pymatgen.io.feff.inputs — pymatgen 2020.7.3 documentation

# Source code for pymatgen.io.feff.inputs

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

    """
    This module defines classes for reading/manipulating/writing the main sections
    of FEFF input file(feff.inp), namely HEADER, ATOMS, POTENTIAL and the program
    control tags.

    XANES and EXAFS input files, are available, for non-spin case at this time.
    """

    import re
    import warnings
    from operator import itemgetter

    from tabulate import tabulate

    import numpy as np

    from monty.io import zopen
    from monty.json import MSONable

    from pymatgen import Structure, Lattice, Element, Molecule
    from pymatgen.io.cif import CifParser
    from pymatgen.symmetry.analyzer import SpacegroupAnalyzer
    from pymatgen.util.io_utils import clean_lines
    from pymatgen.util.string import str_delimited

    __author__ = "Alan Dozier, Kiran Mathew"
    __credits__ = "Anubhav Jain, Shyue Ping Ong"
    __copyright__ = "Copyright 2011, The Materials Project"
    __version__ = "1.0.3"
    __maintainer__ = "Alan Dozier"
    __email__ = "adozier@uky.edu"
    __status__ = "Beta"
    __date__ = "April 7, 2013"

    # **Non-exhaustive** list of valid Feff.inp tags
    VALID_FEFF_TAGS = ("CONTROL", "PRINT", "ATOMS", "POTENTIALS", "RECIPROCAL",
                       "REAL", "MARKER", "LATTICE", "TITLE", "RMULTIPLIER",
                       "SGROUP", "COORDINATES", "EQUIVALENCE", "CIF", "CGRID",
                       "CFAVERAGE", "OVERLAP", "EXAFS", "XANES", "ELNES", "EXELFS",
                       "LDOS", "ELLIPTICITY", "MULTIPOLE", "POLARIZATION",
                       "RHOZZP", "DANES", "FPRIME", "NRIXS", "XES", "XNCD",
                       "XMCD", "XNCDCONTROL", "END", "KMESH", "PRINT", "EGRID",
                       "DIMS", "AFOLP", "EDGE", "COMPTON", "DANES",
                       "FPRIME" "MDFF", "HOLE", "COREHOLE", "S02", "CHBROAD",
                       "EXCHANGE", "FOLP", "NOHOLE", "RGRID", "SCF",
                       "UNFREEZEF", "CHSHIFT", "DEBYE",
                       "INTERSTITIAL", "CHWIDTH", "EGAP", "EPS0", "EXTPOT",
                       "ION", "JUMPRM", "EXPOT", "SPIN", "LJMAX", "LDEC", "MPSE",
                       "PLASMON", "RPHASES", "RSIGMA", "PMBSE", "TDLDA", "FMS",
                       "DEBYA", "OPCONS", "PREP", "RESTART", "SCREEN", "SETE",
                       "STRFACTORS", "BANDSTRUCTURE", "RPATH", "NLEG", "PCRITERIA",
                       "SYMMETRY", "SS", "CRITERIA", "IORDER", "NSTAR", "ABSOLUTE",
                       "CORRECTIONS", "SIG2", "SIG3", "MBCONV", "SFCONV", "RCONV",
                       "SELF", "SFSE", "MAGIC", "TARGET", "STRFAC")

    class Header(MSONable):
        """
        Creates Header for the FEFF input file.

        Has the following format::

            * This feff.inp file generated by pymatgen, www.materialsproject.org
            TITLE comment:
            TITLE Source: CoO19128.cif
            TITLE Structure Summary: (Co2 O2)
            TITLE Reduced formula: CoO
            TITLE space group: P1,   space number: 1
            TITLE abc: 3.297078 3.297078 5.254213
            TITLE angles: 90.0 90.0 120.0
            TITLE sites: 4
            * 1 Co     0.666666     0.333332     0.496324
            * 2 Co     0.333333     0.666667     0.996324
            * 3 O     0.666666     0.333332     0.878676
            * 4 O     0.333333     0.666667     0.378675
        """

        def __init__(self, struct, source='', comment=''):
            """
            Args:
                struct: Structure object, See pymatgen.core.structure.Structure.
                source: User supplied identifier, i.e. for Materials Project this
                    would be the material ID number
                comment: Comment for first header line
            """
            if struct.is_ordered:
                self.struct = struct
                self.source = source
                sym = SpacegroupAnalyzer(struct)
                data = sym.get_symmetry_dataset()
                self.space_number = data["number"]
                self.space_group = data["international"]
                self.comment = comment or "None given"
            else:
                raise ValueError("Structure with partial occupancies cannot be "
                                 "converted into atomic coordinates!")

