import io import numpy as np import warnings import pytest from ase import Atoms from ase.build import molecule from ase.io import read, write from ase.io.cif import CIFLoop, parse_loop, NoStructureData, parse_cif from ase.calculators.calculator import compare_atoms def check_fractional_occupancies(atoms): """ Checks fractional occupancy entries in atoms.info dict """ assert atoms.info['occupancy'] assert list(atoms.arrays['spacegroup_kinds']) occupancies = atoms.info['occupancy'] kinds = atoms.arrays['spacegroup_kinds'] for a in atoms: if a.symbol == 'Na': assert len(occupancies[kinds[a.index]]) == 2 assert occupancies[kinds[a.index]]['K'] == 0.25 assert occupancies[kinds[a.index]]['Na'] == 0.75 else: assert len(occupancies[kinds[a.index]]) == 1 if a.symbol == 'Cl': assert occupancies[kinds[a.index]]['Cl'] == 0.3 content = """ data_1 _chemical_name_common 'Mysterious something' _cell_length_a 5.50000 _cell_length_b 5.50000 _cell_length_c 5.50000 _cell_angle_alpha 90 _cell_angle_beta 90 _cell_angle_gamma 90 _space_group_name_H-M_alt 'F m -3 m' _space_group_IT_number 225 loop_ _space_group_symop_operation_xyz 'x, y, z' '-x, -y, -z' '-x, -y, z' 'x, y, -z' '-x, y, -z' 'x, -y, z' 'x, -y, -z' '-x, y, z' 'z, x, y' '-z, -x, -y' 'z, -x, -y' '-z, x, y' '-z, -x, y' 'z, x, -y' '-z, x, -y' 'z, -x, y' 'y, z, x' '-y, -z, -x' '-y, z, -x' 'y, -z, x' 'y, -z, -x' '-y, z, x' '-y, -z, x' 'y, z, -x' 'y, x, -z' '-y, -x, z' '-y, -x, -z' 'y, x, z' 'y, -x, z' '-y, x, -z' '-y, x, z' 'y, -x, -z' 'x, z, -y' '-x, -z, y' '-x, z, y' 'x, -z, -y' '-x, -z, -y' 'x, z, y' 'x, -z, y' '-x, z, -y' 'z, y, -x' '-z, -y, x' 'z, -y, x' '-z, y, -x' '-z, y, x' 'z, -y, -x' '-z, -y, -x' 'z, y, x' 'x, y+1/2, z+1/2' '-x, -y+1/2, -z+1/2' '-x, -y+1/2, z+1/2' 'x, y+1/2, -z+1/2' '-x, y+1/2, -z+1/2' 'x, -y+1/2, z+1/2' 'x, -y+1/2, -z+1/2' '-x, y+1/2, z+1/2' 'z, x+1/2, y+1/2' '-z, -x+1/2, -y+1/2' 'z, -x+1/2, -y+1/2' '-z, x+1/2, y+1/2' '-z, -x+1/2, y+1/2' 'z, x+1/2, -y+1/2' '-z, x+1/2, -y+1/2' 'z, -x+1/2, y+1/2' 'y, z+1/2, x+1/2' '-y, -z+1/2, -x+1/2' '-y, z+1/2, -x+1/2' 'y, -z+1/2, x+1/2' 'y, -z+1/2, -x+1/2' '-y, z+1/2, x+1/2' '-y, -z+1/2, x+1/2' 'y, z+1/2, -x+1/2' 'y, x+1/2, -z+1/2' '-y, -x+1/2, z+1/2' '-y, -x+1/2, -z+1/2' 'y, x+1/2, z+1/2' 'y, -x+1/2, z+1/2' '-y, x+1/2, -z+1/2' '-y, x+1/2, z+1/2' 'y, -x+1/2, -z+1/2' 'x, z+1/2, -y+1/2' '-x, -z+1/2, y+1/2' '-x, z+1/2, y+1/2' 'x, -z+1/2, -y+1/2' '-x, -z+1/2, -y+1/2' 'x, z+1/2, y+1/2' 'x, -z+1/2, y+1/2' '-x, z+1/2, -y+1/2' 'z, y+1/2, -x+1/2' '-z, -y+1/2, x+1/2' 'z, -y+1/2, x+1/2' '-z, y+1/2, -x+1/2' '-z, y+1/2, x+1/2' 'z, -y+1/2, -x+1/2' '-z, -y+1/2, -x+1/2' 'z, y+1/2, x+1/2' 'x+1/2, y, z+1/2' '-x+1/2, -y, -z+1/2' '-x+1/2, -y, z+1/2' 'x+1/2, y, -z+1/2' '-x+1/2, y, -z+1/2' 'x+1/2, -y, z+1/2' 'x+1/2, -y, -z+1/2' '-x+1/2, y, z+1/2' 'z+1/2, x, y+1/2' '-z+1/2, -x, -y+1/2' 'z+1/2, -x, -y+1/2' '-z+1/2, x, y+1/2' '-z+1/2, -x, y+1/2' 'z+1/2, x, -y+1/2' '-z+1/2, x, -y+1/2' 'z+1/2, -x, y+1/2' 'y+1/2, z, x+1/2' '-y+1/2, -z, -x+1/2' '-y+1/2, z, -x+1/2' 'y+1/2, -z, x+1/2' 'y+1/2, -z, -x+1/2' '-y+1/2, z, x+1/2' '-y+1/2, -z, x+1/2' 'y+1/2, z, -x+1/2' 