empty_spheres

Full name: ase2sprkkr.bindings.es_finder.empty_spheres

ase2sprkkr.bindings.es_finder.empty_spheres(atoms, *, overlap_matrix=0.18, radii_ratios_map=None, max_es_overlap=0.24, adjust_overlap=0.28, min_es_radius=0.2, max_es_radius=1.0, symmetrize_threshold=0.7, max_iterations=100, grid=array([[48, 0, 0], [0, 48, 0], [0, 0, 48]]), verbosity=0)[source]

Compute the best coverage of the primitive cell with spheres.

The function computes:

  • the best radii of atomic-sites spheres

  • the positions of ‘vacuum pseudoatom’ spheres and their radii to be added to the structure

Parameters

  • atoms (Atoms) – The structure, that will be filled in with empty spheres

  • extend – If True, the atoms will be extended by the empty spheres sites

  • overlap_matrix (float | numpy.ndarray) – #TODO

  • radii_ratios_map (Optional[Dict[str, float]]) – Dict, that defines the ratios of radii of used chemical elements. It is dimensionless value (it is not the sizes, only the ratios of the given values, that matter). The default walues are Winger-Seitz radii. If only some of the elements are provided, they are supplemented with the default values.

  • max_es_overlap (float) – Max allowed overlap of empty spheres.

  • adjust_overlap (float) – #TODO

  • max_es_radius (float) – Maximum radius of empty shperes

  • min_es_radius (float) – Minimum radius of empty shperes

  • symetrize_threshold – #TODO Threshold for overlap when symmetrization is used

  • max_iterations (int) – Number of iterations for sphere finding algorithm

  • grid (ndarray) – #TODO

  • verbosity (int) – Verbosity of the output of the algorithm

  • symmetrize_threshold (float) –