pymatgen.apps.borg.hive — pymatgen 2020.7.3 documentation

# Source code for pymatgen.apps.borg.hive

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

    """
    This module define the various drones used to assimilate data.
    """

    import abc
    import os
    import glob
    import logging
    import json
    import warnings

    from monty.io import zopen
    from pymatgen.io.vasp.inputs import Incar, Potcar, Poscar
    from pymatgen.io.vasp.outputs import Vasprun, Oszicar, Dynmat
    from pymatgen.io.gaussian import GaussianOutput
    from pymatgen.entries.computed_entries import ComputedEntry, \
        ComputedStructureEntry
    from monty.json import MSONable

    logger = logging.getLogger(__name__)

    class AbstractDrone(MSONable, metaclass=abc.ABCMeta):
        """
        Abstract drone class that defines the various methods that must be
        implemented by drones. Because of the quirky nature of Python"s
        multiprocessing, the intermediate data representations has to be in the
        form of python primitives. So all objects that drones work with must be
        MSONable. All drones must also implement the standard MSONable as_dict() and
        from_dict API.
        """

        @abc.abstractmethod
        def assimilate(self, path):
            """
            Assimilate data in a directory path into a pymatgen object. Because of
            the quirky nature of Python"s multiprocessing, the object must support
            pymatgen's as_dict() for parallel processing.

            Args:
                path: directory path

            Returns:
                An assimilated object
            """
            return

        @abc.abstractmethod
        def get_valid_paths(self, path):
            """
            Checks if path contains valid data for assimilation, and then returns
            the valid paths. The paths returned can be a list of directory or file
            paths, depending on what kind of data you are assimilating. For
            example, if you are assimilating VASP runs, you are only interested in
            directories containing vasprun.xml files. On the other hand, if you are
            interested converting all POSCARs in a directory tree to cifs for
            example, you will want the file paths.

            Args:
                path: input path as a tuple generated from os.walk, i.e.,
                    (parent, subdirs, files).

            Returns:
                List of valid dir/file paths for assimilation
            """
            return

    class VaspToComputedEntryDrone(AbstractDrone):
        """
        VaspToEntryDrone assimilates directories containing vasp output to
        ComputedEntry/ComputedStructureEntry objects. There are some restrictions
        on the valid directory structures:

        1. There can be only one vasp run in each directory.
        2. Directories designated "relax1", "relax2" are considered to be 2 parts
           of an aflow style run, and only "relax2" is parsed.
        3. The drone parses only the vasprun.xml file.
        """

        def __init__(self, inc_structure=False, parameters=None, data=None):
            """
            Args:
                inc_structure (bool): Set to True if you want
                    ComputedStructureEntries to be returned instead of
                    ComputedEntries.
                parameters (list): Input parameters to include. It has to be one of
                    the properties supported by the Vasprun object. See
                    :class:`pymatgen.io.vasp.Vasprun`. If parameters is None,
                    a default set of parameters that are necessary for typical
                    post-processing will be set.
                data (list): Output data to include. Has to be one of the properties
                    supported by the Vasprun object.
            """
            self._inc_structure = inc_structure
            self._parameters = {"is_hubbard", "hubbards", "potcar_spec",
                                "potcar_symbols", "run_type"}
            if parameters:
                self._parameters.update(parameters)
            self._data = data if data else []

        def assimilate(self, path):
            """
            Assimilate data in a directory path into a ComputedEntry object.

            Args:
                path: directory path

            Returns:
                ComputedEntry
            """
            files = os.listdir(path)
            if "relax1" in files and "relax2" in files:
                filepath = glob.glob(os.path.join(path, "relax2",
                                                  "vasprun.xml*"))[0]
            else:
                vasprun_files = glob.glob(os.path.join(path, "vasprun.xml*"))
                filepath = None
                if len(vasprun_files) == 1:
                    filepath = vasprun_files[0]
                elif len(vasprun_files) > 1:
                    # Since multiple files are ambiguous, we will always read
                    # the one that it the last one alphabetically.
                    filepath = sorted(vasprun_files)[-1]
                    warnings.warn("%d vasprun.xml.* found. %s is being parsed." %
                                  (len(vasprun_files), filepath))

            try:
                vasprun = Vasprun(filepath)
            except Exception as ex:
                logger.debug("error in {}: {}".format(filepath, ex))
                return None

            entry = vasprun.get_computed_entry(self._inc_structure,
                                               parameters=self._parameters,
                                               data=self._data)

            # entry.parameters["history"] = _get_transformation_history(path)
            return entry

        def get_valid_paths(self, path):
            """
            Checks if paths contains vasprun.xml or (POSCAR+OSZICAR)

            Args:
                path: input path as a tuple generated from os.walk, i.e.,
                    (parent, subdirs, files).

