transmission spectrum

[Anurag Chaudhury]

What difference does it make while calculating the bulk transmission spectrum and the device transmission spectrum with the electrodes made up of the same material as the scattering region?

[Petr Khomyakov]

In principle, it should not make any difference as soon as the both calculations of the transmission are numerically converged with respect to computational settings.

[Anurag Chaudhury]

Here are the transmission spectra of bulk and the device from bulk.
The bulk one is clearly different from the latter. Also tr. spectrum of bulk shows integral values of transmission while the other one shows all real values. Why so?

[Petr Khomyakov]

As I said the computational settings for the two calculations are to be effectively similar to get the same result. From the images, it seems that you have adopted too coarse k-grid for the 2D Brillouin zone integration of the Transmission Spectrum in the bulk calculation. You may see that the device-derived spectrum is much smoother compared to that from the bulk calculation. If you posted your python scripts related to these calculations it might make it easier to figure out the cause for this discrepancy.   

[Petr Khomyakov]

Your electrodes in the device are not made of the same material as the scattering region as you do have a sulfur atom (a scatterer) in the middle of the device, whereas there is not sulfur in the electrodes.

In addition, you should always check if the (k_A, k_B)-grid is the same in the two calculations. You have adopted the default values, but the defaults might be different for these two kinds of calculations, in principle. To see the defaults, you would need to save the script details with "Show defaults" instead of "Minimal".   

[Petr Khomyakov]

Thank you for enclosing the scripts, but as I said the two transmission spectrum calculations are done for two different systems. One system is a periodically repeated defect, whereas the second one is a single defect. There is no reason why the two spectra should be identical.

I would suggest reading a book on the electron transport theory to understand the physics behind the electron transport calculations, e.g., see Supriyo Datta, Electronic Transport in Mesoscopic Systems, http://www.cambridge.org/catalogue/catalogue.asp?isbn=0521599431.