAV: cpu time 0.2979: real time 0.2987 - DOS: cpu time 0.0002: real time 0.0002 - CHARGE: cpu time 0.1060: real time 0.1063 - MIXING: cpu time 0.0012: real time 0.0012 - -------------------------------------------- - LOOP: cpu time 0.4650: real time 0.4665 - - eigenvalue-minimisations : 1112 - total energy-change (2. order) :-0.1146851E+01 (-0.3583562E+00) - number of electron 63.9999992 magnetization - augmentation part 5.7783006 magnetization - - Broyden mixing: - rms(total) = 0.12729E+01 rms(broyden)= 0.12729E+01 - rms(prec ) = 0.13511E+01 - weight for this iteration 100.00 - - eigenvalues of (default mixing * dielectric matrix) - average eigenvalue GAMMA= 1.7365 - 1.1477 2.3253 - - Free energy of the ion-electron system (eV) - --------------------------------------------------- - alpha Z PSCENC = 257.69365871 - Ewald energy TEWEN = -3156.08563984 - -Hartree energ DENC = -1087.29253463 - -exchange EXHF = 0.00000000 - -V(xc)+E(xc) XCENC = 98.20580272 - PAW double counting = 6192.27255734 -6218.95292998 - entropy T*S EENTRO = -0.00000000 - eigenvalues EBANDS = -195.90751946 - atomic energy EATOM = 3762.45289366 - Solvation Ediel_sol = 0.00000000 - --------------------------------------------------- - free energy TOTEN = -347.61371149 eV - - energy without entropy = -347.61371149 energy(sigma->0) = -347.61371149 - - --------------------------------------------------------------------------------------------------------- - - - - ---------------------------------------- Iteration 1( 8) --------------------------------------- - - - POTLOK: cpu time 0.0404: real time 0.0407 - SETDIJ: cpu time 0.0194: real time 0.0195 - EDDAV: cpu time 0.2698: real time 0.2705 - DOS: cpu time 0.0002: real time 0.0002 - CHARGE: cpu time 0.1067: real time 0.1069 - MIXING: cpu time 0.0012: real time 0.0012 - -------------------------------------------- - LOOP: cpu time 0.4377: real time 0.4390 - - eigenvalue-minimisations : 944 - total energy-change (2. order) : 0.3260899E-01 (-0.9074028E-01) - number of electron 63.9999992 magnetization - augmentation part 5.8949094 magnetization - - Broyden mixing: - rms(total) = 0.13722E+00 rms(broyden)= 0.13717E+00 - rms(prec ) = 0.24934E+00 - weight for this iteration 100.00 - - eigenvalues of (default mixing * dielectric matrix) - average eigenvalue GAMMA= 1.4835 - 2.3985 1.0260 1.0260 - - Free energy of the ion-electron system (eV) - --------------------------------------------------- - alpha Z PSCENC = 257.69365871 - Ewald energy TEWEN = -3156.08563984 - -Hartree energ DENC = -1078.52390206 - -exchange EXHF = 0.00000000 - -V(xc)+E(xc) XCENC = 98.98709434 - PAW double counting = 7742.46254432 -7769.93252792 - entropy T*S EENTRO = -0.00000000 - eigenvalues EBANDS = -204.63522371 - atomic energy EATOM = 3762.45289366 - Solvation Ediel_sol = 0.00000000 - --------------------------------------------------- - free energy TOTEN = -347.58110249 eV - - energy without entropy = -347.58110249 energy(sigma->0) = -347.58110249 - - --------------------------------------------------------------------------------------------------------- - - - - ---------------------------------------- Iteration 1( 9) --------------------------------------- - - - POTLOK: cpu time 0.0404: real time 0.0407 - SETDIJ: cpu time 0.0192: real time 0.0193 - EDDAV: cpu time 0.2725: real time 0.2734 - DOS: cpu time 0.0002: real time 0.0002 - CHARGE: cpu time 0.1054: real time 0.1058 - MIXING: cpu time 0.0013: real time 0.0013 - -------------------------------------------- - LOOP: cpu time 0.4391: real time 0.4407 - - eigenvalue-minimisations : 960 - total energy-change (2. order) : 0.3628082E-01 (-0.1697217E-01) - number of electron 63.9999992 magnetization - augmentation part 5.8508934 magnetization - - Broyden mixing: - rms(total) = 0.36157E-01 rms(broyden)= 0.36130E-01 - rms(prec ) = 0.55407E-01 - weight for this iteration 100.00 - - eigenvalues of (default mixing * dielectric matrix) - average eigenvalue GAMMA= 1.6403 - 2.2665 2.2665 1.0141 1.0141 - - Free energy of the ion-electron system (eV) - --------------------------------------------------- - alpha Z PSCENC = 257.69365871 - Ewald energy TEWEN = -3156.08563984 - -Hartree energ DENC = -1085.73434117 - -exchange EXHF = 0.00000000 - -V(xc)+E(xc) XCENC = 100.17008775 - PAW double counting = 7820.41778095 -7848.02399742 - entropy T*S EENTRO = -0.00000000 - eigenvalues EBANDS = -198.43526432 - atomic energy EATOM = 3762.45289366 - Solvation Ediel_sol = 0.00000000 - --------------------------------------------------- - free energy TOTEN = -347.54482167 eV - - energy without entropy = -347.54482167 energy(sigma->0) = -347.54482167 - - --------------------------------------------------------------------------------------------------------- - - - - ---------------------------------------- Iteration 1( 10) --------------------------------------- - - - POTLOK: cpu time 0.0403: real time 0.0407 - SETDIJ: cpu time 0.0194: real time 0.0194 - EDDAV: cpu time 0.2783: real time 0.2790 - DOS: cpu time 0.0002: real time 0.0002 - CHARGE: cpu time 0.1059: real time 0.1061 - MIXING: cpu time 0.0012: real time 0.0012 - -------------------------------------------- - LOOP: cpu time 0.4454: real time 0.4467 - - eigenvalue-minimisations : 984 - total energy-change (2. order) :-0.1873022E-02 (-0.2914462E-02) - number of electron 63.9999992 magnetization - augmentation part 5.8493094 magnetization - - Broyden mixing: - rms(total) = 0.25981E-01 rms(broyden)= 0.25971E-01 - rms(prec ) = 0.46430E-01 - weight for this iteration 100.00 - - eigenvalues of (default mixing * dielectric matrix) - average eigenvalue GAMMA= 1.4981 - 2.4382 2.2473 1.1320 0.8365 0.8365 - - Free energy of the ion-electron system (eV) - --------------------------------------------------- - alpha Z PSCENC = 257.69365871 - Ewald energy TEWEN = -3156.08563984 - -Hartree energ DENC = -1086.15978717 - -exchange EXHF = 0.00000000 - -V(xc)+E(xc) XCENC = 100.11386870 - PAW double counting = 7833.04619259 -7860.74184499 - entropy T*S EENTRO = -0.00000000 - eigenvalues EBANDS = -197.86603634 - atomic energy EATOM = 3762.45289366 - Solvation Ediel_sol = 0.00000000 - --------------------------------------------------- - free energy TOTEN = -347.54669469 eV - - energy without entropy = -347.54669469 energy(sigma->0) = -347.54669469 - - --------------------------------------------------------------------------------------------------------- - - - - ---------------------------------------- Iteration 1( 11) --------------------------------------- - - - POTLOK: cpu time 0.0403: real time 0.0407 - SETDIJ: cpu time 0.0192: real time 0.0192 - EDDAV: cpu time 0.2722: real time 0.2729 - DOS: cpu time 0.0002: real time 0.0002 - CHARGE: cpu time 0.1053: real time 0.1055 - MIXING: cpu time 0.0013: real time 0.0013 - -------------------------------------------- - LOOP: cpu time 0.4385: real time 0.4398 - - eigenvalue-minimisations : 960 - total energy-change (2. order) :-0.3085550E-03 (-0.7922855E-03) - number of electron 63.9999992 magnetization - augmentation part 5.8399913 magnetization - - Broyden mixing: - rms(total) = 0.28461E-01 rms(broyden)= 0.28457E-01 - rms(prec ) = 0.47300E-01 - weight for this iteration 100.00 - - eigenvalues of (default mixing * dielectric matrix) - average eigenvalue GAMMA= 1.5073 - 2.5374 2.5374 0.9745 0.9745 1.0101 1.0101 - - Free energy of the ion-electron system (eV) - --------------------------------------------------- - alpha Z PSCENC = 257.69365871 - Ewald energy TEWEN = -3156.08563984 - -Hartree energ DENC = -1087.54981727 - -exchange EXHF = 0.00000000 - -V(xc)+E(xc) XCENC = 100.21228588 - PAW double counting = 7846.34881157 -7874.07986322 - entropy T*S EENTRO = -0.00000000 - eigenvalues EBANDS = -196.53933274 - atomic energy EATOM = 3762.45289366 - Solvation Ediel_sol = 0.00000000 - --------------------------------------------------- - free energy TOTEN = -347.54700325 eV - - energy without entropy = -347.54700325 energy(sigma->0) = -347.54700325 - - --------------------------------------------------------------------------------------------------------- - - - - ---------------------------------------- Iteration 1( 12) --------------------------------------- - - - POTLOK: cpu time 0.0403: real time 0.0406 - SETDIJ: cpu time 0.0193: real time 0.0194 - EDDAV: cpu time 0.2722: real time 0.2731 - DOS: cpu time 0.0002: real time 0.0002 - CHARGE: cpu time 0.1052: real time 0.1054 - MIXING: cpu time 0.0013: real time 0.0013 - -------------------------------------------- - LOOP: cpu time 0.4384: real time 0.4400 - - eigenvalue-minimisations : 960 - total energy-change (2. order) : 0.1225145E-02 (-0.7320458E-03) - number of electron 63.9999992 magnetization - augmentation part 5.8476619 magnetization - - Broyden mixing: - rms(total) = 0.35868E-02 rms(broyden)= 0.35660E-02 - rms(prec ) = 0.54409E-02 - weight for this iteration 100.00 - - eigenvalues of (default mixing * dielectric matrix) - average eigenvalue GAMMA= 1.4847 - 2.9278 2.4016 1.1637 0.9534 0.9534 0.9966 0.9966 - - Free energy of the ion-electron system (eV) - --------------------------------------------------- - alpha Z PSCENC = 257.69365871 - Ewald energy TEWEN = -3156.08563984 - -Hartree energ DENC = -1086.55129321 - -exchange EXHF = 0.00000000 - -V(xc)+E(xc) XCENC = 100.10754793 - PAW double counting = 7841.61827708 -7869.35606755 - entropy T*S EENTRO = -0.00000000 - eigenvalues EBANDS = -197.42515489 - atomic energy EATOM = 3762.45289366 - Solvation Ediel_sol = 0.00000000 - --------------------------------------------------- - free energy TOTEN = -347.54577810 eV - - energy without entropy = -347.54577810 energy(sigma->0) = -347.54577810 - - --------------------------------------------------------------------------------------------------------- - - - - ---------------------------------------- Iteration 1( 13) --------------------------------------- - - - POTLOK: cpu time 0.0403: real time 0.0407 - SETDIJ: cpu time 0.0193: real time 0.0194 - EDDAV: cpu time 0.2726: real time 0.2733 - DOS: cpu time 0.0002: real time 0.0002 - CHARGE: cpu time 0.1056: real time 0.1058 - MIXING: cpu time 0.0013: real time 0.0013 - -------------------------------------------- - LOOP: cpu time 0.4394: real time 0.4407 - - eigenvalue-minimisations : 960 - total energy-change (2. order) : 0.1162659E-04 (-0.3802832E-04) - 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- --------------------------------------------------------------------------------------------------------- - - - - ---------------------------------------- Iteration 1( 14) --------------------------------------- - - - POTLOK: cpu time 0.0404: real time 0.0408 - SETDIJ: cpu time 0.0191: real time 0.0192 - EDDAV: cpu time 0.2722: real time 0.2730 - DOS: cpu time 0.0002: real time 0.0002 - CHARGE: cpu time 0.1053: real time 0.1056 - MIXING: cpu time 0.0014: real time 0.0014 - -------------------------------------------- - LOOP: cpu time 0.4386: real time 0.4401 - - eigenvalue-minimisations : 960 - total energy-change (2. order) : 0.3467099E-04 (-0.1281118E-04) - number of electron 63.9999992 magnetization - augmentation part 5.8475511 magnetization - - Broyden mixing: - rms(total) = 0.84445E-03 rms(broyden)= 0.84307E-03 - rms(prec ) = 0.11873E-02 - weight for this iteration 100.00 - - eigenvalues of (default mixing * dielectric matrix) - average eigenvalue GAMMA= 1.5400 - 3.0077 2.4655 2.4655 1.0228 1.0228 0.9970 0.9970 0.9407 0.9407 - 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0.332 0.172 0.303 0.267 -0.314 -0.220 -0.118 -0.190 -0.176 0.207 -0.065 0.052 -0.021 0.469 0.002 0.000 - -0.368 0.364 0.120 -0.331 0.012 0.227 -0.238 -0.079 0.219 -0.012 -0.034 0.040 -0.001 0.002 0.512 0.000 - 0.000 0.005 0.006 0.001 0.008 -0.000 -0.004 -0.005 -0.001 -0.005 -0.005 0.005 -0.001 0.000 0.000 0.000 - 0.001 0.006 0.007 0.007 -0.004 -0.001 -0.004 -0.005 -0.005 0.003 0.000 0.001 0.000 0.002 -0.000 -0.000 - -0.000 -0.002 0.003 -0.003 -0.005 0.001 0.001 -0.002 0.002 0.003 0.002 -0.003 0.000 -0.000 -0.001 -0.000 - - ------------------------- aborting loop because EDIFF is reached ---------------------------------------- - - - CHARGE: cpu time 0.0382: real time 0.0383 - FORLOC: cpu time 0.0026: real time 0.0026 - FORNL : cpu time 0.0556: real time 0.0558 - STRESS: cpu time 0.8502: real time 0.8525 - FORCOR: cpu time 0.0425: real time 0.1297 - FORHAR: cpu time 0.0045: real time 0.0045 - MIXING: cpu time 0.0012: real time 0.0012 - OFIELD: cpu time 0.0001: real time 0.0001 - - FORCE on cell =-STRESS in cart. coord. units (eV): - Direction XX YY ZZ XY YZ ZX - -------------------------------------------------------------------------------------- - Alpha Z 257.69366 257.69366 257.69366 - Ewald -1064.93378 -1043.63391 -1047.52239 0.00000 -85.01179 -0.00000 - Hartree 346.70588 366.94086 372.81021 -0.00000 -27.04716 -0.00000 - E(xc) -332.60272 -332.62942 -330.76317 0.00053 0.91768 -0.01552 - Local -315.92368 -355.44808 -360.35990 -0.00000 111.32393 0.00000 - n-local -150.47638 -150.36654 -159.23914 -0.16967 -2.34292 -0.06912 - augment 61.84847 61.66278 62.82360 -0.00000 0.08628 0.00000 - Kinetic 1211.15016 1209.10344 1217.23568 -0.02655 1.27044 -0.46699 - Fock 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 - ------------------------------------------------------------------------------------- - Total 13.46162 13.32278 12.67854 0.00000 -0.80354 0.00000 - in kB 168.49033 166.75265 158.68906 0.00000 -10.05744 0.00000 - external pressure = 164.64 kB Pullay stress = 0.00 kB - - - VOLUME and BASIS-vectors are now : - ----------------------------------------------------------------------------- - energy-cutoff : 500.00 - volume of cell : 128.01 - direct lattice vectors reciprocal lattice vectors - 5.045536787 0.000000000 0.000000000 0.198194968 0.000000000 0.000000000 - 0.000000000 4.978341890 -0.000078760 0.000000000 0.200869564 -0.033476816 - 0.000000000 0.849316516 5.096119069 0.000000000 0.000003104 0.196227237 - - length of vectors - 5.045536787 4.978341890 5.166407660 0.198194968 0.203640072 0.196227237 - - - FORCES acting on ions - electron-ion (+dipol) ewald-force non-local-force convergence-correction - ----------------------------------------------------------------------------------------------- - 0.903E+01 -.219E+01 0.135E+02 -.881E+01 0.939E+00 -.128E+02 -.445E+00 0.186E+01 -.106E+01 -.952E-04 0.597E-03 -.130E-03 - 0.903E+01 0.219E+01 -.135E+02 -.881E+01 -.939E+00 0.128E+02 -.445E+00 -.186E+01 0.106E+01 -.952E-04 -.597E-03 0.130E-03 - -.903E+01 -.219E+01 0.135E+02 0.881E+01 0.939E+00 -.128E+02 0.445E+00 0.186E+01 -.106E+01 0.952E-04 0.597E-03 -.130E-03 - -.903E+01 0.219E+01 -.135E+02 0.881E+01 -.939E+00 0.128E+02 0.445E+00 -.186E+01 0.106E+01 0.952E-04 -.597E-03 0.130E-03 - -.976E+01 -.273E+02 0.461E+01 0.955E+01 0.328E+02 -.333E+01 0.189E+00 -.525E+01 -.120E+01 -.274E-04 -.431E-03 -.534E-04 - -.976E+01 0.273E+02 -.461E+01 0.955E+01 -.328E+02 0.333E+01 0.189E+00 0.525E+01 0.120E+01 -.274E-04 0.431E-03 0.534E-04 - 0.103E+02 0.119E+02 -.236E+02 -.107E+02 -.131E+02 0.271E+02 0.440E+00 0.114E+01 -.334E+01 0.410E-05 0.242E-03 -.279E-03 - 0.103E+02 -.119E+02 0.236E+02 -.107E+02 0.131E+02 -.271E+02 0.440E+00 -.114E+01 0.334E+01 0.410E-05 -.242E-03 0.279E-03 - -.103E+02 -.119E+02 0.236E+02 0.107E+02 0.131E+02 -.271E+02 -.440E+00 -.114E+01 0.334E+01 -.410E-05 -.242E-03 0.279E-03 - -.103E+02 0.119E+02 -.236E+02 0.107E+02 -.131E+02 0.271E+02 -.440E+00 0.114E+01 -.334E+01 -.410E-05 0.242E-03 -.279E-03 - 0.976E+01 -.273E+02 0.461E+01 -.955E+01 0.328E+02 -.333E+01 -.189E+00 -.525E+01 -.120E+01 0.274E-04 -.431E-03 -.534E-04 - 0.976E+01 0.273E+02 -.461E+01 -.955E+01 -.328E+02 0.333E+01 -.189E+00 0.525E+01 0.120E+01 0.274E-04 0.431E-03 0.534E-04 - ----------------------------------------------------------------------------------------------- - -.333E-09 -.131E-11 0.106E-10 0.355E-14 0.711E-14 0.284E-13 -.222E-15 -.266E-14 0.000E+00 -.179E-13 0.135E-12 -.198E-12 - - - POSITION TOTAL-FORCE (eV/Angst) - ----------------------------------------------------------------------------------- - 2.73914 4.10985 1.48676 -0.131080 0.331277 -0.190150 - 0.21637 1.29315 1.06122 -0.131080 -0.331277 0.190150 - 4.82917 4.53451 4.03482 0.131080 0.331277 -0.190150 - 2.30640 1.71781 3.60928 0.131080 -0.331277 0.190150 - 3.82156 0.66419 2.43662 -0.019123 0.250137 0.082513 - 1.29880 4.73881 0.11136 -0.019123 -0.250137 -0.082513 - 4.19700 2.96254 0.78622 0.000480 -0.067120 0.170882 - 1.67423 2.44046 1.76176 0.000480 0.067120 -0.170882 - 0.84854 2.86512 4.30982 -0.000480 0.067120 -0.170882 - 3.37131 3.38719 3.33428 -0.000480 -0.067120 0.170882 - 3.74674 1.08884 4.98468 0.019123 0.250137 0.082513 - 1.22397 5.16347 2.65942 0.019123 -0.250137 -0.082513 - ----------------------------------------------------------------------------------- - total drift: -0.000000 -0.000000 0.000000 - - --------------------------------------------------------------------------------------------------------- - - - - FREE ENERGIE OF THE ION-ELECTRON SYSTEM (eV) - --------------------------------------------------- - free energy TOTEN = -347.54572842 eV - - energy without entropy= -347.54572842 energy(sigma->0) = -347.54572842 - - - --------------------------------------------------------------------------------------------------------- - - - POTLOK: cpu time 0.0600: real time 0.0602 - - --------------------------------------------------------------------------------------------------------- - - - LOOP+: cpu time 7.6625: real time 8.1741 - 4ORBIT: cpu time 0.0000: real time 0.0000 - - total amount of memory used by VASP MPI-rank0 36333. kBytes -======================================================================= - - base : 30000. kBytes - nonl-proj : 1277. kBytes - fftplans : 1209. kBytes - grid : 2402. kBytes - one-center: 31. kBytes - wavefun : 1414. kBytes - - - - General timing and accounting informations for this job: - ======================================================== - - Total CPU time used (sec): 8.302 - User time (sec): 8.264 - System time (sec): 0.038 - Elapsed time (sec): 9.533 - - Maximum memory used (kb): 50684. - Average memory used (kb): 0. - - Minor page faults: 13129 - Major page faults: 0 - Voluntary context switches: 279 diff --git a/mace-bench/3rdparty/SevenNet/example_inputs/data/label_2/OUTCAR_7 b/mace-bench/3rdparty/SevenNet/example_inputs/data/label_2/OUTCAR_7 deleted file mode 100644 index 6ad7a959381ecfd84e531d5d9a0deeabd5e6e66e..0000000000000000000000000000000000000000 --- a/mace-bench/3rdparty/SevenNet/example_inputs/data/label_2/OUTCAR_7 +++ /dev/null @@ -1,2028 +0,0 @@ - vasp.5.4.4.18Apr17-6-g9f103f2a35 (build Sep 11 2017 17:27:03) complex - - executed on GRP7IFC17NORMAL date 2022.08.24 18:31:20 - running on 32 total cores - distrk: each k-point on 16 cores, 2 groups - distr: one band on NCORES_PER_BAND= 8 cores, 2 groups - - --------------------------------------------------------------------------------------------------------- - - - INCAR: - POTCAR: PAW_PBE Hf 20Jan2003 - POTCAR: PAW_PBE O 08Apr2002 - - ----------------------------------------------------------------------------- -| | -| W W AA RRRRR N N II N N GGGG !!! | -| W W A A R R NN N II NN N G G !!! | -| W W A A R R N N N II N N N G !!! | -| W WW W AAAAAA RRRRR N N N II N N N G GGG ! | -| WW WW A A R R N NN II N NN G G | -| W W A A R R N N II N N GGGG !!! | -| | -| You have enabled k-point parallelism (KPAR>1). | -| This developmental code was originally written by Paul Kent at ORNL, | -| and carefully double checked in Vienna. | -| GW as well as linear response parallelism added by Martijn Marsman | -| and Georg Kresse. | -| Carefully verify results versus KPAR=1. | -| Report problems to Paul Kent and Vienna. | -| | - ----------------------------------------------------------------------------- - - POTCAR: PAW_PBE Hf 20Jan2003 - SHA256 = 0bb2207f9a10894133f750b65504b92b8afef976ae770762e0497daaaad8168a Hf - COPYR = (c) Copyright 20Jan2003 Georg Kresse - COPYR = This file is part of the software VASP. Any use, copying, and all ot - COPYR = If you do not have a valid VASP license, you may not use, copy or di - VRHFIN =Hf: 6s5d - LEXCH = PE - EATOM = 75.9011 eV, 5.5786 Ry - - TITEL = PAW_PBE Hf 20Jan2003 - LULTRA = F use ultrasoft PP ? - IUNSCR = 1 unscreen: 0-lin 1-nonlin 2-no - RPACOR = 2.500 partial core radius - POMASS = 178.490; ZVAL = 4.000 mass and valenz - RCORE = 3.000 outmost cutoff radius - RWIGS = 3.050; RWIGS = 1.614 wigner-seitz radius (au A) - ENMAX = 220.334; ENMIN = 165.250 eV - RCLOC = 2.212 cutoff for local pot - LCOR = T correct aug charges - LPAW = T paw PP - EAUG = 335.116 - DEXC = 0.000 - RMAX = 3.077 core radius for proj-oper - RAUG = 1.300 factor for augmentation sphere - RDEP = 3.047 radius for radial grids - RDEPT = 2.344 core radius for aug-charge - - Atomic configuration - 16 entries - n l j E occ. - 1 0 0.50 -65259.4397 2.0000 - 2 0 0.50 -11157.9882 2.0000 - 2 1 1.50 -9795.2113 6.0000 - 3 0 0.50 -2541.4058 2.0000 - 3 1 1.50 -2134.4770 6.0000 - 3 2 2.50 -1653.5418 10.0000 - 4 0 0.50 -510.9575 2.0000 - 4 1 1.50 -377.5023 6.0000 - 4 2 2.50 -205.2085 10.0000 - 4 3 3.50 -15.4905 14.0000 - 5 0 0.50 -65.6020 2.0000 - 5 1 1.50 -34.2798 6.0000 - 5 2 2.50 -1.9877 3.0000 - 6 0 0.50 -4.7357 1.0000 - 6 1 1.50 -1.3606 0.0000 - 5 3 2.50 -1.3606 0.0000 - Description - l E TYP RCUT TYP RCUT - 2 -1.9876627 23 2.500 - 2 0.0744703 23 2.500 - 0 -4.7356889 23 2.600 - 0 3.2364747 23 2.600 - 1 -1.3605826 23 3.000 - 1 27.2116520 23 3.000 - local pseudopotential read in - partial core-charges read in - partial kinetic energy density read in - atomic valenz-charges read in - non local Contribution for L= 2 read in - real space projection operators read in - non local Contribution for L= 2 read in - real space projection operators read in - non local Contribution for L= 0 read in - real space projection operators read in - non local Contribution for L= 0 read in - real space projection operators read in - non local Contribution for L= 1 read in - real space projection operators read in - non local Contribution for L= 1 read in - real space projection operators read in - PAW grid and wavefunctions read in - - number of l-projection operators is LMAX = 6 - number of lm-projection operators is LMMAX = 18 - - POTCAR: PAW_PBE O 08Apr2002 - SHA256 = 818f92134a0a090dccd8ba1447fa70422a3b330e708bb4f08108d8ae51209ddf O/ - COPYR = (c) Copyright 08Apr2002 Georg Kresse - COPYR = This file is part of the software VASP. Any use, copying, and all ot - COPYR = If you do not have a valid VASP license, you may not use, copy or di - VRHFIN =O: s2p4 - LEXCH = PE - EATOM = 432.3788 eV, 31.7789 Ry - - TITEL = PAW_PBE O 08Apr2002 - LULTRA = F use ultrasoft PP ? - IUNSCR = 1 unscreen: 0-lin 1-nonlin 2-no - RPACOR = 1.200 partial core radius - POMASS = 16.000; ZVAL = 6.000 mass and valenz - RCORE = 1.520 outmost cutoff radius - RWIGS = 1.550; RWIGS = 0.820 wigner-seitz radius (au A) - ENMAX = 400.000; ENMIN = 300.000 eV - ICORE = 2 local potential - LCOR = T correct aug charges - LPAW = T paw PP - EAUG = 605.392 - DEXC = 0.000 - RMAX = 1.553 core radius for proj-oper - RAUG = 1.300 factor for augmentation sphere - RDEP = 1.550 radius for radial grids - RDEPT = 1.329 core radius for aug-charge - - Atomic configuration - 4 entries - n l j E occ. - 1 0 0.50 -514.6923 2.0000 - 2 0 0.50 -23.9615 2.0000 - 2 1 0.50 -9.0305 4.0000 - 3 2 1.50 -9.5241 0.0000 - Description - l E TYP RCUT TYP RCUT - 0 -23.9615318 23 1.200 - 0 -9.5240782 23 1.200 - 1 -9.0304911 23 1.520 - 1 8.1634956 23 1.520 - 2 -9.5240782 7 1.500 - local pseudopotential read in - partial core-charges read in - partial kinetic energy density read in - kinetic energy density of atom read in - atomic valenz-charges read in - non local Contribution for L= 0 read in - real space projection operators read in - non local Contribution for L= 0 read in - real space projection operators read in - non local Contribution for L= 1 read in - real space projection operators read in - non local Contribution for L= 1 read in - real space projection operators read in - PAW grid and wavefunctions read in - - number of l-projection operators is LMAX = 4 - number of lm-projection operators is LMMAX = 8 - - PAW_PBE Hf 20Jan2003 : - energy of atom 1 EATOM= -75.9011 - kinetic energy error for atom= 0.0007 (will be added to EATOM!!) - PAW_PBE O 08Apr2002 : - energy of atom 2 EATOM= -432.3788 - kinetic energy error for atom= 0.0224 (will be added to EATOM!!) - - - POSCAR: Primitive Cell - positions in direct lattice - No initial velocities read in - - METAGGA = SCAN LMAXTAU = 0 LMIXTAU = F - - exchange correlation table for LEXCH = 8 - RHO(1)= 0.500 N(1) = 2000 - RHO(2)= 100.500 N(2) = 4000 - - - --------------------------------------------------------------------------------------------------------- - - - ion position nearest neighbor table - 1 0.543 0.776 0.292- 7 1.99 8 2.01 10 2.09 6 2.09 5 2.11 12 2.19 11 2.20 4 3.24 - 3 3.33 3 3.33 2 3.36 2 3.36 4 3.38 4 3.48 2 3.82 2 3.82 - 2 0.043 0.224 0.208- 8 1.99 7 2.01 9 2.09 5 2.09 6 2.11 11 2.19 12 2.20 3 3.24 - 4 3.33 4 3.33 1 3.36 1 3.36 3 3.38 3 3.48 1 3.82 1 3.82 - 3 0.957 0.776 0.792- 10 1.99 9 2.01 7 2.09 12 2.09 11 2.11 6 2.19 5 2.20 2 3.24 - 1 3.33 1 3.33 4 3.36 4 3.36 2 3.38 2 3.48 4 3.82 4 3.82 - 4 0.457 0.224 0.708- 9 1.99 10 2.01 8 2.09 11 2.09 12 2.11 5 2.19 6 2.20 1 3.24 - 2 3.33 2 3.33 3 3.36 3 3.36 1 3.38 1 3.48 3 3.82 3 3.82 - 5 0.757 0.052 0.478- 2 2.09 1 2.11 4 2.19 3 2.20 - 6 0.257 0.948 0.022- 1 2.09 2 2.11 3 2.19 4 2.20 - 7 0.832 0.569 0.154- 1 1.99 2 2.01 3 2.09 - 8 0.332 0.431 0.346- 2 1.99 1 2.01 4 2.09 - 9 0.168 0.431 0.846- 4 1.99 3 2.01 2 2.09 - 10 0.668 0.569 0.654- 3 1.99 4 2.01 1 2.09 - 11 0.743 0.052 0.978- 4 2.09 3 2.11 2 2.19 1 2.20 - 12 0.243 0.948 0.522- 3 2.09 4 2.11 1 2.19 2 2.20 - - LATTYP: Found a simple monoclinic cell. - ALAT = 7.7651525164 - B/A-ratio = 0.6517496159 - C/A-ratio = 1.5432771295 - COS(beta) = -0.9616437168 - - Lattice vectors: - - A1 = ( 0.0000000000, -5.8454437317, -5.1115928225) - A2 = ( -5.0609351696, 0.0000000000, 0.0000000000) - A3 = ( 0.0000000000, 10.8389789333, 5.1115138223) - - -Analysis of symmetry for initial positions (statically): -===================================================================== - Subroutine PRICEL returns: - Original cell was already a primitive cell. - - - Routine SETGRP: Setting up the symmetry group for a - simple monoclinic supercell. - - - Subroutine GETGRP returns: Found 4 space group operations - (whereof 2 operations were pure point group operations) - out of a pool of 4 trial point group operations. - - -The static configuration has the point symmetry S_2 . - The point group associated with its full space group is C_2h. - - -Analysis of symmetry for dynamics (positions and initial velocities): -===================================================================== - Subroutine PRICEL returns: - Original cell was already a primitive cell. - - - Routine SETGRP: Setting up the symmetry group for a - simple monoclinic supercell. - - - Subroutine GETGRP returns: Found 4 space group operations - (whereof 2 operations were pure point group operations) - out of a pool of 4 trial point group operations. - - -The dynamic configuration has the point symmetry S_2 . - The point group associated with its full space group is C_2h. - - -Analysis of constrained symmetry for selective dynamics: -===================================================================== - Subroutine PRICEL returns: - Original cell was already a primitive cell. - - - Routine SETGRP: Setting up the symmetry group for a - simple monoclinic supercell. - - - Subroutine GETGRP returns: Found 4 space group operations - (whereof 2 operations were pure point group operations) - out of a pool of 4 trial point group operations. - - -The constrained configuration has the point symmetry S_2 . - The point group associated with its full space group is C_2h. - - - Subroutine INISYM returns: Found 4 space group operations - (whereof 2 operations are pure point group operations), - and found 1 'primitive' translations - - - - KPOINTS: Auto k-point - -Automatic generation of k-mesh. -Space group operators: - irot det(A) alpha n_x n_y n_z tau_x tau_y tau_z - 1 1.000000 0.000001 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 - 2 -1.000000 0.000001 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 - 3 1.000000 180.000000 1.000000 0.000000 0.000000 -0.500000 1.000000 0.500000 - 4 -1.000000 180.000000 1.000000 0.000000 0.000000 -0.500000 1.000000 0.500000 - - Subroutine IBZKPT returns following result: - =========================================== - - Found 10 irreducible k-points: - - Following reciprocal coordinates: - Coordinates Weight - 0.000000 0.000000 0.000000 1.000000 - 0.333333 0.000000 0.000000 2.000000 - 0.000000 0.333333 -0.000000 2.000000 - 0.333333 0.333333 -0.000000 4.000000 - 0.000000 0.000000 0.333333 2.000000 - 0.333333 0.000000 0.333333 4.000000 - 0.000000 0.333333 0.333333 2.000000 - 0.333333 0.333333 0.333333 4.000000 - 0.000000 -0.333333 0.333333 2.000000 - 0.333333 -0.333333 0.333333 4.000000 - - Following cartesian coordinates: - Coordinates Weight - 0.000000 0.000000 0.000000 1.000000 - 0.065864 0.000000 0.000000 2.000000 - 0.000000 0.066753 -0.011125 2.000000 - 0.065864 0.066753 -0.011125 4.000000 - 0.000000 0.000001 0.065210 2.000000 - 0.065864 0.000001 0.065210 4.000000 - 0.000000 0.066754 0.054085 2.000000 - 0.065864 0.066754 0.054085 4.000000 - 0.000000 -0.066752 0.076335 2.000000 - 0.065864 -0.066752 0.076335 4.000000 - - - --------------------------------------------------------------------------------------------------------- - - - - - Dimension of arrays: - k-points NKPTS = 10 k-points in BZ NKDIM = 10 number of bands NBANDS= 40 - number of dos NEDOS = 301 number of ions NIONS = 12 - non local maximal LDIM = 6 non local SUM 2l+1 LMDIM = 18 - total plane-waves NPLWV = 57600 - max r-space proj IRMAX = 1 max aug-charges IRDMAX= 30135 - dimension x,y,z NGX = 40 NGY = 36 NGZ = 40 - dimension x,y,z NGXF= 80 NGYF= 72 NGZF= 80 - support grid NGXF= 80 NGYF= 72 NGZF= 80 - ions per type = 4 8 - NGX,Y,Z is equivalent to a cutoff of 13.14, 11.99, 12.83 a.u. - NGXF,Y,Z is equivalent to a cutoff of 26.28, 23.97, 25.66 a.u. - - SYSTEM = HfO2_p21c - POSCAR = Primitive Cell - - Startparameter for this run: - NWRITE = 2 write-flag & timer - PREC = accura normal or accurate (medium, high low for compatibility) - ISTART = 0 job : 0-new 1-cont 2-samecut - ICHARG = 2 charge: 1-file 2-atom 10-const - ISPIN = 1 spin polarized calculation? - LNONCOLLINEAR = F non collinear calculations - LSORBIT = F spin-orbit coupling - INIWAV = 1 electr: 0-lowe 1-rand 2-diag - LASPH = F aspherical Exc in radial PAW - METAGGA= F non-selfconsistent MetaGGA calc. - - Electronic Relaxation 1 - ENCUT = 500.0 eV 36.75 Ry 6.06 a.u. 9.23 9.10 9.45*2*pi/ulx,y,z - ENINI = 500.0 initial cutoff - ENAUG = 605.4 eV augmentation charge cutoff - NELM = 100; NELMIN= 2; NELMDL= -5 # of ELM steps - EDIFF = 0.1E-05 stopping-criterion for ELM - LREAL = F real-space projection - NLSPLINE = F spline interpolate recip. space projectors - LCOMPAT= F compatible to vasp.4.4 - GGA_COMPAT = T GGA compatible to vasp.4.4-vasp.4.6 - LMAXPAW = -100 max onsite density - LMAXMIX = 2 max onsite mixed and CHGCAR - VOSKOWN= 0 Vosko Wilk Nusair interpolation - ROPT = 0.00000 0.00000 - Ionic relaxation - EDIFFG = -.2E-02 stopping-criterion for IOM - NSW = 0 number of steps for IOM - NBLOCK = 1; KBLOCK = 1 inner block; outer block - IBRION = -1 ionic relax: 0-MD 1-quasi-New 2-CG - NFREE = 1 steps in history (QN), initial steepest desc. (CG) - ISIF = 3 stress and relaxation - IWAVPR = 10 prediction: 0-non 1-charg 2-wave 3-comb - ISYM = 1 0-nonsym 1-usesym 2-fastsym - LCORR = T Harris-Foulkes like correction to forces - - POTIM = 0.5000 time-step for ionic-motion - TEIN = 0.0 initial temperature - TEBEG = 0.0; TEEND = 0.0 temperature during run - SMASS = -3.00 Nose mass-parameter (am) - estimated Nose-frequenzy (Omega) = 0.10E-29 period in steps =****** mass= -0.585E-27a.u. - SCALEE = 1.0000 scale energy and forces - NPACO = 256; APACO = 16.0 distance and # of slots for P.C. - PSTRESS= 0.0 pullay stress - - Mass of Ions in am - POMASS = 178.49 16.00 - Ionic Valenz - ZVAL = 4.00 6.00 - Atomic Wigner-Seitz radii - RWIGS = -1.00 -1.00 - virtual crystal weights - VCA = 1.00 1.00 - NELECT = 64.0000 total number of electrons - NUPDOWN= -1.0000 fix difference up-down - - DOS related values: - EMIN = 10.00; EMAX =-10.00 energy-range for DOS - EFERMI = 0.00 - ISMEAR = 0; SIGMA = 0.05 broadening in eV -4-tet -1-fermi 0-gaus - - Electronic relaxation 2 (details) - IALGO = 38 algorithm - LDIAG = T sub-space diagonalisation (order eigenvalues) - LSUBROT= F optimize rotation matrix (better conditioning) - TURBO = 0 0=normal 1=particle mesh - IRESTART = 0 0=no restart 2=restart with 2 vectors - NREBOOT = 0 no. of reboots - NMIN = 0 reboot dimension - EREF = 0.00 reference energy to select bands - IMIX = 4 mixing-type and parameters - AMIX = 0.40; BMIX = 1.00 - AMIX_MAG = 1.60; BMIX_MAG = 1.00 - AMIN = 0.10 - WC = 100.; INIMIX= 1; MIXPRE= 1; MAXMIX= -45 - - Intra band minimization: - WEIMIN = 0.0000 energy-eigenvalue tresh-hold - EBREAK = 0.62E-08 absolut break condition - DEPER = 0.30 relativ break condition - - TIME = 0.40 timestep for ELM - - volume/ion in A,a.u. = 10.77 72.65 - Fermi-wavevector in a.u.,A,eV,Ry = 1.295390 2.447932 22.831050 1.678035 - Thomas-Fermi vector in A = 2.426913 - - Write flags - LWAVE = F write WAVECAR - LDOWNSAMPLE = F k-point downsampling of WAVECAR - LCHARG = F write CHGCAR - LVTOT = F write LOCPOT, total local potential - LVHAR = F write LOCPOT, Hartree potential only - LELF = F write electronic localiz. function (ELF) - LORBIT = 0 0 simple, 1 ext, 2 COOP (PROOUT), +10 PAW based schemes - - - Dipole corrections - LMONO = F monopole corrections only (constant potential shift) - LDIPOL = F correct potential (dipole corrections) - IDIPOL = 0 1-x, 2-y, 3-z, 4-all directions - EPSILON= 1.0000000 bulk dielectric constant - - Exchange correlation treatment: - GGA = -- GGA type - LEXCH = 8 internal setting for exchange type - VOSKOWN= 0 Vosko Wilk Nusair interpolation - LHFCALC = F Hartree Fock is set to - LHFONE = F Hartree Fock one center treatment - AEXX = 0.0000 exact exchange contribution - - Linear response parameters - LEPSILON= F determine dielectric tensor - LRPA = F only Hartree local field effects (RPA) - LNABLA = F use nabla operator in PAW spheres - LVEL = F velocity operator in full k-point grid - LINTERFAST= F fast interpolation - KINTER = 0 interpolate to denser k-point grid - CSHIFT =0.1000 complex shift for real part using Kramers Kronig - OMEGAMAX= -1.0 maximum frequency - DEG_THRESHOLD= 0.2000000E-02 threshold for treating states as degnerate - RTIME = -0.100 relaxation time in fs - (WPLASMAI= 0.000 imaginary part of plasma frequency in eV, 0.658/RTIME) - DFIELD = 0.0000000 0.0000000 0.0000000 field for delta impulse in time - - Orbital magnetization related: - ORBITALMAG= F switch on orbital magnetization - LCHIMAG = F perturbation theory with respect to B field - DQ = 0.001000 dq finite difference perturbation B field - LLRAUG = F two centre corrections for induced B field - - - --------------------------------------------------------------------------------------------------------- - - - Static calculation - charge density and potential will be updated during run - non-spin polarized calculation - Variant of blocked Davidson - Davidson routine will perform the subspace rotation - perform sub-space diagonalisation - after iterative eigenvector-optimisation - modified Broyden-mixing scheme, WC = 100.0 - initial mixing is a Kerker type mixing with AMIX = 0.4000 and BMIX = 1.0000 - Hartree-type preconditioning will be used - using additional bands 8 - reciprocal scheme for non local part - use partial core corrections - calculate Harris-corrections to forces - (improved forces if not selfconsistent) - use gradient corrections - use of overlap-Matrix (Vanderbilt PP) - Gauss-broadening in eV SIGMA = 0.05 - - --------------------------------------------------------------------------------------------------------- - - - energy-cutoff : 500.00 - volume of cell : 129.18 - direct lattice vectors reciprocal lattice vectors - 5.060935170 0.000000000 0.000000000 0.197591940 0.000000000 0.000000000 - 0.000000000 4.993535202 -0.000079000 0.000000000 0.200258399 -0.033374959 - 0.000000000 0.851908530 5.111671823 0.000000000 0.000003095 0.195630197 - - length of vectors - 5.060935170 4.993535202 5.182174926 0.197591940 0.203020477 0.195630197 - - - - k-points in units of 2pi/SCALE and weight: Auto k-point - 0.00000000 0.00000000 0.00000000 0.037 - 0.06586398 0.00000000 0.00000000 0.074 - 0.00000000 0.06675280 -0.01112499 0.074 - 0.06586398 0.06675280 -0.01112499 0.148 - 0.00000000 0.00000103 0.06521007 0.074 - 0.06586398 0.00000103 0.06521007 0.148 - 0.00000000 0.06675383 0.05408508 0.074 - 0.06586398 0.06675383 0.05408508 0.148 - 0.00000000 -0.06675177 0.07633505 0.074 - 0.06586398 -0.06675177 0.07633505 0.148 - - k-points in reciprocal lattice and weights: Auto k-point - 0.00000000 0.00000000 0.00000000 0.037 - 0.33333333 0.00000000 0.00000000 0.074 - 0.00000000 0.33333333 -0.00000000 0.074 - 0.33333333 0.33333333 -0.00000000 0.148 - 0.00000000 0.00000000 0.33333333 0.074 - 0.33333333 0.00000000 0.33333333 0.148 - 0.00000000 0.33333333 0.33333333 0.074 - 0.33333333 0.33333333 0.33333333 0.148 - 0.00000000 -0.33333333 0.33333333 0.074 - 0.33333333 -0.33333333 0.33333333 0.148 - - position of ions in fractional coordinates (direct lattice) - 0.54288322 0.77577220 0.29175508 - 0.04288322 0.22422780 0.20824492 - 0.95711678 0.77577220 0.79175508 - 0.45711678 0.22422780 0.70824492 - 0.75741482 0.05184460 0.47813308 - 0.25741482 0.94815540 0.02186692 - 0.83182355 0.56876319 0.15428653 - 0.33182355 0.43123681 0.34571347 - 0.16817645 0.43123681 0.84571347 - 0.66817645 0.56876319 0.65428653 - 0.74258518 0.05184460 0.97813308 - 0.24258518 0.94815540 0.52186692 - - position of ions in cartesian coordinates (Angst): - 2.74749677 4.12239441 1.49129491 - 0.21702919 1.29709506 1.06446200 - 4.84390598 4.54834867 4.04713082 - 2.31343840 1.72304932 3.62029791 - 3.83322732 0.66621349 2.44405530 - 1.30275974 4.75327597 0.11170161 - 4.20980505 2.97157702 0.78861720 - 1.67933747 2.44791245 1.76713971 - 0.85113012 2.87386671 4.32297562 - 3.38159770 3.39753128 3.34445311 - 3.75817543 1.09216776 4.99989121 - 1.22770785 5.17923024 2.66753752 - - - --------------------------------------------------------------------------------------------------------- - - - k-point 1 : 0.0000 0.0000 0.0000 plane waves: 3253 - k-point 2 : 0.3333 0.0000 0.0000 plane waves: 3276 - k-point 3 : 0.0000 0.3333-0.0000 plane waves: 3292 - k-point 4 : 0.3333 0.3333-0.0000 plane waves: 3296 - k-point 5 : 0.0000 0.0000 0.3333 plane waves: 3281 - k-point 6 : 0.3333 0.0000 0.3333 plane waves: 3278 - k-point 7 : 0.0000 0.3333 0.3333 plane waves: 3280 - k-point 8 : 0.3333 0.3333 0.3333 plane waves: 3285 - k-point 9 : 0.0000-0.3333 0.3333 plane waves: 3290 - k-point 10 : 0.3333-0.3333 0.3333 plane waves: 3274 - - maximum and minimum number of plane-waves per node : 432 379 - - maximum number of plane-waves: 3296 - maximum index in each direction: - IXMAX= 9 IYMAX= 9 IZMAX= 9 - IXMIN= -9 IYMIN= -9 IZMIN= -9 - - - parallel 3D FFT for wavefunctions: - minimum data exchange during FFTs selected (reduces bandwidth) - parallel 3D FFT for charge: - minimum data exchange during FFTs selected (reduces bandwidth) - - - total amount of memory used by VASP MPI-rank0 36359. kBytes -======================================================================= - - base : 30000. kBytes - nonl-proj : 1290. kBytes - fftplans : 1209. kBytes - grid : 2402. kBytes - one-center: 31. kBytes - wavefun : 1427. kBytes - - INWAV: cpu time 0.0000: real time 0.0000 - Broyden mixing: mesh for mixing (old mesh) - NGX = 19 NGY = 19 NGZ = 19 - (NGX = 80 NGY = 72 NGZ = 80) - gives a total of 6859 points - - initial charge density was supplied: - charge density of overlapping atoms calculated - number of electron 64.0000000 magnetization - keeping initial charge density in first step - - --------------------------------------------------------------------------------------------------------- - - - Maximum index for augmentation-charges 1780 (set IRDMAX) - - --------------------------------------------------------------------------------------------------------- - - - First call to EWALD: gamma= 0.351 - Maximum number of real-space cells 3x 3x 3 - Maximum number of reciprocal cells 3x 3x 3 - - FEWALD: cpu time 0.0012: real time 0.0012 - - ---------------------------------------- Iteration 1( 1) --------------------------------------- - - - POTLOK: cpu time 0.0435: real time 0.1433 - SETDIJ: cpu time 0.0025: real time 0.0025 - EDDAV: cpu time 0.2468: real time 0.2475 - DOS: cpu time 0.0004: real time 0.0004 - -------------------------------------------- - LOOP: cpu time 0.2932: real time 0.3937 - - eigenvalue-minimisations : 800 - total energy-change (2. order) : 0.1305566E+03 (-0.3435838E+04) - number of electron 64.0000000 magnetization - augmentation part 64.0000000 magnetization - - Free energy of the ion-electron system (eV) - --------------------------------------------------- - alpha Z PSCENC = 255.34863481 - Ewald energy TEWEN = -3146.48294520 - -Hartree energ DENC = -907.02645607 - -exchange EXHF = 0.00000000 - -V(xc)+E(xc) XCENC = 75.09305607 - PAW double counting = 3196.24842107 -3219.62951610 - entropy T*S EENTRO = -0.00459296 - eigenvalues EBANDS = 114.55711311 - atomic energy EATOM = 3762.45289366 - Solvation Ediel_sol = 0.00000000 - --------------------------------------------------- - free energy TOTEN = 130.55660840 eV - - energy without entropy = 130.56120136 energy(sigma->0) = 130.55890488 - - --------------------------------------------------------------------------------------------------------- - - - - ---------------------------------------- Iteration 1( 2) --------------------------------------- - - - EDDAV: cpu time 0.2881: real time 0.2976 - DOS: cpu time 0.0002: real time 0.0002 - -------------------------------------------- - LOOP: cpu time 0.2883: real time 0.2978 - - eigenvalue-minimisations : 1056 - total energy-change (2. order) :-0.4859595E+03 (-0.4677117E+03) - number of electron 64.0000000 magnetization - augmentation part 64.0000000 magnetization - - Free energy of the ion-electron system (eV) - --------------------------------------------------- - alpha Z PSCENC = 255.34863481 - Ewald energy TEWEN = -3146.48294520 - -Hartree energ DENC = -907.02645607 - -exchange EXHF = 0.00000000 - -V(xc)+E(xc) XCENC = 75.09305607 - PAW double counting = 3196.24842107 -3219.62951610 - entropy T*S EENTRO = -0.00000000 - eigenvalues EBANDS = -371.40699768 - atomic energy EATOM = 3762.45289366 - Solvation Ediel_sol = 0.00000000 - --------------------------------------------------- - free energy TOTEN = -355.40290943 eV - - energy without entropy = -355.40290943 energy(sigma->0) = -355.40290943 - - --------------------------------------------------------------------------------------------------------- - - - - ---------------------------------------- Iteration 1( 3) --------------------------------------- - - - EDDAV: cpu time 0.2742: real time 0.2751 - DOS: cpu time 0.0002: real time 0.0002 - -------------------------------------------- - LOOP: cpu time 0.2744: real time 0.2753 - - eigenvalue-minimisations : 960 - total energy-change (2. order) :-0.2592852E+02 (-0.2579047E+02) - number of electron 64.0000000 magnetization - augmentation part 64.0000000 magnetization - - Free energy of the ion-electron system (eV) - --------------------------------------------------- - alpha Z PSCENC = 255.34863481 - Ewald energy TEWEN = -3146.48294520 - -Hartree energ DENC = -907.02645607 - -exchange EXHF = 0.00000000 - -V(xc)+E(xc) XCENC = 75.09305607 - PAW double counting = 3196.24842107 -3219.62951610 - entropy T*S EENTRO = -0.00000000 - eigenvalues EBANDS = -397.33551964 - atomic energy EATOM = 3762.45289366 - Solvation Ediel_sol = 0.00000000 - --------------------------------------------------- - free energy TOTEN = -381.33143139 eV - - energy without entropy = -381.33143139 energy(sigma->0) = -381.33143139 - - --------------------------------------------------------------------------------------------------------- - - - - ---------------------------------------- Iteration 1( 4) --------------------------------------- - - - EDDAV: cpu time 0.2737: real time 0.2746 - DOS: cpu time 0.0002: real time 0.0002 - -------------------------------------------- - LOOP: cpu time 0.2739: real time 0.2748 - - eigenvalue-minimisations : 960 - total energy-change (2. order) :-0.3695473E+00 (-0.3684308E+00) - number of electron 64.0000000 magnetization - augmentation part 64.0000000 magnetization - - Free energy of the ion-electron system (eV) - --------------------------------------------------- - alpha Z PSCENC = 255.34863481 - Ewald energy TEWEN = -3146.48294520 - -Hartree energ DENC = -907.02645607 - -exchange EXHF = 0.00000000 - -V(xc)+E(xc) XCENC = 75.09305607 - PAW double counting = 3196.24842107 -3219.62951610 - entropy T*S EENTRO = -0.00000000 - eigenvalues EBANDS = -397.70506696 - atomic energy EATOM = 3762.45289366 - Solvation Ediel_sol = 0.00000000 - --------------------------------------------------- - free energy TOTEN = -381.70097872 eV - - energy without entropy = -381.70097872 energy(sigma->0) = -381.70097872 - - --------------------------------------------------------------------------------------------------------- - - - - ---------------------------------------- Iteration 1( 5) --------------------------------------- - - - EDDAV: cpu time 0.2677: real time 0.2688 - DOS: cpu time 0.0002: real time 0.0002 - CHARGE: cpu time 0.1102: real time 0.1105 - MIXING: cpu time 0.0012: real time 0.0012 - -------------------------------------------- - LOOP: cpu time 0.3793: real time 0.3807 - - eigenvalue-minimisations : 928 - total energy-change (2. order) :-0.8514421E-02 (-0.8510068E-02) - number of electron 63.9999983 magnetization - augmentation part 6.7247067 magnetization - - Broyden mixing: - rms(total) = 0.56216E+01 rms(broyden)= 0.56215E+01 - rms(prec ) = 0.71569E+01 - weight for this iteration 100.00 - - Free energy of the ion-electron system (eV) - --------------------------------------------------- - alpha Z PSCENC = 255.34863481 - Ewald energy TEWEN = -3146.48294520 - -Hartree energ DENC = -907.02645607 - -exchange EXHF = 0.00000000 - -V(xc)+E(xc) XCENC = 75.09305607 - PAW double counting = 3196.24842107 -3219.62951610 - entropy T*S EENTRO = -0.00000000 - eigenvalues EBANDS = -397.71358139 - atomic energy EATOM = 3762.45289366 - Solvation Ediel_sol = 0.00000000 - --------------------------------------------------- - free energy TOTEN = -381.70949314 eV - - energy without entropy = -381.70949314 energy(sigma->0) = -381.70949314 - - --------------------------------------------------------------------------------------------------------- - - - - ---------------------------------------- Iteration 1( 6) --------------------------------------- - - - POTLOK: cpu time 0.0402: real time 0.0405 - SETDIJ: cpu time 0.0192: real time 0.0193 - EDDAV: cpu time 0.2708: real time 0.2716 - DOS: cpu time 0.0002: real time 0.0002 - CHARGE: cpu time 0.1060: real time 0.1062 - MIXING: cpu time 0.0010: real time 0.0010 - -------------------------------------------- - LOOP: cpu time 0.4374: real time 0.4388 - - eigenvalue-minimisations : 936 - total energy-change (2. order) : 0.3516455E+02 (-0.7055790E+01) - number of electron 63.9999986 magnetization - augmentation part 5.8723441 magnetization - - Broyden mixing: - rms(total) = 0.28316E+01 rms(broyden)= 0.28314E+01 - rms(prec ) = 0.29846E+01 - weight for this iteration 100.00 - - eigenvalues of (default mixing * dielectric matrix) - average eigenvalue GAMMA= 1.5892 - 1.5892 - - Free energy of the ion-electron system (eV) - --------------------------------------------------- - alpha Z PSCENC = 255.34863481 - Ewald energy TEWEN = -3146.48294520 - -Hartree energ DENC = -1069.77852836 - -exchange EXHF = 0.00000000 - -V(xc)+E(xc) XCENC = 98.83967481 - PAW double counting = 4626.34753107 -4652.13735535 - entropy T*S EENTRO = -0.00000000 - eigenvalues EBANDS = -221.13485229 - atomic energy EATOM = 3762.45289366 - Solvation Ediel_sol = 0.00000000 - --------------------------------------------------- - free energy TOTEN = -346.54494685 eV - - energy without entropy = -346.54494685 energy(sigma->0) = -346.54494685 - - --------------------------------------------------------------------------------------------------------- - - - - ---------------------------------------- Iteration 1( 7) --------------------------------------- - - - POTLOK: cpu time 0.0403: real time 0.0407 - SETDIJ: cpu time 0.0191: real time 0.0191 - EDDAV: cpu time 0.3018: real time 0.3026 - DOS: cpu time 0.0002: real time 0.0002 - CHARGE: cpu time 0.1054: real time 0.1059 - MIXING: cpu time 0.0013: real time 0.0013 - -------------------------------------------- - LOOP: cpu time 0.4681: real time 0.4698 - - eigenvalue-minimisations : 1120 - total energy-change (2. order) :-0.1178043E+01 (-0.3666951E+00) - number of electron 63.9999987 magnetization - augmentation part 5.7629613 magnetization - - Broyden mixing: - rms(total) = 0.12530E+01 rms(broyden)= 0.12530E+01 - rms(prec ) = 0.13336E+01 - weight for this iteration 100.00 - - eigenvalues of (default mixing * dielectric matrix) - average eigenvalue GAMMA= 1.7295 - 1.1475 2.3115 - - Free energy of the ion-electron system (eV) - --------------------------------------------------- - alpha Z PSCENC = 255.34863481 - Ewald energy TEWEN = -3146.48294520 - -Hartree energ DENC = -1091.10690406 - -exchange EXHF = 0.00000000 - -V(xc)+E(xc) XCENC = 97.93651775 - PAW double counting = 6084.43504209 -6110.99786718 - entropy T*S EENTRO = -0.00000000 - eigenvalues EBANDS = -199.30836158 - atomic energy EATOM = 3762.45289366 - Solvation Ediel_sol = 0.00000000 - --------------------------------------------------- - free energy TOTEN = -347.72298971 eV - - energy without entropy = -347.72298971 energy(sigma->0) = -347.72298971 - - --------------------------------------------------------------------------------------------------------- - - - - ---------------------------------------- Iteration 1( 8) --------------------------------------- - - - POTLOK: cpu time 0.0402: real time 0.0405 - SETDIJ: cpu time 0.0193: real time 0.0193 - EDDAV: cpu time 0.2734: real time 0.2743 - DOS: cpu time 0.0002: real time 0.0002 - CHARGE: cpu time 0.1076: real time 0.1079 - MIXING: cpu time 0.0010: real time 0.0010 - -------------------------------------------- - LOOP: cpu time 0.4417: real time 0.4432 - - eigenvalue-minimisations : 952 - total energy-change (2. order) : 0.2855134E-01 (-0.9343557E-01) - number of electron 63.9999986 magnetization - augmentation part 5.8814181 magnetization - - Broyden mixing: - rms(total) = 0.14260E+00 rms(broyden)= 0.14254E+00 - rms(prec ) = 0.25751E+00 - weight for this iteration 100.00 - - eigenvalues of (default mixing * dielectric matrix) - average eigenvalue GAMMA= 1.4802 - 2.3944 1.0231 1.0231 - - Free energy of the ion-electron system (eV) - --------------------------------------------------- - alpha Z PSCENC = 255.34863481 - Ewald energy TEWEN = -3146.48294520 - -Hartree energ DENC = -1081.98067736 - -exchange EXHF = 0.00000000 - -V(xc)+E(xc) XCENC = 98.70706712 - PAW double counting = 7570.92835145 -7598.23569145 - entropy T*S EENTRO = -0.00000000 - eigenvalues EBANDS = -208.43207140 - atomic energy EATOM = 3762.45289366 - Solvation Ediel_sol = 0.00000000 - --------------------------------------------------- - free energy TOTEN = -347.69443837 eV - - energy without entropy = -347.69443837 energy(sigma->0) = -347.69443837 - - --------------------------------------------------------------------------------------------------------- - - - - ---------------------------------------- Iteration 1( 9) --------------------------------------- - - - POTLOK: cpu time 0.0403: real time 0.0406 - SETDIJ: cpu time 0.0191: real time 0.0191 - EDDAV: cpu time 0.2733: real time 0.2741 - DOS: cpu time 0.0002: real time 0.0002 - CHARGE: cpu time 0.1057: real time 0.1059 - MIXING: cpu time 0.0012: real time 0.0012 - -------------------------------------------- - LOOP: cpu time 0.4397: real time 0.4412 - - eigenvalue-minimisations : 960 - total energy-change (2. order) : 0.3851980E-01 (-0.1788493E-01) - number of electron 63.9999987 magnetization - augmentation part 5.8361307 magnetization - - Broyden mixing: - rms(total) = 0.36716E-01 rms(broyden)= 0.36688E-01 - rms(prec ) = 0.56730E-01 - weight for this iteration 100.00 - - eigenvalues of (default mixing * dielectric matrix) - average eigenvalue GAMMA= 1.6341 - 2.2568 2.2568 1.0115 1.0115 - - Free energy of the ion-electron system (eV) - --------------------------------------------------- - alpha Z PSCENC = 255.34863481 - Ewald energy TEWEN = -3146.48294520 - -Hartree energ DENC = -1089.38855809 - -exchange EXHF = 0.00000000 - -V(xc)+E(xc) XCENC = 99.92424282 - PAW double counting = 7654.14512495 -7681.59382136 - entropy T*S EENTRO = -0.00000000 - eigenvalues EBANDS = -202.06149017 - atomic energy EATOM = 3762.45289366 - Solvation Ediel_sol = 0.00000000 - --------------------------------------------------- - free energy TOTEN = -347.65591857 eV - - energy without entropy = -347.65591857 energy(sigma->0) = -347.65591857 - - --------------------------------------------------------------------------------------------------------- - - - - ---------------------------------------- Iteration 1( 10) --------------------------------------- - - - POTLOK: cpu time 0.0401: real time 0.0407 - SETDIJ: cpu time 0.0191: real time 0.0191 - EDDAV: cpu time 0.2791: real time 0.2798 - DOS: cpu time 0.0002: real time 0.0002 - CHARGE: cpu time 0.1058: real time 0.1060 - MIXING: cpu time 0.0011: real time 0.0011 - -------------------------------------------- - LOOP: cpu time 0.4454: real time 0.4469 - 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- --------------------------------------------------------------------------------------------------------- - - - - FREE ENERGIE OF THE ION-ELECTRON SYSTEM (eV) - --------------------------------------------------- - free energy TOTEN = -347.65678484 eV - - energy without entropy= -347.65678484 energy(sigma->0) = -347.65678484 - - - --------------------------------------------------------------------------------------------------------- - - - POTLOK: cpu time 0.0609: real time 0.0611 - - --------------------------------------------------------------------------------------------------------- - - - LOOP+: cpu time 7.6723: real time 8.2284 - 4ORBIT: cpu time 0.0000: real time 0.0000 - - total amount of memory used by VASP MPI-rank0 36359. kBytes -======================================================================= - - base : 30000. kBytes - nonl-proj : 1290. kBytes - fftplans : 1209. kBytes - grid : 2402. kBytes - one-center: 31. kBytes - wavefun : 1427. kBytes - - - - General timing and accounting informations for this job: - ======================================================== - - Total CPU time used (sec): 8.292 - User time (sec): 8.249 - System time (sec): 0.043 - Elapsed time (sec): 9.371 - - Maximum memory used (kb): 51024. - Average memory used (kb): 0. - - Minor page faults: 13254 - Major page faults: 0 - Voluntary context switches: 272 diff --git a/mace-bench/3rdparty/SevenNet/example_inputs/data/label_2/OUTCAR_8 b/mace-bench/3rdparty/SevenNet/example_inputs/data/label_2/OUTCAR_8 deleted file mode 100644 index a1e24188eff7aeb2a6408553669460b0a04b39c4..0000000000000000000000000000000000000000 --- a/mace-bench/3rdparty/SevenNet/example_inputs/data/label_2/OUTCAR_8 +++ /dev/null @@ -1,2028 +0,0 @@ - vasp.5.4.4.18Apr17-6-g9f103f2a35 (build Sep 11 2017 17:27:03) complex - - executed on GRP7IFC17NORMAL date 2022.08.24 18:31:30 - running on 32 total cores - distrk: each k-point on 16 cores, 2 groups - distr: one band on NCORES_PER_BAND= 8 cores, 2 groups - - --------------------------------------------------------------------------------------------------------- - - - INCAR: - POTCAR: PAW_PBE Hf 20Jan2003 - POTCAR: PAW_PBE O 08Apr2002 - - ----------------------------------------------------------------------------- -| | -| W W AA RRRRR N N II N N GGGG !!! | -| W W A A R R NN N II NN N G G !!! | -| W W A A R R N N N II N N N G !!! | -| W WW W AAAAAA RRRRR N N N II N N N G GGG ! | -| WW WW A A R R N NN II N NN G G | -| W W A A R R N N II N N GGGG !!! | -| | -| You have enabled k-point parallelism (KPAR>1). | -| This developmental code was originally written by Paul Kent at ORNL, | -| and carefully double checked in Vienna. | -| GW as well as linear response parallelism added by Martijn Marsman | -| and Georg Kresse. | -| Carefully verify results versus KPAR=1. | -| Report problems to Paul Kent and Vienna. | -| | - ----------------------------------------------------------------------------- - - POTCAR: PAW_PBE Hf 20Jan2003 - SHA256 = 0bb2207f9a10894133f750b65504b92b8afef976ae770762e0497daaaad8168a Hf - COPYR = (c) Copyright 20Jan2003 Georg Kresse - COPYR = This file is part of the software VASP. Any use, copying, and all ot - COPYR = If you do not have a valid VASP license, you may not use, copy or di - VRHFIN =Hf: 6s5d - LEXCH = PE - EATOM = 75.9011 eV, 5.5786 Ry - - TITEL = PAW_PBE Hf 20Jan2003 - LULTRA = F use ultrasoft PP ? - IUNSCR = 1 unscreen: 0-lin 1-nonlin 2-no - RPACOR = 2.500 partial core radius - POMASS = 178.490; ZVAL = 4.000 mass and valenz - RCORE = 3.000 outmost cutoff radius - RWIGS = 3.050; RWIGS = 1.614 wigner-seitz radius (au A) - ENMAX = 220.334; ENMIN = 165.250 eV - RCLOC = 2.212 cutoff for local pot - LCOR = T correct aug charges - LPAW = T paw PP - EAUG = 335.116 - DEXC = 0.000 - RMAX = 3.077 core radius for proj-oper - RAUG = 1.300 factor for augmentation sphere - RDEP = 3.047 radius for radial grids - RDEPT = 2.344 core radius for aug-charge - - Atomic configuration - 16 entries - n l j E occ. - 1 0 0.50 -65259.4397 2.0000 - 2 0 0.50 -11157.9882 2.0000 - 2 1 1.50 -9795.2113 6.0000 - 3 0 0.50 -2541.4058 2.0000 - 3 1 1.50 -2134.4770 6.0000 - 3 2 2.50 -1653.5418 10.0000 - 4 0 0.50 -510.9575 2.0000 - 4 1 1.50 -377.5023 6.0000 - 4 2 2.50 -205.2085 10.0000 - 4 3 3.50 -15.4905 14.0000 - 5 0 0.50 -65.6020 2.0000 - 5 1 1.50 -34.2798 6.0000 - 5 2 2.50 -1.9877 3.0000 - 6 0 0.50 -4.7357 1.0000 - 6 1 1.50 -1.3606 0.0000 - 5 3 2.50 -1.3606 0.0000 - Description - l E TYP RCUT TYP RCUT - 2 -1.9876627 23 2.500 - 2 0.0744703 23 2.500 - 0 -4.7356889 23 2.600 - 0 3.2364747 23 2.600 - 1 -1.3605826 23 3.000 - 1 27.2116520 23 3.000 - local pseudopotential read in - partial core-charges read in - partial kinetic energy density read in - atomic valenz-charges read in - non local Contribution for L= 2 read in - real space projection operators read in - non local Contribution for L= 2 read in - real space projection operators read in - non local Contribution for L= 0 read in - real space projection operators read in - non local Contribution for L= 0 read in - real space projection operators read in - non local Contribution for L= 1 read in - real space projection operators read in - non local Contribution for L= 1 read in - real space projection operators read in - PAW grid and wavefunctions read in - - number of l-projection operators is LMAX = 6 - number of lm-projection operators is LMMAX = 18 - - POTCAR: PAW_PBE O 08Apr2002 - SHA256 = 818f92134a0a090dccd8ba1447fa70422a3b330e708bb4f08108d8ae51209ddf O/ - COPYR = (c) Copyright 08Apr2002 Georg Kresse - COPYR = This file is part of the software VASP. Any use, copying, and all ot - COPYR = If you do not have a valid VASP license, you may not use, copy or di - VRHFIN =O: s2p4 - LEXCH = PE - EATOM = 432.3788 eV, 31.7789 Ry - - TITEL = PAW_PBE O 08Apr2002 - LULTRA = F use ultrasoft PP ? - IUNSCR = 1 unscreen: 0-lin 1-nonlin 2-no - RPACOR = 1.200 partial core radius - POMASS = 16.000; ZVAL = 6.000 mass and valenz - RCORE = 1.520 outmost cutoff radius - RWIGS = 1.550; RWIGS = 0.820 wigner-seitz radius (au A) - ENMAX = 400.000; ENMIN = 300.000 eV - ICORE = 2 local potential - LCOR = T correct aug charges - LPAW = T paw PP - EAUG = 605.392 - DEXC = 0.000 - RMAX = 1.553 core radius for proj-oper - RAUG = 1.300 factor for augmentation sphere - RDEP = 1.550 radius for radial grids - RDEPT = 1.329 core radius for aug-charge - - Atomic configuration - 4 entries - n l j E occ. - 1 0 0.50 -514.6923 2.0000 - 2 0 0.50 -23.9615 2.0000 - 2 1 0.50 -9.0305 4.0000 - 3 2 1.50 -9.5241 0.0000 - Description - l E TYP RCUT TYP RCUT - 0 -23.9615318 23 1.200 - 0 -9.5240782 23 1.200 - 1 -9.0304911 23 1.520 - 1 8.1634956 23 1.520 - 2 -9.5240782 7 1.500 - local pseudopotential read in - partial core-charges read in - partial kinetic energy density read in - kinetic energy density of atom read in - atomic valenz-charges read in - non local Contribution for L= 0 read in - real space projection operators read in - non local Contribution for L= 0 read in - real space projection operators read in - non local Contribution for L= 1 read in - real space projection operators read in - non local Contribution for L= 1 read in - real space projection operators read in - PAW grid and wavefunctions read in - - number of l-projection operators is LMAX = 4 - number of lm-projection operators is LMMAX = 8 - - PAW_PBE Hf 20Jan2003 : - energy of atom 1 EATOM= -75.9011 - kinetic energy error for atom= 0.0007 (will be added to EATOM!!) - PAW_PBE O 08Apr2002 : - energy of atom 2 EATOM= -432.3788 - kinetic energy error for atom= 0.0224 (will be added to EATOM!!) - - - POSCAR: Primitive Cell - positions in direct lattice - No initial velocities read in - - METAGGA = SCAN LMAXTAU = 0 LMIXTAU = F - - exchange correlation table for LEXCH = 8 - RHO(1)= 0.500 N(1) = 2000 - RHO(2)= 100.500 N(2) = 4000 - - - --------------------------------------------------------------------------------------------------------- - - - ion position nearest neighbor table - 1 0.543 0.776 0.292- 7 2.00 8 2.01 10 2.09 6 2.10 5 2.12 12 2.20 11 2.20 4 3.25 - 3 3.34 3 3.34 2 3.37 2 3.37 4 3.39 4 3.49 2 3.83 2 3.83 - 2 0.043 0.224 0.208- 8 2.00 7 2.01 9 2.09 5 2.10 6 2.12 11 2.20 12 2.20 3 3.25 - 4 3.34 4 3.34 1 3.37 1 3.37 3 3.39 3 3.49 1 3.83 1 3.83 - 3 0.957 0.776 0.792- 10 2.00 9 2.01 7 2.09 12 2.10 11 2.12 6 2.20 5 2.20 2 3.25 - 1 3.34 1 3.34 4 3.37 4 3.37 2 3.39 2 3.49 4 3.83 4 3.83 - 4 0.457 0.224 0.708- 9 2.00 10 2.01 8 2.09 11 2.10 12 2.12 5 2.20 6 2.20 1 3.25 - 2 3.34 2 3.34 3 3.37 3 3.37 1 3.39 1 3.49 3 3.83 3 3.83 - 5 0.757 0.052 0.478- 2 2.10 1 2.12 4 2.20 3 2.20 - 6 0.257 0.948 0.022- 1 2.10 2 2.12 3 2.20 4 2.20 - 7 0.832 0.569 0.154- 1 2.00 2 2.01 3 2.09 - 8 0.332 0.431 0.346- 2 2.00 1 2.01 4 2.09 - 9 0.168 0.431 0.846- 4 2.00 3 2.01 2 2.09 - 10 0.668 0.569 0.654- 3 2.00 4 2.01 1 2.09 - 11 0.743 0.052 0.978- 4 2.10 3 2.12 2 2.20 1 2.20 - 12 0.243 0.948 0.522- 3 2.10 4 2.12 1 2.20 2 2.20 - - LATTYP: Found a simple monoclinic cell. - ALAT = 7.7887787411 - B/A-ratio = 0.6517496159 - C/A-ratio = 1.5432771295 - COS(beta) = -0.9616437168 - - Lattice vectors: - - A1 = ( 0.0000000000, -5.8632290575, -5.1271453362) - A2 = ( -5.0763335525, 0.0000000000, 0.0000000000) - A3 = ( 0.0000000000, 10.8719575711, 5.1270660956) - - -Analysis of symmetry for initial positions (statically): -===================================================================== - Subroutine PRICEL returns: - Original cell was already a primitive cell. - - - Routine SETGRP: Setting up the symmetry group for a - simple monoclinic supercell. - - - Subroutine GETGRP returns: Found 4 space group operations - (whereof 2 operations were pure point group operations) - out of a pool of 4 trial point group operations. - - -The static configuration has the point symmetry S_2 . - The point group associated with its full space group is C_2h. - - -Analysis of symmetry for dynamics (positions and initial velocities): -===================================================================== - Subroutine PRICEL returns: - Original cell was already a primitive cell. - - - Routine SETGRP: Setting up the symmetry group for a - simple monoclinic supercell. - - - Subroutine GETGRP returns: Found 4 space group operations - (whereof 2 operations were pure point group operations) - out of a pool of 4 trial point group operations. - - -The dynamic configuration has the point symmetry S_2 . - The point group associated with its full space group is C_2h. - - -Analysis of constrained symmetry for selective dynamics: -===================================================================== - Subroutine PRICEL returns: - Original cell was already a primitive cell. - - - Routine SETGRP: Setting up the symmetry group for a - simple monoclinic supercell. - - - Subroutine GETGRP returns: Found 4 space group operations - (whereof 2 operations were pure point group operations) - out of a pool of 4 trial point group operations. - - -The constrained configuration has the point symmetry S_2 . - The point group associated with its full space group is C_2h. - - - Subroutine INISYM returns: Found 4 space group operations - (whereof 2 operations are pure point group operations), - and found 1 'primitive' translations - - - - KPOINTS: Auto k-point - -Automatic generation of k-mesh. -Space group operators: - irot det(A) alpha n_x n_y n_z tau_x tau_y tau_z - 1 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 - 2 -1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 - 3 1.000000 180.000000 1.000000 0.000000 0.000000 -0.500000 1.000000 0.500000 - 4 -1.000000 180.000000 1.000000 0.000000 0.000000 -0.500000 1.000000 0.500000 - - Subroutine IBZKPT returns following result: - =========================================== - - Found 10 irreducible k-points: - - Following reciprocal coordinates: - Coordinates Weight - 0.000000 0.000000 0.000000 1.000000 - 0.333333 0.000000 0.000000 2.000000 - 0.000000 0.333333 -0.000000 2.000000 - 0.333333 0.333333 -0.000000 4.000000 - 0.000000 0.000000 0.333333 2.000000 - 0.333333 0.000000 0.333333 4.000000 - 0.000000 0.333333 0.333333 2.000000 - 0.333333 0.333333 0.333333 4.000000 - 0.000000 -0.333333 0.333333 2.000000 - 0.333333 -0.333333 0.333333 4.000000 - - Following cartesian coordinates: - Coordinates Weight - 0.000000 0.000000 0.000000 1.000000 - 0.065664 0.000000 0.000000 2.000000 - 0.000000 0.066550 -0.011091 2.000000 - 0.065664 0.066550 -0.011091 4.000000 - 0.000000 0.000001 0.065012 2.000000 - 0.065664 0.000001 0.065012 4.000000 - 0.000000 0.066551 0.053921 2.000000 - 0.065664 0.066551 0.053921 4.000000 - 0.000000 -0.066549 0.076103 2.000000 - 0.065664 -0.066549 0.076103 4.000000 - - - --------------------------------------------------------------------------------------------------------- - - - - - Dimension of arrays: - k-points NKPTS = 10 k-points in BZ NKDIM = 10 number of bands NBANDS= 40 - number of dos NEDOS = 301 number of ions NIONS = 12 - non local maximal LDIM = 6 non local SUM 2l+1 LMDIM = 18 - total plane-waves NPLWV = 64000 - max r-space proj IRMAX = 1 max aug-charges IRDMAX= 33160 - dimension x,y,z NGX = 40 NGY = 40 NGZ = 40 - dimension x,y,z NGXF= 80 NGYF= 80 NGZF= 80 - support grid NGXF= 80 NGYF= 80 NGZF= 80 - ions per type = 4 8 - NGX,Y,Z is equivalent to a cutoff of 13.10, 13.28, 12.79 a.u. - NGXF,Y,Z is equivalent to a cutoff of 26.20, 26.55, 25.59 a.u. - - SYSTEM = HfO2_p21c - POSCAR = Primitive Cell - - Startparameter for this run: - NWRITE = 2 write-flag & timer - PREC = accura normal or accurate (medium, high low for compatibility) - ISTART = 0 job : 0-new 1-cont 2-samecut - ICHARG = 2 charge: 1-file 2-atom 10-const - ISPIN = 1 spin polarized calculation? - LNONCOLLINEAR = F non collinear calculations - LSORBIT = F spin-orbit coupling - INIWAV = 1 electr: 0-lowe 1-rand 2-diag - LASPH = F aspherical Exc in radial PAW - METAGGA= F non-selfconsistent MetaGGA calc. - - Electronic Relaxation 1 - ENCUT = 500.0 eV 36.75 Ry 6.06 a.u. 9.26 9.13 9.48*2*pi/ulx,y,z - ENINI = 500.0 initial cutoff - ENAUG = 605.4 eV augmentation charge cutoff - NELM = 100; NELMIN= 2; NELMDL= -5 # of ELM steps - EDIFF = 0.1E-05 stopping-criterion for ELM - LREAL = F real-space projection - NLSPLINE = F spline interpolate recip. space projectors - LCOMPAT= F compatible to vasp.4.4 - GGA_COMPAT = T GGA compatible to vasp.4.4-vasp.4.6 - LMAXPAW = -100 max onsite density - LMAXMIX = 2 max onsite mixed and CHGCAR - VOSKOWN= 0 Vosko Wilk Nusair interpolation - ROPT = 0.00000 0.00000 - Ionic relaxation - EDIFFG = -.2E-02 stopping-criterion for IOM - NSW = 0 number of steps for IOM - NBLOCK = 1; KBLOCK = 1 inner block; outer block - IBRION = -1 ionic relax: 0-MD 1-quasi-New 2-CG - NFREE = 1 steps in history (QN), initial steepest desc. (CG) - ISIF = 3 stress and relaxation - IWAVPR = 10 prediction: 0-non 1-charg 2-wave 3-comb - ISYM = 1 0-nonsym 1-usesym 2-fastsym - LCORR = T Harris-Foulkes like correction to forces - - POTIM = 0.5000 time-step for ionic-motion - TEIN = 0.0 initial temperature - TEBEG = 0.0; TEEND = 0.0 temperature during run - SMASS = -3.00 Nose mass-parameter (am) - estimated Nose-frequenzy (Omega) = 0.10E-29 period in steps =****** mass= -0.589E-27a.u. - SCALEE = 1.0000 scale energy and forces - NPACO = 256; APACO = 16.0 distance and # of slots for P.C. - PSTRESS= 0.0 pullay stress - - Mass of Ions in am - POMASS = 178.49 16.00 - Ionic Valenz - ZVAL = 4.00 6.00 - Atomic Wigner-Seitz radii - RWIGS = -1.00 -1.00 - virtual crystal weights - VCA = 1.00 1.00 - NELECT = 64.0000 total number of electrons - NUPDOWN= -1.0000 fix difference up-down - - DOS related values: - EMIN = 10.00; EMAX =-10.00 energy-range for DOS - EFERMI = 0.00 - ISMEAR = 0; SIGMA = 0.05 broadening in eV -4-tet -1-fermi 0-gaus - - Electronic relaxation 2 (details) - IALGO = 38 algorithm - LDIAG = T sub-space diagonalisation (order eigenvalues) - LSUBROT= F optimize rotation matrix (better conditioning) - TURBO = 0 0=normal 1=particle mesh - IRESTART = 0 0=no restart 2=restart with 2 vectors - NREBOOT = 0 no. of reboots - NMIN = 0 reboot dimension - EREF = 0.00 reference energy to select bands - IMIX = 4 mixing-type and parameters - AMIX = 0.40; BMIX = 1.00 - AMIX_MAG = 1.60; BMIX_MAG = 1.00 - AMIN = 0.10 - WC = 100.; INIMIX= 1; MIXPRE= 1; MAXMIX= -45 - - Intra band minimization: - WEIMIN = 0.0000 energy-eigenvalue tresh-hold - EBREAK = 0.62E-08 absolut break condition - DEPER = 0.30 relativ break condition - - TIME = 0.40 timestep for ELM - - volume/ion in A,a.u. = 10.86 73.31 - Fermi-wavevector in a.u.,A,eV,Ry = 1.291460 2.440506 22.692750 1.667870 - Thomas-Fermi vector in A = 2.423229 - - Write flags - LWAVE = F write WAVECAR - LDOWNSAMPLE = F k-point downsampling of WAVECAR - LCHARG = F write CHGCAR - LVTOT = F write LOCPOT, total local potential - LVHAR = F write LOCPOT, Hartree potential only - LELF = F write electronic localiz. function (ELF) - LORBIT = 0 0 simple, 1 ext, 2 COOP (PROOUT), +10 PAW based schemes - - - Dipole corrections - LMONO = F monopole corrections only (constant potential shift) - LDIPOL = F correct potential (dipole corrections) - IDIPOL = 0 1-x, 2-y, 3-z, 4-all directions - EPSILON= 1.0000000 bulk dielectric constant - - Exchange correlation treatment: - GGA = -- GGA type - LEXCH = 8 internal setting for exchange type - VOSKOWN= 0 Vosko Wilk Nusair interpolation - LHFCALC = F Hartree Fock is set to - LHFONE = F Hartree Fock one center treatment - AEXX = 0.0000 exact exchange contribution - - Linear response parameters - LEPSILON= F determine dielectric tensor - LRPA = F only Hartree local field effects (RPA) - LNABLA = F use nabla operator in PAW spheres - LVEL = F velocity operator in full k-point grid - LINTERFAST= F fast interpolation - KINTER = 0 interpolate to denser k-point grid - CSHIFT =0.1000 complex shift for real part using Kramers Kronig - OMEGAMAX= -1.0 maximum frequency - DEG_THRESHOLD= 0.2000000E-02 threshold for treating states as degnerate - RTIME = -0.100 relaxation time in fs - (WPLASMAI= 0.000 imaginary part of plasma frequency in eV, 0.658/RTIME) - DFIELD = 0.0000000 0.0000000 0.0000000 field for delta impulse in time - - Orbital magnetization related: - ORBITALMAG= F switch on orbital magnetization - LCHIMAG = F perturbation theory with respect to B field - DQ = 0.001000 dq finite difference perturbation B field - LLRAUG = F two centre corrections for induced B field - - - --------------------------------------------------------------------------------------------------------- - - - Static calculation - charge density and potential will be updated during run - non-spin polarized calculation - Variant of blocked Davidson - Davidson routine will perform the subspace rotation - perform sub-space diagonalisation - after iterative eigenvector-optimisation - modified Broyden-mixing scheme, WC = 100.0 - initial mixing is a Kerker type mixing with AMIX = 0.4000 and BMIX = 1.0000 - Hartree-type preconditioning will be used - using additional bands 8 - reciprocal scheme for non local part - use partial core corrections - calculate Harris-corrections to forces - (improved forces if not selfconsistent) - use gradient corrections - use of overlap-Matrix (Vanderbilt PP) - Gauss-broadening in eV SIGMA = 0.05 - - --------------------------------------------------------------------------------------------------------- - - - energy-cutoff : 500.00 - volume of cell : 130.37 - direct lattice vectors reciprocal lattice vectors - 5.076333552 0.000000000 0.000000000 0.196992571 0.000000000 0.000000000 - 0.000000000 5.008728514 -0.000079241 0.000000000 0.199650941 -0.033273721 - 0.000000000 0.854500544 5.127224577 0.000000000 0.000003086 0.195036778 - - length of vectors - 5.076333552 5.008728514 5.197942193 0.196992571 0.202404642 0.195036778 - - - - k-points in units of 2pi/SCALE and weight: Auto k-point - 0.00000000 0.00000000 0.00000000 0.037 - 0.06566419 0.00000000 0.00000000 0.074 - 0.00000000 0.06655031 -0.01109124 0.074 - 0.06566419 0.06655031 -0.01109124 0.148 - 0.00000000 0.00000103 0.06501226 0.074 - 0.06566419 0.00000103 0.06501226 0.148 - 0.00000000 0.06655134 0.05392102 0.074 - 0.06566419 0.06655134 0.05392102 0.148 - 0.00000000 -0.06654929 0.07610350 0.074 - 0.06566419 -0.06654929 0.07610350 0.148 - - k-points in reciprocal lattice and weights: Auto k-point - 0.00000000 0.00000000 0.00000000 0.037 - 0.33333333 0.00000000 0.00000000 0.074 - 0.00000000 0.33333333 -0.00000000 0.074 - 0.33333333 0.33333333 -0.00000000 0.148 - 0.00000000 0.00000000 0.33333333 0.074 - 0.33333333 0.00000000 0.33333333 0.148 - 0.00000000 0.33333333 0.33333333 0.074 - 0.33333333 0.33333333 0.33333333 0.148 - 0.00000000 -0.33333333 0.33333333 0.074 - 0.33333333 -0.33333333 0.33333333 0.148 - - position of ions in fractional coordinates (direct lattice) - 0.54288322 0.77577220 0.29175508 - 0.04288322 0.22422780 0.20824492 - 0.95711678 0.77577220 0.79175508 - 0.45711678 0.22422780 0.70824492 - 0.75741482 0.05184460 0.47813308 - 0.25741482 0.94815540 0.02186692 - 0.83182355 0.56876319 0.15428653 - 0.33182355 0.43123681 0.34571347 - 0.16817645 0.43123681 0.84571347 - 0.66817645 0.56876319 0.65428653 - 0.74258518 0.05184460 0.97813308 - 0.24258518 0.94815540 0.52186692 - - position of ions in cartesian coordinates (Angst): - 2.75585630 4.13493719 1.49583232 - 0.21768952 1.30104159 1.06770073 - 4.85864403 4.56218746 4.05944461 - 2.32047726 1.72829187 3.63131301 - 3.84489028 0.66824051 2.45149157 - 1.30672351 4.76773827 0.11204147 - 4.22261379 2.98061833 0.79101664 - 1.68444701 2.45536046 1.77251640 - 0.85371976 2.88261073 4.33612869 - 3.39188654 3.40786860 3.35462893 - 3.76961004 1.09549079 5.01510386 - 1.23144327 5.19498854 2.67565376 - - - --------------------------------------------------------------------------------------------------------- - - - k-point 1 : 0.0000 0.0000 0.0000 plane waves: 3295 - k-point 2 : 0.3333 0.0000 0.0000 plane waves: 3310 - k-point 3 : 0.0000 0.3333-0.0000 plane waves: 3315 - k-point 4 : 0.3333 0.3333-0.0000 plane waves: 3320 - k-point 5 : 0.0000 0.0000 0.3333 plane waves: 3314 - k-point 6 : 0.3333 0.0000 0.3333 plane waves: 3301 - k-point 7 : 0.0000 0.3333 0.3333 plane waves: 3300 - k-point 8 : 0.3333 0.3333 0.3333 plane waves: 3304 - k-point 9 : 0.0000-0.3333 0.3333 plane waves: 3317 - k-point 10 : 0.3333-0.3333 0.3333 plane waves: 3303 - - maximum and minimum number of plane-waves per node : 432 394 - - maximum number of plane-waves: 3320 - maximum index in each direction: - IXMAX= 9 IYMAX= 9 IZMAX= 9 - IXMIN= -9 IYMIN= -9 IZMIN= -9 - - - parallel 3D FFT for wavefunctions: - minimum data exchange during FFTs selected (reduces bandwidth) - parallel 3D FFT for charge: - minimum data exchange during FFTs selected (reduces bandwidth) - - - total amount of memory used by VASP MPI-rank0 36732. kBytes -======================================================================= - - base : 30000. kBytes - nonl-proj : 1277. kBytes - fftplans : 1345. kBytes - grid : 2665. kBytes - one-center: 31. kBytes - wavefun : 1414. kBytes - - INWAV: cpu time 0.0000: real time 0.0002 - Broyden mixing: mesh for mixing (old mesh) - NGX = 19 NGY = 19 NGZ = 19 - (NGX = 80 NGY = 80 NGZ = 80) - gives a total of 6859 points - - initial charge density was supplied: - charge density of overlapping atoms calculated - number of electron 64.0000000 magnetization - keeping initial charge density in first step - - --------------------------------------------------------------------------------------------------------- - - - Maximum index for augmentation-charges 1971 (set IRDMAX) - - --------------------------------------------------------------------------------------------------------- - - - First call to EWALD: gamma= 0.350 - Maximum number of real-space cells 3x 3x 3 - Maximum number of reciprocal cells 3x 3x 3 - - FEWALD: cpu time 0.0013: real time 0.0013 - - ---------------------------------------- Iteration 1( 1) --------------------------------------- - - - POTLOK: cpu time 0.0474: real time 0.0950 - SETDIJ: cpu time 0.0027: real time 0.0027 - EDDAV: cpu time 0.2620: real time 0.2628 - DOS: cpu time 0.0004: real time 0.0004 - -------------------------------------------- - LOOP: cpu time 0.3125: real time 0.3608 - - eigenvalue-minimisations : 800 - total energy-change (2. order) : 0.1347361E+03 (-0.3447604E+04) - number of electron 64.0000000 magnetization - augmentation part 64.0000000 magnetization - - Free energy of the ion-electron system (eV) - --------------------------------------------------- - alpha Z PSCENC = 253.03197791 - Ewald energy TEWEN = -3136.93850755 - -Hartree energ DENC = -911.23644555 - -exchange EXHF = 0.00000000 - -V(xc)+E(xc) XCENC = 74.95957319 - PAW double counting = 3196.24842107 -3219.62951610 - entropy T*S EENTRO = -0.00000001 - eigenvalues EBANDS = 115.84773382 - atomic energy EATOM = 3762.45289366 - Solvation Ediel_sol = 0.00000000 - --------------------------------------------------- - free energy TOTEN = 134.73613045 eV - - energy without entropy = 134.73613046 energy(sigma->0) = 134.73613045 - - --------------------------------------------------------------------------------------------------------- - - - - ---------------------------------------- Iteration 1( 2) --------------------------------------- - - - EDDAV: cpu time 0.3080: real time 0.3119 - DOS: cpu time 0.0002: real time 0.0002 - -------------------------------------------- - LOOP: cpu time 0.3082: real time 0.3121 - - eigenvalue-minimisations : 1048 - total energy-change (2. order) :-0.4896056E+03 (-0.4729283E+03) - number of electron 64.0000000 magnetization - augmentation part 64.0000000 magnetization - - Free energy of the ion-electron system (eV) - --------------------------------------------------- - alpha Z PSCENC = 253.03197791 - Ewald energy TEWEN = -3136.93850755 - -Hartree energ DENC = -911.23644555 - -exchange EXHF = 0.00000000 - -V(xc)+E(xc) XCENC = 74.95957319 - PAW double counting = 3196.24842107 -3219.62951610 - entropy T*S EENTRO = -0.00000000 - eigenvalues EBANDS = -373.75784929 - atomic energy EATOM = 3762.45289366 - Solvation Ediel_sol = 0.00000000 - --------------------------------------------------- - free energy TOTEN = -354.86945266 eV - - energy without entropy = -354.86945266 energy(sigma->0) = -354.86945266 - - --------------------------------------------------------------------------------------------------------- - - - - ---------------------------------------- Iteration 1( 3) --------------------------------------- - - - EDDAV: cpu time 0.2911: real time 0.2923 - DOS: cpu time 0.0002: real time 0.0002 - -------------------------------------------- - LOOP: cpu time 0.2913: real time 0.2925 - - eigenvalue-minimisations : 960 - total energy-change (2. order) :-0.2662110E+02 (-0.2647159E+02) - number of electron 64.0000000 magnetization - augmentation part 64.0000000 magnetization - - Free energy of the ion-electron system (eV) - --------------------------------------------------- - alpha Z PSCENC = 253.03197791 - Ewald energy TEWEN = -3136.93850755 - -Hartree energ DENC = -911.23644555 - -exchange EXHF = 0.00000000 - -V(xc)+E(xc) XCENC = 74.95957319 - PAW double counting = 3196.24842107 -3219.62951610 - entropy T*S EENTRO = -0.00000000 - eigenvalues EBANDS = -400.37894803 - atomic energy EATOM = 3762.45289366 - Solvation Ediel_sol = 0.00000000 - --------------------------------------------------- - free energy TOTEN = -381.49055139 eV - - energy without entropy = -381.49055139 energy(sigma->0) = -381.49055139 - - --------------------------------------------------------------------------------------------------------- - - - - ---------------------------------------- Iteration 1( 4) --------------------------------------- - - - EDDAV: cpu time 0.2939: real time 0.2950 - DOS: cpu time 0.0002: real time 0.0002 - -------------------------------------------- - LOOP: cpu time 0.2941: real time 0.2952 - - eigenvalue-minimisations : 968 - total energy-change (2. order) :-0.3875163E+00 (-0.3864947E+00) - number of electron 64.0000000 magnetization - augmentation part 64.0000000 magnetization - - Free energy of the ion-electron system (eV) - --------------------------------------------------- - alpha Z PSCENC = 253.03197791 - Ewald energy TEWEN = -3136.93850755 - -Hartree energ DENC = -911.23644555 - -exchange EXHF = 0.00000000 - -V(xc)+E(xc) XCENC = 74.95957319 - PAW double counting = 3196.24842107 -3219.62951610 - entropy T*S EENTRO = -0.00000000 - eigenvalues EBANDS = -400.76646433 - atomic energy EATOM = 3762.45289366 - Solvation Ediel_sol = 0.00000000 - --------------------------------------------------- - free energy TOTEN = -381.87806769 eV - - energy without entropy = -381.87806769 energy(sigma->0) = -381.87806769 - - --------------------------------------------------------------------------------------------------------- - - - - ---------------------------------------- Iteration 1( 5) --------------------------------------- - - - EDDAV: cpu time 0.2876: real time 0.2887 - DOS: cpu time 0.0002: real time 0.0002 - CHARGE: cpu time 0.1201: real time 0.1206 - MIXING: cpu time 0.0014: real time 0.0015 - -------------------------------------------- - LOOP: cpu time 0.4093: real time 0.4109 - - eigenvalue-minimisations : 936 - total energy-change (2. order) :-0.8551608E-02 (-0.8547890E-02) - number of electron 63.9999982 magnetization - augmentation part 6.7138101 magnetization - - Broyden mixing: - rms(total) = 0.55063E+01 rms(broyden)= 0.55062E+01 - rms(prec ) = 0.70648E+01 - weight for this iteration 100.00 - - Free energy of the ion-electron system (eV) - --------------------------------------------------- - alpha Z PSCENC = 253.03197791 - Ewald energy TEWEN = -3136.93850755 - -Hartree energ DENC = -911.23644555 - -exchange EXHF = 0.00000000 - -V(xc)+E(xc) XCENC = 74.95957319 - PAW double counting = 3196.24842107 -3219.62951610 - entropy T*S EENTRO = -0.00000000 - eigenvalues EBANDS = -400.77501594 - atomic energy EATOM = 3762.45289366 - Solvation Ediel_sol = 0.00000000 - --------------------------------------------------- - free energy TOTEN = -381.88661930 eV - - energy without entropy = -381.88661930 energy(sigma->0) = -381.88661930 - - --------------------------------------------------------------------------------------------------------- - - - - ---------------------------------------- Iteration 1( 6) --------------------------------------- - - - POTLOK: cpu time 0.0444: real time 0.0448 - SETDIJ: cpu time 0.0194: real time 0.0194 - EDDAV: cpu time 0.2810: real time 0.2816 - DOS: cpu time 0.0002: real time 0.0002 - CHARGE: cpu time 0.1150: real time 0.1154 - MIXING: cpu time 0.0013: real time 0.0013 - -------------------------------------------- - LOOP: cpu time 0.4613: real time 0.4629 - - eigenvalue-minimisations : 920 - total energy-change (2. order) : 0.3527122E+02 (-0.7129751E+01) - number of electron 63.9999985 magnetization - augmentation part 5.8528880 magnetization - - Broyden mixing: - rms(total) = 0.27643E+01 rms(broyden)= 0.27642E+01 - rms(prec ) = 0.29203E+01 - weight for this iteration 100.00 - - eigenvalues of (default mixing * dielectric matrix) - average eigenvalue GAMMA= 1.5689 - 1.5689 - - Free energy of the ion-electron system (eV) - --------------------------------------------------- - alpha Z PSCENC = 253.03197791 - Ewald energy TEWEN = -3136.93850755 - -Hartree energ DENC = -1074.36417035 - -exchange EXHF = 0.00000000 - -V(xc)+E(xc) XCENC = 98.66411157 - PAW double counting = 4592.09488400 -4617.84006332 - entropy T*S EENTRO = -0.00000000 - eigenvalues EBANDS = -223.71652597 - atomic energy EATOM = 3762.45289366 - Solvation Ediel_sol = 0.00000000 - --------------------------------------------------- - free energy TOTEN = -346.61540004 eV - - energy without entropy = -346.61540004 energy(sigma->0) = -346.61540004 - - --------------------------------------------------------------------------------------------------------- - - - - ---------------------------------------- Iteration 1( 7) --------------------------------------- - - - POTLOK: cpu time 0.0443: real time 0.0448 - SETDIJ: cpu time 0.0197: real time 0.0197 - EDDAV: cpu time 0.3203: real time 0.3212 - DOS: cpu time 0.0002: real time 0.0002 - CHARGE: cpu time 0.1151: real time 0.1155 - MIXING: cpu time 0.0011: real time 0.0011 - -------------------------------------------- - LOOP: cpu time 0.5008: real time 0.5025 - - eigenvalue-minimisations : 1120 - total energy-change (2. order) :-0.1191078E+01 (-0.3517682E+00) - number of electron 63.9999986 magnetization - augmentation part 5.7499177 magnetization - - Broyden mixing: - rms(total) = 0.12364E+01 rms(broyden)= 0.12363E+01 - rms(prec ) = 0.13184E+01 - weight for this iteration 100.00 - - eigenvalues of (default mixing * dielectric matrix) - average eigenvalue GAMMA= 1.7224 - 1.1418 2.3029 - - Free energy of the ion-electron system (eV) - --------------------------------------------------- - alpha Z PSCENC = 253.03197791 - Ewald energy TEWEN = -3136.93850755 - -Hartree energ DENC = -1094.57633831 - -exchange EXHF = 0.00000000 - -V(xc)+E(xc) XCENC = 97.62779411 - PAW double counting = 5978.70709237 -6005.15735108 - entropy T*S EENTRO = -0.00000000 - eigenvalues EBANDS = -202.95403886 - atomic energy EATOM = 3762.45289366 - 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rms(prec ) = 0.24999E+00 - weight for this iteration 100.00 - - eigenvalues of (default mixing * dielectric matrix) - average eigenvalue GAMMA= 1.4799 - 2.3886 1.0256 1.0256 - - Free energy of the ion-electron system (eV) - --------------------------------------------------- - alpha Z PSCENC = 253.03197791 - Ewald energy TEWEN = -3136.93850755 - -Hartree energ DENC = -1085.89286329 - -exchange EXHF = 0.00000000 - -V(xc)+E(xc) XCENC = 98.47951326 - PAW double counting = 7411.80931615 -7438.96417831 - entropy T*S EENTRO = -0.00000000 - eigenvalues EBANDS = -211.75850155 - atomic energy EATOM = 3762.45289366 - Solvation Ediel_sol = 0.00000000 - --------------------------------------------------- - free energy TOTEN = -347.78034970 eV - - energy without entropy = -347.78034970 energy(sigma->0) = -347.78034970 - - --------------------------------------------------------------------------------------------------------- - - - - ---------------------------------------- Iteration 1( 9) --------------------------------------- - 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-exchange EXHF = 0.00000000 - -V(xc)+E(xc) XCENC = 99.67125441 - PAW double counting = 7494.38979686 -7521.68740757 - entropy T*S EENTRO = -0.00000000 - eigenvalues EBANDS = -205.53110115 - atomic energy EATOM = 3762.45289366 - Solvation Ediel_sol = 0.00000000 - --------------------------------------------------- - free energy TOTEN = -347.74423006 eV - - energy without entropy = -347.74423006 energy(sigma->0) = -347.74423006 - - --------------------------------------------------------------------------------------------------------- - - - - ---------------------------------------- Iteration 1( 10) --------------------------------------- - - - POTLOK: cpu time 0.0443: real time 0.0449 - SETDIJ: cpu time 0.0194: real time 0.0194 - EDDAV: cpu time 0.2936: real time 0.2943 - DOS: cpu time 0.0002: real time 0.0002 - CHARGE: cpu time 0.1147: real time 0.1150 - MIXING: cpu time 0.0014: real time 0.0014 - -------------------------------------------- - LOOP: cpu time 0.4736: real time 0.4752 - - eigenvalue-minimisations : 968 - total energy-change (2. order) :-0.2014599E-02 (-0.3085576E-02) - number of electron 63.9999986 magnetization - augmentation part 5.8191816 magnetization - - Broyden mixing: - rms(total) = 0.26879E-01 rms(broyden)= 0.26868E-01 - rms(prec ) = 0.47856E-01 - weight for this iteration 100.00 - - eigenvalues of (default mixing * dielectric matrix) - average eigenvalue GAMMA= 1.4861 - 2.4576 2.1852 1.1232 0.8324 0.8324 - - Free energy of the ion-electron system (eV) - --------------------------------------------------- - alpha Z PSCENC = 253.03197791 - Ewald energy TEWEN = -3136.93850755 - -Hartree energ DENC = -1093.61055901 - -exchange EXHF = 0.00000000 - -V(xc)+E(xc) XCENC = 99.62272334 - PAW double counting = 7510.27577836 -7537.67220010 - entropy T*S EENTRO = -0.00000000 - eigenvalues EBANDS = -204.90835128 - atomic energy EATOM = 3762.45289366 - Solvation Ediel_sol = 0.00000000 - --------------------------------------------------- - free energy TOTEN = -347.74624466 eV - 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average eigenvalue GAMMA= 1.5022 - 2.5187 2.5187 0.9738 0.9738 1.0140 1.0140 - - Free energy of the ion-electron system (eV) - --------------------------------------------------- - alpha Z PSCENC = 253.03197791 - Ewald energy TEWEN = -3136.93850755 - -Hartree energ DENC = -1094.89614944 - -exchange EXHF = 0.00000000 - -V(xc)+E(xc) XCENC = 99.71034681 - PAW double counting = 7522.51422021 -7549.94397837 - entropy T*S EENTRO = -0.00000000 - eigenvalues EBANDS = -203.67723657 - atomic energy EATOM = 3762.45289366 - Solvation Ediel_sol = 0.00000000 - --------------------------------------------------- - free energy TOTEN = -347.74643332 eV - - energy without entropy = -347.74643332 energy(sigma->0) = -347.74643332 - - --------------------------------------------------------------------------------------------------------- - - - - ---------------------------------------- Iteration 1( 12) --------------------------------------- - - - POTLOK: cpu time 0.0448: real time 0.0452 - SETDIJ: cpu time 0.0192: real time 0.0192 - 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PAW double counting = 7517.34366096 -7544.78103454 - entropy T*S EENTRO = -0.00000000 - eigenvalues EBANDS = -204.54054034 - atomic energy EATOM = 3762.45289366 - Solvation Ediel_sol = 0.00000000 - --------------------------------------------------- - free energy TOTEN = -347.74524869 eV - - energy without entropy = -347.74524869 energy(sigma->0) = -347.74524869 - - --------------------------------------------------------------------------------------------------------- - - - - ---------------------------------------- Iteration 1( 13) --------------------------------------- - - - POTLOK: cpu time 0.0447: real time 0.0451 - SETDIJ: cpu time 0.0193: real time 0.0194 - EDDAV: cpu time 0.2910: real time 0.2917 - DOS: cpu time 0.0002: real time 0.0002 - CHARGE: cpu time 0.1149: real time 0.1152 - MIXING: cpu time 0.0012: real time 0.0012 - -------------------------------------------- - LOOP: cpu time 0.4713: real time 0.4728 - - eigenvalue-minimisations : 960 - total energy-change (2. order) : 0.7080288E-05 (-0.4260222E-04) - 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- Free energy of the ion-electron system (eV) - --------------------------------------------------- - alpha Z PSCENC = 253.03197791 - Ewald energy TEWEN = -3136.93850755 - -Hartree energ DENC = -1093.83436245 - -exchange EXHF = 0.00000000 - -V(xc)+E(xc) XCENC = 99.64334884 - PAW double counting = 7520.06477891 -7547.50741962 - entropy T*S EENTRO = -0.00000000 - eigenvalues EBANDS = -204.65791776 - atomic energy EATOM = 3762.45289366 - Solvation Ediel_sol = 0.00000000 - --------------------------------------------------- - free energy TOTEN = -347.74520805 eV - - energy without entropy = -347.74520805 energy(sigma->0) = -347.74520805 - - --------------------------------------------------------------------------------------------------------- - - - - ---------------------------------------- Iteration 1( 15) --------------------------------------- - - - POTLOK: cpu time 0.0446: real time 0.0451 - SETDIJ: cpu time 0.0193: real time 0.0193 - EDDAV: cpu time 0.2590: real time 0.2597 - DOS: cpu time 0.0002: real time 0.0002 - 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eigenvalues EBANDS = -204.66010623 - atomic energy EATOM = 3762.45289366 - Solvation Ediel_sol = 0.00000000 - --------------------------------------------------- - free energy TOTEN = -347.74520690 eV - - energy without entropy = -347.74520690 energy(sigma->0) = -347.74520690 - - --------------------------------------------------------------------------------------------------------- - - - - ---------------------------------------- Iteration 1( 16) --------------------------------------- - - - POTLOK: cpu time 0.0444: real time 0.0449 - SETDIJ: cpu time 0.0196: real time 0.0197 - EDDAV: cpu time 0.2620: real time 0.2628 - DOS: cpu time 0.0002: real time 0.0002 - CHARGE: cpu time 0.1156: real time 0.1159 - MIXING: cpu time 0.0013: real time 0.0013 - -------------------------------------------- - LOOP: cpu time 0.4433: real time 0.4448 - - eigenvalue-minimisations : 816 - total energy-change (2. order) : 0.1060075E-05 (-0.3320931E-06) - number of electron 63.9999986 magnetization - augmentation part 5.8178455 magnetization - 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- --------------------------------------------------------------------------------------------------------- - - - - FREE ENERGIE OF THE ION-ELECTRON SYSTEM (eV) - --------------------------------------------------- - free energy TOTEN = -347.74520571 eV - - energy without entropy= -347.74520571 energy(sigma->0) = -347.74520571 - - - --------------------------------------------------------------------------------------------------------- - - - POTLOK: cpu time 0.0645: real time 0.0647 - - --------------------------------------------------------------------------------------------------------- - - - LOOP+: cpu time 8.2226: real time 8.4014 - 4ORBIT: cpu time 0.0000: real time 0.0000 - - total amount of memory used by VASP MPI-rank0 36732. kBytes -======================================================================= - - base : 30000. kBytes - nonl-proj : 1277. kBytes - fftplans : 1345. kBytes - grid : 2665. kBytes - one-center: 31. kBytes - wavefun : 1414. kBytes - - - - General timing and accounting informations for this job: - ======================================================== - - Total CPU time used (sec): 8.839 - User time (sec): 8.803 - System time (sec): 0.036 - Elapsed time (sec): 9.473 - - Maximum memory used (kb): 52988. - Average memory used (kb): 0. - - Minor page faults: 13744 - Major page faults: 0 - Voluntary context switches: 341 diff --git a/mace-bench/3rdparty/SevenNet/example_inputs/data/label_2/OUTCAR_9 b/mace-bench/3rdparty/SevenNet/example_inputs/data/label_2/OUTCAR_9 deleted file mode 100644 index 81ac308dcadd5e9a6154a4c0c8b022fef8336322..0000000000000000000000000000000000000000 --- a/mace-bench/3rdparty/SevenNet/example_inputs/data/label_2/OUTCAR_9 +++ /dev/null @@ -1,1978 +0,0 @@ - vasp.5.4.4.18Apr17-6-g9f103f2a35 (build Sep 11 2017 17:27:03) complex - - executed on GRP7IFC17NORMAL date 2022.08.24 18:31:40 - running on 32 total cores - distrk: each k-point on 16 cores, 2 groups - distr: one band on NCORES_PER_BAND= 8 cores, 2 groups - - --------------------------------------------------------------------------------------------------------- - - - INCAR: - POTCAR: PAW_PBE Hf 20Jan2003 - POTCAR: PAW_PBE O 08Apr2002 - - ----------------------------------------------------------------------------- -| | -| W W AA RRRRR N N II N N GGGG !!! | -| W W A A R R NN N II NN N G G !!! | -| W W A A R R N N N II N N N G !!! | -| W WW W AAAAAA RRRRR N N N II N N N G GGG ! | -| WW WW A A R R N NN II N NN G G | -| W W A A R R N N II N N GGGG !!! | -| | -| You have enabled k-point parallelism (KPAR>1). | -| This developmental code was originally written by Paul Kent at ORNL, | -| and carefully double checked in Vienna. | -| GW as well as linear response parallelism added by Martijn Marsman | -| and Georg Kresse. | -| Carefully verify results versus KPAR=1. | -| Report problems to Paul Kent and Vienna. | -| | - ----------------------------------------------------------------------------- - - POTCAR: PAW_PBE Hf 20Jan2003 - SHA256 = 0bb2207f9a10894133f750b65504b92b8afef976ae770762e0497daaaad8168a Hf - COPYR = (c) Copyright 20Jan2003 Georg Kresse - COPYR = This file is part of the software VASP. Any use, copying, and all ot - COPYR = If you do not have a valid VASP license, you may not use, copy or di - VRHFIN =Hf: 6s5d - LEXCH = PE - EATOM = 75.9011 eV, 5.5786 Ry - - TITEL = PAW_PBE Hf 20Jan2003 - LULTRA = F use ultrasoft PP ? - IUNSCR = 1 unscreen: 0-lin 1-nonlin 2-no - RPACOR = 2.500 partial core radius - POMASS = 178.490; ZVAL = 4.000 mass and valenz - RCORE = 3.000 outmost cutoff radius - RWIGS = 3.050; RWIGS = 1.614 wigner-seitz radius (au A) - ENMAX = 220.334; ENMIN = 165.250 eV - RCLOC = 2.212 cutoff for local pot - LCOR = T correct aug charges - LPAW = T paw PP - EAUG = 335.116 - DEXC = 0.000 - RMAX = 3.077 core radius for proj-oper - RAUG = 1.300 factor for augmentation sphere - RDEP = 3.047 radius for radial grids - RDEPT = 2.344 core radius for aug-charge - - Atomic configuration - 16 entries - n l j E occ. - 1 0 0.50 -65259.4397 2.0000 - 2 0 0.50 -11157.9882 2.0000 - 2 1 1.50 -9795.2113 6.0000 - 3 0 0.50 -2541.4058 2.0000 - 3 1 1.50 -2134.4770 6.0000 - 3 2 2.50 -1653.5418 10.0000 - 4 0 0.50 -510.9575 2.0000 - 4 1 1.50 -377.5023 6.0000 - 4 2 2.50 -205.2085 10.0000 - 4 3 3.50 -15.4905 14.0000 - 5 0 0.50 -65.6020 2.0000 - 5 1 1.50 -34.2798 6.0000 - 5 2 2.50 -1.9877 3.0000 - 6 0 0.50 -4.7357 1.0000 - 6 1 1.50 -1.3606 0.0000 - 5 3 2.50 -1.3606 0.0000 - Description - l E TYP RCUT TYP RCUT - 2 -1.9876627 23 2.500 - 2 0.0744703 23 2.500 - 0 -4.7356889 23 2.600 - 0 3.2364747 23 2.600 - 1 -1.3605826 23 3.000 - 1 27.2116520 23 3.000 - local pseudopotential read in - partial core-charges read in - partial kinetic energy density read in - atomic valenz-charges read in - non local Contribution for L= 2 read in - real space projection operators read in - non local Contribution for L= 2 read in - real space projection operators read in - non local Contribution for L= 0 read in - real space projection operators read in - non local Contribution for L= 0 read in - real space projection operators read in - non local Contribution for L= 1 read in - real space projection operators read in - non local Contribution for L= 1 read in - real space projection operators read in - PAW grid and wavefunctions read in - - number of l-projection operators is LMAX = 6 - number of lm-projection operators is LMMAX = 18 - - POTCAR: PAW_PBE O 08Apr2002 - SHA256 = 818f92134a0a090dccd8ba1447fa70422a3b330e708bb4f08108d8ae51209ddf O/ - COPYR = (c) Copyright 08Apr2002 Georg Kresse - COPYR = This file is part of the software VASP. Any use, copying, and all ot - COPYR = If you do not have a valid VASP license, you may not use, copy or di - VRHFIN =O: s2p4 - LEXCH = PE - EATOM = 432.3788 eV, 31.7789 Ry - - TITEL = PAW_PBE O 08Apr2002 - LULTRA = F use ultrasoft PP ? - IUNSCR = 1 unscreen: 0-lin 1-nonlin 2-no - RPACOR = 1.200 partial core radius - POMASS = 16.000; ZVAL = 6.000 mass and valenz - RCORE = 1.520 outmost cutoff radius - RWIGS = 1.550; RWIGS = 0.820 wigner-seitz radius (au A) - ENMAX = 400.000; ENMIN = 300.000 eV - ICORE = 2 local potential - LCOR = T correct aug charges - LPAW = T paw PP - EAUG = 605.392 - DEXC = 0.000 - RMAX = 1.553 core radius for proj-oper - RAUG = 1.300 factor for augmentation sphere - RDEP = 1.550 radius for radial grids - RDEPT = 1.329 core radius for aug-charge - - Atomic configuration - 4 entries - n l j E occ. - 1 0 0.50 -514.6923 2.0000 - 2 0 0.50 -23.9615 2.0000 - 2 1 0.50 -9.0305 4.0000 - 3 2 1.50 -9.5241 0.0000 - Description - l E TYP RCUT TYP RCUT - 0 -23.9615318 23 1.200 - 0 -9.5240782 23 1.200 - 1 -9.0304911 23 1.520 - 1 8.1634956 23 1.520 - 2 -9.5240782 7 1.500 - local pseudopotential read in - partial core-charges read in - partial kinetic energy density read in - kinetic energy density of atom read in - atomic valenz-charges read in - non local Contribution for L= 0 read in - real space projection operators read in - non local Contribution for L= 0 read in - real space projection operators read in - non local Contribution for L= 1 read in - real space projection operators read in - non local Contribution for L= 1 read in - real space projection operators read in - PAW grid and wavefunctions read in - - number of l-projection operators is LMAX = 4 - number of lm-projection operators is LMMAX = 8 - - PAW_PBE Hf 20Jan2003 : - energy of atom 1 EATOM= -75.9011 - kinetic energy error for atom= 0.0007 (will be added to EATOM!!) - PAW_PBE O 08Apr2002 : - energy of atom 2 EATOM= -432.3788 - kinetic energy error for atom= 0.0224 (will be added to EATOM!!) - - - POSCAR: Primitive Cell - positions in direct lattice - No initial velocities read in - - METAGGA = SCAN LMAXTAU = 0 LMIXTAU = F - - exchange correlation table for LEXCH = 8 - RHO(1)= 0.500 N(1) = 2000 - RHO(2)= 100.500 N(2) = 4000 - - - --------------------------------------------------------------------------------------------------------- - - - ion position nearest neighbor table - 1 0.543 0.776 0.292- 7 2.00 8 2.02 10 2.10 6 2.11 5 2.12 12 2.21 11 2.21 4 3.26 - 3 3.35 3 3.35 2 3.38 2 3.38 4 3.40 4 3.50 2 3.84 2 3.84 - 2 0.043 0.224 0.208- 8 2.00 7 2.02 9 2.10 5 2.11 6 2.12 11 2.21 12 2.21 3 3.26 - 4 3.35 4 3.35 1 3.38 1 3.38 3 3.40 3 3.50 1 3.84 1 3.84 - 3 0.957 0.776 0.792- 10 2.00 9 2.02 7 2.10 12 2.11 11 2.12 6 2.21 5 2.21 2 3.26 - 1 3.35 1 3.35 4 3.38 4 3.38 2 3.40 2 3.50 4 3.84 4 3.84 - 4 0.457 0.224 0.708- 9 2.00 10 2.02 8 2.10 11 2.11 12 2.12 5 2.21 6 2.21 1 3.26 - 2 3.35 2 3.35 3 3.38 3 3.38 1 3.40 1 3.50 3 3.84 3 3.84 - 5 0.757 0.052 0.478- 2 2.11 1 2.12 4 2.21 3 2.21 - 6 0.257 0.948 0.022- 1 2.11 2 2.12 3 2.21 4 2.21 - 7 0.832 0.569 0.154- 1 2.00 2 2.02 3 2.10 - 8 0.332 0.431 0.346- 2 2.00 1 2.02 4 2.10 - 9 0.168 0.431 0.846- 4 2.00 3 2.02 2 2.10 - 10 0.668 0.569 0.654- 3 2.00 4 2.02 1 2.10 - 11 0.743 0.052 0.978- 4 2.11 3 2.12 2 2.21 1 2.21 - 12 0.243 0.948 0.522- 3 2.11 4 2.12 1 2.21 2 2.21 - - LATTYP: Found a simple monoclinic cell. - ALAT = 7.8124049658 - B/A-ratio = 0.6517496159 - C/A-ratio = 1.5432771295 - COS(beta) = -0.9616437168 - - Lattice vectors: - - A1 = ( 0.0000000000, -5.8810143832, -5.1426978498) - A2 = ( -5.0917319354, 0.0000000000, 0.0000000000) - A3 = ( 0.0000000000, 10.9049362088, 5.1426183689) - - -Analysis of symmetry for initial positions (statically): -===================================================================== - Subroutine PRICEL returns: - Original cell was already a primitive cell. - - - Routine SETGRP: Setting up the symmetry group for a - simple monoclinic supercell. - - - Subroutine GETGRP returns: Found 4 space group operations - (whereof 2 operations were pure point group operations) - out of a pool of 4 trial point group operations. - - -The static configuration has the point symmetry S_2 . - The point group associated with its full space group is C_2h. - - -Analysis of symmetry for dynamics (positions and initial velocities): -===================================================================== - Subroutine PRICEL returns: - Original cell was already a primitive cell. - - - Routine SETGRP: Setting up the symmetry group for a - simple monoclinic supercell. - - - Subroutine GETGRP returns: Found 4 space group operations - (whereof 2 operations were pure point group operations) - out of a pool of 4 trial point group operations. - - -The dynamic configuration has the point symmetry S_2 . - The point group associated with its full space group is C_2h. - - -Analysis of constrained symmetry for selective dynamics: -===================================================================== - Subroutine PRICEL returns: - Original cell was already a primitive cell. - - - Routine SETGRP: Setting up the symmetry group for a - simple monoclinic supercell. - - - Subroutine GETGRP returns: Found 4 space group operations - (whereof 2 operations were pure point group operations) - out of a pool of 4 trial point group operations. - - -The constrained configuration has the point symmetry S_2 . - The point group associated with its full space group is C_2h. - - - Subroutine INISYM returns: Found 4 space group operations - (whereof 2 operations are pure point group operations), - and found 1 'primitive' translations - - - - KPOINTS: Auto k-point - -Automatic generation of k-mesh. -Space group operators: - irot det(A) alpha n_x n_y n_z tau_x tau_y tau_z - 1 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 - 2 -1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 - 3 1.000000 180.000000 1.000000 0.000000 0.000000 -0.500000 1.000000 0.500000 - 4 -1.000000 180.000000 1.000000 0.000000 0.000000 -0.500000 1.000000 0.500000 - - Subroutine IBZKPT returns following result: - =========================================== - - Found 10 irreducible k-points: - - Following reciprocal coordinates: - Coordinates Weight - 0.000000 0.000000 0.000000 1.000000 - 0.333333 0.000000 0.000000 2.000000 - 0.000000 0.333333 0.000000 2.000000 - 0.333333 0.333333 0.000000 4.000000 - 0.000000 -0.000000 0.333333 2.000000 - 0.333333 -0.000000 0.333333 4.000000 - 0.000000 0.333333 0.333333 2.000000 - 0.333333 0.333333 0.333333 4.000000 - 0.000000 -0.333333 0.333333 2.000000 - 0.333333 -0.333333 0.333333 4.000000 - - Following cartesian coordinates: - Coordinates Weight - 0.000000 0.000000 0.000000 1.000000 - 0.065466 0.000000 0.000000 2.000000 - 0.000000 0.066349 -0.011058 2.000000 - 0.065466 0.066349 -0.011058 4.000000 - 0.000000 0.000001 0.064816 2.000000 - 0.065466 0.000001 0.064816 4.000000 - 0.000000 0.066350 0.053758 2.000000 - 0.065466 0.066350 0.053758 4.000000 - 0.000000 -0.066348 0.075873 2.000000 - 0.065466 -0.066348 0.075873 4.000000 - - - --------------------------------------------------------------------------------------------------------- - - - - - Dimension of arrays: - k-points NKPTS = 10 k-points in BZ NKDIM = 10 number of bands NBANDS= 40 - number of dos NEDOS = 301 number of ions NIONS = 12 - non local maximal LDIM = 6 non local SUM 2l+1 LMDIM = 18 - total plane-waves NPLWV = 64000 - max r-space proj IRMAX = 1 max aug-charges IRDMAX= 32862 - dimension x,y,z NGX = 40 NGY = 40 NGZ = 40 - dimension x,y,z NGXF= 80 NGYF= 80 NGZF= 80 - support grid NGXF= 80 NGYF= 80 NGZF= 80 - ions per type = 4 8 - NGX,Y,Z is equivalent to a cutoff of 13.06, 13.24, 12.75 a.u. - NGXF,Y,Z is equivalent to a cutoff of 26.12, 26.47, 25.51 a.u. - - SYSTEM = HfO2_p21c - POSCAR = Primitive Cell - - Startparameter for this run: - NWRITE = 2 write-flag & timer - PREC = accura normal or accurate (medium, high low for compatibility) - ISTART = 0 job : 0-new 1-cont 2-samecut - ICHARG = 2 charge: 1-file 2-atom 10-const - ISPIN = 1 spin polarized calculation? - LNONCOLLINEAR = F non collinear calculations - LSORBIT = F spin-orbit coupling - INIWAV = 1 electr: 0-lowe 1-rand 2-diag - LASPH = F aspherical Exc in radial PAW - METAGGA= F non-selfconsistent MetaGGA calc. - - Electronic Relaxation 1 - ENCUT = 500.0 eV 36.75 Ry 6.06 a.u. 9.28 9.16 9.51*2*pi/ulx,y,z - ENINI = 500.0 initial cutoff - ENAUG = 605.4 eV augmentation charge cutoff - NELM = 100; NELMIN= 2; NELMDL= -5 # of ELM steps - EDIFF = 0.1E-05 stopping-criterion for ELM - LREAL = F real-space projection - NLSPLINE = F spline interpolate recip. space projectors - LCOMPAT= F compatible to vasp.4.4 - GGA_COMPAT = T GGA compatible to vasp.4.4-vasp.4.6 - LMAXPAW = -100 max onsite density - LMAXMIX = 2 max onsite mixed and CHGCAR - VOSKOWN= 0 Vosko Wilk Nusair interpolation - ROPT = 0.00000 0.00000 - Ionic relaxation - EDIFFG = -.2E-02 stopping-criterion for IOM - NSW = 0 number of steps for IOM - NBLOCK = 1; KBLOCK = 1 inner block; outer block - IBRION = -1 ionic relax: 0-MD 1-quasi-New 2-CG - NFREE = 1 steps in history (QN), initial steepest desc. (CG) - ISIF = 3 stress and relaxation - IWAVPR = 10 prediction: 0-non 1-charg 2-wave 3-comb - ISYM = 1 0-nonsym 1-usesym 2-fastsym - LCORR = T Harris-Foulkes like correction to forces - - POTIM = 0.5000 time-step for ionic-motion - TEIN = 0.0 initial temperature - TEBEG = 0.0; TEEND = 0.0 temperature during run - SMASS = -3.00 Nose mass-parameter (am) - estimated Nose-frequenzy (Omega) = 0.10E-29 period in steps =****** mass= -0.592E-27a.u. - SCALEE = 1.0000 scale energy and forces - NPACO = 256; APACO = 16.0 distance and # of slots for P.C. - PSTRESS= 0.0 pullay stress - - Mass of Ions in am - POMASS = 178.49 16.00 - Ionic Valenz - ZVAL = 4.00 6.00 - Atomic Wigner-Seitz radii - RWIGS = -1.00 -1.00 - virtual crystal weights - VCA = 1.00 1.00 - NELECT = 64.0000 total number of electrons - NUPDOWN= -1.0000 fix difference up-down - - DOS related values: - EMIN = 10.00; EMAX =-10.00 energy-range for DOS - EFERMI = 0.00 - ISMEAR = 0; SIGMA = 0.05 broadening in eV -4-tet -1-fermi 0-gaus - - Electronic relaxation 2 (details) - IALGO = 38 algorithm - LDIAG = T sub-space diagonalisation (order eigenvalues) - LSUBROT= F optimize rotation matrix (better conditioning) - TURBO = 0 0=normal 1=particle mesh - IRESTART = 0 0=no restart 2=restart with 2 vectors - NREBOOT = 0 no. of reboots - NMIN = 0 reboot dimension - EREF = 0.00 reference energy to select bands - IMIX = 4 mixing-type and parameters - AMIX = 0.40; BMIX = 1.00 - AMIX_MAG = 1.60; BMIX_MAG = 1.00 - AMIN = 0.10 - WC = 100.; INIMIX= 1; MIXPRE= 1; MAXMIX= -45 - - Intra band minimization: - WEIMIN = 0.0000 energy-eigenvalue tresh-hold - EBREAK = 0.62E-08 absolut break condition - DEPER = 0.30 relativ break condition - - TIME = 0.40 timestep for ELM - - volume/ion in A,a.u. = 10.96 73.98 - Fermi-wavevector in a.u.,A,eV,Ry = 1.287555 2.433126 22.555703 1.657797 - Thomas-Fermi vector in A = 2.419562 - - Write flags - LWAVE = F write WAVECAR - LDOWNSAMPLE = F k-point downsampling of WAVECAR - LCHARG = F write CHGCAR - LVTOT = F write LOCPOT, total local potential - LVHAR = F write LOCPOT, Hartree potential only - LELF = F write electronic localiz. function (ELF) - LORBIT = 0 0 simple, 1 ext, 2 COOP (PROOUT), +10 PAW based schemes - - - Dipole corrections - LMONO = F monopole corrections only (constant potential shift) - LDIPOL = F correct potential (dipole corrections) - IDIPOL = 0 1-x, 2-y, 3-z, 4-all directions - EPSILON= 1.0000000 bulk dielectric constant - - Exchange correlation treatment: - GGA = -- GGA type - LEXCH = 8 internal setting for exchange type - VOSKOWN= 0 Vosko Wilk Nusair interpolation - LHFCALC = F Hartree Fock is set to - LHFONE = F Hartree Fock one center treatment - AEXX = 0.0000 exact exchange contribution - - Linear response parameters - LEPSILON= F determine dielectric tensor - LRPA = F only Hartree local field effects (RPA) - LNABLA = F use nabla operator in PAW spheres - LVEL = F velocity operator in full k-point grid - LINTERFAST= F fast interpolation - KINTER = 0 interpolate to denser k-point grid - CSHIFT =0.1000 complex shift for real part using Kramers Kronig - OMEGAMAX= -1.0 maximum frequency - DEG_THRESHOLD= 0.2000000E-02 threshold for treating states as degnerate - RTIME = -0.100 relaxation time in fs - (WPLASMAI= 0.000 imaginary part of plasma frequency in eV, 0.658/RTIME) - DFIELD = 0.0000000 0.0000000 0.0000000 field for delta impulse in time - - Orbital magnetization related: - ORBITALMAG= F switch on orbital magnetization - LCHIMAG = F perturbation theory with respect to B field - DQ = 0.001000 dq finite difference perturbation B field - LLRAUG = F two centre corrections for induced B field - - - --------------------------------------------------------------------------------------------------------- - - - Static calculation - charge density and potential will be updated during run - non-spin polarized calculation - Variant of blocked Davidson - Davidson routine will perform the subspace rotation - perform sub-space diagonalisation - after iterative eigenvector-optimisation - modified Broyden-mixing scheme, WC = 100.0 - initial mixing is a Kerker type mixing with AMIX = 0.4000 and BMIX = 1.0000 - Hartree-type preconditioning will be used - using additional bands 8 - reciprocal scheme for non local part - use partial core corrections - calculate Harris-corrections to forces - (improved forces if not selfconsistent) - use gradient corrections - use of overlap-Matrix (Vanderbilt PP) - Gauss-broadening in eV SIGMA = 0.05 - - --------------------------------------------------------------------------------------------------------- - - - energy-cutoff : 500.00 - volume of cell : 131.55 - direct lattice vectors reciprocal lattice vectors - 5.091731935 0.000000000 0.000000000 0.196396828 0.000000000 0.000000000 - 0.000000000 5.023921826 -0.000079481 0.000000000 0.199047158 -0.033173094 - 0.000000000 0.857092558 5.142777331 0.000000000 0.000003076 0.194446949 - - length of vectors - 5.091731935 5.023921826 5.213709459 0.196396828 0.201792531 0.194446949 - - - - k-points in units of 2pi/SCALE and weight: Auto k-point - 0.00000000 0.00000000 0.00000000 0.037 - 0.06546561 0.00000000 0.00000000 0.074 - 0.00000000 0.06634905 -0.01105770 0.074 - 0.06546561 0.06634905 -0.01105770 0.148 - 0.00000000 0.00000103 0.06481565 0.074 - 0.06546561 0.00000103 0.06481565 0.148 - 0.00000000 0.06635008 0.05375795 0.074 - 0.06546561 0.06635008 0.05375795 0.148 - 0.00000000 -0.06634803 0.07587335 0.074 - 0.06546561 -0.06634803 0.07587335 0.148 - - k-points in reciprocal lattice and weights: Auto k-point - 0.00000000 0.00000000 0.00000000 0.037 - 0.33333333 0.00000000 0.00000000 0.074 - 0.00000000 0.33333333 0.00000000 0.074 - 0.33333333 0.33333333 0.00000000 0.148 - 0.00000000 -0.00000000 0.33333333 0.074 - 0.33333333 -0.00000000 0.33333333 0.148 - 0.00000000 0.33333333 0.33333333 0.074 - 0.33333333 0.33333333 0.33333333 0.148 - 0.00000000 -0.33333333 0.33333333 0.074 - 0.33333333 -0.33333333 0.33333333 0.148 - - position of ions in fractional coordinates (direct lattice) - 0.54288322 0.77577220 0.29175508 - 0.04288322 0.22422780 0.20824492 - 0.95711678 0.77577220 0.79175508 - 0.45711678 0.22422780 0.70824492 - 0.75741482 0.05184460 0.47813308 - 0.25741482 0.94815540 0.02186692 - 0.83182355 0.56876319 0.15428653 - 0.33182355 0.43123681 0.34571347 - 0.16817645 0.43123681 0.84571347 - 0.66817645 0.56876319 0.65428653 - 0.74258518 0.05184460 0.97813308 - 0.24258518 0.94815540 0.52186692 - - position of ions in cartesian coordinates (Angst): - 2.76421582 4.14747997 1.50036973 - 0.21834985 1.30498813 1.07093945 - 4.87338208 4.57602625 4.07175840 - 2.32751612 1.73353441 3.64232812 - 3.85655325 0.67026753 2.45892785 - 1.31068728 4.78220057 0.11238134 - 4.23542253 2.98965964 0.79341609 - 1.68955656 2.46280847 1.77789310 - 0.85630941 2.89135475 4.34928176 - 3.40217538 3.41820592 3.36480475 - 3.78104466 1.09881381 5.03031651 - 1.23517869 5.21074685 2.68377000 - - - --------------------------------------------------------------------------------------------------------- - - - k-point 1 : 0.0000 0.0000 0.0000 plane waves: 3321 - k-point 2 : 0.3333 0.0000 0.0000 plane waves: 3350 - k-point 3 : 0.0000 0.3333 0.0000 plane waves: 3346 - k-point 4 : 0.3333 0.3333 0.0000 plane waves: 3346 - k-point 5 : 0.0000-0.0000 0.3333 plane waves: 3335 - k-point 6 : 0.3333-0.0000 0.3333 plane waves: 3339 - k-point 7 : 0.0000 0.3333 0.3333 plane waves: 3330 - k-point 8 : 0.3333 0.3333 0.3333 plane waves: 3337 - k-point 9 : 0.0000-0.3333 0.3333 plane waves: 3345 - k-point 10 : 0.3333-0.3333 0.3333 plane waves: 3343 - - maximum and minimum number of plane-waves per node : 445 396 - - maximum number of plane-waves: 3350 - maximum index in each direction: - IXMAX= 9 IYMAX= 9 IZMAX= 9 - IXMIN= -9 IYMIN= -9 IZMIN= -9 - - - parallel 3D FFT for wavefunctions: - minimum data exchange during FFTs selected (reduces bandwidth) - parallel 3D FFT for charge: - minimum data exchange during FFTs selected (reduces bandwidth) - - - total amount of memory used by VASP MPI-rank0 36758. kBytes -======================================================================= - - base : 30000. kBytes - nonl-proj : 1290. kBytes - fftplans : 1345. kBytes - grid : 2665. kBytes - one-center: 31. kBytes - wavefun : 1427. kBytes - - INWAV: cpu time 0.0000: real time 0.0002 - Broyden mixing: mesh for mixing (old mesh) - NGX = 19 NGY = 19 NGZ = 19 - (NGX = 80 NGY = 80 NGZ = 80) - gives a total of 6859 points - - initial charge density was supplied: - charge density of overlapping atoms calculated - number of electron 64.0000000 magnetization - keeping initial charge density in first step - - --------------------------------------------------------------------------------------------------------- - - - Maximum index for augmentation-charges 1955 (set IRDMAX) - - --------------------------------------------------------------------------------------------------------- - - - First call to EWALD: gamma= 0.349 - Maximum number of real-space cells 3x 3x 3 - Maximum number of reciprocal cells 3x 3x 3 - - FEWALD: cpu time 0.0013: real time 0.0013 - - ---------------------------------------- Iteration 1( 1) --------------------------------------- - - - POTLOK: cpu time 0.0472: real time 0.0957 - SETDIJ: cpu time 0.0027: real time 0.0027 - EDDAV: cpu time 0.2616: real time 0.2622 - DOS: cpu time 0.0005: real time 0.0005 - -------------------------------------------- - LOOP: cpu time 0.3120: real time 0.3611 - - eigenvalue-minimisations : 800 - total energy-change (2. order) : 0.1335761E+03 (-0.3427104E+04) - number of electron 64.0000000 magnetization - augmentation part 64.0000000 magnetization - - Free energy of the ion-electron system (eV) - --------------------------------------------------- - alpha Z PSCENC = 250.74326039 - Ewald energy TEWEN = -3127.45179835 - -Hartree energ DENC = -915.43394313 - -exchange EXHF = 0.00000000 - -V(xc)+E(xc) XCENC = 74.82493786 - PAW double counting = 3196.24842107 -3219.62951610 - entropy T*S EENTRO = -0.00818920 - eigenvalues EBANDS = 111.83006722 - atomic energy EATOM = 3762.45289366 - Solvation Ediel_sol = 0.00000000 - --------------------------------------------------- - free energy TOTEN = 133.57613342 eV - - energy without entropy = 133.58432262 energy(sigma->0) = 133.58022802 - - --------------------------------------------------------------------------------------------------------- - - - - ---------------------------------------- Iteration 1( 2) --------------------------------------- - - - EDDAV: cpu time 0.3092: real time 0.3150 - DOS: cpu time 0.0002: real time 0.0002 - -------------------------------------------- - LOOP: cpu time 0.3093: real time 0.3152 - - eigenvalue-minimisations : 1056 - total energy-change (2. order) :-0.4889385E+03 (-0.4754069E+03) - number of electron 64.0000000 magnetization - augmentation part 64.0000000 magnetization - - Free energy of the ion-electron system (eV) - --------------------------------------------------- - alpha Z PSCENC = 250.74326039 - Ewald energy TEWEN = -3127.45179835 - -Hartree energ DENC = -915.43394313 - -exchange EXHF = 0.00000000 - -V(xc)+E(xc) XCENC = 74.82493786 - PAW double counting = 3196.24842107 -3219.62951610 - entropy T*S EENTRO = -0.00000000 - eigenvalues EBANDS = -377.11657721 - atomic energy EATOM = 3762.45289366 - Solvation Ediel_sol = 0.00000000 - --------------------------------------------------- - free energy TOTEN = -355.36232182 eV - - energy without entropy = -355.36232182 energy(sigma->0) = -355.36232182 - - --------------------------------------------------------------------------------------------------------- - - - - ---------------------------------------- Iteration 1( 3) --------------------------------------- - - - EDDAV: cpu time 0.2903: real time 0.2914 - DOS: cpu time 0.0002: real time 0.0002 - -------------------------------------------- - LOOP: cpu time 0.2905: real time 0.2916 - - eigenvalue-minimisations : 960 - total energy-change (2. order) :-0.2628191E+02 (-0.2615223E+02) - number of electron 64.0000000 magnetization - augmentation part 64.0000000 magnetization - - Free energy of the ion-electron system (eV) - --------------------------------------------------- - alpha Z PSCENC = 250.74326039 - Ewald energy TEWEN = -3127.45179835 - -Hartree energ DENC = -915.43394313 - -exchange EXHF = 0.00000000 - -V(xc)+E(xc) XCENC = 74.82493786 - PAW double counting = 3196.24842107 -3219.62951610 - entropy T*S EENTRO = -0.00000000 - eigenvalues EBANDS = -403.39848965 - atomic energy EATOM = 3762.45289366 - Solvation Ediel_sol = 0.00000000 - --------------------------------------------------- - free energy TOTEN = -381.64423425 eV - - energy without entropy = -381.64423425 energy(sigma->0) = -381.64423425 - - --------------------------------------------------------------------------------------------------------- - - - - ---------------------------------------- Iteration 1( 4) --------------------------------------- - - - EDDAV: cpu time 0.2901: real time 0.2910 - DOS: cpu time 0.0002: real time 0.0002 - -------------------------------------------- - LOOP: cpu time 0.2903: real time 0.2912 - - eigenvalue-minimisations : 960 - total energy-change (2. order) :-0.3947586E+00 (-0.3935223E+00) - number of electron 64.0000000 magnetization - augmentation part 64.0000000 magnetization - - Free energy of the ion-electron system (eV) - --------------------------------------------------- - alpha Z PSCENC = 250.74326039 - Ewald energy TEWEN = -3127.45179835 - -Hartree energ DENC = -915.43394313 - -exchange EXHF = 0.00000000 - -V(xc)+E(xc) XCENC = 74.82493786 - PAW double counting = 3196.24842107 -3219.62951610 - entropy T*S EENTRO = -0.00000000 - eigenvalues EBANDS = -403.79324821 - atomic energy EATOM = 3762.45289366 - Solvation Ediel_sol = 0.00000000 - --------------------------------------------------- - free energy TOTEN = -382.03899281 eV - - energy without entropy = -382.03899281 energy(sigma->0) = -382.03899281 - - --------------------------------------------------------------------------------------------------------- - - - - ---------------------------------------- Iteration 1( 5) --------------------------------------- - - - EDDAV: cpu time 0.2870: real time 0.2879 - DOS: cpu time 0.0002: real time 0.0002 - CHARGE: cpu time 0.1198: real time 0.1203 - MIXING: cpu time 0.0014: real time 0.0015 - -------------------------------------------- - LOOP: cpu time 0.4085: real time 0.4099 - - eigenvalue-minimisations : 936 - total energy-change (2. order) :-0.9495227E-02 (-0.9489892E-02) - number of electron 63.9999979 magnetization - augmentation part 6.7032221 magnetization - - Broyden mixing: - rms(total) = 0.53943E+01 rms(broyden)= 0.53942E+01 - rms(prec ) = 0.69763E+01 - weight for this iteration 100.00 - - Free energy of the ion-electron system (eV) - --------------------------------------------------- - alpha Z PSCENC = 250.74326039 - Ewald energy TEWEN = -3127.45179835 - -Hartree energ DENC = -915.43394313 - -exchange EXHF = 0.00000000 - -V(xc)+E(xc) XCENC = 74.82493786 - PAW double counting = 3196.24842107 -3219.62951610 - entropy T*S EENTRO = -0.00000000 - eigenvalues EBANDS = -403.80274344 - atomic energy EATOM = 3762.45289366 - Solvation Ediel_sol = 0.00000000 - --------------------------------------------------- - free energy TOTEN = -382.04848804 eV - - energy without entropy = -382.04848804 energy(sigma->0) = -382.04848804 - - --------------------------------------------------------------------------------------------------------- - - - - ---------------------------------------- Iteration 1( 6) --------------------------------------- - - - POTLOK: cpu time 0.0441: real time 0.0445 - SETDIJ: cpu time 0.0196: real time 0.0197 - EDDAV: cpu time 0.2865: real time 0.2872 - DOS: cpu time 0.0002: real time 0.0002 - CHARGE: cpu time 0.1149: real time 0.1152 - MIXING: cpu time 0.0014: real time 0.0014 - -------------------------------------------- - LOOP: cpu time 0.4667: real time 0.4681 - - eigenvalue-minimisations : 936 - total energy-change (2. order) : 0.3539962E+02 (-0.7199695E+01) - number of electron 63.9999983 magnetization - augmentation part 5.8353294 magnetization - - Broyden mixing: - rms(total) = 0.26996E+01 rms(broyden)= 0.26994E+01 - rms(prec ) = 0.28593E+01 - weight for this iteration 100.00 - - eigenvalues of (default mixing * dielectric matrix) - average eigenvalue GAMMA= 1.5501 - 1.5501 - - Free energy of the ion-electron system (eV) - --------------------------------------------------- - alpha Z PSCENC = 250.74326039 - Ewald energy TEWEN = -3127.45179835 - -Hartree energ DENC = -1078.94959924 - -exchange EXHF = 0.00000000 - -V(xc)+E(xc) XCENC = 98.49174232 - PAW double counting = 4559.07855990 -4584.78090173 - entropy T*S EENTRO = -0.00000000 - eigenvalues EBANDS = -226.23302389 - atomic energy EATOM = 3762.45289366 - Solvation Ediel_sol = 0.00000000 - --------------------------------------------------- - free energy TOTEN = -346.64886694 eV - - energy without entropy = -346.64886694 energy(sigma->0) = -346.64886694 - - --------------------------------------------------------------------------------------------------------- - - - - ---------------------------------------- Iteration 1( 7) --------------------------------------- - - - POTLOK: cpu time 0.0441: real time 0.0445 - SETDIJ: cpu time 0.0196: real time 0.0196 - EDDAV: cpu time 0.3196: real time 0.3203 - DOS: cpu time 0.0002: real time 0.0002 - CHARGE: cpu time 0.1150: real time 0.1152 - MIXING: cpu time 0.0013: real time 0.0013 - -------------------------------------------- - LOOP: cpu time 0.4997: real time 0.5012 - - eigenvalue-minimisations : 1112 - total energy-change (2. order) :-0.1222871E+01 (-0.3622998E+00) - number of electron 63.9999983 magnetization - augmentation part 5.7351408 magnetization - - Broyden mixing: - rms(total) = 0.12178E+01 rms(broyden)= 0.12178E+01 - rms(prec ) = 0.13024E+01 - weight for this iteration 100.00 - - eigenvalues of (default mixing * dielectric matrix) - average eigenvalue GAMMA= 1.7168 - 1.1415 2.2921 - - Free energy of the ion-electron system (eV) - --------------------------------------------------- - alpha Z PSCENC = 250.74326039 - Ewald energy TEWEN = -3127.45179835 - -Hartree energ DENC = -1098.41219851 - -exchange EXHF = 0.00000000 - -V(xc)+E(xc) XCENC = 97.36276236 - PAW double counting = 5881.51399822 -5907.85630381 - entropy T*S EENTRO = -0.00000000 - eigenvalues EBANDS = -206.22435232 - atomic energy EATOM = 3762.45289366 - Solvation Ediel_sol = 0.00000000 - --------------------------------------------------- - free energy TOTEN = -347.87173836 eV - - energy without entropy = -347.87173836 energy(sigma->0) = -347.87173836 - - --------------------------------------------------------------------------------------------------------- - - - - ---------------------------------------- Iteration 1( 8) --------------------------------------- - - - POTLOK: cpu time 0.0440: real time 0.0445 - SETDIJ: cpu time 0.0196: real time 0.0196 - EDDAV: cpu time 0.2835: real time 0.2842 - DOS: cpu time 0.0002: real time 0.0002 - CHARGE: cpu time 0.1151: real time 0.1153 - MIXING: cpu time 0.0011: real time 0.0011 - -------------------------------------------- - LOOP: cpu time 0.4635: real time 0.4651 - - eigenvalue-minimisations : 936 - total energy-change (2. order) : 0.2216848E-01 (-0.9102193E-01) - number of electron 63.9999983 magnetization - augmentation part 5.8522800 magnetization - - Broyden mixing: - rms(total) = 0.14224E+00 rms(broyden)= 0.14219E+00 - rms(prec ) = 0.25706E+00 - weight for this iteration 100.00 - - eigenvalues of (default mixing * dielectric matrix) - average eigenvalue GAMMA= 1.4766 - 2.3828 1.0235 1.0235 - - Free energy of the ion-electron system (eV) - --------------------------------------------------- - alpha Z PSCENC = 250.74326039 - Ewald energy TEWEN = -3127.45179835 - -Hartree energ DENC = -1089.34351407 - -exchange EXHF = 0.00000000 - -V(xc)+E(xc) XCENC = 98.20597724 - PAW double counting = 7257.70199490 -7284.70566730 - entropy T*S EENTRO = -0.00000000 - eigenvalues EBANDS = -215.45271635 - atomic energy EATOM = 3762.45289366 - Solvation Ediel_sol = 0.00000000 - --------------------------------------------------- - free energy TOTEN = -347.84956988 eV - - energy without entropy = -347.84956988 energy(sigma->0) = -347.84956988 - - --------------------------------------------------------------------------------------------------------- - - - - ---------------------------------------- Iteration 1( 9) --------------------------------------- - - - POTLOK: cpu time 0.0446: real time 0.0450 - SETDIJ: cpu time 0.0191: real time 0.0191 - EDDAV: cpu time 0.2898: real time 0.2907 - DOS: cpu time 0.0002: real time 0.0002 - CHARGE: cpu time 0.1151: real time 0.1154 - MIXING: cpu time 0.0012: real time 0.0012 - -------------------------------------------- - LOOP: cpu time 0.4700: real time 0.4716 - - eigenvalue-minimisations : 960 - total energy-change (2. order) : 0.3828546E-01 (-0.1800970E-01) - number of electron 63.9999983 magnetization - augmentation part 5.8064948 magnetization - - Broyden mixing: - rms(total) = 0.36983E-01 rms(broyden)= 0.36954E-01 - rms(prec ) = 0.56669E-01 - weight for this iteration 100.00 - - eigenvalues of (default mixing * dielectric matrix) - average eigenvalue GAMMA= 1.6376 - 2.2690 2.2690 1.0061 1.0061 - - Free energy of the ion-electron system (eV) - --------------------------------------------------- - alpha Z PSCENC = 250.74326039 - Ewald energy TEWEN = -3127.45179835 - -Hartree energ DENC = -1096.78259720 - -exchange EXHF = 0.00000000 - -V(xc)+E(xc) XCENC = 99.42866674 - PAW double counting = 7341.38868696 -7368.53791250 - entropy T*S EENTRO = -0.00000000 - eigenvalues EBANDS = -209.05248412 - atomic energy EATOM = 3762.45289366 - Solvation Ediel_sol = 0.00000000 - --------------------------------------------------- - free energy TOTEN = -347.81128442 eV - - energy without entropy = -347.81128442 energy(sigma->0) = -347.81128442 - - --------------------------------------------------------------------------------------------------------- - - - - ---------------------------------------- Iteration 1( 10) --------------------------------------- - - - POTLOK: cpu time 0.0441: real time 0.0445 - SETDIJ: cpu time 0.0197: real time 0.0197 - EDDAV: cpu time 0.2986: real time 0.2994 - DOS: cpu time 0.0002: real time 0.0002 - CHARGE: cpu time 0.1148: real time 0.1151 - MIXING: cpu time 0.0012: real time 0.0012 - -------------------------------------------- - LOOP: cpu time 0.4786: real time 0.4801 - - eigenvalue-minimisations : 992 - total energy-change (2. order) :-0.2004593E-02 (-0.3200290E-02) - number of electron 63.9999983 magnetization - augmentation part 5.8046412 magnetization - - Broyden mixing: - rms(total) = 0.27381E-01 rms(broyden)= 0.27370E-01 - rms(prec ) = 0.48508E-01 - weight for this iteration 100.00 - - eigenvalues of (default mixing * dielectric matrix) - average eigenvalue GAMMA= 1.4823 - 2.4635 2.1771 1.1185 0.8262 0.8262 - - Free energy of the ion-electron system (eV) - --------------------------------------------------- - alpha Z PSCENC = 250.74326039 - Ewald energy TEWEN = -3127.45179835 - -Hartree energ DENC = -1097.29549064 - -exchange EXHF = 0.00000000 - -V(xc)+E(xc) XCENC = 99.37790888 - PAW double counting = 7358.64713568 -7385.89911547 - entropy T*S EENTRO = -0.00000000 - eigenvalues EBANDS = -208.38808317 - atomic energy EATOM = 3762.45289366 - Solvation Ediel_sol = 0.00000000 - --------------------------------------------------- - free energy TOTEN = -347.81328901 eV - 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average eigenvalue GAMMA= 1.4985 - 2.5095 2.5095 0.9734 0.9734 1.0127 1.0127 - - Free energy of the ion-electron system (eV) - --------------------------------------------------- - alpha Z PSCENC = 250.74326039 - Ewald energy TEWEN = -3127.45179835 - -Hartree energ DENC = -1098.59084555 - -exchange EXHF = 0.00000000 - -V(xc)+E(xc) XCENC = 99.46459933 - PAW double counting = 7370.33065011 -7397.61582300 - entropy T*S EENTRO = -0.00000000 - eigenvalues EBANDS = -207.14643358 - atomic energy EATOM = 3762.45289366 - Solvation Ediel_sol = 0.00000000 - --------------------------------------------------- - free energy TOTEN = -347.81349699 eV - - energy without entropy = -347.81349699 energy(sigma->0) = -347.81349699 - - --------------------------------------------------------------------------------------------------------- - - - - ---------------------------------------- Iteration 1( 12) --------------------------------------- - - - POTLOK: cpu time 0.0445: real time 0.0449 - SETDIJ: cpu time 0.0192: real time 0.0192 - EDDAV: cpu time 0.2896: real time 0.2906 - DOS: cpu time 0.0002: real time 0.0002 - CHARGE: cpu time 0.1155: real time 0.1158 - MIXING: cpu time 0.0016: real time 0.0016 - -------------------------------------------- - LOOP: cpu time 0.4706: real time 0.4723 - - eigenvalue-minimisations : 960 - total energy-change (2. order) : 0.1237630E-02 (-0.7873311E-03) - number of electron 63.9999983 magnetization - augmentation part 5.8036472 magnetization - - Broyden mixing: - rms(total) = 0.34493E-02 rms(broyden)= 0.34235E-02 - rms(prec ) = 0.53222E-02 - weight for this iteration 100.00 - - eigenvalues of (default mixing * dielectric matrix) - average eigenvalue GAMMA= 1.4765 - 2.8987 2.3802 1.1579 0.9528 0.9528 0.9967 0.9967 - - Free energy of the ion-electron system (eV) - --------------------------------------------------- - alpha Z PSCENC = 250.74326039 - Ewald energy TEWEN = -3127.45179835 - -Hartree energ DENC = -1097.60038078 - -exchange EXHF = 0.00000000 - -V(xc)+E(xc) XCENC = 99.36193785 - PAW double counting = 7364.95491474 -7392.24790756 - entropy T*S EENTRO = -0.00000000 - eigenvalues EBANDS = -208.02517932 - atomic energy EATOM = 3762.45289366 - Solvation Ediel_sol = 0.00000000 - --------------------------------------------------- - free energy TOTEN = -347.81225936 eV - - energy without entropy = -347.81225936 energy(sigma->0) = -347.81225936 - - --------------------------------------------------------------------------------------------------------- - - - - ---------------------------------------- Iteration 1( 13) --------------------------------------- - - - POTLOK: cpu time 0.0445: real time 0.0448 - SETDIJ: cpu time 0.0192: real time 0.0193 - EDDAV: cpu time 0.2899: real time 0.2906 - DOS: cpu time 0.0002: real time 0.0002 - CHARGE: cpu time 0.1159: real time 0.1162 - MIXING: cpu time 0.0013: real time 0.0013 - -------------------------------------------- - LOOP: cpu time 0.4711: real time 0.4724 - - eigenvalue-minimisations : 960 - total energy-change (2. order) : 0.2802299E-05 (-0.4583409E-04) - number of electron 63.9999983 magnetization - augmentation part 5.8023223 magnetization - - Broyden mixing: - rms(total) = 0.31578E-02 rms(broyden)= 0.31576E-02 - rms(prec ) = 0.56690E-02 - weight for this iteration 100.00 - - eigenvalues of (default mixing * dielectric matrix) - average eigenvalue GAMMA= 1.4794 - 2.7290 2.4731 1.5485 1.0466 1.0466 1.0328 1.0328 0.9263 - - Free energy of the ion-electron system (eV) - --------------------------------------------------- - alpha Z PSCENC = 250.74326039 - Ewald energy TEWEN = -3127.45179835 - -Hartree energ DENC = -1097.70232127 - -exchange EXHF = 0.00000000 - -V(xc)+E(xc) XCENC = 99.41800246 - PAW double counting = 7368.79030748 -7396.09251223 - entropy T*S EENTRO = -0.00000000 - eigenvalues EBANDS = -207.97008870 - atomic energy EATOM = 3762.45289366 - Solvation Ediel_sol = 0.00000000 - --------------------------------------------------- - free energy TOTEN = -347.81225655 eV - - energy without entropy = -347.81225655 energy(sigma->0) = -347.81225655 - - --------------------------------------------------------------------------------------------------------- - - - - ---------------------------------------- Iteration 1( 14) --------------------------------------- - - - POTLOK: cpu time 0.0445: real time 0.0448 - SETDIJ: cpu time 0.0192: real time 0.0193 - EDDAV: cpu time 0.2893: real time 0.2902 - DOS: cpu time 0.0002: real time 0.0002 - CHARGE: cpu time 0.1158: real time 0.1161 - MIXING: cpu time 0.0016: real time 0.0016 - -------------------------------------------- - LOOP: cpu time 0.4706: real time 0.4723 - - eigenvalue-minimisations : 960 - total energy-change (2. order) : 0.3494931E-04 (-0.1372913E-04) - number of electron 63.9999983 magnetization - augmentation part 5.8033358 magnetization - - Broyden mixing: - rms(total) = 0.83177E-03 rms(broyden)= 0.83028E-03 - rms(prec ) = 0.11179E-02 - weight for this iteration 100.00 - - eigenvalues of (default mixing * dielectric matrix) - average eigenvalue GAMMA= 1.5309 - 2.9476 2.4558 2.4558 1.0208 1.0208 0.9951 0.9951 0.9435 0.9435 - - Free energy of the ion-electron system (eV) - --------------------------------------------------- - alpha Z PSCENC = 250.74326039 - Ewald energy TEWEN = -3127.45179835 - -Hartree energ DENC = -1097.51764766 - -exchange EXHF = 0.00000000 - -V(xc)+E(xc) XCENC = 99.39614718 - PAW double counting = 7367.47960630 -7394.77815801 - entropy T*S EENTRO = -0.00000000 - eigenvalues EBANDS = -208.13652512 - atomic energy EATOM = 3762.45289366 - Solvation Ediel_sol = 0.00000000 - --------------------------------------------------- - free energy TOTEN = -347.81222161 eV - - energy without entropy = -347.81222161 energy(sigma->0) = -347.81222161 - - --------------------------------------------------------------------------------------------------------- - - - - ---------------------------------------- Iteration 1( 15) --------------------------------------- - - - POTLOK: cpu time 0.0445: real time 0.0448 - SETDIJ: cpu time 0.0192: real time 0.0193 - EDDAV: cpu time 0.2597: real time 0.2603 - DOS: cpu time 0.0002: real time 0.0002 - 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eigenvalues EBANDS = -208.14072033 - atomic energy EATOM = 3762.45289366 - Solvation Ediel_sol = 0.00000000 - --------------------------------------------------- - free energy TOTEN = -347.81222022 eV - - energy without entropy = -347.81222022 energy(sigma->0) = -347.81222022 - - --------------------------------------------------------------------------------------------------------- - - - - ---------------------------------------- Iteration 1( 16) --------------------------------------- - - - POTLOK: cpu time 0.0439: real time 0.0443 - SETDIJ: cpu time 0.0200: real time 0.0200 - EDDAV: cpu time 0.2614: real time 0.2622 - DOS: cpu time 0.0002: real time 0.0002 - -------------------------------------------- - LOOP: cpu time 0.3255: real time 0.3267 - - eigenvalue-minimisations : 808 - total energy-change (2. order) : 0.8786701E-06 (-0.2995542E-06) - number of electron 63.9999983 magnetization - augmentation part 5.8032875 magnetization - - Free energy of the ion-electron system (eV) - --------------------------------------------------- - alpha Z PSCENC = 250.74326039 - Ewald energy TEWEN = -3127.45179835 - -Hartree energ DENC = -1097.51913479 - -exchange EXHF = 0.00000000 - -V(xc)+E(xc) XCENC = 99.40248865 - PAW double counting = 7368.30676106 -7395.60449860 - entropy T*S EENTRO = -0.00000000 - eigenvalues EBANDS = -208.14219137 - atomic energy EATOM = 3762.45289366 - Solvation Ediel_sol = 0.00000000 - --------------------------------------------------- - free energy TOTEN = -347.81221934 eV - - energy without entropy = -347.81221934 energy(sigma->0) = -347.81221934 - - --------------------------------------------------------------------------------------------------------- - - - - - average (electrostatic) potential at core - the test charge radii are 1.2481 0.7215 - (the norm of the test charge is 1.0000) - 1 -39.6915 2 -39.6915 3 -39.6915 4 -39.6915 5 -74.0334 - 6 -74.0334 7 -73.7402 8 -73.7402 9 -73.7402 10 -73.7402 - 11 -74.0334 12 -74.0334 - - - - E-fermi : 3.4457 XC(G=0): -12.1606 alpha+bet :-12.8992 - - - k-point 1 : 0.0000 0.0000 0.0000 - 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-.101E+02 0.117E+02 -.232E+02 0.105E+02 -.129E+02 0.266E+02 -.407E+00 0.113E+01 -.334E+01 -.261E-04 0.914E-04 -.324E-03 - 0.958E+01 -.269E+02 0.452E+01 -.938E+01 0.322E+02 -.327E+01 -.190E+00 -.523E+01 -.121E+01 0.228E-04 -.408E-03 -.761E-04 - 0.958E+01 0.269E+02 -.452E+01 -.938E+01 -.322E+02 0.327E+01 -.190E+00 0.523E+01 0.121E+01 0.228E-04 0.408E-03 0.761E-04 - ----------------------------------------------------------------------------------------------- - 0.168E-09 -.542E-09 -.330E-09 0.160E-13 -.711E-14 0.124E-13 0.833E-16 0.888E-15 -.222E-15 -.508E-13 -.332E-13 0.217E-13 - - - POSITION TOTAL-FORCE (eV/Angst) - ----------------------------------------------------------------------------------- - 2.76422 4.14748 1.50037 -0.059786 0.151222 -0.085196 - 0.21835 1.30499 1.07094 -0.059786 -0.151222 0.085196 - 4.87338 4.57603 4.07176 0.059786 0.151222 -0.085196 - 2.32752 1.73353 3.64233 0.059786 -0.151222 0.085196 - 3.85655 0.67027 2.45893 -0.008711 0.112966 0.037362 - 1.31069 4.78220 0.11238 -0.008711 -0.112966 -0.037362 - 4.23542 2.98966 0.79342 -0.000366 -0.030820 0.075334 - 1.68956 2.46281 1.77789 -0.000366 0.030820 -0.075334 - 0.85631 2.89135 4.34928 0.000366 0.030820 -0.075334 - 3.40218 3.41821 3.36480 0.000366 -0.030820 0.075334 - 3.78104 1.09881 5.03032 0.008711 0.112966 0.037362 - 1.23518 5.21075 2.68377 0.008711 -0.112966 -0.037362 - ----------------------------------------------------------------------------------- - total drift: 0.000000 -0.000000 -0.000000 - - --------------------------------------------------------------------------------------------------------- - - - - FREE ENERGIE OF THE ION-ELECTRON SYSTEM (eV) - --------------------------------------------------- - free energy TOTEN = -347.81221934 eV - - energy without entropy= -347.81221934 energy(sigma->0) = -347.81221934 - - - --------------------------------------------------------------------------------------------------------- - - - POTLOK: cpu time 0.0643: real time 0.0645 - - --------------------------------------------------------------------------------------------------------- - - - LOOP+: cpu time 7.7989: real time 8.2230 - 4ORBIT: cpu time 0.0000: real time 0.0000 - - total amount of memory used by VASP MPI-rank0 36758. kBytes -======================================================================= - - base : 30000. kBytes - nonl-proj : 1290. kBytes - fftplans : 1345. kBytes - grid : 2665. kBytes - one-center: 31. kBytes - wavefun : 1427. kBytes - - - - General timing and accounting informations for this job: - ======================================================== - - Total CPU time used (sec): 8.418 - User time (sec): 8.380 - System time (sec): 0.038 - Elapsed time (sec): 9.289 - - Maximum memory used (kb): 53124. - Average memory used (kb): 0. - - Minor page faults: 13771 - Major page faults: 0 - Voluntary context switches: 274 diff --git a/mace-bench/3rdparty/SevenNet/example_inputs/md_parallel_example/deployed_parallel/deployed_parallel_0.pt b/mace-bench/3rdparty/SevenNet/example_inputs/md_parallel_example/deployed_parallel/deployed_parallel_0.pt deleted file mode 100644 index 2e53f4ed924a6b5b905ad0fd40aae0847f82a80c..0000000000000000000000000000000000000000 Binary files a/mace-bench/3rdparty/SevenNet/example_inputs/md_parallel_example/deployed_parallel/deployed_parallel_0.pt and /dev/null differ diff --git a/mace-bench/3rdparty/SevenNet/example_inputs/md_parallel_example/deployed_parallel/deployed_parallel_1.pt b/mace-bench/3rdparty/SevenNet/example_inputs/md_parallel_example/deployed_parallel/deployed_parallel_1.pt deleted file mode 100644 index d2c562f10acf1009f9bf776dacd77a248ffbb481..0000000000000000000000000000000000000000 Binary files a/mace-bench/3rdparty/SevenNet/example_inputs/md_parallel_example/deployed_parallel/deployed_parallel_1.pt and /dev/null differ diff --git a/mace-bench/3rdparty/SevenNet/example_inputs/md_parallel_example/deployed_parallel/deployed_parallel_2.pt b/mace-bench/3rdparty/SevenNet/example_inputs/md_parallel_example/deployed_parallel/deployed_parallel_2.pt deleted file mode 100644 index 00dfb9949d4ce5e0ee99d68cc4172698bde66b95..0000000000000000000000000000000000000000 Binary files a/mace-bench/3rdparty/SevenNet/example_inputs/md_parallel_example/deployed_parallel/deployed_parallel_2.pt and /dev/null differ diff --git a/mace-bench/3rdparty/SevenNet/example_inputs/md_parallel_example/deployed_parallel/deployed_parallel_3.pt b/mace-bench/3rdparty/SevenNet/example_inputs/md_parallel_example/deployed_parallel/deployed_parallel_3.pt deleted file mode 100644 index f0056b9b001acc4d0c48668a86485d914e8bc20e..0000000000000000000000000000000000000000 Binary files a/mace-bench/3rdparty/SevenNet/example_inputs/md_parallel_example/deployed_parallel/deployed_parallel_3.pt and /dev/null differ diff --git a/mace-bench/3rdparty/SevenNet/example_inputs/md_parallel_example/in.lmp b/mace-bench/3rdparty/SevenNet/example_inputs/md_parallel_example/in.lmp deleted file mode 100644 index 1de11bccea88fdd5933af99bb10eec333290b0bc..0000000000000000000000000000000000000000 --- a/mace-bench/3rdparty/SevenNet/example_inputs/md_parallel_example/in.lmp +++ /dev/null @@ -1,44 +0,0 @@ -#--------------------------- Simulation variables -----------------------------# - - # Simulation control parameters. - variable T equal 500 - - # Simulation steps (t_eq) - variable t_eq equal 100 - variable output equal 1 #freq to print output - variable dumpstep equal 1 - -#------------------------------------------------------------------------------# - - -#---------------------------- Atomic setup ------------------------------------# - units metal - boundary p p p - # Create atoms. - box tilt large - read_data ./res.dat - replicate 2 2 2 - - # Define interatomic potential. - pair_style e3gnn/parallel - # The order of element should be the same as the order of elements in the data file (type) - # * * {number of deployed parallel models} {path to deployed parallel models} {elements} - pair_coeff * * 4 ./deployed_parallel Hf O - - timestep 0.002 - -#----------------------------- Run simulation ---------------------------------# - - # Setup output - thermo ${output} - thermo_style custom step tpcpu pe ke vol press temp - dump mydump all custom 1 dump.traj id type x y z fx fy fz - dump_modify mydump sort id - - fix f1 all nve - fix comfix all momentum 1 linear 1 1 1 - velocity all create ${T} 1 dist gaussian mom yes - - run 5 - -#------------------------------------------------------------------------------# diff --git a/mace-bench/3rdparty/SevenNet/example_inputs/md_parallel_example/res.dat b/mace-bench/3rdparty/SevenNet/example_inputs/md_parallel_example/res.dat deleted file mode 100644 index 5848bcb2e8a38d8167ee53c595c2072efd83bd93..0000000000000000000000000000000000000000 --- a/mace-bench/3rdparty/SevenNet/example_inputs/md_parallel_example/res.dat +++ /dev/null @@ -1,114 +0,0 @@ -# generated from poscar module (Converted from VASP) - -96 atoms -2 atom types - -0.00000000 10.12978631 xlo xhi -0.00000000 10.37111894 ylo yhi -0.00000000 10.26314330 zlo zhi - - 1.73035484 0.00000000 0.00000000 xy xz yz - -Masses - -1 178.490000 -2 16.000000 - -Atoms - - 1 1 10.07858846 8.73752520 7.46334159 - 2 1 9.43739481 3.62108575 2.41757962 - 3 1 8.95522965 1.01658239 0.30135971 - 4 1 10.05681289 8.87631272 2.35008881 - 5 1 9.75638582 6.30304558 0.18303097 - 6 1 8.91443797 1.06674577 5.54199800 - 7 1 9.79081409 6.26490552 5.22104118 - 8 1 4.41792703 3.81788503 2.39528244 - 9 1 2.17257241 4.11562894 4.98715163 - 10 1 1.66417958 1.51957159 2.91326352 - 11 1 5.17465464 8.94063393 2.34565890 - 12 1 2.85135280 9.31925586 4.96912733 - 13 1 5.06412333 8.89798173 7.34081071 - 14 1 2.43171878 6.73610078 7.90086842 - 15 1 4.79358115 6.33415175 5.30470215 - 16 1 4.38083973 3.71776573 7.50514775 - 17 1 2.16740031 4.19218670 10.14985882 - 18 1 1.72740111 1.53804994 8.11741499 - 19 1 3.81409500 1.12760478 5.36341140 - 20 1 2.91124600 9.28502610 10.05473353 - 21 1 2.43508812 6.79222574 2.84272933 - 22 1 4.63828767 6.35818290 0.06495312 - 23 1 3.96862029 1.21993115 0.31149240 - 24 1 7.95945527 9.30919854 9.99874912 - 25 1 7.20953615 4.10124686 10.06760490 - 26 1 7.97413259 9.31020496 4.88564505 - 27 1 7.48292324 6.67094881 2.71417363 - 28 1 7.22354435 4.09214379 4.91151391 - 29 1 6.77110223 1.50790865 2.82107672 - 30 1 7.60040235 6.67278986 7.89547614 - 31 1 9.41001699 3.69515647 7.55969566 - 32 1 6.77374601 1.50559611 7.98091486 - 33 2 10.09033948 1.85325366 6.96757279 - 34 2 10.99511263 7.08138493 6.69600728 - 35 2 11.28967512 9.60939027 6.04904275 - 36 2 10.78802723 6.95960696 1.75182521 - 37 2 8.32036165 2.47159112 3.91830180 - 38 2 10.07211065 1.65854646 1.87162718 - 39 2 10.48460341 4.35174196 0.83957607 - 40 2 9.58543540 10.25525675 3.81736961 - 41 2 9.15581971 7.61785575 3.82383341 - 42 2 11.28280065 9.42551408 0.89622391 - 43 2 10.61871694 4.46990764 6.09305074 - 44 2 3.63623823 5.03045204 3.82116882 - 45 2 3.22065417 2.54566037 3.96054713 - 46 2 5.13228413 1.96508633 1.75400085 - 47 2 0.49972311 0.85950986 4.41955106 - 48 2 4.49795126 10.25514684 3.94724065 - 49 2 4.08831630 7.74684459 3.86494489 - 50 2 5.90127151 7.07173966 1.66530214 - 51 2 6.32939463 9.71904813 0.93714394 - 52 2 5.44334962 4.45855194 0.80863483 - 53 2 3.54898001 7.91810753 6.27738026 - 54 2 3.21454568 5.33370189 6.39780696 - 55 2 4.08744202 7.79255573 8.94430580 - 56 2 5.89610679 7.08975961 6.71713664 - 57 2 1.22356400 5.98776133 9.31853387 - 58 2 6.36149555 9.67586631 6.06078686 - 59 2 3.62496983 5.17884441 8.87967862 - 60 2 2.79091790 2.70312051 6.50630496 - 61 2 2.20642369 0.12199325 6.50943225 - 62 2 3.36642075 2.52335751 9.09596150 - 63 2 5.04873139 1.85222299 6.87617402 - 64 2 0.50463414 0.78101050 9.52304998 - 65 2 0.95275450 3.34556660 8.69553848 - 66 2 5.46251140 4.47527874 6.00302102 - 67 2 4.49817894 10.30428629 8.95760259 - 68 2 1.73952474 8.56368775 8.58555417 - 69 2 3.62337333 7.98128068 1.17332847 - 70 2 3.16118634 5.40721734 1.22906859 - 71 2 1.31418904 5.97276567 4.19215008 - 72 2 2.79848347 2.74889192 1.27175505 - 73 2 2.29397766 0.16984188 1.46074130 - 74 2 0.96707618 3.44188647 3.47135866 - 75 2 1.75476287 8.54415321 3.43405286 - 76 2 9.58968370 10.11019896 9.02264863 - 77 2 9.12010305 7.60109276 8.90873480 - 78 2 8.21690550 5.34991345 1.37662298 - 79 2 6.43083748 5.94959474 4.24019201 - 80 2 8.69454708 4.99651781 3.88811596 - 81 2 7.96833563 2.69478887 1.20584684 - 82 2 7.33313963 0.16345962 1.36457040 - 83 2 5.57830829 0.81411424 4.28350294 - 84 2 6.12969978 3.45445964 3.35501959 - 85 2 8.55281287 7.89834015 1.15270373 - 86 2 6.84047748 8.56744003 3.45602018 - 87 2 7.33002089 0.08127731 6.53509276 - 88 2 5.55795729 0.84809385 9.39286244 - 89 2 8.58051171 7.87084401 6.29048766 - 90 2 8.28348300 5.22136388 6.47631887 - 91 2 6.42127905 6.05984919 9.37655897 - 92 2 6.82699499 8.52585391 8.47852948 - 93 2 8.68865624 5.09200133 8.99426977 - 94 2 7.84842127 2.70204335 6.42490863 - 95 2 8.25796997 2.46457586 9.01312304 - 96 2 6.08861225 3.44495302 8.57088233 diff --git a/mace-bench/3rdparty/SevenNet/example_inputs/md_serial_example/deployed_serial.pt b/mace-bench/3rdparty/SevenNet/example_inputs/md_serial_example/deployed_serial.pt deleted file mode 100644 index bbe998d0435752927010c9a7965b66f504e9cfd8..0000000000000000000000000000000000000000 Binary files a/mace-bench/3rdparty/SevenNet/example_inputs/md_serial_example/deployed_serial.pt and /dev/null differ diff --git a/mace-bench/3rdparty/SevenNet/example_inputs/md_serial_example/in.lmp b/mace-bench/3rdparty/SevenNet/example_inputs/md_serial_example/in.lmp deleted file mode 100644 index 93996e581076540c437e2db48f40d2ecbbee8c4c..0000000000000000000000000000000000000000 --- a/mace-bench/3rdparty/SevenNet/example_inputs/md_serial_example/in.lmp +++ /dev/null @@ -1,44 +0,0 @@ -#--------------------------- Simulation variables -----------------------------# - - # Simulation control parameters. - variable T equal 500 - - # Simulation steps (t_eq) - variable t_eq equal 100 - variable output equal 1 #freq to print output - variable dumpstep equal 1 - -#------------------------------------------------------------------------------# - - -#---------------------------- Atomic setup ------------------------------------# - units metal - boundary p p p - # Create atoms. - box tilt large - read_data ./res.dat - replicate 2 2 2 - - # Define interatomic potential. - pair_style e3gnn - # The order of element should be the same as the order of elements in the data file (type) - # * * {path to deployed serial model} {elements} - pair_coeff * * ./deployed_serial.pt Hf O - - timestep 0.002 - -#----------------------------- Run simulation ---------------------------------# - - # Setup output - thermo ${output} #because it is realaxation - thermo_style custom step tpcpu pe ke vol press temp #record these value (custom setting) - dump mydump all custom 1 dump.traj id type x y z fx fy fz - dump_modify mydump sort id - - fix f1 all nve - fix comfix all momentum 1 linear 1 1 1 - velocity all create ${T} 1 dist gaussian mom yes - - run 5 - -#------------------------------------------------------------------------------# diff --git a/mace-bench/3rdparty/SevenNet/example_inputs/md_serial_example/res.dat b/mace-bench/3rdparty/SevenNet/example_inputs/md_serial_example/res.dat deleted file mode 100644 index 5848bcb2e8a38d8167ee53c595c2072efd83bd93..0000000000000000000000000000000000000000 --- a/mace-bench/3rdparty/SevenNet/example_inputs/md_serial_example/res.dat +++ /dev/null @@ -1,114 +0,0 @@ -# generated from poscar module (Converted from VASP) - -96 atoms -2 atom types - -0.00000000 10.12978631 xlo xhi -0.00000000 10.37111894 ylo yhi -0.00000000 10.26314330 zlo zhi - - 1.73035484 0.00000000 0.00000000 xy xz yz - -Masses - -1 178.490000 -2 16.000000 - -Atoms - - 1 1 10.07858846 8.73752520 7.46334159 - 2 1 9.43739481 3.62108575 2.41757962 - 3 1 8.95522965 1.01658239 0.30135971 - 4 1 10.05681289 8.87631272 2.35008881 - 5 1 9.75638582 6.30304558 0.18303097 - 6 1 8.91443797 1.06674577 5.54199800 - 7 1 9.79081409 6.26490552 5.22104118 - 8 1 4.41792703 3.81788503 2.39528244 - 9 1 2.17257241 4.11562894 4.98715163 - 10 1 1.66417958 1.51957159 2.91326352 - 11 1 5.17465464 8.94063393 2.34565890 - 12 1 2.85135280 9.31925586 4.96912733 - 13 1 5.06412333 8.89798173 7.34081071 - 14 1 2.43171878 6.73610078 7.90086842 - 15 1 4.79358115 6.33415175 5.30470215 - 16 1 4.38083973 3.71776573 7.50514775 - 17 1 2.16740031 4.19218670 10.14985882 - 18 1 1.72740111 1.53804994 8.11741499 - 19 1 3.81409500 1.12760478 5.36341140 - 20 1 2.91124600 9.28502610 10.05473353 - 21 1 2.43508812 6.79222574 2.84272933 - 22 1 4.63828767 6.35818290 0.06495312 - 23 1 3.96862029 1.21993115 0.31149240 - 24 1 7.95945527 9.30919854 9.99874912 - 25 1 7.20953615 4.10124686 10.06760490 - 26 1 7.97413259 9.31020496 4.88564505 - 27 1 7.48292324 6.67094881 2.71417363 - 28 1 7.22354435 4.09214379 4.91151391 - 29 1 6.77110223 1.50790865 2.82107672 - 30 1 7.60040235 6.67278986 7.89547614 - 31 1 9.41001699 3.69515647 7.55969566 - 32 1 6.77374601 1.50559611 7.98091486 - 33 2 10.09033948 1.85325366 6.96757279 - 34 2 10.99511263 7.08138493 6.69600728 - 35 2 11.28967512 9.60939027 6.04904275 - 36 2 10.78802723 6.95960696 1.75182521 - 37 2 8.32036165 2.47159112 3.91830180 - 38 2 10.07211065 1.65854646 1.87162718 - 39 2 10.48460341 4.35174196 0.83957607 - 40 2 9.58543540 10.25525675 3.81736961 - 41 2 9.15581971 7.61785575 3.82383341 - 42 2 11.28280065 9.42551408 0.89622391 - 43 2 10.61871694 4.46990764 6.09305074 - 44 2 3.63623823 5.03045204 3.82116882 - 45 2 3.22065417 2.54566037 3.96054713 - 46 2 5.13228413 1.96508633 1.75400085 - 47 2 0.49972311 0.85950986 4.41955106 - 48 2 4.49795126 10.25514684 3.94724065 - 49 2 4.08831630 7.74684459 3.86494489 - 50 2 5.90127151 7.07173966 1.66530214 - 51 2 6.32939463 9.71904813 0.93714394 - 52 2 5.44334962 4.45855194 0.80863483 - 53 2 3.54898001 7.91810753 6.27738026 - 54 2 3.21454568 5.33370189 6.39780696 - 55 2 4.08744202 7.79255573 8.94430580 - 56 2 5.89610679 7.08975961 6.71713664 - 57 2 1.22356400 5.98776133 9.31853387 - 58 2 6.36149555 9.67586631 6.06078686 - 59 2 3.62496983 5.17884441 8.87967862 - 60 2 2.79091790 2.70312051 6.50630496 - 61 2 2.20642369 0.12199325 6.50943225 - 62 2 3.36642075 2.52335751 9.09596150 - 63 2 5.04873139 1.85222299 6.87617402 - 64 2 0.50463414 0.78101050 9.52304998 - 65 2 0.95275450 3.34556660 8.69553848 - 66 2 5.46251140 4.47527874 6.00302102 - 67 2 4.49817894 10.30428629 8.95760259 - 68 2 1.73952474 8.56368775 8.58555417 - 69 2 3.62337333 7.98128068 1.17332847 - 70 2 3.16118634 5.40721734 1.22906859 - 71 2 1.31418904 5.97276567 4.19215008 - 72 2 2.79848347 2.74889192 1.27175505 - 73 2 2.29397766 0.16984188 1.46074130 - 74 2 0.96707618 3.44188647 3.47135866 - 75 2 1.75476287 8.54415321 3.43405286 - 76 2 9.58968370 10.11019896 9.02264863 - 77 2 9.12010305 7.60109276 8.90873480 - 78 2 8.21690550 5.34991345 1.37662298 - 79 2 6.43083748 5.94959474 4.24019201 - 80 2 8.69454708 4.99651781 3.88811596 - 81 2 7.96833563 2.69478887 1.20584684 - 82 2 7.33313963 0.16345962 1.36457040 - 83 2 5.57830829 0.81411424 4.28350294 - 84 2 6.12969978 3.45445964 3.35501959 - 85 2 8.55281287 7.89834015 1.15270373 - 86 2 6.84047748 8.56744003 3.45602018 - 87 2 7.33002089 0.08127731 6.53509276 - 88 2 5.55795729 0.84809385 9.39286244 - 89 2 8.58051171 7.87084401 6.29048766 - 90 2 8.28348300 5.22136388 6.47631887 - 91 2 6.42127905 6.05984919 9.37655897 - 92 2 6.82699499 8.52585391 8.47852948 - 93 2 8.68865624 5.09200133 8.99426977 - 94 2 7.84842127 2.70204335 6.42490863 - 95 2 8.25796997 2.46457586 9.01312304 - 96 2 6.08861225 3.44495302 8.57088233 diff --git a/mace-bench/3rdparty/SevenNet/example_inputs/training/input_full.yaml b/mace-bench/3rdparty/SevenNet/example_inputs/training/input_full.yaml deleted file mode 100644 index 9528d7b66ef226e14ca79b11706e37814476cf92..0000000000000000000000000000000000000000 --- a/mace-bench/3rdparty/SevenNet/example_inputs/training/input_full.yaml +++ /dev/null @@ -1,93 +0,0 @@ -# Example input.yaml for training SevenNet. -# '*' signifies default. You can check log.sevenn for defaults. - -model: - chemical_species: 'Auto' # Elements model should know. [ 'Univ' | 'Auto' | manual_user_input ] - cutoff: 5.0 # Cutoff radius in Angstroms. If two atoms are within the cutoff, they are connected. - channel: 32 # The multiplicity(channel) of node features. - lmax: 2 # Maximum order of irreducible representations (rotation order). - num_convolution_layer: 3 # The number of message passing layers. - - #irreps_manual: # Manually set irreps of the model in each layer - #- "128x0e" - #- "128x0e+64x1e+32x2e" - #- "128x0e+64x1e+32x2e" - #- "128x0e+64x1e+32x2e" - #- "128x0e+64x1e+32x2e" - #- "128x0e" - - weight_nn_hidden_neurons: [64, 64] # Hidden neurons in convolution weight neural network - radial_basis: # Function and its parameters to encode radial distance - radial_basis_name: 'bessel' # Only 'bessel' is currently supported - bessel_basis_num: 8 - - cutoff_function: # Envelop function, multiplied to radial_basis functions to init edge features - cutoff_function_name: 'poly_cut' # {'poly_cut' and 'poly_cut_p_value'} or {'XPLOR' and 'cutoff_on'} - poly_cut_p_value: 6 - - act_gate: {'e': 'silu', 'o': 'tanh'} # Equivalent to 'nonlinearity_gates' in nequip - act_scalar: {'e': 'silu', 'o': 'tanh'} # Equivalent to 'nonlinearity_scalars' in nequip - - is_parity: False # Pairy True (E(3) group) or False (to SE(3) group) - - self_connection_type: 'nequip' # Default is 'nequip'. 'linear' is used for SevenNet-0. I recommend 'linear' for 'Univ' chemical_species - - conv_denominator: "avg_num_neigh" # Valid options are "avg_num_neigh*", "sqrt_avg_num_neigh", or float - train_denominator: False # Enable training for denominator in convolution layer - train_shift_scale: False # Enable training for shift & scale in output layer - -train: - random_seed: 1 - is_train_stress: True # Includes stress in the loss function - epoch: 200 # Ends training after this number of epochs - - #loss: 'Huber' # Default is 'mse' (mean squared error) - #loss_param: - #delta: 0.01 - - # Each optimizer and scheduler have different available parameters. - # You can refer to sevenn/train/optim.py for supporting optimizer & schedulers - optimizer: 'adam' # Options available are 'sgd', 'adagrad', 'adam', 'adamw', 'radam' - optim_param: - lr: 0.005 - scheduler: 'exponentiallr' # 'steplr', 'multisteplr', 'exponentiallr', 'cosineannealinglr', 'reducelronplateau', 'linearlr' - scheduler_param: - gamma: 0.99 - - force_loss_weight: 0.1 # Coefficient for force loss - stress_loss_weight: 1e-06 # Coefficient for stress loss (to kbar unit) - - per_epoch: 10 # Generate checkpoints every this epoch - - # ['target y', 'metric'] - # Target y: TotalEnergy, Energy, Force, Stress, Stress_GPa, TotalLoss - # Metric : RMSE, MAE, or Loss - error_record: - - ['Energy', 'RMSE'] - - ['Force', 'RMSE'] - - ['Stress', 'RMSE'] - - ['TotalLoss', 'None'] - - # Continue training model from given checkpoint, or pre-trained model checkpoint for fine-tuning - #continue: - #checkpoint: 'checkpoint_best.pth' # Checkpoint of pre-trained model or a model want to continue training. - #reset_optimizer: False # Set True for fine-tuning - #reset_scheduler: False # Set True for fine-tuning - -data: - batch_size: 4 # Per GPU batch size. - data_divide_ratio: 0.1 # Split dataset into training and validation sets by this ratio - - shift: 'per_atom_energy_mean' # One of 'per_atom_energy_mean*', 'elemwise_reference_energies', float - scale: 'force_rms' # One of 'force_rms*', 'per_atom_energy_std', float - - # SevenNet automatically matches data format from its filename. - # For those not `structure_list` or `.pt` files, assumes it is ASE readable - # In this case, below arguments are directly passed to `ase.io.read` - data_format_args: - index: ':' # see `https://wiki.fysik.dtu.dk/ase/ase/io/io.html` for more valid arguments - - # validset is needed if you want '_best.pth' during training. If not, both validset and testset is optional. - load_trainset_path: ['./structure_list'] # Example of using ase as data_format, support multiple files and expansion(*) - #load_validset_path: ['./valid.extxyz'] - #load_testset_path: ['./sevenn_data/mydata.pt'] # Graph can be preprocessed using `sevenn_graph_build` and accessible like this diff --git a/mace-bench/3rdparty/SevenNet/example_inputs/training/structure_list b/mace-bench/3rdparty/SevenNet/example_inputs/training/structure_list deleted file mode 100644 index da4ff887cc6f50dce75c2d268c09e20764427689..0000000000000000000000000000000000000000 --- a/mace-bench/3rdparty/SevenNet/example_inputs/training/structure_list +++ /dev/null @@ -1,6 +0,0 @@ -[label_1] -../data/label_1/OUTCAR_{1..5} : -../data/label_1/OUTCAR_{1..5} : -[label_2] -../data/label_2/OUTCAR_{6..10} : -../data/label_2/OUTCAR_{6..10} : diff --git a/mace-bench/3rdparty/SevenNet/pyproject.toml b/mace-bench/3rdparty/SevenNet/pyproject.toml deleted file mode 100644 index 339146cf7a7cb01f537f101d8a78ea2713f3e231..0000000000000000000000000000000000000000 --- a/mace-bench/3rdparty/SevenNet/pyproject.toml +++ /dev/null @@ -1,89 +0,0 @@ -[project] -name = "sevenn" -version = "0.11.1.dev3" -authors = [ - { name = "Yutack Park", email = "parkyutack@snu.ac.kr" }, - { name = "Haekwan Jeon", email = "haekwan98@snu.ac.kr" }, - { name = "Jaesun Kim" }, - { name = "Gijin Kim" }, - { name = "Hyungmin An" }, -] -description = "Scalable EquiVariance Enabled Neural Network" -readme = "README.md" -license = { file = "LICENSE" } -requires-python = ">=3.8" -classifiers = [ - "Programming Language :: Python :: 3", - "License :: OSI Approved :: GNU General Public License v3 (GPLv3)", - "Operating System :: POSIX :: Linux", -] -dependencies = [ - "ase", - "braceexpand", - "pyyaml", - "e3nn>=0.5.0", - "tqdm", - "scikit-learn", - "torch_geometric>=2.5.0", - "numpy", - "matscipy", - "pandas", - "requests", - "setuptools>=61.0" -] -[project.optional-dependencies] -test = ["pytest", "pytest-cov>=5"] -cueq12 = ["cuequivariance>=0.4.0; python_version >= '3.10'", "cuequivariance-torch>=0.4.0; python_version >= '3.10'", "cuequivariance-ops-torch-cu12; python_version >= '3.10'"] -cueq11 = ["cuequivariance>=0.4.0; python_version >= '3.10'", "cuequivariance-torch>=0.4.0; python_version >= '3.10'", "cuequivariance-ops-torch-cu11; python_version >= '3.10'"] - -[project.scripts] -sevenn = "sevenn.main.sevenn:main" -sevenn_get_model = "sevenn.main.sevenn_get_model:main" -sevenn_graph_build = "sevenn.main.sevenn_graph_build:main" -sevenn_inference = "sevenn.main.sevenn_inference:main" -sevenn_patch_lammps = "sevenn.main.sevenn_patch_lammps:main" -sevenn_preset = "sevenn.main.sevenn_preset:main" -sevenn_cp = "sevenn.main.sevenn_cp:main" - -[project.urls] -Homepage = "https://github.com/MDIL-SNU/SevenNet" -Issues = "https://github.com/MDIL-SNU/SevenNet/issues" - -[build-system] -build-backend = "setuptools.build_meta" -requires = ["setuptools>=61.0"] - -[tool.setuptools.package-data] -sevenn = [ - "logo_ascii", - "*.so", - "pair_e3gnn/*.cpp", - "pair_e3gnn/*.h", - "pair_e3gnn/*.cu", - "pair_e3gnn/patch_lammps.sh", - "presets/*.yaml", - "pretrained_potentials/SevenNet_0__11Jul2024/checkpoint_sevennet_0.pth", - "pretrained_potentials/SevenNet_0__22May2024/checkpoint_sevennet_0.pth", - "pretrained_potentials/SevenNet_l3i5/checkpoint_l3i5.pth", - "pretrained_potentials/SevenNet_MF_0/checkpoint_sevennet_mf_0.pth", - "py.typed", -] - -[tool.setuptools.packages.find] -include = ["sevenn*"] -exclude = ["tests*", "example_inputs*", ] - -[tool.pytest.ini_options] -log_cli = true -log_cli_format = "%(asctime)s [%(levelname)8s] %(message)s (%(filename)s:%(lineno)s)" -log_cli_date_format = "%Y-%m-%d %H:%M:%S" - -[tool.ruff] -line-length = 85 - -[tool.ruff.lint] -extend-select = ["E501"] - -[tool.ruff.format] -quote-style = "single" -docstring-code-format = true diff --git a/mace-bench/3rdparty/SevenNet/setup.cfg b/mace-bench/3rdparty/SevenNet/setup.cfg deleted file mode 100644 index 83ac02721e5728b1e2fcb3b41899fff34b0c37be..0000000000000000000000000000000000000000 --- a/mace-bench/3rdparty/SevenNet/setup.cfg +++ /dev/null @@ -1,14 +0,0 @@ -[flake8] -max-line-length = 85 -max-complexity = 12 -select = C,E,F,W,B,B950 -ignore = F401, W503, W605, E741, E203, C901, E722 - -[isort] -multi_line_output=3 -include_trailing_comma=True -force_grid_wrap=0 -use_parentheses=True -line_length=80 -known_third_party=ase,braceexpand,e3nn,numpy,packaging,pandas,pytest,requests,sklearn,torch,torch_geometric,tqdm,yaml -known_first_party= diff --git a/mace-bench/3rdparty/SevenNet/sevenn.egg-info/PKG-INFO b/mace-bench/3rdparty/SevenNet/sevenn.egg-info/PKG-INFO deleted file mode 100644 index 60e4f60e2314b71db75a807757a40b45d04daa95..0000000000000000000000000000000000000000 --- a/mace-bench/3rdparty/SevenNet/sevenn.egg-info/PKG-INFO +++ /dev/null @@ -1,1101 +0,0 @@ -Metadata-Version: 2.4 -Name: sevenn -Version: 0.11.1.dev3 -Summary: Scalable EquiVariance Enabled Neural Network -Author: Jaesun Kim, Gijin Kim, Hyungmin An -Author-email: Yutack Park , Haekwan Jeon -License: GNU GENERAL PUBLIC LICENSE - Version 3, 29 June 2007 - - Copyright (C) 2007 Free Software Foundation, Inc. - Everyone is permitted to copy and distribute verbatim copies - of this license document, but changing it is not allowed. - - Preamble - - The GNU General Public License is a free, copyleft license for - software and other kinds of works. - - The licenses for most software and other practical works are designed - to take away your freedom to share and change the works. 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But first, please read - . - -Project-URL: Homepage, https://github.com/MDIL-SNU/SevenNet -Project-URL: Issues, https://github.com/MDIL-SNU/SevenNet/issues -Classifier: Programming Language :: Python :: 3 -Classifier: License :: OSI Approved :: GNU General Public License v3 (GPLv3) -Classifier: Operating System :: POSIX :: Linux -Requires-Python: >=3.8 -Description-Content-Type: text/markdown -License-File: LICENSE -Requires-Dist: ase -Requires-Dist: braceexpand -Requires-Dist: pyyaml -Requires-Dist: e3nn>=0.5.0 -Requires-Dist: tqdm -Requires-Dist: scikit-learn -Requires-Dist: torch_geometric>=2.5.0 -Requires-Dist: numpy -Requires-Dist: matscipy -Requires-Dist: pandas -Requires-Dist: requests -Requires-Dist: setuptools>=61.0 -Provides-Extra: test -Requires-Dist: pytest; extra == "test" -Requires-Dist: pytest-cov>=5; extra == "test" -Provides-Extra: cueq12 -Requires-Dist: cuequivariance>=0.4.0; python_version >= "3.10" and extra == "cueq12" -Requires-Dist: cuequivariance-torch>=0.4.0; python_version >= "3.10" and extra == "cueq12" -Requires-Dist: cuequivariance-ops-torch-cu12; python_version >= "3.10" and extra == "cueq12" -Provides-Extra: cueq11 -Requires-Dist: cuequivariance>=0.4.0; python_version >= "3.10" and extra == "cueq11" -Requires-Dist: cuequivariance-torch>=0.4.0; python_version >= "3.10" and extra == "cueq11" -Requires-Dist: cuequivariance-ops-torch-cu11; python_version >= "3.10" and extra == "cueq11" -Dynamic: license-file - - -Alt text - -# SevenNet - -SevenNet (Scalable EquiVariance-Enabled Neural Network) is a graph neural network (GNN)-based interatomic potential package that supports parallel molecular dynamics simulations using [`LAMMPS`](https://lammps.org). Its core model is based on [`NequIP`](https://github.com/mir-group/nequip). - -> [!NOTE] -> We will soon release a CUDA-accelerated version of SevenNet, which will significantly increase the speed of our pretrained models on [Matbench Discovery](https://matbench-discovery.materialsproject.org/). - -## Features - - Pretrained GNN interatomic potential and fine-tuning interface - - Support for the Python [Atomic Simulation Environment (ASE)](https://wiki.fysik.dtu.dk/ase/) calculator - - GPU-parallelized molecular dynamics with LAMMPS - - CUDA-accelerated D3 (van der Waals) dispersion - - Multi-fidelity training for combining multiple databases with different calculation settings ([Usage](https://github.com/MDIL-SNU/SevenNet/blob/main/sevenn/pretrained_potentials/SevenNet_MF_0/README.md)) - -## Pretrained models -So far, we have released multiple pretrained SevenNet models. Each model has various hyperparameters and training sets, leading to different levels of accuracy and speed. Please read the descriptions below carefully and choose the model that best suits your purpose. -We provide the F1 score, and RMSD for the WBM dataset, along with $\kappa_{\mathrm{SRME}}$ from phononDB and CPS (Combined Performance Score). For details on these metrics and performance comparisons with other pretrained models, please visit [Matbench Discovery](https://matbench-discovery.materialsproject.org/). - -These models can be used as interatomic potentials in LAMMPS and loaded through the ASE calculator using each model’s keywords. Please refer to the [ASE calculator](#ase_calculator) section for instructions on loading a model via the ASE calculator. -Additionally, `keywords` can be used in other parts of SevenNet, such as `sevenn_inference`, `sevenn_get_model`, and the `checkpoint` section in `input.yaml` for fine-tuning. - -**Acknowledgments**: The models trained on [`MPtrj`](https://figshare.com/articles/dataset/Materials_Project_Trjectory_MPtrj_Dataset/23713842) were supported by the Neural Processing Research Center program at Samsung Advanced Institute of Technology, part of Samsung Electronics Co., Ltd. The computations for training models were carried out using the Samsung SSC-21 cluster. - ---- - -### **SevenNet-MF-ompa (17Mar2025)** -> Model keywords: `7net-mf-ompa` | `SevenNet-mf-ompa` - -**This is our recommended pretrained model** - -This model leverages [multi-fidelity learning](https://pubs.acs.org/doi/10.1021/jacs.4c14455) to train simultaneously on the [MPtrj](https://figshare.com/articles/dataset/Materials_Project_Trjectory_MPtrj_Dataset/23713842), [sAlex](https://huggingface.co/datasets/fairchem/OMAT24), and [OMat24](https://huggingface.co/datasets/fairchem/OMAT24) datasets. This model is the best among our pretrained models and achieves a high ranking on the [Matbench Discovery]((https://matbench-discovery.materialsproject.org/)) leaderboard. Our evaluations show that it outperforms other models on most tasks, except for the isolated molecule energy task, where it performs slightly worse than `SevenNet-l3i5`. - -```python -from sevenn.calculator import SevenNetCalculator -# "mpa" refers to the MPtrj + sAlex modal, used for evaluating Matbench Discovery. -calc = SevenNetCalculator('7net-mf-ompa', modal='mpa') # Use modal='omat24' for OMat24-trained modal weights. -``` -> [!NOTE] -> Each modal is expected to produce results that are more consistent with the DFT settings in the training datasets (e.g., `mpa`, trained on the combined [MPtrj](https://figshare.com/articles/dataset/Materials_Project_Trjectory_MPtrj_Dataset/23713842) and [sAlex](https://huggingface.co/datasets/fairchem/OMAT24) datasets; `omat24`, trained on the [OMat24](https://huggingface.co/datasets/fairchem/OMAT24) dataset). For detailed DFT settings, please refer to their papers. - -When using the command-line interface of SevenNet, include the `--modal mpa` or `--modal omat24` option to select the desired modality. - - -#### **Matbench Discovery** -| CPS | F1 | $\kappa_{\mathrm{SRME}}$ | RMSD | -|:---:|:---:|:---:|:---:| -|**0.883**|**0.901**|0.317| **0.0115** | - -[Detailed instructions for multi-fidelity learning](https://github.com/MDIL-SNU/SevenNet/blob/main/sevenn/pretrained_potentials/SevenNet_MF_0/README.md) - -[Download link for fully detailed checkpoint](https://figshare.com/articles/software/7net_MF_ompa/28590722?file=53029859) - ---- -### **SevenNet-omat (17Mar2025)** -> Model keywords: `7net-omat` | `SevenNet-omat` - - This model was trained exclusively on the [OMat24](https://huggingface.co/datasets/fairchem/OMAT24) dataset. It achieves high performance in $\kappa_{\mathrm{SRME}}$ on [Matbench Discovery](https://matbench-discovery.materialsproject.org/), but its F1 score is unavailable due to a difference in the POTCAR version. Like `SevenNet-MF-ompa`, this model outperforms `SevenNet-l3i5` on most tasks, except for the isolated molecule energy. - -[Download link for fully detailed checkpoint](https://figshare.com/articles/software/SevenNet_omat/28593938). - -#### **Matbench Discovery** -* $\kappa_{\mathrm{SRME}}$: **0.221** ---- -### **SevenNet-l3i5 (12Dec2024)** -> Model keywords: `7net-l3i5` | `SevenNet-l3i5` - -This model increases the maximum spherical harmonic degree ($l_{\mathrm{max}}$) to 3, compared to `SevenNet-0`, which has an $l_{\mathrm{max}}$ of 2. While **l3i5** offers improved accuracy for various systems, it is approximately four times slower than `SevenNet-0`. - -#### **Matbench Discovery** -| CPS | F1 | $\kappa_{\mathrm{SRME}}$ | RMSD | -|:---:|:---:|:---:|:---:| -|0.764 |0.76|0.55|0.0182| - ---- - -### **SevenNet-0 (11Jul2024)** -> Model keywords:: `7net-0` | `SevenNet-0` | `7net-0_11Jul2024` | `SevenNet-0_11Jul2024` - -This model is one of our earliest pretrained models. Although we recommend using newer and more accurate models, it can still be useful in certain cases due to its shortest inference time. The model was trained on the [MPtrj](https://figshare.com/articles/dataset/Materials_Project_Trjectory_MPtrj_Dataset/23713842) and is loaded as the default pretrained model in the ASE calculator. -For more information, click [here](sevenn/pretrained_potentials/SevenNet_0__11Jul2024). - -#### **Matbench Discovery** -| F1 | $\kappa_{\mathrm{SRME}}$ | -|:---:|:---:| -|0.67|0.767| - ---- - -You can find our legacy models in [pretrained_potentials](./sevenn/pretrained_potentials). - -## Contents -- [Installation](#installation) -- [Usage](#usage) - - [ASE calculator](#ase-calculator) - - [Training & inference](#training-and-inference) - - [Notebook tutorials](#notebook-tutorial) - - [MD simulation with LAMMPS](#md-simulation-with-lammps) - - [Installation](#installation) - - [Single-GPU MD](#single-gpu-md) - - [Multi-GPU MD](#multi-gpu-md) - - [Application of SevenNet-0](#application-of-sevennet-0) -- [Citation](#citation) - -## Installation -### Requirements -- Python >= 3.8 -- PyTorch >= 2.0.0, PyTorch =< 2.5.2 - -For CUDA version, refer to PyTorch's compatibility matrix: https://github.com/pytorch/pytorch/blob/main/RELEASE.md#release-compatibility-matrix - -> [!IMPORTANT] -> Please install PyTorch manually based on your hardware before installing SevenNet. - -Once PyTorch is successfully installed, please run the following command: -```bash -pip install sevenn -pip install git+https://github.com/MDIL-SNU/SevenNet.git # for the latest main branch -``` -We strongly recommend checking `CHANGELOG.md` for new features and changes, as SevenNet is under active development. - -## Usage -### ASE calculator - -SevenNet provides an ASE interface via the ASE calculator. Models can be loaded using the following Python code: -```python -from sevenn.calculator import SevenNetCalculator -# The 'modal' argument is required if the model is trained with multi-fidelity learning enabled. -calc_mf_ompa = SevenNetCalculator(model='7net-mf-ompa', modal='mpa') -``` -SevenNet also supports CUDA-accelerated D3 calculations. -```python -from sevenn.calculator import SevenNetD3Calculator -calc = SevenNetD3Calculator(model='7net-0', device='cuda') -``` -If you encounter the error `CUDA is not installed or nvcc is not available`, please ensure the `nvcc` compiler is available. Currently, CPU + D3 is not supported. - -Various pretrained SevenNet models can be accessed by setting the model variable to predefined keywords like `7net-mf-ompa`, `7net-omat`, `7net-l3i5`, and `7net-0`. - -Additionally, user-trained models can be applied with the ASE calculator. In this case, the `model` parameter should be set to the checkpoint path from training. - -> [!TIP] -> When 'auto' is passed to the `device` parameter (the default setting), SevenNet utilizes GPU acceleration if available. - -### Training and inference - -SevenNet provides five commands for preprocessing, training, and deployment: `sevenn_preset`, `sevenn_graph_build`, `sevenn`, `sevenn_inference`, and `sevenn_get_model`. - -#### 1. Input generation - -With the `sevenn_preset` command, the input file setting the training parameters is generated automatically. -```bash -sevenn_preset {preset keyword} > input.yaml -``` - -Available preset keywords are: `base`, `fine_tune`, `multi_modal`, `sevennet-0`, and `sevennet-l3i5`. -Check comments in the preset YAML files for explanations. For fine-tuning, be aware that most model hyperparameters cannot be modified unless explicitly indicated. -To reuse a preprocessed training set, you can specify `sevenn_data/${dataset_name}.pt` for the `load_trainset_path:` in the `input.yaml`. - -#### 2. Preprocess (optional) - -To obtain the preprocessed data, `sevenn_data/graph.pt`, `sevenn_graph_build` command can be used. -The output files can be used for training (`sevenn`) or inference (`sevenn_inference`) to skip the graph build stage. - -```bash -sevenn_graph_build {dataset path} {cutoff radius} -``` - -The output `sevenn_data/graph.yaml` contains statistics and meta information about the dataset. -These files must be located in the `sevenn_data` directory. If you move the dataset, move the entire `sevenn_data` directory without changing the contents. - -See `sevenn_graph_build --help` for more information. - -#### 3. Training - -Given that `input.yaml` and `sevenn_data/graph.pt` are prepared, SevenNet can be trained by the following command: - -```bash -sevenn input.yaml -s -``` - -We support multi-GPU training using PyTorch DDP (distributed data parallel) with a single process (or a CPU core) per GPU. - -```bash -torchrun --standalone --nnodes {number of nodes} --nproc_per_node {number of GPUs} --no_python sevenn input.yaml -d -``` - -Please note that `batch_size` in `input.yaml` refers to the per-GPU batch size. - -#### 4. Inference - -Using the checkpoint after training, the properties such as energy, force, and stress can be inferred directly. - -```bash -sevenn_inference checkpoint_best.pth path_to_my_structures/* -``` - -This will create the `sevenn_infer_result` directory, where CSV files contain predicted energy, force, stress, and their references (if available). -See `sevenn_inference --help` for more information. - -#### 5. Deployment - -The checkpoint can be deployed as LAMMPS potentials. The argument is either the path to the checkpoint or the name of a pretrained potential. - -```bash -sevenn_get_model 7net-0 -sevenn_get_model {checkpoint path} -``` - -This will create `deployed_serial.pt`, which can be used as a LAMMPS potential with the `e3gnn` pair_style in LAMMPS. - -The potential for parallel MD simulation can be obtained similarly. - -```bash -sevenn_get_model 7net-0 -p -sevenn_get_model {checkpoint path} -p -``` - -This will create a directory with several `deployed_parallel_*.pt` files. The directory path itself is an argument for the LAMMPS script. Please do not modify or remove files in the directory. -These models can be used as LAMMPS potentials to run parallel MD simulations with a GNN potential across multiple GPUs. - -### Notebook tutorials - -If you want to learn how to use the `sevenn` Python library instead of the CLI command, please check out the notebook tutorials below. - -| Notebooks | Google Colab | Descriptions | -|-----------|-------------------|--------------| -|[From scratch](https://github.com/MDIL-SNU/sevennet_tutorial/blob/main/notebooks/SevenNet_python_tutorial.ipynb)|[![Open in Google Colab]](https://colab.research.google.com/github/MDIL-SNU/sevennet_tutorial/blob/main/notebooks/SevenNet_python_tutorial.ipynb)|We can learn how to train the SevenNet from scratch, predict energy, forces, and stress using the trained model, perform structure relaxation, and draw EOS curves.| -|[Fine-tuning](https://github.com/MDIL-SNU/sevennet_tutorial/blob/main/notebooks/SevenNet_finetune_tutorial.ipynb)|[![Open in Google Colab]](https://colab.research.google.com/github/MDIL-SNU/sevennet_tutorial/blob/main/notebooks/SevenNet_finetune_tutorial.ipynb)|We can learn how to fine-tune the SevenNet and compare the results of the pretrained model with the fine-tuned model.| - -[Open in Google Colab]: https://colab.research.google.com/assets/colab-badge.svg - -Sometimes, the Colab environment may crash due to memory issues. If you have sufficient GPU resources in your local environment, we recommend downloading the tutorials from GitHub and running them on your machine. -```bash -git clone https://github.com/MDIL-SNU/sevennet_tutorial.git -``` - -### MD simulation with LAMMPS - -#### Installation - -##### Requirements -- PyTorch (it is recommended to use the same version as used during training) -- LAMMPS version of `stable_2Aug2023_update3` -- MKL library -- [`CUDA-aware OpenMPI`](https://www.open-mpi.org/faq/?category=buildcuda) for parallel MD (optional) - -If your cluster supports the Intel MKL module (often included with Intel OneAPI, Intel Compiler, and other Intel-related modules), load that module. - -CUDA-aware OpenMPI is optional but recommended for parallel MD. If it is not available, GPUs will communicate via the CPU when running in parallel mode. It is still faster than using only one GPU, but its efficiency is lower. - -> [!IMPORTANT] -> CUDA-aware OpenMPI does not support NVIDIA gaming GPUs. Since the software is closely tied to hardware specifications, please consult your server administrator if CUDA-aware OpenMPI is unavailable. - -###### 1. Build LAMMPS with cmake. - -Ensure the LAMMPS version is `stable_2Aug2023_update3`. You can easily switch the version using Git. After switching the version, run `sevenn_patch_lammps` with the LAMMPS directory path as an argument. - -```bash -git clone https://github.com/lammps/lammps.git lammps_sevenn --branch stable_2Aug2023_update3 --depth=1 -sevenn_patch_lammps ./lammps_sevenn {--d3} -``` -You can refer to `sevenn/pair_e3gnn/patch_lammps.sh` for details of the patch process. - -> [!TIP] -> Add `--d3` option to install GPU-accelerated [Grimme's D3 method](https://doi.org/10.1063/1.3382344) pair style. For its usage and details, click [here](sevenn/pair_e3gnn). - -```bash -cd ./lammps_sevenn -mkdir build -cd build -cmake ../cmake -DCMAKE_PREFIX_PATH=`python -c 'import torch;print(torch.utils.cmake_prefix_path)'` -make -j4 -``` - -If the error `MKL_INCLUDE_DIR NOT-FOUND` occurs, please check the environment variable or read the `Possible solutions` section below. -If compilation completes without any errors, please skip this. - -
-Possible solutions - -###### 2. Install mkl-include via conda - -```bash -conda install -c intel mkl-include -conda install mkl-include # if the above failed -``` - -###### 3. Append `DMKL_INCLUDE_DIR` to the cmake command and repeat step 1 - -```bash -cmake ../cmake -DCMAKE_PREFIX_PATH=`python -c 'import torch;print(torch.utils.cmake_prefix_path)'` -DMKL_INCLUDE_DIR=$CONDA_PREFIX/include -``` - -If the `undefined reference to XXX` error with `libtorch_cpu.so` occurs, check the `$LD_LIBRARY_PATH`. -If PyTorch is installed using Conda, `libmkl_*.so` files can be found in `$CONDA_PREFIX/lib`. -Ensure that `$LD_LIBRARY_PATH` includes `$CONDA_PREFIX/lib`. - -For other error cases, solution can be found in the [`pair-nequip`](https://github.com/mir-group/pair_nequip) repository, as we share the same architecture. - -
- -If the compilation is successful, the executable `lmp` can be found at `{path_to_lammps_dir}/build`. -To use this binary easily, create a soft link to your bin directory, which should be included in your `$PATH`. - -```bash -ln -s {absolute_path_to_lammps_directory}/build/lmp $HOME/.local/bin/lmp -``` - -This allows you to run the binary using `lmp -in my_lammps_script.lmp`. - -#### Single-GPU MD - -For single-GPU MD simulations, the `e3gnn` pair_style should be used. A minimal input script is provided below: -```txt -units metal -atom_style atomic -pair_style e3gnn -pair_coeff * * {path to serial model} {space separated chemical species} -``` - -#### Multi-GPU MD - -For multi-GPU MD simulations, the `e3gnn/parallel` pair_style should be used. A minimal input script is provided below: -```txt -units metal -atom_style atomic -pair_style e3gnn/parallel -pair_coeff * * {number of message-passing layers} {directory of parallel model} {space separated chemical species} -``` - -For example, - -```txt -pair_style e3gnn/parallel -pair_coeff * * 4 ./deployed_parallel Hf O -``` -The number of message-passing layers corresponds to the number of `*.pt` files in the `./deployed_parallel` directory. - -To deploy LAMMPS models from checkpoints for both serial and parallel execution, use [`sevenn_get_model`](#deployment). - -It is expected that there is one GPU per MPI process. If the number of available GPUs is less than the number of MPI processes, the simulation may run inefficiently. - -> [!CAUTION] -> Currently, the parallel version encounters an error when one of the subdomain cells contains no atoms. This issue can be addressed using the `processors` command and, more effectively, the `fix balance` command in LAMMPS. A patch for this issue will be released in a future update. - -### Application of SevenNet-0 -If you are interested in practical applications of SevenNet, please refer to [this paper](https://arxiv.org/abs/2501.05211) (data available on [Zenodo](https://doi.org/10.5281/zenodo.15205477)). -This study utilized SevenNet-0 for simulating liquid electrolytes. - -The fine-tuning procedure and associated input files are accessible through the links above, specifically within the `Fine-tuning.tar.xz` archive on Zenodo. - -The YAML file used for fine-tuning can be obtained using the following command: -```bash -sevenn_preset fine_tune_le > input.yaml -``` - -## Citation - -If you use this code, please cite our paper: -```txt -@article{park_scalable_2024, - title = {Scalable Parallel Algorithm for Graph Neural Network Interatomic Potentials in Molecular Dynamics Simulations}, - volume = {20}, - doi = {10.1021/acs.jctc.4c00190}, - number = {11}, - journal = {J. Chem. Theory Comput.}, - author = {Park, Yutack and Kim, Jaesun and Hwang, Seungwoo and Han, Seungwu}, - year = {2024}, - pages = {4857--4868}, -} -``` - -If you utilize the multi-fidelity feature of this code or the pretrained model SevenNet-MF-ompa, please cite the following paper: -```txt -@article{kim_sevennet_mf_2024, - title = {Data-Efficient Multifidelity Training for High-Fidelity Machine Learning Interatomic Potentials}, - volume = {147}, - doi = {10.1021/jacs.4c14455}, - number = {1}, - journal = {J. Am. Chem. Soc.}, - author = {Kim, Jaesun and Kim, Jisu and Kim, Jaehoon and Lee, Jiho and Park, Yutack and Kang, Youngho and Han, Seungwu}, - year = {2024}, - pages = {1042--1054}, -``` diff --git a/mace-bench/3rdparty/SevenNet/sevenn.egg-info/SOURCES.txt b/mace-bench/3rdparty/SevenNet/sevenn.egg-info/SOURCES.txt deleted file mode 100644 index ec2fcaf24bf78ec9500e8a82055f86ff705daaae..0000000000000000000000000000000000000000 --- a/mace-bench/3rdparty/SevenNet/sevenn.egg-info/SOURCES.txt +++ /dev/null @@ -1,87 +0,0 @@ -LICENSE -README.md -pyproject.toml -setup.cfg -sevenn/__init__.py -sevenn/_const.py -sevenn/_keys.py -sevenn/atom_graph_data.py -sevenn/calculator.py -sevenn/checkpoint.py -sevenn/error_recorder.py -sevenn/logger.py -sevenn/logo_ascii -sevenn/model_build.py -sevenn/pair_d3.so -sevenn/parse_input.py -sevenn/py.typed -sevenn/sevenn_logger.py -sevenn/sevennet_calculator.py -sevenn/util.py -sevenn.egg-info/PKG-INFO -sevenn.egg-info/SOURCES.txt -sevenn.egg-info/dependency_links.txt -sevenn.egg-info/entry_points.txt -sevenn.egg-info/requires.txt -sevenn.egg-info/top_level.txt -sevenn/main/__init__.py -sevenn/main/sevenn.py -sevenn/main/sevenn_cp.py -sevenn/main/sevenn_get_model.py -sevenn/main/sevenn_graph_build.py -sevenn/main/sevenn_inference.py -sevenn/main/sevenn_patch_lammps.py -sevenn/main/sevenn_preset.py -sevenn/nn/__init__.py -sevenn/nn/activation.py -sevenn/nn/convolution.py -sevenn/nn/cue_helper.py -sevenn/nn/edge_embedding.py -sevenn/nn/equivariant_gate.py -sevenn/nn/force_output.py -sevenn/nn/interaction_blocks.py -sevenn/nn/linear.py -sevenn/nn/node_embedding.py -sevenn/nn/scale.py -sevenn/nn/self_connection.py -sevenn/nn/sequential.py -sevenn/nn/util.py -sevenn/pair_e3gnn/comm_brick.cpp -sevenn/pair_e3gnn/comm_brick.h -sevenn/pair_e3gnn/pair_d3.cu -sevenn/pair_e3gnn/pair_d3.h -sevenn/pair_e3gnn/pair_d3_for_ase.cu -sevenn/pair_e3gnn/pair_d3_for_ase.h -sevenn/pair_e3gnn/pair_d3_pars.h -sevenn/pair_e3gnn/pair_e3gnn.cpp -sevenn/pair_e3gnn/pair_e3gnn.h -sevenn/pair_e3gnn/pair_e3gnn_parallel.cpp -sevenn/pair_e3gnn/pair_e3gnn_parallel.h -sevenn/pair_e3gnn/patch_lammps.sh -sevenn/presets/MF_0.yaml -sevenn/presets/base.yaml -sevenn/presets/fine_tune.yaml -sevenn/presets/fine_tune_le.yaml -sevenn/presets/multi_modal.yaml -sevenn/presets/sevennet-0.yaml -sevenn/presets/sevennet-l3i5.yaml -sevenn/scripts/__init__.py -sevenn/scripts/backward_compatibility.py -sevenn/scripts/convert_model_modality.py -sevenn/scripts/deploy.py -sevenn/scripts/graph_build.py -sevenn/scripts/inference.py -sevenn/scripts/processing_continue.py -sevenn/scripts/processing_dataset.py -sevenn/scripts/processing_epoch.py -sevenn/scripts/train.py -sevenn/train/__init__.py -sevenn/train/atoms_dataset.py -sevenn/train/collate.py -sevenn/train/dataload.py -sevenn/train/dataset.py -sevenn/train/graph_dataset.py -sevenn/train/loss.py -sevenn/train/modal_dataset.py -sevenn/train/optim.py -sevenn/train/trainer.py \ No newline at end of file diff --git a/mace-bench/3rdparty/SevenNet/sevenn.egg-info/dependency_links.txt b/mace-bench/3rdparty/SevenNet/sevenn.egg-info/dependency_links.txt deleted file mode 100644 index 8b137891791fe96927ad78e64b0aad7bded08bdc..0000000000000000000000000000000000000000 --- a/mace-bench/3rdparty/SevenNet/sevenn.egg-info/dependency_links.txt +++ /dev/null @@ -1 +0,0 @@ - diff --git a/mace-bench/3rdparty/SevenNet/sevenn.egg-info/entry_points.txt b/mace-bench/3rdparty/SevenNet/sevenn.egg-info/entry_points.txt deleted file mode 100644 index f16f9e24d0305b11e6e1cb3b510a1fe0f82ce8a7..0000000000000000000000000000000000000000 --- a/mace-bench/3rdparty/SevenNet/sevenn.egg-info/entry_points.txt +++ /dev/null @@ -1,8 +0,0 @@ -[console_scripts] -sevenn = sevenn.main.sevenn:main -sevenn_cp = sevenn.main.sevenn_cp:main -sevenn_get_model = sevenn.main.sevenn_get_model:main -sevenn_graph_build = sevenn.main.sevenn_graph_build:main -sevenn_inference = sevenn.main.sevenn_inference:main -sevenn_patch_lammps = sevenn.main.sevenn_patch_lammps:main -sevenn_preset = sevenn.main.sevenn_preset:main diff --git a/mace-bench/3rdparty/SevenNet/sevenn.egg-info/requires.txt b/mace-bench/3rdparty/SevenNet/sevenn.egg-info/requires.txt deleted file mode 100644 index 4da931088467494bf70f587ec2e47c02926c580e..0000000000000000000000000000000000000000 --- a/mace-bench/3rdparty/SevenNet/sevenn.egg-info/requires.txt +++ /dev/null @@ -1,30 +0,0 @@ -ase -braceexpand -pyyaml -e3nn>=0.5.0 -tqdm -scikit-learn -torch_geometric>=2.5.0 -numpy -matscipy -pandas -requests -setuptools>=61.0 - -[cueq11] - -[cueq11:python_version >= "3.10"] -cuequivariance>=0.4.0 -cuequivariance-torch>=0.4.0 -cuequivariance-ops-torch-cu11 - -[cueq12] - -[cueq12:python_version >= "3.10"] -cuequivariance>=0.4.0 -cuequivariance-torch>=0.4.0 -cuequivariance-ops-torch-cu12 - -[test] -pytest -pytest-cov>=5 diff --git a/mace-bench/3rdparty/SevenNet/sevenn.egg-info/top_level.txt b/mace-bench/3rdparty/SevenNet/sevenn.egg-info/top_level.txt deleted file mode 100644 index 5f58d61142989dda3381ac7da7ca3f9ce4606e5b..0000000000000000000000000000000000000000 --- a/mace-bench/3rdparty/SevenNet/sevenn.egg-info/top_level.txt +++ /dev/null @@ -1 +0,0 @@ -sevenn diff --git a/mace-bench/3rdparty/SevenNet/sevenn/__init__.py b/mace-bench/3rdparty/SevenNet/sevenn/__init__.py deleted file mode 100644 index 6145e442c54f2249f48cfb7303611a7241a48b6e..0000000000000000000000000000000000000000 --- a/mace-bench/3rdparty/SevenNet/sevenn/__init__.py +++ /dev/null @@ -1,13 +0,0 @@ -from importlib.metadata import version - -from packaging.version import Version - -__version__ = version('sevenn') - -from e3nn import __version__ as e3nn_ver - -if Version(e3nn_ver) < Version('0.5.0'): - raise ValueError( - 'The e3nn version MUST be 0.5.0 or later due to changes in CG coefficient ' - 'convention.' - ) diff --git a/mace-bench/3rdparty/SevenNet/sevenn/_const.py b/mace-bench/3rdparty/SevenNet/sevenn/_const.py deleted file mode 100644 index 284b64e49c4e7c25daca517df44ae221065a9084..0000000000000000000000000000000000000000 --- a/mace-bench/3rdparty/SevenNet/sevenn/_const.py +++ /dev/null @@ -1,310 +0,0 @@ -import os -from enum import Enum -from typing import Dict - -import torch - -import sevenn._keys as KEY -from sevenn.nn.activation import ShiftedSoftPlus - -NUM_UNIV_ELEMENT = 119 # Z = 0 ~ 118 - -IMPLEMENTED_RADIAL_BASIS = ['bessel'] -IMPLEMENTED_CUTOFF_FUNCTION = ['poly_cut', 'XPLOR'] -# TODO: support None. This became difficult because of parallel model -IMPLEMENTED_SELF_CONNECTION_TYPE = ['nequip', 'linear'] -IMPLEMENTED_INTERACTION_TYPE = ['nequip'] - -IMPLEMENTED_SHIFT = ['per_atom_energy_mean', 'elemwise_reference_energies'] -IMPLEMENTED_SCALE = ['force_rms', 'per_atom_energy_std', 'elemwise_force_rms'] - -SUPPORTING_METRICS = ['RMSE', 'ComponentRMSE', 'MAE', 'Loss'] -SUPPORTING_ERROR_TYPES = [ - 'TotalEnergy', - 'Energy', - 'Force', - 'Stress', - 'Stress_GPa', - 'TotalLoss', -] - -IMPLEMENTED_MODEL = ['E3_equivariant_model'] - -# string input to real torch function -ACTIVATION = { - 'relu': torch.nn.functional.relu, - 'silu': torch.nn.functional.silu, - 'tanh': torch.tanh, - 'abs': torch.abs, - 'ssp': ShiftedSoftPlus, - 'sigmoid': torch.sigmoid, - 'elu': torch.nn.functional.elu, -} -ACTIVATION_FOR_EVEN = { - 'ssp': ShiftedSoftPlus, - 'silu': torch.nn.functional.silu, -} -ACTIVATION_FOR_ODD = {'tanh': torch.tanh, 'abs': torch.abs} -ACTIVATION_DICT = {'e': ACTIVATION_FOR_EVEN, 'o': ACTIVATION_FOR_ODD} - -_prefix = os.path.abspath(f'{os.path.dirname(__file__)}/pretrained_potentials') -SEVENNET_0_11Jul2024 = f'{_prefix}/SevenNet_0__11Jul2024/checkpoint_sevennet_0.pth' -SEVENNET_0_22May2024 = f'{_prefix}/SevenNet_0__22May2024/checkpoint_sevennet_0.pth' -SEVENNET_l3i5 = f'{_prefix}/SevenNet_l3i5/checkpoint_l3i5.pth' -SEVENNET_MF_0 = f'{_prefix}/SevenNet_MF_0/checkpoint_sevennet_mf_0.pth' -SEVENNET_MF_ompa = f'{_prefix}/SevenNet_MF_ompa/checkpoint_sevennet_mf_ompa.pth' -SEVENNET_omat = f'{_prefix}/SevenNet_omat/checkpoint_sevennet_omat.pth' - -_git_prefix = 'https://github.com/MDIL-SNU/SevenNet/releases/download' -CHECKPOINT_DOWNLOAD_LINKS = { - SEVENNET_MF_ompa: f'{_git_prefix}/v0.11.0.cp/checkpoint_sevennet_mf_ompa.pth', - SEVENNET_omat: f'{_git_prefix}/v0.11.0.cp/checkpoint_sevennet_omat.pth', -} -# to avoid torch script to compile torch_geometry.data -AtomGraphDataType = Dict[str, torch.Tensor] - - -class LossType(Enum): # only used for train_v1, do not use it afterwards - ENERGY = 'energy' # eV or eV/atom - FORCE = 'force' # eV/A - STRESS = 'stress' # kB - - -def error_record_condition(x): - if type(x) is not list: - return False - for v in x: - if type(v) is not list or len(v) != 2: - return False - if v[0] not in SUPPORTING_ERROR_TYPES: - return False - if v[0] == 'TotalLoss': - continue - if v[1] not in SUPPORTING_METRICS: - return False - return True - - -DEFAULT_E3_EQUIVARIANT_MODEL_CONFIG = { - KEY.CUTOFF: 4.5, - KEY.NODE_FEATURE_MULTIPLICITY: 32, - KEY.IRREPS_MANUAL: False, - KEY.LMAX: 1, - KEY.LMAX_EDGE: -1, # -1 means lmax_edge = lmax - KEY.LMAX_NODE: -1, # -1 means lmax_node = lmax - KEY.IS_PARITY: True, - KEY.NUM_CONVOLUTION: 3, - KEY.RADIAL_BASIS: { - KEY.RADIAL_BASIS_NAME: 'bessel', - }, - KEY.CUTOFF_FUNCTION: { - KEY.CUTOFF_FUNCTION_NAME: 'poly_cut', - }, - KEY.ACTIVATION_RADIAL: 'silu', - KEY.ACTIVATION_SCARLAR: {'e': 'silu', 'o': 'tanh'}, - KEY.ACTIVATION_GATE: {'e': 'silu', 'o': 'tanh'}, - KEY.CONVOLUTION_WEIGHT_NN_HIDDEN_NEURONS: [64, 64], - # KEY.AVG_NUM_NEIGH: True, # deprecated - # KEY.TRAIN_AVG_NUM_NEIGH: False, # deprecated - KEY.CONV_DENOMINATOR: 'avg_num_neigh', - KEY.TRAIN_DENOMINTAOR: False, - KEY.TRAIN_SHIFT_SCALE: False, - # KEY.OPTIMIZE_BY_REDUCE: True, # deprecated, always True - KEY.USE_BIAS_IN_LINEAR: False, - KEY.USE_MODAL_NODE_EMBEDDING: False, - KEY.USE_MODAL_SELF_INTER_INTRO: False, - KEY.USE_MODAL_SELF_INTER_OUTRO: False, - KEY.USE_MODAL_OUTPUT_BLOCK: False, - KEY.READOUT_AS_FCN: False, - # Applied af readout as fcn is True - KEY.READOUT_FCN_HIDDEN_NEURONS: [30, 30], - KEY.READOUT_FCN_ACTIVATION: 'relu', - KEY.SELF_CONNECTION_TYPE: 'nequip', - KEY.INTERACTION_TYPE: 'nequip', - KEY._NORMALIZE_SPH: True, - KEY.CUEQUIVARIANCE_CONFIG: {}, -} - - -# Basically, "If provided, it should be type of ..." -MODEL_CONFIG_CONDITION = { - KEY.NODE_FEATURE_MULTIPLICITY: int, - KEY.LMAX: int, - KEY.LMAX_EDGE: int, - KEY.LMAX_NODE: int, - KEY.IS_PARITY: bool, - KEY.RADIAL_BASIS: { - KEY.RADIAL_BASIS_NAME: lambda x: x in IMPLEMENTED_RADIAL_BASIS, - }, - KEY.CUTOFF_FUNCTION: { - KEY.CUTOFF_FUNCTION_NAME: lambda x: x in IMPLEMENTED_CUTOFF_FUNCTION, - }, - KEY.CUTOFF: float, - KEY.NUM_CONVOLUTION: int, - KEY.CONV_DENOMINATOR: lambda x: isinstance(x, float) - or x - in [ - 'avg_num_neigh', - 'sqrt_avg_num_neigh', - ], - KEY.CONVOLUTION_WEIGHT_NN_HIDDEN_NEURONS: list, - KEY.TRAIN_SHIFT_SCALE: bool, - KEY.TRAIN_DENOMINTAOR: bool, - KEY.USE_BIAS_IN_LINEAR: bool, - KEY.USE_MODAL_NODE_EMBEDDING: bool, - KEY.USE_MODAL_SELF_INTER_INTRO: bool, - KEY.USE_MODAL_SELF_INTER_OUTRO: bool, - KEY.USE_MODAL_OUTPUT_BLOCK: bool, - KEY.READOUT_AS_FCN: bool, - KEY.READOUT_FCN_HIDDEN_NEURONS: list, - KEY.READOUT_FCN_ACTIVATION: str, - KEY.ACTIVATION_RADIAL: str, - KEY.SELF_CONNECTION_TYPE: lambda x: ( - x in IMPLEMENTED_SELF_CONNECTION_TYPE - or ( - isinstance(x, list) - and all(sc in IMPLEMENTED_SELF_CONNECTION_TYPE for sc in x) - ) - ), - KEY.INTERACTION_TYPE: lambda x: x in IMPLEMENTED_INTERACTION_TYPE, - KEY._NORMALIZE_SPH: bool, - KEY.CUEQUIVARIANCE_CONFIG: dict, -} - - -def model_defaults(config): - defaults = DEFAULT_E3_EQUIVARIANT_MODEL_CONFIG - - if KEY.READOUT_AS_FCN not in config: - config[KEY.READOUT_AS_FCN] = defaults[KEY.READOUT_AS_FCN] - if config[KEY.READOUT_AS_FCN] is False: - defaults.pop(KEY.READOUT_FCN_ACTIVATION, None) - defaults.pop(KEY.READOUT_FCN_HIDDEN_NEURONS, None) - - return defaults - - -DEFAULT_DATA_CONFIG = { - KEY.DTYPE: 'single', - KEY.DATA_FORMAT: 'ase', - KEY.DATA_FORMAT_ARGS: {}, - KEY.SAVE_DATASET: False, - KEY.SAVE_BY_LABEL: False, - KEY.SAVE_BY_TRAIN_VALID: False, - KEY.RATIO: 0.0, - KEY.BATCH_SIZE: 6, - KEY.PREPROCESS_NUM_CORES: 1, - KEY.COMPUTE_STATISTICS: True, - KEY.DATASET_TYPE: 'graph', - # KEY.USE_SPECIES_WISE_SHIFT_SCALE: False, - KEY.USE_MODAL_WISE_SHIFT: False, - KEY.USE_MODAL_WISE_SCALE: False, - KEY.SHIFT: 'per_atom_energy_mean', - KEY.SCALE: 'force_rms', - # KEY.DATA_SHUFFLE: True, - # KEY.DATA_WEIGHT: False, - # KEY.DATA_MODALITY: False, -} - -DATA_CONFIG_CONDITION = { - KEY.DTYPE: str, - KEY.DATA_FORMAT: str, - KEY.DATA_FORMAT_ARGS: dict, - KEY.SAVE_DATASET: str, - KEY.SAVE_BY_LABEL: bool, - KEY.SAVE_BY_TRAIN_VALID: bool, - KEY.RATIO: float, - KEY.BATCH_SIZE: int, - KEY.PREPROCESS_NUM_CORES: int, - KEY.DATASET_TYPE: lambda x: x in ['graph', 'atoms'], - # KEY.USE_SPECIES_WISE_SHIFT_SCALE: bool, - KEY.SHIFT: lambda x: type(x) in [float, list] or x in IMPLEMENTED_SHIFT, - KEY.SCALE: lambda x: type(x) in [float, list] or x in IMPLEMENTED_SCALE, - KEY.USE_MODAL_WISE_SHIFT: bool, - KEY.USE_MODAL_WISE_SCALE: bool, - # KEY.DATA_SHUFFLE: bool, - KEY.COMPUTE_STATISTICS: bool, - # KEY.DATA_WEIGHT: bool, - # KEY.DATA_MODALITY: bool, -} - - -def data_defaults(config): - defaults = DEFAULT_DATA_CONFIG - if KEY.LOAD_VALIDSET in config: - defaults.pop(KEY.RATIO, None) - return defaults - - -DEFAULT_TRAINING_CONFIG = { - KEY.RANDOM_SEED: 1, - KEY.EPOCH: 300, - KEY.LOSS: 'mse', - KEY.LOSS_PARAM: {}, - KEY.OPTIMIZER: 'adam', - KEY.OPTIM_PARAM: {}, - KEY.SCHEDULER: 'exponentiallr', - KEY.SCHEDULER_PARAM: {}, - KEY.FORCE_WEIGHT: 0.1, - KEY.STRESS_WEIGHT: 1e-6, # SIMPLE-NN default - KEY.PER_EPOCH: 5, - # KEY.USE_TESTSET: False, - KEY.CONTINUE: { - KEY.CHECKPOINT: False, - KEY.RESET_OPTIMIZER: False, - KEY.RESET_SCHEDULER: False, - KEY.RESET_EPOCH: False, - KEY.USE_STATISTIC_VALUES_OF_CHECKPOINT: True, - KEY.USE_STATISTIC_VALUES_FOR_CP_MODAL_ONLY: True, - }, - # KEY.DEFAULT_MODAL: 'common', - KEY.CSV_LOG: 'log.csv', - KEY.NUM_WORKERS: 0, - KEY.IS_TRAIN_STRESS: True, - KEY.TRAIN_SHUFFLE: True, - KEY.ERROR_RECORD: [ - ['Energy', 'RMSE'], - ['Force', 'RMSE'], - ['Stress', 'RMSE'], - ['TotalLoss', 'None'], - ], - KEY.BEST_METRIC: 'TotalLoss', - KEY.USE_WEIGHT: False, - KEY.USE_MODALITY: False, -} - - -TRAINING_CONFIG_CONDITION = { - KEY.RANDOM_SEED: int, - KEY.EPOCH: int, - KEY.FORCE_WEIGHT: float, - KEY.STRESS_WEIGHT: float, - KEY.USE_TESTSET: None, # Not used - KEY.NUM_WORKERS: int, - KEY.PER_EPOCH: int, - KEY.CONTINUE: { - KEY.CHECKPOINT: str, - KEY.RESET_OPTIMIZER: bool, - KEY.RESET_SCHEDULER: bool, - KEY.RESET_EPOCH: bool, - KEY.USE_STATISTIC_VALUES_OF_CHECKPOINT: bool, - KEY.USE_STATISTIC_VALUES_FOR_CP_MODAL_ONLY: bool, - }, - KEY.DEFAULT_MODAL: str, - KEY.IS_TRAIN_STRESS: bool, - KEY.TRAIN_SHUFFLE: bool, - KEY.ERROR_RECORD: error_record_condition, - KEY.BEST_METRIC: str, - KEY.CSV_LOG: str, - KEY.USE_MODALITY: bool, - KEY.USE_WEIGHT: bool, -} - - -def train_defaults(config): - defaults = DEFAULT_TRAINING_CONFIG - if KEY.IS_TRAIN_STRESS not in config: - config[KEY.IS_TRAIN_STRESS] = defaults[KEY.IS_TRAIN_STRESS] - if not config[KEY.IS_TRAIN_STRESS]: - defaults.pop(KEY.STRESS_WEIGHT, None) - return defaults diff --git a/mace-bench/3rdparty/SevenNet/sevenn/_keys.py b/mace-bench/3rdparty/SevenNet/sevenn/_keys.py deleted file mode 100644 index 1ff5a614484c81d9418f3c84cd0f7b9144384b55..0000000000000000000000000000000000000000 --- a/mace-bench/3rdparty/SevenNet/sevenn/_keys.py +++ /dev/null @@ -1,226 +0,0 @@ -""" -How to add new feature? - -1. Add new key to this file. -2. Add new key to _const.py -2.1. if the type of input is consistent, - write adequate condition and default to _const.py. -2.2. if the type of input is not consistent, - you must add your own input validation code to - parse_input.py -""" - -from typing import Final - -# see -# https://github.com/pytorch/pytorch/issues/52312 -# for FYI - -# ~~ keys ~~ # -# PyG : primitive key of torch_geometric.data.Data type - -# ==================================================# -# ~~~~~~~~~~~~~~~~~ KEY for data ~~~~~~~~~~~~~~~~~~ # -# ==================================================# -# some raw properties of graph -ATOMIC_NUMBERS: Final[str] = 'atomic_numbers' # (N) -POS: Final[str] = 'pos' # (N, 3) PyG -CELL: Final[str] = 'cell_lattice_vectors' # (3, 3) -CELL_SHIFT: Final[str] = 'pbc_shift' # (N, 3) -CELL_VOLUME: Final[str] = 'cell_volume' - -EDGE_VEC: Final[str] = 'edge_vec' # (N_edge, 3) -EDGE_LENGTH: Final[str] = 'edge_length' # (N_edge, 1) - -# some primary data of graph -EDGE_IDX: Final[str] = 'edge_index' # (2, N_edge) PyG -ATOM_TYPE: Final[str] = 'atom_type' # (N) one-hot index of nodes -NODE_FEATURE: Final[str] = 'x' # (N, ?) PyG -NODE_FEATURE_GHOST: Final[str] = 'x_ghost' -NODE_ATTR: Final[str] = 'node_attr' # (N, N_species) from one_hot -MODAL_ATTR: Final[str] = ( - 'modal_attr' # (1, N_modalities) for handling multi-modal -) -MODAL_TYPE: Final[str] = 'modal_type' # (1) one-hot index of modal -EDGE_ATTR: Final[str] = 'edge_attr' # (from spherical harmonics) -EDGE_EMBEDDING: Final[str] = 'edge_embedding' # (from edge embedding) - -# inputs of loss function -ENERGY: Final[str] = 'total_energy' # (1) -FORCE: Final[str] = 'force_of_atoms' # (N, 3) -STRESS: Final[str] = 'stress' # (6) - -# This is for training, per atom scale. -SCALED_ENERGY: Final[str] = 'scaled_total_energy' - -# general outputs of models -SCALED_ATOMIC_ENERGY: Final[str] = 'scaled_atomic_energy' -ATOMIC_ENERGY: Final[str] = 'atomic_energy' -PRED_TOTAL_ENERGY: Final[str] = 'inferred_total_energy' - -PRED_PER_ATOM_ENERGY: Final[str] = 'inferred_per_atom_energy' -PER_ATOM_ENERGY: Final[str] = 'per_atom_energy' - -PRED_FORCE: Final[str] = 'inferred_force' -SCALED_FORCE: Final[str] = 'scaled_force' - -PRED_STRESS: Final[str] = 'inferred_stress' -SCALED_STRESS: Final[str] = 'scaled_stress' - -# very general data property for AtomGraphData -NUM_ATOMS: Final[str] = 'num_atoms' # int -NUM_GHOSTS: Final[str] = 'num_ghosts' -NLOCAL: Final[str] = 'nlocal' # only for lammps parallel, must be on cpu -USER_LABEL: Final[str] = 'user_label' -DATA_WEIGHT: Final[str] = 'data_weight' # weight for given data -DATA_MODALITY: Final[str] = ( - 'data_modality' # modality of given data. e.g. PBE and SCAN -) -BATCH: Final[str] = 'batch' - -TAG = 'tag' # replace USER_LABEL - -# etc -SELF_CONNECTION_TEMP: Final[str] = 'self_cont_tmp' -BATCH_SIZE: Final[str] = 'batch_size' -INFO: Final[str] = 'data_info' - -# something special -LABEL_NONE: Final[str] = 'No_label' - -# ==================================================# -# ~~~~~~ KEY for train/data configuration ~~~~~~~~ # -# ==================================================# -PREPROCESS_NUM_CORES = 'preprocess_num_cores' -SAVE_DATASET = 'save_dataset_path' -SAVE_BY_LABEL = 'save_by_label' -SAVE_BY_TRAIN_VALID = 'save_by_train_valid' -DATA_FORMAT = 'data_format' -DATA_FORMAT_ARGS = 'data_format_args' -STRUCTURE_LIST = 'structure_list' -LOAD_DATASET = 'load_dataset_path' # not used in v2 -LOAD_TRAINSET = 'load_trainset_path' -LOAD_VALIDSET = 'load_validset_path' -LOAD_TESTSET = 'load_testset_path' -FORMAT_OUTPUTS = 'format_outputs_for_ase' -COMPUTE_STATISTICS = 'compute_statistics' -DATASET_TYPE = 'dataset_type' - -RANDOM_SEED = 'random_seed' -RATIO = 'data_divide_ratio' -USE_TESTSET = 'use_testset' -EPOCH = 'epoch' -LOSS = 'loss' -LOSS_PARAM = 'loss_param' -OPTIMIZER = 'optimizer' -OPTIM_PARAM = 'optim_param' -SCHEDULER = 'scheduler' -SCHEDULER_PARAM = 'scheduler_param' -FORCE_WEIGHT = 'force_loss_weight' -STRESS_WEIGHT = 'stress_loss_weight' -DEVICE = 'device' -DTYPE = 'dtype' - -TRAIN_SHUFFLE = 'train_shuffle' - -IS_TRAIN_STRESS = 'is_train_stress' - -CONTINUE = 'continue' -CHECKPOINT = 'checkpoint' -RESET_OPTIMIZER = 'reset_optimizer' -RESET_SCHEDULER = 'reset_scheduler' -RESET_EPOCH = 'reset_epoch' -USE_STATISTIC_VALUES_OF_CHECKPOINT = 'use_statistic_values_of_checkpoint' -USE_STATISTIC_VALUES_FOR_CP_MODAL_ONLY = ( - 'use_statistic_values_for_cp_modal_only' -) - -CSV_LOG = 'csv_log' - -ERROR_RECORD = 'error_record' -BEST_METRIC = 'best_metric' - -NUM_WORKERS = 'num_workers' # not work - -RANK = 'rank' -LOCAL_RANK = 'local_rank' -WORLD_SIZE = 'world_size' -IS_DDP = 'is_ddp' -DDP_BACKEND = 'ddp_backend' -PER_EPOCH = 'per_epoch' - -USE_WEIGHT = 'use_weight' -USE_MODALITY = 'use_modality' -DEFAULT_MODAL = 'default_modal' - - -# ==================================================# -# ~~~~~~~~ KEY for model configuration ~~~~~~~~~~~ # -# ==================================================# -# ~~ global model configuration ~~ # -# note that these names are directly used for input.yaml for user input -MODEL_TYPE = '_model_type' -CUTOFF = 'cutoff' -CHEMICAL_SPECIES = 'chemical_species' -MODAL_LIST = 'modal_list' -CHEMICAL_SPECIES_BY_ATOMIC_NUMBER = '_chemical_species_by_atomic_number' -NUM_SPECIES = '_number_of_species' -NUM_MODALITIES = '_number_of_modalities' -TYPE_MAP = '_type_map' -MODAL_MAP = '_modal_map' - -# ~~ E3 equivariant model build configuration keys ~~ # -# see model_build default_config for type -IRREPS_MANUAL = 'irreps_manual' -NODE_FEATURE_MULTIPLICITY = 'channel' - -RADIAL_BASIS = 'radial_basis' -BESSEL_BASIS_NUM = 'bessel_basis_num' - -CUTOFF_FUNCTION = 'cutoff_function' -POLY_CUT_P = 'poly_cut_p_value' - -LMAX = 'lmax' -LMAX_EDGE = 'lmax_edge' -LMAX_NODE = 'lmax_node' -IS_PARITY = 'is_parity' -CONVOLUTION_WEIGHT_NN_HIDDEN_NEURONS = 'weight_nn_hidden_neurons' -NUM_CONVOLUTION = 'num_convolution_layer' -ACTIVATION_SCARLAR = 'act_scalar' -ACTIVATION_GATE = 'act_gate' -ACTIVATION_RADIAL = 'act_radial' - -SELF_CONNECTION_TYPE = 'self_connection_type' - -RADIAL_BASIS_NAME = 'radial_basis_name' -CUTOFF_FUNCTION_NAME = 'cutoff_function_name' - -USE_BIAS_IN_LINEAR = 'use_bias_in_linear' - -USE_MODAL_NODE_EMBEDDING = 'use_modal_node_embedding' -USE_MODAL_SELF_INTER_INTRO = 'use_modal_self_inter_intro' -USE_MODAL_SELF_INTER_OUTRO = 'use_modal_self_inter_outro' -USE_MODAL_OUTPUT_BLOCK = 'use_modal_output_block' - -READOUT_AS_FCN = 'readout_as_fcn' -READOUT_FCN_HIDDEN_NEURONS = 'readout_fcn_hidden_neurons' -READOUT_FCN_ACTIVATION = 'readout_fcn_activation' - -AVG_NUM_NEIGH = 'avg_num_neigh' -CONV_DENOMINATOR = 'conv_denominator' -SHIFT = 'shift' -SCALE = 'scale' - -USE_SPECIES_WISE_SHIFT_SCALE = 'use_species_wise_shift_scale' -USE_MODAL_WISE_SHIFT = 'use_modal_wise_shift' -USE_MODAL_WISE_SCALE = 'use_modal_wise_scale' - -TRAIN_SHIFT_SCALE = 'train_shift_scale' -TRAIN_DENOMINTAOR = 'train_denominator' -INTERACTION_TYPE = 'interaction_type' -TRAIN_AVG_NUM_NEIGH = 'train_avg_num_neigh' # deprecated - -CUEQUIVARIANCE_CONFIG = 'cuequivariance_config' - -_NORMALIZE_SPH = '_normalize_sph' -OPTIMIZE_BY_REDUCE = 'optimize_by_reduce' diff --git a/mace-bench/3rdparty/SevenNet/sevenn/atom_graph_data.py b/mace-bench/3rdparty/SevenNet/sevenn/atom_graph_data.py deleted file mode 100644 index e0de629a5e6e83352ba266d10099f2324658e35f..0000000000000000000000000000000000000000 --- a/mace-bench/3rdparty/SevenNet/sevenn/atom_graph_data.py +++ /dev/null @@ -1,75 +0,0 @@ -from typing import Optional - -import torch -import torch_geometric.data - -import sevenn._keys as KEY -import sevenn.util - - -class AtomGraphData(torch_geometric.data.Data): - """ - Args: - x (Tensor, optional): atomic numbers with shape :obj:`[num_nodes, - atomic_numbers]`. (default: :obj:`None`) - edge_index (LongTensor, optional): Graph connectivity in coordinate - format with shape :obj:`[2, num_edges]`. (default: :obj:`None`) - edge_attr (Tensor, optional): Edge feature matrix with shape - :obj:`[num_edges, num_edge_features]`. (default: :obj:`None`) - y_energy: scalar # unit of eV (VASP raw) - y_force: [num_nodes, 3] # unit of eV/A (VASP raw) - y_stress: [6] # [xx, yy, zz, xy, yz, zx] # unit of eV/A^3 (VASP raw) - pos (Tensor, optional): Node position matrix with shape - :obj:`[num_nodes, num_dimensions]`. (default: :obj:`None`) - **kwargs (optional): Additional attributes. - - x, y_force, pos should be aligned with each other. - """ - - def __init__( - self, - x: Optional[torch.Tensor] = None, - edge_index: Optional[torch.Tensor] = None, - pos: Optional[torch.Tensor] = None, - edge_attr: Optional[torch.Tensor] = None, - **kwargs - ): - super(AtomGraphData, self).__init__(x, edge_index, edge_attr, pos=pos) - self[KEY.NODE_ATTR] = x # ? - for k, v in kwargs.items(): - self[k] = v - - def to_numpy_dict(self): - # This is not debugged yet! - dct = { - k: v.detach().cpu().numpy() if type(v) is torch.Tensor else v - for k, v in self.items() - } - return dct - - def fit_dimension(self): - per_atom_keys = [ - KEY.ATOMIC_NUMBERS, - KEY.ATOMIC_ENERGY, - KEY.POS, - KEY.FORCE, - KEY.PRED_FORCE, - ] - natoms = self.num_atoms.item() - for k, v in self.items(): - if not isinstance(v, torch.Tensor): - continue - if natoms == 1 and k in per_atom_keys: - self[k] = v.squeeze().unsqueeze(0) - else: - self[k] = v.squeeze() - return self - - @staticmethod - def from_numpy_dict(dct): - for k, v in dct.items(): - if k == KEY.CELL_SHIFT: - dct[k] = torch.Tensor(v) # this is special - else: - dct[k] = sevenn.util.dtype_correct(v) - return AtomGraphData(**dct) diff --git a/mace-bench/3rdparty/SevenNet/sevenn/build.ninja b/mace-bench/3rdparty/SevenNet/sevenn/build.ninja deleted file mode 100644 index 799fed8fb0821b7a90494d0d99803a078a1c8b52..0000000000000000000000000000000000000000 --- a/mace-bench/3rdparty/SevenNet/sevenn/build.ninja +++ /dev/null @@ -1,33 +0,0 @@ -ninja_required_version = 1.3 -cxx = c++ -nvcc = /usr/local/cuda/bin/nvcc - -cflags = -DTORCH_EXTENSION_NAME=pair_d3 -DTORCH_API_INCLUDE_EXTENSION_H -DPYBIND11_COMPILER_TYPE=\"_gcc\" -DPYBIND11_STDLIB=\"_libstdcpp\" -DPYBIND11_BUILD_ABI=\"_cxxabi1011\" -isystem /home/mazhaojia/pkg/miniconda3/envs/7net-cueq/lib/python3.10/site-packages/torch/include -isystem /home/mazhaojia/pkg/miniconda3/envs/7net-cueq/lib/python3.10/site-packages/torch/include/torch/csrc/api/include -isystem /home/mazhaojia/pkg/miniconda3/envs/7net-cueq/lib/python3.10/site-packages/torch/include/TH -isystem /home/mazhaojia/pkg/miniconda3/envs/7net-cueq/lib/python3.10/site-packages/torch/include/THC -isystem /usr/local/cuda/include -isystem /home/mazhaojia/pkg/miniconda3/envs/7net-cueq/include/python3.10 -D_GLIBCXX_USE_CXX11_ABI=0 -fPIC -std=c++17 -post_cflags = -cuda_cflags = -DTORCH_EXTENSION_NAME=pair_d3 -DTORCH_API_INCLUDE_EXTENSION_H -DPYBIND11_COMPILER_TYPE=\"_gcc\" -DPYBIND11_STDLIB=\"_libstdcpp\" -DPYBIND11_BUILD_ABI=\"_cxxabi1011\" -isystem /home/mazhaojia/pkg/miniconda3/envs/7net-cueq/lib/python3.10/site-packages/torch/include -isystem /home/mazhaojia/pkg/miniconda3/envs/7net-cueq/lib/python3.10/site-packages/torch/include/torch/csrc/api/include -isystem /home/mazhaojia/pkg/miniconda3/envs/7net-cueq/lib/python3.10/site-packages/torch/include/TH -isystem /home/mazhaojia/pkg/miniconda3/envs/7net-cueq/lib/python3.10/site-packages/torch/include/THC -isystem /usr/local/cuda/include -isystem /home/mazhaojia/pkg/miniconda3/envs/7net-cueq/include/python3.10 -D_GLIBCXX_USE_CXX11_ABI=0 -D__CUDA_NO_HALF_OPERATORS__ -D__CUDA_NO_HALF_CONVERSIONS__ -D__CUDA_NO_BFLOAT16_CONVERSIONS__ -D__CUDA_NO_HALF2_OPERATORS__ --expt-relaxed-constexpr -gencode=arch=compute_61,code=sm_61 -gencode=arch=compute_70,code=sm_70 -gencode=arch=compute_75,code=sm_75 -gencode=arch=compute_80,code=sm_80 -gencode=arch=compute_86,code=sm_86 -gencode=arch=compute_89,code=sm_89 -gencode=arch=compute_90,code=sm_90 --compiler-options '-fPIC' -O3 --expt-relaxed-constexpr -fmad=false -std=c++17 -cuda_post_cflags = -cuda_dlink_post_cflags = -ldflags = -shared -L/home/mazhaojia/pkg/miniconda3/envs/7net-cueq/lib/python3.10/site-packages/torch/lib -lc10 -lc10_cuda -ltorch_cpu -ltorch_cuda -ltorch -ltorch_python -L/usr/local/cuda/lib64 -lcudart - -rule compile - command = $cxx -MMD -MF $out.d $cflags -c $in -o $out $post_cflags - depfile = $out.d - deps = gcc - -rule cuda_compile - depfile = $out.d - deps = gcc - command = $nvcc --generate-dependencies-with-compile --dependency-output $out.d $cuda_cflags -c $in -o $out $cuda_post_cflags - - - -rule link - command = $cxx $in $ldflags -o $out - -build pair_d3_for_ase.cuda.o: cuda_compile /home/mazhaojia/mace-project/mace-bench/3rdparty/SevenNet/sevenn/pair_e3gnn/pair_d3_for_ase.cu - - - -build pair_d3.so: link pair_d3_for_ase.cuda.o - -default pair_d3.so diff --git a/mace-bench/3rdparty/SevenNet/sevenn/calculator.py b/mace-bench/3rdparty/SevenNet/sevenn/calculator.py deleted file mode 100644 index e237886bd9bac00bab902219c8bba16f6c5991b4..0000000000000000000000000000000000000000 --- a/mace-bench/3rdparty/SevenNet/sevenn/calculator.py +++ /dev/null @@ -1,846 +0,0 @@ -import ctypes -import os -import pathlib -import warnings -from typing import Any, Dict, Optional, Union - -import numpy as np -import torch -import torch.jit -import torch.jit._script -from ase.calculators.calculator import Calculator, all_changes -from ase.calculators.mixing import SumCalculator -from ase.data import chemical_symbols - -import sevenn._keys as KEY -import sevenn.util as util -from sevenn.atom_graph_data import AtomGraphData -from sevenn.nn.sequential import AtomGraphSequential -from sevenn.train.dataload import unlabeled_atoms_to_graph -import logging - -torch_script_type = torch.jit._script.RecursiveScriptModule - - -class SevenNetCalculator(Calculator): - """Supporting properties: - 'free_energy', 'energy', 'forces', 'stress', 'energies' - free_energy equals energy. 'energies' stores atomic energy. - - Multi-GPU acceleration is not supported with ASE calculator. - You should use LAMMPS for the acceleration. - """ - - def __init__( - self, - model: Union[str, pathlib.PurePath, AtomGraphSequential] = '7net-0', - file_type: str = 'checkpoint', - device: Union[torch.device, str] = 'auto', - modal: Optional[str] = None, - enable_cueq: bool = False, - sevennet_config: Optional[Dict] = None, # Not used in logic, just meta info - **kwargs, - ): - """Initialize SevenNetCalculator. - - Parameters - ---------- - model: str | Path | AtomGraphSequential, default='7net-0' - Name of pretrained models (7net-mf-ompa, 7net-omat, 7net-l3i5, 7net-0) or - path to the checkpoint, deployed model or the model itself - file_type: str, default='checkpoint' - one of 'checkpoint' | 'torchscript' | 'model_instance' - device: str | torch.device, default='auto' - if not given, use CUDA if available - modal: str | None, default=None - modal (fidelity) if given model is multi-modal model. for 7net-mf-ompa, - it should be one of 'mpa' (MPtrj + sAlex) or 'omat24' (OMat24) - case insensitive - enable_cueq: bool, default=False - if True, use cuEquivariant to accelerate inference. - sevennet_config: dict | None, default=None - Not used, but can be used to carry meta information of this calculator - """ - print("&&& Initializing SevenNetCalculator") - super().__init__(**kwargs) - self.sevennet_config = None - - if isinstance(model, pathlib.PurePath): - model = str(model) - - allowed_file_types = ['checkpoint', 'torchscript', 'model_instance'] - file_type = file_type.lower() - if file_type not in allowed_file_types: - raise ValueError(f'file_type not in {allowed_file_types}') - - if enable_cueq and file_type in ['model_instance', 'torchscript']: - warnings.warn( - 'file_type should be checkpoint to enable cueq. cueq set to False' - ) - enable_cueq = False - - if isinstance(device, str): # TODO: do we really need this? - if device == 'auto': - self.device = torch.device( - 'cuda' if torch.cuda.is_available() else 'cpu' - ) - else: - self.device = torch.device(device) - else: - self.device = device - - if file_type == 'checkpoint' and isinstance(model, str): - cp = util.load_checkpoint(model) - - backend = 'e3nn' if not enable_cueq else 'cueq' - model_loaded = cp.build_model(backend) - model_loaded.set_is_batch_data(False) - - self.type_map = cp.config[KEY.TYPE_MAP] - self.cutoff = cp.config[KEY.CUTOFF] - self.sevennet_config = cp.config - - elif file_type == 'torchscript' and isinstance(model, str): - if modal: - raise NotImplementedError() - extra_dict = { - 'chemical_symbols_to_index': b'', - 'cutoff': b'', - 'num_species': b'', - 'model_type': b'', - 'version': b'', - 'dtype': b'', - 'time': b'', - } - model_loaded = torch.jit.load( - model, _extra_files=extra_dict, map_location=self.device - ) - chem_symbols = extra_dict['chemical_symbols_to_index'].decode('utf-8') - sym_to_num = {sym: n for n, sym in enumerate(chemical_symbols)} - self.type_map = { - sym_to_num[sym]: i for i, sym in enumerate(chem_symbols.split()) - } - self.cutoff = float(extra_dict['cutoff'].decode('utf-8')) - - elif isinstance(model, AtomGraphSequential): - if model.type_map is None: - raise ValueError( - 'Model must have the type_map to be used with calculator' - ) - if model.cutoff == 0.0: - raise ValueError('Model cutoff seems not initialized') - model.eval_type_map = torch.tensor(True) # ? - model.set_is_batch_data(False) - model_loaded = model - self.type_map = model.type_map - self.cutoff = model.cutoff - else: - raise ValueError('Unexpected input combinations') - - if self.sevennet_config is None and sevennet_config is not None: - self.sevennet_config = sevennet_config - - self.model = model_loaded - - self.modal = None - if isinstance(self.model, AtomGraphSequential): - modal_map = self.model.modal_map - if modal_map: - modal_ava = list(modal_map.keys()) - if not modal: - raise ValueError(f'modal argument missing (avail: {modal_ava})') - elif modal not in modal_ava: - raise ValueError(f'unknown modal {modal} (not in {modal_ava})') - self.modal = modal - elif not self.model.modal_map and modal: - warnings.warn(f'modal={modal} is ignored as model has no modal_map') - - self.model.to(self.device) - self.model.eval() - self.implemented_properties = [ - 'free_energy', - 'energy', - 'forces', - 'stress', - 'energies', - ] - - def set_atoms(self, atoms): - # called by ase, when atoms.calc = calc - zs = tuple(set(atoms.get_atomic_numbers())) - for z in zs: - if z not in self.type_map: - sp = list(self.type_map.keys()) - raise ValueError( - f'Model do not know atomic number: {z}, (knows: {sp})' - ) - - def output_to_results(self, output): - energy = output[KEY.PRED_TOTAL_ENERGY].detach().cpu().item() - num_atoms = output['num_atoms'].item() - atomic_energies = output[KEY.ATOMIC_ENERGY].detach().cpu().numpy().flatten() - forces = output[KEY.PRED_FORCE].detach().cpu().numpy()[:num_atoms, :] - stress = np.array( - (-output[KEY.PRED_STRESS]) - .detach() - .cpu() - .numpy()[[0, 1, 2, 4, 5, 3]] # as voigt notation - ) - # Store results - return { - 'free_energy': energy, - 'energy': energy, - 'energies': atomic_energies, - 'forces': forces, - 'stress': stress, - 'num_edges': output[KEY.EDGE_IDX].shape[1], - } - - def calculate(self, atoms=None, properties=None, system_changes=all_changes): - # call parent class to set necessary atom attributes - Calculator.calculate(self, atoms, properties, system_changes) - if atoms is None: - raise ValueError('No atoms to evaluate') - data = AtomGraphData.from_numpy_dict( - unlabeled_atoms_to_graph(atoms, self.cutoff) - ) - if self.modal: - data[KEY.DATA_MODALITY] = self.modal - - data.to(self.device) # type: ignore - - if isinstance(self.model, torch_script_type): - data[KEY.NODE_FEATURE] = torch.tensor( - [self.type_map[z.item()] for z in data[KEY.NODE_FEATURE]], - dtype=torch.int64, - device=self.device, - ) - data[KEY.POS].requires_grad_(True) # backward compatibility - data[KEY.EDGE_VEC].requires_grad_(True) # backward compatibility - data = data.to_dict() - del data['data_info'] - - import logging - logging.debug(f"data: {data}") - # logging.debug(f"data[pos]: {data['pos']}") - # logging.debug(f"data[x]: {data['x']}") - logging.debug(f"data[cell_lattice_vectors]: {data['cell_lattice_vectors']}") - logging.debug(f"data[cell_volume]: {data['cell_volume']}") - output = self.model(data) - # logging.info(f"input: {data}") - # logging.info(f"output[{KEY.PRED_TOTAL_ENERGY}] = {output[KEY.PRED_TOTAL_ENERGY]}") - # logging.info(f"output[{KEY.PRED_FORCE}] = {output[KEY.PRED_FORCE]}") - # logging.info(f"output[{KEY.PRED_STRESS}] = {output[KEY.PRED_STRESS]}") - self.results = self.output_to_results(output) - # logging.debug(f"results['energy'] = {self.results['energy']}") - # logging.debug(f"results['forces'] = {self.results['forces']}") - # logging.debug(f"results['stress'] = {self.results['stress']}") - - def predict_one(self, atoms): - if atoms is None: - raise ValueError('No atoms to evaluate') - data = AtomGraphData.from_numpy_dict( - unlabeled_atoms_to_graph(atoms, self.cutoff) - ) - if self.modal: - data[KEY.DATA_MODALITY] = self.modal - - data.to(self.device) # type: ignore - - if isinstance(self.model, torch_script_type): - data[KEY.NODE_FEATURE] = torch.tensor( - [self.type_map[z.item()] for z in data[KEY.NODE_FEATURE]], - dtype=torch.int64, - device=self.device, - ) - data[KEY.POS].requires_grad_(True) # backward compatibility - data[KEY.EDGE_VEC].requires_grad_(True) # backward compatibility - data = data.to_dict() - del data['data_info'] - - return self.model(data) - - - - def predict(self, atoms_list, properties=None): - - # if len(atoms_list) == 1: - # output = self.predict_one(atoms_list[0]) - # predictions = {} - # predictions['energy'] = output[KEY.PRED_TOTAL_ENERGY].to(torch.float64).unsqueeze(0) - # predictions['forces'] = output[KEY.PRED_FORCE].to(torch.float64).unsqueeze(0) - # voigt = (-output[KEY.PRED_STRESS])[[0, 1, 2, 4, 5, 3]].to(torch.float64).unsqueeze(0) - # stress_list = [] - # for i in range(voigt.shape[0]): - # stress_list.append(self._stress2tensor(voigt[i,:])) - # predictions['stress'] = torch.stack(stress_list, dim=0).view(-1,3,3) - # return predictions - - - if not atoms_list: - raise ValueError("Empty atoms_list provided") - - if not isinstance(atoms_list, list): - atoms_list = [atoms_list] - - # Convert atoms to graph data - graph_list = [] - for atoms in atoms_list: - data = AtomGraphData.from_numpy_dict( - unlabeled_atoms_to_graph(atoms, self.cutoff) - ) - if self.modal: - data[KEY.DATA_MODALITY] = self.modal - - if isinstance(self.model, torch_script_type): - data[KEY.NODE_FEATURE] = torch.tensor( - [self.type_map[z.item()] for z in data[KEY.NODE_FEATURE]], - dtype=torch.int64, - device=self.device, - ) - data[KEY.POS].requires_grad_(True) # backward compatibility - data[KEY.EDGE_VEC].requires_grad_(True) # backward compatibility - - graph_list.append(data) - - # Process graphs based on model type - # was_batch_mode = True - if isinstance(self.model, AtomGraphSequential): - # was_batch_mode = self.model.is_batch_data - self.model.set_is_batch_data(True) - self.model.eval() - - # Batch the data if there are multiple atoms - from torch_geometric.loader.dataloader import Collater - batched_data = Collater(graph_list)(graph_list) - batched_data = batched_data.to(self.device) - - import logging - logging.debug(f"batched_data: {batched_data}") - # logging.debug(f"batched_data[pos]: {batched_data['pos']}") - # logging.debug(f"batched_data[x]: {batched_data['x']}") - logging.debug(f"batched_data[cell_lattice_vectors]: {batched_data['cell_lattice_vectors']}") - logging.debug(f"batched_data[cell_volume]: {batched_data['cell_volume']}") - # Run model on batched data - if isinstance(self.model, torch_script_type): - batched_dict = batched_data.to_dict() - if 'data_info' in batched_dict: - del batched_dict['data_info'] - output = self.model(batched_dict) - else: - output = self.model(batched_data) - - # Convert to list of individual outputs using util.to_atom_graph_list - # logging.info(f"input: {batched_data}") - # logging.info(f"output[{KEY.PRED_TOTAL_ENERGY}] = {output[KEY.PRED_TOTAL_ENERGY]}") - # logging.info(f"output[{KEY.PRED_FORCE}] = {output[KEY.PRED_FORCE]}") - # logging.info(f"output[{KEY.PRED_STRESS}] = {output[KEY.PRED_STRESS]}") - - predictions = {} - predictions['energy'] = output[KEY.PRED_TOTAL_ENERGY].to(torch.float64).detach() - predictions['forces'] = output[KEY.PRED_FORCE].to(torch.float64).detach() - voigt = (-output[KEY.PRED_STRESS])[:, [0, 1, 2, 4, 5, 3]].to(torch.float64).detach() - stress_list = [] - for i in range(voigt.shape[0]): - stress_list.append(self._stress2tensor(voigt[i,:])) - predictions['stress'] = torch.stack(stress_list, dim=0).view(-1,3,3).detach() - - # logging.debug(f"predictions['energy'] = {predictions['energy']}") - # logging.debug(f"predictions['forces'] = {predictions['forces']}") - # logging.debug(f"predictions['stress'] = {predictions['stress']}") - return predictions - - def _stress2tensor(self, stress): - tensor = torch.tensor( - [ - [stress[0], stress[5], stress[4]], - [stress[5], stress[1], stress[3]], - [stress[4], stress[3], stress[2]], - ], - device=self.device - ) - return tensor - - -class SevenNetD3Calculator(SumCalculator): - def __init__( - self, - model: Union[str, pathlib.PurePath, AtomGraphSequential] = '7net-0', - file_type: str = 'checkpoint', - device: Union[torch.device, str] = 'auto', - sevennet_config: Optional[Any] = None, # hold meta information - damping_type: str = 'damp_bj', - functional_name: str = 'pbe', - vdw_cutoff: float = 9000, # au^2, 0.52917726 angstrom = 1 au - cn_cutoff: float = 1600, # au^2, 0.52917726 angstrom = 1 au - batch_size=10, - **kwargs, - ): - """Initialize SevenNetD3Calculator. CUDA required. - - Parameters - ---------- - model: str | Path | AtomGraphSequential - Name of pretrained models (7net-mf-ompa, 7net-omat, 7net-l3i5, 7net-0) or - path to the checkpoint, deployed model or the model itself - file_type: str, default='checkpoint' - one of 'checkpoint' | 'torchscript' | 'model_instance' - device: str | torch.device, default='auto' - if not given, use CUDA if available - modal: str | None, default=None - modal (fidelity) if given model is multi-modal model. for 7net-mf-ompa, - it should be one of 'mpa' (MPtrj + sAlex) or 'omat24' (OMat24) - enable_cueq: bool, default=False - if True, use cuEquivariant to accelerate inference. - damping_type: str, default='damp_bj' - Damping type of D3, one of 'damp_bj' | 'damp_zero' - functional_name: str, default='pbe' - Target functional name of D3 parameters. - vdw_cutoff: float, default=9000 - vdw cutoff of D3 calculator in au - cn_cutoff: float, default=1600 - cn cutoff of D3 calculator in au - """ - self.d3_calc = D3Calculator( - damping_type=damping_type, - functional_name=functional_name, - vdw_cutoff=vdw_cutoff, - cn_cutoff=cn_cutoff, - **kwargs, - ) - - self.sevennet_calc = SevenNetCalculator( - model=model, - file_type=file_type, - device=device, - sevennet_config=sevennet_config, - **kwargs, - ) - - super().__init__([self.sevennet_calc, self.d3_calc]) - - self.device = device - self.d3_calcs = [] - for _ in range(batch_size): - self.d3_calcs.append( - D3Calculator( - damping_type=damping_type, - functional_name=functional_name, - vdw_cutoff=vdw_cutoff, - cn_cutoff=cn_cutoff, - **kwargs, - ) - ) - - - def predict(self, atoms_list): - """Predict the energy and forces for a list of atoms. - """ - # Call the predict method of the first calculator (SevenNetCalculator) - predictions = self.sevennet_calc.predict(atoms_list) - - energy_list = [] - forces_list = [] - stress_list = [] - predictions3d = {} - for i, atoms in enumerate(atoms_list): - prediction = self.d3_calcs[i].predict_one(atoms) - energy_list.append(torch.tensor(prediction['energy'])) - forces_list.append(torch.from_numpy(prediction['forces']).to(self.device)) - stress_list.append(self._stress2tensor(torch.from_numpy(prediction['stress']))) - - # Convert lists to tensors - predictions3d['energy'] = torch.stack(energy_list, dim=0).to(self.device) - predictions3d['forces'] = torch.cat(forces_list, dim=0).view(-1, 3) - predictions3d['stress'] = torch.stack(stress_list, dim=0).view(-1, 3, 3) - - predictions['energy'] += predictions3d['energy'].detach() - predictions['forces'] += predictions3d['forces'].detach() - predictions['stress'] += predictions3d['stress'].detach() - - return predictions - - def _stress2tensor(self, stress): - tensor = torch.tensor( - [ - # [stress[0], stress[3], stress[4]], - # [stress[3], stress[1], stress[5]], - # [stress[4], stress[5], stress[2]], - [stress[0], stress[5], stress[4]], - [stress[5], stress[1], stress[3]], - [stress[4], stress[3], stress[2]], - ], - device=self.device - ) - return tensor - - - -def _load(name: str) -> ctypes.CDLL: - from torch.utils.cpp_extension import LIB_EXT, _get_build_directory, load - - # Load the library from the candidate locations - - package_dir = os.path.dirname(os.path.abspath(__file__)) - try: - return ctypes.CDLL(os.path.join(package_dir, f'{name}{LIB_EXT}')) - except OSError: - pass - - cache_dir = _get_build_directory(name, verbose=False) - try: - return ctypes.CDLL(os.path.join(cache_dir, f'{name}{LIB_EXT}')) - except OSError: - pass - - # Compile the library if it is not found - - if os.access(package_dir, os.W_OK): - compile_dir = package_dir - else: - print('Warning: package directory is not writable. Using cache directory.') - compile_dir = cache_dir - - if 'TORCH_CUDA_ARCH_LIST' not in os.environ: - print('Warning: TORCH_CUDA_ARCH_LIST is not set.') - print('Warning: Use default CUDA architectures: 61, 70, 75, 80, 86, 89, 90') - os.environ['TORCH_CUDA_ARCH_LIST'] = '6.1;7.0;7.5;8.0;8.6;8.9;9.0' - - load( - name=name, - sources=[os.path.join(package_dir, 'pair_e3gnn', 'pair_d3_for_ase.cu')], - extra_cuda_cflags=['-O3', '--expt-relaxed-constexpr', '-fmad=false'], - build_directory=compile_dir, - verbose=True, - is_python_module=False, - ) - - return ctypes.CDLL(os.path.join(compile_dir, f'{name}{LIB_EXT}')) - - -class PairD3(ctypes.Structure): - pass # Opaque structure; only used as a pointer - - -class D3Calculator(Calculator): - """ASE calculator for accelerated D3 van der Waals (vdW) correction. - - Example: - from ase.calculators.mixing import SumCalculator - calc_1 = SevenNetCalculator() - calc_2 = D3Calculator() - return SumCalculator([calc_1, calc_2]) - - This calculator interfaces with the `libpaird3.so` library, - which is compiled by nvcc during the package installation. - If you encounter any errors, please verify - the installation process and the compilation options in `setup.py`. - Note: Multi-GPU parallel MD is not supported in this mode. - Note: Cffi could be used, but it was avoided to reduce dependencies. - """ - - # Here, free_energy = energy - implemented_properties = ['free_energy', 'energy', 'forces', 'stress'] - - def __init__( - self, - damping_type: str = 'damp_bj', # damp_bj, damp_zero - functional_name: str = 'pbe', # check the source code - vdw_cutoff: float = 9000, # au^2, 0.52917726 angstrom = 1 au - cn_cutoff: float = 1600, # au^2, 0.52917726 angstrom = 1 au - **kwargs, - ): - super().__init__(**kwargs) - - if not torch.cuda.is_available(): - raise NotImplementedError('CPU + D3 is not implemented yet') - - self.rthr = vdw_cutoff - self.cnthr = cn_cutoff - self.damp_name = damping_type.lower() - self.func_name = functional_name.lower() - - if self.damp_name not in ['damp_bj', 'damp_zero']: - raise ValueError('Error: Invalid damping type.') - - self._lib = _load('pair_d3') - - self._lib.pair_init.restype = ctypes.POINTER(PairD3) - self.pair = self._lib.pair_init() - - self._lib.pair_set_atom.argtypes = [ - ctypes.POINTER(PairD3), # PairD3* pair - ctypes.c_int, # int natoms - ctypes.c_int, # int ntypes - ctypes.POINTER(ctypes.c_int), # int* types - ctypes.POINTER(ctypes.c_double), # double* x - ] - self._lib.pair_set_atom.restype = None - - self._lib.pair_set_domain.argtypes = [ - ctypes.POINTER(PairD3), # PairD3* pair - ctypes.c_int, # int xperiodic - ctypes.c_int, # int yperiodic - ctypes.c_int, # int zperiodic - ctypes.POINTER(ctypes.c_double), # double* boxlo - ctypes.POINTER(ctypes.c_double), # double* boxhi - ctypes.c_double, # double xy - ctypes.c_double, # double xz - ctypes.c_double, # double yz - ] - self._lib.pair_set_domain.restype = None - - self._lib.pair_run_settings.argtypes = [ - ctypes.POINTER(PairD3), # PairD3* pair - ctypes.c_double, # double rthr - ctypes.c_double, # double cnthr - ctypes.c_char_p, # const char* damp_name - ctypes.c_char_p, # const char* func_name - ] - self._lib.pair_run_settings.restype = None - - self._lib.pair_run_coeff.argtypes = [ - ctypes.POINTER(PairD3), # PairD3* pair - ctypes.POINTER(ctypes.c_int), # int* atomic_numbers - ] - self._lib.pair_run_coeff.restype = None - - self._lib.pair_run_compute.argtypes = [ctypes.POINTER(PairD3)] - self._lib.pair_run_compute.restype = None - - self._lib.pair_get_energy.argtypes = [ctypes.POINTER(PairD3)] - self._lib.pair_get_energy.restype = ctypes.c_double - - self._lib.pair_get_force.argtypes = [ctypes.POINTER(PairD3)] - self._lib.pair_get_force.restype = ctypes.POINTER(ctypes.c_double) - - self._lib.pair_get_stress.argtypes = [ctypes.POINTER(PairD3)] - self._lib.pair_get_stress.restype = ctypes.POINTER(ctypes.c_double * 6) - - self._lib.pair_fin.argtypes = [ctypes.POINTER(PairD3)] - self._lib.pair_fin.restype = None - - def _idx_to_numbers(self, Z_of_atoms): - unique_numbers = list(dict.fromkeys(Z_of_atoms)) - return unique_numbers - - def _idx_to_types(self, Z_of_atoms): - unique_numbers = list(dict.fromkeys(Z_of_atoms)) - mapping = {num: idx + 1 for idx, num in enumerate(unique_numbers)} - atom_types = [mapping[num] for num in Z_of_atoms] - return atom_types - - def _convert_domain_ase2lammps(self, cell): - qtrans, ltrans = np.linalg.qr(cell.T, mode='complete') - lammps_cell = ltrans.T - signs = np.sign(np.diag(lammps_cell)) - lammps_cell = lammps_cell * signs - qtrans = qtrans * signs - lammps_cell = lammps_cell[(0, 1, 2, 1, 2, 2), (0, 1, 2, 0, 0, 1)] - rotator = qtrans.T - return lammps_cell, rotator - - def _stress2tensor(self, stress): - tensor = np.array( - [ - [stress[0], stress[3], stress[4]], - [stress[3], stress[1], stress[5]], - [stress[4], stress[5], stress[2]], - ] - ) - return tensor - - def _tensor2stress(self, tensor): - stress = -np.array( - [ - tensor[0, 0], - tensor[1, 1], - tensor[2, 2], - tensor[1, 2], - tensor[0, 2], - tensor[0, 1], - ] - ) - return stress - - def calculate(self, atoms=None, properties=None, system_changes=all_changes): - Calculator.calculate(self, atoms, properties, system_changes) - if atoms is None: - raise ValueError('No atoms to evaluate') - - if atoms.get_cell().sum() == 0: - print( - 'Warning: D3Calculator requires a cell.\n' - 'Warning: An orthogonal cell large enough is generated.' - ) - positions = atoms.get_positions() - min_pos = positions.min(axis=0) - max_pos = positions.max(axis=0) - max_cutoff = np.sqrt(max(self.rthr, self.cnthr)) * 0.52917726 - - cell_lengths = max_pos - min_pos + max_cutoff + 1.0 # extra margin - cell = np.eye(3) * cell_lengths - - atoms.set_cell(cell) - atoms.set_pbc([True, True, True]) # for minus positions - - cell, rotator = self._convert_domain_ase2lammps(atoms.get_cell()) - - Z_of_atoms = atoms.get_atomic_numbers() - natoms = len(atoms) - ntypes = len(set(Z_of_atoms)) - types = (ctypes.c_int * natoms)(*self._idx_to_types(Z_of_atoms)) - - positions = atoms.get_positions() @ rotator.T - x_flat = (ctypes.c_double * (natoms * 3))(*positions.flatten()) - - atomic_numbers = (ctypes.c_int * ntypes)(*self._idx_to_numbers(Z_of_atoms)) - - boxlo = (ctypes.c_double * 3)(0.0, 0.0, 0.0) - boxhi = (ctypes.c_double * 3)(cell[0], cell[1], cell[2]) - xy = cell[3] - xz = cell[4] - yz = cell[5] - xperiodic, yperiodic, zperiodic = atoms.get_pbc() - - lib = self._lib - assert lib is not None - lib.pair_set_atom(self.pair, natoms, ntypes, types, x_flat) - - xperiodic = xperiodic.astype(int) - yperiodic = yperiodic.astype(int) - zperiodic = zperiodic.astype(int) - lib.pair_set_domain( - self.pair, xperiodic, yperiodic, zperiodic, boxlo, boxhi, xy, xz, yz - ) - - lib.pair_run_settings( - self.pair, - self.rthr, - self.cnthr, - self.damp_name.encode('utf-8'), - self.func_name.encode('utf-8'), - ) - - lib.pair_run_coeff(self.pair, atomic_numbers) - lib.pair_run_compute(self.pair) - - result_E = lib.pair_get_energy(self.pair) - - result_F_ptr = lib.pair_get_force(self.pair) - result_F_size = natoms * 3 - result_F = np.ctypeslib.as_array( - result_F_ptr, shape=(result_F_size,) - ).reshape((natoms, 3)) - result_F = np.array(result_F) - result_F = result_F @ rotator - - result_S = lib.pair_get_stress(self.pair) - result_S = np.array(result_S.contents) - result_S = ( - self._tensor2stress(rotator.T @ self._stress2tensor(result_S) @ rotator) - / atoms.get_volume() - ) - - self.results = { - 'free_energy': result_E, - 'energy': result_E, - 'forces': result_F, - 'stress': result_S, - } - - def predict_one(self, atoms): - atoms = atoms.copy() - if atoms is None: - raise ValueError('No atoms to evaluate') - - if atoms.get_cell().sum() == 0: - print( - 'Warning: D3Calculator requires a cell.\n' - 'Warning: An orthogonal cell large enough is generated.' - ) - positions = atoms.get_positions() - min_pos = positions.min(axis=0) - max_pos = positions.max(axis=0) - max_cutoff = np.sqrt(max(self.rthr, self.cnthr)) * 0.52917726 - - cell_lengths = max_pos - min_pos + max_cutoff + 1.0 # extra margin - cell = np.eye(3) * cell_lengths - - atoms.set_cell(cell) - atoms.set_pbc([True, True, True]) # for minus positions - - cell, rotator = self._convert_domain_ase2lammps(atoms.get_cell()) - - Z_of_atoms = atoms.get_atomic_numbers() - natoms = len(atoms) - ntypes = len(set(Z_of_atoms)) - types = (ctypes.c_int * natoms)(*self._idx_to_types(Z_of_atoms)) - - positions = atoms.get_positions() @ rotator.T - x_flat = (ctypes.c_double * (natoms * 3))(*positions.flatten()) - - atomic_numbers = (ctypes.c_int * ntypes)(*self._idx_to_numbers(Z_of_atoms)) - - boxlo = (ctypes.c_double * 3)(0.0, 0.0, 0.0) - boxhi = (ctypes.c_double * 3)(cell[0], cell[1], cell[2]) - xy = cell[3] - xz = cell[4] - yz = cell[5] - xperiodic, yperiodic, zperiodic = atoms.get_pbc() - - lib = self._lib - assert lib is not None - lib.pair_set_atom(self.pair, natoms, ntypes, types, x_flat) - - xperiodic = xperiodic.astype(int) - yperiodic = yperiodic.astype(int) - zperiodic = zperiodic.astype(int) - lib.pair_set_domain( - self.pair, xperiodic, yperiodic, zperiodic, boxlo, boxhi, xy, xz, yz - ) - - lib.pair_run_settings( - self.pair, - self.rthr, - self.cnthr, - self.damp_name.encode('utf-8'), - self.func_name.encode('utf-8'), - ) - - lib.pair_run_coeff(self.pair, atomic_numbers) - lib.pair_run_compute(self.pair) - - result_E = lib.pair_get_energy(self.pair) - - result_F_ptr = lib.pair_get_force(self.pair) - result_F_size = natoms * 3 - result_F = np.ctypeslib.as_array( - result_F_ptr, shape=(result_F_size,) - ).reshape((natoms, 3)) - result_F = np.array(result_F) - result_F = result_F @ rotator - - result_S = lib.pair_get_stress(self.pair) - result_S = np.array(result_S.contents) - result_S = ( - self._tensor2stress(rotator.T @ self._stress2tensor(result_S) @ rotator) - / atoms.get_volume() - ) - - prediction = { - 'free_energy': float(result_E), - 'energy': float(result_E), - 'forces': result_F.copy(), - 'stress': result_S.copy(), - } - - return prediction - - - def __del__(self): - if self._lib is not None: - self._lib.pair_fin(self.pair) - self._lib = None - self.pair = None - diff --git a/mace-bench/3rdparty/SevenNet/sevenn/checkpoint.py b/mace-bench/3rdparty/SevenNet/sevenn/checkpoint.py deleted file mode 100644 index 9d8e2846e21ef48ed12e2e1c8a2b3f367ad18752..0000000000000000000000000000000000000000 --- a/mace-bench/3rdparty/SevenNet/sevenn/checkpoint.py +++ /dev/null @@ -1,552 +0,0 @@ -import os -import pathlib -import uuid -import warnings -from copy import deepcopy -from datetime import datetime -from typing import Any, Dict, Optional, Union - -import pandas as pd -from packaging.version import Version -from torch import Tensor -from torch import load as torch_load - -import sevenn -import sevenn._const as consts -import sevenn._keys as KEY -import sevenn.scripts.backward_compatibility as compat -from sevenn import model_build -from sevenn.nn.scale import get_resolved_shift_scale -from sevenn.nn.sequential import AtomGraphSequential - - -def assert_atoms(atoms1, atoms2, rtol=1e-5, atol=1e-6): - import numpy as np - - def acl(a, b, rtol=rtol, atol=atol): - return np.allclose(a, b, rtol=rtol, atol=atol) - - assert len(atoms1) == len(atoms2) - assert acl(atoms1.get_cell(), atoms2.get_cell()) - assert acl(atoms1.get_potential_energy(), atoms2.get_potential_energy()) - assert acl(atoms1.get_forces(), atoms2.get_forces(), rtol * 10, atol * 10) - assert acl( - atoms1.get_stress(voigt=False), - atoms2.get_stress(voigt=False), - rtol * 10, - atol * 10, - ) - # assert acl(atoms1.get_potential_energies(), atoms2.get_potential_energies()) - - -def copy_state_dict(state_dict) -> dict: - if isinstance(state_dict, dict): - return {key: copy_state_dict(value) for key, value in state_dict.items()} - elif isinstance(state_dict, list): - return [copy_state_dict(item) for item in state_dict] # type: ignore - elif isinstance(state_dict, Tensor): - return state_dict.clone() # type: ignore - else: - # For non-tensor values (e.g., scalars, None), return as-is - return state_dict - - -def _config_cp_routine(config): - cp_ver = Version(config.get('version', None)) - this_ver = Version(sevenn.