atomate2 / OpenMM OPLS-AA Enhancements#1111

Merged

janosh merged 28 commits intomaterialsproject:mainfrom

shehan807:feature/OPLS-AA

Mar 28, 2025

Commits on Jan 16, 2025

added opls_lj function; pre-commit fails for (1) eps._value call, perhaps this is fine? and (2) usused eps14 variable (need to check that eps == eps14)
Shehan M Parmar
committed

Commits on Jan 17, 2025

eps14 is not the correct value, off by 0.5 and eps should be used instead; solution: comment out eps14 line to match original ligpargen code
Shehan M Parmar
committed
initial commit to implementing opls_lj with error checking for proper 14 interaction scale values (i.e., 0.5); changed create_system_from_xml to create_ff_from_xml to enable generate_openmm_interch…
Shehan M Parmar
committed

Commits on Jan 18, 2025

the use of io.StringIO is seemingly a bug? works fine without needing to convert xml to string, leaving this commented for now before checking other cases
Shehan M Parmar
committed
added try/except to handle io.StringIO failure
Shehan M Parmar
committed

Commits on Jan 20, 2025

Commits on Jan 24, 2025

added generate_opls_xml function with placeholder for ligpargen commands
Shehan M Parmar
committed
fixed shutil.copy to shutil.move to avoid redundant files in tmpdir
Shehan M Parmar
committed
fixed linter issues (namely, subprocess.run(...shell=True) was unsafe and solution was to .split() command into a list of strings
Shehan M Parmar
committed
completed OPLS Docker documentation + except for shifter issues, generate_opls_xml(...) is complete
Shehan M Parmar
committed
Merge branch 'materialsproject:main' into feature/OPLS-AA
shehan807
authored

Commits on Jan 25, 2025

completed boss->ligpargen->docker->podman-hpc->subprocess pipeline to generate OPLS .xml files
Shehan M Parmar
committed
minor typo in docs
Shehan M Parmar
committed

Commits on Feb 6, 2025

updated tests for download_ and generate_opls_xml functions
Shehan M Parmar
committed

Commits on Mar 6, 2025

removed defusedxml dependency
Shehan M Parmar
committed
removed textwrap dependency
Shehan M Parmar
committed
replaced tag-based opls flag to ff_kwargs for opls
Shehan M Parmar
committed
added names_params documentation
Shehan M Parmar
committed
test_create_ff_from_xml
Shehan M Parmar
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pre-commit
Shehan M Parmar
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ff_kwargs is not None
Shehan M Parmar
committed

Commits on Mar 7, 2025

all new tests pass pytest
Shehan M Parmar
committed
final pre-commit
Shehan M Parmar
committed

Commits on Mar 10, 2025

added monkeypatching env variables
Shehan M Parmar
committed
fixed docker and/or podman-hpc edge case
Shehan M Parmar
committed
removed rogue file
Shehan M Parmar
committed
Merge pull request #2 from materialsproject/main
shehan807
authored