"""
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.
"""

from __future__ import annotations

import abc
import logging
import math
import os
import sys
import warnings
from copy import deepcopy
from typing import TYPE_CHECKING

import numpy as np
from monty.json import MSONable
from monty.os.path import zpath
from monty.serialization import loadfn

from pymatgen.core.structure import Molecule, Structure
from pymatgen.io.feff.inputs import Atoms, Header, Potential, Tags

if TYPE_CHECKING:
    from typing import Self

__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, abc.ABC):
    """
    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):
        """Get header to be used in feff.inp file from a pymatgen structure."""

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

        Returns:
            Atoms object.
        """

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

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

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

        if "RECIPROCAL" not in self.tags:
            dct |= {"POTENTIALS": self.potential, "ATOMS": self.atoms}

        return dct

    def write_input(self, output_dir=".", make_dir_if_not_present=True):
        """Write a FEFF input set 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:
            os.makedirs(output_dir, exist_ok=True)

        feff = self.all_input()

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

        for k, v in feff.items():
            with open(os.path.join(output_dir, k), mode="w", encoding="utf-8") as file:
                file.write(str(v))

        with open(f"{output_dir}/feff.inp", mode="w", encoding="utf-8") as file:
            file.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: str | int,
        structure: Structure | Molecule,
        radius: float,
        config_dict: dict,
        edge: str = "K",
        spectrum: str = "EXAFS",
        nkpts=1000,
        user_tag_settings: dict | None = None,
        spacegroup_analyzer_settings: dict | None = None,
    ):
        """Initialize a FEFFDictSet.

        Args:
            absorbing_atom (str | int): absorbing atom symbol or site index
            structure: Structure or Molecule object. If a Structure, SpaceGroupAnalyzer is used to
                determine symmetrically-equivalent sites. If a Molecule, there is no symmetry
                checking.
            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"]}
                To specify a net charge on the structure, pass an "IONS" tag containing a list
                    of tuples where the first element is the unique potential value (ipot value)
                    and the second element is the charge to be applied to atoms associated
                    with that potential, e.g. {"IONS": [(0, 0.1), (1, 0.1), (2, 0.1)]}
                    will result in.

                    ION 0 0.1
                    ION 1 0.1
                    ION 2 0.1

                    being written to the input file.
            spacegroup_analyzer_settings (dict): parameters passed to SpacegroupAnalyzer.
                e.g. {"symprec": 0.01, "angle_tolerance": 4}
        """
        self.absorbing_atom = absorbing_atom
        self.user_tag_settings = user_tag_settings or {}
        # make sure there are no partial occupancies
        if structure.is_ordered:
            if isinstance(structure, Structure):
                # charged structures should never be supported b/c periodic boundaries
                # cause problems
                if structure.charge != 0:
                    raise ValueError("Structure objects with a net charge are not supported!")
            elif isinstance(structure, Molecule):
                # charged Molecules should eventually be supported. According to Joshua Kas (FEFF expert),
                # the correct approach is to divide the total charge on the Molecule equally among
                # all atoms. Then, add one ION card with that charge for each atom type (i.e., each
                # unique ipot value)
                # for example, for a cluster with a +1 charge and 10 atoms and 3 unique potentials, you
                # would add
                # ION 0 0.1
                # ION 1 0.1
                # ION 2 0.1
                # This is also most appropriate for self-consistent calculations like XANES.
                # For non-self-consistent calc types, the manual says its best to check results
                # with and without a net charge b/c it's often better not to use charge
                if structure.charge != 0 and not self.user_tag_settings.get("IONS"):
                    warnings.warn(
                        "For Molecule objects with a net charge it is recommended to set one or more"
                        " ION tags in the input file by modifying user_tag_settings."
                        " Consult the FEFFDictSet docstring and the FEFF10 User Guide for more information.",
                        stacklevel=2,
                    )
            else:
                raise ValueError("'structure' argument must be a Structure or Molecule!")
        else:
            raise ValueError("Structure with partial occupancies cannot be converted into atomic coordinates!")
        self.structure = structure
        self.radius = radius
        self.config_dict = deepcopy(config_dict)
        self.edge = edge
        self.spectrum = spectrum
        self.nkpts = nkpts
        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 = len(self.structure) < 14 and "EXAFS" not in self.config_dict
        self.spacegroup_analyzer_settings = spacegroup_analyzer_settings or {}

    def header(self, source: str = "", comment: str = ""):
        """
        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,
            spacegroup_analyzer_settings=self.spacegroup_analyzer_settings,
        )

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

        Returns:
            Tags
        """
        if "RECIPROCAL" in self.config_dict:
            if self.small_system:
                self.config_dict["CIF"] = f"{self.structure.formula.replace(' ', '')}.cif"
                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"):
                    abc = self.structure.lattice.abc
                    mult = (self.nkpts * abc[0] * abc[1] * abc[2]) ** (1 / 3)
                    self.config_dict["KMESH"] = [round(mult / length) for length 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) -> Potential:
        """FEFF potential.

