print(len(electronic_structure['nato_coefficients_multi']))
# Just for testing
# electronic_structure['coefficients'] = electronic_structure['nato_coefficients']
# electronic_structure['mo_energies'] = electronic_structure['nato_occupancies']
print(len(electronic_structure['nato_coefficients_multi']))
print(len(electronic_structure['nato_occupancies_multi']))
print(electronic_structure['nato_occupancies_multi'])
# store original fchk info in file
es = deepcopy(electronic_structure)
es['coefficients'] = electronic_structure['nato_coefficients_multi'][1]
es['mo_energies'] = electronic_structure['nato_occupancies_multi'][1]
open('test.fchk', 'w').write(build_fchk(es))
# print(electronic_structure['nato_coefficients'])
range_f1 = range(0, 6)
range_f2 = range(6, 12)
mo_coeff_f1 = _set_zero_to_coefficients(
electronic_structure['basis'],
electronic_structure['nato_coefficients_multi'][1], range_f2)
# get symmetry classification
electronic_structure['coefficients'] = mo_coeff_f1
electronic_structure['mo_energies'] = electronic_structure['nato_occupancies']
# save test fchk file with new coefficients
molecule = Structure(coordinates=benzene_coordinates,
symbols=symbols,
charge=0,
multiplicity=1)
# define Q-Chem parameters
parameters = {'jobtype': 'sp', 'exchange': 'hf', 'basis': '6-31G'}
# create Q-Chem input
qc_input = create_qchem_input(molecule, **parameters)
# get data from Q-Chem calculation
output, parsed_fchk = get_output_from_qchem(qc_input,
processors=4,
force_recalculation=False,
read_fchk=True,
fchk_only=True)
# write .fchk file copy on disk (for checking purpose)
txt_fchk = build_fchk(parsed_fchk)
open('test_benzene.fchk', 'w').write(txt_fchk)
# get orbital type
orbital_types = get_orbital_classification(parsed_fchk,
center=[0.0, 0.0, 0.0],
orientation=[0.0, 0.0, 1.0])
# print results
print(' {:5} {:5} {:5}'.format('num', 'type', 'overlap'))
for i, ot in enumerate(orbital_types):
print('{:5}: {:5} {:5.3f}'.format(i + 1, ot[0], ot[1]))
benzene_coordinates = np.array(benzene_coordinates)
molecule = Structure(coordinates=benzene_coordinates,
symbols=symbols,
charge=0)
parameters = {'jobtype': 'sp', 'exchange': 'hf', 'basis': '6-31G'}
qc_input = create_qchem_input(molecule, **parameters)
_, _, fchk_data = get_output_from_qchem(qc_input,
processors=4,
force_recalculation=True,
read_fchk=True)
from pyqchem.file_io import build_fchk
open('test.fchk', 'w').write(build_fchk(fchk_data))
mo_coeff = _set_zero_to_coefficients(fchk_data['basis'],
fchk_data['coefficients'],
range(6, 12))
fchk_data['coefficients'] = mo_coeff
structure = fchk_data['structure']
print(structure.get_xyz())
txt_fchk = build_fchk(fchk_data)
open('test2.fchk', 'w').write(txt_fchk)
z_dist = structure.get_coordinates()[0][2]
orbital_type = get_orbital_classification(fchk_data,
print(opt_molecule.get_xyz())
basis_custom_repo = get_basis_from_ccRepo(molecule, 'cc-pVTZ')
qc_input = QchemInput(opt_molecule,
jobtype='sp',
exchange='b3lyp',
basis='sto-3g',
cis_n_roots=5,
cis_singlets=True,
cis_triplets=True,
calc_soc=1,
n_frozen_core=0,
)
print(qc_input.get_txt())
try:
output, electronic_structure = get_output_from_qchem(qc_input,
processors=4,
# parser=basic_cis,
read_fchk=True,
store_full_output=True,
)
except OutputError as e:
print(e.error_lines)
exit()
print(output)
open('benzo_2.fchk', 'w').write(build_fchk(electronic_structure))