GitLab

* Make training benchmark print a warning if not synchronizing, and add a sync before function also

* Take triu_index out since it does not run

* slightly increase default precision

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

ANI1x NNs are updated to be consistent with what we used in the paper

* 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 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

* Simplify triple_by_molecule

* fix

* fix

* fix

* 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