GitLab

* 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

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)

This is copy-pasted from https://github.com/aiqm/torchani/blob/master/.github/workflows/deploy-test-pypi.yml but I forgot to update it...

We should use the tag created on GitHub, not add a new tag named after date

* clean up py2 in setup.py

* Update setup.py

* Use type inference of arange to clean up code

* commit

* 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

* add mypy

* update

* fix

* only core

* add badge

* try

* Use namedtuple to improve API

* improve