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From: | Konrad Hinsen |
Subject: | Re: [h5md-user] Tuples and topology, the return |
Date: | Tue, 08 Jul 2014 08:59:35 +0200 |
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.
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