Re: [h5md-user] fix remaining imprecisions - particle position

[Konrad Hinsen]

Olaf Lenz writes:

 > In some cases it makes sense to store the particle coordinates in
 > absolute coordinates in a periodic system even when they are
 > outside the primary box (for example when tracking the MSD of the
 > particle). In that case 'image' would not be defined.  Also, it
 > might make sense to store coordinates outside the primary box even
 > when 'image' is used (for example, it is common practice that
 > particles can walk out of the box up to skin/2 before the image is
 > updated for performance reasons.

There is one more case I have encountered in practice: all positions
are folded into the box and nothing whatsoever is stored to permit the
reconstruction of absolute coordinates. This is appropriate e.g. for many
Monte-Carlo algorithms where the notion of a trajectory in time doesn't
exist, or doesn't matter for analysis.

So I would like to propose a minor change to your description:

 > The component $d$ of the absolute position of particle $i$ is then
 > computed as $R_{id} = r_{id}  + L_d a_{id}$, where $\vec r_i$ is

If the simulation permits the definition of an absolute position for
each particle, the absolute position of particle $i$ is then ...

 > Finally, I am still wondering about the meaning of the `offset`
 > field, given that we give no guarantees on the limits of the
 > positions. What could anybody do with this value?

I have been wondering about this for a while...

Konrad.
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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
http://dirac.cnrs-orleans.fr/~hinsen/
ORCID: http://orcid.org/0000-0003-0330-9428
Twitter: @khinsen
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