Source code for pymatgen.transformations.advanced_transformations

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

import numpy as np
from fractions import Fraction
from math import gcd
from itertools import groupby, product
from string import ascii_lowercase
from warnings import warn
import logging
import math

import warnings
from monty.fractions import lcm
from monty.json import MSONable

from pymatgen.core.periodic_table import Element, Specie, get_el_sp, DummySpecie
from pymatgen.transformations.transformation_abc import AbstractTransformation
from pymatgen.transformations.standard_transformations import \
    SubstitutionTransformation, OrderDisorderedStructureTransformation
from pymatgen.command_line.enumlib_caller import EnumlibAdaptor, EnumError
from pymatgen.analysis.ewald import EwaldSummation
from pymatgen.core.structure import Structure
from pymatgen.symmetry.analyzer import SpacegroupAnalyzer
from pymatgen.analysis.structure_prediction.substitution_probability import \
from pymatgen.analysis.structure_matcher import StructureMatcher, \
from pymatgen.analysis.energy_models import SymmetryModel
from pymatgen.analysis.bond_valence import BVAnalyzer
from pymatgen.core.surface import SlabGenerator
from pymatgen.electronic_structure.core import Spin
from import GrainBoundaryGenerator

This module implements more advanced transformations.

__author__ = "Shyue Ping Ong, Stephen Dacek, Anubhav Jain, Matthew Horton"
__copyright__ = "Copyright 2012, The Materials Project"
__version__ = "1.0"
__maintainer__ = "Shyue Ping Ong"
__email__ = ""
__date__ = "Jul 24, 2012"

logger = logging.getLogger(__name__)

[docs]class ChargeBalanceTransformation(AbstractTransformation): """ This is a transformation that disorders a structure to make it charge balanced, given an oxidation state-decorated structure. Args: charge_balance_sp: specie to add or remove. Currently only removal is supported """ def __init__(self, charge_balance_sp): self.charge_balance_sp = str(charge_balance_sp)
[docs] def apply_transformation(self, structure): charge = structure.charge specie = get_el_sp(self.charge_balance_sp) num_to_remove = charge / specie.oxi_state num_in_structure = structure.composition[specie] removal_fraction = num_to_remove / num_in_structure if removal_fraction < 0: raise ValueError("addition of specie not yet supported by " "ChargeBalanceTransformation") trans = SubstitutionTransformation( {self.charge_balance_sp: { self.charge_balance_sp: 1 - removal_fraction}}) return trans.apply_transformation(structure)
def __str__(self): return "Charge Balance Transformation : " + \ "Species to remove = {}".format(str(self.charge_balance_sp)) def __repr__(self): return self.__str__() @property def inverse(self): return None @property def is_one_to_many(self): return False
[docs]class SuperTransformation(AbstractTransformation): """ This is a transformation that is inherently one-to-many. It is constructed from a list of transformations and returns one structure for each transformation. The primary use for this class is extending a transmuter object. Args: transformations ([transformations]): List of transformations to apply to a structure. One transformation is applied to each output structure. nstructures_per_trans (int): If the transformations are one-to-many and, nstructures_per_trans structures from each transformation are added to the full list. Defaults to 1, i.e., only best structure. """ def __init__(self, transformations, nstructures_per_trans=1): self._transformations = transformations self.nstructures_per_trans = nstructures_per_trans
[docs] def apply_transformation(self, structure, return_ranked_list=False): if not return_ranked_list: raise ValueError("SuperTransformation has no single best structure" " output. Must use return_ranked_list") structures = [] for t in self._transformations: if t.is_one_to_many: for d in t.apply_transformation( structure, return_ranked_list=self.nstructures_per_trans): d["transformation"] = t structures.append(d) else: structures.append( {"transformation": t, "structure": t.apply_transformation(structure)}) return structures
def __str__(self): return "Super Transformation : Transformations = " + \ "{}".format(" ".join([str(t) for t in self._transformations])) def __repr__(self): return self.__str__() @property def inverse(self): return None @property def is_one_to_many(self): return True
