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Re: [h5md-user] Box image vectors

From: Felix Höfling
Subject: Re: [h5md-user] Box image vectors
Date: Mon, 06 May 2013 16:24:37 +0200
User-agent: Opera Mail/12.15 (Linux)

Am 05.05.2013, 22:19 Uhr, schrieb Peter Colberg


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


It is a good idea to support both choices. All of the subgroups are
optional, so the example in the Draft does not need to be extended, simply
the list of standardised group names.

Instead of making the interpretation of "position" dependent on the
existence of "image", I would prefer to attach an attribute to "position"
stating whether they are absolute or periodically reduced. In the latter
case, the image data group shall exist and is referred to. This helps to
ensure file consistency, e.g., if a user copied the position data but for
some reason not the image vectors.

Note that the image vector is not necessarily an integer, e.g., for
Lees-Edwards boundaries. For such boundaries, also the velocities need to
be corrected for the boundary conditions.


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