#392 mo's of a single atom

Graphics (55)


My real plan at one point in time is to have Jmol show some fake hybrid orbitals for single atoms. (This is why I wrote earlier about the cube file and jvxl file problems/bugs I found).

Now I decided that I should be able to do this by modifying coefficients in a Spartan.spartan file and pretend that Spartan calculated the hybrids (this is how I did it earlier: modify coefficients, calculate surfaces and do screen captures). Then I would like to use the mo xx command to have Jmol show the hybrid orbitals.

To my surprise, I don't see any orbital when I do that for a single atom structure. If I calculate H2O, it works, but not a single atom.
Jmol knows that there are 9 orbitals in the file (since if I ask for mo 12, it tells me an index from 1 to 9 is required). I tried it with C and that worked (for mo's 1-4 of course), but not Fe.

Any idea why?

Just in case, I'll attach the Fe.spartan file.


  • Rene Kanters

    Rene Kanters - 2007-03-26

    The Fe.spartan file that does not show mo's

  • Rene Kanters

    Rene Kanters - 2007-03-26

    Logged In: YES
    Originator: YES

    File Added: C.spartan

  • Rene Kanters

    Rene Kanters - 2007-03-26

    the C.spartan file that does work...

  • Bob Hanson

    Bob Hanson - 2007-06-03

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    Jmol cannot display MOs for calculations using a 5D basis set. (Standard is 6D.) However, the Spartan smol reader was not indicating that the set was 5D, so an exception was being thrown when it came time to do the calculation. (There were too few coefficients.) If you look on your Java console, you will see "Error in MO Calculation" displayed.

    I have made changes to 11.1.47 to handle this better; the Java Console will now read in this case:

    QuantumCalculation.checkCalculationType: can't read 5D basis sets yet: PM3D 1 5D shells -- exit

    At some future date, Jmol might be able to read a 5D basis, but for now, if it is at all possible, try a different basis for the calculation.


  • Bob Hanson

    Bob Hanson - 2007-06-03
    • status: open --> closed-later

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