A Guide to Using Molden on the MSC Computers

The Molden program by Gijs Schaftenaar can be used to view Jaguar orbitals, normal modes, and other features of a QM simulation.

Note in particular that the current version does not support z-matrix geometries, and that some files that use backup basis sets may not be treated properly. Also, there are some problems with effective core potentials. Please let me know asap if you find a bug.

Using Molden to view Jaguar orbitals:

  1. Make sure you have a working version of molden. On the MSC computers, there are versions at /source/molden/linux/molden, /source/molden/IRIX-5.3/molden, and /source/molden/IRIX-6.4/molden. Choose the one appropriate for your platform.
  2. Place the file jag2molf somewhere in your path. Make sure that the script is executable (i.e. chmod +x jag2molf). You can get the script by clicking here. The file is also available on the MSC computers as /source/molden/jag2molf. If you're not running jag2molf on the MSC computers, make sure that the $basis_file_name variable points to the Jaguar basis set file.
  3. To run the jag2molf file, type "jag2molf file.in" where 'file.in' is the name of a jaguar restart file. This will create a file named 'file.molf', which can be loaded into molden by typing "molden file.molf" (provided of course that molden is somewhere in your path).
  4. Alternatively, note that Jaguar now can output molden files directly, so that you don't have to worry about jag2molf at all. Either set ip90=2 in the $gen section, or in the GUI, select Molden Output on the Output: Files dialog box.
  5. To view orbitals, click on the "Dens. Mode" button, which will put up a surface plot of the HOMO. Note positive and negative values of the contours at the right of the graphical screen. Choose a value that is roughly midway in the positive values. Then click on the "Space" button, and enter this contour value in the dialog box that pops up. (This step will take a minute, while the program evaluates the orbital at each gridpoint.) This will give you a standard orbital picture. To view other orbitals, click on the "Orbital" button, and select any of the orbitals there.
  6. Note that you can also view orbital contours this way.

Using Molden to view Jaguar normal modes:

  1. Run a Jaguar job that computes the frequencies of the molecule, e.g. setting &gen ifreq=1 &.
  2. Run this python script on the jaguar output file. This script can be found in /source/molden/molfreq.py on the MSC computers. Capture the output in a file, e.g.:
           % /source/molden/molfreq.py jag.out > jag.molf
           
  3. Now run molden on the file. I.e.:
           % /source/molden/IRIX-6.4/molden jag.molf
           
    Click on the "normal modes" button and select the frequency that corresponds to the mode you want to see.


The Molden manual is available here. I will write more specific Molden notes as time permits.


Here are some preliminary results of using Molden to view molecules and orbitals. In particular, the VRML output viewed through Netscape is quite snazzy. The Molden file that generated all of these pictures is available here.

A geometry viewed in Molden:

The same geometry, taking a snapshot of the VRML output. The whole VRML file is available here (note: your browser must be set up to properly view a .wrl file using the CosmoCode viewer!).

A Molden orbital:

A snapshot of the VRML output of the same orbital. The VRML file that generated it is available here. Note (1) this file is huge (~2.5 Mbytes) and (2) your browser must be properly configured to view VRML.

Obscure VRML tip

You can make the background white by inserting the line:
Background{skyColor[1 1 1]}
at the top (i.e. after the #VRML line) of the file. Also, you can insert the line:
NavigationInfo{type "EXAMINE"}
after that line to automatically put the browser in Examiner mode.