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
|
import numpy as np
import pytest
from ase import Atoms
from ase.formula import Formula
def test_formula_things():
assert Formula('A3B2C2D').format('abc') == 'DB2C2A3'
assert Formula('A3B2C2D').format('ab2') == 'DB2C2A3'
assert Formula('A3B2C2D').format('a2b') == 'A3B2C2D'
assert str(Formula('HHOOO', format='reduce')) == 'H2O3'
assert Formula('HHOOOUO').format('reduce') == 'H2O3UO'
@pytest.mark.parametrize('f',
['SiC', 'MoS2', 'GaAs', 'CO', 'NH3'])
def test_periodic(f):
for fmt in ['ab2', 'a2b', 'periodic']:
assert Formula(f, format=fmt).format('periodic') == f
def test_atoms_formula_things():
assert Atoms('MoS2').get_chemical_formula() == 'MoS2'
assert Atoms('SnO2').get_chemical_formula(mode='metal') == 'SnO2'
def test_h0c1():
f = Formula.from_dict({'H': 0, 'C': 1})
assert f.format('hill') == 'C'
with pytest.raises(ValueError):
Formula.from_dict({'H': -1})
with pytest.raises(ValueError):
Formula.from_dict({'H': 1.5})
with pytest.raises(ValueError):
Formula.from_dict({7: 1})
def test_formula():
for sym in ['', 'Pu', 'Pu2', 'U2Pu2', 'U2((Pu2)2H)']:
for mode in ['all', 'reduce', 'hill', 'metal']:
for empirical in [False, True]:
if empirical and mode in ['all', 'reduce']:
continue
atoms = Atoms(sym)
formula = atoms.get_chemical_formula(mode=mode,
empirical=empirical)
atoms2 = Atoms(formula)
print(repr(sym), '->', repr(formula))
n1 = np.sort(atoms.numbers)
n2 = np.sort(atoms2.numbers)
if empirical and len(atoms) > 0:
reduction = len(n1) // len(n2)
n2 = np.repeat(n2, reduction)
assert (n1 == n2).all()
def test_convert():
assert str(Formula('AgAg').convert('hill')) == 'Ag2'
def test_formula_on_formula():
formula = Formula('CH3CH2OH')
assert formula == Formula(formula)
@pytest.mark.parametrize(
'x',
['H2O', '10H2O', '2(CuO2(H2O)2)10', 'Cu20+H2', 'H' * 15, 'AuBC2', ''])
def test_formulas(x):
f = Formula(x)
y = str(f)
assert y == x
print(f.count(), f'{f:latex}')
a, b = divmod(f, 'H2O')
assert a * Formula('H2O') + b == f
assert f != 117 # check that formula can be compared to non-formula object
|
