def test_rotor_symmetry_determination(self):
"""
Test that the correct symmetry number is determined for rotor potential scans.
"""
path1 = os.path.join(os.path.dirname(os.path.abspath(__file__)), 'data', 'NCC_NRotor.out')
path2 = os.path.join(os.path.dirname(os.path.abspath(__file__)), 'data', 'NCC_CRotor.out')
scan_log1 = QChemLog(path1)
scan_log2 = QChemLog(path2)
v_list1, angle = scan_log1.load_scan_energies()
v_list2, angle = scan_log2.load_scan_energies()
symmetry1 = determine_rotor_symmetry(energies=v_list1, label='NCC', pivots=[])
symmetry2 = determine_rotor_symmetry(energies=v_list2, label='NCC', pivots=[])
self.assertEqual(symmetry1, 1)
self.assertEqual(symmetry2, 3)
def sampling_along_torsion(symbols,
cart_coords,
mode,
internal_object,
conformer,
int_freq,
rotors_dict,
scan_res,
path,
thresh,
ncpus,
charge=None,
multiplicity=None,
rem_variables_dict=None,
gen_basis="",
is_QM_MM_INTERFACE=None,
QM_USER_CONNECT=None,
QM_ATOMS=None,
force_field_params=None,
fixed_molecule_string=None,
opt=None,
label=None):
logging.info('Sampling Mode {}'.format(mode))
XyzDictOfEachMode = {}
EnergyDictOfEachMode = {}
ModeDictOfEachMode = {}
# Extract rotor information
pivots = rotors_dict[mode]['pivots']
top = rotors_dict[mode]['top']
scan = rotors_dict[mode]['scan']
# Determine sampling step size
step_size = np.pi / (180 / scan_res)
# Save information of this mode
ModeDictOfEachMode['mode'] = 'tors'
ModeDictOfEachMode['M'] = conformer.get_internal_reduced_moment_of_inertia(
pivots, top) * constants.Na * 1e23 # in amu*angstrom^2
ModeDictOfEachMode['K'] = (int_freq *
(2 * np.pi * constants.c * 100))**2 # in 1/s^2
ModeDictOfEachMode['step_size'] = step_size # in radian
# Create the unit vector, qk, for displacement along the kth bond torsion
n_rotors = len(rotors_dict)
internal = copy.deepcopy(internal_object)
scan_indices = internal.B_indices[-n_rotors:]
torsion_ind = len(internal.B_indices) - n_rotors + scan_indices.index(
[ind - 1 for ind in scan])
B = internal.B
nrow = B.shape[0]
qk = np.zeros(nrow, dtype=int)
qk[torsion_ind] = 1
if internal.prim_coords[torsion_ind] > 0:
qk *= -1
# Start to sample 1-D PES
logging.info('direction = 1')
nsample = int(360 / scan_res) + 1
initial_geometry = cart_coords.copy()
cart_coords = initial_geometry.copy()
fail_in_torsion_sampling = False
for sample in range(nsample):
xyz = getXYZ(symbols, cart_coords)
file_name = 'tors_{}_{}'.format(mode, sample)
# Calculate electronic energy of each sampling point, and save the result
if is_QM_MM_INTERFACE:
e_elec = get_electronic_energy(xyz, path, file_name, ncpus, charge,
multiplicity, rem_variables_dict,
gen_basis, is_QM_MM_INTERFACE,
QM_USER_CONNECT, QM_ATOMS,
force_field_params,
fixed_molecule_string, opt)
else:
e_elec = get_electronic_energy(xyz, path, file_name, ncpus, charge,
multiplicity, rem_variables_dict,
gen_basis)
XyzDictOfEachMode[sample] = xyz
# Take the electronic energy of stationary point as reference energy, min_elect
if sample == 0:
EnergyDictOfEachMode[sample] = 0
min_elect = e_elec
else:
logging.info('ngrid = {}'.format(sample))
EnergyDictOfEachMode[sample] = e_elec - min_elect
# Check if this mode is a high-barrier hindered rotation
if e_elec - min_elect > thresh:
# Treat this mode as a vibrational normal mode
fail_in_torsion_sampling = True
logging.info(
'\n***********************************************************************'
)
logging.info(
'Since the torsional barrier of mode {} is higher than {} hartree.'
.format(mode, thresh))
logging.info(
'This mode will be treated as vibrational mode later on.')
logging.info(
'***********************************************************************\n'
)
return {}, {}, {}, min_elect
# Update cartesian coordinate of each sampling point
cart_coords += internal.transform_int_step(
(qk * step_size).reshape(-1, )) * BOHR2ANG
# Determine the symmetry number of this internal rotation, and save the result
if fail_in_torsion_sampling is False:
v_list = [
i * (constants.E_h * constants.Na)
for i in EnergyDictOfEachMode.values()
] # in J/mol
symmetry_number = determine_rotor_symmetry(v_list, label, pivots)
# symmetry_number = 3
logging.info('\n')
ModeDictOfEachMode['symmetry_number'] = symmetry_number
return XyzDictOfEachMode, EnergyDictOfEachMode, ModeDictOfEachMode, min_elect