"""This module implements more advanced transformations."""

from __future__ import annotations

import logging
import math
import warnings
from fractions import Fraction
from itertools import groupby, product
from string import ascii_lowercase
from typing import TYPE_CHECKING

import numpy as np
from joblib import Parallel, delayed
from monty.dev import requires
from monty.json import MSONable

from pymatgen.command_line.enumlib_caller import EnumError, EnumlibAdaptor
from pymatgen.command_line.mcsqs_caller import run_mcsqs
from pymatgen.core import DummySpecies, Element, Species, Structure, get_el_sp
from pymatgen.core.adsorption import AdsorbateSiteFinder
from pymatgen.core.bond_valence import BVAnalyzer
from pymatgen.core.energy_models import SymmetryModel
from pymatgen.core.ewald import EwaldSummation
from pymatgen.core.interface import GrainBoundaryGenerator
from pymatgen.core.local_env import MinimumDistanceNN
from pymatgen.core.structure_matcher import SpinComparator, StructureMatcher
from pymatgen.core.structure_prediction.substitution_probability import SubstitutionPredictor
from pymatgen.core.surface import SlabGenerator
from pymatgen.electronic_structure.core import Spin
from pymatgen.io.ase import AseAtomsAdaptor
from pymatgen.io.icet import IcetSQS
from pymatgen.symmetry.analyzer import SpacegroupAnalyzer
from pymatgen.transformations.standard_transformations import (
    OrderDisorderedStructureTransformation,
    SubstitutionTransformation,
    SupercellTransformation,
)
from pymatgen.transformations.transformation_abc import AbstractTransformation

try:
    import hiphive
except ImportError:
    hiphive = None

if TYPE_CHECKING:
    from collections.abc import Callable, Iterable, Sequence
    from typing import Any, Literal

    from numpy.typing import NDArray


__author__ = "Shyue Ping Ong, Stephen Dacek, Anubhav Jain, Matthew Horton, Alex Ganose"

logger = logging.getLogger(__name__)


class ChargeBalanceTransformation(AbstractTransformation):
    """This is a transformation that disorders a structure to make it charge
    balanced, given an oxidation state-decorated structure.
    """

    def __init__(self, charge_balance_sp):
        """Initialize a ChargeBalanceTransformation.

        Args:
            charge_balance_sp: specie to add or remove. Currently only removal
                is supported.
        """
        self.charge_balance_sp = str(charge_balance_sp)

    def __repr__(self):
        return f"Charge Balance Transformation : Species to remove = {self.charge_balance_sp}"

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

        Args:
            structure: Input Structure

        Returns:
            Charge balanced structure.
        """
        charge = structure.charge
        specie = get_el_sp(self.charge_balance_sp)
        num_to_remove = (charge / specie.oxi_state) if specie.oxi_state else 0.0
        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)


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.
    """

    def __init__(self, transformations, nstructures_per_trans=1):
        """Initialize a SuperTransformation.

        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.
        """
        self._transformations = transformations
        self.nstructures_per_trans = nstructures_per_trans

    def __repr__(self):
        return f"Super Transformation : Transformations = {' '.join(map(str, self._transformations))}"

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

        Args:
            structure: Input Structure
            return_ranked_list (bool | int, optional): If return_ranked_list is int, that number of structures

                is returned. If False, only the single lowest energy structure is returned. Defaults to False.

        Returns:
            Structures with all transformations applied.
        """
        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

    @property
    def is_one_to_many(self) -> Literal[True]:
        """Transform one structure to many."""
        return True


class MultipleSubstitutionTransformation:
    """Perform 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,
    ):
        """Perform 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.
            order: Whether to order the structures.
        """
        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

    def __repr__(self):
        return f"Multiple Substitution Transformation : Substitution on {self.sp_to_replace}"

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

        Args:
            structure: Input Structure
            return_ranked_list (bool | int, optional): If return_ranked_list is int, that number of structures

                is returned. If False, only the single lowest energy structure is returned. Defaults to False.

        Returns:
            Structures with all substitutions applied.
        """
        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():
            sign = "+" if charge > 0 else "-"
            dummy_sp = f"X{charge}{sign}"
            mapping = {
                self.sp_to_replace: {
                    self.sp_to_replace: 1 - self.r_fraction,
                    dummy_sp: self.r_fraction,
                }
            }
            trans = SubstitutionTransformation(mapping)  # type: ignore[arg-type]
            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:
                dummy_structure = OrderDisorderedStructureTransformation().apply_transformation(dummy_structure)  # type:ignore[assignment]

            for el in el_list:
                sign = "+" if charge > 0 else "-"
                st = SubstitutionTransformation({f"X{charge}+": f"{el}{charge}{sign}"})
                new_structure = st.apply_transformation(dummy_structure)
                outputs.append({"structure": new_structure})
        return outputs

    @property
    def is_one_to_many(self) -> Literal[True]:
        """Transform one structure to many."""
        return True


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.
    """

    def __init__(
        self,
        min_cell_size: int = 1,
        max_cell_size: int = 1,
        symm_prec: float = 0.1,
        refine_structure: bool = False,
        enum_precision_parameter: float = 0.001,
        check_ordered_symmetry: bool = True,
        max_disordered_sites: int | None = None,
        sort_criteria: str | Callable = "ewald",
        timeout: float | None = None,
        n_jobs: int = -1,
    ):
        """Initialize an EnumerateStructureTransformation.

        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, refinement
                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 or callable): Sort by Ewald energy ("ewald", must have oxidation states and slow) or
                M3GNet relaxed energy ("m3gnet_relax", which is the most accurate but most expensive and provides
                pre-relaxed structures - needs m3gnet package installed) or by M3GNet static energy ("m3gnet_static")
                or by number of sites ("nsites", the fastest, the default). The expense of m3gnet_relax or m3gnet_static
                can be worth it if it significantly reduces the number of structures to be considered. m3gnet_relax
                speeds up the subsequent DFT calculations. Alternatively, a callable can be supplied that returns a
                (Structure, energy) tuple.
            timeout (float): timeout in minutes to pass to EnumlibAdaptor.
            n_jobs (int): Number of parallel jobs used to compute energy criteria. This is used only when the Ewald
                or m3gnet or callable sort_criteria is used. Default is -1, which uses all available CPUs.
        """
        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
        self.n_jobs = n_jobs

        if max_cell_size and max_disordered_sites:
            raise ValueError("Cannot set both max_cell_size and max_disordered_sites!")

    def __repr__(self):
        return "EnumerateStructureTransformation"

    def apply_transformation(
        self, structure: Structure, return_ranked_list: bool | int = False
    ) -> Structure | list[dict]:
        """Get either a single ordered structure or a sequence of all ordered
        structures.

        Args:
            structure: Structure to order.
            return_ranked_list (bool | int, optional): If return_ranked_list is int, that number of structures

                is returned. If False, only the single lowest energy structure is returned. Defaults to False.

