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[h5md-commit] [h5md/h5md] 1ff24a: First commit by Pierre. Added the h5mo
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From: |
Felix Höfling |
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Subject: |
[h5md-commit] [h5md/h5md] 1ff24a: First commit by Pierre. Added the h5mol.rst file w... |
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Date: |
Thu, 26 Sep 2013 13:13:38 -0700 |
Branch: refs/heads/master
Home: https://github.com/h5md/h5md
Commit: 1ff24ac41fc0edc0339387874eb5fe44a49ca904
https://github.com/h5md/h5md/commit/1ff24ac41fc0edc0339387874eb5fe44a49ca904
Author: Pierre de Buyl <address@hidden>
Date: 2011-01-24 (Mon, 24 Jan 2011)
Changed paths:
A h5mol.rst
Log Message:
-----------
First commit by Pierre. Added the h5mol.rst file with the first thougts for a
atomistic simulations file format specification.
Commit: 4ef21263d9eb4cca83b7a65f4ea80d2b736560d3
https://github.com/h5md/h5md/commit/4ef21263d9eb4cca83b7a65f4ea80d2b736560d3
Author: Peter Colberg <address@hidden>
Date: 2011-01-25 (Tue, 25 Jan 2011)
Changed paths:
M h5mol.rst
Log Message:
-----------
h5mol: wrap at 80 chars per line and append underscore to references.
Commit: cac41d24cbabbfa026af610fd11912ebf164b099
https://github.com/h5md/h5md/commit/cac41d24cbabbfa026af610fd11912ebf164b099
Author: Peter Colberg <address@hidden>
Date: 2011-01-25 (Tue, 25 Jan 2011)
Changed paths:
A Makefile
A _static/.placeholder
A conf.py
A index.rst
Log Message:
-----------
Generate sphinx config.
Commit: 663fff3108e0458ca89ceac5f7886a4b733bcd72
https://github.com/h5md/h5md/commit/663fff3108e0458ca89ceac5f7886a4b733bcd72
Author: Peter Colberg <address@hidden>
Date: 2011-01-25 (Tue, 25 Jan 2011)
Changed paths:
M h5mol.rst
Log Message:
-----------
h5mol: convert from latin1 to utf8.
h5mol.rst:33: WARNING: undecodable source characters, replacing with "?": 'All
arrays are stored in C-order as enforced by the HDF5 file format (see
`>>>\xa7<<<'
Commit: 2faca871b0b9706f38b793ca72bd19f98045b265
https://github.com/h5md/h5md/commit/2faca871b0b9706f38b793ca72bd19f98045b265
Author: Peter Colberg <address@hidden>
Date: 2011-01-25 (Tue, 25 Jan 2011)
Changed paths:
A .gitignore
Log Message:
-----------
Add _build to .gitignore.
Commit: 8138f84a87b2bde574af6d1258d7d64296f8784b
https://github.com/h5md/h5md/commit/8138f84a87b2bde574af6d1258d7d64296f8784b
Author: Peter Colberg <address@hidden>
Date: 2011-01-25 (Tue, 25 Jan 2011)
Changed paths:
M index.rst
Log Message:
-----------
Add h5mol to index.
Commit: 346c3dcc83b77f95f862c2dda853dccb327aa697
https://github.com/h5md/h5md/commit/346c3dcc83b77f95f862c2dda853dccb327aa697
Author: Peter Colberg <address@hidden>
Date: 2011-01-25 (Tue, 25 Jan 2011)
Changed paths:
M conf.py
M index.rst
Log Message:
-----------
Remove Documentation from title(s).
Commit: 08591b27470ac5bf993a11c943dc89f7ede505d2
https://github.com/h5md/h5md/commit/08591b27470ac5bf993a11c943dc89f7ede505d2
Author: Pierre de Buyl <address@hidden>
Date: 2011-01-25 (Tue, 25 Jan 2011)
Changed paths:
M h5mol.rst
Log Message:
-----------
Fixed typo (missing parenthesis).
Commit: ccbe7e08836a54fb804d82198d36e5b08e6ce19b
https://github.com/h5md/h5md/commit/ccbe7e08836a54fb804d82198d36e5b08e6ce19b
Author: Pierre de Buyl <address@hidden>
Date: 2011-01-25 (Tue, 25 Jan 2011)
Changed paths:
M h5mol.rst
Log Message:
-----------
Added the 'in discussion' section.
Commit: 50a3dd04852bad0ef4e40b7f358f5bd9422ef25f
https://github.com/h5md/h5md/commit/50a3dd04852bad0ef4e40b7f358f5bd9422ef25f
Author: Pierre de Buyl <address@hidden>
Date: 2011-01-25 (Tue, 25 Jan 2011)
Changed paths:
M h5mol.rst
Log Message:
-----------
Added some elements: force, force field, species mass, box size, time step.
Commit: d7b0c8257e137571eef61bacfce28af861b0ab81
https://github.com/h5md/h5md/commit/d7b0c8257e137571eef61bacfce28af861b0ab81
Author: Pierre de Buyl <address@hidden>
Date: 2011-01-27 (Thu, 27 Jan 2011)
Changed paths:
A h5md.rst
R h5mol.rst
Log Message:
-----------
Changed h5mol in h5md for "hdf5 for molecular data".
Commit: b0f7617366a0f30b148daa9df8d8d68ff4522708
https://github.com/h5md/h5md/commit/b0f7617366a0f30b148daa9df8d8d68ff4522708
Author: Pierre de Buyl <address@hidden>
Date: 2011-01-27 (Thu, 27 Jan 2011)
Changed paths:
M index.rst
Log Message:
-----------
Modified the index.rst file to reflect the change of h5mol in h5md.
Commit: a0e3a4a9f32d37c90d6711904bf61733a801632a
https://github.com/h5md/h5md/commit/a0e3a4a9f32d37c90d6711904bf61733a801632a
Author: Pierre de Buyl <address@hidden>
Date: 2011-01-27 (Thu, 27 Jan 2011)
Changed paths:
M h5md.rst
Log Message:
-----------
Modification to the general informations.
