[h5md-user] H5MD developer's guide

[Konrad Hinsen]

I propose that we write, in addition to the H5MD specification, a
developer's guide that explains how best to do specific tasks related
to trajectories. The motivation is twofold: (1) archive the parts of
the exchanges on this list that are likely to be of use to others
later, and (2) discover omissions and inconsistencies in the
specification by considering how the specification gets applied in
practice. The ideal form for this would be a Wiki, but I don't know
if that's an option on nongnu.org.

As a case in point, we have the current discussion about the box
information. It started with a question of mine which resulted from my
attempts to write a program that reads positions and box shape
information at matching time steps. The current state of this
discussion has shown that

 1) There is no agreement on how box information should be stored, in
    particular if priority should be given to simplicity of storage (a
    single box group per trajectory) or to efficiency of access (a box
    group per position trajectory at matching steps).

 2) A reasonable and useful restriction, monotonicity of step and time
    arrays, is not written down in the specification.

This shows that thinking about doing certain things is definitely
useful.

Here's a first list of standard tasks that should be considered:

- Creating a new trajectory, providing various amounts of
  time-invariant data.

- Appending a step to the trajectory, providing data for various
  quantities.

- Reading positions for a subsystem sequentially, with matching box
  information.

- Reading a specified subset of trajectory data (positions,
  observables ...)  at a specific step number.

- Reading the positions for a (small) subset of the system for all
  times, with matching time labels and box information.

Konrad.
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Konrad Hinsen
Centre de Biophysique Moléculaire, CNRS Orléans
Synchrotron Soleil - Division Expériences
Saint Aubin - BP 48
91192 Gif sur Yvette Cedex, France
Tel. +33-1 69 35 97 15
E-Mail: research AT khinsen DOT fastmail DOT net
http://dirac.cnrs-orleans.fr/~hinsen/
ORCID: http://orcid.org/0000-0003-0330-9428
Twitter: @khinsen
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