PlaneWave

PlaneWave#

class abtem.waves.PlaneWave(extent=None, gpts=None, sampling=None, energy=None, normalize=False, tilt=(0.0, 0.0), device=None)[source]#

Bases: WavesBuilder

Represents electron probe wave functions for simulating experiments with a plane- wave probe, such as HRTEM and SAED.

Parameters:

extent (two float, optional) – Lateral extent of the wave function [Å].
gpts (two int, optional) – Number of grid points describing the wave function.
sampling (two float, optional) – Lateral sampling of the wave functions [Å]. If ‘gpts’ is also given, will be ignored.
energy (float, optional) – Electron energy [eV]. If not provided, inferred from the wave functions.
normalize (bool, optional) – If true, normalizes the wave function such that its reciprocal space intensity sums to one. If false, the wave function takes a value of one everywhere.
tilt (two float, optional) – Small-angle beam tilt [mrad] (default is (0., 0.)). Implemented by shifting the wave functions at every slice.
device (str, optional) – The wave functions are stored on this device (‘cpu’ or ‘gpu’). The default is determined by the user configuration.

__init__(extent=None, gpts=None, sampling=None, energy=None, normalize=False, tilt=(0.0, 0.0), device=None)[source]#

Methods

`__init__`([extent, gpts, sampling, energy, ...])
`apply_transform`(transform[, max_batch, lazy])
`build`([lazy, max_batch])	Build plane-wave wave functions.
`check_can_build`()	Check whether the wave functions can be built.
`copy`()	Make a copy.
`ensemble_blocks`([chunks])	Split the ensemble into an array of smaller ensembles.
`generate_blocks`([chunks])	Generate chunks of the ensemble.
`match_grid`(other[, check_match])	Match the grid to another object with a Grid.
`multislice`(potential[, detectors, ...])	Run the multislice algorithm, after building the plane-wave wave function as needed.

Attributes

`accelerator`	Accelerator object describing the acceleration energy.
`angular_sampling`	Reciprocal-space sampling in units of scattering angles [mrad].
`antialias_cutoff_gpts`	The number of grid points along the x and y direction in the simulation grid at the antialiasing cutoff scattering angle.
`antialias_valid_gpts`	The number of grid points along the x and y direction in the simulation grid for the largest rectangle that fits within antialiasing cutoff scattering angle.
`axes_metadata`	List of AxisMetadata.
`base_axes_metadata`	List of AxisMetadata for the base axes in real space.
`base_shape`	Shape of the base axes of the waves.
`cutoff_angles`	Scattering angles at the antialias cutoff [mrad].
`cutoff_frequencies`	Spatial frequencies at the antialias cutoff [1/Å].
`device`	The device where the waves are created.
`dtype`	The datatype of waves.
`energy`	Electron acceleration energy in electron volts.
`ensemble_axes_metadata`	List of AxisMetadata of the ensemble axes.
`ensemble_shape`	Shape of the ensemble axes of the waves.
`extent`	Extent of grid for each dimension in Ångstrom.
`full_cutoff_angles`	Scattering angles corresponding to the full wave function size [mrad].
`gpts`	Number of grid points for each dimension.
`grid`	Simulation grid.
`metadata`	Metadata stored as a dictionary.
`normalize`	True if the created waves are normalized in reciprocal space.
`reciprocal_space_axes_metadata`	List of AxisMetadata for base axes in reciprocal space.
`reciprocal_space_sampling`	Reciprocal-space sampling in reciprocal Ångstrom.
`rectangle_cutoff_angles`	Scattering angles corresponding to the sides of the largest rectangle within the antialias cutoff [mrad].
`sampling`	Grid sampling for each dimension in Ångstrom per grid point.
`shape`	Shape of the waves.
`tilt`	The small-angle tilt of applied to the Fresnel propagator [mrad].
`wavelength`	Relativistic wavelength in Ångstrom.

property accelerator: Accelerator#: Accelerator object describing the acceleration energy.