        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.elements)

        structures = None

        if structure.is_ordered:
            warnings.warn(
                f"Enumeration skipped for structure with composition {structure.composition} because it is ordered",
                stacklevel=2,
            )
            structures = [structure.copy()]

        if self.max_disordered_sites:
            n_disordered = sum(1 for site in structure if not site.is_ordered)
            if n_disordered > self.max_disordered_sites:
                raise ValueError(f"Too many disordered sites! ({n_disordered} > {self.max_disordered_sites})")
            max_cell_sizes: Iterable[int] = range(
                self.min_cell_size,
                math.floor(self.max_disordered_sites / n_disordered) + 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:
                adaptor.run()
                structures = adaptor.structures
                if structures:
                    break
            except EnumError:
                warnings.warn(f"Unable to enumerate for {max_cell_size = }", stacklevel=2)

        if structures is None:
            raise ValueError("Unable to enumerate")

        original_latt = structure.lattice
        inv_latt = np.linalg.inv(original_latt.matrix)
        ewald_matrices = {}
        m3gnet_model: Relaxer | M3GNetCalculator | None = None

        if not callable(self.sort_criteria) and self.sort_criteria.startswith("m3gnet"):
            import matgl
            from matgl.ext.ase import M3GNetCalculator, Relaxer

            if self.sort_criteria == "m3gnet_relax":
                potential = matgl.load_model("M3GNet-MP-2021.2.8-PES")
                m3gnet_model = Relaxer(potential=potential)
            elif self.sort_criteria == "m3gnet":
                potential = matgl.load_model("M3GNet-MP-2021.2.8-PES")
                m3gnet_model = M3GNetCalculator(potential=potential, stress_weight=0.01)

        def _get_stats(struct):
            if callable(self.sort_criteria):
                struct, energy = self.sort_criteria(struct)
                return {
                    "num_sites": len(struct),
                    "energy": energy,
                    "structure": struct,
                }
            if contains_oxidation_state and self.sort_criteria == "ewald":
                new_latt = struct.lattice
                transformation = np.dot(new_latt.matrix, inv_latt)
                transformation = tuple(tuple(round(cell) for cell in row) for row in transformation)
                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(struct)
                return {"num_sites": len(struct), "energy": energy, "structure": struct}
            if self.sort_criteria.startswith("m3gnet"):
                if self.sort_criteria == "m3gnet_relax":
                    relax_results = m3gnet_model.relax(struct)
                    energy = float(relax_results["trajectory"].energies[-1])
                    struct = relax_results["final_structure"]

                elif self.sort_criteria == "m3gnet":
                    atoms = AseAtomsAdaptor().get_atoms(struct)
                    m3gnet_model.calculate(atoms)
                    energy = float(m3gnet_model.results["energy"])

                else:
                    raise ValueError("Unsupported sort criteria.")

                return {"num_sites": len(struct), "energy": energy, "structure": struct}

            return {"num_sites": len(struct), "structure": struct}

        all_structures = Parallel(n_jobs=self.n_jobs)(delayed(_get_stats)(struct) for struct in structures)

        def sort_func(struct):
            return (
                struct["energy"] / struct["num_sites"]
                if callable(self.sort_criteria)
                or self.sort_criteria.startswith("m3gnet")
                or (contains_oxidation_state and self.sort_criteria == "ewald")
                else struct["num_sites"]
            )

        self._all_structures = sorted(all_structures, key=sort_func)

        if return_ranked_list:
            return self._all_structures[:num_to_return]
        return self._all_structures[0]["structure"]

    @property
    def is_one_to_many(self) -> Literal[True]:
        """Transform one structure to many."""
        return True


class SubstitutionPredictorTransformation(AbstractTransformation):
    """This transformation takes a structure and uses the structure
    prediction module to find likely site substitutions.
    """

    def __init__(self, threshold=1e-2, scale_volumes=True, **kwargs):
        """Initialize a SubstitutionPredictorTransformation.

        Args:
            threshold: Threshold for substitution.
            scale_volumes: Whether to scale volumes after substitution.
            **kwargs: Args for SubstitutionProbability class lambda_table, alpha.
        """
        self.kwargs = kwargs
        self.threshold = threshold
        self.scale_volumes = scale_volumes
        self._substitutor = SubstitutionPredictor(threshold=threshold, **kwargs)

    def __repr__(self):
        return "SubstitutionPredictorTransformation"

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

        Args:
            structure: Input Structure
            return_ranked_list (bool | int, optional): If return_ranked_list is int, that number of structures

                is returned. If False, only the single lowest energy structure is returned. Defaults to False.

        Returns:
            Predicted Structures.
        """
        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

    @property
    def is_one_to_many(self) -> Literal[True]:
        """Transform one structure to many."""
        return True


class MagOrderParameterConstraint(MSONable):
    """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.
    """

    def __init__(
        self,
        order_parameter,
        species_constraints=None,
        site_constraint_name=None,
        site_constraints=None,
    ):
        """Initialize a MagOrderParameterConstraint.

        Args:
            order_parameter (float): any number from 0.0 to 1.0,
                typically 0.5 (antiferromagnetic) or 1.0 (ferromagnetic)
            species_constraints (list): str or list of strings
                of Species symbols that the constraint should apply to
            site_constraint_name (str): name of the site property
                that the constraint should apply to, e.g. "coordination_no"
            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.")
        if 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")
        if not math.isclose(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.",
                stacklevel=2,
            )

        self.order_parameter = order_parameter
        self.species_constraints = species_constraints
        self.site_constraint_name = site_constraint_name
        self.site_constraints = site_constraints

    def satisfies_constraint(self, site):
        """Check if a periodic site satisfies the constraint."""
        if not site.is_ordered:
            return False

        satisfies_constraints = self.species_constraints and str(site.specie) in self.species_constraints

        if self.site_constraint_name and self.site_constraint_name in site.properties:
            prop = site.properties[self.site_constraint_name]
            satisfies_constraints = prop in self.site_constraints

        return satisfies_constraints


class MagOrderingTransformation(AbstractTransformation):
    """This transformation takes a structure and returns a list of collinear
    magnetic orderings. For disordered structures, make an ordered
    approximation first.
    """

    def __init__(self, mag_species_spin, order_parameter=0.5, energy_model=None, **kwargs):
        """Initialize a MagOrderingTransformation.

        Args:
            mag_species_spin: A mapping of elements/species to their
                spin magnitudes, e.g. {"Fe3+": 5, "Mn3+": 4}
            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
                pymatgen.transformations.advanced_transformations.MagOrderParameterConstraint
                to specify more complicated orderings, see documentation for
                MagOrderParameterConstraint more details on usage
            energy_model: Energy model to rank the returned structures,
                see :mod: `pymatgen.core.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.
            kwargs: Additional kwargs that are passed to
                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),
                )
            ]
        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.")  # noqa: TRY004

        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 or SymmetryModel()
        self.enum_kwargs = kwargs

    @staticmethod
    def determine_min_cell(disordered_structure):
        """Determine the smallest supercell that is able to enumerate
        the provided structure with the given order parameter.
        """
        # assumes all order parameters for a given species are the same
        mag_species_order_parameter = {}
        mag_species_occurrences = {}
        for site in disordered_structure:
            if not site.is_ordered:
                # 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(next(iter(site.species))).split(",", maxsplit=1)[0]
                if sp in mag_species_order_parameter:
                    mag_species_occurrences[sp] += 1
                else:
                    op = max(site.species.values())
                    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 = math.gcd(denom, num_atom_per_specie)
            smallest_n.append(math.lcm(int(n_gcd), denom) / n_gcd)

        return max(smallest_n)

    @staticmethod
    def _add_dummy_species(structure, order_parameters):
        """Decorate the structure with DummySpecies based on order-parameter constraints.

        Args:
            structure: ordered Structure
            order_parameters: list of MagOrderParameterConstraints.

