qc_input = QchemInput(
molecule,
jobtype='opt',
exchange='hf',
basis='sto-3g',
geom_opt_tol_gradient=300,
geom_opt_tol_energy=100,
geom_opt_tol_displacement=1200,
geom_opt_max_cycles=50, # reduce this number to test not convergence case
geom_opt_constrains=
constrains # comment/uncomment this line to use or not constrains
)
try:
parsed_data = get_output_from_qchem(qc_input,
processors=4,
parser=basic_optimization,
force_recalculation=False)
opt_molecule = parsed_data['optimized_molecule']
print('Optimized structure')
print(opt_molecule)
print('Final energy:', parsed_data['energy'])
except OutputError as e:
print(e.error_lines)
parsed_data = basic_optimization(e.full_output)
print('Last structure')
print(parsed_data['optimization_steps'][-1]['molecule'])
print('Last energy:', parsed_data['optimization_steps'][-1]['energy'])
ras_act=4,
ras_elec=4,
# ras_occ=66,
ras_spin_mult=1, # singlets only
ras_roots=10, # calculate 8 states
ras_do_hole=True,
ras_do_part=True,
# ras_srdft_cor='srpbe',
# ras_srdft_exc='srpbe',
# ras_omega=300,
set_iter=60)
parsed_data, electronic_structure = get_output_from_qchem(
qc_input,
processors=4,
force_recalculation=False,
parser=rasci_parser,
read_fchk=True,
store_full_output=True)
print('final structure')
print(electronic_structure['structure'])
# Analysis of diabatic states to use in diabatization
print('\nAdiabatic states to use in diabatization (1e, max_jump 4)')
list_diabatic = []
for i, state in enumerate(parsed_data['excited_states']):
ratio = get_ratio_of_condition(state, n_electron=1, max_jump=4)
if ratio > 0.1:
mark = 'X'
# molecule
ethene = [[0.0, 0.0000, 0.65750], [0.0, 0.0000, -0.65750],
[0.0, 0.92281, 1.22792], [0.0, -0.92281, 1.22792],
[0.0, -0.92281, -1.22792], [0.0, 0.92281, -1.22792]]
symbols = ['C', 'C', 'H', 'H', 'H', 'H']
# create molecule
molecule = Structure(coordinates=ethene,
symbols=symbols,
charge=0,
multiplicity=1)
# create Q-Chem input
qc_input = QchemInput(molecule, jobtype='sp', exchange='hf', basis='sto-3g')
print(qc_input.get_txt())
# get data from Q-Chem calculation
output = get_output_from_qchem(qc_input,
processors=1,
force_recalculation=True,
remote=remote_data_pc,
scratch='/Users/abel/Scratch/export/',
parser=basic_parser_qchem)
# Get data
print('OUTPUT')
print(output)
print('the energy is: ', output['scf_energy'])
ncols_remaining -= ncols_block
sline = line.split()
colmin, colmax = int(sline[0]) - 1, int(sline[-1])
line = next(contents_iter)
# iterate over the rows
for row in range(3*N):
sline = line.split()
rowidx = int(sline[0]) - 1
hessian_scf[rowidx, colmin:colmax] = list(map(float, sline[1:]))
line = next(contents_iter, 'break')
return hessian_scf
#Running calcs
#Getting gradient
output_grad = get_output_from_qchem(qc_input1, processors=4)
contents_splitlines = output_grad.splitlines()
gradient = get_gradient(contents_splitlines, 3)
print(gradient)
#Getting hessian
output_hess = get_output_from_qchem(qc_input2, processors=4)
contents_splitlines2 = output_hess.splitlines()
hessian = get_hessian(contents_splitlines2, 3)
print(hessian)
#Getting Energy and Dipole moment
parsed_data = basic_parser_qchem(output_grad)
print(parsed_data)
e = parsed_data['scf_energy']
print(e)
multiplicity=1)
# Transition state optimization
qc_input = QchemInput(molecule,
jobtype='ts',
exchange='hf',
