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

[Felix Höfling]

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:
http://www.hdfgroup.org/HDF5/doc/UG/UG_frame13Attributes.html
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.

Felix