        Returns:
            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
            DummySpecies, 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 DummySpecies 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 = [
            {
                DummySpecies(symbol, spin=Spin.up): constraint.order_parameter,
                DummySpecies(symbol, spin=Spin.down): 1 - constraint.order_parameter,
            }
            for symbol, constraint in zip(dummy_species_symbols, order_parameters, strict=True)
        ]

        for site in 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(f"Order parameter constraints conflict for site: {site.specie}, {site.properties}")
            if 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):
        """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 RuntimeError("Something went wrong with enumeration.")

        sites_to_remove = []
        logger.debug(f"Dummy species structure:\n{structure}")
        for idx, site in enumerate(structure):
            if isinstance(site.specie, DummySpecies):
                sites_to_remove.append(idx)
                spin = getattr(site.specie, "spin", 0)
                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 RuntimeError(f"This shouldn't happen, found {neighbors=}")
                orig_site_idx = neighbors[0][2]
                orig_specie = structure[orig_site_idx].specie
                new_specie = Species(
                    orig_specie.symbol,
                    getattr(orig_specie, "oxi_state", None),
                    spin=spin,
                )
                structure.replace(
                    orig_site_idx,
                    new_specie,
                    properties=structure[orig_site_idx].properties,
                )
        structure.remove_sites(sites_to_remove)
        logger.debug(f"Structure with dummy species removed:\n{structure}")
        return structure

    def _add_spin_magnitudes(self, structure: Structure):
        """Replaces Spin.up/Spin.down with spin magnitudes specified by mag_species_spin.

        Args:
            structure (Structure): Structure to modify.

        Returns:
            Structure: Structure with spin magnitudes added.
        """
        for idx, site in enumerate(structure):
            if getattr(site.specie, "spin", False):
                spin = site.specie.spin
                spin = getattr(site.specie, "spin", None)
                sign = int(spin) if spin else 0
                if spin:
                    # 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(",", maxsplit=1)[0]
                    new_spin = sign * self.mag_species_spin.get(sp, 0)
                    new_specie = Species(
                        site.specie.symbol,
                        getattr(site.specie, "oxi_state", None),
                        spin=new_spin,
                    )
                    structure.replace(idx, new_specie, properties=site.properties)
        logger.debug(f"Structure with spin magnitudes:\n{structure}")
        return structure

    def apply_transformation(
        self, structure: Structure, return_ranked_list: bool | int = False
    ) -> Structure | list[Structure]:
        """Apply MagOrderTransformation to an input structure.

        Args:
            structure (Structure): Any ordered structure.
            return_ranked_list (bool | int, optional): If return_ranked_list is int, that number of structures
                is returned. If False, only the single lowest energy structure is returned. Defaults to False.

        Raises:
            ValueError: On disordered structures.

        Returns:
            Structure | list[Structure]: Structure(s) after MagOrderTransformation.
        """
        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"):
            if enum_kwargs["min_cell_size"] > enum_kwargs["max_cell_size"]:
                warnings.warn(
                    f"Specified max cell size ({enum_kwargs['max_cell_size']}) is "
                    "smaller than the minimum enumerable cell size "
                    f"({enum_kwargs['min_cell_size']}), changing max cell size to "
                    f"{enum_kwargs['min_cell_size']}",
                    stacklevel=2,
                )
                enum_kwargs["max_cell_size"] = enum_kwargs["min_cell_size"]
        else:
            enum_kwargs["max_cell_size"] = enum_kwargs["min_cell_size"]

        trafo = EnumerateStructureTransformation(**enum_kwargs)

        all_structs = trafo.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(all_structs, Structure):
            # remove dummy species and replace Spin.up or Spin.down
            # with spin magnitudes given in mag_species_spin arg
            all_structs = self._remove_dummy_species(all_structs)
            all_structs = self._add_spin_magnitudes(all_structs)  # type: ignore[arg-type]
        else:
            for idx, struct in enumerate(all_structs):
                all_structs[idx]["structure"] = self._remove_dummy_species(struct["structure"])  # type: ignore[index]
                all_structs[idx]["structure"] = self._add_spin_magnitudes(struct["structure"])  # type: ignore[index, arg-type]

        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 all_structs[0]["structure"] if num_to_return else all_structs  # type: ignore[return-value, index]

        # Remove duplicate structures and group according to energy model
        matcher = StructureMatcher(comparator=SpinComparator())

        def key(struct: Structure) -> int:
            return SpacegroupAnalyzer(struct, 0.1).get_space_group_number()

        out = []
        for _, group in groupby(sorted((dct["structure"] for dct in all_structs), key=key), key):  # type: ignore[arg-type, index]
            group = list(group)  # type: ignore[assignment]
            grouped = matcher.group_structures(group)
            out.extend([{"structure": g[0], "energy": self.energy_model.get_energy(g[0])} for g in grouped])

        self._all_structures = sorted(out, key=lambda dct: dct["energy"])

        return self._all_structures[:num_to_return]  # type: ignore[return-value]

    @property
    def is_one_to_many(self) -> Literal[True]:
        """Transform one structure to many."""
        return True


def find_codopant(
    target: Species,
    oxidation_state: float,
    allowed_elements: Sequence[str] | None = None,
) -> Species:
    """Find 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 (Species): provides target ionic radius.
        oxidation_state (float): co-dopant oxidation state.
        allowed_elements (list[str]): List of allowed elements. If None,
            all elements are tried.

    Returns:
        Species: with oxidation_state that has ionic radius closest to target.
    """
    ref_radius = target.ionic_radius
    if ref_radius is None:
        raise ValueError(f"Target species {target} has no ionic radius.")
    candidates: list[tuple[float, Species]] = []
    symbols = allowed_elements or [el.symbol for el in Element]
    for sym in symbols:
        try:
            with warnings.catch_warnings():
                warnings.simplefilter("ignore")
                sp = Species(sym, oxidation_state)
                radius = sp.ionic_radius
                if radius is not None:
                    candidates.append((radius, sp))
        except (ValueError, KeyError):
            pass
    if not candidates:
        raise ValueError(
            f"No species found with oxidation state {oxidation_state} and a known ionic radius "
            f"(target: {target}, allowed_elements: {allowed_elements})."
        )
    return min(candidates, key=lambda tup: abs(tup[0] / ref_radius - 1))[1]


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,
    ):
        """Initialize a DopingTransformation.

        Args:
            dopant (Species-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 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

    def apply_transformation(
        self,
        structure: Structure,
        return_ranked_list: bool | int = False,
    ) -> list[dict[str, Any]] | Structure:
        """Apply the doping transformation to a structure.

        Args:
            structure (Structure): Input structure to dope.
            return_ranked_list (bool | int, optional): If is int, that number of structures is returned.
                If False, only the single lowest energy structure is returned. Defaults to False.

