# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
Input sets for Qchem
"""
import logging
import os
from typing import Dict, List, Optional
from monty.io import zopen
from pymatgen.core.structure import Molecule
from pymatgen.io.qchem.inputs import QCInput
from pymatgen.io.qchem.utils import lower_and_check_unique
__author__ = "Samuel Blau, Brandon Wood, Shyam Dwaraknath, Evan Spotte-Smith, Ryan Kingsbury"
__copyright__ = "Copyright 2018-2021, The Materials Project"
__version__ = "0.1"
logger = logging.getLogger(__name__)
[docs]class QChemDictSet(QCInput):
"""
Build a QCInput given all the various input parameters. Can be extended by standard implementations below.
"""
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,
overwrite_inputs: Optional[Dict] = None,
):
"""
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)
overwrite_inputs (dict): Dictionary of QChem input sections to add or overwrite variables.
The currently available sections (keys) are rem, pcm,
solvent, smx, opt, 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.**
"""
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.overwrite_inputs = overwrite_inputs
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()
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.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 == "plots":
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,
plots=myplots,
)
[docs] def write(self, input_file: str):
"""
Args:
input_file (str): Filename
"""
self.write_file(input_file)
if self.smd_solvent == "custom" or self.smd_solvent == "other":
with zopen(os.path.join(os.path.dirname(input_file), "solvent_data"), "wt") as f:
f.write(self.custom_smd)
[docs]class SinglePointSet(QChemDictSet):
"""
QChemDictSet for a single point calculation
"""
def __init__(
self,
molecule: Molecule,
basis_set: str = "def2-tzvppd",
scf_algorithm: str = "diis",
dft_rung: int = 3,
pcm_dielectric: Optional[float] = None,
smd_solvent: Optional[str] = None,
custom_smd: Optional[str] = None,
max_scf_cycles: int = 200,
plot_cubes: bool = False,
overwrite_inputs: Optional[Dict] = None,
):
"""
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. (Default: "def2-tzvppd")
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.
(Default: "diis")
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: 3)
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.
max_scf_cycles (int): Maximum number of SCF iterations. (Default: 200)
plot_cubes (bool): Whether to write CUBE files of the electron density. (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, 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.**
"""
self.basis_set = basis_set
self.scf_algorithm = scf_algorithm
self.max_scf_cycles = max_scf_cycles
super().__init__(
molecule=molecule,
job_type="sp",
dft_rung=dft_rung,
pcm_dielectric=pcm_dielectric,
smd_solvent=smd_solvent,
custom_smd=custom_smd,
basis_set=self.basis_set,
scf_algorithm=self.scf_algorithm,
max_scf_cycles=self.max_scf_cycles,
plot_cubes=plot_cubes,
overwrite_inputs=overwrite_inputs,
)
[docs]class OptSet(QChemDictSet):
"""
QChemDictSet for a geometry optimization
"""
def __init__(
self,
molecule: Molecule,
basis_set: str = "def2-tzvppd",
scf_algorithm: str = "diis",
dft_rung: int = 3,
pcm_dielectric: Optional[float] = None,
smd_solvent: Optional[str] = None,
custom_smd: Optional[str] = None,
max_scf_cycles: int = 200,
plot_cubes: bool = False,
opt_variables: Optional[Dict[str, List]] = None,
geom_opt_max_cycles: int = 200,
overwrite_inputs: Optional[Dict] = None,
):
"""
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. (Default: "def2-tzvppd")
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.
(Default: "diis")
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: 3)
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.
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)
overwrite_inputs (dict): Dictionary of QChem input sections to add or overwrite variables.
The currently available sections (keys) are rem, pcm, solvent, smx, 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.**
"""
self.basis_set = basis_set
self.scf_algorithm = scf_algorithm
self.max_scf_cycles = max_scf_cycles
self.geom_opt_max_cycles = geom_opt_max_cycles
super().__init__(
molecule=molecule,
job_type="opt",
dft_rung=dft_rung,
pcm_dielectric=pcm_dielectric,
smd_solvent=smd_solvent,
custom_smd=custom_smd,
opt_variables=opt_variables,
basis_set=self.basis_set,
scf_algorithm=self.scf_algorithm,
max_scf_cycles=self.max_scf_cycles,
geom_opt_max_cycles=self.geom_opt_max_cycles,
plot_cubes=plot_cubes,
overwrite_inputs=overwrite_inputs,
)
[docs]class TransitionStateSet(QChemDictSet):
"""
QChemDictSet for a transition-state search
"""
def __init__(
self,
molecule: Molecule,
basis_set: str = "def2-tzvppd",
scf_algorithm: str = "diis",
dft_rung: int = 3,
pcm_dielectric: Optional[float] = None,
smd_solvent: Optional[str] = None,
custom_smd: Optional[str] = None,
max_scf_cycles: int = 200,
plot_cubes: bool = False,
opt_variables: Optional[Dict[str, List]] = None,
geom_opt_max_cycles: int = 200,
overwrite_inputs: Optional[Dict] = None,
):
"""
Args:
molecule (Pymatgen Molecule object)
basis_set (str): Basis set to use. (Default: "def2-tzvppd")
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.
(Default: "diis")
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: 3)
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.
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)
overwrite_inputs (dict): Dictionary of QChem input sections to add or overwrite variables.
