# -*- coding: utf-8 -*-
###########################################################################
# Copyright (c), The AiiDA team. All rights reserved.                     #
# This file is part of the AiiDA code.                                    #
#                                                                         #
# The code is hosted on GitHub at https://github.com/aiidateam/aiida_core #
# For further information on the license, see the LICENSE.txt file        #
# For further information please visit http://www.aiida.net               #
###########################################################################

from aiida.common.constants import elements
import copy
import numpy as np
from aiida.orm.data.structure import Kind, Site, StructureData

__all__ = ['structure_to_spglib_tuple', 'spglib_tuple_to_structure']

def structure_to_spglib_tuple(structure):
    """
    Convert an AiiDA structure to a tuple of the format (cell, scaled_positions, element_numbers).

    :param structure: the AiiDA structure
    :return: (structure_tuple, kind_info, kinds) where structure_tuple
        is a tuple of format (cell, scaled_positions, element_numbers);
        kind_info is a dictionary mapping the kind_names to
        the numbers used in element_numbers. When possible, it uses
        the Z number of the element, otherwise it uses numbers > 1000;
        kinds is a list of the kinds of the structure.
    """
    def get_new_number(the_list, start_from):
        """
        Get the first integer >= start_from not yet in the list
        """
        retval = start_from
        comp_list = sorted(_ for _ in the_list if _ >= start_from)

        current_pos = 0
        found = False
        while not found:
            if len(comp_list) <= current_pos:
                return retval
            if retval == comp_list[current_pos]:
                current_pos += 1
                retval += 1
            else:
                found = True
                return retval

    Z = {v['symbol']: k for k, v in elements.items()}

    cell = np.array(structure.cell)
    abs_pos = np.array([_.position for _ in structure.sites])
    rel_pos = np.dot(abs_pos, np.linalg.inv(cell))
    kinds = {k.name: k for k in structure.kinds}

    kind_numbers = {}
    for kind in structure.kinds:
        if len(kind.symbols) == 1:
            realnumber = Z[kind.symbols[0]]
            if realnumber in list(kind_numbers.values()):
                number = get_new_number(
                    list(kind_numbers.values()), start_from=realnumber * 1000)
            else:
                number = realnumber
            kind_numbers[kind.name] = number
        else:
            number = get_new_number(list(kind_numbers.values()), start_from=200000)
            kind_numbers[kind.name] = number

    numbers = [kind_numbers[s.kind_name] for s in structure.sites]

    return ((cell, rel_pos, numbers), kind_numbers, list(structure.kinds))

def spglib_tuple_to_structure(structure_tuple, kind_info=None, kinds=None):
    """
    Convert a tuple of the format (cell, scaled_positions, element_numbers) to an AiiDA structure.

    Unless the element_numbers are identical to the Z number of the atoms,
    you should pass both kind_info and kinds, with the same format as returned
    by get_tuple_from_aiida_structure.

    :param structure_tuple: the structure in format (structure_tuple, kind_info)
    :param kind_info: a dictionary mapping the kind_names to
       the numbers used in element_numbers. If not provided, assumes {element_name: element_Z}
    :param kinds: a list of the kinds of the structure.
    """
    if kind_info is None and kinds is not None:
        raise ValueError("If you pass kind_info, you should also pass kinds")
    if kinds is None and kind_info is not None:
        raise ValueError("If you pass kinds, you should also pass kind_info")

    Z = {v['symbol']: k for k, v in elements.items()}
    cell, rel_pos, numbers = structure_tuple
    if kind_info:
        _kind_info = copy.copy(kind_info)
        _kinds = copy.copy(kinds)
    else:
        try:
            # For each site
            symbols = [elements[num]['symbol'] for num in numbers]
        except KeyError as e:
            raise ValueError("You did not pass kind_info, but at least one number "
                             "is not a valid Z number: {}".format(e.message))

        _kind_info = {elements[num]['symbol']: num for num in set(numbers)}
        # Get the default kinds
        _kinds = [Kind(symbols=sym) for sym in set(symbols)]