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

    @property
    def atoms(self) -> Atoms:
        """
        absorber + the rest.

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

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

    @classmethod
    def from_directory(cls, input_dir: str) -> Self:
        """
        Read in a set of FEFF input files from a directory, which is
        useful when existing FEFF input needs some adjustment.
        """
        sub_d: dict = {
            "header": Header.from_file(zpath(os.path.join(input_dir, "HEADER"))),
            "parameters": Tags.from_file(zpath(os.path.join(input_dir, "PARAMETERS"))),
        }

        # 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
        feff_inp = zpath(f"{input_dir}/feff.inp")

        if "RECIPROCAL" not in sub_d["parameters"]:
            input_atoms = Atoms.cluster_from_file(feff_inp)
            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
            radius = math.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(float)
                    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(f"{MODULE_DIR}/MPXANESSet.yaml")
            if radius is None:
                radius = 10
            return cls(
                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"],
            )

        raise ValueError("Bad input directory.")


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

    CONFIG = loadfn(f"{MODULE_DIR}/MPXANESSet.yaml")

    def __init__(
        self,
        absorbing_atom,
        structure,
        edge: str = "K",
        radius: float = 10.0,
        nkpts: int = 1000,
        user_tag_settings: dict | None = None,
        **kwargs,
    ):
        r"""
        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
            **kwargs: Passthrough to FEFFDictSet.
        """
        super().__init__(
            absorbing_atom,
            structure,
            radius,
            MPXANESSet.CONFIG,
            edge=edge,
            spectrum="XANES",
            nkpts=nkpts,
            user_tag_settings=user_tag_settings,
            **kwargs,
        )


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

    CONFIG = loadfn(f"{MODULE_DIR}/MPEXAFSSet.yaml")

    def __init__(
        self,
        absorbing_atom,
        structure,
        edge: str = "K",
        radius: float = 10.0,
        nkpts: int = 1000,
        user_tag_settings: dict | None = None,
        **kwargs,
    ):
        r"""
        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
            **kwargs: Passthrough to FEFFDictSet.
        """
        super().__init__(
            absorbing_atom,
            structure,
            radius,
            MPEXAFSSet.CONFIG,
            edge=edge,
            spectrum="EXAFS",
            nkpts=nkpts,
            user_tag_settings=user_tag_settings,
            **kwargs,
        )


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: int = 1000,
        user_tag_settings: dict | None = None,
        **kwargs,
    ):
        """Initialize a MPEELSDictSet.

        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
            **kwargs: Passthrough to FEFFDictSet.
        """
        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,
            **kwargs,
        )


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

    CONFIG = loadfn(f"{MODULE_DIR}/MPELNESSet.yaml")

    def __init__(
        self,
        absorbing_atom,
        structure,
        edge: str = "K",
        radius: float = 10.0,
        beam_energy: float = 100,
        beam_direction=None,
        collection_angle: float = 1,
        convergence_angle: float = 1,
        user_eels_settings=None,
        nkpts: int = 1000,
        user_tag_settings: dict | None = None,
        **kwargs,
    ):
        r"""
        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
            **kwargs: Passthrough to FEFFDictSet.
        """
        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,
            **kwargs,
        )


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

    CONFIG = loadfn(f"{MODULE_DIR}/MPEXELFSSet.yaml")

    def __init__(
        self,
        absorbing_atom,
        structure,
        edge="K",
        radius: float = 10.0,
        beam_energy: float = 100,
        beam_direction=None,
        collection_angle: float = 1,
        convergence_angle: float = 1,
        user_eels_settings=None,
        nkpts: int = 1000,
        user_tag_settings: dict | None = None,
        **kwargs,
    ):
        r"""
        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
            **kwargs: Passthrough to FEFFDictSet.
        """
        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,
            **kwargs,
        )
