# -*- coding: utf-8 -*-
"""Utility class and functions for HubbardStructureData.
Borrowed and adapted from aiida-quantumespresso
"""
# pylint: disable=no-name-in-module, invalid-name
from typing import List, Literal, Tuple
from pymatgen.core import Lattice, PeriodicSite
import numpy as np
from aiida_quantumespresso.common.hubbard import Hubbard, HubbardParameters
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class HubbardGetterMixin:
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def get_hubbard_list(self) -> List[Tuple[int, str, int, str, float, Tuple[int, int, int], str]]:
"""Return the Hubbard `parameters` as a list of lists.
The parameters have the following order within each list:
* atom_index
* atom_manifold
* neighbour_index
* neighbour_manifold
* value
* translation
* hubbard_type
"""
return [params.to_tuple() for params in self.properties.hubbard.parameters]
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class HubbardSetterMixin:
#@staticmethod
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def set_hubbard_from_list(
parameters: List[Tuple[int, str, int, str, float, Tuple[int, int, int], str]],
projectors: str = 'ortho-atomic',
formulation: str = 'dudarev',
):
"""Return a :meth:`~aiida_quantumespresso.common.hubbard.Hubbard` instance from a list of tuples.
Each list must contain the hubbard parameters in the following order:
* atom_index
* atom_manifold
* neighbour_index
* neighbour_manifold
* value
* translation
* hubbard_type
"""
parameters = [HubbardParameters.from_tuple(value) for value in parameters]
self.properties.hubbard = Hubbard(parameters=parameters, projectors=projectors, formulation=formulation)
return
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def append_hubbard_parameter(
self,
atom_index: int,
atom_manifold: str,
neighbour_index: int,
neighbour_manifold: str,
value: float,
translation: Tuple[int, int, int] = None,
hubbard_type: str = 'Ueff',
):
"""Append a :class:`~aiida_quantumespresso.common.hubbard.HubbardParameters`.
:param atom_index: atom index in unitcell
:param atom_manifold: atomic manifold (e.g. 3d, 3d-2p)
:param neighbour_index: neighbouring atom index in unitcell
:param neighbour_manifold: neighbour manifold (e.g. 3d, 3d-2p)
:param value: value of the Hubbard parameter, in eV
:param translation: (3,) list of ints, describing the translation vector
associated with the neighbour atom, defaults to None
:param hubbard_type: hubbard type (U, V, J, ...), defaults to 'Ueff'
(see :class:`~aiida_quantumespresso.common.hubbard.Hubbard` for full allowed values)
"""
sites = [
PeriodicSite(
species=site.species,
coords=site.coords,
lattice=Lattice(self.properties.cell, pbc=self.properties.pbc),
coords_are_cartesian=True
) for site in self.get_pymatgen_structure().sites
]
if any((atom_index > len(sites) - 1, neighbour_index > len(sites) - 1)):
raise ValueError(
'atom_index and neighbour_index must be within the range of the number of sites in the structure'
)
if translation is None:
_, translation = sites[atom_index].distance_and_image(sites[neighbour_index])
translation = np.array(translation, dtype=np.int64).tolist()
hp_tuple = (atom_index, atom_manifold, neighbour_index, neighbour_manifold, value, translation, hubbard_type)
parameters = HubbardParameters.from_tuple(hp_tuple)
hubbard = self.properties.hubbard
if parameters not in hubbard.parameters:
hubbard.parameters.append(parameters)
self.properties.hubbard = hubbard
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def pop_hubbard_parameters(self, index: int = -1):
"""Pop Hubbard parameters in the list.
:param index: index of the Hubbard parameters to pop
"""
hubbard = self.properties.hubbard
hubbard.parameters.pop(index) if index != -1 else hubbard.parameters.pop()
self.properties.hubbard = hubbard
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def clear_hubbard_parameters(self):
"""Clear all the Hubbard parameters."""
hubbard = self.properties.hubbard
hubbard.parameters = []
self.properties.hubbard = hubbard
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def initialize_intersites_hubbard(
self,
atom_name: str,
atom_manifold: str,
neighbour_name: str,
neighbour_manifold: str,
value: float = 1e-8,
hubbard_type: str = 'V',
use_kinds: bool = True,
):
"""Initialize and append intersite Hubbard values between an atom and its neighbour(s).
.. note:: this only initialize the value between the first neighbour. In case
`use_kinds` is False, all the possible combination of couples having
kind name equal to symbol are initialized.
:param atom_name: atom name in unitcell
:param atom_manifold: atomic manifold (e.g. 3d, 3d-2p)
:param neighbour_index: neighbouring atom name in unitcell
:param neighbour_manifold: neighbour manifold (e.g. 3d, 3d-2p)
:param value: value of the Hubbard parameter, in eV
:param hubbard_type: hubbard type (U, V, J, ...), defaults to 'V'
(see :class:`~aiida_quantumespresso.common.hubbard.Hubbard` for full allowed values)
:param use_kinds: whether to use kinds for initializing the parameters; when False, it
initializes all the ``Kinds`` matching the ``atom_name``
"""
sites = self.get_pymatgen_structure().sites
function = self._get_one_kind_index if use_kinds else self._get_symbol_indices
atom_indices = function(atom_name)
neigh_indices = function(neighbour_name)
if atom_indices is None or neigh_indices is None:
raise ValueError('species or kind names not in structure')
for atom_index in atom_indices:
for neighbour_index in neigh_indices:
_, translation = sites[atom_index].distance_and_image(sites[neighbour_index])
translation = np.array(translation, dtype=np.int64).tolist()
args = (
atom_index, atom_manifold, neighbour_index, neighbour_manifold, value, translation, hubbard_type
)
self.append_hubbard_parameter(*args)
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def initialize_onsites_hubbard(
self,
atom_name: str,
atom_manifold: str,
value: float = 1e-8,
hubbard_type: str = 'Ueff',
use_kinds: bool = True,
):
"""Initialize and append onsite Hubbard values of atoms with specific name.
:param atom_name: atom name in unitcell
:param atom_manifold: atomic manifold (e.g. 3d, 3d-2p)
:param value: value of the Hubbard parameter, in eV
:param hubbard_type: hubbard type (U, J, ...), defaults to 'Ueff'
(see :class:`~aiida_quantumespresso.common.hubbard.Hubbard` for full allowed values)
:param use_kinds: whether to use kinds for initializing the parameters; when False, it
initializes all the ``Kinds`` matching the ``atom_name``
"""
function = self._get_one_kind_index if use_kinds else self._get_symbol_indices
atom_indices = function(atom_name)
if atom_indices is None:
raise ValueError('species or kind names not in structure')
for atom_index in atom_indices:
args = (atom_index, atom_manifold, atom_index, atom_manifold, value, [0, 0, 0], hubbard_type)
self.append_hubbard_parameter(*args)
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def _get_one_kind_index(self, kinds: str) -> List[int]:
"""Return the first site index matching with `kinds`."""
for i, site in enumerate(self.properties.sites):
if site.kind_name == kinds:
return [i]
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def _get_symbol_indices(self, symbol: str) -> List[int]:
"""Return one site index for each kind name matching symbol."""
matching_kinds = [kind for kind, symbols in zip(self.properties.kind_names,self.properties.symbols)
if symbol == symbols]
return [self.properties.kind_names.index(kind) for kind in matching_kinds]
