atoms

Module for modifying ASE Atoms objects for use in abTEM.

Functions

atoms_in_cell(atoms[, margin])	Crop atoms outside the cell.
best_orthogonal_cell(cell[, ...])	Find the closest orthogonal cell for a given cell given a maximum number of repetitions in all directions.
cut_cell(atoms[, cell, plane, origin, margin])	Fit the given atoms into a given cell by cropping atoms that are outside the cell, ignoring periodicity.
decompose_affine_transform(affine_transform)	Decompose an affine transform into rotation, scale and shear.
euler_sequence(axes, convention)	type axes: str
euler_to_rotation(ai, aj, ak[, axes, convention])	Convert sequence of Euler angles to Cartesian rotation matrix.
flip_atoms(atoms[, axis])	Inverts the positions of atoms along a given axis.
is_cell_hexagonal(atoms)	Check whether the cell of given atoms is hexagonal.
is_cell_orthogonal(cell[, tol])	Check whether atoms have an orthogonal cell.
is_cell_valid(atoms[, tol])	Check whether the cell of given atoms can be converted to a structure usable by abTEM.
merge_close_atoms(atoms[, tol])	Merge atoms that are closer in distance to each other than the given tolerance.
orthogonalize_cell(atoms[, max_repetitions, ...])	Make the cell of the given atoms orthogonal.
pad_atoms(atoms, margins[, directions])	Repeat the atoms in the x and y directions, retaining only the repeated atoms within the margin distance from the cell boundary.
plane_to_axes(plane)	Convert string representation of Cartesian axes to numerical.
pretty_print_transform(decomposed)	Print a decomposed transformation in an easy-to-read manner.
rotate_atoms(atoms[, axes, angles, convention])	Rotate the positions and cell vectors of atoms using Euler angles.
rotate_atoms_to_plane(atoms[, plane])	Rotate atoms so that their xy plane is rotated into a given plane.
rotation_matrix_from_plane([plane])	Give the rotation matrix corresponding to a rotation from a given plane to the xy plane.
rotation_matrix_to_euler(R[, axes, ...])	Convert a Cartesian rotation matrix to Euler angles.
shrink_cell(atoms[, repetitions, tol])	Find and return the smallest non-repeating cell for the given atoms.
standardize_cell(atoms[, tol])	Standardize the cell of given atoms.
wrap_with_tolerance(atoms[, tol])	Wrap atoms that are closer to cell boundaries than the given tolerance.