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

[Gabriele Penazzi]

On 04/29/2014 07:18 PM, anz118466 at cse.iitd.ac.in wrote:
> 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.

Dear Anusha,

if 'slow convergence' means that you need a lot of SCC cycles,
partitioning will not change it (the number of SCC steps does not depend
on partitioning) but a single SCC step will be faster.

How effective the partitioning will be, it depends on the geometry of
your system. A big elongated molecule on top of the ribbon is not a very
fortunate case.

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

Basically you have to parse the coordinates of all the device atoms and
reorder them in the transport direction in a new .gen file.
Then you can define a cutoff distance such that the Nth PL index is
given by the first atomic index such that its coordinate falls within
(N-1)*cutoff and N*cutoff. I have some scripts I'd like to make public
but you have to wait a bit.

Gabriele


>
> 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.
>>>
>>> _______________________________________________
>>> DFTB-Plus-User mailing list
>>> DFTB-Plus-User at dftb-plus.info
>>> http://www.dftb-plus.info/mailman/listinfo/dftb-plus-user
>>
>> --
>> 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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>
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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