On Saturday 14 February 2004 18:40, Miguel Howard wrote:
> >> How and where may I store these information ? :
> >> - Vibrations associated with a molecule.
> >
> > This has not been defined yet.
> >
> > Miguel, have you given thoughts to this?
>
> So far I have not given it much thought. But clearly I need to do so.
>
> At this point, I think that I would rather work on vibrations than on
> animations.
How so? Animations are actually much easier... just a sequence of models it
should display as a time related sequence... But imlementing vibrations is a
bit more challenging and rewarding...
> I will start going back and reading the b6 source code.
Ok, just done that too. (never actually done that before...) Here's what is
happening:
Assuming things are identical to Gaussian98 files for other formats,
vibrations are stored as force vectors acting on atoms, so a double[3] for
each atom. Associated with this, normally, is a frequency, often in cm-1.
Jmol b6 then 'animates' a vibration by creating an animation of X frames,
depending on the frames per second for the vibration. It simply transforms
the force acting on the atom into a displacements using a simple sinus
function (see jmol.app.Vibrate.createVibration)
Once a new animation is created, viewing it is just starting a thread that
views the newly created animation.
Jmol b6 uses one Vibration class associated with one complete molecule,
defining the displacements for all atoms... I will add this class to CDK
tonight...
> If you could point me to any tutorials or background information about
> vibrations that would be useful.
I hope the above helped a bit. More information can be found on the internet
by looking for infra red spectroscopy... the energies for these kind of
molecular vibrations are in the area of infra red light...
These vibrations are very well describes as being two particles (atoms) on a
spring (bond). Therefore, the sinus function is the source code is
appropriate.
> Also, what is the simplest type of file that I can actually *look at* to
> understand what kinds of data structures are behind a vibration?
An example is h20.g03.log...
On line 964 ("Harmonic frequencies") starts the vibration data...
The three IR vibrations given on lines 968-980.
The frequencies are given on line 970, and the displacement vectors on lines
978-980.
> >> - Energy information
> >
> > Miguel, are these currently stored? If not, again, how shall we do that?
>
> Sorry, I don't even know what this is.
Each molecule has an energy. These are negative denoting that the compound is
stable as compared to single atoms. In geometry optimizations, the energy is
lowered during the process. The plot of the energies is indicative for the
process.
Another example when energy is important is when changing the conformation of
a molecule, e.g. rotate ethane around the C-C bond (a classical example, see
conformeren.cml)... when this animation is started the methyl groups are
rotated with respect which each other. When opening this file in Jmol b6, you
and view the energy plot, you will see a sinus function. The hill (higher
energy) is caused by two H's that bump into each other during the rotation.
Try it, it's very informative example of molecular energies, and standard
material for new chemistry students.
I hope this helped. Now that I understand how the vibrations are animated, I
think we can quite quickly add this to HEAD.
Egon
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