"""A collection of functions for building certain lattice types."""
from __future__ import annotations
import itertools
from typing import TYPE_CHECKING
from ase.spacegroup import crystal
if TYPE_CHECKING:
from ase import Atoms
from smact.lattice import Lattice, Site
def _tile_oxidation_states(
base_oxidation_states: list[list[int]],
n_sites: int,
) -> list[list[int]]:
"""Tile the base unit-cell oxidation states to match the number of sites in an expanded cell."""
n_base = len(base_oxidation_states)
if n_sites == n_base:
return base_oxidation_states
if n_sites % n_base != 0:
msg = f"Number of sites ({n_sites}) is not a multiple of the base oxidation states pattern ({n_base})"
raise ValueError(msg)
return list(itertools.islice(itertools.cycle(base_oxidation_states), n_sites))
[docs]
def cubic_perovskite(
species: list[str],
cell_par: list[float] | None = None,
repetitions: list[int] | None = None,
oxidation_states: list[list[int]] | None = None,
) -> tuple[Lattice, Atoms]:
"""
Build a perovskite cell using the crystal function in ASE.
Args:
----
species (list[str]): Element symbols
cell_par (list): Six floats/ints specifying 3 unit cell lengths and 3 unit cell angles.
repetitions (list): Three integers specifying the expansion of the cell in x,y,z directions.
oxidation_states (list): Oxidation states per site in the unit cell basis.
Defaults to ``[[2], [4], [-2], [-2], [-2]]`` for the standard ABX3 perovskite.
Returns:
-------
SMACT Lattice object of the unit cell,
ASE crystal system of the unit cell.
"""
if repetitions is None:
repetitions = [1, 1, 1]
if cell_par is None:
cell_par = [6, 6, 6, 90, 90, 90]
system = crystal(
(species),
basis=[(0, 0, 0), (0.5, 0.5, 0.5), (0.5, 0.5, 0)],
spacegroup=221,
size=repetitions,
cellpar=cell_par,
)
if oxidation_states is None:
oxidation_states = [[2]] + [[4]] + [[-2]] * 3
tiled_oxi = _tile_oxidation_states(oxidation_states, len(system))
sites_list = [Site(pos, ox) for pos, ox in zip(system.get_scaled_positions(), tiled_oxi, strict=True)]
return Lattice(sites_list), system
[docs]
def wurtzite(
species: list[str],
cell_par: list[float] | None = None,
repetitions: list[int] | None = None,
oxidation_states: list[list[int]] | None = None,
) -> tuple[Lattice, Atoms]:
"""
Build a wurtzite cell using the crystal function in ASE.
Args:
----
species (list[str]): Element symbols
cell_par (list): Six floats/ints specifying 3 unit cell lengths and 3 unit cell angles.
repetitions (list): Three integers specifying the expansion of the cell in x,y,z directions.
oxidation_states (list): Oxidation states per site in the unit cell basis.
Defaults to ``[[2], [2], [-2], [-2]]`` for the standard AX wurtzite.
Returns:
-------
SMACT Lattice object of the unit cell,
ASE crystal system of the unit cell.
"""
if repetitions is None:
repetitions = [1, 1, 1]
if cell_par is None:
cell_par = [3, 3, 6, 90, 90, 120]
system = crystal(
(species),
basis=[(2.0 / 3.0, 1.0 / 3.0, 0), (2.0 / 3.0, 1.0 / 3.0, 5.0 / 8.0)],
spacegroup=186,
size=repetitions,
cellpar=cell_par,
)
if oxidation_states is None:
oxidation_states = [[2]] * 2 + [[-2]] * 2
tiled_oxi = _tile_oxidation_states(oxidation_states, len(system))
sites_list = [Site(pos, ox) for pos, ox in zip(system.get_scaled_positions(), tiled_oxi, strict=True)]
return Lattice(sites_list), system
