Source code for aiida_wannier90.orbitals

# -*- coding: utf-8 -*-
################################################################################
# Copyright (c), AiiDA team and individual contributors.                       #
#  All rights reserved.                                                        #
# This file is part of the AiiDA-wannier90 code.                               #
#                                                                              #
# The code is hosted on GitHub at https://github.com/aiidateam/aiida-wannier90 #
# For further information on the license, see the LICENSE.txt file             #
################################################################################
"""
Creating OrbitalData instances
==============================
"""

__all__ = ('generate_projections', )


def _generate_wannier_orbitals( # pylint: disable=too-many-arguments,too-many-locals,too-many-statements # noqa:  disable=MC0001
    position_cart=None,
    structure=None,
    kind_name=None,
    radial=1,
    ang_mtm_name=None,
    ang_mtm_l_list=None,
    ang_mtm_mr_list=None,
    spin=None,
    zona=None,
    zaxis=None,
    xaxis=None,
    spin_axis=None
):
    """
    Use this method to emulate the input style of Wannier90,
    when setting the orbitals (see chapter 3 in the user_guide). Position
    can be provided either in Cartesian coordiantes using ``position_cart``
    or can be assigned based on an input structure and ``kind_name``.

    :param position_cart: position in Cartesian coordinates or list of
                          positions in Cartesian coodriantes
    :param structure: input structure for use with kind_names
    :param kind_name: kind_name, for use with the structure
    :param radial: number of radial nodes
    :param ang_mtm_name: orbital name or list of orbital names, cannot
                         be used in conjunction with ang_mtm_l_list or
                         ang_mtm_mr_list
    :param ang_mtm_l_list: angular momentum (either an integer or a list), if
                 ang_mtm_mr_list is not specified will return all orbitals associated with it
    :param ang_mtm_mr_list: magnetic angular momentum number must be specified
                       along with ang_mtm_l_list. Note that if this is specified,
                       ang_mtm_l_list must be an integer and not a list
    :param spin: the spin, spin up can be specified with 1,u or U and
                 spin down can be specified using -1,d,D
    :param zona: as specified in user guide, applied to all orbitals
    :param zaxis: the zaxis, list of three floats
                  as described in wannier user guide
    :param xaxis: the xaxis, list of three floats as described in the
                  wannier user guide
    :param spin_axis: the spin alignment axis, as described in the
                      user guide
    """
    from aiida.plugins import DataFactory
    from aiida.plugins import OrbitalFactory
    from aiida.common import InputValidationError

    def convert_to_list(item):
        """
        internal method, checks if the item is already a list or tuple.
        if not returns a tuple containing only item, otherwise returns
        tuple(item)
        """
        if isinstance(item, (list, tuple)):
            return tuple(item)
        return tuple([item])

    def combine_dictlists(dict_list1, dict_list2):
        """
        Creates a list of every dict in dict_list1 updated with every
        dict in dict_list2
        """
        out_list = []
        # excpetion handling for the case of empty dicts
        dict_list1_empty = not any([bool(x) for x in dict_list1])
        dict_list2_empty = not any([bool(x) for x in dict_list2])
        if dict_list1_empty and dict_list2_empty:
            raise InputValidationError('One dict must not be empty')
        if dict_list1_empty:
            return dict_list2
        if dict_list2_empty:
            return dict_list2

        for dict_1 in dict_list1:
            for dict_2 in dict_list2:
                temp_1 = dict_1.copy()
                temp_2 = dict_2.copy()
                temp_1.update(temp_2)
                out_list.append(temp_1)
        return out_list

    RealhydrogenOrbital = OrbitalFactory('realhydrogen')

