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
|
import pytest
import ase.build
from ase import Atoms
from ase.lattice.cubic import FaceCenteredCubic
from ase.geometry.dimensionality import (analyze_dimensionality,
isolate_components)
@pytest.mark.parametrize("method", ['TSA', 'RDA'])
def test_mx2(method):
atoms = ase.build.mx2(formula='MoS2', kind='2H', a=3.18, thickness=3.19)
atoms.cell[2, 2] = 7
atoms.set_pbc((1, 1, 1))
atoms *= 2
intervals = analyze_dimensionality(atoms, method=method)
m = intervals[0]
assert m.dimtype == '2D'
assert intervals[0].dimtype == '2D'
assert intervals[0].h == (0, 0, 2, 0)
assert intervals[1].dimtype == '3D'
assert intervals[1].h == (0, 0, 0, 1)
assert intervals[2].dimtype == '0D'
assert intervals[2].h == (24, 0, 0, 0)
@pytest.mark.parametrize("method", ['TSA', 'RDA'])
def test_fcc(method):
atoms = FaceCenteredCubic(size=(2, 2, 2), symbol='Cu', pbc=(1, 1, 1))
intervals = analyze_dimensionality(atoms, method=method)
m = intervals[0]
assert m.dimtype == '3D'
@pytest.mark.parametrize("kcutoff", [None, 1.1])
def test_isolation_0D(kcutoff):
atoms = ase.build.molecule('H2O', vacuum=3.0)
result = isolate_components(atoms, kcutoff=kcutoff)
assert len(result) == 1
key, components = list(result.items())[0]
assert key == '0D'
assert len(components) == 1
molecule = components[0]
assert molecule.get_chemical_formula() == atoms.get_chemical_formula()
def test_isolation_1D():
atoms = Atoms(symbols='Cl6Ti2', pbc=True,
cell=[[6.27, 0, 0],
[-3.135, 5.43, 0],
[0, 0, 5.82]],
positions=[[1.97505, 0, 1.455],
[0.987525, 1.71044347, 4.365],
[-0.987525, 1.71044347, 1.455],
[4.29495, 0, 4.365],
[2.147475, 3.71953581, 1.455],
[-2.147475, 3.71953581, 4.365],
[0, 0, 0],
[0, 0, 2.91]])
result = isolate_components(atoms)
assert len(result) == 1
key, components = list(result.items())[0]
assert key == '1D'
assert len(components) == 1
chain = components[0]
assert (chain.pbc == [False, False, True]).all()
assert chain.get_chemical_formula() == atoms.get_chemical_formula()
def test_isolation_2D():
atoms = ase.build.mx2(formula='MoS2', kind='2H', a=3.18, thickness=3.19)
atoms.cell[2, 2] = 7
atoms.set_pbc((1, 1, 1))
atoms *= 2
result = isolate_components(atoms)
assert len(result) == 1
key, components = list(result.items())[0]
assert key == '2D'
assert len(components) == 2
for layer in components:
empirical = atoms.get_chemical_formula(empirical=True)
assert empirical == layer.get_chemical_formula(empirical=True)
assert (layer.pbc == [True, True, False]).all()
def test_isolation_3D():
atoms = FaceCenteredCubic(size=(2, 2, 2), symbol='Cu', pbc=(1, 1, 1))
result = isolate_components(atoms)
assert len(result) == 1
key, components = list(result.items())[0]
assert key == '3D'
assert len(components) == 1
bulk = components[0]
assert bulk.get_chemical_formula() == atoms.get_chemical_formula()
|
