pymatgen.analysis.prototypes — pymatgen 2020.7.3 documentation

# Source code for pymatgen.analysis.prototypes

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

    """
    This module is intended to match crystal structures against known crystallographic "prototype"
    structures.

    In this module, the AflowPrototypeMatcher uses the AFLOW LIBRARY OF CRYSTALLOGRAPHIC PROTOTYPES.
    If using this particular class, please cite their publication appropriately:

    Mehl, M. J., Hicks, D., Toher, C., Levy, O., Hanson, R. M., Hart, G., & Curtarolo, S. (2017).
    The AFLOW library of crystallographic prototypes: part 1.
    Computational Materials Science, 136, S1-S828.
    https://doi.org/10.1016/j.commatsci.2017.01.017
    """

    import os

    from monty.serialization import loadfn
    from pymatgen.analysis.structure_matcher import StructureMatcher

    module_dir = os.path.dirname(os.path.abspath(__file__))
    AFLOW_PROTOTYPE_LIBRARY = loadfn(os.path.join(os.path.dirname(os.path.abspath(__file__)),
                                                  "aflow_prototypes.json"))

    class AflowPrototypeMatcher:
        """
        This class will match structures to their crystal prototypes, and will
        attempt to group species together to match structures derived from
        prototypes (e.g. an A_xB_1-x_C from a binary prototype), and will
        give these the names the "-like" suffix.

        This class uses data from the AFLOW LIBRARY OF CRYSTALLOGRAPHIC PROTOTYPES.
        If using this class, please cite their publication appropriately:

        Mehl, M. J., Hicks, D., Toher, C., Levy, O., Hanson, R. M., Hart, G., & Curtarolo, S. (2017).
        The AFLOW library of crystallographic prototypes: part 1.
        Computational Materials Science, 136, S1-S828.
        https://doi.org/10.1016/j.commatsci.2017.01.017
        """

        def __init__(self, initial_ltol=0.2, initial_stol=0.3, initial_angle_tol=5):
            """
            Tolerances as defined in StructureMatcher. Tolerances will be
            gradually decreased until only a single match is found (if possible).

            Args:
                initial_ltol: fractional length tolerance
                initial_stol: site tolerance
                initial_angle_tol: angle tolerance
            """
            self.initial_ltol = initial_ltol
            self.initial_stol = initial_stol
            self.initial_angle_tol = initial_angle_tol

        @staticmethod
        def _match_prototype(structure_matcher, structure):
            tags = []
            for d in AFLOW_PROTOTYPE_LIBRARY:
                p = d['snl'].structure
                match = structure_matcher.fit_anonymous(p, structure)
                if match:
                    tags.append(d)
            return tags

        def _match_single_prototype(self, structure):
            sm = StructureMatcher(ltol=self.initial_ltol,
                                  stol=self.initial_stol,
                                  angle_tol=self.initial_angle_tol)
            tags = self._match_prototype(sm, structure)
            while len(tags) > 1:
                sm.ltol *= 0.8
                sm.stol *= 0.8
                sm.angle_tol *= 0.8
                tags = self._match_prototype(sm, structure)
                if sm.ltol < 0.01:
                    break
            return tags

        def get_prototypes(self, structure):
            """
            Get prototype(s) structures for a given
            input structure. If you use this method in
            your work, please cite the appropriate
            AFLOW publication:

            Mehl, M. J., Hicks, D., Toher, C., Levy, O.,
            Hanson, R. M., Hart, G., & Curtarolo, S. (2017).
            The AFLOW library of crystallographic prototypes: part 1.
            Computational Materials Science, 136, S1-S828.
            https://doi.org/10.1016/j.commatsci.2017.01.017

            Args:
                structure: structure to match

            Returns (list): A list of dicts with keys
            'snl' for the matched prototype and 'tags',
            a dict of tags ('mineral', 'strukturbericht'
            and 'aflow') of that prototype. This should
            be a list containing just a single entry,
            but it is possible a material can match
            multiple prototypes.
            """

            tags = self._match_single_prototype(structure)

            if len(tags) == 0:
                return None
            else:
                return tags