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thermal_disp.py
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thermal_disp.py
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#!/usr/bin/env python
# -*- encoding:utf-8 -*-
# Copyright (C) 2016-2019 Ambroise van Roekeghem <[email protected]>
# Copyright (C) 2016-2019 Jesús Carrete Montaña <[email protected]>
# Copyright (C) 2016-2019 Natalio Mingo Bisquert <[email protected]>
#
# This file is part of qSCAILD.
#
# qSCAILD is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# qSCAILD is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with qSCAILD. If not, see <https://www.gnu.org/licenses/>.
import os
import os.path
import sys
import json
import itertools
import multiprocessing
import binascii
import numpy as np
import scipy as sp
import scipy.constants as codata
import phonopy
import phonopy.interface
import phonopy.file_IO
import io
import hashlib
import subprocess
import generate_conf
from mpi4py import MPI
def harmonic_free_energy(f, T):
"""
Return the free energy depending of T, force constants and structure
"""
f = f[f > 1.e-4]
print("frequencies used for the calculation of harmonic free energy", f)
free_ener_har = np.sum(
0.5 * codata.h * f * 1e12 +
codata.k * T * np.log1p(-np.exp(-codata.h * f * 1e12 / codata.k / T)))
free_ener_har /= 1.60217657 * 1e-19 ##put it in eV
print("harmonic free energy in eV: ", free_ener_har)
return free_ener_har
def fBE(f, T):
"""
Bose-Einstein distribution with mu=0.. f is expected to be in THz,
T in K.
"""
if (T == 0.):
return 0.
elif (codata.h * abs(f) * 1e12 / (codata.k * T) < 2):
return 1. / np.expm1(codata.h * abs(f) * 1e12 / (codata.k * T))
else:
return -np.exp(-codata.h * abs(f) * 1e12 / (codata.k * T)) / np.expm1(
-codata.h * abs(f) * 1e12 / (codata.k * T))
def write_displacement_matrix(poscar_file, fcs_file, T, n, use_smalldisp,
imaginary_freq, grid):
"""
Write the displacement matrix depending of T, force constants and
structure, integrated over the Brillouin zone.
"""
SYMPREC = 1e-5
NQ = grid
if not os.path.isfile(poscar_file):
sys.exit("The specified POSCAR file does not exist.")
na, nb, nc = [int(i) for i in n]
if min(na, nb, nc) < 1:
sys.exit("All dimensions must be positive integers")
poscar = generate_conf.read_POSCAR(poscar_file)
natoms = poscar["numbers"].sum()
ntot = na * nb * nc * natoms
nmodes = 3 * natoms
ncells = na * nb * nc
matrix = np.zeros((ncells * nmodes, ncells * nmodes), dtype=np.complex128)
local_matrix = np.zeros((ncells * nmodes, ncells * nmodes),
dtype=np.complex128)
if use_smalldisp:
for idiag in range(ncells * nmodes):
matrix[idiag, idiag] = 0.000001
return matrix
if not os.path.isfile(fcs_file):
sys.exit("The specified FORCE_CONSTANTS file does not exist.")
supercell_matrix = np.diag([na, nb, nc])
structure = phonopy.interface.calculator.read_crystal_structure(poscar_file,
"vasp")[0]
fc = phonopy.file_IO.parse_FORCE_CONSTANTS(fcs_file)
phonon = phonopy.Phonopy(
structure,
supercell_matrix,
primitive_matrix=None,
factor=phonopy.units.VaspToTHz,
dynamical_matrix_decimals=None,
force_constants_decimals=None,
symprec=SYMPREC,
is_symmetry=True,
log_level=0)
if os.path.isfile("BORN"):
nac_params = phonopy.file_IO.get_born_parameters(
open("BORN"), phonon.get_primitive(),
phonon.get_primitive_symmetry())
phonon.set_nac_params(nac_params=nac_params)
phonon.set_force_constants(fc)
masses = phonon.get_supercell().get_masses(
) * codata.physical_constants["atomic mass constant"][0]
qpoints = create_mesh(NQ)
nqpoints = qpoints.shape[0]
# Initializations and preliminaries
comm = MPI.COMM_WORLD # get MPI communicator object
size = comm.size # total number of processes
rank = comm.rank # rank of this process
full_qlist = list(range(nqpoints))
qlist = full_qlist[rank::size]
for qpt in qlist:
local_matrix += qpoint_worker((qpoints[qpt, :], phonon, T, na, nb, nc,
imaginary_freq, poscar["positions"]))
# Reduce all qpoints
comm.Reduce(local_matrix, matrix, op=MPI.SUM, root=0)
if rank == 0:
matrix *= codata.hbar / 2. / nqpoints / 2. / np.pi / 1e12 # m**2
for i, j in itertools.product(
range(ncells * nmodes), range(ncells * nmodes)):
matrix[i, j] /= np.sqrt(masses[i // 3] * masses[j // 3])
matrix = 1e18 * matrix.real # nm**2
comm.Barrier()
return matrix
def write_displacement_matrix_gamma(sposcar_file, fcs_file, T, n,
use_smalldisp, imaginary_freq):
"""
Writes the displacement matrix depending of T, force constants and
structure, using only the gamma-point of the supercell.
