def get_symmetry(bulk, symprec=1e-5, angle_tolerance=-1.0):
"""
Return symmetry operations as hash.
Hash key 'rotations' gives the numpy integer array
of the rotation matrices for scaled positions
Hash key 'translations' gives the numpy double array
of the translation vectors in scaled positions
"""
# Atomic positions have to be specified by scaled positions for spglib.
positions = bulk.get_scaled_positions().copy()
lattice = bulk.get_cell().T.copy()
numbers = np.intc(bulk.get_atomic_numbers()).copy()
# Get number of symmetry operations and allocate symmetry operations
# multi = spg.multiplicity(cell, positions, numbers, symprec)
multi = 48 * bulk.get_number_of_atoms()
rotation = np.zeros((multi, 3, 3), dtype='intc')
translation = np.zeros((multi, 3))
# Get symmetry operations
magmoms = bulk.get_magnetic_moments()
if magmoms == None:
num_sym = spg.symmetry(rotation, translation, lattice, positions,
numbers, symprec, angle_tolerance)
else:
num_sym = spg.symmetry_with_collinear_spin(rotation, translation,
lattice, positions, numbers,
magmoms, symprec,
angle_tolerance)
return {
'rotations': rotation[:num_sym].copy(),
'translations': translation[:num_sym].copy()
}
def get_symmetry(bulk, use_magmoms=False, symprec=1e-5, angle_tolerance=-1.0):
"""
Return symmetry operations as hash.
Hash key 'rotations' gives the numpy integer array
of the rotation matrices for scaled positions
Hash key 'translations' gives the numpy double array
of the translation vectors in scaled positions
"""
# Atomic positions have to be specified by scaled positions for spglib.
positions = np.array(bulk.get_scaled_positions(), dtype='double', order='C')
lattice = np.array(bulk.get_cell().T, dtype='double', order='C')
numbers = np.array(bulk.get_atomic_numbers(), dtype='intc')
# Get number of symmetry operations and allocate symmetry operations
# multi = spg.multiplicity(cell, positions, numbers, symprec)
multi = 48 * bulk.get_number_of_atoms()
rotation = np.zeros((multi, 3, 3), dtype='intc')
translation = np.zeros((multi, 3), dtype='double')
# Get symmetry operations
if use_magmoms:
magmoms = bulk.get_magnetic_moments()
equivalent_atoms = np.zeros(len(magmoms), dtype='intc')
num_sym = spg.symmetry_with_collinear_spin(rotation,
translation,
equivalent_atoms,
lattice,
positions,
numbers,
magmoms,
symprec,
angle_tolerance)
return ({'rotations': np.array(rotation[:num_sym],
dtype='intc', order='C'),
'translations': np.array(translation[:num_sym],
dtype='double', order='C')},
equivalent_atoms)
else:
num_sym = spg.symmetry(rotation,
translation,
lattice,
positions,
numbers,
symprec,
angle_tolerance)
return {'rotations': np.array(rotation[:num_sym],
dtype='intc', order='C'),
'translations': np.array(translation[:num_sym],
dtype='double', order='C')}
def get_symmetry(bulk, use_magmoms=False, symprec=1e-5, angle_tolerance=-1.0):
"""
Return symmetry operations as hash.
Hash key 'rotations' gives the numpy integer array
of the rotation matrices for scaled positions
Hash key 'translations' gives the numpy double array
of the translation vectors in scaled positions
"""
# Atomic positions have to be specified by scaled positions for spglib.
positions = np.array(bulk.get_scaled_positions(), dtype='double', order='C')
lattice = np.array(bulk.get_cell().T, dtype='double', order='C')
numbers = np.array(bulk.get_atomic_numbers(), dtype='intc')
# Get number of symmetry operations and allocate symmetry operations
# multi = spg.multiplicity(cell, positions, numbers, symprec)
multi = 48 * bulk.get_number_of_atoms()
rotation = np.zeros((multi, 3, 3), dtype='intc')
translation = np.zeros((multi, 3), dtype='double')
# Get symmetry operations
if use_magmoms:
magmoms = bulk.get_magnetic_moments()
equivalent_atoms = np.zeros(len(magmoms), dtype='intc')
num_sym = spg.symmetry_with_collinear_spin(rotation,
translation,
equivalent_atoms,
lattice,
positions,
numbers,
magmoms,
symprec,
angle_tolerance)
return ({'rotations': np.array(rotation[:num_sym],
dtype='intc', order='C'),
'translations': np.array(translation[:num_sym],
dtype='double', order='C')},
equivalent_atoms)
else:
num_sym = spg.symmetry(rotation,
translation,
lattice,
positions,
numbers,
symprec,
angle_tolerance)
return {'rotations': np.array(rotation[:num_sym],
dtype='intc', order='C'),
'translations': np.array(translation[:num_sym],
dtype='double', order='C')}
def get_symmetry(bulk, symprec=1e-5, angle_tolerance=-1.0):
"""
Return symmetry operations as hash.
