Using Avogadro for NWCHEM output

Hello all. As the title suggests, I have been trying to figure out how to
use Avogadro to analyze my output from NWCHEM. In principle, outputting a
.cube file using the commands
dplot
TITLE HOMO
vectors oxygen_dimer.movecs
LimitXYZ
-1.0 1.0 50
-1.0 1.0 50
-1.0 1.0 50
spin total
orbitals view; 1;6
gaussian
output lumo.cube
end

task dft energy
task dplot

should work, but when I import the file it only draws the ball and stick and
doesn’t give the options for viewing orbitals (and a few other features for
that matter) as seen in the video
on http://blog.cryos.net/categories/15-Avogadro. Am I doing something wrong
with my NWCHEM output? Is the problem with my version of Avogadro? Am I just
a noob?

Thanks for any help you can give me.

On Sep 13, 2010, at 8:46 PM, Wilhelm Mainville wrote:

should work, but when I import the file it only draws the ball and stick and doesn’t give the options for viewing orbitals (and a few other features for that matter) as seen in the video
on http://blog.cryos.net/categories/15-Avogadro. Am I doing something wrong with my NWCHEM output? Is the problem with my version of Avogadro? Am I just a noob?

No, you’re not doing anything wrong. I greatly need to find time to make up a table for the wiki indicating which formats have support for MO visualization. At the moment, it’s:

  • Gaussian FCHK
  • Q-Chem FCHK
  • MOPAC
  • Molpro

And in the development code, I have GAMESS-US, GAMESS-UK, and Molden support. If you’d be willing to forward me a few NWChem output files with orbital coefficients, etc., I’ll take a look at parsing them for 1.1.

Best regards,
-Geoff

Hmmm…
This suggests that there may be future support for cfour, which produces
molden files. It would be nice to vizualize orbital and vibrational
modes from this code using avogadro.
Steve

On 09/14/2010 04:37 PM, Geoffrey Hutchison wrote:

On Sep 13, 2010, at 8:46 PM, Wilhelm Mainville wrote:

should work, but when I import the file it only draws the ball and stick and doesn’t give the options for viewing orbitals (and a few other features for that matter) as seen in the video
on http://blog.cryos.net/categories/15-Avogadro. Am I doing something wrong with my NWCHEM output? Is the problem with my version of Avogadro? Am I just a noob?

No, you’re not doing anything wrong. I greatly need to find time to make up a table for the wiki indicating which formats have support for MO visualization. At the moment, it’s:

  • Gaussian FCHK
  • Q-Chem FCHK
  • MOPAC
  • Molpro

And in the development code, I have GAMESS-US, GAMESS-UK, and Molden support. If you’d be willing to forward me a few NWChem output files with orbital coefficients, etc., I’ll take a look at parsing them for 1.1.

Best regards,
-Geoff

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molden files. It would be nice to vizualize orbital and vibrational
modes from this code using avogadro.

Yes, anything which can produce molden files would be supported – which is why I thought it was useful to add to Avogadro.

Cheers,
-Geoff