def energy_gradient(self, new_coords):
#Defining molecule
molecule = Structure(coordinates=[[0.0, 0.0, 0.0],
[0.0, 0.0, 0.9],
[0.0, 0.0, -0.9]],
symbols=['O', 'H', 'H'],
charge=0,
multiplicity=1)
#Preparing QCHEM input
qc_input1 = QchemInput(molecule,
jobtype='force',
exchange='hf',
basis='6-31G')
from pyqchem import get_output_from_qchem
from pyqchem.parsers.basic import basic_parser_qchem
import numpy as np
#Defining molecule
molecule = Structure(coordinates=[[0.0, 0.0, 0.0],
[0.0, 0.0, 0.9],
[0.0, 0.0, -0.9]],
symbols=['O', 'H', 'H'],
charge=0,
multiplicity=1)
#Preparing QCHEM input
qc_input1 = QchemInput(molecule,
jobtype='force',
exchange='hf',
basis='6-31G',
extra_rem_keywords={'multipole_field': 'x 0.001'},
extra_sections=['$multipole_field \n x 0.001 \n $end'])
string = '$multipole_field \n x 0.001 \n$end'
print(string)
exit()
print(type(qc_input1))
inp = qc_input1.get_txt()
qc_input_test =
print(inp)
exit()
qc_input2 = QchemInput(molecule,
jobtype='freq',
# 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)
symbols = ['C', 'O', 'C', 'C', 'C', 'C', 'C', 'H', 'C', 'H', 'H', 'H',
'C', 'C', 'C', 'C', 'C', 'H', 'C', 'H', 'H', 'H', 'C', 'H', 'H']
molecule = Structure(coordinates=coordinates,
symbols=symbols,
charge=0,
multiplicity=1)
basis_custom_repo = get_basis_from_ccRepo(molecule, 'cc-pVDZ')
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()
coordinates = [[0.0, 1.0, 0.0], [0.0, 0.0, 1.0], [0.0, 0.0, -1.0]]
symbols = ['O', 'H', 'H']
molecule = Structure(coordinates=coordinates,
symbols=symbols,
charge=0,
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'])
[ 0.3711605704, 1.0377672206, 0.0000000000],
[-0.5903438458, -0.0311449516, 0.0000000000]]
symbols = ['C', 'H', 'N']
molecule = Structure(coordinates=coordinates,
symbols=symbols,
charge=0,
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'])
[ 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())
[-0.53741536, -3.05918866, 0.04995793],
[-2.14073783, -2.12969357, 0.04016267],
[-0.39112115, -0.95974916, 0.00012984],
[0.67884827, -0.96181542, -0.00769025],
[-1.15875076, 0.37505495, -0.02522296],
[-0.62213437, 1.30041753, -0.05065831],
[-2.51391203, 0.37767199, -0.01531698],
[-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],
self._conn.close()
return self._calculation_data
@calculation_data.setter
def calculation_data(self, calculation_data):
self._conn = sqlite3.connect(self._calculation_data_filename)
for key, value in calculation_data.items():
self._conn.execute(
"INSERT or REPLACE into DATA_TABLE (input_hash, parser, qcdata) VALUES (?, ?, ?)",
(key[0], key[1], pickle.dumps(value, protocol=2)))
self._conn.commit()
self._conn.close()
if __name__ == '__main__':
a = SqlCache()
b = SqlCache()
#b.redefine_calculation_data_filename('calculation_data2.db')
from pyqchem import QchemInput, Structure
input = QchemInput(Structure(coordinates=[[0, 0, 0]], symbols=['X']))
b.store_calculation_data(input, 'key1', {'entry1': 454, 'entry2': 2323})
data = b.retrieve_calculation_data(input, 'key1')
print(data)
[ 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())
# Simple single point calculation
from pyqchem import get_output_from_qchem, QchemInput, Structure
from pyqchem.parsers.basic import basic_parser_qchem
import numpy as np
molecule = Structure(coordinates=[[0.0, 0.0, 0.0],
[0.0, 0.0, 0.9]],
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 x_dist in scan_range:
water = [[x_dist, 0.00000000e+00, 2.40297090e-01],
[-1.43261539e+00, -1.75444785e-16, -9.61188362e-01],
[1.43261539e+00, 1.75444785e-16, -9.61188362e-01]]
water = np.array(water) * 0.529177249
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']]
symbols = ['O', 'H', 'H']
molecule = Structure(coordinates=coordinates,
symbols=symbols,
charge=0,
multiplicity=1)
print('Initial structure')
print(molecule)
# optimization
qc_input = QchemInput(molecule,
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, electronic_structure = get_output_from_qchem(
qc_input, processors=4, parser=basic_optimization, read_fchk=True)
opt_molecule = parsed_data['optimized_molecule']
print('Optimized structure')
print(opt_molecule)
# frequencies calculation
qc_input = QchemInput(opt_molecule,
jobtype='freq',
}, {
'atoms': [1, 3],
'value': 0.9
}],
'bend': [{
'atoms': [2, 1, 3],
'value': 110.0
}]
}
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')
]
molecule = Structure(coordinates=coordinates,
symbols=symbols,
charge=0,
multiplicity=1)
#print(molecule.get_xyz())
# draw_molecule(molecule)
print('Initial structure')
print(molecule)
qc_input_hf = QchemInput(molecule,
unrestricted=True,
jobtype='sp',
exchange='hf',
basis='sto-3g')
#print(qc_input.get_txt())
parsed_data, electronic_structure = get_output_from_qchem(
qc_input_hf,
processors=4,
force_recalculation=False,
# parser=rasci,
read_fchk=True,
store_full_output=True,
)
# create qchem input
qc_input = QchemInput(
range_f1 = range(len(coor_monomer1))
range_f2 = range(len(coor_monomer1), len(coordinates))
print('Dimer structure')
print(dimer)
# RASCI qchem input
qc_input = QchemInput(
dimer,
unrestricted=False,
jobtype='sp',
exchange='hf',
correlation='rasci',
basis='sto-3g',
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,
charge=0,
multiplicity=1)
methane_mol = get_geometry_from_pubchem('methane')
ammonia_mol = get_geometry_from_pubchem('ammonia')
water_mol = get_geometry_from_pubchem('water')
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,