Speed up functions for retrieving old/new positions from hybrid positions

[zhang-ivy]

I've noticed that the HybridTopologyFactory functions for retrieving old/new positions from the hybrid positions are very slow.

I've found that these are much faster:

def new_positions(htf, hybrid_positions):
    n_atoms_new = htf._topology_proposal.n_atoms_new
    hybrid_indices = [htf._new_to_hybrid_map[idx] for idx in range(n_atoms_new)]
    return hybrid_positions[hybrid_indices, :]

def old_positions(htf, hybrid_positions):
    n_atoms_old = htf._topology_proposal.n_atoms_old
    hybrid_indices = [htf._old_to_hybrid_map[idx] for idx in range(n_atoms_old)]
    return hybrid_positions[hybrid_indices, :]

We should 1) double check that the functions I wrote do the same thing as the original functions and 2) integrate my functions with the existing ones.