pymatgen.io.feff.outputs — pymatgen 2020.7.3 documentation

# Source code for pymatgen.io.feff.outputs

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

    """
    This module defines classes for parsing the FEFF output files.

    Currently supports the xmu.dat, ldos.dat output files are for non-spin case.
    """

    from collections import defaultdict, OrderedDict
    import re

    import numpy as np

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

    from pymatgen import Orbital, Spin, Element
    from pymatgen.electronic_structure.dos import Dos, CompleteDos
    from pymatgen.io.feff import Header, Potential, Tags

    __author__ = "Alan Dozier, Kiran Mathew, Chen Zheng"
    __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"

    class LDos(MSONable):
        """
        Parser for ldos files ldos01, ldos02, .....
        """

        def __init__(self, complete_dos, charge_transfer):
            """
            Args:
                complete_dos (CompleteDos): complete dos object
                charge_transfer (dict): computed charge transfer between atoms
                    dictionary
            """
            self.complete_dos = complete_dos
            self.charge_transfer = charge_transfer

        @staticmethod
        def from_file(feff_inp_file='feff.inp', ldos_file='ldos'):
            """
            Creates LDos object from raw Feff ldos files by
            by assuming they are numbered consecutively, i.e. ldos01.dat
            ldos02.dat...

            Args:
                feff_inp_file (str): input file of run to obtain structure
                ldos_file (str): output ldos file of run to obtain dos info, etc.
            """
            header_str = Header.header_string_from_file(feff_inp_file)
            header = Header.from_string(header_str)
            structure = header.struct
            nsites = structure.num_sites
            parameters = Tags.from_file(feff_inp_file)

            if "RECIPROCAL" in parameters:
                pot_dict = dict()
                pot_readstart = re.compile('.*iz.*lmaxsc.*xnatph.*xion.*folp.*')
                pot_readend = re.compile('.*ExternalPot.*switch.*')
                pot_inp = re.sub(r'feff.inp', r'pot.inp', feff_inp_file)
                dos_index = 1
                begin = 0

                with zopen(pot_inp, "r") as potfile:
                    for line in potfile:
                        if len(pot_readend.findall(line)) > 0:
                            break

                        if begin == 1:
                            begin += 1
                            continue

                        if begin == 2:
                            z_number = int(line.strip().split()[0])
                            ele_name = Element.from_Z(z_number).name
                            if ele_name not in pot_dict:
                                pot_dict[ele_name] = dos_index
                            else:
                                pot_dict[ele_name] = min(dos_index, pot_dict[ele_name])
                            dos_index += 1

                        if len(pot_readstart.findall(line)) > 0:
                            begin = 1
            else:
                pot_string = Potential.pot_string_from_file(feff_inp_file)
                dicts = Potential.pot_dict_from_string(pot_string)
                pot_dict = dicts[0]

            with zopen(ldos_file + "00.dat", "r") as fobject:
                f = fobject.readlines()
            efermi = float(f[0].split()[4])

            dos_energies = []
            ldos = {}

            for i in range(1, len(pot_dict) + 1):
                if len(str(i)) == 1:
                    ldos[i] = np.loadtxt("{}0{}.dat".format(ldos_file, i))
                else:
                    ldos[i] = np.loadtxt("{}{}.dat".format(ldos_file, i))

            for i in range(0, len(ldos[1])):
                dos_energies.append(ldos[1][i][0])

            all_pdos = []
            vorb = {"s": Orbital.s, "p": Orbital.py, "d": Orbital.dxy,
                    "f": Orbital.f0}
            forb = {"s": 0, "p": 1, "d": 2, "f": 3}

            dlength = len(ldos[1])

            for i in range(nsites):
                pot_index = pot_dict[structure.species[i].symbol]
                all_pdos.append(defaultdict(dict))
                for k, v in vorb.items():
                    density = [ldos[pot_index][j][forb[k] + 1]
                               for j in range(dlength)]
                    updos = density
                    downdos = None
                    if downdos:
                        all_pdos[-1][v] = {Spin.up: updos, Spin.down: downdos}
                    else:
                        all_pdos[-1][v] = {Spin.up: updos}

            pdos = all_pdos
            vorb2 = {0: Orbital.s, 1: Orbital.py, 2: Orbital.dxy, 3: Orbital.f0}
            pdoss = {structure[i]: {v: pdos[i][v]
                                    for v in vorb2.values()}
                     for i in range(len(pdos))}

            forb = {"s": 0, "p": 1, "d": 2, "f": 3}

            tdos = [0] * dlength
            for i in range(nsites):
                pot_index = pot_dict[structure.species[i].symbol]
                for v in forb.values():
                    density = [ldos[pot_index][j][v + 1] for j in range(dlength)]
                    for j in range(dlength):
                        tdos[j] = tdos[j] + density[j]
            tdos = {Spin.up: tdos}

            dos = Dos(efermi, dos_energies, tdos)
            complete_dos = CompleteDos(structure, dos, pdoss)
            charge_transfer = LDos.charge_transfer_from_file(feff_inp_file,
                                                             ldos_file)
            return LDos(complete_dos, charge_transfer)

        @staticmethod
        def charge_transfer_from_file(feff_inp_file, ldos_file):
            """
            Get charge transfer from file.