        @staticmethod
        def from_cif_file(cif_file, source='', comment=''):
            """
            Static method to create Header object from cif_file

            Args:
                cif_file: cif_file path and name
                source: User supplied identifier, i.e. for Materials Project this
                    would be the material ID number
                comment: User comment that goes in header

            Returns:
                Header Object
            """
            r = CifParser(cif_file)
            structure = r.get_structures()[0]
            return Header(structure, source, comment)

        @property
        def structure_symmetry(self):
            """
            Returns space number and space group

            Returns:
                Space number and space group list
            """
            return self.space_group, self.space_number

        @property
        def formula(self):
            """
            Formula of structure
            """
            return self.struct.composition.formula

        @staticmethod
        def from_file(filename):
            """
            Returns Header object from file
            """
            hs = Header.header_string_from_file(filename)
            return Header.from_string(hs)

        @staticmethod
        def header_string_from_file(filename='feff.inp'):
            """
            Reads Header string from either a HEADER file or feff.inp file
            Will also read a header from a non-pymatgen generated feff.inp file

            Args:
                filename: File name containing the Header data.

            Returns:
                Reads header string.
            """
            with zopen(filename, "r") as fobject:
                f = fobject.readlines()
                feff_header_str = []
                ln = 0

                # Checks to see if generated by pymatgen
                try:
                    feffpmg = f[0].find("pymatgen")
                    if feffpmg == -1:
                        feffpmg = False
                except IndexError:
                    feffpmg = False

                # Reads pymatgen generated header or feff.inp file
                if feffpmg:
                    nsites = int(f[8].split()[2])
                    for line in f:
                        ln += 1
                        if ln <= nsites + 9:
                            feff_header_str.append(line)
                else:
                    # Reads header from header from feff.inp file from unknown
                    # source
                    end = 0
                    for line in f:
                        if (line[0] == "*" or line[0] == "T") and end == 0:
                            feff_header_str.append(line.replace("\r", ""))
                        else:
                            end = 1

            return ''.join(feff_header_str)

        @staticmethod
        def from_string(header_str):
            """
            Reads Header string and returns Header object if header was
            generated by pymatgen.
            Note: Checks to see if generated by pymatgen, if not it is impossible
                to generate structure object so it is not possible to generate
                header object and routine ends

            Args:
                header_str: pymatgen generated feff.inp header

            Returns:
                Structure object.
            """
            lines = tuple(clean_lines(header_str.split("\n"), False))
            comment1 = lines[0]
            feffpmg = comment1.find("pymatgen")
            if feffpmg == -1:
                feffpmg = False
            if feffpmg:
                comment2 = ' '.join(lines[1].split()[2:])

                source = ' '.join(lines[2].split()[2:])
                basis_vec = lines[6].split(":")[-1].split()
                # a, b, c
                a = float(basis_vec[0])
                b = float(basis_vec[1])
                c = float(basis_vec[2])
                lengths = [a, b, c]
                # alpha, beta, gamma
                basis_ang = lines[7].split(":")[-1].split()
                alpha = float(basis_ang[0])
                beta = float(basis_ang[1])
                gamma = float(basis_ang[2])
                angles = [alpha, beta, gamma]

                lattice = Lattice.from_parameters(*lengths, *angles)

                natoms = int(lines[8].split(":")[-1].split()[0])

                atomic_symbols = []
                for i in range(9, 9 + natoms):
                    atomic_symbols.append(lines[i].split()[2])

