[DFTB-Plus-User] cylindrical gate set up

Thu Apr 4 17:01:56 CEST 2013

Hi, I appreciate your kind response. The cylindrical gate works now for my problem.
Best,

xiaobao,

At 2013-04-03 18:00:02,dftb-plus-user-request at dftb-plus.info wrote:
>Send DFTB-Plus-User mailing list submissions to
>	dftb-plus-user at dftb-plus.info
>
>To subscribe or unsubscribe via the World Wide Web, visit
>	http://www.dftb-plus.info/mailman/listinfo/dftb-plus-user
>or, via email, send a message with subject or body 'help' to
>	dftb-plus-user-request at dftb-plus.info
>
>You can reach the person managing the list at
>	dftb-plus-user-owner at dftb-plus.info
>
>When replying, please edit your Subject line so it is more specific
>than "Re: Contents of DFTB-Plus-User digest..."
>
>
>Today's Topics:
>
>   1. R:  cylindrical gate set up (Alessandro Pecchia)
>   2. modes Calculations with DFTB+ (Hongxin Yang)
>   3. Re: modes Calculations with DFTB+ (B?lint Aradi)
>   4. Re: Compilation Problem (B?lint Aradi)
>
>
>----------------------------------------------------------------------
>
>Message: 1
>Date: Tue, 02 Apr 2013 23:23:57 +0200
>From: Alessandro Pecchia <pecchia at ing.uniroma2.it>
>To: User list for DFTB+ related questions
>	<dftb-plus-user at dftb-plus.info>
>Subject: [DFTB-Plus-User] R:  cylindrical gate set up
>Message-ID: <fnkobsl9w7iigwnx2u2r6j1w.1364937837831 at email.android.com>
>Content-Type: text/plain; charset="utf-8"
>
>Hi.
>I tested recently cil. Gate on a CNT and it works. However with no insulator.?
>Please try first without. (Do not set insulator radius and kappa.)
>
>Concerning convergence it might depend on the system. I only used (and published) cil gates with CNTs and SiNWs.?
>
>We will try to sort the problems as soon as possible.
>
>
>A. Pecchia
>
>
>Inviato da Samsung MobileXiaobao <xiaobaojsyz at 163.com> ha scritto:?Hi,
>
>Anyone know how to set up a cylindrical gate? I referred the manual, it says now Planar gate is allowed, however, when we check the source code, seems there is some way to set up a cylindrical gate and also there are already some work used cylindrical gate. I would be very appreciated if you can give some idea. My current try is:
>?Gate = Cylindrical{
>??? GateLength [Angstrom] = 10.0
>??? GateRadius [Angstrom] = 18.0
>??? kappa = 3.9
>??? InsulatorLength [Angstrom] = 20.0
>??? InsulatorRadius[Angstrom]=12.0
>??? GatePotential [eV]= 0.001
>??? }
>but the runs are not converge. If I remove this part, then it converges well. I have tried to vary the radius and length, but it did not help. I am guessing there is something wrong with gate setup. Thank you for you r help!
>xiaobao,
>
>
>-------------- next part --------------
>An HTML attachment was scrubbed...
>URL: <http://www.dftb-plus.info/pipermail/dftb-plus-user/attachments/20130402/f4f629ff/attachment-0001.html>
>
>------------------------------
>
>Message: 2
>Date: Wed, 3 Apr 2013 14:14:31 +1100
>From: Hongxin Yang <hongxin.yang.spintec at gmail.com>
>To: dftb-plus-user at dftb-plus.info
>Subject: [DFTB-Plus-User] modes Calculations with DFTB+
>Message-ID:
>	<CAAqwnK-fnPeFvaNDD_bsAw60kq8AqSDutKEdy-A3YuXXtS3hvg at mail.gmail.com>
>Content-Type: text/plain; charset="iso-8859-1"
>
>Hello,
>I tried to calculate vibration spectra by using MODES, while it crashed by
>saying: "Segmentation fault"
>Anyone knows what is wrong with this problem.
>
>below is my input:
>
>Geometry = GenFormat {
> <<< geo.gen
>}
>Atoms = 1:-1
>DisplayModes = {
> PlotModes=1:-1
> Animate = Yes
>}
> SlaterKosterFiles = {
>    C-C = "./C-C.skf"
>    C-O = "./C-O.skf"
>    O-O = "./O-O.skf"
>    O-C = "./O-C.skf"
>    H-H = "./H-H.skf"
>    H-O = "./H-O.skf"
>    O-H = "./O-H.skf"
>    H-C = "./H-C.skf"
>    C-H = "./C-H.skf"
>  }
>
>Hessian = {
>  <<< "hessian.out"
>}
>
>
>
>And the script to run this:
>
>#!/bin/csh
>
>#PBS -q normal
>#PBS -l ncpus=8
>#PBS -l walltime=12:00:00
>#PBS -l vmem=8384MB
>#PBS -j oe
>#PBS -wd
>
>module load dftbp/1.2.1
>
># Assigning thet input and output files names,
># on user choice
>set input = modes_in.hsd
>set output = z.log
>
>
># program execution
