pymatgen.transformations.site_transformations — pymatgen 2020.7.3 documentation

# Source code for pymatgen.transformations.site_transformations

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

    """
    This module defines site transformations which transforms a structure into
    another structure. Site transformations differ from standard transformations
    in that they operate in a site-specific manner.
    All transformations should inherit the AbstractTransformation ABC.
    """

    import math
    import itertools
    import logging
    import time

    from monty.json import MSONable

    import numpy as np

    from pymatgen.symmetry.analyzer import SpacegroupAnalyzer
    from pymatgen.transformations.transformation_abc import AbstractTransformation
    from pymatgen.analysis.ewald import EwaldSummation, EwaldMinimizer

    __author__ = "Shyue Ping Ong, Will Richards"
    __copyright__ = "Copyright 2011, The Materials Project"
    __version__ = "1.2"
    __maintainer__ = "Shyue Ping Ong"
    __email__ = "shyuep@gmail.com"
    __date__ = "Sep 23, 2011"

    class InsertSitesTransformation(AbstractTransformation):
        """
        This transformation substitutes certain sites with certain species.
        """
        def __init__(self, species, coords, coords_are_cartesian=False,
                     validate_proximity=True):
            """
            Args:
                species: A list of species. e.g., ["Li", "Fe"]
                coords: A list of coords corresponding to those species. e.g.,
                    [[0,0,0],[0.5,0.5,0.5]].
                coords_are_cartesian (bool): Set to True if coords are given in
                    cartesian coords. Defaults to False.
                validate_proximity (bool): Set to False if you do not wish to ensure
                    that added sites are not too close to other sites. Defaults to True.
            """
            if len(species) != len(coords):
                raise ValueError("Species and coords must be the same length!")
            self.species = species
            self.coords = coords
            self.coords_are_cartesian = coords_are_cartesian
            self.validate_proximity = validate_proximity

        def apply_transformation(self, structure):
            """
            Apply the transformation.

            Arg:
                structure (Structure): A structurally similar structure in
                    regards to crystal and site positions.

            Return:
                Returns a copy of structure with sites inserted.
            """
            s = structure.copy()
            for i, sp in enumerate(self.species):
                s.insert(i, sp, self.coords[i],
                         coords_are_cartesian=self.coords_are_cartesian,
                         validate_proximity=self.validate_proximity)
            return s.get_sorted_structure()

        def __str__(self):
            return "InsertSiteTransformation : " + \
                "species {}, coords {}".format(self.species, self.coords)

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

        @property
        def inverse(self):
            """Return: None"""
            return None

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

    class ReplaceSiteSpeciesTransformation(AbstractTransformation):
        """
        This transformation substitutes certain sites with certain species.
        """
        def __init__(self, indices_species_map):
            """
            Args:
                indices_species_map: A dict containing the species mapping in
                    int-string pairs. E.g., { 1:"Na"} or {2:"Mn2+"}. Multiple
                    substitutions can be done. Overloaded to accept sp_and_occu
                    dictionary. E.g. {1: {"Ge":0.75, "C":0.25} }, which
                    substitutes a single species with multiple species to generate a
                    disordered structure.
            """
            self.indices_species_map = indices_species_map

        def apply_transformation(self, structure):
            """
            Apply the transformation.

            Arg:
                structure (Structure): A structurally similar structure in
                    regards to crystal and site positions.

            Return:
                Returns a copy of structure with sites replaced.
            """
            s = structure.copy()
            for i, sp in self.indices_species_map.items():
                s[int(i)] = sp
            return s

        def __str__(self):
            return "ReplaceSiteSpeciesTransformation :" + \
                ", ".join(["{}->{}".format(k, v) + v for k, v in
                           self.indices_species_map.items()])

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

        @property
        def inverse(self):
            """Return: None"""
            return None

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

    class RemoveSitesTransformation(AbstractTransformation):
        """
        Remove certain sites in a structure.
        """
        def __init__(self, indices_to_remove):
            """
            Args:
                indices_to_remove: List of indices to remove. E.g., [0, 1, 2]
            """

            self.indices_to_remove = indices_to_remove

        def apply_transformation(self, structure):
            """
            Apply the transformation.

            Arg:
                structure (Structure): A structurally similar structure in
                    regards to crystal and site positions.