Commit: 62c03ed27a6fa1264717e2e0314d888729d11b27
https://github.com/h5md/h5md/commit/62c03ed27a6fa1264717e2e0314d888729d11b27
Author: Peter Colberg <address@hidden>
Date: 2011-02-06 (Sun, 06 Feb 2011)
Changed paths:
M conf.py
Log Message:
-----------
Switch to sphinxdoc theme.
sphinxdoc theme has lighter colours and smaller font size.
Commit: 556a88a7adc1c3eb1aa8b2f6b29a0bda5c8043a2
https://github.com/h5md/h5md/commit/556a88a7adc1c3eb1aa8b2f6b29a0bda5c8043a2
Author: Pierre de Buyl <address@hidden>
Date: 2011-02-08 (Tue, 08 Feb 2011)
Changed paths:
M h5md.rst
Log Message:
-----------
Added a section on reserved names and placed r,v and f into it.
Started a "in discussion" element about the reserved names.
Commit: b7e9688fce74e8cd8f9cfc145c41ffe8e2c8cd12
https://github.com/h5md/h5md/commit/b7e9688fce74e8cd8f9cfc145c41ffe8e2c8cd12
Author: Pierre de Buyl <address@hidden>
Date: 2011-02-23 (Wed, 23 Feb 2011)
Changed paths:
M h5md.rst
Log Message:
-----------
Decided on the naming scheme to be "full names" ('position' instead of 'r',
for instance).
Commit: 95980f5876ec67365e445f0293db14dc686317ff
https://github.com/h5md/h5md/commit/95980f5876ec67365e445f0293db14dc686317ff
Author: Pierre de Buyl <address@hidden>
Date: 2011-02-24 (Thu, 24 Feb 2011)
Changed paths:
M h5md.rst
Log Message:
-----------
Added macroscopic observables information.
Commit: b6ae2d7762473398baeb1679b0f355b04d9e5e56
https://github.com/h5md/h5md/commit/b6ae2d7762473398baeb1679b0f355b04d9e5e56
Author: Pierre de Buyl <address@hidden>
Date: 2011-02-24 (Thu, 24 Feb 2011)
Changed paths:
M h5md.rst
Log Message:
-----------
Added reference to optional units. Specified the species dataset.
Added the link to "step" and "time" as attributes to the trajectory datasets.
Commit: a9d4effea04b25bc0b710aecf492cf5f905e38da
https://github.com/h5md/h5md/commit/a9d4effea04b25bc0b710aecf492cf5f905e38da
Author: Pierre de Buyl <address@hidden>
Date: 2011-02-24 (Thu, 24 Feb 2011)
Changed paths:
M h5md.rst
Log Message:
-----------
Added a paragraph on the "step" and "time" datasets/groups to keep
the time information of the trajectory datasets.
Commit: 71b055ebc9df260892cabbac696ed5c8c9cd7105
https://github.com/h5md/h5md/commit/71b055ebc9df260892cabbac696ed5c8c9cd7105
Author: Pierre de Buyl <address@hidden>
Date: 2011-03-07 (Mon, 07 Mar 2011)
Changed paths:
M h5md.rst
Log Message:
-----------
Added global attributes creator, h5md_version and datetime. Updated the
reserved names accordingly.
Commit: c537b4b7ba510895bfcc740ba66e0a32b5980231
https://github.com/h5md/h5md/commit/c537b4b7ba510895bfcc740ba66e0a32b5980231
Author: Pierre de Buyl <address@hidden>
Date: 2011-03-07 (Mon, 07 Mar 2011)
Changed paths:
M h5md.rst
Log Message:
-----------
Added discussion on simulation box information.
Commit: d47cc64367930fdc5c8764d672595711604ae670
https://github.com/h5md/h5md/commit/d47cc64367930fdc5c8764d672595711604ae670
Author: Pierre de Buyl <address@hidden>
Date: 2011-03-07 (Mon, 07 Mar 2011)
Changed paths:
M h5md.rst
Log Message:
-----------
Added the parameters and profiling groups. Updated the reserved names.
Commit: 76fc86c175e7401153fd0e491af7bfeba9efb9a1
https://github.com/h5md/h5md/commit/76fc86c175e7401153fd0e491af7bfeba9efb9a1
Author: Pierre de Buyl <address@hidden>
Date: 2011-03-07 (Mon, 07 Mar 2011)
Changed paths:
M h5md.rst
Log Message:
-----------
Added a discussion on parallel issues.
Commit: 5bae03648dafbfe5adb60f5df5eecc8981ed15d5
https://github.com/h5md/h5md/commit/5bae03648dafbfe5adb60f5df5eecc8981ed15d5
Author: Pierre de Buyl <address@hidden>
Date: 2011-03-08 (Tue, 08 Mar 2011)
Changed paths:
M h5md.rst
Log Message:
-----------
Added trajectory subgroups information.
Commit: cc8093863103611468d65ca01dedb06c4e5def37
https://github.com/h5md/h5md/commit/cc8093863103611468d65ca01dedb06c4e5def37
Author: Pierre de Buyl <address@hidden>
Date: 2011-03-08 (Tue, 08 Mar 2011)
Changed paths:
M h5md.rst
Log Message:
-----------
Specified 'observables' as an actual group name.
Commit: e37b156ab147de7b78395520ba012dfd144c7e30
https://github.com/h5md/h5md/commit/e37b156ab147de7b78395520ba012dfd144c7e30
Author: Pierre de Buyl <address@hidden>
Date: 2011-03-08 (Tue, 08 Mar 2011)
Changed paths:
M h5md.rst
Log Message:
-----------
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.
Commit: f4ea7a7d9f982fbfa3756ff5686da84a6a8c1771
https://github.com/h5md/h5md/commit/f4ea7a7d9f982fbfa3756ff5686da84a6a8c1771
Author: Pierre de Buyl <address@hidden>
Date: 2011-03-08 (Tue, 08 Mar 2011)
Changed paths:
M h5md.rst
Log Message:
-----------
Moved the global attributes to the 'h5md' group and move the date and time
issue to the discussion section.
