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 <hans...@stolaf.edu> wrote:
> working too fast.... that works now.
>
>
> On Thu, Apr 16, 2009 at 2:55 PM, Xavier Prat-Resina
> <xav...@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 <hans...@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 <
>>> xav...@chem.wisc.edu> wrote:
>>>
>>>> That looks good.
>>>> Thanks Bob!
>>>>
>>>> Xavier
>>>>
>>>> On Thu, Apr 16, 2009 at 9:22 AM, Robert Hanson <hans...@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 <hans...@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 <
>>>>>> xav...@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
>>>>>>> <hans...@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 <
>>>>>>>> xav...@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 <hans...@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
>>>>>>>>>>
>>>>>>>>>> --
>>>>>>>>>> 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
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> ------------------------------------------------------------------------------
>>>>>>>>>> This SF.net email is sponsored by:
>>>>>>>>>> High Quality Requirements in a Collaborative Environment.
>>>>>>>>>> Download a free trial of Rational Requirements Composer Now!
>>>>>>>>>> http://p.sf.net/sfu/www-ibm-com
>>>>>>>>>> _______________________________________________
>>>>>>>>>> Jmol-users mailing list
>>>>>>>>>> Jmol-users@lists.sourceforge.net
>>>>>>>>>> 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
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> ------------------------------------------------------------------------------
>>>>>>>>> This SF.net email is sponsored by:
>>>>>>>>> High Quality Requirements in a Collaborative Environment.
>>>>>>>>> Download a free trial of Rational Requirements Composer Now!
>>>>>>>>> http://p.sf.net/sfu/www-ibm-com
>>>>>>>>> _______________________________________________
>>>>>>>>> Jmol-users mailing list
>>>>>>>>> Jmol-users@lists.sourceforge.net
>>>>>>>>> https://lists.sourceforge.net/lists/listinfo/jmol-users
>>>>>>>>>
>>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> --
>>>>>>>> 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
>>>>>>>>
>>>>>>>>
>>>>>>>> ------------------------------------------------------------------------------
>>>>>>>> This SF.net email is sponsored by:
>>>>>>>> High Quality Requirements in a Collaborative Environment.
>>>>>>>> Download a free trial of Rational Requirements Composer Now!
>>>>>>>> http://p.sf.net/sfu/www-ibm-com
>>>>>>>> _______________________________________________
>>>>>>>> Jmol-users mailing list
>>>>>>>> Jmol-users@lists.sourceforge.net
>>>>>>>> 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
>>>>>>>
>>>>>>>
>>>>>>> ------------------------------------------------------------------------------
>>>>>>> This SF.net email is sponsored by:
>>>>>>> High Quality Requirements in a Collaborative Environment.
>>>>>>> Download a free trial of Rational Requirements Composer Now!
>>>>>>> http://p.sf.net/sfu/www-ibm-com
>>>>>>> _______________________________________________
>>>>>>> Jmol-users mailing list
>>>>>>> Jmol-users@lists.sourceforge.net
>>>>>>> https://lists.sourceforge.net/lists/listinfo/jmol-users
>>>>>>>
>>>>>>>
>>>>>>
>>>>>>
>>>>>> --
>>>>>> 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
>>>>>
>>>>>
>>>>> ------------------------------------------------------------------------------
>>>>> 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
>>>>>
>>>>> _______________________________________________
>>>>> Jmol-users mailing list
>>>>> Jmol-users@lists.sourceforge.net
>>>>> 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
>>>>
>>>>
>>>> ------------------------------------------------------------------------------
>>>> 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
>>>> _______________________________________________
>>>> Jmol-users mailing list
>>>> Jmol-users@lists.sourceforge.net
>>>> https://lists.sourceforge.net/lists/listinfo/jmol-users
>>>>
>>>>
>>>
>>>
>>> --
>>> 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
>>> _______________________________________________
>>> Jmol-users mailing list
>>> Jmol-users@lists.sourceforge.net
>>> 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
>>
>>
>> ------------------------------------------------------------------------------
>> 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
>> _______________________________________________
>> Jmol-users mailing list
>> Jmol-users@lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/jmol-users
>>
>>
>
>
> --
> 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
> _______________________________________________
> Jmol-users mailing list
> Jmol-users@lists.sourceforge.net
> 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
------------------------------------------------------------------------------
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
developing skills, take BlackBerry mobile applications to market and stay
ahead of the curve. Join us from November 9 - 12, 2009. Register now!
http://p.sf.net/sfu/devconference
_______________________________________________
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users
