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
|
from distutils.version import LooseVersion
import numpy as np
import pytest
from ase import Atoms
from ase.io import read
from ase.build import bulk
from .test_mustem import make_STO_atoms
pytestmark = pytest.mark.skipif(LooseVersion(np.__version__) <
LooseVersion("1.14"),
reason="This test requires numpy >= 1.14")
def test_write_read_cycle_xyz_prismatic():
"""Check writing and reading a xtl mustem file."""
# Reproduce the SI100.XYZ file distributed with prismatic
atoms = bulk('Si', cubic=True)
atoms.set_array('occupancies', np.ones(len(atoms)))
rng = np.random.RandomState(42)
atoms.set_array('debye_waller_factors', 0.62 + 0.1 * rng.rand(len(atoms)))
filename = 'SI100.XYZ'
atoms.write(filename=filename, format='prismatic',
comments='one unit cell of 100 silicon')
atoms_loaded = read(filename=filename, format='prismatic')
np.testing.assert_allclose(atoms.positions, atoms_loaded.positions)
np.testing.assert_allclose(atoms.cell, atoms_loaded.cell)
np.testing.assert_allclose(atoms.get_array('occupancies'),
atoms_loaded.get_array('occupancies'))
np.testing.assert_allclose(atoms.get_array('debye_waller_factors'),
atoms_loaded.get_array('debye_waller_factors'),
rtol=1E-5)
def test_write_error():
"""Check missing parameter when writing xyz prismatic file."""
atoms_Si100 = bulk('Si', cubic=True)
atoms_STO = make_STO_atoms()
filename = 'SI100.XYZ'
with pytest.raises(ValueError):
# DW not provided
atoms_Si100.write(filename, format='prismatic')
# Write file with DW provided as scalar
atoms_Si100.write(filename, format='prismatic',
debye_waller_factors=0.076)
# Write file with DW provided as dict
atoms_Si100.write(filename, format='prismatic',
debye_waller_factors={'Si': 0.076})
STO_DW_dict = {'Sr': 0.62, 'O': 0.73, 'Ti': 0.43}
STO_DW_dict_Ti_missing = {key: STO_DW_dict[key] for key in ['Sr', 'O']}
with pytest.raises(ValueError):
# DW missing keys
atoms_STO.write(filename, format='prismatic',
debye_waller_factors=STO_DW_dict_Ti_missing)
atoms_STO.write(filename, format='prismatic',
debye_waller_factors=STO_DW_dict)
with pytest.raises(ValueError):
# Raise an error if the unit cell is not defined.
atoms4 = Atoms(['Sr', 'Ti', 'O', 'O', 'O'],
positions=[[0, 0, 0],
[0.5, 0.5, 0.5],
[0.5, 0.5, 0],
[0.5, 0, 0.5],
[0, 0.5, 0.5]])
atoms4.write(filename, format='prismatic',
debye_waller_factors=STO_DW_dict)
|
