Xiangru Kong wrote: > Maybe I figured out the order of basis in model.hamiltonian_submatrix, > It follows the order of model.sites with the corresponding orbitals
Yes, the degrees of freedom of a Hamiltonian as used by hamiltonian_submatrix (but also elsewhere in Kwant) are grouped by site. The sites appear in the same order as in the ‘sites’ attribute of a finalized builder. For example, if there are two sites and site 0 has 3 orbitals and site 1 has 2, the 5 degrees of freedom are indexed as follows: Index 0: Orbital 0 of site 0 Index 1: Orbital 1 of site 0 Index 2: Orbital 2 of site 0 Index 3: Orbital 0 of site 1 Index 4: Orbital 1 of site 1
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