Re: [h5md-user] [EXTERNAL] Re: H5MD box group

[Pierre de Buyl]

Hi David,

On Tue, Apr 29, 2014 at 07:40:14PM +0000, Hart, David Blaine wrote:
> I’ve re-written this email several times, as I’ve sorted out what I want to do
> in my head. It would seem that I’m looking at two things. The first,
> converting my current dump files to the H5MD format, I can do a little bit
> looser and store things in a separate root group if necessary. The second,
> writing a LAMMPS plugin that would output H5MD files directly, I probably want
> to be a bit more formal, specifying what extra fields are output as particle
> information in an h5md module, so that the LAMMPS code can point to a module
> definition defining the elements within a particles group (like the
> thermodynamics module does with observables) that can be linked to each other
> with the semantic versioning number. Is that the approach you would suggest?
> Or would you still suggest putting the non-standardized particle data in a
> different root group? [You convinced me that adding particles/…/box/offset
> would be a bad idea, but I still think that particles/…/offset would be useful
> with lammps outputs.]

Is there any news on this?

I am toying with lammps currently for some atomic simulations. I'd gladly help
to test the H5MD plugin or contribute if needed.

Also, you would indeed both the plugin and a H5MD "module". You can design the
module later on and just dump whatever data you need in "/lammps" in the
meantime, taking care to use the regular H5MD whenever possible (for position,
etc).

Cheers,

P

> 
> From: address@hidden [mailto:address@hidden On Behalf Of Olaf Lenz
> Sent: Tuesday, April 29, 2014 1:19 AM
> To: Hart, David Blaine
> Cc: address@hidden
> Subject: [EXTERNAL] Re: [h5md-user] H5MD box group
> 
> Hi!
> 
> 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?
> 
> Olaf
> 
> 
> 2014-04-28 20:19 GMT+02:00 Hart, David Blaine 
> <address@hidden<mailto: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