                # read the atomic coordinates
                coords = []
                for i in range(natoms):
                    toks = lines[i + 9].split()
                    coords.append([float(s) for s in toks[3:]])

                struct = Structure(lattice, atomic_symbols, coords, False,
                                   False, False)

                h = Header(struct, source, comment2)

                return h
            else:
                return "Header not generated by pymatgen, cannot return header object"

        def __str__(self):
            """
            String representation of Header.
            """

            def to_s(x):
                return "%0.6f" % x
            output = ["* This FEFF.inp file generated by pymatgen",
                      ''.join(["TITLE comment: ", self.comment]),
                      ''.join(["TITLE Source:  ", self.source]),
                      "TITLE Structure Summary:  {}".format(self.struct.composition.formula),
                      "TITLE Reduced formula:  {}".format(self.struct.composition.reduced_formula),
                      "TITLE space group: ({}), space number:  ({})".format(self.space_group, self.space_number),
                      "TITLE abc:{}".format(" ".join([to_s(i).rjust(10) for i in self.struct.lattice.abc])),
                      "TITLE angles:{}".format(" ".join([to_s(i).rjust(10) for i in self.struct.lattice.angles])),
                      "TITLE sites: {}".format(self.struct.num_sites)]
            for i, site in enumerate(self.struct):
                output.append(" ".join(["*", str(i + 1), site.species_string,
                                        " ".join([to_s(j).rjust(12) for j in site.frac_coords])]))
            return "\n".join(output)

        def write_file(self, filename='HEADER'):
            """
            Writes Header into filename on disk.

            Args:
                filename: Filename and path for file to be written to disk
            """
            with open(filename, "w") as f:
                f.write(str(self) + "\n")

    class Atoms(MSONable):
        """
        Atomic cluster centered around the absorbing atom.
        """

        def __init__(self, struct, absorbing_atom, radius):
            """
            Args:
                struct (Structure): input structure
                absorbing_atom (str/int): Symbol for absorbing atom or site index
                radius (float): radius of the atom cluster in Angstroms.
            """
            if struct.is_ordered:
                self.struct = struct
                self.pot_dict = get_atom_map(struct)
            else:
                raise ValueError("Structure with partial occupancies cannot be "
                                 "converted into atomic coordinates!")

            self.absorbing_atom, self.center_index = \
                get_absorbing_atom_symbol_index(absorbing_atom, struct)
            self.radius = radius
            self._cluster = self._set_cluster()

        def _set_cluster(self):
            """
            Compute and set the cluster of atoms as a Molecule object. The siteato
            coordinates are translated such that the absorbing atom(aka central
            atom) is at the origin.

            Returns:
                Molecule
            """
            center = self.struct[self.center_index].coords
            sphere = self.struct.get_neighbors(self.struct[self.center_index], self.radius)

            symbols = [self.absorbing_atom]
            coords = [[0, 0, 0]]
            for i, site_dist in enumerate(sphere):
                site_symbol = re.sub(r"[^aA-zZ]+", "", site_dist[0].species_string)
                symbols.append(site_symbol)
                coords.append(site_dist[0].coords - center)
            return Molecule(symbols, coords)

        @property
        def cluster(self):
            """
            Returns the atomic cluster as a Molecule object.
            """
            return self._cluster

        @staticmethod
        def atoms_string_from_file(filename):
            """
            Reads atomic shells from file such as feff.inp or ATOMS file
            The lines are arranged as follows:

            x y z   ipot    Atom Symbol   Distance   Number

            with distance being the shell radius and ipot an integer identifying
            the potential used.

            Args:
                filename: File name containing atomic coord data.

            Returns:
                Atoms string.
            """
            with zopen(filename, "rt") as fobject:
                f = fobject.readlines()
                coords = 0
                atoms_str = []

                for line in f:
                    if coords == 0:
                        find_atoms = line.find("ATOMS")
                        if find_atoms >= 0:
                            coords = 1
                    if coords == 1 and not ("END" in line):
                        atoms_str.append(line.replace("\r", ""))

            return ''.join(atoms_str)

        @staticmethod
        def cluster_from_file(filename):
            """
            Parse the feff input file and return the atomic cluster as a Molecule
            object.

            Args:
                filename (str): path the feff input file

            Returns:
                Molecule: the atomic cluster as Molecule object. The absorbing atom
                    is the one at the origin.
            """
            atoms_string = Atoms.atoms_string_from_file(filename)
            line_list = [l.split() for l in atoms_string.splitlines()[3:]]
            coords = []
            symbols = []
            for l in line_list:
                if l:
                    coords.append([float(i) for i in l[:3]])
                    symbols.append(l[4])
            return Molecule(symbols, coords)

        def get_lines(self):
            """
            Returns a list of string representations of the atomic configuration
            information(x, y, z, ipot, atom_symbol, distance, id).