            Returns:
                List of valid dir/file paths for assimilation
            """
            (parent, subdirs, files) = path
            if "relax1" in subdirs and "relax2" in subdirs:
                return [parent]
            if (not parent.endswith("/relax1")) and \
                    (not parent.endswith("/relax2")) and (
                    len(glob.glob(os.path.join(parent, "vasprun.xml*"))) > 0 or (
                    len(glob.glob(os.path.join(parent, "POSCAR*"))) > 0 and
                    len(glob.glob(os.path.join(parent, "OSZICAR*"))) > 0)
            ):
                return [parent]
            return []

        def __str__(self):
            return " VaspToComputedEntryDrone"

        def as_dict(self):
            """
            Returns: MSONABle dict
            """
            return {"init_args": {"inc_structure": self._inc_structure,
                                  "parameters": self._parameters,
                                  "data": self._data},
                    "@module": self.__class__.__module__,
                    "@class": self.__class__.__name__}

        @classmethod
        def from_dict(cls, d):
            """
            Args:
                d (dict): Dict Representation

            Returns:
                VaspToComputedEntryDrone
            """
            return cls(**d["init_args"])

    class SimpleVaspToComputedEntryDrone(VaspToComputedEntryDrone):
        """
        A simpler VaspToComputedEntryDrone. Instead of parsing vasprun.xml, it
        parses only the INCAR, POTCAR, OSZICAR and KPOINTS files, which are much
        smaller and faster to parse. However, much fewer properties are available
        compared to the standard VaspToComputedEntryDrone.
        """

        def __init__(self, inc_structure=False):
            """
            Args:
                inc_structure (bool): Set to True if you want
                    ComputedStructureEntries to be returned instead of
                    ComputedEntries. Structure will be parsed from the CONTCAR.
            """
            self._inc_structure = inc_structure
            self._parameters = {"is_hubbard", "hubbards", "potcar_spec",
                                "run_type"}

        def assimilate(self, path):
            """
            Assimilate data in a directory path into a ComputedEntry object.

            Args:
                path: directory path

            Returns:
                ComputedEntry
            """
            files = os.listdir(path)
            try:
                files_to_parse = {}
                if "relax1" in files and "relax2" in files:
                    for filename in ("INCAR", "POTCAR", "POSCAR"):
                        search_str = os.path.join(path, "relax1", filename + "*")
                        files_to_parse[filename] = glob.glob(search_str)[0]
                    for filename in ("CONTCAR", "OSZICAR"):
                        search_str = os.path.join(path, "relax2", filename + "*")
                        files_to_parse[filename] = glob.glob(search_str)[-1]
                else:
                    for filename in (
                            "INCAR", "POTCAR", "CONTCAR", "OSZICAR", "POSCAR", "DYNMAT"
                    ):
                        files = sorted(glob.glob(os.path.join(path, filename + "*")))
                        if len(files) < 1:
                            continue
                        if len(files) == 1 or filename == "INCAR" or \
                                filename == "POTCAR" or filename == "DYNMAT":
                            files_to_parse[filename] = files[-1] \
                                if filename == "POTCAR" else files[0]
                        elif len(files) > 1:
                            # Since multiple files are ambiguous, we will always
                            # use the first one for POSCAR and the last one
                            # alphabetically for CONTCAR and OSZICAR.

                            if filename == "POSCAR":
                                files_to_parse[filename] = files[0]
                            else:
                                files_to_parse[filename] = files[-1]
                            warnings.warn(
                                "%d files found. %s is being parsed." %
                                (len(files), files_to_parse[filename]))

                poscar, contcar, incar, potcar, oszicar, dynmat = [None] * 6
                if 'POSCAR' in files_to_parse:
                    poscar = Poscar.from_file(files_to_parse["POSCAR"])
                if 'CONTCAR' in files_to_parse:
                    contcar = Poscar.from_file(files_to_parse["CONTCAR"])
                if 'INCAR' in files_to_parse:
                    incar = Incar.from_file(files_to_parse["INCAR"])
                if 'POTCAR' in files_to_parse:
                    potcar = Potcar.from_file(files_to_parse["POTCAR"])
                if 'OSZICAR' in files_to_parse:
                    oszicar = Oszicar(files_to_parse["OSZICAR"])
                if 'DYNMAT' in files_to_parse:
                    dynmat = Dynmat(files_to_parse["DYNMAT"])

                param = {"hubbards": {}}
                if poscar is not None and incar is not None and "LDAUU" in incar:
                    param["hubbards"] = dict(zip(poscar.site_symbols,
                                                 incar["LDAUU"]))
                param["is_hubbard"] = (
                        incar.get("LDAU", True) and sum(param["hubbards"].values()) > 0
                ) if incar is not None else False
                param["run_type"] = None
                param["potcar_spec"] = potcar.spec if potcar is not None else None
                energy = oszicar.final_energy if oszicar is not None else Vasprun.final_energy
                structure = contcar.structure if contcar is not None \
                    else poscar.structure
                initial_vol = poscar.structure.volume if poscar is not None else \
                    None
                final_vol = contcar.structure.volume if contcar is not None else \
                    None
                delta_volume = None
                if initial_vol is not None and final_vol is not None:
                    delta_volume = (final_vol / initial_vol - 1)
                data = {"filename": path, "delta_volume": delta_volume}
                if dynmat is not None:
                    data['phonon_frequencies'] = dynmat.get_phonon_frequencies()
                if self._inc_structure:
                    entry = ComputedStructureEntry(
                        structure, energy, parameters=param, data=data
                    )
                else:
                    entry = ComputedEntry(
                        structure.composition, energy, parameters=param, data=data
                    )
                return entry

