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Re: H5MD proposal for quaternion

From: Konrad Hinsen
Subject: Re: H5MD proposal for quaternion
Date: Tue, 11 Feb 2020 17:28:05 +0100

Hi Pierre,

> Some elements already depend on the creator. This is the case for charge, even
> though H5MD considers some typical scenarios already, for species, and for ID.

True, but charge still has more of a universal meaning than quaternions,
which can represent orientations or rotations, and in the former case
require a reference conformation that should ideally be deducible from
the information in the trajectory.

> I would be in favor, at least for quaternion, to restrict the definition. For
> instance: "The quaternion defines the orientation of the particle as follows.
> Any point on the body represented by the particle, and located at "p0" at an
> arbitrary reference in time, is located at the time corresponding to 
> quaternion
> q1 at p1 = q1 p0 q1* where q1* is the conjugated quaternion to q1 and the
> multiplications in the formula are quaternion products. The position of the
> point so defined is always relative to the position of the particle."

OK, that's a lot more precise, but wouldn't this better be called

> Whatever happens with quaternions, you propose to have a generic ways of 
> storing
> creator-specific elements, is that right? Do you have an idea of how that 
> would
> work out?

Yes, that's what I have in mind. The idea is to use H5MD much like XML
or HDF5, as a foundation of basic data structures to which more specific
data definitions can be added. For example, H5MD defines how to store
scalars, vectors, and quaternions, all of that time-dependent or not,
plus of course the most basic geometric data that the definition already
contains. A creator-specific definition of "orientation", for example,
would then just add "H5MD time-dependent quaternion per particle" plus
the semantics for interpreting the quaternions.

Konrad Hinsen
Centre de Biophysique Moléculaire, CNRS Orléans
Synchrotron Soleil - Division Expériences
Saint Aubin - BP 48
91192 Gif sur Yvette Cedex, France
Tel. +33-1 69 35 97 15
E-Mail: research AT khinsen DOT fastmail DOT net
ORCID: https://orcid.org/0000-0003-0330-9428
Twitter: @khinsen

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