"""
SYMPREC = 1e-5
if not os.path.isfile(sposcar_file):
sys.exit("The specified POSCAR file does not exist.")
na, nb, nc = [1, 1, 1]
poscar = generate_conf.read_POSCAR(sposcar_file)
natoms = poscar["numbers"].sum()
ntot = na * nb * nc * natoms
nmodes = 3 * natoms
ncells = na * nb * nc
matrix = np.zeros((ncells * nmodes, ncells * nmodes), dtype=np.complex128)
if use_smalldisp:
for idiag in range(ncells * nmodes):
matrix[idiag, idiag] = 0.000001
return matrix
if not os.path.isfile(fcs_file):
sys.exit("The specified FORCE_CONSTANTS file does not exist.")
supercell_matrix = np.diag([na, nb, nc])
structure = phonopy.interface.calculator.read_crystal_structure(sposcar_file,
"vasp")[0]
fc = phonopy.file_IO.parse_FORCE_CONSTANTS(fcs_file)
phonon = phonopy.Phonopy(
structure,
supercell_matrix,
primitive_matrix=None,
factor=phonopy.units.VaspToTHz,
dynamical_matrix_decimals=None,
force_constants_decimals=None,
symprec=SYMPREC,
is_symmetry=True,
log_level=0)
if os.path.isfile("BORN"):
nac_params = phonopy.file_IO.get_born_parameters(
open("BORN"), phonon.get_primitive(),
phonon.get_primitive_symmetry())
phonon.set_nac_params(nac_params=nac_params)
phonon.set_force_constants(fc)
masses = phonon.get_supercell().get_masses(
) * codata.physical_constants["atomic mass constant"][0]
nqpoints = 1
print("nqpoints: " + repr(nqpoints))
matrix = qpoint_worker(([0., 0., 0.], phonon, T, na, nb, nc,
imaginary_freq, poscar["positions"]))
matrix *= codata.hbar / 2. / nqpoints / 2. / np.pi / 1e12 # m**2
for i, j in itertools.product(
range(ncells * nmodes), range(ncells * nmodes)):
matrix[i, j] /= np.sqrt(masses[i // 3] * masses[j // 3])
matrix = 1e18 * matrix.real # nm**2
return matrix
def qpoint_worker(args):
"""
Computes the unnormalized contribution to the thermal
displacement matrix from a single q point.
"""
q, phonon, T, na, nb, nc, imaginary_freq, positions = args
natoms = phonon.get_primitive().get_number_of_atoms()
nmodes = 3 * natoms
ncells = na * nb * nc
matrix = np.zeros((ncells * nmodes, ncells * nmodes), dtype=np.complex128)
f, psi = phonon.get_frequencies_with_eigenvectors(q)
for ifreq in range(len(f)):
if (f[ifreq] < -1.e-4):
print("ATTENTION: IMAGINARY FREQUENCIES ->"
" CONVERTED TO POSITIVE VALUE")
if imaginary_freq == -1:
f[ifreq] = abs(f[ifreq])
else:
f[ifreq] = imaginary_freq
n_B = np.array([fBE(fq, T) for fq in f])
r = range(nmodes)
factors = np.empty(ncells, dtype=np.complex128)
for pos, (k, j, i) in enumerate(
itertools.product(range(nc), range(nb), range(na))):
factors[pos] = np.exp(2j * np.pi * np.dot(q, [i, j, k]))
for im in r:
if (f[im] > 1.e-4):
lpsi = np.empty(ncells * nmodes, dtype=np.complex128)
for ia in range(natoms):
for pos, (k, j, i) in enumerate(
itertools.product(range(nc), range(nb), range(na))):
for ic in range(3):
jm = np.ravel_multi_index((ia, ic), (natoms, 3))
li = np.ravel_multi_index((ia, k, j, i, ic),
(natoms, nc, nb, na, 3))
lpsi[li] = psi[jm, im] * factors[pos] * np.exp(
2j * np.pi * np.dot(q, positions[:, ia]))
matrix += np.outer(lpsi, lpsi.conj()) * (1. + 2. * n_B[im]) / f[im]
return matrix
def create_mesh(nq):
"""
Create a MP mesh with nq q points along each
direction. Return the direct coordinates of each point.
"""
nruter = []
for i, j, k in itertools.product(range(nq), range(nq), range(nq)):
nruter.append([float(i) / nq, float(j) / nq, float(k) / nq])
nruter = np.array(nruter)
center = np.mean(nruter, axis=0)
for i in range(nruter.shape[0]):
nruter[i, :] -= center
return nruter