discussions: clean up section on particle number

This suggestion has already become part of the spec.
discussions: add time-dependent data with constant increments

Sampling at constant rate is by far the most common situation.

The idea is due to Konrad Hinsen:

http://article.gmane.org/gmane.science.simulation.h5md.user/406
Remove box from observables group

The specification of multiple different simulation boxes in /particles
conflicts with the specification of a single unique simulation box.
Hard-link step/time datasets of position and box
Add draft of thermodynamics module

Specify a set of thermodynamic observables including physical interpretation.
thermodynamics: add 'volume'

The volume is the conjugate variable to the pressure (compare NVT vs.
NPT simulations). The volume is well-defined for arbitrary geometrical
shapes underlying the definition of the subsystem.

slight rewording of the definition of 'dimension'
thermodynamics: drop per particle quantities, add enthalpy

In thermodynamics, one may equally work with the total sums (extensive)
or with intensive quantities, e.g., per particle or per volume. Instead
of listing all possiblities, we decide for one choice. The others are
easily derived by suitable normalisation.

Rename 'total_energy' to 'internal_energy'.
http://en.wikipedia.org/wiki/Internal_energy

Add 'enthalpy' which plays the role of internal energy in the NPT
ensemble: H = U + pV.
Remove the word 'element' wherever possible.
Introduce H5MD elements.
Use x.y.z version for specification and modules
Fix description of module version
Explicit type and dimension added in the notation, according to Olaf Lenz's suggestion.

http://article.gmane.org/gmane.science.simulation.h5md.user/262
http://article.gmane.org/gmane.science.simulation.h5md.user/462
be more precise about the types

- use "`Integer` type" instead of "integer kind"

- say that position, velocity, force, edges, offset, ... are either
  Float or Integer (and not String or Compound or whatever).

- specify the dataspace of `value` for a generic H5MD element
draft: some clean-up and reformatting

- replace `` by `
- reformat paragraphs to fill the lines (80 chars)
- remove unneeded Oxford comma in lists of two items
draft: revise section on modules slightly

Let modules also define additional data elements and mention that a
module group may carry further metadata.

Use "HDF5 structure" instead of "HDF5 file" or "trajectory".
draft: drop "time series" for observables

Observables may be time-dependent or time-independent.
modules: add a draft for the units module

The text follows the suggestion by Pierre de Buyl, inspired by a similar
text in the Mosaic project by Konrad Hinsen, see
http://article.gmane.org/gmane.science.simulation.h5md.user/455

The list of units is compatible with the specifications by the 'udunits2'
library
http://www.unidata.ucar.edu/software/udunits/udunits-2/udunits2.html#Database
with a few extensions inspired by the Mosaic project, see the file
doc/source/data_model.rst in https://bitbucket.org/molsim/mosaic/src

In contrast to the Mosaic project but in line with udunits2, unit
symbols may always carry any SI prefix (I omitted some extreme powers
added to SI only recently).

In UTF8 encoding, the powers may be given as superscripted characters.
(I think having units strings in the same format as used by scientific
publishers is timely and in the spirit of UTF8.) These characters need
to be lowered before processing by udunits2.

The module does not yet cover Lennard-Jones units and other artificial
unit sets. We could include generic symbols, "σ" for the unit length,
"τ" for the unit time, "ε" for the unit energy.
draft: drop `unit` attribute, refer to 'units' module

Mention that the 'thermodynamics' and 'units' modules are part of the
official H5MD specification.
refine thermodynamics module

Do not require a 1:1 correspondence between the trees in particles and
observables.

Make 'dimension' a mandatory attribute. Make 'particles' and 'volume'
mandatory as well to allow for the conversion from extensive quantities
to intensive ones (per particle, per volume).

Specify datatypes (Integer and Float, as appropriate).
2nd revision of thermodynamics module

* rename particles to particle_number

This avoids a potential confusion between the root group "particles" and
the H5MD element "particles". Further, the field stores no detailed
information about the particles (which somebody could expect from the
name), just the bare particle number.

* store intensive quantities (per particle) instead of extensive ones

This reverts a previous preference for extensive quantities. The latter,
however, can become really huge as they depend trivially on the system
size and are not very practical, for example, it is difficult to compare
them by visual inspection. Intensive quantities on the other hand do not
suffer from such issues and are typically quoted in publications. The
conversion to extensive quantities is always possible since the particle
number must be given as well.