pymatgen.io.feff.sets — pymatgen 2020.7.3 documentation

# Source code for pymatgen.io.feff.sets

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

    """
    This module defines the FeffInputSet abstract base class and a concrete
    implementation for the Materials Project.  The basic concept behind an input
    set is to specify a scheme to generate a consistent set of Feff inputs from a
    structure without further user intervention. This ensures comparability across
    runs.
    """

    import sys
    import os
    import abc
    from copy import deepcopy
    import logging

    from monty.serialization import loadfn
    from monty.json import MSONable
    from monty.os.path import zpath

    from pymatgen.io.feff.inputs import Atoms, Tags, Potential, Header
    import numpy as np

    __author__ = "Kiran Mathew"
    __credits__ = "Alan Dozier, Anubhav Jain, Shyue Ping Ong"
    __version__ = "1.1"
    __maintainer__ = "Kiran Mathew"
    __email__ = "kmathew@lbl.gov"
    __date__ = "Sept 10, 2016"

    MODULE_DIR = os.path.dirname(os.path.abspath(__file__))

    logger = logging.getLogger(__name__)
    logger.setLevel(logging.DEBUG)
    formatter = logging.Formatter('%(asctime)s: %(levelname)s: %(name)s: %(message)s')
    sh = logging.StreamHandler(stream=sys.stdout)
    sh.setFormatter(formatter)
    logger.addHandler(sh)

    class AbstractFeffInputSet(MSONable, metaclass=abc.ABCMeta):
        """
        Abstract base class representing a set of Feff input parameters.
        The idea is that using a FeffInputSet, a complete set of input files
        (feffPOT, feffXANES, feffEXAFS, ATOMS, feff.inp)set_
        can be generated in an automated fashion for any structure.
        """

        @abc.abstractmethod
        def header(self):
            """
            Returns header to be used in feff.inp file from a pymatgen structure
            """
            pass

        @property
        @abc.abstractmethod
        def atoms(self):
            """
            Returns Atoms string from a structure that goes in feff.inp file.

            Returns:
                Atoms object.
            """
            pass

        @property
        @abc.abstractmethod
        def tags(self):
            """
            Returns standard calculation parameters.
            """
            return

        @property
        @abc.abstractmethod
        def potential(self):
            """
            Returns POTENTIAL section used in feff.inp from a structure.
            """
            pass

        def all_input(self):
            """
            Returns all input files as a dict of {filename: feffio object}
            """
            d = {"HEADER": self.header(), "PARAMETERS": self.tags}

            if "RECIPROCAL" not in self.tags:
                d.update({"POTENTIALS": self.potential, "ATOMS": self.atoms})

            return d

        def write_input(self, output_dir=".", make_dir_if_not_present=True):
            """
            Writes a set of FEFF input to a directory.

            Args:
                output_dir: Directory to output the FEFF input files
                make_dir_if_not_present: Set to True if you want the directory (
                    and the whole path) to be created if it is not present.
            """
            if make_dir_if_not_present and not os.path.exists(output_dir):
                os.makedirs(output_dir)

            feff = self.all_input()

            feff_input = "\n\n".join(str(feff[k]) for k in
                                     ["HEADER", "PARAMETERS", "POTENTIALS", "ATOMS"]
                                     if k in feff)

            for k, v in feff.items():
                with open(os.path.join(output_dir, k), "w") as f:
                    f.write(str(v))

            with open(os.path.join(output_dir, "feff.inp"), "w") as f:
                f.write(feff_input)

            # write the structure to cif file
            if "ATOMS" not in feff:
                self.atoms.struct.to(fmt="cif",
                                     filename=os.path.join(
                                         output_dir, feff["PARAMETERS"]["CIF"]))

    class FEFFDictSet(AbstractFeffInputSet):
        """
        Standard implementation of FeffInputSet, which can be extended by specific
        implementations.
        """

        def __init__(self, absorbing_atom, structure, radius, config_dict,
                     edge="K", spectrum="EXAFS", nkpts=1000,
                     user_tag_settings=None):
            """

