def __init__(self,
molecule,
rem,
opt=None,
pcm=None,
solvent=None,
smx=None):
self.molecule = molecule
self.rem = lower_and_check_unique(rem)
self.opt = opt
self.pcm = lower_and_check_unique(pcm)
self.solvent = lower_and_check_unique(solvent)
self.smx = lower_and_check_unique(smx)
# Make sure molecule is valid: either the string "read" or a pymatgen molecule object
if isinstance(self.molecule, str):
self.molecule = self.molecule.lower()
if self.molecule != "read":
raise ValueError(
'The only acceptable text value for molecule is "read"')
elif not isinstance(self.molecule, Molecule):
raise ValueError(
"The molecule must either be the string 'read' or be a pymatgen Molecule object"
)
# Make sure rem is valid:
# - Has a basis
# - Has a method or DFT exchange functional
# - Has a valid job_type or jobtype
valid_job_types = [
"opt", "optimization", "sp", "freq", "frequency", "nmr"
]
if "basis" not in self.rem:
raise ValueError("The rem dictionary must contain a 'basis' entry")
if "method" not in self.rem:
if "exchange" not in self.rem:
raise ValueError(
"The rem dictionary must contain either a 'method' entry or an 'exchange' entry"
)
if "job_type" not in self.rem:
raise ValueError(
"The rem dictionary must contain a 'job_type' entry")
if self.rem.get("job_type").lower() not in valid_job_types:
raise ValueError(
"The rem dictionary must contain a valid 'job_type' entry")
def __init__(self, rem, pcm=None, solvent=None, smx=None):
self.rem = lower_and_check_unique(rem)
self.pcm = lower_and_check_unique(pcm)
self.solvent = lower_and_check_unique(solvent)
self.smx = lower_and_check_unique(smx)
# Only force jobs should be used with GSM
self.rem["job_type"] = "force"
if "basis" not in self.rem:
raise ValueError("The rem dictionary must contain a 'basis' entry")
if "method" not in self.rem:
if "exchange" not in self.rem:
raise ValueError(
"The rem dictionary must contain either a 'method' entry or an 'exchange' entry"
)
def __init__(self,
molecule,
job_type,
basis_set,
scf_algorithm,
dft_rung=4,
pcm_dielectric=None,
smd_solvent=None,
max_scf_cycles=200,
geom_opt_max_cycles=200,
overwrite_inputs=None):
"""
Args:
molecule (Pymatgen molecule object)
job_type (str)
basis_set (str)
scf_algorithm (str)
dft_rung (int)
pcm_dielectric (str)
max_scf_cycles (int)
geom_opt_max_cycles (int)
overwrite_inputs (dict): This is dictionary of QChem input sections to add or overwrite variables,
the available sections are currently rem, pcm, and solvent. So the accepted keys are rem, pcm, or solvent
and the value is a dictionary of key value pairs relevant to the section. An example would be adding a
new variable to the rem section that sets symmetry to false.
ex. overwrite_inputs = {"rem": {"symmetry": "false"}}
***It should be noted that if something like basis is added to the rem dict it will overwrite
the default basis.***
"""
self.molecule = molecule
self.job_type = job_type
self.basis_set = basis_set
self.scf_algorithm = scf_algorithm
self.dft_rung = dft_rung
self.pcm_dielectric = pcm_dielectric
self.smd_solvent = smd_solvent
self.max_scf_cycles = max_scf_cycles
self.geom_opt_max_cycles = geom_opt_max_cycles
self.overwrite_inputs = overwrite_inputs
pcm_defaults = {
"heavypoints": "194",
"hpoints": "194",
"radii": "uff",
"theory": "cpcm",
"vdwscale": "1.1"
}
mypcm = {}
mysolvent = {}
mysmx = {}
myrem = {}
myrem["job_type"] = job_type
myrem["basis"] = self.basis_set
myrem["max_scf_cycles"] = self.max_scf_cycles
myrem["gen_scfman"] = "true"
myrem["scf_algorithm"] = self.scf_algorithm
if self.dft_rung == 1:
myrem["exchange"] = "B3LYP"
elif self.dft_rung == 2:
myrem["method"] = "B97-D3"
myrem["dft_D"] = "D3_BJ"
elif self.dft_rung == 3:
myrem["method"] = "B97M-rV"
elif self.dft_rung == 4:
myrem["method"] = "wb97xd"
elif self.dft_rung == 5:
myrem["method"] = "wB97M-V"
else:
raise ValueError("dft_rung should be between 1 and 5!")
