|
1
|
|
|
import pytest |
|
2
|
|
|
import os |
|
3
|
|
|
import amd |
|
4
|
|
|
import warnings |
|
5
|
|
|
|
|
6
|
|
|
|
|
7
|
|
|
@pytest.fixture(scope='module') |
|
8
|
|
|
def cif_paths(root_dir): |
|
9
|
|
|
cif_names = [ |
|
10
|
|
|
'cubic', |
|
11
|
|
|
'T2_experimental', |
|
12
|
|
|
] |
|
13
|
|
|
return {name: os.path.join(root_dir, f'{name}.cif') for name in cif_names} |
|
14
|
|
|
|
|
15
|
|
|
@pytest.mark.parametrize('reader', ['ase', 'pymatgen', 'gemmi', 'ccdc']) |
|
16
|
|
|
def test_CifReader(reader, cif_paths, reference_data): |
|
17
|
|
|
for name in cif_paths: |
|
18
|
|
|
references = reference_data[name] |
|
19
|
|
|
try: |
|
20
|
|
|
read_in = list(amd.CifReader(cif_paths[name], reader=reader)) |
|
21
|
|
|
except ImportError as _: |
|
22
|
|
|
pytest.skip(f'Skipping test_CifReader for {reader} as it failed to import.') |
|
23
|
|
|
|
|
24
|
|
|
if (not len(references) == len(read_in)) or len(read_in) == 0: |
|
25
|
|
|
pytest.fail(f'There are {len(references)} references, but {len(read_in)} structures were read.') |
|
26
|
|
|
|
|
27
|
|
|
for s, s_ in zip(read_in, references): |
|
28
|
|
|
if not s == s_['PeriodicSet']: |
|
29
|
|
|
pytest.fail(f'Structure {s.name} read with CifReader disagrees with reference.') |
|
30
|
|
|
|
|
31
|
|
|
def test_periodicset_from_ase_atoms(cif_paths, reference_data): |
|
32
|
|
|
try: |
|
33
|
|
|
from ase.io import iread |
|
34
|
|
|
except ImportError as _: |
|
35
|
|
|
pytest.skip(f'Skipping test_periodicset_from_ase_atoms as ase failed to import.') |
|
36
|
|
|
|
|
37
|
|
|
for name in cif_paths: |
|
38
|
|
|
references = reference_data[name] |
|
39
|
|
|
# ignore ase warning: "crystal system x is not interpreted for space |
|
40
|
|
|
# group Spacegroup(1, setting=1). This may result in wrong setting!" |
|
41
|
|
|
with warnings.catch_warnings() as _: |
|
42
|
|
|
warnings.simplefilter('ignore') |
|
43
|
|
|
atoms = list(iread(cif_paths[name])) |
|
44
|
|
|
read_in = [amd.periodicset_from_ase_atoms(a) for a in atoms] |
|
45
|
|
|
if (not len(references) == len(read_in)) or len(read_in) == 0: |
|
46
|
|
|
pytest.fail(f'There are {len(references)} references, but {len(read_in)} structures were read.') |
|
47
|
|
|
|
|
48
|
|
|
for s, s_ in zip(read_in, references): |
|
49
|
|
|
if not s == s_['PeriodicSet']: |
|
50
|
|
|
pytest.fail(f'Structure {s.name} read with ase.io.iread disagrees with reference.') |
|
51
|
|
|
|
|
52
|
|
|
|
|
53
|
|
|
@pytest.fixture(scope='module') |
|
54
|
|
|
def asym_unit_test_cif_path(root_dir): |
|
55
|
|
|
return os.path.join(root_dir, 'OJIGOG.cif') |
|
56
|
|
|
|
|
57
|
|
|
def test_CifReader_equiv_structs(asym_unit_test_cif_path): |
|
58
|
|
|
pdds = [amd.PDD(struct, 100) for struct in amd.CifReader(asym_unit_test_cif_path, show_warnings=False)] |
|
59
|
|
|
if amd.emd(pdds[0], pdds[1]) > 0: |
|
60
|
|
|
pytest.fail(f'Asymmetric structure was read differently than identical expanded version.') |
|
61
|
|
|
|
|
62
|
|
|
|
|
63
|
|
|
@pytest.fixture(scope='module') |
|
64
|
|
|
def equiv_sites_cif_path(root_dir): |
|
65
|
|
|
return os.path.join(root_dir, 'BABMUQ.cif') |
|
66
|
|
|
|
|
67
|
|
|
def test_equiv_sites(equiv_sites_cif_path): |
|
68
|
|
|
pdds = [amd.PDD(s, 100) for s in amd.CifReader(equiv_sites_cif_path, show_warnings=False)] |
|
69
|
|
|
if amd.PDD_pdist(pdds): |
|
70
|
|
|
pytest.fail(f'Equivalent structures by symmetry differ by PDD.') |
|
71
|
|
|
|
|
72
|
|
|
|
|
73
|
|
|
@pytest.fixture(scope='module') |
|
74
|
|
|
def T2_alpha_cif_path(root_dir): |
|
75
|
|
|
return os.path.join(root_dir, 'T2-alpha-solvent.cif') |
|
76
|
|
|
|
|
77
|
|
|
def test_heaviest_component(T2_alpha_cif_path, ccdc_enabled): |
|
78
|
|
|
|
|
79
|
|
|
if not ccdc_enabled: |
|
80
|
|
|
pytest.skip('Skipping test_CSDReader as csd-python-api is not installed.') |
|
81
|
|
|
|
|
82
|
|
|
s = amd.CifReader( |
|
83
|
|
|
T2_alpha_cif_path, |
|
84
|
|
|
reader='ccdc', |
|
85
|
|
|
disorder='all_sites', |
|
86
|
|
|
heaviest_component=True |
|
87
|
|
|
).read() |
|
88
|
|
|
|
|
89
|
|
|
if not s.asymmetric_unit.shape[0] == 26: |
|
90
|
|
|
pytest.fail(f'Heaviest component test failed.') |
|
91
|
|
|
|
dwiddo /
average-minimum-distance