'y+1/2, x, -z+1/2' '-y+1/2, -x, z+1/2' '-y+1/2, -x, -z+1/2' 'y+1/2, x, z+1/2' 'y+1/2, -x, z+1/2' '-y+1/2, x, -z+1/2' '-y+1/2, x, z+1/2' 'y+1/2, -x, -z+1/2' 'x+1/2, z, -y+1/2' '-x+1/2, -z, y+1/2' '-x+1/2, z, y+1/2' 'x+1/2, -z, -y+1/2' '-x+1/2, -z, -y+1/2' 'x+1/2, z, y+1/2' 'x+1/2, -z, y+1/2' '-x+1/2, z, -y+1/2' 'z+1/2, y, -x+1/2' '-z+1/2, -y, x+1/2' 'z+1/2, -y, x+1/2' '-z+1/2, y, -x+1/2' '-z+1/2, y, x+1/2' 'z+1/2, -y, -x+1/2' '-z+1/2, -y, -x+1/2' 'z+1/2, y, x+1/2' 'x+1/2, y+1/2, z' '-x+1/2, -y+1/2, -z' '-x+1/2, -y+1/2, z' 'x+1/2, y+1/2, -z' '-x+1/2, y+1/2, -z' 'x+1/2, -y+1/2, z' 'x+1/2, -y+1/2, -z' '-x+1/2, y+1/2, z' 'z+1/2, x+1/2, y' '-z+1/2, -x+1/2, -y' 'z+1/2, -x+1/2, -y' '-z+1/2, x+1/2, y' '-z+1/2, -x+1/2, y' 'z+1/2, x+1/2, -y' '-z+1/2, x+1/2, -y' 'z+1/2, -x+1/2, y' 'y+1/2, z+1/2, x' '-y+1/2, -z+1/2, -x' '-y+1/2, z+1/2, -x' 'y+1/2, -z+1/2, x' 'y+1/2, -z+1/2, -x' '-y+1/2, z+1/2, x' '-y+1/2, -z+1/2, x' 'y+1/2, z+1/2, -x' 'y+1/2, x+1/2, -z' '-y+1/2, -x+1/2, z' '-y+1/2, -x+1/2, -z' 'y+1/2, x+1/2, z' 'y+1/2, -x+1/2, z' '-y+1/2, x+1/2, -z' '-y+1/2, x+1/2, z' 'y+1/2, -x+1/2, -z' 'x+1/2, z+1/2, -y' '-x+1/2, -z+1/2, y' '-x+1/2, z+1/2, y' 'x+1/2, -z+1/2, -y' '-x+1/2, -z+1/2, -y' 'x+1/2, z+1/2, y' 'x+1/2, -z+1/2, y' '-x+1/2, z+1/2, -y' 'z+1/2, y+1/2, -x' '-z+1/2, -y+1/2, x' 'z+1/2, -y+1/2, x' '-z+1/2, y+1/2, -x' '-z+1/2, y+1/2, x' 'z+1/2, -y+1/2, -x' '-z+1/2, -y+1/2, -x' 'z+1/2, y+1/2, x' loop_ _atom_site_label _atom_site_occupancy _atom_site_fract_x _atom_site_fract_y _atom_site_fract_z _atom_site_adp_type _atom_site_B_iso_or_equiv _atom_site_type_symbol Na 0.7500 0.000000 0.000000 0.000000 Biso 1.000000 Na K 0.2500 0.000000 0.000000 0.000000 Biso 1.000000 K Cl 0.3000 0.500000 0.500000 0.500000 Biso 1.000000 Cl I 0.5000 0.250000 0.250000 0.250000 Biso 1.000000 I """ def test_cif(): cif_file = io.StringIO(content) # legacy behavior is to not read the K atoms with warnings.catch_warnings(): warnings.simplefilter("ignore") atoms_leg = read(cif_file, format='cif', fractional_occupancies=False) elements = np.unique(atoms_leg.get_atomic_numbers()) for n in (11, 17, 53): assert n in elements try: atoms_leg.info['occupancy'] raise AssertionError except KeyError: pass cif_file = io.StringIO(content) # new behavior is to still not read the K atoms, but build info atoms = read(cif_file, format='cif', fractional_occupancies=True) # yield the same old atoms for fractional_occupancies case assert len(atoms_leg) == len(atoms) assert np.all(atoms_leg.get_atomic_numbers() == atoms.get_atomic_numbers()) assert atoms_leg == atoms elements = np.unique(atoms_leg.get_atomic_numbers()) for n in (11, 17, 53): assert n in elements check_fractional_occupancies(atoms) # read/write fname = 'testfile.cif' with open(fname, 'wb') as fd: write(fd, atoms, format='cif') with open(fname) as fd: atoms = read(fd, format='cif', fractional_occupancies=True) check_fractional_occupancies(atoms) # check repeating atoms atoms = atoms.repeat([2, 1, 1]) assert len(atoms.arrays['spacegroup_kinds']) == len(atoms.arrays['numbers']) # ICSD-like file from issue #293 content2 = """ data_global _cell_length_a 9.378(5) _cell_length_b 