if self.job_type.lower() == "opt":
myrem["geom_opt_max_cycles"] = self.geom_opt_max_cycles
if self.pcm_dielectric is not None and self.smd_solvent is not None:
raise ValueError(
"Only one of pcm or smd may be used for solvation.")
if self.pcm_dielectric is not None:
mypcm = pcm_defaults
mysolvent["dielectric"] = self.pcm_dielectric
myrem["solvent_method"] = 'pcm'
if self.smd_solvent is not None:
mysmx["solvent"] = self.smd_solvent
myrem["solvent_method"] = "smd"
if self.overwrite_inputs:
for sec, sec_dict in self.overwrite_inputs.items():
if sec == "rem":
temp_rem = lower_and_check_unique(sec_dict)
for k, v in temp_rem.items():
myrem[k] = v
if sec == "pcm":
temp_pcm = lower_and_check_unique(sec_dict)
for k, v in temp_pcm.items():
mypcm[k] = v
if sec == "solvent":
temp_solvent = lower_and_check_unique(sec_dict)
for k, v in temp_solvent.items():
mysolvent[k] = v
if sec == "smx":
temp_smx = lower_and_check_unique(sec_dict)
for k, v in temp_smx.items():
mysmx[k] = v
super().__init__(self.molecule,
rem=myrem,
pcm=mypcm,
solvent=mysolvent,
smx=mysmx)
def __init__(
self,
molecule: Molecule,
job_type: str,
basis_set: str,
scf_algorithm: str,
dft_rung: int = 4,
pcm_dielectric: Optional[float] = None,
smd_solvent: Optional[str] = None,
custom_smd: Optional[str] = None,
opt_variables: Optional[Dict[str, List]] = None,
scan_variables: Optional[Dict[str, List]] = None,
max_scf_cycles: int = 200,
geom_opt_max_cycles: int = 200,
plot_cubes: bool = False,
nbo_params: Optional[Dict] = None,
overwrite_inputs: Optional[Dict] = None,
vdw_mode: str = "atomic",
):
"""
Args:
molecule (Pymatgen Molecule object)
job_type (str): QChem job type to run. Valid options are "opt" for optimization,
"sp" for single point, "freq" for frequency calculation, or "force" for
force evaluation.
basis_set (str): Basis set to use. For example, "def2-tzvpd".
scf_algorithm (str): Algorithm to use for converging the SCF. Recommended choices are
"DIIS", "GDM", and "DIIS_GDM". Other algorithms supported by Qchem's GEN_SCFMAN
module will also likely perform well. Refer to the QChem manual for further details.
dft_rung (int): Select the DFT functional among 5 recommended levels of theory,
in order of increasing accuracy/cost. 1 = B3LYP, 2=B3lYP+D3, 3=ωB97X-D,
4=ωB97X-V, 5=ωB97M-V. (Default: 4)
To set a functional not given by one of the above, set the overwrite_inputs
argument to {"method":"<NAME OF FUNCTIONAL>"}
**Note that the "rungs" in this argument do NOT correspond to rungs on "Jacob's
Ladder of Density Functional Approxmations"**
pcm_dielectric (float): Dielectric constant to use for PCM implicit solvation model. (Default: None)
smd_solvent (str): Solvent to use for SMD implicit solvation model. (Default: None)
Examples include "water", "ethanol", "methanol", and "acetonitrile". Refer to the QChem
manual for a complete list of solvents available. To define a custom solvent, set this
argument to "custom" and populate custom_smd with the necessary parameters.
