def get_force_constants(self):
"""
calculate the force constants with phonopy using lammps to calculate forces
:return: ForceConstants type object containing force constants
"""
if self._force_constants is None:
phonon = get_phonon(self._structure,
setup_forces=False,
super_cell_phonon=self._supercell_matrix)
phonon.get_displacement_dataset()
phonon.generate_displacements(distance=self._displacement_distance)
cells_with_disp = phonon.get_supercells_with_displacements()
cells_with_disp = [
cell.get_positions() for cell in cells_with_disp
]
data_sets = phonon.get_displacement_dataset()
# Get forces from lammps
for i, cell in enumerate(cells_with_disp):
if self._show_progress:
print('displacement {} / {}'.format(
i + 1, len(cells_with_disp)))
forces = self.get_lammps_forces(cell)
data_sets['first_atoms'][i]['forces'] = forces
phonon.set_displacement_dataset(data_sets)
phonon.produce_force_constants()
self._force_constants = phonon.get_force_constants()
return self._force_constants
def get_force_constants(self, include_data_set=False):
"""
calculate the force constants with phonopy using lammps to calculate forces
:return: ForceConstants type object containing force constants
"""
if self._force_constants is None:
phonon = get_phonon(self._structure,
setup_forces=False,
super_cell_phonon=self._supercell_matrix,
primitive_matrix=self._primitive_matrix,
NAC=self._NAC,
symmetrize=self._symmetrize)
phonon.get_displacement_dataset()
phonon.generate_displacements(distance=self._displacement_distance)
cells_with_disp = phonon.get_supercells_with_displacements()
data_set = phonon.get_displacement_dataset()
# Check forces for non displaced supercell
forces_supercell = self.get_forces(phonon.get_supercell())
if np.max(forces_supercell) > 1e-1:
warnings.warn(
'Large atomic forces found for non displaced structure: '
'{}. Make sure your unit cell is properly optimized'.
format(np.max(forces_supercell)))
# Get forces from lammps
for i, cell in enumerate(cells_with_disp):
if self._show_progress:
print('displacement {} / {}'.format(
i + 1, len(cells_with_disp)))
forces = self.get_forces(cell)
data_set['first_atoms'][i]['forces'] = forces
phonon.set_displacement_dataset(data_set)
phonon.produce_force_constants()
self._force_constants = phonon.get_force_constants()
self._data_set = data_set
if include_data_set:
return [self._force_constants, self._data_set]
else:
return self._force_constants
def get_phonopy_phonon(self):
"""
Return phonopy phonon object with unitcell, primitive cell and
the force constants set.
:return:
"""
phonon = get_phonon(self._structure,
setup_forces=False,
super_cell_phonon=self._supercell_matrix,
primitive_matrix=self._primitive_matrix,
NAC=self._NAC,
symmetrize=self._symmetrize)
phonon.set_force_constants(self.get_force_constants())
return phonon
return forces
if __name__ == '__main__':
structure = get_structure_from_txyz('structure_wrap_min.txyz', 'structure.key')
print(structure)
print(structure.get_connectivity())
print(generate_VASP_structure(structure))
print(structure.get_scaled_positions())
print(structure.get_chemical_symbols())
phonon = get_phonon(structure,
setup_forces=False,
super_cell_phonon=[[2, 0, 0], [0, 2, 0], [0, 0, 2]],
NAC=False,
symmetrize=True)
phonon.get_displacement_dataset()
phonon.generate_displacements(distance=0.0001)
cells_with_disp = phonon.get_supercells_with_displacements()
print(cells_with_disp[0])
print(generate_VASP_structure(cells_with_disp[0]))
supercell_wd = rebuild_connectivity_tinker(structure,
cells_with_disp[0],
phonon.get_supercell_matrix())
print(generate_tinker_txyz_file(supercell_wd))
