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