#175 Accept NBO PLOT format

open
Bob Hanson
5
2010-11-22
2010-03-23
No

Actually, there is a neater way to visualize Natural Bond Orbitals than I asked for in feature request 2974999.
When PLOT (it has no subparameters) is specified in the NBO parameter list, all files needed for visualization are produced. The NBO parameter list ($NBO ... $END) appears in the electronic structure system input if NBO is embedded in the ESS, and appears in the .47 input file to GenNBO if NBO is being run standalone. $NBO AONBO=P $END is not necessary, for $NBO PLOT $END will output what is needed for visualization of all natural orbital types not just NBO in AO basis. Indeed, PNBO (prenormalized NBO) may be more useful for visualization of overlaps than NBO. PLOT causes the generation of these file types:
molname.31 AO
molname.32 PNAO
molname.33 NAO
molname.34 PNHO
molname.35 NHO
molname.36 PNBO
molname.37 NBO
molname.38 PNLMO
molname.39 NLMO
molname.40 MO
molname.41 AO density matrix
molname.46 Basis label file

Regardless of what ESS NBO 5 is imbedded in or what ESS GenNBO 5 derives its input from the format of these files is unchanged, so this is a completely uniform input for natural orbital visualization. Also, these inputs make a visualization tool fully functional for all natural orbital types. Also, all these types of natural orbitals (including PNBO) are available in a machine oriented format rather than having to be picked out of various places in a somewhat more human oriented format of an ESS log or output file or nbo output file (.nbo). Also, the formats .31 .. .41, .46 could be expected to be more stable across NBO updates than that of log files that might see modification in the interests of human readability.

The .31 file must be present for visualization as it contains such good things as atomic number. The different types of natural orbitals are useful depending on what is being investigated. The thing to do would be to supply a directoryname/molname and let all the .31-.41,.46 be loaded with a single command, then specify what basis you wanted to be working in at that moment.

I will attach a zipped sample file of each file type, though the .33 file might have to be compressed with another method, say zipx, to get under the upload limit.

I can imagine Jmol quite rapidly becoming the best tool to visualize natural orbitals.

Discussion

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  • Bob Hanson
    Bob Hanson
    2010-03-24

    The standard default is just the number -- that's what we have here. I'll stick with that. I need the gfprint option in Gaussian so I can compare the bases.

    So I'm pretty sure this is working. Final tests, with Gaussian to compare, would be:

    a calculation with spherical D orbitals.
    a calculation involving chlorine.
    a calculation with cartesian D orbitals
    a calculation with F orbitals.
    a calculation with S and P but not SP atomic orbitals
    an open-shell calculation of a radical
    a calculation having both alpha and beta orbitals (and what you want to do about that)

    That should just about do it.

    You can run tests yourself using the version found in http://chemapps.stolaf.edu/jmol/docs/examples-11

    Only thing missing there is I just got .31 files showing the AOs.

    Bob

     
  • Unexpected end of file after line 2559:
    C 7- H89* C 7- H90* C 7- H78*
    for file D:/temp/1_a_mp2/1_a_mp2.36
    type NBO
    --
    load >> "D:temp\1_a_mp2\1_a_mp2.36"

    Same error for the .35 file.
    Uploading 1_a_mp2.31, 1_a_mp2.36, 1_a_mp2.46 now.

     
  •  
    Attachments
  •  
    Attachments
  •  
    Attachments
  • Gaussian 03 log with GFPrint

     
    Attachments
  • Gaussian 03 log with GFPrint on uploaded
    14_a_gfprint.log.zip
    (for 14_a_b3lyp)

     
  • Error reading file at line 525:
    NBO 198
    String index out of range: 2009
    for file D:/temp/14_a_b3lyp/14_a_b3lyp.35
    type NBO

    The PLOT output files are those already uploaded to the site.
    The error doesn't occur with the .36 file.
    The .35 file is reported as being type NBO, but should be type NHO.

     
  • Bob Hanson
    Bob Hanson
    2010-03-24

    working ok for me. I'll upload another version.

     
  • I am using Java 6 Update 18 here.

    The orbitals shown for .36, .37 files are simpler and more regular than the Natural Boind Orbitals I saw with GaussView 4.1.2 back when that worked here. Don't know if it a problem, might be the default contours are different and a particular level of contour shows the complexity. Could also be the extremely limited basis set I used to get a small and hence uploadable example.

     
  • Bob Hanson
    Bob Hanson
    2010-03-24

    sorry, still no go.

    Gaussian 03 log with GFPrint on uploaded
    14_a_gfprint.log.zip
    (for 14_a_b3lyp)

    does not contain information about NBOs. Expecting a line like:

    NBOs in the AO basis:

    AO 1 2 3 4 5 6 7 8
    ---------- ------- ------- ------- ------- ------- ------- ------- -------
    1. C 1 (s) -0.0399 -0.0455 -0.0439 -0.0439 0.0062 -0.0060 0.0000 -0.0013

     
  • I think you want AONBO=P in the NBO parameter list. I am not really expecting much different than appears in the .31 file, but I will run it and upload the output.

     
  • Bob Hanson
    Bob Hanson
    2010-03-24

    I think you want AONBO=P in the NBO parameter list. I am not really
    expecting much different than appears in the .31 file, but I will run it
    and upload the output.

    That sounds right. Key is that it is there so that I can compare how Jmol performs reading the Gaussian file (which I know is correct) with reading the GenNBO output. I could be putting coefficients or exponents in an incorrect order since I'm just guessing on the format of the .31 file. (If you have code for reading that, I'd love to see it!)

     
  • Bob Hanson
    Bob Hanson
    2010-03-24

    By the way, in case you hadn't noticed, it is really nice that we can drag the .XX files into Jmol and have instant access to the full range of orbitals there.

     
  • with AONBO=P

     
    Attachments
  • Uploaded 14_a_b3lyp.nbo.zip which has AONBO=P in the NBO parameter list.

     
  • Bob Hanson
    Bob Hanson
    2010-03-24

    good. That's what I needed. I'll experiment with appending to Gaussian output, since I have both the log file and the nbo file now. If you can generate more of these with the range of calculation I listed earlier, that would be great. A Gaussian file with associated nbo and .nn files would be perfect. I suggest doing a set of these, zipping them up into a single ZIP file and sending them to me via a service such as YouSendIt.

    Will get back to this later today.
    Bob

     
  • Bob Hanson
    Bob Hanson
    2010-03-25

    for each new file you add, also add a full Gaussian/NBO output please.

     
  • Bob Hanson
    Bob Hanson
    2010-03-25

    Jmol 11.9.36 will read all GenNBO files directly.

     
  • Nicolas
    Nicolas
    2010-11-22

    • assigned_to: nobody --> hansonr
     
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