pymatgen.symmetry.site_symmetries — pymatgen 2020.7.3 documentation

# 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

    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

    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