1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
|
"""Example of NaCl calculation."""
import numpy as np
from phonopy import Phonopy
from phonopy.file_IO import parse_BORN, parse_FORCE_SETS
from phonopy.interface.vasp import read_vasp
# 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-unitcell")
# 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.symmetry
print("Space group: %s" % symmetry.get_international_table())
force_sets = parse_FORCE_SETS()
phonon.dataset = force_sets
phonon.produce_force_constants()
primitive = phonon.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.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.run_band_structure(bands)
band_dict = phonon.get_band_structure_dict()
q_points = band_dict["qpoints"]
distances = band_dict["distances"]
frequencies = band_dict["frequencies"]
eigvecs = band_dict["eigenvectors"]
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.run_mesh(mesh=[20, 20, 20])
phonon.run_thermal_properties(t_step=10, t_max=1000, t_min=0)
# DOS
phonon.run_total_dos(sigma=0.1)
dos_dict = phonon.get_total_dos_dict()
for omega, dos in zip(dos_dict["frequency_points"], dos_dict["total_dos"]):
print("%15.7f%15.7f" % (omega, dos))
phonon.plot_total_dos().show()
# Thermal properties
tprop_dict = phonon.get_thermal_properties_dict()
for t, free_energy, entropy, cv in zip(
tprop_dict["temperatures"],
tprop_dict["free_energy"],
tprop_dict["entropy"],
tprop_dict["heat_capacity"],
):
print(("%12.3f " + "%15.7f" * 3) % (t, free_energy, entropy, cv))
phonon.plot_thermal_properties().show()
# PDOS
phonon.run_mesh(mesh=[10, 10, 10], is_mesh_symmetry=False, with_eigenvectors=True)
phonon.run_projected_dos(use_tetrahedron_method=True)
pdos_dict = phonon.get_projected_dos_dict()
omegas = pdos_dict["frequency_points"]
pdos = pdos_dict["projected_dos"]
pdos_indices = [[0], [1]]
phonon.plot_projected_dos(pdos_indices=pdos_indices, legend=pdos_indices).show()
|
