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import pytest |
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2
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import amd |
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3
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import warnings |
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4
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5
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6
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@pytest.fixture(scope='module') |
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7
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def test_cif_paths(data_dir): |
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8
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cif_names = ['cubic', 'T2_experimental'] |
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9
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return {name: str(data_dir / f'{name}.cif') for name in cif_names} |
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10
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11
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12
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@pytest.mark.parametrize('reader', ['gemmi', 'pymatgen', 'ase', 'ccdc']) |
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def test_CifReader(reader, test_cif_paths, reference_data): |
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for name in test_cif_paths: |
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try: |
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16
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read_in = list(amd.CifReader(test_cif_paths[name], reader=reader)) |
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except ImportError: |
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18
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pytest.skip( |
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f'Skipping test_CifReader[{reader}] as {reader} failed to ' |
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'import.' |
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) |
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references = reference_data[name] |
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if (not len(references) == len(read_in)) or len(read_in) == 0: |
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pytest.fail( |
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f'There are {len(references)} references, but {len(read_in)}' |
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26
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f'structures were read from {name}.' |
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) |
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for s, s_ in zip(read_in, references): |
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29
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if not s == s_['PeriodicSet']: |
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pytest.fail( |
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f'Structure {name}:{s.name} read with CifReader disagrees ' |
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'with reference.' |
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) |
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34
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35
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36
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def test_periodicset_from_ase_atoms(test_cif_paths, reference_data): |
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try: |
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from ase.io import iread |
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except ImportError: |
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40
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pytest.skip( |
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'Skipping test_periodicset_from_ase_atoms as ase failed to import.' |
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42
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) |
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43
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44
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for name in test_cif_paths: |
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references = reference_data[name] |
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# ignore ase warning: "crystal system x is not interpreted for space |
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# group Spacegroup(1, setting=1). This may result in wrong setting!" |
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48
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with warnings.catch_warnings(): |
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warnings.simplefilter('ignore') |
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50
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atoms = list(iread(test_cif_paths[name])) |
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51
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read_in = [amd.periodicset_from_ase_atoms(a) for a in atoms] |
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if (not len(references) == len(read_in)) or len(read_in) == 0: |
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pytest.fail( |
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54
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f'There are {len(references)} references, but {len(read_in)}' |
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f'structures were read from {name}.' |
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56
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) |
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57
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58
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for s, s_ in zip(read_in, references): |
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59
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if not s == s_['PeriodicSet']: |
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60
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n = s_['PeriodicSet'].name |
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61
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pytest.fail( |
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'Structure read with ase.io.iread disagrees with ' |
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f'reference ({n}).' |
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64
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) |
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65
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66
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67
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def test_CifReader_equiv_structs(data_dir): |
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68
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reader = amd.CifReader(data_dir / 'OJIGOG.cif', show_warnings=False) |
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69
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pdds = [amd.PDD(struct, 100) for struct in reader] |
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70
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if amd.emd(pdds[0], pdds[1]) > 0: |
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71
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pytest.fail( |
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'Asymmetric structure was read differently than identical ' |
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'expanded version.' |
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74
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) |
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75
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76
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77
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def test_equiv_sites(data_dir): |
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78
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reader = amd.CifReader(data_dir / 'BABMUQ.cif', show_warnings=False) |
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79
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pdds = [amd.PDD(s, 100) for s in reader] |
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80
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if amd.PDD_pdist(pdds): |
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81
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pytest.fail('Equivalent structures by symmetry differ by PDD.') |
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82
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83
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84
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def test_heaviest_component(data_dir, ccdc_enabled): |
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85
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86
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if not ccdc_enabled: |
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87
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pytest.skip( |
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88
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'Skipping test_CSDReader as csd-python-api failed to import.' |
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89
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) |
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90
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91
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s = amd.CifReader( |
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92
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data_dir / 'T2-alpha-solvent.cif', |
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reader='ccdc', |
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94
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disorder='all_sites', |
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95
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heaviest_component=True |
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96
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).read() |
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97
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98
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if not s.asymmetric_unit.shape[0] == 26: |
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99
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pytest.fail('Heaviest component test failed.') |
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100
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dwiddo /
average-minimum-distance