The currently available sections (keys) are rem, pcm, solvent, smx, 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.**
"""
self.basis_set = basis_set
self.scf_algorithm = scf_algorithm
self.max_scf_cycles = max_scf_cycles
self.geom_opt_max_cycles = geom_opt_max_cycles
super().__init__(
molecule=molecule,
job_type="ts",
dft_rung=dft_rung,
pcm_dielectric=pcm_dielectric,
smd_solvent=smd_solvent,
custom_smd=custom_smd,
opt_variables=opt_variables,
basis_set=self.basis_set,
scf_algorithm=self.scf_algorithm,
max_scf_cycles=self.max_scf_cycles,
geom_opt_max_cycles=self.geom_opt_max_cycles,
plot_cubes=plot_cubes,
overwrite_inputs=overwrite_inputs,
)
[docs]class ForceSet(QChemDictSet):
"""
QChemDictSet for a force (gradient) calculation
"""
def __init__(
self,
molecule: Molecule,
basis_set: str = "def2-tzvppd",
scf_algorithm: str = "diis",
dft_rung: int = 3,
pcm_dielectric: Optional[float] = None,
smd_solvent: Optional[str] = None,
custom_smd: Optional[str] = None,
max_scf_cycles: int = 200,
plot_cubes: bool = False,
overwrite_inputs: Optional[Dict] = None,
):
"""
Args:
molecule (Pymatgen Molecule object)
basis_set (str): Basis set to use. (Default: "def2-tzvppd")
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.
(Default: "diis")
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: 3)
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.
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)
overwrite_inputs (dict): Dictionary of QChem input sections to add or overwrite variables.
The currently available sections (keys) are rem, pcm, solvent, smx, 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.**
"""
self.basis_set = basis_set
self.scf_algorithm = scf_algorithm
self.max_scf_cycles = max_scf_cycles
super().__init__(
molecule=molecule,
job_type="force",
dft_rung=dft_rung,
pcm_dielectric=pcm_dielectric,
smd_solvent=smd_solvent,
custom_smd=custom_smd,
basis_set=self.basis_set,
scf_algorithm=self.scf_algorithm,
max_scf_cycles=self.max_scf_cycles,
plot_cubes=plot_cubes,
overwrite_inputs=overwrite_inputs,
)
[docs]class FreqSet(QChemDictSet):
"""
QChemDictSet for a frequency calculation
"""
def __init__(
self,
molecule: Molecule,
basis_set: str = "def2-tzvppd",
scf_algorithm: str = "diis",
dft_rung: int = 3,
pcm_dielectric: Optional[float] = None,
smd_solvent: Optional[str] = None,
custom_smd: Optional[str] = None,
max_scf_cycles: int = 200,
plot_cubes: bool = False,
overwrite_inputs: Optional[Dict] = None,
):
"""
Args:
molecule (Pymatgen Molecule object)
basis_set (str): Basis set to use. (Default: "def2-tzvppd")
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.
(Default: "diis")
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: 3)
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.
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)
overwrite_inputs (dict): Dictionary of QChem input sections to add or overwrite variables.
The currently available sections (keys) are rem, pcm, solvent, smx, 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.**
"""
self.basis_set = basis_set
self.scf_algorithm = scf_algorithm
self.max_scf_cycles = max_scf_cycles
super().__init__(
molecule=molecule,
job_type="freq",
dft_rung=dft_rung,
pcm_dielectric=pcm_dielectric,
smd_solvent=smd_solvent,
custom_smd=custom_smd,
basis_set=self.basis_set,
scf_algorithm=self.scf_algorithm,
max_scf_cycles=self.max_scf_cycles,
plot_cubes=plot_cubes,
overwrite_inputs=overwrite_inputs,
)
[docs]class PESScanSet(QChemDictSet):
"""
QChemDictSet for a potential energy surface scan (PES_SCAN) calculation,
used primarily to identify possible transition states or to sample different
geometries.
Note: Because there are no defaults that can be used for a PES scan (the
variables are completely dependent on the molecular structure), by default
scan_variables = None. However, a PES Scan job should not be run with less
than one variable (or more than two variables).
"""
def __init__(
self,
molecule: Molecule,
basis_set: str = "def2-tzvppd",
scf_algorithm: str = "diis",
dft_rung: int = 3,
pcm_dielectric: Optional[float] = None,
smd_solvent: Optional[str] = None,
custom_smd: Optional[str] = None,
max_scf_cycles: int = 200,
plot_cubes: bool = False,
opt_variables: Optional[Dict[str, List]] = None,
scan_variables: Optional[Dict[str, List]] = None,
overwrite_inputs: Optional[Dict] = None,
):
"""
Args:
molecule (Pymatgen Molecule object)
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"]}
basis_set (str): Basis set to use. (Default: "def2-tzvppd")
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.
(Default: "diis")
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: 3)
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.
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)
overwrite_inputs (dict): Dictionary of QChem input sections to add or overwrite variables.
The currently available sections (keys) are rem, pcm, solvent, smx, 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.**
"""
self.basis_set = basis_set
self.scf_algorithm = scf_algorithm
self.max_scf_cycles = max_scf_cycles
if scan_variables is None:
raise ValueError("Cannot run a pes_scan job without some variable " "to scan over!")
super().__init__(
molecule=molecule,
job_type="pes_scan",
dft_rung=dft_rung,
pcm_dielectric=pcm_dielectric,
smd_solvent=smd_solvent,
custom_smd=custom_smd,
opt_variables=opt_variables,
scan_variables=scan_variables,
basis_set=self.basis_set,
scf_algorithm=self.scf_algorithm,
max_scf_cycles=self.max_scf_cycles,
plot_cubes=plot_cubes,
overwrite_inputs=overwrite_inputs,
)