Fix import from Castep lattice_abc format #247
Merged
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
Cell files with lattice_abc vectors were broken, and this was not causing test failures because it wasn't tested. Here we: - Create test files with and without explicit dimension units - fix the treatment of lattice_abc data in "two-rows" format (no unit) - support recent versions of Pymatgen by migrating to - Lattice.from_parameters from the deprecated Lattice.from_lengths_and_angles - Note that Lattice.from_parameters does not produce the same cell matrices as CASTEP, and raise a warning if the user has abs_positions. The positions will very likely be wrong in this case; but not many features of Sumo are impacted.
|
After a brief discussion with @jryates : let's error out if the user specifies abs coordinates with lattice_abc. The error message can instruct the user to fix it using |
CASTEP and Pymatgen orientation are likely to be different from the same lattice vectors. To avoid building incorrect structures, refuse to work with lattice_abc and positions_abs simultaneously.
|
@utf I think all is good here, I'll push a release tag in a few days so you have a chance to object! |
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Outdated suggestions cannot be applied.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.
Closes #107
Cell files with lattice_abc vectors were broken, and this was not causing test failures because it wasn't tested. Here we:
abs_positions. The positions will very likely be wrong in this case; but not many features of Sumo are impacted, so perhaps it would be overkill to error out entirely.