As per my knowledge, transmission spectrum for a perfectly periodic structure can be calculated just from the bulk material (unit cell) and does not need device setup. However, in order to see eigenvalues and eigen states device set up is necessary. I am trying to calculate transmission of carbon nanotubes adsorbed with metal chains. However, when I calculate the transmission spectrum using the unit cell bulk material it gives different values and when I set up device by repeating the same structure and converting it to device, it gives different values. Please guide me which one is the correct procedure to calculate transmission spectrum?