        Returns:
            list[dict] | Structure: each dict as {"structure": Structure, "energy": float}.
        """
        comp = structure.composition
        logger.info(f"Composition: {comp}")

        for sp in comp:
            if not hasattr(sp, "oxi_state"):
                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]
            ]

        logger.info(f"Compatible species: {compatible_species}")

        lengths = structure.lattice.abc
        scaling = [max(1, math.ceil(self.min_length / x)) for x in lengths]
        logger.info(f"{lengths=}")
        logger.info(f"{scaling=}")

        all_structures: list[dict] = []
        trafo = 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}})
                logger.info(f"Doping {sp} for {self.dopant} at level {1 / nsp:.3f}")
            elif self.codopant:
                codopant = find_codopant(sp, 2 * sp.oxi_state - ox)  # type: ignore[arg-type, operator]
                supercell.replace_species({sp: {sp: (nsp - 2) / nsp, self.dopant: 1 / nsp, codopant: 1 / nsp}})
                logger.info(f"Doping {sp} for {self.dopant} + {codopant} at level {1 / nsp:.3f}")
            elif abs(sp.oxi_state) < abs(ox):  # type: ignore[arg-type]
                # 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),  # type: ignore[arg-type]
                )

                if sp_to_remove == sp:
                    common_charge = math.lcm(int(abs(sp.oxi_state)), int(abs(ox)))  # type: ignore[arg-type]
                    n_dopant = common_charge / abs(ox)
                    nsp_to_remove = common_charge / abs(sp.oxi_state)  # type: ignore[arg-type]
                    logger.info(f"Doping {nsp_to_remove} {sp} with {n_dopant} {self.dopant}.")
                    supercell.replace_species(
                        {
                            sp: {
                                sp: (nsp - nsp_to_remove) / nsp,
                                self.dopant: n_dopant / nsp,
                            }
                        }
                    )
                else:
                    ox_diff = int(abs(round(sp.oxi_state - ox)))
                    vac_ox = int(abs(sp_to_remove.oxi_state)) * ox_diff  # type: ignore[arg-type]
                    common_charge = math.lcm(vac_ox, ox_diff)
                    n_dopant = common_charge / ox_diff
                    nx_to_remove = common_charge / vac_ox
                    nx = supercell.composition[sp_to_remove]
                    logger.info(
                        f"Doping {n_dopant} {sp} with {self.dopant} and removing {nx_to_remove} {sp_to_remove}."
                    )
                    supercell.replace_species(
                        {
                            sp: {
                                sp: (nsp - n_dopant) / nsp,
                                self.dopant: n_dopant / nsp,
                            },
                            sp_to_remove: {sp_to_remove: (nx - nx_to_remove) / nx},
                        }
                    )
            elif abs(sp.oxi_state) > abs(ox):  # type: ignore[arg-type]
                # 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, key=lambda el: el.X)
                else:
                    sp_to_remove = min(supercell.composition, key=lambda el: el.X)
                # Confirm species are of opposite oxidation states.
                if sp_to_remove.oxi_state * sp.oxi_state >= 0:  # type: ignore[operator]
                    raise ValueError("Species should be of opposite oxidation states.")
                ox_diff = int(abs(round(sp.oxi_state - ox)))
                anion_ox = int(abs(sp_to_remove.oxi_state))  # type: ignore[arg-type]
                nx = supercell.composition[sp_to_remove]
                common_charge = math.lcm(anion_ox, ox_diff)
                n_dopant = common_charge / ox_diff
                nx_to_remove = common_charge / anion_ox
                logger.info(f"Doping {n_dopant} {sp} with {self.dopant} and removing {nx_to_remove} {sp_to_remove}.")
                supercell.replace_species(
                    {
                        sp: {sp: (nsp - n_dopant) / nsp, self.dopant: n_dopant / nsp},
                        sp_to_remove: {sp_to_remove: (nx - nx_to_remove) / nx},
                    }
                )

            structs = trafo.apply_transformation(supercell, return_ranked_list=self.max_structures_per_enum)
            logger.info(f"{len(structs)} distinct structures")
            all_structures.extend(structs)
        logger.info(f"Total {len(all_structures)} doped structures")
        if return_ranked_list:
            return all_structures[:return_ranked_list]

        return all_structures[0]["structure"]

    @property
    def is_one_to_many(self) -> Literal[True]:
        """Transform one structure to many."""
        return True


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,
    ):
        """Initialize a SlabTransformation.

        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
            in_unit_planes (bool): Whether to set min_slab_size and min_vac_size
                in units of hkl planes (True) or Angstrom (False, the default). Setting in
                units of planes is useful for ensuring some slabs have a certain n_layer of
                atoms. e.g. for Cs (100), a 10 Ang slab will result in a slab with only 2
                layer of atoms, whereas Fe (100) will have more layer of atoms. By using units
                of hkl planes instead, we ensure both slabs have the same number of atoms. The
                slab thickness will be in min_slab_size/math.ceil(self._proj_height/dhkl)
                multiples of oriented unit cells.
            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 = tol

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

        Args:
            structure: Input Structure

        Returns:
            Slab Structures.
        """
        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,
        )
        return sg.get_slab(self.shift, self.tol)


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):
        """Initialize a DisorderOrderedTransformation.

        Args:
            max_sites_to_merge: only merge this number of sites together.
        """
        self.max_sites_to_merge = max_sites_to_merge

    def apply_transformation(self, structure: Structure, return_ranked_list: bool | int = False):
        """Apply the disorder-to-ordered transformation to a structure.

        Args:
            structure: ordered structure
            return_ranked_list (bool | int, optional): If return_ranked_list is int, that number of structures.

                is returned. If False, only the single lowest energy structure is returned. Defaults to False.

        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
        if not return_ranked_list:
            return disordered_structures[0]["structure"]
        if len(disordered_structures) > return_ranked_list:
            disordered_structures = disordered_structures[:return_ranked_list]
        return disordered_structures

    @property
    def is_one_to_many(self) -> Literal[True]:
        """Transform one structure to many."""
        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 https://stackoverflow.com/a/30134039

            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

            return [partitions_to_sort[x[0]] for x in partition_indices]

        collection = list(composition)
        partitions = list(_partition(collection))
        return _sort_partitions(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):
            dct = {}  # 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:
                        dct[sp] = merged_comp
            return dct

        return [_get_replacement_dict_from_partition(p) for p in partitions]


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: tuple[float, float] | None = None,
        normal=False,
        ratio=True,
        plane=None,
        max_search=20,
        tol_coi=1e-8,
        rm_ratio=0.7,
        quick_gen=False,
    ):
        """Initialize a GrainBoundaryTransformation.

        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 (tuple[float, float]): in plane shift of two grains in unit of a, b vectors of Gb
            normal (logic):
                determine if need to require the c axis of top grain (first transformation matrix)
                perpendicular to the surface or not.
                default to false.
            ratio (list of integers): lattice axial ratio.
                If True, will try to determine automatically from structure.
                For cubic system, ratio is not needed and can be set to None.
                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).
            rm_ratio (float): the criteria to remove the atoms which are too close with each other.
                rm_ratio * bond_length of bulk system is the criteria of bond length, below which the atom
                will be removed. Default to 0.7.
            quick_gen (bool): whether to quickly generate a supercell, if set to true, no need to
                find the smallest cell.
        """
        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 or (0, 0)
        self.normal = normal
        self.ratio = ratio
        self.plane = plane
        self.max_search = max_search
        self.tol_coi = tol_coi
        self.rm_ratio = rm_ratio
        self.quick_gen = quick_gen

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

        Args:
            structure: Input Structure
            return_ranked_list (bool | int, optional): If return_ranked_list is int, that number of structures
                is returned. If False, only the single lowest energy structure is returned. Defaults to False.

