Re: [h5md-user] Unit attribute versus non-dimensionless quantities

[Felix Höfling]

Am 01.08.2013, 18:28 Uhr, schrieb Peter Colberg
<address@hidden>:

> On Thu, Aug 01, 2013 at 06:13:55PM +0200, Felix Höfling wrote:
> > I think we would miss an important feature of HDF5 if we do not
> > mention (and support) the possibility of annotating data in general,
> > the physical unit is just one important example.
> >
> > Many people in MD, in particular in the context of force fields and
> > protein simulations, use absolute physical quantities and need
> > units. I have seen many situations where even LJ units were
> > translated to nm and fs. Just guessing or assuming physical units is
> > not in the spirit of a self-describing file format.
> >
> > The current specification is not as worse as it seems. The
> > specification of units is possible for all proper datasets, only
> > data stored as attributes can not carry a unit. We could just leave
> > it as it is.
>
> The specification as is cannot be implemented, since an attribute
> cannot have an attribute. Since we seem to disagree on how to
> implement units, this should be postponed.
>
> Note that I would not consider a unit as an annotation. A
> non-dimensionless quantity consists of a number and a unit.
>
> For an example of how units could be implemented on a computer,
> have a look at Boost.Units [1]. The idea is the same: the data
> type is the type of the quantity, not the number.
>
> [1] www.boost.org/libs/units
>
> > I have also asked myself the question whether insisting on storing
> > dimensionful data as HDF5 attributes might be a design flaw of H5MD,
> > but I don't want to re-open this discussion.
>
> That would be the natural consequence of using a "unit" attribute
> attached to the data: the use of attributes would be forbidden for
> most data. I doubt whether that is a good solution. I certainly
> wish to annotate my datasets with non-dimensionless attributes.
>
> Peter

I think we're trying to solve two issues in one step:

1) It should be possible to annotate data in a flexible way, allowing also
for custom annotations. This goes beyond the issue of units, but reflects
an important feature of HDF5.

2) Dimensionful data need to carry a unit. In the case of datasets and
data groups, this could simply be an attribute. For data stored as
attributes, this is not possible and a more involved solution is needed
(and Peter has pointed at such a solution)

I think H5MD would miss something important if neither 1) nor 2) are
addressed in the first release. My suggestion is

- mention that datasets and data groups can be annotated at will in a
user-defined way

- provide two alternatives for specifying units in case of datasets and
data groups (as attribute "unit" or as attribute to a special type)

- attributes can carry a unit only via an annotated, special type

- add a unit attribute to the box, letting edge and offset share the same
unit

The right place to put these things would be a subsection in the general
section following the specification of time-(in)dependent data.

Would that be a reasonable compromise between versatility and usability (a
flexible number of simple attributes) on the one hand side and efficiency
(attributes instead of datasets) on the other?

I'll be on vacation from now on ... sorry that we didn't manage to close
this issue before.

Best regards,

Felix