basis='sto-3g',
geom_opt_tol_gradient=300,
geom_opt_tol_energy=100,
geom_opt_tol_displacement=1200,
geom_opt_max_cycles=50, # reduce this number to test not convergence case
)
opt_data, ee = get_output_from_qchem(qc_input,
processors=4,
parser=basic_optimization,
force_recalculation=False,
read_fchk=True,
store_full_output=True)
print('Transition state')
print(opt_data['optimized_molecule'])
# frequencies calculation
qc_input = QchemInput(opt_data['optimized_molecule'],
jobtype='freq',
exchange='hf',
basis='sto-3g',
sym_ignore=True,
symmetry=False,
scf_guess=ee['coefficients'])
qc_input = QchemInput(molecule,
jobtype='opt',
exchange='b3lyp',
basis='sto-3g',
geom_opt_tol_gradient=300,
geom_opt_tol_energy=100,
geom_opt_tol_displacement=1200,
geom_opt_max_cycles=50,
# n_frozen_core=0,
)
try:
parsed_data, electronic_structure = get_output_from_qchem(qc_input,
processors=4,
parser=basic_optimization,
read_fchk=True,
store_full_output=True
)
except OutputError as e:
print(e.error_lines)
exit()
opt_molecule = parsed_data['optimized_molecule']
print('Optimized molecule')
print(opt_molecule.get_xyz())
basis_custom_repo = get_basis_from_ccRepo(molecule, 'cc-pVTZ')
qc_input = QchemInput(opt_molecule,
jobtype='sp',
symbols=symbols_monomer,
charge=0,
multiplicity=1)
# optimization qchem input
qc_input = QchemInput(monomer,
jobtype='opt',
exchange='hf',
basis='sto-3g',
geom_opt_tol_gradient=300,
geom_opt_tol_energy=100,
geom_opt_coords=-1,
geom_opt_tol_displacement=1200)
parsed_data = get_output_from_qchem(qc_input,
processors=4,
parser=basic_optimization)
opt_monomer = parsed_data['optimized_molecule']
print('Optimized monomer structure')
print(opt_monomer)
# Build dimer from monomer
coor_monomer2 = np.array(opt_monomer.get_coordinates())
coor_monomer2[:, 2] += 6.0 # monomers separation
coordinates = opt_monomer.get_coordinates() + coor_monomer2.tolist()
symbols_dimer = symbols_monomer * 2
dimer = Structure(coordinates=coordinates,
multiplicity=1)
print('Initial structure')
print(molecule)
# Initial calculation with STO-3G basis
qc_input = QchemInput(
molecule,
jobtype='opt',
exchange='hf',
basis='sto-3g',
)
parsed_data, ee = get_output_from_qchem(qc_input,
processors=4,
parser=basic_optimization,
force_recalculation=False,
read_fchk=True)
opt_molecule = parsed_data['optimized_molecule']
print('Optimized structure')
print(opt_molecule)
print('Final energy:', parsed_data['energy'])
# Precise calculation with larger 6-31G basis using previous MO as guess
qc_input = QchemInput(opt_molecule,
jobtype='sp',
exchange='hf',
basis='6-31g',
basis2=ee['basis'],
symbols=symbols_monomer,
charge=0,
multiplicity=1)
# optimization qchem input
qc_input = QchemInput(monomer,
jobtype='opt',
exchange='hf',
basis='sto-3g',
geom_opt_tol_gradient=300,
geom_opt_tol_energy=100,
geom_opt_coords=-1,
geom_opt_tol_displacement=1200)
parsed_data = get_output_from_qchem(qc_input,
processors=4,
parser=basic_optimization)
opt_monomer = parsed_data['optimized_molecule']
print('Optimized monomer structure')
print(opt_monomer)
# Build dimer from monomer
coor_monomer2 = np.array(opt_monomer.get_coordinates())
coor_monomer2[:, 2] += 4.0 # monomers separation
coordinates = opt_monomer.get_coordinates() + coor_monomer2.tolist()
symbols_dimer = symbols_monomer * 2
dimer = Structure(coordinates=coordinates,
