unsymmetrical density of transmission eigenstate around left and right electrode

[anjana]

I have noticed that, the density of transmission eigenstate around left and right electrodes are not symmetrical, even for symmetrical molecules. And, it is always seen that the density in left electrodes is quite high than in the right electrodes, even though the contact molecules attachment is same on the both side. This thing is really confusing me. And I believe this is the reason why I am getting low  value of transmission spectrum. I have been trying to analyze the IV curve for the cages with thiophene. I have attached the relevant figures. Somebody please help me on this

Regards,
Anjana 

[Anders Blom]

There is a fundamental difference between the molecular eigenstate (which is obtained by projecting the device Hamiltonian onto a bulk-like calculation) and the transmission eigenstate. In the latter case, the transport boundary condition is also imposed, which is not least noticeable from the fact that when you compute the transmission eigenstate you have to specify if you want to include contributions from the left or right electrode. Default is left, which would explain the effect you see.

The "low" transmission values can be caused by many things, but looking at your "homo" transmission eigenstate it is probably not very small since there is a coupled wave function extending from the left electrode to the right.

[anjana]

Thank you so much for the reply. But in some cases, even I select the contribution form the left, I see good density around the right side, like in the attached figure. What might be difference in these two cases.

[Anders Blom]

The "amount" of eigenstate to the right is more or less proportional to the transmission coefficient.