Add easy way to create new substances for real numbers of mols#611
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lilyminium merged 2 commits intomainfrom Jan 28, 2025
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Add easy way to create new substances for real numbers of mols#611lilyminium merged 2 commits intomainfrom
lilyminium merged 2 commits intomainfrom
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mattwthompson
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Jan 23, 2025
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LGTM
I looked at the method you refer to and agree that some refactoring would be useful, but that doesn't need to be done right now
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Thanks Matt! |
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* add easy way to create new substances * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
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* add equilibration code * add some preliminary docs * add some docstrings * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * switch greaterthan -> greaterthanorequalto * add updates for equilibrated properties * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * fix equilibration_properties * Add easy way to create new substances for real numbers of mols (#611) * add easy way to create new substances * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * Add new conditions and tests (#614) * add new conditions and tests * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * Add NoBatch mode (#602) * add nobatch * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * add test * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * Migrate `tmpdir` fixture to new `tmp_path` (#615) * [pre-commit.ci] pre-commit autoupdate (#617) * [pre-commit.ci] pre-commit autoupdate updates: - [github.com/psf/black: 24.10.0 → 25.1.0](psf/black@24.10.0...25.1.0) - [github.com/PyCQA/isort: 5.13.2 → 6.0.0](PyCQA/isort@5.13.2...6.0.0) * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * Add AttributeClass initialization (#606) * add failing test * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * add __init__ method --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * Strip out `openmm.CMMotionRemover` force internally (#622) * Automatically strip out `openmm.CMMotionRemover` force internally * More consistently strip force * Fix relative tolerance (#604) * add nobatch * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * add fix * add helper test functions * add test data * Revert "add fix" This reverts commit 3d9f043. * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Revert "Revert "add fix"" This reverts commit 79a8bea. --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Matthew W. Thompson <mattwthompson@protonmail.com> * allow boxes to be retrieved, read, and short-circuit the graph * add data * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * remove additional raise * disallow merging * rm doc stub for now * Update openff/evaluator/workflow/workflow.py * Update openff/evaluator/properties/density.py * remove unused imports * fix imports * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Matt Thompson <matt.thompson@openforcefield.org> Co-authored-by: Matthew W. Thompson <mattwthompson@protonmail.com>
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Description
Fixes #610
Largely just copies very similar code from the BuildCoordinatesPackmol protocol; possibly these could be merged in some way.