GitLab

* 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>

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

* Rename pipelines so that they are better displayed

* Update unittest.yml

* Update clang-format.yml

* Update clang-format.yml

* Update README.md

* Update runnable_submodules.yml

* Update README.md

* 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>

* Add clang-format ci

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

* Simplify pair computation on AEV

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

torch.norm is deprecated and may be removed in a future PyTorch release.

* raise error for unknown species

* make it jittable

* fix dimension bug

* Disable Final for 3.6

* dont run mypy for 3.6

* Distribute source and weel

* trigger

* fix

* Update JCIM issue

* Add cover and retrigger build

* skip downloading into site-packages

* add placeholder files

* add placeholder files

* dont check filesize in local_dir

* fix shutil erro

* use distutils instead of shutils

* Specify dtype for species

For some reason, sometimes species are constructed as int tensors instead of long tensors, this is wrong and should be fixed

* Update __init__.py

* 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

* README for resources [WIP]

* Update README.md

* Update README.md

* Update models.py

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

* Add new test with hardcoded saes

* flake8

* fix bug introduced in previous commit

* add possibility to use custom padding

* Add padding_dict to actual function

* Simplify arguments and fix docs

* typo

* 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

* Remove workaround for TorchScript bug on torch.unique_consecutive

On par with https://github.com/pytorch/pytorch/pull/39339



This breaks the compatibility with PyTorch 1.5.0, but hopefully will be compatible with 1.5.1.

* trigger ci

* trigger

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

* Update model URL

* Update models.py

* Update models.py

* fix

* cleanup

* save

* download resources from ASE_ANI

* update gitignore

* get resources with request

* fix flke8

* rm svn checkout for resources

* update

* fix flake8

* document species_indices

* Improve documentation

* More documentation for data

* More clearly specify behaviour of SpeciesConverter

* improve docs for SpeciesConverter

* flake8

* Add order recommendation to ChemicalSymbolsToInts

* Fix examples where species_to_tensor is used wrong

* Fix argument

* Add possibility of sorting in different order to subtract_self_energies

* make species_to_indices behave the same as subtract_self_energies

* Revert "make species_to_indices behave the same as subtract_self_energies"

This reverts commit a415df29bd6e270f3225f0b6721b3c873aeed40e.

* Fix examples

* make species_to_indices behave the same whithout breaking API

* Improve documentation to reflect correct usage

* Fix typos in docstring

* some more docstring issues

* more docstring

* Fix error in species_to_indices

* 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>