# coding: utf-8
# Copyright (c) Max-Planck-Institut für Eisenforschung GmbH - Computational Materials Design (CM) Department
# Distributed under the terms of "New BSD License", see the LICENSE file.

from collections import OrderedDict
import numpy as np
from pyiron_atomistics.atomistics.structure.atoms import Atoms
import warnings

__author__ = "<NAME>"
__copyright__ = (
    "Copyright 2021, Max-Planck-Institut für Eisenforschung GmbH - "
    "Computational Materials Design (CM) Department"
)
__version__ = "1.0"
__maintainer__ = "<NAME>"
__email__ = "<EMAIL>"
__status__ = "production"
__date__ = "Sep 1, 2017"


def read_atoms(
    filename="CONTCAR",
    return_velocities=False,
    species_list=None,
    species_from_potcar=False,
):
    """
    Routine to read structural static from a POSCAR type file

    Args:
        filename (str): Input filename
        return_velocities (bool): True if the predictor corrector velocities are read (only from MD output)
        species_list (list/numpy.ndarray): A list of the species (if not present in the POSCAR file or a POTCAR in the
        same directory)
        species_from_potcar (bool): True if the species list should be read from the POTCAR file in the same directory

    Returns:
        pyiron.atomistics.structure.atoms.Atoms: The generated structure object

    """
    directory = "/".join(filename.split("/")[0:-1])
    potcar_file = "/".join([directory, "POTCAR"])
    if (species_list is None) and species_from_potcar:
        species_list = get_species_list_from_potcar(potcar_file)
        if len(species_list) == 0:
            warnings.warn("Warning! Unable to read species information from POTCAR")
    file_string = list()
    with open(filename) as f:
        for line in f:
            line = line.strip()
            file_string.append(line)
    return atoms_from_string(
        file_string, read_velocities=return_velocities, species_list=species_list
    )


def get_species_list_from_potcar(filename="POTCAR"):
    """
    Generates the species list from a POTCAR type file

    Args:
        filename (str): Input filename

    Returns:
        list: A list of species symbols

    """
    trigger = "VRHFIN ="
    species_list = list()
    with open(filename) as potcar_file:
        lines = potcar_file.readlines()
        for line in lines:
            line = line.strip()
            if trigger in line:
                str_1 = line.split(trigger)
                str_2 = str_1[-1].split(":")
                species_list.append(str_2[0].replace(" ", ""))
    return species_list


def write_poscar(structure, filename="POSCAR", write_species=True, cartesian=True):
    """
    Writes a POSCAR type file from a structure object

    Args:
        structure (pyiron.atomistics.structure.atoms.Atoms): The structure instance to be written to the POSCAR format
        filename (str): Output filename
        write_species (bool): True if the species should be written to the file
        cartesian (bool): True if the positions are written in Cartesian coordinates

    """
    endline = "\n"
    with open(filename, "w") as f:
        selec_dyn = False
        f.write("Poscar file generated with pyiron" + endline)
        f.write("1.0" + endline)
        for a_i in structure.get_cell():
            x, y, z = a_i
            f.write("{0:.15f} {1:.15f} {2:.15f}".format(x, y, z) + endline)
        atom_numbers = structure.get_number_species_atoms()
        if write_species:
            f.write(" ".join(atom_numbers.keys()) + endline)
        num_str = [str(val) for val in atom_numbers.values()]
        f.write(" ".join(num_str))
        f.write(endline)
        if "selective_dynamics" in structure.get_tags():
            selec_dyn = True
            f.write("Selective dynamics" + endline)
        sorted_coords = list()
        selec_dyn_lst = list()
        for species in atom_numbers.keys():
            indices = structure.select_index(species)
            for i in indices:
                if cartesian:
                    sorted_coords.append(structure.positions[i])
                else:
                    sorted_coords.append(structure.get_scaled_positions()[i])
                if selec_dyn:
                    selec_dyn_lst.append(structure.selective_dynamics[i])
        if cartesian:
            f.write("Cartesian" + endline)
        else:
            f.write("Direct" + endline)
        if selec_dyn:
            for i, vec in enumerate(sorted_coords):
                x, y, z = vec
                sd_string = " ".join(["T" if sd else "F" for sd in selec_dyn_lst[i]])
                f.write(
                    "{0:.15f} {1:.15f} {2:.15f}".format(x, y, z)
                    + " "
                    + sd_string
                    + endline
                )
        else:
            for i, vec in enumerate(sorted_coords):
                x, y, z = vec
                f.write("{0:.15f} {1:.15f} {2:.15f}".format(x, y, z) + endline)


