def getSpeciesListCIF(inputFile):
''' inputFile is the name of an input file
use ASE at this point to quickly parse file
DOES NOTHING ABOUT FRACTIONAL OCCUPANCY '''
from ase.io.cif import parse_cif
aseParser = parse_cif(inputFile)
for name, c in aseParser:
scaled_positions = np.array([
c['_atom_site_fract_x'], c['_atom_site_fract_y'],
c['_atom_site_fract_z']
]).T
crys = crystal(c['_atom_site_type_symbol'],
basis=scaled_positions,
cellpar=[
c['_cell_length_a'], c['_cell_length_b'],
c['_cell_length_c'], c['_cell_angle_alpha'],
c['_cell_angle_beta'], c['_cell_angle_gamma']
],
spacegroup=c['_symmetry_int_tables_number'])
atoms = Atoms(symbols=c['_atom_site_type_symbol'],
scaled_positions=scaled_positions,
cell=[
c['_cell_length_a'], c['_cell_length_b'],
c['_cell_length_c'], c['_cell_angle_alpha'],
c['_cell_angle_beta'], c['_cell_angle_gamma']
],
info={
'spacegroup':
ASESpacegroup(c['_symmetry_int_tables_number'])
})
print 'pbc=False', len(crys), len(atoms)
yield atoms
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_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
def test_loop_with_space():
# Regression test for https://gitlab.com/ase/ase/-/issues/859 .
buf = io.BytesIO(cif_with_whitespace_after_loop)
blocks = list(parse_cif(buf))
assert len(blocks) == 1
assert blocks[0]['_potato'] == 42
import sys;
from ase.io.cif import parse_cif;
cif = parse_cif( 'CeO2.cif' )
for key,value in cif[0][1].items():
print( "{0} -> {1} {2}".format( type( value ), key, value ) )