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LAMMPS non-unique molecule ID hotfix #1000

Merged
merged 18 commits into from
Jul 16, 2024
Merged

LAMMPS non-unique molecule ID hotfix #1000

merged 18 commits into from
Jul 16, 2024

Commits on Jul 9, 2024

  1. Salted hash in _write_atoms() with molecule ID to guarantee unique ID… 

    …s for Molecules with identical chemical tables
    @timbernat
    timbernat committed Jul 9, 2024
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  2. Wrote unit test to check unique molecule IDs in Interchange.to_lammps… 

    …() output
    @timbernat
    timbernat committed Jul 9, 2024
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  3. [pre-commit.ci] auto fixes from pre-commit.com hooks 

    for more information, see https://pre-commit.ci
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Commits on Jul 16, 2024

  1. Apply suggestions from code review 

    Incorporated suggestions for unique mol ID unit test improvements

Co-authored-by: Matt Thompson <[email protected]>
    @timbernat @mattwthompson
    timbernat and mattwthompson authored Jul 16, 2024
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  2. [pre-commit.ci] auto fixes from pre-commit.com hooks 

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  3. Removed unnecessary typing imports

    @timbernat
    timbernat committed Jul 16, 2024
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  4. Consolidated pilot_mol init and conformer generation using MoleculeWi… 

    …thConformer
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  5. [pre-commit.ci] auto fixes from pre-commit.com hooks 

    for more information, see https://pre-commit.ci
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  6. Updated sidelen default, added assertion to enforce test for multiple… 

    … Molecules
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    timbernat committed Jul 16, 2024
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  7. [pre-commit.ci] auto fixes from pre-commit.com hooks 

    for more information, see https://pre-commit.ci
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  8. Wrapped mol ID + CTAB hash with hash() to produce more literal value … 

    …for molecule_hash
    @timbernat
    timbernat committed Jul 16, 2024
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  9. Re-implemented LAMMPS file molecule ID extraction with in-Python lamm… 

    …ps interface
    @timbernat
    timbernat committed Jul 16, 2024
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  10. Merge remote-tracking branch 'refs/remotes/origin/lammps-hotfix' into… 

    … lammps-hotfix
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  11. [pre-commit.ci] auto fixes from pre-commit.com hooks 

    for more information, see https://pre-commit.ci
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  12. Added pytest parametrization of auxiliary args in test_unique_lammps_… 

    …mol_ids()
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    timbernat committed Jul 16, 2024
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  13. [pre-commit.ci] auto fixes from pre-commit.com hooks 

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  14. MAINT: Streamline, skip generating positions

    @mattwthompson
    mattwthompson committed Jul 16, 2024
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  15. FIX: Use benzene, not fulvene

    @mattwthompson
    mattwthompson committed Jul 16, 2024
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