def atoms_from_string(string, read_velocities=False, species_list=None):
    """
    Routine to convert a string list read from a input/output structure file and convert into Atoms instance

    Args:
        string (list): A list of strings (lines) read from the POSCAR/CONTCAR/CHGCAR/LOCPOT file
        read_velocities (bool): True if the velocities from a CONTCAR file should be read (predictor corrector)
        species_list (list/numpy.ndarray): A list of species of the atoms

    Returns:
        pyiron.atomistics.structure.atoms.Atoms: The required structure object

    """
    string = [s.strip() for s in string]
    string_lower = [s.lower() for s in string]
    atoms_dict = dict()
    atoms_dict["first_line"] = string[0]
    # del string[0]
    atoms_dict["selective_dynamics"] = False
    atoms_dict["relative"] = False
    if "direct" in string_lower or "d" in string_lower:
        atoms_dict["relative"] = True
    atoms_dict["scaling_factor"] = float(string[1])
    unscaled_cell = list()
    for i in [2, 3, 4]:
        vec = list()
        for j in range(3):
            vec.append(float(string[i].split()[j]))
        unscaled_cell.append(vec)
    if atoms_dict["scaling_factor"] > 0.0:
        atoms_dict["cell"] = np.array(unscaled_cell) * atoms_dict["scaling_factor"]
    else:
        atoms_dict["cell"] = np.array(unscaled_cell) * (
            (-atoms_dict["scaling_factor"]) ** (1.0 / 3.0)
        )
    if "selective dynamics" in string_lower:
        atoms_dict["selective_dynamics"] = True
    no_of_species = len(string[5].split())
    species_dict = OrderedDict()
    position_index = 7
    if atoms_dict["selective_dynamics"]:
        position_index += 1
    for i in range(no_of_species):
        species_dict["species_" + str(i)] = dict()
        try:
            species_dict["species_" + str(i)]["count"] = int(string[5].split()[i])
        except ValueError:
            species_dict["species_" + str(i)]["species"] = string[5].split()[i]
            species_dict["species_" + str(i)]["count"] = int(string[6].split()[i])
    atoms_dict["species_dict"] = species_dict
    if "species" in atoms_dict["species_dict"]["species_0"].keys():
        position_index += 1
    positions = list()
    selective_dynamics = list()
    n_atoms = sum(
        [
            atoms_dict["species_dict"][key]["count"]
            for key in atoms_dict["species_dict"].keys()
        ]
    )
    try:
        for i in range(position_index, position_index + n_atoms):
            string_list = np.array(string[i].split())
            positions.append([float(val) for val in string_list[0:3]])
            if atoms_dict["selective_dynamics"]:
                selective_dynamics.append(["T" in val for val in string_list[3:6]])
    except (ValueError, IndexError):
        raise AssertionError(
            "The number of positions given does not match the number of atoms"
        )
    atoms_dict["positions"] = np.array(positions)
    if not atoms_dict["relative"]:
        if atoms_dict["scaling_factor"] > 0.0:
            atoms_dict["positions"] *= atoms_dict["scaling_factor"]
        else:
            atoms_dict["positions"] *= (-atoms_dict["scaling_factor"]) ** (1.0 / 3.0)
    velocities = list()
    try:
        atoms = _dict_to_atoms(atoms_dict, species_list=species_list)
    except ValueError:
        atoms = _dict_to_atoms(atoms_dict, read_from_first_line=True)
    if atoms_dict["selective_dynamics"]:
        selective_dynamics = np.array(selective_dynamics)
        unique_sel_dyn, inverse, counts = np.unique(
            selective_dynamics, axis=0, return_counts=True, return_inverse=True
        )
        count_index = np.argmax(counts)
        atoms.add_tag(selective_dynamics=unique_sel_dyn.tolist()[count_index])
        is_not_majority = np.arange(len(unique_sel_dyn), dtype=int) != count_index
        for i, val in enumerate(unique_sel_dyn):
            if is_not_majority[i]:
                for key in np.argwhere(inverse == i).flatten():
                    atoms.selective_dynamics[int(key)] = val.tolist()
    if read_velocities:
        velocity_index = position_index + n_atoms + 1
        for i in range(velocity_index, velocity_index + n_atoms):
            try:
                velocities.append([float(val) for val in string[i].split()[0:3]])
            except IndexError:
                break
        if not (len(velocities) == n_atoms):
            warnings.warn(
                "The velocities are either not available or they are incomplete/corrupted. Returning empty "
                "list instead",
                UserWarning,
            )
            return atoms, list()
        return atoms, velocities
    else:
        return atoms


