def standardize_cell(structure):
import spglib
from phonopy.structure.atoms import Atoms as PhonopyAtoms
from phonopy.structure.atoms import atom_data
bulk = PhonopyAtoms(symbols=[site.kind_name for site in structure.sites],
positions=[site.position for site in structure.sites],
cell=structure.cell)
structure_data = (structure.cell,
bulk.get_scaled_positions(),
bulk.get_atomic_numbers())
#lattice, refined_positions, numbers = spglib.refine_cell(structure_data, symprec=1e-5)
lattice, standardized_positions, numbers = spglib.standardize_cell(structure_data,
symprec=1e-5,
to_primitive=False,
no_idealize=False)
symbols = [atom_data[i][1] for i in numbers]
# print lattice, standardized_positions, numbers
# print [site.kind_name for site in structure.sites]
standardized_bulk = PhonopyAtoms(symbols=symbols,
scaled_positions=standardized_positions,
cell=lattice)
# create new aiida structure object
standarized = StructureData(cell=standardized_bulk.get_cell())
for position, symbol in zip(standardized_bulk.get_positions(), standardized_bulk.get_chemical_symbols()):
standarized.append_atom(position=position,
symbols=symbol)
return {'standardized_structure': standarized}
