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Wed, 18 Dec 2019 22:36:02 +0100
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Thanks for bringing it to the point. So "rotation" is out and
"orientation" sounds attractive, but we may have different representations
of it - also depending on the type of particle.
I see two options:
1) the data field is always called "orientation" and we use an HDF5
attribute to distinguish between "quaternion" or "principal_axis" or so.
This leaves room for other choices too (storing rotation matrices or Euler
angles?). The disadvantage is that one cannot have different
representations next to each other (although one can always use private
names for special tasks).
2) We leave "orientation" for the rather general quaternion and use e.g.,
"first_principal_axis" for the unit vector of the main symmetry axis. Of
course, this can be extended too as the space of English words is pretty
What do you think? My tendency is for 1) which appears to be cleaner and
perhaps slightly more H5MD-ish.
NB: perhaps we should think of a set of body-fixed vectors such as a body
frame instead of only a specific axis. The precise meaning of the vectors
depends on the application, as is the case with H5MD at various places.
Am 18.12.2019, 20:17 Uhr, schrieb Konrad Hinsen
Practical question: is it required (in H5MD) that the quaternions/axis
vectors are normalised? Should it be stated?
For quaternions, normalization is a requirement: only normalized
quaternions form a representation of the rotation group. So I'd say yes,
it should be a requirement, and therefore it should be stated.
For proper rotational motion, the length of such vectors should be
preserved, at least. So choosing them as unit vectors makes sense.
For axis vectors, I have no opinion - I have never used them in
Making the normalisation mandatory in both cases is good practice since
then the file contains sound (=consistent) data.
During the simulation, some people may admit small violations of the
normalisation for performance reasons. Yet from my view, it is not asking
too much to bring this in order before writing to the file.
Re: quaternions, Pierre de Buyl, 2019/12/18