Tutorial: Visualizing Volumetric Data from the Gaussian Cube Files

The Gaussian electronic structure program can calculate many volumetric properties, e.g. electrostatic potential, electron densities etc., which can be visualized via the Gaussian cube file format.

Visualizing Occupied Molecular Orbitals

Provided that we have a checkpoint file after the Gaussian calculation we need first to create a formatted checkpoint file using formchk utility:

formchk water.chk

It will generate file water.fchk (water.fch under MS Windows).

Then we shall create a multi-orbital cube file for all occupied orbitals using cubegen utility:

cubegen 0 MO=occA water.fchk water-occupied-orbitals.cube -2 h

Now load it into


: Select Manage Gaussian Cubes from the Analyze menu:

It will open Manage Gaussian Cubes Dialog:

Press Load Cube button to select a cube file:

Jamberoo will load a cube file and show info about it:

We see that this is a multi-orbital cube file which contains 5 cubes. The Manage Gaussian Cubes Dialog shows now all available cubes:

We can select cubes one by one and press Create Isosurface button each time. Or we can select all cubes (holding down the Shift key and clicking on the first and last cubes) :

The default isovalue for isosurface for molecular orbitals is 0.02. Program will draw two isosurfaces, one for positive and one for negative values, i.e. 0.02 and -0.02. To supress this behaviour one needs to uncheck the Use Opposite Value as well checkbox.

After pressing Create Isosurface button Jamberoo generates all isosurfaces which are superimposed:

To manage multiple isosurfaces we go to the View menu and select Manage Objects menu item:

and program will open a Graphics Object Properties Dialog:

Checking Display Selected Objects Only checkbox will undisplay all isosurfaces in the Main Window

Now selecting Graphics Object from the Graphics Object Properties Dialog

will display isosurfaces only for the selected orbitals and undisplay others:

Using Graphics Object Properties Panel

user can play with different rendering styles

and opacity:

Send all questions, suggestions and comments to Vlad (vvv900@gmail.com)

Dr. Vladislav Vasilyev

Supercomputer Facility,

The Australian National University,

Canberra, ACT, 0200, Australia