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Re: H5MD proposal for quaternion

From: Pierre de Buyl
Subject: Re: H5MD proposal for quaternion
Date: Sun, 2 Feb 2020 20:25:13 +0100
User-agent: NeoMutt/20180716

Hi Konrad,

On Sun, Feb 02, 2020 at 12:42:24PM +0100, Konrad Hinsen wrote:
> "The specific meaning of the quaternion depends on the creator of the data."
> If the interpretation is undefined, why put this into a standard? It looks
> more useful to define a standard method for adding program-specific data to
> a trajectory, and then use that method for adding quaternions or whatever
> else.

Thank you for the comment. Indeed, this might apply to other components.

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.

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."

This is the interpretation for all MD software that I know, and the one that
follows from references such as Arnold's book or papers on the Molecular
Dynamics of rigid bodies.

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?



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