            Args:
                absorbing_atom (str/int): absorbing atom symbol or site index
                structure (Structure): input structure
                radius (float): cluster radius
                config_dict (dict): control tag settings dict
                edge (str): absorption edge
                spectrum (str): type of spectrum to calculate, available options :
                    EXAFS, XANES, DANES, XMCD, ELNES, EXELFS, FPRIME, NRIXS, XES.
                    The default is EXAFS.
                nkpts (int): Total number of kpoints in the brillouin zone. Used
                    only when feff is run in the reciprocal space mode.
                user_tag_settings (dict): override default tag settings. To delete
                    tags, set the key '_del' in the user_tag_settings.
                    eg: user_tag_settings={"_del": ["COREHOLE", "EXCHANGE"]}
            """
            self.absorbing_atom = absorbing_atom
            self.structure = structure
            self.radius = radius
            self.config_dict = deepcopy(config_dict)
            self.edge = edge
            self.spectrum = spectrum
            self.nkpts = nkpts
            self.user_tag_settings = user_tag_settings or {}
            self.config_dict["EDGE"] = self.edge
            self.config_dict.update(self.user_tag_settings)
            if "_del" in self.user_tag_settings:
                for tag in self.user_tag_settings["_del"]:
                    if tag in self.config_dict:
                        del self.config_dict[tag]
                del self.config_dict["_del"]
            # k-space feff only for small systems. The hardcoded system size in
            # feff is around 14 atoms.
            self.small_system = True if (len(self.structure) < 14 and 'EXAFS' not in self.config_dict) else False

        def header(self, source='', comment=''):
            """
            Creates header string from structure object

            Args:
                source: Source identifier used to create structure, can be defined
                    however user wants to organize structures, calculations, etc.
                    example would be Materials Project material ID number.
                comment: comment to include in header

            Returns:
                Header
            """
            return Header(self.structure, source, comment)

        @property
        def tags(self):
            """
            FEFF job parameters.

            Returns:
                Tags
            """
            if "RECIPROCAL" in self.config_dict:
                if self.small_system:
                    self.config_dict["CIF"] = "{}.cif".format(
                        self.structure.formula.replace(" ", ""))
                    self.config_dict["TARGET"] = self.atoms.center_index + 1
                    self.config_dict["COREHOLE"] = "RPA"
                    logger.warning("Setting COREHOLE = RPA for K-space calculation")
                    if not self.config_dict.get("KMESH", None):
                        abc = self.structure.lattice.abc
                        mult = (self.nkpts * abc[0] * abc[1] * abc[2]) ** (1 / 3)
                        self.config_dict["KMESH"] = [int(round(mult / l)) for l in abc]
                else:
                    logger.warning("Large system(>=14 atoms) or EXAFS calculation, \
                                    removing K-space settings")
                    del self.config_dict["RECIPROCAL"]
                    self.config_dict.pop("CIF", None)
                    self.config_dict.pop("TARGET", None)
                    self.config_dict.pop("KMESH", None)
                    self.config_dict.pop("STRFAC", None)

            return Tags(self.config_dict)

        @property
        def potential(self):
            """
            FEFF potential

            Returns:
                Potential
            """
            return Potential(self.structure, self.absorbing_atom)

        @property
        def atoms(self):
            """
            absorber + the rest

            Returns:
                Atoms
            """
            return Atoms(self.structure, self.absorbing_atom, self.radius)

        def __str__(self):
            output = [self.spectrum]
            output.extend(["%s = %s" % (k, str(v))
                           for k, v in self.config_dict.items()])
            output.append("")
            return "\n".join(output)

        @staticmethod
        def from_directory(input_dir):
            """
            Read in a set of FEFF input files from a directory, which is
            useful when existing FEFF input needs some adjustment.
            """
            sub_d = {}
            for fname, ftype in [("HEADER", Header), ("PARAMETERS", Tags)]:
                fullzpath = zpath(os.path.join(input_dir, fname))
                sub_d[fname.lower()] = ftype.from_file(fullzpath)

            # Generation of FEFFDict set requires absorbing atom, need to search
            # the index of absorption atom in the structure according to the
            # distance matrix and shell species information contained in feff.inp

            absorber_index = []
            radius = None
            feffinp = zpath(os.path.join(input_dir, 'feff.inp'))

            if "RECIPROCAL" not in sub_d["parameters"]:
                input_atoms = Atoms.cluster_from_file(feffinp)
                shell_species = np.array([x.species_string for x in input_atoms])

                # First row of distance matrix represents the distance from the absorber to
                # the rest atoms
                distance_matrix = input_atoms.distance_matrix[0, :]