[docs]class MultipleSubstitutionTransformation: """ Performs multiple substitutions on a structure. For example, can do a fractional replacement of Ge in LiGePS with a list of species, creating one structure for each substitution. Ordering is done using a dummy element so only one ordering must be done per substitution oxidation state. Charge balancing of the structure is optionally performed. .. note:: There are no checks to make sure that removal fractions are possible and rounding may occur. Currently charge balancing only works for removal of species. """ def __init__(self, sp_to_replace, r_fraction, substitution_dict, charge_balance_species=None, order=True): """ Performs multiple fractional substitutions on a transmuter. Args: sp_to_replace: species to be replaced r_fraction: fraction of that specie to replace substitution_dict: dictionary of the format {2: ["Mg", "Ti", "V", "As", "Cr", "Ta", "N", "Nb"], 3: ["Ru", "Fe", "Co", "Ce", "As", "Cr", "Ta", "N", "Nb"], 4: ["Ru", "V", "Cr", "Ta", "N", "Nb"], 5: ["Ru", "W", "Mn"] } The number is the charge used for each of the list of elements (an element can be present in multiple lists) charge_balance_species: If specified, will balance the charge on the structure using that specie. """ self.sp_to_replace = sp_to_replace self.r_fraction = r_fraction self.substitution_dict = substitution_dict self.charge_balance_species = charge_balance_species self.order = order
[docs] def apply_transformation(self, structure, return_ranked_list=False): if not return_ranked_list: raise ValueError("MultipleSubstitutionTransformation has no single" " best structure output. Must use" " return_ranked_list.") outputs = [] for charge, el_list in self.substitution_dict.items(): mapping = {} if charge > 0: sign = "+" else: sign = "-" dummy_sp = "X{}{}".format(str(charge), sign) mapping[self.sp_to_replace] = { self.sp_to_replace: 1 - self.r_fraction, dummy_sp: self.r_fraction} trans = SubstitutionTransformation(mapping) dummy_structure = trans.apply_transformation(structure) if self.charge_balance_species is not None: cbt = ChargeBalanceTransformation(self.charge_balance_species) dummy_structure = cbt.apply_transformation(dummy_structure) if self.order: trans = OrderDisorderedStructureTransformation() dummy_structure = trans.apply_transformation(dummy_structure) for el in el_list: if charge > 0: sign = "+" else: sign = "-" st = SubstitutionTransformation( {"X{}+".format(str(charge)): "{}{}{}".format(el, charge, sign)}) new_structure = st.apply_transformation(dummy_structure) outputs.append({"structure": new_structure}) return outputs
def __str__(self): return "Multiple Substitution Transformation : Substitution on " + \ "{}".format(self.sp_to_replace) def __repr__(self): return self.__str__() @property def inverse(self): return None @property def is_one_to_many(self): return True
[docs]class EnumerateStructureTransformation(AbstractTransformation): """ Order a disordered structure using enumlib. For complete orderings, this generally produces fewer structures that the OrderDisorderedStructure transformation, and at a much faster speed. Args: min_cell_size: The minimum cell size wanted. Must be an int. Defaults to 1. max_cell_size: The maximum cell size wanted. Must be an int. Defaults to 1. symm_prec: Tolerance to use for symmetry. refine_structure: This parameter has the same meaning as in enumlib_caller. If you are starting from a structure that has been relaxed via some electronic structure code, it is usually much better to start with symmetry determination and then obtain a refined structure. The refined structure have cell parameters and atomic positions shifted to the expected symmetry positions, which makes it much less sensitive precision issues in enumlib. If you are already starting from an experimental cif, refinment should have already been done and it is not necessary. Defaults to False. enum_precision_parameter (float): Finite precision parameter for enumlib. Default of 0.001 is usually ok, but you might need to tweak it for certain cells. check_ordered_symmetry (bool): Whether to check the symmetry of the ordered sites. If the symmetry of the ordered sites is lower, the lowest symmetry ordered sites is included in the enumeration. This is important if the ordered sites break symmetry in a way that is important getting possible structures. But sometimes including ordered sites slows down enumeration to the point that it cannot be completed. Switch to False in those cases. Defaults to True. max_disordered_sites (int): An alternate parameter to max_cell size. Will sequentially try larger and larger cell sizes until (i) getting a result or (ii) the number of disordered sites in the cell exceeds max_disordered_sites. Must set max_cell_size to None when using this parameter. sort_criteria (str): Sort by Ewald energy ("ewald", must have oxidation states and slow) or by number of sites ("nsites", much faster). timeout (float): timeout in minutes to pass to EnumlibAdaptor """ def __init__(self, min_cell_size=1, max_cell_size=1, symm_prec=0.1, refine_structure=False, enum_precision_parameter=0.001, check_ordered_symmetry=True, max_disordered_sites=None, sort_criteria="ewald", timeout=None): self.symm_prec = symm_prec self.min_cell_size = min_cell_size self.max_cell_size = max_cell_size self.refine_structure = refine_structure self.enum_precision_parameter = enum_precision_parameter self.check_ordered_symmetry = check_ordered_symmetry self.max_disordered_sites = max_disordered_sites self.sort_criteria = sort_criteria self.timeout = timeout if max_cell_size and max_disordered_sites: raise ValueError("Cannot set both max_cell_size and " "max_disordered_sites!")