symbols=['O', 'H'],
charge=-1,
multiplicity=1)
# create qchem input
qc_input = QchemInput(molecule,
jobtype='sp',
exchange='hf',
basis='6-31G',
unrestricted=True)
# calculate and parse qchem output
data = get_output_from_qchem(qc_input,
processors=4,
force_recalculation=True,
parser=basic_parser_qchem,
)
print('scf energy', data['scf_energy'], 'H')
print('Orbital energies (H)')
print(' {:^10} {:^10}'.format('alpha', 'beta'))
for a, b in zip(data['orbital_energies']['alpha'], data['orbital_energies']['beta']):
print('{:10.3f} {:10.3f}'.format(a, b))
print('dipole moment:', data['multipole']['dipole_moment'], data['multipole']['dipole_units'])
print('quadrupole moment ({}):\n'.format(data['multipole']['quadrupole_units']),
np.array(data['multipole']['quadrupole_moment']))
print('octopole moment ({}):\n'.format(data['multipole']['octopole_units']),
molecule_water = Structure(coordinates=water,
symbols=['O', 'H', 'H'],
charge=0,
multiplicity=1)
qc_input = QchemInput(
molecule_water,
jobtype='freq',
exchange='hf',
basis='6-31G',
sym_ignore=True,
)
parsed_data, ee = get_output_from_qchem(qc_input,
parser=basic_frequencies,
read_fchk=True)
molecule_coor = np.array(ee['structure'].get_coordinates())
molecule_symbols = np.array(ee['structure'].get_symbols())
# print(' structure')
print('Final energy:', parsed_data['scf_energy'])
energies.append(parsed_data['scf_energy'])
modes = [np.array(m['displacement']) for m in parsed_data['modes']]
freqs = [m['frequency'] for m in parsed_data['modes']]
print('freqs: ', freqs)
frequencies.append(freqs)
sm = SymmetryModes(group='c2v',
coordinates=molecule_coor,
[-3.04726506, 1.30510083, -0.03293196],
[-3.05052841, -0.54769055, 0.01011971]],
symbols=['C', 'H', 'H', 'C', 'H', 'C', 'H', 'C', 'H', 'H'])
# create qchem input
qc_input = QchemInput(
molecule_cis,
jobtype='sp',
exchange='hf',
basis='sto-3g',
#sym_ignore=True
)
# calculate and parse qchem output
data_cis, ee_cis = get_output_from_qchem(qc_input,
read_fchk=True,
processors=4,
parser=basic_parser_qchem)
molecule_trans = Structure(
coordinates=[[-1.06908233, -2.13352097, -0.00725330],
[-0.53502155, -3.05996561, -0.04439369],
[-2.13778918, -2.13379901, 0.04533562],
[-0.39193053, -0.95978774, -0.02681816],
[0.67677629, -0.95950970, -0.07940766],
[-1.16057856, 0.37359983, 0.02664018],
[-2.22928521, 0.37332175, 0.07923299],
[-0.48342683, 1.54733308, 0.00707382],
[-1.01748758, 2.47377771, 0.04421474],
[0.58527987, 1.54761115, -0.04551805]],
symbols=['C', 'H', 'H', 'C', 'H', 'C', 'H', 'C', 'H', 'H'])
h2o2_mol = get_geometry_from_pubchem('h2o2')
for molecule, group in zip([h2o2_mol, sh6_mol, water_mol, dichloro_mol, methane_mol, ammonia_mol],
['c2', 'Oh', 'c2v', 'c2h', 'Td', 'c3v']):
qc_input = QchemInput(molecule,
jobtype='opt',
exchange='hf',
basis='sto-3g',
#geom_opt_tol_gradient=1,
#geom_opt_tol_energy=1,
#geom_opt_max_cycles=500,
)
parsed_data = get_output_from_qchem(qc_input, parser=basic_optimization, processors=6)
qc_input = QchemInput(parsed_data['optimized_molecule'],
jobtype='freq',
exchange='hf',
basis='sto-3g',
#sym_ignore=True,
)
print(molecule)
parsed_data, ee = get_output_from_qchem(qc_input, parser=basic_frequencies,
read_fchk=True, processors=6)
molecule_coor = np.array(ee['structure'].get_coordinates())
molecule_symbols = np.array(ee['structure'].get_symbols())
