structuretoolkit.common.helper

Functions

apply_strain(structure, epsilon[, ...])	Apply a given strain on the structure.
center_coordinates_in_unit_cell(structure[, ...])	Wrap atomic coordinates within the supercell.
get_average_of_unique_labels(labels, values)	This function returns the average values of those elements, which share the same labels
get_cell(cell)	Get cell of an ase structure, or convert a float or a (3,)-array into a orthogonal cell.
get_extended_positions(structure, width[, ...])	Get all atoms in the boundary around the supercell which have a distance to the supercell boundary of less than dist
get_number_species_atoms(structure)	Returns a dictionary with the species in the structure and the corresponding count in the structure
get_species_indices_dict(structure)	Get a dictionary mapping element symbols to their corresponding indices in the structure.
get_structure_indices(structure)	Get the indices of the elements in the structure.
get_vertical_length(structure[, norm_order])	Return the length of the cell in each direction projected on the vector vertical to the plane.
get_wrapped_coordinates(structure, positions)	Return coordinates in wrapped in the periodic cell
select_index(structure, element)	Select the indices of atoms in the structure that have a specific element.
set_indices(structure, indices)	Set the indices of atoms in the structure to the specified values.