pymatgen.analysis.energy_models — pymatgen 2020.7.3 documentation

# Source code for pymatgen.analysis.energy_models

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

    """
    This module implements a EnergyModel abstract class and some basic
    implementations. Basically, an EnergyModel is any model that returns an
    "energy" for any given structure.
    """

    import abc

    from monty.json import MSONable
    from pymatgen.analysis.ewald import EwaldSummation
    from pymatgen.symmetry.analyzer import SpacegroupAnalyzer

    __version__ = "0.1"

    class EnergyModel(MSONable, metaclass=abc.ABCMeta):
        """
        Abstract structure filter class.
        """

        @abc.abstractmethod
        def get_energy(self, structure) -> float:
            """
            :param structure: Structure
            :return: Energy value
            """
            return 0.0

        @classmethod
        def from_dict(cls, d):
            """
            :param d: Dict representation
            :return: EnergyModel
            """
            return cls(**d['init_args'])

    class EwaldElectrostaticModel(EnergyModel):
        """
        Wrapper around EwaldSum to calculate the electrostatic energy.
        """

        def __init__(self, real_space_cut=None, recip_space_cut=None,
                     eta=None, acc_factor=8.0):
            """
            Initializes the model. Args have the same definitions as in
            :class:`pymatgen.analysis.ewald.EwaldSummation`.

            Args:
                real_space_cut (float): Real space cutoff radius dictating how
                    many terms are used in the real space sum. Defaults to None,
                    which means determine automagically using the formula given
                    in gulp 3.1 documentation.
                recip_space_cut (float): Reciprocal space cutoff radius.
                    Defaults to None, which means determine automagically using
                    the formula given in gulp 3.1 documentation.
                eta (float): Screening parameter. Defaults to None, which means
                    determine automatically.
                acc_factor (float): No. of significant figures each sum is
                    converged to.
            """
            self.real_space_cut = real_space_cut
            self.recip_space_cut = recip_space_cut
            self.eta = eta
            self.acc_factor = acc_factor

        def get_energy(self, structure):
            """
            :param structure: Structure
            :return: Energy value
            """
            e = EwaldSummation(structure, real_space_cut=self.real_space_cut,
                               recip_space_cut=self.recip_space_cut,
                               eta=self.eta,
                               acc_factor=self.acc_factor)
            return e.total_energy

        def as_dict(self):
            """
            :return: MSONable dict
            """
            return {"version": __version__,
                    "@module": self.__class__.__module__,
                    "@class": self.__class__.__name__,
                    "init_args": {"real_space_cut": self.real_space_cut,
                                  "recip_space_cut": self.recip_space_cut,
                                  "eta": self.eta,
                                  "acc_factor": self.acc_factor}}

    class SymmetryModel(EnergyModel):
        """
        Sets the energy to the -ve of the spacegroup number. Higher symmetry =>
        lower "energy".

        Args have same meaning as in
        :class:`pymatgen.symmetry.finder.SpacegroupAnalyzer`.
        """

        def __init__(self, symprec=0.1, angle_tolerance=5):
            """
            Args:
                symprec (float): Symmetry tolerance. Defaults to 0.1.
                angle_tolerance (float): Tolerance for angles. Defaults to 5 degrees.
            """
            self.symprec = symprec
            self.angle_tolerance = angle_tolerance

        def get_energy(self, structure):
            """
            :param structure: Structure
            :return: Energy value
            """
            f = SpacegroupAnalyzer(structure, symprec=self.symprec, angle_tolerance=self.angle_tolerance)
            return -f.get_space_group_number()

        def as_dict(self):
            """
            :return: MSONable dict
            """
            return {"version": __version__,
                    "@module": self.__class__.__module__,
                    "@class": self.__class__.__name__,
                    "init_args": {"symprec": self.symprec,
                                  "angle_tolerance": self.angle_tolerance}}

    class IsingModel(EnergyModel):
        """
        A very simple Ising model, with r^2 decay.
        """

        def __init__(self, j, max_radius):
            """
            Args:
                j (float): The interaction parameter. E = J * spin1 * spin2.
                radius (float): max_radius for the interaction.
            """
            self.j = j
            self.max_radius = max_radius

        def get_energy(self, structure):
            """
            :param structure: Structure
            :return: Energy value
            """
            all_nn = structure.get_all_neighbors(r=self.max_radius)
            energy = 0
            for i, nns in enumerate(all_nn):
                s1 = getattr(structure[i].specie, "spin", 0)
                for nn in nns:
                    energy += self.j * s1 * getattr(nn.specie, "spin",
                                                    0) / (nn.nn_distance ** 2)
            return energy

        def as_dict(self):
            """
            :return: MSONable dict
            """
            return {"version": __version__,
                    "@module": self.__class__.__module__,
                    "@class": self.__class__.__name__,
                    "init_args": {"j": self.j, "max_radius": self.max_radius}}

    class NsitesModel(EnergyModel):
        """
        Sets the energy to the number of sites. More sites => higher "energy".
        Used to rank structures from smallest number of sites to largest number
        of sites after enumeration.
        """

        def get_energy(self, structure):
            """
            :param structure: Structure
            :return: Energy value
            """
            return len(structure)

        def as_dict(self):
            """
            :return: MSONable dict
            """
            return {"version": __version__,
                    "@module": self.__class__.__module__,
                    "@class": self.__class__.__name__,
                    "init_args": {}}