Jmol users -- Dan Berger found two bugs in the Spartan file reader -- in
certain cases MOs were being read improperly (anions only, maybe?) and in
certain cases, for other reasons, some Sparton 08 files could not be read.
Dan, that's what I needed to see. OK, it's a Jmol bug -- It wasn't expecting
the file to contain only a subset of the orbitals -- there are 27 MOs in
reality; only 24 are included in the file for some reason. Jmol was
expecting 27, so it was looping the wrong number of times.
That's fixed for Jmol 11.7.26 and 11.6.17.
See http://chemapps.stolaf.edu/jmol/docs/examples-11/Jmol-11.zip
You should be all set.
Bob
On Wed, Feb 11, 2009 at 3:30 PM, Berger, Daniel <[email protected]>wrote:
> I'm attaching the output text file for pentadienyl_anion.spartan, along
> with the file itself.
>
>
>
>
>
> Daniel J. Berger
> [email protected]
> 419-358-3379
> www.bluffton.edu/~bergerd <http://www.bluffton.edu/%7Ebergerd>
>
> Professor of Chemistry
> Bluffton University 87
> One University Drive
> Bluffton, OH 45817-2104
>
> *From:* Robert Hanson [mailto:[email protected]]
> *Sent:* Wednesday, February 11, 2009 4:23 PM
>
> *To:* Berger, Daniel
> *Subject:* Re: Another Spartan glitch
>
>
>
> I'm guessing Spartan recalculates the values. Say, what does Spartan say
> for the energies of the top five highest-energy MOs in that
> pentadienyl_anion?
>
> On Wed, Feb 11, 2009 at 3:20 PM, Robert Hanson <[email protected]> wrote:
>
> Oh, yes, right. I can't quite see why they would be dropping lines, but it
> sure looks that way. This file is missing the last three numbers for the
> energies of the orbitals. So Jmol is reading numbers three off from where it
> needs to be. There's absolutely no fix, of course, from this end. It's just
> one huge block of numbers.
>
> Bob
>
>
>
> On Wed, Feb 11, 2009 at 2:27 PM, Berger, Daniel <[email protected]>
> wrote:
>
> Could be, but if so, it's Spartan that's doing it.
>
>
>
> Daniel J. Berger that
> [email protected]
> 419-358-3379
> www.bluffton.edu/~bergerd <http://www.bluffton.edu/%7Ebergerd>
>
> Professor of Chemistry
> Bluffton University 87
> One University Drive
> Bluffton, OH 45817-2104
>
> *From:* Robert Hanson [mailto:[email protected]]
> *Sent:* Wednesday, February 11, 2009 3:06 PM
>
>
> *To:* Berger, Daniel
> *Subject:* Re: Another Spartan glitch
>
>
>
> I'm convinced the Spartan files are corrupted.
>
> On Wed, Feb 11, 2009 at 1:48 PM, Robert Hanson <[email protected]> wrote:
>
> Is this happening only with certain files? Can you check with some simpler
> systems? -- water, methanol, benzene, for example.
>
>
>
> On Wed, Feb 11, 2009 at 1:20 PM, Berger, Daniel <[email protected]>
> wrote:
>
> Spartan and Jmol are not agreeing on orbital coefficients even in files
> that read OK. I'm attaching an image of the HOMO (Spartan-generated) and the
> file that it was generated from; paging through the orbitals in Jmol, I
> don't find anything that looks like the HOMO of pentadienyl anion.
>
>
>
> I'm also attaching a screen capture of MO #14 from both pentadienyl cation
> and anion, AM1 calculations in Spartan '08, rendered by Jmol.
>
>
>
> Daniel J. Berger
> [email protected]
> 419-358-3379
> www.bluffton.edu/~bergerd <http://www.bluffton.edu/%7Ebergerd>
>
> Professor of Chemistry
> Bluffton University 87
> One University Drive
> Bluffton, OH 45817-2104
>
> *From:* Robert Hanson [mailto:[email protected]]
>
> *Sent:* Wednesday, February 11, 2009 11:56 AM
> *To:* Berger, Daniel
> *Subject:* Re: Another Spartan glitch
>
>
>
> Sorry you have to be the one to find the problems, Dan, but I sure do
> appreciate your time. In this case Jmol is reading the file just fine, but
> as far as I can tell Spartan did not write the proper information for the
> wave function coefficients. Looks to me like the output is missing four
> lines. I'll pass that file on to my connection at WaveFunction and ask him
> about it. What EXACT version of Spartan are you using?
>
> Bob
>
> On Wed, Feb 11, 2009 at 10:22 AM, Berger, Daniel <[email protected]>
> wrote:
>
> I find that ab initio calculations aren't read properly by Jmol.
>
> Allyl_anion.spartan is a 3-21G optimized file, and gives a "file reading
> error."
> Allyl_anion1.spartan is AM1-optimized, and works fine.
> Allyl_anion_pm3.spartan is PM3-optimized, and works fine.
>
> Also, if I do an ab inito optimization starting with a semi-empirical
> optimization, I get an error.
>
> I appreciate how quickly you addressed the previous problem, and this is
> not terribly urgent, but I thought you ought to know.
>
> Daniel J. Berger
> [email protected]
> 419-358-3379
> www.bluffton.edu/~bergerd <http://www.bluffton.edu/%7Ebergerd>
>
> Professor of Chemistry
> Bluffton University 87
> One University Drive
> Bluffton, OH 45817-2104
>
>
>
>
> --
> Robert M. Hanson
> Professor of Chemistry
> St. Olaf College
> 1520 St. Olaf Ave.
> Northfield, MN 55057
> http://www.stolaf.edu/people/hansonr
> phone: 507-786-3107
>
>
> 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
>
>
>
>
> --
> Robert M. Hanson
> Professor of Chemistry
> St. Olaf College
> 1520 St. Olaf Ave.
> Northfield, MN 55057
> http://www.stolaf.edu/people/hansonr
> phone: 507-786-3107
>
>
> 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
>
>
>
>
> --
> Robert M. Hanson
> Professor of Chemistry
> St. Olaf College
> 1520 St. Olaf Ave.
> Northfield, MN 55057
> http://www.stolaf.edu/people/hansonr
> phone: 507-786-3107
>
>
> 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
>
>
>
>
> --
> Robert M. Hanson
> Professor of Chemistry
> St. Olaf College
> 1520 St. Olaf Ave.
> Northfield, MN 55057
> http://www.stolaf.edu/people/hansonr
> phone: 507-786-3107
>
>
> 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
>
>
>
>
> --
> Robert M. Hanson
> Professor of Chemistry
> St. Olaf College
> 1520 St. Olaf Ave.
> Northfield, MN 55057
> http://www.stolaf.edu/people/hansonr
> phone: 507-786-3107
>
>
> 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
>
--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107
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
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