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"


[docs]class EnergyModel(MSONable, metaclass=abc.ABCMeta): """ Abstract structure filter class. """
[docs] @abc.abstractmethod def get_energy(self, structure) -> float: """ :param structure: Structure :return: Energy value """ return 0.0
[docs] @classmethod def from_dict(cls, d): """ :param d: Dict representation :return: EnergyModel """ return cls(**d['init_args'])
[docs]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
[docs] 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
[docs] 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}}
[docs]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
[docs] 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()
[docs] 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}}
[docs]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
[docs] 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
[docs] 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}}
[docs]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. """
[docs] def get_energy(self, structure): """ :param structure: Structure :return: Energy value """ return len(structure)
[docs] def as_dict(self): """ :return: MSONable dict """ return {"version": __version__, "@module": self.__class__.__module__, "@class": self.__class__.__name__, "init_args": {}}