View source for Quantum Chemistry Community

{{Jmol Community Sections}}
=== 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 ([http://chemie.skku.ac.kr/~wkpark/demos/demo/sample.html broken link]). --WkPark

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

To render Orbitals from GAMESS use [http://www.scl.ameslab.gov/%7Ebrett/MacMolPlt/ MacMolPlt] to generate a grid file of the orbital. Then you can then use a Java application I have written to reformat the file to Gaussian cube files.  I also have written a Java application to generate a web page displaying the orbitals.  These tools are available on my (Jonathan Gutow's) web site at [http://www.uwosh.edu/faculty_staff/gutow/Jmol_Web_Page_Maker/Jmol_Web_Page_Maker.shtml Tools for authoring Jmol web pages].--[[User:Gutow|Gutow]] 18:15, 18 July 2006 (CEST)

Currently Jmol can generate isosurfaces directly from GAMESS.log files and many other ab initio output files.  There are still some bugs in many of the file readers, so be careful.  If you notice any errors in reading output files please report them.--[[User:Gutow|Gutow]] 21:32, 20 December 2007 (CET)

=== Density and Electrostatic Potential Rendering ===

To render electron densities and electrostatic potentials from GAMESS use [http://www.scl.ameslab.gov/%7Ebrett/MacMolPlt/ MacMolPlt] to generate a grid file of the density and/or electrostatic potential. Then you can then use a [http://www.uwosh.edu/faculty_staff/gutow/Orbitals/HowTo/Jmol_to_web_java.html Java application written by Jonathan Gutow] to reformat the file to Gaussian cube files. Examples can be found [http://molecularmodelingbasics.blogspot.com/2009/11/electron-density-reloaded.html here] and [http://molecularmodelingbasics.blogspot.com/2009/12/electrostatic-potential-maps-reloaded.html here].--[[User:Jhjensen|Jhjensen]] 11:13, 31 December 2009 (CET)

=== 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)
* Gamess
* [[Gaussian]]
* Mopac
* [[NWChem]]
* [[Q-Chem]]