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Re: [h5md-user] Minor revisions before H5MD v1.0

From: Felix Höfling
Subject: Re: [h5md-user] Minor revisions before H5MD v1.0
Date: Fri, 03 May 2013 16:03:26 +0200
User-agent: Opera Mail/12.15 (Linux)

Hi Peter,

Am 02.05.2013, 22:57 Uhr, schrieb Peter Colberg <address@hidden>:

Hi all,

As we are closing on the first release of H5MD, I would like to bring
in two minor revisions, one concerning the box group, and one with
regard to the parameters group.

For the box group, in the fixed-size case, I would recommend to store
"edges" and "offset" as attributes. Besides being the “right” way to
store small data, this sets a good example for users with regard to
their custom metadata.

This would be consistent indeed.

I have a bit mixed feelings about "hiding" the actual data of a group as attributes, the issue is most prominent for the /h5md group. On the other hand, attributes are the most efficient way for small pieces of information as you noted earlier.

This ambiguity is already inherent in the HDF5 Manual, see the first sentences of Chapter 8.1:
Further down in this chapter, the maximum reasonable size of an attribute is given as 64k. So in conclusion, storing the fixed box data as attribute would be fine with me.

The "parameters" group is intended as a program-dependent group.
I suggest to remove the "parameters/dimension" attribute, as it
is in contrast to the purpose of this group. The dimension can
be derived from, e.g., the "edges" attributes or "edges/value"
dataset, similar to the number of particles being derived from
"position/value" dataset(s).

I think we should not turn the clock back. There were good reasons to include the dimension parameter explicitly, mainly it cannot be inferred from scalar datasets in /observables. Recall that the box group is not mandatory.


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