GitLab

* Set C++17 for latest pytorch versions. Add flags for CUDA 12 and 11.8

* Update setup.py

* remove import subprocess

* more robust way to compare version

---------
Co-authored-by: Jinze Xue <jinzexue@ufl.edu>

* Fix cub to 1.11.0 for cuda 10.2

* quick save

* quick save

* Fix --cuaev-all-sms

* expecttest

* fix ci

* init

* separate to h cpp cu files

* works

* fix

* clean

* update

* fix

* only keep one copy of Result

* const result&

* move declaration to header

* fix jit

* clean

* fix

* fix jit

* fix ci test

* clean

* revert to autograd in charge of it's result

* update

* fix memory issue of result.aev_t

* Update torchani/cuaev/aev.h
Co-authored-by: Gao, Xiang <qasdfgtyuiop@gmail.com>

* Update torchani/cuaev/aev.h
Co-authored-by: Gao, Xiang <qasdfgtyuiop@gmail.com>

* Update torchani/cuaev/aev.h
Co-authored-by: Gao, Xiang <qasdfgtyuiop@gmail.com>

* save

* Update torchani/cuaev/aev.h
Co-authored-by: Gao, Xiang <qasdfgtyuiop@gmail.com>

* update

* Update torchani/cuaev/cuaev.cpp
Co-authored-by: Gao, Xiang <qasdfgtyuiop@gmail.com>

* Update torchani/cuaev/cuaev.cpp
Co-authored-by: Gao, Xiang <qasdfgtyuiop@gmail.com>

* Update torchani/cuaev/aev.h
Co-authored-by: Gao, Xiang <qasdfgtyuiop@gmail.com>

* remove aev_t after forward

* remove release function

* fix

* fix jit

* update
Co-authored-by: Gao, Xiang <qasdfgtyuiop@gmail.com>

* Update install_cuda.sh

* Update install_cuda.sh

* Update install_cuda.sh

* update

* update

* update

* update

* update

* update

* update

* update

* init

* init

* double backward test

* fix doublebackward test

* add another test

* rm gaev

* radial done

* angular init

* angular done

* update

* force training benchmark

* format

* update

* benchmark

* update

* update

* clean redundancy codes

* update

* adapt review request

* update

* update

* update

* update

* update

* update

* fix

* fix

* cuAngularAEVs code deduplicate

* pairwise double backward

* cuRadialAEVs dedup

* pairwiseDistance dedup

* format

* readme build notes

* save

* update

* save

* save

* update

* fix

* save

* add equations on comments
Co-authored-by: Gao, Xiang <qasdfgtyuiop@gmail.com>

* Fast Build CUAEV

* fix

* --cuaev for fastbuild, --cuaev-all-sms for all

* update readme

* fix

* fix

* fix

* fix

* cuda port for aev computation

* benchmark, setup and import

* fix bug

* fix flake8 and jit

* fix collections.abc for python>3.7

* setup gitingore

* format code with formatter

* ignore more

* Use torch API to set streams

* Use pytorch's caching allocator

* empty line

* fix

* cuaev correntness testr, instruction of install on readme

* readme

* fix readme

* fix readme

* fix readme

* fix readme

* add usage in readme

* fix readme

* add test in readme

* fix readme

* -std=c++14

* bug fix - add async data copy

* bug fix - add missing stream sync

* code refactor and cosmetic changes

* aev benchmark for big protein

* remove mdtraj

* remove print

* move pdb to dataset folder

* cosmetic changes

* Move torchani/extensions -> torchani/cuaev

* clang-format -i

* cleanup

* return aev from cuComputeAEV

* Update aev.py

* Update aev.py

* fix flake8

* fix LGTM unused local variable

* clang-format

* fix

* save

* install change
Co-authored-by: richard <yueyericardo@gmail.com>
Co-authored-by: Xiang Gao <qasdfgtyuiop@gmail.com>

* More about cuaev

* Update setup.py

* save

* clang-format

* 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

* 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>

* clean up py2 in setup.py

* Update setup.py

* Change homepage url

I forgot to change that when I move it from zasdfgbm/torchani to aiqm/torchani...

* Update setup.py

* Move unittest check to GitHub Actions

Tests are parallelized

* Delete tests.yml

* Update setup.py

* Create test_requirements.txt

* Update unittest.yml

* Update unittest.yml

* Update README.md

* Delete install_dependencies.sh

* Delete install_dependencies_python2.sh

* Update unittest.yml

* Fix dependency in setup.py: `torch-nightly` has been renamed to `torch`

`torch-nightly` has been renamed to `torch`

* Update install_dependencies.sh

* Update install_dependencies_python2.sh

* Update deploy-docs.yml

* Update docs.yml

* Update tools.yml

* Update setup.py

* Update start.rst

* Update runnable_submodules.yml

* Update install_dependencies.sh

* Update install_dependencies_python2.sh

* Update start.rst

* Update README.md

* Update README.md

https://pypi.org/project/torchani/

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)

* fix lfs

* dependency on  pytorch-ignite-nightly

temporarily disable l2 support for now, planning to reenable it after adaw get merged into pytorch (#80)

rewrite unittests to completely remove dependency on NeuroChem