Use handwritten cosine similarity #520
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zasdfgbnm
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farhadrgh and
IgnacioJPickering
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farhadrgh
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Nov 1, 2020
zasdfgbnm
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Dec 17, 2020
* Kill python 2.7 style super (aiqm#496) * Specify dtype for species (aiqm#502) * 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 * Include model parameter placeholders in site-packages (aiqm#500) * 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 numer, year (aiqm#506) * Update JCIM issue * Add cover and retrigger build * Distribute source tarball and wheel to PyPI (aiqm#508) * Distribute source and weel * trigger * fix * Disable Final for 3.6 (aiqm#509) * Disable Final for 3.6 * dont run mypy for 3.6 * Update aev.py (aiqm#510) * Raise error for unknown species (aiqm#512) * raise error for unknown species * make it jittable * fix dimension bug * Use torch.linalg.norm instead of torch.norm (aiqm#515) torch.norm is deprecated and may be removed in a future PyTorch release. * Use handwritten cosine similarity (aiqm#520) * Simplify pair computation on AEV (aiqm#519) * Simplify pair computation on AEV * save Co-authored-by: Farhad Ramezanghorbani <[email protected]> * Update CODEOWNERS (aiqm#523) * Add clang-format ci (aiqm#524) * Add clang-format ci * format Co-authored-by: Farhad Ramezanghorbani <[email protected]> * Update installation guide to mention conda (aiqm#525) * Add dummy cuda extension build (aiqm#521) * 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 <[email protected]> * Rename pipelines so that they are better displayed (aiqm#526) * 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 * Update cuda.yml (aiqm#528) * Update setup.py (aiqm#529) * Make CUDA extension TorchScript compatible (aiqm#527) * 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 mypy coverage (aiqm#530) * Use PyTorch autograd's hessian (aiqm#532) * Use PyTorch autograd's hessian * fix test * save * clean * save * save * drop hessian from jit example * delete old commented code (#7) (aiqm#536) Co-authored-by: Ignacio Pickering <[email protected]> * Faster tests (#8) (aiqm#537) * 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 <[email protected]> * Using the lalr parser loads networks x2 faster (#9) (aiqm#538) Co-authored-by: Ignacio Pickering <[email protected]> * Small modifications in code and comments to clarify (#11) (aiqm#539) Co-authored-by: Ignacio Pickering <[email protected]> * delete all python2 style super calls (#14) (aiqm#540) * delete all python2 style super calls * flake8 Co-authored-by: Ignacio Pickering <[email protected]> * Add sync before functions and print a warning if not synching (#17) (aiqm#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 <[email protected]> * Fix periodic table (#23) (aiqm#544) * Change 0th index of periodic table * Change species converter to reflect new convention * Change None for 'Dummy' and fix flake8 Co-authored-by: Ignacio Pickering <[email protected]> * Revert "Use PyTorch autograd's hessian (aiqm#532)" (aiqm#534) This reverts commit bd9d888. * Intuitive aev computer classmethod (#18) (aiqm#543) * 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 <[email protected]> * Cherry-pick #10 (aiqm#545) * 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 <[email protected]> * Use PyTorch's TestCase to compare tensor (aiqm#533) * 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 * Cherry-pick #15 (aiqm#541) * Move parsing resource code to neurochem/ (#15) * Move parsing resource code to neurochem/ * fix bug * fix * fix Co-authored-by: Ignacio Pickering <[email protected]> * Cherry-pick #22 (aiqm#546) * commit farhads and jinzes changes to fix some bugs [WIP] (#22) * commit farhads and jinzes changes to fix some bugs * Add tests for correct inputs * add missing * fix Co-authored-by: Ignacio Pickering <[email protected]> * More about cuaev (aiqm#547) * More about cuaev * Update setup.py * save * clang-format * Add code snippet to save validation and training sets in nnp_training (aiqm#548) * CUDA port for AEV computation (aiqm#516) * 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 <[email protected]> Co-authored-by: Xiang Gao <[email protected]> * provide better error message (aiqm#550) * clang-format line-limit to 120 (aiqm#552) * clang-format * line-limit 120 * CRLF to LF (aiqm#553) * line-limit 120 * CRLF to LF * fix cuaev angular kernel when center atom pairs are more than 32 (aiqm#555) * Update docs.yml (aiqm#557) * 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 <[email protected]> Co-authored-by: Richard Xue <[email protected]> * Do no require grad in ASE calculator (aiqm#559) Co-authored-by: Gao, Xiang <[email protected]> * flake8 Co-authored-by: Gao, Xiang <[email protected]> Co-authored-by: Farhad Ramezanghorbani <[email protected]> Co-authored-by: Richard Xue <[email protected]> Co-authored-by: Alon Grinberg Dana <[email protected]> Co-authored-by: akkamesh <[email protected]> Co-authored-by: zubatyuk <[email protected]>
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because it is faster.
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