[DFTB-Plus-User] DFTB-Plus-User Digest, Vol 17, Issue 2

Faruq, Muhammad MAF2MPO at bolton.ac.uk
Wed Jan 6 12:12:41 CET 2016


Dear Dr. Ben and Gabriele

Thank you very much for your quick and valuable reply. I will definitely check. Let you know the update.

Thanks
Muhammad Faruq
PhD Researcher, IREET
I-zone, Room-G10 
University of Bolton

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Subject: DFTB-Plus-User Digest, Vol 17, Issue 2

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Today's Topics:

   1. Re: Request for Radial distribution function from md output
      and severe (174): SIGSEGV, segmentation fault occurred (Ben Hourahine)
   2. Re: Request for Radial distribution function from md output
      and severe (174): SIGSEGV, segmentation fault occurred
      (Gabriele Penazzi)


----------------------------------------------------------------------

Message: 1
Date: Tue, 5 Jan 2016 12:38:30 +0000
From: Ben Hourahine <benjamin.hourahine at strath.ac.uk>
To: dftb-plus-user at mailman.zfn.uni-bremen.de
Subject: Re: [DFTB-Plus-User] Request for Radial distribution function
	from md output and severe (174): SIGSEGV, segmentation fault occurred
Message-ID: <568BB946.6000700 at strath.ac.uk>
Content-Type: text/plain; charset="windows-1252"

Hello Faruq,

the data in your file velocity.txt are probably in AA / ps, not the atomic units DFTB is expecting (there is no unit modifier for the Velocities block in your input file).

Regards

Ben

On 05/01/16 12:05, Faruq, Muhammad wrote:

Dear Dr Aradi/All

I want to calculate the RDF from the MD output. Could you please let me how can I do it. One more problem is that I am having a segmentation
fault. Please suggest me what to do.   Thanks in advanced.

Here are output and input file.

Output:????..

-- 
      Dr. B. Hourahine, SUPA, Department of Physics,
    University of Strathclyde, John Anderson Building,
            107 Rottenrow, Glasgow G4 0NG, UK.
    +44 141 548 2325, benjamin.hourahine at strath.ac.uk

2013/4 THE Awards Entrepreneurial University of the Year
      2012/13 THE Awards UK University of the Year

   The University of Strathclyde is a charitable body,
        registered in Scotland, number SC015263

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Message: 2
Date: Tue, 5 Jan 2016 15:05:58 +0100
From: Gabriele Penazzi <penazzi at uni-bremen.de>
To: dftb-plus-user at mailman.zfn.uni-bremen.de
Subject: Re: [DFTB-Plus-User] Request for Radial distribution function
	from md output and severe (174): SIGSEGV, segmentation fault occurred
Message-ID: <568BCDC6.7040604 at uni-bremen.de>
Content-Type: text/plain; charset=windows-1252

On 01/05/2016 01:05 PM, Faruq, Muhammad wrote:
> Dear Dr Aradi/All
> 
> I want to calculate the RDF from the MD output. Could you please let 
> me how can I do it.

There's a plugin on VMD you can use.

If you are proficient with python you can also give a look to a
(undocumented) module I wrote sometimes ago (https://bitbucket.org/gpenazzi/dftbtools/src/2885ddd67256ea212aab2a1be7b44ce046fb9db2/analysis.py),
but you need to have Atomic Simulation Environment installed to use it.
Or you can check the script therein rdf_from_pdb.py referenced.


--
Dr. Gabriele Penazzi
BCCMS - University of Bremen

http://www.bccms.uni-bremen.de/
http://sites.google.com/site/gabrielepenazzi/
phone: +49 (0) 421 218 62337
mobile: +49 (0) 151 19650383


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