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Re: [lammps-users] COM g(r) of Polymer molecular
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Re: [lammps-users] COM g(r) of Polymer molecular


From: Axel Kohlmeyer <akohlmey@...24...>
Date: Mon, 16 Apr 2018 12:18:59 -0400

please apply some common sense and just do a web search. there should
be a *ton* of examples for how to compute a g(r) floating around on
the web.
also, if you convert your COM output file into a suitably formatted
trajectory file, you can use existing codes that post-process
trajectories. there are plenty of those around as well.

axel.

On Mon, Apr 16, 2018 at 11:44 AM, Chuanxing Zhan via lammps-users
<lammps-users@lists.sourceforge.net> wrote:
>
> Thanks a lot! If you can send me an example code, that would be great!
>
> Sincerely,
> Kerwin
> On Sunday, 15 April 2018, 9:04:07 PM GMT-5, Shafat Mubin
> <shafatmubin2@...24...> wrote:
>
>
> Hi,
>
> If you are new to programming, you can check out my website:
> www.hypermd.wordpress.com.
>
> Also, I will try to send you my code for calculating g(r) later.
>
> Thanks,
> Shafat
>
> On Sun, Apr 15, 2018, 21:00 Chuanxing Zhan <chuanxingzhan@...16...> wrote:
>
> Thanks for your explanation, I'm wondering if you have any example script
> remained or any helpful information for writing a script. I'm so new in the
> programming language.
> On Friday, 13 April 2018, 6:11:28 PM GMT-5, Shafat Mubin
> <shafatmubin2@...24...> wrote:
>
>
> Hi,
>
> For the second method, you can dump the COM of every molecule into an output
> file, and then write a post-processing script (e.g. in python) to read the
> COM's every iteration and compute the RDF. I have written a similar python
> code a few years ago for the COM of a benzene layer.
>
> Shafat
>
> On Fri, Apr 13, 2018, 17:25 Chuanxing Zhan via lammps-users
> <lammps-users@lists.sourceforge.net> wrote:
>
> Thanks for you information! Can you say anything specific about the second
> method for computing molecular g(r)?  The question is, how to define this
> COM of molecules to particle and output to trajectory which can use to
> compute the molecular g(r)? I used the example command to compute the COM of
> molecule. If i want co continue, what command would be helpful, dump or
> restart ?
> The example command for computing COM of molecule:
> compute cc1 all chunk/atom molecule
> compute myChunk all com/chunk cc1
> fix                  1 all ave/time 100 1 100 c_myChunk[*] file tmp.out mode
> vector
>
>
> Thanks,
> Kerwin
> On Friday, 13 April 2018, 11:56:45 AM GMT-5, Axel Kohlmeyer
> <akohlmey@...24...> wrote:
>
>
> On Fri, Apr 13, 2018 at 12:40 PM, Chuanxing Zhan via lammps-users
> <lammps-users@lists.sourceforge.net> wrote:
>> Dear lammps users,
>> Hello, everyone! I'm trying to compute the g(r) of COM of polymer, the
>> lammps command only compute the g(r) between the atoms. I read previously
>> thread in lammps forum, and what they mentioned is I need to build a
>> script
>> for calculating COM and defined the molecules. I'm wonder anyone have a
>> better way to do the molecular g(r) calculation. Any help would be
>> appreciated.
>
> please keep in mind, that a g(r) is a property which computes the
> relative probability of point particles in a given system versus the
> distribution of an ideal gas.
> so any application to molecular systems is of limited meaning.
>
> the easiest approach is usually to pick the atom that is closest to
> the center of mass, give it a different atom type number (but the same
> force field parameters) and then compute the g(r) for that type of
> atom. if you average over a large enough system and long enough
> trajectory, the differences to the g(r) of the COM should be
> negligible.
>
> a more involved approach would be to compute the COM(s) and output it
> to a file and then compute the g(r) in post-processing.
>
> axel.
>
>
>>
>> Thanks !
>> Kerwin
>>
>>
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>>
>
>
>
> --
> Dr. Axel Kohlmeyer  akohlmey@...24...  http://goo.gl/1wk0
> College of Science & Technology, Temple University, Philadelphia PA, USA
> International Centre for Theoretical Physics, Trieste. Italy.
>
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-- 
Dr. Axel Kohlmeyer  akohlmey@...24...  http://goo.gl/1wk0
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.