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

[anz118466 at cse.iitd.ac.in]

Dear Gabriele,

Thank you for such a lucid explanation of PL definition :) It did help
clear few doubts of mine.

Actually, I did simulate with (FirstLayerAtoms =  1) for my system. The
slow convergence, however, made me wonder if I am doing it right. My
system has a protein molecule on a GNR and is easily 1000+ atoms big. I
think partitioning it would speed up the convergence.

I did not completely understand the script's function to identify blocks
for partitioning the device. Kindly elaborate.

Best Regards,
Anusha



> 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
>
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