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Re: [h5md-user] Conventions/Modules

From: Felix Höfling
Subject: Re: [h5md-user] Conventions/Modules
Date: Mon, 23 Sep 2013 15:00:16 +0200
User-agent: Opera Mail/12.15 (Linux)

Am 09.09.2013, 12:56 Uhr, schrieb Olaf Lenz <address@hidden>:


On 09/09/2013 12:11 PM, Konrad Hinsen wrote:
I think the same approach could work for H5MD: provide a
"convention" field in the H5MD metadata, and let people work out
conventions for their respective domains. For the species
information, this could range from a simple convention such as
"use chemical element numbers" to more elaborate ones such as "the
species is an index into an array named xxx that stores additional

Your concept of "conventions" seems to be pretty similar to what I have
called "modules" in a (off-line) discussion with Pierre and Felix,
however coming from the technical point of view. My idea was that
instead of trying to define everything in the H5MD specs, it would be
nice to allow for "modules" on top of the H5MD specs (which would be the
"base module").

My idea was the following:

1. A module has a name (e.g. "protein description").

2. A module contains further specifications on top of the H5MD
specification that describe how certain fields look like (syntax) and
how they are to be interpreted (semantics). A "protein description"
module would probably contain specs how to describe the type of an atom
and its position in the protein sequence.

3. When a h5md file uses a module, this should be specified in a group
in the file (probably h5md/modules).

4. Modules can be proposed by users and user groups, and they can be
published on the h5md home page.

5. When a module has proven its value, it can be integrated into the
base module.



I'm aware that the thread is two weeks old by now, but let me make a brief comment:

As I recall our discussion, we planned to implement the modules simply as additional root groups. So the presence of a certain root group (e.g., "lattice_boltzmann" for solvent data) would indicate the use of the respective module. An additional listing in h5md/modules would be redundant.

Konrad's concept of conventions is a bit different if I understand it correctly. The use of a certain convention changes the interpretation of the "core" data, e.g., in the particles group, or even extends the data structures by additional mandatory fields. In such a case, "h5md/conventions" would be helpful to interpret the data. It makes a promise on what fields the reader can expect.


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