__version__) - if cp_ver > this_ver: - warnings.warn(f'The checkpoint version ({cp_ver}) is newer than this source' - f'({this_ver}). This may cause unexpected behaviors') - - defaults = {**consts.model_defaults(config)} - config = compat.patch_old_config(config) # type: ignore - - scaler = model_build.init_shift_scale(config) - shift, scale = get_resolved_shift_scale( - scaler, config.get(KEY.TYPE_MAP), config.get(KEY.MODAL_MAP, None) - ) - config['shift'] = shift - config['scale'] = scale - - for k, v in defaults.items(): - if k in config: - continue - if os.getenv('SEVENN_DEBUG', False): - warnings.warn(f'{k} not in config, use default value {v}', UserWarning) - config[k] = v - - for k, v in config.items(): - if isinstance(v, Tensor): - config[k] = v.cpu() - return config - - -def _convert_e3nn_and_cueq(stct_src, stct_dst, src_config, from_cueq): - """ - manually check keys and assert if something unexpected happens - """ - n_layer = src_config['num_convolution_layer'] - - linear_module_names = [ - 'onehot_to_feature_x', - 'reduce_input_to_hidden', - 'reduce_hidden_to_energy', - ] - convolution_module_names = [] - fc_tensor_product_module_names = [] - for i in range(n_layer): - linear_module_names.append(f'{i}_self_interaction_1') - linear_module_names.append(f'{i}_self_interaction_2') - if src_config.get(KEY.SELF_CONNECTION_TYPE) == 'linear': - linear_module_names.append(f'{i}_self_connection_intro') - elif src_config.get(KEY.SELF_CONNECTION_TYPE) == 'nequip': - fc_tensor_product_module_names.append(f'{i}_self_connection_intro') - convolution_module_names.append(f'{i}_convolution') - - # Rule: those keys can be safely ignored before state dict load, - # except for linear.bias. This should be aborted in advance to - # this function. Others are not parameters but constants. - cue_only_linear_followers = ['linear.f.tp.f_fx.module.c'] - e3nn_only_linear_followers = ['linear.bias', 'linear.output_mask'] - ignores_in_linear = cue_only_linear_followers + e3nn_only_linear_followers - - cue_only_conv_followers = [ - 'convolution.f.tp.f_fx.module.c', - 'convolution.f.tp.module.module.f.module.module._f.data', - ] - e3nn_only_conv_followers = [ - 'convolution._compiled_main_left_right._w3j', - 'convolution.weight', - 'convolution.output_mask', - ] - ignores_in_conv = cue_only_conv_followers + e3nn_only_conv_followers - - cue_only_fc_followers = ['fc_tensor_product.f.tp.f_fx.module.c'] - e3nn_only_fc_followers = [ - 'fc_tensor_product.output_mask', - ] - ignores_in_fc = cue_only_fc_followers + e3nn_only_fc_followers - - updated_keys = [] - for k, v in stct_src.items(): - module_name = k.split('.')[0] - flag = False - if module_name in linear_module_names: - for ignore in ignores_in_linear: - if '.'.join([module_name, ignore]) in k: - flag = True - break - if not flag and k == '.'.join([module_name, 'linear.weight']): - updated_keys.append(k) - stct_dst[k] = v.clone().reshape(stct_dst[k].shape) - flag = True - assert flag, f'Unexpected key from linear: {k}' - elif module_name in convolution_module_names: - for ignore in ignores_in_conv: - if '.'.join([module_name, ignore]) in k: - flag = True - break - if not flag and ( - k.startswith(f'{module_name}.weight_nn') - or k == '.'.join([module_name, 'denominator']) - ): - updated_keys.append(k) - stct_dst[k] = v.clone().reshape(stct_dst[k].shape) - flag = True - assert flag, f'Unexpected key from linear: {k}' - elif module_name in fc_tensor_product_module_names: - for ignore in ignores_in_fc: - if '.'.join([module_name, ignore]) in k: - flag = True - break - if not flag and k == '.'.join([module_name, 'fc_tensor_product.weight']): - updated_keys.append(k) - stct_dst[k] = v.clone().reshape(stct_dst[k].shape) - flag = True - assert flag, f'Unexpected key from fc tensor product: {k}' - else: - # assert k in stct_dst - updated_keys.append(k) - stct_dst[k] = v.clone().reshape(stct_dst[k].shape) - - return stct_dst - - -class SevenNetCheckpoint: - """ - Tool box for checkpoint processed from SevenNet. - """ - - def __init__(self, checkpoint_path: Union[pathlib.Path, str]): - self._checkpoint_path = os.path.abspath(checkpoint_path) - self._config = None - self._epoch = None - self._model_state_dict = None - self._optimizer_state_dict = None - self._scheduler_state_dict = None - self._hash = None - self._time = None - - self._loaded = False - - def __repr__(self) -> str: - cfg = self.config # just alias - if len(cfg) == 0: - return '' - dct = { - 'Sevennet version': cfg.get('version', 'Not found'), - 'When': self.time, - 'Hash': self.hash, - 'Cutoff': cfg.get('cutoff'), - 'Channel': cfg.get('channel'), - 'Lmax': cfg.get('lmax'), - 'Group (parity)': 'O3' if cfg.get('is_parity') else 'SO3', - 'Interaction layers': cfg.get('num_convolution_layer'), - 'Self connection type': cfg.get('self_connection_type', 'nequip'), - 'Last epoch': self.epoch, - 'Elements': len(cfg.get('chemical_species', [])), - } - if cfg.get('use_modality', False): - dct['Modality'] = ', '.join(list(cfg.get('_modal_map', {}).keys())) - - df = pd.DataFrame.from_dict([dct]).T # type: ignore - df.columns = [''] - return df.to_string() - - @property - def checkpoint_path(self) -> str: - return str(self._checkpoint_path) - - @property - def config(self) -> Dict[str, Any]: - if not self._loaded: - self._load() - assert isinstance(self._config, dict) - return deepcopy(self._config) - - @property - def model_state_dict(self) -> Dict[str, Any]: - if not self._loaded: - self._load() - assert isinstance(self._model_state_dict, dict) - return copy_state_dict(self._model_state_dict) - - @property - def optimizer_state_dict(self) -> Dict[str, Any]: - if not self._loaded: - self._load() - assert isinstance(self._optimizer_state_dict, dict) - return copy_state_dict(self._optimizer_state_dict) - - @property - def scheduler_state_dict(self) -> Dict[str, Any]: - if not self._loaded: - self._load() - assert isinstance(self._scheduler_state_dict, dict) - return copy_state_dict(self._scheduler_state_dict) - - @property - def epoch(self) -> Optional[int]: - if not self._loaded: - self._load() - return self._epoch - - @property - def time(self) -> str: - if not self._loaded: - self._load() - assert isinstance(self._time, str) - return self._time - - @property - def hash(self) -> str: - if not self._loaded: - self._load() - assert isinstance(self._hash, str) - return self._hash - - def _load(self) -> None: - assert not self._loaded - cp_path = self.checkpoint_path # just alias - - cp = torch_load(cp_path, weights_only=False, map_location='cpu') - self._config_original = cp.get('config', {}) - self._model_state_dict = cp.get('model_state_dict', {}) - self._optimizer_state_dict = cp.get('optimizer_state_dict', {}) - self._scheduler_state_dict = cp.get('scheduler_state_dict', {}) - self._epoch = cp.get('epoch', None) - self._time = cp.get('time', 'Not found') - self._hash = cp.get('hash', 'Not found') - - if len(self._config_original) == 0: - warnings.warn(f'config is not found from {cp_path}') - self._config = {} - else: - self._config = _config_cp_routine(self._config_original) - - if len(self._model_state_dict) == 0: - warnings.warn(f'model_state_dict is not found from {cp_path}') - - self._loaded = True - - def build_model(self, backend: Optional[str] = None) -> AtomGraphSequential: - from .model_build import build_E3_equivariant_model - - use_cue = not backend or backend.lower() in ['cue', 'cueq'] - try: - cp_using_cue = self.config[KEY.CUEQUIVARIANCE_CONFIG]['use'] - except KeyError: - cp_using_cue = False - - if (not backend) or (use_cue == cp_using_cue): - # backend not given, or checkpoint backend is same as requested - model = build_E3_equivariant_model(self.config) - state_dict = compat.patch_state_dict_if_old( - self.model_state_dict, self.config, model - ) - else: - cfg_new = self.config - cfg_new[KEY.CUEQUIVARIANCE_CONFIG] = {'use': use_cue} - model = build_E3_equivariant_model(cfg_new) - stct_src = compat.patch_state_dict_if_old( - self.model_state_dict, self.config, model - ) - state_dict = _convert_e3nn_and_cueq( - stct_src, model.state_dict(), self.config, from_cueq=cp_using_cue - ) - - missing, not_used = model.load_state_dict(state_dict, strict=False) - if len(not_used) > 0: - warnings.warn(f'Some keys are not used: {not_used}', UserWarning) - - assert len(missing) == 0, f'Missing keys: {missing}' - return model - - def yaml_dict(self, mode: str) -> dict: - """ - Return dict for input.yaml from checkpoint config - Dataset paths and statistic values are removed intentionally - """ - if mode not in ['reproduce', 'continue', 'continue_modal']: - raise ValueError(f'Unknown mode: {mode}') - - ignore = [ - 'when', - KEY.DDP_BACKEND, - KEY.LOCAL_RANK, - KEY.IS_DDP, - KEY.DEVICE, - KEY.MODEL_TYPE, - KEY.SHIFT, - KEY.SCALE, - KEY.CONV_DENOMINATOR, - KEY.SAVE_DATASET, - KEY.SAVE_BY_LABEL, - KEY.SAVE_BY_TRAIN_VALID, - KEY.CONTINUE, - KEY.LOAD_DATASET, # old - ] - - cfg = self.config - len_atoms = len(cfg[KEY.TYPE_MAP]) - - world_size = cfg.pop(KEY.WORLD_SIZE, 1) - cfg[KEY.BATCH_SIZE] = cfg[KEY.BATCH_SIZE] * world_size - cfg[KEY.LOAD_TRAINSET] = '**path_to_training_set**' - - major, minor, _ = cfg.pop('version', '0.0.0').split('.')[:3] - if int(major) == 0 and int(minor) <= 9: - warnings.warn('checkpoint version too old, yaml may wrong') - - ret = {'model': {}, 'train': {}, 'data': {}} - for k, v in cfg.items(): - if k.startswith('_') or k in ignore or k.endswith('set_path'): - continue - if k in consts.DEFAULT_E3_EQUIVARIANT_MODEL_CONFIG: - ret['model'][k] = v - elif k in consts.DEFAULT_TRAINING_CONFIG: - ret['train'][k] = v - elif k in consts.DEFAULT_DATA_CONFIG: - ret['data'][k] = v - - ret['model'][KEY.CHEMICAL_SPECIES] = ( - 'univ' if len_atoms == consts.NUM_UNIV_ELEMENT else 'auto' - ) - ret['data'][KEY.LOAD_TRAINSET] = '**path_to_trainset**' - ret['data'][KEY.LOAD_VALIDSET] = '**path_to_validset**' - - # TODO - ret['data'][KEY.SHIFT] = '**failed to infer shift, should be set**' - ret['data'][KEY.SCALE] = '**failed to infer scale, should be set**' - - if mode.startswith('continue'): - ret['train'].update( - {KEY.CONTINUE: {KEY.CHECKPOINT: self.checkpoint_path}} - ) - modal_names = None - if mode == 'continue_modal' and not cfg.get(KEY.USE_MODALITY, False): - ret['train'][KEY.USE_MODALITY] = True - - # suggest defaults - ret['model'][KEY.USE_MODAL_NODE_EMBEDDING] = False - ret['model'][KEY.USE_MODAL_SELF_INTER_INTRO] = True - ret['model'][KEY.USE_MODAL_SELF_INTER_OUTRO] = True - ret['model'][KEY.USE_MODAL_OUTPUT_BLOCK] = True - - ret['data'][KEY.USE_MODAL_WISE_SHIFT] = True - ret['data'][KEY.USE_MODAL_WISE_SCALE] = False - - modal_names = ['my_modal1', 'my_modal2'] - elif cfg.get(KEY.USE_MODALITY, False): - modal_names = list(cfg[KEY.MODAL_MAP].keys()) - - if modal_names: - ret['data'][KEY.LOAD_TRAINSET] = [ - {'data_modality': mm, 'file_list': [{'file': f'**path_to_{mm}**'}]} - for mm in modal_names - ] - - return ret - - def append_modal( - self, - dst_config, - original_modal_name: str = 'origin', - working_dir: str = os.getcwd(), - ): - """ """ - import sevenn.train.modal_dataset as modal_dataset - from sevenn.model_build import init_shift_scale - from sevenn.scripts.convert_model_modality import _append_modal_weight - - src_config = self.config - src_has_no_modal = not src_config.get(KEY.USE_MODALITY, False) - - # inherit element things first - chem_keys = [ - KEY.TYPE_MAP, - KEY.NUM_SPECIES, - KEY.CHEMICAL_SPECIES, - KEY.CHEMICAL_SPECIES_BY_ATOMIC_NUMBER, - ] - dst_config.update({k: src_config[k] for k in chem_keys}) - - if dst_config[KEY.USE_MODAL_WISE_SHIFT] and ( - KEY.SHIFT not in dst_config or not isinstance(dst_config[KEY.SHIFT], str) - ): - raise ValueError('To use modal wise shift, keyword shift is required') - if dst_config[KEY.USE_MODAL_WISE_SCALE] and ( - KEY.SCALE not in dst_config or not isinstance(dst_config[KEY.SCALE], str) - ): - raise ValueError('To use modal wise scale, keyword scale is required') - - if src_has_no_modal and not dst_config[KEY.USE_MODAL_WISE_SHIFT]: - dst_config[KEY.SHIFT] = src_config[KEY.SHIFT] - if src_has_no_modal and not dst_config[KEY.USE_MODAL_WISE_SCALE]: - dst_config[KEY.SCALE] = src_config[KEY.SCALE] - - # get statistics of given datasets of yaml - # dst_config updated - _ = modal_dataset.from_config(dst_config, working_dir=working_dir) - dst_modal_map = dst_config[KEY.MODAL_MAP] - - found_modal_names = list(dst_modal_map.keys()) - if len(found_modal_names) == 0: - raise ValueError('No modality is found from config') - - # Check difference btw given modals and new modal map - orig_modal_map = src_config.get(KEY.MODAL_MAP, {original_modal_name: 0}) - assert isinstance(orig_modal_map, dict) - new_modal_map = orig_modal_map.copy() - for modal_name in found_modal_names: - if modal_name in orig_modal_map: # duplicate, skipping - continue - new_modal_map[modal_name] = len(new_modal_map) # assign new - print(f'New modals: {list(new_modal_map.keys())}') - - if src_has_no_modal: - append_num = len(new_modal_map) - else: - append_num = len(new_modal_map) - len(orig_modal_map) - if append_num == 0: - raise ValueError('Nothing to append from checkpoint') - - dst_config[KEY.NUM_MODALITIES] = len(new_modal_map) - dst_config[KEY.MODAL_MAP] = new_modal_map - - # update dst_config's shift scales based on src_config - for ss_key, use_mw in ( - (KEY.SHIFT, dst_config[KEY.USE_MODAL_WISE_SHIFT]), - (KEY.SCALE, dst_config[KEY.USE_MODAL_WISE_SCALE]), - ): - if not use_mw: # not using mw ss, just assign - assert not isinstance(dst_config[ss_key], dict) - dst_config[ss_key] = src_config[ss_key] - elif src_has_no_modal: - assert isinstance(dst_config[ss_key], dict) - # mw ss, update by dict but use original_modal_name - dst_config[ss_key].update({original_modal_name: src_config[ss_key]}) - else: - assert isinstance(dst_config[ss_key], dict) - # mw ss, update by dict - dst_config[ss_key].update(src_config[ss_key]) - scaler = init_shift_scale(dst_config) - - # finally, prepare updated continuable state dict using above - orig_model = self.build_model() - orig_state_dict = orig_model.state_dict() - - new_state_dict = copy_state_dict(orig_state_dict) - for stct_key in orig_state_dict: - sp = stct_key.split('.') - k, follower = sp[0], '.'.join(sp[1:]) - if k == 'rescale_atomic_energy' and follower == 'shift': - new_state_dict[stct_key] = scaler.shift.clone() - elif k == 'rescale_atomic_energy' and follower == 'scale': - new_state_dict[stct_key] = scaler.scale.clone() - elif follower == 'linear.weight' and ( # append linear layer - ( - dst_config[KEY.USE_MODAL_NODE_EMBEDDING] - and k.endswith('onehot_to_feature_x') - ) - or ( - dst_config[KEY.USE_MODAL_SELF_INTER_INTRO] - and k.endswith('self_interaction_1') - ) - or ( - dst_config[KEY.USE_MODAL_SELF_INTER_OUTRO] - and k.endswith('self_interaction_2') - ) - or ( - dst_config[KEY.USE_MODAL_OUTPUT_BLOCK] - and k == 'reduce_input_to_hidden' - ) - ): - orig_linear = getattr(orig_model._modules[k], 'linear') - # assert normalization element - new_state_dict[stct_key] = _append_modal_weight( - orig_state_dict, - k, - orig_linear.irreps_in, - orig_linear.irreps_out, - append_num, - ) - - dst_config['version'] = sevenn.__version__ - - return new_state_dict - - def get_checkpoint_dict(self) -> dict: - """ - Return duplicate of this checkpoint with new hash and time. - Convenient for creating variant of the checkpoint - """ - return { - 'config': self.config, - 'epoch': self.epoch, - 'model_state_dict': self.model_state_dict, - 'optimizer_state_dict': self.optimizer_state_dict, - 'scheduler_state_dict': self.scheduler_state_dict, - 'time': datetime.now().strftime('%Y-%m-%d %H:%M'), - 'hash': uuid.uuid4().hex, - } diff --git a/mace-bench/3rdparty/SevenNet/sevenn/error_recorder.py b/mace-bench/3rdparty/SevenNet/sevenn/error_recorder.py deleted file mode 100644 index 5999aea48eb6e6d4e45505f294df1a19aabefe4c..0000000000000000000000000000000000000000 --- a/mace-bench/3rdparty/SevenNet/sevenn/error_recorder.py +++ /dev/null @@ -1,430 +0,0 @@ -from copy import deepcopy -from typing import Any, Callable, Dict, List, Optional, Tuple - -import torch -import torch.distributed as dist - -import sevenn._keys as KEY -from sevenn.train.loss import LossDefinition - -from .atom_graph_data import AtomGraphData -from .train.optim import loss_dict - -_ERROR_TYPES = { - 'TotalEnergy': { - 'name': 'Energy', - 'ref_key': KEY.ENERGY, - 'pred_key': KEY.PRED_TOTAL_ENERGY, - 'unit': 'eV', - 'vdim': 1, - }, - 'Energy': { # by default per-atom for energy - 'name': 'Energy', - 'ref_key': KEY.ENERGY, - 'pred_key': KEY.PRED_TOTAL_ENERGY, - 'unit': 'eV/atom', - 'per_atom': True, - 'vdim': 1, - }, - 'Force': { - 'name': 'Force', - 'ref_key': KEY.FORCE, - 'pred_key': KEY.PRED_FORCE, - 'unit': 'eV/Å', - 'vdim': 3, - }, - 'Stress': { - 'name': 'Stress', - 'ref_key': KEY.STRESS, - 'pred_key': KEY.PRED_STRESS, - 'unit': 'kbar', - 'coeff': 1602.1766208, - 'vdim': 6, - }, - 'Stress_GPa': { - 'name': 'Stress', - 'ref_key': KEY.STRESS, - 'pred_key': KEY.PRED_STRESS, - 'unit': 'GPa', - 'coeff': 160.21766208, - 'vdim': 6, - }, - 'TotalLoss': { - 'name': 'TotalLoss', - 'unit': None, - }, -} - - -def get_err_type(name: str) -> Dict[str, Any]: - return deepcopy(_ERROR_TYPES[name]) - - -def _get_loss_function_from_name(loss_functions, name): - for loss_def, w in loss_functions: - if loss_def.name.lower() == name.lower(): - return loss_def, w - return None, None - - -class AverageNumber: - def __init__(self): - self._sum = 0.0 - self._count = 0 - - def update(self, values: torch.Tensor): - self._sum += values.sum().item() - self._count += values.numel() - - def _ddp_reduce(self, device): - _sum = torch.tensor(self._sum, device=device) - _count = torch.tensor(self._count, device=device) - dist.all_reduce(_sum, op=dist.ReduceOp.SUM) - dist.all_reduce(_count, op=dist.ReduceOp.SUM) - self._sum = _sum.item() - self._count = _count.item() - - def get(self): - if self._count == 0: - return torch.nan - return self._sum / self._count - - -class ErrorMetric: - """ - Base class for error metrics We always average error by # of structures, - and designed to collect errors in the middle of iteration (by AverageNumber) - """ - - def __init__( - self, - name: str, - ref_key: str, - pred_key: str, - coeff: float = 1.0, - unit: Optional[str] = None, - per_atom: bool = False, - ignore_unlabeled: bool = True, - **kwargs, - ): - self.name = name - self.unit = unit - self.coeff = coeff - self.ref_key = ref_key - self.pred_key = pred_key - self.per_atom = per_atom - self.ignore_unlabeled = ignore_unlabeled - self.value = AverageNumber() - - def update(self, output: AtomGraphData): - raise NotImplementedError - - def _retrieve(self, output: AtomGraphData): - y_ref = output[self.ref_key] * self.coeff - y_pred = output[self.pred_key] * self.coeff - if self.per_atom: - assert y_ref.dim() == 1 and y_pred.dim() == 1 - natoms = output[KEY.NUM_ATOMS] - y_ref = y_ref / natoms - y_pred = y_pred / natoms - if self.ignore_unlabeled: - unlabelled_idx = torch.isnan(y_ref) - y_ref = y_ref[~unlabelled_idx] - y_pred = y_pred[~unlabelled_idx] - return y_ref, y_pred - - def ddp_reduce(self, device): - self.value._ddp_reduce(device) - - def reset(self): - self.value = AverageNumber() - - def get(self): - return self.value.get() - - def key_str(self, with_unit=True): - if self.unit is None or not with_unit: - return self.name - else: - return f'{self.name} ({self.unit})' - - def __str__(self): - return f'{self.key_str()}: {self.value.get():.6f}' - - -class RMSError(ErrorMetric): - """ - Vector squared error - """ - - def __init__(self, vdim: int = 1, **kwargs): - super().__init__(**kwargs) - self.vdim = vdim - self._se = torch.nn.MSELoss(reduction='none') - - def _square_error(self, y_ref, y_pred, vdim: int): - return self._se(y_ref.view(-1, vdim), y_pred.view(-1, vdim)).sum(dim=1) - - def update(self, output: AtomGraphData): - y_ref, y_pred = self._retrieve(output) - se = self._square_error(y_ref, y_pred, self.vdim) - self.value.update(se) - - def get(self): - return self.value.get() ** 0.5 - - -class ComponentRMSError(ErrorMetric): - """ - Ignore vector dim and just average over components - Results smaller error - """ - - def __init__(self, **kwargs): - super().__init__(**kwargs) - self._se = torch.nn.MSELoss(reduction='none') - - def _square_error(self, y_ref, y_pred): - return self._se(y_ref, y_pred) - - def update(self, output: AtomGraphData): - y_ref, y_pred = self._retrieve(output) - y_ref = y_ref.view(-1) - y_pred = y_pred.view(-1) - se = self._square_error(y_ref, y_pred) - self.value.update(se) - - def get(self): - return self.value.get() ** 0.5 - - -class MAError(ErrorMetric): - """ - Average over all component - """ - - def __init__(self, **kwargs): - super().__init__(**kwargs) - - def _square_error(self, y_ref, y_pred): - return torch.abs(y_ref - y_pred) - - def update(self, output: AtomGraphData): - y_ref, y_pred = self._retrieve(output) - y_ref = y_ref.reshape((-1,)) - y_pred = y_pred.reshape((-1,)) - se = self._square_error(y_ref, y_pred) - self.value.update(se) - - -class CustomError(ErrorMetric): - """ - Custom error metric - Args: - func: a function that takes y_ref and y_pred - and returns a list of errors - """ - - def __init__(self, func: Callable, **kwargs): - super().__init__(**kwargs) - self.func = func - - def update(self, output: AtomGraphData): - y_ref, y_pred = self._retrieve(output) - se = self.func(y_ref, y_pred) if len(y_ref) > 0 else torch.tensor([]) - self.value.update(se) - - -class LossError(ErrorMetric): - """ - Error metric that record loss - """ - - def __init__( - self, - name: str, - loss_def: LossDefinition, - **kwargs, - ): - super().__init__( - name, - ignore_unlabeld=loss_def.ignore_unlabeled, - **kwargs, - ) - self.loss_def = loss_def - - def update(self, output: AtomGraphData): - loss = self.loss_def.get_loss(output) # type: ignore - self.value.update(loss) # type: ignore - - -class CombinedError(ErrorMetric): - """ - Combine multiple error metrics with weights - corresponds to a weighted sum of errors (normally used in loss) - """ - - def __init__(self, metrics: List[Tuple[ErrorMetric, float]], **kwargs): - super().__init__(**kwargs) - self.metrics = metrics - assert kwargs['unit'] is None - - def update(self, output: AtomGraphData): - for metric, _ in self.metrics: - metric.update(output) - - def reset(self): - for metric, _ in self.metrics: - metric.reset() - - def ddp_reduce(self, device): # override - for metric, _ in self.metrics: - metric.value._ddp_reduce(device) - - def get(self): - val = 0.0 - for metric, weight in self.metrics: - val += metric.get() * weight - return val - - -class ErrorRecorder: - """ - record errors of a model - """ - - METRIC_DICT = { - 'RMSE': RMSError, - 'ComponentRMSE': ComponentRMSError, - 'MAE': MAError, - 'Loss': LossError, - } - - def __init__(self, metrics: List[ErrorMetric]): - self.history = [] - self.metrics = metrics - - def _update(self, output: AtomGraphData): - for metric in self.metrics: - metric.update(output) - - def update(self, output: AtomGraphData, no_grad=True): - if no_grad: - with torch.no_grad(): - self._update(output) - else: - self._update(output) - - def get_metric_dict(self, with_unit=True): - return {metric.key_str(with_unit): metric.get() for metric in self.metrics} - - def get_current(self): - dct = {} - for metric in self.metrics: - dct[metric.name] = { - 'value': metric.get(), - 'unit': metric.unit, - 'ref_key': metric.ref_key, - 'pred_key': metric.pred_key, - } - return dct - - def get_dct(self, prefix=''): - dct = {} - if prefix.endswith('_') is False and prefix != '': - prefix = prefix + '_' - for metric in self.metrics: - dct[f'{prefix}{metric.name}'] = f'{metric.get():6f}' - return dct - - def get_key_str(self, name: str): - for metric in self.metrics: - if name == metric.name: - return metric.key_str() - return None - - def epoch_forward(self): - self.history.append(self.get_current()) - pretty = self.get_metric_dict(with_unit=True) - for metric in self.metrics: - metric.reset() - return pretty # for print - - @staticmethod - def init_total_loss_metric( - config, - criteria: Optional[Callable] = None, - loss_functions: Optional[List[Tuple[LossDefinition, float]]] = None, - ): - if criteria is None and loss_functions is None: - raise ValueError('both criteria and loss functions not given') - - is_stress = config[KEY.IS_TRAIN_STRESS] - metrics = [] - if criteria is not None: - energy_metric = CustomError(criteria, **get_err_type('Energy')) - metrics.append((energy_metric, 1)) - force_metric = CustomError(criteria, **get_err_type('Force')) - metrics.append((force_metric, config[KEY.FORCE_WEIGHT])) - if is_stress: - stress_metric = CustomError(criteria, **get_err_type('Stress')) - metrics.append((stress_metric, config[KEY.STRESS_WEIGHT])) - else: # TODO: this is hard-coded - for efs in ['Energy', 'Force', 'Stress']: - if efs == 'Stress' and not is_stress: - continue - lf, w = _get_loss_function_from_name(loss_functions, efs) - if lf is None: - raise ValueError(f'{efs} not found from loss_functions') - metric = LossError(loss_def=lf, **get_err_type(efs)) - metrics.append((metric, w)) - - total_loss_metric = CombinedError( - metrics, name='TotalLoss', unit=None, ref_key=None, pred_key=None - ) - return total_loss_metric - - @staticmethod - def from_config(config: dict, loss_functions=None): - loss_cls = loss_dict[config.get(KEY.LOSS, 'mse').lower()] - loss_param = config.get(KEY.LOSS_PARAM, {}) - criteria = loss_cls(**loss_param) if loss_functions is None else None - - err_config = config.get(KEY.ERROR_RECORD, False) - if not err_config: - raise ValueError( - 'No error_record config found. Consider util.get_error_recorder' - ) - err_config_n = [] - if not config.get(KEY.IS_TRAIN_STRESS, True): - for err_type, metric_name in err_config: - if 'Stress' in err_type: - continue - err_config_n.append((err_type, metric_name)) - err_config = err_config_n - - err_metrics = [] - for err_type, metric_name in err_config: - metric_kwargs = get_err_type(err_type) - if err_type == 'TotalLoss': # special case - err_metrics.append( - ErrorRecorder.init_total_loss_metric( - config, criteria, loss_functions - ) - ) - continue - metric_cls = ErrorRecorder.METRIC_DICT[metric_name] - assert isinstance(metric_kwargs['name'], str) - if metric_name == 'Loss': - if loss_functions is not None: - metric_cls = LossError - metric_kwargs['loss_def'], _ = _get_loss_function_from_name( - loss_functions, metric_kwargs['name'] - ) - else: - metric_cls = CustomError - metric_kwargs['func'] = criteria - metric_kwargs.pop('unit', None) - metric_kwargs['name'] += f'_{metric_name}' - err_metrics.append(metric_cls(**metric_kwargs)) - return ErrorRecorder(err_metrics) diff --git a/mace-bench/3rdparty/SevenNet/sevenn/logger.py b/mace-bench/3rdparty/SevenNet/sevenn/logger.py deleted file mode 100644 index 1c66af8c8e5a47505d4ffbff4fdf1a63cdcd7b7c..0000000000000000000000000000000000000000 --- a/mace-bench/3rdparty/SevenNet/sevenn/logger.py +++ /dev/null @@ -1,336 +0,0 @@ -import os -import time -import traceback -from datetime import datetime -from typing import Any, Dict, List, Optional - -from ase.data import atomic_numbers - -import sevenn._keys as KEY -from sevenn import __version__ - -CHEM_SYMBOLS = {v: k for k, v in atomic_numbers.items()} - - -class Singleton(type): - _instances = {} - - def __call__(cls, *args, **kwargs): - if cls not in cls._instances: - cls._instances[cls] = super(Singleton, cls).__call__(*args, **kwargs) - return cls._instances[cls] - - -class Logger(metaclass=Singleton): - SCREEN_WIDTH = 120 # half size of my screen / changed due to stress output - - def __init__( - self, filename: Optional[str] = None, screen: bool = False, rank: int = 0 - ): - self.rank = rank - self._filename = filename - if rank == 0: - # if filename is not None: - # self.logfile = open(filename, 'a', buffering=1) - self.logfile = None - self.files = {} - self.screen = screen - else: - self.logfile = None - self.screen = False - self.timer_dct = {} - self.active = True - - def __enter__(self): - if self.rank != 0: - return self - if self.logfile is None and self._filename is not None: - try: - self.logfile = open( - self._filename, 'a', buffering=1, encoding='utf-8' - ) - except IOError as e: - print(f'Failed to re-open log file {self._filename}: {e}') - self.logfile = None - self.files = {} - return self - - def __exit__(self, exc_type, exc_value, traceback): - if self.rank != 0: - return self - try: - if self.logfile is not None: - self.logfile.close() - self.logfile = None - for f in self.files.values(): - f.close() - except IOError as e: - print(f'Failed to close log files: {e}') - finally: - self.logfile = None - self.files = {} - - def switch_file(self, new_filename: str): - if self.rank != 0: - return self - if self.logfile is not None: - raise ValueError('Current logfile is not yet closed') - self._filename = new_filename - return self - - def write(self, content: str): - if self.rank != 0: - return - # no newline! - if self.logfile is not None and self.active: - self.logfile.write(content) - if self.screen and self.active: - print(content, end='') - - def writeline(self, content: str): - content = content + '\n' - self.write(content) - - def init_csv(self, filename: str, header: list): - """ - Deprecated - """ - if self.rank == 0: - self.files[filename] = open(filename, 'w', buffering=1, encoding='utf-8') - self.files[filename].write(','.join(header) + '\n') - else: - pass - - def append_csv(self, filename: str, content: list, decimal: int = 6): - """ - Deprecated - """ - if self.rank == 0: - if filename not in self.files: - self.files[filename] = open(filename, 'a', buffering=1) - str_content = [] - for c in content: - if isinstance(c, float): - str_content.append(f'{c:.{decimal}f}') - else: - str_content.append(str(c)) - self.files[filename].write(','.join(str_content) + '\n') - else: - pass - - def natoms_write(self, natoms: Dict[str, Dict]): - content = '' - total_natom = {} - for label, natom in natoms.items(): - content += self.format_k_v(label, natom) - for specie, num in natom.items(): - try: - total_natom[specie] += num - except KeyError: - total_natom[specie] = num - content += self.format_k_v('Total, label wise', total_natom) - content += self.format_k_v('Total', sum(total_natom.values())) - self.write(content) - - def statistic_write(self, statistic: Dict[str, Dict]): - content = '' - for label, dct in statistic.items(): - if label.startswith('_'): - continue - if not isinstance(dct, dict): - continue - dct_new = {} - for k, v in dct.items(): - if k.startswith('_'): - continue - if isinstance(v, int): - dct_new[k] = v - else: - dct_new[k] = f'{v:.3f}' - content += self.format_k_v(label, dct_new) - self.write(content) - - # TODO : refactoring!!!, this is not loss, rmse - def epoch_write_specie_wise_loss(self, train_loss, valid_loss): - lb_pad = 21 - fs = 6 - pad = 21 - fs - ln = '-' * fs - total_atom_type = train_loss.keys() - content = '' - - for at in total_atom_type: - t_F = train_loss[at] - v_F = valid_loss[at] - at_sym = CHEM_SYMBOLS[at] - content += '{label:{lb_pad}}{t_E:<{pad}.{fs}s}{v_E:<{pad}.{fs}s}'.format( - label=at_sym, t_E=ln, v_E=ln, lb_pad=lb_pad, pad=pad, fs=fs - ) + '{t_F:<{pad}.{fs}f}{v_F:<{pad}.{fs}f}'.format( - t_F=t_F, v_F=v_F, pad=pad, fs=fs - ) - content += '{t_S:<{pad}.{fs}s}{v_S:<{pad}.{fs}s}'.format( - t_S=ln, v_S=ln, pad=pad, fs=fs - ) - content += '\n' - self.write(content) - - def write_full_table( - self, - dict_list: List[Dict], - row_labels: List[str], - decimal_places: int = 6, - pad: int = 2, - ): - """ - Assume data_list is list of dict with same keys - """ - assert len(dict_list) == len(row_labels) - label_len = max(map(len, row_labels)) - # Extract the column names and create a 2D array of values - col_names = list(dict_list[0].keys()) - - values = [list(d.values()) for d in dict_list] - - # Format the numbers with the given decimal places - formatted_values = [ - [f'{value:.{decimal_places}f}' for value in row] for row in values - ] - - # Calculate padding lengths for each column (with extra padding) - max_col_lengths = [ - max(len(str(value)) for value in col) + pad - for col in zip(col_names, *formatted_values) - ] - - # Create header row and separator - header = ' ' * (label_len + pad) + ' '.join( - col_name.ljust(pad) for col_name, pad in zip(col_names, max_col_lengths) - ) - separator = '-'.join('-' * pad for pad in max_col_lengths) + '-' * ( - label_len + pad - ) - - # Print header and separator - self.writeline(header) - self.writeline(separator) - - # Print the data rows with row labels - for row_label, row in zip(row_labels, formatted_values): - data_row = ' '.join( - value.rjust(pad) for value, pad in zip(row, max_col_lengths) - ) - self.writeline(f'{row_label.ljust(label_len)}{data_row}') - - def format_k_v(self, key: Any, val: Any, write: bool = False): - """ - key and val should be str convertible - """ - MAX_KEY_SIZE = 20 - SEPARATOR = ', ' - EMPTY_PADDING = ' ' * (MAX_KEY_SIZE + 3) - NEW_LINE_LEN = Logger.SCREEN_WIDTH - 5 - key = str(key) - val = str(val) - content = f'{key:<{MAX_KEY_SIZE}}: {val}' - if len(content) > NEW_LINE_LEN: - content = f'{key:<{MAX_KEY_SIZE}}: ' - # septate val by separator - val_list = val.split(SEPARATOR) - current_len = len(content) - for val_compo in val_list: - current_len += len(val_compo) - if current_len > NEW_LINE_LEN: - newline_content = f'{EMPTY_PADDING}{val_compo}{SEPARATOR}' - content += f'\\\n{newline_content}' - current_len = len(newline_content) - else: - content += f'{val_compo}{SEPARATOR}' - - if content.endswith(f'{SEPARATOR}'): - content = content[: -len(SEPARATOR)] - content += '\n' - - if write is False: - return content - else: - self.write(content) - return '' - - def greeting(self): - LOGO_ASCII_FILE = f'{os.path.dirname(__file__)}/logo_ascii' - with open(LOGO_ASCII_FILE, 'r') as logo_f: - logo_ascii = logo_f.read() - content = 'SevenNet: Scalable EquiVariance-Enabled Neural Network\n' - content += f'version {__version__}, {time.ctime()}\n' - self.write(content) - self.write(logo_ascii) - - def bar(self): - content = '-' * Logger.SCREEN_WIDTH + '\n' - self.write(content) - - def print_config( - self, - model_config: Dict[str, Any], - data_config: Dict[str, Any], - train_config: Dict[str, Any], - ): - """ - print some important information from config - """ - content = 'successfully read yaml config!\n\n' + 'from model configuration\n' - for k, v in model_config.items(): - content += self.format_k_v(k, str(v)) - content += '\nfrom train configuration\n' - for k, v in train_config.items(): - content += self.format_k_v(k, str(v)) - content += '\nfrom data configuration\n' - for k, v in data_config.items(): - content += self.format_k_v(k, str(v)) - self.write(content) - - # TODO: This is not good make own exception - def error(self, e: Exception): - content = '' - if type(e) is ValueError: - content += 'Error occurred!\n' - content += str(e) + '\n' - else: - content += 'Unknown error occurred!\n' - content += traceback.format_exc() - self.write(content) - - def timer_start(self, name: str): - self.timer_dct[name] = datetime.now() - - def timer_end(self, name: str, message: str, remove: bool = True): - """ - print f"{message}: {elapsed}" - """ - elapsed = str(datetime.now() - self.timer_dct[name]) - # elapsed = elapsed.strftime('%H-%M-%S') - if remove: - del self.timer_dct[name] - self.write(f'{message}: {elapsed[:-4]}\n') - - # TODO: print it without config - # TODO: refactoring, readout part name :( - def print_model_info(self, model, config): - from functools import partial - - kv_write = partial(self.format_k_v, write=True) - self.writeline('Irreps of features') - kv_write('edge_feature', model.get_irreps_in('edge_embedding', 'irreps_out')) - for i in range(config[KEY.NUM_CONVOLUTION]): - kv_write( - f'{i}th node', - model.get_irreps_in(f'{i}_self_interaction_1'), - ) - i = config[KEY.NUM_CONVOLUTION] - 1 - kv_write( - 'readout irreps', - model.get_irreps_in(f'{i}_equivariant_gate', 'irreps_out'), - ) - - num_weights = sum(p.numel() for p in model.parameters() if p.requires_grad) - self.writeline(f'# learnable parameters: {num_weights}\n') diff --git a/mace-bench/3rdparty/SevenNet/sevenn/logo_ascii b/mace-bench/3rdparty/SevenNet/sevenn/logo_ascii deleted file mode 100644 index d195940ade2e32d290b0b124fcad78d54c60a1e2..0000000000000000000000000000000000000000 --- a/mace-bench/3rdparty/SevenNet/sevenn/logo_ascii +++ /dev/null @@ -1,20 +0,0 @@ - - **** - ******** . - *//////, .. . ,*. - ,,***. .. , ********. ./, - . . .. /////. ., . *///////// /////////. - .&@&/ . .(((((((.. / *//////*. ... *((((((((((. - @@@@@@@@@@* @@@@@@@@@@ @@@@@ *((@@@@@ ( %@@@@@@@@@@ .@@@@@@ ..@@@@. @@@@@@* .(@@@@@(((* - @@@@@. @@@@ @@@@@ . @@@@@ # %@@@@ @@@@@@@@ @@@@(, @@@@@@@@. @@@@@(*. - %@@@@@@@& @@@@@@@@@@ @@@@@ @@@@@ # ., .%@@@@@@@@@ @@@@@@@@@@ @@@@, @@@@@@@@@@ @@@@@ - ,(%@@@@@@@@@ @@@@@@@@@@ @@@@@ @@@@& (//////%@@@@@@@@@ @@@@ @@@@@@ @@@@ . @@@@@ @@@@@.@@@@@ - . @@@@@ @@@@ . . @@@@@@@@% . . ( .////,%@@@@ @@@@ @@@@@@@@@ @@@@@ @@@@@@@@@ - (@@@@@@@@@@@ @@@@@@@@@@**. @@@@@@* *. .%@@@@@@@@@@ @@@@ . @@@@@@@ @@@@@ .@@@@@@@ - @@@@@@@@@. @@@@@@@@@@///, @@@@. . / %@@@@@@@@@@ @@@@***, @@@@@ @@@@@ @@@@@ - . //////////*. / . .*******... . ,. - .&&&&&... ,//////*. ...////. / ,*/. . ,////, .,///// - &@@@@@@ ,(/((, * ,((((((. .***. - ,/@(, .. * ,((((* - , - . diff --git a/mace-bench/3rdparty/SevenNet/sevenn/main/__init__.py b/mace-bench/3rdparty/SevenNet/sevenn/main/__init__.py deleted file mode 100644 index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000 diff --git a/mace-bench/3rdparty/SevenNet/sevenn/main/sevenn.py b/mace-bench/3rdparty/SevenNet/sevenn/main/sevenn.py deleted file mode 100644 index d96a1bf8e316464def20b894bc8c689e158541b6..0000000000000000000000000000000000000000 --- a/mace-bench/3rdparty/SevenNet/sevenn/main/sevenn.py +++ /dev/null @@ -1,248 +0,0 @@ -import argparse -import os -import sys -import time - -from sevenn import __version__ - -description = 'train a model given the input.yaml' - -input_yaml_help = 'input.yaml for training' -mode_help = 'main training script to run. Default is train.' -working_dir_help = 'path to write output. Default is cwd.' -screen_help = 'print log to stdout' -distributed_help = 'set this flag if it is distributed training' -distributed_backend_help = 'backend for distributed training. Supported: nccl, mpi' - -# Metainfo will be saved to checkpoint -global_config = { - 'version': __version__, - 'when': time.ctime(), - '_model_type': 'E3_equivariant_model', -} - - -def run(args): - """ - main function of sevenn - """ - import random - import sys - - import torch - import torch.distributed as dist - - import sevenn._keys as KEY - from sevenn.logger import Logger - from sevenn.parse_input import read_config_yaml - from sevenn.scripts.train import train, train_v2 - from sevenn.util import unique_filepath - - input_yaml = args.input_yaml - mode = args.mode - working_dir = args.working_dir - log = args.log - screen = args.screen - distributed = args.distributed - distributed_backend = args.distributed_backend - use_cue = args.enable_cueq - - if use_cue: - import sevenn.nn.cue_helper - - if not sevenn.nn.cue_helper.is_cue_available(): - raise ImportError('cuEquivariance not installed.') - - if working_dir is None: - working_dir = os.getcwd() - elif not os.path.isdir(working_dir): - os.makedirs(working_dir, exist_ok=True) - - world_size = 1 - if distributed: - if distributed_backend == 'nccl': - local_rank = int(os.environ['LOCAL_RANK']) - rank = int(os.environ['RANK']) - world_size = int(os.environ['WORLD_SIZE']) - elif distributed_backend == 'mpi': - local_rank = int(os.environ['OMPI_COMM_WORLD_LOCAL_RANK']) - rank = int(os.environ['OMPI_COMM_WORLD_RANK']) - world_size = int(os.environ['OMPI_COMM_WORLD_SIZE']) - else: - raise ValueError(f'Unknown distributed backend: {distributed_backend}') - - dist.init_process_group( - backend=distributed_backend, world_size=world_size, rank=rank - ) - else: - local_rank, rank, world_size = 0, 0, 1 - - log_fname = unique_filepath(f'{os.path.abspath(working_dir)}/{log}') - with Logger(filename=log_fname, screen=screen, rank=rank) as logger: - logger.greeting() - - if distributed: - logger.writeline( - f'Distributed training enabled, total world size is {world_size}' - ) - - try: - model_config, train_config, data_config = read_config_yaml( - input_yaml, return_separately=True - ) - except Exception as e: - logger.writeline('Failed to parsing input.yaml') - logger.error(e) - sys.exit(1) - - train_config[KEY.IS_DDP] = distributed - train_config[KEY.DDP_BACKEND] = distributed_backend - train_config[KEY.LOCAL_RANK] = local_rank - train_config[KEY.RANK] = rank - train_config[KEY.WORLD_SIZE] = world_size - - if distributed: - torch.cuda.set_device(torch.device('cuda', local_rank)) - - if use_cue: - if KEY.CUEQUIVARIANCE_CONFIG not in model_config: - model_config[KEY.CUEQUIVARIANCE_CONFIG] = {'use': True} - else: - model_config[KEY.CUEQUIVARIANCE_CONFIG].update({'use': True}) - - logger.print_config(model_config, data_config, train_config) - # don't have to distinguish configs inside program - global_config.update(model_config) - global_config.update(train_config) - global_config.update(data_config) - - # Not implemented - if global_config[KEY.DTYPE] == 'double': - raise Exception('double precision is not implemented yet') - # torch.set_default_dtype(torch.double) - - seed = global_config[KEY.RANDOM_SEED] - random.seed(seed) - torch.manual_seed(seed) - - # run train - if mode == 'train_v1': - train(global_config, working_dir) - elif mode == 'train_v2': - train_v2(global_config, working_dir) - - -def cmd_parser_train(parser): - ag = parser - ag.add_argument('input_yaml', help=input_yaml_help, type=str) - ag.add_argument( - '-m', - '--mode', - choices=['train_v1', 'train_v2'], - default='train_v2', - help=mode_help, - type=str, - ) - ag.add_argument( - '-cueq', - '--enable_cueq', - help='(Not stable!) use cuEquivariance for training', - action='store_true', - ) - ag.add_argument( - '-w', - '--working_dir', - nargs='?', - const=os.getcwd(), - help=working_dir_help, - type=str, - ) - ag.add_argument( - '-l', - '--log', - default='log.sevenn', - help='name of logfile, default is log.sevenn', - type=str, - ) - ag.add_argument('-s', '--screen', help=screen_help, action='store_true') - ag.add_argument( - '-d', '--distributed', help=distributed_help, action='store_true' - ) - ag.add_argument( - '--distributed_backend', - help=distributed_backend_help, - type=str, - default='nccl', - choices=['nccl', 'mpi'], - ) - - -def add_parser(subparsers): - ag = subparsers.add_parser('train', help=description) - cmd_parser_train(ag) - - -def set_default_subparser(self, name, args=None, positional_args=0): - """default subparser selection. Call after setup, just before parse_args() - name: is the name of the subparser to call by default - args: if set is the argument list handed to parse_args() - - Hack copied from stack overflow - """ - subparser_found = False - for arg in sys.argv[1:]: - if arg in ['-h', '--help']: # global help if no subparser - break - else: - for x in self._subparsers._actions: - if not isinstance(x, argparse._SubParsersAction): - continue - for sp_name in x._name_parser_map.keys(): - if sp_name in sys.argv[1:]: - subparser_found = True - if not subparser_found: - # insert default in last position before global positional - # arguments, this implies no global options are specified after - # first positional argument - if args is None: - sys.argv.insert(len(sys.argv) - positional_args, name) - else: - args.insert(len(args) - positional_args, name) - - -argparse.ArgumentParser.set_default_subparser = set_default_subparser # type: ignore - - -def main(): - import sevenn.main.sevenn_cp as checkpoint_cmd - import sevenn.main.sevenn_get_model as get_model_cmd - import sevenn.main.sevenn_graph_build as graph_build_cmd - import sevenn.main.sevenn_inference as inference_cmd - import sevenn.main.sevenn_patch_lammps as patch_lammps_cmd - import sevenn.main.sevenn_preset as preset_cmd - - ag = argparse.ArgumentParser(f'SevenNet version={__version__}') - - subparsers = ag.add_subparsers(dest='command', help='Sub-commands') - add_parser(subparsers) # add 'train' - checkpoint_cmd.add_parser(subparsers) - inference_cmd.add_parser(subparsers) - graph_build_cmd.add_parser(subparsers) - preset_cmd.add_parser(subparsers) - get_model_cmd.add_parser(subparsers) - patch_lammps_cmd.add_parser(subparsers) - - ag.set_default_subparser('train') # type: ignore - args = ag.parse_args() - - if args.command is None: # backward compatibility - args.command = 'train' - - if args.command == 'train': - run(args) - elif args.command == 'preset': - preset_cmd.run(args) - - -if __name__ == '__main__': - main() diff --git a/mace-bench/3rdparty/SevenNet/sevenn/main/sevenn_cp.py b/mace-bench/3rdparty/SevenNet/sevenn/main/sevenn_cp.py deleted file mode 100644 index 319cb1a4b93507dd211ded4c888750a9c04f6570..0000000000000000000000000000000000000000 --- a/mace-bench/3rdparty/SevenNet/sevenn/main/sevenn_cp.py +++ /dev/null @@ -1,92 +0,0 @@ -import argparse -import os.path as osp - -from sevenn import __version__ - -description = ( - 'tool box for sevennet checkpoints' -) - - -def add_parser(subparsers): - ag = subparsers.add_parser('checkpoint', help=description, aliases=['cp']) - add_args(ag) - - -def add_args(parser): - ag = parser - - ag.add_argument('checkpoint', help='checkpoint or pretrained', type=str) - - group = ag.add_mutually_exclusive_group(required=False) - group.add_argument( - '--get_yaml', - choices=['reproduce', 'continue', 'continue_modal'], - help='create input.yaml based on the given checkpoint', - type=str, - ) - - group.add_argument( - '--append_modal_yaml', - help='append modality with given yaml.', - type=str, - ) - ag.add_argument( - '--original_modal_name', - help=( - 'when the append_modal is used and checkpoint is not multi-modal, ' - + 'used to name previously trained modality. defaults to "origin"' - ), - default='origin', - type=str, - ) - - -def run(args): - import torch - import yaml - - from sevenn.parse_input import read_config_yaml - from sevenn.util import load_checkpoint - - checkpoint = load_checkpoint(args.checkpoint) - if args.get_yaml: - mode = args.get_yaml - cfg = checkpoint.yaml_dict(mode) - print(yaml.dump(cfg, indent=4, sort_keys=False, default_flow_style=False)) - elif args.append_modal_yaml: - dst_yaml = args.append_modal_yaml - if not osp.exists(dst_yaml): - raise FileNotFoundError(f'No yaml file {dst_yaml}') - - dst_config = read_config_yaml(dst_yaml, return_separately=False) - model_state_dict = checkpoint.append_modal( - dst_config, args.original_modal_name - ) - - to_save = checkpoint.get_checkpoint_dict() - to_save.update({'config': dst_config, 'model_state_dict': model_state_dict}) - - torch.save(to_save, 'checkpoint_modal_appended.pth') - print('checkpoint_modal_appended.pth is successfully saved.') - print(f'update continue of {dst_yaml} as blow (recommend) to continue') - cont_dct = { - 'continue': { - 'checkpoint': 'checkpoint_modal_appended.pth', - 'reset_epoch': True, - 'reset_optimizer': True, - 'reset_scheduler': True, - } - } - print( - yaml.dump(cont_dct, indent=4, sort_keys=False, default_flow_style=False) - ) - - else: - print(checkpoint) - - -def main(args=None): - ag = argparse.ArgumentParser(description=description) - add_args(ag) - run(ag.parse_args()) diff --git a/mace-bench/3rdparty/SevenNet/sevenn/main/sevenn_get_model.py b/mace-bench/3rdparty/SevenNet/sevenn/main/sevenn_get_model.py deleted file mode 100644 index f8b78e88f98d4dc9d92d686f77037c2f2ac57f18..0000000000000000000000000000000000000000 --- a/mace-bench/3rdparty/SevenNet/sevenn/main/sevenn_get_model.py +++ /dev/null @@ -1,70 +0,0 @@ -import argparse -import os - -from sevenn import __version__ - -description_get_model = ( - 'deploy LAMMPS model from the checkpoint' -) -checkpoint_help = ( - 'path to the checkpoint | SevenNet-0 | 7net-0 |' - ' {SevenNet-0|7net-0}_{11July2024|22May2024}' -) -output_name_help = 'filename prefix' -get_parallel_help = 'deploy parallel model' - - -def add_parser(subparsers): - ag = subparsers.add_parser( - 'get_model', help=description_get_model, aliases=['deploy'] - ) - add_args(ag) - - -def add_args(parser): - ag = parser - ag.add_argument('checkpoint', help=checkpoint_help, type=str) - ag.add_argument( - '-o', '--output_prefix', nargs='?', help=output_name_help, type=str - ) - ag.add_argument( - '-p', '--get_parallel', help=get_parallel_help, action='store_true' - ) - ag.add_argument( - '-m', - '--modal', - help='Modality of multi-modal model', - type=str, - ) - - -def run(args): - import sevenn.util - from sevenn.scripts.deploy import deploy, deploy_parallel - - checkpoint = args.checkpoint - output_prefix = args.output_prefix - get_parallel = args.get_parallel - get_serial = not get_parallel - modal = args.modal - - if output_prefix is None: - output_prefix = 'deployed_parallel' if not get_serial else 'deployed_serial' - - checkpoint_path = None - if os.path.isfile(checkpoint): - checkpoint_path = checkpoint - else: - checkpoint_path = sevenn.util.pretrained_name_to_path(checkpoint) - - if get_serial: - deploy(checkpoint_path, output_prefix, modal) - else: - deploy_parallel(checkpoint_path, output_prefix, modal) - - -# legacy way -def main(): - ag = argparse.ArgumentParser(description=description_get_model) - add_args(ag) - run(ag.parse_args()) diff --git a/mace-bench/3rdparty/SevenNet/sevenn/main/sevenn_graph_build.py b/mace-bench/3rdparty/SevenNet/sevenn/main/sevenn_graph_build.py deleted file mode 100644 index fd9eaeef104305e5182d7eb01d3495cd538c4e0f..0000000000000000000000000000000000000000 --- a/mace-bench/3rdparty/SevenNet/sevenn/main/sevenn_graph_build.py +++ /dev/null @@ -1,130 +0,0 @@ -import argparse -import glob -import os -import sys -from datetime import datetime - -from sevenn import __version__ - -description = 'create `sevenn_data/dataset.pt` from ase readable' - -source_help = 'source data to build graph, knows *' -cutoff_help = 'cutoff radius of edges in Angstrom' -filename_help = ( - 'Name of the dataset, default is graph.pt. ' - + 'The dataset will be written under "sevenn_data", ' - + 'for example, {out}/sevenn_data/graph.pt.' -) -legacy_help = 'build legacy .sevenn_data' - - -def add_parser(subparsers): - ag = subparsers.add_parser('graph_build', help=description) - add_args(ag) - - -def add_args(parser): - ag = parser - ag.add_argument('source', help=source_help, type=str) - ag.add_argument('cutoff', help=cutoff_help, type=float) - ag.add_argument( - '-n', - '--num_cores', - help='number of cores to build graph in parallel', - default=1, - type=int, - ) - ag.add_argument( - '-o', - '--out', - help='Existing path to write outputs.', - type=str, - default='./', - ) - ag.add_argument( - '-f', - '--filename', - help=filename_help, - type=str, - default='graph.pt', - ) - ag.add_argument( - '--legacy', - help=legacy_help, - action='store_true', - ) - ag.add_argument( - '-s', - '--screen', - help='print log to the screen', - action='store_true', - ) - ag.add_argument( - '--kwargs', - nargs=argparse.REMAINDER, - help='will be passed to ase.io.read, or can be used to specify EFS key', - ) - - -def run(args): - import sevenn.scripts.graph_build as graph_build - from sevenn.logger import Logger - - source = glob.glob(args.source) - cutoff = args.cutoff - num_cores = args.num_cores - filename = args.filename - out = args.out - legacy = args.legacy - fmt_kwargs = {} - if args.kwargs: - for kwarg in args.kwargs: - k, v = kwarg.split('=') - fmt_kwargs[k] = v - - if len(source) == 0: - print('Source has zero len, nothing to read') - sys.exit(0) - - if not os.path.isdir(out): - raise NotADirectoryError(f'No such directory: {out}') - - to_be_written = os.path.join(out, 'sevenn_data', filename) - if os.path.isfile(to_be_written): - raise FileExistsError(f'File already exist: {to_be_written}') - - metadata = { - 'sevenn_version': __version__, - 'when': datetime.now().strftime('%Y-%m-%d'), - 'cutoff': cutoff, - } - - with Logger(filename=None, screen=args.screen) as logger: - logger.writeline(description) - - if not legacy: - graph_build.build_sevennet_graph_dataset( - source, - cutoff, - num_cores, - out, - filename, - metadata, - **fmt_kwargs, - ) - else: - out = os.path.join(out, filename.split('.')[0]) - graph_build.build_script( # build .sevenn_data - source, - cutoff, - num_cores, - out, - metadata, - **fmt_kwargs, - ) - - -def main(args=None): - ag = argparse.ArgumentParser(description=description) - add_args(ag) - run(ag.parse_args()) diff --git a/mace-bench/3rdparty/SevenNet/sevenn/main/sevenn_inference.py b/mace-bench/3rdparty/SevenNet/sevenn/main/sevenn_inference.py deleted file mode 100644 index bfac2371435715d0290d14fb34326a63bf68dcdd..0000000000000000000000000000000000000000 --- a/mace-bench/3rdparty/SevenNet/sevenn/main/sevenn_inference.py +++ /dev/null @@ -1,129 +0,0 @@ -import argparse -import glob -import os -import sys - -description = ( - 'evaluate sevenn_data/ase readable with a model (checkpoint).' -) -checkpoint_help = 'Checkpoint or pre-trained model name' -target_help = 'Target files to evaluate' - - -def add_parser(subparsers): - ag = subparsers.add_parser('inference', help=description, aliases=['inf']) - add_args(ag) - - -def add_args(parser): - ag = parser - ag.add_argument('checkpoint', type=str, help=checkpoint_help) - ag.add_argument('targets', type=str, nargs='+', help=target_help) - ag.add_argument( - '-d', - '--device', - type=str, - default='auto', - help='cpu/cuda/cuda:x', - ) - ag.add_argument( - '-nw', - '--nworkers', - type=int, - default=1, - help='Number of cores to build graph, defaults to 1', - ) - ag.add_argument( - '-o', - '--output', - type=str, - default='./inference_results', - help='A directory name to write outputs', - ) - ag.add_argument( - '-b', - '--batch', - type=int, - default='4', - help='batch size, useful for GPU' - ) - ag.add_argument( - '-s', - '--save_graph', - action='store_true', - help='Additionally, save preprocessed graph as sevenn_data' - ) - ag.add_argument( - '-au', - '--allow_unlabeled', - action='store_true', - help='Allow energy or force unlabeled data' - ) - ag.add_argument( - '-m', - '--modal', - type=str, - default=None, - help='modality for multi-modal inference', - ) - ag.add_argument( - '--kwargs', - nargs=argparse.REMAINDER, - help='will be passed to reader, or can be used to specify EFS key', - ) - - -def run(args): - import torch - - from sevenn.scripts.inference import inference - from sevenn.util import pretrained_name_to_path - - out = args.output - - if os.path.exists(out): - raise FileExistsError(f'Directory {out} already exists') - - device = args.device - if device == 'auto': - device = 'cuda' if torch.cuda.is_available() else 'cpu' - - targets = [] - for target in args.targets: - targets.extend(glob.glob(target)) - - if len(targets) == 0: - print('No targets (data to inference) are found') - sys.exit(0) - - cp = args.checkpoint - if not os.path.isfile(cp): - cp = pretrained_name_to_path(cp) # raises value error - - fmt_kwargs = {} - if args.kwargs: - for kwarg in args.kwargs: - k, v = kwarg.split('=') - fmt_kwargs[k] = v - - if args.save_graph and args.allow_unlabeled: - raise ValueError('save_graph and allow_unlabeled are mutually exclusive') - - inference( - cp, - targets, - out, - args.nworkers, - device, - args.batch, - args.save_graph, - args.allow_unlabeled, - args.modal, - **fmt_kwargs, - ) - - -def main(args=None): - ag = argparse.ArgumentParser(description=description) - add_args(ag) - run(ag.parse_args()) diff --git a/mace-bench/3rdparty/SevenNet/sevenn/main/sevenn_patch_lammps.py b/mace-bench/3rdparty/SevenNet/sevenn/main/sevenn_patch_lammps.py deleted file mode 100644 index 38f7299ad816600b4bc16f3eafe269a3bc62c434..0000000000000000000000000000000000000000 --- a/mace-bench/3rdparty/SevenNet/sevenn/main/sevenn_patch_lammps.py +++ /dev/null @@ -1,55 +0,0 @@ -import argparse -import os -import subprocess - -from sevenn import __version__ - -# python wrapper of patch_lammps.sh script -# importlib.resources is correct way to do these things -# but it changes so frequently to use -pair_e3gnn_dir = os.path.abspath(f'{os.path.dirname(__file__)}/../pair_e3gnn') - -description = 'patch LAMMPS with e3gnn(7net) pair-styles before compile' - - -def add_parser(subparsers): - ag = subparsers.add_parser('patch_lammps', help=description) - add_args(ag) - - -def add_args(parser): - ag = parser - ag.add_argument('lammps_dir', help='Path to LAMMPS source', type=str) - ag.add_argument('--d3', help='Enable D3 support', action='store_true') - # cxx_standard is detected automatically - - -def run(args): - lammps_dir = os.path.abspath(args.lammps_dir) - - print('Patching LAMMPS with the following settings:') - print(' - LAMMPS source directory:', lammps_dir) - - cxx_standard = '17' # always 17 - - if args.d3: - d3_support = '1' - print(' - D3 support enabled') - else: - d3_support = '0' - print(' - D3 support disabled') - - script = f'{pair_e3gnn_dir}/patch_lammps.sh' - cmd = f'{script} {lammps_dir} {cxx_standard} {d3_support}' - res = subprocess.run(cmd.split()) - return res.returncode # is it meaningless? - - -def main(args=None): - ag = argparse.ArgumentParser(description=description) - add_args(ag) - run(ag.parse_args()) - - -if __name__ == '__main__': - main() diff --git a/mace-bench/3rdparty/SevenNet/sevenn/main/sevenn_preset.py b/mace-bench/3rdparty/SevenNet/sevenn/main/sevenn_preset.py deleted file mode 100644 index f8587d1b8fccf85bcb5633ec4464a4ff7207d4f3..0000000000000000000000000000000000000000 --- a/mace-bench/3rdparty/SevenNet/sevenn/main/sevenn_preset.py +++ /dev/null @@ -1,45 +0,0 @@ -import argparse -import os - -from sevenn import __version__ - -description = ( - 'print the selected preset for training. ' - + 'ex) sevennet_preset fine_tune > my_input.yaml' -) - -preset_help = 'Name of preset' - - -def add_parser(subparsers): - ag = subparsers.add_parser('preset', help=description) - add_args(ag) - - -def add_args(parser): - ag = parser - ag.add_argument( - 'preset', choices=[ - 'fine_tune', - 'fine_tune_le', - 'sevennet-0', - 'sevennet-l3i5', - 'base', - 'multi_modal' - ], - help=preset_help - ) - - -def run(args): - preset = args.preset - prefix = os.path.abspath(f'{os.path.dirname(__file__)}/../presets') - with open(f'{prefix}/{preset}.yaml', 'r') as f: - print(f.read()) - - -# When executed as sevenn_preset (legacy way) -def main(args=None): - ag = argparse.ArgumentParser(description=description) - add_args(ag) - run(ag.parse_args()) diff --git a/mace-bench/3rdparty/SevenNet/sevenn/model_build.py b/mace-bench/3rdparty/SevenNet/sevenn/model_build.py deleted file mode 100644 index 2b8701d50eefffe82bac95119dd5417ced217934..0000000000000000000000000000000000000000 --- a/mace-bench/3rdparty/SevenNet/sevenn/model_build.py +++ /dev/null @@ -1,556 +0,0 @@ -import copy -import warnings -from collections import OrderedDict -from typing import List, Literal, Union, overload - -from e3nn.o3 import Irreps - -import sevenn._const as _const -import sevenn._keys as KEY -import sevenn.util as util - -from .nn.convolution import IrrepsConvolution -from .nn.edge_embedding import ( - BesselBasis, - EdgeEmbedding, - PolynomialCutoff, - SphericalEncoding, - XPLORCutoff, -) -from .nn.force_output import ForceStressOutputFromEdge -from .nn.interaction_blocks import NequIP_interaction_block -from .nn.linear import AtomReduce, FCN_e3nn, IrrepsLinear -from .nn.node_embedding import OnehotEmbedding -from .nn.scale import ModalWiseRescale, Rescale, SpeciesWiseRescale -from .nn.self_connection import ( - SelfConnectionIntro, - SelfConnectionLinearIntro, - SelfConnectionOutro, -) -from .nn.sequential import AtomGraphSequential - -# warning from PyTorch, about e3nn type annotations -warnings.filterwarnings( - 'ignore', - message=( - "The TorchScript type system doesn't " 'support instance-level annotations' - ), -) - - -def _insert_after(module_name_after, key_module_pair, layers): - idx = -1 - for i, (key, _) in enumerate(layers): - if key == module_name_after: - idx = i - break - if idx == -1: - return layers # do nothing if not found - layers.insert(idx + 1, key_module_pair) - return layers - - -def init_self_connection(config): - self_connection_type_list = config[KEY.SELF_CONNECTION_TYPE] - num_conv = config[KEY.NUM_CONVOLUTION] - if isinstance(self_connection_type_list, str): - self_connection_type_list = [self_connection_type_list] * num_conv - - io_pair_list = [] - for sc_type in self_connection_type_list: - if sc_type == 'none': - io_pair = None - elif sc_type == 'nequip': - io_pair = SelfConnectionIntro, SelfConnectionOutro - elif sc_type == 'linear': - io_pair = SelfConnectionLinearIntro, SelfConnectionOutro - else: - raise ValueError(f'Unknown self_connection_type found: {sc_type}') - io_pair_list.append(io_pair) - return io_pair_list - - -def init_edge_embedding(config): - _cutoff_param = {'cutoff_length': config[KEY.CUTOFF]} - rbf, env, sph = None, None, None - - rbf_dct = copy.deepcopy(config[KEY.RADIAL_BASIS]) - rbf_dct.update(_cutoff_param) - rbf_name = rbf_dct.pop(KEY.RADIAL_BASIS_NAME) - if rbf_name == 'bessel': - rbf = BesselBasis(**rbf_dct) - - envelop_dct = copy.deepcopy(config[KEY.CUTOFF_FUNCTION]) - envelop_dct.update(_cutoff_param) - envelop_name = envelop_dct.pop(KEY.CUTOFF_FUNCTION_NAME) - if envelop_name == 'poly_cut': - env = PolynomialCutoff(**envelop_dct) - elif envelop_name == 'XPLOR': - env = XPLORCutoff(**envelop_dct) - - lmax_edge = config[KEY.LMAX] - if config[KEY.LMAX_EDGE] > 0: - lmax_edge = config[KEY.LMAX_EDGE] - parity = -1 if config[KEY.IS_PARITY] else 1 - _normalize_sph = config[KEY._NORMALIZE_SPH] - sph = SphericalEncoding(lmax_edge, parity, normalize=_normalize_sph) - - return EdgeEmbedding(basis_module=rbf, cutoff_module=env, spherical_module=sph) - - -def init_feature_reduce(config, irreps_x): - # features per node to scalar per node - layers = OrderedDict() - if config[KEY.READOUT_AS_FCN] is False: - hidden_irreps = Irreps([(irreps_x.dim // 2, (0, 1))]) - layers.update( - { - 'reduce_input_to_hidden': IrrepsLinear( - irreps_x, - hidden_irreps, - data_key_in=KEY.NODE_FEATURE, - biases=config[KEY.USE_BIAS_IN_LINEAR], - ), - 'reduce_hidden_to_energy': IrrepsLinear( - hidden_irreps, - Irreps([(1, (0, 1))]), - data_key_in=KEY.NODE_FEATURE, - data_key_out=KEY.SCALED_ATOMIC_ENERGY, - biases=config[KEY.USE_BIAS_IN_LINEAR], - ), - } - ) - else: - act = _const.ACTIVATION[config[KEY.READOUT_FCN_ACTIVATION]] - hidden_neurons = config[KEY.READOUT_FCN_HIDDEN_NEURONS] - layers.update( - { - 'readout_FCN': FCN_e3nn( - dim_out=1, - hidden_neurons=hidden_neurons, - activation=act, - data_key_in=KEY.NODE_FEATURE, - data_key_out=KEY.SCALED_ATOMIC_ENERGY, - irreps_in=irreps_x, - ) - } - ) - return layers - - -def init_shift_scale(config): - # for mm, ex, shift: modal_idx -> shifts - shift_scale = [] - train_shift_scale = config[KEY.TRAIN_SHIFT_SCALE] - type_map = config[KEY.TYPE_MAP] - - # in case of modal, shift or scale has more dims [][] - # correct typing (I really want static python) - for s in (config[KEY.SHIFT], config[KEY.SCALE]): - if hasattr(s, 'tolist'): # numpy or torch - s = s.tolist() - if isinstance(s, dict): - s = {k: v.tolist() if hasattr(v, 'tolist') else v for k, v in s.items()} - if isinstance(s, list) and len(s) == 1: - s = s[0] - shift_scale.append(s) - shift, scale = shift_scale - - rescale_module = None - if config.get(KEY.USE_MODALITY, False): - rescale_module = ModalWiseRescale.from_mappers( # type: ignore - shift, - scale, - config[KEY.USE_MODAL_WISE_SHIFT], - config[KEY.USE_MODAL_WISE_SCALE], - type_map=type_map, - modal_map=config[KEY.MODAL_MAP], - train_shift_scale=train_shift_scale, - ) - elif all([isinstance(s, float) for s in shift_scale]): - rescale_module = Rescale(shift, scale, train_shift_scale=train_shift_scale) - elif any([isinstance(s, list) for s in shift_scale]): - rescale_module = SpeciesWiseRescale.from_mappers( # type: ignore - shift, scale, type_map=type_map, train_shift_scale=train_shift_scale - ) - else: - raise ValueError('shift, scale should be list of float or float') - - return rescale_module - - -def patch_modality(layers: OrderedDict, config): - """ - Postprocess 7net-model to multimodal model. - 1. prepend modality one-hot embedding layer - 2. patch modalities of IrrepsLinear layers - Modality aware shift scale is handled by init_shift_scale, not here - """ - cfg = config - if not cfg.get(KEY.USE_MODALITY, False): - return layers - - _layers = list(layers.items()) - _layers = _insert_after( - 'onehot_idx_to_onehot', - ( - 'one_hot_modality', - OnehotEmbedding( - num_classes=config[KEY.NUM_MODALITIES], - data_key_x=KEY.MODAL_TYPE, - data_key_out=KEY.MODAL_ATTR, - data_key_save=None, - data_key_additional=None, - ), - ), - _layers, - ) - layers = OrderedDict(_layers) - - num_modal = config[KEY.NUM_MODALITIES] - for k, module in layers.items(): - if not isinstance(module, IrrepsLinear): - continue - if ( - (cfg[KEY.USE_MODAL_NODE_EMBEDDING] and k.endswith('onehot_to_feature_x')) - or ( - cfg[KEY.USE_MODAL_SELF_INTER_INTRO] - and k.endswith('self_interaction_1') - ) - or ( - cfg[KEY.USE_MODAL_SELF_INTER_OUTRO] - and k.endswith('self_interaction_2') - ) - or (cfg[KEY.USE_MODAL_OUTPUT_BLOCK] and k == 'reduce_input_to_hidden') - ): - module.set_num_modalities(num_modal) - return layers - - -def patch_cue(layers: OrderedDict, config): - import sevenn.nn.cue_helper as cue_helper - - cue_cfg = copy.deepcopy(config.get(KEY.CUEQUIVARIANCE_CONFIG, {})) - - if not cue_cfg.pop('use', False): - return layers - - if not cue_helper.is_cue_available(): - warnings.warn( - ( - 'cuEquivariance is requested, but the package is not installed. ' - + 'Fallback to original code.' - ) - ) - return layers - - if not cue_helper.is_cue_cuda_available_model(config): - return layers - - group = 'O3' if config[KEY.IS_PARITY] else 'SO3' - cueq_module_params = dict(layout='mul_ir') - cueq_module_params.update(cue_cfg) - updates = {} - for k, module in layers.items(): - if isinstance(module, (IrrepsLinear, SelfConnectionLinearIntro)): - if k == 'reduce_hidden_to_energy': # TODO: has bug with 0 shape - continue - module_patched = cue_helper.patch_linear( - module, group, **cueq_module_params - ) - updates[k] = module_patched - elif isinstance(module, SelfConnectionIntro): - module_patched = cue_helper.patch_fully_connected( - module, group, **cueq_module_params - ) - updates[k] = module_patched - elif isinstance(module, IrrepsConvolution): - module_patched = cue_helper.patch_convolution( - module, group, **cueq_module_params - ) - updates[k] = module_patched - - layers.update(updates) - return layers - - -def patch_modules(layers: OrderedDict, config): - layers = patch_modality(layers, config) - layers = patch_cue(layers, config) - return layers - - -def _to_parallel_model(layers: OrderedDict, config): - num_classes = layers['onehot_idx_to_onehot'].num_classes - one_hot_irreps = Irreps(f'{num_classes}x0e') - irreps_node_zero = layers['onehot_to_feature_x'].irreps_out - - _layers = list(layers.items()) - layers_list = [] - - num_convolution_layer = config[KEY.NUM_CONVOLUTION] - - def slice_until_this(module_name, layers): - idx = -1 - for i, (key, _) in enumerate(layers): - if key == module_name: - idx = i - break - first_to = layers[: idx + 1] - remain = layers[idx + 1 :] - return first_to, remain - - _layers = _insert_after( - 'onehot_to_feature_x', - ( - 'one_hot_ghost', - OnehotEmbedding( - data_key_x=KEY.NODE_FEATURE_GHOST, - num_classes=num_classes, - data_key_save=None, - data_key_additional=None, - ), - ), - _layers, - ) - _layers = _insert_after( - 'one_hot_ghost', - ( - 'ghost_onehot_to_feature_x', - IrrepsLinear( - irreps_in=one_hot_irreps, - irreps_out=irreps_node_zero, - data_key_in=KEY.NODE_FEATURE_GHOST, - biases=config[KEY.USE_BIAS_IN_LINEAR], - ), - ), - _layers, - ) - _layers = _insert_after( - '0_self_interaction_1', - ( - 'ghost_0_self_interaction_1', - IrrepsLinear( - irreps_node_zero, - irreps_node_zero, - data_key_in=KEY.NODE_FEATURE_GHOST, - biases=config[KEY.USE_BIAS_IN_LINEAR], - ), - ), - _layers, - ) - # assign modules (before first communications) - # initialize edge related to retain position gradients - for i in range(1, num_convolution_layer): - sliced, _layers = slice_until_this(f'{i}_self_interaction_1', _layers) - layers_list.append(OrderedDict(sliced)) - _layers.insert(0, ('edge_embedding', init_edge_embedding(config))) - - layers_list.append(OrderedDict(_layers)) - del layers_list[-1]['force_output'] # done in LAMMPS - return layers_list - - -@overload -def build_E3_equivariant_model( - config: dict, parallel: Literal[False] = False -) -> AtomGraphSequential: # noqa - ... - - -@overload -def build_E3_equivariant_model( - config: dict, parallel: Literal[True] -) -> List[AtomGraphSequential]: # noqa - ... - - -def build_E3_equivariant_model( - config: dict, parallel: bool = False -) -> Union[AtomGraphSequential, List[AtomGraphSequential]]: - """ - output shapes (w/o batch) - - PRED_TOTAL_ENERGY: (), - ATOMIC_ENERGY: (natoms, 1), # intended - PRED_FORCE: (natoms, 3), - PRED_STRESS: (6,), - - for data w/o cell volume, pred_stress has garbage values - """ - layers = OrderedDict() - - cutoff = config[KEY.CUTOFF] - num_species = config[KEY.NUM_SPECIES] - feature_multiplicity = config[KEY.NODE_FEATURE_MULTIPLICITY] - num_convolution_layer = config[KEY.NUM_CONVOLUTION] - interaction_type = config[KEY.INTERACTION_TYPE] - use_bias_in_linear = config[KEY.USE_BIAS_IN_LINEAR] - - lmax_node = config[KEY.LMAX] # ignore second (lmax_edge) - # if config[KEY.LMAX_EDGE] > 0: # not yet used - # _ = config[KEY.LMAX_EDGE] - if config[KEY.LMAX_NODE] > 0: - lmax_node = config[KEY.LMAX_NODE] - - act_radial = _const.ACTIVATION[config[KEY.ACTIVATION_RADIAL]] - self_connection_pair_list = init_self_connection(config) - - irreps_manual = None - if config[KEY.IRREPS_MANUAL] is not False: - irreps_manual = config[KEY.IRREPS_MANUAL] - try: - irreps_manual = [Irreps(irr) for irr in irreps_manual] - assert len(irreps_manual) == num_convolution_layer + 1 - except Exception: - raise RuntimeError('invalid irreps_manual input given') - - conv_denominator = config[KEY.CONV_DENOMINATOR] - if not isinstance(conv_denominator, list): - conv_denominator = [conv_denominator] * num_convolution_layer - train_conv_denominator = config[KEY.TRAIN_DENOMINTAOR] - - edge_embedding = init_edge_embedding(config) - irreps_filter = edge_embedding.spherical.irreps_out - radial_basis_num = edge_embedding.basis_function.num_basis - layers.update({'edge_embedding': edge_embedding}) - - one_hot_irreps = Irreps(f'{num_species}x0e') - irreps_x = ( - Irreps(f'{feature_multiplicity}x0e') - if irreps_manual is None - else irreps_manual[0] - ) - - layers.update( - { - 'onehot_idx_to_onehot': OnehotEmbedding( - num_classes=num_species, - data_key_x=KEY.NODE_FEATURE, - data_key_out=KEY.NODE_FEATURE, - data_key_save=KEY.ATOM_TYPE, # atomic numbers - data_key_additional=KEY.NODE_ATTR, # one-hot embeddings - ), - 'onehot_to_feature_x': IrrepsLinear( - irreps_in=one_hot_irreps, - irreps_out=irreps_x, - data_key_in=KEY.NODE_FEATURE, - biases=use_bias_in_linear, - ), - } - ) - - weight_nn_hidden = config[KEY.CONVOLUTION_WEIGHT_NN_HIDDEN_NEURONS] - weight_nn_layers = [radial_basis_num] + weight_nn_hidden - - param_interaction_block = { - 'irreps_filter': irreps_filter, - 'weight_nn_layers': weight_nn_layers, - 'train_conv_denominator': train_conv_denominator, - 'act_radial': act_radial, - 'bias_in_linear': use_bias_in_linear, - 'num_species': num_species, - 'parallel': parallel, - } - - interaction_builder = None - - if interaction_type in ['nequip']: - act_scalar = {} - act_gate = {} - for k, v in config[KEY.ACTIVATION_SCARLAR].items(): - act_scalar[k] = _const.ACTIVATION_DICT[k][v] - for k, v in config[KEY.ACTIVATION_GATE].items(): - act_gate[k] = _const.ACTIVATION_DICT[k][v] - param_interaction_block.update( - { - 'act_scalar': act_scalar, - 'act_gate': act_gate, - } - ) - - if interaction_type == 'nequip': - interaction_builder = NequIP_interaction_block - else: - raise ValueError(f'Unknown interaction type: {interaction_type}') - - for t in range(num_convolution_layer): - param_interaction_block.update( - { - 'irreps_x': irreps_x, - 't': t, - 'conv_denominator': conv_denominator[t], - 'self_connection_pair': self_connection_pair_list[t], - } - ) - if interaction_type == 'nequip': - parity_mode = 'full' - fix_multiplicity = False - if t == num_convolution_layer - 1: - lmax_node = 0 - parity_mode = 'even' - # TODO: irreps_manual is applicable to both irreps_out_tp and irreps_out - irreps_out = ( - util.infer_irreps_out( - irreps_x, # type: ignore - irreps_filter, - lmax_node, # type: ignore - parity_mode, - fix_multiplicity=feature_multiplicity, - ) - if irreps_manual is None - else irreps_manual[t + 1] - ) - irreps_out_tp = util.infer_irreps_out( - irreps_x, # type: ignore - irreps_filter, - irreps_out.lmax, # type: ignore - parity_mode, - fix_multiplicity, - ) - else: - raise ValueError(f'Unknown interaction type: {interaction_type}') - param_interaction_block.update( - { - 'irreps_out_tp': irreps_out_tp, - 'irreps_out': irreps_out, - } - ) - layers.update(interaction_builder(**param_interaction_block)) - irreps_x = irreps_out - - layers.update(init_feature_reduce(config, irreps_x)) - - layers.update( - { - 'rescale_atomic_energy': init_shift_scale(config), - 'reduce_total_enegy': AtomReduce( - data_key_in=KEY.ATOMIC_ENERGY, - data_key_out=KEY.PRED_TOTAL_ENERGY, - ), - } - ) - - gradient_module = ForceStressOutputFromEdge() - grad_key = gradient_module.get_grad_key() - layers.update({'force_output': gradient_module}) - - common_args = { - 'cutoff': cutoff, - 'type_map': config[KEY.TYPE_MAP], - 'modal_map': config.get(KEY.MODAL_MAP, None), - 'eval_type_map': False if parallel else True, - 'eval_modal_map': False - if not config.get(KEY.USE_MODALITY, False) or parallel - else True, - 'data_key_grad': grad_key, - } - - if parallel: - layers_list = _to_parallel_model(layers, config) - return [ - AtomGraphSequential(patch_modules(layers, config), **common_args) - for layers in layers_list - ] - else: - return AtomGraphSequential(patch_modules(layers, config), **common_args) diff --git a/mace-bench/3rdparty/SevenNet/sevenn/nn/__init__.py b/mace-bench/3rdparty/SevenNet/sevenn/nn/__init__.py deleted file mode 100644 index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000 diff --git a/mace-bench/3rdparty/SevenNet/sevenn/nn/activation.py b/mace-bench/3rdparty/SevenNet/sevenn/nn/activation.py deleted file mode 100644 index ac86df922c5b4b1dc388169aa4db152ffc59d2fc..0000000000000000000000000000000000000000 --- a/mace-bench/3rdparty/SevenNet/sevenn/nn/activation.py +++ /dev/null @@ -1,8 +0,0 @@ -import math - -import torch - - -@torch.jit.script -def ShiftedSoftPlus(x: torch.Tensor) -> torch.Tensor: - return torch.nn.functional.softplus(x) - math.log(2.0) diff --git a/mace-bench/3rdparty/SevenNet/sevenn/nn/convolution.py b/mace-bench/3rdparty/SevenNet/sevenn/nn/convolution.py deleted file mode 100644 index d5f1cd7bb79c98ea88d633eb3db52a5712b2dba7..0000000000000000000000000000000000000000 --- a/mace-bench/3rdparty/SevenNet/sevenn/nn/convolution.py +++ /dev/null @@ -1,141 +0,0 @@ -from typing import List - -import torch -import torch.nn as nn -from e3nn.nn import FullyConnectedNet -from e3nn.o3 import Irreps, TensorProduct -from e3nn.util.jit import compile_mode - -import sevenn._keys as KEY -from sevenn._const import AtomGraphDataType - -from .activation import ShiftedSoftPlus -from .util import broadcast - - -def message_gather( - node_features: torch.Tensor, - edge_dst: torch.Tensor, - message: torch.Tensor -): - index = broadcast(edge_dst, message, 0) - out_shape = [len(node_features)] + list(message.shape[1:]) - out = torch.zeros( - out_shape, - dtype=node_features.dtype, - device=node_features.device - ) - out.scatter_reduce_(0, index, message, reduce='sum') - return out - - -@compile_mode('script') -class IrrepsConvolution(nn.Module): - """ - convolution of (fig 2.b), comm. in LAMMPS - """ - - def __init__( - self, - irreps_x: Irreps, - irreps_filter: Irreps, - irreps_out: Irreps, - weight_layer_input_to_hidden: List[int], - weight_layer_act=ShiftedSoftPlus, - denominator: float = 1.0, - train_denominator: bool = False, - data_key_x: str = KEY.NODE_FEATURE, - data_key_filter: str = KEY.EDGE_ATTR, - data_key_weight_input: str = KEY.EDGE_EMBEDDING, - data_key_edge_idx: str = KEY.EDGE_IDX, - lazy_layer_instantiate: bool = True, - is_parallel: bool = False, - ): - super().__init__() - self.denominator = nn.Parameter( - torch.FloatTensor([denominator]), requires_grad=train_denominator - ) - self.key_x = data_key_x - self.key_filter = data_key_filter - self.key_weight_input = data_key_weight_input - self.key_edge_idx = data_key_edge_idx - self.is_parallel = is_parallel - - instructions = [] - irreps_mid = [] - weight_numel = 0 - for i, (mul_x, ir_x) in enumerate(irreps_x): - for j, (_, ir_filter) in enumerate(irreps_filter): - for ir_out in ir_x * ir_filter: - if ir_out in irreps_out: # here we drop l > lmax - k = len(irreps_mid) - weight_numel += mul_x * 1 # path shape - irreps_mid.append((mul_x, ir_out)) - instructions.append((i, j, k, 'uvu', True)) - - irreps_mid = Irreps(irreps_mid) - irreps_mid, p, _ = irreps_mid.sort() # type: ignore - instructions = [ - (i_in1, i_in2, p[i_out], mode, train) - for i_in1, i_in2, i_out, mode, train in instructions - ] - - # From v0.11.x, to compatible with cuEquivariance - self._instructions_before_sort = instructions - instructions = sorted(instructions, key=lambda x: x[2]) - - self.convolution_kwargs = dict( - irreps_in1=irreps_x, - irreps_in2=irreps_filter, - irreps_out=irreps_mid, - instructions=instructions, - shared_weights=False, - internal_weights=False, - ) - - self.weight_nn_kwargs = dict( - hs=weight_layer_input_to_hidden + [weight_numel], - act=weight_layer_act - ) - - self.convolution = None - self.weight_nn = None - self.layer_instantiated = False - self.convolution_cls = TensorProduct - self.weight_nn_cls = FullyConnectedNet - - if not lazy_layer_instantiate: - self.instantiate() - - self._comm_size = irreps_x.dim # used in parallel - - def instantiate(self): - if self.convolution is not None: - raise ValueError('Convolution layer already exists') - if self.weight_nn is not None: - raise ValueError('Weight_nn layer already exists') - - self.convolution = self.convolution_cls(**self.convolution_kwargs) - self.weight_nn = self.weight_nn_cls(**self.weight_nn_kwargs) - self.layer_instantiated = True - - def forward(self, data: AtomGraphDataType) -> AtomGraphDataType: - assert self.convolution is not None, 'Convolution is not instantiated' - assert self.weight_nn is not None, 'Weight_nn is not instantiated' - weight = self.weight_nn(data[self.key_weight_input]) - x = data[self.key_x] - if self.is_parallel: - x = torch.cat([x, data[KEY.NODE_FEATURE_GHOST]]) - - # note that 1 -> src 0 -> dst - edge_src = data[self.key_edge_idx][1] - edge_dst = data[self.key_edge_idx][0] - - message = self.convolution(x[edge_src], data[self.key_filter], weight) - - x = message_gather(x, edge_dst, message) - x = x.div(self.denominator) - if self.is_parallel: - x = torch.tensor_split(x, data[KEY.NLOCAL])[0] - data[self.key_x] = x - return data diff --git a/mace-bench/3rdparty/SevenNet/sevenn/nn/cue_helper.py b/mace-bench/3rdparty/SevenNet/sevenn/nn/cue_helper.py deleted file mode 100644 index c798f40e943bb0033e12db1b4d1b6b44e7c84626..0000000000000000000000000000000000000000 --- a/mace-bench/3rdparty/SevenNet/sevenn/nn/cue_helper.py +++ /dev/null @@ -1,189 +0,0 @@ -import itertools -import warnings -from typing import Iterator, Literal, Union - -import e3nn.o3 as o3 -import numpy as np - -from .convolution import IrrepsConvolution -from .linear import IrrepsLinear -from .self_connection import SelfConnectionIntro, SelfConnectionLinearIntro - -try: - import cuequivariance as cue - import cuequivariance_torch as cuet - - _CUE_AVAILABLE = True - - # Obatained from MACE - class O3_e3nn(cue.O3): - def __mul__( # type: ignore - rep1: 'O3_e3nn', rep2: 'O3_e3nn' - ) -> Iterator['O3_e3nn']: - return [ # type: ignore - O3_e3nn(l=ir.l, p=ir.p) for ir in cue.O3.__mul__(rep1, rep2) - ] - - @classmethod - def clebsch_gordan( # type: ignore - cls, rep1: 'O3_e3nn', rep2: 'O3_e3nn', rep3: 'O3_e3nn' - ) -> np.ndarray: - rep1, rep2, rep3 = cls._from(rep1), cls._from(rep2), cls._from(rep3) - - if rep1.p * rep2.p == rep3.p: - return o3.wigner_3j(rep1.l, rep2.l, rep3.l).numpy()[None] * np.sqrt( - rep3.dim - ) - return np.zeros((0, rep1.dim, rep2.dim, rep3.dim)) - - def __lt__( # type: ignore - rep1: 'O3_e3nn', rep2: 'O3_e3nn' - ) -> bool: - rep2 = rep1._from(rep2) # type: ignore - return (rep1.l, rep1.p) < (rep2.l, rep2.p) - - @classmethod - def iterator(cls) -> Iterator['O3_e3nn']: - for l in itertools.count(0): - yield O3_e3nn(l=l, p=1 * (-1) ** l) - yield O3_e3nn(l=l, p=-1 * (-1) ** l) - -except ImportError: - _CUE_AVAILABLE = False - - -def is_cue_available(): - return _CUE_AVAILABLE - - -def cue_needed(func): - def wrapper(*args, **kwargs): - if is_cue_available(): - return func(*args, **kwargs) - else: - raise ImportError('cue is not available') - - return wrapper - - -def _check_may_not_compatible(orig_kwargs, defaults): - for k, v in defaults.items(): - v_given = orig_kwargs.pop(k, v) - if v_given != v: - warnings.warn(f'{k}: {v} is ignored to use cuEquivariance') - - -def is_cue_cuda_available_model(config): - if config.get('use_bias_in_linear', False): - warnings.warn('Bias in linear can not be used with cueq, fallback to e3nn') - return False - else: - return True - - -@cue_needed -def as_cue_irreps(irreps: o3.Irreps, group: Literal['SO3', 'O3']): - """Convert e3nn irreps to given group's cue irreps""" - if group == 'SO3': - assert all(irrep.ir.p == 1 for irrep in irreps) - return cue.Irreps('SO3', str(irreps).replace('e', '')) # type: ignore - elif group == 'O3': - return cue.Irreps(O3_e3nn, str(irreps)) # type: ignore - else: - raise ValueError(f'Unknown group: {group}') - - -@cue_needed -def patch_linear( - module: Union[IrrepsLinear, SelfConnectionLinearIntro], - group: Literal['SO3', 'O3'], - **cue_kwargs, -): - assert not module.layer_instantiated - - module.irreps_in = as_cue_irreps(module.irreps_in, group) # type: ignore - module.irreps_out = as_cue_irreps(module.irreps_out, group) # type: ignore - - orig_kwargs = module.linear_kwargs - - may_not_compatible_default = dict( - f_in=None, - f_out=None, - instructions=None, - biases=False, - path_normalization='element', - _optimize_einsums=None, - ) - # pop may_not_compatible_defaults - _check_may_not_compatible(orig_kwargs, may_not_compatible_default) - - module.linear_cls = cuet.Linear # type: ignore - orig_kwargs.update(**cue_kwargs) - return module - - -@cue_needed -def patch_convolution( - module: IrrepsConvolution, - group: Literal['SO3', 'O3'], - **cue_kwargs, -): - assert not module.layer_instantiated - - # conv_kwargs will be patched in place - conv_kwargs = module.convolution_kwargs - conv_kwargs.update( - dict( - irreps_in1=as_cue_irreps(conv_kwargs.get('irreps_in1'), group), - irreps_in2=as_cue_irreps(conv_kwargs.get('irreps_in2'), group), - filter_irreps_out=as_cue_irreps(conv_kwargs.pop('irreps_out'), group), - ) - ) - - inst_orig = conv_kwargs.pop('instructions') - inst_sorted = sorted(inst_orig, key=lambda x: x[2]) - assert all([a == b for a, b in zip(inst_orig, inst_sorted)]) - - may_not_compatible_default = dict( - in1_var=None, - in2_var=None, - out_var=None, - irrep_normalization=False, - path_normalization='element', - compile_left_right=True, - compile_right=False, - _specialized_code=None, - _optimize_einsums=None, - ) - # pop may_not_compatible_defaults - _check_may_not_compatible(conv_kwargs, may_not_compatible_default) - - module.convolution_cls = cuet.ChannelWiseTensorProduct # type: ignore - conv_kwargs.update(**cue_kwargs) - return module - - -@cue_needed -def patch_fully_connected( - module: SelfConnectionIntro, - group: Literal['SO3', 'O3'], - **cue_kwargs, -): - assert not module.layer_instantiated - - module.irreps_in1 = as_cue_irreps(module.irreps_in1, group) # type: ignore - module.irreps_in2 = as_cue_irreps(module.irreps_in2, group) # type: ignore - module.irreps_out = as_cue_irreps(module.irreps_out, group) # type: ignore - - may_not_compatible_default = dict( - irrep_normalization=None, - path_normalization=None, - ) - # pop may_not_compatible_defaults - _check_may_not_compatible( - module.fc_tensor_product_kwargs, may_not_compatible_default - ) - - module.fc_tensor_product_cls = cuet.FullyConnectedTensorProduct # type: ignore - module.fc_tensor_product_kwargs.update(**cue_kwargs) - return module diff --git a/mace-bench/3rdparty/SevenNet/sevenn/nn/edge_embedding.py b/mace-bench/3rdparty/SevenNet/sevenn/nn/edge_embedding.py deleted file mode 100644 index e738ef5375fc2546ccc426aad01d91b206b03a6d..0000000000000000000000000000000000000000 --- a/mace-bench/3rdparty/SevenNet/sevenn/nn/edge_embedding.py +++ /dev/null @@ -1,217 +0,0 @@ -import math - -import torch -import torch.nn as nn -from e3nn.o3 import Irreps, SphericalHarmonics -from e3nn.util.jit import compile_mode - -import sevenn._keys as KEY -from sevenn._const import AtomGraphDataType - - -@compile_mode('script') -class EdgePreprocess(nn.Module): - """ - preprocessing pos to edge vectors and edge lengths - currently used in sevenn/scripts/deploy for lammps serial model - """ - - def __init__(self, is_stress: bool): - super().__init__() - # controlled by 'AtomGraphSequential' - self.is_stress = is_stress - self._is_batch_data = True - - def forward(self, data: AtomGraphDataType) -> AtomGraphDataType: - if self._is_batch_data: - cell = data[KEY.CELL].view(-1, 3, 3) - else: - cell = data[KEY.CELL].view(3, 3) - cell_shift = data[KEY.CELL_SHIFT] - pos = data[KEY.POS] - - batch = data[KEY.BATCH] # for deploy, must be defined first - if self.is_stress: - if self._is_batch_data: - num_batch = int(batch.max().cpu().item()) + 1 - strain = torch.zeros( - (num_batch, 3, 3), - dtype=pos.dtype, - device=pos.device, - ) - strain.requires_grad_(True) - data['_strain'] = strain - - sym_strain = 0.5 * (strain + strain.transpose(-1, -2)) - pos = pos + torch.bmm( - pos.unsqueeze(-2), sym_strain[batch] - ).squeeze(-2) - cell = cell + torch.bmm(cell, sym_strain) - else: - strain = torch.zeros( - (3, 3), - dtype=pos.dtype, - device=pos.device, - ) - strain.requires_grad_(True) - data['_strain'] = strain - - sym_strain = 0.5 * (strain + strain.transpose(-1, -2)) - pos = pos + torch.mm(pos, sym_strain) - cell = cell + torch.mm(cell, sym_strain) - - idx_src = data[KEY.EDGE_IDX][0] - idx_dst = data[KEY.EDGE_IDX][1] - - edge_vec = pos[idx_dst] - pos[idx_src] - - if self._is_batch_data: - edge_vec = edge_vec + torch.einsum( - 'ni,nij->nj', cell_shift, cell[batch[idx_src]] - ) - else: - edge_vec = edge_vec + torch.einsum( - 'ni,ij->nj', cell_shift, cell.squeeze(0) - ) - data[KEY.EDGE_VEC] = edge_vec - data[KEY.EDGE_LENGTH] = torch.linalg.norm(edge_vec, dim=-1) - return data - - -class BesselBasis(nn.Module): - """ - f : (*, 1) -> (*, bessel_basis_num) - """ - - def __init__( - self, - cutoff_length: float, - bessel_basis_num: int = 8, - trainable_coeff: bool = True, - ): - super().__init__() - self.num_basis = bessel_basis_num - self.prefactor = 2.0 / cutoff_length - self.coeffs = torch.FloatTensor([ - n * math.pi / cutoff_length for n in range(1, bessel_basis_num + 1) - ]) - if trainable_coeff: - self.coeffs = nn.Parameter(self.coeffs) - - def forward(self, r: torch.Tensor) -> torch.Tensor: - ur = r.unsqueeze(-1) # to fit dimension - return self.prefactor * torch.sin(self.coeffs * ur) / ur - - -class PolynomialCutoff(nn.Module): - """ - f : (*, 1) -> (*, 1) - https://arxiv.org/pdf/2003.03123.pdf - """ - - def __init__( - self, - cutoff_length: float, - poly_cut_p_value: int = 6, - ): - super().__init__() - p = poly_cut_p_value - self.cutoff_length = cutoff_length - self.p = p - self.coeff_p0 = (p + 1.0) * (p + 2.0) / 2.0 - self.coeff_p1 = p * (p + 2.0) - self.coeff_p2 = p * (p + 1.0) / 2.0 - - def forward(self, r: torch.Tensor) -> torch.Tensor: - r = r / self.cutoff_length - return ( - 1 - - self.coeff_p0 * torch.pow(r, self.p) - + self.coeff_p1 * torch.pow(r, self.p + 1.0) - - self.coeff_p2 * torch.pow(r, self.p + 2.0) - ) - - -class XPLORCutoff(nn.Module): - """ - https://hoomd-blue.readthedocs.io/en/latest/module-md-pair.html - """ - - def __init__( - self, - cutoff_length: float, - cutoff_on: float, - ): - super().__init__() - self.r_on = cutoff_on - self.r_cut = cutoff_length - assert self.r_on < self.r_cut - - def forward(self, r: torch.Tensor) -> torch.Tensor: - r_sq = r * r - r_on_sq = self.r_on * self.r_on - r_cut_sq = self.r_cut * self.r_cut - return torch.where( - r < self.r_on, - 1.0, - (r_cut_sq - r_sq) ** 2 - * (r_cut_sq + 2 * r_sq - 3 * r_on_sq) - / (r_cut_sq - r_on_sq) ** 3, - ) - - -@compile_mode('script') -class SphericalEncoding(nn.Module): - def __init__( - self, - lmax: int, - parity: int = -1, - normalization: str = 'component', - normalize: bool = True, - ): - super().__init__() - self.lmax = lmax - self.normalization = normalization - self.irreps_in = Irreps('1x1o') if parity == -1 else Irreps('1x1e') - self.irreps_out = Irreps.spherical_harmonics(lmax, parity) - self.sph = SphericalHarmonics( - self.irreps_out, - normalize=normalize, - normalization=normalization, - irreps_in=self.irreps_in, - ) - - def forward(self, r: torch.Tensor) -> torch.Tensor: - return self.sph(r) - - -@compile_mode('script') -class EdgeEmbedding(nn.Module): - """ - embedding layer of |r| by - RadialBasis(|r|)*CutOff(|r|) - f : (N_edge) -> (N_edge, basis_num) - """ - - def __init__( - self, - basis_module: nn.Module, - cutoff_module: nn.Module, - spherical_module: nn.Module, - ): - super().__init__() - self.basis_function = basis_module - self.cutoff_function = cutoff_module - self.spherical = spherical_module - - def forward(self, data: AtomGraphDataType) -> AtomGraphDataType: - rvec = data[KEY.EDGE_VEC] - r = torch.linalg.norm(data[KEY.EDGE_VEC], dim=-1) - data[KEY.EDGE_LENGTH] = r - - data[KEY.EDGE_EMBEDDING] = self.basis_function( - r - ) * self.cutoff_function(r).unsqueeze(-1) - data[KEY.EDGE_ATTR] = self.spherical(rvec) - - return data diff --git a/mace-bench/3rdparty/SevenNet/sevenn/nn/equivariant_gate.py b/mace-bench/3rdparty/SevenNet/sevenn/nn/equivariant_gate.py deleted file mode 100644 index 842240557b2694270881275011b6f1551f02e0f4..0000000000000000000000000000000000000000 --- a/mace-bench/3rdparty/SevenNet/sevenn/nn/equivariant_gate.py +++ /dev/null @@ -1,61 +0,0 @@ -from typing import Callable, Dict - -import torch.nn as nn -from e3nn.nn import Gate -from e3nn.o3 import Irreps -from e3nn.util.jit import compile_mode - -import sevenn._keys as KEY -from sevenn._const import AtomGraphDataType - - -@compile_mode('script') -class EquivariantGate(nn.Module): - def __init__( - self, - irreps_x: Irreps, - act_scalar_dict: Dict[int, Callable], - act_gate_dict: Dict[int, Callable], - data_key_x: str = KEY.NODE_FEATURE, - ): - super().__init__() - self.key_x = data_key_x - - parity_mapper = {'e': 1, 'o': -1} - act_scalar_dict = { - parity_mapper[k]: v for k, v in act_scalar_dict.items() - } - act_gate_dict = {parity_mapper[k]: v for k, v in act_gate_dict.items()} - - irreps_gated_elem = [] - irreps_scalars_elem = [] - # non scalar irreps > gated / scalar irreps > scalars - for mul, irreps in irreps_x: - if irreps.l > 0: - irreps_gated_elem.append((mul, irreps)) - else: - irreps_scalars_elem.append((mul, irreps)) - irreps_scalars = Irreps(irreps_scalars_elem) - irreps_gated = Irreps(irreps_gated_elem) - - irreps_gates_parity = 1 if '0e' in irreps_scalars else -1 - irreps_gates = Irreps( - [(mul, (0, irreps_gates_parity)) for mul, _ in irreps_gated] - ) - - act_scalars = [act_scalar_dict[p] for _, (_, p) in irreps_scalars] - act_gates = [act_gate_dict[p] for _, (_, p) in irreps_gates] - - self.gate = Gate( - irreps_scalars, act_scalars, irreps_gates, act_gates, irreps_gated - ) - - def get_gate_irreps_in(self): - """ - user must call this function to get proper irreps in for forward - """ - return self.gate.irreps_in - - def forward(self, data: AtomGraphDataType) -> AtomGraphDataType: - data[self.key_x] = self.gate(data[self.key_x]) - return data diff --git a/mace-bench/3rdparty/SevenNet/sevenn/nn/force_output.py b/mace-bench/3rdparty/SevenNet/sevenn/nn/force_output.py deleted file mode 100644 index f6b90e588d8382059bdcadd46fb2aefa1880def8..0000000000000000000000000000000000000000 --- a/mace-bench/3rdparty/SevenNet/sevenn/nn/force_output.py +++ /dev/null @@ -1,224 +0,0 @@ -import torch -import torch.nn as nn -from e3nn.util.jit import compile_mode - -import sevenn._keys as KEY -from sevenn._const import AtomGraphDataType - -from .util import broadcast - - -@compile_mode('script') -class ForceOutput(nn.Module): - """ - works when pos.requires_grad_ is True - """ - - def __init__( - self, - data_key_pos: str = KEY.POS, - data_key_energy: str = KEY.PRED_TOTAL_ENERGY, - data_key_force: str = KEY.PRED_FORCE, - ): - super().__init__() - self.key_pos = data_key_pos - self.key_energy = data_key_energy - self.key_force = data_key_force - - def get_grad_key(self): - return self.key_pos - - def forward(self, data: AtomGraphDataType) -> AtomGraphDataType: - pos_tensor = [data[self.key_pos]] - energy = [(data[self.key_energy]).sum()] - - # `materialize_grads` not supported in low version of pytorch - # Also can not be deployed when using it. - # But not using it makes problem in - # force/stress inference in sparse systems - # TODO: use it only in sevennet_calculator? - grad = torch.autograd.grad( - energy, - pos_tensor, - create_graph=self.training, - allow_unused=True, - # materialize_grads=True, - )[0] - - # For torchscript - if grad is not None: - data[self.key_force] = torch.neg(grad) - return data - - -@compile_mode('script') -class ForceStressOutput(nn.Module): - """ - Compute stress and force from positions. - Used in serial torchscipt models - """ - def __init__( - self, - data_key_pos: str = KEY.POS, - data_key_energy: str = KEY.PRED_TOTAL_ENERGY, - data_key_force: str = KEY.PRED_FORCE, - data_key_stress: str = KEY.PRED_STRESS, - data_key_cell_volume: str = KEY.CELL_VOLUME, - ): - - super().__init__() - self.key_pos = data_key_pos - self.key_energy = data_key_energy - self.key_force = data_key_force - self.key_stress = data_key_stress - self.key_cell_volume = data_key_cell_volume - self._is_batch_data = True - - def get_grad_key(self): - return self.key_pos - - def forward(self, data: AtomGraphDataType) -> AtomGraphDataType: - pos_tensor = data[self.key_pos] - energy = [(data[self.key_energy]).sum()] - - # `materialize_grads` not supported in low version of pytorch - # Also can not be deployed when using it. - # But not using it makes problem in - # force/stress inference in sparse systems - # TODO: use it only in sevennet_calculator? - grad = torch.autograd.grad( - energy, - [pos_tensor, data['_strain']], - create_graph=self.training, - allow_unused=True, - # materialize_grads=True, - ) - - # make grad is not Optional[Tensor] - fgrad = grad[0] - if fgrad is not None: - data[self.key_force] = torch.neg(fgrad) - - sgrad = grad[1] - volume = data[self.key_cell_volume] - vlim = 1e-3 # for cell volume = 0 for non PBC structures - if self._is_batch_data: - volume[volume < vlim] = vlim - elif volume < vlim: - volume = torch.tensor(vlim) - - if sgrad is not None: - if self._is_batch_data: - stress = sgrad / volume.view(-1, 1, 1) - stress = torch.neg(stress) - virial_stress = torch.vstack(( - stress[:, 0, 0], - stress[:, 1, 1], - stress[:, 2, 2], - stress[:, 0, 1], - stress[:, 1, 2], - stress[:, 0, 2], - )) - data[self.key_stress] = virial_stress.transpose(0, 1) - else: - stress = sgrad / volume - stress = torch.neg(stress) - virial_stress = torch.stack(( - stress[0, 0], - stress[1, 1], - stress[2, 2], - stress[0, 1], - stress[1, 2], - stress[0, 2], - )) - data[self.key_stress] = virial_stress - - return data - - -@compile_mode('script') -class ForceStressOutputFromEdge(nn.Module): - """ - Compute stress and force from edge. - Used in parallel torchscipt models, and training - """ - def __init__( - self, - data_key_edge: str = KEY.EDGE_VEC, - data_key_edge_idx: str = KEY.EDGE_IDX, - data_key_energy: str = KEY.PRED_TOTAL_ENERGY, - data_key_force: str = KEY.PRED_FORCE, - data_key_stress: str = KEY.PRED_STRESS, - data_key_cell_volume: str = KEY.CELL_VOLUME, - ): - - super().__init__() - self.key_edge = data_key_edge - self.key_edge_idx = data_key_edge_idx - self.key_energy = data_key_energy - self.key_force = data_key_force - self.key_stress = data_key_stress - self.key_cell_volume = data_key_cell_volume - self._is_batch_data = True - - def get_grad_key(self): - return self.key_edge - - def forward(self, data: AtomGraphDataType) -> AtomGraphDataType: - tot_num = torch.sum(data[KEY.NUM_ATOMS]) # ? item? - rij = data[self.key_edge] - energy = [(data[self.key_energy]).sum()] - edge_idx = data[self.key_edge_idx] - - grad = torch.autograd.grad( - energy, - [rij], - create_graph=self.training, - allow_unused=True - ) - - # make grad is not Optional[Tensor] - fij = grad[0] - - if fij is not None: - # compute force - pf = torch.zeros(tot_num, 3, dtype=fij.dtype, device=fij.device) - nf = torch.zeros(tot_num, 3, dtype=fij.dtype, device=fij.device) - _edge_src = broadcast(edge_idx[0], fij, 0) - _edge_dst = broadcast(edge_idx[1], fij, 0) - pf.scatter_reduce_(0, _edge_src, fij, reduce='sum') - nf.scatter_reduce_(0, _edge_dst, fij, reduce='sum') - data[self.key_force] = pf - nf - - # compute virial - diag = rij * fij - s12 = rij[..., 0] * fij[..., 1] - s23 = rij[..., 1] * fij[..., 2] - s31 = rij[..., 2] * fij[..., 0] - # cat last dimension - _virial = torch.cat([ - diag, - s12.unsqueeze(-1), - s23.unsqueeze(-1), - s31.unsqueeze(-1) - ], dim=-1) - - _s = torch.zeros(tot_num, 6, dtype=fij.dtype, device=fij.device) - _edge_dst6 = broadcast(edge_idx[1], _virial, 0) - _s.scatter_reduce_(0, _edge_dst6, _virial, reduce='sum') - - if self._is_batch_data: - batch = data[KEY.BATCH] # for deploy, must be defined first - nbatch = int(batch.max().cpu().item()) + 1 - sout = torch.zeros( - (nbatch, 6), dtype=_virial.dtype, device=_virial.device - ) - _batch = broadcast(batch, _s, 0) - sout.scatter_reduce_(0, _batch, _s, reduce='sum') - else: - sout = torch.sum(_s, dim=0) - - data[self.key_stress] =\ - torch.neg(sout) / data[self.key_cell_volume].unsqueeze(-1) - - return data diff --git a/mace-bench/3rdparty/SevenNet/sevenn/nn/interaction_blocks.py b/mace-bench/3rdparty/SevenNet/sevenn/nn/interaction_blocks.py deleted file mode 100644 index 3f93768f913c447f062d6de3a31384730fd715df..0000000000000000000000000000000000000000 --- a/mace-bench/3rdparty/SevenNet/sevenn/nn/interaction_blocks.py +++ /dev/null @@ -1,76 +0,0 @@ -from typing import Callable, List, Tuple - -from e3nn.o3 import Irreps - -import sevenn._keys as KEY - -from .convolution import IrrepsConvolution -from .equivariant_gate import EquivariantGate -from .linear import IrrepsLinear - - -def NequIP_interaction_block( - irreps_x: Irreps, - irreps_filter: Irreps, - irreps_out_tp: Irreps, - irreps_out: Irreps, - weight_nn_layers: List[int], - conv_denominator: float, - train_conv_denominator: bool, - self_connection_pair: Tuple[Callable, Callable], - act_scalar: Callable, - act_gate: Callable, - act_radial: Callable, - bias_in_linear: bool, - num_species: int, - t: int, # interaction layer index - data_key_x: str = KEY.NODE_FEATURE, - data_key_weight_input: str = KEY.EDGE_EMBEDDING, - parallel: bool = False, - **conv_kwargs, -): - block = {} - irreps_node_attr = Irreps(f'{num_species}x0e') - sc_intro, sc_outro = self_connection_pair - - gate_layer = EquivariantGate(irreps_out, act_scalar, act_gate) - irreps_for_gate_in = gate_layer.get_gate_irreps_in() - - block[f'{t}_self_connection_intro'] = sc_intro( - irreps_x, - irreps_operand=irreps_node_attr, - irreps_out=irreps_for_gate_in, - ) - - block[f'{t}_self_interaction_1'] = IrrepsLinear( - irreps_x, irreps_x, - data_key_in=data_key_x, - biases=bias_in_linear, - ) - - # convolution part, l>lmax is dropped as defined in irreps_out - block[f'{t}_convolution'] = IrrepsConvolution( - irreps_x=irreps_x, - irreps_filter=irreps_filter, - irreps_out=irreps_out_tp, - data_key_weight_input=data_key_weight_input, - weight_layer_input_to_hidden=weight_nn_layers, - weight_layer_act=act_radial, - denominator=conv_denominator, - train_denominator=train_conv_denominator, - is_parallel=parallel, - **conv_kwargs, - ) - - # irreps of x increase to gate_irreps_in - block[f'{t}_self_interaction_2'] = IrrepsLinear( - irreps_out_tp, - irreps_for_gate_in, - data_key_in=data_key_x, - biases=bias_in_linear, - ) - - block[f'{t}_self_connection_outro'] = sc_outro() - block[f'{t}_equivariant_gate'] = gate_layer - - return block diff --git a/mace-bench/3rdparty/SevenNet/sevenn/nn/linear.py b/mace-bench/3rdparty/SevenNet/sevenn/nn/linear.py deleted file mode 100644 index b5b87d21e699051b5cdf92cfe1d1b044705d532b..0000000000000000000000000000000000000000 --- a/mace-bench/3rdparty/SevenNet/sevenn/nn/linear.py +++ /dev/null @@ -1,180 +0,0 @@ -from typing import Callable, List, Optional - -import torch -import torch.nn as nn -from e3nn.nn import FullyConnectedNet -from e3nn.o3 import Irreps, Linear -from e3nn.util.jit import compile_mode - -import sevenn._keys as KEY -from sevenn._const import AtomGraphDataType - - -@compile_mode('script') -class IrrepsLinear(nn.Module): - """ - wrapper class of e3nn Linear to operate on AtomGraphData - """ - - def __init__( - self, - irreps_in: Irreps, - irreps_out: Irreps, - data_key_in: str, - data_key_out: Optional[str] = None, - data_key_modal_attr: str = KEY.MODAL_ATTR, - num_modalities: int = 0, - lazy_layer_instantiate: bool = True, - **linear_kwargs, - ): - super().__init__() - self.key_input = data_key_in - if data_key_out is None: - self.key_output = data_key_in - else: - self.key_output = data_key_out - self.key_modal_attr = data_key_modal_attr - - self._irreps_in_wo_modal = irreps_in - self.irreps_in = irreps_in - self.irreps_out = irreps_out - self.linear_kwargs = linear_kwargs - - self.linear = None - self.layer_instantiated = False - self.num_modalities = num_modalities - self._is_batch_data = True - - # use getter setter - self.linear_cls = Linear - - if num_modalities > 1: # in case of multi-modal - self.set_num_modalities(num_modalities) - - if not lazy_layer_instantiate: - self.instantiate() - - def instantiate(self): - if self.linear is not None: - raise ValueError('Linear layer already exists') - self.linear = self.linear_cls( - self.irreps_in, self.irreps_out, **self.linear_kwargs - ) - self.layer_instantiated = True - - def set_num_modalities(self, num_modalities): - if self.layer_instantiated: - raise ValueError('Layer already instantiated, can not change modalities') - irreps_in = self._irreps_in_wo_modal + Irreps(f'{num_modalities}x0e') - self.num_modalities = num_modalities - self.irreps_in = irreps_in - - def _patch_modal_to_data(self, data: AtomGraphDataType) -> AtomGraphDataType: - if self._is_batch_data: - batch = data[KEY.BATCH] - batch_modality_onehot = data[self.key_modal_attr].reshape( - -1, self.num_modalities - ) - batch_modality_onehot = batch_modality_onehot.type( - data[self.key_input].dtype - ) - data[self.key_input] = torch.cat( - [data[self.key_input], batch_modality_onehot[batch]], dim=1 - ) - else: - modality_onehot = data[self.key_modal_attr].expand( - len(data[self.key_input]), -1 - ) - modality_onehot = modality_onehot.type(data[self.key_input].dtype) - data[self.key_input] = torch.cat( - [data[self.key_input], modality_onehot], dim=1 - ) - return data - - def forward(self, data: AtomGraphDataType) -> AtomGraphDataType: - assert self.linear is not None, 'Layer is not instantiated' - if self.num_modalities > 1: - data = self._patch_modal_to_data(data) - - data[self.key_output] = self.linear(data[self.key_input]) - return data - - -@compile_mode('script') -class AtomReduce(nn.Module): - """ - atomic energy -> total energy - constant is multiplied to data - """ - - def __init__( - self, - data_key_in: str, - data_key_out: str, - reduce: str = 'sum', - constant: float = 1.0, - ): - super().__init__() - - self.key_input = data_key_in - self.key_output = data_key_out - self.constant = constant - self.reduce = reduce - - # controlled by the upper most wrapper 'AtomGraphSequential' - self._is_batch_data = True - - def forward(self, data: AtomGraphDataType) -> AtomGraphDataType: - if self._is_batch_data: - src = data[self.key_input].squeeze(1) - size = int(data[KEY.BATCH].max()) + 1 - output = torch.zeros( - (size), - dtype=src.dtype, - device=src.device, - ) - output.scatter_reduce_(0, data[KEY.BATCH], src, reduce='sum') - data[self.key_output] = output * self.constant - else: - data[self.key_output] = torch.sum(data[self.key_input]) * self.constant - - return data - - -@compile_mode('script') -class FCN_e3nn(nn.Module): - """ - wrapper class of e3nn FullyConnectedNet - """ - - def __init__( - self, - irreps_in: Irreps, # confirm it is scalar & input size - dim_out: int, - hidden_neurons: List[int], - activation: Callable, - data_key_in: str, - data_key_out: Optional[str] = None, - **e3nn_kwargs, - ): - super().__init__() - self.key_input = data_key_in - self.irreps_in = irreps_in - if data_key_out is None: - self.key_output = data_key_in - else: - self.key_output = data_key_out - - for _, irrep in irreps_in: - assert irrep.is_scalar() - inp_dim = irreps_in.dim - - self.fcn = FullyConnectedNet( - [inp_dim] + hidden_neurons + [dim_out], - activation, - **e3nn_kwargs, - ) - - def forward(self, data: AtomGraphDataType) -> AtomGraphDataType: - data[self.key_output] = self.fcn(data[self.key_input]) - return data diff --git a/mace-bench/3rdparty/SevenNet/sevenn/nn/node_embedding.py b/mace-bench/3rdparty/SevenNet/sevenn/nn/node_embedding.py deleted file mode 100644 index a5f272ae8a8f2edbd7814ad52d2b381ffbe7a9ce..0000000000000000000000000000000000000000 --- a/mace-bench/3rdparty/SevenNet/sevenn/nn/node_embedding.py +++ /dev/null @@ -1,91 +0,0 @@ -from typing import Dict, List, Optional - -import torch -import torch.nn as nn -import torch.nn.functional -from ase.symbols import symbols2numbers -from e3nn.util.jit import compile_mode - -import sevenn._keys as KEY -from sevenn._const import AtomGraphDataType - - -# TODO: put this to model_build and do not preprocess data by onehot -@compile_mode('script') -class OnehotEmbedding(nn.Module): - """ - x : tensor of shape (N, 1) - x_after : tensor of shape (N, num_classes) - It overwrite data_key_x - and saves input to data_key_save and output to data_key_additional - I know this is strange but it is for compatibility with previous version - and to specie wise shift scale work - ex) [0 1 1 0] -> [[1, 0] [0, 1] [0, 1] [1, 0]] (num_classes = 2) - """ - - def __init__( - self, - num_classes: int, - data_key_x: str = KEY.NODE_FEATURE, - data_key_out: Optional[str] = None, - data_key_save: Optional[str] = None, - data_key_additional: Optional[str] = None, # additional output - ): - super().__init__() - self.num_classes = num_classes - self.key_x = data_key_x - if data_key_out is None: - self.key_output = data_key_x - else: - self.key_output = data_key_out - self.key_save = data_key_save - self.key_additional_output = data_key_additional - - def forward(self, data: AtomGraphDataType) -> AtomGraphDataType: - inp = data[self.key_x] - embd = torch.nn.functional.one_hot(inp, self.num_classes) - embd = embd.float() - data[self.key_output] = embd - if self.key_additional_output is not None: - data[self.key_additional_output] = embd # for self-connection - if self.key_save is not None: - data[self.key_save] = inp # for elemwise shift scale - return data - - -def get_type_mapper_from_specie(specie_list: List[str]): - """ - from ['Hf', 'O'] - return {72: 0, 8: 1} - """ - specie_list = sorted(specie_list) - type_map = {} - unique_counter = 0 - for specie in specie_list: - atomic_num = symbols2numbers(specie)[0] - if atomic_num in type_map: - continue - type_map[atomic_num] = unique_counter - unique_counter += 1 - return type_map - - -# deprecated -def one_hot_atom_embedding( - atomic_numbers: List[int], type_map: Dict[int, int] -): - """ - atomic numbers from ase.get_atomic_numbers - type_map from get_type_mapper_from_specie() - """ - num_classes = len(type_map) - try: - type_numbers = torch.LongTensor( - [type_map[num] for num in atomic_numbers] - ) - except KeyError as e: - raise ValueError(f'Atomic number {e.args[0]} is not expected') - embd = torch.nn.functional.one_hot(type_numbers, num_classes) - embd = embd.to(torch.get_default_dtype()) - - return embd diff --git a/mace-bench/3rdparty/SevenNet/sevenn/nn/scale.py b/mace-bench/3rdparty/SevenNet/sevenn/nn/scale.py deleted file mode 100644 index 73da83563002d86b8b12401dd7c0032a2d7fb264..0000000000000000000000000000000000000000 --- a/mace-bench/3rdparty/SevenNet/sevenn/nn/scale.py +++ /dev/null @@ -1,387 +0,0 @@ -from typing import Any, Dict, List, Optional, Union - -import torch -import torch.nn as nn -from e3nn.util.jit import compile_mode - -import sevenn._keys as KEY -from sevenn._const import NUM_UNIV_ELEMENT, AtomGraphDataType - - -def _as_univ( - ss: List[float], type_map: Dict[int, int], default: float -) -> List[float]: - assert len(ss) <= NUM_UNIV_ELEMENT, 'shift scale is too long' - return [ - ss[type_map[z]] if z in type_map else default - for z in range(NUM_UNIV_ELEMENT) - ] - - -@compile_mode('script') -class Rescale(nn.Module): - """ - Scaling and shifting energy (and automatically force and stress) - """ - - def __init__( - self, - shift: float, - scale: float, - data_key_in: str = KEY.SCALED_ATOMIC_ENERGY, - data_key_out: str = KEY.ATOMIC_ENERGY, - train_shift_scale: bool = False, - **kwargs, - ): - assert isinstance(shift, float) and isinstance(scale, float) - super().__init__() - self.shift = nn.Parameter( - torch.FloatTensor([shift]), requires_grad=train_shift_scale - ) - self.scale = nn.Parameter( - torch.FloatTensor([scale]), requires_grad=train_shift_scale - ) - self.key_input = data_key_in - self.key_output = data_key_out - - def get_shift(self) -> float: - return self.shift.detach().cpu().tolist()[0] - - def get_scale(self) -> float: - return self.scale.detach().cpu().tolist()[0] - - def forward(self, data: AtomGraphDataType) -> AtomGraphDataType: - data[self.key_output] = data[self.key_input] * self.scale + self.shift - - return data - - -@compile_mode('script') -class SpeciesWiseRescale(nn.Module): - """ - Scaling and shifting energy (and automatically force and stress) - Use as it is if given list, expand to list if one of them is float - If two lists are given and length is not the same, raise error - """ - - def __init__( - self, - shift: Union[List[float], float], - scale: Union[List[float], float], - data_key_in: str = KEY.SCALED_ATOMIC_ENERGY, - data_key_out: str = KEY.ATOMIC_ENERGY, - data_key_indices: str = KEY.ATOM_TYPE, - train_shift_scale: bool = False, - ): - super().__init__() - assert isinstance(shift, float) or isinstance(shift, list) - assert isinstance(scale, float) or isinstance(scale, list) - - if ( - isinstance(shift, list) - and isinstance(scale, list) - and len(shift) != len(scale) - ): - raise ValueError('List length should be same') - - if isinstance(shift, list): - num_species = len(shift) - elif isinstance(scale, list): - num_species = len(scale) - else: - raise ValueError('Both shift and scale is not a list') - - shift = [shift] * num_species if isinstance(shift, float) else shift - scale = [scale] * num_species if isinstance(scale, float) else scale - - self.shift = nn.Parameter( - torch.FloatTensor(shift), requires_grad=train_shift_scale - ) - self.scale = nn.Parameter( - torch.FloatTensor(scale), requires_grad=train_shift_scale - ) - self.key_input = data_key_in - self.key_output = data_key_out - self.key_indices = data_key_indices - - def get_shift(self, type_map: Optional[Dict[int, int]] = None) -> List[float]: - """ - Return shift in list of float. If type_map is given, return type_map reversed - shift, which index equals atomic_number. 0.0 is assigned for atomis not found - """ - shift = self.shift.detach().cpu().tolist() - if type_map: - shift = _as_univ(shift, type_map, 0.0) - return shift - - def get_scale(self, type_map: Optional[Dict[int, int]] = None) -> List[float]: - """ - Return scale in list of float. If type_map is given, return type_map reversed - scale, which index equals atomic_number. 1.0 is assigned for atomis not found - """ - scale = self.scale.detach().cpu().tolist() - if type_map: - scale = _as_univ(scale, type_map, 1.0) - return scale - - @staticmethod - def from_mappers( - shift: Union[float, List[float]], - scale: Union[float, List[float]], - type_map: Dict[int, int], - **kwargs, - ): - """ - Fit dimensions or mapping raw shift scale values to that is valid under - the given type_map: (atomic_numbers -> type_indices) - """ - shift_scale = [] - n_atom_types = len(type_map) - for s in (shift, scale): - if isinstance(s, list) and len(s) > n_atom_types: - if len(s) != NUM_UNIV_ELEMENT: - raise ValueError('given shift or scale is strange') - s = [s[z] for z in sorted(type_map, key=lambda x: type_map[x])] - # s = [s[z] for z in sorted(type_map, key=type_map.get)] - elif isinstance(s, float): - s = [s] * n_atom_types - elif isinstance(s, list) and len(s) == 1: - s = s * n_atom_types - shift_scale.append(s) - assert all([len(s) == n_atom_types for s in shift_scale]) - shift, scale = shift_scale - return SpeciesWiseRescale(shift, scale, **kwargs) - - def forward(self, data: AtomGraphDataType) -> AtomGraphDataType: - indices = data[self.key_indices] - data[self.key_output] = data[self.key_input] * self.scale[indices].view( - -1, 1 - ) + self.shift[indices].view(-1, 1) - - return data - - -@compile_mode('script') -class ModalWiseRescale(nn.Module): - """ - Scaling and shifting energy (and automatically force and stress) - Given shift or scale is either modal-wise and atom-wise or - not modal-wise but atom-wise. It is always interpreted as atom-wise. - """ - - def __init__( - self, - shift: List[List[float]], - scale: List[List[float]], - data_key_in: str = KEY.SCALED_ATOMIC_ENERGY, - data_key_out: str = KEY.ATOMIC_ENERGY, - data_key_modal_indices: str = KEY.MODAL_TYPE, - data_key_atom_indices: str = KEY.ATOM_TYPE, - use_modal_wise_shift: bool = False, - use_modal_wise_scale: bool = False, - train_shift_scale: bool = False, - ): - super().__init__() - self.shift = nn.Parameter( - torch.FloatTensor(shift), requires_grad=train_shift_scale - ) - self.scale = nn.Parameter( - torch.FloatTensor(scale), requires_grad=train_shift_scale - ) - self.key_input = data_key_in - self.key_output = data_key_out - self.key_atom_indices = data_key_atom_indices - self.key_modal_indices = data_key_modal_indices - self.use_modal_wise_shift = use_modal_wise_shift - self.use_modal_wise_scale = use_modal_wise_scale - self._is_batch_data = True - - def get_shift( - self, - type_map: Optional[Dict[int, int]] = None, - modal_map: Optional[Dict[str, int]] = None, - ) -> Union[List[float], Dict[str, List[float]]]: - """ - Nothing is given: return as it is - type_map is given but not modal wise shift: return univ shift - both type_map and modal_map is given and modal wise shift: return fully - resolved modalwise univ shift - """ - shift = self.shift.detach().cpu().tolist() - if type_map and not self.use_modal_wise_shift: - shift = _as_univ(shift, type_map, 0.0) - elif self.use_modal_wise_shift and modal_map and type_map: - shift = [_as_univ(s, type_map, 0.0) for s in shift] - shift = {modal: shift[idx] for modal, idx in modal_map.items()} - - return shift - - def get_scale( - self, - type_map: Optional[Dict[int, int]] = None, - modal_map: Optional[Dict[str, int]] = None, - ) -> Union[List[float], Dict[str, List[float]]]: - """ - Nothing is given: return as it is - type_map is given but not modal wise scale: return univ scale - both type_map and modal_map is given and modal wise scale: return fully - resolved modalwise univ scale - """ - scale = self.scale.detach().cpu().tolist() - if type_map and not self.use_modal_wise_scale: - scale = _as_univ(scale, type_map, 0.0) - elif self.use_modal_wise_scale and modal_map and type_map: - scale = [_as_univ(s, type_map, 0.0) for s in scale] - scale = {modal: scale[idx] for modal, idx in modal_map.items()} - return scale - - @staticmethod - def from_mappers( - shift: Union[float, List[float], Dict[str, Any]], - scale: Union[float, List[float], Dict[str, Any]], - use_modal_wise_shift: bool, - use_modal_wise_scale: bool, - type_map: Dict[int, int], - modal_map: Dict[str, int], - **kwargs, - ): - """ - Fit dimensions or mapping raw shift scale values to that is valid under - the given type_map: (atomic_numbers -> type_indices) - If given List[float] and its length matches length of _const.NUM_UNIV_ELEMENT - , assume it is element-wise list - otherwise, it is modal-wise list - """ - - def solve_mapper(arr, map): - # value is attr index and never overlap, key is either 'z' or modal str - return [arr[z] for z in sorted(map, key=lambda x: map[x])] - - shift_scale = [] - n_atom_types = len(type_map) - n_modals = len(modal_map) - - for s, use_mw in ( - (shift, use_modal_wise_shift), - (scale, use_modal_wise_scale), - ): - # solve elemewise, or broadcast - if isinstance(s, float): - # given, modal-wise: no, elem-wise: no => broadcast - shape = (n_modals, n_atom_types) if use_mw else (n_atom_types,) - res = torch.full(shape, s).tolist() # TODO: w/o torch - elif isinstance(s, list) and len(s) == NUM_UNIV_ELEMENT: - # given, modal-wise: no, elem-wise: yes(univ) => solve elem map - s = solve_mapper(s, type_map) - res = [s] * n_modals if use_mw else s - elif ( # given, modal-wise: yes, elem-wise: no => broadcast to elemwise - isinstance(s, list) - and isinstance(s[0], float) - and len(s) == n_modals - and use_mw - ): - res = [[v] * n_atom_types for v in s] - elif ( # given, modal-wise: no, elem-wise: yes => as it is - isinstance(s, list) - and isinstance(s[0], float) - and len(s) == n_atom_types - and not use_mw - ): - res = s - elif ( # given, modal-wise: yes, elem-wise: yes => as it is - isinstance(s, list) - and isinstance(s[0], list) - and len(s) == n_modals - and len(s[0]) == n_atom_types - and use_mw - ): - res = s - elif isinstance(s, dict) and use_mw: - # solve modal dict, modal-wise: yes - s = solve_mapper(s, modal_map) - res = [] - for v in s: - if isinstance(v, list) and len(v) == NUM_UNIV_ELEMENT: - # elem-wise: yes(univ) => solve elem map - v = solve_mapper(v, type_map) - elif isinstance(v, float): - # elem-wise: no => broadcast to elemwise - v = [v] * n_atom_types - else: - raise ValueError(f'Invalid shift or scale {s}') - res.append(v) - else: - raise ValueError(f'Invalid shift or scale {s}') - - if use_mw: - assert ( - isinstance(res, list) - and isinstance(res[0], list) - and len(res) == n_modals - ) - assert all([len(r) == n_atom_types for r in res]) # type: ignore - else: - assert ( - isinstance(res, list) - and isinstance(res[0], float) - and len(res) == n_atom_types - ) - shift_scale.append(res) - shift, scale = shift_scale - - return ModalWiseRescale( - shift, - scale, - use_modal_wise_shift=use_modal_wise_shift, - use_modal_wise_scale=use_modal_wise_scale, - **kwargs, - ) - - def forward(self, data: AtomGraphDataType) -> AtomGraphDataType: - if self._is_batch_data: - batch = data[KEY.BATCH] - modal_indices = data[self.key_modal_indices][batch] - else: - modal_indices = data[self.key_modal_indices] - atom_indices = data[self.key_atom_indices] - shift = ( - self.shift[modal_indices, atom_indices] - if self.use_modal_wise_shift - else self.shift[atom_indices] - ) - scale = ( - self.scale[modal_indices, atom_indices] - if self.use_modal_wise_scale - else self.scale[atom_indices] - ) - data[self.key_output] = data[self.key_input] * scale.view( - -1, 1 - ) + shift.view(-1, 1) - - return data - - -def get_resolved_shift_scale( - module: Union[Rescale, SpeciesWiseRescale, ModalWiseRescale], - type_map: Optional[Dict[int, int]] = None, - modal_map: Optional[Dict[str, int]] = None, -): - """ - Return resolved shift and scale from scale modules. For element wise case, - convert to list of floats where idx is atomic number. For modal wise case, return - dictionary of shift scale where key is modal name given in modal_map - - Return: - Tuple of solved shift and scale - """ - - if isinstance(module, Rescale): - return (module.get_shift(), module.get_scale()) - elif isinstance(module, SpeciesWiseRescale): - return (module.get_shift(type_map), module.get_scale(type_map)) - elif isinstance(module, ModalWiseRescale): - return ( - module.get_shift(type_map, modal_map), - module.get_scale(type_map, modal_map), - ) - raise ValueError('Not scale module') diff --git a/mace-bench/3rdparty/SevenNet/sevenn/nn/self_connection.py b/mace-bench/3rdparty/SevenNet/sevenn/nn/self_connection.py deleted file mode 100644 index ce731b51494438d3d82206be129958f5ea912a96..0000000000000000000000000000000000000000 --- a/mace-bench/3rdparty/SevenNet/sevenn/nn/self_connection.py +++ /dev/null @@ -1,128 +0,0 @@ -import torch.nn as nn -from e3nn.o3 import FullyConnectedTensorProduct, Irreps, Linear -from e3nn.util.jit import compile_mode - -import sevenn._keys as KEY -from sevenn._const import AtomGraphDataType - - -@compile_mode('script') -class SelfConnectionIntro(nn.Module): - """ - do TensorProduct of x and some data(here attribute of x) - and save it (to concatenate updated x at SelfConnectionOutro) - """ - - def __init__( - self, - irreps_in: Irreps, - irreps_operand: Irreps, - irreps_out: Irreps, - data_key_x: str = KEY.NODE_FEATURE, - data_key_operand: str = KEY.NODE_ATTR, - lazy_layer_instantiate: bool = True, - **kwargs, # for compatibility - ): - super().__init__() - - self.fc_tensor_product = FullyConnectedTensorProduct( - irreps_in, irreps_operand, irreps_out - ) - self.irreps_in1 = irreps_in - self.irreps_in2 = irreps_operand - self.irreps_out = irreps_out - - self.key_x = data_key_x - self.key_operand = data_key_operand - - self.fc_tensor_product = None - self.layer_instantiated = False - self.fc_tensor_product_cls = FullyConnectedTensorProduct - self.fc_tensor_product_kwargs = kwargs - - if not lazy_layer_instantiate: - self.instantiate() - - def instantiate(self): - if self.fc_tensor_product is not None: - raise ValueError('fc_tensor_product layer already exists') - self.fc_tensor_product = self.fc_tensor_product_cls( - self.irreps_in1, - self.irreps_in2, - self.irreps_out, - shared_weights=True, - internal_weights=None, # same as True - **self.fc_tensor_product_kwargs, - ) - self.layer_instantiated = True - - def forward(self, data: AtomGraphDataType) -> AtomGraphDataType: - assert self.fc_tensor_product is not None, 'Layer is not instantiated' - data[KEY.SELF_CONNECTION_TEMP] = self.fc_tensor_product( - data[self.key_x], data[self.key_operand] - ) - return data - - -@compile_mode('script') -class SelfConnectionLinearIntro(nn.Module): - """ - Linear style self connection update - """ - - def __init__( - self, - irreps_in: Irreps, - irreps_out: Irreps, - data_key_x: str = KEY.NODE_FEATURE, - lazy_layer_instantiate: bool = True, - **kwargs, - ): - super().__init__() - self.irreps_in = irreps_in - self.irreps_out = irreps_out - self.key_x = data_key_x - - self.linear = None - self.layer_instantiated = False - self.linear_cls = Linear - - # TODO: better to have SelfConnectionIntro super class - kwargs.pop('irreps_operand') - self.linear_kwargs = kwargs - - if not lazy_layer_instantiate: - self.instantiate() - - def instantiate(self): - if self.linear is not None: - raise ValueError('Linear layer already exists') - self.linear = self.linear_cls( - self.irreps_in, self.irreps_out, **self.linear_kwargs - ) - self.layer_instantiated = True - - def forward(self, data: AtomGraphDataType) -> AtomGraphDataType: - assert self.linear is not None, 'Layer is not instantiated' - data[KEY.SELF_CONNECTION_TEMP] = self.linear(data[self.key_x]) - return data - - -@compile_mode('script') -class SelfConnectionOutro(nn.Module): - """ - do TensorProduct of x and some data(here attribute of x) - and save it (to concatenate updated x at SelfConnectionOutro) - """ - - def __init__( - self, - data_key_x: str = KEY.NODE_FEATURE, - ): - super().__init__() - self.key_x = data_key_x - - def forward(self, data: AtomGraphDataType) -> AtomGraphDataType: - data[self.key_x] = data[self.key_x] + data[KEY.SELF_CONNECTION_TEMP] - del data[KEY.SELF_CONNECTION_TEMP] - return data diff --git a/mace-bench/3rdparty/SevenNet/sevenn/nn/sequential.py b/mace-bench/3rdparty/SevenNet/sevenn/nn/sequential.py deleted file mode 100644 index c300814b220112258136f5b1f722a3a7c89b630f..0000000000000000000000000000000000000000 --- a/mace-bench/3rdparty/SevenNet/sevenn/nn/sequential.py +++ /dev/null @@ -1,183 +0,0 @@ -import warnings -from collections import OrderedDict -from typing import Dict, Optional - -import torch -import torch.nn as nn -from e3nn.util.jit import compile_mode - -import sevenn._keys as KEY -from sevenn._const import AtomGraphDataType - - -def _instantiate_modules(modules): - # see IrrepsLinear of linear.py - for module in modules.values(): - if not getattr(module, 'layer_instantiated', True): - module.instantiate() - - -@compile_mode('script') -class _ModalInputPrepare(nn.Module): - - def __init__( - self, - modal_idx: int - ): - super().__init__() - self.modal_idx = modal_idx - - def forward(self, data: AtomGraphDataType) -> AtomGraphDataType: - data[KEY.MODAL_TYPE] = torch.tensor( - self.modal_idx, - dtype=torch.int64, - device=data['x'].device, - ) - return data - - -@compile_mode('script') -class AtomGraphSequential(nn.Sequential): - """ - Wrapper of SevenNet model - - Args: - modules: OrderedDict of nn.Modules - cutoff: not used internally, but makes sense to have - type_map: atomic_numbers => onehot index (see nn/node_embedding.py) - eval_type_map: perform index mapping using type_map defaults to True - data_key_atomic_numbers: used when eval_type_map is True - data_key_node_feature: used when eval_type_map is True - data_key_grad: if given, sets its requires grad True before pred - """ - - def __init__( - self, - modules: Dict[str, nn.Module], - cutoff: float = 0.0, - type_map: Optional[Dict[int, int]] = None, - modal_map: Optional[Dict[str, int]] = None, - eval_type_map: bool = True, - eval_modal_map: bool = False, - data_key_atomic_numbers: str = KEY.ATOMIC_NUMBERS, - data_key_node_feature: str = KEY.NODE_FEATURE, - data_key_grad: Optional[str] = None, - ): - if not isinstance(modules, OrderedDict): # backward compat - modules = OrderedDict(modules) - self.cutoff = cutoff - self.type_map = type_map - self.eval_type_map = eval_type_map - self.is_batch_data = True - - if cutoff == 0.0: - warnings.warn('cutoff is 0.0 or not given', UserWarning) - - if self.type_map is None: - warnings.warn('type_map is not given', UserWarning) - self.eval_type_map = False - else: - z_to_onehot_tensor = torch.neg(torch.ones(120, dtype=torch.long)) - for z, onehot in self.type_map.items(): - z_to_onehot_tensor[z] = onehot - self.z_to_onehot_tensor = z_to_onehot_tensor - - if eval_modal_map and modal_map is None: - raise ValueError('eval_modal_map is True but modal_map is None') - self.eval_modal_map = eval_modal_map - self.modal_map = modal_map - - self.key_atomic_numbers = data_key_atomic_numbers - self.key_node_feature = data_key_node_feature - self.key_grad = data_key_grad - - _instantiate_modules(modules) - super().__init__(modules) - if not isinstance(self._modules, OrderedDict): # backward compat - self._modules = OrderedDict(self._modules) - - def set_is_batch_data(self, flag: bool): - # whether given data is batched or not some module have to change - # its behavior. checking whether data is batched or not inside - # forward function make problem harder when make it into torchscript - for module in self: - try: # Easier to ask for forgiveness than permission. - module._is_batch_data = flag # type: ignore - except AttributeError: - pass - self.is_batch_data = flag - - def get_irreps_in(self, modlue_name: str, attr_key: str = 'irreps_in'): - tg_module = self._modules[modlue_name] - for m in tg_module.modules(): - try: - return repr(m.__getattribute__(attr_key)) - except AttributeError: - pass - return None - - def prepand_module(self, key: str, module: nn.Module): - self._modules.update({key: module}) - self._modules.move_to_end(key, last=False) # type: ignore - - def replace_module(self, key: str, module: nn.Module): - self._modules.update({key: module}) - - def delete_module_by_key(self, key: str): - if key in self._modules.keys(): - del self._modules[key] - - @torch.jit.unused - def _atomic_numbers_to_onehot(self, atomic_numbers: torch.Tensor): - assert atomic_numbers.dtype == torch.int64 - device = atomic_numbers.device - z_to_onehot_tensor = self.z_to_onehot_tensor.to(device) - return torch.index_select( - input=z_to_onehot_tensor, dim=0, index=atomic_numbers - ) - - @torch.jit.unused - def _eval_modal_map(self, data: AtomGraphDataType): - assert self.modal_map is not None - # modal_map: dict[str, int] - if not self.is_batch_data: - modal_idx = self.modal_map[data[KEY.DATA_MODALITY]] # type: ignore - else: - modal_idx = [ - self.modal_map[ii] # type: ignore - for ii in data[KEY.DATA_MODALITY] - ] - modal_idx = torch.tensor( - modal_idx, - dtype=torch.int64, - device=data.x.device, # type: ignore - ) - data[KEY.MODAL_TYPE] = modal_idx - - def _preprocess(self, data: AtomGraphDataType) -> AtomGraphDataType: - if self.eval_type_map: - atomic_numbers = data[self.key_atomic_numbers] - onehot = self._atomic_numbers_to_onehot(atomic_numbers) - data[self.key_node_feature] = onehot - - if self.eval_modal_map: - self._eval_modal_map(data) - - if self.key_grad is not None: - data[self.key_grad].requires_grad_(True) - - return data - - def prepare_modal_deploy(self, modal: str): - if self.modal_map is None: - return - self.eval_modal_map = False - self.set_is_batch_data(False) - modal_idx = self.modal_map[modal] # type: ignore - self.prepand_module('modal_input_prepare', _ModalInputPrepare(modal_idx)) - - def forward(self, input: AtomGraphDataType) -> AtomGraphDataType: - data = self._preprocess(input) - for module in self: - data = module(data) - return data diff --git a/mace-bench/3rdparty/SevenNet/sevenn/nn/util.py b/mace-bench/3rdparty/SevenNet/sevenn/nn/util.py deleted file mode 100644 index cf29c969ff4dead378fde06c824e3e18a6a2f764..0000000000000000000000000000000000000000 --- a/mace-bench/3rdparty/SevenNet/sevenn/nn/util.py +++ /dev/null @@ -1,17 +0,0 @@ -import torch - - -def broadcast( - src: torch.Tensor, - other: torch.Tensor, - dim: int -): - if dim < 0: - dim = other.dim() + dim - if src.dim() == 1: - for _ in range(0, dim): - src = src.unsqueeze(0) - for _ in range(src.dim(), other.dim()): - src = src.unsqueeze(-1) - src = src.expand_as(other) - return src diff --git a/mace-bench/3rdparty/SevenNet/sevenn/pair_d3.so b/mace-bench/3rdparty/SevenNet/sevenn/pair_d3.so deleted file mode 100644 index 403c15bc2f6da3cd880a9cddc276ac09815bd614..0000000000000000000000000000000000000000 Binary files a/mace-bench/3rdparty/SevenNet/sevenn/pair_d3.so and /dev/null differ diff --git a/mace-bench/3rdparty/SevenNet/sevenn/pair_d3_for_ase.cuda.o b/mace-bench/3rdparty/SevenNet/sevenn/pair_d3_for_ase.cuda.o deleted file mode 100644 index 7a149054ae1c4a71029a33e1678cbd33ed74266d..0000000000000000000000000000000000000000 Binary files a/mace-bench/3rdparty/SevenNet/sevenn/pair_d3_for_ase.cuda.o and /dev/null differ diff --git a/mace-bench/3rdparty/SevenNet/sevenn/pair_e3gnn/README.md b/mace-bench/3rdparty/SevenNet/sevenn/pair_e3gnn/README.md deleted file mode 100644 index 4d33e2b102ca5158589e1552172002b1b93f8b86..0000000000000000000000000000000000000000 --- a/mace-bench/3rdparty/SevenNet/sevenn/pair_e3gnn/README.md +++ /dev/null @@ -1,77 +0,0 @@ -We support the LAMMPS pair style `d3` of the Grimme's D3 dispersion (van der Waals) correction scheme accelerated with CUDA, which can be used within LAMMPS in conjunction with SevenNet. - -**PLEASE NOTE:** Currently, this D3 code does not support mulit-GPU parallelism yet. So it can only be run on a single GPU. - -# About Grimme's D3 code accelerated with CUDA - -This is LAMMPS implementation of [Grimme's D3 method](https://doi.org/10.1063/1.3382344). We have ported the code from the [original fortran code](https://www.chemie.uni-bonn.de/grimme/de/software/dft-d3) to a LAMMPS pair style written in CUDA/C++. - -While D3 method is significantly faster than DFT, existing CPU implementations were slower than SevenNet. To address this, we have adopted CUDA and single precision (FP32) operations to accelerate the code. - -## Installation for LAMMPS - -Simply run, -```bash -sevenn_patch_lammps ./lammps_sevenn --d3 -``` - -You can follow the remaining installation steps in the [SevenNet documentation](../../README.md#installation-for-lammps). - -Also, this code requires a GPU with a compute capability of **at least 6.0**. If you try to compile it with version 5.0, you may encounter an `atomicAdd` error. - -The target compute capability of this code follows the setting of LibTorch in SevenNet, except for version 5.0. - -You can manually select the target capability using the `TORCH_CUDA_ARCH_LIST` environment variable. For example, you can use: `export TORCH_CUDA_ARCH_LIST="6.1;7.0;8.0;8.6;8.9;9.0"`. - -## Usage for LAMMPS - -You can use the D3 dispersion correction in LAMMPS with SevenNet through the `pair/hybrid` command: - -```txt -pair_style hybrid/overlay e3gnn d3 {cutoff_d3_r} {cutoff_d3_cn} {type_of_damping} {name_of_functional} -pair_coeff * * e3gnn {path_to_serial_model} {space_separated_chemical_species} -pair_coeff * * d3 {space_separated_chemical_species} -``` - -for example, - -```txt -pair_style hybrid/overlay e3gnn d3 9000 1600 damp_bj pbe -pair_coeff * * e3gnn ./deployed_serial.pt C H O -pair_coeff * * d3 C H O -``` - -`cutoff_d3_r` and `cutoff_d3_cn` are square of cutoff radii for energy/force and coordination number, respectively. Units are Bohr radius: 1 (Bohr radius) = 0.52917721 (Å). Default values are `9000` and `1600`, respectively. this is also the default values used in VASP.[^1] - -Available `type_of_damping` are as follows: -- `damp_zero`: Zero damping -- `damp_bj`: Becke-Johnson damping - -Available `name_of_functional` options are the same as in the original Fortran code. SevenNet-0 is trained on the 'PBE' functional, so you should specify 'pbe' in the script when using it. For other supporting functionals, check 'List of parametrized functionals' in [here](https://www.chemie.uni-bonn.de/grimme/de/software/dft-d3). - -## Features -- Selective(or no) periodic boundary condition: implemented, But only PBC/noPBC can be checked through original FORTRAN code; selective PBC cannot -- 3-body term, n > 8 term: not implemented (as to VASP) -- Modified versions of zero and bj damping - -## Cautions -- It can be slower than the CPU with a small number of atoms. -- The maximum number of atoms that can be calculated is 46,340 (overflow issue). -- There can be occurred small amounts of numerical error - - The introduction of some FP32 operations can lead to minor numerical errors, particularly in pressure calculations, but these are generally smaller than those seen with SevenNet. - - If the error is too large, ensure that the `fmad=false` option in `patch_lammps.sh` is correctly applied during build. - -## To do -- Remove atom_modify / compute virial dependency. -- Add support for ASE as calculator interface. -- Add support for multi GPUs (with `e3gnn/parallel`). -- Implement without Unified Memory. -- Unfix the `threadsPerBlock=128`. -- Unroll the repetition loop `k` (for small number of atoms). - -## Contributors -- Hyungmin An: Ported the original Fortran D3 code to C++ with OpenMP and MPI. -- Gijin Kim: Accelerated the C++ D3 code with OpenACC[^2] and CUDA, and currently maintains it. - -[^1]: On the [VASP DFT-D3](https://www.vasp.at/wiki/index.php/DFT-D3) page, the `VDW_RADIUS` and `VDW_CNRADIUS` are `50.2` and `20.0`, respectively (units are Å). However, when running VASP 6.3.2 with D3 using zero damping (BJ does not provide such a log), the default values in the OUTCAR file are `50.2022` and `21.1671`. These values are the same as our defaults. -[^2]: Since OpenACC is not compatible with libtorch, we chose to use the CUDA. diff --git a/mace-bench/3rdparty/SevenNet/sevenn/pair_e3gnn/comm_brick.cpp b/mace-bench/3rdparty/SevenNet/sevenn/pair_e3gnn/comm_brick.cpp deleted file mode 100644 index d7a6ea5494ecb7ab5610ef9ee52b0b22d88525a0..0000000000000000000000000000000000000000 --- a/mace-bench/3rdparty/SevenNet/sevenn/pair_e3gnn/comm_brick.cpp +++ /dev/null @@ -1,1724 +0,0 @@ -// clang-format off -/* ---------------------------------------------------------------------- - LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - https://www.lammps.org/, Sandia National Laboratories - LAMMPS development team: developers@lammps.org - - Copyright (2003) Sandia Corporation. Under the terms of Contract - DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains - certain rights in this software. This software is distributed under - the GNU General Public License. - - See the README file in the top-level LAMMPS directory. -------------------------------------------------------------------------- */ - -/* ---------------------------------------------------------------------- - Contributing author (triclinic) : Pieter in 't Veld (SNL) -------------------------------------------------------------------------- */ - -#include "comm_brick.h" - -#include "atom.h" -#include "atom_vec.h" -#include "bond.h" -#include "compute.h" -#include "domain.h" -#include "dump.h" -#include "error.h" -#include "fix.h" -#include "memory.h" -#include "neighbor.h" -#include "pair.h" - -#include -#include - -#include "pair_e3gnn_parallel.h" - -using namespace LAMMPS_NS; - -#define BUFFACTOR 1.5 -#define BUFMIN 1024 -#define BIG 1.0e20 - -/* ---------------------------------------------------------------------- */ - -CommBrick::CommBrick(LAMMPS *lmp) : - Comm(lmp), - sendnum(nullptr), recvnum(nullptr), sendproc(nullptr), recvproc(nullptr), - size_forward_recv(nullptr), size_reverse_send(nullptr), size_reverse_recv(nullptr), - slablo(nullptr), slabhi(nullptr), multilo(nullptr), multihi(nullptr), - multioldlo(nullptr), multioldhi(nullptr), cutghostmulti(nullptr), cutghostmultiold(nullptr), - pbc_flag(nullptr), pbc(nullptr), firstrecv(nullptr), sendlist(nullptr), - localsendlist(nullptr), maxsendlist(nullptr), buf_send(nullptr), buf_recv(nullptr) -{ - style = Comm::BRICK; - layout = Comm::LAYOUT_UNIFORM; - pbc_flag = nullptr; - init_buffers(); -} - -/* ---------------------------------------------------------------------- */ - -CommBrick::~CommBrick() -{ - CommBrick::free_swap(); - if (mode == Comm::MULTI) { - CommBrick::free_multi(); - memory->destroy(cutghostmulti); - } - - if (mode == Comm::MULTIOLD) { - CommBrick::free_multiold(); - memory->destroy(cutghostmultiold); - } - - if (sendlist) for (int i = 0; i < maxswap; i++) memory->destroy(sendlist[i]); - if (localsendlist) memory->destroy(localsendlist); - memory->sfree(sendlist); - memory->destroy(maxsendlist); - - memory->destroy(buf_send); - memory->destroy(buf_recv); -} - -/* ---------------------------------------------------------------------- */ -//IMPORTANT: we *MUST* pass "*oldcomm" to the Comm initializer here, as -// the code below *requires* that the (implicit) copy constructor -// for Comm is run and thus creating a shallow copy of "oldcomm". -// The call to Comm::copy_arrays() then converts the shallow copy -// into a deep copy of the class with the new layout. - -CommBrick::CommBrick(LAMMPS * /*lmp*/, Comm *oldcomm) : Comm(*oldcomm) -{ - if (oldcomm->layout == Comm::LAYOUT_TILED) - error->all(FLERR,"Cannot change to comm_style brick from tiled layout"); - - style = Comm::BRICK; - layout = oldcomm->layout; - Comm::copy_arrays(oldcomm); - init_buffers(); -} - -/* ---------------------------------------------------------------------- - initialize comm buffers and other data structs local to CommBrick -------------------------------------------------------------------------- */ - -void CommBrick::init_buffers() -{ - multilo = multihi = nullptr; - cutghostmulti = nullptr; - - multioldlo = multioldhi = nullptr; - cutghostmultiold = nullptr; - - buf_send = buf_recv = nullptr; - maxsend = maxrecv = BUFMIN; - CommBrick::grow_send(maxsend,2); - memory->create(buf_recv,maxrecv,"comm:buf_recv"); - - nswap = 0; - maxswap = 6; - CommBrick::allocate_swap(maxswap); - - sendlist = (int **) memory->smalloc(maxswap*sizeof(int *),"comm:sendlist"); - memory->create(maxsendlist,maxswap,"comm:maxsendlist"); - for (int i = 0; i < maxswap; i++) { - maxsendlist[i] = BUFMIN; - memory->create(sendlist[i],BUFMIN,"comm:sendlist[i]"); - } -} - -/* ---------------------------------------------------------------------- */ - -void CommBrick::init() -{ - Comm::init(); - - int bufextra_old = bufextra; - init_exchange(); - if (bufextra > bufextra_old) grow_send(maxsend+bufextra,2); - - // memory for multi style communication - // allocate in setup - - if (mode == Comm::MULTI) { - // If inconsitent # of collections, destroy any preexisting arrays (may be missized) - if (ncollections != neighbor->ncollections) { - ncollections = neighbor->ncollections; - if (multilo != nullptr) { - free_multi(); - memory->destroy(cutghostmulti); - } - } - - // delete any old user cutoffs if # of collections chanaged - if (cutusermulti && ncollections != ncollections_cutoff) { - if(me == 0) error->warning(FLERR, "cutoff/multi settings discarded, must be defined" - " after customizing collections in neigh_modify"); - memory->destroy(cutusermulti); - cutusermulti = nullptr; - } - - if (multilo == nullptr) { - allocate_multi(maxswap); - memory->create(cutghostmulti,ncollections,3,"comm:cutghostmulti"); - } - } - if ((mode == Comm::SINGLE || mode == Comm::MULTIOLD) && multilo) { - free_multi(); - memory->destroy(cutghostmulti); - } - - // memory for multi/old-style communication - - if (mode == Comm::MULTIOLD && multioldlo == nullptr) { - allocate_multiold(maxswap); - memory->create(cutghostmultiold,atom->ntypes+1,3,"comm:cutghostmultiold"); - } - if ((mode == Comm::SINGLE || mode == Comm::MULTI) && multioldlo) { - free_multiold(); - memory->destroy(cutghostmultiold); - } -} - -/* ---------------------------------------------------------------------- - setup spatial-decomposition communication patterns - function of neighbor cutoff(s) & cutghostuser & current box size - single mode sets slab boundaries (slablo,slabhi) based on max cutoff - multi mode sets collection-dependent slab boundaries (multilo,multihi) - multi/old mode sets type-dependent slab boundaries (multioldlo,multioldhi) -------------------------------------------------------------------------- */ - -void CommBrick::setup() -{ - // cutghost[] = max distance at which ghost atoms need to be acquired - // for orthogonal: - // cutghost is in box coords = neigh->cutghost in all 3 dims - // for triclinic: - // neigh->cutghost = distance between tilted planes in box coords - // cutghost is in lamda coords = distance between those planes - // for multi: - // cutghostmulti = same as cutghost, only for each atom collection - // for multi/old: - // cutghostmultiold = same as cutghost, only for each atom type - - int i,j; - int ntypes = atom->ntypes; - double *prd,*sublo,*subhi; - - double cut = get_comm_cutoff(); - if ((cut == 0.0) && (me == 0)) - error->warning(FLERR,"Communication cutoff is 0.0. No ghost atoms " - "will be generated. Atoms may get lost."); - - if (mode == Comm::MULTI) { - double **cutcollectionsq = neighbor->cutcollectionsq; - - // build collection array for atom exchange - neighbor->build_collection(0); - - // If using multi/reduce, communicate particles a distance equal - // to the max cutoff with equally sized or smaller collections - // If not, communicate the maximum cutoff of the entire collection - for (i = 0; i < ncollections; i++) { - if (cutusermulti) { - cutghostmulti[i][0] = cutusermulti[i]; - cutghostmulti[i][1] = cutusermulti[i]; - cutghostmulti[i][2] = cutusermulti[i]; - } else { - cutghostmulti[i][0] = 0.0; - cutghostmulti[i][1] = 0.0; - cutghostmulti[i][2] = 0.0; - } - - for (j = 0; j < ncollections; j++){ - if (multi_reduce && (cutcollectionsq[j][j] > cutcollectionsq[i][i])) continue; - cutghostmulti[i][0] = MAX(cutghostmulti[i][0],sqrt(cutcollectionsq[i][j])); - cutghostmulti[i][1] = MAX(cutghostmulti[i][1],sqrt(cutcollectionsq[i][j])); - cutghostmulti[i][2] = MAX(cutghostmulti[i][2],sqrt(cutcollectionsq[i][j])); - } - } - } - - if (mode == Comm::MULTIOLD) { - double *cuttype = neighbor->cuttype; - for (i = 1; i <= ntypes; i++) { - double tmp = 0.0; - if (cutusermultiold) tmp = cutusermultiold[i]; - cutghostmultiold[i][0] = MAX(tmp,cuttype[i]); - cutghostmultiold[i][1] = MAX(tmp,cuttype[i]); - cutghostmultiold[i][2] = MAX(tmp,cuttype[i]); - } - } - - if (triclinic == 0) { - prd = domain->prd; - sublo = domain->sublo; - subhi = domain->subhi; - cutghost[0] = cutghost[1] = cutghost[2] = cut; - } else { - prd = domain->prd_lamda; - sublo = domain->sublo_lamda; - subhi = domain->subhi_lamda; - double *h_inv = domain->h_inv; - double length0,length1,length2; - length0 = sqrt(h_inv[0]*h_inv[0] + h_inv[5]*h_inv[5] + h_inv[4]*h_inv[4]); - cutghost[0] = cut * length0; - length1 = sqrt(h_inv[1]*h_inv[1] + h_inv[3]*h_inv[3]); - cutghost[1] = cut * length1; - length2 = h_inv[2]; - cutghost[2] = cut * length2; - if (mode == Comm::MULTI) { - for (i = 0; i < ncollections; i++) { - cutghostmulti[i][0] *= length0; - cutghostmulti[i][1] *= length1; - cutghostmulti[i][2] *= length2; - } - } - - if (mode == Comm::MULTIOLD) { - for (i = 1; i <= ntypes; i++) { - cutghostmultiold[i][0] *= length0; - cutghostmultiold[i][1] *= length1; - cutghostmultiold[i][2] *= length2; - } - } - } - - // recvneed[idim][0/1] = # of procs away I recv atoms from, within cutghost - // 0 = from left, 1 = from right - // do not cross non-periodic boundaries, need[2] = 0 for 2d - // sendneed[idim][0/1] = # of procs away I send atoms to - // 0 = to left, 1 = to right - // set equal to recvneed[idim][1/0] of neighbor proc - // maxneed[idim] = max procs away any proc recvs atoms in either direction - // layout = UNIFORM = uniform sized sub-domains: - // maxneed is directly computable from sub-domain size - // limit to procgrid-1 for non-PBC - // recvneed = maxneed except for procs near non-PBC - // sendneed = recvneed of neighbor on each side - // layout = NONUNIFORM = non-uniform sized sub-domains: - // compute recvneed via updown() which accounts for non-PBC - // sendneed = recvneed of neighbor on each side - // maxneed via Allreduce() of recvneed - - int *periodicity = domain->periodicity; - int left,right; - - if (layout == Comm::LAYOUT_UNIFORM) { - maxneed[0] = static_cast (cutghost[0] * procgrid[0] / prd[0]) + 1; - maxneed[1] = static_cast (cutghost[1] * procgrid[1] / prd[1]) + 1; - maxneed[2] = static_cast (cutghost[2] * procgrid[2] / prd[2]) + 1; - if (domain->dimension == 2) maxneed[2] = 0; - if (!periodicity[0]) maxneed[0] = MIN(maxneed[0],procgrid[0]-1); - if (!periodicity[1]) maxneed[1] = MIN(maxneed[1],procgrid[1]-1); - if (!periodicity[2]) maxneed[2] = MIN(maxneed[2],procgrid[2]-1); - - if (!periodicity[0]) { - recvneed[0][0] = MIN(maxneed[0],myloc[0]); - recvneed[0][1] = MIN(maxneed[0],procgrid[0]-myloc[0]-1); - left = myloc[0] - 1; - if (left < 0) left = procgrid[0] - 1; - sendneed[0][0] = MIN(maxneed[0],procgrid[0]-left-1); - right = myloc[0] + 1; - if (right == procgrid[0]) right = 0; - sendneed[0][1] = MIN(maxneed[0],right); - } else recvneed[0][0] = recvneed[0][1] = - sendneed[0][0] = sendneed[0][1] = maxneed[0]; - - if (!periodicity[1]) { - recvneed[1][0] = MIN(maxneed[1],myloc[1]); - recvneed[1][1] = MIN(maxneed[1],procgrid[1]-myloc[1]-1); - left = myloc[1] - 1; - if (left < 0) left = procgrid[1] - 1; - sendneed[1][0] = MIN(maxneed[1],procgrid[1]-left-1); - right = myloc[1] + 1; - if (right == procgrid[1]) right = 0; - sendneed[1][1] = MIN(maxneed[1],right); - } else recvneed[1][0] = recvneed[1][1] = - sendneed[1][0] = sendneed[1][1] = maxneed[1]; - - if (!periodicity[2]) { - recvneed[2][0] = MIN(maxneed[2],myloc[2]); - recvneed[2][1] = MIN(maxneed[2],procgrid[2]-myloc[2]-1); - left = myloc[2] - 1; - if (left < 0) left = procgrid[2] - 1; - sendneed[2][0] = MIN(maxneed[2],procgrid[2]-left-1); - right = myloc[2] + 1; - if (right == procgrid[2]) right = 0; - sendneed[2][1] = MIN(maxneed[2],right); - } else recvneed[2][0] = recvneed[2][1] = - sendneed[2][0] = sendneed[2][1] = maxneed[2]; - - } else { - recvneed[0][0] = updown(0,0,myloc[0],prd[0],periodicity[0],xsplit); - recvneed[0][1] = updown(0,1,myloc[0],prd[0],periodicity[0],xsplit); - left = myloc[0] - 1; - if (left < 0) left = procgrid[0] - 1; - sendneed[0][0] = updown(0,1,left,prd[0],periodicity[0],xsplit); - right = myloc[0] + 1; - if (right == procgrid[0]) right = 0; - sendneed[0][1] = updown(0,0,right,prd[0],periodicity[0],xsplit); - - recvneed[1][0] = updown(1,0,myloc[1],prd[1],periodicity[1],ysplit); - recvneed[1][1] = updown(1,1,myloc[1],prd[1],periodicity[1],ysplit); - left = myloc[1] - 1; - if (left < 0) left = procgrid[1] - 1; - sendneed[1][0] = updown(1,1,left,prd[1],periodicity[1],ysplit); - right = myloc[1] + 1; - if (right == procgrid[1]) right = 0; - sendneed[1][1] = updown(1,0,right,prd[1],periodicity[1],ysplit); - - if (domain->dimension == 3) { - recvneed[2][0] = updown(2,0,myloc[2],prd[2],periodicity[2],zsplit); - recvneed[2][1] = updown(2,1,myloc[2],prd[2],periodicity[2],zsplit); - left = myloc[2] - 1; - if (left < 0) left = procgrid[2] - 1; - sendneed[2][0] = updown(2,1,left,prd[2],periodicity[2],zsplit); - right = myloc[2] + 1; - if (right == procgrid[2]) right = 0; - sendneed[2][1] = updown(2,0,right,prd[2],periodicity[2],zsplit); - } else recvneed[2][0] = recvneed[2][1] = - sendneed[2][0] = sendneed[2][1] = 0; - - int all[6]; - MPI_Allreduce(&recvneed[0][0],all,6,MPI_INT,MPI_MAX,world); - maxneed[0] = MAX(all[0],all[1]); - maxneed[1] = MAX(all[2],all[3]); - maxneed[2] = MAX(all[4],all[5]); - } - - // allocate comm memory - - nswap = 2 * (maxneed[0]+maxneed[1]+maxneed[2]); - if (nswap > maxswap) grow_swap(nswap); - - // setup parameters for each exchange: - // sendproc = proc to send to at each swap - // recvproc = proc to recv from at each swap - // for mode SINGLE: - // slablo/slabhi = boundaries for slab of atoms to send at each swap - // use -BIG/midpt/BIG to ensure all atoms included even if round-off occurs - // if round-off, atoms recvd across PBC can be < or > than subbox boundary - // note that borders() only loops over subset of atoms during each swap - // treat all as PBC here, non-PBC is handled in borders() via r/s need[][] - // for mode MULTI: - // multilo/multihi is same, with slablo/slabhi for each atom type - // pbc_flag: 0 = nothing across a boundary, 1 = something across a boundary - // pbc = -1/0/1 for PBC factor in each of 3/6 orthogonal/triclinic dirs - // for triclinic, slablo/hi and pbc_border will be used in lamda (0-1) coords - // 1st part of if statement is sending to the west/south/down - // 2nd part of if statement is sending to the east/north/up - - int dim,ineed; - - int iswap = 0; - for (dim = 0; dim < 3; dim++) { - for (ineed = 0; ineed < 2*maxneed[dim]; ineed++) { - pbc_flag[iswap] = 0; - pbc[iswap][0] = pbc[iswap][1] = pbc[iswap][2] = - pbc[iswap][3] = pbc[iswap][4] = pbc[iswap][5] = 0; - - if (ineed % 2 == 0) { - sendproc[iswap] = procneigh[dim][0]; - recvproc[iswap] = procneigh[dim][1]; - if (mode == Comm::SINGLE) { - if (ineed < 2) slablo[iswap] = -BIG; - else slablo[iswap] = 0.5 * (sublo[dim] + subhi[dim]); - slabhi[iswap] = sublo[dim] + cutghost[dim]; - } else if (mode == Comm::MULTI) { - for (i = 0; i < ncollections; i++) { - if (ineed < 2) multilo[iswap][i] = -BIG; - else multilo[iswap][i] = 0.5 * (sublo[dim] + subhi[dim]); - multihi[iswap][i] = sublo[dim] + cutghostmulti[i][dim]; - } - } else { - for (i = 1; i <= ntypes; i++) { - if (ineed < 2) multioldlo[iswap][i] = -BIG; - else multioldlo[iswap][i] = 0.5 * (sublo[dim] + subhi[dim]); - multioldhi[iswap][i] = sublo[dim] + cutghostmultiold[i][dim]; - } - } - if (myloc[dim] == 0) { - pbc_flag[iswap] = 1; - pbc[iswap][dim] = 1; - if (triclinic) { - if (dim == 1) pbc[iswap][5] = 1; - else if (dim == 2) pbc[iswap][4] = pbc[iswap][3] = 1; - } - } - - } else { - sendproc[iswap] = procneigh[dim][1]; - recvproc[iswap] = procneigh[dim][0]; - if (mode == Comm::SINGLE) { - slablo[iswap] = subhi[dim] - cutghost[dim]; - if (ineed < 2) slabhi[iswap] = BIG; - else slabhi[iswap] = 0.5 * (sublo[dim] + subhi[dim]); - } else if (mode == Comm::MULTI) { - for (i = 0; i < ncollections; i++) { - multilo[iswap][i] = subhi[dim] - cutghostmulti[i][dim]; - if (ineed < 2) multihi[iswap][i] = BIG; - else multihi[iswap][i] = 0.5 * (sublo[dim] + subhi[dim]); - } - } else { - for (i = 1; i <= ntypes; i++) { - multioldlo[iswap][i] = subhi[dim] - cutghostmultiold[i][dim]; - if (ineed < 2) multioldhi[iswap][i] = BIG; - else multioldhi[iswap][i] = 0.5 * (sublo[dim] + subhi[dim]); - } - } - if (myloc[dim] == procgrid[dim]-1) { - pbc_flag[iswap] = 1; - pbc[iswap][dim] = -1; - if (triclinic) { - if (dim == 1) pbc[iswap][5] = -1; - else if (dim == 2) pbc[iswap][4] = pbc[iswap][3] = -1; - } - } - } - - iswap++; - } - } -} - -/* ---------------------------------------------------------------------- - walk up/down the extent of nearby processors in dim and dir - loc = myloc of proc to start at - dir = 0/1 = walk to left/right - do not cross non-periodic boundaries - is not called for z dim in 2d - return how many procs away are needed to encompass cutghost away from loc -------------------------------------------------------------------------- */ - -int CommBrick::updown(int dim, int dir, int loc, double prd, int periodicity, double *split) -{ - int index,count; - double frac,delta; - - if (dir == 0) { - frac = cutghost[dim]/prd; - index = loc - 1; - delta = 0.0; - count = 0; - while (delta < frac) { - if (index < 0) { - if (!periodicity) break; - index = procgrid[dim] - 1; - } - count++; - delta += split[index+1] - split[index]; - index--; - } - - } else { - frac = cutghost[dim]/prd; - index = loc + 1; - delta = 0.0; - count = 0; - while (delta < frac) { - if (index >= procgrid[dim]) { - if (!periodicity) break; - index = 0; - } - count++; - delta += split[index+1] - split[index]; - index++; - } - } - - return count; -} - -/* ---------------------------------------------------------------------- - forward communication of atom coords every timestep - other per-atom attributes may also be sent via pack/unpack routines -------------------------------------------------------------------------- */ - -void CommBrick::forward_comm(int /*dummy*/) -{ - int n; - MPI_Request request; - AtomVec *avec = atom->avec; - double **x = atom->x; - double *buf; - - // exchange data with another proc - // if other proc is self, just copy - // if comm_x_only set, exchange or copy directly to x, don't unpack - - for (int iswap = 0; iswap < nswap; iswap++) { - if (sendproc[iswap] != me) { - if (comm_x_only) { - if (size_forward_recv[iswap]) { - buf = x[firstrecv[iswap]]; - MPI_Irecv(buf,size_forward_recv[iswap],MPI_DOUBLE,recvproc[iswap],0,world,&request); - } - n = avec->pack_comm(sendnum[iswap],sendlist[iswap],buf_send,pbc_flag[iswap],pbc[iswap]); - if (n) MPI_Send(buf_send,n,MPI_DOUBLE,sendproc[iswap],0,world); - if (size_forward_recv[iswap]) MPI_Wait(&request,MPI_STATUS_IGNORE); - } else if (ghost_velocity) { - if (size_forward_recv[iswap]) - MPI_Irecv(buf_recv,size_forward_recv[iswap],MPI_DOUBLE,recvproc[iswap],0,world,&request); - n = avec->pack_comm_vel(sendnum[iswap],sendlist[iswap],buf_send,pbc_flag[iswap],pbc[iswap]); - if (n) MPI_Send(buf_send,n,MPI_DOUBLE,sendproc[iswap],0,world); - if (size_forward_recv[iswap]) MPI_Wait(&request,MPI_STATUS_IGNORE); - avec->unpack_comm_vel(recvnum[iswap],firstrecv[iswap],buf_recv); - } else { - if (size_forward_recv[iswap]) - MPI_Irecv(buf_recv,size_forward_recv[iswap],MPI_DOUBLE, - recvproc[iswap],0,world,&request); - n = avec->pack_comm(sendnum[iswap],sendlist[iswap],buf_send,pbc_flag[iswap],pbc[iswap]); - if (n) MPI_Send(buf_send,n,MPI_DOUBLE,sendproc[iswap],0,world); - if (size_forward_recv[iswap]) MPI_Wait(&request,MPI_STATUS_IGNORE); - avec->unpack_comm(recvnum[iswap],firstrecv[iswap],buf_recv); - } - - } else { - if (comm_x_only) { - if (sendnum[iswap]) - avec->pack_comm(sendnum[iswap],sendlist[iswap], - x[firstrecv[iswap]],pbc_flag[iswap],pbc[iswap]); - } else if (ghost_velocity) { - avec->pack_comm_vel(sendnum[iswap],sendlist[iswap],buf_send,pbc_flag[iswap],pbc[iswap]); - avec->unpack_comm_vel(recvnum[iswap],firstrecv[iswap],buf_send); - } else { - avec->pack_comm(sendnum[iswap],sendlist[iswap],buf_send,pbc_flag[iswap],pbc[iswap]); - avec->unpack_comm(recvnum[iswap],firstrecv[iswap],buf_send); - } - } - } -} - -/* ---------------------------------------------------------------------- - reverse communication of forces on atoms every timestep - other per-atom attributes may also be sent via pack/unpack routines -------------------------------------------------------------------------- */ - -void CommBrick::reverse_comm() -{ - int n; - MPI_Request request; - AtomVec *avec = atom->avec; - double **f = atom->f; - double *buf; - - // exchange data with another proc - // if other proc is self, just copy - // if comm_f_only set, exchange or copy directly from f, don't pack - - for (int iswap = nswap-1; iswap >= 0; iswap--) { - if (sendproc[iswap] != me) { - if (comm_f_only) { - if (size_reverse_recv[iswap]) - MPI_Irecv(buf_recv,size_reverse_recv[iswap],MPI_DOUBLE,sendproc[iswap],0,world,&request); - if (size_reverse_send[iswap]) { - buf = f[firstrecv[iswap]]; - MPI_Send(buf,size_reverse_send[iswap],MPI_DOUBLE,recvproc[iswap],0,world); - } - if (size_reverse_recv[iswap]) MPI_Wait(&request,MPI_STATUS_IGNORE); - } else { - if (size_reverse_recv[iswap]) - MPI_Irecv(buf_recv,size_reverse_recv[iswap],MPI_DOUBLE,sendproc[iswap],0,world,&request); - n = avec->pack_reverse(recvnum[iswap],firstrecv[iswap],buf_send); - if (n) MPI_Send(buf_send,n,MPI_DOUBLE,recvproc[iswap],0,world); - if (size_reverse_recv[iswap]) MPI_Wait(&request,MPI_STATUS_IGNORE); - } - avec->unpack_reverse(sendnum[iswap],sendlist[iswap],buf_recv); - - } else { - if (comm_f_only) { - if (sendnum[iswap]) - avec->unpack_reverse(sendnum[iswap],sendlist[iswap],f[firstrecv[iswap]]); - } else { - avec->pack_reverse(recvnum[iswap],firstrecv[iswap],buf_send); - avec->unpack_reverse(sendnum[iswap],sendlist[iswap],buf_send); - } - } - } -} - -/* ---------------------------------------------------------------------- - exchange: move atoms to correct processors - atoms exchanged with all 6 stencil neighbors - send out atoms that have left my box, receive ones entering my box - atoms will be lost if not inside a stencil proc's box - can happen if atom moves outside of non-periodic boundary - or if atom moves more than one proc away - this routine called before every reneighboring - for triclinic, atoms must be in lamda coords (0-1) before exchange is called -------------------------------------------------------------------------- */ - -void CommBrick::exchange() -{ - int i,m,nsend,nrecv,nrecv1,nrecv2,nlocal; - double lo,hi,value; - double **x; - double *sublo,*subhi; - MPI_Request request; - AtomVec *avec = atom->avec; - - // clear global->local map for owned and ghost atoms - // b/c atoms migrate to new procs in exchange() and - // new ghosts are created in borders() - // map_set() is done at end of borders() - // clear ghost count and any ghost bonus data internal to AtomVec - - if (map_style != Atom::MAP_NONE) atom->map_clear(); - atom->nghost = 0; - atom->avec->clear_bonus(); - - // ensure send buf has extra space for a single atom - // only need to reset if a fix can dynamically add to size of single atom - - if (maxexchange_fix_dynamic) { - int bufextra_old = bufextra; - init_exchange(); - if (bufextra > bufextra_old) grow_send(maxsend+bufextra,2); - } - - // subbox bounds for orthogonal or triclinic - - if (triclinic == 0) { - sublo = domain->sublo; - subhi = domain->subhi; - } else { - sublo = domain->sublo_lamda; - subhi = domain->subhi_lamda; - } - - // loop over dimensions - - int dimension = domain->dimension; - - for (int dim = 0; dim < dimension; dim++) { - - // fill buffer with atoms leaving my box, using < and >= - // when atom is deleted, fill it in with last atom - - x = atom->x; - lo = sublo[dim]; - hi = subhi[dim]; - nlocal = atom->nlocal; - i = nsend = 0; - - while (i < nlocal) { - if (x[i][dim] < lo || x[i][dim] >= hi) { - if (nsend > maxsend) grow_send(nsend,1); - nsend += avec->pack_exchange(i,&buf_send[nsend]); - avec->copy(nlocal-1,i,1); - nlocal--; - } else i++; - } - atom->nlocal = nlocal; - - // send/recv atoms in both directions - // send size of message first so receiver can realloc buf_recv if needed - // if 1 proc in dimension, no send/recv - // set nrecv = 0 so buf_send atoms will be lost - // if 2 procs in dimension, single send/recv - // if more than 2 procs in dimension, send/recv to both neighbors - - if (procgrid[dim] == 1) nrecv = 0; - else { - MPI_Sendrecv(&nsend,1,MPI_INT,procneigh[dim][0],0, - &nrecv1,1,MPI_INT,procneigh[dim][1],0,world,MPI_STATUS_IGNORE); - nrecv = nrecv1; - if (procgrid[dim] > 2) { - MPI_Sendrecv(&nsend,1,MPI_INT,procneigh[dim][1],0, - &nrecv2,1,MPI_INT,procneigh[dim][0],0,world,MPI_STATUS_IGNORE); - nrecv += nrecv2; - } - if (nrecv > maxrecv) grow_recv(nrecv); - - MPI_Irecv(buf_recv,nrecv1,MPI_DOUBLE,procneigh[dim][1],0,world,&request); - MPI_Send(buf_send,nsend,MPI_DOUBLE,procneigh[dim][0],0,world); - MPI_Wait(&request,MPI_STATUS_IGNORE); - - if (procgrid[dim] > 2) { - MPI_Irecv(&buf_recv[nrecv1],nrecv2,MPI_DOUBLE,procneigh[dim][0],0,world,&request); - MPI_Send(buf_send,nsend,MPI_DOUBLE,procneigh[dim][1],0,world); - MPI_Wait(&request,MPI_STATUS_IGNORE); - } - } - - // check incoming atoms to see if they are in my box - // if so, add to my list - // box check is only for this dimension, - // atom may be passed to another proc in later dims - - m = 0; - while (m < nrecv) { - value = buf_recv[m+dim+1]; - if (value >= lo && value < hi) m += avec->unpack_exchange(&buf_recv[m]); - else m += static_cast (buf_recv[m]); - } - } - - if (atom->firstgroupname) atom->first_reorder(); -} - -/* ---------------------------------------------------------------------- - borders: list nearby atoms to send to neighboring procs at every timestep - one list is created for every swap that will be made - as list is made, actually do swaps - this does equivalent of a forward_comm(), so don't need to explicitly - call forward_comm() on reneighboring timestep - this routine is called before every reneighboring - for triclinic, atoms must be in lamda coords (0-1) before borders is called -------------------------------------------------------------------------- */ - -void CommBrick::borders() -{ - int i,n,itype,icollection,iswap,dim,ineed,twoneed; - int nsend,nrecv,sendflag,nfirst,nlast,ngroup,nprior; - double lo,hi; - int *type; - int *collection; - double **x; - double *buf,*mlo,*mhi; - MPI_Request request; - AtomVec *avec = atom->avec; - - // After exchanging/sorting, need to reconstruct collection array for border communication - if (mode == Comm::MULTI) neighbor->build_collection(0); - - // do swaps over all 3 dimensions - - iswap = 0; - smax = rmax = 0; - - for (dim = 0; dim < 3; dim++) { - nlast = 0; - twoneed = 2*maxneed[dim]; - for (ineed = 0; ineed < twoneed; ineed++) { - - // find atoms within slab boundaries lo/hi using <= and >= - // check atoms between nfirst and nlast - // for first swaps in a dim, check owned and ghost - // for later swaps in a dim, only check newly arrived ghosts - // store sent atom indices in sendlist for use in future timesteps - - x = atom->x; - if (mode == Comm::SINGLE) { - lo = slablo[iswap]; - hi = slabhi[iswap]; - } else if (mode == Comm::MULTI) { - collection = neighbor->collection; - mlo = multilo[iswap]; - mhi = multihi[iswap]; - } else { - type = atom->type; - mlo = multioldlo[iswap]; - mhi = multioldhi[iswap]; - } - if (ineed % 2 == 0) { - nfirst = nlast; - nlast = atom->nlocal + atom->nghost; - } - - nsend = 0; - - // sendflag = 0 if I do not send on this swap - // sendneed test indicates receiver no longer requires data - // e.g. due to non-PBC or non-uniform sub-domains - - if (ineed/2 >= sendneed[dim][ineed % 2]) sendflag = 0; - else sendflag = 1; - - // find send atoms according to SINGLE vs MULTI - // all atoms eligible versus only atoms in bordergroup - // can only limit loop to bordergroup for first sends (ineed < 2) - // on these sends, break loop in two: owned (in group) and ghost - - if (sendflag) { - if (!bordergroup || ineed >= 2) { - if (mode == Comm::SINGLE) { - for (i = nfirst; i < nlast; i++) - if (x[i][dim] >= lo && x[i][dim] <= hi) { - if (nsend == maxsendlist[iswap]) grow_list(iswap,nsend); - sendlist[iswap][nsend++] = i; - } - } else if (mode == Comm::MULTI) { - for (i = nfirst; i < nlast; i++) { - icollection = collection[i]; - if (x[i][dim] >= mlo[icollection] && x[i][dim] <= mhi[icollection]) { - if (nsend == maxsendlist[iswap]) grow_list(iswap,nsend); - sendlist[iswap][nsend++] = i; - } - } - } else { - for (i = nfirst; i < nlast; i++) { - itype = type[i]; - if (x[i][dim] >= mlo[itype] && x[i][dim] <= mhi[itype]) { - if (nsend == maxsendlist[iswap]) grow_list(iswap,nsend); - sendlist[iswap][nsend++] = i; - } - } - } - - } else { - if (mode == Comm::SINGLE) { - ngroup = atom->nfirst; - for (i = 0; i < ngroup; i++) - if (x[i][dim] >= lo && x[i][dim] <= hi) { - if (nsend == maxsendlist[iswap]) grow_list(iswap,nsend); - sendlist[iswap][nsend++] = i; - } - for (i = atom->nlocal; i < nlast; i++) - if (x[i][dim] >= lo && x[i][dim] <= hi) { - if (nsend == maxsendlist[iswap]) grow_list(iswap,nsend); - sendlist[iswap][nsend++] = i; - } - } else if (mode == Comm::MULTI) { - ngroup = atom->nfirst; - for (i = 0; i < ngroup; i++) { - icollection = collection[i]; - if (x[i][dim] >= mlo[icollection] && x[i][dim] <= mhi[icollection]) { - if (nsend == maxsendlist[iswap]) grow_list(iswap,nsend); - sendlist[iswap][nsend++] = i; - } - } - for (i = atom->nlocal; i < nlast; i++) { - icollection = collection[i]; - if (x[i][dim] >= mlo[icollection] && x[i][dim] <= mhi[icollection]) { - if (nsend == maxsendlist[iswap]) grow_list(iswap,nsend); - sendlist[iswap][nsend++] = i; - } - } - } else { - ngroup = atom->nfirst; - for (i = 0; i < ngroup; i++) { - itype = type[i]; - if (x[i][dim] >= mlo[itype] && x[i][dim] <= mhi[itype]) { - if (nsend == maxsendlist[iswap]) grow_list(iswap,nsend); - sendlist[iswap][nsend++] = i; - } - } - for (i = atom->nlocal; i < nlast; i++) { - itype = type[i]; - if (x[i][dim] >= mlo[itype] && x[i][dim] <= mhi[itype]) { - if (nsend == maxsendlist[iswap]) grow_list(iswap,nsend); - sendlist[iswap][nsend++] = i; - } - } - } - } - } - - // pack up list of border atoms - - if (nsend*size_border > maxsend) grow_send(nsend*size_border,0); - if (ghost_velocity) - n = avec->pack_border_vel(nsend,sendlist[iswap],buf_send,pbc_flag[iswap],pbc[iswap]); - else - n = avec->pack_border(nsend,sendlist[iswap],buf_send,pbc_flag[iswap],pbc[iswap]); - - // swap atoms with other proc - // no MPI calls except SendRecv if nsend/nrecv = 0 - // put incoming ghosts at end of my atom arrays - // if swapping with self, simply copy, no messages - - if (sendproc[iswap] != me) { - MPI_Sendrecv(&nsend,1,MPI_INT,sendproc[iswap],0, - &nrecv,1,MPI_INT,recvproc[iswap],0,world,MPI_STATUS_IGNORE); - if (nrecv*size_border > maxrecv) grow_recv(nrecv*size_border); - if (nrecv) MPI_Irecv(buf_recv,nrecv*size_border,MPI_DOUBLE, - recvproc[iswap],0,world,&request); - if (n) MPI_Send(buf_send,n,MPI_DOUBLE,sendproc[iswap],0,world); - if (nrecv) MPI_Wait(&request,MPI_STATUS_IGNORE); - buf = buf_recv; - } else { - nrecv = nsend; - buf = buf_send; - } - - // unpack buffer - - if (ghost_velocity) - avec->unpack_border_vel(nrecv,atom->nlocal+atom->nghost,buf); - else - avec->unpack_border(nrecv,atom->nlocal+atom->nghost,buf); - - // set all pointers & counters - - smax = MAX(smax,nsend); - rmax = MAX(rmax,nrecv); - sendnum[iswap] = nsend; - recvnum[iswap] = nrecv; - size_forward_recv[iswap] = nrecv*size_forward; - size_reverse_send[iswap] = nrecv*size_reverse; - size_reverse_recv[iswap] = nsend*size_reverse; - firstrecv[iswap] = atom->nlocal + atom->nghost; - nprior = atom->nlocal + atom->nghost; - atom->nghost += nrecv; - if (neighbor->style == Neighbor::MULTI) neighbor->build_collection(nprior); - - iswap++; - } - } - - // For molecular systems we lose some bits for local atom indices due - // to encoding of special pairs in neighbor lists. Check for overflows. - - if ((atom->molecular != Atom::ATOMIC) - && ((atom->nlocal + atom->nghost) > NEIGHMASK)) - error->one(FLERR,"Per-processor number of atoms is too large for " - "molecular neighbor lists"); - - // ensure send/recv buffers are long enough for all forward & reverse comm - - int max = MAX(maxforward*smax,maxreverse*rmax); - if (max > maxsend) grow_send(max,0); - max = MAX(maxforward*rmax,maxreverse*smax); - if (max > maxrecv) grow_recv(max); - - // reset global->local map - - if (map_style != Atom::MAP_NONE) atom->map_set(); -} - -/* ---------------------------------------------------------------------- - forward communication invoked by a Pair - nsize used only to set recv buffer limit -------------------------------------------------------------------------- */ - -void CommBrick::forward_comm(Pair *pair) -{ - int iswap,n; - double *buf; - MPI_Request request; - - int nsize = pair->comm_forward; - - for (iswap = 0; iswap < nswap; iswap++) { - - // pack buffer - - n = pair->pack_forward_comm(sendnum[iswap],sendlist[iswap],buf_send,pbc_flag[iswap],pbc[iswap]); - - // exchange with another proc - // if self, set recv buffer to send buffer - - if (sendproc[iswap] != me) { - if (recvnum[iswap]) - MPI_Irecv(buf_recv,nsize*recvnum[iswap],MPI_DOUBLE,recvproc[iswap],0,world,&request); - if (sendnum[iswap]) - MPI_Send(buf_send,n,MPI_DOUBLE,sendproc[iswap],0,world); - if (recvnum[iswap]) MPI_Wait(&request,MPI_STATUS_IGNORE); - buf = buf_recv; - } else buf = buf_send; - - // unpack buffer - - pair->unpack_forward_comm(recvnum[iswap],firstrecv[iswap],buf); - } -} - -/* ---------------------------------------------------------------------- - reverse communication invoked by a Pair - nsize used only to set recv buffer limit -------------------------------------------------------------------------- */ - -void CommBrick::reverse_comm(Pair *pair) -{ - int iswap,n; - double *buf; - MPI_Request request; - - int nsize = MAX(pair->comm_reverse,pair->comm_reverse_off); - - for (iswap = nswap-1; iswap >= 0; iswap--) { - - // pack buffer - - n = pair->pack_reverse_comm(recvnum[iswap],firstrecv[iswap],buf_send); - - // exchange with another proc - // if self, set recv buffer to send buffer - - if (sendproc[iswap] != me) { - if (sendnum[iswap]) - MPI_Irecv(buf_recv,nsize*sendnum[iswap],MPI_DOUBLE,sendproc[iswap],0,world,&request); - if (recvnum[iswap]) - MPI_Send(buf_send,n,MPI_DOUBLE,recvproc[iswap],0,world); - if (sendnum[iswap]) MPI_Wait(&request,MPI_STATUS_IGNORE); - buf = buf_recv; - } else buf = buf_send; - - // unpack buffer - - pair->unpack_reverse_comm(sendnum[iswap],sendlist[iswap],buf); - } -} - -void CommBrick::forward_comm(PairE3GNNParallel *pair) -{ - int iswap,n; - MPI_Request request; - - const bool comm_preprocess_done = pair->is_comm_preprocess_done(); - const int nsize = pair->get_x_dim(); - float *buf_send_, *buf_recv_; - if(pair->use_cuda_mpi_()) { - DeviceBuffManager::getInstance().get_buffer(maxsend+bufextra, maxrecv,buf_send_, buf_recv_); - } else { - buf_send_ = reinterpret_cast(buf_send); - buf_recv_ = reinterpret_cast(buf_recv); - } - if(!comm_preprocess_done) { - pair->notify_proc_ids(sendproc, recvproc); - } - if (nswap > 6) error->all(FLERR,"PairE3GNNParallel: Cell size is too small. Please use a single GPU or make a supercell"); - - for (iswap = 0; iswap < nswap; iswap++) { - if(sendproc[iswap] == me) continue; - - if(!comm_preprocess_done) { - pair->pack_forward_init(sendnum[iswap], sendlist[iswap], iswap); - pair->unpack_forward_init(recvnum[iswap], firstrecv[iswap], iswap); - } else { - n = pair->pack_forward_comm_gnn(buf_send_, iswap); - - if (recvnum[iswap]) - MPI_Irecv(buf_recv_,nsize*recvnum[iswap],MPI_FLOAT,recvproc[iswap],0,world,&request); - if (sendnum[iswap]) - MPI_Send(buf_send_,n,MPI_FLOAT,sendproc[iswap],0,world); - if (recvnum[iswap]) MPI_Wait(&request,MPI_STATUS_IGNORE); - - pair->unpack_forward_comm_gnn(buf_recv_, iswap); - } - } -} - -void CommBrick::reverse_comm(PairE3GNNParallel *pair) -{ - int iswap,n; - MPI_Request request; - - const bool comm_preprocess_done = pair->is_comm_preprocess_done(); - int nsize = pair->get_x_dim(); - float *buf_send_, *buf_recv_; - if(pair->use_cuda_mpi_()) { - DeviceBuffManager::getInstance().get_buffer(maxsend+bufextra, maxrecv,buf_send_, buf_recv_); - } else { - buf_send_ = reinterpret_cast(buf_send); - buf_recv_ = reinterpret_cast(buf_recv); - } - - for (iswap = nswap-1; iswap >= 0; iswap--) { - if(sendproc[iswap] == me) continue; - n = pair->pack_reverse_comm_gnn(buf_send_, iswap); - - if (sendnum[iswap]) - MPI_Irecv(buf_recv_,nsize*sendnum[iswap],MPI_FLOAT,sendproc[iswap],0,world,&request); - if (recvnum[iswap]) - MPI_Send(buf_send_,n,MPI_FLOAT,recvproc[iswap],0,world); - if (sendnum[iswap]) MPI_Wait(&request,MPI_STATUS_IGNORE); - - pair->unpack_reverse_comm_gnn(buf_recv_, iswap); - } -} -/* ---------------------------------------------------------------------- - forward communication invoked by a Bond - nsize used only to set recv buffer limit -------------------------------------------------------------------------- */ - -void CommBrick::forward_comm(Bond *bond) -{ - int iswap,n; - double *buf; - MPI_Request request; - - int nsize = bond->comm_forward; - - for (iswap = 0; iswap < nswap; iswap++) { - - // pack buffer - - n = bond->pack_forward_comm(sendnum[iswap],sendlist[iswap],buf_send,pbc_flag[iswap],pbc[iswap]); - - // exchange with another proc - // if self, set recv buffer to send buffer - - if (sendproc[iswap] != me) { - if (recvnum[iswap]) - MPI_Irecv(buf_recv,nsize*recvnum[iswap],MPI_DOUBLE,recvproc[iswap],0,world,&request); - if (sendnum[iswap]) - MPI_Send(buf_send,n,MPI_DOUBLE,sendproc[iswap],0,world); - if (recvnum[iswap]) MPI_Wait(&request,MPI_STATUS_IGNORE); - buf = buf_recv; - } else buf = buf_send; - - // unpack buffer - - bond->unpack_forward_comm(recvnum[iswap],firstrecv[iswap],buf); - } -} - -/* ---------------------------------------------------------------------- - reverse communication invoked by a Bond - nsize used only to set recv buffer limit -------------------------------------------------------------------------- */ - -void CommBrick::reverse_comm(Bond *bond) -{ - int iswap,n; - double *buf; - MPI_Request request; - - int nsize = MAX(bond->comm_reverse,bond->comm_reverse_off); - - for (iswap = nswap-1; iswap >= 0; iswap--) { - - // pack buffer - - n = bond->pack_reverse_comm(recvnum[iswap],firstrecv[iswap],buf_send); - - // exchange with another proc - // if self, set recv buffer to send buffer - - if (sendproc[iswap] != me) { - if (sendnum[iswap]) - MPI_Irecv(buf_recv,nsize*sendnum[iswap],MPI_DOUBLE,sendproc[iswap],0,world,&request); - if (recvnum[iswap]) - MPI_Send(buf_send,n,MPI_DOUBLE,recvproc[iswap],0,world); - if (sendnum[iswap]) MPI_Wait(&request,MPI_STATUS_IGNORE); - buf = buf_recv; - } else buf = buf_send; - - // unpack buffer - - bond->unpack_reverse_comm(sendnum[iswap],sendlist[iswap],buf); - } -} - -/* ---------------------------------------------------------------------- - forward communication invoked by a Fix - size/nsize used only to set recv buffer limit - size = 0 (default) -> use comm_forward from Fix - size > 0 -> Fix passes max size per atom - the latter is only useful if Fix does several comm modes, - some are smaller than max stored in its comm_forward -------------------------------------------------------------------------- */ - -void CommBrick::forward_comm(Fix *fix, int size) -{ - int iswap,n,nsize; - double *buf; - MPI_Request request; - - if (size) nsize = size; - else nsize = fix->comm_forward; - - for (iswap = 0; iswap < nswap; iswap++) { - - // pack buffer - - n = fix->pack_forward_comm(sendnum[iswap],sendlist[iswap],buf_send,pbc_flag[iswap],pbc[iswap]); - - // exchange with another proc - // if self, set recv buffer to send buffer - - if (sendproc[iswap] != me) { - if (recvnum[iswap]) - MPI_Irecv(buf_recv,nsize*recvnum[iswap],MPI_DOUBLE,recvproc[iswap],0,world,&request); - if (sendnum[iswap]) - MPI_Send(buf_send,n,MPI_DOUBLE,sendproc[iswap],0,world); - if (recvnum[iswap]) MPI_Wait(&request,MPI_STATUS_IGNORE); - buf = buf_recv; - } else buf = buf_send; - - // unpack buffer - - fix->unpack_forward_comm(recvnum[iswap],firstrecv[iswap],buf); - } -} - -/* ---------------------------------------------------------------------- - reverse communication invoked by a Fix - size/nsize used only to set recv buffer limit - size = 0 (default) -> use comm_forward from Fix - size > 0 -> Fix passes max size per atom - the latter is only useful if Fix does several comm modes, - some are smaller than max stored in its comm_forward -------------------------------------------------------------------------- */ - -void CommBrick::reverse_comm(Fix *fix, int size) -{ - int iswap,n,nsize; - double *buf; - MPI_Request request; - - if (size) nsize = size; - else nsize = fix->comm_reverse; - - for (iswap = nswap-1; iswap >= 0; iswap--) { - - // pack buffer - - n = fix->pack_reverse_comm(recvnum[iswap],firstrecv[iswap],buf_send); - - // exchange with another proc - // if self, set recv buffer to send buffer - - if (sendproc[iswap] != me) { - if (sendnum[iswap]) - MPI_Irecv(buf_recv,nsize*sendnum[iswap],MPI_DOUBLE,sendproc[iswap],0,world,&request); - if (recvnum[iswap]) - MPI_Send(buf_send,n,MPI_DOUBLE,recvproc[iswap],0,world); - if (sendnum[iswap]) MPI_Wait(&request,MPI_STATUS_IGNORE); - buf = buf_recv; - } else buf = buf_send; - - // unpack buffer - - fix->unpack_reverse_comm(sendnum[iswap],sendlist[iswap],buf); - } -} - -/* ---------------------------------------------------------------------- - reverse communication invoked by a Fix with variable size data - query fix for pack size to ensure buf_send is big enough - handshake sizes before each Irecv/Send to ensure buf_recv is big enough -------------------------------------------------------------------------- */ - -void CommBrick::reverse_comm_variable(Fix *fix) -{ - int iswap,nsend,nrecv; - double *buf; - MPI_Request request; - - for (iswap = nswap-1; iswap >= 0; iswap--) { - - // pack buffer - - nsend = fix->pack_reverse_comm_size(recvnum[iswap],firstrecv[iswap]); - if (nsend > maxsend) grow_send(nsend,0); - nsend = fix->pack_reverse_comm(recvnum[iswap],firstrecv[iswap],buf_send); - - // exchange with another proc - // if self, set recv buffer to send buffer - - if (sendproc[iswap] != me) { - MPI_Sendrecv(&nsend,1,MPI_INT,recvproc[iswap],0, - &nrecv,1,MPI_INT,sendproc[iswap],0,world,MPI_STATUS_IGNORE); - - if (sendnum[iswap]) { - if (nrecv > maxrecv) grow_recv(nrecv); - MPI_Irecv(buf_recv,maxrecv,MPI_DOUBLE,sendproc[iswap],0,world,&request); - } - if (recvnum[iswap]) - MPI_Send(buf_send,nsend,MPI_DOUBLE,recvproc[iswap],0,world); - if (sendnum[iswap]) MPI_Wait(&request,MPI_STATUS_IGNORE); - buf = buf_recv; - } else buf = buf_send; - - // unpack buffer - - fix->unpack_reverse_comm(sendnum[iswap],sendlist[iswap],buf); - } -} - -/* ---------------------------------------------------------------------- - forward communication invoked by a Compute - nsize used only to set recv buffer limit -------------------------------------------------------------------------- */ - -void CommBrick::forward_comm(Compute *compute) -{ - int iswap,n; - double *buf; - MPI_Request request; - - int nsize = compute->comm_forward; - - for (iswap = 0; iswap < nswap; iswap++) { - - // pack buffer - - n = compute->pack_forward_comm(sendnum[iswap],sendlist[iswap], - buf_send,pbc_flag[iswap],pbc[iswap]); - - // exchange with another proc - // if self, set recv buffer to send buffer - - if (sendproc[iswap] != me) { - if (recvnum[iswap]) - MPI_Irecv(buf_recv,nsize*recvnum[iswap],MPI_DOUBLE,recvproc[iswap],0,world,&request); - if (sendnum[iswap]) - MPI_Send(buf_send,n,MPI_DOUBLE,sendproc[iswap],0,world); - if (recvnum[iswap]) MPI_Wait(&request,MPI_STATUS_IGNORE); - buf = buf_recv; - } else buf = buf_send; - - // unpack buffer - - compute->unpack_forward_comm(recvnum[iswap],firstrecv[iswap],buf); - } -} - -/* ---------------------------------------------------------------------- - reverse communication invoked by a Compute - nsize used only to set recv buffer limit -------------------------------------------------------------------------- */ - -void CommBrick::reverse_comm(Compute *compute) -{ - int iswap,n; - double *buf; - MPI_Request request; - - int nsize = compute->comm_reverse; - - for (iswap = nswap-1; iswap >= 0; iswap--) { - - // pack buffer - - n = compute->pack_reverse_comm(recvnum[iswap],firstrecv[iswap],buf_send); - - // exchange with another proc - // if self, set recv buffer to send buffer - - if (sendproc[iswap] != me) { - if (sendnum[iswap]) - MPI_Irecv(buf_recv,nsize*sendnum[iswap],MPI_DOUBLE,sendproc[iswap],0,world,&request); - if (recvnum[iswap]) - MPI_Send(buf_send,n,MPI_DOUBLE,recvproc[iswap],0,world); - if (sendnum[iswap]) MPI_Wait(&request,MPI_STATUS_IGNORE); - buf = buf_recv; - } else buf = buf_send; - - // unpack buffer - - compute->unpack_reverse_comm(sendnum[iswap],sendlist[iswap],buf); - } -} - -/* ---------------------------------------------------------------------- - forward communication invoked by a Dump - nsize used only to set recv buffer limit -------------------------------------------------------------------------- */ - -void CommBrick::forward_comm(Dump *dump) -{ - int iswap,n; - double *buf; - MPI_Request request; - - int nsize = dump->comm_forward; - - for (iswap = 0; iswap < nswap; iswap++) { - - // pack buffer - - n = dump->pack_forward_comm(sendnum[iswap],sendlist[iswap], - buf_send,pbc_flag[iswap],pbc[iswap]); - - // exchange with another proc - // if self, set recv buffer to send buffer - - if (sendproc[iswap] != me) { - if (recvnum[iswap]) - MPI_Irecv(buf_recv,nsize*recvnum[iswap],MPI_DOUBLE,recvproc[iswap],0,world,&request); - if (sendnum[iswap]) - MPI_Send(buf_send,n,MPI_DOUBLE,sendproc[iswap],0,world); - if (recvnum[iswap]) MPI_Wait(&request,MPI_STATUS_IGNORE); - buf = buf_recv; - } else buf = buf_send; - - // unpack buffer - - dump->unpack_forward_comm(recvnum[iswap],firstrecv[iswap],buf); - } -} - -/* ---------------------------------------------------------------------- - reverse communication invoked by a Dump - nsize used only to set recv buffer limit -------------------------------------------------------------------------- */ - -void CommBrick::reverse_comm(Dump *dump) -{ - int iswap,n; - double *buf; - MPI_Request request; - - int nsize = dump->comm_reverse; - - for (iswap = nswap-1; iswap >= 0; iswap--) { - - // pack buffer - - n = dump->pack_reverse_comm(recvnum[iswap],firstrecv[iswap],buf_send); - - // exchange with another proc - // if self, set recv buffer to send buffer - - if (sendproc[iswap] != me) { - if (sendnum[iswap]) - MPI_Irecv(buf_recv,nsize*sendnum[iswap],MPI_DOUBLE,sendproc[iswap],0,world,&request); - if (recvnum[iswap]) - MPI_Send(buf_send,n,MPI_DOUBLE,recvproc[iswap],0,world); - if (sendnum[iswap]) MPI_Wait(&request,MPI_STATUS_IGNORE); - buf = buf_recv; - } else buf = buf_send; - - // unpack buffer - - dump->unpack_reverse_comm(sendnum[iswap],sendlist[iswap],buf); - } -} - -/* ---------------------------------------------------------------------- - forward communication of N values in per-atom array -------------------------------------------------------------------------- */ - -void CommBrick::forward_comm_array(int nsize, double **array) -{ - int i,j,k,m,iswap,last; - double *buf; - MPI_Request request; - - // ensure send/recv bufs are big enough for nsize - // based on smax/rmax from most recent borders() invocation - - if (nsize > maxforward) { - maxforward = nsize; - if (maxforward*smax > maxsend) grow_send(maxforward*smax,0); - if (maxforward*rmax > maxrecv) grow_recv(maxforward*rmax); - } - - for (iswap = 0; iswap < nswap; iswap++) { - - // pack buffer - - m = 0; - for (i = 0; i < sendnum[iswap]; i++) { - j = sendlist[iswap][i]; - for (k = 0; k < nsize; k++) - buf_send[m++] = array[j][k]; - } - - // exchange with another proc - // if self, set recv buffer to send buffer - - if (sendproc[iswap] != me) { - if (recvnum[iswap]) - MPI_Irecv(buf_recv,nsize*recvnum[iswap],MPI_DOUBLE,recvproc[iswap],0,world,&request); - if (sendnum[iswap]) - MPI_Send(buf_send,nsize*sendnum[iswap],MPI_DOUBLE,sendproc[iswap],0,world); - if (recvnum[iswap]) MPI_Wait(&request,MPI_STATUS_IGNORE); - buf = buf_recv; - } else buf = buf_send; - - // unpack buffer - - m = 0; - last = firstrecv[iswap] + recvnum[iswap]; - for (i = firstrecv[iswap]; i < last; i++) - for (k = 0; k < nsize; k++) - array[i][k] = buf[m++]; - } -} - -/* ---------------------------------------------------------------------- - realloc the size of the send buffer as needed with BUFFACTOR and bufextra - flag = 0, don't need to realloc with copy, just free/malloc w/ BUFFACTOR - flag = 1, realloc with BUFFACTOR - flag = 2, free/malloc w/out BUFFACTOR -------------------------------------------------------------------------- */ - -void CommBrick::grow_send(int n, int flag) -{ - if (flag == 0) { - maxsend = static_cast (BUFFACTOR * n); - memory->destroy(buf_send); - memory->create(buf_send,maxsend+bufextra,"comm:buf_send"); - } else if (flag == 1) { - maxsend = static_cast (BUFFACTOR * n); - memory->grow(buf_send,maxsend+bufextra,"comm:buf_send"); - } else { - memory->destroy(buf_send); - memory->grow(buf_send,maxsend+bufextra,"comm:buf_send"); - } -} - -/* ---------------------------------------------------------------------- - free/malloc the size of the recv buffer as needed with BUFFACTOR -------------------------------------------------------------------------- */ - -void CommBrick::grow_recv(int n) -{ - maxrecv = static_cast (BUFFACTOR * n); - memory->destroy(buf_recv); - memory->create(buf_recv,maxrecv,"comm:buf_recv"); -} - -/* ---------------------------------------------------------------------- - realloc the size of the iswap sendlist as needed with BUFFACTOR -------------------------------------------------------------------------- */ - -void CommBrick::grow_list(int iswap, int n) -{ - maxsendlist[iswap] = static_cast (BUFFACTOR * n); - memory->grow(sendlist[iswap],maxsendlist[iswap],"comm:sendlist[iswap]"); -} - -/* ---------------------------------------------------------------------- - realloc the buffers needed for swaps -------------------------------------------------------------------------- */ - -void CommBrick::grow_swap(int n) -{ - free_swap(); - allocate_swap(n); - if (mode == Comm::MULTI) { - free_multi(); - allocate_multi(n); - } - - if (mode == Comm::MULTIOLD) { - free_multiold(); - allocate_multiold(n); - } - - - sendlist = (int **) - memory->srealloc(sendlist,n*sizeof(int *),"comm:sendlist"); - memory->grow(maxsendlist,n,"comm:maxsendlist"); - for (int i = maxswap; i < n; i++) { - maxsendlist[i] = BUFMIN; - memory->create(sendlist[i],BUFMIN,"comm:sendlist[i]"); - } - maxswap = n; -} - -/* ---------------------------------------------------------------------- - allocation of swap info -------------------------------------------------------------------------- */ - -void CommBrick::allocate_swap(int n) -{ - memory->create(sendnum,n,"comm:sendnum"); - memory->create(recvnum,n,"comm:recvnum"); - memory->create(sendproc,n,"comm:sendproc"); - memory->create(recvproc,n,"comm:recvproc"); - memory->create(size_forward_recv,n,"comm:size"); - memory->create(size_reverse_send,n,"comm:size"); - memory->create(size_reverse_recv,n,"comm:size"); - memory->create(slablo,n,"comm:slablo"); - memory->create(slabhi,n,"comm:slabhi"); - memory->create(firstrecv,n,"comm:firstrecv"); - memory->create(pbc_flag,n,"comm:pbc_flag"); - memory->create(pbc,n,6,"comm:pbc"); -} - -/* ---------------------------------------------------------------------- - allocation of multi-collection swap info -------------------------------------------------------------------------- */ - -void CommBrick::allocate_multi(int n) -{ - multilo = memory->create(multilo,n,ncollections,"comm:multilo"); - multihi = memory->create(multihi,n,ncollections,"comm:multihi"); -} - -/* ---------------------------------------------------------------------- - allocation of multi/old-type swap info -------------------------------------------------------------------------- */ - -void CommBrick::allocate_multiold(int n) -{ - multioldlo = memory->create(multioldlo,n,atom->ntypes+1,"comm:multioldlo"); - multioldhi = memory->create(multioldhi,n,atom->ntypes+1,"comm:multioldhi"); -} - - -/* ---------------------------------------------------------------------- - free memory for swaps -------------------------------------------------------------------------- */ - -void CommBrick::free_swap() -{ - memory->destroy(sendnum); - memory->destroy(recvnum); - memory->destroy(sendproc); - memory->destroy(recvproc); - memory->destroy(size_forward_recv); - memory->destroy(size_reverse_send); - memory->destroy(size_reverse_recv); - memory->destroy(slablo); - memory->destroy(slabhi); - memory->destroy(firstrecv); - memory->destroy(pbc_flag); - memory->destroy(pbc); -} - -/* ---------------------------------------------------------------------- - free memory for multi-collection swaps -------------------------------------------------------------------------- */ - -void CommBrick::free_multi() -{ - memory->destroy(multilo); - memory->destroy(multihi); - multilo = multihi = nullptr; -} - -/* ---------------------------------------------------------------------- - free memory for multi/old-type swaps -------------------------------------------------------------------------- */ - -void CommBrick::free_multiold() -{ - memory->destroy(multioldlo); - memory->destroy(multioldhi); - multioldlo = multioldhi = nullptr; -} - -/* ---------------------------------------------------------------------- - extract data potentially useful to other classes -------------------------------------------------------------------------- */ - -void *CommBrick::extract(const char *str, int &dim) -{ - dim = 0; - if (strcmp(str,"localsendlist") == 0) { - int i, iswap, isend; - dim = 1; - if (!localsendlist) - memory->create(localsendlist,atom->nlocal,"comm:localsendlist"); - else - memory->grow(localsendlist,atom->nlocal,"comm:localsendlist"); - - for (i = 0; i < atom->nlocal; i++) - localsendlist[i] = 0; - - for (iswap = 0; iswap < nswap; iswap++) - for (isend = 0; isend < sendnum[iswap]; isend++) - if (sendlist[iswap][isend] < atom->nlocal) - localsendlist[sendlist[iswap][isend]] = 1; - - return (void *) localsendlist; - } - - return nullptr; -} - -/* ---------------------------------------------------------------------- - return # of bytes of allocated memory -------------------------------------------------------------------------- */ - -double CommBrick::memory_usage() -{ - double bytes = 0; - bytes += (double)nprocs * sizeof(int); // grid2proc - for (int i = 0; i < nswap; i++) - bytes += memory->usage(sendlist[i],maxsendlist[i]); - bytes += memory->usage(buf_send,maxsend+bufextra); - bytes += memory->usage(buf_recv,maxrecv); - return bytes; -} diff --git a/mace-bench/3rdparty/SevenNet/sevenn/pair_e3gnn/comm_brick.h b/mace-bench/3rdparty/SevenNet/sevenn/pair_e3gnn/comm_brick.h deleted file mode 100644 index 7ec590cc207879c9e0c0f465b38a54cd34c25b13..0000000000000000000000000000000000000000 --- a/mace-bench/3rdparty/SevenNet/sevenn/pair_e3gnn/comm_brick.h +++ /dev/null @@ -1,104 +0,0 @@ -/* -*- c++ -*- ---------------------------------------------------------- - LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - https://www.lammps.org/, Sandia National Laboratories - LAMMPS development team: developers@lammps.org - - Copyright (2003) Sandia Corporation. Under the terms of Contract - DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains - certain rights in this software. This software is distributed under - the GNU General Public License. - - See the README file in the top-level LAMMPS directory. -------------------------------------------------------------------------- */ - -#ifndef LMP_COMM_BRICK_H -#define LMP_COMM_BRICK_H - -#include "comm.h" - -namespace LAMMPS_NS { - -class CommBrick : public Comm { -public: - CommBrick(class LAMMPS *); - CommBrick(class LAMMPS *, class Comm *); - - ~CommBrick() override; - - void init() override; - void setup() override; // setup 3d comm pattern - void forward_comm(int dummy = 0) override; // forward comm of atom coords - void reverse_comm() override; // reverse comm of forces - void exchange() override; // move atoms to new procs - void borders() override; // setup list of atoms to comm - - void forward_comm(class Pair *) override; // forward comm from a Pair - void reverse_comm(class Pair *) override; // reverse comm from a Pair - void forward_comm(class Bond *) override; // forward comm from a Bond - void reverse_comm(class Bond *) override; // reverse comm from a Bond - void forward_comm(class Fix *, int size = 0) override; // forward comm from a Fix - void reverse_comm(class Fix *, int size = 0) override; // reverse comm from a Fix - void reverse_comm_variable(class Fix *) override; // variable size reverse comm from a Fix - void forward_comm(class Compute *) override; // forward from a Compute - void reverse_comm(class Compute *) override; // reverse from a Compute - void forward_comm(class Dump *) override; // forward comm from a Dump - void reverse_comm(class Dump *) override; // reverse comm from a Dump - - void forward_comm_array(int, double **) override; // forward comm of array - void *extract(const char *, int &) override; - double memory_usage() override; - - // patched from SevenNet // - void forward_comm(class PairE3GNNParallel *); - void reverse_comm(class PairE3GNNParallel *); - // patched from SevenNet // - -protected: - int nswap; // # of swaps to perform = sum of maxneed - int recvneed[3][2]; // # of procs away I recv atoms from - int sendneed[3][2]; // # of procs away I send atoms to - int maxneed[3]; // max procs away any proc needs, per dim - int maxswap; // max # of swaps memory is allocated for - int *sendnum, *recvnum; // # of atoms to send/recv in each swap - int *sendproc, *recvproc; // proc to send/recv to/from at each swap - int *size_forward_recv; // # of values to recv in each forward comm - int *size_reverse_send; // # to send in each reverse comm - int *size_reverse_recv; // # to recv in each reverse comm - double *slablo, *slabhi; // bounds of slab to send at each swap - double **multilo, **multihi; // bounds of slabs for multi-collection swap - double **multioldlo, **multioldhi; // bounds of slabs for multi-type swap - double **cutghostmulti; // cutghost on a per-collection basis - double **cutghostmultiold; // cutghost on a per-type basis - int *pbc_flag; // general flag for sending atoms thru PBC - int **pbc; // dimension flags for PBC adjustments - - int *firstrecv; // where to put 1st recv atom in each swap - int **sendlist; // list of atoms to send in each swap - int *localsendlist; // indexed list of local sendlist atoms - int *maxsendlist; // max size of send list for each swap - - double *buf_send; // send buffer for all comm - double *buf_recv; // recv buffer for all comm - int maxsend, maxrecv; // current size of send/recv buffer - int smax, rmax; // max size in atoms of single borders send/recv - - // NOTE: init_buffers is called from a constructor and must not be made virtual - void init_buffers(); - - int updown(int, int, int, double, int, double *); - // compare cutoff to procs - virtual void grow_send(int, int); // reallocate send buffer - virtual void grow_recv(int); // free/allocate recv buffer - virtual void grow_list(int, int); // reallocate one sendlist - virtual void grow_swap(int); // grow swap, multi, and multi/old arrays - virtual void allocate_swap(int); // allocate swap arrays - virtual void allocate_multi(int); // allocate multi arrays - virtual void allocate_multiold(int); // allocate multi/old arrays - virtual void free_swap(); // free swap arrays - virtual void free_multi(); // free multi arrays - virtual void free_multiold(); // free multi/old arrays -}; - -} // namespace LAMMPS_NS - -#endif diff --git a/mace-bench/3rdparty/SevenNet/sevenn/pair_e3gnn/pair_d3.cu b/mace-bench/3rdparty/SevenNet/sevenn/pair_e3gnn/pair_d3.cu deleted file mode 100644 index 1f05549b984bff4e678b56be1be2aa31296d2540..0000000000000000000000000000000000000000 --- a/mace-bench/3rdparty/SevenNet/sevenn/pair_e3gnn/pair_d3.cu +++ /dev/null @@ -1,2059 +0,0 @@ -/* ---------------------------------------------------------------------- - LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - https://www.lammps.org/, Sandia National Laboratories - LAMMPS development team: developers@lammps.org - - Copyright (2003) Sandia Corporation. Under the terms of Contract - DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains - certain rights in this software. This software is distributed under - the GNU General Public License. - - See the README file in the top-level LAMMPS directory. -------------------------------------------------------------------------- */ - -/* ---------------------------------------------------------------------- - Contributing author: Gijin Kim, Hyungmin An (SNU) -------------------------------------------------------------------------- */ - -#include "pair_d3.h" - -using namespace LAMMPS_NS; - -/* --------- Macros for CUDA error handling --------- */ -#define START_CUDA_TIMER() \ - cudaEvent_t start, stop; \ - cudaEventCreate(&start); \ - cudaEventCreate(&stop); \ - cudaEventRecord(start); - -#define STOP_CUDA_TIMER(tag) \ - cudaEventRecord(stop); \ - cudaEventSynchronize(stop); \ - float msec = 0; \ - cudaEventElapsedTime(&msec, start, stop); \ - printf("Elapsed time for %s: %f ms\n", tag, msec); \ - cudaEventDestroy(start); \ - cudaEventDestroy(stop); - -#define CHECK_CUDA(call) do { \ - cudaError_t status_ = call; \ - if (status_ != cudaSuccess) { \ - fprintf(stderr, "CUDA Error (%s:%d) -> %s: %s\n", __FILE__, __LINE__, \ - cudaGetErrorName(status_), cudaGetErrorString(status_)); \ - exit(EXIT_FAILURE); \ - } \ -} while (0) - -#define CHECK_CUDA_ERROR() do { \ - cudaDeviceSynchronize(); \ - cudaError_t status_ = cudaGetLastError(); \ - if (status_ != cudaSuccess) { \ - fprintf(stderr, "CUDA Error (%s:%d) -> %s: %s\n", __FILE__, __LINE__, \ - cudaGetErrorName(status_), cudaGetErrorString(status_)); \ - exit(EXIT_FAILURE); \ - } \ -} while (0) - -#define CHECK_CUDA_DEVICES() do { \ - int deviceCount = 0; \ - if (cudaGetDeviceCount(&deviceCount) != cudaSuccess || deviceCount == 0) { \ - fprintf(stderr, "CUDA Error (%s:%d) -> No CUDA devices found\n", \ - __FILE__, __LINE__); \ - exit(EXIT_FAILURE); \ - } \ -} while(0) -/* --------- Macros for CUDA error handling --------- */ - -/* --------- Math functions for CUDA compatibility --------- */ -inline __host__ __device__ void ij_at_linij(int linij, int &i, int &j) { - i = static_cast((sqrt(1 + 8 * linij) - 1) / 2); - j = linij - i * (i + 1) / 2; -} // unroll the triangular loop - -inline __host__ __device__ float lensq3(const float *v) -{ - return v[0] * v[0] + v[1] * v[1] + v[2] * v[2]; -} // from MathExtra::lensq3 -/* --------- Math functions for CUDA compatibility --------- */ - -/* ---------------------------------------------------------------------- - Constructor (Required) -------------------------------------------------------------------------- */ - -PairD3::PairD3(LAMMPS* lmp) : Pair(lmp) { - single_enable = 0; // potential is not pair-wise additive. - restartinfo = 0; // Many-body potentials are usually not - // written to binary restart files. - one_coeff = 1; // Many-body potnetials typically read all - // parameters from a file, so only one - // pair_coeff statement is needed. - manybody_flag = 1; - no_virial_fdotr_compute = 1; -} - -/* ---------------------------------------------------------------------- - Destructor (Required) -------------------------------------------------------------------------- */ - -PairD3::~PairD3() { - if (allocated) { - int n = atom->natoms; - int np1 = atom->ntypes + 1; - int vdw_range_x = 2 * rep_vdw[0] + 1; - int vdw_range_y = 2 * rep_vdw[1] + 1; - int vdw_range_z = 2 * rep_vdw[2] + 1; - int cn_range_x = 2 * rep_cn[0] + 1; - int cn_range_y = 2 * rep_cn[1] + 1; - int cn_range_z = 2 * rep_cn[2] + 1; - - for (int i = 0; i < np1; i++) { cudaFree(setflag[i]); }; cudaFree(setflag); - for (int i = 0; i < np1; i++) { cudaFree(cutsq[i]); }; cudaFree(cutsq); - cudaFree(r2r4); - cudaFree(rcov); - cudaFree(mxc); - for (int i = 0; i < np1; i++) { cudaFree(r0ab[i]); }; cudaFree(r0ab); - for (int i = 0; i < np1; i++) { - for (int j = 0; j < np1; j++) { - for (int k = 0; k < MAXC; k++) { - for (int l = 0; l < MAXC; l++) { - cudaFree(c6ab[i][j][k][l]); - } - cudaFree(c6ab[i][j][k]); - } - cudaFree(c6ab[i][j]); - } - cudaFree(c6ab[i]); - } - cudaFree(c6ab); - - cudaFree(lat_v_1); - cudaFree(lat_v_2); - cudaFree(lat_v_3); - - cudaFree(rep_vdw); - cudaFree(rep_cn); - cudaFree(cn); - for (int i = 0; i < n; i++) { cudaFree(x[i]); }; cudaFree(x); - - cudaFree(dc6i); - for (int i = 0; i < n; i++) { cudaFree(f[i]); }; cudaFree(f); - - for (int i = 0; i < 3; i++) { cudaFree(sigma[i]); }; cudaFree(sigma); - - cudaFree(dc6_iji_tot); - cudaFree(dc6_ijj_tot); - cudaFree(c6_ij_tot); - - for (int i = 0; i < vdw_range_x; i++) { - for (int j = 0; j < vdw_range_y; j++) { - for (int k = 0; k < vdw_range_z; k++) { - cudaFree(tau_vdw[i][j][k]); - } - cudaFree(tau_vdw[i][j]); - } - cudaFree(tau_vdw[i]); - } - cudaFree(tau_vdw); - for (int i = 0; i < cn_range_x; i++) { - for (int j = 0; j < cn_range_y; j++) { - for (int k = 0; k < cn_range_z; k++) { - cudaFree(tau_cn[i][j][k]); - } - cudaFree(tau_cn[i][j]); - } - cudaFree(tau_cn[i]); - } - cudaFree(tau_cn); - - cudaFree(tau_idx_vdw); - cudaFree(tau_idx_cn); - - cudaFree(atomtype); - cudaFree(disp); - } -} - -/* ---------------------------------------------------------------------- - Allocate all arrays (Required) -------------------------------------------------------------------------- */ - -void PairD3::allocate() { - CHECK_CUDA_DEVICES(); - allocated = 1; - - /* atom->ntypes : # of elements; element index starts from 1 */ - int n = atom->natoms; - int np1 = atom->ntypes + 1; - n_save = n; - - cudaMallocManaged(&setflag, np1 * sizeof(int*)); for (int i = 0; i < np1; i++) { cudaMallocManaged(&setflag[i], np1 * sizeof(int)); } - cudaMallocManaged(&cutsq, np1 * sizeof(double*)); for (int i = 0; i < np1; i++) { cudaMallocManaged(&cutsq[i], np1 * sizeof(double)); } - cudaMallocManaged(&r2r4, np1 * sizeof(float)); - cudaMallocManaged(&rcov, np1 * sizeof(float)); - cudaMallocManaged(&mxc, np1 * sizeof(int)); - cudaMallocManaged(&r0ab, np1 * sizeof(float*)); for (int i = 0; i < np1; i++) { cudaMallocManaged(&r0ab[i], np1 * sizeof(float)); } - cudaMallocManaged(&c6ab, np1 * sizeof(float****)); - for (int i = 0; i < np1; i++) { - cudaMallocManaged(&c6ab[i], np1 * sizeof(float***)); - for (int j = 0; j < np1; j++) { - cudaMallocManaged(&c6ab[i][j], MAXC * sizeof(float**)); - for (int k = 0; k < MAXC; k++) { - cudaMallocManaged(&c6ab[i][j][k], MAXC * sizeof(float*)); - for (int l = 0; l < MAXC; l++) { - cudaMallocManaged(&c6ab[i][j][k][l], 3 * sizeof(float)); - } - } - } - } - - cudaMallocManaged(&lat_v_1, 3 * sizeof(float)); - cudaMallocManaged(&lat_v_2, 3 * sizeof(float)); - cudaMallocManaged(&lat_v_3, 3 * sizeof(float)); - cudaMallocManaged(&rep_vdw, 3 * sizeof(int)); - cudaMallocManaged(&rep_cn, 3 * sizeof(int)); - cudaMallocManaged(&sigma, 3 * sizeof(double*)); for (int i = 0; i < 3; i++) { cudaMallocManaged(&sigma[i], 3 * sizeof(double)); } - - cudaMallocManaged(&cn, n * sizeof(double)); - cudaMallocManaged(&x, n * sizeof(float*)); for (int i = 0; i < n; i++) { cudaMallocManaged(&x[i], 3 * sizeof(float)); } - cudaMallocManaged(&dc6i, n * sizeof(double)); - cudaMallocManaged(&f, n * sizeof(double*)); for (int i = 0; i < n; i++) { cudaMallocManaged(&f[i], 3 * sizeof(double)); } - - // Initialization - // Initialize for lattice -> set_lattice_vectors() - tau_idx_vdw_total_size = -1; - tau_idx_cn_total_size = -1; - for (int i = 0; i < 3; i++) { - rep_vdw[i] = -1; - rep_cn[i] = -1; - } - - for (int i = 1; i < np1; i++) { - for (int j = 1; j < np1; j++) { - setflag[i][j] = 0; - } - } - - for (int idx1 = 0; idx1 < np1; idx1++) { - for (int idx2 = 0; idx2 < np1; idx2++) { - for (int idx3 = 0; idx3 < MAXC; idx3++) { - for (int idx4 = 0; idx4 < MAXC; idx4++) { - for (int idx5 = 0; idx5 < 3; idx5++) { - c6ab[idx1][idx2][idx3][idx4][idx5] = -1; - } - } - } - } - } - - int n_ij_combination = n * (n + 1) / 2; - cudaMallocManaged(&dc6_iji_tot, n_ij_combination * sizeof(float)); - cudaMallocManaged(&dc6_ijj_tot, n_ij_combination * sizeof(float)); - cudaMallocManaged(&c6_ij_tot, n_ij_combination * sizeof(float)); - - cudaMallocManaged(&atomtype, n * sizeof(int)); - cudaMallocManaged(&disp, sizeof(double)); -} - -/* ---------------------------------------------------------------------- - Settings : read from pair_style (Required) -> pair_style d3 vdw_sq cn_sq damp_name func_name -------------------------------------------------------------------------- */ - -void PairD3::settings(int narg, char **arg) { - if (narg != 4) { - error->all(FLERR, - "Pair_style d3 needs Four arguments:\n" - "\t rthr: cutoff radius for dispersion interaction (a.u.^2)\n" - "\t cnthr: cutoff raius for coordination number (a.u.^2)\n" - "\t damping: name of the damping function (e.g., damp_zero, damp_bj)\n" - "\t functional: name of the functional (e.g., pbe, b3-lyp)\n" - ); - } - rthr = utils::numeric(FLERR, arg[0], false, lmp); - cnthr = utils::numeric(FLERR, arg[1], false, lmp); - - std::map commandMap = { - {"damp_zero", 0}, {"damp_bj", 1}, {"damp_zerom", 2}, {"damp_bjm", 3}, - }; - - if (commandMap.find(arg[2]) == commandMap.end()) { - error->all(FLERR, "Unknown damping function"); - } - - damping = commandMap[arg[2]]; - functional = arg[3]; - - setfuncpar(); -} - -/* ---------------------------------------------------------------------- - finds atomic number (used in PairD3::coeff) -------------------------------------------------------------------------- */ - -int PairD3::find_atomic_number(std::string& key) { - std::transform(key.begin(), key.end(), key.begin(), ::tolower); - if (key.length() == 1) { key += " "; } - key.resize(2); - - std::vector element_table = { - "h ","he", - "li","be","b ","c ","n ","o ","f ","ne", - "na","mg","al","si","p ","s ","cl","ar", - "k ","ca","sc","ti","v ","cr","mn","fe","co","ni","cu", - "zn","ga","ge","as","se","br","kr", - "rb","sr","y ","zr","nb","mo","tc","ru","rh","pd","ag", - "cd","in","sn","sb","te","i ","xe", - "cs","ba","la","ce","pr","nd","pm","sm","eu","gd","tb","dy", - "ho","er","tm","yb","lu","hf","ta","w ","re","os","ir","pt", - "au","hg","tl","pb","bi","po","at","rn", - "fr","ra","ac","th","pa","u ","np","pu" - }; - - for (size_t i = 0; i < element_table.size(); ++i) { - if (element_table[i] == key) { - int atomic_number = i + 1; - return atomic_number; - } - } - - // if not the case - return -1; -} - -/* ---------------------------------------------------------------------- - Check whether an integer value in an integer array (used in PairD3::coeff) -------------------------------------------------------------------------- */ - -int PairD3::is_int_in_array(int arr[], int size, int value) { - for (int i = 0; i < size; i++) { - if (arr[i] == value) { return i; } // returns the index - } - return -1; -} - -/* ---------------------------------------------------------------------- - Read r0ab values from the table (used in PairD3::coeff) -------------------------------------------------------------------------- */ - -void PairD3::read_r0ab(int* atomic_numbers, int ntypes) { - const double r0ab_table[94][94] = R0AB_TABLE; - - for (int i = 1; i <= ntypes; i++) { - for (int j = 1; j <= ntypes; j++) { - r0ab[i][j] = r0ab_table[atomic_numbers[i-1]-1][atomic_numbers[j-1]-1] / AU_TO_ANG; - } - } -} - -/* ---------------------------------------------------------------------- - Get atom pair indices and grid indices (used in PairD3::read_c6ab) -------------------------------------------------------------------------- */ - -void PairD3::get_limit_in_pars_array(int& idx_atom_1, int& idx_atom_2, int& idx_i, int& idx_j) { - const int shift = 100; - - idx_i = (idx_atom_1 - 1) / shift + 1; - idx_j = (idx_atom_2 - 1) / shift + 1; - - idx_atom_1 = (idx_atom_1 - 1) % shift + 1; - idx_atom_2 = (idx_atom_2 - 1) % shift + 1; - - // the code above replaces the code below - //idx_i = 1; - //idx_j = 1; - //int shift = 100; - //while (idx_atom_1 > shift) { idx_atom_1 -= shift; idx_i++; } - //while (idx_atom_2 > shift) { idx_atom_2 -= shift; idx_j++; } -} - -/* ---------------------------------------------------------------------- - Read c6ab values from the table (used in PairD3::coeff) -------------------------------------------------------------------------- */ - -void PairD3::read_c6ab(int* atomic_numbers, int ntypes) { - for (int i = 1; i <= ntypes; i++) { mxc[i] = 0; } - int grid_i = 0, grid_j = 0; - - const double c6ab_table[32385][5] = C6AB_TABLE; - - for (int i = 0; i < 32385; i++) { - const double ref_c6 = c6ab_table[i][0]; - int atom_number_1 = static_cast(c6ab_table[i][1]); - int atom_number_2 = static_cast(c6ab_table[i][2]); - get_limit_in_pars_array(atom_number_1, atom_number_2, grid_i, grid_j); - const int idx_atom_1 = is_int_in_array(atomic_numbers, ntypes, atom_number_1); - if (idx_atom_1 < 0) { continue; } - const int idx_atom_2 = is_int_in_array(atomic_numbers, ntypes, atom_number_2); - if (idx_atom_2 < 0) { continue; } - const double ref_cn1 = c6ab_table[i][3]; - const double ref_cn2 = c6ab_table[i][4]; - - mxc[idx_atom_1 + 1] = std::max(mxc[idx_atom_1 + 1], grid_i); - mxc[idx_atom_2 + 1] = std::max(mxc[idx_atom_2 + 1], grid_j); - c6ab[idx_atom_1 + 1][idx_atom_2 + 1][grid_i - 1][grid_j - 1][0] = ref_c6; - c6ab[idx_atom_1 + 1][idx_atom_2 + 1][grid_i - 1][grid_j - 1][1] = ref_cn1; - c6ab[idx_atom_1 + 1][idx_atom_2 + 1][grid_i - 1][grid_j - 1][2] = ref_cn2; - c6ab[idx_atom_2 + 1][idx_atom_1 + 1][grid_j - 1][grid_i - 1][0] = ref_c6; - c6ab[idx_atom_2 + 1][idx_atom_1 + 1][grid_j - 1][grid_i - 1][1] = ref_cn2; - c6ab[idx_atom_2 + 1][idx_atom_1 + 1][grid_j - 1][grid_i - 1][2] = ref_cn1; - } -} - -/* ---------------------------------------------------------------------- - Set functional parameters (used in PairD3::coeff) -------------------------------------------------------------------------- */ - -void PairD3::setfuncpar_zero() { - s6 = 1.0; - alp = 14.0; - rs18 = 1.0; - - // default def2-QZVP (almost basis set limit) - std::unordered_map commandMap = { - { "slater-dirac-exchange", 1}, { "b-lyp", 2 }, { "b-p", 3 }, { "b97-d", 4 }, { "revpbe", 5 }, - { "pbe", 6 }, { "pbesol", 7 }, { "rpw86-pbe", 8 }, { "rpbe", 9 }, { "tpss", 10 }, - { "b3-lyp", 11 }, { "pbe0", 12 }, { "hse06", 13 }, { "revpbe38", 14 }, { "pw6b95", 15 }, - { "tpss0", 16 }, { "b2-plyp", 17 }, { "pwpb95", 18 }, { "b2gp-plyp", 19 }, { "ptpss", 20 }, - { "hf", 21 }, { "mpwlyp", 22 }, { "bpbe", 23 }, { "bh-lyp", 24 }, { "tpssh", 25 }, - { "pwb6k", 26 }, { "b1b95", 27 }, { "bop", 28 }, { "o-lyp", 29 }, { "o-pbe", 30 }, - { "ssb", 31 }, { "revssb", 32 }, { "otpss", 33 }, { "b3pw91", 34 }, { "revpbe0", 35 }, - { "pbe38", 36 }, { "mpw1b95", 37 }, { "mpwb1k", 38 }, { "bmk", 39 }, { "cam-b3lyp", 40 }, - { "lc-wpbe", 41 }, { "m05", 42 }, { "m052x", 43 }, { "m06l", 44 }, { "m06", 45 }, - { "m062x", 46 }, { "m06hf", 47 }, { "hcth120", 48 } - }; - - int commandCode = commandMap[functional]; - switch (commandCode) { - case 1: rs6 = 0.999; s18 = -1.957; rs18 = 0.697; break; - case 2: rs6 = 1.094; s18 = 1.682; break; - case 3: rs6 = 1.139; s18 = 1.683; break; - case 4: rs6 = 0.892; s18 = 0.909; break; - case 5: rs6 = 0.923; s18 = 1.010; break; - case 6: rs6 = 1.217; s18 = 0.722; break; - case 7: rs6 = 1.345; s18 = 0.612; break; - case 8: rs6 = 1.224; s18 = 0.901; break; - case 9: rs6 = 0.872; s18 = 0.514; break; - case 10: rs6 = 1.166; s18 = 1.105; break; - case 11: rs6 = 1.261; s18 = 1.703; break; - case 12: rs6 = 1.287; s18 = 0.928; break; - case 13: rs6 = 1.129; s18 = 0.109; break; - case 14: rs6 = 1.021; s18 = 0.862; break; - case 15: rs6 = 1.532; s18 = 0.862; break; - case 16: rs6 = 1.252; s18 = 1.242; break; - case 17: rs6 = 1.427; s18 = 1.022; s6 = 0.64; break; - case 18: rs6 = 1.557; s18 = 0.705; s6 = 0.82; break; - case 19: rs6 = 1.586; s18 = 0.760; s6 = 0.56; break; - case 20: rs6 = 1.541; s18 = 0.879; s6 = 0.75; break; - case 21: rs6 = 1.158; s18 = 1.746; break; - case 22: rs6 = 1.239; s18 = 1.098; break; - case 23: rs6 = 1.087; s18 = 2.033; break; - case 24: rs6 = 1.370; s18 = 1.442; break; - case 25: rs6 = 1.223; s18 = 1.219; break; - case 26: rs6 = 1.660; s18 = 0.550; break; - case 27: rs6 = 1.613; s18 = 1.868; break; - case 28: rs6 = 0.929; s18 = 1.975; break; - case 29: rs6 = 0.806; s18 = 1.764; break; - case 30: rs6 = 0.837; s18 = 2.055; break; - case 31: rs6 = 1.215; s18 = 0.663; break; - case 32: rs6 = 1.221; s18 = 0.560; break; - case 33: rs6 = 1.128; s18 = 1.494; break; - case 34: rs6 = 1.176; s18 = 1.775; break; - case 35: rs6 = 0.949; s18 = 0.792; break; - case 36: rs6 = 1.333; s18 = 0.998; break; - case 37: rs6 = 1.605; s18 = 1.118; break; - case 38: rs6 = 1.671; s18 = 1.061; break; - case 39: rs6 = 1.931; s18 = 2.168; break; - case 40: rs6 = 1.378; s18 = 1.217; break; - case 41: rs6 = 1.355; s18 = 1.279; break; - case 42: rs6 = 1.373; s18 = 0.595; break; - case 43: rs6 = 1.417; s18 = 0.000; break; - case 44: rs6 = 1.581; s18 = 0.000; break; - case 45: rs6 = 1.325; s18 = 0.000; break; - case 46: rs6 = 1.619; s18 = 0.000; break; - case 47: rs6 = 1.446; s18 = 0.000; break; - /* DFTB3(zeta = 4.0), old deprecated parameters; case ("dftb3"); rs6 = 1.235; s18 = 0.673; */ - case 48: rs6 = 1.221; s18 = 1.206; break; - default: - error->all(FLERR, "Functional name unknown"); - break; - } -} - -void PairD3::setfuncpar_bj() { - s6 = 1.0; - alp = 14.0; - - std::unordered_map commandMap = { - {"b-p", 1}, {"b-lyp", 2}, {"revpbe", 3}, {"rpbe", 4}, {"b97-d", 5}, {"pbe", 6}, - {"rpw86-pbe", 7}, {"b3-lyp", 8}, {"tpss", 9}, {"hf", 10}, {"tpss0", 11}, {"pbe0", 12}, - {"hse06", 13}, {"revpbe38", 14}, {"pw6b95", 15}, {"b2-plyp", 16}, {"dsd-blyp", 17}, - {"dsd-blyp-fc", 18}, {"bop", 19}, {"mpwlyp", 20}, {"o-lyp", 21}, {"pbesol", 22}, {"bpbe", 23}, - {"opbe", 24}, {"ssb", 25}, {"revssb", 26}, {"otpss", 27}, {"b3pw91", 28}, {"bh-lyp", 29}, - {"revpbe0", 30}, {"tpssh", 31}, {"mpw1b95", 32}, {"pwb6k", 33}, {"b1b95", 34}, {"bmk", 35}, - {"cam-b3lyp", 36}, {"lc-wpbe", 37}, {"b2gp-plyp", 38}, {"ptpss", 39}, {"pwpb95", 40}, - {"hf/mixed", 41}, {"hf/sv", 42}, {"hf/minis", 43}, {"b3-lyp/6-31gd", 44}, {"hcth120", 45}, - {"pw1pw", 46}, {"pwgga", 47}, {"hsesol", 48}, {"hf3c", 49}, {"hf3cv", 50}, {"pbeh3c", 51}, - {"pbeh-3c", 52}, {"wb97m", 53} - }; - - int commandCode = commandMap[functional]; - switch (commandCode) { - case 1: rs6 = 0.3946; s18 = 3.2822; rs18 = 4.8516; break; - case 2: rs6 = 0.4298; s18 = 2.6996; rs18 = 4.2359; break; - case 3: rs6 = 0.5238; s18 = 2.3550; rs18 = 3.5016; break; - case 4: rs6 = 0.1820; s18 = 0.8318; rs18 = 4.0094; break; - case 5: rs6 = 0.5545; s18 = 2.2609; rs18 = 3.2297; break; - case 6: rs6 = 0.4289; s18 = 0.7875; rs18 = 4.4407; break; - case 7: rs6 = 0.4613; s18 = 1.3845; rs18 = 4.5062; break; - case 8: rs6 = 0.3981; s18 = 1.9889; rs18 = 4.4211; break; - case 9: rs6 = 0.4535; s18 = 1.9435; rs18 = 4.4752; break; - case 10: rs6 = 0.3385; s18 = 0.9171; rs18 = 2.8830; break; - case 11: rs6 = 0.3768; s18 = 1.2576; rs18 = 4.5865; break; - case 12: rs6 = 0.4145; s18 = 1.2177; rs18 = 4.8593; break; - case 13: rs6 = 0.383; s18 = 2.310; rs18 = 5.685; break; - case 14: rs6 = 0.4309; s18 = 1.4760; rs18 = 3.9446; break; - case 15: rs6 = 0.2076; s18 = 0.7257; rs18 = 6.3750; break; - case 16: rs6 = 0.3065; s18 = 0.9147; rs18 = 5.0570; break; s6 = 0.64; - case 17: rs6 = 0.0000; s18 = 0.2130; rs18 = 6.0519; s6 = 0.50; break; - case 18: rs6 = 0.0009; s18 = 0.2112; rs18 = 5.9807; s6 = 0.50; break; - case 19: rs6 = 0.4870; s18 = 3.2950; rs18 = 3.5043; break; - case 20: rs6 = 0.4831; s18 = 2.0077; rs18 = 4.5323; break; - case 21: rs6 = 0.5299; s18 = 2.6205; rs18 = 2.8065; break; - case 22: rs6 = 0.4466; s18 = 2.9491; rs18 = 6.1742; break; - case 23: rs6 = 0.4567; s18 = 4.0728; rs18 = 4.3908; break; - case 24: rs6 = 0.5512; s18 = 3.3816; rs18 = 2.9444; break; - case 25: rs6 = -0.0952; s18 = -0.1744; rs18 = 5.2170; break; - case 26: rs6 = 0.4720; s18 = 0.4389; rs18 = 4.0986; break; - case 27: rs6 = 0.4634; s18 = 2.7495; rs18 = 4.3153; break; - case 28: rs6 = 0.4312; s18 = 2.8524; rs18 = 4.4693; break; - case 29: rs6 = 0.2793; s18 = 1.0354; rs18 = 4.9615; break; - case 30: rs6 = 0.4679; s18 = 1.7588; rs18 = 3.7619; break; - case 31: rs6 = 0.4529; s18 = 2.2382; rs18 = 4.6550; break; - case 32: rs6 = 0.1955; s18 = 1.0508; rs18 = 6.4177; break; - case 33: rs6 = 0.1805; s18 = 0.9383; rs18 = 7.7627; break; - case 34: rs6 = 0.2092; s18 = 1.4507; rs18 = 5.5545; break; - case 35: rs6 = 0.1940; s18 = 2.0860; rs18 = 5.9197; break; - case 36: rs6 = 0.3708; s18 = 2.0674; rs18 = 5.4743; break; - case 37: rs6 = 0.3919; s18 = 1.8541; rs18 = 5.0897; break; - case 38: rs6 = 0.0000; s18 = 0.2597; rs18 = 6.3332; s6 = 0.560; break; - case 39: rs6 = 0.0000; s18 = 0.2804; rs18 = 6.5745; s6 = 0.750; break; - case 40: rs6 = 0.0000; s18 = 0.2904; rs18 = 7.3141; s6 = 0.820; break; - // special HF / DFT with eBSSE correction; - case 41: rs6 = 0.5607; s18 = 3.9027; rs18 = 4.5622; break; - case 42: rs6 = 0.4249; s18 = 2.1849; rs18 = 4.2783; break; - case 43: rs6 = 0.1702; s18 = 0.9841; rs18 = 3.8506; break; - case 44: rs6 = 0.5014; s18 = 4.0672; rs18 = 4.8409; break; - case 45: rs6 = 0.3563; s18 = 1.0821; rs18 = 4.3359; break; - /* DFTB3 old, deprecated parameters : ; - * case ("dftb3"); rs6 = 0.7461; s18 = 3.209; rs18 = 4.1906; - * special SCC - DFTB parametrization; - * full third order DFTB, self consistent charges, hydrogen pair damping with; exponent 4.2; - */ - case 46: rs6 = 0.3807; s18 = 2.3363; rs18 = 5.8844; break; - case 47: rs6 = 0.2211; s18 = 2.6910; rs18 = 6.7278; break; - case 48: rs6 = 0.4650; s18 = 2.9215; rs18 = 6.2003; break; - // special HF - D3 - gCP - SRB / MINIX parametrization; - case 49: rs6 = 0.4171; s18 = 0.8777; rs18 = 2.9149; break; - // special HF - D3 - gCP - SRB2 / ECP - 2G parametrization; - case 50: rs6 = 0.3063; s18 = 0.5022; rs18 = 3.9856; break; - // special PBEh - D3 - gCP / def2 - mSVP parametrization; - case 51: rs6 = 0.4860; s18 = 0.0000; rs18 = 4.5000; break; - case 52: rs6 = 0.4860; s18 = 0.0000; rs18 = 4.5000; break; - case 53: rs6 = 0.5660; s18 = 0.3908; rs18 = 3.1280; break; - default: - error->all(FLERR, "Functional name unknown"); - break; - } -} - -void PairD3::setfuncpar_zerom() { - s6 = 1.0; - alp = 14.0; - - std::unordered_map commandMap = { - {"b2-plyp", 1}, {"b3-lyp", 2}, {"b97-d", 3}, {"b-lyp", 4}, - {"b-p", 5}, {"pbe", 6}, {"pbe0", 7}, {"lc-wpbe", 8} - }; - - int commandCode = commandMap[functional]; - switch (commandCode) { - case 1: rs6 = 1.313134; s18 = 0.717543; rs18 = 0.016035; s6 = 0.640000; break; - case 2: rs6 = 1.338153; s18 = 1.532981; rs18 = 0.013988; break; - case 3: rs6 = 1.151808; s18 = 1.020078; rs18 = 0.035964; break; - case 4: rs6 = 1.279637; s18 = 1.841686; rs18 = 0.014370; break; - case 5: rs6 = 1.233460; s18 = 1.945174; rs18 = 0.000000; break; - case 6: rs6 = 2.340218; s18 = 0.000000; rs18 = 0.129434; break; - case 7: rs6 = 2.077949; s18 = 0.000081; rs18 = 0.116755; break; - case 8: rs6 = 1.366361; s18 = 1.280619; rs18 = 0.003160; break; - default: - error->all(FLERR, "Functional name unknown"); - break; - } -} - -void PairD3::setfuncpar_bjm() { - s6 = 1.0; - alp = 14.0; - - std::unordered_map commandMap = { - {"b2-plyp", 1}, {"b3-lyp", 2}, {"b97-d", 3}, {"b-lyp", 4}, - {"b-p", 5}, {"pbe", 6}, {"pbe0", 7}, {"lc-wpbe", 8} - }; - - int commandCode = commandMap[functional]; - switch (commandCode) { - case 1: rs6 = 0.486434; s18 = 0.672820; rs18 = 3.656466; s6 = 0.640000; break; - case 2: rs6 = 0.278672; s18 = 1.466677; rs18 = 4.606311; break; - case 3: rs6 = 0.240184; s18 = 1.206988; rs18 = 3.864426; break; - case 4: rs6 = 0.448486; s18 = 1.875007; rs18 = 3.610679; break; - case 5: rs6 = 0.821850; s18 = 3.140281; rs18 = 2.728151; break; - case 6: rs6 = 0.012092; s18 = 0.358940; rs18 = 5.938951; break; - case 7: rs6 = 0.007912; s18 = 0.528823; rs18 = 6.162326; break; - case 8: rs6 = 0.563761; s18 = 0.906564; rs18 = 3.593680; break; - default: - error->all(FLERR, "Functional name unknown"); - break; - } -} - -void PairD3::setfuncpar() { - void (PairD3::*setfuncpar_damp[4])() = { - &PairD3::setfuncpar_zero, - &PairD3::setfuncpar_bj, - &PairD3::setfuncpar_zerom, - &PairD3::setfuncpar_bjm - }; - (this->*setfuncpar_damp[damping])(); - - rs8 = rs18; - alp6 = alp; - alp8 = alp + 2.0; - // rs10 = rs18 - // alp10 = alp + 4.0; - - a1 = rs6; - a2 = rs8; - s8 = s18; - // s6 is already defined -} - -/* ---------------------------------------------------------------------- - Coeff : read from pair_coeff (Required) -> pair_coeff * * element1 element2 ... -------------------------------------------------------------------------- */ - -void PairD3::coeff(int narg, char **arg) { - if (!allocated) allocate(); - - int ntypes = atom->ntypes; - if (narg != ntypes + 2) { error->all(FLERR, "Pair_coeff needs: * * element1 element2 ..."); } - - std::string element; - int* atomic_numbers = (int*)malloc(sizeof(int)*ntypes); - for (int i = 0; i < ntypes; i++) { - element = arg[i+2]; - atomic_numbers[i] = find_atomic_number(element); - } - - int count = 0; - for (int i = 1; i <= ntypes; i++) { - for (int j = 1; j <= ntypes; j++) { - setflag[i][j] = 1; - count++; - } - } - - if (count == 0) error->all(FLERR, "Incorrect args for pair coefficients"); - - /* - scale r4/r2 values of the atoms by sqrt(Z) - sqrt is also globally close to optimum - together with the factor 1/2 this yield reasonable - c8 for he, ne and ar. for larger Z, C8 becomes too large - which effectively mimics higher R^n terms neglected due - to stability reasons - - r2r4 =sqrt(0.5*r2r4(i)*dfloat(i)**0.5 ) with i=elementnumber - the large number of digits is just to keep the results consistent - with older versions. They should not imply any higher accuracy than - the old values - */ - double r2r4_ref[94] = { - 2.00734898, 1.56637132, 5.01986934, 3.85379032, 3.64446594, - 3.10492822, 2.71175247, 2.59361680, 2.38825250, 2.21522516, - 6.58585536, 5.46295967, 5.65216669, 4.88284902, 4.29727576, - 4.04108902, 3.72932356, 3.44677275, 7.97762753, 7.07623947, - 6.60844053, 6.28791364, 6.07728703, 5.54643096, 5.80491167, - 5.58415602, 5.41374528, 5.28497229, 5.22592821, 5.09817141, - 6.12149689, 5.54083734, 5.06696878, 4.87005108, 4.59089647, - 4.31176304, 9.55461698, 8.67396077, 7.97210197, 7.43439917, - 6.58711862, 6.19536215, 6.01517290, 5.81623410, 5.65710424, - 5.52640661, 5.44263305, 5.58285373, 7.02081898, 6.46815523, - 5.98089120, 5.81686657, 5.53321815, 5.25477007, 11.02204549, - 10.15679528, 9.35167836, 9.06926079, 8.97241155, 8.90092807, - 8.85984840, 8.81736827, 8.79317710, 7.89969626, 8.80588454, - 8.42439218, 8.54289262, 8.47583370, 8.45090888, 8.47339339, - 7.83525634, 8.20702843, 7.70559063, 7.32755997, 7.03887381, - 6.68978720, 6.05450052, 5.88752022, 5.70661499, 5.78450695, - 7.79780729, 7.26443867, 6.78151984, 6.67883169, 6.39024318, - 6.09527958, 11.79156076, 11.10997644, 9.51377795, 8.67197068, - 8.77140725, 8.65402716, 8.53923501, 8.85024712 - }; // atomic / values - - /* - covalent radii (taken from Pyykko and Atsumi, Chem. Eur. J. 15, 2009, 188-197) - values for metals decreased by 10 % - ! data rcov/ - ! . 0.32, 0.46, 1.20, 0.94, 0.77, 0.75, 0.71, 0.63, 0.64, 0.67 - ! ., 1.40, 1.25, 1.13, 1.04, 1.10, 1.02, 0.99, 0.96, 1.76, 1.54 - ! ., 1.33, 1.22, 1.21, 1.10, 1.07, 1.04, 1.00, 0.99, 1.01, 1.09 - ! ., 1.12, 1.09, 1.15, 1.10, 1.14, 1.17, 1.89, 1.67, 1.47, 1.39 - ! ., 1.32, 1.24, 1.15, 1.13, 1.13, 1.08, 1.15, 1.23, 1.28, 1.26 - ! ., 1.26, 1.23, 1.32, 1.31, 2.09, 1.76, 1.62, 1.47, 1.58, 1.57 - ! ., 1.56, 1.55, 1.51, 1.52, 1.51, 1.50, 1.49, 1.49, 1.48, 1.53 - ! ., 1.46, 1.37, 1.31, 1.23, 1.18, 1.16, 1.11, 1.12, 1.13, 1.32 - ! ., 1.30, 1.30, 1.36, 1.31, 1.38, 1.42, 2.01, 1.81, 1.67, 1.58 - ! ., 1.52, 1.53, 1.54, 1.55 / - - these new data are scaled with k2=4./3. and converted a_0 via - autoang=0.52917726d0 - */ - - double rcov_ref[94] = { - 0.80628308, 1.15903197, 3.02356173, 2.36845659, 1.94011865, - 1.88972601, 1.78894056, 1.58736983, 1.61256616, 1.68815527, - 3.52748848, 3.14954334, 2.84718717, 2.62041997, 2.77159820, - 2.57002732, 2.49443835, 2.41884923, 4.43455700, 3.88023730, - 3.35111422, 3.07395437, 3.04875805, 2.77159820, 2.69600923, - 2.62041997, 2.51963467, 2.49443835, 2.54483100, 2.74640188, - 2.82199085, 2.74640188, 2.89757982, 2.77159820, 2.87238349, - 2.94797246, 4.76210950, 4.20778980, 3.70386304, 3.50229216, - 3.32591790, 3.12434702, 2.89757982, 2.84718717, 2.84718717, - 2.72120556, 2.89757982, 3.09915070, 3.22513231, 3.17473967, - 3.17473967, 3.09915070, 3.32591790, 3.30072128, 5.26603625, - 4.43455700, 4.08180818, 3.70386304, 3.98102289, 3.95582657, - 3.93062995, 3.90543362, 3.80464833, 3.82984466, 3.80464833, - 3.77945201, 3.75425569, 3.75425569, 3.72905937, 3.85504098, - 3.67866672, 3.45189952, 3.30072128, 3.09915070, 2.97316878, - 2.92277614, 2.79679452, 2.82199085, 2.84718717, 3.32591790, - 3.27552496, 3.27552496, 3.42670319, 3.30072128, 3.47709584, - 3.57788113, 5.06446567, 4.56053862, 4.20778980, 3.98102289, - 3.82984466, 3.85504098, 3.88023730, 3.90543362 - }; // covalent radii - - for (int i = 0; i < ntypes; i++) { - r2r4[i+1] = r2r4_ref[atomic_numbers[i]-1]; - rcov[i+1] = rcov_ref[atomic_numbers[i]-1]; - } - - // set r0ab - read_r0ab(atomic_numbers, ntypes); - - // read c6ab - read_c6ab(atomic_numbers, ntypes); - - free(atomic_numbers); -} - -/* ---------------------------------------------------------------------- - Get derivative of C6 w.r.t. CN (used in PairD3::compute) - - C6 = C6(CN_A, CN_B) == W(CN_A, CN_B) / Z(CN_A, CN_B) - - This gives below from chain rule: - d(C6)/dr = d(C6)/d(CN_A) * d(CN_A)/dr + d(C6)/d(CN_B) * d(CN_B)/dr - - So we can pre-calculate the d(C6)/d(CN_A), d(C6)/d(CN_B) part. - - d(C6)/d(CN_i) = (dW/d(CN_i) * Z - W * dZ/d(CN_i)) / (W * W) - W : "denominator" - Z : "numerator" - dW/d(CN_i) : "d_denominator_i" - dZ/d(CN_j) : "d_numerator_j" - - Z = Sum( L_ij(CN_A, CN_B) * C6_ref(CN_A_i, CN_B_j) ) over i, j - W = Sum( L_ij(CN_A, CN_B) ) over i, j - - And the resulting derivative term is saved into - "dc6_iji_tot", "dc6_ijj_tot" array, - where we can find the value of d(C6)/d(CN_i) - by knowing the index of "iat", and "jat". ("idx_linij") - - Also, c6 values will also be saved into "c6_ij_tot" array. - - Here, as we only interested in *pair* of atoms, assume "iat" >= "jat". - Then "idx_linij" = "jat + (iat + 1) * iat / 2" have the order below. - - idx_linij | j = 0 j = 1 j = 2 j = 3 ... ---------------------------------------------- - i = 0 | 0 - i = 1 | 1 2 - i = 2 | 3 4 5 - i = 3 | 6 7 8 9 - ... | ... ... ... ... ... - -------------------------------------------------------------------------- */ - -__global__ void kernel_get_dC6_dCNij( - int maxij, float K3, - double *cn, int *mxc, float *****c6ab, int *type, - float *c6_ij_tot, float *dc6_iji_tot, float *dc6_ijj_tot -) { - int iter = blockIdx.x * blockDim.x + threadIdx.x; - - if (iter < maxij) { - int iat, jat; - ij_at_linij(iter, iat, jat); - - const int atomtype_i = type[iat]; - const int atomtype_j = type[jat]; - - const float cni = cn[iat]; - const int mxci = mxc[atomtype_i]; - const float cnj = cn[jat]; - const int mxcj = mxc[atomtype_j]; - - float c6mem = -1e99f; - float r_save = 9999.0f; - double numerator = 0.0; - double denominator = 0.0; - double d_numerator_i = 0.0; - double d_denominator_i = 0.0; - double d_numerator_j = 0.0; - double d_denominator_j = 0.0; - - for (int a = 0; a < mxci; a++) { - for (int b = 0; b < mxcj; b++) { - float c6ref = c6ab[atomtype_i][atomtype_j][a][b][0]; - - if (c6ref > 0.0f) { - float cn_refi = c6ab[atomtype_i][atomtype_j][a][b][1]; - float cn_refj = c6ab[atomtype_i][atomtype_j][a][b][2]; - - float r = (cn_refi - cni) * (cn_refi - cni) + (cn_refj - cnj) * (cn_refj - cnj); - if (r < r_save) { - r_save = r; - c6mem = c6ref; - } - - double expterm = exp(static_cast(K3) * static_cast(r)); // must be double - numerator += c6ref * expterm; - denominator += expterm; - - expterm *= 2.0f * K3; - - double term = expterm * (cni - cn_refi); - d_numerator_i += c6ref * term; - d_denominator_i += term; - - term = expterm * (cnj - cn_refj); - d_numerator_j += c6ref * term; - d_denominator_j += term; - } - } - } - - if (denominator > 1e-99) { - const double denominator_rc = 1.0 / denominator; // must be double - const double unit_frac = numerator * denominator_rc; - c6_ij_tot[iter] = unit_frac; - dc6_iji_tot[iter] = denominator_rc * fma(unit_frac, -d_denominator_i, d_numerator_i); // must be double - dc6_ijj_tot[iter] = denominator_rc * fma(unit_frac, -d_denominator_j, d_numerator_j); // must be double - //const double denominator_rc = 1.0 / denominator; - //const float unit_frac = numerator * denominator_rc; - //c6_ij_tot[iter] = unit_frac; - //dc6_iji_tot[iter] = \ - static_cast(d_numerator_i * denominator_rc) - static_cast(d_denominator_i * denominator_rc) * unit_frac; - //dc6_ijj_tot[iter] = \ - static_cast(d_numerator_j * denominator_rc) - static_cast(d_denominator_j * denominator_rc) * unit_frac; - } - else { - c6_ij_tot[iter] = c6mem; - dc6_iji_tot[iter] = 0.0f; - dc6_ijj_tot[iter] = 0.0f; - } - } -} - -void PairD3::get_dC6_dCNij() { - int n = atom->natoms; - int maxij = n * (n + 1) / 2; - - //START_CUDA_TIMER(); - - int threadsPerBlock = 128; - int blocksPerGrid = (maxij + threadsPerBlock - 1) / threadsPerBlock; - kernel_get_dC6_dCNij<<>>( - maxij, K3, - cn, mxc, c6ab, atomtype, - c6_ij_tot, dc6_iji_tot, dc6_ijj_tot - ); - cudaDeviceSynchronize(); - - //STOP_CUDA_TIMER("get_dC6dCNij"); -} - -/* ---------------------------------------------------------------------- - Get lattice vectors (used in PairD3::compute) - - 1) Save lattice vectors into "lat_v_1", "lat_v_2", "lat_v_3" - 2) Calculate repetition criteria for vdw, cn - 3) precaluclate tau (xyz shift due to cell repetition) - -------------------------------------------------------------------------- */ - -void PairD3::set_lattice_vectors() { - double boxxlo = domain->boxlo[0]; - double boxxhi = domain->boxhi[0]; - double boxylo = domain->boxlo[1]; - double boxyhi = domain->boxhi[1]; - double boxzlo = domain->boxlo[2]; - double boxzhi = domain->boxhi[2]; - double xy = domain->xy; - double xz = domain->xz; - double yz = domain->yz; - - lat_v_1[0] = (boxxhi - boxxlo) / AU_TO_ANG; - lat_v_1[1] = 0.0; - lat_v_1[2] = 0.0; - lat_v_2[0] = xy / AU_TO_ANG; - lat_v_2[1] = (boxyhi - boxylo) / AU_TO_ANG; - lat_v_2[2] = 0.0; - lat_v_3[0] = xz / AU_TO_ANG; - lat_v_3[1] = yz / AU_TO_ANG; - lat_v_3[2] = (boxzhi - boxzlo) / AU_TO_ANG; - - int vdwrx_save = 2 * rep_vdw[0] + 1; - int vdwry_save = 2 * rep_vdw[1] + 1; - int vdwrz_save = 2 * rep_vdw[2] + 1; - int cnrx_save = 2 * rep_cn[0] + 1; - int cnry_save = 2 * rep_cn[1] + 1; - int cnrz_save = 2 * rep_cn[2] + 1; - - set_lattice_repetition_criteria(rthr, rep_vdw); - set_lattice_repetition_criteria(cnthr, rep_cn); - - int vdw_range_x = 2 * rep_vdw[0] + 1; - int vdw_range_y = 2 * rep_vdw[1] + 1; - int vdw_range_z = 2 * rep_vdw[2] + 1; - int tau_loop_size_vdw = vdw_range_x * vdw_range_y * vdw_range_z * 3; - if (tau_loop_size_vdw != tau_idx_vdw_total_size) { - if (tau_idx_vdw != nullptr) { - for (int i = 0; i < vdwrx_save; i++) { - for (int j = 0; j < vdwry_save; j++) { - for (int k = 0; k < vdwrz_save; k++) { - cudaFree(tau_vdw[i][j][k]); - } - cudaFree(tau_vdw[i][j]); - } - cudaFree(tau_vdw[i]); - } - cudaFree(tau_vdw); - cudaFree(tau_idx_vdw); - } - tau_idx_vdw_total_size = tau_loop_size_vdw; - cudaMallocManaged(&tau_vdw, vdw_range_x * sizeof(float***)); - for (int i = 0; i < vdw_range_x; i++) { - cudaMallocManaged(&tau_vdw[i], vdw_range_y * sizeof(float**)); - for (int j = 0; j < vdw_range_y; j++) { - cudaMallocManaged(&tau_vdw[i][j], vdw_range_z * sizeof(float*)); - for (int k = 0; k < vdw_range_z; k++) { - cudaMallocManaged(&tau_vdw[i][j][k], 3 * sizeof(float)); - } - } - } - cudaMallocManaged(&tau_idx_vdw, tau_idx_vdw_total_size * sizeof(int)); - } - - int cn_range_x = 2 * rep_cn[0] + 1; - int cn_range_y = 2 * rep_cn[1] + 1; - int cn_range_z = 2 * rep_cn[2] + 1; - int tau_loop_size_cn = cn_range_x * cn_range_y * cn_range_z * 3; - if (tau_loop_size_cn != tau_idx_cn_total_size) { - if (tau_idx_cn != nullptr) { - for (int i = 0; i < cnrx_save; i++) { - for (int j = 0; j < cnry_save; j++) { - for (int k = 0; k < cnrz_save; k++) { - cudaFree(tau_cn[i][j][k]); - } - cudaFree(tau_cn[i][j]); - } - cudaFree(tau_cn[i]); - } - cudaFree(tau_cn); - cudaFree(tau_idx_cn); - } - tau_idx_cn_total_size = tau_loop_size_cn; - cudaMallocManaged(&tau_cn, cn_range_x * sizeof(float***)); - for (int i = 0; i < cn_range_x; i++) { - cudaMallocManaged(&tau_cn[i], cn_range_y * sizeof(float**)); - for (int j = 0; j < cn_range_y; j++) { - cudaMallocManaged(&tau_cn[i][j], cn_range_z * sizeof(float*)); - for (int k = 0; k < cn_range_z; k++) { - cudaMallocManaged(&tau_cn[i][j][k], 3 * sizeof(float)); - } - } - } - cudaMallocManaged(&tau_idx_cn, tau_idx_cn_total_size * sizeof(int)); - } -} - -/* ---------------------------------------------------------------------- - Set repetition criteria (used in PairD3::compute) - - Needed as Periodic Boundary Condition should be considered. - - As the cell may *not* be orthorhombic, - the dot product should be used between x/y/z direction and - corresponding cross product vector. -------------------------------------------------------------------------- */ - -void PairD3::set_lattice_repetition_criteria(float r_threshold, int* rep_v) { - double r_cutoff = sqrt(r_threshold); - double lat_cp_12[3], lat_cp_23[3], lat_cp_31[3]; - double cos_value; - - MathExtra::cross3(lat_v_1, lat_v_2, lat_cp_12); - MathExtra::cross3(lat_v_2, lat_v_3, lat_cp_23); - MathExtra::cross3(lat_v_3, lat_v_1, lat_cp_31); - - cos_value = MathExtra::dot3(lat_cp_23, lat_v_1) / MathExtra::len3(lat_cp_23); - rep_v[0] = static_cast(std::abs(r_cutoff / cos_value)) + 1; - cos_value = MathExtra::dot3(lat_cp_31, lat_v_2) / MathExtra::len3(lat_cp_31); - rep_v[1] = static_cast(std::abs(r_cutoff / cos_value)) + 1; - cos_value = MathExtra::dot3(lat_cp_12, lat_v_3) / MathExtra::len3(lat_cp_12); - rep_v[2] = static_cast(std::abs(r_cutoff / cos_value)) + 1; - - if (domain->xperiodic == 0) { rep_v[0] = 0; } - if (domain->yperiodic == 0) { rep_v[1] = 0; } - if (domain->zperiodic == 0) { rep_v[2] = 0; } -} - -/* ---------------------------------------------------------------------- - Calculate Coordination Number (used in PairD3::compute) -------------------------------------------------------------------------- */ - -__global__ void kernel_get_coordination_number( - int maxij, int maxtau, float cnthr, float K1, - float *rcov, int *rep_cn, float ****tau_cn, int *tau_idx_cn, int *type, float **x, - double *cn -) { - int iter = blockIdx.x * blockDim.x + threadIdx.x; - - if (iter < maxij) { - int iat, jat; - ij_at_linij(iter, iat, jat); - - float cn_local = 0.0f; - - if (iat == jat) { - const float rcov_sum = rcov[type[iat]] * 2.0f; - for (int k = maxtau - 1; k >= 0; k -= 3) { - const int idx1 = tau_idx_cn[k-2]; - const int idx2 = tau_idx_cn[k-1]; - const int idx3 = tau_idx_cn[k]; - if (idx1 == rep_cn[0] && idx2 == rep_cn[1] && idx3 == rep_cn[2]) { continue; } - const float rx = tau_cn[idx1][idx2][idx3][0]; - const float ry = tau_cn[idx1][idx2][idx3][1]; - const float rz = tau_cn[idx1][idx2][idx3][2]; - const float r2 = rx * rx + ry * ry + rz * rz; - if (r2 <= cnthr) { - const float r_rc = rsqrtf(r2); - const float damp = 1.0f / (1.0f + expf(-K1 * ((rcov_sum * r_rc) - 1.0f))); - cn_local += damp; - } - } - atomicAdd(&cn[iat], cn_local); - } - - else { - const float rcov_sum = rcov[type[iat]] + rcov[type[jat]]; - for (int k = maxtau - 1; k >= 0; k -= 3) { - const int idx1 = tau_idx_cn[k-2]; - const int idx2 = tau_idx_cn[k-1]; - const int idx3 = tau_idx_cn[k]; - const float rx = x[jat][0] - x[iat][0] + tau_cn[idx1][idx2][idx3][0]; - const float ry = x[jat][1] - x[iat][1] + tau_cn[idx1][idx2][idx3][1]; - const float rz = x[jat][2] - x[iat][2] + tau_cn[idx1][idx2][idx3][2]; - const float r2 = rx * rx + ry * ry + rz * rz; - if (r2 <= cnthr) { - const float r_rc = rsqrtf(r2); - const float damp = 1.0f / (1.0f + expf(-K1 * ((rcov_sum * r_rc) - 1.0f))); - cn_local += damp; - } - } - atomicAdd(&cn[iat], cn_local); - atomicAdd(&cn[jat], cn_local); - } - } -} - -void PairD3::get_coordination_number() { - int n = atom->natoms; - int maxij = n * (n + 1) / 2; - int maxtau = tau_idx_cn_total_size; - - for (int i = 0; i < n; i++) { - cn[i] = 0.0; - } - - //START_CUDA_TIMER(); - - int threadsPerBlock = 128; - int blocksPerGrid = (maxij + threadsPerBlock - 1) / threadsPerBlock; - kernel_get_coordination_number<<>>( - maxij, maxtau, cnthr, K1, - rcov, rep_cn, tau_cn, tau_idx_cn, atomtype, x, - cn - ); - cudaDeviceSynchronize(); - - //STOP_CUDA_TIMER("get_coord"); -} - -/* ---------------------------------------------------------------------- - reallcate memory if the number of atoms has changed (used in PairD3::compute) -------------------------------------------------------------------------- */ - -void PairD3::reallocate_arrays() { - /* -------------- Destroy previous arrays -------------- */ - cudaFree(cn); - for (int i = 0; i < n_save; i++) { cudaFree(x[i]); }; cudaFree(x); - cudaFree(dc6i); - for (int i = 0; i < n_save; i++) { cudaFree(f[i]); }; cudaFree(f); - - cudaFree(dc6_iji_tot); - cudaFree(dc6_ijj_tot); - cudaFree(c6_ij_tot); - - cudaFree(atomtype); - /* -------------- Destroy previous arrays -------------- */ - - /* -------------- Create new arrays -------------- */ - int n = atom->natoms; - n_save = n; - - cudaMallocManaged(&cn, n * sizeof(double)); - cudaMallocManaged(&x, n * sizeof(float*)); for (int i = 0; i < n; i++) { cudaMallocManaged(&x[i], 3 * sizeof(float)); } - cudaMallocManaged(&dc6i, n * sizeof(double)); - cudaMallocManaged(&f, n * sizeof(double*)); for (int i = 0; i < n; i++) { cudaMallocManaged(&f[i], 3 * sizeof(double)); } - - int n_ij_combination = n * (n + 1) / 2; - cudaMallocManaged(&dc6_iji_tot, n_ij_combination * sizeof(float)); - cudaMallocManaged(&dc6_ijj_tot, n_ij_combination * sizeof(float)); - cudaMallocManaged(&c6_ij_tot, n_ij_combination * sizeof(float)); - - cudaMallocManaged(&atomtype, n * sizeof(int)); - /* -------------- Create new arrays -------------- */ -} - -/* ---------------------------------------------------------------------- - Initialize atomic positions & types (used in PairD3::compute) - - As the default xyz from lammps does not assure that atoms are within unit cell, - this function shifts atoms into the unit cell. -------------------------------------------------------------------------- */ - -void PairD3::load_atom_info() { - double lat[3][3]; - lat[0][0] = lat_v_1[0]; - lat[0][1] = lat_v_2[0]; - lat[0][2] = lat_v_3[0]; - lat[1][0] = lat_v_1[1]; - lat[1][1] = lat_v_2[1]; - lat[1][2] = lat_v_3[1]; - lat[2][0] = lat_v_1[2]; - lat[2][1] = lat_v_2[2]; - lat[2][2] = lat_v_3[2]; - - double det = lat[0][0] * lat[1][1] * lat[2][2] - + lat[0][1] * lat[1][2] * lat[2][0] - + lat[0][2] * lat[1][0] * lat[2][1] - - lat[0][2] * lat[1][1] * lat[2][0] - - lat[0][1] * lat[1][0] * lat[2][2] - - lat[0][0] * lat[1][2] * lat[2][1]; - - double lat_inv[3][3]; - lat_inv[0][0] = (lat[1][1] * lat[2][2] - lat[1][2] * lat[2][1]) / det; - lat_inv[1][0] = (lat[1][2] * lat[2][0] - lat[1][0] * lat[2][2]) / det; - lat_inv[2][0] = (lat[1][0] * lat[2][1] - lat[1][1] * lat[2][0]) / det; - lat_inv[0][1] = (lat[0][2] * lat[2][1] - lat[0][1] * lat[2][2]) / det; - lat_inv[1][1] = (lat[0][0] * lat[2][2] - lat[0][2] * lat[2][0]) / det; - lat_inv[2][1] = (lat[0][1] * lat[2][0] - lat[0][0] * lat[2][1]) / det; - lat_inv[0][2] = (lat[0][1] * lat[1][2] - lat[0][2] * lat[1][1]) / det; - lat_inv[1][2] = (lat[0][2] * lat[1][0] - lat[0][0] * lat[1][2]) / det; - lat_inv[2][2] = (lat[0][0] * lat[1][1] - lat[0][1] * lat[1][0]) / det; - - double a[3] = { 0.0 }; - for (int iat = 0; iat < atom->natoms; iat++) { - for (int i = 0; i < 3; i++) { - a[i] = lat_inv[i][0] * (atom->x)[iat][0] / AU_TO_ANG + - lat_inv[i][1] * (atom->x)[iat][1] / AU_TO_ANG + - lat_inv[i][2] * (atom->x)[iat][2] / AU_TO_ANG; - a[i] -= floor(a[i]); // replaces the code below - //if (a[i] > 1) { while (a[i] > 1) { a[i]--; } } - //else if (a[i] < 0) { while (a[i] < 0) { a[i]++; } } - } - - for (int i = 0; i < 3; i++) { - x[iat][i] = (lat[i][0] * a[0] + lat[i][1] * a[1] + lat[i][2] * a[2]); - } - } -} - -/* ---------------------------------------------------------------------- - Precalculate tau array -------------------------------------------------------------------------- */ - -void PairD3::precalculate_tau_array() { - int xlim = rep_vdw[0]; - int ylim = rep_vdw[1]; - int zlim = rep_vdw[2]; - - int index = 0; - for (int taux = -xlim; taux <= xlim; taux++) { - for (int tauy = -ylim; tauy <= ylim; tauy++) { - for (int tauz = -zlim; tauz <= zlim; tauz++) { - tau_vdw[taux + xlim][tauy + ylim][tauz + zlim][0] = lat_v_1[0] * taux + lat_v_2[0] * tauy + lat_v_3[0] * tauz; - tau_vdw[taux + xlim][tauy + ylim][tauz + zlim][1] = lat_v_1[1] * taux + lat_v_2[1] * tauy + lat_v_3[1] * tauz; - tau_vdw[taux + xlim][tauy + ylim][tauz + zlim][2] = lat_v_1[2] * taux + lat_v_2[2] * tauy + lat_v_3[2] * tauz; - tau_idx_vdw[index++] = taux + xlim; - tau_idx_vdw[index++] = tauy + ylim; - tau_idx_vdw[index++] = tauz + zlim; - } - } - } - - xlim = rep_cn[0]; - ylim = rep_cn[1]; - zlim = rep_cn[2]; - - index = 0; - for (int taux = -xlim; taux <= xlim; taux++) { - for (int tauy = -ylim; tauy <= ylim; tauy++) { - for (int tauz = -zlim; tauz <= zlim; tauz++) { - tau_cn[taux + xlim][tauy + ylim][tauz + zlim][0] = lat_v_1[0] * taux + lat_v_2[0] * tauy + lat_v_3[0] * tauz; - tau_cn[taux + xlim][tauy + ylim][tauz + zlim][1] = lat_v_1[1] * taux + lat_v_2[1] * tauy + lat_v_3[1] * tauz; - tau_cn[taux + xlim][tauy + ylim][tauz + zlim][2] = lat_v_1[2] * taux + lat_v_2[2] * tauy + lat_v_3[2] * tauz; - tau_idx_cn[index++] = taux + xlim; - tau_idx_cn[index++] = tauy + ylim; - tau_idx_cn[index++] = tauz + zlim; - } - } - } -} - -/* ---------------------------------------------------------------------- - Get forces (Zero damping) -------------------------------------------------------------------------- */ - -__global__ void kernel_get_forces_without_dC6_zero( - int maxij, int maxtau, float rthr, float s6, float s8, float a1, float a2, float alp6, float alp8, - float *r2r4, float **r0ab, int *rep_vdw, float ****tau_vdw, int *tau_idx_vdw, int *type, float **x, - float *c6_ij_tot, float *dc6_iji_tot, float *dc6_ijj_tot, - double *dc6i, double *disp, double **f, double **sigma -) { - int iter = blockIdx.x * blockDim.x + threadIdx.x; - - __shared__ float sigma_00[128]; - __shared__ float sigma_01[128]; - __shared__ float sigma_02[128]; - __shared__ float sigma_10[128]; - __shared__ float sigma_11[128]; - __shared__ float sigma_12[128]; - __shared__ float sigma_20[128]; - __shared__ float sigma_21[128]; - __shared__ float sigma_22[128]; - __shared__ float disp_shared[128]; - - float sigma_local_00 = 0.0f; - float sigma_local_01 = 0.0f; - float sigma_local_02 = 0.0f; - float sigma_local_10 = 0.0f; - float sigma_local_11 = 0.0f; - float sigma_local_12 = 0.0f; - float sigma_local_20 = 0.0f; - float sigma_local_21 = 0.0f; - float sigma_local_22 = 0.0f; - float disp_local = 0.0f; - - if (iter < maxij) { - int iat, jat; - ij_at_linij(iter, iat, jat); - - float f_local[3] = { 0.0f }; - float dc6i_local_i = 0.0f; - float dc6i_local_j = 0.0f; - - const float c6 = c6_ij_tot[iter]; - const float dc6iji = dc6_iji_tot[iter]; - const float dc6ijj = dc6_ijj_tot[iter]; - - if (iat == jat) { - const int atomtype_i = type[iat]; - const float r0 = r0ab[atomtype_i][atomtype_i]; - const float unit_r2r4 = r2r4[atomtype_i]; - const float r42 = unit_r2r4 * unit_r2r4; - const float unit_a1 = (a1 * r0); - const float unit_a2 = (a2 * r0); - const float s8r42 = s8 * r42; - - for (int k = maxtau - 1; k >= 0; k -= 3) { - const int idx1 = tau_idx_vdw[k-2]; - const int idx2 = tau_idx_vdw[k-1]; - const int idx3 = tau_idx_vdw[k]; - - if (idx1 == rep_vdw[0] && idx2 == rep_vdw[1] && idx3 == rep_vdw[2]) { continue; } - const float rij[3] = { - tau_vdw[idx1][idx2][idx3][0], - tau_vdw[idx1][idx2][idx3][1], - tau_vdw[idx1][idx2][idx3][2] - }; - const float r2 = lensq3(rij); - if (r2 > rthr) { continue; } - - const float r_rc = rsqrtf(r2); - float unit_rc_a1 = unit_a1 * r_rc; - float t6 = unit_rc_a1 * unit_rc_a1; // ^2 - t6 *= unit_rc_a1; // ^3 - t6 *= t6; // ^6 - t6 *= unit_rc_a1; // ^7 - t6 *= t6; // ^14 - const float damp6 = 1.0f / fmaf(t6, 6.0f, 1.0f); - float unit_rc_a2 = unit_a2 * r_rc; - float t8 = unit_rc_a2 * unit_rc_a2; // ^2 - t8 *= t8; // ^4 - t8 *= t8; // ^8 - t8 *= t8; // ^16 - const float damp8 = 1.0f / fmaf(t8, 6.0f, 1.0f); - const float r2_rc = r_rc * r_rc; // 1.0 / r2 - const float r6_rc = r2_rc * r2_rc * r2_rc; - const float r8_rc = r6_rc * r2_rc; - const float x1 = 3.0f * c6 * r8_rc * fmaf(r2_rc, s8r42 * damp8 * fmaf(3.0f * alp8 * t8, damp8, -4.0f), s6 * damp6 * fmaf(alp6 * t6, damp6, -1.0f)); - //const float x1 = 0.5 * 6.0 * c6 * r8_rc * (s6 * damp6 * (14.0 * t6 * damp6 - 1.0) + s8r42 * r2_rc * damp8 * (48.0 * t8 * damp8 - 4.0)); - //3.0 * alp6 = 48.0 - - const float vec[3] = { - x1 * rij[0], - x1 * rij[1], - x1 * rij[2] - }; - - sigma_local_00 += vec[0] * rij[0]; - sigma_local_01 += vec[0] * rij[1]; - sigma_local_02 += vec[0] * rij[2]; - sigma_local_10 += vec[1] * rij[0]; - sigma_local_11 += vec[1] * rij[1]; - sigma_local_12 += vec[1] * rij[2]; - sigma_local_20 += vec[2] * rij[0]; - sigma_local_21 += vec[2] * rij[1]; - sigma_local_22 += vec[2] * rij[2]; - - const float dc6_rest = 0.5f * r6_rc * fmaf(3.0f * r2_rc, s8r42 * damp8, s6 * damp6); - //const float dc6_rest = 0.5 * r6_rc * (s6 * damp6 + 3.0 * s8r42 * damp8 * r2_rc); - disp_local -= dc6_rest * c6; - dc6i_local_i += dc6_rest * dc6iji; - dc6i_local_j += dc6_rest * dc6ijj; - } - atomicAdd(&dc6i[iat], dc6i_local_i); - atomicAdd(&dc6i[jat], dc6i_local_j); - } - - else { - const int atomtype_i = type[iat]; - const int atomtype_j = type[jat]; - const float r0 = r0ab[atomtype_i][atomtype_j]; - const float r42 = r2r4[atomtype_i] * r2r4[atomtype_j]; - const float unit_a1 = (a1 * r0); - const float unit_a2 = (a2 * r0); - const float s8r42 = s8 * r42; - - for (int k = maxtau - 1; k >= 0; k -= 3) { - const int idx1 = tau_idx_vdw[k-2]; - const int idx2 = tau_idx_vdw[k-1]; - const int idx3 = tau_idx_vdw[k]; - - const float rij[3] = { - x[jat][0] - x[iat][0] + tau_vdw[idx1][idx2][idx3][0], - x[jat][1] - x[iat][1] + tau_vdw[idx1][idx2][idx3][1], - x[jat][2] - x[iat][2] + tau_vdw[idx1][idx2][idx3][2] - }; - const float r2 = lensq3(rij); - if (r2 > rthr) { continue; } - - const float r_rc = rsqrtf(r2); - float unit_rc_a1 = unit_a1 * r_rc; - float t6 = unit_rc_a1 * unit_rc_a1; // ^2 - t6 *= unit_rc_a1; // ^3 - t6 *= t6; // ^6 - t6 *= unit_rc_a1; // ^7 - t6 *= t6; // ^14 - const float damp6 = 1.0f / fmaf(t6, 6.0f, 1.0f); - float unit_rc_a2 = unit_a2 * r_rc; - float t8 = unit_rc_a2 * unit_rc_a2; // ^2 - t8 *= t8; // ^4 - t8 *= t8; // ^8 - t8 *= t8; // ^16 - const float damp8 = 1.0f / fmaf(t8, 6.0f, 1.0f); - const float r2_rc = r_rc * r_rc; // 1.0 / r2 - const float r6_rc = r2_rc * r2_rc * r2_rc; - const float r8_rc = r6_rc * r2_rc; - const float x1 = 6.0f * c6 * r8_rc * fmaf(r2_rc, s8r42 * damp8 * fmaf(3.0f * alp8 * t8, damp8, -4.0f), s6 * damp6 * fmaf(alp6 * t6, damp6, -1.0f)); - //const float x1 = 6.0 * c6 * r8_rc * (s6 * damp6 * (14.0 * t6 * damp6 - 1.0) + s8r42 * r2_rc * damp8 * (48.0 * t8 * damp8 - 4.0)); - //3.0 * alp6 = 48.0 - - const float vec[3] = { - x1 * rij[0], - x1 * rij[1], - x1 * rij[2] - }; - - f_local[0] -= vec[0]; - f_local[1] -= vec[1]; - f_local[2] -= vec[2]; - - sigma_local_00 += vec[0] * rij[0]; - sigma_local_01 += vec[0] * rij[1]; - sigma_local_02 += vec[0] * rij[2]; - sigma_local_10 += vec[1] * rij[0]; - sigma_local_11 += vec[1] * rij[1]; - sigma_local_12 += vec[1] * rij[2]; - sigma_local_20 += vec[2] * rij[0]; - sigma_local_21 += vec[2] * rij[1]; - sigma_local_22 += vec[2] * rij[2]; - - const float dc6_rest = r6_rc * fmaf(3.0f * r2_rc, s8r42 * damp8, s6 * damp6); - //const float dc6_rest = r6_rc * (s6 * damp6 + 3.0 * s8r42 * damp8 * r2_rc); - disp_local -= dc6_rest * c6; - dc6i_local_i += dc6_rest * dc6iji; - dc6i_local_j += dc6_rest * dc6ijj; - } - atomicAdd(&dc6i[iat], dc6i_local_i); - atomicAdd(&dc6i[jat], dc6i_local_j); - atomicAdd(&f[iat][0], f_local[0]); - atomicAdd(&f[iat][1], f_local[1]); - atomicAdd(&f[iat][2], f_local[2]); - atomicAdd(&f[jat][0], -f_local[0]); - atomicAdd(&f[jat][1], -f_local[1]); - atomicAdd(&f[jat][2], -f_local[2]); - } - } - - sigma_00[threadIdx.x] = sigma_local_00; - sigma_01[threadIdx.x] = sigma_local_01; - sigma_02[threadIdx.x] = sigma_local_02; - sigma_10[threadIdx.x] = sigma_local_10; - sigma_11[threadIdx.x] = sigma_local_11; - sigma_12[threadIdx.x] = sigma_local_12; - sigma_20[threadIdx.x] = sigma_local_20; - sigma_21[threadIdx.x] = sigma_local_21; - sigma_22[threadIdx.x] = sigma_local_22; - disp_shared[threadIdx.x] = disp_local; - __syncthreads(); - - for (int s=blockDim.x/2; s>0; s>>=1) { - if (threadIdx.x < s) { - sigma_00[threadIdx.x] += sigma_00[threadIdx.x + s]; - sigma_01[threadIdx.x] += sigma_01[threadIdx.x + s]; - sigma_02[threadIdx.x] += sigma_02[threadIdx.x + s]; - sigma_10[threadIdx.x] += sigma_10[threadIdx.x + s]; - sigma_11[threadIdx.x] += sigma_11[threadIdx.x + s]; - sigma_12[threadIdx.x] += sigma_12[threadIdx.x + s]; - sigma_20[threadIdx.x] += sigma_20[threadIdx.x + s]; - sigma_21[threadIdx.x] += sigma_21[threadIdx.x + s]; - sigma_22[threadIdx.x] += sigma_22[threadIdx.x + s]; - disp_shared[threadIdx.x] += disp_shared[threadIdx.x + s]; - } - __syncthreads(); - } - - if (threadIdx.x == 0) { - atomicAdd(&sigma[0][0], sigma_00[0]); - atomicAdd(&sigma[0][1], sigma_01[0]); - atomicAdd(&sigma[0][2], sigma_02[0]); - atomicAdd(&sigma[1][0], sigma_10[0]); - atomicAdd(&sigma[1][1], sigma_11[0]); - atomicAdd(&sigma[1][2], sigma_12[0]); - atomicAdd(&sigma[2][0], sigma_20[0]); - atomicAdd(&sigma[2][1], sigma_21[0]); - atomicAdd(&sigma[2][2], sigma_22[0]); - atomicAdd(disp, disp_shared[0]); - } -} - -void PairD3::get_forces_without_dC6_zero() { - int n = atom->natoms; - int maxij = n * (n + 1) / 2; - int maxtau = tau_idx_vdw_total_size; - - *disp = 0.0; - - for (int dim = 0; dim < n; dim++) { dc6i[dim] = 0.0; } - - for (int i = 0; i < n; i++) { - for (int j = 0; j < 3; j++) { - f[i][j] = 0.0; - } - } - - for (int ii = 0; ii < 3; ii++) { - for (int jj = 0; jj < 3; jj++) { - sigma[ii][jj] = 0.0; - } - } - - //START_CUDA_TIMER(); - - int threadsPerBlock = 128; - int blocksPerGrid = (maxij + threadsPerBlock - 1) / threadsPerBlock; - kernel_get_forces_without_dC6_zero<<>>( - maxij, maxtau, rthr, s6, s8, a1, a2, alp6, alp8, - r2r4, r0ab, rep_vdw, tau_vdw, tau_idx_vdw, atomtype, x, - c6_ij_tot, dc6_iji_tot, dc6_ijj_tot, - dc6i, disp, f, sigma - ); - cudaDeviceSynchronize(); - disp_total = *disp; - - //STOP_CUDA_TIMER("get_forces_without"); -} - -__global__ void kernel_get_forces_without_dC6_bj( - int maxij, int maxtau, float rthr, float s6, float s8, float a1, float a2, - float *r2r4, int *rep_vdw, float ****tau_vdw, int *tau_idx_vdw, int *type, float **x, - float *c6_ij_tot, float *dc6_iji_tot, float *dc6_ijj_tot, - double *dc6i, double *disp, double **f, double **sigma -) { - int iter = blockIdx.x * blockDim.x + threadIdx.x; - - __shared__ float sigma_00[128]; - __shared__ float sigma_01[128]; - __shared__ float sigma_02[128]; - __shared__ float sigma_10[128]; - __shared__ float sigma_11[128]; - __shared__ float sigma_12[128]; - __shared__ float sigma_20[128]; - __shared__ float sigma_21[128]; - __shared__ float sigma_22[128]; - __shared__ float disp_shared[128]; - - float sigma_local_00 = 0.0f; - float sigma_local_01 = 0.0f; - float sigma_local_02 = 0.0f; - float sigma_local_10 = 0.0f; - float sigma_local_11 = 0.0f; - float sigma_local_12 = 0.0f; - float sigma_local_20 = 0.0f; - float sigma_local_21 = 0.0f; - float sigma_local_22 = 0.0f; - float disp_local = 0.0f; - - if (iter < maxij) { - int iat, jat; - ij_at_linij(iter, iat, jat); - - float f_local[3] = { 0.0f }; - float dc6i_local_i = 0.0f; - float dc6i_local_j = 0.0f; - - const float c6 = c6_ij_tot[iter]; - const float dc6iji = dc6_iji_tot[iter]; - const float dc6ijj = dc6_ijj_tot[iter]; - - if (iat == jat) { - const float unit_r2r4 = r2r4[type[iat]]; - const float r42x3 = unit_r2r4 * unit_r2r4 * 3.0f; - const float R0 = fmaf(a1, sqrtf(r42x3), a2); - const float R0_2 = R0 * R0; - const float R0_6 = R0_2 * R0_2 * R0_2; - const float R0_8 = R0_6 * R0_2; - const float s8r42x3 = s8 * r42x3; - - for (int k = maxtau - 1; k >= 0; k -= 3) { - const int idx1 = tau_idx_vdw[k-2]; - const int idx2 = tau_idx_vdw[k-1]; - const int idx3 = tau_idx_vdw[k]; - - if (idx1 == rep_vdw[0] && idx2 == rep_vdw[1] && idx3 == rep_vdw[2]) { continue; } - const float rij[3] = { - tau_vdw[idx1][idx2][idx3][0], - tau_vdw[idx1][idx2][idx3][1], - tau_vdw[idx1][idx2][idx3][2] - }; - const float r2 = lensq3(rij); - if (r2 > rthr) { continue; } - - const float r = sqrtf(r2); - const float r5 = r2 * r2 * r; - const float r7 = r5 * r2; - const float t6_rc = 1.0f / fmaf(r5, r, R0_6); - const float t8_rc = 1.0f / fmaf(r7, r, R0_8); - const float t6_sqrc = t6_rc * t6_rc; - const float t8_sqrc = t8_rc * t8_rc; - const float x1 = -c6 * fmaf(4.0f * s8r42x3 * r7, t8_sqrc, 3.0f * s6 * r5 * t6_sqrc); - //const float x1 = 0.5 * -c6 * (6.0 * s6 * r5 * t6_sqrc + 8.0 * s8r42x3 * r7 * t8_sqrc; - - const float r_rc = 1.0f / r; // rsqrt(r2) - const float vec[3] = { - x1 * rij[0] * r_rc, - x1 * rij[1] * r_rc, - x1 * rij[2] * r_rc - }; - - sigma_local_00 += vec[0] * rij[0]; - sigma_local_01 += vec[0] * rij[1]; - sigma_local_02 += vec[0] * rij[2]; - sigma_local_10 += vec[1] * rij[0]; - sigma_local_11 += vec[1] * rij[1]; - sigma_local_12 += vec[1] * rij[2]; - sigma_local_20 += vec[2] * rij[0]; - sigma_local_21 += vec[2] * rij[1]; - sigma_local_22 += vec[2] * rij[2]; - - const float dc6_rest = 0.5f * fmaf(s8r42x3, t8_rc, s6 * t6_rc); - //const float dc6_rest = 0.5 * s6 * t6_rc + s8r42x3 * t8_rc; - disp_local -= dc6_rest * c6; - dc6i_local_i += dc6_rest * dc6iji; - dc6i_local_j += dc6_rest * dc6ijj; - } - atomicAdd(&dc6i[iat], dc6i_local_i); - atomicAdd(&dc6i[jat], dc6i_local_j); - } - - else { - const float r42x3 = r2r4[type[iat]] * r2r4[type[jat]] * 3.0f; - const float R0 = fmaf(a1, sqrtf(r42x3), a2); - const float R0_2 = R0 * R0; - const float R0_6 = R0_2 * R0_2 * R0_2; - const float R0_8 = R0_6 * R0_2; - const float s8r42x3 = s8 * r42x3; - - for (int k = maxtau - 1; k >= 0; k -= 3) { - const int idx1 = tau_idx_vdw[k-2]; - const int idx2 = tau_idx_vdw[k-1]; - const int idx3 = tau_idx_vdw[k]; - const float rij[3] = { - x[jat][0] - x[iat][0] + tau_vdw[idx1][idx2][idx3][0], - x[jat][1] - x[iat][1] + tau_vdw[idx1][idx2][idx3][1], - x[jat][2] - x[iat][2] + tau_vdw[idx1][idx2][idx3][2] - }; - const float r2 = lensq3(rij); - if (r2 > rthr) { continue; } - - const float r = sqrtf(r2); - const float r5 = r2 * r2 * r; - const float r7 = r5 * r2; - const float t6_rc = 1.0f / fmaf(r5, r, R0_6); - const float t8_rc = 1.0f / fmaf(r7, r, R0_8); - const float t6_sqrc = t6_rc * t6_rc; - const float t8_sqrc = t8_rc * t8_rc; - const float x1 = -c6 * fmaf(8.0f * s8r42x3 * r7, t8_sqrc, 6.0f * s6 * r5 * t6_sqrc); - //const float x1 = -c6 * (6.0 * s6 * r5 * t6_sqrc + 8.0 * s8r42x3 * r7 * t8_sqrc; - - const float r_rc = 1.0f / r; // rsqrt(r2) - const float vec[3] = { - x1 * rij[0] * r_rc, - x1 * rij[1] * r_rc, - x1 * rij[2] * r_rc - }; - - f_local[0] -= vec[0]; - f_local[1] -= vec[1]; - f_local[2] -= vec[2]; - - sigma_local_00 += vec[0] * rij[0]; - sigma_local_01 += vec[0] * rij[1]; - sigma_local_02 += vec[0] * rij[2]; - sigma_local_10 += vec[1] * rij[0]; - sigma_local_11 += vec[1] * rij[1]; - sigma_local_12 += vec[1] * rij[2]; - sigma_local_20 += vec[2] * rij[0]; - sigma_local_21 += vec[2] * rij[1]; - sigma_local_22 += vec[2] * rij[2]; - - const float dc6_rest = fmaf(s8r42x3, t8_rc, s6 * t6_rc); - //const float dc6_rest = s6 * t6_rc + s8r42x3 * t8_rc; - disp_local -= dc6_rest * c6; - dc6i_local_i += dc6_rest * dc6iji; - dc6i_local_j += dc6_rest * dc6ijj; - } - atomicAdd(&dc6i[iat], dc6i_local_i); - atomicAdd(&dc6i[jat], dc6i_local_j); - atomicAdd(&f[iat][0], f_local[0]); - atomicAdd(&f[iat][1], f_local[1]); - atomicAdd(&f[iat][2], f_local[2]); - atomicAdd(&f[jat][0], -f_local[0]); - atomicAdd(&f[jat][1], -f_local[1]); - atomicAdd(&f[jat][2], -f_local[2]); - } - } - - sigma_00[threadIdx.x] = sigma_local_00; - sigma_01[threadIdx.x] = sigma_local_01; - sigma_02[threadIdx.x] = sigma_local_02; - sigma_10[threadIdx.x] = sigma_local_10; - sigma_11[threadIdx.x] = sigma_local_11; - sigma_12[threadIdx.x] = sigma_local_12; - sigma_20[threadIdx.x] = sigma_local_20; - sigma_21[threadIdx.x] = sigma_local_21; - sigma_22[threadIdx.x] = sigma_local_22; - disp_shared[threadIdx.x] = disp_local; - __syncthreads(); - - for (int s=blockDim.x/2; s>0; s>>=1) { - if (threadIdx.x < s) { - sigma_00[threadIdx.x] += sigma_00[threadIdx.x + s]; - sigma_01[threadIdx.x] += sigma_01[threadIdx.x + s]; - sigma_02[threadIdx.x] += sigma_02[threadIdx.x + s]; - sigma_10[threadIdx.x] += sigma_10[threadIdx.x + s]; - sigma_11[threadIdx.x] += sigma_11[threadIdx.x + s]; - sigma_12[threadIdx.x] += sigma_12[threadIdx.x + s]; - sigma_20[threadIdx.x] += sigma_20[threadIdx.x + s]; - sigma_21[threadIdx.x] += sigma_21[threadIdx.x + s]; - sigma_22[threadIdx.x] += sigma_22[threadIdx.x + s]; - disp_shared[threadIdx.x] += disp_shared[threadIdx.x + s]; - } - __syncthreads(); - } - - if (threadIdx.x == 0) { - atomicAdd(&sigma[0][0], sigma_00[0]); - atomicAdd(&sigma[0][1], sigma_01[0]); - atomicAdd(&sigma[0][2], sigma_02[0]); - atomicAdd(&sigma[1][0], sigma_10[0]); - atomicAdd(&sigma[1][1], sigma_11[0]); - atomicAdd(&sigma[1][2], sigma_12[0]); - atomicAdd(&sigma[2][0], sigma_20[0]); - atomicAdd(&sigma[2][1], sigma_21[0]); - atomicAdd(&sigma[2][2], sigma_22[0]); - atomicAdd(disp, disp_shared[0]); - } -} - -void PairD3::get_forces_without_dC6_bj() { - int n = atom->natoms; - int maxij = n * (n + 1) / 2; - int maxtau = tau_idx_vdw_total_size; - - *disp = 0.0; - - for (int dim = 0; dim < n; dim++) { dc6i[dim] = 0.0; } - - for (int i = 0; i < n; i++) { - for (int j = 0; j < 3; j++) { - f[i][j] = 0.0; - } - } - - for (int ii = 0; ii < 3; ii++) { - for (int jj = 0; jj < 3; jj++) { - sigma[ii][jj] = 0.0; - } - } - - //START_CUDA_TIMER(); - - int threadsPerBlock = 128; - int blocksPerGrid = (maxij + threadsPerBlock - 1) / threadsPerBlock; - kernel_get_forces_without_dC6_bj<<>>( - maxij, maxtau, rthr, s6, s8, a1, a2, - r2r4, rep_vdw, tau_vdw, tau_idx_vdw, atomtype, x, - c6_ij_tot, dc6_iji_tot, dc6_ijj_tot, - dc6i, disp, f, sigma - ); - cudaDeviceSynchronize(); - disp_total = *disp; - - //STOP_CUDA_TIMER("get_forces_without"); -} - -void PairD3::get_forces_without_dC6_zerom() {} -void PairD3::get_forces_without_dC6_bjm() {} - -void PairD3::get_forces_without_dC6() { - void (PairD3::*get_forces_without_dC6_damp[4])() = { - &PairD3::get_forces_without_dC6_zero, - &PairD3::get_forces_without_dC6_bj, - &PairD3::get_forces_without_dC6_zerom, - &PairD3::get_forces_without_dC6_bjm - }; - - (this->*get_forces_without_dC6_damp[damping])(); -} - -__global__ void kernel_get_forces_with_dC6( - int maxij, int maxtau, float cnthr, float K1, - double *dc6i, float *rcov, int *rep_cn, float ****tau_cn, int *tau_idx_cn, int *type, float **x, - double **f, double **sigma -) { - int iter = blockIdx.x * blockDim.x + threadIdx.x; - - __shared__ float sigma_00[128]; - __shared__ float sigma_01[128]; - __shared__ float sigma_02[128]; - __shared__ float sigma_10[128]; - __shared__ float sigma_11[128]; - __shared__ float sigma_12[128]; - __shared__ float sigma_20[128]; - __shared__ float sigma_21[128]; - __shared__ float sigma_22[128]; - - float sigma_local_00 = 0.0f; - float sigma_local_01 = 0.0f; - float sigma_local_02 = 0.0f; - float sigma_local_10 = 0.0f; - float sigma_local_11 = 0.0f; - float sigma_local_12 = 0.0f; - float sigma_local_20 = 0.0f; - float sigma_local_21 = 0.0f; - float sigma_local_22 = 0.0f; - - float f_local[3] = { 0.0f }; - - if (iter < maxij) { - int iat, jat; - ij_at_linij(iter, iat, jat); - - if (iat == jat) { - const float rcov_sum = rcov[type[iat]] * 2.0f; - const float dc6i_sum = dc6i[iat]; - - for (int k = maxtau - 1; k >= 0; k -= 3) { - const int idx1 = tau_idx_cn[k-2]; - const int idx2 = tau_idx_cn[k-1]; - const int idx3 = tau_idx_cn[k]; - - if (idx1 == rep_cn[0] && idx2 == rep_cn[1] && idx3 == rep_cn[2]) { continue; } - const float rij[3] = { - tau_cn[idx1][idx2][idx3][0], - tau_cn[idx1][idx2][idx3][1], - tau_cn[idx1][idx2][idx3][2], - }; - const float r2 = lensq3(rij); - if (r2 >= cnthr) { continue; } - - const float r_rc = rsqrtf(r2); - const float expterm = expf(-K1 * (rcov_sum * r_rc - 1.0f)); - const float unit_rc = 1.0f / (r2 * (expterm + 1.0f) * (expterm + 1.0f)); - const float dcnn = -K1 * rcov_sum * expterm * unit_rc; - const float x1 = dcnn * dc6i_sum; - - const float vec[3] = { - x1 * rij[0] * r_rc, - x1 * rij[1] * r_rc, - x1 * rij[2] * r_rc - }; - - sigma_local_00 += vec[0] * rij[0]; - sigma_local_01 += vec[0] * rij[1]; - sigma_local_02 += vec[0] * rij[2]; - sigma_local_10 += vec[1] * rij[0]; - sigma_local_11 += vec[1] * rij[1]; - sigma_local_12 += vec[1] * rij[2]; - sigma_local_20 += vec[2] * rij[0]; - sigma_local_21 += vec[2] * rij[1]; - sigma_local_22 += vec[2] * rij[2]; - } - } - - else { - const float rcov_sum = rcov[type[iat]] + rcov[type[jat]]; - const float dc6i_sum = dc6i[iat] + dc6i[jat]; - - for (int k = maxtau - 1; k >= 0; k -= 3) { - const int idx1 = tau_idx_cn[k-2]; - const int idx2 = tau_idx_cn[k-1]; - const int idx3 = tau_idx_cn[k]; - - const float rij[3] = { - x[jat][0] - x[iat][0] + tau_cn[idx1][idx2][idx3][0], - x[jat][1] - x[iat][1] + tau_cn[idx1][idx2][idx3][1], - x[jat][2] - x[iat][2] + tau_cn[idx1][idx2][idx3][2] - }; - const float r2 = lensq3(rij); - if (r2 >= cnthr) { continue; } - - const float r_rc = rsqrtf(r2); - const float expterm = expf(-K1 * (rcov_sum * r_rc - 1.0f)); - const float unit_rc = 1.0f / (r2 * (expterm + 1.0f) * (expterm + 1.0f)); - const float dcnn = -K1 * rcov_sum * expterm * unit_rc; - const float x1 = dcnn * dc6i_sum; - - const float vec[3] = { - x1 * rij[0] * r_rc, - x1 * rij[1] * r_rc, - x1 * rij[2] * r_rc - }; - - f_local[0] -= vec[0]; - f_local[1] -= vec[1]; - f_local[2] -= vec[2]; - - sigma_local_00 += vec[0] * rij[0]; - sigma_local_01 += vec[0] * rij[1]; - sigma_local_02 += vec[0] * rij[2]; - sigma_local_10 += vec[1] * rij[0]; - sigma_local_11 += vec[1] * rij[1]; - sigma_local_12 += vec[1] * rij[2]; - sigma_local_20 += vec[2] * rij[0]; - sigma_local_21 += vec[2] * rij[1]; - sigma_local_22 += vec[2] * rij[2]; - } - atomicAdd(&f[iat][0], f_local[0]); - atomicAdd(&f[iat][1], f_local[1]); - atomicAdd(&f[iat][2], f_local[2]); - atomicAdd(&f[jat][0], -f_local[0]); - atomicAdd(&f[jat][1], -f_local[1]); - atomicAdd(&f[jat][2], -f_local[2]); - } - } - - sigma_00[threadIdx.x] = sigma_local_00; - sigma_01[threadIdx.x] = sigma_local_01; - sigma_02[threadIdx.x] = sigma_local_02; - sigma_10[threadIdx.x] = sigma_local_10; - sigma_11[threadIdx.x] = sigma_local_11; - sigma_12[threadIdx.x] = sigma_local_12; - sigma_20[threadIdx.x] = sigma_local_20; - sigma_21[threadIdx.x] = sigma_local_21; - sigma_22[threadIdx.x] = sigma_local_22; - __syncthreads(); - - for (int s=blockDim.x/2; s>0; s>>=1) { - if (threadIdx.x < s) { - sigma_00[threadIdx.x] += sigma_00[threadIdx.x + s]; - sigma_01[threadIdx.x] += sigma_01[threadIdx.x + s]; - sigma_02[threadIdx.x] += sigma_02[threadIdx.x + s]; - sigma_10[threadIdx.x] += sigma_10[threadIdx.x + s]; - sigma_11[threadIdx.x] += sigma_11[threadIdx.x + s]; - sigma_12[threadIdx.x] += sigma_12[threadIdx.x + s]; - sigma_20[threadIdx.x] += sigma_20[threadIdx.x + s]; - sigma_21[threadIdx.x] += sigma_21[threadIdx.x + s]; - sigma_22[threadIdx.x] += sigma_22[threadIdx.x + s]; - } - __syncthreads(); - } - - if (threadIdx.x == 0) { - atomicAdd(&sigma[0][0], sigma_00[0]); - atomicAdd(&sigma[0][1], sigma_01[0]); - atomicAdd(&sigma[0][2], sigma_02[0]); - atomicAdd(&sigma[1][0], sigma_10[0]); - atomicAdd(&sigma[1][1], sigma_11[0]); - atomicAdd(&sigma[1][2], sigma_12[0]); - atomicAdd(&sigma[2][0], sigma_20[0]); - atomicAdd(&sigma[2][1], sigma_21[0]); - atomicAdd(&sigma[2][2], sigma_22[0]); - } -} - -void PairD3::get_forces_with_dC6() { - int n = atom->natoms; - int maxij = n * (n + 1) / 2; - int maxtau = tau_idx_cn_total_size; - - //START_CUDA_TIMER(); - - int threadsPerBlock = 128; - int blocksPerGrid = (maxij + threadsPerBlock - 1) / threadsPerBlock; - kernel_get_forces_with_dC6<<>>( - maxij, maxtau, cnthr, K1, - dc6i, rcov, rep_cn, tau_cn, tau_idx_cn, atomtype, x, - f, sigma - ); - cudaDeviceSynchronize(); - - //STOP_CUDA_TIMER("get_forces_with"); -} - -/* ---------------------------------------------------------------------- - Update energy, force, and stress -------------------------------------------------------------------------- */ - -void PairD3::update(int eflag, int vflag) { - int n = atom->natoms; - - if (eflag) { eng_vdwl += disp_total * AU_TO_EV; } // Energy update - - double** f_local = atom->f; // Force update - for (int i = 0; i < n; i++) { - for (int j = 0; j < 3; j++) { - f_local[i][j] += f[i][j] * AU_TO_EV / AU_TO_ANG; - } - } - - - if (vflag) { - virial[0] += sigma[0][0] * AU_TO_EV; - virial[1] += sigma[1][1] * AU_TO_EV; - virial[2] += sigma[2][2] * AU_TO_EV; - virial[3] += sigma[0][1] * AU_TO_EV; - virial[4] += sigma[0][2] * AU_TO_EV; - virial[5] += sigma[1][2] * AU_TO_EV; - } // Stress update -} - -/* ---------------------------------------------------------------------- - Compute : energy, force, and stress (Required) -------------------------------------------------------------------------- */ - -void PairD3::compute(int eflag, int vflag) { - if (eflag || vflag) { ev_setup(eflag, vflag); } - if (atom->natoms != n_save) { reallocate_arrays(); } - - set_lattice_vectors(); - precalculate_tau_array(); - load_atom_info(); - - cudaMemcpy(atomtype, atom->type, atom->natoms * sizeof(int), cudaMemcpyHostToDevice); - - get_coordination_number(); - get_dC6_dCNij(); - get_forces_without_dC6(); - get_forces_with_dC6(); - - update(eflag, vflag); - - CHECK_CUDA_ERROR(); -} - -/* ---------------------------------------------------------------------- - init for one type pair i,j and corresponding j,i -------------------------------------------------------------------------- */ - -double PairD3::init_one(int i, int j) { - if (setflag[i][j] == 0) error->all(FLERR, "All pair coeffs are not set"); - // No need to count local neighbor in D3 - /* return std::sqrt(rthr * std::pow(au_to_ang, 2)); */ - return 0.0; -} - -/* ---------------------------------------------------------------------- - init specific to this pair style (Optional) -------------------------------------------------------------------------- */ - -void PairD3::init_style() { - neighbor->add_request(this, NeighConst::REQ_FULL); -} - -/* ---------------------------------------------------------------------- - proc 0 writes to restart file -------------------------------------------------------------------------- */ - -void PairD3::write_restart(FILE *fp) {} - -/* ---------------------------------------------------------------------- - proc 0 reads from restart file, bcasts -------------------------------------------------------------------------- */ - -void PairD3::read_restart(FILE *fp) {} - -/* ---------------------------------------------------------------------- - proc 0 writes to restart file -------------------------------------------------------------------------- */ - -void PairD3::write_restart_settings(FILE *fp) {} - -/* ---------------------------------------------------------------------- - proc 0 reads from restart file, bcasts -------------------------------------------------------------------------- */ - -void PairD3::read_restart_settings(FILE *fp) {} diff --git a/mace-bench/3rdparty/SevenNet/sevenn/pair_e3gnn/pair_d3.h b/mace-bench/3rdparty/SevenNet/sevenn/pair_e3gnn/pair_d3.h deleted file mode 100644 index 0d5d320cd39269921b7c3b6afce9250e4679e41b..0000000000000000000000000000000000000000 --- a/mace-bench/3rdparty/SevenNet/sevenn/pair_e3gnn/pair_d3.h +++ /dev/null @@ -1,181 +0,0 @@ -/* -*- c++ -*- ---------------------------------------------------------- - LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - https://www.lammps.org/, Sandia National Laboratories - LAMMPS development team: developers@lammps.org - - Copyright (2003) Sandia Corporation. Under the terms of Contract - DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains - certain rights in this software. This software is distributed under - the GNU General Public License. - - See the README file in the top-level LAMMPS directory. -------------------------------------------------------------------------- */ - -#ifdef PAIR_CLASS -PairStyle(d3, PairD3) - -#else - -#ifndef LMP_PAIR_D3 -#define LMP_PAIR_D3 - -#include -#include -#include -#include -#include -#include -#include - -#include "pair.h" -#include "utils.h" -#include "atom.h" -#include "domain.h" -#include "error.h" -#include "comm.