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[h5md-user] particle number

From: Felix Höfling
Subject: [h5md-user] particle number
Date: Fri, 25 Jan 2013 16:10:49 +0100
User-agent: Opera Mail/12.12 (Linux)

Hi all,

Let's go on with H5MD after the Christmas break.

I would like to suggest 2 additional attributes:

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.

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 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?



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