VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Tue Jun 30 2009 - 12:53:26 CDT

On Tue, 2009-06-30 at 17:19 +0000, Heidenreich, Joseph David wrote:
> All,
>

> I have two files: an XYZ file for the specific time step extracted from
> the Lammps dump file, and a file containing the scalars I'd like to
> color the atoms by. From my reading, the closest thing I've found to
> complete this task is at the following link:

> http://www.theochem.ruhr-uni-bochum.de/~axel.kohlmeyer/cpmd-vmd/part3.html#chap5_sect4
> (Thanks for all the tutorials and help Axel).

you're welcome. ;-)

> I'm assuming that this is still the best way to complete this.
> Essentially, it loads the data into the charge field for each atom,
> then the atoms are colored by charge. If this is the best way to do

the best way to do this, is to read the data into the "user" field.
see the previous example with the deformed buckyballs. the charge field
is per molecule, while "user" is per timestep. values you don't set
default to 0.0.

> this, is there a way I could complete this in one swoop by merging the
> XYZ file and the scalars I have into one file (I'm assuming a
> different format than XYZ). And if so, could I be pointed toward a
> direction that shows the standards and syntax of said file format?

there is currently no way to read data into "user" with the molfile
plugin API. we are working on reworking it, so that many more optional
data can be passed from trajectory files to VMD. with the latest
revision of the lammps dump file reader. the information can already
be parsed from within the molfile plugins, but so far only an API to
pass on velocity information exists.

you could in principle create a lammps dump that has the relevant
information in the vx, vy, vz fields and then afterwards copy it
to user, user1, user2 and then color by user, but reading the
information from a secondary file, is about as straightforward,
and i would consider this to be cleaner.

cheers,
   axel.

> Thanks for the time,
>
> Joe Heidenreich 

-- 
=======================================================================
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.