def _create_supercell(self, unitcell, symprec):
mat = self._supercell_matrix
frame = self._get_surrounding_frame(mat)
sur_cell, u2sur_map = self._get_simple_supercell(frame, unitcell)
# Trim the simple supercell by the supercell matrix
trim_frame = np.array([mat[0] / float(frame[0]),
mat[1] / float(frame[1]),
mat[2] / float(frame[2])])
supercell, sur2s_map = trim_cell(trim_frame,
sur_cell,
symprec)
multi = supercell.get_number_of_atoms() / unitcell.get_number_of_atoms()
if multi != determinant(self._supercell_matrix):
print "Supercell creation failed."
Atoms.__init__(self)
else:
Atoms.__init__(self,
numbers=supercell.get_atomic_numbers(),
masses=supercell.get_masses(),
magmoms=supercell.get_magnetic_moments(),
scaled_positions=supercell.get_scaled_positions(),
cell=supercell.get_cell(),
pbc=True)
self._u2s_map = np.arange(unitcell.get_number_of_atoms()) * multi
self._u2u_map = dict([(j, i) for i, j in enumerate(self._u2s_map)])
self._s2u_map = np.array(u2sur_map)[sur2s_map] * multi
def _create_supercell(self, unitcell, symprec):
mat = self._supercell_matrix
frame = self._get_surrounding_frame(mat)
sur_cell, u2sur_map = self._get_simple_supercell(frame, unitcell)
# Trim the simple supercell by the supercell matrix
trim_frame = np.array([
mat[0] / float(frame[0]), mat[1] / float(frame[1]),
mat[2] / float(frame[2])
])
supercell, sur2s_map = trim_cell(trim_frame, sur_cell, symprec)
multi = supercell.get_number_of_atoms() / unitcell.get_number_of_atoms(
)
if multi != determinant(self._supercell_matrix):
print "Supercell creation failed."
Atoms.__init__(self)
else:
Atoms.__init__(self,
numbers=supercell.get_atomic_numbers(),
masses=supercell.get_masses(),
magmoms=supercell.get_magnetic_moments(),
scaled_positions=supercell.get_scaled_positions(),
cell=supercell.get_cell(),
pbc=True)
self._u2s_map = np.arange(unitcell.get_number_of_atoms()) * multi
self._u2u_map = dict([(j, i) for i, j in enumerate(self._u2s_map)])
self._s2u_map = np.array(u2sur_map)[sur2s_map] * multi
def __init__( self, supercell, supercell_to_unitcell_map ):
Atoms.__init__( self,
numbers = supercell.get_atomic_numbers(),
masses = supercell.get_masses(),
scaled_positions = supercell.get_scaled_positions(),
cell = supercell.get_cell(),
pbc = True )
self.s2u_map = supercell_to_unitcell_map
def __init__(self, supercell, supercell_to_unitcell_map):
Atoms.__init__(self,
numbers = supercell.get_atomic_numbers(),
masses = supercell.get_masses(),
magmoms = supercell.get_magnetic_moments(),
scaled_positions = supercell.get_scaled_positions(),
cell = supercell.get_cell(),
pbc = True)
self.s2u_map = supercell_to_unitcell_map
def _primitive_cell(self, supercell):
trimed_cell, p2s_map = trim_cell(self.frame, supercell, self.symprec)
Atoms.__init__(self,
numbers=trimed_cell.get_atomic_numbers(),
masses=trimed_cell.get_masses(),
magmoms=trimed_cell.get_magnetic_moments(),
scaled_positions=trimed_cell.get_scaled_positions(),
cell=trimed_cell.get_cell(),
pbc=True)
self.p2s_map = p2s_map
def _primitive_cell(self, supercell):
trimed_cell, p2s_map = trim_cell(self._primitive_matrix, supercell,
self._symprec)
Atoms.__init__(self,
numbers=trimed_cell.get_atomic_numbers(),
masses=trimed_cell.get_masses(),
magmoms=trimed_cell.get_magnetic_moments(),
scaled_positions=trimed_cell.get_scaled_positions(),
cell=trimed_cell.get_cell(),
pbc=True)
self._p2s_map = np.array(p2s_map, dtype='intc')
def __primitive_cell(self, supercell):
trimed_cell, p2s_map = trim_cell( self.frame,
supercell,
self.symprec )
Atoms.__init__( self,
numbers = trimed_cell.get_atomic_numbers(),
masses = trimed_cell.get_masses(),
scaled_positions = trimed_cell.get_scaled_positions(),
cell = trimed_cell.get_cell(),
pbc = True )
self.p2s_map = p2s_map
def _primitive_cell(self, supercell):
trimed_cell, p2s_map = trim_cell(self._primitive_matrix,
supercell,
self._symprec)
Atoms.__init__(self,
numbers=trimed_cell.get_atomic_numbers(),
masses=trimed_cell.get_masses(),
magmoms=trimed_cell.get_magnetic_moments(),
scaled_positions=trimed_cell.get_scaled_positions(),
cell=trimed_cell.get_cell(),
pbc=True)
self._p2s_map = np.array(p2s_map, dtype='intc')