Commit: 6409058f0a2d995c089d74f14f1969a8298725d2
https://github.com/h5md/h5md/commit/6409058f0a2d995c089d74f14f1969a8298725d2
Author: Pierre de Buyl <address@hidden>
Date: 2011-03-10 (Thu, 10 Mar 2011)
Changed paths:
M h5md.rst
Log Message:
-----------
Changed the 'time' and 'step' structure in the trajectory group. No use is
made of attributes as links.
Commit: bf703a39c45fd05473dc305a1873d949d11ac5fc
https://github.com/h5md/h5md/commit/bf703a39c45fd05473dc305a1873d949d11ac5fc
Author: Pierre de Buyl <address@hidden>
Date: 2011-03-10 (Thu, 10 Mar 2011)
Changed paths:
M h5md.rst
Log Message:
-----------
Put creation_time as global attribute, specifying RFC 822 format.
Commit: 0a0c7ddd659e07a27dfe0a2c243bdcabdacc7bbe
https://github.com/h5md/h5md/commit/0a0c7ddd659e07a27dfe0a2c243bdcabdacc7bbe
Author: Pierre de Buyl <address@hidden>
Date: 2011-03-11 (Fri, 11 Mar 2011)
Changed paths:
M h5md.rst
Log Message:
-----------
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.
Commit: 249ba5a786a2e1e93f27cb875d19b4abc5d72810
https://github.com/h5md/h5md/commit/249ba5a786a2e1e93f27cb875d19b4abc5d72810
Author: Pierre de Buyl <address@hidden>
Date: 2011-03-14 (Mon, 14 Mar 2011)
Changed paths:
M h5md.rst
Log Message:
-----------
Changed name from h5md to H5MD (capitalization).
Commit: f0e3c2344c565c10c13376e06d2db5c26da23c5c
https://github.com/h5md/h5md/commit/f0e3c2344c565c10c13376e06d2db5c26da23c5c
Author: Pierre de Buyl <address@hidden>
Date: 2011-03-15 (Tue, 15 Mar 2011)
Changed paths:
M h5md.rst
Log Message:
-----------
Changed creation_time to be seconds since Epoch.
Commit: 323057e46326c38aeaa940d04b9288532c1d4ee2
https://github.com/h5md/h5md/commit/323057e46326c38aeaa940d04b9288532c1d4ee2
Author: Pierre de Buyl <address@hidden>
Date: 2011-03-16 (Wed, 16 Mar 2011)
Changed paths:
M h5md.rst
Log Message:
-----------
Updated observables to hold also vector observables.
Commit: df4fbf0768bc3da48ec3011bb4ee5236ee944818
https://github.com/h5md/h5md/commit/df4fbf0768bc3da48ec3011bb4ee5236ee944818
Author: Pierre de Buyl <address@hidden>
Date: 2011-03-16 (Wed, 16 Mar 2011)
Changed paths:
M h5md.rst
Log Message:
-----------
Added minimum[D] and maximum[D] attributes to the position dataset to know
the box size when displaying positions.
Commit: fad70510aa9ccc0ec32216bb8afd107be198cc26
https://github.com/h5md/h5md/commit/fad70510aa9ccc0ec32216bb8afd107be198cc26
Author: Pierre de Buyl <address@hidden>
Date: 2011-03-16 (Wed, 16 Mar 2011)
Changed paths:
M h5md.rst
Log Message:
-----------
Changed minimum and maximum positions as optional attributes.
Commit: 1b4574fdabf9df9f7f917afd2e742d8c8702ff7a
https://github.com/h5md/h5md/commit/1b4574fdabf9df9f7f917afd2e742d8c8702ff7a
Author: Pierre de Buyl <address@hidden>
Date: 2011-03-22 (Tue, 22 Mar 2011)
Changed paths:
M h5md.rst
Log Message:
-----------
Added H5MD group example structure.
Commit: f0432df78d46a937f0886aceffaece3b59167e53
https://github.com/h5md/h5md/commit/f0432df78d46a937f0886aceffaece3b59167e53
Author: Pierre de Buyl <address@hidden>
Date: 2011-03-22 (Tue, 22 Mar 2011)
Changed paths:
M h5md.rst
Log Message:
-----------
Modified layout for structure example.
Commit: bfd0d18becc4b8b8cad883fa94fc9b0eb4ffd2a2
https://github.com/h5md/h5md/commit/bfd0d18becc4b8b8cad883fa94fc9b0eb4ffd2a2
Author: Pierre de Buyl <address@hidden>
Date: 2011-03-22 (Tue, 22 Mar 2011)
Changed paths:
M h5md.rst
Log Message:
-----------
Added structure layout to trajectory group.
Commit: 1f27b55dbbeb8f85993a825b01abd856213bccfa
https://github.com/h5md/h5md/commit/1f27b55dbbeb8f85993a825b01abd856213bccfa
Author: Pierre de Buyl <address@hidden>
Date: 2011-03-24 (Thu, 24 Mar 2011)
Changed paths:
M h5md.rst
Log Message:
-----------
Removed the species part from the discussions as it is present in the
specification.
Commit: 963e1bd441aa692019fdbca080eda8581677376e
https://github.com/h5md/h5md/commit/963e1bd441aa692019fdbca080eda8581677376e
Author: Pierre de Buyl <address@hidden>
Date: 2011-03-24 (Thu, 24 Mar 2011)
Changed paths:
M h5md.rst
Log Message:
-----------
Modified the 'simulation box information' discussion.
Commit: ab432de45b9e5c4813ad35737718c9a8c206ee4b
https://github.com/h5md/h5md/commit/ab432de45b9e5c4813ad35737718c9a8c206ee4b
Author: Pierre de Buyl <address@hidden>
Date: 2011-03-24 (Thu, 24 Mar 2011)
Changed paths:
M h5md.rst
Log Message:
-----------
Added an example layout for observables.
