def get_spacegroup(self, subtrans_included) -> Spacegroup:
# XXX The logic in this method needs serious cleaning up!
# The setting needs to be passed as either 1 or two, not None (default)
no = self._get_spacegroup_number()
hm_symbol = self._get_spacegroup_name()
sitesym = self._get_sitesym()
setting = 1
spacegroup = 1
if sitesym is not None:
subtrans = [(0.0, 0.0, 0.0)] if subtrans_included else None
spacegroup = spacegroup_from_data(no=no,
symbol=hm_symbol,
sitesym=sitesym,
subtrans=subtrans,
setting=setting)
elif no is not None:
spacegroup = no
elif hm_symbol is not None:
spacegroup = hm_symbol
else:
spacegroup = 1
setting_std = self._get_setting()
setting_name = None
if '_symmetry_space_group_setting' in self:
assert setting_std is not None
setting = setting_std
elif '_space_group_crystal_system' in self:
setting_name = self['_space_group_crystal_system']
elif '_symmetry_cell_setting' in self:
setting_name = self['_symmetry_cell_setting']
if setting_name:
no = Spacegroup(spacegroup).no
if no in rhombohedral_spacegroups:
if setting_name == 'hexagonal':
setting = 1
elif setting_name in ('trigonal', 'rhombohedral'):
setting = 2
else:
warnings.warn(
'unexpected crystal system %r for space group %r' %
(setting_name, spacegroup))
# FIXME - check for more crystal systems...
else:
warnings.warn(
'crystal system %r is not interpreted for space group %r. '
'This may result in wrong setting!' %
(setting_name, spacegroup))
spg = Spacegroup(spacegroup, setting)
if no is not None:
assert int(spg) == no, (int(spg), no)
return spg
def tags2atoms(tags,
store_tags=False,
primitive_cell=False,
subtrans_included=True,
fractional_occupancies=True):
"""Returns an Atoms object from a cif tags dictionary. See read_cif()
for a description of the arguments."""
if primitive_cell and subtrans_included:
raise RuntimeError(
'Primitive cell cannot be determined when sublattice translations '
'are included in the symmetry operations listed in the CIF file, '
'i.e. when `subtrans_included` is True.')
cell_tags = [
'_cell_length_a', '_cell_length_b', '_cell_length_c',
'_cell_angle_alpha', '_cell_angle_beta', '_cell_angle_gamma'
]
# If any value is missing, ditch periodic boundary conditions
has_pbc = True
try:
cell_values = [tags[ct] for ct in cell_tags]
a, b, c, alpha, beta, gamma = cell_values
except KeyError:
has_pbc = False
# Now get positions
try:
scaled_positions = np.array([
tags['_atom_site_fract_x'], tags['_atom_site_fract_y'],
tags['_atom_site_fract_z']
]).T
except KeyError:
scaled_positions = None
try:
positions = np.array([
tags['_atom_site_cartn_x'], tags['_atom_site_cartn_y'],
tags['_atom_site_cartn_z']
]).T
except KeyError:
positions = None
if (positions is None) and (scaled_positions is None):
raise RuntimeError('No positions found in structure')
elif scaled_positions is not None and not has_pbc:
raise RuntimeError('Structure has fractional coordinates but not '
'lattice parameters')
symbols = []
if '_atom_site_type_symbol' in tags:
labels = tags['_atom_site_type_symbol']
else:
labels = tags['_atom_site_label']
for s in labels:
# Strip off additional labeling on chemical symbols
m = re.search(r'([A-Z][a-z]?)', s)
symbol = m.group(0)
symbols.append(symbol)
# Symmetry specification, see
# http://www.iucr.org/resources/cif/dictionaries/cif_sym for a
# complete list of official keys. In addition we also try to
# support some commonly used depricated notations
no = None
if '_space_group.it_number' in tags:
no = tags['_space_group.it_number']
elif '_space_group_it_number' in tags:
no = tags['_space_group_it_number']
elif '_symmetry_int_tables_number' in tags:
no = tags['_symmetry_int_tables_number']
symbolHM = None
if '_space_group.Patterson_name_h-m' in tags:
symbolHM = tags['_space_group.patterson_name_h-m']
elif '_symmetry_space_group_name_h-m' in tags:
symbolHM = tags['_symmetry_space_group_name_h-m']
elif '_space_group_name_h-m_alt' in tags:
symbolHM = tags['_space_group_name_h-m_alt']
if symbolHM is not None:
symbolHM = old_spacegroup_names.get(symbolHM.strip(), symbolHM)
for name in [
'_space_group_symop_operation_xyz',
'_space_group_symop.operation_xyz', '_symmetry_equiv_pos_as_xyz'
]:
if name in tags:
sitesym = tags[name]
break
else:
sitesym = None
# The setting needs to be passed as either 1 or two, not None (default)
setting = 1
spacegroup = 1
if sitesym is not None:
if isinstance(sitesym, str):
sitesym = [sitesym]
subtrans = [(0.0, 0.0, 0.0)] if subtrans_included else None
spacegroup = spacegroup_from_data(no=no,
symbol=symbolHM,
sitesym=sitesym,
subtrans=subtrans,
setting=setting)
elif no is not None:
spacegroup = no
elif symbolHM is not None:
spacegroup = symbolHM
else:
spacegroup = 1
kwargs = {}
if store_tags:
kwargs['info'] = tags.copy()
if 'D' in symbols:
deuterium = [symbol == 'D' for symbol in symbols]
symbols = [symbol if symbol != 'D' else 'H' for symbol in symbols]
else:
deuterium = False
setting_name = None
if '_space_group_crystal_system' in tags:
setting_name = tags['_space_group_crystal_system']
elif '_symmetry_cell_setting' in tags:
setting_name = tags['_symmetry_cell_setting']
if setting_name:
no = Spacegroup(spacegroup).no
# rhombohedral systems
if no in (146, 148, 155, 160, 161, 166, 167):
if setting_name == 'hexagonal':
setting = 1
elif setting_name in ('trigonal', 'rhombohedral'):
setting = 2
else:
warnings.warn(
'unexpected crystal system %r for space group %r' %
(setting_name, spacegroup))
