corresponds to the flat of the matroid that consists of those elements of the matroid that are atoms

Like a geometric lattice, a matroid is endowed with a rank function, but that function maps a set of matroid elements to a number rather than taking a lattice element as its argument. The rank function of a matroid must be monotonic (adding an element to a set can never decrease its rank) and it must be submodular, meaning that it obeys an inequality similar