Hey Anton, Thank you for the reply.
It is indeed a honeycomb lattice I am working with, and I attempting to connecting the two sublattices the honeycomb lattices to create a superconducting lead. Since the site.pos of honeycomb(electron)-sublattice-a is the same as the site.pos of honeycomb(hole)-sublattice-c, should this method not also work for this lattice? Maybe I will just rewrite it in the orbital method. Regards, Henry