pymatgen.io.qchem.inputs — pymatgen 2020.7.3 documentation

# Source code for pymatgen.io.qchem.inputs

    # coding: utf-8
    # Copyright (c) Pymatgen Development Team.
    # Distributed under the terms of the MIT License.

    """
    Classes for reading/manipulating/writing QChem input files.
    """

    import logging
    from monty.json import MSONable
    from monty.io import zopen
    from pymatgen.core import Molecule
    from .utils import read_table_pattern, read_pattern, lower_and_check_unique

    __author__ = "Brandon Wood, Samuel Blau, Shyam Dwaraknath, Julian Self"
    __copyright__ = "Copyright 2018, The Materials Project"
    __version__ = "0.1"
    __email__ = "b.wood@berkeley.edu"
    __credits__ = "Xiaohui Qu"

    logger = logging.getLogger(__name__)

    class QCInput(MSONable):
        """
        An object representing a QChem input file. QCInput attributes represent different sections of a QChem input file.
        To add a new section one needs to modify __init__, __str__, from_sting and add staticmethods
        to read and write the new section i.e. section_template and read_section. By design, there is very little (or no)
        checking that input parameters conform to the appropriate QChem format, this responsible lands on the user or a
        separate error handling software.
        """

        def __init__(self, molecule, rem, opt=None, pcm=None, solvent=None, smx=None):
            """
            Args:
                molecule (pymatgen Molecule object or "read"):
                    Input molecule. molecule can be set as either a pymatgen Molecule object or as the str "read".
                    "read" can be used in multi_job QChem input files where the molecule is read in from the
                    previous calculation.
                rem (dict):
                    A dictionary of all the input parameters for the rem section of QChem input file.
                    Ex. rem = {'method': 'rimp2', 'basis': '6-31*G++' ... }
                opt (dict of lists):
                    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"]}
            """
            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", "force", "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")

            # Still to do:
            #   - Check that the method or functional is valid
            #   - Check that basis is valid
            #   - Check that basis is defined for all species in the molecule
            #   - Validity checks specific to job type?
            #   - Check OPT and PCM sections?

        def __str__(self):
            combined_list = []
            # molecule section
            combined_list.append(self.molecule_template(self.molecule))
            combined_list.append("")
            # rem section
            combined_list.append(self.rem_template(self.rem))
            combined_list.append("")
            # opt section
            if self.opt:
                combined_list.append(self.opt_template(self.opt))
                combined_list.append("")
            # pcm section
            if self.pcm:
                combined_list.append(self.pcm_template(self.pcm))
                combined_list.append("")
            # solvent section
            if self.solvent:
                combined_list.append(self.solvent_template(self.solvent))
                combined_list.append("")
            if self.smx:
                combined_list.append(self.smx_template(self.smx))
                combined_list.append("")
            return '\n'.join(combined_list)

        @staticmethod
        def multi_job_string(job_list):
            """
            Args:
                job_list (): List of jobs

            Returns:
                (str) String representation of multi job input file.
            """
            multi_job_string = str()
            for i, job_i in enumerate(job_list):
                if i < len(job_list) - 1:
                    multi_job_string += job_i.__str__() + "\n@@@\n\n"
                else:
                    multi_job_string += job_i.__str__()
            return multi_job_string

        @classmethod
        def from_string(cls, string):
            """
            Read QcInput from string.

            Args:
                string (str): String input.

            Returns:
                QcInput
            """
            sections = cls.find_sections(string)
            molecule = cls.read_molecule(string)
            rem = cls.read_rem(string)
            # only molecule and rem are necessary everything else is checked
            opt = None
            pcm = None
            solvent = None
            smx = None
            if "opt" in sections:
                opt = cls.read_opt(string)
            if "pcm" in sections:
                pcm = cls.read_pcm(string)
            if "solvent" in sections:
                solvent = cls.read_solvent(string)
            if "smx" in sections:
                smx = cls.read_smx(string)
            return cls(molecule, rem, opt=opt, pcm=pcm, solvent=solvent, smx=smx)

        def write_file(self, filename):
            """
            Write QcInput to file.

            Args:
                filename (str): Filename
            """
            with zopen(filename, 'wt') as f:
                f.write(self.__str__())

        @staticmethod
        def write_multi_job_file(job_list, filename):
            """
            Write a multijob file.

            Args:
                job_list (): List of jobs.
                filename (): Filename
            """
            with zopen(filename, 'wt') as f:
                f.write(QCInput.multi_job_string(job_list))

        @staticmethod
        def from_file(filename):
            """
            Create QcInput from file.
            Args:
                filename (str): Filename

            Returns:
                QcInput
            """
            with zopen(filename, 'rt') as f:
                return QCInput.from_string(f.read())

        @classmethod
        def from_multi_jobs_file(cls, filename):
            """
            Create list of QcInput from a file.
            Args:
                filename (str): Filename

            Returns:
                List of QCInput objects
            """
            with zopen(filename, 'rt') as f:
                # the delimiter between QChem jobs is @@@
                multi_job_strings = f.read().split("@@@")
                # list of individual QChem jobs
                input_list = [cls.from_string(i) for i in multi_job_strings]
                return input_list