**Note that only one of smd_solvent and pcm_dielectric may be set.**
custom_smd (str): List of parameters to define a custom solvent in SMD. (Default: None)
Must be given as a string of seven comma separated values in the following order:
"dielectric, refractive index, acidity, basicity, surface tension, aromaticity,
electronegative halogenicity"
Refer to the QChem manual for further details.
opt_variables (dict): A dictionary of opt sections, where each opt section is a key
and the corresponding values are a list of strings. Stings must be formatted
as instructed by the QChem manual. The different opt sections are: CONSTRAINT, FIXED,
DUMMY, and CONNECT.
Ex. opt = {"CONSTRAINT": ["tors 2 3 4 5 25.0", "tors 2 5 7 9 80.0"], "FIXED": ["2 XY"]}
scan_variables (dict): A dictionary of scan variables. Because two constraints of the
same type are allowed (for instance, two torsions or two bond stretches), each TYPE of
variable (stre, bend, tors) should be its own key in the dict, rather than each variable.
Note that the total number of variable (sum of lengths of all lists) CANNOT be more than two.
Ex. scan_variables = {"stre": ["3 6 1.5 1.9 0.1"], "tors": ["1 2 3 4 -180 180 15"]}
max_scf_cycles (int): Maximum number of SCF iterations. (Default: 200)
geom_opt_max_cycles (int): Maximum number of geometry optimization iterations. (Default: 200)
plot_cubes (bool): Whether to write CUBE files of the electron density. (Default: False)
nbo_params (list): A list of strings for the desired NBO params. If an empty list is passed,
default NBO analysis will be performed. (Default: False)
overwrite_inputs (dict): Dictionary of QChem input sections to add or overwrite variables.
The currently available sections (keys) are rem, pcm,
solvent, smx, opt, scan, van_der_waals, and plots. The value of each key is a
dictionary of key value pairs relevant to that section. For example, to add
a new variable to the rem section that sets symmetry to false, use
overwrite_inputs = {"rem": {"symmetry": "false"}}
**Note that if something like basis is added to the rem dict it will overwrite
the default basis.**
**Note that supplying a van_der_waals section here will automatically modify
the PCM "radii" setting to "read".**
**Note that all keys must be given as strings, even when they are numbers!**
vdw_mode (str): Method of specifying custom van der Waals radii. Applies only if
you are using overwrite_inputs to add a $van_der_waals section to the input.
Valid value are 'atomic' and 'sequential'. In 'atomic' mode (default), dict
keys represent the atomic number associated with each radius (e.g., '12' = carbon).
In 'sequential' mode, dict keys represent the sequential position of a single
specific atom in the input structure.
"""
self.molecule = molecule
self.job_type = job_type
self.basis_set = basis_set
self.scf_algorithm = scf_algorithm
self.dft_rung = dft_rung
self.pcm_dielectric = pcm_dielectric
self.smd_solvent = smd_solvent
self.custom_smd = custom_smd
self.opt_variables = opt_variables
self.scan_variables = scan_variables
self.max_scf_cycles = max_scf_cycles
self.geom_opt_max_cycles = geom_opt_max_cycles
self.plot_cubes = plot_cubes
self.nbo_params = nbo_params
self.overwrite_inputs = overwrite_inputs
self.vdw_mode = vdw_mode
pcm_defaults = {
"heavypoints": "194",
"hpoints": "194",
"radii": "uff",
"theory": "cpcm",
"vdwscale": "1.1",
}
plots_defaults = {"grid_spacing": "0.05", "total_density": "0"}
if self.opt_variables is None:
myopt = dict()
else:
myopt = self.opt_variables
if self.scan_variables is None:
myscan = dict()
else:
myscan = self.scan_variables
mypcm = dict()
mysolvent = dict()
mysmx = dict()
myvdw = dict()
myplots = dict()
myrem = dict()
myrem["job_type"] = job_type
myrem["basis"] = self.basis_set
myrem["max_scf_cycles"] = str(self.max_scf_cycles)
myrem["gen_scfman"] = "true"
myrem["xc_grid"] = "3"
myrem["scf_algorithm"] = self.scf_algorithm
myrem["resp_charges"] = "true"
myrem["symmetry"] = "false"
myrem["sym_ignore"] = "true"
if self.dft_rung == 1:
myrem["method"] = "b3lyp"
elif self.dft_rung == 2:
myrem["method"] = "b3lyp"
myrem["dft_D"] = "D3_BJ"
elif self.dft_rung == 3:
myrem["method"] = "wb97xd"
elif self.dft_rung == 4:
myrem["method"] = "wb97xv"
elif self.dft_rung == 5:
myrem["method"] = "wb97mv"
else:
raise ValueError("dft_rung should be between 1 and 5!")
