Source code for pymatgen.symmetry.site_symmetries

Provides analysis of site symmetries.

import numpy as np
from pymatgen.symmetry.analyzer import SpacegroupAnalyzer as sga
from pymatgen.core.operations import SymmOp

[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 in range(len(ops)): if all(ops[site2].translation_vector == [0, 0, 0]): pointops[site1].append(ops[site2]) 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 in range(len(pointops[site1])): for op2 in range(len(pointops[site2])): if np.allclose( pointops[site1][op1].rotation_matrix, pointops[site2][op2].rotation_matrix, ): sharedops[site1][site2].append(pointops[site1][op1]) for site1 in range(len(sharedops)): for site2 in range(len(sharedops[site1])): uniqueops = [] for ops in range(len(sharedops[site1][site2])): op = SymmOp.from_rotation_and_translation( rotation_matrix=sharedops[site1][site2][ops].rotation_matrix, translation_vec=(0, 0, 0), tol=tol, ) if op in uniqueops: continue else: uniqueops.append(op) sharedops[site1][site2] = uniqueops return sharedops