def standardize_cell(bulk,
to_primitive=0,
no_idealize=0,
symprec=1e-5,
angle_tolerance=-1.0):
"""
Return standardized cell
"""
# Atomic positions have to be specified by scaled positions for spglib.
num_atom = bulk.get_number_of_atoms()
lattice = np.array(bulk.get_cell().T, dtype='double', order='C')
pos = np.zeros((num_atom * 4, 3), dtype='double')
pos[:num_atom] = bulk.get_scaled_positions()
numbers = np.zeros(num_atom * 4, dtype='intc')
numbers[:num_atom] = np.array(bulk.get_atomic_numbers(), dtype='intc')
num_atom_std = spg.standardize_cell(lattice,
pos,
numbers,
num_atom,
to_primitive,
no_idealize,
symprec,
angle_tolerance)
return (np.array(lattice.T, dtype='double', order='C'),
np.array(pos[:num_atom_std], dtype='double', order='C'),
np.array(numbers[:num_atom_std], dtype='intc'))
def standardize_cell(cell,
to_primitive=0,
no_idealize=0,
symprec=1e-5,
angle_tolerance=-1.0):
"""
Return standardized cell
"""
lattice, _positions, _numbers, _ = _expand_cell(cell)
# Atomic positions have to be specified by scaled positions for spglib.
num_atom = len(_positions)
positions = np.zeros((num_atom * 4, 3), dtype='double', order='C')
positions[:num_atom] = _positions
numbers = np.zeros(num_atom * 4, dtype='intc')
numbers[:num_atom] = _numbers
num_atom_std = spg.standardize_cell(lattice, positions, numbers, num_atom,
to_primitive, no_idealize, symprec,
angle_tolerance)
return (np.array(lattice.T, dtype='double', order='C'),
np.array(positions[:num_atom_std], dtype='double',
order='C'), np.array(numbers[:num_atom_std],
dtype='intc'))
def standardize_cell(cell,
to_primitive=0,
no_idealize=0,
symprec=1e-5,
angle_tolerance=-1.0):
"""
Return standardized cell
"""
lattice, _positions, _numbers, _ = _expand_cell(cell)
# Atomic positions have to be specified by scaled positions for spglib.
num_atom = len(_positions)
positions = np.zeros((num_atom * 4, 3), dtype='double', order='C')
positions[:num_atom] = _positions
numbers = np.zeros(num_atom * 4, dtype='intc')
numbers[:num_atom] = _numbers
num_atom_std = spg.standardize_cell(lattice,
positions,
numbers,
num_atom,
to_primitive,
no_idealize,
symprec,
angle_tolerance)
return (np.array(lattice.T, dtype='double', order='C'),
np.array(positions[:num_atom_std], dtype='double', order='C'),
np.array(numbers[:num_atom_std], dtype='intc'))
def standardize_cell(bulk,
to_primitive=0,
no_idealize=0,
symprec=1e-5,
angle_tolerance=-1.0):
"""
Return standardized cell
"""
# Atomic positions have to be specified by scaled positions for spglib.
num_atom = bulk.get_number_of_atoms()
lattice = np.array(bulk.get_cell().T, dtype='double', order='C')
pos = np.zeros((num_atom * 4, 3), dtype='double')
pos[:num_atom] = bulk.get_scaled_positions()
numbers = np.zeros(num_atom * 4, dtype='intc')
numbers[:num_atom] = np.array(bulk.get_atomic_numbers(), dtype='intc')
num_atom_std = spg.standardize_cell(lattice,
pos,
numbers,
num_atom,
to_primitive,
no_idealize,
symprec,
angle_tolerance)
return (np.array(lattice.T, dtype='double', order='C'),
np.array(pos[:num_atom_std], dtype='double', order='C'),
np.array(numbers[:num_atom_std], dtype='intc'))
def standardize_cell(cell,
to_primitive=False,
no_idealize=False,
symprec=1e-5,
angle_tolerance=-1.0):
"""Return standardized cell.
Args:
cell, symprec, angle_tolerance:
See the docstring of get_symmetry.
to_primitive:
bool: If True, the standardized primitive cell is created.
no_idealize:
bool: If True, it is disabled to idealize lengths and angles of
basis vectors and positions of atoms according to crystal
symmetry.
Return:
The standardized unit cell or primitive cell is returned by a tuple of
(lattice, positions, numbers).
If it fails, None is returned.
"""
_set_no_error()
lattice, _positions, _numbers, _ = _expand_cell(cell)
if lattice is None:
return None
# Atomic positions have to be specified by scaled positions for spglib.
num_atom = len(_positions)
positions = np.zeros((num_atom * 4, 3), dtype='double', order='C')
positions[:num_atom] = _positions
numbers = np.zeros(num_atom * 4, dtype='intc')
numbers[:num_atom] = _numbers
num_atom_std = spg.standardize_cell(lattice,
positions,
numbers,
num_atom,
to_primitive * 1,
no_idealize * 1,
symprec,
angle_tolerance)
_set_error_message()
if num_atom_std > 0:
return (np.array(lattice.T, dtype='double', order='C'),
np.array(positions[:num_atom_std], dtype='double', order='C'),
np.array(numbers[:num_atom_std], dtype='intc'))
else:
return None
def standardize_cell(cell,
to_primitive=False,
no_idealize=False,
symprec=1e-5,
angle_tolerance=-1.0):
"""Return standardized cell.
Args:
cell, symprec, angle_tolerance:
See the docstring of get_symmetry.
to_primitive:
bool: If True, the standardized primitive cell is created.
no_idealize:
bool: If True, it is disabled to idealize lengths and angles of
basis vectors and positions of atoms according to crystal
symmetry.
Return:
The standardized unit cell or primitive cell is returned by a tuple of
(lattice, positions, numbers).
If it fails, None is returned.
"""
_set_no_error()
lattice, _positions, _numbers, _ = _expand_cell(cell)
if lattice is None:
return None
# Atomic positions have to be specified by scaled positions for spglib.
num_atom = len(_positions)
positions = np.zeros((num_atom * 4, 3), dtype='double', order='C')
positions[:num_atom] = _positions
numbers = np.zeros(num_atom * 4, dtype='intc')
numbers[:num_atom] = _numbers
num_atom_std = spg.standardize_cell(lattice,
positions,
numbers,
num_atom,
to_primitive * 1,
no_idealize * 1,
symprec,
angle_tolerance)
_set_error_message()
if num_atom_std > 0:
return (np.array(lattice.T, dtype='double', order='C'),
np.array(positions[:num_atom_std], dtype='double', order='C'),
np.array(numbers[:num_atom_std], dtype='intc'))
else:
return None