            Return:
                Returns a copy of structure with sites removed.
            """
            s = structure.copy()
            s.remove_sites(self.indices_to_remove)
            return s

        def __str__(self):
            return "RemoveSitesTransformation :" + ", ".join(
                map(str, self.indices_to_remove))

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

        @property
        def inverse(self):
            """Return: None"""
            return None

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

    class TranslateSitesTransformation(AbstractTransformation):
        """
        This class translates a set of sites by a certain vector.
        """
        def __init__(self, indices_to_move, translation_vector,
                     vector_in_frac_coords=True):
            """
            Args:
                indices_to_move: The indices of the sites to move
                translation_vector: Vector to move the sites. If a list of list or numpy
                    array of shape, (len(indices_to_move), 3), is provided then each
                    translation vector is applied to the corresponding site in the
                    indices_to_move.
                vector_in_frac_coords: Set to True if the translation vector is in
                    fractional coordinates, and False if it is in cartesian
                    coordinations. Defaults to True.
            """
            self.indices_to_move = indices_to_move
            self.translation_vector = np.array(translation_vector)
            self.vector_in_frac_coords = vector_in_frac_coords

        def apply_transformation(self, structure):
            """
            Apply the transformation.

            Arg:
                structure (Structure): A structurally similar structure in
                    regards to crystal and site positions.

            Return:
                Returns a copy of structure with sites translated.
            """
            s = structure.copy()
            if self.translation_vector.shape == (len(self.indices_to_move), 3):
                for i, idx in enumerate(self.indices_to_move):
                    s.translate_sites(idx, self.translation_vector[i],
                                      self.vector_in_frac_coords)
            else:
                s.translate_sites(self.indices_to_move, self.translation_vector,
                                  self.vector_in_frac_coords)
            return s

        def __str__(self):
            return "TranslateSitesTransformation for indices " + \
                "{}, vect {} and vect_in_frac_coords = {}".format(
                    self.indices_to_move, self.translation_vector,
                    self.vector_in_frac_coords)

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

        @property
        def inverse(self):
            """
            Returns:
                TranslateSitesTranformation with the reverse translation.
            """
            return TranslateSitesTransformation(
                self.indices_to_move, -self.translation_vector,
                self.vector_in_frac_coords)

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

        def as_dict(self):
            """
            Json-serializable dict representation.
            """
            d = MSONable.as_dict(self)
            d["translation_vector"] = self.translation_vector.tolist()
            return d

    class PartialRemoveSitesTransformation(AbstractTransformation):
        """
        Remove fraction of specie from a structure.
        Requires an oxidation state decorated structure for ewald sum to be
        computed.

        Given that the solution to selecting the right removals is NP-hard, there
        are several algorithms provided with varying degrees of accuracy and speed.
        The options are as follows:

        ALGO_FAST:
            This is a highly optimized algorithm to quickly go through the search
            tree. It is guaranteed to find the optimal solution, but will return
            only a single lowest energy structure. Typically, you will want to use
            this.

        ALGO_COMPLETE:
            The complete algo ensures that you get all symmetrically distinct
            orderings, ranked by the estimated Ewald energy. But this can be an
            extremely time-consuming process if the number of possible orderings is
            very large. Use this if you really want all possible orderings. If you
            want just the lowest energy ordering, ALGO_FAST is accurate and faster.

        ALGO_BEST_FIRST:
            This algorithm is for ordering the really large cells that defeats even
            ALGO_FAST.  For example, if you have 48 sites of which you want to
            remove 16 of them, the number of possible orderings is around
            2 x 10^12. ALGO_BEST_FIRST shortcircuits the entire search tree by
            removing the highest energy site first, then followed by the next
            highest energy site, and so on. It is guaranteed to find a solution
            in a reasonable time, but it is also likely to be highly inaccurate.

        ALGO_ENUMERATE:
            This algorithm uses the EnumerateStructureTransformation to perform
            ordering. This algo returns *complete* orderings up to a single unit
            cell size. It is more robust than the ALGO_COMPLETE, but requires
            Gus Hart's enumlib to be installed.
        """

        ALGO_FAST = 0
        ALGO_COMPLETE = 1
        ALGO_BEST_FIRST = 2
        ALGO_ENUMERATE = 3

        def __init__(self, indices, fractions, algo=ALGO_COMPLETE):
            """
            Args:
                indices:
                    A list of list of indices.
                    e.g. [[0, 1], [2, 3, 4, 5]]
                fractions:
                    The corresponding fractions to remove. Must be same length as
                    indices. e.g., [0.5, 0.25]
                algo:
                    This parameter allows you to choose the algorithm to perform
                    ordering. Use one of PartialRemoveSpecieTransformation.ALGO_*
                    variables to set the algo.
            """
            self.indices = indices
            self.fractions = fractions
            self.algo = algo
            self.logger = logging.getLogger(self.__class__.__name__)

        def _best_first_ordering(self, structure, num_remove_dict):
            self.logger.debug("Performing best first ordering")
            starttime = time.time()
            self.logger.debug("Performing initial ewald sum...")
            ewaldsum = EwaldSummation(structure)
            self.logger.debug("Ewald sum took {} seconds."
                              .format(time.time() - starttime))
            starttime = time.time()

