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


[docs]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]
[docs] def copy(self): """ :return: Copy of structure. """ return self.__class__(self, spacegroup=self.spacegroup, equivalent_positions=self.site_labels, wyckoff_letters=self.wyckoff_letters)
[docs] 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)
[docs] 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 }
[docs] @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"] )