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Re: [h5md-user] H5MD box group

From: Olaf Lenz
Subject: Re: [h5md-user] H5MD box group
Date: Tue, 29 Apr 2014 09:18:30 +0200


In general, the H5MD-Format only specifies how to interpret certain groups/datasets if they exist. However, there is nothing that prevents a user to add arbitrary further groups/datasets to any other group - only they are not standardized. So there is no problem, you can easily supply an offset in the box vector. However, I would suggest to put data that is not standardized in h5md into an own, application-specific group.

As for the "offset", the discussion was that we (i.e. at least Konrad and me) did not see any use for it, and (as far as I remember) nobody was able to provide us with an actual use case. The only application that we saw was that the offset plus the edges would provide a bounding box of the particles in the system. However, the use of that would be limited, as a h5md reader should still not rely that all particles are in that box.
Can you provide another use case? Why would you need to store an offset, and what exactly would it mean?


2014-04-28 20:19 GMT+02:00 Hart, David Blaine <address@hidden>:

I am interested in using H5MD to store converted trajectories from LAMMPS text dumps, but eventually also writing an H5MD dump plugin to LAMMPS to avoid the conversion step. As I’ve read through the mailing list archive, it seems that the particles->…->box->offset group has come and gone as part of the specification. Does the spec. require that only ‘edges’ be present in ‘box’, or can offset also be present?


I realize that if I’m only using my own tools, that I can do as I see fit, but I’d like to conform to the specification as much as possible, especially as I move towards direct HDF5 output from LAMMPS. Is the definition of extra groups, like offset within box, the purpose of the modules?


Thanks, and I am excited that the specification has been published!


David Hart

Dr. rer. nat. Olaf Lenz
Institut für Computerphysik, Allmandring 3, D-70569 Stuttgart
Phone: +49-711-685-63607

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