7.488(5) _cell_length_c 6.513(5) _cell_angle_alpha 90. _cell_angle_beta 91.15(5) _cell_angle_gamma 90. _cell_volume 457.27 _cell_formula_units_Z 2 _symmetry_space_group_name_H-M 'P 1 n 1' _symmetry_Int_Tables_number 7 _refine_ls_R_factor_all 0.071 loop_ _symmetry_equiv_pos_site_id _symmetry_equiv_pos_as_xyz 1 'x+1/2, -y, z+1/2' 2 'x, y, z' loop_ _atom_type_symbol _atom_type_oxidation_number Sn2+ 2 As4+ 4 Se2- -2 loop_ _atom_site_label _atom_site_type_symbol _atom_site_symmetry_multiplicity _atom_site_Wyckoff_symbol _atom_site_fract_x _atom_site_fract_y _atom_site_fract_z _atom_site_B_iso_or_equiv _atom_site_occupancy _atom_site_attached_hydrogens Sn1 Sn2+ 2 a 0.5270(2) 0.3856(2) 0.7224(3) 0.0266(4) 1. 0 Sn2 Sn2+ 2 a 0.0279(2) 0.1245(2) 0.7870(2) 0.0209(4) 1. 0 As1 As4+ 2 a 0.6836(4) 0.1608(5) 0.8108(6) 0.0067(7) 1. 0 As2 As4+ 2 a 0.8174(4) 0.6447(6) 0.1908(6) 0.0057(6) 1. 0 Se1 Se2- 2 a 0.4898(4) 0.7511(6) 0.8491(6) 0.0110(6) 1. 0 Se2 Se2- 2 a 0.7788(4) 0.6462(6) 0.2750(6) 0.0097(6) 1. 0 Se3 Se2- 2 a 0.6942(4) 0.0517(5) 0.5921(6) 0.2095(6) 1. 0 Se4 Se2- 2 a 0.0149(4) 0.3437(6) 0.5497(7) 0.1123(7) 1. 0 Se5 Se2- 2 a 0.1147(4) 0.5633(4) 0.3288(6) 0.1078(6) 1. 0 Se6 Se2- 2 a 0.0050(4) 0.4480(6) 0.9025(6) 0.9102(6) 1. 0 """ def test_cif_icsd(): cif_file = io.StringIO(content2) atoms = read(cif_file, format='cif') # test something random so atoms is not unused assert 'occupancy' in atoms.info @pytest.fixture def cif_atoms(): cif_file = io.StringIO(content) return read(cif_file, format='cif') def test_cif_loop_keys(cif_atoms): data = {} # test case has 20 entries data['someKey'] = [[str(i) + "test" for i in range(20)]] # test case has 20 entries data['someIntKey'] = [[str(i) + "123" for i in range(20)]] cif_atoms.write('testfile.cif', loop_keys=data) atoms1 = read('testfile.cif', store_tags=True) # keys are read lowercase only r_data = {'someKey': atoms1.info['_somekey'], 'someIntKey': atoms1.info['_someintkey']} assert r_data['someKey'] == data['someKey'][0] # data reading auto converts strins assert r_data['someIntKey'] == [int(x) for x in data['someIntKey'][0]] # test if automatic numbers written after elements are correct def test_cif_writer_label_numbers(cif_atoms): cif_atoms.write('testfile.cif') atoms1 = read('testfile.cif', store_tags=True) labels = atoms1.info['_atom_site_label'] # cannot use atoms.symbols as K is missing there elements = atoms1.info['_atom_site_type_symbol'] build_labels = [ "{:}{:}".format( x, i) for x in set(elements) for i in range( 1, elements.count(x) + 1)] assert build_labels.sort() == labels.sort() def test_cif_labels(cif_atoms): data = [["label" + str(i) for i in range(20)]] # test case has 20 entries cif_atoms.write('testfile.cif', labels=data) atoms1 = read('testfile.cif', store_tags=True) print(atoms1.info) assert data[0] == atoms1.info['_atom_site_label'] def test_cifloop(): dct = {'_eggs': range(4), '_potatoes': [1.3, 7.1, -1, 0]} loop = CIFLoop() loop.add('_eggs', dct['_eggs'], '{:<2d}') loop.add('_potatoes', dct['_potatoes'], '{:.4f}') string = loop.tostring() + '\n\n' lines = string.splitlines()[::-1] assert