    #########################################################################
    # Validation of inputs                                                  #
    #########################################################################
    if position_cart is None and kind_name is None:
        raise InputValidationError('Must supply a kind_name or position')
    if position_cart is not None and kind_name is not None:
        raise InputValidationError(
            'Must supply position or kind_name'
            ' not both'
        )

    structure_class = DataFactory('structure')
    if kind_name is not None:
        if not isinstance(structure, structure_class):
            raise InputValidationError(
                'Must supply a StructureData as '
                'structure if using kind_name'
            )
        if not isinstance(kind_name, str):
            raise InputValidationError('kind_name must be a string')

    if ang_mtm_name is None and ang_mtm_l_list is None:
        raise InputValidationError(
            "Must supply ang_mtm_name or ang_mtm_l_list"
        )
    if ang_mtm_name is not None and (
        ang_mtm_l_list is not None or ang_mtm_mr_list is not None
    ):
        raise InputValidationError(
            "Cannot supply ang_mtm_l_list or ang_mtm_mr_list"
            " but not both"
        )
    if ang_mtm_l_list is None and ang_mtm_mr_list is not None:
        raise InputValidationError(
            "Cannot supply ang_mtm_mr_list without "
            "ang_mtm_l_list"
        )

    ####################################################################
    #Setting up initial basic parameters
    ####################################################################
    projection_dict = {}
    if radial:
        projection_dict['radial_nodes'] = radial - 1
    if xaxis:
        projection_dict['x_orientation'] = xaxis
    if zaxis:
        projection_dict['z_orientation'] = zaxis
    if kind_name:
        projection_dict['kind_name'] = kind_name
    if spin_axis:
        projection_dict['spin_orientation'] = spin_axis
    if zona:
        projection_dict['diffusivity'] = zona

    projection_dicts = [projection_dict]

    #####################################################################
    # Setting up Positions                                              #
    #####################################################################
    # finds all the positions to append the orbitals to (if applicable)
    position_list = []
    if kind_name:
        for site in structure.sites:
            if site.kind_name == kind_name:
                position_list.append(site.position)
        if not position_list:
            raise InputValidationError(
                "No valid positions found in structure "
                "using {}".format(kind_name)
            )
    # otherwise turns position into position_list
    else:
        position_list = [convert_to_list(position_cart)]
    position_dicts = [{"position": v} for v in position_list]
    projection_dicts = combine_dictlists(projection_dicts, position_dicts)

    #######################################################################
    # Setting up angular momentum                                         #
    #######################################################################
    # if ang_mtm_l_list, ang_mtm_mr_list provided, setup dicts
    if ang_mtm_l_list is not None:
        ang_mtm_l_list = convert_to_list(ang_mtm_l_list)
        ang_mtm_dicts = []
        for ang_mtm_l in ang_mtm_l_list:
            if ang_mtm_l >= 0:
                ang_mtm_dicts += [{
                    'angular_momentum': ang_mtm_l,
                    'magnetic_number': i
                } for i in range(2 * ang_mtm_l + 1)]
            else:
                ang_mtm_dicts += [{
                    'angular_momentum': ang_mtm_l,
                    'magnetic_number': i
                } for i in range(-ang_mtm_l + 1)]
        if ang_mtm_mr_list is not None:
            if len(ang_mtm_l_list) > 1:
                raise InputValidationError(
                    "If you are giving specific"
                    " magnetic numbers please do"
                    " not supply more than one"
                    " angular number."
                )
            ang_mtm_mr_list = convert_to_list(ang_mtm_mr_list)
            ang_mtm_l_num = ang_mtm_l_list[0]
            ang_mtm_dicts = [{
                'angular_momentum': ang_mtm_l_num,
                'magnetic_number': j - 1
            } for j in ang_mtm_mr_list]
    if ang_mtm_name is not None:
        ang_mtm_names = convert_to_list(ang_mtm_name)
        ang_mtm_dicts = []
        for name in ang_mtm_names:
            # get_quantum_numbers_from_name (in AiiDA) might not return
            # a consistent order since it creates the list from a dictionary
            # This might be considered a bug in AiiDA, but since AiiDA is going
            # to drop py2 support soon, this might not be fixed, so we work
            # around the issue here.
            ang_mtm_dicts += sorted(
                RealhydrogenOrbital.get_quantum_numbers_from_name(name),
                key=lambda qnums:
                (qnums['angular_momentum'], qnums['magnetic_number'])
            )
    projection_dicts = combine_dictlists(projection_dicts, ang_mtm_dicts)