    _kinds_dict = {k.name: k for k in _kinds}
    # Now I will use in any case _kinds and _kind_info
    if len(_kind_info.values()) != len(set(_kind_info.values())):
        raise ValueError(
            "There is at least a number repeated twice in kind_info!")
    # Invert the mapping
    mapping_num_kindname = {v: k for k, v in _kind_info.items()}
    # Create the actual mapping
    try:
        mapping_to_kinds = {num: _kinds_dict[kindname] for num, kindname
                            in mapping_num_kindname.items()}
    except KeyError as e:
        raise ValueError(
            "Unable to find '{}' in the kinds list".format(e.message))

    try:
        site_kinds = [mapping_to_kinds[num] for num in numbers]
    except KeyError as e:
        raise ValueError(
            "Unable to find kind in kind_info for number {}".format(e.message))

    structure = StructureData(cell=cell)
    for k in _kinds:
        structure.append_kind(k)
    abs_pos = np.dot(rel_pos, cell)
    if len(abs_pos) != len(site_kinds):
        raise ValueError("The length of the positions array is different from the "
                         "length of the element numbers")

    for kind, pos in zip(site_kinds, abs_pos):
        structure.append_site(Site(kind_name=kind.name, position=pos))

    return structure

# -*- coding: utf-8 -*-
###########################################################################
# Copyright (c), The AiiDA team. All rights reserved.                     #
# This file is part of the AiiDA code.                                    #
#                                                                         #
# The code is hosted on GitHub at https://github.com/aiidateam/aiida_core #
# For further information on the license, see the LICENSE.txt file        #
# For further information please visit http://www.aiida.net               #
###########################################################################

from aiida.common.constants import elements
import copy
import numpy as np
from aiida.orm.data.structure import Kind, Site, StructureData

__all__ = ['structure_to_spglib_tuple', 'spglib_tuple_to_structure']

def structure_to_spglib_tuple(structure):
    """
    Convert an AiiDA structure to a tuple of the format (cell, scaled_positions, element_numbers).

    :param structure: the AiiDA structure
    :return: (structure_tuple, kind_info, kinds) where structure_tuple
        is a tuple of format (cell, scaled_positions, element_numbers);
        kind_info is a dictionary mapping the kind_names to
        the numbers used in element_numbers. When possible, it uses
        the Z number of the element, otherwise it uses numbers > 1000;
        kinds is a list of the kinds of the structure.
    """
    def get_new_number(the_list, start_from):
        """
        Get the first integer >= start_from not yet in the list
        """
        retval = start_from
        comp_list = sorted(_ for _ in the_list if _ >= start_from)

        current_pos = 0
        found = False
        while not found:
            if len(comp_list) <= current_pos:
                return retval
            if retval == comp_list[current_pos]:
                current_pos += 1
                retval += 1
            else:
                found = True
                return retval

    Z = {v['symbol']: k for k, v in elements.items()}

    cell = np.array(structure.cell)
    abs_pos = np.array([_.position for _ in structure.sites])
    rel_pos = np.dot(abs_pos, np.linalg.inv(cell))
    kinds = {k.name: k for k in structure.kinds}

    kind_numbers = {}
    for kind in structure.kinds:
        if len(kind.symbols) == 1:
            realnumber = Z[kind.symbols[0]]
            if realnumber in list(kind_numbers.values()):
                number = get_new_number(
                    list(kind_numbers.values()), start_from=realnumber * 1000)
            else:
                number = realnumber
            kind_numbers[kind.name] = number
        else:
            number = get_new_number(list(kind_numbers.values()), start_from=200000)
            kind_numbers[kind.name] = number

    numbers = [kind_numbers[s.kind_name] for s in structure.sites]

    return ((cell, rel_pos, numbers), kind_numbers, list(structure.kinds))

def spglib_tuple_to_structure(structure_tuple, kind_info=None, kinds=None):
    """
    Convert a tuple of the format (cell, scaled_positions, element_numbers) to an AiiDA structure.