Commit: 0beed1f7971add4338475a1abc7844d34804ceca
https://github.com/h5md/h5md/commit/0beed1f7971add4338475a1abc7844d34804ceca
Author: Pierre de Buyl <address@hidden>
Date: 2011-03-24 (Thu, 24 Mar 2011)
Changed paths:
M h5md.rst
Log Message:
-----------
Changed the h5md group name to be lower-case.
Commit: ad1999a054e23f2112bf1a2fe74fa36c08f25216
https://github.com/h5md/h5md/commit/ad1999a054e23f2112bf1a2fe74fa36c08f25216
Author: Pierre de Buyl <address@hidden>
Date: 2011-05-27 (Fri, 27 May 2011)
Changed paths:
M h5md.rst
Log Message:
-----------
Lower-cased the example observables.
Commit: 64de61927caac3c482d68a4b03c344331a04da90
https://github.com/h5md/h5md/commit/64de61927caac3c482d68a4b03c344331a04da90
Author: Pierre de Buyl <address@hidden>
Date: 2011-05-30 (Mon, 30 May 2011)
Changed paths:
M h5md.rst
Log Message:
-----------
Added density and velocity_field trajectory elements.
Corrected datetime h5md attribute to creation time in the example.
Commit: 0a5ab7d608ec44590007b36dc2a33dfd9f558b0d
https://github.com/h5md/h5md/commit/0a5ab7d608ec44590007b36dc2a33dfd9f558b0d
Author: Pierre de Buyl <address@hidden>
Date: 2011-06-14 (Tue, 14 Jun 2011)
Changed paths:
M h5md.rst
Log Message:
-----------
Removed the fields from the trajectory group and moved them back
to the discussion section.
Updated the trajectory group to contain only subgroups that comply
to the specification.
Updated the example structure for trajectories.
Commit: 36eb87ba71225b3402cbcdba8b55f9b758b83c04
https://github.com/h5md/h5md/commit/36eb87ba71225b3402cbcdba8b55f9b758b83c04
Author: Pierre de Buyl <address@hidden>
Date: 2011-06-14 (Tue, 14 Jun 2011)
Changed paths:
M h5md.rst
Log Message:
-----------
Changed "interaction_energy" to "potential_energy" and updated the
observables paragraph.
Commit: 85c31fd483f442b41de3e98ed2e48b12cd5e64f7
https://github.com/h5md/h5md/commit/85c31fd483f442b41de3e98ed2e48b12cd5e64f7
Author: Pierre de Buyl <address@hidden>
Date: 2011-06-14 (Tue, 14 Jun 2011)
Changed paths:
M h5md.rst
Log Message:
-----------
Changed species: should be an integer dataset. Also, if the
species at a given time is missing, it is assumed that the most
recent entry is still valid.
Commit: f1d83b5884c08c1a311fe51da82bc84fe0638ae3
https://github.com/h5md/h5md/commit/f1d83b5884c08c1a311fe51da82bc84fe0638ae3
Author: Pierre de Buyl <address@hidden>
Date: 2011-06-14 (Tue, 14 Jun 2011)
Changed paths:
M h5md.rst
Log Message:
-----------
Added creator_version to the h5md attributes.
Commit: ed364740e93829820548142b6eeaea0d93d88dcd
https://github.com/h5md/h5md/commit/ed364740e93829820548142b6eeaea0d93d88dcd
Author: Pierre de Buyl <address@hidden>
Date: 2011-06-19 (Sun, 19 Jun 2011)
Changed paths:
A LICENSE
A discussion.rst
A draft.rst
R h5md.rst
M index.rst
Log Message:
-----------
Added GPLv3: LICENSE file and headers everywhere.
Split the specification in a draft and a discussion.
Added some info in the index.
Commit: d1768c4347b8a80bbedcb3d9852fb76eb965ef34
https://github.com/h5md/h5md/commit/d1768c4347b8a80bbedcb3d9852fb76eb965ef34
Author: Pierre de Buyl <address@hidden>
Date: 2011-06-19 (Sun, 19 Jun 2011)
Changed paths:
M discussion.rst
M draft.rst
M index.rst
Log Message:
-----------
Added the copyright notice in all .rst files.
Commit: 4124cf7c2aa49202199809fde984eeef97d432c2
https://github.com/h5md/h5md/commit/4124cf7c2aa49202199809fde984eeef97d432c2
Author: Peter Colberg <address@hidden>
Date: 2011-06-19 (Sun, 19 Jun 2011)
Changed paths:
M index.rst
Log Message:
-----------
index: fix UTF8 character in Felix's name.
Commit: d8ba3555dc9eeb0f2d74ad747bd95325e797bc92
https://github.com/h5md/h5md/commit/d8ba3555dc9eeb0f2d74ad747bd95325e797bc92
Author: Peter Colberg <address@hidden>
Date: 2011-06-19 (Sun, 19 Jun 2011)
Changed paths:
M discussion.rst
M index.rst
Log Message:
-----------
Fix minor typos.
Commit: 6f8e7bd9118075ad6d67a3268fc42eb8b6d6a708
https://github.com/h5md/h5md/commit/6f8e7bd9118075ad6d67a3268fc42eb8b6d6a708
Author: Pierre de Buyl <address@hidden>
Date: 2011-07-20 (Wed, 20 Jul 2011)
Changed paths:
A README
Log Message:
-----------
Added a README file.
Commit: 5a3988691ff4588673d9561ccd1f3cd1bb741c5c
https://github.com/h5md/h5md/commit/5a3988691ff4588673d9561ccd1f3cd1bb741c5c
Author: Pierre de Buyl <address@hidden>
Date: 2011-07-27 (Wed, 27 Jul 2011)
Changed paths:
M Makefile
M README
M conf.py
M index.rst
Log Message:
-----------
Changed GPL into GNU General Public License.
Added license information to Makefile and conf.py.
Commit: 3b8e6e5a672df19b290689e4b9a58bbbde6e0d88
https://github.com/h5md/h5md/commit/3b8e6e5a672df19b290689e4b9a58bbbde6e0d88
Author: Peter Colberg <address@hidden>
Date: 2011-08-05 (Fri, 05 Aug 2011)
Changed paths:
M conf.py
Log Message:
-----------
conf.py: fix missing UTF-8 header.
