Menu
▾
▴
Re: [Jmol-developers] Molecular Orbitals from Gaussian output
|
From: Bob H. <ha...@st...> - 2008-02-26 22:51:13
|
It's fixed and committed. Nico, please release 11.5.9 and 11.4.RC7. Thanks, Bob Xavier Prat-Resina wrote: > Alright, I understand the problem. > > When you mentioned the symmetry issue it reminded me of an old > discussion in the quantum chemistry community. > see the CCL link > http://www.ccl.net/chemistry/resources/messages/2003/12/12.006-dir/index.html > > Basically Gaussian adds an additional basis function which is not 'd' > but 's'. > (5d + 1s) > My understanding is that 10 4XX -0.00745 -0.00699 -0.01650 -0.01153 0.00145 11 4YY -0.00745 -0.00699 -0.01650 -0.01153 0.00145 12 4ZZ -0.00613 -0.00600 0.01480 0.02179 0.01193 13 4XY 0.00000 0.00000 0.00000 0.00000 0.00000 14 4XZ 0.00000 0.00000 0.00000 0.00000 0.00000 15 4YZ 0.00000 0.00000 0.00000 0.00000 0.00000 means cartesian 6D set; all 6 are D functions. Correct me if I'm wrong, but I don't see anything about S orbitals here. I think the second poster on that list is mistaken. > For a temporary solution users will have to specify 5D in the Gaussian > input. The calculation will contain just a bit smaller basis set in > comparison > with the default one, but at least it can be read by jmol: > I tested this in the previous examples, and now it works!! > http://144.92.39.89/xavier/mo/5d.html > Thanks Bob! > > Xavier > > On Tue, Feb 26, 2008 at 3:02 PM, Bob Hanson <ha...@st... > <mailto:ha...@st...>> wrote: > > OK, I'm pretty sure this is not a bug. First, I note that the STO-3G > orbitals are just fine. (right?) > > > Here's your problem, I think, with the 6-31G(d) set: > > There are 4 symmetry adapted basis functions of A1 symmetry. > There are 0 symmetry adapted basis functions of A2 symmetry. > There are 1 symmetry adapted basis functions of B1 symmetry. > There are 2 symmetry adapted basis functions of B2 symmetry. > > > Two-electron integral symmetry is turned on. > 19 basis functions, 36 primitive gaussians, 19 cartesian > basis > functions > 5 alpha electrons 5 beta electrons > > I think it's just a symmetry problem. Are there any other options you > know of that you can test in regard to orbital symmetry? > > That's not an excuse, just the fact that Jmol isn't set up for > recombining symmetry-adapted (or not adapted?) wavefunctions to > what you > might see with Gaussian itself. I'll need help from someone to explain > to me how that works. If someone wants to teach me how orbital > symmetry > is recorded in these files and how one transforms that information > back > into symmetric orbitals, I'll be happy to look at that. > > > Bob > > > Xavier Prat-Resina 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/examples-11/isosurface.htm > > when it loads "water-G03W.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 > 6-31g(d) > > For third or higher row elements, these d functions are always > > included (with the exception of sto-3g 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 Prat-Resina > > Research Associate > > Journal of Chemical Education and University of Wisconsin > > 209 N. Brooks St. Madison, WI 53715-1116 > > > > Tel: 608 8901702 // Fax: 608 2627145 > > e-mail: xavier.prat.resina + gmail.com <http://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/ > > > >------------------------------------------------------------------------ > > > >_______________________________________________ > >Jmol-developers mailing list > >Jmo...@li... > <mailto:Jmo...@li...> > >https://lists.sourceforge.net/lists/listinfo/jmol-developers > > > > > > > -- > 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 > > > > ------------------------------------------------------------------------- > 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/ > _______________________________________________ > Jmol-developers mailing list > Jmo...@li... > <mailto:Jmo...@li...> > https://lists.sourceforge.net/lists/listinfo/jmol-developers > > > > > -- > Xavier Prat-Resina > Research Associate > Journal of Chemical Education and University of Wisconsin > 209 N. Brooks St. Madison, WI 53715-1116 > > Tel: 608 8901702 // Fax: 608 2627145 > e-mail: 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/ > >------------------------------------------------------------------------ > >_______________________________________________ >Jmol-developers mailing list >Jmo...@li... >https://lists.sourceforge.net/lists/listinfo/jmol-developers > > -- 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 |