Fix Molecule.get_boxed_structure when reorder=False #4419
Merged
Conversation
This file contains hidden or 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
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Outdated suggestions cannot be applied.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
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.