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Re: [h5md-user] particle number

From: Pierre de Buyl
Subject: Re: [h5md-user] particle number
Date: Fri, 25 Jan 2013 20:19:48 +0100
User-agent: Mutt/1.5.21 (2010-09-15)

Hi Felix,

Thanks for relaunching the discussion :-)

On Fri, Jan 25, 2013 at 04:10:49PM +0100, Felix Höfling wrote:
> 1) The space dimension shall be stored in /parameters+dimension (as
> integer attribute).
> In principle, it can be deduced from the size of the box offset, but
> this appears pretty cumbersome. Apart from handiness, the box may be
> found either in observables or in trajectory, requiring a
> distinction of cases—just to obtain the space dimension.

This seems reasonable enough :-)

> 2) If data are present only in /observables, the number of particles
> can not be inferred. My suggestion is to supplement each observable
> group with an attribute indicating the number of particles that lead
> to this specific average. (So far, all macroscopic observables
> result from an average over particles.) Thereby, also partial
> observables of particle subgroups are handled correctly. The
> attribute may be attached either to the top groups ('all', 'A', and
> so on), or to individual data groups like 'total_energy'.

I have mixed feelings about this one. For the moment (this does not mean that
this should be the final solution, btw) I run multispecies simulations. The
number of particles is in /observables/solvent_N and is a [:,N_species] dataset.
In all generality, the number of particles depends on time and on the species.
The variety of situations makes me think that this should not go into the first
published version (FPV).

> I believe that both attributes are of sufficient generality to
> deserve a place in H5MD, and I will add them if there are no urgent
> objections.
> BTW, what is missing as well is an (optional) error field (=standard
> deviation) for the observables. What do you think?

Is this critical for the FPV?



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