def _dict_to_atoms(atoms_dict, species_list=None, read_from_first_line=False):
    """
    Function to convert a generated dict into an structure object

    Args:
        atoms_dict (dict): Dictionary with the details (from string_to_atom)
        species_list (list/numpy.ndarray): List of species
        read_from_first_line (bool): True if we are to read the species information from the first line in the file

    Returns:
        pyiron.atomistics.structure.atoms.Atoms: The required structure object
    """
    is_absolute = not (atoms_dict["relative"])
    positions = atoms_dict["positions"]
    cell = atoms_dict["cell"]
    symbol = str()
    elements = list()
    el_list = list()
    for i, sp_key in enumerate(atoms_dict["species_dict"].keys()):
        if species_list is not None:
            try:
                el_list = np.array([species_list[i]])
                el_list = np.tile(el_list, atoms_dict["species_dict"][sp_key]["count"])
                if isinstance(species_list[i], str):
                    symbol += species_list[i] + str(
                        atoms_dict["species_dict"][sp_key]["count"]
                    )
                else:
                    symbol += species_list[i].Abbreviation + str(
                        atoms_dict["species_dict"][sp_key]["count"]
                    )
            except IndexError:
                raise ValueError(
                    "Number of species in the specified species list does not match that in the file"
                )
        elif "species" in atoms_dict["species_dict"][sp_key].keys():
            el_list = np.array([atoms_dict["species_dict"][sp_key]["species"]])
            el_list = np.tile(el_list, atoms_dict["species_dict"][sp_key]["count"])
            symbol += atoms_dict["species_dict"][sp_key]["species"]
            symbol += str(atoms_dict["species_dict"][sp_key]["count"])
        elif read_from_first_line:
            if not (
                len(atoms_dict["first_line"].split())
                == len(atoms_dict["species_dict"].keys())
            ):
                raise AssertionError()
            el_list = np.array(atoms_dict["first_line"].split()[i])
            el_list = np.tile(el_list, atoms_dict["species_dict"][sp_key]["count"])
            symbol += atoms_dict["first_line"].split()[i]
            symbol += str(atoms_dict["species_dict"][sp_key]["count"])
        elif species_list is None:
            raise ValueError(
                "Species list should be provided since pyiron can't detect species information"
            )
        elements.append(el_list)
    elements_new = list()
    for ele in elements:
        for e in ele:
            elements_new.append(e)
    elements = elements_new
    if is_absolute:
        atoms = Atoms(elements, positions=positions, cell=cell, pbc=True)
    else:
        atoms = Atoms(elements, scaled_positions=positions, cell=cell, pbc=True)
    return atoms


def vasp_sorter(structure):
    """
    Routine to sort the indices of a structure as it would be when written to a POSCAR file

