# Copyright (c) Max-Planck-Institut für Eisenforschung GmbH - Computational Materials Design (CM) Department
# Distributed under the terms of "New BSD License", see the LICENSE file.
from warnings import warn
import numpy as np
from ase.atoms import Atoms
from structuretoolkit.common.pymatgen import ase_to_pymatgen, pymatgen_to_ase
__author__ = "Ujjal Saikia"
__copyright__ = (
"Copyright 2021, Max-Planck-Institut für Eisenforschung GmbH - "
"Computational Materials Design (CM) Department"
)
__version__ = "1.0"
__maintainer__ = "Liam Huber"
__email__ = "liamhuber@greyhavensolutions.com"
__status__ = "production"
__date__ = "Sept 7, 2023"
[docs]
def get_grainboundary_info(axis: np.ndarray, max_sigma: int):
"""
Provides a list of possible GB structures for a given rotational axis and upto the given maximum sigma value.
Args:
axis : Rotational axis for the GB you want to construct (for example, axis=[1,0,0])
max_sigma (int) : The maximum value of sigma upto which you want to consider for your
GB (for example, sigma=5)
Returns:
A list of possible GB structures in the format:
{sigma value: {'theta': [theta value],
'plane': the GB planes")
'rot_matrix': array([the rotational matrix]),
'csl': [array([the csl matrix])]}}
To construct the grain boundary select a GB plane and sigma value from the list and pass it to the
GBBuilder.gb_build() function along with the rotational axis and initial bulk structure.
"""
from aimsgb import GBInformation
return GBInformation(axis=axis, max_sigma=max_sigma)
[docs]
def grainboundary(
axis: np.ndarray,
sigma: int,
plane: np.ndarray,
initial_struct: Atoms,
*,
uc_a: int = 1,
uc_b: int = 1,
vacuum: float = 0.0,
gap: float = 0.0,
delete_layer: str = "0b0t0b0t",
tol: float = 0.25,
to_primitive: bool = False,
add_if_dist: float | None = None,
):
"""
Generate a grain boundary structure based on aimsgb.
Args:
axis : Rotational axis for the GB you want to construct (for example, axis=[1,0,0])
sigma (int) : The sigma value of the GB you want to construct (for example, sigma=5)
plane: The grain boundary plane of the GB you want to construct (for example, plane=[2,1,0])
initial_struct : Initial bulk structure from which you want to construct the GB (a ase
structure object).
uc_a (int): Number of unit cell of grain A. (Default is 1.)
uc_b (int): Number of unit cell of grain B. (Default is 1.)
vacuum (float): Adds space between the grains at _one_ of the two interfaces
that must exist due to periodic boundary conditions. (Default is 0.0.)
gap (float): Adds space between the grains at _both_ of the two interfaces
that must exist due to periodic boundary conditions. When used together with
`vacuum`, these spaces add at one of the two interfaces. (Default is 0.0.)
delete_layer (str) : To delete layers of the GB. For example, `delete_layer='1b0t1b0t'`. The first
4 characters is for first grain and the other 4 is for second grain. b means
bottom layer and t means top layer. Integer represents the number of layers
to be deleted. The first t and second b from the left hand side represents
the layers at the GB interface. Default value is `delete_layer='0b0t0b0t'`, which
means no deletion of layers.
tol (float): Tolerance factor (in distance units) to determine whether two atoms
are in the same plane. (Default is 0.25.)
to_primitive : To generate primitive or non-primitive GB structure. (Default
value is False.)
add_if_dist (float): (Deprecated) Use `gap`.
Returns:
:class:`ase.Atoms`: final grain boundary structure
"""
from aimsgb import Grain, GrainBoundary
if add_if_dist is not None:
warn("`add_if_dist` is deprecated, please use `gap` instead.", stacklevel=2)
gap = add_if_dist
basis_pymatgen = ase_to_pymatgen(structure=initial_struct)
grain_init = Grain(
basis_pymatgen.lattice, basis_pymatgen.species, basis_pymatgen.frac_coords
)
gb = GrainBoundary(
axis=axis,
sigma=sigma,
plane=plane,
initial_struct=grain_init,
uc_a=uc_a,
uc_b=uc_b,
)
return pymatgen_to_ase(
structure=Grain.stack_grains(
grain_a=gb.grain_a,
grain_b=gb.grain_b,
vacuum=vacuum,
gap=gap,
direction=gb.direction,
delete_layer=delete_layer,
tol=tol,
to_primitive=to_primitive,
)
)