GitLab

* Use PyTorch's TestCase to compare tensor

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* Update test_energies.py

* Update test_ase.py

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* flake8

* Make CUDA extension TorchScript compatible

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* fix

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* Update install_dependencies.sh

* trigger ci

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* fix

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* try

* fix

* revert

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* mypy

* Add dummy cuda extension build

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* run tests

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* fix

* pytorch cu110

* no vision

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* nl

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* autopep8

* more autopep8

* optional=True

* no todo

* fix

* refactor ci

* mypy

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* flake8

* os error

* Run cuaev test

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* 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>

* Adding ANI-2x parameters

* Moving 2x to seperate branch

* Adding ANI-2x to new branch

* Adding 2x network

* Update models.py

* Update api.rst

* Update __init__.py
Co-authored-by: Christian Devereux <cdever01@ufl.edu>
Co-authored-by: Farhad Ramezanghorbani <farhadrgh@users.noreply.github.com>

* switch AdamW from torchany to pytorch

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

* 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

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)

* Remove ignite

* remove neurochem-test

* remove cache-aev

Add AdamW optimizer, Add docs of nnp training to train a real ANI-1x model, remove h5py and ignite from dependencies, rename MAEMetric -> MaxAEMetric, use torch.utils.tensorboard to replace tensorboardX (#224)

* add ANI model zoo

* Update cache_aev.py

rewrite unittests to completely remove dependency on NeuroChem