def generate_freq_input(qoutfile,
qinfile,
basis_set="6-311++G*",
pcm_dielectric=None,
overwrite_inputs=None):
"""
Parses a QChem output file for ideal structure and then returns a QChem
input file for frequency calculations (to determine enthalpy and entropy).
:param qoutfile: Absolute path to the QChem output file (.out)
:param qinfile: Absolute path to the QChem input file (.in)
:return:
"""
output = QCOutput(qoutfile)
if len(output.data.get("molecule_from_optimized_geometry", [])) > 0:
mol = output.data["molecule_from_optimized_geometry"]
else:
try:
mol = output.data["molecule_from_last_geometry"]
except KeyError:
raise RuntimeError("No molecule to use as input")
qcinput = FreqSet(mol,
basis_set=basis_set,
pcm_dielectric=pcm_dielectric,
overwrite_inputs=overwrite_inputs)
qcinput.write_file(qinfile)
def test_pcm_init(self):
test_molecule = QCInput.from_file(os.path.join(test_dir, "new_qchem_files/pcm.qin")).molecule
test_FreqSet = FreqSet(molecule=test_molecule, pcm_dielectric=10.0)
self.assertEqual(
test_FreqSet.rem,
{
"job_type": "freq",
"gen_scfman": "true",
"basis": "def2-tzvppd",
"max_scf_cycles": "200",
"method": "wb97xd",
"scf_algorithm": "diis",
"xc_grid": "3",
"solvent_method": "pcm",
"symmetry": "false",
"sym_ignore": "true",
"resp_charges": "true",
},
)
self.assertEqual(
test_FreqSet.pcm,
{
"heavypoints": "194",
"hpoints": "194",
"radii": "uff",
"theory": "cpcm",
"vdwscale": "1.1",
},
)
self.assertEqual(test_FreqSet.solvent, {"dielectric": 10.0})
self.assertEqual(test_FreqSet.molecule, test_molecule)
def test_smd_init(self):
test_molecule = QCInput.from_file(
os.path.join(test_dir, "new_qchem_files/pcm.qin")).molecule
test_FreqSet = FreqSet(molecule=test_molecule, smd_solvent="water")
self.assertEqual(
test_FreqSet.rem,
{
"job_type": "freq",
"gen_scfman": "true",
"basis": "def2-tzvppd",
"max_scf_cycles": "100",
"method": "wb97xd",
"scf_algorithm": "diis",
"xc_grid": "3",
"thresh": "14",
"s2thresh": "16",
"solvent_method": "smd",
"ideriv": "1",
"symmetry": "false",
"sym_ignore": "true",
"resp_charges": "true",
},
)
self.assertEqual(test_FreqSet.smx, {"solvent": "water"})
self.assertEqual(test_FreqSet.molecule, test_molecule)
def test_init(self):
test_molecule = QCInput.from_file(os.path.join(test_dir, "new_qchem_files/pcm.qin")).molecule
test_FreqSet = FreqSet(molecule=test_molecule)
self.assertEqual(
test_FreqSet.rem,
{
"job_type": "freq",
"gen_scfman": "true",
"basis": "def2-tzvppd",
"max_scf_cycles": "200",
"method": "wb97xd",
"scf_algorithm": "diis",
"xc_grid": "3",
"symmetry": "false",
"sym_ignore": "true",
"resp_charges": "true",
},
)
self.assertEqual(test_FreqSet.pcm, {})
self.assertEqual(test_FreqSet.solvent, {})
self.assertEqual(test_FreqSet.molecule, test_molecule)