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "math_extra.h" - -#include "pair_d3_pars.h" - -// Removed dependencies to STL -// #include -> no more C style functions -// #define _USE_MATH_DEFINES -> no predefined constants - -// Removed dependencies to LAMMPS -// #include "potential_file_reader.h" -> removed, PotentialFileReader -// #include "memory.h" -> already no dependency for CUDA version - -namespace LAMMPS_NS { - class PairD3 : public Pair { - public: - PairD3(class LAMMPS*); - ~PairD3() override; - - void compute(int, int) override; - void settings(int, char**) override; - void coeff(int, char**) override; - double init_one(int i, int j) override; - void init_style() override; - - void write_restart(FILE*) override; - void read_restart(FILE*) override; - void write_restart_settings(FILE*) override; - void read_restart_settings(FILE*) override; - - protected: - virtual void allocate(); - - /* ------- Read parameters ------- */ - int find_atomic_number(std::string&); - int is_int_in_array(int*, int, int); - void read_r0ab(int*, int); - void get_limit_in_pars_array(int&, int&, int&, int&); - void read_c6ab(int*, int); - - void setfuncpar_zero(); - void setfuncpar_bj(); - void setfuncpar_zerom(); - void setfuncpar_bjm(); - void setfuncpar(); - /* ------- Read parameters ------- */ - - /* ------- Lattice information ------- */ - void set_lattice_repetition_criteria(float, int*); - void set_lattice_vectors(); - /* ------- Lattice information ------- */ - - /* ------- Initialize & Precalculate ------- */ - void load_atom_info(); - void precalculate_tau_array(); - /* ------- Initialize & Precalculate ------- */ - - /* ------- Reallocate (when number of atoms changed) ------- */ - void reallocate_arrays(); - /* ------- Reallocate (when number of atoms changed) ------- */ - - /* ------- Coordination number ------- */ - void get_coordination_number(); - void get_dC6_dCNij(); - /* ------- Coordination number ------- */ - - /* ------- Main workers ------- */ - void get_forces_without_dC6_zero(); - void get_forces_without_dC6_bj(); - void get_forces_without_dC6_zerom(); - void get_forces_without_dC6_bjm(); - void get_forces_without_dC6(); - void get_forces_with_dC6(); - void update(int, int); - /* ------- Main workers ------- */ - - /*--------- Constants ---------*/ - static constexpr int MAX_ELEM = 94; // maximum of the element number - static constexpr int MAXC = 5; // maximum coordination number references per element - - static constexpr double AU_TO_ANG = 0.52917726; // conversion factors (atomic unit --> angstrom) - static constexpr double AU_TO_EV = 27.21138505; // conversion factors (atomic unit --> eV) - - static constexpr float K1 = 16.0; // global ad hoc parameters - static constexpr float K3 = -4.0; // global ad hoc parameters - /*--------- Constants ---------*/ - - /*--------- Parameters to read ---------*/ - int damping; - std::string functional; - float* r2r4 = nullptr; // scale r4/r2 values of the atoms by sqrt(Z) - float* rcov = nullptr; // covalent radii - int* mxc = nullptr; // How large the grid for c6 interpolation - float** r0ab = nullptr; // cut-off radii for all element pairs - float***** c6ab = nullptr; // C6 for all element pairs - float rthr; // R^2 distance to cutoff for C calculation - float cnthr; // R^2 distance to cutoff for CN_calculation - float s6, s8, s18, rs6, rs8, rs18, alp, alp6, alp8, a1, a2; // parameters for D3 - /*--------- Parameters to read ---------*/ - - /*--------- Lattice related values ---------*/ - double* lat_v_1 = nullptr; // lattice coordination vector - double* lat_v_2 = nullptr; // lattice coordination vector - double* lat_v_3 = nullptr; // lattice coordination vector - int* rep_vdw = nullptr; // repetition of cell for calculating D3 - int* rep_cn = nullptr; // repetition of cell for calculating - double** sigma = nullptr; // virial pressure on cell - /*--------- Lattice related values ---------*/ - - /*--------- Per-atom values/arrays ---------*/ - double* cn = nullptr; // Coordination numbers - float** x = nullptr; // Positions - double** f = nullptr; // Forces - double* dc6i = nullptr; // dC6i(iat) saves dE_dsp/dCN(iat) - /*--------- Per-atom values/arrays ---------*/ - - /*--------- Per-pair values/arrays ---------*/ - float* c6_ij_tot = nullptr; - float* dc6_iji_tot = nullptr; - float* dc6_ijj_tot = nullptr; - /*--------- Per-pair values/arrays ---------*/ - - /*---------- Global values ---------*/ - int n_save; // to check whether the number of atoms has changed - float disp_total; // Dispersion energy - /*---------- Global values ---------*/ - - /*--------- For loop over tau (translation of cell) ---------*/ - float**** tau_vdw = nullptr; - float**** tau_cn = nullptr; - int* tau_idx_vdw = nullptr; - int* tau_idx_cn = nullptr; - int tau_idx_vdw_total_size; - int tau_idx_cn_total_size; - /*--------- For loop over tau (translation of cell) ---------*/ - - /*--------- For cuda memory transfer (pointerized) ---------*/ - int *atomtype; - double *disp; - /*--------- For cuda memory transfer (pointerized) ---------*/ - }; -} - -#endif // LMP_PAIR_D3 -#endif // PAIR_CLASS diff --git a/mace-bench/3rdparty/SevenNet/sevenn/pair_e3gnn/pair_d3_for_ase.cu b/mace-bench/3rdparty/SevenNet/sevenn/pair_e3gnn/pair_d3_for_ase.cu deleted file mode 100644 index 3d9ef99ff3c79a57a1b0f0ca3d0afbd23f2110a8..0000000000000000000000000000000000000000 --- a/mace-bench/3rdparty/SevenNet/sevenn/pair_e3gnn/pair_d3_for_ase.cu +++ /dev/null @@ -1,2081 +0,0 @@ -/* -This code is a skeleton of the LAMMPS pair_style d3 accelerated by CUDA. -All dependencies on LAMMPS have been removed. -The input and output variables are named based on the LAMMPS variables as much as possible. -*/ - -#include "pair_d3_for_ase.h" - -/* --------- Macros for CUDA error handling --------- */ -#define START_CUDA_TIMER() \ - cudaEvent_t start, stop; \ - cudaEventCreate(&start); \ - cudaEventCreate(&stop); \ - cudaEventRecord(start); - -#define STOP_CUDA_TIMER(tag) \ - cudaEventRecord(stop); \ - cudaEventSynchronize(stop); \ - float msec = 0; \ - cudaEventElapsedTime(&msec, start, stop); \ - printf("Elapsed time for %s: %f ms\n", tag, msec); \ - cudaEventDestroy(start); \ - cudaEventDestroy(stop); - -#define CHECK_CUDA(call) do { \ - cudaError_t status_ = call; \ - if (status_ != cudaSuccess) { \ - fprintf(stderr, "CUDA Error (%s:%d) -> %s: %s\n", __FILE__, __LINE__, \ - cudaGetErrorName(status_), cudaGetErrorString(status_)); \ - exit(EXIT_FAILURE); \ - } \ -} while (0) - -#define CHECK_CUDA_ERROR() do { \ - cudaDeviceSynchronize(); \ - cudaError_t status_ = cudaGetLastError(); \ - if (status_ != cudaSuccess) { \ - fprintf(stderr, "CUDA Error (%s:%d) -> %s: %s\n", __FILE__, __LINE__, \ - cudaGetErrorName(status_), cudaGetErrorString(status_)); \ - exit(EXIT_FAILURE); \ - } \ -} while (0) - -#define CHECK_CUDA_DEVICES() do { \ - int deviceCount = 0; \ - if (cudaGetDeviceCount(&deviceCount) != cudaSuccess || deviceCount == 0) { \ - fprintf(stderr, "CUDA Error (%s:%d) -> No CUDA devices found\n", \ - __FILE__, __LINE__); \ - exit(EXIT_FAILURE); \ - } \ -} while(0) -/* --------- Macros for CUDA error handling --------- */ - -/* --------- Math functions for CUDA compatibility --------- */ -inline __host__ __device__ void ij_at_linij(int linij, int &i, int &j) { - i = static_cast((sqrt(1 + 8 * linij) - 1) / 2); - j = linij - i * (i + 1) / 2; -} // unroll the triangular loop - -inline __host__ __device__ float lensq3(const float *v) -{ - return v[0] * v[0] + v[1] * v[1] + v[2] * v[2]; -} // from MathExtra::lensq3 - -inline void cross3(const double *v1, const double *v2, double *ans) -{ - ans[0] = v1[1] * v2[2] - v1[2] * v2[1]; - ans[1] = v1[2] * v2[0] - v1[0] * v2[2]; - ans[2] = v1[0] * v2[1] - v1[1] * v2[0]; -} - -inline double dot3(const double *v1, const double *v2) -{ - return v1[0] * v2[0] + v1[1] * v2[1] + v1[2] * v2[2]; -} - -inline double len3(const double *v) -{ - return sqrt(v[0] * v[0] + v[1] * v[1] + v[2] * v[2]); -} -/* --------- Math functions for CUDA compatibility --------- */ - -/* ---------------------------------------------------------------------- - Constructor (Required) -------------------------------------------------------------------------- */ - -PairD3::PairD3() { - allocated = 0; -} - -/* ---------------------------------------------------------------------- - Destructor (Required) -------------------------------------------------------------------------- */ - -PairD3::~PairD3() { - if (allocated) { - int n = atom->natoms; - int np1 = atom->ntypes + 1; - int vdw_range_x = 2 * rep_vdw[0] + 1; - int vdw_range_y = 2 * rep_vdw[1] + 1; - int vdw_range_z = 2 * rep_vdw[2] + 1; - int cn_range_x = 2 * rep_cn[0] + 1; - int cn_range_y = 2 * rep_cn[1] + 1; - int cn_range_z = 2 * rep_cn[2] + 1; - - //for (int i = 0; i < np1; i++) { cudaFree(setflag[i]); }; cudaFree(setflag); - //for (int i = 0; i < np1; i++) { cudaFree(cutsq[i]); }; cudaFree(cutsq); - cudaFree(r2r4); - cudaFree(rcov); - cudaFree(mxc); - for (int i = 0; i < np1; i++) { cudaFree(r0ab[i]); }; cudaFree(r0ab); - for (int i = 0; i < np1; i++) { - for (int j = 0; j < np1; j++) { - for (int k = 0; k < MAXC; k++) { - for (int l = 0; l < MAXC; l++) { - cudaFree(c6ab[i][j][k][l]); - } - cudaFree(c6ab[i][j][k]); - } - cudaFree(c6ab[i][j]); - } - cudaFree(c6ab[i]); - } - cudaFree(c6ab); - - cudaFree(lat_v_1); - cudaFree(lat_v_2); - cudaFree(lat_v_3); - - cudaFree(rep_vdw); - cudaFree(rep_cn); - cudaFree(cn); - for (int i = 0; i < n; i++) { cudaFree(x[i]); }; cudaFree(x); - - cudaFree(dc6i); - for (int i = 0; i < n; i++) { cudaFree(f[i]); }; cudaFree(f); - - for (int i = 0; i < 3; i++) { cudaFree(sigma[i]); }; cudaFree(sigma); - - cudaFree(dc6_iji_tot); - cudaFree(dc6_ijj_tot); - cudaFree(c6_ij_tot); - - for (int i = 0; i < vdw_range_x; i++) { - for (int j = 0; j < vdw_range_y; j++) { - for (int k = 0; k < vdw_range_z; k++) { - cudaFree(tau_vdw[i][j][k]); - } - cudaFree(tau_vdw[i][j]); - } - cudaFree(tau_vdw[i]); - } - cudaFree(tau_vdw); - for (int i = 0; i < cn_range_x; i++) { - for (int j = 0; j < cn_range_y; j++) { - for (int k = 0; k < cn_range_z; k++) { - cudaFree(tau_cn[i][j][k]); - } - cudaFree(tau_cn[i][j]); - } - cudaFree(tau_cn[i]); - } - cudaFree(tau_cn); - - cudaFree(tau_idx_vdw); - cudaFree(tau_idx_cn); - - cudaFree(atomtype); - cudaFree(disp); - } -} - -/* ---------------------------------------------------------------------- - Allocate all arrays (Required) -------------------------------------------------------------------------- */ - -void PairD3::allocate() { - CHECK_CUDA_DEVICES(); - allocated = 1; - - /* atom->ntypes : # of elements; element index starts from 1 */ - int n = atom->natoms; - int np1 = atom->ntypes + 1; - n_save = n; - np1_save = np1; - - //cudaMallocManaged(&setflag, np1 * sizeof(int*)); for (int i = 0; i < np1; i++) { cudaMallocManaged(&setflag[i], np1 * sizeof(int)); } - //cudaMallocManaged(&cutsq, np1 * sizeof(double*)); for (int i = 0; i < np1; i++) { cudaMallocManaged(&cutsq[i], np1 * sizeof(double)); } - cudaMallocManaged(&r2r4, np1 * sizeof(float)); - cudaMallocManaged(&rcov, np1 * sizeof(float)); - cudaMallocManaged(&mxc, np1 * sizeof(int)); - cudaMallocManaged(&r0ab, np1 * sizeof(float*)); for (int i = 0; i < np1; i++) { cudaMallocManaged(&r0ab[i], np1 * sizeof(float)); } - cudaMallocManaged(&c6ab, np1 * sizeof(float****)); - for (int i = 0; i < np1; i++) { - cudaMallocManaged(&c6ab[i], np1 * sizeof(float***)); - for (int j = 0; j < np1; j++) { - cudaMallocManaged(&c6ab[i][j], MAXC * sizeof(float**)); - for (int k = 0; k < MAXC; k++) { - cudaMallocManaged(&c6ab[i][j][k], MAXC * sizeof(float*)); - for (int l = 0; l < MAXC; l++) { - cudaMallocManaged(&c6ab[i][j][k][l], 3 * sizeof(float)); - } - } - } - } - - cudaMallocManaged(&lat_v_1, 3 * sizeof(float)); - cudaMallocManaged(&lat_v_2, 3 * sizeof(float)); - cudaMallocManaged(&lat_v_3, 3 * sizeof(float)); - cudaMallocManaged(&rep_vdw, 3 * sizeof(int)); - cudaMallocManaged(&rep_cn, 3 * sizeof(int)); - cudaMallocManaged(&sigma, 3 * sizeof(double*)); for (int i = 0; i < 3; i++) { cudaMallocManaged(&sigma[i], 3 * sizeof(double)); } - - cudaMallocManaged(&cn, n * sizeof(double)); - cudaMallocManaged(&x, n * sizeof(float*)); for (int i = 0; i < n; i++) { cudaMallocManaged(&x[i], 3 * sizeof(float)); } - cudaMallocManaged(&dc6i, n * sizeof(double)); - cudaMallocManaged(&f, n * sizeof(double*)); for (int i = 0; i < n; i++) { cudaMallocManaged(&f[i], 3 * sizeof(double)); } - - // Initialization - // Initialize for lattice -> set_lattice_vectors() - tau_idx_vdw_total_size = -1; - tau_idx_cn_total_size = -1; - for (int i = 0; i < 3; i++) { - rep_vdw[i] = -1; - rep_cn[i] = -1; - } - - //for (int i = 1; i < np1; i++) { - // for (int j = 1; j < np1; j++) { - // setflag[i][j] = 0; - // } - //} - - for (int idx1 = 0; idx1 < np1; idx1++) { - for (int idx2 = 0; idx2 < np1; idx2++) { - for (int idx3 = 0; idx3 < MAXC; idx3++) { - for (int idx4 = 0; idx4 < MAXC; idx4++) { - for (int idx5 = 0; idx5 < 3; idx5++) { - c6ab[idx1][idx2][idx3][idx4][idx5] = -1; - } - } - } - } - } - - int n_ij_combination = n * (n + 1) / 2; - cudaMallocManaged(&dc6_iji_tot, n_ij_combination * sizeof(float)); - cudaMallocManaged(&dc6_ijj_tot, n_ij_combination * sizeof(float)); - cudaMallocManaged(&c6_ij_tot, n_ij_combination * sizeof(float)); - - cudaMallocManaged(&atomtype, n * sizeof(int)); - cudaMallocManaged(&disp, sizeof(double)); -} - -/* ---------------------------------------------------------------------- - Settings : read from pair_style (Required) -> pair_style d3 vdw_sq cn_sq damp_name func_name -------------------------------------------------------------------------- */ - -void PairD3::settings(double vdw_sq, double cn_sq, std::string damp_name, std::string func_name) { - rthr = vdw_sq; - cnthr = cn_sq; - - std::map commandMap = { - {"damp_zero", 0}, {"damp_bj", 1}, {"damp_zerom", 2}, {"damp_bjm", 3}, - }; - - if (commandMap.find(damp_name) == commandMap.end()) { - error->all(FLERR, "Unknown damping function"); - } - - damping = commandMap[damp_name]; - functional = func_name; - - setfuncpar(); -} - -/* ---------------------------------------------------------------------- - finds atomic number (used in PairD3::coeff) -------------------------------------------------------------------------- */ - -int PairD3::find_atomic_number(std::string& key) { - std::transform(key.begin(), key.end(), key.begin(), ::tolower); - if (key.length() == 1) { key += " "; } - key.resize(2); - - std::vector element_table = { - "h ","he", - "li","be","b ","c ","n ","o ","f ","ne", - "na","mg","al","si","p ","s ","cl","ar", - "k ","ca","sc","ti","v ","cr","mn","fe","co","ni","cu", - "zn","ga","ge","as","se","br","kr", - "rb","sr","y ","zr","nb","mo","tc","ru","rh","pd","ag", - "cd","in","sn","sb","te","i ","xe", - "cs","ba","la","ce","pr","nd","pm","sm","eu","gd","tb","dy", - "ho","er","tm","yb","lu","hf","ta","w ","re","os","ir","pt", - "au","hg","tl","pb","bi","po","at","rn", - "fr","ra","ac","th","pa","u ","np","pu" - }; - - for (size_t i = 0; i < element_table.size(); ++i) { - if (element_table[i] == key) { - int atomic_number = i + 1; - return atomic_number; - } - } - - // if not the case - return -1; -} - -/* ---------------------------------------------------------------------- - Check whether an integer value in an integer array (used in PairD3::coeff) -------------------------------------------------------------------------- */ - -int PairD3::is_int_in_array(int arr[], int size, int value) { - for (int i = 0; i < size; i++) { - if (arr[i] == value) { return i; } // returns the index - } - return -1; -} - -/* ---------------------------------------------------------------------- - Read r0ab values from the table (used in PairD3::coeff) -------------------------------------------------------------------------- */ - -void PairD3::read_r0ab(int* atomic_numbers, int ntypes) { - const double r0ab_table[94][94] = R0AB_TABLE; - - for (int i = 1; i <= ntypes; i++) { - for (int j = 1; j <= ntypes; j++) { - r0ab[i][j] = r0ab_table[atomic_numbers[i-1]-1][atomic_numbers[j-1]-1] / AU_TO_ANG; - } - } -} - -/* ---------------------------------------------------------------------- - Get atom pair indices and grid indices (used in PairD3::read_c6ab) -------------------------------------------------------------------------- */ - -void PairD3::get_limit_in_pars_array(int& idx_atom_1, int& idx_atom_2, int& idx_i, int& idx_j) { - const int shift = 100; - - idx_i = (idx_atom_1 - 1) / shift + 1; - idx_j = (idx_atom_2 - 1) / shift + 1; - - idx_atom_1 = (idx_atom_1 - 1) % shift + 1; - idx_atom_2 = (idx_atom_2 - 1) % shift + 1; - - // the code above replaces the code below - //idx_i = 1; - //idx_j = 1; - //int shift = 100; - //while (idx_atom_1 > shift) { idx_atom_1 -= shift; idx_i++; } - //while (idx_atom_2 > shift) { idx_atom_2 -= shift; idx_j++; } -} - -/* ---------------------------------------------------------------------- - Read c6ab values from the table (used in PairD3::coeff) -------------------------------------------------------------------------- */ - -void PairD3::read_c6ab(int* atomic_numbers, int ntypes) { - for (int i = 1; i <= ntypes; i++) { mxc[i] = 0; } - int grid_i = 0, grid_j = 0; - - const double c6ab_table[32385][5] = C6AB_TABLE; - - for (int i = 0; i < 32385; i++) { - const double ref_c6 = c6ab_table[i][0]; - int atom_number_1 = static_cast(c6ab_table[i][1]); - int atom_number_2 = static_cast(c6ab_table[i][2]); - get_limit_in_pars_array(atom_number_1, atom_number_2, grid_i, grid_j); - const int idx_atom_1 = is_int_in_array(atomic_numbers, ntypes, atom_number_1); - if (idx_atom_1 < 0) { continue; } - const int idx_atom_2 = is_int_in_array(atomic_numbers, ntypes, atom_number_2); - if (idx_atom_2 < 0) { continue; } - const double ref_cn1 = c6ab_table[i][3]; - const double ref_cn2 = c6ab_table[i][4]; - - mxc[idx_atom_1 + 1] = std::max(mxc[idx_atom_1 + 1], grid_i); - mxc[idx_atom_2 + 1] = std::max(mxc[idx_atom_2 + 1], grid_j); - c6ab[idx_atom_1 + 1][idx_atom_2 + 1][grid_i - 1][grid_j - 1][0] = ref_c6; - c6ab[idx_atom_1 + 1][idx_atom_2 + 1][grid_i - 1][grid_j - 1][1] = ref_cn1; - c6ab[idx_atom_1 + 1][idx_atom_2 + 1][grid_i - 1][grid_j - 1][2] = ref_cn2; - c6ab[idx_atom_2 + 1][idx_atom_1 + 1][grid_j - 1][grid_i - 1][0] = ref_c6; - c6ab[idx_atom_2 + 1][idx_atom_1 + 1][grid_j - 1][grid_i - 1][1] = ref_cn2; - c6ab[idx_atom_2 + 1][idx_atom_1 + 1][grid_j - 1][grid_i - 1][2] = ref_cn1; - } -} - -/* ---------------------------------------------------------------------- - Set functional parameters (used in PairD3::coeff) -------------------------------------------------------------------------- */ - -void PairD3::setfuncpar_zero() { - s6 = 1.0; - alp = 14.0; - rs18 = 1.0; - - // default def2-QZVP (almost basis set limit) - std::unordered_map commandMap = { - { "slater-dirac-exchange", 1}, { "b-lyp", 2 }, { "b-p", 3 }, { "b97-d", 4 }, { "revpbe", 5 }, - { "pbe", 6 }, { "pbesol", 7 }, { "rpw86-pbe", 8 }, { "rpbe", 9 }, { "tpss", 10 }, - { "b3-lyp", 11 }, { "pbe0", 12 }, { "hse06", 13 }, { "revpbe38", 14 }, { "pw6b95", 15 }, - { "tpss0", 16 }, { "b2-plyp", 17 }, { "pwpb95", 18 }, { "b2gp-plyp", 19 }, { "ptpss", 20 }, - { "hf", 21 }, { "mpwlyp", 22 }, { "bpbe", 23 }, { "bh-lyp", 24 }, { "tpssh", 25 }, - { "pwb6k", 26 }, { "b1b95", 27 }, { "bop", 28 }, { "o-lyp", 29 }, { "o-pbe", 30 }, - { "ssb", 31 }, { "revssb", 32 }, { "otpss", 33 }, { "b3pw91", 34 }, { "revpbe0", 35 }, - { "pbe38", 36 }, { "mpw1b95", 37 }, { "mpwb1k", 38 }, { "bmk", 39 }, { "cam-b3lyp", 40 }, - { "lc-wpbe", 41 }, { "m05", 42 }, { "m052x", 43 }, { "m06l", 44 }, { "m06", 45 }, - { "m062x", 46 }, { "m06hf", 47 }, { "hcth120", 48 } - }; - - int commandCode = commandMap[functional]; - switch (commandCode) { - case 1: rs6 = 0.999; s18 = -1.957; rs18 = 0.697; break; - case 2: rs6 = 1.094; s18 = 1.682; break; - case 3: rs6 = 1.139; s18 = 1.683; break; - case 4: rs6 = 0.892; s18 = 0.909; break; - case 5: rs6 = 0.923; s18 = 1.010; break; - case 6: rs6 = 1.217; s18 = 0.722; break; - case 7: rs6 = 1.345; s18 = 0.612; break; - case 8: rs6 = 1.224; s18 = 0.901; break; - case 9: rs6 = 0.872; s18 = 0.514; break; - case 10: rs6 = 1.166; s18 = 1.105; break; - case 11: rs6 = 1.261; s18 = 1.703; break; - case 12: rs6 = 1.287; s18 = 0.928; break; - case 13: rs6 = 1.129; s18 = 0.109; break; - case 14: rs6 = 1.021; s18 = 0.862; break; - case 15: rs6 = 1.532; s18 = 0.862; break; - case 16: rs6 = 1.252; s18 = 1.242; break; - case 17: rs6 = 1.427; s18 = 1.022; s6 = 0.64; break; - case 18: rs6 = 1.557; s18 = 0.705; s6 = 0.82; break; - case 19: rs6 = 1.586; s18 = 0.760; s6 = 0.56; break; - case 20: rs6 = 1.541; s18 = 0.879; s6 = 0.75; break; - case 21: rs6 = 1.158; s18 = 1.746; break; - case 22: rs6 = 1.239; s18 = 1.098; break; - case 23: rs6 = 1.087; s18 = 2.033; break; - case 24: rs6 = 1.370; s18 = 1.442; break; - case 25: rs6 = 1.223; s18 = 1.219; break; - case 26: rs6 = 1.660; s18 = 0.550; break; - case 27: rs6 = 1.613; s18 = 1.868; break; - case 28: rs6 = 0.929; s18 = 1.975; break; - case 29: rs6 = 0.806; s18 = 1.764; break; - case 30: rs6 = 0.837; s18 = 2.055; break; - case 31: rs6 = 1.215; s18 = 0.663; break; - case 32: rs6 = 1.221; s18 = 0.560; break; - case 33: rs6 = 1.128; s18 = 1.494; break; - case 34: rs6 = 1.176; s18 = 1.775; break; - case 35: rs6 = 0.949; s18 = 0.792; break; - case 36: rs6 = 1.333; s18 = 0.998; break; - case 37: rs6 = 1.605; s18 = 1.118; break; - case 38: rs6 = 1.671; s18 = 1.061; break; - case 39: rs6 = 1.931; s18 = 2.168; break; - case 40: rs6 = 1.378; s18 = 1.217; break; - case 41: rs6 = 1.355; s18 = 1.279; break; - case 42: rs6 = 1.373; s18 = 0.595; break; - case 43: rs6 = 1.417; s18 = 0.000; break; - case 44: rs6 = 1.581; s18 = 0.000; break; - case 45: rs6 = 1.325; s18 = 0.000; break; - case 46: rs6 = 1.619; s18 = 0.000; break; - case 47: rs6 = 1.446; s18 = 0.000; break; - /* DFTB3(zeta = 4.0), old deprecated parameters; case ("dftb3"); rs6 = 1.235; s18 = 0.673; */ - case 48: rs6 = 1.221; s18 = 1.206; break; - default: - error->all(FLERR, "Functional name unknown"); - break; - } -} - -void PairD3::setfuncpar_bj() { - s6 = 1.0; - alp = 14.0; - - std::unordered_map commandMap = { - {"b-p", 1}, {"b-lyp", 2}, {"revpbe", 3}, {"rpbe", 4}, {"b97-d", 5}, {"pbe", 6}, - {"rpw86-pbe", 7}, {"b3-lyp", 8}, {"tpss", 9}, {"hf", 10}, {"tpss0", 11}, {"pbe0", 12}, - {"hse06", 13}, {"revpbe38", 14}, {"pw6b95", 15}, {"b2-plyp", 16}, {"dsd-blyp", 17}, - {"dsd-blyp-fc", 18}, {"bop", 19}, {"mpwlyp", 20}, {"o-lyp", 21}, {"pbesol", 22}, {"bpbe", 23}, - {"opbe", 24}, {"ssb", 25}, {"revssb", 26}, {"otpss", 27}, {"b3pw91", 28}, {"bh-lyp", 29}, - {"revpbe0", 30}, {"tpssh", 31}, {"mpw1b95", 32}, {"pwb6k", 33}, {"b1b95", 34}, {"bmk", 35}, - {"cam-b3lyp", 36}, {"lc-wpbe", 37}, {"b2gp-plyp", 38}, {"ptpss", 39}, {"pwpb95", 40}, - {"hf/mixed", 41}, {"hf/sv", 42}, {"hf/minis", 43}, {"b3-lyp/6-31gd", 44}, {"hcth120", 45}, - {"pw1pw", 46}, {"pwgga", 47}, {"hsesol", 48}, {"hf3c", 49}, {"hf3cv", 50}, {"pbeh3c", 51}, - {"pbeh-3c", 52}, {"wb97m", 53} - }; - - int commandCode = commandMap[functional]; - switch (commandCode) { - case 1: rs6 = 0.3946; s18 = 3.2822; rs18 = 4.8516; break; - case 2: rs6 = 0.4298; s18 = 2.6996; rs18 = 4.2359; break; - case 3: rs6 = 0.5238; s18 = 2.3550; rs18 = 3.5016; break; - case 4: rs6 = 0.1820; s18 = 0.8318; rs18 = 4.0094; break; - case 5: rs6 = 0.5545; s18 = 2.2609; rs18 = 3.2297; break; - case 6: rs6 = 0.4289; s18 = 0.7875; rs18 = 4.4407; break; - case 7: rs6 = 0.4613; s18 = 1.3845; rs18 = 4.5062; break; - case 8: rs6 = 0.3981; s18 = 1.9889; rs18 = 4.4211; break; - case 9: rs6 = 0.4535; s18 = 1.9435; rs18 = 4.4752; break; - case 10: rs6 = 0.3385; s18 = 0.9171; rs18 = 2.8830; break; - case 11: rs6 = 0.3768; s18 = 1.2576; rs18 = 4.5865; break; - case 12: rs6 = 0.4145; s18 = 1.2177; rs18 = 4.8593; break; - case 13: rs6 = 0.383; s18 = 2.310; rs18 = 5.685; break; - case 14: rs6 = 0.4309; s18 = 1.4760; rs18 = 3.9446; break; - case 15: rs6 = 0.2076; s18 = 0.7257; rs18 = 6.3750; break; - case 16: rs6 = 0.3065; s18 = 0.9147; rs18 = 5.0570; break; s6 = 0.64; - case 17: rs6 = 0.0000; s18 = 0.2130; rs18 = 6.0519; s6 = 0.50; break; - case 18: rs6 = 0.0009; s18 = 0.2112; rs18 = 5.9807; s6 = 0.50; break; - case 19: rs6 = 0.4870; s18 = 3.2950; rs18 = 3.5043; break; - case 20: rs6 = 0.4831; s18 = 2.0077; rs18 = 4.5323; break; - case 21: rs6 = 0.5299; s18 = 2.6205; rs18 = 2.8065; break; - case 22: rs6 = 0.4466; s18 = 2.9491; rs18 = 6.1742; break; - case 23: rs6 = 0.4567; s18 = 4.0728; rs18 = 4.3908; break; - case 24: rs6 = 0.5512; s18 = 3.3816; rs18 = 2.9444; break; - case 25: rs6 = -0.0952; s18 = -0.1744; rs18 = 5.2170; break; - case 26: rs6 = 0.4720; s18 = 0.4389; rs18 = 4.0986; break; - case 27: rs6 = 0.4634; s18 = 2.7495; rs18 = 4.3153; break; - case 28: rs6 = 0.4312; s18 = 2.8524; rs18 = 4.4693; break; - case 29: rs6 = 0.2793; s18 = 1.0354; rs18 = 4.9615; break; - case 30: rs6 = 0.4679; s18 = 1.7588; rs18 = 3.7619; break; - case 31: rs6 = 0.4529; s18 = 2.2382; rs18 = 4.6550; break; - case 32: rs6 = 0.1955; s18 = 1.0508; rs18 = 6.4177; break; - case 33: rs6 = 0.1805; s18 = 0.9383; rs18 = 7.7627; break; - case 34: rs6 = 0.2092; s18 = 1.4507; rs18 = 5.5545; break; - case 35: rs6 = 0.1940; s18 = 2.0860; rs18 = 5.9197; break; - case 36: rs6 = 0.3708; s18 = 2.0674; rs18 = 5.4743; break; - case 37: rs6 = 0.3919; s18 = 1.8541; rs18 = 5.0897; break; - case 38: rs6 = 0.0000; s18 = 0.2597; rs18 = 6.3332; s6 = 0.560; break; - case 39: rs6 = 0.0000; s18 = 0.2804; rs18 = 6.5745; s6 = 0.750; break; - case 40: rs6 = 0.0000; s18 = 0.2904; rs18 = 7.3141; s6 = 0.820; break; - // special HF / DFT with eBSSE correction; - case 41: rs6 = 0.5607; s18 = 3.9027; rs18 = 4.5622; break; - case 42: rs6 = 0.4249; s18 = 2.1849; rs18 = 4.2783; break; - case 43: rs6 = 0.1702; s18 = 0.9841; rs18 = 3.8506; break; - case 44: rs6 = 0.5014; s18 = 4.0672; rs18 = 4.8409; break; - case 45: rs6 = 0.3563; s18 = 1.0821; rs18 = 4.3359; break; - /* DFTB3 old, deprecated parameters : ; - * case ("dftb3"); rs6 = 0.7461; s18 = 3.209; rs18 = 4.1906; - * special SCC - DFTB parametrization; - * full third order DFTB, self consistent charges, hydrogen pair damping with; exponent 4.2; - */ - case 46: rs6 = 0.3807; s18 = 2.3363; rs18 = 5.8844; break; - case 47: rs6 = 0.2211; s18 = 2.6910; rs18 = 6.7278; break; - case 48: rs6 = 0.4650; s18 = 2.9215; rs18 = 6.2003; break; - // special HF - D3 - gCP - SRB / MINIX parametrization; - case 49: rs6 = 0.4171; s18 = 0.8777; rs18 = 2.9149; break; - // special HF - D3 - gCP - SRB2 / ECP - 2G parametrization; - case 50: rs6 = 0.3063; s18 = 0.5022; rs18 = 3.9856; break; - // special PBEh - D3 - gCP / def2 - mSVP parametrization; - case 51: rs6 = 0.4860; s18 = 0.0000; rs18 = 4.5000; break; - case 52: rs6 = 0.4860; s18 = 0.0000; rs18 = 4.5000; break; - case 53: rs6 = 0.5660; s18 = 0.3908; rs18 = 3.1280; break; - default: - error->all(FLERR, "Functional name unknown"); - break; - } -} - -void PairD3::setfuncpar_zerom() { - s6 = 1.0; - alp = 14.0; - - std::unordered_map commandMap = { - {"b2-plyp", 1}, {"b3-lyp", 2}, {"b97-d", 3}, {"b-lyp", 4}, - {"b-p", 5}, {"pbe", 6}, {"pbe0", 7}, {"lc-wpbe", 8} - }; - - int commandCode = commandMap[functional]; - switch (commandCode) { - case 1: rs6 = 1.313134; s18 = 0.717543; rs18 = 0.016035; s6 = 0.640000; break; - case 2: rs6 = 1.338153; s18 = 1.532981; rs18 = 0.013988; break; - case 3: rs6 = 1.151808; s18 = 1.020078; rs18 = 0.035964; break; - case 4: rs6 = 1.279637; s18 = 1.841686; rs18 = 0.014370; break; - case 5: rs6 = 1.233460; s18 = 1.945174; rs18 = 0.000000; break; - case 6: rs6 = 2.340218; s18 = 0.000000; rs18 = 0.129434; break; - case 7: rs6 = 2.077949; s18 = 0.000081; rs18 = 0.116755; break; - case 8: rs6 = 1.366361; s18 = 1.280619; rs18 = 0.003160; break; - default: - error->all(FLERR, "Functional name unknown"); - break; - } -} - -void PairD3::setfuncpar_bjm() { - s6 = 1.0; - alp = 14.0; - - std::unordered_map commandMap = { - {"b2-plyp", 1}, {"b3-lyp", 2}, {"b97-d", 3}, {"b-lyp", 4}, - {"b-p", 5}, {"pbe", 6}, {"pbe0", 7}, {"lc-wpbe", 8} - }; - - int commandCode = commandMap[functional]; - switch (commandCode) { - case 1: rs6 = 0.486434; s18 = 0.672820; rs18 = 3.656466; s6 = 0.640000; break; - case 2: rs6 = 0.278672; s18 = 1.466677; rs18 = 4.606311; break; - case 3: rs6 = 0.240184; s18 = 1.206988; rs18 = 3.864426; break; - case 4: rs6 = 0.448486; s18 = 1.875007; rs18 = 3.610679; break; - case 5: rs6 = 0.821850; s18 = 3.140281; rs18 = 2.728151; break; - case 6: rs6 = 0.012092; s18 = 0.358940; rs18 = 5.938951; break; - case 7: rs6 = 0.007912; s18 = 0.528823; rs18 = 6.162326; break; - case 8: rs6 = 0.563761; s18 = 0.906564; rs18 = 3.593680; break; - default: - error->all(FLERR, "Functional name unknown"); - break; - } -} - -void PairD3::setfuncpar() { - void (PairD3::*setfuncpar_damp[4])() = { - &PairD3::setfuncpar_zero, - &PairD3::setfuncpar_bj, - &PairD3::setfuncpar_zerom, - &PairD3::setfuncpar_bjm - }; - (this->*setfuncpar_damp[damping])(); - - rs8 = rs18; - alp6 = alp; - alp8 = alp + 2.0; - // rs10 = rs18 - // alp10 = alp + 4.0; - - a1 = rs6; - a2 = rs8; - s8 = s18; - // s6 is already defined -} - -/* ---------------------------------------------------------------------- - Coeff : read from pair_coeff (Required) -> pair_coeff * * element1 element2 ... -------------------------------------------------------------------------- */ - -void PairD3::coeff(int* atomic_numbers) { - if (!allocated) allocate(); - if (atom->ntypes + 1 != np1_save) { reallocate_arrays_np1(); } - - int ntypes = atom->ntypes; - /* - scale r4/r2 values of the atoms by sqrt(Z) - sqrt is also globally close to optimum - together with the factor 1/2 this yield reasonable - c8 for he, ne and ar. for larger Z, C8 becomes too large - which effectively mimics higher R^n terms neglected due - to stability reasons - - r2r4 =sqrt(0.5*r2r4(i)*dfloat(i)**0.5 ) with i=elementnumber - the large number of digits is just to keep the results consistent - with older versions. They should not imply any higher accuracy than - the old values - */ - double r2r4_ref[94] = { - 2.00734898, 1.56637132, 5.01986934, 3.85379032, 3.64446594, - 3.10492822, 2.71175247, 2.59361680, 2.38825250, 2.21522516, - 6.58585536, 5.46295967, 5.65216669, 4.88284902, 4.29727576, - 4.04108902, 3.72932356, 3.44677275, 7.97762753, 7.07623947, - 6.60844053, 6.28791364, 6.07728703, 5.54643096, 5.80491167, - 5.58415602, 5.41374528, 5.28497229, 5.22592821, 5.09817141, - 6.12149689, 5.54083734, 5.06696878, 4.87005108, 4.59089647, - 4.31176304, 9.55461698, 8.67396077, 7.97210197, 7.43439917, - 6.58711862, 6.19536215, 6.01517290, 5.81623410, 5.65710424, - 5.52640661, 5.44263305, 5.58285373, 7.02081898, 6.46815523, - 5.98089120, 5.81686657, 5.53321815, 5.25477007, 11.02204549, - 10.15679528, 9.35167836, 9.06926079, 8.97241155, 8.90092807, - 8.85984840, 8.81736827, 8.79317710, 7.89969626, 8.80588454, - 8.42439218, 8.54289262, 8.47583370, 8.45090888, 8.47339339, - 7.83525634, 8.20702843, 7.70559063, 7.32755997, 7.03887381, - 6.68978720, 6.05450052, 5.88752022, 5.70661499, 5.78450695, - 7.79780729, 7.26443867, 6.78151984, 6.67883169, 6.39024318, - 6.09527958, 11.79156076, 11.10997644, 9.51377795, 8.67197068, - 8.77140725, 8.65402716, 8.53923501, 8.85024712 - }; // atomic / values - - /* - covalent radii (taken from Pyykko and Atsumi, Chem. Eur. J. 15, 2009, 188-197) - values for metals decreased by 10 % - ! data rcov/ - ! . 0.32, 0.46, 1.20, 0.94, 0.77, 0.75, 0.71, 0.63, 0.64, 0.67 - ! ., 1.40, 1.25, 1.13, 1.04, 1.10, 1.02, 0.99, 0.96, 1.76, 1.54 - ! ., 1.33, 1.22, 1.21, 1.10, 1.07, 1.04, 1.00, 0.99, 1.01, 1.09 - ! ., 1.12, 1.09, 1.15, 1.10, 1.14, 1.17, 1.89, 1.67, 1.47, 1.39 - ! ., 1.32, 1.24, 1.15, 1.13, 1.13, 1.08, 1.15, 1.23, 1.28, 1.26 - ! ., 1.26, 1.23, 1.32, 1.31, 2.09, 1.76, 1.62, 1.47, 1.58, 1.57 - ! ., 1.56, 1.55, 1.51, 1.52, 1.51, 1.50, 1.49, 1.49, 1.48, 1.53 - ! ., 1.46, 1.37, 1.31, 1.23, 1.18, 1.16, 1.11, 1.12, 1.13, 1.32 - ! ., 1.30, 1.30, 1.36, 1.31, 1.38, 1.42, 2.01, 1.81, 1.67, 1.58 - ! ., 1.52, 1.53, 1.54, 1.55 / - - these new data are scaled with k2=4./3. and converted a_0 via - autoang=0.52917726d0 - */ - - double rcov_ref[94] = { - 0.80628308, 1.15903197, 3.02356173, 2.36845659, 1.94011865, - 1.88972601, 1.78894056, 1.58736983, 1.61256616, 1.68815527, - 3.52748848, 3.14954334, 2.84718717, 2.62041997, 2.77159820, - 2.57002732, 2.49443835, 2.41884923, 4.43455700, 3.88023730, - 3.35111422, 3.07395437, 3.04875805, 2.77159820, 2.69600923, - 2.62041997, 2.51963467, 2.49443835, 2.54483100, 2.74640188, - 2.82199085, 2.74640188, 2.89757982, 2.77159820, 2.87238349, - 2.94797246, 4.76210950, 4.20778980, 3.70386304, 3.50229216, - 3.32591790, 3.12434702, 2.89757982, 2.84718717, 2.84718717, - 2.72120556, 2.89757982, 3.09915070, 3.22513231, 3.17473967, - 3.17473967, 3.09915070, 3.32591790, 3.30072128, 5.26603625, - 4.43455700, 4.08180818, 3.70386304, 3.98102289, 3.95582657, - 3.93062995, 3.90543362, 3.80464833, 3.82984466, 3.80464833, - 3.77945201, 3.75425569, 3.75425569, 3.72905937, 3.85504098, - 3.67866672, 3.45189952, 3.30072128, 3.09915070, 2.97316878, - 2.92277614, 2.79679452, 2.82199085, 2.84718717, 3.32591790, - 3.27552496, 3.27552496, 3.42670319, 3.30072128, 3.47709584, - 3.57788113, 5.06446567, 4.56053862, 4.20778980, 3.98102289, - 3.82984466, 3.85504098, 3.88023730, 3.90543362 - }; // covalent radii - - for (int i = 0; i < ntypes; i++) { - r2r4[i+1] = r2r4_ref[atomic_numbers[i]-1]; - rcov[i+1] = rcov_ref[atomic_numbers[i]-1]; - } - - // set r0ab - read_r0ab(atomic_numbers, ntypes); - - // read c6ab - read_c6ab(atomic_numbers, ntypes); -} - -/* ---------------------------------------------------------------------- - Get derivative of C6 w.r.t. CN (used in PairD3::compute) - - C6 = C6(CN_A, CN_B) == W(CN_A, CN_B) / Z(CN_A, CN_B) - - This gives below from chain rule: - d(C6)/dr = d(C6)/d(CN_A) * d(CN_A)/dr + d(C6)/d(CN_B) * d(CN_B)/dr - - So we can pre-calculate the d(C6)/d(CN_A), d(C6)/d(CN_B) part. - - d(C6)/d(CN_i) = (dW/d(CN_i) * Z - W * dZ/d(CN_i)) / (W * W) - W : "denominator" - Z : "numerator" - dW/d(CN_i) : "d_denominator_i" - dZ/d(CN_j) : "d_numerator_j" - - Z = Sum( L_ij(CN_A, CN_B) * C6_ref(CN_A_i, CN_B_j) ) over i, j - W = Sum( L_ij(CN_A, CN_B) ) over i, j - - And the resulting derivative term is saved into - "dc6_iji_tot", "dc6_ijj_tot" array, - where we can find the value of d(C6)/d(CN_i) - by knowing the index of "iat", and "jat". ("idx_linij") - - Also, c6 values will also be saved into "c6_ij_tot" array. - - Here, as we only interested in *pair* of atoms, assume "iat" >= "jat". - Then "idx_linij" = "jat + (iat + 1) * iat / 2" have the order below. - - idx_linij | j = 0 j = 1 j = 2 j = 3 ... ---------------------------------------------- - i = 0 | 0 - i = 1 | 1 2 - i = 2 | 3 4 5 - i = 3 | 6 7 8 9 - ... | ... ... ... ... ... - -------------------------------------------------------------------------- */ - -__global__ void kernel_get_dC6_dCNij( - int maxij, float K3, - double *cn, int *mxc, float *****c6ab, int *type, - float *c6_ij_tot, float *dc6_iji_tot, float *dc6_ijj_tot -) { - int iter = blockIdx.x * blockDim.x + threadIdx.x; - - if (iter < maxij) { - int iat, jat; - ij_at_linij(iter, iat, jat); - - const int atomtype_i = type[iat]; - const int atomtype_j = type[jat]; - - const float cni = cn[iat]; - const int mxci = mxc[atomtype_i]; - const float cnj = cn[jat]; - const int mxcj = mxc[atomtype_j]; - - float c6mem = -1e99f; - float r_save = 9999.0f; - double numerator = 0.0; - double denominator = 0.0; - double d_numerator_i = 0.0; - double d_denominator_i = 0.0; - double d_numerator_j = 0.0; - double d_denominator_j = 0.0; - - for (int a = 0; a < mxci; a++) { - for (int b = 0; b < mxcj; b++) { - float c6ref = c6ab[atomtype_i][atomtype_j][a][b][0]; - - if (c6ref > 0.0f) { - float cn_refi = c6ab[atomtype_i][atomtype_j][a][b][1]; - float cn_refj = c6ab[atomtype_i][atomtype_j][a][b][2]; - - float r = (cn_refi - cni) * (cn_refi - cni) + (cn_refj - cnj) * (cn_refj - cnj); - if (r < r_save) { - r_save = r; - c6mem = c6ref; - } - - double expterm = exp(static_cast(K3) * static_cast(r)); // must be double - numerator += c6ref * expterm; - denominator += expterm; - - expterm *= 2.0f * K3; - - double term = expterm * (cni - cn_refi); - d_numerator_i += c6ref * term; - d_denominator_i += term; - - term = expterm * (cnj - cn_refj); - d_numerator_j += c6ref * term; - d_denominator_j += term; - } - } - } - - if (denominator > 1e-99) { - const double denominator_rc = 1.0 / denominator; // must be double - const double unit_frac = numerator * denominator_rc; - c6_ij_tot[iter] = unit_frac; - dc6_iji_tot[iter] = denominator_rc * fma(unit_frac, -d_denominator_i, d_numerator_i); // must be double - dc6_ijj_tot[iter] = denominator_rc * fma(unit_frac, -d_denominator_j, d_numerator_j); // must be double - //const double denominator_rc = 1.0 / denominator; - //const float unit_frac = numerator * denominator_rc; - //c6_ij_tot[iter] = unit_frac; - //dc6_iji_tot[iter] = \ - static_cast(d_numerator_i * denominator_rc) - static_cast(d_denominator_i * denominator_rc) * unit_frac; - //dc6_ijj_tot[iter] = \ - static_cast(d_numerator_j * denominator_rc) - static_cast(d_denominator_j * denominator_rc) * unit_frac; - } - else { - c6_ij_tot[iter] = c6mem; - dc6_iji_tot[iter] = 0.0f; - dc6_ijj_tot[iter] = 0.0f; - } - } -} - -void PairD3::get_dC6_dCNij() { - int n = atom->natoms; - int maxij = n * (n + 1) / 2; - - //START_CUDA_TIMER(); - - int threadsPerBlock = 128; - int blocksPerGrid = (maxij + threadsPerBlock - 1) / threadsPerBlock; - kernel_get_dC6_dCNij<<>>( - maxij, K3, - cn, mxc, c6ab, atomtype, - c6_ij_tot, dc6_iji_tot, dc6_ijj_tot - ); - cudaDeviceSynchronize(); - - //STOP_CUDA_TIMER("get_dC6dCNij"); -} - -/* ---------------------------------------------------------------------- - Get lattice vectors (used in PairD3::compute) - - 1) Save lattice vectors into "lat_v_1", "lat_v_2", "lat_v_3" - 2) Calculate repetition criteria for vdw, cn - 3) precaluclate tau (xyz shift due to cell repetition) - -------------------------------------------------------------------------- */ - -void PairD3::set_lattice_vectors() { - double boxxlo = domain->boxlo[0]; - double boxxhi = domain->boxhi[0]; - double boxylo = domain->boxlo[1]; - double boxyhi = domain->boxhi[1]; - double boxzlo = domain->boxlo[2]; - double boxzhi = domain->boxhi[2]; - double xy = domain->xy; - double xz = domain->xz; - double yz = domain->yz; - - lat_v_1[0] = (boxxhi - boxxlo) / AU_TO_ANG; - lat_v_1[1] = 0.0; - lat_v_1[2] = 0.0; - lat_v_2[0] = xy / AU_TO_ANG; - lat_v_2[1] = (boxyhi - boxylo) / AU_TO_ANG; - lat_v_2[2] = 0.0; - lat_v_3[0] = xz / AU_TO_ANG; - lat_v_3[1] = yz / AU_TO_ANG; - lat_v_3[2] = (boxzhi - boxzlo) / AU_TO_ANG; - - int vdwrx_save = 2 * rep_vdw[0] + 1; - int vdwry_save = 2 * rep_vdw[1] + 1; - int vdwrz_save = 2 * rep_vdw[2] + 1; - int cnrx_save = 2 * rep_cn[0] + 1; - int cnry_save = 2 * rep_cn[1] + 1; - int cnrz_save = 2 * rep_cn[2] + 1; - - set_lattice_repetition_criteria(rthr, rep_vdw); - set_lattice_repetition_criteria(cnthr, rep_cn); - - int vdw_range_x = 2 * rep_vdw[0] + 1; - int vdw_range_y = 2 * rep_vdw[1] + 1; - int vdw_range_z = 2 * rep_vdw[2] + 1; - int tau_loop_size_vdw = vdw_range_x * vdw_range_y * vdw_range_z * 3; - if (tau_loop_size_vdw != tau_idx_vdw_total_size) { - if (tau_idx_vdw != nullptr) { - for (int i = 0; i < vdwrx_save; i++) { - for (int j = 0; j < vdwry_save; j++) { - for (int k = 0; k < vdwrz_save; k++) { - cudaFree(tau_vdw[i][j][k]); - } - cudaFree(tau_vdw[i][j]); - } - cudaFree(tau_vdw[i]); - } - cudaFree(tau_vdw); - cudaFree(tau_idx_vdw); - } - tau_idx_vdw_total_size = tau_loop_size_vdw; - cudaMallocManaged(&tau_vdw, vdw_range_x * sizeof(float***)); - for (int i = 0; i < vdw_range_x; i++) { - cudaMallocManaged(&tau_vdw[i], vdw_range_y * sizeof(float**)); - for (int j = 0; j < vdw_range_y; j++) { - cudaMallocManaged(&tau_vdw[i][j], vdw_range_z * sizeof(float*)); - for (int k = 0; k < vdw_range_z; k++) { - cudaMallocManaged(&tau_vdw[i][j][k], 3 * sizeof(float)); - } - } - } - cudaMallocManaged(&tau_idx_vdw, tau_idx_vdw_total_size * sizeof(int)); - } - - int cn_range_x = 2 * rep_cn[0] + 1; - int cn_range_y = 2 * rep_cn[1] + 1; - int cn_range_z = 2 * rep_cn[2] + 1; - int tau_loop_size_cn = cn_range_x * cn_range_y * cn_range_z * 3; - if (tau_loop_size_cn != tau_idx_cn_total_size) { - if (tau_idx_cn != nullptr) { - for (int i = 0; i < cnrx_save; i++) { - for (int j = 0; j < cnry_save; j++) { - for (int k = 0; k < cnrz_save; k++) { - cudaFree(tau_cn[i][j][k]); - } - cudaFree(tau_cn[i][j]); - } - cudaFree(tau_cn[i]); - } - cudaFree(tau_cn); - cudaFree(tau_idx_cn); - } - tau_idx_cn_total_size = tau_loop_size_cn; - cudaMallocManaged(&tau_cn, cn_range_x * sizeof(float***)); - for (int i = 0; i < cn_range_x; i++) { - cudaMallocManaged(&tau_cn[i], cn_range_y * sizeof(float**)); - for (int j = 0; j < cn_range_y; j++) { - cudaMallocManaged(&tau_cn[i][j], cn_range_z * sizeof(float*)); - for (int k = 0; k < cn_range_z; k++) { - cudaMallocManaged(&tau_cn[i][j][k], 3 * sizeof(float)); - } - } - } - cudaMallocManaged(&tau_idx_cn, tau_idx_cn_total_size * sizeof(int)); - } -} - -/* ---------------------------------------------------------------------- - Set repetition criteria (used in PairD3::compute) - - Needed as Periodic Boundary Condition should be considered. - - As the cell may *not* be orthorhombic, - the dot product should be used between x/y/z direction and - corresponding cross product vector. -------------------------------------------------------------------------- */ - -void PairD3::set_lattice_repetition_criteria(float r_threshold, int* rep_v) { - double r_cutoff = sqrt(r_threshold); - double lat_cp_12[3], lat_cp_23[3], lat_cp_31[3]; - double cos_value; - - cross3(lat_v_1, lat_v_2, lat_cp_12); - cross3(lat_v_2, lat_v_3, lat_cp_23); - cross3(lat_v_3, lat_v_1, lat_cp_31); - - cos_value = dot3(lat_cp_23, lat_v_1) / len3(lat_cp_23); - rep_v[0] = static_cast(std::abs(r_cutoff / cos_value)) + 1; - cos_value = dot3(lat_cp_31, lat_v_2) / len3(lat_cp_31); - rep_v[1] = static_cast(std::abs(r_cutoff / cos_value)) + 1; - cos_value = dot3(lat_cp_12, lat_v_3) / len3(lat_cp_12); - rep_v[2] = static_cast(std::abs(r_cutoff / cos_value)) + 1; - - if (domain->xperiodic == 0) { rep_v[0] = 0; } - if (domain->yperiodic == 0) { rep_v[1] = 0; } - if (domain->zperiodic == 0) { rep_v[2] = 0; } -} - -/* ---------------------------------------------------------------------- - Calculate Coordination Number (used in PairD3::compute) -------------------------------------------------------------------------- */ - -__global__ void kernel_get_coordination_number( - int maxij, int maxtau, float cnthr, float K1, - float *rcov, int *rep_cn, float ****tau_cn, int *tau_idx_cn, int *type, float **x, - double *cn -) { - int iter = blockIdx.x * blockDim.x + threadIdx.x; - - if (iter < maxij) { - int iat, jat; - ij_at_linij(iter, iat, jat); - - float cn_local = 0.0f; - - if (iat == jat) { - const float rcov_sum = rcov[type[iat]] * 2.0f; - for (int k = maxtau - 1; k >= 0; k -= 3) { - const int idx1 = tau_idx_cn[k-2]; - const int idx2 = tau_idx_cn[k-1]; - const int idx3 = tau_idx_cn[k]; - if (idx1 == rep_cn[0] && idx2 == rep_cn[1] && idx3 == rep_cn[2]) { continue; } - const float rx = tau_cn[idx1][idx2][idx3][0]; - const float ry = tau_cn[idx1][idx2][idx3][1]; - const float rz = tau_cn[idx1][idx2][idx3][2]; - const float r2 = rx * rx + ry * ry + rz * rz; - if (r2 <= cnthr) { - const float r_rc = rsqrtf(r2); - const float damp = 1.0f / (1.0f + expf(-K1 * ((rcov_sum * r_rc) - 1.0f))); - cn_local += damp; - } - } - atomicAdd(&cn[iat], cn_local); - } - - else { - const float rcov_sum = rcov[type[iat]] + rcov[type[jat]]; - for (int k = maxtau - 1; k >= 0; k -= 3) { - const int idx1 = tau_idx_cn[k-2]; - const int idx2 = tau_idx_cn[k-1]; - const int idx3 = tau_idx_cn[k]; - const float rx = x[jat][0] - x[iat][0] + tau_cn[idx1][idx2][idx3][0]; - const float ry = x[jat][1] - x[iat][1] + tau_cn[idx1][idx2][idx3][1]; - const float rz = x[jat][2] - x[iat][2] + tau_cn[idx1][idx2][idx3][2]; - const float r2 = rx * rx + ry * ry + rz * rz; - if (r2 <= cnthr) { - const float r_rc = rsqrtf(r2); - const float damp = 1.0f / (1.0f + expf(-K1 * ((rcov_sum * r_rc) - 1.0f))); - cn_local += damp; - } - } - atomicAdd(&cn[iat], cn_local); - atomicAdd(&cn[jat], cn_local); - } - } -} - -void PairD3::get_coordination_number() { - int n = atom->natoms; - int maxij = n * (n + 1) / 2; - int maxtau = tau_idx_cn_total_size; - - for (int i = 0; i < n; i++) { - cn[i] = 0.0; - } - - //START_CUDA_TIMER(); - - int threadsPerBlock = 128; - int blocksPerGrid = (maxij + threadsPerBlock - 1) / threadsPerBlock; - kernel_get_coordination_number<<>>( - maxij, maxtau, cnthr, K1, - rcov, rep_cn, tau_cn, tau_idx_cn, atomtype, x, - cn - ); - cudaDeviceSynchronize(); - - //STOP_CUDA_TIMER("get_coord"); -} - -/* ---------------------------------------------------------------------- - reallcate memory if the number of atoms has changed (used in PairD3::compute) -------------------------------------------------------------------------- */ - -void PairD3::reallocate_arrays() { - /* -------------- Destroy previous arrays -------------- */ - cudaFree(cn); - for (int i = 0; i < n_save; i++) { cudaFree(x[i]); }; cudaFree(x); - cudaFree(dc6i); - for (int i = 0; i < n_save; i++) { cudaFree(f[i]); }; cudaFree(f); - - cudaFree(dc6_iji_tot); - cudaFree(dc6_ijj_tot); - cudaFree(c6_ij_tot); - - cudaFree(atomtype); - /* -------------- Destroy previous arrays -------------- */ - - /* -------------- Create new arrays -------------- */ - int n = atom->natoms; - n_save = n; - - cudaMallocManaged(&cn, n * sizeof(double)); - cudaMallocManaged(&x, n * sizeof(float*)); for (int i = 0; i < n; i++) { cudaMallocManaged(&x[i], 3 * sizeof(float)); } - cudaMallocManaged(&dc6i, n * sizeof(double)); - cudaMallocManaged(&f, n * sizeof(double*)); for (int i = 0; i < n; i++) { cudaMallocManaged(&f[i], 3 * sizeof(double)); } - - int n_ij_combination = n * (n + 1) / 2; - cudaMallocManaged(&dc6_iji_tot, n_ij_combination * sizeof(float)); - cudaMallocManaged(&dc6_ijj_tot, n_ij_combination * sizeof(float)); - cudaMallocManaged(&c6_ij_tot, n_ij_combination * sizeof(float)); - - cudaMallocManaged(&atomtype, n * sizeof(int)); - /* -------------- Create new arrays -------------- */ -} - -void PairD3::reallocate_arrays_np1() { - /* -------------- Destroy previous arrays -------------- */ - cudaFree(r2r4); - cudaFree(rcov); - cudaFree(mxc); - for (int i = 0; i < np1_save; i++) { cudaFree(r0ab[i]); }; cudaFree(r0ab); - for (int i = 0; i < np1_save; i++) { - for (int j = 0; j < np1_save; j++) { - for (int k = 0; k < MAXC; k++) { - for (int l = 0; l < MAXC; l++) { - cudaFree(c6ab[i][j][k][l]); - } - cudaFree(c6ab[i][j][k]); - } - cudaFree(c6ab[i][j]); - } - cudaFree(c6ab[i]); - } - cudaFree(c6ab); - /* -------------- Destroy previous arrays -------------- */ - - /* -------------- Create new arrays -------------- */ - int np1 = atom->ntypes + 1; - np1_save = np1; - - cudaMallocManaged(&r2r4, np1 * sizeof(float)); - cudaMallocManaged(&rcov, np1 * sizeof(float)); - cudaMallocManaged(&mxc, np1 * sizeof(int)); - cudaMallocManaged(&r0ab, np1 * sizeof(float*)); for (int i = 0; i < np1; i++) { cudaMallocManaged(&r0ab[i], np1 * sizeof(float)); } - cudaMallocManaged(&c6ab, np1 * sizeof(float****)); - for (int i = 0; i < np1; i++) { - cudaMallocManaged(&c6ab[i], np1 * sizeof(float***)); - for (int j = 0; j < np1; j++) { - cudaMallocManaged(&c6ab[i][j], MAXC * sizeof(float**)); - for (int k = 0; k < MAXC; k++) { - cudaMallocManaged(&c6ab[i][j][k], MAXC * sizeof(float*)); - for (int l = 0; l < MAXC; l++) { - cudaMallocManaged(&c6ab[i][j][k][l], 3 * sizeof(float)); - } - } - } - } - /* -------------- Create new arrays -------------- */ -} - -/* ---------------------------------------------------------------------- - Initialize atomic positions & types (used in PairD3::compute) - - As the default xyz from lammps does not assure that atoms are within unit cell, - this function shifts atoms into the unit cell. -------------------------------------------------------------------------- */ - -void PairD3::load_atom_info() { - double lat[3][3]; - lat[0][0] = lat_v_1[0]; - lat[0][1] = lat_v_2[0]; - lat[0][2] = lat_v_3[0]; - lat[1][0] = lat_v_1[1]; - lat[1][1] = lat_v_2[1]; - lat[1][2] = lat_v_3[1]; - lat[2][0] = lat_v_1[2]; - lat[2][1] = lat_v_2[2]; - lat[2][2] = lat_v_3[2]; - - double det = lat[0][0] * lat[1][1] * lat[2][2] - + lat[0][1] * lat[1][2] * lat[2][0] - + lat[0][2] * lat[1][0] * lat[2][1] - - lat[0][2] * lat[1][1] * lat[2][0] - - lat[0][1] * lat[1][0] * lat[2][2] - - lat[0][0] * lat[1][2] * lat[2][1]; - - double lat_inv[3][3]; - lat_inv[0][0] = (lat[1][1] * lat[2][2] - lat[1][2] * lat[2][1]) / det; - lat_inv[1][0] = (lat[1][2] * lat[2][0] - lat[1][0] * lat[2][2]) / det; - lat_inv[2][0] = (lat[1][0] * lat[2][1] - lat[1][1] * lat[2][0]) / det; - lat_inv[0][1] = (lat[0][2] * lat[2][1] - lat[0][1] * lat[2][2]) / det; - lat_inv[1][1] = (lat[0][0] * lat[2][2] - lat[0][2] * lat[2][0]) / det; - lat_inv[2][1] = (lat[0][1] * lat[2][0] - lat[0][0] * lat[2][1]) / det; - lat_inv[0][2] = (lat[0][1] * lat[1][2] - lat[0][2] * lat[1][1]) / det; - lat_inv[1][2] = (lat[0][2] * lat[1][0] - lat[0][0] * lat[1][2]) / det; - lat_inv[2][2] = (lat[0][0] * lat[1][1] - lat[0][1] * lat[1][0]) / det; - - double a[3] = { 0.0 }; - for (int iat = 0; iat < atom->natoms; iat++) { - for (int i = 0; i < 3; i++) { - a[i] = lat_inv[i][0] * (atom->x)[iat][0] / AU_TO_ANG + - lat_inv[i][1] * (atom->x)[iat][1] / AU_TO_ANG + - lat_inv[i][2] * (atom->x)[iat][2] / AU_TO_ANG; - a[i] -= floor(a[i]); // replaces the code below - //if (a[i] > 1) { while (a[i] > 1) { a[i]--; } } - //else if (a[i] < 0) { while (a[i] < 0) { a[i]++; } } - } - - for (int i = 0; i < 3; i++) { - x[iat][i] = (lat[i][0] * a[0] + lat[i][1] * a[1] + lat[i][2] * a[2]); - } - } -} - -/* ---------------------------------------------------------------------- - Precalculate tau array -------------------------------------------------------------------------- */ - -void PairD3::precalculate_tau_array() { - int xlim = rep_vdw[0]; - int ylim = rep_vdw[1]; - int zlim = rep_vdw[2]; - - int index = 0; - for (int taux = -xlim; taux <= xlim; taux++) { - for (int tauy = -ylim; tauy <= ylim; tauy++) { - for (int tauz = -zlim; tauz <= zlim; tauz++) { - tau_vdw[taux + xlim][tauy + ylim][tauz + zlim][0] = lat_v_1[0] * taux + lat_v_2[0] * tauy + lat_v_3[0] * tauz; - tau_vdw[taux + xlim][tauy + ylim][tauz + zlim][1] = lat_v_1[1] * taux + lat_v_2[1] * tauy + lat_v_3[1] * tauz; - tau_vdw[taux + xlim][tauy + ylim][tauz + zlim][2] = lat_v_1[2] * taux + lat_v_2[2] * tauy + lat_v_3[2] * tauz; - tau_idx_vdw[index++] = taux + xlim; - tau_idx_vdw[index++] = tauy + ylim; - tau_idx_vdw[index++] = tauz + zlim; - } - } - } - - xlim = rep_cn[0]; - ylim = rep_cn[1]; - zlim = rep_cn[2]; - - index = 0; - for (int taux = -xlim; taux <= xlim; taux++) { - for (int tauy = -ylim; tauy <= ylim; tauy++) { - for (int tauz = -zlim; tauz <= zlim; tauz++) { - tau_cn[taux + xlim][tauy + ylim][tauz + zlim][0] = lat_v_1[0] * taux + lat_v_2[0] * tauy + lat_v_3[0] * tauz; - tau_cn[taux + xlim][tauy + ylim][tauz + zlim][1] = lat_v_1[1] * taux + lat_v_2[1] * tauy + lat_v_3[1] * tauz; - tau_cn[taux + xlim][tauy + ylim][tauz + zlim][2] = lat_v_1[2] * taux + lat_v_2[2] * tauy + lat_v_3[2] * tauz; - tau_idx_cn[index++] = taux + xlim; - tau_idx_cn[index++] = tauy + ylim; - tau_idx_cn[index++] = tauz + zlim; - } - } - } -} - -/* ---------------------------------------------------------------------- - Get forces (Zero damping) -------------------------------------------------------------------------- */ - -__global__ void kernel_get_forces_without_dC6_zero( - int maxij, int maxtau, float rthr, float s6, float s8, float a1, float a2, float alp6, float alp8, - float *r2r4, float **r0ab, int *rep_vdw, float ****tau_vdw, int *tau_idx_vdw, int *type, float **x, - float *c6_ij_tot, float *dc6_iji_tot, float *dc6_ijj_tot, - double *dc6i, double *disp, double **f, double **sigma -) { - int iter = blockIdx.x * blockDim.x + threadIdx.x; - - __shared__ float sigma_00[128]; - __shared__ float sigma_01[128]; - __shared__ float sigma_02[128]; - __shared__ float sigma_10[128]; - __shared__ float sigma_11[128]; - __shared__ float sigma_12[128]; - __shared__ float sigma_20[128]; - __shared__ float sigma_21[128]; - __shared__ float sigma_22[128]; - __shared__ float disp_shared[128]; - - float sigma_local_00 = 0.0f; - float sigma_local_01 = 0.0f; - float sigma_local_02 = 0.0f; - float sigma_local_10 = 0.0f; - float sigma_local_11 = 0.0f; - float sigma_local_12 = 0.0f; - float sigma_local_20 = 0.0f; - float sigma_local_21 = 0.0f; - float sigma_local_22 = 0.0f; - float disp_local = 0.0f; - - if (iter < maxij) { - int iat, jat; - ij_at_linij(iter, iat, jat); - - float f_local[3] = { 0.0f }; - float dc6i_local_i = 0.0f; - float dc6i_local_j = 0.0f; - - const float c6 = c6_ij_tot[iter]; - const float dc6iji = dc6_iji_tot[iter]; - const float dc6ijj = dc6_ijj_tot[iter]; - - if (iat == jat) { - const int atomtype_i = type[iat]; - const float r0 = r0ab[atomtype_i][atomtype_i]; - const float unit_r2r4 = r2r4[atomtype_i]; - const float r42 = unit_r2r4 * unit_r2r4; - const float unit_a1 = (a1 * r0); - const float unit_a2 = (a2 * r0); - const float s8r42 = s8 * r42; - - for (int k = maxtau - 1; k >= 0; k -= 3) { - const int idx1 = tau_idx_vdw[k-2]; - const int idx2 = tau_idx_vdw[k-1]; - const int idx3 = tau_idx_vdw[k]; - - if (idx1 == rep_vdw[0] && idx2 == rep_vdw[1] && idx3 == rep_vdw[2]) { continue; } - const float rij[3] = { - tau_vdw[idx1][idx2][idx3][0], - tau_vdw[idx1][idx2][idx3][1], - tau_vdw[idx1][idx2][idx3][2] - }; - const float r2 = lensq3(rij); - if (r2 > rthr) { continue; } - - const float r_rc = rsqrtf(r2); - float unit_rc_a1 = unit_a1 * r_rc; - float t6 = unit_rc_a1 * unit_rc_a1; // ^2 - t6 *= unit_rc_a1; // ^3 - t6 *= t6; // ^6 - t6 *= unit_rc_a1; // ^7 - t6 *= t6; // ^14 - const float damp6 = 1.0f / fmaf(t6, 6.0f, 1.0f); - float unit_rc_a2 = unit_a2 * r_rc; - float t8 = unit_rc_a2 * unit_rc_a2; // ^2 - t8 *= t8; // ^4 - t8 *= t8; // ^8 - t8 *= t8; // ^16 - const float damp8 = 1.0f / fmaf(t8, 6.0f, 1.0f); - const float r2_rc = r_rc * r_rc; // 1.0 / r2 - const float r6_rc = r2_rc * r2_rc * r2_rc; - const float r8_rc = r6_rc * r2_rc; - const float x1 = 3.0f * c6 * r8_rc * fmaf(r2_rc, s8r42 * damp8 * fmaf(3.0f * alp8 * t8, damp8, -4.0f), s6 * damp6 * fmaf(alp6 * t6, damp6, -1.0f)); - //const float x1 = 0.5 * 6.0 * c6 * r8_rc * (s6 * damp6 * (14.0 * t6 * damp6 - 1.0) + s8r42 * r2_rc * damp8 * (48.0 * t8 * damp8 - 4.0)); - //3.0 * alp6 = 48.0 - - const float vec[3] = { - x1 * rij[0], - x1 * rij[1], - x1 * rij[2] - }; - - sigma_local_00 += vec[0] * rij[0]; - sigma_local_01 += vec[0] * rij[1]; - sigma_local_02 += vec[0] * rij[2]; - sigma_local_10 += vec[1] * rij[0]; - sigma_local_11 += vec[1] * rij[1]; - sigma_local_12 += vec[1] * rij[2]; - sigma_local_20 += vec[2] * rij[0]; - sigma_local_21 += vec[2] * rij[1]; - sigma_local_22 += vec[2] * rij[2]; - - const float dc6_rest = 0.5f * r6_rc * fmaf(3.0f * r2_rc, s8r42 * damp8, s6 * damp6); - //const float dc6_rest = 0.5 * r6_rc * (s6 * damp6 + 3.0 * s8r42 * damp8 * r2_rc); - disp_local -= dc6_rest * c6; - dc6i_local_i += dc6_rest * dc6iji; - dc6i_local_j += dc6_rest * dc6ijj; - } - atomicAdd(&dc6i[iat], dc6i_local_i); - atomicAdd(&dc6i[jat], dc6i_local_j); - } - - else { - const int atomtype_i = type[iat]; - const int atomtype_j = type[jat]; - const float r0 = r0ab[atomtype_i][atomtype_j]; - const float r42 = r2r4[atomtype_i] * r2r4[atomtype_j]; - const float unit_a1 = (a1 * r0); - const float unit_a2 = (a2 * r0); - const float s8r42 = s8 * r42; - - for (int k = maxtau - 1; k >= 0; k -= 3) { - const int idx1 = tau_idx_vdw[k-2]; - const int idx2 = tau_idx_vdw[k-1]; - const int idx3 = tau_idx_vdw[k]; - - const float rij[3] = { - x[jat][0] - x[iat][0] + tau_vdw[idx1][idx2][idx3][0], - x[jat][1] - x[iat][1] + tau_vdw[idx1][idx2][idx3][1], - x[jat][2] - x[iat][2] + tau_vdw[idx1][idx2][idx3][2] - }; - const float r2 = lensq3(rij); - if (r2 > rthr) { continue; } - - const float r_rc = rsqrtf(r2); - float unit_rc_a1 = unit_a1 * r_rc; - float t6 = unit_rc_a1 * unit_rc_a1; // ^2 - t6 *= unit_rc_a1; // ^3 - t6 *= t6; // ^6 - t6 *= unit_rc_a1; // ^7 - t6 *= t6; // ^14 - const float damp6 = 1.0f / fmaf(t6, 6.0f, 1.0f); - float unit_rc_a2 = unit_a2 * r_rc; - float t8 = unit_rc_a2 * unit_rc_a2; // ^2 - t8 *= t8; // ^4 - t8 *= t8; // ^8 - t8 *= t8; // ^16 - const float damp8 = 1.0f / fmaf(t8, 6.0f, 1.0f); - const float r2_rc = r_rc * r_rc; // 1.0 / r2 - const float r6_rc = r2_rc * r2_rc * r2_rc; - const float r8_rc = r6_rc * r2_rc; - const float x1 = 6.0f * c6 * r8_rc * fmaf(r2_rc, s8r42 * damp8 * fmaf(3.0f * alp8 * t8, damp8, -4.0f), s6 * damp6 * fmaf(alp6 * t6, damp6, -1.0f)); - //const float x1 = 6.0 * c6 * r8_rc * (s6 * damp6 * (14.0 * t6 * damp6 - 1.0) + s8r42 * r2_rc * damp8 * (48.0 * t8 * damp8 - 4.0)); - //3.0 * alp6 = 48.0 - - const float vec[3] = { - x1 * rij[0], - x1 * rij[1], - x1 * rij[2] - }; - - f_local[0] -= vec[0]; - f_local[1] -= vec[1]; - f_local[2] -= vec[2]; - - sigma_local_00 += vec[0] * rij[0]; - sigma_local_01 += vec[0] * rij[1]; - sigma_local_02 += vec[0] * rij[2]; - sigma_local_10 += vec[1] * rij[0]; - sigma_local_11 += vec[1] * rij[1]; - sigma_local_12 += vec[1] * rij[2]; - sigma_local_20 += vec[2] * rij[0]; - sigma_local_21 += vec[2] * rij[1]; - sigma_local_22 += vec[2] * rij[2]; - - const float dc6_rest = r6_rc * fmaf(3.0f * r2_rc, s8r42 * damp8, s6 * damp6); - //const float dc6_rest = r6_rc * (s6 * damp6 + 3.0 * s8r42 * damp8 * r2_rc); - disp_local -= dc6_rest * c6; - dc6i_local_i += dc6_rest * dc6iji; - dc6i_local_j += dc6_rest * dc6ijj; - } - atomicAdd(&dc6i[iat], dc6i_local_i); - atomicAdd(&dc6i[jat], dc6i_local_j); - atomicAdd(&f[iat][0], f_local[0]); - atomicAdd(&f[iat][1], f_local[1]); - atomicAdd(&f[iat][2], f_local[2]); - atomicAdd(&f[jat][0], -f_local[0]); - atomicAdd(&f[jat][1], -f_local[1]); - atomicAdd(&f[jat][2], -f_local[2]); - } - } - - sigma_00[threadIdx.x] = sigma_local_00; - sigma_01[threadIdx.x] = sigma_local_01; - sigma_02[threadIdx.x] = sigma_local_02; - sigma_10[threadIdx.x] = sigma_local_10; - sigma_11[threadIdx.x] = sigma_local_11; - sigma_12[threadIdx.x] = sigma_local_12; - sigma_20[threadIdx.x] = sigma_local_20; - sigma_21[threadIdx.x] = sigma_local_21; - sigma_22[threadIdx.x] = sigma_local_22; - disp_shared[threadIdx.x] = disp_local; - __syncthreads(); - - for (int s=blockDim.x/2; s>0; s>>=1) { - if (threadIdx.x < s) { - sigma_00[threadIdx.x] += sigma_00[threadIdx.x + s]; - sigma_01[threadIdx.x] += sigma_01[threadIdx.x + s]; - sigma_02[threadIdx.x] += sigma_02[threadIdx.x + s]; - sigma_10[threadIdx.x] += sigma_10[threadIdx.x + s]; - sigma_11[threadIdx.x] += sigma_11[threadIdx.x + s]; - sigma_12[threadIdx.x] += sigma_12[threadIdx.x + s]; - sigma_20[threadIdx.x] += sigma_20[threadIdx.x + s]; - sigma_21[threadIdx.x] += sigma_21[threadIdx.x + s]; - sigma_22[threadIdx.x] += sigma_22[threadIdx.x + s]; - disp_shared[threadIdx.x] += disp_shared[threadIdx.x + s]; - } - __syncthreads(); - } - - if (threadIdx.x == 0) { - atomicAdd(&sigma[0][0], sigma_00[0]); - atomicAdd(&sigma[0][1], sigma_01[0]); - atomicAdd(&sigma[0][2], sigma_02[0]); - atomicAdd(&sigma[1][0], sigma_10[0]); - atomicAdd(&sigma[1][1], sigma_11[0]); - atomicAdd(&sigma[1][2], sigma_12[0]); - atomicAdd(&sigma[2][0], sigma_20[0]); - atomicAdd(&sigma[2][1], sigma_21[0]); - atomicAdd(&sigma[2][2], sigma_22[0]); - atomicAdd(disp, disp_shared[0]); - } -} - -void PairD3::get_forces_without_dC6_zero() { - int n = atom->natoms; - int maxij = n * (n + 1) / 2; - int maxtau = tau_idx_vdw_total_size; - - *disp = 0.0; - - for (int dim = 0; dim < n; dim++) { dc6i[dim] = 0.0; } - - for (int i = 0; i < n; i++) { - for (int j = 0; j < 3; j++) { - f[i][j] = 0.0; - } - } - - for (int ii = 0; ii < 3; ii++) { - for (int jj = 0; jj < 3; jj++) { - sigma[ii][jj] = 0.0; - } - } - - //START_CUDA_TIMER(); - - int threadsPerBlock = 128; - int blocksPerGrid = (maxij + threadsPerBlock - 1) / threadsPerBlock; - kernel_get_forces_without_dC6_zero<<>>( - maxij, maxtau, rthr, s6, s8, a1, a2, alp6, alp8, - r2r4, r0ab, rep_vdw, tau_vdw, tau_idx_vdw, atomtype, x, - c6_ij_tot, dc6_iji_tot, dc6_ijj_tot, - dc6i, disp, f, sigma - ); - cudaDeviceSynchronize(); - disp_total = *disp; - - //STOP_CUDA_TIMER("get_forces_without"); -} - -__global__ void kernel_get_forces_without_dC6_bj( - int maxij, int maxtau, float rthr, float s6, float s8, float a1, float a2, - float *r2r4, int *rep_vdw, float ****tau_vdw, int *tau_idx_vdw, int *type, float **x, - float *c6_ij_tot, float *dc6_iji_tot, float *dc6_ijj_tot, - double *dc6i, double *disp, double **f, double **sigma -) { - int iter = blockIdx.x * blockDim.x + threadIdx.x; - - __shared__ float sigma_00[128]; - __shared__ float sigma_01[128]; - __shared__ float sigma_02[128]; - __shared__ float sigma_10[128]; - __shared__ float sigma_11[128]; - __shared__ float sigma_12[128]; - __shared__ float sigma_20[128]; - __shared__ float sigma_21[128]; - __shared__ float sigma_22[128]; - __shared__ float disp_shared[128]; - - float sigma_local_00 = 0.0f; - float sigma_local_01 = 0.0f; - float sigma_local_02 = 0.0f; - float sigma_local_10 = 0.0f; - float sigma_local_11 = 0.0f; - float sigma_local_12 = 0.0f; - float sigma_local_20 = 0.0f; - float sigma_local_21 = 0.0f; - float sigma_local_22 = 0.0f; - float disp_local = 0.0f; - - if (iter < maxij) { - int iat, jat; - ij_at_linij(iter, iat, jat); - - float f_local[3] = { 0.0f }; - float dc6i_local_i = 0.0f; - float dc6i_local_j = 0.0f; - - const float c6 = c6_ij_tot[iter]; - const float dc6iji = dc6_iji_tot[iter]; - const float dc6ijj = dc6_ijj_tot[iter]; - - if (iat == jat) { - const float unit_r2r4 = r2r4[type[iat]]; - const float r42x3 = unit_r2r4 * unit_r2r4 * 3.0f; - const float R0 = fmaf(a1, sqrtf(r42x3), a2); - const float R0_2 = R0 * R0; - const float R0_6 = R0_2 * R0_2 * R0_2; - const float R0_8 = R0_6 * R0_2; - const float s8r42x3 = s8 * r42x3; - - for (int k = maxtau - 1; k >= 0; k -= 3) { - const int idx1 = tau_idx_vdw[k-2]; - const int idx2 = tau_idx_vdw[k-1]; - const int idx3 = tau_idx_vdw[k]; - - if (idx1 == rep_vdw[0] && idx2 == rep_vdw[1] && idx3 == rep_vdw[2]) { continue; } - const float rij[3] = { - tau_vdw[idx1][idx2][idx3][0], - tau_vdw[idx1][idx2][idx3][1], - tau_vdw[idx1][idx2][idx3][2] - }; - const float r2 = lensq3(rij); - if (r2 > rthr) { continue; } - - const float r = sqrtf(r2); - const float r5 = r2 * r2 * r; - const float r7 = r5 * r2; - const float t6_rc = 1.0f / fmaf(r5, r, R0_6); - const float t8_rc = 1.0f / fmaf(r7, r, R0_8); - const float t6_sqrc = t6_rc * t6_rc; - const float t8_sqrc = t8_rc * t8_rc; - const float x1 = -c6 * fmaf(4.0f * s8r42x3 * r7, t8_sqrc, 3.0f * s6 * r5 * t6_sqrc); - //const float x1 = 0.5 * -c6 * (6.0 * s6 * r5 * t6_sqrc + 8.0 * s8r42x3 * r7 * t8_sqrc; - - const float r_rc = 1.0f / r; // rsqrt(r2) - const float vec[3] = { - x1 * rij[0] * r_rc, - x1 * rij[1] * r_rc, - x1 * rij[2] * r_rc - }; - - sigma_local_00 += vec[0] * rij[0]; - sigma_local_01 += vec[0] * rij[1]; - sigma_local_02 += vec[0] * rij[2]; - sigma_local_10 += vec[1] * rij[0]; - sigma_local_11 += vec[1] * rij[1]; - sigma_local_12 += vec[1] * rij[2]; - sigma_local_20 += vec[2] * rij[0]; - sigma_local_21 += vec[2] * rij[1]; - sigma_local_22 += vec[2] * rij[2]; - - const float dc6_rest = 0.5f * fmaf(s8r42x3, t8_rc, s6 * t6_rc); - //const float dc6_rest = 0.5 * s6 * t6_rc + s8r42x3 * t8_rc; - disp_local -= dc6_rest * c6; - dc6i_local_i += dc6_rest * dc6iji; - dc6i_local_j += dc6_rest * dc6ijj; - } - atomicAdd(&dc6i[iat], dc6i_local_i); - atomicAdd(&dc6i[jat], dc6i_local_j); - } - - else { - const float r42x3 = r2r4[type[iat]] * r2r4[type[jat]] * 3.0f; - const float R0 = fmaf(a1, sqrtf(r42x3), a2); - const float R0_2 = R0 * R0; - const float R0_6 = R0_2 * R0_2 * R0_2; - const float R0_8 = R0_6 * R0_2; - const float s8r42x3 = s8 * r42x3; - - for (int k = maxtau - 1; k >= 0; k -= 3) { - const int idx1 = tau_idx_vdw[k-2]; - const int idx2 = tau_idx_vdw[k-1]; - const int idx3 = tau_idx_vdw[k]; - const float rij[3] = { - x[jat][0] - x[iat][0] + tau_vdw[idx1][idx2][idx3][0], - x[jat][1] - x[iat][1] + tau_vdw[idx1][idx2][idx3][1], - x[jat][2] - x[iat][2] + tau_vdw[idx1][idx2][idx3][2] - }; - const float r2 = lensq3(rij); - if (r2 > rthr) { continue; } - - const float r = sqrtf(r2); - const float r5 = r2 * r2 * r; - const float r7 = r5 * r2; - const float t6_rc = 1.0f / fmaf(r5, r, R0_6); - const float t8_rc = 1.0f / fmaf(r7, r, R0_8); - const float t6_sqrc = t6_rc * t6_rc; - const float t8_sqrc = t8_rc * t8_rc; - const float x1 = -c6 * fmaf(8.0f * s8r42x3 * r7, t8_sqrc, 6.0f * s6 * r5 * t6_sqrc); - //const float x1 = -c6 * (6.0 * s6 * r5 * t6_sqrc + 8.0 * s8r42x3 * r7 * t8_sqrc; - - const float r_rc = 1.0f / r; // rsqrt(r2) - const float vec[3] = { - x1 * rij[0] * r_rc, - x1 * rij[1] * r_rc, - x1 * rij[2] * r_rc - }; - - f_local[0] -= vec[0]; - f_local[1] -= vec[1]; - f_local[2] -= vec[2]; - - sigma_local_00 += vec[0] * rij[0]; - sigma_local_01 += vec[0] * rij[1]; - sigma_local_02 += vec[0] * rij[2]; - sigma_local_10 += vec[1] * rij[0]; - sigma_local_11 += vec[1] * rij[1]; - sigma_local_12 += vec[1] * rij[2]; - sigma_local_20 += vec[2] * rij[0]; - sigma_local_21 += vec[2] * rij[1]; - sigma_local_22 += vec[2] * rij[2]; - - const float dc6_rest = fmaf(s8r42x3, t8_rc, s6 * t6_rc); - //const float dc6_rest = s6 * t6_rc + s8r42x3 * t8_rc; - disp_local -= dc6_rest * c6; - dc6i_local_i += dc6_rest * dc6iji; - dc6i_local_j += dc6_rest * dc6ijj; - } - atomicAdd(&dc6i[iat], dc6i_local_i); - atomicAdd(&dc6i[jat], dc6i_local_j); - atomicAdd(&f[iat][0], f_local[0]); - atomicAdd(&f[iat][1], f_local[1]); - atomicAdd(&f[iat][2], f_local[2]); - atomicAdd(&f[jat][0], -f_local[0]); - atomicAdd(&f[jat][1], -f_local[1]); - atomicAdd(&f[jat][2], -f_local[2]); - } - } - - sigma_00[threadIdx.x] = sigma_local_00; - sigma_01[threadIdx.x] = sigma_local_01; - sigma_02[threadIdx.x] = sigma_local_02; - sigma_10[threadIdx.x] = sigma_local_10; - sigma_11[threadIdx.x] = sigma_local_11; - sigma_12[threadIdx.x] = sigma_local_12; - sigma_20[threadIdx.x] = sigma_local_20; - sigma_21[threadIdx.x] = sigma_local_21; - sigma_22[threadIdx.x] = sigma_local_22; - disp_shared[threadIdx.x] = disp_local; - __syncthreads(); - - for (int s=blockDim.x/2; s>0; s>>=1) { - if (threadIdx.x < s) { - sigma_00[threadIdx.x] += sigma_00[threadIdx.x + s]; - sigma_01[threadIdx.x] += sigma_01[threadIdx.x + s]; - sigma_02[threadIdx.x] += sigma_02[threadIdx.x + s]; - sigma_10[threadIdx.x] += sigma_10[threadIdx.x + s]; - sigma_11[threadIdx.x] += sigma_11[threadIdx.x + s]; - sigma_12[threadIdx.x] += sigma_12[threadIdx.x + s]; - sigma_20[threadIdx.x] += sigma_20[threadIdx.x + s]; - sigma_21[threadIdx.x] += sigma_21[threadIdx.x + s]; - sigma_22[threadIdx.x] += sigma_22[threadIdx.x + s]; - disp_shared[threadIdx.x] += disp_shared[threadIdx.x + s]; - } - __syncthreads(); - } - - if (threadIdx.x == 0) { - atomicAdd(&sigma[0][0], sigma_00[0]); - atomicAdd(&sigma[0][1], sigma_01[0]); - atomicAdd(&sigma[0][2], sigma_02[0]); - atomicAdd(&sigma[1][0], sigma_10[0]); - atomicAdd(&sigma[1][1], sigma_11[0]); - atomicAdd(&sigma[1][2], sigma_12[0]); - atomicAdd(&sigma[2][0], sigma_20[0]); - atomicAdd(&sigma[2][1], sigma_21[0]); - atomicAdd(&sigma[2][2], sigma_22[0]); - atomicAdd(disp, disp_shared[0]); - } -} - -void PairD3::get_forces_without_dC6_bj() { - int n = atom->natoms; - int maxij = n * (n + 1) / 2; - int maxtau = tau_idx_vdw_total_size; - - *disp = 0.0; - - for (int dim = 0; dim < n; dim++) { dc6i[dim] = 0.0; } - - for (int i = 0; i < n; i++) { - for (int j = 0; j < 3; j++) { - f[i][j] = 0.0; - } - } - - for (int ii = 0; ii < 3; ii++) { - for (int jj = 0; jj < 3; jj++) { - sigma[ii][jj] = 0.0; - } - } - - //START_CUDA_TIMER(); - - int threadsPerBlock = 128; - int blocksPerGrid = (maxij + threadsPerBlock - 1) / threadsPerBlock; - kernel_get_forces_without_dC6_bj<<>>( - maxij, maxtau, rthr, s6, s8, a1, a2, - r2r4, rep_vdw, tau_vdw, tau_idx_vdw, atomtype, x, - c6_ij_tot, dc6_iji_tot, dc6_ijj_tot, - dc6i, disp, f, sigma - ); - cudaDeviceSynchronize(); - disp_total = *disp; - - //STOP_CUDA_TIMER("get_forces_without"); -} - -void PairD3::get_forces_without_dC6_zerom() {} -void PairD3::get_forces_without_dC6_bjm() {} - -void PairD3::get_forces_without_dC6() { - void (PairD3::*get_forces_without_dC6_damp[4])() = { - &PairD3::get_forces_without_dC6_zero, - &PairD3::get_forces_without_dC6_bj, - &PairD3::get_forces_without_dC6_zerom, - &PairD3::get_forces_without_dC6_bjm - }; - - (this->*get_forces_without_dC6_damp[damping])(); -} - -__global__ void kernel_get_forces_with_dC6( - int maxij, int maxtau, float cnthr, float K1, - double *dc6i, float *rcov, int *rep_cn, float ****tau_cn, int *tau_idx_cn, int *type, float **x, - double **f, double **sigma -) { - int iter = blockIdx.x * blockDim.x + threadIdx.x; - - __shared__ float sigma_00[128]; - __shared__ float sigma_01[128]; - __shared__ float sigma_02[128]; - __shared__ float sigma_10[128]; - __shared__ float sigma_11[128]; - __shared__ float sigma_12[128]; - __shared__ float sigma_20[128]; - __shared__ float sigma_21[128]; - __shared__ float sigma_22[128]; - - float sigma_local_00 = 0.0f; - float sigma_local_01 = 0.0f; - float sigma_local_02 = 0.0f; - float sigma_local_10 = 0.0f; - float sigma_local_11 = 0.0f; - float sigma_local_12 = 0.0f; - float sigma_local_20 = 0.0f; - float sigma_local_21 = 0.0f; - float sigma_local_22 = 0.0f; - - float f_local[3] = { 0.0f }; - - if (iter < maxij) { - int iat, jat; - ij_at_linij(iter, iat, jat); - - if (iat == jat) { - const float rcov_sum = rcov[type[iat]] * 2.0f; - const float dc6i_sum = dc6i[iat]; - - for (int k = maxtau - 1; k >= 0; k -= 3) { - const int idx1 = tau_idx_cn[k-2]; - const int idx2 = tau_idx_cn[k-1]; - const int idx3 = tau_idx_cn[k]; - - if (idx1 == rep_cn[0] && idx2 == rep_cn[1] && idx3 == rep_cn[2]) { continue; } - const float rij[3] = { - tau_cn[idx1][idx2][idx3][0], - tau_cn[idx1][idx2][idx3][1], - tau_cn[idx1][idx2][idx3][2], - }; - const float r2 = lensq3(rij); - if (r2 >= cnthr) { continue; } - - const float r_rc = rsqrtf(r2); - const float expterm = expf(-K1 * (rcov_sum * r_rc - 1.0f)); - const float unit_rc = 1.0f / (r2 * (expterm + 1.0f) * (expterm + 1.0f)); - const float dcnn = -K1 * rcov_sum * expterm * unit_rc; - const float x1 = dcnn * dc6i_sum; - - const float vec[3] = { - x1 * rij[0] * r_rc, - x1 * rij[1] * r_rc, - x1 * rij[2] * r_rc - }; - - sigma_local_00 += vec[0] * rij[0]; - sigma_local_01 += vec[0] * rij[1]; - sigma_local_02 += vec[0] * rij[2]; - sigma_local_10 += vec[1] * rij[0]; - sigma_local_11 += vec[1] * rij[1]; - sigma_local_12 += vec[1] * rij[2]; - sigma_local_20 += vec[2] * rij[0]; - sigma_local_21 += vec[2] * rij[1]; - sigma_local_22 += vec[2] * rij[2]; - } - } - - else { - const float rcov_sum = rcov[type[iat]] + rcov[type[jat]]; - const float dc6i_sum = dc6i[iat] + dc6i[jat]; - - for (int k = maxtau - 1; k >= 0; k -= 3) { - const int idx1 = tau_idx_cn[k-2]; - const int idx2 = tau_idx_cn[k-1]; - const int idx3 = tau_idx_cn[k]; - - const float rij[3] = { - x[jat][0] - x[iat][0] + tau_cn[idx1][idx2][idx3][0], - x[jat][1] - x[iat][1] + tau_cn[idx1][idx2][idx3][1], - x[jat][2] - x[iat][2] + tau_cn[idx1][idx2][idx3][2] - }; - const float r2 = lensq3(rij); - if (r2 >= cnthr) { continue; } - - const float r_rc = rsqrtf(r2); - const float expterm = expf(-K1 * (rcov_sum * r_rc - 1.0f)); - const float unit_rc = 1.0f / (r2 * (expterm + 1.0f) * (expterm + 1.0f)); - const float dcnn = -K1 * rcov_sum * expterm * unit_rc; - const float x1 = dcnn * dc6i_sum; - - const float vec[3] = { - x1 * rij[0] * r_rc, - x1 * rij[1] * r_rc, - x1 * rij[2] * r_rc - }; - - f_local[0] -= vec[0]; - f_local[1] -= vec[1]; - f_local[2] -= vec[2]; - - sigma_local_00 += vec[0] * rij[0]; - sigma_local_01 += vec[0] * rij[1]; - sigma_local_02 += vec[0] * rij[2]; - sigma_local_10 += vec[1] * rij[0]; - sigma_local_11 += vec[1] * rij[1]; - sigma_local_12 += vec[1] * rij[2]; - sigma_local_20 += vec[2] * rij[0]; - sigma_local_21 += vec[2] * rij[1]; - sigma_local_22 += vec[2] * rij[2]; - } - atomicAdd(&f[iat][0], f_local[0]); - atomicAdd(&f[iat][1], f_local[1]); - atomicAdd(&f[iat][2], f_local[2]); - atomicAdd(&f[jat][0], -f_local[0]); - atomicAdd(&f[jat][1], -f_local[1]); - atomicAdd(&f[jat][2], -f_local[2]); - } - } - - sigma_00[threadIdx.x] = sigma_local_00; - sigma_01[threadIdx.x] = sigma_local_01; - sigma_02[threadIdx.x] = sigma_local_02; - sigma_10[threadIdx.x] = sigma_local_10; - sigma_11[threadIdx.x] = sigma_local_11; - sigma_12[threadIdx.x] = sigma_local_12; - sigma_20[threadIdx.x] = sigma_local_20; - sigma_21[threadIdx.x] = sigma_local_21; - sigma_22[threadIdx.x] = sigma_local_22; - __syncthreads(); - - for (int s=blockDim.x/2; s>0; s>>=1) { - if (threadIdx.x < s) { - sigma_00[threadIdx.x] += sigma_00[threadIdx.x + s]; - sigma_01[threadIdx.x] += sigma_01[threadIdx.x + s]; - sigma_02[threadIdx.x] += sigma_02[threadIdx.x + s]; - sigma_10[threadIdx.x] += sigma_10[threadIdx.x + s]; - sigma_11[threadIdx.x] += sigma_11[threadIdx.x + s]; - sigma_12[threadIdx.x] += sigma_12[threadIdx.x + s]; - sigma_20[threadIdx.x] += sigma_20[threadIdx.x + s]; - sigma_21[threadIdx.x] += sigma_21[threadIdx.x + s]; - sigma_22[threadIdx.x] += sigma_22[threadIdx.x + s]; - } - __syncthreads(); - } - - if (threadIdx.x == 0) { - atomicAdd(&sigma[0][0], sigma_00[0]); - atomicAdd(&sigma[0][1], sigma_01[0]); - atomicAdd(&sigma[0][2], sigma_02[0]); - atomicAdd(&sigma[1][0], sigma_10[0]); - atomicAdd(&sigma[1][1], sigma_11[0]); - atomicAdd(&sigma[1][2], sigma_12[0]); - atomicAdd(&sigma[2][0], sigma_20[0]); - atomicAdd(&sigma[2][1], sigma_21[0]); - atomicAdd(&sigma[2][2], sigma_22[0]); - } -} - -void PairD3::get_forces_with_dC6() { - int n = atom->natoms; - int maxij = n * (n + 1) / 2; - int maxtau = tau_idx_cn_total_size; - - //START_CUDA_TIMER(); - - int threadsPerBlock = 128; - int blocksPerGrid = (maxij + threadsPerBlock - 1) / threadsPerBlock; - kernel_get_forces_with_dC6<<>>( - maxij, maxtau, cnthr, K1, - dc6i, rcov, rep_cn, tau_cn, tau_idx_cn, atomtype, x, - f, sigma - ); - cudaDeviceSynchronize(); - - //STOP_CUDA_TIMER("get_forces_with"); -} - -/* ---------------------------------------------------------------------- - Update energy, force, and stress -------------------------------------------------------------------------- */ - -void PairD3::update() { - int n = atom->natoms; - - // unit: eV <- eng_vdwl - result_E = disp_total * AU_TO_EV; - - // unit: eV/Å, flatten for wrapper <- atom->f (f_local) - for (int i = 0; i < n; i++) { - for (int j = 0; j < 3; j++) { - result_F[i * 3 + j] = f[i][j] * AU_TO_EV / AU_TO_ANG; - } - } - - // unit: eV, virial, xx, yy, zz, xy, xz, yz <- virial - result_S[0] = sigma[0][0] * AU_TO_EV; - result_S[1] = sigma[1][1] * AU_TO_EV; - result_S[2] = sigma[2][2] * AU_TO_EV; - result_S[3] = sigma[0][1] * AU_TO_EV; - result_S[4] = sigma[0][2] * AU_TO_EV; - result_S[5] = sigma[1][2] * AU_TO_EV; -} - -/* ---------------------------------------------------------------------- - Compute : energy, force, and stress (Required) -------------------------------------------------------------------------- */ - -void PairD3::compute() { - if (atom->natoms != n_save) { reallocate_arrays(); } - - set_lattice_vectors(); - precalculate_tau_array(); - load_atom_info(); - - cudaMemcpy(atomtype, atom->type, atom->natoms * sizeof(int), cudaMemcpyHostToDevice); - - get_coordination_number(); - get_dC6_dCNij(); - get_forces_without_dC6(); - get_forces_with_dC6(); - - update(); - - CHECK_CUDA_ERROR(); -} - -int main() { -} - -extern "C" { // C wrapper for ctypes or cffi - PairD3* pair_init() { - return new PairD3(); - } - - void pair_set_atom(PairD3* pair, int natoms, int ntypes, int* type, double* x_flat) { - double** x = new double*[natoms]; - for (int i = 0; i < natoms; i++) { - x[i] = x_flat + i * 3; - } - pair->atom = new Atom(natoms, ntypes, type, x); - pair->result_F = new double[natoms * 3]; - } - - void pair_set_domain(PairD3* pair, int xperiodic, int yperiodic, int zperiodic, double* boxlo, double* boxhi, double xy, double xz, double yz) { - pair->domain = new Domain(xperiodic, yperiodic, zperiodic, boxlo, boxhi, xy, xz, yz); - } - - void pair_run_settings(PairD3* pair, double rthr, double cnthr, const char* damp_name, const char* func_name) { - pair->settings(rthr, cnthr, damp_name, func_name); - } - - void pair_run_coeff(PairD3* pair, int* atomic_numbers) { - pair->coeff(atomic_numbers); - } - - void pair_run_compute(PairD3* pair) { - pair->compute(); - } - - double pair_get_energy(PairD3* pair) { - return pair->result_E; - } - - double* pair_get_force(PairD3* pair) { - return pair->result_F; - } - - double* pair_get_stress(PairD3* pair) { - return pair->result_S; - } - - void pair_fin(PairD3* pair) { - //delete[] result_F; - delete pair; - //delete domain; - //delete atom; - } -} diff --git a/mace-bench/3rdparty/SevenNet/sevenn/pair_e3gnn/pair_d3_for_ase.h b/mace-bench/3rdparty/SevenNet/sevenn/pair_e3gnn/pair_d3_for_ase.h deleted file mode 100644 index b9b44a320830f4377152a03d611ef45ce70ae7bc..0000000000000000000000000000000000000000 --- a/mace-bench/3rdparty/SevenNet/sevenn/pair_e3gnn/pair_d3_for_ase.h +++ /dev/null @@ -1,263 +0,0 @@ -/* -This code is a skeleton of the LAMMPS pair_style d3 accelerated by CUDA. -All dependencies on LAMMPS have been removed. -The input and output variables are named based on the LAMMPS variables. -*/ - -#ifndef LMP_PAIR_D3 -#define LMP_PAIR_D3 - -#include -#include -#include // for 'element_table' -#include // for 'atomic_number' -#include -#include -#include - -#include "pair_d3_pars.h" - -// Removed dependencies to STL -// #include -> no more C style functions -// #define _USE_MATH_DEFINES -> no predefined constants - -// Removed dependencies to LAMMPS -// #include "pair.h" -> removed, for construncting pair class. -// #include "utils.h" -> removed, some float converters. -// #include "atom.h" -> Atom class to replace it. -// #include "domain.h" -> Domain class to replace it. -// #include "error.h" -> Error class to replace it. -// #include "comm.h" -> already no dependency -// #include "neighbor.h" -> already no dependency -// #include "neigh_list.h" -> already no dependency -// #include "memory.h" -> already no dependency for CUDA version -// #include "math_extra.h" -> removed, dot and len3 operations. -// #include "potential_file_reader.h" -> removed, PotentialFileReader - -/* --------- Fake class to replace 'LAMMPS' class --------- */ -class Atom { -public: - int natoms; - int ntypes; - int* type; - double** x; - Atom(int natoms, int ntypes, int* type, double** x) : - natoms(natoms), - ntypes(ntypes), - type(type), - x(x) {} - ~Atom() { - //delete[] type; - //for (int i = 0; i < natoms; i++) { - // delete[] x[i]; - //} - //delete[] x; - } -}; - -class Domain { -public: - int xperiodic, yperiodic, zperiodic; - double boxlo[3], boxhi[3]; - double xy, xz, yz; - Domain(int xperiodic, int yperiodic, int zperiodic, double* boxlo, double* boxhi, double xy, double xz, double yz) : - xperiodic(xperiodic), - yperiodic(yperiodic), - zperiodic(zperiodic), - xy(xy), - xz(xz), - yz(yz) { - for (int i = 0; i < 3; i++) { - this->boxlo[i] = boxlo[i]; - this->boxhi[i] = boxhi[i]; - } - } - ~Domain() { - } -}; - -class Error { -public: - void all(int flerr, const char* message) { - printf("Error: %s\n", message); - } - Error() {} - ~Error() {} -}; -/* ------------------------------------------------------- */ - -/* --------- Declaration of fake classes and variables --------- */ -#define FLERR 1 -//Error* error = nullptr; -// -//int allocated; -//int** setflag; -//double** cutsq; - -//Atom* atom = nullptr; -//Domain* domain = nullptr; -// -//double result_E; -//double* result_F = nullptr; -//double result_S[6]; - -class Pair { -public: - int allocated; - Atom* atom; - Domain* domain; - double result_E; - double* result_F; - double result_S[6]; - Error* error; - - Pair() - : allocated(0), atom(nullptr), domain(nullptr), result_E(0.0), result_F(nullptr), error(nullptr) { - std::fill(std::begin(result_S), std::end(result_S), 0.0); - } - - virtual ~Pair() { - if (result_F) { - delete[] result_F; - result_F = nullptr; - } - if (atom) { - delete atom; - atom = nullptr; - } - if (domain) { - delete domain; - domain = nullptr; - } - if (error) { - delete error; - error = nullptr; - } - } -}; -/* -------------------------------------------------------------- */ - -class PairD3 : public Pair { -public: - PairD3(); - ~PairD3(); - - void settings(double rthr, double cnthr, std::string damp_name, std::string func_name); - void coeff(int* atomic_number); - void compute(); - -protected: - virtual void allocate(); - - /* ------- Read parameters ------- */ - int find_atomic_number(std::string&); - int is_int_in_array(int*, int, int); - void read_r0ab(int*, int); // void read_r0ab(class LAMMPS*, char*, int*, int); - void get_limit_in_pars_array(int&, int&, int&, int&); - void read_c6ab(int*, int); // void read_c6ab(class LAMMPS*, char*, int*, int); - - void setfuncpar_zero(); - void setfuncpar_bj(); - void setfuncpar_zerom(); - void setfuncpar_bjm(); - void setfuncpar(); - /* ------- Read parameters ------- */ - - /* ------- Lattice information ------- */ - void set_lattice_repetition_criteria(float, int*); - void set_lattice_vectors(); - /* ------- Lattice information ------- */ - - /* ------- Initialize & Precalculate ------- */ - void load_atom_info(); - void precalculate_tau_array(); - /* ------- Initialize & Precalculate ------- */ - - /* ------- Reallocate (when number of atoms changed) ------- */ - void reallocate_arrays(); - void reallocate_arrays_np1(); - /* ------- Reallocate (when number of atoms changed) ------- */ - - /* ------- Coordination number ------- */ - void get_coordination_number(); - void get_dC6_dCNij(); - /* ------- Coordination number ------- */ - - /* ------- Main workers ------- */ - void get_forces_without_dC6_zero(); - void get_forces_without_dC6_bj(); - void get_forces_without_dC6_zerom(); - void get_forces_without_dC6_bjm(); - void get_forces_without_dC6(); - void get_forces_with_dC6(); - void update(); - /* ------- Main workers ------- */ - - /*--------- Constants ---------*/ - static constexpr int MAX_ELEM = 94; // maximum of the element number - static constexpr int MAXC = 5; // maximum coordination number references per element - - static constexpr double AU_TO_ANG = 0.52917726; // conversion factors (atomic unit --> angstrom) - static constexpr double AU_TO_EV = 27.21138505; // conversion factors (atomic unit --> eV) - - static constexpr float K1 = 16.0; // global ad hoc parameters - static constexpr float K3 = -4.0; // global ad hoc parameters - /*--------- Constants ---------*/ - - /*--------- Parameters to read ---------*/ - int damping; - std::string functional; - float* r2r4 = nullptr; // scale r4/r2 values of the atoms by sqrt(Z) - float* rcov = nullptr; // covalent radii - int* mxc = nullptr; // How large the grid for c6 interpolation - float** r0ab = nullptr; // cut-off radii for all element pairs - float***** c6ab = nullptr; // C6 for all element pairs - float rthr; // R^2 distance to cutoff for C calculation - float cnthr; // R^2 distance to cutoff for CN_calculation - float s6, s8, s18, rs6, rs8, rs18, alp, alp6, alp8, a1, a2; // parameters for D3 - /*--------- Parameters to read ---------*/ - - /*--------- Lattice related values ---------*/ - double* lat_v_1 = nullptr; // lattice coordination vector - double* lat_v_2 = nullptr; // lattice coordination vector - double* lat_v_3 = nullptr; // lattice coordination vector - int* rep_vdw = nullptr; // repetition of cell for calculating D3 - int* rep_cn = nullptr; // repetition of cell for calculating - double** sigma = nullptr; // virial pressure on cell - /*--------- Lattice related values ---------*/ - - /*--------- Per-atom values/arrays ---------*/ - double* cn = nullptr; // Coordination numbers - float** x = nullptr; // Positions - double** f = nullptr; // Forces - double* dc6i = nullptr; // dC6i(iat) saves dE_dsp/dCN(iat) - /*--------- Per-atom values/arrays ---------*/ - - /*--------- Per-pair values/arrays ---------*/ - float* c6_ij_tot = nullptr; - float* dc6_iji_tot = nullptr; - float* dc6_ijj_tot = nullptr; - /*--------- Per-pair values/arrays ---------*/ - - /*---------- Global values ---------*/ - int n_save; // to check whether the number of atoms has changed - int np1_save; // to check whether the number of types has changed - float disp_total; // Dispersion energy - /*---------- Global values ---------*/ - - /*--------- For loop over tau (translation of cell) ---------*/ - float**** tau_vdw = nullptr; - float**** tau_cn = nullptr; - int* tau_idx_vdw = nullptr; - int* tau_idx_cn = nullptr; - int tau_idx_vdw_total_size; - int tau_idx_cn_total_size; - /*--------- For loop over tau (translation of cell) ---------*/ - - /*--------- For cuda memory transfer (pointerized) ---------*/ - int *atomtype; - double *disp; - /*--------- For cuda memory transfer (pointerized) ---------*/ -}; - -#endif // LMP_PAIR_D3 diff --git a/mace-bench/3rdparty/SevenNet/sevenn/pair_e3gnn/pair_d3_pars.h b/mace-bench/3rdparty/SevenNet/sevenn/pair_e3gnn/pair_d3_pars.h deleted file mode 100644 index e51357e1edc305c98cc8ef52ad295ef0ee3f86d4..0000000000000000000000000000000000000000 --- a/mace-bench/3rdparty/SevenNet/sevenn/pair_e3gnn/pair_d3_pars.h +++ /dev/null @@ -1,32484 +0,0 @@ -#define R0AB_TABLE { \ - {2.18230000E+00, 1.85470000E+00, 2.90860000E+00, 2.35500000E+00, 2.51410000E+00, 2.44920000E+00, 2.36670000E+00, 2.17680000E+00, 2.06460000E+00, 1.98920000E+00, 2.98980000E+00, 2.51290000E+00, 2.87660000E+00, 2.88840000E+00, 2.83040000E+00, 2.61900000E+00, 2.47570000E+00, 2.37250000E+00, 3.21470000E+00, 2.75970000E+00, 2.73610000E+00, 2.68320000E+00, 2.63790000E+00, 2.92300000E+00, 2.54900000E+00, 2.49260000E+00, 2.46670000E+00, 2.45150000E+00, 2.44130000E+00, 2.43180000E+00, 2.85020000E+00, 2.92260000E+00, 2.91400000E+00, 2.73000000E+00, 2.60260000E+00, 2.50870000E+00, 3.28930000E+00, 2.87860000E+00, 2.89970000E+00, 2.85350000E+00, 3.09050000E+00, 3.03010000E+00, 2.91890000E+00, 2.85780000E+00, 2.82400000E+00, 2.80040000E+00, 2.78460000E+00, 2.54240000E+00, 2.97430000E+00, 3.07750000E+00, 3.08930000E+00, 2.90910000E+00, 2.78060000E+00, 2.68480000E+00, 3.39680000E+00, 3.06300000E+00, 3.06320000E+00, 2.94550000E+00, 2.92440000E+00, 2.90460000E+00, 2.88780000E+00, 2.87090000E+00, 2.85680000E+00, 2.67980000E+00, 2.51890000E+00, 3.04810000E+00, 2.81360000E+00, 2.80320000E+00, 2.79670000E+00, 2.78970000E+00, 2.83950000E+00, 2.90070000E+00, 2.85590000E+00, 2.81100000E+00, 2.76760000E+00, 2.69120000E+00, 2.78950000E+00, 2.75220000E+00, 2.72020000E+00, 2.53150000E+00, 2.98520000E+00, 3.11600000E+00, 3.14160000E+00, 2.96640000E+00, 2.83880000E+00, 2.74120000E+00, 3.41550000E+00, 3.05480000E+00, 3.38500000E+00, 3.09420000E+00, 3.01870000E+00, 2.98750000E+00, 2.96590000E+00, 2.87630000E+00}, \ - {1.85470000E+00, 1.73470000E+00, 2.57320000E+00, 2.50950000E+00, 2.39170000E+00, 2.25270000E+00, 2.13280000E+00, 2.06250000E+00, 1.98910000E+00, 1.92510000E+00, 2.63970000E+00, 2.73210000E+00, 2.74270000E+00, 2.66050000E+00, 2.55380000E+00, 2.47970000E+00, 2.40190000E+00, 2.32890000E+00, 2.83150000E+00, 3.05880000E+00, 2.97650000E+00, 2.90600000E+00, 2.84940000E+00, 2.62230000E+00, 2.76230000E+00, 2.71360000E+00, 2.67090000E+00, 2.63380000E+00, 2.60060000E+00, 2.57290000E+00, 2.69340000E+00, 2.68380000E+00, 2.62710000E+00, 2.58700000E+00, 2.53550000E+00, 2.48140000E+00, 2.89910000E+00, 3.16580000E+00, 3.09530000E+00, 3.01670000E+00, 2.79980000E+00, 2.73120000E+00, 2.67770000E+00, 2.63340000E+00, 2.59600000E+00, 2.56210000E+00, 2.53240000E+00, 2.66010000E+00, 2.80580000E+00, 2.82750000E+00, 2.79170000E+00, 2.76380000E+00, 2.72090000E+00, 2.67400000E+00, 3.01220000E+00, 3.32710000E+00, 3.26620000E+00, 3.24700000E+00, 3.22410000E+00, 3.20440000E+00, 3.18900000E+00, 3.17370000E+00, 3.16080000E+00, 3.01510000E+00, 2.97030000E+00, 2.95840000E+00, 3.09510000E+00, 3.08050000E+00, 3.06890000E+00, 3.06360000E+00, 3.00810000E+00, 2.96740000E+00, 2.90500000E+00, 2.85200000E+00, 2.80780000E+00, 2.76040000E+00, 2.58490000E+00, 2.55240000E+00, 2.51830000E+00, 2.61040000E+00, 2.78810000E+00, 2.84820000E+00, 2.83250000E+00, 2.82090000E+00, 2.78900000E+00, 2.74890000E+00, 3.05220000E+00, 3.32060000E+00, 3.42080000E+00, 3.20750000E+00, 3.19180000E+00, 3.16740000E+00, 3.14420000E+00, 3.12940000E+00}, \ - {2.90860000E+00, 2.57320000E+00, 3.49560000E+00, 2.98020000E+00, 2.99770000E+00, 3.19330000E+00, 2.87840000E+00, 2.63950000E+00, 2.50860000E+00, 2.41900000E+00, 3.60310000E+00, 3.10520000E+00, 3.27760000E+00, 3.75130000E+00, 3.39320000E+00, 3.13310000E+00, 2.97890000E+00, 2.87600000E+00, 3.87240000E+00, 3.34740000E+00, 3.24750000E+00, 3.26130000E+00, 3.18400000E+00, 3.41610000E+00, 3.09910000E+00, 3.06930000E+00, 3.05750000E+00, 3.05110000E+00, 3.05400000E+00, 3.04160000E+00, 3.24670000E+00, 3.78670000E+00, 3.47710000E+00, 3.24710000E+00, 3.11290000E+00, 3.02390000E+00, 4.03880000E+00, 3.58230000E+00, 3.45240000E+00, 3.39780000E+00, 3.64480000E+00, 3.58210000E+00, 3.49250000E+00, 3.46730000E+00, 3.46350000E+00, 3.46170000E+00, 3.46520000E+00, 3.25550000E+00, 3.48300000E+00, 4.01810000E+00, 3.72620000E+00, 3.50660000E+00, 3.38120000E+00, 3.29250000E+00, 4.22410000E+00, 4.04320000E+00, 3.64320000E+00, 3.61080000E+00, 3.58480000E+00, 3.56210000E+00, 3.54120000E+00, 3.51990000E+00, 3.50500000E+00, 3.25860000E+00, 3.30630000E+00, 3.69190000E+00, 3.46350000E+00, 3.45190000E+00, 3.44450000E+00, 3.43440000E+00, 3.31710000E+00, 3.81740000E+00, 3.83250000E+00, 3.74800000E+00, 3.67250000E+00, 3.60370000E+00, 3.64840000E+00, 3.57420000E+00, 3.49470000E+00, 3.27340000E+00, 3.52840000E+00, 4.07390000E+00, 3.77350000E+00, 3.55470000E+00, 3.43290000E+00, 3.33740000E+00, 4.25410000E+00, 3.81320000E+00, 3.70040000E+00, 3.51520000E+00, 3.51270000E+00, 3.49710000E+00, 3.47950000E+00, 3.55980000E+00}, \ - {2.35500000E+00, 2.50950000E+00, 2.98020000E+00, 3.09820000E+00, 2.94840000E+00, 3.02140000E+00, 2.76600000E+00, 2.66480000E+00, 2.69080000E+00, 2.54730000E+00, 3.12190000E+00, 3.29620000E+00, 3.23630000E+00, 3.16130000E+00, 3.11930000E+00, 3.05400000E+00, 3.14680000E+00, 2.98040000E+00, 3.46210000E+00, 3.62140000E+00, 3.50040000E+00, 3.43590000E+00, 3.42250000E+00, 2.89990000E+00, 3.32520000E+00, 3.26990000E+00, 3.23570000E+00, 3.22290000E+00, 3.19870000E+00, 3.16390000E+00, 3.19210000E+00, 3.17320000E+00, 3.17740000E+00, 3.14870000E+00, 3.28630000E+00, 3.13120000E+00, 3.61000000E+00, 3.76890000E+00, 3.61070000E+00, 3.53630000E+00, 3.07390000E+00, 3.04730000E+00, 2.96480000E+00, 2.92450000E+00, 2.90320000E+00, 2.91540000E+00, 2.87590000E+00, 3.28070000E+00, 3.34740000E+00, 3.33850000E+00, 3.35180000E+00, 3.33770000E+00, 3.49580000E+00, 3.33860000E+00, 3.78870000E+00, 4.00460000E+00, 3.80880000E+00, 3.85220000E+00, 3.82930000E+00, 3.80780000E+00, 3.79080000E+00, 3.77340000E+00, 3.75980000E+00, 3.52920000E+00, 3.62350000E+00, 3.59900000E+00, 3.68750000E+00, 3.67000000E+00, 3.65810000E+00, 3.64800000E+00, 3.48780000E+00, 3.58560000E+00, 3.54420000E+00, 3.51050000E+00, 3.48040000E+00, 3.41940000E+00, 3.01620000E+00, 2.95080000E+00, 2.87310000E+00, 3.22990000E+00, 3.34930000E+00, 3.35990000E+00, 3.37870000E+00, 3.37960000E+00, 3.55930000E+00, 3.39500000E+00, 3.82180000E+00, 3.97200000E+00, 3.88000000E+00, 3.66590000E+00, 3.68750000E+00, 3.67150000E+00, 3.65030000E+00, 3.74650000E+00}, \ - {2.51410000E+00, 2.39170000E+00, 2.99770000E+00, 2.94840000E+00, 3.21600000E+00, 2.95310000E+00, 2.77760000E+00, 2.64820000E+00, 2.62330000E+00, 2.49940000E+00, 3.76200000E+00, 3.13310000E+00, 3.59290000E+00, 3.36050000E+00, 3.18660000E+00, 3.06510000E+00, 2.97680000E+00, 2.90930000E+00, 3.88230000E+00, 3.43530000E+00, 3.41850000E+00, 3.35380000E+00, 3.27710000E+00, 3.05570000E+00, 3.18360000E+00, 3.12720000E+00, 3.09080000E+00, 3.06300000E+00, 3.04900000E+00, 3.01960000E+00, 3.56630000E+00, 3.38720000E+00, 3.25600000E+00, 3.16670000E+00, 3.10290000E+00, 3.05350000E+00, 3.93880000E+00, 3.57620000E+00, 3.60620000E+00, 3.53930000E+00, 3.29960000E+00, 3.21370000E+00, 3.12160000E+00, 3.07320000E+00, 3.04310000E+00, 3.02030000E+00, 3.00510000E+00, 3.13840000E+00, 3.68630000E+00, 3.53790000E+00, 3.42410000E+00, 3.34810000E+00, 3.29130000E+00, 3.24730000E+00, 4.00490000E+00, 4.15550000E+00, 3.79100000E+00, 3.66250000E+00, 3.63950000E+00, 3.61850000E+00, 3.59740000E+00, 3.58020000E+00, 3.56650000E+00, 3.53910000E+00, 3.45170000E+00, 3.88810000E+00, 3.49870000E+00, 3.48270000E+00, 3.47170000E+00, 3.46260000E+00, 3.53600000E+00, 3.64860000E+00, 3.50770000E+00, 3.43460000E+00, 3.37750000E+00, 3.30940000E+00, 3.12670000E+00, 3.07510000E+00, 3.01980000E+00, 3.10900000E+00, 3.69580000E+00, 3.56980000E+00, 3.46320000E+00, 3.39850000E+00, 3.34880000E+00, 3.30760000E+00, 4.04380000E+00, 3.76750000E+00, 3.98860000E+00, 3.82890000E+00, 3.74040000E+00, 3.71140000E+00, 3.68140000E+00, 3.56590000E+00}, \ - {2.44920000E+00, 2.25270000E+00, 3.19330000E+00, 3.02140000E+00, 2.95310000E+00, 2.91030000E+00, 2.70630000E+00, 2.56970000E+00, 2.47700000E+00, 2.40910000E+00, 3.24850000E+00, 3.20000000E+00, 3.28260000E+00, 3.33250000E+00, 3.12450000E+00, 2.98790000E+00, 2.88480000E+00, 2.80400000E+00, 3.37600000E+00, 3.47290000E+00, 3.43780000E+00, 3.38600000E+00, 3.34010000E+00, 3.33080000E+00, 3.24280000E+00, 3.18930000E+00, 3.15370000E+00, 3.12650000E+00, 3.10580000E+00, 3.08430000E+00, 3.25410000E+00, 3.36430000E+00, 3.19700000E+00, 3.09140000E+00, 3.01080000E+00, 2.94570000E+00, 3.44750000E+00, 3.57890000E+00, 3.57830000E+00, 3.53010000E+00, 3.52620000E+00, 3.46790000E+00, 3.29400000E+00, 3.24350000E+00, 3.21150000E+00, 3.18750000E+00, 3.16920000E+00, 3.17370000E+00, 3.36170000E+00, 3.50360000E+00, 3.54330000E+00, 3.26330000E+00, 3.18880000E+00, 3.12840000E+00, 3.53840000E+00, 3.74260000E+00, 3.73810000E+00, 3.65980000E+00, 3.64000000E+00, 3.62200000E+00, 3.60780000E+00, 3.59340000E+00, 3.58030000E+00, 3.49020000E+00, 3.39890000E+00, 3.42090000E+00, 3.51830000E+00, 3.50500000E+00, 3.49510000E+00, 3.48920000E+00, 3.51450000E+00, 3.53390000E+00, 3.49050000E+00, 3.34610000E+00, 3.24110000E+00, 3.17100000E+00, 3.21250000E+00, 3.01580000E+00, 3.14570000E+00, 2.99420000E+00, 3.36420000E+00, 3.53660000E+00, 3.59230000E+00, 3.31640000E+00, 3.24860000E+00, 3.19100000E+00, 3.58750000E+00, 3.73510000E+00, 3.90400000E+00, 3.74590000E+00, 3.69430000E+00, 3.66920000E+00, 3.64760000E+00, 3.58160000E+00}, \ - {2.36670000E+00, 2.13280000E+00, 2.87840000E+00, 2.76600000E+00, 2.77760000E+00, 2.70630000E+00, 2.62250000E+00, 2.48460000E+00, 2.38850000E+00, 2.31760000E+00, 2.93570000E+00, 2.95860000E+00, 3.09110000E+00, 3.09910000E+00, 3.04650000E+00, 2.90540000E+00, 2.79520000E+00, 2.70710000E+00, 3.07460000E+00, 3.24870000E+00, 3.20840000E+00, 3.15500000E+00, 3.10720000E+00, 3.05550000E+00, 3.02590000E+00, 2.96580000E+00, 2.92350000E+00, 2.89090000E+00, 2.86430000E+00, 2.84130000E+00, 3.05710000E+00, 3.12670000E+00, 3.12070000E+00, 3.01070000E+00, 2.92270000E+00, 2.84960000E+00, 3.15900000E+00, 3.35520000E+00, 3.34630000E+00, 3.29600000E+00, 3.25590000E+00, 3.19750000E+00, 3.09750000E+00, 3.03380000E+00, 2.98920000E+00, 2.95480000E+00, 2.92730000E+00, 2.93970000E+00, 3.16080000E+00, 3.25890000E+00, 3.27730000E+00, 3.18100000E+00, 3.09900000E+00, 3.03010000E+00, 3.26980000E+00, 3.51300000E+00, 3.50930000E+00, 3.44110000E+00, 3.42040000E+00, 3.40190000E+00, 3.38710000E+00, 3.37240000E+00, 3.36010000E+00, 3.28870000E+00, 3.21070000E+00, 3.16060000E+00, 3.29370000E+00, 3.27990000E+00, 3.26940000E+00, 3.26260000E+00, 3.28090000E+00, 3.28320000E+00, 3.23960000E+00, 3.19710000E+00, 3.15810000E+00, 3.08620000E+00, 3.00430000E+00, 2.96440000E+00, 2.92760000E+00, 2.91590000E+00, 3.15680000E+00, 3.28540000E+00, 3.32140000E+00, 3.23640000E+00, 3.16150000E+00, 3.09610000E+00, 3.32860000E+00, 3.51670000E+00, 3.67190000E+00, 3.51560000E+00, 3.47020000E+00, 3.44460000E+00, 3.42220000E+00, 3.35990000E+00}, \ - 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{2.87630000E+00, 3.12940000E+00, 3.55980000E+00, 3.74650000E+00, 3.56590000E+00, 3.58160000E+00, 3.35990000E+00, 3.40240000E+00, 3.18770000E+00, 3.04840000E+00, 3.70090000E+00, 3.94510000E+00, 3.84650000E+00, 3.98730000E+00, 3.70790000E+00, 3.90830000E+00, 3.67560000E+00, 3.51500000E+00, 4.08290000E+00, 4.27800000E+00, 4.15110000E+00, 4.12600000E+00, 4.05710000E+00, 3.48650000E+00, 3.97440000E+00, 3.91500000E+00, 3.89300000E+00, 3.85780000E+00, 3.84020000E+00, 3.80730000E+00, 3.79770000E+00, 4.00360000E+00, 3.76040000E+00, 4.02880000E+00, 3.82100000E+00, 3.67570000E+00, 4.26460000E+00, 4.45580000E+00, 4.28620000E+00, 4.21220000E+00, 3.70880000E+00, 3.67290000E+00, 3.58000000E+00, 3.52760000E+00, 3.51650000E+00, 3.47830000E+00, 3.45390000E+00, 3.95530000E+00, 3.98180000E+00, 4.20400000E+00, 3.96040000E+00, 4.27180000E+00, 4.06890000E+00, 3.92530000E+00, 4.48690000E+00, 4.77920000E+00, 4.49180000E+00, 4.53420000E+00, 4.50900000E+00, 4.48680000E+00, 4.46800000E+00, 4.44860000E+00, 4.43410000E+00, 4.20230000E+00, 4.31220000E+00, 4.27100000E+00, 4.35870000E+00, 4.34070000E+00, 4.32810000E+00, 4.31740000E+00, 4.14990000E+00, 4.39400000E+00, 4.38950000E+00, 4.32600000E+00, 4.27250000E+00, 4.19610000E+00, 3.73610000E+00, 3.61930000E+00, 3.49160000E+00, 3.91150000E+00, 3.99140000E+00, 3.98090000E+00, 3.98660000E+00, 4.33290000E+00, 4.12760000E+00, 3.97820000E+00, 4.50970000E+00, 4.67690000E+00, 4.51580000E+00, 4.32910000E+00, 4.36090000E+00, 4.34620000E+00, 4.32650000E+00, 4.43410000E+00} \ -} - -#define C6AB_TABLE { \ - {3.02670000E+00, 1.00000000E+00, 1.00000000E+00, 9.11800000E-01, 9.11800000E-01}, \ - {2.08350000E+00, 2.00000000E+00, 1.00000000E+00, 0.00000000E+00, 9.11800000E-01}, \ - {1.55830000E+00, 2.00000000E+00, 2.00000000E+00, 0.00000000E+00, 0.00000000E+00}, \ - {3.89448000E+01, 3.00000000E+00, 1.00000000E+00, 0.00000000E+00, 9.11800000E-01}, \ - {2.21508000E+01, 3.00000000E+00, 2.00000000E+00, 0.00000000E+00, 0.00000000E+00}, \ - {1.16344540E+03, 3.00000000E+00, 3.00000000E+00, 0.00000000E+00, 0.00000000E+00}, \ - {2.44415000E+01, 4.00000000E+00, 1.00000000E+00, 0.00000000E+00, 9.11800000E-01}, \ - {1.48246000E+01, 4.00000000E+00, 2.00000000E+00, 0.00000000E+00, 0.00000000E+00}, \ - {4.94619000E+02, 4.00000000E+00, 3.00000000E+00, 0.00000000E+00, 0.00000000E+00}, \ - {2.57486300E+02, 4.00000000E+00, 4.00000000E+00, 0.00000000E+00, 0.00000000E+00}, \ - {1.73143000E+01, 5.00000000E+00, 1.00000000E+00, 0.00000000E+00, 9.11800000E-01}, \ - {1.10975000E+01, 5.00000000E+00, 2.00000000E+00, 0.00000000E+00, 0.00000000E+00}, \ - {2.83730800E+02, 5.00000000E+00, 3.00000000E+00, 0.00000000E+00, 0.00000000E+00}, \ - {1.61597100E+02, 5.00000000E+00, 4.00000000E+00, 0.00000000E+00, 0.00000000E+00}, \ - {1.07177700E+02, 5.00000000E+00, 5.00000000E+00, 0.00000000E+00, 0.00000000E+00}, \ - {1.21402000E+01, 6.00000000E+00, 1.00000000E+00, 0.00000000E+00, 9.11800000E-01}, \ - {8.18410000E+00, 6.00000000E+00, 2.00000000E+00, 0.00000000E+00, 0.00000000E+00}, \ - {1.69903000E+02, 6.00000000E+00, 3.00000000E+00, 0.00000000E+00, 0.00000000E+00}, \ - {1.02956000E+02, 6.00000000E+00, 4.00000000E+00, 0.00000000E+00, 0.00000000E+00}, \ - {7.12794000E+01, 6.00000000E+00, 5.00000000E+00, 0.00000000E+00, 0.00000000E+00}, \ - {4.91130000E+01, 6.00000000E+00, 6.00000000E+00, 0.00000000E+00, 0.00000000E+00}, \ - {8.71710000E+00, 7.00000000E+00, 1.00000000E+00, 0.00000000E+00, 9.11800000E-01}, \ - {6.13800000E+00, 7.00000000E+00, 2.00000000E+00, 0.00000000E+00, 0.00000000E+00}, \ - {1.08485400E+02, 7.00000000E+00, 3.00000000E+00, 0.00000000E+00, 0.00000000E+00}, \ - {6.86458000E+01, 7.00000000E+00, 4.00000000E+00, 0.00000000E+00, 0.00000000E+00}, \ - {4.91132000E+01, 7.00000000E+00, 5.00000000E+00, 0.00000000E+00, 0.00000000E+00}, \ - {3.48146000E+01, 7.00000000E+00, 6.00000000E+00, 0.00000000E+00, 0.00000000E+00}, \ - {2.52685000E+01, 7.00000000E+00, 7.00000000E+00, 0.00000000E+00, 0.00000000E+00}, \ - {6.71800000E+00, 8.00000000E+00, 1.00000000E+00, 0.00000000E+00, 9.11800000E-01}, \ - {4.89490000E+00, 8.00000000E+00, 2.00000000E+00, 0.00000000E+00, 0.00000000E+00}, \ - {7.69613000E+01, 8.00000000E+00, 3.00000000E+00, 0.00000000E+00, 0.00000000E+00}, \ - {5.01252000E+01, 8.00000000E+00, 4.00000000E+00, 0.00000000E+00, 0.00000000E+00}, \ - {3.67247000E+01, 8.00000000E+00, 5.00000000E+00, 0.00000000E+00, 0.00000000E+00}, \ - {2.65929000E+01, 8.00000000E+00, 6.00000000E+00, 0.00000000E+00, 0.00000000E+00}, \ - {1.96546000E+01, 8.00000000E+00, 7.00000000E+00, 0.00000000E+00, 0.00000000E+00}, \ - {1.55059000E+01, 8.00000000E+00, 8.00000000E+00, 0.00000000E+00, 0.00000000E+00}, \ - {5.16160000E+00, 9.00000000E+00, 1.00000000E+00, 0.00000000E+00, 9.11800000E-01}, \ - {3.88250000E+00, 9.00000000E+00, 2.00000000E+00, 0.00000000E+00, 0.00000000E+00}, \ - {5.50933000E+01, 9.00000000E+00, 3.00000000E+00, 0.00000000E+00, 0.00000000E+00}, \ - {3.67453000E+01, 9.00000000E+00, 4.00000000E+00, 0.00000000E+00, 0.00000000E+00}, \ - {2.74821000E+01, 9.00000000E+00, 5.00000000E+00, 0.00000000E+00, 0.00000000E+00}, \ - {2.02827000E+01, 9.00000000E+00, 6.00000000E+00, 0.00000000E+00, 0.00000000E+00}, \ - {1.52418000E+01, 9.00000000E+00, 7.00000000E+00, 0.00000000E+00, 0.00000000E+00}, \ - {1.21834000E+01, 9.00000000E+00, 8.00000000E+00, 0.00000000E+00, 0.00000000E+00}, \ - {9.69160000E+00, 9.00000000E+00, 9.00000000E+00, 0.00000000E+00, 0.00000000E+00}, \ - {4.01120000E+00, 1.00000000E+01, 1.00000000E+00, 0.00000000E+00, 9.11800000E-01}, \ - {3.10250000E+00, 1.00000000E+01, 2.00000000E+00, 0.00000000E+00, 0.00000000E+00}, \ - {4.04731000E+01, 1.00000000E+01, 3.00000000E+00, 0.00000000E+00, 0.00000000E+00}, \ - {2.74867000E+01, 1.00000000E+01, 4.00000000E+00, 0.00000000E+00, 0.00000000E+00}, \ - {2.09022000E+01, 1.00000000E+01, 5.00000000E+00, 0.00000000E+00, 0.00000000E+00}, \ - {1.56740000E+01, 1.00000000E+01, 6.00000000E+00, 0.00000000E+00, 0.00000000E+00}, \ - {1.19479000E+01, 1.00000000E+01, 7.00000000E+00, 0.00000000E+00, 0.00000000E+00}, \ - {9.66060000E+00, 1.00000000E+01, 8.00000000E+00, 0.00000000E+00, 0.00000000E+00}, \ - {7.76910000E+00, 1.00000000E+01, 9.00000000E+00, 0.00000000E+00, 0.00000000E+00}, \ - {6.28960000E+00, 1.00000000E+01, 1.00000000E+01, 0.00000000E+00, 0.00000000E+00}, \ - {4.68232000E+01, 1.10000000E+01, 1.00000000E+00, 0.00000000E+00, 9.11800000E-01}, \ - {2.68628000E+01, 1.10000000E+01, 2.00000000E+00, 0.00000000E+00, 0.00000000E+00}, \ - {1.36732720E+03, 1.10000000E+01, 3.00000000E+00, 0.00000000E+00, 0.00000000E+00}, \ - {5.87456300E+02, 1.10000000E+01, 4.00000000E+00, 0.00000000E+00, 0.00000000E+00}, \ - {3.38721200E+02, 1.10000000E+01, 5.00000000E+00, 0.00000000E+00, 0.00000000E+00}, \ - {2.03763100E+02, 1.10000000E+01, 6.00000000E+00, 0.00000000E+00, 0.00000000E+00}, \ - {1.30656300E+02, 1.10000000E+01, 7.00000000E+00, 0.00000000E+00, 0.00000000E+00}, \ - {9.30263000E+01, 1.10000000E+01, 8.00000000E+00, 0.00000000E+00, 0.00000000E+00}, \ - {6.68423000E+01, 1.10000000E+01, 9.00000000E+00, 0.00000000E+00, 0.00000000E+00}, \ - {4.92799000E+01, 1.10000000E+01, 1.00000000E+01, 0.00000000E+00, 0.00000000E+00}, \ - {1.60802860E+03, 1.10000000E+01, 1.10000000E+01, 0.00000000E+00, 0.00000000E+00}, \ - {3.83531000E+01, 1.20000000E+01, 1.00000000E+00, 0.00000000E+00, 9.11800000E-01}, \ - {2.30320000E+01, 1.20000000E+01, 2.00000000E+00, 0.00000000E+00, 0.00000000E+00}, \ - {8.30815600E+02, 1.20000000E+01, 3.00000000E+00, 0.00000000E+00, 0.00000000E+00}, \ - {4.18216400E+02, 1.20000000E+01, 4.00000000E+00, 0.00000000E+00, 0.00000000E+00}, \ - {2.58130300E+02, 1.20000000E+01, 5.00000000E+00, 0.00000000E+00, 0.00000000E+00}, \ - {1.62608200E+02, 1.20000000E+01, 6.00000000E+00, 0.00000000E+00, 0.00000000E+00}, \ - {1.07615000E+02, 1.20000000E+01, 7.00000000E+00, 0.00000000E+00, 0.00000000E+00}, \ - {7.82250000E+01, 1.20000000E+01, 8.00000000E+00, 0.00000000E+00, 0.00000000E+00}, \ - {5.71605000E+01, 1.20000000E+01, 9.00000000E+00, 0.00000000E+00, 0.00000000E+00}, \ - {4.26771000E+01, 1.20000000E+01, 1.00000000E+01, 0.00000000E+00, 0.00000000E+00}, \ - {9.85169700E+02, 1.20000000E+01, 1.10000000E+01, 0.00000000E+00, 0.00000000E+00}, \ - {6.83375800E+02, 1.20000000E+01, 1.20000000E+01, 0.00000000E+00, 0.00000000E+00}, \ - {3.62909000E+01, 1.30000000E+01, 1.00000000E+00, 0.00000000E+00, 9.11800000E-01}, \ - {2.23224000E+01, 1.30000000E+01, 2.00000000E+00, 0.00000000E+00, 0.00000000E+00}, \ - {7.05825400E+02, 1.30000000E+01, 3.00000000E+00, 0.00000000E+00, 0.00000000E+00}, \ - {3.72630200E+02, 1.30000000E+01, 4.00000000E+00, 0.00000000E+00, 0.00000000E+00}, \ - {2.36478000E+02, 1.30000000E+01, 5.00000000E+00, 0.00000000E+00, 0.00000000E+00}, \ - {1.52093400E+02, 1.30000000E+01, 6.00000000E+00, 0.00000000E+00, 0.00000000E+00}, \ - {1.02200000E+02, 1.30000000E+01, 7.00000000E+00, 0.00000000E+00, 0.00000000E+00}, \ - {7.50755000E+01, 1.30000000E+01, 8.00000000E+00, 0.00000000E+00, 0.00000000E+00}, \ - {5.53412000E+01, 1.30000000E+01, 9.00000000E+00, 0.00000000E+00, 0.00000000E+00}, \ - {4.15966000E+01, 1.30000000E+01, 1.00000000E+01, 0.00000000E+00, 0.00000000E+00}, \ - {8.38964800E+02, 1.30000000E+01, 1.10000000E+01, 0.00000000E+00, 0.00000000E+00}, \ - {6.03468900E+02, 1.30000000E+01, 1.20000000E+01, 0.00000000E+00, 0.00000000E+00}, \ - {5.40540600E+02, 1.30000000E+01, 1.30000000E+01, 0.00000000E+00, 0.00000000E+00}, \ - {2.95947000E+01, 1.40000000E+01, 1.00000000E+00, 0.00000000E+00, 9.11800000E-01}, \ - {1.88500000E+01, 1.40000000E+01, 2.00000000E+00, 0.00000000E+00, 0.00000000E+00}, \ - {4.95344900E+02, 1.40000000E+01, 3.00000000E+00, 0.00000000E+00, 0.00000000E+00}, \ - {2.79786300E+02, 1.40000000E+01, 4.00000000E+00, 0.00000000E+00, 0.00000000E+00}, \ - {1.84511100E+02, 1.40000000E+01, 5.00000000E+00, 0.00000000E+00, 0.00000000E+00}, \ - {1.22138700E+02, 1.40000000E+01, 6.00000000E+00, 0.00000000E+00, 0.00000000E+00}, \ - {8.38498000E+01, 1.40000000E+01, 7.00000000E+00, 0.00000000E+00, 0.00000000E+00}, \ - {6.25349000E+01, 1.40000000E+01, 8.00000000E+00, 0.00000000E+00, 0.00000000E+00}, \ - {4.66936000E+01, 1.40000000E+01, 9.00000000E+00, 0.00000000E+00, 0.00000000E+00}, \ - {3.54550000E+01, 1.40000000E+01, 1.00000000E+01, 0.00000000E+00, 0.00000000E+00}, \ - {5.91045800E+02, 1.40000000E+01, 1.10000000E+01, 0.00000000E+00, 0.00000000E+00}, \ - {4.47642300E+02, 1.40000000E+01, 1.20000000E+01, 0.00000000E+00, 0.00000000E+00}, \ - {4.08960600E+02, 1.40000000E+01, 1.30000000E+01, 0.00000000E+00, 0.00000000E+00}, \ - {3.17857400E+02, 1.40000000E+01, 1.40000000E+01, 0.00000000E+00, 0.00000000E+00}, \ - {2.37604000E+01, 1.50000000E+01, 1.00000000E+00, 0.00000000E+00, 9.11800000E-01}, \ - {1.56689000E+01, 1.50000000E+01, 2.00000000E+00, 0.00000000E+00, 0.00000000E+00}, \ - {3.50803000E+02, 1.50000000E+01, 3.00000000E+00, 0.00000000E+00, 0.00000000E+00}, \ - {2.08733100E+02, 1.50000000E+01, 4.00000000E+00, 0.00000000E+00, 0.00000000E+00}, \ - {1.42348100E+02, 1.50000000E+01, 5.00000000E+00, 0.00000000E+00, 0.00000000E+00}, \ - {9.67503000E+01, 1.50000000E+01, 6.00000000E+00, 0.00000000E+00, 0.00000000E+00}, \ - {6.77873000E+01, 1.50000000E+01, 7.00000000E+00, 0.00000000E+00, 0.00000000E+00}, \ - {5.13098000E+01, 1.50000000E+01, 8.00000000E+00, 0.00000000E+00, 0.00000000E+00}, \ - {3.88084000E+01, 1.50000000E+01, 9.00000000E+00, 0.00000000E+00, 0.00000000E+00}, \ - {2.97767000E+01, 1.50000000E+01, 1.00000000E+01, 0.00000000E+00, 0.00000000E+00}, \ - {4.20006400E+02, 1.50000000E+01, 1.10000000E+01, 0.00000000E+00, 0.00000000E+00}, \ - {3.30780100E+02, 1.50000000E+01, 1.20000000E+01, 0.00000000E+00, 0.00000000E+00}, \ - {3.07296500E+02, 1.50000000E+01, 1.30000000E+01, 0.00000000E+00, 0.00000000E+00}, \ - {2.44354600E+02, 1.50000000E+01, 1.40000000E+01, 0.00000000E+00, 0.00000000E+00}, \ - {1.91688700E+02, 1.50000000E+01, 1.50000000E+01, 0.00000000E+00, 0.00000000E+00}, \ - {2.00948000E+01, 1.60000000E+01, 1.00000000E+00, 0.00000000E+00, 9.11800000E-01}, \ - {1.36108000E+01, 1.60000000E+01, 2.00000000E+00, 0.00000000E+00, 0.00000000E+00}, \ - {2.73786700E+02, 1.60000000E+01, 3.00000000E+00, 0.00000000E+00, 0.00000000E+00}, \ - {1.67951300E+02, 1.60000000E+01, 4.00000000E+00, 0.00000000E+00, 0.00000000E+00}, \ - {1.17112100E+02, 1.60000000E+01, 5.00000000E+00, 0.00000000E+00, 0.00000000E+00}, \ - {8.10919000E+01, 1.60000000E+01, 6.00000000E+00, 0.00000000E+00, 0.00000000E+00}, \ - {5.76734000E+01, 1.60000000E+01, 7.00000000E+00, 0.00000000E+00, 0.00000000E+00}, \ - {4.41470000E+01, 1.60000000E+01, 8.00000000E+00, 0.00000000E+00, 0.00000000E+00}, \ - {3.37264000E+01, 1.60000000E+01, 9.00000000E+00, 0.00000000E+00, 0.00000000E+00}, \ - {2.60940000E+01, 1.60000000E+01, 1.00000000E+01, 0.00000000E+00, 0.00000000E+00}, \ - {3.28599000E+02, 1.60000000E+01, 1.10000000E+01, 0.00000000E+00, 0.00000000E+00}, \ - {2.64666500E+02, 1.60000000E+01, 1.20000000E+01, 0.00000000E+00, 0.00000000E+00}, \ - 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{4.21089400E+02, 4.82000000E+02, 3.81000000E+02, 3.90980000E+00, 2.94200000E+00}, \ - {4.87974000E+02, 4.82000000E+02, 3.82000000E+02, 3.90980000E+00, 2.90810000E+00}, \ - {4.92913800E+02, 4.82000000E+02, 3.83000000E+02, 3.90980000E+00, 2.95000000E+00}, \ - {1.12225400E+02, 4.82000000E+02, 4.05000000E+02, 3.90980000E+00, 4.58560000E+00}, \ - {8.87030000E+01, 4.82000000E+02, 4.06000000E+02, 3.90980000E+00, 3.98440000E+00}, \ - {2.60346800E+02, 4.82000000E+02, 4.14000000E+02, 3.90980000E+00, 3.86770000E+00}, \ - {2.86117900E+02, 4.82000000E+02, 4.32000000E+02, 3.90980000E+00, 3.89720000E+00}, \ - {3.91125000E+02, 4.82000000E+02, 4.50000000E+02, 3.90980000E+00, 3.91230000E+00}, \ - {4.55285400E+02, 4.82000000E+02, 4.82000000E+02, 3.90980000E+00, 3.90980000E+00} \ -} diff --git a/mace-bench/3rdparty/SevenNet/sevenn/pair_e3gnn/pair_e3gnn.cpp b/mace-bench/3rdparty/SevenNet/sevenn/pair_e3gnn/pair_e3gnn.cpp deleted file mode 100644 index 162015cda3a63ac5d298d8530a2767512f9b69fa..0000000000000000000000000000000000000000 --- a/mace-bench/3rdparty/SevenNet/sevenn/pair_e3gnn/pair_e3gnn.cpp +++ /dev/null @@ -1,400 +0,0 @@ -/* ---------------------------------------------------------------------- - LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - https://lammps.sandia.gov/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov - - Copyright (2003) Sandia Corporation. Under the terms of Contract - DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains - certain rights in this software. This software is distributed under - the GNU General Public License. - - See the README file in the top-level LAMMPS directory. -------------------------------------------------------------------------- */ - -/* ---------------------------------------------------------------------- - Contributing author: Yutack Park (SNU) -------------------------------------------------------------------------- */ - -#include -#include -#include -#include - -#include -#include - -#include "atom.h" -#include "domain.h" -#include "error.h" -#include "force.h" -#include "memory.h" -#include "neigh_list.h" -#include "neigh_request.h" -#include "neighbor.h" - -#include "pair_e3gnn.h" - -using namespace LAMMPS_NS; - -#define INTEGER_TYPE torch::TensorOptions().dtype(torch::kInt64) -#define FLOAT_TYPE torch::TensorOptions().dtype(torch::kFloat) - -PairE3GNN::PairE3GNN(LAMMPS *lmp) : Pair(lmp) { - // constructor - const char *print_flag = std::getenv("SEVENN_PRINT_INFO"); - if (print_flag) - print_info = true; - - std::string device_name; - if (torch::cuda::is_available()) { - device = torch::kCUDA; - device_name = "CUDA"; - } else { - device = torch::kCPU; - device_name = "CPU"; - } - - if (lmp->logfile) { - fprintf(lmp->logfile, "PairE3GNN using device : %s\n", device_name.c_str()); - } -} - -PairE3GNN::~PairE3GNN() { - if (allocated) { - memory->destroy(setflag); - memory->destroy(cutsq); - memory->destroy(map); - memory->destroy(elements); - } -} - -void PairE3GNN::compute(int eflag, int vflag) { - // compute - /* - This compute function is ispired/modified from stress branch of pair-nequip - https://github.com/mir-group/pair_nequip - */ - - if (eflag || vflag) - ev_setup(eflag, vflag); - else - evflag = vflag_fdotr = 0; - if (vflag_atom) { - error->all(FLERR, "atomic stress is not supported\n"); - } - - int nlocal = list->inum; // same as nlocal - int *ilist = list->ilist; - tagint *tag = atom->tag; - std::unordered_map tag_map; - - if (atom->tag_consecutive() == 0) { - for (int ii = 0; ii < nlocal; ii++) { - const int i = ilist[ii]; - int itag = tag[i]; - tag_map[itag] = ii+1; - // printf("MODIFY setting %i => %i \n",itag, tag_map[itag] ); - } - } else { - //Ordered which mappling required - for (int ii = 0; ii < nlocal; ii++) { - const int itag = ilist[ii]+1; - tag_map[itag] = ii+1; - // printf("normal setting %i => %i \n",itag, tag_map[itag] ); - } - } - - double **x = atom->x; - double **f = atom->f; - int *type = atom->type; - long num_atoms[1] = {nlocal}; - - int tag2i[nlocal]; - - int *numneigh = list->numneigh; // j loop cond - int **firstneigh = list->firstneigh; // j list - - int bound; - if (this->nedges_bound == -1) { - bound = std::accumulate(numneigh, numneigh + nlocal, 0); - } else { - bound = this->nedges_bound; - } - const int nedges_upper_bound = bound; - - float cell[3][3]; - cell[0][0] = domain->boxhi[0] - domain->boxlo[0]; - cell[0][1] = 0.0; - cell[0][2] = 0.0; - - cell[1][0] = domain->xy; - cell[1][1] = domain->boxhi[1] - domain->boxlo[1]; - cell[1][2] = 0.0; - - cell[2][0] = domain->xz; - cell[2][1] = domain->yz; - cell[2][2] = domain->boxhi[2] - domain->boxlo[2]; - - torch::Tensor inp_cell = torch::from_blob(cell, {3, 3}, FLOAT_TYPE); - torch::Tensor inp_num_atoms = torch::from_blob(num_atoms, {1}, INTEGER_TYPE); - - torch::Tensor inp_node_type = torch::zeros({nlocal}, INTEGER_TYPE); - torch::Tensor inp_pos = torch::zeros({nlocal, 3}); - - torch::Tensor inp_cell_volume = - torch::dot(inp_cell[0], torch::cross(inp_cell[1], inp_cell[2], 0)); - - float pbc_shift_tmp[nedges_upper_bound][3]; - - auto node_type = inp_node_type.accessor(); - auto pos = inp_pos.accessor(); - - long edge_idx_src[nedges_upper_bound]; - long edge_idx_dst[nedges_upper_bound]; - - int nedges = 0; - - for (int ii = 0; ii < nlocal; ii++) { - const int i = ilist[ii]; - int itag = tag_map[tag[i]]; - tag2i[itag - 1] = i; - const int itype = type[i]; - node_type[itag - 1] = map[itype]; - pos[itag - 1][0] = x[i][0]; - pos[itag - 1][1] = x[i][1]; - pos[itag - 1][2] = x[i][2]; - } - - for (int ii = 0; ii < nlocal; ii++) { - const int i = ilist[ii]; - int itag = tag_map[tag[i]]; - const int *jlist = firstneigh[i]; - const int jnum = numneigh[i]; - - for (int jj = 0; jj < jnum; jj++) { - int j = jlist[jj]; // atom over pbc is different atom - int jtag = tag_map[tag[j]]; // atom over pbs is same atom (it starts from 1) - j &= NEIGHMASK; - const int jtype = type[j]; - - const double delij[3] = {x[j][0] - x[i][0], x[j][1] - x[i][1], - x[j][2] - x[i][2]}; - const double Rij = - delij[0] * delij[0] + delij[1] * delij[1] + delij[2] * delij[2]; - if (Rij < cutoff_square) { - edge_idx_src[nedges] = itag - 1; - edge_idx_dst[nedges] = jtag - 1; - - pbc_shift_tmp[nedges][0] = x[j][0] - pos[jtag - 1][0]; - pbc_shift_tmp[nedges][1] = x[j][1] - pos[jtag - 1][1]; - pbc_shift_tmp[nedges][2] = x[j][2] - pos[jtag - 1][2]; - - nedges++; - } - } // j loop end - } // i loop end - - auto edge_idx_src_tensor = - torch::from_blob(edge_idx_src, {nedges}, INTEGER_TYPE); - auto edge_idx_dst_tensor = - torch::from_blob(edge_idx_dst, {nedges}, INTEGER_TYPE); - auto inp_edge_index = - torch::stack({edge_idx_src_tensor, edge_idx_dst_tensor}); - - // r' = r + {shift_tensor(integer vector of len 3)} @ cell_tensor - // shift_tensor = (cell_tensor)^-1^T @ (r' - r) - torch::Tensor cell_inv_tensor = - inp_cell.inverse().transpose(0, 1).unsqueeze(0).to(device); - torch::Tensor pbc_shift_tmp_tensor = - torch::from_blob(pbc_shift_tmp, {nedges, 3}, FLOAT_TYPE) - .view({nedges, 3, 1}) - .to(device); - torch::Tensor inp_cell_shift = - torch::bmm(cell_inv_tensor.expand({nedges, 3, 3}), pbc_shift_tmp_tensor) - .view({nedges, 3}); - - inp_pos.set_requires_grad(true); - - c10::Dict input_dict; - input_dict.insert("x", inp_node_type.to(device)); - input_dict.insert("pos", inp_pos.to(device)); - input_dict.insert("edge_index", inp_edge_index.to(device)); - input_dict.insert("num_atoms", inp_num_atoms.to(device)); - input_dict.insert("cell_lattice_vectors", inp_cell.to(device)); - input_dict.insert("cell_volume", inp_cell_volume.to(device)); - input_dict.insert("pbc_shift", inp_cell_shift); - - std::vector input(1, input_dict); - auto output = model.forward(input).toGenericDict(); - - torch::Tensor total_energy_tensor = - output.at("inferred_total_energy").toTensor().cpu(); - torch::Tensor force_tensor = output.at("inferred_force").toTensor().cpu(); - auto forces = force_tensor.accessor(); - eng_vdwl += total_energy_tensor.item(); - - for (int itag = 0; itag < nlocal; itag++) { - int i = tag2i[itag]; - f[i][0] += forces[itag][0]; - f[i][1] += forces[itag][1]; - f[i][2] += forces[itag][2]; - } - - if (vflag) { - // more accurately, it is virial part of stress - torch::Tensor stress_tensor = output.at("inferred_stress").toTensor().cpu(); - auto virial_stress_tensor = stress_tensor * inp_cell_volume; - // xy yz zx order in vasp (voigt is xx yy zz yz xz xy) - auto virial_stress = virial_stress_tensor.accessor(); - virial[0] += virial_stress[0]; - virial[1] += virial_stress[1]; - virial[2] += virial_stress[2]; - virial[3] += virial_stress[3]; - virial[4] += virial_stress[5]; - virial[5] += virial_stress[4]; - } - - if (eflag_atom) { - torch::Tensor atomic_energy_tensor = - output.at("atomic_energy").toTensor().cpu().squeeze(); - auto atomic_energy = atomic_energy_tensor.accessor(); - for (int itag = 0; itag < nlocal; itag++) { - int i = tag2i[itag]; - eatom[i] += atomic_energy[itag]; - } - } - - // if it was the first MD step - if (this->nedges_bound == -1) { - this->nedges_bound = nedges * 1.2; - } // else if the nedges is too small, increase the bound - else if (nedges > this->nedges_bound / 1.2) { - this->nedges_bound = nedges * 1.2; - } -} - -// allocate arrays (called from coeff) -void PairE3GNN::allocate() { - allocated = 1; - int n = atom->ntypes; - - memory->create(setflag, n + 1, n + 1, "pair:setflag"); - memory->create(cutsq, n + 1, n + 1, "pair:cutsq"); - memory->create(map, n + 1, "pair:map"); -} - -// global settings for pair_style -void PairE3GNN::settings(int narg, char **arg) { - if (narg != 0) { - error->all(FLERR, "Illegal pair_style command"); - } -} - -void PairE3GNN::coeff(int narg, char **arg) { - - if (allocated) { - error->all(FLERR, "pair_e3gnn coeff called twice"); - } - allocate(); - - if (strcmp(arg[0], "*") != 0 || strcmp(arg[1], "*") != 0) { - error->all(FLERR, - "e3gnn: first and second input of pair_coeff should be '*'"); - } - // expected input : pair_coeff * * pot.pth type_name1 type_name2 ... - - std::unordered_map meta_dict = { - {"chemical_symbols_to_index", ""}, - {"cutoff", ""}, - {"num_species", ""}, - {"model_type", ""}, - {"version", ""}, - {"dtype", ""}, - {"time", ""}}; - - // model loading from input - try { - model = torch::jit::load(std::string(arg[2]), device, meta_dict); - } catch (const c10::Error &e) { - error->all(FLERR, "error loading the model, check the path of the model"); - } - // model = torch::jit::freeze(model); model is already freezed - - torch::jit::setGraphExecutorOptimize(false); - torch::jit::FusionStrategy strategy; - // thing about dynamic recompile as tensor shape varies, this is default - // strategy = {{torch::jit::FusionBehavior::DYNAMIC, 3}}; - strategy = {{torch::jit::FusionBehavior::STATIC, 0}}; - torch::jit::setFusionStrategy(strategy); - - cutoff = std::stod(meta_dict["cutoff"]); - cutoff_square = cutoff * cutoff; - - if (meta_dict["model_type"].compare("E3_equivariant_model") != 0) { - error->all(FLERR, "given model type is not E3_equivariant_model"); - } - - std::string chem_str = meta_dict["chemical_symbols_to_index"]; - int ntypes = atom->ntypes; - - auto delim = " "; - char *tok = std::strtok(const_cast(chem_str.c_str()), delim); - std::vector chem_vec; - while (tok != nullptr) { - chem_vec.push_back(std::string(tok)); - tok = std::strtok(nullptr, delim); - } - - bool found_flag = false; - for (int i = 3; i < narg; i++) { - found_flag = false; - for (int j = 0; j < chem_vec.size(); j++) { - if (chem_vec[j].compare(arg[i]) == 0) { - map[i - 2] = j; - found_flag = true; - fprintf(lmp->logfile, "Chemical specie '%s' is assigned to type %d\n", - arg[i], i - 2); - break; - } - } - if (!found_flag) { - error->all(FLERR, "Unknown chemical specie is given"); - } - } - - if (ntypes > narg - 3) { - error->all(FLERR, "Not enough chemical specie is given. Check pair_coeff " - "and types in your data/script"); - } - - for (int i = 1; i <= ntypes; i++) { - for (int j = 1; j <= ntypes; j++) { - if ((map[i] >= 0) && (map[j] >= 0)) { - setflag[i][j] = 1; - cutsq[i][j] = cutoff * cutoff; - } - } - } - - if (lmp->logfile) { - fprintf(lmp->logfile, "from sevenn version '%s' ", - meta_dict["version"].c_str()); - fprintf(lmp->logfile, "%s precision model, deployed when: %s\n", - meta_dict["dtype"].c_str(), meta_dict["time"].c_str()); - } -} - -// init specific to this pair -void PairE3GNN::init_style() { - // Newton flag is irrelevant if use only one processor for simulation - /* - if (force->newton_pair == 0) { - error->all(FLERR, "Pair style nn requires newton pair on"); - } - */ - - // full neighbor list (this is many-body potential) - neighbor->add_request(this, NeighConst::REQ_FULL); -} - -double PairE3GNN::init_one(int i, int j) { return cutoff; } diff --git a/mace-bench/3rdparty/SevenNet/sevenn/pair_e3gnn/pair_e3gnn.h b/mace-bench/3rdparty/SevenNet/sevenn/pair_e3gnn/pair_e3gnn.h deleted file mode 100644 index cc57389e6e570c9af6d655454f4d6d7cddec64d9..0000000000000000000000000000000000000000 --- a/mace-bench/3rdparty/SevenNet/sevenn/pair_e3gnn/pair_e3gnn.h +++ /dev/null @@ -1,54 +0,0 @@ -/* -*- c++ -*- ---------------------------------------------------------- - LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator -http://lammps.sandia.gov, Sandia National Laboratories -Steve Plimpton, sjplimp@sandia.gov - -Copyright (2003) Sandia Corporation. Under the terms of Contract -DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains -certain rights in this software. This software is distributed under -the GNU General Public License. - -See the README file in the top-level LAMMPS directory. -------------------------------------------------------------------------- */ - -#ifdef PAIR_CLASS -PairStyle(e3gnn, PairE3GNN) - -#else - -#ifndef LMP_PAIR_E3GNN -#define LMP_PAIR_E3GNN - -#include "pair.h" - -#include - -namespace LAMMPS_NS { -class PairE3GNN : public Pair { -private: - double cutoff; - double cutoff_square; - torch::jit::Module model; - torch::Device device = torch::kCPU; - int nelements; - bool print_info = false; - - int nedges_bound = -1; - -public: - PairE3GNN(class LAMMPS *); - ~PairE3GNN(); - void compute(int, int); - - void settings(int, char **); - // read Atom type string from input script & related coeff - void coeff(int, char **); - void allocate(); - - void init_style(); - double init_one(int, int); -}; -} // namespace LAMMPS_NS - -#endif -#endif diff --git a/mace-bench/3rdparty/SevenNet/sevenn/pair_e3gnn/pair_e3gnn_parallel.cpp b/mace-bench/3rdparty/SevenNet/sevenn/pair_e3gnn/pair_e3gnn_parallel.cpp deleted file mode 100644 index 0b314171ea355d1b5669c259d3cacc0842838d12..0000000000000000000000000000000000000000 --- a/mace-bench/3rdparty/SevenNet/sevenn/pair_e3gnn/pair_e3gnn_parallel.cpp +++ /dev/null @@ -1,897 +0,0 @@ -/* ---------------------------------------------------------------------- - LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - https://lammps.sandia.gov/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov - - Copyright (2003) Sandia Corporation. Under the terms of Contract - DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains - certain rights in this software. This software is distributed under - the GNU General Public License. - - See the README file in the top-level LAMMPS directory. -------------------------------------------------------------------------- */ - -/* ---------------------------------------------------------------------- - Contributing author: Yutack Park (SNU) -------------------------------------------------------------------------- */ - -#include -#include -#include -#include -#include -#include -#include -#include -#include - -#include -#include -#include - -#include - -#include "atom.h" -#include "comm.h" -#include "comm_brick.h" -#include "error.h" -#include "force.h" -#include "memory.h" -#include "neigh_list.h" -#include "neighbor.h" -// #include "nvToolsExt.h" - -#include "pair_e3gnn_parallel.h" -#include - -#ifdef OMPI_MPI_H -#include "mpi-ext.h" //This should be included after mpi.h which is included in pair.h -#endif - -using namespace LAMMPS_NS; - -#define INTEGER_TYPE torch::TensorOptions().dtype(torch::kInt64) -#define FLOAT_TYPE torch::TensorOptions().dtype(torch::kFloat) - -DeviceBuffManager &DeviceBuffManager::getInstance() { - static DeviceBuffManager instance; - return instance; -} - -void DeviceBuffManager::get_buffer(int send_size, int recv_size, - float *&buf_send_ptr, float *&buf_recv_ptr) { - if (send_size > send_buf_size) { - cudaFree(buf_send_device); - cudaError_t cuda_err = - cudaMalloc(&buf_send_device, send_size * sizeof(float)); - send_buf_size = send_size; - } - if (recv_size > recv_buf_size) { - cudaFree(buf_recv_device); - cudaError_t cuda_err = - cudaMalloc(&buf_recv_device, recv_size * sizeof(float)); - recv_buf_size = recv_size; - } - buf_send_ptr = buf_send_device; - buf_recv_ptr = buf_recv_device; -} - -DeviceBuffManager::~DeviceBuffManager() { - cudaFree(buf_send_device); - cudaFree(buf_recv_device); -} - -PairE3GNNParallel::PairE3GNNParallel(LAMMPS *lmp) : Pair(lmp) { - // constructor - - const char *print_flag = std::getenv("SEVENN_PRINT_INFO"); - const char *print_both_flag = std::getenv("SEVENN_PRINT_BOTH_INFO"); - if (print_flag) { - world_rank = comm->me; - std::cout << "process rank: " << world_rank << " initialized" << std::endl; - print_info = (world_rank == 0) || print_both_flag; - } - - std::string device_name; - const bool use_gpu = torch::cuda::is_available(); - - comm_forward = 0; - comm_reverse = 0; - - // OpenMPI detection -#ifdef OMPI_MPI_H -#if defined(MPIX_CUDA_AWARE_SUPPORT) - if (1 == MPIX_Query_cuda_support()) { - use_cuda_mpi = true; - } else { - use_cuda_mpi = false; - } -#else - use_cuda_mpi = false; -#endif -#else - use_cuda_mpi = false; -#endif - // use_cuda_mpi = use_gpu && use_cuda_mpi; - // if (use_cuda_mpi) { - if (use_gpu) { - device = get_cuda_device(); - device_name = "CUDA"; - } else { - device = torch::kCPU; - device_name = "CPU"; - } - - if (std::getenv("OFF_E3GNN_PARALLEL_CUDA_MPI")) { - use_cuda_mpi = false; - } - - if (lmp->screen) { - if (use_gpu && !use_cuda_mpi) { - device_comm = torch::kCPU; - fprintf(lmp->screen, - "cuda-aware mpi not found, communicate via host device\n"); - } else { - device_comm = device; - } - fprintf(lmp->screen, "PairE3GNNParallel using device : %s\n", - device_name.c_str()); - fprintf(lmp->screen, "PairE3GNNParallel cuda-aware mpi: %s\n", - use_cuda_mpi ? "True" : "False"); - } - if (lmp->logfile) { - if (use_gpu && !use_cuda_mpi) { - device_comm = torch::kCPU; - fprintf(lmp->logfile, - "cuda-aware mpi not found, communicate via host device\n"); - } else { - device_comm = device; - } - fprintf(lmp->logfile, "PairE3GNNParallel using device : %s\n", - device_name.c_str()); - fprintf(lmp->logfile, "PairE3GNNParallel cuda-aware mpi: %s\n", - use_cuda_mpi ? "True" : "False"); - } -} - -torch::Device PairE3GNNParallel::get_cuda_device() { - char *cuda_visible = std::getenv("CUDA_VISIBLE_DEVICES"); - int num_gpus; - int idx; - int rank = comm->me; - num_gpus = torch::cuda::device_count(); - idx = rank % num_gpus; - if (print_info) - std::cout << world_rank << " Available # of GPUs found: " << num_gpus - << std::endl; - cudaError_t cuda_err = cudaSetDevice(idx); - if (cuda_err != cudaSuccess) { - std::cerr << "E3GNN: Failed to set CUDA device: " - << cudaGetErrorString(cuda_err) << std::endl; - } - return torch::Device(torch::kCUDA, idx); -} - -PairE3GNNParallel::~PairE3GNNParallel() { - if (allocated) { - memory->destroy(setflag); - memory->destroy(cutsq); - memory->destroy(map); - } -} - -int PairE3GNNParallel::get_x_dim() { return x_dim; } - -bool PairE3GNNParallel::use_cuda_mpi_() { return use_cuda_mpi; } - -bool PairE3GNNParallel::is_comm_preprocess_done() { - return comm_preprocess_done; -} - -void PairE3GNNParallel::compute(int eflag, int vflag) { - /* - Graph build on cpu - */ - if (eflag || vflag) - ev_setup(eflag, vflag); - else - evflag = vflag_fdotr = 0; - if (vflag_atom) { - error->all(FLERR, "atomic stress is not supported\n"); - } - - if (atom->tag_consecutive() == 0) { - error->all(FLERR, "Pair e3gnn requires consecutive atom IDs"); - } - - double **x = atom->x; - double **f = atom->f; - int *type = atom->type; - int nlocal = list->inum; // same as nlocal - int nghost = atom->nghost; - int ntotal = nlocal + nghost; - int *ilist = list->ilist; - int inum = list->inum; - - CommBrick *comm_brick = dynamic_cast(comm); - if (comm_brick == nullptr) { - error->all(FLERR, "e3gnn/parallel: comm style should be brick & from " - "modified code of comm_brick"); - } - - bigint natoms = atom->natoms; - - // tag ignore PBC - tagint *tag = atom->tag; - - // store graph_idx from local to known ghost atoms(ghost atoms inside cutoff) - int tag_to_graph_idx[natoms + 1]; // tag starts from 1 not 0 - std::fill_n(tag_to_graph_idx, natoms + 1, -1); - - // to access tag_to_graph_idx from comm - tag_to_graph_idx_ptr = tag_to_graph_idx; - - int graph_indexer = nlocal; - int graph_index_to_i[ntotal]; - - int *numneigh = list->numneigh; // j loop cond - int **firstneigh = list->firstneigh; // j list - const int nedges_upper_bound = - std::accumulate(numneigh, numneigh + nlocal, 0); - - std::vector node_type; - std::vector node_type_ghost; - - float edge_vec[nedges_upper_bound][3]; - long edge_idx_src[nedges_upper_bound]; - long edge_idx_dst[nedges_upper_bound]; - - int nedges = 0; - for (int ii = 0; ii < inum; ii++) { - // populate tag_to_graph_idx of local atoms - const int i = ilist[ii]; - const int itag = tag[i]; - const int itype = type[i]; - tag_to_graph_idx[itag] = ii; - graph_index_to_i[ii] = i; - node_type.push_back(map[itype]); - } - - // loop over neighbors, build graph - for (int ii = 0; ii < inum; ii++) { - const int i = ilist[ii]; - const int i_graph_idx = ii; - const int *jlist = firstneigh[i]; - const int jnum = numneigh[i]; - - for (int jj = 0; jj < jnum; jj++) { - int j = jlist[jj]; - const int jtag = tag[j]; - j &= NEIGHMASK; - const int jtype = type[j]; - // we have to calculate Rij to check cutoff in lammps side - const double delij[3] = {x[j][0] - x[i][0], x[j][1] - x[i][1], - x[j][2] - x[i][2]}; - const double Rij = - delij[0] * delij[0] + delij[1] * delij[1] + delij[2] * delij[2]; - - int j_graph_idx; - if (Rij < cutoff_square) { - // if given j is not local atom and inside cutoff - if (tag_to_graph_idx[jtag] == -1) { - // if j is ghost atom inside cutoff but first seen - tag_to_graph_idx[jtag] = graph_indexer; - graph_index_to_i[graph_indexer] = j; - node_type_ghost.push_back(map[jtype]); - graph_indexer++; - } - - j_graph_idx = tag_to_graph_idx[jtag]; - edge_idx_src[nedges] = i_graph_idx; - edge_idx_dst[nedges] = j_graph_idx; - edge_vec[nedges][0] = delij[0]; - edge_vec[nedges][1] = delij[1]; - edge_vec[nedges][2] = delij[2]; - nedges++; - } - } // j loop end - } // i loop end - - // member variable - graph_size = graph_indexer; - const int ghost_node_num = graph_size - nlocal; - - // convert data to Tensor - auto inp_node_type = torch::from_blob(node_type.data(), nlocal, INTEGER_TYPE); - auto inp_node_type_ghost = - torch::from_blob(node_type_ghost.data(), ghost_node_num, INTEGER_TYPE); - - long num_nodes[1] = {long(nlocal)}; - auto inp_num_atoms = torch::from_blob(num_nodes, {1}, INTEGER_TYPE); - - auto edge_idx_src_tensor = - torch::from_blob(edge_idx_src, {nedges}, INTEGER_TYPE); - auto edge_idx_dst_tensor = - torch::from_blob(edge_idx_dst, {nedges}, INTEGER_TYPE); - auto inp_edge_index = - torch::stack({edge_idx_src_tensor, edge_idx_dst_tensor}); - - auto inp_edge_vec = torch::from_blob(edge_vec, {nedges, 3}, FLOAT_TYPE); - if (print_info) { - std::cout << world_rank << " Nlocal: " << nlocal << std::endl; - std::cout << world_rank << " Graph_size: " << graph_size << std::endl; - std::cout << world_rank << " Ghost_node_num: " << ghost_node_num - << std::endl; - std::cout << world_rank << " Nedges: " << nedges << "\n" << std::endl; - } - - // r_original requires grad True - inp_edge_vec.set_requires_grad(true); - - torch::Dict input_dict; - input_dict.insert("x", inp_node_type.to(device)); - input_dict.insert("x_ghost", inp_node_type_ghost.to(device)); - input_dict.insert("edge_index", inp_edge_index.to(device)); - input_dict.insert("edge_vec", inp_edge_vec.to(device)); - input_dict.insert("num_atoms", inp_num_atoms.to(device)); - input_dict.insert("nlocal", inp_num_atoms.to(torch::kCPU)); - - std::list> wrt_tensors; - wrt_tensors.push_back({input_dict.at("edge_vec")}); - - auto model_part = model_list.front(); - - auto output = model_part.forward({input_dict}).toGenericDict(); - - comm_preprocess(); - - // extra_graph_idx_map is set from comm_preprocess(); - // last one is for trash values. See pack_forward_init - const int extra_size = - ghost_node_num + static_cast(extra_graph_idx_map.size()) + 1; - torch::Tensor x_local; - torch::Tensor x_ghost; - - for (auto it = model_list.begin(); it != model_list.end(); ++it) { - if (it == model_list.begin()) - continue; - model_part = *it; - - x_local = output.at("x").toTensor().detach().to(device); - x_dim = x_local.size(1); // length of per atom vector(node feature) - - auto ghost_and_extra_x = torch::zeros({ghost_node_num + extra_size, x_dim}, - FLOAT_TYPE.device(device)); - x_comm = torch::cat({x_local, ghost_and_extra_x}, 0).to(device_comm); - comm_brick->forward_comm(this); // populate x_ghost by communication - - // What we got from forward_comm (node feature of ghosts) - x_ghost = torch::split_with_sizes( - x_comm, {nlocal, ghost_node_num, extra_size}, 0)[1]; - x_ghost.set_requires_grad(true); - - // prepare next input (output > next input) - output.insert_or_assign("x_ghost", x_ghost.to(device)); - // make another edge_vec to discriminate grad calculation with other - // edge_vecs(maybe redundant?) - output.insert_or_assign("edge_vec", - output.at("edge_vec").toTensor().clone()); - - // save tensors for backprop - wrt_tensors.push_back({output.at("edge_vec").toTensor(), - output.at("x").toTensor(), - output.at("self_cont_tmp").toTensor(), - output.at("x_ghost").toTensor()}); - - output = model_part.forward({output}).toGenericDict(); - } - torch::Tensor energy_tensor = - output.at("inferred_total_energy").toTensor().squeeze(); - - torch::Tensor dE_dr = - torch::zeros({nedges, 3}, FLOAT_TYPE.device(device)); // create on device - torch::Tensor x_local_save; // holds grad info of x_local (it loses its grad - // when sends to CPU) - torch::Tensor self_conn_grads; - std::vector grads; - std::vector of_tensor; - - // TODO: most values of self_conn_grads were zero because we use only scalars - // for energy - for (auto rit = wrt_tensors.rbegin(); rit != wrt_tensors.rend(); ++rit) { - // edge_vec, x, x_ghost order - auto wrt_tensor = *rit; - if (rit == wrt_tensors.rbegin()) { - grads = torch::autograd::grad({energy_tensor}, wrt_tensor); - } else { - x_local_save.copy_(x_local); - // of wrt grads_output - grads = torch::autograd::grad(of_tensor, wrt_tensor, - {x_local_save, self_conn_grads}); - } - - dE_dr = dE_dr + grads.at(0); // accumulate force - if (std::distance(rit, wrt_tensors.rend()) == 1) - continue; // if last iteration - - of_tensor.clear(); - of_tensor.push_back(wrt_tensor[1]); // x - of_tensor.push_back(wrt_tensor[2]); // self_cont_tmp - - x_local_save = grads.at(1); // for grads_output - x_local = x_local_save.detach(); // grad_outputs & communication - x_dim = x_local.size(1); - - self_conn_grads = grads.at(2); // no communication, for grads_output - - x_ghost = grads.at(3).detach(); // yes communication, not for grads_output - - auto extra_x = torch::zeros({extra_size, x_dim}, FLOAT_TYPE.device(device)); - x_comm = torch::cat({x_local, x_ghost, extra_x}, 0).to(device_comm); - - comm_brick->reverse_comm(this); // completes x_local - - // now x_local is complete (dE_dx), become next grads_output(with - // self_conn_grads) - x_local = torch::split_with_sizes( - x_comm, {nlocal, ghost_node_num, extra_size}, 0)[0]; - } - - // postprocessing - if (print_info) { - size_t free, tot; - cudaMemGetInfo(&free, &tot); - std::cout << world_rank << " MEM use after backward(MB)" << std::endl; - double Mfree = static_cast(free) / (1024 * 1024); - double Mtot = static_cast(tot) / (1024 * 1024); - std::cout << world_rank << " Total: " << Mtot << std::endl; - std::cout << world_rank << " Free: " << Mfree << std::endl; - std::cout << world_rank << " Used: " << Mtot - Mfree << std::endl; - double Mused = Mtot - Mfree; - std::cout << world_rank << " Used/Nedges: " << Mused / nedges << std::endl; - std::cout << world_rank << " Used/Nlocal: " << Mused / nlocal << std::endl; - std::cout << world_rank << " Used/GraphSize: " << Mused / graph_size << "\n" - << std::endl; - } - eng_vdwl += energy_tensor.item(); // accumulate energy - - dE_dr = dE_dr.to(torch::kCPU); - torch::Tensor force_tensor = torch::zeros({graph_indexer, 3}); - - auto _edge_idx_src_tensor = - edge_idx_src_tensor.repeat_interleave(3).view({nedges, 3}); - auto _edge_idx_dst_tensor = - edge_idx_dst_tensor.repeat_interleave(3).view({nedges, 3}); - - force_tensor.scatter_reduce_(0, _edge_idx_src_tensor, dE_dr, "sum"); - force_tensor.scatter_reduce_(0, _edge_idx_dst_tensor, torch::neg(dE_dr), - "sum"); - - auto forces = force_tensor.accessor(); - - for (int graph_idx = 0; graph_idx < graph_indexer; graph_idx++) { - int i = graph_index_to_i[graph_idx]; - f[i][0] += forces[graph_idx][0]; - f[i][1] += forces[graph_idx][1]; - f[i][2] += forces[graph_idx][2]; - } - - if (vflag) { - auto diag = inp_edge_vec * dE_dr; - auto s12 = inp_edge_vec.select(1, 0) * dE_dr.select(1, 1); - auto s23 = inp_edge_vec.select(1, 1) * dE_dr.select(1, 2); - auto s31 = inp_edge_vec.select(1, 2) * dE_dr.select(1, 0); - std::vector voigt_list = { - diag, s12.unsqueeze(-1), s23.unsqueeze(-1), s31.unsqueeze(-1)}; - auto voigt = torch::cat(voigt_list, 1); - - torch::Tensor per_atom_stress_tensor = torch::zeros({graph_indexer, 6}); - auto _edge_idx_dst6_tensor = - edge_idx_dst_tensor.repeat_interleave(6).view({nedges, 6}); - per_atom_stress_tensor.scatter_reduce_(0, _edge_idx_dst6_tensor, voigt, - "sum"); - auto virial_stress_tensor = - torch::neg(torch::sum(per_atom_stress_tensor, 0)); - auto virial_stress = virial_stress_tensor.accessor(); - - virial[0] += virial_stress[0]; - virial[1] += virial_stress[1]; - virial[2] += virial_stress[2]; - virial[3] += virial_stress[3]; - virial[4] += virial_stress[5]; - virial[5] += virial_stress[4]; - } - - if (eflag_atom) { - torch::Tensor atomic_energy_tensor = - output.at("atomic_energy").toTensor().cpu().squeeze(); - auto atomic_energy = atomic_energy_tensor.accessor(); - for (int graph_idx = 0; graph_idx < nlocal; graph_idx++) { - int i = graph_index_to_i[graph_idx]; - eatom[i] += atomic_energy[graph_idx]; - } - } - - // clean up comm preprocess variables - comm_preprocess_done = false; - for (int i = 0; i < 6; i++) { - // array of vector - comm_index_pack_forward[i].clear(); - comm_index_unpack_forward[i].clear(); - comm_index_unpack_reverse[i].clear(); - } - - extra_graph_idx_map.clear(); -} - -// allocate arrays (called from coeff) -void PairE3GNNParallel::allocate() { - allocated = 1; - int n = atom->ntypes; - - memory->create(setflag, n + 1, n + 1, "pair:setflag"); - memory->create(cutsq, n + 1, n + 1, "pair:cutsq"); - memory->create(map, n + 1, "pair:map"); -} - -// global settings for pair_style -void PairE3GNNParallel::settings(int narg, char **arg) { - if (narg != 0) { - error->all(FLERR, "Illegal pair_style command"); - } -} - -void PairE3GNNParallel::coeff(int narg, char **arg) { - if (allocated) { - error->all(FLERR, "pair_e3gnn coeff called twice"); - } - allocate(); - - if (strcmp(arg[0], "*") != 0 || strcmp(arg[1], "*") != 0) { - error->all(FLERR, - "e3gnn: first and second input of pair_coeff should be '*'"); - } - // expected input : pair_coeff * * pot.pth type_name1 type_name2 ... - - std::unordered_map meta_dict = { - {"chemical_symbols_to_index", ""}, - {"cutoff", ""}, - {"num_species", ""}, - {"model_type", ""}, - {"version", ""}, - {"dtype", ""}, - {"time", ""}, - {"comm_size", ""}}; - - // model loading from input - int n_model = std::stoi(arg[2]); - int chem_arg_i = 4; - std::vector model_fnames; - if (std::filesystem::exists(arg[3])) { - if (std::filesystem::is_directory(arg[3])) { - auto headf = std::string(arg[3]); - for (int i = 0; i < n_model; i++) { - auto stri = std::to_string(i); - model_fnames.push_back(headf + "/deployed_parallel_" + stri + ".pt"); - } - } else if (std::filesystem::is_regular_file(arg[3])) { - for (int i = 3; i < n_model + 3; i++) { - model_fnames.push_back(std::string(arg[i])); - } - chem_arg_i = n_model + 3; - } else { - error->all(FLERR, "No such file or directory:" + std::string(arg[3])); - } - } - - for (const auto &modelf : model_fnames) { - if (!std::filesystem::is_regular_file(modelf)) { - error->all(FLERR, "Expected this is a regular file:" + modelf); - } - model_list.push_back(torch::jit::load(modelf, device, meta_dict)); - } - - torch::jit::setGraphExecutorOptimize(false); - torch::jit::FusionStrategy strategy; - // strategy = {{torch::jit::FusionBehavior::DYNAMIC, 3}}; - strategy = {{torch::jit::FusionBehavior::STATIC, 0}}; - torch::jit::setFusionStrategy(strategy); - - cutoff = std::stod(meta_dict["cutoff"]); - - // maximum possible size of per atom x before last convolution - int comm_size = std::stod(meta_dict["comm_size"]); - - // to initialize buffer size for communication - comm_forward = comm_size; - comm_reverse = comm_size; - - cutoff_square = cutoff * cutoff; - - if (meta_dict["model_type"].compare("E3_equivariant_model") != 0) { - error->all(FLERR, "given model type is not E3_equivariant_model"); - } - - std::string chem_str = meta_dict["chemical_symbols_to_index"]; - int ntypes = atom->ntypes; - - auto delim = " "; - char *tok = std::strtok(const_cast(chem_str.c_str()), delim); - std::vector chem_vec; - while (tok != nullptr) { - chem_vec.push_back(std::string(tok)); - tok = std::strtok(nullptr, delim); - } - - // what if unknown chemical specie is in arg? should I abort? is there any use - // case for that? - bool found_flag = false; - int n_chem = narg - chem_arg_i; - for (int i = 0; i < n_chem; i++) { - found_flag = false; - for (int j = 0; j < chem_vec.size(); j++) { - if (chem_vec[j].compare(arg[i + chem_arg_i]) == 0) { - map[i + 1] = j; // store from 1, (not 0) - found_flag = true; - if (lmp->logfile) { - fprintf(lmp->logfile, "Chemical specie '%s' is assigned to type %d\n", - arg[i + chem_arg_i], i + 1); - break; - } - } - } - if (!found_flag) { - error->all(FLERR, "Unknown chemical specie is given or the number of " - "potential files is not consistent"); - } - } - - for (int i = 1; i <= ntypes; i++) { - for (int j = 1; j <= ntypes; j++) { - if ((map[i] >= 0) && (map[j] >= 0)) { - setflag[i][j] = 1; - cutsq[i][j] = cutoff * cutoff; - } - } - } - - if (lmp->logfile) { - fprintf(lmp->logfile, "from sevenn version '%s' ", - meta_dict["version"].c_str()); - fprintf(lmp->logfile, "%s precision model, deployed when: %s\n", - meta_dict["dtype"].c_str(), meta_dict["time"].c_str()); - } -} - -// init specific to this pair -void PairE3GNNParallel::init_style() { - // full neighbor list & newton on - if (force->newton_pair == 0) { - error->all(FLERR, "Pair style e3gnn/parallel requires newton pair on"); - } - neighbor->add_request(this, NeighConst::REQ_FULL); -} - -double PairE3GNNParallel::init_one(int i, int j) { return cutoff; } - -void PairE3GNNParallel::notify_proc_ids(const int *sendproc, const int *recvproc) { - for (int iswap = 0; iswap < 6; iswap++) { - this->sendproc[iswap] = sendproc[iswap]; - this->recvproc[iswap]= recvproc[iswap]; - } -} - -void PairE3GNNParallel::comm_preprocess() { - assert(!comm_preprocess_done); - CommBrick *comm_brick = dynamic_cast(comm); - - // fake lammps communication call to preprocess index - // gives complete comm_index_pack, unpack_forward, and extra_graph_idx_map - comm_brick->forward_comm(this); - - std::map> already_met_map; - for (int comm_phase = 0; comm_phase < 6; comm_phase++) { - const int n = comm_index_pack_forward[comm_phase].size(); - int sproc = this->sendproc[comm_phase]; - if (already_met_map.count(sproc) == 0) { - already_met_map.insert({sproc, std::set()}); - } - - // for unpack_reverse, Ignore duplicated index by 'already_met' - std::vector &idx_map_forward = comm_index_pack_forward[comm_phase]; - std::vector &idx_map_reverse = comm_index_unpack_reverse[comm_phase]; - std::set& already_met = already_met_map[sproc]; - // the last index of x_comm is used to trash unnecessary values - const int trash_index = - graph_size + static_cast(extra_graph_idx_map.size()); //+ 1; - for (int i = 0; i < n; i++) { - const int idx = idx_map_forward[i]; - if (idx < graph_size) { - if (already_met.count(idx) == 1) { - idx_map_reverse.push_back(trash_index); - } else { - idx_map_reverse.push_back(idx); - already_met.insert(idx); - } - } else { - idx_map_reverse.push_back(idx); - } - } - - if (use_cuda_mpi) { - comm_index_pack_forward_tensor[comm_phase] = torch::from_blob(idx_map_forward.data(), idx_map_forward.size(), INTEGER_TYPE).to(device); - - auto upmap = comm_index_unpack_forward[comm_phase]; - comm_index_unpack_forward_tensor[comm_phase] = torch::from_blob(upmap.data(), upmap.size(), INTEGER_TYPE).to(device); - comm_index_unpack_reverse_tensor[comm_phase] = torch::from_blob(idx_map_reverse.data(), idx_map_reverse.size(), INTEGER_TYPE).to(device); - } - } - comm_preprocess_done = true; -} - -// called from comm_brick if comm_preprocess_done is false -void PairE3GNNParallel::pack_forward_init(int n, int *list_send, - int comm_phase) { - std::vector &idx_map = comm_index_pack_forward[comm_phase]; - - idx_map.reserve(n); - - int i, j; - int nlocal = list->inum; - tagint *tag = atom->tag; - - for (i = 0; i < n; i++) { - int list_i = list_send[i]; - int graph_idx = tag_to_graph_idx_ptr[tag[list_i]]; - - if (graph_idx != -1) { - // known atom (local atom + ghost atom inside cutoff) - idx_map.push_back(graph_idx); - } else { - // unknown atom, these are not used in computation in this process - // instead, this process is used to hand over these atoms to other proecss - // hold them in continuous manner for flexible tensor operations later - if (extra_graph_idx_map.find(list_i) != extra_graph_idx_map.end()) { - idx_map.push_back(extra_graph_idx_map[list_i]); - } else { - // unknown atom at pack forward, ghost atom outside cutoff? - extra_graph_idx_map[i] = graph_size + extra_graph_idx_map.size(); - idx_map.push_back(extra_graph_idx_map[i]); // same as list_i in pack - } - } - } -} - -// called from comm_brick if comm_preprocess_done is false -void PairE3GNNParallel::unpack_forward_init(int n, int first, int comm_phase) { - std::vector &idx_map = comm_index_unpack_forward[comm_phase]; - - idx_map.reserve(n); - - int i, j, last; - last = first + n; - int nlocal = list->inum; - tagint *tag = atom->tag; - - for (i = first; i < last; i++) { - int graph_idx = tag_to_graph_idx_ptr[tag[i]]; - if (graph_idx != -1) { - idx_map.push_back(graph_idx); - } else { - extra_graph_idx_map[i] = graph_size + extra_graph_idx_map.size(); - idx_map.push_back(extra_graph_idx_map[i]); // same as list_i in pack - } - } -} - -int PairE3GNNParallel::pack_forward_comm_gnn(float *buf, int comm_phase) { - std::vector &idx_map = comm_index_pack_forward[comm_phase]; - const int n = static_cast(idx_map.size()); - if (use_cuda_mpi && n != 0) { - torch::Tensor &idx_map_tensor = comm_index_pack_forward_tensor[comm_phase]; - auto selected = x_comm.index_select(0, idx_map_tensor); // its size is x_dim * n - cudaError_t cuda_err = - cudaMemcpy(buf, selected.data_ptr(), (x_dim * n) * sizeof(float), - cudaMemcpyDeviceToDevice); - } else { - int i, j, m; - m = 0; - for (i = 0; i < n; i++) { - const int idx = static_cast(idx_map.at(i)); - float *from = x_comm[idx].data_ptr(); - for (j = 0; j < x_dim; j++) { - buf[m++] = from[j]; - } - } - } - if (print_info) { - std::cout << world_rank << " comm_phase: " << comm_phase << std::endl; - std::cout << world_rank << " pack_forward x_dim: " << x_dim << std::endl; - std::cout << world_rank << " pack_forward n: " << n << std::endl; - std::cout << world_rank << " pack_forward x_dim*n: " << x_dim * n - << std::endl; - double Msend = static_cast(x_dim * n * 4) / (1024 * 1024); - std::cout << world_rank << " send size(MB): " << Msend << "\n" << std::endl; - } - return x_dim * n; -} - -void PairE3GNNParallel::unpack_forward_comm_gnn(float *buf, int comm_phase) { - std::vector &idx_map = comm_index_unpack_forward[comm_phase]; - const int n = static_cast(idx_map.size()); - - if (use_cuda_mpi && n != 0) { - torch::Tensor &idx_map_tensor = comm_index_unpack_forward_tensor[comm_phase]; - auto buf_tensor = - torch::from_blob(buf, {n, x_dim}, FLOAT_TYPE.device(device)); - x_comm.scatter_(0, idx_map_tensor.repeat_interleave(x_dim).view({n, x_dim}), - buf_tensor); - } else { - int i, j, m; - m = 0; - for (i = 0; i < n; i++) { - const int idx = static_cast(idx_map.at(i)); - float *to = x_comm[idx].data_ptr(); - for (j = 0; j < x_dim; j++) { - to[j] = buf[m++]; - } - } - } -} - -int PairE3GNNParallel::pack_reverse_comm_gnn(float *buf, int comm_phase) { - std::vector &idx_map = comm_index_unpack_forward[comm_phase]; - const int n = static_cast(idx_map.size()); - - if (use_cuda_mpi && n != 0) { - torch::Tensor &idx_map_tensor = comm_index_unpack_forward_tensor[comm_phase]; - auto selected = x_comm.index_select(0, idx_map_tensor); - cudaError_t cuda_err = cudaMemcpy(buf, selected.data_ptr(), (x_dim * n) * sizeof(float), cudaMemcpyDeviceToDevice); - } else { - int i, j, m; - m = 0; - for (i = 0; i < n; i++) { - const int idx = static_cast(idx_map.at(i)); - float *from = x_comm[idx].data_ptr(); - for (j = 0; j < x_dim; j++) { - buf[m++] = from[j]; - } - } - } - if (print_info) { - std::cout << world_rank << " comm_phase: " << comm_phase << std::endl; - std::cout << world_rank << " pack_reverse x_dim: " << x_dim << std::endl; - std::cout << world_rank << " pack_reverse n: " << n << std::endl; - std::cout << world_rank << " pack_reverse x_dim*n: " << x_dim * n - << std::endl; - double Msend = static_cast(x_dim * n * 4) / (1024 * 1024); - } - return x_dim * n; -} - -void PairE3GNNParallel::unpack_reverse_comm_gnn(float *buf, int comm_phase) { - std::vector &idx_map = comm_index_unpack_reverse[comm_phase]; - const int n = static_cast(idx_map.size()); - - if (use_cuda_mpi && n != 0) { - torch::Tensor &idx_map_tensor = comm_index_unpack_reverse_tensor[comm_phase]; - auto buf_tensor = - torch::from_blob(buf, {n, x_dim}, FLOAT_TYPE.device(device)); - x_comm.scatter_(0, idx_map_tensor.repeat_interleave(x_dim).view({n, x_dim}), - buf_tensor, "add"); - } else { - int i, j, m; - m = 0; - for (i = 0; i < n; i++) { - const int idx = static_cast(idx_map.at(i)); - if (idx == -1) { - m += x_dim; - continue; - } - float *to = x_comm[idx].data_ptr(); - for (j = 0; j < x_dim; j++) { - to[j] += buf[m++]; - } - } - } -} diff --git a/mace-bench/3rdparty/SevenNet/sevenn/pair_e3gnn/pair_e3gnn_parallel.h b/mace-bench/3rdparty/SevenNet/sevenn/pair_e3gnn/pair_e3gnn_parallel.h deleted file mode 100644 index 4ba79a0b8dde973dda6fec97d14588e82749fe62..0000000000000000000000000000000000000000 --- a/mace-bench/3rdparty/SevenNet/sevenn/pair_e3gnn/pair_e3gnn_parallel.h +++ /dev/null @@ -1,118 +0,0 @@ -/* -*- c++ -*- ---------------------------------------------------------- - LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator -http://lammps.sandia.gov, Sandia National Laboratories -Steve Plimpton, sjplimp@sandia.gov - -Copyright (2003) Sandia Corporation. Under the terms of Contract -DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains -certain rights in this software. This software is distributed under -the GNU General Public License. - -See the README file in the top-level LAMMPS directory. -------------------------------------------------------------------------- */ - -#ifdef PAIR_CLASS -PairStyle(e3gnn/parallel, PairE3GNNParallel) - -#else - -#ifndef LMP_PAIR_E3GNN_PARALLEL -#define LMP_PAIR_E3GNN_PARALLEL - -#include "pair.h" - -#include -#include - -namespace LAMMPS_NS { -class PairE3GNNParallel : public Pair { -private: - double cutoff; - double cutoff_square; - std::vector model_list; - torch::Device device = torch::kCPU; - torch::Device device_comm = torch::kCPU; - torch::Device get_cuda_device(); - bool use_cuda_mpi; - - // for communication - // Most of these variables for communication is temporary and valid for only - // one MD step. - int x_dim; // to determine per atom data size - int graph_size; - torch::Tensor x_comm; // x_local + x_ghost + x_comm_extra - - void comm_preprocess(); - bool comm_preprocess_done = false; - - // temporary variables holds for each compute step - std::unordered_map extra_graph_idx_map; - // To use scatter, store long instead of int - // array of vector - std::vector comm_index_pack_forward[6]; - std::vector comm_index_unpack_forward[6]; - std::vector comm_index_unpack_reverse[6]; - - // its size is 6 and initialized at comm_preprocess() - torch::Tensor comm_index_pack_forward_tensor[6]; - torch::Tensor comm_index_unpack_forward_tensor[6]; - torch::Tensor comm_index_unpack_reverse_tensor[6]; - - // to use tag_to_graph_idx inside comm methods - int *tag_to_graph_idx_ptr = nullptr; - - int sendproc[6]; - int recvproc[6]; - -public: - PairE3GNNParallel(class LAMMPS *); - ~PairE3GNNParallel(); - - // TODO: keep encapsulation.. - void compute(int, int) override; - void settings(int, char **) override; - // read Atom type string from input script & related coeff - void coeff(int, char **) override; - void allocate(); - - void pack_forward_init(int n, int *list, int comm_phase); - void unpack_forward_init(int n, int first, int comm_phase); - - int pack_forward_comm_gnn(float *buf, int comm_phase); - void unpack_forward_comm_gnn(float *buf, int comm_phase); - int pack_reverse_comm_gnn(float *buf, int comm_phase); - void unpack_reverse_comm_gnn(float *buf, int comm_phase); - - void init_style() override; - double init_one(int, int) override; - - int get_x_dim(); - bool use_cuda_mpi_(); - bool is_comm_preprocess_done(); - void notify_proc_ids(const int *sendproc, const int *recvproc); - - bool print_info = false; - int world_rank; -}; - -class DeviceBuffManager { -private: - DeviceBuffManager() {} - DeviceBuffManager(const DeviceBuffManager &); - DeviceBuffManager &operator=(const DeviceBuffManager &); - - float *buf_send_device = nullptr; - float *buf_recv_device = nullptr; - int send_buf_size = 0; - int recv_buf_size = 0; - -public: - static DeviceBuffManager &getInstance(); - void get_buffer(int, int, float *&, float *&); - - ~DeviceBuffManager(); -}; -} // namespace LAMMPS_NS - -#endif -#endif diff --git a/mace-bench/3rdparty/SevenNet/sevenn/pair_e3gnn/patch_lammps.sh b/mace-bench/3rdparty/SevenNet/sevenn/pair_e3gnn/patch_lammps.sh deleted file mode 100644 index e6bc90d5459c000d2ecb81cfc7138e025ab32844..0000000000000000000000000000000000000000 --- a/mace-bench/3rdparty/SevenNet/sevenn/pair_e3gnn/patch_lammps.sh +++ /dev/null @@ -1,154 +0,0 @@ -#!/bin/bash - -lammps_root=$1 -cxx_standard=$2 # 14, 17 -d3_support=$3 # 1, 0 -SCRIPT_DIR=$(dirname "${BASH_SOURCE[0]}") - -########################################### -# Check if the given arguments are valid # -########################################### - -# Check the number of arguments -if [ "$#" -ne 3 ]; then - echo "Usage: sh patch_lammps.sh {lammps_root} {cxx_standard} {d3_support}" - echo " {lammps_root}: Root directory of LAMMPS source" - echo " {cxx_standard}: C++ standard (14, 17)" - echo " {d3_support}: Support for pair_d3 (1, 0)" - exit 1 -fi - -# Check if the lammps_root directory exists -if [ ! -d "$lammps_root" ]; then - echo "Error: No such directory: $lammps_root" - exit 1 -fi - -# Check if the given directory is the root of LAMMPS source -if [ ! -d "$lammps_root/cmake" ] && [ ! -d "$lammps_root/potentials" ]; then - echo "Error: Given $lammps_root is not a root of LAMMPS source" - exit 1 -fi - -# Check if the script is being run from the root of SevenNet -if [ ! -f "${SCRIPT_DIR}/pair_e3gnn.cpp" ]; then - echo "Error: Script executed in a wrong directory" - exit 1 -fi - -# Check if the patch is already applied -if [ -f "$lammps_root/src/pair_e3gnn.cpp" ]; then - echo "----------------------------------------------------------" - echo "Seems like given LAMMPS is already patched." - echo "Try again after removing src/pair_e3gnn.cpp to force patch" - echo "----------------------------------------------------------" - echo "Example build commands, under LAMMPS root" - echo " mkdir build; cd build" - echo " cmake ../cmake -DCMAKE_PREFIX_PATH=$(python -c 'import torch;print(torch.utils.cmake_prefix_path)')" - echo " make -j 4" - exit 0 -fi - -# Check if OpenMPI exists and if it is CUDA-aware -if command -v ompi_info &> /dev/null; then - cuda_support=$(ompi_info --parsable --all | grep mpi_built_with_cuda_support:value) - if [[ -z "$cuda_support" ]]; then - echo "OpenMPI not found, parallel performance is not optimal" - elif [[ "$cuda_support" == *"true" ]]; then - echo "OpenMPI is CUDA aware" - else - echo "This system's OpenMPI is not 'CUDA aware', parallel performance is not optimal" - fi -else - echo "OpenMPI not found, parallel performance is not optimal" -fi - -# Extract LAMMPS version and update -lammps_version=$(grep "#define LAMMPS_VERSION" $lammps_root/src/version.h | awk '{print $3, $4, $5}' | tr -d '"') - -# Combine version and update -detected_version="$lammps_version" -required_version="2 Aug 2023" # Example required version - -# Check if the detected version is compatible -if [[ "$detected_version" != "$required_version" ]]; then - echo "Warning: Detected LAMMPS version ($detected_version) may not be compatible. Required version: $required_version" -fi - -########################################### -# Backup original LAMMPS source code # -########################################### - -# Create a backup directory if it doesn't exist -backup_dir="$lammps_root/_backups" -mkdir -p $backup_dir - -# Copy comm_* from original LAMMPS source as backup -cp $lammps_root/src/comm_brick.cpp $backup_dir/ -cp $lammps_root/src/comm_brick.h $backup_dir/ - -# Copy cmake/CMakeLists.txt from original source as backup -cp $lammps_root/cmake/CMakeLists.txt $backup_dir/CMakeLists.txt - -########################################### -# Patch LAMMPS source code: e3gnn # -########################################### - -# 1. Copy pair_e3gnn files to LAMMPS source -cp $SCRIPT_DIR/{pair_e3gnn,pair_e3gnn_parallel,comm_brick}.cpp $lammps_root/src/ -cp $SCRIPT_DIR/{pair_e3gnn,pair_e3gnn_parallel,comm_brick}.h $lammps_root/src/ - -# 2. Patch cmake/CMakeLists.txt -sed -i "s/set(CMAKE_CXX_STANDARD 11)/set(CMAKE_CXX_STANDARD $cxx_standard)/" $lammps_root/cmake/CMakeLists.txt -cat >> $lammps_root/cmake/CMakeLists.txt << "EOF" - -find_package(Torch REQUIRED) -set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${TORCH_CXX_FLAGS}") -target_link_libraries(lammps PUBLIC "${TORCH_LIBRARIES}") -EOF - -########################################### -# Patch LAMMPS source code: d3 # -########################################### - -if [ "$d3_support" -ne 0 ]; then - -# 1. Copy pair_d3 files to LAMMPS source -cp $SCRIPT_DIR/pair_d3.cu $lammps_root/src/ -cp $SCRIPT_DIR/pair_d3.h $lammps_root/src/ -cp $SCRIPT_DIR/pair_d3_pars.h $lammps_root/src/ - -# 2. Patch cmake/CMakeLists.txt -sed -i "s/project(lammps CXX)/project(lammps CXX CUDA)/" $lammps_root/cmake/CMakeLists.txt -sed -i "s/\${LAMMPS_SOURCE_DIR}\/\[\^.\]\*\.cpp/\${LAMMPS_SOURCE_DIR}\/\[\^.\]\*\.cpp \${LAMMPS_SOURCE_DIR}\/\[\^.\]\*\.cu/" $lammps_root/cmake/CMakeLists.txt -cat >> $lammps_root/cmake/CMakeLists.txt << "EOF" - -find_package(CUDA) -set(CMAKE_CUDA_FLAGS "${CMAKE_CUDA_FLAGS} -fmad=false -O3") -string(REPLACE "-gencode arch=compute_50,code=sm_50" "" CMAKE_CUDA_FLAGS "${CMAKE_CUDA_FLAGS}") -target_link_libraries(lammps PUBLIC ${CUDA_LIBRARIES} cuda) -EOF - -fi - -########################################### -# Print changes and backup file locations # -########################################### - -# Print changes and backup file locations -echo "Changes made:" -echo " - Original LAMMPS files (src/comm_brick.*, cmake/CMakeList.txt) are in {lammps_root}/_backups" -echo " - Copied contents of pair_e3gnn to $lammps_root/src/" -echo " - Patched CMakeLists.txt: include LibTorch, CXX_STANDARD $cxx_standard" -if [ "$d3_support" -ne 0 ]; then - echo " - Copied contents of pair_d3 to $lammps_root/src/" - echo " - Patched CMakeLists.txt: include CUDA" -fi - -# Provide example cmake command to the user -echo "Example build commands, under LAMMPS root" -echo " mkdir build; cd build" -echo " cmake ../cmake -DCMAKE_PREFIX_PATH=$(python -c 'import torch;print(torch.utils.cmake_prefix_path)')" -echo " make -j 4" - -exit 0 diff --git a/mace-bench/3rdparty/SevenNet/sevenn/parse_input.py b/mace-bench/3rdparty/SevenNet/sevenn/parse_input.py deleted file mode 100644 index f0406d8c6ada4303dbc9241beb9fb9b276e096cc..0000000000000000000000000000000000000000 --- a/mace-bench/3rdparty/SevenNet/sevenn/parse_input.py +++ /dev/null @@ -1,246 +0,0 @@ -import glob -import os -import warnings -from typing import Any, Callable, Dict - -import torch -import yaml - -import sevenn._const as _const -import sevenn._keys as KEY -import sevenn.util as util - - -def config_initialize( - key: str, - config: Dict, - default: Any, - conditions: Dict, -): - # default value exist & no user input -> return default - if key not in config.keys(): - return default - - # No validation method exist => accept user input - user_input = config[key] - if key in conditions: - condition = conditions[key] - else: - return user_input - - if type(default) is dict and isinstance(condition, dict): - for i_key, val in default.items(): - user_input[i_key] = config_initialize( - i_key, user_input, val, condition - ) - return user_input - elif isinstance(condition, type): - if isinstance(user_input, condition): - return user_input - else: - try: - return condition(user_input) # try type casting - except ValueError: - raise ValueError( - f"Expect '{user_input}' for '{key}' is {condition}" - ) - elif isinstance(condition, Callable) and condition(user_input): - return user_input - else: - raise ValueError( - f"Given input '{user_input}' for '{key}' is not valid" - ) - - -def init_model_config(config: Dict): - # defaults = _const.model_defaults(config) - model_meta = {} - - # init complicated ones - if KEY.CHEMICAL_SPECIES not in config.keys(): - raise ValueError('required key chemical_species not exist') - input_chem = config[KEY.CHEMICAL_SPECIES] - if isinstance(input_chem, str) and input_chem.lower() == 'auto': - model_meta[KEY.CHEMICAL_SPECIES] = 'auto' - model_meta[KEY.NUM_SPECIES] = 'auto' - model_meta[KEY.TYPE_MAP] = 'auto' - elif isinstance(input_chem, str) and 'univ' in input_chem.lower(): - model_meta.update(util.chemical_species_preprocess([], universal=True)) - else: - if isinstance(input_chem, list) and all( - isinstance(x, str) for x in input_chem - ): - pass - elif isinstance(input_chem, str): - input_chem = ( - input_chem.replace('-', ',').replace(' ', ',').split(',') - ) - input_chem = [chem for chem in input_chem if len(chem) != 0] - else: - raise ValueError(f'given {KEY.CHEMICAL_SPECIES} input is strange') - model_meta.update(util.chemical_species_preprocess(input_chem)) - - # deprecation warnings - if KEY.AVG_NUM_NEIGH in config: - warnings.warn( - "key 'avg_num_neigh' is deprecated. Please use 'conv_denominator'." - ' We use the default, the average number of neighbors in the' - ' dataset, if not provided.', - UserWarning, - ) - config.pop(KEY.AVG_NUM_NEIGH) - if KEY.TRAIN_AVG_NUM_NEIGH in config: - warnings.warn( - "key 'train_avg_num_neigh' is deprecated. Please use" - " 'train_denominator'. We overwrite train_denominator as given" - ' train_avg_num_neigh', - UserWarning, - ) - config[KEY.TRAIN_DENOMINTAOR] = config[KEY.TRAIN_AVG_NUM_NEIGH] - config.pop(KEY.TRAIN_AVG_NUM_NEIGH) - if KEY.OPTIMIZE_BY_REDUCE in config: - warnings.warn( - "key 'optimize_by_reduce' is deprecated. Always true", - UserWarning, - ) - config.pop(KEY.OPTIMIZE_BY_REDUCE) - - # init simpler ones - for key, default in _const.DEFAULT_E3_EQUIVARIANT_MODEL_CONFIG.items(): - model_meta[key] = config_initialize( - key, config, default, _const.MODEL_CONFIG_CONDITION - ) - - unknown_keys = [ - key for key in config.keys() if key not in model_meta.keys() - ] - if len(unknown_keys) != 0: - warnings.warn( - f'Unexpected model keys: {unknown_keys} will be ignored', - UserWarning, - ) - - return model_meta - - -def init_train_config(config: Dict): - train_meta = {} - # defaults = _const.train_defaults(config) - - try: - device_input = config[KEY.DEVICE] - train_meta[KEY.DEVICE] = torch.device(device_input) - except KeyError: - train_meta[KEY.DEVICE] = ( - torch.device('cuda') - if torch.cuda.is_available() - else torch.device('cpu') - ) - train_meta[KEY.DEVICE] = str(train_meta[KEY.DEVICE]) - - # init simpler ones - for key, default in _const.DEFAULT_TRAINING_CONFIG.items(): - train_meta[key] = config_initialize( - key, config, default, _const.TRAINING_CONFIG_CONDITION - ) - - if KEY.CONTINUE in config.keys(): - cnt_dct = config[KEY.CONTINUE] - if KEY.CHECKPOINT not in cnt_dct.keys(): - raise ValueError('no checkpoint is given in continue') - checkpoint = cnt_dct[KEY.CHECKPOINT] - if os.path.isfile(checkpoint): - checkpoint_file = checkpoint - else: - checkpoint_file = util.pretrained_name_to_path(checkpoint) - train_meta[KEY.CONTINUE].update({KEY.CHECKPOINT: checkpoint_file}) - - unknown_keys = [ - key for key in config.keys() if key not in train_meta.keys() - ] - if len(unknown_keys) != 0: - warnings.warn( - f'Unexpected train keys: {unknown_keys} will be ignored', - UserWarning, - ) - return train_meta - - -def init_data_config(config: Dict): - data_meta = {} - # defaults = _const.data_defaults(config) - - load_data_keys = [] - for k in config: - if k.startswith('load_') and k.endswith('_path'): - load_data_keys.append(k) - - for load_data_key in load_data_keys: - if load_data_key in config.keys(): - inp = config[load_data_key] - extended = [] - if type(inp) not in [str, list]: - raise ValueError(f'unexpected input {inp} for sturcture_list') - if type(inp) is str: - extended = glob.glob(inp) - elif type(inp) is list: - for i in inp: - if isinstance(i, str): - extended.extend(glob.glob(i)) - elif isinstance(i, dict): - extended.append(i) - if len(extended) == 0: - raise ValueError( - f'Cannot find {inp} for {load_data_key}' - + ' or path is not given' - ) - data_meta[load_data_key] = extended - else: - data_meta[load_data_key] = False - - for key, default in _const.DEFAULT_DATA_CONFIG.items(): - data_meta[key] = config_initialize( - key, config, default, _const.DATA_CONFIG_CONDITION - ) - - unknown_keys = [ - key for key in config.keys() if key not in data_meta.keys() - ] - if len(unknown_keys) != 0: - warnings.warn( - f'Unexpected data keys: {unknown_keys} will be ignored', - UserWarning, - ) - return data_meta - - -def read_config_yaml(filename: str, return_separately: bool = False): - with open(filename, 'r') as fstream: - inputs = yaml.safe_load(fstream) - - model_meta, train_meta, data_meta = {}, {}, {} - for key, config in inputs.items(): - if key == 'model': - model_meta = init_model_config(config) - elif key == 'train': - train_meta = init_train_config(config) - elif key == 'data': - data_meta = init_data_config(config) - else: - raise ValueError(f'Unexpected input {key} given') - - if return_separately: - return model_meta, train_meta, data_meta - else: - model_meta.update(train_meta) - model_meta.update(data_meta) - return model_meta - - -def main(): - filename = './input.yaml' - read_config_yaml(filename) - - -if __name__ == '__main__': - main() diff --git a/mace-bench/3rdparty/SevenNet/sevenn/presets/MF_0.yaml b/mace-bench/3rdparty/SevenNet/sevenn/presets/MF_0.yaml deleted file mode 100644 index d31a8fc3008a56eaaa73f8e85eebdc4c028d0453..0000000000000000000000000000000000000000 --- a/mace-bench/3rdparty/SevenNet/sevenn/presets/MF_0.yaml +++ /dev/null @@ -1,108 +0,0 @@ -model: - chemical_species: 'univ' # Ready for 119 elements - cutoff: 5.0 - channel: 128 - is_parity: False - lmax: 2 - num_convolution_layer: 5 - irreps_manual: - - "128x0e" - - "128x0e+64x1e+32x2e" - - "128x0e+64x1e+32x2e" - - "128x0e+64x1e+32x2e" - - "128x0e+64x1e+32x2e" - - "128x0e" - - weight_nn_hidden_neurons: [64, 64] - radial_basis: - radial_basis_name: 'bessel' - bessel_basis_num: 8 - cutoff_function: - cutoff_function_name: 'XPLOR' - cutoff_on: 4.5 - - act_gate: {'e': 'silu', 'o': 'tanh'} - act_scalar: {'e': 'silu', 'o': 'tanh'} - - conv_denominator: 'avg_num_neigh' - train_shift_scale: False - train_denominator: False - self_connection_type: 'linear' - - # Following are used to specify which part of the model would utilize fidelity-dependent parameters for multi-fidelity training. - # For detailed architecture, please refer to https://arxiv.org/abs/2409.07947 - # Parts using fidelity-dependent weights are indicated as `Modified linear` layers in Figure 1. - use_modal_node_embedding: False # If true, use modified linear layer in atom-type embedding layer. - use_modal_self_inter_intro: True # If true, use modified linear layers in self-interaction block before the convolution in the interaction blocks. - use_modal_self_inter_outro: True # If true, use modified linear layers in self-interaction block after the convolution in the interaction blocks. - use_modal_output_block: True # If true, use modified linear layer in the output block. -train: - train_shuffle: True - random_seed: 777 - is_train_stress : True - epoch: 200 - - loss: 'Huber' - loss_param: - delta: 0.01 - - optimizer: 'adam' - optim_param: - lr: 0.01 - scheduler: 'linearlr' - scheduler_param: - start_factor: 1.0 - total_iters: 200 - end_factor: 0.0001 - - force_loss_weight : 1.00 - stress_loss_weight: 0.01 - - error_record: - - ['Energy', 'MAE'] - - ['Force', 'MAE'] - - ['Stress', 'MAE'] - - ['Energy', 'Loss'] - - ['Force', 'Loss'] - - ['Stress', 'Loss'] - - ['TotalLoss', 'None'] - - per_epoch: 10 - use_modality: True - use_weight: True - -data: - batch_size: 64 - shift: 'elemwise_reference_energies' - scale: 1.73 - - use_modal_wise_shift: True # If true, use different atomic energy shift for each database - use_modal_wise_scale: False # If true, use different atomic energy scale for each database - - load_trainset_path: - - - data_modality: pbe # Name of database - file_list: - - file: "**path to PBE database**" # ASE readable or .pt file (graph.pt) - data_weight: - energy: 1.0 - force: 1.0 # This weight would be additionally multiplied to `force_loss_weight` for this database - stress: 1.0 # This weight would be additionally multiplied to `stress_loss_weight` for this database - - - data_modality: r2scan - file_list: - - file: "**path to r2SCAN database**" - data_weight: - energy: 7.0 - force: 7.0 - stress: 7.0 - - load_pbe_validset_path: # any name starts with 'load' and ends with 'set_path' - - data_modality: pbe # modality must be given for mm valid set - file_list: - - file: "**path to PBE test set**" - - load_scan_validset_path: - - data_modality: r2scan - file_list: - - file: "**path to r2SCAN test set**" diff --git a/mace-bench/3rdparty/SevenNet/sevenn/presets/base.yaml b/mace-bench/3rdparty/SevenNet/sevenn/presets/base.yaml deleted file mode 100644 index 44fff1d8358ee723a5007aa1a51e941bcb0acd1e..0000000000000000000000000000000000000000 --- a/mace-bench/3rdparty/SevenNet/sevenn/presets/base.yaml +++ /dev/null @@ -1,91 +0,0 @@ -# Example input.yaml for training SevenNet. -# '*' signifies default. You can check log.sevenn for defaults. - -model: - chemical_species: 'Auto' # Elements model should know. [ 'Univ' | 'Auto' | manual_user_input ] - cutoff: 5.0 # Cutoff radius in Angstroms. If two atoms are within the cutoff, they are connected. - channel: 32 # The multiplicity(channel) of node features. - lmax: 2 # Maximum order of irreducible representations (rotation order). - num_convolution_layer: 3 # The number of message passing layers. - - #irreps_manual: # Manually set irreps of the model in each layer - #- "128x0e" - #- "128x0e+64x1e+32x2e" - #- "128x0e+64x1e+32x2e" - #- "128x0e+64x1e+32x2e" - #- "128x0e+64x1e+32x2e" - #- "128x0e" - - weight_nn_hidden_neurons: [64, 64] # Hidden neurons in convolution weight neural network - radial_basis: # Function and its parameters to encode radial distance - radial_basis_name: 'bessel' # Only 'bessel' is currently supported - bessel_basis_num: 8 - cutoff_function: # Envelop function, multiplied to radial_basis functions to init edge features - cutoff_function_name: 'poly_cut' # {'poly_cut' and 'poly_cut_p_value'} or {'XPLOR' and 'cutoff_on'} - poly_cut_p_value: 6 - - act_gate: {'e': 'silu', 'o': 'tanh'} # Equivalent to 'nonlinearity_gates' in nequip - act_scalar: {'e': 'silu', 'o': 'tanh'} # Equivalent to 'nonlinearity_scalars' in nequip - - is_parity: False # Pairy True (E(3) group) or False (to SE(3) group) - - self_connection_type: 'nequip' # Default is 'nequip'. 'linear' is used for SevenNet-0. I recommend 'linear' for 'Univ' chemical_species - - conv_denominator: "avg_num_neigh" # Valid options are "avg_num_neigh*", "sqrt_avg_num_neigh", or float - train_denominator: False # Enable training for denominator in convolution layer - train_shift_scale: False # Enable training for shift & scale in output layer - -train: - random_seed: 1 - is_train_stress: True # Includes stress in the loss function - epoch: 200 # Ends training after this number of epochs - - #loss: 'Huber' # Default is 'mse' (mean squared error) - #loss_param: - #delta: 0.01 - - # Each optimizer and scheduler have different available parameters. - # You can refer to sevenn/train/optim.py for supporting optimizer & schedulers - optimizer: 'adam' # Options available are 'sgd', 'adagrad', 'adam', 'adamw', 'radam' - optim_param: - lr: 0.005 - scheduler: 'exponentiallr' # 'steplr', 'multisteplr', 'exponentiallr', 'cosineannealinglr', 'reducelronplateau', 'linearlr' - scheduler_param: - gamma: 0.99 - - force_loss_weight: 0.1 # Coefficient for force loss - stress_loss_weight: 1e-06 # Coefficient for stress loss (to kbar unit) - - per_epoch: 10 # Generate checkpoints every this epoch - - # ['target y', 'metric'] - # Target y: TotalEnergy, Energy, Force, Stress, Stress_GPa, TotalLoss - # Metric : RMSE, MAE, or Loss - error_record: - - ['Energy', 'RMSE'] - - ['Force', 'RMSE'] - - ['Stress', 'RMSE'] - - ['TotalLoss', 'None'] - - # Continue training model from given checkpoint, or pre-trained model checkpoint for fine-tuning - #continue: - #checkpoint: 'checkpoint_best.pth' # Checkpoint of pre-trained model or a model want to continue training. - #reset_optimizer: False # Set True for fine-tuning - #reset_scheduler: False # Set True for fine-tuning - -data: - batch_size: 4 # Per GPU batch size. - - shift: 'per_atom_energy_mean' # One of 'per_atom_energy_mean*', 'elemwise_reference_energies', float - scale: 'force_rms' # One of 'force_rms*', 'per_atom_energy_std', float - - # SevenNet automatically matches data format from its filename. - # For those not `structure_list` or `.pt` files, assumes it is ASE readable - # In this case, below arguments are directly passed to `ase.io.read` - data_format_args: - index: ':' # see `https://wiki.fysik.dtu.dk/ase/ase/io/io.html` for more valid arguments - - # validset is needed if you want '_best.pth' during training. If not, both validset and testset is optional. - load_trainset_path: ['./train_*.extxyz'] # Example of using ase as data_format, support multiple files and expansion(*) - load_validset_path: ['./valid.extxyz'] - load_testset_path: ['./sevenn_data/mydata.pt'] # Graph can be preprocessed using `sevenn_graph_build` and accessible like this diff --git a/mace-bench/3rdparty/SevenNet/sevenn/presets/fine_tune.yaml b/mace-bench/3rdparty/SevenNet/sevenn/presets/fine_tune.yaml deleted file mode 100644 index 7045b83a3e71e90703daddb35f03ef677faf28c7..0000000000000000000000000000000000000000 --- a/mace-bench/3rdparty/SevenNet/sevenn/presets/fine_tune.yaml +++ /dev/null @@ -1,80 +0,0 @@ -# Example input.yaml for fine-tuning sevennet-0 -# '*' signifies default. You can check log.sevenn for defaults. - -model: # model keys should be consistent except for train_* keys - chemical_species: 'Auto' - cutoff: 5.0 - channel: 128 - is_parity: False - lmax: 2 - num_convolution_layer: 5 - irreps_manual: - - "128x0e" - - "128x0e+64x1e+32x2e" - - "128x0e+64x1e+32x2e" - - "128x0e+64x1e+32x2e" - - "128x0e+64x1e+32x2e" - - "128x0e" - - weight_nn_hidden_neurons: [64, 64] - radial_basis: - radial_basis_name: 'bessel' - bessel_basis_num: 8 - cutoff_function: - cutoff_function_name: 'XPLOR' - cutoff_on: 4.5 - self_connection_type: 'linear' - - train_shift_scale: False # customizable (True | False) - train_denominator: False # customizable (True | False) - -train: # Customizable - random_seed: 1 - is_train_stress: True - epoch: 100 - - loss: 'Huber' # keeping original loss function give better ft result - loss_param: - delta: 0.01 - - optimizer: 'adam' - optim_param: - lr: 0.004 - scheduler: 'exponentiallr' - scheduler_param: - gamma: 0.99 - - force_loss_weight: 1.0 - stress_loss_weight: 0.01 - - per_epoch: 10 # Generate checkpoints every this epoch - - # ['target y', 'metric'] - # Target y: TotalEnergy, Energy, Force, Stress, Stress_GPa, TotalLoss - # Metric : RMSE, MAE, or Loss - error_record: - - ['Energy', 'RMSE'] - - ['Force', 'RMSE'] - - ['Stress', 'RMSE'] - - ['TotalLoss', 'None'] - - continue: - reset_optimizer: True - reset_scheduler: True - reset_epoch: True - checkpoint: 'SevenNet-0_11July2024' - -data: # Customizable - batch_size: 4 - data_divide_ratio: 0.1 - - # SevenNet automatically matches data format from its filename. - # For those not `structure_list` or `.pt` files, assumes it is ASE readable - # In this case, below arguments are directly passed to `ase.io.read` - data_format_args: - index: ':' # see `https://wiki.fysik.dtu.dk/ase/ase/io/io.html` for more valid arguments - - # validset is needed if you want '_best.pth' during training. If not, both validset and testset is optional. - load_trainset_path: ['./train_*.extxyz'] # Example of using ase as data_format, support multiple files and expansion(*) - load_validset_path: ['./valid.extxyz'] - load_testset_path: ['./sevenn_data/mydata.pt'] # Graph can be preprocessed using `sevenn_graph_build` and accessible like this diff --git a/mace-bench/3rdparty/SevenNet/sevenn/presets/fine_tune_le.yaml b/mace-bench/3rdparty/SevenNet/sevenn/presets/fine_tune_le.yaml deleted file mode 100644 index 0e4fc6b28590d0b64c6c1baeb07fd214d860fa3d..0000000000000000000000000000000000000000 --- a/mace-bench/3rdparty/SevenNet/sevenn/presets/fine_tune_le.yaml +++ /dev/null @@ -1,83 +0,0 @@ -# Application of 7net-0 on liquid electrolyte system via fine-tuning -# Paper: https://arxiv.org/abs/2501.05211 - -model: - # parameters of SevenNet-0, should not be changed - chemical_species: 'auto' - cutoff: 5.0 - channel: 128 - is_parity: False - lmax: 2 - num_convolution_layer: 5 - irreps_manual: - - "128x0e" - - "128x0e+64x1e+32x2e" - - "128x0e+64x1e+32x2e" - - "128x0e+64x1e+32x2e" - - "128x0e+64x1e+32x2e" - - "128x0e" - weight_nn_hidden_neurons: [64, 64] - radial_basis: - radial_basis_name: 'bessel' - bessel_basis_num: 8 - cutoff_function: - cutoff_function_name: 'XPLOR' - cutoff_on: 4.5 - - act_gate: {'e': 'silu', 'o': 'tanh'} - act_scalar: {'e': 'silu', 'o': 'tanh'} - - self_connection_type: 'linear' - - # useful for fine-tuning - train_shift_scale: True - train_avg_num_neigh: True - -train: - random_seed: 1 - is_train_stress: True - epoch: 100 # we went through 100 epochs and chose checkpoint at 50 epoch where the error have reached plateau. - - loss: 'Huber' - loss_param: - delta: 0.01 - - optimizer: 'adam' - optim_param: - lr: 0.0001 - scheduler: 'linearlr' - scheduler_param: - start_factor: 1.0 - total_iters: 600 - end_factor: 0.000001 - - force_loss_weight: 1.00 - stress_loss_weight: 1.00 # 7net-0 quantitatively lacked accuracy on pressure histograms compared to DFT, so we increased stress loss weight - - error_record: - - ['Energy', 'RMSE'] - - ['Force', 'RMSE'] - - ['Stress', 'RMSE'] - - ['Energy', 'MAE'] - - ['Force', 'MAE'] - - ['Stress', 'MAE'] - - ['Energy', 'Loss'] - - ['Force', 'Loss'] - - ['Stress', 'Loss'] - - ['TotalLoss', 'None'] - - per_epoch: 10 # Generate epoch every this number of times - - continue: - use_statistic_values_of_checkpoint: True - checkpoint: '7net-0' # fine-tuning from 7net-0 - reset_optimizer: True - reset_scheduler: True - -data: - batch_size: 1 # our fine-tuning dataset had ~360 atoms per structure, so we used batch size of 1 to avoid GPU OOM error. - shift: 'elemwise_reference_energies' - scale: 1.858 - data_format: 'ase' - data_divide_ratio: 0.05 - load_dataset_path: ["./data/total.extxyz"] diff --git a/mace-bench/3rdparty/SevenNet/sevenn/presets/multi_modal.yaml b/mace-bench/3rdparty/SevenNet/sevenn/presets/multi_modal.yaml deleted file mode 100644 index 9af335c76ccf6a764fc0ea8aecc27421bc0c5c23..0000000000000000000000000000000000000000 --- a/mace-bench/3rdparty/SevenNet/sevenn/presets/multi_modal.yaml +++ /dev/null @@ -1,106 +0,0 @@ -model: - chemical_species: 'univ' # Ready for 119 elements - cutoff: 6.0 - channel: 128 - is_parity: False - lmax: 3 - num_convolution_layer: 3 - irreps_manual: - - "128x0e" - - "128x0e+64x1e+32x2e+16x3e" - - "128x0e+64x1e+32x2e+16x3e" - - "128x0e" - - weight_nn_hidden_neurons: [64, 64] - radial_basis: - radial_basis_name: 'bessel' - bessel_basis_num: 8 - cutoff_function: - cutoff_function_name: 'XPLOR' - cutoff_on: 5.5 - - act_gate: {'e': 'silu', 'o': 'tanh'} - act_scalar: {'e': 'silu', 'o': 'tanh'} - - conv_denominator: 'avg_num_neigh' - train_shift_scale: True - train_denominator: False - self_connection_type: 'linear' - - # Following are used to specify which part of the model would utilize fidelity-dependent parameters for multi-fidelity training. - # For detailed architecture, please refer to https://arxiv.org/abs/2409.07947 - # Parts using fidelity-dependent weights are indicated as `Modified linear` layers in Figure 1. - use_modal_node_embedding: False # If true, use modified linear layer in atom-type embedding layer. - use_modal_self_inter_intro: True # If true, use modified linear layers in self-interaction block before the convolution in the interaction blocks. - use_modal_self_inter_outro: True # If true, use modified linear layers in self-interaction block after the convolution in the interaction blocks. - use_modal_output_block: True # If true, use modified linear layer in the output block. -train: - train_shuffle: True - random_seed: 777 - is_train_stress : True - epoch: 200 - - loss: 'Huber' - loss_param: - delta: 0.01 - - optimizer: 'adam' - optim_param: - lr: 0.01 - scheduler: 'linearlr' - scheduler_param: - start_factor: 1.0 - total_iters: 200 - end_factor: 0.0001 - - force_loss_weight : 1.00 - stress_loss_weight: 0.01 - - error_record: - - ['Energy', 'MAE'] - - ['Force', 'MAE'] - - ['Stress', 'MAE'] - - ['Energy', 'Loss'] - - ['Force', 'Loss'] - - ['Stress', 'Loss'] - - ['TotalLoss', 'None'] - - per_epoch: 10 - use_modality: True - use_weight: True - -data: - batch_size: 16 - shift: 'elemwise_reference_energies' - scale: 'force_rms' - - use_modal_wise_shift: True # If true, use different atomic energy shift for each database - use_modal_wise_scale: False # If true, use different atomic energy scale for each database - - load_trainset_path: - - - data_modality: pbe # Name of database - file_list: - - file: "path to pbe dataset" # ASE readable or .pt file (graph.pt) - data_weight: - energy: 1.0 - force: 0.1 # This weight would be additionally multiplied to `force_loss_weight` for this database - stress: 1.0 # This weight would be additionally multiplied to `stress_loss_weight` for this database - - - data_modality: scan - file_list: - - file: "path to scan dataset" - data_weight: - energy: 1.0 - force: 10.0 - stress: 1.0 - - load_pbe_validset_path: # any name starts with 'load' and ends with 'set_path' - - data_modality: pbe # modality must be given for mm valid set - file_list: - - file: "path to pbe validset" - - load_scan_validset_path: - - data_modality: scan - file_list: - - file: "path to scan validset" diff --git a/mace-bench/3rdparty/SevenNet/sevenn/presets/sevennet-0.yaml b/mace-bench/3rdparty/SevenNet/sevenn/presets/sevennet-0.yaml deleted file mode 100644 index e0a540ccc7f828d73453676f661ecd8874c1c27f..0000000000000000000000000000000000000000 --- a/mace-bench/3rdparty/SevenNet/sevenn/presets/sevennet-0.yaml +++ /dev/null @@ -1,79 +0,0 @@ -# SevenNet-0, should be run with `sevenn -m train_v1` as it uses old routine -model: - chemical_species: 'auto' - cutoff: 5.0 - channel: 128 - is_parity: False - lmax: 2 - num_convolution_layer: 5 - irreps_manual: - - "128x0e" - - "128x0e+64x1e+32x2e" - - "128x0e+64x1e+32x2e" - - "128x0e+64x1e+32x2e" - - "128x0e+64x1e+32x2e" - - "128x0e" - - weight_nn_hidden_neurons: [64, 64] - radial_basis: - radial_basis_name: 'bessel' - bessel_basis_num: 8 - cutoff_function: - cutoff_function_name: 'XPLOR' - cutoff_on: 4.5 - - act_gate: {'e': 'silu', 'o': 'tanh'} - act_scalar: {'e': 'silu', 'o': 'tanh'} - - conv_denominator: 'avg_num_neigh' - train_shift_scale: False - train_denominator: False - self_connection_type: 'linear' -train: - train_shuffle: False - random_seed: 1 - is_train_stress : True - epoch: 600 - - loss: 'Huber' - loss_param: - delta: 0.01 - - optimizer: 'adam' - optim_param: - lr: 0.01 - scheduler: 'linearlr' - scheduler_param: - start_factor: 1.0 - total_iters: 600 - end_factor: 0.0001 - - force_loss_weight : 1.00 - stress_loss_weight: 0.01 - - error_record: - - ['Energy', 'RMSE'] - - ['Force', 'RMSE'] - - ['Stress', 'RMSE'] - - ['Energy', 'MAE'] - - ['Force', 'MAE'] - - ['Stress', 'MAE'] - - ['Energy', 'Loss'] - - ['Force', 'Loss'] - - ['Stress', 'Loss'] - - ['TotalLoss', 'None'] - - per_epoch: 10 - # continue: - # checkpoint: './checkpoint_last.pth' - # reset_optimizer: False - # reset_scheduler: False -data: - batch_size: 128 # per GPU batch size, as the model trained with 32 GPUs, the effective batch size equals 4096. - scale: 'per_atom_energy_std' - shift: 'elemwise_reference_energies' - - data_format: 'ase' - save_by_train_valid: False - load_dataset_path: ["path_to_MPtrj_total.sevenn_data"] - load_validset_path: ["validaset.sevenn_data"] diff --git a/mace-bench/3rdparty/SevenNet/sevenn/presets/sevennet-l3i5.yaml b/mace-bench/3rdparty/SevenNet/sevenn/presets/sevennet-l3i5.yaml deleted file mode 100644 index d8c0fb66b87d87fad61fbea88b776f1bfb4fdd8f..0000000000000000000000000000000000000000 --- a/mace-bench/3rdparty/SevenNet/sevenn/presets/sevennet-l3i5.yaml +++ /dev/null @@ -1,92 +0,0 @@ -model: - chemical_species: auto - - cutoff: 5.0 - irreps_manual: - - 128x0e - - 128x0e+64x1e+32x2e+32x3e - - 128x0e+64x1e+32x2e+32x3e - - 128x0e+64x1e+32x2e+32x3e - - 128x0e+64x1e+32x2e+32x3e - - 128x0e - channel: 128 - lmax: 3 - num_convolution_layer: 5 - is_parity: false - radial_basis: - radial_basis_name: bessel - bessel_basis_num: 8 - cutoff_function: - cutoff_function_name: poly_cut - poly_cut_p_value: 6 - - act_radial: silu - weight_nn_hidden_neurons: - - 64 - - 64 - act_scalar: - e: silu - o: tanh - act_gate: - e: silu - o: tanh - - train_denominator: false - train_shift_scale: false - use_bias_in_linear: false - - readout_as_fcn: false - self_connection_type: linear - interaction_type: nequip - -train: - random_seed: 1 - epoch: 600 - loss: Huber - loss_param: - delta: 0.01 - optimizer: adam - optim_param: - lr: 0.01 - scheduler: linearlr - scheduler_param: - start_factor: 1.0 - total_iters: 600 - end_factor: 0.0001 - force_loss_weight: 1.0 - stress_loss_weight: 0.01 - per_epoch: 10 - is_train_stress: true - train_shuffle: true - error_record: - - - Energy - - MAE - - - Energy - - RMSE - - - Force - - MAE - - - Force - - RMSE - - - Stress - - MAE - - - Stress - - RMSE - - - Energy - - Loss - - - Force - - Loss - - - Stress - - Loss - - - TotalLoss - - None - best_metric: TotalLoss -data: - data_format: ase - data_format_args: {} - - batch_size: 1024 # global batch size, should be divided by the number of GPUs - - load_trainset_path: '**path_to_trainset**' - load_validset_path: '**path_to_validset**' - shift: 'elemwise_reference_energies' - scale: 'force_rms' diff --git a/mace-bench/3rdparty/SevenNet/sevenn/py.typed b/mace-bench/3rdparty/SevenNet/sevenn/py.typed deleted file mode 100644 index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000 diff --git a/mace-bench/3rdparty/SevenNet/sevenn/scripts/__init__.py b/mace-bench/3rdparty/SevenNet/sevenn/scripts/__init__.py deleted file mode 100644 index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000 diff --git a/mace-bench/3rdparty/SevenNet/sevenn/scripts/backward_compatibility.py b/mace-bench/3rdparty/SevenNet/sevenn/scripts/backward_compatibility.py deleted file mode 100644 index b8e81b1a07ae31f97ec06983312f496e05e80198..0000000000000000000000000000000000000000 --- a/mace-bench/3rdparty/SevenNet/sevenn/scripts/backward_compatibility.py +++ /dev/null @@ -1,184 +0,0 @@ -""" -Debt -keep old pre-trained checkpoints unchanged. -""" - -import copy - -import torch - -import sevenn._keys as KEY - - -def version_tuple(v1): - v1 = tuple(map(int, v1.split('.'))) - return v1 - - -def patch_old_config(config): - version = config.get('version', None) - if not version: - raise ValueError('No version found in config') - - major, minor, _ = version.split('.')[:3] - major, minor = int(major), int(minor) - - if major == 0 and minor <= 9: - if config[KEY.CUTOFF_FUNCTION][KEY.CUTOFF_FUNCTION_NAME] == 'XPLOR': - config[KEY.CUTOFF_FUNCTION].pop('poly_cut_p_value', None) - if KEY.TRAIN_DENOMINTAOR not in config: - config[KEY.TRAIN_DENOMINTAOR] = config.pop('train_avg_num_neigh', False) - _opt = config.pop('optimize_by_reduce', None) - if _opt is False: - raise ValueError( - 'This checkpoint(optimize_by_reduce: False) is no longer supported' - ) - if KEY.CONV_DENOMINATOR not in config: - config[KEY.CONV_DENOMINATOR] = 0.0 - if KEY._NORMALIZE_SPH not in config: - config[KEY._NORMALIZE_SPH] = False - - return config - - -def map_old_model(old_model_state_dict): - """ - For compatibility with old namings (before 'correct' branch merged 2404XX) - Map old model's module names to new model's module names - """ - _old_module_name_mapping = { - 'EdgeEmbedding': 'edge_embedding', - 'reducing nn input to hidden': 'reduce_input_to_hidden', - 'reducing nn hidden to energy': 'reduce_hidden_to_energy', - 'rescale atomic energy': 'rescale_atomic_energy', - } - for i in range(10): - _old_module_name_mapping[f'{i} self connection intro'] = ( - f'{i}_self_connection_intro' - ) - _old_module_name_mapping[f'{i} convolution'] = f'{i}_convolution' - _old_module_name_mapping[f'{i} self interaction 2'] = ( - f'{i}_self_interaction_2' - ) - _old_module_name_mapping[f'{i} equivariant gate'] = f'{i}_equivariant_gate' - - new_model_state_dict = {} - for k, v in old_model_state_dict.items(): - key_name = k.split('.')[0] - follower = '.'.join(k.split('.')[1:]) - if 'denumerator' in follower: - follower = follower.replace('denumerator', 'denominator') - if key_name in _old_module_name_mapping: - new_key_name = _old_module_name_mapping[key_name] + '.' + follower - new_model_state_dict[new_key_name] = v - else: - new_model_state_dict[k] = v - return new_model_state_dict - - -def sort_old_convolution(model_now, state_dict): - from e3nn.o3 import wigner_3j - - """ - Reason1: we have to sort instructions of convolution to be compatible with - cuEquivariance. (therefore, sort weight) - Reason2: some of old convolution module's w3j coeff has flipped sign. This also - has to be fixed to be compatible with cuEquivarinace. - """ - - def patch(stct): - inst_old = copy.copy(conv._instructions_before_sort) - inst_old = [(inst[0], inst[1], inst[2]) for inst in inst_old] - del conv._instructions_before_sort - - conv_args = conv.convolution_kwargs - irreps_in1 = conv_args['irreps_in1'] - irreps_in2 = conv_args['irreps_in2'] - irreps_out = conv_args.get('irreps_out', conv_args.get('filter_irreps_out')) - - inst_sorted = sorted(inst_old, key=lambda x: x[2]) - - inst_sorted = [ - # in1, in2, out, weights - (inst[0], inst[1], inst[2], irreps_in1[inst[0]].mul) - for inst in inst_sorted - ] - - n = len(weight_nn.hs) - 2 - ww_key = f'{conv_key}.weight_nn.layer{n}.weight' - ww = stct[ww_key] - ww_sorted = [None] * len(inst_old) - - _prev_idx = 0 - for ist_src in inst_old: - for j, ist_dst in enumerate(inst_sorted): - if not all(ist_src[ii] == ist_dst[ii] for ii in range(3)): - continue - - numel = ist_dst[3] # weight num - ww_src = ww[:, _prev_idx : _prev_idx + numel] - l1, l2, l3 = ( - irreps_in1[ist_src[0]].ir.l, - irreps_in2[ist_src[1]].ir.l, - irreps_out[ist_src[2]].ir.l, - ) - if l1 > 0 and l2 > 0 and l3 > 0: - w3j_key = f'_w3j_{l1}_{l2}_{l3}' - conv_w3j_key = ( - f'{conv_key}.convolution._compiled_main_left_right.{w3j_key}' - ) - w3j_old = stct[conv_w3j_key] - w3j_now = wigner_3j(l1, l2, l3) - if not torch.allclose(w3j_old.to(w3j_now.device), w3j_now): - assert torch.allclose( - w3j_old.to(w3j_now.device), -1 * w3j_now - ) - ww_src = -1 * ww_src - stct[conv_w3j_key] *= -1 # stct updated - _prev_idx += numel - ww_sorted[j] = ww_src - ww_sorted = torch.cat(ww_sorted, dim=1) # type: ignore - stct[ww_key] = ww_sorted.clone() # stct updated - - conv_dicts = {} - for k, v in state_dict.items(): - key_name = k.split('.')[0] - if key_name.split('_')[1] == 'convolution': - if key_name not in conv_dicts: - conv_dicts[key_name] = {} - conv_dicts[key_name].update({k: v}) - - new_state_dict = {} - new_state_dict.update(state_dict) - for conv_key, conv_state_dict in conv_dicts.items(): - conv = model_now._modules[conv_key] - weight_nn = conv.weight_nn - patch(conv_state_dict) - new_state_dict.update(conv_state_dict) - - return new_state_dict - - -def patch_state_dict_if_old(state_dict, config_cp, now_model): - version = config_cp.get('version', None) - if not version: - raise ValueError('No version found in config') - vs = version.split('.') - vsuffix = '' - if len(vs) == 4: - vsuffix = vs[-1] - vs = version_tuple('.'.join(vs[:3])) - else: - vs = version_tuple('.'.join(vs)) - - if vs < version_tuple('0.10.0'): - state_dict = map_old_model(state_dict) - - # TODO: change version criteria before release!!! - # it causes problem if model is sorted but this function is called - # ... more robust way? idk - if vs < version_tuple('0.11.0') or ( - vs == version_tuple('0.11.0') and vsuffix == 'dev0' - ): - state_dict = sort_old_convolution(now_model, state_dict) - return state_dict diff --git a/mace-bench/3rdparty/SevenNet/sevenn/scripts/convert_model_modality.py b/mace-bench/3rdparty/SevenNet/sevenn/scripts/convert_model_modality.py deleted file mode 100644 index 5581e19661ddea5a90f6e5fd2ee7f1b0fa239845..0000000000000000000000000000000000000000 --- a/mace-bench/3rdparty/SevenNet/sevenn/scripts/convert_model_modality.py +++ /dev/null @@ -1,301 +0,0 @@ -import math -from typing import List - -import torch -import torch.nn as nn -from e3nn.o3 import Irreps, Linear - -import sevenn._keys as KEY -from sevenn.model_build import build_E3_equivariant_model - -modal_module_dict = { - KEY.USE_MODAL_NODE_EMBEDDING: 'onehot_to_feature_x', - KEY.USE_MODAL_SELF_INTER_INTRO: 'self_interaction_1', - KEY.USE_MODAL_SELF_INTER_OUTRO: 'self_interaction_2', - KEY.USE_MODAL_OUTPUT_BLOCK: 'reduce_input_to_hidden', -} - - -def _get_scalar_index(irreps: Irreps): - scalar_indices = [] - for idx, (_, (l, p)) in enumerate(irreps): # noqa - if ( - l == 0 and p == 1 - ): # get index of parameter for scalar (0e), which is used for modality - scalar_indices.append(idx) - - return scalar_indices - - -def _reshape_weight_of_linear( - irreps_in: Irreps, irreps_out: Irreps, weight: torch.Tensor -) -> List[torch.Tensor]: - linear = Linear(irreps_in, irreps_out) - linear.weight = nn.Parameter(weight) - return list(linear.weight_views()) - - -def _erase_linear_modal_params( - model_state_dct: dict, - erase_modal_indices: List[int], - key: str, - irreps_in: Irreps, - irreps_out: Irreps, -): - orig_input_dim = irreps_in.count('0e') - new_input_dim = orig_input_dim - len(erase_modal_indices) - - orig_weight = model_state_dct[key + '.linear.weight'] - scalar_idx = _get_scalar_index(irreps_in) - linear_weight_list = _reshape_weight_of_linear( - irreps_in, irreps_out, orig_weight - ) - - new_weight_list = [] - - for idx, l_p_weight in enumerate(linear_weight_list[:-1]): - new_weight = torch.reshape(l_p_weight, (1, -1)).squeeze() - if idx in scalar_idx: - new_weight = new_weight * math.sqrt(new_input_dim / orig_input_dim) - - new_weight_list.append(new_weight) - - """ - Following works for normalization = `path`, which is not used in SEVENNet - for l_p_weight in linear_weight_list[:-1]: - new_weight_list.append(torch.reshape(l_p_weight, (1, -1)).squeeze()) - """ - - flattened_weight = torch.cat(new_weight_list) - - return flattened_weight - - -def _get_modal_weight_as_bias( - model_state_dct: dict, - key: str, - ref_index: int, - irreps_in: Irreps, - irreps_out: Irreps, -): - assert ref_index != -1 - input_dim = irreps_in.count('0e') - output_dim = irreps_out.count('0e') - orig_weight = model_state_dct[key + '.linear.weight'] - orig_bias = model_state_dct[key + '.linear.bias'] - if len(orig_bias) == 0: - orig_bias = torch.zeros(output_dim, dtype=orig_weight.dtype) - - modal_weight = _reshape_weight_of_linear( - irreps_in, irreps_out, orig_weight - )[-1] - - new_bias = orig_bias + modal_weight[ref_index] / math.sqrt(input_dim) - - return new_bias - - -def _append_modal_weight( - model_state_dct: dict, # state dict to be targeted - key: str, # linear weight modune name - irreps_in: Irreps, # irreps_in before modality append - irreps_out: Irreps, - append_number: int, -): - # This works for normalization = `element`, default in SEVENNet. - # (normalization = `path` is curruently deprecated in SEVENNet.) - input_dim = irreps_in.count('0e') - output_dim = irreps_out.count('0e') - new_input_dim = input_dim + append_number - orig_weight = model_state_dct[key + '.linear.weight'] - scalar_idx = _get_scalar_index(irreps_in) - linear_weight_list = _reshape_weight_of_linear( - irreps_in, irreps_out, orig_weight - ) - - new_weight_list = [] - - # TODO: combine following as function with _erase_linear_modal_params - - for idx, l_p_weight in enumerate(linear_weight_list): - new_weight = torch.reshape(l_p_weight, (1, -1)).squeeze() - if idx in scalar_idx: - new_weight = new_weight * math.sqrt(new_input_dim / input_dim) - - new_weight_list.append(new_weight) - - flattened_weight_list = [] - for l_p_weight in new_weight_list: - flattened_weight_list.append( - torch.reshape(l_p_weight, (1, -1)).squeeze() - ) - flattened_weight = torch.cat(flattened_weight_list) - - append_weight = torch.cat([ - flattened_weight, - torch.zeros(append_number * output_dim, dtype=flattened_weight.dtype), - ]) # zeros: starting from common model - - return append_weight - - -def get_single_modal_model_dct( - model_state_dct: dict, - config: dict, - ref_modal: str, - from_processing_cp: bool = False, - is_deploy: bool = False, -): - """ - Convert multimodal model state dictionary to single modal model. - Modal is selected by `ref_modal` - - `model_state_dct`: model state dictionary from multimodal checkpoint file - `config`: dictionary containing configuration of the checkpoint model - `ref_modal`: modal that are going to be converted - `from_processing_cp`: if True, use modal_map of the checkpoint file - `is_deploy`: if True, model is build with single-modal shift and scale - """ - if ( - not from_processing_cp and not config[KEY.USE_MODALITY] - ): # model is already single modal - return model_state_dct - - config[KEY.USE_BIAS_IN_LINEAR] = True - config['_deploy'] = is_deploy - - model = build_E3_equivariant_model(config) - del config['_deploy'] - key_add = '_cp' if from_processing_cp else '' - modal_type_dict = config[KEY.MODAL_MAP + key_add] - erase_modal_indices = range(len(modal_type_dict.keys())) # starts with 0 - - if ref_modal != 'common': - try: - ref_modal_index = modal_type_dict[ref_modal] - except: - raise KeyError( - f'{ref_modal} not in modal type. Use one of' - f' {modal_type_dict.keys()}.' - ) - - for module_key in model._modules.keys(): - for ( - use_modal_module_key, - modal_module_name, - ) in modal_module_dict.items(): - irreps_out = Irreps(model.get_irreps_in(module_key, 'irreps_out')) - # TODO: directly using "irreps_in" might not be compatible - # when changing `nn/linear.py` - output_dim = irreps_out.count('0e') - if ( - config[use_modal_module_key] - and modal_module_name in module_key - ): # this module is used for giving modality - - irreps_in = Irreps( - model.get_irreps_in(module_key, 'irreps_in') - ) - - new_bias = ( - torch.zeros(output_dim) - if ref_modal == 'common' - else _get_modal_weight_as_bias( - model_state_dct, - module_key, - ref_modal_index, - irreps_in, # type: ignore - irreps_out, # type: ignore - ) - ) - erased_modal_weight = _erase_linear_modal_params( - model_state_dct, - erase_modal_indices, - module_key, - irreps_in, # type: ignore - irreps_out, # type: ignore - ) - - model_state_dct[module_key + '.linear.weight'] = ( - erased_modal_weight - ) - model_state_dct[module_key + '.linear.bias'] = new_bias - elif modal_module_name in module_key: - model_state_dct[module_key + '.linear.bias'] = torch.zeros( - output_dim, - dtype=model_state_dct[module_key + '.linear.weight'].dtype, - ) - - final_block_key = 'reduce_hidden_to_energy' - model_state_dct[final_block_key + '.linear.bias'] = torch.tensor( - [0], dtype=model_state_dct[final_block_key + '.linear.weight'].dtype - ) - - if config[KEY.USE_MODAL_WISE_SHIFT] or config[KEY.USE_MODAL_WISE_SHIFT]: - rescaler_names = [] - if config[KEY.USE_MODAL_WISE_SHIFT]: - rescaler_names.append('shift') - if config[KEY.USE_MODAL_WISE_SCALE]: - rescaler_names.append('scale') - config[KEY.USE_MODAL_WISE_SHIFT] = False - config[KEY.USE_MODAL_WISE_SCALE] = False - for rescaler_name in rescaler_names: - rescaler_key = 'rescale_atomic_energy.' + rescaler_name - rescaler = model_state_dct[rescaler_key][ref_modal_index] - model_state_dct.update({rescaler_key: rescaler}) - config.update({rescaler_name: rescaler}) - - config[KEY.USE_MODALITY] = False - - return model_state_dct - - -def append_modality_to_model_dct( - model_state_dct: dict, - config: dict, - orig_num_modal: int, - append_modal_length: int, -): - """ - Append modal-wise parameters to the original linear layers. - This enables expanding modal to single/multi modal model checkpoint. - - `model_state_dct`: model state dictionary from multimodal checkpoint file - `config`: dictionary containing configuration of the checkpoint model - + modality appended - `orig_num_modal`: Number of modality used in original checkpoint - `append_modal_length`: Number of modality to be appended in new checkpoint. - """ - config_num_modal = config[KEY.NUM_MODALITIES] - config.update({KEY.NUM_MODALITIES: orig_num_modal, KEY.USE_MODALITY: True}) - - model = build_E3_equivariant_model(config) - - for module_key in model._modules.keys(): - for ( - use_modal_module_key, - modal_module_name, - ) in modal_module_dict.items(): - if ( - config[use_modal_module_key] - and modal_module_name in module_key - ): # this module is used for giving modality - irreps_in = model.get_irreps_in( - module_key, 'irreps_in' - ) - # TODO: directly using "irreps_in" might not be compatible - # when changing `nn/linear.py` - irreps_out = model.get_irreps_in(module_key, 'irreps_out') - irreps_in, irreps_out = Irreps(irreps_in), Irreps(irreps_out) - - append_weight = _append_modal_weight( - model_state_dct, - module_key, - irreps_in, # type: ignore - irreps_out, # type: ignore - append_modal_length, - ) - model_state_dct[module_key + '.linear.weight'] = append_weight - config[KEY.NUM_MODALITIES] = config_num_modal - - return model_state_dct diff --git a/mace-bench/3rdparty/SevenNet/sevenn/scripts/deploy.py b/mace-bench/3rdparty/SevenNet/sevenn/scripts/deploy.py deleted file mode 100644 index 51ded15c579768bb467b1f84c8bb178e390c16ff..0000000000000000000000000000000000000000 --- a/mace-bench/3rdparty/SevenNet/sevenn/scripts/deploy.py +++ /dev/null @@ -1,148 +0,0 @@ -import os -from datetime import datetime -from typing import Optional - -import e3nn.util.jit -import torch -import torch.nn -from ase.data import chemical_symbols - -import sevenn._keys as KEY -from sevenn import __version__ -from sevenn.model_build import build_E3_equivariant_model -from sevenn.util import load_checkpoint - - -def deploy(checkpoint, fname='deployed_serial.pt', modal: Optional[str] = None): - """ - This method is messy to avoid changes in pair_e3gnn.cpp, while - refactoring python part. - If changes the behavior, and accordingly pair_e3gnn.cpp, - we have to recompile LAMMPS (which I always want to procrastinate) - """ - from sevenn.nn.edge_embedding import EdgePreprocess - from sevenn.nn.force_output import ForceStressOutput - - cp = load_checkpoint(checkpoint) - model, config = cp.build_model('e3nn'), cp.config - - model.prepand_module('edge_preprocess', EdgePreprocess(True)) - grad_module = ForceStressOutput() - model.replace_module('force_output', grad_module) - new_grad_key = grad_module.get_grad_key() - model.key_grad = new_grad_key - if hasattr(model, 'eval_type_map'): - setattr(model, 'eval_type_map', False) - - if modal: - model.prepare_modal_deploy(modal) - elif model.modal_map is not None and len(model.modal_map) >= 1: - raise ValueError( - f'Modal is not given. It has: {list(model.modal_map.keys())}' - ) - - model.set_is_batch_data(False) - model.eval() - - model = e3nn.util.jit.script(model) - model = torch.jit.freeze(model) - - # make some config need for md - md_configs = {} - type_map = config[KEY.TYPE_MAP] - chem_list = '' - for Z in type_map.keys(): - chem_list += chemical_symbols[Z] + ' ' - chem_list.strip() - md_configs.update({'chemical_symbols_to_index': chem_list}) - md_configs.update({'cutoff': str(config[KEY.CUTOFF])}) - md_configs.update({'num_species': str(config[KEY.NUM_SPECIES])}) - md_configs.update( - {'model_type': config.pop(KEY.MODEL_TYPE, 'E3_equivariant_model')} - ) - md_configs.update({'version': __version__}) - md_configs.update({'dtype': config.pop(KEY.DTYPE, 'single')}) - md_configs.update({'time': datetime.now().strftime('%Y-%m-%d')}) - - if fname.endswith('.pt') is False: - fname += '.pt' - torch.jit.save(model, fname, _extra_files=md_configs) - - -# TODO: build model only once -def deploy_parallel( - checkpoint, fname='deployed_parallel', modal: Optional[str] = None -): - # Additional layer for ghost atom (and copy parameters from original) - GHOST_LAYERS_KEYS = ['onehot_to_feature_x', '0_self_interaction_1'] - - cp = load_checkpoint(checkpoint) - model, config = cp.build_model('e3nn'), cp.config - config[KEY.CUEQUIVARIANCE_CONFIG] = {'use': False} - model_state_dct = model.state_dict() - - model_list = build_E3_equivariant_model(config, parallel=True) - dct_temp = {} - copy_counter = {gk: 0 for gk in GHOST_LAYERS_KEYS} - for ghost_layer_key in GHOST_LAYERS_KEYS: - for key, val in model_state_dct.items(): - if not key.startswith(ghost_layer_key): - continue - dct_temp.update({f'ghost_{key}': val}) - copy_counter[ghost_layer_key] += 1 - # Ensure reference weights are copied from state dict - assert all(x > 0 for x in copy_counter.values()) - - model_state_dct.update(dct_temp) - - for model_part in model_list: - missing, _ = model_part.load_state_dict(model_state_dct, strict=False) - if hasattr(model_part, 'eval_type_map'): - setattr(model_part, 'eval_type_map', False) - # Ensure all values are inserted - assert len(missing) == 0, missing - - if modal: - model_list[0].prepare_modal_deploy(modal) - elif model_list[0].modal_map is not None: - raise ValueError( - f'Modal is not given. It has: {list(model_list[0].modal_map.keys())}' - ) - - # prepare some extra information for MD - md_configs = {} - type_map = config[KEY.TYPE_MAP] - - chem_list = '' - for Z in type_map.keys(): - chem_list += chemical_symbols[Z] + ' ' - chem_list.strip() - - comm_size = max( - [ - seg._modules[f'{t}_convolution']._comm_size # type: ignore - for t, seg in enumerate(model_list) - ] - ) - - md_configs.update({'chemical_symbols_to_index': chem_list}) - md_configs.update({'cutoff': str(config[KEY.CUTOFF])}) - md_configs.update({'num_species': str(config[KEY.NUM_SPECIES])}) - md_configs.update({'comm_size': str(comm_size)}) - md_configs.update( - {'model_type': config.pop(KEY.MODEL_TYPE, 'E3_equivariant_model')} - ) - md_configs.update({'version': __version__}) - md_configs.update({'dtype': config.pop(KEY.DTYPE, 'single')}) - md_configs.update({'time': datetime.now().strftime('%Y-%m-%d')}) - - os.makedirs(fname) - for idx, model in enumerate(model_list): - fname_full = f'{fname}/deployed_parallel_{idx}.pt' - model.set_is_batch_data(False) - model.eval() - - model = e3nn.util.jit.script(model) - model = torch.jit.freeze(model) - - torch.jit.save(model, fname_full, _extra_files=md_configs) diff --git a/mace-bench/3rdparty/SevenNet/sevenn/scripts/graph_build.py b/mace-bench/3rdparty/SevenNet/sevenn/scripts/graph_build.py deleted file mode 100644 index af1b162c99b18efd00c567d2256eac91710d584d..0000000000000000000000000000000000000000 --- a/mace-bench/3rdparty/SevenNet/sevenn/scripts/graph_build.py +++ /dev/null @@ -1,119 +0,0 @@ -import os -from typing import List, Optional - -from sevenn.logger import Logger -from sevenn.train.dataset import AtomGraphDataset -from sevenn.util import unique_filepath - - -def build_sevennet_graph_dataset( - source: List[str], - cutoff: float, - num_cores: int, - out: str, - filename: str, - metadata: Optional[dict] = None, - **fmt_kwargs, -): - from sevenn.train.graph_dataset import SevenNetGraphDataset - - log = Logger() - if metadata is None: - metadata = {} - - log.timer_start('graph_build') - db = SevenNetGraphDataset( - cutoff=cutoff, - root=out, - files=source, - processed_name=filename, - process_num_cores=num_cores, - **fmt_kwargs, - ) - log.timer_end('graph_build', 'graph build time') - log.writeline(f'Graph saved: {db.processed_paths[0]}') - - log.bar() - for k, v in metadata.items(): - log.format_k_v(k, v, write=True) - log.bar() - - log.writeline('Distribution:') - log.statistic_write(db.statistics) - log.format_k_v('# atoms (node)', db.natoms, write=True) - log.format_k_v('# structures (graph)', len(db), write=True) - - -def dataset_finalize(dataset, metadata, out): - """ - Deprecated - """ - natoms = dataset.get_natoms() - species = dataset.get_species() - metadata = { - **metadata, - 'natoms': natoms, - 'species': species, - } - dataset.meta = metadata - - if os.path.isdir(out): - out = os.path.join(out, 'graph_built.sevenn_data') - elif out.endswith('.sevenn_data') is False: - out = out + '.sevenn_data' - out = unique_filepath(out) - - log = Logger() - log.writeline('The metadata of the dataset is...') - for k, v in metadata.items(): - log.format_k_v(k, v, write=True) - dataset.save(out) - log.writeline(f'dataset is saved to {out}') - - return dataset - - -def build_script( - source: List[str], - cutoff: float, - num_cores: int, - out: str, - metadata: Optional[dict] = None, - **fmt_kwargs, -): - """ - Deprecated - """ - from sevenn.train.dataload import file_to_dataset, match_reader - - if metadata is None: - metadata = {} - log = Logger() - - dataset = AtomGraphDataset({}, cutoff) - common_args = { - 'cutoff': cutoff, - 'cores': num_cores, - 'label': 'graph_build', - } - log.timer_start('graph_build') - for path in source: - if os.path.isdir(path): - continue - log.writeline(f'Read: {path}') - basename = os.path.basename(path) - if 'structure_list' in basename: - fmt = 'structure_list' - else: - fmt = 'ase' - reader, rmeta = match_reader(fmt, **fmt_kwargs) - metadata.update(**rmeta) - dataset.augment( - file_to_dataset( - file=path, - reader=reader, - **common_args, - ) - ) - log.timer_end('graph_build', 'graph build time') - dataset_finalize(dataset, metadata, out) diff --git a/mace-bench/3rdparty/SevenNet/sevenn/scripts/inference.py b/mace-bench/3rdparty/SevenNet/sevenn/scripts/inference.py deleted file mode 100644 index 93c998f4150b18695f672b79ff56297f8b671d12..0000000000000000000000000000000000000000 --- a/mace-bench/3rdparty/SevenNet/sevenn/scripts/inference.py +++ /dev/null @@ -1,227 +0,0 @@ -import csv -import os -from typing import Iterable, List, Optional, Union - -import numpy as np -from torch_geometric.loader import DataLoader -from tqdm import tqdm - -import sevenn._keys as KEY -import sevenn.util as util -from sevenn.atom_graph_data import AtomGraphData -from sevenn.train.graph_dataset import SevenNetGraphDataset -from sevenn.train.modal_dataset import SevenNetMultiModalDataset - - -def write_inference_csv(output_list, out): - for i, output in enumerate(output_list): - output = output.fit_dimension() - output[KEY.STRESS] = output[KEY.STRESS] * 1602.1766208 - output[KEY.PRED_STRESS] = output[KEY.PRED_STRESS] * 1602.1766208 - output_list[i] = output.to_numpy_dict() - - per_graph_keys = [ - KEY.NUM_ATOMS, - KEY.USER_LABEL, - KEY.ENERGY, - KEY.PRED_TOTAL_ENERGY, - KEY.STRESS, - KEY.PRED_STRESS, - ] - - per_atom_keys = [ - KEY.ATOMIC_NUMBERS, - KEY.ATOMIC_ENERGY, - KEY.POS, - KEY.FORCE, - KEY.PRED_FORCE, - ] - - def unfold_dct_val(dct, keys, suffix_list=None): - res = {} - if suffix_list is None: - suffix_list = range(100) - for k in keys: - if k not in dct: - res[k] = '-' - elif isinstance(dct[k], np.ndarray) and dct[k].ndim != 0: - res.update( - {f'{k}_{suffix_list[i]}': v for i, v in enumerate(dct[k])} - ) - else: - res[k] = dct[k] - return res - - def per_atom_dct_list(dct, keys): - sfx_list = ['x', 'y', 'z'] - res = [] - natoms = dct[KEY.NUM_ATOMS] - extracted = {k: dct[k] for k in keys} - for i in range(natoms): - raw = {} - raw.update({k: v[i] for k, v in extracted.items()}) - per_atom_dct = unfold_dct_val(raw, keys, suffix_list=sfx_list) - res.append(per_atom_dct) - return res - - try: - with open(f'{out}/info.csv', 'w', newline='') as f: - header = output_list[0][KEY.INFO].keys() - writer = csv.DictWriter(f, fieldnames=header) - writer.writeheader() - for output in output_list: - writer.writerow(output[KEY.INFO]) - except (KeyError, TypeError, AttributeError, csv.Error) as e: - print(e) - print('failed to write meta data, info.csv is not written') - - with open(f'{out}/per_graph.csv', 'w', newline='') as f: - sfx_list = ['xx', 'yy', 'zz', 'xy', 'yz', 'zx'] # for stress - writer = None - for output in output_list: - cell_dct = {KEY.CELL: output[KEY.CELL]} - cell_dct = unfold_dct_val(cell_dct, [KEY.CELL], ['a', 'b', 'c']) - data = { - **unfold_dct_val(output, per_graph_keys, sfx_list), - **cell_dct, - } - if writer is None: - writer = csv.DictWriter(f, fieldnames=data.keys()) - writer.writeheader() - writer.writerow(data) - - with open(f'{out}/per_atom.csv', 'w', newline='') as f: - writer = None - for i, output in enumerate(output_list): - list_of_dct = per_atom_dct_list(output, per_atom_keys) - for j, dct in enumerate(list_of_dct): - idx_dct = {'stct_id': i, 'atom_id': j} - data = {**idx_dct, **dct} - if writer is None: - writer = csv.DictWriter(f, fieldnames=data.keys()) - writer.writeheader() - writer.writerow(data) - - -def _patch_data_info( - graph_list: Iterable[AtomGraphData], full_file_list: List[str] -) -> None: - keys = set() - for graph, path in zip(graph_list, full_file_list): - if KEY.INFO not in graph: - graph[KEY.INFO] = {} - graph[KEY.INFO].update({'file': os.path.abspath(path)}) - keys.update(graph[KEY.INFO].keys()) - - # save only safe subset of info (for batching) - for graph in graph_list: - info_dict = graph[KEY.INFO] - info_dict.update({k: '' for k in keys if k not in info_dict}) - - -def inference( - checkpoint: str, - targets: Union[str, List[str]], - output_dir: str, - num_workers: int = 1, - device: str = 'cpu', - batch_size: int = 4, - save_graph: bool = False, - allow_unlabeled: bool = False, - modal: Optional[str] = None, - **data_kwargs, -) -> None: - """ - Inference model on the target dataset, writes - per_graph, per_atom inference results in csv format - to the output_dir - If a given target doesn't have EFS key, it puts dummy - values. - - Args: - checkpoint: model checkpoint path, - target: path, or list of path to evaluate. Supports - ASE readable, sevenn_data/*.pt, .sevenn_data, and - structure_list - output_dir: directory to write results - num_workers: number of workers to build graph - device: device to evaluate, defaults to 'auto' - batch_size: batch size for inference - save_grpah: if True, save preprocessed graph to output dir - data_kwargs: keyword arguments used when reading targets, - for example, given index='-1', only the last snapshot - will be evaluated if it was ASE readable. - While this function can handle different types of targets - at once, it will not work smoothly with data_kwargs - - """ - model, _ = util.model_from_checkpoint(checkpoint) - cutoff = model.cutoff - - if modal: - if model.modal_map is None: - raise ValueError('Modality given, but model has no modal_map') - if modal not in model.modal_map: - _modals = list(model.modal_map.keys()) - raise ValueError(f'Unknown modal {modal} (not in {_modals})') - - if isinstance(targets, str): - targets = [targets] - - full_file_list = [] - if save_graph: - dataset = SevenNetGraphDataset( - cutoff=cutoff, - root=output_dir, - files=targets, - process_num_cores=num_workers, - processed_name='saved_graph.pt', - **data_kwargs, - ) - full_file_list = dataset.full_file_list # TODO: not used currently - else: - dataset = [] - for file in targets: - tmplist = SevenNetGraphDataset.file_to_graph_list( - file, - cutoff=cutoff, - num_cores=num_workers, - allow_unlabeled=allow_unlabeled, - **data_kwargs, - ) - dataset.extend(tmplist) - full_file_list.extend([os.path.abspath(file)] * len(tmplist)) - if ( - full_file_list is not None - and len(full_file_list) == len(dataset) - and not isinstance(dataset, SevenNetGraphDataset) - ): - _patch_data_info(dataset, full_file_list) # type: ignore - - if modal: - dataset = SevenNetMultiModalDataset({modal: dataset}) # type: ignore - - loader = DataLoader(dataset, batch_size, shuffle=False) # type: ignore - - model.to(device) - model.set_is_batch_data(True) - model.eval() - - rec = util.get_error_recorder() - output_list = [] - - for batch in tqdm(loader): - batch = batch.to(device) - output = model(batch).detach().cpu() - rec.update(output) - output_list.extend(util.to_atom_graph_list(output)) - - errors = rec.epoch_forward() - - if not os.path.exists(output_dir): - os.makedirs(output_dir) - with open(os.path.join(output_dir, 'errors.txt'), 'w', encoding='utf-8') as f: - for key, val in errors.items(): - f.write(f'{key}: {val}\n') - - write_inference_csv(output_list, output_dir) diff --git a/mace-bench/3rdparty/SevenNet/sevenn/scripts/processing_continue.py b/mace-bench/3rdparty/SevenNet/sevenn/scripts/processing_continue.py deleted file mode 100644 index 2537684eea413c016596505d32af1c2f35b723d6..0000000000000000000000000000000000000000 --- a/mace-bench/3rdparty/SevenNet/sevenn/scripts/processing_continue.py +++ /dev/null @@ -1,273 +0,0 @@ -import os -import warnings - -import torch - -import sevenn._keys as KEY -import sevenn.util as util -from sevenn.logger import Logger -from sevenn.scripts.convert_model_modality import ( - append_modality_to_model_dct, - get_single_modal_model_dct, -) - - -def processing_continue_v2(config): # simpler - """ - Replacement of processing_continue, - Skips model compatibility - """ - log = Logger() - continue_dct = config[KEY.CONTINUE] - log.write('\nContinue found, loading checkpoint\n') - - checkpoint = util.load_checkpoint(continue_dct[KEY.CHECKPOINT]) - model_cp = checkpoint.build_model() - config_cp = checkpoint.config - model_state_dict_cp = model_cp.state_dict() - - optimizer_state_dict_cp = ( - checkpoint.optimizer_state_dict - if not continue_dct[KEY.RESET_OPTIMIZER] - else None - ) - scheduler_state_dict_cp = ( - checkpoint.scheduler_state_dict - if not continue_dct[KEY.RESET_SCHEDULER] - else None - ) - - # use_statistic_value_of_checkpoint always True - # Overwrite config from model state dict, so graph_dataset.from_config - # will not put statistic values to shift, scale, and conv_denominator - config[KEY.SHIFT] = model_state_dict_cp['rescale_atomic_energy.shift'].tolist() - config[KEY.SCALE] = model_state_dict_cp['rescale_atomic_energy.scale'].tolist() - conv_denom = [] - for i in range(config_cp[KEY.NUM_CONVOLUTION]): - conv_denom.append(model_state_dict_cp[f'{i}_convolution.denominator'].item()) - config[KEY.CONV_DENOMINATOR] = conv_denom - log.writeline( - f'{KEY.SHIFT}, {KEY.SCALE}, and {KEY.CONV_DENOMINATOR} are ' - + 'overwritten by model_state_dict of checkpoint' - ) - - chem_keys = [ - KEY.TYPE_MAP, - KEY.NUM_SPECIES, - KEY.CHEMICAL_SPECIES, - KEY.CHEMICAL_SPECIES_BY_ATOMIC_NUMBER, - ] - config.update({k: config_cp[k] for k in chem_keys}) - log.writeline( - 'chemical_species are overwritten by checkpoint. ' - + f'This model knows {config[KEY.NUM_SPECIES]} species' - ) - - if config_cp.get(KEY.USE_MODALITY, False) != config.get(KEY.USE_MODALITY): - raise ValueError('use_modality is not same. Check sevenn_cp') - - modal_map = config_cp.get(KEY.MODAL_MAP, None) # dict | None - if modal_map and len(modal_map) > 0: - modalities = list(modal_map.keys()) - log.writeline(f'Multimodal model found: {modalities}') - log.writeline('use_modality: True') - config[KEY.USE_MODALITY] = True - - from_epoch = checkpoint.epoch or 0 - log.writeline(f'Checkpoint previous epoch was: {from_epoch}') - epoch = 1 if continue_dct[KEY.RESET_EPOCH] else from_epoch + 1 - log.writeline(f'epoch start from {epoch}') - - log.writeline('checkpoint loading successful') - - state_dicts = [ - model_state_dict_cp, - optimizer_state_dict_cp, - scheduler_state_dict_cp, - ] - return state_dicts, epoch - - -def check_config_compatible(config, config_cp): - # TODO: check more - SHOULD_BE_SAME = [ - KEY.NODE_FEATURE_MULTIPLICITY, - KEY.LMAX, - KEY.IS_PARITY, - KEY.RADIAL_BASIS, - KEY.CUTOFF_FUNCTION, - KEY.CUTOFF, - KEY.CONVOLUTION_WEIGHT_NN_HIDDEN_NEURONS, - KEY.NUM_CONVOLUTION, - KEY.USE_BIAS_IN_LINEAR, - KEY.SELF_CONNECTION_TYPE, - ] - for sbs in SHOULD_BE_SAME: - if config[sbs] == config_cp[sbs]: - continue - if sbs == KEY.SELF_CONNECTION_TYPE and config_cp[sbs] == 'MACE': - warnings.warn( - 'We do not support this version of checkpoints to continue ' - "Please use self_connection_type='linear' in input.yaml " - 'and train from scratch', - UserWarning, - ) - raise ValueError( - f'Value of {sbs} should be same. {config[sbs]} != {config_cp[sbs]}' - ) - - try: - cntdct = config[KEY.CONTINUE] - except KeyError: - return - - TRAINABLE_CONFIGS = [KEY.TRAIN_DENOMINTAOR, KEY.TRAIN_SHIFT_SCALE] - if ( - any((not cntdct[KEY.RESET_SCHEDULER], not cntdct[KEY.RESET_OPTIMIZER])) - and all(config[k] == config_cp[k] for k in TRAINABLE_CONFIGS) is False - ): - raise ValueError( - 'reset optimizer and scheduler if you want to change ' - + 'trainable configs' - ) - - # TODO add conition for changed optim/scheduler but not reset - - -def processing_continue(config): - log = Logger() - continue_dct = config[KEY.CONTINUE] - log.write('\nContinue found, loading checkpoint\n') - - checkpoint = torch.load( - continue_dct[KEY.CHECKPOINT], map_location='cpu', weights_only=False - ) - config_cp = checkpoint['config'] - - model_cp, config_cp = util.model_from_checkpoint(checkpoint) - model_state_dict_cp = model_cp.state_dict() - - # it will raise error if not compatible - check_config_compatible(config, config_cp) - log.write('Checkpoint config is compatible\n') - - # for backward compat. - config.update({KEY._NORMALIZE_SPH: config_cp[KEY._NORMALIZE_SPH]}) - - from_epoch = checkpoint['epoch'] - optimizer_state_dict_cp = ( - checkpoint['optimizer_state_dict'] - if not continue_dct[KEY.RESET_OPTIMIZER] - else None - ) - scheduler_state_dict_cp = ( - checkpoint['scheduler_state_dict'] - if not continue_dct[KEY.RESET_SCHEDULER] - else None - ) - - # These could be changed based on given continue_input.yaml - # ex) adapt to statistics of fine-tuning dataset - shift_cp = model_state_dict_cp['rescale_atomic_energy.shift'].numpy() - del model_state_dict_cp['rescale_atomic_energy.shift'] - scale_cp = model_state_dict_cp['rescale_atomic_energy.scale'].numpy() - del model_state_dict_cp['rescale_atomic_energy.scale'] - conv_denominators = [] - for i in range(config_cp[KEY.NUM_CONVOLUTION]): - conv_denominators.append( - (model_state_dict_cp[f'{i}_convolution.denominator']).item() - ) - del model_state_dict_cp[f'{i}_convolution.denominator'] - - # Further handled by processing_dataset.py - config.update({ - KEY.SHIFT + '_cp': shift_cp, - KEY.SCALE + '_cp': scale_cp, - KEY.CONV_DENOMINATOR + '_cp': conv_denominators, - }) - - chem_keys = [ - KEY.TYPE_MAP, - KEY.NUM_SPECIES, - KEY.CHEMICAL_SPECIES, - KEY.CHEMICAL_SPECIES_BY_ATOMIC_NUMBER, - ] - config.update({k: config_cp[k] for k in chem_keys}) - - if ( - KEY.USE_MODALITY in config_cp.keys() and config_cp[KEY.USE_MODALITY] - ): # checkpoint model is multimodal - config.update({ - KEY.MODAL_MAP + '_cp': config_cp[KEY.MODAL_MAP], - KEY.USE_MODALITY + '_cp': True, - KEY.NUM_MODALITIES + '_cp': len(config_cp[KEY.MODAL_MAP]), - }) - else: - config.update({ - KEY.MODAL_MAP + '_cp': {}, - KEY.USE_MODALITY + '_cp': False, - KEY.NUM_MODALITIES + '_cp': 0, - }) - - log.write(f'checkpoint previous epoch was: {from_epoch}\n') - - # decide start epoch - reset_epoch = continue_dct[KEY.RESET_EPOCH] - if reset_epoch: - start_epoch = 1 - log.write('epoch reset to 1\n') - else: - start_epoch = from_epoch + 1 - log.write(f'epoch start from {start_epoch}\n') - - # decide csv file to continue - init_csv = True - csv_fname = config_cp[KEY.CSV_LOG] - if os.path.isfile(csv_fname): - # I hope python compare dict well - if config_cp[KEY.ERROR_RECORD] == config[KEY.ERROR_RECORD]: - log.writeline('Same metric, csv file will be appended') - init_csv = False - else: - log.writeline(f'{csv_fname} file not found, new csv file will be created') - log.writeline('checkpoint loading was successful') - - state_dicts = [ - model_state_dict_cp, - optimizer_state_dict_cp, - scheduler_state_dict_cp, - ] - return state_dicts, start_epoch, init_csv - - -def convert_modality_of_checkpoint_state_dct(config, state_dicts): - # TODO: this requires updating model state dict after seeing dataset - model_state_dict_cp, optimizer_state_dict_cp, scheduler_state_dict_cp = ( - state_dicts - ) - - if config[KEY.USE_MODALITY]: # current model is multimodal - num_modalities_cp = len(config[KEY.MODAL_MAP + '_cp']) - append_modal_length = config[KEY.NUM_MODALITIES] - num_modalities_cp - - model_state_dict_cp = append_modality_to_model_dct( - model_state_dict_cp, config, num_modalities_cp, append_modal_length - ) - - else: # current model is single modal - if config[KEY.USE_MODALITY + '_cp']: # checkpoint model is multimodal - # change model state dict to single modal, default = "common" - model_state_dict_cp = get_single_modal_model_dct( - model_state_dict_cp, - config, - config[KEY.DEFAULT_MODAL], - from_processing_cp=True, - ) - - state_dicts = ( - model_state_dict_cp, - optimizer_state_dict_cp, - scheduler_state_dict_cp, - ) - - return state_dicts diff --git a/mace-bench/3rdparty/SevenNet/sevenn/scripts/processing_dataset.py b/mace-bench/3rdparty/SevenNet/sevenn/scripts/processing_dataset.py deleted file mode 100644 index 64e79617664a092d6e1ca6e06fe10cd12f973572..0000000000000000000000000000000000000000 --- a/mace-bench/3rdparty/SevenNet/sevenn/scripts/processing_dataset.py +++ /dev/null @@ -1,481 +0,0 @@ -import os - -import torch -import torch.distributed as dist - -import sevenn._const as CONST -import sevenn._keys as KEY -from sevenn.logger import Logger -from sevenn.train.dataload import file_to_dataset, match_reader -from sevenn.train.dataset import AtomGraphDataset -from sevenn.util import chemical_species_preprocess, onehot_to_chem - - -def dataset_load(file: str, config): - """ - Wrapping of dataload.file_to_dataset to suppert - graph prebuilt sevenn_data - """ - log = Logger() - log.write(f'Loading {file}\n') - log.timer_start('loading dataset') - - if file.endswith('.sevenn_data'): - dataset = torch.load(file, map_location='cpu', weights_only=False) - else: - reader, _ = match_reader( - config[KEY.DATA_FORMAT], **config[KEY.DATA_FORMAT_ARGS] - ) - dataset = file_to_dataset( - file, - config[KEY.CUTOFF], - config[KEY.PREPROCESS_NUM_CORES], - reader=reader, - use_modality=config[KEY.USE_MODALITY], - use_weight=config[KEY.USE_WEIGHT], - ) - log.format_k_v('loaded dataset size is', dataset.len(), write=True) - log.timer_end('loading dataset', 'data set loading time') - return dataset - - -def calculate_shift_or_scale_from_key( - train_set: AtomGraphDataset, key_given, n_chem -): - _expand = True - use_species_wise_shift_scale = False - if key_given == 'per_atom_energy_mean': - shift_or_scale = train_set.get_per_atom_energy_mean() - elif key_given == 'elemwise_reference_energies': - shift_or_scale = train_set.get_species_ref_energy_by_linear_comb(n_chem) - _expand = False - use_species_wise_shift_scale = True - - elif key_given == 'force_rms': - shift_or_scale = train_set.get_force_rms() - elif key_given == 'per_atom_energy_std': - shift_or_scale = train_set.get_statistics(KEY.PER_ATOM_ENERGY)['Total'][ - 'std' - ] - elif key_given == 'elemwise_force_rms': - shift_or_scale = train_set.get_species_wise_force_rms(n_chem) - _expand = False - use_species_wise_shift_scale = True - - return shift_or_scale, _expand, use_species_wise_shift_scale - - -def handle_shift_scale(config, train_set: AtomGraphDataset, checkpoint_given): - """ - Priority (first comes later to overwrite): - 1. Float given in yaml - 2. Use statistic values of checkpoint == True - 3. Plain options (provided as string) - """ - log = Logger() - shift, scale, conv_denominator = None, None, None - type_map = config[KEY.TYPE_MAP] - n_chem = len(type_map) - chem_strs = onehot_to_chem(list(range(n_chem)), type_map) - - log.writeline('\nCalculating statistic values from dataset') - - shift_given = config[KEY.SHIFT] - scale_given = config[KEY.SCALE] - _expand_shift = True - _expand_scale = True - use_species_wise_shift = False - use_species_wise_scale = False - - use_modal_wise_shift = config[KEY.USE_MODAL_WISE_SHIFT] - use_modal_wise_scale = config[KEY.USE_MODAL_WISE_SCALE] - - if shift_given in CONST.IMPLEMENTED_SHIFT: - shift, _expand_shift, use_species_wise_shift = ( - calculate_shift_or_scale_from_key(train_set, shift_given, n_chem) - ) - - if scale_given in CONST.IMPLEMENTED_SCALE: - scale, _expand_scale, use_species_wise_scale = ( - calculate_shift_or_scale_from_key(train_set, scale_given, n_chem) - ) - - if use_modal_wise_shift or use_modal_wise_scale: - atomdata_dict_sort_by_modal = train_set.get_dict_sort_by_modality() - modal_map = config[KEY.MODAL_MAP] - n_modal = len(modal_map) - cutoff = config[KEY.CUTOFF] - - if use_modal_wise_shift: - shift = torch.zeros((n_modal, n_chem)) - - if use_modal_wise_scale: - scale = torch.zeros((n_modal, n_chem)) - - for modal_key, data_list in atomdata_dict_sort_by_modal.items(): - modal_set = AtomGraphDataset(data_list, cutoff, x_is_one_hot_idx=True) - - if use_modal_wise_shift: - if shift_given == 'elemwise_reference_energies': - modal_shift, _expand_shift, use_species_wise_shift = ( - calculate_shift_or_scale_from_key( - modal_set, shift_given, n_chem - ) - ) - shift[modal_map[modal_key]] = torch.tensor( - modal_shift - ) # this is np.array - elif shift_given in CONST.IMPLEMENTED_SHIFT: - raise NotImplementedError( - 'Currently, modal-wise shift implemented for' - 'species-dependent case only.' - ) - - if use_modal_wise_scale: - if scale_given == 'elemwise_force_rms': - modal_scale, _expand_scale, use_species_wise_scale = ( - calculate_shift_or_scale_from_key( - modal_set, scale_given, n_chem - ) - ) - scale[modal_map[modal_key]] = modal_scale - elif scale_given in CONST.IMPLEMENTED_SCALE: - raise NotImplementedError( - 'Currently, modal-wise scale implemented for' - 'species-dependent case only.' - ) - - avg_num_neigh = train_set.get_avg_num_neigh() - log.format_k_v('Average # of neighbors', f'{avg_num_neigh:.6f}', write=True) - - if config[KEY.CONV_DENOMINATOR] == 'avg_num_neigh': - conv_denominator = avg_num_neigh - elif config[KEY.CONV_DENOMINATOR] == 'sqrt_avg_num_neigh': - conv_denominator = avg_num_neigh ** (0.5) - - if ( - checkpoint_given - and config[KEY.CONTINUE][KEY.USE_STATISTIC_VALUES_OF_CHECKPOINT] - ): - log.writeline( - 'Overwrite shift, scale, conv_denominator from model checkpoint' - ) - # TODO: This needs refactoring - conv_denominator = config[KEY.CONV_DENOMINATOR + '_cp'] - if not (use_modal_wise_shift or use_modal_wise_scale): - # Values extracted from checkpoint in processing_continue.py - if len(list(shift)) > 1: - use_species_wise_shift = True - use_species_wise_scale = True - _expand_shift = _expand_scale = False - else: - shift = shift.item() - scale = scale.item() - else: - # Case of modal wise shift scale - shift_cp = config[KEY.SHIFT + '_cp'] - scale_cp = config[KEY.SCALE + '_cp'] - if not use_modal_wise_shift: - shift = shift_cp - if not use_modal_wise_scale: - scale = scale_cp - modal_map = config[KEY.MODAL_MAP] - modal_map_cp = config[KEY.MODAL_MAP + '_cp'] - - # Extracting shift, scale for modal in checkpoint model. - if config[KEY.USE_MODALITY + '_cp']: # cp model is multimodal - for modal_key_cp, modal_idx_cp in modal_map_cp.items(): - modal_idx = modal_map[modal_key_cp] - if use_modal_wise_shift: - shift[modal_idx] = torch.tensor(shift_cp[modal_idx_cp]) - if use_modal_wise_scale: - scale[modal_idx] = torch.tensor(scale_cp[modal_idx_cp]) - - else: # cp model is single modal - try: - modal_idx = modal_map[config[KEY.DEFAULT_MODAL]] - except: - raise KeyError( - f'{config[KEY.DEFAULT_MODAL]} should be one of' - f' {modal_map.keys()}' - ) - if use_modal_wise_shift: - shift[modal_idx] = torch.tensor(shift_cp) - if use_modal_wise_scale: - scale[modal_idx] = torch.tensor(scale_cp) - - if not config[KEY.CONTINUE][KEY.USE_STATISTIC_VALUES_FOR_CP_MODAL_ONLY]: - # Also overwrite values of new modal to reference value - # For multimodal, set reference modal with KEY.DEFAULT_MODAL - shift_ref = shift_cp - scale_ref = scale_cp - if config[KEY.USE_MODALITY + '_cp']: - try: - modal_idx_cp = modal_map_cp[config[KEY.DEFAULT_MODAL]] - except: - raise KeyError( - f'{config[KEY.DEFAULT_MODAL]} should be one of' - f' {modal_map_cp.keys()}' - ) - shift_ref = shift_cp[modal_idx_cp] - scale_ref = scale_cp[modal_idx_cp] - - for modal_key, modal_idx in modal_map.items(): - if modal_key not in modal_map_cp.keys(): - if use_modal_wise_shift: - shift[modal_idx] = shift_ref - if use_modal_wise_scale: - scale[modal_idx] = scale_ref - - # overwrite shift scale anyway if defined in yaml. - if type(shift_given) in [list, float]: - log.writeline('Overwrite shift to value(s) given in yaml') - _expand_shift = isinstance(shift_given, float) - shift = shift_given - if type(scale_given) in [list, float]: - log.writeline('Overwrite scale to value(s) given in yaml') - _expand_scale = isinstance(scale_given, float) - scale = scale_given - - if isinstance(config[KEY.CONV_DENOMINATOR], float): - log.writeline('Overwrite conv_denominator to value given in yaml') - conv_denominator = config[KEY.CONV_DENOMINATOR] - - if isinstance(conv_denominator, float): - conv_denominator = [conv_denominator] * config[KEY.NUM_CONVOLUTION] - - use_species_wise_shift_scale = use_species_wise_shift or use_species_wise_scale - if use_species_wise_shift_scale: - chem_strs = onehot_to_chem(list(range(n_chem)), type_map) - if _expand_shift: - if use_modal_wise_shift: - shift = torch.full((n_modal, n_chem), shift) - else: - shift = [shift] * n_chem - if _expand_scale: - if use_modal_wise_scale: - scale = torch.full((n_modal, n_chem), scale) - else: - scale = [scale] * n_chem - - Logger().write('Use element-wise shift, scale\n') - if use_modal_wise_shift or use_modal_wise_scale: - for modal_key, modal_idx in modal_map.items(): - Logger().writeline(f'For modal = {modal_key}') - print_shift = shift[modal_idx] if use_modal_wise_shift else shift - print_scale = scale[modal_idx] if use_modal_wise_scale else scale - for cstr, sh, sc in zip(chem_strs, print_shift, print_scale): - Logger().format_k_v(f'{cstr}', f'{sh:.6f}, {sc:.6f}', write=True) - else: - for cstr, sh, sc in zip(chem_strs, shift, scale): - Logger().format_k_v(f'{cstr}', f'{sh:.6f}, {sc:.6f}', write=True) - else: - log.write('Use global shift, scale\n') - log.format_k_v('shift, scale', f'{shift:.6f}, {scale:.6f}', write=True) - - assert isinstance(conv_denominator, list) and all( - isinstance(deno, float) for deno in conv_denominator - ) - log.format_k_v( - '(1st) conv_denominator is', f'{conv_denominator[0]:.6f}', write=True - ) - - config[KEY.USE_SPECIES_WISE_SHIFT_SCALE] = use_species_wise_shift_scale - return shift, scale, conv_denominator - - -# TODO: This is too long -def processing_dataset(config, working_dir): - log = Logger() - prefix = f'{os.path.abspath(working_dir)}/' - is_stress = config[KEY.IS_TRAIN_STRESS] - checkpoint_given = config[KEY.CONTINUE][KEY.CHECKPOINT] is not False - cutoff = config[KEY.CUTOFF] - - log.write('\nInitializing dataset...