Re: [h5md-user] Writing vs reading

[Pierre de Buyl]

Hello :-)

On Fri, Jan 24, 2014 at 09:58:29AM +0100, Felix Höfling wrote:
> Am 23.01.2014, 19:29 Uhr, schrieb Olaf Lenz <address@hidden>:
> >2014/1/14 Pierre de Buyl <address@hidden>
> >>
> >>> The most important feature for me is that any given combination of
> >>> data arrays has a clear and unambiguous meaning. That criterion still
> >>> leaves a lot of freedom, where as you say the question is whose life
> >>> we want to simplify most.
> >>
> >
> >I'd like to add some thoughts. It is most easy to discuss this on
> >an actual
> >example, therefore I'd like to review the discussion on how to store
> >positions.
> >
> >First of all, as Felix remarked, the most important criterion for h5md
> >seems to be **flexibility**: h5md should allow to express everything that
> >people could possibly want. We do not want to sacrifice any
> >flexibility in
> >exchange for reader-friendliness. For example, in the case of the
> >particle
> >positions we deemed it to be important that the number of particles can
> >change, even though this makes writing and reading them more complex.
> >
> >What remains open is the question what happens in those cases where there
> >are more than one possibilities to express the same thing? When there are
> >several alternative representations of the same thing? As an
> >example, think
> >of writing the positions in periodic boundary conditions. Currently, we
> >allow for three methods to store the position: using the "image",
> >not using
> >the image, forcing the positions to be within the central image, or not.
> >All of these variants are equivalent: one can always transform
> >between the
> >different variants. This is the "writer-friendly" approach.
> >
> >For a reader, this makes it more complex to read the file. In a
> >"reader-friendly" approach, we would allow only one variant of
> >these, e.g.
> >not using the "image" at all, and always storing the absolute position,
> >even if it is outside the central image. For a reader, that would be
> >definitely the simplest variant, as he can always transform into his own
> >model. Insofar I wonder whether it wouldn't be the best to simply
> >throw out
> >the "image" from the specs.
> >
> >Olaf
> >
> 
> The situation is indeed somewhat confusing because of the various
> possibilities. Note that this arbitrariness is expressed now clearly in
> the spec (since a recent update):
> 
>       "..., the data indicate for each particle the component k of the 
> absolute
> position in space of an arbitrary periodic image of that particle."
> 
> As far as I remember, the main reason for adding the image is that the
> simulation program can dump the data directly from memory, without sorting
> or extending positions to absolute values. This is desirable because of:
> 
> i) Folding and unfolding particle positions comes with round-off errors,
> in particular for large box sizes (which become more amenable with
> progress in computing power). This means that the last digits are simply
> thrown away. As consequence, H5MD could not serve for storing simulation
> snapshots which allow for faithfully resuming the simulation.
> 
> ii) Performance when writing. I consider this aspect not important: disc
> access is slow anyway and should be minimised. Further, it seems better to
> let the (potentially parallelised) writer software do these operations
> rather than a reader.
> 
> In general, I think that the spec has reached a relatively broad consensus
> now. I would prefer to mainly fine-tune the wording and avoid drastic
> changes. I feel that dropping the image field would be of the latter kind.

As for as "particles/<group_name>/image" is concerned, I am all for keeping it.
I do not see it as complex to read. The cases you presented [1] make it clear
for both writing and reading.

Also, I am very keen on keeping the changes to a strict minimum from now on.

Best,

Pierre

[1] http://article.gmane.org/gmane.science.simulation.h5md.user/540