Bug fix: change CifWriter to save only the element symbol, and not the entire species string #3071
+7
−2
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
Change the atom site type symbol, such that the element symbol is saved instead of the full species string (which includes site properties)
|
@kamronald does this still handle species with oxidation state correctly? |
|
@mkhorton good point, I just checked and it does not handle them properly, I'll fix that |
atom_site_type_symbol now saves the element and oxidation state, without the other site properties
|
@mkhorton oxidation states are now properly saved |
|
Thanks @kamronald! 👍 IIUC @mkhorton in #3065 (comment), he's suggesting we continue saving scalar magmoms to regular CIF using the local data name Also, would be great if you could refactor your repro #3065 (comment) into a new test case. |
janosh
added
needs testing
Codecov ReportPatch coverage:
Additional details and impacted files@@ Coverage Diff @@
## master #3071 +/- ##
==========================================
- Coverage 74.65% 74.09% -0.57%
==========================================
Files 230 230
Lines 69377 69382 +5
Branches 16154 16154
==========================================
- Hits 51796 51410 -386
- Misses 14513 14937 +424
+ Partials 3068 3035 -33
☔ View full report in Codecov by Sentry. |
janosh
force-pushed
the
master
branch
2 times, most recently
from
3c23114
to
36e289c
Compare
janosh
force-pushed
the
master
branch
4 times, most recently
from
d725325
to
dca98be
Compare
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Outdated suggestions cannot be applied.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.
Change the "atom site type symbol", such that the element symbol is saved instead of the full species string (which includes site properties). This fixes Issue #3065, allowing for accurate writing of structures containing species properties to CIF and MCIF files.
Summary
Major updates:
Change the "atom site type symbol", such that the element symbol is saved instead of the full species string (which includes site properties).
Todos
Checklist
Ensure:
ruff.mypy.