property angular_sampling: tuple[float, float]#: Reciprocal-space sampling in units of scattering angles [mrad].

property antialias_cutoff_gpts: tuple[int, int]#: The number of grid points along the x and y direction in the simulation grid at the antialiasing cutoff scattering angle.

property antialias_valid_gpts: tuple[int, int]#: The number of grid points along the x and y direction in the simulation grid for the largest rectangle that fits within antialiasing cutoff scattering angle.

property axes_metadata: AxesMetadataList#: List of AxisMetadata.

property base_axes_metadata: list[AxisMetadata]#: List of AxisMetadata for the base axes in real space.

property base_shape: tuple[int, int]#: Shape of the base axes of the waves.

build(lazy=None, max_batch='auto')[source]#

Build plane-wave wave functions.

Parameters:

lazy (bool, optional) – If True, create the wave functions lazily, otherwise, calculate instantly. If not given, defaults to the setting in the user configuration file.
max_batch (int or str, optional) – The number of wave functions in each chunk of the Dask array. If ‘auto’ (default), the batch size is automatically chosen based on the abtem user configuration settings “dask.chunk-size” and “dask.chunk-size-gpu”.

Returns:

plane_waves – The wave functions.

Return type:

Waves

check_can_build()#: Check whether the wave functions can be built.

copy()#

Make a copy.

Return type:: Self

property cutoff_angles: tuple[float, float]#: Scattering angles at the antialias cutoff [mrad].

property cutoff_frequencies: tuple[float, float]#: Spatial frequencies at the antialias cutoff [1/Å].

property device: str#: The device where the waves are created.

property dtype: dtype#: The datatype of waves.

property energy: float | None#: Electron acceleration energy in electron volts.

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#: Shape of the ensemble axes of the waves.

property extent: tuple[float, float] | None#: Extent of grid for each dimension in Ångstrom.

property full_cutoff_angles: tuple[float, float]#: Scattering angles corresponding to the full wave function size [mrad].

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.

property metadata#: Metadata stored as a dictionary.

multislice(potential, detectors=None, max_batch='auto', lazy=None)[source]#

Run the multislice algorithm, after building the plane-wave wave function as needed. The grid of the wave functions will be set to the grid of the potential.

Parameters:

potential (BasePotential, Atoms) – The potential through which to propagate the wave function. Optionally atoms can be directly given.
detectors (Detector, list of detectors, optional) – A detector or a list of detectors defining how the wave functions should be converted to measurements after running the multislice algorithm.
max_batch (int, optional) – The number of wave functions in each chunk of the Dask array. If ‘auto’ (default), the batch size is automatically chosen based on the abtem user configuration settings “dask.chunk-size” and “dask.chunk-size-gpu”.
lazy (bool, optional) – If True, create the wave functions lazily, otherwise, calculate instantly. If None, this defaults to the setting in the user configuration file.

Return type:

Union[BaseMeasurements, Waves, list[Union[BaseMeasurements, Waves]]]

Returns:

measurements (BaseMeasurements or ComputableList of BaseMeasurement) – The detected measurement (if detector(s) given).
exit_waves (Waves) – Wave functions at the exit plane(s) of the potential (if no detector(s) given).

property normalize#: True if the created waves are normalized in reciprocal space.

property reciprocal_space_axes_metadata: list[AxisMetadata]#: List of AxisMetadata for base axes in reciprocal space.

property reciprocal_space_sampling: tuple[float, float]#: Reciprocal-space sampling in reciprocal Ångstrom.

property rectangle_cutoff_angles: tuple[float, float]#: Scattering angles corresponding to the sides of the largest rectangle within the antialias cutoff [mrad].

property sampling: tuple[float, float] | None#: Grid sampling for each dimension in Ångstrom per grid point.

property shape: tuple[int, ...]#: Shape of the waves.

property tilt#: The small-angle tilt of applied to the Fresnel propagator [mrad].

property wavelength: float#: Relativistic wavelength in Ångstrom.

PlaneWave

Contents

PlaneWave#