Dear Sudin, The sites in the finalized system are stored in an arbitrary order. You can check which site is which by looking at the sys.sites list. You can trivially sort the sites by using the following code (here sys is a finalized system): sort_order = sorted(range(len(sys.sites)), key=(lambda x: sys.sites[x])) # Calculate which permutation will order the sites. h = sys.hamiltonian_submatrix(args) # Calculate the system Hamiltonian sorted_h = h[sort_order][:, sort_order] # Reorder the Hamiltonian Best, Anton On Fri, Apr 17, 2015 at 10:12 PM, Sudin Ganguly <sudin@iitg.ernet.in> wrote:

Dear Sir,

Thank you for the reply.

The main motivation of my question was ----

How the Hamiltonian of the scattering region is going into the 'sys'?

If I want to check the Hamiltonian with the help of Hamiltonian_submatrix(), from the output matrix I am unable to understand how the onsite and hopping terms are positioned in that matrix.

I read the post about 'Site position in hamiltonian matrix', but still I'm not getting this.

With regards, Sudin