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

[Pierre de Buyl]

On Fri, Jan 10, 2014 at 04:06:01PM +0100, Konrad Hinsen wrote:
> 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.

I modestly propose that this issue remains for a later version. In the context
of a database with validated submissions, a criterion could also be imposed on
the H5MD version that is used.

P