Re: [h5md-user] Tuples and topology, the return

[Pierre de Buyl]

Hi Felix,

On Mon, Jul 07, 2014 at 03:55:56PM +0200, Felix Höfling wrote:
> Good to see progress here :-) I'm not (yet) using molecules with a
> topology, so I can't comment on the semantics.
> 
> Your draft seems to repeat the definition of the H5MD element (twice), so
> it may be made more concise by defining a list of N k-tuples simply as
> H5MD element of rank 2 with dimensions [N, k]. (Especially the distinction
> between time-dependent and -independent should be clear.) The speciality
> that the values refer to particle indices goes beyond a general data
> structure and should be part of the topology module.

It depends if the tuples here systematically refer to particles indices/ids. If
so, this point should be there.

> topology module:
> 
> * one may want to store different bond types for the same group (implying
> that each tuple list collects bonds of the same type)

One <bond_list> per interaction type, no problem with that. 

> * can one define a set of names for the bond lists which imply the kind of
> bond (similarly to the fields in the thermodynamics module)? The PDB
> format may give an inspiration for possible bond types.

This goes further and would actually be the start of program specific modules.
Interaction parameters between programs can have minor differences in their
definitions. As PDB considers "real" atoms only it might be too restrictive.

> *  the wording "The step and time datasets must match exactly" should be
> replaced by "... must be hard links to". Compare to the specification of
> particles/image: "For time-dependent data, the step and time datasets of
> image must equal those of position, which must be accomplished by
> hard-linking the respective datasets."

Sounds more consistent, thanks :-)

P