[DFTB-Plus-User] single molecule transmission
Gabriele Penazzi
penazzi at uni-bremen.de
Sat Apr 9 16:40:19 CEST 2016
[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>
> [mailto: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 <mailto: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 <mailto: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>
> [mailto: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:* 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 <mailto: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
> <mailto:dftb-plus-user-bounces at mailman.zfn.uni-bremen.de>
> [mailto: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:* 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
> <mailto: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
>
> 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 <mailto:alessandro.pirrotta at chem.ku.dk>
>
> http://nano.ku.dk/english/research/nanochemistry/solomon_group/
>
> www.ki.ku.dk <http://www.ki.ku.dk/>
>
> On 05 Apr 2016, at 08:54, Raha khalili
> <khadije.khalili at gmail.com <mailto: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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>
>
> --
>
> 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.
>
> 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,
>
> (ii) please notify sender of your receipt by reply email and
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>
>
> --
> Khadijeh Khalili
> Nanotechnology group, Physics department, university of Mazandaran
> Babolsar, Iran
>
>
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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 9328
fax: +49 (0) 421 218 4764
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