Add keyword check_occu: bool = True to CifParser.get_structures()
#2836
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add tests to skip_checks
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Could you move the test into the existing |
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Additional details and impacted files@@ Coverage Diff @@
## master #2836 +/- ##
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- Coverage 74.63% 74.06% -0.58%
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Files 230 230
Lines 69403 69426 +23
Branches 16161 16169 +8
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- Hits 51802 51422 -380
- Misses 14528 14959 +431
+ Partials 3073 3045 -28
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…pymatgen into Add-Skip_checks
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@janosh I believe everything is working as it should now. I added the description you wanted as well. |
pymatgen/io/cif.py
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| if skip_occu_checks: | ||
| struct_2 = Structure( | ||
| lattice, all_species, all_coords, site_properties=site_properties, labels=all_labels | ||
| ) | ||
| for idx in range(len(struct_2)): | ||
| struct_2[idx] = PeriodicSite( | ||
| all_species_noedit[idx], all_coords[idx], lattice, properties=site_properties, skip_checks=True | ||
| ) |
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This looks needlessly complicated. What's the reason for creating struct_2?
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I think the reason struct_2 was there is no longer in cif.py. I've updated the file so that it doesn't make a new object.
pymatgen/io/cif.py
Outdated
| if skip_occu_checks: | ||
| struct_2 = SymmetrizedStructure(struct, sg, equivalent_indices, wyckoffs) | ||
| for idx in range(len(struct_2)): | ||
| struct_2[idx] = PeriodicSite( | ||
| all_species_noedit[idx], | ||
| all_coords[idx], | ||
| lattice, | ||
| properties=site_properties, | ||
| skip_checks=True, | ||
| ) | ||
| return struct_2 | ||
|
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janosh
changed the title
check_occu: bool = True to CifParser.get_structures()
janosh
added
enhancement
If
check_occu=False, site occupancy will not be checked, allowing unphysical occupancy != 1. Useful for experimental results in which occupancy was allowed to refine to unphysical values. Warning: unphysical site occupancies are incompatible with many pymatgen features.