        Returns:
            Grain boundary Structures.
        """
        gbg = GrainBoundaryGenerator(structure)

        return gbg.gb_from_parameters(
            self.rotation_axis,
            self.rotation_angle,
            expand_times=self.expand_times,
            vacuum_thickness=self.vacuum_thickness,
            ab_shift=self.ab_shift,
            normal=self.normal,
            ratio=gbg.get_ratio() if self.ratio is True else self.ratio,
            plane=self.plane,
            max_search=self.max_search,
            tol_coi=self.tol_coi,
            rm_ratio=self.rm_ratio,
            quick_gen=self.quick_gen,
        )


class CubicSupercellTransformation(AbstractTransformation):
    """A transformation that aims to generate a nearly cubic supercell structure
    from a structure.

    The algorithm solves for a transformation matrix that makes the supercell
    cubic. The matrix must have integer entries, so entries are rounded (in such
    a way that forces the matrix to be non-singular). From the supercell
    resulting from this transformation matrix, vector projections are used to
    determine the side length of the largest cube that can fit inside the
    supercell. The algorithm will iteratively increase the size of the supercell
    until the largest inscribed cube's side length is at least 'min_length'
    and the number of atoms in the supercell falls in the range
    ``min_atoms < n < max_atoms``.
    """

    def __init__(
        self,
        min_atoms: int | None = None,
        max_atoms: int | None = None,
        min_length: float = 15.0,
        max_length: float | None = None,
        force_diagonal: bool = False,
        force_90_degrees: bool = False,
        allow_orthorhombic: bool = False,
        angle_tolerance: float = 1e-3,
        step_size: float = 0.1,
    ):
        """Initialize a CubicSupercellTransformation.

        Args:
            max_atoms: Maximum number of atoms allowed in the supercell.
            min_atoms: Minimum number of atoms allowed in the supercell.
            min_length: Minimum length of the smallest supercell lattice vector.
            max_length: Maximum length of the larger supercell lattice vector.
            force_diagonal: If True, return a transformation with a diagonal
                transformation matrix.
            force_90_degrees: If True, return a transformation for a supercell
                with 90 degree angles (if possible). To avoid long run times,
                please use max_atoms or max_length
            allow_orthorhombic: Instead of a cubic cell, also orthorhombic cells
                are allowed. max_length is required for this option.
            angle_tolerance: tolerance to determine the 90 degree angles.
            step_size (float): step_size which is used to increase the supercell.
                If allow_orthorhombic and force_90_degrees is both set to True,
                the chosen step_size will be automatically multiplied by 5 to
                prevent a too long search for the possible supercell.
        """
        self.min_atoms = min_atoms or -np.inf
        self.max_atoms = max_atoms or np.inf
        self.min_length = min_length
        self.max_length = max_length
        self.force_diagonal = force_diagonal
        self.force_90_degrees = force_90_degrees
        self.allow_orthorhombic = allow_orthorhombic
        self.angle_tolerance = angle_tolerance
        self.transformation_matrix = None
        self.step_size = step_size

    def apply_transformation(self, structure: Structure) -> Structure:
        """The algorithm solves for a transformation matrix that makes the
        supercell cubic. The matrix must have integer entries, so entries are
        rounded (in such a way that forces the matrix to be non-singular). From
        the supercell resulting from this transformation matrix, vector
        projections are used to determine the side length of the largest cube
        that can fit inside the supercell. The algorithm will iteratively
        increase the size of the supercell until the largest inscribed cube's
        side length is at least 'num_nn_dists' times the nearest neighbor
        distance and the number of atoms in the supercell falls in the range
        defined by min_atoms and max_atoms.

        Returns:
            supercell: Transformed supercell.
        """
        lat_vecs = structure.lattice.matrix

        if self.max_length is None and self.allow_orthorhombic:
            raise AttributeError("max_length is required for orthorhombic cells")

        if self.force_diagonal:
            scale = self.min_length / np.array(structure.lattice.abc)
            self.transformation_matrix = np.diag(np.ceil(scale).astype(int))  # type: ignore[assignment]
            st = SupercellTransformation(self.transformation_matrix)
            return st.apply_transformation(structure)

        if not self.allow_orthorhombic:
            # boolean for if a sufficiently large supercell has been created
            sc_not_found = True

            # target_threshold is used as the desired cubic side lengths
            target_sc_size = self.min_length
            while sc_not_found:
                target_sc_lat_vecs = np.eye(3, 3) * target_sc_size
                length_vecs, n_atoms, superstructure, self.transformation_matrix = self.get_possible_supercell(
                    lat_vecs, structure, target_sc_lat_vecs
                )
                # Check if constraints are satisfied
                if self.check_constraints(
                    length_vecs=length_vecs,
                    n_atoms=n_atoms,
                    superstructure=superstructure,
                ):
                    return superstructure

                # Increase threshold until proposed supercell meets requirements
                target_sc_size += self.step_size
                self.check_exceptions(length_vecs, n_atoms)

            raise AttributeError("Unable to find cubic supercell")

        if self.force_90_degrees:
            # prevent a too long search for the supercell
            self.step_size *= 5

        combined_list = [
            [size_a, size_b, size_c]
            for size_a in np.arange(self.min_length, self.max_length, self.step_size)
            for size_b in np.arange(self.min_length, self.max_length, self.step_size)
            for size_c in np.arange(self.min_length, self.max_length, self.step_size)
        ]
        combined_list = sorted(combined_list, key=sum)

        for size_a, size_b, size_c in combined_list:
            target_sc_lat_vecs = np.array([[size_a, 0, 0], [0, size_b, 0], [0, 0, size_c]])
            length_vecs, n_atoms, superstructure, self.transformation_matrix = self.get_possible_supercell(
                lat_vecs, structure, target_sc_lat_vecs
            )
            # Check if constraints are satisfied
            if self.check_constraints(length_vecs=length_vecs, n_atoms=n_atoms, superstructure=superstructure):
                return superstructure

            self.check_exceptions(length_vecs, n_atoms)
        raise AttributeError("Unable to find orthorhombic supercell")

    def check_exceptions(self, length_vecs, n_atoms):
        """Check supercell exceptions."""
        if n_atoms > self.max_atoms:
            raise AttributeError(
                "While trying to solve for the supercell, the max "
                "number of atoms was exceeded. Try lowering the number"
                "of nearest neighbor distances."
            )
        if self.max_length is not None and np.max(np.linalg.norm(length_vecs, axis=1)) >= self.max_length:
            raise AttributeError("While trying to solve for the supercell, the max length was exceeded.")

    def check_constraints(self, length_vecs, n_atoms, superstructure):
        """
        Check if the supercell constraints are met.

        Returns:
            bool

        """
        return bool(
            (
                np.min(np.linalg.norm(length_vecs, axis=1)) >= self.min_length
                and self.min_atoms <= n_atoms <= self.max_atoms
            )
            and (
                not self.force_90_degrees
                or np.all(np.absolute(np.array(superstructure.lattice.angles) - 90) < self.angle_tolerance)
            )
        )

    @staticmethod
    def get_possible_supercell(lat_vecs, structure, target_sc_lat_vecs):
        """
        Get the supercell possible with the set conditions.