if self.job_type.lower() in ["opt", "ts", "pes_scan"]:
myrem["geom_opt_max_cycles"] = str(self.geom_opt_max_cycles)
if self.pcm_dielectric is not None and self.smd_solvent is not None:
raise ValueError(
"Only one of pcm or smd may be used for solvation.")
if self.pcm_dielectric is not None:
mypcm = pcm_defaults
mysolvent["dielectric"] = self.pcm_dielectric
myrem["solvent_method"] = "pcm"
if self.smd_solvent is not None:
if self.smd_solvent == "custom":
mysmx["solvent"] = "other"
else:
mysmx["solvent"] = self.smd_solvent
myrem["solvent_method"] = "smd"
myrem["ideriv"] = "1"
if self.smd_solvent == "custom" or self.smd_solvent == "other":
if self.custom_smd is None:
raise ValueError(
"A user-defined SMD requires passing custom_smd, a string"
+
" of seven comma separated values in the following order:"
+
" dielectric, refractive index, acidity, basicity, surface"
+
" tension, aromaticity, electronegative halogenicity")
if self.plot_cubes:
myplots = plots_defaults
myrem["plots"] = "true"
myrem["make_cube_files"] = "true"
if self.nbo_params is not None:
myrem["nbo"] = "true"
if self.overwrite_inputs:
for sec, sec_dict in self.overwrite_inputs.items():
if sec == "rem":
temp_rem = lower_and_check_unique(sec_dict)
for k, v in temp_rem.items():
myrem[k] = v
if sec == "pcm":
temp_pcm = lower_and_check_unique(sec_dict)
for k, v in temp_pcm.items():
mypcm[k] = v
if sec == "solvent":
temp_solvent = lower_and_check_unique(sec_dict)
for k, v in temp_solvent.items():
mysolvent[k] = v
if sec == "smx":
temp_smx = lower_and_check_unique(sec_dict)
for k, v in temp_smx.items():
mysmx[k] = v
if sec == "scan":
temp_scan = lower_and_check_unique(sec_dict)
for k, v in temp_scan.items():
myscan[k] = v
if sec == "van_der_waals":
temp_vdw = lower_and_check_unique(sec_dict)
for k, v in temp_vdw.items():
myvdw[k] = v
# set the PCM section to read custom radii
mypcm["radii"] = "read"
if sec == "plots":
temp_plots = lower_and_check_unique(sec_dict)
for k, v in temp_plots.items():
myplots[k] = v
if sec == "nbo":
temp_plots = lower_and_check_unique(sec_dict)
for k, v in temp_plots.items():
myplots[k] = v
if sec == "opt":
temp_opts = lower_and_check_unique(sec_dict)
for k, v in temp_opts.items():
myopt[k] = v
super().__init__(
self.molecule,
rem=myrem,
opt=myopt,
pcm=mypcm,
solvent=mysolvent,
smx=mysmx,
scan=myscan,
van_der_waals=myvdw,
vdw_mode=self.vdw_mode,
plots=myplots,
nbo=self.nbo_params,
)
def __init__(
self,
molecule,
job_type,
basis_set,
scf_algorithm,
dft_rung=4,
pcm_dielectric=None,
smd_solvent=None,
custom_smd=None,
max_scf_cycles=200,
geom_opt_max_cycles=200,
overwrite_inputs=None,
):
"""
Args:
molecule (Pymatgen molecule object)
job_type (str)
basis_set (str)
scf_algorithm (str)
dft_rung (int)
pcm_dielectric (str)
max_scf_cycles (int)
geom_opt_max_cycles (int)
overwrite_inputs (dict): This is dictionary of QChem input sections to add or overwrite variables,
the available sections are currently rem, pcm, and solvent. So the accepted keys are rem, pcm, or solvent
and the value is a dictionary of key value pairs relevant to the section. An example would be adding a
new variable to the rem section that sets symmetry to false.