    Args:
        structure (pyiron.atomistics.structure.atoms.Atoms): The structure whose indices need to be sorted

    Returns:
        list: A list of indices which is sorted by the corresponding species for writing to POSCAR

    """
    atom_numbers = structure.get_number_species_atoms()
    sorted_indices = list()
    for species in atom_numbers.keys():
        indices = structure.select_index(species)
        for i in indices:
            sorted_indices.append(i)
    return np.array(sorted_indices)


def manip_contcar(filename, new_filename, add_pos):
    """
    Manipulate a CONTCAR/POSCAR file by adding something to the positions

    Args:
        filename (str):  Filename/path of the input file
        new_filename (str): Filename/path of the output file
        add_pos (list/numpy.ndarray): Array of values to be added to the positions of the input

    """
    actual_struct = read_atoms(filename)
    n = 0
    direct = True
    with open(filename, "r") as f:
        lines = f.readlines()
        for line in lines:
            if "Direct" in line or "Cartesian" in line:
                direct = "Direct" in line
                break
            n += 1
    pos_list = list()
    sd_list = list()
    if len(lines[n + 1].split()) == 6:
        for line in lines[n + 1 : n + 1 + len(actual_struct)]:
            pos_list.append([float(val) for val in line.split()[0:3]])
            sd_list.append(["T" in val for val in line.split()[3:]])
    else:
        for line in lines[n + 1 : n + 1 + len(actual_struct)]:
            pos_list.append([float(val) for val in line.split()[0:3]])
    old_pos = np.array(pos_list)
    if direct:
        add_pos_rel = np.dot(add_pos, np.linalg.inv(actual_struct.cell))
        new_pos = old_pos + add_pos_rel
    else:
        new_pos = old_pos + add_pos
    new_lines = lines
    new_pos_str = np.array(new_pos, dtype=str)
    if len(sd_list) > 0:
        bool_list = np.zeros_like(old_pos, dtype=str)
        bool_list[:] = "F"
        bool_list[np.array(sd_list)] = "T"
        for i, pos in enumerate(new_pos_str):
            linestr = np.append(pos, bool_list[i])
            new_lines[n + 1 + i] = " ".join([str(val) for val in linestr]) + "\n"
    else:
        for i, pos in enumerate(new_pos_str):
            linestr = pos
            new_lines[n + 1 + i] = " ".join([str(val) for val in linestr]) + "\n"

    # Exclude predictor corrector positions
    if len(new_lines[n + len(new_pos_str) :]) >= 2 * len(new_pos_str):
        new_lines = new_lines[: n + 2 * (len(new_pos_str)) + 2]

    with open(new_filename, "w") as f:
        for new_line in new_lines:
            f.write(new_line)

# coding: utf-8
# Copyright (c) Max-Planck-Institut für Eisenforschung GmbH - Computational Materials Design (CM) Department
# Distributed under the terms of "New BSD License", see the LICENSE file.

from collections import OrderedDict
import numpy as np
from pyiron_atomistics.atomistics.structure.atoms import Atoms
import warnings

__author__ = "<NAME>"
__copyright__ = (
    "Copyright 2021, Max-Planck-Institut für Eisenforschung GmbH - "
    "Computational Materials Design (CM) Department"
)
__version__ = "1.0"
__maintainer__ = "<NAME>"
__email__ = "<EMAIL>"
__status__ = "production"
__date__ = "Sep 1, 2017"


def read_atoms(
    filename="CONTCAR",
    return_velocities=False,
    species_list=None,
    species_from_potcar=False,
):
    """
    Routine to read structural static from a POSCAR type file

    Args:
        filename (str): Input filename
        return_velocities (bool): True if the predictor corrector velocities are read (only from MD output)
        species_list (list/numpy.ndarray): A list of the species (if not present in the POSCAR file or a POTCAR in the
        same directory)
        species_from_potcar (bool): True if the species list should be read from the POTCAR file in the same directory