            Returns:
                list: list of strings, sorted by the distance from the absorbing
                    atom.
            """
            lines = [["{:f}".format(self._cluster[0].x),
                      "{:f}".format(self._cluster[0].y),
                      "{:f}".format(self._cluster[0].z),
                      0, self.absorbing_atom, "0.0", 0]]
            for i, site in enumerate(self._cluster[1:]):
                site_symbol = re.sub(r"[^aA-zZ]+", "", site.species_string)
                ipot = self.pot_dict[site_symbol]
                lines.append(["{:f}".format(site.x), "{:f}".format(site.y),
                              "{:f}".format(site.z), ipot, site_symbol,
                              "{:f}".format(self._cluster.get_distance(0, i + 1)), i + 1])

            return sorted(lines, key=itemgetter(5))

        def __str__(self):
            """
            String representation of Atoms file.
            """
            lines_sorted = self.get_lines()
            # TODO: remove the formatting and update the unittests
            lines_formatted = str(tabulate(lines_sorted,
                                           headers=["*       x", "y", "z", "ipot",
                                                    "Atom", "Distance", "Number"]))
            atom_list = lines_formatted.replace("--", "**")
            return ''.join(["ATOMS\n", atom_list, "\nEND\n"])

        def write_file(self, filename='ATOMS'):
            """
            Write Atoms list to file.

            Args:
               filename: path for file to be written
            """
            with zopen(filename, "wt") as f:
                f.write(str(self) + "\n")

    class Tags(dict):
        """
        FEFF control parameters.
        """

        def __init__(self, params=None):
            """
            Args:
                params: A set of input parameters as a dictionary.
            """
            super().__init__()
            if params:
                self.update(params)

        def __setitem__(self, key, val):
            """
            Add parameter-val pair.  Warns if parameter is not in list of valid
            Feff tags. Also cleans the parameter and val by stripping leading and
            trailing white spaces.

            Arg:
                key: dict key value
                value: value associated with key in dictionary
            """
            if key.strip().upper() not in VALID_FEFF_TAGS:
                warnings.warn(key.strip() + " not in VALID_FEFF_TAGS list")
            super().__setitem__(key.strip(), Tags.proc_val(key.strip(), val.strip()) if isinstance(val, str) else val)

        def as_dict(self):
            """
            Dict representation.

            Returns:
                Dictionary of parameters from fefftags object
            """
            tags_dict = dict(self)
            tags_dict['@module'] = self.__class__.__module__
            tags_dict['@class'] = self.__class__.__name__
            return tags_dict

        @staticmethod
        def from_dict(d):
            """
            Creates Tags object from a dictionary.

            Args:
                d: Dict of feff parameters and values.

            Returns:
                Tags object
            """
            i = Tags()
            for k, v in d.items():
                if k not in ("@module", "@class"):
                    i[k] = v
            return i

        def get_string(self, sort_keys=False, pretty=False):
            """
            Returns a string representation of the Tags.  The reason why this
            method is different from the __str__ method is to provide options
            for pretty printing.

            Args:
                sort_keys: Set to True to sort the Feff parameters alphabetically.
                    Defaults to False.
                pretty: Set to True for pretty aligned output. Defaults to False.

            Returns:
                String representation of Tags.
            """
            keys = self.keys()
            if sort_keys:
                keys = sorted(keys)
            lines = []
            for k in keys:
                if isinstance(self[k], dict):
                    if k in ["ELNES", "EXELFS"]:
                        lines.append([k, self._stringify_val(self[k]["ENERGY"])])
                        beam_energy = self._stringify_val(self[k]["BEAM_ENERGY"])
                        beam_energy_list = beam_energy.split()
                        if int(beam_energy_list[1]) == 0:  # aver=0, specific beam direction
                            lines.append([beam_energy])
                            lines.append([self._stringify_val(self[k]["BEAM_DIRECTION"])])
                        else:
                            # no cross terms for orientation averaged spectrum
                            beam_energy_list[2] = str(0)
                            lines.append([self._stringify_val(beam_energy_list)])
                        lines.append([self._stringify_val(self[k]["ANGLES"])])
                        lines.append([self._stringify_val(self[k]["MESH"])])
                        lines.append([self._stringify_val(self[k]["POSITION"])])
                else:
                    lines.append([k, self._stringify_val(self[k])])
            if pretty:
                return tabulate(lines)
            else:
                return str_delimited(lines, None, " ")

        @staticmethod
        def _stringify_val(val):
            """
            Convert the given value to string.
            """
            if isinstance(val, list):
                return " ".join([str(i) for i in val])
            else:
                return str(val)

        def __str__(self):
            return self.get_string()

        def write_file(self, filename='PARAMETERS'):
            """
            Write Tags to a Feff parameter tag file.

