HI Ville,
I'm trying to use Kwant to investigate behavior of a lattice between two superconductors, namely trying to figure out the Josephson current. The task is basically to diagonalize the related Bogoliubov-de Gennes Hamiltonian and use the eigenvectors and eigenvalues to calculate the current in the lattice. I basically follow the example 2.6. in Kwant documentation to build up the Hamiltonian but let the both leads be superconductors and establish the system in between. I introduce the phase difference between the leads by multiplying the Delta parameter of the other lead by e^(i phi). However, I'm a bit stuck there as I don't know how to utilize the obtained eigenvectors to make wave functions which I could input to t current operator in Kwant.