def get_forces(self, cell_with_disp):
"""
Calculate the forces of a supercell using tinker
:param cell_with_disp: supercell (PhonopyAtoms) from which determine the forces
:return array: numpy array matrix with forces of atoms [Natoms x 3]
"""
import tempfile
import subprocess
import os
from subprocess import PIPE
temp_file_name = tempfile.gettempdir() + '/tinker_temp' + '_' + str(
os.getpid())
# temp_file_name = 'test_calc'
supercell_wd = rebuild_connectivity_tinker(self._structure,
cell_with_disp,
self._supercell_matrix)
tinker_input_file = open(temp_file_name + '.txyz', mode='w')
tinker_input_file.write(generate_tinker_txyz_file(supercell_wd))
tinker_key_file = open(temp_file_name + '.key', mode='w')
tinker_key_file.write(generate_tinker_key_file(supercell_wd))
tinker_input_file.close()
tinker_key_file.close()
tinker_command = './testgrad ' + tinker_input_file.name + \
' ' + self.force_field + ' Y N N ' + ' -k ' + tinker_key_file.name
tinker_process = subprocess.Popen(tinker_command,
stdin=PIPE,
stderr=PIPE,
stdout=PIPE,
shell=True)
(output, err) = tinker_process.communicate()
tinker_process.wait()
if len(err.split()) != 0:
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
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))
print(generate_tinker_key_file(supercell_wd))
print(generate_VASP_structure(structure))
import tempfile
import subprocess
import os
from subprocess import PIPE
force_field = 'mm3'
temp_file_name = tempfile.gettempdir() + '/tinker_temp'+ '_' + str(os.getpid())