            Args:
                filename: filename and path to write to.
            """
            with zopen(filename, "wt") as f:
                f.write(self.__str__() + "\n")

        @staticmethod
        def from_file(filename="feff.inp"):
            """
            Creates a Feff_tag dictionary from a PARAMETER or feff.inp file.

            Args:
                filename: Filename for either PARAMETER or feff.inp file

            Returns:
                Feff_tag object
            """
            with zopen(filename, "rt") as f:
                lines = list(clean_lines(f.readlines()))
            params = {}
            eels_params = []
            ieels = -1
            ieels_max = -1
            for i, line in enumerate(lines):
                m = re.match(r"([A-Z]+\d*\d*)\s*(.*)", line)
                if m:
                    key = m.group(1).strip()
                    val = m.group(2).strip()
                    val = Tags.proc_val(key, val)
                    if key not in ("ATOMS", "POTENTIALS", "END", "TITLE"):
                        if key in ["ELNES", "EXELFS"]:
                            ieels = i
                            ieels_max = ieels + 5
                        else:
                            params[key] = val
                if ieels >= 0:
                    if i >= ieels and i <= ieels_max:
                        if i == ieels + 1:
                            if int(line.split()[1]) == 1:
                                ieels_max -= 1
                        eels_params.append(line)

            if eels_params:
                if len(eels_params) == 6:
                    eels_keys = ['BEAM_ENERGY', 'BEAM_DIRECTION', 'ANGLES', 'MESH', 'POSITION']
                else:
                    eels_keys = ['BEAM_ENERGY', 'ANGLES', 'MESH', 'POSITION']
                eels_dict = {"ENERGY": Tags._stringify_val(eels_params[0].split()[1:])}
                for k, v in zip(eels_keys, eels_params[1:]):
                    eels_dict[k] = str(v)
                params[str(eels_params[0].split()[0])] = eels_dict

            return Tags(params)

        @staticmethod
        def proc_val(key, val):
            """
            Static helper method to convert Feff parameters to proper types, e.g.
            integers, floats, lists, etc.

            Args:
                key: Feff parameter key
                val: Actual value of Feff parameter.
            """

            list_type_keys = list(VALID_FEFF_TAGS)
            del list_type_keys[list_type_keys.index("ELNES")]
            del list_type_keys[list_type_keys.index("EXELFS")]
            boolean_type_keys = ()
            float_type_keys = ("S02", "EXAFS", "RPATH")

            def smart_int_or_float(numstr):
                if numstr.find(".") != -1 or numstr.lower().find("e") != -1:
                    return float(numstr)
                else:
                    return int(numstr)

            try:
                if key.lower() == 'cif':
                    m = re.search(r"\w+.cif", val)
                    return m.group(0)

                if key in list_type_keys:
                    output = list()
                    toks = re.split(r"\s+", val)

                    for tok in toks:
                        m = re.match(r"(\d+)\*([\d\.\-\+]+)", tok)
                        if m:
                            output.extend([smart_int_or_float(m.group(2))] *
                                          int(m.group(1)))
                        else:
                            output.append(smart_int_or_float(tok))
                    return output
                if key in boolean_type_keys:
                    m = re.search(r"^\W+([TtFf])", val)
                    if m:
                        if m.group(1) == "T" or m.group(1) == "t":
                            return True
                        else:
                            return False
                    raise ValueError(key + " should be a boolean type!")

                if key in float_type_keys:
                    return float(val)

            except ValueError:
                return val.capitalize()

            return val.capitalize()

        def diff(self, other):
            """
            Diff function.  Compares two PARAMETER files and indicates which
            parameters are the same and which are not. Useful for checking whether
            two runs were done using the same parameters.