            ematrix = ewaldsum.total_energy_matrix
            to_delete = []

            totalremovals = sum(num_remove_dict.values())
            removed = {k: 0 for k in num_remove_dict.keys()}
            for i in range(totalremovals):
                maxindex = None
                maxe = float("-inf")
                maxindices = None
                for indices in num_remove_dict.keys():
                    if removed[indices] < num_remove_dict[indices]:
                        for ind in indices:
                            if ind not in to_delete:
                                energy = sum(ematrix[:, ind]) + \
                                    sum(ematrix[:, ind]) - ematrix[ind, ind]
                                if energy > maxe:
                                    maxindex = ind
                                    maxe = energy
                                    maxindices = indices
                removed[maxindices] += 1
                to_delete.append(maxindex)
                ematrix[:, maxindex] = 0
                ematrix[maxindex, :] = 0
            s = structure.copy()
            s.remove_sites(to_delete)
            self.logger.debug("Minimizing Ewald took {} seconds."
                              .format(time.time() - starttime))
            return [{"energy": sum(sum(ematrix)),
                     "structure": s.get_sorted_structure()}]

        def _complete_ordering(self, structure, num_remove_dict):
            self.logger.debug("Performing complete ordering...")
            all_structures = []
            symprec = 0.2
            s = SpacegroupAnalyzer(structure, symprec=symprec)
            self.logger.debug("Symmetry of structure is determined to be {}."
                              .format(s.get_space_group_symbol()))
            sg = s.get_space_group_operations()
            tested_sites = []
            starttime = time.time()
            self.logger.debug("Performing initial ewald sum...")
            ewaldsum = EwaldSummation(structure)
            self.logger.debug("Ewald sum took {} seconds."
                              .format(time.time() - starttime))
            starttime = time.time()

            allcombis = []
            for ind, num in num_remove_dict.items():
                allcombis.append(itertools.combinations(ind, num))

            count = 0
            for allindices in itertools.product(*allcombis):
                sites_to_remove = []
                indices_list = []
                for indices in allindices:
                    sites_to_remove.extend([structure[i] for i in indices])
                    indices_list.extend(indices)
                s_new = structure.copy()
                s_new.remove_sites(indices_list)
                energy = ewaldsum.compute_partial_energy(indices_list)
                already_tested = False
                for i, tsites in enumerate(tested_sites):
                    tenergy = all_structures[i]["energy"]
                    if abs((energy - tenergy) / len(s_new)) < 1e-5 and \
                            sg.are_symmetrically_equivalent(sites_to_remove,
                                                            tsites,
                                                            symm_prec=symprec):
                        already_tested = True

                if not already_tested:
                    tested_sites.append(sites_to_remove)
                    all_structures.append({"structure": s_new, "energy": energy})

                count += 1
                if count % 10 == 0:
                    timenow = time.time()
                    self.logger.debug("{} structures, {:.2f} seconds."
                                      .format(count, timenow - starttime))
                    self.logger.debug("Average time per combi = {} seconds"
                                      .format((timenow - starttime) / count))
                    self.logger.debug("{} symmetrically distinct structures found."
                                      .format(len(all_structures)))

            self.logger.debug("Total symmetrically distinct structures found = {}"
                              .format(len(all_structures)))
            all_structures = sorted(all_structures, key=lambda s: s["energy"])
            return all_structures

        def _fast_ordering(self, structure, num_remove_dict, num_to_return=1):
            """
            This method uses the matrix form of ewaldsum to calculate the ewald
            sums of the potential structures. This is on the order of 4 orders of
            magnitude faster when there are large numbers of permutations to
            consider. There are further optimizations possible (doing a smarter
            search of permutations for example), but this wont make a difference
            until the number of permutations is on the order of 30,000.
            """
            self.logger.debug("Performing fast ordering")
            starttime = time.time()
            self.logger.debug("Performing initial ewald sum...")