    Returns:
        pyiron.atomistics.structure.atoms.Atoms: The generated structure object

    """
    directory = "/".join(filename.split("/")[0:-1])
    potcar_file = "/".join([directory, "POTCAR"])
    if (species_list is None) and species_from_potcar:
        species_list = get_species_list_from_potcar(potcar_file)
        if len(species_list) == 0:
            warnings.warn("Warning! Unable to read species information from POTCAR")
    file_string = list()
    with open(filename) as f:
        for line in f:
            line = line.strip()
            file_string.append(line)
    return atoms_from_string(
        file_string, read_velocities=return_velocities, species_list=species_list
    )


def get_species_list_from_potcar(filename="POTCAR"):
    """
    Generates the species list from a POTCAR type file

    Args:
        filename (str): Input filename

    Returns:
        list: A list of species symbols

    """
    trigger = "VRHFIN ="
    species_list = list()
    with open(filename) as potcar_file:
        lines = potcar_file.readlines()
        for line in lines:
            line = line.strip()
            if trigger in line:
                str_1 = line.split(trigger)
                str_2 = str_1[-1].split(":")
                species_list.append(str_2[0].replace(" ", ""))
    return species_list


def write_poscar(structure, filename="POSCAR", write_species=True, cartesian=True):
    """
    Writes a POSCAR type file from a structure object

    Args:
        structure (pyiron.atomistics.structure.atoms.Atoms): The structure instance to be written to the POSCAR format
        filename (str): Output filename
        write_species (bool): True if the species should be written to the file
        cartesian (bool): True if the positions are written in Cartesian coordinates

    """
    endline = "\n"
    with open(filename, "w") as f:
        selec_dyn = False
        f.write("Poscar file generated with pyiron" + endline)
        f.write("1.0" + endline)
        for a_i in structure.get_cell():
            x, y, z = a_i
            f.write("{0:.15f} {1:.15f} {2:.15f}".format(x, y, z) + endline)
        atom_numbers = structure.get_number_species_atoms()
        if write_species:
            f.write(" ".join(atom_numbers.keys()) + endline)
        num_str = [str(val) for val in atom_numbers.values()]
        f.write(" ".join(num_str))
        f.write(endline)
        if "selective_dynamics" in structure.get_tags():
            selec_dyn = True
            f.write("Selective dynamics" + endline)
        sorted_coords = list()
        selec_dyn_lst = list()
        for species in atom_numbers.keys():
            indices = structure.select_index(species)
            for i in indices:
                if cartesian:
                    sorted_coords.append(structure.positions[i])
                else:
                    sorted_coords.append(structure.get_scaled_positions()[i])
                if selec_dyn:
                    selec_dyn_lst.append(structure.selective_dynamics[i])
        if cartesian:
            f.write("Cartesian" + endline)
        else:
            f.write("Direct" + endline)
        if selec_dyn:
            for i, vec in enumerate(sorted_coords):
                x, y, z = vec
                sd_string = " ".join(["T" if sd else "F" for sd in selec_dyn_lst[i]])
                f.write(
                    "{0:.15f} {1:.15f} {2:.15f}".format(x, y, z)
                    + " "
                    + sd_string
                    + endline
                )
        else:
            for i, vec in enumerate(sorted_coords):
                x, y, z = vec
                f.write("{0:.15f} {1:.15f} {2:.15f}".format(x, y, z) + endline)


def atoms_from_string(string, read_velocities=False, species_list=None):
    """
    Routine to convert a string list read from a input/output structure file and convert into Atoms instance

    Args:
        string (list): A list of strings (lines) read from the POSCAR/CONTCAR/CHGCAR/LOCPOT file
        read_velocities (bool): True if the velocities from a CONTCAR file should be read (predictor corrector)
        species_list (list/numpy.ndarray): A list of species of the atoms

    Returns:
        pyiron.atomistics.structure.atoms.Atoms: The required structure object

