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Update to Grain.stack_grains per aimsgb deprecation warning #67

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Merged
merged 4 commits into from
Sep 11, 2023
Merged

Update to Grain.stack_grains per aimsgb deprecation warning #67

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7f4dfd4
Update to Grain.stack_grains per aimsgb deprecation warning
liamhuber Sep 7, 2023
8bbd43f
Update module metadata
liamhuber Sep 7, 2023
36ec749
Update structuretoolkit/build/aimsgb.py
liamhuber Sep 8, 2023
e13a46f
Force kwargs to be keyword only
liamhuber Sep 11, 2023
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60 changes: 41 additions & 19 deletions structuretoolkit/build/aimsgb.py
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Original file line number Diff line number Diff line change
Expand Up @@ -2,6 +2,8 @@
# 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

from structuretoolkit.common.pymatgen import ase_to_pymatgen, pymatgen_to_ase

__author__ = "Ujjal Saikia"
Expand All @@ -11,9 +13,9 @@
)
__version__ = "1.0"
__maintainer__ = "Liam Huber"
__email__ = "huber@mpie.de"
__email__ = "liamhuber@greyhavensolutions.com"
__status__ = "production"
__date__ = "Feb 26, 2021"
__date__ = "Sept 7, 2023"


def get_grainboundary_info(axis, max_sigma):
Expand Down Expand Up @@ -45,43 +47,58 @@ def grainboundary(
sigma,
plane,
initial_struct,
to_primitive=False,
delete_layer="0b0t0b0t",
add_if_dist=0.0,
*,
uc_a=1,
uc_b=1,
vacuum=0.0,
gap=0.0,
delete_layer="0b0t0b0t",
tol=0.25,
to_primitive=False,
add_if_dist=None,
Comment on lines +53 to +58
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Is it necessary to change the order of the arguments?

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Not necessary, but beneficial.

Previously the arguments were GrainBoundary.__init__ args, then an arbitrary mixture of GrainBoudary.__init__ and GrainBoundary.build_gb kwargs. This rationalizes things so that it's GrainBoundary.__init__ args, GrainBoundary.__init__ kwargs, Grain.stack_grains kwargs, then deprecated kwargs, with user-facing kwargs appearing in the same order as they do in the underlying library.

Since we need to change the signature anyways to handle the new kwarg and the renamed kwarg, I thought we might as well tighten the API up at the same time.

):
"""
Generate a grain boundary structure based on the aimsgb.GrainBoundary module.
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).
delete_layer : To delete layers of the GB. For example, delete_layer='1b0t1b0t'. The first
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
the layers at the GB interface. Default value is `delete_layer='0b0t0b0t'`, which
means no deletion of layers.
add_if_dist : If you want to add extra interface distance, you can specify add_if_dist.
Default value is add_if_dist=0.0
to_primitive : To generate primitive or non-primitive GB structure. Default value is
to_primitive=False
uc_a (int): Number of unit cell of grain A. Default to 1.
uc_b (int): Number of unit cell of grain B. Default to 1.
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:`.Atoms`: final grain boundary structure
:class:`ase.Atoms`: final grain boundary structure
"""
from aimsgb import GrainBoundary, Grain

if add_if_dist is not None:
warn("`add_if_dist` is deprecated, please use `gap` instead.")
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_obj = GrainBoundary(
gb = GrainBoundary(
axis=axis,
sigma=sigma,
plane=plane,
Expand All @@ -91,9 +108,14 @@ def grainboundary(
)

return pymatgen_to_ase(
structure=gb_obj.build_gb(
to_primitive=to_primitive,
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,
add_if_dist=add_if_dist,
tol=tol,
to_primitive=to_primitive,
)
)