            Args:
                other: The other PARAMETER dictionary to compare to.

            Returns:
                Dict of the format {"Same" : parameters_that_are_the_same,
                "Different": parameters_that_are_different} Note that the
                parameters are return as full dictionaries of values.
            """
            similar_param = {}
            different_param = {}
            for k1, v1 in self.items():
                if k1 not in other:
                    different_param[k1] = {"FEFF_TAGS1": v1,
                                           "FEFF_TAGS2": "Default"}
                elif v1 != other[k1]:
                    different_param[k1] = {"FEFF_TAGS1": v1,
                                           "FEFF_TAGS2": other[k1]}
                else:
                    similar_param[k1] = v1
            for k2, v2 in other.items():
                if k2 not in similar_param and k2 not in different_param:
                    if k2 not in self:
                        different_param[k2] = {"FEFF_TAGS1": "Default",
                                               "FEFF_TAGS2": v2}
            return {"Same": similar_param, "Different": different_param}

        def __add__(self, other):
            """
            Add all the values of another Tags object to this object
            Facilitates the use of "standard" Tags
            """
            params = dict(self)
            for k, v in other.items():
                if k in self and v != self[k]:
                    raise ValueError("Tags have conflicting values!")
                else:
                    params[k] = v
            return Tags(params)

    class Potential(MSONable):
        """
        FEFF atomic potential.
        """

        def __init__(self, struct, absorbing_atom):
            """
            Args:
                struct (Structure): Structure object.
                absorbing_atom (str/int): Absorbing atom symbol or site index
            """
            if struct.is_ordered:
                self.struct = struct
                self.pot_dict = get_atom_map(struct)
            else:
                raise ValueError("Structure with partial occupancies cannot be "
                                 "converted into atomic coordinates!")

            self.absorbing_atom, _ = \
                get_absorbing_atom_symbol_index(absorbing_atom, struct)

        @staticmethod
        def pot_string_from_file(filename='feff.inp'):
            """
            Reads Potential parameters from a feff.inp or FEFFPOT file.
            The lines are arranged as follows:

              ipot   Z   element   lmax1   lmax2   stoichometry   spinph

            Args:
                filename: file name containing potential data.

            Returns:
                FEFFPOT string.
            """
            with zopen(filename, "rt") as f_object:
                f = f_object.readlines()
                ln = -1
                pot_str = ["POTENTIALS\n"]
                pot_tag = -1
                pot_data = 0
                pot_data_over = 1

                sep_line_pattern = [re.compile('ipot.*Z.*tag.*lmax1.*lmax2.*spinph'),
                                    re.compile('^[*]+.*[*]+$')]

                for line in f:
                    if pot_data_over == 1:
                        ln += 1
                        if pot_tag == -1:
                            pot_tag = line.find("POTENTIALS")
                            ln = 0
                        if pot_tag >= 0 and ln > 0 and pot_data_over > 0:
                            try:
                                if len(sep_line_pattern[0].findall(line)) > 0 or \
                                                len(sep_line_pattern[1].findall(line)) > 0:
                                    pot_str.append(line)
                                elif int(line.split()[0]) == pot_data:
                                    pot_data += 1
                                    pot_str.append(line.replace("\r", ""))
                            except (ValueError, IndexError):
                                if pot_data > 0:
                                    pot_data_over = 0

            return ''.join(pot_str).rstrip('\n')

        @staticmethod
        def pot_dict_from_string(pot_data):
            """
            Creates atomic symbol/potential number dictionary
            forward and reverse

            Arg:
                pot_data: potential data in string format

            Returns:
                forward and reverse atom symbol and potential number dictionaries.
            """

            pot_dict = {}
            pot_dict_reverse = {}
            begin = 0
            ln = -1

            for line in pot_data.split("\n"):
                try:
                    if begin == 0 and line.split()[0] == "0":
                        begin += 1
                        ln = 0
                    if begin == 1:
                        ln += 1
                    if ln > 0:
                        atom = line.split()[2]
                        index = int(line.split()[0])
                        pot_dict[atom] = index
                        pot_dict_reverse[index] = atom
                except (ValueError, IndexError):
                    pass
            return pot_dict, pot_dict_reverse

        def __str__(self):
            """
            Returns a string representation of potential parameters to be used in
            the feff.inp file,
            determined from structure object.