    Unless the element_numbers are identical to the Z number of the atoms,
    you should pass both kind_info and kinds, with the same format as returned
    by get_tuple_from_aiida_structure.

    :param structure_tuple: the structure in format (structure_tuple, kind_info)
    :param kind_info: a dictionary mapping the kind_names to
       the numbers used in element_numbers. If not provided, assumes {element_name: element_Z}
    :param kinds: a list of the kinds of the structure.
    """
    if kind_info is None and kinds is not None:
        raise ValueError("If you pass kind_info, you should also pass kinds")
    if kinds is None and kind_info is not None:
        raise ValueError("If you pass kinds, you should also pass kind_info")

    Z = {v['symbol']: k for k, v in elements.items()}
    cell, rel_pos, numbers = structure_tuple
    if kind_info:
        _kind_info = copy.copy(kind_info)
        _kinds = copy.copy(kinds)
    else:
        try:
            # For each site
            symbols = [elements[num]['symbol'] for num in numbers]
        except KeyError as e:
            raise ValueError("You did not pass kind_info, but at least one number "
                             "is not a valid Z number: {}".format(e.message))

        _kind_info = {elements[num]['symbol']: num for num in set(numbers)}
        # Get the default kinds
        _kinds = [Kind(symbols=sym) for sym in set(symbols)]

    _kinds_dict = {k.name: k for k in _kinds}
    # Now I will use in any case _kinds and _kind_info
    if len(_kind_info.values()) != len(set(_kind_info.values())):
        raise ValueError(
            "There is at least a number repeated twice in kind_info!")
    # Invert the mapping
    mapping_num_kindname = {v: k for k, v in _kind_info.items()}
    # Create the actual mapping
    try:
        mapping_to_kinds = {num: _kinds_dict[kindname] for num, kindname
                            in mapping_num_kindname.items()}
    except KeyError as e:
        raise ValueError(
            "Unable to find '{}' in the kinds list".format(e.message))

    try:
        site_kinds = [mapping_to_kinds[num] for num in numbers]
    except KeyError as e:
        raise ValueError(
            "Unable to find kind in kind_info for number {}".format(e.message))

    structure = StructureData(cell=cell)
    for k in _kinds:
        structure.append_kind(k)
    abs_pos = np.dot(rel_pos, cell)
    if len(abs_pos) != len(site_kinds):
        raise ValueError("The length of the positions array is different from the "
                         "length of the element numbers")

    for kind, pos in zip(site_kinds, abs_pos):
        structure.append_site(Site(kind_name=kind.name, position=pos))

    return structure

# -*- coding: utf-8 -*- ########################################################################### # Copyright (c), The AiiDA team. All rights reserved.                     # # This file is part of the AiiDA code.                                    # #                                                                         # # The code is hosted on GitHub at https://github.com/aiidateam/aiida_core # # For further information on the license, see the LICENSE.txt file        # # For further information please visit http://www.aiida.net               # ########################################################################### Convert an AiiDA structure to a tuple of the format (cell, scaled_positions, element_numbers).      :param structure: the AiiDA structure     :return: (structure_tuple, kind_info, kinds) where structure_tuple         is a tuple of format (cell, scaled_positions, element_numbers);         kind_info is a dictionary mapping the kind_names to         the numbers used in element_numbers. When possible, it uses         the Z number of the element, otherwise it uses numbers > 1000;         kinds is a list of the kinds of the structure. Get the first integer >= start_from not yet in the list Convert a tuple of the format (cell, scaled_positions, element_numbers) to an AiiDA structure.      Unless the element_numbers are identical to the Z number of the atoms,     you should pass both kind_info and kinds, with the same format as returned     by get_tuple_from_aiida_structure.      :param structure_tuple: the structure in format (structure_tuple, kind_info)     :param kind_info: a dictionary mapping the kind_names to        the numbers used in element_numbers. If not provided, assumes {element_name: element_Z}     :param kinds: a list of the kinds of the structure. # For each site # Get the default kinds # Now I will use in any case _kinds and _kind_info # Invert the mapping # Create the actual mapping