ex. overwrite_inputs = {"rem": {"symmetry": "false"}}
***It should be noted that if something like basis is added to the rem dict it will overwrite
the default basis.***
"""
self.molecule = molecule
self.job_type = job_type
self.basis_set = basis_set
self.scf_algorithm = scf_algorithm
self.dft_rung = dft_rung
self.pcm_dielectric = pcm_dielectric
self.smd_solvent = smd_solvent
self.custom_smd = custom_smd
self.max_scf_cycles = max_scf_cycles
self.geom_opt_max_cycles = geom_opt_max_cycles
self.overwrite_inputs = overwrite_inputs
pcm_defaults = {
"heavypoints": "194",
"hpoints": "194",
"radii": "uff",
"theory": "cpcm",
"vdwscale": "1.1",
}
mypcm = {}
mysolvent = {}
mysmx = {}
myrem = {}
myrem["job_type"] = job_type
myrem["basis"] = self.basis_set
myrem["max_scf_cycles"] = self.max_scf_cycles
myrem["gen_scfman"] = "true"
myrem["xc_grid"] = "3"
myrem["scf_algorithm"] = self.scf_algorithm
myrem["resp_charges"] = "true"
myrem["symmetry"] = "false"
myrem["sym_ignore"] = "true"
if self.dft_rung == 1:
myrem["method"] = "b3lyp"
elif self.dft_rung == 2:
myrem["method"] = "b3lyp"
myrem["dft_D"] = "D3_BJ"
elif self.dft_rung == 3:
myrem["method"] = "wb97xd"
elif self.dft_rung == 4:
myrem["method"] = "wb97xv"
elif self.dft_rung == 5:
myrem["method"] = "wb97mv"
else:
raise ValueError("dft_rung should be between 1 and 5!")
if self.job_type.lower() == "opt":
myrem["geom_opt_max_cycles"] = self.geom_opt_max_cycles
if self.pcm_dielectric is not None and self.smd_solvent is not None:
raise ValueError(
"Only one of pcm or smd may be used for solvation.")