                    The lines are arranged as follows:

              ipot   Z   element   lmax1   lmax2   stoichiometry   spinph

            Returns:
                String representation of Atomic Coordinate Shells.
            """
            central_element = Element(self.absorbing_atom)
            ipotrow = [[0, central_element.Z, central_element.symbol, -1, -1, .0001, 0]]
            for el, amt in self.struct.composition.items():
                ipot = self.pot_dict[el.symbol]
                ipotrow.append([ipot, el.Z, el.symbol, -1, -1, amt, 0])
            ipot_sorted = sorted(ipotrow, key=itemgetter(0))
            ipotrow = str(tabulate(ipot_sorted,
                                   headers=["*ipot", "Z", "tag", "lmax1",
                                            "lmax2", "xnatph(stoichometry)",
                                            "spinph"]))
            ipotlist = ipotrow.replace("--", "**")
            ipotlist = ''.join(["POTENTIALS\n", ipotlist])

            return ipotlist

        def write_file(self, filename='POTENTIALS'):
            """
            Write to file.

            Args:
                filename: filename and path to write potential file to.
            """
            with zopen(filename, "wt") as f:
                f.write(str(self) + "\n")

    class Paths(MSONable):
        """
        Set FEFF scattering paths('paths.dat' file used by the 'genfmt' module).
        """

        def __init__(self, atoms, paths, degeneracies=None):
            """
            Args:
                atoms (Atoms): Atoms object
                paths (list(list)): list of paths. Each path is a list of atom indices in the atomic
                    cluster(the molecular cluster created by Atoms class).
                    e.g. [[0, 1, 2], [5, 9, 4, 1]] -> 2 paths: one with 3 legs and the other with 4 legs.
                degeneracies (list): list of degeneracies, one for each path. Set to 1 if not specified.
            """
            self.atoms = atoms
            self.paths = paths
            self.degeneracies = degeneracies or [1] * len(paths)
            assert len(self.degeneracies) == len(self.paths)

        def __str__(self):
            lines = ["PATH", "---------------"]
            # max possible, to avoid name collision count down from max value.
            path_index = 9999
            for i, legs in enumerate(self.paths):
                lines.append("{} {} {}".format(path_index, len(legs), self.degeneracies[i]))
                lines.append("x y z ipot label")
                for l in legs:
                    coords = self.atoms.cluster[l].coords.tolist()
                    tmp = "{:.6f} {:.6f} {:.6f}".format(*tuple(coords))
                    element = str(self.atoms.cluster[l].specie.name)
                    # the potential index for the absorbing atom(the one at the cluster origin) is 0
                    potential = 0 if np.linalg.norm(coords) <= 1e-6 else self.atoms.pot_dict[element]
                    tmp = "{} {} {}".format(tmp, potential, element)
                    lines.append(tmp)
                path_index -= 1
            return "\n".join(lines)

        def write_file(self, filename="paths.dat"):
            """
            Write paths.dat.
            """
            with zopen(filename, "wt") as f:
                f.write(str(self) + "\n")

    class FeffParserError(Exception):
        """
        Exception class for Structure.
        Raised when the structure has problems, e.g., atoms that are too close.
        """

    def get_atom_map(structure):
        """
        Returns a dict that maps each atomic symbol to a unique integer starting
        from 1.

        Args:
            structure (Structure)

        Returns:
            dict
        """
        syms = [site.specie.symbol for site in structure]
        unique_pot_atoms = []
        [unique_pot_atoms.append(i) for i in syms if not unique_pot_atoms.count(i)]
        atom_map = {}
        for i, atom in enumerate(unique_pot_atoms):
            atom_map[atom] = i + 1
        return atom_map

    def get_absorbing_atom_symbol_index(absorbing_atom, structure):
        """
        Return the absorbing atom symboll and site index in the given structure.

        Args:
            absorbing_atom (str/int): symbol or site index
            structure (Structure)

        Returns:
            str, int: symbol and site index
        """
        if isinstance(absorbing_atom, str):
            return absorbing_atom, structure.indices_from_symbol(absorbing_atom)[0]
        elif isinstance(absorbing_atom, int):
            return str(structure[absorbing_atom].specie), absorbing_atom
        else:
            raise ValueError("absorbing_atom must be either specie symbol or site index")