Python expects the UTF-8 header in the first line.
sphinx-build -b html -d _build/doctrees . _build/html
Making output directory...
Running Sphinx v1.0.7
Configuration error:
There is a syntax error in your configuration file: Non-ASCII character '\xc2'
in file h5md/conf.py on line 1, but no encoding declared; see
http://www.python.org/peps/pep-0263.html for details (conf.py, line 1)
Commit: e856003b7cda6815fd1d07ace7e6e8bcf2d30e73
https://github.com/h5md/h5md/commit/e856003b7cda6815fd1d07ace7e6e8bcf2d30e73
Author: Peter Colberg <address@hidden>
Date: 2011-08-06 (Sat, 06 Aug 2011)
Changed paths:
M discussion.rst
M draft.rst
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Commit: b60e6a9789e9f7ffd81262e488158462116329ee
https://github.com/h5md/h5md/commit/b60e6a9789e9f7ffd81262e488158462116329ee
Author: Pierre de Buyl <address@hidden>
Date: 2011-08-15 (Mon, 15 Aug 2011)
Changed paths:
M draft.rst
Log Message:
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Added author info to /h5md.
Commit: c2895750d35d106e32acf96b0bd0c3cb731924ff
https://github.com/h5md/h5md/commit/c2895750d35d106e32acf96b0bd0c3cb731924ff
Author: Pierre de Buyl <address@hidden>
Date: 2011-08-15 (Mon, 15 Aug 2011)
Changed paths:
M draft.rst
Log Message:
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Corrected encoding typo.
Commit: d44c0c1aef90cad3aa69a502f3f008efa5884699
https://github.com/h5md/h5md/commit/d44c0c1aef90cad3aa69a502f3f008efa5884699
Author: Peter Colberg <address@hidden>
Date: 2011-08-17 (Wed, 17 Aug 2011)
Changed paths:
M Makefile
M conf.py
M draft.rst
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Purge trailing whitespace at end of line.
Commit: dbcbbdc4d1314cd8d77bf61b390813b2ca056d2b
https://github.com/h5md/h5md/commit/dbcbbdc4d1314cd8d77bf61b390813b2ca056d2b
Author: Peter Colberg <address@hidden>
Date: 2011-08-25 (Thu, 25 Aug 2011)
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M conf.py
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conf.py: substitute leftover “Molecular Simulation” with “H5MD”.
Commit: 74a28be0e82d4babfadbb92429636753b1f849fd
https://github.com/h5md/h5md/commit/74a28be0e82d4babfadbb92429636753b1f849fd
Author: Peter Colberg <address@hidden>
Date: 2011-08-25 (Thu, 25 Aug 2011)
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M conf.py
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conf.py: replace version 0.0.1 with 0.0.
The first release will be tagged 0.1.
Commit: 9d7ee050b56a321ffd7fc32f72e90396af1306ca
https://github.com/h5md/h5md/commit/9d7ee050b56a321ffd7fc32f72e90396af1306ca
Author: Felix Höfling <address@hidden>
Date: 2011-08-29 (Mon, 29 Aug 2011)
Changed paths:
M draft.rst
Log Message:
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rename 'samples' and 'coordinates' to 'sample'
This unifies the subgroups describing a specific time series. We will prefer
the singular form for datasets or groups of datasets, and plural for groups
that collect other groups.
Remove 'coordinates' from the list of reserved names.
Commit: ddc2864335b2449545cf94da83dacfc74b5d650c
https://github.com/h5md/h5md/commit/ddc2864335b2449545cf94da83dacfc74b5d650c
Author: Pierre de Buyl <address@hidden>
Date: 2011-09-01 (Thu, 01 Sep 2011)
Changed paths:
M draft.rst
Log Message:
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Changed attributes notation to "+--" and optional items are
enclosed in square brackets.
Commit: c787ebb6c08261f75a419ec2d1a8ff6a2a58551d
https://github.com/h5md/h5md/commit/c787ebb6c08261f75a419ec2d1a8ff6a2a58551d
Author: Pierre de Buyl <address@hidden>
Date: 2011-10-21 (Fri, 21 Oct 2011)
Changed paths:
M draft.rst
Log Message:
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Added, in "general organization", a list of all root groups.
Updated the box information.
Commit: fa0467b2e6ad784d035bdb94065b89e3271e80db
https://github.com/h5md/h5md/commit/fa0467b2e6ad784d035bdb94065b89e3271e80db
Author: Pierre de Buyl <address@hidden>
Date: 2012-01-04 (Wed, 04 Jan 2012)
Changed paths:
M draft.rst
Log Message:
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Added a sentence on the structure of time-dependent data groups in
the intro.
Commit: 2b89c13f75102167f64bae8445cdbbc89f7c73b6
https://github.com/h5md/h5md/commit/2b89c13f75102167f64bae8445cdbbc89f7c73b6
Author: Pierre de Buyl <address@hidden>
Date: 2012-02-10 (Fri, 10 Feb 2012)
Changed paths:
M draft.rst
Log Message:
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Moved the "time data" information to be separated from the
trajectory group, as it is now generalized.
Commit: 64800b08c248942e23709e209fb26eaf1831ba89
https://github.com/h5md/h5md/commit/64800b08c248942e23709e209fb26eaf1831ba89
Author: Pierre de Buyl <address@hidden>
Date: 2012-02-10 (Fri, 10 Feb 2012)
Changed paths:
M draft.rst
Log Message:
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Removed extraneous box information from the trajectory group.
Commit: 9c15daed2a30e51125161140548be198e223f7b3
https://github.com/h5md/h5md/commit/9c15daed2a30e51125161140548be198e223f7b3
Author: Pierre de Buyl <address@hidden>
Date: 2012-02-10 (Fri, 10 Feb 2012)
Changed paths:
M draft.rst
Log Message:
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Added an example for the information found in "parameters".