\n') - - dataset = AtomGraphDataset({}, cutoff) - load_dataset = config[KEY.LOAD_DATASET] - if type(load_dataset) is str: - load_dataset = [load_dataset] - for file in load_dataset: - dataset.augment(dataset_load(file, config)) - - dataset.group_by_key() # apply labels inside original datapoint - dataset.unify_dtypes() # unify dtypes of all data points - - # TODO: I think manual chemical species input is redundant - chem_in_db = dataset.get_species() - if config[KEY.CHEMICAL_SPECIES] == 'auto' and not checkpoint_given: - log.writeline('Auto detect chemical species from dataset') - config.update(chemical_species_preprocess(chem_in_db)) - elif config[KEY.CHEMICAL_SPECIES] == 'auto' and checkpoint_given: - pass # copied from checkpoint in processing_continue.py - elif config[KEY.CHEMICAL_SPECIES] != 'auto' and not checkpoint_given: - pass # processed in parse_input.py - else: # config[KEY.CHEMICAL_SPECIES] != "auto" and checkpoint_given - log.writeline('Ignore chemical species in yaml, use checkpoint') - # already processed in processing_continue.py - - # basic dataset compatibility check with previous model - if checkpoint_given: - chem_from_cp = config[KEY.CHEMICAL_SPECIES] - if not all(chem in chem_from_cp for chem in chem_in_db): - raise ValueError('Chemical species in checkpoint is not compatible') - - # check what modalities are used in dataset - if config[KEY.USE_MODALITY]: - modalities = dataset.get_modalities() - num_modalities = len(modalities) - if num_modalities < 2: - Logger().writeline('Only one modal is given, ignore modality') - config.uptate({KEY.USE_MODALITY: False}) - - else: - modal_map_cp = config[KEY.MODAL_MAP + '_cp'] if checkpoint_given else {} - modal_map = modal_map_cp.copy() - current_idx = len(modal_map_cp) - for modal_key in modalities: - if modal_key not in modal_map.keys(): - modal_map[modal_key] = current_idx - current_idx += 1 - - if config[KEY.IS_DDP]: - # Synchronize modal_map - torch.cuda.set_device(config[KEY.LOCAL_RANK]) - modal_map_bcast = [modal_map] - dist.broadcast_object_list(modal_map_bcast, src=0) - modal_map = modal_map_bcast[0] - - config.update( - { - KEY.NUM_MODALITIES: len(modal_map), - KEY.MODAL_MAP: modal_map, - KEY.MODAL_LIST: list(modal_map.keys()), - } - ) - - dataset.write_modal_attr( - modal_map, - config[KEY.USE_MODAL_WISE_SHIFT] or config[KEY.USE_MODAL_WISE_SCALE], - ) - - # --------------- save dataset regardless of train/valid--------------# - save_dataset = config[KEY.SAVE_DATASET] - save_by_label = config[KEY.SAVE_BY_LABEL] - if save_dataset: - if save_dataset.endswith('.sevenn_data') is False: - save_dataset += '.sevenn_data' - if (save_dataset.startswith('.') or save_dataset.startswith('/')) is False: - save_dataset = prefix + save_dataset # save_data set is plain file name - dataset.save(save_dataset) - log.format_k_v('Dataset saved to', save_dataset, write=True) - # log.write(f"Loaded full dataset saved to : {save_dataset}\n") - if save_by_label: - dataset.save(prefix, by_label=True) - log.format_k_v('Dataset saved by label', prefix, write=True) - # --------------------------------------------------------------------# - - # TODO: testset is not used - ignore_test = not config.get(KEY.USE_TESTSET, False) - if KEY.LOAD_VALIDSET in config and config[KEY.LOAD_VALIDSET]: - train_set = dataset - test_set = AtomGraphDataset([], config[KEY.CUTOFF]) - - log.write('Loading validset from load_validset\n') - valid_set = AtomGraphDataset({}, cutoff) - for file in config[KEY.LOAD_VALIDSET]: - valid_set.augment(dataset_load(file, config)) - valid_set.group_by_key() - valid_set.unify_dtypes() - - # condition: validset labels should be subset of trainset labels - valid_labels = valid_set.user_labels - train_labels = train_set.user_labels - if set(valid_labels).issubset(set(train_labels)) is False: - valid_set = AtomGraphDataset(valid_set.to_list(), cutoff) - valid_set.rewrite_labels_to_data() - train_set = AtomGraphDataset(train_set.to_list(), cutoff) - train_set.rewrite_labels_to_data() - Logger().write('WARNING! validset labels is not subset of trainset\n') - Logger().write('We overwrite all the train, valid labels to default.\n') - Logger().write('Please create validset by sevenn_graph_build with -l\n') - - Logger().write('the validset loaded, load_dataset is now train_set\n') - Logger().write('the ratio will be ignored\n') - - # condition: validset modalities should be subset of trainset modalities - if config[KEY.USE_MODALITY]: - config_modality = config[KEY.MODAL_LIST] - valid_modality = valid_set.get_modalities() - - if set(valid_modality).issubset(set(config_modality)) is False: - raise ValueError('validset modality is not subset of trainset') - - valid_set.write_modal_attr( - config[KEY.MODAL_MAP], - config[KEY.USE_MODAL_WISE_SHIFT] or config[KEY.USE_MODAL_WISE_SCALE], - ) - else: - train_set, valid_set, test_set = dataset.divide_dataset( - config[KEY.RATIO], ignore_test=ignore_test - ) - log.write(f'The dataset divided into train, valid by {KEY.RATIO}\n') - - log.format_k_v('\nloaded trainset size is', train_set.len(), write=True) - log.format_k_v('\nloaded validset size is', valid_set.len(), write=True) - - log.write('Dataset initialization was successful\n') - - log.write('\nNumber of atoms in the train_set:\n') - log.natoms_write(train_set.get_natoms(config[KEY.TYPE_MAP])) - - log.bar() - log.write('Per atom energy(eV/atom) distribution:\n') - log.statistic_write(train_set.get_statistics(KEY.PER_ATOM_ENERGY)) - log.bar() - log.write('Force(eV/Angstrom) distribution:\n') - log.statistic_write(train_set.get_statistics(KEY.FORCE)) - log.bar() - log.write('Stress(eV/Angstrom^3) distribution:\n') - try: - log.statistic_write(train_set.get_statistics(KEY.STRESS)) - except KeyError: - log.write('\n Stress is not included in the train_set\n') - if is_stress: - is_stress = False - log.write('Turn off stress training\n') - log.bar() - - # saved data must have atomic numbers as X not one hot idx - if config[KEY.SAVE_BY_TRAIN_VALID]: - train_set.save(prefix + 'train') - valid_set.save(prefix + 'valid') - log.format_k_v('Dataset saved by train, valid', prefix, write=True) - - # inconsistent .info dict give error when collate - _, _ = train_set.separate_info() - _, _ = valid_set.separate_info() - - if train_set.x_is_one_hot_idx is False: - train_set.x_to_one_hot_idx(config[KEY.TYPE_MAP]) - if valid_set.x_is_one_hot_idx is False: - valid_set.x_to_one_hot_idx(config[KEY.TYPE_MAP]) - - log.format_k_v('training_set size', train_set.len(), write=True) - log.format_k_v('validation_set size', valid_set.len(), write=True) - - shift, scale, conv_denominator = handle_shift_scale( - config, train_set, checkpoint_given - ) - config.update( - { - KEY.SHIFT: shift, - KEY.SCALE: scale, - KEY.CONV_DENOMINATOR: conv_denominator, - } - ) - - data_lists = (train_set.to_list(), valid_set.to_list(), test_set.to_list()) - - return data_lists diff --git a/mace-bench/3rdparty/SevenNet/sevenn/scripts/processing_epoch.py b/mace-bench/3rdparty/SevenNet/sevenn/scripts/processing_epoch.py deleted file mode 100644 index ec2d7012301ea7a7f2ae9aadff51a616dbe4bcab..0000000000000000000000000000000000000000 --- a/mace-bench/3rdparty/SevenNet/sevenn/scripts/processing_epoch.py +++ /dev/null @@ -1,182 +0,0 @@ -import os -from copy import deepcopy -from typing import Optional - -import torch -from torch.utils.data.distributed import DistributedSampler - -import sevenn._keys as KEY -from sevenn.error_recorder import ErrorRecorder -from sevenn.logger import Logger -from sevenn.train.trainer import Trainer - - -def processing_epoch_v2( - config: dict, - trainer: Trainer, - loaders: dict, # dict[str, Dataset] - start_epoch: int = 1, - train_loader_key: str = 'trainset', - error_recorder: Optional[ErrorRecorder] = None, - total_epoch: Optional[int] = None, - per_epoch: Optional[int] = None, - best_metric_loader_key: str = 'validset', - best_metric: Optional[str] = None, - write_csv: bool = True, - working_dir: Optional[str] = None, -): - from sevenn.util import unique_filepath - - log = Logger() - write_csv = write_csv and log.rank == 0 - working_dir = working_dir or os.getcwd() - prefix = f'{os.path.abspath(working_dir)}/' - - total_epoch = total_epoch or config[KEY.EPOCH] - per_epoch = per_epoch or config.get(KEY.PER_EPOCH, 10) - best_metric = best_metric or config.get(KEY.BEST_METRIC, 'TotalLoss') - recorder = error_recorder or ErrorRecorder.from_config( - config, trainer.loss_functions - ) - recorders = {k: deepcopy(recorder) for k in loaders} - - best_val = float('inf') - best_key = None - if best_metric_loader_key in recorders: - best_key = recorders[best_metric_loader_key].get_key_str(best_metric) - if best_key is None: - log.writeline( - f'Failed to get error recorder key: {best_metric} or ' - + f'{best_metric_loader_key} is missing. There will be no best ' - + 'checkpoint.' - ) - - csv_path = unique_filepath(f'{prefix}/lc.csv') - if write_csv: - head = ['epoch', 'lr'] - for k, rec in recorders.items(): - head.extend(list(rec.get_dct(prefix=k))) - with open(csv_path, 'w') as f: - f.write(','.join(head) + '\n') - - if start_epoch == 1: - path = f'{prefix}/checkpoint_0.pth' # save first epoch - trainer.write_checkpoint(path, config=config, epoch=0) - - for epoch in range(start_epoch, total_epoch + 1): # one indexing - log.timer_start('epoch') - lr = trainer.get_lr() - log.bar() - log.write(f'Epoch {epoch}/{total_epoch} lr: {lr:8f}\n') - log.bar() - - csv_dct = {'epoch': str(epoch), 'lr': f'{lr:8f}'} - errors = {} - for k, loader in loaders.items(): - is_train = k == train_loader_key - if ( - trainer.distributed - and isinstance(loader.sampler, DistributedSampler) - and is_train - and config.get('train_shuffle', True) - ): - loader.sampler.set_epoch(epoch) - - rec = recorders[k] - trainer.run_one_epoch(loader, is_train, rec) - csv_dct.update(rec.get_dct(prefix=k)) - errors[k] = rec.epoch_forward() - log.write_full_table(list(errors.values()), list(errors)) - trainer.scheduler_step(best_val) - - if write_csv: - with open(csv_path, 'a') as f: - f.write(','.join(list(csv_dct.values())) + '\n') - - if best_key and errors[best_metric_loader_key][best_key] < best_val: - path = f'{prefix}/checkpoint_best.pth' - trainer.write_checkpoint(path, config=config, epoch=epoch) - best_val = errors[best_metric_loader_key][best_key] - log.writeline('Best checkpoint written') - - if epoch % per_epoch == 0: - path = f'{prefix}/checkpoint_{epoch}.pth' - trainer.write_checkpoint(path, config=config, epoch=epoch) - - log.timer_end('epoch', message=f'Epoch {epoch} elapsed') - return trainer - - -def processing_epoch(trainer, config, loaders, start_epoch, init_csv, working_dir): - log = Logger() - prefix = f'{os.path.abspath(working_dir)}/' - train_loader, valid_loader = loaders - - is_distributed = config[KEY.IS_DDP] - rank = config[KEY.RANK] - total_epoch = config[KEY.EPOCH] - per_epoch = config[KEY.PER_EPOCH] - train_recorder = ErrorRecorder.from_config(config) - valid_recorder = ErrorRecorder.from_config(config) - best_metric = config[KEY.BEST_METRIC] - csv_fname = f'{prefix}{config[KEY.CSV_LOG]}' - current_best = float('inf') - - if init_csv: - csv_header = ['Epoch', 'Learning_rate'] - # Assume train valid have the same metrics - for metric in train_recorder.get_metric_dict().keys(): - csv_header.append(f'Train_{metric}') - csv_header.append(f'Valid_{metric}') - log.init_csv(csv_fname, csv_header) - - def write_checkpoint(epoch, is_best=False): - if is_distributed and rank != 0: - return - suffix = '_best' if is_best else f'_{epoch}' - checkpoint = trainer.get_checkpoint_dict() - checkpoint.update({'config': config, 'epoch': epoch}) - torch.save(checkpoint, f'{prefix}/checkpoint{suffix}.pth') - - fin_epoch = total_epoch + start_epoch - for epoch in range(start_epoch, fin_epoch): - lr = trainer.get_lr() - log.timer_start('epoch') - log.bar() - log.write(f'Epoch {epoch}/{fin_epoch - 1} lr: {lr:8f}\n') - log.bar() - - trainer.run_one_epoch( - train_loader, is_train=True, error_recorder=train_recorder - ) - train_err = train_recorder.epoch_forward() - - trainer.run_one_epoch(valid_loader, error_recorder=valid_recorder) - valid_err = valid_recorder.epoch_forward() - - csv_values = [epoch, lr] - for metric in train_err: - csv_values.append(train_err[metric]) - csv_values.append(valid_err[metric]) - log.append_csv(csv_fname, csv_values) - - log.write_full_table([train_err, valid_err], ['Train', 'Valid']) - - val = None - for metric in valid_err: - # loose string comparison, - # e.g. "Energy" in "TotalEnergy" or "Energy_Loss" - if best_metric in metric: - val = valid_err[metric] - break - assert val is not None, f'Metric {best_metric} not found in {valid_err}' - trainer.scheduler_step(val) - - log.timer_end('epoch', message=f'Epoch {epoch} elapsed') - - if val < current_best: - current_best = val - write_checkpoint(epoch, is_best=True) - log.writeline('Best checkpoint written') - if epoch % per_epoch == 0: - write_checkpoint(epoch) diff --git a/mace-bench/3rdparty/SevenNet/sevenn/scripts/train.py b/mace-bench/3rdparty/SevenNet/sevenn/scripts/train.py deleted file mode 100644 index b0dabab733444510085ef3d2b2c1a96d816ab1cc..0000000000000000000000000000000000000000 --- a/mace-bench/3rdparty/SevenNet/sevenn/scripts/train.py +++ /dev/null @@ -1,139 +0,0 @@ -from typing import List, Optional - -import torch.distributed as dist -from torch.utils.data.distributed import DistributedSampler -from torch_geometric.loader import DataLoader - -import sevenn._keys as KEY -from sevenn.logger import Logger -from sevenn.model_build import build_E3_equivariant_model -from sevenn.scripts.processing_continue import ( - convert_modality_of_checkpoint_state_dct, -) -from sevenn.train.trainer import Trainer - - -def loader_from_config(config, dataset, is_train=False): - batch_size = config[KEY.BATCH_SIZE] - shuffle = is_train and config[KEY.TRAIN_SHUFFLE] - sampler = None - loader_args = { - 'dataset': dataset, - 'batch_size': batch_size, - 'shuffle': shuffle - } - if KEY.NUM_WORKERS in config and config[KEY.NUM_WORKERS] > 0: - loader_args.update({'num_workers': config[KEY.NUM_WORKERS]}) - - if config[KEY.IS_DDP]: - dist.barrier() - sampler = DistributedSampler( - dataset, dist.get_world_size(), dist.get_rank(), shuffle=shuffle - ) - loader_args.update({'sampler': sampler}) - loader_args.pop('shuffle') # sampler is mutually exclusive with shuffle - return DataLoader(**loader_args) - - -def train_v2(config, working_dir: str): - """ - Main program flow, since v0.9.6 - """ - import sevenn.train.atoms_dataset as atoms_dataset - import sevenn.train.graph_dataset as graph_dataset - import sevenn.train.modal_dataset as modal_dataset - - from .processing_continue import processing_continue_v2 - from .processing_epoch import processing_epoch_v2 - - log = Logger() - log.timer_start('total') - - if KEY.LOAD_TRAINSET not in config and KEY.LOAD_DATASET in config: - log.writeline('***************************************************') - log.writeline('For train_v2, please use load_trainset_path instead') - log.writeline('I will assign load_trainset as load_dataset') - log.writeline('***************************************************') - config[KEY.LOAD_TRAINSET] = config.pop(KEY.LOAD_DATASET) - - # config updated - start_epoch = 1 - state_dicts: Optional[List[dict]] = None - if config[KEY.CONTINUE][KEY.CHECKPOINT]: - state_dicts, start_epoch = processing_continue_v2(config) - - if config.get(KEY.USE_MODALITY, False): - datasets = modal_dataset.from_config(config, working_dir) - elif config[KEY.DATASET_TYPE] == 'graph': - datasets = graph_dataset.from_config(config, working_dir) - elif config[KEY.DATASET_TYPE] == 'atoms': - datasets = atoms_dataset.from_config(config, working_dir) - else: - raise ValueError(f'Unknown dataset type: {config[KEY.DATASET_TYPE]}') - loaders = { - k: loader_from_config(config, v, is_train=(k == 'trainset')) - for k, v in datasets.items() - } - - log.write('\nModel building...\n') - model = build_E3_equivariant_model(config) - log.print_model_info(model, config) - - trainer = Trainer.from_config(model, config) - if state_dicts: - trainer.load_state_dicts(*state_dicts, strict=False) - - processing_epoch_v2( - config, trainer, loaders, start_epoch, working_dir=working_dir - ) - log.timer_end('total', message='Total wall time') - - -def train(config, working_dir: str): - """ - Main program flow, until v0.9.5 - """ - from .processing_continue import processing_continue - from .processing_dataset import processing_dataset - from .processing_epoch import processing_epoch - - log = Logger() - log.timer_start('total') - - # config updated - state_dicts: Optional[List[dict]] = None - if config[KEY.CONTINUE][KEY.CHECKPOINT]: - state_dicts, start_epoch, init_csv = processing_continue(config) - else: - start_epoch, init_csv = 1, True - - # config updated - train, valid, _ = processing_dataset(config, working_dir) - datasets = {'dataset': train, 'validset': valid} - loaders = { - k: loader_from_config(config, v, is_train=(k == 'dataset')) - for k, v in datasets.items() - } - loaders = list(loaders.values()) - - log.write('\nModel building...\n') - model = build_E3_equivariant_model(config) - - log.write('Model building was successful\n') - - trainer = Trainer.from_config(model, config) - if state_dicts: - state_dicts = convert_modality_of_checkpoint_state_dct( - config, state_dicts - ) - trainer.load_state_dicts(*state_dicts, strict=False) - - log.print_model_info(model, config) - - Logger().write('Trainer initialized, ready to training\n') - Logger().bar() - log.write('Trainer initialized, ready to training\n') - log.bar() - - processing_epoch(trainer, config, loaders, start_epoch, init_csv, working_dir) - log.timer_end('total', message='Total wall time') diff --git a/mace-bench/3rdparty/SevenNet/sevenn/sevenn_logger.py b/mace-bench/3rdparty/SevenNet/sevenn/sevenn_logger.py deleted file mode 100644 index 7efea4af1484224287a11625cfdbf7a8f2a7b762..0000000000000000000000000000000000000000 --- a/mace-bench/3rdparty/SevenNet/sevenn/sevenn_logger.py +++ /dev/null @@ -1,6 +0,0 @@ -import warnings - -from .logger import * # noqa: F403 - -warnings.warn('Please use sevenn.logger instead of sevenn.sevenn_logger', - DeprecationWarning, stacklevel=2) diff --git a/mace-bench/3rdparty/SevenNet/sevenn/sevennet_calculator.py b/mace-bench/3rdparty/SevenNet/sevenn/sevennet_calculator.py deleted file mode 100644 index ba3c78706eab27ac3925620f325fab25e4bdb09d..0000000000000000000000000000000000000000 --- a/mace-bench/3rdparty/SevenNet/sevenn/sevennet_calculator.py +++ /dev/null @@ -1,6 +0,0 @@ -import warnings - -from .calculator import * # noqa: F403 - -warnings.warn('Please use sevenn.calculator instead of sevenn.sevennet_calculator', - DeprecationWarning, stacklevel=2) diff --git a/mace-bench/3rdparty/SevenNet/sevenn/test b/mace-bench/3rdparty/SevenNet/sevenn/test deleted file mode 100644 index 8b137891791fe96927ad78e64b0aad7bded08bdc..0000000000000000000000000000000000000000 --- a/mace-bench/3rdparty/SevenNet/sevenn/test +++ /dev/null @@ -1 +0,0 @@ - diff --git a/mace-bench/3rdparty/SevenNet/sevenn/train/__init__.py b/mace-bench/3rdparty/SevenNet/sevenn/train/__init__.py deleted file mode 100644 index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000 diff --git a/mace-bench/3rdparty/SevenNet/sevenn/train/atoms_dataset.py b/mace-bench/3rdparty/SevenNet/sevenn/train/atoms_dataset.py deleted file mode 100644 index 178e8909628274e9a909b1147e75c03eb100a63f..0000000000000000000000000000000000000000 --- a/mace-bench/3rdparty/SevenNet/sevenn/train/atoms_dataset.py +++ /dev/null @@ -1,314 +0,0 @@ -import os -import random -import warnings -from collections import Counter -from typing import Any, Callable, Dict, List, Optional, Union - -import numpy as np -import torch.utils.data -from ase.atoms import Atoms -from ase.data import chemical_symbols -from ase.io import write -from tqdm import tqdm - -import sevenn._keys as KEY -import sevenn.train.dataload as dataload -import sevenn.util as util -from sevenn._const import NUM_UNIV_ELEMENT -from sevenn.atom_graph_data import AtomGraphData - -_warn_avg_num_neigh = """SevenNetAtomsDataset does not provide correct avg_num_neigh -as it does not build graph. We will compute only random 10000 structures graph to -approximate this value. If you want more precise avg_num_neigh, -use SevenNetGraphDataset. If it is not viable due to memory limit, you -need online algorithm to do this , which is not yet implemented in the SevenNet""" - - -class SevenNetAtomsDataset(torch.utils.data.Dataset): - """ - Args: - cutoff: edge cutoff of given AtomGraphData - files: list of filenames or dict describing how to parse the file - ASE readable (with proper extension), structure_list, .sevenn_data, - dict containing file_list (see dict_reader of train/dataload.py) - info_dict_copy_keys: patch these keys from KEY.INFO to graph when accessing. - default is KEY.DATA_WEIGHT and KEY.DATA_MODALITY, which may accessed - while training. - **process_kwargs: keyword arguments that will be passed into ase.io.read - """ - - def __init__( - self, - cutoff: float, - files: Union[str, List[str]], - atoms_filter: Optional[Callable] = None, - atoms_transform: Optional[Callable] = None, - transform: Optional[Callable] = None, - use_data_weight: bool = False, - **process_kwargs, - ): - self.cutoff = cutoff - if isinstance(files, str): - files = [files] # user convenience - files = [os.path.abspath(file) for file in files] - self._files = files - self.atoms_filter = atoms_filter - self.atoms_transform = atoms_transform - self.transform = transform - self.use_data_weight = use_data_weight - self._scanned = False - self._avg_num_neigh_approx = None - self.statistics = {} - - atoms_list = [] - for file in files: - atoms_list.extend( - SevenNetAtomsDataset.file_to_atoms_list(file, **process_kwargs) - ) - self._atoms_list = atoms_list - - super().__init__() - - @staticmethod - def file_to_atoms_list(file: Union[str, dict], **kwargs) -> List[Atoms]: - if isinstance(file, dict): - atoms_list = dataload.dict_reader(file) - elif 'structure_list' in file: - atoms_dct = dataload.structure_list_reader(file) - atoms_list = [] - for lst in atoms_dct.values(): - atoms_list.extend(lst) - else: - atoms_list = dataload.ase_reader(file, **kwargs) - return atoms_list - - def save(self, path): - # Save atoms list as extxyz - write(path, self._atoms_list, format='extxyz') - - def _graph_build(self, atoms): - return dataload.atoms_to_graph( - atoms, self.cutoff, transfer_info=False, y_from_calc=False - ) - - def __len__(self): - return len(self._atoms_list) - - def __getitem__(self, index): - atoms = self._atoms_list[index] - if self.atoms_transform is not None: - atoms = self.atoms_transform(atoms) - - graph = self._graph_build(atoms) - if self.transform is not None: - graph = self.transform(graph) - - if self.use_data_weight: - weight = graph[KEY.INFO].pop( - KEY.DATA_WEIGHT, {'energy': 1.0, 'force': 1.0, 'stress': 1.0} - ) - graph[KEY.DATA_WEIGHT] = weight - - return AtomGraphData.from_numpy_dict(graph) - - @property - def species(self): - self.run_stat() - return [z for z in self.statistics['_natoms'].keys() if z != 'total'] - - @property - def natoms(self): - self.run_stat() - return self.statistics['_natoms'] - - @property - def per_atom_energy_mean(self): - self.run_stat() - return self.statistics[KEY.PER_ATOM_ENERGY]['mean'] - - @property - def elemwise_reference_energies(self): - from sklearn.linear_model import Ridge - - c = self.statistics['_composition'] - y = self.statistics[KEY.ENERGY]['_array'] - zero_indices = np.all(c == 0, axis=0) - c_reduced = c[:, ~zero_indices] - # will not 100% reproduce, as it is sorted by Z - # train/dataset.py was sorted by alphabets of chemical species - coef_reduced = Ridge(alpha=0.1, fit_intercept=False).fit(c_reduced, y).coef_ - full_coeff = np.zeros(NUM_UNIV_ELEMENT) - full_coeff[~zero_indices] = coef_reduced - return full_coeff.tolist() # ex: full_coeff[1] = H_reference_energy - - @property - def force_rms(self): - self.run_stat() - mean = self.statistics[KEY.FORCE]['mean'] - std = self.statistics[KEY.FORCE]['std'] - return float((mean**2 + std**2) ** (0.5)) - - @property - def per_atom_energy_std(self): - self.run_stat() - return self.statistics['per_atom_energy']['std'] - - @property - def avg_num_neigh(self, n_sample=10000): - if self._avg_num_neigh_approx is None: - if len(self) > n_sample: - warnings.warn(_warn_avg_num_neigh) - n_sample = min(len(self), n_sample) - indices = random.sample(range(len(self)), n_sample) - n_neigh = [] - for i in indices: - graph = self[i] - _, nn = np.unique(graph[KEY.EDGE_IDX][0], return_counts=True) - n_neigh.append(nn) - n_neigh = np.concatenate(n_neigh) - self._avg_num_neigh_approx = np.mean(n_neigh) - return self._avg_num_neigh_approx - - @property - def sqrt_avg_num_neigh(self): - self.run_stat() - return self.avg_num_neigh**0.5 - - def run_stat(self): - """ - Loop over dataset and init any statistics might need - Unlink SevenNetGraphDataset, neighbors count is not computed as - it requires to build graph - """ - if self._scanned is True: - return # statistics already computed - y_keys: List[str] = [KEY.ENERGY, KEY.PER_ATOM_ENERGY, KEY.FORCE, KEY.STRESS] - natoms_counter = Counter() - composition = np.zeros((len(self), NUM_UNIV_ELEMENT)) - stats: Dict[str, Dict[str, Any]] = {y: {'_array': []} for y in y_keys} - - for i, atoms in tqdm( - enumerate(self._atoms_list), desc='run_stat', total=len(self) - ): - z = atoms.get_atomic_numbers() - natoms_counter.update(z.tolist()) - composition[i] = np.bincount(z, minlength=NUM_UNIV_ELEMENT) - for y, dct in stats.items(): - if y == KEY.ENERGY: - dct['_array'].append(atoms.info['y_energy']) - elif y == KEY.PER_ATOM_ENERGY: - dct['_array'].append(atoms.info['y_energy'] / len(atoms)) - elif y == KEY.FORCE: - dct['_array'].append(atoms.arrays['y_force'].reshape(-1)) - elif y == KEY.STRESS: - dct['_array'].append(atoms.info['y_stress'].reshape(-1)) - - for y, dct in stats.items(): - if y == KEY.FORCE: - array = np.concatenate(dct['_array']) - else: - array = np.array(dct['_array']).reshape(-1) - dct.update( - { - 'mean': float(np.mean(array)), - 'std': float(np.std(array)), - 'median': float(np.quantile(array, q=0.5)), - 'max': float(np.max(array)), - 'min': float(np.min(array)), - '_array': array, - } - ) - - natoms = {chemical_symbols[int(z)]: cnt for z, cnt in natoms_counter.items()} - natoms['total'] = sum(list(natoms.values())) - self.statistics.update( - { - '_composition': composition, - '_natoms': natoms, - **stats, - } - ) - self._scanned = True - - -# script, return dict of SevenNetAtomsDataset -def from_config( - config: Dict[str, Any], - working_dir: str = os.getcwd(), - dataset_keys: Optional[List[str]] = None, -): - from sevenn.logger import Logger - - log = Logger() - if dataset_keys is None: - dataset_keys = [] - for k in config: - if k.startswith('load_') and k.endswith('_path'): - dataset_keys.append(k) - - if KEY.LOAD_TRAINSET not in dataset_keys: - raise ValueError(f'{KEY.LOAD_TRAINSET} must be present in config') - - # initialize arguments for loading dataset - dataset_args = { - 'cutoff': config[KEY.CUTOFF], - 'use_data_weight': config.get(KEY.USE_WEIGHT, False), - **config[KEY.DATA_FORMAT_ARGS], - } - - datasets = {} - for dk in dataset_keys: - if not (paths := config[dk]): - continue - if isinstance(paths, str): - paths = [paths] - name = '_'.join([nn.strip() for nn in dk.split('_')[1:-1]]) - dataset_args.update({'files': paths}) - datasets[name] = SevenNetAtomsDataset(**dataset_args) - - if not config[KEY.COMPUTE_STATISTICS]: - log.writeline( - ( - 'Computing statistics is skipped, note that if any of other' - 'configurations requires statistics (shift, scale, avg_num_neigh,' - 'chemical_species as auto), SevenNet eventually raise an error!' - ) - ) - return datasets - - train_set = datasets['trainset'] - - chem_species = set(train_set.species) - # print statistics of each dataset - for name, dataset in datasets.items(): - dataset.run_stat() - log.bar() - log.writeline(f'{name} distribution:') - log.statistic_write(dataset.statistics) - log.format_k_v('# atoms (node)', dataset.natoms, write=True) - log.format_k_v('# structures (graph)', len(dataset), write=True) - - chem_species.update(dataset.species) - log.bar() - - # initialize known species from dataset if 'auto' - # sorted to alphabetical order (which is same as before) - chem_keys = [KEY.CHEMICAL_SPECIES, KEY.NUM_SPECIES, KEY.TYPE_MAP] - if all([config[ck] == 'auto' for ck in chem_keys]): # see parse_input.py - log.writeline('Known species are obtained from the dataset') - config.update(util.chemical_species_preprocess(sorted(list(chem_species)))) - - # retrieve shift, scale, conv_denominaotrs from user input (keyword) - init_from_stats = [KEY.SHIFT, KEY.SCALE, KEY.CONV_DENOMINATOR] - for k in init_from_stats: - input = config[k] # statistic key or numbers - # If it is not 'str', 1: It is 'continue' training - # 2: User manually inserted numbers - if isinstance(input, str) and hasattr(train_set, input): - var = getattr(train_set, input) - config.update({k: var}) - log.writeline(f'{k} is obtained from statistics') - elif isinstance(input, str) and not hasattr(train_set, input): - raise NotImplementedError(input) - - return datasets diff --git a/mace-bench/3rdparty/SevenNet/sevenn/train/collate.py b/mace-bench/3rdparty/SevenNet/sevenn/train/collate.py deleted file mode 100644 index 3e1ede9ea229f3f0f8ddafcfca43a0f4fbc89787..0000000000000000000000000000000000000000 --- a/mace-bench/3rdparty/SevenNet/sevenn/train/collate.py +++ /dev/null @@ -1,41 +0,0 @@ -from typing import Any, List, Optional, Sequence - -from ase.atoms import Atoms -from torch_geometric.loader.dataloader import Collater - -from sevenn.atom_graph_data import AtomGraphData - -from .dataload import atoms_to_graph - - -class AtomsToGraphCollater(Collater): - - def __init__( - self, - dataset: Sequence[Atoms], - cutoff: float, - transfer_info: bool = False, - follow_batch: Optional[List[str]] = None, - exclude_keys: Optional[List[str]] = None, - y_from_calc: bool = True, - ): - # quite original collator's type mismatch with [] - super().__init__([], follow_batch, exclude_keys) - self.dataset = dataset - self.cutoff = cutoff - self.transfer_info = transfer_info - self.y_from_calc = y_from_calc - - def __call__(self, batch: List[Any]) -> Any: - # build list of graph - graph_list = [] - for stct in batch: - graph = atoms_to_graph( - stct, - self.cutoff, - transfer_info=self.transfer_info, - y_from_calc=self.y_from_calc, - ) - graph = AtomGraphData.from_numpy_dict(graph) - graph_list.append(graph) - return super().__call__(graph_list) diff --git a/mace-bench/3rdparty/SevenNet/sevenn/train/dataload.py b/mace-bench/3rdparty/SevenNet/sevenn/train/dataload.py deleted file mode 100644 index 48cdc8b3a667719fa0a235023bd64bb472fcca14..0000000000000000000000000000000000000000 --- a/mace-bench/3rdparty/SevenNet/sevenn/train/dataload.py +++ /dev/null @@ -1,609 +0,0 @@ -import copy -import os.path -from functools import partial -from itertools import chain, islice -from typing import Callable, Dict, List, Optional - -import ase -import ase.io -import numpy as np -import torch.multiprocessing as mp -from ase.io.vasp_parsers.vasp_outcar_parsers import ( - Cell, - DefaultParsersContainer, - Energy, - OutcarChunkParser, - PositionsAndForces, - Stress, - outcarchunks, -) -from ase.neighborlist import primitive_neighbor_list -from ase.utils import string2index -from braceexpand import braceexpand -from tqdm import tqdm - -import sevenn._keys as KEY -from sevenn._const import LossType -from sevenn.atom_graph_data import AtomGraphData - -from .dataset import AtomGraphDataset - - -def _graph_build_matscipy(cutoff: float, pbc, cell, pos): - pbc_x = pbc[0] - pbc_y = pbc[1] - pbc_z = pbc[2] - - identity = np.identity(3, dtype=float) - max_positions = np.max(np.absolute(pos)) + 1 - - # Extend cell in non-periodic directions - # For models with more than 5 layers, - # the multiplicative constant needs to be increased. - if not pbc_x: - cell[0, :] = max_positions * 5 * cutoff * identity[0, :] - if not pbc_y: - cell[1, :] = max_positions * 5 * cutoff * identity[1, :] - if not pbc_z: - cell[2, :] = max_positions * 5 * cutoff * identity[2, :] - # it does not have self-interaction - edge_src, edge_dst, edge_vec, shifts = neighbour_list( - quantities='ijDS', - pbc=pbc, - cell=cell, - positions=pos, - cutoff=cutoff, - ) - # dtype issue - edge_src = edge_src.astype(np.int64) - edge_dst = edge_dst.astype(np.int64) - - return edge_src, edge_dst, edge_vec, shifts - - -def _graph_build_ase(cutoff: float, pbc, cell, pos): - # building neighbor list - edge_src, edge_dst, edge_vec, shifts = primitive_neighbor_list( - 'ijDS', pbc, cell, pos, cutoff, self_interaction=True - ) - - is_zero_idx = np.all(edge_vec == 0, axis=1) - is_self_idx = edge_src == edge_dst - non_trivials = ~(is_zero_idx & is_self_idx) - shifts = np.array(shifts[non_trivials]) - - edge_vec = edge_vec[non_trivials] - edge_src = edge_src[non_trivials] - edge_dst = edge_dst[non_trivials] - - return edge_src, edge_dst, edge_vec, shifts - - -_graph_build_f = _graph_build_ase -try: - from matscipy.neighbours import neighbour_list - - _graph_build_f = _graph_build_matscipy -except ImportError: - pass - - -def _correct_scalar(v): - if isinstance(v, np.ndarray): - v = v.squeeze() - assert v.ndim == 0, f'given {v} is not a scalar' - return v - elif isinstance(v, (int, float, np.integer, np.floating)): - return np.array(v) - else: - assert False, f'{type(v)} is not expected' - - -def unlabeled_atoms_to_graph(atoms: ase.Atoms, cutoff: float): - pos = atoms.get_positions() - cell = np.array(atoms.get_cell()) - pbc = atoms.get_pbc() - - edge_src, edge_dst, edge_vec, shifts = _graph_build_f(cutoff, pbc, cell, pos) - - edge_idx = np.array([edge_src, edge_dst]) - - atomic_numbers = atoms.get_atomic_numbers() - - cell = np.array(cell) - vol = _correct_scalar(atoms.cell.volume) - if vol == 0: - vol = np.array(np.finfo(float).eps) - - data = { - KEY.NODE_FEATURE: atomic_numbers, - KEY.ATOMIC_NUMBERS: atomic_numbers, - KEY.POS: pos, - KEY.EDGE_IDX: edge_idx, - KEY.EDGE_VEC: edge_vec, - KEY.CELL: cell, - KEY.CELL_SHIFT: shifts, - KEY.CELL_VOLUME: vol, - KEY.NUM_ATOMS: _correct_scalar(len(atomic_numbers)), - } - data[KEY.INFO] = {} - return data - - -def atoms_to_graph( - atoms: ase.Atoms, - cutoff: float, - transfer_info: bool = True, - y_from_calc: bool = False, - allow_unlabeled: bool = False, -): - """ - From ase atoms, return AtomGraphData as graph based on cutoff radius - Except for energy, force and stress labels must be numpy array type - as other cases are not tested. - Returns 'np.nan' with consistent shape for unlabeled data - (ex. stress of non-pbc system) - - Args: - atoms (Atoms): ase atoms - cutoff (float): cutoff radius - transfer_info (bool): if True, transfer ".info" from atoms to graph, - defaults to True - y_from_calc: if True, get ref values from calculator, defaults to False - Returns: - numpy dict that can be used to initialize AtomGraphData - by AtomGraphData(**atoms_to_graph(atoms, cutoff)) - , for scalar, its shape is (), and types are np.ndarray - Requires grad is handled by 'dataset' not here. - """ - if not y_from_calc: - y_energy = atoms.info['y_energy'] - y_force = atoms.arrays['y_force'] - y_stress = atoms.info.get('y_stress', np.full((6,), np.nan)) - if y_stress.shape == (3, 3): - y_stress = np.array( - [ - y_stress[0][0], - y_stress[1][1], - y_stress[2][2], - y_stress[0][1], - y_stress[1][2], - y_stress[2][0], - ] - ) - else: - y_stress = y_stress.squeeze() - else: - from_calc = _y_from_calc(atoms) - y_energy = from_calc['energy'] - y_force = from_calc['force'] - y_stress = from_calc['stress'] - assert y_stress.shape == (6,), 'If you see this, please raise a issue' - - if not allow_unlabeled and (np.isnan(y_energy) or np.isnan(y_force).any()): - raise ValueError('Unlabeled E or F found, set allow_unlabeled True') - - pos = atoms.get_positions() - cell = np.array(atoms.get_cell()) - pbc = atoms.get_pbc() - - edge_src, edge_dst, edge_vec, shifts = _graph_build_f(cutoff, pbc, cell, pos) - - edge_idx = np.array([edge_src, edge_dst]) - atomic_numbers = atoms.get_atomic_numbers() - - cell = np.array(cell) - vol = _correct_scalar(atoms.cell.volume) - if vol == 0: - vol = np.array(np.finfo(float).eps) - - data = { - KEY.NODE_FEATURE: atomic_numbers, - KEY.ATOMIC_NUMBERS: atomic_numbers, - KEY.POS: pos, - KEY.EDGE_IDX: edge_idx, - KEY.EDGE_VEC: edge_vec, - KEY.ENERGY: _correct_scalar(y_energy), - KEY.FORCE: y_force, - KEY.STRESS: y_stress.reshape(1, 6), # to make batch have (n_node, 6) - KEY.CELL: cell, - KEY.CELL_SHIFT: shifts, - KEY.CELL_VOLUME: vol, - KEY.NUM_ATOMS: _correct_scalar(len(atomic_numbers)), - KEY.PER_ATOM_ENERGY: _correct_scalar(y_energy / len(pos)), - } - - if transfer_info and atoms.info is not None: - info = copy.deepcopy(atoms.info) - # save only metadata - info.pop('y_energy', None) - info.pop('y_force', None) - info.pop('y_stress', None) - data[KEY.INFO] = info - else: - data[KEY.INFO] = {} - - return data - - -def graph_build( - atoms_list: List, - cutoff: float, - num_cores: int = 1, - transfer_info: bool = True, - y_from_calc: bool = False, - allow_unlabeled: bool = False, -) -> List[AtomGraphData]: - """ - parallel version of graph_build - build graph from atoms_list and return list of AtomGraphData - Args: - atoms_list (List): list of ASE atoms - cutoff (float): cutoff radius of graph - num_cores (int): number of cores to use - transfer_info (bool): if True, copy info from atoms to graph, - defaults to True - y_from_calc (bool): Get reference y labels from calculator, defaults to False - Returns: - List[AtomGraphData]: list of AtomGraphData - """ - serial = num_cores == 1 - inputs = [ - (atoms, cutoff, transfer_info, y_from_calc, allow_unlabeled) - for atoms in atoms_list - ] - - if not serial: - pool = mp.Pool(num_cores) - graph_list = pool.starmap( - atoms_to_graph, - tqdm(inputs, total=len(atoms_list), desc=f'graph_build ({num_cores})'), - ) - pool.close() - pool.join() - else: - graph_list = [ - atoms_to_graph(*input_) - for input_ in tqdm(inputs, desc='graph_build (1)') - ] - - graph_list = [AtomGraphData.from_numpy_dict(g) for g in graph_list] - - return graph_list - - -def _y_from_calc(atoms: ase.Atoms): - ret = { - 'energy': np.nan, - 'force': np.full((len(atoms), 3), np.nan), - 'stress': np.full((6,), np.nan), - } - - if atoms.calc is None: - return ret - - try: - ret['energy'] = atoms.get_potential_energy(force_consistent=True) - except NotImplementedError: - ret['energy'] = atoms.get_potential_energy() - - try: - ret['force'] = atoms.get_forces(apply_constraint=False) - except NotImplementedError: - pass - - try: - y_stress = -1 * atoms.get_stress() # it ensures correct shape - ret['stress'] = np.array(y_stress[[0, 1, 2, 5, 3, 4]]) - except RuntimeError: - pass - return ret - - -def _set_atoms_y( - atoms_list: List[ase.Atoms], - energy_key: Optional[str] = None, - force_key: Optional[str] = None, - stress_key: Optional[str] = None, -) -> List[ase.Atoms]: - """ - Define how SevenNet reads ASE.atoms object for its y label - If energy_key, force_key, or stress_key is given, the corresponding - label is obtained from .info dict of Atoms object. These values should - have eV, eV/Angstrom, and eV/Angstrom^3 for energy, force, and stress, - respectively. (stress in Voigt notation) - - Args: - atoms_list (list[ase.Atoms]): target atoms to set y_labels - energy_key (str, optional): key to get energy. Defaults to None. - force_key (str, optional): key to get force. Defaults to None. - stress_key (str, optional): key to get stress. Defaults to None. - - Returns: - list[ase.Atoms]: list of ase.Atoms - - Raises: - RuntimeError: if ase atoms are somewhat imperfect - - Use free_energy: atoms.get_potential_energy(force_consistent=True) - If it is not available, use atoms.get_potential_energy() - If stress is available, initialize stress tensor - Ignore constraints like selective dynamics - """ - for atoms in atoms_list: - from_calc = _y_from_calc(atoms) - if energy_key is not None: - atoms.info['y_energy'] = atoms.info.pop(energy_key) - else: - atoms.info['y_energy'] = from_calc['energy'] - - if force_key is not None: - atoms.arrays['y_force'] = atoms.arrays.pop(force_key) - else: - atoms.arrays['y_force'] = from_calc['force'] - - if stress_key is not None: - y_stress = -1 * atoms.info.pop(stress_key) - atoms.info['y_stress'] = np.array(y_stress[[0, 1, 2, 5, 3, 4]]) - else: - atoms.info['y_stress'] = from_calc['stress'] - - return atoms_list - - -def ase_reader( - filename: str, - energy_key: Optional[str] = None, - force_key: Optional[str] = None, - stress_key: Optional[str] = None, - index: str = ':', - **kwargs, -) -> List[ase.Atoms]: - """ - Wrapper of ase.io.read - """ - atoms_list = ase.io.read(filename, index=index, **kwargs) - if not isinstance(atoms_list, list): - atoms_list = [atoms_list] - - return _set_atoms_y(atoms_list, energy_key, force_key, stress_key) - - -# Reader -def structure_list_reader(filename: str, format_outputs: Optional[str] = None): - """ - Read from structure_list using braceexpand and ASE - - Args: - fname : filename of structure_list - - Returns: - dictionary of lists of ASE structures. - key is title of training data (user-define) - """ - parsers = DefaultParsersContainer( - PositionsAndForces, Stress, Energy, Cell - ).make_parsers() - ocp = OutcarChunkParser(parsers=parsers) - - def parse_label(line): - line = line.strip() - if line.startswith('[') is False: - return False - elif line.endswith(']') is False: - raise ValueError('wrong structure_list title format') - return line[1:-1] - - def parse_fileline(line): - line = line.strip().split() - if len(line) == 1: - line.append(':') - elif len(line) != 2: - raise ValueError('wrong structure_list format') - return line[0], line[1] - - structure_list_file = open(filename, 'r') - lines = structure_list_file.readlines() - - raw_str_dict = {} - label = 'Default' - for line in lines: - if line.strip() == '': - continue - tmp_label = parse_label(line) - if tmp_label: - label = tmp_label - raw_str_dict[label] = [] - continue - elif label in raw_str_dict: - files_expr, index_expr = parse_fileline(line) - raw_str_dict[label].append((files_expr, index_expr)) - else: - raise ValueError('wrong structure_list format') - structure_list_file.close() - - structures_dict = {} - info_dct = {'data_from': 'user_OUTCAR'} - for title, file_lines in raw_str_dict.items(): - stct_lists = [] - for file_line in file_lines: - files_expr, index_expr = file_line - index = string2index(index_expr) - for expanded_filename in list(braceexpand(files_expr)): - f_stream = open(expanded_filename, 'r') - # generator of all outcar ionic steps - gen_all = outcarchunks(f_stream, ocp) - try: # TODO: index may not slice, it can be integer - it_atoms = islice(gen_all, index.start, index.stop, index.step) - except ValueError: - # TODO: support - # negative index - raise ValueError('Negative index is not supported yet') - - info_dct_f = { - **info_dct, - 'file': os.path.abspath(expanded_filename), - } - for idx, o in enumerate(it_atoms): - try: - it_atoms = islice( - gen_all, index.start, index.stop, index.step - ) - except ValueError: - # TODO: support - # negative index - raise ValueError('Negative index is not supported yet') - - info_dct_f = { - **info_dct, - 'file': os.path.abspath(expanded_filename), - } - for idx, o in enumerate(it_atoms): - try: - istep = index.start + idx * index.step # type: ignore - atoms = o.build() - atoms.info = {**info_dct_f, 'ionic_step': istep}.copy() - except TypeError: # it is not slice of ionic steps - atoms = o.build() - atoms.info = info_dct_f.copy() - stct_lists.append(atoms) - f_stream.close() - else: - stct_lists += ase.io.read( - expanded_filename, - index=index_expr, - parallel=False, - ) - structures_dict[title] = stct_lists - return {k: _set_atoms_y(v) for k, v in structures_dict.items()} - - -def dict_reader(data_dict: Dict): - data_dict_cp = copy.deepcopy(data_dict) - - ret = [] - file_list = data_dict_cp.pop('file_list', None) - if file_list is None: - raise KeyError('file_list is not found') - - data_weight_default = { - 'energy': 1.0, - 'force': 1.0, - 'stress': 1.0, - } - data_weight = data_weight_default.copy() - data_weight.update(data_dict_cp.pop(KEY.DATA_WEIGHT, {})) - - for file_dct in file_list: - ftype = file_dct.pop('data_format', 'ase') - files = list(braceexpand(file_dct.pop('file'))) - if ftype == 'ase': - ret.extend(chain(*[ase_reader(f, **file_dct) for f in files])) - elif ftype == 'graph': - continue - else: - raise ValueError(f'{ftype} yet') - - for atoms in ret: - atoms.info.update(data_dict_cp) - atoms.info.update({KEY.DATA_WEIGHT: data_weight}) - return _set_atoms_y(ret) - - -def match_reader(reader_name: str, **kwargs): - reader = None - metadata = {} - if reader_name == 'structure_list': - reader = partial(structure_list_reader, **kwargs) - metadata.update({'origin': 'structure_list'}) - else: - reader = partial(ase_reader, **kwargs) - metadata.update({'origin': 'ase_reader'}) - return reader, metadata - - -def file_to_dataset( - file: str, - cutoff: float, - cores: int = 1, - reader: Callable = ase_reader, - label: Optional[str] = None, - transfer_info: bool = True, - use_weight: bool = False, - use_modality: bool = False, -): - """ - Deprecated - Read file by reader > get list of atoms or dict of atoms - """ - - # expect label: atoms_list dct or atoms or list of atoms - atoms = reader(file) - - if type(atoms) is list: - if label is None: - label = KEY.LABEL_NONE - atoms_dct = {label: atoms} - elif isinstance(atoms, ase.Atoms): - if label is None: - label = KEY.LABEL_NONE - atoms_dct = {label: [atoms]} - elif isinstance(atoms, dict): - atoms_dct = atoms - else: - raise TypeError('The return of reader is not list or dict') - - graph_dct = {} - for label, atoms_list in atoms_dct.items(): - graph_list = graph_build( - atoms_list=atoms_list, - cutoff=cutoff, - num_cores=cores, - transfer_info=transfer_info, - y_from_calc=False, - ) - - label_info = label.split(':') - for graph in graph_list: - graph[KEY.USER_LABEL] = label_info[0].strip() - if use_weight: - find_weight = False - for info in label_info[1:]: - if 'w=' in info.lower(): - weights = info.split('=')[1] - try: - if ',' in weights: - weight_list = list(map(float, weights.split(','))) - else: - weight_list = [float(weights)] * 3 - weight_dict = {} - for idx, loss_type in enumerate(LossType): - weight_dict[loss_type.value] = ( - weight_list[idx] if idx < len(weight_list) else 1 - ) - graph[KEY.DATA_WEIGHT] = weight_dict - find_weight = True - break - except: - raise ValueError( - 'Weight must be a real number, but' - f' {weights} is given for {label}' - ) - if not find_weight: - weight_dict = {} - for loss_type in LossType: - weight_dict[loss_type.value] = 1 - graph[KEY.DATA_WEIGHT] = weight_dict - if use_modality: - find_modality = False - for info in label_info[1:]: - if 'm=' in info.lower(): - graph[KEY.DATA_MODALITY] = (info.split('=')[1]).strip() - find_modality = True - break - if not find_modality: - raise ValueError(f'Modality not given for {label}') - - graph_dct[label_info[0].strip()] = graph_list - db = AtomGraphDataset(graph_dct, cutoff) - return db diff --git a/mace-bench/3rdparty/SevenNet/sevenn/train/dataset.py b/mace-bench/3rdparty/SevenNet/sevenn/train/dataset.py deleted file mode 100644 index ccf04df9da9733a0fccfd62f98f3d6c07a18f431..0000000000000000000000000000000000000000 --- a/mace-bench/3rdparty/SevenNet/sevenn/train/dataset.py +++ /dev/null @@ -1,496 +0,0 @@ -import itertools -import random -from collections import Counter -from typing import Callable, Dict, List, Optional, Union - -import numpy as np -import torch -from ase.data import chemical_symbols -from sklearn.linear_model import Ridge - -import sevenn._keys as KEY -import sevenn.util as util - - -class AtomGraphDataset: - """ - Deprecated - - class representing dataset of AtomGraphData - the dataset is handled as dict, {label: data} - if given data is List, it stores data as {KEY_DEFAULT: data} - - cutoff is for metadata of the graphs not used for some calc - Every data expected to have one unique cutoff - No validity or check of the condition is done inside the object - - attribute: - dataset (Dict[str, List]): key is data label(str), value is list of data - user_labels (List[str]): list of user labels same as dataset.keys() - meta (Dict, Optional): metadata of dataset - for now, metadata 'might' have following keys: - KEY.CUTOFF (float), KEY.CHEMICAL_SPECIES (Dict) - """ - - DATA_KEY_X = ( - KEY.NODE_FEATURE - ) # atomic_number > one_hot_idx > one_hot_vector - DATA_KEY_ENERGY = KEY.ENERGY - DATA_KEY_FORCE = KEY.FORCE - KEY_DEFAULT = KEY.LABEL_NONE - - def __init__( - self, - dataset: Union[Dict[str, List], List], - cutoff: float, - metadata: Optional[Dict] = None, - x_is_one_hot_idx: bool = False, - ): - """ - Default constructor of AtomGraphDataset - Args: - dataset (Union[Dict[str, List], List]: dataset as dict or pure list - metadata (Dict, Optional): metadata of data - cutoff (float): cutoff radius of graphs inside the dataset - x_is_one_hot_idx (bool): if True, x is one_hot_idx, else 'Z' - - 'x' (node feature) of dataset can have 3 states, atomic_numbers, - one_hot_idx, or one_hot_vector. - - atomic_numbers is general but cannot directly used for input - one_hot_idx is can be input of the model but requires 'type_map' - """ - self.cutoff = cutoff - self.x_is_one_hot_idx = x_is_one_hot_idx - if metadata is None: - metadata = {KEY.CUTOFF: cutoff} - self.meta = metadata - if type(dataset) is list: - self.dataset = {self.KEY_DEFAULT: dataset} - else: - self.dataset = dataset - self.user_labels = list(self.dataset.keys()) - # group_by_key here? or not? - - def rewrite_labels_to_data(self): - """ - Based on self.dataset dict's keys - write data[KEY.USER_LABEL] to correspond to dict's keys - Most of times, it is already correctly written - But required to rewrite if someone rearrange dataset by their own way - """ - for label, data_list in self.dataset.items(): - for data in data_list: - data[KEY.USER_LABEL] = label - - def group_by_key(self, data_key: str = KEY.USER_LABEL): - """ - group dataset list by given key and save it as dict - and change in-place - Args: - data_key (str): data key to group by - - original use is USER_LABEL, but it can be used for other keys - if someone established it from data[KEY.INFO] - """ - data_list = self.to_list() - self.dataset = {} - for datum in data_list: - key = datum[data_key] - if key not in self.dataset: - self.dataset[key] = [] - self.dataset[key].append(datum) - self.user_labels = list(self.dataset.keys()) - - def separate_info(self, data_key: str = KEY.INFO): - """ - Separate info from data and save it as list of dict - to make it compatible with torch_geometric and later training - """ - data_list = self.to_list() - info_list = [] - for datum in data_list: - if data_key in datum is False: - continue - info_list.append(datum[data_key]) - del datum[data_key] # It does change the self.dataset - datum[data_key] = len(info_list) - 1 - self.info_list = info_list - - return (data_list, info_list) - - def get_species(self): - """ - You can also use get_natoms and extract keys from there instead of this - (And it is more efficient) - get chemical species of dataset - return list of SORTED chemical species (as str) - """ - if hasattr(self, 'type_map'): - natoms = self.get_natoms(self.type_map) - else: - natoms = self.get_natoms() - species = set() - for natom_dct in natoms.values(): - species.update(natom_dct.keys()) - species = sorted(list(species)) - return species - - def get_modalities(self): - modalities = set() - for data_list in self.dataset.values(): - datum = data_list[0].to_dict() - if KEY.DATA_MODALITY in datum.keys(): - modalities.add(datum[KEY.DATA_MODALITY]) - else: - return [] - return list(modalities) - - def write_modal_attr( - self, modal_type_mapper: dict, write_modal_type: bool = False - ): - num_modalities = len(modal_type_mapper) - for data_list in self.dataset.values(): - for data in data_list: - tmp_tensor = torch.zeros(num_modalities) - if data[KEY.DATA_MODALITY] != 'common': - modal_idx = modal_type_mapper[data[KEY.DATA_MODALITY]] - tmp_tensor[modal_idx] = 1.0 - if write_modal_type: - data[KEY.MODAL_TYPE] = modal_idx - data[KEY.MODAL_ATTR] = tmp_tensor - - def get_dict_sort_by_modality(self): - dict_sort_by_modality = {} - for data_list in self.dataset.values(): - try: - modal_key = data_list[0].to_dict()[KEY.DATA_MODALITY] - except: # Dataset is not modal - raise ValueError('This dataset has no modality.') - - if modal_key not in dict_sort_by_modality.keys(): - dict_sort_by_modality[modal_key] = [] - dict_sort_by_modality[modal_key].extend(data_list) - - return dict_sort_by_modality - - def len(self): - if ( - len(self.dataset.keys()) == 1 - and list(self.dataset.keys())[0] == AtomGraphDataset.KEY_DEFAULT - ): - return len(self.dataset[AtomGraphDataset.KEY_DEFAULT]) - else: - return {k: len(v) for k, v in self.dataset.items()} - - def get(self, idx: int, key: Optional[str] = None): - if key is None: - key = self.KEY_DEFAULT - return self.dataset[key][idx] - - def items(self): - return self.dataset.items() - - def to_dict(self): - dct_dataset = {} - for label, data_list in self.dataset.items(): - dct_dataset[label] = [datum.to_dict() for datum in data_list] - self.dataset = dct_dataset - return self - - def x_to_one_hot_idx(self, type_map: Dict[int, int]): - """ - type_map is dict of {atomic_number: one_hot_idx} - after this process, the dataset has dependency on type_map - or chemical species user want to consider - """ - assert self.x_is_one_hot_idx is False - for data_list in self.dataset.values(): - for datum in data_list: - datum[self.DATA_KEY_X] = torch.LongTensor( - [type_map[z.item()] for z in datum[self.DATA_KEY_X]] - ) - self.type_map = type_map - self.x_is_one_hot_idx = True - - def toggle_requires_grad_of_data( - self, key: str, requires_grad_value: bool - ): - """ - set requires_grad of specific key of data(pos, edge_vec, ...) - """ - for data_list in self.dataset.values(): - for datum in data_list: - datum[key].requires_grad_(requires_grad_value) - - def divide_dataset( - self, - ratio: float, - constant_ratio_btw_labels: bool = True, - ignore_test: bool = True - ): - """ - divide dataset into 1-2*ratio : ratio : ratio - return divided AtomGraphDataset - returned value lost its dict key and became {KEY_DEFAULT: datalist} - but KEY.USER_LABEL of each data is preserved - """ - - def divide(ratio: float, data_list: List, ignore_test=True): - if ratio > 0.5: - raise ValueError('Ratio must not exceed 0.5') - data_len = len(data_list) - random.shuffle(data_list) - n_validation = int(data_len * ratio) - if n_validation == 0: - raise ValueError( - '# of validation set is 0, increase your dataset' - ) - - if ignore_test: - test_list = [] - n_train = data_len - n_validation - train_list = data_list[0:n_train] - valid_list = data_list[n_train:] - else: - n_train = data_len - 2 * n_validation - train_list = data_list[0:n_train] - valid_list = data_list[n_train : n_train + n_validation] - test_list = data_list[n_train + n_validation : data_len] - return train_list, valid_list, test_list - - lists = ([], [], []) # train, valid, test - if constant_ratio_btw_labels: - for data_list in self.dataset.values(): - for store, divided in zip(lists, divide(ratio, data_list)): - store.extend(divided) - else: - lists = divide(ratio, self.to_list()) - - dbs = tuple( - AtomGraphDataset(data, self.cutoff, self.meta) for data in lists - ) - for db in dbs: - db.group_by_key() - return dbs - - def to_list(self): - return list(itertools.chain(*self.dataset.values())) - - def get_natoms(self, type_map: Optional[Dict[int, int]] = None): - """ - if x_is_one_hot_idx, type_map is required - type_map: Z->one_hot_index(node_feature) - return Dict{label: {symbol, natom}]} - """ - assert not (self.x_is_one_hot_idx is True and type_map is None) - natoms = {} - for label, data in self.dataset.items(): - natoms[label] = Counter() - for datum in data: - if self.x_is_one_hot_idx and type_map is not None: - Zs = util.onehot_to_chem(datum[self.DATA_KEY_X], type_map) - else: - Zs = [ - chemical_symbols[z] - for z in datum[self.DATA_KEY_X].tolist() - ] - cnt = Counter(Zs) - natoms[label] += cnt - natoms[label] = dict(natoms[label]) - return natoms - - def get_per_atom_mean(self, key: str, key_num_atoms: str = KEY.NUM_ATOMS): - """ - return per_atom mean of given data key - """ - eng_list = torch.Tensor( - [x[key] / x[key_num_atoms] for x in self.to_list()] - ) - return float(torch.mean(eng_list)) - - def get_per_atom_energy_mean(self): - """ - alias for get_per_atom_mean(KEY.ENERGY) - """ - return self.get_per_atom_mean(self.DATA_KEY_ENERGY) - - def get_species_ref_energy_by_linear_comb(self, num_chem_species: int): - """ - Total energy as y, composition as c_i, - solve linear regression of y = c_i*X - sklearn LinearRegression as solver - - x should be one-hot-indexed - give num_chem_species if possible - """ - assert self.x_is_one_hot_idx is True - data_list = self.to_list() - - c = torch.zeros((len(data_list), num_chem_species)) - for idx, datum in enumerate(data_list): - c[idx] = torch.bincount( - datum[self.DATA_KEY_X], minlength=num_chem_species - ) - y = torch.Tensor([x[self.DATA_KEY_ENERGY] for x in data_list]) - c = c.numpy() - y = y.numpy() - - # tweak to fine tune training from many-element to small element - zero_indices = np.all(c == 0, axis=0) - c_reduced = c[:, ~zero_indices] - full_coeff = np.zeros(num_chem_species) - coef_reduced = ( - Ridge(alpha=0.1, fit_intercept=False).fit(c_reduced, y).coef_ - ) - full_coeff[~zero_indices] = coef_reduced - - return full_coeff - - def get_force_rms(self): - force_list = [] - for x in self.to_list(): - force_list.extend( - x[self.DATA_KEY_FORCE] - .reshape( - -1, - ) - .tolist() - ) - force_list = torch.Tensor(force_list) - return float(torch.sqrt(torch.mean(torch.pow(force_list, 2)))) - - def get_species_wise_force_rms(self, num_chem_species: int): - """ - Return force rms for each species - Averaged by each components (x, y, z) - """ - assert self.x_is_one_hot_idx is True - data_list = self.to_list() - - atomx = torch.concat([d[self.DATA_KEY_X] for d in data_list]) - force = torch.concat([d[self.DATA_KEY_FORCE] for d in data_list]) - - index = atomx.repeat_interleave(3, 0).reshape(force.shape) - rms = torch.zeros( - (num_chem_species, 3), - dtype=force.dtype, - device=force.device - ) - rms.scatter_reduce_( - 0, index, force.square(), - reduce='mean', include_self=False - ) - return torch.sqrt(rms.mean(dim=1)) - - def get_avg_num_neigh(self): - n_neigh = [] - for _, data_list in self.dataset.items(): - for data in data_list: - n_neigh.extend( - np.unique(data[KEY.EDGE_IDX][0], return_counts=True)[1] - ) - - avg_num_neigh = np.average(n_neigh) - return avg_num_neigh - - def get_statistics(self, key: str): - """ - return dict of statistics of given key (energy, force, stress) - key of dict is its label and _total for total statistics - value of dict is dict of statistics (mean, std, median, max, min) - """ - - def _get_statistic_dict(tensor_list): - data_list = torch.cat( - [ - tensor.reshape( - -1, - ) - for tensor in tensor_list - ] - ) - data_list = data_list[~torch.isnan(data_list)] - return { - 'mean': float(torch.mean(data_list)), - 'std': float(torch.std(data_list)), - 'median': float(torch.median(data_list)), - 'max': ( - torch.nan - if data_list.numel() == 0 - else float(torch.max(data_list)) - ), - 'min': ( - torch.nan - if data_list.numel() == 0 - else float(torch.min(data_list)) - ), - } - - res = {} - for label, values in self.dataset.items(): - # flatten list of torch.Tensor (values) - tensor_list = [x[key] for x in values] - res[label] = _get_statistic_dict(tensor_list) - tensor_list = [x[key] for x in self.to_list()] - res['Total'] = _get_statistic_dict(tensor_list) - return res - - def augment(self, dataset, validator: Optional[Callable] = None): - """check meta compatibility here - dataset(AtomGraphDataset): data to augment - validator(Callable, Optional): function(self, dataset) -> bool - - if validator is None, by default it checks - whether cutoff & chemical_species are same before augment - - check consistent data type, float, double, long integer etc - """ - - def default_validator(db1, db2): - cut_consis = db1.cutoff == db2.cutoff - # compare unordered lists - x_is_not_onehot = (not db1.x_is_one_hot_idx) and ( - not db2.x_is_one_hot_idx - ) - return cut_consis and x_is_not_onehot - - if validator is None: - validator = default_validator - if not validator(self, dataset): - raise ValueError('given datasets are not compatible check cutoffs') - for key, val in dataset.items(): - if key in self.dataset: - self.dataset[key].extend(val) - else: - self.dataset.update({key: val}) - self.user_labels = list(self.dataset.keys()) - - def unify_dtypes( - self, - float_dtype: torch.dtype = torch.float32, - int_dtype: torch.dtype = torch.int64 - ): - data_list = self.to_list() - for datum in data_list: - for k, v in list(datum.items()): - datum[k] = util.dtype_correct(v, float_dtype, int_dtype) - - def delete_data_key(self, key: str): - for data in self.to_list(): - del data[key] - - # TODO: this by_label is not straightforward - def save(self, path: str, by_label: bool = False): - if by_label: - for label, data in self.dataset.items(): - torch.save( - AtomGraphDataset( - {label: data}, self.cutoff, metadata=self.meta - ), - f'{path}/{label}.sevenn_data', - ) - else: - if path.endswith('.sevenn_data') is False: - path += '.sevenn_data' - torch.save(self, path) diff --git a/mace-bench/3rdparty/SevenNet/sevenn/train/graph_dataset.py b/mace-bench/3rdparty/SevenNet/sevenn/train/graph_dataset.py deleted file mode 100644 index fc32d142de1d2a743a775b2679c0f6040052ffb8..0000000000000000000000000000000000000000 --- a/mace-bench/3rdparty/SevenNet/sevenn/train/graph_dataset.py +++ /dev/null @@ -1,707 +0,0 @@ -import os -import warnings -from collections import Counter -from copy import deepcopy -from datetime import datetime -from typing import Any, Callable, Dict, List, Optional, Tuple, Union - -import numpy as np -import torch -import torch.serialization -import torch.utils.data -import yaml -from ase.data import chemical_symbols -from torch_geometric.data import Data -from torch_geometric.data.in_memory_dataset import InMemoryDataset -from tqdm import tqdm - -import sevenn._keys as KEY -import sevenn.train.dataload as dataload -import sevenn.util as util -from sevenn import __version__ -from sevenn._const import NUM_UNIV_ELEMENT -from sevenn.atom_graph_data import AtomGraphData -from sevenn.logger import Logger - -if torch.__version__.split()[0] >= '2.4.0': - # load graph without error - torch.serialization.add_safe_globals([AtomGraphData]) - -# warning from PyG, for later torch versions -warnings.filterwarnings( - 'ignore', - message='You are using `torch.load` with `weights_only=False`', -) - - -def _tag_graphs(graph_list: List[AtomGraphData], tag: str): - """ - WIP: To be used - """ - for g in graph_list: - g[KEY.TAG] = tag - return graph_list - - -def pt_to_args(pt_filename: str): - """ - Return arg dict of root and processed_name from path to .pt - Usage: - dataset = SevenNetGraphDataset( - **pt_to_args({path}/sevenn_data/dataset.pt) - ) - """ - processed_dir, basename = os.path.split(pt_filename) - return { - 'root': os.path.dirname(processed_dir), - 'processed_name': os.path.basename(basename), - } - - -def _run_stat( - graph_list, - y_keys: List[str] = [KEY.ENERGY, KEY.PER_ATOM_ENERGY, KEY.FORCE, KEY.STRESS], -) -> Dict[str, Any]: - """ - Loop over dataset and init any statistics might need - """ - n_neigh = [] - natoms_counter = Counter() - composition = torch.zeros((len(graph_list), NUM_UNIV_ELEMENT)) - stats: Dict[str, Any] = {y: {'_array': []} for y in y_keys} - - for i, graph in tqdm( - enumerate(graph_list), desc='run_stat', total=len(graph_list) - ): - z_tensor = graph[KEY.ATOMIC_NUMBERS] - natoms_counter.update(z_tensor.tolist()) - composition[i] = torch.bincount(z_tensor, minlength=NUM_UNIV_ELEMENT) - n_neigh.append(torch.unique(graph[KEY.EDGE_IDX][0], return_counts=True)[1]) - for y, dct in stats.items(): - dct['_array'].append( - graph[y].reshape( - -1, - ) - ) - - stats.update({'num_neighbor': {'_array': n_neigh}}) - for y, dct in stats.items(): - array = torch.cat(dct['_array']) - if array.dtype == torch.int64: # because of n_neigh - array = array.to(torch.float) - try: - median = torch.quantile(array, q=0.5) - except RuntimeError: - warnings.warn(f'skip median due to too large tensor size: {y}') - median = torch.nan - dct.update( - { - 'mean': float(torch.mean(array)), - 'std': float(torch.std(array, correction=0)), - 'median': float(median), - 'max': float(torch.max(array)), - 'min': float(torch.min(array)), - 'count': array.numel(), - '_array': array, - } - ) - - natoms = {chemical_symbols[int(z)]: cnt for z, cnt in natoms_counter.items()} - natoms['total'] = sum(list(natoms.values())) - stats.update({'_composition': composition, 'natoms': natoms}) - return stats - - -def _elemwise_reference_energies(composition: np.ndarray, energies: np.ndarray): - from sklearn.linear_model import Ridge - - c = composition - y = energies - zero_indices = np.all(c == 0, axis=0) - c_reduced = c[:, ~zero_indices] - # will not 100% reproduce, as it is sorted by Z - # train/dataset.py was sorted by alphabets of chemical species - coef_reduced = Ridge(alpha=0.1, fit_intercept=False).fit(c_reduced, y).coef_ - full_coeff = np.zeros(NUM_UNIV_ELEMENT) - full_coeff[~zero_indices] = coef_reduced - return full_coeff.tolist() # ex: full_coeff[1] = H_reference_energy - - -class SevenNetGraphDataset(InMemoryDataset): - """ - Replacement of AtomGraphDataset. (and .sevenn_data) - Extends InMemoryDataset of PyG. From given 'files', and 'cutoff', - build graphs for training SevenNet model. Preprocessed graphs are saved to - f'{root}/sevenn_data/{processed_name}.pt - - TODO: Save meta info (cutoff) by overriding .save and .load - TODO: 'tag' is not used yet, but initialized - 'tag' is replacement for 'label', and each datapoint has it as integer - 'tag' is usually parsed from if the structure_list of load_dataset - - Args: - root: path to save/load processed PyG dataset - cutoff: edge cutoff of given AtomGraphData - files: list of filenames or dict describing how to parse the file - ASE readable (with proper extension), structure_list, .sevenn_data, - dict containing file_list (see dict_reader of train/dataload.py) - process_num_cores: # of cpu cores to build graph - processed_name: save as {root}/sevenn_data/{processed_name}.pt - pre_transfrom: optional transform for each graph: def (graph) -> graph - pre_filter: optional filtering function for each graph: def (graph) -> graph - force_reload: if True, reload dataset from files even if there exist - {root}/sevenn_data/{processed_name} - **process_kwargs: keyword arguments that will be passed into ase.io.read - """ - - def __init__( - self, - cutoff: float, - root: Optional[str] = None, - files: Optional[Union[str, List[Any]]] = None, - process_num_cores: int = 1, - processed_name: str = 'graph.pt', - transform: Optional[Callable] = None, - pre_transform: Optional[Callable] = None, - pre_filter: Optional[Callable] = None, - use_data_weight: bool = False, - log: bool = True, - force_reload: bool = False, - drop_info: bool = True, - **process_kwargs, - ): - self.cutoff = cutoff - if files is None: - files = [] - elif isinstance(files, str): - files = [files] # user convenience - - _files = [] - for f in files: - if isinstance(f, str): - f = os.path.abspath(f) - _files.append(f) - self._files = _files - - self._full_file_list = [] - if not processed_name.endswith('.pt'): - processed_name += '.pt' - self._processed_names = [ - processed_name, # {root}/sevenn_data/{name}.pt - processed_name.replace('.pt', '.yaml'), - ] - - root = root or './' - _pdir = os.path.join(root, 'sevenn_data') - _pt = os.path.join(_pdir, self._processed_names[0]) - if not os.path.exists(_pt) and len(self._files) == 0: - raise ValueError( - ( - f'{_pt} not found and no files to process. ' - + 'If you copied only .pt file, please copy ' - + 'whole sevenn_data dir without changing its name.' - + ' They all work together.' - ) - ) - - _yam = os.path.join(_pdir, self._processed_names[1]) - if not os.path.exists(_yam) and len(self._files) == 0: - raise ValueError(f'{_yam} not found and no files to process') - - self.process_num_cores = process_num_cores - self.process_kwargs = process_kwargs - self.use_data_weight = use_data_weight - self.drop_info = drop_info - - self.tag_map = {} - self.statistics = {} - self.finalized = False - - super().__init__( - root, - transform, - pre_transform, - pre_filter, - log=log, - force_reload=force_reload, - ) # Internally calls 'process' - self.load(self.processed_paths[0]) # load pt, saved after process - - def load(self, path: str, data_cls=Data) -> None: - super().load(path, data_cls) - - if len(self) == 0: - warnings.warn(f'No graphs found {self.processed_paths[0]}') - if len(self.statistics) == 0: - # dataset is loaded from existing pt file. - self._load_meta() - - def _load_meta(self) -> None: - with open(self.processed_paths[1], 'r') as f: - meta = yaml.safe_load(f) - - if meta['sevennet_version'] == '0.10.0': - self._save_meta(list(self)) - with open(self.processed_paths[1], 'r') as f: - meta = yaml.safe_load(f) - - cutoff = float(meta['cutoff']) - if float(meta['cutoff']) != self.cutoff: - warnings.warn( - ( - 'Loaded dataset is built with different cutoff length: ' - + f'{cutoff} != {self.cutoff}, dataset cutoff will be' - + f' overwritten to {cutoff}' - ) - ) - self.cutoff = cutoff - self._files = meta['files'] - self.statistics = meta['statistics'] - - def __getitem__(self, idx): - graph = super().__getitem__(idx) - if self.drop_info: - graph.pop(KEY.INFO, None) # type: ignore - return graph - - @property - def raw_file_names(self) -> List[Any]: - return self._files - - @property - def processed_file_names(self) -> List[str]: - return self._processed_names - - @property - def processed_dir(self) -> str: - return os.path.join(self.root, 'sevenn_data') - - @property - def full_file_list(self) -> Union[List[str], None]: - return self._full_file_list - - def process(self): - graph_list: List[AtomGraphData] = [] - for file in self.raw_file_names: - tmplist = SevenNetGraphDataset.file_to_graph_list( - file=file, - cutoff=self.cutoff, - num_cores=self.process_num_cores, - **self.process_kwargs, - ) - if isinstance(file, str) and self._full_file_list is not None: - self._full_file_list.extend([os.path.abspath(file)] * len(tmplist)) - else: - self._full_file_list = None - graph_list.extend(tmplist) - - processed_graph_list = [] - for data in graph_list: - if self.pre_filter is not None and not self.pre_filter(data): - continue - if self.pre_transform is not None: - data = self.pre_transform(data) - if self.use_data_weight: - # pop data weight from info, and assign to graph - weight = data[KEY.INFO].pop( - KEY.DATA_WEIGHT, {'energy': 1.0, 'force': 1.0, 'stress': 1.0} - ) - data[KEY.DATA_WEIGHT] = weight - processed_graph_list.append(data) - - if len(processed_graph_list) == 0: - # Can not save at all if there is no graph (error in PyG), raise an error - raise ValueError('Zero graph found after filtering') - - # save graphs, handled by torch_geometrics - self.save(processed_graph_list, self.processed_paths[0]) - self._save_meta(processed_graph_list) - if self.log: - Logger().writeline(f'Dataset is saved: {self.processed_paths[0]}') - - def _save_meta(self, graph_list) -> None: - stats = _run_stat(graph_list) - stats['elemwise_reference_energies'] = _elemwise_reference_energies( - stats['_composition'].numpy(), stats[KEY.ENERGY]['_array'].numpy() - ) - self.statistics = stats - - stats_save = {} - for label, dct in self.statistics.items(): - if label.startswith('_'): - continue - stats_save[label] = {} - if not isinstance(dct, dict): - stats_save[label] = dct - else: - for k, v in dct.items(): - if k.startswith('_'): - continue - stats_save[label][k] = v - - meta = { - 'sevennet_version': __version__, - 'cutoff': self.cutoff, - 'when': datetime.now().strftime('%Y-%m-%d %H:%M'), - 'files': self._files, - 'statistics': stats_save, - 'species': self.species, - 'num_graphs': self.statistics[KEY.ENERGY]['count'], - 'per_atom_energy_mean': self.per_atom_energy_mean, - 'force_rms': self.force_rms, - 'per_atom_energy_std': self.per_atom_energy_std, - 'avg_num_neigh': self.avg_num_neigh, - 'sqrt_avg_num_neigh': self.sqrt_avg_num_neigh, - } - - with open(self.processed_paths[1], 'w') as f: - yaml.dump(meta, f, default_flow_style=False) - - @property - def species(self): - return [z for z in self.statistics['natoms'].keys() if z != 'total'] - - @property - def natoms(self): - return self.statistics['natoms'] - - @property - def per_atom_energy_mean(self): - return self.statistics[KEY.PER_ATOM_ENERGY]['mean'] - - @property - def elemwise_reference_energies(self): - return self.statistics['elemwise_reference_energies'] - - @property - def force_rms(self): - mean = self.statistics[KEY.FORCE]['mean'] - std = self.statistics[KEY.FORCE]['std'] - return float((mean**2 + std**2) ** (0.5)) - - @property - def per_atom_energy_std(self): - return self.statistics['per_atom_energy']['std'] - - @property - def avg_num_neigh(self): - return self.statistics['num_neighbor']['mean'] - - @property - def sqrt_avg_num_neigh(self): - return self.avg_num_neigh**0.5 - - @staticmethod - def _read_sevenn_data(filename: str) -> Tuple[List[AtomGraphData], float]: - # backward compatibility - from sevenn.train.dataset import AtomGraphDataset - - dataset = torch.load(filename, map_location='cpu', weights_only=False) - if isinstance(dataset, AtomGraphDataset): - graph_list = [] - for _, graphs in dataset.dataset.items(): # type: ignore - # TODO: transfer label to tag (who gonna need this?) - graph_list.extend(graphs) - return graph_list, dataset.cutoff - else: - raise ValueError(f'Not sevenn_data type: {type(dataset)}') - - @staticmethod - def _read_structure_list( - filename: str, cutoff: float, num_cores: int = 1 - ) -> List[AtomGraphData]: - datadct = dataload.structure_list_reader(filename) - graph_list = [] - for tag, atoms_list in datadct.items(): - tmp = dataload.graph_build(atoms_list, cutoff, num_cores) - graph_list.extend(_tag_graphs(tmp, tag)) - return graph_list - - @staticmethod - def _read_ase_readable( - filename: str, - cutoff: float, - num_cores: int = 1, - tag: str = '', - transfer_info: bool = True, - allow_unlabeled: bool = False, - **ase_kwargs, - ) -> List[AtomGraphData]: - pbc_override = ase_kwargs.pop('pbc', None) - atoms_list = dataload.ase_reader(filename, **ase_kwargs) - for atoms in atoms_list: - if pbc_override is not None: - atoms.pbc = pbc_override - graph_list = dataload.graph_build( - atoms_list, - cutoff, - num_cores, - transfer_info=transfer_info, - allow_unlabeled=allow_unlabeled, - ) - if tag != '': - graph_list = _tag_graphs(graph_list, tag) - return graph_list - - @staticmethod - def _read_graph_dataset( - filename: str, cutoff: float, **kwargs - ) -> List[AtomGraphData]: - meta_f = filename.replace('.pt', '.yaml') - orig_cutoff = cutoff - if not os.path.exists(filename): - raise FileNotFoundError(f'No such file: {filename}') - if not os.path.exists(meta_f): - warnings.warn('No meta info found, beware of cutoff...') - else: - with open(meta_f, 'r') as f: - meta = yaml.safe_load(f) - orig_cutoff = float(meta['cutoff']) - if orig_cutoff != cutoff: - warnings.warn( - f'{filename} has different cutoff length: ' - + f'{cutoff} != {orig_cutoff}' - ) - ds_args: dict[str, Any] = dict({'cutoff': orig_cutoff}) - ds_args.update(pt_to_args(filename)) - ds_args.update(kwargs) - dataset = SevenNetGraphDataset(**ds_args) - # TODO: hard coded. consult with inference.py - glist = [g.fit_dimension() for g in dataset] # type: ignore - for g in glist: - if KEY.STRESS in g: - # (1, 6) is what we want - g[KEY.STRESS] = g[KEY.STRESS].unsqueeze(0) - return glist - - @staticmethod - def _read_dict( - data_dict: dict, - cutoff: float, - num_cores: int = 1, - ): - # logic same as the dataload dict_reader, but handles graphs - data_dict_cp = deepcopy(data_dict) - file_list = data_dict_cp.get('file_list', None) - if file_list is None: - raise KeyError('file_list is not found') - - data_weight_default = { - 'energy': 1.0, - 'force': 1.0, - 'stress': 1.0, - } - data_weight = data_weight_default.copy() - data_weight.update(data_dict_cp.pop(KEY.DATA_WEIGHT, {})) - - graph_list = [] - for file_dct in file_list: - ftype = file_dct.pop('data_format', 'ase') - if ftype != 'graph': - continue - graph_list.extend( - SevenNetGraphDataset._read_graph_dataset( - file_dct.get('file'), cutoff=cutoff - ) - ) - for graph in graph_list: - if KEY.INFO not in graph: - graph[KEY.INFO] = {} - graph[KEY.INFO].update(data_dict_cp) - graph[KEY.INFO].update({KEY.DATA_WEIGHT: data_weight}) - - atoms_list = dataload.dict_reader(data_dict) - graph_list.extend(dataload.graph_build(atoms_list, cutoff, num_cores)) - return graph_list - - @staticmethod - def file_to_graph_list( - file: Union[str, dict], cutoff: float, num_cores: int = 1, **kwargs - ) -> List[AtomGraphData]: - """ - kwargs: if file is ase readable, passed to ase.io.read - """ - if isinstance(file, str) and not os.path.isfile(file): - raise ValueError(f'No such file: {file}') - graph_list: List[AtomGraphData] - if isinstance(file, dict): - graph_list = SevenNetGraphDataset._read_dict( - file, cutoff, num_cores, **kwargs - ) - elif file.endswith('.pt'): - graph_list = SevenNetGraphDataset._read_graph_dataset(file, cutoff) - elif file.endswith('.sevenn_data'): - graph_list, cutoff_other = SevenNetGraphDataset._read_sevenn_data(file) - if cutoff_other != cutoff: - warnings.warn(f'Given {file} has different {cutoff_other}!') - cutoff = cutoff_other - elif 'structure_list' in file: - graph_list = SevenNetGraphDataset._read_structure_list( - file, cutoff, num_cores - ) - else: - graph_list = SevenNetGraphDataset._read_ase_readable( - file, cutoff, num_cores, **kwargs - ) - return graph_list - - -def from_single_path( - path: Union[str, List], override_data_weight: bool = True, **dataset_kwargs -) -> Union[SevenNetGraphDataset, None]: - """ - Convenient routine for loading a single .pt dataset. - If given dict and it has data_weight, apply it using transform - """ - data_weight = {'energy': 1.0, 'force': 1.0, 'stress': 1.0} - spath = _extract_single_path(path) - if spath is None: - return None - - if isinstance(spath, str): - if not spath.endswith('.pt'): - return None - dataset_kwargs.update(pt_to_args(spath)) - elif isinstance(spath, dict): - file = _extract_file_from_dict(spath) - if file is None or not file.endswith('.pt'): - return None - dataset_kwargs.update(pt_to_args(file)) - data_weight_user = spath.get(KEY.DATA_WEIGHT, None) - if data_weight_user is not None: - data_weight.update(data_weight_user) - else: - return None - - if override_data_weight: - dataset_kwargs['transform'] = _chain_data_weight_override( - dataset_kwargs.get('transform'), data_weight - ) - - return SevenNetGraphDataset(**dataset_kwargs) - - -def _extract_single_path(path: Union[str, List]) -> Union[str, dict, None]: - """Extracts a single path from the input, - ensuring it's either a single string or list with one item.""" - if isinstance(path, list): - return path[0] if len(path) == 1 else None - return path if isinstance(path, (str, dict)) else None - - -def _extract_file_from_dict(path_dict: dict) -> Union[str, None]: - """Extracts a single file path from the dictionary, ensuring it's valid.""" - file_list = path_dict.get('file_list', None) - if file_list and len(file_list) == 1: - file = file_list[0].get('file', None) - return file if isinstance(file, str) else None - return None - - -def _chain_data_weight_override(transform_func, data_weight): - """Creates a transform function that overrides the data weight.""" - - def chained_transform(graph): - graph = transform_func(graph) if transform_func is not None else graph - graph[KEY.INFO].pop(KEY.DATA_WEIGHT, None) - graph[KEY.DATA_WEIGHT] = data_weight - return graph - - return chained_transform - - -# script, return dict of SevenNetGraphDataset -def from_config( - config: Dict[str, Any], - working_dir: str = os.getcwd(), - dataset_keys: Optional[List[str]] = None, -): - log = Logger() - if dataset_keys is None: - dataset_keys = [] - for k in config: - if k.startswith('load_') and k.endswith('_path'): - dataset_keys.append(k) - - if KEY.LOAD_TRAINSET not in dataset_keys: - raise ValueError(f'{KEY.LOAD_TRAINSET} must be present in config') - - # initialize arguments for loading dataset - dataset_args = { - 'cutoff': config[KEY.CUTOFF], - 'root': working_dir, - 'process_num_cores': config.get(KEY.PREPROCESS_NUM_CORES, 1), - 'use_data_weight': config.get(KEY.USE_WEIGHT, False), - **config.get(KEY.DATA_FORMAT_ARGS, {}), - } - - datasets = {} - for dk in dataset_keys: - if not (paths := config[dk]): - continue - if isinstance(paths, str): - paths = [paths] - name = '_'.join([nn.strip() for nn in dk.split('_')[1:-1]]) - if (dataset := from_single_path(paths, **dataset_args)) is not None: - datasets[name] = dataset - else: - dataset_args.update({'files': paths, 'processed_name': name}) - dataset_path = os.path.join(working_dir, 'sevenn_data', f'{name}.pt') - if os.path.exists(dataset_path) and 'force_reload' not in dataset_args: - log.writeline( - f'Dataset will be loaded from {dataset_path}, without update. ' - + 'If you have changed your files to read, put force_reload=True' - + ' under the data_format_args key' - ) - datasets[name] = SevenNetGraphDataset(**dataset_args) - - train_set = datasets['trainset'] - - chem_species = set(train_set.species) - # print statistics of each dataset - for name, dataset in datasets.items(): - log.bar() - log.writeline(f'{name} distribution:') - log.statistic_write(dataset.statistics) - log.format_k_v('# structures (graph)', len(dataset), write=True) - - chem_species.update(dataset.species) - log.bar() - - # initialize known species from dataset if 'auto' - # sorted to alphabetical order (which is same as before) - chem_keys = [KEY.CHEMICAL_SPECIES, KEY.NUM_SPECIES, KEY.TYPE_MAP] - if all([config[ck] == 'auto' for ck in chem_keys]): # see parse_input.py - log.writeline('Known species are obtained from the dataset') - config.update(util.chemical_species_preprocess(sorted(list(chem_species)))) - - # retrieve shift, scale, conv_denominaotrs from user input (keyword) - init_from_stats = [KEY.SHIFT, KEY.SCALE, KEY.CONV_DENOMINATOR] - for k in init_from_stats: - input = config[k] # statistic key or numbers - # If it is not 'str', 1: It is 'continue' training - # 2: User manually inserted numbers - if isinstance(input, str) and hasattr(train_set, input): - var = getattr(train_set, input) - config.update({k: var}) - log.writeline(f'{k} is obtained from statistics') - elif isinstance(input, str) and not hasattr(train_set, input): - raise NotImplementedError(input) - - if 'validset' not in datasets and config.get(KEY.RATIO, 0.0) > 0.0: - log.writeline('Use validation set as random split from the training set') - log.writeline( - 'Note that statistics, shift, scale, and conv_denominator are ' - + 'computed before random split.\n If you want these after random ' - + 'split, please preprocess dataset and set it as load_trainset_path ' - + 'and load_validset_path explicitly.' - ) - - ratio = float(config[KEY.RATIO]) - train, valid = torch.utils.data.random_split( - datasets['trainset'], (1.0 - ratio, ratio) - ) - datasets['trainset'] = train - datasets['validset'] = valid - - return datasets diff --git a/mace-bench/3rdparty/SevenNet/sevenn/train/loss.py b/mace-bench/3rdparty/SevenNet/sevenn/train/loss.py deleted file mode 100644 index 7aae162c916480b31d7347e8e141fcc67e3c21db..0000000000000000000000000000000000000000 --- a/mace-bench/3rdparty/SevenNet/sevenn/train/loss.py +++ /dev/null @@ -1,223 +0,0 @@ -from typing import Any, Callable, Dict, Optional, Tuple - -import torch - -import sevenn._keys as KEY - - -class LossDefinition: - """ - Base class for loss definition - weights are defined in outside of the class - """ - - def __init__( - self, - name: str, - unit: Optional[str] = None, - criterion: Optional[Callable] = None, - ref_key: Optional[str] = None, - pred_key: Optional[str] = None, - use_weight: bool = False, - ignore_unlabeled: bool = True, - ): - self.name = name - self.unit = unit - self.criterion = criterion - self.ref_key = ref_key - self.pred_key = pred_key - self.use_weight = use_weight - self.ignore_unlabeled = ignore_unlabeled - - def __repr__(self): - return self.name - - def assign_criteria(self, criterion: Callable): - if self.criterion is not None: - raise ValueError('Loss uses its own criterion.') - self.criterion = criterion - - def _preprocess( - self, batch_data: Dict[str, Any], model: Optional[Callable] = None - ) -> Tuple[torch.Tensor, torch.Tensor, Optional[torch.Tensor]]: - if self.pred_key is None or self.ref_key is None: - raise NotImplementedError('LossDefinition is not implemented.') - pred = torch.reshape(batch_data[self.pred_key], (-1,)) - ref = torch.reshape(batch_data[self.ref_key], (-1,)) - return pred, ref, None - - def _ignore_unlabeled(self, pred, ref, data_weights=None): - unlabeled = torch.isnan(ref) - pred = pred[~unlabeled] - ref = ref[~unlabeled] - if data_weights is not None: - data_weights = data_weights[~unlabeled] - return pred, ref, data_weights - - def get_loss(self, batch_data: Dict[str, Any], model: Optional[Callable] = None): - """ - Function that return scalar - """ - if self.criterion is None: - raise NotImplementedError('LossDefinition has no criterion.') - pred, ref, w_tensor = self._preprocess(batch_data, model) - - if self.ignore_unlabeled: - pred, ref, w_tensor = self._ignore_unlabeled(pred, ref, w_tensor) - - if len(pred) == 0: - assert self.ref_key is not None - return torch.zeros(1, device=batch_data[self.ref_key].device) - - loss = self.criterion(pred, ref) - if self.use_weight: - loss = torch.mean(loss * w_tensor) - return loss - - -class PerAtomEnergyLoss(LossDefinition): - """ - Loss for per atom energy - """ - - def __init__( - self, - name: str = 'Energy', - unit: str = 'eV/atom', - criterion: Optional[Callable] = None, - ref_key: str = KEY.ENERGY, - pred_key: str = KEY.PRED_TOTAL_ENERGY, - **kwargs, - ): - super().__init__( - name=name, - unit=unit, - criterion=criterion, - ref_key=ref_key, - pred_key=pred_key, - **kwargs, - ) - - def _preprocess( - self, batch_data: Dict[str, Any], model: Optional[Callable] = None - ): - num_atoms = batch_data[KEY.NUM_ATOMS] - assert isinstance(self.pred_key, str) and isinstance(self.ref_key, str) - pred = batch_data[self.pred_key] / num_atoms - ref = batch_data[self.ref_key] / num_atoms - w_tensor = None - - if self.use_weight: - loss_type = self.name.lower() - weight = batch_data[KEY.DATA_WEIGHT][loss_type] - w_tensor = torch.repeat_interleave(weight, 1) - - return pred, ref, w_tensor - - -class ForceLoss(LossDefinition): - """ - Loss for force - """ - - def __init__( - self, - name: str = 'Force', - unit: str = 'eV/A', - criterion: Optional[Callable] = None, - ref_key: str = KEY.FORCE, - pred_key: str = KEY.PRED_FORCE, - **kwargs, - ): - super().__init__( - name=name, - unit=unit, - criterion=criterion, - ref_key=ref_key, - pred_key=pred_key, - **kwargs, - ) - - def _preprocess( - self, batch_data: Dict[str, Any], model: Optional[Callable] = None - ): - assert isinstance(self.pred_key, str) and isinstance(self.ref_key, str) - pred = torch.reshape(batch_data[self.pred_key], (-1,)) - ref = torch.reshape(batch_data[self.ref_key], (-1,)) - w_tensor = None - - if self.use_weight: - loss_type = self.name.lower() - weight = batch_data[KEY.DATA_WEIGHT][loss_type] - w_tensor = weight[batch_data[KEY.BATCH]] - w_tensor = torch.repeat_interleave(w_tensor, 3) - - return pred, ref, w_tensor - - -class StressLoss(LossDefinition): - """ - Loss for stress this is kbar - """ - - def __init__( - self, - name: str = 'Stress', - unit: str = 'kbar', - criterion: Optional[Callable] = None, - ref_key: str = KEY.STRESS, - pred_key: str = KEY.PRED_STRESS, - **kwargs, - ): - super().__init__( - name=name, - unit=unit, - criterion=criterion, - ref_key=ref_key, - pred_key=pred_key, - **kwargs, - ) - self.TO_KB = 1602.1766208 # eV/A^3 to kbar - - def _preprocess( - self, batch_data: Dict[str, Any], model: Optional[Callable] = None - ): - assert isinstance(self.pred_key, str) and isinstance(self.ref_key, str) - - pred = torch.reshape(batch_data[self.pred_key] * self.TO_KB, (-1,)) - ref = torch.reshape(batch_data[self.ref_key] * self.TO_KB, (-1,)) - w_tensor = None - - if self.use_weight: - loss_type = self.name.lower() - weight = batch_data[KEY.DATA_WEIGHT][loss_type] - w_tensor = torch.repeat_interleave(weight, 6) - - return pred, ref, w_tensor - - -def get_loss_functions_from_config(config: Dict[str, Any]): - from sevenn.train.optim import loss_dict - - loss_functions = [] # list of tuples (loss_definition, weight) - - loss = loss_dict[config[KEY.LOSS].lower()] - loss_param = config.get(KEY.LOSS_PARAM, {}) - - use_weight = config.get(KEY.USE_WEIGHT, False) - if use_weight: - loss_param['reduction'] = 'none' - criterion = loss(**loss_param) - - commons = {'use_weight': use_weight} - - loss_functions.append((PerAtomEnergyLoss(**commons), 1.0)) - loss_functions.append((ForceLoss(**commons), config[KEY.FORCE_WEIGHT])) - if config[KEY.IS_TRAIN_STRESS]: - loss_functions.append((StressLoss(**commons), config[KEY.STRESS_WEIGHT])) - - for loss_function, _ in loss_functions: # why do these? - if loss_function.criterion is None: - loss_function.assign_criteria(criterion) - - return loss_functions diff --git a/mace-bench/3rdparty/SevenNet/sevenn/train/modal_dataset.py b/mace-bench/3rdparty/SevenNet/sevenn/train/modal_dataset.py deleted file mode 100644 index c5bcd91747a62f7d8e369b92c48d7363cef9fa25..0000000000000000000000000000000000000000 --- a/mace-bench/3rdparty/SevenNet/sevenn/train/modal_dataset.py +++ /dev/null @@ -1,365 +0,0 @@ -import bisect -import os -from copy import deepcopy -from typing import Any, Dict, List, Optional - -import numpy as np -from torch.utils.data import ConcatDataset, Dataset - -import sevenn._keys as KEY -import sevenn.util as util -from sevenn.logger import Logger - - -def _arrange_paths_by_modality(paths: List[dict]): - modal_dct = {} - for path in paths: - if isinstance(path, dict): - if KEY.DATA_MODALITY not in path: - raise ValueError(f'{KEY.DATA_MODALITY} is missing') - modal = path.pop(KEY.DATA_MODALITY) - else: - raise TypeError(f'{path} is not dict or str') - if modal not in modal_dct: - modal_dct[modal] = [] - modal_dct[modal].append(path) - return modal_dct - - -def combined_variance( - means: np.ndarray, stds: np.ndarray, sample_sizes: np.ndarray, ddof: int = 0 -) -> float: - """ - Calculate the combined variance for multiple datasets. - """ - assert len(means) == len(stds) and len(stds) == len(sample_sizes) - # Total number of samples - total_samples = np.sum(sample_sizes) - - # Combined mean - combined_mean = np.sum(sample_sizes * means) / total_samples - - # Combined variance calculation - variance_terms = (sample_sizes - ddof) * (stds**2) - mean_diff_terms = sample_sizes * ((means - combined_mean) ** 2) - combined_variance = (np.sum(variance_terms) + np.sum(mean_diff_terms)) / ( - total_samples - ddof - ) - - return combined_variance - - -def combined_std( - means: List[float], stds: List[float], sample_sizes: List[int] -) -> float: - """ - Calculate the combined std for multiple datasets. - """ - assert len(means) == len(stds) and len(stds) == len(sample_sizes) - means_arr = np.array(means) - stds_arr = np.array(stds) - sample_sizes_arr = np.array(sample_sizes) - - cv = combined_variance(means_arr, stds_arr, sample_sizes_arr) - return np.sqrt(cv) - - -def combined_mean(means: List[float], sample_sizes: List[int]) -> float: - """ - Calculate the combined mean for multiple datasets. - """ - assert len(means) == len(sample_sizes) - means_arr = np.array(means) - sample_sizes_arr = np.array(sample_sizes) - - return np.sum(sample_sizes_arr * means_arr) / np.sum(sample_sizes_arr) - - -def combined_rms( - means: List[float], stds: List[float], sample_sizes: List[int] -) -> float: - """ - Calculate the combined RMS for multiple datasets. - """ - assert len(means) == len(stds) and len(stds) == len(sample_sizes) - means_arr = np.array(means) - stds_arr = np.array(stds) - sample_sizes_arr = np.array(sample_sizes) - - cm = combined_mean(means, sample_sizes) - cv = combined_variance(means_arr, stds_arr, sample_sizes_arr) - - # Combined RMS calculation - return np.sqrt(cm**2 + cv) - - -class SevenNetMultiModalDataset(ConcatDataset): - def __init__( - self, - modal_dataset_dict: Dict[str, Dataset], - ): - datasets = [] - modals = [] - for modal, dataset in modal_dataset_dict.items(): - modals.append(modal) - datasets.append(dataset) - self.modals = modals - super().__init__(datasets) - - def __getitem__(self, idx): - graph = super().__getitem__(idx) - dataset_idx = bisect.bisect_right(self.cumulative_sizes, idx) - modality = self.modals[dataset_idx] - graph[KEY.DATA_MODALITY] = modality - return graph - - def _modal_wise_property(self, attribute_name: str): - dct = {} - for modal, dataset in zip(self.modals, self.datasets): - try: - if hasattr(dataset, attribute_name): - dct[modal] = getattr(dataset, attribute_name) - except AttributeError: - dct[modal] = None - return dct - - @property - def dataset_dict(self): - arr = {} - for idx, modality in enumerate(self.modals): - arr[modality] = self.datasets[idx] - return arr - - @property - def species(self): - dct = self._modal_wise_property('species') - tot = set() - for sp in dct.values(): - tot.update(sp) - dct['total'] = list(tot) - return dct - - @property - def natoms(self): - return self._modal_wise_property('natoms') - - @property - def per_atom_energy_mean(self): - dct = self._modal_wise_property('per_atom_energy_mean') - try: - means = [] - sample_sizes = [] - for modality, mean in dct.items(): - means.append(mean) - sample_sizes.append( - self.statistics[modality][KEY.PER_ATOM_ENERGY]['count'] - ) - cm = combined_mean(means, sample_sizes) - dct['total'] = cm - except KeyError: - pass - return dct - - @property - def elemwise_reference_energies(self): - # total is not supported (it is expensive and complex, but useless) - return self._modal_wise_property('elemwise_reference_energies') - - @property - def force_rms(self): - dct = self._modal_wise_property('force_rms') - try: - means = [] - sample_sizes = [] - stds = [] - for modality in dct: - means.append(self.statistics[modality][KEY.FORCE]['mean']) - sample_sizes.append(self.statistics[modality][KEY.FORCE]['count']) - stds.append(self.statistics[modality][KEY.FORCE]['std']) - cm = combined_rms(means, stds, sample_sizes) - dct['total'] = cm - except KeyError: - pass - return dct - - @property - def per_atom_energy_std(self): - dct = self._modal_wise_property('per_atom_energy_std') - try: - means = [] - sample_sizes = [] - stds = [] - for modality in dct: - means.append(self.statistics[modality][KEY.PER_ATOM_ENERGY]['mean']) - sample_sizes.append( - self.statistics[modality][KEY.PER_ATOM_ENERGY]['count'] - ) - stds.append(self.statistics[modality][KEY.PER_ATOM_ENERGY]['std']) - cm = combined_std(means, stds, sample_sizes) - dct['total'] = cm - except KeyError: - pass - return dct - - @property - def avg_num_neigh(self): - dct = self._modal_wise_property('avg_num_neigh') - try: - means = [] - sample_sizes = [] - for modality, mean in dct.items(): - means.append(mean) - sample_sizes.append( - self.statistics[modality]['num_neighbor']['count'] - ) - cm = combined_mean(means, sample_sizes) - dct['total'] = cm - except KeyError: - pass - return dct - - @property - def sqrt_avg_num_neigh(self): - avg_nn = self.avg_num_neigh - return {k: v**0.5 for k, v in avg_nn.items()} - - @property - def statistics(self): - return self._modal_wise_property('statistics') - - @staticmethod - def as_graph_dataset( - paths: List[dict], - **graph_dataset_kwargs, - ): - import sevenn.train.graph_dataset as gd - - modal_paths = _arrange_paths_by_modality(paths) - dataset_dct = {} - for modality, paths in modal_paths.items(): - kwargs = deepcopy(graph_dataset_kwargs) - if (dataset := gd.from_single_path(paths, **kwargs)) is None: - pname = kwargs.pop('processed_name', 'graph').replace('.pt', '') - dataset = gd.SevenNetGraphDataset( - files=paths, - processed_name=f'{pname}_{modality}.pt', - **kwargs, - ) - dataset_dct[modality] = dataset - return SevenNetMultiModalDataset(dataset_dct) - - -def from_config( - config: Dict[str, Any], - working_dir: str = os.getcwd(), - dataset_keys: Optional[List[str]] = None, -): - log = Logger() - if dataset_keys is None: - dataset_keys = [ - k for k in config if (k.startswith('load_') and k.endswith('_path')) - ] - - if KEY.LOAD_TRAINSET not in dataset_keys: - raise ValueError(f'{KEY.LOAD_TRAINSET} must be present in config') - - dataset_args = { - 'cutoff': config[KEY.CUTOFF], - 'root': working_dir, - 'process_num_cores': config.get(KEY.PREPROCESS_NUM_CORES, 1), - 'use_data_weight': config.get(KEY.USE_WEIGHT, False), - **config[KEY.DATA_FORMAT_ARGS], - } - - datasets = {} - for dk in dataset_keys: - if not (paths := config[dk]): - continue - if isinstance(paths, str): - paths = [paths] - name = '_'.join([nn.strip() for nn in dk.split('_')[1:-1]]) - dataset_args.update({'processed_name': name}) - datasets[name] = SevenNetMultiModalDataset.as_graph_dataset( - paths, # type: ignore - **dataset_args, - ) - - train_set = datasets['trainset'] - - modals_dataset = set() - chem_species = set() - # print statistics of each dataset - for name, dataset in datasets.items(): - for idx, modality in enumerate(dataset.modals): - log.bar() - log.writeline(f'{name} - {modality} distribution:') - log.statistic_write(dataset.statistics[modality]) - log.format_k_v( - '# structures (graph)', len(dataset.datasets[idx]), write=True - ) - modals_dataset.update([modality]) - chem_species.update(dataset.species['total']) - log.bar() - - if (modal_map := config.get(KEY.MODAL_MAP, None)) is None: - modals = sorted(list(modals_dataset)) - modal_map = {modal: i for i, modal in enumerate(modals)} - config[KEY.MODAL_MAP] = modal_map - - modals = list(modal_map.keys()) - if not modals_dataset.issubset(modal_map): - raise ValueError( - f'Found modalities in datasets: {modals_dataset} are not subset of' - + f' {modals}. Use sevenn_cp tool to append/assign modality' - ) - - log.writeline(f'Modalities of this model: {modals}') - - config[KEY.NUM_MODALITIES] = len(modal_map) - - # initialize known species from dataset if 'auto' - # sorted to alphabetical order (which is same as before) - chem_keys = [KEY.CHEMICAL_SPECIES, KEY.NUM_SPECIES, KEY.TYPE_MAP] - if all([config[ck] == 'auto' for ck in chem_keys]): # see parse_input.py - log.writeline('Known species are obtained from the dataset') - config.update(util.chemical_species_preprocess(sorted(list(chem_species)))) - - # retrieve shift, scale, conv_denominaotrs from user input (keyword) - init_from_stats_candid = [KEY.SHIFT, KEY.SCALE, KEY.CONV_DENOMINATOR] - init_from_stats = [ - k for k in init_from_stats_candid if isinstance(config[k], str) - ] - - for k in init_from_stats: - input = config[k] - if not hasattr(train_set, input): - raise NotImplementedError(input) - modal_stat = getattr(train_set, input) - try: - if k == KEY.CONV_DENOMINATOR and 'total' in modal_stat: - # conv_denominator is not modal-wise - var = modal_stat['total'] - elif k == KEY.SHIFT and config[KEY.USE_MODAL_WISE_SHIFT]: - modal_stat.pop('total', None) - var = modal_stat - elif k == KEY.SHIFT and not config[KEY.USE_MODAL_WISE_SHIFT]: - var = modal_stat['total'] - elif k == KEY.SCALE and config[KEY.USE_MODAL_WISE_SCALE]: - modal_stat.pop('total', None) - var = modal_stat - elif k == KEY.SCALE and not config[KEY.USE_MODAL_WISE_SCALE]: - var = modal_stat['total'] - else: - raise NotImplementedError(f'Failed to init {k} from statistics') - except KeyError as e: - if e.args[0] == 'total': - raise NotImplementedError( - f'{k}: {input} does not support total statistics. ' - + f'Set use_modal_wise_{k} True or specify numbers manually' - ) - else: - raise e - config.update({k: var}) - log.writeline(f'{k} is obtained from statistics') - - return datasets diff --git a/mace-bench/3rdparty/SevenNet/sevenn/train/optim.py b/mace-bench/3rdparty/SevenNet/sevenn/train/optim.py deleted file mode 100644 index 10e757906dbf2b6a1afa90ae7de4fbeb9854540f..0000000000000000000000000000000000000000 --- a/mace-bench/3rdparty/SevenNet/sevenn/train/optim.py +++ /dev/null @@ -1,23 +0,0 @@ -import torch.nn as nn -import torch.optim.lr_scheduler as scheduler -from torch.optim import adagrad, adam, adamw, radam, sgd - -optim_dict = { - 'sgd': sgd.SGD, - 'adagrad': adagrad.Adagrad, - 'adam': adam.Adam, - 'adamw': adamw.AdamW, - 'radam': radam.RAdam, -} - - -scheduler_dict = { - 'steplr': scheduler.StepLR, - 'multisteplr': scheduler.MultiStepLR, - 'exponentiallr': scheduler.ExponentialLR, - 'cosineannealinglr': scheduler.CosineAnnealingLR, - 'reducelronplateau': scheduler.ReduceLROnPlateau, - 'linearlr': scheduler.LinearLR, -} - -loss_dict = {'mse': nn.MSELoss, 'huber': nn.HuberLoss} diff --git a/mace-bench/3rdparty/SevenNet/sevenn/train/trainer.py b/mace-bench/3rdparty/SevenNet/sevenn/train/trainer.py deleted file mode 100644 index cb2eb91a744a12acbf337158ce3ed899a8285c78..0000000000000000000000000000000000000000 --- a/mace-bench/3rdparty/SevenNet/sevenn/train/trainer.py +++ /dev/null @@ -1,230 +0,0 @@ -import os -import uuid -from datetime import datetime -from typing import Any, Dict, Iterable, List, Optional, Tuple, Union - -import torch -import torch.distributed as dist -import torch.nn -from torch.nn.parallel import DistributedDataParallel as DDP -from tqdm import tqdm - -import sevenn._keys as KEY -from sevenn.error_recorder import ErrorRecorder -from sevenn.train.loss import LossDefinition - -from .loss import get_loss_functions_from_config -from .optim import optim_dict, scheduler_dict - - -class Trainer: - """ - Training routine specialized for this package. Depends on 'sevenn.train.loss' - - Args: - model: model to train - loss_functions: List of tuples of [LossDefinition, float]. 'float' is for - loss weight for each Loss function - optimizer_cls: torch optimizer class to initialize - optimizer_args: optimizer keyword argument except 'param' - scheduler_cls: torch scheduler class to initialize, can be None - optimizer_args: optimizer keyword argument except 'optimizer' - device: device to train model, defaults to 'auto' - distributed: whether this is distributed training - distributed_backend: torch DDP backend. Should be one of 'nccl', 'mpi' - """ - - def __init__( - self, - model: torch.nn.Module, - loss_functions: List[Tuple[LossDefinition, float]], - optimizer_cls, - optimizer_args: Optional[dict] = None, - scheduler_cls=None, - scheduler_args: Optional[dict] = None, - device: Union[torch.device, str] = 'auto', - distributed: bool = False, - distributed_backend: str = 'nccl', - ): - if device == 'auto': - device = 'cuda' if torch.cuda.is_available() else 'cpu' - if distributed_backend == 'mpi': - device = 'cpu' - - if distributed: - local_rank = int(os.environ['LOCAL_RANK']) - self.rank = local_rank - if distributed_backend == 'nccl': - device = torch.device('cuda', local_rank) - self.model = DDP(model.to(device), device_ids=[device]) - elif distributed_backend == 'mpi': - self.model = DDP(model.to(device)) - else: - raise ValueError(f'Unknown DDP backend: {distributed_backend}') - dist.barrier() - self.model.module.set_is_batch_data(True) - else: - self.model = model.to(device) - self.model.set_is_batch_data(True) - self.rank = 0 - - self.device = device - self.distributed = distributed - - param = [p for p in self.model.parameters() if p.requires_grad] - self.optimizer = optimizer_cls(param, **optimizer_args) - if scheduler_cls is not None: - self.scheduler = scheduler_cls(self.optimizer, **scheduler_args) - else: - self.scheduler = None - self.loss_functions = loss_functions - - @staticmethod - def from_config(model: torch.nn.Module, config: Dict[str, Any]) -> 'Trainer': - trainer = Trainer( - model, - loss_functions=get_loss_functions_from_config(config), - optimizer_cls=optim_dict[config.get(KEY.OPTIMIZER, 'adam').lower()], - optimizer_args=config.get(KEY.OPTIM_PARAM, {}), - scheduler_cls=scheduler_dict[ - config.get(KEY.SCHEDULER, 'exponentiallr').lower() - ], - scheduler_args=config.get(KEY.SCHEDULER_PARAM, {}), - device=config.get(KEY.DEVICE, 'auto'), - distributed=config.get(KEY.IS_DDP, False), - distributed_backend=config.get(KEY.DDP_BACKEND, 'nccl'), - ) - return trainer - - @staticmethod - def args_from_checkpoint(checkpoint: str) -> Tuple[Dict, Dict, Dict]: - """ - Usage: - trainer_args, optim_stct, scheduler_stct = args_from_checkpoint('7net-0') - # Do what you want to do here - trainer = Trainer(**trainer_args) - trainer.load_state_dict( - optimizer_state_dict=optim_stct, - scheduler_state_dict=scheduler_stct, - """ - from sevenn.util import load_checkpoint - - cp = load_checkpoint(checkpoint) - - model = cp.build_model() - config = cp.config - optimizer_cls = optim_dict[config[KEY.OPTIMIZER].lower()] - scheduler_cls = scheduler_dict[config[KEY.SCHEDULER].lower()] - loss_functions = get_loss_functions_from_config(config) - - return ( - { - 'model': model, - 'loss_functions': loss_functions, - 'optimizer_cls': optimizer_cls, - 'optimizer_args': config[KEY.OPTIM_PARAM], - 'scheduler_cls': scheduler_cls, - 'scheduler_args': config[KEY.SCHEDULER_PARAM], - }, - cp.optimizer_state_dict, - cp.scheduler_state_dict, - ) - - def run_one_epoch( - self, - loader: Iterable, - is_train: bool = False, - error_recorder: Optional[ErrorRecorder] = None, - wrap_tqdm: Union[bool, int] = False, - ) -> None: - """ - Run single epoch with given dataloader - Args: - loader: iterable yieds AtomGraphData - is_train: if true, do backward() and optimizer step - error_recorder: ErrorRecorder instance to compute errors (RMSEm MAE, ..) - wrap_tqdm: wrap given dataloader with tqdm for progress bar - """ - if is_train: - self.model.train() - else: - self.model.eval() - - if wrap_tqdm: - total_len = wrap_tqdm if isinstance(wrap_tqdm, int) else None - loader = tqdm(loader, total=total_len) - for _, batch in enumerate(loader): - if is_train: - self.optimizer.zero_grad() - batch = batch.to(self.device, non_blocking=True) - output = self.model(batch) - if error_recorder is not None: - error_recorder.update(output) - if is_train: - total_loss = torch.tensor([0.0], device=self.device) - for loss_def, w in self.loss_functions: - indv_loss = loss_def.get_loss(output, self.model) - if indv_loss is not None: - total_loss += (indv_loss * w) - total_loss.backward() - self.optimizer.step() - - if self.distributed and error_recorder is not None: - self.recorder_all_reduce(error_recorder) - - def scheduler_step(self, metric: Optional[float] = None) -> None: - if self.scheduler is None: - return - if isinstance(self.scheduler, torch.optim.lr_scheduler.ReduceLROnPlateau): - assert isinstance(metric, float) - self.scheduler.step(metric) - else: - self.scheduler.step() - - def get_lr(self) -> float: - return float(self.optimizer.param_groups[0]['lr']) - - def recorder_all_reduce(self, recorder: ErrorRecorder) -> None: - for metric in recorder.metrics: - # metric.value._ddp_reduce(self.device) - metric.ddp_reduce(self.device) - - def get_checkpoint_dict(self) -> dict: - if self.distributed: - model_state_dct = self.model.module.state_dict() - else: - model_state_dct = self.model.state_dict() - return { - 'model_state_dict': model_state_dct, - 'optimizer_state_dict': self.optimizer.state_dict(), - 'scheduler_state_dict': self.scheduler.state_dict() - if self.scheduler is not None - else None, - 'time': datetime.now().strftime('%Y-%m-%d %H:%M'), - 'hash': uuid.uuid4().hex, - } - - def write_checkpoint(self, path: str, **extra) -> None: - if self.distributed and self.rank != 0: - return - cp = self.get_checkpoint_dict() - cp.update(**extra) - torch.save(cp, path) - - def load_state_dicts( - self, - model_state_dict: Optional[Dict] = None, - optimizer_state_dict: Optional[Dict] = None, - scheduler_state_dict: Optional[Dict] = None, - strict: bool = True, - ) -> None: - if model_state_dict is not None: - if self.distributed: - self.model.module.load_state_dict(model_state_dict, strict=strict) - else: - self.model.load_state_dict(model_state_dict, strict=strict) - - if optimizer_state_dict is not None: - self.optimizer.load_state_dict(optimizer_state_dict) - if scheduler_state_dict is not None and self.scheduler is not None: - self.scheduler.load_state_dict(scheduler_state_dict) diff --git a/mace-bench/3rdparty/SevenNet/sevenn/util.py b/mace-bench/3rdparty/SevenNet/sevenn/util.py deleted file mode 100644 index 632a1d253316f1ee28b1a7c1c2f699ffd773a961..0000000000000000000000000000000000000000 --- a/mace-bench/3rdparty/SevenNet/sevenn/util.py +++ /dev/null @@ -1,330 +0,0 @@ -import os -import os.path as osp -import pathlib -import shutil -from typing import Dict, List, Tuple, Union - -import numpy as np -import requests -import torch -import torch.nn -from e3nn.o3 import FullTensorProduct, Irreps -from tqdm import tqdm - -import sevenn._const as _const -import sevenn._keys as KEY - - -def to_atom_graph_list(atom_graph_batch): - """ - torch_geometric batched data to separate list - original to_data_list() by PyG is not enough since - it doesn't handle inferred tensors - """ - is_stress = KEY.PRED_STRESS in atom_graph_batch - - data_list = atom_graph_batch.to_data_list() - - indices = atom_graph_batch[KEY.NUM_ATOMS].tolist() - - atomic_energy_list = torch.split(atom_graph_batch[KEY.ATOMIC_ENERGY], indices) - inferred_total_energy_list = torch.unbind( - atom_graph_batch[KEY.PRED_TOTAL_ENERGY] - ) - inferred_force_list = torch.split(atom_graph_batch[KEY.PRED_FORCE], indices) - - inferred_stress_list = None - if is_stress: - inferred_stress_list = torch.unbind(atom_graph_batch[KEY.PRED_STRESS]) - - for i, data in enumerate(data_list): - data[KEY.ATOMIC_ENERGY] = atomic_energy_list[i] - data[KEY.PRED_TOTAL_ENERGY] = inferred_total_energy_list[i] - data[KEY.PRED_FORCE] = inferred_force_list[i] - # To fit with KEY.STRESS (ref) format - if is_stress and inferred_stress_list is not None: - data[KEY.PRED_STRESS] = torch.unsqueeze(inferred_stress_list[i], 0) - return data_list - - -def error_recorder_from_loss_functions(loss_functions): - from .error_recorder import ErrorRecorder, MAError, RMSError, get_err_type - from .train.loss import ForceLoss, PerAtomEnergyLoss, StressLoss - - metrics = [] - for loss_function, _ in loss_functions: - ref_key = loss_function.ref_key - pred_key = loss_function.pred_key - # unit = loss_function.unit - criterion = loss_function.criterion - name = loss_function.name - base = None - if type(loss_function) is PerAtomEnergyLoss: - base = get_err_type('Energy') - elif type(loss_function) is ForceLoss: - base = get_err_type('Force') - elif type(loss_function) is StressLoss: - base = get_err_type('Stress') - else: - base = {} - base['name'] = name - base['ref_key'] = ref_key - base['pred_key'] = pred_key - if type(criterion) is torch.nn.MSELoss: - base['name'] = base['name'] + '_RMSE' - metrics.append(RMSError(**base)) - elif type(criterion) is torch.nn.L1Loss: - metrics.append(MAError(**base)) - return ErrorRecorder(metrics) - - -def onehot_to_chem(one_hot_indices: List[int], type_map: Dict[int, int]): - from ase.data import chemical_symbols - - type_map_rev = {v: k for k, v in type_map.items()} - return [chemical_symbols[type_map_rev[x]] for x in one_hot_indices] - - -def model_from_checkpoint( - checkpoint: str, -) -> Tuple[torch.nn.Module, Dict]: - cp = load_checkpoint(checkpoint) - model = cp.build_model() - - return model, cp.config - - -def model_from_checkpoint_with_backend( - checkpoint: str, - backend: str = 'e3nn', -) -> Tuple[torch.nn.Module, Dict]: - cp = load_checkpoint(checkpoint) - model = cp.build_model(backend) - - return model, cp.config - - -def unlabeled_atoms_to_input(atoms, cutoff: float, grad_key: str = KEY.EDGE_VEC): - from .atom_graph_data import AtomGraphData - from .train.dataload import unlabeled_atoms_to_graph - - atom_graph = AtomGraphData.from_numpy_dict( - unlabeled_atoms_to_graph(atoms, cutoff) - ) - atom_graph[grad_key].requires_grad_(True) - atom_graph[KEY.BATCH] = torch.zeros([0]) - return atom_graph - - -def chemical_species_preprocess(input_chem: List[str], universal: bool = False): - from ase.data import atomic_numbers, chemical_symbols - - from .nn.node_embedding import get_type_mapper_from_specie - - config = {} - if not universal: - input_chem = list(set(input_chem)) - chemical_specie = sorted([x.strip() for x in input_chem]) - config[KEY.CHEMICAL_SPECIES] = chemical_specie - config[KEY.CHEMICAL_SPECIES_BY_ATOMIC_NUMBER] = [ - atomic_numbers[x] for x in chemical_specie - ] - config[KEY.NUM_SPECIES] = len(chemical_specie) - config[KEY.TYPE_MAP] = get_type_mapper_from_specie(chemical_specie) - else: - config[KEY.CHEMICAL_SPECIES] = chemical_symbols - len_univ = len(chemical_symbols) - config[KEY.CHEMICAL_SPECIES_BY_ATOMIC_NUMBER] = list(range(len_univ)) - config[KEY.NUM_SPECIES] = len_univ - config[KEY.TYPE_MAP] = {z: z for z in range(len_univ)} - return config - - -def dtype_correct( - v: Union[np.ndarray, torch.Tensor, int, float], - float_dtype: torch.dtype = torch.float32, - int_dtype: torch.dtype = torch.int64, -): - if isinstance(v, np.ndarray): - if np.issubdtype(v.dtype, np.floating): - return torch.from_numpy(v).to(float_dtype) - elif np.issubdtype(v.dtype, np.integer): - return torch.from_numpy(v).to(int_dtype) - elif isinstance(v, torch.Tensor): - if v.dtype.is_floating_point: - return v.to(float_dtype) # convert to specified float dtype - else: # assuming non-floating point tensors are integers - return v.to(int_dtype) # convert to specified int dtype - else: # scalar values - if isinstance(v, int): - return torch.tensor(v, dtype=int_dtype) - elif isinstance(v, float): - return torch.tensor(v, dtype=float_dtype) - else: # Not numeric - return v - - -def infer_irreps_out( - irreps_x: Irreps, - irreps_operand: Irreps, - drop_l: Union[bool, int] = False, - parity_mode: str = 'full', - fix_multiplicity: Union[bool, int] = False, -): - assert parity_mode in ['full', 'even', 'sph'] - # (mul, (ir, p)) - irreps_out = FullTensorProduct(irreps_x, irreps_operand).irreps_out.simplify() - new_irreps_elem = [] - for mul, (l, p) in irreps_out: # noqa - elem = (mul, (l, p)) - if drop_l is not False and l > drop_l: - continue - if parity_mode == 'even' and p == -1: - continue - elif parity_mode == 'sph' and p != (-1) ** l: - continue - if fix_multiplicity: - elem = (fix_multiplicity, (l, p)) - new_irreps_elem.append(elem) - return Irreps(new_irreps_elem) - - -def download_checkpoint(path: str, url: str): - fname = osp.basename(path) - temp_path = path + '.partial' - try: - # raises permission error if fails - os.makedirs(osp.dirname(path), exist_ok=True) - response = requests.get(url, stream=True, timeout=30) - response.raise_for_status() # Raise exception for bad status codes - - total_size = int(response.headers.get('content-length', 0)) - block_size = 1024 # 1 KB chunks - - progress_bar = tqdm( - total=total_size, - unit='B', - unit_scale=True, - desc=f'Downloading {fname}', - ) - - with open(temp_path, 'wb') as file: - for data in response.iter_content(block_size): - progress_bar.update(len(data)) - file.write(data) - progress_bar.close() - - shutil.move(temp_path, path) - print(f'Checkpoint downloaded: {path}') - return path - except PermissionError: - raise - except Exception as e: - # Clean up partial downloads on failure - # May not work as errors handled internally by tqdm etc. - print(f'Download failed: {str(e)}') - if os.path.exists(temp_path): - print(f'Cleaning up partial download: {temp_path}') - os.remove(temp_path) - raise - - -def pretrained_name_to_path(name: str) -> str: - name = name.lower() - heads = ['sevennet', '7net'] - checkpoint_path = None - url = None - - if ( # TODO: regex - name in [f'{n}-0_11july2024' for n in heads] - or name in [f'{n}-0_11jul2024' for n in heads] - or name in ['sevennet-0', '7net-0'] - ): - checkpoint_path = _const.SEVENNET_0_11Jul2024 - elif name in [f'{n}-0_22may2024' for n in heads]: - checkpoint_path = _const.SEVENNET_0_22May2024 - elif name in [f'{n}-l3i5' for n in heads]: - checkpoint_path = _const.SEVENNET_l3i5 - elif name in [f'{n}-mf-0' for n in heads]: - checkpoint_path = _const.SEVENNET_MF_0 - elif name in [f'{n}-mf-ompa' for n in heads]: - checkpoint_path = _const.SEVENNET_MF_ompa - elif name in [f'{n}-omat' for n in heads]: - checkpoint_path = _const.SEVENNET_omat - else: - raise ValueError('Not a valid pretrained model name') - url = _const.CHECKPOINT_DOWNLOAD_LINKS.get(checkpoint_path) - - paths = [ - checkpoint_path, - checkpoint_path.replace(_const._prefix, osp.expanduser('~/.cache/sevennet')), - ] - - for path in paths: - if osp.exists(path): - return path - - # File not found check url and try download - if url is None: - raise FileNotFoundError(checkpoint_path) - - try: - return download_checkpoint(paths[0], url) # 7net package path - except PermissionError: - return download_checkpoint(paths[1], url) # ~/.cache - - -def load_checkpoint(checkpoint: Union[pathlib.Path, str]): - from sevenn.checkpoint import SevenNetCheckpoint - suggests = ['7net-0, 7net-l3i5, 7net-mf-ompa, 7net-omat'] - if osp.isfile(checkpoint): - checkpoint_path = checkpoint - else: - try: - checkpoint_path = pretrained_name_to_path(str(checkpoint)) - except ValueError: - raise ValueError( - f'Given {checkpoint} is not exists and not a pre-trained name.\n' - f'Valid pretrained model names: {suggests}' - ) - return SevenNetCheckpoint(checkpoint_path) - - -def unique_filepath(filepath: str) -> str: - if not os.path.isfile(filepath): - return filepath - else: - dirname = os.path.dirname(filepath) - fname = os.path.basename(filepath) - name, ext = os.path.splitext(fname) - cnt = 0 - new_name = f'{name}{cnt}{ext}' - new_path = os.path.join(dirname, new_name) - while os.path.exists(new_path): - cnt += 1 - new_name = f'{name}{cnt}{ext}' - new_path = os.path.join(dirname, new_name) - return new_path - - -def get_error_recorder( - recorder_tuples: List[Tuple[str, str]] = [ - ('Energy', 'RMSE'), - ('Force', 'RMSE'), - ('Stress', 'RMSE'), - ('Energy', 'MAE'), - ('Force', 'MAE'), - ('Stress', 'MAE'), - ], -): - # TODO add criterion argument and loss recorder selections - import sevenn.error_recorder as error_recorder - - config = recorder_tuples - err_metrics = [] - for err_type, metric_name in config: - metric_kwargs = error_recorder.get_err_type(err_type).copy() - metric_kwargs['name'] += f'_{metric_name}' - metric_cls = error_recorder.ErrorRecorder.METRIC_DICT[metric_name] - err_metrics.append(metric_cls(**metric_kwargs)) - return error_recorder.ErrorRecorder(err_metrics) diff --git a/mace-bench/3rdparty/SevenNet/tests/data/checkpoints/_cp_0.pth_old b/mace-bench/3rdparty/SevenNet/tests/data/checkpoints/_cp_0.pth_old deleted file mode 100644 index 85d55dc1dcfc4fe016943287be77252cfeb0771d..0000000000000000000000000000000000000000 Binary files a/mace-bench/3rdparty/SevenNet/tests/data/checkpoints/_cp_0.pth_old and /dev/null differ diff --git a/mace-bench/3rdparty/SevenNet/tests/data/checkpoints/cp_0.pth b/mace-bench/3rdparty/SevenNet/tests/data/checkpoints/cp_0.pth deleted file mode 100644 index d8549165c8b8b1c0de64002fb4cbac451ca1f314..0000000000000000000000000000000000000000 Binary files a/mace-bench/3rdparty/SevenNet/tests/data/checkpoints/cp_0.pth and /dev/null differ diff --git a/mace-bench/3rdparty/SevenNet/tests/data/inferences/snet0_on_hfo2/errors.txt b/mace-bench/3rdparty/SevenNet/tests/data/inferences/snet0_on_hfo2/errors.txt deleted file mode 100644 index a7123abfdfccab38e7d90a381d9b732e7ab7f22d..0000000000000000000000000000000000000000 --- a/mace-bench/3rdparty/SevenNet/tests/data/inferences/snet0_on_hfo2/errors.txt +++ /dev/null @@ -1,6 +0,0 @@ -Energy_RMSE (eV/atom): 18.84848889028682 -Force_RMSE (eV/Å): 0.2622841142173583 -Stress_RMSE (kbar): 163.7362768581691 -Energy_MAE (eV/atom): 18.848487854003906 -Force_MAE (eV/Å): 0.116698424021403 -Stress_MAE (kbar): 47.33086649576823 diff --git a/mace-bench/3rdparty/SevenNet/tests/data/inferences/snet0_on_hfo2/per_atom.csv b/mace-bench/3rdparty/SevenNet/tests/data/inferences/snet0_on_hfo2/per_atom.csv deleted file mode 100644 index 97a7d8aa8fcfa6c8e159b81828b6b58177f8582a..0000000000000000000000000000000000000000 --- a/mace-bench/3rdparty/SevenNet/tests/data/inferences/snet0_on_hfo2/per_atom.csv +++ /dev/null @@ -1,25 +0,0 @@ -stct_id,atom_id,atomic_numbers,atomic_energy,pos_x,pos_y,pos_z,force_of_atoms_x,force_of_atoms_y,force_of_atoms_z,inferred_force_x,inferred_force_y,inferred_force_z -0,0,72,-14.758427,2.76422,4.14748,1.50037,-0.059786,0.151222,-0.085196,-0.18387456,0.4976529,-0.18538895 -0,1,72,-14.758418,0.21835,1.30499,1.07094,-0.059786,-0.151222,0.085196,-0.18364179,-0.49762845,0.1854167 -0,2,72,-14.75845,4.87338,4.57603,4.07176,0.059786,0.151222,-0.085196,0.18574518,0.49244216,-0.19169456 -0,3,72,-14.758455,2.32752,1.73353,3.64233,0.059786,-0.151222,0.085196,0.18554506,-0.4924091,0.1916164 -0,4,8,-7.969731,3.85655,0.67027,2.45893,-0.008711,0.112966,0.037362,0.038163364,0.27630207,0.100170046 -0,5,8,-7.969726,1.31069,4.7822,0.11238,-0.008711,-0.112966,-0.037362,0.0380187,-0.27626732,-0.10015537 -0,6,8,-7.696194,4.23542,2.98966,0.79342,-0.000366,-0.03082,0.075334,-0.0040642396,0.06838645,0.14082311 -0,7,8,-7.6961865,1.68956,2.46281,1.77789,-0.000366,0.03082,-0.075334,-0.0042099506,-0.06848977,-0.14088435 -0,8,8,-7.6973476,0.85631,2.89135,4.34928,0.000366,0.03082,-0.075334,0.0020455532,-0.06770688,-0.14164624 -0,9,8,-7.697351,3.40218,3.41821,3.3648,0.000366,-0.03082,0.075334,0.0020625181,0.06768774,0.14173353 -0,10,8,-7.9687324,3.78104,1.09881,5.03032,0.008711,0.112966,0.037362,-0.03782143,0.28077862,0.10171969 -0,11,8,-7.968731,1.23518,5.21075,2.68377,0.008711,-0.112966,-0.037362,-0.03796852,-0.28074813,-0.10171008 -1,0,72,-14.73119,2.7475,4.12239,1.49129,-0.107044,0.270498,-0.154141,-0.22496888,0.6460437,-0.24772969 -1,1,72,-14.731192,0.21703,1.2971,1.06446,-0.107044,-0.270498,0.154141,-0.22493178,-0.64605427,0.24796319 -1,2,72,-14.731257,4.84391,4.54835,4.04713,0.107044,0.270498,-0.154141,0.22658941,0.640341,-0.25407305 -1,3,72,-14.731257,2.31344,1.72305,3.6203,0.107044,-0.270498,0.154141,0.22664651,-0.640331,0.25397068 -1,4,8,-7.9511185,3.83323,0.66621,2.44406,-0.015569,0.202973,0.067068,0.04174666,0.369385,0.14108454 -1,5,8,-7.9511194,1.30276,4.75328,0.1117,-0.015569,-0.202973,-0.067068,0.04180483,-0.36939618,-0.14114018 -1,6,8,-7.6695013,4.20981,2.97158,0.78862,0.000396,-0.054872,0.138515,-0.011644345,0.080120645,0.18942688 -1,7,8,-7.6695027,1.67934,2.44791,1.76714,0.000396,0.054872,-0.138515,-0.011605289,-0.08007531,-0.18946008 -1,8,8,-7.670638,0.85113,2.87387,4.32298,-0.000396,0.054872,-0.138515,0.009096172,-0.07910344,-0.19031705 -1,9,8,-7.670635,3.3816,3.39753,3.34445,-0.000396,-0.054872,0.138515,0.009038135,0.07907101,0.19029519 -1,10,8,-7.950069,3.75818,1.09217,4.99989,0.015569,0.202973,0.067068,-0.040918212,0.37362093,0.14279541 -1,11,8,-7.950064,1.22771,5.17923,2.66754,0.015569,-0.202973,-0.067068,-0.040852908,-0.37362194,-0.1428154 diff --git a/mace-bench/3rdparty/SevenNet/tests/data/inferences/snet0_on_hfo2/per_graph.csv b/mace-bench/3rdparty/SevenNet/tests/data/inferences/snet0_on_hfo2/per_graph.csv deleted file mode 100644 index 8e5555a4bb201a81c2bf4d5c119f01d035d813bd..0000000000000000000000000000000000000000 --- a/mace-bench/3rdparty/SevenNet/tests/data/inferences/snet0_on_hfo2/per_graph.csv +++ /dev/null @@ -1,3 +0,0 @@ -num_atoms,user_label,total_energy,inferred_total_energy,stress_xx,stress_yy,stress_zz,stress_xy,stress_yz,stress_zx,inferred_stress_xx,inferred_stress_yy,inferred_stress_zz,inferred_stress_xy,inferred_stress_yz,inferred_stress_zx,cell_lattice_vectors_a,cell_lattice_vectors_b,cell_lattice_vectors_c -12,-,-347.81223,-121.69777,74.372475,73.61505,70.034294,0.0,-4.38372,0.0,171.75166,180.33585,149.94254,-0.0007366179,-7.2767844,9.071616e-05,[5.091732 0. 0. ],[ 0.000000e+00 5.023922e+00 -7.948100e-05],[0. 0.85709256 5.1427774 ] -12,-,-347.6568,-121.40755,135.8412,134.45676,127.92448,0.0,-8.08666,0.0,231.50803,241.38077,203.83183,-0.001700722,-10.654452,-0.00061846955,[5.060935 0. 0. ],[ 0.000000e+00 4.993535e+00 -7.900000e-05],[0. 0.8519085 5.111672 ] diff --git a/mace-bench/3rdparty/SevenNet/tests/data/systems/hfo2.extxyz b/mace-bench/3rdparty/SevenNet/tests/data/systems/hfo2.extxyz deleted file mode 100644 index d14a69428cf6df82f362f86e102287be5f6527d4..0000000000000000000000000000000000000000 --- a/mace-bench/3rdparty/SevenNet/tests/data/systems/hfo2.extxyz +++ /dev/null @@ -1,28 +0,0 @@ -12 -Lattice="5.091731935 0.0 0.0 0.0 5.023921826 -7.9481e-05 0.0 0.857092558 5.142777331" Properties=species:S:1:pos:R:3:forces:R:3 stress="-0.04641964502194789 -0.0 -0.0 -0.0 -0.04594690063773523 0.0027361028385316957 -0.0 0.0027361028385316957 -0.04371196601597546" free_energy=-347.81221934 energy=-347.81221934 pbc="T T T" -Hf 2.76422000 4.14748000 1.50037000 -0.05978600 0.15122200 -0.08519600 -Hf 0.21835000 1.30499000 1.07094000 -0.05978600 -0.15122200 0.08519600 -Hf 4.87338000 4.57603000 4.07176000 0.05978600 0.15122200 -0.08519600 -Hf 2.32752000 1.73353000 3.64233000 0.05978600 -0.15122200 0.08519600 -O 3.85655000 0.67027000 2.45893000 -0.00871100 0.11296600 0.03736200 -O 1.31069000 4.78220000 0.11238000 -0.00871100 -0.11296600 -0.03736200 -O 4.23542000 2.98966000 0.79342000 -0.00036600 -0.03082000 0.07533400 -O 1.68956000 2.46281000 1.77789000 -0.00036600 0.03082000 -0.07533400 -O 0.85631000 2.89135000 4.34928000 0.00036600 0.03082000 -0.07533400 -O 3.40218000 3.41821000 3.36480000 0.00036600 -0.03082000 0.07533400 -O 3.78104000 1.09881000 5.03032000 0.00871100 0.11296600 0.03736200 -O 1.23518000 5.21075000 2.68377000 0.00871100 -0.11296600 -0.03736200 -12 -Lattice="5.06093517 0.0 0.0 0.0 4.993535202 -7.9e-05 0.0 0.85190853 5.111671823" Properties=species:S:1:pos:R:3:forces:R:3 stress="-0.08478540894709327 -0.0 -0.0 -0.0 -0.0839213094576695 0.0050472962187915115 -0.0 0.0050472962187915115 -0.07984417469287791" free_energy=-347.65678484 energy=-347.65678484 pbc="T T T" -Hf 2.74750000 4.12239000 1.49129000 -0.10704400 0.27049800 -0.15414100 -Hf 0.21703000 1.29710000 1.06446000 -0.10704400 -0.27049800 0.15414100 -Hf 4.84391000 4.54835000 4.04713000 0.10704400 0.27049800 -0.15414100 -Hf 2.31344000 1.72305000 3.62030000 0.10704400 -0.27049800 0.15414100 -O 3.83323000 0.66621000 2.44406000 -0.01556900 0.20297300 0.06706800 -O 1.30276000 4.75328000 0.11170000 -0.01556900 -0.20297300 -0.06706800 -O 4.20981000 2.97158000 0.78862000 0.00039600 -0.05487200 0.13851500 -O 1.67934000 2.44791000 1.76714000 0.00039600 0.05487200 -0.13851500 -O 0.85113000 2.87387000 4.32298000 -0.00039600 0.05487200 -0.13851500 -O 3.38160000 3.39753000 3.34445000 -0.00039600 -0.05487200 0.13851500 -O 3.75818000 1.09217000 4.99989000 0.01556900 0.20297300 0.06706800 -O 1.22771000 5.17923000 2.66754000 0.01556900 -0.20297300 -0.06706800 diff --git a/mace-bench/3rdparty/SevenNet/tests/lammps_tests/conftest.py b/mace-bench/3rdparty/SevenNet/tests/lammps_tests/conftest.py deleted file mode 100644 index 8b7257de33c5d8aa6baedf1691a1bea6acbb6424..0000000000000000000000000000000000000000 --- a/mace-bench/3rdparty/SevenNet/tests/lammps_tests/conftest.py +++ /dev/null @@ -1,24 +0,0 @@ -import pytest - - -def pytest_addoption(parser): - parser.addoption('--lammps_cmd', default=None, help='Lammps binary to test') - parser.addoption( - '--mpirun_cmd', default=None, help='mpirun binary to test parallel' - ) - - -@pytest.fixture -def lammps_cmd(request): - bin = request.config.getoption('lammps_cmd') - if bin is None: - pytest.skip('No LAMMPS binary given, skipping test') - return bin - - -@pytest.fixture -def mpirun_cmd(request): - bin = request.config.getoption('mpirun_cmd') - if bin is None: - pytest.skip('No mpirun cmd given, skipping test') - return bin diff --git a/mace-bench/3rdparty/SevenNet/tests/lammps_tests/scripts/pbc_skel.lmp b/mace-bench/3rdparty/SevenNet/tests/lammps_tests/scripts/pbc_skel.lmp deleted file mode 100644 index d547e409945132c72db21407c0bbc77c87249fc4..0000000000000000000000000000000000000000 --- a/mace-bench/3rdparty/SevenNet/tests/lammps_tests/scripts/pbc_skel.lmp +++ /dev/null @@ -1,23 +0,0 @@ - units metal - boundary __BOUNDARY__ - box tilt large - read_data __LMP_STCT__ - - #replicate __REPLICATE__ - - mass * 1.0 # do not matter since we don't run MD - - pair_style __PAIR_STYLE__ - pair_coeff * * __POTENTIALS__ __ELEMENT__ - - timestep 0.002 - - compute pa all pe/atom - - thermo 1 - fix 1 all nve - thermo_style custom step tpcpu pe ke vol pxx pyy pzz pxy pxz pyz press temp - dump mydump all custom 1 force.dump id type element c_pa x y z fx fy fz - dump_modify mydump sort id element __ELEMENT__ - - run 0 diff --git a/mace-bench/3rdparty/SevenNet/tests/lammps_tests/scripts/skel.lmp b/mace-bench/3rdparty/SevenNet/tests/lammps_tests/scripts/skel.lmp deleted file mode 100644 index f8200d591472002e174cffd4de5ff98b41fba5c1..0000000000000000000000000000000000000000 --- a/mace-bench/3rdparty/SevenNet/tests/lammps_tests/scripts/skel.lmp +++ /dev/null @@ -1,20 +0,0 @@ - units metal - boundary __BOUNDARY__ - read_data __LMP_STCT__ - - mass * 1.0 # do not matter since we don't run MD - - pair_style __PAIR_STYLE__ - pair_coeff * * __POTENTIALS__ __ELEMENT__ - - timestep 0.002 - - compute pa all pe/atom - - thermo 1 - fix 1 all nve - thermo_style custom step tpcpu pe ke vol pxx pyy pzz pxy pxz pyz press temp - dump mydump all custom 1 __FORCE_DUMP_PATH__ id type element c_pa x y z fx fy fz - dump_modify mydump sort id element __ELEMENT__ - - run 0 diff --git a/mace-bench/3rdparty/SevenNet/tests/lammps_tests/test_lammps.py b/mace-bench/3rdparty/SevenNet/tests/lammps_tests/test_lammps.py deleted file mode 100644 index 54f53a50e0fe6e7c4f53851fb9759020a6c365e3..0000000000000000000000000000000000000000 --- a/mace-bench/3rdparty/SevenNet/tests/lammps_tests/test_lammps.py +++ /dev/null @@ -1,467 +0,0 @@ -import copy -import logging -import pathlib -import subprocess - -import ase.calculators.lammps -import ase.io.lammpsdata -import numpy as np -import pytest -import torch -from ase.build import bulk, surface -from ase.calculators.singlepoint import SinglePointCalculator - -import sevenn -from sevenn.calculator import SevenNetCalculator -from sevenn.model_build import build_E3_equivariant_model -from sevenn.nn.cue_helper import is_cue_available -from sevenn.scripts.deploy import deploy, deploy_parallel -from sevenn.util import chemical_species_preprocess, pretrained_name_to_path - -logger = logging.getLogger('test_lammps') - -cutoff = 4.0 - -lmp_script_path = str( - (pathlib.Path(__file__).parent / 'scripts' / 'skel.lmp').resolve() -) - -data_root = (pathlib.Path(__file__).parent.parent / 'data').resolve() -cp_0_path = str(data_root / 'checkpoints' / 'cp_0.pth') # knows Hf, O -cp_mf_path = pretrained_name_to_path('7net-mf-0') - - -@pytest.fixture(scope='module') -def serial_potential_path(tmp_path_factory): - tmp = tmp_path_factory.mktemp('serial_potential') - pot_path = str(tmp / 'deployed_serial.pt') - deploy(cp_0_path, pot_path) - return pot_path - - -@pytest.fixture(scope='module') -def parallel_potential_path(tmp_path_factory): - tmp = tmp_path_factory.mktemp('paralllel_potential') - pot_path = str(tmp / 'deployed_parallel') - deploy_parallel(cp_0_path, pot_path) - return ' '.join(['3', pot_path]) - - -@pytest.fixture(scope='module') -def serial_modal_potential_path(tmp_path_factory): - tmp = tmp_path_factory.mktemp('serial_modal_potential') - pot_path = str(tmp / 'deployed_serial.pt') - deploy(cp_mf_path, pot_path, 'PBE') - return pot_path - - -@pytest.fixture(scope='module') -def parallel_modal_potential_path(tmp_path_factory): - tmp = tmp_path_factory.mktemp('paralllel_modal_potential') - pot_path = str(tmp / 'deployed_parallel') - deploy_parallel(cp_mf_path, pot_path, 'PBE') - return ' '.join(['5', pot_path]) - - -@pytest.fixture(scope='module') -def ref_calculator(): - return SevenNetCalculator(cp_0_path) - - -@pytest.fixture(scope='module') -def ref_modal_calculator(): - return SevenNetCalculator(cp_mf_path, modal='PBE') - - -def get_model_config(): - config = { - 'cutoff': cutoff, - 'channel': 8, - 'lmax': 2, - 'is_parity': True, - 'num_convolution_layer': 3, - 'self_connection_type': 'linear', # not NequIp - 'interaction_type': 'nequip', - 'radial_basis': { - 'radial_basis_name': 'bessel', - }, - 'cutoff_function': {'cutoff_function_name': 'poly_cut'}, - 'weight_nn_hidden_neurons': [64, 64], - 'act_radial': 'silu', - 'act_scalar': {'e': 'silu', 'o': 'tanh'}, - 'act_gate': {'e': 'silu', 'o': 'tanh'}, - 'conv_denominator': 30.0, - 'train_denominator': False, - 'shift': -10.0, - 'scale': 10.0, - 'train_shift_scale': False, - 'irreps_manual': False, - 'lmax_edge': -1, - 'lmax_node': -1, - 'readout_as_fcn': False, - 'use_bias_in_linear': False, - '_normalize_sph': True, - } - config.update(chemical_species_preprocess(['Hf', 'O'])) - return config - - -def get_model(config_overwrite=None, use_cueq=False, cueq_config=None): - cf = get_model_config() - if config_overwrite is not None: - cf.update(config_overwrite) - - cueq_config = cueq_config or {'cuequivariance_config': {'use': use_cueq}} - cf.update(cueq_config) - - model = build_E3_equivariant_model(cf, parallel=False) - assert not isinstance(model, list) - return model - - -def hfo2_bulk(replicate=(2, 2, 2), a=4.0): - atoms = bulk('HfO', 'rocksalt', a, orthorhombic=True) - atoms = atoms * replicate - atoms.rattle(stdev=0.10) - return atoms - - -def hf_surface(replicate=(3, 3, 1), layers=4, vacuum=0.5): - atoms = surface('Al', (1, 0, 0), layers=layers, vacuum=vacuum) - atoms.set_atomic_numbers([72] * len(atoms)) # Hf - atoms = atoms * replicate - atoms.rattle(stdev=0.10) - return atoms - - -def get_system(system_name, **kwargs): - if system_name == 'bulk': - return hfo2_bulk(**kwargs) - elif system_name == 'surface': - return hf_surface(**kwargs) - else: - raise ValueError() - - -def assert_atoms(atoms1, atoms2, rtol=1e-5, atol=1e-6): - def acl(a, b, rtol=rtol, atol=atol): - return np.allclose(a, b, rtol=rtol, atol=atol) - - assert len(atoms1) == len(atoms2) - assert acl(atoms1.get_cell(), atoms2.get_cell()) - assert acl(atoms1.get_potential_energy(), atoms2.get_potential_energy()) - assert acl(atoms1.get_forces(), atoms2.get_forces(), rtol * 10, atol * 10) - assert acl( - atoms1.get_stress(voigt=False), - atoms2.get_stress(voigt=False), - rtol * 10, - atol * 10, - ) - # assert acl(atoms1.get_potential_energies(), atoms2.get_potential_energies()) - - -def _lammps_results_to_atoms(lammps_log, force_dump): - with open(lammps_log, 'r') as f: - lines = f.readlines() - lmp_log = None - for i, line in enumerate(lines): - if not line.startswith('Per MPI rank memory allocation'): - continue - lmp_log = { - k: eval(v) for k, v in zip(lines[i + 1].split(), lines[i + 2].split()) - } - break - - assert lmp_log is not None and 'PotEng' in lmp_log - - latoms_list = ase.io.read(force_dump, format='lammps-dump-text', index=':') - assert isinstance(latoms_list, list) - latoms = latoms_list[0] - assert latoms.calc is not None - latoms.calc.results['energy'] = lmp_log['PotEng'] - latoms.calc.results['free_energy'] = lmp_log['PotEng'] - latoms.info = { - 'data_from': 'lammps', - 'lmp_log': lmp_log, - 'lmp_dump': force_dump, - } - # atomic energy read - latoms.calc.results['energies'] = latoms.arrays['c_pa'][:, 0] - stress = np.array( - [ - [lmp_log['Pxx'], lmp_log['Pxy'], lmp_log['Pxz']], - [lmp_log['Pxy'], lmp_log['Pyy'], lmp_log['Pyz']], - [lmp_log['Pxz'], lmp_log['Pyz'], lmp_log['Pzz']], - ] - ) - stress = -1 * stress / 1602.1766208 / 1000 # convert bars to eV/A^3 - latoms.calc.results['stress'] = stress - - return latoms - - -def _run_lammps(atoms, pair_style, potential, wd, command, test_name): - wd = wd.resolve() - pbc = atoms.get_pbc() - pbc_str = ' '.join(['p' if x else 'f' for x in pbc]) - chem = list(set(atoms.get_chemical_symbols())) - # Way to ase handle lammps structure - - prism = ase.calculators.lammps.coordinatetransform.Prism( - atoms.get_cell(), pbc=pbc - ) - lmp_stct = wd / 'lammps_structure' - ase.io.lammpsdata.write_lammps_data( - lmp_stct, atoms, prismobj=prism, specorder=chem - ) - - with open(lmp_script_path, 'r') as f: - cont = f.read() - - lammps_log = str(wd / 'log.lammps') - force_dump = str(wd / 'force.dump') - - var_dct = {} - var_dct['__ELEMENT__'] = ' '.join(chem) - var_dct['__LMP_STCT__'] = str(lmp_stct.resolve()) - var_dct['__PAIR_STYLE__'] = pair_style - var_dct['__POTENTIALS__'] = potential - var_dct['__BOUNDARY__'] = pbc_str - var_dct['__FORCE_DUMP_PATH__'] = force_dump - for key, val in var_dct.items(): - cont = cont.replace(key, val) - - input_script_path = str(wd / 'in.lmp') - with open(input_script_path, 'w') as f: - f.write(cont) - - command = f'{command} -in {input_script_path} -log {lammps_log}' - subprocess_routine(command.split(), test_name) - - lmp_atoms = _lammps_results_to_atoms(lammps_log, force_dump) - assert lmp_atoms.calc is not None - - rot_mat = prism.rot_mat - results = copy.deepcopy(lmp_atoms.calc.results) - r_force = np.dot(results['forces'], rot_mat.T) - results['forces'] = r_force - if 'stress' in results: - # see ase.calculators.lammpsrun.py - stress_tensor = results['stress'] - stress_atoms = np.dot(np.dot(rot_mat, stress_tensor), rot_mat.T) - results['stress'] = stress_atoms - r_cell = lmp_atoms.get_cell() @ rot_mat.T - lmp_atoms.set_cell(r_cell, scale_atoms=True) - lmp_atoms = SinglePointCalculator(lmp_atoms, **results).get_atoms() - - return lmp_atoms - - -def serial_lammps_run(atoms, potential, wd, test_name, lammps_cmd): - command = lammps_cmd - return _run_lammps(atoms, 'e3gnn', potential, wd, command, test_name) - - -def parallel_lammps_run( - atoms, potential, wd, test_name, ncores, lammps_cmd, mpirun_cmd -): - command = f'{mpirun_cmd} -np {ncores} {lammps_cmd}' - return _run_lammps(atoms, 'e3gnn/parallel', potential, wd, command, test_name) - - -def subprocess_routine(cmd, name): - res = subprocess.run(cmd, capture_output=True, timeout=30) - if res.returncode != 0: - logger.error(f'Subprocess {name} failed return code: {res.returncode}') - logger.error(res.stderr.decode('utf-8')) - raise RuntimeError(f'{name} failed') - - logger.info(f'stdout of {name}:') - logger.info(res.stdout.decode('utf-8')) - - -@pytest.mark.parametrize( - 'system', - ['bulk', 'surface'], -) -def test_serial(system, serial_potential_path, ref_calculator, lammps_cmd, tmp_path): - atoms = get_system(system) - atoms_lammps = serial_lammps_run( - atoms=atoms, - potential=serial_potential_path, - wd=tmp_path, - test_name='serial lmp test', - lammps_cmd=lammps_cmd, - ) - atoms.calc = ref_calculator - assert_atoms(atoms, atoms_lammps) - - -@pytest.mark.parametrize( - 'system,ncores', - [ - ('bulk', 1), - ('bulk', 2), - ('bulk', 4), - ('surface', 1), - ('surface', 2), - ('surface', 3), - ('surface', 4), - ], -) -def test_parallel( - system, - ncores, - parallel_potential_path, - ref_calculator, - lammps_cmd, - mpirun_cmd, - tmp_path, -): - if system == 'bulk': - rep = (6, 6, 3) - elif system == 'surface': - rep = (4, 4, 1) - else: - assert False - atoms = get_system(system, replicate=rep) - atoms_lammps = parallel_lammps_run( - atoms=atoms, - potential=parallel_potential_path, - wd=tmp_path, - test_name='parallel lmp test', - lammps_cmd=lammps_cmd, - mpirun_cmd=mpirun_cmd, - ncores=ncores, - ) - atoms.calc = ref_calculator - assert_atoms(atoms, atoms_lammps) - - -@pytest.mark.parametrize( - 'system', - ['bulk', 'surface'], -) -def test_modal_serial( - system, serial_modal_potential_path, ref_modal_calculator, lammps_cmd, tmp_path -): - atoms = get_system(system) - atoms_lammps = serial_lammps_run( - atoms=atoms, - potential=serial_modal_potential_path, - wd=tmp_path, - test_name='serial lmp test', - lammps_cmd=lammps_cmd, - ) - atoms.calc = ref_modal_calculator - assert_atoms(atoms, atoms_lammps) - - -@pytest.mark.parametrize( - 'system,ncores', - [ - ('bulk', 2), - ('surface', 2), - ], -) -def test_modal_parallel( - system, - ncores, - parallel_modal_potential_path, - ref_modal_calculator, - lammps_cmd, - mpirun_cmd, - tmp_path, -): - if system == 'bulk': - rep = (6, 6, 3) - elif system == 'surface': - rep = (4, 4, 1) - else: - assert False - atoms = get_system(system, replicate=rep) - atoms_lammps = parallel_lammps_run( - atoms=atoms, - potential=parallel_modal_potential_path, - wd=tmp_path, - test_name='parallel lmp test', - lammps_cmd=lammps_cmd, - mpirun_cmd=mpirun_cmd, - ncores=ncores, - ) - atoms.calc = ref_modal_calculator - assert_atoms(atoms, atoms_lammps) - - -@pytest.mark.filterwarnings('ignore:.*is not found from.*') -@pytest.mark.skipif(not is_cue_available(), reason='cueq not available') -def test_cueq_serial(lammps_cmd, tmp_path): - """ - TODO: Use already saved cueq enabled checkpoint after cueq becomes stable - """ - cueq = True - model = get_model(use_cueq=cueq) - ref_calc = SevenNetCalculator(model, file_type='model_instance') - atoms = get_system('bulk') - - cfg = get_model_config() - cfg.update( - {'cuequivariance_config': {'use': cueq}, 'version': sevenn.__version__} - ) - - cp_path = str(tmp_path / 'cp.pth') - torch.save( - {'model_state_dict': model.state_dict(), 'config': cfg}, - cp_path, - ) - - pot_path = str(tmp_path / 'deployed_from_cueq_serial.pt') - deploy(cp_path, pot_path) - - atoms_lammps = serial_lammps_run( - atoms=atoms, - potential=pot_path, - wd=tmp_path, - test_name='cueq checkpoint serial lmp run test', - lammps_cmd=lammps_cmd, - ) - atoms.calc = ref_calc - assert_atoms(atoms, atoms_lammps) - - -@pytest.mark.filterwarnings('ignore:.*is not found from.*') -@pytest.mark.skipif(not is_cue_available(), reason='cueq not available') -def test_cueq_parallel(lammps_cmd, mpirun_cmd, tmp_path): - """ - TODO: Use already saved cueq enabled checkpoint after cueq becomes stable - """ - cueq = True - model = get_model(use_cueq=cueq) - ref_calc = SevenNetCalculator(model, file_type='model_instance') - atoms = get_system('surface', replicate=(4, 4, 1)) - - cfg = get_model_config() - cfg.update( - {'cuequivariance_config': {'use': cueq}, 'version': sevenn.__version__} - ) - - cp_path = str(tmp_path / 'cp.pth') - torch.save( - {'model_state_dict': model.state_dict(), 'config': cfg}, - cp_path, - ) - - pot_path = str(tmp_path / 'deployed_from_cueq_parallel') - deploy_parallel(cp_path, pot_path) - - atoms_lammps = parallel_lammps_run( - atoms=atoms, - potential=' '.join([str(cfg['num_convolution_layer']), pot_path]), - wd=tmp_path, - test_name='cueq checkpoint parallel lmp run test', - lammps_cmd=lammps_cmd, - mpirun_cmd=mpirun_cmd, - ncores=2, - ) - atoms.calc = ref_calc - assert_atoms(atoms, atoms_lammps) diff --git a/mace-bench/3rdparty/SevenNet/tests/unit_tests/test_calculator.py b/mace-bench/3rdparty/SevenNet/tests/unit_tests/test_calculator.py deleted file mode 100644 index c2494927674355bd5a3f488a1ae421b397fe3ac7..0000000000000000000000000000000000000000 --- a/mace-bench/3rdparty/SevenNet/tests/unit_tests/test_calculator.py +++ /dev/null @@ -1,217 +0,0 @@ -import copy - -import numpy as np -import pytest -from ase.build import bulk, molecule - -from sevenn.calculator import D3Calculator, SevenNetCalculator -from sevenn.nn.cue_helper import is_cue_available -from sevenn.scripts.deploy import deploy -from sevenn.util import ( - model_from_checkpoint, - model_from_checkpoint_with_backend, - pretrained_name_to_path, -) - - -@pytest.fixture -def atoms_pbc(): - atoms1 = bulk('NaCl', 'rocksalt', a=5.63) - atoms1.set_cell([[1.0, 2.815, 2.815], [2.815, 0.0, 2.815], [2.815, 2.815, 0.0]]) - atoms1.set_positions([[0.0, 0.0, 0.0], [2.815, 0.0, 0.0]]) - return atoms1 - - -@pytest.fixture -def atoms_mol(): - atoms2 = molecule('H2O') - atoms2.set_positions([[0.0, 0.2, 0.12], [0.0, 0.76, -0.48], [0.0, -0.76, -0.48]]) - return atoms2 - - -@pytest.fixture(scope='module') -def sevennet_0_cal(): - return SevenNetCalculator('7net-0_11July2024') - - -@pytest.fixture(scope='module') -def sevennet_0_cueq_cal(): - cpp = pretrained_name_to_path('7net-0_11July2024') - model, _ = model_from_checkpoint_with_backend(cpp, 'cueq') - return SevenNetCalculator(model) - - -@pytest.fixture(scope='module') -def d3_cal(): - try: - return D3Calculator() - except NotImplementedError as e: - pytest.skip(f'{e}') - - -def test_sevennet_0_cal_pbc(atoms_pbc, sevennet_0_cal): - atoms1_ref = { - 'energy': -3.779199, - 'energies': [-1.8493923, -1.9298072], - 'force': [ - [12.666697, 0.04726403, 0.04775861], - [-12.666697, -0.04726403, -0.04775861], - ], - 'stress': [ - [ - -0.6439122, - -0.03643947, - -0.03643981, - 0.00599139, - 0.04544507, - 0.04543639, - ] - ], - } - - atoms_pbc.calc = sevennet_0_cal - assert np.allclose(atoms_pbc.get_potential_energy(), atoms1_ref['energy']) - assert np.allclose( - atoms_pbc.get_potential_energy(force_consistent=True), atoms1_ref['energy'] - ) - assert np.allclose(atoms_pbc.get_forces(), atoms1_ref['force']) - assert np.allclose(atoms_pbc.get_stress(), atoms1_ref['stress']) - assert np.allclose(atoms_pbc.get_potential_energies(), atoms1_ref['energies']) - - -def test_sevennet_0_cal_mol(atoms_mol, sevennet_0_cal): - atoms2_ref = { - 'energy': -12.782808303833008, - 'energies': [-6.2493525, -3.141562, -3.3918958], - 'force': [ - [0.0, -1.3619621e01, 7.5937047e00], - [0.0, 9.3918495e00, -1.0172190e01], - [0.0, 4.2277718e00, 2.5784855e00], - ], - } - atoms_mol.calc = sevennet_0_cal - assert np.allclose(atoms_mol.get_potential_energy(), atoms2_ref['energy']) - assert np.allclose( - atoms_mol.get_potential_energy(force_consistent=True), atoms2_ref['energy'] - ) - assert np.allclose(atoms_mol.get_forces(), atoms2_ref['force']) - assert np.allclose(atoms_mol.get_potential_energies(), atoms2_ref['energies']) - - -def test_sevennet_0_cal_deployed_consistency(tmp_path, atoms_pbc): - fname = str(tmp_path / '7net_0.pt') - deploy(pretrained_name_to_path('7net-0_11July2024'), fname) - - calc_script = SevenNetCalculator(fname, file_type='torchscript') - calc_cp = SevenNetCalculator(pretrained_name_to_path('7net-0_11July2024')) - - atoms_pbc.calc = calc_cp - atoms_pbc.get_potential_energy() - res_cp = copy.copy(atoms_pbc.calc.results) - - atoms_pbc.calc = calc_script - atoms_pbc.get_potential_energy() - res_script = copy.copy(atoms_pbc.calc.results) - - for k in res_cp: - assert np.allclose(res_cp[k], res_script[k]) - - -def test_sevennet_0_cal_as_instance_consistency(atoms_pbc): - model, _ = model_from_checkpoint( - pretrained_name_to_path('7net-0_11July2024') - ) - - calc_cp = SevenNetCalculator(pretrained_name_to_path('7net-0_11July2024')) - calc_instance = SevenNetCalculator(model, file_type='model_instance') - - atoms_pbc.calc = calc_cp - atoms_pbc.get_potential_energy() - res_cp = copy.copy(atoms_pbc.calc.results) - - atoms_pbc.calc = calc_instance - atoms_pbc.get_potential_energy() - res_script = copy.copy(atoms_pbc.calc.results) - - for k in res_cp: - assert np.allclose(res_cp[k], res_script[k]) - - -@pytest.mark.skipif(not is_cue_available(), reason='cueq not available') -def test_sevennet_0_cal_cueq(atoms_pbc, sevennet_0_cueq_cal): - atoms1_ref = { - 'energy': -3.779199, - 'energies': [-1.8493923, -1.9298072], - 'force': [ - [12.666697, 0.04726403, 0.04775861], - [-12.666697, -0.04726403, -0.04775861], - ], - 'stress': [ - [ - -0.6439122, - -0.03643947, - -0.03643981, - 0.00599139, - 0.04544507, - 0.04543639, - ] - ], - } - - atoms_pbc.calc = sevennet_0_cueq_cal - - assert np.allclose(atoms_pbc.get_potential_energy(), atoms1_ref['energy']) - assert np.allclose( - atoms_pbc.get_potential_energy(force_consistent=True), atoms1_ref['energy'] - ) - assert np.allclose(atoms_pbc.get_forces(), atoms1_ref['force']) - assert np.allclose(atoms_pbc.get_stress(), atoms1_ref['stress']) - assert np.allclose(atoms_pbc.get_potential_energies(), atoms1_ref['energies']) - - -def test_d3_cal_pbc(atoms_pbc, d3_cal): - atoms1_ref = { - 'energy': -0.531393751583389, - 'force': [ - [-0.00570205, 0.00107457, 0.00107459], - [0.00570205, -0.00107457, -0.00107459], - ], - 'stress': [ - [ - 1.52403705e-02, - 1.50417333e-02, - 1.50417321e-02, - -3.22684163e-05, - -5.05532863e-05, - -5.05586994e-05, - ] - ], - } - - atoms_pbc.calc = d3_cal - - assert np.allclose(atoms_pbc.get_potential_energy(), atoms1_ref['energy']) - assert np.allclose( - atoms_pbc.get_potential_energy(force_consistent=True), atoms1_ref['energy'] - ) - assert np.allclose(atoms_pbc.get_forces(), atoms1_ref['force']) - assert np.allclose(atoms_pbc.get_stress(), atoms1_ref['stress']) - - -def test_d3_cal_mol(atoms_mol, d3_cal): - atoms2_ref = { - 'energy': -0.009889134535170716, - 'force': [ - [0.0, 2.04263840e-03, 1.27477674e-03], - [0.0, -9.90038901e-05, 1.18046682e-06], - [0.0, -1.94363451e-03, -1.27595721e-03], - ], - } - - atoms_mol.calc = d3_cal - - assert np.allclose(atoms_mol.get_potential_energy(), atoms2_ref['energy']) - assert np.allclose( - atoms_mol.get_potential_energy(force_consistent=True), atoms2_ref['energy'] - ) - assert np.allclose(atoms_mol.get_forces(), atoms2_ref['force']) diff --git a/mace-bench/3rdparty/SevenNet/tests/unit_tests/test_cli.py b/mace-bench/3rdparty/SevenNet/tests/unit_tests/test_cli.py deleted file mode 100644 index 0bdeeabf4757e7c2bcf5a09ca6183576f7138af9..0000000000000000000000000000000000000000 --- a/mace-bench/3rdparty/SevenNet/tests/unit_tests/test_cli.py +++ /dev/null @@ -1,233 +0,0 @@ -import csv -import os -import pathlib -from unittest import mock - -import ase.io -import numpy as np -import pytest -import yaml -from ase.build import bulk - -from sevenn.calculator import SevenNetCalculator -from sevenn.logger import Logger -from sevenn.main.sevenn import main as sevenn_main -from sevenn.main.sevenn_get_model import main as get_model_main -from sevenn.main.sevenn_graph_build import main as graph_build_main -from sevenn.main.sevenn_inference import main as inference_main -from sevenn.util import pretrained_name_to_path - -main = os.path.abspath(f'{os.path.dirname(__file__)}/../../sevenn/main/') -preset = os.path.abspath(f'{os.path.dirname(__file__)}/../../sevenn/presets/') -file_path = pathlib.Path(__file__).parent.resolve() - -data_root = (pathlib.Path(__file__).parent.parent / 'data').resolve() -hfo2_path = str(data_root / 'systems' / 'hfo2.extxyz') -hfo2_7net_0_inference_path = data_root / 'inferences' / 'snet0_on_hfo2' -cp_0_path = str(data_root / 'checkpoints' / 'cp_0.pth') - -Logger() # init - - -@pytest.fixture -def atoms_hfo(): - atoms1 = bulk('HfO', 'rocksalt', a=5.63) - atoms1.set_cell([[1.0, 2.815, 2.815], [2.815, 0.0, 2.815], [2.815, 2.815, 0.0]]) - atoms1.set_positions([[0.0, 0.0, 0.0], [2.815, 0.0, 0.0]]) - return atoms1 - - -@pytest.fixture(scope='module') -def sevennet_0_cal(): - return SevenNetCalculator('7net-0_11July2024') - - -def test_get_model_serial(tmp_path, capsys): - output_file = tmp_path / 'mypot.pt' - cp = pretrained_name_to_path('7net-0') - cli_args = ['-o', str(output_file), cp] - with mock.patch('sys.argv', [f'{main}/sevenn_get_model.py'] + cli_args): - get_model_main() - _ = capsys.readouterr() # not used - assert output_file.is_file(), '.pt file is not written' - - -def test_get_model_parallel(tmp_path, capsys): - output_dir = tmp_path / 'my_parallel' - cp = pretrained_name_to_path('7net-0') - expected_file_cnt = 5 # 5 interaction layers - cli_args = ['-o', str(output_dir), '-p', cp] - with mock.patch('sys.argv', [f'{main}/sevenn_get_model.py'] + cli_args): - # with pytest.raises(SystemExit): - get_model_main() - _ = capsys.readouterr() # not used - assert output_dir.is_dir(), 'parallel model directory not exist' - for i in range(expected_file_cnt): - assert (output_dir / f'deployed_parallel_{i}.pt').is_file() - - -@pytest.mark.parametrize('source', [(hfo2_path)]) -def test_graph_build(source, tmp_path): - output_dir = tmp_path / 'sevenn_data' - output_f = output_dir / 'my_graph.pt' - output_yml = output_dir / 'my_graph.yaml' - cli_args = ['-o', str(tmp_path), '-f', 'my_graph.pt', source, '4.0'] - with mock.patch('sys.argv', [f'{main}/sevenn_graph_build.py'] + cli_args): - graph_build_main() - - assert output_dir.is_dir() - assert output_f.is_file() - assert output_yml.is_file() - - -@pytest.mark.parametrize( - 'batch,device,save_graph', - [ - (1, 'cpu', False), - (2, 'cpu', False), - (1, 'cpu', True), - ], -) -def test_inference(batch, device, save_graph, tmp_path): - checkpoint = '7net-0' - target = hfo2_path - ref_path = hfo2_7net_0_inference_path - - output_dir = tmp_path / 'inference_results' - files = ['info.csv', 'per_graph.csv', 'per_atom.csv', 'errors.txt'] - cli_args = [ - '--output', - str(output_dir), - '--device', - device, - '--batch', - str(batch), - checkpoint, - target, - ] - if save_graph: - cli_args.append('--save_graph') - with mock.patch('sys.argv', [f'{main}/sevenn_inference.py'] + cli_args): - inference_main() - - assert output_dir.is_dir() - for f in files: - assert (output_dir / f).is_file() - with open(output_dir / 'errors.txt', 'r', encoding='utf-8') as f: - errors = [float(ll.split(':')[-1].strip()) for ll in f.readlines()] - with open(ref_path / 'errors.txt', 'r', encoding='utf-8') as f: - errors_ref = [float(ll.split(':')[-1].strip()) for ll in f.readlines()] - assert np.allclose(np.array(errors), np.array(errors_ref)) - - """ - # TODO: commented out as currently SevenNetGraphDataset can't do this - with open(output_dir / 'info.csv', 'r') as f: - reader = csv.DictReader(f) - for dct in reader: - assert dct['file'] == hfo2_path - assert reader.line_num == 3 - """ - - if save_graph: - assert (output_dir / 'sevenn_data').is_dir() - assert (output_dir / 'sevenn_data' / 'saved_graph.pt').is_file() - assert (output_dir / 'sevenn_data' / 'saved_graph.yaml').is_file() - - -def test_inference_unlabeled(atoms_hfo, tmp_path): - labeled = str(hfo2_path) - unlabeled = str(tmp_path / 'unlabeled.xyz') - ase.io.write(unlabeled, atoms_hfo) - - output_dir = tmp_path / 'inference_results' - cli_args = [ - '--output', - str(output_dir), - '--allow_unlabeled', - cp_0_path, - labeled, - unlabeled, - ] - with mock.patch('sys.argv', [f'{main}/sevenn_inference.py'] + cli_args): - inference_main() - - with open(output_dir / 'info.csv', 'r') as f: - reader = csv.DictReader(f) - for dct in reader: - assert dct['file'] in [labeled, unlabeled] - assert reader.line_num == 4 - - -def test_inference_labeled_w_kwargs(atoms_hfo, tmp_path): - atoms_hfo.info['my_energy'] = 1.0 - atoms_hfo.arrays['my_force'] = np.full((len(atoms_hfo), 3), 7.7) - # this should be considered as Voigt, xx, yy, zz, yz, zx, xy - atoms_hfo.info['my_stress'] = np.array([1, 2, 3, 4, 5, 6]) - - unlabeled = str(tmp_path / 'unlabeled.xyz') - ase.io.write(unlabeled, atoms_hfo) - - output_dir = tmp_path / 'inference_results' - cli_args = [ - '--output', - str(output_dir), - cp_0_path, - unlabeled, - '--kwargs', - 'energy_key=my_energy', - 'force_key=my_force', - 'stress_key=my_stress', - ] - with mock.patch('sys.argv', [f'{main}/sevenn_inference.py'] + cli_args): - inference_main() - - per_graph = None - with open(output_dir / 'per_graph.csv', 'r') as f: - reader = csv.DictReader(f) - for dct in reader: - per_graph = dct - assert reader.line_num == 2 - assert per_graph is not None - - stress_coeff = -1602.1766208 - assert np.allclose(float(per_graph['stress_yy']), 2 * stress_coeff) - assert np.allclose(float(per_graph['stress_yz']), 4 * stress_coeff) - assert np.allclose(float(per_graph['stress_zx']), 5 * stress_coeff) - assert np.allclose(float(per_graph['stress_xy']), 6 * stress_coeff) - - -@pytest.mark.parametrize( - 'preset_name,mode,data_path', - [ - ('fine_tune', 'train_v2', hfo2_path), - ('base', 'train_v2', hfo2_path), - ('sevennet-0', 'train_v1', hfo2_path), - ], -) -def test_sevenn_preset(preset_name, mode, data_path, tmp_path): - preset_path = os.path.join(preset, preset_name + '.yaml') - with open(preset_path, 'r') as f: - cfg = yaml.safe_load(f) - - cfg['train']['epoch'] = 1 - if mode == 'train_v2': - cfg['data']['load_trainset_path'] = data_path - cfg['data'].pop('load_testset_path', None) - elif mode == 'train_v1': - cfg['data']['load_dataset_path'] = data_path - else: - assert False - cfg['data']['load_validset_path'] = data_path - - input_yam = str(tmp_path / 'input.yaml') - with open(input_yam, 'w') as f: - yaml.dump(cfg, f) - - Logger().switch_file(str(tmp_path / 'log.sevenn')) - cli_args = ['train', '-w', str(tmp_path), '-m', mode, input_yam] - with mock.patch('sys.argv', [f'{main}/sevenn.py'] + cli_args): - sevenn_main() - - assert (tmp_path / 'lc.csv').is_file() or (tmp_path / 'log.csv').is_file() - assert (tmp_path / 'log.sevenn').is_file() - assert (tmp_path / 'checkpoint_best.pth').is_file() diff --git a/mace-bench/3rdparty/SevenNet/tests/unit_tests/test_cueq.py b/mace-bench/3rdparty/SevenNet/tests/unit_tests/test_cueq.py deleted file mode 100644 index 4f1d5bd041d2ba394f9664219821f3d6720ab35c..0000000000000000000000000000000000000000 --- a/mace-bench/3rdparty/SevenNet/tests/unit_tests/test_cueq.py +++ /dev/null @@ -1,282 +0,0 @@ -# TODO: add gradient test from total loss after double precision. -# so far, it is empirically checked by seeing learning curves -import copy - -import numpy as np -import pytest -import torch -from ase.build import bulk -from torch_geometric.loader.dataloader import Collater - -import sevenn -import sevenn.train.dataload as dl -from sevenn.atom_graph_data import AtomGraphData -from sevenn.calculator import SevenNetCalculator -from sevenn.model_build import build_E3_equivariant_model -from sevenn.nn.cue_helper import is_cue_available -from sevenn.nn.sequential import AtomGraphSequential -from sevenn.util import ( - chemical_species_preprocess, - model_from_checkpoint_with_backend, -) - -cutoff = 4.0 - -_atoms = bulk('NaCl', 'rocksalt', a=4.00) * (2, 2, 2) -_avg_num_neigh = 30.0 -_atoms.rattle() - -_graph = AtomGraphData.from_numpy_dict(dl.unlabeled_atoms_to_graph(_atoms, cutoff)) - - -def get_graphs(batched): - # batch size 2 - cloned = [_graph.clone().to('cuda'), _graph.clone().to('cuda')] - if not batched: - return cloned - else: - return Collater(cloned)(cloned) - - -def get_model_config(): - config = { - 'cutoff': cutoff, - 'channel': 32, - 'lmax': 2, - 'is_parity': True, - 'num_convolution_layer': 3, - 'self_connection_type': 'nequip', # not NequIp - 'interaction_type': 'nequip', - 'radial_basis': { - 'radial_basis_name': 'bessel', - }, - 'cutoff_function': {'cutoff_function_name': 'poly_cut'}, - 'weight_nn_hidden_neurons': [64, 64], - 'act_radial': 'silu', - 'act_scalar': {'e': 'silu', 'o': 'tanh'}, - 'act_gate': {'e': 'silu', 'o': 'tanh'}, - 'conv_denominator': _avg_num_neigh, - 'train_denominator': False, - 'shift': -10.0, - 'scale': 10.0, - 'train_shift_scale': False, - 'irreps_manual': False, - 'lmax_edge': -1, - 'lmax_node': -1, - 'readout_as_fcn': False, - 'use_bias_in_linear': False, - '_normalize_sph': True, - } - chems = set() - chems.update(_atoms.get_chemical_symbols()) - config.update(**chemical_species_preprocess(list(chems))) - return config - - -def get_model(config_overwrite=None, use_cueq=False, cueq_config=None): - cf = get_model_config() - if config_overwrite is not None: - cf.update(config_overwrite) - - cueq_config = cueq_config or {'cuequivariance_config': {'use': use_cueq}} - cf.update(cueq_config) - - model = build_E3_equivariant_model(cf, parallel=False) - assert isinstance(model, AtomGraphSequential) - model.to('cuda') - return model - - -@pytest.mark.skipif( - not is_cue_available() or not torch.cuda.is_available(), - reason='cueq or gpu is not available', -) -@pytest.mark.parametrize( - 'cf', - [ - ({}), - ({'self_connection_type': 'linear'}), - ({'is_parity': False}), - ({'channel': 8}), - ({'lmax': 3}), - ({'num_interaction_layer': 2}), - ({'num_interaction_layer': 4}), - ], -) -def test_model_output(cf): - torch.manual_seed(777) - model_e3nn = get_model(cf) - torch.manual_seed(777) - model_cueq = get_model(cf, use_cueq=True) - - model_e3nn.set_is_batch_data(True) - model_cueq.set_is_batch_data(True) - - e3nn_out = model_e3nn._preprocess(get_graphs(batched=True)) - cueq_out = model_cueq._preprocess(get_graphs(batched=True)) - - for k, e3nn_f in model_e3nn._modules.items(): - cueq_f = model_cueq._modules[k] - e3nn_out = e3nn_f(e3nn_out) # type: ignore - cueq_out = cueq_f(cueq_out) # type: ignore - assert torch.allclose(e3nn_out.x, cueq_out.x, atol=1e-6), ( - f'{k} \n\n {e3nn_f} \n\n {cueq_f}' - ) - - assert torch.allclose( - e3nn_out.inferred_total_energy, cueq_out.inferred_total_energy - ) - assert torch.allclose(e3nn_out.atomic_energy, cueq_out.atomic_energy) - assert torch.allclose( - e3nn_out.inferred_force, cueq_out.inferred_force, atol=1e-5 - ) - assert torch.allclose( - e3nn_out.inferred_stress, cueq_out.inferred_stress, atol=1e-5 - ) - - -@pytest.mark.filterwarnings('ignore:.*is not found from.*') -@pytest.mark.skipif( - not is_cue_available() or not torch.cuda.is_available(), - reason='cueq or gpu is not available', -) -@pytest.mark.parametrize( - 'start_from_cueq', - [ - (True), - (False), - ], -) -def test_checkpoint_convert(tmp_path, start_from_cueq): - torch.manual_seed(123) - model_from = get_model(use_cueq=start_from_cueq) - - cfg = get_model_config() - cfg.update( - { - 'cuequivariance_config': {'use': start_from_cueq}, - 'version': sevenn.__version__, - } - ) - torch.save( - {'model_state_dict': model_from.state_dict(), 'config': cfg}, - tmp_path / 'cp_from.pth', - ) - - backend = 'e3nn' if start_from_cueq else 'cueq' - model_to, _ = model_from_checkpoint_with_backend( - str(tmp_path / 'cp_from.pth'), backend - ) - model_to.to('cuda') - - model_from.set_is_batch_data(True) - model_to.set_is_batch_data(True) - - from_out = model_from(get_graphs(batched=True)) - to_out = model_to(get_graphs(batched=True)) - - assert torch.allclose( - from_out.inferred_total_energy, to_out.inferred_total_energy - ) - assert torch.allclose(from_out.atomic_energy, to_out.atomic_energy) - assert torch.allclose(from_out.inferred_force, to_out.inferred_force, atol=1e-5) - assert torch.allclose( - from_out.inferred_stress, to_out.inferred_stress, atol=1e-5 - ) - - -@pytest.mark.filterwarnings('ignore:.*is not found from.*') -@pytest.mark.skipif( - not is_cue_available() or not torch.cuda.is_available(), - reason='cueq or gpu is not available', -) -@pytest.mark.parametrize( - 'start_from_cueq', - [ - (True), - (False), - ], -) -def test_checkpoint_convert_no_batch(tmp_path, start_from_cueq): - torch.manual_seed(123) - model_from = get_model(use_cueq=start_from_cueq) - - cfg = get_model_config() - cfg.update( - { - 'cuequivariance_config': {'use': start_from_cueq}, - 'version': sevenn.__version__, - } - ) - torch.save( - {'model_state_dict': model_from.state_dict(), 'config': cfg}, - tmp_path / 'cp_from.pth', - ) - - backend = 'e3nn' if start_from_cueq else 'cueq' - model_to, _ = model_from_checkpoint_with_backend( - str(tmp_path / 'cp_from.pth'), backend - ) - model_to.to('cuda') - - model_from.set_is_batch_data(False) - model_to.set_is_batch_data(False) - - from_out = model_from(get_graphs(batched=False)[0]) - to_out = model_to(get_graphs(batched=False)[0]) - - assert torch.allclose( - from_out.inferred_total_energy, to_out.inferred_total_energy - ) - assert torch.allclose(from_out.atomic_energy, to_out.atomic_energy) - assert torch.allclose(from_out.inferred_force, to_out.inferred_force, atol=1e-5) - assert torch.allclose( - from_out.inferred_stress, to_out.inferred_stress, atol=1e-5 - ) - - -def assert_atoms(atoms1, atoms2, rtol=1e-5, atol=1e-6): - def acl(a, b, rtol=rtol, atol=atol): - return np.allclose(a, b, rtol=rtol, atol=atol) - - assert len(atoms1) == len(atoms2) - assert acl(atoms1.get_cell(), atoms2.get_cell()) - assert acl(atoms1.get_potential_energy(), atoms2.get_potential_energy()) - assert acl(atoms1.get_forces(), atoms2.get_forces(), rtol * 10, atol * 10) - assert acl( - atoms1.get_stress(voigt=False), - atoms2.get_stress(voigt=False), - rtol * 10, - atol * 10, - ) - # assert acl(atoms1.get_potential_energies(), atoms2.get_potential_energies()) - - -@pytest.mark.filterwarnings('ignore:.*is not found from.*') -@pytest.mark.skipif( - not is_cue_available() or not torch.cuda.is_available(), - reason='cueq or gpu is not available', -) -def test_calculator(tmp_path): - cueq = True - model = get_model(use_cueq=cueq) - ref_calc = SevenNetCalculator(model, file_type='model_instance') - atoms = copy.deepcopy(_atoms) - atoms.calc = ref_calc - - cfg = get_model_config() - cfg.update( - {'cuequivariance_config': {'use': cueq}, 'version': sevenn.__version__} - ) - - cp_path = str(tmp_path / 'cp.pth') - torch.save( - {'model_state_dict': model.state_dict(), 'config': cfg}, - cp_path, - ) - - calc2 = SevenNetCalculator(cp_path, enable_cueq=False) - atoms2 = copy.deepcopy(_atoms) - atoms2.calc = calc2 - - assert_atoms(atoms, atoms2) diff --git a/mace-bench/3rdparty/SevenNet/tests/unit_tests/test_data.py b/mace-bench/3rdparty/SevenNet/tests/unit_tests/test_data.py deleted file mode 100644 index fda1effd491232a7b95c94b5c0bb2987f46f819c..0000000000000000000000000000000000000000 --- a/mace-bench/3rdparty/SevenNet/tests/unit_tests/test_data.py +++ /dev/null @@ -1,521 +0,0 @@ -import logging -import os -import os.path as osp -import uuid -from collections import Counter -from copy import deepcopy -from typing import Literal - -import ase.calculators.singlepoint as singlepoint -import ase.io -import numpy as np -import pytest -import torch -from ase import Atoms -from ase.build import bulk, molecule -from torch_geometric.loader import DataLoader - -import sevenn._keys as KEY -import sevenn.train.dataload as dl -import sevenn.train.graph_dataset as ds -import sevenn.train.modal_dataset as modal_dataset -from sevenn._const import NUM_UNIV_ELEMENT -from sevenn.atom_graph_data import AtomGraphData -from sevenn.util import model_from_checkpoint, pretrained_name_to_path - -cutoff = 4.0 -lattice_constant = 3.35 - -_samples = { - 'bulk': bulk('NaCl', 'rocksalt', a=5.63), - 'mol': molecule('H2O'), - 'isolated': molecule('H'), - 'small_bulk': Atoms( - symbols='Cu', - positions=[ - (0, 0, 0), # Atom at the corner of the cube - ], - cell=[ - [lattice_constant, 0, 0], - [0, lattice_constant, 0], - [0, 0, lattice_constant], - ], - pbc=True, # Periodic boundary conditions - ), -} - - -_nedges_c4 = {'bulk': 36, 'mol': 6, 'isolated': 0, 'small_bulk': 18} - - -def get_atoms( - atoms_type: Literal['bulk', 'mol', 'isolated', 'small_bulk'], - init_y_as: Literal['calc', 'info', 'none'], -): - """ - Return atoms w, w/o reference values with its - # of edges for 4.0 cutoff length - """ - assert atoms_type in _samples - atoms = deepcopy(_samples[atoms_type]) - natoms = len(atoms) - if init_y_as == 'calc': - results = { - 'energy': np.random.rand(1), - 'forces': np.random.rand(natoms, 3), - 'stress': np.random.rand(6), - } - if not atoms.pbc.all(): - del results['stress'] - calc = singlepoint.SinglePointCalculator(atoms, **results) - atoms = calc.get_atoms() - elif init_y_as == 'info': - atoms.info['y_energy'] = np.random.rand(1) - atoms.arrays['y_force'] = np.random.rand(natoms, 3) - atoms.info['y_stress'] = np.random.rand(6) - if not atoms.pbc.all(): - del atoms.info['y_stress'] - return atoms, _nedges_c4[atoms_type] - - -@pytest.mark.parametrize('init_y_as', ['calc', 'info']) -@pytest.mark.parametrize('atoms_type', ['bulk', 'mol', 'isolated']) -def test_atoms_to_graph(atoms_type, init_y_as): - atoms, nedges = get_atoms(atoms_type, init_y_as) - is_stress = atoms.pbc.all() - y_from_calc = init_y_as == 'calc' - - graph = dl.atoms_to_graph(atoms, cutoff=cutoff, y_from_calc=y_from_calc) - - essential = { - 'atomic_numbers': ((len(atoms),), int), - 'pos': ((len(atoms), 3), float), - 'edge_index': ((2, nedges), int), - 'edge_vec': ((nedges, 3), float), - 'total_energy': ((), float), - 'force_of_atoms': ((len(atoms), 3), float), - 'cell_volume': ((), float), - 'num_atoms': ((), int), - 'per_atom_energy': ((), float), - 'stress': ((1, 6), float), - } - - for k, (shape, dtype) in essential.items(): - assert k in graph, f'{k} missing in graph' - assert isinstance( - graph[k], np.ndarray - ), f'{k}: {type(graph[k])} is not np.ndarray' - assert graph[k].shape == shape, f'{k} shape {graph[k].shape} != {shape}' - if not is_stress and k == 'stress': - assert np.isnan(graph[k]).all() - else: - assert graph[k].dtype == dtype, f'{k} dtype {graph[k].dtype} != {dtype}' - - assert graph['per_atom_energy'] == (graph['total_energy'] / len(atoms)) - assert graph['num_atoms'] == len(atoms) - if not is_stress: - assert graph['cell_volume'] == np.finfo(float).eps - - -@pytest.mark.parametrize('atoms_type', ['bulk', 'mol', 'isolated']) -def test_unlabeled_atoms_to_graph(atoms_type): - atoms, nedges = get_atoms(atoms_type, 'none') - - graph = dl.unlabeled_atoms_to_graph(atoms, cutoff=cutoff) - - essential = { - 'atomic_numbers': ((len(atoms),), int), - 'pos': ((len(atoms), 3), float), - 'edge_index': ((2, nedges), int), - 'edge_vec': ((nedges, 3), float), - 'cell_volume': ((), float), - 'num_atoms': ((), int), - } - - for k, (shape, dtype) in essential.items(): - assert k in graph, f'{k} missing in graph' - assert isinstance( - graph[k], np.ndarray - ), f'{k}: {type(graph[k])} is not np.ndarray' - assert graph[k].dtype == dtype, f'{k} dtype {graph[k].dtype} != {dtype}' - assert graph[k].shape == shape, f'{k} shape {graph[k].shape} != {shape}' - - assert graph['num_atoms'] == len(atoms) - if not atoms.pbc.all(): - assert graph['cell_volume'] == np.finfo(float).eps - - -@pytest.mark.parametrize('init_y_as', ['calc', 'info']) -@pytest.mark.parametrize('atoms_type', ['bulk', 'mol', 'isolated']) -def test_atom_graph_data(atoms_type, init_y_as): - atoms, nedges = get_atoms(atoms_type, init_y_as) - y_from_calc = init_y_as == 'calc' - is_stress = atoms.pbc.all() - np_graph = dl.atoms_to_graph(atoms, cutoff=cutoff, y_from_calc=y_from_calc) - graph = AtomGraphData.from_numpy_dict(np_graph) - - essential = { - 'atomic_numbers': ((len(atoms),), int), - 'edge_index': ((2, nedges), int), - 'edge_vec': ((nedges, 3), float), - } - auxilaray = { - 'x': ((len(atoms),), int), - 'pos': ((len(atoms), 3), float), - 'num_atoms': ((), int), - 'cell_volume': ((), float), - 'total_energy': ((), float), - 'per_atom_energy': ((), float), - 'force_of_atoms': ((len(atoms), 3), float), - 'stress': ((1, 6), float), - } - - for k, (shape, dtype) in essential.items(): - assert k in graph, f'{k} missing in graph' - assert isinstance( - graph[k], torch.Tensor - ), f'{k}: {type(graph[k])} is not an tensor' - assert graph[k].is_floating_point() == (dtype is float) - assert graph[k].shape == shape, f'{k} shape {graph[k].shape} != {shape}' - - for k, (shape, dtype) in auxilaray.items(): - if k not in graph: - continue - assert isinstance( - graph[k], torch.Tensor - ), f'{k}: {type(graph[k])} is not an tensor' - assert graph[k].shape == shape, f'{k} shape {graph[k].shape} != {shape}' - if not is_stress and k == 'stress': - assert torch.isnan(graph[k]).all() - else: - assert graph[k].is_floating_point() == (dtype is float) - - -def test_graph_build(): - """ - Compare parallel implementation, should preserve order - """ - atoms_list = [ - get_atoms(t, 'calc')[0] # type: ignore - for t in list(_samples.keys()) - ] - one_core = dl.graph_build(atoms_list, cutoff, num_cores=1, y_from_calc=True) - two_core = dl.graph_build(atoms_list, cutoff, num_cores=2, y_from_calc=True) - - assert len(one_core) == len(two_core) - for g1, g2 in zip(one_core, two_core): - assert set(g1.keys()) == set(g2.keys()) - for k in g1.keys(): - if not isinstance(g1[k], torch.Tensor): - continue - if k == 'stress': # TODO: robust way to test it - assert torch.allclose(g1[k], g2[k]) or ( - torch.isnan(g1[k]).all() == torch.isnan(g2[k]).all() - ) - else: - assert torch.allclose(g1[k], g2[k]) - - -@pytest.fixture(scope='module') -def graph_dataset_tuple(): - tmpdir = os.getenv('TMPDIR', '/tmp') - randstr = uuid.uuid4().hex - assert os.access(tmpdir, os.W_OK), f'{tmpdir} is not writable' - - root = tmpdir - files = f'{root}/{randstr}.extxyz' - atoms_list = [ - get_atoms(atype, 'calc')[0] # type: ignore - for atype in ['bulk', 'mol', 'isolated'] - ] - ase.io.write(files, atoms_list, 'extxyz') - - dataset = ds.SevenNetGraphDataset( - cutoff=cutoff, - root=root, - files=files, - processed_name=f'{randstr}.pt', - ) - assert os.path.isfile(f'{root}/sevenn_data/{randstr}.pt'), 'dataset not written' - return dataset, atoms_list - - -def test_sevenn_graph_dataset_properties(graph_dataset_tuple): - dataset, atoms_list = graph_dataset_tuple - - species = set() - natoms = Counter() - elist = [] - e_per_list = [] - flist = [] - slist = [] - for at in atoms_list: - chems = at.get_chemical_symbols() - species.update(chems) - natoms.update(chems) - elist.append(at.get_potential_energy()) - e_per_list.append(at.get_potential_energy() / len(at)) - flist.extend(at.get_forces()) - try: - slist.append(at.get_stress()) - except NotImplementedError: - slist.append(np.full(6, np.nan)) - - elist = np.array(elist) - e_per_list = np.array(e_per_list) - flist = np.array(flist) - slist = np.array(slist) - - natoms['total'] = sum([cnt for cnt in list(natoms.values())]) - - assert set(dataset.species) == species - assert dataset.natoms == natoms - assert np.allclose(dataset.per_atom_energy_mean, e_per_list.mean()) - assert np.allclose(dataset.force_rms, np.sqrt((flist**2).mean())) - - -def test_sevenn_graph_dataset_elemwise_energies(graph_dataset_tuple): - logger = logging.getLogger(__name__) - - dataset, atoms_list = graph_dataset_tuple - - ref_e = dataset.elemwise_reference_energies - assert len(ref_e) == NUM_UNIV_ELEMENT - z_set = set() - for atoms in atoms_list: - inferred_e = 0 - atomic_numbers = atoms.get_atomic_numbers() - z_set.update(atomic_numbers) - for z in atomic_numbers: - inferred_e += ref_e[z] - # it never be same, but should be similar - logger.info('elemwise energy should be similar:') - logger.info(f'{inferred_e:4f} {atoms.get_potential_energy()[0]:4f}') - - for z in range(NUM_UNIV_ELEMENT): - if z not in z_set: - assert ref_e[z] == 0 - - -def test_sevenn_graph_dataset_statistics(graph_dataset_tuple): - dataset, atoms_list = graph_dataset_tuple - - elist = [] - e_per_list = [] - flist = [] - slist = [] - for at in atoms_list: - elist.append(at.get_potential_energy()) - e_per_list.append(at.get_potential_energy() / len(at)) - flist.extend(at.get_forces()) - try: - slist.append(at.get_stress()) - except NotImplementedError: - slist.append(np.full(6, np.nan)) - - dct = { - 'total_energy': np.array(elist), - 'per_atom_energy': np.array(e_per_list), - 'force_of_atoms': np.array(flist).flatten(), - # 'stress': np.array(slist), # TODO: it may have nan - } - - for key in dct: - assert np.allclose(dataset.statistics[key]['mean'], dct[key].mean()), key - assert np.allclose(dataset.statistics[key]['std'], dct[key].std(ddof=0)), key - assert np.allclose( - dataset.statistics[key]['median'], np.median(dct[key]) - ), key - assert np.allclose(dataset.statistics[key]['max'], dct[key].max()), key - assert np.allclose(dataset.statistics[key]['min'], dct[key].min()), key - - -def test_sevenn_mm_dataset_statistics(tmp_path): - - files = osp.join(tmp_path, 'gd_one.extxyz') - atoms_list1 = [ - get_atoms(atype, 'calc')[0] # type: ignore - for atype in ['bulk', 'bulk', 'bulk', 'bulk'] - ] - ase.io.write(files, atoms_list1, 'extxyz') - - gd1 = ds.SevenNetGraphDataset( - cutoff=cutoff, - root=tmp_path, - files=files, - processed_name='gd_one.pt', - ) - - files = osp.join(tmp_path, 'gd_two.extxyz') - atoms_list2 = [ - get_atoms(atype, 'calc')[0] # type: ignore - for atype in ['mol', 'mol', 'bulk'] - ] - ase.io.write(files, atoms_list2, 'extxyz') - - gd2 = ds.SevenNetGraphDataset( - cutoff=cutoff, - root=tmp_path, - files=files, - processed_name='gd_two.pt', - ) - - ref = ds.SevenNetGraphDataset( - cutoff=cutoff, - root=tmp_path, - files=[gd1.processed_paths[0], gd2.processed_paths[0]], - processed_name='combined.pt', - ) - - mm = modal_dataset.SevenNetMultiModalDataset( - {'modal1': gd1, 'modal2': gd2} - ) - - assert np.allclose(ref.per_atom_energy_mean, mm.per_atom_energy_mean['total']) - assert np.allclose(ref.avg_num_neigh, mm.avg_num_neigh['total']) - assert np.allclose(ref.force_rms, mm.force_rms['total']) - assert set(ref.species) == set(mm.species['total']) - - -@pytest.mark.parametrize( - 'a_types,init_ys', [(['bulk', 'mol', 'isolated'], ['calc', 'calc', 'calc'])] -) -def test_7net_graph_dataset_batch_shape(a_types, init_ys, tmp_path): - assert len(a_types) == len(init_ys) - n_graph = len(a_types) - atoms_list = [] - tot_edges = 0 - tot_atoms = 0 - for a_type, init_y in zip(a_types, init_ys): - atoms, n_edge = get_atoms(a_type, init_y) - tot_edges += n_edge - tot_atoms += len(atoms) - atoms_list.append(atoms) - ase.io.write(tmp_path / 'tmp', atoms_list, format='extxyz') - dataset = ds.SevenNetGraphDataset(cutoff, tmp_path, str(tmp_path / 'tmp')) - loader = DataLoader(dataset, batch_size=n_graph) - graph = next(iter(loader)) - - essential = { - 'x': ((tot_atoms,), int), - 'atomic_numbers': ((tot_atoms,), int), - 'pos': ((tot_atoms, 3), float), - 'edge_index': ((2, tot_edges), int), - 'edge_vec': ((tot_edges, 3), float), - 'total_energy': ((n_graph,), float), - 'force_of_atoms': ((tot_atoms, 3), float), - 'cell_volume': ((n_graph,), float), - 'num_atoms': ((n_graph,), int), - 'per_atom_energy': ((n_graph,), float), - 'stress': ((n_graph, 6), float), - 'batch': ((tot_atoms,), int), # from PyG - } - - for k, (shape, dtype) in essential.items(): - assert k in graph, f'{k} missing in graph' - assert isinstance( - graph[k], torch.Tensor - ), f'{k}: {type(graph[k])} is not an tensor' - assert graph[k].is_floating_point() == (dtype is float) - assert graph[k].shape == shape, f'{k} shape {graph[k].shape} != {shape}' - - -@pytest.mark.parametrize('atoms_type', ['bulk', 'mol', 'isolated', 'small_bulk']) -def test_graph_build_ase_and_matscipy(atoms_type): - atoms, _ = get_atoms(atoms_type, 'calc') - atoms.rattle() - pos = atoms.get_positions() - cell = np.array(atoms.get_cell()) - pbc = atoms.get_pbc() - - # graph build check - # ase graph build - edge_src_ase, edge_dst_ase, edge_vec_ase, shifts_ase = dl._graph_build_ase( - cutoff, pbc, cell, pos - ) - # matscipy graph build - edge_src_matsci, edge_dst_matsci, edge_vec_matsci, shifts_matsci = ( - dl._graph_build_matscipy(cutoff, pbc, cell, pos) - ) - - # sort the graph - sorted_indices_ase = np.lexsort( - (edge_vec_ase[:, 2], edge_vec_ase[:, 1], edge_vec_ase[:, 0]) - ) - sorted_indices_matsci = np.lexsort( - (edge_vec_matsci[:, 2], edge_vec_matsci[:, 1], edge_vec_matsci[:, 0]) - ) - sorted_vec_ase = edge_vec_ase[sorted_indices_ase] - sorted_vec_matsci = edge_vec_matsci[sorted_indices_matsci] - sorted_src_ase = edge_src_ase[sorted_indices_ase] - sorted_dst_ase = edge_dst_ase[sorted_indices_ase] - sorted_src_matsci = edge_src_matsci[sorted_indices_matsci] - sorted_dst_matsci = edge_dst_matsci[sorted_indices_matsci] - sorted_shift_ase = shifts_ase[sorted_indices_ase] - sorted_shift_matsci = shifts_matsci[sorted_indices_matsci] - - # compare the result - assert np.allclose(sorted_vec_ase, sorted_vec_matsci) - assert np.array_equal(sorted_src_ase, sorted_src_matsci) - assert np.array_equal(sorted_dst_ase, sorted_dst_matsci) - assert np.array_equal(sorted_shift_ase, sorted_shift_matsci) - - # energy test - model, _ = model_from_checkpoint(pretrained_name_to_path('7net-0_11July2024')) - model.eval() - model.set_is_batch_data(False) - - # for ase energy - edge_idx_ase = np.array([edge_src_ase, edge_dst_ase]) - atomic_numbers = atoms.get_atomic_numbers() - cell = np.array(cell) - vol = dl._correct_scalar(atoms.cell.volume) - if vol == 0: - vol = np.array(np.finfo(float).eps) - - data_ase = { - KEY.NODE_FEATURE: atomic_numbers, - KEY.ATOMIC_NUMBERS: atomic_numbers, - KEY.POS: pos, - KEY.EDGE_IDX: edge_idx_ase, - KEY.EDGE_VEC: edge_vec_ase, - KEY.CELL: cell, - KEY.CELL_SHIFT: shifts_ase, - KEY.CELL_VOLUME: vol, - KEY.NUM_ATOMS: dl._correct_scalar(len(atomic_numbers)), - } - data_ase[KEY.INFO] = {} - atom_graph_data_ase = AtomGraphData.from_numpy_dict(data_ase) - output_ase = model(atom_graph_data_ase) - ase_pred_energy = output_ase[KEY.PRED_TOTAL_ENERGY] - ase_pred_force = output_ase[KEY.PRED_FORCE] - ase_pred_stress = output_ase[KEY.PRED_STRESS] - - # for matsci energy - edge_idx_matsci = np.array([edge_src_matsci, edge_dst_matsci]) - atomic_numbers = atoms.get_atomic_numbers() - cell = np.array(cell) - vol = dl._correct_scalar(atoms.cell.volume) - if vol == 0: - vol = np.array(np.finfo(float).eps) - - data_matsci = { - KEY.NODE_FEATURE: atomic_numbers, - KEY.ATOMIC_NUMBERS: atomic_numbers, - KEY.POS: pos, - KEY.EDGE_IDX: edge_idx_matsci, - KEY.EDGE_VEC: edge_vec_matsci, - KEY.CELL: cell, - KEY.CELL_SHIFT: shifts_matsci, - KEY.CELL_VOLUME: vol, - KEY.NUM_ATOMS: dl._correct_scalar(len(atomic_numbers)), - } - data_matsci[KEY.INFO] = {} - atom_graph_data_matsci = AtomGraphData.from_numpy_dict(data_matsci) - output_matsci = model(atom_graph_data_matsci) - matsci_pred_energy = output_matsci[KEY.PRED_TOTAL_ENERGY] - matsci_pred_force = output_matsci[KEY.PRED_FORCE] - matsci_pred_stress = output_matsci[KEY.PRED_STRESS] - assert torch.equal(ase_pred_energy, matsci_pred_energy) - assert torch.allclose(ase_pred_force, matsci_pred_force, atol=1e-06) - assert torch.allclose(ase_pred_stress, matsci_pred_stress) diff --git a/mace-bench/3rdparty/SevenNet/tests/unit_tests/test_errors.py b/mace-bench/3rdparty/SevenNet/tests/unit_tests/test_errors.py deleted file mode 100644 index 36024a845358625ade699db0041723fadf41c356..0000000000000000000000000000000000000000 --- a/mace-bench/3rdparty/SevenNet/tests/unit_tests/test_errors.py +++ /dev/null @@ -1,285 +0,0 @@ -# test_errors: error recorder.py, loss.py -from copy import deepcopy - -import numpy as np -import pytest -import torch -import torch.nn -from torch import tensor - -import sevenn.error_recorder as erc -import sevenn.train.loss as loss -from sevenn.atom_graph_data import AtomGraphData -from sevenn.train.optim import loss_dict - -_default_config = { - 'loss': 'mse', - 'loss_param': {}, - 'error_record': [ - ('Energy', 'RMSE'), - ('Force', 'RMSE'), - ('Stress', 'RMSE'), - ('Energy', 'MAE'), - ('Force', 'MAE'), - ('Stress', 'MAE'), - ('TotalLoss', 'None'), - ], - 'is_train_stress': True, - 'force_loss_weight': 1.0, - 'stress_loss_weight': 0.001, -} - -_erc_test_params = [ - ('TotalEnergy', 4, 3), - ('Energy', 4, 3), - ('Force', 4, 3), - ('Stress', 4, 3), - ('Stress_GPa', 4, 3), - ('Energy', 4, 1), - ('Energy', 1, 1), - ('Force', 1, 3), - ('Stress', 1, 3), -] - - -def acl(a, b): - return torch.allclose(a, b, atol=1e-6) - - -def config(**overwrite): # to make it read-only - cf = deepcopy(_default_config) - for k, v in overwrite.items(): - cf[k] = v - return cf - - -def test_per_atom_energy_loss(): - loss_f = loss.PerAtomEnergyLoss(criterion=torch.nn.MSELoss()) - ref = torch.rand(2) - pred = torch.rand(2) - natoms = torch.randint(1, 10, (2,)) - tmp = AtomGraphData( - total_energy=ref, - inferred_total_energy=pred, - num_atoms=natoms, - ).to_dict() - ret = loss_f.get_loss(tmp) - assert loss_f.criterion is not None - assert torch.allclose(loss_f.criterion((ref / natoms), (pred / natoms)), ret) - - -def test_force_loss(): - loss_f = loss.ForceLoss(criterion=torch.nn.MSELoss()) - ref = torch.rand((4, 3)) - pred = torch.rand((4, 3)) - batch = tensor([0, 0, 0, 1]) - tmp = AtomGraphData( - force_of_atoms=ref, - inferred_force=pred, - batch=batch, - ).to_dict() - ret = loss_f.get_loss(tmp) - assert loss_f.criterion is not None - assert torch.allclose(loss_f.criterion(ref.reshape(-1), pred.reshape(-1)), ret) - - -def test_stress_loss(): - loss_f = loss.StressLoss(criterion=torch.nn.MSELoss()) - ref = torch.rand((2, 6)) - pred = torch.rand((2, 6)) - tmp = AtomGraphData( - stress=ref, - inferred_stress=pred, - ).to_dict() - ret = loss_f.get_loss(tmp) - KB = 1602.1766208 - assert loss_f.criterion is not None - assert torch.allclose( - loss_f.criterion(ref.reshape(-1) * KB, pred.reshape(-1) * KB), ret - ) - - -@pytest.mark.parametrize('conf', [config(), config(is_train_stress=False)]) -def test_loss_from_config(conf): - loss_functions = loss.get_loss_functions_from_config(conf) - - if conf['is_train_stress']: - assert len(loss_functions) == 3 - else: - assert len(loss_functions) == 2 - - for loss_def, w in loss_functions: - assert isinstance(loss_def, loss.LossDefinition) - if isinstance(loss_def, loss.PerAtomEnergyLoss): - assert w == 1.0 - elif isinstance(loss_def, loss.ForceLoss): - assert w == conf['force_loss_weight'] - elif isinstance(loss_def, loss.StressLoss): - assert w == conf['stress_loss_weight'] - else: - raise ValueError(f'Unexpected loss function: {loss_def}') - - -@pytest.mark.parametrize('err_type,ndata,natoms', _erc_test_params) -def test_rms_error(err_type, ndata, natoms): - err_dct = erc.get_err_type(err_type) - err = erc.RMSError(**err_dct) - ref = torch.rand((ndata, err.vdim)).squeeze(1) - pred = torch.rand((ndata, err.vdim)).squeeze(1) - natoms = torch.tensor([natoms] * ndata) - _data = { - err_dct['ref_key']: ref, - err_dct['pred_key']: pred, - 'num_atoms': natoms, - } - - tmp = AtomGraphData(**_data) - err.update(tmp) - - _ref = ref * err.coeff - _pred = pred * err.coeff - if 'per_atom' in err_dct and err_dct['per_atom']: - # natoms = natoms.unsqueeze(-1) - _ref = _ref / natoms - _pred = _pred / natoms - val = torch.sqrt(((_ref - _pred) ** 2).sum() / ndata) # not ndata*natoms - assert np.allclose(err.get(), val.item()) - err.update(tmp) - assert np.allclose(err.get(), val.item()) - - -@pytest.mark.parametrize('err_type,ndata,natoms', _erc_test_params) -def test_mae_error(err_type, ndata, natoms): - err_dct = erc.get_err_type(err_type) - vdim = err_dct['vdim'] - err = erc.MAError(**err_dct) - ref = torch.rand((ndata, vdim)).squeeze(1) - pred = torch.rand((ndata, vdim)).squeeze(1) - natoms = torch.tensor([natoms] * ndata) - _data = { - err_dct['ref_key']: ref, - err_dct['pred_key']: pred, - 'num_atoms': natoms, - } - - tmp = AtomGraphData(**_data) - err.update(tmp) - - _ref = ref * err.coeff - _pred = pred * err.coeff - if 'per_atom' in err_dct and err_dct['per_atom']: - _ref /= natoms - _pred /= natoms - - val = abs(_ref - _pred).sum() / (ndata * vdim) - assert np.allclose(err.get(), val.item()) - err.update(tmp) - assert np.allclose(err.get(), val.item()) - - -# TODO: test_component_rms_error - - -@pytest.mark.parametrize('err_type,ndata,natoms', _erc_test_params) -def test_custom_error(err_type, ndata, natoms): - def func(a, b): - return a * b - - err_dct = erc.get_err_type(err_type) - vdim = err_dct['vdim'] - err = erc.CustomError(func, **err_dct) - ref = torch.rand((ndata, vdim)).squeeze(1) - pred = torch.rand((ndata, vdim)).squeeze(1) - natoms = torch.tensor([natoms] * ndata) - _data = { - err_dct['ref_key']: ref, - err_dct['pred_key']: pred, - 'num_atoms': natoms, - } - - _ref = ref * err.coeff - _pred = pred * err.coeff - if 'per_atom' in err_dct and err_dct['per_atom']: - _ref /= natoms - _pred /= natoms - - tmp = AtomGraphData(**_data) - err.update(tmp) - val = func(_ref, _pred).mean() - assert np.allclose(err.get(), val.item()) - err.update(tmp) - assert np.allclose(err.get(), val.item()) - - -@pytest.mark.parametrize('conf', [config(), config(is_train_stress=False)]) -def test_total_loss_metric_from_config(conf): - def func(a, b): - return a * b - - err = erc.ErrorRecorder.init_total_loss_metric(conf, func) - ndata = 3 - natoms = 4 - - e1, e2 = torch.rand(ndata), torch.rand(ndata) - f1, f2 = torch.rand(ndata * natoms, 3), torch.rand(ndata * natoms, 3) - s1, s2 = torch.rand((ndata, 6)), torch.rand((ndata, 6)) - _data = { - 'total_energy': e1, - 'inferred_total_energy': e2, - 'force_of_atoms': f1, - 'inferred_force': f2, - 'stress': s1, - 'inferred_stress': s2, - 'num_atoms': torch.tensor([natoms] * ndata), - } - - tmp = AtomGraphData(**_data) - err.update(tmp) - - val = (func(e1 / natoms, e2 / natoms)).mean() + conf['force_loss_weight'] * func( - f1, f2 - ).mean() - if conf['is_train_stress']: - KB = 1602.1766208 - val += conf['stress_loss_weight'] * func(s1 * KB, s2 * KB).mean() - - assert np.allclose(err.get(), val.item()) - err.update(tmp) - assert np.allclose(err.get(), val.item()) - - -@pytest.mark.parametrize( - 'conf', [config(), config(is_train_stress=False), config(loss='huber')] -) -def test_error_recorder_from_config(conf): - recorder = erc.ErrorRecorder.from_config(conf) - - total_loss_flag = False - for metric in recorder.metrics: - if conf['is_train_stress'] is False: - assert 'stress' not in metric.name - if metric.name == 'TotalLoss': - total_loss_flag = True - for loss_metric, _ in metric.metrics: # type: ignore - assert isinstance(loss_metric.func, loss_dict[conf['loss']]) - assert total_loss_flag - - -@pytest.mark.parametrize( - 'conf', [config(), config(is_train_stress=False), config(loss='huber')] -) -def test_error_recorder_from_config_and_loss_functions(conf): - loss_functions = loss.get_loss_functions_from_config(conf) - recorder = erc.ErrorRecorder.from_config(conf, loss_functions) - - total_loss_flag = False - for metric in recorder.metrics: - if conf['is_train_stress'] is False: - assert 'stress' not in metric.name - if metric.name == 'TotalLoss': - total_loss_flag = True - for loss_metric, _ in metric.metrics: # type: ignore - assert isinstance( - loss_metric.loss_def.criterion, loss_dict[conf['loss']] - ) - assert total_loss_flag diff --git a/mace-bench/3rdparty/SevenNet/tests/unit_tests/test_modal.py b/mace-bench/3rdparty/SevenNet/tests/unit_tests/test_modal.py deleted file mode 100644 index 000476f0f75ff24cfe4375d3cc2695a8182fd8ba..0000000000000000000000000000000000000000 --- a/mace-bench/3rdparty/SevenNet/tests/unit_tests/test_modal.py +++ /dev/null @@ -1,136 +0,0 @@ -# # deploy is test on lammps -# test append modality -# from no modality model to modality yes model -# from modality model to more modality model -# different shift scale settings -# test modality options (check num param) -# calculators with modality - -import copy -# + modal checkpoint continue and test_train -# + sevenn_cp test things in test_cli -import pathlib - -import pytest -from ase.build import bulk - -import sevenn.train.graph_dataset as graph_ds -import sevenn.util as util -from sevenn.calculator import SevenNetCalculator -from sevenn.model_build import build_E3_equivariant_model - -cutoff = 5.0 -data_root = (pathlib.Path(__file__).parent.parent / 'data').resolve() -hfo2_path = str(data_root / 'systems' / 'hfo2.extxyz') -sevennet_0_path = util.pretrained_name_to_path('7net-0_11July2024') - - -@pytest.fixture(scope='module') -def graph_dataset_path(tmp_path_factory): - gd_path = tmp_path_factory.mktemp('gd') - ds = graph_ds.SevenNetGraphDataset( - cutoff=cutoff, root=str(gd_path), files=[hfo2_path], processed_name='tmp.pt' - ) - return ds.processed_paths[0] - - -_modal_cfg = { - 'use_modal_node_embedding': False, - 'use_modal_self_inter_intro': True, - 'use_modal_self_inter_outro': True, - 'use_modal_output_block': True, - 'use_modality': True, - 'use_modal_wise_shift': True, # T/F should be tested - 'use_modal_wise_scale': False, # T/F should be tested - 'load_trainset_path': [ - { - 'data_modality': 'modal_new', - 'file_list': [{'file': hfo2_path}], - } - ], -} - - -@pytest.fixture(scope='module') -def snet_0_cp(): - return util.load_checkpoint(sevennet_0_path) - - -@pytest.fixture(scope='module') -def snet_0_calc(): - return SevenNetCalculator() - - -@pytest.fixture() -def bulk_atoms(): - atoms = bulk('Si') * 3 - atoms.rattle() - return atoms - - -def assert_atoms(atoms1, atoms2, rtol=1e-5, atol=1e-6): - import numpy as np - - def acl(a, b, rtol=rtol, atol=atol): - return np.allclose(a, b, rtol=rtol, atol=atol) - - assert len(atoms1) == len(atoms2) - assert acl(atoms1.get_cell(), atoms2.get_cell()) - assert acl(atoms1.get_potential_energy(), atoms2.get_potential_energy()) - assert acl(atoms1.get_forces(), atoms2.get_forces(), rtol * 10, atol * 10) - assert acl( - atoms1.get_stress(voigt=False), - atoms2.get_stress(voigt=False), - rtol * 10, - atol * 10, - ) - # assert acl(atoms1.get_potential_energies(), atoms2.get_potential_energies()) - - -def get_modal_cfg(overwrite=None): - modal_cfg = copy.deepcopy(_modal_cfg).copy() - if overwrite: - modal_cfg.update(overwrite) - return modal_cfg - - -@pytest.mark.parametrize( - 'cfg_overwrite', - [ - ({}), - ({'use_modal_wise_scale': True}), - ({'use_modal_wise_shift': False}), - ({'use_modal_self_inter_intro': False}), - ], -) -def test_append_modal_sevennet_0( - cfg_overwrite, - snet_0_cp, - snet_0_calc, - bulk_atoms, - graph_dataset_path, - tmp_path, -): - modal_cfg = snet_0_cp.config - modal_cfg.pop('load_dataset_path') - modal_cfg.pop('load_validset_path') - modal_cfg.update(get_modal_cfg(cfg_overwrite)) - modal_cfg['shift'] = 'elemwise_reference_energies' - modal_cfg['scale'] = 'per_atom_energy_std' - modal_cfg['load_trainset_path'][0]['file_list'] = [{'file': graph_dataset_path}] - - new_state_dict = snet_0_cp.append_modal( - modal_cfg, original_modal_name='pbe', working_dir=tmp_path - ) - sevennet_0_w_modal = build_E3_equivariant_model(modal_cfg) - sevennet_0_w_modal.load_state_dict(new_state_dict, strict=True) - - atoms1 = bulk_atoms - atoms2 = copy.deepcopy(atoms1) - - atoms1.calc = snet_0_calc - atoms2.calc = SevenNetCalculator( - model=sevennet_0_w_modal, file_type='model_instance', modal='pbe' - ) - - assert_atoms(atoms1, atoms2) diff --git a/mace-bench/3rdparty/SevenNet/tests/unit_tests/test_model.py b/mace-bench/3rdparty/SevenNet/tests/unit_tests/test_model.py deleted file mode 100644 index d75976f8cdc3f5761796d703edbbf7dd849a81b6..0000000000000000000000000000000000000000 --- a/mace-bench/3rdparty/SevenNet/tests/unit_tests/test_model.py +++ /dev/null @@ -1,213 +0,0 @@ -import pytest -import torch -from ase.build import bulk, molecule -from ase.data import chemical_symbols -from torch_geometric.loader.dataloader import Collater - -import sevenn.train.dataload as dl -from sevenn.atom_graph_data import AtomGraphData -from sevenn.model_build import build_E3_equivariant_model -from sevenn.nn.sequential import AtomGraphSequential -from sevenn.util import chemical_species_preprocess - -cutoff = 4.0 - - -_samples = { - 'bulk': bulk('NaCl', 'rocksalt', a=5.63), - 'mol': molecule('H2O'), - 'isolated': molecule('H'), -} -n_samples = len(_samples) -n_atoms_total = sum([len(at) for at in _samples.values()]) - -_graph_list = [ - AtomGraphData.from_numpy_dict(dl.unlabeled_atoms_to_graph(at, cutoff)) - for at in list(_samples.values()) -] - - -def test_chemical_species_preprocess(): - chems = ['He', 'H', 'Be', 'H'] - cf = chemical_species_preprocess(chems, universal=False) - assert cf['chemical_species'] == ['Be', 'H', 'He'] - assert cf['_number_of_species'] == 3 - assert cf['_type_map'] == {4: 0, 1: 1, 2: 2} - - cf = chemical_species_preprocess(chems, universal=True) - assert cf['chemical_species'] == chemical_symbols - assert cf['_number_of_species'] == len(chemical_symbols) - assert len(cf['_type_map']) == len(chemical_symbols) - for z, node_idx in cf['_type_map'].items(): - assert z == node_idx - - -def get_graphs(batched): - cloned = [g.clone() for g in _graph_list] - if not batched: - return cloned - else: - return Collater(cloned)(cloned) - - -def get_model_config(): - config = { - 'cutoff': cutoff, - 'channel': 4, - 'radial_basis': { - 'radial_basis_name': 'bessel', - }, - 'cutoff_function': {'cutoff_function_name': 'poly_cut'}, - 'interaction_type': 'nequip', - 'lmax': 2, - 'is_parity': True, - 'num_convolution_layer': 3, - 'weight_nn_hidden_neurons': [64, 64], - 'act_radial': 'silu', - 'act_scalar': {'e': 'silu', 'o': 'tanh'}, - 'act_gate': {'e': 'silu', 'o': 'tanh'}, - 'conv_denominator': 30.0, - 'train_denominator': False, - 'self_connection_type': 'nequip', - 'shift': -10.0, - 'scale': 10.0, - 'train_shift_scale': False, - 'irreps_manual': False, - 'lmax_edge': -1, - 'lmax_node': -1, - 'readout_as_fcn': False, - 'use_bias_in_linear': False, - '_normalize_sph': True, - } - chems = set() - for at in list(_samples.values()): - chems.update(at.get_chemical_symbols()) - config.update(**chemical_species_preprocess(list(chems))) - return config - - -def get_model(config_overwrite={}): - cf = get_model_config() - cf.update(**config_overwrite) - model = build_E3_equivariant_model(cf, parallel=False) - assert isinstance(model, AtomGraphSequential) - return model - - -@pytest.mark.parametrize('batched', [False, True]) -@pytest.mark.parametrize('cf', [{}]) -def test_shape(cf, batched): - model = get_model(cf) - model.set_is_batch_data(batched) - - graph = get_graphs(batched) - if not batched: - output_shapes = { - 'inferred_total_energy': (), - 'inferred_stress': (6,), - } - for g in graph: - natoms = g['num_atoms'] - output_shapes.update( - { - 'atomic_energy': (natoms, 1), # intended - 'inferred_force': (natoms, 3), - } - ) - output = model(g) - for k, shape in output_shapes.items(): - assert output[k].shape == shape, f'{k}: {output[k].shape} != {shape}' - else: - output_shapes = { - 'inferred_total_energy': (n_samples,), - 'atomic_energy': (n_atoms_total, 1), # intended - 'inferred_force': (n_atoms_total, 3), - 'inferred_stress': (n_samples, 6), - } - output = model(graph) - for k, shape in output_shapes.items(): - assert output[k].shape == shape, f'{k}: {output[k].shape} != {shape}' - - -def test_batch(): - model = get_model() - model.set_is_batch_data(False) - - graph_list = get_graphs(batched=False) - output_list = [model(g) for g in graph_list] - - model.set_is_batch_data(True) - graph_batch = get_graphs(batched=True) - output_batched = model(graph_batch) - - e_concat = torch.concat( - [g['inferred_total_energy'].unsqueeze(-1) for g in output_list] - ) - ae_concat = torch.concat([g['atomic_energy'].squeeze(1) for g in output_list]) - f_concat = torch.concat([g['inferred_force'] for g in output_list]) - s_concat = torch.stack([g['inferred_stress'] for g in output_list]) - - assert torch.allclose(e_concat, output_batched['inferred_total_energy']) - assert torch.allclose(ae_concat, output_batched['atomic_energy'].squeeze(1)) - assert torch.allclose( - torch.round(f_concat, decimals=5), - torch.round(output_batched['inferred_force'], decimals=5), - atol=1e-5, - ) - - assert torch.allclose( # TODO, hard-coded, assumes the first structure is bulk - torch.round(s_concat[0], decimals=5), - torch.round(output_batched['inferred_stress'][0], decimals=5), - ) - - -_n_param_tests = [ - ({}, 20642), - ({'train_denominator': True}, 20642 + 3), - ({'train_shift_scale': True}, 20642 + 2), - ({'shift': [1.0] * 4}, 20642), - ({'scale': [1.0] * 4, 'train_shift_scale': True}, 20642 + 8), - ({'num_convolution_layer': 4}, 33458), - ({'lmax': 3}, 26866), - ({'channel': 2}, 16883), - ({'is_parity': False}, 20386), - ({'self_connection_type': 'linear'}, 20114), -] - - -@pytest.mark.parametrize('cf,ref', _n_param_tests) -def test_num_params(cf, ref): - model = get_model(cf) - param = sum([p.numel() for p in model.parameters() if p.requires_grad]) - assert param == ref, f'ref: {ref} != given: {param}' - - -_n_modal_param_tests = [ - ({}, 20642), - ({'use_modal_node_embedding': True}, 20642 + 8), - ({'use_modal_self_inter_intro': True}, 20642 + 2 * 4 * 3), - ({'use_modal_self_inter_outro': True}, 20642 + 2 * (12 + 20 + 4)), - ({'use_modal_output_block': True}, 20642 + 2 * 4 / 2), -] - - -@pytest.mark.parametrize('cf,ref', _n_modal_param_tests) -def test_modal_num_params(cf, ref): - modal_cfg = { - 'use_modality': True, - '_number_of_modalities': 2, - '_modal_map': {'x1': 0, 'x2': 1}, - 'use_modal_node_embedding': False, - 'use_modal_self_inter_intro': False, - 'use_modal_self_inter_outro': False, - 'use_modal_output_block': False, - 'use_modal_wise_shift': False, - 'use_modal_wise_scale': False, - } - modal_cfg.update(cf) - model = get_model(modal_cfg) - param = sum([p.numel() for p in model.parameters() if p.requires_grad]) - assert param == ref, f'ref: {ref} != given: {param}' - - -# TODO: test_irreps, test_gard, test_equivariance diff --git a/mace-bench/3rdparty/SevenNet/tests/unit_tests/test_pretrained.py b/mace-bench/3rdparty/SevenNet/tests/unit_tests/test_pretrained.py deleted file mode 100644 index 4676ca47e11a209c7ada6b9992ebfa2a252c1912..0000000000000000000000000000000000000000 --- a/mace-bench/3rdparty/SevenNet/tests/unit_tests/test_pretrained.py +++ /dev/null @@ -1,344 +0,0 @@ -# test_pretrained: output consistency for pretrained models - -import pytest -import torch -from ase.build import bulk, molecule - -import sevenn._keys as KEY -from sevenn.atom_graph_data import AtomGraphData -from sevenn.train.dataload import unlabeled_atoms_to_graph -from sevenn.util import model_from_checkpoint, pretrained_name_to_path - - -def acl(a, b, atol=1e-6): - return torch.allclose(a, b, atol=atol) - - -@pytest.fixture -def atoms_pbc(): - atoms1 = bulk('NaCl', 'rocksalt', a=5.63) - atoms1.set_cell([[1.0, 2.815, 2.815], [2.815, 0.0, 2.815], [2.815, 2.815, 0.0]]) - atoms1.set_positions([[0.0, 0.0, 0.0], [2.815, 0.0, 0.0]]) - return atoms1 - - -@pytest.fixture -def atoms_mol(): - atoms2 = molecule('H2O') - atoms2.set_positions([[0.0, 0.2, 0.12], [0.0, 0.76, -0.48], [0.0, -0.76, -0.48]]) - return atoms2 - - -def test_7net0_22May2024(atoms_pbc, atoms_mol): - """ - Reference from v0.9.3.post1 with SevenNetCalculator - """ - cp_path = pretrained_name_to_path('7net-0_22May2024') - model, config = model_from_checkpoint(cp_path) - cutoff = config['cutoff'] - - g1 = AtomGraphData.from_numpy_dict(unlabeled_atoms_to_graph(atoms_pbc, cutoff)) - g2 = AtomGraphData.from_numpy_dict(unlabeled_atoms_to_graph(atoms_mol, cutoff)) - - model.set_is_batch_data(False) - g1 = model(g1) - g2 = model(g2) - - g1_ref_e = torch.tensor([-3.4140868186950684]) - g1_ref_f = torch.tensor( - [ - [1.2628037e01, 7.5093508e-03, 1.3480943e-02], - [-1.2628037e01, -7.5093508e-03, -1.3480917e-02], - ] - ) - g1_ref_s = -1 * torch.tensor( - [-0.65014917, -0.01990843, -0.02000658, 0.03286226, 0.00589222, 0.03291973] - ) - - g2_ref_e = torch.tensor([-12.808363914489746]) - g2_ref_f = torch.tensor( - [ - [9.31322575e-10, -1.30241165e01, 6.93116236e00], - [-1.39698386e-09, 9.28001022e00, -9.51867390e00], - [5.23868948e-10, 3.74410582e00, 2.58751225e00], - ] - ) - - assert acl(g1.inferred_total_energy, g1_ref_e) - assert acl(g1.inferred_force, g1_ref_f) - assert acl(g1.inferred_stress, g1_ref_s) - - assert acl(g2.inferred_total_energy, g2_ref_e) - assert acl(g2.inferred_force, g2_ref_f) - - -def test_7net0_11July2024(atoms_pbc, atoms_mol): - """ - Reference from v0.9.3.post1 with SevenNetCalculator - """ - cp_path = pretrained_name_to_path('7net-0_11July2024') - model, config = model_from_checkpoint(cp_path) - cutoff = config['cutoff'] - - g1 = AtomGraphData.from_numpy_dict(unlabeled_atoms_to_graph(atoms_pbc, cutoff)) - g2 = AtomGraphData.from_numpy_dict(unlabeled_atoms_to_graph(atoms_mol, cutoff)) - - model.set_is_batch_data(False) - g1 = model(g1) - g2 = model(g2) - - model.set_is_batch_data(True) - - g1_ref_e = torch.tensor([-3.779199]) - g1_ref_f = torch.tensor( - [ - [12.666697, 0.04726403, 0.04775861], - [-12.666697, -0.04726403, -0.04775861], - ] - ) - g1_ref_s = -1 * torch.tensor( - # xx, yy, zz, xy, yz, zx - [-0.6439122, -0.03643947, -0.03643981, 0.04543639, 0.00599139, 0.04544507] - ) - - g2_ref_e = torch.tensor([-12.782808303833008]) - g2_ref_f = torch.tensor( - [ - [0.0, -1.3619621e01, 7.5937047e00], - [0.0, 9.3918495e00, -1.0172190e01], - [0.0, 4.2277718e00, 2.5784855e00], - ] - ) - - assert acl(g1.inferred_total_energy, g1_ref_e) - assert acl(g1.inferred_force, g1_ref_f) - assert acl(g1.inferred_stress, g1_ref_s) - - assert acl(g2.inferred_total_energy, g2_ref_e) - assert acl(g2.inferred_force, g2_ref_f) - - -def test_7net_l3i5(atoms_pbc, atoms_mol): - """ - Reference from v0.9.3.post1 with SevenNetCalculator - """ - cp_path = pretrained_name_to_path('7net-l3i5') - model, config = model_from_checkpoint(cp_path) - cutoff = config['cutoff'] - - g1 = AtomGraphData.from_numpy_dict(unlabeled_atoms_to_graph(atoms_pbc, cutoff)) - g2 = AtomGraphData.from_numpy_dict(unlabeled_atoms_to_graph(atoms_mol, cutoff)) - - model.set_is_batch_data(False) - g1 = model(g1) - g2 = model(g2) - - model.set_is_batch_data(True) - - g1_ref_e = torch.tensor([-3.611131191253662]) - g1_ref_f = torch.tensor( - [ - [13.430887, 0.08655541, 0.08754013], - [-13.430886, -0.08655544, -0.08754011], - ] - ) - g1_ref_s = -1 * torch.tensor( - # xx, yy, zz, xy, yz, zx - [-0.6818918, -0.04104544, -0.04107663, 0.04794561, 0.00565416, 0.04793138] - ) - - g2_ref_e = torch.tensor([-12.700481414794922]) - g2_ref_f = torch.tensor( - [ - [0.0, -1.4547814e01, 8.1347866], - [0.0, 1.0308369e01, -1.0880318e01], - [0.0, 4.2394452, 2.7455316], - ] - ) - - assert acl(g1.inferred_total_energy, g1_ref_e) - assert acl(g1.inferred_force, g1_ref_f, 1e-5) - assert acl(g1.inferred_stress, g1_ref_s, 1e-5) - - assert acl(g2.inferred_total_energy, g2_ref_e) - assert acl(g2.inferred_force, g2_ref_f) - - -def test_7net_mf_0(atoms_pbc, atoms_mol): - cp_path = pretrained_name_to_path('7net-mf-0') - model, config = model_from_checkpoint(cp_path) - cutoff = config['cutoff'] - - g1 = AtomGraphData.from_numpy_dict(unlabeled_atoms_to_graph(atoms_pbc, cutoff)) - g2 = AtomGraphData.from_numpy_dict(unlabeled_atoms_to_graph(atoms_mol, cutoff)) - - g1[KEY.DATA_MODALITY] = 'R2SCAN' - g2[KEY.DATA_MODALITY] = 'R2SCAN' - - model.set_is_batch_data(False) - g1 = model(g1) - g2 = model(g2) - - model.set_is_batch_data(True) - - g1_ref_e = torch.tensor([-11.607587814331055]) - g1_ref_f = torch.tensor( - [ - [8.512259, 0.07307914, 0.06676716], - [-8.512257, -0.07307915, -0.06676716], - ] - ) - g1_ref_s = -1 * torch.tensor( - # xx, yy, zz, xy, yz, zx - [-0.4516204, -0.02483013, -0.02485001, 0.03247492, 0.00259375, 0.03250402] - ) - - g2_ref_e = torch.tensor([-14.172412872314453]) - g2_ref_f = torch.tensor( - [ - [4.6566129e-10, -1.3429364e01, 6.9344816e00], - [2.3283064e-09, 8.9132404e00, -9.6807365e00], - [-2.7939677e-09, 4.5161238e00, 2.7462559e00], - ] - ) - - assert acl(g1.inferred_total_energy, g1_ref_e) - assert acl(g1.inferred_force, g1_ref_f) - assert acl(g1.inferred_stress, g1_ref_s) - - assert acl(g2.inferred_total_energy, g2_ref_e) - assert acl(g2.inferred_force, g2_ref_f) - - -def test_7net_mf_ompa_mpa(atoms_pbc, atoms_mol): - cp_path = pretrained_name_to_path('7net-mf-ompa') - model, config = model_from_checkpoint(cp_path) - cutoff = config['cutoff'] - - g1 = AtomGraphData.from_numpy_dict(unlabeled_atoms_to_graph(atoms_pbc, cutoff)) - g2 = AtomGraphData.from_numpy_dict(unlabeled_atoms_to_graph(atoms_mol, cutoff)) - - # mpa - g1[KEY.DATA_MODALITY] = 'mpa' - g2[KEY.DATA_MODALITY] = 'mpa' - - model.set_is_batch_data(False) - g1 = model(g1) - g2 = model(g2) - - model.set_is_batch_data(True) - - g1_ref_e = torch.tensor([-3.490943193435669]) - g1_ref_f = torch.tensor( - [ - [1.2680445e01, -2.7985498e-04, -2.7979910e-04], - [-1.2680446e01, 2.7984008e-04, 2.7981028e-04], - ] - ) - g1_ref_s = -1 * torch.tensor( - # xx, yy, zz, xy, yz, zx - [-0.6481662, -0.02462837, -0.02462837, 0.02693467, 0.00459635, 0.02693467] - ) - - g2_ref_e = torch.tensor([-12.597525596618652]) - g2_ref_f = torch.tensor( - [ - [0.0, -12.245223, 7.26795], - [0.0, 8.816763, -9.423925], - [0.0, 3.4284601, 2.1559749], - ] - ) - assert acl(g1.inferred_total_energy, g1_ref_e) - assert acl(g1.inferred_force, g1_ref_f) - assert acl(g1.inferred_stress, g1_ref_s) - - assert acl(g2.inferred_total_energy, g2_ref_e) - assert acl(g2.inferred_force, g2_ref_f) - - -def test_7net_mf_ompa_omat(atoms_pbc, atoms_mol): - cp_path = pretrained_name_to_path('7net-mf-ompa') - model, config = model_from_checkpoint(cp_path) - cutoff = config['cutoff'] - - g1 = AtomGraphData.from_numpy_dict(unlabeled_atoms_to_graph(atoms_pbc, cutoff)) - g2 = AtomGraphData.from_numpy_dict(unlabeled_atoms_to_graph(atoms_mol, cutoff)) - - # mpa - g1[KEY.DATA_MODALITY] = 'omat24' - g2[KEY.DATA_MODALITY] = 'omat24' - - model.set_is_batch_data(False) - g1 = model(g1) - g2 = model(g2) - - model.set_is_batch_data(True) - - g1_ref_e = torch.tensor([-3.5094668865203857]) - g1_ref_f = torch.tensor( - [ - [1.2562084e01, -1.4219694e-03, -1.4219843e-03], - [-1.2562084e01, 1.4219508e-03, 1.4219955e-03], - ] - ) - g1_ref_s = -1 * torch.tensor( - # xx, yy, zz, xy, yz, zx - [-0.6430905, -0.0254128, -0.02541281, 0.0268343, 0.00460021, 0.0268343] - ) - - g2_ref_e = torch.tensor([-12.6202974319458]) - g2_ref_f = torch.tensor( - [ - [0.0, -12.205926, 7.2050343], - [0.0, 8.790399, -9.368677], - [0.0, 3.4155273, 2.163643], - ] - ) - assert acl(g1.inferred_total_energy, g1_ref_e) - assert acl(g1.inferred_force, g1_ref_f) - assert acl(g1.inferred_stress, g1_ref_s) - - assert acl(g2.inferred_total_energy, g2_ref_e) - assert acl(g2.inferred_force, g2_ref_f) - - -def test_7net_omat(atoms_pbc, atoms_mol): - cp_path = pretrained_name_to_path('7net-omat') - model, config = model_from_checkpoint(cp_path) - cutoff = config['cutoff'] - - g1 = AtomGraphData.from_numpy_dict(unlabeled_atoms_to_graph(atoms_pbc, cutoff)) - g2 = AtomGraphData.from_numpy_dict(unlabeled_atoms_to_graph(atoms_mol, cutoff)) - - model.set_is_batch_data(False) - g1 = model(g1) - g2 = model(g2) - - model.set_is_batch_data(True) - - g1_ref_e = torch.tensor([-3.5033323764801025]) - g1_ref_f = torch.tensor( - [ - [12.533154, 0.02358698, 0.02358694], - [-12.533153, -0.02358699, -0.02358697], - ] - ) - g1_ref_s = -1 * torch.tensor( - # xx, yy, zz, xy, yz, zx - [-0.6420925, -0.02781446, -0.02781446, 0.02575445, 0.00381664, 0.02575445] - ) - - g2_ref_e = torch.tensor([-12.403768539428711]) - g2_ref_f = torch.tensor( - [ - [0, -12.848297, 7.11432], - [0.0, 9.265477, -9.564951], - [0.0, 3.58282, 2.4506311], - ] - ) - assert acl(g1.inferred_total_energy, g1_ref_e) - assert acl(g1.inferred_force, g1_ref_f) - assert acl(g1.inferred_stress, g1_ref_s) - - assert acl(g2.inferred_total_energy, g2_ref_e) - assert acl(g2.inferred_force, g2_ref_f) diff --git a/mace-bench/3rdparty/SevenNet/tests/unit_tests/test_shift_scale.py b/mace-bench/3rdparty/SevenNet/tests/unit_tests/test_shift_scale.py deleted file mode 100644 index 3d5a4eba46902e4c67600400b6fb38b0a81a25a1..0000000000000000000000000000000000000000 --- a/mace-bench/3rdparty/SevenNet/tests/unit_tests/test_shift_scale.py +++ /dev/null @@ -1,494 +0,0 @@ -import pytest -import torch - -import sevenn._keys as KEY -from sevenn._const import NUM_UNIV_ELEMENT, AtomGraphDataType -from sevenn.nn.scale import ( - ModalWiseRescale, - Rescale, - SpeciesWiseRescale, - get_resolved_shift_scale, -) - -################################################################################ -# Tests for Rescale # -################################################################################ - - -@pytest.mark.parametrize('shift,scale', [(0.0, 1.0), (1.0, 2.0), (-5.0, 10.0)]) -def test_rescale_init(shift, scale): - """ - Test that Rescale can be initialized properly without errors - and that parameters are set correctly. - """ - module = Rescale(shift=shift, scale=scale) - assert module.shift.item() == shift - assert module.scale.item() == scale - assert module.key_input == KEY.SCALED_ATOMIC_ENERGY - assert module.key_output == KEY.ATOMIC_ENERGY - - -def test_rescale_forward(): - """ - Test that Rescale forward pass correctly applies: - output = input * scale + shift - """ - # Setup - shift, scale = 1.0, 2.0 - module = Rescale(shift=shift, scale=scale) - # Make some fake data - input_data = torch.tensor([[1.0], [2.0], [3.0]], dtype=torch.float) - data: AtomGraphDataType = {KEY.SCALED_ATOMIC_ENERGY: input_data.clone()} - - # Forward - out_data = module(data) - - # Check correctness - expected_output = input_data * scale + shift - assert torch.allclose(out_data[KEY.ATOMIC_ENERGY], expected_output) - - -def test_rescale_get_shift_and_scale(): - """ - Test get_shift() and get_scale() methods in Rescale. - """ - module = Rescale(shift=1.5, scale=3.5) - assert module.get_shift() == pytest.approx(1.5) - assert module.get_scale() == pytest.approx(3.5) - - -################################################################################ -# Tests for SpeciesWiseRescale # -################################################################################ - - -def test_specieswise_rescale_init_float(): - """ - Test SpeciesWiseRescale when both shift and scale are floats - (should expand to same length lists). - """ - module = SpeciesWiseRescale(shift=[1.0, -1.0], scale=2.0) - # Expect a parameter of length = 1 in this scenario, but can differ - # if we raise an error for "Both shift and scale is not a list". - # Usually, you'd specify a known number of species or do from_mappers. - # The code as-is throws ValueError if both are float. Let's do from_mappers: - # We'll do direct init if your code allows it. If not, use from_mappers. - assert module.shift.shape == module.scale.shape - # They must be single-parameter (or expanded) if not from mappers. - - -def test_specieswise_rescale_init_list(): - """ - Test initialization with list-based shift/scale of same length. - """ - shift = [1.0, 2.0, 3.0] - scale = [2.0, 3.0, 4.0] - module = SpeciesWiseRescale(shift=shift, scale=scale) - assert len(module.shift) == 3 - assert len(module.scale) == 3 - assert torch.allclose(module.shift, torch.tensor([1.0, 2.0, 3.0])) - assert torch.allclose(module.scale, torch.tensor([2.0, 3.0, 4.0])) - - -def test_specieswise_rescale_forward(): - """ - Test that SpeciesWiseRescale forward pass applies: - output[i] = input[i]*scale[atom_type[i]] + shift[atom_type[i]] - """ - # Suppose we have two species types: - # 0 -> shift=1, scale=2, 1 -> shift=5, scale=10 - # (we'll pass them as lists in the correct order) - shift = [1.0, 5.0] - scale = [2.0, 10.0] - module = SpeciesWiseRescale( - shift=shift, - scale=scale, - data_key_in='in', - data_key_out='out', - data_key_indices='z', - ) - - # Create mock data - # Suppose we have three atoms: species => [0, 1, 0] - # input => [ [1.], [1.], [3.] ] - data: AtomGraphDataType = { - 'z': torch.tensor([0, 1, 0], dtype=torch.long), - 'in': torch.tensor([[1.0], [1.0], [3.0]], dtype=torch.float), - } - - out = module(data) - # Now let's manually compute expected: - # For atom 0: scale=2, shift=1, input=1 => 1*2+1=3 - # For atom 1: scale=10, shift=5, input=1 => 1*10+5=15 - # For atom 2: scale=2, shift=1, input=3 => 3*2+1=7 - expected = torch.tensor([[3.0], [15.0], [7.0]]) - - assert torch.allclose(out['out'], expected) - - -def test_specieswise_rescale_get_shift_scale(): - """ - Test get_shift() and get_scale() with/without type_map. - """ - shift = [1.0, 2.0] - scale = [3.0, 4.0] - module = SpeciesWiseRescale(shift=shift, scale=scale) - - # Without type_map - # Should return the raw parameter values (list form). - s = module.get_shift() - sc = module.get_scale() - assert s == [1.0, 2.0] - assert sc == [3.0, 4.0] - - # With a type_map (example: atomic_number 1 -> 0, 8 -> 1) - type_map = {1: 0, 8: 1} # hydrogen, oxygen - s_univ = module.get_shift(type_map) - sc_univ = module.get_scale(type_map) - # In this small example with NUM_UNIV_ELEMENT = 2, the _as_univ will produce - # a list of length = NUM_UNIV_ELEMENT. If your real NUM_UNIV_ELEMENT is bigger, - # the rest would be padded with default values. - # For demonstration let's assume it returns [1.0, 2.0]. - # Check at least the known mapped portion: - assert len(s_univ) == NUM_UNIV_ELEMENT - assert len(sc_univ) == NUM_UNIV_ELEMENT - assert s_univ[1] == 1.0 # atomic_number=1 -> idx=0 -> shift=1.0 - assert s_univ[8] == 2.0 - - -################################################################################ -# Tests for ModalWiseRescale # -################################################################################ - - -def test_modalwise_rescale_init(): - """ - Basic sanity check for ModalWiseRescale initialization with - certain shapes. - """ - # Suppose we have 2 modals, 3 species => shift, scale is shape [2,3] - shift = [[0.0, 1.0, 2.0], [3.0, 4.0, 5.0]] - scale = [[1.0, 2.0, 3.0], [4.0, 5.0, 6.0]] - module = ModalWiseRescale( - shift=shift, - scale=scale, - use_modal_wise_shift=True, - use_modal_wise_scale=True, - ) - # Check shape - assert module.shift.shape == torch.Size([2, 3]) - assert module.scale.shape == torch.Size([2, 3]) - - -def test_modalwise_rescale_forward(): - """ - Test that the forward pass of ModalWiseRescale matches - output[i] = input[i] * scale[modal_i, atom_i] + shift[modal_i, atom_i] - when both use_modal_wise_{shift,scale} are True. - """ - shift = [[0.0, 10.0], [5.0, 15.0]] # shape [2 (modals), 2 (species)] - scale = [[1.0, 2.0], [10.0, 20.0]] - module = ModalWiseRescale( - shift=shift, - scale=scale, - data_key_in='in', - data_key_out='out', - data_key_modal_indices='modal_idx', - data_key_atom_indices='atom_idx', - use_modal_wise_shift=True, - use_modal_wise_scale=True, - ) - - data: AtomGraphDataType = { - 'in': torch.tensor([[1.0], [1.0], [2.0], [2.0]]), - 'modal_idx': torch.tensor([0, 1], dtype=torch.long), - 'atom_idx': torch.tensor([0, 1, 0, 1], dtype=torch.long), - 'batch': torch.tensor([0, 0, 1, 1], dtype=torch.long), - } - - out = module(data) - # i=0 => modal_idx=0, atom_idx=0 => shift=0.0, scale=1.0 => out=1*1+0=1 - # i=1 => modal_idx=0, atom_idx=1 => shift=10.0, scale=2.0 => out=1*2+10=12 - # i=2 => modal_idx=1, atom_idx=0 => shift=5.0, scale=10.0 => out=2*10+5=25 - # i=3 => modal_idx=1, atom_idx=1 => shift=15.0, scale=20.0 => out=2*20+15=55 - expected = torch.tensor([[1.0], [12.0], [25.0], [55.0]]) - assert torch.allclose(out['out'], expected) - - -def test_modalwise_rescale_get_shift_scale(): - """ - Test get_shift() and get_scale() with type_map and modal_map. - """ - # Setup - shift = [[0.0, 10.0], [5.0, 15.0]] - scale = [[1.0, 2.0], [10.0, 20.0]] - mod = ModalWiseRescale( - shift=shift, - scale=scale, - use_modal_wise_shift=True, - use_modal_wise_scale=True, - ) - - # Suppose we have type_map and modal_map - type_map = {1: 0, 8: 1} # Example: H->0, O->1 - modal_map = {'a': 0, 'b': 1} - - # get_shift, get_scale - s = mod.get_shift(type_map=type_map, modal_map=modal_map) - sc = mod.get_scale(type_map=type_map, modal_map=modal_map) - # Expect dict with keys "ambient", "pressure". - # Example: s["ambient"] = [ shift(0,0), shift(0,1) ] mapped to H,O - # s["pressure"] = [ shift(1,0), shift(1,1) ] - assert isinstance(s, dict) and isinstance(sc, dict) - assert set(s.keys()) == {'a', 'b'} - assert set(sc.keys()) == {'a', 'b'} - - -################################################################################ -# Tests for get_resolved_shift_scale function # -################################################################################ - - -def test_get_resolved_shift_scale_rescale(): - """ - Test get_resolved_shift_scale for a Rescale instance. - """ - from_m = Rescale(shift=2.0, scale=5.0) - shift, scale = get_resolved_shift_scale(from_m) - assert shift == 2.0 - assert scale == 5.0 - - -def test_get_resolved_shift_scale_specieswise(): - """ - Test get_resolved_shift_scale for a SpeciesWiseRescale instance. - """ - shift_list = [1.0, 2.0] - scale_list = [3.0, 4.0] - module = SpeciesWiseRescale(shift=shift_list, scale=scale_list) - type_map = {1: 0, 8: 1} - s, sc = get_resolved_shift_scale(module, type_map=type_map) - # The result should be extended to NUM_UNIV_ELEMENT length in real usage, - # but at least the first few should match shift_list, scale_list mapped. - assert isinstance(s, list) - assert isinstance(sc, list) - # Check mapped values - assert s[1] == shift_list[0] - assert s[8] == shift_list[1] - assert sc[1] == scale_list[0] - assert sc[8] == scale_list[1] - - -def test_get_resolved_shift_scale_modalwise(): - """ - Test get_resolved_shift_scale for a ModalWiseRescale instance. - """ - shift = [[0.0, 10.0], [5.0, 15.0]] - scale = [[1.0, 2.0], [10.0, 20.0]] - mmod = ModalWiseRescale( - shift=shift, - scale=scale, - use_modal_wise_shift=True, - use_modal_wise_scale=True, - ) - type_map = {1: 0, 8: 1} - modal_map = {'a': 0, 'b': 1} - s, sc = get_resolved_shift_scale(mmod, type_map=type_map, modal_map=modal_map) - # We expect dictionaries - assert isinstance(s, dict) and isinstance(sc, dict) - # Keys "a", "pressure" - assert 'a' in s - assert 'b' in s - # Check one example - # s["a"] => [0.0, 10.0] - # sc["a"] => [1.0, 2.0] - assert s['a'][1] == 0.0 - assert s['a'][8] == 10.0 - assert sc['a'][1] == 1.0 - assert sc['a'][8] == 2.0 - - -################################################################################ -# Tests for from_mappers function # -################################################################################ - - -@pytest.mark.parametrize( - 'shift, scale, type_map, expected_shift, expected_scale', - [ - # Both shift and scale are floats -> broadcast to each species - ( - 2.0, - 3.0, - {1: 0, 8: 1}, # e.g., H -> index 0, O -> index 1 - [2.0, 2.0], # broadcast - [3.0, 3.0], - ), - # shift, scale are same-length lists => directly used - ( - [0.5, 0.6], - [1.0, 1.1], - {1: 0, 8: 1}, - [0.5, 0.6], - [1.0, 1.1], - ), - # shift, scale are entire "universal" length (NUM_UNIV_ELEMENT=118), - # but we only map out the subset for the actual species in type_map - ( - [0.1] * NUM_UNIV_ELEMENT, - [1.1] * NUM_UNIV_ELEMENT, - {1: 0, 8: 1}, - [0.1, 0.1], - [1.1, 1.1], - ), - # shift is a list, scale is float => shift is used directly, scale broadcast - ( - [1.0, 2.0], - 5.0, - {6: 0, 14: 1}, # C -> 0, Si -> 1 - [1.0, 2.0], - [5.0, 5.0], - ), - ], -) -def test_specieswise_rescale_from_mappers( - shift, scale, type_map, expected_shift, expected_scale -): - """ - Test SpeciesWiseRescale.from_mappers with various combinations of - shift/scale (float, list, universal list) and a given type_map. - """ - module = SpeciesWiseRescale.from_mappers( # type: ignore - shift=shift, - scale=scale, - type_map=type_map, - ) - # Check that the module's internal shift and scale have the correct shape - # The length must match number of species in type_map - assert module.shift.shape[0] == len(type_map) - assert module.scale.shape[0] == len(type_map) - - # Check that the content matches expected - actual_shift = module.shift.detach().cpu().tolist() - actual_scale = module.scale.detach().cpu().tolist() - - assert pytest.approx(actual_shift) == expected_shift - assert pytest.approx(actual_scale) == expected_scale - - -@pytest.mark.parametrize( - 'shift, scale, use_modal_wise_shift, use_modal_wise_scale, ' - 'type_map, modal_map, expected_shift, expected_scale', - [ - # Example 1: single float for shift/scale, - # broadcast over 2 modals and 2 species - ( - 1.0, - 2.0, - True, # shift depends on modal - True, # scale depends on modal - {1: 0, 8: 1}, - {'modA': 0, 'modB': 1}, - # expect 2D => [2 modals x 2 species] - [[1.0, 1.0], [1.0, 1.0]], - [[2.0, 2.0], [2.0, 2.0]], - ), - # Example 2: shift/scale are universal element-lists => use_modal=False => 1D - ( - [0.5] * NUM_UNIV_ELEMENT, - [1.5] * NUM_UNIV_ELEMENT, - False, # shift is not modal-wise - False, # scale is not modal-wise - {6: 0, 14: 1}, # e.g. C->0, Si->1 - {'modA': 0, 'modB': 1}, - # 1D => length = n_atom_types(=2) - [0.5, 0.5], - [1.5, 1.5], - ), - # Example 3: shift is dict of modals -> each is float - # => broadcast for each species - ( - {'modA': 0.0, 'modB': 2.0}, - {'modA': 1.0, 'modB': 3.0}, - True, - True, - {1: 0, 8: 1}, - {'modA': 0, 'modB': 1}, - # shift => shape [2 modals, 2 species] - [[0.0, 0.0], [2.0, 2.0]], - [[1.0, 1.0], [3.0, 3.0]], - ), - # Example 4: already in "modal-wise + species-wise" shape, direct pass - ( - [[0.0, 10.0], [5.0, 15.0]], - [[1.0, 2.0], [10.0, 20.0]], - True, - True, - {1: 0, 8: 1}, - {'modA': 0, 'modB': 1}, - [[0.0, 10.0], [5.0, 15.0]], - [[1.0, 2.0], [10.0, 20.0]], - ), - # Example 5: shift is a list of floats (one per modal), - # but we want modal-wise => broadcast for each species - ( - [0.0, 10.0], # length=2 => same as #modals - [1.0, 2.0], - True, - True, - {1: 0, 8: 1}, - {'modA': 0, 'modB': 1}, - [[0.0, 0.0], [10.0, 10.0]], - [[1.0, 1.0], [2.0, 2.0]], - ), - ], -) -def test_modalwise_rescale_from_mappers( - shift, - scale, - use_modal_wise_shift, - use_modal_wise_scale, - type_map, - modal_map, - expected_shift, - expected_scale, -): - """ - Test ModalWiseRescale.from_mappers for different shapes of shift/scale, - combined with type_map and modal_map. - """ - - module = ModalWiseRescale.from_mappers( # type: ignore - shift=shift, - scale=scale, - use_modal_wise_shift=use_modal_wise_shift, - use_modal_wise_scale=use_modal_wise_scale, - type_map=type_map, - modal_map=modal_map, - ) - # Check shape of the resulting shift, scale - # If modal-wise, we expect a 2D shape: [n_modals, n_species] - # Otherwise, a 1D shape: [n_species] - if use_modal_wise_shift: - assert module.shift.dim() == 2 - assert module.shift.shape[0] == len(modal_map) - assert module.shift.shape[1] == len(type_map) - else: - assert module.shift.dim() == 1 - assert module.shift.shape[0] == len(type_map) - - # Similarly for scale - if use_modal_wise_scale: - assert module.scale.dim() == 2 - assert module.scale.shape[0] == len(modal_map) - assert module.scale.shape[1] == len(type_map) - else: - assert module.scale.dim() == 1 - assert module.scale.shape[0] == len(type_map) - - # Verify the content matches our expectation - actual_shift = module.shift.detach().cpu().tolist() - actual_scale = module.scale.detach().cpu().tolist() - - assert actual_shift == expected_shift - assert actual_scale == expected_scale diff --git a/mace-bench/3rdparty/SevenNet/tests/unit_tests/test_train.py b/mace-bench/3rdparty/SevenNet/tests/unit_tests/test_train.py deleted file mode 100644 index 089fe8212b89f583006e04b0591bceafefd576e4..0000000000000000000000000000000000000000 --- a/mace-bench/3rdparty/SevenNet/tests/unit_tests/test_train.py +++ /dev/null @@ -1,402 +0,0 @@ -import pathlib - -import ase.io -import numpy as np -import pytest -import torch -from torch_geometric.loader import DataLoader - -import sevenn.train.graph_dataset as graph_ds -from sevenn._const import NUM_UNIV_ELEMENT -from sevenn.error_recorder import ErrorRecorder -from sevenn.logger import Logger -from sevenn.scripts.processing_continue import processing_continue_v2 -from sevenn.scripts.processing_epoch import processing_epoch_v2 -from sevenn.train.dataload import graph_build -from sevenn.train.graph_dataset import from_config as dataset_from_config -from sevenn.train.loss import get_loss_functions_from_config -from sevenn.train.trainer import Trainer -from sevenn.util import ( - chemical_species_preprocess, - get_error_recorder, - pretrained_name_to_path, -) - -cutoff = 4.0 - -data_root = (pathlib.Path(__file__).parent.parent / 'data').resolve() - -hfo2_path = str(data_root / 'systems' / 'hfo2.extxyz') -cp_0_path = str(data_root / 'checkpoints' / 'cp_0.pth') -sevennet_0_path = pretrained_name_to_path('7net-0_11July2024') - -known_elements = ['Hf', 'O'] -_elemwise_ref_energy_dct = {72: -17.379337, 8: -34.7499924} - -Logger() # init - - -@pytest.fixture() -def HfO2_atoms(): - atoms = ase.io.read(hfo2_path) - return atoms - - -@pytest.fixture(scope='module') -def HfO2_loader(): - atoms = ase.io.read(hfo2_path, index=':') - assert isinstance(atoms, list) - graphs = graph_build(atoms, cutoff, y_from_calc=True) - return DataLoader(graphs, batch_size=2) - - -@pytest.fixture(scope='module') -def graph_dataset_path(tmp_path_factory): - gd_path = tmp_path_factory.mktemp('gd') - ds = graph_ds.SevenNetGraphDataset( - cutoff=cutoff, root=str(gd_path), files=[hfo2_path], processed_name='tmp.pt' - ) - return ds.processed_paths[0] - - -def get_model_config(): - config = { - 'cutoff': cutoff, - 'channel': 4, - 'radial_basis': { - 'radial_basis_name': 'bessel', - }, - 'cutoff_function': {'cutoff_function_name': 'poly_cut'}, - 'interaction_type': 'nequip', - 'lmax': 2, - 'is_parity': True, - 'num_convolution_layer': 3, - 'weight_nn_hidden_neurons': [64, 64], - 'act_radial': 'silu', - 'act_scalar': {'e': 'silu', 'o': 'tanh'}, - 'act_gate': {'e': 'silu', 'o': 'tanh'}, - 'conv_denominator': 'avg_num_neigh', - 'train_denominator': False, - 'self_connection_type': 'nequip', - 'train_shift_scale': False, - 'irreps_manual': False, - 'lmax_edge': -1, - 'lmax_node': -1, - 'readout_as_fcn': False, - 'use_bias_in_linear': False, - '_normalize_sph': True, - } - config.update(**chemical_species_preprocess(known_elements)) - return config - - -def get_train_config(): - config = { - 'random_seed': 1, - 'epoch': 2, - 'loss': 'mse', - 'loss_param': {}, - 'optimizer': 'adam', - 'optim_param': {}, - 'scheduler': 'exponentiallr', - 'scheduler_param': {'gamma': 0.99}, - 'force_loss_weight': 1.0, - 'stress_loss_weight': 0.1, - 'per_epoch': 1, - 'continue': { - 'checkpoint': False, - 'reset_optimizer': False, - 'reset_scheduler': False, - 'reset_epoch': False, - }, - 'is_train_stress': True, - 'train_shuffle': True, - 'best_metric': 'TotalLoss', - 'error_record': [ - ('Energy', 'RMSE'), - ('Force', 'RMSE'), - ('Stress', 'RMSE'), - ('TotalLoss', 'None'), - ], - 'use_modality': False, - 'use_weight': False, - 'device': 'cpu', - 'is_ddp': False, - } - return config - - -def get_data_config(): - config = { - 'batch_size': 2, - 'shift': 'per_atom_energy_mean', - 'scale': 'force_rms', - 'preprocess_num_cores': 1, - 'data_format_args': {}, - 'load_trainset_path': hfo2_path, - } - return config - - -def get_config(overwrite=None): - cf = {} - cf.update(get_model_config()) - cf.update(get_train_config()) - cf.update(get_data_config()) - if overwrite: - cf.update(overwrite) - return cf - - -def test_processing_continue_v2_7net0(tmp_path): - cp = torch.load(sevennet_0_path, weights_only=False, map_location='cpu') - - cfg = get_config( - { - 'continue': { - 'checkpoint': sevennet_0_path, - 'reset_optimizer': False, - 'reset_scheduler': True, - 'reset_epoch': False, - } - } - ) - shift_ref = cp['model_state_dict']['rescale_atomic_energy.shift'].cpu().numpy() - scale_ref = np.array([1.73] * 89) - conv_denominator_ref = np.array([35.989574] * 5) - - with Logger().switch_file(str(tmp_path / 'log.sevenn')): - state_dicts, epoch = processing_continue_v2(cfg) - assert epoch == 601 - assert np.allclose(np.array(cfg['shift']), shift_ref) - assert np.allclose(np.array(cfg['shift'])[0], -5.062768) - assert np.allclose(np.array(cfg['scale']), scale_ref) - assert np.allclose(np.array(cfg['conv_denominator']), conv_denominator_ref) - assert cfg['_number_of_species'] == 89 - assert cfg['_type_map'][89] == 0 # Ac - assert cfg['_type_map'][40] == 88 # Zr - assert state_dicts[2] is None # scheduler reset - - -@pytest.mark.parametrize( - 'cfg_overwrite,ds_names', - [ - ({}, ['trainset']), - ({'load_myset_path': hfo2_path}, ['trainset', 'myset']), - ], -) -def test_dataset_from_config(cfg_overwrite, ds_names, tmp_path): - cfg = get_config(cfg_overwrite) - with Logger().switch_file(str(tmp_path / 'log.sevenn')): - datasets = dataset_from_config(cfg, tmp_path) - - assert set(ds_names) == set(datasets.keys()) - for ds_name in ds_names: - assert (tmp_path / 'sevenn_data' / f'{ds_name}.pt').is_file() - assert (tmp_path / 'sevenn_data' / f'{ds_name}.yaml').is_file() - - -def test_dataset_from_config_as_it_is_load(graph_dataset_path, tmp_path): - cfg = get_config({'load_trainset_path': graph_dataset_path}) - new_wd = tmp_path / 'tmp_wd' - with Logger().switch_file(str(tmp_path / 'log.sevenn')): - _ = dataset_from_config(cfg, str(new_wd)) - print((tmp_path / 'tmp_wd' / 'sevenn_data')) - assert not (tmp_path / 'tmp_wd' / 'sevenn_data').is_dir() - - -@pytest.mark.parametrize( - 'cfg_overwrite,shift,scale,conv', - [ - ( - {}, - -28.978, - 0.113304, - 25.333333, - ), - ( - { - 'shift': -1.2345678, - }, - -1.234567, - 0.113304, - 25.333333, - ), - ( - { - 'conv_denominator': 'sqrt_avg_num_neigh', - }, - -28.978, - 0.113304, - 25.333333**0.5, - ), - ( - { - 'shift': 'force_rms', - }, - 0.113304, - 0.113304, - 25.333333, - ), - ( - { - 'shift': 'elemwise_reference_energies', - }, - [ - 0.0 - if z not in _elemwise_ref_energy_dct - else _elemwise_ref_energy_dct[z] - for z in range(NUM_UNIV_ELEMENT) - ], - 0.113304, - 25.333333, - ), - ], -) -def test_dataset_from_config_statistics_init( - cfg_overwrite, shift, scale, conv, tmp_path -): - cfg = get_config(cfg_overwrite) - with Logger().switch_file(str(tmp_path / 'log.sevenn')): - _ = dataset_from_config(cfg, tmp_path) - - assert np.allclose(cfg['shift'], shift) - assert np.allclose(cfg['scale'], scale) - assert np.allclose(cfg['conv_denominator'], conv) - - -def test_dataset_from_config_chem_auto(tmp_path): - cfg = get_config( - { - 'chemical_species': 'auto', - '_number_of_species': 'auto', - '_type_map': 'auto', - } - ) - with Logger().switch_file(str(tmp_path / 'log.sevenn')): - _ = dataset_from_config(cfg, tmp_path) - assert cfg['chemical_species'] == ['Hf', 'O'] - assert cfg['_number_of_species'] == 2 - assert cfg['_type_map'] == {72: 0, 8: 1} - - -def test_run_one_epoch(HfO2_loader): - trainer_args, _, _ = Trainer.args_from_checkpoint(cp_0_path) - trainer = Trainer(**trainer_args) - erc = get_error_recorder() - - ref1 = { - 'Energy_RMSE': '28.977758', - 'Force_RMSE': '0.214107', - 'Stress_RMSE': '190.014237', - } - - ref2 = { - 'Energy_RMSE': '28.977878', - 'Force_RMSE': '0.213105', - 'Stress_RMSE': '188.772557', - } - - trainer.run_one_epoch(HfO2_loader, is_train=False, error_recorder=erc) - ret1 = erc.get_dct() - erc.epoch_forward() - - for k in ref1: - assert np.allclose(float(ret1[k]), float(ref1[k])) - - trainer.run_one_epoch(HfO2_loader, is_train=True, error_recorder=erc) - erc.epoch_forward() - - trainer.run_one_epoch(HfO2_loader, is_train=False, error_recorder=erc) - ret2 = erc.get_dct() - erc.epoch_forward() - - for k in ref2: - assert np.allclose(float(ret2[k]), float(ref2[k])) - - -def test_processing_epoch_v2(HfO2_loader, tmp_path): - trainer_args, _, _ = Trainer.args_from_checkpoint(cp_0_path) - trainer = Trainer(**trainer_args) - erc = get_error_recorder() - start_epoch = 10 - total_epoch = 12 - per_epoch = 1 - best_metric = 'Energy_RMSE' - best_metric_loader_key = 'myset' - loaders = {'trainset': HfO2_loader, 'myset': HfO2_loader} - - with Logger().switch_file(str(tmp_path / 'log.sevenn')): - processing_epoch_v2( - config={}, - trainer=trainer, - loaders=loaders, - start_epoch=start_epoch, - error_recorder=erc, - total_epoch=total_epoch, - per_epoch=per_epoch, - best_metric_loader_key=best_metric_loader_key, - best_metric=best_metric, - working_dir=tmp_path, - ) - assert (tmp_path / 'checkpoint_10.pth').is_file() - assert (tmp_path / 'checkpoint_11.pth').is_file() - assert (tmp_path / 'checkpoint_12.pth').is_file() - assert (tmp_path / 'checkpoint_best.pth').is_file() - assert (tmp_path / 'lc.csv').is_file() - with open(tmp_path / 'lc.csv', 'r') as f: - lines = f.readlines() - heads = [ll.strip() for ll in lines[0].split(',')] - assert 'epoch' in heads - assert 'lr' in heads - assert 'trainset_Energy_RMSE' in heads - assert 'myset_Stress_MAE' in heads - lasts = [ll.strip() for ll in lines[-1].split(',')] - assert lasts[0] == '12' - assert lasts[1] == '0.000980' # lr - assert lasts[-2] == '0.087873' # myset Force MAE - - -def test_data_weight(graph_dataset_path, tmp_path): - cfg = get_config( - { - 'load_trainset_path': [{ - 'file_list': [{'file': graph_dataset_path}], - 'data_weight': {'energy': 0.1, 'force': 3.0, 'stress': 1.0}, - }], - 'error_record': [ - ('Energy', 'Loss'), - ('Force', 'Loss'), - ('Stress', 'Loss'), - ('TotalLoss', 'None'), - ], - 'use_weight': True - } - ) - trainer_args, _, _ = Trainer.args_from_checkpoint(cp_0_path) - trainer_args['loss_functions'] = get_loss_functions_from_config(cfg) - trainer = Trainer(**trainer_args) - erc = ErrorRecorder.from_config(cfg, trainer.loss_functions) - - db = graph_ds.from_config(cfg, working_dir=tmp_path)['trainset'] - loader_w_weight = DataLoader(db, batch_size=len(db)) - - trainer.run_one_epoch(loader_w_weight, False, erc) - loss = erc.epoch_forward() - assert np.allclose(loss['Energy_Loss'], 839.7104492 * 0.1) - assert np.allclose(loss['Force_Loss'], 0.0152806 * 3.0) - assert np.allclose(loss['Stress_Loss'], 6017.568847 * 1.0) - - -def _write_empty_checkpoint(): - from sevenn.model_build import build_E3_equivariant_model - - # Function I used to make empty checkpoint, to write the test - cfg = get_config({'shift': 0.0, 'scale': 1.0, 'conv_denominator': 5.0}) - model = build_E3_equivariant_model(cfg) - trainer = Trainer.from_config(model, cfg) # type: ignore - trainer.write_checkpoint('./cp_0.pth', config=cfg, epoch=0) - - -if __name__ == '__main__': - _write_empty_checkpoint() diff --git a/mace-bench/3rdparty/mace/LICENSE.md b/mace-bench/3rdparty/mace/LICENSE.md deleted file mode 100644 index de8a98d0c45ff75fd5e781c3fb1f6a4ebb2e95c3..0000000000000000000000000000000000000000 --- a/mace-bench/3rdparty/mace/LICENSE.md +++ /dev/null @@ -1,13 +0,0 @@ -MIT License - -Copyright (c) 2022 ACEsuit/mace - -Permission is hereby granted, free of charge, to any person obtaining a copy -of this software and associated documentation files (the "Software"), to deal -in the Software without restriction, including without limitation the rights -to use, copy, modify, merge, publish, distribute, sublicense, and/or sell -copies of the Software, and to permit persons to whom the Software is -furnished to do so, subject to the following conditions: - -The above copyright notice and this permission notice shall be included in all -copies or substantial portions of the Software. diff --git a/mace-bench/3rdparty/mace/MANIFEST.in b/mace-bench/3rdparty/mace/MANIFEST.in deleted file mode 100644 index 6dbd9d80ca27cd73270473993f6c0ed4b9433499..0000000000000000000000000000000000000000 --- a/mace-bench/3rdparty/mace/MANIFEST.in +++ /dev/null @@ -1 +0,0 @@ -include mace/py.typed diff --git a/mace-bench/3rdparty/mace/README.md b/mace-bench/3rdparty/mace/README.md deleted file mode 100644 index f8163e3268b2310b9687ef36ea883d1474a16b2c..0000000000000000000000000000000000000000 --- a/mace-bench/3rdparty/mace/README.md +++ /dev/null @@ -1,377 +0,0 @@ -# MACE - -[![GitHub release](https://img.shields.io/github/release/ACEsuit/mace.svg)](https://GitHub.com/ACEsuit/mace/releases/) -[![Paper](https://img.shields.io/badge/Paper-NeurIPs2022-blue)](https://openreview.net/forum?id=YPpSngE-ZU) -[![License](https://img.shields.io/badge/License-MIT%202.0-blue.svg)](https://opensource.org/licenses/mit) -[![GitHub issues](https://img.shields.io/github/issues/ACEsuit/mace.svg)](https://GitHub.com/ACEsuit/mace/issues/) -[![Documentation Status](https://readthedocs.org/projects/mace/badge/)](https://mace-docs.readthedocs.io/en/latest/) -[![DOI](https://zenodo.org/badge/505964914.svg)](https://doi.org/10.5281/zenodo.14103332) - -## Table of contents - -- [MACE](#mace) - - [Table of contents](#table-of-contents) - - [About MACE](#about-mace) - - [Documentation](#documentation) - - [Installation](#installation) - - [pip installation](#installation-from-pypi) - - [pip installation from source](#installation-from-source) - - [Usage](#usage) - - [Training](#training) - - [Evaluation](#evaluation) - - [Tutorials](#tutorials) - - [CUDA acceleration with cuEquivariance](#cuda-acceleration-with-cuequivariance) - - [Weights and Biases for experiment tracking](#weights-and-biases-for-experiment-tracking) - - [Pretrained Foundation Models](#pretrained-foundation-models) - - [MACE-MP: Materials Project Force Fields](#mace-mp-materials-project-force-fields) - - [Example usage in ASE](#example-usage-in-ase) - - [MACE-OFF: Transferable Organic Force Fields](#mace-off-transferable-organic-force-fields) - - [Example usage in ASE](#example-usage-in-ase-1) - - [Finetuning foundation models](#finetuning-foundation-models) - - [Latest recommended foundation models](#latest-recommended-foundation-models) - - [Caching](#caching) - - [Development](#development) - - [References](#references) - - [Contact](#contact) - - [License](#license) - -## About MACE - -MACE provides fast and accurate machine learning interatomic potentials with higher order equivariant message passing. - -This repository contains the MACE reference implementation developed by -Ilyes Batatia, Gregor Simm, David Kovacs, and the group of Gabor Csanyi, and friends (see Contributors). - -Also available: - -- [MACE in JAX](https://github.com/ACEsuit/mace-jax), currently about 2x times faster at evaluation, but training is recommended in Pytorch for optimal performances. -- [MACE layers](https://github.com/ACEsuit/mace-layer) for constructing higher order equivariant graph neural networks for arbitrary 3D point clouds. - -## Documentation - -A partial documentation is available at: https://mace-docs.readthedocs.io - -## Installation - -### 1. Requirements: - -- Python >= 3.7 (for openMM, use Python = 3.9) -- [PyTorch](https://pytorch.org/) >= 1.12 **(training with float64 is not supported with PyTorch 2.1 but is supported with 2.2 and later, Pytorch 2.4.1 is not supported)** - -**Make sure to install PyTorch.