            except Exception as ex:
                logger.debug("error in {}: {}".format(path, ex))
                return None

        def __str__(self):
            return "SimpleVaspToComputedEntryDrone"

        def as_dict(self):
            """
            Returns: MSONAble dict
            """
            return {"init_args": {"inc_structure": self._inc_structure},
                    "@module": self.__class__.__module__,
                    "@class": self.__class__.__name__}

        @classmethod
        def from_dict(cls, d):
            """
            Args:
                d (dict): Dict Representation

            Returns:
                SimpleVaspToComputedEntryDrone
            """
            return cls(**d["init_args"])

    class GaussianToComputedEntryDrone(AbstractDrone):
        """
        GaussianToEntryDrone assimilates directories containing Gaussian output to
        ComputedEntry/ComputedStructureEntry objects. By default, it is assumed
        that Gaussian output files have a ".log" extension.

        .. note::

            Like the GaussianOutput class, this is still in early beta.
        """

        def __init__(self, inc_structure=False, parameters=None, data=None,
                     file_extensions=(".log",)):
            """
            Args:
                inc_structure (bool): Set to True if you want
                    ComputedStructureEntries to be returned instead of
                    ComputedEntries.
                parameters (list): Input parameters to include. It has to be one of
                    the properties supported by the GaussianOutput object. See
                    :class:`pymatgen.io.gaussianio GaussianOutput`. The parameters
                    have to be one of python"s primitive types, i.e., list, dict of
                    strings and integers. If parameters is None, a default set of
                    parameters will be set.
                data (list): Output data to include. Has to be one of the properties
                    supported by the GaussianOutput object. The parameters have to
                    be one of python"s primitive types, i.e. list, dict of strings
                    and integers. If data is None, a default set will be set.
                file_extensions (list):
                    File extensions to be considered as Gaussian output files.
                    Defaults to just the typical "log" extension.
            """
            self._inc_structure = inc_structure
            self._parameters = {"functional", "basis_set", "charge",
                                "spin_multiplicity", "route_parameters"}

            if parameters:
                self._parameters.update(parameters)

            self._data = {"stationary_type", "properly_terminated"}
            if data:
                self._data.update(data)

            self._file_extensions = file_extensions

        def assimilate(self, path):
            """
            Assimilate data in a directory path into a ComputedEntry object.

            Args:
                path: directory path

            Returns:
                ComputedEntry
            """
            try:
                gaurun = GaussianOutput(path)
            except Exception as ex:
                logger.debug("error in {}: {}".format(path, ex))
                return None
            param = {}
            for p in self._parameters:
                param[p] = getattr(gaurun, p)
            data = {}
            for d in self._data:
                data[d] = getattr(gaurun, d)
            if self._inc_structure:
                entry = ComputedStructureEntry(gaurun.final_structure,
                                               gaurun.final_energy,
                                               parameters=param,
                                               data=data)
            else:
                entry = ComputedEntry(gaurun.final_structure.composition,
                                      gaurun.final_energy, parameters=param,
                                      data=data)
            return entry

        def get_valid_paths(self, path):
            """
            Checks if path contains files with define extensions.

            Args:
                path: input path as a tuple generated from os.walk, i.e.,
                    (parent, subdirs, files).

            Returns:
                List of valid dir/file paths for assimilation
            """
            parent, subdirs, files = path
            return [os.path.join(parent, f) for f in files
                    if os.path.splitext(f)[1] in self._file_extensions]

        def __str__(self):
            return " GaussianToComputedEntryDrone"

        def as_dict(self):
            """
            Returns: MSONable dict
            """
            return {"init_args": {"inc_structure": self._inc_structure,
                                  "parameters": self._parameters,
                                  "data": self._data,
                                  "file_extensions": self._file_extensions},
                    "@module": self.__class__.__module__,
                    "@class": self.__class__.__name__}

        @classmethod
        def from_dict(cls, d):
            """
            Args:
                d (dict): Dict Representation

            Returns:
                GaussianToComputedEntryDrone
            """
            return cls(**d["init_args"])

    def _get_transformation_history(path):
        """
        Checks for a transformations.json* file and returns the history.
        """
        trans_json = glob.glob(os.path.join(path, "transformations.json*"))
        if trans_json:
            try:
                with zopen(trans_json[0]) as f:
                    return json.load(f)["history"]
            except Exception:
                return None
        return None