pymatgen.symmetry.structure — pymatgen 2020.7.3 documentation

# Source code for pymatgen.symmetry.structure

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

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

    from typing import Sequence, List

    import numpy as np

    from tabulate import tabulate

    from pymatgen.core.structure import Structure, PeriodicSite

    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.

        .. attribute: equivalent_indices

            indices of structure grouped by equivalency
        """

        def __init__(self, structure: Structure,
                     spacegroup,
                     equivalent_positions: Sequence[int],
                     wyckoff_letters: Sequence[str]):
            """
            Args:
                structure (Structure): Original structure
                spacegroup (SpacegroupOperations): An input SpacegroupOperations from
                    SpacegroupAnalyzer.
                equivalent_positions: Equivalent positions from SpacegroupAnalyzer.
                wyckoff_letters: Wyckoff letters
            """
            self.spacegroup = spacegroup
            u, inv = np.unique(equivalent_positions, return_inverse=True)
            self.site_labels = equivalent_positions

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

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

        def copy(self):
            """
            :return: Copy of structure.
            """
            return self.__class__(self, spacegroup=self.spacegroup,
                                  equivalent_positions=self.site_labels,
                                  wyckoff_letters=self.wyckoff_letters)

        def find_equivalent_sites(self, site) -> List[PeriodicSite]:
            """
            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")

        def __repr__(self):
            return self.__str__()

        def __str__(self):
            outs = [
                "SymmetrizedStructure",
                "Full Formula ({s})".format(s=self.composition.formula),
                "Reduced Formula: {}".format(self.composition.reduced_formula)]

            def to_s(x):
                return "%0.6f" % x
            outs.append("abc   : " + " ".join([to_s(i).rjust(10)
                                               for i in self.lattice.abc]))
            outs.append("angles: " + " ".join([to_s(i).rjust(10)
                                               for i in self.lattice.angles]))
            if self._charge:
                if self._charge >= 0:
                    outs.append("Overall Charge: +{}".format(self._charge))
                else:
                    outs.append("Overall Charge: -{}".format(self._charge))
            outs.append("Sites ({i})".format(i=len(self)))
            data = []
            props = self.site_properties
            keys = sorted(props.keys())
            for i, sites in enumerate(self.equivalent_sites):
                site = sites[0]
                row = [str(i), site.species_string]
                row.extend([to_s(j) for j in site.frac_coords])
                row.append(self.wyckoff_symbols[i])
                for k in keys:
                    row.append(props[k][i])
                data.append(row)
            outs.append(tabulate(data, headers=["#", "SP", "a", "b", "c", "Wyckoff"] + keys,
                                 ))
            return "\n".join(outs)

        def as_dict(self):
            """
            :return: MSONAble dict
            """
            return {
                "structure": super().as_dict(),
                "spacegroup": self.spacegroup,
                "equivalent_positions": self.site_labels,
                "wyckoff_letters": self.wyckoff_letters
            }

        @classmethod
        def from_dict(cls, d):
            """
            :param d: Dict representation
            :return: SymmetrizedStructure
            """
            return SymmetrizedStructure(
                Structure.from_dict(d["structure"]),
                spacegroup=d["spacegroup"],
                equivalent_positions=d["equivalent_positions"],
                wyckoff_letters=d["wyckoff_letters"]
            )