        @staticmethod
        def molecule_template(molecule):
            """
            Args:
                molecule (Molecule): molecule

            Returns:
                (str) Molecule template.
            """
            # todo: add ghost atoms
            mol_list = []
            mol_list.append("$molecule")
            if isinstance(molecule, str):
                if molecule == "read":
                    mol_list.append(" read")
                else:
                    raise ValueError('The only acceptable text value for molecule is "read"')
            else:
                mol_list.append(" {charge} {spin_mult}".format(
                    charge=int(molecule.charge),
                    spin_mult=molecule.spin_multiplicity))
                for site in molecule.sites:
                    mol_list.append(
                        " {atom}     {x: .10f}     {y: .10f}     {z: .10f}".format(
                            atom=site.species_string, x=site.x, y=site.y,
                            z=site.z))
            mol_list.append("$end")
            return '\n'.join(mol_list)

        @staticmethod
        def rem_template(rem):
            """
            Args:
                rem ():

            Returns:
                (str)
            """
            rem_list = []
            rem_list.append("$rem")
            for key, value in rem.items():
                rem_list.append("   {key} = {value}".format(key=key, value=value))
            rem_list.append("$end")
            return '\n'.join(rem_list)

        @staticmethod
        def opt_template(opt):
            """
            Optimization template.

            Args:
                opt ():

            Returns:
                (str)
            """
            opt_list = []
            opt_list.append("$opt")
            # loops over all opt sections
            for key, value in opt.items():
                opt_list.append("{section}".format(section=key))
                # loops over all values within the section
                for i in value:
                    opt_list.append("   {val}".format(val=i))
                opt_list.append("END{section}".format(section=key))
                opt_list.append("")
            # this deletes the empty space after the last section
            del opt_list[-1]
            opt_list.append("$end")
            return '\n'.join(opt_list)

        @staticmethod
        def pcm_template(pcm):
            """
            Pcm run template.

            Args:
                pcm ():

            Returns:
                (str)
            """
            pcm_list = []
            pcm_list.append("$pcm")
            for key, value in pcm.items():
                pcm_list.append("   {key} {value}".format(key=key, value=value))
            pcm_list.append("$end")
            return '\n'.join(pcm_list)

        @staticmethod
        def solvent_template(solvent):
            """
            Solvent template.

            Args:
                solvent ():

            Returns:
                (str)
            """
            solvent_list = []
            solvent_list.append("$solvent")
            for key, value in solvent.items():
                solvent_list.append("   {key} {value}".format(
                    key=key, value=value))
            solvent_list.append("$end")
            return '\n'.join(solvent_list)

        @staticmethod
        def smx_template(smx):
            """
            Args:
                smx ():

            Returns:
                (str)
            """
            smx_list = []
            smx_list.append("$smx")
            for key, value in smx.items():
                if value == "tetrahydrofuran":
                    smx_list.append("   {key} {value}".format(
                        key=key, value="thf"))
                else:
                    smx_list.append("   {key} {value}".format(
                        key=key, value=value))
            smx_list.append("$end")
            return '\n'.join(smx_list)

        @staticmethod
        def find_sections(string):
            """
            Find sections in the string.

            Args:
                string (str): String

            Returns:
                List of sections.
            """
            patterns = {"sections": r"^\s*?\$([a-z]+)", "multiple_jobs": r"(@@@)"}
            matches = read_pattern(string, patterns)
            # list of the sections present
            sections = [val[0] for val in matches["sections"]]
            # remove end from sections
            sections = [sec for sec in sections if sec != 'end']
            # this error should be replaced by a multi job read function when it is added
            if "multiple_jobs" in matches.keys():
                raise ValueError(
                    "Output file contains multiple qchem jobs please parse separately"
                )
            if "molecule" not in sections:
                raise ValueError("Output file does not contain a molecule section")
            if "rem" not in sections:
                raise ValueError("Output file does not contain a rem section")
            return sections

        @staticmethod
        def read_molecule(string):
            """
            Read molecule from string.

            Args:
                string (str): String

            Returns:
                Molecule
            """
            charge = None
            spin_mult = None
            patterns = {
                "read": r"^\s*\$molecule\n\s*(read)",
                "charge": r"^\s*\$molecule\n\s*((?:\-)*\d+)\s+\d",
                "spin_mult": r"^\s*\$molecule\n\s(?:\-)*\d+\s*(\d)"
            }
            matches = read_pattern(string, patterns)
            if "read" in matches.keys():
                return "read"
            if "charge" in matches.keys():
                charge = float(matches["charge"][0][0])
            if "spin_mult" in matches.keys():
                spin_mult = int(matches["spin_mult"][0][0])
            header = r"^\s*\$molecule\n\s*(?:\-)*\d+\s*\d"
            row = r"\s*((?i)[a-z]+)\s+([\d\-\.]+)\s+([\d\-\.]+)\s+([\d\-\.]+)"
            footer = r"^\$end"
            mol_table = read_table_pattern(
                string,
                header_pattern=header,
                row_pattern=row,
                footer_pattern=footer)
            species = [val[0] for val in mol_table[0]]
            coords = [[float(val[1]), float(val[2]),
                       float(val[3])] for val in mol_table[0]]
            mol = Molecule(
                species=species,
                coords=coords,
                charge=charge,
                spin_multiplicity=spin_mult)
            return mol

        @staticmethod
        def read_rem(string):
            """
            Parse rem from string.

