[DFTB-Plus-User] single molecule transmission

Fri Apr 8 19:38:16 CEST 2016

Dear Martin,

On Thu, Apr 7, 2016 at 6:56 PM, PERSSON Martin <Martin.PERSSON at 3ds.com>
wrote:

> Dear Raha,
>
>
>
> I would suggest try setting up the ideal wire first and make sure you get
> the correct ideal Transmission.
>
>
>
> I few questions about your input file:
>
> Why do you set k-points? For the device calculation there are no k-points.
>

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?

> 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>
> 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>
> 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] *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>
> 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] *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> 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
>
> http://nano.ku.dk/english/research/nanochemistry/solomon_group/
>
> www.ki.ku.dk
>
>
>
> On 05 Apr 2016, at 08:54, Raha khalili <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
>
> *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
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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 delete this
> email and all attachments,
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> (iii) Dassault Systemes does not accept or assume any liability or
> responsibility for any use of or reliance on this email.
>
> For other languages, go to http://www.3ds.com/terms/email-disclaimer
>
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-- 
Khadijeh Khalili
Nanotechnology group, Physics department, university of Mazandaran
Babolsar, Iran
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