>setenv OMP_NUM_THREADS $PBS_NCPUS
>modes > $output
>
>
>the output is:
>
>================================================================================
>     MODES  0.01
>================================================================================
>
>Interpreting input file 'modes_in.hsd'
>--------------------------------------------------------------------------------
>
>Thank you very much for help!
>Best,
>Hongixn
>-- 
>
>~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
>Hongxin YANG
>CSIRO's Office of the Chief Executive Postdoc Fellow
>CSIRO, Materials Science and Engineering
>343 Royal Pde, Parkville, VIC, 3052, Australia
>Tel:   +61 (03) 9662 7105
>FAX: +61 (03) 9662 7145
>Email: hongxin.yang at csiro.au
>          hongxin.yang.spintec at gmail.com
>~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
>-------------- next part --------------
>An HTML attachment was scrubbed...
>URL: <http://www.dftb-plus.info/pipermail/dftb-plus-user/attachments/20130403/34d7e37a/attachment-0001.html>
>
>------------------------------
>
>Message: 3
>Date: Wed, 03 Apr 2013 09:09:45 +0200
>From: B?lint Aradi <balint.aradi at bccms.uni-bremen.de>
>To: User list for DFTB+ related questions
>	<dftb-plus-user at dftb-plus.info>
>Subject: Re: [DFTB-Plus-User] modes Calculations with DFTB+
>Message-ID: <515BD5B9.6020504 at bccms.uni-bremen.de>
>Content-Type: text/plain; charset="iso-8859-1"
>
>Hi,
>
>> Hello,
>> I tried to calculate vibration spectra by using MODES, while it crashed by
>> saying: "Segmentation fault"
>> Anyone knows what is wrong with this problem.
>> 
>
>Do you use the binary from the website? Could you then try to set the
>usual stack limit to unlimited, that may solve your problem. Just do
>depending on your shell
>
>ulimit -s unlimited (in BASH)
>or
>limit stack unlimited (in (T)CSH)
>
>  Best regards,
>
>  B?lint
>
>
>-- 
>Dr. B?lint Aradi
>Bremen Center for Computational Materials Science, University of Bremen
>http://www.bccms.uni-bremen.de/cms/people/b_aradi/
>
>
>-------------- next part --------------
>A non-text attachment was scrubbed...
>Name: signature.asc
>Type: application/pgp-signature
>Size: 261 bytes
>Desc: OpenPGP digital signature
>URL: <http://www.dftb-plus.info/pipermail/dftb-plus-user/attachments/20130403/b43ca23d/attachment-0001.pgp>
>
>------------------------------
>
>Message: 4
>Date: Wed, 03 Apr 2013 09:15:21 +0200
>From: B?lint Aradi <balint.aradi at bccms.uni-bremen.de>
>To: User list for DFTB+ related questions
>	<dftb-plus-user at dftb-plus.info>
>Subject: Re: [DFTB-Plus-User] Compilation Problem
>Message-ID: <515BD709.4020507 at bccms.uni-bremen.de>
>Content-Type: text/plain; charset="iso-8859-1"
>
>On 04/02/2013 01:43 PM, debs at iitk.ac.in wrote:
>> Hi,
>>  I am new with DFTB+ and I am trying to install it in my Ubuntu 12.04 OS.
>> I am getting some error which I can not able to sort out. I am using
>> make.x86_64-linux-gfortran file. I have modified the make file and it is
>> given below.
>
> You could try to take the binary provided on the website, that should
>run on your system (provided it is a 64 bit system) and it will be
>probably also faster as the one you're going to build.
>
>  Best regards,
>
>  B?lint
>
>-- 
>Dr. B?lint Aradi
>Bremen Center for Computational Materials Science, University of Bremen
>http://www.bccms.uni-bremen.de/cms/people/b_aradi/
>
>
>-------------- next part --------------
>A non-text attachment was scrubbed...
>Name: signature.asc
>Type: application/pgp-signature
>Size: 261 bytes
>Desc: OpenPGP digital signature
>URL: <http://www.dftb-plus.info/pipermail/dftb-plus-user/attachments/20130403/648bd362/attachment-0001.pgp>
>
>------------------------------
>
>_______________________________________________
>DFTB-Plus-User mailing list
>DFTB-Plus-User at dftb-plus.info
>http://www.dftb-plus.info/mailman/listinfo/dftb-plus-user
>
>
>End of DFTB-Plus-User Digest, Vol 63, Issue 2
>*********************************************
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.zfn.uni-bremen.de/pipermail/dftb-plus-user/attachments/20130404/12ebd557/attachment.htm>