[DFTB-Plus-User] single molecule transmission

[Raha khalili]

Hello Gabriele,

Many thanks for the explanation.

Bests,
Raha

On Sat, Apr 9, 2016 at 7:10 PM, Gabriele Penazzi <penazzi at uni-bremen.de>
wrote:

> [cut]
>
>
> As I know, for transport calculation, it is needed to set at least one
> direction periodic that in dftb+ z-direction should be. So, I have to set
> up a supper cell for my geometry and define k-point sampling for my T
> calculation. Isn't it correct?
>
>
>
> No, you don't need to have periodicity along z. I think it is in this way
> maybe in transiesta, but in DFTB periodicity along transport direction is
> ignored as the boundary conditions are substituted by open ones. The
> periodicity is needed when you have periodicity in the other directions (2D
> system or bulk electrodes)
>
>
> And you should not use OrbitalResolvedSCC = Yes with mio.
>>
>
> Yes, good point. It was a mistake. Thanks for mention it. I removed this
> line but the problem hasn't solved!!
>
> Bests,
> Raha
>
>>
>>
>> /Martin
>>
>>
>>
>>
>>
>> *From:* dftb-plus-user-bounces at mailman.zfn.uni-bremen.de [mailto:
>> dftb-plus-user-bounces at mailman.zfn.uni-bremen.de] *On Behalf Of *Raha
>> khalili
>> *Sent:* Thursday, April 07, 2016 2:59 PM
>>
>> *To:* User list for DFTB+ related questions
>> *Subject:* Re: [DFTB-Plus-User] single molecule transmission
>>
>>
>>
>> Dear Martin,
>>
>> So sorry for my too my many emails. I've repeated T calculation with the
>> geometry you already sent. I only changed z direction to periodic but
>> interestingly problem persists. The final T result is attached. Any advice
>> will be really appreciated.
>>
>> Kind regards,
>>
>> Raha
>>
>>
>>
>> On Wed, Apr 6, 2016 at 2:34 PM, Raha khalili <
>> <khadije.khalili at gmail.com>khadije.khalili at gmail.com> wrote:
>>
>> Dear Martin,
>>
>> I really appreciate your attention. It helped a lot. Yes, It can be a
>> good reason for the difference.
>>
>> I'll do my calculation again.
>>
>> Kind wishes,
>>
>> Raha
>>
>>
>>
>> On Wed, Apr 6, 2016 at 2:15 PM, PERSSON Martin < <Martin.PERSSON at 3ds.com>
>> Martin.PERSSON at 3ds.com> wrote:
>>
>> Dear Raha,
>>
>>
>>
>> I ran the calculation with a k-point separation of 0.02 1/Å.
>>
>>
>>
>> I had a quick  comparison between our input files.
>>
>> I am running with a significantly larger structure. I noticed that you
>> only have about 80 atoms in your electrode. Are you sure that is big
>> enough? My electrode is about 120 atoms, the Materials Studio setup
>> automatically calculate a safe electrode size using the skf input and
>> expands the initial structure to allow for the larger electrode. So my
>> calculation had larger electrodes and a longer device section.
>>
>>
>>
>> I attached the hsd file used for the transmission calculation.
>>
>>
>>
>> Best Regards,
>>
>> Martin
>>
>>
>>
>> *From:* dftb-plus-user-bounces at mailman.zfn.uni-bremen.de [mailto:
>> <dftb-plus-user-bounces at mailman.zfn.uni-bremen.de>
>> dftb-plus-user-bounces at mailman.zfn.uni-bremen.de] *On Behalf Of *Raha
>> khalili
>> *Sent:* Tuesday, April 05, 2016 5:15 PM
>>
>>
>> *To:* User list for DFTB+ related questions
>> *Subject:* Re: [DFTB-Plus-User] single molecule transmission
>>
>>
>>
>> Dear Martin,
>>
>> Thanks a lot for your email. Quite interesting!! Here is attached the
>> final transmission plot for my calculation in addition to input files. I
>> also used mio parameter set.
>>
>> May I ask you which k-point sampling did you use? I am trying to change
>> different parameters to find the solution.
>>
>> Best,
>>
>> Raha
>>
>>
>>
>> On Tue, Apr 5, 2016 at 5:17 PM, PERSSON Martin < <Martin.PERSSON at 3ds.com>
>> Martin.PERSSON at 3ds.com> wrote:
>>
>> I took your geometry and ran it through the Materials Studio version of
>> DFTB+ using the mio library.
>>
>> I don’t get any peak at the Fermi level.
>>
>>
>>
>> Best Regards,
>>
>> Martin
>>
>>
>>
>> *From:* <dftb-plus-user-bounces at mailman.zfn.uni-bremen.de>
>> dftb-plus-user-bounces at mailman.zfn.uni-bremen.de [mailto:
>> <dftb-plus-user-bounces at mailman.zfn.uni-bremen.de>
>> dftb-plus-user-bounces at mailman.zfn.uni-bremen.de] *On Behalf Of *Raha
>> khalili
>> *Sent:* Tuesday, April 05, 2016 11:41 AM
