Modify FHI-aims inputs to not use species string

materialsproject / pymatgen

Python Materials Genomics (pymatgen) is a robust materials analysis code that defines classes for structures and molecules with support for many electronic structure codes. It powers the Materials Project.

https://pymatgen.org

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Modify FHI-aims inputs to not use species string #4177

Open tpurcell90 opened 1 week ago

tpurcell90 commented 1 week ago

FHI-aims does not read spin from the species and that causes issues with magnetic calculations

Summary

Major changes:

fix 1: Don't use species_string for FHI-aims

Checklist

[x] Google format doc strings added. Check with ruff.
[x] Type annotations included. Check with mypy.
[x] Tests added for new features/fixes.
[x] If applicable, new classes/functions/modules have duecredit @due.dcite decorators to reference relevant papers by DOI (example)

tpurcell90 commented 1 week ago

@ansobolev Does this work for your things?

ansobolev commented 1 week ago

@tpurcell90 This seems to work for the defect workflow, thanks; however, as aims accepts anything in the species line (it's just a label), I would rather use something like site.label for site description in geometry.in. This will allow more precise accounting for species defaults in heterogeneous calculations (something like adsorbate on the surface). But that's for sure open for discussion and not the blocking issue.

tpurcell90 commented 1 week ago

FHI-aims can accept an arbitrary label, but pymatgen requires a CompositionLike or SpeciesLike object for species, which requires an element to be present from what I can tell.

I think this is ready for review.

ansobolev commented 1 week ago

For writing geometry.in pymatgen perspective does not matter, as the file is intended for FHI-aims; when reading the element can be defined by species defaults in control.in, or element can be explicitly included (like site.element_site.label) in the species label.