VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Sat May 21 2011 - 22:55:46 CDT

Hi,
  You can set environment variables inside of VMD (while you're running)
like this (standard Tcl syntax):
  set env(SOMEVARIABLE) valueyouwanttosetitto

So, for this case:
  set env(LAMMPSREMAPFIELDS) "vx=v_stress"

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Sat, May 21, 2011 at 09:10:17PM -0500, Shaorui Yang wrote:
> Hi Axel:
> Thanks for your reply. I should have been more specific. It is indeed a
> LAMMPS dump file (see attachment). How could I define the environment
> variable, through VMD text interface? If so, what does the syntax look
> like? I tried to search in the manual but didn't find what I want.
> Thanks.
> Shaorui
> On Sat, May 21, 2011 at 4:25 PM, Axel Kohlmeyer <akohlmey_at_gmail.com>
> wrote:
>
> On Sat, May 21, 2011 at 4:23 PM, Shaorui Yang <yangshaoruigt_at_gmail.com>
> wrote:
> > Dear VMD Users:
> > I have a single step dump file containing the following informations
>
> please be more specific about the file format. this sounds like you
> have a lammps custom trajectory dump. remember that most people
> cannot read minds. thanks.
> > id type xu yu zu per-atom stress.
> > I wish I can color the atoms by their stress magnitude. How should I
> do
> > this?
>
> there are a number of options. however, the major problem is to feed
> the information you want into some internal data field. the default
> molfile plugin API currently only supports a subset of data that is read
> to be communicate to VMD. per-timestep data is even more limited.
> practically only coordinates and velocities can currently passed on.
> for the LAMMPS trajectory plugin a little hack exists, to disguise any
> data as velocity components.
>
> just define the environment variable LAMMPSREMAPFIELDS
> e.g. to 'vx=v_stress' which will then read the v_stress column
> should doe the trick.
>
> then you can visualize the stress with the velocity coloring method.
>
> alternative methods are described here.
> http://docs.google.com/viewer?a=v&pid=sites&srcid=ZGVmYXVsdGRvbWFpbnxha29obG1leXxneDo0MzMwYzUwMmIyODU5NDFk
>
> cheers,
> axel.
>
> > Thanks a lot.
> > Shaorui
>
> --
> Dr. Axel Kohlmeyer
> akohlmey_at_gmail.com http://goo.gl/1wk0
>
> Institute for Computational Molecular Science
> Temple University, Philadelphia PA, USA. 

-- 
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