[docs] def apply_transformation(self, structure, return_ranked_list=False): """ Return either a single ordered structure or a sequence of all ordered structures. Args: structure: Structure to order. 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 list of ordered structures is ranked by ewald energy / atom, if the input structure is an oxidation state decorated structure. Otherwise, it is ranked by number of sites, with smallest number of sites first. """ try: num_to_return = int(return_ranked_list) except ValueError: num_to_return = 1 if self.refine_structure: finder = SpacegroupAnalyzer(structure, self.symm_prec) structure = finder.get_refined_structure() contains_oxidation_state = all( [hasattr(sp, "oxi_state") and sp.oxi_state != 0 for sp in structure.composition.elements] ) structures = None if structure.is_ordered: warn("Enumeration skipped for structure with composition {} " "because it is ordered".format(structure.composition)) structures = [structure.copy()] if self.max_disordered_sites: ndisordered = sum([1 for site in structure if not site.is_ordered]) if ndisordered > self.max_disordered_sites: raise ValueError( "Too many disordered sites! ({} > {})".format( ndisordered, self.max_disordered_sites)) max_cell_sizes = range(self.min_cell_size, int( math.floor(self.max_disordered_sites / ndisordered)) + 1) else: max_cell_sizes = [self.max_cell_size] for max_cell_size in max_cell_sizes: adaptor = EnumlibAdaptor( structure, min_cell_size=self.min_cell_size, max_cell_size=max_cell_size, symm_prec=self.symm_prec, refine_structure=False, enum_precision_parameter=self.enum_precision_parameter, check_ordered_symmetry=self.check_ordered_symmetry, timeout=self.timeout) try: except EnumError: warn("Unable to enumerate for max_cell_size = %d".format( max_cell_size)) structures = adaptor.structures if structures: break if structures is None: raise ValueError("Unable to enumerate") original_latt = structure.lattice inv_latt = np.linalg.inv(original_latt.matrix) ewald_matrices = {} all_structures = [] for s in structures: new_latt = s.lattice transformation =, inv_latt) transformation = tuple([tuple([int(round(cell)) for cell in row]) for row in transformation]) if contains_oxidation_state and self.sort_criteria == "ewald": if transformation not in ewald_matrices: s_supercell = structure * transformation ewald = EwaldSummation(s_supercell) ewald_matrices[transformation] = ewald else: ewald = ewald_matrices[transformation] energy = ewald.compute_sub_structure(s) all_structures.append({"num_sites": len(s), "energy": energy, "structure": s}) else: all_structures.append({"num_sites": len(s), "structure": s}) def sort_func(s): return s["energy"] / s["num_sites"] \ if contains_oxidation_state and self.sort_criteria == "ewald" \ else s["num_sites"] self._all_structures = sorted(all_structures, key=sort_func) if return_ranked_list: return self._all_structures[0:num_to_return] else: return self._all_structures[0]["structure"]
def __str__(self): return "EnumerateStructureTransformation" def __repr__(self): return self.__str__() @property def inverse(self): return None @property def is_one_to_many(self): return True
[docs]class SubstitutionPredictorTransformation(AbstractTransformation): """ This transformation takes a structure and uses the structure prediction module to find likely site substitutions. Args: threshold: Threshold for substitution. **kwargs: Args for SubstitutionProbability class lambda_table, alpha """ def __init__(self, threshold=1e-2, scale_volumes=True, **kwargs): self.kwargs = kwargs self.threshold = threshold self.scale_volumes = scale_volumes self._substitutor = SubstitutionPredictor(threshold=threshold, **kwargs)
[docs] def apply_transformation(self, structure, return_ranked_list=False): if not return_ranked_list: raise ValueError("SubstitutionPredictorTransformation doesn't" " support returning 1 structure") preds = self._substitutor.composition_prediction( structure.composition, to_this_composition=False) preds.sort(key=lambda x: x['probability'], reverse=True) outputs = [] for pred in preds: st = SubstitutionTransformation(pred['substitutions']) output = {'structure': st.apply_transformation(structure), 'probability': pred['probability'], 'threshold': self.threshold, 'substitutions': {}} # dictionary keys have to be converted to strings for JSON for key, value in pred['substitutions'].items(): output['substitutions'][str(key)] = str(value) outputs.append(output) return outputs
def __str__(self): return "SubstitutionPredictorTransformation" def __repr__(self): return self.__str__() @property def inverse(self): return None @property def is_one_to_many(self): return True
[docs]class MagOrderParameterConstraint(MSONable): def __init__(self, order_parameter, species_constraints=None, site_constraint_name=None, site_constraints=None): """ This class can be used to supply MagOrderingTransformation to just a specific subset of species or sites that satisfy the provided constraints. This can be useful for setting an order parameters for, for example, ferrimagnetic structures which might order on certain motifs, with the global order parameter dependent on how many sites satisfy that motif. :param order_parameter (float): any number from 0.0 to 1.0, typically 0.5 (antiferromagnetic) or 1.0 (ferromagnetic) :param species_constraint (list): str or list of strings of Specie symbols that the constraint should apply to :param site_constraint_name (str): name of the site property that the constraint should apply to, e.g. "coordination_no" :param site_constraints (list): list of values of