            ewaldmatrix = EwaldSummation(structure).total_energy_matrix
            self.logger.debug("Ewald sum took {} seconds."
                              .format(time.time() - starttime))
            starttime = time.time()
            m_list = []
            for indices, num in num_remove_dict.items():
                m_list.append([0, num, list(indices), None])

            self.logger.debug("Calling EwaldMinimizer...")
            minimizer = EwaldMinimizer(ewaldmatrix, m_list, num_to_return,
                                       PartialRemoveSitesTransformation.ALGO_FAST)
            self.logger.debug("Minimizing Ewald took {} seconds."
                              .format(time.time() - starttime))

            all_structures = []

            lowest_energy = minimizer.output_lists[0][0]
            num_atoms = sum(structure.composition.values())

            for output in minimizer.output_lists:
                s = structure.copy()
                del_indices = []

                for manipulation in output[1]:
                    if manipulation[1] is None:
                        del_indices.append(manipulation[0])
                    else:
                        s.replace(manipulation[0], manipulation[1])
                s.remove_sites(del_indices)
                struct = s.get_sorted_structure()
                all_structures.append(
                    {"energy": output[0],
                     "energy_above_minimum": (output[0] - lowest_energy)
                        / num_atoms,
                     "structure": struct})

            return all_structures

        def _enumerate_ordering(self, structure):
            # Generate the disordered structure first.
            s = structure.copy()
            for indices, fraction in zip(self.indices, self.fractions):
                for ind in indices:
                    new_sp = {sp: occu * fraction
                              for sp, occu
                              in structure[ind].species.items()}
                    s[ind] = new_sp
            # Perform enumeration
            from pymatgen.transformations.advanced_transformations import \
                EnumerateStructureTransformation
            trans = EnumerateStructureTransformation()
            return trans.apply_transformation(s, 10000)

        def apply_transformation(self, structure, return_ranked_list=False):
            """
            Apply the transformation.

            Args:
                structure: input structure
                return_ranked_list (bool): Whether or not multiple structures are
                    returned. If return_ranked_list is a number, that number of
                    structures is returned.

            Returns:
                Depending on returned_ranked list, either a transformed structure
                or a list of dictionaries, where each dictionary is of the form
                {"structure" = .... , "other_arguments"}
                the key "transformation" is reserved for the transformation that
                was actually applied to the structure.
                This transformation is parsed by the alchemy classes for generating
                a more specific transformation history. Any other information will
                be stored in the transformation_parameters dictionary in the
                transmuted structure class.
            """
            num_remove_dict = {}
            total_combis = 0
            for indices, frac in zip(self.indices, self.fractions):
                num_to_remove = len(indices) * frac
                if abs(num_to_remove - int(round(num_to_remove))) > 1e-3:
                    raise ValueError("Fraction to remove must be consistent with "
                                     "integer amounts in structure.")
                else:
                    num_to_remove = int(round(num_to_remove))
                num_remove_dict[tuple(indices)] = num_to_remove
                n = len(indices)
                total_combis += int(round(math.factorial(n) /
                                          math.factorial(num_to_remove) /
                                          math.factorial(n - num_to_remove)))

            self.logger.debug("Total combinations = {}".format(total_combis))

            try:
                num_to_return = int(return_ranked_list)
            except ValueError:
                num_to_return = 1

            num_to_return = max(1, num_to_return)
            self.logger.debug("Will return {} best structures."
                              .format(num_to_return))

            if self.algo == PartialRemoveSitesTransformation.ALGO_FAST:
                all_structures = self._fast_ordering(structure, num_remove_dict,
                                                     num_to_return)
            elif self.algo == PartialRemoveSitesTransformation.ALGO_COMPLETE:
                all_structures = self._complete_ordering(structure, num_remove_dict)
            elif self.algo == PartialRemoveSitesTransformation.ALGO_BEST_FIRST:
                all_structures = self._best_first_ordering(structure,
                                                           num_remove_dict)
            elif self.algo == PartialRemoveSitesTransformation.ALGO_ENUMERATE:
                all_structures = self._enumerate_ordering(structure)
            else:
                raise ValueError("Invalid algo.")

            opt_s = all_structures[0]["structure"]
            return opt_s if not return_ranked_list \
                else all_structures[0:num_to_return]

        def __str__(self):
            return "PartialRemoveSitesTransformation : Indices and fraction" + \
                   " to remove = {}, ALGO = {}".format(self.indices, self.algo)

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

        @property
        def inverse(self):
            """Return: None"""
            return None

        @property
        def is_one_to_many(self):
            """Return: True"""
            return True

    class AddSitePropertyTransformation(AbstractTransformation):
        """
        Simple transformation to add site properties to a given structure
        """
        def __init__(self, site_properties):
            """
            Args:
                site_properties (dict): site properties to be added to a structure
            """
            self.site_properties = site_properties

        def apply_transformation(self, structure):
            """
            Apply the transformation.

            Arg:
                structure (Structure): A structurally similar structure in
                    regards to crystal and site positions.

            Return:
                Returns a copy of structure with sites properties added.
            """
            new_structure = structure.copy()
            for prop in self.site_properties.keys():
                new_structure.add_site_property(prop, self.site_properties[prop])
            return new_structure

        @property
        def inverse(self):
            """Return: None"""
            return None

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