Orbital movie

I played around a little bit with visualization of charge transfer dynamics. And I think it looks kind of cool. The video is related to the one shown here (the background is described here and in this paper). But now I am directly plotting the singly occupied orbital to give a more direct impression of what happens. To represent the surface hopping dynamics, I am changing the color of this orbital to indicate when the system is in the excited state.

You can notice that there are some discontinuities when the system changes between the states. This is because after passing through the crossing region the system is in a coherent superposition between transfer and no-transfer (I think). And the dynamics samples one of these options, and switches between them by stochastic hoppings. An important point is that in many cases it is not possible to average the potential, which would lead to Ehrenfest dynamics. But you really have to consider the wave packet as two distinct entities. Eventually the wave function "collapses" and the charge is clearly localized on one side. In this formalism this is actually realized through an ad-hoc decoherence correction.

This was a dynamics simulation at the state averaged MCSCF level, performed with Newton-X coupled to Columbus (with its new highly efficient SA-MCSCF gradients). I saved the Molden files with orbitals from the dynamics and plotted these with Jmol. For Jmol I used a long script looking like this, containing the commands for every frame:

load DEBUG/HYBR.0.5000/JOBEX_1.columbus/MOLDEN/molden_no_mc.drt1.st01.sp
background white
mo fill
mo cutoff 0.03
mo titleformat ""
mo 24
rotate -z
rotate -z
mo color red blue
write image png "frames/frame000.50.png"

load DEBUG/HYBR.1.0000/JOBEX_1.columbus/MOLDEN/molden_no_mc.drt1.st01.sp
background white
mo fill
mo cutoff 0.03
mo titleformat ""
mo 24
rotate -z
rotate -z
mo color red blue
write image png "frames/frame001.00.png"
...

And this script was in turn created with a python script, since I do not know how to program in Jmol itself. In the jmol console all I had to do was setting up the frame and executing

script movie.jmol

Open Access Journals

In response to that post, a quick comment about open access journals. I do not think they are the solution to everything but I think it is good to have some competition on the publication market. And not just always the same big players, like Elsevier, Springer, ACS.

Elsevier has apparently recently been criticized.

Aside from that I do not like the fact that I seem to publish everything for the American Chemical Society. Not only that my English girlfriend frowns everytime I write "neighbor" or "analyze". But I am appalled by their disgracefully unprofessional "exclusive invitation letter" everyone of us gets about once every month (I don't understand why they think it makes sense to do that).

I do think that the big publication companies play an important role in science. And they surely have the know-how and infrastructure to produce quality publications. But just as I sometimes like to buy fruit at the local market, rather than the big super market, I think it makes sense to consider alternative journals as part of a healthy science world. And in fact if I see PLoS publications or arXiv links in someone's publication list, I already think of that person as dynamic and open-minded.