def test_write_file_from_OptSet(self):
from pymatgen.io.qchem.sets import OptSet
odd_dict = loadfn(os.path.join(os.path.dirname(__file__), "odd.json"))
odd_mol = odd_dict["spec"]["_tasks"][0]["molecule"]
qcinp = OptSet(odd_mol)
qcinp.write_file(os.path.join(os.path.dirname(__file__), "test.qin"))
test_dict = QCInput.from_file(os.path.join(os.path.dirname(__file__), "test.qin")).as_dict()
test_ref_dict = QCInput.from_file(os.path.join(os.path.dirname(__file__), "test_ref.qin")).as_dict()
for key in test_dict:
self.assertEqual(test_dict[key], test_ref_dict[key])
os.remove(os.path.join(os.path.dirname(__file__), "test.qin"))
def test_write_file_from_OptSet(self):
from pymatgen.io.qchem.sets import OptSet
odd_dict = loadfn(os.path.join(os.path.dirname(__file__), "odd.json"))
odd_mol = odd_dict["spec"]["_tasks"][0]["molecule"]
qcinp = OptSet(odd_mol)
qcinp.write_file(os.path.join(os.path.dirname(__file__), "test.qin"))
test_dict = QCInput.from_file(os.path.join(os.path.dirname(__file__), "test.qin")).as_dict()
test_ref_dict = QCInput.from_file(os.path.join(os.path.dirname(__file__), "test_ref.qin")).as_dict()
for key in test_dict:
self.assertEqual(test_dict[key], test_ref_dict[key])
os.remove(os.path.join(os.path.dirname(__file__), "test.qin"))
def test_pcm_init(self):
test_molecule = QCInput.from_file(os.path.join(test_dir, "new_qchem_files/pcm.qin")).molecule
test_OptSet = OptSet(molecule=test_molecule, pcm_dielectric=10.0)
self.assertEqual(
test_OptSet.rem,
{
"job_type": "opt",
"gen_scfman": "true",
"basis": "def2-tzvppd",
"max_scf_cycles": "200",
"method": "wb97xd",
"geom_opt_max_cycles": "200",
"scf_algorithm": "diis",
"xc_grid": "3",
"solvent_method": "pcm",
"symmetry": "false",
"sym_ignore": "true",
"resp_charges": "true",
},
)
self.assertEqual(
test_OptSet.pcm,
{
"heavypoints": "194",
"hpoints": "194",
"radii": "uff",
"theory": "cpcm",
"vdwscale": "1.1",
},
)
self.assertEqual(test_OptSet.solvent, {"dielectric": 10.0})
self.assertEqual(test_OptSet.molecule, test_molecule)
def test_overwrite_input(self):
test_molecule = QCInput.from_file(os.path.join(test_dir, "new_qchem_files/pcm.qin")).molecule
overwrite_inputs = {
"rem": {
"method": "b3lyp",
"basis": "6-31g*",
"thresh": 10,
"xc_grid": "000150000302",
}
}
test_OptSet = OptSet(molecule=test_molecule, overwrite_inputs=overwrite_inputs)
act_rem = {
"job_type": "opt",
"gen_scfman": "true",
"basis": "6-31g*",
"max_scf_cycles": "200",
"method": "b3lyp",
"scf_algorithm": "diis",
"xc_grid": "000150000302",
"geom_opt_max_cycles": "200",
"thresh": 10,
"symmetry": "false",
"sym_ignore": "true",
"resp_charges": "true",
}
self.assertDictEqual(act_rem, test_OptSet.rem)
def test_nbo_init(self):
test_molecule = QCInput.from_file(
os.path.join(test_dir, "new_qchem_files/pcm.qin")).molecule
test_OptSet = OptSet(molecule=test_molecule, nbo_params={})
self.assertEqual(
test_OptSet.rem,
{
"job_type": "opt",
"gen_scfman": "true",
"geom_opt_max_cycles": "200",
"basis": "def2-tzvppd",
"max_scf_cycles": "100",
"method": "wb97xd",
"scf_algorithm": "diis",
"xc_grid": "3",
"thresh": "14",
"s2thresh": "16",
"symmetry": "false",
"sym_ignore": "true",
"resp_charges": "true",
"nbo": "true",
},
)
self.assertEqual(test_OptSet.nbo, {})
self.assertEqual(test_OptSet.molecule, test_molecule)
def test_write_file_from_OptSet_with_vdw(self):
from pymatgen.io.qchem.sets import OptSet
odd_dict = loadfn(os.path.join(os.path.dirname(__file__), "odd.json"))
odd_mol = odd_dict["spec"]["_tasks"][0]["molecule"]
qcinp = OptSet(odd_mol, overwrite_inputs={"van_der_waals": {"16": 3.14159}})
qcinp.write_file(os.path.join(os.path.dirname(__file__), "test_vdw.qin"))
test_file = open(os.path.join(os.path.dirname(__file__), "test_vdw.qin"))
ref_file = open(os.path.join(os.path.dirname(__file__), "test_ref_vdw.qin"))
for l_test, l_ref in zip(test_file, ref_file):
# By default, if this statement fails the offending line will be printed
assert l_test == l_ref
test_file.close()
ref_file.close()
os.remove(os.path.join(os.path.dirname(__file__), "test_vdw.qin"))
def test_overwrite_opt_input(self):
test_molecule = QCInput.from_file(
os.path.join(test_dir, "new_qchem_files/pcm.qin")).molecule
overwrite_inputs = {"opt": {"FIXED": ["1 XYZ", "2 XY"]}}
test_OptSet = OptSet(molecule=test_molecule,
overwrite_inputs=overwrite_inputs)
act_opt = {"fixed": ["1 XYZ", "2 XY"]}
self.assertDictEqual(act_opt, test_OptSet.opt)
def generate_opt_input(molfile,
qinfile,
basis_set="6-311++G*",
pcm_dielectric=None,
overwrite_inputs=None):
"""
Generates a QChem input file from Molecule after conformer search.
:param molfile: Absolute path to the input file (.mol, .sdf, etc.)
:param qinfile: Absolute path to the output file (.in)
:param basis_set: To overwrite default basis.
:param pcm_dielectric: To use solvent
:param overwrite_inputs: To overwrite any set defaults
:return:
"""
mol = get_molecule(molfile)
qcinput = OptSet(mol,
basis_set=basis_set,
pcm_dielectric=pcm_dielectric,
overwrite_inputs=overwrite_inputs)
qcinput.write_file(qinfile)
def test_smd_init(self):
test_molecule = QCInput.from_file(os.path.join(test_dir, "new_qchem_files/pcm.qin")).molecule
test_OptSet = OptSet(molecule=test_molecule, smd_solvent="water")
self.assertEqual(
test_OptSet.rem,
{
"job_type": "opt",
"gen_scfman": "true",
"basis": "def2-tzvppd",
"max_scf_cycles": "200",
"method": "wb97xd",
"geom_opt_max_cycles": "200",
"scf_algorithm": "diis",
"xc_grid": "3",
"solvent_method": "smd",
"ideriv": "1",
"symmetry": "false",
"sym_ignore": "true",
"resp_charges": "true",
},
)
self.assertEqual(test_OptSet.smx, {"solvent": "water"})
self.assertEqual(test_OptSet.molecule, test_molecule)