> Q: What are these atom vectors used for? What do they represent?
They can be used for many things. Particularly:
1) The normal mode calculations in many quantum chemistry packages
show the directions the atoms travel as one perturbs along that
normal mode. This has traditionally been represented in Jmol as a
vector starting at the atom center.
2) In classical trajectory simulations, the vectors can be used to
denote instantaneous velocities with appropriate scaling to the
fundamental velocity units being used in the simulation package.
Alternatively, one can calculate forces on the atoms and use the
vectors to denote the direction and magnitude of the force
instead of the instantaneous velocity.
3) In calculations involving models with point dipoles (as opposed
to point charges), the vectors can be used to store the directional
information for the dipoles.
> Q: For me, the name is confusingly similar to the other Vectors. Can you
> suggest a better name?
I'd suggest UnitVector, but the length doesn't have to be fixed.
> Q: How important are these atom vectors? Who uses them?
Very important. That's one of the prime diagnostics I use to test
trajectory code. I'd imagine that people who worry about normal modes
also find the vectors an important visualization tool.
> - There seem to be several "fudge factors" related to the screen
> representation of these atoms. Is the magnitude of them really not that
> important?
Probably not. Ideally the vectors would be drawn correctly, but there
were many fudge factors in the early versions of Jmol. I'm the guilty
party responsible for most of them.
> - I could only find one example of an Atom Vector in samples ...
> samples/cs2.xyz.
Look at the normal mode calculations in the Gaussian log files to see
more examples.
--Dan
P.S. It is great to see so much activity from the Jmol team!
--
***********************************************
J. Daniel Gezelter
Assistant Professor
Department of Chemistry and Biochemistry
251 Nieuwland Science Hall
University of Notre Dame
Notre Dame, IN 46556-5670
phone: +1 (574) 631-7595
fax: +1 (574) 631-6652
e-mail: [EMAIL PROTECTED]
web: http://www.nd.edu/~gezelter
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