Fix Molecule.get_boxed_structure when reorder=False#4419
Merged
shyuep merged 1 commit intomaterialsproject:masterfrom May 28, 2025
Merged
Fix Molecule.get_boxed_structure when reorder=False#4419shyuep merged 1 commit intomaterialsproject:masterfrom
shyuep merged 1 commit intomaterialsproject:masterfrom
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Summary
In
Molecule.get_boxed_structure, whenreorder=False, in the current version of the code does not use the processed new coordinates, but the initial ones of the Molecule. This usually results for example in a Molecule not being centered in the box.Unless I am missing something there should be no reason not to use the modified coordinates in the case of
reorder=False. This PR switches to use the same coordinates independently of the final sorting.I added a test based on the coordinates that would have failed in the previous implementation due to the molecule not being centered in the box.