Viewing Jaguar Orbitals Using Python Tools

Overview

This page details some tools developed at the MSC to view Jaguar orbitals. I wish to simplify the process so that people interested in viewing their orbitals don't have to go through the hassles of either Cerius or Molden.

The good news is that this is our software, which means that we can customize practically everything about it: colors of the atoms, bonds, and orbitals, sizes of everything, background color, bounding boxes and more. The bad news is that this is still under development, and currently is not as easy as it will ultimately be.

Notice: This is developmental software! Use at your own risk!!

Step One:

Converge the wave function whose orbitals you wish to display. Edit the restart file for that run. You need to specify the $plot section. The script /ul/rpm/python/plotsection.py can help in creating this section. To run it, type
% /ul/rpm/python/plotsection.py (output file name)
where (output file name) is the name of the output file that generated the restart file you wish to visualize. This will give a decent &plot section that can be appended to the end of your restart file. Replace the question marks with the orbital you wish to see. Now run this restart file. This should only take a minute, because Jaguar does not rerun the job, it simply evaluates the wave function on the specified grid.

The source code to the plotsection script is available here. There's nothing magic, or even necessarily correct, about the script, and if you feel like rewriting it with different parameters, by all means do so.

Step Two:

View the orbitals via the command
% /ul/rpm/python/orbviewer.py (plot file name)
The plot file name should be the same as the restart file name, with '.plt' appended to it instead of '.in'. The source code to the orbital plotting script is available here. Feel free to experiment!

More Gratuitous Images

Source Code

The source code for these routines are available here.
Richard P. Muller <rpm@wag.caltech.edu>
Last modified: Thu Mar 17 08:06:50 2005