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Re: [h5md-user] box and observables
From: |
Pierre de Buyl |
Subject: |
Re: [h5md-user] box and observables |
Date: |
Tue, 24 Sep 2013 16:22:57 +0200 |
User-agent: |
Mutt/1.5.21 (2010-09-15) |
Hi,
Just replying a bit on the box issue, as I cannot keep track of all the topics
currently discussed on the list.
On Mon, Sep 23, 2013 at 11:48:27AM +0200, Konrad Hinsen wrote:
> Felix Höfling writes:
>
> > The reason that there are several box groups is primarily that different
> > subgroups have different sampling intervals. For trajectory subgroups, the
>
>
> That was my understanding as well (there is even a sentence saying
> so), but apparently Peter disagrees.
Within a particles group, data can be sampled at different intervals. To make
the point clear, else we would have unique step/time datasets for a particles
group. One may wish to sample different coordinates at different time intervals.
> > For this reason (and since the /particle root group may be absent),
> > the box is also stored in /observables where it is considered a
> > physical observable (NPT simulations), not just an appendage to
> > some real data.
>
> Having the box as an observable is indeed quite reasonable.
We had a realllllly long discussion on whether to put the box in /particles or
in /observables. The current solution is the result of that.
> > Assuming that there is only one simulation box, the
> > box is not stored inside each particle subgroup but at the main
> > level. Actually, this latter point deviates from the structure in
> > /particles and may be debated.
>
> Now that I understand the reasoning behind the current layout, I'd say
> the fundamental problem is elsewhere: it's that the "observables" group
> can contain two very distinct kinds of subgroups: those that define
> systems-wide observables, and those that group together observables for
> different subsystems.
>
> There is no such distinction in the "particles" group, where all data
> is stored by subsystem, implying that the whole system is just a special
> case of a subsystem.
>
> Why not take the same point of view for "observables"? We'd then have
> only subsystem-naming groups at the top level, and all observables,
> including "box", inside them.
I cannot comment on this yet but I have the impression that starting to give a
rigid structure to /observables might lead to premature complexification [1].
Cheers,
Pierre
[1] Can I say "Premature complexification is the root of all evil" ?
- Re: [h5md-user] box and observables, (continued)
- Re: [h5md-user] box and observables, Konrad Hinsen, 2013/09/25
- Re: [h5md-user] box and observables, Felix Höfling, 2013/09/25
- Re: [h5md-user] box and observables, Konrad Hinsen, 2013/09/25
- Re: [h5md-user] box and observables, Peter Colberg, 2013/09/25
- Re: [h5md-user] box and observables, Felix Höfling, 2013/09/25
- Re: [h5md-user] box and observables, Peter Colberg, 2013/09/25
- Re: [h5md-user] box and observables,
Pierre de Buyl <=
- Re: [h5md-user] box and observables, Peter Colberg, 2013/09/23
- Re: [h5md-user] box and observables, Felix Höfling, 2013/09/23
- Re: [h5md-user] box and observables, Peter Colberg, 2013/09/23
- Re: [h5md-user] box and observables, Pierre de Buyl, 2013/09/24