VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Sat Jul 20 2013 - 07:46:18 CDT

On Sat, Jul 20, 2013 at 2:31 PM, amit kunte <amit7kunte_at_gmail.com> wrote:
> 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

for the most part, it is simply that i personally don't care enough. i
consider the readvarxyz thing an ugly hack that solved a specific
problem that i was involved in and *did* care about. for xyz files,
this way fairly simple to do, since the xyz file format does not
contain a lot of information. the LAMMPS dump format, on the other
hand is complex and support many (optional) features. it would be
comparatively easy to adapt the xyz reader/parse for the one specific
format that you are using, but i cannot put such a version into the
distribution, since then a lot of other people will want *their*
version to be supported, too.

> 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.

the situation is pretty simple. you have several choices
- figure out how to do proper Tcl scripting and adapt the code in
topotools for your needs
- figure out how to do proper Python scripting and adapt Pizza.py to
output a suitable .xyz file for you
- figure out a way to compel me to do what you are not willing or able to do
- have your boss/adviser make me an offer i cannot refuse

axel.

> 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.
>
> 

--
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com  http://goo.gl/1wk0
International Centre for Theoretical Physics, Trieste. Italy.