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

[Konrad Hinsen]

--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.

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 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.

Konrad.