BasePotential

class abtem.potentials.iam.BasePotential

Bases: BaseField

Base class of all potentials. Documented in the subclasses.

__init__()

Methods

__init__()
build([first_slice, last_slice, chunks, lazy])
copy()	Make a copy.
depth_profile([projection_axis, depth])	Create a depth profile by projecting the potential along a spatial axis.
ensemble_blocks([chunks])	Split the ensemble into an array of smaller ensembles.
generate_blocks([chunks])	Generate chunks of the ensemble.
generate_slices([first_slice, last_slice])
match_grid(other[, check_match])	Match the grid to another object with a Grid.
project()	Sum of the potential slices as an image.
show([project])	Show the potential projection.
show_depth_profile([projection_axis, depth, ...])	Show a depth cross-section of the potential.
to_images()	Converts the potential to an ensemble of images.

Attributes

axes_metadata	List of AxisMetadata.
base_axes_metadata	List of AxisMetadata for the base axes.
base_shape	Shape of the base axes of the potential.
ensemble_axes_metadata	List of AxisMetadata of the ensemble axes.
ensemble_shape	Shape of the ensemble axes.
exit_planes	The "exit planes" of the potential.
exit_thicknesses	The "exit thicknesses" of the potential.
extent	Extent of grid for each dimension in Ångstrom.
gpts	Number of grid points for each dimension.
grid	Simulation grid.
num_configurations	Number of frozen phonons in the ensemble of potentials.
num_exit_planes	Number of exit planes.
num_slices	Number of projected potential slices.
reciprocal_space_sampling	Reciprocal-space sampling in reciprocal Ångstrom.
sampling	Grid sampling for each dimension in Ångstrom per grid point.
shape	Shape of the ensemble.
slice_limits	The entrance and exit thicknesses of each slice [Å].
slice_thickness	Slice thicknesses for each slice.
thickness	Thickness of the potential [Å].

property axes_metadata: AxesMetadataList

List of AxisMetadata.

property base_axes_metadata

List of AxisMetadata for the base axes.

property base_shape

Shape of the base axes of the potential.

copy()

Make a copy.

Return type:

Self

depth_profile(projection_axis='y', depth=None)

Create a depth profile by projecting the potential along a spatial axis.

Parameters:

• projection_axis (str) – Spatial axis to project (sum) along. "y" (default) produces an x–z cross-section; "x" produces a y–z cross-section.

• depth (float, optional) – If given, project only over a finite slab of this thickness [Å], centered on the midpoint of the projected axis. The number of grid points is rounded to the nearest integer. If None, the full extent is projected.

Returns:

depth_profile – 2D image(s) with the remaining spatial axis horizontal and depth (z) vertical. Any ensemble axes (e.g. frozen phonons) are preserved.

Return type:

Images

property ensemble_axes_metadata: list[AxisMetadata]

List of AxisMetadata of the ensemble axes.

ensemble_blocks(chunks=None)

Split the ensemble into an array of smaller ensembles.

Parameters:

chunks (iterable of tuples) – Block sizes along each dimension.

Return type:

Array

property ensemble_shape: tuple[int, ...]

Shape of the ensemble axes.

abstract property exit_planes: tuple[int, ...]

The “exit planes” of the potential. The indices of slices where a measurement is returned.

property exit_thicknesses: tuple[float, ...]

The “exit thicknesses” of the potential. The thicknesses in the potential where a measurement is returned.

property extent: tuple[float, float] | None

Extent of grid for each dimension in Ångstrom.

generate_blocks(chunks=1)

Generate chunks of the ensemble.

Parameters:

chunks (iterable of tuples) – Block sizes along each dimension.

Return type:

Generator[tuple[tuple[int, ...], tuple[slice, ...], ndarray], None, None]

property gpts: tuple[int, int] | None

Number of grid points for each dimension.

property grid: Grid

Simulation grid.

match_grid(other, check_match=False)

Match the grid to another object with a Grid.

abstract property num_configurations

Number of frozen phonons in the ensemble of potentials.

property num_exit_planes: int

Number of exit planes.

property num_slices: int

Number of projected potential slices.

project()

Sum of the potential slices as an image.

Returns:

projected – The projected potential.

Return type:

Images

property reciprocal_space_sampling: tuple[float, float]

Reciprocal-space sampling in reciprocal Ångstrom.

property sampling: tuple[float, float] | None

Grid sampling for each dimension in Ångstrom per grid point.

property shape: tuple[int, ...]

Shape of the ensemble.

show(project=True, **kwargs)

Show the potential projection. This requires building all potential slices.

Parameters:

• project (bool, optional) – Show the projected potential (True, default) or show all potential slices. It is recommended to index a subset of the potential slices when this keyword set to False.

• kwargs – Additional keyword arguments for the show method of Images.

show_depth_profile(projection_axis='y', depth=None, z_scale=1.0, slice_lines=True, ax=None, cbar=False, cmap=None, vmin=None, vmax=None, power=1.0, common_color_scale=False, explode=(), figsize=None, title=True, **kwargs)

Show a depth cross-section of the potential.

Parameters:

• projection_axis (str) – Spatial axis to project (sum) along. "y" (default) produces an x–z cross-section; "x" produces a y–z cross-section.

• depth (float, optional) – If given, project only over a finite slab of this thickness [Å], centered on the midpoint of the projected axis. The number of grid points is rounded to the nearest integer. If None, the full extent is projected.

• z_scale (float) – Scaling factor for the z-axis relative to the spatial axis. Values less than 1 compress the z-axis, making panels of thick specimens more compact. Default is 1.0 (equal scaling).

• slice_lines (bool) – If True (default), draw horizontal lines at slice boundaries.

• ax (matplotlib.axes.Axes, optional) – If given the plot is added to the axis.

• cbar (bool, optional) – Add a colorbar to the plot. Default is False.

• cmap (str, optional) – Matplotlib colormap name.

• vmin (float, optional) – Minimum of the color scale.

• vmax (float, optional) – Maximum of the color scale.

• power (float) – Show image on a power scale.

• common_color_scale (bool, optional) – If True, all images in a grid share the same color scale.

• explode (bool or sequence of int, optional) – If True, create a grid of images for ensemble items.

• figsize (two int, optional) – Figure size as (width, height) in inches.

• title (bool or str, optional) – Column title for the images.

• **kwargs – Additional keyword arguments passed to the show method.

Returns:

visualization

Return type:

Visualization

property slice_limits: list[tuple[float, float]]

The entrance and exit thicknesses of each slice [Å].

abstract property slice_thickness: tuple[float, ...]

Slice thicknesses for each slice.

property thickness: float

Thickness of the potential [Å].

to_images()

Converts the potential to an ensemble of images.

Returns:

image_ensemble – The potential slices as images.

Return type:

Images