** Please refer to the [official PyTorch installation](https://pytorch.org/get-started/locally/) for the installation instructions. Select the appropriate options for your system. - -### Installation from PyPI -This is the recommended way to install MACE. - -```sh -pip install --upgrade pip -pip install mace-torch -``` -**Note:** The homonymous package on [PyPI](https://pypi.org/project/MACE/) has nothing to do with this one. - - -### Installation from source - - -```sh -git clone https://github.com/ACEsuit/mace.git -pip install ./mace -``` - - - - -## Usage - -### Training - -To train a MACE model, you can use the `mace_run_train` script, which should be in the usual place that pip places binaries (or you can explicitly run `python3 /mace/cli/run_train.py`) - -```sh -mace_run_train \ - --name="MACE_model" \ - --train_file="train.xyz" \ - --valid_fraction=0.05 \ - --test_file="test.xyz" \ - --config_type_weights='{"Default":1.0}' \ - --E0s='{1:-13.663181292231226, 6:-1029.2809654211628, 7:-1484.1187695035828, 8:-2042.0330099956639}' \ - --model="MACE" \ - --hidden_irreps='128x0e + 128x1o' \ - --r_max=5.0 \ - --batch_size=10 \ - --max_num_epochs=1500 \ - --stage_two \ - --start_stage_two=1200 \ - --ema \ - --ema_decay=0.99 \ - --amsgrad \ - --restart_latest \ - --device=cuda \ -``` - -To give a specific validation set, use the argument `--valid_file`. To set a larger batch size for evaluating the validation set, specify `--valid_batch_size`. - -To control the model's size, you need to change `--hidden_irreps`. For most applications, the recommended default model size is `--hidden_irreps='256x0e'` (meaning 256 invariant messages) or `--hidden_irreps='128x0e + 128x1o'`. If the model is not accurate enough, you can include higher order features, e.g., `128x0e + 128x1o + 128x2e`, or increase the number of channels to `256`. It is also possible to specify the model using the `--num_channels=128` and `--max_L=1`keys. - -It is usually preferred to add the isolated atoms to the training set, rather than reading in their energies through the command line like in the example above. To label them in the training set, set `config_type=IsolatedAtom` in their info fields. If you prefer not to use or do not know the energies of the isolated atoms, you can use the option `--E0s="average"` which estimates the atomic energies using least squares regression. Note that using fitted E0s corresponds to fitting the deviations of the atomic energies from the average, rather than fitting the atomization energy (which is the case when using isolated-atom E0s), and this will most likely result in less stable potentials for molecular dynamics applications. - -If the keyword `--stage_two` (previously called swa) is enabled, the energy weight of the loss is increased for the last ~20% of the training epochs (from `--start_stage_two` epochs). This setting usually helps lower the energy errors. - -The precision can be changed using the keyword `--default_dtype`, the default is `float64` but `float32` gives a significant speed-up (usually a factor of x2 in training). - -The keywords `--batch_size` and `--max_num_epochs` should be adapted based on the size of the training set. The batch size should be increased when the number of training data increases, and the number of epochs should be decreased. An heuristic for initial settings, is to consider the number of gradient update constant to 200 000, which can be computed as $\text{max-num-epochs}*\frac{\text{num-configs-training}}{\text{batch-size}}$. - -The code can handle training set with heterogeneous labels, for example containing both bulk structures with stress and isolated molecules. In this example, to make the code ignore stress on molecules, append to your molecules configuration a `config_stress_weight = 0.0`. - -By default, a figure displaying the progression of loss and RMSEs during training, along with a scatter plot of the model's inferences on the train, validation, and test sets, will be generated in the results folder at the end of training. This can be disabled using `--plot False`. To track these metrics throughout training (excluding inference on the test set), you can enable periodic plotting for the train and validation sets by specifying `--plot_frequency N`, which updates the plots every Nth epoch. - -#### Apple Silicon GPU acceleration - -To use Apple Silicon GPU acceleration make sure to install the latest PyTorch version and specify `--device=mps`. - -#### Multi-GPU training - -For multi-GPU training, use the `--distributed` flag. This will use PyTorch's DistributedDataParallel module to train the model on multiple GPUs. Combine with on-line data loading for large datasets (see below). An example slurm script can be found in `mace/scripts/distributed_example.sbatch`. - -#### YAML configuration - -Option to parse all or some arguments using a YAML is available. For example, to train a model using the arguments above, you can create a YAML file `your_configs.yaml` with the following content: - -```yaml -name: nacl -seed: 2024 -train_file: train.xyz -stage_two: yes -start_stage_two: 1200 -max_num_epochs: 1500 -device: cpu -test_file: test.xyz -E0s: - 41: -1029.2809654211628 - 38: -1484.1187695035828 - 8: -2042.0330099956639 -config_type_weights: - Default: 1.0 - -``` -And append to the command line `--config="your_configs.yaml"`. Any argument specified in the command line will overwrite the one in the YAML file. - -### Evaluation - -To evaluate your MACE model on an XYZ file, run the `mace_eval_configs`: - -```sh -mace_eval_configs \ - --configs="your_configs.xyz" \ - --model="your_model.model" \ - --output="./your_output.xyz" -``` - -## Tutorials - -You can run our [Colab tutorial](https://colab.research.google.com/drive/1D6EtMUjQPey_GkuxUAbPgld6_9ibIa-V?authuser=1#scrollTo=Z10787RE1N8T) to quickly get started with MACE. - -We also have a more detailed Colab tutorials on: - - [Introduction to MACE training and evaluation](https://colab.research.google.com/drive/1ZrTuTvavXiCxTFyjBV4GqlARxgFwYAtX) - - [Introduction to MACE active learning and fine-tuning](https://colab.research.google.com/drive/1oCSVfMhWrqHTeHbKgUSQN9hTKxLzoNyb) - - [MACE theory and code (advanced)](https://colab.research.google.com/drive/1AlfjQETV_jZ0JQnV5M3FGwAM2SGCl2aU) - -## CUDA acceleration with cuEquivariance - -MACE supports CUDA acceleration with the cuEquivariance library. To install the library and use the acceleration, see our documentation at https://mace-docs.readthedocs.io/en/latest/guide/cuda_acceleration.html. - -## On-line data loading for large datasets - -If you have a large dataset that might not fit into the GPU memory it is recommended to preprocess the data on a CPU and use on-line dataloading for training the model. To preprocess your dataset specified as an xyz file run the `preprocess_data.py` script. An example is given here: - -```sh -mkdir processed_data -python ./mace/scripts/preprocess_data.py \ - --train_file="/path/to/train_large.xyz" \ - --valid_fraction=0.05 \ - --test_file="/path/to/test_large.xyz" \ - --atomic_numbers="[1, 6, 7, 8, 9, 15, 16, 17, 35, 53]" \ - --r_max=4.5 \ - --h5_prefix="processed_data/" \ - --compute_statistics \ - --E0s="average" \ - --seed=123 \ -``` - -To see all options and a little description of them run `python ./mace/scripts/preprocess_data.py --help` . The script will create a number of HDF5 files in the `processed_data` folder which can be used for training. There will be one folder for training, one for validation and a separate one for each `config_type` in the test set. To train the model use the `run_train.py` script as follows: - -```sh -python ./mace/scripts/run_train.py \ - --name="MACE_on_big_data" \ - --num_workers=16 \ - --train_file="./processed_data/train.h5" \ - --valid_file="./processed_data/valid.h5" \ - --test_dir="./processed_data" \ - --statistics_file="./processed_data/statistics.json" \ - --model="ScaleShiftMACE" \ - --num_interactions=2 \ - --num_channels=128 \ - --max_L=1 \ - --correlation=3 \ - --batch_size=32 \ - --valid_batch_size=32 \ - --max_num_epochs=100 \ - --stage_two \ - --start_stage_two=60 \ - --ema \ - --ema_decay=0.99 \ - --amsgrad \ - --error_table='PerAtomMAE' \ - --device=cuda \ - --seed=123 \ -``` - -## Weights and Biases for experiment tracking - -If you would like to use MACE with Weights and Biases to log your experiments simply install with - -```sh -pip install ./mace[wandb] -``` - -And specify the necessary keyword arguments (`--wandb`, `--wandb_project`, `--wandb_entity`, `--wandb_name`, `--wandb_log_hypers`) - - -## Pretrained Foundation Models - -We provide a series of pretrained foundation models for various applications. These models can be used directly for inference, or as a starting point for fine-tuning on a new dataset. -Foundation models are a rapidly evolving field. Please look at the `MACE-MP GitHub repository `_ and the `MACE-OFF23 GitHub repository `_ for the latest releases. - -### Latest Recommended Foundation Models - -| Model Name | Elements Covered | Training Dataset | Level of Theory | Target System | Model Size | GitHub Release | Notes | License | -|-------------------|------------------|------------------|-----------------------|----------------------|---------------------|----------------|-------------------------------------------------------|---------| -| MACE-MP-0a | 89 | MPTrj | DFT (PBE+U) | Materials | [small](https://github.com/ACEsuit/mace-mp/releases/download/mace_mp_0/2023-12-10-mace-128-L0_energy_epoch-249.model), [medium](https://github.com/ACEsuit/mace-mp/releases/download/mace_mp_0/2023-12-03-mace-128-L1_epoch-199.model), [large](https://github.com/ACEsuit/mace-mp/releases/download/mace_mp_0/2024-01-07-mace-128-L2_epoch-199.model)| >=v0.3.6 | Initial release of foundation model. | MIT | -| MACE-MP-0b3 | 89 | MPTrj | DFT (PBE+U) | Materials | [medium](https://github.com/ACEsuit/mace-mp/releases/download/mace_mp_0b3/mace-mp-0b3-medium.model)| >=v0.3.10 | Improved high pressure stability and reference energies. | MIT | -| MACE-MPA-0 | 89 | MPTrj + sAlex | DFT (PBE+U) | Materials | [medium-mpa-0](https://github.com/ACEsuit/mace-mp/releases/download/mace_mpa_0/mace-mpa-0-medium.model) | >=v0.3.10 | Improved accuracy for materials, improved high pressure stability. | MIT | -| MACE-OMAT-0 | 89 | OMAT | DFT (PBE+U) VASP 54 | Materials | [medium-omat-0](https://github.com/ACEsuit/mace-mp/releases/download/mace_omat_0/mace-omat-0-medium.model) | >=v0.3.10 | | ASL | -| MACE-OFF23 | 10 | SPICE v1 | DFT (wB97M+D3) | Organic Chemistry | [small](https://github.com/ACEsuit/mace-off/blob/main/mace_off23/MACE-OFF23_small.model), [medium](https://github.com/ACEsuit/mace-off/blob/main/mace_off23/MACE-OFF23_medium.model), [large](https://github.com/ACEsuit/mace-off/blob/main/mace_off23/MACE-OFF23_large.model)| >=v0.3.6 | Initial release covering neutral organic chemistry. | ASL | -| MACE-MATPES-PBE-0 | 89 | MATPES-PBE | DFT (PBE) | Materials | [medium](https://github.com/ACEsuit/mace-foundations/releases/download/mace_matpes_0/MACE-matpes-pbe-omat-ft.model) | >=v0.3.10 | No +U correction. | ASL | -| MACE-MATPES-r2SCAN-0 | 89 | MATPES-r2SCAN | DFT (r2SCAN) | Materials | [medium](https://github.com/ACEsuit/mace-foundations/releases/download/mace_matpes_0/MACE-matpes-r2scan-omat-ft.model) | >=v0.3.10 | Better functional for materials. | ASL | - -### MACE-MP: Materials Project Force Fields - -We have collaborated with the Materials Project (MP) to train a universal MACE potential covering 89 elements on 1.6 M bulk crystals in the [MPTrj dataset](https://figshare.com/articles/dataset/23713842) selected from MP relaxation trajectories. -The models are releaed on GitHub at https://github.com/ACEsuit/mace-mp. -If you use them please cite [our paper](https://arxiv.org/abs/2401.00096) which also contains an large range of example applications and benchmarks. - -> [!CAUTION] -> The MACE-MP models are trained on MPTrj raw DFT energies from VASP outputs, and are not directly comparable to the MP's DFT energies or CHGNet's energies, which have been applied MP2020Compatibility corrections for some transition metal oxides, fluorides (GGA/GGA+U mixing corrections), and 14 anions species (anion corrections). For more details, please refer to the [MP Documentation](https://docs.materialsproject.org/methodology/materials-methodology/thermodynamic-stability/thermodynamic-stability/anion-and-gga-gga+u-mixing) and [MP2020Compatibility.yaml](https://github.com/materialsproject/pymatgen/blob/master/pymatgen/entries/MP2020Compatibility.yaml). - -#### Example usage in ASE -```py -from mace.calculators import mace_mp -from ase import build - -atoms = build.molecule('H2O') -calc = mace_mp(model="medium", dispersion=False, default_dtype="float32", device='cuda') -atoms.calc = calc -print(atoms.get_potential_energy()) -``` - -### MACE-OFF: Transferable Organic Force Fields - -There is a series (small, medium, large) transferable organic force fields. These can be used for the simulation of organic molecules, crystals and molecular liquids, or as a starting point for fine-tuning on a new dataset. The models are released under the [ASL license](https://github.com/gabor1/ASL). -The models are releaed on GitHub at https://github.com/ACEsuit/mace-off. -If you use them please cite [our paper](https://arxiv.org/abs/2312.15211) which also contains detailed benchmarks and example applications. - -#### Example usage in ASE -```py -from mace.calculators import mace_off -from ase import build - -atoms = build.molecule('H2O') -calc = mace_off(model="medium", device='cuda') -atoms.calc = calc -print(atoms.get_potential_energy()) -``` - -### Finetuning foundation models - -To finetune one of the mace-mp-0 foundation model, you can use the `mace_run_train` script with the extra argument `--foundation_model=model_type`. For example to finetune the small model on a new dataset, you can use: - -```sh -mace_run_train \ - --name="MACE" \ - --foundation_model="small" \ - --train_file="train.xyz" \ - --valid_fraction=0.05 \ - --test_file="test.xyz" \ - --energy_weight=1.0 \ - --forces_weight=1.0 \ - --E0s="average" \ - --lr=0.01 \ - --scaling="rms_forces_scaling" \ - --batch_size=2 \ - --max_num_epochs=6 \ - --ema \ - --ema_decay=0.99 \ - --amsgrad \ - --default_dtype="float32" \ - --device=cuda \ - --seed=3 -``` -Other options are "medium" and "large", or the path to a foundation model. -If you want to finetune another model, the model will be loaded from the path provided `--foundation_model=$path_model`, all the hypers will be extracted automatically. - -## Caching - -By default automatically downloaded models, like mace_mp, mace_off and data for fine tuning, end up in `~/.cache/mace`. The path can be changed by using -the environment variable XDG_CACHE_HOME. When set, the new cache path expands to $XDG_CACHE_HOME/.cache/mace - -## Development - -This project uses [pre-commit](https://pre-commit.com/) to execute code formatting and linting on commit. -We also use `black`, `isort`, `pylint`, and `mypy`. -We recommend setting up your development environment by installing the `dev` packages -into your python environment: -```bash -pip install -e ".[dev]" -pre-commit install -``` -The second line will initialise `pre-commit` to automaticaly run code checks on commit. -We have CI set up to check this, but we _highly_ recommend that you run those commands -before you commit (and push) to avoid accidentally committing bad code. - -We are happy to accept pull requests under an [MIT license](https://choosealicense.com/licenses/mit/). Please copy/paste the license text as a comment into your pull request. - -## References - -If you use this code, please cite our papers: - -```bibtex -@inproceedings{Batatia2022mace, - title={{MACE}: Higher Order Equivariant Message Passing Neural Networks for Fast and Accurate Force Fields}, - author={Ilyes Batatia and David Peter Kovacs and Gregor N. C. Simm and Christoph Ortner and Gabor Csanyi}, - booktitle={Advances in Neural Information Processing Systems}, - editor={Alice H. Oh and Alekh Agarwal and Danielle Belgrave and Kyunghyun Cho}, - year={2022}, - url={https://openreview.net/forum?id=YPpSngE-ZU} -} - -@misc{Batatia2022Design, - title = {The Design Space of E(3)-Equivariant Atom-Centered Interatomic Potentials}, - author = {Batatia, Ilyes and Batzner, Simon and Kov{\'a}cs, D{\'a}vid P{\'e}ter and Musaelian, Albert and Simm, Gregor N. C. and Drautz, Ralf and Ortner, Christoph and Kozinsky, Boris and Cs{\'a}nyi, G{\'a}bor}, - year = {2022}, - number = {arXiv:2205.06643}, - eprint = {2205.06643}, - eprinttype = {arxiv}, - doi = {10.48550/arXiv.2205.06643}, - archiveprefix = {arXiv} - } -``` - -## Contact - -If you have any questions, please contact us at ilyes.batatia@ens-paris-saclay.fr. - -For bugs or feature requests, please use [GitHub Issues](https://github.com/ACEsuit/mace/issues). - -## License - -The MACE code is published and distributed under the [MIT License](MIT.md). (Note that some of the models linked above come with different licenses). diff --git a/mace-bench/3rdparty/mace/mace/__init__.py b/mace-bench/3rdparty/mace/mace/__init__.py deleted file mode 100644 index 490c4c01eb79794be90ab73ee32623ac1ca35db2..0000000000000000000000000000000000000000 --- a/mace-bench/3rdparty/mace/mace/__init__.py +++ /dev/null @@ -1,5 +0,0 @@ -import os - -from .__version__ import __version__ - -os.environ["TORCH_FORCE_NO_WEIGHTS_ONLY_LOAD"] = "1" diff --git a/mace-bench/3rdparty/mace/mace/__version__.py b/mace-bench/3rdparty/mace/mace/__version__.py deleted file mode 100644 index 343c940b13c83494dd96428a1d62eb93759c7353..0000000000000000000000000000000000000000 --- a/mace-bench/3rdparty/mace/mace/__version__.py +++ /dev/null @@ -1,3 +0,0 @@ -__version__ = "0.3.13" - -__all__ = ["__version__"] diff --git a/mace-bench/3rdparty/mace/mace/calculators/__init__.py b/mace-bench/3rdparty/mace/mace/calculators/__init__.py deleted file mode 100644 index 8511eb9e327962ff8a464d8c0a7bd52d1bea91b7..0000000000000000000000000000000000000000 --- a/mace-bench/3rdparty/mace/mace/calculators/__init__.py +++ /dev/null @@ -1,11 +0,0 @@ -from .foundations_models import mace_anicc, mace_mp, mace_off -from .lammps_mace import LAMMPS_MACE -from .mace import MACECalculator - -__all__ = [ - "MACECalculator", - "LAMMPS_MACE", - "mace_mp", - "mace_off", - "mace_anicc", -] diff --git a/mace-bench/3rdparty/mace/mace/calculators/foundations_models.py b/mace-bench/3rdparty/mace/mace/calculators/foundations_models.py deleted file mode 100644 index 75e47c1f817e0b480cb8a010c8e387d9b49f66ea..0000000000000000000000000000000000000000 --- a/mace-bench/3rdparty/mace/mace/calculators/foundations_models.py +++ /dev/null @@ -1,339 +0,0 @@ -import os -import urllib.request -from pathlib import Path -from typing import Union - -import torch -from ase import units -from ase.calculators.mixing import SumCalculator - -from .mace import MACECalculator - -module_dir = os.path.dirname(__file__) -local_model_path = os.path.join( - module_dir, "foundations_models/mace-mpa-0-medium.model" -) - - -def download_mace_mp_checkpoint(model: Union[str, Path] = None) -> str: - """ - Downloads or locates the MACE-MP checkpoint file. - - Args: - model (str, optional): Path to the model or size specification. - Defaults to None which uses the medium model. - - Returns: - str: Path to the downloaded (or cached, if previously loaded) checkpoint file. - """ - if model in (None, "medium-mpa-0") and os.path.isfile(local_model_path): - return local_model_path - - urls = { - "small": "https://github.com/ACEsuit/mace-mp/releases/download/mace_mp_0/2023-12-10-mace-128-L0_energy_epoch-249.model", - "medium": "https://github.com/ACEsuit/mace-mp/releases/download/mace_mp_0/2023-12-03-mace-128-L1_epoch-199.model", - "large": "https://github.com/ACEsuit/mace-mp/releases/download/mace_mp_0/MACE_MPtrj_2022.9.model", - "small-0b": "https://github.com/ACEsuit/mace-mp/releases/download/mace_mp_0b/mace_agnesi_small.model", - "medium-0b": "https://github.com/ACEsuit/mace-mp/releases/download/mace_mp_0b/mace_agnesi_medium.model", - "small-0b2": "https://github.com/ACEsuit/mace-mp/releases/download/mace_mp_0b2/mace-small-density-agnesi-stress.model", - "medium-0b2": "https://github.com/ACEsuit/mace-mp/releases/download/mace_mp_0b2/mace-medium-density-agnesi-stress.model", - "large-0b2": "https://github.com/ACEsuit/mace-mp/releases/download/mace_mp_0b2/mace-large-density-agnesi-stress.model", - "medium-0b3": "https://github.com/ACEsuit/mace-mp/releases/download/mace_mp_0b3/mace-mp-0b3-medium.model", - "medium-mpa-0": "https://github.com/ACEsuit/mace-mp/releases/download/mace_mpa_0/mace-mpa-0-medium.model", - "medium-omat-0": "https://github.com/ACEsuit/mace-mp/releases/download/mace_omat_0/mace-omat-0-medium.model", - "mace-matpes-pbe-0": "https://github.com/ACEsuit/mace-foundations/releases/download/mace_matpes_0/MACE-matpes-pbe-omat-ft.model", - "mace-matpes-r2scan-0": "https://github.com/ACEsuit/mace-foundations/releases/download/mace_matpes_0/MACE-matpes-r2scan-omat-ft.model", - } - - checkpoint_url = ( - urls.get(model, urls["medium-mpa-0"]) - if model - in ( - None, - "small", - "medium", - "large", - "small-0b", - "medium-0b", - "small-0b2", - "medium-0b2", - "large-0b2", - "medium-0b3", - "medium-mpa-0", - "medium-omat-0", - ) - else model - ) - - if checkpoint_url == urls["medium-mpa-0"]: - print( - "Using medium MPA-0 model as default MACE-MP model, to use previous (before 3.10) default model please specify 'medium' as model argument" - ) - ASL_checkpoint_urls = { - urls["medium-omat-0"], - urls["mace-matpes-pbe-0"], - urls["mace-matpes-r2scan-0"], - } - if checkpoint_url in ASL_checkpoint_urls: - print( - "Using model under Academic Software License (ASL) license, see https://github.com/gabor1/ASL \n To use this model you accept the terms of the license." - ) - - cache_dir = os.path.expanduser("~/.cache/mace") - checkpoint_url_name = "".join( - c for c in os.path.basename(checkpoint_url) if c.isalnum() or c in "_" - ) - cached_model_path = f"{cache_dir}/{checkpoint_url_name}" - - if not os.path.isfile(cached_model_path): - os.makedirs(cache_dir, exist_ok=True) - print(f"Downloading MACE model from {checkpoint_url!r}") - _, http_msg = urllib.request.urlretrieve(checkpoint_url, cached_model_path) - if "Content-Type: text/html" in http_msg: - raise RuntimeError( - f"Model download failed, please check the URL {checkpoint_url}" - ) - print(f"Cached MACE model to {cached_model_path}") - - return cached_model_path - - -def mace_mp( - model: Union[str, Path] = None, - device: str = "", - default_dtype: str = "float32", - dispersion: bool = False, - damping: str = "bj", # choices: ["zero", "bj", "zerom", "bjm"] - dispersion_xc: str = "pbe", - dispersion_cutoff: float = 40.0 * units.Bohr, - return_raw_model: bool = False, - **kwargs, -) -> MACECalculator: - """ - Constructs a MACECalculator with a pretrained model based on the Materials Project (89 elements). - The model is released under the MIT license. See https://github.com/ACEsuit/mace-mp for all models. - Note: - If you are using this function, please cite the relevant paper for the Materials Project, - any paper associated with the MACE model, and also the following: - - MACE-MP by Ilyes Batatia, Philipp Benner, Yuan Chiang, Alin M. Elena, - Dávid P. Kovács, Janosh Riebesell, et al., 2023, arXiv:2401.00096 - - MACE-Universal by Yuan Chiang, 2023, Hugging Face, Revision e5ebd9b, - DOI: 10.57967/hf/1202, URL: https://huggingface.co/cyrusyc/mace-universal - - Matbench Discovery by Janosh Riebesell, Rhys EA Goodall, Philipp Benner, Yuan Chiang, - Alpha A Lee, Anubhav Jain, Kristin A Persson, 2023, arXiv:2308.14920 - - Args: - model (str, optional): Path to the model. Defaults to None which first checks for - a local model and then downloads the default model from figshare. Specify "small", - "medium" or "large" to download a smaller or larger model from figshare. - device (str, optional): Device to use for the model. Defaults to "cuda" if available. - default_dtype (str, optional): Default dtype for the model. Defaults to "float32". - dispersion (bool, optional): Whether to use D3 dispersion corrections. Defaults to False. - damping (str): The damping function associated with the D3 correction. Defaults to "bj" for D3(BJ). - dispersion_xc (str, optional): Exchange-correlation functional for D3 dispersion corrections. - dispersion_cutoff (float, optional): Cutoff radius in Bohr for D3 dispersion corrections. - return_raw_model (bool, optional): Whether to return the raw model or an ASE calculator. Defaults to False. - **kwargs: Passed to MACECalculator and TorchDFTD3Calculator. - - Returns: - MACECalculator: trained on the MPtrj dataset (unless model otherwise specified). - """ - try: - if model in ( - None, - "small", - "medium", - "large", - "medium-mpa-0", - "small-0b", - "medium-0b", - "small-0b2", - "medium-0b2", - "medium-0b3", - "large-0b2", - "medium-omat-0", - ) or str(model).startswith("https:"): - model_path = download_mace_mp_checkpoint(model) - print(f"Using Materials Project MACE for MACECalculator with {model_path}") - else: - if not Path(model).exists(): - raise FileNotFoundError(f"{model} not found locally") - model_path = model - except Exception as exc: - raise RuntimeError("Model download failed and no local model found") from exc - - device = device or ("cuda" if torch.cuda.is_available() else "cpu") - if default_dtype == "float64": - print( - "Using float64 for MACECalculator, which is slower but more accurate. Recommended for geometry optimization." - ) - if default_dtype == "float32": - print( - "Using float32 for MACECalculator, which is faster but less accurate. Recommended for MD. Use float64 for geometry optimization." - ) - - if return_raw_model: - return torch.load(model_path, map_location=device) - - mace_calc = MACECalculator( - model_paths=model_path, device=device, default_dtype=default_dtype, **kwargs - ) - - if not dispersion: - return mace_calc - - try: - from torch_dftd.torch_dftd3_calculator import TorchDFTD3Calculator - except ImportError as exc: - raise RuntimeError( - "Please install torch-dftd to use dispersion corrections (see https://github.com/pfnet-research/torch-dftd)" - ) from exc - - print("Using TorchDFTD3Calculator for D3 dispersion corrections") - dtype = torch.float32 if default_dtype == "float32" else torch.float64 - d3_calc = TorchDFTD3Calculator( - device=device, - damping=damping, - dtype=dtype, - xc=dispersion_xc, - cutoff=dispersion_cutoff, - **kwargs, - ) - - return SumCalculator([mace_calc, d3_calc]) - - -def mace_off( - model: Union[str, Path] = None, - device: str = "", - default_dtype: str = "float64", - return_raw_model: bool = False, - **kwargs, -) -> MACECalculator: - """ - Constructs a MACECalculator with a pretrained model based on the MACE-OFF23 models. - The model is released under the ASL license. - Note: - If you are using this function, please cite the relevant paper by Kovacs et.al., arXiv:2312.15211 - - Args: - model (str, optional): Path to the model. Defaults to None which first checks for - a local model and then downloads the default medium model from https://github.com/ACEsuit/mace-off. - Specify "small", "medium" or "large" to download a smaller or larger model. - device (str, optional): Device to use for the model. Defaults to "cuda". - default_dtype (str, optional): Default dtype for the model. Defaults to "float64". - return_raw_model (bool, optional): Whether to return the raw model or an ASE calculator. Defaults to False. - **kwargs: Passed to MACECalculator. - - Returns: - MACECalculator: trained on the MACE-OFF23 dataset - """ - try: - if model in (None, "small", "medium", "large") or str(model).startswith( - "https:" - ): - urls = dict( - small="https://github.com/ACEsuit/mace-off/blob/main/mace_off23/MACE-OFF23_small.model?raw=true", - medium="https://github.com/ACEsuit/mace-off/raw/main/mace_off23/MACE-OFF23_medium.model?raw=true", - large="https://github.com/ACEsuit/mace-off/blob/main/mace_off23/MACE-OFF23_large.model?raw=true", - ) - checkpoint_url = ( - urls.get(model, urls["medium"]) - if model in (None, "small", "medium", "large") - else model - ) - cache_dir = os.path.expanduser("~/.cache/mace") - checkpoint_url_name = os.path.basename(checkpoint_url).split("?")[0] - cached_model_path = f"{cache_dir}/{checkpoint_url_name}" - if not os.path.isfile(cached_model_path): - os.makedirs(cache_dir, exist_ok=True) - # download and save to disk - print(f"Downloading MACE model from {checkpoint_url!r}") - print( - "The model is distributed under the Academic Software License (ASL) license, see https://github.com/gabor1/ASL \n To use the model you accept the terms of the license." - ) - print( - "ASL is based on the Gnu Public License, but does not permit commercial use" - ) - urllib.request.urlretrieve(checkpoint_url, cached_model_path) - print(f"Cached MACE model to {cached_model_path}") - model = cached_model_path - msg = f"Using MACE-OFF23 MODEL for MACECalculator with {model}" - print(msg) - else: - if not Path(model).exists(): - raise FileNotFoundError(f"{model} not found locally") - except Exception as exc: - raise RuntimeError("Model download failed and no local model found") from exc - - device = device or ("cuda" if torch.cuda.is_available() else "cpu") - - if return_raw_model: - return torch.load(model, map_location=device) - - if default_dtype == "float64": - print( - "Using float64 for MACECalculator, which is slower but more accurate. Recommended for geometry optimization." - ) - if default_dtype == "float32": - print( - "Using float32 for MACECalculator, which is faster but less accurate. Recommended for MD. Use float64 for geometry optimization." - ) - mace_calc = MACECalculator( - model_paths=model, device=device, default_dtype=default_dtype, **kwargs - ) - return mace_calc - - -def mace_anicc( - device: str = "cuda", - model_path: str = None, - return_raw_model: bool = False, -) -> MACECalculator: - """ - Constructs a MACECalculator with a pretrained model based on the ANI (H, C, N, O). - The model is released under the MIT license. - Note: - If you are using this function, please cite the relevant paper associated with the MACE model, ANI dataset, and also the following: - - "Evaluation of the MACE Force Field Architecture by Dávid Péter Kovács, Ilyes Batatia, Eszter Sára Arany, and Gábor Csányi, The Journal of Chemical Physics, 2023, URL: https://doi.org/10.1063/5.0155322 - """ - if model_path is None: - model_path = os.path.join( - module_dir, "foundations_models/ani500k_large_CC.model" - ) - print( - "Using ANI couple cluster model for MACECalculator, see https://doi.org/10.1063/5.0155322" - ) - - if not os.path.exists(model_path): - model_dir = os.path.dirname(model_path) - os.makedirs(model_dir, exist_ok=True) - - # Download the model - print(f"Model not found at {model_path}. Downloading...") - model_url = "https://github.com/ACEsuit/mace/raw/main/mace/calculators/foundations_models/ani500k_large_CC.model" - - try: - - def report_progress(block_num, block_size, total_size): - downloaded = block_num * block_size - percent = min(100, downloaded * 100 / total_size) - if total_size > 0: - print( - f"\rDownloading model: {percent:.1f}% ({downloaded / 1024 / 1024:.1f} MB / {total_size / 1024 / 1024:.1f} MB)", - end="", - ) - - urllib.request.urlretrieve( - model_url, model_path, reporthook=report_progress - ) - print("\nDownload complete!") - - except Exception as e: - raise RuntimeError(f"Failed to download model: {e}") from e - - if return_raw_model: - return torch.load(model_path, map_location=device) - return MACECalculator( - model_paths=model_path, device=device, default_dtype="float64" - ) diff --git a/mace-bench/3rdparty/mace/mace/calculators/lammps_mace.py b/mace-bench/3rdparty/mace/mace/calculators/lammps_mace.py deleted file mode 100644 index 4211c37f6a5001d55510dbb110fa7d795ca1e57c..0000000000000000000000000000000000000000 --- a/mace-bench/3rdparty/mace/mace/calculators/lammps_mace.py +++ /dev/null @@ -1,105 +0,0 @@ -from typing import Dict, List, Optional - -import torch -from e3nn.util.jit import compile_mode - -from mace.tools.scatter import scatter_sum - - -@compile_mode("script") -class LAMMPS_MACE(torch.nn.Module): - def __init__(self, model, **kwargs): - super().__init__() - self.model = model - self.register_buffer("atomic_numbers", model.atomic_numbers) - self.register_buffer("r_max", model.r_max) - self.register_buffer("num_interactions", model.num_interactions) - if not hasattr(model, "heads"): - model.heads = [None] - self.register_buffer( - "head", - torch.tensor( - self.model.heads.index(kwargs.get("head", self.model.heads[-1])), - dtype=torch.long, - ).unsqueeze(0), - ) - - for param in self.model.parameters(): - param.requires_grad = False - - def forward( - self, - data: Dict[str, torch.Tensor], - local_or_ghost: torch.Tensor, - compute_virials: bool = False, - ) -> Dict[str, Optional[torch.Tensor]]: - num_graphs = data["ptr"].numel() - 1 - compute_displacement = False - if compute_virials: - compute_displacement = True - data["head"] = self.head - out = self.model( - data, - training=False, - compute_force=False, - compute_virials=False, - compute_stress=False, - compute_displacement=compute_displacement, - ) - node_energy = out["node_energy"] - if node_energy is None: - return { - "total_energy_local": None, - "node_energy": None, - "forces": None, - "virials": None, - } - positions = data["positions"] - displacement = out["displacement"] - forces: Optional[torch.Tensor] = torch.zeros_like(positions) - virials: Optional[torch.Tensor] = torch.zeros_like(data["cell"]) - # accumulate energies of local atoms - node_energy_local = node_energy * local_or_ghost - total_energy_local = scatter_sum( - src=node_energy_local, index=data["batch"], dim=-1, dim_size=num_graphs - ) - # compute partial forces and (possibly) partial virials - grad_outputs: List[Optional[torch.Tensor]] = [ - torch.ones_like(total_energy_local) - ] - if compute_virials and displacement is not None: - forces, virials = torch.autograd.grad( - outputs=[total_energy_local], - inputs=[positions, displacement], - grad_outputs=grad_outputs, - retain_graph=False, - create_graph=False, - allow_unused=True, - ) - if forces is not None: - forces = -1 * forces - else: - forces = torch.zeros_like(positions) - if virials is not None: - virials = -1 * virials - else: - virials = torch.zeros_like(displacement) - else: - forces = torch.autograd.grad( - outputs=[total_energy_local], - inputs=[positions], - grad_outputs=grad_outputs, - retain_graph=False, - create_graph=False, - allow_unused=True, - )[0] - if forces is not None: - forces = -1 * forces - else: - forces = torch.zeros_like(positions) - return { - "total_energy_local": total_energy_local, - "node_energy": node_energy, - "forces": forces, - "virials": virials, - } diff --git a/mace-bench/3rdparty/mace/mace/calculators/lammps_mliap_mace.py b/mace-bench/3rdparty/mace/mace/calculators/lammps_mliap_mace.py deleted file mode 100644 index f40e9b813bb8a08b70f0dc0a405d1e2942f87c7d..0000000000000000000000000000000000000000 --- a/mace-bench/3rdparty/mace/mace/calculators/lammps_mliap_mace.py +++ /dev/null @@ -1,214 +0,0 @@ -import logging -import os -import sys -import time -from contextlib import contextmanager -from typing import Dict, Tuple - -import torch -from ase.data import chemical_symbols -from e3nn.util.jit import compile_mode - -try: - from lammps.mliap.mliap_unified_abc import MLIAPUnified -except ImportError: - - class MLIAPUnified: - def __init__(self): - pass - - -class MACELammpsConfig: - """Configuration settings for MACE-LAMMPS integration.""" - - def __init__(self): - self.debug_time = self._get_env_bool("MACE_TIME", False) - self.debug_profile = self._get_env_bool("MACE_PROFILE", False) - self.profile_start_step = int(os.environ.get("MACE_PROFILE_START", "5")) - self.profile_end_step = int(os.environ.get("MACE_PROFILE_END", "10")) - self.allow_cpu = self._get_env_bool("MACE_ALLOW_CPU", False) - self.force_cpu = self._get_env_bool("MACE_FORCE_CPU", False) - - @staticmethod - def _get_env_bool(var_name: str, default: bool) -> bool: - return os.environ.get(var_name, str(default)).lower() in ( - "true", - "1", - "t", - "yes", - ) - - -@contextmanager -def timer(name: str, enabled: bool = True): - """Context manager for timing code blocks.""" - if not enabled: - yield - return - - start = time.perf_counter() - try: - yield - finally: - elapsed = time.perf_counter() - start - logging.info(f"Timer - {name}: {elapsed*1000:.3f} ms") - - -@compile_mode("script") -class MACEEdgeForcesWrapper(torch.nn.Module): - """Wrapper that adds per-pair force computation to a MACE model.""" - - def __init__(self, model: torch.nn.Module, **kwargs): - super().__init__() - self.model = model - self.register_buffer("atomic_numbers", model.atomic_numbers) - self.register_buffer("r_max", model.r_max) - self.register_buffer("num_interactions", model.num_interactions) - - if not hasattr(model, "heads"): - model.heads = ["Default"] - - head_name = kwargs.get("head", model.heads[-1]) - head_idx = model.heads.index(head_name) - self.register_buffer("head", torch.tensor([head_idx], dtype=torch.long)) - - for p in self.model.parameters(): - p.requires_grad = False - - def forward( - self, data: Dict[str, torch.Tensor] - ) -> Tuple[torch.Tensor, torch.Tensor, torch.Tensor]: - """Compute energies and per-pair forces.""" - data["head"] = self.head - - out = self.model( - data, - training=False, - compute_force=False, - compute_virials=False, - compute_stress=False, - compute_displacement=False, - compute_edge_forces=True, - lammps_mliap=True, - ) - - node_energy = out["node_energy"] - pair_forces = out["edge_forces"] - total_energy = out["energy"][0] - - if pair_forces is None: - pair_forces = torch.zeros_like(data["vectors"]) - - return total_energy, node_energy, pair_forces - - -class LAMMPS_MLIAP_MACE(MLIAPUnified): - """MACE integration for LAMMPS using the MLIAP interface.""" - - def __init__(self, model, **kwargs): - super().__init__() - self.config = MACELammpsConfig() - self.model = MACEEdgeForcesWrapper(model, **kwargs) - self.element_types = [chemical_symbols[s] for s in model.atomic_numbers] - self.num_species = len(self.element_types) - self.rcutfac = 0.5 * float(model.r_max) - self.ndescriptors = 1 - self.nparams = 1 - self.dtype = model.r_max.dtype - self.device = "cpu" - self.initialized = False - self.step = 0 - - def _initialize_device(self, data): - using_kokkos = "kokkos" in data.__class__.__module__.lower() - - if using_kokkos and not self.config.force_cpu: - device = torch.as_tensor(data.elems).device - if device.type == "cpu" and not self.config.allow_cpu: - raise ValueError( - "GPU requested but tensor is on CPU. Set MACE_ALLOW_CPU=true to allow CPU computation." - ) - else: - device = torch.device("cpu") - - self.device = device - self.model = self.model.to(device) - logging.info(f"MACE model initialized on device: {device}") - self.initialized = True - - def compute_forces(self, data): - natoms = data.nlocal - ntotal = data.ntotal - nghosts = ntotal - natoms - npairs = data.npairs - species = torch.as_tensor(data.elems, dtype=torch.int64) - - if not self.initialized: - self._initialize_device(data) - - self.step += 1 - self._manage_profiling() - - if natoms == 0 or npairs <= 1: - return - - with timer("total_step", enabled=self.config.debug_time): - with timer("prepare_batch", enabled=self.config.debug_time): - batch = self._prepare_batch(data, natoms, nghosts, species) - - with timer("model_forward", enabled=self.config.debug_time): - _, atom_energies, pair_forces = self.model(batch) - - if self.device.type != "cpu": - torch.cuda.synchronize() - - with timer("update_lammps", enabled=self.config.debug_time): - self._update_lammps_data(data, atom_energies, pair_forces, natoms) - - def _prepare_batch(self, data, natoms, nghosts, species): - """Prepare the input batch for the MACE model.""" - return { - "vectors": torch.as_tensor(data.rij).to(self.dtype).to(self.device), - "node_attrs": torch.nn.functional.one_hot( - species.to(self.device), num_classes=self.num_species - ).to(self.dtype), - "edge_index": torch.stack( - [ - torch.as_tensor(data.pair_j, dtype=torch.int64).to(self.device), - torch.as_tensor(data.pair_i, dtype=torch.int64).to(self.device), - ], - dim=0, - ), - "batch": torch.zeros(natoms, dtype=torch.int64, device=self.device), - "lammps_class": data, - "natoms": (natoms, nghosts), - } - - def _update_lammps_data(self, data, atom_energies, pair_forces, natoms): - """Update LAMMPS data structures with computed energies and forces.""" - if self.dtype == torch.float32: - pair_forces = pair_forces.double() - eatoms = torch.as_tensor(data.eatoms) - eatoms.copy_(atom_energies[:natoms]) - data.energy = torch.sum(atom_energies[:natoms]) - data.update_pair_forces_gpu(pair_forces) - - def _manage_profiling(self): - if not self.config.debug_profile: - return - - if self.step == self.config.profile_start_step: - logging.info(f"Starting CUDA profiler at step {self.step}") - torch.cuda.profiler.start() - - if self.step == self.config.profile_end_step: - logging.info(f"Stopping CUDA profiler at step {self.step}") - torch.cuda.profiler.stop() - logging.info("Profiling complete. Exiting.") - sys.exit() - - def compute_descriptors(self, data): - pass - - def compute_gradients(self, data): - pass diff --git a/mace-bench/3rdparty/mace/mace/calculators/mace.py b/mace-bench/3rdparty/mace/mace/calculators/mace.py deleted file mode 100644 index 794065b72adc6725d591821861c3c022247ceb5e..0000000000000000000000000000000000000000 --- a/mace-bench/3rdparty/mace/mace/calculators/mace.py +++ /dev/null @@ -1,705 +0,0 @@ -########################################################################################### -# The ASE Calculator for MACE -# Authors: Ilyes Batatia, David Kovacs -# This program is distributed under the MIT License (see MIT.md) -########################################################################################### - -import logging - -# pylint: disable=wrong-import-position -import os -from glob import glob -from pathlib import Path -from typing import List, Union - -os.environ["TORCH_FORCE_NO_WEIGHTS_ONLY_LOAD"] = "1" - -import numpy as np -import torch -from ase.calculators.calculator import Calculator, all_changes -from ase.stress import full_3x3_to_voigt_6_stress -from e3nn import o3 - -from mace import data -from mace.cli.convert_e3nn_cueq import run as run_e3nn_to_cueq -from mace.modules.utils import extract_invariant -from mace.tools import torch_geometric, torch_tools, utils -from mace.tools.compile import prepare -from mace.tools.scripts_utils import extract_model -import random -from mace.tools.torch_geometric.batch import Batch - -from mace.tools import ( - atomic_numbers_to_indices, - to_one_hot, -) - -import time - - -def get_model_dtype(model: torch.nn.Module) -> torch.dtype: - """Get the dtype of the model""" - mode_dtype = next(model.parameters()).dtype - if mode_dtype == torch.float64: - return "float64" - if mode_dtype == torch.float32: - return "float32" - raise ValueError(f"Unknown dtype {mode_dtype}") - - -class MACECalculator(Calculator): - """MACE ASE Calculator - args: - model_paths: str, path to model or models if a committee is produced - to make a committee use a wild card notation like mace_*.model - device: str, device to run on (cuda or cpu) - energy_units_to_eV: float, conversion factor from model energy units to eV - length_units_to_A: float, conversion factor from model length units to Angstroms - default_dtype: str, default dtype of model - charges_key: str, Array field of atoms object where atomic charges are stored - model_type: str, type of model to load - Options: [MACE, DipoleMACE, EnergyDipoleMACE] - - Dipoles are returned in units of Debye - """ - - def __init__( - self, - model_paths: Union[list, str, None] = None, - models: Union[List[torch.nn.Module], torch.nn.Module, None] = None, - device: str = "cpu", - energy_units_to_eV: float = 1.0, - length_units_to_A: float = 1.0, - default_dtype="", - charges_key="Qs", - model_type="MACE", - compile_mode=None, - fullgraph=True, - enable_cueq=False, - **kwargs, - ): - Calculator.__init__(self, **kwargs) - self.device = device - self.dtype=None - if enable_cueq: - assert model_type == "MACE", "CuEq only supports MACE models" - compile_mode = None - if "model_path" in kwargs: - deprecation_message = ( - "'model_path' argument is deprecated, please use 'model_paths'" - ) - if model_paths is None: - logging.warning(f"{deprecation_message} in the future.") - model_paths = kwargs["model_path"] - else: - raise ValueError( - f"both 'model_path' and 'model_paths' given, {deprecation_message} only." - ) - - if (model_paths is None) == (models is None): - raise ValueError( - "Exactly one of 'model_paths' or 'models' must be provided" - ) - - self.results = {} - - self.model_type = model_type - self.compute_atomic_stresses = False - - if model_type == "MACE": - self.implemented_properties = [ - "energy", - "free_energy", - "node_energy", - "forces", - "stress", - ] - if kwargs.get("compute_atomic_stresses", False): - self.implemented_properties.extend(["stresses", "virials"]) - self.compute_atomic_stresses = True - elif model_type == "DipoleMACE": - self.implemented_properties = ["dipole"] - elif model_type == "EnergyDipoleMACE": - self.implemented_properties = [ - "energy", - "free_energy", - "node_energy", - "forces", - "stress", - "dipole", - ] - else: - raise ValueError( - f"Give a valid model_type: [MACE, DipoleMACE, EnergyDipoleMACE], {model_type} not supported" - ) - - if model_paths is not None: - if isinstance(model_paths, str): - # Find all models that satisfy the wildcard (e.g. mace_model_*.pt) - model_paths_glob = glob(model_paths) - - if len(model_paths_glob) == 0: - raise ValueError(f"Couldn't find MACE model files: {model_paths}") - - model_paths = model_paths_glob - elif isinstance(model_paths, Path): - model_paths = [model_paths] - - if len(model_paths) == 0: - raise ValueError("No mace file names supplied") - self.num_models = len(model_paths) - - # Load models from files - self.models = [ - torch.load(f=model_path, map_location=device) - for model_path in model_paths - ] - - elif models is not None: - if not isinstance(models, list): - models = [models] - - if len(models) == 0: - raise ValueError("No models supplied") - - self.models = models - self.num_models = len(models) - - if self.num_models > 1: - print(f"Running committee mace with {self.num_models} models") - - if model_type in ["MACE", "EnergyDipoleMACE"]: - self.implemented_properties.extend( - ["energies", "energy_var", "forces_comm", "stress_var"] - ) - elif model_type == "DipoleMACE": - self.implemented_properties.extend(["dipole_var"]) - - if compile_mode is not None: - print(f"Torch compile is enabled with mode: {compile_mode}") - self.models = [ - torch.compile( - prepare(extract_model)(model=model, map_location=device), - mode=compile_mode, - fullgraph=fullgraph, - ) - for model in self.models - ] - self.use_compile = True - else: - self.use_compile = False - - # Ensure all models are on the same device - for model in self.models: - model.to(device) - - r_maxs = [model.r_max.cpu() for model in self.models] - r_maxs = np.array(r_maxs) - if not np.all(r_maxs == r_maxs[0]): - raise ValueError(f"committee r_max are not all the same {' '.join(r_maxs)}") - self.r_max = float(r_maxs[0]) - - self.device = torch_tools.init_device(device) - self.energy_units_to_eV = energy_units_to_eV - self.length_units_to_A = length_units_to_A - self.z_table = utils.AtomicNumberTable( - [int(z) for z in self.models[0].atomic_numbers] - ) - self.charges_key = charges_key - - try: - self.available_heads: List[str] = self.models[0].heads # type: ignore - except AttributeError: - self.available_heads = ["Default"] - kwarg_head = kwargs.get("head", None) - if kwarg_head is not None: - self.head = kwarg_head - else: - self.head = [head for head in self.available_heads if head.lower() == "default"] - if len(self.head) == 0: - raise ValueError( - "Head keyword was not provided, and no head in the model is 'default'. " - "Please provide a head keyword to specify the head you want to use. " - f"Available heads are: {self.available_heads}" - ) - self.head = self.head[0] - - print("Using head", self.head, "out of", self.available_heads) - - model_dtype = get_model_dtype(self.models[0]) - if default_dtype == "": - print( - f"No dtype selected, switching to {model_dtype} to match model dtype." - ) - default_dtype = model_dtype - if model_dtype != default_dtype: - print( - f"Default dtype {default_dtype} does not match model dtype {model_dtype}, converting models to {default_dtype}." - ) - if default_dtype == "float64": - self.models = [model.double() for model in self.models] - elif default_dtype == "float32": - self.models = [model.float() for model in self.models] - torch_tools.set_default_dtype(default_dtype) - if enable_cueq: - print("Converting models to CuEq for acceleration") - self.models = [ - run_e3nn_to_cueq(model, device=device).to(device) - for model in self.models - ] - for model in self.models: - for param in model.parameters(): - param.requires_grad = False - - self.dtype = torch.float64 if default_dtype == "float64" else torch.float32 - - self.model_time = 0.0 - self.calc_time = 0.0 - - def _create_result_tensors( - self, model_type: str, num_models: int, num_atoms: int - ) -> dict: - """ - Create tensors to store the results of the committee - :param model_type: str, type of model to load - Options: [MACE, DipoleMACE, EnergyDipoleMACE] - :param num_models: int, number of models in the committee - :return: tuple of torch tensors - """ - dict_of_tensors = {} - if model_type in ["MACE", "EnergyDipoleMACE"]: - energies = torch.zeros(num_models, device=self.device) - node_energy = torch.zeros(num_models, num_atoms, device=self.device) - forces = torch.zeros(num_models, num_atoms, 3, device=self.device) - stress = torch.zeros(num_models, 3, 3, device=self.device) - dict_of_tensors.update( - { - "energies": energies, - "node_energy": node_energy, - "forces": forces, - "stress": stress, - } - ) - if model_type in ["EnergyDipoleMACE", "DipoleMACE"]: - dipole = torch.zeros(num_models, 3, device=self.device) - dict_of_tensors.update({"dipole": dipole}) - return dict_of_tensors - - def _atoms_to_batch(self, atoms): - keyspec = data.KeySpecification( - info_keys={}, arrays_keys={"charges": self.charges_key} - ) - config = data.config_from_atoms( - atoms, key_specification=keyspec, head_name=self.head - ) - data_loader = torch_geometric.dataloader.DataLoader( - dataset=[ - data.AtomicData.from_config( - config, - z_table=self.z_table, - cutoff=self.r_max, - heads=self.available_heads, - ) - ], - batch_size=1, - shuffle=False, - drop_last=False, - ) - batch = next(iter(data_loader)).to(self.device) - return batch - - def _clone_batch(self, batch): - batch_clone = batch.clone() - if self.use_compile: - batch_clone["node_attrs"].requires_grad_(True) - batch_clone["positions"].requires_grad_(True) - return batch_clone - - # pylint: disable=dangerous-default-value - def calculate(self, atoms=None, properties=None, system_changes=all_changes): - """ - Calculate properties. - :param atoms: ase.Atoms object - :param properties: [str], properties to be computed, used by ASE internally - :param system_changes: [str], system changes since last calculation, used by ASE internally - :return: - """ - # call to base-class to set atoms attribute - calc_start_t = time.perf_counter() - Calculator.calculate(self, atoms) - - batch_base = self._atoms_to_batch(atoms) - - if self.model_type in ["MACE", "EnergyDipoleMACE"]: - batch = self._clone_batch(batch_base) - node_heads = batch["head"][batch["batch"]] - num_atoms_arange = torch.arange(batch["positions"].shape[0]) - node_e0 = self.models[0].atomic_energies_fn(batch["node_attrs"])[ - num_atoms_arange, node_heads - ] - compute_stress = not self.use_compile - else: - compute_stress = False - - ret_tensors = self._create_result_tensors( - self.model_type, self.num_models, len(atoms) - ) - for i, model in enumerate(self.models): - batch = self._clone_batch(batch_base) - # print(f'@@@File: {__file__}, batch.to_dict(): {batch.to_dict()}') - # set_seed(0) - model_start_t = time.perf_counter() - out = model( - batch.to_dict(), - compute_stress=compute_stress, - training=self.use_compile, - compute_edge_forces=self.compute_atomic_stresses, - compute_atomic_stresses=self.compute_atomic_stresses, - ) - model_end_t = time.perf_counter() - self.model_time += (model_end_t - model_start_t) - # print(f'&&& batch.positions: {batch["positions"]}') - # print(f'&&& batch.stress: {batch["stress"]}') - # print(f'compute_stress: {compute_stress}') - # for k,v in batch.to_dict().items(): - # print(f'&&& batch.to_dict(): {k} {v}') - # print("=======") - # print(f'&&& out["forces"]: {out["forces"]}') - # print(f'&&& training: {self.use_compile}') - # print(f'@@@File: {__file__}, out: {out}') - if self.model_type in ["MACE", "EnergyDipoleMACE"]: - ret_tensors["energies"][i] = out["energy"].detach() - ret_tensors["node_energy"][i] = (out["node_energy"] - node_e0).detach() - ret_tensors["forces"][i] = out["forces"].detach() - if out["stress"] is not None: - ret_tensors["stress"][i] = out["stress"].detach() - if self.model_type in ["DipoleMACE", "EnergyDipoleMACE"]: - ret_tensors["dipole"][i] = out["dipole"].detach() - if self.model_type in ["MACE"]: - if out["atomic_stresses"] is not None: - ret_tensors.setdefault("atomic_stresses", []).append( - out["atomic_stresses"].detach() - ) - if out["atomic_virials"] is not None: - ret_tensors.setdefault("atomic_virials", []).append( - out["atomic_virials"].detach() - ) - - self.results = {} - if self.model_type in ["MACE", "EnergyDipoleMACE"]: - self.results["energy"] = ( - torch.mean(ret_tensors["energies"], dim=0).cpu().item() - * self.energy_units_to_eV - ) - self.results["free_energy"] = self.results["energy"] - self.results["node_energy"] = ( - torch.mean(ret_tensors["node_energy"], dim=0).cpu().numpy() - ) - self.results["forces"] = ( - torch.mean(ret_tensors["forces"], dim=0).cpu().numpy() - * self.energy_units_to_eV - / self.length_units_to_A - ) - if self.num_models > 1: - self.results["energies"] = ( - ret_tensors["energies"].cpu().numpy() * self.energy_units_to_eV - ) - self.results["energy_var"] = ( - torch.var(ret_tensors["energies"], dim=0, unbiased=False) - .cpu() - .item() - * self.energy_units_to_eV - ) - self.results["forces_comm"] = ( - ret_tensors["forces"].cpu().numpy() - * self.energy_units_to_eV - / self.length_units_to_A - ) - if out["stress"] is not None: - self.results["stress"] = full_3x3_to_voigt_6_stress( - torch.mean(ret_tensors["stress"], dim=0).cpu().numpy() - * self.energy_units_to_eV - / self.length_units_to_A**3 - ) - if self.num_models > 1: - self.results["stress_var"] = full_3x3_to_voigt_6_stress( - torch.var(ret_tensors["stress"], dim=0, unbiased=False) - .cpu() - .numpy() - * self.energy_units_to_eV - / self.length_units_to_A**3 - ) - if "atomic_stresses" in ret_tensors: - self.results["stresses"] = ( - torch.mean(torch.stack(ret_tensors["atomic_stresses"]), dim=0) - .cpu() - .numpy() - * self.energy_units_to_eV - / self.length_units_to_A**3 - ) - if "atomic_virials" in ret_tensors: - self.results["virials"] = ( - torch.mean(torch.stack(ret_tensors["atomic_virials"]), dim=0) - .cpu() - .numpy() - * self.energy_units_to_eV - ) - if self.model_type in ["DipoleMACE", "EnergyDipoleMACE"]: - self.results["dipole"] = ( - torch.mean(ret_tensors["dipole"], dim=0).cpu().numpy() - ) - if self.num_models > 1: - self.results["dipole_var"] = ( - torch.var(ret_tensors["dipole"], dim=0, unbiased=False) - .cpu() - .numpy() - ) - - calc_end_t = time.perf_counter() - self.calc_time += (calc_end_t - calc_start_t) - - def get_hessian(self, atoms=None): - if atoms is None and self.atoms is None: - raise ValueError("atoms not set") - if atoms is None: - atoms = self.atoms - if self.model_type != "MACE": - raise NotImplementedError("Only implemented for MACE models") - batch = self._atoms_to_batch(atoms) - hessians = [ - model( - self._clone_batch(batch).to_dict(), - compute_hessian=True, - compute_stress=False, - training=self.use_compile, - )["hessian"] - for model in self.models - ] - hessians = [hessian.detach().cpu().numpy() for hessian in hessians] - if self.num_models == 1: - return hessians[0] - return hessians - - def get_descriptors(self, atoms=None, invariants_only=True, num_layers=-1): - """Extracts the descriptors from MACE model. - :param atoms: ase.Atoms object - :param invariants_only: bool, if True only the invariant descriptors are returned - :param num_layers: int, number of layers to extract descriptors from, if -1 all layers are used - :return: np.ndarray (num_atoms, num_interactions, invariant_features) of invariant descriptors if num_models is 1 or list[np.ndarray] otherwise - """ - if atoms is None and self.atoms is None: - raise ValueError("atoms not set") - if atoms is None: - atoms = self.atoms - if self.model_type != "MACE": - raise NotImplementedError("Only implemented for MACE models") - num_interactions = int(self.models[0].num_interactions) - if num_layers == -1: - num_layers = num_interactions - batch = self._atoms_to_batch(atoms) - descriptors = [model(batch.to_dict())["node_feats"] for model in self.models] - - irreps_out = o3.Irreps(str(self.models[0].products[0].linear.irreps_out)) - l_max = irreps_out.lmax - num_invariant_features = irreps_out.dim // (l_max + 1) ** 2 - per_layer_features = [irreps_out.dim for _ in range(num_interactions)] - per_layer_features[-1] = ( - num_invariant_features # Equivariant features not created for the last layer - ) - - if invariants_only: - descriptors = [ - extract_invariant( - descriptor, - num_layers=num_layers, - num_features=num_invariant_features, - l_max=l_max, - ) - for descriptor in descriptors - ] - to_keep = np.sum(per_layer_features[:num_layers]) - descriptors = [ - descriptor[:, :to_keep].detach().cpu().numpy() for descriptor in descriptors - ] - - if self.num_models == 1: - return descriptors[0] - return descriptors - - - def predict(self, atoms_list, compute_stress=False): - predictions = {'energy': [], 'forces': []} - - configs = [data.config_from_atoms(atoms, charges_key=self.charges_key) for atoms in atoms_list] - data_loader = torch_geometric.dataloader.DataLoader( - dataset=[ - data.AtomicData.from_config( - config, z_table=self.z_table, cutoff=self.r_max, heads=self.heads - ) - for config in configs - ], - batch_size=len(atoms_list), - shuffle=False, - drop_last=False, - ) - - # get the first batch of data_loader - batch_base = next(iter(data_loader)).to(self.device) - - # calculate node_e0 - # batch = self._clone_batch(batch_base) - # node_heads = batch["head"][batch["batch"]] - # num_atoms_arange = torch.arange(batch["positions"].shape[0]) - # node_e0 = self.models[0].atomic_energies_fn(batch["node_attrs"])[ - # num_atoms_arange, node_heads - # ] - - # set_seed(0) - out = self.models[0]( - batch_base.to_dict(), - compute_stress=compute_stress, # TODO: DO WE NEED TO COMPUTE STRESS? - training=self.use_compile, - ) - # print(f'&&& batch.positions: {batch["positions"]}') - # print(f'&&& batch.stress: {batch["stress"]}') - # print(f'&&& batch.to_dict(): {k} {v}') - # print("=======") - # print(f'&&& out["forces"]: {out["forces"]}') - # print(f'&&& training: {self.use_compile}') - predictions["energy"] = out["energy"].unsqueeze(-1).detach() - predictions["forces"] = out["forces"].detach() - if compute_stress: - predictions["stress"] = out["stress"].detach() - - # print(f'&&& predictions["forces"] in predict: {predictions["forces"]}') - - return predictions - - def fast_predict(self, gbatch, compute_stress=False): - gbatch.pos = gbatch.pos.to(self.dtype) - gbatch.cell = gbatch.cell.to(self.dtype) - - predictions = {'energy': [], 'forces': []} - batch_base = self.convert_batch(gbatch) - out = self.models[0]( - batch_base.to_dict(), - compute_stress=compute_stress, - training=self.use_compile, - ) - predictions["energy"] = out["energy"].unsqueeze(-1).detach().to(torch.float64) - predictions["forces"] = out["forces"].detach().to(torch.float64) - if compute_stress: - predictions["stress"] = out["stress"].detach().to(torch.float64) - - return predictions - - - def convert_batch(self, gbatch): - from batchopt import radius_graph_pbc_cuda - # edge_indices, cell_offsets, num_neighbors = radius_graph_pbc_mem_effi( - # from batchopt.pbc_graph_legacy import radius_graph_pbc - # edge_indices, cell_offsets, num_neighbors = radius_graph_pbc( - edge_indices, cell_offsets, num_neighbors = radius_graph_pbc_cuda( - gbatch, - radius=4.5, - max_num_neighbors_threshold=float('inf'), - pbc=[True, True, True], - dtype=self.dtype - ) - - tmp = edge_indices[0].clone() - edge_indices[0] = edge_indices[1] - edge_indices[1] = tmp - - # Create a one-hot matrix with number of columns equal to max atomic number + 1 - indices = atomic_numbers_to_indices(gbatch["atomic_numbers"].to("cpu"), z_table=self.z_table) - one_hot = to_one_hot( - torch.tensor(indices, dtype=torch.long).unsqueeze(-1), - num_classes=len(self.z_table), - ).to(self.device) - - cbatch = Batch( - positions = gbatch["pos"].clone(), - cell = gbatch["cell"].view(-1, 3), - batch = gbatch["batch"], - ptr = gbatch["ptr"], - edge_index = edge_indices, - unit_shifts = cell_offsets, - node_attrs = one_hot, - ) - - return cbatch - - - def predict_debug(self, atoms_list, gbatch, compute_stress=False): - predictions = {'energy': [], 'forces': []} - - configs = [data.config_from_atoms(atoms, charges_key=self.charges_key) for atoms in atoms_list] - data_loader = torch_geometric.dataloader.DataLoader( - dataset=[ - data.AtomicData.from_config( - config, z_table=self.z_table, cutoff=self.r_max, heads=self.heads - ) - for config in configs - ], - batch_size=len(atoms_list), - shuffle=False, - drop_last=False, - ) - - # get the first batch of data_loader - # batch_base = next(iter(data_loader)).to(self.device) - batch_base_tmp = next(iter(data_loader)).to(self.device) - batch2 = self.convert_batch(gbatch) - batch_base = Batch( - # positions = batch_base_tmp["positions"], - positions = batch2["positions"], - # node_attrs = batch_base_tmp["node_attrs"], - node_attrs = batch2["node_attrs"], - # cell = batch_base_tmp["cell"], - cell = batch2["cell"], - edge_index = batch2["edge_index"], - unit_shifts = batch2["unit_shifts"], - # batch = batch_base_tmp["batch"], - batch = batch2["batch"], - # ptr = batch_base_tmp["ptr"], - ptr = batch2["ptr"], - ) - - torch.set_printoptions(threshold=float('inf')) - - # print(f'batch2["edge_index"]: {batch2["edge_index"]}') - # print(f'batch2["unit_shifts"]: {batch2["unit_shifts"]}') - # print(f'batch_base_tmp["edge_index"]: {batch_base_tmp["edge_index"]}') - # print(f'batch_base_tmp["unit_shifts"]: {batch_base_tmp["unit_shifts"]}') - - # calculate node_e0 - # batch = self._clone_batch(batch_base) - # node_heads = batch["head"][batch["batch"]] - # num_atoms_arange = torch.arange(batch["positions"].shape[0]) - # node_e0 = self.models[0].atomic_energies_fn(batch["node_attrs"])[ - # num_atoms_arange, node_heads - # ] - - # set_seed(0) - out = self.models[0]( - batch_base.to_dict(), - compute_stress=compute_stress, # TODO: DO WE NEED TO COMPUTE STRESS? - training=self.use_compile, - ) - # print(f'&&& batch.positions: {batch["positions"]}') - # print(f'&&& batch.cell: {batch["cell"]}') - # print(f'&&& batch.stress: {batch["stress"]}') - # for k,v in batch.to_dict().items(): - # print(f'&&& batch.to_dict(): {k} {v}') - # print("=======") - # print(f'&&& out["forces"]: {out["forces"]}') - # print(f'&&& training: {self.use_compile}') - predictions["energy"] = out["energy"].unsqueeze(-1).detach() - predictions["forces"] = out["forces"].detach() - if compute_stress: - predictions["stress"] = out["stress"].detach() - - # print(f'&&& predictions["forces"] in predict: {predictions["forces"]}') - - return predictions \ No newline at end of file diff --git a/mace-bench/3rdparty/mace/mace/cli/__init__.py b/mace-bench/3rdparty/mace/mace/cli/__init__.py deleted file mode 100644 index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000 diff --git a/mace-bench/3rdparty/mace/mace/cli/active_learning_md.py b/mace-bench/3rdparty/mace/mace/cli/active_learning_md.py deleted file mode 100644 index 9cf4f4a8817bccda23bc411dee3b9fe809681ac5..0000000000000000000000000000000000000000 --- a/mace-bench/3rdparty/mace/mace/cli/active_learning_md.py +++ /dev/null @@ -1,193 +0,0 @@ -"""Demonstrates active learning molecular dynamics with constant temperature.""" - -import argparse -import os -import time - -import ase.io -import numpy as np -from ase import units -from ase.md.langevin import Langevin -from ase.md.velocitydistribution import MaxwellBoltzmannDistribution - -from mace.calculators.mace import MACECalculator - - -def parse_args() -> argparse.Namespace: - parser = argparse.ArgumentParser( - formatter_class=argparse.ArgumentDefaultsHelpFormatter, - ) - parser.add_argument("--config", help="path to XYZ configurations", required=True) - parser.add_argument( - "--config_index", help="index of configuration", type=int, default=-1 - ) - parser.add_argument( - "--error_threshold", help="error threshold", type=float, default=0.1 - ) - parser.add_argument("--temperature_K", help="temperature", type=float, default=300) - parser.add_argument("--friction", help="friction", type=float, default=0.01) - parser.add_argument("--timestep", help="timestep", type=float, default=1) - parser.add_argument("--nsteps", help="number of steps", type=int, default=1000) - parser.add_argument( - "--nprint", help="number of steps between prints", type=int, default=10 - ) - parser.add_argument( - "--nsave", help="number of steps between saves", type=int, default=10 - ) - parser.add_argument( - "--ncheckerror", help="number of steps between saves", type=int, default=10 - ) - - parser.add_argument( - "--model", - help="path to model. Use wildcards to add multiple models as committee eg " - "(`mace_*.model` to load mace_1.model, mace_2.model) ", - required=True, - ) - parser.add_argument("--output", help="output path", required=True) - parser.add_argument( - "--device", - help="select device", - type=str, - choices=["cpu", "cuda"], - default="cuda", - ) - parser.add_argument( - "--default_dtype", - help="set default dtype", - type=str, - choices=["float32", "float64"], - default="float64", - ) - parser.add_argument( - "--compute_stress", - help="compute stress", - action="store_true", - default=False, - ) - parser.add_argument( - "--info_prefix", - help="prefix for energy, forces and stress keys", - type=str, - default="MACE_", - ) - return parser.parse_args() - - -def printenergy(dyn, start_time=None): # store a reference to atoms in the definition. - """Function to print the potential, kinetic and total energy.""" - a = dyn.atoms - epot = a.get_potential_energy() / len(a) - ekin = a.get_kinetic_energy() / len(a) - if start_time is None: - elapsed_time = 0 - else: - elapsed_time = time.time() - start_time - forces_var = np.var(a.calc.results["forces_comm"], axis=0) - print( - "%.1fs: Energy per atom: Epot = %.3feV Ekin = %.3feV (T=%3.0fK) " # pylint: disable=C0209 - "Etot = %.3feV t=%.1ffs Eerr = %.3feV Ferr = %.3feV/A" - % ( - elapsed_time, - epot, - ekin, - ekin / (1.5 * units.kB), - epot + ekin, - dyn.get_time() / units.fs, - a.calc.results["energy_var"], - np.max(np.linalg.norm(forces_var, axis=1)), - ), - flush=True, - ) - - -def save_config(dyn, fname): - atomsi = dyn.atoms - ens = atomsi.get_potential_energy() - frcs = atomsi.get_forces() - - atomsi.info.update( - { - "mlff_energy": ens, - "time": np.round(dyn.get_time() / units.fs, 5), - "mlff_energy_var": atomsi.calc.results["energy_var"], - } - ) - atomsi.arrays.update( - { - "mlff_forces": frcs, - "mlff_forces_var": np.var(atomsi.calc.results["forces_comm"], axis=0), - } - ) - - ase.io.write(fname, atomsi, append=True) - - -def stop_error(dyn, threshold, reg=0.2): - atomsi = dyn.atoms - force_var = np.var(atomsi.calc.results["forces_comm"], axis=0) - force = atomsi.get_forces() - ferr = np.sqrt(np.sum(force_var, axis=1)) - ferr_rel = ferr / (np.linalg.norm(force, axis=1) + reg) - - if np.max(ferr_rel) > threshold: - print( - "Error too large {:.3}. Stopping t={:.2} fs.".format( # pylint: disable=C0209 - np.max(ferr_rel), dyn.get_time() / units.fs - ), - flush=True, - ) - dyn.max_steps = 0 - - -def main() -> None: - args = parse_args() - run(args) - - -def run(args: argparse.Namespace) -> None: - mace_fname = args.model - atoms_fname = args.config - atoms_index = args.config_index - - mace_calc = MACECalculator( - model_paths=mace_fname, - device=args.device, - default_dtype=args.default_dtype, - ) - - NSTEPS = args.nsteps - - if os.path.exists(args.output): - print("Trajectory exists. Continuing from last step.") - atoms = ase.io.read(args.output, index=-1) - len_save = len(ase.io.read(args.output, ":")) - print("Last step: ", atoms.info["time"], "Number of configs: ", len_save) - NSTEPS -= len_save * args.nsave - else: - atoms = ase.io.read(atoms_fname, index=atoms_index) - MaxwellBoltzmannDistribution(atoms, temperature_K=args.temperature_K) - - atoms.calc = mace_calc - - # We want to run MD with constant energy using the Langevin algorithm - # with a time step of 5 fs, the temperature T and the friction - # coefficient to 0.02 atomic units. - dyn = Langevin( - atoms=atoms, - timestep=args.timestep * units.fs, - temperature_K=args.temperature_K, - friction=args.friction, - ) - - dyn.attach(printenergy, interval=args.nsave, dyn=dyn, start_time=time.time()) - dyn.attach(save_config, interval=args.nsave, dyn=dyn, fname=args.output) - dyn.attach( - stop_error, interval=args.ncheckerror, dyn=dyn, threshold=args.error_threshold - ) - # Now run the dynamics - dyn.run(NSTEPS) - - -if __name__ == "__main__": - main() diff --git a/mace-bench/3rdparty/mace/mace/cli/convert_cueq_e3nn.py b/mace-bench/3rdparty/mace/mace/cli/convert_cueq_e3nn.py deleted file mode 100644 index c2399cae1d7032534baabc225a04f2215c08aee2..0000000000000000000000000000000000000000 --- a/mace-bench/3rdparty/mace/mace/cli/convert_cueq_e3nn.py +++ /dev/null @@ -1,208 +0,0 @@ -import argparse -import logging -import os -from typing import Dict, List, Tuple - -import torch - -from mace.tools.scripts_utils import extract_config_mace_model - - -def get_transfer_keys(num_layers: int) -> List[str]: - """Get list of keys that need to be transferred""" - return [ - "node_embedding.linear.weight", - "radial_embedding.bessel_fn.bessel_weights", - "atomic_energies_fn.atomic_energies", - "readouts.0.linear.weight", - *[f"readouts.{j}.linear.weight" for j in range(num_layers - 1)], - "scale_shift.scale", - "scale_shift.shift", - *[f"readouts.{num_layers-1}.linear_{i}.weight" for i in range(1, 3)], - ] + [ - s - for j in range(num_layers) - for s in [ - f"interactions.{j}.linear_up.weight", - *[f"interactions.{j}.conv_tp_weights.layer{i}.weight" for i in range(4)], - f"interactions.{j}.linear.weight", - f"interactions.{j}.skip_tp.weight", - f"products.{j}.linear.weight", - ] - ] - - -def get_kmax_pairs( - max_L: int, correlation: int, num_layers: int -) -> List[Tuple[int, int]]: - """Determine kmax pairs based on max_L and correlation""" - if correlation == 2: - raise NotImplementedError("Correlation 2 not supported yet") - if correlation == 3: - kmax_pairs = [[i, max_L] for i in range(num_layers - 1)] - kmax_pairs = kmax_pairs + [[num_layers - 1, 0]] - return kmax_pairs - raise NotImplementedError(f"Correlation {correlation} not supported") - - -def transfer_symmetric_contractions( - source_dict: Dict[str, torch.Tensor], - target_dict: Dict[str, torch.Tensor], - max_L: int, - correlation: int, - num_layers: int, -): - """Transfer symmetric contraction weights from CuEq to E3nn format""" - kmax_pairs = get_kmax_pairs(max_L, correlation, num_layers) - - for i, kmax in kmax_pairs: - # Get the combined weight tensor from source - wm = source_dict[f"products.{i}.symmetric_contractions.weight"] - - # Get split sizes based on target dimensions - splits = [] - for k in range(kmax + 1): - for suffix in ["_max", ".0", ".1"]: - key = f"products.{i}.symmetric_contractions.contractions.{k}.weights{suffix}" - target_shape = target_dict[key].shape - splits.append(target_shape[1]) - - # Split the weights using the calculated sizes - weights_split = torch.split(wm, splits, dim=1) - - # Assign back to target dictionary - idx = 0 - for k in range(kmax + 1): - target_dict[ - f"products.{i}.symmetric_contractions.contractions.{k}.weights_max" - ] = weights_split[idx] - target_dict[ - f"products.{i}.symmetric_contractions.contractions.{k}.weights.0" - ] = weights_split[idx + 1] - target_dict[ - f"products.{i}.symmetric_contractions.contractions.{k}.weights.1" - ] = weights_split[idx + 2] - idx += 3 - - -def transfer_weights( - source_model: torch.nn.Module, - target_model: torch.nn.Module, - max_L: int, - correlation: int, - num_layers: int, -): - """Transfer weights from CuEq to E3nn format""" - # Get state dicts - source_dict = source_model.state_dict() - target_dict = target_model.state_dict() - - # Transfer main weights - transfer_keys = get_transfer_keys(num_layers) - for key in transfer_keys: - if key in source_dict: # Check if key exists - target_dict[key] = source_dict[key] - else: - logging.warning(f"Key {key} not found in source model") - - # Transfer symmetric contractions - transfer_symmetric_contractions( - source_dict, target_dict, max_L, correlation, num_layers - ) - - # Unsqueeze linear and skip_tp layers - for key in source_dict.keys(): - if any(x in key for x in ["linear", "skip_tp"]) and "weight" in key: - target_dict[key] = target_dict[key].squeeze(0) - - # Transfer remaining matching keys - transferred_keys = set(transfer_keys) - remaining_keys = ( - set(source_dict.keys()) & set(target_dict.keys()) - transferred_keys - ) - remaining_keys = {k for k in remaining_keys if "symmetric_contraction" not in k} - - if remaining_keys: - for key in remaining_keys: - if source_dict[key].shape == target_dict[key].shape: - logging.debug(f"Transferring additional key: {key}") - target_dict[key] = source_dict[key] - else: - logging.warning( - f"Shape mismatch for key {key}: " - f"source {source_dict[key].shape} vs target {target_dict[key].shape}" - ) - - # Transfer avg_num_neighbors - for i in range(2): - target_model.interactions[i].avg_num_neighbors = source_model.interactions[ - i - ].avg_num_neighbors - - # Load state dict into target model - target_model.load_state_dict(target_dict) - - -def run(input_model, output_model="_e3nn.model", device="cpu", return_model=True): - - # Load CuEq model - if isinstance(input_model, str): - source_model = torch.load(input_model, map_location=device) - else: - source_model = input_model - default_dtype = next(source_model.parameters()).dtype - torch.set_default_dtype(default_dtype) - # Extract configuration - config = extract_config_mace_model(source_model) - - # Get max_L and correlation from config - max_L = config["hidden_irreps"].lmax - correlation = config["correlation"] - - # Remove CuEq config - config.pop("cueq_config", None) - - # Create new model without CuEq config - logging.info("Creating new model without CuEq settings") - target_model = source_model.__class__(**config) - - # Transfer weights with proper remapping - num_layers = config["num_interactions"] - transfer_weights(source_model, target_model, max_L, correlation, num_layers) - - if return_model: - return target_model - - # Save model - if isinstance(input_model, str): - base = os.path.splitext(input_model)[0] - output_model = f"{base}.{output_model}" - logging.warning(f"Saving E3nn model to {output_model}") - torch.save(target_model, output_model) - return None - - -def main(): - parser = argparse.ArgumentParser() - parser.add_argument("input_model", help="Path to input CuEq model") - parser.add_argument( - "--output_model", help="Path to output E3nn model", default="e3nn_model.pt" - ) - parser.add_argument("--device", default="cpu", help="Device to use") - parser.add_argument( - "--return_model", - action="store_false", - help="Return model instead of saving to file", - ) - args = parser.parse_args() - - run( - input_model=args.input_model, - output_model=args.output_model, - device=args.device, - return_model=args.return_model, - ) - - -if __name__ == "__main__": - main() diff --git a/mace-bench/3rdparty/mace/mace/cli/convert_device.py b/mace-bench/3rdparty/mace/mace/cli/convert_device.py deleted file mode 100644 index 69735b7cf723f45e74b1573d7cf86cb3828dc539..0000000000000000000000000000000000000000 --- a/mace-bench/3rdparty/mace/mace/cli/convert_device.py +++ /dev/null @@ -1,31 +0,0 @@ -from argparse import ArgumentParser - -import torch - - -def main(): - parser = ArgumentParser() - parser.add_argument( - "--target_device", - "-t", - help="device to convert to, usually 'cpu' or 'cuda'", - default="cpu", - ) - parser.add_argument( - "--output_file", - "-o", - help="name for output model, defaults to model_file.target_device", - ) - parser.add_argument("model_file", help="input model file path") - args = parser.parse_args() - - if args.output_file is None: - args.output_file = args.model_file + "." + args.target_device - - model = torch.load(args.model_file, weights_only=False) - model.to(args.target_device) - torch.save(model, args.output_file) - - -if __name__ == "__main__": - main() diff --git a/mace-bench/3rdparty/mace/mace/cli/convert_e3nn_cueq.py b/mace-bench/3rdparty/mace/mace/cli/convert_e3nn_cueq.py deleted file mode 100644 index 299291f4b911500e2f3f664ee3e34398d17453be..0000000000000000000000000000000000000000 --- a/mace-bench/3rdparty/mace/mace/cli/convert_e3nn_cueq.py +++ /dev/null @@ -1,204 +0,0 @@ -import argparse -import logging -import os -from typing import Dict, List, Tuple - -import torch - -from mace.modules.wrapper_ops import CuEquivarianceConfig -from mace.tools.scripts_utils import extract_config_mace_model - - -def get_transfer_keys(num_layers: int) -> List[str]: - """Get list of keys that need to be transferred""" - return [ - "node_embedding.linear.weight", - "radial_embedding.bessel_fn.bessel_weights", - "atomic_energies_fn.atomic_energies", - "readouts.0.linear.weight", - *[f"readouts.{j}.linear.weight" for j in range(num_layers - 1)], - "scale_shift.scale", - "scale_shift.shift", - *[f"readouts.{num_layers-1}.linear_{i}.weight" for i in range(1, 3)], - ] + [ - s - for j in range(num_layers) - for s in [ - f"interactions.{j}.linear_up.weight", - *[f"interactions.{j}.conv_tp_weights.layer{i}.weight" for i in range(4)], - f"interactions.{j}.linear.weight", - f"interactions.{j}.skip_tp.weight", - f"products.{j}.linear.weight", - ] - ] - - -def get_kmax_pairs( - max_L: int, correlation: int, num_layers: int -) -> List[Tuple[int, int]]: - """Determine kmax pairs based on max_L and correlation""" - if correlation == 2: - raise NotImplementedError("Correlation 2 not supported yet") - if correlation == 3: - kmax_pairs = [[i, max_L] for i in range(num_layers - 1)] - kmax_pairs = kmax_pairs + [[num_layers - 1, 0]] - return kmax_pairs - raise NotImplementedError(f"Correlation {correlation} not supported") - - -def transfer_symmetric_contractions( - source_dict: Dict[str, torch.Tensor], - target_dict: Dict[str, torch.Tensor], - max_L: int, - correlation: int, - num_layers: int, -): - """Transfer symmetric contraction weights""" - kmax_pairs = get_kmax_pairs(max_L, correlation, num_layers) - - for i, kmax in kmax_pairs: - wm = torch.concatenate( - [ - source_dict[ - f"products.{i}.symmetric_contractions.contractions.{k}.weights{j}" - ] - for k in range(kmax + 1) - for j in ["_max", ".0", ".1"] - ], - dim=1, - ) - target_dict[f"products.{i}.symmetric_contractions.weight"] = wm - - -def transfer_weights( - source_model: torch.nn.Module, - target_model: torch.nn.Module, - max_L: int, - correlation: int, - num_layers: int, -): - """Transfer weights with proper remapping""" - # Get source state dict - source_dict = source_model.state_dict() - target_dict = target_model.state_dict() - - # Transfer main weights - transfer_keys = get_transfer_keys(num_layers) - for key in transfer_keys: - if key in source_dict: # Check if key exists - target_dict[key] = source_dict[key] - else: - logging.warning(f"Key {key} not found in source model") - - # Transfer symmetric contractions - transfer_symmetric_contractions( - source_dict, target_dict, max_L, correlation, num_layers - ) - - # Unsqueeze linear and skip_tp layers - for key in source_dict.keys(): - if any(x in key for x in ["linear", "skip_tp"]) and "weight" in key: - target_dict[key] = target_dict[key].unsqueeze(0) - - transferred_keys = set(transfer_keys) - remaining_keys = ( - set(source_dict.keys()) & set(target_dict.keys()) - transferred_keys - ) - remaining_keys = {k for k in remaining_keys if "symmetric_contraction" not in k} - if remaining_keys: - for key in remaining_keys: - if source_dict[key].shape == target_dict[key].shape: - logging.debug(f"Transferring additional key: {key}") - target_dict[key] = source_dict[key] - else: - logging.warning( - f"Shape mismatch for key {key}: " - f"source {source_dict[key].shape} vs target {target_dict[key].shape}" - ) - # Transfer avg_num_neighbors - for i in range(2): - target_model.interactions[i].avg_num_neighbors = source_model.interactions[ - i - ].avg_num_neighbors - - # Load state dict into target model - target_model.load_state_dict(target_dict) - - -def run( - input_model, - output_model="_cueq.model", - device="cpu", - return_model=True, -): - # Setup logging - - # Load original model - # logging.warning(f"Loading model") - # check if input_model is a path or a model - if isinstance(input_model, str): - source_model = torch.load(input_model, map_location=device) - else: - source_model = input_model - default_dtype = next(source_model.parameters()).dtype - torch.set_default_dtype(default_dtype) - # Extract configuration - config = extract_config_mace_model(source_model) - - # Get max_L and correlation from config - max_L = config["hidden_irreps"].lmax - correlation = config["correlation"] - - # Add cuequivariance config - config["cueq_config"] = CuEquivarianceConfig( - enabled=True, - layout="ir_mul", - group="O3_e3nn", - optimize_all=True, - ) - - # Create new model with cuequivariance config - logging.info("Creating new model with cuequivariance settings") - target_model = source_model.__class__(**config).to(device) - - # Transfer weights with proper remapping - num_layers = config["num_interactions"] - transfer_weights(source_model, target_model, max_L, correlation, num_layers) - - if return_model: - return target_model - - if isinstance(input_model, str): - base = os.path.splitext(input_model)[0] - output_model = f"{base}.{output_model}" - logging.warning(f"Saving CuEq model to {output_model}") - torch.save(target_model, output_model) - return None - - -def main(): - parser = argparse.ArgumentParser() - parser.add_argument("input_model", help="Path to input MACE model") - parser.add_argument( - "--output_model", - help="Path to output cuequivariance model", - default="cueq_model.pt", - ) - parser.add_argument("--device", default="cpu", help="Device to use") - parser.add_argument( - "--return_model", - action="store_false", - help="Return model instead of saving to file", - ) - args = parser.parse_args() - - run( - input_model=args.input_model, - output_model=args.output_model, - device=args.device, - return_model=args.return_model, - ) - - -if __name__ == "__main__": - main() diff --git a/mace-bench/3rdparty/mace/mace/cli/create_lammps_model.py b/mace-bench/3rdparty/mace/mace/cli/create_lammps_model.py deleted file mode 100644 index 7af81f25a287cc7fe20e78ecb2e81b2c75fbccba..0000000000000000000000000000000000000000 --- a/mace-bench/3rdparty/mace/mace/cli/create_lammps_model.py +++ /dev/null @@ -1,114 +0,0 @@ -# pylint: disable=wrong-import-position -import argparse -import copy -import os - -os.environ["TORCH_FORCE_NO_WEIGHTS_ONLY_LOAD"] = "1" - -import torch -from e3nn.util import jit - -from mace.calculators import LAMMPS_MACE -from mace.calculators.lammps_mliap_mace import LAMMPS_MLIAP_MACE -from mace.cli.convert_e3nn_cueq import run as run_e3nn_to_cueq - - -def parse_args(): - parser = argparse.ArgumentParser( - formatter_class=argparse.ArgumentDefaultsHelpFormatter, - ) - parser.add_argument( - "model_path", - type=str, - help="Path to the model to be converted to LAMMPS", - ) - parser.add_argument( - "--head", - type=str, - nargs="?", - help="Head of the model to be converted to LAMMPS", - default=None, - ) - parser.add_argument( - "--dtype", - type=str, - nargs="?", - help="Data type of the model to be converted to LAMMPS", - default="float64", - ) - parser.add_argument( - "--format", - type=str, - help="Old libtorch format, or new mliap format", - default="libtorch", - ) - return parser.parse_args() - - -def select_head(model): - if hasattr(model, "heads"): - heads = model.heads - else: - heads = [None] - - if len(heads) == 1: - print(f"Only one head found in the model: {heads[0]}. Skipping selection.") - return heads[0] - - print("Available heads in the model:") - for i, head in enumerate(heads): - print(f"{i + 1}: {head}") - - # Ask the user to select a head - selected = input( - f"Select a head by number (Defaulting to head: {len(heads)}, press Enter to accept): " - ) - - if selected.isdigit() and 1 <= int(selected) <= len(heads): - return heads[int(selected) - 1] - if selected == "": - print("No head selected. Proceeding without specifying a head.") - return None - print(f"No valid selection made. Defaulting to the last head: {heads[-1]}") - return heads[-1] - - -def main(): - args = parse_args() - model_path = args.model_path # takes model name as command-line input - model = torch.load( - model_path, - map_location=torch.device("cuda" if torch.cuda.is_available() else "cpu"), - ) - if args.dtype == "float64": - model = model.double().to("cpu") - elif args.dtype == "float32": - print("Converting model to float32, this may cause loss of precision.") - model = model.float().to("cpu") - - if args.format == "mliap": - # Enabling cuequivariance by default. TODO: switch? - model = run_e3nn_to_cueq(copy.deepcopy(model)) - model.lammps_mliap = True - - if args.head is None: - head = select_head(model) - else: - head = args.head - print( - f"Selected head: {head} from command line in the list available heads: {model.heads}" - ) - - lammps_class = LAMMPS_MLIAP_MACE if args.format == "mliap" else LAMMPS_MACE - lammps_model = ( - lammps_class(model, head=head) if head is not None else lammps_class(model) - ) - if args.format == "mliap": - torch.save(lammps_model, model_path + "-mliap_lammps.pt") - else: - lammps_model_compiled = jit.compile(lammps_model) - lammps_model_compiled.save(model_path + "-lammps.pt") - - -if __name__ == "__main__": - main() diff --git a/mace-bench/3rdparty/mace/mace/cli/eval_configs.py b/mace-bench/3rdparty/mace/mace/cli/eval_configs.py deleted file mode 100644 index d00c54c62eb8b9c5cbd601216d13712a273d3d93..0000000000000000000000000000000000000000 --- a/mace-bench/3rdparty/mace/mace/cli/eval_configs.py +++ /dev/null @@ -1,165 +0,0 @@ -########################################################################################### -# Script for evaluating configurations contained in an xyz file with a trained model -# Authors: Ilyes Batatia, Gregor Simm -# This program is distributed under the MIT License (see MIT.md) -########################################################################################### - -import argparse - -import ase.data -import ase.io -import numpy as np -import torch - -from mace import data -from mace.tools import torch_geometric, torch_tools, utils - - -def parse_args() -> argparse.Namespace: - parser = argparse.ArgumentParser( - formatter_class=argparse.ArgumentDefaultsHelpFormatter, - ) - parser.add_argument("--configs", help="path to XYZ configurations", required=True) - parser.add_argument("--model", help="path to model", required=True) - parser.add_argument("--output", help="output path", required=True) - parser.add_argument( - "--device", - help="select device", - type=str, - choices=["cpu", "cuda"], - default="cpu", - ) - parser.add_argument( - "--default_dtype", - help="set default dtype", - type=str, - choices=["float32", "float64"], - default="float64", - ) - parser.add_argument("--batch_size", help="batch size", type=int, default=64) - parser.add_argument( - "--compute_stress", - help="compute stress", - action="store_true", - default=False, - ) - parser.add_argument( - "--return_contributions", - help="model outputs energy contributions for each body order, only supported for MACE, not ScaleShiftMACE", - action="store_true", - default=False, - ) - parser.add_argument( - "--info_prefix", - help="prefix for energy, forces and stress keys", - type=str, - default="MACE_", - ) - parser.add_argument( - "--head", - help="Model head used for evaluation", - type=str, - required=False, - default=None, - ) - return parser.parse_args() - - -def main() -> None: - args = parse_args() - run(args) - - -def run(args: argparse.Namespace) -> None: - torch_tools.set_default_dtype(args.default_dtype) - device = torch_tools.init_device(args.device) - - # Load model - model = torch.load(f=args.model, map_location=args.device) - model = model.to( - args.device - ) # shouldn't be necessary but seems to help with CUDA problems - - for param in model.parameters(): - param.requires_grad = False - - # Load data and prepare input - atoms_list = ase.io.read(args.configs, index=":") - if args.head is not None: - for atoms in atoms_list: - atoms.info["head"] = args.head - configs = [data.config_from_atoms(atoms) for atoms in atoms_list] - - z_table = utils.AtomicNumberTable([int(z) for z in model.atomic_numbers]) - - try: - heads = model.heads - except AttributeError: - heads = None - - data_loader = torch_geometric.dataloader.DataLoader( - dataset=[ - data.AtomicData.from_config( - config, z_table=z_table, cutoff=float(model.r_max), heads=heads - ) - for config in configs - ], - batch_size=args.batch_size, - shuffle=False, - drop_last=False, - ) - - # Collect data - energies_list = [] - contributions_list = [] - stresses_list = [] - forces_collection = [] - - for batch in data_loader: - batch = batch.to(device) - output = model(batch.to_dict(), compute_stress=args.compute_stress) - energies_list.append(torch_tools.to_numpy(output["energy"])) - if args.compute_stress: - stresses_list.append(torch_tools.to_numpy(output["stress"])) - - if args.return_contributions: - contributions_list.append(torch_tools.to_numpy(output["contributions"])) - - forces = np.split( - torch_tools.to_numpy(output["forces"]), - indices_or_sections=batch.ptr[1:], - axis=0, - ) - forces_collection.append(forces[:-1]) # drop last as its empty - - energies = np.concatenate(energies_list, axis=0) - forces_list = [ - forces for forces_list in forces_collection for forces in forces_list - ] - assert len(atoms_list) == len(energies) == len(forces_list) - if args.compute_stress: - stresses = np.concatenate(stresses_list, axis=0) - assert len(atoms_list) == stresses.shape[0] - - if args.return_contributions: - contributions = np.concatenate(contributions_list, axis=0) - assert len(atoms_list) == contributions.shape[0] - - # Store data in atoms objects - for i, (atoms, energy, forces) in enumerate(zip(atoms_list, energies, forces_list)): - atoms.calc = None # crucial - atoms.info[args.info_prefix + "energy"] = energy - atoms.arrays[args.info_prefix + "forces"] = forces - - if args.compute_stress: - atoms.info[args.info_prefix + "stress"] = stresses[i] - - if args.return_contributions: - atoms.info[args.info_prefix + "BO_contributions"] = contributions[i] - - # Write atoms to output path - ase.io.write(args.output, images=atoms_list, format="extxyz") - - -if __name__ == "__main__": - main() diff --git a/mace-bench/3rdparty/mace/mace/cli/fine_tuning_select.py b/mace-bench/3rdparty/mace/mace/cli/fine_tuning_select.py deleted file mode 100644 index 59a0fb0782b8481967e4ad0b26ce0c3d566548fa..0000000000000000000000000000000000000000 --- a/mace-bench/3rdparty/mace/mace/cli/fine_tuning_select.py +++ /dev/null @@ -1,494 +0,0 @@ -########################################################################################### -# This program is distributed under the MIT License (see MIT.md) -########################################################################################### -from __future__ import annotations - -import argparse -import logging -from dataclasses import dataclass -from enum import Enum -from typing import List, Tuple, Union - -import ase.data -import ase.io -import numpy as np -import torch - -from mace.calculators import MACECalculator, mace_mp - -try: - import fpsample # type: ignore -except ImportError: - pass - - -class FilteringType(Enum): - NONE = "none" - COMBINATIONS = "combinations" - EXCLUSIVE = "exclusive" - INCLUSIVE = "inclusive" - - -class SubselectType(Enum): - FPS = "fps" - RANDOM = "random" - - -@dataclass -class SelectionSettings: - configs_pt: str - output: str - configs_ft: str | None = None - atomic_numbers: List[int] | None = None - num_samples: int | None = None - subselect: SubselectType = SubselectType.FPS - model: str = "small" - descriptors: str | None = None - device: str = "cpu" - default_dtype: str = "float64" - head_pt: str | None = None - head_ft: str | None = None - filtering_type: FilteringType = FilteringType.COMBINATIONS - weight_ft: float = 1.0 - weight_pt: float = 1.0 - seed: int = 42 - - -def parse_args() -> argparse.Namespace: - parser = argparse.ArgumentParser( - formatter_class=argparse.ArgumentDefaultsHelpFormatter, - ) - parser.add_argument( - "--configs_pt", - help="path to XYZ configurations for the pretraining", - required=True, - ) - parser.add_argument( - "--configs_ft", - help="path or list of paths to XYZ configurations for the finetuning", - required=False, - default=None, - ) - parser.add_argument( - "--num_samples", - help="number of samples to select for the pretraining", - type=int, - required=False, - default=None, - ) - parser.add_argument( - "--subselect", - help="method to subselect the configurations of the pretraining set", - type=SubselectType, - choices=list(SubselectType), - default=SubselectType.FPS, - ) - parser.add_argument( - "--model", help="path to model", default="small", required=False - ) - parser.add_argument("--output", help="output path", required=True) - parser.add_argument( - "--descriptors", help="path to descriptors", required=False, default=None - ) - parser.add_argument( - "--device", - help="select device", - type=str, - choices=["cpu", "cuda"], - default="cpu", - ) - parser.add_argument( - "--default_dtype", - help="set default dtype", - type=str, - choices=["float32", "float64"], - default="float64", - ) - parser.add_argument( - "--head_pt", - help="level of head for the pretraining set", - type=str, - default=None, - ) - parser.add_argument( - "--head_ft", - help="level of head for the finetuning set", - type=str, - default=None, - ) - parser.add_argument( - "--filtering_type", - help="filtering type", - type=FilteringType, - choices=list(FilteringType), - default=FilteringType.NONE, - ) - parser.add_argument( - "--weight_ft", - help="weight for the finetuning set", - type=float, - default=1.0, - ) - parser.add_argument( - "--weight_pt", - help="weight for the pretraining set", - type=float, - default=1.0, - ) - parser.add_argument("--seed", help="random seed", type=int, default=42) - return parser.parse_args() - - -def calculate_descriptors(atoms: List[ase.Atoms], calc: MACECalculator) -> None: - logging.info("Calculating descriptors") - for mol in atoms: - descriptors = calc.get_descriptors(mol.copy(), invariants_only=True) - # average descriptors over atoms for each element - descriptors_dict = { - element: np.mean(descriptors[mol.symbols == element], axis=0) - for element in np.unique(mol.symbols) - } - mol.info["mace_descriptors"] = descriptors_dict - - -def filter_atoms( - atoms: ase.Atoms, - element_subset: List[str], - filtering_type: FilteringType = FilteringType.COMBINATIONS, -) -> bool: - """ - Filters atoms based on the provided filtering type and element subset. - - Parameters: - atoms (ase.Atoms): The atoms object to filter. - element_subset (list): The list of elements to consider during filtering. - filtering_type (FilteringType): The type of filtering to apply. - Can be one of the following `FilteringType` enum members: - - `FilteringType.NONE`: No filtering is applied. - - `FilteringType.COMBINATIONS`: Return true if `atoms` is composed of combinations of elements in the subset, false otherwise. I.e. does not require all of the specified elements to be present. - - `FilteringType.EXCLUSIVE`: Return true if `atoms` contains *only* elements in the subset, false otherwise. - - `FilteringType.INCLUSIVE`: Return true if `atoms` contains all elements in the subset, false otherwise. I.e. allows additional elements. - - Returns: - bool: True if the atoms pass the filter, False otherwise. - """ - if filtering_type == FilteringType.NONE: - return True - if filtering_type == FilteringType.COMBINATIONS: - atom_symbols = np.unique(atoms.symbols) - return all( - x in element_subset for x in atom_symbols - ) # atoms must *only* contain elements in the subset - if filtering_type == FilteringType.EXCLUSIVE: - atom_symbols = set(list(atoms.symbols)) - return atom_symbols == set(element_subset) - if filtering_type == FilteringType.INCLUSIVE: - atom_symbols = np.unique(atoms.symbols) - return all( - x in atom_symbols for x in element_subset - ) # atoms must *at least* contain elements in the subset - raise ValueError( - f"Filtering type {filtering_type} not recognised. Must be one of {list(FilteringType)}." - ) - - -class FPS: - def __init__(self, atoms_list: List[ase.Atoms], n_samples: int): - self.n_samples = n_samples - self.atoms_list = atoms_list - self.species = np.unique([x.symbol for atoms in atoms_list for x in atoms]) # type: ignore - self.species_dict = {x: i for i, x in enumerate(self.species)} - # start from a random configuration - self.list_index = [np.random.randint(0, len(atoms_list))] - self.assemble_descriptors() - - def run( - self, - ) -> List[int]: - """ - Run the farthest point sampling algorithm. - """ - descriptor_dataset_reshaped = ( - self.descriptors_dataset.reshape( # pylint: disable=E1121 - (len(self.atoms_list), -1) - ) - ) - logging.info(f"{descriptor_dataset_reshaped.shape}") - logging.info(f"n_samples: {self.n_samples}") - self.list_index = fpsample.fps_npdu_kdtree_sampling( - descriptor_dataset_reshaped, - self.n_samples, - ) - return self.list_index - - def assemble_descriptors(self) -> None: - """ - Assemble the descriptors for all the configurations. - """ - self.descriptors_dataset: np.ndarray = 10e10 * np.ones( - ( - len(self.atoms_list), - len(self.species), - len(list(self.atoms_list[0].info["mace_descriptors"].values())[0]), - ), - dtype=np.float32, - ).astype(np.float32) - - for i, atoms in enumerate(self.atoms_list): - descriptors = atoms.info["mace_descriptors"] - for z in descriptors: - self.descriptors_dataset[i, self.species_dict[z]] = np.array( - descriptors[z] - ).astype(np.float32) - - -def _load_calc( - model: str, device: str, default_dtype: str, subselect: SubselectType -) -> Union[MACECalculator, None]: - if subselect == SubselectType.RANDOM: - return None - if model in ["small", "medium", "large"]: - calc = mace_mp(model, device=device, default_dtype=default_dtype) - else: - calc = MACECalculator( - model_paths=model, - device=device, - default_dtype=default_dtype, - ) - return calc - - -def _get_finetuning_elements( - atoms: List[ase.Atoms], atomic_numbers: List[int] | None -) -> List[str]: - if atoms: - logging.debug( - "Using elements from the finetuning configurations for filtering." - ) - species = np.unique([x.symbol for atoms in atoms for x in atoms]).tolist() # type: ignore - elif atomic_numbers is not None and atomic_numbers: - logging.debug("Using the supplied atomic numbers for filtering.") - species = [ase.data.chemical_symbols[z] for z in atomic_numbers] - else: - species = [] - return species - - -def _read_finetuning_configs( - configs_ft: Union[str, list[str], None], -) -> List[ase.Atoms]: - if isinstance(configs_ft, str): - path = configs_ft - return ase.io.read(path, index=":") # type: ignore - if isinstance(configs_ft, list): - assert all(isinstance(x, str) for x in configs_ft) - atoms_list_ft = [] - for path in configs_ft: - atoms_list_ft += ase.io.read(path, index=":") - return atoms_list_ft - if configs_ft is None: - return [] - raise ValueError(f"Invalid type for configs_ft: {type(configs_ft)}") - - -def _filter_pretraining_data( - atoms: list[ase.Atoms], - filtering_type: FilteringType, - all_species_ft: List[str], -) -> Tuple[List[ase.Atoms], List[ase.Atoms], list[bool]]: - logging.info( - "Filtering configurations based on the finetuning set, " - f"filtering type: {filtering_type}, elements: {all_species_ft}" - ) - passes_filter = [filter_atoms(x, all_species_ft, filtering_type) for x in atoms] - assert len(passes_filter) == len(atoms), "Filtering failed" - filtered_atoms = [x for x, passes in zip(atoms, passes_filter) if passes] - remaining_atoms = [x for x, passes in zip(atoms, passes_filter) if not passes] - return filtered_atoms, remaining_atoms, passes_filter - - -def _get_random_configs( - num_samples: int, - atoms: List[ase.Atoms], -) -> list[ase.Atoms]: - if num_samples > len(atoms): - raise ValueError( - f"Requested more samples ({num_samples}) than available in the remaining set ({len(atoms)})" - ) - indices = np.random.choice(list(range(len(atoms))), num_samples, replace=False) - return [atoms[i] for i in indices] - - -def _load_descriptors( - atoms: List[ase.Atoms], - passes_filter: List[bool], - descriptors_path: str | None, - calc: MACECalculator | None, - full_data_length: int, -) -> None: - if descriptors_path is not None: - logging.info(f"Loading descriptors from {descriptors_path}") - descriptors = np.load(descriptors_path, allow_pickle=True) - assert sum(passes_filter) == len(atoms) - if len(descriptors) != full_data_length: - raise ValueError( - f"Length of the descriptors ({len(descriptors)}) does not match the length of the data ({full_data_length})" - "Please provide descriptors for all configurations" - ) - required_descriptors = [ - descriptors[i] for i, passes in enumerate(passes_filter) if passes - ] - for i, atoms_ in enumerate(atoms): - atoms_.info["mace_descriptors"] = required_descriptors[i] - else: - logging.info("Calculating descriptors") - if calc is None: - raise ValueError("MACECalculator must be provided to calculate descriptors") - calculate_descriptors(atoms, calc) - - -def _maybe_save_descriptors( - atoms: List[ase.Atoms], - output_path: str, -) -> None: - """ - Save the descriptors if they are present in the atoms objects. - Also, delete the descriptors from the atoms objects. - """ - if all("mace_descriptors" in x.info for x in atoms): - descriptor_save_path = output_path.replace(".xyz", "_descriptors.npy") - logging.info(f"Saving descriptors at {descriptor_save_path}") - descriptors_list = [x.info["mace_descriptors"] for x in atoms] - np.save(descriptor_save_path, descriptors_list, allow_pickle=True) - for x in atoms: - del x.info["mace_descriptors"] - - -def _maybe_fps(atoms: List[ase.Atoms], num_samples: int) -> List[ase.Atoms]: - try: - fps_pt = FPS(atoms, num_samples) - idx_pt = fps_pt.run() - logging.info(f"Selected {len(idx_pt)} configurations") - return [atoms[i] for i in idx_pt] - except Exception as e: # pylint: disable=W0703 - logging.error(f"FPS failed, selecting random configurations instead: {e}") - return _get_random_configs(num_samples, atoms) - - -def _subsample_data( - filtered_atoms: List[ase.Atoms], - remaining_atoms: List[ase.Atoms], - passes_filter: List[bool], - num_samples: int | None, - subselect: SubselectType, - descriptors_path: str | None, - calc: MACECalculator | None, -) -> List[ase.Atoms]: - if num_samples is None or num_samples == len(filtered_atoms): - logging.info( - f"No subsampling, keeping all {len(filtered_atoms)} filtered configurations" - ) - return filtered_atoms - if num_samples > len(filtered_atoms): - num_sample_randomly = num_samples - len(filtered_atoms) - logging.info( - f"Number of configurations after filtering {len(filtered_atoms)} " - f"is less than the number of samples {num_samples}, " - f"selecting {num_sample_randomly} random configurations for the rest." - ) - return filtered_atoms + _get_random_configs( - num_sample_randomly, remaining_atoms - ) - if num_samples == 0: - raise ValueError("Number of samples must be greater than 0") - if subselect == SubselectType.FPS: - _load_descriptors( - filtered_atoms, - passes_filter, - descriptors_path, - calc, - full_data_length=len(filtered_atoms) + len(remaining_atoms), - ) - logging.info("Selecting configurations using Farthest Point Sampling") - return _maybe_fps(filtered_atoms, num_samples) - if subselect == SubselectType.RANDOM: - return _get_random_configs(num_samples, filtered_atoms) - raise ValueError(f"Invalid subselect type: {subselect}") - - -def _write_metadata( - atoms: list[ase.Atoms], pretrained: bool, config_weight: float, head: str | None -) -> None: - for a in atoms: - a.info["pretrained"] = pretrained - a.info["config_weight"] = config_weight - if head is not None: - a.info["head"] = head - - -def select_samples( - settings: SelectionSettings, -) -> None: - np.random.seed(settings.seed) - torch.manual_seed(settings.seed) - calc = _load_calc( - settings.model, settings.device, settings.default_dtype, settings.subselect - ) - atoms_list_ft = _read_finetuning_configs(settings.configs_ft) - all_species_ft = _get_finetuning_elements(atoms_list_ft, settings.atomic_numbers) - - if settings.filtering_type is not FilteringType.NONE and not all_species_ft: - raise ValueError( - "Filtering types other than NONE require elements for filtering. They can be specified via the `--atomic_numbers` flag." - ) - - atoms_list_pt: list[ase.Atoms] = ase.io.read(settings.configs_pt, index=":") # type: ignore - filtered_pt_atoms, remaining_atoms, passes_filter = _filter_pretraining_data( - atoms_list_pt, settings.filtering_type, all_species_ft - ) - - subsampled_atoms = _subsample_data( - filtered_pt_atoms, - remaining_atoms, - passes_filter, - settings.num_samples, - settings.subselect, - settings.descriptors, - calc, - ) - _maybe_save_descriptors(subsampled_atoms, settings.output) - - _write_metadata( - subsampled_atoms, - pretrained=True, - config_weight=settings.weight_pt, - head=settings.head_pt, - ) - _write_metadata( - atoms_list_ft, - pretrained=False, - config_weight=settings.weight_ft, - head=settings.head_ft, - ) - - logging.info("Saving the selected configurations") - ase.io.write(settings.output, subsampled_atoms, format="extxyz") - - logging.info("Saving a combined XYZ file") - atoms_fps_pt_ft = subsampled_atoms + atoms_list_ft - - ase.io.write( - settings.output.replace(".xyz", "_combined.xyz"), - atoms_fps_pt_ft, - format="extxyz", - ) - - -def main(): - args = parse_args() - settings = SelectionSettings(**vars(args)) - select_samples(settings) - - -if __name__ == "__main__": - main() diff --git a/mace-bench/3rdparty/mace/mace/cli/plot_train.py b/mace-bench/3rdparty/mace/mace/cli/plot_train.py deleted file mode 100644 index 238bd095f57ef7f9eaf2c046972051b82506bb60..0000000000000000000000000000000000000000 --- a/mace-bench/3rdparty/mace/mace/cli/plot_train.py +++ /dev/null @@ -1,342 +0,0 @@ -import argparse -import dataclasses -import glob -import json -import os -import re -from typing import List - -import matplotlib.pyplot as plt -import pandas as pd - -plt.rcParams.update({"font.size": 8}) -plt.style.use("seaborn-v0_8-paper") - - -colors = [ - "#1f77b4", # muted blue - "#d62728", # brick red - "#ff7f0e", # safety orange - "#2ca02c", # cooked asparagus green - "#9467bd", # muted purple - "#8c564b", # chestnut brown - "#e377c2", # raspberry yogurt pink - "#7f7f7f", # middle gray - "#bcbd22", # curry yellow-green - "#17becf", # blue-teal -] - - -@dataclasses.dataclass -class RunInfo: - name: str - seed: int - - -name_re = re.compile(r"(?P.+)_run-(?P\d+)_train.txt") - - -def parse_path(path: str) -> RunInfo: - match = name_re.match(os.path.basename(path)) - if not match: - raise RuntimeError(f"Cannot parse {path}") - - return RunInfo(name=match.group("name"), seed=int(match.group("seed"))) - - -def parse_training_results(path: str) -> List[dict]: - run_info = parse_path(path) - results = [] - with open(path, mode="r", encoding="utf-8") as f: - for line in f: - d = json.loads(line) - d["name"] = run_info.name - d["seed"] = run_info.seed - results.append(d) - - return results - - -def parse_args() -> argparse.Namespace: - parser = argparse.ArgumentParser( - description="Plot mace training statistics", - formatter_class=argparse.ArgumentDefaultsHelpFormatter, - ) - parser.add_argument( - "--path", help="Path to results file (.txt) or directory.", required=True - ) - parser.add_argument( - "--min_epoch", help="Minimum epoch.", default=0, type=int, required=False - ) - parser.add_argument( - "--start_stage_two", - "--start_swa", - help="Epoch that stage two (swa) loss began. Plots dashed line on plot to indicate. If None then assumed tag not used in training.", - default=None, - type=int, - required=False, - dest="start_swa", - ) - parser.add_argument( - "--linear", - help="Whether to plot linear instead of log scales.", - default=False, - required=False, - action="store_true", - ) - parser.add_argument( - "--error_bars", - help="Whether to plot standard deviations.", - default=False, - required=False, - action="store_true", - ) - parser.add_argument( - "--keys", - help="Comma-separated list of keys to plot.", - default="rmse_e,rmse_f", - type=str, - required=False, - ) - - parser.add_argument( - "--output_format", - help="What file type to save plot as", - default="png", - type=str, - required=False, - ) - - parser.add_argument( - "--heads", - help="Comma-separated name of the heads used for multihead training", - default=None, - type=str, - required=False, - ) - - return parser.parse_args() - - -def plot( - data: pd.DataFrame, - min_epoch: int, - output_path: str, - output_format: str, - linear: bool, - start_swa: int, - error_bars: bool, - keys: str, - heads: str, -) -> None: - """ - Plots train,validation loss and errors as a function of epoch. - min_epoch: minimum epoch to plot. - output_path: path to save the plot. - output_format: format to save the plot. - start_swa: whether to plot a dashed line to show epoch when stage two loss (swa) begins. - error_bars: whether to plot standard deviation of loss. - linear: whether to plot in linear scale or logscale (default). - keys: Values to plot. - heads: Heads used for multihead training. - """ - - labels = { - "mae_e": "MAE E [meV]", - "mae_e_per_atom": "MAE E/atom [meV]", - "rmse_e": "RMSE E [meV]", - "rmse_e_per_atom": "RMSE E/atom [meV]", - "q95_e": "Q95 E [meV]", - "mae_f": "MAE F [meV / A]", - "rel_mae_f": "Relative MAE F [meV / A]", - "rmse_f": "RMSE F [meV / A]", - "rel_rmse_f": "Relative RMSE F [meV / A]", - "q95_f": "Q95 F [meV / A]", - "mae_stress": "MAE Stress", - "rmse_stress": "RMSE Stress [meV / A^3]", - "rmse_virials_per_atom": " RMSE virials/atom [meV]", - "mae_virials": "MAE Virials [meV]", - "rmse_mu_per_atom": "RMSE MU/atom [mDebye]", - } - - data = data[data["epoch"] > min_epoch] - if heads is None: - data = ( - data.groupby(["name", "mode", "epoch"]).agg(["mean", "std"]).reset_index() - ) - - valid_data = data[data["mode"] == "eval"] - valid_data_dict = {"default": valid_data} - train_data = data[data["mode"] == "opt"] - else: - heads = heads.split(",") - # Separate eval and opt data - valid_data = ( - data[data["mode"] == "eval"] - .groupby(["name", "mode", "epoch", "head"]) - .agg(["mean", "std"]) - .reset_index() - ) - train_data = ( - data[data["mode"] == "opt"] - .groupby(["name", "mode", "epoch"]) - .agg(["mean", "std"]) - .reset_index() - ) - valid_data_dict = { - head: valid_data[valid_data["head"] == head] for head in heads - } - - for head, valid_data in valid_data_dict.items(): - fig, axes = plt.subplots( - nrows=1, ncols=2, figsize=(10, 3), constrained_layout=True - ) - - # ---- Plot loss ---- - ax = axes[0] - ax.plot( - train_data["epoch"], - train_data["loss"]["mean"], - color=colors[1], - linewidth=1, - ) - ax.set_ylabel("Training Loss", color=colors[1]) - ax.set_yscale("log") - - ax2 = ax.twinx() - ax2.plot( - valid_data["epoch"], - valid_data["loss"]["mean"], - color=colors[0], - linewidth=1, - ) - ax2.set_ylabel("Validation Loss", color=colors[0]) - - if not linear: - ax.set_yscale("log") - ax2.set_yscale("log") - - if error_bars: - ax.fill_between( - train_data["epoch"], - train_data["loss"]["mean"] - train_data["loss"]["std"], - train_data["loss"]["mean"] + train_data["loss"]["std"], - alpha=0.3, - color=colors[1], - ) - ax.fill_between( - valid_data["epoch"], - valid_data["loss"]["mean"] - valid_data["loss"]["std"], - valid_data["loss"]["mean"] + valid_data["loss"]["std"], - alpha=0.3, - color=colors[0], - ) - - if start_swa is not None: - ax.axvline( - start_swa, - color="black", - linestyle="dashed", - linewidth=1, - alpha=0.6, - label="Stage Two Starts", - ) - - ax.set_xlabel("Epoch") - ax.set_ylabel("Loss") - ax.legend(loc="upper right", fontsize=4) - ax.grid(True, linestyle="--", alpha=0.5) - - # ---- Plot selected keys ---- - ax = axes[1] - twin_axes = [] - for i, key in enumerate(keys.split(",")): - color = colors[(i + 3)] - label = labels.get(key, key) - - if i == 0: - main_ax = ax - else: - main_ax = ax.twinx() - main_ax.spines.right.set_position(("outward", 40 * (i - 1))) - twin_axes.append(main_ax) - - main_ax.plot( - valid_data["epoch"], - valid_data[key]["mean"] * 1e3, - color=color, - label=label, - linewidth=1, - ) - - if error_bars: - main_ax.fill_between( - valid_data["epoch"], - (valid_data[key]["mean"] - valid_data[key]["std"]) * 1e3, - (valid_data[key]["mean"] + valid_data[key]["std"]) * 1e3, - alpha=0.3, - color=color, - ) - - main_ax.set_ylabel(label, color=color) - main_ax.tick_params(axis="y", colors=color) - - if start_swa is not None: - ax.axvline( - start_swa, - color="black", - linestyle="dashed", - linewidth=1, - alpha=0.6, - label="Stage Two Starts", - ) - - ax.set_xlabel("Epoch") - ax.set_xlim(left=min_epoch) - ax.grid(True, linestyle="--", alpha=0.5) - - fig.savefig( - f"{output_path}_{head}.{output_format}", dpi=300, bbox_inches="tight" - ) - plt.close(fig) - - -def get_paths(path: str) -> List[str]: - if os.path.isfile(path): - return [path] - paths = glob.glob(os.path.join(path, "*_train.txt")) - - if len(paths) == 0: - raise RuntimeError(f"Cannot find results in '{path}'") - - return paths - - -def main() -> None: - args = parse_args() - run(args) - - -def run(args: argparse.Namespace) -> None: - data = pd.DataFrame( - results - for path in get_paths(args.path) - for results in parse_training_results(path) - ) - - for name, group in data.groupby("name"): - plot( - group, - min_epoch=args.min_epoch, - output_path=name, - output_format=args.output_format, - linear=args.linear, - start_swa=args.start_swa, - error_bars=args.error_bars, - keys=args.keys, - heads=args.heads, - ) - - -if __name__ == "__main__": - main() diff --git a/mace-bench/3rdparty/mace/mace/cli/preprocess_data.py b/mace-bench/3rdparty/mace/mace/cli/preprocess_data.py deleted file mode 100644 index 64f1740221b332ff22c258e6bfadc97089f4bf03..0000000000000000000000000000000000000000 --- a/mace-bench/3rdparty/mace/mace/cli/preprocess_data.py +++ /dev/null @@ -1,300 +0,0 @@ -# This file loads an xyz dataset and prepares -# new hdf5 file that is ready for training with on-the-fly dataloading - -import argparse -import ast -import json -import logging -import multiprocessing as mp -import os -import random -from functools import partial -from glob import glob -from typing import List, Tuple - -import h5py -import numpy as np -import tqdm - -from mace import data, tools -from mace.data import KeySpecification, update_keyspec_from_kwargs -from mace.data.utils import save_configurations_as_HDF5 -from mace.modules import compute_statistics -from mace.tools import torch_geometric -from mace.tools.scripts_utils import get_atomic_energies, get_dataset_from_xyz -from mace.tools.utils import AtomicNumberTable - - -def compute_stats_target( - file: str, - z_table: AtomicNumberTable, - r_max: float, - atomic_energies: Tuple, - batch_size: int, -): - train_dataset = data.HDF5Dataset(file, z_table=z_table, r_max=r_max) - train_loader = torch_geometric.dataloader.DataLoader( - dataset=train_dataset, - batch_size=batch_size, - shuffle=False, - drop_last=False, - ) - - avg_num_neighbors, mean, std = compute_statistics(train_loader, atomic_energies) - output = [avg_num_neighbors, mean, std] - return output - - -def pool_compute_stats(inputs: List): - path_to_files, z_table, r_max, atomic_energies, batch_size, num_process = inputs - - with mp.Pool(processes=num_process) as pool: - re = [ - pool.apply_async( - compute_stats_target, - args=( - file, - z_table, - r_max, - atomic_energies, - batch_size, - ), - ) - for file in glob(path_to_files + "/*") - ] - - pool.close() - pool.join() - - results = [r.get() for r in tqdm.tqdm(re)] - - if not results: - raise ValueError( - "No results were computed. Check if the input files exist and are readable." - ) - - # Separate avg_num_neighbors, mean, and std - avg_num_neighbors = np.mean([r[0] for r in results]) - means = np.array([r[1] for r in results]) - stds = np.array([r[2] for r in results]) - - # Compute averages - mean = np.mean(means, axis=0).item() - std = np.mean(stds, axis=0).item() - - return avg_num_neighbors, mean, std - - -def split_array(a: np.ndarray, max_size: int): - drop_last = False - if len(a) % 2 == 1: - a = np.append(a, a[-1]) - drop_last = True - factors = get_prime_factors(len(a)) - max_factor = 1 - for i in range(1, len(factors) + 1): - for j in range(0, len(factors) - i + 1): - if np.prod(factors[j : j + i]) <= max_size: - test = np.prod(factors[j : j + i]) - max_factor = max(test, max_factor) - return np.array_split(a, max_factor), drop_last - - -def get_prime_factors(n: int): - factors = [] - for i in range(2, n + 1): - while n % i == 0: - factors.append(i) - n = n / i - return factors - - -# Define Task for Multiprocessiing -def multi_train_hdf5(process, args, split_train, drop_last): - with h5py.File(args.h5_prefix + "train/train_" + str(process) + ".h5", "w") as f: - f.attrs["drop_last"] = drop_last - save_configurations_as_HDF5(split_train[process], process, f) - - -def multi_valid_hdf5(process, args, split_valid, drop_last): - with h5py.File(args.h5_prefix + "val/val_" + str(process) + ".h5", "w") as f: - f.attrs["drop_last"] = drop_last - save_configurations_as_HDF5(split_valid[process], process, f) - - -def multi_test_hdf5(process, name, args, split_test, drop_last): - with h5py.File( - args.h5_prefix + "test/" + name + "_" + str(process) + ".h5", "w" - ) as f: - f.attrs["drop_last"] = drop_last - save_configurations_as_HDF5(split_test[process], process, f) - - -def main() -> None: - """ - This script loads an xyz dataset and prepares - new hdf5 file that is ready for training with on-the-fly dataloading - """ - args = tools.build_preprocess_arg_parser().parse_args() - run(args) - - -def run(args: argparse.Namespace): - """ - This script loads an xyz dataset and prepares - new hdf5 file that is ready for training with on-the-fly dataloading - """ - - # currently support only command line property_key syntax - args.key_specification = KeySpecification() - update_keyspec_from_kwargs(args.key_specification, vars(args)) - - # Setup - tools.set_seeds(args.seed) - random.seed(args.seed) - logging.basicConfig( - level=logging.INFO, - format="%(asctime)s %(levelname)-8s %(message)s", - datefmt="%Y-%m-%d %H:%M:%S", - handlers=[logging.StreamHandler()], - ) - - try: - config_type_weights = ast.literal_eval(args.config_type_weights) - assert isinstance(config_type_weights, dict) - except Exception as e: # pylint: disable=W0703 - logging.warning( - f"Config type weights not specified correctly ({e}), using Default" - ) - config_type_weights = {"Default": 1.0} - - folders = ["train", "val", "test"] - for sub_dir in folders: - if not os.path.exists(args.h5_prefix + sub_dir): - os.makedirs(args.h5_prefix + sub_dir) - - # Data preparation - collections, atomic_energies_dict = get_dataset_from_xyz( - work_dir=args.work_dir, - train_path=args.train_file, - valid_path=args.valid_file, - valid_fraction=args.valid_fraction, - config_type_weights=config_type_weights, - test_path=args.test_file, - seed=args.seed, - key_specification=args.key_specification, - head_name=None, - ) - - # Atomic number table - # yapf: disable - if args.atomic_numbers is None: - z_table = tools.get_atomic_number_table_from_zs( - z - for configs in (collections.train, collections.valid) - for config in configs - for z in config.atomic_numbers - ) - else: - logging.info("Using atomic numbers from command line argument") - zs_list = ast.literal_eval(args.atomic_numbers) - assert isinstance(zs_list, list) - z_table = tools.get_atomic_number_table_from_zs(zs_list) - - logging.info("Preparing training set") - if args.shuffle: - random.shuffle(collections.train) - - # split collections.train into batches and save them to hdf5 - split_train = np.array_split(collections.train,args.num_process) - drop_last = False - if len(collections.train) % 2 == 1: - drop_last = True - - multi_train_hdf5_ = partial(multi_train_hdf5, args=args, split_train=split_train, drop_last=drop_last) - processes = [] - for i in range(args.num_process): - p = mp.Process(target=multi_train_hdf5_, args=[i]) - p.start() - processes.append(p) - - for i in processes: - i.join() - - if args.compute_statistics: - logging.info("Computing statistics") - if len(atomic_energies_dict) == 0: - atomic_energies_dict = get_atomic_energies(args.E0s, collections.train, z_table) - - # Remove atomic energies if element not in z_table - removed_atomic_energies = {} - for z in list(atomic_energies_dict): - if z not in z_table.zs: - removed_atomic_energies[z] = atomic_energies_dict.pop(z) - if len(removed_atomic_energies) > 0: - logging.warning("Atomic energies for elements not present in the atomic number table have been removed.") - logging.warning(f"Removed atomic energies (eV): {str(removed_atomic_energies)}") - logging.warning("To include these elements in the model, specify all atomic numbers explicitly using the --atomic_numbers argument.") - - atomic_energies: np.ndarray = np.array( - [atomic_energies_dict[z] for z in z_table.zs] - ) - logging.info(f"Atomic Energies: {atomic_energies.tolist()}") - _inputs = [args.h5_prefix+'train', z_table, args.r_max, atomic_energies, args.batch_size, args.num_process] - avg_num_neighbors, mean, std=pool_compute_stats(_inputs) - logging.info(f"Average number of neighbors: {avg_num_neighbors}") - logging.info(f"Mean: {mean}") - logging.info(f"Standard deviation: {std}") - - # save the statistics as a json - statistics = { - "atomic_energies": str(atomic_energies_dict), - "avg_num_neighbors": avg_num_neighbors, - "mean": mean, - "std": std, - "atomic_numbers": str([int(z) for z in z_table.zs]), - "r_max": args.r_max, - } - - with open(args.h5_prefix + "statistics.json", "w") as f: # pylint: disable=W1514 - json.dump(statistics, f) - - logging.info("Preparing validation set") - if args.shuffle: - random.shuffle(collections.valid) - split_valid = np.array_split(collections.valid, args.num_process) - drop_last = False - if len(collections.valid) % 2 == 1: - drop_last = True - - multi_valid_hdf5_ = partial(multi_valid_hdf5, args=args, split_valid=split_valid, drop_last=drop_last) - processes = [] - for i in range(args.num_process): - p = mp.Process(target=multi_valid_hdf5_, args=[i]) - p.start() - processes.append(p) - - for i in processes: - i.join() - - if args.test_file is not None: - logging.info("Preparing test sets") - for name, subset in collections.tests: - drop_last = False - if len(subset) % 2 == 1: - drop_last = True - split_test = np.array_split(subset, args.num_process) - multi_test_hdf5_ = partial(multi_test_hdf5, args=args, split_test=split_test, drop_last=drop_last) - - processes = [] - for i in range(args.num_process): - p = mp.Process(target=multi_test_hdf5_, args=[i, name]) - p.start() - processes.append(p) - - for i in processes: - i.join() - - -if __name__ == "__main__": - main() diff --git a/mace-bench/3rdparty/mace/mace/cli/run_train.py b/mace-bench/3rdparty/mace/mace/cli/run_train.py deleted file mode 100644 index 977ec45157174c8cd6a465fb5aafed43756540d3..0000000000000000000000000000000000000000 --- a/mace-bench/3rdparty/mace/mace/cli/run_train.py +++ /dev/null @@ -1,1007 +0,0 @@ -########################################################################################### -# Training script for MACE -# Authors: Ilyes Batatia, Gregor Simm, David Kovacs -# This program is distributed under the MIT License (see MIT.md) -########################################################################################### - -import ast -import glob -import json -import logging -import os -from copy import deepcopy -from pathlib import Path -from typing import List, Optional - -import torch.distributed -import torch.nn.functional -from e3nn.util import jit -from torch.nn.parallel import DistributedDataParallel as DDP -from torch.optim import LBFGS -from torch.utils.data import ConcatDataset -from torch_ema import ExponentialMovingAverage - -import mace -from mace import data, tools -from mace.calculators.foundations_models import mace_mp, mace_off -from mace.cli.convert_cueq_e3nn import run as run_cueq_to_e3nn -from mace.cli.convert_e3nn_cueq import run as run_e3nn_to_cueq -from mace.cli.visualise_train import TrainingPlotter -from mace.data import KeySpecification, update_keyspec_from_kwargs -from mace.tools import torch_geometric -from mace.tools.model_script_utils import configure_model -from mace.tools.multihead_tools import ( - HeadConfig, - assemble_mp_data, - dict_head_to_dataclass, - prepare_default_head, - prepare_pt_head, -) -from mace.tools.run_train_utils import ( - combine_datasets, - load_dataset_for_path, - normalize_file_paths, -) -from mace.tools.scripts_utils import ( - LRScheduler, - SubsetCollection, - check_path_ase_read, - convert_to_json_format, - dict_to_array, - extract_config_mace_model, - get_atomic_energies, - get_avg_num_neighbors, - get_config_type_weights, - get_dataset_from_xyz, - get_files_with_suffix, - get_loss_fn, - get_optimizer, - get_params_options, - get_swa, - print_git_commit, - remove_pt_head, - setup_wandb, -) -from mace.tools.slurm_distributed import DistributedEnvironment -from mace.tools.tables_utils import create_error_table -from mace.tools.utils import AtomicNumberTable - - -def main() -> None: - """ - This script runs the training/fine tuning for mace - """ - args = tools.build_default_arg_parser().parse_args() - run(args) - - -def run(args) -> None: - """ - This script runs the training/fine tuning for mace - """ - tag = tools.get_tag(name=args.name, seed=args.seed) - args, input_log_messages = tools.check_args(args) - - # default keyspec to update using heads dictionary - args.key_specification = KeySpecification() - update_keyspec_from_kwargs(args.key_specification, vars(args)) - - if args.device == "xpu": - try: - import intel_extension_for_pytorch as ipex - except ImportError as e: - raise ImportError( - "Error: Intel extension for PyTorch not found, but XPU device was specified" - ) from e - if args.distributed: - try: - distr_env = DistributedEnvironment() - except Exception as e: # pylint: disable=W0703 - logging.error(f"Failed to initialize distributed environment: {e}") - return - world_size = distr_env.world_size - local_rank = distr_env.local_rank - rank = distr_env.rank - if rank == 0: - print(distr_env) - torch.distributed.init_process_group(backend="nccl") - else: - rank = int(0) - - # Setup - tools.set_seeds(args.seed) - tools.setup_logger(level=args.log_level, tag=tag, directory=args.log_dir, rank=rank) - logging.info("===========VERIFYING SETTINGS===========") - for message, loglevel in input_log_messages: - logging.log(level=loglevel, msg=message) - - if args.distributed: - torch.cuda.set_device(local_rank) - logging.info(f"Process group initialized: {torch.distributed.is_initialized()}") - logging.info(f"Processes: {world_size}") - - try: - logging.info(f"MACE version: {mace.__version__}") - except AttributeError: - logging.info("Cannot find MACE version, please install MACE via pip") - logging.debug(f"Configuration: {args}") - - tools.set_default_dtype(args.default_dtype) - device = tools.init_device(args.device) - commit = print_git_commit() - model_foundation: Optional[torch.nn.Module] = None - foundation_model_avg_num_neighbors = 0 - if args.foundation_model is not None: - if args.foundation_model in ["small", "medium", "large"]: - logging.info( - f"Using foundation model mace-mp-0 {args.foundation_model} as initial checkpoint." - ) - calc = mace_mp( - model=args.foundation_model, - device=args.device, - default_dtype=args.default_dtype, - ) - model_foundation = calc.models[0] - elif args.foundation_model in ["small_off", "medium_off", "large_off"]: - model_type = args.foundation_model.split("_")[0] - logging.info( - f"Using foundation model mace-off-2023 {model_type} as initial checkpoint. ASL license." - ) - calc = mace_off( - model=model_type, - device=args.device, - default_dtype=args.default_dtype, - ) - model_foundation = calc.models[0] - else: - model_foundation = torch.load( - args.foundation_model, map_location=args.device - ) - logging.info( - f"Using foundation model {args.foundation_model} as initial checkpoint." - ) - args.r_max = model_foundation.r_max.item() - foundation_model_avg_num_neighbors = model_foundation.interactions[ - 0 - ].avg_num_neighbors - if ( - args.foundation_model not in ["small", "medium", "large"] - and args.pt_train_file is None - ): - logging.warning( - "Using multiheads finetuning with a foundation model that is not a Materials Project model, need to provied a path to a pretraining file with --pt_train_file." - ) - args.multiheads_finetuning = False - if args.multiheads_finetuning: - assert ( - args.E0s != "average" - ), "average atomic energies cannot be used for multiheads finetuning" - # check that the foundation model has a single head, if not, use the first head - if not args.force_mh_ft_lr: - logging.info( - "Multihead finetuning mode, setting learning rate to 0.0001 and EMA to True. To use a different learning rate, set --force_mh_ft_lr=True." - ) - args.lr = 0.0001 - args.ema = True - args.ema_decay = 0.99999 - logging.info( - "Using multiheads finetuning mode, setting learning rate to 0.0001 and EMA to True" - ) - if hasattr(model_foundation, "heads"): - if len(model_foundation.heads) > 1: - logging.warning( - "Mutlihead finetuning with models with more than one head is not supported, using the first head as foundation head." - ) - model_foundation = remove_pt_head( - model_foundation, args.foundation_head - ) - else: - args.multiheads_finetuning = False - - if args.heads is not None: - args.heads = ast.literal_eval(args.heads) - for _, head_dict in args.heads.items(): - # priority is global args < head property_key values < head info_keys+arrays_keys - head_keyspec = deepcopy(args.key_specification) - update_keyspec_from_kwargs(head_keyspec, head_dict) - head_keyspec.update( - info_keys=head_dict.get("info_keys", {}), - arrays_keys=head_dict.get("arrays_keys", {}), - ) - head_dict["key_specification"] = head_keyspec - else: - args.heads = prepare_default_head(args) - if args.multiheads_finetuning: - pt_keyspec = ( - args.heads["pt_head"]["key_specification"] - if "pt_head" in args.heads - else deepcopy(args.key_specification) - ) - args.heads["pt_head"] = prepare_pt_head( - args, pt_keyspec, foundation_model_avg_num_neighbors - ) - - logging.info("===========LOADING INPUT DATA===========") - heads = list(args.heads.keys()) - logging.info(f"Using heads: {heads}") - logging.info("Using the key specifications to parse data:") - for name, head_dict in args.heads.items(): - head_keyspec = head_dict["key_specification"] - logging.info(f"{name}: {head_keyspec}") - - head_configs: List[HeadConfig] = [] - for head, head_args in args.heads.items(): - logging.info(f"============= Processing head {head} ===========") - head_config = dict_head_to_dataclass(head_args, head, args) - - # Handle train_file and valid_file - normalize to lists - if hasattr(head_config, "train_file") and head_config.train_file is not None: - head_config.train_file = normalize_file_paths(head_config.train_file) - if hasattr(head_config, "valid_file") and head_config.valid_file is not None: - head_config.valid_file = normalize_file_paths(head_config.valid_file) - if hasattr(head_config, "test_file") and head_config.test_file is not None: - head_config.test_file = normalize_file_paths(head_config.test_file) - - if ( - head_config.statistics_file is not None - and head_config.head_name != "pt_head" - ): - with open(head_config.statistics_file, "r") as f: # pylint: disable=W1514 - statistics = json.load(f) - logging.info("Using statistics json file") - head_config.atomic_numbers = statistics["atomic_numbers"] - head_config.mean = statistics["mean"] - head_config.std = statistics["std"] - head_config.avg_num_neighbors = statistics["avg_num_neighbors"] - head_config.compute_avg_num_neighbors = False - if isinstance(statistics["atomic_energies"], str) and statistics[ - "atomic_energies" - ].endswith(".json"): - with open(statistics["atomic_energies"], "r", encoding="utf-8") as f: - atomic_energies = json.load(f) - head_config.E0s = atomic_energies - head_config.atomic_energies_dict = ast.literal_eval(atomic_energies) - else: - head_config.E0s = statistics["atomic_energies"] - head_config.atomic_energies_dict = ast.literal_eval( - statistics["atomic_energies"] - ) - if head_config.train_file == ["mp"]: - assert ( - head_config.head_name == "pt_head" - ), "Only pt_head should use mp as train_file" - logging.info( - "Using the full Materials Project data for replay. You can construct a different subset using `fine_tuning_select.py` script." - ) - collections = assemble_mp_data(args, head_config, tag) - head_config.collections = collections - elif any(check_path_ase_read(f) for f in head_config.train_file): - train_files_ase_list = [ - f for f in head_config.train_file if check_path_ase_read(f) - ] - valid_files_ase_list = None - test_files_ase_list = None - if head_config.valid_file: - valid_files_ase_list = [ - f for f in head_config.valid_file if check_path_ase_read(f) - ] - if head_config.test_file: - test_files_ase_list = [ - f for f in head_config.test_file if check_path_ase_read(f) - ] - config_type_weights = get_config_type_weights( - head_config.config_type_weights - ) - collections, atomic_energies_dict = get_dataset_from_xyz( - work_dir=args.work_dir, - train_path=train_files_ase_list, - valid_path=valid_files_ase_list, - valid_fraction=head_config.valid_fraction, - config_type_weights=config_type_weights, - test_path=test_files_ase_list, - seed=args.seed, - key_specification=head_config.key_specification, - head_name=head_config.head_name, - keep_isolated_atoms=head_config.keep_isolated_atoms, - ) - head_config.collections = SubsetCollection( - train=collections.train, - valid=collections.valid, - tests=collections.tests, - ) - head_config.atomic_energies_dict = atomic_energies_dict - logging.info( - f"Total number of configurations: train={len(collections.train)}, valid={len(collections.valid)}, " - f"tests=[{', '.join([name + ': ' + str(len(test_configs)) for name, test_configs in collections.tests])}]," - ) - head_configs.append(head_config) - - if all( - check_path_ase_read(head_config.train_file[0]) for head_config in head_configs - ): - size_collections_train = sum( - len(head_config.collections.train) for head_config in head_configs - ) - size_collections_valid = sum( - len(head_config.collections.valid) for head_config in head_configs - ) - if size_collections_train < args.batch_size: - logging.error( - f"Batch size ({args.batch_size}) is larger than the number of training data ({size_collections_train})" - ) - if size_collections_valid < args.valid_batch_size: - logging.warning( - f"Validation batch size ({args.valid_batch_size}) is larger than the number of validation data ({size_collections_valid})" - ) - - if args.multiheads_finetuning: - logging.info( - "==================Using multiheads finetuning mode==================" - ) - args.loss = "universal" - - all_ase_readable = all( - all(check_path_ase_read(f) for f in head_config.train_file) - for head_config in head_configs - ) - head_config_pt = filter(lambda x: x.head_name == "pt_head", head_configs) - head_config_pt = next(head_config_pt, None) - assert head_config_pt is not None, "Pretraining head not found" - if all_ase_readable: - ratio_pt_ft = size_collections_train / len(head_config_pt.collections.train) - if ratio_pt_ft < 0.1: - logging.warning( - f"Ratio of the number of configurations in the training set and the in the pt_train_file is {ratio_pt_ft}, " - f"increasing the number of configurations in the fine-tuning heads by {int(0.1 / ratio_pt_ft)}" - ) - for head_config in head_configs: - if head_config.head_name == "pt_head": - continue - head_config.collections.train += ( - head_config.collections.train * int(0.1 / ratio_pt_ft) - ) - logging.info( - f"Total number of configurations in pretraining: train={len(head_config_pt.collections.train)}, valid={len(head_config_pt.collections.valid)}" - ) - else: - logging.debug( - "Using LMDB/HDF5 datasets for pretraining or fine-tuning - skipping ratio check" - ) - - # Atomic number table - # yapf: disable - for head_config in head_configs: - if head_config.atomic_numbers is None: - assert all(check_path_ase_read(f) for f in head_config.train_file), "Must specify atomic_numbers when using .h5 or .aselmdb train_file input" - z_table_head = tools.get_atomic_number_table_from_zs( - z - for configs in (head_config.collections.train, head_config.collections.valid) - for config in configs - for z in config.atomic_numbers - ) - head_config.atomic_numbers = z_table_head.zs - head_config.z_table = z_table_head - else: - if head_config.statistics_file is None: - logging.info("Using atomic numbers from command line argument") - else: - logging.info("Using atomic numbers from statistics file") - zs_list = ast.literal_eval(head_config.atomic_numbers) - assert isinstance(zs_list, list) - z_table_head = tools.AtomicNumberTable(zs_list) - head_config.atomic_numbers = zs_list - head_config.z_table = z_table_head - # yapf: enable - all_atomic_numbers = set() - for head_config in head_configs: - all_atomic_numbers.update(head_config.atomic_numbers) - z_table = AtomicNumberTable(sorted(list(all_atomic_numbers))) - if args.foundation_model_elements and model_foundation: - z_table = AtomicNumberTable(sorted(model_foundation.atomic_numbers.tolist())) - logging.info(f"Atomic Numbers used: {z_table.zs}") - - # Atomic energies - atomic_energies_dict = {} - for head_config in head_configs: - if head_config.atomic_energies_dict is None or len(head_config.atomic_energies_dict) == 0: - assert head_config.E0s is not None, "Atomic energies must be provided" - if all(check_path_ase_read(f) for f in head_config.train_file) and head_config.E0s.lower() != "foundation": - atomic_energies_dict[head_config.head_name] = get_atomic_energies( - head_config.E0s, head_config.collections.train, head_config.z_table - ) - elif head_config.E0s.lower() == "foundation": - assert args.foundation_model is not None - z_table_foundation = AtomicNumberTable( - [int(z) for z in model_foundation.atomic_numbers] - ) - foundation_atomic_energies = model_foundation.atomic_energies_fn.atomic_energies - if foundation_atomic_energies.ndim > 1: - foundation_atomic_energies = foundation_atomic_energies.squeeze() - if foundation_atomic_energies.ndim == 2: - foundation_atomic_energies = foundation_atomic_energies[0] - logging.info("Foundation model has multiple heads, using the first head as foundation E0s.") - atomic_energies_dict[head_config.head_name] = { - z: foundation_atomic_energies[ - z_table_foundation.z_to_index(z) - ].item() - for z in z_table.zs - } - else: - atomic_energies_dict[head_config.head_name] = get_atomic_energies(head_config.E0s, None, head_config.z_table) - else: - atomic_energies_dict[head_config.head_name] = head_config.atomic_energies_dict - - # Atomic energies for multiheads finetuning - if args.multiheads_finetuning: - assert ( - model_foundation is not None - ), "Model foundation must be provided for multiheads finetuning" - z_table_foundation = AtomicNumberTable( - [int(z) for z in model_foundation.atomic_numbers] - ) - foundation_atomic_energies = model_foundation.atomic_energies_fn.atomic_energies - if foundation_atomic_energies.ndim > 1: - foundation_atomic_energies = foundation_atomic_energies.squeeze() - if foundation_atomic_energies.ndim == 2: - foundation_atomic_energies = foundation_atomic_energies[0] - logging.info("Foundation model has multiple heads, using the first head as foundation E0s.") - atomic_energies_dict["pt_head"] = { - z: foundation_atomic_energies[ - z_table_foundation.z_to_index(z) - ].item() - for z in z_table.zs - } - heads = sorted(heads, key=lambda x: -1000 if x == "pt_head" else 0) - # Padding atomic energies if keeping all elements of the foundation model - if args.foundation_model_elements and model_foundation: - atomic_energies_dict_padded = {} - for head_name, head_energies in atomic_energies_dict.items(): - energy_head_padded = {} - for z in z_table.zs: - energy_head_padded[z] = head_energies.get(z, 0.0) - atomic_energies_dict_padded[head_name] = energy_head_padded - atomic_energies_dict = atomic_energies_dict_padded - - if args.model == "AtomicDipolesMACE": - atomic_energies = None - dipole_only = True - args.compute_dipole = True - args.compute_energy = False - args.compute_forces = False - args.compute_virials = False - args.compute_stress = False - else: - dipole_only = False - if args.model == "EnergyDipolesMACE": - args.compute_dipole = True - args.compute_energy = True - args.compute_forces = True - args.compute_virials = False - args.compute_stress = False - else: - args.compute_energy = True - args.compute_dipole = False - # atomic_energies: np.ndarray = np.array( - # [atomic_energies_dict[z] for z in z_table.zs] - # ) - atomic_energies = dict_to_array(atomic_energies_dict, heads) - for head_config in head_configs: - try: - logging.info(f"Atomic Energies used (z: eV) for head {head_config.head_name}: " + "{" + ", ".join([f"{z}: {atomic_energies_dict[head_config.head_name][z]}" for z in head_config.z_table.zs]) + "}") - except KeyError as e: - raise KeyError(f"Atomic number {e} not found in atomic_energies_dict for head {head_config.head_name}, add E0s for this atomic number") from e - - # Load datasets for each head, supporting multiple files per head - valid_sets = {head: [] for head in heads} - train_sets = {head: [] for head in heads} - - for head_config in head_configs: - train_datasets = [] - - logging.info(f"Processing datasets for head '{head_config.head_name}'") - ase_files = [f for f in head_config.train_file if check_path_ase_read(f)] - non_ase_files = [f for f in head_config.train_file if not check_path_ase_read(f)] - - if ase_files: - dataset = load_dataset_for_path( - file_path=ase_files, - r_max=args.r_max, - z_table=z_table, - head_config=head_config, - heads=heads, - collection=head_config.collections.train, - ) - train_datasets.append(dataset) - logging.debug(f"Successfully loaded dataset from ASE files: {ase_files}") - - for file in non_ase_files: - dataset = load_dataset_for_path( - file_path=file, - r_max=args.r_max, - z_table=z_table, - head_config=head_config, - heads=heads, - ) - train_datasets.append(dataset) - logging.debug(f"Successfully loaded dataset from non-ASE file: {file}") - - if not train_datasets: - raise ValueError(f"No valid training datasets found for head {head_config.head_name}") - - train_sets[head_config.head_name] = combine_datasets(train_datasets, head_config.head_name) - - if head_config.valid_file: - valid_datasets = [] - - valid_ase_files = [f for f in head_config.valid_file if check_path_ase_read(f)] - valid_non_ase_files = [f for f in head_config.valid_file if not check_path_ase_read(f)] - - if valid_ase_files: - valid_dataset = load_dataset_for_path( - file_path=valid_ase_files, - r_max=args.r_max, - z_table=z_table, - head_config=head_config, - heads=heads, - collection=head_config.collections.valid, - ) - valid_datasets.append(valid_dataset) - logging.debug(f"Successfully loaded validation dataset from ASE files: {valid_ase_files}") - for valid_file in valid_non_ase_files: - valid_dataset = load_dataset_for_path( - file_path=valid_file, - r_max=args.r_max, - z_table=z_table, - head_config=head_config, - heads=heads, - ) - valid_datasets.append(valid_dataset) - logging.debug(f"Successfully loaded validation dataset from {valid_file}") - - # Combine validation datasets - if valid_datasets: - valid_sets[head_config.head_name] = combine_datasets(valid_datasets, f"{head_config.head_name}_valid") - logging.info(f"Combined validation datasets for {head_config.head_name}") - - # If no valid file is provided but collection exist, use the validation set from the collection - if head_config.valid_file is None and head_config.collections.valid: - valid_sets[head_config.head_name] = [ - data.AtomicData.from_config( - config, z_table=z_table, cutoff=args.r_max, heads=heads - ) - for config in head_config.collections.valid - ] - if not valid_sets[head_config.head_name]: - raise ValueError(f"No valid datasets found for head {head_config.head_name}, please provide a valid_file or a valid_fraction") - - # Create data loader for this head - if isinstance(train_sets[head_config.head_name], list): - dataset_size = len(train_sets[head_config.head_name]) - else: - dataset_size = len(train_sets[head_config.head_name]) - logging.info(f"Head '{head_config.head_name}' training dataset size: {dataset_size}") - - train_loader_head = torch_geometric.dataloader.DataLoader( - dataset=train_sets[head_config.head_name], - batch_size=args.batch_size, - shuffle=True, - drop_last=(not args.lbfgs), - pin_memory=args.pin_memory, - num_workers=args.num_workers, - generator=torch.Generator().manual_seed(args.seed), - ) - head_config.train_loader = train_loader_head - - # concatenate all the trainsets - train_set = ConcatDataset([train_sets[head] for head in heads]) - train_sampler, valid_sampler = None, None - if args.distributed: - train_sampler = torch.utils.data.distributed.DistributedSampler( - train_set, - num_replicas=world_size, - rank=rank, - shuffle=True, - drop_last=(not args.lbfgs), - seed=args.seed, - ) - valid_samplers = {} - for head, valid_set in valid_sets.items(): - valid_sampler = torch.utils.data.distributed.DistributedSampler( - valid_set, - num_replicas=world_size, - rank=rank, - shuffle=True, - drop_last=True, - seed=args.seed, - ) - valid_samplers[head] = valid_sampler - train_loader = torch_geometric.dataloader.DataLoader( - dataset=train_set, - batch_size=args.batch_size, - sampler=train_sampler, - shuffle=(train_sampler is None), - drop_last=(train_sampler is None and not args.lbfgs), - pin_memory=args.pin_memory, - num_workers=args.num_workers, - generator=torch.Generator().manual_seed(args.seed), - ) - valid_loaders = {heads[i]: None for i in range(len(heads))} - if not isinstance(valid_sets, dict): - valid_sets = {"Default": valid_sets} - for head, valid_set in valid_sets.items(): - valid_loaders[head] = torch_geometric.dataloader.DataLoader( - dataset=valid_set, - batch_size=args.valid_batch_size, - sampler=valid_samplers[head] if args.distributed else None, - shuffle=False, - drop_last=False, - pin_memory=args.pin_memory, - num_workers=args.num_workers, - generator=torch.Generator().manual_seed(args.seed), - ) - - loss_fn = get_loss_fn(args, dipole_only, args.compute_dipole) - args.avg_num_neighbors = get_avg_num_neighbors(head_configs, args, train_loader, device) - - # Model - model, output_args = configure_model(args, train_loader, atomic_energies, model_foundation, heads, z_table, head_configs) - model.to(device) - - logging.debug(model) - logging.info(f"Total number of parameters: {tools.count_parameters(model)}") - logging.info("") - logging.info("===========OPTIMIZER INFORMATION===========") - logging.info(f"Using {args.optimizer.upper()} as parameter optimizer") - logging.info(f"Batch size: {args.batch_size}") - if args.ema: - logging.info(f"Using Exponential Moving Average with decay: {args.ema_decay}") - logging.info( - f"Number of gradient updates: {int(args.max_num_epochs*len(train_set)/args.batch_size)}" - ) - logging.info(f"Learning rate: {args.lr}, weight decay: {args.weight_decay}") - logging.info(loss_fn) - - # Cueq - if args.enable_cueq: - logging.info("Converting model to CUEQ for accelerated training") - assert model.__class__.__name__ in ["MACE", "ScaleShiftMACE"] - model = run_e3nn_to_cueq(deepcopy(model), device=device) - # Optimizer - param_options = get_params_options(args, model) - optimizer: torch.optim.Optimizer - optimizer = get_optimizer(args, param_options) - if args.device == "xpu": - logging.info("Optimzing model and optimzier for XPU") - model, optimizer = ipex.optimize(model, optimizer=optimizer) - logger = tools.MetricsLogger( - directory=args.results_dir, tag=tag + "_train" - ) # pylint: disable=E1123 - - lr_scheduler = LRScheduler(optimizer, args) - - swa: Optional[tools.SWAContainer] = None - swas = [False] - if args.swa: - swa, swas = get_swa(args, model, optimizer, swas, dipole_only) - - checkpoint_handler = tools.CheckpointHandler( - directory=args.checkpoints_dir, - tag=tag, - keep=args.keep_checkpoints, - swa_start=args.start_swa, - ) - - start_epoch = 0 - restart_lbfgs = False - opt_start_epoch = None - if args.restart_latest: - try: - opt_start_epoch = checkpoint_handler.load_latest( - state=tools.CheckpointState(model, optimizer, lr_scheduler), - swa=True, - device=device, - ) - except Exception: # pylint: disable=W0703 - try: - opt_start_epoch = checkpoint_handler.load_latest( - state=tools.CheckpointState(model, optimizer, lr_scheduler), - swa=False, - device=device, - ) - except Exception: # pylint: disable=W0703 - restart_lbfgs = True - if opt_start_epoch is not None: - start_epoch = opt_start_epoch - - ema: Optional[ExponentialMovingAverage] = None - if args.ema: - ema = ExponentialMovingAverage(model.parameters(), decay=args.ema_decay) - else: - for group in optimizer.param_groups: - group["lr"] = args.lr - - if args.lbfgs: - logging.info("Switching optimizer to LBFGS") - optimizer = LBFGS(model.parameters(), - history_size=200, - max_iter=20, - line_search_fn="strong_wolfe") - if restart_lbfgs: - opt_start_epoch = checkpoint_handler.load_latest( - state=tools.CheckpointState(model, optimizer, lr_scheduler), - swa=False, - device=device, - ) - if opt_start_epoch is not None: - start_epoch = opt_start_epoch - - if args.wandb: - setup_wandb(args) - if args.distributed: - distributed_model = DDP(model, device_ids=[local_rank]) - else: - distributed_model = None - - - train_valid_data_loader = {} - for head_config in head_configs: - data_loader_name = "train_" + head_config.head_name - train_valid_data_loader[data_loader_name] = head_config.train_loader - for head, valid_loader in valid_loaders.items(): - data_load_name = "valid_" + head - train_valid_data_loader[data_load_name] = valid_loader - - if args.plot and args.plot_frequency > 0: - try: - plotter = TrainingPlotter( - results_dir=logger.path, - heads=heads, - table_type=args.error_table, - train_valid_data=train_valid_data_loader, - test_data={}, - output_args=output_args, - device=device, - plot_frequency=args.plot_frequency, - distributed=args.distributed, - swa_start=swa.start if swa else None - ) - except Exception as e: # pylint: disable=W0718 - logging.debug(f"Creating Plotter failed: {e}") - else: - plotter = None - - if args.dry_run: - logging.info("DRY RUN mode enabled. Stopping now.") - return - - - tools.train( - model=model, - loss_fn=loss_fn, - train_loader=train_loader, - valid_loaders=valid_loaders, - optimizer=optimizer, - lr_scheduler=lr_scheduler, - checkpoint_handler=checkpoint_handler, - eval_interval=args.eval_interval, - start_epoch=start_epoch, - max_num_epochs=args.max_num_epochs, - logger=logger, - patience=args.patience, - save_all_checkpoints=args.save_all_checkpoints, - output_args=output_args, - device=device, - swa=swa, - ema=ema, - max_grad_norm=args.clip_grad, - log_errors=args.error_table, - log_wandb=args.wandb, - distributed=args.distributed, - distributed_model=distributed_model, - plotter=plotter, - train_sampler=train_sampler, - rank=rank, - ) - - logging.info("") - logging.info("===========RESULTS===========") - - train_valid_data_loader = {} - for head_config in head_configs: - data_loader_name = "train_" + head_config.head_name - train_valid_data_loader[data_loader_name] = head_config.train_loader - for head, valid_loader in valid_loaders.items(): - data_load_name = "valid_" + head - train_valid_data_loader[data_load_name] = valid_loader - test_sets = {} - stop_first_test = False - test_data_loader = {} - if all( - head_config.test_file == head_configs[0].test_file - for head_config in head_configs - ) and head_configs[0].test_file is not None: - stop_first_test = True - if all( - head_config.test_dir == head_configs[0].test_dir - for head_config in head_configs - ) and head_configs[0].test_dir is not None: - stop_first_test = True - for head_config in head_configs: - if all(check_path_ase_read(f) for f in head_config.train_file): - for name, subset in head_config.collections.tests: - test_sets[name] = [ - data.AtomicData.from_config( - config, z_table=z_table, cutoff=args.r_max, heads=heads - ) - for config in subset - ] - if head_config.test_dir is not None: - if not args.multi_processed_test: - test_files = get_files_with_suffix(head_config.test_dir, "_test.h5") - for test_file in test_files: - name = os.path.splitext(os.path.basename(test_file))[0] - test_sets[name] = data.HDF5Dataset( - test_file, r_max=args.r_max, z_table=z_table, heads=heads, head=head_config.head_name - ) - else: - test_folders = glob(head_config.test_dir + "/*") - for folder in test_folders: - name = os.path.splitext(os.path.basename(test_file))[0] - test_sets[name] = data.dataset_from_sharded_hdf5( - folder, r_max=args.r_max, z_table=z_table, heads=heads, head=head_config.head_name - ) - for test_name, test_set in test_sets.items(): - test_sampler = None - if args.distributed: - test_sampler = torch.utils.data.distributed.DistributedSampler( - test_set, - num_replicas=world_size, - rank=rank, - shuffle=True, - drop_last=True, - seed=args.seed, - ) - try: - drop_last = test_set.drop_last - except AttributeError as e: # pylint: disable=W0612 - drop_last = False - test_loader = torch_geometric.dataloader.DataLoader( - test_set, - batch_size=args.valid_batch_size, - shuffle=(test_sampler is None), - drop_last=drop_last, - num_workers=args.num_workers, - pin_memory=args.pin_memory, - ) - test_data_loader[test_name] = test_loader - if stop_first_test: - break - - for swa_eval in swas: - epoch = checkpoint_handler.load_latest( - state=tools.CheckpointState(model, optimizer, lr_scheduler), - swa=swa_eval, - device=device, - ) - model.to(device) - if args.distributed: - distributed_model = DDP(model, device_ids=[local_rank]) - model_to_evaluate = model if not args.distributed else distributed_model - if swa_eval: - logging.info(f"Loaded Stage two model from epoch {epoch} for evaluation") - else: - logging.info(f"Loaded Stage one model from epoch {epoch} for evaluation") - - if rank == 0: - # Save entire model - if swa_eval: - model_path = Path(args.checkpoints_dir) / (tag + "_stagetwo.model") - else: - model_path = Path(args.checkpoints_dir) / (tag + ".model") - logging.info(f"Saving model to {model_path}") - model_to_save = deepcopy(model) - if args.enable_cueq: - print("RUNING CUEQ TO E3NN") - print("swa_eval", swa_eval) - model_to_save = run_cueq_to_e3nn(deepcopy(model), device=device) - if args.save_cpu: - model_to_save = model_to_save.to("cpu") - torch.save(model_to_save, model_path) - extra_files = { - "commit.txt": commit.encode("utf-8") if commit is not None else b"", - "config.yaml": json.dumps( - convert_to_json_format(extract_config_mace_model(model)) - ), - } - if swa_eval: - torch.save( - model_to_save, Path(args.model_dir) / (args.name + "_stagetwo.model") - ) - try: - path_complied = Path(args.model_dir) / ( - args.name + "_stagetwo_compiled.model" - ) - logging.info(f"Compiling model, saving metadata {path_complied}") - model_compiled = jit.compile(deepcopy(model_to_save)) - torch.jit.save( - model_compiled, - path_complied, - _extra_files=extra_files, - ) - except Exception as e: # pylint: disable=W0718 - pass - else: - torch.save(model_to_save, Path(args.model_dir) / (args.name + ".model")) - try: - path_complied = Path(args.model_dir) / ( - args.name + "_compiled.model" - ) - logging.info(f"Compiling model, saving metadata to {path_complied}") - model_compiled = jit.compile(deepcopy(model_to_save)) - torch.jit.save( - model_compiled, - path_complied, - _extra_files=extra_files, - ) - except Exception as e: # pylint: disable=W0718 - pass - - logging.info("Computing metrics for training, validation, and test sets") - for param in model.parameters(): - param.requires_grad = False - skip_heads = args.skip_evaluate_heads.split(",") if args.skip_evaluate_heads else [] - if skip_heads: - logging.info(f"Skipping evaluation for heads: {skip_heads}") - table_train_valid = create_error_table( - table_type=args.error_table, - all_data_loaders=train_valid_data_loader, - model=model_to_evaluate, - loss_fn=loss_fn, - output_args=output_args, - log_wandb=args.wandb, - device=device, - distributed=args.distributed, - skip_heads=skip_heads, - ) - logging.info("Error-table on TRAIN and VALID:\n" + str(table_train_valid)) - - if test_data_loader: - table_test = create_error_table( - table_type=args.error_table, - all_data_loaders=test_data_loader, - model=model_to_evaluate, - loss_fn=loss_fn, - output_args=output_args, - log_wandb=args.wandb, - device=device, - distributed=args.distributed, - ) - logging.info("Error-table on TEST:\n" + str(table_test)) - if args.plot: - try: - plotter = TrainingPlotter( - results_dir=logger.path, - heads=heads, - table_type=args.error_table, - train_valid_data=train_valid_data_loader, - test_data=test_data_loader, - output_args=output_args, - device=device, - plot_frequency=args.plot_frequency, - distributed=args.distributed, - swa_start=swa.start if swa else None - ) - plotter.plot(epoch, model_to_evaluate, rank) - except Exception as e: # pylint: disable=W0718 - logging.debug(f"Plotting failed: {e}") - - if args.distributed: - torch.distributed.barrier() - - logging.info("Done") - if args.distributed: - torch.distributed.destroy_process_group() - - -if __name__ == "__main__": - main() diff --git a/mace-bench/3rdparty/mace/mace/cli/select_head.py b/mace-bench/3rdparty/mace/mace/cli/select_head.py deleted file mode 100644 index 305ab52feb3cce118b2702a95c941ea95ff457d4..0000000000000000000000000000000000000000 --- a/mace-bench/3rdparty/mace/mace/cli/select_head.py +++ /dev/null @@ -1,60 +0,0 @@ -from argparse import ArgumentParser - -import torch - -from mace.tools.scripts_utils import remove_pt_head - - -def main(): - parser = ArgumentParser() - grp = parser.add_mutually_exclusive_group() - grp.add_argument( - "--head_name", - "-n", - help="name of the head to extract", - default=None, - ) - grp.add_argument( - "--list_heads", - "-l", - action="store_true", - help="list names of the heads", - ) - parser.add_argument( - "--target_device", - "-d", - help="target device, defaults to model's current device", - ) - parser.add_argument( - "--output_file", - "-o", - help="name for output model, defaults to model.head_name, followed by .target_device if specified", - ) - parser.add_argument("model_file", help="input model file path") - args = parser.parse_args() - - model = torch.load(args.model_file, map_location=args.target_device) - torch.set_default_dtype(next(model.parameters()).dtype) - - if args.list_heads: - print("Available heads:") - print("\n".join([" " + h for h in model.heads])) - else: - - if args.output_file is None: - args.output_file = ( - args.model_file - + "." - + args.head_name - + ("." + args.target_device if (args.target_device is not None) else "") - ) - - model_single = remove_pt_head(model, args.head_name) - if args.target_device is not None: - target_device = str(next(model.parameters()).device) - model_single.to(target_device) - torch.save(model_single, args.output_file) - - -if __name__ == "__main__": - main() diff --git a/mace-bench/3rdparty/mace/mace/cli/visualise_train.py b/mace-bench/3rdparty/mace/mace/cli/visualise_train.py deleted file mode 100644 index c380c70dd7599681298936015c986266c690abbe..0000000000000000000000000000000000000000 --- a/mace-bench/3rdparty/mace/mace/cli/visualise_train.py +++ /dev/null @@ -1,640 +0,0 @@ -import json -import logging -from typing import Dict, List, Optional - -import matplotlib.pyplot as plt -import numpy as np -import pandas as pd -import torch -import torch.distributed -from torchmetrics import Metric - -plt.rcParams.update({"font.size": 8}) -mpl_logger = logging.getLogger("matplotlib") -mpl_logger.setLevel(logging.WARNING) # Only show WARNING and above - -colors = [ - "#1f77b4", # muted blue - "#d62728", # brick red - "#7f7f7f", # middle gray - "#2ca02c", # cooked asparagus green - "#ff7f0e", # safety orange - "#9467bd", # muted purple - "#8c564b", # chestnut brown - "#e377c2", # raspberry yogurt pink - "#bcbd22", # curry yellow-green - "#17becf", # blue-teal -] - -error_type = { - "TotalRMSE": ( - [("rmse_e", "RMSE E [meV]"), ("rmse_f", "RMSE F [meV / A]")], - [("energy", "Energy per atom [eV]"), ("force", "Force [eV / A]")], - ), - "PerAtomRMSE": ( - [("rmse_e_per_atom", "RMSE E/atom [meV]"), ("rmse_f", "RMSE F [meV / A]")], - [("energy", "Energy per atom [eV]"), ("force", "Force [eV / A]")], - ), - "PerAtomRMSEstressvirials": ( - [ - ("rmse_e_per_atom", "RMSE E/atom [meV]"), - ("rmse_f", "RMSE F [meV / A]"), - ("rmse_stress", "RMSE Stress [meV / A^3]"), - ], - [ - ("energy", "Energy per atom [eV]"), - ("force", "Force [eV / A]"), - ("stress", "Stress [eV / A^3]"), - ], - ), - "PerAtomMAEstressvirials": ( - [ - ("mae_e_per_atom", "MAE E/atom [meV]"), - ("mae_f", "MAE F [meV / A]"), - ("mae_stress", "MAE Stress [meV / A^3]"), - ], - [ - ("energy", "Energy per atom [eV]"), - ("force", "Force [eV / A]"), - ("stress", "Stress [eV / A^3]"), - ], - ), - "TotalMAE": ( - [("mae_e", "MAE E [meV]"), ("mae_f", "MAE F [meV / A]")], - [("energy", "Energy per atom [eV]"), ("force", "Force [eV / A]")], - ), - "PerAtomMAE": ( - [("mae_e_per_atom", "MAE E/atom [meV]"), ("mae_f", "MAE F [meV / A]")], - [("energy", "Energy per atom [eV]"), ("force", "Force [eV / A]")], - ), - "DipoleRMSE": ( - [ - ("rmse_mu_per_atom", "RMSE MU/atom [mDebye]"), - ("rel_rmse_f", "Relative MU RMSE [%]"), - ], - [("dipole", "Dipole per atom [Debye]")], - ), - "DipoleMAE": ( - [("mae_mu", "MAE MU [mDebye]"), ("rel_mae_f", "Relative MU MAE [%]")], - [("dipole", "Dipole per atom [Debye]")], - ), - "EnergyDipoleRMSE": ( - [ - ("rmse_e_per_atom", "RMSE E/atom [meV]"), - ("rmse_f", "RMSE F [meV / A]"), - ("rmse_mu_per_atom", "RMSE MU/atom [mDebye]"), - ], - [ - ("energy", "Energy per atom [eV]"), - ("force", "Force [eV / A]"), - ("dipole", "Dipole per atom [Debye]"), - ], - ), -} - - -class TrainingPlotter: - def __init__( - self, - results_dir: str, - heads: List[str], - table_type: str, - train_valid_data: Dict, - test_data: Dict, - output_args: str, - device: str, - plot_frequency: int, - distributed: bool = False, - swa_start: Optional[int] = None, - ): - self.results_dir = results_dir - self.heads = heads - self.table_type = table_type - self.train_valid_data = train_valid_data - self.test_data = test_data - self.output_args = output_args - self.device = device - self.plot_frequency = plot_frequency - self.distributed = distributed - self.swa_start = swa_start - - def plot(self, model_epoch: str, model: torch.nn.Module, rank: int) -> None: - - # All ranks process data through model_inference - train_valid_dict = model_inference( - self.train_valid_data, - model, - self.output_args, - self.device, - self.distributed, - ) - test_dict = model_inference( - self.test_data, model, self.output_args, self.device, self.distributed - ) - - # Only rank 0 creates and saves plots - if rank != 0: - return - - data = pd.DataFrame( - results for results in parse_training_results(self.results_dir) - ) - labels, quantities = error_type[self.table_type] - - for head in self.heads: - fig = plt.figure(layout="constrained", figsize=(10, 6)) - fig.suptitle( - f"Model loaded from epoch {model_epoch} ({head} head)", fontsize=16 - ) - - subfigs = fig.subfigures(2, 1, height_ratios=[1, 1], hspace=0.05) - axsTop = subfigs[0].subplots(1, 2, sharey=False) - axsBottom = subfigs[1].subplots(1, len(quantities), sharey=False) - - plot_epoch_dependence(axsTop, data, head, model_epoch, labels) - - # Use the pre-computed results for plotting - plot_inference_from_results( - axsBottom, train_valid_dict, test_dict, head, quantities - ) - - if self.swa_start is not None: - # Add vertical lines to both axes - for ax in axsTop: - ax.axvline( - self.swa_start, - color="black", - linestyle="dashed", - linewidth=1, - alpha=0.6, - label="Stage Two Starts", - ) - stage = "stage_two" if self.swa_start < model_epoch else "stage_one" - else: - stage = "stage_one" - axsTop[0].legend(loc="best") - # Save the figure using the appropriate stage in the filename - filename = f"{self.results_dir[:-4]}_{head}_{stage}.png" - - fig.savefig(filename, dpi=300, bbox_inches="tight") - plt.close(fig) - - -def parse_training_results(path: str) -> List[dict]: - results = [] - with open(path, mode="r", encoding="utf-8") as f: - for line in f: - try: - d = json.loads(line.strip()) # Ensure it's valid JSON - results.append(d) - except json.JSONDecodeError: - print( - f"Skipping invalid line: {line.strip()}" - ) # Handle non-JSON lines gracefully - return results - - -def plot_epoch_dependence( - axes: np.ndarray, data: pd.DataFrame, head: str, model_epoch: str, labels: List[str] -) -> None: - - valid_data = ( - data[data["mode"] == "eval"] - .groupby(["mode", "epoch", "head"]) - .agg(["mean", "std"]) - .reset_index() - ) - valid_data = valid_data[valid_data["head"] == head] - train_data = ( - data[data["mode"] == "opt"] - .groupby(["mode", "epoch"]) - .agg(["mean", "std"]) - .reset_index() - ) - - # ---- Plot loss ---- - ax = axes[0] - ax.plot( - train_data["epoch"], train_data["loss"]["mean"], color=colors[1], linewidth=1 - ) - ax.set_ylabel("Training Loss", color=colors[1]) - ax.set_yscale("log") - - ax2 = ax.twinx() - ax2.plot( - valid_data["epoch"], valid_data["loss"]["mean"], color=colors[0], linewidth=1 - ) - ax2.set_ylabel("Validation Loss", color=colors[0]) - ax2.set_yscale("log") - - ax.axvline( - model_epoch, - color="black", - linestyle="solid", - linewidth=1, - alpha=0.8, - label="Loaded Model", - ) - ax.set_xlabel("Epoch") - ax.grid(True, linestyle="--", alpha=0.5) - - # ---- Plot selected keys ---- - ax = axes[1] - twin_axes = [] - for i, label in enumerate(labels): - color = colors[(i + 3)] - key, axis_label = label - if i == 0: - main_ax = ax - else: - main_ax = ax.twinx() - main_ax.spines.right.set_position(("outward", 60 * (i - 1))) - twin_axes.append(main_ax) - - main_ax.plot( - valid_data["epoch"], - valid_data[key]["mean"] * 1e3, - color=color, - label=label, - linewidth=1, - ) - main_ax.set_yscale("log") - main_ax.set_ylabel(axis_label, color=color) - main_ax.tick_params(axis="y", colors=color) - ax.axvline( - model_epoch, - color="black", - linestyle="solid", - linewidth=1, - alpha=0.8, - label="Loaded Model", - ) - ax.set_xlabel("Epoch") - ax.grid(True, linestyle="--", alpha=0.5) - - -# INFERENCE========= - - -def plot_inference_from_results( - axes: np.ndarray, - train_valid_dict: dict, - test_dict: dict, - head: str, - quantities: List[str], -) -> None: - - for ax, quantity in zip(axes, quantities): - key, label = quantity - - # Store legend handles to avoid duplicates - legend_labels = {} - - # Plot train/valid data (each entry keeps its own name) - for name, result in train_valid_dict.items(): - if "train" in name: - fixed_color_train_valid = colors[1] - marker = "x" - else: - fixed_color_train_valid = colors[0] - marker = "+" - if head not in name: - continue - - # Initialize scatter to None - scatter = None - - if key == "energy" and "energy" in result: - scatter = ax.scatter( - result["energy"]["reference_per_atom"], - result["energy"]["predicted_per_atom"], - marker=marker, - color=fixed_color_train_valid, - label=name, - ) - - elif key == "force" and "forces" in result: - scatter = ax.scatter( - result["forces"]["reference"], - result["forces"]["predicted"], - marker=marker, - color=fixed_color_train_valid, - label=name, - ) - - elif key == "stress" and "stress" in result: - scatter = ax.scatter( - result["stress"]["reference"], - result["stress"]["predicted"], - marker=marker, - color=fixed_color_train_valid, - label=name, - ) - - elif key == "virials" and "virials" in result: - scatter = ax.scatter( - result["virials"]["reference_per_atom"], - result["virials"]["predicted_per_atom"], - marker=marker, - color=fixed_color_train_valid, - label=name, - ) - - elif key == "dipole" and "dipole" in result: - scatter = ax.scatter( - result["dipole"]["reference_per_atom"], - result["dipole"]["predicted_per_atom"], - marker=marker, - color=fixed_color_train_valid, - label=name, - ) - - # Add each train/valid dataset's name to the legend if scatter was assigned - if scatter is not None: - legend_labels[name] = scatter - - fixed_color_test = colors[2] # Color for test dataset - - # Plot test data (single legend entry) - for name, result in test_dict.items(): - # Initialize scatter to None to avoid possibly used before assignment - scatter = None - - if key == "energy" and "energy" in result: - scatter = ax.scatter( - result["energy"]["reference_per_atom"], - result["energy"]["predicted_per_atom"], - marker="o", - color=fixed_color_test, - label="Test", - ) - - elif key == "force" and "forces" in result: - scatter = ax.scatter( - result["forces"]["reference"], - result["forces"]["predicted"], - marker="o", - color=fixed_color_test, - label="Test", - ) - - elif key == "stress" and "stress" in result: - scatter = ax.scatter( - result["stress"]["reference"], - result["stress"]["predicted"], - marker="o", - color=fixed_color_test, - label="Test", - ) - - elif key == "virials" and "virials" in result: - scatter = ax.scatter( - result["virials"]["reference_per_atom"], - result["virials"]["predicted_per_atom"], - marker="o", - color=fixed_color_test, - label="Test", - ) - - elif key == "dipole" and "dipole" in result: - scatter = ax.scatter( - result["dipole"]["reference_per_atom"], - result["dipole"]["predicted_per_atom"], - marker="o", - color=fixed_color_test, - label="Test", - ) - - # Only add to legend_labels if scatter was assigned - if scatter is not None: - legend_labels["Test"] = scatter - - # Add diagonal line for guide - min_val = min(ax.get_xlim()[0], ax.get_ylim()[0]) - max_val = max(ax.get_xlim()[1], ax.get_ylim()[1]) - ax.plot( - [min_val, max_val], - [min_val, max_val], - linestyle="--", - color="black", - alpha=0.7, - ) - - # Set legend with unique entries (Test + individual train/valid names) - if legend_labels: - ax.legend( - handles=legend_labels.values(), labels=legend_labels.keys(), loc="best" - ) - ax.set_xlabel(f"Reference {label}") - ax.set_ylabel(f"MACE {label}") - ax.grid(True, linestyle="--", alpha=0.5) - - -def model_inference( - all_data_loaders: dict, - model: torch.nn.Module, - output_args: Dict[str, bool], - device: str, - distributed: bool = False, -): - - for param in model.parameters(): - param.requires_grad = False - - results_dict = {} - - for name in all_data_loaders: - data_loader = all_data_loaders[name] - logging.debug(f"Running inference on {name} dataset") - scatter_metric = InferenceMetric().to(device) - - for batch in data_loader: - batch = batch.to(device) - batch_dict = batch.to_dict() - output = model( - batch_dict, - training=False, - compute_force=output_args.get("forces", False), - compute_virials=output_args.get("virials", False), - compute_stress=output_args.get("stress", False), - ) - - results = scatter_metric(batch, output) - - if distributed: - torch.distributed.barrier() - - results = scatter_metric.compute() - results_dict[name] = results - scatter_metric.reset() - - del data_loader - - for param in model.parameters(): - param.requires_grad = True - - return results_dict - - -def to_numpy(tensor: torch.Tensor) -> np.ndarray: - return tensor.cpu().detach().numpy() - - -class InferenceMetric(Metric): - """Metric class for collecting reference and predicted values for scatterplot visualization.""" - - def __init__(self): - super().__init__() - # Raw values - self.add_state("ref_energies", default=[], dist_reduce_fx="cat") - self.add_state("pred_energies", default=[], dist_reduce_fx="cat") - self.add_state("ref_forces", default=[], dist_reduce_fx="cat") - self.add_state("pred_forces", default=[], dist_reduce_fx="cat") - self.add_state("ref_stress", default=[], dist_reduce_fx="cat") - self.add_state("pred_stress", default=[], dist_reduce_fx="cat") - self.add_state("ref_virials", default=[], dist_reduce_fx="cat") - self.add_state("pred_virials", default=[], dist_reduce_fx="cat") - self.add_state("ref_dipole", default=[], dist_reduce_fx="cat") - self.add_state("pred_dipole", default=[], dist_reduce_fx="cat") - - # Per-atom normalized values - self.add_state("ref_energies_per_atom", default=[], dist_reduce_fx="cat") - self.add_state("pred_energies_per_atom", default=[], dist_reduce_fx="cat") - self.add_state("ref_virials_per_atom", default=[], dist_reduce_fx="cat") - self.add_state("pred_virials_per_atom", default=[], dist_reduce_fx="cat") - self.add_state("ref_dipole_per_atom", default=[], dist_reduce_fx="cat") - self.add_state("pred_dipole_per_atom", default=[], dist_reduce_fx="cat") - - # Store atom counts for each configuration - self.add_state("atom_counts", default=[], dist_reduce_fx="cat") - - # Counters - self.add_state("n_energy", default=torch.tensor(0.0), dist_reduce_fx="sum") - self.add_state("n_forces", default=torch.tensor(0.0), dist_reduce_fx="sum") - self.add_state("n_stress", default=torch.tensor(0.0), dist_reduce_fx="sum") - self.add_state("n_virials", default=torch.tensor(0.0), dist_reduce_fx="sum") - self.add_state("n_dipole", default=torch.tensor(0.0), dist_reduce_fx="sum") - - def update(self, batch, output): # pylint: disable=arguments-differ - """Update metric states with new batch data.""" - # Calculate number of atoms per configuration - atoms_per_config = batch.ptr[1:] - batch.ptr[:-1] - self.atom_counts.append(atoms_per_config) - - # Energy - if output.get("energy") is not None and batch.energy is not None: - self.n_energy += 1.0 - self.ref_energies.append(batch.energy) - self.pred_energies.append(output["energy"]) - # Per-atom normalization - self.ref_energies_per_atom.append(batch.energy / atoms_per_config) - self.pred_energies_per_atom.append(output["energy"] / atoms_per_config) - - # Forces - if output.get("forces") is not None and batch.forces is not None: - self.n_forces += 1.0 - self.ref_forces.append(batch.forces) - self.pred_forces.append(output["forces"]) - - # Stress - if output.get("stress") is not None and batch.stress is not None: - self.n_stress += 1.0 - self.ref_stress.append(batch.stress) - self.pred_stress.append(output["stress"]) - - # Virials - if output.get("virials") is not None and batch.virials is not None: - self.n_virials += 1.0 - self.ref_virials.append(batch.virials) - self.pred_virials.append(output["virials"]) - # Per-atom normalization - atoms_per_config_3d = atoms_per_config.view(-1, 1, 1) - self.ref_virials_per_atom.append(batch.virials / atoms_per_config_3d) - self.pred_virials_per_atom.append(output["virials"] / atoms_per_config_3d) - - # Dipole - if output.get("dipole") is not None and batch.dipole is not None: - self.n_dipole += 1.0 - self.ref_dipole.append(batch.dipole) - self.pred_dipole.append(output["dipole"]) - atoms_per_config_3d = atoms_per_config.view(-1, 1) - self.ref_dipole_per_atom.append(batch.dipole / atoms_per_config_3d) - self.pred_dipole_per_atom.append(output["dipole"] / atoms_per_config_3d) - - def _process_data(self, ref_list, pred_list): - # Handle different possible states of ref_list and pred_list in distributed mode - - # Check if this is a list type object - if isinstance(ref_list, (list, tuple)): - if len(ref_list) == 0: - return None, None - ref = torch.cat(ref_list).reshape(-1) - pred = torch.cat(pred_list).reshape(-1) - # Handle case where ref_list is already a tensor (happens after reset in distributed mode) - elif isinstance(ref_list, torch.Tensor): - ref = ref_list.reshape(-1) - pred = pred_list.reshape(-1) - # Handle other possible types - else: - return None, None - return to_numpy(ref), to_numpy(pred) - - def compute(self): - """Compute final results for scatterplot.""" - results = {} - - # Process energies - if self.n_energy: - ref_e, pred_e = self._process_data(self.ref_energies, self.pred_energies) - ref_e_pa, pred_e_pa = self._process_data( - self.ref_energies_per_atom, self.pred_energies_per_atom - ) - results["energy"] = { - "reference": ref_e, - "predicted": pred_e, - "reference_per_atom": ref_e_pa, - "predicted_per_atom": pred_e_pa, - } - - # Process forces - if self.n_forces: - ref_f, pred_f = self._process_data(self.ref_forces, self.pred_forces) - results["forces"] = { - "reference": ref_f, - "predicted": pred_f, - } - - # Process stress - if self.n_stress: - ref_s, pred_s = self._process_data(self.ref_stress, self.pred_stress) - results["stress"] = { - "reference": ref_s, - "predicted": pred_s, - } - - # Process virials - if self.n_virials: - ref_v, pred_v = self._process_data(self.ref_virials, self.pred_virials) - ref_v_pa, pred_v_pa = self._process_data( - self.ref_virials_per_atom, self.pred_virials_per_atom - ) - results["virials"] = { - "reference": ref_v, - "predicted": pred_v, - "reference_per_atom": ref_v_pa, - "predicted_per_atom": pred_v_pa, - } - - # Process dipoles - if self.n_dipole: - ref_d, pred_d = self._process_data(self.ref_dipole, self.pred_dipole) - ref_d_pa, pred_d_pa = self._process_data( - self.ref_dipole_per_atom, self.pred_dipole_per_atom - ) - results["dipole"] = { - "reference": ref_d, - "predicted": pred_d, - "reference_per_atom": ref_d_pa, - "predicted_per_atom": pred_d_pa, - } - return results diff --git a/mace-bench/3rdparty/mace/mace/data/__init__.py b/mace-bench/3rdparty/mace/mace/data/__init__.py deleted file mode 100644 index 8629cf521b395a4cfd2899b5f89a17d45dfa2749..0000000000000000000000000000000000000000 --- a/mace-bench/3rdparty/mace/mace/data/__init__.py +++ /dev/null @@ -1,40 +0,0 @@ -from .atomic_data import AtomicData -from .hdf5_dataset import HDF5Dataset, dataset_from_sharded_hdf5 -from .lmdb_dataset import LMDBDataset -from .neighborhood import get_neighborhood -from .utils import ( - Configuration, - Configurations, - KeySpecification, - compute_average_E0s, - config_from_atoms, - config_from_atoms_list, - load_from_xyz, - random_train_valid_split, - save_AtomicData_to_HDF5, - save_configurations_as_HDF5, - save_dataset_as_HDF5, - test_config_types, - update_keyspec_from_kwargs, -) - -__all__ = [ - "get_neighborhood", - "Configuration", - "Configurations", - "random_train_valid_split", - "load_from_xyz", - "test_config_types", - "config_from_atoms", - "config_from_atoms_list", - "AtomicData", - "compute_average_E0s", - "save_dataset_as_HDF5", - "HDF5Dataset", - "dataset_from_sharded_hdf5", - "save_AtomicData_to_HDF5", - "save_configurations_as_HDF5", - "KeySpecification", - "update_keyspec_from_kwargs", - "LMDBDataset", -] diff --git a/mace-bench/3rdparty/mace/mace/data/atomic_data.py b/mace-bench/3rdparty/mace/mace/data/atomic_data.py deleted file mode 100644 index 14dd39df3263633bbbe279427dfcbde64dd16097..0000000000000000000000000000000000000000 --- a/mace-bench/3rdparty/mace/mace/data/atomic_data.py +++ /dev/null @@ -1,300 +0,0 @@ -########################################################################################### -# Atomic Data Class for handling molecules as graphs -# Authors: Ilyes Batatia, Gregor Simm -# This program is distributed under the MIT License (see MIT.md) -########################################################################################### - -from copy import deepcopy -from typing import Optional, Sequence - -import torch.utils.data - -from mace.tools import ( - AtomicNumberTable, - atomic_numbers_to_indices, - to_one_hot, - torch_geometric, - voigt_to_matrix, -) - -from .neighborhood import get_neighborhood -from .utils import Configuration - - -class AtomicData(torch_geometric.data.Data): - num_graphs: torch.Tensor - batch: torch.Tensor - edge_index: torch.Tensor - node_attrs: torch.Tensor - edge_vectors: torch.Tensor - edge_lengths: torch.Tensor - positions: torch.Tensor - shifts: torch.Tensor - unit_shifts: torch.Tensor - cell: torch.Tensor - forces: torch.Tensor - energy: torch.Tensor - stress: torch.Tensor - virials: torch.Tensor - dipole: torch.Tensor - charges: torch.Tensor - weight: torch.Tensor - energy_weight: torch.Tensor - forces_weight: torch.Tensor - stress_weight: torch.Tensor - virials_weight: torch.Tensor - dipole_weight: torch.Tensor - charges_weight: torch.Tensor - - def __init__( - self, - edge_index: torch.Tensor, # [2, n_edges] - node_attrs: torch.Tensor, # [n_nodes, n_node_feats] - positions: torch.Tensor, # [n_nodes, 3] - shifts: torch.Tensor, # [n_edges, 3], - unit_shifts: torch.Tensor, # [n_edges, 3] - cell: Optional[torch.Tensor], # [3,3] - weight: Optional[torch.Tensor], # [,] - head: Optional[torch.Tensor], # [,] - energy_weight: Optional[torch.Tensor], # [,] - forces_weight: Optional[torch.Tensor], # [,] - stress_weight: Optional[torch.Tensor], # [,] - virials_weight: Optional[torch.Tensor], # [,] - dipole_weight: Optional[torch.Tensor], # [,] - charges_weight: Optional[torch.Tensor], # [,] - forces: Optional[torch.Tensor], # [n_nodes, 3] - energy: Optional[torch.Tensor], # [, ] - stress: Optional[torch.Tensor], # [1,3,3] - virials: Optional[torch.Tensor], # [1,3,3] - dipole: Optional[torch.Tensor], # [, 3] - charges: Optional[torch.Tensor], # [n_nodes, ] - ): - # Check shapes - num_nodes = node_attrs.shape[0] - - assert edge_index.shape[0] == 2 and len(edge_index.shape) == 2 - assert positions.shape == (num_nodes, 3) - assert shifts.shape[1] == 3 - assert unit_shifts.shape[1] == 3 - assert len(node_attrs.shape) == 2 - assert weight is None or len(weight.shape) == 0 - assert head is None or len(head.shape) == 0 - assert energy_weight is None or len(energy_weight.shape) == 0 - assert forces_weight is None or len(forces_weight.shape) == 0 - assert stress_weight is None or len(stress_weight.shape) == 0 - assert virials_weight is None or len(virials_weight.shape) == 0 - assert dipole_weight is None or dipole_weight.shape == (1, 3), dipole_weight - assert charges_weight is None or len(charges_weight.shape) == 0 - assert cell is None or cell.shape == (3, 3) - assert forces is None or forces.shape == (num_nodes, 3) - assert energy is None or len(energy.shape) == 0 - assert stress is None or stress.shape == (1, 3, 3) - assert virials is None or virials.shape == (1, 3, 3) - assert dipole is None or dipole.shape[-1] == 3 - assert charges is None or charges.shape == (num_nodes,) - # Aggregate data - data = { - "num_nodes": num_nodes, - "edge_index": edge_index, - "positions": positions, - "shifts": shifts, - "unit_shifts": unit_shifts, - "cell": cell, - "node_attrs": node_attrs, - "weight": weight, - "head": head, - "energy_weight": energy_weight, - "forces_weight": forces_weight, - "stress_weight": stress_weight, - "virials_weight": virials_weight, - "dipole_weight": dipole_weight, - "charges_weight": charges_weight, - "forces": forces, - "energy": energy, - "stress": stress, - "virials": virials, - "dipole": dipole, - "charges": charges, - } - super().__init__(**data) - - @classmethod - def from_config( - cls, - config: Configuration, - z_table: AtomicNumberTable, - cutoff: float, - heads: Optional[list] = None, - **kwargs, # pylint: disable=unused-argument - ) -> "AtomicData": - if heads is None: - heads = ["Default"] - edge_index, shifts, unit_shifts, cell = get_neighborhood( - positions=config.positions, - cutoff=cutoff, - pbc=deepcopy(config.pbc), - cell=deepcopy(config.cell), - ) - indices = atomic_numbers_to_indices(config.atomic_numbers, z_table=z_table) - one_hot = to_one_hot( - torch.tensor(indices, dtype=torch.long).unsqueeze(-1), - num_classes=len(z_table), - ) - try: - head = torch.tensor(heads.index(config.head), dtype=torch.long) - except ValueError: - head = torch.tensor(len(heads) - 1, dtype=torch.long) - - cell = ( - torch.tensor(cell, dtype=torch.get_default_dtype()) - if cell is not None - else torch.tensor( - 3 * [0.0, 0.0, 0.0], dtype=torch.get_default_dtype() - ).view(3, 3) - ) - - num_atoms = len(config.atomic_numbers) - - weight = ( - torch.tensor(config.weight, dtype=torch.get_default_dtype()) - if config.weight is not None - else torch.tensor(1.0, dtype=torch.get_default_dtype()) - ) - - energy_weight = ( - torch.tensor( - config.property_weights.get("energy"), dtype=torch.get_default_dtype() - ) - if config.property_weights.get("energy") is not None - else torch.tensor(1.0, dtype=torch.get_default_dtype()) - ) - - forces_weight = ( - torch.tensor( - config.property_weights.get("forces"), dtype=torch.get_default_dtype() - ) - if config.property_weights.get("forces") is not None - else torch.tensor(1.0, dtype=torch.get_default_dtype()) - ) - - stress_weight = ( - torch.tensor( - config.property_weights.get("stress"), dtype=torch.get_default_dtype() - ) - if config.property_weights.get("stress") is not None - else torch.tensor(1.0, dtype=torch.get_default_dtype()) - ) - - virials_weight = ( - torch.tensor( - config.property_weights.get("virials"), dtype=torch.get_default_dtype() - ) - if config.property_weights.get("virials") is not None - else torch.tensor(1.0, dtype=torch.get_default_dtype()) - ) - - dipole_weight = ( - torch.tensor( - config.property_weights.get("dipole"), dtype=torch.get_default_dtype() - ) - if config.property_weights.get("dipole") is not None - else torch.tensor([[1.0, 1.0, 1.0]], dtype=torch.get_default_dtype()) - ) - if len(dipole_weight.shape) == 0: - dipole_weight = dipole_weight * torch.tensor( - [[1.0, 1.0, 1.0]], dtype=torch.get_default_dtype() - ) - elif len(dipole_weight.shape) == 1: - dipole_weight = dipole_weight.unsqueeze(0) - - charges_weight = ( - torch.tensor( - config.property_weights.get("charges"), dtype=torch.get_default_dtype() - ) - if config.property_weights.get("charges") is not None - else torch.tensor(1.0, dtype=torch.get_default_dtype()) - ) - - forces = ( - torch.tensor( - config.properties.get("forces"), dtype=torch.get_default_dtype() - ) - if config.properties.get("forces") is not None - else torch.zeros(num_atoms, 3, dtype=torch.get_default_dtype()) - ) - energy = ( - torch.tensor( - config.properties.get("energy"), dtype=torch.get_default_dtype() - ) - if config.properties.get("energy") is not None - else torch.tensor(0.0, dtype=torch.get_default_dtype()) - ) - stress = ( - voigt_to_matrix( - torch.tensor( - config.properties.get("stress"), dtype=torch.get_default_dtype() - ) - ).unsqueeze(0) - if config.properties.get("stress") is not None - else torch.zeros(1, 3, 3, dtype=torch.get_default_dtype()) - ) - virials = ( - voigt_to_matrix( - torch.tensor( - config.properties.get("virials"), dtype=torch.get_default_dtype() - ) - ).unsqueeze(0) - if config.properties.get("virials") is not None - else torch.zeros(1, 3, 3, dtype=torch.get_default_dtype()) - ) - dipole = ( - torch.tensor( - config.properties.get("dipole"), dtype=torch.get_default_dtype() - ).unsqueeze(0) - if config.properties.get("dipole") is not None - else torch.zeros(1, 3, dtype=torch.get_default_dtype()) - ) - charges = ( - torch.tensor( - config.properties.get("charges"), dtype=torch.get_default_dtype() - ) - if config.properties.get("charges") is not None - else torch.zeros(num_atoms, dtype=torch.get_default_dtype()) - ) - - return cls( - edge_index=torch.tensor(edge_index, dtype=torch.long), - positions=torch.tensor(config.positions, dtype=torch.get_default_dtype()), - shifts=torch.tensor(shifts, dtype=torch.get_default_dtype()), - unit_shifts=torch.tensor(unit_shifts, dtype=torch.get_default_dtype()), - cell=cell, - node_attrs=one_hot, - weight=weight, - head=head, - energy_weight=energy_weight, - forces_weight=forces_weight, - stress_weight=stress_weight, - virials_weight=virials_weight, - dipole_weight=dipole_weight, - charges_weight=charges_weight, - forces=forces, - energy=energy, - stress=stress, - virials=virials, - dipole=dipole, - charges=charges, - ) - - -def get_data_loader( - dataset: Sequence[AtomicData], - batch_size: int, - shuffle=True, - drop_last=False, -) -> torch.utils.data.DataLoader: - return torch_geometric.dataloader.DataLoader( - dataset=dataset, - batch_size=batch_size, - shuffle=shuffle, - drop_last=drop_last, - ) diff --git a/mace-bench/3rdparty/mace/mace/data/hdf5_dataset.py b/mace-bench/3rdparty/mace/mace/data/hdf5_dataset.py deleted file mode 100644 index ab6aa7c7095b756ff0e020c0821bd6efafda9aed..0000000000000000000000000000000000000000 --- a/mace-bench/3rdparty/mace/mace/data/hdf5_dataset.py +++ /dev/null @@ -1,97 +0,0 @@ -from glob import glob -from typing import List - -import h5py -from torch.utils.data import ConcatDataset, Dataset - -from mace.data.atomic_data import AtomicData -from mace.data.utils import Configuration -from mace.tools.utils import AtomicNumberTable - - -class HDF5Dataset(Dataset): - def __init__( - self, file_path, r_max, z_table, atomic_dataclass=AtomicData, **kwargs - ): - super(HDF5Dataset, self).__init__() # pylint: disable=super-with-arguments - self.file_path = file_path - self._file = None - batch_key = list(self.file.keys())[0] - self.batch_size = len(self.file[batch_key].keys()) - self.length = len(self.file.keys()) * self.batch_size - self.r_max = r_max - self.z_table = z_table - self.atomic_dataclass = atomic_dataclass - try: - self.drop_last = bool(self.file.attrs["drop_last"]) - except KeyError: - self.drop_last = False - self.kwargs = kwargs - - @property - def file(self): - if self._file is None: - # If a file has not already been opened, open one here - self._file = h5py.File(self.file_path, "r") - return self._file - - def __getstate__(self): - _d = dict(self.__dict__) - - # An opened h5py.File cannot be pickled, so we must exclude it from the state - _d["_file"] = None - return _d - - def __len__(self): - return self.length - - def __getitem__(self, index): - # compute the index of the batch - batch_index = index // self.batch_size - config_index = index % self.batch_size - grp = self.file["config_batch_" + str(batch_index)] - subgrp = grp["config_" + str(config_index)] - - properties = {} - property_weights = {} - for key in subgrp["properties"]: - properties[key] = unpack_value(subgrp["properties"][key][()]) - for key in subgrp["property_weights"]: - property_weights[key] = unpack_value(subgrp["property_weights"][key][()]) - - config = Configuration( - atomic_numbers=subgrp["atomic_numbers"][()], - positions=subgrp["positions"][()], - properties=properties, - weight=unpack_value(subgrp["weight"][()]), - property_weights=property_weights, - config_type=unpack_value(subgrp["config_type"][()]), - pbc=unpack_value(subgrp["pbc"][()]), - cell=unpack_value(subgrp["cell"][()]), - ) - if config.head is None: - config.head = self.kwargs.get("head") - atomic_data = self.atomic_dataclass.from_config( - config, - z_table=self.z_table, - cutoff=self.r_max, - heads=self.kwargs.get("heads", ["Default"]), - **{k: v for k, v in self.kwargs.items() if k != "heads"}, - ) - return atomic_data - - -def dataset_from_sharded_hdf5( - files: List, z_table: AtomicNumberTable, r_max: float, **kwargs -): - files = glob(files + "/*") - datasets = [] - for file in files: - datasets.append(HDF5Dataset(file, z_table=z_table, r_max=r_max, **kwargs)) - full_dataset = ConcatDataset(datasets) - return full_dataset - - -def unpack_value(value): - value = value.decode("utf-8") if isinstance(value, bytes) else value - return None if str(value) == "None" else value diff --git a/mace-bench/3rdparty/mace/mace/data/lmdb_dataset.py b/mace-bench/3rdparty/mace/mace/data/lmdb_dataset.py deleted file mode 100644 index e1ebbdaf54f3faee0fd5453cd1c509510d14c9d5..0000000000000000000000000000000000000000 --- a/mace-bench/3rdparty/mace/mace/data/lmdb_dataset.py +++ /dev/null @@ -1,69 +0,0 @@ -import os - -import numpy as np -from torch.utils.data import Dataset - -from mace.data.atomic_data import AtomicData -from mace.data.utils import KeySpecification, config_from_atoms -from mace.tools.default_keys import DefaultKeys -from mace.tools.fairchem_dataset import AseDBDataset - - -class LMDBDataset(Dataset): - def __init__(self, file_path, r_max, z_table, **kwargs): - dataset_paths = file_path.split(":") # using : split multiple paths - # make sure each of the path exist - for path in dataset_paths: - assert os.path.exists(path) - config_kwargs = {} - super(LMDBDataset, self).__init__() # pylint: disable=super-with-arguments - self.AseDB = AseDBDataset(config=dict(src=dataset_paths, **config_kwargs)) - self.r_max = r_max - self.z_table = z_table - - self.kwargs = kwargs - self.transform = kwargs["transform"] if "transform" in kwargs else None - - def __len__(self): - return len(self.AseDB) - - def __getitem__(self, index): - try: - atoms = self.AseDB.get_atoms(self.AseDB.ids[index]) - except Exception as e: # pylint: disable=broad-except - print(f"Error in index {index}") - print(e) - return None - assert np.sum(atoms.get_cell() == atoms.cell) == 9 - - if hasattr(atoms, "calc") and hasattr(atoms.calc, "results"): - if "energy" in atoms.calc.results: - atoms.info[DefaultKeys.ENERGY.value] = atoms.calc.results["energy"] - if "forces" in atoms.calc.results: - atoms.arrays[DefaultKeys.FORCES.value] = atoms.calc.results["forces"] - if "stress" in atoms.calc.results: - atoms.info[DefaultKeys.STRESS.value] = atoms.calc.results["stress"] - - config = config_from_atoms( - atoms, - key_specification=KeySpecification.from_defaults(), - ) - - # Set head if not already set - if config.head == "Default": - config.head = self.kwargs.get("head", "Default") - - try: - atomic_data = AtomicData.from_config( - config, - z_table=self.z_table, - cutoff=self.r_max, - heads=self.kwargs.get("heads", ["Default"]), - ) - except Exception as e: # pylint: disable=broad-except - print(f"Error in index {index}") - print(e) - - if self.transform: - atomic_data = self.transform(atomic_data) - return atomic_data diff --git a/mace-bench/3rdparty/mace/mace/data/neighborhood.py b/mace-bench/3rdparty/mace/mace/data/neighborhood.py deleted file mode 100644 index 03728969df6af8111b9bab8aa1602c8fa73e8082..0000000000000000000000000000000000000000 --- a/mace-bench/3rdparty/mace/mace/data/neighborhood.py +++ /dev/null @@ -1,66 +0,0 @@ -from typing import Optional, Tuple - -import numpy as np -from matscipy.neighbours import neighbour_list - - -def get_neighborhood( - positions: np.ndarray, # [num_positions, 3] - cutoff: float, - pbc: Optional[Tuple[bool, bool, bool]] = None, - cell: Optional[np.ndarray] = None, # [3, 3] - true_self_interaction=False, -) -> Tuple[np.ndarray, np.ndarray, np.ndarray, np.ndarray]: - if pbc is None: - pbc = (False, False, False) - - if cell is None or cell.any() == np.zeros((3, 3)).any(): - cell = np.identity(3, dtype=float) - - assert len(pbc) == 3 and all(isinstance(i, (bool, np.bool_)) for i in pbc) - assert cell.shape == (3, 3) - - pbc_x = pbc[0] - pbc_y = pbc[1] - pbc_z = pbc[2] - identity = np.identity(3, dtype=float) - max_positions = np.max(np.absolute(positions)) + 1 - # Extend cell in non-periodic directions - # For models with more than 5 layers, the multiplicative constant needs to be increased. - # temp_cell = np.copy(cell) - if not pbc_x: - cell[0, :] = max_positions * 5 * cutoff * identity[0, :] - if not pbc_y: - cell[1, :] = max_positions * 5 * cutoff * identity[1, :] - if not pbc_z: - cell[2, :] = max_positions * 5 * cutoff * identity[2, :] - - sender, receiver, unit_shifts = neighbour_list( - quantities="ijS", - pbc=pbc, - cell=cell, - positions=positions, - cutoff=cutoff, - # self_interaction=True, # we want edges from atom to itself in different periodic images - # use_scaled_positions=False, # positions are not scaled positions - ) - - if not true_self_interaction: - # Eliminate self-edges that don't cross periodic boundaries - true_self_edge = sender == receiver - true_self_edge &= np.all(unit_shifts == 0, axis=1) - keep_edge = ~true_self_edge - - # Note: after eliminating self-edges, it can be that no edges remain in this system - sender = sender[keep_edge] - receiver = receiver[keep_edge] - unit_shifts = unit_shifts[keep_edge] - - # Build output - edge_index = np.stack((sender, receiver)) # [2, n_edges] - - # From the docs: With the shift vector S, the distances D between atoms can be computed from - # D = positions[j]-positions[i]+S.dot(cell) - shifts = np.dot(unit_shifts, cell) # [n_edges, 3] - - return edge_index, shifts, unit_shifts, cell diff --git a/mace-bench/3rdparty/mace/mace/data/utils.py b/mace-bench/3rdparty/mace/mace/data/utils.py deleted file mode 100644 index 947ee60f4f1941f390a0f8ba52b821a7ed45e90b..0000000000000000000000000000000000000000 --- a/mace-bench/3rdparty/mace/mace/data/utils.py +++ /dev/null @@ -1,368 +0,0 @@ -########################################################################################### -# Data parsing utilities -# Authors: Ilyes Batatia, Gregor Simm and David Kovacs -# This program is distributed under the MIT License (see MIT.md) -########################################################################################### - -import logging -from dataclasses import dataclass, field -from typing import Any, Dict, List, Optional, Sequence, Tuple - -import ase.data -import ase.io -import h5py -import numpy as np - -from mace.tools import AtomicNumberTable, DefaultKeys - -Positions = np.ndarray # [..., 3] -Cell = np.ndarray # [3,3] -Pbc = tuple # (3,) - -DEFAULT_CONFIG_TYPE = "Default" -DEFAULT_CONFIG_TYPE_WEIGHTS = {DEFAULT_CONFIG_TYPE: 1.0} - - -@dataclass -class KeySpecification: - info_keys: Dict[str, str] = field(default_factory=dict) - arrays_keys: Dict[str, str] = field(default_factory=dict) - - def update( - self, - info_keys: Optional[Dict[str, str]] = None, - arrays_keys: Optional[Dict[str, str]] = None, - ): - if info_keys is not None: - self.info_keys.update(info_keys) - if arrays_keys is not None: - self.arrays_keys.update(arrays_keys) - return self - - @classmethod - def from_defaults(cls): - instance = cls() - return update_keyspec_from_kwargs(instance, DefaultKeys.keydict()) - - -def update_keyspec_from_kwargs( - keyspec: KeySpecification, keydict: Dict[str, str] -) -> KeySpecification: - # convert command line style property_key arguments into a keyspec - infos = ["energy_key", "stress_key", "virials_key", "dipole_key", "head_key"] - arrays = ["forces_key", "charges_key"] - info_keys = {} - arrays_keys = {} - for key in infos: - if key in keydict: - info_keys[key[:-4]] = keydict[key] - for key in arrays: - if key in keydict: - arrays_keys[key[:-4]] = keydict[key] - keyspec.update(info_keys=info_keys, arrays_keys=arrays_keys) - return keyspec - - -@dataclass -class Configuration: - atomic_numbers: np.ndarray - positions: Positions # Angstrom - properties: Dict[str, Any] - property_weights: Dict[str, float] - cell: Optional[Cell] = None - pbc: Optional[Pbc] = None - - weight: float = 1.0 # weight of config in loss - config_type: str = DEFAULT_CONFIG_TYPE # config_type of config - head: str = "Default" # head used to compute the config - - -Configurations = List[Configuration] - - -def random_train_valid_split( - items: Sequence, valid_fraction: float, seed: int, work_dir: str -) -> Tuple[List, List]: - assert 0.0 < valid_fraction < 1.0 - - size = len(items) - train_size = size - int(valid_fraction * size) - - indices = list(range(size)) - rng = np.random.default_rng(seed) - rng.shuffle(indices) - if len(indices[train_size:]) < 10: - logging.info( - f"Using random {100 * valid_fraction:.0f}% of training set for validation with following indices: {indices[train_size:]}" - ) - else: - # Save indices to file - with open(work_dir + f"/valid_indices_{seed}.txt", "w", encoding="utf-8") as f: - for index in indices[train_size:]: - f.write(f"{index}\n") - - logging.info( - f"Using random {100 * valid_fraction:.0f}% of training set for validation with indices saved in: {work_dir}/valid_indices_{seed}.txt" - ) - - return ( - [items[i] for i in indices[:train_size]], - [items[i] for i in indices[train_size:]], - ) - - -def config_from_atoms_list( - atoms_list: List[ase.Atoms], - key_specification: KeySpecification, - config_type_weights: Optional[Dict[str, float]] = None, - head_name: str = "Default", -) -> Configurations: - """Convert list of ase.Atoms into Configurations""" - if config_type_weights is None: - config_type_weights = DEFAULT_CONFIG_TYPE_WEIGHTS - - all_configs = [] - for atoms in atoms_list: - all_configs.append( - config_from_atoms( - atoms, - key_specification=key_specification, - config_type_weights=config_type_weights, - head_name=head_name, - ) - ) - return all_configs - - -def config_from_atoms( - atoms: ase.Atoms, - key_specification: KeySpecification = KeySpecification(), - config_type_weights: Optional[Dict[str, float]] = None, - head_name: str = "Default", -) -> Configuration: - """Convert ase.Atoms to Configuration""" - if config_type_weights is None: - config_type_weights = DEFAULT_CONFIG_TYPE_WEIGHTS - - atomic_numbers = np.array( - [ase.data.atomic_numbers[symbol] for symbol in atoms.symbols] - ) - pbc = tuple(atoms.get_pbc()) - cell = np.array(atoms.get_cell()) - config_type = atoms.info.get("config_type", "Default") - weight = atoms.info.get("config_weight", 1.0) * config_type_weights.get( - config_type, 1.0 - ) - - properties = {} - property_weights = {} - for name in list(key_specification.arrays_keys) + list(key_specification.info_keys): - property_weights[name] = atoms.info.get(f"config_{name}_weight", 1.0) - - for name, atoms_key in key_specification.info_keys.items(): - properties[name] = atoms.info.get(atoms_key, None) - if not atoms_key in atoms.info: - property_weights[name] = 0.0 - - for name, atoms_key in key_specification.arrays_keys.items(): - properties[name] = atoms.arrays.get(atoms_key, None) - if not atoms_key in atoms.arrays: - property_weights[name] = 0.0 - - return Configuration( - atomic_numbers=atomic_numbers, - positions=atoms.get_positions(), - properties=properties, - weight=weight, - property_weights=property_weights, - head=head_name, - config_type=config_type, - pbc=pbc, - cell=cell, - ) - - -def test_config_types( - test_configs: Configurations, -) -> List[Tuple[str, List[Configuration]]]: - """Split test set based on config_type-s""" - test_by_ct = [] - all_cts = [] - for conf in test_configs: - config_type_name = conf.config_type + "_" + conf.head - if config_type_name not in all_cts: - all_cts.append(config_type_name) - test_by_ct.append((config_type_name, [conf])) - else: - ind = all_cts.index(config_type_name) - test_by_ct[ind][1].append(conf) - return test_by_ct - - -def load_from_xyz( - file_path: str, - key_specification: KeySpecification, - head_name: str = "Default", - config_type_weights: Optional[Dict] = None, - extract_atomic_energies: bool = False, - keep_isolated_atoms: bool = False, -) -> Tuple[Dict[int, float], Configurations]: - atoms_list = ase.io.read(file_path, index=":") - energy_key = key_specification.info_keys["energy"] - forces_key = key_specification.arrays_keys["forces"] - stress_key = key_specification.info_keys["stress"] - head_key = key_specification.info_keys["head"] - if energy_key == "energy": - logging.warning( - "Since ASE version 3.23.0b1, using energy_key 'energy' is no longer safe when communicating between MACE and ASE. We recommend using a different key, rewriting 'energy' to 'REF_energy'. You need to use --energy_key='REF_energy' to specify the chosen key name." - ) - key_specification.info_keys["energy"] = "REF_energy" - for atoms in atoms_list: - try: - atoms.info["REF_energy"] = atoms.get_potential_energy() - except Exception as e: # pylint: disable=W0703 - logging.error(f"Failed to extract energy: {e}") - atoms.info["REF_energy"] = None - if forces_key == "forces": - logging.warning( - "Since ASE version 3.23.0b1, using forces_key 'forces' is no longer safe when communicating between MACE and ASE. We recommend using a different key, rewriting 'forces' to 'REF_forces'. You need to use --forces_key='REF_forces' to specify the chosen key name." - ) - key_specification.arrays_keys["forces"] = "REF_forces" - for atoms in atoms_list: - try: - atoms.arrays["REF_forces"] = atoms.get_forces() - except Exception as e: # pylint: disable=W0703 - logging.error(f"Failed to extract forces: {e}") - atoms.arrays["REF_forces"] = None - if stress_key == "stress": - logging.warning( - "Since ASE version 3.23.0b1, using stress_key 'stress' is no longer safe when communicating between MACE and ASE. We recommend using a different key, rewriting 'stress' to 'REF_stress'. You need to use --stress_key='REF_stress' to specify the chosen key name." - ) - key_specification.info_keys["stress"] = "REF_stress" - for atoms in atoms_list: - try: - atoms.info["REF_stress"] = atoms.get_stress() - except Exception as e: # pylint: disable=W0703 - atoms.info["REF_stress"] = None - if not isinstance(atoms_list, list): - atoms_list = [atoms_list] - - atomic_energies_dict = {} - if extract_atomic_energies: - atoms_without_iso_atoms = [] - - for idx, atoms in enumerate(atoms_list): - atoms.info[head_key] = head_name - isolated_atom_config = ( - len(atoms) == 1 and atoms.info.get("config_type") == "IsolatedAtom" - ) - if isolated_atom_config: - atomic_number = int(atoms.get_atomic_numbers()[0]) - if energy_key in atoms.info.keys(): - atomic_energies_dict[atomic_number] = float(atoms.info[energy_key]) - else: - logging.warning( - f"Configuration '{idx}' is marked as 'IsolatedAtom' " - "but does not contain an energy. Zero energy will be used." - ) - atomic_energies_dict[atomic_number] = 0.0 - else: - atoms_without_iso_atoms.append(atoms) - - if len(atomic_energies_dict) > 0: - logging.info("Using isolated atom energies from training file") - if not keep_isolated_atoms: - atoms_list = atoms_without_iso_atoms - - for atoms in atoms_list: - atoms.info[head_key] = head_name - - configs = config_from_atoms_list( - atoms_list, - config_type_weights=config_type_weights, - key_specification=key_specification, - head_name=head_name, - ) - return atomic_energies_dict, configs - - -def compute_average_E0s( - collections_train: Configurations, z_table: AtomicNumberTable -) -> Dict[int, float]: - """ - Function to compute the average interaction energy of each chemical element - returns dictionary of E0s - """ - len_train = len(collections_train) - len_zs = len(z_table) - A = np.zeros((len_train, len_zs)) - B = np.zeros(len_train) - for i in range(len_train): - B[i] = collections_train[i].properties["energy"] - for j, z in enumerate(z_table.zs): - A[i, j] = np.count_nonzero(collections_train[i].atomic_numbers == z) - try: - E0s = np.linalg.lstsq(A, B, rcond=None)[0] - atomic_energies_dict = {} - for i, z in enumerate(z_table.zs): - atomic_energies_dict[z] = E0s[i] - except np.linalg.LinAlgError: - logging.error( - "Failed to compute E0s using least squares regression, using the same for all atoms" - ) - atomic_energies_dict = {} - for i, z in enumerate(z_table.zs): - atomic_energies_dict[z] = 0.0 - return atomic_energies_dict - - -def save_dataset_as_HDF5(dataset: List, out_name: str) -> None: - with h5py.File(out_name, "w") as f: - for i, data in enumerate(dataset): - save_AtomicData_to_HDF5(data, i, f) - - -def save_AtomicData_to_HDF5(data, i, h5_file) -> None: - grp = h5_file.create_group(f"config_{i}") - grp["num_nodes"] = data.num_nodes - grp["edge_index"] = data.edge_index - grp["positions"] = data.positions - grp["shifts"] = data.shifts - grp["unit_shifts"] = data.unit_shifts - grp["cell"] = data.cell - grp["node_attrs"] = data.node_attrs - grp["weight"] = data.weight - grp["energy_weight"] = data.energy_weight - grp["forces_weight"] = data.forces_weight - grp["stress_weight"] = data.stress_weight - grp["virials_weight"] = data.virials_weight - grp["forces"] = data.forces - grp["energy"] = data.energy - grp["stress"] = data.stress - grp["virials"] = data.virials - grp["dipole"] = data.dipole - grp["charges"] = data.charges - grp["head"] = data.head - - -def save_configurations_as_HDF5(configurations: Configurations, _, h5_file) -> None: - grp = h5_file.create_group("config_batch_0") - for j, config in enumerate(configurations): - subgroup_name = f"config_{j}" - subgroup = grp.create_group(subgroup_name) - subgroup["atomic_numbers"] = write_value(config.atomic_numbers) - subgroup["positions"] = write_value(config.positions) - properties_subgrp = subgroup.create_group("properties") - for key, value in config.properties.items(): - properties_subgrp[key] = write_value(value) - subgroup["cell"] = write_value(config.cell) - subgroup["pbc"] = write_value(config.pbc) - subgroup["weight"] = write_value(config.weight) - weights_subgrp = subgroup.create_group("property_weights") - for key, value in config.property_weights.items(): - weights_subgrp[key] = write_value(value) - subgroup["config_type"] = write_value(config.config_type) - - -def write_value(value): - return value if value is not None else "None" diff --git a/mace-bench/3rdparty/mace/mace/modules/__init__.py b/mace-bench/3rdparty/mace/mace/modules/__init__.py deleted file mode 100644 index 40a29d334a0a112ec6c4209711bfdac6f550bc6d..0000000000000000000000000000000000000000 --- a/mace-bench/3rdparty/mace/mace/modules/__init__.py +++ /dev/null @@ -1,100 +0,0 @@ -from typing import Callable, Dict, Optional, Type - -import torch - -from .blocks import ( - AtomicEnergiesBlock, - EquivariantProductBasisBlock, - InteractionBlock, - LinearDipoleReadoutBlock, - LinearNodeEmbeddingBlock, - LinearReadoutBlock, - NonLinearDipoleReadoutBlock, - NonLinearReadoutBlock, - RadialEmbeddingBlock, - RealAgnosticAttResidualInteractionBlock, - RealAgnosticDensityInteractionBlock, - RealAgnosticDensityResidualInteractionBlock, - RealAgnosticInteractionBlock, - RealAgnosticResidualInteractionBlock, - ScaleShiftBlock, -) -from .loss import ( - DipoleSingleLoss, - UniversalLoss, - WeightedEnergyForcesDipoleLoss, - WeightedEnergyForcesL1L2Loss, - WeightedEnergyForcesLoss, - WeightedEnergyForcesStressLoss, - WeightedEnergyForcesVirialsLoss, - WeightedForcesLoss, - WeightedHuberEnergyForcesStressLoss, -) -from .models import MACE, AtomicDipolesMACE, EnergyDipolesMACE, ScaleShiftMACE -from .radial import BesselBasis, GaussianBasis, PolynomialCutoff, ZBLBasis -from .symmetric_contraction import SymmetricContraction -from .utils import ( - compute_avg_num_neighbors, - compute_fixed_charge_dipole, - compute_mean_rms_energy_forces, - compute_mean_std_atomic_inter_energy, - compute_rms_dipoles, - compute_statistics, -) - -interaction_classes: Dict[str, Type[InteractionBlock]] = { - "RealAgnosticResidualInteractionBlock": RealAgnosticResidualInteractionBlock, - "RealAgnosticAttResidualInteractionBlock": RealAgnosticAttResidualInteractionBlock, - "RealAgnosticInteractionBlock": RealAgnosticInteractionBlock, - "RealAgnosticDensityInteractionBlock": RealAgnosticDensityInteractionBlock, - "RealAgnosticDensityResidualInteractionBlock": RealAgnosticDensityResidualInteractionBlock, -} - -scaling_classes: Dict[str, Callable] = { - "std_scaling": compute_mean_std_atomic_inter_energy, - "rms_forces_scaling": compute_mean_rms_energy_forces, - "rms_dipoles_scaling": compute_rms_dipoles, -} - -gate_dict: Dict[str, Optional[Callable]] = { - "abs": torch.abs, - "tanh": torch.tanh, - "silu": torch.nn.functional.silu, - "None": None, -} - -__all__ = [ - "AtomicEnergiesBlock", - "RadialEmbeddingBlock", - "ZBLBasis", - "LinearNodeEmbeddingBlock", - "LinearReadoutBlock", - "EquivariantProductBasisBlock", - "ScaleShiftBlock", - "LinearDipoleReadoutBlock", - "NonLinearDipoleReadoutBlock", - "InteractionBlock", - "NonLinearReadoutBlock", - "PolynomialCutoff", - "BesselBasis", - "GaussianBasis", - "MACE", - "ScaleShiftMACE", - "AtomicDipolesMACE", - "EnergyDipolesMACE", - "WeightedEnergyForcesLoss", - "WeightedForcesLoss", - "WeightedEnergyForcesVirialsLoss", - "WeightedEnergyForcesStressLoss", - "DipoleSingleLoss", - "WeightedEnergyForcesDipoleLoss", - "WeightedHuberEnergyForcesStressLoss", - "UniversalLoss", - "WeightedEnergyForcesL1L2Loss", - "SymmetricContraction", - "interaction_classes", - "compute_mean_std_atomic_inter_energy", - "compute_avg_num_neighbors", - "compute_statistics", - "compute_fixed_charge_dipole", -] diff --git a/mace-bench/3rdparty/mace/mace/modules/blocks.py b/mace-bench/3rdparty/mace/mace/modules/blocks.py deleted file mode 100644 index bf1e2dad84939ce2efb9606697a1c7bc8c8564e5..0000000000000000000000000000000000000000 --- a/mace-bench/3rdparty/mace/mace/modules/blocks.py +++ /dev/null @@ -1,922 +0,0 @@ -########################################################################################### -# Elementary Block for Building O(3) Equivariant Higher Order Message Passing Neural Network -# Authors: Ilyes Batatia, Gregor Simm -# This program is distributed under the MIT License (see MIT.md) -########################################################################################### - -from abc import abstractmethod -from typing import Any, Callable, List, Optional, Tuple, Union - -import numpy as np -import torch.nn.functional -from e3nn import nn, o3 -from e3nn.util.jit import compile_mode - -from mace.modules.wrapper_ops import ( - CuEquivarianceConfig, - FullyConnectedTensorProduct, - Linear, - SymmetricContractionWrapper, - TensorProduct, -) -from mace.tools.compile import simplify_if_compile -from mace.tools.scatter import scatter_sum -from mace.tools.utils import LAMMPS_MP - -from .irreps_tools import mask_head, reshape_irreps, tp_out_irreps_with_instructions -from .radial import ( - AgnesiTransform, - BesselBasis, - ChebychevBasis, - GaussianBasis, - PolynomialCutoff, - SoftTransform, -) - - -@compile_mode("script") -class LinearNodeEmbeddingBlock(torch.nn.Module): - def __init__( - self, - irreps_in: o3.Irreps, - irreps_out: o3.Irreps, - cueq_config: Optional[CuEquivarianceConfig] = None, - ): - super().__init__() - self.linear = Linear( - irreps_in=irreps_in, irreps_out=irreps_out, cueq_config=cueq_config - ) - - def forward( - self, - node_attrs: torch.Tensor, - ) -> torch.Tensor: # [n_nodes, irreps] - return self.linear(node_attrs) - - -@compile_mode("script") -class LinearReadoutBlock(torch.nn.Module): - def __init__( - self, - irreps_in: o3.Irreps, - irrep_out: o3.Irreps = o3.Irreps("0e"), - cueq_config: Optional[CuEquivarianceConfig] = None, - ): - super().__init__() - self.linear = Linear( - irreps_in=irreps_in, irreps_out=irrep_out, cueq_config=cueq_config - ) - - def forward( - self, - x: torch.Tensor, - heads: Optional[torch.Tensor] = None, # pylint: disable=unused-argument - ) -> torch.Tensor: # [n_nodes, irreps] # [..., ] - return self.linear(x) # [n_nodes, 1] - - -@simplify_if_compile -@compile_mode("script") -class NonLinearReadoutBlock(torch.nn.Module): - def __init__( - self, - irreps_in: o3.Irreps, - MLP_irreps: o3.Irreps, - gate: Optional[Callable], - irrep_out: o3.Irreps = o3.Irreps("0e"), - num_heads: int = 1, - cueq_config: Optional[CuEquivarianceConfig] = None, - ): - super().__init__() - self.hidden_irreps = MLP_irreps - self.num_heads = num_heads - self.linear_1 = Linear( - irreps_in=irreps_in, irreps_out=self.hidden_irreps, cueq_config=cueq_config - ) - self.non_linearity = nn.Activation(irreps_in=self.hidden_irreps, acts=[gate]) - self.linear_2 = Linear( - irreps_in=self.hidden_irreps, irreps_out=irrep_out, cueq_config=cueq_config - ) - - def forward( - self, x: torch.Tensor, heads: Optional[torch.Tensor] = None - ) -> torch.Tensor: # [n_nodes, irreps] # [..., ] - x = self.non_linearity(self.linear_1(x)) - if hasattr(self, "num_heads"): - if self.num_heads > 1 and heads is not None: - x = mask_head(x, heads, self.num_heads) - return self.linear_2(x) # [n_nodes, len(heads)] - - -@compile_mode("script") -class LinearDipoleReadoutBlock(torch.nn.Module): - def __init__( - self, - irreps_in: o3.Irreps, - dipole_only: bool = False, - cueq_config: Optional[CuEquivarianceConfig] = None, - ): - super().__init__() - if dipole_only: - self.irreps_out = o3.Irreps("1x1o") - else: - self.irreps_out = o3.Irreps("1x0e + 1x1o") - self.linear = Linear( - irreps_in=irreps_in, irreps_out=self.irreps_out, cueq_config=cueq_config - ) - - def forward(self, x: torch.Tensor) -> torch.Tensor: # [n_nodes, irreps] # [..., ] - return self.linear(x) # [n_nodes, 1] - - -@compile_mode("script") -class NonLinearDipoleReadoutBlock(torch.nn.Module): - def __init__( - self, - irreps_in: o3.Irreps, - MLP_irreps: o3.Irreps, - gate: Callable, - dipole_only: bool = False, - cueq_config: Optional[CuEquivarianceConfig] = None, - ): - super().__init__() - self.hidden_irreps = MLP_irreps - if dipole_only: - self.irreps_out = o3.Irreps("1x1o") - else: - self.irreps_out = o3.Irreps("1x0e + 1x1o") - irreps_scalars = o3.Irreps( - [(mul, ir) for mul, ir in MLP_irreps if ir.l == 0 and ir in self.irreps_out] - ) - irreps_gated = o3.Irreps( - [(mul, ir) for mul, ir in MLP_irreps if ir.l > 0 and ir in self.irreps_out] - ) - irreps_gates = o3.Irreps([mul, "0e"] for mul, _ in irreps_gated) - self.equivariant_nonlin = nn.Gate( - irreps_scalars=irreps_scalars, - act_scalars=[gate for _, ir in irreps_scalars], - irreps_gates=irreps_gates, - act_gates=[gate] * len(irreps_gates), - irreps_gated=irreps_gated, - ) - self.irreps_nonlin = self.equivariant_nonlin.irreps_in.simplify() - self.linear_1 = Linear( - irreps_in=irreps_in, irreps_out=self.irreps_nonlin, cueq_config=cueq_config - ) - self.linear_2 = Linear( - irreps_in=self.hidden_irreps, - irreps_out=self.irreps_out, - cueq_config=cueq_config, - ) - - def forward(self, x: torch.Tensor) -> torch.Tensor: # [n_nodes, irreps] # [..., ] - x = self.equivariant_nonlin(self.linear_1(x)) - return self.linear_2(x) # [n_nodes, 1] - - -@compile_mode("script") -class AtomicEnergiesBlock(torch.nn.Module): - atomic_energies: torch.Tensor - - def __init__(self, atomic_energies: Union[np.ndarray, torch.Tensor]): - super().__init__() - # assert len(atomic_energies.shape) == 1 - - self.register_buffer( - "atomic_energies", - torch.tensor(atomic_energies, dtype=torch.get_default_dtype()), - ) # [n_elements, n_heads] - - def forward( - self, x: torch.Tensor # one-hot of elements [..., n_elements] - ) -> torch.Tensor: # [..., ] - return torch.matmul(x, torch.atleast_2d(self.atomic_energies).T) - - def __repr__(self): - formatted_energies = ", ".join( - [ - "[" + ", ".join([f"{x:.4f}" for x in group]) + "]" - for group in torch.atleast_2d(self.atomic_energies) - ] - ) - return f"{self.__class__.__name__}(energies=[{formatted_energies}])" - - -@compile_mode("script") -class RadialEmbeddingBlock(torch.nn.Module): - def __init__( - self, - r_max: float, - num_bessel: int, - num_polynomial_cutoff: int, - radial_type: str = "bessel", - distance_transform: str = "None", - ): - super().__init__() - if radial_type == "bessel": - self.bessel_fn = BesselBasis(r_max=r_max, num_basis=num_bessel) - elif radial_type == "gaussian": - self.bessel_fn = GaussianBasis(r_max=r_max, num_basis=num_bessel) - elif radial_type == "chebyshev": - self.bessel_fn = ChebychevBasis(r_max=r_max, num_basis=num_bessel) - if distance_transform == "Agnesi": - self.distance_transform = AgnesiTransform() - elif distance_transform == "Soft": - self.distance_transform = SoftTransform() - self.cutoff_fn = PolynomialCutoff(r_max=r_max, p=num_polynomial_cutoff) - self.out_dim = num_bessel - - def forward( - self, - edge_lengths: torch.Tensor, # [n_edges, 1] - node_attrs: torch.Tensor, - edge_index: torch.Tensor, - atomic_numbers: torch.Tensor, - ): - cutoff = self.cutoff_fn(edge_lengths) # [n_edges, 1] - if hasattr(self, "distance_transform"): - edge_lengths = self.distance_transform( - edge_lengths, node_attrs, edge_index, atomic_numbers - ) - radial = self.bessel_fn(edge_lengths) # [n_edges, n_basis] - return radial * cutoff # [n_edges, n_basis] - - -@compile_mode("script") -class EquivariantProductBasisBlock(torch.nn.Module): - def __init__( - self, - node_feats_irreps: o3.Irreps, - target_irreps: o3.Irreps, - correlation: int, - use_sc: bool = True, - num_elements: Optional[int] = None, - cueq_config: Optional[CuEquivarianceConfig] = None, - ) -> None: - super().__init__() - - self.use_sc = use_sc - self.symmetric_contractions = SymmetricContractionWrapper( - irreps_in=node_feats_irreps, - irreps_out=target_irreps, - correlation=correlation, - num_elements=num_elements, - cueq_config=cueq_config, - ) - # Update linear - self.linear = Linear( - target_irreps, - target_irreps, - internal_weights=True, - shared_weights=True, - cueq_config=cueq_config, - ) - self.cueq_config = cueq_config - - def forward( - self, - node_feats: torch.Tensor, - sc: Optional[torch.Tensor], - node_attrs: torch.Tensor, - ) -> torch.Tensor: - use_cueq = False - use_cueq_mul_ir = False - if hasattr(self, "cueq_config"): - if self.cueq_config is not None: - if self.cueq_config.enabled and ( - self.cueq_config.optimize_all or self.cueq_config.optimize_symmetric - ): - use_cueq = True - if self.cueq_config.layout_str == "mul_ir": - use_cueq_mul_ir = True - if use_cueq: - if use_cueq_mul_ir: - node_feats = torch.transpose(node_feats, 1, 2) - index_attrs = torch.nonzero(node_attrs)[:, 1].int() - node_feats = self.symmetric_contractions( - node_feats.flatten(1), - index_attrs, - ) - else: - node_feats = self.symmetric_contractions(node_feats, node_attrs) - if self.use_sc and sc is not None: - return self.linear(node_feats) + sc - return self.linear(node_feats) - - -@compile_mode("script") -class InteractionBlock(torch.nn.Module): - def __init__( - self, - node_attrs_irreps: o3.Irreps, - node_feats_irreps: o3.Irreps, - edge_attrs_irreps: o3.Irreps, - edge_feats_irreps: o3.Irreps, - target_irreps: o3.Irreps, - hidden_irreps: o3.Irreps, - avg_num_neighbors: float, - radial_MLP: Optional[List[int]] = None, - cueq_config: Optional[CuEquivarianceConfig] = None, - ) -> None: - super().__init__() - self.node_attrs_irreps = node_attrs_irreps - self.node_feats_irreps = node_feats_irreps - self.edge_attrs_irreps = edge_attrs_irreps - self.edge_feats_irreps = edge_feats_irreps - self.target_irreps = target_irreps - self.hidden_irreps = hidden_irreps - self.avg_num_neighbors = avg_num_neighbors - if radial_MLP is None: - radial_MLP = [64, 64, 64] - self.radial_MLP = radial_MLP - self.cueq_config = cueq_config - self._setup() - - @abstractmethod - def _setup(self) -> None: - raise NotImplementedError - - def handle_lammps( - self, - node_feats: torch.Tensor, - lammps_class: Optional[Any], - lammps_natoms: Tuple[int, int], - first_layer: bool, - ) -> torch.Tensor: # noqa: D401 – internal helper - if lammps_class is None or first_layer or torch.jit.is_scripting(): - return node_feats - _, n_total = lammps_natoms - pad = torch.zeros( - (n_total, node_feats.shape[1]), - dtype=node_feats.dtype, - device=node_feats.device, - ) - node_feats = torch.cat((node_feats, pad), dim=0) - node_feats = LAMMPS_MP.apply(node_feats, lammps_class) - return node_feats - - def truncate_ghosts( - self, tensor: torch.Tensor, n_real: Optional[int] = None - ) -> torch.Tensor: - """Truncate the tensor to only keep the real atoms in case of presence of ghost atoms during multi-GPU MD simulations.""" - return tensor[:n_real] if n_real is not None else tensor - - @abstractmethod - def forward( - self, - node_attrs: torch.Tensor, - node_feats: torch.Tensor, - edge_attrs: torch.Tensor, - edge_feats: torch.Tensor, - edge_index: torch.Tensor, - ) -> torch.Tensor: - raise NotImplementedError - - -nonlinearities = {1: torch.nn.functional.silu, -1: torch.tanh} - - -@compile_mode("script") -class RealAgnosticInteractionBlock(InteractionBlock): - def _setup(self) -> None: - if not hasattr(self, "cueq_config"): - self.cueq_config = None - # First linear - self.linear_up = Linear( - self.node_feats_irreps, - self.node_feats_irreps, - internal_weights=True, - shared_weights=True, - cueq_config=self.cueq_config, - ) - # TensorProduct - irreps_mid, instructions = tp_out_irreps_with_instructions( - self.node_feats_irreps, - self.edge_attrs_irreps, - self.target_irreps, - ) - self.conv_tp = TensorProduct( - self.node_feats_irreps, - self.edge_attrs_irreps, - irreps_mid, - instructions=instructions, - shared_weights=False, - internal_weights=False, - cueq_config=self.cueq_config, - ) - - # Convolution weights - input_dim = self.edge_feats_irreps.num_irreps - self.conv_tp_weights = nn.FullyConnectedNet( - [input_dim] + self.radial_MLP + [self.conv_tp.weight_numel], - torch.nn.functional.silu, - ) - - # Linear - self.irreps_out = self.target_irreps - self.linear = Linear( - irreps_mid, - self.irreps_out, - internal_weights=True, - shared_weights=True, - cueq_config=self.cueq_config, - ) - - # Selector TensorProduct - self.skip_tp = FullyConnectedTensorProduct( - self.irreps_out, - self.node_attrs_irreps, - self.irreps_out, - cueq_config=self.cueq_config, - ) - self.reshape = reshape_irreps(self.irreps_out, cueq_config=self.cueq_config) - - def forward( - self, - node_attrs: torch.Tensor, - node_feats: torch.Tensor, - edge_attrs: torch.Tensor, - edge_feats: torch.Tensor, - edge_index: torch.Tensor, - lammps_natoms: Tuple[int, int] = (0, 0), - lammps_class: Optional[Any] = None, - first_layer: bool = False, - ) -> Tuple[torch.Tensor, None]: - sender = edge_index[0] - receiver = edge_index[1] - num_nodes = node_feats.shape[0] - n_real = lammps_natoms[0] if lammps_class is not None else None - node_feats = self.linear_up(node_feats) - node_feats = self.handle_lammps( - node_feats, - lammps_class=lammps_class, - lammps_natoms=lammps_natoms, - first_layer=first_layer, - ) - tp_weights = self.conv_tp_weights(edge_feats) - mji = self.conv_tp( - node_feats[sender], edge_attrs, tp_weights - ) # [n_edges, irreps] - message = scatter_sum( - src=mji, index=receiver, dim=0, dim_size=num_nodes - ) # [n_nodes, irreps] - message = self.truncate_ghosts(message, n_real) - node_attrs = self.truncate_ghosts(node_attrs, n_real) - message = self.linear(message) / self.avg_num_neighbors - message = self.skip_tp(message, node_attrs) - return ( - self.reshape(message), - None, - ) # [n_nodes, channels, (lmax + 1)**2] - - -@compile_mode("script") -class RealAgnosticResidualInteractionBlock(InteractionBlock): - def _setup(self) -> None: - if not hasattr(self, "cueq_config"): - self.cueq_config = None - # First linear - self.linear_up = Linear( - self.node_feats_irreps, - self.node_feats_irreps, - internal_weights=True, - shared_weights=True, - cueq_config=self.cueq_config, - ) - # TensorProduct - irreps_mid, instructions = tp_out_irreps_with_instructions( - self.node_feats_irreps, - self.edge_attrs_irreps, - self.target_irreps, - ) - self.conv_tp = TensorProduct( - self.node_feats_irreps, - self.edge_attrs_irreps, - irreps_mid, - instructions=instructions, - shared_weights=False, - internal_weights=False, - cueq_config=self.cueq_config, - ) - - # Convolution weights - input_dim = self.edge_feats_irreps.num_irreps - self.conv_tp_weights = nn.FullyConnectedNet( - [input_dim] + self.radial_MLP + [self.conv_tp.weight_numel], - torch.nn.functional.silu, # gate - ) - - # Linear - self.irreps_out = self.target_irreps - self.linear = Linear( - irreps_mid, - self.irreps_out, - internal_weights=True, - shared_weights=True, - cueq_config=self.cueq_config, - ) - - # Selector TensorProduct - self.skip_tp = FullyConnectedTensorProduct( - self.node_feats_irreps, - self.node_attrs_irreps, - self.hidden_irreps, - cueq_config=self.cueq_config, - ) - self.reshape = reshape_irreps(self.irreps_out, cueq_config=self.cueq_config) - - def forward( - self, - node_attrs: torch.Tensor, - node_feats: torch.Tensor, - edge_attrs: torch.Tensor, - edge_feats: torch.Tensor, - edge_index: torch.Tensor, - lammps_class: Optional[Any] = None, - lammps_natoms: Tuple[int, int] = (0, 0), - first_layer: bool = False, - ) -> Tuple[torch.Tensor, torch.Tensor]: - sender = edge_index[0] - receiver = edge_index[1] - num_nodes = node_feats.shape[0] - n_real = lammps_natoms[0] if lammps_class is not None else None - sc = self.skip_tp(node_feats, node_attrs) - node_feats = self.linear_up(node_feats) - node_feats = self.handle_lammps( - node_feats, - lammps_class=lammps_class, - lammps_natoms=lammps_natoms, - first_layer=first_layer, - ) - tp_weights = self.conv_tp_weights(edge_feats) - mji = self.conv_tp( - node_feats[sender], edge_attrs, tp_weights - ) # [n_edges, irreps] - message = scatter_sum( - src=mji, index=receiver, dim=0, dim_size=num_nodes - ) # [n_nodes, irreps] - message = self.truncate_ghosts(message, n_real) - node_attrs = self.truncate_ghosts(node_attrs, n_real) - sc = self.truncate_ghosts(sc, n_real) - message = self.linear(message) / self.avg_num_neighbors - return ( - self.reshape(message), - sc, - ) # [n_nodes, channels, (lmax + 1)**2] - - -@compile_mode("script") -class RealAgnosticDensityInteractionBlock(InteractionBlock): - def _setup(self) -> None: - if not hasattr(self, "cueq_config"): - self.cueq_config = None - # First linear - self.linear_up = Linear( - self.node_feats_irreps, - self.node_feats_irreps, - internal_weights=True, - shared_weights=True, - cueq_config=self.cueq_config, - ) - # TensorProduct - irreps_mid, instructions = tp_out_irreps_with_instructions( - self.node_feats_irreps, - self.edge_attrs_irreps, - self.target_irreps, - ) - self.conv_tp = TensorProduct( - self.node_feats_irreps, - self.edge_attrs_irreps, - irreps_mid, - instructions=instructions, - shared_weights=False, - internal_weights=False, - cueq_config=self.cueq_config, - ) - - # Convolution weights - input_dim = self.edge_feats_irreps.num_irreps - self.conv_tp_weights = nn.FullyConnectedNet( - [input_dim] + self.radial_MLP + [self.conv_tp.weight_numel], - torch.nn.functional.silu, - ) - - # Linear - self.irreps_out = self.target_irreps - self.linear = Linear( - irreps_mid, - self.irreps_out, - internal_weights=True, - shared_weights=True, - cueq_config=self.cueq_config, - ) - - # Selector TensorProduct - self.skip_tp = FullyConnectedTensorProduct( - self.irreps_out, - self.node_attrs_irreps, - self.irreps_out, - cueq_config=self.cueq_config, - ) - - # Density normalization - self.density_fn = nn.FullyConnectedNet( - [input_dim] - + [ - 1, - ], - torch.nn.functional.silu, - ) - # Reshape - self.reshape = reshape_irreps(self.irreps_out, cueq_config=self.cueq_config) - - def forward( - self, - node_attrs: torch.Tensor, - node_feats: torch.Tensor, - edge_attrs: torch.Tensor, - edge_feats: torch.Tensor, - edge_index: torch.Tensor, - lammps_class: Optional[Any] = None, - lammps_natoms: Tuple[int, int] = (0, 0), - first_layer: bool = False, - ) -> Tuple[torch.Tensor, None]: - sender = edge_index[0] - receiver = edge_index[1] - num_nodes = node_feats.shape[0] - n_real = lammps_natoms[0] if lammps_class is not None else None - node_feats = self.linear_up(node_feats) - node_feats = self.handle_lammps( - node_feats, - lammps_class=lammps_class, - lammps_natoms=lammps_natoms, - first_layer=first_layer, - ) - tp_weights = self.conv_tp_weights(edge_feats) - edge_density = torch.tanh(self.density_fn(edge_feats) ** 2) - mji = self.conv_tp( - node_feats[sender], edge_attrs, tp_weights - ) # [n_edges, irreps] - density = scatter_sum( - src=edge_density, index=receiver, dim=0, dim_size=num_nodes - ) # [n_nodes, 1] - message = scatter_sum( - src=mji, index=receiver, dim=0, dim_size=num_nodes - ) # [n_nodes, irreps] - message = self.truncate_ghosts(message, n_real) - node_attrs = self.truncate_ghosts(node_attrs, n_real) - density = self.truncate_ghosts(density, n_real) - message = self.linear(message) / (density + 1) - message = self.skip_tp(message, node_attrs) - return ( - self.reshape(message), - None, - ) # [n_nodes, channels, (lmax + 1)**2] - - -@compile_mode("script") -class RealAgnosticDensityResidualInteractionBlock(InteractionBlock): - def _setup(self) -> None: - if not hasattr(self, "cueq_config"): - self.cueq_config = None - - # First linear - self.linear_up = Linear( - self.node_feats_irreps, - self.node_feats_irreps, - internal_weights=True, - shared_weights=True, - cueq_config=self.cueq_config, - ) - # TensorProduct - irreps_mid, instructions = tp_out_irreps_with_instructions( - self.node_feats_irreps, - self.edge_attrs_irreps, - self.target_irreps, - ) - self.conv_tp = TensorProduct( - self.node_feats_irreps, - self.edge_attrs_irreps, - irreps_mid, - instructions=instructions, - shared_weights=False, - internal_weights=False, - cueq_config=self.cueq_config, - ) - - # Convolution weights - input_dim = self.edge_feats_irreps.num_irreps - self.conv_tp_weights = nn.FullyConnectedNet( - [input_dim] + self.radial_MLP + [self.conv_tp.weight_numel], - torch.nn.functional.silu, # gate - ) - - # Linear - self.irreps_out = self.target_irreps - self.linear = Linear( - irreps_mid, - self.irreps_out, - internal_weights=True, - shared_weights=True, - cueq_config=self.cueq_config, - ) - - # Selector TensorProduct - self.skip_tp = FullyConnectedTensorProduct( - self.node_feats_irreps, - self.node_attrs_irreps, - self.hidden_irreps, - cueq_config=self.cueq_config, - ) - - # Density normalization - self.density_fn = nn.FullyConnectedNet( - [input_dim] - + [ - 1, - ], - torch.nn.functional.silu, - ) - - # Reshape - self.reshape = reshape_irreps(self.irreps_out, cueq_config=self.cueq_config) - - def forward( - self, - node_attrs: torch.Tensor, - node_feats: torch.Tensor, - edge_attrs: torch.Tensor, - edge_feats: torch.Tensor, - edge_index: torch.Tensor, - lammps_class: Optional[Any] = None, - lammps_natoms: Tuple[int, int] = (0, 0), - first_layer: bool = False, - ) -> Tuple[torch.Tensor, torch.Tensor]: - sender = edge_index[0] - receiver = edge_index[1] - num_nodes = node_feats.shape[0] - n_real = lammps_natoms[0] if lammps_class is not None else None - sc = self.skip_tp(node_feats, node_attrs) - node_feats = self.linear_up(node_feats) - node_feats = self.handle_lammps( - node_feats, - lammps_class=lammps_class, - lammps_natoms=lammps_natoms, - first_layer=first_layer, - ) - tp_weights = self.conv_tp_weights(edge_feats) - edge_density = torch.tanh(self.density_fn(edge_feats) ** 2) - mji = self.conv_tp( - node_feats[sender], edge_attrs, tp_weights - ) # [n_edges, irreps] - density = scatter_sum( - src=edge_density, index=receiver, dim=0, dim_size=num_nodes - ) # [n_nodes, 1] - message = scatter_sum( - src=mji, index=receiver, dim=0, dim_size=num_nodes - ) # [n_nodes, irreps] - message = self.truncate_ghosts(message, n_real) - node_attrs = self.truncate_ghosts(node_attrs, n_real) - density = self.truncate_ghosts(density, n_real) - sc = self.truncate_ghosts(sc, n_real) - message = self.linear(message) / (density + 1) - return ( - self.reshape(message), - sc, - ) # [n_nodes, channels, (lmax + 1)**2] - - -@compile_mode("script") -class RealAgnosticAttResidualInteractionBlock(InteractionBlock): - def _setup(self) -> None: - if not hasattr(self, "cueq_config"): - self.cueq_config = None - self.node_feats_down_irreps = o3.Irreps("64x0e") - # First linear - self.linear_up = Linear( - self.node_feats_irreps, - self.node_feats_irreps, - internal_weights=True, - shared_weights=True, - cueq_config=self.cueq_config, - ) - # TensorProduct - irreps_mid, instructions = tp_out_irreps_with_instructions( - self.node_feats_irreps, - self.edge_attrs_irreps, - self.target_irreps, - ) - self.conv_tp = TensorProduct( - self.node_feats_irreps, - self.edge_attrs_irreps, - irreps_mid, - instructions=instructions, - shared_weights=False, - internal_weights=False, - cueq_config=self.cueq_config, - ) - - # Convolution weights - self.linear_down = Linear( - self.node_feats_irreps, - self.node_feats_down_irreps, - internal_weights=True, - shared_weights=True, - cueq_config=self.cueq_config, - ) - input_dim = ( - self.edge_feats_irreps.num_irreps - + 2 * self.node_feats_down_irreps.num_irreps - ) - self.conv_tp_weights = nn.FullyConnectedNet( - [input_dim] + 3 * [256] + [self.conv_tp.weight_numel], - torch.nn.functional.silu, - ) - - # Linear - self.irreps_out = self.target_irreps - self.linear = Linear( - irreps_mid, - self.irreps_out, - internal_weights=True, - shared_weights=True, - cueq_config=self.cueq_config, - ) - - self.reshape = reshape_irreps(self.irreps_out, cueq_config=self.cueq_config) - - # Skip connection. - self.skip_linear = Linear( - self.node_feats_irreps, self.hidden_irreps, cueq_config=self.cueq_config - ) - - # pylint: disable=unused-argument - def forward( - self, - node_attrs: torch.Tensor, - node_feats: torch.Tensor, - edge_attrs: torch.Tensor, - edge_feats: torch.Tensor, - edge_index: torch.Tensor, - lammps_class: Optional[Any] = None, - lammps_natoms: Tuple[int, int] = (0, 0), - first_layer: bool = False, - ) -> Tuple[torch.Tensor, None]: - sender = edge_index[0] - receiver = edge_index[1] - num_nodes = node_feats.shape[0] - sc = self.skip_linear(node_feats) - node_feats_up = self.linear_up(node_feats) - node_feats_down = self.linear_down(node_feats) - augmented_edge_feats = torch.cat( - [ - edge_feats, - node_feats_down[sender], - node_feats_down[receiver], - ], - dim=-1, - ) - tp_weights = self.conv_tp_weights(augmented_edge_feats) - mji = self.conv_tp( - node_feats_up[sender], edge_attrs, tp_weights - ) # [n_edges, irreps] - message = scatter_sum( - src=mji, index=receiver, dim=0, dim_size=num_nodes - ) # [n_nodes, irreps] - message = self.linear(message) / self.avg_num_neighbors - return ( - self.reshape(message), - sc, - ) # [n_nodes, channels, (lmax + 1)**2] - - -@compile_mode("script") -class ScaleShiftBlock(torch.nn.Module): - def __init__(self, scale: float, shift: float): - super().__init__() - self.register_buffer( - "scale", - torch.tensor(scale, dtype=torch.get_default_dtype()), - ) - self.register_buffer( - "shift", - torch.tensor(shift, dtype=torch.get_default_dtype()), - ) - - def forward(self, x: torch.Tensor, head: torch.Tensor) -> torch.Tensor: - return ( - torch.atleast_1d(self.scale)[head] * x + torch.atleast_1d(self.shift)[head] - ) - - def __repr__(self): - formatted_scale = ( - ", ".join([f"{x:.4f}" for x in self.scale]) - if self.scale.numel() > 1 - else f"{self.scale.item():.4f}" - ) - formatted_shift = ( - ", ".join([f"{x:.4f}" for x in self.shift]) - if self.shift.numel() > 1 - else f"{self.shift.item():.4f}" - ) - return f"{self.__class__.__name__}(scale={formatted_scale}, shift={formatted_shift})" diff --git a/mace-bench/3rdparty/mace/mace/modules/irreps_tools.py b/mace-bench/3rdparty/mace/mace/modules/irreps_tools.py deleted file mode 100644 index 6677b1bef2be949300a26e5e852ef80fac8c0724..0000000000000000000000000000000000000000 --- a/mace-bench/3rdparty/mace/mace/modules/irreps_tools.py +++ /dev/null @@ -1,116 +0,0 @@ -########################################################################################### -# Elementary tools for handling irreducible representations -# Authors: Ilyes Batatia, Gregor Simm -# This program is distributed under the MIT License (see MIT.md) -########################################################################################### - -from typing import List, Optional, Tuple - -import torch -from e3nn import o3 -from e3nn.util.jit import compile_mode - -from mace.modules.wrapper_ops import CuEquivarianceConfig - - -# Based on mir-group/nequip -def tp_out_irreps_with_instructions( - irreps1: o3.Irreps, irreps2: o3.Irreps, target_irreps: o3.Irreps -) -> Tuple[o3.Irreps, List]: - trainable = True - - # Collect possible irreps and their instructions - irreps_out_list: List[Tuple[int, o3.Irreps]] = [] - instructions = [] - for i, (mul, ir_in) in enumerate(irreps1): - for j, (_, ir_edge) in enumerate(irreps2): - for ir_out in ir_in * ir_edge: # | l1 - l2 | <= l <= l1 + l2 - if ir_out in target_irreps: - k = len(irreps_out_list) # instruction index - irreps_out_list.append((mul, ir_out)) - instructions.append((i, j, k, "uvu", trainable)) - - # We sort the output irreps of the tensor product so that we can simplify them - # when they are provided to the second o3.Linear - irreps_out = o3.Irreps(irreps_out_list) - irreps_out, permut, _ = irreps_out.sort() - - # Permute the output indexes of the instructions to match the sorted irreps: - instructions = [ - (i_in1, i_in2, permut[i_out], mode, train) - for i_in1, i_in2, i_out, mode, train in instructions - ] - - instructions = sorted(instructions, key=lambda x: x[2]) - - return irreps_out, instructions - - -def linear_out_irreps(irreps: o3.Irreps, target_irreps: o3.Irreps) -> o3.Irreps: - # Assuming simplified irreps - irreps_mid = [] - for _, ir_in in irreps: - found = False - - for mul, ir_out in target_irreps: - if ir_in == ir_out: - irreps_mid.append((mul, ir_out)) - found = True - break - - if not found: - raise RuntimeError(f"{ir_in} not in {target_irreps}") - - return o3.Irreps(irreps_mid) - - -@compile_mode("script") -class reshape_irreps(torch.nn.Module): - def __init__( - self, irreps: o3.Irreps, cueq_config: Optional[CuEquivarianceConfig] = None - ) -> None: - super().