Quantum Chemistry Community - Revision history

Jhjensen at 10:20, 31 December 2009

2009-12-31T10:20:12Z

AngelHerraez: advise of broken link

2009-03-30T11:20:06Z

advise of broken link

Rkanters at 14:39, 18 March 2009

2009-03-18T14:39:00Z

Gutow: /* Orbital Rendering */

2007-12-20T20:32:09Z

‎Orbital Rendering

Pimpim at 11:50, 10 July 2007

2007-07-10T11:50:13Z

Pimpim at 11:49, 10 July 2007

2007-07-10T11:49:51Z

Pimpim: Added jmol community sections template

2007-07-10T11:49:22Z

Added jmol community sections template

Gutow: /* Orbital Rendering */

2006-07-18T16:15:55Z

‎Orbital Rendering

Gutow: /* Visualisation of IR Vibrations */

2006-06-15T15:08:06Z

‎Visualisation of IR Vibrations

Gutow: /* Orbital Rendering */

2006-06-15T15:06:54Z

‎Orbital Rendering

← Older revision		Revision as of 10:20, 31 December 2009
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	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)		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 ===		=== Visualisation of IR Vibrations ===

@@ Line 8: / Line 8: @@
 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. [http://chemie.skku.ac.kr/~wkpark/demos/demo/sample.html Orbital example with the Jmol] generated by the modified isovis. --WkPark
+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.

← Older revision		Revision as of 14:39, 18 March 2009
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	* Mopac		* Mopac
	* [[NWChem]]		* [[NWChem]]
		+	* [[Q-Chem]]

← Older revision		Revision as of 20:32, 20 December 2007
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	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)		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)

	=== Visualisation of IR Vibrations ===		=== Visualisation of IR Vibrations ===

← Older revision		Revision as of 11:50, 10 July 2007
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−	{{Jmol ~~Communitiy~~ Sections}}	+	{{Jmol Community Sections}}
	=== Quantum Chemistry Community ===		=== Quantum Chemistry Community ===

← Older revision		Revision as of 11:49, 10 July 2007
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−	{{Jmol ~~Communtiy~~ Sections}}	+	{{Jmol Communitiy Sections}}
	=== Quantum Chemistry Community ===		=== Quantum Chemistry Community ===

@@ Line 11: / Line 11: @@
 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/Orbitals/HowTo/Jmol_to_web_java.html Tools for authoring Jmol web pages].
+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)
 === Visualisation of IR Vibrations ===

@@ Line 19: / Line 19: @@
 (In alphabetical order)
 * [[Gaussian]]
 * Mopac
 * [[NWChem]]