Source code for pymatgen.phonon.dos

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

"""
This module defines classes to represent the phonon density of states, etc.
"""

import numpy as np
import scipy.constants as const

from pymatgen.core.structure import Structure
from pymatgen.util.coord import get_linear_interpolated_value
from monty.json import MSONable
from monty.functools import lazy_property


BOLTZ_THZ_PER_K = const.value("Boltzmann constant in Hz/K") / const.tera  # Boltzmann constant in THz/K
THZ_TO_J = const.value("hertz-joule relationship") * const.tera


[docs]def coth(x): """ Coth function. Args: x (): value Returns: coth(x) """ return 1.0 / np.tanh(x)
[docs]class PhononDos(MSONable): """ Basic DOS object. All other DOS objects are extended versions of this object. """ def __init__(self, frequencies, densities): """ Args: frequencies: A sequences of frequencies in THz densities: A list representing the density of states. """ self.frequencies = np.array(frequencies) self.densities = np.array(densities)
[docs] def get_smeared_densities(self, sigma): """ Returns the densities, but with a Gaussian smearing of std dev sigma applied. Args: sigma: Std dev of Gaussian smearing function. Returns: Gaussian-smeared densities. """ from scipy.ndimage.filters import gaussian_filter1d diff = [self.frequencies[i + 1] - self.frequencies[i] for i in range(len(self.frequencies) - 1)] avgdiff = sum(diff) / len(diff) smeared_dens = gaussian_filter1d(self.densities, sigma / avgdiff) return smeared_dens
def __add__(self, other): """ Adds two DOS together. Checks that frequency scales are the same. Otherwise, a ValueError is thrown. Args: other: Another DOS object. Returns: Sum of the two DOSs. """ if not all(np.equal(self.frequencies, other.frequencies)): raise ValueError("Frequencies of both DOS are not compatible!") densities = self.densities + other.densities return PhononDos(self.frequencies, densities) def __radd__(self, other): """ Reflected addition of two DOS objects Args: other: Another DOS object. Returns: Sum of the two DOSs. """ return self.__add__(other)
[docs] def get_interpolated_value(self, frequency): """ Returns interpolated density for a particular frequency. Args: frequency: frequency to return the density for. """ return get_linear_interpolated_value(self.frequencies, self.densities, frequency)
def __str__(self): """ Returns a string which can be easily plotted (using gnuplot). """ stringarray = ["#{:30s} {:30s}".format("Frequency", "Density")] for i, frequency in enumerate(self.frequencies): stringarray.append("{:.5f} {:.5f}" .format(frequency, self.densities[i])) return "\n".join(stringarray)
[docs] @classmethod def from_dict(cls, d): """ Returns PhononDos object from dict representation of PhononDos. """ return cls(d["frequencies"], d["densities"])
[docs] def as_dict(self): """ Json-serializable dict representation of PhononDos. """ return {"@module": self.__class__.__module__, "@class": self.__class__.__name__, "frequencies": list(self.frequencies), "densities": list(self.densities)}
[docs] @lazy_property def ind_zero_freq(self): """ Index of the first point for which the freqencies are equal or greater than zero. """ ind = np.searchsorted(self.frequencies, 0) if ind >= len(self.frequencies): raise ValueError("No positive frequencies found") return ind
@lazy_property def _positive_frequencies(self): """ Numpy array containing the list of positive frequencies """ return self.frequencies[self.ind_zero_freq:] @lazy_property def _positive_densities(self): """ Numpy array containing the list of densities corresponding to positive frequencies """ return self.densities[self.ind_zero_freq:]
[docs] def cv(self, t, structure=None): """ Constant volume specific heat C_v at temperature T obtained from the integration of the DOS. Only positive frequencies will be used. Result in J/(K*mol-c). A mol-c is the abbreviation of a mole-cell, that is, the number of Avogadro times the atoms in a unit cell. To compare with experimental data the result should be divided by the number of unit formulas in the cell. If the structure is provided the division is performed internally and the result is in J/(K*mol) Args: t: a temperature in K structure: the structure of the system. If not None it will be used to determine the numer of formula units Returns: Constant volume specific heat C_v """ if t == 0: return 0 freqs = self._positive_frequencies dens = self._positive_densities def csch2(x): return 1.0 / (np.sinh(x) ** 2) wd2kt = freqs / (2 * BOLTZ_THZ_PER_K * t) cv = np.trapz(wd2kt ** 2 * csch2(wd2kt) * dens, x=freqs) cv *= const.Boltzmann * const.Avogadro if structure: formula_units = structure.composition.num_atoms / structure.composition.reduced_composition.num_atoms cv /= formula_units return cv
[docs] def entropy(self, t, structure=None): """ Vibrational entropy at temperature T obtained from the integration of the DOS. Only positive frequencies will be used. Result in J/(K*mol-c). A mol-c is the abbreviation of a mole-cell, that is, the number of Avogadro times the atoms in a unit cell. To compare with experimental data the result should be divided by the number of unit formulas in the cell. If the structure is provided the division is performed internally and the result is in J/(K*mol) Args: t: a temperature in K structure: the structure of the system. If not None it will be used to determine the numer of formula units Returns: Vibrational entropy """ if t == 0: return 0 freqs = self._positive_frequencies dens = self._positive_densities wd2kt = freqs / (2 * BOLTZ_THZ_PER_K * t) s = np.trapz((wd2kt * coth(wd2kt) - np.log(2 * np.sinh(wd2kt))) * dens, x=freqs) s *= const.Boltzmann * const.Avogadro if structure: formula_units = structure.composition.num_atoms / structure.composition.reduced_composition.num_atoms s /= formula_units return s