Commit: eff7ae6559a9fe119f5a5b7774c31aa1930e1bf8
https://github.com/h5md/h5md/commit/eff7ae6559a9fe119f5a5b7774c31aa1930e1bf8
Author: Pierre de Buyl <address@hidden>
Date: 2012-02-10 (Fri, 10 Feb 2012)
Changed paths:
M draft.rst
Log Message:
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Changed "sample" dataset name to "value" everywhere.
Commit: aff1f2f567b231933eb55854784b84c0654c4eea
https://github.com/h5md/h5md/commit/aff1f2f567b231933eb55854784b84c0654c4eea
Author: Pierre de Buyl <address@hidden>
Date: 2012-07-15 (Sun, 15 Jul 2012)
Changed paths:
M draft.rst
Log Message:
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Changed cubic to cuboid.
Commit: 3092738fbe0687ec60ec8a6b1c244ab83447c111
https://github.com/h5md/h5md/commit/3092738fbe0687ec60ec8a6b1c244ab83447c111
Author: Pierre de Buyl <address@hidden>
Date: 2012-07-15 (Sun, 15 Jul 2012)
Changed paths:
M draft.rst
Log Message:
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Corrected cuboid subtitle underlining.
Commit: a39257fe2b702c6e7dcd15ffbf8fbb22f4c75b7e
https://github.com/h5md/h5md/commit/a39257fe2b702c6e7dcd15ffbf8fbb22f4c75b7e
Author: Pierre de Buyl <address@hidden>
Date: 2012-07-15 (Sun, 15 Jul 2012)
Changed paths:
M draft.rst
Log Message:
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Removed the reserved names section.
Commit: 44c9bcefc258e31f4043edfd2ebaa815a69644ce
https://github.com/h5md/h5md/commit/44c9bcefc258e31f4043edfd2ebaa815a69644ce
Author: Pierre de Buyl <address@hidden>
Date: 2012-07-21 (Sat, 21 Jul 2012)
Changed paths:
M discussion.rst
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Modified discussion to take into account latest updates of the draft.
Commit: 5bd007c352802a1a1e8070e004cacccf8adf818f
https://github.com/h5md/h5md/commit/5bd007c352802a1a1e8070e004cacccf8adf818f
Author: Felix Höfling <address@hidden>
Date: 2012-07-31 (Tue, 31 Jul 2012)
Changed paths:
M draft.rst
Log Message:
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observables: allow subgroups, add "pressure", matrix of edge vectors
We shall allow subgroups in the "observables" group as we do in "trajectory".
We shall not forget the pressue, which is of similar importance as the
potential energy or the temperature (aka kinetic energy).
For the triclinic box, the set of D D-dimensional vectors may be considered a
D×D matrix which makes essentially no difference how the data are stored
finally. But it is clearer that the full set of edge vectors is to be
considered a single entity, e.g., the determinant of which readily yields the
box volume.
Commit: 05c78ca8849c17dc69335ed62dbd313d29bb42cd
https://github.com/h5md/h5md/commit/05c78ca8849c17dc69335ed62dbd313d29bb42cd
Author: Pierre de Buyl <address@hidden>
Date: 2012-08-13 (Mon, 13 Aug 2012)
Changed paths:
M draft.rst
Log Message:
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The optional character of most groups in a file is made explicit in the
specification.
Commit: 9b70b6ae561e0df374b1e40882bfbc6823d5edfa
https://github.com/h5md/h5md/commit/9b70b6ae561e0df374b1e40882bfbc6823d5edfa
Author: Pierre de Buyl <address@hidden>
Date: 2012-08-13 (Mon, 13 Aug 2012)
Changed paths:
M draft.rst
Log Message:
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Removed the "profiling" group from the draft, its inclusion is not relevant at
this time.
Only "parameters" is a program-dependent group, it has been promoted in the
document hierarchy by one level.
Commit: e5e862ed8dd46a97d26fdcb2303bcec23f61ec96
https://github.com/h5md/h5md/commit/e5e862ed8dd46a97d26fdcb2303bcec23f61ec96
Author: Pierre de Buyl <address@hidden>
Date: 2012-08-13 (Mon, 13 Aug 2012)
Changed paths:
M draft.rst
Log Message:
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Specified the name of the "units" attribute in the trajectory group.
Commit: b215f4b65034f6c769a019528253e16f9038645d
https://github.com/h5md/h5md/commit/b215f4b65034f6c769a019528253e16f9038645d
Author: Pierre de Buyl <address@hidden>
Date: 2012-10-14 (Sun, 14 Oct 2012)
Changed paths:
M draft.rst
Log Message:
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Added a section for the notation.
Commit: 96323ee12149046e6a95c282f88381d56e27905a
https://github.com/h5md/h5md/commit/96323ee12149046e6a95c282f88381d56e27905a
Author: Pierre de Buyl <address@hidden>
Date: 2012-11-19 (Mon, 19 Nov 2012)
Changed paths:
M draft.rst
Log Message:
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Promoted 'trajectory group', 'box specification' and 'observables group' so
that they appear in the toc.
Commit: 54654b76a1a5bdf96aaa5de7d2b8bab622419611
https://github.com/h5md/h5md/commit/54654b76a1a5bdf96aaa5de7d2b8bab622419611
Author: Pierre de Buyl <address@hidden>
Date: 2012-11-19 (Mon, 19 Nov 2012)
Changed paths:
M draft.rst
Log Message:
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Added structure display for the root of the file.
Commit: 6fba3944c0f682b957940eccddeaa1357a634cd3
https://github.com/h5md/h5md/commit/6fba3944c0f682b957940eccddeaa1357a634cd3
Author: Pierre de Buyl <address@hidden>
Date: 2012-11-19 (Mon, 19 Nov 2012)
Changed paths:
M draft.rst
Log Message:
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Fixed typos.
Commit: 23e87cf9a2b067666beac652a9aaeaddd8638f87
https://github.com/h5md/h5md/commit/23e87cf9a2b067666beac652a9aaeaddd8638f87
Author: Pierre de Buyl <address@hidden>
Date: 2012-11-19 (Mon, 19 Nov 2012)
Changed paths:
M draft.rst
Log Message:
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Added example of fixed-in-time triclinic box.