            Args:
                string (str): String

            Returns:
                (dict) rem
            """
            header = r"^\s*\$rem"
            row = r"\s*([a-zA-Z\_]+)\s*=?\s*(\S+)"
            footer = r"^\s*\$end"
            rem_table = read_table_pattern(
                string,
                header_pattern=header,
                row_pattern=row,
                footer_pattern=footer)
            rem = {key: val for key, val in rem_table[0]}
            return rem

        @staticmethod
        def read_opt(string):
            """
            Read opt section from string.

            Args:
                string (str): String

            Returns:
                (dict) Opt section
            """
            patterns = {
                "CONSTRAINT": r"^\s*CONSTRAINT",
                "FIXED": r"^\s*FIXED",
                "DUMMY": r"^\s*DUMMY",
                "CONNECT": r"^\s*CONNECT"
            }
            opt_matches = read_pattern(string, patterns)
            opt_sections = [key for key in opt_matches.keys()]
            opt = {}
            if "CONSTRAINT" in opt_sections:
                c_header = r"^\s*CONSTRAINT\n"
                c_row = r"(\w.*)\n"
                c_footer = r"^\s*ENDCONSTRAINT\n"
                c_table = read_table_pattern(
                    string,
                    header_pattern=c_header,
                    row_pattern=c_row,
                    footer_pattern=c_footer)
                opt["CONSTRAINT"] = [val[0] for val in c_table[0]]
            if "FIXED" in opt_sections:
                f_header = r"^\s*FIXED\n"
                f_row = r"(\w.*)\n"
                f_footer = r"^\s*ENDFIXED\n"
                f_table = read_table_pattern(
                    string,
                    header_pattern=f_header,
                    row_pattern=f_row,
                    footer_pattern=f_footer)
                opt["FIXED"] = [val[0] for val in f_table[0]]
            if "DUMMY" in opt_sections:
                d_header = r"^\s*DUMMY\n"
                d_row = r"(\w.*)\n"
                d_footer = r"^\s*ENDDUMMY\n"
                d_table = read_table_pattern(
                    string,
                    header_pattern=d_header,
                    row_pattern=d_row,
                    footer_pattern=d_footer)
                opt["DUMMY"] = [val[0] for val in d_table[0]]
            if "CONNECT" in opt_sections:
                cc_header = r"^\s*CONNECT\n"
                cc_row = r"(\w.*)\n"
                cc_footer = r"^\s*ENDCONNECT\n"
                cc_table = read_table_pattern(
                    string,
                    header_pattern=cc_header,
                    row_pattern=cc_row,
                    footer_pattern=cc_footer)
                opt["CONNECT"] = [val[0] for val in cc_table[0]]
            return opt

        @staticmethod
        def read_pcm(string):
            """
            Read pcm parameters from string.

            Args:
                string (str): String

            Returns:
                (dict) PCM parameters
            """
            header = r"^\s*\$pcm"
            row = r"\s*([a-zA-Z\_]+)\s+(\S+)"
            footer = r"^\s*\$end"
            pcm_table = read_table_pattern(
                string,
                header_pattern=header,
                row_pattern=row,
                footer_pattern=footer)
            if pcm_table == []:
                print(
                    "No valid PCM inputs found. Note that there should be no '=' chracters in PCM input lines."
                )
                return {}
            else:
                pcm = {key: val for key, val in pcm_table[0]}
                return pcm

        @staticmethod
        def read_solvent(string):
            """
            Read solvent parameters from string.

            Args:
                string (str): String

            Returns:
                (dict) Solvent parameters
            """
            header = r"^\s*\$solvent"
            row = r"\s*([a-zA-Z\_]+)\s+(\S+)"
            footer = r"^\s*\$end"
            solvent_table = read_table_pattern(
                string,
                header_pattern=header,
                row_pattern=row,
                footer_pattern=footer)
            if solvent_table == []:
                print(
                    "No valid solvent inputs found. Note that there should be no '=' chracters in solvent input lines."
                )
                return {}
            else:
                solvent = {key: val for key, val in solvent_table[0]}
                return solvent

        @staticmethod
        def read_smx(string):
            """
            Read smx parameters from string.

            Args:
                string (str): String

            Returns:
                (dict) SMX parameters.
            """
            header = r"^\s*\$smx"
            row = r"\s*([a-zA-Z\_]+)\s+(\S+)"
            footer = r"^\s*\$end"
            smx_table = read_table_pattern(
                string,
                header_pattern=header,
                row_pattern=row,
                footer_pattern=footer)
            if smx_table == []:
                print(
                    "No valid smx inputs found. Note that there should be no '=' chracters in smx input lines."
                )
                return {}
            else:
                smx = {key: val for key, val in smx_table[0]}
                if smx["solvent"] == "tetrahydrofuran":
                    smx["solvent"] = "thf"
                return smx