VMD-L Mailing List

From: Heidenreich, Joseph David (joheiden_at_imail.iu.edu)
Date: Tue Jun 30 2009 - 12:19:29 CDT

All,

I have been using Lammps to run NEMD simulations. At specific time steps in the simulation, I would like to visualize the system with the atoms colored by a scalar (in specific the PE of each atom and Pxx). I have not included these values in the dump file created by Lammps for storage space reasons, so I've written a code that extracts the needed time step from the dump file, and converts it into an input Lammps will take. Then, this is fed into Lammps and the PE and other values are calculated.

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).

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 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?

Thanks for the time,

Joe Heidenreich