        Returns:
            length_vecs, n_atoms, superstructure, transformation_matrix
        """
        transformation_matrix = target_sc_lat_vecs @ np.linalg.inv(lat_vecs)
        # round the entries of T and force T to be non-singular
        transformation_matrix = _round_and_make_arr_singular(  # type: ignore[assignment]
            transformation_matrix  # type: ignore[arg-type]
        )
        proposed_sc_lat_vecs = transformation_matrix @ lat_vecs
        # Find the shortest dimension length and direction
        a = proposed_sc_lat_vecs[0]
        b = proposed_sc_lat_vecs[1]
        c = proposed_sc_lat_vecs[2]
        length1_vec = c - _proj(c, a)  # a-c plane
        length2_vec = a - _proj(a, c)
        length3_vec = b - _proj(b, a)  # b-a plane
        length4_vec = a - _proj(a, b)
        length5_vec = b - _proj(b, c)  # b-c plane
        length6_vec = c - _proj(c, b)
        length_vecs = np.array(
            [
                length1_vec,
                length2_vec,
                length3_vec,
                length4_vec,
                length5_vec,
                length6_vec,
            ]
        )
        # Get number of atoms
        st = SupercellTransformation(transformation_matrix)
        superstructure = st.apply_transformation(structure)
        n_atoms = len(superstructure)
        return length_vecs, n_atoms, superstructure, transformation_matrix


class AddAdsorbateTransformation(AbstractTransformation):
    """Create adsorbate structures."""

    def __init__(
        self,
        adsorbate,
        selective_dynamics=False,
        height=0.9,
        mi_vec=None,
        repeat=None,
        min_lw=5.0,
        translate=True,
        reorient=True,
        find_args=None,
    ):
        """Use AdsorbateSiteFinder to add an adsorbate to a slab.

        Args:
            adsorbate (Molecule): molecule to add as adsorbate
            selective_dynamics (bool): flag for whether to assign
                non-surface sites as fixed for selective dynamics
            height (float): height criteria for selection of surface sites
            mi_vec : vector corresponding to the vector
                concurrent with the miller index, this enables use with
                slabs that have been reoriented, but the miller vector
                must be supplied manually
            repeat (3-tuple or list): repeat argument for supercell generation
            min_lw (float): minimum length and width of the slab, only used
                if repeat is None
            translate (bool): flag on whether to translate the molecule so
                that its CoM is at the origin prior to adding it to the surface
            reorient (bool): flag on whether or not to reorient adsorbate
                along the miller index
            find_args (dict): dictionary of arguments to be passed to the
                call to self.find_adsorption_sites, e.g. {"distance":2.0}
        """
        self.adsorbate = adsorbate
        self.selective_dynamics = selective_dynamics
        self.height = height
        self.mi_vec = mi_vec
        self.repeat = repeat
        self.min_lw = min_lw
        self.translate = translate
        self.reorient = reorient
        self.find_args = find_args

    def apply_transformation(self, structure: Structure, return_ranked_list: bool | int = False):
        """Apply the slab adsorbate transformation to a Slab structure.

        Args:
            structure: Must be a Slab structure
            return_ranked_list (bool | int, optional): If return_ranked_list is int, that number of structures.

                is returned. If False, only the single lowest energy structure is returned. Defaults to False.

        Returns:
            Slab: with adsorbate
        """
        site_finder = AdsorbateSiteFinder(
            structure,  # type:ignore[arg-type]
            selective_dynamics=self.selective_dynamics,
            height=self.height,
            mi_vec=self.mi_vec,
        )

        structures = site_finder.generate_adsorption_structures(
            self.adsorbate,
            repeat=self.repeat,
            min_lw=self.min_lw,
            translate=self.translate,
            reorient=self.reorient,
            find_args=self.find_args,
        )

        if not return_ranked_list:
            return structures[0]
        return [{"structure": structure} for structure in structures[:return_ranked_list]]

    @property
    def is_one_to_many(self) -> Literal[True]:
        """Transform one structure to many."""
        return True


def _round_and_make_arr_singular(arr: np.ndarray) -> np.ndarray:
    """This function rounds all elements of a matrix to the nearest integer,
    unless the rounding scheme causes the matrix to be singular, in which
    case elements of zero rows or columns in the rounded matrix with the
    largest absolute valued magnitude in the unrounded matrix will be
    rounded to the next integer away from zero rather than to the
    nearest integer.

    The transformation is as follows. First, all entries in 'arr' will be
    rounded to the nearest integer to yield 'arr_rounded'. If 'arr_rounded'
    has any zero rows, then one element in each zero row of 'arr_rounded'
    corresponding to the element in 'arr' of that row with the largest
    absolute valued magnitude will be rounded to the next integer away from
    zero (see the '_round_away_from_zero(x)' function) rather than the
    nearest integer. This process is then repeated for zero columns. Also
    note that if 'arr' already has zero rows or columns, then this function
    will not change those rows/columns.

    Args:
        arr: Input matrix

    Returns:
        Transformed matrix.
    """

    def round_away_from_zero(x):
        """Get 'x' rounded to the next integer away from 0.
        If 'x' is zero, then returns zero.
        E.g. -1.2 rounds to -2.0. 1.2 rounds to 2.0.
        """
        abs_x = abs(x)
        return math.ceil(abs_x) * (abs_x / x) if x != 0 else 0

    arr_rounded = np.around(arr)

    # Zero rows in 'arr_rounded' make the array singular, so force zero rows to
    # be nonzero
    if (~arr_rounded.any(axis=1)).any():
        # Check for zero rows in T_rounded

        # indices of zero rows
        zero_row_idxs = np.where(~arr_rounded.any(axis=1))[0]

        for zero_row_idx in zero_row_idxs:  # loop over zero rows
            zero_row = arr[zero_row_idx, :]

            # Find the element of the zero row with the largest absolute
            # magnitude in the original (non-rounded) array (i.e. 'arr')
            matches = np.absolute(zero_row) == np.amax(np.absolute(zero_row))
            col_idx_to_fix = np.where(matches)[0]

            # Break ties for the largest absolute magnitude
            r_idx = np.random.default_rng().integers(len(col_idx_to_fix))
            col_idx_to_fix = col_idx_to_fix[r_idx]

            # Round the chosen element away from zero
            arr_rounded[zero_row_idx, col_idx_to_fix] = round_away_from_zero(arr[zero_row_idx, col_idx_to_fix])

    # Repeat process for zero columns
    if (~arr_rounded.any(axis=0)).any():
        # Check for zero columns in T_rounded
        zero_col_idxs = np.where(~arr_rounded.any(axis=0))[0]
        for zero_col_idx in zero_col_idxs:
            zero_col = arr[:, zero_col_idx]
            matches = np.absolute(zero_col) == np.amax(np.absolute(zero_col))
            row_idx_to_fix = np.where(matches)[0]

            for idx in row_idx_to_fix:
                arr_rounded[idx, zero_col_idx] = round_away_from_zero(arr[idx, zero_col_idx])
    return arr_rounded.astype(int)


class SubstituteSurfaceSiteTransformation(AbstractTransformation):
    """Use AdsorptionSiteFinder to perform substitution-type doping on the surface
    and returns all possible configurations where one dopant is substituted
    per surface. Can substitute one surface or both.
    """

    def __init__(
        self,
        atom,
        selective_dynamics=False,
        height=0.9,
        mi_vec=None,
        target_species=None,
        sub_both_sides=False,
        range_tol=1e-2,
        dist_from_surf=0,
    ):
        """Initialize a SubstituteSurfaceSiteTransformation.