    """
    string = [s.strip() for s in string]
    string_lower = [s.lower() for s in string]
    atoms_dict = dict()
    atoms_dict["first_line"] = string[0]
    # del string[0]
    atoms_dict["selective_dynamics"] = False
    atoms_dict["relative"] = False
    if "direct" in string_lower or "d" in string_lower:
        atoms_dict["relative"] = True
    atoms_dict["scaling_factor"] = float(string[1])
    unscaled_cell = list()
    for i in [2, 3, 4]:
        vec = list()
        for j in range(3):
            vec.append(float(string[i].split()[j]))
        unscaled_cell.append(vec)
    if atoms_dict["scaling_factor"] > 0.0:
        atoms_dict["cell"] = np.array(unscaled_cell) * atoms_dict["scaling_factor"]
    else:
        atoms_dict["cell"] = np.array(unscaled_cell) * (
            (-atoms_dict["scaling_factor"]) ** (1.0 / 3.0)
        )
    if "selective dynamics" in string_lower:
        atoms_dict["selective_dynamics"] = True
    no_of_species = len(string[5].split())
    species_dict = OrderedDict()
    position_index = 7
    if atoms_dict["selective_dynamics"]:
        position_index += 1
    for i in range(no_of_species):
        species_dict["species_" + str(i)] = dict()
        try:
            species_dict["species_" + str(i)]["count"] = int(string[5].split()[i])
        except ValueError:
            species_dict["species_" + str(i)]["species"] = string[5].split()[i]
            species_dict["species_" + str(i)]["count"] = int(string[6].split()[i])
    atoms_dict["species_dict"] = species_dict
    if "species" in atoms_dict["species_dict"]["species_0"].keys():
        position_index += 1
    positions = list()
    selective_dynamics = list()
    n_atoms = sum(
        [
            atoms_dict["species_dict"][key]["count"]
            for key in atoms_dict["species_dict"].keys()
        ]
    )
    try:
        for i in range(position_index, position_index + n_atoms):
            string_list = np.array(string[i].split())
            positions.append([float(val) for val in string_list[0:3]])
            if atoms_dict["selective_dynamics"]:
                selective_dynamics.append(["T" in val for val in string_list[3:6]])
    except (ValueError, IndexError):
        raise AssertionError(
            "The number of positions given does not match the number of atoms"
        )
    atoms_dict["positions"] = np.array(positions)
    if not atoms_dict["relative"]:
        if atoms_dict["scaling_factor"] > 0.0:
            atoms_dict["positions"] *= atoms_dict["scaling_factor"]
        else:
            atoms_dict["positions"] *= (-atoms_dict["scaling_factor"]) ** (1.0 / 3.0)
    velocities = list()
    try:
        atoms = _dict_to_atoms(atoms_dict, species_list=species_list)
    except ValueError:
        atoms = _dict_to_atoms(atoms_dict, read_from_first_line=True)
    if atoms_dict["selective_dynamics"]:
        selective_dynamics = np.array(selective_dynamics)
        unique_sel_dyn, inverse, counts = np.unique(
            selective_dynamics, axis=0, return_counts=True, return_inverse=True
        )
        count_index = np.argmax(counts)
        atoms.add_tag(selective_dynamics=unique_sel_dyn.tolist()[count_index])
        is_not_majority = np.arange(len(unique_sel_dyn), dtype=int) != count_index
        for i, val in enumerate(unique_sel_dyn):
            if is_not_majority[i]:
                for key in np.argwhere(inverse == i).flatten():
                    atoms.selective_dynamics[int(key)] = val.tolist()
    if read_velocities:
        velocity_index = position_index + n_atoms + 1
        for i in range(velocity_index, velocity_index + n_atoms):
            try:
                velocities.append([float(val) for val in string[i].split()[0:3]])
            except IndexError:
                break
        if not (len(velocities) == n_atoms):
            warnings.warn(
                "The velocities are either not available or they are incomplete/corrupted. Returning empty "
                "list instead",
                UserWarning,
            )
            return atoms, list()
        return atoms, velocities
    else:
        return atoms


def _dict_to_atoms(atoms_dict, species_list=None, read_from_first_line=False):
    """
    Function to convert a generated dict into an structure object