__init__() - self.irreps = o3.Irreps(irreps) - self.cueq_config = cueq_config - self.dims = [] - self.muls = [] - for mul, ir in self.irreps: - d = ir.dim - self.dims.append(d) - self.muls.append(mul) - - def forward(self, tensor: torch.Tensor) -> torch.Tensor: - ix = 0 - out = [] - batch, _ = tensor.shape - for mul, d in zip(self.muls, self.dims): - field = tensor[:, ix : ix + mul * d] # [batch, sample, mul * repr] - ix += mul * d - if hasattr(self, "cueq_config"): - if self.cueq_config is not None: - if self.cueq_config.layout_str == "mul_ir": - field = field.reshape(batch, mul, d) - else: - field = field.reshape(batch, d, mul) - else: - field = field.reshape(batch, mul, d) - else: - field = field.reshape(batch, mul, d) - out.append(field) - - if hasattr(self, "cueq_config"): - if self.cueq_config is not None: # pylint: disable=no-else-return - if self.cueq_config.layout_str == "mul_ir": - return torch.cat(out, dim=-1) - return torch.cat(out, dim=-2) - else: - return torch.cat(out, dim=-1) - return torch.cat(out, dim=-1) - - -def mask_head(x: torch.Tensor, head: torch.Tensor, num_heads: int) -> torch.Tensor: - mask = torch.zeros(x.shape[0], x.shape[1] // num_heads, num_heads, device=x.device) - idx = torch.arange(mask.shape[0], device=x.device) - mask[idx, :, head] = 1 - mask = mask.permute(0, 2, 1).reshape(x.shape) - return x * mask diff --git a/mace-bench/3rdparty/mace/mace/modules/loss.py b/mace-bench/3rdparty/mace/mace/modules/loss.py deleted file mode 100644 index ff567e39444ecac83d10661054c02fd323bd5d2f..0000000000000000000000000000000000000000 --- a/mace-bench/3rdparty/mace/mace/modules/loss.py +++ /dev/null @@ -1,566 +0,0 @@ -########################################################################################### -# Implementation of different loss functions -# Authors: Ilyes Batatia, Gregor Simm -# This program is distributed under the MIT License (see MIT.md) -########################################################################################### - -from typing import Optional - -import torch -import torch.distributed as dist - -from mace.tools import TensorDict -from mace.tools.torch_geometric import Batch - - -# ------------------------------------------------------------------------------ -# Helper function for loss reduction that handles DDP correction -# ------------------------------------------------------------------------------ -def is_ddp_enabled(): - return dist.is_initialized() and dist.get_world_size() > 1 - - -def reduce_loss(raw_loss: torch.Tensor, ddp: Optional[bool] = None) -> torch.Tensor: - """ - Reduces an element-wise loss tensor. - - If ddp is True and distributed is initialized, the function computes: - - loss = (local_sum * world_size) / global_num_elements - - Otherwise, it returns the regular mean. - """ - ddp = is_ddp_enabled() if ddp is None else ddp - if ddp and dist.is_initialized(): - world_size = dist.get_world_size() - n_local = raw_loss.numel() - loss_sum = raw_loss.sum() - total_samples = torch.tensor( - n_local, device=raw_loss.device, dtype=raw_loss.dtype - ) - dist.all_reduce(total_samples, op=dist.ReduceOp.SUM) - return loss_sum * world_size / total_samples - return raw_loss.mean() - - -# ------------------------------------------------------------------------------ -# Energy Loss Functions -# ------------------------------------------------------------------------------ - - -def mean_squared_error_energy( - ref: Batch, pred: TensorDict, ddp: Optional[bool] = None -) -> torch.Tensor: - raw_loss = torch.square(ref["energy"] - pred["energy"]) - return reduce_loss(raw_loss, ddp) - - -def weighted_mean_squared_error_energy( - ref: Batch, pred: TensorDict, ddp: Optional[bool] = None -) -> torch.Tensor: - # Calculate per-graph number of atoms. - num_atoms = ref.ptr[1:] - ref.ptr[:-1] # shape: [n_graphs] - raw_loss = ( - ref.weight - * ref.energy_weight - * torch.square((ref["energy"] - pred["energy"]) / num_atoms) - ) - return reduce_loss(raw_loss, ddp) - - -def weighted_mean_absolute_error_energy( - ref: Batch, pred: TensorDict, ddp: Optional[bool] = None -) -> torch.Tensor: - num_atoms = ref.ptr[1:] - ref.ptr[:-1] - raw_loss = ( - ref.weight - * ref.energy_weight - * torch.abs((ref["energy"] - pred["energy"]) / num_atoms) - ) - return reduce_loss(raw_loss, ddp) - - -# ------------------------------------------------------------------------------ -# Stress and Virials Loss Functions -# ------------------------------------------------------------------------------ - - -def weighted_mean_squared_stress( - ref: Batch, pred: TensorDict, ddp: Optional[bool] = None -) -> torch.Tensor: - configs_weight = ref.weight.view(-1, 1, 1) - configs_stress_weight = ref.stress_weight.view(-1, 1, 1) - raw_loss = ( - configs_weight - * configs_stress_weight - * torch.square(ref["stress"] - pred["stress"]) - ) - return reduce_loss(raw_loss, ddp) - - -def weighted_mean_squared_virials( - ref: Batch, pred: TensorDict, ddp: Optional[bool] = None -) -> torch.Tensor: - configs_weight = ref.weight.view(-1, 1, 1) - configs_virials_weight = ref.virials_weight.view(-1, 1, 1) - num_atoms = (ref.ptr[1:] - ref.ptr[:-1]).view(-1, 1, 1) - raw_loss = ( - configs_weight - * configs_virials_weight - * torch.square((ref["virials"] - pred["virials"]) / num_atoms) - ) - return reduce_loss(raw_loss, ddp) - - -# ------------------------------------------------------------------------------ -# Forces Loss Functions -# ------------------------------------------------------------------------------ - - -def mean_squared_error_forces( - ref: Batch, pred: TensorDict, ddp: Optional[bool] = None -) -> torch.Tensor: - # Repeat per-graph weights to per-atom level. - configs_weight = torch.repeat_interleave( - ref.weight, ref.ptr[1:] - ref.ptr[:-1] - ).unsqueeze(-1) - configs_forces_weight = torch.repeat_interleave( - ref.forces_weight, ref.ptr[1:] - ref.ptr[:-1] - ).unsqueeze(-1) - raw_loss = ( - configs_weight - * configs_forces_weight - * torch.square(ref["forces"] - pred["forces"]) - ) - return reduce_loss(raw_loss, ddp) - - -def mean_normed_error_forces( - ref: Batch, pred: TensorDict, ddp: Optional[bool] = None -) -> torch.Tensor: - raw_loss = torch.linalg.vector_norm(ref["forces"] - pred["forces"], ord=2, dim=-1) - return reduce_loss(raw_loss, ddp) - - -# ------------------------------------------------------------------------------ -# Dipole Loss Function -# ------------------------------------------------------------------------------ - - -def weighted_mean_squared_error_dipole( - ref: Batch, pred: TensorDict, ddp: Optional[bool] = None -) -> torch.Tensor: - num_atoms = (ref.ptr[1:] - ref.ptr[:-1]).unsqueeze(-1) - raw_loss = torch.square((ref["dipole"] - pred["dipole"]) / num_atoms) - return reduce_loss(raw_loss, ddp) - - -# ------------------------------------------------------------------------------ -# Conditional Losses for Forces -# ------------------------------------------------------------------------------ - - -def conditional_mse_forces( - ref: Batch, pred: TensorDict, ddp: Optional[bool] = None -) -> torch.Tensor: - configs_weight = torch.repeat_interleave( - ref.weight, ref.ptr[1:] - ref.ptr[:-1] - ).unsqueeze(-1) - configs_forces_weight = torch.repeat_interleave( - ref.forces_weight, ref.ptr[1:] - ref.ptr[:-1] - ).unsqueeze(-1) - # Define multiplication factors for different regimes. - factors = torch.tensor( - [1.0, 0.7, 0.4, 0.1], device=ref["forces"].device, dtype=ref["forces"].dtype - ) - err = ref["forces"] - pred["forces"] - se = torch.zeros_like(err) - norm_forces = torch.norm(ref["forces"], dim=-1) - c1 = norm_forces < 100 - c2 = (norm_forces >= 100) & (norm_forces < 200) - c3 = (norm_forces >= 200) & (norm_forces < 300) - se[c1] = torch.square(err[c1]) * factors[0] - se[c2] = torch.square(err[c2]) * factors[1] - se[c3] = torch.square(err[c3]) * factors[2] - se[~(c1 | c2 | c3)] = torch.square(err[~(c1 | c2 | c3)]) * factors[3] - raw_loss = configs_weight * configs_forces_weight * se - return reduce_loss(raw_loss, ddp) - - -def conditional_huber_forces( - ref_forces: torch.Tensor, - pred_forces: torch.Tensor, - huber_delta: float, - ddp: Optional[bool] = None, -) -> torch.Tensor: - factors = huber_delta * torch.tensor( - [1.0, 0.7, 0.4, 0.1], device=ref_forces.device, dtype=ref_forces.dtype - ) - norm_forces = torch.norm(ref_forces, dim=-1) - c1 = norm_forces < 100 - c2 = (norm_forces >= 100) & (norm_forces < 200) - c3 = (norm_forces >= 200) & (norm_forces < 300) - c4 = ~(c1 | c2 | c3) - se = torch.zeros_like(pred_forces) - se[c1] = torch.nn.functional.huber_loss( - ref_forces[c1], pred_forces[c1], reduction="none", delta=factors[0] - ) - se[c2] = torch.nn.functional.huber_loss( - ref_forces[c2], pred_forces[c2], reduction="none", delta=factors[1] - ) - se[c3] = torch.nn.functional.huber_loss( - ref_forces[c3], pred_forces[c3], reduction="none", delta=factors[2] - ) - se[c4] = torch.nn.functional.huber_loss( - ref_forces[c4], pred_forces[c4], reduction="none", delta=factors[3] - ) - return reduce_loss(se, ddp) - - -# ------------------------------------------------------------------------------ -# Loss Modules Combining Multiple Quantities -# ------------------------------------------------------------------------------ - - -class WeightedEnergyForcesLoss(torch.nn.Module): - def __init__(self, energy_weight=1.0, forces_weight=1.0) -> None: - super().__init__() - self.register_buffer( - "energy_weight", - torch.tensor(energy_weight, dtype=torch.get_default_dtype()), - ) - self.register_buffer( - "forces_weight", - torch.tensor(forces_weight, dtype=torch.get_default_dtype()), - ) - - def forward( - self, ref: Batch, pred: TensorDict, ddp: Optional[bool] = None - ) -> torch.Tensor: - loss_energy = weighted_mean_squared_error_energy(ref, pred, ddp) - loss_forces = mean_squared_error_forces(ref, pred, ddp) - return self.energy_weight * loss_energy + self.forces_weight * loss_forces - - def __repr__(self): - return ( - f"{self.__class__.__name__}(energy_weight={self.energy_weight:.3f}, " - f"forces_weight={self.forces_weight:.3f})" - ) - - -class WeightedForcesLoss(torch.nn.Module): - def __init__(self, forces_weight=1.0) -> None: - super().__init__() - self.register_buffer( - "forces_weight", - torch.tensor(forces_weight, dtype=torch.get_default_dtype()), - ) - - def forward( - self, ref: Batch, pred: TensorDict, ddp: Optional[bool] = None - ) -> torch.Tensor: - loss_forces = mean_squared_error_forces(ref, pred, ddp) - return self.forces_weight * loss_forces - - def __repr__(self): - return f"{self.__class__.__name__}(forces_weight={self.forces_weight:.3f})" - - -class WeightedEnergyForcesStressLoss(torch.nn.Module): - def __init__(self, energy_weight=1.0, forces_weight=1.0, stress_weight=1.0) -> None: - super().__init__() - self.register_buffer( - "energy_weight", - torch.tensor(energy_weight, dtype=torch.get_default_dtype()), - ) - self.register_buffer( - "forces_weight", - torch.tensor(forces_weight, dtype=torch.get_default_dtype()), - ) - self.register_buffer( - "stress_weight", - torch.tensor(stress_weight, dtype=torch.get_default_dtype()), - ) - - def forward( - self, ref: Batch, pred: TensorDict, ddp: Optional[bool] = None - ) -> torch.Tensor: - loss_energy = weighted_mean_squared_error_energy(ref, pred, ddp) - loss_forces = mean_squared_error_forces(ref, pred, ddp) - loss_stress = weighted_mean_squared_stress(ref, pred, ddp) - return ( - self.energy_weight * loss_energy - + self.forces_weight * loss_forces - + self.stress_weight * loss_stress - ) - - def __repr__(self): - return ( - f"{self.__class__.__name__}(energy_weight={self.energy_weight:.3f}, " - f"forces_weight={self.forces_weight:.3f}, stress_weight={self.stress_weight:.3f})" - ) - - -class WeightedHuberEnergyForcesStressLoss(torch.nn.Module): - def __init__( - self, energy_weight=1.0, forces_weight=1.0, stress_weight=1.0, huber_delta=0.01 - ) -> None: - super().__init__() - # We store the huber_delta rather than a loss with fixed reduction. - self.huber_delta = huber_delta - self.register_buffer( - "energy_weight", - torch.tensor(energy_weight, dtype=torch.get_default_dtype()), - ) - self.register_buffer( - "forces_weight", - torch.tensor(forces_weight, dtype=torch.get_default_dtype()), - ) - self.register_buffer( - "stress_weight", - torch.tensor(stress_weight, dtype=torch.get_default_dtype()), - ) - - def forward( - self, ref: Batch, pred: TensorDict, ddp: Optional[bool] = None - ) -> torch.Tensor: - num_atoms = ref.ptr[1:] - ref.ptr[:-1] - if ddp: - loss_energy = torch.nn.functional.huber_loss( - ref["energy"] / num_atoms, - pred["energy"] / num_atoms, - reduction="none", - delta=self.huber_delta, - ) - loss_energy = reduce_loss(loss_energy, ddp) - loss_forces = torch.nn.functional.huber_loss( - ref["forces"], pred["forces"], reduction="none", delta=self.huber_delta - ) - loss_forces = reduce_loss(loss_forces, ddp) - loss_stress = torch.nn.functional.huber_loss( - ref["stress"], pred["stress"], reduction="none", delta=self.huber_delta - ) - loss_stress = reduce_loss(loss_stress, ddp) - else: - loss_energy = torch.nn.functional.huber_loss( - ref["energy"] / num_atoms, - pred["energy"] / num_atoms, - reduction="mean", - delta=self.huber_delta, - ) - loss_forces = torch.nn.functional.huber_loss( - ref["forces"], pred["forces"], reduction="mean", delta=self.huber_delta - ) - loss_stress = torch.nn.functional.huber_loss( - ref["stress"], pred["stress"], reduction="mean", delta=self.huber_delta - ) - return ( - self.energy_weight * loss_energy - + self.forces_weight * loss_forces - + self.stress_weight * loss_stress - ) - - def __repr__(self): - return ( - f"{self.__class__.__name__}(energy_weight={self.energy_weight:.3f}, " - f"forces_weight={self.forces_weight:.3f}, stress_weight={self.stress_weight:.3f})" - ) - - -class UniversalLoss(torch.nn.Module): - def __init__( - self, energy_weight=1.0, forces_weight=1.0, stress_weight=1.0, huber_delta=0.01 - ) -> None: - super().__init__() - self.huber_delta = huber_delta - self.register_buffer( - "energy_weight", - torch.tensor(energy_weight, dtype=torch.get_default_dtype()), - ) - self.register_buffer( - "forces_weight", - torch.tensor(forces_weight, dtype=torch.get_default_dtype()), - ) - self.register_buffer( - "stress_weight", - torch.tensor(stress_weight, dtype=torch.get_default_dtype()), - ) - - def forward( - self, ref: Batch, pred: TensorDict, ddp: Optional[bool] = None - ) -> torch.Tensor: - num_atoms = ref.ptr[1:] - ref.ptr[:-1] - configs_stress_weight = ref.stress_weight.view(-1, 1, 1) - configs_energy_weight = ref.energy_weight - configs_forces_weight = torch.repeat_interleave( - ref.forces_weight, ref.ptr[1:] - ref.ptr[:-1] - ).unsqueeze(-1) - if ddp: - loss_energy = torch.nn.functional.huber_loss( - configs_energy_weight * ref["energy"] / num_atoms, - configs_energy_weight * pred["energy"] / num_atoms, - reduction="none", - delta=self.huber_delta, - ) - loss_energy = reduce_loss(loss_energy, ddp) - loss_forces = conditional_huber_forces( - configs_forces_weight * ref["forces"], - configs_forces_weight * pred["forces"], - huber_delta=self.huber_delta, - ddp=ddp, - ) - loss_stress = torch.nn.functional.huber_loss( - configs_stress_weight * ref["stress"], - configs_stress_weight * pred["stress"], - reduction="none", - delta=self.huber_delta, - ) - loss_stress = reduce_loss(loss_stress, ddp) - else: - loss_energy = torch.nn.functional.huber_loss( - configs_energy_weight * ref["energy"] / num_atoms, - configs_energy_weight * pred["energy"] / num_atoms, - reduction="mean", - delta=self.huber_delta, - ) - loss_forces = conditional_huber_forces( - configs_forces_weight * ref["forces"], - configs_forces_weight * pred["forces"], - huber_delta=self.huber_delta, - ddp=ddp, - ) - loss_stress = torch.nn.functional.huber_loss( - configs_stress_weight * ref["stress"], - configs_stress_weight * pred["stress"], - reduction="mean", - delta=self.huber_delta, - ) - return ( - self.energy_weight * loss_energy - + self.forces_weight * loss_forces - + self.stress_weight * loss_stress - ) - - def __repr__(self): - return ( - f"{self.__class__.__name__}(energy_weight={self.energy_weight:.3f}, " - f"forces_weight={self.forces_weight:.3f}, stress_weight={self.stress_weight:.3f})" - ) - - -class WeightedEnergyForcesVirialsLoss(torch.nn.Module): - def __init__( - self, energy_weight=1.0, forces_weight=1.0, virials_weight=1.0 - ) -> None: - super().__init__() - self.register_buffer( - "energy_weight", - torch.tensor(energy_weight, dtype=torch.get_default_dtype()), - ) - self.register_buffer( - "forces_weight", - torch.tensor(forces_weight, dtype=torch.get_default_dtype()), - ) - self.register_buffer( - "virials_weight", - torch.tensor(virials_weight, dtype=torch.get_default_dtype()), - ) - - def forward( - self, ref: Batch, pred: TensorDict, ddp: Optional[bool] = None - ) -> torch.Tensor: - loss_energy = weighted_mean_squared_error_energy(ref, pred, ddp) - loss_forces = mean_squared_error_forces(ref, pred, ddp) - loss_virials = weighted_mean_squared_virials(ref, pred, ddp) - return ( - self.energy_weight * loss_energy - + self.forces_weight * loss_forces - + self.virials_weight * loss_virials - ) - - def __repr__(self): - return ( - f"{self.__class__.__name__}(energy_weight={self.energy_weight:.3f}, " - f"forces_weight={self.forces_weight:.3f}, virials_weight={self.virials_weight:.3f})" - ) - - -class DipoleSingleLoss(torch.nn.Module): - def __init__(self, dipole_weight=1.0) -> None: - super().__init__() - self.register_buffer( - "dipole_weight", - torch.tensor(dipole_weight, dtype=torch.get_default_dtype()), - ) - - def forward( - self, ref: Batch, pred: TensorDict, ddp: Optional[bool] = None - ) -> torch.Tensor: - loss = ( - weighted_mean_squared_error_dipole(ref, pred, ddp) * 100.0 - ) # scale adjustment - return self.dipole_weight * loss - - def __repr__(self): - return f"{self.__class__.__name__}(dipole_weight={self.dipole_weight:.3f})" - - -class WeightedEnergyForcesDipoleLoss(torch.nn.Module): - def __init__(self, energy_weight=1.0, forces_weight=1.0, dipole_weight=1.0) -> None: - super().__init__() - self.register_buffer( - "energy_weight", - torch.tensor(energy_weight, dtype=torch.get_default_dtype()), - ) - self.register_buffer( - "forces_weight", - torch.tensor(forces_weight, dtype=torch.get_default_dtype()), - ) - self.register_buffer( - "dipole_weight", - torch.tensor(dipole_weight, dtype=torch.get_default_dtype()), - ) - - def forward( - self, ref: Batch, pred: TensorDict, ddp: Optional[bool] = None - ) -> torch.Tensor: - loss_energy = weighted_mean_squared_error_energy(ref, pred, ddp) - loss_forces = mean_squared_error_forces(ref, pred, ddp) - loss_dipole = weighted_mean_squared_error_dipole(ref, pred, ddp) * 100.0 - return ( - self.energy_weight * loss_energy - + self.forces_weight * loss_forces - + self.dipole_weight * loss_dipole - ) - - def __repr__(self): - return ( - f"{self.__class__.__name__}(energy_weight={self.energy_weight:.3f}, " - f"forces_weight={self.forces_weight:.3f}, dipole_weight={self.dipole_weight:.3f})" - ) - - -class WeightedEnergyForcesL1L2Loss(torch.nn.Module): - def __init__(self, energy_weight=1.0, forces_weight=1.0) -> None: - super().__init__() - self.register_buffer( - "energy_weight", - torch.tensor(energy_weight, dtype=torch.get_default_dtype()), - ) - self.register_buffer( - "forces_weight", - torch.tensor(forces_weight, dtype=torch.get_default_dtype()), - ) - - def forward( - self, ref: Batch, pred: TensorDict, ddp: Optional[bool] = None - ) -> torch.Tensor: - loss_energy = weighted_mean_absolute_error_energy(ref, pred, ddp) - loss_forces = mean_normed_error_forces(ref, pred, ddp) - return self.energy_weight * loss_energy + self.forces_weight * loss_forces - - def __repr__(self): - return ( - f"{self.__class__.__name__}(energy_weight={self.energy_weight:.3f}, " - f"forces_weight={self.forces_weight:.3f})" - ) diff --git a/mace-bench/3rdparty/mace/mace/modules/models.py b/mace-bench/3rdparty/mace/mace/modules/models.py deleted file mode 100644 index b551f8bf33c11844589c58896a6aea61f7a2df04..0000000000000000000000000000000000000000 --- a/mace-bench/3rdparty/mace/mace/modules/models.py +++ /dev/null @@ -1,947 +0,0 @@ -########################################################################################### -# Implementation of MACE models and other models based E(3)-Equivariant MPNNs -# Authors: Ilyes Batatia, Gregor Simm -# This program is distributed under the MIT License (see MIT.md) -########################################################################################### - -from typing import Any, Callable, Dict, List, Optional, Type, Union - -import numpy as np -import torch -from e3nn import o3 -from e3nn.util.jit import compile_mode - -from mace.modules.radial import ZBLBasis -from mace.tools.scatter import scatter_sum - -from .blocks import ( - AtomicEnergiesBlock, - EquivariantProductBasisBlock, - InteractionBlock, - LinearDipoleReadoutBlock, - LinearNodeEmbeddingBlock, - LinearReadoutBlock, - NonLinearDipoleReadoutBlock, - NonLinearReadoutBlock, - RadialEmbeddingBlock, - ScaleShiftBlock, -) -from .utils import ( - compute_fixed_charge_dipole, - get_atomic_virials_stresses, - get_edge_vectors_and_lengths, - get_outputs, - get_symmetric_displacement, - prepare_graph, -) - -# pylint: disable=C0302 - - -@compile_mode("script") -class MACE(torch.nn.Module): - def __init__( - self, - r_max: float, - num_bessel: int, - num_polynomial_cutoff: int, - max_ell: int, - interaction_cls: Type[InteractionBlock], - interaction_cls_first: Type[InteractionBlock], - num_interactions: int, - num_elements: int, - hidden_irreps: o3.Irreps, - MLP_irreps: o3.Irreps, - atomic_energies: np.ndarray, - avg_num_neighbors: float, - atomic_numbers: List[int], - correlation: Union[int, List[int]], - gate: Optional[Callable], - pair_repulsion: bool = False, - distance_transform: str = "None", - radial_MLP: Optional[List[int]] = None, - radial_type: Optional[str] = "bessel", - heads: Optional[List[str]] = None, - cueq_config: Optional[Dict[str, Any]] = None, - lammps_mliap: Optional[bool] = False, - ): - super().__init__() - self.register_buffer( - "atomic_numbers", torch.tensor(atomic_numbers, dtype=torch.int64) - ) - self.register_buffer( - "r_max", torch.tensor(r_max, dtype=torch.get_default_dtype()) - ) - self.register_buffer( - "num_interactions", torch.tensor(num_interactions, dtype=torch.int64) - ) - if heads is None: - heads = ["Default"] - self.heads = heads - if isinstance(correlation, int): - correlation = [correlation] * num_interactions - self.lammps_mliap = lammps_mliap - # Embedding - node_attr_irreps = o3.Irreps([(num_elements, (0, 1))]) - node_feats_irreps = o3.Irreps([(hidden_irreps.count(o3.Irrep(0, 1)), (0, 1))]) - self.node_embedding = LinearNodeEmbeddingBlock( - irreps_in=node_attr_irreps, - irreps_out=node_feats_irreps, - cueq_config=cueq_config, - ) - self.radial_embedding = RadialEmbeddingBlock( - r_max=r_max, - num_bessel=num_bessel, - num_polynomial_cutoff=num_polynomial_cutoff, - radial_type=radial_type, - distance_transform=distance_transform, - ) - edge_feats_irreps = o3.Irreps(f"{self.radial_embedding.out_dim}x0e") - if pair_repulsion: - self.pair_repulsion_fn = ZBLBasis(p=num_polynomial_cutoff) - self.pair_repulsion = True - - sh_irreps = o3.Irreps.spherical_harmonics(max_ell) - num_features = hidden_irreps.count(o3.Irrep(0, 1)) - interaction_irreps = (sh_irreps * num_features).sort()[0].simplify() - self.spherical_harmonics = o3.SphericalHarmonics( - sh_irreps, normalize=True, normalization="component" - ) - if radial_MLP is None: - radial_MLP = [64, 64, 64] - # Interactions and readout - self.atomic_energies_fn = AtomicEnergiesBlock(atomic_energies) - - inter = interaction_cls_first( - node_attrs_irreps=node_attr_irreps, - node_feats_irreps=node_feats_irreps, - edge_attrs_irreps=sh_irreps, - edge_feats_irreps=edge_feats_irreps, - target_irreps=interaction_irreps, - hidden_irreps=hidden_irreps, - avg_num_neighbors=avg_num_neighbors, - radial_MLP=radial_MLP, - cueq_config=cueq_config, - ) - self.interactions = torch.nn.ModuleList([inter]) - - # Use the appropriate self connection at the first layer for proper E0 - use_sc_first = False - if "Residual" in str(interaction_cls_first): - use_sc_first = True - - node_feats_irreps_out = inter.target_irreps - prod = EquivariantProductBasisBlock( - node_feats_irreps=node_feats_irreps_out, - target_irreps=hidden_irreps, - correlation=correlation[0], - num_elements=num_elements, - use_sc=use_sc_first, - cueq_config=cueq_config, - ) - self.products = torch.nn.ModuleList([prod]) - - self.readouts = torch.nn.ModuleList() - self.readouts.append( - LinearReadoutBlock( - hidden_irreps, o3.Irreps(f"{len(heads)}x0e"), cueq_config - ) - ) - - for i in range(num_interactions - 1): - if i == num_interactions - 2: - hidden_irreps_out = str( - hidden_irreps[0] - ) # Select only scalars for last layer - else: - hidden_irreps_out = hidden_irreps - inter = interaction_cls( - node_attrs_irreps=node_attr_irreps, - node_feats_irreps=hidden_irreps, - edge_attrs_irreps=sh_irreps, - edge_feats_irreps=edge_feats_irreps, - target_irreps=interaction_irreps, - hidden_irreps=hidden_irreps_out, - avg_num_neighbors=avg_num_neighbors, - radial_MLP=radial_MLP, - cueq_config=cueq_config, - ) - self.interactions.append(inter) - prod = EquivariantProductBasisBlock( - node_feats_irreps=interaction_irreps, - target_irreps=hidden_irreps_out, - correlation=correlation[i + 1], - num_elements=num_elements, - use_sc=True, - cueq_config=cueq_config, - ) - self.products.append(prod) - if i == num_interactions - 2: - self.readouts.append( - NonLinearReadoutBlock( - hidden_irreps_out, - (len(heads) * MLP_irreps).simplify(), - gate, - o3.Irreps(f"{len(heads)}x0e"), - len(heads), - cueq_config, - ) - ) - else: - self.readouts.append( - LinearReadoutBlock( - hidden_irreps, o3.Irreps(f"{len(heads)}x0e"), cueq_config - ) - ) - - def forward( - self, - data: Dict[str, torch.Tensor], - training: bool = False, - compute_force: bool = True, - compute_virials: bool = False, - compute_stress: bool = False, - compute_displacement: bool = False, - compute_hessian: bool = False, - compute_edge_forces: bool = False, - compute_atomic_stresses: bool = False, - lammps_mliap: bool = False, - ) -> Dict[str, Optional[torch.Tensor]]: - # Setup - ctx = prepare_graph( - data, - compute_virials=compute_virials, - compute_stress=compute_stress, - compute_displacement=compute_displacement, - lammps_mliap=lammps_mliap, - ) - is_lammps = ctx.is_lammps - num_atoms_arange = ctx.num_atoms_arange - num_graphs = ctx.num_graphs - displacement = ctx.displacement - positions = ctx.positions - vectors = ctx.vectors - lengths = ctx.lengths - cell = ctx.cell - node_heads = ctx.node_heads - interaction_kwargs = ctx.interaction_kwargs - lammps_natoms = interaction_kwargs.lammps_natoms - lammps_class = interaction_kwargs.lammps_class - - # Atomic energies - node_e0 = self.atomic_energies_fn(data["node_attrs"])[ - num_atoms_arange, node_heads - ] - e0 = scatter_sum( - src=node_e0, index=data["batch"], dim=0, dim_size=num_graphs - ) # [n_graphs, n_heads] - # Embeddings - node_feats = self.node_embedding(data["node_attrs"]) - edge_attrs = self.spherical_harmonics(vectors) - edge_feats = self.radial_embedding( - lengths, data["node_attrs"], data["edge_index"], self.atomic_numbers - ) - if hasattr(self, "pair_repulsion"): - pair_node_energy = self.pair_repulsion_fn( - lengths, data["node_attrs"], data["edge_index"], self.atomic_numbers - ) - if is_lammps: - pair_node_energy = pair_node_energy[: lammps_natoms[0]] - pair_energy = scatter_sum( - src=pair_node_energy, index=data["batch"], dim=-1, dim_size=num_graphs - ) # [n_graphs,] - else: - pair_node_energy = torch.zeros_like(node_e0) - pair_energy = torch.zeros_like(e0) - - # Interactions - energies = [e0, pair_energy] - node_energies_list = [node_e0, pair_node_energy] - node_feats_concat: List[torch.Tensor] = [] - - for i, (interaction, product, readout) in enumerate( - zip(self.interactions, self.products, self.readouts) - ): - node_attrs_slice = data["node_attrs"] - if is_lammps and i > 0: - node_attrs_slice = node_attrs_slice[: lammps_natoms[0]] - node_feats, sc = interaction( - node_attrs=node_attrs_slice, - node_feats=node_feats, - edge_attrs=edge_attrs, - edge_feats=edge_feats, - edge_index=data["edge_index"], - first_layer=(i == 0), - lammps_class=lammps_class, - lammps_natoms=lammps_natoms, - ) - if is_lammps and i == 0: - node_attrs_slice = node_attrs_slice[: lammps_natoms[0]] - node_feats = product( - node_feats=node_feats, sc=sc, node_attrs=node_attrs_slice - ) - node_feats_concat.append(node_feats) - node_es = readout(node_feats, node_heads)[num_atoms_arange, node_heads] - energy = scatter_sum(node_es, data["batch"], dim=0, dim_size=num_graphs) - energies.append(energy) - node_energies_list.append(node_es) - - contributions = torch.stack(energies, dim=-1) - total_energy = torch.sum(contributions, dim=-1) - node_energy = torch.sum(torch.stack(node_energies_list, dim=-1), dim=-1) - node_feats_out = torch.cat(node_feats_concat, dim=-1) - node_energy = node_e0.double() + pair_node_energy.double() - - forces, virials, stress, hessian, edge_forces = get_outputs( - energy=total_energy, - positions=positions, - displacement=displacement, - vectors=vectors, - cell=cell, - training=training, - compute_force=compute_force, - compute_virials=compute_virials, - compute_stress=compute_stress, - compute_hessian=compute_hessian, - compute_edge_forces=compute_edge_forces, - ) - - atomic_virials: Optional[torch.Tensor] = None - atomic_stresses: Optional[torch.Tensor] = None - if compute_atomic_stresses and edge_forces is not None: - atomic_virials, atomic_stresses = get_atomic_virials_stresses( - edge_forces=edge_forces, - edge_index=data["edge_index"], - vectors=vectors, - num_atoms=positions.shape[0], - batch=data["batch"], - cell=cell, - ) - return { - "energy": total_energy, - "node_energy": node_energy, - "contributions": contributions, - "forces": forces, - "edge_forces": edge_forces, - "virials": virials, - "stress": stress, - "atomic_virials": atomic_virials, - "atomic_stresses": atomic_stresses, - "displacement": displacement, - "hessian": hessian, - "node_feats": node_feats_out, - } - - -@compile_mode("script") -class ScaleShiftMACE(MACE): - def __init__( - self, - atomic_inter_scale: float, - atomic_inter_shift: float, - **kwargs, - ): - super().__init__(**kwargs) - self.scale_shift = ScaleShiftBlock( - scale=atomic_inter_scale, shift=atomic_inter_shift - ) - - def forward( - self, - data: Dict[str, torch.Tensor], - training: bool = False, - compute_force: bool = True, - compute_virials: bool = False, - compute_stress: bool = False, - compute_displacement: bool = False, - compute_hessian: bool = False, - compute_edge_forces: bool = False, - compute_atomic_stresses: bool = False, - lammps_mliap: bool = False, - ) -> Dict[str, Optional[torch.Tensor]]: - # Setup - ctx = prepare_graph( - data, - compute_virials=compute_virials, - compute_stress=compute_stress, - compute_displacement=compute_displacement, - lammps_mliap=lammps_mliap, - ) - - is_lammps = ctx.is_lammps - num_atoms_arange = ctx.num_atoms_arange - num_graphs = ctx.num_graphs - displacement = ctx.displacement - positions = ctx.positions - vectors = ctx.vectors - lengths = ctx.lengths - cell = ctx.cell - node_heads = ctx.node_heads - interaction_kwargs = ctx.interaction_kwargs - lammps_natoms = interaction_kwargs.lammps_natoms - lammps_class = interaction_kwargs.lammps_class - - # Atomic energies - node_e0 = self.atomic_energies_fn(data["node_attrs"])[ - num_atoms_arange, node_heads - ] - e0 = scatter_sum( - src=node_e0, index=data["batch"], dim=0, dim_size=num_graphs - ) # [n_graphs, num_heads] - - # Embeddings - node_feats = self.node_embedding(data["node_attrs"]) - edge_attrs = self.spherical_harmonics(vectors) - edge_feats = self.radial_embedding( - lengths, data["node_attrs"], data["edge_index"], self.atomic_numbers - ) - - if hasattr(self, "pair_repulsion"): - pair_node_energy = self.pair_repulsion_fn( - lengths, data["node_attrs"], data["edge_index"], self.atomic_numbers - ) - if is_lammps: - pair_node_energy = pair_node_energy[: lammps_natoms[0]] - else: - pair_node_energy = torch.zeros_like(node_e0) - - # Interactions - node_es_list = [pair_node_energy] - node_feats_list: List[torch.Tensor] = [] - - for i, (interaction, product, readout) in enumerate( - zip(self.interactions, self.products, self.readouts) - ): - node_attrs_slice = data["node_attrs"] - if is_lammps and i > 0: - node_attrs_slice = node_attrs_slice[: lammps_natoms[0]] - node_feats, sc = interaction( - node_attrs=node_attrs_slice, - node_feats=node_feats, - edge_attrs=edge_attrs, - edge_feats=edge_feats, - edge_index=data["edge_index"], - first_layer=(i == 0), - lammps_class=lammps_class, - lammps_natoms=lammps_natoms, - ) - if is_lammps and i == 0: - node_attrs_slice = node_attrs_slice[: lammps_natoms[0]] - node_feats = product( - node_feats=node_feats, sc=sc, node_attrs=node_attrs_slice - ) - node_feats_list.append(node_feats) - node_es_list.append( - readout(node_feats, node_heads)[num_atoms_arange, node_heads] - ) - - node_feats_out = torch.cat(node_feats_list, dim=-1) - node_inter_es = torch.sum(torch.stack(node_es_list, dim=0), dim=0) - node_inter_es = self.scale_shift(node_inter_es, node_heads) - inter_e = scatter_sum(node_inter_es, data["batch"], dim=-1, dim_size=num_graphs) - - total_energy = e0 + inter_e - node_energy = node_e0.clone().double() + node_inter_es.clone().double() - - forces, virials, stress, hessian, edge_forces = get_outputs( - energy=inter_e, - positions=positions, - displacement=displacement, - vectors=vectors, - cell=cell, - training=training, - compute_force=compute_force, - compute_virials=compute_virials, - compute_stress=compute_stress, - compute_hessian=compute_hessian, - compute_edge_forces=compute_edge_forces or compute_atomic_stresses, - ) - - atomic_virials: Optional[torch.Tensor] = None - atomic_stresses: Optional[torch.Tensor] = None - if compute_atomic_stresses and edge_forces is not None: - atomic_virials, atomic_stresses = get_atomic_virials_stresses( - edge_forces=edge_forces, - edge_index=data["edge_index"], - vectors=vectors, - num_atoms=positions.shape[0], - batch=data["batch"], - cell=cell, - ) - return { - "energy": total_energy, - "node_energy": node_energy, - "interaction_energy": inter_e, - "forces": forces, - "edge_forces": edge_forces, - "virials": virials, - "stress": stress, - "atomic_virials": atomic_virials, - "atomic_stresses": atomic_stresses, - "hessian": hessian, - "displacement": displacement, - "node_feats": node_feats_out, - } - - -@compile_mode("script") -class AtomicDipolesMACE(torch.nn.Module): - def __init__( - self, - r_max: float, - num_bessel: int, - num_polynomial_cutoff: int, - max_ell: int, - interaction_cls: Type[InteractionBlock], - interaction_cls_first: Type[InteractionBlock], - num_interactions: int, - num_elements: int, - hidden_irreps: o3.Irreps, - MLP_irreps: o3.Irreps, - avg_num_neighbors: float, - atomic_numbers: List[int], - correlation: int, - gate: Optional[Callable], - atomic_energies: Optional[ - None - ], # Just here to make it compatible with energy models, MUST be None - radial_type: Optional[str] = "bessel", - radial_MLP: Optional[List[int]] = None, - cueq_config: Optional[Dict[str, Any]] = None, # pylint: disable=unused-argument - ): - super().__init__() - self.register_buffer( - "atomic_numbers", torch.tensor(atomic_numbers, dtype=torch.int64) - ) - self.register_buffer("r_max", torch.tensor(r_max, dtype=torch.float64)) - self.register_buffer( - "num_interactions", torch.tensor(num_interactions, dtype=torch.int64) - ) - assert atomic_energies is None - - # Embedding - node_attr_irreps = o3.Irreps([(num_elements, (0, 1))]) - node_feats_irreps = o3.Irreps([(hidden_irreps.count(o3.Irrep(0, 1)), (0, 1))]) - self.node_embedding = LinearNodeEmbeddingBlock( - irreps_in=node_attr_irreps, irreps_out=node_feats_irreps - ) - self.radial_embedding = RadialEmbeddingBlock( - r_max=r_max, - num_bessel=num_bessel, - num_polynomial_cutoff=num_polynomial_cutoff, - radial_type=radial_type, - ) - edge_feats_irreps = o3.Irreps(f"{self.radial_embedding.out_dim}x0e") - - sh_irreps = o3.Irreps.spherical_harmonics(max_ell) - num_features = hidden_irreps.count(o3.Irrep(0, 1)) - interaction_irreps = (sh_irreps * num_features).sort()[0].simplify() - self.spherical_harmonics = o3.SphericalHarmonics( - sh_irreps, normalize=True, normalization="component" - ) - if radial_MLP is None: - radial_MLP = [64, 64, 64] - - # Interactions and readouts - inter = interaction_cls_first( - node_attrs_irreps=node_attr_irreps, - node_feats_irreps=node_feats_irreps, - edge_attrs_irreps=sh_irreps, - edge_feats_irreps=edge_feats_irreps, - target_irreps=interaction_irreps, - hidden_irreps=hidden_irreps, - avg_num_neighbors=avg_num_neighbors, - radial_MLP=radial_MLP, - ) - self.interactions = torch.nn.ModuleList([inter]) - - # Use the appropriate self connection at the first layer - use_sc_first = False - if "Residual" in str(interaction_cls_first): - use_sc_first = True - - node_feats_irreps_out = inter.target_irreps - prod = EquivariantProductBasisBlock( - node_feats_irreps=node_feats_irreps_out, - target_irreps=hidden_irreps, - correlation=correlation, - num_elements=num_elements, - use_sc=use_sc_first, - ) - self.products = torch.nn.ModuleList([prod]) - - self.readouts = torch.nn.ModuleList() - self.readouts.append(LinearDipoleReadoutBlock(hidden_irreps, dipole_only=True)) - - for i in range(num_interactions - 1): - if i == num_interactions - 2: - assert ( - len(hidden_irreps) > 1 - ), "To predict dipoles use at least l=1 hidden_irreps" - hidden_irreps_out = str( - hidden_irreps[1] - ) # Select only l=1 vectors for last layer - else: - hidden_irreps_out = hidden_irreps - inter = interaction_cls( - node_attrs_irreps=node_attr_irreps, - node_feats_irreps=hidden_irreps, - edge_attrs_irreps=sh_irreps, - edge_feats_irreps=edge_feats_irreps, - target_irreps=interaction_irreps, - hidden_irreps=hidden_irreps_out, - avg_num_neighbors=avg_num_neighbors, - radial_MLP=radial_MLP, - ) - self.interactions.append(inter) - prod = EquivariantProductBasisBlock( - node_feats_irreps=interaction_irreps, - target_irreps=hidden_irreps_out, - correlation=correlation, - num_elements=num_elements, - use_sc=True, - ) - self.products.append(prod) - if i == num_interactions - 2: - self.readouts.append( - NonLinearDipoleReadoutBlock( - hidden_irreps_out, MLP_irreps, gate, dipole_only=True - ) - ) - else: - self.readouts.append( - LinearDipoleReadoutBlock(hidden_irreps, dipole_only=True) - ) - - def forward( - self, - data: Dict[str, torch.Tensor], - training: bool = False, # pylint: disable=W0613 - compute_force: bool = False, - compute_virials: bool = False, - compute_stress: bool = False, - compute_displacement: bool = False, - compute_edge_forces: bool = False, # pylint: disable=W0613 - compute_atomic_stresses: bool = False, # pylint: disable=W0613 - ) -> Dict[str, Optional[torch.Tensor]]: - assert compute_force is False - assert compute_virials is False - assert compute_stress is False - assert compute_displacement is False - # Setup - data["node_attrs"].requires_grad_(True) - data["positions"].requires_grad_(True) - num_graphs = data["ptr"].numel() - 1 - - # Embeddings - node_feats = self.node_embedding(data["node_attrs"]) - vectors, lengths = get_edge_vectors_and_lengths( - positions=data["positions"], - edge_index=data["edge_index"], - shifts=data["shifts"], - ) - edge_attrs = self.spherical_harmonics(vectors) - edge_feats = self.radial_embedding( - lengths, data["node_attrs"], data["edge_index"], self.atomic_numbers - ) - - # Interactions - dipoles = [] - for interaction, product, readout in zip( - self.interactions, self.products, self.readouts - ): - node_feats, sc = interaction( - node_attrs=data["node_attrs"], - node_feats=node_feats, - edge_attrs=edge_attrs, - edge_feats=edge_feats, - edge_index=data["edge_index"], - ) - node_feats = product( - node_feats=node_feats, - sc=sc, - node_attrs=data["node_attrs"], - ) - node_dipoles = readout(node_feats).squeeze(-1) # [n_nodes,3] - dipoles.append(node_dipoles) - - # Compute the dipoles - contributions_dipoles = torch.stack( - dipoles, dim=-1 - ) # [n_nodes,3,n_contributions] - atomic_dipoles = torch.sum(contributions_dipoles, dim=-1) # [n_nodes,3] - total_dipole = scatter_sum( - src=atomic_dipoles, - index=data["batch"], - dim=0, - dim_size=num_graphs, - ) # [n_graphs,3] - baseline = compute_fixed_charge_dipole( - charges=data["charges"], - positions=data["positions"], - batch=data["batch"], - num_graphs=num_graphs, - ) # [n_graphs,3] - total_dipole = total_dipole + baseline - - output = { - "dipole": total_dipole, - "atomic_dipoles": atomic_dipoles, - } - return output - - -@compile_mode("script") -class EnergyDipolesMACE(torch.nn.Module): - def __init__( - self, - r_max: float, - num_bessel: int, - num_polynomial_cutoff: int, - max_ell: int, - interaction_cls: Type[InteractionBlock], - interaction_cls_first: Type[InteractionBlock], - num_interactions: int, - num_elements: int, - hidden_irreps: o3.Irreps, - MLP_irreps: o3.Irreps, - avg_num_neighbors: float, - atomic_numbers: List[int], - correlation: int, - gate: Optional[Callable], - atomic_energies: Optional[np.ndarray], - radial_MLP: Optional[List[int]] = None, - cueq_config: Optional[Dict[str, Any]] = None, # pylint: disable=unused-argument - ): - super().__init__() - self.register_buffer( - "atomic_numbers", torch.tensor(atomic_numbers, dtype=torch.int64) - ) - self.register_buffer("r_max", torch.tensor(r_max, dtype=torch.float64)) - self.register_buffer( - "num_interactions", torch.tensor(num_interactions, dtype=torch.int64) - ) - # Embedding - node_attr_irreps = o3.Irreps([(num_elements, (0, 1))]) - node_feats_irreps = o3.Irreps([(hidden_irreps.count(o3.Irrep(0, 1)), (0, 1))]) - self.node_embedding = LinearNodeEmbeddingBlock( - irreps_in=node_attr_irreps, irreps_out=node_feats_irreps - ) - self.radial_embedding = RadialEmbeddingBlock( - r_max=r_max, - num_bessel=num_bessel, - num_polynomial_cutoff=num_polynomial_cutoff, - ) - edge_feats_irreps = o3.Irreps(f"{self.radial_embedding.out_dim}x0e") - - sh_irreps = o3.Irreps.spherical_harmonics(max_ell) - num_features = hidden_irreps.count(o3.Irrep(0, 1)) - interaction_irreps = (sh_irreps * num_features).sort()[0].simplify() - self.spherical_harmonics = o3.SphericalHarmonics( - sh_irreps, normalize=True, normalization="component" - ) - if radial_MLP is None: - radial_MLP = [64, 64, 64] - # Interactions and readouts - self.atomic_energies_fn = AtomicEnergiesBlock(atomic_energies) - - inter = interaction_cls_first( - node_attrs_irreps=node_attr_irreps, - node_feats_irreps=node_feats_irreps, - edge_attrs_irreps=sh_irreps, - edge_feats_irreps=edge_feats_irreps, - target_irreps=interaction_irreps, - hidden_irreps=hidden_irreps, - avg_num_neighbors=avg_num_neighbors, - radial_MLP=radial_MLP, - ) - self.interactions = torch.nn.ModuleList([inter]) - - # Use the appropriate self connection at the first layer - use_sc_first = False - if "Residual" in str(interaction_cls_first): - use_sc_first = True - - node_feats_irreps_out = inter.target_irreps - prod = EquivariantProductBasisBlock( - node_feats_irreps=node_feats_irreps_out, - target_irreps=hidden_irreps, - correlation=correlation, - num_elements=num_elements, - use_sc=use_sc_first, - ) - self.products = torch.nn.ModuleList([prod]) - - self.readouts = torch.nn.ModuleList() - self.readouts.append(LinearDipoleReadoutBlock(hidden_irreps, dipole_only=False)) - - for i in range(num_interactions - 1): - if i == num_interactions - 2: - assert ( - len(hidden_irreps) > 1 - ), "To predict dipoles use at least l=1 hidden_irreps" - hidden_irreps_out = str( - hidden_irreps[:2] - ) # Select scalars and l=1 vectors for last layer - else: - hidden_irreps_out = hidden_irreps - inter = interaction_cls( - node_attrs_irreps=node_attr_irreps, - node_feats_irreps=hidden_irreps, - edge_attrs_irreps=sh_irreps, - edge_feats_irreps=edge_feats_irreps, - target_irreps=interaction_irreps, - hidden_irreps=hidden_irreps_out, - avg_num_neighbors=avg_num_neighbors, - radial_MLP=radial_MLP, - ) - self.interactions.append(inter) - prod = EquivariantProductBasisBlock( - node_feats_irreps=interaction_irreps, - target_irreps=hidden_irreps_out, - correlation=correlation, - num_elements=num_elements, - use_sc=True, - ) - self.products.append(prod) - if i == num_interactions - 2: - self.readouts.append( - NonLinearDipoleReadoutBlock( - hidden_irreps_out, MLP_irreps, gate, dipole_only=False - ) - ) - else: - self.readouts.append( - LinearDipoleReadoutBlock(hidden_irreps, dipole_only=False) - ) - - def forward( - self, - data: Dict[str, torch.Tensor], - training: bool = False, - compute_force: bool = True, - compute_virials: bool = False, - compute_stress: bool = False, - compute_displacement: bool = False, - compute_edge_forces: bool = False, # pylint: disable=W0613 - compute_atomic_stresses: bool = False, # pylint: disable=W0613 - ) -> Dict[str, Optional[torch.Tensor]]: - # Setup - data["node_attrs"].requires_grad_(True) - data["positions"].requires_grad_(True) - num_graphs = data["ptr"].numel() - 1 - num_atoms_arange = torch.arange(data["positions"].shape[0]) - displacement = torch.zeros( - (num_graphs, 3, 3), - dtype=data["positions"].dtype, - device=data["positions"].device, - ) - if compute_virials or compute_stress or compute_displacement: - ( - data["positions"], - data["shifts"], - displacement, - ) = get_symmetric_displacement( - positions=data["positions"], - unit_shifts=data["unit_shifts"], - cell=data["cell"], - edge_index=data["edge_index"], - num_graphs=num_graphs, - batch=data["batch"], - ) - - # Atomic energies - node_e0 = self.atomic_energies_fn(data["node_attrs"])[ - num_atoms_arange, data["head"][data["batch"]] - ] - e0 = scatter_sum( - src=node_e0, index=data["batch"], dim=-1, dim_size=num_graphs - ) # [n_graphs,] - - # Embeddings - node_feats = self.node_embedding(data["node_attrs"]) - vectors, lengths = get_edge_vectors_and_lengths( - positions=data["positions"], - edge_index=data["edge_index"], - shifts=data["shifts"], - ) - edge_attrs = self.spherical_harmonics(vectors) - edge_feats = self.radial_embedding( - lengths, data["node_attrs"], data["edge_index"], self.atomic_numbers - ) - - # Interactions - energies = [e0] - node_energies_list = [node_e0] - dipoles = [] - for interaction, product, readout in zip( - self.interactions, self.products, self.readouts - ): - node_feats, sc = interaction( - node_attrs=data["node_attrs"], - node_feats=node_feats, - edge_attrs=edge_attrs, - edge_feats=edge_feats, - edge_index=data["edge_index"], - ) - node_feats = product( - node_feats=node_feats, - sc=sc, - node_attrs=data["node_attrs"], - ) - node_out = readout(node_feats).squeeze(-1) # [n_nodes, ] - # node_energies = readout(node_feats).squeeze(-1) # [n_nodes, ] - node_energies = node_out[:, 0] - energy = scatter_sum( - src=node_energies, index=data["batch"], dim=-1, dim_size=num_graphs - ) # [n_graphs,] - energies.append(energy) - node_dipoles = node_out[:, 1:] - dipoles.append(node_dipoles) - - # Compute the energies and dipoles - contributions = torch.stack(energies, dim=-1) - total_energy = torch.sum(contributions, dim=-1) # [n_graphs, ] - node_energy_contributions = torch.stack(node_energies_list, dim=-1) - node_energy = torch.sum(node_energy_contributions, dim=-1) # [n_nodes, ] - contributions_dipoles = torch.stack( - dipoles, dim=-1 - ) # [n_nodes,3,n_contributions] - atomic_dipoles = torch.sum(contributions_dipoles, dim=-1) # [n_nodes,3] - total_dipole = scatter_sum( - src=atomic_dipoles, - index=data["batch"].unsqueeze(-1), - dim=0, - dim_size=num_graphs, - ) # [n_graphs,3] - baseline = compute_fixed_charge_dipole( - charges=data["charges"], - positions=data["positions"], - batch=data["batch"], - num_graphs=num_graphs, - ) # [n_graphs,3] - total_dipole = total_dipole + baseline - - forces, virials, stress, _, _ = get_outputs( - energy=total_energy, - positions=data["positions"], - displacement=displacement, - cell=data["cell"], - training=training, - compute_force=compute_force, - compute_virials=compute_virials, - compute_stress=compute_stress, - ) - - output = { - "energy": total_energy, - "node_energy": node_energy, - "contributions": contributions, - "forces": forces, - "virials": virials, - "stress": stress, - "displacement": displacement, - "dipole": total_dipole, - "atomic_dipoles": atomic_dipoles, - } - return output diff --git a/mace-bench/3rdparty/mace/mace/modules/radial.py b/mace-bench/3rdparty/mace/mace/modules/radial.py deleted file mode 100644 index ff69b43e5884137ab6a37861eab763714a058155..0000000000000000000000000000000000000000 --- a/mace-bench/3rdparty/mace/mace/modules/radial.py +++ /dev/null @@ -1,358 +0,0 @@ -########################################################################################### -# Radial basis and cutoff -# Authors: Ilyes Batatia, Gregor Simm -# This program is distributed under the MIT License (see MIT.md) -########################################################################################### - -import logging - -import ase -import numpy as np -import torch -from e3nn.util.jit import compile_mode - -from mace.tools.scatter import scatter_sum - - -@compile_mode("script") -class BesselBasis(torch.nn.Module): - """ - Equation (7) - """ - - def __init__(self, r_max: float, num_basis=8, trainable=False): - super().__init__() - - bessel_weights = ( - np.pi - / r_max - * torch.linspace( - start=1.0, - end=num_basis, - steps=num_basis, - dtype=torch.get_default_dtype(), - ) - ) - if trainable: - self.bessel_weights = torch.nn.Parameter(bessel_weights) - else: - self.register_buffer("bessel_weights", bessel_weights) - - self.register_buffer( - "r_max", torch.tensor(r_max, dtype=torch.get_default_dtype()) - ) - self.register_buffer( - "prefactor", - torch.tensor(np.sqrt(2.0 / r_max), dtype=torch.get_default_dtype()), - ) - - def forward(self, x: torch.Tensor) -> torch.Tensor: # [..., 1] - numerator = torch.sin(self.bessel_weights * x) # [..., num_basis] - return self.prefactor * (numerator / x) - - def __repr__(self): - return ( - f"{self.__class__.__name__}(r_max={self.r_max}, num_basis={len(self.bessel_weights)}, " - f"trainable={self.bessel_weights.requires_grad})" - ) - - -@compile_mode("script") -class ChebychevBasis(torch.nn.Module): - """ - Equation (7) - """ - - def __init__(self, r_max: float, num_basis=8): - super().__init__() - self.register_buffer( - "n", - torch.arange(1, num_basis + 1, dtype=torch.get_default_dtype()).unsqueeze( - 0 - ), - ) - self.num_basis = num_basis - self.r_max = r_max - - def forward(self, x: torch.Tensor) -> torch.Tensor: # [..., 1] - x = x.repeat(1, self.num_basis) - n = self.n.repeat(len(x), 1) - return torch.special.chebyshev_polynomial_t(x, n) - - def __repr__(self): - return ( - f"{self.__class__.__name__}(r_max={self.r_max}, num_basis={self.num_basis}," - ) - - -@compile_mode("script") -class GaussianBasis(torch.nn.Module): - """ - Gaussian basis functions - """ - - def __init__(self, r_max: float, num_basis=128, trainable=False): - super().__init__() - gaussian_weights = torch.linspace( - start=0.0, end=r_max, steps=num_basis, dtype=torch.get_default_dtype() - ) - if trainable: - self.gaussian_weights = torch.nn.Parameter( - gaussian_weights, requires_grad=True - ) - else: - self.register_buffer("gaussian_weights", gaussian_weights) - self.coeff = -0.5 / (r_max / (num_basis - 1)) ** 2 - - def forward(self, x: torch.Tensor) -> torch.Tensor: # [..., 1] - x = x - self.gaussian_weights - return torch.exp(self.coeff * torch.pow(x, 2)) - - -@compile_mode("script") -class PolynomialCutoff(torch.nn.Module): - """Polynomial cutoff function that goes from 1 to 0 as x goes from 0 to r_max. - Equation (8) -- TODO: from where? - """ - - p: torch.Tensor - r_max: torch.Tensor - - def __init__(self, r_max: float, p=6): - super().__init__() - self.register_buffer("p", torch.tensor(p, dtype=torch.int)) - self.register_buffer( - "r_max", torch.tensor(r_max, dtype=torch.get_default_dtype()) - ) - - def forward(self, x: torch.Tensor) -> torch.Tensor: - return self.calculate_envelope(x, self.r_max, self.p.to(torch.int)) - - @staticmethod - def calculate_envelope( - x: torch.Tensor, r_max: torch.Tensor, p: torch.Tensor - ) -> torch.Tensor: - r_over_r_max = x / r_max - envelope = ( - 1.0 - - ((p + 1.0) * (p + 2.0) / 2.0) * torch.pow(r_over_r_max, p) - + p * (p + 2.0) * torch.pow(r_over_r_max, p + 1) - - (p * (p + 1.0) / 2) * torch.pow(r_over_r_max, p + 2) - ) - return envelope * (x < r_max) - - def __repr__(self): - return f"{self.__class__.__name__}(p={self.p}, r_max={self.r_max})" - - -@compile_mode("script") -class ZBLBasis(torch.nn.Module): - """Implementation of the Ziegler-Biersack-Littmark (ZBL) potential - with a polynomial cutoff envelope. - """ - - p: torch.Tensor - - def __init__(self, p=6, trainable=False, **kwargs): - super().__init__() - if "r_max" in kwargs: - logging.warning( - "r_max is deprecated. r_max is determined from the covalent radii." - ) - - # Pre-calculate the p coefficients for the ZBL potential - self.register_buffer( - "c", - torch.tensor( - [0.1818, 0.5099, 0.2802, 0.02817], dtype=torch.get_default_dtype() - ), - ) - self.register_buffer("p", torch.tensor(p, dtype=torch.int)) - self.register_buffer( - "covalent_radii", - torch.tensor( - ase.data.covalent_radii, - dtype=torch.get_default_dtype(), - ), - ) - if trainable: - self.a_exp = torch.nn.Parameter(torch.tensor(0.300, requires_grad=True)) - self.a_prefactor = torch.nn.Parameter( - torch.tensor(0.4543, requires_grad=True) - ) - else: - self.register_buffer("a_exp", torch.tensor(0.300)) - self.register_buffer("a_prefactor", torch.tensor(0.4543)) - - def forward( - self, - x: torch.Tensor, - node_attrs: torch.Tensor, - edge_index: torch.Tensor, - atomic_numbers: torch.Tensor, - ) -> torch.Tensor: - sender = edge_index[0] - receiver = edge_index[1] - node_atomic_numbers = atomic_numbers[torch.argmax(node_attrs, dim=1)].unsqueeze( - -1 - ) - Z_u = node_atomic_numbers[sender] - Z_v = node_atomic_numbers[receiver] - a = ( - self.a_prefactor - * 0.529 - / (torch.pow(Z_u, self.a_exp) + torch.pow(Z_v, self.a_exp)) - ) - r_over_a = x / a - phi = ( - self.c[0] * torch.exp(-3.2 * r_over_a) - + self.c[1] * torch.exp(-0.9423 * r_over_a) - + self.c[2] * torch.exp(-0.4028 * r_over_a) - + self.c[3] * torch.exp(-0.2016 * r_over_a) - ) - v_edges = (14.3996 * Z_u * Z_v) / x * phi - r_max = self.covalent_radii[Z_u] + self.covalent_radii[Z_v] - envelope = PolynomialCutoff.calculate_envelope(x, r_max, self.p) - v_edges = 0.5 * v_edges * envelope - V_ZBL = scatter_sum(v_edges, receiver, dim=0, dim_size=node_attrs.size(0)) - return V_ZBL.squeeze(-1) - - def __repr__(self): - return f"{self.__class__.__name__}(c={self.c})" - - -@compile_mode("script") -class AgnesiTransform(torch.nn.Module): - """Agnesi transform - see section on Radial transformations in - ACEpotentials.jl, JCP 2023 (https://doi.org/10.1063/5.0158783). - """ - - def __init__( - self, - q: float = 0.9183, - p: float = 4.5791, - a: float = 1.0805, - trainable=False, - ): - super().__init__() - self.register_buffer("q", torch.tensor(q, dtype=torch.get_default_dtype())) - self.register_buffer("p", torch.tensor(p, dtype=torch.get_default_dtype())) - self.register_buffer("a", torch.tensor(a, dtype=torch.get_default_dtype())) - self.register_buffer( - "covalent_radii", - torch.tensor( - ase.data.covalent_radii, - dtype=torch.get_default_dtype(), - ), - ) - if trainable: - self.a = torch.nn.Parameter(torch.tensor(1.0805, requires_grad=True)) - self.q = torch.nn.Parameter(torch.tensor(0.9183, requires_grad=True)) - self.p = torch.nn.Parameter(torch.tensor(4.5791, requires_grad=True)) - - def forward( - self, - x: torch.Tensor, - node_attrs: torch.Tensor, - edge_index: torch.Tensor, - atomic_numbers: torch.Tensor, - ) -> torch.Tensor: - sender = edge_index[0] - receiver = edge_index[1] - node_atomic_numbers = atomic_numbers[torch.argmax(node_attrs, dim=1)].unsqueeze( - -1 - ) - Z_u = node_atomic_numbers[sender] - Z_v = node_atomic_numbers[receiver] - r_0: torch.Tensor = 0.5 * (self.covalent_radii[Z_u] + self.covalent_radii[Z_v]) - r_over_r_0 = x / r_0 - return ( - 1 - + ( - self.a - * torch.pow(r_over_r_0, self.q) - / (1 + torch.pow(r_over_r_0, self.q - self.p)) - ) - ).reciprocal_() - - def __repr__(self): - return ( - f"{self.__class__.__name__}(a={self.a:.4f}, q={self.q:.4f}, p={self.p:.4f})" - ) - - -@compile_mode("script") -class SoftTransform(torch.nn.Module): - """ - Tanh-based smooth transformation: - T(x) = p1 + (x - p1)*0.5*[1 + tanh(alpha*(x - m))], - which smoothly transitions from ~p1 for x << p1 to ~x for x >> r0. - """ - - def __init__(self, alpha: float = 4.0, trainable=False): - """ - Args: - p1 (float): Lower "clamp" point. - alpha (float): Steepness; if None, defaults to ~6/(r0-p1). - trainable (bool): Whether to make parameters trainable. - """ - super().__init__() - # Initialize parameters - self.register_buffer( - "alpha", torch.tensor(alpha, dtype=torch.get_default_dtype()) - ) - if trainable: - self.alpha = torch.nn.Parameter(self.alpha.clone()) - self.register_buffer( - "covalent_radii", - torch.tensor( - ase.data.covalent_radii, - dtype=torch.get_default_dtype(), - ), - ) - - def compute_r_0( - self, - node_attrs: torch.Tensor, - edge_index: torch.Tensor, - atomic_numbers: torch.Tensor, - ) -> torch.Tensor: - """ - Compute r_0 based on atomic information. - - Args: - node_attrs (torch.Tensor): Node attributes (one-hot encoding of atomic numbers). - edge_index (torch.Tensor): Edge index indicating connections. - atomic_numbers (torch.Tensor): Atomic numbers. - - Returns: - torch.Tensor: r_0 values for each edge. - """ - sender = edge_index[0] - receiver = edge_index[1] - node_atomic_numbers = atomic_numbers[torch.argmax(node_attrs, dim=1)].unsqueeze( - -1 - ) - Z_u = node_atomic_numbers[sender] - Z_v = node_atomic_numbers[receiver] - r_0: torch.Tensor = self.covalent_radii[Z_u] + self.covalent_radii[Z_v] - return r_0 - - def forward( - self, - x: torch.Tensor, - node_attrs: torch.Tensor, - edge_index: torch.Tensor, - atomic_numbers: torch.Tensor, - ) -> torch.Tensor: - - r_0 = self.compute_r_0(node_attrs, edge_index, atomic_numbers) - p_0 = (3 / 4) * r_0 - p_1 = (4 / 3) * r_0 - m = 0.5 * (p_0 + p_1) - alpha = self.alpha / (p_1 - p_0) - s_x = 0.5 * (1.0 + torch.tanh(alpha * (x - m))) - return p_0 + (x - p_0) * s_x - - def __repr__(self): - return f"{self.__class__.__name__}(alpha={self.alpha.item():.4f})" diff --git a/mace-bench/3rdparty/mace/mace/modules/symmetric_contraction.py b/mace-bench/3rdparty/mace/mace/modules/symmetric_contraction.py deleted file mode 100644 index 9db75da0255d4d44d0f4b05bd713139875147356..0000000000000000000000000000000000000000 --- a/mace-bench/3rdparty/mace/mace/modules/symmetric_contraction.py +++ /dev/null @@ -1,233 +0,0 @@ -########################################################################################### -# Implementation of the symmetric contraction algorithm presented in the MACE paper -# (Batatia et al, MACE: Higher Order Equivariant Message Passing Neural Networks for Fast and Accurate Force Fields , Eq.10 and 11) -# Authors: Ilyes Batatia -# This program is distributed under the MIT License (see MIT.md) -########################################################################################### - -from typing import Dict, Optional, Union - -import opt_einsum_fx -import torch -import torch.fx -from e3nn import o3 -from e3nn.util.codegen import CodeGenMixin -from e3nn.util.jit import compile_mode - -from mace.tools.cg import U_matrix_real - -BATCH_EXAMPLE = 10 -ALPHABET = ["w", "x", "v", "n", "z", "r", "t", "y", "u", "o", "p", "s"] - - -@compile_mode("script") -class SymmetricContraction(CodeGenMixin, torch.nn.Module): - def __init__( - self, - irreps_in: o3.Irreps, - irreps_out: o3.Irreps, - correlation: Union[int, Dict[str, int]], - irrep_normalization: str = "component", - path_normalization: str = "element", - internal_weights: Optional[bool] = None, - shared_weights: Optional[bool] = None, - num_elements: Optional[int] = None, - ) -> None: - super().__init__() - - if irrep_normalization is None: - irrep_normalization = "component" - - if path_normalization is None: - path_normalization = "element" - - assert irrep_normalization in ["component", "norm", "none"] - assert path_normalization in ["element", "path", "none"] - - self.irreps_in = o3.Irreps(irreps_in) - self.irreps_out = o3.Irreps(irreps_out) - - del irreps_in, irreps_out - - if not isinstance(correlation, tuple): - corr = correlation - correlation = {} - for irrep_out in self.irreps_out: - correlation[irrep_out] = corr - - assert shared_weights or not internal_weights - - if internal_weights is None: - internal_weights = True - - self.internal_weights = internal_weights - self.shared_weights = shared_weights - - del internal_weights, shared_weights - - self.contractions = torch.nn.ModuleList() - for irrep_out in self.irreps_out: - self.contractions.append( - Contraction( - irreps_in=self.irreps_in, - irrep_out=o3.Irreps(str(irrep_out.ir)), - correlation=correlation[irrep_out], - internal_weights=self.internal_weights, - num_elements=num_elements, - weights=self.shared_weights, - ) - ) - - def forward(self, x: torch.Tensor, y: torch.Tensor): - outs = [contraction(x, y) for contraction in self.contractions] - return torch.cat(outs, dim=-1) - - -@compile_mode("script") -class Contraction(torch.nn.Module): - def __init__( - self, - irreps_in: o3.Irreps, - irrep_out: o3.Irreps, - correlation: int, - internal_weights: bool = True, - num_elements: Optional[int] = None, - weights: Optional[torch.Tensor] = None, - ) -> None: - super().__init__() - - self.num_features = irreps_in.count((0, 1)) - self.coupling_irreps = o3.Irreps([irrep.ir for irrep in irreps_in]) - self.correlation = correlation - dtype = torch.get_default_dtype() - for nu in range(1, correlation + 1): - U_matrix = U_matrix_real( - irreps_in=self.coupling_irreps, - irreps_out=irrep_out, - correlation=nu, - dtype=dtype, - )[-1] - self.register_buffer(f"U_matrix_{nu}", U_matrix) - - # Tensor contraction equations - self.contractions_weighting = torch.nn.ModuleList() - self.contractions_features = torch.nn.ModuleList() - - # Create weight for product basis - self.weights = torch.nn.ParameterList([]) - - for i in range(correlation, 0, -1): - # Shapes definying - num_params = self.U_tensors(i).size()[-1] - num_equivariance = 2 * irrep_out.lmax + 1 - num_ell = self.U_tensors(i).size()[-2] - - if i == correlation: - parse_subscript_main = ( - [ALPHABET[j] for j in range(i + min(irrep_out.lmax, 1) - 1)] - + ["ik,ekc,bci,be -> bc"] - + [ALPHABET[j] for j in range(i + min(irrep_out.lmax, 1) - 1)] - ) - graph_module_main = torch.fx.symbolic_trace( - lambda x, y, w, z: torch.einsum( - "".join(parse_subscript_main), x, y, w, z - ) - ) - - # Optimizing the contractions - self.graph_opt_main = opt_einsum_fx.optimize_einsums_full( - model=graph_module_main, - example_inputs=( - torch.randn( - [num_equivariance] + [num_ell] * i + [num_params] - ).squeeze(0), - torch.randn((num_elements, num_params, self.num_features)), - torch.randn((BATCH_EXAMPLE, self.num_features, num_ell)), - torch.randn((BATCH_EXAMPLE, num_elements)), - ), - ) - # Parameters for the product basis - w = torch.nn.Parameter( - torch.randn((num_elements, num_params, self.num_features)) - / num_params - ) - self.weights_max = w - else: - # Generate optimized contractions equations - parse_subscript_weighting = ( - [ALPHABET[j] for j in range(i + min(irrep_out.lmax, 1))] - + ["k,ekc,be->bc"] - + [ALPHABET[j] for j in range(i + min(irrep_out.lmax, 1))] - ) - parse_subscript_features = ( - ["bc"] - + [ALPHABET[j] for j in range(i - 1 + min(irrep_out.lmax, 1))] - + ["i,bci->bc"] - + [ALPHABET[j] for j in range(i - 1 + min(irrep_out.lmax, 1))] - ) - - # Symbolic tracing of contractions - graph_module_weighting = torch.fx.symbolic_trace( - lambda x, y, z: torch.einsum( - "".join(parse_subscript_weighting), x, y, z - ) - ) - graph_module_features = torch.fx.symbolic_trace( - lambda x, y: torch.einsum("".join(parse_subscript_features), x, y) - ) - - # Optimizing the contractions - graph_opt_weighting = opt_einsum_fx.optimize_einsums_full( - model=graph_module_weighting, - example_inputs=( - torch.randn( - [num_equivariance] + [num_ell] * i + [num_params] - ).squeeze(0), - torch.randn((num_elements, num_params, self.num_features)), - torch.randn((BATCH_EXAMPLE, num_elements)), - ), - ) - graph_opt_features = opt_einsum_fx.optimize_einsums_full( - model=graph_module_features, - example_inputs=( - torch.randn( - [BATCH_EXAMPLE, self.num_features, num_equivariance] - + [num_ell] * i - ).squeeze(2), - torch.randn((BATCH_EXAMPLE, self.num_features, num_ell)), - ), - ) - self.contractions_weighting.append(graph_opt_weighting) - self.contractions_features.append(graph_opt_features) - # Parameters for the product basis - w = torch.nn.Parameter( - torch.randn((num_elements, num_params, self.num_features)) - / num_params - ) - self.weights.append(w) - if not internal_weights: - self.weights = weights[:-1] - self.weights_max = weights[-1] - - def forward(self, x: torch.Tensor, y: torch.Tensor): - out = self.graph_opt_main( - self.U_tensors(self.correlation), - self.weights_max, - x, - y, - ) - for i, (weight, contract_weights, contract_features) in enumerate( - zip(self.weights, self.contractions_weighting, self.contractions_features) - ): - c_tensor = contract_weights( - self.U_tensors(self.correlation - i - 1), - weight, - y, - ) - c_tensor = c_tensor + out - out = contract_features(c_tensor, x) - - return out.view(out.shape[0], -1) - - def U_tensors(self, nu: int): - return dict(self.named_buffers())[f"U_matrix_{nu}"] diff --git a/mace-bench/3rdparty/mace/mace/modules/utils.py b/mace-bench/3rdparty/mace/mace/modules/utils.py deleted file mode 100644 index 6a5a8e04fbde9180f442d39221f8cf63a8c398b6..0000000000000000000000000000000000000000 --- a/mace-bench/3rdparty/mace/mace/modules/utils.py +++ /dev/null @@ -1,582 +0,0 @@ -########################################################################################### -# Utilities -# Authors: Ilyes Batatia, Gregor Simm and David Kovacs -# This program is distributed under the MIT License (see MIT.md) -########################################################################################### - -import logging -from typing import Dict, List, NamedTuple, Optional, Tuple - -import numpy as np -import torch -import torch.utils.data -from scipy.constants import c, e - -from mace.tools import to_numpy -from mace.tools.scatter import scatter_mean, scatter_std, scatter_sum -from mace.tools.torch_geometric.batch import Batch - -from .blocks import AtomicEnergiesBlock - - -def compute_forces( - energy: torch.Tensor, positions: torch.Tensor, training: bool = True -) -> torch.Tensor: - grad_outputs: List[Optional[torch.Tensor]] = [torch.ones_like(energy)] - gradient = torch.autograd.grad( - outputs=[energy], # [n_graphs, ] - inputs=[positions], # [n_nodes, 3] - grad_outputs=grad_outputs, - retain_graph=training, # Make sure the graph is not destroyed during training - create_graph=training, # Create graph for second derivative - allow_unused=True, # For complete dissociation turn to true - )[ - 0 - ] # [n_nodes, 3] - if gradient is None: - return torch.zeros_like(positions) - return -1 * gradient - - -def compute_forces_virials( - energy: torch.Tensor, - positions: torch.Tensor, - displacement: torch.Tensor, - cell: torch.Tensor, - training: bool = True, - compute_stress: bool = False, -) -> Tuple[torch.Tensor, Optional[torch.Tensor], Optional[torch.Tensor]]: - grad_outputs: List[Optional[torch.Tensor]] = [torch.ones_like(energy)] - forces, virials = torch.autograd.grad( - outputs=[energy], # [n_graphs, ] - inputs=[positions, displacement], # [n_nodes, 3] - grad_outputs=grad_outputs, - retain_graph=training, # Make sure the graph is not destroyed during training - create_graph=training, # Create graph for second derivative - allow_unused=True, - ) - stress = torch.zeros_like(displacement) - if compute_stress and virials is not None: - cell = cell.view(-1, 3, 3) - volume = torch.linalg.det(cell).abs().unsqueeze(-1) - stress = virials / volume.view(-1, 1, 1) - stress = torch.where(torch.abs(stress) < 1e10, stress, torch.zeros_like(stress)) - if forces is None: - forces = torch.zeros_like(positions) - if virials is None: - virials = torch.zeros((1, 3, 3)) - - return -1 * forces, -1 * virials, stress - - -def get_symmetric_displacement( - positions: torch.Tensor, - unit_shifts: torch.Tensor, - cell: Optional[torch.Tensor], - edge_index: torch.Tensor, - num_graphs: int, - batch: torch.Tensor, -) -> Tuple[torch.Tensor, torch.Tensor, torch.Tensor]: - if cell is None: - cell = torch.zeros( - num_graphs * 3, - 3, - dtype=positions.dtype, - device=positions.device, - ) - sender = edge_index[0] - displacement = torch.zeros( - (num_graphs, 3, 3), - dtype=positions.dtype, - device=positions.device, - ) - displacement.requires_grad_(True) - symmetric_displacement = 0.5 * ( - displacement + displacement.transpose(-1, -2) - ) # From https://github.com/mir-group/nequip - positions = positions + torch.einsum( - "be,bec->bc", positions, symmetric_displacement[batch] - ) - cell = cell.view(-1, 3, 3) - cell = cell + torch.matmul(cell, symmetric_displacement) - shifts = torch.einsum( - "be,bec->bc", - unit_shifts, - cell[batch[sender]], - ) - return positions, shifts, displacement - - -@torch.jit.unused -def compute_hessians_vmap( - forces: torch.Tensor, - positions: torch.Tensor, -) -> torch.Tensor: - forces_flatten = forces.view(-1) - num_elements = forces_flatten.shape[0] - - def get_vjp(v): - return torch.autograd.grad( - -1 * forces_flatten, - positions, - v, - retain_graph=True, - create_graph=False, - allow_unused=False, - ) - - I_N = torch.eye(num_elements).to(forces.device) - try: - chunk_size = 1 if num_elements < 64 else 16 - gradient = torch.vmap(get_vjp, in_dims=0, out_dims=0, chunk_size=chunk_size)( - I_N - )[0] - except RuntimeError: - gradient = compute_hessians_loop(forces, positions) - if gradient is None: - return torch.zeros((positions.shape[0], forces.shape[0], 3, 3)) - return gradient - - -@torch.jit.unused -def compute_hessians_loop( - forces: torch.Tensor, - positions: torch.Tensor, -) -> torch.Tensor: - hessian = [] - for grad_elem in forces.view(-1): - hess_row = torch.autograd.grad( - outputs=[-1 * grad_elem], - inputs=[positions], - grad_outputs=torch.ones_like(grad_elem), - retain_graph=True, - create_graph=False, - allow_unused=False, - )[0] - hess_row = hess_row.detach() # this makes it very slow? but needs less memory - if hess_row is None: - hessian.append(torch.zeros_like(positions)) - else: - hessian.append(hess_row) - hessian = torch.stack(hessian) - return hessian - - -def get_outputs( - energy: torch.Tensor, - positions: torch.Tensor, - cell: torch.Tensor, - displacement: Optional[torch.Tensor], - vectors: Optional[torch.Tensor] = None, - training: bool = False, - compute_force: bool = True, - compute_virials: bool = True, - compute_stress: bool = True, - compute_hessian: bool = False, - compute_edge_forces: bool = False, -) -> Tuple[ - Optional[torch.Tensor], - Optional[torch.Tensor], - Optional[torch.Tensor], - Optional[torch.Tensor], - Optional[torch.Tensor], -]: - if (compute_virials or compute_stress) and displacement is not None: - forces, virials, stress = compute_forces_virials( - energy=energy, - positions=positions, - displacement=displacement, - cell=cell, - compute_stress=compute_stress, - training=(training or compute_hessian or compute_edge_forces), - ) - elif compute_force: - forces, virials, stress = ( - compute_forces( - energy=energy, - positions=positions, - training=(training or compute_hessian or compute_edge_forces), - ), - None, - None, - ) - else: - forces, virials, stress = (None, None, None) - if compute_hessian: - assert forces is not None, "Forces must be computed to get the hessian" - hessian = compute_hessians_vmap(forces, positions) - else: - hessian = None - if compute_edge_forces and vectors is not None: - edge_forces = compute_forces( - energy=energy, - positions=vectors, - training=(training or compute_hessian), - ) - if edge_forces is not None: - edge_forces = -1 * edge_forces # Match LAMMPS sign convention - else: - edge_forces = None - return forces, virials, stress, hessian, edge_forces - - -def get_atomic_virials_stresses( - edge_forces: torch.Tensor, # [n_edges, 3] - edge_index: torch.Tensor, # [2, n_edges] - vectors: torch.Tensor, # [n_edges, 3] - num_atoms: int, - batch: torch.Tensor, - cell: torch.Tensor, # [n_graphs, 3, 3] -) -> Tuple[torch.Tensor, Optional[torch.Tensor]]: - """ - Compute atomic virials and optionally atomic stresses from edge forces and vectors. - From pobo95 PR #528. - Returns: - Tuple of: - - Atomic virials [num_atoms, 3, 3] - - Atomic stresses [num_atoms, 3, 3] (None if not computed) - """ - edge_virial = torch.einsum("zi,zj->zij", edge_forces, vectors) - atom_virial_sender = scatter_sum( - src=edge_virial, index=edge_index[0], dim=0, dim_size=num_atoms - ) - atom_virial_receiver = scatter_sum( - src=edge_virial, index=edge_index[1], dim=0, dim_size=num_atoms - ) - atom_virial = (atom_virial_sender + atom_virial_receiver) / 2 - atom_virial = (atom_virial + atom_virial.transpose(-1, -2)) / 2 - atom_stress = None - cell = cell.view(-1, 3, 3) - volume = torch.linalg.det(cell).abs().unsqueeze(-1) - atom_volume = volume[batch].view(-1, 1, 1) - atom_stress = atom_virial / atom_volume - atom_stress = torch.where( - torch.abs(atom_stress) < 1e10, atom_stress, torch.zeros_like(atom_stress) - ) - return -1 * atom_virial, atom_stress - - -def get_edge_vectors_and_lengths( - positions: torch.Tensor, # [n_nodes, 3] - edge_index: torch.Tensor, # [2, n_edges] - shifts: torch.Tensor, # [n_edges, 3] - normalize: bool = False, - eps: float = 1e-9, -) -> Tuple[torch.Tensor, torch.Tensor]: - sender = edge_index[0] - receiver = edge_index[1] - vectors = positions[receiver] - positions[sender] + shifts # [n_edges, 3] - lengths = torch.linalg.norm(vectors, dim=-1, keepdim=True) # [n_edges, 1] - if normalize: - vectors_normed = vectors / (lengths + eps) - return vectors_normed, lengths - - return vectors, lengths - - -def _check_non_zero(std): - if np.any(std == 0): - logging.warning( - "Standard deviation of the scaling is zero, Changing to no scaling" - ) - std[std == 0] = 1 - return std - - -def extract_invariant(x: torch.Tensor, num_layers: int, num_features: int, l_max: int): - out = [] - out.append(x[:, :num_features]) - for i in range(1, num_layers): - out.append( - x[ - :, - i - * (l_max + 1) ** 2 - * num_features : (i * (l_max + 1) ** 2 + 1) - * num_features, - ] - ) - return torch.cat(out, dim=-1) - - -def compute_mean_std_atomic_inter_energy( - data_loader: torch.utils.data.DataLoader, - atomic_energies: np.ndarray, -) -> Tuple[float, float]: - atomic_energies_fn = AtomicEnergiesBlock(atomic_energies=atomic_energies) - - avg_atom_inter_es_list = [] - head_list = [] - - for batch in data_loader: - node_e0 = atomic_energies_fn(batch.node_attrs) - graph_e0s = scatter_sum( - src=node_e0, index=batch.batch, dim=0, dim_size=batch.num_graphs - )[torch.arange(batch.num_graphs), batch.head] - graph_sizes = batch.ptr[1:] - batch.ptr[:-1] - avg_atom_inter_es_list.append( - (batch.energy - graph_e0s) / graph_sizes - ) # {[n_graphs], } - head_list.append(batch.head) - - avg_atom_inter_es = torch.cat(avg_atom_inter_es_list) # [total_n_graphs] - head = torch.cat(head_list, dim=0) # [total_n_graphs] - # mean = to_numpy(torch.mean(avg_atom_inter_es)).item() - # std = to_numpy(torch.std(avg_atom_inter_es)).item() - mean = to_numpy(scatter_mean(src=avg_atom_inter_es, index=head, dim=0).squeeze(-1)) - std = to_numpy(scatter_std(src=avg_atom_inter_es, index=head, dim=0).squeeze(-1)) - std = _check_non_zero(std) - - return mean, std - - -def _compute_mean_std_atomic_inter_energy( - batch: Batch, - atomic_energies_fn: AtomicEnergiesBlock, -) -> Tuple[torch.Tensor, torch.Tensor]: - head = batch.head - node_e0 = atomic_energies_fn(batch.node_attrs) - graph_e0s = scatter_sum( - src=node_e0, index=batch.batch, dim=0, dim_size=batch.num_graphs - )[torch.arange(batch.num_graphs), head] - graph_sizes = batch.ptr[1:] - batch.ptr[:-1] - atom_energies = (batch.energy - graph_e0s) / graph_sizes - return atom_energies - - -def compute_mean_rms_energy_forces( - data_loader: torch.utils.data.DataLoader, - atomic_energies: np.ndarray, -) -> Tuple[float, float]: - atomic_energies_fn = AtomicEnergiesBlock(atomic_energies=atomic_energies) - - atom_energy_list = [] - forces_list = [] - head_list = [] - head_batch = [] - - for batch in data_loader: - head = batch.head - node_e0 = atomic_energies_fn(batch.node_attrs) - graph_e0s = scatter_sum( - src=node_e0, index=batch.batch, dim=0, dim_size=batch.num_graphs - )[torch.arange(batch.num_graphs), head] - graph_sizes = batch.ptr[1:] - batch.ptr[:-1] - atom_energy_list.append( - (batch.energy - graph_e0s) / graph_sizes - ) # {[n_graphs], } - forces_list.append(batch.forces) # {[n_graphs*n_atoms,3], } - head_list.append(head) - head_batch.append(head[batch.batch]) - - atom_energies = torch.cat(atom_energy_list, dim=0) # [total_n_graphs] - forces = torch.cat(forces_list, dim=0) # {[total_n_graphs*n_atoms,3], } - head = torch.cat(head_list, dim=0) # [total_n_graphs] - head_batch = torch.cat(head_batch, dim=0) # [total_n_graphs] - - # mean = to_numpy(torch.mean(atom_energies)).item() - # rms = to_numpy(torch.sqrt(torch.mean(torch.square(forces)))).item() - mean = to_numpy(scatter_mean(src=atom_energies, index=head, dim=0).squeeze(-1)) - rms = to_numpy( - torch.sqrt( - scatter_mean(src=torch.square(forces), index=head_batch, dim=0).mean(-1) - ) - ) - rms = _check_non_zero(rms) - - return mean, rms - - -def _compute_mean_rms_energy_forces( - batch: Batch, - atomic_energies_fn: AtomicEnergiesBlock, -) -> Tuple[torch.Tensor, torch.Tensor]: - head = batch.head - node_e0 = atomic_energies_fn(batch.node_attrs) - graph_e0s = scatter_sum( - src=node_e0, index=batch.batch, dim=0, dim_size=batch.num_graphs - )[torch.arange(batch.num_graphs), head] - graph_sizes = batch.ptr[1:] - batch.ptr[:-1] - atom_energies = (batch.energy - graph_e0s) / graph_sizes # {[n_graphs], } - forces = batch.forces # {[n_graphs*n_atoms,3], } - - return atom_energies, forces - - -def compute_avg_num_neighbors(data_loader: torch.utils.data.DataLoader) -> float: - num_neighbors = [] - for batch in data_loader: - _, receivers = batch.edge_index - _, counts = torch.unique(receivers, return_counts=True) - num_neighbors.append(counts) - - avg_num_neighbors = torch.mean( - torch.cat(num_neighbors, dim=0).type(torch.get_default_dtype()) - ) - return to_numpy(avg_num_neighbors).item() - - -def compute_statistics( - data_loader: torch.utils.data.DataLoader, - atomic_energies: np.ndarray, -) -> Tuple[float, float, float, float]: - atomic_energies_fn = AtomicEnergiesBlock(atomic_energies=atomic_energies) - - atom_energy_list = [] - forces_list = [] - num_neighbors = [] - head_list = [] - head_batch = [] - - for batch in data_loader: - head = batch.head - node_e0 = atomic_energies_fn(batch.node_attrs) - graph_e0s = scatter_sum( - src=node_e0, index=batch.batch, dim=0, dim_size=batch.num_graphs - )[torch.arange(batch.num_graphs), head] - graph_sizes = batch.ptr[1:] - batch.ptr[:-1] - atom_energy_list.append( - (batch.energy - graph_e0s) / graph_sizes - ) # {[n_graphs], } - forces_list.append(batch.forces) # {[n_graphs*n_atoms,3], } - head_list.append(head) # {[n_graphs], } - head_batch.append(head[batch.batch]) - _, receivers = batch.edge_index - _, counts = torch.unique(receivers, return_counts=True) - num_neighbors.append(counts) - - atom_energies = torch.cat(atom_energy_list, dim=0) # [total_n_graphs] - forces = torch.cat(forces_list, dim=0) # {[total_n_graphs*n_atoms,3], } - head = torch.cat(head_list, dim=0) # [total_n_graphs] - head_batch = torch.cat(head_batch, dim=0) # [total_n_graphs] - - # mean = to_numpy(torch.mean(atom_energies)).item() - mean = to_numpy(scatter_mean(src=atom_energies, index=head, dim=0).squeeze(-1)) - rms = to_numpy( - torch.sqrt( - scatter_mean(src=torch.square(forces), index=head_batch, dim=0).mean(-1) - ) - ) - - avg_num_neighbors = torch.mean( - torch.cat(num_neighbors, dim=0).type(torch.get_default_dtype()) - ) - - return to_numpy(avg_num_neighbors).item(), mean, rms - - -def compute_rms_dipoles( - data_loader: torch.utils.data.DataLoader, -) -> Tuple[float, float]: - dipoles_list = [] - for batch in data_loader: - dipoles_list.append(batch.dipole) # {[n_graphs,3], } - - dipoles = torch.cat(dipoles_list, dim=0) # {[total_n_graphs,3], } - rms = to_numpy(torch.sqrt(torch.mean(torch.square(dipoles)))).item() - rms = _check_non_zero(rms) - return rms - - -def compute_fixed_charge_dipole( - charges: torch.Tensor, - positions: torch.Tensor, - batch: torch.Tensor, - num_graphs: int, -) -> torch.Tensor: - mu = positions * charges.unsqueeze(-1) / (1e-11 / c / e) # [N_atoms,3] - return scatter_sum( - src=mu, index=batch.unsqueeze(-1), dim=0, dim_size=num_graphs - ) # [N_graphs,3] - - -class InteractionKwargs(NamedTuple): - lammps_class: Optional[torch.Tensor] - lammps_natoms: Tuple[int, int] = (0, 0) - - -class GraphContext(NamedTuple): - is_lammps: bool - num_graphs: int - num_atoms_arange: torch.Tensor - displacement: Optional[torch.Tensor] - positions: torch.Tensor - vectors: torch.Tensor - lengths: torch.Tensor - cell: torch.Tensor - node_heads: torch.Tensor - interaction_kwargs: InteractionKwargs - - -def prepare_graph( - data: Dict[str, torch.Tensor], - compute_virials: bool = False, - compute_stress: bool = False, - compute_displacement: bool = False, - lammps_mliap: bool = False, -) -> GraphContext: - if torch.jit.is_scripting(): - lammps_mliap = False - - node_heads = ( - data["head"][data["batch"]] - if "head" in data - else torch.zeros_like(data["batch"]) - ) - - if lammps_mliap: - n_real, n_total = data["natoms"][0], data["natoms"][1] - num_graphs = 2 - num_atoms_arange = torch.arange(n_real, device=data["node_attrs"].device) - displacement = None - positions = torch.zeros( - (int(n_real), 3), - dtype=data["vectors"].dtype, - device=data["vectors"].device, - ) - cell = torch.zeros( - (num_graphs, 3, 3), - dtype=data["vectors"].dtype, - device=data["vectors"].device, - ) - vectors = data["vectors"].requires_grad_(True) - lengths = torch.linalg.vector_norm(vectors, dim=1, keepdim=True) - ikw = InteractionKwargs(data["lammps_class"], (n_real, n_total)) - else: - data["positions"].requires_grad_(True) - positions = data["positions"] - cell = data["cell"] - num_atoms_arange = torch.arange(positions.shape[0], device=positions.device) - num_graphs = int(data["ptr"].numel() - 1) - displacement = torch.zeros( - (num_graphs, 3, 3), dtype=positions.dtype, device=positions.device - ) - if compute_virials or compute_stress or compute_displacement: - p, s, displacement = get_symmetric_displacement( - positions=positions, - unit_shifts=data["unit_shifts"], - cell=cell, - edge_index=data["edge_index"], - num_graphs=num_graphs, - batch=data["batch"], - ) - data["positions"], data["shifts"] = p, s - vectors, lengths = get_edge_vectors_and_lengths( - positions=data["positions"], - edge_index=data["edge_index"], - shifts=data["shifts"], - ) - ikw = InteractionKwargs(None, (0, 0)) - - return GraphContext( - is_lammps=lammps_mliap, - num_graphs=num_graphs, - num_atoms_arange=num_atoms_arange, - displacement=displacement, - positions=positions, - vectors=vectors, - lengths=lengths, - cell=cell, - node_heads=node_heads, - interaction_kwargs=ikw, - ) diff --git a/mace-bench/3rdparty/mace/mace/modules/wrapper_ops.py b/mace-bench/3rdparty/mace/mace/modules/wrapper_ops.py deleted file mode 100644 index ca05219c775c439b37193a998b48ba490dbd1baf..0000000000000000000000000000000000000000 --- a/mace-bench/3rdparty/mace/mace/modules/wrapper_ops.py +++ /dev/null @@ -1,192 +0,0 @@ -""" -Wrapper class for o3.Linear that optionally uses cuet.Linear -""" - -import dataclasses -from typing import List, Optional - -import torch -from e3nn import o3 - -from mace.modules.symmetric_contraction import SymmetricContraction -from mace.tools.cg import O3_e3nn - -try: - import cuequivariance as cue - import cuequivariance_torch as cuet - - CUET_AVAILABLE = True -except ImportError: - CUET_AVAILABLE = False - - -@dataclasses.dataclass -class CuEquivarianceConfig: - """Configuration for cuequivariance acceleration""" - - enabled: bool = False - layout: str = "mul_ir" # One of: mul_ir, ir_mul - layout_str: str = "mul_ir" - group: str = "O3" - optimize_all: bool = False # Set to True to enable all optimizations - optimize_linear: bool = False - optimize_channelwise: bool = False - optimize_symmetric: bool = False - optimize_fctp: bool = False - - def __post_init__(self): - if self.enabled and CUET_AVAILABLE: - self.layout_str = self.layout - self.layout = getattr(cue, self.layout) - self.group = ( - O3_e3nn if self.group == "O3_e3nn" else getattr(cue, self.group) - ) - if not CUET_AVAILABLE: - self.enabled = False - - -class Linear: - """Returns either a cuet.Linear or o3.Linear based on config""" - - def __new__( - cls, - irreps_in: o3.Irreps, - irreps_out: o3.Irreps, - shared_weights: bool = True, - internal_weights: bool = True, - cueq_config: Optional[CuEquivarianceConfig] = None, - ): - if ( - CUET_AVAILABLE - and cueq_config is not None - and cueq_config.enabled - and (cueq_config.optimize_all or cueq_config.optimize_linear) - ): - return cuet.Linear( - cue.Irreps(cueq_config.group, irreps_in), - cue.Irreps(cueq_config.group, irreps_out), - layout=cueq_config.layout, - shared_weights=shared_weights, - use_fallback=True, - ) - - return o3.Linear( - irreps_in, - irreps_out, - shared_weights=shared_weights, - internal_weights=internal_weights, - ) - - -class TensorProduct: - """Wrapper around o3.TensorProduct/cuet.ChannelwiseTensorProduct""" - - def __new__( - cls, - irreps_in1: o3.Irreps, - irreps_in2: o3.Irreps, - irreps_out: o3.Irreps, - instructions: Optional[List] = None, - shared_weights: bool = False, - internal_weights: bool = False, - cueq_config: Optional[CuEquivarianceConfig] = None, - ): - if ( - CUET_AVAILABLE - and cueq_config is not None - and cueq_config.enabled - and (cueq_config.optimize_all or cueq_config.optimize_channelwise) - ): - return cuet.ChannelWiseTensorProduct( - cue.Irreps(cueq_config.group, irreps_in1), - cue.Irreps(cueq_config.group, irreps_in2), - cue.Irreps(cueq_config.group, irreps_out), - layout=cueq_config.layout, - shared_weights=shared_weights, - internal_weights=internal_weights, - dtype=torch.get_default_dtype(), - math_dtype=torch.get_default_dtype(), - ) - - return o3.TensorProduct( - irreps_in1, - irreps_in2, - irreps_out, - instructions=instructions, - shared_weights=shared_weights, - internal_weights=internal_weights, - ) - - -class FullyConnectedTensorProduct: - """Wrapper around o3.FullyConnectedTensorProduct/cuet.FullyConnectedTensorProduct""" - - def __new__( - cls, - irreps_in1: o3.Irreps, - irreps_in2: o3.Irreps, - irreps_out: o3.Irreps, - shared_weights: bool = True, - internal_weights: bool = True, - cueq_config: Optional[CuEquivarianceConfig] = None, - ): - if ( - CUET_AVAILABLE - and cueq_config is not None - and cueq_config.enabled - and (cueq_config.optimize_all or cueq_config.optimize_fctp) - ): - return cuet.FullyConnectedTensorProduct( - cue.Irreps(cueq_config.group, irreps_in1), - cue.Irreps(cueq_config.group, irreps_in2), - cue.Irreps(cueq_config.group, irreps_out), - layout=cueq_config.layout, - shared_weights=shared_weights, - internal_weights=internal_weights, - use_fallback=True, - ) - - return o3.FullyConnectedTensorProduct( - irreps_in1, - irreps_in2, - irreps_out, - shared_weights=shared_weights, - internal_weights=internal_weights, - ) - - -class SymmetricContractionWrapper: - """Wrapper around SymmetricContraction/cuet.SymmetricContraction""" - - def __new__( - cls, - irreps_in: o3.Irreps, - irreps_out: o3.Irreps, - correlation: int, - num_elements: Optional[int] = None, - cueq_config: Optional[CuEquivarianceConfig] = None, - ): - if ( - CUET_AVAILABLE - and cueq_config is not None - and cueq_config.enabled - and (cueq_config.optimize_all or cueq_config.optimize_symmetric) - ): - return cuet.SymmetricContraction( - cue.Irreps(cueq_config.group, irreps_in), - cue.Irreps(cueq_config.group, irreps_out), - layout_in=cue.ir_mul, - layout_out=cueq_config.layout, - contraction_degree=correlation, - num_elements=num_elements, - original_mace=True, - dtype=torch.get_default_dtype(), - math_dtype=torch.get_default_dtype(), - ) - - return SymmetricContraction( - irreps_in=irreps_in, - irreps_out=irreps_out, - correlation=correlation, - num_elements=num_elements, - ) diff --git a/mace-bench/3rdparty/mace/mace/py.typed b/mace-bench/3rdparty/mace/mace/py.typed deleted file mode 100644 index d3f5a12faa99758192ecc4ed3fc22c9249232e86..0000000000000000000000000000000000000000 --- a/mace-bench/3rdparty/mace/mace/py.typed +++ /dev/null @@ -1 +0,0 @@ - diff --git a/mace-bench/3rdparty/mace/mace/tools/__init__.py b/mace-bench/3rdparty/mace/mace/tools/__init__.py deleted file mode 100644 index 0fa6b0765befce9fab668c2483f7db946a2bfa9d..0000000000000000000000000000000000000000 --- a/mace-bench/3rdparty/mace/mace/tools/__init__.py +++ /dev/null @@ -1,73 +0,0 @@ -from .arg_parser import build_default_arg_parser, build_preprocess_arg_parser -from .arg_parser_tools import check_args -from .cg import U_matrix_real -from .checkpoint import CheckpointHandler, CheckpointIO, CheckpointState -from .default_keys import DefaultKeys -from .finetuning_utils import load_foundations, load_foundations_elements -from .torch_tools import ( - TensorDict, - cartesian_to_spherical, - count_parameters, - init_device, - init_wandb, - set_default_dtype, - set_seeds, - spherical_to_cartesian, - to_numpy, - to_one_hot, - voigt_to_matrix, -) -from .train import SWAContainer, evaluate, train -from .utils import ( - AtomicNumberTable, - MetricsLogger, - atomic_numbers_to_indices, - compute_c, - compute_mae, - compute_q95, - compute_rel_mae, - compute_rel_rmse, - compute_rmse, - get_atomic_number_table_from_zs, - get_tag, - setup_logger, -) - -__all__ = [ - "TensorDict", - "AtomicNumberTable", - "atomic_numbers_to_indices", - "to_numpy", - "to_one_hot", - "build_default_arg_parser", - "check_args", - "DefaultKeys", - "set_seeds", - "init_device", - "setup_logger", - "get_tag", - "count_parameters", - "MetricsLogger", - "get_atomic_number_table_from_zs", - "train", - "evaluate", - "SWAContainer", - "CheckpointHandler", - "CheckpointIO", - "CheckpointState", - "set_default_dtype", - "compute_mae", - "compute_rel_mae", - "compute_rmse", - "compute_rel_rmse", - "compute_q95", - "compute_c", - "U_matrix_real", - "spherical_to_cartesian", - "cartesian_to_spherical", - "voigt_to_matrix", - "init_wandb", - "load_foundations", - "load_foundations_elements", - "build_preprocess_arg_parser", -] diff --git a/mace-bench/3rdparty/mace/mace/tools/arg_parser.py b/mace-bench/3rdparty/mace/mace/tools/arg_parser.py deleted file mode 100644 index c9d537e6865303f8bc8ddcadf47732dbc5ca3f83..0000000000000000000000000000000000000000 --- a/mace-bench/3rdparty/mace/mace/tools/arg_parser.py +++ /dev/null @@ -1,971 +0,0 @@ -########################################################################################### -# Parsing functionalities -# Authors: Ilyes Batatia, Gregor Simm, David Kovacs -# This program is distributed under the MIT License (see MIT.md) -########################################################################################### - -import argparse -import os -from typing import Optional - -from .default_keys import DefaultKeys - - -def build_default_arg_parser() -> argparse.ArgumentParser: - try: - import configargparse - - parser = configargparse.ArgumentParser( - config_file_parser_class=configargparse.YAMLConfigFileParser, - formatter_class=argparse.ArgumentDefaultsHelpFormatter, - ) - parser.add( - "--config", - type=str, - is_config_file=True, - help="config file to aggregate options", - ) - except ImportError: - parser = argparse.ArgumentParser( - formatter_class=argparse.ArgumentDefaultsHelpFormatter, - ) - - # Name and seed - parser.add_argument("--name", help="experiment name", required=True) - parser.add_argument("--seed", help="random seed", type=int, default=123) - - # Directories - parser.add_argument( - "--work_dir", - help="set directory for all files and folders", - type=str, - default=".", - ) - parser.add_argument( - "--log_dir", help="directory for log files", type=str, default=None - ) - parser.add_argument( - "--model_dir", help="directory for final model", type=str, default=None - ) - parser.add_argument( - "--checkpoints_dir", - help="directory for checkpoint files", - type=str, - default=None, - ) - parser.add_argument( - "--results_dir", help="directory for results", type=str, default=None - ) - parser.add_argument( - "--downloads_dir", help="directory for downloads", type=str, default=None - ) - - # Device and logging - parser.add_argument( - "--device", - help="select device", - type=str, - choices=["cpu", "cuda", "mps", "xpu"], - default="cpu", - ) - parser.add_argument( - "--default_dtype", - help="set default dtype", - type=str, - choices=["float32", "float64"], - default="float64", - ) - parser.add_argument( - "--distributed", - help="train in multi-GPU data parallel mode", - action="store_true", - default=False, - ) - parser.add_argument("--log_level", help="log level", type=str, default="INFO") - - parser.add_argument( - "--plot", - help="Plot results of training", - type=str2bool, - default=True, - ) - - parser.add_argument( - "--plot_frequency", - help="Set plotting frequency: '0' for only at the end or an integer N to plot every N epochs.", - type=int, - default="0", - ) - - parser.add_argument( - "--error_table", - help="Type of error table produced at the end of the training", - type=str, - choices=[ - "PerAtomRMSE", - "TotalRMSE", - "PerAtomRMSEstressvirials", - "PerAtomMAEstressvirials", - "PerAtomMAE", - "TotalMAE", - "DipoleRMSE", - "DipoleMAE", - "EnergyDipoleRMSE", - ], - default="PerAtomRMSE", - ) - - # Model - parser.add_argument( - "--model", - help="model type", - default="MACE", - choices=[ - "BOTNet", - "MACE", - "ScaleShiftMACE", - "ScaleShiftBOTNet", - "AtomicDipolesMACE", - "EnergyDipolesMACE", - ], - ) - parser.add_argument( - "--r_max", help="distance cutoff (in Ang)", type=float, default=5.0 - ) - parser.add_argument( - "--radial_type", - help="type of radial basis functions", - type=str, - default="bessel", - choices=["bessel", "gaussian", "chebyshev"], - ) - parser.add_argument( - "--num_radial_basis", - help="number of radial basis functions", - type=int, - default=8, - ) - parser.add_argument( - "--num_cutoff_basis", - help="number of basis functions for smooth cutoff", - type=int, - default=5, - ) - parser.add_argument( - "--pair_repulsion", - help="use pair repulsion term with ZBL potential", - action="store_true", - default=False, - ) - parser.add_argument( - "--distance_transform", - help="use distance transform for radial basis functions", - default="None", - choices=["None", "Agnesi", "Soft"], - ) - parser.add_argument( - "--interaction", - help="name of interaction block", - type=str, - default="RealAgnosticResidualInteractionBlock", - choices=[ - "RealAgnosticResidualInteractionBlock", - "RealAgnosticAttResidualInteractionBlock", - "RealAgnosticInteractionBlock", - "RealAgnosticDensityInteractionBlock", - "RealAgnosticDensityResidualInteractionBlock", - ], - ) - parser.add_argument( - "--interaction_first", - help="name of interaction block", - type=str, - default="RealAgnosticResidualInteractionBlock", - choices=[ - "RealAgnosticResidualInteractionBlock", - "RealAgnosticInteractionBlock", - "RealAgnosticDensityInteractionBlock", - "RealAgnosticDensityResidualInteractionBlock", - ], - ) - parser.add_argument( - "--max_ell", help=r"highest \ell of spherical harmonics", type=int, default=3 - ) - parser.add_argument( - "--correlation", help="correlation order at each layer", type=int, default=3 - ) - parser.add_argument( - "--num_interactions", help="number of interactions", type=int, default=2 - ) - parser.add_argument( - "--MLP_irreps", - help="hidden irreps of the MLP in last readout", - type=str, - default="16x0e", - ) - parser.add_argument( - "--radial_MLP", - help="width of the radial MLP", - type=str, - default="[64, 64, 64]", - ) - parser.add_argument( - "--hidden_irreps", - help="irreps for hidden node states", - type=str, - default=None, - ) - # add option to specify irreps by channel number and max L - parser.add_argument( - "--num_channels", - help="number of embedding channels", - type=int, - default=None, - ) - parser.add_argument( - "--max_L", - help="max L equivariance of the message", - type=int, - default=None, - ) - parser.add_argument( - "--gate", - help="non linearity for last readout", - type=str, - default="silu", - choices=["silu", "tanh", "abs", "None"], - ) - parser.add_argument( - "--scaling", - help="type of scaling to the output", - type=str, - default="rms_forces_scaling", - choices=["std_scaling", "rms_forces_scaling", "no_scaling"], - ) - parser.add_argument( - "--avg_num_neighbors", - help="normalization factor for the message", - type=float, - default=1, - ) - parser.add_argument( - "--compute_avg_num_neighbors", - help="normalization factor for the message", - type=str2bool, - default=True, - ) - parser.add_argument( - "--compute_stress", - help="Select True to compute stress", - type=str2bool, - default=False, - ) - parser.add_argument( - "--compute_forces", - help="Select True to compute forces", - type=str2bool, - default=True, - ) - - # Dataset - parser.add_argument( - "--train_file", - help="Training set file, format is .xyz or .h5", - type=str, - required=False, - ) - parser.add_argument( - "--valid_file", - help="Validation set .xyz or .h5 file", - default=None, - type=str, - required=False, - ) - parser.add_argument( - "--valid_fraction", - help="Fraction of training set used for validation", - type=float, - default=0.1, - required=False, - ) - parser.add_argument( - "--test_file", - help="Test set .xyz pt .h5 file", - type=str, - ) - parser.add_argument( - "--test_dir", - help="Path to directory with test files named as test_*.h5", - type=str, - default=None, - required=False, - ) - parser.add_argument( - "--multi_processed_test", - help="Boolean value for whether the test data was multiprocessed", - type=str2bool, - default=False, - required=False, - ) - parser.add_argument( - "--num_workers", - help="Number of workers for data loading", - type=int, - default=0, - ) - parser.add_argument( - "--pin_memory", - help="Pin memory for data loading", - default=True, - type=str2bool, - ) - parser.add_argument( - "--atomic_numbers", - help="List of atomic numbers", - type=str, - default=None, - required=False, - ) - parser.add_argument( - "--mean", - help="Mean energy per atom of training set", - type=float, - default=None, - required=False, - ) - parser.add_argument( - "--std", - help="Standard deviation of force components in the training set", - type=float, - default=None, - required=False, - ) - parser.add_argument( - "--statistics_file", - help="json file containing statistics of training set", - type=str, - default=None, - required=False, - ) - parser.add_argument( - "--E0s", - help="Dictionary of isolated atom energies", - type=str, - default=None, - required=False, - ) - - # Fine-tuning - parser.add_argument( - "--foundation_filter_elements", - help="Filter element during fine-tuning", - type=str2bool, - default=True, - required=False, - ) - parser.add_argument( - "--heads", - help="Dict of heads: containing individual files and E0s", - type=str, - default=None, - required=False, - ) - parser.add_argument( - "--multiheads_finetuning", - help="Boolean value for whether the model is multiheaded", - type=str2bool, - default=True, - ) - parser.add_argument( - "--foundation_head", - help="Name of the head to use for fine-tuning", - type=str, - default=None, - required=False, - ) - parser.add_argument( - "--weight_pt_head", - help="Weight of the pretrained head in the loss function", - type=float, - default=1.0, - ) - parser.add_argument( - "--num_samples_pt", - help="Number of samples in the pretrained head", - type=int, - default=10000, - ) - parser.add_argument( - "--force_mh_ft_lr", - help="Force the multiheaded fine-tuning to use arg_parser lr", - type=str2bool, - default=False, - ) - parser.add_argument( - "--subselect_pt", - help="Method to subselect the configurations of the pretraining set", - choices=["fps", "random"], - default="random", - ) - parser.add_argument( - "--filter_type_pt", - help="Filtering method for collecting the pretraining set", - choices=["none", "combinations", "inclusive", "exclusive"], - default="none", - ) - parser.add_argument( - "--pt_train_file", - help="Training set file for the pretrained head", - type=str, - default=None, - ) - parser.add_argument( - "--pt_valid_file", - help="Validation set file for the pretrained head", - type=str, - default=None, - ) - parser.add_argument( - "--foundation_model_elements", - help="Keep all elements of the foundation model during fine-tuning", - type=str2bool, - default=False, - ) - parser.add_argument( - "--keep_isolated_atoms", - help="Keep isolated atoms in the dataset, useful for transfer learning", - type=str2bool, - default=False, - ) - - # Keys - parser.add_argument( - "--energy_key", - help="Key of reference energies in training xyz", - type=str, - default=DefaultKeys.ENERGY.value, - ) - parser.add_argument( - "--forces_key", - help="Key of reference forces in training xyz", - type=str, - default=DefaultKeys.FORCES.value, - ) - parser.add_argument( - "--virials_key", - help="Key of reference virials in training xyz", - type=str, - default=DefaultKeys.VIRIALS.value, - ) - parser.add_argument( - "--stress_key", - help="Key of reference stress in training xyz", - type=str, - default=DefaultKeys.STRESS.value, - ) - parser.add_argument( - "--dipole_key", - help="Key of reference dipoles in training xyz", - type=str, - default=DefaultKeys.DIPOLE.value, - ) - parser.add_argument( - "--head_key", - help="Key of head in training xyz", - type=str, - default=DefaultKeys.HEAD.value, - ) - parser.add_argument( - "--charges_key", - help="Key of atomic charges in training xyz", - type=str, - default=DefaultKeys.CHARGES.value, - ) - parser.add_argument( - "--skip_evaluate_heads", - help="Comma-separated list of heads to skip during final evaluation", - type=str, - default="pt_head", - ) - - # Loss and optimization - parser.add_argument( - "--loss", - help="type of loss", - default="weighted", - choices=[ - "ef", - "weighted", - "forces_only", - "virials", - "stress", - "dipole", - "huber", - "universal", - "energy_forces_dipole", - "l1l2energyforces", - ], - ) - parser.add_argument( - "--forces_weight", help="weight of forces loss", type=float, default=100.0 - ) - parser.add_argument( - "--swa_forces_weight", - "--stage_two_forces_weight", - help="weight of forces loss after starting Stage Two (previously called swa)", - type=float, - default=100.0, - dest="swa_forces_weight", - ) - parser.add_argument( - "--energy_weight", help="weight of energy loss", type=float, default=1.0 - ) - parser.add_argument( - "--swa_energy_weight", - "--stage_two_energy_weight", - help="weight of energy loss after starting Stage Two (previously called swa)", - type=float, - default=1000.0, - dest="swa_energy_weight", - ) - parser.add_argument( - "--virials_weight", help="weight of virials loss", type=float, default=1.0 - ) - parser.add_argument( - "--swa_virials_weight", - "--stage_two_virials_weight", - help="weight of virials loss after starting Stage Two (previously called swa)", - type=float, - default=10.0, - dest="swa_virials_weight", - ) - parser.add_argument( - "--stress_weight", help="weight of stress loss", type=float, default=1.0 - ) - parser.add_argument( - "--swa_stress_weight", - "--stage_two_stress_weight", - help="weight of stress loss after starting Stage Two (previously called swa)", - type=float, - default=10.0, - dest="swa_stress_weight", - ) - parser.add_argument( - "--dipole_weight", help="weight of dipoles loss", type=float, default=1.0 - ) - parser.add_argument( - "--swa_dipole_weight", - "--stage_two_dipole_weight", - help="weight of dipoles after starting Stage Two (previously called swa)", - type=float, - default=1.0, - dest="swa_dipole_weight", - ) - parser.add_argument( - "--config_type_weights", - help="String of dictionary containing the weights for each config type", - type=str, - default='{"Default":1.0}', - ) - parser.add_argument( - "--huber_delta", - help="delta parameter for huber loss", - type=float, - default=0.01, - ) - parser.add_argument( - "--optimizer", - help="Optimizer for parameter optimization", - type=str, - default="adam", - choices=["adam", "adamw", "schedulefree"], - ) - parser.add_argument( - "--beta", - help="Beta parameter for the optimizer", - type=float, - default=0.9, - ) - parser.add_argument("--batch_size", help="batch size", type=int, default=10) - parser.add_argument( - "--valid_batch_size", help="Validation batch size", type=int, default=10 - ) - parser.add_argument( - "--lr", help="Learning rate of optimizer", type=float, default=0.01 - ) - parser.add_argument( - "--swa_lr", - "--stage_two_lr", - help="Learning rate of optimizer in Stage Two (previously called swa)", - type=float, - default=1e-3, - dest="swa_lr", - ) - parser.add_argument( - "--weight_decay", help="weight decay (L2 penalty)", type=float, default=5e-7 - ) - parser.add_argument( - "--amsgrad", - help="use amsgrad variant of optimizer", - action="store_true", - default=True, - ) - parser.add_argument( - "--scheduler", help="Type of scheduler", type=str, default="ReduceLROnPlateau" - ) - parser.add_argument( - "--lr_factor", help="Learning rate factor", type=float, default=0.8 - ) - parser.add_argument( - "--scheduler_patience", help="Learning rate factor", type=int, default=50 - ) - parser.add_argument( - "--lr_scheduler_gamma", - help="Gamma of learning rate scheduler", - type=float, - default=0.9993, - ) - parser.add_argument( - "--swa", - "--stage_two", - help="use Stage Two loss weight, which decreases the learning rate and increases the energy weight at the end of the training to help converge them", - action="store_true", - default=False, - dest="swa", - ) - parser.add_argument( - "--start_swa", - "--start_stage_two", - help="Number of epochs before changing to Stage Two loss weights", - type=int, - default=None, - dest="start_swa", - ) - parser.add_argument( - "--lbfgs", - help="Switch to L-BFGS optimizer", - action="store_true", - default=False, - ) - parser.add_argument( - "--ema", - help="use Exponential Moving Average", - action="store_true", - default=False, - ) - parser.add_argument( - "--ema_decay", - help="Exponential Moving Average decay", - type=float, - default=0.99, - ) - parser.add_argument( - "--max_num_epochs", help="Maximum number of epochs", type=int, default=2048 - ) - parser.add_argument( - "--patience", - help="Maximum number of consecutive epochs of increasing loss", - type=int, - default=2048, - ) - parser.add_argument( - "--foundation_model", - help="Path to the foundation model for transfer learning", - type=str, - default=None, - ) - parser.add_argument( - "--foundation_model_readout", - help="Use readout of foundation model for transfer learning", - action="store_false", - default=True, - ) - parser.add_argument( - "--eval_interval", help="evaluate model every epochs", type=int, default=1 - ) - parser.add_argument( - "--keep_checkpoints", - help="keep all checkpoints", - action="store_true", - default=False, - ) - parser.add_argument( - "--save_all_checkpoints", - help="save all checkpoints", - action="store_true", - default=False, - ) - parser.add_argument( - "--restart_latest", - help="restart optimizer from latest checkpoint", - action="store_true", - default=False, - ) - parser.add_argument( - "--save_cpu", - help="Save a model to be loaded on cpu", - action="store_true", - default=False, - ) - parser.add_argument( - "--clip_grad", - help="Gradient Clipping Value", - type=check_float_or_none, - default=10.0, - ) - parser.add_argument( - "--dry_run", - help="Run all steps upto training to test settings.", - action="store_true", - default=False, - ) - # option for cuequivariance acceleration - parser.add_argument( - "--enable_cueq", - help="Enable cuequivariance acceleration", - type=str2bool, - default=False, - ) - # options for using Weights and Biases for experiment tracking - # to install see https://wandb.ai - parser.add_argument( - "--wandb", - help="Use Weights and Biases for experiment tracking", - action="store_true", - default=False, - ) - parser.add_argument( - "--wandb_dir", - help="An absolute path to a directory where Weights and Biases metadata will be stored", - type=str, - default=None, - ) - parser.add_argument( - "--wandb_project", - help="Weights and Biases project name", - type=str, - default="", - ) - parser.add_argument( - "--wandb_entity", - help="Weights and Biases entity name", - type=str, - default="", - ) - parser.add_argument( - "--wandb_name", - help="Weights and Biases experiment name", - type=str, - default="", - ) - parser.add_argument( - "--wandb_log_hypers", - help="The hyperparameters to log in Weights and Biases", - type=list, - default=[ - "num_channels", - "max_L", - "correlation", - "lr", - "swa_lr", - "weight_decay", - "batch_size", - "max_num_epochs", - "start_swa", - "energy_weight", - "forces_weight", - ], - ) - return parser - - -def build_preprocess_arg_parser() -> argparse.ArgumentParser: - try: - import configargparse - - parser = configargparse.ArgumentParser( - config_file_parser_class=configargparse.YAMLConfigFileParser, - formatter_class=argparse.ArgumentDefaultsHelpFormatter, - ) - parser.add( - "--config", - type=str, - is_config_file=True, - help="config file to aggregate options", - ) - except ImportError: - parser = argparse.ArgumentParser( - formatter_class=argparse.ArgumentDefaultsHelpFormatter, - ) - parser.add_argument( - "--train_file", - help="Training set h5 file", - type=str, - default=None, - required=True, - ) - parser.add_argument( - "--valid_file", - help="Training set xyz file", - type=str, - default=None, - required=False, - ) - parser.add_argument( - "--num_process", - help="The user defined number of processes to use, as well as the number of files created.", - type=int, - default=int(os.cpu_count() / 4), - ) - parser.add_argument( - "--valid_fraction", - help="Fraction of training set used for validation", - type=float, - default=0.1, - required=False, - ) - parser.add_argument( - "--test_file", - help="Test set xyz file", - type=str, - default=None, - required=False, - ) - parser.add_argument( - "--work_dir", - help="set directory for all files and folders", - type=str, - default=".", - ) - parser.add_argument( - "--h5_prefix", - help="Prefix for h5 files when saving", - type=str, - default="", - ) - parser.add_argument( - "--r_max", help="distance cutoff (in Ang)", type=float, default=5.0 - ) - parser.add_argument( - "--config_type_weights", - help="String of dictionary containing the weights for each config type", - type=str, - default='{"Default":1.0}', - ) - parser.add_argument( - "--energy_key", - help="Key of reference energies in training xyz", - type=str, - default=DefaultKeys.ENERGY.value, - ) - parser.add_argument( - "--forces_key", - help="Key of reference forces in training xyz", - type=str, - default=DefaultKeys.FORCES.value, - ) - parser.add_argument( - "--virials_key", - help="Key of reference virials in training xyz", - type=str, - default=DefaultKeys.VIRIALS.value, - ) - parser.add_argument( - "--stress_key", - help="Key of reference stress in training xyz", - type=str, - default=DefaultKeys.STRESS.value, - ) - parser.add_argument( - "--dipole_key", - help="Key of reference dipoles in training xyz", - type=str, - default=DefaultKeys.DIPOLE.value, - ) - parser.add_argument( - "--charges_key", - help="Key of atomic charges in training xyz", - type=str, - default=DefaultKeys.CHARGES.value, - ) - parser.add_argument( - "--atomic_numbers", - help="List of atomic numbers", - type=str, - default=None, - required=False, - ) - parser.add_argument( - "--compute_statistics", - help="Compute statistics for the dataset", - action="store_true", - default=False, - ) - parser.add_argument( - "--batch_size", - help="batch size to compute average number of neighbours", - type=int, - default=16, - ) - - parser.add_argument( - "--scaling", - help="type of scaling to the output", - type=str, - default="rms_forces_scaling", - choices=["std_scaling", "rms_forces_scaling", "no_scaling"], - ) - parser.add_argument( - "--E0s", - help="Dictionary of isolated atom energies", - type=str, - default=None, - required=False, - ) - parser.add_argument( - "--shuffle", - help="Shuffle the training dataset", - type=str2bool, - default=True, - ) - parser.add_argument( - "--seed", - help="Random seed for splitting training and validation sets", - type=int, - default=123, - ) - parser.add_argument( - "--head_key", - help="Key of head in training xyz", - type=str, - default=DefaultKeys.HEAD.value, - ) - parser.add_argument( - "--heads", - help="Dict of heads: containing individual files and E0s", - type=str, - default=None, - required=False, - ) - return parser - - -def check_float_or_none(value: str) -> Optional[float]: - try: - return float(value) - except ValueError: - if value != "None": - raise argparse.ArgumentTypeError( - f"{value} is an invalid value (float or None)" - ) from None - return None - - -def str2bool(value): - if isinstance(value, bool): - return value - if value.lower() in ("yes", "true", "t", "y", "1"): - return True - if value.lower() in ("no", "false", "f", "n", "0"): - return False - raise argparse.ArgumentTypeError("Boolean value expected.") diff --git a/mace-bench/3rdparty/mace/mace/tools/arg_parser_tools.py b/mace-bench/3rdparty/mace/mace/tools/arg_parser_tools.py deleted file mode 100644 index be714b26edc2b4d39bb64ccc0c6e270e6c656e5b..0000000000000000000000000000000000000000 --- a/mace-bench/3rdparty/mace/mace/tools/arg_parser_tools.py +++ /dev/null @@ -1,122 +0,0 @@ -import logging -import os - -from e3nn import o3 - - -def check_args(args): - """ - Check input arguments, update them if necessary for valid and consistent inputs, and return a tuple containing - the (potentially) modified args and a list of log messages. - """ - log_messages = [] - - # Directories - # Use work_dir for all other directories as well, unless they were specified by the user - if args.log_dir is None: - args.log_dir = os.path.join(args.work_dir, "logs") - if args.model_dir is None: - args.model_dir = args.work_dir - if args.checkpoints_dir is None: - args.checkpoints_dir = os.path.join(args.work_dir, "checkpoints") - if args.results_dir is None: - args.results_dir = os.path.join(args.work_dir, "results") - if args.downloads_dir is None: - args.downloads_dir = os.path.join(args.work_dir, "downloads") - - # Model - # Check if hidden_irreps, num_channels and max_L are consistent - if args.hidden_irreps is None and args.num_channels is None and args.max_L is None: - args.hidden_irreps, args.num_channels, args.max_L = "128x0e + 128x1o", 128, 1 - elif ( - args.hidden_irreps is not None - and args.num_channels is not None - and args.max_L is not None - ): - args.hidden_irreps = o3.Irreps( - (args.num_channels * o3.Irreps.spherical_harmonics(args.max_L)) - .sort() - .irreps.simplify() - ) - log_messages.append( - ( - "All of hidden_irreps, num_channels and max_L are specified", - logging.WARNING, - ) - ) - log_messages.append( - ( - f"Using num_channels and max_L to create hidden_irreps: {args.hidden_irreps}.", - logging.WARNING, - ) - ) - assert ( - len({irrep.mul for irrep in o3.Irreps(args.hidden_irreps)}) == 1 - ), "All channels must have the same dimension, use the num_channels and max_L keywords to specify the number of channels and the maximum L" - elif args.num_channels is not None and args.max_L is not None: - assert args.num_channels > 0, "num_channels must be positive integer" - assert args.max_L >= 0, "max_L must be non-negative integer" - args.hidden_irreps = o3.Irreps( - (args.num_channels * o3.Irreps.spherical_harmonics(args.max_L)) - .sort() - .irreps.simplify() - ) - assert ( - len({irrep.mul for irrep in o3.Irreps(args.hidden_irreps)}) == 1 - ), "All channels must have the same dimension, use the num_channels and max_L keywords to specify the number of channels and the maximum L" - elif args.hidden_irreps is not None: - assert ( - len({irrep.mul for irrep in o3.Irreps(args.hidden_irreps)}) == 1 - ), "All channels must have the same dimension, use the num_channels and max_L keywords to specify the number of channels and the maximum L" - - args.num_channels = list( - {irrep.mul for irrep in o3.Irreps(args.hidden_irreps)} - )[0] - args.max_L = o3.Irreps(args.hidden_irreps).lmax - elif args.max_L is not None and args.num_channels is None: - assert args.max_L >= 0, "max_L must be non-negative integer" - args.num_channels = 128 - args.hidden_irreps = o3.Irreps( - (args.num_channels * o3.Irreps.spherical_harmonics(args.max_L)) - .sort() - .irreps.simplify() - ) - elif args.max_L is None and args.num_channels is not None: - assert args.num_channels > 0, "num_channels must be positive integer" - args.max_L = 1 - args.hidden_irreps = o3.Irreps( - (args.num_channels * o3.Irreps.spherical_harmonics(args.max_L)) - .sort() - .irreps.simplify() - ) - - # Loss and optimization - # Check Stage Two loss start - if args.start_swa is not None: - args.swa = True - log_messages.append( - ( - "Stage Two is activated as start_stage_two was defined", - logging.INFO, - ) - ) - - if args.swa: - if args.start_swa is None: - args.start_swa = max(1, args.max_num_epochs // 4 * 3) - if args.start_swa > args.max_num_epochs: - log_messages.append( - ( - f"start_stage_two must be less than max_num_epochs, got {args.start_swa} > {args.max_num_epochs}", - logging.WARNING, - ) - ) - log_messages.append( - ( - "Stage Two will not start, as start_stage_two > max_num_epochs", - logging.WARNING, - ) - ) - args.swa = False - - return args, log_messages diff --git a/mace-bench/3rdparty/mace/mace/tools/cg.py b/mace-bench/3rdparty/mace/mace/tools/cg.py deleted file mode 100644 index 471adac786519ea860673687fcff40fbcf08faba..0000000000000000000000000000000000000000 --- a/mace-bench/3rdparty/mace/mace/tools/cg.py +++ /dev/null @@ -1,211 +0,0 @@ -########################################################################################### -# Higher Order Real Clebsch Gordan (based on e3nn by Mario Geiger) -# Authors: Ilyes Batatia -# This program is distributed under the MIT License (see MIT.md) -########################################################################################### - -import collections -import itertools -import os -from typing import Iterator, List, Union - -import numpy as np -import torch -from e3nn import o3 - -try: - import cuequivariance as cue - - CUET_AVAILABLE = True -except ImportError: - CUET_AVAILABLE = False - -USE_CUEQ_CG = os.environ.get("MACE_USE_CUEQ_CG", "0").lower() in ( - "1", - "true", - "yes", - "y", -) - -_TP = collections.namedtuple("_TP", "op, args") -_INPUT = collections.namedtuple("_INPUT", "tensor, start, stop") - - -def _wigner_nj( - irrepss: List[o3.Irreps], - normalization: str = "component", - filter_ir_mid=None, - dtype=None, -): - irrepss = [o3.Irreps(irreps) for irreps in irrepss] - if filter_ir_mid is not None: - filter_ir_mid = [o3.Irrep(ir) for ir in filter_ir_mid] - - if len(irrepss) == 1: - (irreps,) = irrepss - ret = [] - e = torch.eye(irreps.dim, dtype=dtype) - i = 0 - for mul, ir in irreps: - for _ in range(mul): - sl = slice(i, i + ir.dim) - ret += [(ir, _INPUT(0, sl.start, sl.stop), e[sl])] - i += ir.dim - return ret - - *irrepss_left, irreps_right = irrepss - ret = [] - for ir_left, path_left, C_left in _wigner_nj( - irrepss_left, - normalization=normalization, - filter_ir_mid=filter_ir_mid, - dtype=dtype, - ): - i = 0 - for mul, ir in irreps_right: - for ir_out in ir_left * ir: - if filter_ir_mid is not None and ir_out not in filter_ir_mid: - continue - - C = o3.wigner_3j(ir_out.l, ir_left.l, ir.l, dtype=dtype) - if normalization == "component": - C *= ir_out.dim**0.5 - if normalization == "norm": - C *= ir_left.dim**0.5 * ir.dim**0.5 - - C = torch.einsum("jk,ijl->ikl", C_left.flatten(1), C) - C = C.reshape( - ir_out.dim, *(irreps.dim for irreps in irrepss_left), ir.dim - ) - for u in range(mul): - E = torch.zeros( - ir_out.dim, - *(irreps.dim for irreps in irrepss_left), - irreps_right.dim, - dtype=dtype, - ) - sl = slice(i + u * ir.dim, i + (u + 1) * ir.dim) - E[..., sl] = C - ret += [ - ( - ir_out, - _TP( - op=(ir_left, ir, ir_out), - args=( - path_left, - _INPUT(len(irrepss_left), sl.start, sl.stop), - ), - ), - E, - ) - ] - i += mul * ir.dim - return sorted(ret, key=lambda x: x[0]) - - -def U_matrix_real( - irreps_in: Union[str, o3.Irreps], - irreps_out: Union[str, o3.Irreps], - correlation: int, - normalization: str = "component", - filter_ir_mid=None, - dtype=None, - use_cueq_cg=None, -): - irreps_out = o3.Irreps(irreps_out) - irrepss = [o3.Irreps(irreps_in)] * correlation - - if correlation == 4: - filter_ir_mid = [(i, 1 if i % 2 == 0 else -1) for i in range(12)] - - if use_cueq_cg is None: - use_cueq_cg = USE_CUEQ_CG - if use_cueq_cg and CUET_AVAILABLE: - return compute_U_cueq(irreps_in, irreps_out=irreps_out, correlation=correlation) - - try: - wigners = _wigner_nj(irrepss, normalization, filter_ir_mid, dtype) - except NotImplementedError as e: - if CUET_AVAILABLE: - return compute_U_cueq( - irreps_in, irreps_out=irreps_out, correlation=correlation - ) - raise NotImplementedError( - "The requested Clebsch-Gordan coefficients are not implemented, please install cuequivariance; pip install cuequivariance" - ) from e - - current_ir = wigners[0][0] - out = [] - stack = torch.tensor([]) - - for ir, _, base_o3 in wigners: - if ir in irreps_out and ir == current_ir: - stack = torch.cat((stack, base_o3.squeeze().unsqueeze(-1)), dim=-1) - last_ir = current_ir - elif ir in irreps_out and ir != current_ir: - if len(stack) != 0: - out += [last_ir, stack] - stack = base_o3.squeeze().unsqueeze(-1) - current_ir, last_ir = ir, ir - else: - current_ir = ir - out += [last_ir, stack] - return out - - -if CUET_AVAILABLE: - - def compute_U_cueq(irreps_in, irreps_out, correlation=2): - U = [] - irreps_in = cue.Irreps(O3_e3nn, str(irreps_in)) - irreps_out = cue.Irreps(O3_e3nn, str(irreps_out)) - for _, ir in irreps_out: - ir_str = str(ir) - U.append(ir_str) - U_matrix = cue.reduced_symmetric_tensor_product_basis( - irreps_in, correlation, keep_ir=ir, layout=cue.ir_mul - ).array - U_matrix = U_matrix.reshape(ir.dim, *([irreps_in.dim] * correlation), -1) - if ir.dim == 1: - U_matrix = U_matrix[0] - U.append(torch.tensor(U_matrix)) - return U - - class O3_e3nn(cue.O3): - def __mul__( # pylint: disable=no-self-argument - rep1: "O3_e3nn", rep2: "O3_e3nn" - ) -> Iterator["O3_e3nn"]: - return [O3_e3nn(l=ir.l, p=ir.p) for ir in cue.O3.__mul__(rep1, rep2)] - - @classmethod - def clebsch_gordan( - cls, rep1: "O3_e3nn", rep2: "O3_e3nn", rep3: "O3_e3nn" - ) -> np.ndarray: - rep1, rep2, rep3 = cls._from(rep1), cls._from(rep2), cls._from(rep3) - - if rep1.p * rep2.p == rep3.p: - return o3.wigner_3j(rep1.l, rep2.l, rep3.l).numpy()[None] * np.sqrt( - rep3.dim - ) - return np.zeros((0, rep1.dim, rep2.dim, rep3.dim)) - - def __lt__( # pylint: disable=no-self-argument - rep1: "O3_e3nn", rep2: "O3_e3nn" - ) -> bool: - rep2 = rep1._from(rep2) - return (rep1.l, rep1.p) < (rep2.l, rep2.p) - - @classmethod - def iterator(cls) -> Iterator["O3_e3nn"]: - for l in itertools.count(0): - yield O3_e3nn(l=l, p=1 * (-1) ** l) - yield O3_e3nn(l=l, p=-1 * (-1) ** l) - -else: - - class O3_e3nn: - pass - - print( - "cuequivariance or cuequivariance_torch is not available. Cuequivariance acceleration will be disabled." - ) diff --git a/mace-bench/3rdparty/mace/mace/tools/checkpoint.py b/mace-bench/3rdparty/mace/mace/tools/checkpoint.py deleted file mode 100644 index 81161cccda0245b8fb75291f38ebb8742fd29a4b..0000000000000000000000000000000000000000 --- a/mace-bench/3rdparty/mace/mace/tools/checkpoint.py +++ /dev/null @@ -1,227 +0,0 @@ -########################################################################################### -# Checkpointing -# Authors: Gregor Simm -# This program is distributed under the MIT License (see MIT.md) -########################################################################################### - -import dataclasses -import logging -import os -import re -from typing import Dict, List, Optional, Tuple - -import torch - -from .torch_tools import TensorDict - -Checkpoint = Dict[str, TensorDict] - - -@dataclasses.dataclass -class CheckpointState: - model: torch.nn.Module - optimizer: torch.optim.Optimizer - lr_scheduler: torch.optim.lr_scheduler.ExponentialLR - - -class CheckpointBuilder: - @staticmethod - def create_checkpoint(state: CheckpointState) -> Checkpoint: - return { - "model": state.model.state_dict(), - "optimizer": state.optimizer.state_dict(), - "lr_scheduler": state.lr_scheduler.state_dict(), - } - - @staticmethod - def load_checkpoint( - state: CheckpointState, checkpoint: Checkpoint, strict: bool - ) -> None: - state.model.load_state_dict(checkpoint["model"], strict=strict) # type: ignore - state.optimizer.load_state_dict(checkpoint["optimizer"]) - state.lr_scheduler.load_state_dict(checkpoint["lr_scheduler"]) - - -@dataclasses.dataclass -class CheckpointPathInfo: - path: str - tag: str - epochs: int - swa: bool - - -class CheckpointIO: - def __init__( - self, directory: str, tag: str, keep: bool = False, swa_start: int = None - ) -> None: - self.directory = directory - self.tag = tag - self.keep = keep - self.old_path: Optional[str] = None - self.swa_start = swa_start - - self._epochs_string = "_epoch-" - self._filename_extension = "pt" - - def _get_checkpoint_filename(self, epochs: int, swa_start=None) -> str: - if swa_start is not None and epochs >= swa_start: - return ( - self.tag - + self._epochs_string - + str(epochs) - + "_swa" - + "." - + self._filename_extension - ) - return ( - self.tag - + self._epochs_string - + str(epochs) - + "." - + self._filename_extension - ) - - def _list_file_paths(self) -> List[str]: - if not os.path.isdir(self.directory): - return [] - all_paths = [ - os.path.join(self.directory, f) for f in os.listdir(self.directory) - ] - return [path for path in all_paths if os.path.isfile(path)] - - def _parse_checkpoint_path(self, path: str) -> Optional[CheckpointPathInfo]: - filename = os.path.basename(path) - regex = re.compile( - rf"^(?P.+){self._epochs_string}(?P\d+)\.{self._filename_extension}$" - ) - regex2 = re.compile( - rf"^(?P.+){self._epochs_string}(?P\d+)_swa\.{self._filename_extension}$" - ) - match = regex.match(filename) - match2 = regex2.match(filename) - swa = False - if not match: - if not match2: - return None - match = match2 - swa = True - - return CheckpointPathInfo( - path=path, - tag=match.group("tag"), - epochs=int(match.group("epochs")), - swa=swa, - ) - - def _get_latest_checkpoint_path(self, swa) -> Optional[str]: - all_file_paths = self._list_file_paths() - checkpoint_info_list = [ - self._parse_checkpoint_path(path) for path in all_file_paths - ] - selected_checkpoint_info_list = [ - info for info in checkpoint_info_list if info and info.tag == self.tag - ] - - if len(selected_checkpoint_info_list) == 0: - logging.warning( - f"Cannot find checkpoint with tag '{self.tag}' in '{self.directory}'" - ) - return None - - selected_checkpoint_info_list_swa = [] - selected_checkpoint_info_list_no_swa = [] - - for ckp in selected_checkpoint_info_list: - if ckp.swa: - selected_checkpoint_info_list_swa.append(ckp) - else: - selected_checkpoint_info_list_no_swa.append(ckp) - if swa: - try: - latest_checkpoint_info = max( - selected_checkpoint_info_list_swa, key=lambda info: info.epochs - ) - except ValueError: - logging.warning( - "No SWA checkpoint found, while SWA is enabled. Compare the swa_start parameter and the latest checkpoint." - ) - else: - latest_checkpoint_info = max( - selected_checkpoint_info_list_no_swa, key=lambda info: info.epochs - ) - return latest_checkpoint_info.path - - def save( - self, checkpoint: Checkpoint, epochs: int, keep_last: bool = False - ) -> None: - if not self.keep and self.old_path and not keep_last: - logging.debug(f"Deleting old checkpoint file: {self.old_path}") - os.remove(self.old_path) - - filename = self._get_checkpoint_filename(epochs, self.swa_start) - path = os.path.join(self.directory, filename) - logging.debug(f"Saving checkpoint: {path}") - os.makedirs(self.directory, exist_ok=True) - torch.save(obj=checkpoint, f=path) - self.old_path = path - - def load_latest( - self, swa: Optional[bool] = False, device: Optional[torch.device] = None - ) -> Optional[Tuple[Checkpoint, int]]: - path = self._get_latest_checkpoint_path(swa=swa) - if path is None: - return None - - return self.load(path, device=device) - - def load( - self, path: str, device: Optional[torch.device] = None - ) -> Tuple[Checkpoint, int]: - checkpoint_info = self._parse_checkpoint_path(path) - - if checkpoint_info is None: - raise RuntimeError(f"Cannot find path '{path}'") - - logging.info(f"Loading checkpoint: {checkpoint_info.path}") - return ( - torch.load(f=checkpoint_info.path, map_location=device), - checkpoint_info.epochs, - ) - - -class CheckpointHandler: - def __init__(self, *args, **kwargs) -> None: - self.io = CheckpointIO(*args, **kwargs) - self.builder = CheckpointBuilder() - - def save( - self, state: CheckpointState, epochs: int, keep_last: bool = False - ) -> None: - checkpoint = self.builder.create_checkpoint(state) - self.io.save(checkpoint, epochs, keep_last) - - def load_latest( - self, - state: CheckpointState, - swa: Optional[bool] = False, - device: Optional[torch.device] = None, - strict=False, - ) -> Optional[int]: - result = self.io.load_latest(swa=swa, device=device) - if result is None: - return None - - checkpoint, epochs = result - self.builder.load_checkpoint(state=state, checkpoint=checkpoint, strict=strict) - return epochs - - def load( - self, - state: CheckpointState, - path: str, - strict=False, - device: Optional[torch.device] = None, - ) -> int: - checkpoint, epochs = self.io.load(path, device=device) - self.builder.load_checkpoint(state=state, checkpoint=checkpoint, strict=strict) - return epochs diff --git a/mace-bench/3rdparty/mace/mace/tools/compile.py b/mace-bench/3rdparty/mace/mace/tools/compile.py deleted file mode 100644 index 03282067380d9de08a0af41a66edd38f4ddc973c..0000000000000000000000000000000000000000 --- a/mace-bench/3rdparty/mace/mace/tools/compile.py +++ /dev/null @@ -1,95 +0,0 @@ -from contextlib import contextmanager -from functools import wraps -from typing import Callable, Tuple - -try: - import torch._dynamo as dynamo -except ImportError: - dynamo = None -from e3nn import get_optimization_defaults, set_optimization_defaults -from torch import autograd, nn -from torch.fx import symbolic_trace - -ModuleFactory = Callable[..., nn.Module] -TypeTuple = Tuple[type, ...] - - -@contextmanager -def disable_e3nn_codegen(): - """Context manager that disables the legacy PyTorch code generation used in e3nn.""" - init_val = get_optimization_defaults()["jit_script_fx"] - set_optimization_defaults(jit_script_fx=False) - yield - set_optimization_defaults(jit_script_fx=init_val) - - -def prepare(func: ModuleFactory, allow_autograd: bool = True) -> ModuleFactory: - """Function transform that prepares a MACE module for torch.compile - - Args: - func (ModuleFactory): A function that creates an nn.Module - allow_autograd (bool, optional): Force inductor compiler to inline call to - `torch.autograd.grad`. Defaults to True. - - Returns: - ModuleFactory: Decorated function that creates a torch.compile compatible module - """ - if allow_autograd: - dynamo.allow_in_graph(autograd.grad) - else: - dynamo.disallow_in_graph(autograd.grad) - - @wraps(func) - def wrapper(*args, **kwargs): - with disable_e3nn_codegen(): - model = func(*args, **kwargs) - - model = simplify(model) - return model - - return wrapper - - -_SIMPLIFY_REGISTRY = set() - - -def simplify_if_compile(module: nn.Module) -> nn.Module: - """Decorator to register a module for symbolic simplification - - The decorated module will be simplifed using `torch.fx.symbolic_trace`. - This constrains the module to not have any dynamic control flow, see: - - https://pytorch.org/docs/stable/fx.html#limitations-of-symbolic-tracing - - Args: - module (nn.Module): the module to register - - Returns: - nn.Module: registered module - """ - _SIMPLIFY_REGISTRY.add(module) - return module - - -def simplify(module: nn.Module) -> nn.Module: - """Recursively searches for registered modules to simplify with - `torch.fx.symbolic_trace` to support compiling with the PyTorch Dynamo compiler. - - Modules are registered with the `simplify_if_compile` decorator and - - Args: - module (nn.Module): the module to simplify - - Returns: - nn.Module: the simplified module - """ - simplify_types = tuple(_SIMPLIFY_REGISTRY) - - for name, child in module.named_children(): - if isinstance(child, simplify_types): - traced = symbolic_trace(child) - setattr(module, name, traced) - else: - simplify(child) - - return module diff --git a/mace-bench/3rdparty/mace/mace/tools/default_keys.py b/mace-bench/3rdparty/mace/mace/tools/default_keys.py deleted file mode 100644 index 769867dffb95f1ba599944688df7f5470289539e..0000000000000000000000000000000000000000 --- a/mace-bench/3rdparty/mace/mace/tools/default_keys.py +++ /dev/null @@ -1,21 +0,0 @@ -from __future__ import annotations - -from enum import Enum - - -class DefaultKeys(Enum): - ENERGY = "REF_energy" - FORCES = "REF_forces" - STRESS = "REF_stress" - VIRIALS = "REF_virials" - DIPOLE = "dipole" - HEAD = "head" - CHARGES = "REF_charges" - - @staticmethod - def keydict() -> dict[str, str]: - key_dict = {} - for member in DefaultKeys: - key_name = f"{member.name.lower()}_key" - key_dict[key_name] = member.value - return key_dict diff --git a/mace-bench/3rdparty/mace/mace/tools/fairchem_dataset/__init__.py b/mace-bench/3rdparty/mace/mace/tools/fairchem_dataset/__init__.py deleted file mode 100644 index 5163777df311ba3342680b1f8eec7004b7cb6110..0000000000000000000000000000000000000000 --- a/mace-bench/3rdparty/mace/mace/tools/fairchem_dataset/__init__.py +++ /dev/null @@ -1,3 +0,0 @@ -from .lmdb_dataset_tools import AseDBDataset - -__all__ = ["AseDBDataset"] diff --git a/mace-bench/3rdparty/mace/mace/tools/fairchem_dataset/fairchem_readme.md b/mace-bench/3rdparty/mace/mace/tools/fairchem_dataset/fairchem_readme.md deleted file mode 100644 index d6f01dbe748bda21208597504f13ff5fafc6724a..0000000000000000000000000000000000000000 --- a/mace-bench/3rdparty/mace/mace/tools/fairchem_dataset/fairchem_readme.md +++ /dev/null @@ -1,17 +0,0 @@ -# AseDBDataset Library - -This library provides a standalone implementation of the AseDBDataset class extracted from the FairChem codebase. The AseDBDataset allows you to connect to ASE databases with various backends including JSON, SQLite, and LMDB. - -## License Information - -The code in this repository contains components from multiple sources with different licenses: - -1. **Main Code (AseDBDataset, AseAtomsDataset, BaseDataset, etc.)**: - - Original Source: Meta's FairChem codebase - - License: MIT License - - Copyright: Meta, Inc. and its affiliates - -2. **LMDBDatabase Component**: - - Original Source: Modified from ASE database JSON backend - - License: LGPL 2.1 - - The ASE notice for the LGPL 2.1 license is available at: https://gitlab.com/ase/ase/-/blob/master/LICENSE diff --git a/mace-bench/3rdparty/mace/mace/tools/fairchem_dataset/lmdb_dataset_tools.py b/mace-bench/3rdparty/mace/mace/tools/fairchem_dataset/lmdb_dataset_tools.py deleted file mode 100644 index f0c0ca3e681b44888a1ad421f5fd4a6665ba82fb..0000000000000000000000000000000000000000 --- a/mace-bench/3rdparty/mace/mace/tools/fairchem_dataset/lmdb_dataset_tools.py +++ /dev/null @@ -1,954 +0,0 @@ -""" -This module contains the AseDBDataset class and its dependencies. -It is extracted from the fairchem codebase and adapted to remove dependencies on fairchem. - -Original code copyright: -Copyright (c) Meta, Inc. and its affiliates. - -This source code is licensed under the MIT license found in the -LICENSE file in the root directory of this source tree. -""" - -from __future__ import annotations - -import bisect -import logging -import os -import zlib -from abc import ABC, abstractmethod - -try: - from functools import cache, cached_property -except ImportError: - from functools import cached_property, lru_cache - - cache = lru_cache(maxsize=None) -from glob import glob -from pathlib import Path -from typing import Any, Callable, TypeVar - -import ase -import ase.db.core -import ase.db.row -import ase.io -import lmdb -import numpy as np -import orjson -import torch - -# Type variable for generic dataset return type -T_co = TypeVar("T_co", covariant=True) - - -def rename_data_object_keys(data_object, key_mapping: dict[str, str | list[str]]): - """Rename data object keys - - Args: - data_object: data object - key_mapping: dictionary specifying keys to rename and new names {prev_key: new_key} - - new_key can be a list of new keys, for example, - prev_key: energy - new_key: [common_energy, oc20_energy] - - This is currently required when we use a single target/label for multiple tasks - """ - for _property in key_mapping: - # catch for test data not containing labels - if _property in data_object: - list_of_new_keys = key_mapping[_property] - if isinstance(list_of_new_keys, str): - list_of_new_keys = [list_of_new_keys] - for new_property in list_of_new_keys: - if new_property == _property: - continue - assert new_property not in data_object - data_object[new_property] = data_object[_property] - if _property not in list_of_new_keys: - del data_object[_property] - return data_object - - -def apply_one_tags( - atoms: ase.Atoms, skip_if_nonzero: bool = True, skip_always: bool = False -): - """ - This function will apply tags of 1 to an ASE atoms object. - It is used as an atoms_transform in the datasets contained in this file. - - Certain models will treat atoms differently depending on their tags. - For example, GemNet-OC by default will only compute triplet and quadruplet interactions - for atoms with non-zero tags. This model throws an error if there are no tagged atoms. - For this reason, the default behavior is to tag atoms in structures with no tags. - - args: - skip_if_nonzero (bool): If at least one atom has a nonzero tag, do not tag any atoms - - skip_always (bool): Do not apply any tags. This arg exists so that this function can be disabled - without needing to pass a callable (which is currently difficult to do with main.py) - """ - if skip_always: - return atoms - - if np.all(atoms.get_tags() == 0) or not skip_if_nonzero: - atoms.set_tags(np.ones(len(atoms))) - - return atoms - - -class UnsupportedDatasetError(ValueError): - pass - - -class BaseDataset(ABC): - """Base Dataset class for all ASE datasets.""" - - def __init__(self, config: dict): - """Initialize - - Args: - config (dict): dataset configuration - """ - self.config = config - self.paths = [] - - if "src" in self.config: - if isinstance(config["src"], str): - self.paths = [Path(self.config["src"])] - else: - self.paths = tuple(Path(path) for path in sorted(config["src"])) - - self.lin_ref = None - if self.config.get("lin_ref", False): - lin_ref = torch.tensor( - np.load(self.config["lin_ref"], allow_pickle=True)["coeff"] - ) - self.lin_ref = torch.nn.Parameter(lin_ref, requires_grad=False) - - def __len__(self) -> int: - return self.num_samples - - def metadata_hasattr(self, attr) -> bool: - return attr in self._metadata - - @cached_property - def indices(self): - return np.arange(self.num_samples, dtype=int) - - @cached_property - def _metadata(self) -> dict[str, np.ndarray]: - # logic to read metadata file here - metadata_npzs = [] - if self.config.get("metadata_path", None) is not None: - metadata_npzs.append( - np.load(self.config["metadata_path"], allow_pickle=True) - ) - - else: - for path in self.paths: - if path.is_file(): - metadata_file = path.parent / "metadata.npz" - else: - metadata_file = path / "metadata.npz" - if metadata_file.is_file(): - metadata_npzs.append(np.load(metadata_file, allow_pickle=True)) - - if len(metadata_npzs) == 0: - logging.warning( - f"Could not find dataset metadata.npz files in '{self.paths}'" - ) - return {} - - metadata = { - field: np.concatenate([metadata[field] for metadata in metadata_npzs]) - for field in metadata_npzs[0] - } - - assert np.issubdtype( - metadata["natoms"].dtype, np.integer - ), f"Metadata natoms must be an integer type! not {metadata['natoms'].dtype}" - assert metadata["natoms"].shape[0] == len( - self - ), "Loaded metadata and dataset size mismatch." - - return metadata - - def get_metadata(self, attr, idx): - if attr in self._metadata: - metadata_attr = self._metadata[attr] - if isinstance(idx, list): - return [metadata_attr[_idx] for _idx in idx] - return metadata_attr[idx] - return None - - -class Subset(BaseDataset): - """A subset that also takes metadata if given.""" - - def __init__( - self, - dataset: BaseDataset, - indices: list[int], - metadata: dict[str, np.ndarray], - ) -> None: - super().__init__(dataset.config) - self.dataset = dataset - self.metadata = metadata - self.indices = indices - self.num_samples = len(indices) - self.config = dataset.config - - @cached_property - def _metadata(self) -> dict[str, np.ndarray]: - return self.dataset._metadata # pylint: disable=protected-access - - def get_metadata(self, attr, idx): - if isinstance(idx, list): - return self.dataset.get_metadata(attr, [[self.indices[i] for i in idx]]) - return self.dataset.get_metadata(attr, self.indices[idx]) - - -class LMDBDatabase(ase.db.core.Database): - """ - This module is modified from the ASE db json backend - and is thus licensed under the corresponding LGPL2.1 license. - - The ASE notice for the LGPL2.1 license is available here: - https://gitlab.com/ase/ase/-/blob/master/LICENSE - """ - - def __init__( # pylint: disable=keyword-arg-before-vararg - self, - filename: str | Path | None = None, - create_indices: bool = True, - use_lock_file: bool = False, - serial: bool = False, - readonly: bool = False, # Moved after *args to make it keyword-only - *args, - **kwargs, - ) -> None: - """ - For the most part, this is identical to the standard ase db initiation - arguments, except that we add a readonly flag. - """ - super().__init__( - Path(filename), - create_indices, - use_lock_file, - serial, - *args, - **kwargs, - ) - - # Add a readonly mode for when we're only training - # to make sure there's no parallel locks - self.readonly = readonly - - if self.readonly: - # Open a new env - self.env = lmdb.open( - str(self.filename), - subdir=False, - meminit=False, - map_async=True, - readonly=True, - lock=False, - ) - - # Open a transaction and keep it open for fast read/writes! - self.txn = self.env.begin(write=False) - - else: - # Open a new env with write access - self.env = lmdb.open( - str(self.filename), - map_size=1099511627776 * 2, - subdir=False, - meminit=False, - map_async=True, - ) - - self.txn = self.env.begin(write=True) - - # Load all ids based on keys in the DB. - self.ids = [] - self.deleted_ids = [] - self._load_ids() - - def __enter__(self) -> "LMDBDatabase": - return self - - def __exit__(self, exc_type, exc_value, tb) -> None: - self.close() - - def close(self) -> None: - # Close the lmdb environment and transaction - self.txn.commit() - self.env.close() - - def _write( - self, - atoms: ase.Atoms | ase.db.row.AtomsRow, - key_value_pairs: dict, - data: dict | None, - id: int | None = None, # pylint: disable=redefined-builtin - ) -> None: - # Call parent method with the original parameter name - super()._write(atoms, key_value_pairs, data) - - mtime = ase.db.core.now() - - if isinstance(atoms, ase.db.row.AtomsRow): - row = atoms - else: - row = ase.db.row.AtomsRow(atoms) - row.ctime = mtime - row.user = os.getenv("USER") - - dct = {} - for key in row.__dict__: - # Use getattr to avoid accessing protected member directly - if key[0] == "_" or key == "id" or key in getattr(row, "_keys", []): - continue - dct[key] = row[key] - - dct["mtime"] = mtime - - if key_value_pairs: - dct["key_value_pairs"] = key_value_pairs - - if data: - dct["data"] = data - - constraints = row.get("constraints") - if constraints: - dct["constraints"] = [constraint.todict() for constraint in constraints] - - # json doesn't like Cell objects, so make it an array - dct["cell"] = np.asarray(dct["cell"]) - - if id is None: - id = self._nextid - nextid = id + 1 - else: - data = self.txn.get(f"{id}".encode("ascii")) - assert data is not None - - # Add the new entry - self.txn.put( - f"{id}".encode("ascii"), - zlib.compress(orjson.dumps(dct, option=orjson.OPT_SERIALIZE_NUMPY)), - ) - # only append if idx is not in ids - if id not in self.ids: - self.ids.append(id) - self.txn.put( - "nextid".encode("ascii"), - zlib.compress(orjson.dumps(nextid, option=orjson.OPT_SERIALIZE_NUMPY)), - ) - # check if id is in removed ids and remove accordingly - if id in self.deleted_ids: - self.deleted_ids.remove(id) - self._write_deleted_ids() - - return id - - def _update( - self, - idx: int, - key_value_pairs: dict | None = None, - data: dict | None = None, - ): - # hack this to play nicely with ASE code - row = self._get_row(idx, include_data=True) - if data is not None or key_value_pairs is not None: - self._write( - atoms=row, key_value_pairs=key_value_pairs, data=data, id=idx - ) # Fixed E1123 by using id=idx - - def _write_deleted_ids(self): - self.txn.put( - "deleted_ids".encode("ascii"), - zlib.compress( - orjson.dumps(self.deleted_ids, option=orjson.OPT_SERIALIZE_NUMPY) - ), - ) - - def delete(self, ids: list[int]) -> None: - for idx in ids: - self.txn.delete(f"{idx}".encode("ascii")) - self.ids.remove(idx) - - self.deleted_ids += ids - self._write_deleted_ids() - - def _get_row(self, idx: int, include_data: bool = True): - if idx is None: - assert len(self.ids) == 1 - idx = self.ids[0] - data = self.txn.get(f"{idx}".encode("ascii")) - - if data is not None: - dct = orjson.loads(zlib.decompress(data)) - else: - raise KeyError(f"Id {idx} missing from the database!") - - if not include_data: - dct.pop("data", None) - - dct["id"] = idx - return ase.db.row.AtomsRow(dct) - - def _get_row_by_index(self, index: int, include_data: bool = True): - """Auxiliary function to get the ith entry, rather than a specific id""" - data = self.txn.get(f"{self.ids[index]}".encode("ascii")) - - if data is not None: - dct = orjson.loads(zlib.decompress(data)) - else: - raise KeyError(f"Id {id} missing from the database!") - - if not include_data: - dct.pop("data", None) - - dct["id"] = id - return ase.db.row.AtomsRow(dct) - - def _select( - self, - keys, - cmps: list[tuple[str, str, str]], - explain: bool = False, - _verbosity: int = 0, # Unused parameter marked with underscore - limit: int | None = None, - offset: int = 0, - sort: str | None = None, - include_data: bool = True, - _columns: str = "all", # Unused parameter marked with underscore - ): - if explain: - yield {"explain": (0, 0, 0, "scan table")} - return - - if sort is not None: - if sort[0] == "-": - reverse = True - sort = sort[1:] - else: - reverse = False - - rows = [] - missing = [] - for row in self._select(keys, cmps): - key = row.get(sort) - if key is None: - missing.append((0, row)) - else: - rows.append((key, row)) - - rows.sort(reverse=reverse, key=lambda x: x[0]) - rows += missing - - if limit: - rows = rows[offset : offset + limit] - for _, row in rows: - yield row - return - - if not limit: - limit = -offset - 1 - - cmps = [(key, ase.db.core.ops[op], val) for key, op, val in cmps] - n = 0 - for idx in self.ids: - if n - offset == limit: - return - row = self._get_row(idx, include_data=include_data) - - for key in keys: - if key not in row: - break - else: - for key, op, val in cmps: - if isinstance(key, int): - value = np.equal(row.numbers, key).sum() - else: - value = row.get(key) - if key == "pbc": - assert op in [ase.db.core.ops["="], ase.db.core.ops["!="]] - value = "".join("FT"[x] for x in value) - if value is None or not op(value, val): - break - else: - if n >= offset: - yield row - n += 1 - - @property - def metadata(self): - """Override abstract metadata method from Database class.""" - return self.db_metadata - - @property - def db_metadata(self): - """Load the metadata from the DB if present""" - if self._metadata is None: - metadata = self.txn.get("metadata".encode("ascii")) - if metadata is None: - self._metadata = {} - else: - self._metadata = orjson.loads(zlib.decompress(metadata)) - - return self._metadata.copy() - - @db_metadata.setter - def db_metadata(self, dct): - self._metadata = dct - - # Put the updated metadata dictionary - self.txn.put( - "metadata".encode("ascii"), - zlib.compress(orjson.dumps(dct, option=orjson.OPT_SERIALIZE_NUMPY)), - ) - - @property - def _nextid(self): - """Get the id of the next row to be written""" - # Get the nextid - nextid_data = self.txn.get("nextid".encode("ascii")) - if nextid_data: - return orjson.loads(zlib.decompress(nextid_data)) - return 1 # Removed unnecessary else (R1705) - - def count(self, selection=None, **kwargs) -> int: - """Count rows. - - See the select() method for the selection syntax. Use db.count() or - len(db) to count all rows. - """ - if selection is not None: - n = 0 - for _row in self.select(selection, **kwargs): - n += 1 - return n - return len(self.ids) - - def _load_ids(self) -> None: - """Load ids from the DB - - Since ASE db ids are mostly 1-N integers, but can be missing entries - if ids have been deleted. To save space and operating under the assumption - that there will probably not be many deletions in most OCP datasets, - we just store the deleted ids. - """ - # Load the deleted ids - deleted_ids_data = self.txn.get("deleted_ids".encode("ascii")) - if deleted_ids_data is not None: - self.deleted_ids = orjson.loads(zlib.decompress(deleted_ids_data)) - - # Reconstruct the full id list - self.ids = [i for i in range(1, self._nextid) if i not in set(self.deleted_ids)] - - -# Placeholder for AtomsToGraphs class -# This is a minimal implementation without the full functionality -class AtomsToGraphs: - """Enhanced AtomsToGraphs implementation with proper property handling.""" - - def __init__( - self, - r_edges=False, - r_pbc=True, - r_energy=False, - r_forces=False, - r_stress=False, - r_data_keys=None, - **kwargs, - ): - self.r_edges = r_edges - self.r_pbc = r_pbc - self.r_energy = r_energy - self.r_forces = r_forces - self.r_stress = r_stress - self.r_data_keys = r_data_keys or {} - self.kwargs = kwargs - - def convert(self, atoms, sid=None): - """ - Convert ASE atoms to graph data format with proper property handling. - """ - from mace.tools.torch_geometric.data import Data - - # Create a minimal data object with required properties - data = Data() - - # Set positions - data.pos = torch.tensor(atoms.get_positions(), dtype=torch.float) - - # Set atomic numbers - data.atomic_numbers = torch.tensor(atoms.get_atomic_numbers(), dtype=torch.long) - - # Set cell if available - if atoms.cell is not None: - data.cell = torch.tensor(atoms.get_cell(), dtype=torch.float) - - # Set PBC if requested - if self.r_pbc: - data.pbc = torch.tensor(atoms.get_pbc(), dtype=torch.bool) - - # Set energy if requested - if self.r_energy: - energy = self._get_property(atoms, "energy") - if energy is not None: - data.energy = torch.tensor(energy, dtype=torch.float) - - # Set forces if requested - if self.r_forces: - forces = self._get_property(atoms, "forces") - if forces is not None: - data.forces = torch.tensor(forces, dtype=torch.float) - - # Set stress if requested - if self.r_stress: - stress = self._get_property(atoms, "stress") - if stress is not None: - data.stress = torch.tensor(stress, dtype=torch.float) - - # Set sid if provided - if sid is not None: - data.sid = sid - - return data - - def _get_property(self, atoms, prop_name): - """Get property from atoms, checking custom names first then standard methods.""" - # Check if we have a custom name for this property - custom_name = self.r_data_keys.get(prop_name) - - # Try custom name in info dict - if custom_name and custom_name in atoms.info: - return atoms.info[custom_name] - - # Try custom name in arrays dict - if custom_name and custom_name in atoms.arrays: - return atoms.arrays[custom_name] - - # Try standard name in info dict - if prop_name in atoms.info: - return atoms.info[prop_name] - - # Try standard name in arrays dict - if prop_name in atoms.arrays: - return atoms.arrays[prop_name] - - # Try standard ASE methods - method_map = { - "energy": "get_potential_energy", - "forces": "get_forces", - "stress": "get_stress", - } - - if prop_name in method_map and hasattr(atoms, method_map[prop_name]): - try: - method = getattr(atoms, method_map[prop_name]) - return method() - except ( - AttributeError, - RuntimeError, - ) as exc: # Fixed W0718 by specifying exceptions - logging.debug(f"Error getting property {prop_name}: {exc}") - # Removed unnecessary pass (W0107) - - return None - - -# Placeholder for DataTransforms class -class DataTransforms: - """Minimal implementation of DataTransforms to satisfy dependencies.""" - - def __init__(self, transforms_config=None): - self.transforms_config = transforms_config or {} - - def __call__(self, data): - """Apply transforms to data""" - # No transforms applied in this minimal implementation - return data - - -class AseAtomsDataset(BaseDataset, ABC): - """ - This is an abstract Dataset that includes helpful utilities for turning - ASE atoms objects into OCP-usable data objects. This should not be instantiated directly - as get_atoms_object and load_dataset_get_ids are not implemented in this base class. - - Derived classes must add at least two things: - self.get_atoms_object(id): a function that takes an identifier and returns a corresponding atoms object - - self.load_dataset_get_ids(config: dict): This function is responsible for any initialization/loads - of the dataset and importantly must return a list of all possible identifiers that can be passed into - self.get_atoms_object(id) - - Identifiers need not be any particular type. - """ - - def __init__( - self, - config: dict, - atoms_transform: Callable[[ase.Atoms, Any], ase.Atoms] = apply_one_tags, - ) -> None: - super().__init__(config) - - a2g_args = config.get("a2g_args", {}) or {} - - # set default to False if not set by user, assuming otf_graph will be used - if "r_edges" not in a2g_args: - a2g_args["r_edges"] = False - - # Make sure we always include PBC info in the resulting atoms objects - a2g_args["r_pbc"] = True - self.a2g = AtomsToGraphs(**a2g_args) - - self.key_mapping = self.config.get("key_mapping", None) - self.transforms = DataTransforms(self.config.get("transforms", {})) - - self.atoms_transform = atoms_transform - - if self.config.get("keep_in_memory", False): - self.__getitem__ = cache(self.__getitem__) - - self.ids = self._load_dataset_get_ids(config) - self.num_samples = len(self.ids) - - if len(self.ids) == 0: - raise ValueError( - rf"No valid ase data found! \n" - f"Double check that the src path and/or glob search pattern gives ASE compatible data: {config['src']}" - ) - - def __getitem__(self, idx): # pylint: disable=method-hidden - # Handle slicing - if isinstance(idx, slice): - return [self[i] for i in range(*idx.indices(len(self)))] - - # Get atoms object via derived class method - atoms = self.get_atoms(self.ids[idx]) - - # Transform atoms object - if self.atoms_transform is not None: - atoms = self.atoms_transform( - atoms, **self.config.get("atoms_transform_args", {}) - ) - - sid = atoms.info.get("sid", self.ids[idx]) - fid = atoms.info.get("fid", torch.tensor([0])) - - # Convert to data object - data_object = self.a2g.convert(atoms, sid) - data_object.fid = fid - data_object.natoms = len(atoms) - - # apply linear reference - if self.a2g.r_energy is True and self.lin_ref is not None: - data_object.energy -= sum(self.lin_ref[data_object.atomic_numbers.long()]) - - # Transform data object - data_object = self.transforms(data_object) - - if self.key_mapping is not None: - data_object = rename_data_object_keys(data_object, self.key_mapping) - - if self.config.get("include_relaxed_energy", False): - data_object.energy_relaxed = self.get_relaxed_energy(self.ids[idx]) - - return data_object - - @abstractmethod - def get_atoms(self, idx: str | int) -> ase.Atoms: - # This function should return an ASE atoms object. - raise NotImplementedError( - "Returns an ASE atoms object. Derived classes should implement this function." - ) - - @abstractmethod - def _load_dataset_get_ids(self, config): - # This function should return a list of ids that can be used to index into the database - raise NotImplementedError( - "Every ASE dataset needs to declare a function to load the dataset and return a list of ids." - ) - - def get_relaxed_energy(self, identifier): - raise NotImplementedError( - "Reading relaxed energy from trajectory or file is not implemented with this dataset. " - "If relaxed energies are saved with the atoms info dictionary, they can be used by passing the keys in " - "the r_data_keys argument under a2g_args." - ) - - def get_metadata(self, attr, idx): - # try the parent method - metadata = super().get_metadata(attr, idx) - if metadata is not None: - return metadata - # try to resolve it here - if attr != "natoms": - return None - if isinstance(idx, (list, np.ndarray)): - return np.array([self.get_metadata(attr, i) for i in idx]) - return len(self.get_atoms(idx)) - - -class AseDBDataset(AseAtomsDataset): - """ - This Dataset connects to an ASE Database, allowing the storage of atoms objects - with a variety of backends including JSON, SQLite, and database server options. - """ - - def _load_dataset_get_ids(self, config: dict) -> list[int]: - if isinstance(config["src"], list): - filepaths = [] - for path in sorted(config["src"]): - if os.path.isdir(path): - filepaths.extend(sorted(glob(f"{path}/*"))) - elif os.path.isfile(path): - filepaths.append(path) - else: - raise RuntimeError(f"Error reading dataset in {path}!") - elif os.path.isfile(config["src"]): - filepaths = [config["src"]] - elif os.path.isdir(config["src"]): - filepaths = sorted(glob(f'{config["src"]}/*')) - else: - filepaths = sorted(glob(config["src"])) - - self.dbs = [] - - for path in filepaths: - try: - self.dbs.append(self.connect_db(path, config.get("connect_args", {}))) - except ValueError: - logging.debug( - f"Tried to connect to {path} but it's not an ASE database!" - ) - - self.select_args = config.get("select_args", {}) - if self.select_args is None: - self.select_args = {} - - # Get all unique IDs from the databases - self.db_ids = [] - for db in self.dbs: - if hasattr(db, "ids") and self.select_args == {}: - self.db_ids.append(db.ids) - else: - # this is the slow alternative - self.db_ids.append([row.id for row in db.select(**self.select_args)]) - - idlens = [len(ids) for ids in self.db_ids] - self._idlen_cumulative = np.cumsum(idlens).tolist() - - return list(range(sum(idlens))) - - def get_atoms(self, idx: int) -> ase.Atoms: - """Get atoms object corresponding to datapoint idx. - Args: - idx (int): index in dataset - - Returns: - atoms: ASE atoms corresponding to datapoint idx - """ - # Figure out which db this should be indexed from - db_idx = bisect.bisect(self._idlen_cumulative, idx) - - # Extract index of element within that db - el_idx = idx - if db_idx != 0: - el_idx = idx - self._idlen_cumulative[db_idx - 1] - assert el_idx >= 0 - - # Use a wrapper method to avoid protected access warning - atoms_row = self.get_row_from_db(db_idx, el_idx) - - # Convert to atoms object - atoms = atoms_row.toatoms() - - # Put data back into atoms info - if isinstance(atoms_row.data, dict): - atoms.info.update(atoms_row.data) - - # Add key-value pairs directly to atoms.info - if hasattr(atoms_row, "key_value_pairs") and atoms_row.key_value_pairs: - atoms.info.update(atoms_row.key_value_pairs) - - # Create a SinglePointCalculator to attach energy, forces and stress to atoms - calc_kwargs = {} - - # Check for energy, forces, stress in atoms_row and store in info & calc_kwargs - for prop in ["energy", "forces", "stress", "free_energy"]: - if hasattr(atoms_row, prop) and getattr(atoms_row, prop) is not None: - value = getattr(atoms_row, prop) - calc_kwargs[prop] = value - atoms.info[prop] = value - - # If we have custom data mappings, copy the standard properties to the custom names - a2g_args = self.config.get("a2g_args", {}) or {} - r_data_keys = a2g_args.get("r_data_keys", {}) - if r_data_keys: - # Map from standard names to custom names (in reverse of how they'll be used) - for custom_key, standard_key in r_data_keys.items(): - if standard_key in atoms.info: - atoms.info[custom_key] = atoms.info[standard_key] - elif standard_key in atoms.arrays: - atoms.arrays[custom_key] = atoms.arrays[standard_key] - - # Create calculator if we have any properties - if calc_kwargs: - from ase.calculators.singlepoint import SinglePointCalculator - - calc = SinglePointCalculator(atoms, **calc_kwargs) - atoms.calc = calc - - return atoms - - def get_row_from_db(self, db_idx, el_idx): - """Get a row from the database at the given indices.""" - db = self.dbs[db_idx] - row_id = self.db_ids[db_idx][el_idx] - if isinstance(db, LMDBDatabase): - return db._get_row(row_id) # pylint: disable=protected-access - return db.get(row_id) - - @staticmethod - def connect_db( - address: str | Path, connect_args: dict | None = None - ) -> ase.db.core.Database: - if connect_args is None: - connect_args = {} - db_type = connect_args.get("type", "extract_from_name") - if db_type in ("lmdb", "aselmdb") or ( - db_type == "extract_from_name" - and str(address).rsplit(".", maxsplit=1)[-1] in ("lmdb", "aselmdb") - ): - return LMDBDatabase(address, readonly=True, **connect_args) - - return ase.db.connect(address, **connect_args) - - def __del__(self): - for db in self.dbs: - if hasattr(db, "close"): - db.close() - - def sample_property_metadata( - self, - ) -> dict: # Removed unused argument num_samples (W0613) - """ - Sample property metadata from the database. - - This method was previously using the copy module which is now removed. - """ - logging.warning( - "You specified a folder of ASE dbs, so it's impossible to know which metadata to use. Using the first!" - ) - if self.dbs[0].metadata == {}: - return {} - - # Fixed unnecessary comprehension (R1721) - return dict(self.dbs[0].metadata.items()) diff --git a/mace-bench/3rdparty/mace/mace/tools/finetuning_utils.py b/mace-bench/3rdparty/mace/mace/tools/finetuning_utils.py deleted file mode 100644 index 8df0b0d1f7309995ea1417264190d5f7749c2acd..0000000000000000000000000000000000000000 --- a/mace-bench/3rdparty/mace/mace/tools/finetuning_utils.py +++ /dev/null @@ -1,204 +0,0 @@ -import torch - -from mace.tools.utils import AtomicNumberTable - - -def load_foundations_elements( - model: torch.nn.Module, - model_foundations: torch.nn.Module, - table: AtomicNumberTable, - load_readout=False, - use_shift=True, - use_scale=True, - max_L=2, -): - """ - Load the foundations of a model into a model for fine-tuning. - """ - assert model_foundations.r_max == model.r_max - z_table = AtomicNumberTable([int(z) for z in model_foundations.atomic_numbers]) - model_heads = model.heads - new_z_table = table - num_species_foundations = len(z_table.zs) - num_channels_foundation = ( - model_foundations.node_embedding.linear.weight.shape[0] - // num_species_foundations - ) - indices_weights = [z_table.z_to_index(z) for z in new_z_table.zs] - num_radial = model.radial_embedding.out_dim - num_species = len(indices_weights) - max_ell = model.spherical_harmonics._lmax # pylint: disable=protected-access - model.node_embedding.linear.weight = torch.nn.Parameter( - model_foundations.node_embedding.linear.weight.view( - num_species_foundations, -1 - )[indices_weights, :] - .flatten() - .clone() - / (num_species_foundations / num_species) ** 0.5 - ) - if model.radial_embedding.bessel_fn.__class__.__name__ == "BesselBasis": - model.radial_embedding.bessel_fn.bessel_weights = torch.nn.Parameter( - model_foundations.radial_embedding.bessel_fn.bessel_weights.clone() - ) - for i in range(int(model.num_interactions)): - model.interactions[i].linear_up.weight = torch.nn.Parameter( - model_foundations.interactions[i].linear_up.weight.clone() - ) - model.interactions[i].avg_num_neighbors = model_foundations.interactions[ - i - ].avg_num_neighbors - for j in range(4): # Assuming 4 layers in conv_tp_weights, - layer_name = f"layer{j}" - if j == 0: - getattr(model.interactions[i].conv_tp_weights, layer_name).weight = ( - torch.nn.Parameter( - getattr( - model_foundations.interactions[i].conv_tp_weights, - layer_name, - ) - .weight[:num_radial, :] - .clone() - ) - ) - else: - getattr(model.interactions[i].conv_tp_weights, layer_name).weight = ( - torch.nn.Parameter( - getattr( - model_foundations.interactions[i].conv_tp_weights, - layer_name, - ).weight.clone() - ) - ) - - model.interactions[i].linear.weight = torch.nn.Parameter( - model_foundations.interactions[i].linear.weight.clone() - ) - if model.interactions[i].__class__.__name__ in [ - "RealAgnosticResidualInteractionBlock", - "RealAgnosticDensityResidualInteractionBlock", - ]: - model.interactions[i].skip_tp.weight = torch.nn.Parameter( - model_foundations.interactions[i] - .skip_tp.weight.reshape( - num_channels_foundation, - num_species_foundations, - num_channels_foundation, - )[:, indices_weights, :] - .flatten() - .clone() - / (num_species_foundations / num_species) ** 0.5 - ) - else: - model.interactions[i].skip_tp.weight = torch.nn.Parameter( - model_foundations.interactions[i] - .skip_tp.weight.reshape( - num_channels_foundation, - (max_ell + 1), - num_species_foundations, - num_channels_foundation, - )[:, :, indices_weights, :] - .flatten() - .clone() - / (num_species_foundations / num_species) ** 0.5 - ) - if model.interactions[i].__class__.__name__ in [ - "RealAgnosticDensityInteractionBlock", - "RealAgnosticDensityResidualInteractionBlock", - ]: - # Assuming only 1 layer in density_fn - getattr(model.interactions[i].density_fn, "layer0").weight = ( - torch.nn.Parameter( - getattr( - model_foundations.interactions[i].density_fn, - "layer0", - ).weight.clone() - ) - ) - # Transferring products - for i in range(2): # Assuming 2 products modules - max_range = max_L + 1 if i == 0 else 1 - for j in range(max_range): # Assuming 3 contractions in symmetric_contractions - model.products[i].symmetric_contractions.contractions[j].weights_max = ( - torch.nn.Parameter( - model_foundations.products[i] - .symmetric_contractions.contractions[j] - .weights_max[indices_weights, :, :] - .clone() - ) - ) - - for k in range(2): # Assuming 2 weights in each contraction - model.products[i].symmetric_contractions.contractions[j].weights[k] = ( - torch.nn.Parameter( - model_foundations.products[i] - .symmetric_contractions.contractions[j] - .weights[k][indices_weights, :, :] - .clone() - ) - ) - - model.products[i].linear.weight = torch.nn.Parameter( - model_foundations.products[i].linear.weight.clone() - ) - - if load_readout: - # Transferring readouts - model_readouts_zero_linear_weight = model.readouts[0].linear.weight.clone() - model_readouts_zero_linear_weight = ( - model_foundations.readouts[0] - .linear.weight.view(num_channels_foundation, -1) - .repeat(1, len(model_heads)) - .flatten() - .clone() - ) - model.readouts[0].linear.weight = torch.nn.Parameter( - model_readouts_zero_linear_weight - ) - - shape_input_1 = ( - model_foundations.readouts[1].linear_1.__dict__["irreps_out"].num_irreps - ) - shape_output_1 = model.readouts[1].linear_1.__dict__["irreps_out"].num_irreps - model_readouts_one_linear_1_weight = model.readouts[1].linear_1.weight.clone() - model_readouts_one_linear_1_weight = ( - model_foundations.readouts[1] - .linear_1.weight.view(num_channels_foundation, -1) - .repeat(1, len(model_heads)) - .flatten() - .clone() - ) - model.readouts[1].linear_1.weight = torch.nn.Parameter( - model_readouts_one_linear_1_weight - ) - model_readouts_one_linear_2_weight = model.readouts[1].linear_2.weight.clone() - model_readouts_one_linear_2_weight = model_foundations.readouts[ - 1 - ].linear_2.weight.view(shape_input_1, -1).repeat( - len(model_heads), len(model_heads) - ).flatten().clone() / ( - ((shape_input_1) / (shape_output_1)) ** 0.5 - ) - model.readouts[1].linear_2.weight = torch.nn.Parameter( - model_readouts_one_linear_2_weight - ) - if model_foundations.scale_shift is not None: - if use_scale: - model.scale_shift.scale = model_foundations.scale_shift.scale.repeat( - len(model_heads) - ).clone() - if use_shift: - model.scale_shift.shift = model_foundations.scale_shift.shift.repeat( - len(model_heads) - ).clone() - return model - - -def load_foundations( - model, - model_foundations, -): - for name, param in model_foundations.named_parameters(): - if name in model.state_dict().keys(): - if "readouts" not in name: - model.state_dict()[name].copy_(param) - return model diff --git a/mace-bench/3rdparty/mace/mace/tools/model_script_utils.py b/mace-bench/3rdparty/mace/mace/tools/model_script_utils.py deleted file mode 100644 index c9de08b9f34abb957f3407fedd32e13ea68779d7..0000000000000000000000000000000000000000 --- a/mace-bench/3rdparty/mace/mace/tools/model_script_utils.py +++ /dev/null @@ -1,265 +0,0 @@ -import ast -import logging - -import numpy as np -from e3nn import o3 - -from mace import modules -from mace.tools.finetuning_utils import load_foundations_elements -from mace.tools.scripts_utils import extract_config_mace_model -from mace.tools.utils import AtomicNumberTable - - -def configure_model( - args, - train_loader, - atomic_energies, - model_foundation=None, - heads=None, - z_table=None, - head_configs=None, -): - # Selecting outputs - compute_virials = args.loss == "virials" - compute_stress = args.loss in ("stress", "huber", "universal") - - if compute_virials: - args.compute_virials = True - args.error_table = "PerAtomRMSEstressvirials" - elif compute_stress: - args.compute_stress = True - args.error_table = "PerAtomRMSEstressvirials" - - output_args = { - "energy": args.compute_energy, - "forces": args.compute_forces, - "virials": compute_virials, - "stress": compute_stress, - "dipoles": args.compute_dipole, - } - logging.info( - f"During training the following quantities will be reported: {', '.join([f'{report}' for report, value in output_args.items() if value])}" - ) - logging.info("===========MODEL DETAILS===========") - - if args.scaling == "no_scaling": - args.std = 1.0 - if head_configs is not None: - for head_config in head_configs: - head_config.std = 1.0 - logging.info("No scaling selected") - - if ( - head_configs is not None - and args.std is not None - and not isinstance(args.std, list) - ): - atomic_inter_scale = [] - for head_config in head_configs: - if hasattr(head_config, "std") and head_config.std is not None: - atomic_inter_scale.append(head_config.std) - elif args.std is not None: - atomic_inter_scale.append( - args.std if isinstance(args.std, float) else 1.0 - ) - args.std = atomic_inter_scale - - elif (args.mean is None or args.std is None) and args.model != "AtomicDipolesMACE": - args.mean, args.std = modules.scaling_classes[args.scaling]( - train_loader, atomic_energies - ) - - # Build model - if model_foundation is not None and args.model in ["MACE", "ScaleShiftMACE"]: - logging.info("Loading FOUNDATION model") - model_config_foundation = extract_config_mace_model(model_foundation) - model_config_foundation["atomic_energies"] = atomic_energies - - if args.foundation_model_elements: - foundation_z_table = AtomicNumberTable( - [int(z) for z in model_foundation.atomic_numbers] - ) - model_config_foundation["atomic_numbers"] = foundation_z_table.zs - model_config_foundation["num_elements"] = len(foundation_z_table) - z_table = foundation_z_table - logging.info( - f"Using all elements from foundation model: {foundation_z_table.zs}" - ) - else: - model_config_foundation["atomic_numbers"] = z_table.zs - model_config_foundation["num_elements"] = len(z_table) - logging.info(f"Using filtered elements: {z_table.zs}") - - args.max_L = model_config_foundation["hidden_irreps"].lmax - - if args.model == "MACE" and model_foundation.__class__.__name__ == "MACE": - model_config_foundation["atomic_inter_shift"] = [0.0] * len(heads) - else: - model_config_foundation["atomic_inter_shift"] = ( - _determine_atomic_inter_shift(args.mean, heads) - ) - model_config_foundation["atomic_inter_scale"] = [1.0] * len(heads) - args.avg_num_neighbors = model_config_foundation["avg_num_neighbors"] - args.model = "FoundationMACE" - model_config_foundation["heads"] = heads - model_config = model_config_foundation - - logging.info("Model configuration extracted from foundation model") - logging.info("Using universal loss function for fine-tuning") - logging.info( - f"Message passing with hidden irreps {model_config_foundation['hidden_irreps']})" - ) - logging.info( - f"{model_config_foundation['num_interactions']} layers, each with correlation order: {model_config_foundation['correlation']} (body order: {model_config_foundation['correlation']+1}) and spherical harmonics up to: l={model_config_foundation['max_ell']}" - ) - logging.info( - f"Radial cutoff: {model_config_foundation['r_max']} A (total receptive field for each atom: {model_config_foundation['r_max'] * model_config_foundation['num_interactions']} A)" - ) - logging.info( - f"Distance transform for radial basis functions: {model_config_foundation['distance_transform']}" - ) - else: - logging.info("Building model") - logging.info( - f"Message passing with {args.num_channels} channels and max_L={args.max_L} ({args.hidden_irreps})" - ) - logging.info( - f"{args.num_interactions} layers, each with correlation order: {args.correlation} (body order: {args.correlation+1}) and spherical harmonics up to: l={args.max_ell}" - ) - logging.info( - f"{args.num_radial_basis} radial and {args.num_cutoff_basis} basis functions" - ) - logging.info( - f"Radial cutoff: {args.r_max} A (total receptive field for each atom: {args.r_max * args.num_interactions} A)" - ) - logging.info( - f"Distance transform for radial basis functions: {args.distance_transform}" - ) - - assert ( - len({irrep.mul for irrep in o3.Irreps(args.hidden_irreps)}) == 1 - ), "All channels must have the same dimension, use the num_channels and max_L keywords to specify the number of channels and the maximum L" - - logging.info(f"Hidden irreps: {args.hidden_irreps}") - - model_config = dict( - r_max=args.r_max, - num_bessel=args.num_radial_basis, - num_polynomial_cutoff=args.num_cutoff_basis, - max_ell=args.max_ell, - interaction_cls=modules.interaction_classes[args.interaction], - num_interactions=args.num_interactions, - num_elements=len(z_table), - hidden_irreps=o3.Irreps(args.hidden_irreps), - atomic_energies=atomic_energies, - avg_num_neighbors=args.avg_num_neighbors, - atomic_numbers=z_table.zs, - ) - model_config_foundation = None - - model = _build_model(args, model_config, model_config_foundation, heads) - - if model_foundation is not None: - model = load_foundations_elements( - model, - model_foundation, - z_table, - load_readout=args.foundation_filter_elements, - max_L=args.max_L, - ) - - return model, output_args - - -def _determine_atomic_inter_shift(mean, heads): - if isinstance(mean, np.ndarray): - if mean.size == 1: - return mean.item() - if mean.size == len(heads): - return mean.tolist() - logging.info("Mean not in correct format, using default value of 0.0") - return [0.0] * len(heads) - if isinstance(mean, list) and len(mean) == len(heads): - return mean - if isinstance(mean, float): - return [mean] * len(heads) - logging.info("Mean not in correct format, using default value of 0.0") - return [0.0] * len(heads) - - -def _build_model( - args, model_config, model_config_foundation, heads -): # pylint: disable=too-many-return-statements - if args.model == "MACE": - if args.interaction_first not in [ - "RealAgnosticInteractionBlock", - "RealAgnosticDensityInteractionBlock", - ]: - args.interaction_first = "RealAgnosticInteractionBlock" - return modules.ScaleShiftMACE( - **model_config, - pair_repulsion=args.pair_repulsion, - distance_transform=args.distance_transform, - correlation=args.correlation, - gate=modules.gate_dict[args.gate], - interaction_cls_first=modules.interaction_classes[args.interaction_first], - MLP_irreps=o3.Irreps(args.MLP_irreps), - atomic_inter_scale=args.std, - atomic_inter_shift=[0.0] * len(heads), - radial_MLP=ast.literal_eval(args.radial_MLP), - radial_type=args.radial_type, - heads=heads, - ) - if args.model == "ScaleShiftMACE": - return modules.ScaleShiftMACE( - **model_config, - pair_repulsion=args.pair_repulsion, - distance_transform=args.distance_transform, - correlation=args.correlation, - gate=modules.gate_dict[args.gate], - interaction_cls_first=modules.interaction_classes[args.interaction_first], - MLP_irreps=o3.Irreps(args.MLP_irreps), - atomic_inter_scale=args.std, - atomic_inter_shift=args.mean, - radial_MLP=ast.literal_eval(args.radial_MLP), - radial_type=args.radial_type, - heads=heads, - ) - if args.model == "FoundationMACE": - return modules.ScaleShiftMACE(**model_config_foundation) - if args.model == "ScaleShiftBOTNet": - # say it is deprecated - raise RuntimeError("ScaleShiftBOTNet is deprecated, use MACE instead") - if args.model == "BOTNet": - raise RuntimeError("BOTNet is deprecated, use MACE instead") - if args.model == "AtomicDipolesMACE": - assert args.loss == "dipole", "Use dipole loss with AtomicDipolesMACE model" - assert ( - args.error_table == "DipoleRMSE" - ), "Use error_table DipoleRMSE with AtomicDipolesMACE model" - return modules.AtomicDipolesMACE( - **model_config, - correlation=args.correlation, - gate=modules.gate_dict[args.gate], - interaction_cls_first=modules.interaction_classes[ - "RealAgnosticInteractionBlock" - ], - MLP_irreps=o3.Irreps(args.MLP_irreps), - ) - if args.model == "EnergyDipolesMACE": - assert ( - args.loss == "energy_forces_dipole" - ), "Use energy_forces_dipole loss with EnergyDipolesMACE model" - assert ( - args.error_table == "EnergyDipoleRMSE" - ), "Use error_table EnergyDipoleRMSE with AtomicDipolesMACE model" - return modules.EnergyDipolesMACE( - **model_config, - correlation=args.correlation, - gate=modules.gate_dict[args.gate], - interaction_cls_first=modules.interaction_classes[ - "RealAgnosticInteractionBlock" - ], - MLP_irreps=o3.Irreps(args.MLP_irreps), - ) - raise RuntimeError(f"Unknown model: '{args.model}'") diff --git a/mace-bench/3rdparty/mace/mace/tools/multihead_tools.py b/mace-bench/3rdparty/mace/mace/tools/multihead_tools.py deleted file mode 100644 index f321af390f8d45a63b68a62c1a95f49d88fa7756..0000000000000000000000000000000000000000 --- a/mace-bench/3rdparty/mace/mace/tools/multihead_tools.py +++ /dev/null @@ -1,200 +0,0 @@ -import argparse -import ast -import dataclasses -import logging -import os -import urllib.request -from pathlib import Path -from typing import Any, Dict, List, Optional, Union - -import torch - -from mace.cli.fine_tuning_select import ( - FilteringType, - SelectionSettings, - SubselectType, - select_samples, -) -from mace.data import KeySpecification -from mace.tools.scripts_utils import SubsetCollection, get_dataset_from_xyz - - -@dataclasses.dataclass -class HeadConfig: - head_name: str - key_specification: KeySpecification - train_file: Optional[Union[str, List[str]]] = None - valid_file: Optional[Union[str, List[str]]] = None - test_file: Optional[str] = None - test_dir: Optional[str] = None - E0s: Optional[Any] = None - statistics_file: Optional[str] = None - valid_fraction: Optional[float] = None - config_type_weights: Optional[Dict[str, float]] = None - keep_isolated_atoms: Optional[bool] = None - atomic_numbers: Optional[Union[List[int], List[str]]] = None - mean: Optional[float] = None - std: Optional[float] = None - avg_num_neighbors: Optional[float] = None - compute_avg_num_neighbors: Optional[bool] = None - collections: Optional[SubsetCollection] = None - train_loader: Optional[torch.utils.data.DataLoader] = None - z_table: Optional[Any] = None - atomic_energies_dict: Optional[Dict[str, float]] = None - - -def dict_head_to_dataclass( - head: Dict[str, Any], head_name: str, args: argparse.Namespace -) -> HeadConfig: - """Convert head dictionary to HeadConfig dataclass.""" - # parser+head args that have no defaults but are required - if (args.train_file is None) and (head.get("train_file", None) is None): - raise ValueError( - "train file is not set in the head config yaml or via command line args" - ) - - return HeadConfig( - head_name=head_name, - train_file=head.get("train_file", args.train_file), - valid_file=head.get("valid_file", args.valid_file), - test_file=head.get("test_file", None), - test_dir=head.get("test_dir", None), - E0s=head.get("E0s", args.E0s), - statistics_file=head.get("statistics_file", args.statistics_file), - valid_fraction=head.get("valid_fraction", args.valid_fraction), - config_type_weights=head.get("config_type_weights", args.config_type_weights), - compute_avg_num_neighbors=head.get( - "compute_avg_num_neighbors", args.compute_avg_num_neighbors - ), - atomic_numbers=head.get("atomic_numbers", args.atomic_numbers), - mean=head.get("mean", args.mean), - std=head.get("std", args.std), - avg_num_neighbors=head.get("avg_num_neighbors", args.avg_num_neighbors), - key_specification=head["key_specification"], - keep_isolated_atoms=head.get("keep_isolated_atoms", args.keep_isolated_atoms), - ) - - -def prepare_default_head(args: argparse.Namespace) -> Dict[str, Any]: - """Prepare a default head from args.""" - return { - "Default": { - "train_file": args.train_file, - "valid_file": args.valid_file, - "test_file": args.test_file, - "test_dir": args.test_dir, - "E0s": args.E0s, - "statistics_file": args.statistics_file, - "key_specification": args.key_specification, - "valid_fraction": args.valid_fraction, - "config_type_weights": args.config_type_weights, - "keep_isolated_atoms": args.keep_isolated_atoms, - } - } - - -def prepare_pt_head( - args: argparse.Namespace, - pt_keyspec: KeySpecification, - foundation_model_num_neighbours: float, -) -> Dict[str, Any]: - """Prepare a pretraining head from args.""" - if ( - args.foundation_model in ["small", "medium", "large"] - or args.pt_train_file == "mp" - ): - logging.info( - "Using foundation model for multiheads finetuning with Materials Project data" - ) - pt_keyspec.update( - info_keys={"energy": "energy", "stress": "stress"}, - arrays_keys={"forces": "forces"}, - ) - pt_head = { - "train_file": "mp", - "E0s": "foundation", - "statistics_file": None, - "key_specification": pt_keyspec, - "avg_num_neighbors": foundation_model_num_neighbours, - "compute_avg_num_neighbors": False, - } - else: - pt_head = { - "train_file": args.pt_train_file, - "valid_file": args.pt_valid_file, - "E0s": "foundation", - "statistics_file": args.statistics_file, - "valid_fraction": args.valid_fraction, - "key_specification": pt_keyspec, - "avg_num_neighbors": foundation_model_num_neighbours, - "keep_isolated_atoms": args.keep_isolated_atoms, - "compute_avg_num_neighbors": False, - } - - return pt_head - - -def assemble_mp_data( - args: argparse.Namespace, - head_config_pt: HeadConfig, - tag: str, -) -> SubsetCollection: - """Assemble Materials Project data for fine-tuning.""" - try: - checkpoint_url = "https://github.com/ACEsuit/mace-mp/releases/download/mace_mp_0b/mp_traj_combined.xyz" - cache_dir = ( - Path(os.environ.get("XDG_CACHE_HOME", "~/")).expanduser() / ".cache/mace" - ) - checkpoint_url_name = "".join( - c for c in os.path.basename(checkpoint_url) if c.isalnum() or c in "_" - ) - cached_dataset_path = f"{cache_dir}/{checkpoint_url_name}" - if not os.path.isfile(cached_dataset_path): - os.makedirs(cache_dir, exist_ok=True) - # download and save to disk - logging.info("Downloading MP structures for finetuning") - _, http_msg = urllib.request.urlretrieve( - checkpoint_url, cached_dataset_path - ) - if "Content-Type: text/html" in http_msg: - raise RuntimeError( - f"Dataset download failed, please check the URL {checkpoint_url}" - ) - logging.info(f"Materials Project dataset to {cached_dataset_path}") - output = f"mp_finetuning-{tag}.xyz" - atomic_numbers = ( - ast.literal_eval(args.atomic_numbers) - if args.atomic_numbers is not None - else None - ) - settings = SelectionSettings( - configs_pt=cached_dataset_path, - output=f"mp_finetuning-{tag}.xyz", - atomic_numbers=atomic_numbers, - num_samples=args.num_samples_pt, - seed=args.seed, - head_pt="pbe_mp", - weight_pt=args.weight_pt_head, - filtering_type=FilteringType(args.filter_type_pt), - subselect=SubselectType(args.subselect_pt), - default_dtype=args.default_dtype, - ) - select_samples(settings) - head_config_pt.train_file = [output] - collections_mp, _ = get_dataset_from_xyz( - work_dir=args.work_dir, - train_path=output, - valid_path=None, - valid_fraction=args.valid_fraction, - config_type_weights=None, - test_path=None, - seed=args.seed, - key_specification=head_config_pt.key_specification, - head_name="pt_head", - keep_isolated_atoms=args.keep_isolated_atoms, - ) - return collections_mp - except Exception as exc: - raise RuntimeError( - "Model or descriptors download failed and no local model found" - ) from exc diff --git a/mace-bench/3rdparty/mace/mace/tools/run_train_utils.py b/mace-bench/3rdparty/mace/mace/tools/run_train_utils.py deleted file mode 100644 index ce37e0edc345f7367eac550af822e6ee03c7e9f4..0000000000000000000000000000000000000000 --- a/mace-bench/3rdparty/mace/mace/tools/run_train_utils.py +++ /dev/null @@ -1,217 +0,0 @@ -import logging -import os -from pathlib import Path -from typing import Any, List, Optional, Union - -import torch -from torch.utils.data import ConcatDataset - -from mace import data -from mace.tools.scripts_utils import check_path_ase_read -from mace.tools.torch_geometric.dataset import Dataset -from mace.tools.utils import AtomicNumberTable - - -def normalize_file_paths(file_paths: Union[str, List[str]]) -> List[str]: - """ - Normalize file paths to a list format. - - Args: - file_paths: Either a string or a list of strings representing file paths - - Returns: - A list of file paths - """ - if isinstance(file_paths, str): - return [file_paths] - if isinstance(file_paths, list): - return file_paths - raise ValueError(f"Unexpected file paths format: {type(file_paths)}") - - -def load_dataset_for_path( - file_path: Union[str, Path, List[str]], - r_max: float, - z_table: AtomicNumberTable, - heads: List[str], - head_config: Any, - collection: Optional[Any] = None, -) -> Union[Dataset, List]: - """ - Load a dataset from a file path based on its format. - - Args: - file_path: Path to the dataset file - r_max: Cutoff radius - z_table: Atomic number table - heads: List of head names - head_name: Current head name - **kwargs: Additional arguments - - Returns: - Loaded dataset - """ - if isinstance(file_path, list): - if len(file_path) == 1: - file_path = file_path[0] - if isinstance(file_path, list): - is_ase_readable = all(check_path_ase_read(p) for p in file_path) - if not is_ase_readable: - raise ValueError( - "Not all paths in the list are ASE readable, not supported" - ) - if isinstance(file_path, str): - is_ase_readable = check_path_ase_read(file_path) - - if is_ase_readable: - assert ( - collection is not None - ), "Collection must be provided for ASE readable files" - return [ - data.AtomicData.from_config( - config, z_table=z_table, cutoff=r_max, heads=heads - ) - for config in collection - ] - - filepath = Path(file_path) - if filepath.is_dir(): - - if filepath.name.endswith("_lmdb") or any( - f.endswith(".lmdb") or f.endswith(".aselmdb") for f in os.listdir(filepath) - ): - logging.info(f"Loading LMDB dataset from {file_path}") - return data.LMDBDataset( - file_path, - r_max=r_max, - z_table=z_table, - heads=heads, - head=head_config.head_name, - ) - - h5_files = list(filepath.glob("*.h5")) + list(filepath.glob("*.hdf5")) - if h5_files: - logging.info(f"Loading HDF5 dataset from directory {file_path}") - try: - return data.dataset_from_sharded_hdf5( - file_path, - r_max=r_max, - z_table=z_table, - heads=heads, - head=head_config.head_name, - ) - except Exception as e: - logging.error(f"Error loading sharded HDF5 dataset: {e}") - raise - - if "lmdb" in str(filepath).lower() or "aselmdb" in str(filepath).lower(): - logging.info(f"Loading LMDB dataset based on path name: {file_path}") - return data.LMDBDataset( - file_path, - r_max=r_max, - z_table=z_table, - heads=heads, - head=head_config.head_name, - ) - - logging.info(f"Attempting to load directory as HDF5 dataset: {file_path}") - try: - return data.dataset_from_sharded_hdf5( - file_path, - r_max=r_max, - z_table=z_table, - heads=heads, - head=head_config.head_name, - ) - except Exception as e: - logging.error(f"Error loading as sharded HDF5: {e}") - raise - - suffix = filepath.suffix.lower() - if suffix in (".h5", ".hdf5"): - logging.info(f"Loading single HDF5 file: {file_path}") - return data.HDF5Dataset( - file_path, - r_max=r_max, - z_table=z_table, - heads=heads, - head=head_config.head_name, - ) - - if suffix in (".lmdb", ".aselmdb", ".db"): - logging.info(f"Loading single LMDB file: {file_path}") - return data.LMDBDataset( - file_path, - r_max=r_max, - z_table=z_table, - heads=heads, - head=head_config.head_name, - ) - - logging.info(f"Attempting to load as LMDB: {file_path}") - return data.LMDBDataset( - file_path, - r_max=r_max, - z_table=z_table, - heads=heads, - head=head_config.head_name, - ) - - -def combine_datasets(datasets, head_name): - """ - Combine multiple datasets which might be of different types. - - Args: - datasets: List of datasets (can be mixed types) - head_name: Name of the current head - - Returns: - Combined dataset - """ - if not datasets: - return [] - - if all(isinstance(ds, list) for ds in datasets): - logging.info(f"Combining {len(datasets)} list datasets for head '{head_name}'") - return [item for sublist in datasets for item in sublist] - - if all(not isinstance(ds, list) for ds in datasets): - logging.info( - f"Combining {len(datasets)} Dataset objects for head '{head_name}'" - ) - return ConcatDataset(datasets) if len(datasets) > 1 else datasets[0] - - logging.info(f"Converting mixed dataset types for head '{head_name}'") - - try: - all_items = [] - for ds in datasets: - if isinstance(ds, list): - all_items.extend(ds) - else: - all_items.extend([ds[i] for i in range(len(ds))]) - return all_items - except Exception as e: # pylint: disable=W0703 - logging.warning(f"Failed to convert mixed datasets to list: {e}") - - try: - dataset_objects = [] - for ds in datasets: - if isinstance(ds, list): - from torch.utils.data import TensorDataset - - # Convert list to a Dataset - dataset_objects.append( - TensorDataset(*[torch.tensor([i]) for i in range(len(ds))]) - ) - else: - dataset_objects.append(ds) - return ConcatDataset(dataset_objects) - except Exception as e: # pylint: disable=W0703 - logging.warning(f"Failed to convert mixed datasets to ConcatDataset: {e}") - - logging.warning( - "Could not combine datasets of different types. Using only the first dataset." - ) - return datasets[0] diff --git a/mace-bench/3rdparty/mace/mace/tools/scatter.py b/mace-bench/3rdparty/mace/mace/tools/scatter.py deleted file mode 100644 index 7e1139a999e5d741b0b57f500d1d349a10092db9..0000000000000000000000000000000000000000 --- a/mace-bench/3rdparty/mace/mace/tools/scatter.py +++ /dev/null @@ -1,112 +0,0 @@ -"""basic scatter_sum operations from torch_scatter from -https://github.com/mir-group/pytorch_runstats/blob/main/torch_runstats/scatter_sum.py -Using code from https://github.com/rusty1s/pytorch_scatter, but cut down to avoid a dependency. -PyTorch plans to move these features into the main repo, but until then, -to make installation simpler, we need this pure python set of wrappers -that don't require installing PyTorch C++ extensions. -See https://github.com/pytorch/pytorch/issues/63780. -""" - -from typing import Optional - -import torch - - -def _broadcast(src: torch.Tensor, other: torch.Tensor, dim: int): - if dim < 0: - dim = other.dim() + dim - if src.dim() == 1: - for _ in range(0, dim): - src = src.unsqueeze(0) - for _ in range(src.dim(), other.dim()): - src = src.unsqueeze(-1) - src = src.expand_as(other) - return src - - -def scatter_sum( - src: torch.Tensor, - index: torch.Tensor, - dim: int = -1, - out: Optional[torch.Tensor] = None, - dim_size: Optional[int] = None, - reduce: str = "sum", -) -> torch.Tensor: - assert reduce == "sum" # for now, TODO - index = _broadcast(index, src, dim) - if out is None: - size = list(src.size()) - if dim_size is not None: - size[dim] = dim_size - elif index.numel() == 0: - size[dim] = 0 - else: - size[dim] = int(index.max()) + 1 - out = torch.zeros(size, dtype=src.dtype, device=src.device) - return out.scatter_add_(dim, index, src) - else: - return out.scatter_add_(dim, index, src) - - -def scatter_std( - src: torch.Tensor, - index: torch.Tensor, - dim: int = -1, - out: Optional[torch.Tensor] = None, - dim_size: Optional[int] = None, - unbiased: bool = True, -) -> torch.Tensor: - if out is not None: - dim_size = out.size(dim) - - if dim < 0: - dim = src.dim() + dim - - count_dim = dim - if index.dim() <= dim: - count_dim = index.dim() - 1 - - ones = torch.ones(index.size(), dtype=src.dtype, device=src.device) - count = scatter_sum(ones, index, count_dim, dim_size=dim_size) - - index = _broadcast(index, src, dim) - tmp = scatter_sum(src, index, dim, dim_size=dim_size) - count = _broadcast(count, tmp, dim).clamp(1) - mean = tmp.div(count) - - var = src - mean.gather(dim, index) - var = var * var - out = scatter_sum(var, index, dim, out, dim_size) - - if unbiased: - count = count.sub(1).clamp_(1) - out = out.div(count + 1e-6).sqrt() - - return out - - -def scatter_mean( - src: torch.Tensor, - index: torch.Tensor, - dim: int = -1, - out: Optional[torch.Tensor] = None, - dim_size: Optional[int] = None, -) -> torch.Tensor: - out = scatter_sum(src, index, dim, out, dim_size) - dim_size = out.size(dim) - - index_dim = dim - if index_dim < 0: - index_dim = index_dim + src.dim() - if index.dim() <= index_dim: - index_dim = index.dim() - 1 - - ones = torch.ones(index.size(), dtype=src.dtype, device=src.device) - count = scatter_sum(ones, index, index_dim, None, dim_size) - count[count < 1] = 1 - count = _broadcast(count, out, dim) - if out.is_floating_point(): - out.true_divide_(count) - else: - out.div_(count, rounding_mode="floor") - return out diff --git a/mace-bench/3rdparty/mace/mace/tools/scripts_utils.py b/mace-bench/3rdparty/mace/mace/tools/scripts_utils.py deleted file mode 100644 index bb7f79efe84cf8e3c81237bdb34e31f28fc9ca13..0000000000000000000000000000000000000000 --- a/mace-bench/3rdparty/mace/mace/tools/scripts_utils.py +++ /dev/null @@ -1,888 +0,0 @@ -########################################################################################### -# Training utils -# Authors: David Kovacs, Ilyes Batatia -# This program is distributed under the MIT License (see MIT.md) -########################################################################################### - -import argparse -import ast -import dataclasses -import json -import logging -import os -from pathlib import Path -from typing import Any, Dict, List, Optional, Tuple, Union - -import numpy as np -import torch -import torch.distributed -from e3nn import o3 -from torch.optim.swa_utils import SWALR, AveragedModel - -from mace import data, modules, tools -from mace.data import KeySpecification -from mace.tools.train import SWAContainer - - -@dataclasses.dataclass -class SubsetCollection: - train: data.Configurations - valid: data.Configurations - tests: List[Tuple[str, data.Configurations]] - - -def log_dataset_contents(dataset: data.Configurations, dataset_name: str) -> None: - log_string = f"{dataset_name} [" - for prop_name in dataset[0].properties.keys(): - if prop_name == "dipole": - log_string += f"{prop_name} components: {int(np.sum([np.sum(config.property_weights[prop_name]) for config in dataset]))}, " - else: - log_string += f"{prop_name}: {int(np.sum([config.property_weights[prop_name] for config in dataset]))}, " - log_string = log_string[:-2] + "]" - logging.info(log_string) - - -def get_dataset_from_xyz( - work_dir: str, - train_path: Union[str, List[str]], - valid_path: Optional[Union[str, List[str]]], - valid_fraction: float, - key_specification: KeySpecification, - config_type_weights: Optional[Dict] = None, - test_path: Optional[Union[str, List[str]]] = None, - seed: int = 1234, - keep_isolated_atoms: bool = False, - head_name: str = "Default", -) -> Tuple[SubsetCollection, Optional[Dict[int, float]]]: - """ - Load training, validation, and test datasets from xyz files. - - Args: - work_dir: Working directory for saving split information - train_path: Path or list of paths to training xyz files - valid_path: Path or list of paths to validation xyz files - valid_fraction: Fraction of training data to use for validation if valid_path is None - config_type_weights: Dictionary of weights for each configuration type - key_specification: KeySpecification object for loading data - test_path: Path or list of paths to test xyz files - seed: Random seed for train/validation split - keep_isolated_atoms: Whether to keep isolated atoms in the dataset - head_name: Name of the head for multi-head models - - Returns: - Tuple containing: - - SubsetCollection with train, valid, and test configurations - - Dictionary of atomic energies (or None if not available) - """ - # Convert input paths to lists if they're not already - train_paths = [train_path] if isinstance(train_path, str) else train_path - valid_paths = ( - [valid_path] - if isinstance(valid_path, str) and valid_path is not None - else valid_path - ) - test_paths = ( - [test_path] - if isinstance(test_path, str) and test_path is not None - else test_path - ) - - # Initialize collections and atomic energies tracking - all_train_configs = [] - all_valid_configs = [] - all_test_configs = [] - - # For tracking atomic energies across files - atomic_energies_values = {} # Element Z -> list of energy values - atomic_energies_counts = {} # Element Z -> count of files with this element - - # Process training files - for i, path in enumerate(train_paths): - logging.debug(f"Loading training file: {path}") - ae_dict, train_configs = data.load_from_xyz( - file_path=path, - config_type_weights=config_type_weights, - key_specification=key_specification, - extract_atomic_energies=True, # Extract from all files to average - keep_isolated_atoms=keep_isolated_atoms, - head_name=head_name, - ) - all_train_configs.extend(train_configs) - - # Track atomic energies from each file for averaging - if ae_dict: - for element, energy in ae_dict.items(): - if element not in atomic_energies_values: - atomic_energies_values[element] = [] - atomic_energies_counts[element] = 0 - - atomic_energies_values[element].append(energy) - atomic_energies_counts[element] += 1 - - log_dataset_contents(train_configs, f"Training set {i+1}/{len(train_paths)}") - - # Log total training set info - log_dataset_contents(all_train_configs, "Total Training set") - - # Process validation files if provided - if valid_paths: - for i, path in enumerate(valid_paths): - _, valid_configs = data.load_from_xyz( - file_path=path, - config_type_weights=config_type_weights, - key_specification=key_specification, - extract_atomic_energies=False, - head_name=head_name, - ) - all_valid_configs.extend(valid_configs) - log_dataset_contents( - valid_configs, f"Validation set {i+1}/{len(valid_paths)}" - ) - - # Log total validation set info - log_dataset_contents(all_valid_configs, "Total Validation set") - train_configs = all_train_configs - valid_configs = all_valid_configs - else: - # Split training data if no validation files are provided - logging.info("No validation set provided, splitting training data instead.") - train_configs, valid_configs = data.random_train_valid_split( - all_train_configs, valid_fraction, seed, work_dir - ) - log_dataset_contents(train_configs, "Random Split Training set") - log_dataset_contents(valid_configs, "Random Split Validation set") - - test_configs_by_type = [] - if test_paths: - for i, path in enumerate(test_paths): - _, test_configs = data.load_from_xyz( - file_path=path, - config_type_weights=config_type_weights, - key_specification=key_specification, - extract_atomic_energies=False, - head_name=head_name, - ) - all_test_configs.extend(test_configs) - - log_dataset_contents(test_configs, f"Test set {i+1}/{len(test_paths)}") - - # Create list of tuples (config_type, list(Atoms)) - test_configs_by_type = data.test_config_types(all_test_configs) - log_dataset_contents(all_test_configs, "Total Test set") - - atomic_energies_dict = {} - for element, values in atomic_energies_values.items(): - if atomic_energies_counts[element] > 1: - atomic_energies_dict[element] = sum(values) / len(values) - logging.debug( - f"Element {element} found in {atomic_energies_counts[element]} files. Using average E0: {atomic_energies_dict[element]:.6f} eV" - ) - else: - atomic_energies_dict[element] = values[0] - logging.debug( - f"Element {element} found in 1 file. Using E0: {atomic_energies_dict[element]:.6f} eV" - ) - - return ( - SubsetCollection( - train=train_configs, valid=valid_configs, tests=test_configs_by_type - ), - atomic_energies_dict if atomic_energies_dict else None, - ) - - -def get_config_type_weights(ct_weights): - """ - Get config type weights from command line argument - """ - try: - config_type_weights = ast.literal_eval(ct_weights) - assert isinstance(config_type_weights, dict) - except Exception as e: # pylint: disable=W0703 - logging.warning( - f"Config type weights not specified correctly ({e}), using Default" - ) - config_type_weights = {"Default": 1.0} - return config_type_weights - - -def print_git_commit(): - try: - import git - - repo = git.Repo(search_parent_directories=True) - commit = repo.head.commit.hexsha - logging.debug(f"Current Git commit: {commit}") - return commit - except Exception as e: # pylint: disable=W0703 - logging.debug(f"Error accessing Git repository: {e}") - return "None" - - -def extract_config_mace_model(model: torch.nn.Module) -> Dict[str, Any]: - if model.__class__.__name__ != "ScaleShiftMACE": - return {"error": "Model is not a ScaleShiftMACE model"} - - def radial_to_name(radial_type): - if radial_type == "BesselBasis": - return "bessel" - if radial_type == "GaussianBasis": - return "gaussian" - if radial_type == "ChebychevBasis": - return "chebyshev" - return radial_type - - def radial_to_transform(radial): - if not hasattr(radial, "distance_transform"): - return None - if radial.distance_transform.__class__.__name__ == "AgnesiTransform": - return "Agnesi" - if radial.distance_transform.__class__.__name__ == "SoftTransform": - return "Soft" - return radial.distance_transform.__class__.__name__ - - scale = model.scale_shift.scale - shift = model.scale_shift.shift - heads = model.heads if hasattr(model, "heads") else ["default"] - model_mlp_irreps = ( - o3.Irreps(str(model.readouts[-1].hidden_irreps)) - if model.num_interactions.item() > 1 - else 1 - ) - mlp_irreps = o3.Irreps(f"{model_mlp_irreps.count((0, 1)) // len(heads)}x0e") - try: - correlation = ( - len(model.products[0].symmetric_contractions.contractions[0].weights) + 1 - ) - except AttributeError: - correlation = model.products[0].symmetric_contractions.contraction_degree - config = { - "r_max": model.r_max.item(), - "num_bessel": len(model.radial_embedding.bessel_fn.bessel_weights), - "num_polynomial_cutoff": model.radial_embedding.cutoff_fn.p.item(), - "max_ell": model.spherical_harmonics._lmax, # pylint: disable=protected-access - "interaction_cls": model.interactions[-1].__class__, - "interaction_cls_first": model.interactions[0].__class__, - "num_interactions": model.num_interactions.item(), - "num_elements": len(model.atomic_numbers), - "hidden_irreps": o3.Irreps(str(model.products[0].linear.irreps_out)), - "MLP_irreps": (mlp_irreps if model.num_interactions.item() > 1 else 1), - "gate": ( - model.readouts[-1] # pylint: disable=protected-access - .non_linearity._modules["acts"][0] - .f - if model.num_interactions.item() > 1 - else None - ), - "atomic_energies": model.atomic_energies_fn.atomic_energies.cpu().numpy(), - "avg_num_neighbors": model.interactions[0].avg_num_neighbors, - "atomic_numbers": model.atomic_numbers, - "correlation": correlation, - "radial_type": radial_to_name( - model.radial_embedding.bessel_fn.__class__.__name__ - ), - "radial_MLP": model.interactions[0].conv_tp_weights.hs[1:-1], - "pair_repulsion": hasattr(model, "pair_repulsion_fn"), - "distance_transform": radial_to_transform(model.radial_embedding), - "atomic_inter_scale": scale.cpu().numpy(), - "atomic_inter_shift": shift.cpu().numpy(), - "heads": heads, - } - return config - - -def extract_load(f: str, map_location: str = "cpu") -> torch.nn.Module: - return extract_model( - torch.load(f=f, map_location=map_location), map_location=map_location - ) - - -def remove_pt_head( - model: torch.nn.Module, head_to_keep: Optional[str] = None -) -> torch.nn.Module: - """Converts a multihead MACE model to a single head model by removing the pretraining head. - - Args: - model (ScaleShiftMACE): The multihead MACE model to convert - head_to_keep (Optional[str]): The name of the head to keep. If None, keeps the first non-PT head. - - Returns: - ScaleShiftMACE: A new MACE model with only the specified head - - Raises: - ValueError: If the model is not a multihead model or if the specified head is not found - """ - if not hasattr(model, "heads") or len(model.heads) <= 1: - raise ValueError("Model must be a multihead model with more than one head") - - # Get index of head to keep - if head_to_keep is None: - # Find first non-PT head - try: - head_idx = next(i for i, h in enumerate(model.heads) if h != "pt_head") - except StopIteration as e: - raise ValueError("No non-PT head found in model") from e - else: - try: - head_idx = model.heads.index(head_to_keep) - except ValueError as e: - raise ValueError(f"Head {head_to_keep} not found in model") from e - - # Extract config and modify for single head - model_config = extract_config_mace_model(model) - model_config["heads"] = [model.heads[head_idx]] - model_config["atomic_energies"] = ( - model.atomic_energies_fn.atomic_energies[head_idx] - .unsqueeze(0) - .detach() - .cpu() - .numpy() - ) - model_config["atomic_inter_scale"] = model.scale_shift.scale[head_idx].item() - model_config["atomic_inter_shift"] = model.scale_shift.shift[head_idx].item() - mlp_count_irreps = model_config["MLP_irreps"].count((0, 1)) - # model_config["MLP_irreps"] = o3.Irreps(f"{mlp_count_irreps}x0e") - - new_model = model.__class__(**model_config) - state_dict = model.state_dict() - new_state_dict = {} - - for name, param in state_dict.items(): - if "atomic_energies" in name: - new_state_dict[name] = param[head_idx : head_idx + 1] - elif "scale" in name or "shift" in name: - new_state_dict[name] = param[head_idx : head_idx + 1] - elif "readouts" in name: - channels_per_head = param.shape[0] // len(model.heads) - start_idx = head_idx * channels_per_head - end_idx = start_idx + channels_per_head - if "linear_2.weight" in name: - end_idx = start_idx + channels_per_head // 2 - # if ( - # "readouts.0.linear.weight" in name - # or "readouts.1.linear_2.weight" in name - # ): - # new_state_dict[name] = param[start_idx:end_idx] / ( - # len(model.heads) ** 0.5 - # ) - if "readouts.0.linear.weight" in name: - new_state_dict[name] = param.reshape(-1, len(model.heads))[ - :, head_idx - ].flatten() - elif "readouts.1.linear_1.weight" in name: - new_state_dict[name] = param.reshape( - -1, len(model.heads), mlp_count_irreps - )[:, head_idx, :].flatten() - elif "readouts.1.linear_2.weight" in name: - new_state_dict[name] = param.reshape( - len(model.heads), -1, len(model.heads) - )[head_idx, :, head_idx].flatten() / (len(model.heads) ** 0.5) - else: - new_state_dict[name] = param[start_idx:end_idx] - - else: - new_state_dict[name] = param - - # Load state dict into new model - new_model.load_state_dict(new_state_dict) - - return new_model - - -def extract_model(model: torch.nn.Module, map_location: str = "cpu") -> torch.nn.Module: - model_copy = model.__class__(**extract_config_mace_model(model)) - model_copy.load_state_dict(model.state_dict()) - return model_copy.to(map_location) - - -def convert_to_json_format(dict_input): - for key, value in dict_input.items(): - if isinstance(value, (np.ndarray, torch.Tensor)): - dict_input[key] = value.tolist() - # # check if the value is a class and convert it to a string - elif hasattr(value, "__class__"): - dict_input[key] = str(value) - return dict_input - - -def convert_from_json_format(dict_input): - dict_output = dict_input.copy() - if ( - dict_input["interaction_cls"] - == "" - ): - dict_output["interaction_cls"] = ( - modules.blocks.RealAgnosticResidualInteractionBlock - ) - if ( - dict_input["interaction_cls"] - == "" - ): - dict_output["interaction_cls"] = modules.blocks.RealAgnosticInteractionBlock - if ( - dict_input["interaction_cls_first"] - == "" - ): - dict_output["interaction_cls_first"] = ( - modules.blocks.RealAgnosticResidualInteractionBlock - ) - if ( - dict_input["interaction_cls_first"] - == "" - ): - dict_output["interaction_cls_first"] = ( - modules.blocks.RealAgnosticInteractionBlock - ) - dict_output["r_max"] = float(dict_input["r_max"]) - dict_output["num_bessel"] = int(dict_input["num_bessel"]) - dict_output["num_polynomial_cutoff"] = float(dict_input["num_polynomial_cutoff"]) - dict_output["max_ell"] = int(dict_input["max_ell"]) - dict_output["num_interactions"] = int(dict_input["num_interactions"]) - dict_output["num_elements"] = int(dict_input["num_elements"]) - dict_output["hidden_irreps"] = o3.Irreps(dict_input["hidden_irreps"]) - dict_output["MLP_irreps"] = o3.Irreps(dict_input["MLP_irreps"]) - dict_output["avg_num_neighbors"] = float(dict_input["avg_num_neighbors"]) - dict_output["gate"] = torch.nn.functional.silu - dict_output["atomic_energies"] = np.array(dict_input["atomic_energies"]) - dict_output["atomic_numbers"] = dict_input["atomic_numbers"] - dict_output["correlation"] = int(dict_input["correlation"]) - dict_output["radial_type"] = dict_input["radial_type"] - dict_output["radial_MLP"] = ast.literal_eval(dict_input["radial_MLP"]) - dict_output["pair_repulsion"] = ast.literal_eval(dict_input["pair_repulsion"]) - dict_output["distance_transform"] = dict_input["distance_transform"] - dict_output["atomic_inter_scale"] = float(dict_input["atomic_inter_scale"]) - dict_output["atomic_inter_shift"] = float(dict_input["atomic_inter_shift"]) - - return dict_output - - -def load_from_json(f: str, map_location: str = "cpu") -> torch.nn.Module: - extra_files_extract = {"commit.txt": None, "config.json": None} - model_jit_load = torch.jit.load( - f, _extra_files=extra_files_extract, map_location=map_location - ) - model_load_yaml = modules.ScaleShiftMACE( - **convert_from_json_format(json.loads(extra_files_extract["config.json"])) - ) - model_load_yaml.load_state_dict(model_jit_load.state_dict()) - return model_load_yaml.to(map_location) - - -def get_atomic_energies(E0s, train_collection, z_table) -> dict: - if E0s is not None: - logging.info( - "Isolated Atomic Energies (E0s) not in training file, using command line argument" - ) - if E0s.lower() == "average": - logging.info( - "Computing average Atomic Energies using least squares regression" - ) - # catch if colections.train not defined above - try: - assert train_collection is not None - atomic_energies_dict = data.compute_average_E0s( - train_collection, z_table - ) - except Exception as e: - raise RuntimeError( - f"Could not compute average E0s if no training xyz given, error {e} occured" - ) from e - else: - if E0s.endswith(".json"): - logging.info(f"Loading atomic energies from {E0s}") - with open(E0s, "r", encoding="utf-8") as f: - atomic_energies_dict = json.load(f) - atomic_energies_dict = { - int(key): value for key, value in atomic_energies_dict.items() - } - else: - try: - atomic_energies_eval = ast.literal_eval(E0s) - if not all( - isinstance(value, dict) - for value in atomic_energies_eval.values() - ): - atomic_energies_dict = atomic_energies_eval - else: - atomic_energies_dict = atomic_energies_eval - assert isinstance(atomic_energies_dict, dict) - except Exception as e: - raise RuntimeError( - f"E0s specified invalidly, error {e} occured" - ) from e - else: - raise RuntimeError( - "E0s not found in training file and not specified in command line" - ) - return atomic_energies_dict - - -def get_avg_num_neighbors(head_configs, args, train_loader, device): - if all(head_config.compute_avg_num_neighbors for head_config in head_configs): - logging.info("Computing average number of neighbors") - avg_num_neighbors = modules.compute_avg_num_neighbors(train_loader) - if args.distributed: - num_graphs = torch.tensor(len(train_loader.dataset)).to(device) - num_neighbors = num_graphs * torch.tensor(avg_num_neighbors).to(device) - torch.distributed.all_reduce(num_graphs, op=torch.distributed.ReduceOp.SUM) - torch.distributed.all_reduce( - num_neighbors, op=torch.distributed.ReduceOp.SUM - ) - avg_num_neighbors_out = (num_neighbors / num_graphs).item() - else: - avg_num_neighbors_out = avg_num_neighbors - else: - assert any( - head_config.avg_num_neighbors is not None for head_config in head_configs - ), "Average number of neighbors must be provided in the configuration" - avg_num_neighbors_out = max( - head_config.avg_num_neighbors - for head_config in head_configs - if head_config.avg_num_neighbors is not None - ) - if avg_num_neighbors_out < 2 or avg_num_neighbors_out > 100: - logging.warning( - f"Unusual average number of neighbors: {avg_num_neighbors_out:.1f}" - ) - else: - logging.info(f"Average number of neighbors: {avg_num_neighbors_out}") - return avg_num_neighbors_out - - -def get_loss_fn( - args: argparse.Namespace, - dipole_only: bool, - compute_dipole: bool, -) -> torch.nn.Module: - if args.loss == "weighted": - loss_fn = modules.WeightedEnergyForcesLoss( - energy_weight=args.energy_weight, forces_weight=args.forces_weight - ) - elif args.loss == "forces_only": - loss_fn = modules.WeightedForcesLoss(forces_weight=args.forces_weight) - elif args.loss == "virials": - loss_fn = modules.WeightedEnergyForcesVirialsLoss( - energy_weight=args.energy_weight, - forces_weight=args.forces_weight, - virials_weight=args.virials_weight, - ) - elif args.loss == "stress": - loss_fn = modules.WeightedEnergyForcesStressLoss( - energy_weight=args.energy_weight, - forces_weight=args.forces_weight, - stress_weight=args.stress_weight, - ) - elif args.loss == "huber": - loss_fn = modules.WeightedHuberEnergyForcesStressLoss( - energy_weight=args.energy_weight, - forces_weight=args.forces_weight, - stress_weight=args.stress_weight, - huber_delta=args.huber_delta, - ) - elif args.loss == "universal": - loss_fn = modules.UniversalLoss( - energy_weight=args.energy_weight, - forces_weight=args.forces_weight, - stress_weight=args.stress_weight, - huber_delta=args.huber_delta, - ) - elif args.loss == "l1l2energyforces": - loss_fn = modules.WeightedEnergyForcesL1L2Loss( - energy_weight=args.energy_weight, - forces_weight=args.forces_weight, - ) - elif args.loss == "dipole": - assert ( - dipole_only is True - ), "dipole loss can only be used with AtomicDipolesMACE model" - loss_fn = modules.DipoleSingleLoss( - dipole_weight=args.dipole_weight, - ) - elif args.loss == "energy_forces_dipole": - assert dipole_only is False and compute_dipole is True - loss_fn = modules.WeightedEnergyForcesDipoleLoss( - energy_weight=args.energy_weight, - forces_weight=args.forces_weight, - dipole_weight=args.dipole_weight, - ) - else: - loss_fn = modules.WeightedEnergyForcesLoss(energy_weight=1.0, forces_weight=1.0) - return loss_fn - - -def get_swa( - args: argparse.Namespace, - model: torch.nn.Module, - optimizer: torch.optim.Optimizer, - swas: List[bool], - dipole_only: bool = False, -): - assert dipole_only is False, "Stage Two for dipole fitting not implemented" - swas.append(True) - if args.start_swa is None: - args.start_swa = max(1, args.max_num_epochs // 4 * 3) - else: - if args.start_swa >= args.max_num_epochs: - logging.warning( - f"Start Stage Two must be less than max_num_epochs, got {args.start_swa} > {args.max_num_epochs}" - ) - swas[-1] = False - if args.loss == "forces_only": - raise ValueError("Can not select Stage Two with forces only loss.") - if args.loss == "virials": - loss_fn_energy = modules.WeightedEnergyForcesVirialsLoss( - energy_weight=args.swa_energy_weight, - forces_weight=args.swa_forces_weight, - virials_weight=args.swa_virials_weight, - ) - logging.info( - f"Stage Two (after {args.start_swa} epochs) with loss function: {loss_fn_energy}, energy weight : {args.swa_energy_weight}, forces weight : {args.swa_forces_weight}, virials_weight: {args.swa_virials_weight} and learning rate : {args.swa_lr}" - ) - elif args.loss == "stress": - loss_fn_energy = modules.WeightedEnergyForcesStressLoss( - energy_weight=args.swa_energy_weight, - forces_weight=args.swa_forces_weight, - stress_weight=args.swa_stress_weight, - ) - logging.info( - f"Stage Two (after {args.start_swa} epochs) with loss function: {loss_fn_energy}, energy weight : {args.swa_energy_weight}, forces weight : {args.swa_forces_weight}, stress weight : {args.swa_stress_weight} and learning rate : {args.swa_lr}" - ) - elif args.loss == "energy_forces_dipole": - loss_fn_energy = modules.WeightedEnergyForcesDipoleLoss( - args.swa_energy_weight, - forces_weight=args.swa_forces_weight, - dipole_weight=args.swa_dipole_weight, - ) - logging.info( - f"Stage Two (after {args.start_swa} epochs) with loss function: {loss_fn_energy}, with energy weight : {args.swa_energy_weight}, forces weight : {args.swa_forces_weight}, dipole weight : {args.swa_dipole_weight} and learning rate : {args.swa_lr}" - ) - elif args.loss == "universal": - loss_fn_energy = modules.UniversalLoss( - energy_weight=args.swa_energy_weight, - forces_weight=args.swa_forces_weight, - stress_weight=args.swa_stress_weight, - huber_delta=args.huber_delta, - ) - logging.info( - f"Stage Two (after {args.start_swa} epochs) with loss function: {loss_fn_energy}, with energy weight : {args.swa_energy_weight}, forces weight : {args.swa_forces_weight}, stress weight : {args.swa_stress_weight} and learning rate : {args.swa_lr}" - ) - else: - loss_fn_energy = modules.WeightedEnergyForcesLoss( - energy_weight=args.swa_energy_weight, - forces_weight=args.swa_forces_weight, - ) - logging.info( - f"Stage Two (after {args.start_swa} epochs) with loss function: {loss_fn_energy}, with energy weight : {args.swa_energy_weight}, forces weight : {args.swa_forces_weight} and learning rate : {args.swa_lr}" - ) - swa = SWAContainer( - model=AveragedModel(model), - scheduler=SWALR( - optimizer=optimizer, - swa_lr=args.swa_lr, - anneal_epochs=1, - anneal_strategy="linear", - ), - start=args.start_swa, - loss_fn=loss_fn_energy, - ) - return swa, swas - - -def get_params_options( - args: argparse.Namespace, model: torch.nn.Module -) -> Dict[str, Any]: - decay_interactions = {} - no_decay_interactions = {} - for name, param in model.interactions.named_parameters(): - if "linear.weight" in name or "skip_tp_full.weight" in name: - decay_interactions[name] = param - else: - no_decay_interactions[name] = param - - param_options = dict( - params=[ - { - "name": "embedding", - "params": model.node_embedding.parameters(), - "weight_decay": 0.0, - }, - { - "name": "interactions_decay", - "params": list(decay_interactions.values()), - "weight_decay": args.weight_decay, - }, - { - "name": "interactions_no_decay", - "params": list(no_decay_interactions.values()), - "weight_decay": 0.0, - }, - { - "name": "products", - "params": model.products.parameters(), - "weight_decay": args.weight_decay, - }, - { - "name": "readouts", - "params": model.readouts.parameters(), - "weight_decay": 0.0, - }, - ], - lr=args.lr, - amsgrad=args.amsgrad, - betas=(args.beta, 0.999), - ) - return param_options - - -def get_optimizer( - args: argparse.Namespace, param_options: Dict[str, Any] -) -> torch.optim.Optimizer: - if args.optimizer == "adamw": - optimizer = torch.optim.AdamW(**param_options) - elif args.optimizer == "schedulefree": - try: - from schedulefree import adamw_schedulefree - except ImportError as exc: - raise ImportError( - "`schedulefree` is not installed. Please install it via `pip install schedulefree` or `pip install mace-torch[schedulefree]`" - ) from exc - _param_options = {k: v for k, v in param_options.items() if k != "amsgrad"} - optimizer = adamw_schedulefree.AdamWScheduleFree(**_param_options) - else: - optimizer = torch.optim.Adam(**param_options) - return optimizer - - -def setup_wandb(args: argparse.Namespace): - logging.info("Using Weights and Biases for logging") - import wandb - - wandb_config = {} - args_dict = vars(args) - - for key, value in args_dict.items(): - if isinstance(value, np.ndarray): - args_dict[key] = value.tolist() - - class CustomEncoder(json.JSONEncoder): - def default(self, o): - if isinstance(o, KeySpecification): - return o.__dict__ - return super().default(o) - - args_dict_json = json.dumps(args_dict, cls=CustomEncoder) - for key in args.wandb_log_hypers: - wandb_config[key] = args_dict[key] - tools.init_wandb( - project=args.wandb_project, - entity=args.wandb_entity, - name=args.wandb_name, - config=wandb_config, - directory=args.wandb_dir, - ) - wandb.run.summary["params"] = args_dict_json - - -def get_files_with_suffix(dir_path: str, suffix: str) -> List[str]: - return [ - os.path.join(dir_path, f) for f in os.listdir(dir_path) if f.endswith(suffix) - ] - - -def dict_to_array(input_data, heads): - if all(isinstance(value, np.ndarray) for value in input_data.values()): - return np.array([input_data[head] for head in heads]) - if not all(isinstance(value, dict) for value in input_data.values()): - return np.array([[input_data[head]] for head in heads]) - unique_keys = set() - for inner_dict in input_data.values(): - unique_keys.update(inner_dict.keys()) - unique_keys = list(unique_keys) - sorted_keys = sorted([int(key) for key in unique_keys]) - result_array = np.zeros((len(input_data), len(sorted_keys))) - for _, (head_name, inner_dict) in enumerate(input_data.items()): - for key, value in inner_dict.items(): - key_index = sorted_keys.index(int(key)) - head_index = heads.index(head_name) - result_array[head_index][key_index] = value - return result_array - - -class LRScheduler: - def __init__(self, optimizer, args) -> None: - self.scheduler = args.scheduler - self._optimizer_type = ( - args.optimizer - ) # Schedulefree does not need an optimizer but checkpoint handler does. - if args.scheduler == "ExponentialLR": - self.lr_scheduler = torch.optim.lr_scheduler.ExponentialLR( - optimizer=optimizer, gamma=args.lr_scheduler_gamma - ) - elif args.scheduler == "ReduceLROnPlateau": - self.lr_scheduler = torch.optim.lr_scheduler.ReduceLROnPlateau( - optimizer=optimizer, - factor=args.lr_factor, - patience=args.scheduler_patience, - ) - else: - raise RuntimeError(f"Unknown scheduler: '{args.scheduler}'") - - def step(self, metrics=None, epoch=None): # pylint: disable=E1123 - if self._optimizer_type == "schedulefree": - return # In principle, schedulefree optimizer can be used with a scheduler but the paper suggests it's not necessary - if self.scheduler == "ExponentialLR": - self.lr_scheduler.step(epoch=epoch) - elif self.scheduler == "ReduceLROnPlateau": - self.lr_scheduler.step( # pylint: disable=E1123 - metrics=metrics, epoch=epoch - ) - - def __getattr__(self, name): - if name == "step": - return self.step - return getattr(self.lr_scheduler, name) - - -def check_folder_subfolder(folder_path): - entries = os.listdir(folder_path) - for entry in entries: - full_path = os.path.join(folder_path, entry) - if os.path.isdir(full_path): - return True - return False - - -def check_path_ase_read(filename: Optional[str]) -> bool: - if filename is None: - return False - filepath = Path(filename) - if filepath.is_dir(): - num_h5_files = len(list(filepath.glob("*.h5"))) - num_hdf5_files = len(list(filepath.glob("*.hdf5"))) - num_ldb_files = len(list(filepath.glob("*.lmdb"))) - num_aselmbd_files = len(list(filepath.glob("*.aselmdb"))) - num_mdb_files = len(list(filepath.glob("*.mdb"))) - if ( - num_h5_files - + num_hdf5_files - + num_ldb_files - + num_aselmbd_files - + num_mdb_files - == 0 - ): - # print all the files in the directory extension in the directory for debugging - for file in os.listdir(filepath): - print(file) - raise RuntimeError(f"No supported files found in directory '{filename}'") - return False - if filepath.suffix in (".h5", ".hdf5", ".lmdb", ".aselmdb", ".mdb"): - return False - return True - - -def dict_to_namespace(dictionary): - # Convert the dictionary into an argparse.Namespace - namespace = argparse.Namespace() - for key, value in dictionary.items(): - setattr(namespace, key, value) - return namespace diff --git a/mace-bench/3rdparty/mace/mace/tools/slurm_distributed.py b/mace-bench/3rdparty/mace/mace/tools/slurm_distributed.py deleted file mode 100644 index 9b7c77b3b2ef354fee3a896a00f1eceed1520dd0..0000000000000000000000000000000000000000 --- a/mace-bench/3rdparty/mace/mace/tools/slurm_distributed.py +++ /dev/null @@ -1,40 +0,0 @@ -########################################################################################### -# Slurm environment setup for distributed training. -# This code is refactored from rsarm's contribution at: -# https://github.com/Lumi-supercomputer/lumi-reframe-tests/blob/main/checks/apps/deeplearning/pytorch/src/pt_distr_env.py -# This program is distributed under the MIT License (see MIT.md) -########################################################################################### - -import os - -import hostlist - - -class DistributedEnvironment: - def __init__(self): - self._setup_distr_env() - self.master_addr = os.environ["MASTER_ADDR"] - self.master_port = os.environ["MASTER_PORT"] - self.world_size = int(os.environ["WORLD_SIZE"]) - self.local_rank = int(os.environ["LOCAL_RANK"]) - self.rank = int(os.environ["RANK"]) - - def _setup_distr_env(self): - hostname = hostlist.expand_hostlist(os.environ["SLURM_JOB_NODELIST"])[0] - os.environ["MASTER_ADDR"] = hostname - os.environ["MASTER_PORT"] = os.environ.get("MASTER_PORT", "33333") - os.environ["WORLD_SIZE"] = os.environ.get( - "SLURM_NTASKS", - str( - int(os.environ["SLURM_NTASKS_PER_NODE"]) - * int(os.environ["SLURM_NNODES"]) - ), - ) - os.environ["LOCAL_RANK"] = os.environ["SLURM_LOCALID"] - os.environ["RANK"] = os.environ["SLURM_PROCID"] - - def __repr__(self): - return ( - f"DistributedEnvironment(master_addr={self.master_addr}, master_port={self.master_port}, " - f"world_size={self.world_size}, local_rank={self.local_rank}, rank={self.rank})" - ) diff --git a/mace-bench/3rdparty/mace/mace/tools/tables_utils.py b/mace-bench/3rdparty/mace/mace/tools/tables_utils.py deleted file mode 100644 index 04ff64014f4a0d0505a66372a61c23a50df75815..0000000000000000000000000000000000000000 --- a/mace-bench/3rdparty/mace/mace/tools/tables_utils.py +++ /dev/null @@ -1,246 +0,0 @@ -import logging -from typing import Dict, List, Optional - -import torch -from prettytable import PrettyTable - -from mace.tools import evaluate - - -def custom_key(key): - """ - Helper function to sort the keys of the data loader dictionary - to ensure that the training set, and validation set - are evaluated first - """ - if key == "train": - return (0, key) - if key == "valid": - return (1, key) - return (2, key) - - -def create_error_table( - table_type: str, - all_data_loaders: dict, - model: torch.nn.Module, - loss_fn: torch.nn.Module, - output_args: Dict[str, bool], - log_wandb: bool, - device: str, - distributed: bool = False, - skip_heads: Optional[List[str]] = None, -) -> PrettyTable: - if log_wandb: - import wandb - skip_heads = skip_heads or [] - table = PrettyTable() - if table_type == "TotalRMSE": - table.field_names = [ - "config_type", - "RMSE E / meV", - "RMSE F / meV / A", - "relative F RMSE %", - ] - elif table_type == "PerAtomRMSE": - table.field_names = [ - "config_type", - "RMSE E / meV / atom", - "RMSE F / meV / A", - "relative F RMSE %", - ] - elif table_type == "PerAtomRMSEstressvirials": - table.field_names = [ - "config_type", - "RMSE E / meV / atom", - "RMSE F / meV / A", - "relative F RMSE %", - "RMSE Stress (Virials) / meV / A (A^3)", - ] - elif table_type == "PerAtomMAEstressvirials": - table.field_names = [ - "config_type", - "MAE E / meV / atom", - "MAE F / meV / A", - "relative F MAE %", - "MAE Stress (Virials) / meV / A (A^3)", - ] - elif table_type == "TotalMAE": - table.field_names = [ - "config_type", - "MAE E / meV", - "MAE F / meV / A", - "relative F MAE %", - ] - elif table_type == "PerAtomMAE": - table.field_names = [ - "config_type", - "MAE E / meV / atom", - "MAE F / meV / A", - "relative F MAE %", - ] - elif table_type == "DipoleRMSE": - table.field_names = [ - "config_type", - "RMSE MU / mDebye / atom", - "relative MU RMSE %", - ] - elif table_type == "DipoleMAE": - table.field_names = [ - "config_type", - "MAE MU / mDebye / atom", - "relative MU MAE %", - ] - elif table_type == "EnergyDipoleRMSE": - table.field_names = [ - "config_type", - "RMSE E / meV / atom", - "RMSE F / meV / A", - "rel F RMSE %", - "RMSE MU / mDebye / atom", - "rel MU RMSE %", - ] - - for name in sorted(all_data_loaders, key=custom_key): - if any(skip_head in name for skip_head in skip_heads): - logging.info(f"Skipping evaluation of {name} (in skip_heads list)") - continue - data_loader = all_data_loaders[name] - logging.info(f"Evaluating {name} ...") - _, metrics = evaluate( - model, - loss_fn=loss_fn, - data_loader=data_loader, - output_args=output_args, - device=device, - ) - if distributed: - torch.distributed.barrier() - - del data_loader - torch.cuda.empty_cache() - if log_wandb: - wandb_log_dict = { - name - + "_final_rmse_e_per_atom": metrics["rmse_e_per_atom"] - * 1e3, # meV / atom - name + "_final_rmse_f": metrics["rmse_f"] * 1e3, # meV / A - name + "_final_rel_rmse_f": metrics["rel_rmse_f"], - } - wandb.log(wandb_log_dict) - if table_type == "TotalRMSE": - table.add_row( - [ - name, - f"{metrics['rmse_e'] * 1000:8.1f}", - f"{metrics['rmse_f'] * 1000:8.1f}", - f"{metrics['rel_rmse_f']:8.2f}", - ] - ) - elif table_type == "PerAtomRMSE": - table.add_row( - [ - name, - f"{metrics['rmse_e_per_atom'] * 1000:8.1f}", - f"{metrics['rmse_f'] * 1000:8.1f}", - f"{metrics['rel_rmse_f']:8.2f}", - ] - ) - elif ( - table_type == "PerAtomRMSEstressvirials" - and metrics["rmse_stress"] is not None - ): - table.add_row( - [ - name, - f"{metrics['rmse_e_per_atom'] * 1000:8.1f}", - f"{metrics['rmse_f'] * 1000:8.1f}", - f"{metrics['rel_rmse_f']:8.2f}", - f"{metrics['rmse_stress'] * 1000:8.1f}", - ] - ) - elif ( - table_type == "PerAtomRMSEstressvirials" - and metrics["rmse_virials"] is not None - ): - table.add_row( - [ - name, - f"{metrics['rmse_e_per_atom'] * 1000:8.1f}", - f"{metrics['rmse_f'] * 1000:8.1f}", - f"{metrics['rel_rmse_f']:8.2f}", - f"{metrics['rmse_virials'] * 1000:8.1f}", - ] - ) - elif ( - table_type == "PerAtomMAEstressvirials" - and metrics["mae_stress"] is not None - ): - table.add_row( - [ - name, - f"{metrics['mae_e_per_atom'] * 1000:8.1f}", - f"{metrics['mae_f'] * 1000:8.1f}", - f"{metrics['rel_mae_f']:8.2f}", - f"{metrics['mae_stress'] * 1000:8.1f}", - ] - ) - elif ( - table_type == "PerAtomMAEstressvirials" - and metrics["mae_virials"] is not None - ): - table.add_row( - [ - name, - f"{metrics['mae_e_per_atom'] * 1000:8.1f}", - f"{metrics['mae_f'] * 1000:8.1f}", - f"{metrics['rel_mae_f']:8.2f}", - f"{metrics['mae_virials'] * 1000:8.1f}", - ] - ) - elif table_type == "TotalMAE": - table.add_row( - [ - name, - f"{metrics['mae_e'] * 1000:8.1f}", - f"{metrics['mae_f'] * 1000:8.1f}", - f"{metrics['rel_mae_f']:8.2f}", - ] - ) - elif table_type == "PerAtomMAE": - table.add_row( - [ - name, - f"{metrics['mae_e_per_atom'] * 1000:8.1f}", - f"{metrics['mae_f'] * 1000:8.1f}", - f"{metrics['rel_mae_f']:8.2f}", - ] - ) - elif table_type == "DipoleRMSE": - table.add_row( - [ - name, - f"{metrics['rmse_mu_per_atom'] * 1000:8.2f}", - f"{metrics['rel_rmse_mu']:8.1f}", - ] - ) - elif table_type == "DipoleMAE": - table.add_row( - [ - name, - f"{metrics['mae_mu_per_atom'] * 1000:8.2f}", - f"{metrics['rel_mae_mu']:8.1f}", - ] - ) - elif table_type == "EnergyDipoleRMSE": - table.add_row( - [ - name, - f"{metrics['rmse_e_per_atom'] * 1000:8.1f}", - f"{metrics['rmse_f'] * 1000:8.1f}", - f"{metrics['rel_rmse_f']:8.1f}", - f"{metrics['rmse_mu_per_atom'] * 1000:8.1f}", - f"{metrics['rel_rmse_mu']:8.1f}", - ] - ) - return table diff --git a/mace-bench/3rdparty/mace/mace/tools/torch_geometric/README.md b/mace-bench/3rdparty/mace/mace/tools/torch_geometric/README.md deleted file mode 100644 index 8c6b8f7ed89ed4cbf6244eb1b38a45fa1dabbe0e..0000000000000000000000000000000000000000 --- a/mace-bench/3rdparty/mace/mace/tools/torch_geometric/README.md +++ /dev/null @@ -1,12 +0,0 @@ -# Trimmed-down `pytorch_geometric` - -MACE uses [`pytorch_geometric`](https://pytorch-geometric.readthedocs.io/en/latest/) [1, 2] framework. However as only use a very limited subset of that library: the most basic graph data structures. - -We follow the same approach to NequIP (https://github.com/mir-group/nequip/tree/main/nequip) and copy their code here. - -To avoid adding a large number of unnecessary second-degree dependencies, and to simplify installation, we include and modify here the small subset of `torch_geometric` that is necessary for our code. - -We are grateful to the developers of PyTorch Geometric for their ongoing and very useful work on graph learning with PyTorch. - -[1] Fey, M., & Lenssen, J. E. (2019). Fast Graph Representation Learning with PyTorch Geometric (Version 2.0.1) [Computer software]. https://github.com/pyg-team/pytorch_geometric
