iOpenShell » Technical questions » viewing NWCHE density/orbitals etc

viewing NWCHE density/orbitals etc

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Member
Registered: Jun 2010
Posts: 4
Hello all. Does anyone have any experience in viewing the more detailed output from NWCHEM? It's easy for Gaussian or GAMESS where the outputs themselves are inputs for molden or other programs, but for NWCHEM you have to specify in the input file exactly what sort of output you want for the orbitals etc and I can't figure out how to look at things.

Supposedly once you convert the .cube file you can look at it with gOpenMol, but so far it doesn't seem to be able to do what I want and is difficult to use. There are keywords that you can add in the input file to output the info needed by molden to view the orbitals, but when I try to do this the orbitals don't show up in the viewing menu.

Does anyone have any advice?

Thanks,
Wil
Member
Registered: Mar 2010
Posts: 40
Location: New York, NY
How about using Avogadro or VMD? I've been using these to visualize .cube files from Q-Chem, and these should be the same as those from NWChem.

Eric
Member
Registered: Jun 2010
Posts: 4
I've tried Avogadro, but when I import the .cube file I don't see the option of looking at the orbitals as seen in the video on the Avogadro website:
http://blog.cryos.net/categories/15-Avogadro

When I try to use the same .cube file in Molden I get essentially the same thing; it plots the ball and stick figures and knows the identity of the atoms, but all of the rest of the info in the .cube file doesn't seem to be a) in the file or b)readable. I'm not sure how to check on which it is or what to do if I'm somehow specifying the output incorrectly (it's taken straight from the manual).
Member
Registered: Mar 2010
Posts: 40
Location: New York, NY
Are you going to Extensions --> Create Surfaces... and then selecting the cube file under "Surface Type" and "Color By"? There are some options in the menu for the Surfaces display type once this is done, too.

I would check to see if you can get VMD to read the .cube files also. If this doesn't work, then it's possible that there is something wrong in the formatting of the file. A while back I remember not being able to open up a few .cube files and it turned out that there mistakenly were some blank lines between a few of the blocks of data in the file. http://local.wasp.uwa.edu.au/~pbourke/dataformats/cube/ seems to explain the basic formatting.

Hope this helps,
Eric

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iOpenShell » Technical questions » viewing NWCHE density/orbitals etc