def create_pattern():
"Read the atom positions and transform them to the flat coordinates"
active, inactive = universe.get_active_inactive()
tmp_cell = UnitCell()
tmp_cell.add_cell_vector(universe.cell[:,active[0]])
tmp_cell.add_cell_vector(universe.cell[:,active[1]])
r = tmp_cell.calc_align_rotation_matrix()
return [
(atom.number, numpy.dot(r, atom.get_absolute_frame().t))
for atom in yield_atoms([universe])
]