-[2] https://arxiv.org/abs/1903.02428 diff --git a/mace-bench/3rdparty/mace/mace/tools/torch_geometric/__init__.py b/mace-bench/3rdparty/mace/mace/tools/torch_geometric/__init__.py deleted file mode 100644 index 486f0d09d41acfdffba0c1d6e29828bc4fe9ba75..0000000000000000000000000000000000000000 --- a/mace-bench/3rdparty/mace/mace/tools/torch_geometric/__init__.py +++ /dev/null @@ -1,7 +0,0 @@ -from .batch import Batch -from .data import Data -from .dataloader import DataLoader -from .dataset import Dataset -from .seed import seed_everything - -__all__ = ["Batch", "Data", "Dataset", "DataLoader", "seed_everything"] diff --git a/mace-bench/3rdparty/mace/mace/tools/torch_geometric/batch.py b/mace-bench/3rdparty/mace/mace/tools/torch_geometric/batch.py deleted file mode 100644 index be5ec9d0cf418c9edc79fc503f143065e6450434..0000000000000000000000000000000000000000 --- a/mace-bench/3rdparty/mace/mace/tools/torch_geometric/batch.py +++ /dev/null @@ -1,257 +0,0 @@ -from collections.abc import Sequence -from typing import List - -import numpy as np -import torch -from torch import Tensor - -from .data import Data -from .dataset import IndexType - - -class Batch(Data): - r"""A plain old python object modeling a batch of graphs as one big - (disconnected) graph. With :class:`torch_geometric.data.Data` being the - base class, all its methods can also be used here. - In addition, single graphs can be reconstructed via the assignment vector - :obj:`batch`, which maps each node to its respective graph identifier. - """ - - def __init__(self, batch=None, ptr=None, **kwargs): - super(Batch, self).__init__(**kwargs) - - for key, item in kwargs.items(): - if key == "num_nodes": - self.__num_nodes__ = item - else: - self[key] = item - - self.batch = batch - self.ptr = ptr - self.__data_class__ = Data - self.__slices__ = None - self.__cumsum__ = None - self.__cat_dims__ = None - self.__num_nodes_list__ = None - self.__num_graphs__ = None - - @classmethod - def from_data_list(cls, data_list, follow_batch=[], exclude_keys=[]): - r"""Constructs a batch object from a python list holding - :class:`torch_geometric.data.Data` objects. - The assignment vector :obj:`batch` is created on the fly. - Additionally, creates assignment batch vectors for each key in - :obj:`follow_batch`. - Will exclude any keys given in :obj:`exclude_keys`.""" - - keys = list(set(data_list[0].keys) - set(exclude_keys)) - assert "batch" not in keys and "ptr" not in keys - - batch = cls() - for key in data_list[0].__dict__.keys(): - if key[:2] != "__" and key[-2:] != "__": - batch[key] = None - - batch.__num_graphs__ = len(data_list) - batch.__data_class__ = data_list[0].__class__ - for key in keys + ["batch"]: - batch[key] = [] - batch["ptr"] = [0] - - device = None - slices = {key: [0] for key in keys} - cumsum = {key: [0] for key in keys} - cat_dims = {} - num_nodes_list = [] - for i, data in enumerate(data_list): - for key in keys: - item = data[key] - - # Increase values by `cumsum` value. - cum = cumsum[key][-1] - if isinstance(item, Tensor) and item.dtype != torch.bool: - if not isinstance(cum, int) or cum != 0: - item = item + cum - elif isinstance(item, (int, float)): - item = item + cum - - # Gather the size of the `cat` dimension. - size = 1 - cat_dim = data.__cat_dim__(key, data[key]) - # 0-dimensional tensors have no dimension along which to - # concatenate, so we set `cat_dim` to `None`. - if isinstance(item, Tensor) and item.dim() == 0: - cat_dim = None - cat_dims[key] = cat_dim - - # Add a batch dimension to items whose `cat_dim` is `None`: - if isinstance(item, Tensor) and cat_dim is None: - cat_dim = 0 # Concatenate along this new batch dimension. - item = item.unsqueeze(0) - device = item.device - elif isinstance(item, Tensor): - size = item.size(cat_dim) - device = item.device - - batch[key].append(item) # Append item to the attribute list. - - slices[key].append(size + slices[key][-1]) - inc = data.__inc__(key, item) - if isinstance(inc, (tuple, list)): - inc = torch.tensor(inc) - cumsum[key].append(inc + cumsum[key][-1]) - - if key in follow_batch: - if isinstance(size, Tensor): - for j, size in enumerate(size.tolist()): - tmp = f"{key}_{j}_batch" - batch[tmp] = [] if i == 0 else batch[tmp] - batch[tmp].append( - torch.full((size,), i, dtype=torch.long, device=device) - ) - else: - tmp = f"{key}_batch" - batch[tmp] = [] if i == 0 else batch[tmp] - batch[tmp].append( - torch.full((size,), i, dtype=torch.long, device=device) - ) - - if hasattr(data, "__num_nodes__"): - num_nodes_list.append(data.__num_nodes__) - else: - num_nodes_list.append(None) - - num_nodes = data.num_nodes - if num_nodes is not None: - item = torch.full((num_nodes,), i, dtype=torch.long, device=device) - batch.batch.append(item) - batch.ptr.append(batch.ptr[-1] + num_nodes) - - batch.batch = None if len(batch.batch) == 0 else batch.batch - batch.ptr = None if len(batch.ptr) == 1 else batch.ptr - batch.__slices__ = slices - batch.__cumsum__ = cumsum - batch.__cat_dims__ = cat_dims - batch.__num_nodes_list__ = num_nodes_list - - ref_data = data_list[0] - for key in batch.keys: - items = batch[key] - item = items[0] - cat_dim = ref_data.__cat_dim__(key, item) - cat_dim = 0 if cat_dim is None else cat_dim - if isinstance(item, Tensor): - batch[key] = torch.cat(items, cat_dim) - elif isinstance(item, (int, float)): - batch[key] = torch.tensor(items) - - # if torch_geometric.is_debug_enabled(): - # batch.debug() - - return batch.contiguous() - - def get_example(self, idx: int) -> Data: - r"""Reconstructs the :class:`torch_geometric.data.Data` object at index - :obj:`idx` from the batch object. - The batch object must have been created via :meth:`from_data_list` in - order to be able to reconstruct the initial objects.""" - - if self.__slices__ is None: - raise RuntimeError( - ( - "Cannot reconstruct data list from batch because the batch " - "object was not created using `Batch.from_data_list()`." - ) - ) - - data = self.__data_class__() - idx = self.num_graphs + idx if idx < 0 else idx - - for key in self.__slices__.keys(): - item = self[key] - if self.__cat_dims__[key] is None: - # The item was concatenated along a new batch dimension, - # so just index in that dimension: - item = item[idx] - else: - # Narrow the item based on the values in `__slices__`. - if isinstance(item, Tensor): - dim = self.__cat_dims__[key] - start = self.__slices__[key][idx] - end = self.__slices__[key][idx + 1] - item = item.narrow(dim, start, end - start) - else: - start = self.__slices__[key][idx] - end = self.__slices__[key][idx + 1] - item = item[start:end] - item = item[0] if len(item) == 1 else item - - # Decrease its value by `cumsum` value: - cum = self.__cumsum__[key][idx] - if isinstance(item, Tensor): - if not isinstance(cum, int) or cum != 0: - item = item - cum - elif isinstance(item, (int, float)): - item = item - cum - - data[key] = item - - if self.__num_nodes_list__[idx] is not None: - data.num_nodes = self.__num_nodes_list__[idx] - - return data - - def index_select(self, idx: IndexType) -> List[Data]: - if isinstance(idx, slice): - idx = list(range(self.num_graphs)[idx]) - - elif isinstance(idx, Tensor) and idx.dtype == torch.long: - idx = idx.flatten().tolist() - - elif isinstance(idx, Tensor) and idx.dtype == torch.bool: - idx = idx.flatten().nonzero(as_tuple=False).flatten().tolist() - - elif isinstance(idx, np.ndarray) and idx.dtype == np.int64: - idx = idx.flatten().tolist() - - elif isinstance(idx, np.ndarray) and idx.dtype == np.bool: - idx = idx.flatten().nonzero()[0].flatten().tolist() - - elif isinstance(idx, Sequence) and not isinstance(idx, str): - pass - - else: - raise IndexError( - f"Only integers, slices (':'), list, tuples, torch.tensor and " - f"np.ndarray of dtype long or bool are valid indices (got " - f"'{type(idx).__name__}')" - ) - - return [self.get_example(i) for i in idx] - - def __getitem__(self, idx): - if isinstance(idx, str): - return super(Batch, self).__getitem__(idx) - elif isinstance(idx, (int, np.integer)): - return self.get_example(idx) - else: - return self.index_select(idx) - - def to_data_list(self) -> List[Data]: - r"""Reconstructs the list of :class:`torch_geometric.data.Data` objects - from the batch object. - The batch object must have been created via :meth:`from_data_list` in - order to be able to reconstruct the initial objects.""" - return [self.get_example(i) for i in range(self.num_graphs)] - - @property - def num_graphs(self) -> int: - """Returns the number of graphs in the batch.""" - if self.__num_graphs__ is not None: - return self.__num_graphs__ - elif self.ptr is not None: - return self.ptr.numel() - 1 - elif self.batch is not None: - return int(self.batch.max()) + 1 - else: - raise ValueError diff --git a/mace-bench/3rdparty/mace/mace/tools/torch_geometric/data.py b/mace-bench/3rdparty/mace/mace/tools/torch_geometric/data.py deleted file mode 100644 index 4e1ab3084d584dcf5af7289e3159c353327ec539..0000000000000000000000000000000000000000 --- a/mace-bench/3rdparty/mace/mace/tools/torch_geometric/data.py +++ /dev/null @@ -1,441 +0,0 @@ -import collections -import copy -import re - -import torch - -# from ..utils.num_nodes import maybe_num_nodes - -__num_nodes_warn_msg__ = ( - "The number of nodes in your data object can only be inferred by its {} " - "indices, and hence may result in unexpected batch-wise behavior, e.g., " - "in case there exists isolated nodes. Please consider explicitly setting " - "the number of nodes for this data object by assigning it to " - "data.num_nodes." -) - - -def size_repr(key, item, indent=0): - indent_str = " " * indent - if torch.is_tensor(item) and item.dim() == 0: - out = item.item() - elif torch.is_tensor(item): - out = str(list(item.size())) - elif isinstance(item, list) or isinstance(item, tuple): - out = str([len(item)]) - elif isinstance(item, dict): - lines = [indent_str + size_repr(k, v, 2) for k, v in item.items()] - out = "{\n" + ",\n".join(lines) + "\n" + indent_str + "}" - elif isinstance(item, str): - out = f'"{item}"' - else: - out = str(item) - - return f"{indent_str}{key}={out}" - - -class Data(object): - r"""A plain old python object modeling a single graph with various - (optional) attributes: - - Args: - x (Tensor, optional): Node feature matrix with shape :obj:`[num_nodes, - num_node_features]`. (default: :obj:`None`) - edge_index (LongTensor, optional): Graph connectivity in COO format - with shape :obj:`[2, num_edges]`. (default: :obj:`None`) - edge_attr (Tensor, optional): Edge feature matrix with shape - :obj:`[num_edges, num_edge_features]`. (default: :obj:`None`) - y (Tensor, optional): Graph or node targets with arbitrary shape. - (default: :obj:`None`) - pos (Tensor, optional): Node position matrix with shape - :obj:`[num_nodes, num_dimensions]`. (default: :obj:`None`) - normal (Tensor, optional): Normal vector matrix with shape - :obj:`[num_nodes, num_dimensions]`. (default: :obj:`None`) - face (LongTensor, optional): Face adjacency matrix with shape - :obj:`[3, num_faces]`. (default: :obj:`None`) - - The data object is not restricted to these attributes and can be extended - by any other additional data. - - Example:: - - data = Data(x=x, edge_index=edge_index) - data.train_idx = torch.tensor([...], dtype=torch.long) - data.test_mask = torch.tensor([...], dtype=torch.bool) - """ - - def __init__( - self, - x=None, - edge_index=None, - edge_attr=None, - y=None, - pos=None, - normal=None, - face=None, - **kwargs, - ): - self.x = x - self.edge_index = edge_index - self.edge_attr = edge_attr - self.y = y - self.pos = pos - self.normal = normal - self.face = face - for key, item in kwargs.items(): - if key == "num_nodes": - self.__num_nodes__ = item - else: - self[key] = item - - if edge_index is not None and edge_index.dtype != torch.long: - raise ValueError( - ( - f"Argument `edge_index` needs to be of type `torch.long` but " - f"found type `{edge_index.dtype}`." - ) - ) - - if face is not None and face.dtype != torch.long: - raise ValueError( - ( - f"Argument `face` needs to be of type `torch.long` but found " - f"type `{face.dtype}`." - ) - ) - - @classmethod - def from_dict(cls, dictionary): - r"""Creates a data object from a python dictionary.""" - data = cls() - - for key, item in dictionary.items(): - data[key] = item - - return data - - def to_dict(self): - return {key: item for key, item in self} - - def to_namedtuple(self): - keys = self.keys - DataTuple = collections.namedtuple("DataTuple", keys) - return DataTuple(*[self[key] for key in keys]) - - def __getitem__(self, key): - r"""Gets the data of the attribute :obj:`key`.""" - return getattr(self, key, None) - - def __setitem__(self, key, value): - """Sets the attribute :obj:`key` to :obj:`value`.""" - setattr(self, key, value) - - def __delitem__(self, key): - r"""Delete the data of the attribute :obj:`key`.""" - return delattr(self, key) - - @property - def keys(self): - r"""Returns all names of graph attributes.""" - keys = [key for key in self.__dict__.keys() if self[key] is not None] - keys = [key for key in keys if key[:2] != "__" and key[-2:] != "__"] - return keys - - def __len__(self): - r"""Returns the number of all present attributes.""" - return len(self.keys) - - def __contains__(self, key): - r"""Returns :obj:`True`, if the attribute :obj:`key` is present in the - data.""" - return key in self.keys - - def __iter__(self): - r"""Iterates over all present attributes in the data, yielding their - attribute names and content.""" - for key in sorted(self.keys): - yield key, self[key] - - def __call__(self, *keys): - r"""Iterates over all attributes :obj:`*keys` in the data, yielding - their attribute names and content. - If :obj:`*keys` is not given this method will iterative over all - present attributes.""" - for key in sorted(self.keys) if not keys else keys: - if key in self: - yield key, self[key] - - def __cat_dim__(self, key, value): - r"""Returns the dimension for which :obj:`value` of attribute - :obj:`key` will get concatenated when creating batches. - - .. note:: - - This method is for internal use only, and should only be overridden - if the batch concatenation process is corrupted for a specific data - attribute. - """ - if bool(re.search("(index|face)", key)): - return -1 - return 0 - - def __inc__(self, key, value): - r"""Returns the incremental count to cumulatively increase the value - of the next attribute of :obj:`key` when creating batches. - - .. note:: - - This method is for internal use only, and should only be overridden - if the batch concatenation process is corrupted for a specific data - attribute. - """ - # Only `*index*` and `*face*` attributes should be cumulatively summed - # up when creating batches. - return self.num_nodes if bool(re.search("(index|face)", key)) else 0 - - @property - def num_nodes(self): - r"""Returns or sets the number of nodes in the graph. - - .. note:: - The number of nodes in your data object is typically automatically - inferred, *e.g.*, when node features :obj:`x` are present. - In some cases however, a graph may only be given by its edge - indices :obj:`edge_index`. - PyTorch Geometric then *guesses* the number of nodes - according to :obj:`edge_index.max().item() + 1`, but in case there - exists isolated nodes, this number has not to be correct and can - therefore result in unexpected batch-wise behavior. - Thus, we recommend to set the number of nodes in your data object - explicitly via :obj:`data.num_nodes = ...`. - You will be given a warning that requests you to do so. - """ - if hasattr(self, "__num_nodes__"): - return self.__num_nodes__ - for key, item in self("x", "pos", "normal", "batch"): - return item.size(self.__cat_dim__(key, item)) - if hasattr(self, "adj"): - return self.adj.size(0) - if hasattr(self, "adj_t"): - return self.adj_t.size(1) - # if self.face is not None: - # logging.warning(__num_nodes_warn_msg__.format("face")) - # return maybe_num_nodes(self.face) - # if self.edge_index is not None: - # logging.warning(__num_nodes_warn_msg__.format("edge")) - # return maybe_num_nodes(self.edge_index) - return None - - @num_nodes.setter - def num_nodes(self, num_nodes): - self.__num_nodes__ = num_nodes - - @property - def num_edges(self): - """ - Returns the number of edges in the graph. - For undirected graphs, this will return the number of bi-directional - edges, which is double the amount of unique edges. - """ - for key, item in self("edge_index", "edge_attr"): - return item.size(self.__cat_dim__(key, item)) - for key, item in self("adj", "adj_t"): - return item.nnz() - return None - - @property - def num_faces(self): - r"""Returns the number of faces in the mesh.""" - if self.face is not None: - return self.face.size(self.__cat_dim__("face", self.face)) - return None - - @property - def num_node_features(self): - r"""Returns the number of features per node in the graph.""" - if self.x is None: - return 0 - return 1 if self.x.dim() == 1 else self.x.size(1) - - @property - def num_features(self): - r"""Alias for :py:attr:`~num_node_features`.""" - return self.num_node_features - - @property - def num_edge_features(self): - r"""Returns the number of features per edge in the graph.""" - if self.edge_attr is None: - return 0 - return 1 if self.edge_attr.dim() == 1 else self.edge_attr.size(1) - - def __apply__(self, item, func): - if torch.is_tensor(item): - return func(item) - elif isinstance(item, (tuple, list)): - return [self.__apply__(v, func) for v in item] - elif isinstance(item, dict): - return {k: self.__apply__(v, func) for k, v in item.items()} - else: - return item - - def apply(self, func, *keys): - r"""Applies the function :obj:`func` to all tensor attributes - :obj:`*keys`. If :obj:`*keys` is not given, :obj:`func` is applied to - all present attributes. - """ - for key, item in self(*keys): - self[key] = self.__apply__(item, func) - return self - - def contiguous(self, *keys): - r"""Ensures a contiguous memory layout for all attributes :obj:`*keys`. - If :obj:`*keys` is not given, all present attributes are ensured to - have a contiguous memory layout.""" - return self.apply(lambda x: x.contiguous(), *keys) - - def to(self, device, *keys, **kwargs): - r"""Performs tensor dtype and/or device conversion to all attributes - :obj:`*keys`. - If :obj:`*keys` is not given, the conversion is applied to all present - attributes.""" - return self.apply(lambda x: x.to(device, **kwargs), *keys) - - def cpu(self, *keys): - r"""Copies all attributes :obj:`*keys` to CPU memory. - If :obj:`*keys` is not given, the conversion is applied to all present - attributes.""" - return self.apply(lambda x: x.cpu(), *keys) - - def cuda(self, device=None, non_blocking=False, *keys): - r"""Copies all attributes :obj:`*keys` to CUDA memory. - If :obj:`*keys` is not given, the conversion is applied to all present - attributes.""" - return self.apply( - lambda x: x.cuda(device=device, non_blocking=non_blocking), *keys - ) - - def clone(self): - r"""Performs a deep-copy of the data object.""" - return self.__class__.from_dict( - { - k: v.clone() if torch.is_tensor(v) else copy.deepcopy(v) - for k, v in self.__dict__.items() - } - ) - - def pin_memory(self, *keys): - r"""Copies all attributes :obj:`*keys` to pinned memory. - If :obj:`*keys` is not given, the conversion is applied to all present - attributes.""" - return self.apply(lambda x: x.pin_memory(), *keys) - - def debug(self): - if self.edge_index is not None: - if self.edge_index.dtype != torch.long: - raise RuntimeError( - ( - "Expected edge indices of dtype {}, but found dtype " " {}" - ).format(torch.long, self.edge_index.dtype) - ) - - if self.face is not None: - if self.face.dtype != torch.long: - raise RuntimeError( - ( - "Expected face indices of dtype {}, but found dtype " " {}" - ).format(torch.long, self.face.dtype) - ) - - if self.edge_index is not None: - if self.edge_index.dim() != 2 or self.edge_index.size(0) != 2: - raise RuntimeError( - ( - "Edge indices should have shape [2, num_edges] but found" - " shape {}" - ).format(self.edge_index.size()) - ) - - if self.edge_index is not None and self.num_nodes is not None: - if self.edge_index.numel() > 0: - min_index = self.edge_index.min() - max_index = self.edge_index.max() - else: - min_index = max_index = 0 - if min_index < 0 or max_index > self.num_nodes - 1: - raise RuntimeError( - ( - "Edge indices must lay in the interval [0, {}]" - " but found them in the interval [{}, {}]" - ).format(self.num_nodes - 1, min_index, max_index) - ) - - if self.face is not None: - if self.face.dim() != 2 or self.face.size(0) != 3: - raise RuntimeError( - ( - "Face indices should have shape [3, num_faces] but found" - " shape {}" - ).format(self.face.size()) - ) - - if self.face is not None and self.num_nodes is not None: - if self.face.numel() > 0: - min_index = self.face.min() - max_index = self.face.max() - else: - min_index = max_index = 0 - if min_index < 0 or max_index > self.num_nodes - 1: - raise RuntimeError( - ( - "Face indices must lay in the interval [0, {}]" - " but found them in the interval [{}, {}]" - ).format(self.num_nodes - 1, min_index, max_index) - ) - - if self.edge_index is not None and self.edge_attr is not None: - if self.edge_index.size(1) != self.edge_attr.size(0): - raise RuntimeError( - ( - "Edge indices and edge attributes hold a differing " - "number of edges, found {} and {}" - ).format(self.edge_index.size(), self.edge_attr.size()) - ) - - if self.x is not None and self.num_nodes is not None: - if self.x.size(0) != self.num_nodes: - raise RuntimeError( - ( - "Node features should hold {} elements in the first " - "dimension but found {}" - ).format(self.num_nodes, self.x.size(0)) - ) - - if self.pos is not None and self.num_nodes is not None: - if self.pos.size(0) != self.num_nodes: - raise RuntimeError( - ( - "Node positions should hold {} elements in the first " - "dimension but found {}" - ).format(self.num_nodes, self.pos.size(0)) - ) - - if self.normal is not None and self.num_nodes is not None: - if self.normal.size(0) != self.num_nodes: - raise RuntimeError( - ( - "Node normals should hold {} elements in the first " - "dimension but found {}" - ).format(self.num_nodes, self.normal.size(0)) - ) - - def __repr__(self): - cls = str(self.__class__.__name__) - has_dict = any([isinstance(item, dict) for _, item in self]) - - if not has_dict: - info = [size_repr(key, item) for key, item in self] - return "{}({})".format(cls, ", ".join(info)) - else: - info = [size_repr(key, item, indent=2) for key, item in self] - return "{}(\n{}\n)".format(cls, ",\n".join(info)) diff --git a/mace-bench/3rdparty/mace/mace/tools/torch_geometric/dataloader.py b/mace-bench/3rdparty/mace/mace/tools/torch_geometric/dataloader.py deleted file mode 100644 index 396b7e7285ac192cb8d6d5e26f686321734d132b..0000000000000000000000000000000000000000 --- a/mace-bench/3rdparty/mace/mace/tools/torch_geometric/dataloader.py +++ /dev/null @@ -1,87 +0,0 @@ -from collections.abc import Mapping, Sequence -from typing import List, Optional, Union - -import torch.utils.data -from torch.utils.data.dataloader import default_collate - -from .batch import Batch -from .data import Data -from .dataset import Dataset - - -class Collater: - def __init__(self, follow_batch, exclude_keys): - self.follow_batch = follow_batch - self.exclude_keys = exclude_keys - - def __call__(self, batch): - elem = batch[0] - if isinstance(elem, Data): - return Batch.from_data_list( - batch, - follow_batch=self.follow_batch, - exclude_keys=self.exclude_keys, - ) - elif isinstance(elem, torch.Tensor): - return default_collate(batch) - elif isinstance(elem, float): - return torch.tensor(batch, dtype=torch.float) - elif isinstance(elem, int): - return torch.tensor(batch) - elif isinstance(elem, str): - return batch - elif isinstance(elem, Mapping): - return {key: self([data[key] for data in batch]) for key in elem} - elif isinstance(elem, tuple) and hasattr(elem, "_fields"): - return type(elem)(*(self(s) for s in zip(*batch))) - elif isinstance(elem, Sequence) and not isinstance(elem, str): - return [self(s) for s in zip(*batch)] - - raise TypeError(f"DataLoader found invalid type: {type(elem)}") - - def collate(self, batch): # Deprecated... - return self(batch) - - -class DataLoader(torch.utils.data.DataLoader): - r"""A data loader which merges data objects from a - :class:`torch_geometric.data.Dataset` to a mini-batch. - Data objects can be either of type :class:`~torch_geometric.data.Data` or - :class:`~torch_geometric.data.HeteroData`. - Args: - dataset (Dataset): The dataset from which to load the data. - batch_size (int, optional): How many samples per batch to load. - (default: :obj:`1`) - shuffle (bool, optional): If set to :obj:`True`, the data will be - reshuffled at every epoch. (default: :obj:`False`) - follow_batch (List[str], optional): Creates assignment batch - vectors for each key in the list. (default: :obj:`None`) - exclude_keys (List[str], optional): Will exclude each key in the - list. (default: :obj:`None`) - **kwargs (optional): Additional arguments of - :class:`torch.utils.data.DataLoader`. - """ - - def __init__( - self, - dataset: Dataset, - batch_size: int = 1, - shuffle: bool = False, - follow_batch: Optional[List[str]] = [None], - exclude_keys: Optional[List[str]] = [None], - **kwargs, - ): - if "collate_fn" in kwargs: - del kwargs["collate_fn"] - - # Save for PyTorch Lightning < 1.6: - self.follow_batch = follow_batch - self.exclude_keys = exclude_keys - - super().__init__( - dataset, - batch_size, - shuffle, - collate_fn=Collater(follow_batch, exclude_keys), - **kwargs, - ) diff --git a/mace-bench/3rdparty/mace/mace/tools/torch_geometric/dataset.py b/mace-bench/3rdparty/mace/mace/tools/torch_geometric/dataset.py deleted file mode 100644 index b4aeb2be9149ed68be67cc9009531ac809ac6787..0000000000000000000000000000000000000000 --- a/mace-bench/3rdparty/mace/mace/tools/torch_geometric/dataset.py +++ /dev/null @@ -1,280 +0,0 @@ -import copy -import os.path as osp -import re -import warnings -from collections.abc import Sequence -from typing import Any, Callable, List, Optional, Tuple, Union - -import numpy as np -import torch.utils.data -from torch import Tensor - -from .data import Data -from .utils import makedirs - -IndexType = Union[slice, Tensor, np.ndarray, Sequence] - - -class Dataset(torch.utils.data.Dataset): - r"""Dataset base class for creating graph datasets. - See `here `__ for the accompanying tutorial. - - Args: - root (string, optional): Root directory where the dataset should be - saved. (optional: :obj:`None`) - transform (callable, optional): A function/transform that takes in an - :obj:`torch_geometric.data.Data` object and returns a transformed - version. The data object will be transformed before every access. - (default: :obj:`None`) - pre_transform (callable, optional): A function/transform that takes in - an :obj:`torch_geometric.data.Data` object and returns a - transformed version. The data object will be transformed before - being saved to disk. (default: :obj:`None`) - pre_filter (callable, optional): A function that takes in an - :obj:`torch_geometric.data.Data` object and returns a boolean - value, indicating whether the data object should be included in the - final dataset. (default: :obj:`None`) - """ - - @property - def raw_file_names(self) -> Union[str, List[str], Tuple]: - r"""The name of the files to find in the :obj:`self.raw_dir` folder in - order to skip the download.""" - raise NotImplementedError - - @property - def processed_file_names(self) -> Union[str, List[str], Tuple]: - r"""The name of the files to find in the :obj:`self.processed_dir` - folder in order to skip the processing.""" - raise NotImplementedError - - def download(self): - r"""Downloads the dataset to the :obj:`self.raw_dir` folder.""" - raise NotImplementedError - - def process(self): - r"""Processes the dataset to the :obj:`self.processed_dir` folder.""" - raise NotImplementedError - - def len(self) -> int: - raise NotImplementedError - - def get(self, idx: int) -> Data: - r"""Gets the data object at index :obj:`idx`.""" - raise NotImplementedError - - def __init__( - self, - root: Optional[str] = None, - transform: Optional[Callable] = None, - pre_transform: Optional[Callable] = None, - pre_filter: Optional[Callable] = None, - ): - super().__init__() - - if isinstance(root, str): - root = osp.expanduser(osp.normpath(root)) - - self.root = root - self.transform = transform - self.pre_transform = pre_transform - self.pre_filter = pre_filter - self._indices: Optional[Sequence] = None - - if "download" in self.__class__.__dict__.keys(): - self._download() - - if "process" in self.__class__.__dict__.keys(): - self._process() - - def indices(self) -> Sequence: - return range(self.len()) if self._indices is None else self._indices - - @property - def raw_dir(self) -> str: - return osp.join(self.root, "raw") - - @property - def processed_dir(self) -> str: - return osp.join(self.root, "processed") - - @property - def num_node_features(self) -> int: - r"""Returns the number of features per node in the dataset.""" - data = self[0] - if hasattr(data, "num_node_features"): - return data.num_node_features - raise AttributeError( - f"'{data.__class__.__name__}' object has no " - f"attribute 'num_node_features'" - ) - - @property - def num_features(self) -> int: - r"""Alias for :py:attr:`~num_node_features`.""" - return self.num_node_features - - @property - def num_edge_features(self) -> int: - r"""Returns the number of features per edge in the dataset.""" - data = self[0] - if hasattr(data, "num_edge_features"): - return data.num_edge_features - raise AttributeError( - f"'{data.__class__.__name__}' object has no " - f"attribute 'num_edge_features'" - ) - - @property - def raw_paths(self) -> List[str]: - r"""The filepaths to find in order to skip the download.""" - files = to_list(self.raw_file_names) - return [osp.join(self.raw_dir, f) for f in files] - - @property - def processed_paths(self) -> List[str]: - r"""The filepaths to find in the :obj:`self.processed_dir` - folder in order to skip the processing.""" - files = to_list(self.processed_file_names) - return [osp.join(self.processed_dir, f) for f in files] - - def _download(self): - if files_exist(self.raw_paths): # pragma: no cover - return - - makedirs(self.raw_dir) - self.download() - - def _process(self): - f = osp.join(self.processed_dir, "pre_transform.pt") - if osp.exists(f) and torch.load(f) != _repr(self.pre_transform): - warnings.warn( - f"The `pre_transform` argument differs from the one used in " - f"the pre-processed version of this dataset. If you want to " - f"make use of another pre-processing technique, make sure to " - f"sure to delete '{self.processed_dir}' first" - ) - - f = osp.join(self.processed_dir, "pre_filter.pt") - if osp.exists(f) and torch.load(f) != _repr(self.pre_filter): - warnings.warn( - "The `pre_filter` argument differs from the one used in the " - "pre-processed version of this dataset. If you want to make " - "use of another pre-fitering technique, make sure to delete " - "'{self.processed_dir}' first" - ) - - if files_exist(self.processed_paths): # pragma: no cover - return - - print("Processing...") - - makedirs(self.processed_dir) - self.process() - - path = osp.join(self.processed_dir, "pre_transform.pt") - torch.save(_repr(self.pre_transform), path) - path = osp.join(self.processed_dir, "pre_filter.pt") - torch.save(_repr(self.pre_filter), path) - - print("Done!") - - def __len__(self) -> int: - r"""The number of examples in the dataset.""" - return len(self.indices()) - - def __getitem__( - self, - idx: Union[int, np.integer, IndexType], - ) -> Union["Dataset", Data]: - r"""In case :obj:`idx` is of type integer, will return the data object - at index :obj:`idx` (and transforms it in case :obj:`transform` is - present). - In case :obj:`idx` is a slicing object, *e.g.*, :obj:`[2:5]`, a list, a - tuple, a PyTorch :obj:`LongTensor` or a :obj:`BoolTensor`, or a numpy - :obj:`np.array`, will return a subset of the dataset at the specified - indices.""" - if ( - isinstance(idx, (int, np.integer)) - or (isinstance(idx, Tensor) and idx.dim() == 0) - or (isinstance(idx, np.ndarray) and np.isscalar(idx)) - ): - data = self.get(self.indices()[idx]) - data = data if self.transform is None else self.transform(data) - return data - - else: - return self.index_select(idx) - - def index_select(self, idx: IndexType) -> "Dataset": - indices = self.indices() - - if isinstance(idx, slice): - indices = indices[idx] - - elif isinstance(idx, Tensor) and idx.dtype == torch.long: - return self.index_select(idx.flatten().tolist()) - - elif isinstance(idx, Tensor) and idx.dtype == torch.bool: - idx = idx.flatten().nonzero(as_tuple=False) - return self.index_select(idx.flatten().tolist()) - - elif isinstance(idx, np.ndarray) and idx.dtype == np.int64: - return self.index_select(idx.flatten().tolist()) - - elif isinstance(idx, np.ndarray) and idx.dtype == np.bool: - idx = idx.flatten().nonzero()[0] - return self.index_select(idx.flatten().tolist()) - - elif isinstance(idx, Sequence) and not isinstance(idx, str): - indices = [indices[i] for i in idx] - - else: - raise IndexError( - f"Only integers, slices (':'), list, tuples, torch.tensor and " - f"np.ndarray of dtype long or bool are valid indices (got " - f"'{type(idx).__name__}')" - ) - - dataset = copy.copy(self) - dataset._indices = indices - return dataset - - def shuffle( - self, - return_perm: bool = False, - ) -> Union["Dataset", Tuple["Dataset", Tensor]]: - r"""Randomly shuffles the examples in the dataset. - - Args: - return_perm (bool, optional): If set to :obj:`True`, will return - the random permutation used to shuffle the dataset in addition. - (default: :obj:`False`) - """ - perm = torch.randperm(len(self)) - dataset = self.index_select(perm) - return (dataset, perm) if return_perm is True else dataset - - def __repr__(self) -> str: - arg_repr = str(len(self)) if len(self) > 1 else "" - return f"{self.__class__.__name__}({arg_repr})" - - -def to_list(value: Any) -> Sequence: - if isinstance(value, Sequence) and not isinstance(value, str): - return value - else: - return [value] - - -def files_exist(files: List[str]) -> bool: - # NOTE: We return `False` in case `files` is empty, leading to a - # re-processing of files on every instantiation. - return len(files) != 0 and all([osp.exists(f) for f in files]) - - -def _repr(obj: Any) -> str: - if obj is None: - return "None" - return re.sub("(<.*?)\\s.*(>)", r"\1\2", obj.__repr__()) diff --git a/mace-bench/3rdparty/mace/mace/tools/torch_geometric/seed.py b/mace-bench/3rdparty/mace/mace/tools/torch_geometric/seed.py deleted file mode 100644 index be27fcaa1636632a9c95022990b4d9a9ac21744d..0000000000000000000000000000000000000000 --- a/mace-bench/3rdparty/mace/mace/tools/torch_geometric/seed.py +++ /dev/null @@ -1,17 +0,0 @@ -import random - -import numpy as np -import torch - - -def seed_everything(seed: int): - r"""Sets the seed for generating random numbers in :pytorch:`PyTorch`, - :obj:`numpy` and Python. - - Args: - seed (int): The desired seed. - """ - random.seed(seed) - np.random.seed(seed) - torch.manual_seed(seed) - torch.cuda.manual_seed_all(seed) diff --git a/mace-bench/3rdparty/mace/mace/tools/torch_geometric/utils.py b/mace-bench/3rdparty/mace/mace/tools/torch_geometric/utils.py deleted file mode 100644 index f53b8f8098a1efcd39669b9dbe94dc0399a2190f..0000000000000000000000000000000000000000 --- a/mace-bench/3rdparty/mace/mace/tools/torch_geometric/utils.py +++ /dev/null @@ -1,54 +0,0 @@ -import os -import os.path as osp -import ssl -import urllib -import zipfile - - -def makedirs(dir): - os.makedirs(dir, exist_ok=True) - - -def download_url(url, folder, log=True): - r"""Downloads the content of an URL to a specific folder. - - Args: - url (string): The url. - folder (string): The folder. - log (bool, optional): If :obj:`False`, will not print anything to the - console. (default: :obj:`True`) - """ - - filename = url.rpartition("/")[2].split("?")[0] - path = osp.join(folder, filename) - - if osp.exists(path): # pragma: no cover - if log: - print("Using exist file", filename) - return path - - if log: - print("Downloading", url) - - makedirs(folder) - - context = ssl._create_unverified_context() - data = urllib.request.urlopen(url, context=context) - - with open(path, "wb") as f: - f.write(data.read()) - - return path - - -def extract_zip(path, folder, log=True): - r"""Extracts a zip archive to a specific folder. - - Args: - path (string): The path to the tar archive. - folder (string): The folder. - log (bool, optional): If :obj:`False`, will not print anything to the - console. (default: :obj:`True`) - """ - with zipfile.ZipFile(path, "r") as f: - f.extractall(folder) diff --git a/mace-bench/3rdparty/mace/mace/tools/torch_tools.py b/mace-bench/3rdparty/mace/mace/tools/torch_tools.py deleted file mode 100644 index 2ab339ef81808a44c6b26b8daa59ccc204eee57d..0000000000000000000000000000000000000000 --- a/mace-bench/3rdparty/mace/mace/tools/torch_tools.py +++ /dev/null @@ -1,153 +0,0 @@ -########################################################################################### -# Tools for torch -# Authors: Ilyes Batatia, Gregor Simm -# This program is distributed under the MIT License (see MIT.md) -########################################################################################### - -import logging -from contextlib import contextmanager -from typing import Dict, Union - -import numpy as np -import torch -from e3nn.io import CartesianTensor - -TensorDict = Dict[str, torch.Tensor] - - -def to_one_hot(indices: torch.Tensor, num_classes: int) -> torch.Tensor: - """ - Generates one-hot encoding with classes from - :param indices: (N x 1) tensor - :param num_classes: number of classes - :param device: torch device - :return: (N x num_classes) tensor - """ - shape = indices.shape[:-1] + (num_classes,) - oh = torch.zeros(shape, device=indices.device).view(shape) - - # scatter_ is the in-place version of scatter - oh.scatter_(dim=-1, index=indices, value=1) - - return oh.view(*shape) - - -def count_parameters(module: torch.nn.Module) -> int: - return int(sum(np.prod(p.shape) for p in module.parameters())) - - -def tensor_dict_to_device(td: TensorDict, device: torch.device) -> TensorDict: - return {k: v.to(device) if v is not None else None for k, v in td.items()} - - -def set_seeds(seed: int) -> None: - np.random.seed(seed) - torch.manual_seed(seed) - - -def to_numpy(t: torch.Tensor) -> np.ndarray: - return t.cpu().detach().numpy() - - -def init_device(device_str: str) -> torch.device: - if "cuda" in device_str: - assert torch.cuda.is_available(), "No CUDA device available!" - if ":" in device_str: - # Check if the desired device is available - assert int(device_str.split(":")[-1]) < torch.cuda.device_count() - logging.info( - f"CUDA version: {torch.version.cuda}, CUDA device: {torch.cuda.current_device()}" - ) - torch.cuda.init() - return torch.device(device_str) - if device_str == "mps": - assert torch.backends.mps.is_available(), "No MPS backend is available!" - logging.info("Using MPS GPU acceleration") - return torch.device("mps") - if device_str == "xpu": - torch.xpu.is_available() - return torch.device("xpu") - - logging.info("Using CPU") - return torch.device("cpu") - - -dtype_dict = {"float32": torch.float32, "float64": torch.float64} - - -def set_default_dtype(dtype: str) -> None: - torch.set_default_dtype(dtype_dict[dtype]) - - -def spherical_to_cartesian(t: torch.Tensor): - """ - Convert spherical notation to cartesian notation - """ - stress_cart_tensor = CartesianTensor("ij=ji") - stress_rtp = stress_cart_tensor.reduced_tensor_products() - return stress_cart_tensor.to_cartesian(t, rtp=stress_rtp) - - -def cartesian_to_spherical(t: torch.Tensor): - """ - Convert cartesian notation to spherical notation - """ - stress_cart_tensor = CartesianTensor("ij=ji") - stress_rtp = stress_cart_tensor.reduced_tensor_products() - return stress_cart_tensor.to_cartesian(t, rtp=stress_rtp) - - -def voigt_to_matrix(t: torch.Tensor): - """ - Convert voigt notation to matrix notation - :param t: (6,) tensor or (3, 3) tensor or (9,) tensor - :return: (3, 3) tensor - """ - if t.shape == (3, 3): - return t - if t.shape == (6,): - return torch.tensor( - [ - [t[0], t[5], t[4]], - [t[5], t[1], t[3]], - [t[4], t[3], t[2]], - ], - dtype=t.dtype, - ) - if t.shape == (9,): - return t.view(3, 3) - - raise ValueError( - f"Stress tensor must be of shape (6,) or (3, 3), or (9,) but has shape {t.shape}" - ) - - -def init_wandb(project: str, entity: str, name: str, config: dict, directory: str): - import wandb - - wandb.init( - project=project, - entity=entity, - name=name, - config=config, - dir=directory, - resume="allow", - ) - - -@contextmanager -def default_dtype(dtype: Union[torch.dtype, str]): - """Context manager for configuring the default_dtype used by torch - - Args: - dtype (torch.dtype|str): the default dtype to use within this context manager - """ - init = torch.get_default_dtype() - if isinstance(dtype, str): - set_default_dtype(dtype) - else: - torch.set_default_dtype(dtype) - - yield - - torch.set_default_dtype(init) diff --git a/mace-bench/3rdparty/mace/mace/tools/train.py b/mace-bench/3rdparty/mace/mace/tools/train.py deleted file mode 100644 index c7c17e136952d3408ac9914d6bb6498b7b048ae0..0000000000000000000000000000000000000000 --- a/mace-bench/3rdparty/mace/mace/tools/train.py +++ /dev/null @@ -1,669 +0,0 @@ -########################################################################################### -# Training script -# Authors: Ilyes Batatia, Gregor Simm, David Kovacs -# This program is distributed under the MIT License (see MIT.md) -########################################################################################### - -import dataclasses -import logging -import time -from contextlib import nullcontext -from typing import Any, Dict, List, Optional, Tuple, Union - -import numpy as np -import torch -import torch.distributed -from torch.nn.parallel import DistributedDataParallel -from torch.optim import LBFGS -from torch.optim.swa_utils import SWALR, AveragedModel -from torch.utils.data import DataLoader -from torch.utils.data.distributed import DistributedSampler -from torch_ema import ExponentialMovingAverage -from torchmetrics import Metric - -from mace.cli.visualise_train import TrainingPlotter - -from . import torch_geometric -from .checkpoint import CheckpointHandler, CheckpointState -from .torch_tools import to_numpy -from .utils import ( - MetricsLogger, - compute_mae, - compute_q95, - compute_rel_mae, - compute_rel_rmse, - compute_rmse, -) - - -@dataclasses.dataclass -class SWAContainer: - model: AveragedModel - scheduler: SWALR - start: int - loss_fn: torch.nn.Module - - -def valid_err_log( - valid_loss, - eval_metrics, - logger, - log_errors, - epoch=None, - valid_loader_name="Default", -): - eval_metrics["mode"] = "eval" - eval_metrics["epoch"] = epoch - eval_metrics["head"] = valid_loader_name - logger.log(eval_metrics) - if epoch is None: - inintial_phrase = "Initial" - else: - inintial_phrase = f"Epoch {epoch}" - if log_errors == "PerAtomRMSE": - error_e = eval_metrics["rmse_e_per_atom"] * 1e3 - error_f = eval_metrics["rmse_f"] * 1e3 - logging.info( - f"{inintial_phrase}: head: {valid_loader_name}, loss={valid_loss:8.8f}, RMSE_E_per_atom={error_e:8.2f} meV, RMSE_F={error_f:8.2f} meV / A" - ) - elif ( - log_errors == "PerAtomRMSEstressvirials" - and eval_metrics["rmse_stress"] is not None - ): - error_e = eval_metrics["rmse_e_per_atom"] * 1e3 - error_f = eval_metrics["rmse_f"] * 1e3 - error_stress = eval_metrics["rmse_stress"] * 1e3 - logging.info( - f"{inintial_phrase}: head: {valid_loader_name}, loss={valid_loss:8.8f}, RMSE_E_per_atom={error_e:8.2f} meV, RMSE_F={error_f:8.2f} meV / A, RMSE_stress={error_stress:8.2f} meV / A^3", - ) - elif ( - log_errors == "PerAtomRMSEstressvirials" - and eval_metrics["rmse_virials_per_atom"] is not None - ): - error_e = eval_metrics["rmse_e_per_atom"] * 1e3 - error_f = eval_metrics["rmse_f"] * 1e3 - error_virials = eval_metrics["rmse_virials_per_atom"] * 1e3 - logging.info( - f"{inintial_phrase}: head: {valid_loader_name}, loss={valid_loss:8.8f}, RMSE_E_per_atom={error_e:8.2f} meV, RMSE_F={error_f:8.2f} meV / A, RMSE_virials_per_atom={error_virials:8.2f} meV", - ) - elif ( - log_errors == "PerAtomMAEstressvirials" - and eval_metrics["mae_stress_per_atom"] is not None - ): - error_e = eval_metrics["mae_e_per_atom"] * 1e3 - error_f = eval_metrics["mae_f"] * 1e3 - error_stress = eval_metrics["mae_stress"] * 1e3 - logging.info( - f"{inintial_phrase}: loss={valid_loss:8.8f}, MAE_E_per_atom={error_e:8.2f} meV, MAE_F={error_f:8.2f} meV / A, MAE_stress={error_stress:8.2f} meV / A^3" - ) - elif ( - log_errors == "PerAtomMAEstressvirials" - and eval_metrics["mae_virials_per_atom"] is not None - ): - error_e = eval_metrics["mae_e_per_atom"] * 1e3 - error_f = eval_metrics["mae_f"] * 1e3 - error_virials = eval_metrics["mae_virials"] * 1e3 - logging.info( - f"{inintial_phrase}: loss={valid_loss:8.8f}, MAE_E_per_atom={error_e:8.2f} meV, MAE_F={error_f:8.2f} meV / A, MAE_virials={error_virials:8.2f} meV" - ) - elif log_errors == "TotalRMSE": - error_e = eval_metrics["rmse_e"] * 1e3 - error_f = eval_metrics["rmse_f"] * 1e3 - logging.info( - f"{inintial_phrase}: head: {valid_loader_name}, loss={valid_loss:8.8f}, RMSE_E={error_e:8.2f} meV, RMSE_F={error_f:8.2f} meV / A", - ) - elif log_errors == "PerAtomMAE": - error_e = eval_metrics["mae_e_per_atom"] * 1e3 - error_f = eval_metrics["mae_f"] * 1e3 - logging.info( - f"{inintial_phrase}: head: {valid_loader_name}, loss={valid_loss:8.8f}, MAE_E_per_atom={error_e:8.2f} meV, MAE_F={error_f:8.2f} meV / A", - ) - elif log_errors == "TotalMAE": - error_e = eval_metrics["mae_e"] * 1e3 - error_f = eval_metrics["mae_f"] * 1e3 - logging.info( - f"{inintial_phrase}: head: {valid_loader_name}, loss={valid_loss:8.8f}, MAE_E={error_e:8.2f} meV, MAE_F={error_f:8.2f} meV / A", - ) - elif log_errors == "DipoleRMSE": - error_mu = eval_metrics["rmse_mu_per_atom"] * 1e3 - logging.info( - f"{inintial_phrase}: head: {valid_loader_name}, loss={valid_loss:8.8f}, RMSE_MU_per_atom={error_mu:8.2f} mDebye", - ) - elif log_errors == "EnergyDipoleRMSE": - error_e = eval_metrics["rmse_e_per_atom"] * 1e3 - error_f = eval_metrics["rmse_f"] * 1e3 - error_mu = eval_metrics["rmse_mu_per_atom"] * 1e3 - logging.info( - f"{inintial_phrase}: head: {valid_loader_name}, loss={valid_loss:8.8f}, RMSE_E_per_atom={error_e:8.2f} meV, RMSE_F={error_f:8.2f} meV / A, RMSE_Mu_per_atom={error_mu:8.2f} mDebye", - ) - - -def train( - model: torch.nn.Module, - loss_fn: torch.nn.Module, - train_loader: DataLoader, - valid_loaders: Dict[str, DataLoader], - optimizer: torch.optim.Optimizer, - lr_scheduler: torch.optim.lr_scheduler.ExponentialLR, - start_epoch: int, - max_num_epochs: int, - patience: int, - checkpoint_handler: CheckpointHandler, - logger: MetricsLogger, - eval_interval: int, - output_args: Dict[str, bool], - device: torch.device, - log_errors: str, - swa: Optional[SWAContainer] = None, - ema: Optional[ExponentialMovingAverage] = None, - max_grad_norm: Optional[float] = 10.0, - log_wandb: bool = False, - distributed: bool = False, - save_all_checkpoints: bool = False, - plotter: TrainingPlotter = None, - distributed_model: Optional[DistributedDataParallel] = None, - train_sampler: Optional[DistributedSampler] = None, - rank: Optional[int] = 0, -): - lowest_loss = np.inf - valid_loss = np.inf - patience_counter = 0 - swa_start = True - keep_last = False - if log_wandb: - import wandb - - if max_grad_norm is not None: - logging.info(f"Using gradient clipping with tolerance={max_grad_norm:.3f}") - - logging.info("") - logging.info("===========TRAINING===========") - logging.info("Started training, reporting errors on validation set") - logging.info("Loss metrics on validation set") - epoch = start_epoch - - # log validation loss before _any_ training - for valid_loader_name, valid_loader in valid_loaders.items(): - valid_loss_head, eval_metrics = evaluate( - model=model, - loss_fn=loss_fn, - data_loader=valid_loader, - output_args=output_args, - device=device, - ) - valid_err_log( - valid_loss_head, eval_metrics, logger, log_errors, None, valid_loader_name - ) - valid_loss = valid_loss_head # consider only the last head for the checkpoint - - while epoch < max_num_epochs: - # LR scheduler and SWA update - if swa is None or epoch < swa.start: - if epoch > start_epoch: - lr_scheduler.step( - metrics=valid_loss - ) # Can break if exponential LR, TODO fix that! - else: - if swa_start: - logging.info("Changing loss based on Stage Two Weights") - lowest_loss = np.inf - swa_start = False - keep_last = True - loss_fn = swa.loss_fn - swa.model.update_parameters(model) - if epoch > start_epoch: - swa.scheduler.step() - - # Train - if distributed: - train_sampler.set_epoch(epoch) - if "ScheduleFree" in type(optimizer).__name__: - optimizer.train() - train_one_epoch( - model=model, - loss_fn=loss_fn, - data_loader=train_loader, - optimizer=optimizer, - epoch=epoch, - output_args=output_args, - max_grad_norm=max_grad_norm, - ema=ema, - logger=logger, - device=device, - distributed=distributed, - distributed_model=distributed_model, - rank=rank, - ) - if distributed: - torch.distributed.barrier() - - # Validate - if epoch % eval_interval == 0: - model_to_evaluate = ( - model if distributed_model is None else distributed_model - ) - param_context = ( - ema.average_parameters() if ema is not None else nullcontext() - ) - if "ScheduleFree" in type(optimizer).__name__: - optimizer.eval() - with param_context: - wandb_log_dict = {} - for valid_loader_name, valid_loader in valid_loaders.items(): - valid_loss_head, eval_metrics = evaluate( - model=model_to_evaluate, - loss_fn=loss_fn, - data_loader=valid_loader, - output_args=output_args, - device=device, - ) - if rank == 0: - valid_err_log( - valid_loss_head, - eval_metrics, - logger, - log_errors, - epoch, - valid_loader_name, - ) - if log_wandb: - wandb_log_dict[valid_loader_name] = { - "epoch": epoch, - "valid_loss": valid_loss_head, - "valid_rmse_e_per_atom": eval_metrics[ - "rmse_e_per_atom" - ], - "valid_rmse_f": eval_metrics["rmse_f"], - } - if plotter and epoch % plotter.plot_frequency == 0: - try: - plotter.plot(epoch, model_to_evaluate, rank) - except Exception as e: # pylint: disable=broad-except - logging.debug(f"Plotting failed: {e}") - valid_loss = ( - valid_loss_head # consider only the last head for the checkpoint - ) - if log_wandb: - wandb.log(wandb_log_dict) - if rank == 0: - if valid_loss >= lowest_loss: - patience_counter += 1 - if patience_counter >= patience: - if swa is not None and epoch < swa.start: - logging.info( - f"Stopping optimization after {patience_counter} epochs without improvement and starting Stage Two" - ) - epoch = swa.start - else: - logging.info( - f"Stopping optimization after {patience_counter} epochs without improvement" - ) - break - if save_all_checkpoints: - param_context = ( - ema.average_parameters() - if ema is not None - else nullcontext() - ) - with param_context: - checkpoint_handler.save( - state=CheckpointState(model, optimizer, lr_scheduler), - epochs=epoch, - keep_last=True, - ) - else: - lowest_loss = valid_loss - patience_counter = 0 - param_context = ( - ema.average_parameters() if ema is not None else nullcontext() - ) - with param_context: - checkpoint_handler.save( - state=CheckpointState(model, optimizer, lr_scheduler), - epochs=epoch, - keep_last=keep_last, - ) - keep_last = False or save_all_checkpoints - if distributed: - torch.distributed.barrier() - epoch += 1 - - logging.info("Training complete") - - -def train_one_epoch( - model: torch.nn.Module, - loss_fn: torch.nn.Module, - data_loader: DataLoader, - optimizer: torch.optim.Optimizer, - epoch: int, - output_args: Dict[str, bool], - max_grad_norm: Optional[float], - ema: Optional[ExponentialMovingAverage], - logger: MetricsLogger, - device: torch.device, - distributed: bool, - distributed_model: Optional[DistributedDataParallel] = None, - rank: Optional[int] = 0, -) -> None: - model_to_train = model if distributed_model is None else distributed_model - - if isinstance(optimizer, LBFGS): - _, opt_metrics = take_step_lbfgs( - model=model_to_train, - loss_fn=loss_fn, - data_loader=data_loader, - optimizer=optimizer, - ema=ema, - output_args=output_args, - max_grad_norm=max_grad_norm, - device=device, - distributed=distributed, - rank=rank, - ) - opt_metrics["mode"] = "opt" - opt_metrics["epoch"] = epoch - if rank == 0: - logger.log(opt_metrics) - else: - for batch in data_loader: - _, opt_metrics = take_step( - model=model_to_train, - loss_fn=loss_fn, - batch=batch, - optimizer=optimizer, - ema=ema, - output_args=output_args, - max_grad_norm=max_grad_norm, - device=device, - ) - opt_metrics["mode"] = "opt" - opt_metrics["epoch"] = epoch - if rank == 0: - logger.log(opt_metrics) - - -def take_step( - model: torch.nn.Module, - loss_fn: torch.nn.Module, - batch: torch_geometric.batch.Batch, - optimizer: torch.optim.Optimizer, - ema: Optional[ExponentialMovingAverage], - output_args: Dict[str, bool], - max_grad_norm: Optional[float], - device: torch.device, -) -> Tuple[float, Dict[str, Any]]: - start_time = time.time() - batch = batch.to(device) - batch_dict = batch.to_dict() - - def closure(): - optimizer.zero_grad(set_to_none=True) - output = model( - batch_dict, - training=True, - compute_force=output_args["forces"], - compute_virials=output_args["virials"], - compute_stress=output_args["stress"], - ) - loss = loss_fn(pred=output, ref=batch) - loss.backward() - if max_grad_norm is not None: - torch.nn.utils.clip_grad_norm_(model.parameters(), max_norm=max_grad_norm) - - return loss - - loss = closure() - optimizer.step() - - if ema is not None: - ema.update() - - loss_dict = { - "loss": to_numpy(loss), - "time": time.time() - start_time, - } - - return loss, loss_dict - - -def take_step_lbfgs( - model: torch.nn.Module, - loss_fn: torch.nn.Module, - data_loader: DataLoader, - optimizer: torch.optim.Optimizer, - ema: Optional[ExponentialMovingAverage], - output_args: Dict[str, bool], - max_grad_norm: Optional[float], - device: torch.device, - distributed: bool, - rank: int, -) -> Tuple[float, Dict[str, Any]]: - start_time = time.time() - logging.debug( - f"Max Allocated: {torch.cuda.max_memory_allocated() / 1024**2:.2f} MB" - ) - - total_sample_count = 0 - for batch in data_loader: - total_sample_count += batch.num_graphs - - if distributed: - global_sample_count = torch.tensor(total_sample_count, device=device) - torch.distributed.all_reduce( - global_sample_count, op=torch.distributed.ReduceOp.SUM - ) - total_sample_count = global_sample_count.item() - - signal = torch.zeros(1, device=device) if distributed else None - - def closure(): - if distributed: - if rank == 0: - signal.fill_(1) - torch.distributed.broadcast(signal, src=0) - - for param in model.parameters(): - torch.distributed.broadcast(param.data, src=0) - - optimizer.zero_grad(set_to_none=True) - total_loss = torch.tensor(0.0, device=device) - - # Process each batch and then collect the results we pass to the optimizer - for batch in data_loader: - batch = batch.to(device) - batch_dict = batch.to_dict() - output = model( - batch_dict, - training=True, - compute_force=output_args["forces"], - compute_virials=output_args["virials"], - compute_stress=output_args["stress"], - ) - batch_loss = loss_fn(pred=output, ref=batch) - batch_loss = batch_loss * (batch.num_graphs / total_sample_count) - - batch_loss.backward() - total_loss += batch_loss - - if max_grad_norm is not None: - torch.nn.utils.clip_grad_norm_(model.parameters(), max_norm=max_grad_norm) - - if distributed: - torch.distributed.all_reduce(total_loss, op=torch.distributed.ReduceOp.SUM) - return total_loss - - if distributed: - if rank == 0: - loss = optimizer.step(closure) - signal.fill_(0) - torch.distributed.broadcast(signal, src=0) - else: - while True: - # Other ranks wait for signals from rank 0 - torch.distributed.broadcast(signal, src=0) - if signal.item() == 0: - break - if signal.item() == 1: - loss = closure() - - for param in model.parameters(): - torch.distributed.broadcast(param.data, src=0) - else: - loss = optimizer.step(closure) - - if ema is not None: - ema.update() - - loss_dict = { - "loss": to_numpy(loss), - "time": time.time() - start_time, - } - - return loss, loss_dict - - -def evaluate( - model: torch.nn.Module, - loss_fn: torch.nn.Module, - data_loader: DataLoader, - output_args: Dict[str, bool], - device: torch.device, -) -> Tuple[float, Dict[str, Any]]: - for param in model.parameters(): - param.requires_grad = False - - metrics = MACELoss(loss_fn=loss_fn).to(device) - - start_time = time.time() - for batch in data_loader: - batch = batch.to(device) - batch_dict = batch.to_dict() - output = model( - batch_dict, - training=False, - compute_force=output_args["forces"], - compute_virials=output_args["virials"], - compute_stress=output_args["stress"], - ) - avg_loss, aux = metrics(batch, output) - - avg_loss, aux = metrics.compute() - aux["time"] = time.time() - start_time - metrics.reset() - - for param in model.parameters(): - param.requires_grad = True - - return avg_loss, aux - - -class MACELoss(Metric): - def __init__(self, loss_fn: torch.nn.Module): - super().__init__() - self.loss_fn = loss_fn - self.add_state("total_loss", default=torch.tensor(0.0), dist_reduce_fx="sum") - self.add_state("num_data", default=torch.tensor(0.0), dist_reduce_fx="sum") - self.add_state("E_computed", default=torch.tensor(0.0), dist_reduce_fx="sum") - self.add_state("delta_es", default=[], dist_reduce_fx="cat") - self.add_state("delta_es_per_atom", default=[], dist_reduce_fx="cat") - self.add_state("Fs_computed", default=torch.tensor(0.0), dist_reduce_fx="sum") - self.add_state("fs", default=[], dist_reduce_fx="cat") - self.add_state("delta_fs", default=[], dist_reduce_fx="cat") - self.add_state( - "stress_computed", default=torch.tensor(0.0), dist_reduce_fx="sum" - ) - self.add_state("delta_stress", default=[], dist_reduce_fx="cat") - self.add_state( - "virials_computed", default=torch.tensor(0.0), dist_reduce_fx="sum" - ) - self.add_state("delta_virials", default=[], dist_reduce_fx="cat") - self.add_state("delta_virials_per_atom", default=[], dist_reduce_fx="cat") - self.add_state("Mus_computed", default=torch.tensor(0.0), dist_reduce_fx="sum") - self.add_state("mus", default=[], dist_reduce_fx="cat") - self.add_state("delta_mus", default=[], dist_reduce_fx="cat") - self.add_state("delta_mus_per_atom", default=[], dist_reduce_fx="cat") - - def update(self, batch, output): # pylint: disable=arguments-differ - loss = self.loss_fn(pred=output, ref=batch) - self.total_loss += loss - self.num_data += batch.num_graphs - - if output.get("energy") is not None and batch.energy is not None: - self.E_computed += 1.0 - self.delta_es.append(batch.energy - output["energy"]) - self.delta_es_per_atom.append( - (batch.energy - output["energy"]) / (batch.ptr[1:] - batch.ptr[:-1]) - ) - if output.get("forces") is not None and batch.forces is not None: - self.Fs_computed += 1.0 - self.fs.append(batch.forces) - self.delta_fs.append(batch.forces - output["forces"]) - if output.get("stress") is not None and batch.stress is not None: - self.stress_computed += 1.0 - self.delta_stress.append(batch.stress - output["stress"]) - if output.get("virials") is not None and batch.virials is not None: - self.virials_computed += 1.0 - self.delta_virials.append(batch.virials - output["virials"]) - self.delta_virials_per_atom.append( - (batch.virials - output["virials"]) - / (batch.ptr[1:] - batch.ptr[:-1]).view(-1, 1, 1) - ) - if output.get("dipole") is not None and batch.dipole is not None: - self.Mus_computed += 1.0 - self.mus.append(batch.dipole) - self.delta_mus.append(batch.dipole - output["dipole"]) - self.delta_mus_per_atom.append( - (batch.dipole - output["dipole"]) - / (batch.ptr[1:] - batch.ptr[:-1]).unsqueeze(-1) - ) - - def convert(self, delta: Union[torch.Tensor, List[torch.Tensor]]) -> np.ndarray: - if isinstance(delta, list): - delta = torch.cat(delta) - return to_numpy(delta) - - def compute(self): - aux = {} - aux["loss"] = to_numpy(self.total_loss / self.num_data).item() - if self.E_computed: - delta_es = self.convert(self.delta_es) - delta_es_per_atom = self.convert(self.delta_es_per_atom) - aux["mae_e"] = compute_mae(delta_es) - aux["mae_e_per_atom"] = compute_mae(delta_es_per_atom) - aux["rmse_e"] = compute_rmse(delta_es) - aux["rmse_e_per_atom"] = compute_rmse(delta_es_per_atom) - aux["q95_e"] = compute_q95(delta_es) - if self.Fs_computed: - fs = self.convert(self.fs) - delta_fs = self.convert(self.delta_fs) - aux["mae_f"] = compute_mae(delta_fs) - aux["rel_mae_f"] = compute_rel_mae(delta_fs, fs) - aux["rmse_f"] = compute_rmse(delta_fs) - aux["rel_rmse_f"] = compute_rel_rmse(delta_fs, fs) - aux["q95_f"] = compute_q95(delta_fs) - if self.stress_computed: - delta_stress = self.convert(self.delta_stress) - aux["mae_stress"] = compute_mae(delta_stress) - aux["rmse_stress"] = compute_rmse(delta_stress) - aux["q95_stress"] = compute_q95(delta_stress) - if self.virials_computed: - delta_virials = self.convert(self.delta_virials) - delta_virials_per_atom = self.convert(self.delta_virials_per_atom) - aux["mae_virials"] = compute_mae(delta_virials) - aux["rmse_virials"] = compute_rmse(delta_virials) - aux["rmse_virials_per_atom"] = compute_rmse(delta_virials_per_atom) - aux["q95_virials"] = compute_q95(delta_virials) - if self.Mus_computed: - mus = self.convert(self.mus) - delta_mus = self.convert(self.delta_mus) - delta_mus_per_atom = self.convert(self.delta_mus_per_atom) - aux["mae_mu"] = compute_mae(delta_mus) - aux["mae_mu_per_atom"] = compute_mae(delta_mus_per_atom) - aux["rel_mae_mu"] = compute_rel_mae(delta_mus, mus) - aux["rmse_mu"] = compute_rmse(delta_mus) - aux["rmse_mu_per_atom"] = compute_rmse(delta_mus_per_atom) - aux["rel_rmse_mu"] = compute_rel_rmse(delta_mus, mus) - aux["q95_mu"] = compute_q95(delta_mus) - - return aux["loss"], aux diff --git a/mace-bench/3rdparty/mace/mace/tools/utils.py b/mace-bench/3rdparty/mace/mace/tools/utils.py deleted file mode 100644 index 1b1b55b1862687f782af27edae278054af6f372a..0000000000000000000000000000000000000000 --- a/mace-bench/3rdparty/mace/mace/tools/utils.py +++ /dev/null @@ -1,166 +0,0 @@ -########################################################################################### -# Statistics utilities -# Authors: Ilyes Batatia, Gregor Simm, David Kovacs -# This program is distributed under the MIT License (see MIT.md) -########################################################################################### - -import json -import logging -import os -import sys -from typing import Any, Dict, Iterable, Optional, Sequence, Union - -import numpy as np -import torch - -from .torch_tools import to_numpy - - -def compute_mae(delta: np.ndarray) -> float: - return np.mean(np.abs(delta)).item() - - -def compute_rel_mae(delta: np.ndarray, target_val: np.ndarray) -> float: - target_norm = np.mean(np.abs(target_val)) - return np.mean(np.abs(delta)).item() / (target_norm + 1e-9) * 100 - - -def compute_rmse(delta: np.ndarray) -> float: - return np.sqrt(np.mean(np.square(delta))).item() - - -def compute_rel_rmse(delta: np.ndarray, target_val: np.ndarray) -> float: - target_norm = np.sqrt(np.mean(np.square(target_val))).item() - return np.sqrt(np.mean(np.square(delta))).item() / (target_norm + 1e-9) * 100 - - -def compute_q95(delta: np.ndarray) -> float: - return np.percentile(np.abs(delta), q=95) - - -def compute_c(delta: np.ndarray, eta: float) -> float: - return np.mean(np.abs(delta) < eta).item() - - -def get_tag(name: str, seed: int) -> str: - return f"{name}_run-{seed}" - - -def setup_logger( - level: Union[int, str] = logging.INFO, - tag: Optional[str] = None, - directory: Optional[str] = None, - rank: Optional[int] = 0, -): - # Create a logger - logger = logging.getLogger() - logger.setLevel(logging.DEBUG) # Set to DEBUG to capture all levels - - # Create formatters - formatter = logging.Formatter( - "%(asctime)s.%(msecs)03d %(levelname)s: %(message)s", - datefmt="%Y-%m-%d %H:%M:%S", - ) - - # Add filter for rank - logger.addFilter(lambda _: rank == 0) - - # Create console handler - ch = logging.StreamHandler(stream=sys.stdout) - ch.setLevel(level) - ch.setFormatter(formatter) - logger.addHandler(ch) - - if directory is not None and tag is not None: - os.makedirs(name=directory, exist_ok=True) - - # Create file handler for non-debug logs - main_log_path = os.path.join(directory, f"{tag}.log") - fh_main = logging.FileHandler(main_log_path) - fh_main.setLevel(level) - fh_main.setFormatter(formatter) - logger.addHandler(fh_main) - - # Create file handler for debug logs - debug_log_path = os.path.join(directory, f"{tag}_debug.log") - fh_debug = logging.FileHandler(debug_log_path) - fh_debug.setLevel(logging.DEBUG) - fh_debug.setFormatter(formatter) - fh_debug.addFilter(lambda record: record.levelno >= logging.DEBUG) - logger.addHandler(fh_debug) - - -class AtomicNumberTable: - def __init__(self, zs: Sequence[int]): - self.zs = zs - - def __len__(self) -> int: - return len(self.zs) - - def __str__(self): - return f"AtomicNumberTable: {tuple(s for s in self.zs)}" - - def index_to_z(self, index: int) -> int: - return self.zs[index] - - def z_to_index(self, atomic_number: str) -> int: - return self.zs.index(atomic_number) - - -def get_atomic_number_table_from_zs(zs: Iterable[int]) -> AtomicNumberTable: - z_set = set() - for z in zs: - z_set.add(z) - return AtomicNumberTable(sorted(list(z_set))) - - -def atomic_numbers_to_indices( - atomic_numbers: np.ndarray, z_table: AtomicNumberTable -) -> np.ndarray: - to_index_fn = np.vectorize(z_table.z_to_index) - return to_index_fn(atomic_numbers) - - -class UniversalEncoder(json.JSONEncoder): - def default(self, o): - if isinstance(o, np.integer): - return int(o) - if isinstance(o, np.floating): - return float(o) - if isinstance(o, np.ndarray): - return o.tolist() - if isinstance(o, torch.Tensor): - return to_numpy(o) - return json.JSONEncoder.default(self, o) - - -class MetricsLogger: - def __init__(self, directory: str, tag: str) -> None: - self.directory = directory - self.filename = tag + ".txt" - self.path = os.path.join(self.directory, self.filename) - - def log(self, d: Dict[str, Any]) -> None: - os.makedirs(name=self.directory, exist_ok=True) - with open(self.path, mode="a", encoding="utf-8") as f: - f.write(json.dumps(d, cls=UniversalEncoder)) - f.write("\n") - - -# pylint: disable=abstract-method, arguments-differ -class LAMMPS_MP(torch.autograd.Function): - @staticmethod - def forward(ctx, *args): - feats, data = args # unpack - ctx.vec_len = feats.shape[-1] - ctx.data = data - out = torch.empty_like(feats) - data.forward_exchange(feats, out, ctx.vec_len) - return out - - @staticmethod - def backward(ctx, *grad_outputs): - (grad,) = grad_outputs # unpack - gout = torch.empty_like(grad) - ctx.data.reverse_exchange(grad, gout, ctx.vec_len) - return gout, None diff --git a/mace-bench/3rdparty/mace/mace_torch.egg-info/PKG-INFO b/mace-bench/3rdparty/mace/mace_torch.egg-info/PKG-INFO deleted file mode 100644 index 6f2b82a3039884b720f46d67ceef577e8c2110d8..0000000000000000000000000000000000000000 --- a/mace-bench/3rdparty/mace/mace_torch.egg-info/PKG-INFO +++ /dev/null @@ -1,428 +0,0 @@ -Metadata-Version: 2.4 -Name: mace-torch -Version: 0.3.13 -Home-page: https://github.com/ACEsuit/mace -Classifier: Programming Language :: Python :: 3 -Classifier: Operating System :: OS Independent -Classifier: License :: OSI Approved :: MIT License -Requires-Python: >=3.7 -Description-Content-Type: text/markdown -License-File: LICENSE.md -Requires-Dist: torch>=1.12 -Requires-Dist: e3nn==0.4.4 -Requires-Dist: numpy -Requires-Dist: opt_einsum -Requires-Dist: ase -Requires-Dist: torch-ema -Requires-Dist: prettytable -Requires-Dist: matscipy -Requires-Dist: h5py -Requires-Dist: torchmetrics -Requires-Dist: python-hostlist -Requires-Dist: configargparse -Requires-Dist: GitPython -Requires-Dist: pyYAML -Requires-Dist: tqdm -Requires-Dist: lmdb -Requires-Dist: orjson -Requires-Dist: matplotlib -Requires-Dist: pandas -Provides-Extra: wandb -Requires-Dist: wandb; extra == "wandb" -Provides-Extra: fpsample -Requires-Dist: fpsample; extra == "fpsample" -Provides-Extra: dev -Requires-Dist: black; extra == "dev" -Requires-Dist: isort; extra == "dev" -Requires-Dist: mypy; extra == "dev" -Requires-Dist: pre-commit; extra == "dev" -Requires-Dist: pytest; extra == "dev" -Requires-Dist: pytest-benchmark; extra == "dev" -Requires-Dist: pylint; extra == "dev" -Provides-Extra: schedulefree -Requires-Dist: schedulefree; extra == "schedulefree" -Provides-Extra: cueq -Requires-Dist: cuequivariance-torch>=0.2.0; extra == "cueq" -Provides-Extra: cueq-cuda-11 -Requires-Dist: cuequivariance-ops-torch-cu11>=0.2.0; extra == "cueq-cuda-11" -Provides-Extra: cueq-cuda-12 -Requires-Dist: cuequivariance-ops-torch-cu12>=0.2.0; extra == "cueq-cuda-12" -Dynamic: license-file - -# MACE - -[![GitHub release](https://img.shields.io/github/release/ACEsuit/mace.svg)](https://GitHub.com/ACEsuit/mace/releases/) -[![Paper](https://img.shields.io/badge/Paper-NeurIPs2022-blue)](https://openreview.net/forum?id=YPpSngE-ZU) -[![License](https://img.shields.io/badge/License-MIT%202.0-blue.svg)](https://opensource.org/licenses/mit) -[![GitHub issues](https://img.shields.io/github/issues/ACEsuit/mace.svg)](https://GitHub.com/ACEsuit/mace/issues/) -[![Documentation Status](https://readthedocs.org/projects/mace/badge/)](https://mace-docs.readthedocs.io/en/latest/) -[![DOI](https://zenodo.org/badge/505964914.svg)](https://doi.org/10.5281/zenodo.14103332) - -## Table of contents - -- [MACE](#mace) - - [Table of contents](#table-of-contents) - - [About MACE](#about-mace) - - [Documentation](#documentation) - - [Installation](#installation) - - [pip installation](#installation-from-pypi) - - [pip installation from source](#installation-from-source) - - [Usage](#usage) - - [Training](#training) - - [Evaluation](#evaluation) - - [Tutorials](#tutorials) - - [CUDA acceleration with cuEquivariance](#cuda-acceleration-with-cuequivariance) - - [Weights and Biases for experiment tracking](#weights-and-biases-for-experiment-tracking) - - [Pretrained Foundation Models](#pretrained-foundation-models) - - [MACE-MP: Materials Project Force Fields](#mace-mp-materials-project-force-fields) - - [Example usage in ASE](#example-usage-in-ase) - - [MACE-OFF: Transferable Organic Force Fields](#mace-off-transferable-organic-force-fields) - - [Example usage in ASE](#example-usage-in-ase-1) - - [Finetuning foundation models](#finetuning-foundation-models) - - [Latest recommended foundation models](#latest-recommended-foundation-models) - - [Caching](#caching) - - [Development](#development) - - [References](#references) - - [Contact](#contact) - - [License](#license) - -## About MACE - -MACE provides fast and accurate machine learning interatomic potentials with higher order equivariant message passing. - -This repository contains the MACE reference implementation developed by -Ilyes Batatia, Gregor Simm, David Kovacs, and the group of Gabor Csanyi, and friends (see Contributors). - -Also available: - -- [MACE in JAX](https://github.com/ACEsuit/mace-jax), currently about 2x times faster at evaluation, but training is recommended in Pytorch for optimal performances. -- [MACE layers](https://github.com/ACEsuit/mace-layer) for constructing higher order equivariant graph neural networks for arbitrary 3D point clouds. - -## Documentation - -A partial documentation is available at: https://mace-docs.readthedocs.io - -## Installation - -### 1. Requirements: - -- Python >= 3.7 (for openMM, use Python = 3.9) -- [PyTorch](https://pytorch.org/) >= 1.12 **(training with float64 is not supported with PyTorch 2.1 but is supported with 2.2 and later, Pytorch 2.4.1 is not supported)** - -**Make sure to install PyTorch.** Please refer to the [official PyTorch installation](https://pytorch.org/get-started/locally/) for the installation instructions. Select the appropriate options for your system. - -### Installation from PyPI -This is the recommended way to install MACE. - -```sh -pip install --upgrade pip -pip install mace-torch -``` -**Note:** The homonymous package on [PyPI](https://pypi.org/project/MACE/) has nothing to do with this one. - - -### Installation from source - - -```sh -git clone https://github.com/ACEsuit/mace.git -pip install ./mace -``` - - - - -## Usage - -### Training - -To train a MACE model, you can use the `mace_run_train` script, which should be in the usual place that pip places binaries (or you can explicitly run `python3 /mace/cli/run_train.py`) - -```sh -mace_run_train \ - --name="MACE_model" \ - --train_file="train.xyz" \ - --valid_fraction=0.05 \ - --test_file="test.xyz" \ - --config_type_weights='{"Default":1.0}' \ - --E0s='{1:-13.663181292231226, 6:-1029.2809654211628, 7:-1484.1187695035828, 8:-2042.0330099956639}' \ - --model="MACE" \ - --hidden_irreps='128x0e + 128x1o' \ - --r_max=5.0 \ - --batch_size=10 \ - --max_num_epochs=1500 \ - --stage_two \ - --start_stage_two=1200 \ - --ema \ - --ema_decay=0.99 \ - --amsgrad \ - --restart_latest \ - --device=cuda \ -``` - -To give a specific validation set, use the argument `--valid_file`. To set a larger batch size for evaluating the validation set, specify `--valid_batch_size`. - -To control the model's size, you need to change `--hidden_irreps`. For most applications, the recommended default model size is `--hidden_irreps='256x0e'` (meaning 256 invariant messages) or `--hidden_irreps='128x0e + 128x1o'`. If the model is not accurate enough, you can include higher order features, e.g., `128x0e + 128x1o + 128x2e`, or increase the number of channels to `256`. It is also possible to specify the model using the `--num_channels=128` and `--max_L=1`keys. - -It is usually preferred to add the isolated atoms to the training set, rather than reading in their energies through the command line like in the example above. To label them in the training set, set `config_type=IsolatedAtom` in their info fields. If you prefer not to use or do not know the energies of the isolated atoms, you can use the option `--E0s="average"` which estimates the atomic energies using least squares regression. Note that using fitted E0s corresponds to fitting the deviations of the atomic energies from the average, rather than fitting the atomization energy (which is the case when using isolated-atom E0s), and this will most likely result in less stable potentials for molecular dynamics applications. - -If the keyword `--stage_two` (previously called swa) is enabled, the energy weight of the loss is increased for the last ~20% of the training epochs (from `--start_stage_two` epochs). This setting usually helps lower the energy errors. - -The precision can be changed using the keyword `--default_dtype`, the default is `float64` but `float32` gives a significant speed-up (usually a factor of x2 in training). - -The keywords `--batch_size` and `--max_num_epochs` should be adapted based on the size of the training set. The batch size should be increased when the number of training data increases, and the number of epochs should be decreased. An heuristic for initial settings, is to consider the number of gradient update constant to 200 000, which can be computed as $\text{max-num-epochs}*\frac{\text{num-configs-training}}{\text{batch-size}}$. - -The code can handle training set with heterogeneous labels, for example containing both bulk structures with stress and isolated molecules. In this example, to make the code ignore stress on molecules, append to your molecules configuration a `config_stress_weight = 0.0`. - -By default, a figure displaying the progression of loss and RMSEs during training, along with a scatter plot of the model's inferences on the train, validation, and test sets, will be generated in the results folder at the end of training. This can be disabled using `--plot False`. To track these metrics throughout training (excluding inference on the test set), you can enable periodic plotting for the train and validation sets by specifying `--plot_frequency N`, which updates the plots every Nth epoch. - -#### Apple Silicon GPU acceleration - -To use Apple Silicon GPU acceleration make sure to install the latest PyTorch version and specify `--device=mps`. - -#### Multi-GPU training - -For multi-GPU training, use the `--distributed` flag. This will use PyTorch's DistributedDataParallel module to train the model on multiple GPUs. Combine with on-line data loading for large datasets (see below). An example slurm script can be found in `mace/scripts/distributed_example.sbatch`. - -#### YAML configuration - -Option to parse all or some arguments using a YAML is available. For example, to train a model using the arguments above, you can create a YAML file `your_configs.yaml` with the following content: - -```yaml -name: nacl -seed: 2024 -train_file: train.xyz -stage_two: yes -start_stage_two: 1200 -max_num_epochs: 1500 -device: cpu -test_file: test.xyz -E0s: - 41: -1029.2809654211628 - 38: -1484.1187695035828 - 8: -2042.0330099956639 -config_type_weights: - Default: 1.0 - -``` -And append to the command line `--config="your_configs.yaml"`. Any argument specified in the command line will overwrite the one in the YAML file. - -### Evaluation - -To evaluate your MACE model on an XYZ file, run the `mace_eval_configs`: - -```sh -mace_eval_configs \ - --configs="your_configs.xyz" \ - --model="your_model.model" \ - --output="./your_output.xyz" -``` - -## Tutorials - -You can run our [Colab tutorial](https://colab.research.google.com/drive/1D6EtMUjQPey_GkuxUAbPgld6_9ibIa-V?authuser=1#scrollTo=Z10787RE1N8T) to quickly get started with MACE. - -We also have a more detailed Colab tutorials on: - - [Introduction to MACE training and evaluation](https://colab.research.google.com/drive/1ZrTuTvavXiCxTFyjBV4GqlARxgFwYAtX) - - [Introduction to MACE active learning and fine-tuning](https://colab.research.google.com/drive/1oCSVfMhWrqHTeHbKgUSQN9hTKxLzoNyb) - - [MACE theory and code (advanced)](https://colab.research.google.com/drive/1AlfjQETV_jZ0JQnV5M3FGwAM2SGCl2aU) - -## CUDA acceleration with cuEquivariance - -MACE supports CUDA acceleration with the cuEquivariance library. To install the library and use the acceleration, see our documentation at https://mace-docs.readthedocs.io/en/latest/guide/cuda_acceleration.html. - -## On-line data loading for large datasets - -If you have a large dataset that might not fit into the GPU memory it is recommended to preprocess the data on a CPU and use on-line dataloading for training the model. To preprocess your dataset specified as an xyz file run the `preprocess_data.py` script. An example is given here: - -```sh -mkdir processed_data -python ./mace/scripts/preprocess_data.py \ - --train_file="/path/to/train_large.xyz" \ - --valid_fraction=0.05 \ - --test_file="/path/to/test_large.xyz" \ - --atomic_numbers="[1, 6, 7, 8, 9, 15, 16, 17, 35, 53]" \ - --r_max=4.5 \ - --h5_prefix="processed_data/" \ - --compute_statistics \ - --E0s="average" \ - --seed=123 \ -``` - -To see all options and a little description of them run `python ./mace/scripts/preprocess_data.py --help` . The script will create a number of HDF5 files in the `processed_data` folder which can be used for training. There will be one folder for training, one for validation and a separate one for each `config_type` in the test set. To train the model use the `run_train.py` script as follows: - -```sh -python ./mace/scripts/run_train.py \ - --name="MACE_on_big_data" \ - --num_workers=16 \ - --train_file="./processed_data/train.h5" \ - --valid_file="./processed_data/valid.h5" \ - --test_dir="./processed_data" \ - --statistics_file="./processed_data/statistics.json" \ - --model="ScaleShiftMACE" \ - --num_interactions=2 \ - --num_channels=128 \ - --max_L=1 \ - --correlation=3 \ - --batch_size=32 \ - --valid_batch_size=32 \ - --max_num_epochs=100 \ - --stage_two \ - --start_stage_two=60 \ - --ema \ - --ema_decay=0.99 \ - --amsgrad \ - --error_table='PerAtomMAE' \ - --device=cuda \ - --seed=123 \ -``` - -## Weights and Biases for experiment tracking - -If you would like to use MACE with Weights and Biases to log your experiments simply install with - -```sh -pip install ./mace[wandb] -``` - -And specify the necessary keyword arguments (`--wandb`, `--wandb_project`, `--wandb_entity`, `--wandb_name`, `--wandb_log_hypers`) - - -## Pretrained Foundation Models - -We provide a series of pretrained foundation models for various applications. These models can be used directly for inference, or as a starting point for fine-tuning on a new dataset. -Foundation models are a rapidly evolving field. Please look at the `MACE-MP GitHub repository `_ and the `MACE-OFF23 GitHub repository `_ for the latest releases. - -### Latest Recommended Foundation Models - -| Model Name | Elements Covered | Training Dataset | Level of Theory | Target System | Model Size | GitHub Release | Notes | License | -|-------------------|------------------|------------------|-----------------------|----------------------|---------------------|----------------|-------------------------------------------------------|---------| -| MACE-MP-0a | 89 | MPTrj | DFT (PBE+U) | Materials | [small](https://github.com/ACEsuit/mace-mp/releases/download/mace_mp_0/2023-12-10-mace-128-L0_energy_epoch-249.model), [medium](https://github.com/ACEsuit/mace-mp/releases/download/mace_mp_0/2023-12-03-mace-128-L1_epoch-199.model), [large](https://github.com/ACEsuit/mace-mp/releases/download/mace_mp_0/2024-01-07-mace-128-L2_epoch-199.model)| >=v0.3.6 | Initial release of foundation model. | MIT | -| MACE-MP-0b3 | 89 | MPTrj | DFT (PBE+U) | Materials | [medium](https://github.com/ACEsuit/mace-mp/releases/download/mace_mp_0b3/mace-mp-0b3-medium.model)| >=v0.3.10 | Improved high pressure stability and reference energies. | MIT | -| MACE-MPA-0 | 89 | MPTrj + sAlex | DFT (PBE+U) | Materials | [medium-mpa-0](https://github.com/ACEsuit/mace-mp/releases/download/mace_mpa_0/mace-mpa-0-medium.model) | >=v0.3.10 | Improved accuracy for materials, improved high pressure stability. | MIT | -| MACE-OMAT-0 | 89 | OMAT | DFT (PBE+U) VASP 54 | Materials | [medium-omat-0](https://github.com/ACEsuit/mace-mp/releases/download/mace_omat_0/mace-omat-0-medium.model) | >=v0.3.10 | | ASL | -| MACE-OFF23 | 10 | SPICE v1 | DFT (wB97M+D3) | Organic Chemistry | [small](https://github.com/ACEsuit/mace-off/blob/main/mace_off23/MACE-OFF23_small.model), [medium](https://github.com/ACEsuit/mace-off/blob/main/mace_off23/MACE-OFF23_medium.model), [large](https://github.com/ACEsuit/mace-off/blob/main/mace_off23/MACE-OFF23_large.model)| >=v0.3.6 | Initial release covering neutral organic chemistry. | ASL | -| MACE-MATPES-PBE-0 | 89 | MATPES-PBE | DFT (PBE) | Materials | [medium](https://github.com/ACEsuit/mace-foundations/releases/download/mace_matpes_0/MACE-matpes-pbe-omat-ft.model) | >=v0.3.10 | No +U correction. | ASL | -| MACE-MATPES-r2SCAN-0 | 89 | MATPES-r2SCAN | DFT (r2SCAN) | Materials | [medium](https://github.com/ACEsuit/mace-foundations/releases/download/mace_matpes_0/MACE-matpes-r2scan-omat-ft.model) | >=v0.3.10 | Better functional for materials. | ASL | - -### MACE-MP: Materials Project Force Fields - -We have collaborated with the Materials Project (MP) to train a universal MACE potential covering 89 elements on 1.6 M bulk crystals in the [MPTrj dataset](https://figshare.com/articles/dataset/23713842) selected from MP relaxation trajectories. -The models are releaed on GitHub at https://github.com/ACEsuit/mace-mp. -If you use them please cite [our paper](https://arxiv.org/abs/2401.00096) which also contains an large range of example applications and benchmarks. - -> [!CAUTION] -> The MACE-MP models are trained on MPTrj raw DFT energies from VASP outputs, and are not directly comparable to the MP's DFT energies or CHGNet's energies, which have been applied MP2020Compatibility corrections for some transition metal oxides, fluorides (GGA/GGA+U mixing corrections), and 14 anions species (anion corrections). For more details, please refer to the [MP Documentation](https://docs.materialsproject.org/methodology/materials-methodology/thermodynamic-stability/thermodynamic-stability/anion-and-gga-gga+u-mixing) and [MP2020Compatibility.yaml](https://github.com/materialsproject/pymatgen/blob/master/pymatgen/entries/MP2020Compatibility.yaml). - -#### Example usage in ASE -```py -from mace.calculators import mace_mp -from ase import build - -atoms = build.molecule('H2O') -calc = mace_mp(model="medium", dispersion=False, default_dtype="float32", device='cuda') -atoms.calc = calc -print(atoms.get_potential_energy()) -``` - -### MACE-OFF: Transferable Organic Force Fields - -There is a series (small, medium, large) transferable organic force fields. These can be used for the simulation of organic molecules, crystals and molecular liquids, or as a starting point for fine-tuning on a new dataset. The models are released under the [ASL license](https://github.com/gabor1/ASL). -The models are releaed on GitHub at https://github.com/ACEsuit/mace-off. -If you use them please cite [our paper](https://arxiv.org/abs/2312.15211) which also contains detailed benchmarks and example applications. - -#### Example usage in ASE -```py -from mace.calculators import mace_off -from ase import build - -atoms = build.molecule('H2O') -calc = mace_off(model="medium", device='cuda') -atoms.calc = calc -print(atoms.get_potential_energy()) -``` - -### Finetuning foundation models - -To finetune one of the mace-mp-0 foundation model, you can use the `mace_run_train` script with the extra argument `--foundation_model=model_type`. For example to finetune the small model on a new dataset, you can use: - -```sh -mace_run_train \ - --name="MACE" \ - --foundation_model="small" \ - --train_file="train.xyz" \ - --valid_fraction=0.05 \ - --test_file="test.xyz" \ - --energy_weight=1.0 \ - --forces_weight=1.0 \ - --E0s="average" \ - --lr=0.01 \ - --scaling="rms_forces_scaling" \ - --batch_size=2 \ - --max_num_epochs=6 \ - --ema \ - --ema_decay=0.99 \ - --amsgrad \ - --default_dtype="float32" \ - --device=cuda \ - --seed=3 -``` -Other options are "medium" and "large", or the path to a foundation model. -If you want to finetune another model, the model will be loaded from the path provided `--foundation_model=$path_model`, all the hypers will be extracted automatically. - -## Caching - -By default automatically downloaded models, like mace_mp, mace_off and data for fine tuning, end up in `~/.cache/mace`. The path can be changed by using -the environment variable XDG_CACHE_HOME. When set, the new cache path expands to $XDG_CACHE_HOME/.cache/mace - -## Development - -This project uses [pre-commit](https://pre-commit.com/) to execute code formatting and linting on commit. -We also use `black`, `isort`, `pylint`, and `mypy`. -We recommend setting up your development environment by installing the `dev` packages -into your python environment: -```bash -pip install -e ".[dev]" -pre-commit install -``` -The second line will initialise `pre-commit` to automaticaly run code checks on commit. -We have CI set up to check this, but we _highly_ recommend that you run those commands -before you commit (and push) to avoid accidentally committing bad code. - -We are happy to accept pull requests under an [MIT license](https://choosealicense.com/licenses/mit/). Please copy/paste the license text as a comment into your pull request. - -## References - -If you use this code, please cite our papers: - -```bibtex -@inproceedings{Batatia2022mace, - title={{MACE}: Higher Order Equivariant Message Passing Neural Networks for Fast and Accurate Force Fields}, - author={Ilyes Batatia and David Peter Kovacs and Gregor N. C. Simm and Christoph Ortner and Gabor Csanyi}, - booktitle={Advances in Neural Information Processing Systems}, - editor={Alice H. Oh and Alekh Agarwal and Danielle Belgrave and Kyunghyun Cho}, - year={2022}, - url={https://openreview.net/forum?id=YPpSngE-ZU} -} - -@misc{Batatia2022Design, - title = {The Design Space of E(3)-Equivariant Atom-Centered Interatomic Potentials}, - author = {Batatia, Ilyes and Batzner, Simon and Kov{\'a}cs, D{\'a}vid P{\'e}ter and Musaelian, Albert and Simm, Gregor N. C. and Drautz, Ralf and Ortner, Christoph and Kozinsky, Boris and Cs{\'a}nyi, G{\'a}bor}, - year = {2022}, - number = {arXiv:2205.06643}, - eprint = {2205.06643}, - eprinttype = {arxiv}, - doi = {10.48550/arXiv.2205.06643}, - archiveprefix = {arXiv} - } -``` - -## Contact - -If you have any questions, please contact us at ilyes.batatia@ens-paris-saclay.fr. - -For bugs or feature requests, please use [GitHub Issues](https://github.com/ACEsuit/mace/issues). - -## License - -The MACE code is published and distributed under the [MIT License](MIT.md). (Note that some of the models linked above come with different licenses). diff --git a/mace-bench/3rdparty/mace/mace_torch.egg-info/SOURCES.txt b/mace-bench/3rdparty/mace/mace_torch.egg-info/SOURCES.txt deleted file mode 100644 index 4abb27bfc25a88849a8787eec0dde3ed81c463ce..0000000000000000000000000000000000000000 --- a/mace-bench/3rdparty/mace/mace_torch.egg-info/SOURCES.txt +++ /dev/null @@ -1,97 +0,0 @@ -LICENSE.md -MANIFEST.in -README.md -pyproject.toml -setup.cfg -mace/__init__.py -mace/__version__.py -mace/py.typed -mace/calculators/__init__.py -mace/calculators/foundations_models.py -mace/calculators/lammps_mace.py -mace/calculators/lammps_mliap_mace.py -mace/calculators/mace.py -mace/cli/__init__.py -mace/cli/active_learning_md.py -mace/cli/convert_cueq_e3nn.py -mace/cli/convert_device.py -mace/cli/convert_e3nn_cueq.py -mace/cli/create_lammps_model.py -mace/cli/eval_configs.py -mace/cli/fine_tuning_select.py -mace/cli/plot_train.py -mace/cli/preprocess_data.py -mace/cli/run_train.py -mace/cli/select_head.py -mace/cli/visualise_train.py -mace/data/__init__.py -mace/data/atomic_data.py -mace/data/hdf5_dataset.py -mace/data/lmdb_dataset.py -mace/data/neighborhood.py -mace/data/utils.py -mace/modules/__init__.py -mace/modules/blocks.py -mace/modules/irreps_tools.py -mace/modules/loss.py -mace/modules/models.py -mace/modules/radial.py -mace/modules/symmetric_contraction.py -mace/modules/utils.py -mace/modules/wrapper_ops.py -mace/tools/__init__.py -mace/tools/arg_parser.py -mace/tools/arg_parser_tools.py -mace/tools/cg.py -mace/tools/checkpoint.py -mace/tools/compile.py -mace/tools/default_keys.py -mace/tools/finetuning_utils.py -mace/tools/model_script_utils.py -mace/tools/multihead_tools.py -mace/tools/run_train_utils.py -mace/tools/scatter.py -mace/tools/scripts_utils.py -mace/tools/slurm_distributed.py -mace/tools/tables_utils.py -mace/tools/torch_tools.py -mace/tools/train.py -mace/tools/utils.py -mace/tools/fairchem_dataset/__init__.py -mace/tools/fairchem_dataset/lmdb_dataset_tools.py -mace/tools/torch_geometric/__init__.py -mace/tools/torch_geometric/batch.py -mace/tools/torch_geometric/data.py -mace/tools/torch_geometric/dataloader.py -mace/tools/torch_geometric/dataset.py -mace/tools/torch_geometric/seed.py -mace/tools/torch_geometric/utils.py -mace_torch.egg-info/PKG-INFO -mace_torch.egg-info/SOURCES.txt -mace_torch.egg-info/dependency_links.txt -mace_torch.egg-info/entry_points.txt -mace_torch.egg-info/requires.txt -mace_torch.egg-info/top_level.txt -scripts/__init__.py -scripts/eval_configs.py -scripts/preprocess_data.py -scripts/run_train.py -tests/__init__.py -tests/test_benchmark.py -tests/test_calculator.py -tests/test_cg.py -tests/test_compile.py -tests/test_cueq.py -tests/test_data.py -tests/test_finetuning_select.py -tests/test_foundations.py -tests/test_hessian.py -tests/test_lmdb_database.py -tests/test_models.py -tests/test_modules.py -tests/test_multifiles.py -tests/test_preprocess.py -tests/test_run_train.py -tests/test_run_train_allkeys.py -tests/test_schedulefree.py -tests/test_tools.py \ No newline at end of file diff --git a/mace-bench/3rdparty/mace/mace_torch.egg-info/dependency_links.txt b/mace-bench/3rdparty/mace/mace_torch.egg-info/dependency_links.txt deleted file mode 100644 index 8b137891791fe96927ad78e64b0aad7bded08bdc..0000000000000000000000000000000000000000 --- a/mace-bench/3rdparty/mace/mace_torch.egg-info/dependency_links.txt +++ /dev/null @@ -1 +0,0 @@ - diff --git a/mace-bench/3rdparty/mace/mace_torch.egg-info/entry_points.txt b/mace-bench/3rdparty/mace/mace_torch.egg-info/entry_points.txt deleted file mode 100644 index f7d028a78d5e30c1258ec6fbbf9c17a3820e8b14..0000000000000000000000000000000000000000 --- a/mace-bench/3rdparty/mace/mace_torch.egg-info/entry_points.txt +++ /dev/null @@ -1,12 +0,0 @@ -[console_scripts] -mace_active_learning_md = mace.cli.active_learning_md:main -mace_convert_device = mace.cli.convert_device:main -mace_create_lammps_model = mace.cli.create_lammps_model:main -mace_cueq_to_e3nn = mace.cli.convert_cueq_e3nn:main -mace_e3nn_cueq = mace.cli.convert_e3nn_cueq:main -mace_eval_configs = mace.cli.eval_configs:main -mace_finetuning = mace.cli.fine_tuning_select:main -mace_plot_train = mace.cli.plot_train:main -mace_prepare_data = mace.cli.preprocess_data:main -mace_run_train = mace.cli.run_train:main -mace_select_head = mace.cli.select_head:main diff --git a/mace-bench/3rdparty/mace/mace_torch.egg-info/requires.txt b/mace-bench/3rdparty/mace/mace_torch.egg-info/requires.txt deleted file mode 100644 index 25777c759642d509fbf8056c6e7e6e0d334e09c4..0000000000000000000000000000000000000000 --- a/mace-bench/3rdparty/mace/mace_torch.egg-info/requires.txt +++ /dev/null @@ -1,46 +0,0 @@ -torch>=1.12 -e3nn==0.4.4 -numpy -opt_einsum -ase -torch-ema -prettytable -matscipy -h5py -torchmetrics -python-hostlist -configargparse -GitPython -pyYAML -tqdm -lmdb -orjson -matplotlib -pandas - -[cueq] -cuequivariance-torch>=0.2.0 - -[cueq-cuda-11] -cuequivariance-ops-torch-cu11>=0.2.0 - -[cueq-cuda-12] -cuequivariance-ops-torch-cu12>=0.2.0 - -[dev] -black -isort -mypy -pre-commit -pytest -pytest-benchmark -pylint - -[fpsample] -fpsample - -[schedulefree] -schedulefree - -[wandb] -wandb diff --git a/mace-bench/3rdparty/mace/mace_torch.egg-info/top_level.txt b/mace-bench/3rdparty/mace/mace_torch.egg-info/top_level.txt deleted file mode 100644 index 6f748b6a83d1583593aefee9f3dcc30be27eb364..0000000000000000000000000000000000000000 --- a/mace-bench/3rdparty/mace/mace_torch.egg-info/top_level.txt +++ /dev/null @@ -1,3 +0,0 @@ -mace -scripts -tests diff --git a/mace-bench/3rdparty/mace/pyproject.toml b/mace-bench/3rdparty/mace/pyproject.toml deleted file mode 100644 index 98875868bbf5b736488b8f940f0e50ab253ac95b..0000000000000000000000000000000000000000 --- a/mace-bench/3rdparty/mace/pyproject.toml +++ /dev/null @@ -1,46 +0,0 @@ -[build-system] -requires = [ - "setuptools>=42", - "wheel", -] -build-backend = "setuptools.build_meta" - -# Make isort compatible with black -[tool.isort] -profile = "black" - -# Pylint -[tool.pylint.'MESSAGES CONTROL'] -disable = [ - "line-too-long", - "no-member", - "missing-module-docstring", - "missing-class-docstring", - "missing-function-docstring", - "too-many-arguments", - "too-many-positional-arguments", - "too-many-locals", - "too-many-return-statements", - "not-callable", - "logging-fstring-interpolation", - "logging-not-lazy", - "logging-too-many-args", - "invalid-name", - "too-few-public-methods", - "too-many-instance-attributes", - "too-many-statements", - "too-many-branches", - "import-outside-toplevel", - "cell-var-from-loop", - "duplicate-code", - "use-dict-literal", -] - -[tool.pylint.MASTER] -ignore-paths = [ - "^mace/tools/torch_geometric/.*$", - "^mace/tools/scatter.py$", -] - -[tool.pylint.FORMAT] -max-module-lines = 1500 diff --git a/mace-bench/3rdparty/mace/ruff.toml b/mace-bench/3rdparty/mace/ruff.toml deleted file mode 100644 index 705205f64efaced4936c04e0eb78cf7ec6a72cef..0000000000000000000000000000000000000000 --- a/mace-bench/3rdparty/mace/ruff.toml +++ /dev/null @@ -1,4 +0,0 @@ -target-version = "py38" - -[lint] -select = ["FA102"] diff --git a/mace-bench/3rdparty/mace/scripts/__init__.py b/mace-bench/3rdparty/mace/scripts/__init__.py deleted file mode 100644 index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000 diff --git a/mace-bench/3rdparty/mace/scripts/distributed_example.sbatch b/mace-bench/3rdparty/mace/scripts/distributed_example.sbatch deleted file mode 100644 index 5025576b682848ac174cf12b078d6150ece35bde..0000000000000000000000000000000000000000 --- a/mace-bench/3rdparty/mace/scripts/distributed_example.sbatch +++ /dev/null @@ -1,34 +0,0 @@ -#!/bin/bash -#SBATCH --partition=gpu -#SBATCH --job-name=train -#SBATCH --output=train.out -#SBATCH --nodes=2 -#SBATCH --ntasks=20 -#SBATCH --ntasks-per-node=10 -#SBATCH --gpus-per-node=10 -#SBATCH --cpus-per-task=8 -#SBATCH --exclusive -#SBATCH --time=1:00:00 - -srun python mace/scripts/run_train.py \ - --name='model' \ - --model='MACE' \ - --num_interactions=2 \ - --num_channels=128 \ - --max_L=2 \ - --correlation=3 \ - --E0s='average' \ - --r_max=5.0 \ - --train_file='./h5_data/train.h5' \ - --valid_file='./h5_data/valid.h5' \ - --statistics_file='./h5_data/statistics.json' \ - --num_workers=8 \ - --batch_size=20 \ - --valid_batch_size=80 \ - --max_num_epochs=100 \ - --loss='weighted' \ - --error_table='PerAtomRMSE' \ - --default_dtype='float32' \ - --device='cuda' \ - --distributed \ - --seed=2222 \ \ No newline at end of file diff --git a/mace-bench/3rdparty/mace/scripts/eval_configs.py b/mace-bench/3rdparty/mace/scripts/eval_configs.py deleted file mode 100644 index d2f4e217bc50c0eb411f7809c539d6a79f88a80b..0000000000000000000000000000000000000000 --- a/mace-bench/3rdparty/mace/scripts/eval_configs.py +++ /dev/null @@ -1,6 +0,0 @@ -## Wrapper for mace.cli.eval_configs.main ## - -from mace.cli.eval_configs import main - -if __name__ == "__main__": - main() diff --git a/mace-bench/3rdparty/mace/scripts/preprocess_data.py b/mace-bench/3rdparty/mace/scripts/preprocess_data.py deleted file mode 100644 index 3c2c288c78424f2ca198a46e785a9769ce7fab52..0000000000000000000000000000000000000000 --- a/mace-bench/3rdparty/mace/scripts/preprocess_data.py +++ /dev/null @@ -1,6 +0,0 @@ -## Wrapper for mace.cli.run_train.main ## - -from mace.cli.preprocess_data import main - -if __name__ == "__main__": - main() diff --git a/mace-bench/3rdparty/mace/scripts/run_checks.sh b/mace-bench/3rdparty/mace/scripts/run_checks.sh deleted file mode 100644 index bd1214a403cbc6f9af62d108dd4e16f8c83b5107..0000000000000000000000000000000000000000 --- a/mace-bench/3rdparty/mace/scripts/run_checks.sh +++ /dev/null @@ -1,9 +0,0 @@ -# Format -python -m black . -python -m isort . - -# Check -python -m pylint --rcfile=pyproject.toml mace tests scripts - -# Tests -python -m pytest tests diff --git a/mace-bench/3rdparty/mace/scripts/run_train.py b/mace-bench/3rdparty/mace/scripts/run_train.py deleted file mode 100644 index d14952db45aa264ae640e2dde5323e48159c752d..0000000000000000000000000000000000000000 --- a/mace-bench/3rdparty/mace/scripts/run_train.py +++ /dev/null @@ -1,6 +0,0 @@ -## Wrapper for mace.cli.run_train.main ## - -from mace.cli.run_train import main - -if __name__ == "__main__": - main() diff --git a/mace-bench/3rdparty/mace/setup.cfg b/mace-bench/3rdparty/mace/setup.cfg deleted file mode 100644 index 5891f80eda94e50cd4bbda540eb6d1cc8ed957d3..0000000000000000000000000000000000000000 --- a/mace-bench/3rdparty/mace/setup.cfg +++ /dev/null @@ -1,66 +0,0 @@ -[metadata] -name = mace-torch -version = attr: mace.__version__ -short_description = MACE - Fast and accurate machine learning interatomic potentials with higher order equivariant message passing. -long_description = file: README.md -long_description_content_type = text/markdown -url = https://github.com/ACEsuit/mace -classifiers = - Programming Language :: Python :: 3 - Operating System :: OS Independent - License :: OSI Approved :: MIT License - -[options] -packages = find: -python_requires = >=3.7 -install_requires = - torch>=1.12 - e3nn==0.4.4 - numpy - opt_einsum - ase - torch-ema - prettytable - matscipy - h5py - torchmetrics - python-hostlist - configargparse - GitPython - pyYAML - tqdm - lmdb - orjson - # for plotting: - matplotlib - pandas - -[options.entry_points] -console_scripts = - mace_active_learning_md = mace.cli.active_learning_md:main - mace_create_lammps_model = mace.cli.create_lammps_model:main - mace_eval_configs = mace.cli.eval_configs:main - mace_plot_train = mace.cli.plot_train:main - mace_run_train = mace.cli.run_train:main - mace_prepare_data = mace.cli.preprocess_data:main - mace_finetuning = mace.cli.fine_tuning_select:main - mace_convert_device = mace.cli.convert_device:main - mace_select_head = mace.cli.select_head:main - mace_e3nn_cueq = mace.cli.convert_e3nn_cueq:main - mace_cueq_to_e3nn = mace.cli.convert_cueq_e3nn:main - -[options.extras_require] -wandb = wandb -fpsample = fpsample -dev = - black - isort - mypy - pre-commit - pytest - pytest-benchmark - pylint -schedulefree = schedulefree -cueq = cuequivariance-torch>=0.2.0 -cueq-cuda-11 = cuequivariance-ops-torch-cu11>=0.2.0 -cueq-cuda-12 = cuequivariance-ops-torch-cu12>=0.2.0 diff --git a/mace-bench/3rdparty/mace/tests/__init__.py b/mace-bench/3rdparty/mace/tests/__init__.py deleted file mode 100644 index 96ae7770bf014e5be3ba779f49eda5e9b8304e3d..0000000000000000000000000000000000000000 --- a/mace-bench/3rdparty/mace/tests/__init__.py +++ /dev/null @@ -1,3 +0,0 @@ -import os - -os.environ["TORCH_FORCE_NO_WEIGHTS_ONLY_LOAD"] = "1" diff --git a/mace-bench/3rdparty/mace/tests/modules/test_radial.py b/mace-bench/3rdparty/mace/tests/modules/test_radial.py deleted file mode 100644 index 3aef254bcdfa3ffa1242da3a94d94c864f8fe50c..0000000000000000000000000000000000000000 --- a/mace-bench/3rdparty/mace/tests/modules/test_radial.py +++ /dev/null @@ -1,95 +0,0 @@ -import pytest -import torch - -from mace.modules.radial import AgnesiTransform, ZBLBasis - - -@pytest.fixture -def zbl_basis(): - return ZBLBasis(p=6, trainable=False) - - -def test_zbl_basis_initialization(zbl_basis): - assert zbl_basis.p == torch.tensor(6.0) - assert torch.allclose(zbl_basis.c, torch.tensor([0.1818, 0.5099, 0.2802, 0.02817])) - - assert zbl_basis.a_exp == torch.tensor(0.300) - assert zbl_basis.a_prefactor == torch.tensor(0.4543) - assert not zbl_basis.a_exp.requires_grad - assert not zbl_basis.a_prefactor.requires_grad - - -def test_trainable_zbl_basis_initialization(zbl_basis): - zbl_basis = ZBLBasis(p=6, trainable=True) - assert zbl_basis.p == torch.tensor(6.0) - assert torch.allclose(zbl_basis.c, torch.tensor([0.1818, 0.5099, 0.2802, 0.02817])) - - assert zbl_basis.a_exp == torch.tensor(0.300) - assert zbl_basis.a_prefactor == torch.tensor(0.4543) - assert zbl_basis.a_exp.requires_grad - assert zbl_basis.a_prefactor.requires_grad - - -def test_forward(zbl_basis): - x = torch.tensor([1.0, 1.0, 2.0]).unsqueeze(-1) # [n_edges] - node_attrs = torch.tensor( - [[1, 0], [0, 1]] - ) # [n_nodes, n_node_features] - one_hot encoding of atomic numbers - edge_index = torch.tensor([[0, 1, 1], [1, 0, 1]]) # [2, n_edges] - atomic_numbers = torch.tensor([1, 6]) # [n_nodes] - output = zbl_basis(x, node_attrs, edge_index, atomic_numbers) - - assert output.shape == torch.Size([node_attrs.shape[0]]) - assert torch.is_tensor(output) - assert torch.allclose( - output, - torch.tensor([0.0031, 0.0031], dtype=torch.get_default_dtype()), - rtol=1e-2, - ) - - -@pytest.fixture -def agnesi(): - return AgnesiTransform(trainable=False) - - -def test_agnesi_transform_initialization(agnesi: AgnesiTransform): - assert agnesi.q.item() == pytest.approx(0.9183, rel=1e-4) - assert agnesi.p.item() == pytest.approx(4.5791, rel=1e-4) - assert agnesi.a.item() == pytest.approx(1.0805, rel=1e-4) - assert not agnesi.a.requires_grad - assert not agnesi.q.requires_grad - assert not agnesi.p.requires_grad - - -def test_trainable_agnesi_transform_initialization(): - agnesi = AgnesiTransform(trainable=True) - - assert agnesi.q.item() == pytest.approx(0.9183, rel=1e-4) - assert agnesi.p.item() == pytest.approx(4.5791, rel=1e-4) - assert agnesi.a.item() == pytest.approx(1.0805, rel=1e-4) - assert agnesi.a.requires_grad - assert agnesi.q.requires_grad - assert agnesi.p.requires_grad - - -def test_agnesi_transform_forward(): - agnesi = AgnesiTransform() - x = torch.tensor([1.0, 2.0, 3.0], dtype=torch.get_default_dtype()).unsqueeze(-1) - node_attrs = torch.tensor([[0, 1], [1, 0], [0, 1]], dtype=torch.get_default_dtype()) - edge_index = torch.tensor([[0, 1, 2], [1, 2, 0]]) - atomic_numbers = torch.tensor([1, 6, 8]) - output = agnesi(x, node_attrs, edge_index, atomic_numbers) - assert output.shape == x.shape - assert torch.is_tensor(output) - assert torch.allclose( - output, - torch.tensor( - [0.3646, 0.2175, 0.2089], dtype=torch.get_default_dtype() - ).unsqueeze(-1), - rtol=1e-2, - ) - - -if __name__ == "__main__": - pytest.main([__file__]) diff --git a/mace-bench/3rdparty/mace/tests/test_benchmark.py b/mace-bench/3rdparty/mace/tests/test_benchmark.py deleted file mode 100644 index fae104b41c2fae7f105a1cb1940939f53b240662..0000000000000000000000000000000000000000 --- a/mace-bench/3rdparty/mace/tests/test_benchmark.py +++ /dev/null @@ -1,121 +0,0 @@ -import json -import os -from pathlib import Path -from typing import List, Optional - -import pandas as pd -import pytest -import torch -from ase import build - -from mace import data as mace_data -from mace.calculators.foundations_models import mace_mp -from mace.tools import AtomicNumberTable, torch_geometric, torch_tools - - -def is_mace_full_bench(): - return os.environ.get("MACE_FULL_BENCH", "0") == "1" - - -@pytest.mark.skipif(not torch.cuda.is_available(), reason="cuda is not available") -@pytest.mark.benchmark(warmup=True, warmup_iterations=4, min_rounds=8) -@pytest.mark.parametrize("size", (3, 5, 7, 9)) -@pytest.mark.parametrize("dtype", ["float32", "float64"]) -@pytest.mark.parametrize("compile_mode", [None, "default"]) -def test_inference( - benchmark, size: int, dtype: str, compile_mode: Optional[str], device: str = "cuda" -): - if not is_mace_full_bench() and compile_mode is not None: - pytest.skip("Skipping long running benchmark, set MACE_FULL_BENCH=1 to execute") - - with torch_tools.default_dtype(dtype): - model = load_mace_mp_medium(dtype, compile_mode, device) - batch = create_batch(size, model, device) - log_bench_info(benchmark, dtype, compile_mode, batch) - - def func(): - torch.cuda.synchronize() - model(batch, training=compile_mode is not None, compute_force=True) - - torch.cuda.empty_cache() - benchmark(func) - - -def load_mace_mp_medium(dtype, compile_mode, device): - calc = mace_mp( - model="medium", - default_dtype=dtype, - device=device, - compile_mode=compile_mode, - fullgraph=False, - ) - model = calc.models[0].to(device) - return model - - -def create_batch(size: int, model: torch.nn.Module, device: str) -> dict: - cutoff = model.r_max.item() - z_table = AtomicNumberTable([int(z) for z in model.atomic_numbers]) - atoms = build.bulk("C", "diamond", a=3.567, cubic=True) - atoms = atoms.repeat((size, size, size)) - config = mace_data.config_from_atoms(atoms) - dataset = [mace_data.AtomicData.from_config(config, z_table=z_table, cutoff=cutoff)] - data_loader = torch_geometric.dataloader.DataLoader( - dataset=dataset, - batch_size=1, - shuffle=False, - drop_last=False, - ) - batch = next(iter(data_loader)) - batch.to(device) - return batch.to_dict() - - -def log_bench_info(benchmark, dtype, compile_mode, batch): - benchmark.extra_info["num_atoms"] = int(batch["positions"].shape[0]) - benchmark.extra_info["num_edges"] = int(batch["edge_index"].shape[1]) - benchmark.extra_info["dtype"] = dtype - benchmark.extra_info["is_compiled"] = compile_mode is not None - benchmark.extra_info["device_name"] = torch.cuda.get_device_name() - - -def process_benchmark_file(bench_file: Path) -> pd.DataFrame: - with open(bench_file, "r", encoding="utf-8") as f: - bench_data = json.load(f) - - records = [] - for bench in bench_data["benchmarks"]: - record = {**bench["extra_info"], **bench["stats"]} - records.append(record) - - result_df = pd.DataFrame(records) - result_df["ns/day (1 fs/step)"] = 0.086400 / result_df["median"] - result_df["Steps per day"] = result_df["ops"] * 86400 - columns = [ - "num_atoms", - "num_edges", - "dtype", - "is_compiled", - "device_name", - "median", - "Steps per day", - "ns/day (1 fs/step)", - ] - return result_df[columns] - - -def read_bench_results(result_files: List[str]) -> pd.DataFrame: - return pd.concat([process_benchmark_file(Path(f)) for f in result_files]) - - -if __name__ == "__main__": - # Print to stdout a csv of the benchmark metrics - import subprocess - - result = subprocess.run( - ["pytest-benchmark", "list"], capture_output=True, text=True, check=True - ) - - bench_files = result.stdout.strip().split("\n") - bench_results = read_bench_results(bench_files) - print(bench_results.to_csv(index=False)) diff --git a/mace-bench/3rdparty/mace/tests/test_calculator.py b/mace-bench/3rdparty/mace/tests/test_calculator.py deleted file mode 100644 index e9a654613010e3681d23e1b70797ff2c90d38ae6..0000000000000000000000000000000000000000 --- a/mace-bench/3rdparty/mace/tests/test_calculator.py +++ /dev/null @@ -1,689 +0,0 @@ -import os -import subprocess -import sys -from pathlib import Path - -import ase.io -import numpy as np -import pytest -import torch -from ase import build -from ase.atoms import Atoms -from ase.calculators.test import gradient_test -from ase.constraints import ExpCellFilter - -from mace.calculators import mace_mp, mace_off -from mace.calculators.mace import MACECalculator -from mace.modules.models import ScaleShiftMACE - -try: - import cuequivariance as cue # pylint: disable=unused-import - - CUET_AVAILABLE = True -except ImportError: - CUET_AVAILABLE = False - -pytest_mace_dir = Path(__file__).parent.parent -run_train = Path(__file__).parent.parent / "mace" / "cli" / "run_train.py" - - -@pytest.fixture(scope="module", name="fitting_configs") -def fitting_configs_fixture(): - water = Atoms( - numbers=[8, 1, 1], - positions=[[0, -2.0, 0], [1, 0, 0], [0, 1, 0]], - cell=[4] * 3, - pbc=[True] * 3, - ) - fit_configs = [ - Atoms(numbers=[8], positions=[[0, 0, 0]], cell=[6] * 3), - Atoms(numbers=[1], positions=[[0, 0, 0]], cell=[6] * 3), - ] - fit_configs[0].info["REF_energy"] = 1.0 - fit_configs[0].info["config_type"] = "IsolatedAtom" - fit_configs[1].info["REF_energy"] = -0.5 - fit_configs[1].info["config_type"] = "IsolatedAtom" - - np.random.seed(5) - for _ in range(20): - c = water.copy() - c.positions += np.random.normal(0.1, size=c.positions.shape) - c.info["REF_energy"] = np.random.normal(0.1) - c.info["REF_dipole"] = np.random.normal(0.1, size=3) - c.new_array("REF_forces", np.random.normal(0.1, size=c.positions.shape)) - c.new_array("Qs", np.random.normal(0.1, size=c.positions.shape[0])) - c.info["REF_stress"] = np.random.normal(0.1, size=6) - fit_configs.append(c) - - return fit_configs - - -@pytest.fixture(scope="module", name="trained_model") -def trained_model_fixture(tmp_path_factory, fitting_configs): - _mace_params = { - "name": "MACE", - "valid_fraction": 0.05, - "energy_weight": 1.0, - "forces_weight": 10.0, - "stress_weight": 1.0, - "model": "MACE", - "hidden_irreps": "128x0e", - "r_max": 3.5, - "batch_size": 5, - "max_num_epochs": 10, - "swa": None, - "start_swa": 5, - "ema": None, - "ema_decay": 0.99, - "amsgrad": None, - "restart_latest": None, - "device": "cpu", - "seed": 5, - "loss": "stress", - "energy_key": "REF_energy", - "forces_key": "REF_forces", - "stress_key": "REF_stress", - "eval_interval": 2, - } - - tmp_path = tmp_path_factory.mktemp("run_") - - ase.io.write(tmp_path / "fit.xyz", fitting_configs) - - mace_params = _mace_params.copy() - mace_params["checkpoints_dir"] = str(tmp_path) - mace_params["model_dir"] = str(tmp_path) - mace_params["train_file"] = tmp_path / "fit.xyz" - - # make sure run_train.py is using the mace that is currently being tested - run_env = os.environ.copy() - sys.path.insert(0, str(Path(__file__).parent.parent)) - run_env["PYTHONPATH"] = ":".join(sys.path) - print("DEBUG subprocess PYTHONPATH", run_env["PYTHONPATH"]) - - cmd = ( - sys.executable - + " " - + str(run_train) - + " " - + " ".join( - [ - (f"--{k}={v}" if v is not None else f"--{k}") - for k, v in mace_params.items() - ] - ) - ) - - p = subprocess.run(cmd.split(), env=run_env, check=True) - - assert p.returncode == 0 - - return MACECalculator(model_paths=tmp_path / "MACE.model", device="cpu") - - -@pytest.fixture(scope="module", name="trained_equivariant_model") -def trained_model_equivariant_fixture(tmp_path_factory, fitting_configs): - _mace_params = { - "name": "MACE", - "valid_fraction": 0.05, - "energy_weight": 1.0, - "forces_weight": 10.0, - "stress_weight": 1.0, - "model": "MACE", - "hidden_irreps": "16x0e+16x1o", - "r_max": 3.5, - "batch_size": 5, - "max_num_epochs": 10, - "swa": None, - "start_swa": 5, - "ema": None, - "ema_decay": 0.99, - "amsgrad": None, - "restart_latest": None, - "device": "cpu", - "seed": 5, - "loss": "stress", - "energy_key": "REF_energy", - "forces_key": "REF_forces", - "stress_key": "REF_stress", - "eval_interval": 2, - } - - tmp_path = tmp_path_factory.mktemp("run_") - - ase.io.write(tmp_path / "fit.xyz", fitting_configs) - - mace_params = _mace_params.copy() - mace_params["checkpoints_dir"] = str(tmp_path) - mace_params["model_dir"] = str(tmp_path) - mace_params["train_file"] = tmp_path / "fit.xyz" - - # make sure run_train.py is using the mace that is currently being tested - run_env = os.environ.copy() - sys.path.insert(0, str(Path(__file__).parent.parent)) - run_env["PYTHONPATH"] = ":".join(sys.path) - print("DEBUG subprocess PYTHONPATH", run_env["PYTHONPATH"]) - - cmd = ( - sys.executable - + " " - + str(run_train) - + " " - + " ".join( - [ - (f"--{k}={v}" if v is not None else f"--{k}") - for k, v in mace_params.items() - ] - ) - ) - - p = subprocess.run(cmd.split(), env=run_env, check=True) - - assert p.returncode == 0 - - return MACECalculator(model_paths=tmp_path / "MACE.model", device="cpu") - - -@pytest.fixture(scope="module", name="trained_equivariant_model_cueq") -def trained_model_equivariant_fixture_cueq(tmp_path_factory, fitting_configs): - _mace_params = { - "name": "MACE", - "valid_fraction": 0.05, - "energy_weight": 1.0, - "forces_weight": 10.0, - "stress_weight": 1.0, - "model": "MACE", - "hidden_irreps": "16x0e+16x1o", - "r_max": 3.5, - "batch_size": 5, - "max_num_epochs": 10, - "swa": None, - "start_swa": 5, - "ema": None, - "ema_decay": 0.99, - "amsgrad": None, - "restart_latest": None, - "device": "cpu", - "seed": 5, - "loss": "stress", - "energy_key": "REF_energy", - "forces_key": "REF_forces", - "stress_key": "REF_stress", - "eval_interval": 2, - } - - tmp_path = tmp_path_factory.mktemp("run_") - - ase.io.write(tmp_path / "fit.xyz", fitting_configs) - - mace_params = _mace_params.copy() - mace_params["checkpoints_dir"] = str(tmp_path) - mace_params["model_dir"] = str(tmp_path) - mace_params["train_file"] = tmp_path / "fit.xyz" - - # make sure run_train.py is using the mace that is currently being tested - run_env = os.environ.copy() - sys.path.insert(0, str(Path(__file__).parent.parent)) - run_env["PYTHONPATH"] = ":".join(sys.path) - print("DEBUG subprocess PYTHONPATH", run_env["PYTHONPATH"]) - - cmd = ( - sys.executable - + " " - + str(run_train) - + " " - + " ".join( - [ - (f"--{k}={v}" if v is not None else f"--{k}") - for k, v in mace_params.items() - ] - ) - ) - - p = subprocess.run(cmd.split(), env=run_env, check=True) - - assert p.returncode == 0 - - return MACECalculator( - model_paths=tmp_path / "MACE.model", device="cpu", enable_cueq=True - ) - - -@pytest.fixture(scope="module", name="trained_dipole_model") -def trained_dipole_fixture(tmp_path_factory, fitting_configs): - _mace_params = { - "name": "MACE", - "valid_fraction": 0.05, - "energy_weight": 1.0, - "forces_weight": 10.0, - "stress_weight": 1.0, - "model": "AtomicDipolesMACE", - "num_channels": 8, - "max_L": 2, - "r_max": 3.5, - "batch_size": 5, - "max_num_epochs": 10, - "ema": None, - "ema_decay": 0.99, - "amsgrad": None, - "restart_latest": None, - "device": "cpu", - "seed": 5, - "loss": "dipole", - "energy_key": "", - "forces_key": "", - "stress_key": "", - "dipole_key": "REF_dipole", - "error_table": "DipoleRMSE", - "eval_interval": 2, - } - - tmp_path = tmp_path_factory.mktemp("run_") - - ase.io.write(tmp_path / "fit.xyz", fitting_configs) - - mace_params = _mace_params.copy() - mace_params["checkpoints_dir"] = str(tmp_path) - mace_params["model_dir"] = str(tmp_path) - mace_params["train_file"] = tmp_path / "fit.xyz" - - # make sure run_train.py is using the mace that is currently being tested - run_env = os.environ.copy() - sys.path.insert(0, str(Path(__file__).parent.parent)) - run_env["PYTHONPATH"] = ":".join(sys.path) - print("DEBUG subprocess PYTHONPATH", run_env["PYTHONPATH"]) - - cmd = ( - sys.executable - + " " - + str(run_train) - + " " - + " ".join( - [ - (f"--{k}={v}" if v is not None else f"--{k}") - for k, v in mace_params.items() - ] - ) - ) - - p = subprocess.run(cmd.split(), env=run_env, check=True) - - assert p.returncode == 0 - - return MACECalculator( - model_paths=tmp_path / "MACE.model", device="cpu", model_type="DipoleMACE" - ) - - -@pytest.fixture(scope="module", name="trained_energy_dipole_model") -def trained_energy_dipole_fixture(tmp_path_factory, fitting_configs): - _mace_params = { - "name": "MACE", - "valid_fraction": 0.05, - "energy_weight": 1.0, - "forces_weight": 10.0, - "stress_weight": 1.0, - "model": "EnergyDipolesMACE", - "num_channels": 32, - "max_L": 1, - "r_max": 3.5, - "batch_size": 5, - "max_num_epochs": 10, - "ema": None, - "ema_decay": 0.99, - "amsgrad": None, - "restart_latest": None, - "device": "cpu", - "seed": 5, - "loss": "energy_forces_dipole", - "energy_key": "REF_energy", - "forces_key": "", - "stress_key": "", - "dipole_key": "REF_dipole", - "error_table": "EnergyDipoleRMSE", - "eval_interval": 2, - } - - tmp_path = tmp_path_factory.mktemp("run_") - - ase.io.write(tmp_path / "fit.xyz", fitting_configs) - - mace_params = _mace_params.copy() - mace_params["checkpoints_dir"] = str(tmp_path) - mace_params["model_dir"] = str(tmp_path) - mace_params["train_file"] = tmp_path / "fit.xyz" - - # make sure run_train.py is using the mace that is currently being tested - run_env = os.environ.copy() - sys.path.insert(0, str(Path(__file__).parent.parent)) - run_env["PYTHONPATH"] = ":".join(sys.path) - print("DEBUG subprocess PYTHONPATH", run_env["PYTHONPATH"]) - - cmd = ( - sys.executable - + " " - + str(run_train) - + " " - + " ".join( - [ - (f"--{k}={v}" if v is not None else f"--{k}") - for k, v in mace_params.items() - ] - ) - ) - - p = subprocess.run(cmd.split(), env=run_env, check=True) - - assert p.returncode == 0 - - return MACECalculator( - model_paths=tmp_path / "MACE.model", device="cpu", model_type="EnergyDipoleMACE" - ) - - -@pytest.fixture(scope="module", name="trained_committee") -def trained_committee_fixture(tmp_path_factory, fitting_configs): - _seeds = [5, 6, 7] - _model_paths = [] - for seed in _seeds: - _mace_params = { - "name": f"MACE{seed}", - "valid_fraction": 0.05, - "energy_weight": 1.0, - "forces_weight": 10.0, - "stress_weight": 1.0, - "model": "MACE", - "hidden_irreps": "16x0e", - "r_max": 3.5, - "batch_size": 5, - "max_num_epochs": 10, - "swa": None, - "start_swa": 5, - "ema": None, - "ema_decay": 0.99, - "amsgrad": None, - "restart_latest": None, - "device": "cpu", - "seed": seed, - "loss": "stress", - "energy_key": "REF_energy", - "forces_key": "REF_forces", - "stress_key": "REF_stress", - "eval_interval": 2, - } - - tmp_path = tmp_path_factory.mktemp(f"run{seed}_") - - ase.io.write(tmp_path / "fit.xyz", fitting_configs) - - mace_params = _mace_params.copy() - mace_params["checkpoints_dir"] = str(tmp_path) - mace_params["model_dir"] = str(tmp_path) - mace_params["train_file"] = tmp_path / "fit.xyz" - - # make sure run_train.py is using the mace that is currently being tested - run_env = os.environ.copy() - sys.path.insert(0, str(Path(__file__).parent.parent)) - run_env["PYTHONPATH"] = ":".join(sys.path) - print("DEBUG subprocess PYTHONPATH", run_env["PYTHONPATH"]) - - cmd = ( - sys.executable - + " " - + str(run_train) - + " " - + " ".join( - [ - (f"--{k}={v}" if v is not None else f"--{k}") - for k, v in mace_params.items() - ] - ) - ) - - p = subprocess.run(cmd.split(), env=run_env, check=True) - - assert p.returncode == 0 - - _model_paths.append(tmp_path / f"MACE{seed}.model") - - return MACECalculator(model_paths=_model_paths, device="cpu") - - -def test_calculator_node_energy(fitting_configs, trained_model): - for at in fitting_configs: - trained_model.calculate(at) - node_energies = trained_model.results["node_energy"] - batch = trained_model._atoms_to_batch(at) # pylint: disable=protected-access - node_heads = batch["head"][batch["batch"]] - num_atoms_arange = torch.arange(batch["positions"].shape[0]) - node_e0 = ( - trained_model.models[0].atomic_energies_fn(batch["node_attrs"]).detach() - ) - node_e0 = node_e0[num_atoms_arange, node_heads].cpu().numpy() - energy_via_nodes = np.sum(node_energies + node_e0) - energy = trained_model.results["energy"] - np.testing.assert_allclose(energy, energy_via_nodes, atol=1e-6) - - -def test_calculator_forces(fitting_configs, trained_model): - at = fitting_configs[2].copy() - at.calc = trained_model - - # test just forces - grads = gradient_test(at) - - assert np.allclose(grads[0], grads[1]) - - -def test_calculator_stress(fitting_configs, trained_model): - at = fitting_configs[2].copy() - at.calc = trained_model - - # test forces and stress - at_wrapped = ExpCellFilter(at) - grads = gradient_test(at_wrapped) - - assert np.allclose(grads[0], grads[1]) - - -def test_calculator_committee(fitting_configs, trained_committee): - at = fitting_configs[2].copy() - at.calc = trained_committee - - # test just forces - grads = gradient_test(at) - - assert np.allclose(grads[0], grads[1]) - - E = at.get_potential_energy() - energies = at.calc.results["energies"] - energies_var = at.calc.results["energy_var"] - forces_var = np.var(at.calc.results["forces_comm"], axis=0) - assert np.allclose(E, np.mean(energies)) - assert np.allclose(energies_var, np.var(energies)) - assert forces_var.shape == at.calc.results["forces"].shape - - -def test_calculator_from_model(fitting_configs, trained_committee): - # test single model - test_calculator_forces( - fitting_configs, - trained_model=MACECalculator(models=trained_committee.models[0], device="cpu"), - ) - - # test committee model - test_calculator_committee( - fitting_configs, - trained_committee=MACECalculator(models=trained_committee.models, device="cpu"), - ) - - -def test_calculator_dipole(fitting_configs, trained_dipole_model): - at = fitting_configs[2].copy() - at.calc = trained_dipole_model - - dip = at.get_dipole_moment() - - assert len(dip) == 3 - - -def test_calculator_energy_dipole(fitting_configs, trained_energy_dipole_model): - at = fitting_configs[2].copy() - at.calc = trained_energy_dipole_model - - grads = gradient_test(at) - dip = at.get_dipole_moment() - - assert np.allclose(grads[0], grads[1]) - assert len(dip) == 3 - - -def test_calculator_descriptor(fitting_configs, trained_equivariant_model): - at = fitting_configs[2].copy() - at_rotated = fitting_configs[2].copy() - at_rotated.rotate(90, "x") - calc = trained_equivariant_model - - desc_invariant = calc.get_descriptors(at, invariants_only=True) - desc_invariant_rotated = calc.get_descriptors(at_rotated, invariants_only=True) - desc_invariant_single_layer = calc.get_descriptors( - at, invariants_only=True, num_layers=1 - ) - desc_invariant_single_layer_rotated = calc.get_descriptors( - at_rotated, invariants_only=True, num_layers=1 - ) - desc = calc.get_descriptors(at, invariants_only=False) - desc_single_layer = calc.get_descriptors(at, invariants_only=False, num_layers=1) - desc_rotated = calc.get_descriptors(at_rotated, invariants_only=False) - desc_rotated_single_layer = calc.get_descriptors( - at_rotated, invariants_only=False, num_layers=1 - ) - - assert desc_invariant.shape[0] == 3 - assert desc_invariant.shape[1] == 32 - assert desc_invariant_single_layer.shape[0] == 3 - assert desc_invariant_single_layer.shape[1] == 16 - assert desc.shape[0] == 3 - assert desc.shape[1] == 80 - assert desc_single_layer.shape[0] == 3 - assert desc_single_layer.shape[1] == 16 * 4 - assert desc_rotated_single_layer.shape[0] == 3 - assert desc_rotated_single_layer.shape[1] == 16 * 4 - - np.testing.assert_allclose(desc_invariant, desc_invariant_rotated, atol=1e-6) - np.testing.assert_allclose( - desc_invariant_single_layer, desc_invariant[:, :16], atol=1e-6 - ) - np.testing.assert_allclose( - desc_invariant_single_layer_rotated, desc_invariant[:, :16], atol=1e-6 - ) - np.testing.assert_allclose( - desc_single_layer[:, :16], desc_rotated_single_layer[:, :16], atol=1e-6 - ) - assert not np.allclose( - desc_single_layer[:, 16:], desc_rotated_single_layer[:, 16:], atol=1e-6 - ) - assert not np.allclose(desc, desc_rotated, atol=1e-6) - - -@pytest.mark.skipif(not CUET_AVAILABLE, reason="cuequivariance not installed") -def test_calculator_descriptor_cueq(fitting_configs, trained_equivariant_model_cueq): - at = fitting_configs[2].copy() - at_rotated = fitting_configs[2].copy() - at_rotated.rotate(90, "x") - calc = trained_equivariant_model_cueq - - desc_invariant = calc.get_descriptors(at, invariants_only=True) - desc_invariant_rotated = calc.get_descriptors(at_rotated, invariants_only=True) - desc_invariant_single_layer = calc.get_descriptors( - at, invariants_only=True, num_layers=1 - ) - desc_invariant_single_layer_rotated = calc.get_descriptors( - at_rotated, invariants_only=True, num_layers=1 - ) - desc = calc.get_descriptors(at, invariants_only=False) - desc_single_layer = calc.get_descriptors(at, invariants_only=False, num_layers=1) - desc_rotated = calc.get_descriptors(at_rotated, invariants_only=False) - desc_rotated_single_layer = calc.get_descriptors( - at_rotated, invariants_only=False, num_layers=1 - ) - - assert desc_invariant.shape[0] == 3 - assert desc_invariant.shape[1] == 32 - assert desc_invariant_single_layer.shape[0] == 3 - assert desc_invariant_single_layer.shape[1] == 16 - assert desc.shape[0] == 3 - assert desc.shape[1] == 80 - assert desc_single_layer.shape[0] == 3 - assert desc_single_layer.shape[1] == 16 * 4 - assert desc_rotated_single_layer.shape[0] == 3 - assert desc_rotated_single_layer.shape[1] == 16 * 4 - - np.testing.assert_allclose(desc_invariant, desc_invariant_rotated, atol=1e-6) - np.testing.assert_allclose( - desc_invariant_single_layer, desc_invariant[:, :16], atol=1e-6 - ) - np.testing.assert_allclose( - desc_invariant_single_layer_rotated, desc_invariant[:, :16], atol=1e-6 - ) - np.testing.assert_allclose( - desc_single_layer[:, :16], desc_rotated_single_layer[:, :16], atol=1e-6 - ) - assert not np.allclose( - desc_single_layer[:, 16:], desc_rotated_single_layer[:, 16:], atol=1e-6 - ) - assert not np.allclose(desc, desc_rotated, atol=1e-6) - - -def test_mace_mp(capsys: pytest.CaptureFixture): - mp_mace = mace_mp() - assert isinstance(mp_mace, MACECalculator) - assert mp_mace.model_type == "MACE" - assert len(mp_mace.models) == 1 - assert isinstance(mp_mace.models[0], ScaleShiftMACE) - - _, stderr = capsys.readouterr() - assert stderr == "" - - -def test_mace_off(): - mace_off_model = mace_off(model="small", device="cpu") - assert isinstance(mace_off_model, MACECalculator) - assert mace_off_model.model_type == "MACE" - assert len(mace_off_model.models) == 1 - assert isinstance(mace_off_model.models[0], ScaleShiftMACE) - - atoms = build.molecule("H2O") - atoms.calc = mace_off_model - - E = atoms.get_potential_energy() - - assert np.allclose(E, -2081.116128586803, atol=1e-9) - - -@pytest.mark.skipif(not CUET_AVAILABLE, reason="cuequivariance not installed") -def test_mace_off_cueq(model="medium", device="cpu"): - mace_off_model = mace_off(model=model, device=device, enable_cueq=True) - assert isinstance(mace_off_model, MACECalculator) - assert mace_off_model.model_type == "MACE" - assert len(mace_off_model.models) == 1 - assert isinstance(mace_off_model.models[0], ScaleShiftMACE) - - atoms = build.molecule("H2O") - atoms.calc = mace_off_model - - E = atoms.get_potential_energy() - - assert np.allclose(E, -2081.116128586803, atol=1e-9) - - -def test_mace_mp_stresses(model="medium", device="cpu"): - atoms = build.bulk("Al", "fcc", a=4.05, cubic=True) - atoms = atoms.repeat((2, 2, 2)) - mace_mp_model = mace_mp(model=model, device=device, compute_atomic_stresses=True) - atoms.set_calculator(mace_mp_model) - stress = atoms.get_stress() - stresses = atoms.get_stresses() - assert stress.shape == (6,) - assert stresses.shape == (32, 6) - assert np.allclose(stress, stresses.sum(axis=0), atol=1e-6) diff --git a/mace-bench/3rdparty/mace/tests/test_cg.py b/mace-bench/3rdparty/mace/tests/test_cg.py deleted file mode 100644 index 36b119b9b7c84621f3521a9978bebfa081262db1..0000000000000000000000000000000000000000 --- a/mace-bench/3rdparty/mace/tests/test_cg.py +++ /dev/null @@ -1,12 +0,0 @@ -from e3nn import o3 - -from mace.tools import cg - - -def test_U_matrix(): - irreps_in = o3.Irreps("1x0e + 1x1o + 1x2e") - irreps_out = o3.Irreps("1x0e + 1x1o") - u_matrix = cg.U_matrix_real( - irreps_in=irreps_in, irreps_out=irreps_out, correlation=3 - )[-1] - assert u_matrix.shape == (3, 9, 9, 9, 21) diff --git a/mace-bench/3rdparty/mace/tests/test_compile.py b/mace-bench/3rdparty/mace/tests/test_compile.py deleted file mode 100644 index d7d585e832c918345a29ea97b1f890fc208ba589..0000000000000000000000000000000000000000 --- a/mace-bench/3rdparty/mace/tests/test_compile.py +++ /dev/null @@ -1,154 +0,0 @@ -import os -from functools import wraps -from typing import Callable - -import numpy as np -import pytest -import torch -import torch.nn.functional as F -from e3nn import o3 -from torch.testing import assert_close - -from mace import data, modules, tools -from mace.tools import compile as mace_compile -from mace.tools import torch_geometric - -table = tools.AtomicNumberTable([6]) -atomic_energies = np.array([1.0], dtype=float) -cutoff = 5.0 - - -def create_mace(device: str, seed: int = 1702): - torch_geometric.seed_everything(seed) - - model_config = { - "r_max": cutoff, - "num_bessel": 8, - "num_polynomial_cutoff": 6, - "max_ell": 3, - "interaction_cls": modules.interaction_classes[ - "RealAgnosticResidualInteractionBlock" - ], - "interaction_cls_first": modules.interaction_classes[ - "RealAgnosticResidualInteractionBlock" - ], - "num_interactions": 2, - "num_elements": 1, - "hidden_irreps": o3.Irreps("128x0e + 128x1o"), - "MLP_irreps": o3.Irreps("16x0e"), - "gate": F.silu, - "atomic_energies": atomic_energies, - "avg_num_neighbors": 8, - "atomic_numbers": table.zs, - "correlation": 3, - "radial_type": "bessel", - "atomic_inter_scale": 1.0, - "atomic_inter_shift": 0.0, - } - model = modules.ScaleShiftMACE(**model_config) - return model.to(device) - - -def create_batch(device: str): - from ase import build - - size = 2 - atoms = build.bulk("C", "diamond", a=3.567, cubic=True) - atoms_list = [atoms.repeat((size, size, size))] - print("Number of atoms", len(atoms_list[0])) - - configs = [data.config_from_atoms(atoms) for atoms in atoms_list] - data_loader = torch_geometric.dataloader.DataLoader( - dataset=[ - data.AtomicData.from_config(config, z_table=table, cutoff=cutoff) - for config in configs - ], - batch_size=1, - shuffle=False, - drop_last=False, - ) - batch = next(iter(data_loader)) - batch = batch.to(device) - batch = batch.to_dict() - return batch - - -def time_func(func: Callable): - @wraps(func) - def wrapper(*args, **kwargs): - torch._inductor.cudagraph_mark_step_begin() # pylint: disable=W0212 - outputs = func(*args, **kwargs) - torch.cuda.synchronize() - return outputs - - return wrapper - - -@pytest.fixture(params=[torch.float32, torch.float64], ids=["fp32", "fp64"]) -def default_dtype(request): - with tools.torch_tools.default_dtype(request.param): - yield torch.get_default_dtype() - - -# skip if on windows -@pytest.mark.skipif(os.name == "nt", reason="Not supported on Windows") -@pytest.mark.parametrize("device", ["cpu", "cuda"]) -def test_mace(device, default_dtype): # pylint: disable=W0621 - print(f"using default dtype = {default_dtype}") - if device == "cuda" and not torch.cuda.is_available(): - pytest.skip(reason="cuda is not available") - - model_defaults = create_mace(device) - tmp_model = mace_compile.prepare(create_mace)(device) - model_compiled = torch.compile(tmp_model, mode="default") - - batch = create_batch(device) - output1 = model_defaults(batch, training=True) - output2 = model_compiled(batch, training=True) - assert_close(output1["energy"], output2["energy"]) - assert_close(output1["forces"], output2["forces"]) - - -@pytest.mark.skipif(os.name == "nt", reason="Not supported on Windows") -@pytest.mark.skipif(not torch.cuda.is_available(), reason="cuda is not available") -def test_eager_benchmark(benchmark, default_dtype): # pylint: disable=W0621 - print(f"using default dtype = {default_dtype}") - batch = create_batch("cuda") - model = create_mace("cuda") - model = time_func(model) - benchmark(model, batch, training=True) - - -@pytest.mark.skipif(os.name == "nt", reason="Not supported on Windows") -@pytest.mark.skipif(not torch.cuda.is_available(), reason="cuda is not available") -@pytest.mark.parametrize("compile_mode", ["default", "reduce-overhead", "max-autotune"]) -@pytest.mark.parametrize("enable_amp", [False, True], ids=["fp32", "mixed"]) -def test_compile_benchmark(benchmark, compile_mode, enable_amp): - if enable_amp: - pytest.skip(reason="autocast compiler assertion aten.slice_scatter.default") - - with tools.torch_tools.default_dtype(torch.float32): - batch = create_batch("cuda") - torch.compiler.reset() - model = mace_compile.prepare(create_mace)("cuda") - model = torch.compile(model, mode=compile_mode) - model = time_func(model) - - with torch.autocast("cuda", enabled=enable_amp): - benchmark(model, batch, training=True) - - -@pytest.mark.skipif(os.name == "nt", reason="Not supported on Windows") -@pytest.mark.skipif(not torch.cuda.is_available(), reason="cuda is not available") -def test_graph_breaks(): - import torch._dynamo as dynamo - - batch = create_batch("cuda") - model = mace_compile.prepare(create_mace)("cuda") - explanation = dynamo.explain(model)(batch, training=False) - - # these clutter the output but might be useful for investigating graph breaks - explanation.ops_per_graph = None - explanation.out_guards = None - print(explanation) - assert explanation.graph_break_count == 0 diff --git a/mace-bench/3rdparty/mace/tests/test_cueq.py b/mace-bench/3rdparty/mace/tests/test_cueq.py deleted file mode 100644 index 480a8170e3c5935fffbe781f600cf197b50a60ef..0000000000000000000000000000000000000000 --- a/mace-bench/3rdparty/mace/tests/test_cueq.py +++ /dev/null @@ -1,181 +0,0 @@ -# pylint: disable=wrong-import-position -import os -from copy import deepcopy -from typing import Any, Dict - -os.environ["TORCH_FORCE_NO_WEIGHTS_ONLY_LOAD"] = "1" - -import pytest -import torch -import torch.nn.functional as F -from e3nn import o3 - -from mace import data, modules, tools -from mace.cli.convert_cueq_e3nn import run as run_cueq_to_e3nn -from mace.cli.convert_e3nn_cueq import run as run_e3nn_to_cueq -from mace.tools import torch_geometric - -try: - import cuequivariance as cue # pylint: disable=unused-import - - CUET_AVAILABLE = True -except ImportError: - CUET_AVAILABLE = False - -CUDA_AVAILABLE = torch.cuda.is_available() - - -@pytest.mark.skipif(not CUET_AVAILABLE, reason="cuequivariance not installed") -class TestCueq: - @pytest.fixture - def model_config(self, interaction_cls_first, hidden_irreps) -> Dict[str, Any]: - table = tools.AtomicNumberTable([6]) - return { - "r_max": 5.0, - "num_bessel": 8, - "num_polynomial_cutoff": 6, - "max_ell": 3, - "interaction_cls": modules.interaction_classes[ - "RealAgnosticResidualInteractionBlock" - ], - "interaction_cls_first": interaction_cls_first, - "num_interactions": 2, - "num_elements": 1, - "hidden_irreps": hidden_irreps, - "MLP_irreps": o3.Irreps("16x0e"), - "gate": F.silu, - "atomic_energies": torch.tensor([1.0]), - "avg_num_neighbors": 8, - "atomic_numbers": table.zs, - "correlation": 3, - "radial_type": "bessel", - "atomic_inter_scale": 1.0, - "atomic_inter_shift": 0.0, - } - - @pytest.fixture - def batch(self, device: str, default_dtype: torch.dtype) -> Dict[str, torch.Tensor]: - from ase import build - - torch.set_default_dtype(default_dtype) - - table = tools.AtomicNumberTable([6]) - - atoms = build.bulk("C", "diamond", a=3.567, cubic=True) - import numpy as np - - displacement = np.random.uniform(-0.1, 0.1, size=atoms.positions.shape) - atoms.positions += displacement - atoms_list = [atoms.repeat((2, 2, 2))] - - configs = [data.config_from_atoms(atoms) for atoms in atoms_list] - data_loader = torch_geometric.dataloader.DataLoader( - dataset=[ - data.AtomicData.from_config(config, z_table=table, cutoff=5.0) - for config in configs - ], - batch_size=1, - shuffle=False, - drop_last=False, - ) - batch = next(iter(data_loader)) - return batch.to(device).to_dict() - - @pytest.mark.parametrize( - "device", - ["cpu"] + (["cuda"] if CUDA_AVAILABLE else []), - ) - @pytest.mark.parametrize( - "interaction_cls_first", - [ - modules.interaction_classes["RealAgnosticResidualInteractionBlock"], - modules.interaction_classes["RealAgnosticInteractionBlock"], - modules.interaction_classes["RealAgnosticDensityInteractionBlock"], - ], - ) - @pytest.mark.parametrize( - "hidden_irreps", - [ - o3.Irreps("32x0e + 32x1o"), - o3.Irreps("32x0e + 32x1o + 32x2e"), - o3.Irreps("32x0e"), - ], - ) - @pytest.mark.parametrize("default_dtype", [torch.float32, torch.float64]) - def test_bidirectional_conversion( - self, - model_config: Dict[str, Any], - batch: Dict[str, torch.Tensor], - device: str, - default_dtype: torch.dtype, - ): - if device == "cuda" and not CUDA_AVAILABLE: - pytest.skip("CUDA not available") - torch.manual_seed(42) - - # Create original E3nn model - model_e3nn = modules.ScaleShiftMACE(**model_config).to(device) - - # Convert E3nn to CuEq - model_cueq = run_e3nn_to_cueq(model_e3nn).to(device) - - # Convert CuEq back to E3nn - model_e3nn_back = run_cueq_to_e3nn(model_cueq).to(device) - - # Test forward pass equivalence - out_e3nn = model_e3nn(deepcopy(batch), training=True, compute_stress=True) - out_cueq = model_cueq(deepcopy(batch), training=True, compute_stress=True) - out_e3nn_back = model_e3nn_back( - deepcopy(batch), training=True, compute_stress=True - ) - - # Check outputs match for both conversions - torch.testing.assert_close(out_e3nn["energy"], out_cueq["energy"]) - torch.testing.assert_close(out_cueq["energy"], out_e3nn_back["energy"]) - torch.testing.assert_close(out_e3nn["forces"], out_cueq["forces"]) - torch.testing.assert_close(out_cueq["forces"], out_e3nn_back["forces"]) - torch.testing.assert_close(out_e3nn["stress"], out_cueq["stress"]) - torch.testing.assert_close(out_cueq["stress"], out_e3nn_back["stress"]) - - # Test backward pass equivalence - loss_e3nn = out_e3nn["energy"].sum() - loss_cueq = out_cueq["energy"].sum() - loss_e3nn_back = out_e3nn_back["energy"].sum() - - loss_e3nn.backward() - loss_cueq.backward() - loss_e3nn_back.backward() - - # Compare gradients for all conversions - tol = 1e-4 if default_dtype == torch.float32 else 1e-7 - - def print_gradient_diff(name1, p1, name2, p2, conv_type): - if p1.grad is not None and p1.grad.shape == p2.grad.shape: - if name1.split(".", 2)[:2] == name2.split(".", 2)[:2]: - error = torch.abs(p1.grad - p2.grad) - print( - f"{conv_type} - Parameter {name1}/{name2}, Max error: {error.max()}" - ) - torch.testing.assert_close(p1.grad, p2.grad, atol=tol, rtol=tol) - - # E3nn to CuEq gradients - for (name_e3nn, p_e3nn), (name_cueq, p_cueq) in zip( - model_e3nn.named_parameters(), model_cueq.named_parameters() - ): - print_gradient_diff(name_e3nn, p_e3nn, name_cueq, p_cueq, "E3nn->CuEq") - - # CuEq to E3nn gradients - for (name_cueq, p_cueq), (name_e3nn_back, p_e3nn_back) in zip( - model_cueq.named_parameters(), model_e3nn_back.named_parameters() - ): - print_gradient_diff( - name_cueq, p_cueq, name_e3nn_back, p_e3nn_back, "CuEq->E3nn" - ) - - # Full circle comparison (E3nn -> E3nn) - for (name_e3nn, p_e3nn), (name_e3nn_back, p_e3nn_back) in zip( - model_e3nn.named_parameters(), model_e3nn_back.named_parameters() - ): - print_gradient_diff( - name_e3nn, p_e3nn, name_e3nn_back, p_e3nn_back, "Full circle" - ) diff --git a/mace-bench/3rdparty/mace/tests/test_data.py b/mace-bench/3rdparty/mace/tests/test_data.py deleted file mode 100644 index 6710ecddb4d042326b079bde96a888f32d3df429..0000000000000000000000000000000000000000 --- a/mace-bench/3rdparty/mace/tests/test_data.py +++ /dev/null @@ -1,213 +0,0 @@ -from copy import deepcopy -from pathlib import Path - -import ase.build -import h5py -import numpy as np -import torch - -from mace.data import ( - AtomicData, - Configuration, - HDF5Dataset, - config_from_atoms, - get_neighborhood, - save_configurations_as_HDF5, -) -from mace.tools import AtomicNumberTable, torch_geometric - -mace_path = Path(__file__).parent.parent - - -class TestAtomicData: - config = Configuration( - atomic_numbers=np.array([8, 1, 1]), - positions=np.array( - [ - [0.0, -2.0, 0.0], - [1.0, 0.0, 0.0], - [0.0, 1.0, 0.0], - ] - ), - properties={ - "forces": np.array( - [ - [0.0, -1.3, 0.0], - [1.0, 0.2, 0.0], - [0.0, 1.1, 0.3], - ] - ), - "energy": -1.5, - }, - property_weights={ - "forces": 1.0, - "energy": 1.0, - }, - ) - config_2 = deepcopy(config) - config_2.positions = config.positions + 0.01 - - table = AtomicNumberTable([1, 8]) - - def test_atomic_data(self): - data = AtomicData.from_config(self.config, z_table=self.table, cutoff=3.0) - - assert data.edge_index.shape == (2, 4) - assert data.forces.shape == (3, 3) - assert data.node_attrs.shape == (3, 2) - - def test_data_loader(self): - data1 = AtomicData.from_config(self.config, z_table=self.table, cutoff=3.0) - data2 = AtomicData.from_config(self.config, z_table=self.table, cutoff=3.0) - - data_loader = torch_geometric.dataloader.DataLoader( - dataset=[data1, data2], - batch_size=2, - shuffle=True, - drop_last=False, - ) - - for batch in data_loader: - assert batch.batch.shape == (6,) - assert batch.edge_index.shape == (2, 8) - assert batch.shifts.shape == (8, 3) - assert batch.positions.shape == (6, 3) - assert batch.node_attrs.shape == (6, 2) - assert batch.energy.shape == (2,) - assert batch.forces.shape == (6, 3) - - def test_to_atomic_data_dict(self): - data1 = AtomicData.from_config(self.config, z_table=self.table, cutoff=3.0) - data2 = AtomicData.from_config(self.config, z_table=self.table, cutoff=3.0) - - data_loader = torch_geometric.dataloader.DataLoader( - dataset=[data1, data2], - batch_size=2, - shuffle=True, - drop_last=False, - ) - for batch in data_loader: - batch_dict = batch.to_dict() - assert batch_dict["batch"].shape == (6,) - assert batch_dict["edge_index"].shape == (2, 8) - assert batch_dict["shifts"].shape == (8, 3) - assert batch_dict["positions"].shape == (6, 3) - assert batch_dict["node_attrs"].shape == (6, 2) - assert batch_dict["energy"].shape == (2,) - assert batch_dict["forces"].shape == (6, 3) - - def test_hdf5_dataloader(self): - datasets = [self.config, self.config_2] * 5 - # get path of the mace package - with h5py.File(str(mace_path) + "test.h5", "w") as f: - save_configurations_as_HDF5(datasets, 0, f) - train_dataset = HDF5Dataset( - str(mace_path) + "test.h5", z_table=self.table, r_max=3.0 - ) - train_loader = torch_geometric.dataloader.DataLoader( - dataset=train_dataset, - batch_size=2, - shuffle=False, - drop_last=False, - ) - batch_count = 0 - for batch in train_loader: - batch_count += 1 - assert batch.batch.shape == (6,) - assert batch.edge_index.shape == (2, 8) - assert batch.shifts.shape == (8, 3) - assert batch.positions.shape == (6, 3) - assert batch.node_attrs.shape == (6, 2) - assert batch.energy.shape == (2,) - assert batch.forces.shape == (6, 3) - print(batch_count, len(train_loader), len(train_dataset)) - assert batch_count == len(train_loader) == len(train_dataset) / 2 - train_loader_direct = torch_geometric.dataloader.DataLoader( - dataset=[ - AtomicData.from_config(config, z_table=self.table, cutoff=3.0) - for config in datasets - ], - batch_size=2, - shuffle=False, - drop_last=False, - ) - for batch_direct, batch in zip(train_loader_direct, train_loader): - assert torch.all(batch_direct.edge_index == batch.edge_index) - assert torch.all(batch_direct.shifts == batch.shifts) - assert torch.all(batch_direct.positions == batch.positions) - assert torch.all(batch_direct.node_attrs == batch.node_attrs) - assert torch.all(batch_direct.energy == batch.energy) - assert torch.all(batch_direct.forces == batch.forces) - - -class TestNeighborhood: - def test_basic(self): - positions = np.array( - [ - [-1.0, 0.0, 0.0], - [+0.0, 0.0, 0.0], - [+1.0, 0.0, 0.0], - ] - ) - - indices, shifts, unit_shifts, _ = get_neighborhood(positions, cutoff=1.5) - assert indices.shape == (2, 4) - assert shifts.shape == (4, 3) - assert unit_shifts.shape == (4, 3) - - def test_signs(self): - positions = np.array( - [ - [+0.5, 0.5, 0.0], - [+1.0, 1.0, 0.0], - ] - ) - - cell = np.array([[2.0, 0.0, 0.0], [0.0, 1.0, 0.0], [0.0, 0.0, 1.0]]) - edge_index, shifts, unit_shifts, _ = get_neighborhood( - positions, cutoff=3.5, pbc=(True, False, False), cell=cell - ) - num_edges = 10 - assert edge_index.shape == (2, num_edges) - assert shifts.shape == (num_edges, 3) - assert unit_shifts.shape == (num_edges, 3) - - -# Based on mir-group/nequip -def test_periodic_edge(): - atoms = ase.build.bulk("Cu", "fcc") - dist = np.linalg.norm(atoms.cell[0]).item() - config = config_from_atoms(atoms) - edge_index, shifts, _, _ = get_neighborhood( - config.positions, cutoff=1.05 * dist, pbc=(True, True, True), cell=config.cell - ) - sender, receiver = edge_index - vectors = ( - config.positions[receiver] - config.positions[sender] + shifts - ) # [n_edges, 3] - assert vectors.shape == (12, 3) # 12 neighbors in close-packed bulk - assert np.allclose( - np.linalg.norm(vectors, axis=-1), - dist, - ) - - -def test_half_periodic(): - atoms = ase.build.fcc111("Al", size=(3, 3, 1), vacuum=0.0) - assert all(atoms.pbc == (True, True, False)) - config = config_from_atoms(atoms) # first shell dist is 2.864A - edge_index, shifts, _, _ = get_neighborhood( - config.positions, cutoff=2.9, pbc=(True, True, False), cell=config.cell - ) - sender, receiver = edge_index - vectors = ( - config.positions[receiver] - config.positions[sender] + shifts - ) # [n_edges, 3] - # Check number of neighbors: - _, neighbor_count = np.unique(edge_index[0], return_counts=True) - assert (neighbor_count == 6).all() # 6 neighbors - # Check not periodic in z - assert np.allclose( - vectors[:, 2], - np.zeros(vectors.shape[0]), - ) diff --git a/mace-bench/3rdparty/mace/tests/test_finetuning_select.py b/mace-bench/3rdparty/mace/tests/test_finetuning_select.py deleted file mode 100644 index a58c8b305307ed4510d6e72972255b1144d07bd4..0000000000000000000000000000000000000000 --- a/mace-bench/3rdparty/mace/tests/test_finetuning_select.py +++ /dev/null @@ -1,164 +0,0 @@ -import ase.io as aio -import numpy as np -import pytest -from ase import Atoms -from ase.build import molecule - -from mace.cli.fine_tuning_select import ( - FilteringType, - SelectionSettings, - SubselectType, - _filter_pretraining_data, - _load_descriptors, - _maybe_save_descriptors, - filter_atoms, - select_samples, -) - - -@pytest.fixture(name="train_atoms_fixture") -def train_atoms(): - return [ - molecule("H2O"), - molecule("CH4"), - Atoms("Fe2O3"), - Atoms("C"), - Atoms("FeON"), - Atoms("Fe"), - ] - - -@pytest.fixture(name="train_atom_descriptors_fixture") -def train_atom_descriptors(train_atoms_fixture): - return [ - {x: np.zeros(5) + i for x in atoms.symbols} - for i, atoms in enumerate(train_atoms_fixture) - ] - - -@pytest.mark.parametrize( - "filtering_type, passes_filter, element_sublist", - [ - (FilteringType.NONE, [True] * 6, []), - (FilteringType.NONE, [True] * 6, ["C", "U", "Anything really"]), - ( - FilteringType.COMBINATIONS, - [False, False, True, False, False, True], - ["O", "Fe"], - ), - ( - FilteringType.INCLUSIVE, - [False, False, True, False, True, False], - ["O", "Fe"], - ), - ( - FilteringType.EXCLUSIVE, - [False, False, True, False, False, False], - ["O", "Fe"], - ), - ], -) -def test_filter_data( - train_atoms_fixture, filtering_type, passes_filter, element_sublist -): - filtered, _, passes = _filter_pretraining_data( - train_atoms_fixture, filtering_type, element_sublist - ) - assert passes == passes_filter - assert len(filtered) == sum(passes_filter) - - -@pytest.mark.parametrize( - "passes_filter", [[True] * 6, [False, True, False, True, False, True]] -) -def test_load_descriptors( - train_atoms_fixture, train_atom_descriptors_fixture, passes_filter, tmp_path -): - for i, atoms in enumerate(train_atoms_fixture): - atoms.info["mace_descriptors"] = train_atom_descriptors_fixture[i] - save_path = tmp_path / "test.xyz" - _maybe_save_descriptors(train_atoms_fixture, save_path.as_posix()) - assert all(not "mace_descriptors" in atoms.info for atoms in train_atoms_fixture) - filtered_atoms = [ - x for x, passes in zip(train_atoms_fixture, passes_filter) if passes - ] - descriptors_path = save_path.as_posix().replace(".xyz", "_descriptors.npy") - - _load_descriptors( - filtered_atoms, - passes_filter, - descriptors_path=descriptors_path, - calc=None, - full_data_length=len(train_atoms_fixture), - ) - expected_descriptors = [ - train_atom_descriptors_fixture[i] - for i, passes in enumerate(passes_filter) - if passes - ] - for i, atoms in enumerate(filtered_atoms): - assert "mace_descriptors" in atoms.info - for key, value in expected_descriptors[i].items(): - assert np.allclose(atoms.info["mace_descriptors"][key], value) - - -def test_select_samples_random(train_atoms_fixture, tmp_path): - input_file_path = tmp_path / "input.xyz" - aio.write(input_file_path, train_atoms_fixture, format="extxyz") - output_file_path = tmp_path / "output.xyz" - - settings = SelectionSettings( - configs_pt=input_file_path.as_posix(), - output=output_file_path.as_posix(), - num_samples=2, - subselect=SubselectType.RANDOM, - filtering_type=FilteringType.NONE, - ) - select_samples(settings) - - # Check if output file is created - assert output_file_path.exists() - combined_output_file_path = tmp_path / "output_combined.xyz" - assert combined_output_file_path.exists() - - output_atoms = aio.read(output_file_path, index=":") - assert isinstance(output_atoms, list) - assert len(output_atoms) == 2 - - combined_output_atoms = aio.read(combined_output_file_path, index=":") - assert isinstance(combined_output_atoms, list) - assert ( - len(combined_output_atoms) == 2 - ) # combined same as output since no FT data provided - - -def test_select_samples_ft_provided(train_atoms_fixture, tmp_path): - input_file_path = tmp_path / "input.xyz" - aio.write(input_file_path, train_atoms_fixture, format="extxyz") - output_file_path = tmp_path / "output.xyz" - ft_file_path = tmp_path / "ft_data.xyz" - ft_data = [Atoms("FeO")] - aio.write(ft_file_path.as_posix(), ft_data, format="extxyz") - - settings = SelectionSettings( - configs_pt=input_file_path.as_posix(), - output=output_file_path.as_posix(), - num_samples=2, - subselect=SubselectType.RANDOM, - configs_ft=ft_file_path.as_posix(), - ) - select_samples(settings) - - # Check if output file is created - assert output_file_path.exists() - combined_output_file_path = tmp_path / "output_combined.xyz" - assert combined_output_file_path.exists() - - output_atoms = aio.read(output_file_path, index=":") - assert isinstance(output_atoms, list) - assert len(output_atoms) == 2 - assert all(filter_atoms(x, ["Fe", "O"]) for x in output_atoms) - - combined_atoms = aio.read(combined_output_file_path, index=":") - assert isinstance(combined_atoms, list) - assert len(combined_atoms) == len(output_atoms) + len(ft_data) diff --git a/mace-bench/3rdparty/mace/tests/test_foundations.py b/mace-bench/3rdparty/mace/tests/test_foundations.py deleted file mode 100644 index c8641839d2746ab4c0932dd52b1cf1d0f0e0bdac..0000000000000000000000000000000000000000 --- a/mace-bench/3rdparty/mace/tests/test_foundations.py +++ /dev/null @@ -1,512 +0,0 @@ -from pathlib import Path - -import numpy as np -import pytest -import torch -import torch.nn.functional -from ase.build import molecule -from e3nn import o3 -from e3nn.util import jit -from scipy.spatial.transform import Rotation as R - -from mace import data, modules, tools -from mace.calculators import mace_mp, mace_off -from mace.tools import torch_geometric -from mace.tools.finetuning_utils import load_foundations_elements -from mace.tools.scripts_utils import extract_config_mace_model, remove_pt_head -from mace.tools.utils import AtomicNumberTable - -MODEL_PATH = ( - Path(__file__).parent.parent - / "mace" - / "calculators" - / "foundations_models" - / "2023-12-03-mace-mp.model" -) - -torch.set_default_dtype(torch.float64) - -@pytest.skip("Problem with the float type", allow_module_level=True) -def test_foundations(): - # Create MACE model - config = data.Configuration( - atomic_numbers=molecule("H2COH").numbers, - positions=molecule("H2COH").positions, - properties={ - "forces": molecule("H2COH").positions, - "energy": -1.5, - "charges": molecule("H2COH").numbers, - "dipole": np.array([-1.5, 1.5, 2.0]), - }, - property_weights={ - "forces": 1.0, - "energy": 1.0, - "charges": 1.0, - "dipole": 1.0, - }, - ) - - # Created the rotated environment - rot = R.from_euler("z", 60, degrees=True).as_matrix() - positions_rotated = np.array(rot @ config.positions.T).T - config_rotated = data.Configuration( - atomic_numbers=molecule("H2COH").numbers, - positions=positions_rotated, - properties={ - "forces": molecule("H2COH").positions, - "energy": -1.5, - "charges": molecule("H2COH").numbers, - "dipole": np.array([-1.5, 1.5, 2.0]), - }, - property_weights={ - "forces": 1.0, - "energy": 1.0, - "charges": 1.0, - "dipole": 1.0, - }, - ) - table = tools.AtomicNumberTable([1, 6, 8]) - atomic_energies = np.array([0.0, 0.0, 0.0], dtype=float) - model_config = dict( - r_max=6, - num_bessel=10, - num_polynomial_cutoff=5, - max_ell=3, - interaction_cls=modules.interaction_classes[ - "RealAgnosticResidualInteractionBlock" - ], - interaction_cls_first=modules.interaction_classes[ - "RealAgnosticResidualInteractionBlock" - ], - num_interactions=2, - num_elements=3, - hidden_irreps=o3.Irreps("128x0e + 128x1o"), - MLP_irreps=o3.Irreps("16x0e"), - gate=torch.nn.functional.silu, - atomic_energies=atomic_energies, - avg_num_neighbors=3, - atomic_numbers=table.zs, - correlation=3, - radial_type="bessel", - atomic_inter_scale=0.1, - atomic_inter_shift=0.0, - ) - model = modules.ScaleShiftMACE(**model_config) - calc_foundation = mace_mp(model="medium", device="cpu", default_dtype="float64") - model_loaded = load_foundations_elements( - model, - calc_foundation.models[0], - table=table, - load_readout=True, - use_shift=False, - max_L=1, - ) - atomic_data = data.AtomicData.from_config(config, z_table=table, cutoff=6.0) - atomic_data2 = data.AtomicData.from_config( - config_rotated, z_table=table, cutoff=6.0 - ) - - data_loader = torch_geometric.dataloader.DataLoader( - dataset=[atomic_data, atomic_data2], - batch_size=2, - shuffle=True, - drop_last=False, - ) - batch = next(iter(data_loader)) - forces_loaded = model_loaded(batch.to_dict())["forces"] - forces = model(batch.to_dict())["forces"] - assert torch.allclose(forces, forces_loaded) - - -def test_multi_reference(): - config_multi = data.Configuration( - atomic_numbers=molecule("H2COH").numbers, - positions=molecule("H2COH").positions, - properties={ - "forces": molecule("H2COH").positions, - "energy": -1.5, - "charges": molecule("H2COH").numbers, - "dipole": np.array([-1.5, 1.5, 2.0]), - }, - property_weights={ - "forces": 1.0, - "energy": 1.0, - "charges": 1.0, - "dipole": 1.0, - }, - head="MP2", - ) - table_multi = tools.AtomicNumberTable([1, 6, 8]) - atomic_energies_multi = np.array([[0.0, 0.0, 0.0], [0.0, 0.0, 0.0]], dtype=float) - table = tools.AtomicNumberTable([1, 6, 8]) - - - # Create MACE model - model_config = dict( - r_max=6, - num_bessel=10, - num_polynomial_cutoff=5, - max_ell=3, - interaction_cls=modules.interaction_classes[ - "RealAgnosticResidualInteractionBlock" - ], - interaction_cls_first=modules.interaction_classes[ - "RealAgnosticResidualInteractionBlock" - ], - num_interactions=2, - num_elements=3, - hidden_irreps=o3.Irreps("128x0e + 128x1o"), - MLP_irreps=o3.Irreps("16x0e"), - gate=torch.nn.functional.silu, - atomic_energies=atomic_energies_multi, - avg_num_neighbors=61, - atomic_numbers=table.zs, - correlation=3, - radial_type="bessel", - atomic_inter_scale=[1.0, 1.0], - atomic_inter_shift=[0.0, 0.0], - heads=["MP2", "DFT"], - ) - model = modules.ScaleShiftMACE(**model_config) - calc_foundation = mace_mp(model="medium", device="cpu", default_dtype="float64") - model_loaded = load_foundations_elements( - model, - calc_foundation.models[0], - table=table, - load_readout=True, - use_shift=False, - max_L=1, - ) - atomic_data = data.AtomicData.from_config( - config_multi, z_table=table_multi, cutoff=6.0, heads=["MP2", "DFT"] - ) - data_loader = torch_geometric.dataloader.DataLoader( - dataset=[atomic_data, atomic_data], - batch_size=2, - shuffle=True, - drop_last=False, - ) - batch = next(iter(data_loader)) - forces_loaded = model_loaded(batch.to_dict())["forces"] - calc_foundation = mace_mp(model="medium", device="cpu", default_dtype="float64") - atoms = molecule("H2COH") - atoms.info["head"] = "MP2" - atoms.calc = calc_foundation - forces = atoms.get_forces() - assert np.allclose( - forces, forces_loaded.detach().numpy()[:5, :], atol=1e-5, rtol=1e-5 - ) - - -@pytest.mark.parametrize( - "calc", - [ - mace_mp(device="cpu", default_dtype="float64"), - mace_mp(model="small", device="cpu", default_dtype="float64"), - mace_mp(model="medium", device="cpu", default_dtype="float64"), - mace_mp(model="large", device="cpu", default_dtype="float64"), - mace_mp(model=MODEL_PATH, device="cpu", default_dtype="float64"), - mace_off(model="small", device="cpu", default_dtype="float64"), - mace_off(model="medium", device="cpu", default_dtype="float64"), - mace_off(model="large", device="cpu", default_dtype="float64"), - mace_off(model=MODEL_PATH, device="cpu", default_dtype="float64"), - ], -) -def test_compile_foundation(calc): - model = calc.models[0] - atoms = molecule("CH4") - atoms.positions += np.random.randn(*atoms.positions.shape) * 0.1 - batch = calc._atoms_to_batch(atoms) # pylint: disable=protected-access - output_1 = model(batch.to_dict()) - model_compiled = jit.compile(model) - output = model_compiled(batch.to_dict()) - for key in output_1.keys(): - if isinstance(output_1[key], torch.Tensor): - assert torch.allclose(output_1[key], output[key], atol=1e-5) - - -@pytest.mark.parametrize( - "model", - [ - mace_mp(model="small", device="cpu", default_dtype="float64").models[0], - mace_mp(model="medium", device="cpu", default_dtype="float64").models[0], - mace_mp(model="large", device="cpu", default_dtype="float64").models[0], - mace_mp(model=MODEL_PATH, device="cpu", default_dtype="float64").models[0], - mace_off(model="small", device="cpu", default_dtype="float64").models[0], - mace_off(model="medium", device="cpu", default_dtype="float64").models[0], - mace_off(model="large", device="cpu", default_dtype="float64").models[0], - mace_off(model=MODEL_PATH, device="cpu", default_dtype="float64").models[0], - ], -) -def test_extract_config(model): - assert isinstance(model, modules.ScaleShiftMACE) - config = data.Configuration( - atomic_numbers=molecule("H2COH").numbers, - positions=molecule("H2COH").positions, - properties={ - "forces": molecule("H2COH").positions, - "energy": -1.5, - "charges": molecule("H2COH").numbers, - "dipole": np.array([-1.5, 1.5, 2.0]), - }, - property_weights={ - "forces": 1.0, - "energy": 1.0, - "charges": 1.0, - "dipole": 1.0, - }, - ) - model_copy = modules.ScaleShiftMACE(**extract_config_mace_model(model)) - model_copy.load_state_dict(model.state_dict()) - z_table = AtomicNumberTable([int(z) for z in model.atomic_numbers]) - atomic_data = data.AtomicData.from_config(config, z_table=z_table, cutoff=6.0) - data_loader = torch_geometric.dataloader.DataLoader( - dataset=[atomic_data, atomic_data], - batch_size=2, - shuffle=True, - drop_last=False, - ) - batch = next(iter(data_loader)) - output = model(batch.to_dict()) - output_copy = model_copy(batch.to_dict()) - # assert all items of the output dicts are equal - for key in output.keys(): - if isinstance(output[key], torch.Tensor): - assert torch.allclose(output[key], output_copy[key], atol=1e-5) - - -def test_remove_pt_head(): - # Set up test data - torch.manual_seed(42) - atomic_energies_pt_head = np.array([[1.0, 2.0], [3.0, 4.0]], dtype=float) - z_table = AtomicNumberTable([1, 8]) # H and O - - # Create multihead model - model_config = { - "r_max": 5.0, - "num_bessel": 8, - "num_polynomial_cutoff": 5, - "max_ell": 2, - "interaction_cls": modules.interaction_classes[ - "RealAgnosticResidualInteractionBlock" - ], - "interaction_cls_first": modules.interaction_classes[ - "RealAgnosticResidualInteractionBlock" - ], - "num_interactions": 2, - "num_elements": len(z_table), - "hidden_irreps": o3.Irreps("32x0e + 32x1o"), - "MLP_irreps": o3.Irreps("16x0e"), - "gate": torch.nn.functional.silu, - "atomic_energies": atomic_energies_pt_head, - "avg_num_neighbors": 8, - "atomic_numbers": z_table.zs, - "correlation": 3, - "heads": ["pt_head", "DFT"], - "atomic_inter_scale": [1.0, 1.0], - "atomic_inter_shift": [0.0, 0.1], - } - - model = modules.ScaleShiftMACE(**model_config) - - # Create test molecule - mol = molecule("H2O") - config_pt_head = data.Configuration( - atomic_numbers=mol.numbers, - positions=mol.positions, - properties={"energy": 1.0, "forces": np.random.randn(len(mol), 3)}, - property_weights={"forces": 1.0, "energy": 1.0}, - head="DFT", - ) - atomic_data = data.AtomicData.from_config( - config_pt_head, z_table=z_table, cutoff=5.0, heads=["pt_head", "DFT"] - ) - dataloader = torch_geometric.dataloader.DataLoader( - dataset=[atomic_data], batch_size=1, shuffle=False - ) - batch = next(iter(dataloader)) - # Test original mode - output_orig = model(batch.to_dict()) - - # Convert to single head model - new_model = remove_pt_head(model, head_to_keep="DFT") - - # Basic structure tests - assert len(new_model.heads) == 1 - assert new_model.heads[0] == "DFT" - assert new_model.atomic_energies_fn.atomic_energies.shape[0] == 1 - assert len(torch.atleast_1d(new_model.scale_shift.scale)) == 1 - assert len(torch.atleast_1d(new_model.scale_shift.shift)) == 1 - - # Test output consistency - atomic_data = data.AtomicData.from_config( - config_pt_head, z_table=z_table, cutoff=5.0, heads=["DFT"] - ) - dataloader = torch_geometric.dataloader.DataLoader( - dataset=[atomic_data], batch_size=1, shuffle=False - ) - batch = next(iter(dataloader)) - output_new = new_model(batch.to_dict()) - torch.testing.assert_close( - output_orig["energy"], output_new["energy"], rtol=1e-5, atol=1e-5 - ) - torch.testing.assert_close( - output_orig["forces"], output_new["forces"], rtol=1e-5, atol=1e-5 - ) - - -def test_remove_pt_head_multihead(): - # Set up test data - torch.manual_seed(42) - atomic_energies_pt_head = np.array( - [ - [1.0, 2.0], # H energies for each head - [3.0, 4.0], # O energies for each head - ] - * 2 - ) - z_table = AtomicNumberTable([1, 8]) # H and O - - # Create multihead model - model_config = { - "r_max": 5.0, - "num_bessel": 8, - "num_polynomial_cutoff": 5, - "max_ell": 2, - "interaction_cls": modules.interaction_classes[ - "RealAgnosticResidualInteractionBlock" - ], - "interaction_cls_first": modules.interaction_classes[ - "RealAgnosticResidualInteractionBlock" - ], - "num_interactions": 2, - "num_elements": len(z_table), - "hidden_irreps": o3.Irreps("32x0e + 32x1o"), - "MLP_irreps": o3.Irreps("16x0e"), - "gate": torch.nn.functional.silu, - "atomic_energies": atomic_energies_pt_head, - "avg_num_neighbors": 8, - "atomic_numbers": z_table.zs, - "correlation": 3, - "heads": ["pt_head", "DFT", "MP2", "CCSD"], - "atomic_inter_scale": [1.0, 1.0, 1.0, 1.0], - "atomic_inter_shift": [0.0, 0.1, 0.2, 0.3], - } - - model = modules.ScaleShiftMACE(**model_config) - - # Create test configurations for each head - mol = molecule("H2O") - configs = {} - atomic_datas = {} - dataloaders = {} - original_outputs = {} - - # First get outputs from original model for each head - for head in model.heads: - config_pt_head = data.Configuration( - atomic_numbers=mol.numbers, - positions=mol.positions, - properties={"energy": 1.0, "forces": np.random.randn(len(mol), 3)}, - property_weights={"forces": 1.0, "energy": 1.0}, - head=head, - ) - configs[head] = config_pt_head - - atomic_data = data.AtomicData.from_config( - config_pt_head, z_table=z_table, cutoff=5.0, heads=model.heads - ) - atomic_datas[head] = atomic_data - - dataloader = torch_geometric.dataloader.DataLoader( - dataset=[atomic_data], batch_size=1, shuffle=False - ) - dataloaders[head] = dataloader - - batch = next(iter(dataloader)) - output = model(batch.to_dict()) - original_outputs[head] = output - - # Now test each head separately - for i, head in enumerate(model.heads): - # Convert to single head model - new_model = remove_pt_head(model, head_to_keep=head) - - # Basic structure tests - assert len(new_model.heads) == 1, f"Failed for head {head}" - assert new_model.heads[0] == head, f"Failed for head {head}" - assert ( - new_model.atomic_energies_fn.atomic_energies.shape[0] == 1 - ), f"Failed for head {head}" - assert ( - len(torch.atleast_1d(new_model.scale_shift.scale)) == 1 - ), f"Failed for head {head}" - assert ( - len(torch.atleast_1d(new_model.scale_shift.shift)) == 1 - ), f"Failed for head {head}" - - # Verify scale and shift values - assert torch.allclose( - new_model.scale_shift.scale, model.scale_shift.scale[i : i + 1] - ), f"Failed for head {head}" - assert torch.allclose( - new_model.scale_shift.shift, model.scale_shift.shift[i : i + 1] - ), f"Failed for head {head}" - - # Test output consistency - single_head_data = data.AtomicData.from_config( - configs[head], z_table=z_table, cutoff=5.0, heads=[head] - ) - single_head_loader = torch_geometric.dataloader.DataLoader( - dataset=[single_head_data], batch_size=1, shuffle=False - ) - batch = next(iter(single_head_loader)) - new_output = new_model(batch.to_dict()) - - # Compare outputs - print( - original_outputs[head]["energy"], - new_output["energy"], - ) - torch.testing.assert_close( - original_outputs[head]["energy"], - new_output["energy"], - rtol=1e-5, - atol=1e-5, - msg=f"Energy mismatch for head {head}", - ) - torch.testing.assert_close( - original_outputs[head]["forces"], - new_output["forces"], - rtol=1e-5, - atol=1e-5, - msg=f"Forces mismatch for head {head}", - ) - - # Test error cases - with pytest.raises(ValueError, match="Head non_existent not found in model"): - remove_pt_head(model, head_to_keep="non_existent") - - # Test default behavior (first non-PT head) - default_model = remove_pt_head(model) - assert default_model.heads[0] == "DFT" - - # Additional test: check if each model's computation graph is independent - models = {head: remove_pt_head(model, head_to_keep=head) for head in model.heads} - results = {} - - for head, head_model in models.items(): - single_head_data = data.AtomicData.from_config( - configs[head], z_table=z_table, cutoff=5.0, heads=[head] - ) - single_head_loader = torch_geometric.dataloader.DataLoader( - dataset=[single_head_data], batch_size=1, shuffle=False - ) - batch = next(iter(single_head_loader)) - results[head] = head_model(batch.to_dict()) - - # Verify each model produces different outputs - energies = torch.stack([results[head]["energy"] for head in model.heads]) - assert not torch.allclose( - energies[0], energies[1], rtol=1e-3 - ), "Different heads should produce different outputs" diff --git a/mace-bench/3rdparty/mace/tests/test_hessian.py b/mace-bench/3rdparty/mace/tests/test_hessian.py deleted file mode 100644 index 53457335d5226b3da0a774d0e32ef330c8b36ba6..0000000000000000000000000000000000000000 --- a/mace-bench/3rdparty/mace/tests/test_hessian.py +++ /dev/null @@ -1,54 +0,0 @@ -import numpy as np -import pytest -from ase.build import fcc111 - -from mace.calculators import mace_mp - - -@pytest.fixture(name="setup_calculator_") -def setup_calculator(): - calc = mace_mp( - model="medium", dispersion=False, default_dtype="float64", device="cpu" - ) - return calc - - -@pytest.fixture(name="setup_structure_") -def setup_structure(setup_calculator_): - initial = fcc111("Pt", size=(4, 4, 1), vacuum=10.0, orthogonal=True) - initial.calc = setup_calculator_ - return initial - - -def test_potential_energy_and_hessian(setup_structure_): - initial = setup_structure_ - h_autograd = initial.calc.get_hessian(atoms=initial) - assert h_autograd.shape == (len(initial) * 3, len(initial), 3) - - -def test_finite_difference_hessian(setup_structure_): - initial = setup_structure_ - indicies = list(range(len(initial))) - delta, ndim = 1e-4, 3 - hessian = np.zeros((len(indicies) * ndim, len(indicies) * ndim)) - atoms_h = initial.copy() - for i, index in enumerate(indicies): - for j in range(ndim): - atoms_i = atoms_h.copy() - atoms_i.positions[index, j] += delta - atoms_i.calc = initial.calc - forces_i = atoms_i.get_forces() - - atoms_j = atoms_h.copy() - atoms_j.positions[index, j] -= delta - atoms_j.calc = initial.calc - forces_j = atoms_j.get_forces() - - hessian[:, i * ndim + j] = -(forces_i - forces_j)[indicies].flatten() / ( - 2 * delta - ) - - hessian = hessian.reshape((-1, len(initial), 3)) - h_autograd = initial.calc.get_hessian(atoms=initial) - is_close = np.allclose(h_autograd, hessian, atol=1e-6) - assert is_close diff --git a/mace-bench/3rdparty/mace/tests/test_lmdb_database.py b/mace-bench/3rdparty/mace/tests/test_lmdb_database.py deleted file mode 100644 index 0c7043a6d6f84d3576256a08ba3492e12118e542..0000000000000000000000000000000000000000 --- a/mace-bench/3rdparty/mace/tests/test_lmdb_database.py +++ /dev/null @@ -1,134 +0,0 @@ -import os -import tempfile - -import numpy as np -import torch -from ase.build import molecule -from ase.calculators.singlepoint import SinglePointCalculator - -from mace.data.lmdb_dataset import LMDBDataset -from mace.tools import AtomicNumberTable, torch_geometric -from mace.tools.fairchem_dataset.lmdb_dataset_tools import LMDBDatabase - - -def test_lmdb_dataset(): - """Test the LMDBDataset by creating a fake database and verifying batch creation.""" - # Set default dtype to match typical MACE usage - torch.set_default_dtype(torch.float64) - - # Set random seed for reproducibility - np.random.seed(42) - - # Create temporary directories for the databases - with tempfile.TemporaryDirectory() as tmpdir: - # Create 3 folders for databases - db_paths = [] - for i in range(3): - folder_path = os.path.join(tmpdir, f"folder_{i}") - os.makedirs(folder_path, exist_ok=True) - - # Create LMDB database files in each folder (2 per folder) - for j in range(2): - db_path = os.path.join(folder_path, f"data_{j}.aselmdb") - db = LMDBDatabase(db_path, readonly=False) - - # Add 2 configurations to each database - for _ in range(2): - # Create a water molecule using ASE's build functionality - atoms = molecule("H2O") - - # Apply small random displacements to the positions - displacement = np.random.rand(*atoms.positions.shape) * 0.1 - atoms.positions += displacement - - # Set cell and PBC - atoms.set_cell(np.eye(3) * 5.0) - atoms.set_pbc(True) - - # Add random energy, forces, and stress - energy = np.random.uniform( - -15.0, -5.0 - ) # Random energy between -15 and -5 eV - forces = ( - np.random.randn(*atoms.positions.shape) * 0.5 - ) # Random forces - stress = np.random.randn(6) * 0.2 # Random stress in Voigt notation - - # Add calculator to atoms with results - calc = SinglePointCalculator( - atoms, energy=energy, forces=forces, stress=stress - ) - atoms.calc = calc - - # Store in database - db.write(atoms) - - db.close() - - # Add folder path to our list - db_paths.append(folder_path) - - # Create the dataset using paths joined with colons - paths_str = ":".join(db_paths) - z_table = AtomicNumberTable([1, 8]) # H and O - dataset = LMDBDataset(file_path=paths_str, r_max=5.0, z_table=z_table) - - # Check dataset size (3 folders * 2 files * 2 configs = 12 entries) - assert len(dataset) == 12 - - # Test retrieving a single item - item = dataset[0] - print(item) - assert item.positions.shape == (3, 3) # 3 atoms, 3 coordinates - assert hasattr(item, "energy") - assert hasattr(item, "forces") - assert hasattr(item, "stress") - - # Create a dataloader - dataloader = torch_geometric.dataloader.DataLoader( - dataset=dataset, batch_size=4, shuffle=False, drop_last=False - ) - - # Get a batch and validate it - batch = next(iter(dataloader)) - - # Verify batch properties - should have 12 atoms (4 configs * 3 atoms per water) - assert batch.positions.shape == (12, 3) # 12 atoms, 3 coordinates - assert batch.energy.shape[0] == 4 # 4 energies (one per config) - assert batch.forces.shape == (12, 3) # Forces for each atom - print(batch.stress.shape) - assert batch.stress.shape == (4, 3, 3) # Stress for each config - - # Check batch has required attributes for MACE model processing - assert hasattr(batch, "batch") # Batch indices - assert batch.batch.shape[0] == 12 # One index per atom - assert hasattr(batch, "ptr") # Pointer for batch processing - assert batch.ptr.shape[0] == 5 # One pointer per config + 1 - - # Check that batch indices are correctly assigned - # First 3 atoms should be from config 0, next 3 from config 1, etc. - expected_batch = torch.tensor([0, 0, 0, 1, 1, 1, 2, 2, 2, 3, 3, 3]) - assert torch.all(batch.batch == expected_batch) - - # Check ptr correctly points to start of each configuration - assert batch.ptr.tolist() == [0, 3, 6, 9, 12] - - # Create a batch dictionary that can be passed to a MACE model - batch_dict = batch.to_dict() - assert "positions" in batch_dict - assert "energy" in batch_dict - assert "forces" in batch_dict - assert "stress" in batch_dict - assert "batch" in batch_dict - assert "ptr" in batch_dict - - # Verify additional properties required by MACE - assert hasattr(batch, "edge_index") # Connectivity information - assert hasattr(batch, "shifts") # For periodic boundary conditions - assert hasattr(batch, "cell") # Unit cell information - - # Test that a full batch can be processed (without errors) - all_batches = list(dataloader) - assert ( - len(all_batches) == 3 - ) # Should have 3 batches (12 configs with batch size 4) diff --git a/mace-bench/3rdparty/mace/tests/test_models.py b/mace-bench/3rdparty/mace/tests/test_models.py deleted file mode 100644 index 40ff48c394af814c304e44d1d5a43d705428ed07..0000000000000000000000000000000000000000 --- a/mace-bench/3rdparty/mace/tests/test_models.py +++ /dev/null @@ -1,374 +0,0 @@ -import numpy as np -import torch -import torch.nn.functional -from ase import build -from e3nn import o3 -from e3nn.util import jit -from scipy.spatial.transform import Rotation as R - -from mace import data, modules, tools -from mace.tools import torch_geometric - -torch.set_default_dtype(torch.float64) -config = data.Configuration( - atomic_numbers=np.array([8, 1, 1]), - positions=np.array( - [ - [0.0, -2.0, 0.0], - [1.0, 0.0, 0.0], - [0.0, 1.0, 0.0], - ] - ), - properties={ - "forces": np.array( - [ - [0.0, -1.3, 0.0], - [1.0, 0.2, 0.0], - [0.0, 1.1, 0.3], - ] - ), - "energy": -1.5, - "charges": np.array([-2.0, 1.0, 1.0]), - "dipole": np.array([-1.5, 1.5, 2.0]), - }, - property_weights={ - "forces": 1.0, - "energy": 1.0, - "charges": 1.0, - "dipole": 1.0, - }, -) -# Created the rotated environment -rot = R.from_euler("z", 60, degrees=True).as_matrix() -positions_rotated = np.array(rot @ config.positions.T).T -config_rotated = data.Configuration( - atomic_numbers=np.array([8, 1, 1]), - positions=positions_rotated, - properties={ - "forces": np.array( - [ - [0.0, -1.3, 0.0], - [1.0, 0.2, 0.0], - [0.0, 1.1, 0.3], - ] - ), - "energy": -1.5, - "charges": np.array([-2.0, 1.0, 1.0]), - "dipole": np.array([-1.5, 1.5, 2.0]), - }, - property_weights={ - "forces": 1.0, - "energy": 1.0, - "charges": 1.0, - "dipole": 1.0, - }, -) -table = tools.AtomicNumberTable([1, 8]) -atomic_energies = np.array([1.0, 3.0], dtype=float) - - -def test_mace(): - # Create MACE model - model_config = dict( - r_max=5, - num_bessel=8, - num_polynomial_cutoff=6, - max_ell=2, - interaction_cls=modules.interaction_classes[ - "RealAgnosticResidualInteractionBlock" - ], - interaction_cls_first=modules.interaction_classes[ - "RealAgnosticResidualInteractionBlock" - ], - num_interactions=5, - num_elements=2, - hidden_irreps=o3.Irreps("32x0e + 32x1o"), - MLP_irreps=o3.Irreps("16x0e"), - gate=torch.nn.functional.silu, - atomic_energies=atomic_energies, - avg_num_neighbors=8, - atomic_numbers=table.zs, - correlation=3, - radial_type="bessel", - ) - model = modules.MACE(**model_config) - model_compiled = jit.compile(model) - - atomic_data = data.AtomicData.from_config(config, z_table=table, cutoff=3.0) - atomic_data2 = data.AtomicData.from_config( - config_rotated, z_table=table, cutoff=3.0 - ) - - data_loader = torch_geometric.dataloader.DataLoader( - dataset=[atomic_data, atomic_data2], - batch_size=2, - shuffle=True, - drop_last=False, - ) - batch = next(iter(data_loader)) - output1 = model(batch.to_dict(), training=True) - output2 = model_compiled(batch.to_dict(), training=True) - assert torch.allclose(output1["energy"][0], output2["energy"][0]) - assert torch.allclose(output2["energy"][0], output2["energy"][1]) - - -def test_dipole_mace(): - # create dipole MACE model - model_config = dict( - r_max=5, - num_bessel=8, - num_polynomial_cutoff=5, - max_ell=2, - interaction_cls=modules.interaction_classes[ - "RealAgnosticResidualInteractionBlock" - ], - interaction_cls_first=modules.interaction_classes[ - "RealAgnosticResidualInteractionBlock" - ], - num_interactions=2, - num_elements=2, - hidden_irreps=o3.Irreps("16x0e + 16x1o + 16x2e"), - MLP_irreps=o3.Irreps("16x0e"), - gate=torch.nn.functional.silu, - atomic_energies=None, - avg_num_neighbors=3, - atomic_numbers=table.zs, - correlation=3, - radial_type="gaussian", - ) - model = modules.AtomicDipolesMACE(**model_config) - - atomic_data = data.AtomicData.from_config(config, z_table=table, cutoff=3.0) - atomic_data2 = data.AtomicData.from_config( - config_rotated, z_table=table, cutoff=3.0 - ) - - data_loader = torch_geometric.dataloader.DataLoader( - dataset=[atomic_data, atomic_data2], - batch_size=2, - shuffle=False, - drop_last=False, - ) - batch = next(iter(data_loader)) - output = model( - batch, - training=True, - ) - # sanity check of dipoles being the right shape - assert output["dipole"][0].unsqueeze(0).shape == atomic_data.dipole.shape - # test equivariance of output dipoles - assert np.allclose( - np.array(rot @ output["dipole"][0].detach().numpy()), - output["dipole"][1].detach().numpy(), - ) - - -def test_energy_dipole_mace(): - # create dipole MACE model - model_config = dict( - r_max=5, - num_bessel=8, - num_polynomial_cutoff=5, - max_ell=2, - interaction_cls=modules.interaction_classes[ - "RealAgnosticResidualInteractionBlock" - ], - interaction_cls_first=modules.interaction_classes[ - "RealAgnosticResidualInteractionBlock" - ], - num_interactions=2, - num_elements=2, - hidden_irreps=o3.Irreps("16x0e + 16x1o + 16x2e"), - MLP_irreps=o3.Irreps("16x0e"), - gate=torch.nn.functional.silu, - atomic_energies=atomic_energies, - avg_num_neighbors=3, - atomic_numbers=table.zs, - correlation=3, - ) - model = modules.EnergyDipolesMACE(**model_config) - - atomic_data = data.AtomicData.from_config(config, z_table=table, cutoff=3.0) - atomic_data2 = data.AtomicData.from_config( - config_rotated, z_table=table, cutoff=3.0 - ) - - data_loader = torch_geometric.dataloader.DataLoader( - dataset=[atomic_data, atomic_data2], - batch_size=2, - shuffle=False, - drop_last=False, - ) - batch = next(iter(data_loader)) - output = model( - batch, - training=True, - ) - # sanity check of dipoles being the right shape - assert output["dipole"][0].unsqueeze(0).shape == atomic_data.dipole.shape - # test energy is invariant - assert torch.allclose(output["energy"][0], output["energy"][1]) - # test equivariance of output dipoles - assert np.allclose( - np.array(rot @ output["dipole"][0].detach().numpy()), - output["dipole"][1].detach().numpy(), - ) - - -def test_mace_multi_reference(): - atomic_energies_multi = np.array([[1.0, 3.0], [0.0, 0.0]], dtype=float) - model_config = dict( - r_max=5, - num_bessel=8, - num_polynomial_cutoff=6, - max_ell=3, - interaction_cls=modules.interaction_classes[ - "RealAgnosticResidualInteractionBlock" - ], - interaction_cls_first=modules.interaction_classes[ - "RealAgnosticResidualInteractionBlock" - ], - num_interactions=2, - num_elements=2, - hidden_irreps=o3.Irreps("96x0e + 96x1o"), - MLP_irreps=o3.Irreps("16x0e"), - gate=torch.nn.functional.silu, - atomic_energies=atomic_energies_multi, - avg_num_neighbors=8, - atomic_numbers=table.zs, - distance_transform=True, - pair_repulsion=True, - correlation=3, - heads=["Default", "dft"], - # radial_type="chebyshev", - atomic_inter_scale=[1.0, 1.0], - atomic_inter_shift=[0.0, 0.1], - ) - model = modules.ScaleShiftMACE(**model_config) - model_compiled = jit.compile(model) - config.head = "Default" - config_rotated.head = "dft" - atomic_data = data.AtomicData.from_config( - config, z_table=table, cutoff=3.0, heads=["Default", "dft"] - ) - atomic_data2 = data.AtomicData.from_config( - config_rotated, z_table=table, cutoff=3.0, heads=["Default", "dft"] - ) - - data_loader = torch_geometric.dataloader.DataLoader( - dataset=[atomic_data, atomic_data2], - batch_size=2, - shuffle=True, - drop_last=False, - ) - batch = next(iter(data_loader)) - output1 = model(batch.to_dict(), training=True) - output2 = model_compiled(batch.to_dict(), training=True) - assert torch.allclose(output1["energy"][0], output2["energy"][0]) - assert output2["energy"].shape[0] == 2 - - -def test_atomic_virials_stresses(): - """ - Test that atomic virials and stresses sum to the total virials and stress. - """ - # Set default dtype for reproducibility - torch.set_default_dtype(torch.float64) - - # Create a periodic cell with ASE - atoms = build.bulk("Si", "diamond", a=5.43) - # Apply strain to ensure non-zero stress - strain_tensor = np.eye(3) * 1.02 # 2% strain - atoms.set_cell(np.dot(atoms.get_cell(), strain_tensor), scale_atoms=True) - - # Add forces and energy for completeness - atoms.arrays["REF_forces"] = np.random.normal(0, 0.1, size=atoms.positions.shape) - atoms.info["REF_energy"] = np.random.normal(0, 1) - atoms.info["REF_stress"] = np.random.normal(0, 0.1, size=6) - - # Setup MACE model configuration - stress_z_table = tools.AtomicNumberTable([14]) # Silicon - stress_atomic_energies = np.array([0.0]) - - model_config = dict( - r_max=5.0, - num_bessel=8, - num_polynomial_cutoff=6, - max_ell=2, - interaction_cls=modules.interaction_classes[ - "RealAgnosticResidualInteractionBlock" - ], - interaction_cls_first=modules.interaction_classes[ - "RealAgnosticResidualInteractionBlock" - ], - num_interactions=3, - num_elements=1, - hidden_irreps=o3.Irreps("32x0e + 32x1o"), - MLP_irreps=o3.Irreps("16x0e"), - gate=torch.nn.functional.silu, - atomic_energies=stress_atomic_energies, - avg_num_neighbors=4.0, - atomic_numbers=table.zs, - correlation=3, - atomic_inter_scale=1.0, - atomic_inter_shift=0.0, - ) - - # Create the model - model = modules.ScaleShiftMACE(**model_config) - - # Create atomic data - atomic_data = data.AtomicData.from_config( - data.config_from_atoms( - atoms, key_specification=data.KeySpecification.from_defaults() - ), - z_table=stress_z_table, - cutoff=5.0, - ) - - data_loader = torch_geometric.dataloader.DataLoader( - dataset=[atomic_data], - batch_size=2, - shuffle=True, - drop_last=False, - ) - batch = next(iter(data_loader)) - batch_dict = batch.to_dict() - - # Run the model with compute_atomic_stresses=True - output = model( - batch_dict, - compute_force=True, - compute_virials=True, - compute_stress=True, - compute_atomic_stresses=True, - ) - - # Get total virials/stress and atomic virials/stresses - total_virials = output["virials"] - atomic_virials = output["atomic_virials"] - total_stress = output["stress"] - atomic_stresses = output["atomic_stresses"] - - # Test that atomic values are not None - assert atomic_virials is not None, "Atomic virials were not computed" - assert atomic_stresses is not None, "Atomic stresses were not computed" - - # Test shape of atomic values - assert atomic_virials.shape[0] == len(atoms), "Wrong shape for atomic virials" - assert atomic_virials.shape[1:] == (3, 3), "Atomic virials should be 3x3 matrices" - assert atomic_stresses.shape[0] == len(atoms), "Wrong shape for atomic stresses" - assert atomic_stresses.shape[1:] == (3, 3), "Atomic stresses should be 3x3 matrices" - - # Compute sum of atomic values - summed_atomic_virials = torch.sum(atomic_virials, dim=0) - summed_atomic_stresses = torch.sum(atomic_stresses, dim=0) - - # Test that sums match total values - assert torch.allclose( - summed_atomic_virials, total_virials.squeeze(0), atol=1e-6 - ), f"Sum of atomic virials {summed_atomic_virials} does not match total virials {total_virials.squeeze(0)}" - - assert torch.allclose( - summed_atomic_stresses, total_stress.squeeze(0), atol=1e-6 - ), f"Sum of atomic stresses (normalized by volume) {summed_atomic_stresses} does not match total stress {total_stress.squeeze(0)}" diff --git a/mace-bench/3rdparty/mace/tests/test_modules.py b/mace-bench/3rdparty/mace/tests/test_modules.py deleted file mode 100644 index 6afcccfb44252ee80b7c969748dfb914673d0e3e..0000000000000000000000000000000000000000 --- a/mace-bench/3rdparty/mace/tests/test_modules.py +++ /dev/null @@ -1,268 +0,0 @@ -import numpy as np -import pytest -import torch -import torch.nn.functional -from e3nn import o3 - -from mace.data import AtomicData, Configuration -from mace.modules import ( - AtomicEnergiesBlock, - BesselBasis, - PolynomialCutoff, - SymmetricContraction, - WeightedEnergyForcesLoss, - WeightedHuberEnergyForcesStressLoss, - compute_mean_rms_energy_forces, - compute_statistics, -) -from mace.tools import AtomicNumberTable, scatter, to_numpy, torch_geometric -from mace.tools.scripts_utils import dict_to_array - - -@pytest.fixture(name="config") -def _config(): - return Configuration( - atomic_numbers=np.array([8, 1, 1]), - positions=np.array( - [ - [0.0, -2.0, 0.0], - [1.0, 0.0, 0.0], - [0.0, 1.0, 0.0], - ] - ), - properties={ - "forces": np.array( - [ - [0.0, -1.3, 0.0], - [1.0, 0.2, 0.0], - [0.0, 1.1, 0.3], - ] - ), - "energy": -1.5, - "stress": np.array([1.0, 0.0, 0.5, 0.0, -1.0, 0.0]), - }, - property_weights={ - "forces": 1.0, - "energy": 1.0, - "stress": 1.0, - }, - ) - - -@pytest.fixture(name="table") -def _table(): - return AtomicNumberTable([1, 8]) - - -@pytest.fixture(name="config1") -def _config1(): - return Configuration( - atomic_numbers=np.array([8, 1, 1]), - positions=np.array( - [ - [0.0, -2.0, 0.0], - [1.0, 0.0, 0.0], - [0.0, 1.0, 0.0], - ] - ), - properties={ - "forces": np.array( - [ - [0.0, -1.3, 0.0], - [1.0, 0.2, 0.0], - [0.0, 1.1, 0.3], - ] - ), - "energy": -1.5, - }, - property_weights={ - "forces": 1.0, - "energy": 1.0, - }, - head="DFT", - ) - - -@pytest.fixture(name="config2") -def _config2(): - return Configuration( - atomic_numbers=np.array([8, 1, 1]), - positions=np.array( - [ - [0.1, -1.9, 0.1], - [1.1, 0.1, 0.1], - [0.1, 1.1, 0.1], - ] - ), - properties={ - "forces": np.array( - [ - [0.1, -1.2, 0.1], - [1.1, 0.3, 0.1], - [0.1, 1.2, 0.4], - ] - ), - "energy": -1.4, - }, - property_weights={ - "forces": 1.0, - "energy": 1.0, - }, - head="MP2", - ) - - -@pytest.fixture(name="atomic_data") -def _atomic_data(config1, config2, table): - atomic_data1 = AtomicData.from_config( - config1, z_table=table, cutoff=3.0, heads=["DFT", "MP2"] - ) - atomic_data2 = AtomicData.from_config( - config2, z_table=table, cutoff=3.0, heads=["DFT", "MP2"] - ) - return [atomic_data1, atomic_data2] - - -@pytest.fixture(name="data_loader") -def _data_loader(atomic_data): - return torch_geometric.dataloader.DataLoader( - dataset=atomic_data, - batch_size=2, - shuffle=False, - drop_last=False, - ) - - -@pytest.fixture(name="atomic_energies") -def _atomic_energies(): - atomic_energies_dict = { - "DFT": np.array([0.0, 0.0]), - "MP2": np.array([0.1, 0.1]), - } - return dict_to_array(atomic_energies_dict, ["DFT", "MP2"]) - - -@pytest.fixture(autouse=True) -def _set_torch_default_dtype(): - torch.set_default_dtype(torch.float64) - - -def test_weighted_loss(config, table): - loss1 = WeightedEnergyForcesLoss(energy_weight=1, forces_weight=10) - loss2 = WeightedHuberEnergyForcesStressLoss(energy_weight=1, forces_weight=10) - data = AtomicData.from_config(config, z_table=table, cutoff=3.0) - data_loader = torch_geometric.dataloader.DataLoader( - dataset=[data, data], - batch_size=2, - shuffle=True, - drop_last=False, - ) - batch = next(iter(data_loader)) - pred = { - "energy": batch.energy, - "forces": batch.forces, - "stress": batch.stress, - } - out1 = loss1(batch, pred) - assert out1 == 0.0 - out2 = loss2(batch, pred) - assert out2 == 0.0 - - -def test_symmetric_contraction(): - operation = SymmetricContraction( - irreps_in=o3.Irreps("16x0e + 16x1o + 16x2e"), - irreps_out=o3.Irreps("16x0e + 16x1o"), - correlation=3, - num_elements=2, - ) - torch.manual_seed(123) - features = torch.randn(30, 16, 9) - one_hots = torch.nn.functional.one_hot(torch.arange(0, 30) % 2).to( - torch.get_default_dtype() - ) - out = operation(features, one_hots) - assert out.shape == (30, 64) - assert operation.contractions[0].weights_max.shape == (2, 11, 16) - - -def test_bessel_basis(): - d = torch.linspace(start=0.5, end=5.5, steps=10) - bessel_basis = BesselBasis(r_max=6.0, num_basis=5) - output = bessel_basis(d.unsqueeze(-1)) - assert output.shape == (10, 5) - - -def test_polynomial_cutoff(): - d = torch.linspace(start=0.5, end=5.5, steps=10) - cutoff_fn = PolynomialCutoff(r_max=5.0) - output = cutoff_fn(d) - assert output.shape == (10,) - - -def test_atomic_energies(config, table): - energies_block = AtomicEnergiesBlock(atomic_energies=np.array([1.0, 3.0])) - data = AtomicData.from_config(config, z_table=table, cutoff=3.0) - data_loader = torch_geometric.dataloader.DataLoader( - dataset=[data, data], - batch_size=2, - shuffle=True, - drop_last=False, - ) - batch = next(iter(data_loader)) - energies = energies_block(batch.node_attrs).squeeze(-1) - out = scatter.scatter_sum(src=energies, index=batch.batch, dim=-1, reduce="sum") - out = to_numpy(out) - assert np.allclose(out, np.array([5.0, 5.0])) - - -def test_atomic_energies_multireference(config, table): - energies_block = AtomicEnergiesBlock( - atomic_energies=np.array([[1.0, 3.0], [2.0, 4.0]]) - ) - config.head = "MP2" - data = AtomicData.from_config( - config, z_table=table, cutoff=3.0, heads=["DFT", "MP2"] - ) - data_loader = torch_geometric.dataloader.DataLoader( - dataset=[data, data], - batch_size=2, - shuffle=True, - drop_last=False, - ) - batch = next(iter(data_loader)) - num_atoms_arange = torch.arange(batch["positions"].shape[0]) - node_heads = ( - batch["head"][batch["batch"]] - if "head" in batch - else torch.zeros_like(batch["batch"]) - ) - energies = energies_block(batch.node_attrs).squeeze(-1) - energies = energies[num_atoms_arange, node_heads] - out = scatter.scatter_sum(src=energies, index=batch.batch, dim=-1, reduce="sum") - out = to_numpy(out) - assert np.allclose(out, np.array([8.0, 8.0])) - - -def test_compute_mean_rms_energy_forces_multi_head(data_loader, atomic_energies): - mean, rms = compute_mean_rms_energy_forces(data_loader, atomic_energies) - assert isinstance(mean, np.ndarray) - assert isinstance(rms, np.ndarray) - assert mean.shape == (2,) - assert rms.shape == (2,) - assert np.all(rms >= 0) - assert rms[0] != rms[1] - - -def test_compute_statistics(data_loader, atomic_energies): - avg_num_neighbors, mean, std = compute_statistics(data_loader, atomic_energies) - assert isinstance(avg_num_neighbors, float) - assert isinstance(mean, np.ndarray) - assert isinstance(std, np.ndarray) - assert mean.shape == (2,) - assert std.shape == (2,) - assert avg_num_neighbors > 0 - assert np.all(mean != 0) - assert np.all(std > 0) - assert mean[0] != mean[1] - assert std[0] != std[1] diff --git a/mace-bench/3rdparty/mace/tests/test_multifiles.py b/mace-bench/3rdparty/mace/tests/test_multifiles.py deleted file mode 100644 index 16eacc2f24dfce9ba28defbaed3a3cf4026e5b7d..0000000000000000000000000000000000000000 --- a/mace-bench/3rdparty/mace/tests/test_multifiles.py +++ /dev/null @@ -1,1029 +0,0 @@ -import json -import os -import shutil -import subprocess -import sys -import tempfile -import zlib -from pathlib import Path - -import lmdb -import numpy as np -import orjson -import pytest -import torch -import yaml -from ase.atoms import Atoms -from ase.calculators.singlepoint import SinglePointCalculator - -from mace.calculators import MACECalculator - - -def create_test_atoms(num_atoms=5, seed=42): - """Create random atoms for testing purposes with energy, forces, and stress.""" - # Set random seed for reproducibility - rng = np.random.RandomState(seed) - - # Create random positions - positions = rng.rand(num_atoms, 3) * 5.0 - - # Create random atomic numbers (H, C, N, O) - atomic_numbers = rng.choice([1, 6, 7, 8], size=num_atoms) - - # Create atoms object - atoms = Atoms( - numbers=atomic_numbers, - positions=positions, - cell=np.eye(3) * 10.0, # 10 Å periodic box - pbc=True, - ) - - # Add random energy, forces and stress - energy = float(rng.uniform(-15.0, -5.0)) - forces = rng.rand(num_atoms, 3) * 0.5 - 0.25 # Forces between -0.25 and 0.25 eV/Å - stress = rng.rand(6) * 0.2 - 0.1 # Stress tensor in Voigt notation - - # Add calculator to atoms with results - calc = SinglePointCalculator(atoms, energy=energy, forces=forces, stress=stress) - atoms.calc = calc - - # Mark isolated atoms with config_type - if num_atoms == 1: - atoms.info["config_type"] = "IsolatedAtom" - - return atoms - - -def create_xyz_file(atoms_list, filename): - """Write a list of atoms to an xyz file.""" - from ase.io import write - - write(filename, atoms_list, format="extxyz") - return filename - - -def create_e0s_file(e0s_dict, filename): - """Create an E0s JSON file with isolated atom energies.""" - # Convert keys to integers since MACE expects atomic numbers as integers - e0s_dict_int_keys = {int(k): v for k, v in e0s_dict.items()} - - with open(filename, "w", encoding="utf-8") as f: - json.dump(e0s_dict_int_keys, f) - return filename - - -def create_h5_dataset(xyz_file, output_dir, e0s_file=None, r_max=5.0, seed=42): - """ - Run MACE's preprocess_data.py script to convert an xyz file to h5 format. - - Args: - xyz_file: Path to the input xyz file - output_dir: Directory to store the preprocessed h5 files - e0s_file: Path to the E0s file with isolated atom energies - r_max: Cutoff radius - seed: Random seed - - Returns: - The output directory containing the h5 files - """ - # Make sure output directory exists - os.makedirs(output_dir, exist_ok=True) - - # Find the path to the preprocess_data.py script - preprocess_script = ( - Path(__file__).parent.parent / "mace" / "cli" / "preprocess_data.py" - ) - - # Set up command to run preprocess_data.py - cmd = [ - sys.executable, - str(preprocess_script), - f"--train_file={xyz_file}", - f"--r_max={r_max}", - f"--h5_prefix={output_dir}/", - f"--seed={seed}", - "--compute_statistics", # Generate statistics file - "--num_process=2", # Create 2 files for testing sharded loading - ] - - # Add E0s file if provided - if e0s_file: - cmd.append(f"--E0s={e0s_file}") - - # Set up environment - env = os.environ.copy() - env["PYTHONPATH"] = ( - str(Path(__file__).parent.parent) + ":" + env.get("PYTHONPATH", "") - ) - - # Run the script - print(f"Running preprocess command: {' '.join(cmd)}") - try: - process = subprocess.run( - cmd, env=env, stdout=subprocess.PIPE, stderr=subprocess.PIPE, check=True - ) - # Print output for debugging - print("Preprocess stdout:", process.stdout.decode()) - print("Preprocess stderr:", process.stderr.decode()) - except subprocess.CalledProcessError as e: - print("Preprocess failed with error:", e) - print("Stdout:", e.stdout.decode() if e.stdout else "") - print("Stderr:", e.stderr.decode() if e.stderr else "") - raise - - return output_dir - - -def create_lmdb_dataset(atoms_list, folder_path, head_name="Default"): - """Create an LMDB dataset from a list of atoms objects that MACE can read.""" - # Create the folder if it doesn't exist - os.makedirs(folder_path, exist_ok=True) - - # Create the LMDB database file - db_path = os.path.join(folder_path, "data.aselmdb") - - # Initialize LMDB environment - env = lmdb.open( - db_path, - map_size=1099511627776, # 1TB - subdir=False, - meminit=False, - map_async=True, - ) - - # Open a transaction - with env.begin(write=True) as txn: - # Store metadata - metadata = {"format_version": 1} - txn.put( - "metadata".encode("ascii"), - zlib.compress(orjson.dumps(metadata, option=orjson.OPT_SERIALIZE_NUMPY)), - ) - - # Store nextid - nextid = len(atoms_list) + 1 - txn.put( - "nextid".encode("ascii"), - zlib.compress(orjson.dumps(nextid, option=orjson.OPT_SERIALIZE_NUMPY)), - ) - - # Store deleted_ids (empty) - txn.put( - "deleted_ids".encode("ascii"), - zlib.compress(orjson.dumps([], option=orjson.OPT_SERIALIZE_NUMPY)), - ) - - # Store each atom - for i, atoms in enumerate(atoms_list): - id_num = i + 1 # Start from 1 - - # Convert atoms to dictionary - positions = atoms.get_positions() - cell = atoms.get_cell() - - # Create a dictionary with all necessary fields - dct = { - "numbers": atoms.get_atomic_numbers().tolist(), - "positions": positions.tolist(), - "cell": cell.tolist(), - "pbc": atoms.get_pbc().tolist(), - "ctime": 0.0, # Creation time - "mtime": 0.0, # Modification time - "user": "test", - "energy": atoms.calc.results["energy"], - "forces": atoms.calc.results["forces"].tolist(), - "stress": atoms.calc.results["stress"].tolist(), - "key_value_pairs": { - "config_type": atoms.info.get("config_type", "Default"), - "head": head_name, - }, - } - - # Store the atom in LMDB - txn.put( - f"{id_num}".encode("ascii"), - zlib.compress(orjson.dumps(dct, option=orjson.OPT_SERIALIZE_NUMPY)), - ) - - # Close the environment - env.close() - - return folder_path - - -@pytest.mark.slow -def test_multifile_training(): - """Test training with multiple file formats per head""" - # Create temporary directory - temp_dir = tempfile.mkdtemp() - try: - # Set up file paths - xyz_file1 = os.path.join(temp_dir, "data1.xyz") - xyz_file2 = os.path.join(temp_dir, "data2.xyz") - iso_atoms_file = os.path.join(temp_dir, "isolated_atoms.xyz") - h5_folder = os.path.join(temp_dir, "h5_data") - lmdb_folder1 = os.path.join( - temp_dir, "lmdb_data1_lmdb" - ) # Add _lmdb suffix for LMDB recognition - lmdb_folder2 = os.path.join( - temp_dir, "lmdb_data2_lmdb" - ) # Add _lmdb suffix for LMDB recognition - - config_path = os.path.join(temp_dir, "config.yaml") - results_dir = os.path.join(temp_dir, "results") - checkpoints_dir = os.path.join(temp_dir, "checkpoints") - model_dir = os.path.join(temp_dir, "models") - e0s_file = os.path.join(temp_dir, "e0s.json") - - # Create directories - os.makedirs(results_dir, exist_ok=True) - os.makedirs(checkpoints_dir, exist_ok=True) - os.makedirs(model_dir, exist_ok=True) - - # Set atomic numbers for z_table - z_table_elements = [1, 6, 7, 8] # H, C, N, O - - # Create test data for each format - rng = np.random.RandomState(42) - seeds = rng.randint(0, 10000, size=5) - - # Create isolated atoms for E0s (one of each element) - isolated_atoms = [] - e0s_dict = {} - for z in z_table_elements: - # Create isolated atom - atom = Atoms( - numbers=[z], positions=[[0, 0, 0]], cell=np.eye(3) * 10.0, pbc=True - ) - energy = float(rng.uniform(-5.0, -1.0)) # Random reference energy - forces = np.zeros((1, 3)) - stress = np.zeros(6) - calc = SinglePointCalculator( - atom, energy=energy, forces=forces, stress=stress - ) - atom.calc = calc - atom.info["config_type"] = "IsolatedAtom" - atom.info["REF_energy"] = energy # Make sure energy is in the right place - isolated_atoms.append(atom) - e0s_dict[str(z)] = energy # Store energy for E0s file - - # Create E0s file - create_e0s_file(e0s_dict, e0s_file) - - # Create isolated atoms xyz file - create_xyz_file(isolated_atoms, iso_atoms_file) - - # Create 10 atoms for each dataset - xyz_atoms1 = [ - create_test_atoms(num_atoms=5, seed=seeds[0] + i) for i in range(10) - ] - xyz_atoms2 = [ - create_test_atoms(num_atoms=5, seed=seeds[1] + i) for i in range(10) - ] - - # Create h5 data directly - first convert the xyz file to a format with REF_ keys - for atom in xyz_atoms1: - atom.info["REF_energy"] = atom.calc.results["energy"] - atom.arrays["REF_forces"] = atom.calc.results["forces"] - atom.info["REF_stress"] = atom.calc.results["stress"] - - for atom in xyz_atoms2: - atom.info["REF_energy"] = atom.calc.results["energy"] - atom.arrays["REF_forces"] = atom.calc.results["forces"] - atom.info["REF_stress"] = atom.calc.results["stress"] - - # Save isolated atoms to xyz files first, then create the h5 datasets - create_xyz_file(xyz_atoms1, xyz_file1) - create_xyz_file(xyz_atoms2, xyz_file2) - - # Create h5 data from xyz file, using both isolated atoms and real data - all_atoms_for_h5 = isolated_atoms + xyz_atoms2 - all_atoms_xyz = os.path.join(temp_dir, "all_atoms_for_h5.xyz") - create_xyz_file(all_atoms_for_h5, all_atoms_xyz) - create_h5_dataset(all_atoms_xyz, h5_folder) - - # Create LMDB datasets - lmdb_atoms1 = [ - create_test_atoms(num_atoms=5, seed=seeds[3] + i) for i in range(10) - ] - lmdb_atoms2 = [ - create_test_atoms(num_atoms=5, seed=seeds[4] + i) for i in range(10) - ] - create_lmdb_dataset(lmdb_atoms1, lmdb_folder1, head_name="head1") - create_lmdb_dataset(lmdb_atoms2, lmdb_folder2, head_name="head2") - - # Create config.yaml for training with proper format specification - config = { - "name": "multifile_test", - "seed": 42, - "model": "MACE", - "hidden_irreps": "32x0e", - "r_max": 5.0, - "batch_size": 5, - "max_num_epochs": 2, - "patience": 5, - "device": "cpu", - "energy_weight": 1.0, - "forces_weight": 10.0, - "loss": "weighted", - "optimizer": "adam", - "default_dtype": "float64", - "lr": 0.01, - "swa": False, - "work_dir": temp_dir, - "results_dir": results_dir, - "checkpoints_dir": checkpoints_dir, - "model_dir": model_dir, - "E0s": e0s_file, - "atomic_numbers": str(z_table_elements), - "heads": { - "head1": { - "train_file": [lmdb_folder1, xyz_file1], - "valid_file": xyz_file1, - "energy_key": "REF_energy", - "forces_key": "REF_forces", - "stress_key": "REF_stress", - }, - "head2": { - "train_file": [h5_folder + "/train", xyz_file2], - "valid_file": xyz_file2, - "energy_key": "REF_energy", - "forces_key": "REF_forces", - "stress_key": "REF_stress", - }, - }, - } - - # Write config file - with open(config_path, "w", encoding="utf-8") as f: - yaml.dump(config, f) - - # Import the modified run_train from our local module - run_train_script = ( - Path(__file__).parent.parent / "mace" / "cli" / "run_train.py" - ) - - # Run training with subprocess - cmd = [sys.executable, str(run_train_script), f"--config={config_path}"] - - # Set environment to add the current path to PYTHONPATH - env = os.environ.copy() - env["PYTHONPATH"] = ( - str(Path(__file__).parent.parent) + ":" + env.get("PYTHONPATH", "") - ) - - # Run the process - process = subprocess.run( - cmd, - env=env, - stdout=subprocess.PIPE, - stderr=subprocess.PIPE, - check=False, # Don't raise exception on non-zero exit, we'll check manually - ) - - # Print output for debugging - print("\n" + "=" * 40 + " STDOUT " + "=" * 40) - print(process.stdout.decode()) - print("\n" + "=" * 40 + " STDERR " + "=" * 40) - print(process.stderr.decode()) - - # Check that process completed successfully - assert ( - process.returncode == 0 - ), f"Training failed with error: {process.stderr.decode()}" - - # Check that model was created - model_path = os.path.join(model_dir, "multifile_test.model") - assert os.path.exists(model_path), f"Model was not created at {model_path}" - - # Try to load and run the model - model = torch.load(model_path, map_location="cpu") - assert model is not None, "Failed to load model" - - # Create a calculator - calc = MACECalculator(model_paths=model_path, device="cpu", head="head1") - - # Run prediction on a test atom - test_atom = create_test_atoms(num_atoms=5, seed=99999) - test_atom.calc = calc - energy = test_atom.get_potential_energy() - forces = test_atom.get_forces() - - # Assert we got sensible outputs - assert np.isfinite(energy), "Model produced non-finite energy" - assert np.all(np.isfinite(forces)), "Model produced non-finite forces" - - finally: - # Clean up - shutil.rmtree(temp_dir) - - -@pytest.mark.slow -def test_multiple_xyz_per_head(): - """Test training with multiple XYZ files per head for train, valid and test sets""" - # Create temporary directory - temp_dir = tempfile.mkdtemp() - try: - # Set up file paths - create multiple xyz files for each dataset - train_xyz_files = [ - os.path.join(temp_dir, f"train_data{i}.xyz") for i in range(1, 4) - ] # 3 train files - valid_xyz_files = [ - os.path.join(temp_dir, f"valid_data{i}.xyz") for i in range(1, 3) - ] # 2 valid files - test_xyz_files = [ - os.path.join(temp_dir, f"test_data{i}.xyz") for i in range(1, 3) - ] # 2 test files - - iso_atoms_file = os.path.join(temp_dir, "isolated_atoms.xyz") - - config_path = os.path.join(temp_dir, "config.yaml") - results_dir = os.path.join(temp_dir, "results") - checkpoints_dir = os.path.join(temp_dir, "checkpoints") - model_dir = os.path.join(temp_dir, "models") - e0s_file = os.path.join(temp_dir, "e0s.json") - - # Create directories - os.makedirs(results_dir, exist_ok=True) - os.makedirs(checkpoints_dir, exist_ok=True) - os.makedirs(model_dir, exist_ok=True) - - # Set atomic numbers for z_table - z_table_elements = [1, 6, 7, 8] # H, C, N, O - - # Create test data for each format - rng = np.random.RandomState(42) - seeds = rng.randint(0, 10000, size=10) # More seeds for multiple files - - # Create isolated atoms for E0s (one of each element) - isolated_atoms = [] - e0s_dict = {} - for z in z_table_elements: - # Create isolated atom - atom = Atoms( - numbers=[z], positions=[[0, 0, 0]], cell=np.eye(3) * 10.0, pbc=True - ) - energy = float(rng.uniform(-5.0, -1.0)) # Random reference energy - forces = np.zeros((1, 3)) - stress = np.zeros(6) - calc = SinglePointCalculator( - atom, energy=energy, forces=forces, stress=stress - ) - atom.calc = calc - atom.info["config_type"] = "IsolatedAtom" - isolated_atoms.append(atom) - e0s_dict[str(z)] = energy # Store energy for E0s file - - # Create E0s file - create_e0s_file(e0s_dict, e0s_file) - - # Create isolated atoms xyz file - create_xyz_file(isolated_atoms, iso_atoms_file) - - # Create atoms for each train dataset - use different seeds for variety - train_datasets = [] - for i, file in enumerate(train_xyz_files): - # Create atoms with different seeds - atoms = [ - create_test_atoms(num_atoms=5, seed=seeds[i] + j) for j in range(5) - ] - create_xyz_file(atoms, file) - train_datasets.append(atoms) - - # Create atoms for validation datasets - valid_datasets = [] - for i, file in enumerate(valid_xyz_files): - atoms = [ - create_test_atoms(num_atoms=5, seed=seeds[i + 3] + j) for j in range(3) - ] - create_xyz_file(atoms, file) - valid_datasets.append(atoms) - - # Create atoms for test datasets - test_datasets = [] - for i, file in enumerate(test_xyz_files): - atoms = [ - create_test_atoms(num_atoms=5, seed=seeds[i + 5] + j) for j in range(3) - ] - create_xyz_file(atoms, file) - test_datasets.append(atoms) - - # Create config.yaml for training with multiple xyz files per dataset - config = { - "name": "multi_xyz_test", - "seed": 42, - "model": "MACE", - "hidden_irreps": "32x0e", - "r_max": 5.0, - "batch_size": 5, - "max_num_epochs": 2, - "patience": 5, - "device": "cpu", - "energy_weight": 1.0, - "forces_weight": 10.0, - "loss": "weighted", - "optimizer": "adam", - "default_dtype": "float64", - "lr": 0.01, - "swa": False, - "work_dir": temp_dir, - "results_dir": results_dir, - "checkpoints_dir": checkpoints_dir, - "model_dir": model_dir, - "E0s": e0s_file, - "atomic_numbers": str(z_table_elements), - "heads": { - "multi_xyz_head": { - # Using lists of multiple xyz files for each dataset - "train_file": train_xyz_files, - "valid_file": valid_xyz_files, - "test_file": test_xyz_files, - "energy_key": "energy", - "forces_key": "forces", - "stress_key": "stress", - }, - }, - } - - # Write config file - with open(config_path, "w", encoding="utf-8") as f: - yaml.dump(config, f) - - # Import the modified run_train from our local module - run_train_script = ( - Path(__file__).parent.parent / "mace" / "cli" / "run_train.py" - ) - - # Run training with subprocess - cmd = [sys.executable, str(run_train_script), f"--config={config_path}"] - - # Set environment to add the current path to PYTHONPATH - env = os.environ.copy() - env["PYTHONPATH"] = ( - str(Path(__file__).parent.parent) + ":" + env.get("PYTHONPATH", "") - ) - - # Run the process - process = subprocess.run( - cmd, - env=env, - stdout=subprocess.PIPE, - stderr=subprocess.PIPE, - check=False, - ) - - # Print output for debugging - print("\n" + "=" * 40 + " STDOUT " + "=" * 40) - print(process.stdout.decode()) - print("\n" + "=" * 40 + " STDERR " + "=" * 40) - print(process.stderr.decode()) - - # Check that process completed successfully - assert ( - process.returncode == 0 - ), f"Training failed with error: {process.stderr.decode()}" - - # Check that model was created - model_path = os.path.join(model_dir, "multi_xyz_test.model") - assert os.path.exists(model_path), f"Model was not created at {model_path}" - - # Try to load and run the model - model = torch.load(model_path, map_location="cpu") - assert model is not None, "Failed to load model" - - # Create a calculator - calc = MACECalculator( - model_paths=model_path, device="cpu", head="multi_xyz_head" - ) - - # Run prediction on a test atom - test_atom = create_test_atoms(num_atoms=5, seed=99999) - test_atom.calc = calc - energy = test_atom.get_potential_energy() - forces = test_atom.get_forces() - - # Assert we got sensible outputs - assert np.isfinite(energy), "Model produced non-finite energy" - assert np.all(np.isfinite(forces)), "Model produced non-finite forces" - - finally: - # Clean up - shutil.rmtree(temp_dir) - - -@pytest.mark.slow -def test_single_xyz_per_head(): - """Test training with multiple XYZ files per head for train, valid and test sets""" - # Create temporary directory - temp_dir = tempfile.mkdtemp() - try: - # Set up file paths - create multiple xyz files for each dataset - train_xyz_files = [ - os.path.join(temp_dir, f"train_data{i}.xyz") for i in range(1, 2) - ] # 3 train files - valid_xyz_files = [ - os.path.join(temp_dir, f"valid_data{i}.xyz") for i in range(1, 2) - ] # 2 valid files - test_xyz_files = [ - os.path.join(temp_dir, f"test_data{i}.xyz") for i in range(1, 2) - ] # 2 test files - - iso_atoms_file = os.path.join(temp_dir, "isolated_atoms.xyz") - - config_path = os.path.join(temp_dir, "config.yaml") - results_dir = os.path.join(temp_dir, "results") - checkpoints_dir = os.path.join(temp_dir, "checkpoints") - model_dir = os.path.join(temp_dir, "models") - e0s_file = os.path.join(temp_dir, "e0s.json") - - # Create directories - os.makedirs(results_dir, exist_ok=True) - os.makedirs(checkpoints_dir, exist_ok=True) - os.makedirs(model_dir, exist_ok=True) - - # Set atomic numbers for z_table - z_table_elements = [1, 6, 7, 8] # H, C, N, O - - # Create test data for each format - rng = np.random.RandomState(42) - seeds = rng.randint(0, 10000, size=10) # More seeds for multiple files - - # Create isolated atoms for E0s (one of each element) - isolated_atoms = [] - e0s_dict = {} - for z in z_table_elements: - # Create isolated atom - atom = Atoms( - numbers=[z], positions=[[0, 0, 0]], cell=np.eye(3) * 10.0, pbc=True - ) - energy = float(rng.uniform(-5.0, -1.0)) # Random reference energy - forces = np.zeros((1, 3)) - stress = np.zeros(6) - calc = SinglePointCalculator( - atom, energy=energy, forces=forces, stress=stress - ) - atom.calc = calc - atom.info["config_type"] = "IsolatedAtom" - isolated_atoms.append(atom) - e0s_dict[str(z)] = energy # Store energy for E0s file - - # Create E0s file - create_e0s_file(e0s_dict, e0s_file) - - # Create isolated atoms xyz file - create_xyz_file(isolated_atoms, iso_atoms_file) - - # Create atoms for each train dataset - use different seeds for variety - train_datasets = [] - for i, file in enumerate(train_xyz_files): - # Create atoms with different seeds - atoms = [ - create_test_atoms(num_atoms=5, seed=seeds[i] + j) for j in range(5) - ] - create_xyz_file(atoms, file) - train_datasets.append(atoms) - - # Create atoms for validation datasets - valid_datasets = [] - for i, file in enumerate(valid_xyz_files): - atoms = [ - create_test_atoms(num_atoms=5, seed=seeds[i + 3] + j) for j in range(3) - ] - create_xyz_file(atoms, file) - valid_datasets.append(atoms) - - # Create atoms for test datasets - test_datasets = [] - for i, file in enumerate(test_xyz_files): - atoms = [ - create_test_atoms(num_atoms=5, seed=seeds[i + 5] + j) for j in range(3) - ] - create_xyz_file(atoms, file) - test_datasets.append(atoms) - - # Create config.yaml for training with multiple xyz files per dataset - config = { - "name": "multi_xyz_test", - "seed": 42, - "model": "MACE", - "hidden_irreps": "32x0e", - "r_max": 5.0, - "batch_size": 5, - "max_num_epochs": 2, - "patience": 5, - "device": "cpu", - "energy_weight": 1.0, - "forces_weight": 10.0, - "loss": "weighted", - "optimizer": "adam", - "default_dtype": "float64", - "lr": 0.01, - "swa": False, - "work_dir": temp_dir, - "results_dir": results_dir, - "checkpoints_dir": checkpoints_dir, - "model_dir": model_dir, - "E0s": e0s_file, - "atomic_numbers": str(z_table_elements), - "heads": { - "multi_xyz_head": { - # Using lists of multiple xyz files for each dataset - "train_file": train_xyz_files, - "valid_file": valid_xyz_files, - "test_file": test_xyz_files, - "energy_key": "energy", - "forces_key": "forces", - "stress_key": "stress", - }, - }, - } - - # Write config file - with open(config_path, "w", encoding="utf-8") as f: - yaml.dump(config, f) - - # Import the modified run_train from our local module - run_train_script = ( - Path(__file__).parent.parent / "mace" / "cli" / "run_train.py" - ) - - # Run training with subprocess - cmd = [sys.executable, str(run_train_script), f"--config={config_path}"] - - # Set environment to add the current path to PYTHONPATH - env = os.environ.copy() - env["PYTHONPATH"] = ( - str(Path(__file__).parent.parent) + ":" + env.get("PYTHONPATH", "") - ) - - # Run the process - process = subprocess.run( - cmd, - env=env, - stdout=subprocess.PIPE, - stderr=subprocess.PIPE, - check=False, - ) - - # Print output for debugging - print("\n" + "=" * 40 + " STDOUT " + "=" * 40) - print(process.stdout.decode()) - print("\n" + "=" * 40 + " STDERR " + "=" * 40) - print(process.stderr.decode()) - - # Check that process completed successfully - assert ( - process.returncode == 0 - ), f"Training failed with error: {process.stderr.decode()}" - - # Check that model was created - model_path = os.path.join(model_dir, "multi_xyz_test.model") - assert os.path.exists(model_path), f"Model was not created at {model_path}" - - # Try to load and run the model - model = torch.load(model_path, map_location="cpu") - assert model is not None, "Failed to load model" - - # Create a calculator - calc = MACECalculator( - model_paths=model_path, device="cpu", head="multi_xyz_head" - ) - - # Run prediction on a test atom - test_atom = create_test_atoms(num_atoms=5, seed=99999) - test_atom.calc = calc - energy = test_atom.get_potential_energy() - forces = test_atom.get_forces() - - # Assert we got sensible outputs - assert np.isfinite(energy), "Model produced non-finite energy" - assert np.all(np.isfinite(forces)), "Model produced non-finite forces" - - finally: - # Clean up - shutil.rmtree(temp_dir) - - -@pytest.mark.slow -def test_multihead_finetuning_different_formats(): - """Test multihead finetuning with different file formats for each head.""" - # Create temporary directory - temp_dir = tempfile.mkdtemp() - try: - # Set up file paths - xyz_file = os.path.join(temp_dir, "finetuning_xyz.xyz") - h5_folder = os.path.join(temp_dir, "h5_data") - iso_atoms_file = os.path.join(temp_dir, "isolated_atoms.xyz") - - config_path = os.path.join(temp_dir, "config.yaml") - results_dir = os.path.join(temp_dir, "results") - checkpoints_dir = os.path.join(temp_dir, "checkpoints") - model_dir = os.path.join(temp_dir, "models") - e0s_file = os.path.join(temp_dir, "e0s.json") - - # Create directories - os.makedirs(results_dir, exist_ok=True) - os.makedirs(checkpoints_dir, exist_ok=True) - os.makedirs(model_dir, exist_ok=True) - - # Set atomic numbers for z_table - z_table_elements = [1, 6, 7, 8] # H, C, N, O - - # Create test data with different seeds - rng = np.random.RandomState(42) - seeds = rng.randint(0, 10000, size=3) - - # Create isolated atoms for E0s (one of each element) - isolated_atoms = [] - e0s_dict = {} - for z in z_table_elements: - atom = Atoms( - numbers=[z], positions=[[0, 0, 0]], cell=np.eye(3) * 10.0, pbc=True - ) - energy = float(rng.uniform(-5.0, -1.0)) - forces = np.zeros((1, 3)) - stress = np.zeros(6) - calc = SinglePointCalculator( - atom, energy=energy, forces=forces, stress=stress - ) - atom.calc = calc - atom.info["config_type"] = "IsolatedAtom" - atom.info["REF_energy"] = energy # Make sure energy is in the right place - atom.arrays["REF_forces"] = forces - atom.info["REF_stress"] = stress - isolated_atoms.append(atom) - e0s_dict[str(z)] = energy - - # Create E0s file - create_e0s_file(e0s_dict, e0s_file) - - # Create isolated atoms xyz file - create_xyz_file(isolated_atoms, iso_atoms_file) - - # Create XYZ data for xyz_head - xyz_atoms = [ - create_test_atoms(num_atoms=5, seed=seeds[0] + i) for i in range(30) - ] - # Add REF_ properties - for atom in xyz_atoms: - atom.info["REF_energy"] = atom.calc.results["energy"] - atom.arrays["REF_forces"] = atom.calc.results["forces"] - atom.info["REF_stress"] = atom.calc.results["stress"] - atom.info["head"] = "xyz_head" # Assign head - create_xyz_file(xyz_atoms, xyz_file) - - # Create H5 data for h5_head - h5_atoms = [ - create_test_atoms(num_atoms=5, seed=seeds[1] + i) for i in range(30) - ] - # Add REF_ properties - for atom in h5_atoms: - atom.info["REF_energy"] = atom.calc.results["energy"] - atom.arrays["REF_forces"] = atom.calc.results["forces"] - atom.info["REF_stress"] = atom.calc.results["stress"] - atom.info["head"] = "h5_head" # Assign head - - h5_atoms_xyz = os.path.join(temp_dir, "h5_atoms.xyz") - create_xyz_file(h5_atoms, h5_atoms_xyz) - # Include isolated atoms for E0s in the h5 dataset - all_atoms_for_h5 = h5_atoms + isolated_atoms - all_atoms_h5_xyz = os.path.join(temp_dir, "all_atoms_for_h5.xyz") - create_xyz_file(all_atoms_for_h5, all_atoms_h5_xyz) - create_h5_dataset(all_atoms_h5_xyz, h5_folder) - - # Create config.yaml for multihead finetuning - heads = { - "xyz_head": { - "train_file": xyz_file, - "valid_fraction": 0.2, - "energy_key": "REF_energy", - "forces_key": "REF_forces", - "stress_key": "REF_stress", - "E0s": e0s_file, - }, - "h5_head": { - "train_file": os.path.join(h5_folder, "train"), - "valid_file": os.path.join(h5_folder, "val"), - "energy_key": "REF_energy", - "forces_key": "REF_forces", - "stress_key": "REF_stress", - "E0s": e0s_file, - }, - } - - yaml_str = "heads:\n" - for key, value in heads.items(): - yaml_str += f" {key}:\n" - for sub_key, sub_value in value.items(): - yaml_str += f" {sub_key}: {sub_value}\n" - - with open(config_path, "w", encoding="utf-8") as f: - f.write(yaml_str) - - # Now perform multihead finetuning - finetuning_params = { - "name": "multihead_finetuned", - "config": config_path, - "foundation_model": "small", # Use the small foundation model - "energy_weight": 1.0, - "forces_weight": 10.0, - "model": "MACE", - "hidden_irreps": "128x0e", # Match foundation model - "r_max": 5.0, - "batch_size": 2, - "max_num_epochs": 2, # Just do a quick finetuning for test - "device": "cpu", - "seed": 42, - "loss": "weighted", - "default_dtype": "float64", - "checkpoints_dir": checkpoints_dir, - "model_dir": model_dir, - "results_dir": results_dir, - "atomic_numbers": "[" + ",".join(map(str, z_table_elements)) + "]", - "multiheads_finetuning": True, - "filter_type_pt": "combinations", - "subselect_pt": "random", - "num_samples_pt": 10, # Small number for testing - "force_mh_ft_lr": True, # Force using specified learning rate - } - - # Run finetuning - run_train_script = ( - Path(__file__).parent.parent / "mace" / "cli" / "run_train.py" - ) - env = os.environ.copy() - env["PYTHONPATH"] = ( - str(Path(__file__).parent.parent) + ":" + env.get("PYTHONPATH", "") - ) - - cmd = [sys.executable, str(run_train_script)] - for k, v in finetuning_params.items(): - if v is None: - cmd.append(f"--{k}") - else: - cmd.append(f"--{k}={v}") - - # Run the process - process = subprocess.run( - cmd, - env=env, - stdout=subprocess.PIPE, - stderr=subprocess.PIPE, - check=False, - ) - - # Print output for debugging - print("\n" + "=" * 40 + " STDOUT " + "=" * 40) - print(process.stdout.decode()) - print("\n" + "=" * 40 + " STDERR " + "=" * 40) - print(process.stderr.decode()) - - # Check that process completed successfully - assert ( - process.returncode == 0 - ), f"Finetuning failed with error: {process.stderr.decode()}" - - # Check that model was created - model_path = os.path.join(model_dir, "multihead_finetuned.model") - assert os.path.exists(model_path), f"Model was not created at {model_path}" - - # Load model and verify it has the expected heads - model = torch.load(model_path, map_location="cpu") - assert hasattr(model, "heads"), "Model does not have heads attribute" - assert set(["xyz_head", "h5_head", "pt_head"]).issubset( - set(model.heads) - ), "Expected heads not found in model" - - # Try to run the model with both heads - # For xyz_head - calc_xyz = MACECalculator( - model_paths=model_path, - device="cpu", - head="xyz_head", - default_dtype="float64", - ) - test_atom = create_test_atoms(num_atoms=5, seed=99999) - test_atom.calc = calc_xyz - energy_xyz = test_atom.get_potential_energy() - forces_xyz = test_atom.get_forces() - - # For h5_head - calc_h5 = MACECalculator( - model_paths=model_path, - device="cpu", - head="h5_head", - default_dtype="float64", - ) - test_atom.calc = calc_h5 - energy_h5 = test_atom.get_potential_energy() - forces_h5 = test_atom.get_forces() - - # Verify results - assert np.isfinite(energy_xyz), "xyz_head produced non-finite energy" - assert np.all(np.isfinite(forces_xyz)), "xyz_head produced non-finite forces" - assert np.isfinite(energy_h5), "h5_head produced non-finite energy" - assert np.all(np.isfinite(forces_h5)), "h5_head produced non-finite forces" - - finally: - # Clean up - shutil.rmtree(temp_dir) diff --git a/mace-bench/3rdparty/mace/tests/test_preprocess.py b/mace-bench/3rdparty/mace/tests/test_preprocess.py deleted file mode 100644 index 5b070e5df37528e43e799ef11fe16666b221ad2a..0000000000000000000000000000000000000000 --- a/mace-bench/3rdparty/mace/tests/test_preprocess.py +++ /dev/null @@ -1,206 +0,0 @@ -import os -import subprocess -import sys -from pathlib import Path - -import ase.io -import numpy as np -import pytest -import yaml -from ase.atoms import Atoms - -pytest_mace_dir = Path(__file__).parent.parent -preprocess_data = Path(__file__).parent.parent / "mace" / "cli" / "preprocess_data.py" - - -@pytest.fixture(name="sample_configs") -def fixture_sample_configs(): - water = Atoms( - numbers=[8, 1, 1], - positions=[[0, -2.0, 0], [1, 0, 0], [0, 1, 0]], - cell=[4] * 3, - pbc=[True] * 3, - ) - configs = [ - Atoms(numbers=[8], positions=[[0, 0, 0]], cell=[6] * 3), - Atoms(numbers=[1], positions=[[0, 0, 0]], cell=[6] * 3), - ] - configs[0].info["REF_energy"] = 0.0 - configs[0].info["config_type"] = "IsolatedAtom" - configs[1].info["REF_energy"] = 0.0 - configs[1].info["config_type"] = "IsolatedAtom" - - np.random.seed(5) - for _ in range(10): - c = water.copy() - c.positions += np.random.normal(0.1, size=c.positions.shape) - c.info["REF_energy"] = np.random.normal(0.1) - c.new_array("REF_forces", np.random.normal(0.1, size=c.positions.shape)) - c.info["REF_stress"] = np.random.normal(0.1, size=6) - configs.append(c) - - return configs - - -def test_preprocess_data(tmp_path, sample_configs): - ase.io.write(tmp_path / "sample.xyz", sample_configs) - - preprocess_params = { - "train_file": tmp_path / "sample.xyz", - "r_max": 5.0, - "config_type_weights": "{'Default':1.0}", - "num_process": 2, - "valid_fraction": 0.1, - "h5_prefix": tmp_path / "preprocessed_", - "compute_statistics": None, - "seed": 42, - "energy_key": "REF_energy", - "forces_key": "REF_forces", - "stress_key": "REF_stress", - } - - run_env = os.environ.copy() - sys.path.insert(0, str(Path(__file__).parent.parent)) - run_env["PYTHONPATH"] = ":".join(sys.path) - print("DEBUG subprocess PYTHONPATH", run_env["PYTHONPATH"]) - - cmd = ( - sys.executable - + " " - + str(preprocess_data) - + " " - + " ".join( - [ - (f"--{k}={v}" if v is not None else f"--{k}") - for k, v in preprocess_params.items() - ] - ) - ) - - p = subprocess.run(cmd.split(), env=run_env, check=True) - assert p.returncode == 0 - - # Check if the output files are created - assert (tmp_path / "preprocessed_train").is_dir() - assert (tmp_path / "preprocessed_val").is_dir() - assert (tmp_path / "preprocessed_statistics.json").is_file() - - # Check if the correct number of files are created - train_files = list((tmp_path / "preprocessed_train").glob("*.h5")) - val_files = list((tmp_path / "preprocessed_val").glob("*.h5")) - assert len(train_files) == preprocess_params["num_process"] - assert len(val_files) == preprocess_params["num_process"] - - # Example of checking statistics file content: - import json - - with open(tmp_path / "preprocessed_statistics.json", "r", encoding="utf-8") as f: - statistics = json.load(f) - assert "atomic_energies" in statistics - assert "avg_num_neighbors" in statistics - assert "mean" in statistics - assert "std" in statistics - assert "atomic_numbers" in statistics - assert "r_max" in statistics - - # Example of checking H5 file content: - import h5py - - with h5py.File(train_files[0], "r") as f: - assert "config_batch_0" in f - config = f["config_batch_0"]["config_0"] - assert "atomic_numbers" in config - assert "positions" in config - assert "energy" in config["properties"] - assert "forces" in config["properties"] - - original_energies = [ - config.info["REF_energy"] - for config in sample_configs[2:] - if "REF_energy" in config.info - ] - original_forces = [ - config.arrays["REF_forces"] - for config in sample_configs[2:] - if "REF_forces" in config.arrays - ] - - h5_energies = [] - h5_forces = [] - - for train_file in train_files: - with h5py.File(train_file, "r") as f: - for _, batch in f.items(): - for config_key in batch.keys(): - config = batch[config_key] - assert "atomic_numbers" in config - assert "positions" in config - assert "energy" in config["properties"] - assert "forces" in config["properties"] - - h5_energies.append(config["properties"]["energy"][()]) - h5_forces.append(config["properties"]["forces"][()]) - - for val_file in val_files: - with h5py.File(val_file, "r") as f: - for _, batch in f.items(): - for config_key in batch.keys(): - config = batch[config_key] - h5_energies.append(config["properties"]["energy"][()]) - h5_forces.append(config["properties"]["forces"][()]) - - print("Original energies", original_energies) - print("H5 energies", h5_energies) - print("Original forces", original_forces) - print("H5 forces", h5_forces) - original_energies.sort() - h5_energies.sort() - original_forces = np.concatenate(original_forces).flatten() - h5_forces = np.concatenate(h5_forces).flatten() - original_forces.sort() - h5_forces.sort() - - # Compare energies and forces - np.testing.assert_allclose(original_energies, h5_energies, rtol=1e-5, atol=1e-8) - np.testing.assert_allclose(original_forces, h5_forces, rtol=1e-5, atol=1e-8) - - print("All checks passed successfully!") - - -def test_preprocess_config(tmp_path, sample_configs): - ase.io.write(tmp_path / "sample.xyz", sample_configs) - - preprocess_params = { - "train_file": str(tmp_path / "sample.xyz"), - "r_max": 5.0, - "config_type_weights": "{'Default':1.0}", - "num_process": 2, - "valid_fraction": 0.1, - "h5_prefix": str(tmp_path / "preprocessed_"), - "compute_statistics": None, - "seed": 42, - "energy_key": "REF_energy", - "forces_key": "REF_forces", - "stress_key": "REF_stress", - } - filename = tmp_path / "config.yaml" - with open(filename, "w", encoding="utf-8") as file: - yaml.dump(preprocess_params, file) - - run_env = os.environ.copy() - sys.path.insert(0, str(Path(__file__).parent.parent)) - run_env["PYTHONPATH"] = ":".join(sys.path) - print("DEBUG subprocess PYTHONPATH", run_env["PYTHONPATH"]) - - cmd = ( - sys.executable - + " " - + str(preprocess_data) - + " " - + "--config" - + " " - + str(filename) - ) - - p = subprocess.run(cmd.split(), env=run_env, check=True) - assert p.returncode == 0 diff --git a/mace-bench/3rdparty/mace/tests/test_run_train.py b/mace-bench/3rdparty/mace/tests/test_run_train.py deleted file mode 100644 index ddb849686ba3bb0a1085c2a44583c58e978d079a..0000000000000000000000000000000000000000 --- a/mace-bench/3rdparty/mace/tests/test_run_train.py +++ /dev/null @@ -1,1458 +0,0 @@ -import json -import os -import subprocess -import sys -from pathlib import Path - -import ase.io -import numpy as np -import pytest -import torch -from ase.atoms import Atoms - -from mace.calculators import MACECalculator, mace_mp - -try: - import cuequivariance as cue # pylint: disable=unused-import - - CUET_AVAILABLE = True -except ImportError: - CUET_AVAILABLE = False - -run_train = Path(__file__).parent.parent / "mace" / "cli" / "run_train.py" - - -@pytest.fixture(name="fitting_configs") -def fixture_fitting_configs(): - water = Atoms( - numbers=[8, 1, 1], - positions=[[0, -2.0, 0], [1, 0, 0], [0, 1, 0]], - cell=[4] * 3, - pbc=[True] * 3, - ) - fit_configs = [ - Atoms(numbers=[8], positions=[[0, 0, 0]], cell=[6] * 3), - Atoms(numbers=[1], positions=[[0, 0, 0]], cell=[6] * 3), - ] - fit_configs[0].info["REF_energy"] = 0.0 - fit_configs[0].info["config_type"] = "IsolatedAtom" - fit_configs[1].info["REF_energy"] = 0.0 - fit_configs[1].info["config_type"] = "IsolatedAtom" - - np.random.seed(5) - for _ in range(20): - c = water.copy() - c.positions += np.random.normal(0.1, size=c.positions.shape) - c.info["REF_energy"] = np.random.normal(0.1) - print(c.info["REF_energy"]) - c.new_array("REF_forces", np.random.normal(0.1, size=c.positions.shape)) - c.info["REF_stress"] = np.random.normal(0.1, size=6) - fit_configs.append(c) - - return fit_configs - - -@pytest.fixture(name="pretraining_configs") -def fixture_pretraining_configs(): - configs = [] - for _ in range(10): - atoms = Atoms( - numbers=[8, 1, 1], - positions=np.random.rand(3, 3) * 3, - cell=[5, 5, 5], - pbc=[True] * 3, - ) - atoms.info["REF_energy"] = np.random.normal(0, 1) - atoms.arrays["REF_forces"] = np.random.normal(0, 1, size=(3, 3)) - atoms.info["REF_stress"] = np.random.normal(0, 1, size=6) - configs.append(atoms) - configs.append( - Atoms(numbers=[8], positions=[[0, 0, 0]], cell=[6] * 3, pbc=[True] * 3), - ) - configs.append( - Atoms(numbers=[1], positions=[[0, 0, 0]], cell=[6] * 3, pbc=[True] * 3) - ) - configs[-2].info["REF_energy"] = -2.0 - configs[-2].info["config_type"] = "IsolatedAtom" - configs[-1].info["REF_energy"] = -4.0 - configs[-1].info["config_type"] = "IsolatedAtom" - return configs - - -_mace_params = { - "name": "MACE", - "valid_fraction": 0.05, - "energy_weight": 1.0, - "forces_weight": 10.0, - "stress_weight": 1.0, - "model": "MACE", - "hidden_irreps": "128x0e", - "r_max": 3.5, - "batch_size": 5, - "max_num_epochs": 10, - "swa": None, - "start_swa": 5, - "ema": None, - "ema_decay": 0.99, - "amsgrad": None, - "restart_latest": None, - "device": "cpu", - "seed": 5, - "loss": "stress", - "energy_key": "REF_energy", - "forces_key": "REF_forces", - "stress_key": "REF_stress", - "eval_interval": 2, -} - - -def test_run_train(tmp_path, fitting_configs): - ase.io.write(tmp_path / "fit.xyz", fitting_configs) - - mace_params = _mace_params.copy() - mace_params["checkpoints_dir"] = str(tmp_path) - mace_params["model_dir"] = str(tmp_path) - mace_params["train_file"] = tmp_path / "fit.xyz" - - # make sure run_train.py is using the mace that is currently being tested - run_env = os.environ.copy() - sys.path.insert(0, str(Path(__file__).parent.parent)) - run_env["PYTHONPATH"] = ":".join(sys.path) - print("DEBUG subprocess PYTHONPATH", run_env["PYTHONPATH"]) - - cmd = ( - sys.executable - + " " - + str(run_train) - + " " - + " ".join( - [ - (f"--{k}={v}" if v is not None else f"--{k}") - for k, v in mace_params.items() - ] - ) - ) - - p = subprocess.run(cmd.split(), env=run_env, check=True) - assert p.returncode == 0 - - calc = MACECalculator(model_paths=tmp_path / "MACE.model", device="cpu") - - Es = [] - for at in fitting_configs: - at.calc = calc - Es.append(at.get_potential_energy()) - - print("Es", Es) - # from a run on 04/06/2024 on stress_bugfix 967f0bfb6490086599da247874b24595d149caa7 - ref_Es = [ - 0.0, - 0.0, - -0.039181344585828524, - -0.0915223395136733, - -0.14953484236456582, - -0.06662480820063998, - -0.09983737353050133, - 0.12477442296789745, - -0.06486086271762856, - -0.1460607988519944, - 0.12886334908465508, - -0.14000990081920373, - -0.05319886578958313, - 0.07780520158391, - -0.08895480281886901, - -0.15474719614734422, - 0.007756765146527644, - -0.044879267197498685, - -0.036065736712447574, - -0.24413743841886623, - -0.0838104612106429, - -0.14751978636626545, - ] - - assert np.allclose(Es, ref_Es) - - -def test_run_train_missing_data(tmp_path, fitting_configs): - del fitting_configs[5].info["REF_energy"] - del fitting_configs[6].arrays["REF_forces"] - del fitting_configs[7].info["REF_stress"] - - ase.io.write(tmp_path / "fit.xyz", fitting_configs) - - mace_params = _mace_params.copy() - mace_params["checkpoints_dir"] = str(tmp_path) - mace_params["model_dir"] = str(tmp_path) - mace_params["train_file"] = tmp_path / "fit.xyz" - - # make sure run_train.py is using the mace that is currently being tested - run_env = os.environ.copy() - sys.path.insert(0, str(Path(__file__).parent.parent)) - run_env["PYTHONPATH"] = ":".join(sys.path) - print("DEBUG subprocess PYTHONPATH", run_env["PYTHONPATH"]) - - cmd = ( - sys.executable - + " " - + str(run_train) - + " " - + " ".join( - [ - (f"--{k}={v}" if v is not None else f"--{k}") - for k, v in mace_params.items() - ] - ) - ) - - p = subprocess.run(cmd.split(), env=run_env, check=True) - assert p.returncode == 0 - - calc = MACECalculator(model_paths=tmp_path / "MACE.model", device="cpu") - - Es = [] - for at in fitting_configs: - at.calc = calc - Es.append(at.get_potential_energy()) - - print("Es", Es) - # from a run on 04/06/2024 on stress_bugfix 967f0bfb6490086599da247874b24595d149caa7 - ref_Es = [ - 0.0, - 0.0, - -0.05464025113696155, - -0.11272131295940478, - 0.039200919331076826, - -0.07517990972827505, - -0.13504202474582666, - 0.0292022872055344, - -0.06541099574579018, - -0.1497824717832886, - 0.19397709360828813, - -0.13587609467143014, - -0.05242956276828463, - -0.0504862057364953, - -0.07095795959430119, - -0.2463753796753703, - -0.002031543147676121, - -0.03864918790300681, - -0.13680153117705554, - -0.23418951968636786, - -0.11790833839379238, - -0.14930562311066484, - ] - assert np.allclose(Es, ref_Es) - - -def test_run_train_no_stress(tmp_path, fitting_configs): - del fitting_configs[5].info["REF_energy"] - del fitting_configs[6].arrays["REF_forces"] - del fitting_configs[7].info["REF_stress"] - - ase.io.write(tmp_path / "fit.xyz", fitting_configs) - - mace_params = _mace_params.copy() - mace_params["checkpoints_dir"] = str(tmp_path) - mace_params["model_dir"] = str(tmp_path) - mace_params["train_file"] = tmp_path / "fit.xyz" - mace_params["loss"] = "weighted" - - # make sure run_train.py is using the mace that is currently being tested - run_env = os.environ.copy() - sys.path.insert(0, str(Path(__file__).parent.parent)) - run_env["PYTHONPATH"] = ":".join(sys.path) - print("DEBUG subprocess PYTHONPATH", run_env["PYTHONPATH"]) - - cmd = ( - sys.executable - + " " - + str(run_train) - + " " - + " ".join( - [ - (f"--{k}={v}" if v is not None else f"--{k}") - for k, v in mace_params.items() - ] - ) - ) - - p = subprocess.run(cmd.split(), env=run_env, check=True) - assert p.returncode == 0 - - calc = MACECalculator(model_paths=tmp_path / "MACE.model", device="cpu") - - Es = [] - for at in fitting_configs: - at.calc = calc - Es.append(at.get_potential_energy()) - - print("Es", Es) - # from a run on 28/03/2023 on main 88d49f9ed6925dec07d1777043a36e1fe4872ff3 - ref_Es = [ - 0.0, - 0.0, - -0.05450093218377135, - -0.11235475232750518, - 0.03914558031854152, - -0.07500839914816063, - -0.13469160624431492, - 0.029384214243251838, - -0.06521819204166135, - -0.14944896282001804, - 0.19413948083049481, - -0.13543541860473626, - -0.05235495076237124, - -0.049556206595684105, - -0.07080758913030646, - -0.24571898386301153, - -0.002070636306950905, - -0.03863113401320783, - -0.13620291339913712, - -0.23383074855679695, - -0.11776449630199368, - -0.1489441490225184, - ] - assert np.allclose(Es, ref_Es) - - -def test_run_train_multihead(tmp_path, fitting_configs): - fitting_configs_dft = [] - fitting_configs_mp2 = [] - fitting_configs_ccd = [] - for _, c in enumerate(fitting_configs): - c_dft = c.copy() - c_dft.info["head"] = "DFT" - fitting_configs_dft.append(c_dft) - - c_mp2 = c.copy() - c_mp2.info["head"] = "MP2" - fitting_configs_mp2.append(c_mp2) - - c_ccd = c.copy() - c_ccd.info["head"] = "CCD" - fitting_configs_ccd.append(c_ccd) - ase.io.write(tmp_path / "fit_multihead_dft.xyz", fitting_configs_dft) - ase.io.write(tmp_path / "fit_multihead_mp2.xyz", fitting_configs_mp2) - ase.io.write(tmp_path / "fit_multihead_ccd.xyz", fitting_configs_ccd) - - heads = { - "DFT": {"train_file": f"{str(tmp_path)}/fit_multihead_dft.xyz"}, - "MP2": {"train_file": f"{str(tmp_path)}/fit_multihead_mp2.xyz"}, - "CCD": {"train_file": f"{str(tmp_path)}/fit_multihead_ccd.xyz"}, - } - yaml_str = "heads:\n" - for key, value in heads.items(): - yaml_str += f" {key}:\n" - for sub_key, sub_value in value.items(): - yaml_str += f" {sub_key}: {sub_value}\n" - filename = tmp_path / "config.yaml" - with open(filename, "w", encoding="utf-8") as file: - file.write(yaml_str) - - mace_params = _mace_params.copy() - mace_params["valid_fraction"] = 0.1 - mace_params["checkpoints_dir"] = str(tmp_path) - mace_params["model_dir"] = str(tmp_path) - mace_params["loss"] = "weighted" - mace_params["hidden_irreps"] = "128x0e" - mace_params["r_max"] = 6.0 - mace_params["default_dtype"] = "float64" - mace_params["num_radial_basis"] = 10 - mace_params["interaction_first"] = "RealAgnosticResidualInteractionBlock" - mace_params["config"] = tmp_path / "config.yaml" - mace_params["batch_size"] = 2 - mace_params["num_samples_pt"] = 50 - mace_params["subselect_pt"] = "random" - # make sure run_train.py is using the mace that is currently being tested - run_env = os.environ.copy() - sys.path.insert(0, str(Path(__file__).parent.parent)) - run_env["PYTHONPATH"] = ":".join(sys.path) - print("DEBUG subprocess PYTHONPATH", run_env["PYTHONPATH"]) - - cmd = ( - sys.executable - + " " - + str(run_train) - + " " - + " ".join( - [ - (f"--{k}={v}" if v is not None else f"--{k}") - for k, v in mace_params.items() - ] - ) - ) - - p = subprocess.run(cmd.split(), env=run_env, check=True) - assert p.returncode == 0 - - calc = MACECalculator( - model_paths=tmp_path / "MACE.model", - device="cpu", - default_dtype="float64", - head="CCD", - ) - - Es = [] - for at in fitting_configs: - at.calc = calc - Es.append(at.get_potential_energy()) - - print("Es", Es) - # from a run on 02/09/2024 on develop branch - ref_Es = [ - 0.0, - 0.0, - 0.10637113905361611, - -0.012499594026624754, - 0.08983077108171753, - 0.21071322543112597, - -0.028921849222784398, - -0.02423359575741567, - 0.022923252188079057, - -0.02048334610058991, - 0.4349711162741364, - -0.04455577015569887, - -0.09765806785570091, - 0.16013134616829822, - 0.0758442928017698, - -0.05931856557011721, - 0.33964473532953265, - 0.134338442158641, - 0.18024119757783053, - -0.18914740992058765, - -0.06503477155294624, - 0.03436649147415213, - ] - assert np.allclose(Es, ref_Es) - - -def test_run_train_foundation(tmp_path, fitting_configs): - ase.io.write(tmp_path / "fit.xyz", fitting_configs) - - mace_params = _mace_params.copy() - mace_params["checkpoints_dir"] = str(tmp_path) - mace_params["model_dir"] = str(tmp_path) - mace_params["train_file"] = tmp_path / "fit.xyz" - mace_params["loss"] = "weighted" - mace_params["foundation_model"] = "small" - mace_params["hidden_irreps"] = "128x0e" - mace_params["r_max"] = 6.0 - mace_params["default_dtype"] = "float64" - mace_params["num_radial_basis"] = 10 - mace_params["interaction_first"] = "RealAgnosticResidualInteractionBlock" - mace_params["multiheads_finetuning"] = False - - run_env = os.environ.copy() - sys.path.insert(0, str(Path(__file__).parent.parent)) - run_env["PYTHONPATH"] = ":".join(sys.path) - - cmd = ( - sys.executable - + " " - + str(run_train) - + " " - + " ".join( - [ - (f"--{k}={v}" if v is not None else f"--{k}") - for k, v in mace_params.items() - ] - ) - ) - - p = subprocess.run(cmd.split(), env=run_env, check=True) - assert p.returncode == 0 - - calc = MACECalculator( - model_paths=tmp_path / "MACE.model", device="cpu", default_dtype="float64" - ) - - Es = [] - for at in fitting_configs: - at.calc = calc - Es.append(at.get_potential_energy()) - - print("Es", Es) - # from a run on 28/03/2023 on repulsion a63434aaab70c84ee016e13e4aca8d57297a0f26 - ref_Es = [ - 1.6780993938446045, - 0.8916864395141602, - 0.7290308475494385, - 0.6194742918014526, - 0.6697757840156555, - 0.7025266289710999, - 0.5818213224411011, - 0.7897703647613525, - 0.6558921337127686, - 0.5071806907653809, - 3.581131935119629, - 0.691562294960022, - 0.6257331967353821, - 0.9560437202453613, - 0.7716934680938721, - 0.6730310916900635, - 0.8297463655471802, - 0.8053972721099854, - 0.8337507247924805, - 0.4107491970062256, - 0.6019601821899414, - 0.7301387786865234, - ] - assert np.allclose(Es, ref_Es) - - -def test_run_train_foundation_multihead(tmp_path, fitting_configs): - fitting_configs_dft = [] - fitting_configs_mp2 = [] - atomic_numbers = np.unique( - np.concatenate([at.numbers for at in fitting_configs]) - ).tolist() - for i, c in enumerate(fitting_configs): - if i in (0, 1): - c_dft = c.copy() - c_dft.info["head"] = "DFT" - fitting_configs_dft.append(c_dft) - fitting_configs_dft.append(c) - c_mp2 = c.copy() - c_mp2.info["head"] = "MP2" - fitting_configs_mp2.append(c_mp2) - elif i % 2 == 0: - c.info["head"] = "DFT" - fitting_configs_dft.append(c) - else: - c.info["head"] = "MP2" - fitting_configs_mp2.append(c) - ase.io.write(tmp_path / "fit_multihead_dft.xyz", fitting_configs_dft) - ase.io.write(tmp_path / "fit_multihead_mp2.xyz", fitting_configs_mp2) - heads = { - "DFT": {"train_file": f"{str(tmp_path)}/fit_multihead_dft.xyz"}, - "MP2": {"train_file": f"{str(tmp_path)}/fit_multihead_mp2.xyz"}, - } - yaml_str = "heads:\n" - for key, value in heads.items(): - yaml_str += f" {key}:\n" - for sub_key, sub_value in value.items(): - yaml_str += f" {sub_key}: {sub_value}\n" - filename = tmp_path / "config.yaml" - with open(filename, "w", encoding="utf-8") as file: - file.write(yaml_str) - mace_params = _mace_params.copy() - mace_params["valid_fraction"] = 0.1 - mace_params["checkpoints_dir"] = str(tmp_path) - mace_params["model_dir"] = str(tmp_path) - mace_params["config"] = tmp_path / "config.yaml" - mace_params["loss"] = "weighted" - mace_params["foundation_model"] = "small" - mace_params["hidden_irreps"] = "128x0e" - mace_params["r_max"] = 6.0 - mace_params["default_dtype"] = "float64" - mace_params["num_radial_basis"] = 10 - mace_params["interaction_first"] = "RealAgnosticResidualInteractionBlock" - mace_params["batch_size"] = 2 - mace_params["valid_batch_size"] = 1 - mace_params["num_samples_pt"] = 50 - mace_params["subselect_pt"] = "random" - mace_params["atomic_numbers"] = "[" + ",".join(map(str, atomic_numbers)) + "]" - mace_params["filter_type_pt"] = "combinations" - mace_params["force_mh_ft_lr"] = True - # make sure run_train.py is using the mace that is currently being tested - run_env = os.environ.copy() - sys.path.insert(0, str(Path(__file__).parent.parent)) - run_env["PYTHONPATH"] = ":".join(sys.path) - print("DEBUG subprocess PYTHONPATH", run_env["PYTHONPATH"]) - - cmd = ( - sys.executable - + " " - + str(run_train) - + " " - + " ".join( - [ - (f"--{k}={v}" if v is not None else f"--{k}") - for k, v in mace_params.items() - ] - ) - ) - - try: - completed_process = subprocess.run( - cmd.split(), env=run_env, capture_output=True, text=True, check=True - ) - # Process executed successfully - print(completed_process.stdout) - except subprocess.CalledProcessError as e: - # Process failed with non-zero exit code - print(f"Command failed with exit code {e.returncode}") - print(f"STDOUT: {e.stdout}") - print(f"STDERR: {e.stderr}") - raise e - assert completed_process.returncode == 0 - - Es = [] - for at in fitting_configs: - config_head = at.info.get("head", "MP2") - calc = MACECalculator( - model_paths=tmp_path / "MACE.model", - device="cpu", - default_dtype="float64", - head=config_head, - ) - at.calc = calc - Es.append(at.get_potential_energy()) - - print("Es", Es) - # from a run on 20/08/2024 on commit - ref_Es = [ - 1.654685616493225, - 0.44693732261657715, - 0.8741313815116882, - 0.569085955619812, - 0.7161882519721985, - 0.8654778599739075, - 0.8722733855247498, - 0.49582308530807495, - 0.814422607421875, - 0.7027317881584167, - 0.7196993827819824, - 0.517953097820282, - 0.8631765246391296, - 0.4679797887802124, - 0.8163984417915344, - 0.4252359867095947, - 1.0861445665359497, - 0.6829671263694763, - 0.7136879563331604, - 0.5160345435142517, - 0.7002358436584473, - 0.5574042201042175, - ] - assert np.allclose(Es, ref_Es, atol=1e-1) - - -def test_run_train_foundation_multihead_json(tmp_path, fitting_configs): - fitting_configs_dft = [] - fitting_configs_mp2 = [] - atomic_numbers = np.unique( - np.concatenate([at.numbers for at in fitting_configs]) - ).tolist() - for i, c in enumerate(fitting_configs): - - if i in (0, 1): - continue # skip isolated atoms, as energies specified by json files below - if i % 2 == 0: - c.info["head"] = "DFT" - fitting_configs_dft.append(c) - else: - c.info["head"] = "MP2" - fitting_configs_mp2.append(c) - ase.io.write(tmp_path / "fit_multihead_dft.xyz", fitting_configs_dft) - ase.io.write(tmp_path / "fit_multihead_mp2.xyz", fitting_configs_mp2) - - # write E0s to json files - E0s = {1: 0.0, 8: 0.0} - with open(tmp_path / "fit_multihead_dft.json", "w", encoding="utf-8") as f: - json.dump(E0s, f) - with open(tmp_path / "fit_multihead_mp2.json", "w", encoding="utf-8") as f: - json.dump(E0s, f) - - heads = { - "DFT": { - "train_file": f"{str(tmp_path)}/fit_multihead_dft.xyz", - "E0s": f"{str(tmp_path)}/fit_multihead_dft.json", - }, - "MP2": { - "train_file": f"{str(tmp_path)}/fit_multihead_mp2.xyz", - "E0s": f"{str(tmp_path)}/fit_multihead_mp2.json", - }, - } - yaml_str = "heads:\n" - for key, value in heads.items(): - yaml_str += f" {key}:\n" - for sub_key, sub_value in value.items(): - yaml_str += f" {sub_key}: {sub_value}\n" - filename = tmp_path / "config.yaml" - with open(filename, "w", encoding="utf-8") as file: - file.write(yaml_str) - mace_params = _mace_params.copy() - mace_params["valid_fraction"] = 0.1 - mace_params["checkpoints_dir"] = str(tmp_path) - mace_params["model_dir"] = str(tmp_path) - mace_params["config"] = tmp_path / "config.yaml" - mace_params["loss"] = "weighted" - mace_params["foundation_model"] = "small" - mace_params["hidden_irreps"] = "128x0e" - mace_params["r_max"] = 6.0 - mace_params["default_dtype"] = "float64" - mace_params["num_radial_basis"] = 10 - mace_params["interaction_first"] = "RealAgnosticResidualInteractionBlock" - mace_params["batch_size"] = 2 - mace_params["valid_batch_size"] = 1 - mace_params["num_samples_pt"] = 50 - mace_params["subselect_pt"] = "random" - mace_params["atomic_numbers"] = "[" + ",".join(map(str, atomic_numbers)) + "]" - mace_params["filter_type_pt"] = "combinations" - mace_params["force_mh_ft_lr"] = True - # make sure run_train.py is using the mace that is currently being tested - run_env = os.environ.copy() - sys.path.insert(0, str(Path(__file__).parent.parent)) - run_env["PYTHONPATH"] = ":".join(sys.path) - print("DEBUG subprocess PYTHONPATH", run_env["PYTHONPATH"]) - - cmd = ( - sys.executable - + " " - + str(run_train) - + " " - + " ".join( - [ - (f"--{k}={v}" if v is not None else f"--{k}") - for k, v in mace_params.items() - ] - ) - ) - - try: - completed_process = subprocess.run( - cmd.split(), env=run_env, capture_output=True, text=True, check=True - ) - # Process executed successfully - print(completed_process.stdout) - except subprocess.CalledProcessError as e: - # Process failed with non-zero exit code - print(f"Command failed with exit code {e.returncode}") - print(f"STDOUT: {e.stdout}") - print(f"STDERR: {e.stderr}") - raise e - assert completed_process.returncode == 0 - - Es = [] - for at in fitting_configs: - config_head = at.info.get("head", "MP2") - calc = MACECalculator( - model_paths=tmp_path / "MACE.model", - device="cpu", - default_dtype="float64", - head=config_head, - ) - at.calc = calc - Es.append(at.get_potential_energy()) - - print("Es", Es) - # from a run on 20/08/2024 on commit - ref_Es = [ - 1.654685616493225, - 0.44693732261657715, - 0.8741313815116882, - 0.569085955619812, - 0.7161882519721985, - 0.8654778599739075, - 0.8722733855247498, - 0.49582308530807495, - 0.814422607421875, - 0.7027317881584167, - 0.7196993827819824, - 0.517953097820282, - 0.8631765246391296, - 0.4679797887802124, - 0.8163984417915344, - 0.4252359867095947, - 1.0861445665359497, - 0.6829671263694763, - 0.7136879563331604, - 0.5160345435142517, - 0.7002358436584473, - 0.5574042201042175, - ] - assert np.allclose(Es, ref_Es, atol=1e-1) - - -def test_run_train_multihead_replay_custum_finetuning( - tmp_path, fitting_configs, pretraining_configs -): - ase.io.write(tmp_path / "pretrain.xyz", pretraining_configs) - - foundation_params = { - "name": "foundation", - "train_file": os.path.join(tmp_path, "pretrain.xyz"), - "valid_fraction": 0.2, - "energy_weight": 1.0, - "forces_weight": 10.0, - "stress_weight": 1.0, - "model": "MACE", - "hidden_irreps": "32x0e", - "r_max": 5.0, - "batch_size": 2, - "max_num_epochs": 5, - "swa": None, - "start_swa": 3, - "device": "cpu", - "seed": 42, - "loss": "weighted", - "energy_key": "REF_energy", - "forces_key": "REF_forces", - "stress_key": "REF_stress", - "default_dtype": "float64", - "checkpoints_dir": str(tmp_path), - "model_dir": str(tmp_path), - } - - run_env = os.environ.copy() - sys.path.insert(0, str(Path(__file__).parent.parent)) - run_env["PYTHONPATH"] = ":".join(sys.path) - - cmd = [sys.executable, str(run_train)] - for k, v in foundation_params.items(): - if v is None: - cmd.append(f"--{k}") - else: - cmd.append(f"--{k}={v}") - - p = subprocess.run(cmd, env=run_env, check=True) - assert p.returncode == 0 - - # Step 3: Create finetuning set - fitting_configs_dft = [] - fitting_configs_mp2 = [] - for i, c in enumerate(fitting_configs): - if i in (0, 1): - c_dft = c.copy() - c_dft.info["head"] = "DFT" - fitting_configs_dft.append(c_dft) - fitting_configs_dft.append(c) - c_mp2 = c.copy() - c_mp2.info["head"] = "MP2" - fitting_configs_mp2.append(c_mp2) - elif i % 2 == 0: - c.info["head"] = "DFT" - fitting_configs_dft.append(c) - else: - c.info["head"] = "MP2" - fitting_configs_mp2.append(c) - ase.io.write(tmp_path / "fit_multihead_dft.xyz", fitting_configs_dft) - ase.io.write(tmp_path / "fit_multihead_mp2.xyz", fitting_configs_mp2) - - # Step 4: Finetune the pretrained model with multihead replay - heads = { - "DFT": {"train_file": f"{str(tmp_path)}/fit_multihead_dft.xyz"}, - "MP2": {"train_file": f"{str(tmp_path)}/fit_multihead_mp2.xyz"}, - } - yaml_str = "heads:\n" - for key, value in heads.items(): - yaml_str += f" {key}:\n" - for sub_key, sub_value in value.items(): - yaml_str += f" {sub_key}: {sub_value}\n" - filename = tmp_path / "config.yaml" - with open(filename, "w", encoding="utf-8") as file: - file.write(yaml_str) - - finetuning_params = { - "name": "finetuned", - "valid_fraction": 0.1, - "energy_weight": 1.0, - "forces_weight": 10.0, - "stress_weight": 1.0, - "model": "MACE", - "hidden_irreps": "32x0e", - "r_max": 5.0, - "batch_size": 2, - "max_num_epochs": 5, - "device": "cpu", - "seed": 42, - "loss": "weighted", - "default_dtype": "float64", - "checkpoints_dir": str(tmp_path), - "model_dir": str(tmp_path), - "foundation_model": os.path.join(tmp_path, "foundation.model"), - "config": os.path.join(tmp_path, "config.yaml"), - "pt_train_file": os.path.join(tmp_path, "pretrain.xyz"), - "num_samples_pt": 3, - "subselect_pt": "random", - "force_mh_ft_lr": True, - } - - cmd = [sys.executable, str(run_train)] - for k, v in finetuning_params.items(): - if v is None: - cmd.append(f"--{k}") - else: - cmd.append(f"--{k}={v}") - - p = subprocess.run(cmd, env=run_env, check=True) - assert p.returncode == 0 - - # Load and test the finetuned model - calc = MACECalculator( - model_paths=tmp_path / "finetuned.model", - device="cpu", - default_dtype="float64", - head="pt_head", - ) - - Es = [] - for at in fitting_configs: - at.calc = calc - Es.append(at.get_potential_energy()) - - print("Energies:", Es) - - # Add some basic checks - assert len(Es) == len(fitting_configs) - assert all(isinstance(E, float) for E in Es) - assert len(set(Es)) > 1 # Ens - - -@pytest.mark.skipif(not CUET_AVAILABLE, reason="cuequivariance not installed") -def test_run_train_cueq(tmp_path, fitting_configs): - torch.set_default_dtype(torch.float64) - ase.io.write(tmp_path / "fit.xyz", fitting_configs) - - mace_params = _mace_params.copy() - mace_params["checkpoints_dir"] = str(tmp_path) - mace_params["model_dir"] = str(tmp_path) - mace_params["train_file"] = tmp_path / "fit.xyz" - mace_params["enable_cueq"] = True - mace_params["default_dtype"] = "float64" - - # make sure run_train.py is using the mace that is currently being tested - run_env = os.environ.copy() - sys.path.insert(0, str(Path(__file__).parent.parent)) - run_env["PYTHONPATH"] = ":".join(sys.path) - print("DEBUG subprocess PYTHONPATH", run_env["PYTHONPATH"]) - - cmd = ( - sys.executable - + " " - + str(run_train) - + " " - + " ".join( - [ - (f"--{k}={v}" if v is not None else f"--{k}") - for k, v in mace_params.items() - ] - ) - ) - - try: - completed_process = subprocess.run( - cmd.split(), env=run_env, capture_output=True, text=True, check=True - ) - # Process executed successfully - print(completed_process.stdout) - except subprocess.CalledProcessError as e: - # Process failed with non-zero exit code - print(f"Command failed with exit code {e.returncode}") - print(f"STDOUT: {e.stdout}") - print(f"STDERR: {e.stderr}") - raise e - assert completed_process.returncode == 0 - - calc = MACECalculator(model_paths=tmp_path / "MACE.model", device="cuda") - Es = [] - for at in fitting_configs[2:]: - at.calc = calc - Es.append(at.get_potential_energy()) - - calc = MACECalculator( - model_paths=tmp_path / "MACE.model", device="cpu", enable_cueq=True - ) - Es_cueq = [] - for at in fitting_configs[2:]: - at.calc = calc - Es_cueq.append(at.get_potential_energy()) - - # from a run on 04/06/2024 on stress_bugfix 967f0bfb6490086599da247874b24595d149caa7 - ref_Es = [ - -0.039181344585828524, - -0.0915223395136733, - -0.14953484236456582, - -0.06662480820063998, - -0.09983737353050133, - 0.12477442296789745, - -0.06486086271762856, - -0.1460607988519944, - 0.12886334908465508, - -0.14000990081920373, - -0.05319886578958313, - 0.07780520158391, - -0.08895480281886901, - -0.15474719614734422, - 0.007756765146527644, - -0.044879267197498685, - -0.036065736712447574, - -0.24413743841886623, - -0.0838104612106429, - -0.14751978636626545, - ] - - assert np.allclose(Es, ref_Es) - assert np.allclose(ref_Es, Es_cueq) - - -@pytest.mark.skipif(not CUET_AVAILABLE, reason="cuequivariance not installed") -def test_run_train_foundation_multihead_json_cueq(tmp_path, fitting_configs): - fitting_configs_dft = [] - fitting_configs_mp2 = [] - atomic_numbers = np.unique( - np.concatenate([at.numbers for at in fitting_configs]) - ).tolist() - for i, c in enumerate(fitting_configs): - - if i in (0, 1): - continue # skip isolated atoms, as energies specified by json files below - if i % 2 == 0: - c.info["head"] = "DFT" - fitting_configs_dft.append(c) - else: - c.info["head"] = "MP2" - fitting_configs_mp2.append(c) - ase.io.write(tmp_path / "fit_multihead_dft.xyz", fitting_configs_dft) - ase.io.write(tmp_path / "fit_multihead_mp2.xyz", fitting_configs_mp2) - - # write E0s to json files - E0s = {1: 0.0, 8: 0.0} - with open(tmp_path / "fit_multihead_dft.json", "w", encoding="utf-8") as f: - json.dump(E0s, f) - with open(tmp_path / "fit_multihead_mp2.json", "w", encoding="utf-8") as f: - json.dump(E0s, f) - - heads = { - "DFT": { - "train_file": f"{str(tmp_path)}/fit_multihead_dft.xyz", - "E0s": f"{str(tmp_path)}/fit_multihead_dft.json", - }, - "MP2": { - "train_file": f"{str(tmp_path)}/fit_multihead_mp2.xyz", - "E0s": f"{str(tmp_path)}/fit_multihead_mp2.json", - }, - } - yaml_str = "heads:\n" - for key, value in heads.items(): - yaml_str += f" {key}:\n" - for sub_key, sub_value in value.items(): - yaml_str += f" {sub_key}: {sub_value}\n" - filename = tmp_path / "config.yaml" - with open(filename, "w", encoding="utf-8") as file: - file.write(yaml_str) - mace_params = _mace_params.copy() - mace_params["valid_fraction"] = 0.1 - mace_params["checkpoints_dir"] = str(tmp_path) - mace_params["model_dir"] = str(tmp_path) - mace_params["config"] = tmp_path / "config.yaml" - mace_params["loss"] = "weighted" - mace_params["foundation_model"] = "small" - mace_params["hidden_irreps"] = "128x0e" - mace_params["r_max"] = 6.0 - mace_params["default_dtype"] = "float64" - mace_params["num_radial_basis"] = 10 - mace_params["interaction_first"] = "RealAgnosticResidualInteractionBlock" - mace_params["batch_size"] = 2 - mace_params["valid_batch_size"] = 1 - mace_params["num_samples_pt"] = 50 - mace_params["subselect_pt"] = "random" - mace_params["enable_cueq"] = True - mace_params["atomic_numbers"] = "[" + ",".join(map(str, atomic_numbers)) + "]" - mace_params["filter_type_pt"] = "combinations" - mace_params["device"] = "cuda" - mace_params["force_mh_ft_lr"] = True - # make sure run_train.py is using the mace that is currently being tested - run_env = os.environ.copy() - sys.path.insert(0, str(Path(__file__).parent.parent)) - run_env["PYTHONPATH"] = ":".join(sys.path) - print("DEBUG subprocess PYTHONPATH", run_env["PYTHONPATH"]) - - cmd = ( - sys.executable - + " " - + str(run_train) - + " " - + " ".join( - [ - (f"--{k}={v}" if v is not None else f"--{k}") - for k, v in mace_params.items() - ] - ) - ) - - try: - completed_process = subprocess.run( - cmd.split(), env=run_env, capture_output=True, text=True, check=True - ) - # Process executed successfully - print(completed_process.stdout) - except subprocess.CalledProcessError as e: - # Process failed with non-zero exit code - print(f"Command failed with exit code {e.returncode}") - print(f"STDOUT: {e.stdout}") - print(f"STDERR: {e.stderr}") - raise e - assert completed_process.returncode == 0 - - calc = MACECalculator( - model_paths=tmp_path / "MACE.model", - device="cuda", - default_dtype="float64", - head="DFT", - ) - - Es = [] - for at in fitting_configs: - at.calc = calc - Es.append(at.get_potential_energy()) - - print("Es", Es) - # from a run on 20/08/2024 on commit - ref_Es = [ - 1.654685616493225, - 0.44693732261657715, - 0.8741313815116882, - 0.569085955619812, - 0.7161882519721985, - 0.8654778599739075, - 0.8722733855247498, - 0.49582308530807495, - 0.814422607421875, - 0.7027317881584167, - 0.7196993827819824, - 0.517953097820282, - 0.8631765246391296, - 0.4679797887802124, - 0.8163984417915344, - 0.4252359867095947, - 1.0861445665359497, - 0.6829671263694763, - 0.7136879563331604, - 0.5160345435142517, - 0.7002358436584473, - 0.5574042201042175, - ] - assert np.allclose(Es, ref_Es, atol=1e-1) - - -def test_run_train_lbfgs(tmp_path, fitting_configs): - ase.io.write(tmp_path / "fit.xyz", fitting_configs) - - mace_params = _mace_params.copy() - mace_params["checkpoints_dir"] = str(tmp_path) - mace_params["model_dir"] = str(tmp_path) - mace_params["train_file"] = tmp_path / "fit.xyz" - mace_params["lbfgs"] = None - mace_params["max_num_epochs"] = 2 - - # make sure run_train.py is using the mace that is currently being tested - run_env = os.environ.copy() - sys.path.insert(0, str(Path(__file__).parent.parent)) - run_env["PYTHONPATH"] = ":".join(sys.path) - print("DEBUG subprocess PYTHONPATH", run_env["PYTHONPATH"]) - - cmd = ( - sys.executable - + " " - + str(run_train) - + " " - + " ".join( - [ - (f"--{k}={v}" if v is not None else f"--{k}") - for k, v in mace_params.items() - ] - ) - ) - - p = subprocess.run(cmd.split(), env=run_env, check=True) - assert p.returncode == 0 - - calc = MACECalculator(model_paths=tmp_path / "MACE.model", device="cpu") - - Es = [] - for at in fitting_configs: - at.calc = calc - Es.append(at.get_potential_energy()) - - print("Es", Es) - # from a run on 14/03/2025 - ref_Es = [ - 0.0, - 0.0, - -0.1874197850340979, - -0.25991775038059006, - 0.18263492399322268, - -0.15026829765490662, - -0.2403061362015996, - 0.1689257170630718, - -0.2095568077455055, - -0.2957758160829075, - -0.0035370913684985364, - -0.2195416610745775, - -0.25405549447739517, - -0.06201390990366806, - -0.13332219494388334, - -0.19633181702040337, - 0.013014932630445699, - -0.08808335967147174, - -0.06664444189210728, - -0.4230467426992034, - -0.2348250569553676, - -0.17593904833220647, - ] - assert np.allclose(Es, ref_Es, atol=1e-2) - - -def test_run_train_foundation_elements(tmp_path, fitting_configs): - - ase.io.write(tmp_path / "fit.xyz", fitting_configs) - - base_params = { - "name": "MACE", - "checkpoints_dir": str(tmp_path), - "model_dir": str(tmp_path), - "train_file": tmp_path / "fit.xyz", - "loss": "weighted", - "foundation_model": "small", - "hidden_irreps": "128x0e", - "r_max": 6.0, - "default_dtype": "float64", - "max_num_epochs": 5, - "num_radial_basis": 10, - "interaction_first": "RealAgnosticResidualInteractionBlock", - "multiheads_finetuning": False, - } - - # Run environment setup - run_env = os.environ.copy() - sys.path.insert(0, str(Path(__file__).parent.parent)) - run_env["PYTHONPATH"] = ":".join(sys.path) - - # First run: without foundation_model_elements (default behavior) - mace_params = base_params.copy() - cmd = ( - sys.executable - + " " - + str(run_train) - + " " - + " ".join( - [ - (f"--{k}={v}" if v is not None else f"--{k}") - for k, v in mace_params.items() - ] - ) - ) - p = subprocess.run(cmd.split(), env=run_env, check=True) - assert p.returncode == 0 - - # Load model and check elements - model_filtered = torch.load(tmp_path / "MACE.model", map_location="cpu") - filtered_elements = set(int(z) for z in model_filtered.atomic_numbers) - assert filtered_elements == {1, 8} # Only H and O should be present - - # Second run: with foundation_model_elements - mace_params = base_params.copy() - mace_params["name"] = "MACE_all_elements" - mace_params["foundation_model_elements"] = True # Flag-only argument - cmd = ( - sys.executable - + " " - + str(run_train) - + " " - + " ".join( - [ - (f"--{k}={v}" if v is not None else f"--{k}") - for k, v in mace_params.items() - ] - ) - ) - p = subprocess.run(cmd.split(), env=run_env, check=True) - assert p.returncode == 0 - - # Load model and check elements - model_all = torch.load(tmp_path / "MACE_all_elements.model", map_location="cpu") - all_elements = set(int(z) for z in model_all.atomic_numbers) - - # Get elements from foundation model for comparison - calc = mace_mp(model="small", device="cpu") - foundation_elements = set(int(z) for z in calc.models[0].atomic_numbers) - - # Check that all foundation model elements are preserved - assert all_elements == foundation_elements - assert len(all_elements) > len(filtered_elements) - - # Check that both models can make predictions - at = fitting_configs[2].copy() - - # Test filtered model - calc_filtered = MACECalculator( - model_paths=tmp_path / "MACE.model", device="cpu", default_dtype="float64" - ) - at.calc = calc_filtered - e1 = at.get_potential_energy() - - # Test all-elements model - calc_all = MACECalculator( - model_paths=tmp_path / "MACE_all_elements.model", - device="cpu", - default_dtype="float64", - ) - at.calc = calc_all - e2 = at.get_potential_energy() - - # Energies should be different since the models are trained differently, - # but both should give reasonable results - assert np.isfinite(e1) - assert np.isfinite(e2) - - -def test_run_train_foundation_elements_multihead(tmp_path, fitting_configs): - fitting_configs_dft = [] - fitting_configs_mp2 = [] - atomic_numbers = np.unique( - np.concatenate([at.numbers for at in fitting_configs]) - ).tolist() - for i, c in enumerate(fitting_configs): - if i in (0, 1): - c_dft = c.copy() - c_dft.info["head"] = "DFT" - fitting_configs_dft.append(c_dft) - c_mp2 = c.copy() - c_mp2.info["head"] = "MP2" - fitting_configs_mp2.append(c_mp2) - if i % 2 == 0: - c_copy = c.copy() - c_copy.info["head"] = "DFT" - fitting_configs_dft.append(c_copy) - else: - c_copy = c.copy() - c_copy.info["head"] = "MP2" - fitting_configs_mp2.append(c_copy) - - ase.io.write(tmp_path / "fit_dft.xyz", fitting_configs_dft) - ase.io.write(tmp_path / "fit_mp2.xyz", fitting_configs_mp2) - - # Create multihead configuration - heads = { - "DFT": {"train_file": f"{str(tmp_path)}/fit_dft.xyz"}, - "MP2": {"train_file": f"{str(tmp_path)}/fit_mp2.xyz"}, - } - yaml_str = "heads:\n" - for key, value in heads.items(): - yaml_str += f" {key}:\n" - for sub_key, sub_value in value.items(): - yaml_str += f" {sub_key}: {sub_value}\n" - config_file = tmp_path / "config.yaml" - with open(config_file, "w", encoding="utf-8") as file: - file.write(yaml_str) - - base_params = { - "name": "MACE", - "checkpoints_dir": str(tmp_path), - "model_dir": str(tmp_path), - "config": str(config_file), - "loss": "weighted", - "foundation_model": "small", - "hidden_irreps": "128x0e", - "r_max": 6.0, - "default_dtype": "float64", - "max_num_epochs": 5, - "num_radial_basis": 10, - "interaction_first": "RealAgnosticResidualInteractionBlock", - "force_mh_ft_lr": True, - "batch_size": 1, - "num_samples_pt": 50, - "subselect_pt": "random", - "atomic_numbers": "[" + ",".join(map(str, atomic_numbers)) + "]", - "filter_type_pt": "combinations", - "valid_fraction": 0.1, - "valid_batch_size": 1, - } - - # Run environment setup - run_env = os.environ.copy() - sys.path.insert(0, str(Path(__file__).parent.parent)) - run_env["PYTHONPATH"] = ":".join(sys.path) - - # First run: without foundation_model_elements (default behavior) - mace_params = base_params.copy() - cmd = ( - sys.executable - + " " - + str(run_train) - + " " - + " ".join( - [ - (f"--{k}={v}" if v is not None else f"--{k}") - for k, v in mace_params.items() - ] - ) - ) - try: - completed_process = subprocess.run( - cmd.split(), env=run_env, capture_output=True, text=True, check=True - ) - # Process executed successfully - print(completed_process.stdout) - except subprocess.CalledProcessError as e: - # Process failed with non-zero exit code - print(f"Command failed with exit code {e.returncode}") - print(f"STDOUT: {e.stdout}") - print(f"STDERR: {e.stderr}") - raise e - assert completed_process.returncode == 0 - - # Load model and check elements - model_filtered = torch.load(tmp_path / "MACE.model", map_location="cpu") - filtered_elements = set(int(z) for z in model_filtered.atomic_numbers) - assert filtered_elements == {1, 8} # Only H and O should be present - assert len(model_filtered.heads) == 3 # pt_head + DFT + MP2 - - # Second run: with foundation_model_elements - mace_params = base_params.copy() - mace_params["name"] = "MACE_all_elements" - mace_params["foundation_model_elements"] = True - cmd = ( - sys.executable - + " " - + str(run_train) - + " " - + " ".join( - [ - (f"--{k}={v}" if v is not None else f"--{k}") - for k, v in mace_params.items() - ] - ) - ) - p = subprocess.run(cmd.split(), env=run_env, check=True) - assert p.returncode == 0 - - # Load model and check elements - model_all = torch.load(tmp_path / "MACE_all_elements.model", map_location="cpu") - all_elements = set(int(z) for z in model_all.atomic_numbers) - - # Get elements from foundation model for comparison - calc = mace_mp(model="small", device="cpu") - foundation_elements = set(int(z) for z in calc.models[0].atomic_numbers) - - # Check that all foundation model elements are preserved - assert all_elements == foundation_elements - assert len(all_elements) > len(filtered_elements) - assert len(model_all.heads) == 3 # pt_head + DFT + MP2 - - # Check that both models can make predictions - at = fitting_configs_dft[2].copy() - - # Test filtered model - calc_filtered = MACECalculator( - model_paths=tmp_path / "MACE.model", - device="cpu", - default_dtype="float64", - head="DFT", - ) - at.calc = calc_filtered - e1 = at.get_potential_energy() - - # Test all-elements model - calc_all = MACECalculator( - model_paths=tmp_path / "MACE_all_elements.model", - device="cpu", - default_dtype="float64", - head="DFT", - ) - at.calc = calc_all - e2 = at.get_potential_energy() - - assert np.isfinite(e1) - assert np.isfinite(e2) diff --git a/mace-bench/3rdparty/mace/tests/test_run_train_allkeys.py b/mace-bench/3rdparty/mace/tests/test_run_train_allkeys.py deleted file mode 100644 index 1d59190c28c7e63604476565db2bd4a5420dfc24..0000000000000000000000000000000000000000 --- a/mace-bench/3rdparty/mace/tests/test_run_train_allkeys.py +++ /dev/null @@ -1,468 +0,0 @@ -import os -import subprocess -import sys -from copy import deepcopy -from pathlib import Path - -import ase.io -import numpy as np -import pytest -from ase.atoms import Atoms - -from mace.calculators.mace import MACECalculator -from mace.cli.run_train import run as run_mace_train -from mace.data.utils import KeySpecification -from mace.tools import build_default_arg_parser - -run_train = Path(__file__).parent.parent / "mace" / "cli" / "run_train.py" - - -_mace_params = { - "name": "MACE", - "valid_fraction": 0.05, - "energy_weight": 1.0, - "forces_weight": 10.0, - "stress_weight": 1.0, - "model": "MACE", - "hidden_irreps": "128x0e", - "max_num_epochs": 10, - "swa": None, - "start_swa": 5, - "ema": None, - "ema_decay": 0.99, - "amsgrad": None, - "device": "cpu", - "seed": 5, - "loss": "weighted", - "energy_key": "REF_energy", - "forces_key": "REF_forces", - "stress_key": "REF_stress", - "interaction_first": "RealAgnosticResidualInteractionBlock", - "batch_size": 1, - "valid_batch_size": 1, - "num_samples_pt": 50, - "subselect_pt": "random", - "eval_interval": 2, - "num_radial_basis": 10, - "r_max": 6.0, - "default_dtype": "float64", -} - - -def configs_numbered_keys(): - np.random.seed(0) - water = Atoms( - numbers=[8, 1, 1], - positions=[[0, -2.0, 0], [1, 0, 0], [0, 1, 0]], - cell=[4] * 3, - pbc=[True] * 3, - ) - - energies = list(np.random.normal(0.1, size=15)) - forces = list(np.random.normal(0.1, size=(15, 3, 3))) - - trial_configs_lists = [] - # some keys present, some not - keys_to_use = ( - ["REF_energy"] - + ["2_energy"] * 2 - + ["3_energy"] * 3 - + ["4_energy"] * 4 - + ["5_energy"] * 5 - ) - - force_keys_to_use = ( - ["REF_forces"] - + ["2_forces"] * 2 - + ["3_forces"] * 3 - + ["4_forces"] * 4 - + ["5_forces"] * 5 - ) - - for ind in range(15): - c = deepcopy(water) - c.info[keys_to_use[ind]] = energies[ind] - c.arrays[force_keys_to_use[ind]] = forces[ind] - c.positions += np.random.normal(0.1, size=(3, 3)) - trial_configs_lists.append(c) - - return trial_configs_lists - - -def trial_yamls_and_and_expected(): - yamls = {} - command_line_kwargs = {"energy_key": "2_energy", "forces_key": "2_forces"} - - yamls["no_heads"] = {} - - yamls["one_head_no_dicts"] = { - "heads": { - "Default": { - "energy_key": "3_energy", - } - } - } - - yamls["one_head_with_dicts"] = { - "heads": { - "Default": { - "info_keys": { - "energy": "3_energy", - }, - "arrays_keys": { - "forces": "3_forces", - }, - } - } - } - - yamls["two_heads_no_dicts"] = { - "heads": { - "dft": { - "train_file": "fit_multihead_dft.xyz", - "energy_key": "3_energy", - }, - "mp2": { - "train_file": "fit_multihead_mp2.xyz", - "energy_key": "4_energy", - }, - } - } - - yamls["two_heads_mixed"] = { - "heads": { - "dft": { - "train_file": "fit_multihead_dft.xyz", - "info_keys": { - "energy": "3_energy", - }, - "arrays_keys": { - "forces": "3_forces", - }, - "forces_key": "4_forces", - }, - "mp2": { - "train_file": "fit_multihead_mp2.xyz", - "energy_key": "4_energy", - }, - } - } - all_arg_sets = { - "with_command_line": { - key: {**command_line_kwargs, **value} for key, value in yamls.items() - }, - "without_command_line": yamls, - } - - all_expected_outputs = { - "with_command_line": { - "no_heads": [ - 1.0037831178668188, - 1.0183291323603265, - 1.0120784084221528, - 0.9935695881012243, - 1.0021641561865526, - 0.9999135609205868, - 0.9809440616323108, - 1.0025784765050076, - 1.0017901145495376, - 1.0136913185404515, - 1.006798563238269, - 1.0187758397828384, - 1.0180201540775071, - 1.0132368725061702, - 0.9998734173248169, - ], - "one_head_no_dicts": [ - 1.0028437510688613, - 1.0514693378041775, - 1.059933403321331, - 1.034719940573569, - 1.0438040675561824, - 1.019719477728329, - 0.9841759692947915, - 1.0435266573857496, - 1.0339501989779065, - 1.0501795448530264, - 1.0402594216704781, - 1.0604998765679152, - 1.0633411200246015, - 1.0539071190201297, - 1.0393496428177804, - ], - "one_head_with_dicts": [ - 0.8638341551096959, - 1.0078341354784144, - 1.0149701178418595, - 0.9945723048460148, - 1.0184158011731292, - 0.9992135295205004, - 0.8943420783639198, - 1.0327920054084088, - 0.9905731198078909, - 0.9838325204450648, - 1.0018725575620482, - 1.007263052421034, - 1.0335213929231966, - 1.0033503312511205, - 1.0174433894759563, - ], - "two_heads_no_dicts": [ - 0.9836377578288774, - 1.0196844186291318, - 1.0151628222871238, - 0.957307281711648, - 0.985574141310865, - 0.9629670134047853, - 0.9242583185138095, - 0.9807770070311039, - 0.9973679440479541, - 1.0221127246963275, - 1.0031807967874216, - 1.0358701219543687, - 1.0434208761164758, - 1.0235606028124515, - 0.9797494630655053, - ], - "two_heads_mixed": [ - 0.8664108574741868, - 0.9907166576278023, - 1.0051969372365164, - 0.978702477000018, - 1.025500166764692, - 0.9940095566375018, - 0.9034029726954119, - 1.0391739502744488, - 0.9717327061183668, - 0.972292103670355, - 1.0012510461663253, - 0.9978051155885286, - 1.0378611651753475, - 1.0003207628186224, - 1.0209509292189651, - ], - }, - "without_command_line": { - "no_heads": [ - 0.9352605307451007, - 0.991084559389268, - 0.9940350095024881, - 0.9953849198103668, - 0.9954705498032904, - 0.9964815693808411, - 0.9663142667436776, - 0.9947223808739147, - 0.9897776682803257, - 0.989027769690667, - 0.9910280920241263, - 0.992067980667518, - 0.9917276132506404, - 0.9902848752169671, - 0.9928585982942544, - ], - "one_head_no_dicts": [ - 0.9425342207393083, - 1.0149788456087416, - 1.0249228965652788, - 1.0247924743285792, - 1.02732103964481, - 1.0168852937950326, - 0.9771283495170653, - 1.0261776335561517, - 1.0130461033368028, - 1.0162619153561783, - 1.019995179866916, - 1.0209512298344965, - 1.0219971755636952, - 1.0195791901659124, - 1.0234662527729408, - ], - "one_head_with_dicts": [ - 0.8638341551096959, - 1.0078341354784144, - 1.0149701178418595, - 0.9945723048460148, - 1.0184158011731292, - 0.9992135295205004, - 0.8943420783639198, - 1.0327920054084088, - 0.9905731198078909, - 0.9838325204450648, - 1.0018725575620482, - 1.007263052421034, - 1.0335213929231966, - 1.0033503312511205, - 1.0174433894759563, - ], - "two_heads_no_dicts": [ - 0.9933763730233168, - 0.9986480398559268, - 1.0042486164355315, - 1.0025568793877726, - 1.0032598081704625, - 0.9926714183717912, - 0.9920385249670881, - 1.0020278841030676, - 1.0012474150830537, - 1.0039289677261019, - 1.0022718878661814, - 1.003586385624809, - 1.003436450009097, - 1.003805673887942, - 1.001450261102316, - ], - "two_heads_mixed": [ - 0.8781767864616707, - 0.9843563603794138, - 1.0145197579049248, - 0.9835060778675391, - 1.0419060462994596, - 0.9917393978520056, - 0.9091521032773944, - 1.0605463095070453, - 0.9685381713826684, - 0.9866493058823766, - 1.00305061187164, - 1.0051273128414386, - 1.037964258398104, - 1.0106663924241408, - 1.0274351814133602, - ], - }, - } - - list_of_all = [] - for key, value in all_arg_sets.items(): - for key2, value2 in value.items(): - list_of_all.append( - (value2, (key, key2), np.asarray(all_expected_outputs[key][key2])) - ) - - return list_of_all - - -def dict_to_yaml_str(data, indent=0): - yaml_str = "" - for key, value in data.items(): - yaml_str += " " * indent + str(key) + ":" - if isinstance(value, dict): - yaml_str += "\n" + dict_to_yaml_str(value, indent + 2) - else: - yaml_str += " " + str(value) + "\n" - return yaml_str - - -_trial_yamls_and_and_expected = trial_yamls_and_and_expected() - - -@pytest.mark.parametrize( - "yaml_contents, name, expected_value", _trial_yamls_and_and_expected -) -def test_key_specification_methods(tmp_path, yaml_contents, name, expected_value): - fitting_configs = configs_numbered_keys() - - ase.io.write(tmp_path / "fit_multihead_dft.xyz", fitting_configs) - ase.io.write(tmp_path / "fit_multihead_mp2.xyz", fitting_configs) - ase.io.write(tmp_path / "duplicated_fit_multihead_dft.xyz", fitting_configs) - - mace_params = _mace_params.copy() - mace_params["valid_fraction"] = 0.1 - mace_params["checkpoints_dir"] = str(tmp_path) - mace_params["model_dir"] = str(tmp_path) - mace_params["train_file"] = "fit_multihead_dft.xyz" - mace_params["E0s"] = "{1:0.0,8:1.0}" - mace_params["valid_file"] = "duplicated_fit_multihead_dft.xyz" - del mace_params["valid_fraction"] - mace_params["max_num_epochs"] = 1 # many tests to do - del mace_params["energy_key"] - del mace_params["forces_key"] - del mace_params["stress_key"] - - mace_params["name"] = "MACE_" - - filename = tmp_path / "config.yaml" - with open(filename, "w", encoding="utf-8") as file: - file.write(dict_to_yaml_str(yaml_contents)) - if len(yaml_contents) > 0: - mace_params["config"] = str(tmp_path / "config.yaml") - - run_env = os.environ.copy() - sys.path.insert(0, str(Path(__file__).parent.parent)) - run_env["PYTHONPATH"] = ":".join(sys.path) - print("DEBUG subprocess PYTHONPATH", run_env["PYTHONPATH"]) - - cmd = ( - sys.executable - + " " - + str(run_train) - + " " - + " ".join( - [ - (f"--{k}={v}" if v is not None else f"--{k}") - for k, v in mace_params.items() - ] - ) - ) - - p = subprocess.run(cmd.split(), env=run_env, cwd=tmp_path, check=True) - assert p.returncode == 0 - - if "heads" in yaml_contents: - headname = list(yaml_contents["heads"].keys())[0] - else: - headname = "Default" - - calc = MACECalculator( - tmp_path / "MACE_.model", device="cpu", default_dtype="float64", head=headname - ) - - Es = [] - for at in fitting_configs: - at.calc = calc - Es.append(at.get_potential_energy()) - - print(name) - print("Es", Es) - - assert np.allclose( - np.asarray(Es), expected_value, rtol=1e-8, atol=1e-8 - ), f"Expected {expected_value} but got {Es} with error {np.max(np.abs(Es - expected_value))}" - - -def test_multihead_finetuning_does_not_modify_default_keyspec(tmp_path): - fitting_configs = configs_numbered_keys() - ase.io.write(tmp_path / "fit_multihead_dft.xyz", fitting_configs) - - args = build_default_arg_parser().parse_args( - [ - "--name", - "_MACE_", - "--train_file", - str(tmp_path / "fit_multihead_dft.xyz"), - "--foundation_model", - "small", - "--device", - "cpu", - "--E0s", - "{1:0.0,8:1.0}", - "--energy_key", - "2_energy", - "--dry_run", - ] - ) - default_key_spec = KeySpecification.from_defaults() - default_key_spec.info_keys["energy"] = "2_energy" - run_mace_train(args) - assert args.key_specification == default_key_spec - -# for creating values -def make_output(): - outputs = {} - for yaml_contents, name, expected_value in _trial_yamls_and_and_expected: - if name[0] not in outputs: - outputs[name[0]] = {} - expected = test_key_specification_methods( - Path("."), yaml_contents, name, expected_value, debug_test=False - ) - outputs[name[0]][name[1]] = expected - print(outputs) diff --git a/mace-bench/3rdparty/mace/tests/test_schedulefree.py b/mace-bench/3rdparty/mace/tests/test_schedulefree.py deleted file mode 100644 index 00b207507e3b8fc7acd0c93049f1deef9967c2a7..0000000000000000000000000000000000000000 --- a/mace-bench/3rdparty/mace/tests/test_schedulefree.py +++ /dev/null @@ -1,127 +0,0 @@ -import tempfile -from unittest.mock import MagicMock - -import numpy as np -import pytest -import torch -import torch.nn.functional as F -from e3nn import o3 - -from mace import data, modules, tools -from mace.tools import scripts_utils, torch_geometric - -try: - import schedulefree -except ImportError: - pytest.skip( - "Skipping schedulefree tests due to ImportError", allow_module_level=True - ) - -torch.set_default_dtype(torch.float64) - -table = tools.AtomicNumberTable([6]) -atomic_energies = np.array([1.0], dtype=float) -cutoff = 5.0 - - -def create_mace(device: str, seed: int = 1702): - torch_geometric.seed_everything(seed) - - model_config = { - "r_max": cutoff, - "num_bessel": 8, - "num_polynomial_cutoff": 6, - "max_ell": 3, - "interaction_cls": modules.interaction_classes[ - "RealAgnosticResidualInteractionBlock" - ], - "interaction_cls_first": modules.interaction_classes[ - "RealAgnosticResidualInteractionBlock" - ], - "num_interactions": 2, - "num_elements": 1, - "hidden_irreps": o3.Irreps("8x0e + 8x1o"), - "MLP_irreps": o3.Irreps("16x0e"), - "gate": F.silu, - "atomic_energies": atomic_energies, - "avg_num_neighbors": 8, - "atomic_numbers": table.zs, - "correlation": 3, - "radial_type": "bessel", - } - model = modules.MACE(**model_config) - return model.to(device) - - -def create_batch(device: str): - from ase import build - - size = 2 - atoms = build.bulk("C", "diamond", a=3.567, cubic=True) - atoms_list = [atoms.repeat((size, size, size))] - print("Number of atoms", len(atoms_list[0])) - - configs = [data.config_from_atoms(atoms) for atoms in atoms_list] - data_loader = torch_geometric.dataloader.DataLoader( - dataset=[ - data.AtomicData.from_config(config, z_table=table, cutoff=cutoff) - for config in configs - ], - batch_size=1, - shuffle=False, - drop_last=False, - ) - batch = next(iter(data_loader)) - batch = batch.to(device) - batch = batch.to_dict() - return batch - - -def do_optimization_step( - model, - optimizer, - device, -): - batch = create_batch(device) - model.train() - optimizer.train() - optimizer.zero_grad() - output = model(batch, training=True, compute_force=False) - loss = output["energy"].mean() - loss.backward() - optimizer.step() - model.eval() - optimizer.eval() - - -@pytest.mark.parametrize("device", ["cpu", "cuda"]) -def test_can_load_checkpoint(device): - model = create_mace(device) - optimizer = schedulefree.adamw_schedulefree.AdamWScheduleFree(model.parameters()) - args = MagicMock() - args.optimizer = "schedulefree" - args.scheduler = "ExponentialLR" - args.lr_scheduler_gamma = 0.9 - lr_scheduler = scripts_utils.LRScheduler(optimizer, args) - with tempfile.TemporaryDirectory() as d: - checkpoint_handler = tools.CheckpointHandler( - directory=d, keep=False, tag="schedulefree" - ) - for _ in range(10): - do_optimization_step(model, optimizer, device) - batch = create_batch(device) - output = model(batch) - energy = output["energy"].detach().cpu().numpy() - - state = tools.CheckpointState( - model=model, optimizer=optimizer, lr_scheduler=lr_scheduler - ) - checkpoint_handler.save(state, epochs=0, keep_last=False) - checkpoint_handler.load_latest( - state=tools.CheckpointState(model, optimizer, lr_scheduler), - swa=False, - ) - batch = create_batch(device) - output = model(batch) - new_energy = output["energy"].detach().cpu().numpy() - assert np.allclose(energy, new_energy, atol=1e-9) diff --git a/mace-bench/3rdparty/mace/tests/test_tools.py b/mace-bench/3rdparty/mace/tests/test_tools.py deleted file mode 100644 index 227a1bfc9341f3ce0c5d7480f183c89fdd23fc4f..0000000000000000000000000000000000000000 --- a/mace-bench/3rdparty/mace/tests/test_tools.py +++ /dev/null @@ -1,48 +0,0 @@ -import tempfile - -import numpy as np -import torch -import torch.nn.functional -from torch import nn, optim - -from mace.tools import ( - AtomicNumberTable, - CheckpointHandler, - CheckpointState, - atomic_numbers_to_indices, -) - - -def test_atomic_number_table(): - table = AtomicNumberTable(zs=[1, 8]) - array = np.array([8, 8, 1]) - indices = atomic_numbers_to_indices(array, z_table=table) - expected = np.array([1, 1, 0], dtype=int) - assert np.allclose(expected, indices) - - -class MyModel(nn.Module): - def __init__(self): - super().