def __init__(self,
txyz_input_file,
key_input_file,
force_field_file,
supercell_matrix=np.identity(3),
primitive_matrix=np.identity(3),
displacement_distance=0.01,
show_log=False,
show_progress=False,
use_NAC=False,
symmetrize=True):
"""
Experimental class to use Tinker to calculate forces, can be used
as an example to how to expand phonoLAMMPS to other software
:param txyz_input_file: TXYZ input file name (see example)
:param supercell_matrix: 3x3 matrix supercell
:param primitive cell: 3x3 matrix primitive cell
:param displacement_distance: displacement distance in Angstroms
:param show_log: set true to display lammps log info
:param show_progress: set true to display progress of calculation
:param use_NAC: set true to use Non-Analytical corrections or not
:param symmetrize: set true to use symmetrization of the force constants
"""
self._structure = get_structure_from_txyz(txyz_input_file,
key_input_file)
self._txyz_input_file = txyz_input_file
self._supercell_matrix = supercell_matrix
self._primitive_matrix = primitive_matrix
self._displacement_distance = displacement_distance
self._show_log = show_log
self._show_progress = show_progress
self._symmetrize = symmetrize
self._NAC = use_NAC
self._force_constants = None
self._data_set = None
self.units = 'tinker'
self.force_field = force_field_file
if not self.units in unit_factors.keys():
print('Units style not supported, use: {}'.format(
unit_factors.keys()))
exit()
print(err)
print('Something wrong in forces calculation!')
exit()
# print(output)
os.unlink(tinker_input_file.name)
os.unlink(tinker_key_file.name)
forces = parse_tinker_forces(output) * unit_factors[self.units]
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)