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Proposal making protocol and specialized H5MD schemas

From: Joseph Rudzinski
Subject: Proposal making protocol and specialized H5MD schemas
Date: Mon, 24 Jul 2023 09:04:52 +0200

Hello all,

I am new to H5MD and looking for guidance in making a proposal:

I am part of the materials data infrastructure project FAIRmat (https://www.fairmat-nfdi.eu/fairmat/), which develops the software and repository NOMAD (https://nomad-lab.eu/nomad-lab/). We are expanding to support molecular dynamics simulations, and already have parsers for Gromacs and Lammps. However, I am very interested in using the H5MD schema as a route for uploading a broader range of simulation data to NOMAD. 

Question 1: What is the exact protocol for making proposals for amendments of the H5MD schema? I can see the proposal markdown files in the repo. Is it as simple as writing such a markdown file? Is this done via the Git repo or via the mailing list (as I have seen proposals posted here)?

To accomplish my aims, there are certain specifications (mostly added restrictions) that I would require within the general H5MD format. Some of these may be general things which could be adopted into the general H5MD schema, but others may be more of an additional “specialized" schema on top of H5MD, which COULD be useful in general but may be too restrictive for the H5MD schema generally, but MUST be used if the user wants to upload to NOMAD. 

Question 2: Is there any current approach for such “suggested” or “specialized” schemas on top of H5MD for a particular use / application?

Thanks in advance for the assistance!


Dr. Joseph F. Rudzinski 

Domain Expert for Soft Matter Simulations
FAIRmat Consortium / NFDI
Humboldt-Universität zu Berlin

Affiliated Group Leader 
Theory Group, Max Planck Institute for Polymer Research 

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