lines.pop() == 'loop_' newdct = parse_loop(lines) print(newdct) assert set(dct) == set(newdct) for name in dct: assert dct[name] == pytest.approx(newdct[name]) @pytest.mark.parametrize('data', [b'', b'data_dummy']) def test_empty_or_atomless(data): ciffile = io.BytesIO(data) images = read(ciffile, index=':', format='cif') assert len(images) == 0 def test_empty_or_atomless_cifblock(): ciffile = io.BytesIO(b'data_dummy') blocks = list(parse_cif(ciffile)) assert len(blocks) == 1 assert not blocks[0].has_structure() with pytest.raises(NoStructureData): blocks[0].get_atoms() def test_symbols_questionmark(): ciffile = io.BytesIO( b'data_dummy\n' b'loop_\n' b'_atom_site_label\n' b'?\n') blocks = list(parse_cif(ciffile)) assert not blocks[0].has_structure() with pytest.raises(NoStructureData, match='undetermined'): blocks[0].get_atoms() def test_bad_occupancies(cif_atoms): assert 'Au' not in cif_atoms.symbols cif_atoms.symbols[0] = 'Au' with pytest.warns(UserWarning, match='no occupancy info'): write('tmp.cif', cif_atoms) @pytest.mark.parametrize( 'setting_name, ref_setting', [ ('hexagonal', 1), ('trigonal', 2), ('rhombohedral', 2) ] ) def test_spacegroup_named_setting(setting_name, ref_setting): """The rhombohedral crystal system signifies setting=2""" ciffile = io.BytesIO("""\ data_test _space_group_crystal_system {} _symmetry_space_group_name_H-M 'R-3m' """.format(setting_name).encode('ascii')) blocks = list(parse_cif(ciffile)) assert len(blocks) == 1 spg = blocks[0].get_spacegroup(False) assert int(spg) == 166 assert spg.setting == ref_setting @pytest.fixture def atoms(): return Atoms('CO', cell=[2., 3., 4., 50., 60., 70.], pbc=True, scaled_positions=[[0.1, 0.2, 0.3], [0.4, 0.5, 0.6]]) def roundtrip(atoms): from ase.io.bytes import to_bytes, parse_atoms buf = to_bytes(atoms, format='cif') return parse_atoms(buf, format='cif') def test_cif_roundtrip_periodic(atoms): # Reading and writing the cell loses the rotation information, # but preserves cellpar and scaled positions. atoms1 = roundtrip(atoms) assert str(atoms1.symbols) == 'CO' assert all(atoms1.pbc) assert atoms.cell.cellpar() == pytest.approx( atoms1.cell.cellpar(), abs=1e-5) assert atoms.get_scaled_positions() == pytest.approx( atoms1.get_scaled_positions(), abs=1e-5) def test_cif_roundtrip_nonperiodic(): atoms = molecule('H2O') atoms1 = roundtrip(atoms) assert not compare_atoms(atoms, atoms1, tol=1e-5) def test_cif_missingvector(atoms): # We don't know any way to represent only 2 cell vectors in CIF. # So we discard them and warn the user. atoms.cell[0] = 0.0 atoms.pbc[0] = False assert atoms.cell.rank == 2 with pytest.raises(ValueError, match='CIF format can only'): roundtrip(atoms) def test_cif_roundtrip_mixed(): atoms = Atoms('Au', cell=[1., 2., 3.], pbc=[1, 1, 0]) atoms1 = roundtrip(atoms) # We cannot preserve PBC info for this case: assert all(atoms1.pbc) assert compare_atoms(atoms, atoms1, tol=1e-5) == ['pbc'] assert atoms.get_scaled_positions() == pytest.approx( atoms1.get_scaled_positions(), abs=1e-5) #assert pytest.approx(atoms.positions) == atoms1.positions #assert atoms1.cell.rank == 0