def find_structure_symmetry(structure,
method='spglib',
symprec=1e-5,
angle_tolerance=-1.0):
"""
Return the rotatiosn and translations which are possessed by the structure.
Examples::
>>> from qmpy.io import read
>>> from qmpy.analysis.symmetry import find_structure_symmetry
>>> structure = read('POSCAR')
>>> find_structure_symmetry(structure)
"""
# Get number of symmetry operations and allocate symmetry operations
multi = 48 * len(structure)
rotation = np.zeros((multi, 3, 3), dtype='intc')
translation = np.zeros((multi, 3))
cell = structure.cell.T.copy()
coords = structure.site_coords.copy()
numbers = np.array(structure.site_ids, dtype='intc')
# Get symmetry operations
magmoms = structure.magmoms
if not any(magmoms):
num_sym = spg.symmetry(rotation, translation, cell, coords, numbers,
symprec, angle_tolerance)
else:
num_sym = spg.symmetry_with_collinear_spin(rotation, translation, cell,
coords, numbers, magmoms,
symprec, angle_tolerance)
return rotation[:num_sym], translation[:num_sym]
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, 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')
positions = np.array([
np.dot(atom.pos, np.linalg.inv(np.transpose(bulk.cell)))
for atom in bulk
],
dtype='double',
order='C')
lattice = np.array(bulk.cell * bulk.scale, dtype='double', order='C')
numbers = np.array(
[periodic_table.symbols.index(atom.type) + 1 for atom in bulk],
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()
multi = 48 * len(bulk)
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()
# num_sym = spg.symmetry_with_collinear_spin(rotation,
# translation,
# lattice,
# positions,
# numbers,
# magmoms,
# symprec,
# angle_tolerance)
# else:
# num_sym = spg.symmetry(rotation,
# translation,
# lattice,
# positions,
# numbers,
# symprec,
# angle_tolerance)
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, 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(self):
"""
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 float64 array
of the translation vectors in scaled positions
"""
# Get number of symmetry operations and allocate symmetry operations
# multi = spg.multiplicity(cell, positions, numbers, symprec)
multi = 48 * self._structure.num_sites
rotation = np.zeros((multi, 3, 3), dtype=int)
translation = np.zeros((multi, 3))
num_sym = spg.symmetry(rotation, translation, self._lattice.transpose().copy(),
self._positions, self._numbers, self._symprec, self._angle_tol)
return (rotation[:num_sym], translation[:num_sym])
def find_structure_symmetry(structure, method='spglib',
symprec=1e-5, angle_tolerance=-1.0):
"""
Return the rotatiosn and translations which are possessed by the structure.
Examples::
>>> from qmpy.io import read
>>> from qmpy.analysis.symmetry import find_structure_symmetry
>>> structure = read('POSCAR')
>>> find_structure_symmetry(structure)
"""
# Get number of symmetry operations and allocate symmetry operations
multi = 48 * len(structure)
rotation = np.zeros((multi, 3, 3), dtype='intc')
translation = np.zeros((multi, 3))
cell = structure.cell.T.copy()
coords = structure.site_coords.copy()
numbers = np.array(structure.site_ids, dtype='intc')
# Get symmetry operations
magmoms = structure.magmoms
if not any(magmoms):
num_sym = spg.symmetry(rotation,
translation,
cell,
coords,
numbers,
symprec,
angle_tolerance)
else:
num_sym = spg.symmetry_with_collinear_spin(rotation,
translation,
cell,
coords,
numbers,
magmoms,
symprec,
angle_tolerance)
return rotation[:num_sym], translation[:num_sym]
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()}