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Re: [h5md-user] H5MD

From: Peter Colberg
Subject: Re: [h5md-user] H5MD
Date: Tue, 7 May 2013 17:05:36 -0400
User-agent: Mutt/1.5.21 (2010-09-15)

Dear Valérie,

Welcome to the community of H5MD users!

On Mon, May 06, 2013 at 02:17:01PM -0500, Valérie Vallet wrote:
> I am writing to you regarding your project on H5MD. I came across
> H5MD when searching for MD-codes and vizualisation tools that would
> write/read HDF5 files for MD trajectories. From the mailing list
> discussion, I realize that you should soon release a first version
> of H5MD. When do you exactly schedule this? Will the H5MD be C, F90,
> python compatible? These are some of the question I have for the
> moment. 
> It looks like you library will exactly do what we want in terms of
> generating a structured MD file.
> Will you also work with visualization programs to include H5MD
> reading features in there? I am thinking of VMD for instance.
> Thanks a lot in advance for your answer.

H5MD itself is a specification for storing molecular data using the
HDF5 [1] file format, so any HDF5 software can be used to read and
write H5MD files.

[1] http://www.hdfgroup.org/HDF5/

The HDF5 library provides interfaces for C and Fortran, which one
would typically use for the heavy-duty output in simulation codes.
The main “low-level” HDF5 API [2] seems vast at first, but you will
only need a small subset for reading and writing H5MD files.

[2] http://www.hdfgroup.org/HDF5/doc/RM/RM_H5Front.html#LowLevelAPIs

A good starting point for learning the C/Fortan interfaces are the
HDF5 tutorial [3] and the examples shipped with the HDF5 source [4].

[3] http://www.hdfgroup.org/HDF5/Tutor/introductory.html
[4] http://www.hdfgroup.org/ftp/HDF5/current/src/

If you are thinking of more high-level use, e.g., using Python
scripting, there is the excellent h5py [5] and documentation [6].

[5] https://code.google.com/p/h5py/
[6] http://www.h5py.org/docs/

h5py is most useful in post-simulation analysis of H5MD files,
together with NumPy and SciPy. Specifically for H5MD, Pierre de Buyl
has written a Python module pyh5md [7], which will get you started.
For another example of plotting H5MD data, see the h5md-tools [8]
by Felix Höfling.

[7] http://article.gmane.org/gmane.science.simulation.h5md.user/124
[8] http://github.com/fhoefling/h5md-tools

For visualization, Olaf Lenz recently posted a message [8] that a
student is working on an H5MD file reader plugin for VMD.

[8] http://article.gmane.org/gmane.science.simulation.h5md.user/122

As for the release schedule, we are currently working on the
manuscript introducing H5MD to the community of researchers,
which should be submitted for publication soon.

You are invited to subscribe to the mailing list [9] and join the
discussion. We would be very interested to get your feedback and
suggestions for improvements of H5MD.

[9] https://lists.nongnu.org/mailman/listinfo/h5md-user


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