>> *To:* User list for DFTB+ related questions
>> *Subject:* Re: [DFTB-Plus-User] single molecule transmission
>>
>>
>>
>> Dear Alessandro,
>>
>> Very thanks for your kind helping. It worked well. I changed the geometry
>> and found the transmission  (here is attached) but i am not sure whether it
>> is correct or not. It seems to have a peak at fermi level means the
>> structure behaves metallic that may not be in agreement with DFT
>> calculation for benzene+cnt electrodes (J. Phys. Chem. A 2009, 113,
>> 4100–4104). It will be very kind of to help me in this case.
>>
>> Best regards,
>>
>> Raha
>>
>>
>>
>> On Tue, Apr 5, 2016 at 12:50 PM, Alessandro Pirrotta <
>> <alessandro.pirrotta at chem.ku.dk>alessandro.pirrotta at chem.ku.dk> wrote:
>>
>> Dear Raha,
>>
>>
>>
>> I have encountered this issue before. I think your only problem is the
>> ordering of the atoms of your contacts.
>>
>> Please, have a look at section 2.1.1.2 of this guide
>> <http://www.dftb-plus.info/fileadmin/DFTB-Plus/public/recipes-negf/html/transport/specifying_geometry.html>
>>
>>
>>
>> <http://www.dftb-plus.info/fileadmin/DFTB-Plus/public/recipes-negf/html/transport/specifying_geometry.html>
>> http://www.dftb-plus.info/fileadmin/DFTB-Plus/public/recipes-negf/html/transport/specifying_geometry.html
>>
>>
>>
>> Cheers,
>>
>> Alessandro
>>
>>
>>
>> *Alessandro Pirrotta*
>> PhD student
>>
>>
>>
>> *Faculty of Science*
>> Department of Chemistry &
>> Nano-Science Center
>> University of Copenhagen
>> Universitetsparken 5, C321
>> 2100 Copenhagen Ø
>> Denmark
>>
>> DIR +45 21 18 11 90
>> MOB +45 52 81 23 41
>>
>> alessandro.pirrotta at chem.ku.dk
>>
>> <http://nano.ku.dk/english/research/nanochemistry/solomon_group/>
>> http://nano.ku.dk/english/research/nanochemistry/solomon_group/
>>
>> <http://www.ki.ku.dk/>www.ki.ku.dk
>>
>>
>>
>> On 05 Apr 2016, at 08:54, Raha khalili < <khadije.khalili at gmail.com>
>> khadije.khalili at gmail.com> wrote:
>>
>>
>>
>> Hello!
>>
>> I am trying to find transmission of a single molecule sandwiched between
>> two CNT electrodes. My calculations got converged but the final
>> transmission order is very low, almost zero.
>> Here are attached the input and ouput files. Any help will be really
>> appreciated.
>>
>> Best regards,
>>
>> Raha
>>
>>
>> --
>>
>> Khadijeh Khalili
>>
>> Nanotechnology group, Physics department, university of Mazandaran
>>
>> Babolsar, Iran
>>
>>
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>> --
>>
>> Khadijeh Khalili
>>
>> Nanotechnology group, Physics department, university of Mazandaran
>>
>> Babolsar, Iran
>>
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>> --
>>
>> Khadijeh Khalili
>>
>> Nanotechnology group, Physics department, university of Mazandaran
>>
>> Babolsar, Iran
>>
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>> individual or entity to whom it is addressed and may be confidential and/or
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>>
>> --
>>
>> Khadijeh Khalili
>>
>> Nanotechnology group, Physics department, university of Mazandaran
>>
>> Babolsar, Iran
>>
>>
>>
>>
>> --
>>
>> Khadijeh Khalili
>>
>> Nanotechnology group, Physics department, university of Mazandaran
>>
>> Babolsar, Iran
>>
>> This email and any attachments are intended solely for the use of the
>> individual or entity to whom it is addressed and may be confidential and/or
>> privileged.
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>> If you are not one of the named recipients or have received this email in
>> error,
>>
>> (i) you should not read, disclose, or copy it,
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>
>
> --
> Khadijeh Khalili
> Nanotechnology group, Physics department, university of Mazandaran
> Babolsar, Iran
>
>
> _______________________________________________
> DFTB-Plus-User mailing listDFTB-Plus-User at mailman.zfn.uni-bremen.dehttps://mailman.zfn.uni-bremen.de/cgi-bin/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 9328
> fax: +49 (0) 421 218 4764
>
>
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-- 
Khadijeh Khalili
Nanotechnology group, Physics department, university of Mazandaran
Babolsar, Iran
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