# FIXME - check for more crystal systems...
else:
warnings.warn(
'crystal system %r is not interpreted for space group %r. '
'This may result in wrong setting!' %
(setting_name, spacegroup))
occupancies = None
if fractional_occupancies:
try:
occupancies = tags['_atom_site_occupancy']
# no warnings in this case
kwargs['onduplicates'] = 'keep'
except KeyError:
pass
else:
try:
if not np.allclose(tags['_atom_site_occupancy'], 1.):
warnings.warn(
'Cif file containes mixed/fractional occupancies. '
'Consider using `fractional_occupancies=True`')
kwargs['onduplicates'] = 'keep'
except KeyError:
pass
if has_pbc:
if scaled_positions is None:
_ = Atoms(symbols,
positions=positions,
cell=[a, b, c, alpha, beta, gamma])
scaled_positions = _.get_scaled_positions()
if deuterium:
numbers = np.array([atomic_numbers[s] for s in symbols])
masses = atomic_masses[numbers]
masses[deuterium] = 2.01355
kwargs['masses'] = masses
atoms = crystal(symbols,
basis=scaled_positions,
cellpar=[a, b, c, alpha, beta, gamma],
spacegroup=spacegroup,
occupancies=occupancies,
setting=setting,
primitive_cell=primitive_cell,
**kwargs)
else:
atoms = Atoms(symbols,
positions=positions,
info=kwargs.get('info', None))
if occupancies is not None:
# Compile an occupancies dictionary
occ_dict = {}
for i, sym in enumerate(symbols):
occ_dict[i] = {sym: occupancies[i]}
atoms.info['occupancy'] = occ_dict
if deuterium:
masses = atoms.get_masses()
masses[atoms.numbers == 1] = 1.00783
masses[deuterium] = 2.01355
atoms.set_masses(masses)
return atoms
def tags2atoms(tags,
store_tags=False,
primitive_cell=False,
subtrans_included=True):
"""Returns an Atoms object from a cif tags dictionary. See read_cif()
for a description of the arguments."""
if primitive_cell and subtrans_included:
raise RuntimeError(
'Primitive cell cannot be determined when sublattice translations '
'are included in the symmetry operations listed in the CIF file, '
'i.e. when `subtrans_included` is True.')
