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* 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
* 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
* Update JCIM issue * Add cover and retrigger build
* Distribute source and weel * trigger * fix
* Disable Final for 3.6 * dont run mypy for 3.6
* raise error for unknown species * make it jittable * fix dimension bug
torch.norm is deprecated and may be removed in a future PyTorch release.
* Simplify pair computation on AEV * save 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>
* 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>
* 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
* 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
* Use PyTorch autograd's hessian * fix test * save * clean * save * save * drop hessian from jit example
* 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>
…iqm#542) * 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>
* Add classmethod for conveniently building AEVComputer * Fix bug * Add test * flake8 * Small change in assert * rename to zeta for consistency with other code * trigger tests * What the hell Dropbox?! -.- Co-authored-by: Ignacio Pickering <ign.pickering@gmail.com>
* Add convenience functions useful for active learning [WIP] (#10) * Add convenience functions useful for active learning * avoid training outputs * modify gitignore * Add convenience functions to directly get atomic energies * fix bug * fix mypy * flake8 * fix bugs * flake8 * mypy * Add tests for functions * add test to workflows and flake8 * empty to trigger tests * trigger * delete new test * readd new test * avoid training outputs * trigger * trigger tests again, they are all passing on my side * fix isclose in tests * save * fix Co-authored-by: Ignacio Pickering <ign.pickering@gmail.com>
* Use PyTorch's TestCase to compare tensor * save * save * save * save * save * save * save * save * save * Update test_energies.py * Update test_ase.py * save * flake8
* More about cuaev * Update setup.py * save * clang-format
* 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>
* clang-format * line-limit 120
* line-limit 120 * CRLF to LF
* Update docs.yml * Update docs.yml * Update docs.yml * Update docs.yml * Update docs.yml * Update docs.yml * Apply suggestions from code review Co-authored-by: Richard Xue <yueyericardo@gmail.com> Co-authored-by: Richard Xue <yueyericardo@gmail.com>
Co-authored-by: Gao, Xiang <qasdfgtyuiop@gmail.com>
IgnacioJPickering
requested review from
farhadrgh,
yueyericardo and
zasdfgbnm
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zasdfgbnm
approved these changes
Dec 17, 2020
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Merge changes from public torchani