                # Get radius value
                from math import ceil
                radius = int(ceil(input_atoms.get_distance(input_atoms.index(input_atoms[0]),
                                                           input_atoms.index(input_atoms[-1]))))

                for site_index, site in enumerate(sub_d['header'].struct):

                    if site.specie == input_atoms[0].specie:
                        site_atoms = Atoms(sub_d['header'].struct, absorbing_atom=site_index,
                                           radius=radius)
                        site_distance = np.array(site_atoms.get_lines())[:, 5].astype(np.float64)
                        site_shell_species = np.array(site_atoms.get_lines())[:, 4]
                        shell_overlap = min(shell_species.shape[0], site_shell_species.shape[0])

                        if np.allclose(distance_matrix[:shell_overlap], site_distance[:shell_overlap]) and \
                                np.all(site_shell_species[:shell_overlap] == shell_species[:shell_overlap]):
                            absorber_index.append(site_index)

            if "RECIPROCAL" in sub_d["parameters"]:
                absorber_index = sub_d["parameters"]["TARGET"]
                absorber_index[0] = int(absorber_index[0]) - 1

            # Generate the input set
            if 'XANES' in sub_d["parameters"]:
                CONFIG = loadfn(os.path.join(MODULE_DIR, "MPXANESSet.yaml"))
                if radius is None:
                    radius = 10
                return FEFFDictSet(absorber_index[0], sub_d['header'].struct, radius=radius,
                                   config_dict=CONFIG, edge=sub_d["parameters"]["EDGE"],
                                   nkpts=1000, user_tag_settings=sub_d["parameters"])

    class MPXANESSet(FEFFDictSet):
        """
        FeffDictSet for XANES spectroscopy.
        """

        CONFIG = loadfn(os.path.join(MODULE_DIR, "MPXANESSet.yaml"))

        def __init__(self, absorbing_atom, structure, edge="K", radius=10.,
                     nkpts=1000, user_tag_settings=None):
            """
            Args:
                absorbing_atom (str/int): absorbing atom symbol or site index
                structure (Structure): input
                edge (str): absorption edge
                radius (float): cluster radius in Angstroms.
                nkpts (int): Total number of kpoints in the brillouin zone. Used
                    only when feff is run in the reciprocal space mode.
                user_tag_settings (dict): override default tag settings
            """
            super().__init__(absorbing_atom, structure, radius,
                             MPXANESSet.CONFIG, edge=edge,
                             spectrum="XANES", nkpts=nkpts,
                             user_tag_settings=user_tag_settings)

    class MPEXAFSSet(FEFFDictSet):
        """
        FeffDictSet for EXAFS spectroscopy.
        """

        CONFIG = loadfn(os.path.join(MODULE_DIR, "MPEXAFSSet.yaml"))

        def __init__(self, absorbing_atom, structure, edge="K", radius=10.,
                     nkpts=1000, user_tag_settings=None):
            """
            Args:
                absorbing_atom (str/int): absorbing atom symbol or site index
                structure (Structure): input structure
                edge (str): absorption edge
                radius (float): cluster radius in Angstroms.
                nkpts (int): Total number of kpoints in the brillouin zone. Used
                    only when feff is run in the reciprocal space mode.
                user_tag_settings (dict): override default tag settings
            """
            super().__init__(absorbing_atom, structure, radius,
                             MPEXAFSSet.CONFIG, edge=edge,
                             spectrum="EXAFS", nkpts=nkpts,
                             user_tag_settings=user_tag_settings)

    class MPEELSDictSet(FEFFDictSet):
        """
        FeffDictSet for ELNES spectroscopy.
        """

        def __init__(self, absorbing_atom, structure, edge, spectrum, radius,
                     beam_energy, beam_direction, collection_angle,
                     convergence_angle, config_dict, user_eels_settings=None,
                     nkpts=1000, user_tag_settings=None):
            """
            Args:
                absorbing_atom (str/int): absorbing atom symbol or site index
                structure (Structure): input structure
                edge (str): absorption edge
                spectrum (str): ELNES or EXELFS
                radius (float): cluster radius in Angstroms.
                beam_energy (float): Incident beam energy in keV
                beam_direction (list): Incident beam direction. If None, the
                    cross section will be averaged.
                collection_angle (float): Detector collection angle in mrad.
                convergence_angle (float): Beam convergence angle in mrad.
                user_eels_settings (dict): override default EELS config.
                    See MPELNESSet.yaml for supported keys.
                nkpts (int): Total number of kpoints in the brillouin zone. Used
                    only when feff is run in the reciprocal space mode.
                user_tag_settings (dict): override default tag settings
            """
            self.beam_energy = beam_energy
            self.beam_direction = beam_direction
            self.collection_angle = collection_angle
            self.convergence_angle = convergence_angle
            self.user_eels_settings = user_eels_settings
            eels_config_dict = deepcopy(config_dict)

