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Re: [h5md-user] box and observables

From: Felix Höfling
Subject: Re: [h5md-user] box and observables
Date: Mon, 23 Sep 2013 14:23:05 +0200
User-agent: Opera Mail/12.15 (Linux)

Am 23.09.2013, 11:48 Uhr, schrieb Konrad Hinsen

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.

 > 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.

 > 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.


Indeed, such a structure would be cleaner and also better to parse. The
name of the subgroup referring to the whole system should be specified
("all", "global", "system") to give stuff like the box or the system
temperature a defined location. I tend to choose "global" since the box is
a global property and for some observables there are global conservation

I have attached a patch with the proposed change.


Attachment: 0001-observables-move-global-observables-to-subgroup.patch
Description: Text document

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