            Args:
                feff_inp_file (str): name of feff.inp file for run
                ldos_file (str): ldos filename for run, assume consequetive order,
                    i.e., ldos01.dat, ldos02.dat....

            Returns:
                dictionary of dictionaries in order of potential sites
                ({"p": 0.154, "s": 0.078, "d": 0.0, "tot": 0.232}, ...)
            """
            cht = OrderedDict()
            parameters = Tags.from_file(feff_inp_file)

            if 'RECIPROCAL' in parameters:
                dicts = [dict()]
                pot_dict = dict()
                dos_index = 1
                begin = 0
                pot_inp = re.sub(r'feff.inp', r'pot.inp', feff_inp_file)
                pot_readstart = re.compile('.*iz.*lmaxsc.*xnatph.*xion.*folp.*')
                pot_readend = re.compile('.*ExternalPot.*switch.*')
                with zopen(pot_inp, "r") as potfile:
                    for line in potfile:
                        if len(pot_readend.findall(line)) > 0:
                            break
                        if begin == 1:
                            z_number = int(line.strip().split()[0])
                            ele_name = Element.from_Z(z_number).name
                            if len(pot_dict) == 0:
                                pot_dict[0] = ele_name
                            elif len(pot_dict) > 0:
                                pot_dict[max(pot_dict.keys()) + 1] = ele_name
                            begin += 1
                            continue
                        if begin == 2:
                            z_number = int(line.strip().split()[0])
                            ele_name = Element.from_Z(z_number).name
                            dicts[0][ele_name] = dos_index
                            dos_index += 1
                            if len(pot_dict) == 0:
                                pot_dict[0] = ele_name
                            elif len(pot_dict) > 0:
                                pot_dict[max(pot_dict.keys()) + 1] = ele_name
                        if len(pot_readstart.findall(line)) > 0:
                            begin = 1
            else:
                pot_string = Potential.pot_string_from_file(feff_inp_file)
                dicts = Potential.pot_dict_from_string(pot_string)
                pot_dict = dicts[1]

            for i in range(0, len(dicts[0]) + 1):
                if len(str(i)) == 1:
                    with zopen("{}0{}.dat".format(ldos_file, i), "rt") \
                            as fobject:
                        f = fobject.readlines()
                        s = float(f[3].split()[2])
                        p = float(f[4].split()[2])
                        d = float(f[5].split()[2])
                        f1 = float(f[6].split()[2])
                        tot = float(f[1].split()[4])
                        cht[str(i)] = {pot_dict[i]: {'s': s, 'p': p, 'd': d,
                                                     'f': f1,
                                                     'tot': tot}}
                else:
                    with zopen(ldos_file + str(i) + ".dat", "rt") as fid:
                        f = fid.readlines()
                        s = float(f[3].split()[2])
                        p = float(f[4].split()[2])
                        d = float(f[5].split()[2])
                        f1 = float(f[6].split()[2])
                        tot = float(f[1].split()[4])
                        cht[str(i)] = {pot_dict[i]: {'s': s, 'p': p, 'd': d,
                                                     'f': f1,
                                                     'tot': tot}}

            return cht

        def charge_transfer_to_string(self):
            """returns shrage transfer as string"""
            ch = self.charge_transfer
            chts = ['\nCharge Transfer\n\nabsorbing atom']
            for i in range(len(ch)):
                for atom, v2 in ch[str(i)].items():
                    a = ['\n', atom, '\n', 's   ', str(v2['s']), '\n',
                         'p   ', str(v2['p']), '\n',
                         'd   ', str(v2['d']), '\n',
                         'f   ', str(v2['f']), '\n',
                         'tot ', str(v2['tot']), '\n']
                    chts.extend(a)
            return ''.join(chts)

    class Xmu(MSONable):
        r"""
        Parser for data in 'xmu.dat' file.
        The file 'xmu.dat' contains XANES, EXAFS or NRIXS data depending on the
        situation; \\mu, \\mu_0, and \\chi = \\chi * \\mu_0/ \\mu_0/(edge+50eV) as
        functions of absolute energy E, relative energy E − E_f and wave number k.

