[h5md-commit] [SCM] UNNAMED PROJECT annotated tag, v1.0_rc2, created. v1.0_rc2

[Pierre de Buyl]

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The annotated tag, v1.0_rc2 has been created
        at  ddcc364d709170c30706615cefeab7e7f025a554 (tag)
   tagging  5b9da536eff563b70a72ab7132479821d3a7c3f7 (commit)
 tagged by  Pierre de Buyl
        on  Wed Jul 24 21:13:54 2013 +0200

- Log -----------------------------------------------------------------
H5MD v1.0_rc2
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Felix Höfling (16):
      rename 'samples' and 'coordinates' to 'sample'
      observables: allow subgroups, add "pressure", matrix of edge vectors
      Add attribute "dimension" to parameters group
      revise text for tajectory group
      Revise description of observables group
      rename "count" to "particles" in observables groups
      Generalise optional "unit" attribute for all datasets
      add attribute "dimension" to the box group
      revise section on box specification
      observables group: minor editing
      fix graphical tree for /observables
      revise section on time-dependent data
      revise trajectory group
      draft: update years covered by copyright
      discussion: add accumulators and particle count
      discussion: add note on author/creator tracking

Olaf Lenz (1):
      Added "How to contribute".

Peter Colberg (26):
      h5mol: wrap at 80 chars per line and append underscore to references.
      Generate sphinx config.
      h5mol: convert from latin1 to utf8.
      Add _build to .gitignore.
      Add h5mol to index.
      Remove Documentation from title(s).
      Switch to sphinxdoc theme.
      index: fix UTF8 character in Felix's name.
      Fix minor typos.
      conf.py: fix missing UTF-8 header.
      Purge trailing whitespace at end of line.
      Purge trailing whitespace at end of line.
      conf.py: substitute leftover “Molecular Simulation” with “H5MD”.
      conf.py: replace version 0.0.1 with 0.0.
      Remove Peter from list of developers.
      Store edges and offset as attributes for fixed-size box.
      Specify "parameters" group for user-defined parameters.
      Replace creation_time attribute with automatic object time tracking.
      Add implementation hints for the H5MD file format.
      Add Free/Libre software for H5MD files.
      Add h5md html theme
      Reduce html body margins and sidebar width for wider text.
      Update copyright years.
      Name implementation sections after language.
      Omit duplicate word.
      Add simulation subsection to software.

Pierre de Buyl (93):
      First commit by Pierre. Added the h5mol.rst file with the first thougts 
for a atomistic simulations file format specification.
      Fixed typo (missing parenthesis).
      Added the 'in discussion' section.
      Added some elements: force, force field, species mass, box size, time 
step.
      Changed h5mol in h5md for "hdf5 for molecular data".
      Modified the index.rst file to reflect the change of h5mol in h5md.
      Modification to the general informations.
      Added a section on reserved names and placed r,v and f into it.
      Decided on the naming scheme to be "full names" ('position' instead of 
'r', for instance).
      Added macroscopic observables information.
      Added reference to optional units. Specified the species dataset.
      Added a paragraph on the "step" and "time" datasets/groups to keep
      Added global attributes creator, h5md_version and datetime. Updated the 
reserved names accordingly.
      Added discussion on simulation box information.
      Added the parameters and profiling groups. Updated the reserved names.
      Added a discussion on parallel issues.
      Added trajectory subgroups information.
      Specified 'observables' as an actual group name.
      A bit of cleanup: typos, sorting of the reserved names, suppression of 
the 'Macroscopic variables' discussion element that has been solved with the 
'observables' group.
      Moved the global attributes to the 'h5md' group and move the date and 
time issue to the discussion section.
      Changed the 'time' and 'step' structure in the trajectory group. No use 
is made of attributes as links.
      Put creation_time as global attribute, specifying RFC 822 format.
      Updated the version global attribute to a 2-component integer dataset for 
the major and minor version numbers. Modified the observables group to hold 
step and time datasets, as for the trajectories.
      Changed name from h5md to H5MD (capitalization).
      Changed creation_time to be seconds since Epoch.
      Updated observables to hold also vector observables.
      Added minimum[D] and maximum[D] attributes to the position dataset to 
know the box size when displaying positions.
      Changed minimum and maximum positions as optional attributes.
      Added H5MD group example structure.
      Modified layout for structure example.
      Added structure layout to trajectory group.
      Removed the species part from the discussions as it is present in the 
specification.
      Modified the 'simulation box information' discussion.
      Added an example layout for observables.
      Changed the h5md group name to be lower-case.
      Lower-cased the example observables.
      Added density and velocity_field trajectory elements.
      Removed the fields from the trajectory group and moved them back
      Changed "interaction_energy" to "potential_energy" and updated the
      Changed species: should be an integer dataset. Also, if the
      Added creator_version to the h5md attributes.
      Added GPLv3: LICENSE file and headers everywhere.
      Added the copyright notice in all .rst files.
      Added a README file.
      Changed GPL into GNU General Public License.
      Added author info to /h5md.
      Corrected encoding typo.
      Changed attributes notation to "+--" and optional items are
      Added, in "general organization", a list of all root groups.
      Added a sentence on the structure of time-dependent data groups in
      Moved the "time data" information to be separated from the
      Removed extraneous box information from the trajectory group.
      Added an example for the information found in "parameters".
      Changed "sample" dataset name to "value" everywhere.
      Changed cubic to cuboid.
      Corrected cuboid subtitle underlining.
      Removed the reserved names section.
      Modified discussion to take into account latest updates of the draft.
      The optional character of most groups in a file is made explicit in the
      Removed the "profiling" group from the draft, its inclusion is not 
relevant at
      Specified the name of the "units" attribute in the trajectory group.
      Added a section for the notation.
      Promoted 'trajectory group', 'box specification' and 'observables group' 
so that they appear in the toc.
      Added structure display for the root of the file.
      Fixed typos.
      Added example of fixed-in-time triclinic box.
      Added HDF5 detail.
      Converted two only single quoted words to double quoted words;
      Moved the box data in the trajectory group.
      Changed the name 'value' to 'data' to avoid any possible confusion in the 
notation section.
      Minor edit in the 'General Organization' section.
      Minor edit for american english.
      Revert "Remove Peter from list of developers."
      Addition of image dataset in the trajectory group.
      Addition of id within the trajectory group.
      Modification of "type" to "geometry" for the box.
      Move notation section at the beginning of the document for clarity.
      Minor rephrase in definition of "id".
      Given the addition of the box boundary information, removal of the fact 
that the absence of "image" means that we have absolute positions.
      Specified that id is of integer kind.
      Make particle attribute/dataset optional in /observables.
      Correct bad indentation for bullet list.
      Changed boundary kinds to periodic/nonperiodic instead of periodic/open.
      Modification of time-dependent section to reflect the general change to 
time-dependence agnosticity.
      Update of Trajectory section to reflect the time-dependence agnosticity.
      Update of trajectory example.
      Remove special case for seldom-changing species that allows to store only 
changing time steps. In such a situation, one may chunk and compress the data.
      Fix typo.
      Clarify sentence.
      Moved parameters down in the general organization section.
      Fix typo.
      Fix typo.
      Change of /trajectory to /particles

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