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Re: [h5md-user] H5MD box group

From: Felix Höfling
Subject: Re: [h5md-user] H5MD box group
Date: Tue, 29 Apr 2014 09:54:47 +0200
User-agent: Opera Mail/12.16 (Linux)

Am 28.04.2014, 20:19 Uhr, schrieb 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

Dear David,

Good to hear that you plan to enable LAMMPS for reading and writing H5MD.
I also planned to use H5MD as an interface between LAMMPS and my own
software HALMD, but haven't yet found time to do anything in that

When checking out various possibilities, I stumpled over the use of VMD
molfile plugins.
Maybe the H5MD plugin could be used? (Olaf is in charge here.)

You may also have a look at the various libraries related to H5MD, hopefully they make life easier:

Best regards,


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