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Document XYZFileWriter chemical_symbols argument - #616

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cw-tan merged 1 commit into
mir-group:developfrom
kumar-miskin:fix/xyz-writer-chemical-symbols
Sep 30, 2026
Merged

cw-tan merged 1 commit into
mir-group:developfrom
kumar-miskin:fix/xyz-writer-chemical-symbols

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@kumar-miskin

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The XYZFileWriter, TestTimeXYZFileWriter, and ValTimeXYZFileWriter docstrings tell users to pass chemical_species, but their constructor accepts chemical_symbols. This changes only those docstrings to use the actual argument name and explains when the mapping is needed: output data without atomic numbers. The mapping order remains aligned with the model's type_names.

Validation: python3 -m compileall -q nequip/train/callbacks/write_xyz.py, a docstring consistency check for all three classes, and git diff --check passed. The full NequIP test suite was not run because it requires the heavier ML dependencies.

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cw-tan changed the base branch from main to develop September 28, 2026 01:53
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cw-tan force-pushed the fix/xyz-writer-chemical-symbols branch from 28e6371 to dad8e84 Compare September 28, 2026 01:53
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cw-tan force-pushed the fix/xyz-writer-chemical-symbols branch from dad8e84 to 2ebe15f Compare September 30, 2026 21:30
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cw-tan commented Sep 30, 2026

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Thanks for the PR @kumar-miskin

@cw-tan
cw-tan merged commit 7b869b0 into mir-group:develop Sep 30, 2026
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2 participants