AtomsEnsemble

class abtem.inelastic.phonons.AtomsEnsemble(trajectory, ensemble_mean=True, ensemble_axes_metadata=None, cell=None)

Bases: BaseFrozenPhonons

Frozen phonons based on a molecular dynamics simulation.

Parameters:

• trajectory (list of ASE.Atoms, dask.core.Array, list of dask.Delayed) – Sequence of atoms representing a distribution of atomic configurations.

• ensemble_mean (True, optional) – If True, the mean of the ensemble of results from a multislice simulation is calculated, otherwise, the result of every frozen phonon is returned.

• ensemble_axes_metadata (list of AxesMetadata, optional) – Axis metadata for each ensemble axis. The axis metadata must be compatible with the shape of the array.

• cell (Cell, optional)

__init__(trajectory, ensemble_mean=True, ensemble_axes_metadata=None, cell=None)

Methods

__init__(trajectory[, ensemble_mean, ...])
copy()	Make a copy.
ensemble_blocks([chunks])	Split the ensemble into an array of smaller ensembles.
generate_blocks([chunks])	Generate chunks of the ensemble.
randomize(atoms)	Randomize the atoms.
select_block(index, chunks)	Select a block from the ensemble.
standard_deviations()	Standard deviation of the positions of each atom in each direction.

Attributes

atomic_numbers	The unique atomic number of the atoms.
atoms	Base atomic configuration used for displacements.
axes_metadata	List of AxisMetadata.
base_axes_metadata	List of AxisMetadata of the base axes.
base_shape	Shape of the base axes.
cell	The cell of the atoms.
ensemble_axes_metadata	List of AxisMetadata of the ensemble axes.
ensemble_mean	The mean of the ensemble of results from a multislice simulation is calculated.
ensemble_shape	Shape of the ensemble axes.
num_configs	Number of atomic configurations.
shape	Shape of the ensemble.
trajectory	Array of atoms representing an ensemble of atomic configurations.

property atomic_numbers: ndarray

The unique atomic number of the atoms.

property atoms: Atoms

Base atomic configuration used for displacements.

property axes_metadata: AxesMetadataList

List of AxisMetadata.

property base_axes_metadata: list[AxisMetadata]

List of AxisMetadata of the base axes.

property base_shape: tuple[int, ...]

Shape of the base axes.

property cell: Cell

The cell of the atoms.

copy()

Make a copy.

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_mean

The mean of the ensemble of results from a multislice simulation is calculated.

property ensemble_shape: tuple[int, ...]

Shape of the ensemble axes.

generate_blocks(chunks=1)

Generate chunks of the ensemble.

Parameters:

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

property num_configs: int

Number of atomic configurations.

randomize(atoms)

Randomize the atoms.

Parameters:

atoms (Atoms)

Return type:

Atoms

select_block(index, chunks)

Select a block from the ensemble.

Parameters:

• index (tuple of ints) – Index of selected block.

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

property shape

Shape of the ensemble.

standard_deviations()

Standard deviation of the positions of each atom in each direction.

Return type:

ndarray

property trajectory: np.ndarray | da.core.Array

Array of atoms representing an ensemble of atomic configurations.