Hash key 'rotations' gives the numpy integer array
of the rotation matrices for scaled positions
Hash key 'translations' gives the numpy double array
of the translation vectors in scaled positions
"""
# Atomic positions have to be specified by scaled positions for spglib.
positions = bulk.get_scaled_positions().copy()
lattice = bulk.get_cell().T.copy()
numbers = np.intc(bulk.get_atomic_numbers()).copy()
# Get number of symmetry operations and allocate symmetry operations
# multi = spg.multiplicity(cell, positions, numbers, symprec)
multi = 48 * bulk.get_number_of_atoms()
rotation = np.zeros((multi, 3, 3), dtype='intc')
translation = np.zeros((multi, 3))
# Get symmetry operations
magmoms = bulk.get_magnetic_moments()
if magmoms == None:
num_sym = spg.symmetry(rotation,
translation,
lattice,
positions,
numbers,
symprec,
angle_tolerance)
else:
num_sym = spg.symmetry_with_collinear_spin(rotation,
translation,
lattice,
positions,
numbers,
magmoms,
symprec,
angle_tolerance)
return {'rotations': rotation[:num_sym].copy(),
'translations': translation[:num_sym].copy()}
def get_symmetry(cell, symprec=1e-5, angle_tolerance=-1.0):
"""This gives crystal symmetry operations from a crystal structure.
Args:
cell: Crystal structrue given either in Atoms object or tuple.
In the case given by a tuple, it has to follow the form below,
(Lattice parameters in a 3x3 array (see the detail below),
Fractional atomic positions in an Nx3 array,
Integer numbers to distinguish species in a length N array,
(optional) Collinear magnetic moments in a length N array),
where N is the number of atoms.
Lattice parameters are given in the form:
[[a_x, a_y, a_z],
[b_x, b_y, b_z],
[c_x, c_y, c_z]]
symprec:
float: Symmetry search tolerance in the unit of length.
angle_tolerance:
float: Symmetry search tolerance in the unit of angle deg.
If the value is negative, an internally optimized routine
is used to judge symmetry.
Return:
dictionary: Rotation parts and translation parts.
'rotations': Gives the numpy 'intc' array of the rotation matrices.
'translations': Gives the numpy 'double' array of fractional
translations with respect to a, b, c axes.
"""
_set_no_error()
lattice, positions, numbers, magmoms = _expand_cell(cell)
if lattice is None:
return None
multi = 48 * len(positions)
rotation = np.zeros((multi, 3, 3), dtype='intc')
translation = np.zeros((multi, 3), dtype='double')
# Get symmetry operations
if magmoms is None:
dataset = get_symmetry_dataset(cell,
symprec=symprec,
angle_tolerance=angle_tolerance)
if dataset is None:
return None
else:
return {'rotations': dataset['rotations'],
'translations': dataset['translations'],
'equivalent_atoms': dataset['equivalent_atoms']}
else:
equivalent_atoms = np.zeros(len(magmoms), dtype='intc')
num_sym = spg.symmetry_with_collinear_spin(rotation,
translation,
equivalent_atoms,
lattice,
positions,
numbers,
magmoms,
symprec,
angle_tolerance)
_set_error_message()
if num_sym == 0:
return None
else:
return {'rotations': np.array(rotation[:num_sym],
dtype='intc', order='C'),
'translations': np.array(translation[:num_sym],
dtype='double', order='C'),
'equivalent_atoms': equivalent_atoms}
def get_symmetry(cell, symprec=1e-5, angle_tolerance=-1.0):
"""This gives crystal symmetry operations from a crystal structure.
Args:
cell: Crystal structrue given either in Atoms object or tuple.
In the case given by a tuple, it has to follow the form below,
(Lattice parameters in a 3x3 array (see the detail below),
Fractional atomic positions in an Nx3 array,
Integer numbers to distinguish species in a length N array,
(optional) Collinear magnetic moments in a length N array),
where N is the number of atoms.
Lattice parameters are given in the form:
[[a_x, a_y, a_z],
[b_x, b_y, b_z],
[c_x, c_y, c_z]]
symprec:
float: Symmetry search tolerance in the unit of length.
angle_tolerance:
float: Symmetry search tolerance in the unit of angle deg.
If the value is negative, an internally optimized routine
is used to judge symmetry.
Return:
dictionary: Rotation parts and translation parts.
'rotations': Gives the numpy 'intc' array of the rotation matrices.
'translations': Gives the numpy 'double' array of fractional
translations with respect to a, b, c axes.
"""
_set_no_error()
lattice, positions, numbers, magmoms = _expand_cell(cell)
if lattice is None:
return None
multi = 48 * len(positions)
rotation = np.zeros((multi, 3, 3), dtype='intc')
translation = np.zeros((multi, 3), dtype='double')
# Get symmetry operations
if magmoms is None:
dataset = get_symmetry_dataset(cell,
symprec=symprec,
angle_tolerance=angle_tolerance)
if dataset is None:
return None
else:
return {
'rotations': dataset['rotations'],
'translations': dataset['translations'],
'equivalent_atoms': dataset['equivalent_atoms']
}
else:
equivalent_atoms = np.zeros(len(magmoms), dtype='intc')
num_sym = spg.symmetry_with_collinear_spin(rotation, translation,
equivalent_atoms, lattice,
positions, numbers, magmoms,
symprec, angle_tolerance)
_set_error_message()
if num_sym == 0:
return None
else:
return {
'rotations':
np.array(rotation[:num_sym], dtype='intc', order='C'),
'translations':
np.array(translation[:num_sym], dtype='double', order='C'),
'equivalent_atoms':
equivalent_atoms
}
