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_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 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)
