VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Sat May 21 2011 - 16:25:18 CDT

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.