        Default attributes:
            xmu: Photon absorption cross section of absorbing atom in material
            Energies: Energies of data point
            relative_energies: E - E_fermi
            wavenumber: k=\\sqrt(E −E_fermi)
            mu: The total absorption cross-section.
            mu0: The embedded atomic background absorption.
            chi: fine structure.
            Edge: Aborption Edge
            Absorbing atom: Species of absorbing atom
            Material: Formula of material
            Source: Source of structure
            Calculation: Type of Feff calculation performed
        """

        def __init__(self, header, parameters, absorbing_atom, data):
            """
            Args:
                header: Header object
                parameters: Tags object
                absorbing_atom (str/int): absorbing atom symbol or index
                data (numpy.ndarray, Nx6): cross_sections
            """
            self.header = header
            self.parameters = parameters
            self.absorbing_atom = absorbing_atom
            self.data = np.array(data)

        @staticmethod
        def from_file(xmu_dat_file="xmu.dat", feff_inp_file="feff.inp"):
            """
            Get Xmu from file.

            Args:
                xmu_dat_file (str): filename and path for xmu.dat
                feff_inp_file (str): filename and path of feff.inp input file

            Returns:
                 Xmu object
            """
            data = np.loadtxt(xmu_dat_file)
            header = Header.from_file(feff_inp_file)
            parameters = Tags.from_file(feff_inp_file)
            pots = Potential.pot_string_from_file(feff_inp_file)
            # site index (Note: in feff it starts from 1)
            if "RECIPROCAL" in parameters:
                absorbing_atom = parameters["TARGET"]
            # species symbol
            else:
                absorbing_atom = pots.splitlines()[3].split()[2]
            return Xmu(header, parameters, absorbing_atom, data)

        @property
        def energies(self):
            """
            Returns the absolute energies in eV.
            """
            return self.data[:, 0]

        @property
        def relative_energies(self):
            """
            Returns energy with respect to the fermi level.
            E - E_f
            """
            return self.data[:, 1]

        @property
        def wavenumber(self):
            r"""
            Returns The wave number in units of \\AA^-1. k=\\sqrt(E −E_f) where E is
            the energy and E_f is the Fermi level computed from electron gas theory
            at the average interstitial charge density.
            """
            return self.data[:, 2]

        @property
        def mu(self):
            """
            Returns the total absorption cross-section.
            """
            return self.data[:, 3]

        @property
        def mu0(self):
            """
            Returns the embedded atomic background absorption.
            """
            return self.data[:, 4]

        @property
        def chi(self):
            """
            Returns the normalized fine structure.
            """
            return self.data[:, 5]

        @property
        def e_fermi(self):
            """
            Returns the fermi level in eV.
            """
            return (self.energies[0] - self.relative_energies[0])

        @property
        def source(self):
            """
            Returns source identification from Header file
            """
            return self.header.source

        @property
        def calc(self):
            """
            Returns type of Feff calculation, XANES or EXAFS
            """
            return "XANES" if "XANES" in self.parameters else "EXAFS"

        @property
        def material_formula(self):
            """
            Returns chemical formula of material from feff.inp file
            """
            try:
                form = self.header.formula
            except IndexError:
                form = 'No formula provided'
            return "".join(map(str, form))

        @property
        def edge(self):
            """
            Returns excitation edge.
            """
            return self.parameters["EDGE"]

        def as_dict(self):
            """
            Returns dict representations of Xmu object
            """
            d = MSONable.as_dict(self)
            d["data"] = self.data.tolist()
            return d

    class Eels(MSONable):
        """
        Parse'eels.dat' file.
        """

        def __init__(self, data):
            """
            Args:
                data (): Eels data.
            """
            self.data = np.array(data)

        @property
        def energies(self):
            """
            Returns the energies in eV.
            """
            return self.data[:, 0]

        @property
        def total_spectrum(self):
            """
            Returns the total eels spectrum.
            """
            return self.data[:, 1]

        @property
        def atomic_background(self):
            """
            Returns: atomic background.
            """
            return self.data[:, 2]

        @property
        def fine_structure(self):
            """
            Returns: Fine structure of EELS.
            """
            return self.data[:, 3]

        @staticmethod
        def from_file(eels_dat_file="eels.dat"):
            """
            Parse eels spectrum.

            Args:
                eels_dat_file (str): filename and path for eels.dat

            Returns:
                 Eels object
            """
            data = np.loadtxt(eels_dat_file)
            return Eels(data)

        def as_dict(self):
            """
            Returns dict representations of Xmu object
            """
            d = MSONable.as_dict(self)
            d["data"] = self.data.tolist()
            return d