[MMTK] principal axes

Jochen Küpper jochen@jochen-kuepper.de
30 Sep 2001 00:03:35 -0400

I need to put GroupOfAtoms (GA) into their principal axis system (PAS)
and am looking for some comments on my ideas:

As I see it I have move all atoms of the GA to new positions so the
implicit axis system is the PAS. As MMTK doesn't provide a method to
do that directly, I am thinking of the following algorithm: 

- get COM and inertial tensor of GA (MMTK), diagonalize tensor (NumPy)
- get atomList() of GA (MMTK)
- translate and rotate every atom to its PAS position 
- setPosition() for atoms (MMTK) 
voila, there's a modified GA with the internal axis system
corresponding to the PAS.

Is this usage of atomList() + setPosition() ok? Are there any obvious
problems I am overseeing?

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