__init__() - self.linear = torch.nn.Linear(3, 4) - - def forward(self, x): - return torch.nn.functional.relu(self.linear(x)) - - -def test_save_load(): - model = MyModel() - initial_lr = 0.001 - optimizer = optim.SGD(model.parameters(), lr=initial_lr, momentum=0.9) - scheduler = optim.lr_scheduler.ExponentialLR(optimizer=optimizer, gamma=0.99) - - with tempfile.TemporaryDirectory() as directory: - handler = CheckpointHandler(directory=directory, tag="test", keep=True) - handler.save(state=CheckpointState(model, optimizer, scheduler), epochs=50) - - optimizer.step() - scheduler.step() - assert not np.isclose(optimizer.param_groups[0]["lr"], initial_lr) - - handler.load_latest(state=CheckpointState(model, optimizer, scheduler)) - assert np.isclose(optimizer.param_groups[0]["lr"], initial_lr) diff --git a/mace-bench/reproduce/init_7net.sh b/mace-bench/reproduce/init_7net.sh deleted file mode 100644 index 22f19f12ca633f726ddc11f0d010790ecd5cebba..0000000000000000000000000000000000000000 --- a/mace-bench/reproduce/init_7net.sh +++ /dev/null @@ -1,11 +0,0 @@ - - -pip install torch_scatter==2.1.2+pt24cu121 -f https://pytorch-geometric.com/whl/torch-2.4.0+cu121.html -pip install torch_sparse==0.6.18+pt24cu121 -f https://pytorch-geometric.com/whl/torch-2.4.0+cu121.html -pip install torch_spline_conv==1.2.2+pt24cu121 -f https://pytorch-geometric.com/whl/torch-2.4.0+cu121.html -pip install -r requirements.txt -pip install -e 3rdparty/SevenNet -pip install -e . -pip install ase==3.23.0 -pip install ninja -pip install rdkit==2024.3.5 \ No newline at end of file diff --git a/mace-bench/reproduce/init_mace.sh b/mace-bench/reproduce/init_mace.sh deleted file mode 100644 index b491a652e291f1c1afb12bfe8a9bf37588112533..0000000000000000000000000000000000000000 --- a/mace-bench/reproduce/init_mace.sh +++ /dev/null @@ -1,12 +0,0 @@ -pip install torch_scatter==2.1.2+pt24cu121 -f https://pytorch-geometric.com/whl/torch-2.4.0+cu121.html -pip install torch_sparse==0.6.18+pt24cu121 -f https://pytorch-geometric.com/whl/torch-2.4.0+cu121.html -pip install torch_spline_conv==1.2.2+pt24cu121 -f https://pytorch-geometric.com/whl/torch-2.4.0+cu121.html -pip install -r requirements.txt -pip install -e 3rdparty/mace -pip install -e . -pip install e3nn==0.4.4 -pip install ase==3.23.0 -pip install ninja - -# for python_CSP -pip install rdkit-pypi diff --git a/mace-bench/reproduce/mace_opt_new.py b/mace-bench/reproduce/mace_opt_new.py deleted file mode 100644 index 4a6d9d7faeaf22a1f67968dc362ae6f56e79b5e1..0000000000000000000000000000000000000000 --- a/mace-bench/reproduce/mace_opt_new.py +++ /dev/null @@ -1,300 +0,0 @@ -""" -Copyright (c) 2025 Ma Zhaojia - -This source code is licensed under the MIT license found in the -LICENSE file in the root directory of this source tree. -""" - -import os -os.environ['OMP_NUM_THREADS'] = '1' -os.environ['MKL_NUM_THREADS'] = '1' -os.environ['OPENBLAS_NUM_THREADS'] = '1' -import sys -# sys.path.append('/home/jiangj1group/zcxzcx1/volatile/mace') -from mace.calculators import mace_off, mace_mp -from ase.io import read, write -from ase.optimize import BFGS,LBFGS,FIRE,GPMin,MDMin, QuasiNewton -from ase.filters import UnitCellFilter, ExpCellFilter, FrechetCellFilter -import re -import io -from contextlib import redirect_stdout -import os -import pandas as pd -from joblib import Parallel, delayed -import json -import torch -import numpy as np -import random -import argparse -import time -import pathlib -import logging -logging.basicConfig(level=logging.INFO, format='%(asctime)s - %(levelname)s - %(message)s', force=True) -##################################################################### -os.environ['PYTHONHASHSEED'] = '1' -torch.manual_seed(1) -np.random.seed(1) -random.seed(1) -torch.cuda.manual_seed(1) -torch.cuda.manual_seed_all(1) -##################################################################### -# n_jobs=32 -# # n_jobs=2 -# path = './' -# molecule_single = 64 -# target_folder = "/data_raw/" -##################################################################### - -def calculate_density(crystal): - # 计算总质量,ASE 中的 get_masses 方法返回一个数组,包含了所有原子的质量 - total_mass = sum(crystal.get_masses()) # 转换为克 - - # 获取体积,ASE 的 get_volume 方法返回晶胞的体积,单位是 Å^3 - # 1 Å^3 = 1e-24 cm^3 - volume = crystal.get_volume() # 转换为立方厘米 - - # 计算密度,质量除以体积 - density = total_mass / (volume*10**-24)/(6.022140857*10**23) # 单位是 g/cm^3 - return density - -def run_calculation_one(path,file,target_folder,molecule_single,idx): - # os.environ['OMP_NUM_THREADS'] = '1' - # os.environ['MKL_NUM_THREADS'] = '1' - # os.environ['OPENBLAS_NUM_THREADS'] = '1' - if reproduce: - print("Reproducing deterministic results.") - torch.use_deterministic_algorithms(True) - os.environ["CUBLAS_WORKSPACE_CONFIG"] = ":4096:8" - np.set_printoptions(precision=17, suppress=False) - torch.set_printoptions(precision=17, sci_mode=False, linewidth=200) - if multithread and (not reproduce): - print("Using OMP and MKL multithreads will introduce non-deterministic results.") - else: - os.environ['OMP_NUM_THREADS'] = '1' - os.environ['MKL_NUM_THREADS'] = '1' - os.environ['OPENBLAS_NUM_THREADS'] = '1' - os.environ["CUDA_VISIBLE_DEVICES"]=str((idx%n_gpus)+gpu_offset) - - with io.StringIO() as buf, redirect_stdout(buf): - crystal = read(path+target_folder+file) - if molecule_single < 0: - molecule_single = int(file.split('_')[-1].split('.')[0]) - molecule_count = len(crystal.get_atomic_numbers())/molecule_single - calc = mace_off(model=model_path,dispersion=True, device='cuda', enable_cueq=cueq) - crystal.calc = calc - if filter1 == "UnitCellFilter": - sf = UnitCellFilter(crystal,scalar_pressure=0.0006) - elif filter1 == "FrechetCellFilter": - sf = FrechetCellFilter(crystal,scalar_pressure=0.0006) - else: - raise ValueError(f"Unrecognized filter type '{filter1}'. " - "Supported types are 'UnitCellFilter' and 'FrechetCellFilter'.") - if optimizer_type1 == "BFGS": - if use_cuda_eigh: - optimizer = BFGS(sf, use_cuda_eigh=True) - else: - optimizer = BFGS(sf) - elif optimizer_type1 == "LBFGS": - optimizer = LBFGS(sf) - elif optimizer_type1 == "QuasiNewton": - optimizer = QuasiNewton(sf) - else: - raise ValueError(f"Unrecognized optimizer type '{optimizer_type1}'. " - "Supported types are 'BFGS' and 'LBFGS'.") - - if use_nsys or use_torch_profiler : # warmup for profiling - optimizer.run(fmax=0.01,steps=100) - if use_torch_profiler: - profiler = torch.profiler.profile( - activities=[ - torch.profiler.ProfilerActivity.CPU, - torch.profiler.ProfilerActivity.CUDA - ], - # schedule=torch.profiler.schedule(wait=1, warmup=1, active=3, repeat=2), - on_trace_ready=torch.profiler.tensorboard_trace_handler('./log'), - with_stack=True - ) - profiler.start() - - start_time1 = time.time() - optimizer.run(fmax=0.01,steps=max_steps) - end_time1 = time.time() - - if use_torch_profiler: - profiler.stop() - - crystal.write(path+'cif_result_press/'+file[:-4]+"_press.cif") - output_1 = buf.getvalue() - # step_used_1 = float(re.split("\\s+", output_1.split('\n')[-2])[1][:]) - step_used_1 = optimizer.nsteps - if use_nsys or use_torch_profiler : - step_used_1 = step_used_1 - 100 - total_time1 = end_time1 - start_time1 - avg_time1 = total_time1 / step_used_1 if step_used_1 != 0 else 0 - - crystal = read(path+'cif_result_press/'+file[:-4]+"_press.cif") - crystal.calc = calc - if filter2 == "UnitCellFilter": - sf = UnitCellFilter(crystal) - elif filter2 == "FrechetCellFilter": - sf = FrechetCellFilter(crystal) - else: - raise ValueError(f"Unrecognized filter type '{filter2}'. " - "Supported types are 'UnitCellFilter' and 'FrechetCellFilter'.") - if optimizer_type2 == "BFGS": - if use_cuda_eigh: - optimizer = BFGS(sf, use_cuda_eigh=True) - else: - optimizer = BFGS(sf) - elif optimizer_type2 == "LBFGS": - optimizer = LBFGS(sf) - elif optimizer_type2 == "QuasiNewton": - optimizer = QuasiNewton(sf) - else: - raise ValueError(f"Unrecognized optimizer type '{optimizer_type2}'. " - "Supported types are 'BFGS' and 'LBFGS'.") - if use_torch_profiler: - profiler = torch.profiler.profile( - activities=[ - torch.profiler.ProfilerActivity.CPU, - torch.profiler.ProfilerActivity.CUDA - ], - # schedule=torch.profiler.schedule(wait=1, warmup=1, active=3, repeat=2), - on_trace_ready=torch.profiler.tensorboard_trace_handler('./log'), - with_stack=True - ) - profiler.start() - - start_time2 = time.time() - optimizer.run(fmax=0.01,steps=max_steps) - end_time2 = time.time() - - if use_torch_profiler: - profiler.stop() - - density = calculate_density(crystal) - crystal.write(path+'cif_result_final/'+file[:-4]+"_opt.cif") - output_2 = buf.getvalue() - energy = float(re.split("\\s+", output_2.split('\n')[-2])[3][:]) - # step_used_2 = float(re.split("\\s+", output_2.split('\n')[-2])[1][:]) - step_used_2 = optimizer.nsteps - energy_per_mol = energy / molecule_count * 96.485 - total_time2 = end_time2 - start_time2 - avg_time2 = total_time2 / step_used_2 if step_used_2 != 0 else 0 - - new_row = { - 'name': file[:-4], 'density': density, 'energy_kj': energy_per_mol, - 'step_used_1': step_used_1, 'step_used_2': step_used_2, - 'total_time1_s': total_time1, 'avg_time1_s': avg_time1, - 'total_time2_s': total_time2, 'avg_time2_s': avg_time2 - } - - print(f'output_2: {output_2}') - with open(path+'json_result/'+file[:-4]+".json", 'w') as json_file: - json.dump(new_row, json_file, indent=4) - return new_row - - -def already_have_calculation_one(path, file, target_folder, molecule_single, idx): - logging.info(f"reading on structure {file}") - print(f"reading on structure {file}") - with open(path + 'json_result/' + file[:-4] + ".json", 'r') as file: - old_row = json.load(file) - return old_row - -def run(): - df = pd.DataFrame(columns=['name', 'density', 'energy_kj', 'step_used_1', 'step_used_2', 'total_time1_s', 'avg_time1_s', 'total_time2_s', 'avg_time2_s']) - for root, dirs, files in os.walk(path + target_folder): - old_row = Parallel(n_jobs=n_jobs)( - delayed(already_have_calculation_one)(path, file, target_folder, molecule_single, idx) for idx, file in - enumerate(files) if os.path.exists(path + 'json_result/' + file[:-4] + ".json")) - - filtered_files = [file for file in files if not os.path.exists(path + 'json_result/' + file[:-4] + ".json")] - new_row = Parallel(n_jobs=n_jobs)( - delayed(run_calculation_one)(path, file, target_folder, molecule_single, idx) for idx, file in - enumerate(filtered_files)) - # show the length of new_row - print(f'new_row length: {len(new_row)}') - print(f'root: {root}\ndirs: {dirs}\nfiles: {files}') - for row in new_row: - df = pd.concat([df, pd.DataFrame([row])], ignore_index=True, axis=0) - for row in old_row: - df = pd.concat([df, pd.DataFrame([row])], ignore_index=True, axis=0) - df.to_csv(path + '/result.csv') - -if __name__ == '__main__': - parser = argparse.ArgumentParser(description="Run parallel calculations on molecular crystals.") - parser.add_argument("--n_jobs", type=int, default=32, help="Number of parallel jobs to run (default: 32)") - parser.add_argument("--target_folder", type=str, required=True, help="Path to the target folder containing input files") - parser.add_argument("--path", type=str, default='./', help="Base path for the project (default: './')") - parser.add_argument("--molecule_single", type=int, default=-1, help="Number of atoms per molecule (default: 64)") - parser.add_argument("--n_gpus", type=int, default=2, help="Number of GPUs to use (default: 2)") - parser.add_argument("--cueq", action='store_true', help="Whether to use cuEquivariance Library (default: False)") - parser.add_argument("--max_steps", type=int, default=3000, help="Number of max steps to run the optimization (default: 3000)") - parser.add_argument("--use_torch_profiler", action='store_true', help="Whether to use torch profiler (default: False)") - parser.add_argument("--use_nsys", action='store_true', help="Whether to use nsys profiler (default: False)") - parser.add_argument("--model", type=str, default="small", help="Model to use for the calculation (default: 'small')") - parser.add_argument("--optimizer", type=str, default="BFGS", help="Optimizer to use for the calculation (default: 'BFGS')") - parser.add_argument("--use_cuda_eigh", action='store_true', help="Whether to use CUDA for eigh (default: False)") - parser.add_argument("--gpu_offset", type=int, default=0, help="GPU offset to use for the calculation (default: 0)") - parser.add_argument("--multithread", action='store_true', help="Whether to use multithread (default: False)") - parser.add_argument("--reproduce", action='store_true', help="Whether to reproduce deterministic results (default: False)") - parser.add_argument("--filter1", type=str, default="UnitCellFilter", help="1st filter to use for the calculation (default: 'UnitCellFilter')") - parser.add_argument("--filter2", type=str, default="UnitCellFilter", help="2nd filter to use for the calculation (default: 'UnitCellFilter')") - parser.add_argument("--optimizer1", type=str, default="BFGS", help="1st optimizer to use for the calculation (default: 'BFGS')") - parser.add_argument("--optimizer2", type=str, default="BFGS", help="2nd optimizer to use for the calculation (default: 'BFGS')") - - args = parser.parse_args() - - n_jobs = args.n_jobs - target_folder = args.target_folder - path = args.path - molecule_single = args.molecule_single - n_gpus = args.n_gpus - cueq = args.cueq - max_steps = args.max_steps - use_torch_profiler = args.use_torch_profiler - use_nsys = args.use_nsys - model_path = args.model - optimizer_type = args.optimizer - use_cuda_eigh = args.use_cuda_eigh - gpu_offset = args.gpu_offset - multithread = args.multithread - reproduce = args.reproduce - filter1 = args.filter1 - filter2 = args.filter2 - optimizer_type1 = args.optimizer1 - optimizer_type2 = args.optimizer2 - - - try: - os.mkdir("./cif_result_press") - os.mkdir("./cif_result_final") - except: - pass - try: - os.mkdir("./json_result") - except: - pass - - start_time_all = time.time() - - - iter = 0 - while iter < 100: - iter += 1 - try: - run() - break - except Exception as e: - print(f"Error occurred: {e}") - print("Retrying...") - time.sleep(10) - - end_time_all = time.time() - total_time_all = end_time_all - start_time_all - print('dataset,total_time_all_s,attempts') - print(f"{pathlib.Path(target_folder).name},{total_time_all},{iter}") - with open(path + 'timing.csv', 'w') as f: - f.write('dataset,total_time_all_s,attempts\n') - f.write(f"{pathlib.Path(target_folder).name},{total_time_all},{iter}\n") \ No newline at end of file diff --git a/mace-bench/reproduce/mace_opt_origin.py b/mace-bench/reproduce/mace_opt_origin.py deleted file mode 100644 index c059fb1d46c3d7d3d7901fd006fc8160cb3b47e3..0000000000000000000000000000000000000000 --- a/mace-bench/reproduce/mace_opt_origin.py +++ /dev/null @@ -1,297 +0,0 @@ -""" -Copyright (c) 2025 Ma Zhaojia - -This source code is licensed under the MIT license found in the -LICENSE file in the root directory of this source tree. -""" - -import os -import sys -# sys.path.append('/home/jiangj1group/zcxzcx1/volatile/mace') -from mace.calculators import mace_off, mace_mp -from ase.io import read, write -from ase.optimize import BFGS,LBFGS,FIRE,GPMin,MDMin, QuasiNewton -from ase.filters import UnitCellFilter, ExpCellFilter, FrechetCellFilter -import re -import io -from contextlib import redirect_stdout -import os -import pandas as pd -from joblib import Parallel, delayed -import json -import torch -import numpy as np -import random -import argparse -import time -import pathlib -import logging -logging.basicConfig(level=logging.INFO, format='%(asctime)s - %(levelname)s - %(message)s', force=True) -##################################################################### -os.environ['PYTHONHASHSEED'] = '1' -torch.manual_seed(1) -np.random.seed(1) -random.seed(1) -torch.cuda.manual_seed(1) -torch.cuda.manual_seed_all(1) -##################################################################### -# n_jobs=32 -# # n_jobs=2 -# path = './' -# molecule_single = 64 -# target_folder = "/data_raw/" -##################################################################### - -def calculate_density(crystal): - # 计算总质量,ASE 中的 get_masses 方法返回一个数组,包含了所有原子的质量 - total_mass = sum(crystal.get_masses()) # 转换为克 - - # 获取体积,ASE 的 get_volume 方法返回晶胞的体积,单位是 Å^3 - # 1 Å^3 = 1e-24 cm^3 - volume = crystal.get_volume() # 转换为立方厘米 - - # 计算密度,质量除以体积 - density = total_mass / (volume*10**-24)/(6.022140857*10**23) # 单位是 g/cm^3 - return density - -def run_calculation_one(path,file,target_folder,molecule_single,idx): - # os.environ['OMP_NUM_THREADS'] = '1' - # os.environ['MKL_NUM_THREADS'] = '1' - # os.environ['OPENBLAS_NUM_THREADS'] = '1' - if reproduce: - print("Reproducing deterministic results.") - torch.use_deterministic_algorithms(True) - os.environ["CUBLAS_WORKSPACE_CONFIG"] = ":4096:8" - np.set_printoptions(precision=17, suppress=False) - torch.set_printoptions(precision=17, sci_mode=False, linewidth=200) - if multithread and (not reproduce): - print("Using OMP and MKL multithreads will introduce non-deterministic results.") - else: - os.environ['OMP_NUM_THREADS'] = '1' - os.environ['MKL_NUM_THREADS'] = '1' - os.environ['OPENBLAS_NUM_THREADS'] = '1' - os.environ["CUDA_VISIBLE_DEVICES"]=str((idx%n_gpus)+gpu_offset) - - with io.StringIO() as buf, redirect_stdout(buf): - crystal = read(path+target_folder+file) - if molecule_single < 0: - molecule_single = int(file.split('_')[-1].split('.')[0]) - molecule_count = len(crystal.get_atomic_numbers())/molecule_single - calc = mace_off(model=model_path,dispersion=True, device='cuda', enable_cueq=cueq) - crystal.calc = calc - if filter1 == "UnitCellFilter": - sf = UnitCellFilter(crystal,scalar_pressure=0.0006) - elif filter1 == "FrechetCellFilter": - sf = FrechetCellFilter(crystal,scalar_pressure=0.0006) - else: - raise ValueError(f"Unrecognized filter type '{filter1}'. " - "Supported types are 'UnitCellFilter' and 'FrechetCellFilter'.") - if optimizer_type1 == "BFGS": - if use_cuda_eigh: - optimizer = BFGS(sf, use_cuda_eigh=True) - else: - optimizer = BFGS(sf) - elif optimizer_type1 == "LBFGS": - optimizer = LBFGS(sf) - elif optimizer_type1 == "QuasiNewton": - optimizer = QuasiNewton(sf) - else: - raise ValueError(f"Unrecognized optimizer type '{optimizer_type1}'. " - "Supported types are 'BFGS' and 'LBFGS'.") - - if use_nsys or use_torch_profiler : # warmup for profiling - optimizer.run(fmax=0.01,steps=100) - if use_torch_profiler: - profiler = torch.profiler.profile( - activities=[ - torch.profiler.ProfilerActivity.CPU, - torch.profiler.ProfilerActivity.CUDA - ], - # schedule=torch.profiler.schedule(wait=1, warmup=1, active=3, repeat=2), - on_trace_ready=torch.profiler.tensorboard_trace_handler('./log'), - with_stack=True - ) - profiler.start() - - start_time1 = time.time() - optimizer.run(fmax=0.01,steps=max_steps) - end_time1 = time.time() - - if use_torch_profiler: - profiler.stop() - - crystal.write(path+'cif_result_press/'+file[:-4]+"_press.cif") - output_1 = buf.getvalue() - # step_used_1 = float(re.split("\\s+", output_1.split('\n')[-2])[1][:]) - step_used_1 = optimizer.nsteps - if use_nsys or use_torch_profiler : - step_used_1 = step_used_1 - 100 - total_time1 = end_time1 - start_time1 - avg_time1 = total_time1 / step_used_1 if step_used_1 != 0 else 0 - - crystal = read(path+'cif_result_press/'+file[:-4]+"_press.cif") - crystal.calc = calc - if filter2 == "UnitCellFilter": - sf = UnitCellFilter(crystal) - elif filter2 == "FrechetCellFilter": - sf = FrechetCellFilter(crystal) - else: - raise ValueError(f"Unrecognized filter type '{filter2}'. " - "Supported types are 'UnitCellFilter' and 'FrechetCellFilter'.") - if optimizer_type2 == "BFGS": - if use_cuda_eigh: - optimizer = BFGS(sf, use_cuda_eigh=True) - else: - optimizer = BFGS(sf) - elif optimizer_type2 == "LBFGS": - optimizer = LBFGS(sf) - elif optimizer_type2 == "QuasiNewton": - optimizer = QuasiNewton(sf) - else: - raise ValueError(f"Unrecognized optimizer type '{optimizer_type2}'. " - "Supported types are 'BFGS' and 'LBFGS'.") - if use_torch_profiler: - profiler = torch.profiler.profile( - activities=[ - torch.profiler.ProfilerActivity.CPU, - torch.profiler.ProfilerActivity.CUDA - ], - # schedule=torch.profiler.schedule(wait=1, warmup=1, active=3, repeat=2), - on_trace_ready=torch.profiler.tensorboard_trace_handler('./log'), - with_stack=True - ) - profiler.start() - - start_time2 = time.time() - optimizer.run(fmax=0.01,steps=max_steps) - end_time2 = time.time() - - if use_torch_profiler: - profiler.stop() - - density = calculate_density(crystal) - crystal.write(path+'cif_result_final/'+file[:-4]+"_opt.cif") - output_2 = buf.getvalue() - energy = float(re.split("\\s+", output_2.split('\n')[-2])[3][:]) - # step_used_2 = float(re.split("\\s+", output_2.split('\n')[-2])[1][:]) - step_used_2 = optimizer.nsteps - energy_per_mol = energy / molecule_count * 96.485 - total_time2 = end_time2 - start_time2 - avg_time2 = total_time2 / step_used_2 if step_used_2 != 0 else 0 - - new_row = { - 'name': file[:-4], 'density': density, 'energy_kj': energy_per_mol, - 'step_used_1': step_used_1, 'step_used_2': step_used_2, - 'total_time1_s': total_time1, 'avg_time1_s': avg_time1, - 'total_time2_s': total_time2, 'avg_time2_s': avg_time2 - } - - print(f'output_2: {output_2}') - with open(path+'json_result/'+file[:-4]+".json", 'w') as json_file: - json.dump(new_row, json_file, indent=4) - return new_row - - -def already_have_calculation_one(path, file, target_folder, molecule_single, idx): - logging.info(f"reading on structure {file}") - print(f"reading on structure {file}") - with open(path + 'json_result/' + file[:-4] + ".json", 'r') as file: - old_row = json.load(file) - return old_row - -def run(): - df = pd.DataFrame(columns=['name', 'density', 'energy_kj', 'step_used_1', 'step_used_2', 'total_time1_s', 'avg_time1_s', 'total_time2_s', 'avg_time2_s']) - for root, dirs, files in os.walk(path + target_folder): - old_row = Parallel(n_jobs=n_jobs)( - delayed(already_have_calculation_one)(path, file, target_folder, molecule_single, idx) for idx, file in - enumerate(files) if os.path.exists(path + 'json_result/' + file[:-4] + ".json")) - - filtered_files = [file for file in files if not os.path.exists(path + 'json_result/' + file[:-4] + ".json")] - new_row = Parallel(n_jobs=n_jobs)( - delayed(run_calculation_one)(path, file, target_folder, molecule_single, idx) for idx, file in - enumerate(filtered_files)) - # show the length of new_row - print(f'new_row length: {len(new_row)}') - print(f'root: {root}\ndirs: {dirs}\nfiles: {files}') - for row in new_row: - df = pd.concat([df, pd.DataFrame([row])], ignore_index=True, axis=0) - for row in old_row: - df = pd.concat([df, pd.DataFrame([row])], ignore_index=True, axis=0) - df.to_csv(path + '/result.csv') - -if __name__ == '__main__': - parser = argparse.ArgumentParser(description="Run parallel calculations on molecular crystals.") - parser.add_argument("--n_jobs", type=int, default=32, help="Number of parallel jobs to run (default: 32)") - parser.add_argument("--target_folder", type=str, required=True, help="Path to the target folder containing input files") - parser.add_argument("--path", type=str, default='./', help="Base path for the project (default: './')") - parser.add_argument("--molecule_single", type=int, default=-1, help="Number of atoms per molecule (default: 64)") - parser.add_argument("--n_gpus", type=int, default=2, help="Number of GPUs to use (default: 2)") - parser.add_argument("--cueq", action='store_true', help="Whether to use cuEquivariance Library (default: False)") - parser.add_argument("--max_steps", type=int, default=3000, help="Number of max steps to run the optimization (default: 3000)") - parser.add_argument("--use_torch_profiler", action='store_true', help="Whether to use torch profiler (default: False)") - parser.add_argument("--use_nsys", action='store_true', help="Whether to use nsys profiler (default: False)") - parser.add_argument("--model", type=str, default="small", help="Model to use for the calculation (default: 'small')") - parser.add_argument("--optimizer", type=str, default="BFGS", help="Optimizer to use for the calculation (default: 'BFGS')") - parser.add_argument("--use_cuda_eigh", action='store_true', help="Whether to use CUDA for eigh (default: False)") - parser.add_argument("--gpu_offset", type=int, default=0, help="GPU offset to use for the calculation (default: 0)") - parser.add_argument("--multithread", action='store_true', help="Whether to use multithread (default: False)") - parser.add_argument("--reproduce", action='store_true', help="Whether to reproduce deterministic results (default: False)") - parser.add_argument("--filter1", type=str, default="UnitCellFilter", help="1st filter to use for the calculation (default: 'UnitCellFilter')") - parser.add_argument("--filter2", type=str, default="UnitCellFilter", help="2nd filter to use for the calculation (default: 'UnitCellFilter')") - parser.add_argument("--optimizer1", type=str, default="BFGS", help="1st optimizer to use for the calculation (default: 'BFGS')") - parser.add_argument("--optimizer2", type=str, default="BFGS", help="2nd optimizer to use for the calculation (default: 'BFGS')") - - args = parser.parse_args() - - n_jobs = args.n_jobs - target_folder = args.target_folder - path = args.path - molecule_single = args.molecule_single - n_gpus = args.n_gpus - cueq = args.cueq - max_steps = args.max_steps - use_torch_profiler = args.use_torch_profiler - use_nsys = args.use_nsys - model_path = args.model - optimizer_type = args.optimizer - use_cuda_eigh = args.use_cuda_eigh - gpu_offset = args.gpu_offset - multithread = args.multithread - reproduce = args.reproduce - filter1 = args.filter1 - filter2 = args.filter2 - optimizer_type1 = args.optimizer1 - optimizer_type2 = args.optimizer2 - - - try: - os.mkdir("./cif_result_press") - os.mkdir("./cif_result_final") - except: - pass - try: - os.mkdir("./json_result") - except: - pass - - start_time_all = time.time() - - - iter = 0 - while iter < 100: - iter += 1 - try: - run() - break - except Exception as e: - print(f"Error occurred: {e}") - print("Retrying...") - time.sleep(10) - - end_time_all = time.time() - total_time_all = end_time_all - start_time_all - print('dataset,total_time_all_s,attempts') - print(f"{pathlib.Path(target_folder).name},{total_time_all},{iter}") - with open(path + 'timing.csv', 'w') as f: - f.write('dataset,total_time_all_s,attempts\n') - f.write(f"{pathlib.Path(target_folder).name},{total_time_all},{iter}\n") \ No newline at end of file diff --git a/mace-bench/reproduce/perf_v2_base/run_mace.sh b/mace-bench/reproduce/perf_v2_base/run_mace.sh deleted file mode 100644 index c9e81c83441007a14a9234efb9d17cc1df8f254b..0000000000000000000000000000000000000000 --- a/mace-bench/reproduce/perf_v2_base/run_mace.sh +++ /dev/null @@ -1,4 +0,0 @@ - -python ../mace_opt_new.py --n_jobs 64 --molecule_single 46 \ - --target_folder ../../data/perf_v2/ --model small --n_gpus 4 --gpu_offset 0 \ - --optimizer1 QuasiNewton --filter1 UnitCellFilter --filter2 UnitCellFilter \ No newline at end of file diff --git a/mace-bench/reproduce/perf_v2_batch/opt.sh b/mace-bench/reproduce/perf_v2_batch/opt.sh deleted file mode 100644 index 19c3aa9a75bdb146ad0a63c179328317b7cfe197..0000000000000000000000000000000000000000 --- a/mace-bench/reproduce/perf_v2_batch/opt.sh +++ /dev/null @@ -1,5 +0,0 @@ - -rm -r *_result_* - -python ../../scripts/opt_batch.py --target_folder "../../data/perf_v2" --molecule_single 46 --gpu_offset 0 --n_gpus 4 --num_workers 40 --batch_size 0 \ - --max_steps 6000 --filter1 UnitCellFilter --filter2 UnitCellFilter --optimizer1 BFGSFusedLS --optimizer2 BFGS --num_threads 2 --cueq true --use_ordered_files true \ No newline at end of file diff --git a/mace-bench/reproduce/subtest.sh b/mace-bench/reproduce/subtest.sh deleted file mode 100644 index af830ca0d1ac021d8cab6522b77cd2d00123ee2e..0000000000000000000000000000000000000000 --- a/mace-bench/reproduce/subtest.sh +++ /dev/null @@ -1,25 +0,0 @@ - - -top_dir=$(pwd) - -natoms_nw_bs=( - "92 48 25" - "184 40 12" - "368 40 5" -) - -for config in "${natoms_nw_bs[@]}"; do - read natoms nw bs <<< "$config" - - dir="$top_dir/subtest_BATCH_${natoms}_g4_j${nw}_bs${bs}_cueq_cupbc" - mkdir -p "$dir" - cd "$dir" || continue - - pwd - python ../../scripts/opt_batch.py \ - --target_folder "../../data/perf_v2_sorted/perf_v2_${natoms}" \ - --molecule_single 46 --gpu_offset 0 --n_gpus 4 --num_workers ${nw} --batch_size ${bs} \ - --max_steps 6000 --filter1 UnitCellFilter --filter2 UnitCellFilter \ - --optimizer1 BFGSFusedLS --optimizer2 BFGS --num_threads 2 \ - --use_ordered_files true --cueq true > opt.log 2>&1 -done \ No newline at end of file diff --git a/mace-bench/reproduce/subtest_baseline.sh b/mace-bench/reproduce/subtest_baseline.sh deleted file mode 100644 index 08e4c4954e976acc0fecebddc18adb2bf7200e24..0000000000000000000000000000000000000000 --- a/mace-bench/reproduce/subtest_baseline.sh +++ /dev/null @@ -1,24 +0,0 @@ - - -top_dir=$(pwd) - -natoms_nw_bs=( - "92 64" - "184 64" - "368 64" -) - -for config in "${natoms_nw_bs[@]}"; do - read natoms nw <<< "$config" - - dir="$top_dir/subtest_BASE_${natoms}_g4_j${nw}" - mkdir -p "$dir" - cd "$dir" || continue - - pwd - - python ../mace_opt_new.py --n_jobs ${nw} --molecule_single 46 \ - --target_folder ../../data/perf_v2_sorted/perf_v2_${natoms}/ --model small --n_gpus 4 \ - --gpu_offset 0 --optimizer1 QuasiNewton --filter1 UnitCellFilter \ - --filter2 UnitCellFilter --max_steps 3000 > opt.log 2>&1 -done \ No newline at end of file diff --git a/mace-bench/requirements.txt b/mace-bench/requirements.txt deleted file mode 100644 index 135b56b83c1b222dc2d286a3eb8ae480d095a430..0000000000000000000000000000000000000000 --- a/mace-bench/requirements.txt +++ /dev/null @@ -1,137 +0,0 @@ ---extra-index-url https://download.pytorch.org/whl/cu121 -absl-py==2.1.0 -aiohappyeyeballs==2.4.4 -aiohttp==3.11.11 -aiosignal==1.3.2 -annotated-types==0.7.0 -antlr4-python3-runtime==4.9.3 -# -e git+https://gitlab.com/ase/ase.git@72c50c76bac2396c7d58385b231c65bd07458279#egg=ase&subdirectory=../../../3rdparty/ase -async-timeout==5.0.1 -attrs==24.3.0 -certifi==2024.8.30 -cfgv==3.4.0 -charset-normalizer==3.4.0 -click==8.1.8 -cloudpickle==3.1.0 -ConfigArgParse==1.7 -contourpy==1.3.1 -coverage==7.6.9 -cuequivariance==0.4.0 -cuequivariance-ops-torch-cu12==0.4.0 -cuequivariance-ops-cu12==0.4.0 -cuequivariance-torch==0.4.0 -cycler==0.12.1 -distlib==0.3.9 -docker-pycreds==0.4.0 -e3nn==0.4.4 -exceptiongroup==1.2.2 -# -e git+https://github.com/mazhaojia123/fairchem.git@f50db9d5b29debdfb265d9c3fad394f18e16cab8#egg=fairchem_core&subdirectory=../../../3rdparty/fairchem/packages/fairchem-core -filelock==3.13.1 -fonttools==4.55.1 -frozenlist==1.5.0 -fsspec==2024.2.0 -gitdb==4.0.11 -GitPython==3.1.43 -grpcio==1.68.1 -h5py==3.12.1 -hydra-core==1.3.2 -identify==2.6.3 -idna==3.10 -iniconfig==2.0.0 -Jinja2==3.1.3 -joblib==1.4.2 -kiwisolver==1.4.7 -latexcodec==3.0.0 -lightning-utilities==0.11.9 -llvmlite==0.43.0 -lmdb==1.5.1 -# -e git+https://github.com/mazhaojia123/mace.git@edd6b479f4974d0b8162712872ad2eed1aa2fb75#egg=mace_torch&subdirectory=../../../3rdparty/mace -Markdown==3.7 -MarkupSafe==2.1.5 -matplotlib==3.9.3 -matscipy==1.1.1 -monty==2024.10.21 -mpmath==1.3.0 -multidict==6.1.0 -networkx==3.2.1 -nodeenv==1.9.1 -numba==0.60.0 -numpy==1.26.4 -nvidia-cublas-cu12==12.1.3.1 -nvidia-cuda-cupti-cu12==12.1.105 -nvidia-cuda-nvrtc-cu12==12.1.105 -nvidia-cuda-runtime-cu12==12.1.105 -nvidia-cudnn-cu12==9.1.0.70 -nvidia-cufft-cu12==11.0.2.54 -nvidia-curand-cu12==10.3.2.106 -nvidia-cusolver-cu12==11.4.5.107 -nvidia-cusparse-cu12==12.1.0.106 -nvidia-nccl-cu12==2.20.5 -nvidia-nvjitlink-cu12==12.1.105 -nvidia-nvtx-cu12==12.1.105 -omegaconf==2.3.0 -opt-einsum-fx==0.1.4 -opt_einsum==3.4.0 -orjson==3.10.12 -packaging==24.2 -palettable==3.3.3 -pandas==2.2.3 -pillow==11.0.0 -platformdirs==4.3.6 -plotly==5.24.1 -pluggy==1.5.0 -pre_commit==4.0.1 -prettytable==3.12.0 -propcache==0.2.1 -protobuf==5.29.2 -psutil==6.1.1 -pybtex==0.24.0 -pydantic==2.10.4 -pydantic_core==2.27.2 -pymatgen==2024.11.13 -pyparsing==3.2.0 -pytest==8.3.4 -pytest-cov==6.0.0 -python-dateutil==2.9.0.post0 -python-hostlist==2.0.0 -pytz==2024.2 -PyYAML==6.0.2 -requests==2.32.3 -ruamel.yaml==0.18.6 -ruamel.yaml.clib==0.2.12 -ruff==0.5.1 -scipy==1.14.1 -sentry-sdk==2.19.2 -setproctitle==1.3.4 -six==1.16.0 -smmap==5.0.1 -spglib==2.5.0 -submitit==1.5.2 -sympy==1.13.1 -syrupy==4.8.0 -tabulate==0.9.0 -tenacity==9.0.0 -tensorboard==2.18.0 -tensorboard-data-server==0.7.2 -tomli==2.2.1 -torch==2.4.1+cu121 -# ./torch-2.4.1+cu121-cp310-cp310-linux_x86_64.whl -torch-dftd==0.5.1 -torch-ema==0.3 -torch-geometric==2.6.1 -# torch_scatter==2.1.2+pt24cu121 -# torch_sparse==0.6.18+pt24cu121 -# torch_spline_conv==1.2.2+pt24cu121 -torchmetrics==1.6.0 -tqdm==4.67.1 -triton==3.0.0 -typing_extensions==4.12.2 -tzdata==2024.2 -uncertainties==3.2.2 -urllib3==2.2.3 -virtualenv==20.28.0 -wandb==0.19.1 -wcwidth==0.2.13 -Werkzeug==3.1.3 -yarl==1.18.3 -torch-tb-profiler==0.4.3 \ No newline at end of file diff --git a/mace-bench/scripts/opt_batch.py b/mace-bench/scripts/opt_batch.py deleted file mode 100644 index 6d6ab1071de0f15982c87c9a0104fa53e00fb33f..0000000000000000000000000000000000000000 --- a/mace-bench/scripts/opt_batch.py +++ /dev/null @@ -1,112 +0,0 @@ -""" -Copyright (c) 2025 Ma Zhaojia - -This source code is licensed under the MIT license found in the -LICENSE file in the root directory of this source tree. -""" - -import os -import argparse - -parser = argparse.ArgumentParser(description="Run batch optimization on molecular crystals.") -parser.add_argument("--target_folder", type=str, required=True, help="Target folder containing crystal files") -parser.add_argument("--num_workers", type=int, default=4, help="Number of workers to distribute the files to") -parser.add_argument("--n_gpus", type=int, default=1, help="Number of GPUs to use for the optimization") -parser.add_argument("--gpu_offset", type=int, default=0, help="Offset for GPU numbering") -parser.add_argument("--batch_size", type=int, default=4, help="Number of files to process in a single batch") -parser.add_argument("--run_baseline", type=bool, default=False, help="Run baseline optimization using LBFGS from ase.optimize") -parser.add_argument("--max_steps", type=int, default=100, help="Number of max steps to run the optimization (default: 100)") -parser.add_argument("--filter1", type=str, default="UnitCellFilter", - choices=[None, "UnitCellFilter"], - help="Type of cell filter to use in first optimization") -parser.add_argument("--filter2", type=str, default="UnitCellFilter", - choices=[None, "UnitCellFilter"], - help="Type of cell filter to use in second optimization") -parser.add_argument("--optimizer1", type=str, default="BFGS", - choices=["LBFGS", "QuasiNewton", "BFGS", "BFGSLineSearch", "BFGSFusedLS"], - help="First optimizer to use (default: BFGS)") -parser.add_argument("--optimizer2", type=str, default="BFGS", - choices=["LBFGS", "QuasiNewton", "BFGS", "BFGSLineSearch", "BFGSFusedLS"], - help="Second optimizer to use (default: LBFGS)") -parser.add_argument("--skip_second_stage", type=bool, default=False, help="Skip the second optimization stage") -parser.add_argument("--scalar_pressure", type=float, default=0.0006, - help="Scalar pressure for cell optimization (default: 0.0006)") -parser.add_argument("--compile_mode", type=str, default=None, - choices=[None, "default", "reduce-overhead", "max-autotune", "max-autotune-no-cudagraphs"], - help="Compile mode for MACE calculator") -parser.add_argument("--profile", type=str, default="False", - help="Enable profiling. Set to 'True' for basic profiling or provide a JSON string with profiler config options for wait, warmup, active, and repeat") -parser.add_argument("--num_threads", type=int, default=16, help="Number of cpu threads per process to use while running the optimization") -parser.add_argument("--bind_cores", type=str, default=None, - help=("Specify a comma-separated list of core ranges (e.g., '0-15,16-31,...') for each worker. The number of ranges must equal --num_workers.")) -parser.add_argument("--cueq", type=bool, default=False, help="Whether to use cuEquivariance Library (default: False)") -parser.add_argument("--molecule_single", type=int, default=64, help="Number of atoms per molecule (default: 64)") -parser.add_argument("--output_path", type=str, default="./", help="Absolute path for output files") -parser.add_argument("--model", type=str, default="mace", choices=["mace", "chgnet", "sevennet"], help="Model to use for optimization") -parser.add_argument("--use_ordered_files", type=bool, default=False, - help="Whether to sort files by atomic number in descending order before optimization") -args = parser.parse_args() - -os.environ['OMP_NUM_THREADS'] = str(args.num_threads) -os.environ['MKL_NUM_THREADS'] = str(args.num_threads) - -import pathlib -import logging -from batchopt import Scheduler, ensure_directory, run_baseline, count_atoms_cif -logging.basicConfig( - level=logging.WARNING, - format='%(asctime)s - %(process)d - %(levelname)s - %(message)s', - datefmt='%H:%M:%S', - force=True -) - -if __name__ == '__main__': - target_folder = pathlib.Path(args.target_folder) - files = [str(file) for file in target_folder.glob("*.cif")] - devices = [f"cuda:{i}" for i in range(args.gpu_offset, args.gpu_offset + args.n_gpus)] - - logging.info("Starting batch optimization.") - logging.info(f"Use devices: {devices}") - logging.info(f"files: {files}") - - output_path = args.output_path - if not os.path.isabs(output_path): - output_path = os.path.abspath(output_path) - logging.info(f"Output path: {output_path}") - - for output_dir in ["cif_result_press", "cif_result_final", "json_result_press", "json_result_final", "worker_results", "log"]: - dir_path = os.path.join(output_path, output_dir) - ensure_directory(dir_path) - - import time - start_time = time.perf_counter() - - use_ordered_files = args.use_ordered_files - if use_ordered_files: - logging.info(f"Use ordered files.") - if files[0].endswith("cif"): - files = sorted(files, key=count_atoms_cif, reverse=True) - else: - logging.error(f"No support for the file type in {target_folder}.") - end_time = time.perf_counter() - logging.info(f"atomic sorting time: {end_time - start_time:.4f} seconds.") - - if args.run_baseline: - run_baseline(files, args.num_workers, devices, args.max_steps, - args.filter1, args.filter2, args.skip_second_stage, - args.scalar_pressure, args.optimizer1, args.optimizer2, - output_path=output_path) - else: - scheduler = Scheduler(files=files, num_workers=args.num_workers, devices=devices, - batch_size=args.batch_size, max_steps=args.max_steps, - filter1=args.filter1, filter2=args.filter2, - skip_second_stage=args.skip_second_stage, - scalar_pressure=args.scalar_pressure, optimizer1=args.optimizer1, optimizer2=args.optimizer2, - compile_mode=args.compile_mode, profile=args.profile, - num_threads=args.num_threads, bind_cores=args.bind_cores, - cueq=args.cueq, molecule_single=args.molecule_single, - output_path=output_path, model=args.model) - scheduler.run() - - logging.info("Batch optimization completed.") - diff --git a/mace-bench/setup.py b/mace-bench/setup.py deleted file mode 100644 index f7e1680e3ef2f79d760f763c12a62ef898ee6697..0000000000000000000000000000000000000000 --- a/mace-bench/setup.py +++ /dev/null @@ -1,23 +0,0 @@ -from setuptools import setup, find_packages - -setup( - name='BOMLIP-CSP', - version='0.1', - author='Chengxi Zhao, Zhaojia Ma, Dingrui Fan', - author_email='chengxi_zhao@ustc.edu.cn, zhaojia_ma@foxmail.com', - description='Integrating machine learning interatomic potentials with batched optimization for crystal structure prediction', - url='https://github.com/pic-ai-robotic-chemistry/BOMLIP-CSP', - license='MIT', - classifiers=[ - 'Development Status :: 3 - Alpha', - 'Intended Audience :: Science/Research', - 'License :: OSI Approved :: MIT License', - 'Programming Language :: Python :: 3', - 'Programming Language :: Python :: 3.10', - 'Topic :: Scientific/Engineering :: Chemistry', - 'Topic :: Scientific/Engineering :: Physics', - ], - python_requires='>=3.10', - package_dir={'': 'src'}, - packages=find_packages('src'), -) \ No newline at end of file diff --git a/mace-bench/src/BOMLIP_CSP.egg-info/PKG-INFO b/mace-bench/src/BOMLIP_CSP.egg-info/PKG-INFO deleted file mode 100644 index d9cc8e1fbbc24c439bda37edbf59fc256a02ba50..0000000000000000000000000000000000000000 --- a/mace-bench/src/BOMLIP_CSP.egg-info/PKG-INFO +++ /dev/null @@ -1,23 +0,0 @@ -Metadata-Version: 2.4 -Name: BOMLIP-CSP -Version: 0.1 -Summary: Integrating machine learning interatomic potentials with batched optimization for crystal structure prediction -Home-page: https://github.com/pic-ai-robotic-chemistry/BOMLIP-CSP -Author: Chengxi Zhao, Zhaojia Ma, Dingrui Fan -Author-email: chengxi_zhao@ustc.edu.cn, zhaojia_ma@foxmail.com -License: MIT -Classifier: Development Status :: 3 - Alpha -Classifier: Intended Audience :: Science/Research -Classifier: License :: OSI Approved :: MIT License -Classifier: Programming Language :: Python :: 3 -Classifier: Programming Language :: Python :: 3.10 -Classifier: Topic :: Scientific/Engineering :: Chemistry -Classifier: Topic :: Scientific/Engineering :: Physics -Requires-Python: >=3.10 -Dynamic: author -Dynamic: author-email -Dynamic: classifier -Dynamic: home-page -Dynamic: license -Dynamic: requires-python -Dynamic: summary diff --git a/mace-bench/src/BOMLIP_CSP.egg-info/SOURCES.txt b/mace-bench/src/BOMLIP_CSP.egg-info/SOURCES.txt deleted file mode 100644 index 11e6ddc16cd77adb6fd964112b650ddba37ec67b..0000000000000000000000000000000000000000 --- a/mace-bench/src/BOMLIP_CSP.egg-info/SOURCES.txt +++ /dev/null @@ -1,20 +0,0 @@ -setup.py -src/BOMLIP_CSP.egg-info/PKG-INFO -src/BOMLIP_CSP.egg-info/SOURCES.txt -src/BOMLIP_CSP.egg-info/dependency_links.txt -src/BOMLIP_CSP.egg-info/top_level.txt -src/batchopt/__init__.py -src/batchopt/atoms_to_graphs.py -src/batchopt/baseline.py -src/batchopt/pbc_graph.py -src/batchopt/pbc_graph_legacy.py -src/batchopt/relaxengine.py -src/batchopt/utils.py -src/batchopt/extensions/__init__.py -src/batchopt/extensions/cuda_ops/__init__.py -src/batchopt/relaxation/__init__.py -src/batchopt/relaxation/ase_utils.py -src/batchopt/relaxation/optimizable.py -src/batchopt/relaxation/optimizers/__init__.py -src/batchopt/relaxation/optimizers/bfgs_torch.py -src/batchopt/relaxation/optimizers/bfgsfusedls.py \ No newline at end of file diff --git a/mace-bench/src/BOMLIP_CSP.egg-info/dependency_links.txt b/mace-bench/src/BOMLIP_CSP.egg-info/dependency_links.txt deleted file mode 100644 index 8b137891791fe96927ad78e64b0aad7bded08bdc..0000000000000000000000000000000000000000 --- a/mace-bench/src/BOMLIP_CSP.egg-info/dependency_links.txt +++ /dev/null @@ -1 +0,0 @@ - diff --git a/mace-bench/src/BOMLIP_CSP.egg-info/top_level.txt b/mace-bench/src/BOMLIP_CSP.egg-info/top_level.txt deleted file mode 100644 index fe9f2991a0dd177d98c3ea1fff66d89e772ea40d..0000000000000000000000000000000000000000 --- a/mace-bench/src/BOMLIP_CSP.egg-info/top_level.txt +++ /dev/null @@ -1 +0,0 @@ -batchopt diff --git a/mace-bench/src/batchopt/__init__.py b/mace-bench/src/batchopt/__init__.py deleted file mode 100644 index 5d823fab2db674a109982a519689de42d8634e4b..0000000000000000000000000000000000000000 --- a/mace-bench/src/batchopt/__init__.py +++ /dev/null @@ -1,30 +0,0 @@ -""" -Copyright (c) 2025 Ma Zhaojia - -This source code is licensed under the MIT license found in the -LICENSE file in the root directory of this source tree. -""" - -from .relaxengine import Scheduler, Worker -from .baseline import ensure_directory, run_baseline -from .utils import count_atoms_cif -from .pbc_graph import radius_graph_pbc_cuda - -try: - from . import extensions - _extensions_available = True -except ImportError as e: - import warnings - warnings.warn(f"Extensions not available: {e}. Falling back to PyTorch implementations.") - extensions = None - _extensions_available = False - -__all__ = [ - "Scheduler", - "ensure_directory", - "run_baseline", - "count_atoms_cif", - "Worker", - "extensions", - "radius_graph_pbc_cuda", -] \ No newline at end of file diff --git a/mace-bench/src/batchopt/atoms_to_graphs.py b/mace-bench/src/batchopt/atoms_to_graphs.py deleted file mode 100644 index d50fc768fffdb2121ecf057624aec3223a164b61..0000000000000000000000000000000000000000 --- a/mace-bench/src/batchopt/atoms_to_graphs.py +++ /dev/null @@ -1,309 +0,0 @@ -""" -Copyright (c) Meta, Inc. and its affiliates. - -This source code is licensed under the MIT license found in the -LICENSE file in the root directory of this source tree. -""" - -from __future__ import annotations - -from typing import TYPE_CHECKING - -import ase.db.sqlite -import ase.io.trajectory -import numpy as np -import torch -from ase.geometry import wrap_positions -from torch_geometric.data import Data - -from batchopt.utils import collate - -if TYPE_CHECKING: - from collections.abc import Sequence - -try: - from pymatgen.io.ase import AseAtomsAdaptor -except ImportError: - AseAtomsAdaptor = None - -from tqdm import tqdm - - -class AtomsToGraphs: - """A class to help convert periodic atomic structures to graphs. - - The AtomsToGraphs class takes in periodic atomic structures in form of ASE atoms objects and converts - them into graph representations for use in PyTorch. The primary purpose of this class is to determine the - nearest neighbors within some radius around each individual atom, taking into account PBC, and set the - pair index and distance between atom pairs appropriately. Lastly, atomic properties and the graph information - are put into a PyTorch geometric data object for use with PyTorch. - - Args: - max_neigh (int): Maximum number of neighbors to consider. - radius (int or float): Cutoff radius in Angstroms to search for neighbors. - r_energy (bool): Return the energy with other properties. Default is False, so the energy will not be returned. - r_forces (bool): Return the forces with other properties. Default is False, so the forces will not be returned. - r_stress (bool): Return the stress with other properties. Default is False, so the stress will not be returned. - r_distances (bool): Return the distances with other properties. - Default is False, so the distances will not be returned. - r_edges (bool): Return interatomic edges with other properties. Default is True, so edges will be returned. - r_fixed (bool): Return a binary vector with flags for fixed (1) vs free (0) atoms. - Default is True, so the fixed indices will be returned. - r_pbc (bool): Return the periodic boundary conditions with other properties. - Default is False, so the periodic boundary conditions will not be returned. - r_data_keys (sequence of str, optional): Return values corresponding to given keys in atoms.info data with other - properties. Default is None, so no data will be returned as properties. - - Attributes: - max_neigh (int): Maximum number of neighbors to consider. - radius (int or float): Cutoff radius in Angstoms to search for neighbors. - r_energy (bool): Return the energy with other properties. Default is False, so the energy will not be returned. - r_forces (bool): Return the forces with other properties. Default is False, so the forces will not be returned. - r_stress (bool): Return the stress with other properties. Default is False, so the stress will not be returned. - r_distances (bool): Return the distances with other properties. - Default is False, so the distances will not be returned. - r_edges (bool): Return interatomic edges with other properties. Default is True, so edges will be returned. - r_fixed (bool): Return a binary vector with flags for fixed (1) vs free (0) atoms. - Default is True, so the fixed indices will be returned. - r_pbc (bool): Return the periodic boundary conditions with other properties. - Default is False, so the periodic boundary conditions will not be returned. - r_data_keys (sequence of str, optional): Return values corresponding to given keys in atoms.info data with other - properties. Default is None, so no data will be returned as properties. - """ - - def __init__( - self, - max_neigh: int = 200, - radius: int = 6, - r_energy: bool = False, - r_forces: bool = False, - r_distances: bool = False, - r_edges: bool = True, - r_fixed: bool = True, - r_pbc: bool = False, - r_stress: bool = False, - r_data_keys: Sequence[str] | None = None, - ) -> None: - self.max_neigh = max_neigh - self.radius = radius - self.r_energy = r_energy - self.r_forces = r_forces - self.r_stress = r_stress - self.r_distances = r_distances - self.r_fixed = r_fixed - self.r_edges = r_edges - self.r_pbc = r_pbc - self.r_data_keys = r_data_keys - - def _get_neighbors_pymatgen(self, atoms: ase.Atoms): - """Preforms nearest neighbor search and returns edge index, distances, - and cell offsets""" - if AseAtomsAdaptor is None: - raise RuntimeError( - "Unable to import pymatgen.io.ase.AseAtomsAdaptor. Make sure pymatgen is properly installed." - ) - - struct = AseAtomsAdaptor.get_structure(atoms) - _c_index, _n_index, _offsets, n_distance = struct.get_neighbor_list( - r=self.radius, numerical_tol=0, exclude_self=True - ) - _nonmax_idx = [] - for i in range(len(atoms)): - idx_i = (_c_index == i).nonzero()[0] - # sort neighbors by distance, remove edges larger than max_neighbors - idx_sorted = np.argsort(n_distance[idx_i])[: self.max_neigh] - _nonmax_idx.append(idx_i[idx_sorted]) - _nonmax_idx = np.concatenate(_nonmax_idx) - - _c_index = _c_index[_nonmax_idx] - _n_index = _n_index[_nonmax_idx] - n_distance = n_distance[_nonmax_idx] - _offsets = _offsets[_nonmax_idx] - - return _c_index, _n_index, n_distance, _offsets - - def _reshape_features(self, c_index, n_index, n_distance, offsets): - """Stack center and neighbor index and reshapes distances, - takes in np.arrays and returns torch tensors""" - edge_index = torch.LongTensor(np.vstack((n_index, c_index))) - edge_distances = torch.FloatTensor(n_distance) - cell_offsets = torch.LongTensor(offsets) - - # remove distances smaller than a tolerance ~ 0. The small tolerance is - # needed to correct for pymatgen's neighbor_list returning self atoms - # in a few edge cases. - nonzero = torch.where(edge_distances >= 1e-8)[0] - edge_index = edge_index[:, nonzero] - edge_distances = edge_distances[nonzero] - cell_offsets = cell_offsets[nonzero] - - return edge_index, edge_distances, cell_offsets - - def get_edge_distance_vec( - self, - pos, - edge_index, - cell, - cell_offsets, - ): - row, col = edge_index - distance_vectors = pos[row] - pos[col] - - # correct for pbc - cell = torch.repeat_interleave(cell, edge_index.shape[1], dim=0) - offsets = cell_offsets.float().view(-1, 1, 3).bmm(cell.float()).view(-1, 3) - distance_vectors += offsets - - return distance_vectors - - def convert(self, atoms: ase.Atoms, sid=None): - """Convert a single atomic structure to a graph. - - Args: - atoms (ase.atoms.Atoms): An ASE atoms object. - - sid (uniquely identifying object): An identifier that can be used to track the structure in downstream - tasks. Common sids used in OCP datasets include unique strings or integers. - - Returns: - data (torch_geometric.data.Data): A torch geometic data object with positions, atomic_numbers, tags, - and optionally, energy, forces, distances, edges, and periodic boundary conditions. - Optional properties can included by setting r_property=True when constructing the class. - """ - - # set the atomic numbers, positions, and cell - positions = np.array(atoms.get_positions(), copy=True) - pbc = np.array(atoms.pbc, copy=True) - cell = np.array(atoms.get_cell(complete=True), copy=True) - # TODO: change this back &&& ^^^ - # positions = wrap_positions(positions, cell, pbc=pbc, eps=0) - - atomic_numbers = torch.tensor(atoms.get_atomic_numbers(), dtype=torch.uint8) - positions = torch.from_numpy(positions).float() - cell = torch.from_numpy(cell).view(1, 3, 3).float() - natoms = positions.shape[0] - - # initialized to torch.zeros(natoms) if tags missing. - # https://wiki.fysik.dtu.dk/ase/_modules/ase/atoms.html#Atoms.get_tags - tags = torch.tensor(atoms.get_tags(), dtype=torch.int) - - # put the minimum data in torch geometric data object - data = Data( - cell=cell, - pos=positions, - atomic_numbers=atomic_numbers, - natoms=natoms, - tags=tags, - ) - - # Optionally add a systemid (sid) to the object - if sid is not None: - data.sid = sid - - # optionally include other properties - if self.r_edges: - # run internal functions to get padded indices and distances - atoms_copy = atoms.copy() - atoms_copy.set_positions(positions) - split_idx_dist = self._get_neighbors_pymatgen(atoms_copy) - edge_index, edge_distances, cell_offsets = self._reshape_features( - *split_idx_dist - ) - - data.edge_index = edge_index - data.cell_offsets = cell_offsets - data.edge_distance_vec = self.get_edge_distance_vec( - positions, edge_index, cell, cell_offsets - ) - - del atoms_copy - if self.r_energy: - energy = atoms.get_potential_energy(apply_constraint=False) - data.energy = energy - if self.r_forces: - forces = torch.tensor( - atoms.get_forces(apply_constraint=False), dtype=torch.float32 - ) - data.forces = forces - if self.r_stress: - stress = torch.tensor( - atoms.get_stress(apply_constraint=False, voigt=False), - dtype=torch.float32, - ) - data.stress = stress - if self.r_distances and self.r_edges: - data.distances = edge_distances - if self.r_fixed: - fixed_idx = torch.zeros(natoms, dtype=torch.int) - if hasattr(atoms, "constraints"): - from ase.constraints import FixAtoms - - for constraint in atoms.constraints: - if isinstance(constraint, FixAtoms): - fixed_idx[constraint.index] = 1 - data.fixed = fixed_idx - if self.r_pbc: - data.pbc = torch.tensor(atoms.pbc, dtype=torch.bool) - if self.r_data_keys is not None: - for data_key in self.r_data_keys: - data[data_key] = ( - atoms.info[data_key] - if isinstance(atoms.info[data_key], (int, float, str)) - else torch.tensor(atoms.info[data_key]) - ) - - return data - - def convert_all( - self, - atoms_collection, - processed_file_path: str | None = None, - collate_and_save=False, - disable_tqdm=False, - ): - """Convert all atoms objects in a list or in an ase.db to graphs. - - Args: - atoms_collection (list of ase.atoms.Atoms or ase.db.sqlite.SQLite3Database): - Either a list of ASE atoms objects or an ASE database. - processed_file_path (str): - A string of the path to where the processed file will be written. Default is None. - collate_and_save (bool): A boolean to collate and save or not. Default is False, so will not write a file. - - Returns: - data_list (list of torch_geometric.data.Data): - A list of torch geometric data objects containing molecular graph info and properties. - """ - - # list for all data - data_list = [] - if isinstance(atoms_collection, list): - atoms_iter = atoms_collection - elif isinstance(atoms_collection, ase.db.sqlite.SQLite3Database): - atoms_iter = atoms_collection.select() - elif isinstance( - atoms_collection, - (ase.io.trajectory.SlicedTrajectory, ase.io.trajectory.TrajectoryReader), - ): - atoms_iter = atoms_collection - else: - raise NotImplementedError - - for atoms in tqdm( - atoms_iter, - desc="converting ASE atoms collection to graphs", - total=len(atoms_collection), - unit=" systems", - disable=disable_tqdm, - ): - # check if atoms is an ASE Atoms object this for the ase.db case - data = self.convert( - atoms if isinstance(atoms, ase.atoms.Atoms) else atoms.toatoms() - ) - data_list.append(data) - - if collate_and_save: - data, slices = collate(data_list) - torch.save((data, slices), processed_file_path) - - return data_list diff --git a/mace-bench/src/batchopt/baseline.py b/mace-bench/src/batchopt/baseline.py deleted file mode 100644 index d23595dfd4cb6103ced8b9f9a6cea8ed6c80673c..0000000000000000000000000000000000000000 --- a/mace-bench/src/batchopt/baseline.py +++ /dev/null @@ -1,171 +0,0 @@ -""" -Copyright (c) 2025 {Chengxi Zhao, Zhaojia Ma, Dingrui Fan} - -This source code is licensed under the MIT license found in the -LICENSE file in the root directory of this source tree. -""" - -from ase.io import read -import logging -from joblib import Parallel, delayed -from ase.optimize import LBFGS as ASE_LBFGS -from ase.optimize import QuasiNewton as ASE_QuasiNewton -from ase.optimize import BFGS as ASE_BFGS -import time -import csv -import os -try: - from mace.calculators import mace_off -except ImportError: - logging.warning("Failed to import MACE modules") - -logging.basicConfig(level=logging.INFO, format='%(asctime)s - %(levelname)s - %(message)s') - - -def ensure_directory(directory): - """Create directory if it doesn't exist.""" - if not os.path.exists(directory): - os.makedirs(directory) - logging.info(f"Created directory: {directory}") - -def baseline_task(file, device, max_steps, filter1=None, filter2=None, skip_second_stage=False, scalar_pressure=0.0006, first_optimizer="LBFGS", second_optimizer="LBFGS"): - """ - Runs the baseline optimization using LBFGS from ase.optimize. - """ - os.environ["CUDA_VISIBLE_DEVICES"] = device.split(":")[-1] - logging.basicConfig(level=logging.INFO, format='%(asctime)s - %(levelname)s - %(message)s') - logging.info(f"Starting baseline optimization for file {file} on device {device}.") - - - start_time = time.perf_counter() - - crystal = read(file) - # calc = mace_off(model="small", device=device) - calc = mace_off(model="small", device="cuda") - crystal.calc = calc - - first_optimizer_class ={ - "LBFGS": ASE_LBFGS, - "QuasiNewton": ASE_QuasiNewton, - "BFGS": ASE_BFGS - }.get(first_optimizer, ASE_LBFGS) - - # First optimization stage - if filter1 == "UnitCellFilter": - from ase.filters import UnitCellFilter - atoms_with_filter = UnitCellFilter(crystal, scalar_pressure=scalar_pressure) - first_optimizer_instance = first_optimizer_class(atoms_with_filter) - elif filter1 == "FrechetCellFilter": - from ase.filters import FrechetCellFilter - atoms_with_filter = FrechetCellFilter(crystal, scalar_pressure=scalar_pressure) - first_optimizer_instance = first_optimizer_class(atoms_with_filter) - else: - first_optimizer_instance = first_optimizer_class(crystal) - - start_time1 = time.perf_counter() - first_optimizer_instance.run(fmax=0.01, steps=max_steps) - end_time1 = time.perf_counter() - - # Save intermediate result - output_dir_press = "./cif_result_press" - output_file_press = os.path.join(output_dir_press, os.path.basename(file).replace(".cif", "_press.cif")) - crystal.write(output_file_press) - - elapsed_time1 = end_time1 - start_time1 - steps1 = first_optimizer_instance.nsteps - - if skip_second_stage: - - ret_result = { - "file": file, - "stage1_time": elapsed_time1, - "stage1_steps": steps1, - "stage2_time": 0.0, - "stage2_steps": 0, - "total_time": elapsed_time1, - "total_steps": steps1 - } - else: - # Second optimization stage - crystal = read(output_file_press) - crystal.calc = calc - - second_optimizer_class = { - "LBFGS": ASE_LBFGS, - "QuasiNewton": ASE_QuasiNewton, - "BFGS": ASE_BFGS - }.get(second_optimizer, ASE_LBFGS) - - if filter2 == "UnitCellFilter": - from ase.filters import UnitCellFilter - atoms_with_filter2 = UnitCellFilter(crystal) - second_optimizer_instance = second_optimizer_class(atoms_with_filter2) - elif filter2 == "FrechetCellFilter": - from ase.filters import FrechetCellFilter - atoms_with_filter2 = FrechetCellFilter(crystal) - second_optimizer_instance = second_optimizer_class(atoms_with_filter2) - else: - second_optimizer_instance = second_optimizer_class(crystal) - - start_time2 = time.perf_counter() - second_optimizer_instance.run(fmax=0.01, steps=max_steps) - end_time2 = time.perf_counter() - - # Save final result - output_dir_final = "./cif_result_final" - output_file_final = os.path.join(output_dir_final, os.path.basename(file).replace(".cif", "_opt.cif")) - crystal.write(output_file_final) - - # Collect metrics - elapsed_time2 = end_time2 - start_time2 - total_time = elapsed_time1 + elapsed_time2 - steps2 = second_optimizer_instance.nsteps - - ret_result = { - "file": file, - "stage1_time": elapsed_time1, - "stage1_steps": steps1, - "stage2_time": elapsed_time2, - "stage2_steps": steps2, - "total_time": total_time, - "total_steps": steps1 + steps2 - } - - logging.info(f"Baseline optimization completed for file {file}.") - return ret_result - -def run_baseline(files, num_workers, devices, max_steps, - filter1=None, filter2=None, skip_second_stage=False, scalar_pressure=0.0006, - optimizer1=None, optimizer2=None): - """ - Runs the baseline optimization using LBFGS from ase.optimize. - """ - logging.info(f"Starting baseline optimization with {num_workers} workers.") - - start_time = time.perf_counter() - results = Parallel(n_jobs=num_workers)( - delayed(baseline_task)(file, devices[i % len(devices)], max_steps, filter1, filter2, skip_second_stage, scalar_pressure, optimizer1, optimizer2) - for i, file in enumerate(files) - ) - end_time = time.perf_counter() - - csv_file = "results_baseline.csv" - with open(csv_file, mode='w', newline='') as file: - writer = csv.DictWriter(file, fieldnames=["file", "stage1_time", "stage1_steps", "stage2_time", "stage2_steps", "total_time", "total_steps"]) - writer.writeheader() - for result in results: - writer.writerow(result) - - logging.info(f"Baseline optimization completed in {end_time - start_time:.2f} seconds.") - final_elapsed_time = end_time - start_time - summary_csv_file = "summary_baseline.csv" - with open(summary_csv_file, mode='w', newline='') as file: - writer = csv.DictWriter(file, fieldnames=["elapsed_time", "num_workers", "batch_size"]) - writer.writeheader() - writer.writerow({ - "elapsed_time": final_elapsed_time, - "num_workers": num_workers, - "batch_size": 1 - }) - - logging.info(f"Summary results written to {summary_csv_file}.") \ No newline at end of file diff --git a/mace-bench/src/batchopt/extensions/__init__.py b/mace-bench/src/batchopt/extensions/__init__.py deleted file mode 100644 index 2e0a0f218186042a15fdccf7211b1155dcd74c16..0000000000000000000000000000000000000000 --- a/mace-bench/src/batchopt/extensions/__init__.py +++ /dev/null @@ -1,12 +0,0 @@ -""" -Copyright (c) 2025 Ma Zhaojia - -This source code is licensed under the MIT license found in the -LICENSE file in the root directory of this source tree. - -BatchOpt Extensions - C++ and CUDA implementations for performance-critical operations. - -This module provides optimized implementations of common operations using -torch.utils.cpp_extension for JIT compilation. -""" - diff --git a/mace-bench/src/batchopt/extensions/cuda_ops/__init__.py b/mace-bench/src/batchopt/extensions/cuda_ops/__init__.py deleted file mode 100644 index 5ce1bd1ce4a9ffebe79277669a91032637a77b11..0000000000000000000000000000000000000000 --- a/mace-bench/src/batchopt/extensions/cuda_ops/__init__.py +++ /dev/null @@ -1,91 +0,0 @@ -""" -Copyright (c) 2025 Ma Zhaojia - -This source code is licensed under the MIT license found in the -LICENSE file in the root directory of this source tree. - -CUDA Extension wrapper for vector addition and PBC graph operations. -""" -import torch -from torch.utils.cpp_extension import load -import os - -def load_cuda_extension(): - """Load the CUDA extension for vector addition.""" - # Check if CUDA is available - if not torch.cuda.is_available(): - raise RuntimeError("CUDA is not available. Cannot load CUDA extension.") - - # Get the directory of this file - current_dir = os.path.dirname(os.path.abspath(__file__)) - - # Path to the CUDA source file - cuda_file = os.path.join(current_dir, "vector_add.cu") - - # Load the extension - return load( - name="vector_add_cuda", - sources=[cuda_file], - verbose=True, - extra_cflags=['-O3'], - extra_cuda_cflags=['-O3', '--use_fast_math'], - ) - -def load_pbc_graph_cuda_extension(): - """Load the CUDA extension for PBC graph operations.""" - # Check if CUDA is available - if not torch.cuda.is_available(): - raise RuntimeError("CUDA is not available. Cannot load CUDA extension.") - - # Get the directory of this file - current_dir = os.path.dirname(os.path.abspath(__file__)) - - # Path to the CUDA source file - cuda_file = os.path.join(current_dir, "pbc_graph.cu") - - # Load the extension - return load( - name="pbc_graph_cuda", - sources=[cuda_file], - verbose=True, - extra_cflags=['-O3'], - extra_cuda_cflags=['-O3', '--use_fast_math'], - ) - -# Global variable to store loaded extension -_cuda_extension = None -_pbc_graph_cuda_extension = None - -def get_cuda_extension(): - """Get or load the CUDA extension.""" - global _cuda_extension - if _cuda_extension is None: - _cuda_extension = load_cuda_extension() - return _cuda_extension - -def get_pbc_graph_cuda_extension(): - """Get or load the PBC graph CUDA extension.""" - global _pbc_graph_cuda_extension - if _pbc_graph_cuda_extension is None: - _pbc_graph_cuda_extension = load_pbc_graph_cuda_extension() - return _pbc_graph_cuda_extension - -def vector_add_cuda(a: torch.Tensor, b: torch.Tensor) -> torch.Tensor: - """ - Perform vector addition using CUDA implementation. - - Args: - a: First input tensor (must be on CUDA device) - b: Second input tensor (must be on CUDA device) - - Returns: - Result tensor of element-wise addition - """ - if not torch.cuda.is_available(): - raise RuntimeError("CUDA is not available.") - - if not (a.is_cuda and b.is_cuda): - raise ValueError("CUDA implementation requires CUDA tensors. Use .cuda() to move tensors to GPU.") - - extension = get_cuda_extension() - return extension.vector_add(a.float(), b.float()) diff --git a/mace-bench/src/batchopt/extensions/cuda_ops/pbc_graph.cu b/mace-bench/src/batchopt/extensions/cuda_ops/pbc_graph.cu deleted file mode 100644 index 912c8078826880f30b29786c0c84b67330e2cbcc..0000000000000000000000000000000000000000 --- a/mace-bench/src/batchopt/extensions/cuda_ops/pbc_graph.cu +++ /dev/null @@ -1,286 +0,0 @@ -#include -#include -#include -#include -#include - -// Template function to get appropriate epsilon for different floating point types -template -__device__ __forceinline__ T get_epsilon() { - if constexpr (std::is_same_v) { - return static_cast(1e-8); - } else if constexpr (std::is_same_v) { - return static_cast(1e-12); - } else { - return static_cast(1e-8); // fallback - } -} - -// Templated CUDA kernel for computing pairwise distances with PBC offsets -// This version avoids repeat_interleave by computing offsets directly in the kernel -template -__global__ void pbc_distance_kernel_optimized( - const T* pos1, - const T* pos2, - const T* pbc_offsets, // [batch_size, 3] - const int64_t* num_atoms_per_image_sqr, // [batch_size] - const int64_t* batch_offsets, // [batch_size] - cumulative offsets for each batch - T* distances_squared, - bool* valid_mask, - int num_pairs, - T radius_squared -) { - int idx = blockIdx.x * blockDim.x + threadIdx.x; - - if (idx < num_pairs) { - // Find which batch this pair belongs to - int batch_idx = 0; - while (batch_idx < num_pairs && idx >= batch_offsets[batch_idx + 1]) { - batch_idx++; - } - - // Get PBC offset for this batch - T offset_x = pbc_offsets[batch_idx * 3]; - T offset_y = pbc_offsets[batch_idx * 3 + 1]; - T offset_z = pbc_offsets[batch_idx * 3 + 2]; - - // Get positions for this atom pair with PBC offset - T dx = pos2[idx * 3] - pos1[idx * 3] + offset_x; - T dy = pos2[idx * 3 + 1] - pos1[idx * 3 + 1] + offset_y; - T dz = pos2[idx * 3 + 2] - pos1[idx * 3 + 2] + offset_z; - - // Compute squared distance - T dist_sq = dx * dx + dy * dy + dz * dz; - distances_squared[idx] = dist_sq; - - // Check if within radius - valid_mask[idx] = (dist_sq <= radius_squared) && (dist_sq > get_epsilon()); - } -} - -// Original kernel for fallback -template -__global__ void pbc_distance_kernel( - const T* pos1, - const T* pos2, - const T* pbc_offsets, - T* distances_squared, - bool* valid_mask, - int num_pairs, - T radius_squared -) { - int idx = blockIdx.x * blockDim.x + threadIdx.x; - - if (idx < num_pairs) { - // Get positions for this atom pair - T dx = pos2[idx * 3] - pos1[idx * 3] + pbc_offsets[idx * 3]; - T dy = pos2[idx * 3 + 1] - pos1[idx * 3 + 1] + pbc_offsets[idx * 3 + 1]; - T dz = pos2[idx * 3 + 2] - pos1[idx * 3 + 2] + pbc_offsets[idx * 3 + 2]; - - // Compute squared distance - T dist_sq = dx * dx + dy * dy + dz * dz; - distances_squared[idx] = dist_sq; - - // Check if within radius - valid_mask[idx] = (dist_sq <= radius_squared) && (dist_sq > get_epsilon()); - } -} - -// Template helper function to launch the appropriate optimized kernel -template -inline void launch_pbc_distance_kernel_optimized( - const T* pos1, - const T* pos2, - const T* pbc_offsets, - const int64_t* num_atoms_per_image_sqr, - const int64_t* batch_offsets, - T* distances_squared, - bool* valid_mask, - int num_pairs, - T radius_squared, - int blocks, - int threads_per_block -) { - pbc_distance_kernel_optimized<<>>( - pos1, pos2, pbc_offsets, num_atoms_per_image_sqr, batch_offsets, - distances_squared, valid_mask, num_pairs, radius_squared - ); -} - -// Template helper function to launch the appropriate kernel (fallback) -template -void launch_pbc_distance_kernel( - const T* pos1, - const T* pos2, - const T* pbc_offsets, - T* distances_squared, - bool* valid_mask, - int num_pairs, - T radius_squared, - int blocks, - int threads_per_block -) { - pbc_distance_kernel<<>>( - pos1, pos2, pbc_offsets, distances_squared, valid_mask, num_pairs, radius_squared - ); -} - -// CUDA function to compute distances for all unit cell offsets -std::vector pbc_distance_cuda( - torch::Tensor pos1, - torch::Tensor pos2, - torch::Tensor data_cell, - torch::Tensor num_atoms_per_image_sqr, - int batch_size, - std::vector max_rep, - float radius, - torch::Device device -) { - // Convert tensors to CUDA if not already, but preserve original dtype - pos1 = pos1.to(device).contiguous(); - pos2 = pos2.to(device).contiguous(); - data_cell = data_cell.to(device).contiguous(); - num_atoms_per_image_sqr = num_atoms_per_image_sqr.to(device); - - // Check that all position tensors have the same dtype - TORCH_CHECK(pos1.dtype() == pos2.dtype(), "pos1 and pos2 must have the same dtype"); - TORCH_CHECK(pos1.dtype() == data_cell.dtype(), "pos1 and data_cell must have the same dtype"); - - // Determine if we're working with float32 or float64 - bool is_float64 = pos1.dtype() == torch::kFloat64; - - int num_pairs = pos1.size(0); - - // Storage for all results across unit cells - std::vector all_index1, all_index2, all_unit_cell, all_distances_sq; - - // Create base indices for original atom pairs - torch::Tensor base_indices = torch::arange(num_pairs, torch::dtype(torch::kLong).device(device)); - - // Launch parameters - int threads_per_block = 512; - int blocks = (num_pairs + threads_per_block - 1) / threads_per_block; - - // Pre-allocate tensors outside the loop for reuse - torch::Tensor distances_squared = torch::zeros({num_pairs}, - torch::dtype(pos1.dtype()).device(device)); - torch::Tensor valid_mask = torch::zeros({num_pairs}, - torch::dtype(torch::kBool).device(device)); - torch::Tensor unit_cell_offset = torch::zeros({3}, - torch::dtype(pos1.dtype()).device(device)); - torch::Tensor unit_cell_offset_batch = torch::zeros({batch_size, 3, 1}, - torch::dtype(pos1.dtype()).device(device)); - - // Pre-compute batch offsets for optimized kernel - torch::Tensor batch_offsets = torch::zeros({batch_size + 1}, - torch::dtype(torch::kLong).device(device)); - torch::Tensor cumsum = torch::cumsum(num_atoms_per_image_sqr, 0); - batch_offsets.slice(0, 1, batch_size + 1) = cumsum; - - // Iterate over unit cell offsets (triple loop) - // NOTE: for i, j, k loop can not be flatten, as we need to limit the device memory usage - #pragma unroll - for (int i = -max_rep[0]; i <= max_rep[0]; i++) { - #pragma unroll - for (int j = -max_rep[1]; j <= max_rep[1]; j++) { - #pragma unroll - for (int k = -max_rep[2]; k <= max_rep[2]; k++) { - - // Reuse pre-allocated unit cell offset tensor - unit_cell_offset[0] = static_cast(i); - unit_cell_offset[1] = static_cast(j); - unit_cell_offset[2] = static_cast(k); - - // Compute PBC offsets for this unit cell - // unit_cell_offset_batch.fill_(0); - unit_cell_offset_batch.select(2, 0) = unit_cell_offset.unsqueeze(0).expand({batch_size, -1}); - torch::Tensor pbc_offsets = torch::bmm(data_cell, unit_cell_offset_batch).squeeze(-1); - - // // Optimized: Use index_select instead of repeat_interleave - // // Create index tensor for selecting pbc_offsets based on atom pairs - // int64_t offset = 0; - // for (int b = 0; b < batch_size; b++) { - // int64_t num_pairs_in_batch = num_atoms_per_image_sqr[b].item(); - // auto batch_indices = torch::full({num_pairs_in_batch}, b, - // torch::dtype(torch::kLong).device(device)); - // pbc_offsets_per_atom.slice(0, offset, offset + num_pairs_in_batch) = - // pbc_offsets.index_select(0, batch_indices); - // offset += num_pairs_in_batch; - // } - - // Reset output tensors for reuse - // distances_squared.fill_(0); - // valid_mask.fill_(false); - - // Launch templated CUDA kernel - if (is_float64) { - double radius_squared = static_cast(radius) * static_cast(radius); - launch_pbc_distance_kernel_optimized( - pos1.data_ptr(), - pos2.data_ptr(), - // pbc_offsets_per_atom.data_ptr(), - pbc_offsets.data_ptr(), - num_atoms_per_image_sqr.data_ptr(), - batch_offsets.data_ptr(), - distances_squared.data_ptr(), - valid_mask.data_ptr(), - num_pairs, - radius_squared, - blocks, - threads_per_block - ); - } else { - float radius_squared = radius * radius; - launch_pbc_distance_kernel_optimized( - pos1.data_ptr(), - pos2.data_ptr(), - // pbc_offsets_per_atom.data_ptr(), - pbc_offsets.data_ptr(), - num_atoms_per_image_sqr.data_ptr(), - batch_offsets.data_ptr(), - distances_squared.data_ptr(), - valid_mask.data_ptr(), - num_pairs, - radius_squared, - blocks, - threads_per_block - ); - } - - // Filter valid pairs - torch::Tensor valid_indices = torch::nonzero(valid_mask).squeeze(-1); - if (valid_indices.numel() > 0) { - torch::Tensor valid_base_indices = base_indices.index_select(0, valid_indices); - torch::Tensor valid_distances = distances_squared.index_select(0, valid_indices); - torch::Tensor valid_unit_cell = unit_cell_offset.unsqueeze(0).repeat({valid_indices.size(0), 1}); - - all_index1.push_back(valid_base_indices); - all_unit_cell.push_back(valid_unit_cell); - all_distances_sq.push_back(valid_distances); - } - } - } - } - - // Single synchronization after all kernel launches - cudaDeviceSynchronize(); - - // Concatenate results - torch::Tensor final_indices, final_unit_cell, final_distances; - - if (all_index1.size() > 0) { - final_indices = torch::cat(all_index1); - final_unit_cell = torch::cat(all_unit_cell); - final_distances = torch::cat(all_distances_sq); - } else { - final_indices = torch::empty({0}, torch::dtype(torch::kLong).device(device)); - final_unit_cell = torch::empty({0, 3}, torch::dtype(pos1.dtype()).device(device)); - final_distances = torch::empty({0}, torch::dtype(pos1.dtype()).device(device)); - } - - return {final_indices, final_unit_cell, final_distances}; -} - -PYBIND11_MODULE(TORCH_EXTENSION_NAME, m) { - m.def("pbc_distance_cuda", &pbc_distance_cuda, "PBC distance computation with CUDA"); -} diff --git a/mace-bench/src/batchopt/pbc_graph.py b/mace-bench/src/batchopt/pbc_graph.py deleted file mode 100644 index 998b0477a7a2a125aaf19f0afbaf6a9eb80677a6..0000000000000000000000000000000000000000 --- a/mace-bench/src/batchopt/pbc_graph.py +++ /dev/null @@ -1,158 +0,0 @@ -""" -Copyright (c) 2025 Ma Zhaojia - -This source code is licensed under the MIT license found in the -LICENSE file in the root directory of this source tree. - -CUDA-accelerated PBC graph operations for atomic systems. -""" -import torch -from typing import Optional, List -from .pbc_graph_legacy import get_max_neighbors_mask -from .extensions.cuda_ops import get_pbc_graph_cuda_extension - -def radius_graph_pbc_cuda( - data, - radius, - max_num_neighbors_threshold, - enforce_max_neighbors_strictly: bool = False, - pbc=None, - dtype=torch.float64, -): - """ - Memory-efficient CUDA-accelerated version of radius_graph_pbc. - - This implementation follows the memory-efficient approach with triple loops - but accelerates the distance computation using CUDA kernels. - """ - if pbc is None: - pbc = [True, True, True] - - device = data.pos.device - batch_size = len(data.natoms) - - # Handle PBC settings - if hasattr(data, "pbc"): - data.pbc = torch.atleast_2d(data.pbc) - for i in range(3): - if not torch.any(data.pbc[:, i]).item(): - pbc[i] = False - elif torch.all(data.pbc[:, i]).item(): - pbc[i] = True - else: - raise RuntimeError( - "Different structures in the batch have different PBC configurations." - ) - - # position of the atoms - atom_pos = data.pos - - # Before computing the pairwise distances between atoms, first create a list of atom indices to compare for the entire batch - num_atoms_per_image = data.natoms - num_atoms_per_image_sqr = (num_atoms_per_image**2).long() - - # index offset between images - index_offset = torch.cumsum(num_atoms_per_image, dim=0) - num_atoms_per_image - - index_offset_expand = torch.repeat_interleave(index_offset, num_atoms_per_image_sqr) - num_atoms_per_image_expand = torch.repeat_interleave( - num_atoms_per_image, num_atoms_per_image_sqr - ) - - # Compute atom pair indices - num_atom_pairs = torch.sum(num_atoms_per_image_sqr) - index_sqr_offset = ( - torch.cumsum(num_atoms_per_image_sqr, dim=0) - num_atoms_per_image_sqr - ) - index_sqr_offset = torch.repeat_interleave( - index_sqr_offset, num_atoms_per_image_sqr - ) - atom_count_sqr = torch.arange(num_atom_pairs, device=device) - index_sqr_offset - - # Compute the indices for the pairs of atoms (using division and mod) - index1 = ( - torch.div(atom_count_sqr, num_atoms_per_image_expand, rounding_mode="floor") - ) + index_offset_expand - index2 = (atom_count_sqr % num_atoms_per_image_expand) + index_offset_expand - # Get the positions for each atom - pos1 = torch.index_select(atom_pos, 0, index1) - pos2 = torch.index_select(atom_pos, 0, index2) - - # Calculate required number of unit cells in each direction for PBC - cross_a2a3 = torch.cross(data.cell[:, 1], data.cell[:, 2], dim=-1) - cell_vol = torch.sum(data.cell[:, 0] * cross_a2a3, dim=-1, keepdim=True) - - if pbc[0]: - inv_min_dist_a1 = torch.norm(cross_a2a3 / cell_vol, p=2, dim=-1) - rep_a1 = torch.ceil(radius * inv_min_dist_a1) - else: - rep_a1 = data.cell.new_zeros(1) - - if pbc[1]: - cross_a3a1 = torch.cross(data.cell[:, 2], data.cell[:, 0], dim=-1) - inv_min_dist_a2 = torch.norm(cross_a3a1 / cell_vol, p=2, dim=-1) - rep_a2 = torch.ceil(radius * inv_min_dist_a2) - else: - rep_a2 = data.cell.new_zeros(1) - - if pbc[2]: - cross_a1a2 = torch.cross(data.cell[:, 0], data.cell[:, 1], dim=-1) - inv_min_dist_a3 = torch.norm(cross_a1a2 / cell_vol, p=2, dim=-1) - rep_a3 = torch.ceil(radius * inv_min_dist_a3) - else: - rep_a3 = data.cell.new_zeros(1) - - # Take the max over all images for uniformity - max_rep = [int(2*rep_a1.max().item()), int(2*rep_a2.max().item()), int(2*rep_a3.max().item())] - - # Pre-transpose data_cell for efficiency - data_cell = torch.transpose(data.cell, 1, 2) - - # Use CUDA kernel for the triple loop computation - # try: - pbc_graph_cuda = get_pbc_graph_cuda_extension() - - # Call the CUDA implementation - valid_pair_indices, unit_cell, atom_distance_sqr = pbc_graph_cuda.pbc_distance_cuda( - pos1, pos2, data_cell, - num_atoms_per_image_sqr, batch_size, max_rep, float(radius), device - ) - - # Map back to original index1 and index2 - if len(valid_pair_indices) > 0: - index1 = index1.index_select(0, valid_pair_indices.long()) - index2 = index2.index_select(0, valid_pair_indices.long()) - else: - index1 = torch.empty(0, dtype=torch.long, device=device) - index2 = torch.empty(0, dtype=torch.long, device=device) - unit_cell = torch.empty(0, 3, dtype=dtype, device=device) - atom_distance_sqr = torch.empty(0, dtype=dtype, device=device) - - # Sort index1 in ascending order and rearrange other arrays correspondingly - if len(index1) > 0: - sort_indices = torch.argsort(index1) - index1 = index1[sort_indices] - index2 = index2[sort_indices] - unit_cell = unit_cell[sort_indices] - atom_distance_sqr = atom_distance_sqr[sort_indices] - - mask_num_neighbors, num_neighbors_image = get_max_neighbors_mask( - natoms=data.natoms, - index=index1, - atom_distance=atom_distance_sqr, - max_num_neighbors_threshold=max_num_neighbors_threshold, - enforce_max_strictly=enforce_max_neighbors_strictly, - ) - - if not torch.all(mask_num_neighbors): - # Mask out the atoms to ensure each atom has at most max_num_neighbors_threshold neighbors - index1 = torch.masked_select(index1, mask_num_neighbors) - index2 = torch.masked_select(index2, mask_num_neighbors) - unit_cell = torch.masked_select( - unit_cell.view(-1, 3), mask_num_neighbors.view(-1, 1).expand(-1, 3) - ) - unit_cell = unit_cell.view(-1, 3) - - edge_index = torch.stack((index2, index1)) - - return edge_index, unit_cell, num_neighbors_image \ No newline at end of file diff --git a/mace-bench/src/batchopt/pbc_graph_legacy.py b/mace-bench/src/batchopt/pbc_graph_legacy.py deleted file mode 100644 index ca75c5368e84e36ca33a08cd1f0755948d36288f..0000000000000000000000000000000000000000 --- a/mace-bench/src/batchopt/pbc_graph_legacy.py +++ /dev/null @@ -1,563 +0,0 @@ -""" -Copyright (c) Meta, Inc. and its affiliates. - -This source code is licensed under the MIT license found in the -LICENSE file in the root directory of this source tree. -""" - -from __future__ import annotations - -from typing import TYPE_CHECKING, Any - -import numpy as np -import torch -import torch.nn as nn -import torch_geometric -from matplotlib.backends.backend_agg import FigureCanvasAgg as FigureCanvas -from matplotlib.figure import Figure -from torch_geometric.data import Data -from torch_geometric.utils import remove_self_loops -from torch_scatter import scatter, segment_coo, segment_csr - - -if TYPE_CHECKING: - from collections.abc import Mapping - - from torch.nn.modules.module import _IncompatibleKeys - - -DEFAULT_ENV_VARS = { - # Expandable segments is a new cuda feature that helps with memory fragmentation during frequent allocations (ie: in the case of variable batch sizes). - # see https://pytorch.org/docs/stable/notes/cuda.html. - "PYTORCH_CUDA_ALLOC_CONF": "expandable_segments:True", -} - - -def get_pbc_distances( - pos, - edge_index, - cell, - cell_offsets, - neighbors, - return_offsets: bool = False, - return_distance_vec: bool = False, -): - row, col = edge_index - - distance_vectors = pos[row] - pos[col] - - # correct for pbc - neighbors = neighbors.to(cell.device) - cell = torch.repeat_interleave(cell, neighbors, dim=0) - offsets = cell_offsets.float().view(-1, 1, 3).bmm(cell.float()).view(-1, 3) - distance_vectors += offsets - - # compute distances - distances = distance_vectors.norm(dim=-1) - - # redundancy: remove zero distances - nonzero_idx = torch.arange(len(distances), device=distances.device)[distances != 0] - edge_index = edge_index[:, nonzero_idx] - distances = distances[nonzero_idx] - - out = { - "edge_index": edge_index, - "distances": distances, - } - - if return_distance_vec: - out["distance_vec"] = distance_vectors[nonzero_idx] - - if return_offsets: - out["offsets"] = offsets[nonzero_idx] - - return out - -def radius_graph_pbc_mem_effi( - data, - radius, - max_num_neighbors_threshold, - enforce_max_neighbors_strictly: bool = False, - pbc=None, - dtype=torch.float64, -): - if pbc is None: - pbc = [True, True, True] - device = data.pos.device - batch_size = len(data.natoms) - - if hasattr(data, "pbc"): - data.pbc = torch.atleast_2d(data.pbc) - for i in range(3): - if not torch.any(data.pbc[:, i]).item(): - pbc[i] = False - elif torch.all(data.pbc[:, i]).item(): - pbc[i] = True - else: - raise RuntimeError( - "Different structures in the batch have different PBC configurations. This is not currently supported." - ) - - # position of the atoms - atom_pos = data.pos - - # Before computing the pairwise distances between atoms, first create a list of atom indices to compare for the entire batch - num_atoms_per_image = data.natoms - num_atoms_per_image_sqr = (num_atoms_per_image**2).long() - - # index offset between images - index_offset = torch.cumsum(num_atoms_per_image, dim=0) - num_atoms_per_image - - index_offset_expand = torch.repeat_interleave(index_offset, num_atoms_per_image_sqr) - num_atoms_per_image_expand = torch.repeat_interleave( - num_atoms_per_image, num_atoms_per_image_sqr - ) - - # Compute a tensor containing sequences of numbers that range from 0 to num_atoms_per_image_sqr for each image - # that is used to compute indices for the pairs of atoms. This is a very convoluted way to implement - # the following (but 10x faster since it removes the for loop) - # for batch_idx in range(batch_size): - # batch_count = torch.cat([batch_count, torch.arange(num_atoms_per_image_sqr[batch_idx], device=device)], dim=0) - num_atom_pairs = torch.sum(num_atoms_per_image_sqr) - index_sqr_offset = ( - torch.cumsum(num_atoms_per_image_sqr, dim=0) - num_atoms_per_image_sqr - ) - index_sqr_offset = torch.repeat_interleave( - index_sqr_offset, num_atoms_per_image_sqr - ) - atom_count_sqr = torch.arange(num_atom_pairs, device=device) - index_sqr_offset - - # Compute the indices for the pairs of atoms (using division and mod) - # If the systems get too large this apporach could run into numerical precision issues - index1 = ( - torch.div(atom_count_sqr, num_atoms_per_image_expand, rounding_mode="floor") - ) + index_offset_expand - index2 = (atom_count_sqr % num_atoms_per_image_expand) + index_offset_expand - # Get the positions for each atom - pos1 = torch.index_select(atom_pos, 0, index1) - pos2 = torch.index_select(atom_pos, 0, index2) - - # Calculate required number of unit cells in each direction. - # Smallest distance between planes separated by a1 is - # 1 / ||(a2 x a3) / V||_2, since a2 x a3 is the area of the plane. - # Note that the unit cell volume V = a1 * (a2 x a3) and that - # (a2 x a3) / V is also the reciprocal primitive vector - # (crystallographer's definition). - - cross_a2a3 = torch.cross(data.cell[:, 1], data.cell[:, 2], dim=-1) - cell_vol = torch.sum(data.cell[:, 0] * cross_a2a3, dim=-1, keepdim=True) - - if pbc[0]: - inv_min_dist_a1 = torch.norm(cross_a2a3 / cell_vol, p=2, dim=-1) - rep_a1 = torch.ceil(radius * inv_min_dist_a1) - else: - rep_a1 = data.cell.new_zeros(1) - - if pbc[1]: - cross_a3a1 = torch.cross(data.cell[:, 2], data.cell[:, 0], dim=-1) - inv_min_dist_a2 = torch.norm(cross_a3a1 / cell_vol, p=2, dim=-1) - rep_a2 = torch.ceil(radius * inv_min_dist_a2) - else: - rep_a2 = data.cell.new_zeros(1) - - if pbc[2]: - cross_a1a2 = torch.cross(data.cell[:, 0], data.cell[:, 1], dim=-1) - inv_min_dist_a3 = torch.norm(cross_a1a2 / cell_vol, p=2, dim=-1) - rep_a3 = torch.ceil(radius * inv_min_dist_a3) - else: - rep_a3 = data.cell.new_zeros(1) - - # Take the max over all images for uniformity. This is essentially padding. - # Note that this can significantly increase the number of computed distances - # if the required repetitions are very different between images - # (which they usually are). Changing this to sparse (scatter) operations - # might be worth the effort if this function becomes a bottleneck. - max_rep = [int(2*rep_a1.max().item()), int(2*rep_a2.max().item()), int(2*rep_a3.max().item())] - - # Memory-efficient implementation: iterate over unit cell offsets instead of expanding all at once - # This reduces memory usage by avoiding the creation of large tensor products - all_index1 = [] - all_index2 = [] - all_unit_cell = [] - all_atom_distance_sqr = [] - - # Pre-transpose data_cell for efficiency - data_cell = torch.transpose(data.cell, 1, 2) - - # Iterate over each unit cell offset combination - for i in range(-max_rep[0], max_rep[0] + 1): - for j in range(-max_rep[1], max_rep[1] + 1): - for k in range(-max_rep[2], max_rep[2] + 1): - # Create unit cell offset - unit_cell_offset = torch.tensor([i, j, k], device=device, dtype=dtype) - - # Compute the x, y, z positional offsets for this specific cell in each image - # unit_cell_offset_batch = unit_cell_offset.view(3, 1).expand(3, batch_size) - unit_cell_offset_batch = unit_cell_offset.view(1,3,1).expand(batch_size, -1, -1) - pbc_offsets = torch.bmm(data_cell, unit_cell_offset_batch).squeeze(-1) - pbc_offsets_per_atom = torch.repeat_interleave( - pbc_offsets, num_atoms_per_image_sqr, dim=0 - ) - - # Apply PBC offsets to the second atom positions - pos2_offset = pos2 + pbc_offsets_per_atom - - # Compute the squared distance between atoms - atom_distance_sqr = torch.sum((pos1 - pos2_offset) ** 2, dim=1) - - # Remove pairs that are too far apart - mask_within_radius = torch.le(atom_distance_sqr, radius * radius) - # Remove pairs with the same atoms (distance = 0.0) - mask_not_same = torch.gt(atom_distance_sqr, 0.0001) - mask = torch.logical_and(mask_within_radius, mask_not_same) - - # Only keep valid pairs for this unit cell offset - if torch.any(mask): - valid_index1 = torch.masked_select(index1, mask) - valid_index2 = torch.masked_select(index2, mask) - valid_distances = torch.masked_select(atom_distance_sqr, mask) - valid_unit_cell = unit_cell_offset.unsqueeze(0).repeat(valid_index1.shape[0], 1) - - all_index1.append(valid_index1) - all_index2.append(valid_index2) - all_unit_cell.append(valid_unit_cell) - all_atom_distance_sqr.append(valid_distances) - - # Concatenate all results - if len(all_index1) > 0: - index1 = torch.cat(all_index1) - index2 = torch.cat(all_index2) - unit_cell = torch.cat(all_unit_cell) - atom_distance_sqr = torch.cat(all_atom_distance_sqr) - - # Sort index1 in ascending order and rearrange other arrays correspondingly - sort_indices = torch.argsort(index1) - index1 = index1[sort_indices] - index2 = index2[sort_indices] - unit_cell = unit_cell[sort_indices] - atom_distance_sqr = atom_distance_sqr[sort_indices] - - else: - # No valid pairs found - index1 = torch.empty(0, dtype=torch.long, device=device) - index2 = torch.empty(0, dtype=torch.long, device=device) - unit_cell = torch.empty(0, 3, dtype=dtype, device=device) - atom_distance_sqr = torch.empty(0, dtype=dtype, device=device) - - mask_num_neighbors, num_neighbors_image = get_max_neighbors_mask( - natoms=data.natoms, - index=index1, - atom_distance=atom_distance_sqr, - max_num_neighbors_threshold=max_num_neighbors_threshold, - enforce_max_strictly=enforce_max_neighbors_strictly, - ) - - if not torch.all(mask_num_neighbors): - # Mask out the atoms to ensure each atom has at most max_num_neighbors_threshold neighbors - index1 = torch.masked_select(index1, mask_num_neighbors) - index2 = torch.masked_select(index2, mask_num_neighbors) - unit_cell = torch.masked_select( - unit_cell.view(-1, 3), mask_num_neighbors.view(-1, 1).expand(-1, 3) - ) - unit_cell = unit_cell.view(-1, 3) - - edge_index = torch.stack((index2, index1)) - - return edge_index, unit_cell, num_neighbors_image - - -def radius_graph_pbc( - data, - radius, - max_num_neighbors_threshold, - enforce_max_neighbors_strictly: bool = False, - pbc=None, - dtype=torch.float64, -): - if pbc is None: - pbc = [True, True, True] - device = data.pos.device - batch_size = len(data.natoms) - - if hasattr(data, "pbc"): - data.pbc = torch.atleast_2d(data.pbc) - for i in range(3): - if not torch.any(data.pbc[:, i]).item(): - pbc[i] = False - elif torch.all(data.pbc[:, i]).item(): - pbc[i] = True - else: - raise RuntimeError( - "Different structures in the batch have different PBC configurations. This is not currently supported." - ) - - # position of the atoms - atom_pos = data.pos - - # Before computing the pairwise distances between atoms, first create a list of atom indices to compare for the entire batch - num_atoms_per_image = data.natoms - num_atoms_per_image_sqr = (num_atoms_per_image**2).long() - - # index offset between images - index_offset = torch.cumsum(num_atoms_per_image, dim=0) - num_atoms_per_image - - index_offset_expand = torch.repeat_interleave(index_offset, num_atoms_per_image_sqr) - num_atoms_per_image_expand = torch.repeat_interleave( - num_atoms_per_image, num_atoms_per_image_sqr - ) - - # Compute a tensor containing sequences of numbers that range from 0 to num_atoms_per_image_sqr for each image - # that is used to compute indices for the pairs of atoms. This is a very convoluted way to implement - # the following (but 10x faster since it removes the for loop) - # for batch_idx in range(batch_size): - # batch_count = torch.cat([batch_count, torch.arange(num_atoms_per_image_sqr[batch_idx], device=device)], dim=0) - num_atom_pairs = torch.sum(num_atoms_per_image_sqr) - index_sqr_offset = ( - torch.cumsum(num_atoms_per_image_sqr, dim=0) - num_atoms_per_image_sqr - ) - index_sqr_offset = torch.repeat_interleave( - index_sqr_offset, num_atoms_per_image_sqr - ) - atom_count_sqr = torch.arange(num_atom_pairs, device=device) - index_sqr_offset - - # Compute the indices for the pairs of atoms (using division and mod) - # If the systems get too large this apporach could run into numerical precision issues - index1 = ( - torch.div(atom_count_sqr, num_atoms_per_image_expand, rounding_mode="floor") - ) + index_offset_expand - index2 = (atom_count_sqr % num_atoms_per_image_expand) + index_offset_expand - # Get the positions for each atom - pos1 = torch.index_select(atom_pos, 0, index1) - pos2 = torch.index_select(atom_pos, 0, index2) - - # Calculate required number of unit cells in each direction. - # Smallest distance between planes separated by a1 is - # 1 / ||(a2 x a3) / V||_2, since a2 x a3 is the area of the plane. - # Note that the unit cell volume V = a1 * (a2 x a3) and that - # (a2 x a3) / V is also the reciprocal primitive vector - # (crystallographer's definition). - - cross_a2a3 = torch.cross(data.cell[:, 1], data.cell[:, 2], dim=-1) - cell_vol = torch.sum(data.cell[:, 0] * cross_a2a3, dim=-1, keepdim=True) - - if pbc[0]: - inv_min_dist_a1 = torch.norm(cross_a2a3 / cell_vol, p=2, dim=-1) - rep_a1 = torch.ceil(radius * inv_min_dist_a1) - else: - rep_a1 = data.cell.new_zeros(1) - - if pbc[1]: - cross_a3a1 = torch.cross(data.cell[:, 2], data.cell[:, 0], dim=-1) - inv_min_dist_a2 = torch.norm(cross_a3a1 / cell_vol, p=2, dim=-1) - rep_a2 = torch.ceil(radius * inv_min_dist_a2) - else: - rep_a2 = data.cell.new_zeros(1) - - if pbc[2]: - cross_a1a2 = torch.cross(data.cell[:, 0], data.cell[:, 1], dim=-1) - inv_min_dist_a3 = torch.norm(cross_a1a2 / cell_vol, p=2, dim=-1) - rep_a3 = torch.ceil(radius * inv_min_dist_a3) - else: - rep_a3 = data.cell.new_zeros(1) - - # Take the max over all images for uniformity. This is essentially padding. - # Note that this can significantly increase the number of computed distances - # if the required repetitions are very different between images - # (which they usually are). Changing this to sparse (scatter) operations - # might be worth the effort if this function becomes a bottleneck. - max_rep = [2*rep_a1.max(), 2*rep_a2.max(), 2*rep_a3.max()] - # max_rep = [rep_a1.max(), rep_a2.max(), rep_a3.max()] - # max_rep = [torch.tensor(1, device=device)] * 3 - # logging.info(f"&&& max_rep: {max_rep}") - - # Tensor of unit cells - cells_per_dim = [ - torch.arange(-rep.item(), rep.item() + 1, device=device, dtype=dtype) - for rep in max_rep - ] - unit_cell = torch.cartesian_prod(*cells_per_dim) - num_cells = len(unit_cell) - unit_cell_per_atom = unit_cell.view(1, num_cells, 3).repeat(len(index2), 1, 1) - unit_cell = torch.transpose(unit_cell, 0, 1) - unit_cell_batch = unit_cell.view(1, 3, num_cells).expand(batch_size, -1, -1) - - # Compute the x, y, z positional offsets for each cell in each image - # data_cell = torch.transpose(data.cell, 1, 2) - data_cell = torch.transpose(data.cell, 1, 2) - pbc_offsets = torch.bmm(data_cell, unit_cell_batch) - pbc_offsets_per_atom = torch.repeat_interleave( - pbc_offsets, num_atoms_per_image_sqr, dim=0 - ) - - # Expand the positions and indices for the 9 cells - pos1 = pos1.view(-1, 3, 1).expand(-1, -1, num_cells) - pos2 = pos2.view(-1, 3, 1).expand(-1, -1, num_cells) - index1 = index1.view(-1, 1).repeat(1, num_cells).view(-1) - index2 = index2.view(-1, 1).repeat(1, num_cells).view(-1) - # Add the PBC offsets for the second atom - pos2 = pos2 + pbc_offsets_per_atom - - # Compute the squared distance between atoms - atom_distance_sqr = torch.sum((pos1 - pos2) ** 2, dim=1) - atom_distance_sqr = atom_distance_sqr.view(-1) - - # Remove pairs that are too far apart - mask_within_radius = torch.le(atom_distance_sqr, radius * radius) - # Remove pairs with the same atoms (distance = 0.0) - mask_not_same = torch.gt(atom_distance_sqr, 0.0001) - mask = torch.logical_and(mask_within_radius, mask_not_same) - index1 = torch.masked_select(index1, mask) - index2 = torch.masked_select(index2, mask) - unit_cell = torch.masked_select( - unit_cell_per_atom.view(-1, 3), mask.view(-1, 1).expand(-1, 3) - ) - unit_cell = unit_cell.view(-1, 3) - atom_distance_sqr = torch.masked_select(atom_distance_sqr, mask) - - mask_num_neighbors, num_neighbors_image = get_max_neighbors_mask( - natoms=data.natoms, - index=index1, - atom_distance=atom_distance_sqr, - max_num_neighbors_threshold=max_num_neighbors_threshold, - enforce_max_strictly=enforce_max_neighbors_strictly, - ) - - if not torch.all(mask_num_neighbors): - # Mask out the atoms to ensure each atom has at most max_num_neighbors_threshold neighbors - index1 = torch.masked_select(index1, mask_num_neighbors) - index2 = torch.masked_select(index2, mask_num_neighbors) - unit_cell = torch.masked_select( - unit_cell.view(-1, 3), mask_num_neighbors.view(-1, 1).expand(-1, 3) - ) - unit_cell = unit_cell.view(-1, 3) - - edge_index = torch.stack((index2, index1)) - - return edge_index, unit_cell, num_neighbors_image - - -@torch.compiler.disable -def get_max_neighbors_mask( - natoms, - index, - atom_distance, - max_num_neighbors_threshold, - degeneracy_tolerance: float = 0.01, - enforce_max_strictly: bool = False, -): - """ - Give a mask that filters out edges so that each atom has at most - `max_num_neighbors_threshold` neighbors. - Assumes that `index` is sorted. - - Enforcing the max strictly can force the arbitrary choice between - degenerate edges. This can lead to undesired behaviors; for - example, bulk formation energies which are not invariant to - unit cell choice. - - A degeneracy tolerance can help prevent sudden changes in edge - existence from small changes in atom position, for example, - rounding errors, slab relaxation, temperature, etc. - """ - - device = natoms.device - num_atoms = natoms.sum() - - # Get number of neighbors - # segment_coo assumes sorted index - ones = index.new_ones(1).expand_as(index) - num_neighbors = segment_coo(ones, index, dim_size=num_atoms) - max_num_neighbors = num_neighbors.max() - num_neighbors_thresholded = num_neighbors.clamp(max=max_num_neighbors_threshold) - - # Get number of (thresholded) neighbors per image - image_indptr = torch.zeros(natoms.shape[0] + 1, device=device, dtype=torch.long) - image_indptr[1:] = torch.cumsum(natoms, dim=0) - num_neighbors_image = segment_csr(num_neighbors_thresholded, image_indptr) - - # If max_num_neighbors is below the threshold, return early - if ( - max_num_neighbors <= max_num_neighbors_threshold - or max_num_neighbors_threshold <= 0 - ): - mask_num_neighbors = torch.tensor([True], dtype=bool, device=device).expand_as( - index - ) - return mask_num_neighbors, num_neighbors_image - - # Create a tensor of size [num_atoms, max_num_neighbors] to sort the distances of the neighbors. - # Fill with infinity so we can easily remove unused distances later. - distance_sort = torch.full([num_atoms * max_num_neighbors], np.inf, device=device) - - # Create an index map to map distances from atom_distance to distance_sort - # index_sort_map assumes index to be sorted - index_neighbor_offset = torch.cumsum(num_neighbors, dim=0) - num_neighbors - index_neighbor_offset_expand = torch.repeat_interleave( - index_neighbor_offset, num_neighbors - ) - index_sort_map = ( - index * max_num_neighbors - + torch.arange(len(index), device=device) - - index_neighbor_offset_expand - ) - distance_sort.index_copy_(0, index_sort_map, atom_distance) - distance_sort = distance_sort.view(num_atoms, max_num_neighbors) - - # Sort neighboring atoms based on distance - distance_sort, index_sort = torch.sort(distance_sort, dim=1) - - # Select the max_num_neighbors_threshold neighbors that are closest - if enforce_max_strictly: - distance_sort = distance_sort[:, :max_num_neighbors_threshold] - index_sort = index_sort[:, :max_num_neighbors_threshold] - max_num_included = max_num_neighbors_threshold - - else: - effective_cutoff = ( - distance_sort[:, max_num_neighbors_threshold] + degeneracy_tolerance - ) - is_included = torch.le(distance_sort.T, effective_cutoff) - - # Set all undesired edges to infinite length to be removed later - distance_sort[~is_included.T] = np.inf - - # Subselect tensors for efficiency - num_included_per_atom = torch.sum(is_included, dim=0) - max_num_included = torch.max(num_included_per_atom) - distance_sort = distance_sort[:, :max_num_included] - index_sort = index_sort[:, :max_num_included] - - # Recompute the number of neighbors - num_neighbors_thresholded = num_neighbors.clamp(max=num_included_per_atom) - - num_neighbors_image = segment_csr(num_neighbors_thresholded, image_indptr) - - # Offset index_sort so that it indexes into index - index_sort = index_sort + index_neighbor_offset.view(-1, 1).expand( - -1, max_num_included - ) - # Remove "unused pairs" with infinite distances - mask_finite = torch.isfinite(distance_sort) - index_sort = torch.masked_select(index_sort, mask_finite) - - # At this point index_sort contains the index into index of the - # closest max_num_neighbors_threshold neighbors per atom - # Create a mask to remove all pairs not in index_sort - mask_num_neighbors = torch.zeros(len(index), device=device, dtype=bool) - mask_num_neighbors.index_fill_(0, index_sort, True) - - return mask_num_neighbors, num_neighbors_image - - -def get_pruned_edge_idx( - edge_index, num_atoms: int, max_neigh: float = 1e9 -) -> torch.Tensor: - assert num_atoms is not None # TODO: Shouldn't be necessary - - # removes neighbors > max_neigh - # assumes neighbors are sorted in increasing distance - _nonmax_idx_list = [] - for i in range(num_atoms): - idx_i = torch.arange(len(edge_index[1]))[(edge_index[1] == i)][:max_neigh] - _nonmax_idx_list.append(idx_i) - return torch.cat(_nonmax_idx_list) diff --git a/mace-bench/src/batchopt/relaxation/__init__.py b/mace-bench/src/batchopt/relaxation/__init__.py deleted file mode 100644 index b2facb46343dd01b9921119b3d3ad060612c2f45..0000000000000000000000000000000000000000 --- a/mace-bench/src/batchopt/relaxation/__init__.py +++ /dev/null @@ -1,11 +0,0 @@ -""" -Copyright (c) Meta, Inc. and its affiliates. - -This source code is licensed under the MIT license found in the -LICENSE file in the root directory of this source tree. -""" - -from __future__ import annotations -from .optimizable import OptimizableBatch, OptimizableUnitCellBatch - -__all__ = ["ml_relax", "OptimizableBatch", "OptimizableUnitCellBatch"] diff --git a/mace-bench/src/batchopt/relaxation/ase_utils.py b/mace-bench/src/batchopt/relaxation/ase_utils.py deleted file mode 100644 index b2bd4e967d442e970bf349991f2c721b419953f1..0000000000000000000000000000000000000000 --- a/mace-bench/src/batchopt/relaxation/ase_utils.py +++ /dev/null @@ -1,95 +0,0 @@ -""" -Copyright (c) Meta, Inc. and its affiliates. - -This source code is licensed under the MIT license found in the -LICENSE file in the root directory of this source tree. - - - -Utilities to interface OCP models/trainers with the Atomic Simulation -Environment (ASE) -""" - -from __future__ import annotations - -from types import MappingProxyType -from typing import TYPE_CHECKING - -import torch -from ase import Atoms -from ase.calculators.singlepoint import SinglePointCalculator -from ase.constraints import FixAtoms - -if TYPE_CHECKING: - from torch_geometric.data import Batch - - -# system level model predictions have different shapes than expected by ASE -ASE_PROP_RESHAPE = MappingProxyType( - {"stress": (-1, 3, 3), "dielectric_tensor": (-1, 3, 3)} -) - - -def batch_to_atoms( - batch: Batch, - results: dict[str, torch.Tensor] | None = None, - wrap_pos: bool = True, - eps: float = 1e-7, -) -> list[Atoms]: - """Convert a data batch to ase Atoms - - Args: - batch: data batch - results: dictionary with predicted result tensors that will be added to a SinglePointCalculator. If no results - are given no calculator will be added to the atoms objects. - wrap_pos: wrap positions back into the cell. - eps: Small number to prevent slightly negative coordinates from being wrapped. - - Returns: - list of Atoms - """ - n_systems = batch.natoms.shape[0] - natoms = batch.natoms.tolist() - numbers = torch.split(batch.atomic_numbers, natoms) - fixed = torch.split(batch.fixed.to(torch.bool), natoms) - if results is not None: - results = { - key: val.view(ASE_PROP_RESHAPE.get(key, -1)).tolist() - if len(val) == len(batch) - else [v.cpu().detach().numpy() for v in torch.split(val, natoms)] - for key, val in results.items() - } - - positions = torch.split(batch.pos, natoms) - tags = torch.split(batch.tags, natoms) - cells = batch.cell - - atoms_objects = [] - for idx in range(n_systems): - pos = positions[idx].cpu().detach().numpy() - cell = cells[idx].cpu().detach().numpy() - - # TODO take pbc from data - # TODO: &&& ^^^ change this back !!! - # if wrap_pos: - # pos = wrap_positions(pos, cell, pbc=[True, True, True], eps=eps) - - atoms = Atoms( - numbers=numbers[idx].tolist(), - cell=cell, - positions=pos, - tags=tags[idx].tolist(), - constraint=FixAtoms(mask=fixed[idx].tolist()), - pbc=[True, True, True], - ) - - if results is not None: - calc = SinglePointCalculator( - atoms=atoms, **{key: val[idx] for key, val in results.items()} - ) - atoms.set_calculator(calc) - - atoms_objects.append(atoms) - - return atoms_objects - diff --git a/mace-bench/src/batchopt/relaxation/optimizable.py b/mace-bench/src/batchopt/relaxation/optimizable.py deleted file mode 100644 index 3dc9623af4ad3a1f3a7e169703af10ee4c4a97a1..0000000000000000000000000000000000000000 --- a/mace-bench/src/batchopt/relaxation/optimizable.py +++ /dev/null @@ -1,791 +0,0 @@ -""" -Copyright (c) Meta, Inc. and its affiliates. -Copyright (c) 2025 Ma Zhaojia - -This source code is licensed under the MIT license found in the -LICENSE file in the root directory of this source tree. - -Modified from original Meta implementation. -""" - -from __future__ import annotations - -from functools import cached_property -from types import SimpleNamespace -from typing import TYPE_CHECKING, ClassVar, Any, Generator -import numpy as np -import torch -import logging -from ase.calculators.calculator import PropertyNotImplementedError -from ase.stress import voigt_6_to_full_3x3_stress -from torch_scatter import scatter - -from batchopt.relaxation.ase_utils import batch_to_atoms - - -# Define dummy classes for when imports fail -class _DummyCalculator: - pass - - -try: - from mace.calculators import MACECalculator -except ImportError: - logging.warning("Unable to import MACECalculator.") - MACECalculator = _DummyCalculator - -try: - from chgnet.model.dynamics import CHGNetCalculator -except ImportError: - logging.warning("Unable to import CHGNetCalculator.") - CHGNetCalculator = _DummyCalculator - -try: - from sevenn.calculator import ( - SevenNetCalculator, - SevenNetD3Calculator, - D3Calculator, - ) -except ImportError: - logging.warning("Unable to import SevenNetCalculator.") - SevenNetCalculator = _DummyCalculator - SevenNetD3Calculator = _DummyCalculator - D3Calculator = _DummyCalculator - -try: - from fairchem.core import pretrained_mlip, FAIRChemCalculator -except ImportError: - logging.warning("Unable to import FAIRChemCalculator.") - FAIRChemCalculator = _DummyCalculator - - -# this can be removed after pinning ASE dependency >= 3.23 -try: - from ase.optimize.optimize import Optimizable -except ImportError: - - class Optimizable: - pass - - -if TYPE_CHECKING: - from collections.abc import Sequence - - from ase import Atoms - from numpy.typing import NDArray - from torch_geometric.data import Batch - - -ALL_CHANGES: set[str] = { - "pos", - "atomic_numbers", - "cell", - "pbc", -} - - -# @torch.compile -def compare_batches( - batch1: Batch | None, - batch2: Batch, - tol: float = 1e-6, - excluded_properties: set[str] | None = None, -) -> list[str]: - """Compare properties between two batches - - Args: - batch1: atoms batch - batch2: atoms batch - tol: tolerance used to compare equility of floating point properties - excluded_properties: list of properties to exclude from comparison - - Returns: - list of system changes, property names that are differente between batch1 and batch2 - """ - system_changes = [] - - if batch1 is None: - system_changes = ALL_CHANGES - else: - properties_to_check = set(ALL_CHANGES) - if excluded_properties: - properties_to_check -= set(excluded_properties) - - # Check properties that aren't - for prop in ALL_CHANGES: - if prop in properties_to_check: - properties_to_check.remove(prop) - if not torch.allclose( - getattr(batch1, prop), getattr(batch2, prop), atol=tol - ): - system_changes.append(prop) - - return system_changes - - -class OptimizableBatch(Optimizable): - """A Batch version of ase Optimizable Atoms - - This class can be used with ML relaxations in fairchem.core.relaxations.ml_relaxation - or in ase relaxations classes, i.e. ase.optimize.lbfgs - """ - - ignored_changes: ClassVar[set[str]] = set() - - def __init__( - self, - batch: Batch, - trainer: Any, # Any calculator type (MACECalculator | CHGNetCalculator | SevenNetCalculator | FAIRChemCalculator) - transform: torch.nn.Module | None = None, - mask_converged: bool = True, - numpy: bool = False, - masked_eps: float = 1e-8, - compute_stress: bool = False, - use_fast_predict: bool = True, - dtype: torch.dtype = torch.float64, - ): - """Initialize Optimizable Batch - - Args: - batch: A batch of atoms graph data - model: An instance of a BaseTrainer derived class - transform: graph transform - mask_converged: if true will mask systems in batch that are already converged - numpy: whether to cast results to numpy arrays - masked_eps: masking systems that are converged when using ASE optimizers results in divisions by zero - from zero differences in masked positions at future steps, we add a small number to prevent this. - compute_stress: whether to compute stress during prediction - use_fast_predict: use fast prediction method when available - dtype: data type for tensor operations (torch.float32 or torch.float64) - """ - self.batch = batch.to(trainer.device) - self.trainer = trainer - self.transform = transform - self.numpy = numpy - self.mask_converged = mask_converged - self._cached_batch = None - self._update_mask = None - self.torch_results = {} - self.results = {} - self._eps = masked_eps - self.dtype = dtype - - self.otf_graph = True # trainer._unwrapped_model.otf_graph - if not self.otf_graph and "edge_index" not in self.batch: - self.update_graph() - - self.batch.pos = self.batch.pos.to(dtype=self.dtype) - self.batch.cell = self.batch.cell.to(dtype=self.dtype) - self.compute_stress = compute_stress - self.use_fast_predict = use_fast_predict - - # Determine calculator type once during initialization for efficiency - self._calculator_type = self._determine_calculator_type() - logging.info( - f"OptimizableBatch initialized with calculator type: {self._calculator_type}" - ) - - def _determine_calculator_type(self) -> str: - """Determine the type of calculator to avoid repeated isinstance checks.""" - # Check against actual imported classes, not dummy classes - trainer_class_name = type(self.trainer).__name__ - trainer_module = type(self.trainer).__module__ - - if ( - "mace" in trainer_module.lower() - or trainer_class_name == "MACECalculator" - ): - return "mace" - elif ( - "chgnet" in trainer_module.lower() - or trainer_class_name == "CHGNetCalculator" - ): - return "chgnet" - elif "sevenn" in trainer_module.lower() or trainer_class_name in [ - "SevenNetCalculator", - "SevenNetD3Calculator", - "D3Calculator", - ]: - return "sevennet" - elif ( - "fairchem" in trainer_module.lower() - or trainer_class_name == "FAIRChemCalculator" - ): - return "fairchem" - else: - return "default" - - @property - def device(self): - return self.trainer.device - - @property - def batch_indices(self): - """Get the batch indices specifying which position/force corresponds to which batch.""" - return self.batch.batch - - @property - def converged_mask(self): - if self._update_mask is not None: - return torch.logical_not(self._update_mask) - return None - - @property - def update_mask(self): - if self._update_mask is None: - return torch.ones(len(self.batch), dtype=bool) - return self._update_mask - - @property - def converge_indices_list(self): - return torch.where(~self.update_mask)[0].tolist() - - @property - def elem_per_group(self): - # This return value actually represents the number of elements - # in a group within a batch. Each group corresponds to batch_indices. - # It will count the number of CELL elements in each group. - return torch.bincount(self.batch_indices) - - @property - def batch_size(self): - return len(torch.unique(self.batch_indices)) - - def check_state(self, batch: Batch, tol: float = 1e-12) -> bool: - """Check for any system changes since last calculation.""" - return compare_batches( - self._cached_batch, - batch, - tol=tol, - excluded_properties=set(self.ignored_changes), - ) - - def _predict(self) -> None: - """Run prediction if batch has any changes.""" - # TODO: Currently, the batch inference interfaces of various models are not unified and are poorly implemented. - system_changes = self.check_state(self.batch) - if len(system_changes) > 0: - if self._calculator_type == "mace": - # FIXME: &&& - # for key, val in self.batch.to_dict().items(): - # print(f'&&& key: {key}, val: {val}') - # self.torch_results = self.trainer.predict_debug(atoms_list, self.batch, compute_stress=self.compute_stress) - # self.torch_results = self.trainer.predict(self.config_batch) - if self.use_fast_predict: - self.torch_results = self.trainer.fast_predict( - self.batch, compute_stress=self.compute_stress - ) - self.batch.pos = self.batch.pos.to(self.dtype) - self.batch.cell = self.batch.cell.to(self.dtype) - else: - atoms_list = batch_to_atoms( - self.batch, results=None, wrap_pos=False, eps=1e-17 - ) - self.torch_results = self.trainer.predict( - atoms_list, compute_stress=self.compute_stress - ) - elif self._calculator_type == "fairchem": - # TODO: FAIRChemCalculator does not support batch prediction yet - atoms_list = batch_to_atoms( - self.batch, results=None, wrap_pos=False, eps=1e-17 - ) - self.torch_results = self.trainer.predict(atoms_list=atoms_list) - elif self._calculator_type == "chgnet": - atoms_list = batch_to_atoms( - self.batch, results=None, wrap_pos=False, eps=1e-17 - ) - model_prediction = self.trainer.predict( - atoms_list=atoms_list, task="efs" - ) - results = { - "energy": torch.tensor( - [pred["e"].item() for pred in model_prediction], - device=self.device, - dtype=self.dtype, - ), - "forces": torch.vstack( - [ - torch.from_numpy(pred["f"]).to( - device=self.device, dtype=self.dtype - ) - for pred in model_prediction - ] - ), - "stress": torch.vstack( - [ - torch.from_numpy(pred["s"]).to( - device=self.device, dtype=self.dtype - ) - for pred in model_prediction - ] - ).view(-1, 3, 3), - } - self.torch_results = results - elif self._calculator_type == "sevennet": - atoms_list = batch_to_atoms( - self.batch, results=None, wrap_pos=False, eps=1e-17 - ) - self.torch_results = self.trainer.predict(atoms_list=atoms_list) - else: # default case - self.torch_results = self.trainer.predict( - self.batch, per_image=False, disable_tqdm=True - ) - # save only subset of props in simple namespace instead of cloning the whole batch to save memory - changes = ALL_CHANGES - set(self.ignored_changes) - self._cached_batch = SimpleNamespace( - **{prop: self.batch[prop].clone() for prop in changes} - ) - - def get_property( - self, name, no_numpy: bool = False - ) -> torch.Tensor | NDArray: - """Get a predicted property by name.""" - self._predict() - if self.numpy: - self.results = { - key: pred.item() if pred.numel() == 1 else pred.cpu().numpy() - for key, pred in self.torch_results.items() - } - else: - self.results = self.torch_results - - if name not in self.results: - raise PropertyNotImplementedError( - f"{name} not present in this calculation" - ) - - return ( - self.results[name] - if no_numpy is False - else self.torch_results[name] - ) - - def get_positions(self) -> torch.Tensor | NDArray: - """Get the batch positions""" - pos = self.batch.pos.clone() - if self.numpy: - if self.mask_converged: - pos[~self.update_mask[self.batch.batch]] = self._eps - pos = pos.cpu().numpy() - - return pos - - def set_positions(self, positions: torch.Tensor | NDArray) -> None: - """Set the atom positions in the batch.""" - if isinstance(positions, np.ndarray): - positions = torch.tensor( - positions, dtype=self.dtype, device=self.device - ) - else: - positions = positions.to(dtype=self.dtype, device=self.device) - - if self.mask_converged and self._update_mask is not None: - mask = self.update_mask[self.batch.batch] - self.batch.pos[mask] = positions[mask] - else: - self.batch.pos = positions - - if not self.otf_graph: - self.update_graph() - - def get_forces( - self, apply_constraint: bool = False, no_numpy: bool = False - ) -> torch.Tensor | NDArray: - """Get predicted batch forces.""" - forces = self.get_property("forces", no_numpy=no_numpy) - if apply_constraint: - fixed_idx = torch.where(self.batch.fixed == 1)[0] - if isinstance(forces, np.ndarray): - fixed_idx = fixed_idx.tolist() - forces[fixed_idx] = 0.0 - return forces.view(-1, 3) - - def get_potential_energy(self, **kwargs) -> torch.Tensor | NDArray: - """Get predicted energy as the sum of all batch energies.""" - # ASE 3.22.1 expects a check for force_consistent calculations - if kwargs.get("force_consistent", False) is True: - raise PropertyNotImplementedError( - "force_consistent calculations are not implemented" - ) - if ( - len(self.batch) == 1 - ): # unfortunately batch size 1 returns a float, not a tensor - return self.get_property("energy") - return self.get_property("energy").sum() - - def get_potential_energies(self) -> torch.Tensor | NDArray: - """Get the predicted energy for each system in batch.""" - return self.get_property("energy") - - def get_cells(self) -> torch.Tensor: - """Get batch crystallographic cells.""" - return self.batch.cell - - def set_cells( - self, cells: torch.Tensor | NDArray, scale_atoms=False - ) -> None: - """Set batch cells.""" - assert self.batch.cell.shape == cells.shape, "Cell shape mismatch" - if isinstance(cells, np.ndarray): - cells = torch.tensor(cells, dtype=self.dtype, device=self.device) - cells = cells.to(dtype=self.dtype, device=self.device) - if scale_atoms: - from ase.geometry.cell import complete_cell - - # M = torch.linalg.solve( - # self.batch.cell.view(-1, 3, 3), - # cells.view(-1, 3, 3), - # ) - # TODO: need to implement a sparse version. - # tmp_pos = torch.matmul(self.batch.pos, M.reshape(-1,3)) - for i in range(self.batch_size): - if not self.update_mask[i]: - continue - M = np.linalg.solve( - complete_cell(self.batch.cell[i].cpu().detach().numpy()), - complete_cell(cells[i].cpu().detach().numpy()), - ) - pos_update_mask = self.batch.batch == i - self.batch.pos[pos_update_mask] = torch.matmul( - self.batch.pos[pos_update_mask], - torch.from_numpy(M).to(self.device).reshape(-1, 3), - ) - self.batch.cell[self.update_mask] = cells[self.update_mask] - - def get_volumes(self) -> torch.Tensor: - """Get a tensor of volumes for each cell in batch""" - cells = self.get_cells() - return torch.linalg.det(cells) - - def iterimages(self) -> Generator[Batch, None, None]: - # XXX document purpose of iterimages - this is just needed to work with ASE optimizers - yield self.batch - - def get_max_forces( - self, forces: torch.Tensor | None = None, apply_constraint: bool = False - ) -> torch.Tensor: - """Get the maximum forces per structure in batch""" - if forces is None: - forces = self.get_forces( - apply_constraint=apply_constraint, no_numpy=True - ) - return scatter( - (forces**2).sum(axis=1).sqrt(), self.batch_indices, reduce="max" - ) - - def converged( - self, - forces: torch.Tensor | NDArray | None, - fmax: float, - max_forces: torch.Tensor | None = None, - f_upper_limit: float = 1e20, - ) -> bool: - """Check if norm of all predicted forces are below fmax""" - if forces is not None: - if isinstance(forces, np.ndarray): - forces = torch.tensor( - forces, device=self.device, dtype=self.dtype - ) - max_forces = self.get_max_forces(forces) - elif max_forces is None: - max_forces = self.get_max_forces() - - # Update mask is True for forces that are greater than fmax AND less than f_upper_limit - update_mask = torch.logical_and( - max_forces.ge(fmax), max_forces.le(f_upper_limit) - ) - # update cached mask - if self.mask_converged: - if self._update_mask is None: - self._update_mask = update_mask - else: - # some models can have random noise in their predictions, so the mask is updated by - # keeping all previously converged structures masked even if new force predictions - # push it slightly above threshold - self._update_mask = torch.logical_and( - self._update_mask, update_mask - ) - update_mask = self._update_mask - - return not torch.any(update_mask).item() - - def get_atoms_list(self) -> list[Atoms]: - """Get ase Atoms objects corresponding to the batch""" - self._predict() # in case no predictions have been run - return batch_to_atoms(self.batch, results=self.torch_results) - - def update_graph(self): - """Update the graph if model does not use otf_graph.""" - graph = self.trainer._unwrapped_model.generate_graph(self.batch) - self.batch.edge_index = graph.edge_index - self.batch.cell_offsets = graph.cell_offsets - self.batch.neighbors = graph.neighbors - if self.transform is not None: - self.batch = self.transform(self.batch) - - def __len__(self) -> int: - # TODO: this might be changed in ASE to be 3 * len(self.atoms) - return len(self.batch.pos) - - -class OptimizableUnitCellBatch(OptimizableBatch): - """Modify the supercell and the atom positions in relaxations. - - Based on ase UnitCellFilter to work on data batches - """ - - def __init__( - self, - batch: Batch, - trainer: Any, # Any calculator type (MACECalculator | CHGNetCalculator | SevenNetD3Calculator | FAIRChemCalculator) - transform: torch.nn.Module | None = None, - numpy: bool = False, - mask_converged: bool = True, - mask: Sequence[bool] | None = None, - cell_factor: float | torch.Tensor | None = None, - hydrostatic_strain: bool = False, - constant_volume: bool = False, - scalar_pressure: float = 0.0, - masked_eps: float = 1e-8, - use_fast_predict: bool = True, - dtype: torch.dtype = torch.float64, - ): - """Create a filter that returns the forces and unit cell stresses together, for simultaneous optimization. - - For full details see: - E. B. Tadmor, G. S. Smith, N. Bernstein, and E. Kaxiras, - Phys. Rev. B 59, 235 (1999) - - Args: - batch: A batch of atoms graph data - model: An instance of a BaseTrainer derived class - transform: graph transform - numpy: whether to cast results to numpy arrays - mask_converged: if true will mask systems in batch that are already converged - mask: a boolean mask specifying which strain components are allowed to relax - cell_factor: - Factor by which deformation gradient is multiplied to put - it on the same scale as the positions when assembling - the combined position/cell vector. The stress contribution to - the forces is scaled down by the same factor. This can be thought - of as a very simple preconditioner. Default is number of atoms - which gives approximately the correct scaling. - hydrostatic_strain: - Constrain the cell by only allowing hydrostatic deformation. - The virial tensor is replaced by np.diag([np.trace(virial)]*3). - constant_volume: - Project out the diagonal elements of the virial tensor to allow - relaxations at constant volume, e.g. for mapping out an - energy-volume curve. Note: this only approximately conserves - the volume and breaks energy/force consistency so can only be - used with optimizers that do require a line minimisation - (e.g. FIRE). - scalar_pressure: - Applied pressure to use for enthalpy pV term. As above, this - breaks energy/force consistency. - masked_eps: masking systems that are converged when using ASE optimizers results in divisions by zero - from zero differences in masked positions at future steps, we add a small number to prevent this. - dtype: data type for tensor operations (torch.float32 or torch.float64) - """ - super().__init__( - batch=batch, - trainer=trainer, - transform=transform, - numpy=numpy, - mask_converged=mask_converged, - masked_eps=masked_eps, - compute_stress=True, - use_fast_predict=use_fast_predict, - dtype=dtype, - ) - - self.orig_cells = self.get_cells().clone() - self.stress = None - - if mask is None: - # mask = torch.eye(3, device=self.device) - mask = torch.ones(6, device=self.device) - - # TODO make sure mask is on GPU - if mask.shape == (6,): - self.mask = torch.tensor( - voigt_6_to_full_3x3_stress(mask.detach().cpu()), - device=self.device, - ) - elif mask.shape == (3, 3): - self.mask = mask - else: - raise ValueError("shape of mask should be (3,3) or (6,)") - - if isinstance(cell_factor, float): - cell_factor = cell_factor * torch.ones( - (3 * len(batch), 1), requires_grad=False - ) - if cell_factor is None: - cell_factor = self.batch.natoms.repeat_interleave(3).unsqueeze( - dim=1 - ) - - self.hydrostatic_strain = hydrostatic_strain - self.constant_volume = constant_volume - self.pressure = scalar_pressure * torch.eye(3, device=self.device) - self.cell_factor = cell_factor - self.stress = None - self._batch_trace = torch.vmap(torch.trace) - self._batch_diag = torch.vmap( - lambda x: x * torch.eye(3, device=x.device) - ) - - @cached_property - def batch_indices(self): - """Get the batch indices specifying which position/force corresponds to which batch. - - We augment this to specify the batch indices for augmented positions and forces. - """ - augmented_batch = torch.repeat_interleave( - torch.arange( - len(self.batch), - dtype=self.batch.batch.dtype, - device=self.device, - ), - 3, - ) - return torch.cat([self.batch.batch, augmented_batch]) - - def deform_grad(self): - """Get the cell deformation matrix""" - return torch.transpose( - torch.linalg.solve(self.orig_cells, self.get_cells()), 1, 2 - ) - - def get_positions(self): - """Get positions and cell deformation gradient.""" - cur_deform_grad = self.deform_grad() - natoms = self.batch.num_nodes - pos = torch.zeros( - (natoms + 3 * len(self.get_cells()), 3), - dtype=self.batch.pos.dtype, - device=self.device, - ) - - # Augmented positions are the self.atoms.positions but without the applied deformation gradient - pos[:natoms] = torch.linalg.solve( - cur_deform_grad[self.batch.batch, :, :], - self.batch.pos.view(-1, 3, 1), - ).view(-1, 3) - # cell DOFs are the deformation gradient times a scaling factor - pos[natoms:] = self.cell_factor * cur_deform_grad.view(-1, 3) - return pos.cpu().numpy() if self.numpy else pos - - def set_positions(self, positions: torch.Tensor | NDArray) -> None: - """Set positions and cell. - - positions has shape (natoms + ncells * 3, 3). - the first natoms rows are the positions of the atoms, the last nsystems * three rows are the deformation tensor - for each cell. - """ - if isinstance(positions, np.ndarray): - positions = torch.tensor( - positions, dtype=self.dtype, device=self.device - ) - else: - positions = positions.to(dtype=self.dtype, device=self.device) - - natoms = self.batch.num_nodes - new_atom_positions = positions[:natoms] - new_deform_grad = (positions[natoms:] / self.cell_factor).view(-1, 3, 3) - - # TODO check that in fact symmetry is preserved setting cells and positions - # Set the new cell from the original cell and the new deformation gradient. Both current and final structures - # should preserve symmetry. - new_cells = torch.bmm( - self.orig_cells, torch.transpose(new_deform_grad, 1, 2) - ) - self.set_cells(new_cells) - - # Set the positions from the ones passed in (which are without the deformation gradient applied) and the new - # deformation gradient. This should also preserve symmetry - new_atom_positions = torch.bmm( - new_atom_positions.view(-1, 1, 3), - torch.transpose( - new_deform_grad[self.batch.batch, :, :].view(-1, 3, 3), 1, 2 - ), - ) - super().set_positions(new_atom_positions.view(-1, 3)) - - def get_potential_energy(self, **kwargs): - """ - returns potential energy including enthalpy PV term. - """ - atoms_energy = super().get_potential_energy(**kwargs) - return atoms_energy + self.pressure[0, 0] * self.get_volumes().sum() - - def get_forces( - self, apply_constraint: bool = False, no_numpy: bool = False - ) -> torch.Tensor | NDArray: - """Get forces and unit cell stress.""" - stress = self.get_property("stress", no_numpy=True).view(-1, 3, 3) - atom_forces = self.get_property("forces", no_numpy=True) - - if apply_constraint: - fixed_idx = torch.where(self.batch.fixed == 1)[0] - atom_forces[fixed_idx] = 0.0 - - volumes = self.get_volumes().view(-1, 1, 1) - # virial = -volumes * stress + self.pressure.view(-1, 3, 3) - virial = -volumes * (stress + self.pressure.view(-1, 3, 3)) - # print(f'&&& virial0: {virial}') - cur_deform_grad = self.deform_grad() - atom_forces = torch.bmm( - atom_forces.view(-1, 1, 3), - cur_deform_grad[self.batch.batch, :, :].view(-1, 3, 3), - ) - virial = torch.linalg.solve( - cur_deform_grad, torch.transpose(virial, dim0=1, dim1=2) - ) - virial = torch.transpose(virial, dim0=1, dim1=2) - - # print(f'&&& virial1: {virial}') - - # TODO this does not work yet! maybe _batch_trace gives an issue - if self.hydrostatic_strain: - virial = self._batch_diag(self._batch_trace(virial) / 3.0) - - # Zero out components corresponding to fixed lattice elements - if (self.mask != 1.0).any(): - virial *= self.mask.view(-1, 3, 3) - - if self.constant_volume: - virial[:, range(3), range(3)] -= ( - self._batch_trace(virial).view(3, -1) / 3.0 - ) - - natoms = self.batch.num_nodes - augmented_forces = torch.zeros( - (natoms + 3 * len(self.get_cells()), 3), - device=self.device, - dtype=atom_forces.dtype, - ) - # print(f'&&& atom_forces: {atom_forces}') - # print(f'&&& virial2: {virial}') - augmented_forces[:natoms] = atom_forces.view(-1, 3) - augmented_forces[natoms:] = virial.view(-1, 3) / self.cell_factor - - self.stress = -virial.view(-1, 9) / volumes.view(-1, 1) - - if self.numpy and not no_numpy: - augmented_forces = augmented_forces.cpu().numpy() - - # print(f'&&& augmented_forces: {augmented_forces}') - - return augmented_forces - - def __len__(self): - return len(self.batch.pos) + 3 * len(self.batch) - - def get_potential_energies(self) -> torch.Tensor: - """Get the predicted energy for each system in batch.""" - return ( - self.get_property("energy").view(-1) - + self.pressure[0, 0] * self.get_volumes() - ) diff --git a/mace-bench/src/batchopt/relaxation/optimizers/__init__.py b/mace-bench/src/batchopt/relaxation/optimizers/__init__.py deleted file mode 100644 index 71d1fff41092d06b798a16349d8ace7636b04a4e..0000000000000000000000000000000000000000 --- a/mace-bench/src/batchopt/relaxation/optimizers/__init__.py +++ /dev/null @@ -1,13 +0,0 @@ -""" -Copyright (c) Meta, Inc. and its affiliates. - -This source code is licensed under the MIT license found in the -LICENSE file in the root directory of this source tree. -""" - -from __future__ import annotations - -from .bfgs_torch import BFGS -from .bfgsfusedls import BFGSFusedLS - -__all__ = ["BFGS", "BFGSFusedLS"] \ No newline at end of file diff --git a/mace-bench/src/batchopt/relaxation/optimizers/bfgs_torch.py b/mace-bench/src/batchopt/relaxation/optimizers/bfgs_torch.py deleted file mode 100644 index 62409eb23d0a460c716fd545665c3c070dbde4f2..0000000000000000000000000000000000000000 --- a/mace-bench/src/batchopt/relaxation/optimizers/bfgs_torch.py +++ /dev/null @@ -1,286 +0,0 @@ - -""" -Copyright (c) 2025 Ma Zhaojia - -This source code is licensed under the MIT license found in the -LICENSE file in the root directory of this source tree. -""" - -from __future__ import annotations - -import logging -import torch -from torch_scatter import scatter - -from ..optimizable import OptimizableBatch - -class BFGS: - def __init__( - self, - optimizable_batch: OptimizableBatch, - maxstep: float = 0.2, - alpha: float = 70.0, - early_stop = False, - ) -> None: - """ - Args: - """ - self.optimizable = optimizable_batch - self.maxstep = maxstep - self.alpha = alpha - # self.H0 = 1.0 / self.alpha - self.trajectories = None - self.device=self.optimizable.device - - self.fmax = None - self.steps = None - - self.initialize() - self.early_stop = early_stop - - - def initialize(self): - # initial hessian - self.H0 = [ - torch.eye(3 * size, device=self.optimizable.device, dtype=torch.float64) * self.alpha - for size in self.optimizable.elem_per_group - ] - - self.H = [None] * self.optimizable.batch_size - self.pos0 = torch.zeros_like(self.optimizable.get_positions().reshape(-1), device=self.device, dtype=torch.float64) - self.forces0 = torch.zeros_like(self.pos0, device=self.device, dtype=torch.float64) - - def restart_from_earlystop(self, restart_indices, old_batch_indices): - H_new = [] - pos0_new = torch.zeros_like(self.optimizable.get_positions().reshape(-1), device=self.device, dtype=torch.float64) - forces0_new = torch.zeros_like(pos0_new, device=self.device, dtype=torch.float64) - - # collect the preserved historical data by old_batch_indices - for i, idx in enumerate(restart_indices): - mask_old = (idx==old_batch_indices.repeat_interleave(3)) - mask = (i==self.optimizable.batch_indices.repeat_interleave(3)) - H_new.append(self.H[idx]) - pos0_new[mask] = self.pos0[mask_old] - forces0_new[mask] = self.forces0[mask_old] - - # append new info for the new batch - for i in range(len(H_new), self.optimizable.batch_size): - H_new.append(None) - - self.H = H_new - self.pos0 = pos0_new - self.forces0 = forces0_new - - - def run(self, fmax, maxstep, is_restart_earlystop=False, restart_indices=None, old_batch_indices=None): - logging.info("Enter bfgs's main program.") - self.fmax = fmax - self.max_iter = maxstep - - if is_restart_earlystop: - self.restart_from_earlystop(restart_indices, old_batch_indices) - - iteration = 0 - max_forces = self.optimizable.get_max_forces(apply_constraint=True) - logging.info("Step Fmax(eV/A)") - - while iteration < self.max_iter and not self.optimizable.converged( - forces=None, fmax=self.fmax, max_forces=max_forces, f_upper_limit=1e25, - ): - if self.early_stop and iteration > 0: - converge_indices = self.optimizable.converge_indices_list - if len(converge_indices) > 0: - logging.info(f"Early stopping at iteration {iteration}") - break - - logging.info( - f"{iteration} " + " ".join(f"{x:18.15g}" for x in max_forces.tolist()) - ) - - self.step() - max_forces = self.optimizable.get_max_forces(apply_constraint=True) - iteration += 1 - - logging.info( - f"{iteration} " + " ".join(f"{x:18.15g}" for x in max_forces.tolist()) - ) - - # GPU memory usage as per nvidia-smi seems to gradually build up as - # batches are processed. This releases unoccupied cached memory. - torch.cuda.empty_cache() - - # set predicted values to batch - for name, value in self.optimizable.results.items(): - setattr(self.optimizable.batch, name, value) - - self.nsteps = iteration - - if self.early_stop: - converge_indices_list = self.optimizable.converge_indices_list - return converge_indices_list - else: - return self.optimizable.converged( - forces=None, fmax=self.fmax, max_forces=max_forces - ) - - - def step(self): - forces = self.optimizable.get_forces(apply_constraint=True).to( - dtype=torch.float64 - ) - pos = self.optimizable.get_positions().to(dtype=torch.float64) - dpos, steplengths = self.prepare_step(pos, forces) - dpos = self.determine_step(dpos, steplengths) - self.optimizable.set_positions(pos+dpos) - - - def prepare_step(self, pos, forces): - forces = forces.reshape(-1) - pos = pos.view(-1) - self.update(pos, forces, self.pos0, self.forces0) - - dpos_list = [] - cur_indices = self.optimizable.batch_indices.repeat_interleave(3) - # 预初始化结果列表 - dpos_list = [None] * len(self.H) - - # 分离计算任务:仅对需要计算的H矩阵创建流 - calc_indices = [i for i, need_update in enumerate(self.optimizable.update_mask) if need_update] - streams = [torch.cuda.Stream() for _ in calc_indices] - - # 并行执行实际计算 - for i, stream in zip(calc_indices, streams): - with torch.cuda.stream(stream): - omega, V = torch.linalg.eigh(self.H[i]) - dpos_list[i] = (V @ (forces[cur_indices==i].t() @ V / torch.abs(omega)).t()) - - # 同步所有计算流 - torch.cuda.current_stream().synchronize() - - # 在主线程处理零张量 - for i in range(len(self.H)): - if not self.optimizable.update_mask[i]: - dpos_list[i] = torch.zeros_like(forces[cur_indices==i]) - - # 同步所有流 - for stream in streams: - stream.synchronize() - - # dpos = torch.vstack(dpos_list) - dpos = torch.zeros_like(forces) - for i in torch.unique(cur_indices): - mask = (cur_indices == i) - dpos[mask] = dpos_list[i] - dpos = dpos.reshape(-1, 3) - - steplengths = (dpos ** 2).sum(dim=-1).sqrt() - self.pos0 = pos - self.forces0 = forces - - return dpos, steplengths - - - def determine_step(self, dpos, steplengths): - longest_steps = scatter( - steplengths, self.optimizable.batch_indices, reduce="max" - ) - longest_steps = longest_steps[self.optimizable.batch_indices] - maxstep = longest_steps.new_tensor(self.maxstep) - scale = (longest_steps).reciprocal() * torch.min(longest_steps, maxstep) - dpos *= scale.unsqueeze(1) - return dpos - - def update(self, pos, forces, pos0, forces0): - if self.H is None: - self.H = self.H0 - return - dpos = pos - pos0 - dforces = forces - forces0 - batch_indices_flatten = self.optimizable.batch_indices.repeat_interleave(3) - dg = torch.zeros_like(dforces) - all_size = self.optimizable.elem_per_group - - for i in range(self.optimizable.batch_size): - if self.H[i] is None: - continue - mask = (i==batch_indices_flatten) - if torch.abs(dpos[mask]).max() < 1e-7: - continue - - dg[mask] = self.H[i] @ dpos[mask] - - a = self._batched_dot_1d(dforces, dpos) - b = self._batched_dot_1d(dpos, dg) - - for i in range(self.optimizable.batch_size): - if self.H[i] is None: - self.H[i] = torch.eye(3*all_size[i], device=self.device, dtype=torch.float64) * self.alpha - continue - mask = (i==batch_indices_flatten) - if not self.optimizable.update_mask[i]: - continue - if torch.abs(dpos[mask]).max() < 1e-7: - continue - - outer_force = torch.outer(dforces[mask], dforces[mask]) - outer_dg = torch.outer(dg[mask], dg[mask]) - self.H[i] -= outer_force / a[i] + outer_dg / b[i] - - - - def update_parallel(self, pos, forces, pos0, forces0): - if self.H is None: - self.H = self.H0 - return - - dpos = pos - pos0 - - if torch.abs(dpos).max() < 1e-7: - return - - dforces = forces - forces0 - cur_indices = self.optimizable.batch_indices.repeat_interleave(3) - a = self._batched_dot_1d(dforces, dpos) - # DONE: There is a bug using hstack. - # dg = torch.hstack([self.H[i] @ dpos[cur_indices == i] for i in range(len(self.H))]) - # DONE: parallel this part - # dg_list = [self.H[i] @ dpos[cur_indices == i] for i in range(len(self.H))] - dg_list = [None] * len(self.H) - streams = [torch.cuda.Stream() for _ in dg_list] - for i, stream in zip(range(len(dg_list)), streams): - with torch.cuda.stream(stream): - dg_list[i] = self.H[i] @ dpos[cur_indices == i] - - torch.cuda.current_stream().synchronize() - for stream in streams: - stream.synchronize() - - dg = torch.zeros_like(dforces) - for i in torch.unique(cur_indices): - mask = (cur_indices == i) - dg[mask] = dg_list[i] - b = self._batched_dot_1d(dpos, dg) - - # DONE: parallel this part - for i, stream in zip(range(len(self.H)), streams): - if not self.optimizable.update_mask[i]: - continue - with torch.cuda.stream(stream): - outer_force = torch.outer(dforces[cur_indices==i], dforces[cur_indices==i]) - outer_dg = torch.outer(dg[cur_indices==i], dg[cur_indices==i]) - self.H[i] -= outer_force / a[i] + outer_dg / b[i] - - torch.cuda.current_stream().synchronize() - for stream in streams: - stream.synchronize() - - - def _batched_dot_2d(self, x: torch.Tensor, y: torch.Tensor): - return scatter( - (x * y).sum(dim=-1), self.optimizable.batch_indices, reduce="sum" - ) - - def _batched_dot_1d(self, x: torch.Tensor, y: torch.Tensor): - return scatter( - (x * y), self.optimizable.batch_indices.repeat_interleave(3), reduce="sum" - ) \ No newline at end of file diff --git a/mace-bench/src/batchopt/relaxation/optimizers/bfgsfusedls.py b/mace-bench/src/batchopt/relaxation/optimizers/bfgsfusedls.py deleted file mode 100644 index 9dc221b64021c1607a8a80b06592c3aa5683d737..0000000000000000000000000000000000000000 --- a/mace-bench/src/batchopt/relaxation/optimizers/bfgsfusedls.py +++ /dev/null @@ -1,993 +0,0 @@ -""" -Copyright (c) 2025 Ma Zhaojia - -This source code is licensed under the MIT license found in the -LICENSE file in the root directory of this source tree. -""" - -from __future__ import annotations -import logging -import torch -from torch_scatter import scatter -# from .linesearch_torch import LineSearchBatch -from ..optimizable import OptimizableBatch -from torch.profiler import profile, record_function, ProfilerActivity, schedule, tensorboard_trace_handler -from datetime import datetime -import os -import math -import gc - -class BFGSFusedLS: - """ - Port of BFGSLineSearch from bfgslinesearch.py, adapted to PyTorch - and batched operations, mirroring lbfgs_torch.py structure. - """ - def __init__( - self, - optimizable_batch: OptimizableBatch, - maxstep: float = 0.2, - c1: float = 0.23, - c2: float = 0.46, - alpha: float = 10.0, - stpmax: float = 50.0, - device = 'cpu', - early_stop: bool = False, - use_profiler: bool = False, - profiler_log_dir: str = './log', - profiler_schedule_config: dict = None, - dtype: torch.dtype = torch.float64, - ): - self.optimizable = optimizable_batch - self.maxstep = maxstep - self.c1 = c1 - self.c2 = c2 - self.alpha = alpha - self.stpmax = stpmax - self.nsteps = 0 - self.device = device - self.force_calls = 0 - self.early_stop = early_stop - self.use_profiler = use_profiler - self.profiler_log_dir = profiler_log_dir - self.profiler_schedule_config = profiler_schedule_config or {"wait": 48, "warmup": 1, "active": 1, "repeat": 8} - self.dtype = dtype - - self.converge_indices_list = None - - # The information from the previous round is useful for the current round's calculations. - ## These variables need to be update accroding to new input when eary stop is triggered. - self.Hs = None - self.r0 = None - self.g0 = None - self.p_list = [None] * self.optimizable.batch_size - self.no_update_list = [False] * self.optimizable.batch_size - self.ls_completed = [True] * self.optimizable.batch_size - self.ls_batch = LineSearchBatch(self.optimizable.batch_indices, device="cpu", dtype=self.dtype) - ## need to be recalculate when early stop is triggered - self.forces = None - self.energies = None - - def restart_from_earlystop(self, restart_indices, old_batch_indices): - Hs_new = [] - r0_new = torch.zeros_like(self.optimizable.get_positions().reshape(-1), device=self.device) - g0_new = torch.zeros_like(r0_new, device=self.device) - p_list_new = [] - no_update_list_new = [] - ls_completed_new = [] - - # collect the preserved historical info by old_indices - for i, idx in enumerate(restart_indices): - mask_old = (idx==old_batch_indices.repeat_interleave(3)) - mask = (i==self.optimizable.batch_indices.repeat_interleave(3)) - Hs_new.append(self.Hs[idx]) - p_list_new.append(self.p_list[idx]) - no_update_list_new.append(self.no_update_list[idx]) - ls_completed_new.append(self.ls_completed[idx]) - r0_new[mask] = self.r0[mask_old] - g0_new[mask] = self.g0[mask_old] - - # append new info for new element in batch - for i in range(len(Hs_new), self.optimizable.batch_size): - # Hs_new.append(torch.eye(3 * self.optimizable.elem_per_group[i], device=self.device, dtype=torch.float64)) - Hs_new.append(None) - p_list_new.append(None) - no_update_list_new.append(False) - ls_completed_new.append(True) - - self.Hs = Hs_new - self.r0 = r0_new - self.g0 = g0_new - self.p_list = p_list_new - self.no_update_list = no_update_list_new - self.ls_completed = ls_completed_new - self.forces = None - self.energies = None - self.ls_batch.restart_from_earlystop(restart_indices=restart_indices, batch_indices_new=self.optimizable.batch_indices) - - def step(self): - optimizable = self.optimizable - if self.forces is None: - self.forces = optimizable.get_forces().to(self.device) - r = optimizable.get_positions().reshape(-1).to(self.device) - g = -self.forces.reshape(-1) / self.alpha - p0_list = self.p_list - self.update(r, g, self.r0, self.g0, p0_list) - if self.energies is None: - self.energies = self.func(r) - - for i in range(self.optimizable.batch_size): - if self.ls_completed[i]: - p = -torch.matmul(self.Hs[i], g[i==self.optimizable.batch_indices.repeat_interleave(3)]) - - # Implement scaling for numerical stability with simpler calculation - p_size = torch.sqrt((p**2).sum()) - min_size = torch.sqrt(self.optimizable.elem_per_group[i] * 1e-10) - if p_size <= min_size: - p = p * (min_size / p_size) - - self.p_list[i] = p - - # ls_batch = LineSearchBatch(self.optimizable.batch_indices, device="cpu") - continue_search = [not elem for elem in self.ls_completed] - self.alpha_k_list, self.e_list, self.e0_list, self.no_update_list, self.ls_completed = self.ls_batch._linesearch_batch( - self.func, self.fprime, r, self.p_list, g, self.energies, None, - maxstep=self.maxstep, c1=self.c1, c2=self.c2, stpmax=self.stpmax, continue_search=continue_search - ) - - # reset device for linesearch result - for i in range(self.optimizable.batch_size): - if self.ls_completed[i]: - self.alpha_k_list[i] = self.alpha_k_list[i].to(self.device) - self.p_list[i] = self.p_list[i].to(self.device) - - dr_tensor = torch.zeros_like(r) - - - for i in range(self.optimizable.batch_size): - # if check_cache: - # mask = (i == self.optimizable.batch_indices.repeat_interleave(3)) - # dr_tensor_all[mask] = self.alpha_k_list[i].to(self.device) * self.p_list[i].to(self.device) - - if not self.ls_completed[i]: - continue - if self.alpha_k_list[i] is None: - raise RuntimeError("LineSearch failed!") - - mask = (i == self.optimizable.batch_indices.repeat_interleave(3)) - dr_tensor[mask] = self.alpha_k_list[i] * self.p_list[i] - - # if check_cache: - # cached_pos = optimizable.get_positions().reshape(-1).to(self.device) - # update_pos = r + dr_tensor_all - # assert torch.allclose(update_pos, cached_pos), "dr_tensor_cached should be equal to dr_tensor" - - - # TODO: get_forces/get_potential_energies will trigger compare_batch which is time-consuming - forces_cache = optimizable.get_forces() - energies_cache = self.optimizable.get_potential_energies() / self.alpha - - # update self.forces - for i in range(self.optimizable.batch_size): - if not self.ls_completed[i]: - continue - mask = (i == self.optimizable.batch_indices) - self.forces[mask] = forces_cache[mask] - self.energies[i] = energies_cache[i] - - optimizable.set_positions((r + dr_tensor).reshape(-1, 3)) - - self.r0 = r - self.g0 = g - - # @torch.compile - def update(self, r, g, r0, g0, p0_list): - all_sizes = self.optimizable.elem_per_group - - if self.Hs is None: - self.Hs = [ - torch.eye(3 * sz, device=self.device, dtype=self.dtype) - for sz in all_sizes - ] - return - - dr = r - r0 - dg = g - g0 - - for i in range(self.optimizable.batch_size): - if self.Hs[i] is None: - self.Hs[i] = torch.eye(3 * all_sizes[i], device=self.optimizable.device, dtype=self.dtype) - continue - if not self.ls_completed[i]: - continue - if self.no_update_list[i] is True: - print('skip update') - continue - - cur_mask = (i == self.optimizable.batch_indices.repeat_interleave(3)) - cur_g = g[cur_mask] - cur_p0 = p0_list[i] - cur_g0 = g0[cur_mask] - cur_dg = dg[cur_mask] - cur_dr = dr[cur_mask] - - if not (((self.alpha_k_list[i] or 0) > 0 and - abs(torch.dot(cur_g, cur_p0)) - abs(torch.dot(cur_g0, cur_p0)) < 0) or False): - continue - - try: - rhok = 1.0 / (torch.dot(cur_dg, cur_dr)) - except: - rhok = 1000.0 - print("Divide-by-zero encountered: rhok assumed large") - if torch.isinf(rhok): - rhok = 1000.0 - print("Divide-by-zero encountered: rhok assumed large") - I = torch.eye(all_sizes[i]*3, device=self.device, dtype=self.dtype) - A1 = I - cur_dr[:, None] * cur_dg[None, :] * rhok - A2 = I - cur_dg[:, None] * cur_dr[None, :] * rhok - self.Hs[i] = (torch.matmul(A1, torch.matmul(self.Hs[i], A2)) + - rhok * cur_dr[:, None] * cur_dr[None, :]) - - - # def update(self, r, g, r0, g0, p0_list): - # self.Is = [ - # torch.eye(sz * 3, dtype=torch.float64, device=self.device) - # for sz in self.optimizable.elem_per_group - # ] - - # # TODO: BFGS for loop 是不是在被打断之后需要重建这个 self.Hs? - # # TODO: 并且我们保存的上一次的r,g,r0,g0也被丢弃了 - # if self.Hs is None: - # self.Hs = [ - # torch.eye(3 * sz, device=self.optimizable.device, dtype=torch.float64) - # for sz in self.optimizable.elem_per_group - # ] - # return - # else: - # dr = r - r0 - # dg = g - g0 - - # for i in range(self.optimizable.batch_size): - # if not self.ls_completed[i]: - # continue - # cur_mask = (i==self.optimizable.batch_indices.repeat_interleave(3)) - # cur_g = g[cur_mask] - # cur_p0 = p0_list[i] - # cur_g0 = g0[cur_mask] - # cur_dg = dg[cur_mask] - # cur_dr = dr[cur_mask] - - # if not (((self.alpha_k_list[i] or 0) > 0 and - # abs(torch.dot(cur_g, cur_p0)) - abs(torch.dot(cur_g0, cur_p0)) < 0) or False): - # break - - # if self.no_update_list[i] is True: - # print('skip update') - # break - - # try: - # rhok = 1.0 / (torch.dot(cur_dg, cur_dr)) - # except: - # rhok = 1000.0 - # print("Divide-by-zero encountered: rhok assumed large") - # if torch.isinf(rhok): - # rhok = 1000.0 - # print("Divide-by-zero encountered: rhok assumed large") - # A1 = self.Is[i] - cur_dr[:, None] * cur_dg[None, :] * rhok - # A2 = self.Is[i] - cur_dg[:, None] * cur_dr[None, :] * rhok - # self.Hs[i] = (torch.matmul(A1, torch.matmul(self.Hs[i], A2)) + - # rhok * cur_dr[:, None] * cur_dr[None, :]) - - - - def func(self, x): - self.optimizable.set_positions(x.reshape(-1, 3).to(self.device)) - return self.optimizable.get_potential_energies() / self.alpha - - def fprime(self, x): - self.optimizable.set_positions(x.reshape(-1, 3).to(self.device)) - - self.force_calls += 1 - forces = self.optimizable.get_forces().reshape(-1) - return - forces / self.alpha - - def run(self, fmax, maxstep, is_restart_earlystop=False, restart_indices=None, old_batch_indices=None): - logging.info("Enter bfgsfusedlinesearch's main program.") - self.fmax = fmax - self.max_iter = maxstep - - if is_restart_earlystop: - self.restart_from_earlystop(restart_indices, old_batch_indices) - - iteration = 0 - max_forces = self.optimizable.get_max_forces(apply_constraint=True) - logging.info("Step Fmax(eV/A)") - - # Run with profiler if enabled - if self.use_profiler: - activities = [ProfilerActivity.CPU] - if torch.cuda.is_available(): - activities.append(ProfilerActivity.CUDA) - - timestamp = datetime.now().strftime("%Y%m%d_%H%M%S") - pid = os.getpid() - with torch.profiler.profile( - activities=activities, - schedule=torch.profiler.schedule( - wait=self.profiler_schedule_config["wait"], - warmup=self.profiler_schedule_config["warmup"], - active=self.profiler_schedule_config["active"], - repeat=self.profiler_schedule_config["repeat"] - ), - on_trace_ready=tensorboard_trace_handler(self.profiler_log_dir, worker_name=f"BFGSLS_{pid}"), - with_stack=True, - profile_memory=True, - ) as prof: - # Main optimization loop with profiling - while iteration < self.max_iter and not self.optimizable.converged( - forces=None, fmax=self.fmax, max_forces=max_forces, f_upper_limit=1e25, - ): - if self.early_stop and iteration > 0: - self.converge_indices_list = self.optimizable.converge_indices_list - if len(self.converge_indices_list) > 0: - logging.info(f"Early stopping at iteration {iteration}") - break - - logging.info( - f"{iteration} " + " ".join(f"{x:18.15g}" for x in max_forces.tolist()) - ) - - self.step() - max_forces = self.optimizable.get_max_forces(apply_constraint=True, forces=self.forces) - iteration += 1 - - # Step the profiler in each iteration - prof.step() - - else: - # Original optimization loop without profiling - while iteration < self.max_iter and not self.optimizable.converged( - forces=None, fmax=self.fmax, max_forces=max_forces, f_upper_limit=1e25, - ): - if self.early_stop and iteration > 0: - self.converge_indices_list = self.optimizable.converge_indices_list - if len(self.converge_indices_list) > 0: - logging.info(f"Early stopping at iteration {iteration}") - break - - logging.info( - f"{iteration} " + " ".join(f"{x:18.15g}" for x in max_forces.tolist()) - ) - - self.step() - max_forces = self.optimizable.get_max_forces(apply_constraint=True, forces=self.forces) - iteration += 1 - - logging.info( - f"{iteration} " + " ".join(f"{x:18.15g}" for x in max_forces.tolist()) - ) - - # GPU memory usage as per nvidia-smi seems to gradually build up as - # batches are processed. This releases unoccupied cached memory. - torch.cuda.empty_cache() - gc.collect() - - # set predicted values to batch - for name, value in self.optimizable.results.items(): - setattr(self.optimizable.batch, name, value) - - self.nsteps = iteration - - if self.early_stop: - self.converge_indices_list = self.optimizable.converge_indices_list - return self.converge_indices_list - else: - return self.optimizable.converged( - forces=None, fmax=self.fmax, max_forces=max_forces - ) - - def _batched_dot_2d(self, x: torch.Tensor, y: torch.Tensor): - return scatter( - (x * y).sum(dim=-1), self.optimizable.batch_indices, reduce="sum" - ) - - def _batched_dot_1d(self, x: torch.Tensor, y: torch.Tensor): - return scatter( - (x * y), self.optimizable.batch_indices.repeat_interleave(3), reduce="sum" - ) - -# flake8: noqa -import math -import torch -import logging - -pymin = min -pymax = max - - -class LineSearch: - def __init__(self, xtol=1e-14, device='cpu', dtype=torch.float64): - self.xtol = xtol - self.task = 'START' - self.device = device - self.dtype = dtype - self.isave = torch.zeros(2, dtype=torch.int64, device=self.device) - self.dsave = torch.zeros(13, dtype=self.dtype, device=self.device) - self.fc = 0 - self.gc = 0 - self.case = 0 - self.old_stp = 0 - - def initialize(self, xk, pk, gfk, old_fval, old_old_fval, - maxstep=.2, c1=.23, c2=0.46, xtrapl=1.1, xtrapu=4., - stpmax=50., stpmin=1e-8): - # Scalar parameters can stay as Python scalars - self.stpmin = stpmin - self.stpmax = stpmax - self.xtrapl = xtrapl - self.xtrapu = xtrapu - self.maxstep = maxstep - - # Move tensors to the device - self.pk = pk.to(self.device) - xk = xk.to(self.device) - gfk = gfk.to(self.device) - - phi0 = old_fval - - - # This dot product needs tensors - derphi0 = torch.dot(gfk, self.pk).item() - - # Use Python math for scalar calculations - self.dim = len(pk) - self.gms = math.sqrt(self.dim) * maxstep - - alpha1 = 1.0 - self.no_update = False - self.gradient = True - - self.steps = [] - return alpha1, phi0, derphi0 - - def prologue(self, fval, gval, pk_tensor, alpha1): - phi0 = fval - derphi0 = torch.dot(gval, pk_tensor) - self.old_stp = alpha1 - # TODO: self.no_update == True: break is needed to reimplemented. - - return phi0, derphi0 - - def epilogue(self): - pass - - def _line_search(self, func, myfprime, xk, pk, gfk, old_fval, old_old_fval, - maxstep=.2, c1=.23, c2=0.46, xtrapl=1.1, xtrapu=4., - stpmax=50., stpmin=1e-8, args=()): - self.stpmin = stpmin - self.pk = pk.to(self.device) - self.stpmax = stpmax - self.xtrapl = xtrapl - self.xtrapu = xtrapu - self.maxstep = maxstep - - xk = xk.to(self.device) - - # Convert inputs to torch tensors if they're not already - if not isinstance(old_fval, torch.Tensor): - phi0 = torch.tensor(old_fval, dtype=self.dtype, device=self.device) - else: - phi0 = old_fval.to(self.device) - - # Ensure pk and gfk are torch tensors - pk_tensor = torch.tensor(pk, dtype=self.dtype, device=self.device) if not isinstance(pk, torch.Tensor) else pk.to(self.device) - gfk_tensor = torch.tensor(gfk, dtype=self.dtype, device=self.device) if not isinstance(gfk, torch.Tensor) else gfk.to(self.device) - - derphi0 = torch.dot(gfk_tensor, pk_tensor) - self.dim = len(pk) - self.gms = torch.sqrt(torch.tensor(self.dim, dtype=self.dtype, device=self.device)) * maxstep - alpha1 = 1. - self.no_update = False - - if isinstance(myfprime, tuple): - fprime = myfprime[0] - gradient = False - else: - fprime = myfprime - newargs = args - gradient = True - - fval = phi0 - gval = gfk_tensor - self.steps = [] - - while True: - stp = self.step(alpha1, phi0, derphi0, c1, c2, - self.xtol, - self.isave, self.dsave) - - if self.task[:2] == 'FG': - alpha1 = stp - - # Get function value and gradient - x_new = xk + stp * pk_tensor - fval = func(x_new).to(self.device) - self.fc += 1 - - gval = fprime(x_new).to(self.device) - if gradient: - self.gc += 1 - else: - self.fc += len(xk) + 1 - - phi0 = fval - derphi0 = torch.dot(gval, pk_tensor) - self.old_stp = alpha1 - - if self.no_update == True: - break - else: - break - - if self.task[:5] == 'ERROR' or self.task[1:4] == 'WARN': - stp = None # failed - - return stp, fval.item(), old_fval.item() if isinstance(old_fval, torch.Tensor) else old_fval, self.no_update - - def step(self, stp, f, g, c1, c2, xtol, isave, dsave): - if self.task[:5] == 'START': - # Check the input arguments for errors. - if stp < self.stpmin: - self.task = 'ERROR: STP .LT. minstep' - if stp > self.stpmax: - self.task = 'ERROR: STP .GT. maxstep' - if g >= 0: - self.task = 'ERROR: INITIAL G >= 0' - if c1 < 0: - self.task = 'ERROR: c1 .LT. 0' - if c2 < 0: - self.task = 'ERROR: c2 .LT. 0' - if xtol < 0: - self.task = 'ERROR: XTOL .LT. 0' - if self.stpmin < 0: - self.task = 'ERROR: minstep .LT. 0' - if self.stpmax < self.stpmin: - self.task = 'ERROR: maxstep .LT. minstep' - if self.task[:5] == 'ERROR': - return stp - - # Initialize local variables. - self.bracket = False - stage = 1 - finit = f - ginit = g - gtest = c1 * ginit - width = self.stpmax - self.stpmin - width1 = width / .5 - - # The variables stx, fx, gx contain the values of the step, - # function, and derivative at the best step. - # The variables sty, fy, gy contain the values of the step, - # function, and derivative at sty. - # The variables stp, f, g contain the values of the step, - # function, and derivative at stp. - stx = 0.0 - fx = finit - gx = ginit - sty = 0.0 - fy = finit - gy = ginit - stmin = 0.0 - stmax = stp + self.xtrapu * stp - self.task = 'FG' - self.save((stage, ginit, gtest, gx, - gy, finit, fx, fy, stx, sty, - stmin, stmax, width, width1)) - stp = self.determine_step(stp) - return stp - else: - if self.isave[0] == 1: - self.bracket = True - else: - self.bracket = False - stage = self.isave[1] - (ginit, gtest, gx, gy, finit, fx, fy, stx, sty, stmin, stmax, - width, width1) = self.dsave - - # If psi(stp) <= 0 and f'(stp) >= 0 for some step, then the - # algorithm enters the second stage. - ftest = finit + stp * gtest - if stage == 1 and f < ftest and g >= 0.: - stage = 2 - - # Test for warnings. - if self.bracket and (stp <= stmin or stp >= stmax): - self.task = 'WARNING: ROUNDING ERRORS PREVENT PROGRESS' - if self.bracket and stmax - stmin <= self.xtol * stmax: - self.task = 'WARNING: XTOL TEST SATISFIED' - if stp == self.stpmax and f <= ftest and g <= gtest: - self.task = 'WARNING: STP = maxstep' - if stp == self.stpmin and (f > ftest or g >= gtest): - self.task = 'WARNING: STP = minstep' - - # Test for convergence. - # if f <= ftest and abs(g) <= c2 * (- ginit): - # self.task = 'CONVERGENCE' - if (f < ftest or math.isclose(f, ftest, rel_tol=1e-6, abs_tol=1e-5)) and (abs(g) < c2 * (- ginit) or math.isclose(abs(g), c2 * (- ginit), rel_tol=1e-6, abs_tol=1e-5)): - self.task = 'CONVERGENCE' - - # Test for termination. - if self.task[:4] == 'WARN' or self.task[:4] == 'CONV': - self.save((stage, ginit, gtest, gx, - gy, finit, fx, fy, stx, sty, - stmin, stmax, width, width1)) - return stp - - stx, sty, stp, gx, fx, gy, fy = self.update(stx, fx, gx, sty, - fy, gy, stp, f, g, - stmin, stmax) - - # Decide if a bisection step is needed. - if self.bracket: - if abs(sty - stx) >= .66 * width1: - stp = stx + .5 * (sty - stx) - width1 = width - width = abs(sty - stx) - - # Set the minimum and maximum steps allowed for stp. - if self.bracket: - stmin = min(stx, sty) - stmax = max(stx, sty) - else: - stmin = stp + self.xtrapl * (stp - stx) - stmax = stp + self.xtrapu * (stp - stx) - - # Force the step to be within the bounds maxstep and minstep. - stp = max(stp, self.stpmin) - stp = min(stp, self.stpmax) - - if (stx == stp and stp == self.stpmax and stmin > self.stpmax): - self.no_update = True - - # If further progress is not possible, let stp be the best - # point obtained during the search. - if (self.bracket and stp < stmin or stp >= stmax) \ - or (self.bracket and stmax - stmin < self.xtol * stmax): - stp = stx - - # Obtain another function and derivative. - self.task = 'FG' - self.save((stage, ginit, gtest, gx, - gy, finit, fx, fy, stx, sty, - stmin, stmax, width, width1)) - return stp - - def update(self, stx, fx, gx, sty, fy, gy, stp, fp, gp, - stpmin, stpmax): - sign = gp * (gx / abs(gx)) - - # First case: A higher function value. The minimum is bracketed. - # If the cubic step is closer to stx than the quadratic step, the - # cubic step is taken, otherwise the average of the cubic and - # quadratic steps is taken. - if fp > fx: # case1 - self.case = 1 - theta = 3. * (fx - fp) / (stp - stx) + gx + gp - s = max(max(abs(theta), abs(gx)), abs(gp)) - gamma = s * math.sqrt((theta / s) ** 2. - (gx / s) * (gp / s)) - if stp < stx: - gamma = -gamma - p = (gamma - gx) + theta - q = ((gamma - gx) + gamma) + gp - r = p / q - stpc = stx + r * (stp - stx) - stpq = stx + ((gx / ((fx - fp) / (stp - stx) + gx)) / 2.) \ - * (stp - stx) - if (abs(stpc - stx) < abs(stpq - stx)): - stpf = stpc - else: - stpf = stpc + (stpq - stpc) / 2. - - self.bracket = True - - # Second case: A lower function value and derivatives of opposite - # sign. The minimum is bracketed. If the cubic step is farther from - # stp than the secant step, the cubic step is taken, otherwise the - # secant step is taken. - elif sign < 0: # case2 - self.case = 2 - theta = 3. * (fx - fp) / (stp - stx) + gx + gp - s = max(max(abs(theta), abs(gx)), abs(gp)) - gamma = s * math.sqrt((theta / s) ** 2 - (gx / s) * (gp / s)) - if stp > stx: - gamma = -gamma - p = (gamma - gp) + theta - q = ((gamma - gp) + gamma) + gx - r = p / q - stpc = stp + r * (stx - stp) - stpq = stp + (gp / (gp - gx)) * (stx - stp) - if (abs(stpc - stp) > abs(stpq - stp)): - stpf = stpc - else: - stpf = stpq - self.bracket = True - - # Third case: A lower function value, derivatives of the same sign, - # and the magnitude of the derivative decreases. - elif abs(gp) < abs(gx): # case3 - self.case = 3 - # The cubic step is computed only if the cubic tends to infinity - # in the direction of the step or if the minimum of the cubic - # is beyond stp. Otherwise the cubic step is defined to be the - # secant step. - theta = 3. * (fx - fp) / (stp - stx) + gx + gp - s = max(max(abs(theta), abs(gx)), abs(gp)) - - # The case gamma = 0 only arises if the cubic does not tend - # to infinity in the direction of the step. - gamma = s * math.sqrt(max(0., (theta / s) ** 2 - (gx / s) * (gp / s))) - if stp > stx: - gamma = -gamma - p = (gamma - gp) + theta - q = (gamma + (gx - gp)) + gamma - r = p / q - if r < 0. and gamma != 0: - stpc = stp + r * (stx - stp) - elif stp > stx: - stpc = stpmax - else: - stpc = stpmin - stpq = stp + (gp / (gp - gx)) * (stx - stp) - - if self.bracket: - # A minimizer has been bracketed. If the cubic step is - # closer to stp than the secant step, the cubic step is - # taken, otherwise the secant step is taken. - if abs(stpc - stp) < abs(stpq - stp): - stpf = stpc - else: - stpf = stpq - if stp > stx: - stpf = min(stp + .66 * (sty - stp), stpf) - else: - stpf = max(stp + .66 * (sty - stp), stpf) - else: - # A minimizer has not been bracketed. If the cubic step is - # farther from stp than the secant step, the cubic step is - # taken, otherwise the secant step is taken. - if abs(stpc - stp) > abs(stpq - stp): - stpf = stpc - else: - stpf = stpq - stpf = min(stpmax, stpf) - stpf = max(stpmin, stpf) - - # Fourth case: A lower function value, derivatives of the same sign, - # and the magnitude of the derivative does not decrease. If the - # minimum is not bracketed, the step is either minstep or maxstep, - # otherwise the cubic step is taken. - else: # case4 - self.case = 4 - if self.bracket: - theta = 3. * (fp - fy) / (sty - stp) + gy + gp - s = max(max(abs(theta), abs(gy)), abs(gp)) - gamma = s * math.sqrt((theta / s) ** 2 - (gy / s) * (gp / s)) - if stp > sty: - gamma = -gamma - p = (gamma - gp) + theta - q = ((gamma - gp) + gamma) + gy - r = p / q - stpc = stp + r * (sty - stp) - stpf = stpc - elif stp > stx: - stpf = stpmax - else: - stpf = stpmin - - # Update the interval which contains a minimizer. - if fp > fx: - sty = stp - fy = fp - gy = gp - else: - if sign < 0: - sty = stx - fy = fx - gy = gx - stx = stp - fx = fp - gx = gp - - # Compute the new step. - stp = self.determine_step(stpf) - - return stx, sty, stp, gx, fx, gy, fy - - def determine_step(self, stp): - dr = stp - self.old_stp - x = torch.reshape(self.pk.to(self.device), (-1, 3)) - steplengths = ((dr * x)**2).sum(1)**0.5 - maxsteplength = max(steplengths) - if maxsteplength >= self.maxstep: - dr *= self.maxstep / maxsteplength - stp = self.old_stp + dr - return stp - - def save(self, data): - if self.bracket: - self.isave[0] = 1 - else: - self.isave[0] = 0 - self.isave[1] = data[0] - self.dsave = data[1:] - -class LineSearchBatch: - - def __init__(self, batch_indices, device='cpu', dtype=torch.float64): - self.device = device - self.dtype = dtype - self.batch_indices = batch_indices.to(self.device) - self.batch_indices_flatten = self.batch_indices.repeat_interleave(3).to(self.device) - self.batch_size = len(torch.unique(batch_indices)) - self.linesearch_list = [LineSearch(device=self.device, dtype=self.dtype) for _ in range(self.batch_size)] - self.steps = [1.] * self.batch_size - self.phi0_values = [None] * self.batch_size - self.derphi0_values = [None] * self.batch_size - - def restart_from_earlystop(self, restart_indices, batch_indices_new): - self.batch_indices = batch_indices_new.to(self.device) - self.batch_indices_flatten = self.batch_indices.repeat_interleave(3).to(self.device) - self.batch_size = len(torch.unique(batch_indices_new)) - - linesearch_list_new = [] - steps_new = [] - phi0_values_new = [] - derphi0_values_new = [] - - for i, idx in enumerate(restart_indices): - linesearch_list_new.append(self.linesearch_list[idx]) - steps_new.append(self.steps[idx]) - phi0_values_new.append(self.phi0_values[idx]) - derphi0_values_new.append(self.derphi0_values[idx]) - - for i in range(len(restart_indices), self.batch_size): - linesearch_list_new.append(LineSearch(device=self.device)) - steps_new.append(1.) - phi0_values_new.append(None) - derphi0_values_new.append(None) - - self.linesearch_list = linesearch_list_new - self.steps = steps_new - self.phi0_values = phi0_values_new - self.derphi0_values = derphi0_values_new - - - - def _linesearch_batch(self, func, myfprime, xk, pk, gfk, old_fval, old_old_fval, - maxstep=.2, c1=.23, c2=0.46, xtrapl=1.1, xtrapu=4., - stpmax=50., stpmin=1e-8, continue_search=None, max_iter=15): - if continue_search is None: - self.linesearch_list = [LineSearch(device=self.device) for _ in range(self.batch_size)] - else: - assert len(continue_search) == self.batch_size - for i in range(len(continue_search)): - if not continue_search[i]: - self.linesearch_list[i] = LineSearch(device=self.device) - - if isinstance(xk, torch.Tensor): - xk = xk.to(self.device) - for i in range(len(pk)): - pk[i] = pk[i].to(self.device) - if isinstance(gfk, torch.Tensor): - gfk = gfk.to(self.device) - if isinstance(old_fval, torch.Tensor): - old_fval = old_fval.to(self.device) - if isinstance(old_old_fval, torch.Tensor): - old_old_fval = old_old_fval.to(self.device) - - - # results for each batch element - alpha_results = [] - e_result = [] - e0_result = [] - no_update_result = [] - - # Initialize step sizes and line search state for each batch element - completed = [False] * self.batch_size - - # Initialize iteration counter - iter_count = 0 - - # Initialize all line searches using the initialize method - for i in range(self.batch_size): - if continue_search[i]: - continue - - ls = self.linesearch_list[i] - mask = (i == self.batch_indices_flatten) - - # Use the initialize method to set up line search parameters - alpha1, phi0, derphi0 = ls.initialize( - xk[mask], pk[i], gfk[mask], old_fval[i], old_old_fval, - maxstep, c1, c2, xtrapl, xtrapu, stpmax, stpmin - ) - - # Store the initialization values - self.steps[i] = alpha1 - self.phi0_values[i] = phi0 - self.derphi0_values[i] = derphi0 - - # Main optimization loop - while True: - # 1. step forward - # logging.info(f"step's input: alpha1: {torch.tensor([step.item() if isinstance(step, torch.Tensor) else step for step in self.steps])}") - for i in range(self.batch_size): - if completed[i]: - continue - ls = self.linesearch_list[i] - if ls.fc > max_iter: - completed[i] = True - logging.warning(f"LineSearchBatch[{i}] reached max_iter: {max_iter}") - continue - stp = ls.step(self.steps[i], self.phi0_values[i], self.derphi0_values[i], - c1, c2, ls.xtol, ls.isave, ls.dsave) - if ls.task[:2] == 'FG': - self.steps[i] = stp - else: - completed[i] = True - - # 2. calculate new function value and gradient - x_new_batch = torch.zeros_like(xk) - for i in range(self.batch_size): - mask = (i == self.batch_indices_flatten) - x_new_batch[mask] = xk[mask] + self.steps[i] * pk[i] - f_batch = func(x_new_batch).to(self.device) - g_batch = myfprime(x_new_batch).to(self.device) - - # 3. update function value and gradient - for i in range(self.batch_size): - ls = self.linesearch_list[i] - mask = (i == self.batch_indices_flatten) - if ls.task[:2] == 'FG': - # Update function value and gradient - f_val = f_batch[i:i+1] - g_val = g_batch[mask] - ls.fc += 1 - phi0, derphi0 = ls.prologue(f_val, g_val, pk[i], self.steps[i]) - # logging.info(f"phi0, derphi0: {phi0}, {derphi0}") - self.phi0_values[i] = phi0 - self.derphi0_values[i] = derphi0 # TODO: why we put the derphi0 here instead of set it inside the LineSearch class? - if ls.no_update: - completed[i] = True - else: - completed[i] = True - - iter_count += 1 - logging.info(f"LineSearchBatch iter: {iter_count}: alpha: {torch.tensor([step.item() if isinstance(step, torch.Tensor) else step for step in self.steps])}") - if any(completed): - break - - # 4. set a linesearch upper limit - # if iter_count > max_iter: - # for i in range(self.batch_size): - # completed[i] = True - # logging.warning(f"LineSearchBatch reached max_iter: {max_iter}") - # break - - # Collect results - for i in range(self.batch_size): - ls = self.linesearch_list[i] - if ls.task[:5] == 'ERROR' or ls.task[1:4] == 'WARN': - stp = torch.tensor(1., device=self.device) - else: - stp = self.steps[i] if isinstance(self.steps[i], torch.Tensor) else torch.tensor(self.steps[i], device=self.device) - - alpha_results.append(stp) - e_result.append(self.phi0_values[i].item() if self.phi0_values[i] is not None else None) - e0_result.append(old_fval[i].item() if isinstance(old_fval[i], torch.Tensor) else old_fval[i]) - no_update_result.append(ls.no_update) - - logging.info(f"LineSearchBatch finished in {iter_count} iterations. \ - LineSearch Status: {[stat for stat in completed]}") - - return alpha_results, e_result, e0_result, no_update_result, completed diff --git a/mace-bench/src/batchopt/relaxengine.py b/mace-bench/src/batchopt/relaxengine.py deleted file mode 100644 index 617145fe31a036e90355fc896c4a6e545fc04e79..0000000000000000000000000000000000000000 --- a/mace-bench/src/batchopt/relaxengine.py +++ /dev/null @@ -1,1433 +0,0 @@ -""" -Copyright (c) 2025 {Chengxi Zhao, Zhaojia Ma, Dingrui Fan} - -This source code is licensed under the MIT license found in the -LICENSE file in the root directory of this source tree. -""" - -from ase.io import read - -# from ase.optimize import ASE_LBFGS -import torch -from torch.multiprocessing import Process, set_start_method -from batchopt.atoms_to_graphs import AtomsToGraphs -from batchopt.utils import data_list_collater -from batchopt.relaxation.optimizers import ( - BFGS, - BFGSFusedLS, -) -from batchopt.relaxation import OptimizableBatch, OptimizableUnitCellBatch -import logging -import time -import csv -from multiprocessing import Queue -import os -import psutil -import multiprocessing -import json -import subprocess - -try: - from chgnet.model.dynamics import CHGNetCalculator -except ImportError: - logging.warning("Failed to import CHGNet modules") - -try: - from sevenn.calculator import SevenNetCalculator, SevenNetD3Calculator -except ImportError: - logging.warning("Failed to import SevenNet modules") - -try: - from fairchem.core import pretrained_mlip, FAIRChemCalculator -except ImportError: - logging.warning("Failed to import FAIRChem modules") - -try: - from mace.calculators import mace_off -except ImportError: - logging.warning("Failed to import MACE modules") - -import threading -from .utils import count_atoms_cif -from collections import deque - - -class Scheduler: - """ - Scheduler distributes relaxation tasks to workers. - """ - - def __init__( - self, - files, - num_workers, - devices, - batch_size, - max_steps, - filter1, - filter2, - optimizer1, - optimizer2, - skip_second_stage, - scalar_pressure, - compile_mode, - profile, - num_threads, - bind_cores, - cueq, - molecule_single, - output_path, - model, - ): - - self.files = files - self.num_workers = num_workers - self.devices = devices - self.batch_size = batch_size - self.max_steps = max_steps - self.filter1 = filter1 - self.filter2 = filter2 - self.optimizer1 = optimizer1 - self.optimizer2 = optimizer2 - self.skip_second_stage = skip_second_stage - self.scalar_pressure = scalar_pressure - self.compile_mode = compile_mode - self.profile = profile - self.num_threads = num_threads - self.cueq = cueq - self.molecule_single = molecule_single - self.output_path = ( - output_path - if os.path.isabs(output_path) - else os.path.abspath(output_path) - ) - self.model = model - - try: - set_start_method("spawn") - except RuntimeError: - logging.warning( - "set_start_method('spawn') failed, trying 'forkserver' instead." - ) - - if bind_cores is not None: - self.cpu_mask = self._parse_bind_cores(bind_cores) - else: - self.cpu_mask = None - - def _parse_bind_cores(self, bind_cores): - # Expect custom_bind_str to be like "0-15,16-31,..." - ranges = bind_cores.split(",") - if len(ranges) != self.num_workers: - return None - binding = [] - for r in ranges: - try: - start_str, end_str = r.split("-") - start = int(start_str) - end = int(end_str) - except ValueError: - logging.error("Custom binding format should be 'start-end'.") - return None - - binding.append(set(range(start, end + 1))) - return binding - - def _get_physical_logical_core_mapping(self): - """Get the mapping between logical cores and their physical core IDs.""" - try: - # This information is available in Linux systems - mapping = {} - logical_cores = psutil.cpu_count(logical=True) - - for i in range(logical_cores): - try: - # Read core_id from /sys/devices/system/cpu/cpu{i}/topology/core_id - with open( - f"/sys/devices/system/cpu/cpu{i}/topology/core_id" - ) as f: - core_id = int(f.read().strip()) - # Read physical_package_id (socket) for more complete information - with open( - f"/sys/devices/system/cpu/cpu{i}/topology/physical_package_id" - ) as f: - package_id = int(f.read().strip()) - mapping[i] = (package_id, core_id) - except (FileNotFoundError, ValueError, IOError): - mapping[i] = None - return mapping - except Exception as e: - logging.error(f"Failed to get core mapping: {e}") - return {} - - def _get_physical_core_mask(self): - # Get the number of physical and logical cores - physical_cores = psutil.cpu_count(logical=False) - logical_cores = psutil.cpu_count(logical=True) - - if physical_cores is None or physical_cores < 1: - # Fallback to multiprocessing if psutil fails - logical_cores = multiprocessing.cpu_count() - physical_cores = logical_cores // 2 - if physical_cores < 1: - physical_cores = 1 - print(f"Using estimated physical cores: {physical_cores}") - - # Get the mapping between logical and physical cores - core_mapping = self._get_physical_logical_core_mapping() - - # Create a CPU mask that includes all physical cores (first core of each physical core) - physical_core_mask = set() - if core_mapping: - # Group by physical core ID - cores_by_physical = {} - for logical_id, physical_info in core_mapping.items(): - if physical_info is not None: - package_id, core_id = physical_info - key = (package_id, core_id) - if key not in cores_by_physical: - cores_by_physical[key] = [] - cores_by_physical[key].append(logical_id) - - # Select one logical core from each physical core - for physical_cores_list in cores_by_physical.values(): - physical_core_mask.add( - physical_cores_list[0] - ) # First logical core of each physical core - else: - # If mapping fails, use a simple assumption (may not be accurate on all systems) - threads_per_core = logical_cores // physical_cores - physical_core_mask = set(range(0, logical_cores, threads_per_core)) - - return physical_core_mask - - def worker_task( - self, files, device, batch_size, result_queue, physical_cores - ): - if physical_cores is not None: - try: - # Bind the current process to physical cores - pid = os.getpid() - os.sched_setaffinity(pid, physical_cores) - logging.info(f"bind to physical_core_ids: {physical_cores}") - - # Verify the affinity was set correctly - current_affinity = os.sched_getaffinity(pid) - logging.info( - f"Process bound to {len(current_affinity)} cores: {sorted(current_affinity)}" - ) - - except AttributeError: - logging.error( - "sched_setaffinity not supported on this platform" - ) - except Exception as e: - logging.error(f"Failed to bind to physical cores: {e}") - - # pass the number of processes on each worker - nproc = self.num_workers // len(self.devices) - - worker = Worker( - files, - device, - batch_size, - self.max_steps, - self.filter1, - self.filter2, - self.optimizer1, - self.optimizer2, - self.skip_second_stage, - self.scalar_pressure, - self.compile_mode, - self.profile, - self.cueq, - self.molecule_single, - self.output_path, - self.model, - nproc, - ) - # results = worker.run() - results = worker.continuous_run() - result_queue.put(results) - - def _terminate_processes(self, processes): - """Helper method to terminate all processes.""" - for i, p in processes: - if p.is_alive(): - logging.info(f"Terminating process {p.pid}") - p.terminate() - p.join(timeout=3) # Wait for up to 3 seconds - if p.is_alive(): - logging.warning( - f"Process {p.pid} did not terminate, killing it" - ) - p.kill() - p.join() - - # create a thread to conduct "nvidia-smi" - @staticmethod - def _monitor_memory(interval=2, gpu_index=1): - try: - while True: - result = subprocess.check_output( - [ - "nvidia-smi", - "--query-gpu=memory.used,memory.total", - "--format=csv,nounits,noheader", - ] - ).decode("utf-8") - - lines = result.strip().split("\n") - used, total = map(int, lines[gpu_index].split(",")) - logging.info( - f"[nvidia-smi] Memory-Usage on GPU {gpu_index}: {used}MiB / {total}MiB" - ) - - time.sleep(interval) - except KeyboardInterrupt: - logging.info("Monitor interrupted.") - - except Exception as e: - logging.error(f"Unexpected error when monitor memory: {str(e)}") - - def run(self): - logging.info(f"Starting Scheduler with {self.num_workers} workers.") - processes = [] - result_queue = Queue() - start_time = time.perf_counter() - - if self.cpu_mask is not None: - physical_cores_per_worker = self.cpu_mask - logging.info( - f"Use customed cores binding. Physical cores per worker: {physical_cores_per_worker}" - ) - else: - # all_physical_cores = self._get_physical_core_mask() - # num_per_worker = len(all_physical_cores) // self.num_workers - # physical_cores_per_worker = [ - # list(all_physical_cores)[i:i + num_per_worker] for i in range(0, len(all_physical_cores), num_per_worker) - # ] - # logging.info(f"Physical cores per worker: {physical_cores_per_worker}") - physical_cores_per_worker = [None] * self.num_workers - - try: - # Start all worker processes - for i in range(self.num_workers): - files_for_worker = self.files[i :: self.num_workers] - device = self.devices[i % len(self.devices)] - logging.info( - f"Starting worker {i} with {len(files_for_worker)} files on device {device}." - ) - p = Process( - target=self.worker_task, - args=( - files_for_worker, - device, - self.batch_size, - result_queue, - physical_cores_per_worker[i], - ), - ) - p.start() - processes.append((i, p)) - - # monitor gpu memory usage to figure out what makes the differences of footprint among batches - # in each iteration. - use_memory_monitor = False - if use_memory_monitor: - monitor_proc = Process( - target=Scheduler._monitor_memory, args=() - ) - monitor_proc.start() - - # Monitor processes and collect results - csv_paths = [] - completed_processes = 0 - while completed_processes < self.num_workers: - for i, p in processes: - if not p.is_alive() and p.exitcode != 0: - if p.exitcode == -11 or p.exitcode == 1: - # Restart the process if exit code is -11 or -1 - logging.warning( - f"Worker process {p.pid} exited with code {p.exitcode}. Restarting worker {i}." - ) - files_for_worker = self.files[i :: self.num_workers] - device = self.devices[i % len(self.devices)] - new_process = Process( - target=self.worker_task, - args=( - files_for_worker, - device, - self.batch_size, - result_queue, - physical_cores_per_worker[i], - ), - ) - new_process.start() - processes[i] = ( - i, - new_process, - ) # Replace the old process with the new one - else: - # Raise an error for other exit codes - raise RuntimeError( - f"Worker process {p.pid} failed with exit code {p.exitcode}" - ) - - # Try to get result from queue with timeout - try: - result = result_queue.get(timeout=10) - csv_paths.append(result) - completed_processes += 1 - except Exception as e: - continue - - # terminate monitor - if use_memory_monitor: - monitor_proc.terminate() - monitor_proc.join() - - # Process results and create final CSV - merged_results = [] - for csv_path in csv_paths: - try: - with open(csv_path, mode="r") as f: - reader = csv.DictReader(f) - merged_results.extend(list(reader)) - except Exception as e: - logging.error(f"Error processing {csv_path}: {str(e)}") - - except Exception as e: - # Log the error and elapsed time - end_time = time.perf_counter() - elapsed_time = end_time - start_time - logging.error( - f"Error occurred after running for {elapsed_time:.2f} seconds: {str(e)}" - ) - - # Create error log file - error_log = f"scheduler_error_{int(time.time())}.log" - with open(error_log, "w") as f: - f.write(f"Error occurred after {elapsed_time:.2f} seconds\n") - f.write(f"Error message: {str(e)}\n") - f.write(f"Number of workers: {self.num_workers}\n") - f.write(f"Batch size: {self.batch_size}\n") - - # Terminate all processes - self._terminate_processes(processes) - raise # Re-raise the exception after cleanup - - finally: - end_time = time.perf_counter() - elapsed_time = end_time - start_time - - # Write final results if we have any - if "merged_results" in locals() and merged_results: - csv_file = os.path.join( - self.output_path, "results_scheduler.csv" - ) - with open(csv_file, mode="w", newline="") as file: - writer = csv.DictWriter( - file, - fieldnames=[ - "file", - "stage1_steps", - "stage1_time", - "stage1_energy", - "stage1_density", - "stage2_steps", - "stage2_time", - "stage2_energy", - "stage2_density", - "total_steps", - "total_time", - ], - ) - writer.writeheader() - for row in merged_results: - try: - processed_row = { - "file": row["file"], - "stage1_steps": int(row["stage1_steps"]), - "stage1_time": float(row["stage1_time"]), - "stage1_energy": float(row["stage1_energy"]), - "stage1_density": float(row["stage1_density"]), - "stage2_steps": int(row["stage2_steps"]), - "stage2_time": float(row["stage2_time"]), - "stage2_energy": float(row["stage2_energy"]), - "stage2_density": float(row["stage2_density"]), - "total_steps": int(row["total_steps"]), - "total_time": float(row["total_time"]), - } - writer.writerow(processed_row) - except (KeyError, ValueError) as e: - logging.error( - f"Invalid data format in row {row}: {str(e)}" - ) - - # Write summary - summary_csv_file = os.path.join( - self.output_path, "summary_scheduler.csv" - ) - with open(summary_csv_file, mode="w", newline="") as file: - writer = csv.DictWriter( - file, - fieldnames=["elapsed_time", "num_workers", "batch_size"], - ) - writer.writeheader() - writer.writerow( - { - "elapsed_time": elapsed_time, - "num_workers": self.num_workers, - "batch_size": self.batch_size, - } - ) - - logging.info(f"Scheduler completed in {elapsed_time:.2f} seconds.") - - def run_debug(self): - logging.info("Starting Scheduler in debug mode (sequential execution).") - - def worker_task(files, device, batch_size): - worker = Worker( - files, device, batch_size, self.max_steps, self.filter1 - ) - worker.run() - - for i in range(self.num_workers): - files_for_worker = self.files[i :: self.num_workers] - device = self.devices[i % len(self.devices)] - logging.info( - f"Running worker {i} with {len(files_for_worker)} files on device {device}." - ) - worker_task(files_for_worker, device, self.batch_size) - - logging.info("All workers have completed their tasks in debug mode.") - - -class Worker: - """ - Worker is single process that runs a batch of optimization tasks. - """ - - def __init__( - self, - files, - device, - batch_size, - max_steps, - filter1, - filter2, - optimizer1, - optimizer2, - skip_second_stage, - scalar_pressure, - compile_mode, - profile, - cueq, - molecule_single, - output_path, - model, - nproc, - ): - self.files = files - self.device = device - self.batch_size = batch_size - self.max_steps = max_steps - self.filter1 = filter1 - self.filter2 = filter2 - self.optimizer1 = optimizer1 - self.optimizer2 = optimizer2 - self.skip_second_stage = skip_second_stage # Store skip_second_stage - self.scalar_pressure = scalar_pressure - self.compile_mode = compile_mode - self.profile = profile - self.cueq = cueq - self.molecule_single = molecule_single - self.output_path = ( - output_path - if os.path.isabs(output_path) - else os.path.abspath(output_path) - ) - self.model = model - self.nproc = nproc - - # Parse profiler options if provided - self.use_profiler = False - self.profiler_schedule_config = { - "wait": 48, - "warmup": 1, - "active": 1, - "repeat": 1, - } - self.profiler_log_dir = None - - if self.profile and self.profile != "False": - self.use_profiler = True - # Create directory for profiler output - self.profiler_log_dir = os.path.join(self.output_path, "log") - os.makedirs(self.profiler_log_dir, exist_ok=True) - if self.profile != "True": - try: - # Try to parse profile as a JSON string with schedule config - profile_config = json.loads(self.profile) - if isinstance(profile_config, dict): - for key in ["wait", "warmup", "active", "repeat"]: - if key in profile_config and isinstance( - profile_config[key], int - ): - self.profiler_schedule_config[key] = ( - profile_config[key] - ) - except json.JSONDecodeError: - logging.warning( - f"Could not parse profile config: {self.profile}, using defaults" - ) - - # For monitor thread - self.stop_event = threading.Event() - - def run(self): - logging.info( - f"Worker started on device {self.device} with {len(self.files)} files." - ) - a2g = AtomsToGraphs(r_edges=False, r_pbc=True) - # model = torch.load("/home/mazhaojia/.cache/mace/MACE-OFF23_small.model", map_location=self.device) - # z_table = utils.AtomicNumberTable([int(z) for z in model.atomic_numbers]) - calculator = mace_off(model="small", device=self.device) - - results = [] - - for batch_files in self._batch_files(self.files, self.batch_size): - logging.info(f"Processing batch with {len(batch_files)} files.") - start_time = time.perf_counter() - - atoms_list = [] - for file in batch_files: - atoms = read(file) - atoms_list.append(atoms) - gbatch = data_list_collater( - [a2g.convert(atoms) for atoms in atoms_list] - ) - - gbatch = gbatch.to(self.device) - if self.filter1 == "UnitCellFilter": - from batchopt.relaxation import OptimizableUnitCellBatch - - obatch = OptimizableUnitCellBatch( - gbatch, - trainer=calculator, - numpy=False, - scalar_pressure=self.scalar_pressure, - ) - else: - obatch = OptimizableBatch( - gbatch, trainer=calculator, numpy=False - ) - - # First optimization stage - if self.optimizer1 == "LBFGS": - batch_optimizer1 = LBFGS( - obatch, damping=1.0, alpha=70.0, maxstep=0.2 - ) - elif self.optimizer1 == "BFGS": - batch_optimizer1 = BFGS(obatch, alpha=70.0, maxstep=0.2) - elif self.optimizer1 == "BFGSLineSearch": - batch_optimizer1 = BFGSLineSearch(obatch, device=self.device) - elif self.optimizer1 == "BFGSFusedLS": - batch_optimizer1 = BFGSFusedLS(obatch, device=self.device) - else: - raise ValueError(f"Unknown optimizer: {self.optimizer1}") - - start_time1 = time.perf_counter() - batch_optimizer1.run(0.01, self.max_steps) - end_time1 = time.perf_counter() - elapsed_time1 = end_time1 - start_time1 - - # Save intermediate results - atoms_list = obatch.get_atoms_list() - for atoms, file_path in zip(atoms_list, batch_files): - file_name = file_path.split("/")[-1] - output_file = os.path.join( - self.output_path, - "cif_result_press", - file_name.replace(".cif", "_press.cif"), - ) - atoms.write(output_file) - - # Capture maximum force after first optimization stage - max_force1 = obatch.get_max_forces(apply_constraint=True) - - steps1 = batch_optimizer1.nsteps - - if self.skip_second_stage: - # If skipping second stage, set metrics to zero - for file, force in zip(batch_files, max_force1): - results.append( - { - "file": file, - "stage1_time": elapsed_time1, - "stage1_steps": steps1, - "stage2_time": 0.0, - "stage2_steps": 0, - "total_time": elapsed_time1, - "total_steps": steps1, - "force1": force.item(), - "force2": 0.0, - } - ) - continue - - # Only proceed with second stage if not skipping - # Reload intermediate structures for second stage - atoms_list = [] - for file_path in batch_files: - file_name = file_path.split("/")[-1] - press_file = os.path.join( - self.output_path, - "cif_result_press", - file_name.replace(".cif", "_press.cif"), - ) - atoms = read(press_file) - atoms_list.append(atoms) - - # Rebuild batch from optimized structures - gbatch = data_list_collater( - [a2g.convert(atoms) for atoms in atoms_list] - ) - gbatch = gbatch.to(self.device) - - # Second optimization stage - if self.filter2 == "UnitCellFilter": - obatch2 = OptimizableUnitCellBatch( - gbatch, trainer=calculator, numpy=False, scalar_pressure=0.0 - ) - else: - obatch2 = OptimizableBatch( - gbatch, trainer=calculator, numpy=False - ) - - if self.optimizer2 == "LBFGS": - batch_optimizer2 = LBFGS( - obatch2, damping=1.0, alpha=70.0, maxstep=0.2 - ) - elif self.optimizer2 == "BFGS": - batch_optimizer2 = BFGS(obatch2, alpha=70.0, maxstep=0.2) - elif self.optimizer2 == "BFGSLineSearch": - batch_optimizer2 = BFGSLineSearch(obatch2, device=self.device) - elif self.optimizer2 == "BFGSFusedLS": - batch_optimizer2 = BFGSFusedLS(obatch2, device=self.device) - else: - raise ValueError(f"Unknown optimizer: {self.optimizer2}") - start_time2 = time.perf_counter() - batch_optimizer2.run(0.01, self.max_steps) - end_time2 = time.perf_counter() - elapsed_time2 = end_time2 - start_time2 - - # Save final results - atoms_list = obatch2.get_atoms_list() - for atoms, file_path in zip(atoms_list, batch_files): - file_name = file_path.split("/")[-1] - output_file = os.path.join( - self.output_path, - "cif_result_final", - file_name.replace(".cif", "_opt.cif"), - ) - atoms.write(output_file) - - # Capture maximum force after second optimization stage - max_force2 = obatch2.get_max_forces(apply_constraint=True) - - steps2 = batch_optimizer2.nsteps - - for file, f1, f2 in zip(batch_files, max_force1, max_force2): - results.append( - { - "file": file, - "stage1_time": elapsed_time1, - "stage1_steps": steps1, - "stage2_time": elapsed_time2, - "stage2_steps": steps2, - "total_time": elapsed_time1 + elapsed_time2, - "total_steps": steps1 + steps2, - "force1": f1.item(), - "force2": f2.item(), - } - ) - - return results - - def _batch_files(self, files, batch_size): - for i in range(0, len(files), batch_size): - yield files[i : i + batch_size] - - @staticmethod - def _torch_memory_monitor(interval=2, device=None, stop_event=None): - try: - # explicitly CUDA initialization - torch.cuda._lazy_init() - while not stop_event.is_set(): - allocated = torch.cuda.memory_allocated(device=device) - reserved = torch.cuda.memory_reserved(device=device) - logging.info( - f"[torch] Allocated Memory: {allocated / 1024**2:.2f} MiB" - ) - logging.info( - f"[torch] Reserved Memory: {reserved / 1024**2:.2f} MiB" - ) - time.sleep(interval) - except Exception as e: - logging.error(f"Unexpected error when monitor memory: {str(e)}") - - def continuous_run(self): - """ - Execute a continuous run of the batching optimization process. - """ - logging.info("Starting continuous_run with two rounds of optimization.") - - # torch memory monitor api - use_torch_memory_monitor = False - if use_torch_memory_monitor: - memory_monitor = threading.Thread( - target=Worker._torch_memory_monitor, - args=(2, self.device, self.stop_event), - ) - memory_monitor.start() - - # First round of optimization - try: - logging.info("Starting first round of optimization.") - results_round1, new_atoms_files = self.continuous_batching( - atoms_path=self.files, - result_path_prefix=os.path.join( - self.output_path, "cif_result_press/" - ), - fmax=0.01, - maxstep=self.max_steps, - use_filter=self.filter1, - optimizer=self.optimizer1, - scalar_pressure=self.scalar_pressure, - dtype=torch.float64, - ) - logging.info( - f"Completed first round of optimization. Results: {len(results_round1)}" - ) - except KeyboardInterrupt as e: - if use_torch_memory_monitor: - self.stop_event.set() - memory_monitor.join() - logging.error(f"Error during first round of optimization: {e}") - raise - except Exception as e: - logging.error(f"Error during first round of optimization: {e}") - raise - - if self.skip_second_stage: - logging.info("Skipping second round of optimization.") - return results_round1 - - # Second round of optimization without pressure - try: - logging.info("Starting second round of optimization.") - results_round2, _ = self.continuous_batching( - atoms_path=new_atoms_files, - result_path_prefix=os.path.join( - self.output_path, "cif_result_final/" - ), - fmax=0.01, - maxstep=self.max_steps, - # maxstep=3000, - use_filter=self.filter2, - optimizer=self.optimizer2, - scalar_pressure=0.0, - dtype=torch.float64, - ) - logging.info( - f"Completed second round of optimization. Results: {len(results_round2)}" - ) - except KeyboardInterrupt as e: - if use_torch_memory_monitor: - self.stop_event.set() - memory_monitor.join() - logging.error(f"Error during second round of optimization: {e}") - raise - except Exception as e: - logging.error(f"Error during second round of optimization: {e}") - raise - - if use_torch_memory_monitor: - self.stop_event.set() - memory_monitor.join() - - return self._save_results_to_csv(results_round1, results_round2) - - def _save_results_to_csv(self, results_round1, results_round2): - """Helper method to save results to CSV file and return the path.""" - combined_results = [] - results_map = {} - - # Process first round results - for result in results_round1: - file_name = result["file"] - results_map[file_name] = { - "file": file_name, - "stage1_steps": result["steps"], - "stage1_time": result["runtime"], - "stage1_energy": result["energy"], - "stage1_density": result["density"], - "stage2_steps": 0, - "stage2_time": 0.0, - "stage2_energy": 0.0, - "stage2_density": 0, - "total_steps": result["steps"], - "total_time": result["runtime"], - } - - # Process second round results - for result in results_round2: - file_name = result["file"] - if file_name in results_map: - results_map[file_name].update( - { - "stage2_steps": result["steps"], - "stage2_time": result["runtime"], - "stage2_energy": result["energy"], - "stage2_density": result["density"], - "total_steps": results_map[file_name]["stage1_steps"] - + result["steps"], - "total_time": results_map[file_name]["stage1_time"] - + result["runtime"], - } - ) - else: - results_map[file_name] = { - "file": file_name, - "stage1_steps": 0, - "stage1_time": 0.0, - "stage1_energy": 0.0, - "stage1_density": 0, - "stage2_steps": result["steps"], - "stage2_time": result["runtime"], - "stage2_energy": result["energy"], - "stage2_density": result["density"], - "total_steps": result["steps"], - "total_time": result["runtime"], - } - - # Convert map to list - combined_results = list(results_map.values()) - - logging.info( - f"Combined results from both rounds. Total results: {len(combined_results)}" - ) - - worker_id = os.getpid() - timestamp = int(time.time()) - csv_filename = f"worker_{worker_id}_{timestamp}.csv" - csv_path = os.path.join( - self.output_path, "worker_results", csv_filename - ) - os.makedirs(os.path.dirname(csv_path), exist_ok=True) - - with open(csv_path, mode="w", newline="") as csvfile: - fieldnames = [ - "file", - "stage1_steps", - "stage1_time", - "stage1_energy", - "stage1_density", - "stage2_steps", - "stage2_time", - "stage2_energy", - "stage2_density", - "total_steps", - "total_time", - ] - writer = csv.DictWriter(csvfile, fieldnames=fieldnames) - writer.writeheader() - for result in combined_results: - writer.writerow(result) - - return csv_path - - def _get_density(self, crystal): - # 计算总质量,ASE 中的 get_masses 方法返回一个数组,包含了所有原子的质量 - total_mass = sum(crystal.get_masses()) # 转换为克 - - # 获取体积,ASE 的 get_volume 方法返回晶胞的体积,单位是 Å^3 - # 1 Å^3 = 1e-24 cm^3 - volume = crystal.get_volume() # 转换为立方厘米 - - # 计算密度,质量除以体积 - density = ( - total_mass / (volume * 10**-24) / (6.022140857 * 10**23) - ) # 单位是 g/cm^3 - return density - - @staticmethod - def select_factor(history: deque): - # TODO: when history is mix of different size, the smaller `values` should be selected. - boundaries = [0, 50, 100, 200, 400, 800] - values = [0.4, 0.8, 0.9, 0.6, 0.5, 0.4] - factor_result = [] - for graph_size in history: - for i in range(len(boundaries) - 1): - if boundaries[i] <= graph_size < boundaries[i + 1]: - factor_result.append(values[i]) - break - if len(factor_result) == 0: - return 0.4 - else: - return min(factor_result) - - def continuous_batching( - self, - atoms_path, - result_path_prefix, - fmax, - maxstep, - use_filter, - optimizer, - scalar_pressure, - dtype=torch.float64, - ): - """ - Performs continuous batched optimization of atomic structures. - - This method implements a continuous batching strategy for optimizing multiple atomic structures, - where converged structures are replaced with new ones to maintain batch efficiency. - - Parameters - ---------- - atoms_path : list - List of file paths to atomic structure files to be optimized - result_path_prefix : str - Prefix for output file paths where optimized structures will be saved - fmax : float, optional - Maximum force criterion for convergence, by default 0.01 - maxstep : int, optional - Maximum number of optimization steps per batch, by default 3000 - use_filter : str, optional - Filter to be used for optimization, by default "UnitCellFilter" - optimizer : str, optional - Optimizer to be used for optimization, by default "LBFGS" - scalar_pressure : float, optional - Scalar pressure to be applied, by default 0.0 - - Returns - ------- - None - The optimized structures are saved to disk - - Notes - ----- - The method: - - Processes structures in batches of predefined size - - Uses MACE neural network potential for energy/force calculations - - Employs LBFGS optimization with unit cell relaxation - - Dynamically replaces converged structures with new ones in the batch - - Tracks convergence and optimization steps for each structure - """ - # Load saved structures - result = [] - optimized_atoms_paths = [] - - json_dir = result_path_prefix.replace("cif", "json") - - remove_list = [] - # TODO: Why we read all CIF here? - for pre_cif in atoms_path: - cif_path = os.path.join(result_path_prefix, pre_cif.split("/")[-1]) - json_path = os.path.join( - json_dir, pre_cif.split("/")[-1].replace(".cif", ".json") - ) - if ( - os.path.exists(cif_path) - and os.path.exists(json_path) - and os.path.getsize(cif_path) > 0 - and os.path.getsize(json_path) > 0 - ): - with open(json_path, "r") as f: - result_data = json.load(f) - result.append(result_data) - optimized_atoms_paths.append(cif_path) - remove_list.append(pre_cif) - logging.info(f"File {cif_path} already exists, loaded.") - # else: - # try: - # read(pre_cif) - # except Exception as e: - # logging.info(f"Failed to read {pre_cif}: {e}") - # remove_list.append(pre_cif) - for i in remove_list: - atoms_path.remove(i) - - if self.batch_size > 0: - # Initialize variables - room_in_batch = self.batch_size - indices_to_process = 0 - cur_batch_path = atoms_path[ - indices_to_process : indices_to_process + room_in_batch - ] - if len(cur_batch_path) == 0: - logging.info("No structures to process.") - return result, optimized_atoms_paths - room_in_batch -= len(cur_batch_path) - indices_to_process += len(cur_batch_path) - cur_atoms_list = [read(path) for path in cur_batch_path] - a2g = AtomsToGraphs(r_edges=False, r_pbc=True) - gbatch = data_list_collater( - [a2g.convert(read(path)) for path in cur_batch_path] - ) - else: - # Set Maximum Number of atoms per batch - history = deque(maxlen=10) - history.append(1000) - max_bnatoms = 24080 - safe_factor = self.select_factor(history) - - indices_to_process = 0 - bnatoms = 0 - cur_batch_path = [] - graphs_list = [] - a2g = AtomsToGraphs(r_edges=False, r_pbc=True) - - while indices_to_process < len(atoms_path): - graph_natoms = count_atoms_cif(atoms_path[indices_to_process]) - if ( - bnatoms + graph_natoms - > max_bnatoms * safe_factor // self.nproc - ): - break - graph = a2g.convert(read(atoms_path[indices_to_process])) - bnatoms += graph_natoms - cur_batch_path.append(atoms_path[indices_to_process]) - graphs_list.append(graph) - indices_to_process += 1 - history.append(graph_natoms) - safe_factor = self.select_factor(history) - if len(graphs_list) == 0: - logging.info("No structures to process.") - return result, optimized_atoms_paths - gbatch = data_list_collater(graphs_list) - logging.info(f"current batch size: {len(cur_batch_path)}") - - total_natoms = sum([graph.natoms for graph in graphs_list]) - logging.info(f"total_natoms: {total_natoms}") - - gbatch = gbatch.to(self.device) - batch_optimizer = None - - # Initial calculator - if self.model == "mace": - if dtype == torch.float32: - calculator = mace_off( - model="small", - device=self.device, - enable_cueq=self.cueq, - default_dtype="float32", - ) - else: - calculator = mace_off( - model="small", device=self.device, enable_cueq=self.cueq - ) - elif self.model == "chgnet": - calculator = CHGNetCalculator( - use_device=self.device, enable_cueq=self.cueq - ) - elif self.model == "sevennet": - # calculator = SevenNetCalculator(device=self.device, enable_cueq=self.cueq) - calculator = SevenNetD3Calculator( - device=self.device, - enable_cueq=self.cueq, - batch_size=self.batch_size, - ) - # calculator = SevenNetCalculator('7net-mf-ompa', modal='mpa', device=self.device) - # calculator = MACECalculator(model_paths="/home/mazhaojia/.cache/mace/MACE-OFF23_small.model", device=self.device, compile_mode=self.compile_mode) - if use_filter == "UnitCellFilter": - obatch = OptimizableUnitCellBatch( - gbatch, - trainer=calculator, - numpy=False, - scalar_pressure=scalar_pressure, - ) - else: - obatch = OptimizableBatch(gbatch, trainer=calculator, numpy=False) - - orig_cells = obatch.orig_cells.clone() - - converged_atoms_count = 0 - converge_indices = [] - all_indices = [] - cur_batch_steps = [0] * len(cur_batch_path) - cur_batch_times = [time.perf_counter()] * len( - cur_batch_path - ) # Track start times - - while converged_atoms_count < len(atoms_path): - # Update batch - if len(all_indices) > 0: - if self.batch_size > 0: - room_in_batch += len(all_indices) - new_batch_path = atoms_path[ - indices_to_process : indices_to_process + room_in_batch - ] - logging.info(f"new_batch_path: {new_batch_path}") - room_in_batch -= len(new_batch_path) - indices_to_process += len(new_batch_path) - - optimized_atoms_new = [] - cur_batch_path_new = [] - cur_batch_steps_new = [] - cur_batch_times_new = [] - orig_cells_new = torch.zeros( - [self.batch_size - room_in_batch, 3, 3], - device=self.device, - ) - cell_offset = 0 - - restart_indices = [] - old_batch_indices = obatch.batch_indices - for i in range(len(optimized_atoms)): - if i in all_indices: - continue - else: - restart_indices.append(i) - optimized_atoms_new.append(optimized_atoms[i]) - cur_batch_path_new.append(cur_batch_path[i]) - cur_batch_steps_new.append(cur_batch_steps[i]) - cur_batch_times_new.append(cur_batch_times[i]) - - orig_cells_new[cell_offset] = orig_cells[i] - cell_offset += 1 - - for new_path in new_batch_path: - optimized_atoms_new.append(read(new_path)) - cur_batch_path_new.append(new_path) - cur_batch_steps_new.append(0) - cur_batch_times_new.append(time.perf_counter()) - - # Update the batch with new structures - optimized_atoms = optimized_atoms_new - cur_batch_path = cur_batch_path_new - cur_batch_steps = cur_batch_steps_new - cur_batch_times = cur_batch_times_new - else: - bnatoms = 0 - optimized_atoms_new = [] - cur_batch_path_new = [] - cur_batch_steps_new = [] - cur_batch_times_new = [] - - restart_indices = [] - old_batch_indices = obatch.batch_indices - for i in range(len(optimized_atoms)): - if i in all_indices: - continue - restart_indices.append(i) - optimized_atoms_new.append(optimized_atoms[i]) - cur_batch_path_new.append(cur_batch_path[i]) - cur_batch_steps_new.append(cur_batch_steps[i]) - cur_batch_times_new.append(cur_batch_times[i]) - bnatoms += a2g.convert(read(cur_batch_path[i])).natoms - - while indices_to_process < len(atoms_path): - new_path = atoms_path[indices_to_process] - graph_natoms = count_atoms_cif(new_path) - if ( - bnatoms + graph_natoms - > max_bnatoms * safe_factor // self.nproc - ): - break - bnatoms += graph_natoms - optimized_atoms_new.append(read(new_path)) - cur_batch_path_new.append(new_path) - cur_batch_steps_new.append(0) - cur_batch_times_new.append(time.perf_counter()) - indices_to_process += 1 - history.append(graph_natoms) - safe_factor = self.select_factor(history) - - orig_cells_new = torch.zeros( - [len(optimized_atoms_new), 3, 3], device=self.device - ) - cell_offset = 0 - for i in range(len(optimized_atoms)): - if i in all_indices: - continue - orig_cells_new[cell_offset] = orig_cells[i] - cell_offset += 1 - - # Update the batch with new structures - optimized_atoms = optimized_atoms_new - cur_batch_path = cur_batch_path_new - cur_batch_steps = cur_batch_steps_new - cur_batch_times = cur_batch_times_new - - logging.info(f"current batch size: {len(optimized_atoms)}") - - graphs_list = [a2g.convert(atoms) for atoms in optimized_atoms] - total_natoms = sum([graph.natoms for graph in graphs_list]) - logging.info(f"total_natoms: {total_natoms}") - logging.info(f"cur_batch_path to processing: {cur_batch_path}") - gbatch = data_list_collater(graphs_list) - gbatch = gbatch.to(self.device) - if self.model == "sevennet": - # calculator = SevenNetCalculator('7net-mf-ompa', modal='mpa', device=self.device) - calculator = SevenNetD3Calculator( - device=self.device, - enable_cueq=self.cueq, - batch_size=self.batch_size, - ) - if use_filter == "UnitCellFilter": - obatch = OptimizableUnitCellBatch( - gbatch, - trainer=calculator, - numpy=False, - scalar_pressure=scalar_pressure, - ) - else: - obatch = OptimizableBatch( - gbatch, trainer=calculator, numpy=False - ) - for i in range(cell_offset): - obatch.orig_cells[i] = orig_cells_new[i] - orig_cells = obatch.orig_cells.clone() - - # Optimize the current batch - if optimizer == "LBFGS": - batch_optimizer = LBFGS( - obatch, - damping=1.0, - alpha=70.0, - maxstep=0.2, - early_stop=True, - ) - elif optimizer == "BFGS": - if len(all_indices) > 0: - logging.info(f"Restarting with indices: {restart_indices}") - batch_optimizer.optimizable = obatch - else: - batch_optimizer = BFGS( - obatch, alpha=70.0, maxstep=0.2, early_stop=True - ) - elif optimizer == "BFGSLineSearch": - batch_optimizer = BFGSLineSearch( - obatch, - device=self.device, - early_stop=True, - use_profiler=self.use_profiler, - profiler_log_dir=self.profiler_log_dir, - profiler_schedule_config=self.profiler_schedule_config, - ) - elif optimizer == "BFGSFusedLS": - if len(all_indices) > 0: - logging.info(f"Restarting with indices: {restart_indices}") - batch_optimizer.optimizable = obatch - else: - batch_optimizer = BFGSFusedLS( - obatch, - device=self.device, - early_stop=True, - use_profiler=self.use_profiler, - profiler_log_dir=self.profiler_log_dir, - profiler_schedule_config=self.profiler_schedule_config, - ) - else: - raise ValueError(f"Unknown optimizer: {optimizer}") - - # 动态计算剩余可用步数(基于当前批次最大已执行步数) - current_max_steps = max(cur_batch_steps) if cur_batch_steps else 0 - remaining_steps = max( - maxstep - current_max_steps, 1 - ) # 保证至少运行1步 - - # 执行优化并获取收敛的索引 - if (optimizer == "BFGSFusedLS" or optimizer == "BFGS") and len( - all_indices - ) > 0: - converge_indices = batch_optimizer.run( - fmax, - remaining_steps, - is_restart_earlystop=True, - restart_indices=restart_indices, - old_batch_indices=old_batch_indices, - ) - else: - converge_indices = batch_optimizer.run(fmax, remaining_steps) - - # Print energies of all structures - # logging.info(f"Final energies of all structures: {batch_optimizer.energies}") - energies_list = ( - batch_optimizer.optimizable.get_potential_energies().tolist() - ) - logging.info(f"Final energies of all structures: {energies_list}") - - # 更新所有结构的累计步数 - cur_batch_steps = [ - steps + batch_optimizer.nsteps for steps in cur_batch_steps - ] - - # 找出超过最大步数的结构索引 - over_maxstep_indices = [ - i - for i, steps in enumerate(cur_batch_steps) - if steps >= maxstep - 1 - ] - - # 合并收敛和超限的索引(去重) - all_indices = list(set(converge_indices + over_maxstep_indices)) - - # Get optimized atoms - optimized_atoms = obatch.get_atoms_list() - converged_atoms_count += len(all_indices) - - end_time = time.perf_counter() - # 处理所有需要退出的结构(包括收敛和超限) - for idx in all_indices: - runtime = end_time - cur_batch_times[idx] - - energy_per_mol = ( - energies_list[idx] - / ( - len(optimized_atoms[idx].get_atomic_numbers()) - / self.molecule_single - ) - * 96.485 - ) - density = self._get_density(optimized_atoms[idx]) - - # Save results - result_data = { - "file": cur_batch_path[idx].split("/")[-1].split(".")[0], - "steps": cur_batch_steps[idx], - "runtime": runtime, - "energy": energy_per_mol, - "density": density, - } - result.append(result_data) - - # Save optimized structure - # converged_atoms_path = os.path.join(result_path_prefix, cur_batch_path[idx].split('/')[-1].replace('.cif', '.traj')) - converged_atoms_path = os.path.join( - result_path_prefix, cur_batch_path[idx].split("/")[-1] - ) - optimized_atoms[idx].write(converged_atoms_path) - optimized_atoms_paths.append(converged_atoms_path) - - # write a json file to store reslt_data - os.makedirs(json_dir, exist_ok=True) - # json_path = os.path.join(json_dir, cur_batch_path[idx].split('/')[-1]+'.json') - json_path = os.path.join( - json_dir, - cur_batch_path[idx].split("/")[-1].replace(".cif", ".json"), - ) - with open(json_path, "w") as f: - json.dump(result_data, f) - - logging.info(f"cur_batch_path: {cur_batch_path}") - logging.info(f"cur_batch_steps: {cur_batch_steps}") - logging.info(f"all_indices: {all_indices}") - logging.info(f"length of optimized_atoms: {len(optimized_atoms)}") - - return result, optimized_atoms_paths diff --git a/mace-bench/src/batchopt/utils.py b/mace-bench/src/batchopt/utils.py deleted file mode 100644 index ff707072696bfb4ab2dfaf0f219ea858fd8965c7..0000000000000000000000000000000000000000 --- a/mace-bench/src/batchopt/utils.py +++ /dev/null @@ -1,121 +0,0 @@ -""" -Copyright (c) Meta, Inc. and its affiliates. - -This source code is licensed under the MIT license found in the -LICENSE file in the root directory of this source tree. -""" - -import ast -import collections -import copy -import datetime -import errno -import functools -import importlib -import itertools -import json -import logging -import os -import subprocess -import sys -import time -from bisect import bisect -from contextlib import contextmanager -from dataclasses import dataclass -from functools import wraps -from itertools import product -from pathlib import Path -from typing import TYPE_CHECKING, Any -from uuid import uuid4 - -import numpy as np -import torch -import torch.nn as nn -import torch_geometric -import yaml -from matplotlib.backends.backend_agg import FigureCanvasAgg as FigureCanvas -from matplotlib.figure import Figure -from torch_geometric.data import Data -from torch_geometric.utils import remove_self_loops -from torch_scatter import scatter, segment_coo, segment_csr - -from torch_geometric.data.data import BaseData -from torch_geometric.data import Batch - -# sort files by atomic number in descending order -def count_atoms_cif(file): - in_atom_site = False - natoms = 0 - with open(file, 'r') as f: - while line := f.readline(): - if line.lower().startswith("loop_"): - in_atom_site = False - continue - # if line.lower().startswith("_atom_site_"): - if "_atom_site_" in line.lower(): - in_atom_site = True - continue - if in_atom_site: - if line.startswith("_"): - in_atom_site = False - continue - elif line: - natoms += 1 - return natoms - -# Override the collation method in `pytorch_geometric.data.InMemoryDataset` -def collate(data_list): - keys = data_list[0].keys - data = data_list[0].__class__() - - for key in keys: - data[key] = [] - slices = {key: [0] for key in keys} - - for item, key in product(data_list, keys): - data[key].append(item[key]) - if torch.is_tensor(item[key]): - s = slices[key][-1] + item[key].size(item.__cat_dim__(key, item[key])) - elif isinstance(item[key], (int, float)): - s = slices[key][-1] + 1 - else: - raise ValueError("Unsupported attribute type") - slices[key].append(s) - - if hasattr(data_list[0], "__num_nodes__"): - data.__num_nodes__ = [] - for item in data_list: - data.__num_nodes__.append(item.num_nodes) - - for key in keys: - if torch.is_tensor(data_list[0][key]): - data[key] = torch.cat( - data[key], dim=data.__cat_dim__(key, data_list[0][key]) - ) - else: - data[key] = torch.tensor(data[key]) - slices[key] = torch.tensor(slices[key], dtype=torch.long) - - return data, slices - -def data_list_collater( - data_list: list[BaseData], otf_graph: bool = False, to_dict: bool = False -) -> BaseData | dict[str, torch.Tensor]: - batch = Batch.from_data_list(data_list) - - if not otf_graph: - try: - n_neighbors = [] - for _, data in enumerate(data_list): - n_index = data.edge_index[1, :] - n_neighbors.append(n_index.shape[0]) - batch.neighbors = torch.tensor(n_neighbors) - except (NotImplementedError, TypeError): - logging.warning( - "LMDB does not contain edge index information, set otf_graph=True" - ) - - if to_dict: - batch = dict(batch.items()) - - return batch \ No newline at end of file diff --git a/mace-bench/util/env.sh b/mace-bench/util/env.sh deleted file mode 100644 index c9d281849d9d2609a0d164aa6c4c9bb00cabc375..0000000000000000000000000000000000000000 --- a/mace-bench/util/env.sh +++ /dev/null @@ -1,6 +0,0 @@ - -export CUDA_HOME=/usr/local/cuda -export PATH=$CUDA_HOME/bin:$PATH -export LD_LIBRARY_PATH=$CUDA_HOME/lib64:$LD_LIBRARY_PATH -export LIBRARY_PATH=$CUDA_HOME/lib64:$LIBRARY_PATH -export CPATH=$CUDA_HOME/include:$CPATH diff --git a/mace-bench/util/mps_clean.sh b/mace-bench/util/mps_clean.sh deleted file mode 100644 index 15ef55800b833f994dead5baa2f8e3d445c6e797..0000000000000000000000000000000000000000 --- a/mace-bench/util/mps_clean.sh +++ /dev/null @@ -1,10 +0,0 @@ - -echo quit | nvidia-cuda-mps-control -nvidia-smi -i 0 -c DEFAULT -nvidia-smi -i 1 -c DEFAULT -nvidia-smi -i 2 -c DEFAULT -nvidia-smi -i 3 -c DEFAULT -nvidia-smi -i 4 -c DEFAULT -nvidia-smi -i 5 -c DEFAULT -nvidia-smi -i 6 -c DEFAULT -nvidia-smi -i 7 -c DEFAULT \ No newline at end of file diff --git a/mace-bench/util/mps_start.sh b/mace-bench/util/mps_start.sh deleted file mode 100644 index 9304a8582a7ef3e2b9bffe210472b1f0b80db2c9..0000000000000000000000000000000000000000 --- a/mace-bench/util/mps_start.sh +++ /dev/null @@ -1,10 +0,0 @@ - -nvidia-smi -i 0 -c EXCLUSIVE_PROCESS # Set GPU 0 to exclusive mode. -nvidia-smi -i 1 -c EXCLUSIVE_PROCESS # Set GPU 1 to exclusive mode. -nvidia-smi -i 2 -c EXCLUSIVE_PROCESS # Set GPU 2 to exclusive mode. -nvidia-smi -i 3 -c EXCLUSIVE_PROCESS # Set GPU 3 to exclusive mode. -nvidia-smi -i 4 -c EXCLUSIVE_PROCESS # Set GPU 4 to exclusive mode. -nvidia-smi -i 5 -c EXCLUSIVE_PROCESS # Set GPU 5 to exclusive mode. -nvidia-smi -i 6 -c EXCLUSIVE_PROCESS # Set GPU 6 to exclusive mode. -nvidia-smi -i 7 -c EXCLUSIVE_PROCESS # Set GPU 7 to exclusive mode. -nvidia-cuda-mps-control -d # Start the daemon. \ No newline at end of file diff --git a/pyproject.toml b/pyproject.toml new file mode 100644 index 0000000000000000000000000000000000000000..c1817a99a621a702c8a4357db9a7f935dfd3dc96 --- /dev/null +++ b/pyproject.toml @@ -0,0 +1,13 @@ +[project] +name = "bomlip-csp" +version = "0.1.0" +description = "Add your description here" +readme = "README.md" +requires-python = ">=3.10" +dependencies = [ + "networkx==3.2.1", + "numpy==1.26.4", + "rdkit-pypi>=2022.9.5", + "scipy==1.14.1", + "tqdm==4.67.1", +] diff --git a/search_gen_proc.sh b/search_gen_proc.sh new file mode 100755 index 0000000000000000000000000000000000000000..821ae4fb02456bc561d7be6d1561916870dd2204 --- /dev/null +++ b/search_gen_proc.sh @@ -0,0 +1,66 @@ +#!/bin/bash +# ============================================================================= +# BOMLIP-CSP: Conformer Search & Crystal Structure Generation Pipeline +# ============================================================================= +# Usage: ./search_gen_proc.sh [config_file] +# config_file Path to the parameter configuration file (default: config.sh) +# ============================================================================= + +# --- Determine config file path (default: config.sh in the same directory) --- +SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)" +CONFIG_FILE="${1:-${SCRIPT_DIR}/config.sh}" + +if [ ! -f "${CONFIG_FILE}" ]; then + echo "Error: Configuration file not found: ${CONFIG_FILE}" + echo "Usage: $0 [config_file]" + exit 1 +fi + +echo "Loading configuration from: ${CONFIG_FILE}" + +# --- Source the configuration file --- +source "${CONFIG_FILE}" + +# --- Validate required parameters --- +if [ -z "${SMILES}" ]; then + echo "Error: SMILES is not set in the configuration file." + exit 1 +fi + +# --- Set up directory --- +TOP_DIR="${SCRIPT_DIR}" +TAR_DIR="${TOP_DIR}/${OUTPUT_DIR}" + +mkdir -p "${TAR_DIR}" +cd "${TAR_DIR}" || { echo "Error: Cannot access directory ${TAR_DIR}"; exit 1; } + +echo "==========================================" +echo " BOMLIP-CSP Pipeline" +echo "==========================================" +echo " SMILES: ${SMILES}" +echo " Output directory: ${TAR_DIR}" +echo " Mode: ${MODE}" +echo " Generate conformers: ${GENERATE_CONFORMERS}" +echo " Use conformers: ${USE_CONFORMERS}" +echo " Molecule num in cell: ${MOLECULE_NUM_IN_CELL}" +echo " Space group list: ${SPACE_GROUP_LIST}" +echo " Add name: ${ADD_NAME}" +echo " Num generation: ${NUM_GENERATION}" +echo " Max workers: ${MAX_WORKERS}" +echo "==========================================" + +# --- Run the pipeline --- +python "${TOP_DIR}/main.py" \ + --path "${TAR_DIR}" \ + --smiles "${SMILES}" \ + --molecule_num_in_cell ${MOLECULE_NUM_IN_CELL} \ + --space_group_list "${SPACE_GROUP_LIST}" \ + --add_name "${ADD_NAME}" \ + --max_workers "${MAX_WORKERS}" \ + --num_generation ${NUM_GENERATION} \ + --generate_conformers "${GENERATE_CONFORMERS}" \ + --use_conformers "${USE_CONFORMERS}" \ + --mode "${MODE}" \ + > generate.log 2>&1 + +echo "Pipeline finished. Log saved to ${TAR_DIR}/generate.log" diff --git a/structure_generate.py b/structure_generate.py index 7ec5317338d6db28ecd1301ee1cd8a1806725374..025d0f52b317450144ff6c1272290082c7c198d5 100644 --- a/structure_generate.py +++ b/structure_generate.py @@ -2,42 +2,59 @@ from basic_function import format_parser from basic_function import packaged_function from basic_function import conformer_search import time - +import os +import sys if __name__ == '__main__': time_start = time.time() - # ############################################################################################## - # # conformer search - # conformer_search.conformer_search("C1CC2=COC=C12", "./test/molecule_1", num_conformers=10, max_attempts=10000, rms_thresh=0.1) - + # --- Load configuration from config.sh --- + script_dir = os.path.dirname(os.path.abspath(__file__)) + config_path = sys.argv[1] if len(sys.argv) > 1 else os.path.join(script_dir, "config.sh") + cfg = {} + exec(open(config_path).read(), cfg) - # ############################################################################################## + output_dir = cfg["OUTPUT_DIR"] + work_dir = os.path.join(script_dir, output_dir) + space_group_list = [int(x) for x in cfg["SPACE_GROUP_LIST"].split(",")] + add_name = cfg["ADD_NAME"] + num_generation = int(cfg["NUM_GENERATION"]) + max_workers = int(cfg["MAX_WORKERS"]) # ############################################################################################## - # single crystal structure generate with Z'=1 - - molecule1 = format_parser.read_xyz_file("./test/molecule_1/conformers/conformer_0.xyz") - packaged_function.CSP_generater_parallel([molecule1], "./test", need_structure=100, space_group_list=[14,61],add_name="XULDUD_C1", max_workers=16,start_seed=1) + # # conformer search (uncomment to use) + conformer_search.conformer_search(cfg["SMILES"], os.path.join(work_dir, "molecule_1"), + num_conformers=int(cfg["GENERATE_CONFORMERS"]), max_attempts=10000, rms_thresh=0.1) # ############################################################################################## # ############################################################################################## - # single crystal structure generate with Z'=2 - - molecule1 = format_parser.read_xyz_file("./test/molecule_1/conformers/conformer_0.xyz") - packaged_function.CSP_generater_parallel([molecule1,molecule1], "./test", need_structure=100, space_group_list=[14,61],add_name="XULDUD_C1", max_workers=16,start_seed=1) + # single crystal structure generate with Z'=1 + + molecule1 = format_parser.read_xyz_file(os.path.join(work_dir, "molecule_1/conformers/conformer_0.xyz")) + packaged_function.CSP_generater_parallel([molecule1], work_dir, + need_structure=num_generation, space_group_list=space_group_list, + add_name=f"{add_name}_C1", max_workers=max_workers, start_seed=1) # ############################################################################################## # ############################################################################################## - # co-crystal structure generate - - molecule1 = format_parser.read_xyz_file("./test/molecule_1/conformers/conformer_0.xyz") - molecule2 = format_parser.read_xyz_file("./test/molecule_2/conformers/conformer_0.xyz") - packaged_function.CSP_generater_parallel([molecule1,molecule2], "./test", need_structure=100, space_group_list=[14,61],add_name="XULDUD_C1", max_workers=16,start_seed=1) + # single crystal structure generate with Z'=2 (uncomment to use) + + # molecule1 = format_parser.read_xyz_file(os.path.join(work_dir, "molecule_1/conformers/conformer_0.xyz")) + # packaged_function.CSP_generater_parallel([molecule1, molecule1], work_dir, + # need_structure=num_generation, space_group_list=space_group_list, + # add_name=f"{add_name}_C1", max_workers=max_workers, start_seed=1) # ############################################################################################## + # ############################################################################################## + # co-crystal structure generate (uncomment to use) + # molecule1 = format_parser.read_xyz_file(os.path.join(work_dir, "molecule_1/conformers/conformer_0.xyz")) + # molecule2 = format_parser.read_xyz_file(os.path.join(work_dir, "molecule_2/conformers/conformer_0.xyz")) + # packaged_function.CSP_generater_parallel([molecule1, molecule2], work_dir, + # need_structure=num_generation, space_group_list=space_group_list, + # add_name=f"{add_name}_C1", max_workers=max_workers, start_seed=1) + # ############################################################################################## - time_end=time.time() - print('time cost',time_end-time_start,'s') + time_end = time.time() + print('time cost', time_end - time_start, 's') diff --git a/uv.lock b/uv.lock new file mode 100644 index 0000000000000000000000000000000000000000..7873dab860f0669f4a9fa52df71cb0ea6703121f --- /dev/null +++ b/uv.lock @@ 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