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
|
"""Tests for the QLM calculator interface."""
import os
import tempfile
import numpy as np
from phonopy.interface.qlm import (
parse_set_of_forces,
read_qlm,
)
def test_parse_set_of_forces():
"""Test parse_set_of_forces."""
force_ref = """% rows 2 cols 3 real
0.00000000 -0.00406659 -0.00406659
-0.00000000 0.00406659 0.00406659"""
# when min py v3.12+ move from try..finally to "with" and delete_on_close=False
# for windows
try:
tfl = tempfile.NamedTemporaryFile(delete=False)
tfl.write(force_ref.encode())
tfl.close()
frs = parse_set_of_forces(2, (tfl.name,), verbose=False)
np.testing.assert_allclose(
frs,
[
np.array(
[
[0.00000000, -0.00406659, -0.00406659],
[-0.00000000, 0.00406659, 0.00406659],
]
)
],
atol=1e-7,
)
finally:
os.unlink(tfl.name)
def test_cell2struct_and_read_qlm():
"""Test read_qlm and get_qlm_structure."""
sitex_ref = (
"""% site-data vn=3.0 xpos fast io=15 nbas=8"""
+ """ alat=10.7531113565 plat= 1.0 0.0 0.0 0.0 1.0 0.0 0.0 0.0 1.0
# pos
Na 0.0000000000 0.0000000000 0.0000000000
Na 0.0000000000 0.5000000000 0.5000000000
Na2 0.5000000000 0.0000000000 0.5000000000
Na3 0.5000000000 0.5000000000 0.0000000000
Cl 0.5000000000 0.5000000000 0.5000000000
Clu 0.5000000000 0.0000000000 0.0000000000
Cl 0.0000000000 0.5000000000 0.0000000000
Cld 0.0000000000 0.0000000000 0.5000000000
"""
)
try:
fl1 = tempfile.NamedTemporaryFile(delete=False)
fl1.write(sitex_ref.encode())
fl1.close()
cell1, (inst1,) = read_qlm(fl1.name)
fl2 = tempfile.NamedTemporaryFile(delete=False)
fl2.write(inst1.to_site_str(cell1).encode())
fl2.close()
cell2, _ = read_qlm(fl2.name)
np.testing.assert_allclose(cell1.cell, cell2.cell, atol=1e-7)
np.testing.assert_allclose(
cell1.scaled_positions, cell2.scaled_positions, atol=1e-7
)
assert cell1.symbols == cell2.symbols
finally:
os.unlink(fl1.name)
os.unlink(fl2.name)
|