a = tags['_cell_length_a']
b = tags['_cell_length_b']
c = tags['_cell_length_c']
alpha = tags['_cell_angle_alpha']
beta = tags['_cell_angle_beta']
gamma = tags['_cell_angle_gamma']
scaled_positions = np.array([
tags['_atom_site_fract_x'], tags['_atom_site_fract_y'],
tags['_atom_site_fract_z']
]).T
symbols = []
if '_atom_site_type_symbol' in tags:
labels = tags['_atom_site_type_symbol']
else:
labels = tags['_atom_site_label']
for s in labels:
# Strip off additional labeling on chemical symbols
m = re.search(r'([A-Z][a-z]?)', s)
symbol = m.group(0)
symbols.append(symbol)
# Symmetry specification, see
# http://www.iucr.org/resources/cif/dictionaries/cif_sym for a
# complete list of official keys. In addition we also try to
# support some commonly used depricated notations
no = None
if '_space_group.it_number' in tags:
no = tags['_space_group.it_number']
elif '_space_group_it_number' in tags:
no = tags['_space_group_it_number']
elif '_symmetry_int_tables_number' in tags:
no = tags['_symmetry_int_tables_number']
symbolHM = None
if '_space_group.Patterson_name_h-m' in tags:
symbolHM = tags['_space_group.patterson_name_h-m']
elif '_symmetry_space_group_name_h-m' in tags:
symbolHM = tags['_symmetry_space_group_name_h-m']
elif '_space_group_name_h-m_alt' in tags:
symbolHM = tags['_space_group_name_h-m_alt']
if symbolHM is not None:
symbolHM = old_spacegroup_names.get(symbolHM.strip(), symbolHM)
for name in [
'_space_group_symop_operation_xyz',
'_space_group_symop.operation_xyz', '_symmetry_equiv_pos_as_xyz'
]:
if name in tags:
sitesym = tags[name]
break
else:
sitesym = None
spacegroup = 1
if sitesym is not None:
subtrans = [(0.0, 0.0, 0.0)] if subtrans_included else None
spacegroup = spacegroup_from_data(no=no,
symbol=symbolHM,
sitesym=sitesym,
subtrans=subtrans)
elif no is not None:
spacegroup = no
elif symbolHM is not None:
spacegroup = symbolHM
else:
spacegroup = 1
if store_tags:
kwargs = {'info': tags.copy()}
else:
kwargs = {}
if 'D' in symbols:
deuterium = [symbol == 'D' for symbol in symbols]
symbols = [symbol if symbol != 'D' else 'H' for symbol in symbols]
else:
deuterium = False
atoms = crystal(symbols,
basis=scaled_positions,
cellpar=[a, b, c, alpha, beta, gamma],
spacegroup=spacegroup,
primitive_cell=primitive_cell,
**kwargs)
if deuterium:
masses = atoms.get_masses()
masses[atoms.numbers == 1] = 1.00783
masses[deuterium] = 2.01355
atoms.set_masses(masses)
return atoms
def tags2atoms(tags, store_tags=False, primitive_cell=False,
subtrans_included=True):
"""Returns an Atoms object from a cif tags dictionary. See read_cif()
for a description of the arguments."""
if primitive_cell and subtrans_included:
raise RuntimeError(
'Primitive cell cannot be determined when sublattice translations '
'are included in the symmetry operations listed in the CIF file, '
'i.e. when `subtrans_included` is True.')
a = tags['_cell_length_a']
b = tags['_cell_length_b']
c = tags['_cell_length_c']
alpha = tags['_cell_angle_alpha']
beta = tags['_cell_angle_beta']
gamma = tags['_cell_angle_gamma']
scaled_positions = np.array([tags['_atom_site_fract_x'],
tags['_atom_site_fract_y'],
tags['_atom_site_fract_z']]).T
symbols = []
if '_atom_site_type_symbol' in tags:
labels = tags['_atom_site_type_symbol']
else:
labels = tags['_atom_site_label']
for s in labels:
# Strip off additional labeling on chemical symbols
m = re.search(r'([A-Z][a-z]?)', s)
symbol = m.group(0)
symbols.append(symbol)
# Symmetry specification, see
# http://www.iucr.org/resources/cif/dictionaries/cif_sym for a
# complete list of official keys. In addition we also try to
# support some commonly used depricated notations
no = None
if '_space_group.it_number' in tags:
no = tags['_space_group.it_number']
elif '_space_group_it_number' in tags:
no = tags['_space_group_it_number']
elif '_symmetry_int_tables_number' in tags:
no = tags['_symmetry_int_tables_number']
symbolHM = None
if '_space_group.Patterson_name_h-m' in tags:
symbolHM = tags['_space_group.patterson_name_h-m']
elif '_symmetry_space_group_name_h-m' in tags:
symbolHM = tags['_symmetry_space_group_name_h-m']
elif '_space_group_name_h-m_alt' in tags:
symbolHM = tags['_space_group_name_h-m_alt']
if symbolHM is not None:
symbolHM = old_spacegroup_names.get(symbolHM.strip(), symbolHM)
for name in ['_space_group_symop_operation_xyz',
'_space_group_symop.operation_xyz',
'_symmetry_equiv_pos_as_xyz']:
if name in tags:
sitesym = tags[name]
break
else:
sitesym = None
spacegroup = 1
if sitesym is not None:
subtrans = [(0.0, 0.0, 0.0)] if subtrans_included else None
spacegroup = spacegroup_from_data(
no=no, symbol=symbolHM, sitesym=sitesym, subtrans=subtrans)
elif no is not None:
spacegroup = no
elif symbolHM is not None:
spacegroup = symbolHM
else:
spacegroup = 1
if store_tags:
kwargs = {'info': tags.copy()}
else:
kwargs = {}
if 'D' in symbols:
deuterium = [symbol == 'D' for symbol in symbols]
symbols = [symbol if symbol != 'D' else 'H' for symbol in symbols]
else:
deuterium = False
atoms = crystal(symbols, basis=scaled_positions,
cellpar=[a, b, c, alpha, beta, gamma],
spacegroup=spacegroup, primitive_cell=primitive_cell,
**kwargs)
if deuterium:
masses = atoms.get_masses()
masses[atoms.numbers == 1] = 1.00783
masses[deuterium] = 2.01355
atoms.set_masses(masses)
return atoms
