From: JeJoon Yeon (
Date: Thu Jul 30 2015 - 19:36:27 CDT


I have a lammps custom file result, which have
atom type, x, y, z, stress values, pe, and ke

I can draw the pictures of stress distribution in the system with velocity
coloring (change the name as vx in the file). At the same time, I clearly
know that user field or other options from cpmd-vmd manual are needed, if I
want to give transparency/size/color modification with respect to the
stress values.

I really need some guidance here.

1) CPMD-VMD manual
I downloaded the pdf, but I can't open the example files linked. Is this
because all links for the example files are closed? Or something I missed
to see the files in pdf here?

2) tcl script
To achieve my task (atom transparency / size / color modification w.r.t
velocity (or atom name)), I'm trying to follow and modify the CPMD-VMD's
manual 6.4, "Using the user field for computed selections" Is this right
choice for my task?

3) executing tcl script
Should I need to execute the tcl script inside the VMD, after I read the
lammpstrj file? Or should I need to execute the tcl script without opening
VMD and lammps custom file? (like vmd -dispdev text command) I also saw
some example scripts inside the mailing list, but I don't know when and how
to execute them.