Source code for pymatgen.symmetry.site_symmetries
"""
Provides analysis of site symmetries.
"""
import numpy as np
from pymatgen.core.operations import SymmOp
from pymatgen.symmetry.analyzer import SpacegroupAnalyzer as sga
[docs]def get_site_symmetries(struc, precision=0.1):
"""
Get all the point group operations centered on each atomic site
in the form [[point operations of site index 1]...[[point operations of site index N]]]
Args:
struc: Pymatgen structure
precision (float): tolerance to find symmetry operaitons
Return:
list of lists of point operations for each atomic site
"""
pointops = []
# Point symmetries of each atom
for site1 in range(len(struc.sites)):
tempstruc = struc.copy()
# Place the origin of the cell at each atomic site
pointops.append([])
for site2 in range(len(struc.sites)):
tempstruc.replace(
site2,
tempstruc.sites[site2].specie,
tempstruc.frac_coords[site2] - struc.frac_coords[site1],
)
sgastruc = sga(tempstruc, symprec=precision)
ops = sgastruc.get_symmetry_operations(cartesian=True)
for site2, op in enumerate(ops):
if all(op.translation_vector == [0, 0, 0]):
pointops[site1].append(op)
return pointops
[docs]def get_shared_symmetry_operations(struc, pointops, tol=0.1):
"""
Get all the point group operations shared by a pair of atomic sites
in the form [[point operations of site index 1],[],...,[]]
Args:
struc: Pymatgen structure
pointops: list of point group operations from get_site_symmetries method
Return:
list of lists of shared point operations for each pair of atomic sites
"""
numsites = len(struc)
sharedops = [[0 for x in range(numsites)] for y in range(numsites)]
for site1 in range(numsites):
for site2 in range(numsites):
sharedops[site1][site2] = []
for op1, pop1 in enumerate(pointops[site1]):
for op2, pop2 in enumerate(pointops[site2]):
if np.allclose(pop1.rotation_matrix, pop2.rotation_matrix):
sharedops[site1][site2].append(pop1)
for site1, sops in enumerate(sharedops):
for site2, sop in enumerate(sops):
uniqueops = []
for ops in sop:
op = SymmOp.from_rotation_and_translation(
rotation_matrix=ops.rotation_matrix,
translation_vec=(0, 0, 0),
tol=tol,
)
if op not in uniqueops:
uniqueops.append(op)
sharedops[site1][site2] = uniqueops
return sharedops