[DFTB-Plus-User] single molecule transmission

PERSSON Martin Martin.PERSSON at 3ds.com
Thu Apr 7 16:26:48 CEST 2016


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.
And you should not use OrbitalResolvedSCC = Yes with mio.

/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<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
<geom.gen><tunneling.dat><dftb_in.hsd.device><detailed.out>_______________________________________________
DFTB-Plus-User mailing list
DFTB-Plus-User at mailman.zfn.uni-bremen.de<mailto:DFTB-Plus-User at mailman.zfn.uni-bremen.de>
https://mailman.zfn.uni-bremen.de/cgi-bin/mailman/listinfo/dftb-plus-user


_______________________________________________
DFTB-Plus-User mailing list
DFTB-Plus-User at mailman.zfn.uni-bremen.de<mailto:DFTB-Plus-User at mailman.zfn.uni-bremen.de>
https://mailman.zfn.uni-bremen.de/cgi-bin/mailman/listinfo/dftb-plus-user



--
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,

(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

_______________________________________________
DFTB-Plus-User mailing list
DFTB-Plus-User at mailman.zfn.uni-bremen.de<mailto:DFTB-Plus-User at mailman.zfn.uni-bremen.de>
https://mailman.zfn.uni-bremen.de/cgi-bin/mailman/listinfo/dftb-plus-user



--
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,

(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

_______________________________________________
DFTB-Plus-User mailing list
DFTB-Plus-User at mailman.zfn.uni-bremen.de<mailto:DFTB-Plus-User at mailman.zfn.uni-bremen.de>
https://mailman.zfn.uni-bremen.de/cgi-bin/mailman/listinfo/dftb-plus-user



--
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,

(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
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.zfn.uni-bremen.de/pipermail/dftb-plus-user/attachments/20160407/c3e8bc44/attachment-0001.html>


More information about the DFTB-Plus-User mailing list