load h2so4_nbo.log filter "NBOCharges MO"
model 2;label %P;mo 10

On Tue, Oct 27, 2009 at 6:38 PM, Xavier Prat-Resina <xavier@chem.wisc.edu> wrote:
Thanks for the fast response Bob.

I meant to have access to the NBO charges at the same time as the regular MOs,
not the Natural Bond Orbitals.
I'm using the same Gaussian file that contains a lot of information to display
MOs, MEPs...etc and I prefer NBO charges rather than Mulliken.

If I FILTER "NBOCharges NBO" I lose the MOs and the NBO charges are in frame 2 of
the Gaussian file (in frame 1 charges are 0).
On the other hand if I try something like FILTER "NBOCharges !NBO"
I can display the MOs on frame 2 but I lose the NBOCharges and only Mulliken
seem to be available.

I've been testing this in the same h2so4_nbo.log file that it's available in the repository.
http://xpr.chemeddl.org/~xavier/nbo/test2.html
Thanks for the help!!

Xavier

On Tue, Oct 27, 2009 at 5:24 PM, Robert Hanson <hansonr@stolaf.edu> wrote:
That doesn't surprise me. Try FILTER "NBOCharges NBO"

but also send me a file.

On Tue, Oct 27, 2009 at 4:58 PM, Xavier Prat-Resina <xavier@chem.wisc.edu> wrote:
Hi,

when I apply the NBOCharges filter

load myfile.out FILTER "NBOCharges"

it seems that the molecular orbitals are no longer available.
Is that what is supposed to happen?
Thanks

Xavier


On Thu, Apr 16, 2009 at 3:26 PM, Robert Hanson <hansonr@stolaf.edu> wrote:
working too fast.... that works now.


On Thu, Apr 16, 2009 at 2:55 PM, Xavier Prat-Resina <xavier@chem.wisc.edu> wrote:
Bob,
I don't know why, but with the new changes (rev. 10811) I can only load the gaussian file with
the NBO filter, otherwise I get a java.lang.NullPointerException
Is it just me?

Xavier


On Thu, Apr 16, 2009 at 1:01 PM, Robert Hanson <hansonr@stolaf.edu> wrote:
just made some more changes -- it will have to be 0 charges for frame 1 and NBO for frame 2, with no Mulliken.

Bob



On Thu, Apr 16, 2009 at 10:05 AM, Xavier Prat-Resina <xavier@chem.wisc.edu> wrote:
That looks good.
Thanks Bob!

Xavier

On Thu, Apr 16, 2009 at 9:22 AM, Robert Hanson <hansonr@stolaf.edu> wrote:
Xavier, take a look now. The charges were beta-spin charges. I've corrected that, and yes, I think it will be nice to have Mulliken charges in frame 1 and NBO charges in frame 2. Let's leave it that way. Interesting comparison.



On Thu, Apr 16, 2009 at 8:54 AM, Robert Hanson <hansonr@stolaf.edu> wrote:
Xavier, can you put together an output that involves dummy atoms? I see this in the partial charge code:

      // first skip over the dummy atoms

Will that be important with the NBO charges?

Bob



On Wed, Apr 15, 2009 at 10:13 AM, Xavier Prat-Resina <xavier@chem.wisc.edu> wrote:
Wonderful! Thanks!
NBO charges describe the electronic density of the molecule much better than mulliken charges.

I noticed though that in Gaussian the filter "NBOcharges" only works for frame 1. When I switch to frame 2 to view the
NBO orbitals it shows the mulliken charges again. Is that the expected behavior?

Xavier


On Wed, Apr 15, 2009 at 9:00 AM, Robert Hanson <hansonr@stolaf.edu> wrote:
done.

load xxx.xxx FILTER "NBOcharges"

or, with the NBOs:

load xxx.xxx FILTER "NBO;NBOcharges"



On Mon, Apr 13, 2009 at 10:40 AM, Xavier Prat-Resina <xavier@chem.wisc.edu> wrote:
Bob,

when applying the NBO filter, would it be possible to display NBO charges instead of mulliken?

                                     Natural Population
|             Natural    ---------------------------------------------
   Atom No    Charge        Core      Valence    Rydberg      Total
  --------------------------------------------------------------------
     S  1    2.57261      9.99930     3.21446    0.21363    13.42739



Xavier


On Sat, Apr 11, 2009 at 7:40 PM, Robert Hanson <hansonr@stolaf.edu> wrote:
Jmol users --

Jmol now displays NBOs in GAMESS and Gaussian if the NBO "AONBO" option is included.

See examples at http://chemapps.stolaf.edu/jmol/docs/examples-11/new.htm
 
If people can find me examples of output for QChem, I can try them as well. The version at that site might even work with QChem already; I don't know.

Bob

--
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St. Olaf College
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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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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 ( ) chem.wisc.edu ; skype: xavierprat
http://x.prat.resina.googlepages.com

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--
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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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 ( ) chem.wisc.edu ; skype: xavierprat
http://x.prat.resina.googlepages.com

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--
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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around Java (TM) technology - register by April 22, and save
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--
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 ( ) chem.wisc.edu ; skype: xavierprat
http://x.prat.resina.googlepages.com

------------------------------------------------------------------------------
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_______________________________________________
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--
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

------------------------------------------------------------------------------
Stay on top of everything new and different, both inside and
around Java (TM) technology - register by April 22, and save
$200 on the JavaOne (SM) conference, June 2-5, 2009, San Francisco.
300 plus technical and hands-on sessions. Register today.
Use priority code J9JMT32. http://p.sf.net/sfu/p
_______________________________________________
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https://lists.sourceforge.net/lists/listinfo/jmol-users




--
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 ( ) chem.wisc.edu ; skype: xavierprat
http://x.prat.resina.googlepages.com

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--
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

------------------------------------------------------------------------------
Come build with us! The BlackBerry(R) Developer Conference in SF, CA
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--
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 ( ) chem.wisc.edu ; skype: xavierprat
http://x.prat.resina.googlepages.com

------------------------------------------------------------------------------
Come build with us! The BlackBerry(R) Developer Conference in SF, CA
is the only developer event you need to attend this year. Jumpstart your
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_______________________________________________
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--
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