Commit: 02be5edff9f2152175cd5b4a064c7b88e425afde
https://github.com/h5md/h5md/commit/02be5edff9f2152175cd5b4a064c7b88e425afde
Author: Pierre de Buyl <address@hidden>
Date: 2012-11-19 (Mon, 19 Nov 2012)
Changed paths:
M draft.rst
Log Message:
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Added HDF5 detail.
Commit: 862ef3dda1bf627f9bfae06549b3b5bd5c6436d4
https://github.com/h5md/h5md/commit/862ef3dda1bf627f9bfae06549b3b5bd5c6436d4
Author: Pierre de Buyl <address@hidden>
Date: 2012-11-19 (Mon, 19 Nov 2012)
Changed paths:
M draft.rst
Log Message:
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Converted two only single quoted words to double quoted words;
Commit: 20f772b17b856f0c68d5dfb01e94d28d8cef2702
https://github.com/h5md/h5md/commit/20f772b17b856f0c68d5dfb01e94d28d8cef2702
Author: Pierre de Buyl <address@hidden>
Date: 2012-12-21 (Fri, 21 Dec 2012)
Changed paths:
M draft.rst
Log Message:
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Moved the box data in the trajectory group.
Commit: d8b8eba5eab005ab584fd0ab4ba91b17a1fe42db
https://github.com/h5md/h5md/commit/d8b8eba5eab005ab584fd0ab4ba91b17a1fe42db
Author: Pierre de Buyl <address@hidden>
Date: 2012-12-21 (Fri, 21 Dec 2012)
Changed paths:
M draft.rst
Log Message:
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Changed the name 'value' to 'data' to avoid any possible confusion in the
notation section.
Commit: c4729428fcd40c054ce276566ba21c6e43d38a83
https://github.com/h5md/h5md/commit/c4729428fcd40c054ce276566ba21c6e43d38a83
Author: Pierre de Buyl <address@hidden>
Date: 2012-12-21 (Fri, 21 Dec 2012)
Changed paths:
M draft.rst
Log Message:
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Minor edit in the 'General Organization' section.
Commit: d978e3e2e90b0904fdfed27dbb55e0c721a58587
https://github.com/h5md/h5md/commit/d978e3e2e90b0904fdfed27dbb55e0c721a58587
Author: Pierre de Buyl <address@hidden>
Date: 2012-12-21 (Fri, 21 Dec 2012)
Changed paths:
M draft.rst
Log Message:
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Minor edit for american english.
Commit: e0ea7891b998744ec6c386e66e6dac7796c82493
https://github.com/h5md/h5md/commit/e0ea7891b998744ec6c386e66e6dac7796c82493
Author: Peter Colberg <address@hidden>
Date: 2013-02-08 (Fri, 08 Feb 2013)
Changed paths:
M index.rst
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Remove Peter from list of developers.
Commit: f8c49b1fe5cbc97bf4949e7eb2f1925d4df54b1f
https://github.com/h5md/h5md/commit/f8c49b1fe5cbc97bf4949e7eb2f1925d4df54b1f
Author: Felix Höfling <address@hidden>
Date: 2013-02-22 (Fri, 22 Feb 2013)
Changed paths:
M draft.rst
Log Message:
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Add attribute "dimension" to parameters group
Commit: 3e424003ecb01be26cf006453dc086eb69ab64b5
https://github.com/h5md/h5md/commit/3e424003ecb01be26cf006453dc086eb69ab64b5
Author: Pierre de Buyl <address@hidden>
Date: 2013-02-26 (Tue, 26 Feb 2013)
Changed paths:
M index.rst
Log Message:
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Revert "Remove Peter from list of developers."
This reverts commit e0ea7891b998744ec6c386e66e6dac7796c82493.
Commit: 0fd560c1e04255d6f40324052c409c5ac63d9a1c
https://github.com/h5md/h5md/commit/0fd560c1e04255d6f40324052c409c5ac63d9a1c
Author: Peter Colberg <address@hidden>
Date: 2013-05-05 (Sun, 05 May 2013)
Changed paths:
M draft.rst
Log Message:
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Store edges and offset as attributes for fixed-size box.
http://article.gmane.org/gmane.science.simulation.h5md.user/125
Commit: d26d8e96a29693f7cd76a7489d0414c9f850b61f
https://github.com/h5md/h5md/commit/d26d8e96a29693f7cd76a7489d0414c9f850b61f
Author: Peter Colberg <address@hidden>
Date: 2013-05-05 (Sun, 05 May 2013)
Changed paths:
M draft.rst
Log Message:
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Specify "parameters" group for user-defined parameters.
http://article.gmane.org/gmane.science.simulation.h5md.user/131
Commit: 8e0f25f657d5221ca47c9b2681725d4d79e8dde3
https://github.com/h5md/h5md/commit/8e0f25f657d5221ca47c9b2681725d4d79e8dde3
Author: Felix Höfling <address@hidden>
Date: 2013-05-06 (Mon, 06 May 2013)
Changed paths:
M draft.rst
Log Message:
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revise text for tajectory group
* revise introducory paragraph, add general definition of what is meant
by "trajectory" information
* add semi-grandcanonical Monte-Carlo as example for fluctuating species
Commit: dd4faedca244b94e2bec2c5c6162f534f85da064
https://github.com/h5md/h5md/commit/dd4faedca244b94e2bec2c5c6162f534f85da064
Author: Felix Höfling <address@hidden>
Date: 2013-05-06 (Mon, 06 May 2013)
Changed paths:
M draft.rst
Log Message:
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Revise description of observables group
* clean up introductory paragraph
* add count attribute as discussed in
http://lists.nongnu.org/archive/html/h5md-user/2013-02/msg00001.html
* allow for observables of higher tensor rank, e.g., the stress tensor
* add note what "temperature" actually means. The true thermodynamic
temperature is only defined as ensemble average and does not fluctuate
in NVT simulations (the kinetic energy does).
