From: Bob Hanson <hansonr@st...>  20080227 07:41:26

Xavier I checked all the files you provided on that web site, and the orbitals look terrific now. By the way, I note that the following script commands could be quite useful: print getProperty("auxiliaryInfo", "models", 2, "modata","mos") energy 20.24444 coefficients float[7] array(0.00584,0.99416006,0.02631,0.0,0.0,0.0042700004,0.00584) symmetry "(A1)O" energy 1.26376 coefficients float[7] array(0.15775,0.23316002,0.83750004,0.0,0.0,0.12662,0.15775) symmetry "(A1)O" energy 0.61038 coefficients float[7] array(0.44628,0.0,0.0,0.0,0.60745007,0.0,0.44628) symmetry "(B2)O" energy 0.45392 coefficients float[7] array(0.28342,0.10317,0.53590995,0.0,0.0,0.77124995,0.28342) symmetry "(A1)O" energy 0.39124 coefficients float[7] array(0.0,0.0,0.0,1.0,0.0,0.0,0.0) symmetry "(B1)O" energy 0.59607 coefficients float[7] array(0.78786004,0.13034,0.8628,0.0,0.0,0.74679,0.78786004) symmetry "(A1)V" energy 0.72617 coefficients float[7] array(0.82911,0.0,0.0,0.0,0.98133,0.0,0.82911) symmetry "(B2)V" or just one MO: print getProperty("auxiliaryInfo", "models", 2, "modata","mos", 1) energy 20.24444 coefficients float[7] array(0.00584,0.99416006,0.02631,0.0,0.0,0.0042700004,0.00584) symmetry "(A1)O" or the highest: print getProperty("auxiliaryInfo", "models", 2, "modata","mos", 0) energy 0.72617 coefficients float[7] array(0.82911,0.0,0.0,0.0,0.98133,0.0,0.82911) symmetry "(B2)V" or how many: print getProperty("auxiliaryInfo", "models", 2, "modata","mos").size 7 or the basis function parameters: print getProperty("auxiliaryInfo", "models", 2, "modata", "gaussians").split("f").join("\nf") float[][] [ float[2] array(3.425251,0.15432896), float[2] array(0.6239137,0.53532815), float[2] array(0.1688554,0.44463456), float[2] array(130.7093,0.15432896), float[2] array(23.808867,0.53532815), float[2] array(6.443609,0.44463456), float[3] array(5.033152,0.099967234,0.15591627), float[3] array(1.1695961,0.39951286,0.6076837), float[3] array(0.38038892,0.7001155,0.3919574), float[2] array(3.425251,0.15432896), float[2] array(0.6239137,0.53532815), float[2] array(0.1688554,0.44463456)] or the shells array, indicating (atomNumber, spdfType, pointerToGaussians, numberOfGaussians) print getProperty("auxiliaryInfo", "models", 2, "modata", "shells") int[4] array(0,0,0,3) int[4] array(1,0,3,3) int[4] array(1,2,6,3) int[4] array(2,0,9,3) or the calculation type: print getProperty("auxiliaryInfo", "models", 2, "modata", "calculationType") STO3G (5D, 7F) or the energy units, if they are present: print getProperty("auxiliaryInfo", "models", 2, "modata", "energyUnits") That sort of thing. To see all of what's there, just use print getProperty("auxiliaryInfo") Also, though this is probably not generally desired, did you know that if you use the "isosurface mo" command rather than the MO command itself, then you can select specific atoms and only see the electron density specifically due to that atom's orbitals? select oxygen isosurface mo 6 Kind of interesting. Bob Xavier PratResina wrote: > Jmol developers, > > it's seems that Jmol is not able to display the right shape of > some Molecular Orbitals when the data is read form Gaussian outputs > (not cube files). > This anomaly can already be seen in > http://chemapps.stolaf.edu/jmol/docs/examples11/isosurface.htm > when it loads "waterG03W.out" and the 6th MO has the wrong shape. > > I tested it myself comparing it with cube files > (for water, the discrepancy starts at MO=6) > http://144.92.39.89/xavier/mo/index.html > (for ethyne the very first MO is not symmetric) > http://144.92.39.89/xavier/mo/ethyne.html > > It seems to me that Jmol has problems with the d functions, > labeled in Gaussian as XX, YY, ZZ, XY, XZ, YZ (just a guess). > For water or ethyne this basis set is used with keywords like 631g(d) > For third or higher row elements, these d functions are always > included (with the exception of sto3g basis) > I tested this for Br: > http://144.92.39.89/xavier/mo/brf5.html > > I've been looking at the source code but I have no clue where the > problem is. > I would be willing to do it myself if I get a hint :) > Is there any standard/XML format for molecular properties such > as vibrations, molecular orbitals etc? This would save Jmol a lot > of trouble when reading formatted files. > > Thanks for your help > > > Xavier > >  > Xavier PratResina > Research Associate > Journal of Chemical Education and University of Wisconsin > 209 N. Brooks St. Madison, WI 537151116 > > Tel: 608 8901702 // Fax: 608 2627145 > email: xavier.prat.resina + gmail.com <http://gmail.com>;; skype: > xavierprat > http://x.prat.resina.googlepages.com > > > > >This SF.net email is sponsored by: Microsoft >Defy all challenges. Microsoft(R) Visual Studio 2008. >http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ > > > >_______________________________________________ >Jmoldevelopers mailing list >Jmoldevelopers@... >https://lists.sourceforge.net/lists/listinfo/jmoldevelopers > >  Robert M. Hanson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr If nature does not answer first what we want, it is better to take what answer we get.  Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 