NaCl.py

import numpy as np
from phonopy import Phonopy
from phonopy.interface.vasp import read_vasp
from phonopy.file_IO import parse_FORCE_SETS, parse_BORN
from phonopy.structure.atoms import PhonopyAtoms

def append_band(bands, q_start, q_end):
    band = []
    for i in range(51):
        band.append(np.array(q_start) +
                    (np.array(q_end) - np.array(q_start)) / 50 * i)
    bands.append(band)


# NaCl crystal structure is read from POSCAR.
unitcell = read_vasp("POSCAR")
# This can be given via a PhonopyAtoms class as follows:
# unitcell = PhonopyAtoms(symbols=(['Na'] * 4 + ['Cl'] * 4),
#                         cell=(np.eye(3) * 5.6903014761756712),
#                         scaled_positions=[[0, 0, 0],
#                                           [0, 0.5, 0.5],
#                                           [0.5, 0, 0.5],
#                                           [0.5, 0.5, 0],
#                                           [0.5, 0.5, 0.5],
#                                           [0.5, 0, 0],
#                                           [0, 0.5, 0],
#                                           [0, 0, 0.5]])

phonon = Phonopy(unitcell,
                 [[2, 0, 0],
                  [0, 2, 0],
                  [0, 0, 2]],
                 primitive_matrix=[[0, 0.5, 0.5],
                                   [0.5, 0, 0.5],
                                   [0.5, 0.5, 0]])

symmetry = phonon.get_symmetry()
print("Space group: %s" % symmetry.get_international_table())

force_sets = parse_FORCE_SETS()
phonon.set_displacement_dataset(force_sets)
phonon.produce_force_constants()
primitive = phonon.get_primitive()

# Born effective charges and dielectric constants are read from BORN file.
nac_params = parse_BORN(primitive, filename="BORN")
# Or it can be of course given by hand as follows:
# born = [[[1.08703, 0, 0],
#          [0, 1.08703, 0],
#          [0, 0, 1.08703]],
#         [[-1.08672, 0, 0],
#          [0, -1.08672, 0],
#          [0, 0, -1.08672]]]
# epsilon = [[2.43533967, 0, 0],
#            [0, 2.43533967, 0],
#            [0, 0, 2.43533967]]
# factors = 14.400
# nac_params = {'born': born,
#               'factor': factors,
#               'dielectric': epsilon}
phonon.set_nac_params(nac_params)

# BAND = 0.0 0.0 0.0  0.5 0.0 0.0  0.5 0.5 0.0  0.0 0.0 0.0  0.5 0.5 0.5
bands = []
append_band(bands, [0.0, 0.0, 0.0], [0.5, 0.0, 0.0])
append_band(bands, [0.5, 0.0, 0.0], [0.5, 0.5, 0.0])
append_band(bands, [0.5, 0.5, 0.0], [0.0, 0.0, 0.0])
append_band(bands, [0.0, 0.0, 0.0], [0.5, 0.5, 0.5])
phonon.set_band_structure(bands)
q_points, distances, frequencies, eigvecs = phonon.get_band_structure()
for q_path, d_path, freq_path in zip(q_points, distances, frequencies):
    for q, d, freq in zip(q_path, d_path, freq_path):
        print(("%10.5f  %5.2f %5.2f %5.2f " + (" %7.3f" * len(freq)))
              % ((d, q[0], q[1], q[2]) + tuple(freq)))

phonon.plot_band_structure().show()

# Mesh sampling 20x20x20
phonon.set_mesh([20, 20, 20])
phonon.set_thermal_properties(t_step=10,
                              t_max=1000,
                              t_min=0)

# DOS
phonon.set_total_DOS(sigma=0.1)
for omega, dos in np.array(phonon.get_total_DOS()).T:
    print("%15.7f%15.7f" % (omega, dos))
phonon.plot_total_DOS().show()

# Thermal properties
for t, free_energy, entropy, cv in np.array(phonon.get_thermal_properties()).T:
    print(("%12.3f " + "%15.7f" * 3) % ( t, free_energy, entropy, cv))
phonon.plot_thermal_properties().show()

# PDOS
phonon.set_mesh([10, 10, 10],
                is_mesh_symmetry=False,
                is_eigenvectors=True)
phonon.set_partial_DOS(tetrahedron_method=True)
omegas, pdos = phonon.get_partial_DOS()
pdos_indices = [[0], [1]]
phonon.plot_partial_DOS(pdos_indices=pdos_indices,
                        legend=pdos_indices).show()