{
'method': 'DQ',
'states': [1, 2, 3, 4],
'parameters': 0.0
}
]
# create Q-Chem input
qc_input = QchemInput(
dimer,
jobtype='sp',
exchange='hf',
correlation='rasci',
ras_act=6,
ras_elec=4,
basis='sto-3g',
ras_spin_mult=1, # singlets only
ras_roots=8,
ras_do_hole=False,
ras_do_part=False,
ras_diabatization_states=[3, 4, 5, 6
], # adiabatic states selected for diabatization
ras_diabatization_scheme=diabatization_scheme,
)
print(qc_input.get_txt())
# get data from Q-Chem calculation
output, err, electronic_structure = get_output_from_qchem(
qc_input,
processors=4,
force_recalculation=False,
def create_qchem_input(*args, **kwargs):
return QchemInput(*args, **kwargs)
basis_custom_repo = trucate_basis(basis_custom_repo,
shells=['G', 'H', 'I', 'J', 'K'])
qc_input_s = QchemInput(
atom,
jobtype='sp',
exchange='hf',
correlation='rasci',
unrestricted='False',
thresh=14,
scf_convergence=11,
cis_convergence=9,
max_cis_cycles=150,
max_scf_cycles=100,
basis=basis_custom_repo,
ras_elec_alpha=active_spaces['singlet'][0][0],
ras_elec_beta=active_spaces['singlet'][0][1],
ras_act=active_spaces['singlet'][1],
ras_occ=active_spaces['singlet'][2],
ras_spin_mult=0,
ras_roots=10,
calc_soc=1,
n_frozen_core=0,
# ras_do_part=False,
set_iter=1000,
mem_total=15000,
mem_static=900)
qc_input_t = QchemInput(atom,
jobtype='sp',
exchange='hf',
energies = []
for dist in distances:
# generate molecule
molecule = Structure(coordinates=[[0.0, 0.0, 0.0], [0.0, 0.0, dist]],
symbols=['H', 'H'],
charge=0,
multiplicity=1)
# create qchem input
qc_input = QchemInput(molecule,
jobtype='sp',
exchange='hf',
correlation='rasci',
basis='sto-3g',
ras_act=2,
ras_elec=2,
ras_spin_mult=0,
ras_roots=2,
ras_do_part=False,
ras_do_hole=False)
# calculate and parse qchem output
data = get_output_from_qchem(
qc_input,
processors=4,
parser=parser_rasci,
store_full_output=True,
)
# store energies of excited states states in list
if_missing=basis_name.replace('cc-pC', 'cc-p'))
basis_custom_repo = trucate_basis(basis_custom_repo,
shells=['G', 'H', 'I', 'J', 'K'])
qc_input = QchemInput(molecule,
jobtype='sp',
exchange='hf',
correlation='rasci',
purecart='1111',
unrestricted='False',
thresh=14,
scf_convergence=8,
max_cis_cycles=150,
basis=basis_custom_repo,
ras_elec=active_space[0],
ras_act=active_space[1],
ras_occ=active_space[2],
ras_spin_mult=0,
ras_roots=2, # calculate 2 states
calc_soc=calc_soc,
set_iter=60,
# n_frozen_core=0,
mem_total=15000,
mem_static=200
)
# print(qc_input.get_txt())
try:
output = get_output_from_qchem(qc_input,
processors=4,
# create molecule
molecule = Structure(coordinates=ethene,
symbols=symbols,
charge=0,
multiplicity=1)
point_group = molecule.get_point_symmetry()
print('Point group: {}\n'.format(point_group))
# create Q-Chem input
qc_input = QchemInput(molecule,
jobtype='sp',
exchange='hf',
correlation='rasci',
ras_act=6,
ras_elec=6,
basis='6-311(2+,2+)G**',
ras_roots=10,
ras_do_hole=False,
ras_do_part=False)
# get data from Q-Chem calculation
output, electronic_structure = get_output_from_qchem(qc_input,
processors=4,
force_recalculation=False,
read_fchk=True,
parser=parser_rasci,
store_full_output=True)
# get plane from coordinates to determine orientation using the plane of the molecule
coordinates_mat = np.array(electronic_structure['structure'].get_coordinates())
from pyqchem.structure import Structure
from pyqchem.parsers.basic import basic_parser_qchem
from pyqchem.basis import get_basis_from_ccRepo
from pyqchem.basis import get_basis_from_BSE
# create molecule
molecule = Structure(coordinates=[[0.0, 0.0, 0.0000],
[0.0, 0.0, 1.5811]],
symbols=['Se', 'H'],
charge=-1,
multiplicity=1)
# Standard input using 6-31G basis
qc_input = QchemInput(molecule,
jobtype='sp',
exchange='hf',
basis='6-31G')
