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, mapping_table = 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.")
print("Probably some atoms are overwrapped. "
"The mapping table is give below.")
print(mapping_table)
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, mapping_table = trim_cell(
trim_frame, sur_cell, symprec)
num_satom = supercell.get_number_of_atoms()
num_uatom = unitcell.get_number_of_atoms()
multi = num_satom // num_uatom
if multi != determinant(self._supercell_matrix):
print("Supercell creation failed.")
print("Probably some atoms are overwrapped. "
"The mapping table is give below.")
print(mapping_table)
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(num_uatom) * 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 _primitive_cell(self, supercell):
trimed_cell, p2s_map, mapping_table = 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 _create_supercell(self, unitcell, symprec):
mat = self._supercell_matrix
if self._is_old_style:
P = None
multi = self._get_surrounding_frame(mat)
# trim_fram is to trim overlapping atoms.
trim_frame = np.array([
mat[0] / float(multi[0]), mat[1] / float(multi[1]),
mat[2] / float(multi[2])
])
else:
# In the new style, it is unnecessary to trim atoms,
if (np.diag(np.diagonal(mat)) != mat).any():
snf = SNF3x3(mat)
snf.run()
P = snf.P
multi = np.diagonal(snf.A)
else:
P = None
multi = np.diagonal(mat)
trim_frame = np.eye(3)
sur_cell, u2sur_map = self._get_simple_supercell(unitcell, multi, P)
trimmed_cell_ = _trim_cell(trim_frame, sur_cell, symprec)
if trimmed_cell_:
supercell, sur2s_map, mapping_table = trimmed_cell_
else:
return False
num_satom = supercell.get_number_of_atoms()
num_uatom = unitcell.get_number_of_atoms()
N = num_satom // num_uatom
if N != determinant(self._supercell_matrix):
print("Supercell creation failed.")
print("Probably some atoms are overwrapped. "
"The mapping table is give below.")
print(mapping_table)
PhonopyAtoms.__init__(self)
else:
PhonopyAtoms.__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(num_uatom) * N
self._u2u_map = {j: i for i, j in enumerate(self._u2s_map)}
self._s2u_map = np.array(u2sur_map)[sur2s_map] * N
def _primitive_cell(self, supercell):
trimed_cell, p2s_map, mapping_table = 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 _create_supercell(self, unitcell, symprec):
mat = self._supercell_matrix
if self._is_old_style:
P = None
multi = self._get_surrounding_frame(mat)
# trim_fram is to trim overlapping atoms.
trim_frame = np.array([mat[0] / float(multi[0]),
mat[1] / float(multi[1]),
mat[2] / float(multi[2])])
else:
# In the new style, it is unnecessary to trim atoms,
if (np.diag(np.diagonal(mat)) != mat).any():
snf = SNF3x3(mat)
snf.run()
P = snf.P
multi = np.diagonal(snf.A)
else:
P = None
multi = np.diagonal(mat)
trim_frame = np.eye(3)
sur_cell, u2sur_map = self._get_simple_supercell(unitcell, multi, P)
trimmed_cell_ = _trim_cell(trim_frame, sur_cell, symprec)
if trimmed_cell_:
supercell, sur2s_map, mapping_table = trimmed_cell_
else:
return False
num_satom = supercell.get_number_of_atoms()
num_uatom = unitcell.get_number_of_atoms()
N = num_satom // num_uatom
if N != determinant(self._supercell_matrix):
print("Supercell creation failed.")
print("Probably some atoms are overwrapped. "
"The mapping table is give below.")
print(mapping_table)
PhonopyAtoms.__init__(self)
else:
PhonopyAtoms.__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(num_uatom) * N
self._u2u_map = {j: i for i, j in enumerate(self._u2s_map)}
self._s2u_map = np.array(u2sur_map)[sur2s_map] * N
