Quantum Chemistry Community

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Revision as of 16:34, 24 May 2006 by Gutow (talk | contribs) (Orbital Rendering)
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Quantum Chemistry Community

This subcommunity of for Jmol users that use Jmol for display and analysis of quantum chemistry calculations.

Orbital Rendering

By means of the pmesh command, Jmol can render pmesh surfaces. But most QM programs do not output pmesh files for orbitals, and a isosurface rendering step is needed in between. It would be nice if Jmol would contain an algorithm that can perform this conversion step, or an interface to an opensource program that can do this.

The Isovis can generate isosurface with hdf/cube file (hdf is 3d cube/grid data file) and I patch it to generate the pmesh file. Orbital example with the Jmol generated by the modified isovis. --WkPark

Currently Jmol can generate isosurfaces directly from GaussianXX cube files !! See Gaussian link below.

To render Orbitals from GAMESS use MacMolPlt to generate a grid file of the orbital. Then you can then use a Perl script, I provide here, to reformat the file to Gaussian cube files. I've made an example page that uses these files which allows viewing Cl AOs. Instructions for creating a page like this using a script I wrote may be accessed here.

Visualisation of IR Vibrations

Jmol can render molecular vibrations outputed by programs like Gaussian and Nwchem. QM Programs that Work with Jmol (or should)

(In alphabetical order)