[docs] def internal_energy(self, t, structure=None): """ Phonon contribution to the internal energy at temperature T obtained from the integration of the DOS. Only positive frequencies will be used. Result in J/mol-c. A mol-c is the abbreviation of a mole-cell, that is, the number of Avogadro times the atoms in a unit cell. To compare with experimental data the result should be divided by the number of unit formulas in the cell. If the structure is provided the division is performed internally and the result is in J/mol Args: t: a temperature in K structure: the structure of the system. If not None it will be used to determine the numer of formula units Returns: Phonon contribution to the internal energy """ if t == 0: return self.zero_point_energy(structure=structure) freqs = self._positive_frequencies dens = self._positive_densities wd2kt = freqs / (2 * BOLTZ_THZ_PER_K * t) e = np.trapz(freqs * coth(wd2kt) * dens, x=freqs) / 2 e *= THZ_TO_J * const.Avogadro if structure: formula_units = structure.composition.num_atoms / structure.composition.reduced_composition.num_atoms e /= formula_units return e
[docs] def helmholtz_free_energy(self, t, structure=None): """ Phonon contribution to the Helmholtz free energy at temperature T obtained from the integration of the DOS. Only positive frequencies will be used. Result in J/mol-c. A mol-c is the abbreviation of a mole-cell, that is, the number of Avogadro times the atoms in a unit cell. To compare with experimental data the result should be divided by the number of unit formulas in the cell. If the structure is provided the division is performed internally and the result is in J/mol Args: t: a temperature in K structure: the structure of the system. If not None it will be used to determine the numer of formula units Returns: Phonon contribution to the Helmholtz free energy """ if t == 0: return self.zero_point_energy(structure=structure) freqs = self._positive_frequencies dens = self._positive_densities wd2kt = freqs / (2 * BOLTZ_THZ_PER_K * t) f = np.trapz(np.log(2 * np.sinh(wd2kt)) * dens, x=freqs) f *= const.Boltzmann * const.Avogadro * t if structure: formula_units = structure.composition.num_atoms / structure.composition.reduced_composition.num_atoms f /= formula_units return f
[docs] def zero_point_energy(self, structure=None): """ Zero point energy energy of the system. Only positive frequencies will be used. Result in J/mol-c. A mol-c is the abbreviation of a mole-cell, that is, the number of Avogadro times the atoms in a unit cell. To compare with experimental data the result should be divided by the number of unit formulas in the cell. If the structure is provided the division is performed internally and the result is in J/mol Args: t: a temperature in K structure: the structure of the system. If not None it will be used to determine the numer of formula units Returns: Phonon contribution to the internal energy """ freqs = self._positive_frequencies dens = self._positive_densities zpe = 0.5 * np.trapz(freqs * dens, x=freqs) zpe *= THZ_TO_J * const.Avogadro if structure: formula_units = structure.composition.num_atoms / structure.composition.reduced_composition.num_atoms zpe /= formula_units return zpe
[docs]class CompletePhononDos(PhononDos): """ This wrapper class defines a total dos, and also provides a list of PDos. .. attribute:: pdos Dict of partial densities of the form {Site:Densities} """ def __init__(self, structure, total_dos, pdoss): """ Args: structure: Structure associated with this particular DOS. total_dos: total Dos for structure pdoss: The pdoss are supplied as an {Site: Densities} """ super().__init__( frequencies=total_dos.frequencies, densities=total_dos.densities) self.pdos = {s: np.array(d) for s, d in pdoss.items()} self.structure = structure
[docs] def get_site_dos(self, site): """ Get the Dos for a site. Args: site: Site in Structure associated with CompletePhononDos. Returns: PhononDos containing summed orbital densities for site. """ return PhononDos(self.frequencies, self.pdos[site])
[docs] def get_element_dos(self): """ Get element projected Dos. Returns: dict of {Element: Dos} """ el_dos = {} for site, atom_dos in self.pdos.items(): el = site.specie if el not in el_dos: el_dos[el] = np.array(atom_dos) else: el_dos[el] += np.array(atom_dos) return {el: PhononDos(self.frequencies, densities) for el, densities in el_dos.items()}
[docs] @classmethod def from_dict(cls, d): """ Returns CompleteDos object from dict representation. """ tdos = PhononDos.from_dict(d) struct = Structure.from_dict(d["structure"]) pdoss = {} for at, pdos in zip(struct, d["pdos"]): pdoss[at] = pdos return cls(struct, tdos, pdoss)
[docs] def as_dict(self): """ Json-serializable dict representation of CompletePhononDos. """ d = {"@module": self.__class__.__module__, "@class": self.__class__.__name__, "structure": self.structure.as_dict(), "frequencies": list(self.frequencies), "densities": list(self.densities), "pdos": []} if len(self.pdos) > 0: for at in self.structure: d["pdos"].append(list(self.pdos[at])) return d
def __str__(self): return "Complete phonon DOS for " + str(self.structure)