Manual for gOpenMol


Import and display a contour

gOpenMol can display both transparent and non-transparent isocontour solid surfaces in a grid mesh. In fact gOpenMol does not know what kind of surface it is displaying, so as long as you can describe your property as a grid mesh data you can display it with gOpenMol. If your data points (in the mesh) are vectors you can colour the points according to the vector norm and plot the vectors at the respective points.

The contour manager widget controls the display of the isocontour surfaces:

Main contour control widget:

Select contour colour:

Select contour file:



The display of orbitals or electron densities from a GaussianXX calculation


  1. Make first your calculation using the GaussianXX-program. Before you submit the job you have to know a few things:
  2. Use the gcube2plt-program to convert the grid mesh produced by GaussianXX into the plt-format recognized by gOpenMol.
    +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
     This program converts the Gaussian output using the 'cube'
     command to a form understandable to gopenmol.
     Usage:
     gcube2plt -iinput.cube -ooutput.plt
     Options:  -mXXX , where XXX is the molecular orbital number to be
                       placed in the plot file (you dont need this for 
                       electron densities) 
               -p      prevent the output of the coordinate file
    +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
    
    Where the input file is the cube mesh data and the output file is the plt-file. The conversion program will also produce a coordinate input file based on the coordinates GaussianXX used to generate the mesh data. This coordinate file (or an other file) has to be read into gOpenMol before you read in the mesh data (in the plt-format).
  3. From the View menu choose the Contour option and you will get the Contour manager widget. Double click on the file name in the Files-widget. gOpenMol will now open the file (which you will see in the widget on the right side) and reports the minimum and maximum values of the grid data in the file.
  4. Write an isocontour value in the isocontour input widget.
  5. Press one of the (small) colour buttons or use the sliders and you will se that the button above the small button or sliders will be coloured according to the colour you just picked/chose. Press now this button and you have defined a colour for your isocontour value. The small button beside the isocontour value widget shows you also the colour you have chosen. You can define several isocontour values by the same procedure.
  6. Now you can press the Apply button and you should see the defined surface.


Maintained by Leif Laaksonen (Leif.Laaksonen@csc.fi)

Last modified 1995/11/23