def test_get_hall_number_from_symmetry(self):
for fname in self._filenames:
cell = read_vasp(fname)
if 'distorted' in fname:
dataset = get_symmetry_dataset(cell, symprec=1e-1)
hall_number = get_hall_number_from_symmetry(
dataset['rotations'],
dataset['translations'],
symprec=1e-1)
if hall_number != dataset['hall_number']:
print("%d != %d in %s" %
(hall_number, dataset['hall_number'], fname))
ref_cell = (dataset['std_lattice'],
dataset['std_positions'], dataset['std_types'])
dataset = get_symmetry_dataset(ref_cell, symprec=1e-5)
hall_number = get_hall_number_from_symmetry(
dataset['rotations'],
dataset['translations'],
symprec=1e-5)
print("Using refinced cell: %d, %d in %s" %
(hall_number, dataset['hall_number'], fname))
else:
dataset = get_symmetry_dataset(cell, symprec=1e-5)
hall_number = get_hall_number_from_symmetry(
dataset['rotations'],
dataset['translations'],
symprec=1e-5)
self.assertEqual(
hall_number,
dataset['hall_number'],
msg=("%d != %d in %s" %
(hall_number, dataset['hall_number'], fname)))
def test_get_hall_number_from_symmetry(self):
for fname in self._filenames:
cell = read_vasp(fname)
if 'distorted' in fname:
dataset = get_symmetry_dataset(cell, symprec=1e-1)
hall_number = get_hall_number_from_symmetry(
dataset['rotations'],
dataset['translations'],
symprec=1e-1)
if hall_number != dataset['hall_number']:
print("%d != %d in %s" %
(hall_number, dataset['hall_number'], fname))
ref_cell = (dataset['std_lattice'],
dataset['std_positions'],
dataset['std_types'])
dataset = get_symmetry_dataset(ref_cell, symprec=1e-5)
hall_number = get_hall_number_from_symmetry(
dataset['rotations'],
dataset['translations'],
symprec=1e-5)
print("Using refinced cell: %d, %d in %s" %
(hall_number, dataset['hall_number'], fname))
else:
dataset = get_symmetry_dataset(cell, symprec=1e-5)
hall_number = get_hall_number_from_symmetry(
dataset['rotations'],
dataset['translations'],
symprec=1e-5)
self.assertEqual(
hall_number, dataset['hall_number'],
msg=("%d != %d in %s" %
(hall_number, dataset['hall_number'], fname)))
def get_hall_number_from_symmetry(operations,
basis="fractional",
lattice=None,
symprec=1e-5):
"""obtain the Hall number from the symmetry operations
Parameters
----------
operations: list
Nx12 flattened list of symmetry operations
basis: str
"fractional" or "cartesian"
Returns
-------
int
"""
if basis == "cartesian":
operations = operations_cart_to_frac(operations, lattice)
elif basis != "fractional":
raise ValueError("basis should be cartesian or fractional")
rotations = [[o[0:3], o[3:6], o[6:9]] for o in operations]
translations = [o[9:12] for o in operations]
return spglib.get_hall_number_from_symmetry(rotations,
translations,
symprec=symprec)
def get_spglib_hall_number(self, symprec=1e-5):
"""
Uses spglib.get_hall_number_from_symmetry to determine the hall number
based on the symmetry operations. Useful when the space group number
is not available, but the symmetries are (e.g. the DDB file)
Args:
symprec: distance tolerance in fractional coordinates (not the standard
in cartesian coordinates). See spglib docs for more details.
Returns:
int: the hall number.
"""
return spglib.get_hall_number_from_symmetry(self.symrel, self.tnons, symprec=symprec)
def get_iso(self, symprec):
DG = self.matrices
mat_list = [mat.rotation_matrix for mat in DG]
vec_list = [mat.translation_vector for mat in DG]
h_number = spglib.get_hall_number_from_symmetry(np.around(
mat_list, decimals=4), np.around(vec_list, decimals=6), symprec = symprec)
sg_type_data=spglib.get_spacegroup_type(h_number)
iso_sg=sg_type_data['international_short']
iso_sg_num=sg_type_data['number']
return iso_sg, iso_sg_num
def get_iso(path, iv):
DG = path.get_DG()
outputfile = open(iv.image_dir + "/../results/output.out", "a")
h_number = spglib.get_hall_number_from_symmetry(np.around(DG[0][:],
decimals=4),
np.around(DG[1][:],
decimals=6),
symprec=iv.gentol)
sg_type_data = spglib.get_spacegroup_type(h_number)
iso_sg = sg_type_data['international_short']
iso_sg_num = sg_type_data['number']
return iso_sg, iso_sg_num
def read(self, file):
"""Read and parse fort.34 file"""
if isinstance(file, str):
with open(file) as f:
data = f.read()
else:
data = file.read()
parsed_data = _parse_string(f34_parser(), data)
self.dimensionality, self.centring, self.crystal_type = parsed_data['header']
if self.dimensionality != 3:
raise NotImplementedError('Structure with dimensionality < 3 currently not supported')
# primitive cell vectors and basis positions in cartesian coordinates
abc = np.array(parsed_data['abc'].asList()).reshape((3, 3))
positions = np.array([d[1:] for d in parsed_data['geometry']])
# convert positions to fractional
positions = np.dot(np.linalg.inv(abc).T, positions.T).T
atomic_numbers = [d[0] for d in parsed_data['geometry']]
# convert to conventional cell
cell = (abc, positions, atomic_numbers)
cell = spglib.standardize_cell(cell, to_primitive=False, no_idealize=False)
self.abc, self.positions, atomic_numbers = cell
# ECPs
self.atomic_numbers = [num if num < 201 else num - 200 for num in atomic_numbers]
# get symmetry operations
self.n_symops = parsed_data['n_symops']
self.symops = np.array(parsed_data['symops'].asList()).reshape(self.n_symops * 4, 3)
rotations = np.zeros((self.n_symops, 3, 3))
for i in range(3):
rotations[:, i] = self.symops[i::4]
# convert symmetry operations from cartesian to fractional
rotations = np.dot(np.dot(np.linalg.inv(abc.T), rotations), abc.T)
# have to round rotations matrix as it is used to find symmetry group
rotations = np.round(np.swapaxes(rotations, 0, 1), 9)
translations = np.dot(self.symops[3::4], np.linalg.inv(abc))
hall = spglib.get_hall_number_from_symmetry(rotations, translations)
self.space_group = int(spglib.get_spacegroup_type(hall)['number'])
# we have conventional cell now
return self
