################################################################################
# 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 #
################################################################################
"""Create OrbitalData instances."""
__all__ = ("generate_projections",)
def _generate_wannier_orbitals( # pylint: disable=too-many-arguments,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,
):
"""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.common import InputValidationError
from aiida.plugins import DataFactory, OrbitalFactory
def convert_to_list(item):
"""Check 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):
"""Create 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("core.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("core.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(
f"No valid positions found in structure using {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):
"""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("core.orbital")()
orbitaldata.set_orbitals(orbitals)
return orbitaldata