def find_primitive(structure, symprec=1e-4, angle_tolerance=-1.0):
"""
A primitive cell in the input cell is searched and returned
as an object of Atoms class.
If no primitive cell is found, (None, None, None) is returned.
"""
cell = structure.cell.T.copy()
coords = np.array(structure.site_coords.copy(), dtype='double')
comps = structure.site_compositions
numbers = [ comps.index(c) for c in comps ]
numbers = np.array(numbers*4, dtype='intc')
num_atom_prim = spg.primitive(cell,
coords,
numbers,
symprec,
angle_tolerance)
coords = wrap(coords)
comps = [ comps[i] for i in numbers ]
if num_atom_prim > 0:
structure.cell = cell.T
structure.set_nsites(num_atom_prim)
structure.site_coords = coords[:num_atom_prim]
structure.site_compositions = comps[:num_atom_prim]
return structure
else:
return structure
def find_primitive(structure, symprec=1e-4, angle_tolerance=-1.0):
"""
A primitive cell in the input cell is searched and returned
as an object of Atoms class.
If no primitive cell is found, (None, None, None) is returned.
"""
cell = structure.cell.T.copy()
coords = np.array(structure.site_coords.copy(), dtype='double')
comps = structure.site_compositions
numbers = [comps.index(c) for c in comps]
numbers = np.array(numbers * 4, dtype='intc')
num_atom_prim = spg.primitive(cell, coords, numbers, symprec,
angle_tolerance)
coords = wrap(coords)
comps = [comps[i] for i in numbers]
if num_atom_prim > 0:
structure.cell = cell.T
structure.set_nsites(num_atom_prim)
structure.site_coords = coords[:num_atom_prim]
structure.site_compositions = comps[:num_atom_prim]
return structure
else:
return structure
def find_primitive(bulk, symprec=1e-5, angle_tolerance=-1.0):
"""
A primitive cell in the input cell is searched and returned
as an object of Atoms class.
If no primitive cell is found, (None, None, None) is returned.
"""
# 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()
# lattice is transposed with respect to the definition of Atoms class
num_atom_prim = spg.primitive(lattice, positions, numbers, symprec,
angle_tolerance)
if num_atom_prim > 0:
return (lattice.T.copy(), positions[:num_atom_prim].copy(),
numbers[:num_atom_prim].copy())
else:
return None, None, None
def find_primitive(self):
"""
A primitive cell in the input cell is searched and returned
as an Structure object.
If no primitive cell is found, (None, None, None) is returned.
"""
# Atomic positions have to be specified by scaled positions for spglib.
positions = self._positions.copy()
lattice = self._lattice.T.copy()
numbers = self._numbers.copy()
# lattice is transposed with respect to the definition of Atoms class
num_atom_prim = spg.primitive(lattice, positions, numbers, self._symprec, self._angle_tol)
zs = numbers[:num_atom_prim]
species = [self._unique_species[i - 1] for i in zs]
if num_atom_prim > 0:
return Structure(lattice.T, species, positions[:num_atom_prim])
else:
#Not sure if we should return None or just return the full structure.
return None
def find_primitive(bulk, symprec=1e-5, angle_tolerance=-1.0):
"""
A primitive cell in the input cell is searched and returned
as an object of Atoms class.
If no primitive cell is found, (None, None, None) is returned.
"""
# 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')
# lattice is transposed with respect to the definition of Atoms class
num_atom_prim = spg.primitive(lattice,
positions,
numbers,
symprec,
angle_tolerance)
if num_atom_prim > 0:
return (np.array(lattice.T, dtype='double', order='C'),
np.array(positions[:num_atom_prim], dtype='double', order='C'),
np.array(numbers[:num_atom_prim], dtype='intc'))
else:
return None, None, None
