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[h5md-user] Box image vectors

From: Peter Colberg
Subject: [h5md-user] Box image vectors
Date: Sun, 5 May 2013 16:19:28 -0400
User-agent: Mutt/1.5.21 (2010-09-15)


While implementing the trajectory I/O for my new simulation codes,
I noticed that H5MD does not yet specify box image vectors in the
trajectory subgroup(s).

I suggest to specify a trajectory subgroup as follows:

     \-- group1
          \-- position
          |    \-- value
          |    \-- step
          |    \-- time
          \-- velocity
          |    \-- value
          |    \-- step
          |    \-- time
          \-- force
          |    \-- value
          |    \-- step
          |    \-- time
          \-- image
          |    \-- value
          |    \-- step
          |    \-- time
          \-- species
          |    \-- value
          |    \-- step
          |    \-- time

The "image" group contains the signed integer box image vectors, which
represent the periodic image of a particle given periodic boundary
conditions. The group is optional. If present, "position" is to be
interpreted as periodically reduced coordinates. If absent, "position"
is to be interpreted as periodically extended coordinates.

The choice of the position format is up to the user, but H5MD should
specify the periodically reduced case, which is common in existing
molecular simulation software [HOOMD]. The format has its benefits,
e.g., it allows to store a representation of the data as commonly
stored in memory.

[HOOMD] http://codeblue.umich.edu/hoomd-blue/doc/page_xml_file_format.html


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