def test_custom_smd_write(self):
dict_set = GSMDictSet(basis_set='6-31g*',
scf_algorithm='diis',
dft_rung=5,
smd_solvent="custom",
custom_smd="90.00,1.415,0.00,0.735,20.2,0.00,0.00",
max_scf_cycles=35)
dict_set.write("mol.qin")
test_dict = QCTemplate.from_file("mol.qin").as_dict()
rem = {
"job_type": "force",
"basis": "6-31G*",
"max_scf_cycles": '35',
"method": "wb97mv",
"gen_scfman": 'true',
"scf_algorithm": "diis",
"xc_grid": '3',
"solvent_method": "smd",
"ideriv": "1",
'symmetry': 'false',
'sym_ignore': 'true',
'resp_charges': 'true'
}
qc_input = QCTemplate(rem=rem, smx={"solvent": "other"})
for k, v in qc_input.as_dict().items():
self.assertEqual(v, test_dict[k])
os.remove("mol.qin")
with open("solvent_data") as sd:
lines = sd.readlines()
self.assertEqual(lines[0], "90.00,1.415,0.00,0.735,20.2,0.00,0.00")
os.remove("solvent_data")
def test_pcm_write(self):
dict_set = GSMDictSet(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 = QCTemplate.from_file("mol.qin").as_dict()
rem = {
"job_type": "force",
"basis": "6-31G*",
"max_scf_cycles": '35',
"method": "wb97mv",
"gen_scfman": 'true',
"scf_algorithm": "diis",
"xc_grid": '3',
"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 = QCTemplate(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_full_init(self):
test_DictSet = GSMDictSet(
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': 'force',
'gen_scfman': 'true',
'basis': '6-31g*',
'max_scf_cycles': 35,
'method': 'b3lyp',
'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})
test_DictSet = GSMDictSet(
basis_set='6-31g*',
scf_algorithm='diis',
dft_rung=1,
smd_solvent='water',
max_scf_cycles=35)
self.assertEqual(
test_DictSet.rem, {
'job_type': 'force',
'gen_scfman': 'true',
'basis': '6-31g*',
'max_scf_cycles': 35,
'method': 'b3lyp',
'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'})
def test_double_solvation(self):
raised_error = False
dict_set = None
try:
dict_set = GSMDictSet(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_DictSet = GSMDictSet(
basis_set='6-31G*',
scf_algorithm='diis')
self.assertEqual(
test_DictSet.rem, {
'job_type': 'force',
'gen_scfman': 'true',
'basis': '6-31g*',
'max_scf_cycles': 200,
'method': 'wb97xv',
'scf_algorithm': 'diis',
'xc_grid': '3',
'symmetry': 'false',
'sym_ignore': 'true',
'resp_charges': 'true'
})
self.assertEqual(test_DictSet.pcm, {})
self.assertEqual(test_DictSet.solvent, {})
self.assertEqual(test_DictSet.smx, {})
def test_overwrite_input(self):
overwrite_inputs = {
"rem": {
'method': 'b3lyp',
'basis': '6-31g*',
'thresh': 10,
"xc_grid": "000150000302"
}
}
test_set = GSMDictSet(overwrite_inputs=overwrite_inputs)
act_rem = {
'job_type': 'force',
'gen_scfman': 'true',
'basis': '6-31g*',
'max_scf_cycles': 200,
'method': 'b3lyp',
'scf_algorithm': 'diis',
'xc_grid': '000150000302',
'thresh': 10,
'symmetry': 'false',
'sym_ignore': 'true',
'resp_charges': 'true'
}
self.assertDictEqual(act_rem, test_set.rem)
def __init__(self,
molecule,
isomers,
base_command="gsm",
num_nodes=30,
fixed_endpoints=True,
name="single-ended GSM",
max_cores=32,
input_params=None,
db_file=None,
parents=None,
**kwargs):
"""
Args:
molecule (Molecule): Input molecule.
isomers (dict): list of coordinates to vary to find transition states
base_command (str): Way to call pyGSM. By default this is "gsm".
num_nodes (int): Maximum number of nodes along the reaction path.
Default is 30.
fixed_endpoint (bool): If True (default), do not optimize the input
node.
name (str): Name for the Firework.
max_cores (int): Maximum number of cores to parallelize over. Supports env_chk.
input_params (dict): Specify kwargs for instantiating the input set parameters.
Basic uses would be to modify the default inputs of the set,
such as dft_rung, basis_set, pcm_dielectric, scf_algorithm,
or max_scf_cycles. See pymatgen/io/gsm/sets.py for default
values of all input parameters. For instance, if a user wanted
to use a more advanced DFT functional, include a pcm with a
dielectric of 30, and use a larger basis, the user would set
qchem_input_params = {"dft_rung": 5, "pcm_dielectric": 30,
"basis_set": "6-311++g**"}. However, more advanced customization
of the input is also possible through the overwrite_inputs key
which allows the user to directly modify the rem, pcm, smd, and
solvent dictionaries that QChemDictSet passes to inputs.py to
print an actual input file. For instance, if a user wanted to
set the sym_ignore flag in the rem section of the input file
to true, then they would set qchem_input_params = {"overwrite_inputs":
"rem": {"sym_ignore": "true"}}. Of course, overwrite_inputs
could be used in conjuction with more typical modifications.
db_file (str): Path to file specifying db credentials to place output parsing.
parents ([Firework]): Parents of this particular Firework.
**kwargs: Other kwargs that are passed to Firework.__init__.
"""
input_params = input_params or dict()
molecule_file = "input.xyz"
lot_file = "qin"
isomers_file = "isomers.txt"
output_file = "gsm.out"
flags = [
base_command, "-mode", "SE_GSM", "-xyzfile", molecule_file,
"-package", "QChem", "-lot_inp_file", lot_file, "-num_nodes",
str(num_nodes), "-isomers", isomers_file, "-charge",
str(molecule.charge), "-multiplicity",
str(molecule.spin_multiplicity), "-nproc",
str(max_cores)
]
if fixed_endpoints:
flags.append("-reactant_geom_fixed")
flags.append(">")
flags.append(output_file)
t = list()
input_set = GSMDictSet(**input_params)
t.append(
WriteInputFromIOSet(input_set=input_set,
molecules=[molecule],
molecule_file=molecule_file,
lot_file=lot_file))
t.append(WriteIsomer(isomers=isomers, isomers_file=isomers_file))
t.append(RunGSMDirect(cmd=" ".join(flags)))
t.append(
GSMToDb(db_file=db_file,
molecule_file=molecule_file,
template_file=lot_file,
output_file=output_file,
isomers_file=isomers_file,
additional_fields={"task_label": name}))
super(SingleEndedGSMFW, self).__init__(t,
parents=parents,
name=name,
**kwargs)