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

[Pierre de Buyl]

Hi Konrad,

On Tue, Jul 08, 2014 at 08:59:35AM +0200, Konrad Hinsen wrote:
> --On 7 juillet 2014 11:50:06 +0200 Pierre de Buyl
> <address@hidden> wrote:
> 
> >and the ensuing discussion, I modified my proposal.
> >
> >1. a module "tuple", defining n-tuples
> >2. a module "topology", similar to the previous proposal but made more
> >precise.
> 
> A comment on naming:
> 
> 1) The term "topology" is used in at least two very different
> meanings in molecular simulations [(1) bond connectivity, (2)
> universe topology], so it's perhaps better to avoid it in a
> specification.

Right, I forgot your point about that. bond_connectivity, bonded_interactions, ?

> 2) Unless someone comes up with a definition that suits all
> molecular simulation techniques (which I consider highly unlikely),
> we should expect to have multiple modules that address the issue of
> molecular structure and interactions, and not use a name that
> suggests universality for any one of them.
> 
> Point 2 also suggests that any specific module should state its
> intended field of application, with its limitations, which yours
> currently doesn't.

The actual field of application is coarse-grained molecular models. In practice,
there should be a lot in common with atomistic force fields but I don't
currently use them.

So the name should reflect this? cg_connectivity cg_bonds
coarse_grained_connectivity coarse_grained_bonds ? That would be too specific.

> >The idea is that "tuple" would be included somehow in the main
> >specification so that it can serve as the basis to further functionality.
> 
> Yes, that's a good idea.
> 
> >I've put TODO items in each module:
> >Tuples
> >1. Provide a way link unambiguously to a particle group.
> 
> The name of each particle groups is unique, so we could just have a
> "particle group" attribute in the tuple that contains the name of
> the group.

That's fine for randomly placed tuple lists but in a structure like

/clever_name_for_connectivity/<group_name>/FENE

it would be redundant, a problem that we have succeeded in avoiding until now,
unless I am just being too optimistic with the state of H5MD :-)

Another solution would be: either be in a structured paths (like above) or have
the attribute "particles_group".

So, I need a name for a connectivity module for bonded interaction that applies
to coarse-grained molecular models but is likely to also apply to atomistic
force fields. Suggestions welcome :-)

Pierre