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

[Felix Höfling]

Am 08.07.2014, 10:49 Uhr, schrieb Pierre de Buyl <address@hidden>:

> 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.
"there" means in the topology module?

> > 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.
I meant that we should allow for this, but it is not a requirement. The  
user may also collect all (pair) bonds in a single data field.

> > * 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.

From Olaf (whom I consider an expert in PDB) I got the information that  
PDB only stores connections, no bond types. Thus we can leave the names of  
the H5MD elements unspecified. They have no defined meaning and simply  
serve to group bonds (by whatever criterion, similarly as for the groups  
in particles/).

Felix