GitLab

* 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)

* 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

* add mypy

* update

* fix

* only core

* add badge

* try

* Use namedtuple to improve API

* improve

* __constants__ is deprecated

* commit

* Use modern type annotations for utils.py

* update (#377)

* Remove python2 support from CI, _six, etc. (#370)

* Remove python2 step 1

* badge

* Delete _six.py

* Simplify triple_by_molecule (#368)

* Simplify triple_by_molecule

* fix

* fix

* fix

* Use @ syntax (#371)

* Use modern type annotations for nn.py (#373)

* Use modern type annotations for nn.py

* flake8

* Use modern type annotations for models.py (#374)

* Use modern type annotations for aev.py

* commit

* Use modern type annotations for nn.py

* flake8

* Simplify triple_by_molecule

* fix

* fix

* fix

* Remove python2 step 1

* badge

* Delete _six.py

* Simplify code using torch.triu_indices

* Update aev.py

* Remove AEV cacher

* more

* more

* more

* flake8

* further cleanup

* Don't hard code ensemble size

* flake8

* fix

* Remove ignite

* remove neurochem-test

* remove cache-aev

* fix cuda support

* Update aev.py

* Update utils.py

* Update utils.py

* Update utils.py

* Update utils.py

* remove float32 dtypes from comp6.py

* fix device type

* Update utils.py

* Update utils.py

fix typo!

* 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

* Update utils.py

if I train molecule like Oxygen which contains only one element, the self.self_energies is a scalar and will make the operation self_energies = self.self_energies[species] crash. Besides, the species of Oxygen is [[3,3]] and is over the boundary of the energy list, so need to minus the minimum.

* Update utils.py

* 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