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
|
# fmt: off
import numpy as np
import pytest
from ase import Atoms
from ase.build import bulk, molecule
from ase.constraints import FixAtoms, FixCartesian
from ase.io.jsonio import decode, encode
@pytest.fixture()
def silver_bulk() -> Atoms:
return bulk('Ag', cubic=True)
def test_jsonio_atoms():
def assert_equal(atoms1, atoms2):
assert atoms1 == atoms2
assert set(atoms1.arrays) == set(atoms2.arrays)
for name in atoms1.arrays:
assert np.array_equal(
atoms1.arrays[name], atoms2.arrays[name]), name
atoms = bulk('Ti')
txt = encode(atoms)
atoms1 = decode(txt)
txt1 = encode(atoms1)
assert txt == txt1
assert_equal(atoms, atoms1)
BeH = molecule('BeH')
assert BeH.has('initial_magmoms')
new_BeH = decode(encode(BeH))
assert_equal(BeH, new_BeH)
assert new_BeH.has('initial_magmoms')
atoms = bulk('Ti')
atoms.constraints = FixAtoms(indices=[0])
new_atoms = decode(encode(atoms))
c1 = atoms.constraints
c2 = new_atoms.constraints
assert len(c1) == len(c2) == 1
# Can we check constraint equality somehow?
# Would make sense for FixAtoms
assert np.array_equal(c1[0].index, c2[0].index)
def test_jsonio_constraints_cartesian(silver_bulk):
a = [0, 1]
mask = [[False, False, True], [False, False, True]]
silver_bulk.constraints = FixCartesian(a, mask=mask)
new_atoms = decode(encode(silver_bulk))
c1 = silver_bulk.constraints
c2 = new_atoms.constraints
assert len(c1) == len(c2) == 1
assert np.array_equal(c1[0].index, c2[0].index)
assert np.array_equal(c1[0].mask, c2[0].mask)
def test_jsonio_constraints_fix_atoms_empty(silver_bulk: Atoms) -> None:
a = np.empty(0, dtype=int)
silver_bulk.set_constraint(FixAtoms(a))
new_atoms: Atoms = decode(encode(silver_bulk))
decoded_constraints = new_atoms.constraints[0]
assert isinstance(decoded_constraints, FixAtoms)
assert len(decoded_constraints.get_indices()) == 0
|