        Args:
            atom (str): atom corresponding to substitutional dopant
            selective_dynamics (bool): flag for whether to assign
                non-surface sites as fixed for selective dynamics
            height (float): height criteria for selection of surface sites
            mi_vec : vector corresponding to the vector
                concurrent with the miller index, this enables use with
                slabs that have been reoriented, but the miller vector
                must be supplied manually
            target_species: List of specific species to substitute
            sub_both_sides (bool): If true, substitute an equivalent
                site on the other surface
            range_tol (float): Find viable substitution sites at a specific
                distance from the surface +- this tolerance
            dist_from_surf (float): Distance from the surface to find viable
                substitution sites, defaults to 0 to substitute at the surface.
        """
        self.atom = atom
        self.selective_dynamics = selective_dynamics
        self.height = height
        self.mi_vec = mi_vec
        self.target_species = target_species
        self.sub_both_sides = sub_both_sides
        self.range_tol = range_tol
        self.dist_from_surf = dist_from_surf

    def apply_transformation(
        self, structure: Structure, return_ranked_list: bool | int = False
    ) -> list[dict] | Structure:
        """Apply the slab substitution transformation to a Slab structure.

        Args:
            structure: Must be a Slab structure
            return_ranked_list (bool | int, optional): If return_ranked_list is int, that number of structures.

                is returned. If False, only the single lowest energy structure is returned. Defaults to False.

        Returns:
            list[dict]: each dict has key 'structure' which is a Slab with sites substituted
        """
        site_finder = AdsorbateSiteFinder(
            structure,  # type:ignore[arg-type]
            selective_dynamics=self.selective_dynamics,
            height=self.height,
            mi_vec=self.mi_vec,
        )

        structures = site_finder.generate_substitution_structures(
            self.atom,
            target_species=self.target_species,
            sub_both_sides=self.sub_both_sides,
            range_tol=self.range_tol,
            dist_from_surf=self.dist_from_surf,
        )

        if not return_ranked_list:
            return structures[0]
        return [{"structure": structure} for structure in structures[:return_ranked_list]]

    @property
    def is_one_to_many(self) -> Literal[True]:
        """Transform one structure to many."""
        return True


def _proj(b: NDArray, a: NDArray) -> NDArray:
    """Get vector projection of vector b onto vector a.

    Args:
        b (NDArray): Vector to be projected.
        a (NDArray): Vector onto which `b` is projected.

    Returns:
        NDArray: Projection of `b` onto `a`.
    """
    a = np.asarray(a)
    b = np.asarray(b)

    return (np.dot(b, a) / np.dot(a, a)) * a


class SQSTransformation(AbstractTransformation):
    """A transformation that creates a special quasi-random structure (SQS)
    from a structure with partial occupancies.
    """

    def __init__(
        self,
        scaling: int | list[int],
        cluster_size_and_shell: dict[int, int] | None = None,
        search_time: float = 60,
        directory: str | None = None,
        instances: int | None = None,
        temperature: float = 1,
        wr: float = 1,
        wn: float = 1,
        wd: float = 0.5,
        tol: float = 1e-3,
        icet_sqs_kwargs: dict[str, Any] | None = None,
        best_only: bool = True,
        remove_duplicate_structures: bool = True,
        reduction_algo: Literal["niggli", "LLL"] = "LLL",
        sqs_method: Literal["mcsqs", "icet-enumeration", "icet-monte_carlo"] = "mcsqs",
    ):
        """Initialize a SQSTransformation.

        Args:
            scaling (int or list): Scaling factor to determine supercell. Two options are possible:
                a. (preferred) Scales number of atoms, e.g. for a structure with 8 atoms,
                    scaling=4 would lead to a 32 atom supercell
                b. A sequence of three scaling factors, e.g. [2, 1, 1], which
                    specifies that the supercell should have dimensions 2a x b x c
            cluster_size_and_shell (dict[int, int] | None): Dictionary of cluster interactions with entries in
                the form number of atoms: nearest neighbor shell
            search_time (float, optional): If sqs_method == "mcsqs", the time spent looking for the ideal SQS
                in minutes (default: 60)
            directory (str, optional): Directory to run mcsqs calculation and store files (default: None
                runs calculations in a temp directory)
            instances (int, optional): Specifies the number of parallel instances of mcsqs to run
                (default: number of cpu cores detected by Python)
            temperature (float, optional): Monte Carlo temperature (default: 1), "T" in atat code
            wr (float, optional): Weight assigned to range of perfect correlation match in objective
                function (default = 1)
            wn (float, optional): Multiplicative decrease in weight per additional point in cluster (default: 1)
            wd (float, optional): Exponent of decay in weight as function of cluster diameter (default: 0)
            tol (float, optional): Tolerance for matching correlations (default: 1e-3)
            icet_sqs_kwargs (dict) : If icet is used for the SQS search, kwargs to pass to
                pymatgen.io.icet.IcetSQS
            best_only (bool, optional): only return structures with lowest objective function
            remove_duplicate_structures (bool, optional): only return unique structures
            reduction_algo (str, optional): The lattice reduction algorithm to use.
                One of "niggli" or "LLL". Passing False does not reduce structure.
            sqs_method (str): One of "mcsqs" (MCSQS method from ATAT), "icet-enumeration"
                (enumeration of all possible SQS structures of a given size with icet),
                or "icet-monte_carlo" (Monte Carlo search with icet, similar to MCSQS).
        """
        self.scaling = scaling
        self.search_time = search_time
        self.cluster_size_and_shell = cluster_size_and_shell
        self.directory = directory
        self.instances = instances
        self.temperature = temperature
        self.wr = wr
        self.wn = wn
        self.wd = wd
        self.tol = tol
        self.icet_sqs_kwargs = icet_sqs_kwargs or {}
        self.best_only = best_only
        self.remove_duplicate_structures = remove_duplicate_structures
        self.reduction_algo = reduction_algo
        self.sqs_method = sqs_method

    @staticmethod
    def _get_max_neighbor_distance(struct, shell):
        """Calculate maximum nearest neighbor distance.

        Args:
            struct: pymatgen Structure object
            shell: nearest neighbor shell, such that shell=1 is the first nearest
                neighbor, etc.

        Returns:
            maximum nearest neighbor distance, in angstroms
        """
        min_dist_nn = MinimumDistanceNN()
        distances = []

        for site_num, site in enumerate(struct):
            shell_info = min_dist_nn.get_nn_shell_info(struct, site_num, shell)
            for entry in shell_info:
                image = entry["image"]
                distance = site.distance(struct[entry["site_index"]], jimage=image)
                distances.append(distance)

        return max(distances)

    @staticmethod
    def _get_disordered_substructure(struct_disordered):
        """Convert disordered structure into a substructure consisting of only disordered sites.

        Args:
            struct_disordered: pymatgen disordered Structure object.

        Returns:
            pymatgen Structure object representing a substructure of disordered sites.
        """
        disordered_substructure = struct_disordered.copy()

        idx_to_remove = [idx for idx, site in enumerate(disordered_substructure) if site.is_ordered]
        disordered_substructure.remove_sites(idx_to_remove)

        return disordered_substructure

    @staticmethod
    def _sqs_cluster_estimate(struct_disordered, cluster_size_and_shell: dict[int, int] | None = None):
        """Set up an ATAT cluster.out file for a given structure and set of constraints.

        Args:
            struct_disordered: disordered pymatgen Structure object
            cluster_size_and_shell: dict of integers {cluster: shell}.

        Returns:
            dict of {cluster size: distance in angstroms} for mcsqs calculation
        """
        cluster_size_and_shell = cluster_size_and_shell or {2: 3, 3: 2, 4: 1}

        disordered_substructure = SQSTransformation._get_disordered_substructure(struct_disordered)

        clusters = {}
        for cluster_size, shell in cluster_size_and_shell.items():
            max_distance = SQSTransformation._get_max_neighbor_distance(disordered_substructure, shell)
            clusters[cluster_size] = max_distance + 0.01  # add small tolerance

        return clusters

    def apply_transformation(self, structure: Structure, return_ranked_list: bool | int = False):
        """Apply SQS transformation.

