>> - 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,
I tried to take a look at some of the Gaussian files ... and ran into a
problem.
The vectors that are being read by the Gaussian readers are *not* the same
vectors as the ones I am calling "AtomVectors". The ones which I am
calling "AtomVectors" are only read from .xyz files.
These are not the same as the "Vibration Atom Vectors" which are read by
the Gaussian readers. (Nor are they the same as the "CrystalFrame
Vectors".)
>> 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.
This was my motivation for asking about using different names for these
different types of vectors.
Here is what the situation looks like to me:
- There are AtomVectors which are constructed *only* by the XYZReader.
* The data structure is an instance variable of Atom called "vector"
* Atom.vector is of type Point3f
* These are rendered to the screen as arrows
* The code samples I sent previously are associated with these vectors
* there are bugs in the rendering (in Release 5)
- There are vibration vectors associated with the Gaussian readers.
* It is an instance variable of Vibration called "atomVectors"
* Vibration.atomVectors is of type ... Vector ... java.util.Vector ;^)
* I may be mistaken but ... in Release 5 these vectors
are *not* rendered to the screen (!)
* Based upon your previous email, I assume you *want* them rendered (!)
- Chemical frames have their own types of vectors
* I haven't looked at the code
* I think they define outline the crystal frame box
* they *do* get rendered to the screen
(As an aside, none of these vectors is ever rendered in Povray)
My current goal is to get my head around the situation.
Q: Are the "xyz atom vectors" related to the "gaussian vibration atom
vectors"?
If yes
Q: should the data structures be the same?
If no
Q: Which one should have the name "UnitVector"?
Q: What should the other one be called?
Q: Should the gaussian vibration vectors be rendered to the screen?
�Gracias!
Miguel
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