Source code for pymatgen.io.qchem.sets

# 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 monty.io import zopen
from pymatgen.io.qchem.inputs import QCInput
from pymatgen.io.qchem.utils import lower_and_check_unique


__author__ = "Samuel Blau, Brandon Wood, Shyam Dwaraknath"
__copyright__ = "Copyright 2018, 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, 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)
[docs] def write(self, input_file): """ 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 OptSet(QChemDictSet): """ QChemDictSet for a geometry optimization """ def __init__(self, molecule, dft_rung=3, basis_set="def2-tzvppd", pcm_dielectric=None, smd_solvent=None, custom_smd=None, scf_algorithm="diis", max_scf_cycles=200, geom_opt_max_cycles=200, overwrite_inputs=None): """ Args: molecule (): dft_rung (): basis_set (): pcm_dielectric (): smd_solvent (): custom_smd (): scf_algorithm (): max_scf_cycles (): geom_opt_max_cycles (): overwrite_inputs (): """ 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, 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, overwrite_inputs=overwrite_inputs)
[docs]class SinglePointSet(QChemDictSet): """ QChemDictSet for a single point calculation """ def __init__(self, molecule, dft_rung=3, basis_set="def2-tzvppd", pcm_dielectric=None, smd_solvent=None, custom_smd=None, scf_algorithm="diis", max_scf_cycles=200, overwrite_inputs=None): """ Args: molecule (): dft_rung (): basis_set (): pcm_dielectric (): smd_solvent (): custom_smd (): scf_algorithm (): max_scf_cycles (): overwrite_inputs (): """ 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, overwrite_inputs=overwrite_inputs)
[docs]class FreqSet(QChemDictSet): """ QChemDictSet for a single point calculation """ def __init__(self, molecule, dft_rung=3, basis_set="def2-tzvppd", pcm_dielectric=None, smd_solvent=None, custom_smd=None, scf_algorithm="diis", max_scf_cycles=200, overwrite_inputs=None): """ Args: molecule (): dft_rung (): basis_set (): pcm_dielectric (): smd_solvent (): custom_smd (): scf_algorithm (): max_scf_cycles (): overwrite_inputs (): """ 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, overwrite_inputs=overwrite_inputs)