the site property that the constraints should apply to """ # validation if site_constraints and site_constraints != [None] \ and not site_constraint_name: raise ValueError("Specify the name of the site constraint.") elif not site_constraints and site_constraint_name: raise ValueError("Please specify some site constraints.") if not isinstance(species_constraints, list): species_constraints = [species_constraints] if not isinstance(site_constraints, list): site_constraints = [site_constraints] if order_parameter > 1 or order_parameter < 0: raise ValueError('Order parameter must lie between 0 and 1') elif order_parameter != 0.5: warnings.warn("Use care when using a non-standard order parameter, " "though it can be useful in some cases it can also " "lead to unintended behavior. Consult documentation.") self.order_parameter = order_parameter self.species_constraints = species_constraints self.site_constraint_name = site_constraint_name self.site_constraints = site_constraints
[docs] def satisfies_constraint(self, site): """ Checks if a periodic site satisfies the constraint. """ if not site.is_ordered: return False if self.species_constraints \ and str(site.specie) in self.species_constraints: satisfies_constraints = True else: satisfies_constraints = False if self.site_constraint_name \ and self.site_constraint_name in prop =[self.site_constraint_name] if prop in self.site_constraints: satisfies_constraints = True else: satisfies_constraints = False return satisfies_constraints
[docs]class MagOrderingTransformation(AbstractTransformation): def __init__(self, mag_species_spin, order_parameter=0.5, energy_model=SymmetryModel(), **kwargs): """ This transformation takes a structure and returns a list of collinear magnetic orderings. For disordered structures, make an ordered approximation first. :param mag_species_spin: A mapping of elements/species to their spin magnitudes, e.g. {"Fe3+": 5, "Mn3+": 4} :param order_parameter (float or list): if float, a specifies a global order parameter and can take values from 0.0 to 1.0 (e.g. 0.5 for antiferromagnetic or 1.0 for ferromagnetic), if list has to be a list of :class: `pymatgen.transformations.advanced_transformations.MagOrderParameterConstraint` to specify more complicated orderings, see documentation for MagOrderParameterConstraint more details on usage :param energy_model: Energy model to rank the returned structures, see :mod: `pymatgen.analysis.energy_models` for more information (note that this is not necessarily a physical energy). By default, returned structures use SymmetryModel() which ranks structures from most symmetric to least. :param kwargs: Additional kwargs that are passed to :class:`EnumerateStructureTransformation` such as min_cell_size etc. """ # checking for sensible order_parameter values if isinstance(order_parameter, float): # convert to constraint format order_parameter = [MagOrderParameterConstraint(order_parameter=order_parameter, species_constraints= list(mag_species_spin.keys()))] elif isinstance(order_parameter, list): ops = [isinstance(item, MagOrderParameterConstraint) for item in order_parameter] if not any(ops): raise ValueError("Order parameter not correctly defined.") else: raise ValueError("Order parameter not correctly defined.") self.mag_species_spin = mag_species_spin # store order parameter constraints as dicts to save implementing # to/from dict methods for MSONable compatibility self.order_parameter = [op.as_dict() for op in order_parameter] self.energy_model = energy_model self.enum_kwargs = kwargs
[docs] @staticmethod def determine_min_cell(disordered_structure): """ Determine the smallest supercell that is able to enumerate the provided structure with the given order parameter """ def lcm(n1, n2): """ Find least common multiple of two numbers """ return n1 * n2 / gcd(n1, n2) # assumes all order parameters for a given species are the same mag_species_order_parameter = {} mag_species_occurrences = {} for idx, site in enumerate(disordered_structure): if not site.is_ordered: op = max(site.species.values()) # this very hacky bit of code only works because we know # that on disordered sites in this class, all species are the same # but have different spins, and this is comma-delimited sp = str(list(site.species.keys())[0]).split(",")[0] if sp in mag_species_order_parameter: mag_species_occurrences[sp] += 1 else: mag_species_order_parameter[sp] = op mag_species_occurrences[sp] = 1 smallest_n = [] for sp, order_parameter in mag_species_order_parameter.items(): denom = Fraction(order_parameter).limit_denominator(100).denominator num_atom_per_specie = mag_species_occurrences[sp] n_gcd = gcd(denom, num_atom_per_specie) smallest_n.append(lcm(int(n_gcd), denom) / n_gcd) return max(smallest_n)
