pymatgen.analysis.aflow_prototypes — pymatgen 2020.3.2 documentation

# Source code for pymatgen.analysis.aflow_prototypes

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

    import os

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

    """
    This module uses data from the AFLOW LIBRARY OF CRYSTALLOGRAPHIC PROTOTYPES.
    If using this module, 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
    """

    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