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

[Konrad Hinsen]

Olaf Lenz writes:

 > 2014/1/10 Konrad Hinsen <address@hidden>
 > 
 >     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.
 > 
 > ​Yes, there is a distinction, and I think it needs to exist: the absolute 
 > position is

In a platonic sense, the distinction exists, but for a particular
simulation universe, it may make no sense.

 >     1) Having both "minimum" and "maximum" is redundant, as the difference
 >        must be "edge".
 > 
 > ​No, it is not​! "edge" defines the size of the boundaries, it is a physical 
 > property of
 > the system.
 > "minimum" and "maximum" define the bounding box of "position". It has no 
 > physical
 > meaning, but is a hint for the person reading the file. However, I'm not 
 > really

OK, so it's a time-dependent quantity even if the box is rigid, right?
I have never seen anyone provide such information, and I wouldn't know
what to do with it. If I need the bounding box, I can always compute
it from the positions.

The one information that I see a potential use for is a guarantee
about the range in which all folded coordinates will stay.

 > convinced that it is actually very useful: even when it is given, a
 > reader should still always check whether the positions really are
 > within the bounding box, otherwise he might get into trouble with
 > badly crafted files.

True. But there is one kind of software that could very well use this
information: a trajectory verification tool, used for example by a database
before accepting a submission.

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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