#175 Accept NBO PLOT format

open
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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  • Granger Hermitage

     
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  • Granger Hermitage

    zipx format to get under upload limit

     
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  • Bob Hanson

    Bob Hanson - 2010-03-23

    ok, I will look at that. Not sure that's exactly "easier"!

     
  • Bob Hanson

    Bob Hanson - 2010-03-23

    I can't decompress the 33 file. (gzip would work) -- you can send that to hansonr@stolaf.edu directly if you want.

    We can look into this as a long-term project. It would be a pretty big job that would need quite a bit more information to create a totally new reader for these. While I appreciate the fact that it adds capabilities that the ESS programs don't have, I would have to think hard about how to implement this properly considering the complexity of having all those files to worry about.

    OK, there are two possibilities. We do also read Spartan directories, so the idea of reading a directory or reading a zip file with included files is possible, but it relies on Jmol first reading ALL the files and then parsing the concatenated script. It's really not ideal with these big files. In principle that could be adapted a bit.

    Jmol does not use file extensions for identifying files, so it's a bit problematic to think about doing this just from a list of file names. For example, you can drag and drop into Jmol, but that doesn't work if you want a specific SET of files.

    By the way, where are the energies stored? Or doesn't that apply in the case of NBOs?

     
  • Bob Hanson

    Bob Hanson - 2010-03-23

    More thoughts. What do you think of using the OUT file as the file that is indicated (or dragged) to read. Then, if the information such as AO Basis is missing, because this is NOT part of an ESS output, then we have Jmol automatically look for and load the .31 file. And if certain FILTER options are given (which we would agree upon), then it will also read another .NN file. Could be something like

    load "xxx.nbo" FILTER "PNBO"

    load "xxx.nbo" FILTER "PNLMO"

    That could work. The reader would know then to go grab the data in whichever file is appropriate.

    Bob

     
  • Granger Hermitage

    It would be okay to load one file in the range .32 to .40 at a time
    For files .32 to .40 as .yy :
    load "molname.yy"
    this load could get the molname.31 and molname.46 behind the scenes.
    A visualization session most often (perhaps always) compares and contrasts orbitals of the same type e.g. orbitals appearing in just one type in the range .32 .. .40

    Files .32 to .40 are likely to be of the same format, so code for one should work for all. A visualization tool isn't aware of the difference in meaning of orbital type.

     
  • Bob Hanson

    Bob Hanson - 2010-03-23

    OK. We could do that. Where is the description of the .31 file?

    Bob

     
  • Bob Hanson

    Bob Hanson - 2010-03-23

    OK, Jmol is now reading the .nbo file and .31-.41 files. At least, provisionally. No orbitals yet, because I don't have any idea what the format of those files is.

    I'll need the .nbo output file for 14a, please. Also, if this comes from an ESS calc, can you please send me the ESS output file as well, showing the AO basis functions used? This will allow me to verify the file reading.

    Thanks

    Thanks.

     
  • Granger Hermitage

    Gaussian 03 output

     
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  • Granger Hermitage

    GenNBO 5 output

     
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  • Granger Hermitage

    14_a_b3lyp.nbo.zip (GenNBO output) and 14_a.log.zip (Gaussian 03 output) uploaded, 14_a_b3lyp.33.zip sent.

     
  • Bob Hanson

    Bob Hanson - 2010-03-23

    Jmol 11.9.36_dev can provisionally read .nbo files provided 0.31 file is present, 0.31 file for structure only, and 0.32-0.41 files provided 0.31 and 0.46 are present in the directory. See http://chemapps.stolaf.edu/jmol/docs/examples-11/Jmol-11.zip

     
  • Bob Hanson

    Bob Hanson - 2010-03-23

    14_a.log needs basis functions listed, please.

     
  • Bob Hanson

    Bob Hanson - 2010-03-23

    Question: The .46 file has names for only AO, NAO, NHO, and NBO orbitals. Then (a) there are no names for MO orbitals, and (b) the names of PXXX are the same as XXX?

    Names do seem to match pretty well with depictions...

    Bob

     
  • Granger Hermitage

    (a) I would just give the MOs a number as they are read in and use that number as a label.
    (b) Yes, give the PXXX the same names as XXX.

    For a 14_a.log basis functions listing, do you want an option switched on in the ESS parameter list or the NBO parameter list?

     
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