    Args:
        atoms_dict (dict): Dictionary with the details (from string_to_atom)
        species_list (list/numpy.ndarray): List of species
        read_from_first_line (bool): True if we are to read the species information from the first line in the file

    Returns:
        pyiron.atomistics.structure.atoms.Atoms: The required structure object
    """
    is_absolute = not (atoms_dict["relative"])
    positions = atoms_dict["positions"]
    cell = atoms_dict["cell"]
    symbol = str()
    elements = list()
    el_list = list()
    for i, sp_key in enumerate(atoms_dict["species_dict"].keys()):
        if species_list is not None:
            try:
                el_list = np.array([species_list[i]])
                el_list = np.tile(el_list, atoms_dict["species_dict"][sp_key]["count"])
                if isinstance(species_list[i], str):
                    symbol += species_list[i] + str(
                        atoms_dict["species_dict"][sp_key]["count"]
                    )
                else:
                    symbol += species_list[i].Abbreviation + str(
                        atoms_dict["species_dict"][sp_key]["count"]
                    )
            except IndexError:
                raise ValueError(
                    "Number of species in the specified species list does not match that in the file"
                )
        elif "species" in atoms_dict["species_dict"][sp_key].keys():
            el_list = np.array([atoms_dict["species_dict"][sp_key]["species"]])
            el_list = np.tile(el_list, atoms_dict["species_dict"][sp_key]["count"])
            symbol += atoms_dict["species_dict"][sp_key]["species"]
            symbol += str(atoms_dict["species_dict"][sp_key]["count"])
        elif read_from_first_line:
            if not (
                len(atoms_dict["first_line"].split())
                == len(atoms_dict["species_dict"].keys())
            ):
                raise AssertionError()
            el_list = np.array(atoms_dict["first_line"].split()[i])
            el_list = np.tile(el_list, atoms_dict["species_dict"][sp_key]["count"])
            symbol += atoms_dict["first_line"].split()[i]
            symbol += str(atoms_dict["species_dict"][sp_key]["count"])
        elif species_list is None:
            raise ValueError(
                "Species list should be provided since pyiron can't detect species information"
            )
        elements.append(el_list)
    elements_new = list()
    for ele in elements:
        for e in ele:
            elements_new.append(e)
    elements = elements_new
    if is_absolute:
        atoms = Atoms(elements, positions=positions, cell=cell, pbc=True)
    else:
        atoms = Atoms(elements, scaled_positions=positions, cell=cell, pbc=True)
    return atoms


def vasp_sorter(structure):
    """
    Routine to sort the indices of a structure as it would be when written to a POSCAR file

    Args:
        structure (pyiron.atomistics.structure.atoms.Atoms): The structure whose indices need to be sorted

    Returns:
        list: A list of indices which is sorted by the corresponding species for writing to POSCAR

    """
    atom_numbers = structure.get_number_species_atoms()
    sorted_indices = list()
    for species in atom_numbers.keys():
        indices = structure.select_index(species)
        for i in indices:
            sorted_indices.append(i)
    return np.array(sorted_indices)


def manip_contcar(filename, new_filename, add_pos):
    """
    Manipulate a CONTCAR/POSCAR file by adding something to the positions

    Args:
        filename (str):  Filename/path of the input file
        new_filename (str): Filename/path of the output file
        add_pos (list/numpy.ndarray): Array of values to be added to the positions of the input

