pymatgen.io.qchem.sets — pymatgen 2020.7.3 documentation

# 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__)

    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)

        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)

    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)

    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)

    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)