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Re: [h5md-user] fix remaining imprecisions - particle position
From: |
Pierre de Buyl |
Subject: |
Re: [h5md-user] fix remaining imprecisions - particle position |
Date: |
Fri, 10 Jan 2014 21:29:44 +0100 |
User-agent: |
Mutt/1.5.21 (2010-09-15) |
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
- Re: [h5md-user] fix remaining imprecisions - particle position, Felix Höfling, 2014/01/07
- Re: [h5md-user] fix remaining imprecisions - particle position, Olaf Lenz, 2014/01/08
- Re: [h5md-user] fix remaining imprecisions - particle position, Felix Höfling, 2014/01/08
- Re: [h5md-user] fix remaining imprecisions - particle position, Konrad Hinsen, 2014/01/09
- Re: [h5md-user] fix remaining imprecisions - particle position, Felix Höfling, 2014/01/09
- Re: [h5md-user] fix remaining imprecisions - particle position, Konrad Hinsen, 2014/01/10
- Re: [h5md-user] fix remaining imprecisions - particle position, Olaf Lenz, 2014/01/10
- Re: [h5md-user] fix remaining imprecisions - particle position, Konrad Hinsen, 2014/01/10
- Re: [h5md-user] fix remaining imprecisions - particle position,
Pierre de Buyl <=
- Re: [h5md-user] fix remaining imprecisions - particle position, Pierre de Buyl, 2014/01/13
- Re: [h5md-user] fix remaining imprecisions - particle position, Felix Höfling, 2014/01/13
- Re: [h5md-user] fix remaining imprecisions - particle position, Felix Höfling, 2014/01/10
- Re: [h5md-user] fix remaining imprecisions - particle position, Pierre de Buyl, 2014/01/10
- Re: [h5md-user] fix remaining imprecisions - particle position, Felix Höfling, 2014/01/10
- Re: [h5md-user] fix remaining imprecisions - particle position, Pierre de Buyl, 2014/01/10
- Re: [h5md-user] fix remaining imprecisions - particle position, Olaf Lenz, 2014/01/10
- Re: [h5md-user] fix remaining imprecisions - particle position, Felix Höfling, 2014/01/10
- Re: [h5md-user] fix remaining imprecisions - particle position, Pierre de Buyl, 2014/01/10
- Re: [h5md-user] fix remaining imprecisions - particle position, Pierre de Buyl, 2014/01/10