if self.pcm_dielectric is not None:
mypcm = pcm_defaults
mysolvent["dielectric"] = self.pcm_dielectric
myrem["solvent_method"] = "pcm"
if self.smd_solvent is not None:
if self.smd_solvent == "custom":
mysmx["solvent"] = "other"
else:
mysmx["solvent"] = self.smd_solvent
myrem["solvent_method"] = "smd"
myrem["ideriv"] = "1"
if self.smd_solvent == "custom" or self.smd_solvent == "other":
if self.custom_smd is None:
raise ValueError(
"A user-defined SMD requires passing custom_smd, a string"
+
" of seven comma separated values in the following order:"
+
" dielectric, refractive index, acidity, basicity, surface"
+
" tension, aromaticity, electronegative halogenicity")
if self.overwrite_inputs:
for sec, sec_dict in self.overwrite_inputs.items():
if sec == "rem":
temp_rem = lower_and_check_unique(sec_dict)
for k, v in temp_rem.items():
myrem[k] = v
if sec == "pcm":
temp_pcm = lower_and_check_unique(sec_dict)
for k, v in temp_pcm.items():
mypcm[k] = v
if sec == "solvent":
temp_solvent = lower_and_check_unique(sec_dict)
for k, v in temp_solvent.items():
mysolvent[k] = v
if sec == "smx":
temp_smx = lower_and_check_unique(sec_dict)
for k, v in temp_smx.items():
mysmx[k] = v
super().__init__(self.molecule,
rem=myrem,
pcm=mypcm,
solvent=mysolvent,
smx=mysmx)
def __init__(self,
molecule,
job_type,
basis_set,
scf_algorithm,
dft_rung=4,
pcm_dielectric=None,
max_scf_cycles=200,
geom_opt_max_cycles=200,
overwrite_inputs=None):
"""
Args:
molecule (Pymatgen molecule object)
job_type (str)
basis_set (str)
scf_algorithm (str)
dft_rung (int)
pcm_dielectric (str)
max_scf_cycles (int)
geom_opt_max_cycles (int)
overwrite_inputs (dict): This is dictionary of QChem input sections to add or overwrite variables,
the available sections are currently rem, pcm, and solvent. So the accepted keys are rem, pcm, or solvent
and the value is a dictionary of key value pairs relevant to the section. An example would be adding a
new variable to the rem section that sets symmetry to false.
ex. overwrite_inputs = {"rem": {"symmetry": "false"}}
***It should be noted that if something like basis is added to the rem dict it will overwrite
the default basis.***
"""
self.molecule = molecule
self.job_type = job_type
self.basis_set = basis_set
self.scf_algorithm = scf_algorithm
self.dft_rung = dft_rung
self.pcm_dielectric = pcm_dielectric
self.max_scf_cycles = max_scf_cycles
self.geom_opt_max_cycles = geom_opt_max_cycles
self.overwrite_inputs = overwrite_inputs
pcm_defaults = {
"heavypoints": "194",
"hpoints": "194",
"radii": "uff",
"theory": "cpcm",
"vdwscale": "1.1"
}
mypcm = {}
mysolvent = {}
myrem = {}
myrem["job_type"] = job_type
myrem["basis"] = self.basis_set
myrem["max_scf_cycles"] = self.max_scf_cycles
myrem["gen_scfman"] = "true"
myrem["scf_algorithm"] = self.scf_algorithm
if self.dft_rung == 1:
myrem["exchange"] = "B3LYP"
elif self.dft_rung == 2:
myrem["method"] = "B97-D3"
myrem["dft_D"] = "D3_BJ"
elif self.dft_rung == 3:
myrem["method"] = "B97M-rV"
elif self.dft_rung == 4:
myrem["method"] = "wb97xd"
elif self.dft_rung == 5:
myrem["method"] = "wB97M-V"
else:
raise ValueError("dft_rung should be between 1 and 5!")
if self.job_type.lower() == "opt":
myrem["geom_opt_max_cycles"] = self.geom_opt_max_cycles
if self.pcm_dielectric != None:
mypcm = pcm_defaults
mysolvent["dielectric"] = self.pcm_dielectric
myrem["solvent_method"] = 'pcm'
if self.overwrite_inputs:
for sec, sec_dict in self.overwrite_inputs.items():
if sec == "rem":
temp_rem = lower_and_check_unique(sec_dict)
for k, v in temp_rem.items():
myrem[k] = v
if sec == "pcm":
temp_pcm = lower_and_check_unique(sec_dict)
for k, v in temp_pcm.items():
mypcm[k] = v
if sec == "solvent":
temp_solvent = lower_and_check_unique(sec_dict)
for k, v in temp_solvent.items():
mysolvent[k] = v
super(QChemDictSet, self).__init__(
self.molecule, rem=myrem, pcm=mypcm, solvent=mysolvent)