Re: quaternions

[Felix Höfling]

> > My own HALMD software is close to support quaternions as well. Here a
> > question came up, which we may address now: What is the relation of the
> > quaternion to the axis vector for axisymmetric particles (e.g.,
> > ellipsoids)? A natural name for both properties would be "orientation" -
> > so how should we distinguish them in H5MD? Of course, we could call the
> > quaternion representation "orientation" and the axis representation  
> > "axis"
> > or "direction" or so. Any thoughts on this?
>
> No thought yet. It is true that for axisymmetric bodies, quaternions are  
> not
> necessary. For quaternions, I see no issue with the name "quaternion",  
> it is
> unambiguous and actually used internally (even though "q" or "quat"  
> would be the
> variable name, the data is named quaternion in the code and  
> documentation such
> as "the quaternion" as one would say "the position").

What I find a bit weird about the name "quaternion" is that it refers to  
the data type, just as "vector" or "complex number", and not to the  
property it describes. Admittedly, I don't know about any other use of  
quaternions than for representing rotations, at least in MD.

By the way, "rotation" would be a nice name too. How is it named in the  
LAMMPS or Espresso interfaces (not necessarily the code)?

> What you refer to as axis is the unit vector pointing along the "long"  
> axis of
> the ellipsoid, right? If so, I can think of "axis", "u", "unit_vector",  
> or even
> "orientation" actually. All current names in the particles group (even  
> the new
> quaternion) are unambiguous. Apart from "id", we even have full english  
> names
> for all elements :-)
"axis" sounds good, or "orientation"

Practical question: is it required (in H5MD) that the quaternions/axis  
vectors are normalised? Should it be stated?

Felix