VMD-L Mailing List

From: amit kunte (amit7kunte_at_gmail.com)
Date: Sat Jul 20 2013 - 07:31:42 CDT

Hi Axel,
Will it be possible for you without costing too much time to write a
similar parser for lammps dump as there is for xyz. If not, is it too steep
a learning curve for someone like me who is not conversant with tcl
scripting to write it on his own? It would require too much time to rerun
all my simulations with xyz as the output format.

Regards
Amit

On Sat, Jul 20, 2013 at 5:12 PM, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:

> On Sat, Jul 20, 2013 at 12:36 PM, amit kunte <amit7kunte_at_gmail.com> wrote:
> > Hi vmd users
> > I have a lammps dump file where the number of atoms change per
> > timestep(due to fix pour). I want to visualize it in vmd and I know the
> > subsequent limitation of vmd of variant atom visualization and that
> > readvarxyz circumvents this problem. Is there a way to visualize with
> native
> > lammps file without converting it to XYZ format? ( If i am not wrong, XYZ
>
> you would have to write a parser similar to the xyz format parser for
> topotools.
>
> > does not contain diameter info of particles and i have a polydisperse
>
> if you assign a different atom type for each radius, you can handle
> this with .xyz format as well. all you'd need is to run a little Tcl
> script in VMD after loading the .xyz file that assigns the
> corresponding radii to the atom types.
>
> > system to visualize). If no other way please suggest me a tool to convert
> > lammps dump to xyz file.
>
> i don't know. have you checked out Pizza.py?
>
> axel.
>
> > Regards
> > Amit
>
>
>
> --
> Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0
> International Centre for Theoretical Physics, Trieste. Italy.
>