    #####################################################################
    # Setting up the spin                                               #
    #####################################################################
    if spin:
        spin_dict = {'U': 1, 'u': 1, 1: 1, 'D': -1, 'd': -1, -1: -1}
        if isinstance(spin, (list, tuple)):
            spin = [spin_dict[x] for x in spin]
        else:
            spin = [spin_dict[spin]]
        spin_dicts = [{'spin': v} for v in spin]
        projection_dicts = combine_dictlists(projection_dicts, spin_dicts)

    # generating and returning a list of all corresponding orbitals
    orbital_out = []
    for projection_dict in projection_dicts:
        realh = RealhydrogenOrbital(**projection_dict)
        orbital_out.append(realh)
    return orbital_out


[docs]def generate_projections(list_of_projection_dicts, structure): """ Use this method to emulate the input style of Wannier90, when setting the orbitals (see chapter 3 in the Wannier90 user guide). Position can be provided either in Cartesian coordinates using ``position_cart`` or can be assigned based on an input structure and ``kind_name``. Pass a list of dictionaries, in which the keys of each dictionary correspond to those below. Also note that ``radial`` and ``ang_mtm_mr_list`` both use 0-based indexing as opposed to 1-based indexing, effectively meaning that both should be offset by 1. E.g., an orbital with two radial nodes would use ``radial=2`` (Wannier90 syntax), and then be converted to ``radial_nodes=1`` (AiiDA plugin syntax) inside the stored orbital. .. note:: The key entries used here do not correspond to the keys used internally by the orbital objects. For example, ``ang_mtm_mr_list`` will be converted to ``magnetic_number`` in the :py:class:`~aiida.orm.OrbitalData` node (the internal key is mentioned in brackets). :param position_cart: position in Cartesian coordinates or list of positions in Cartesian coordinates (``position``) :param kind_name: kind name in the input :py:class:`~aiida.orm.StructureData` node (``kind_name``) :param radial: number of radial nodes (``radial_nodes + 1``) :param ang_mtm_name: orbital name or list of orbital names, cannot be used in conjunction with ``ang_mtm_l_list`` or ``ang_mtm_mr_list`` (see ``ang_mtm_l_list`` and ``ang_mtm_mr_list``). :param ang_mtm_l_list: angular momentum (either an integer or a list), if ``ang_mtm_mr_list`` is not specified will return all orbitals associated with it (``angular_momentum``). :param ang_mtm_mr_list: magnetic angular momentum number must be specified along with ``ang_mtm_l_list`` (``magnetic_number + 1``). Note that if this is specified, ``ang_mtm_l_list`` must be an integer and not a list. :param spin: the spin, spin up can be specified with ``1``, ``'u'`` or ``'U'`` and spin down can be specified using ``-1``, ``'d'`` or ``'D'`` (``spin``) :param zona: as specified in user guide, applied to all orbitals (``diffusivity``) :param zaxis: the z-axis of the orbital, a list of three floats as described in wannier user guide (``z_orientation``) :param xaxis: the x-axis of the orbital, a list of three floats as described in the Wannier user guide (``x_orientation``) :param spin_axis: the spin alignment axis, as described in the user guide (``spin_orientation``) """ from aiida.plugins import DataFactory if not isinstance(list_of_projection_dicts, (list, tuple)): list_of_projection_dicts = [list_of_projection_dicts] orbitals = [] for this_dict in list_of_projection_dicts: if 'kind_name' in this_dict: this_dict.update({'structure': structure}) orbitals += _generate_wannier_orbitals(**this_dict) orbitaldata = DataFactory('orbital')() orbitaldata.set_orbitals(orbitals) return orbitaldata