Screenshot instructions:
Windows
Mac
Red Hat Linux
Ubuntu
Click URL instructions:
Rightclick on ad, choose "Copy Link", then paste here →
(This may not be possible with some types of ads)
From: Xavier PratResina <xavier@ch...>  20080226 20:20:30
Attachments:
Message as HTML

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; skype: xavierprat http://x.prat.resina.googlepages.com 
From: Bob Hanson <hansonr@st...>  20080226 20:32:17

Very much appreciate your finding that, Xavier. We did a lot of testing of that, but it's still possible that there is a bug there. I will definitely look into it immediately. By the way, you can deliver those cube files as JVXL format surfaces with very little files space if you want to. http://chemapps.stolaf.edu/jmol/docs/misc/JVXLformat.pdf 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 
From: Bob Hanson <hansonr@st...>  20080226 21:04:57

OK, I'm pretty sure this is not a bug. First, I note that the STO3G orbitals are just fine. (right?) Here's your problem, I think, with the 631G(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. Twoelectron 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 symmetryadapted (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 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 
From: Xavier PratResina <xavier@ch...>  20080226 21:50:30
Attachments:
Message as HTML

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/2003/12/12.006dir/index.html Basically Gaussian adds an additional basis function which is not 'd' but 's'. (5d + 1s) 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 <hansonr@...> wrote: > OK, I'm pretty sure this is not a bug. First, I note that the STO3G > orbitals are just fine. (right?) > > Here's your problem, I think, with the 631G(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. > > > Twoelectron 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 symmetryadapted (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 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 > > > >  > 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 > >  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; skype: xavierprat http://x.prat.resina.googlepages.com 
From: Bob Hanson <hansonr@st...>  20080226 22:51:13

It's fixed and committed. Nico, please release 11.5.9 and 11.4.RC7. Thanks, Bob Xavier PratResina 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/2003/12/12.006dir/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 <hansonr@... > <mailto:hansonr@...>> wrote: > > OK, I'm pretty sure this is not a bug. First, I note that the STO3G > orbitals are just fine. (right?) > > > Here's your problem, I think, with the 631G(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. > > > Twoelectron 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 symmetryadapted (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 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>; > <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@... > <mailto: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 > > > >  > 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@... > <mailto:Jmoldevelopers@...> > https://lists.sourceforge.net/lists/listinfo/jmoldevelopers > > > > >  > 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 
From: Bob Hanson <hansonr@st...>  20080226 22:16:29

OK, I found it. It is a bug. Introduced when we added spherical (5D) sets. The 7F functions present here fool Jmol into thinking that these are spherical sets. So when we added F orbitals, we didn't realize that the 7F might be combined with a 6D instead of a 5D. I can fix this.... Thank you ever so much, Xavier! 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 
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 
Sign up for the SourceForge newsletter:
No, thanks