# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import division, unicode_literals
import abc
import six
from monty.json import MSONable
from pymatgen.analysis.ewald import EwaldSummation
from pymatgen.symmetry.analyzer import SpacegroupAnalyzer
"""
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.
"""
__author__ = "Shyue Ping Ong"
__copyright__ = "Copyright 2012, The Materials Project"
__version__ = "0.1"
__maintainer__ = "Shyue Ping Ong"
__email__ = "shyuep@gmail.com"
__date__ = "11/19/13"
[docs]class EnergyModel(six.with_metaclass(abc.ABCMeta, MSONable)):
"""
Abstract structure filter class.
"""
[docs] @abc.abstractmethod
def get_energy(self, structure):
"""
Returns a boolean for any structure. Structures that return true are
kept in the Transmuter object during filtering.
"""
return
[docs] @classmethod
def from_dict(cls, d):
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):
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 {"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`.
Args:
symprec (float): Symmetry tolerance. Defaults to 0.1.
angle_tolerance (float): Tolerance for angles. Defaults to 5 degrees.
"""
def __init__(self, symprec=0.1, angle_tolerance=5):
self.symprec = symprec
self.angle_tolerance = angle_tolerance
[docs] def get_energy(self, structure):
f = SpacegroupAnalyzer(structure, symprec=self.symprec,
angle_tolerance=self.angle_tolerance)
return -f.get_space_group_number()
[docs] def as_dict(self):
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.
Args:
j (float): The interaction parameter. E = J * spin1 * spin2.
radius (float): max_radius for the interaction.
"""
def __init__(self, j, max_radius):
self.j = j
self.max_radius = max_radius
[docs] def get_energy(self, structure):
all_nn = structure.get_all_neighbors(r=self.max_radius)
energy = 0
for i, nn in enumerate(all_nn):
s1 = getattr(structure[i].specie, "spin", 0)
for site, dist in nn:
energy += self.j * s1 * getattr(site.specie, "spin",
0) / (dist ** 2)
return energy
[docs] def as_dict(self):
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):
return len(structure)
[docs] def as_dict(self):
return {"version": __version__,
"@module": self.__class__.__module__,
"@class": self.__class__.__name__,
"init_args": {}}