Structures

Module for modifying ASE atoms objects for use in abTEM.

abtem.structures.cut_rectangle(atoms, origin, extent, margin=0.0)[source]

Cuts out a cell starting at the origin to a given extent from a sufficiently repeated copy of atoms.

Parameters
  • atoms (ASE atoms object) – This should correspond to a repeatable unit cell.

  • origin (two float) – Origin of the new cell. Units of Angstrom.

  • extent (two float) – xy-extent of the new cell. Units of Angstrom.

  • margin (float) – Atoms within margin from the border of the new cell will be included. Units of Angstrom. Default is 0.

Returns

Return type

ASE atoms object

abtem.structures.is_cell_hexagonal(atoms)[source]

Function to check whether the cell of an ASE atoms object is hexagonal.

Parameters

atoms (ASE atoms object) – The atoms that should be checked.

abtem.structures.is_cell_orthogonal(atoms, tol=1e-12)[source]

Check whether an Atoms object has an orthogonal cell.

Parameters
  • atoms (ASE atoms object) – The atoms that should be checked.

  • tol (float) – Components of the lattice vectors below this value are considered to be zero.

abtem.structures.is_cell_valid(atoms, tol=1e-12)[source]

Check whether the cell of an ASE atoms object can be converted to a structure that is usable by abTEM.

Parameters
  • atoms (ASE atoms object) – The atoms that should be checked.

  • tol (float) – Components of the lattice vectors below this value are considered to be zero.

Returns

If true, the atomic structure is usable by abTEM.

Return type

bool

abtem.structures.orthogonalize_cell(atoms, limit_denominator=10, return_strain=False)[source]

Make the cell of an ASE atoms object orthogonal. This is accomplished by repeating the cell until the x-component of the lattice vectors in the xy-plane closely matches. If the ratio between the x-components is irrational this may not be possible without introducing some strain. However, the amount of strain can be made arbitrarily small by using many repetitions.

Parameters
  • atoms (ASE atoms object) – The non-orthogonal atoms object.

  • limit_denominator (int) – The maximum denominator in the rational approximation. Increase this to allow more repetitions and hence less strain.

  • return_strain (bool) – If true, return the strain tensor that were applied to make the atoms orthogonal.

Returns

  • atoms (ASE atoms object) – The orthogonal atoms.

  • strain_tensor (2x2 array) – The applied strain tensor. Only provided if return_strain is true.

abtem.structures.pad_atoms(atoms, margin, directions='xy', in_place=False)[source]

Repeat the atoms in x and y, retaining only the repeated atoms within the margin distance from the cell boundary.

Parameters
  • atoms (ASE Atoms object) – The atoms that should be padded.

  • margin (float) – The padding margin.

Returns

Padded atoms.

Return type

ASE Atoms object

abtem.structures.standardize_cell(atoms, tol=1e-12)[source]

Standardize the cell of an ASE atoms object. The atoms are rotated so one of the lattice vectors in the xy-plane aligns with the x-axis, then all of the lattice vectors are made positive.

Parameters
  • atoms (ASE atoms object) – The atoms that should be standardized

  • tol (float) – Components of the lattice vectors below this value are considered to be zero.

Returns

atoms – The standardized atoms.

Return type

ASE atoms object