def test_smd_write(self):
test_molecule = QCInput.from_file(os.path.join(test_dir, "new_qchem_files/pcm.qin")).molecule
dict_set = QChemDictSet(
molecule=test_molecule,
job_type="opt",
basis_set="6-31g*",
scf_algorithm="diis",
dft_rung=5,
smd_solvent="water",
max_scf_cycles=35,
)
dict_set.write("mol.qin")
test_dict = QCInput.from_file("mol.qin").as_dict()
rem = {
"job_type": "opt",
"basis": "6-31G*",
"max_scf_cycles": "35",
"method": "wb97mv",
"geom_opt_max_cycles": "200",
"gen_scfman": "true",
"scf_algorithm": "diis",
"xc_grid": "3",
"solvent_method": "smd",
"ideriv": "1",
"symmetry": "false",
"sym_ignore": "true",
"resp_charges": "true",
}
qc_input = QCInput(molecule=test_molecule, rem=rem, smx={"solvent": "water"})
for k, v in qc_input.as_dict().items():
self.assertEqual(v, test_dict[k])
os.remove("mol.qin")
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/pes_scan.qin")).molecule
test_pes_scan = PESScanSet(
molecule=test_molecule, smd_solvent="water", scan_variables={"stre": ["3 6 1.5 1.9 0.01"]}
)
self.assertEqual(
test_pes_scan.rem,
{
"job_type": "pes_scan",
"gen_scfman": "true",
"basis": "def2-tzvppd",
"max_scf_cycles": "200",
"geom_opt_max_cycles": "200",
"method": "wb97xd",
"scf_algorithm": "diis",
"xc_grid": "3",
"solvent_method": "smd",
"ideriv": "1",
"resp_charges": "true",
"sym_ignore": "true",
"symmetry": "false",
},
)
self.assertEqual(test_pes_scan.smx, {"solvent": "water"})
self.assertEqual(test_pes_scan.scan, {"stre": ["3 6 1.5 1.9 0.01"]})
self.assertEqual(test_pes_scan.molecule, test_molecule)
def test_pcm_init(self):
test_molecule = QCInput.from_file(os.path.join(test_dir, "new_qchem_files/pes_scan.qin")).molecule
test_pes_scan = PESScanSet(
molecule=test_molecule, pcm_dielectric=10.0, scan_variables={"stre": ["3 6 1.5 1.9 0.01"]}
)
self.assertEqual(
test_pes_scan.rem,
{
"job_type": "pes_scan",
"gen_scfman": "true",
"basis": "def2-tzvppd",
"max_scf_cycles": "200",
"geom_opt_max_cycles": "200",
"method": "wb97xd",
"scf_algorithm": "diis",
"xc_grid": "3",
"solvent_method": "pcm",
"resp_charges": "true",
"sym_ignore": "true",
"symmetry": "false",
},
)
self.assertEqual(
test_pes_scan.pcm,
{"heavypoints": "194", "hpoints": "194", "radii": "uff", "theory": "cpcm", "vdwscale": "1.1"},
)
self.assertEqual(test_pes_scan.solvent, {"dielectric": 10.0})
self.assertEqual(test_pes_scan.scan, {"stre": ["3 6 1.5 1.9 0.01"]})
self.assertEqual(test_pes_scan.molecule, test_molecule)
def test_plots_init(self):
test_molecule = QCInput.from_file(os.path.join(test_dir, "new_qchem_files/pcm.qin")).molecule
test_SPSet = SinglePointSet(molecule=test_molecule, smd_solvent="water", plot_cubes=True)
self.assertEqual(
test_SPSet.rem,
{
"job_type": "sp",
"gen_scfman": "true",
"basis": "def2-tzvppd",
"max_scf_cycles": "200",
"method": "wb97xd",
"scf_algorithm": "diis",
"xc_grid": "3",
"solvent_method": "smd",
"ideriv": "1",
"symmetry": "false",
"sym_ignore": "true",
"resp_charges": "true",
"plots": "true",
"make_cube_files": "true",
},
)
self.assertEqual(test_SPSet.plots, {"grid_spacing": "0.05", "total_density": "0"})
self.assertEqual(test_SPSet.smx, {"solvent": "water"})
self.assertEqual(test_SPSet.molecule, test_molecule)
def test_init(self):
test_molecule = QCInput.from_file(os.path.join(test_dir, "new_qchem_files/pcm.qin")).molecule
test_DictSet = QChemDictSet(
molecule=test_molecule,
job_type="opt",
basis_set="6-31G*",
scf_algorithm="diis",
)
self.assertEqual(
test_DictSet.rem,
{
"job_type": "opt",
"gen_scfman": "true",
"basis": "6-31g*",
"max_scf_cycles": "200",
"method": "wb97xv",
"scf_algorithm": "diis",
"xc_grid": "3",
"geom_opt_max_cycles": "200",
"symmetry": "false",
"sym_ignore": "true",
"resp_charges": "true",
},
)
self.assertEqual(test_DictSet.pcm, {})
self.assertEqual(test_DictSet.solvent, {})
self.assertEqual(test_DictSet.smx, {})