@staticmethod def _add_dummy_species(structure, order_parameters): """ :param structure: ordered Structure :param order_parameters: list of MagOrderParameterConstraints :return: A structure decorated with disordered DummySpecies on which to perform the enumeration. Note that the DummySpecies are super-imposed on to the original sites, to make it easier to retrieve the original site after enumeration is performed (this approach is preferred over a simple mapping since multiple species may have the same DummySpecie, depending on the constraints specified). This approach can also preserve site properties even after enumeration. """ dummy_struct = structure.copy() def generate_dummy_specie(): """ Generator which returns DummySpecie symbols Mma, Mmb, etc. """ subscript_length = 1 while True: for subscript in product(ascii_lowercase, repeat=subscript_length): yield "Mm" + "".join(subscript) subscript_length += 1 dummy_species_gen = generate_dummy_specie() # one dummy species for each order parameter constraint dummy_species_symbols = [next(dummy_species_gen) for i in range(len(order_parameters))] dummy_species = [{ DummySpecie(symbol, properties={'spin': Spin.up}): constraint.order_parameter, DummySpecie(symbol, properties={'spin': Spin.down}): 1 - constraint.order_parameter } for symbol, constraint in zip(dummy_species_symbols, order_parameters)] sites_to_add = [] for idx, site in enumerate(dummy_struct): satisfies_constraints = [c.satisfies_constraint(site) for c in order_parameters] if satisfies_constraints.count(True) > 1: # site should either not satisfy any constraints, or satisfy # one constraint raise ValueError("Order parameter constraints conflict for site: {}, {}" .format(str(site.specie), elif any(satisfies_constraints): dummy_specie_idx = satisfies_constraints.index(True) dummy_struct.append( dummy_species[dummy_specie_idx], site.coords, site.lattice ) return dummy_struct @staticmethod def _remove_dummy_species(structure): """ :return: Structure with dummy species removed, but their corresponding spin properties merged with the original sites. Used after performing enumeration. """ if not structure.is_ordered: raise Exception("Something went wrong with enumeration.") sites_to_remove = [] logger.debug('Dummy species structure:\n{}'.format(str(structure))) for idx, site in enumerate(structure): if isinstance(site.specie, DummySpecie): sites_to_remove.append(idx) spin = site.specie._properties.get('spin', None) neighbors = structure.get_neighbors( site, 0.05, # arbitrary threshold, needs to be << any bond length # but >> floating point precision issues include_index=True ) if len(neighbors) != 1: raise Exception("This shouldn't happen, found neighbors: {}" .format(neighbors)) orig_site_idx = neighbors[0][2] orig_specie = structure[orig_site_idx].specie new_specie = Specie(orig_specie.symbol, getattr(orig_specie, 'oxi_state', None), properties={'spin': spin}) structure.replace(orig_site_idx, new_specie, properties=structure[orig_site_idx].properties) structure.remove_sites(sites_to_remove) logger.debug('Structure with dummy species removed:\n{}'.format(str(structure))) return structure def _add_spin_magnitudes(self, structure): """ Replaces Spin.up/Spin.down with spin magnitudes specified by mag_species_spin. :param structure: :return: """ for idx, site in enumerate(structure): if getattr(site.specie, '_properties', None): spin = site.specie._properties.get('spin', None) sign = int(spin) if spin else 0 if spin: new_properties = site.specie._properties.copy() # this very hacky bit of code only works because we know # that on disordered sites in this class, all species are the same # but have different spins, and this is comma-delimited sp = str(site.specie).split(",")[0] new_properties.update({ 'spin': sign * self.mag_species_spin.get(sp, 0) }) new_specie = Specie(site.specie.symbol, getattr(site.specie, 'oxi_state', None), new_properties) structure.replace(idx, new_specie, logger.debug('Structure with spin magnitudes:\n{}'.format(str(structure))) return structure
[docs] def apply_transformation(self, structure, return_ranked_list=False): """ Apply MagOrderTransformation to an input structure. :param structure: Any ordered structure. :param return_ranked_list: As in other Transformations. :return: """ if not structure.is_ordered: raise ValueError("Create an ordered approximation of " "your input structure first.") # retrieve order parameters order_parameters = [MagOrderParameterConstraint.from_dict(op_dict) for op_dict in self.order_parameter] # add dummy species on which to perform enumeration structure = self._add_dummy_species(structure, order_parameters) # trivial case if structure.is_ordered: structure = self._remove_dummy_species(structure) return [structure] if return_ranked_list > 1 else structure enum_kwargs = self.enum_kwargs.copy() enum_kwargs["min_cell_size"] = max( int(self.determine_min_cell(structure)), enum_kwargs.get("min_cell_size", 1) ) if enum_kwargs.get("max_cell_size", None): if enum_kwargs["min_cell_size"] > enum_kwargs["max_cell_size"]: warnings.warn("Specified max cell size ({}) is smaller " "than the minimum enumerable cell size ({}), " "changing max cell size to {}".format(enum_kwargs["max_cell_size"], enum_kwargs["min_cell_size"], enum_kwargs["min_cell_size"])) enum_kwargs["max_cell_size"] = enum_kwargs["min_cell_size"] else: enum_kwargs["max_cell_size"] = enum_kwargs["min_cell_size"] t = EnumerateStructureTransformation(**enum_kwargs) alls = t.apply_transformation(structure, return_ranked_list=return_ranked_list) # handle the fact that EnumerateStructureTransformation can either # return a single Structure or a list if isinstance(alls, Structure): # remove dummy species and replace Spin.up or Spin.down # with spin magnitudes given in mag_species_spin arg alls = self._remove_dummy_species(alls) alls = self._add_spin_magnitudes(alls) else: for idx, _ in enumerate(alls): alls[idx]["structure"] = self._remove_dummy_species(alls[idx]["structure"]) alls[idx]["structure"] = self._add_spin_magnitudes(alls[idx]["structure"]) try: num_to_return = int(return_ranked_list) except ValueError: num_to_return = 1 if num_to_return == 1 or not return_ranked_list: return alls[0]["structure"] if num_to_return else alls # remove duplicate structures and group according to energy model m = StructureMatcher(comparator=SpinComparator()) key = lambda x: SpacegroupAnalyzer(x, 0.1).get_space_group_number() out = [] for _, g in groupby(sorted([d["structure"] for d in alls], key=key), key): g = list(g) grouped = m.group_structures(g) out.extend([{"structure": g[0], "energy": self.energy_model.get_energy(g[0])} for g in grouped]) self._all_structures = sorted(out, key=lambda d: d["energy"]) return self._all_structures[0:num_to_return]