    """
    actual_struct = read_atoms(filename)
    n = 0
    direct = True
    with open(filename, "r") as f:
        lines = f.readlines()
        for line in lines:
            if "Direct" in line or "Cartesian" in line:
                direct = "Direct" in line
                break
            n += 1
    pos_list = list()
    sd_list = list()
    if len(lines[n + 1].split()) == 6:
        for line in lines[n + 1 : n + 1 + len(actual_struct)]:
            pos_list.append([float(val) for val in line.split()[0:3]])
            sd_list.append(["T" in val for val in line.split()[3:]])
    else:
        for line in lines[n + 1 : n + 1 + len(actual_struct)]:
            pos_list.append([float(val) for val in line.split()[0:3]])
    old_pos = np.array(pos_list)
    if direct:
        add_pos_rel = np.dot(add_pos, np.linalg.inv(actual_struct.cell))
        new_pos = old_pos + add_pos_rel
    else:
        new_pos = old_pos + add_pos
    new_lines = lines
    new_pos_str = np.array(new_pos, dtype=str)
    if len(sd_list) > 0:
        bool_list = np.zeros_like(old_pos, dtype=str)
        bool_list[:] = "F"
        bool_list[np.array(sd_list)] = "T"
        for i, pos in enumerate(new_pos_str):
            linestr = np.append(pos, bool_list[i])
            new_lines[n + 1 + i] = " ".join([str(val) for val in linestr]) + "\n"
    else:
        for i, pos in enumerate(new_pos_str):
            linestr = pos
            new_lines[n + 1 + i] = " ".join([str(val) for val in linestr]) + "\n"

    # Exclude predictor corrector positions
    if len(new_lines[n + len(new_pos_str) :]) >= 2 * len(new_pos_str):
        new_lines = new_lines[: n + 2 * (len(new_pos_str)) + 2]

    with open(new_filename, "w") as f:
        for new_line in new_lines:
            f.write(new_line)

# coding: utf-8 # Copyright (c) Max-Planck-Institut für Eisenforschung GmbH - Computational Materials Design (CM) Department # Distributed under the terms of "New BSD License", see the LICENSE file. Routine to read structural static from a POSCAR type file      Args:         filename (str): Input filename         return_velocities (bool): True if the predictor corrector velocities are read (only from MD output)         species_list (list/numpy.ndarray): A list of the species (if not present in the POSCAR file or a POTCAR in the         same directory)         species_from_potcar (bool): True if the species list should be read from the POTCAR file in the same directory      Returns:         pyiron.atomistics.structure.atoms.Atoms: The generated structure object Generates the species list from a POTCAR type file      Args:         filename (str): Input filename      Returns:         list: A list of species symbols Writes a POSCAR type file from a structure object      Args:         structure (pyiron.atomistics.structure.atoms.Atoms): The structure instance to be written to the POSCAR format         filename (str): Output filename         write_species (bool): True if the species should be written to the file         cartesian (bool): True if the positions are written in Cartesian coordinates Routine to convert a string list read from a input/output structure file and convert into Atoms instance      Args:         string (list): A list of strings (lines) read from the POSCAR/CONTCAR/CHGCAR/LOCPOT file         read_velocities (bool): True if the velocities from a CONTCAR file should be read (predictor corrector)         species_list (list/numpy.ndarray): A list of species of the atoms      Returns:         pyiron.atomistics.structure.atoms.Atoms: The required structure object # del string[0] Function to convert a generated dict into an structure object      Args:         atoms_dict (dict): Dictionary with the details (from string_to_atom)         species_list (list/numpy.ndarray): List of species         read_from_first_line (bool): True if we are to read the species information from the first line in the file      Returns:         pyiron.atomistics.structure.atoms.Atoms: The required structure object Routine to sort the indices of a structure as it would be when written to a POSCAR file      Args:         structure (pyiron.atomistics.structure.atoms.Atoms): The structure whose indices need to be sorted      Returns:         list: A list of indices which is sorted by the corresponding species for writing to POSCAR Manipulate a CONTCAR/POSCAR file by adding something to the positions      Args:         filename (str):  Filename/path of the input file         new_filename (str): Filename/path of the output file         add_pos (list/numpy.ndarray): Array of values to be added to the positions of the input # Exclude predictor corrector positions