# print input
print(qc_input.get_txt())
output, electronic_structure = get_output_from_qchem(qc_input,
processors=4,
force_recalculation=False,
read_fchk=True,
parser=basic_parser_qchem,
store_full_output=False)
print('scf_energy 6-31G: ', output['scf_energy'])
ethene = Structure(coordinates=coordinates,
symbols=['C', 'C', 'H', 'H', 'H', 'H'],
charge=0,
multiplicity=1)
# create qchem input
qc_input = QchemInput(ethene,
jobtype='sp',
exchange='hf',
correlation='rasci',
basis='6-31G',
ras_act=4,
ras_elec=2,
ras_spin_mult=0,
ras_roots=2,
ras_do_part=False,
ras_do_hole=False,
# ras_srdft_spinpol=True,
ras_omega=400,
max_scf_cycles=100,
ras_srdft_cor='srPBE',
# ras_srdft_exc='srPBE'
)
# calculate and parse qchem output
data, ee = get_output_from_qchem(qc_input,
processors=3,
parser=parser_rasci,
read_fchk=True,
# store_full_output=True,
coor_monomer = [[0.6695, 0.0000, 0.0000], [-0.6695, 0.0000, 0.0000],
[1.2321, 0.9289, 0.0000], [1.2321, -0.9289, 0.0000],
[-1.2321, 0.9289, 0.0000], [-1.2321, -0.9289, 0.0000]]
symbols_monomer = ['C', 'C', 'H', 'H', 'H', 'H']
monomer = Structure(coordinates=coor_monomer,
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())
charge=-2,
multiplicity=1,
name='C')
basis_name = '6-31G**'
# RAS_CI calculation
qc_input_rasci = QchemInput(atom_c,
jobtype='sp',
exchange='hf',
correlation='rasci',
unrestricted=True,
thresh=14,
scf_convergence=8,
max_cis_cycles=150,
max_scf_cycles=100,
basis=basis_name,
ras_elec_alpha=3,
ras_elec_beta=1,
ras_act=4,
ras_occ=1,
ras_spin_mult=0,
ras_roots=8,
calc_soc=1,
n_frozen_core=0,
)
# CIS calculation
qc_input_cis = QchemInput(atom_c,
jobtype='sp',
exchange='b3lyp',
basis=basis_name,
energies = []
for dist in distances:
# generate molecule
molecule = Structure(coordinates=[[0.0, 0.0, 0.0], [0.0, 0.0, dist]],
symbols=['H', 'H'],
charge=0,
multiplicity=1)
# create qchem input
qc_input = QchemInput(molecule,
jobtype='sp',
exchange='b3lyp',
unrestricted=False,
basis='sto-3g',
cis_n_roots=4,
cis_convergence=14,
cis_singlets=True,
cis_triplets=True)
# calculate and parse qchem output
data = get_output_from_qchem(
qc_input,
processors=4,
parser=basic_cis,
store_full_output=True,
)
# store energies of excited states states in list
energies.append(
basis_custom_repo = trucate_basis(basis_custom_repo,
shells=['G', 'H', 'I', 'J', 'K'])
qc_input = QchemInput(atom,
jobtype='sp',
exchange='hf',
correlation='rasci',
unrestricted='False',
thresh=14,
scf_convergence=8,
max_cis_cycles=150,
max_scf_cycles=100,
basis=basis_custom_repo,
# ras_elec=active_space[0],
ras_elec_alpha=active_space[0][0],
ras_elec_beta=active_space[0][1],
ras_act=active_space[1],
ras_occ=active_space[2],
ras_spin_mult=0,
ras_roots=8, # calculate 5 states
calc_soc=1,
# n_frozen_core=0,
set_iter=1000,
mem_total=15000,
mem_static=900
)
try:
output = get_output_from_qchem(qc_input,
processors=4,
[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',
correlation='rasci',
ras_act=6,
ras_elec=6,
basis='sto-3g',
ras_roots=10,
ras_do_hole=False,
ras_do_part=False)
print(qc_input.get_txt())
# get data from Q-Chem calculation
output, electronic_structure = get_output_from_qchem(qc_input,
processors=4,
force_recalculation=False,
read_fchk=True,
parser=parser_rasci,
store_full_output=True)
symbols=['C', 'C', 'C', 'H', 'H', 'H', 'H', 'H', 'H'],
charge=0,
multiplicity=3)
basis_name = 'cc-pVDZ'
qc_input_rasci = QchemInput(
molecule,
jobtype='sp',
exchange='hf',
correlation='rasci',
unrestricted=False,
# thresh=14,
scf_convergence=8,
max_cis_cycles=100,
max_scf_cycles=100,
basis=basis_name,
ras_elec=6,
ras_act=5,
ras_occ=9,
ras_spin_mult=0,
ras_roots=4,
calc_soc=1,
n_frozen_core=0,
state_analysis=True,
set_iter=300,
)
output = get_output_from_qchem(
qc_input_rasci,
processors=4,
force_recalculation=False,