def _set_phonon(self):
if self._supercell_matrix is None:
cell = sort_cell_by_symbols(
get_crystallographic_cell(self.get_cell()))
self._supercell_matrix = estimate_supercell_matrix(
cell,
max_num_atoms=self._max_num_atoms)
else:
cell = self.get_cell()
phonopy_cell = cell2atoms(cell)
self._phonon = Phonopy(phonopy_cell,
self._supercell_matrix,
primitive_matrix=self._primitive_matrix,
dynamical_matrix_decimals=14,
force_constants_decimals=14,
symprec=self._symmetry_tolerance)
self._phonon.generate_displacements(
distance=self._distance,
is_plusminus=self._displace_plusminus,
is_diagonal=self._displace_diagonal)
supercell = self._phonon.get_supercell()
displacements = self._phonon.get_displacements()
write_poscar(cell, filename="POSCAR-unitcell")
write_poscar_yaml(cell, filename="POSCAR-unitcell.yaml")
write_disp_yaml(displacements, supercell)
def _set_phonon_fc3(self):
cell = self.get_cell()
phonopy_cell = cell2atoms(cell)
self._phonon = Phonopy(phonopy_cell,
self._supercell_matrix,
primitive_matrix=self._primitive_matrix,
dynamical_matrix_decimals=14,
force_constants_decimals=14)
self._phonon_fc3 = Phono3py(phonopy_cell,
self._supercell_matrix,
primitive_matrix=self._primitive_matrix)
self._phonon_fc3.generate_displacements(distance=self._distance,
is_diagonal=self._is_diagonal)
supercell = self._phonon_fc3.get_supercell()
disp_dataset = self._phonon_fc3.get_displacement_dataset()
self._phonon.set_displacement_dataset(disp_dataset)
write_poscar(cell, "POSCAR-unitcell")
write_disp_yaml(self._phonon.get_displacements(),
supercell,
directions=self._phonon.get_displacement_directions())
write_disp_fc3_yaml(disp_dataset, supercell)
def _set_phonon(self):
cell = self.get_cell()
if self._supercell_matrix is None:
self._supercell_matrix = estimate_supercell_matrix(
cell,
max_num_atoms=self._max_num_atoms)
phonopy_cell = cell2atoms(cell)
self._phonon = Phonopy(phonopy_cell,
self._supercell_matrix,
primitive_matrix=self._primitive_matrix,
is_auto_displacements=False,
dynamical_matrix_decimals=14,
force_constants_decimals=14)
self._phonon.generate_displacements(
distance=self._distance,
is_plusminus=self._displace_plusminus,
is_diagonal=self._displace_diagonal)
supercell = self._phonon.get_supercell()
displacements = self._phonon.get_displacements()
write_poscar(cell, "POSCAR-unitcell")
write_disp_yaml(displacements, supercell)