self.assertEqual(test_DictSet.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_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_TSSet = TransitionStateSet(molecule=test_molecule)
self.assertEqual(
test_TSSet.rem,
{
"job_type": "ts",
"gen_scfman": "true",
"basis": "def2-tzvppd",
"max_scf_cycles": "100",
"method": "wb97xd",
"scf_algorithm": "diis",
"xc_grid": "3",
"thresh": "14",
"s2thresh": "16",
"geom_opt_max_cycles": "200",
"resp_charges": "true",
"sym_ignore": "true",
"symmetry": "false",
},
)
self.assertEqual(test_TSSet.pcm, {})
self.assertEqual(test_TSSet.solvent, {})
self.assertEqual(test_TSSet.smx, {})
self.assertEqual(test_TSSet.molecule, test_molecule)
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 test_pcm_write(self):
test_molecule = QCInput.from_file(
os.path.join(test_dir, "new_qchem_files/pcm.qin")).molecule
dict_set = QChemDictSet(
molecule=test_molecule,
job_type="opt",
basis_set="6-31g*",
scf_algorithm="diis",
dft_rung=5,
pcm_dielectric=10.0,
max_scf_cycles=35,
)
dict_set.write("mol.qin")
test_dict = QCInput.from_file("mol.qin").as_dict()
rem = {
"job_type": "opt",
"basis": "6-31G*",
"max_scf_cycles": "35",
"method": "wb97mv",
"geom_opt_max_cycles": "200",
"gen_scfman": "true",
"scf_algorithm": "diis",
"xc_grid": "3",
"thresh": "14",
"s2thresh": "16",
"solvent_method": "pcm",
"symmetry": "false",
"sym_ignore": "true",
"resp_charges": "true",
}
pcm = {
"heavypoints": "194",
"hpoints": "194",
"radii": "uff",
"theory": "cpcm",
"vdwscale": "1.1",
}
qc_input = QCInput(molecule=test_molecule,
rem=rem,
pcm=pcm,
solvent={"dielectric": "10.0"})
for k, v in qc_input.as_dict().items():
self.assertEqual(v, test_dict[k])
os.remove("mol.qin")
def test_double_solvation(self):
test_molecule = QCInput.from_file(os.path.join(test_dir, "new_qchem_files/pcm.qin")).molecule
raised_error = False
dict_set = None
try:
dict_set = QChemDictSet(
molecule=test_molecule,
job_type="opt",
basis_set="6-31g*",
scf_algorithm="diis",
dft_rung=1,
pcm_dielectric=10.0,
smd_solvent="water",
max_scf_cycles=35,
)
except ValueError:
raised_error = True
self.assertTrue(raised_error)
self.assertEqual(dict_set, None)
def test_init(self):
test_molecule = QCInput.from_file(os.path.join(test_dir, "new_qchem_files/pcm.qin")).molecule
test_SPSet = SinglePointSet(molecule=test_molecule)
self.assertEqual(
test_SPSet.rem,
{
"job_type": "sp",
"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_SPSet.pcm, {})
self.assertEqual(test_SPSet.solvent, {})
self.assertEqual(test_SPSet.molecule, test_molecule)
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": "200",
"method": "wb97xd",
"scf_algorithm": "diis",
"xc_grid": "3",
"symmetry": "false",
"sym_ignore": "true",
"resp_charges": "true",
"nbo": "true",
},
)
self.assertEqual(test_OptSet.nbo, {})
self.assertEqual(test_OptSet.molecule, test_molecule)
def test_full_init(self):
test_molecule = QCInput.from_file(os.path.join(test_dir, "new_qchem_files/pcm.qin")).molecule
test_DictSet = QChemDictSet(
molecule=test_molecule,
job_type="opt",
basis_set="6-31g*",
scf_algorithm="diis",
dft_rung=1,
pcm_dielectric=10.0,
max_scf_cycles=35,
)
self.assertEqual(
test_DictSet.rem,
{
"job_type": "opt",
"gen_scfman": "true",
"basis": "6-31g*",
"max_scf_cycles": "35",
"method": "b3lyp",
"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_DictSet.pcm,
{
"heavypoints": "194",
"hpoints": "194",
"radii": "uff",
"theory": "cpcm",
"vdwscale": "1.1",
},
)
self.assertEqual(test_DictSet.solvent, {"dielectric": 10.0})
self.assertEqual(test_DictSet.molecule, test_molecule)
test_DictSet = QChemDictSet(
molecule=test_molecule,
job_type="opt",
basis_set="6-31g*",
scf_algorithm="diis",
dft_rung=1,
smd_solvent="water",
max_scf_cycles=35,
)
self.assertEqual(
test_DictSet.rem,
{
"job_type": "opt",
"gen_scfman": "true",
"basis": "6-31g*",
"max_scf_cycles": "35",
"method": "b3lyp",
"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_DictSet.smx, {"solvent": "water"})