coor_monomer2 = np.array(
[rotate_vector(coor, [0.0, 0.0, 0.0]) for coor in coor_monomer2])
coor_monomer2[:, 0] += 4.0 # monomers separation
coor_monomer2[:, 1] += 0.0 # monomers separation
coor_monomer2[:, 2] += 0.0 # monomers separation
coordinates = ethene + coor_monomer2.tolist()
symbols_dimer = symbols * 2
dimer = Structure(coordinates=coordinates,
symbols=symbols_dimer,
charge=0,
multiplicity=1)
print(dimer.get_xyz())
diabatization_scheme = [
# {'method': 'ER', 'states': [1, 2, 3, 4]}, # in order with respect to selected states
{
'method': 'DQ',
'states': [1, 2, 3, 4],
'parameters': 0.0
}
]
# create Q-Chem input
qc_input = QchemInput(
dimer,
jobtype='sp',
exchange='hf',
if args.show_plot:
txt_input = create_qchem_input(mol,
jobtype='freq',
method='b3lyp',
basis='cc-pVDZ')
parsed_data = get_output_from_qchem(txt_input,
processors=4,
force_recalculation=False,
parser=basic_frequencies)
energy = parsed_data['energy']
data_for_plot.append(
[d, (energy - energy_i) * hartree_to_kcalmol,
energy2]) # kcal/mol
f.write(
mol.get_xyz(title='{:8.5f} kcal/mol rmsd: {:10.8f}\n'.format(
energy2, rmsd)))
f2.write(
mol.get_xyz(title='{:8.5f} kcal/mol rmsd: {:10.8f}\n'.format(
energy2, rmsd)))
if args.show_plot:
import matplotlib.pyplot as plt
plt.plot(np.array(data_for_plot)[:, 0], np.array(data_for_plot)[:, 1:])
plt.show()
f.close()
f2.close()