Export "structure" class to .xyz file?

pymatgen
2

Here’s a simple way to do the conversion and retain lattice information as the comment line in the xyz file. For more context, take a look at this forum post.

from pymatgen.core import Molecule
from mp_api.client import MPRester
import json

mpid = "mp-1227591"
with MPRester() as mpr:
    structure = mpr.get_structure_by_material_id(mpid)

# perform operations on the structure here

lattice_comment = "# lattice = " + json.dumps(structure.lattice.matrix.tolist())

mol = Molecule(
    structure.species,
    structure.cart_coords,
    charge = structure.charge,
    site_properties=structure.site_properties,
)
xyz_str = mol.to(fmt="xyz")
xyz_lines = xyz_str.splitlines()
xyz_str = "\n".join([xyz_lines[0],lattice_comment,*xyz_lines[2:]])

with open(f"{mpid}.xyz","w") as f:
    f.write(xyz_str)
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