Temperature

Module to describe the effect of temperature on the atomic positions.

class abtem.temperature.AbstractFrozenPhonons

Abstract base class for frozen phonons objects.

copy()

Make a copy.

abstract generate_atoms()

Generate frozen phonon configurations.

class abtem.temperature.DummyFrozenPhonons(atoms)

Dummy frozen phonons object.

Generates the input Atoms object. Used as a stand-in for simulations without frozen phonons.

Parameters

atoms (ASE Atoms object) – Generated Atoms object.

copy()

Make a copy.

generate_atoms()

Generate frozen phonon configurations.

class abtem.temperature.FrozenPhonons(atoms, num_configs, sigmas, directions='xyz', seed=None)

Frozen phonons object.

Generates atomic configurations for thermal diffuse scattering. Randomly displaces the atomic positions of an ASE Atoms object to emulate thermal vibrations.

Parameters

• atoms (ASE Atoms object) – Atoms with the average atomic configuration.

• num_configs (int) – Number of frozen phonon configurations.

• sigmas (float or dict or list) – If float, the standard deviation of the displacements is assumed to be identical for all atoms. If dict, a displacement standard deviation should be provided for each species. The atomic species can be specified as atomic number or symbol. If list or array, a displacement standard deviation should be provided for each atom.

• directions (str) – The displacement directions of the atoms as a string; for example ‘xy’ for displacement in the x- and y-direction.

• seed (int) – Seed for random number generator.

copy()

Make a copy.

generate_atoms()

Generate frozen phonon configurations.

class abtem.temperature.MDFrozenPhonons(trajectory)

Molecular dynamics frozen phonons object.

Parameters

trajectory (List of ASE Atoms objects) – Sequence of Atoms objects representing a thermal distribution of atomic configurations.

copy()

Make a copy.

generate_atoms()

Generate frozen phonon configurations.