Tuesday 18 October 2011

Orbitals in Jmol

Actually automatic plotting of orbitals in Jmol is even easier than in VMD, considering that Jmol can directly read the output of many major quantum chemical programs, or alternatively Molden format files.

The only thing is that Jmol does not have all of its functionality easily available over a menu, so you should always have the scripting manual ready and use the console inside the program. But then it is rather easy to use. And the advantage of script based input is that you can naturally automatize repetitive tasks. For visualizing orbitals it can look something like this (you can just copy this directly into the Jmol console):

background white
mo fill
mo cutoff 0.03

mo homo

At this point you would probably play with the perspective a little bit. Then you continue by saving this picture and all other pictures of orbitals you are interested in, e.g.

write image png "homo.png"
mo homo-1
write image png "homo1.png"
mo homo-2
write image png "homo2.png"
mo lumo
write image png "lumo.png"
mo lumo+1
write image png "lumo1.png"

And you have what you wanted.

Actually the new Jmol lets you do even more and you can make linear combinations. For example if we combine the HOMO (14bg) with the HOMO-1 (13au), we get an orbital, which is localized on one half of the molecule.

mo [1 183 1 182]

It is even possible to put up interactive models with Jmol. I used to do that, but then I lost my account on the server where I had this, and I did not want to set it up again. So nothing of that now ...

Edit: The functionality described here is available through the jmol_MOs.py script within the TheoDORE wavefunction analysis package.

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