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

[Konrad Hinsen]

Felix Höfling writes:

 > In some sense, this case is already included in the current version. If
 > `image` is absent, the `position` data are taken as absolute positions
 > (which then are all inside the box). However, the file format doesn't say
 > anything about the existence of a meaningful (continuous) trajectory. Do
 > you see a need for such information?

My understanding of the original text is that there is a distinction
between the position in the primary box and some "absolute"
position. My point is that this distinction need not exist.

This doesn't make any difference in practice, of course, so it's not a
very important issue for H5MD.

 > Originally, `offset` together with `edges` was meant to provide the range
 > of folded particle positions. As of Olaf's pointing at the box skin, this
 > use has become meaningless. As nobody is using `offset` AFAIK, we may drop
 > it in favour of `minimum` and `maximum` which provide a guarantee on the
 > range of particle positions. What do you think?

Sounds good in principle, but again the devil is in the details.

1) Having both "minimum" and "maximum" is redundant, as the difference
   must be "edge".

2) Any such specification should be optional, for trajectories that
   don't make any promises.

3) In simulation of small-molecule liquids, it is common to apply
   periodic boundary conditions to the centers of mass of the molecules,
   rather than to individual atoms. The guarantee on the positions thus
   applies to something else than the stored coordinates.

   It's OK with me to say that no minimum/maximum should be specified
   in this situation, but I think it's worth saying so explicitly to
   avoid misunderstandings.

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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