It seems that your structure is now correctly shaped as you expect. As was
stated by Cristoph, the physics of the system with or without reshaping the
system with sym.add_site_family(..) is the same.
you said *Still, there are one supercell's extra sites added in blue
connecting the original central region and the lead*
I guess you mean an extra cell in the lead. This extracell would cause
additional modes in the energy band which are not necessary and would
affect more or less your transport calculation.
Maybe if you write neg_direc[*1/2**direcI]) instead of neg_direc[direcI])
you will get the correct periodicity in the lead.
I Hope this helps.
Le ven. 8 oct. 2021 à 15:22, Jerry xhm
Thank you Adel and Christoph! sym.add_site_family(lat, other_vectors=[v]) with v orthogonal to the translation symmetry vector places the lead in the way I expected. Still, there are one supercell's extra sites added in blue connecting the original central region and the lead ( https://www.dropbox.com/s/3c1uioclcbsez4g/lattice2.pdf?dl=0). If I put disorder in the central region, I presume these added sites although in blue color will be the same as the lead Hamiltonian and thus do not have disorder? If so, I guess it might only very slightly affect the physics once the central region is not too small. And these extra sites are currently unavoidable?