Support magmoms in get_phonopy_structure()

[tomdemeyere]

Summary

Phonopy needs magnetic moments to calculate the symmetry etc, currently pymatgen does not send it.

Checklist

• Google format doc strings added. Check with ruff.
• Type annotations included. Check with mypy.
• Tests added for new features/fixes.

python -m pytest tests/io/test_phonopy.py fails with "ImportError: cannot import name 'coord_cython' from 'pymatgen.util'", any ideas?

[JaGeo]

Tagging @JonathanSchmidt1 as I have seen a similar fix in one of his atomate2 branches.

[janosh]

Thanks @tomdemeyere! 👍

[JonathanSchmidt1]

@JaGeo My solution basically was the same as here.
Maybe sth relevant for you is that when I added magnetic moments it broke sth in atomate2 because some of the functionalities of phonopy did not work with magnetic moments at the time.
I assume this change in the materials project will lead to the workflow accepting magnetic structures automatically.

 get_phonopy_structure(structure)
 if use_symmetrized_structure == "primitive" and kpath_scheme != "seekpath":
        primitive_matrix: list[list[float]] | str = [
            [1.0, 0.0, 0.0],
            [0.0, 1.0, 0.0],
            [0.0, 0.0, 1.0],
        ]
    else:
        primitive_matrix = "auto"

For me auto was not working with magmoms so I had to remove it. If this is still the case, it might be an option to give a warning in atomate2 and specifically disable auto for magnetic structures.

[JaGeo]

@JonathanSchmidt1 Thanks! I will keep the potential issue for atomate2 in mind.