            if beam_direction:
                beam_energy_list = [beam_energy, 0, 1, 1]
                eels_config_dict[spectrum]["BEAM_DIRECTION"] = beam_direction
            else:
                beam_energy_list = [beam_energy, 1, 0, 1]
                del eels_config_dict[spectrum]["BEAM_DIRECTION"]
            eels_config_dict[spectrum]["BEAM_ENERGY"] = beam_energy_list
            eels_config_dict[spectrum]["ANGLES"] = [collection_angle,
                                                    convergence_angle]

            if user_eels_settings:
                eels_config_dict[spectrum].update(user_eels_settings)

            super().__init__(absorbing_atom, structure, radius,
                             eels_config_dict, edge=edge,
                             spectrum=spectrum, nkpts=nkpts,
                             user_tag_settings=user_tag_settings)

    class MPELNESSet(MPEELSDictSet):
        """
        FeffDictSet for ELNES spectroscopy.
        """

        CONFIG = loadfn(os.path.join(MODULE_DIR, "MPELNESSet.yaml"))

        def __init__(self, absorbing_atom, structure, edge="K", radius=10.,
                     beam_energy=100, beam_direction=None, collection_angle=1,
                     convergence_angle=1, user_eels_settings=None, nkpts=1000,
                     user_tag_settings=None):
            """
            Args:
                absorbing_atom (str/int): absorbing atom symbol or site index
                structure (Structure): input structure
                edge (str): absorption edge
                radius (float): cluster radius in Angstroms.
                beam_energy (float): Incident beam energy in keV
                beam_direction (list): Incident beam direction. If None, the
                    cross section will be averaged.
                collection_angle (float): Detector collection angle in mrad.
                convergence_angle (float): Beam convergence angle in mrad.
                user_eels_settings (dict): override default EELS config.
                    See MPELNESSet.yaml for supported keys.
                nkpts (int): Total number of kpoints in the brillouin zone. Used
                    only when feff is run in the reciprocal space mode.
                user_tag_settings (dict): override default tag settings
            """

            super().__init__(absorbing_atom, structure, edge,
                             "ELNES", radius, beam_energy,
                             beam_direction, collection_angle,
                             convergence_angle, MPELNESSet.CONFIG,
                             user_eels_settings=user_eels_settings,
                             nkpts=nkpts, user_tag_settings=user_tag_settings)

    class MPEXELFSSet(MPEELSDictSet):
        """
        FeffDictSet for EXELFS spectroscopy.
        """

        CONFIG = loadfn(os.path.join(MODULE_DIR, "MPEXELFSSet.yaml"))

        def __init__(self, absorbing_atom, structure, edge="K", radius=10.,
                     beam_energy=100, beam_direction=None, collection_angle=1,
                     convergence_angle=1, user_eels_settings=None, nkpts=1000,
                     user_tag_settings=None):
            """
            Args:
                absorbing_atom (str/int): absorbing atom symbol or site index
                structure (Structure): input structure
                edge (str): absorption edge
                radius (float): cluster radius in Angstroms.
                beam_energy (float): Incident beam energy in keV
                beam_direction (list): Incident beam direction. If None, the
                    cross section will be averaged.
                collection_angle (float): Detector collection angle in mrad.
                convergence_angle (float): Beam convergence angle in mrad.
                user_eels_settings (dict): override default EELS config.
                    See MPEXELFSSet.yaml for supported keys.
                nkpts (int): Total number of kpoints in the brillouin zone. Used
                    only when feff is run in the reciprocal space mode.
                user_tag_settings (dict): override default tag settings
            """

            super().__init__(absorbing_atom, structure, edge,
                             "EXELFS", radius, beam_energy,
                             beam_direction, collection_angle,
                             convergence_angle, MPEXELFSSet.CONFIG,
                             user_eels_settings=user_eels_settings,
                             nkpts=nkpts, user_tag_settings=user_tag_settings)