GitLab

* Add convenience functions useful for active learning [WIP] (#10)

* Add convenience functions useful for active learning

* avoid training outputs

* modify gitignore

* Add convenience functions to directly get atomic energies

* fix bug

* fix mypy

* flake8

* fix bugs

* flake8

* mypy

* Add tests for functions

* add test to workflows and flake8

* empty to trigger tests

* trigger

* delete new test

* readd new test

* avoid training outputs

* trigger

* trigger tests again, they are all passing on my side

* fix isclose in tests

* save

* fix
Co-authored-by: Ignacio Pickering <ign.pickering@gmail.com>

* Add classmethod for conveniently building AEVComputer

* Fix bug

* Add test

* flake8

* Small change in assert

* rename to zeta for consistency with other code

* trigger tests

* What the hell Dropbox?! -.-
Co-authored-by: Ignacio Pickering <ign.pickering@gmail.com>

This reverts commit bd9d888a.

* modifications to make tests faster

* Now ani1x is not loaded for any aev_computer necessary

* flake*

* Avoid test warnings by loading from json and setting initial velocities to a small number

* Avoid loading from cif in ManualMirror and Repeat also

* Add comments to clarify test_energies and delete unused variable

* Fix inaccurate comment

* Delete unused variable in test_ensemble

* Add comments and clarifications to test_ase

* flake8
Co-authored-by: Ignacio Pickering <ign.pickering@gmail.com>

* Use PyTorch autograd's hessian

* fix test

* save

* clean

* save

* save

* drop hessian from jit example

* Make CUDA extension TorchScript compatible

* save

* save

* fix

* save

* save

* save

* save

* Update install_dependencies.sh

* trigger ci

* save

* fix

* save

* save

* save

* save

* try

* fix

* revert

* save

* save

* mypy

* Add dummy cuda extension build

* save

* run tests

* save

* fix

* pytorch cu110

* no vision

* save

* nl

* save

* save

* save

* save

* save

* save

* save

* autopep8

* more autopep8

* optional=True

* no todo

* fix

* refactor ci

* mypy

* save

* flake8

* os error

* Run cuaev test

* save

* clang format

* Delete delete-me.cu

* Search for cub in pytorch include paths

* nl

* instructions on test

* Add better handle cuaev install/not install

* test_cuaev.py

* clean

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

* Remove test gradient from aev tests

* Add a dedicated test gradient for one model, and make it feasible

* add test_grad to unittests

* Add some comments and fix formatting

* flake8

* flake8

* remove unused var

* delete transform function, which was legacy from old pytorch probably

* Delete random_skip function, which was unused

* Allow testNeuroChem to use cuda if available, which makes it much faster

* small modification for consistency

* remove unused import

* simplify device call

* remove unused variable

* add main to test_grad

* Remove test gradient from aev tests

* Add a dedicated test gradient for one model, and make it feasible

* add test_grad to unittests

* Add some comments and fix formatting

* flake8

* flake8

* remove unused var

* Add new test with hardcoded saes

* flake8

* fix bug introduced in previous commit

* cleanup after test_vibrational to avoid .pckl files everywhere

* only dump test_neurochem's runs into torchani/tests

* avoid runs inside tests/

* Add coverage to gitignore

* consts is unnecessary here

* Allow easily loading individual models

* Hopefully make the tests a tiny bit faster by not loading the whole network each time

* Refactor BuiltinNet into BuiltinModel and BuiltinEnsemble

* Change test name

* flake8 whitespace

* Get rid of redundant comparison

* remove unused import

* Fix info file bug

* flake8

* don't use nonlocal on get_resource

* Revert "don't use nonlocal on get_resource"

This reverts commit efe221bb4f7ce4a1ccb8c3c73b886bdbad019ab0.

* Fix get_resource bug

* Add missing init call

* Fix species_to_tensor bug

* Add species attribute

* Add some extra attributes

* Fix bug in getitem

* Always assign species_converter

* Species to tensor is also an entry point

* Lets not make it an entry point for now

* delete duplicated definition

* cleanup

* move forces to additional_properties

* fix typo

* 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>

* 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

* 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

* 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

* Support jit hessian

* fix

* fix

* Support  periodic table Indexing in builtin models

* flake8

* more

* fix

* fix cuda

* Add element names to ANIModel

* nc trainer

Add helper module to convert species from element id in periodic table to 0, 1, 2, 3, ... format (#396)

* Init

* fix test

* flake8

* try fix

* Fix stupidity of len(self)

* Allow passing pbc and cell to sequential

* revert

* Simplify ase interface

* fix

* fix

* fix

* flake8

* Update ase.py

* fix

* Try latest ASE

Just to see if ASE fixes its bug

* fix

* Remove AEV cacher

* more

* more

* more

* flake8

* further cleanup

* Remove ignite

* remove neurochem-test

* remove cache-aev

* Add unit test for builtin models

* flake8

* add test for scripted ensemble

* use torchani.nn.Sequential

* change OrderedDict to module list

* fix

* fix nn.py

* try more fix

* try

* more

* more

* fix more

* rename

* bring ensemble back

* make ANIModel iterable

* Move unittest check to GitHub Actions

Tests are parallelized

* Delete tests.yml

* Update setup.py

* Create test_requirements.txt

* Update unittest.yml

* Update unittest.yml

* Update README.md

* Delete install_dependencies.sh

* Delete install_dependencies_python2.sh

* Update unittest.yml

* split

* split

* fix

* fix

* -v

* more

* more

* fix

* fix

* flake8

* transform

* reduce testBenzeneMD

* version

* reduce number of epoches

* further reduce time

* Update docs.yml

* enable EnergyShifter scripting

* fix

* fix

* make aev,model compatible with jit

* add type annotation to nn

* flake8 fix

* refactor AEVComputer

* fix doc

* an example with padding

* use Optional type instead of padding

* fix

* fix

* make pbc and cell keyword arguments in test_aev

* fix

* make pbc and cell keyword arguments in ase

* fix

* fix

* fix dtype

* fix

* aev_computer dtype to double

* change test files to have aev_computer with keyword argument

* fix JIT types

* add TestAEVJIT

* fix LGTM alerts

* fix TestAEVJIT

* Update aev.py

workaround for dtype in `torch.arange`

* More arange bugs

* Even more arange

* fix LGTM alert

* cached

* typo and comments

* easy to read

* change some names

* fix unit test

* empty line

* fix

* fix

* add docs and add whether include_energies

* docs

* other properties for shuffled dataset

* docs

* dtype for benchmark

* add properties to test

* style

* split

* clean

* docs

* docs

* Update new.py