VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Mon Jul 13 2009 - 14:21:03 CDT

On Mon, 2009-07-13 at 19:44 +0100, Dan Lussier wrote:

dan,

> I had a question about using other data beyond just x,y,z from LAMMPS
> ascii files produced by 'dump custom ...' command.

> As it stands I am loading the LAMMPS ascii dump files using a loop
> over a list of files like:
>
> set x 0
> foreach filename [glob $search] {
> set file_num [scan $filename "$filespec%d"]
>
> if { ($file_num >= $ilo) && ($file_num <= $ihi)} {
> puts "Processing: $filename ($x)"
>
> if {$x == 0} {
> mol new $filename type lammpstrj
> set mol_name $filename
> } else {
> mol addfile $filename type lammpstrj
> }
> incr x
> }
> }
>
> This does a good job loading the system's geometry but as expected
> leaves out the other values from the dump file.
>
> I'm interested in loading data from other columns of the dump files
> (i.e. atom-wise potential energy, atom-wise coordination number, etc.)
> and was hoping there was a VMD friendly way to do this either as the
> files are loaded or after the fact by looping over the frames.

sorry, but as of the very latest version of the LAMMPS plugin in VMD,
you can only retrieve the information about atom velocities.

for everything else, the corresponding APIs are not yet available
in the molfile plugin interface. the LAMMPS plugin parser does
recognize a lot of entries, but has no way to pass this on.

plans to adjust the API to have additional (and at some point
arbitrary) properties passed along are underway, but will have
to wait until after the release of 1.8.7 and then will need to
be implemented on a case by case basis depending on demand,
usefulness and ease of implementation.

since for the increasing likelihood of multimillion particle
simulations and the impracticality to do lots of analysis in
postprocessing, i expect the demand and usefulness to increase
steeply over the next couple of years...
our group will definitely have demand along those lines.

cheers,
   axel.
> Any advice would be great.
>
> Many thanks.
>
> Dan 

-- 
=======================================================================
Axel Kohlmeyer   akohlmey_at_cmm.chem.upenn.edu   http://www.cmm.upenn.edu
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
=======================================================================
If you make something idiot-proof, the universe creates a better idiot.