VMD-L Mailing List

From: Shaorui Yang (yangshaoruigt_at_gmail.com)
Date: Sat May 21 2011 - 21:10:17 CDT

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.
>