def __str__(self): return "MagOrderingTransformation" def __repr__(self): return self.__str__() @property def inverse(self): return None @property def is_one_to_many(self): return True
def _find_codopant(target, oxidation_state, allowed_elements=None): """ Finds the element from "allowed elements" that (i) possesses the desired "oxidation state" and (ii) is closest in ionic radius to the target specie Args: target: (Specie) provides target ionic radius. oxidation_state: (float) codopant oxidation state. allowed_elements: ([str]) List of allowed elements. If None, all elements are tried. Returns: (Specie) with oxidation_state that has ionic radius closest to target. """ ref_radius = target.ionic_radius candidates = [] symbols = allowed_elements or [el.symbol for el in Element] for sym in symbols: try: with warnings.catch_warnings(): warnings.simplefilter("ignore") sp = Specie(sym, oxidation_state) r = sp.ionic_radius if r is not None: candidates.append((r, sp)) except: pass return min(candidates, key=lambda l: abs(l[0] / ref_radius - 1))[1]
[docs]class DopingTransformation(AbstractTransformation): """ A transformation that performs doping of a structure. """ def __init__(self, dopant, ionic_radius_tol=float("inf"), min_length=10, alio_tol=0, codopant=False, max_structures_per_enum=100, allowed_doping_species=None, **kwargs): """ Args: dopant (Specie-like): E.g., Al3+. Must have oxidation state. ionic_radius_tol (float): E.g., Fractional allowable ionic radii mismatch for dopant to fit into a site. Default of inf means that any dopant with the right oxidation state is allowed. min_Length (float): Min. lattice parameter between periodic images of dopant. Defaults to 10A for now. alio_tol (int): If this is not 0, attempt will be made to dope sites with oxidation_states +- alio_tol of the dopant. E.g., 1 means that the ions like Ca2+ and Ti4+ are considered as potential doping sites for Al3+. codopant (bool): If True, doping will be carried out with a codopant to maintain charge neutrality. Otherwise, vacancies will be used. max_structures_per_enum (float): Maximum number of structures to return per enumeration. Note that there can be more than one candidate doping site, and each site enumeration will return at max max_structures_per_enum structures. Defaults to 100. allowed_doping_species (list): Species that are allowed to be doping sites. This is an inclusionary list. If specified, any sites which are not \\*\\*kwargs: Same keyword args as :class:`EnumerateStructureTransformation`, i.e., min_cell_size, etc. """ self.dopant = get_el_sp(dopant) self.ionic_radius_tol = ionic_radius_tol self.min_length = min_length self.alio_tol = alio_tol self.codopant = codopant self.max_structures_per_enum = max_structures_per_enum self.allowed_doping_species = allowed_doping_species self.kwargs = kwargs
[docs] def apply_transformation(self, structure, return_ranked_list=False): """ Args: structure (Structure): Input structure to dope Returns: [{"structure": Structure, "energy": float}] """ comp = structure.composition"Composition: %s" % comp) for sp in comp: try: sp.oxi_state except AttributeError: analyzer = BVAnalyzer() structure = analyzer.get_oxi_state_decorated_structure( structure) comp = structure.composition break ox = self.dopant.oxi_state radius = self.dopant.ionic_radius compatible_species = [ sp for sp in comp if sp.oxi_state == ox and abs(sp.ionic_radius / radius - 1) < self.ionic_radius_tol] if (not compatible_species) and self.alio_tol: # We only consider aliovalent doping if there are no compatible # isovalent species. compatible_species = [ sp for sp in comp if abs(sp.oxi_state - ox) <= self.alio_tol and abs(sp.ionic_radius / radius - 1) < self.ionic_radius_tol and sp.oxi_state * ox >= 0] if self.allowed_doping_species is not None: # Only keep allowed doping species. compatible_species = [ sp for sp in compatible_species if sp in [get_el_sp(s) for s in self.allowed_doping_species]]"Compatible species: %s" % compatible_species) lengths = scaling = [max(1, int(round(math.ceil(self.min_length / x)))) for x in lengths]"Lengths are %s" % str(lengths))"Scaling = %s" % str(scaling)) all_structures = [] t = EnumerateStructureTransformation(**self.kwargs) for sp in compatible_species: supercell = structure * scaling nsp = supercell.composition[sp] if sp.oxi_state == ox: supercell.replace_species({sp: {sp: (nsp - 1) / nsp, self.dopant: 1 / nsp}})"Doping %s for %s at level %.3f" % ( sp, self.dopant, 1 / nsp)) elif self.codopant: codopant = _find_codopant(sp, 2 * sp.oxi_state - ox) supercell.replace_species({sp: {sp: (nsp - 2) / nsp, self.dopant: 1 / nsp, codopant: 1 / nsp}})"Doping %s for %s + %s at level %.3f" % ( sp, self.dopant, codopant, 1 / nsp)) elif abs(sp.oxi_state) < abs(ox): # Strategy: replace the target species with a # combination of dopant and vacancy. # We will choose the lowest oxidation state species as a # vacancy compensation species as it is likely to be lower in # energy sp_to_remove = min([s for s in comp if s.oxi_state * ox > 0], key=lambda ss: abs(ss.oxi_state)) if sp_to_remove == sp: common_charge = lcm(int(abs(sp.oxi_state)), int(abs(ox))) ndopant = common_charge / abs(ox) nsp_to_remove = common_charge / abs(sp.oxi_state)"Doping %d %s with %d %s." % (nsp_to_remove, sp, ndopant, self.dopant)) supercell.replace_species( {sp: {sp: (nsp - nsp_to_remove) / nsp, self.dopant: ndopant / nsp}}) else: ox_diff = int(abs(round(sp.oxi_state - ox))) vac_ox = int(abs(sp_to_remove.oxi_state)) common_charge = lcm(vac_ox, ox_diff) ndopant = common_charge / ox_diff nx_to_remove = common_charge / vac_ox nx = supercell.composition[sp_to_remove]"Doping %d %s with %s and removing %d %s." % (ndopant, sp, self.dopant, nx_to_remove, sp_to_remove)) supercell.replace_species( {sp: {sp: (nsp - ndopant) / nsp, self.dopant: ndopant / nsp}, sp_to_remove: { sp_to_remove: (nx - nx_to_remove) / nx}}) elif abs(sp.oxi_state) > abs(ox): # Strategy: replace the target species with dopant and also # remove some opposite charged species for charge neutrality if ox > 0: sp_to_remove = max(supercell.composition.keys(), key=lambda el: el.X) else: sp_to_remove = min(supercell.composition.keys(), key=lambda el: el.X) # Confirm species are of opposite oxidation states. assert sp_to_remove.oxi_state * sp.oxi_state < 0 ox_diff = int(abs(round(sp.oxi_state - ox))) anion_ox = int(abs(sp_to_remove.oxi_state)) nx = supercell.composition[sp_to_remove] common_charge = lcm(anion_ox, ox_diff) ndopant = common_charge / ox_diff nx_to_remove = common_charge / anion_ox"Doping %d %s with %s and removing %d %s." % (ndopant, sp, self.dopant, nx_to_remove, sp_to_remove)) supercell.replace_species( {sp: {sp: (nsp - ndopant) / nsp, self.dopant: ndopant / nsp}, sp_to_remove: {sp_to_remove: (nx - nx_to_remove) / nx}}) ss = t.apply_transformation( supercell, return_ranked_list=self.max_structures_per_enum)"%s distinct structures" % len(ss)) all_structures.extend(ss)"Total %s doped structures" % len(all_structures)) if return_ranked_list: return all_structures[:return_ranked_list] return all_structures[0]["structure"]
@property def inverse(self): return None @property def is_one_to_many(self): return True
[docs]class SlabTransformation(AbstractTransformation): """ A transformation that creates a slab from a structure. """ def __init__(self, miller_index, min_slab_size, min_vacuum_size, lll_reduce=False, center_slab=False, in_unit_planes=False, primitive=True, max_normal_search=None, shift=0, tol=0.1): """ Args: miller_index (3-tuple or list): miller index of slab min_slab_size (float): minimum slab size in angstroms min_vacuum_size (float): minimum size of vacuum lll_reduce (bool): whether to apply LLL reduction center_slab (bool): whether to center the slab primitive (bool): whether to reduce slabs to most primitive cell max_normal_search (int): maximum index to include in linear combinations of indices to find c lattice vector orthogonal to slab surface shift (float): shift to get termination tol (float): tolerance for primitive cell finding """ self.miller_index = miller_index self.min_slab_size = min_slab_size self.min_vacuum_size = min_vacuum_size self.lll_reduce = lll_reduce self.center_slab = center_slab self.in_unit_planes = in_unit_planes self.primitive = primitive self.max_normal_search = max_normal_search self.shift = shift self.tol = 0.1
[docs] def apply_transformation(self, structure): sg = SlabGenerator(structure, self.miller_index, self.min_slab_size, self.min_vacuum_size, self.lll_reduce, self.center_slab, self.in_unit_planes, self.primitive, self.max_normal_search) slab = sg.get_slab(self.shift, self.tol) return slab
@property def inverse(self): return None @property def is_one_to_many(self): return None
[docs]class DisorderOrderedTransformation(AbstractTransformation): """ Not to be confused with OrderDisorderedTransformation, this transformation attempts to obtain a *disordered* structure from an input ordered structure. This may or may not be physically plausible, further inspection of the returned structures is advised. The main purpose for this transformation is for structure matching to crystal prototypes for structures that have been derived from a parent prototype structure by substitutions or alloying additions. """ def __init__(self, max_sites_to_merge=2): """ Args: max_sites_to_merge: only merge this number of sites together """ self.max_sites_to_merge = max_sites_to_merge
[docs] def apply_transformation(self, structure, return_ranked_list=False): """ Args: structure: ordered structure return_ranked_list: as in other pymatgen Transformations Returns: transformed disordered structure(s) """ if not structure.is_ordered: raise ValueError("This transformation is for disordered structures only.") partitions = self._partition_species(structure.composition, max_components=self.max_sites_to_merge) disorder_mappings = self._get_disorder_mappings(structure.composition, partitions) disordered_structures = [] for mapping in disorder_mappings: disordered_structure = structure.copy() disordered_structure.replace_species(mapping) disordered_structures.append({'structure': disordered_structure, 'mapping': mapping}) if len(disordered_structures) == 0: return None elif not return_ranked_list: return disordered_structures[0]['structure'] else: if len(disordered_structures) > return_ranked_list: disordered_structures = disordered_structures[0:return_ranked_list] return disordered_structures
