pymatgen.transformations.defect_transformations — pymatgen 2020.7.3 documentation

# Source code for pymatgen.transformations.defect_transformations

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

    """
    This module defines classes for point defect transformations on structures
    """

    from pymatgen.transformations.transformation_abc import AbstractTransformation

    __author__ = "Danny Broberg, Shyam Dwaraknath"
    __copyright__ = "Copyright 2018, The Materials Project"
    __version__ = "1.0"
    __maintainer__ = "Shyam Dwaraknath"
    __email__ = "shyamd@lbl.gov"
    __status__ = "Development"
    __date__ = "Mar 15, 2018"

    class DefectTransformation(AbstractTransformation):
        """
        Generates Defect structures based on pymatgen Defect Core classes
        """

        def __init__(self, scaling_matrix, defect):
            """
            :param scaling_matrix: Supercell scaling matrix
            :param defect: Defect pymatgen object
                NOTE: defect.bulk_structure should be same as provided structure in the apply_transformation step
            """
            self.scaling_matrix = scaling_matrix
            self.defect = defect

        def apply_transformation(self, structure):
            """
            :param structure: (bulk structure to be scaled up - typically conventional unit cell)
            :return: defect_structure, with charge applied
            """
            if structure != self.defect.bulk_structure:
                raise ValueError("Defect bulk_structure is not the same as input structure.")

            def_structure = self.defect.generate_defect_structure(self.scaling_matrix)

            return def_structure

        def __str__(self):
            inp_args = ["Supercell scaling matrix = {}".format(self.scaling_matrix), "Defect = {}".format(self.defect)]
            return "Defect Transformation : " + ", ".join(inp_args)

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

        @property
        def inverse(self):
            """
            Not implemented
            """
            raise NotImplementedError()

        @property
        def is_one_to_many(self):
            """
            Returns: False
            """
            return False