        Args:
            structure (pymatgen Structure): pymatgen Structure with partial occupancies
            return_ranked_list (bool | int, optional): If return_ranked_list is int, that number of structures

                is returned. If False, only the single lowest energy structure is returned. Defaults to False.

        Returns:
            pymatgen Structure which is an SQS of the input structure
        """
        if return_ranked_list and self.instances is None:
            raise ValueError(f"{type(self).__name__} has no instances, so cannot return a ranked list")
        if (
            isinstance(return_ranked_list, int)
            and isinstance(self.instances, int)
            and return_ranked_list > self.instances
        ):
            raise ValueError(f"{return_ranked_list=} cannot be greater than {self.instances=}")

        clusters = self._sqs_cluster_estimate(structure, self.cluster_size_and_shell)

        # useful for debugging and understanding
        self._last_used_clusters = clusters

        if self.sqs_method == "mcsqs":
            sqs = run_mcsqs(
                structure=structure,
                clusters=clusters,
                scaling=self.scaling,
                search_time=self.search_time,
                directory=self.directory,
                instances=self.instances,
                temperature=self.temperature,
                wr=self.wr,
                wn=self.wn,
                wd=self.wd,
                tol=self.tol,
            )

        elif self.sqs_method.startswith("icet-"):
            if not isinstance(self.scaling, int) or self.scaling < 1:
                raise ValueError(
                    f"icet can only scale the input cell by a positive integer factor, not {self.scaling}."
                )
            self.icet_sqs_kwargs.setdefault("optimality_weight", self.wr)
            self.icet_sqs_kwargs.setdefault("T_start", self.temperature)

            sqs = IcetSQS(
                structure=structure,
                scaling=self.scaling,
                instances=self.instances,
                sqs_method=self.sqs_method.split("icet-")[1],
                cluster_cutoffs=clusters,
                sqs_kwargs=self.icet_sqs_kwargs,
            ).run()

        else:
            raise RuntimeError(f"Unsupported SQS method {self.sqs_method}.")

        return self._get_unique_best_sqs_structs(
            sqs,
            best_only=self.best_only,
            return_ranked_list=return_ranked_list,
            remove_duplicate_structures=self.remove_duplicate_structures,
            reduction_algo=self.reduction_algo,
        )

    @staticmethod
    def _get_unique_best_sqs_structs(sqs, best_only, return_ranked_list, remove_duplicate_structures, reduction_algo):
        """Get unique sqs structures with lowest objective function. Requires an mcsqs output that has been run
            in parallel, otherwise returns Sqs.bestsqs.

        Args:
            sqs (Sqs): Sqs class object.
            best_only (bool): only return structures with lowest objective function.
            return_ranked_list (bool | int, optional): If return_ranked_list is int, that number of structures.

                is returned. If False, only the single lowest energy structure is returned. Defaults to False.
            remove_duplicate_structures (bool): only return unique structures.
            reduction_algo (str): The lattice reduction algorithm to use. One of "niggli" or "LLL".
                reduction_algo=False does not reduce structure.

        Returns:
            list[dict[str, Structure | Callable]]: of the form {'structure': Structure, 'objective_function': ...},
                unless run in serial (returns a single structure Sqs.bestsqs)
        """
        if not return_ranked_list:
            return_struct = sqs.bestsqs

            # reduce structure
            if reduction_algo:
                return_struct = return_struct.get_reduced_structure(reduction_algo=reduction_algo)

            # return just the structure
            return return_struct

        structs = []
        for dct in sqs.allsqs:
            # filter for best structures only if enabled, else use full sqs.all_sqs list
            if (not best_only) or (best_only and dct["objective_function"] == sqs.objective_function):
                struct = dct["structure"]
                # add temporary objective_function attribute to access objective_function after grouping
                struct.objective_function = dct["objective_function"]
                structs.append(struct)

        if remove_duplicate_structures:
            matcher = StructureMatcher()
            # sort by unique structures ... can take a while for a long list of structs
            unique_structs_grouped = matcher.group_structures(structs)
            # get unique structures only
            structs = [group[0] for group in unique_structs_grouped]

        # sort structures by objective function
        structs.sort(key=lambda x: x.objective_function if isinstance(x.objective_function, float) else -np.inf)

        to_return = [{"structure": struct, "objective_function": struct.objective_function} for struct in structs]

        for dct in to_return:
            # delete temporary objective_function attribute
            del dct["structure"].objective_function

            # reduce structure
            if reduction_algo:
                dct["structure"] = dct["structure"].get_reduced_structure(reduction_algo=reduction_algo)

        # because bools are subclasses of ints, cannot just check that returned_ranked_list is int
        if isinstance(return_ranked_list, int) and not isinstance(return_ranked_list, bool):
            return to_return[:return_ranked_list]
        return to_return

    @property
    def is_one_to_many(self) -> Literal[True]:
        """Transform one structure to many."""
        return True


class MonteCarloRattleTransformation(AbstractTransformation):
    r"""Uses a Monte Carlo rattle procedure to randomly perturb the sites in a
    structure.

    This class requires the hiPhive package to be installed.

    Rattling atom `i` is carried out as a Monte Carlo move that is accepted with
    a probability determined from the minimum interatomic distance
    :math:`d_{ij}`. If :math:`\\min(d_{ij})` is smaller than :math:`d_{min}`
    the move is only accepted with a low probability.

    This process is repeated for each atom a number of times meaning
    the magnitude of the final displacements is not *directly*
    connected to `rattle_std`.
    """

    @requires(hiphive, "hiphive is required for MonteCarloRattleTransformation")
    def __init__(self, rattle_std: float, min_distance: float, seed: int | None = None, **kwargs):
        """Initialize a MonteCarloRattleTransformation.

        Args:
            rattle_std: Rattle amplitude (standard deviation in normal
                distribution). Note: this value is not *directly* connected to the
                final average displacement for the structures
            min_distance: Interatomic distance used for computing the probability
                for each rattle move.
            seed: Seed for setting up NumPy random state from which random numbers
                are generated. If ``None``, a random seed will be generated
                (default). This option allows the output of this transformation
                to be deterministic.
            **kwargs: Additional keyword arguments to be passed to the hiPhive
                mc_rattle function.
        """
        self.rattle_std = rattle_std
        self.min_distance = min_distance
        self.seed = seed or np.random.default_rng().integers(1, 1000000000)
        # if seed is None, use a random RandomState seed but make sure
        # we store that the original seed was None

        self.random_state = np.random.RandomState(self.seed)
        self.kwargs = kwargs

    def __repr__(self):
        return f"{__name__} : rattle_std = {self.rattle_std}"

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

        Args:
            structure: Input Structure

        Returns:
            Structure with sites perturbed.
        """
        from hiphive.structure_generation.rattle import mc_rattle

        atoms = AseAtomsAdaptor.get_atoms(structure)
        seed = self.random_state.randint(1, 1000000000)
        displacements = mc_rattle(atoms, self.rattle_std, self.min_distance, seed=seed, **self.kwargs)

        return Structure(
            structure.lattice,
            structure.species,
            structure.cart_coords + displacements,
            coords_are_cartesian=True,
        )