@property def inverse(self): return None @property def is_one_to_many(self): return True @staticmethod def _partition_species(composition, max_components=2): """ Private method to split a list of species into various partitions. """ def _partition(collection): # thanks if len(collection) == 1: yield [collection] return first = collection[0] for smaller in _partition(collection[1:]): # insert `first` in each of the subpartition's subsets for n, subset in enumerate(smaller): yield smaller[:n] + [[first] + subset] + smaller[n + 1:] # put `first` in its own subset yield [[first]] + smaller def _sort_partitions(partitions_to_sort): """ Sort partitions by those we want to check first (typically, merging two sites into one is the one to try first). """ partition_indices = [(idx, [len(p) for p in partition]) for idx, partition in enumerate(partitions_to_sort)] # sort by maximum length of partition first (try smallest maximums first) # and secondarily by number of partitions (most partitions first, i.e. # create the 'least disordered' structures first) partition_indices = sorted(partition_indices, key=lambda x: (max(x[1]), -len(x[1]))) # merge at most max_component sites, # e.g. merge at most 2 species into 1 disordered site partition_indices = [x for x in partition_indices if max(x[1]) <= max_components] partition_indices.pop(0) # this is just the input structure sorted_partitions = [partitions_to_sort[x[0]] for x in partition_indices] return sorted_partitions collection = list(composition.keys()) partitions = list(_partition(collection)) partitions = _sort_partitions(partitions) return partitions @staticmethod def _get_disorder_mappings(composition, partitions): """ Private method to obtain the mapping to create a disordered structure from a given partition. """ def _get_replacement_dict_from_partition(partition): d = {} # to be passed to Structure.replace_species() for sp_list in partition: if len(sp_list) > 1: total_occ = sum([composition[sp] for sp in sp_list]) merged_comp = {sp: composition[sp] / total_occ for sp in sp_list} for sp in sp_list: d[sp] = merged_comp return d disorder_mapping = [_get_replacement_dict_from_partition(p) for p in partitions] return disorder_mapping
[docs]class GrainBoundaryTransformation(AbstractTransformation): """ A transformation that creates a gb from a bulk structure. """ def __init__(self, rotation_axis, rotation_angle, expand_times=4, vacuum_thickness=0.0, ab_shift=[0, 0], normal=False, ratio=None, plane=None, max_search=50, tol_coi=1.e-3): """ Args: rotation_axis (list): Rotation axis of GB in the form of a list of integer e.g.: [1, 1, 0] rotation_angle (float, in unit of degree): rotation angle used to generate GB. Make sure the angle is accurate enough. You can use the enum* functions in this class to extract the accurate angle. e.g.: The rotation angle of sigma 3 twist GB with the rotation axis [1, 1, 1] and GB plane (1, 1, 1) can be 60.000000000 degree. If you do not know the rotation angle, but know the sigma value, we have provide the function get_rotation_angle_from_sigma which is able to return all the rotation angles of sigma value you provided. expand_times (int): The multiple times used to expand one unit grain to larger grain. This is used to tune the grain length of GB to warrant that the two GBs in one cell do not interact with each other. Default set to 4. vacuum_thickness (float): The thickness of vacuum that you want to insert between two grains of the GB. Default to 0. ab_shift (list of float, in unit of a, b vectors of Gb): in plane shift of two grains normal (logic): determine if need to require the c axis of top grain (first transformation matrix) perperdicular to the surface or not. default to false. ratio (list of integers): lattice axial ratio. For cubic system, ratio is not needed. For tetragonal system, ratio = [mu, mv], list of two integers, that is, mu/mv = c2/a2. If it is irrational, set it to none. For orthorhombic system, ratio = [mu, lam, mv], list of three integers, that is, mu:lam:mv = c2:b2:a2. If irrational for one axis, set it to None. e.g. mu:lam:mv = c2,None,a2, means b2 is irrational. For rhombohedral system, ratio = [mu, mv], list of two integers, that is, mu/mv is the ratio of (1+2*cos(alpha))/cos(alpha). If irrational, set it to None. For hexagonal system, ratio = [mu, mv], list of two integers, that is, mu/mv = c2/a2. If it is irrational, set it to none. plane (list): Grain boundary plane in the form of a list of integers e.g.: [1, 2, 3]. If none, we set it as twist GB. The plane will be perpendicular to the rotation axis. max_search (int): max search for the GB lattice vectors that give the smallest GB lattice. If normal is true, also max search the GB c vector that perpendicular to the plane. For complex GB, if you want to speed up, you can reduce this value. But too small of this value may lead to error. tol_coi (float): tolerance to find the coincidence sites. When making approximations to the ratio needed to generate the GB, you probably need to increase this tolerance to obtain the correct number of coincidence sites. To check the number of coincidence sites are correct or not, you can compare the generated Gb object's sigma with enum* sigma values (what user expected by input). Returns: Grain boundary structure (Gb (Structure) object). """ self.rotation_axis = rotation_axis self.rotation_angle = rotation_angle self.expand_times = expand_times self.vacuum_thickness = vacuum_thickness self.ab_shift = ab_shift self.normal = normal self.ratio = ratio self.plane = plane self.max_search = max_search self.tol_coi = tol_coi
[docs] def apply_transformation(self, structure): gbg = GrainBoundaryGenerator(structure) gb_struct = gbg.gb_from_parameters( self.rotation_axis, self.rotation_angle, self.expand_times, self.vacuum_thickness, self.ab_shift, self.normal, self.ratio, self.plane, self.max_search, self.tol_coi) return gb_struct
@property def inverse(self): return None @property def is_one_to_many(self): return False