Bugfix: Structure/ase.Atoms interconversion side effects #4297
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
this fixes bug where atoms/structure objects were themselves modified when converted
wolearyc
changed the title
in keeping with style of ase.py
wolearyc
changed the title
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
Summary
This PR resolves #4289. There were bugs in
pymatgen.io.ase.AseAtomsAdaptorin whichStructureandase.Atomsobjects were modified when converted into one another. Specifically,Atoms.infoandStructure.propertiesshared memory, leading to side effects.Minor changes:
AseAtomsAdaptornow usesdeepcopywhen convertingAtoms.infotoStructure.propertiesand vice versa 3d47747ase.spacegroup.Spacegroupinterconversion 1730f29Checklist
ruff.mypy.duecredit@due.dcitedecorators to reference relevant papers by DOI (example) (N/A)