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Re: [h5md-user] topology

From: Felix Höfling
Subject: Re: [h5md-user] topology
Date: Fri, 25 Apr 2014 14:12:52 +0200
User-agent: Opera Mail/12.16 (Linux)

Am 24.04.2014, 14:35 Uhr, schrieb Pierre de Buyl <address@hidden>:

Hi Felix,

On Wed, Apr 23, 2014 at 10:00:17AM +0200, Felix Höfling wrote:
Am 22.04.2014, 13:59 Uhr, schrieb Pierre de Buyl

We better keep the topology separate from the /particles tree. The
information complements the information in /particles, but is quite
different in structure. In /particles, there is one entry per
particle while the topology is about subsets of pairs, triples, etc.

It is true that the information in /topology is structured quite differently than in /particles. I don't see a hard reason to choose any of the solutions
yet, though. An advantage of putting it in /particles could be that the
particles' positions and topologies could be copied more simply from a file to

Eventually, everything is somehow related to /particles. But following this argument we end up in putting everything in this tree, which is probably not intended. Let's stick to the (informal) definition that the data in /particles scale as O(N), one entry per particle.

Second argument: as I will outline below, the topology is not a single H5MD element, but a group of such elements. And I would like to avoid too nested structures for clarity. It should be as simple as
/<top level>/<group>/<H5MD element>

I realize that I forgot also that topology information could be pairs of
particles combined with an equilibrium/constraint distance. I have no idea on
how to add that yet.

What is missing is to specify interaction parameters for each bond (even if the functional form of the interaction is the same). The problem is similar to the 'species' field in /particles and we could implement it similarly as an additional H5MD element parallel to the list of bonds, indicating the bond parameters. (It would require an additional intermediate group though.) The bond parameters themselves have to be specified elsewhere, as per bond species. Alternatively, there is an H5MD element 'bond_length' which gives the parameter for each bond in the list. The analogy would be the "mass" field in /particles (which could also be specified on a per-species basis).

Actually, the spec 1.0 does not contain the possibility of providing per-species properties. An generic extension would be most welcome. Such data, of course, would not be stored inside /particle (no O(N) scaling), but in a different top-level group. As of 1.0, the user may store such information in /parameters.



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