GitLab

* Reduce number of kernel calls in AEV

* try

* Revert "try"

This reverts commit 04e56fde671c5168cb7825ab3c33f64a24196d98.

* more

* more

* merge more for angular terms

* neighbor_pairs

* more

* more

* save

* save

* save

* save
Co-authored-by: Farhad Ramezanghorbani <farhadrgh@users.noreply.github.com>

Co-authored-by: Farhad Ramezanghorbani <farhadrgh@users.noreply.github.com>

Co-authored-by: Farhad Ramezanghorbani <farhadrgh@users.noreply.github.com>

* ../aten/src/ATen/native/BinaryOps.cpp:81: UserWarning: Integer division of tensors using div or / is deprecated, and in a future release div will perform true division as in Python 3. Use true_divide or floor_divide (// in Python) instead.

* Update aev.py
Co-authored-by: Farhad Ramezanghorbani <farhadrgh@users.noreply.github.com>

* Clean up unused args

* fix
Co-authored-by: Farhad Ramezanghorbani <farhadrgh@users.noreply.github.com>

* Improve new dataset API

* Improve more on new dataset API

* fix

* fix reentrance

* Allow all intermediate state of transformation to be reentered

* Add length inference

* fix

* split by ratio

* add dataloader example

* add test for data loader

* Remove everything about chunking

* aev.py

* neurochem trainer

* training-benchmark-nsys-profile.py

* fix eval

* training-benchmark.py

* nnp_training.py

* flake8

* nnp_training_force.py

* fix dtype of species

* fix

* flake8

* requires_grad_

* git ignore

* fix

* original

* fix

* fix

* fix

* fix

* save

* save

* save

* save

* save

* save

* save

* save

* save

* collate

* fix

* save

* fix

* save

* save

* fix

* save

* fix

* fix

* no len

* float

* save

* save

* save

* save

* save

* save

* save

* save

* save

* fix

* save

* save

* save

* save

* fix

* fix

* fix

* fix mypy

* don't remove outliers

* save

* save

* save

* fix

* flake8

* save

* fix

* flake8

* docs

* more docs

* fix test_data

* remove test_data_new

* fix

* massive training time improvement

* flake8

* improve validation also

* improve training-benchmark.py

* fix devices

* send num_atoms to GPU

* rerun

* Add an argument for inserting synchronization

* Update training-benchmark.py

* Update training-benchmark.py
Co-authored-by: Farhad Ramezanghorbani <farhadrgh@users.noreply.github.com>

* Add tuple of atomic masses

* Add get_atomic_masses function, to get masses from periodic table indices (znumbers)

* Fix bug that prevented using ASE together with periodic_table_index

* ASE has to know if the model has PTI or not

* Allow for models that don't have a periodic_table_index attribute

* now vibrational analysis can be computed without explicit masses if periodic_table_index=True

* Add atomic masses calculator to docs

* flake8

* flake8

* flake8
Co-authored-by: Gao, Xiang <qasdfgtyuiop@gmail.com>

* Remove deprecated API and add a docstring to PaddedBatchChunkDataset

* Remove reference to deprecated API

* Added PaddedBatchChunkDataset to docs

* remove unused warnings

* Fix bug that prevented using ASE together with periodic_table_index

* ASE has to know if the model has PTI or not

* Allow for models that don't have a periodic_table_index attribute

* Add warning to ChemicalSymbolsToInts

* Change ocurrences of ChemicalSymbolsToInts in the code to reflect safe usage

* flake8

* Add warning to call also

* Add clarification

* docs dont fetch magic functions so documentation is moved to the class docstring

* fix clarification

* flake8

* bypass slow code

* delete reference to all_atoms which was unused

* delete whitespace

* make flake8 happy

* rerun

* actual change was off

* typo did not turn on bypassing code

* Add CODATA and IUPAC unit conversion factors

* Add units to main module

* change neurochem and training-benchmark to use the new hartree2kcalmol conversion

* change training-benchmark to use hartree2kcalmol conversion

* change comp6 to use the new hartree2kcalmol conversion

* change training-benchmark without nsys to also use hartree2kcalmol conversion

* change examples to use hartree2kcalmol conversion

* Rename ase to ase_ani to avoid naming conflicts that come from naming internal module the same as an external one we are using

* fix import

* Add ASE's hartree_to_ev conversion to compare with codata 2018

* Standarize our units to be essentially the same as ASE and CODATA 2014

* Change vibration_analysis to use the consistent constants

* Fix explanation in docstring

* Add millieV conversion factor

* Add millieV conversion factor to vibrational analysis

* Add clarification

* flake8

* revert name change

* Fix typo in function name

* Add units to __all__'

* Improve units docstring and comments in preparation for docs

* delete pad from docs

* Add units to api.rst

* minor formatting of docstrings and comments

* Add functions into the API

* final formatting changes

* flake8

* try to make mypy happy

* Checking if mypy prefers this

* rerun

* bypass slow code

* delete reference to all_atoms which was unused

* delete whitespace

* make flake8 happy

* rerun

* actual change was off

* typo did not turn on bypassing code

This PR resolves #415
Thanks @mhellstr for pointing it out

* try

* try

* try

* fix

* fix

* Delete pad from utils

* Delete pad_species
Co-authored-by: Farhad Ramezanghorbani <farhadrgh@users.noreply.github.com>
Co-authored-by: Gao, Xiang <qasdfgtyuiop@gmail.com>

* Add force constants, reduced masses and normalized normal modes to vibrational analysis

* Formatting to make flake8 happy

* nvidia profiling for md

* 1 model

* hook functions

* Update md-benchmark-nsys-profile.py

* nvidia profiling for md

* 1 model

* Add Python 3.8 to CI

* only oldest + latest
Co-authored-by: Farhad Ramezanghorbani <farhadrgh@users.noreply.github.com>

* Improvements on docs

* Add tips

* add example to customize JIT models

* cleanup

* fix list

* Update jit.py

* Support jit hessian

* fix

* fix

* Add badge to display stable torch compatibility

* more

* more

* don't run on PR

* nl

* Support  periodic table Indexing in builtin models

* flake8

* more

* fix

* fix cuda

* Add element names to ANIModel

* nc trainer