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

[Gabriele Penazzi]

Dear Anusha,

the construction rule to define a valid PL is the following: there
should be non-zero interactions only between adjacent PLs. Therefore
some kind of 1D partitioning is usually possible for any transport
geometry. Note that the PLs in the device region do not need to have the
same size.

The definition of PLs in the contacts is crucial and needs to be
ensured. This point is usually easy because the contacts should be given
by a semi-infinite bulk structure. Partitioning in the device region is
not mandatory, but it is useful to take advantage of the iterative
scheme, speed up the calculation and decrease the memory usage. In line
of principle, you can define a single PL containing all the device atoms
(FirstLayerAtoms =  1), and if the system is small enough the code would
still work. Alternatively you can write a script which orders all the
device atoms along the transport direction and identify the atom indexes
collecting blocks of atoms within blocks spaced by a reasonable cutoff
range (10 atomic units, for example).

Note that 'contiguous' does not mean necessarily bonded, or in-plane.
For example, if you have an homogeneous ribbon with an adatom on the top
and the atoms in the gen file are ordered along the transport direction,
you will have that the corresponding PL will contain one more atom (i.e.
the adatom itself)

Hope this helped, otherwise I can maybe send you an example later.

Best,
Gabriele


On 04/29/2014 12:10 PM, anz118466 at cse.iitd.ac.in wrote:
> 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.
>
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-- 
Dr. Gabriele Penazzi
BCCMS - University of Bremen

http://www.bccms.uni-bremen.de/
http://sites.google.com/site/gabrielepenazzi/

phone: +49 (0) 421 218 62337
fax: +49 (0) 421 218 62770