gsv instrumented

gsv_instrumented.py

def _get_equivalent_smallest_vectors_simple(frac_vector,
                                            reduced_bases,
                                            symprec):

    def get_lattice_points():
        return np.array([
            [i, j, k] for i in (-1, 0, 1)
                      for j in (-1, 0, 1)
                      for k in (-1, 0, 1)
        ])
    lattice_points = get_lattice_points()

    def do_addition():
        return frac_vector + lattice_points
    candidates = do_addition()

    def do_squares():
        return np.dot(candidates, reduced_bases)**2
    squares = do_squares()

    def do_sums():
        return np.sum(squares, axis=1)
    norm_sqs = do_sums()

    def do_roots():
        return np.sqrt(norm_sqs)
    lengths = do_roots()

    def filtered():
        return candidates[lengths - lengths.min() < symprec]
    return filtered()

def _get_smallest_vectors(supercell, primitive, symprec):

    p2s_map, size_super, size_prim, shortest_vectors, multiplicity = [None]*5
    reduced_bases, reduced_bases_inv, primitive_lattice, primitive_lattice_inv = [None]*4
    supercell_fracs = None
    supercell_to_primitive_frac = None
    def prep():
        ...
        # omitted: initialization for all of the above
        ...
    prep()

    for s_index, s_pos in enumerate(supercell_fracs): # run in supercell
        for j, p_index in enumerate(p2s_map): # run in primitive
            p_pos = supercell_fracs[p_index]

            vectors = _get_equivalent_smallest_vectors_simple(s_pos - p_pos,
                                                              reduced_bases,
                                                              symprec)

            def fill_it():
                nonlocal vectors
                vectors = [np.dot(v, supercell_to_primitive_frac) for v in vectors]
    
                multiplicity[s_index][j] = len(vectors)
                for k, elem in enumerate(vectors):
                    shortest_vectors[s_index][j][k] = elem
            fill_it()

    return shortest_vectors, multiplicity