sorry -- said GAMESS, meant GAUSSIAN. Well, Jmol takes the orbitals as
they come. So use GenNBO files if you want the that sort of NBO order (as
far as I know we don't sort them by energy, but I can't say for sure), and
use Gaussian if you want standard energy-order.
Bob
On Mon, Feb 20, 2012 at 1:36 AM, E.P.A. Couzijn <[email protected]>wrote:
> Dear Jörg,
>
> Actually, I only know about stand-alone NBO5 vs NBO 3.1 as interfaced with
> Gaussian, but there might be similarities with Gamess.
>
> - The data in the FILE31 -- FILE41 files is sorted as numbered in the NBO
> output.
> For the NBOs first all bonds are given, followed by all core orbitals,
> all lone pairs, then all Rydberg states, and finally all antibonds.
> Likewise, NAOs ar sorted by atom number, then angular momentum, then
> core--valence--Rydberg.
> Thus, it should be very straightforward to find the number of any
> orbital that you want plotted.
>
> - In Gaussian, with the option SaveNBOs, all NBOs are reordered by their
> energy for storage in the checkpoint file.
> These energies are listed in the NBO output under "Natural Bond Orbitals
> (Summary):".
> Furthermore, Gaussian prints the new order (by rows of 10) and the
> labels of the NBOs (CR/BD/LP/BD*/RY*).
> Thus, one needs to do some counting to get the correct orbital number...
>
> Does the Gamess output give any hint of such a reordering?
> If you visualize the first few, do those correspond to core orbitals on
> the heaviest/most electronegative atoms? That would suggest that they are
> sorted by energy.
>
> Kind regards,
>
> Dr. Erik P.A. Couzijn
> Laboratorium für Organische Chemie
> ETH Zürich HCI G 204
> CH-8093 Zürich
> http://couzijn.125mb.com/<https://mail.ethz.ch/owa/redir.aspx?C=e6453ff64ac44c37ad9d582b9fea7ff0&URL=http%3a%2f%2fcouzijn.125mb.com%2f>
>
> ------------------------------
> *From:* Jörg Saßmannshausen <[email protected]>
> *To:* [email protected]
> *Sent:* Saturday, February 18, 2012 11:33 PM
> *Subject:* [Jmol-users] MO numbers in NBO outputfile different from
> logfile?
>
> Dear all,
>
> I was playing around with a relative 'new' feature of JMOL. I have found
> out
> tonight whilst I was struggling to get some NBO orbitals drawn that JMOL
> now
> can load the output files of the NBO5 program directly instead of loading
> the
> log-file of the calculation. That is great!
>
> However, I am a bit puzzled. If I am loading the log file of a GAMESS
> calculation and I issue:
> $ frame 1.2; isosurface t2 cutoff 0.05 mo 121 fill translucent 0.5
>
> I get the correct orbital. So far, so good.
> However, if I am loading the nbo.31 file and issue the same command, I get
> a
> complete different orbital drawn. Somehow there seems to be no correlation
> between the orbital numbers in the log file and the ones in the nbo.31 -
> nbo.41
> files. Is that the way one would expect it? How would I then find out
> which
> orbital number I need to supply when I want to use the nbo.31 - nbo.41
> files?
>
> All the best from London!
>
> Jörg
>
>
> --
> *************************************************************
> Jörg Saßmannshausen
> University College London
> Department of Chemistry
> Gordon Street
> London
> WC1H 0AJ
>
> email: [email protected]
> web: http://sassy.formativ.net
>
> Please avoid sending me Word or PowerPoint attachments.
> See http://www.gnu.org/philosophy/no-word-attachments.html
>
>
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