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

From: Hart, David Blaine
Subject: Re: [h5md-user] [EXTERNAL] Re: H5MD box group
Date: Tue, 29 Apr 2014 19:52:06 +0000

Hi Felix,

I have looked at the Python H5MD tools already, and they look very useful. Part 
of the reason I was wondering about an 'offset' element was because there is no 
way get at such an item within the Box class, only at the 'edges' element. I 
realized as I wrote back to Olaf's response that leaving 'offset' out of 'box' 
makes sense, and that if I place 'offset' as a trajectory group, just like 
'position' or 'velocity', the PyH4MD module can already handle that.

I've not used the dump_molfile plugin before, but I do use the dump_xtc plugin 
to get VMD visualizations, and was planning on starting a dump_h5md plugin that 
would start from one of the existing dump_* modules. The lammps log files are 
less important to me (mainly because they aren't tens of gigabytes) at the 
moment, but the h5md thermodynamics module seems to include everything that 
would be needed for a log_h5md plugin too. 



-----Original Message-----
From: address@hidden [mailto:address@hidden On Behalf Of Felix Höfling
Sent: Tuesday, April 29, 2014 1:55 AM
To: address@hidden
Subject: [EXTERNAL] Re: [h5md-user] H5MD box group

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 direction.

When checking out various possibilities, I stumpled over the use of VMD molfile 
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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