[DFTB-Plus-User] DFTB+NEGF device geometry definition for non-contiguous atoms

[anz118466 at cse.iitd.ac.in]

Dear all,

I am a new user of DFTB+ and am looking at plotting the transmission
function of a graphene nanoribbon in the presence/absence of a biomolecule
using the DFTB+NEGF package. I have a confusion related to basic geometry
definition of the device region, which I am sharing here.

>From the example given in
(http://www.dftb-plus.info/fileadmin/DFTB-Plus/public/recipes-negf/html/transport/specifying_geometry.html),
I understand that my system needs to be partitioned into PLs. As per the
reference link, a PL is a contiguous group of atoms. Since my system
consists of a biomolecule placed on top of a continuous GNR sheet, I am
unable to decide upon the PL definition for my device region. How does one
define a multiple layer device in DFTB+?

I believe I might have misunderstood a fundamental point here. Any
clarification would be extremely helpful.

Thanks in advance.

Kind regards,
Anusha Iyer
PhD student at Indian Institute of Technology, Delhi.