Source code for pymatgen.symmetry.structure

# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.

from __future__ import division, unicode_literals
import numpy as np
from pymatgen.core.structure import Structure

"""
This module implements symmetry-related structure forms.
"""


__author__ = "Shyue Ping Ong"
__copyright__ = "Copyright 2012, The Materials Project"
__version__ = "0.1"
__maintainer__ = "Shyue Ping Ong"
__email__ = "shyuep@gmail.com"
__date__ = "Mar 9, 2012"


class SymmetrizedStructure(Structure):
    """
    This class represents a symmetrized structure, i.e. a structure
    where the spacegroup and symmetry operations are defined. This class is
    typically not called but instead is typically obtained by calling
    pymatgen.symmetry.analyzer.SpacegroupAnalyzer.get_symmetrized_structure.

    Args:
        structure (Structure): Original structure
        spacegroup (SpacegroupOperations): An input SpacegroupOperations from 
            SpacegroupAnalyzer.
        equivalent_positions: Equivalent positions from SpacegroupAnalyzer.

    .. attribute: equivalent_indices

        indices of structure grouped by equivalency
    """

    def __init__(self, structure, spacegroup, equivalent_positions,
                 wyckoff_letters):
        self.spacegroup = spacegroup
        u, inv = np.unique(equivalent_positions, return_inverse=True)
        self.site_labels = equivalent_positions

        # site_properties = structure.site_properties
        # site_properties["wyckoff"] = [
        #     "%d%s" % (list(self.site_labels).count(self.site_labels[i]),
        #               wyckoff_letters[i]) for i in range(len(structure))]

        super(SymmetrizedStructure, self).__init__(
            structure.lattice, [site.species_and_occu for site in structure],
            structure.frac_coords, site_properties=structure.site_properties)

        self.equivalent_indices = [[] for i in range(len(u))]
        self.equivalent_sites = [[] for i in range(len(u))]
        wyckoff_symbols = [[] for i in range(len(u))]
        for i, inv in enumerate(inv):
            self.equivalent_indices[inv].append(i)
            self.equivalent_sites[inv].append(self.sites[i])
            wyckoff_symbols[inv].append(wyckoff_letters[i])
        self.wyckoff_symbols = ["%d%s" % (len(w), w[0])
                                for w in wyckoff_symbols]

    def find_equivalent_sites(self, site):
        """
        Finds all symmetrically equivalent sites for a particular site

        Args:
            site (PeriodicSite): A site in the structure

        Returns:
            ([PeriodicSite]): List of all symmetrically equivalent sites.
        """
        for sites in self.equivalent_sites:
            if site in sites:
                return sites

        raise ValueError("Site not in structure")