Commit: 39fe4b694b7ad374e8226b038b2fc7ed5ac58f8d
https://github.com/h5md/h5md/commit/39fe4b694b7ad374e8226b038b2fc7ed5ac58f8d
Author: Pierre de Buyl <address@hidden>
Date: 2013-05-29 (Wed, 29 May 2013)
Changed paths:
M draft.rst
Log Message:
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Addition of image dataset in the trajectory group.
Commit: c234149781bfa9f5dc81aa139038e7dc6689b64d
https://github.com/h5md/h5md/commit/c234149781bfa9f5dc81aa139038e7dc6689b64d
Author: Felix Höfling <address@hidden>
Date: 2013-05-29 (Wed, 29 May 2013)
Changed paths:
M draft.rst
Log Message:
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rename "count" to "particles" in observables groups
This avoids a potential name clash with a future extension to store
time-averaged observables adding optional fields like "error", "count"
etc.
http://article.gmane.org/gmane.science.simulation.h5md.user/149
Commit: fe80364a43befcd01d43347e0fb7672f565a1b86
https://github.com/h5md/h5md/commit/fe80364a43befcd01d43347e0fb7672f565a1b86
Author: Felix Höfling <address@hidden>
Date: 2013-05-29 (Wed, 29 May 2013)
Changed paths:
M draft.rst
Log Message:
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Generalise optional "unit" attribute for all datasets
Move the description of the "unit" attribute from the trajectory group
to the general section on time-dependent data groups.
Commit: 6f6ccb6348fe3077334a009a09e42db9c1d16b31
https://github.com/h5md/h5md/commit/6f6ccb6348fe3077334a009a09e42db9c1d16b31
Author: Felix Höfling <address@hidden>
Date: 2013-05-29 (Wed, 29 May 2013)
Changed paths:
M draft.rst
Log Message:
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add attribute "dimension" to the box group
http://permalink.gmane.org/gmane.science.simulation.h5md.user/147
Commit: 4335c814fa532c886deb046b42d44577836edd10
https://github.com/h5md/h5md/commit/4335c814fa532c886deb046b42d44577836edd10
Author: Felix Höfling <address@hidden>
Date: 2013-05-29 (Wed, 29 May 2013)
Changed paths:
M draft.rst
Log Message:
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revise section on box specification
* Make the box group mandatory in both the trajectory and the
observables groups (recall that both root groups are optional and may
not be present).
http://thread.gmane.org/gmane.science.simulation.h5md.user/126
* Revise and rephrase some of the text.
Commit: a6b2336dda2822b7e79a46bb7289279bb7bbb420
https://github.com/h5md/h5md/commit/a6b2336dda2822b7e79a46bb7289279bb7bbb420
Author: Felix Höfling <address@hidden>
Date: 2013-05-29 (Wed, 29 May 2013)
Changed paths:
M draft.rst
Log Message:
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observables group: minor editing
Commit: f012b09b547751d409bc04cc642f250ca622970f
https://github.com/h5md/h5md/commit/f012b09b547751d409bc04cc642f250ca622970f
Author: Felix Höfling <address@hidden>
Date: 2013-05-29 (Wed, 29 May 2013)
Changed paths:
M draft.rst
Log Message:
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fix graphical tree for /observables
This amends commit a6b2336.
Commit: ff0e8689aa5c214fc8dedbdbc648ccf10f0217e2
https://github.com/h5md/h5md/commit/ff0e8689aa5c214fc8dedbdbc648ccf10f0217e2
Author: Felix Höfling <address@hidden>
Date: 2013-05-29 (Wed, 29 May 2013)
Changed paths:
M draft.rst
Log Message:
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revise section on time-dependent data
* mention that the "unit" attribute is a string
* slightly rephrase the text, copying some text from the trajectory
group
* adapt form to the other sections with a bullet list describing each
item
Commit: 0757824ef085c567ef2795f05d0b07219682bf05
https://github.com/h5md/h5md/commit/0757824ef085c567ef2795f05d0b07219682bf05
Author: Felix Höfling <address@hidden>
Date: 2013-05-29 (Wed, 29 May 2013)
Changed paths:
M draft.rst
Log Message:
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revise trajectory group
* add particle mass as standardised identifier. It was the only missing
quantity to make Newtons equations of motion complete.
* describe image vectors and give an example.
http://thread.gmane.org/gmane.science.simulation.h5md.user/134/focus=155
* some further editing of the text, delete description of
value/step/time as it duplicates the section on time-dependent data.
Commit: e46043d291310f4fa6ce76b24086af76a146f443
https://github.com/h5md/h5md/commit/e46043d291310f4fa6ce76b24086af76a146f443
Author: Olaf Lenz <address@hidden>
Date: 2013-05-31 (Fri, 31 May 2013)
Changed paths:
M index.rst
Log Message:
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Added "How to contribute".
Commit: e8ab18ae4480a77639f08886f540c117cb2329f3
https://github.com/h5md/h5md/commit/e8ab18ae4480a77639f08886f540c117cb2329f3
Author: Felix Höfling <address@hidden>
Date: 2013-06-21 (Fri, 21 Jun 2013)
Changed paths:
M draft.rst
Log Message:
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draft: update years covered by copyright
fix typo
Commit: 5f9df9e63bc59745c9cf9515d26aaedceb2bef74
https://github.com/h5md/h5md/commit/5f9df9e63bc59745c9cf9515d26aaedceb2bef74
Author: Felix Höfling <address@hidden>
Date: 2013-06-21 (Fri, 21 Jun 2013)
Changed paths:
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Log Message:
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discussion: add accumulators and particle count
Commit: 3dc18aae640b99b077572ca678b3ae32b31cfc9d
https://github.com/h5md/h5md/commit/3dc18aae640b99b077572ca678b3ae32b31cfc9d
Author: Felix Höfling <address@hidden>
Date: 2013-06-21 (Fri, 21 Jun 2013)
Changed paths:
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Log Message:
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discussion: add note on author/creator tracking
Commit: 4267fbfe33c3f798e076e56f76e97bd788954384
https://github.com/h5md/h5md/commit/4267fbfe33c3f798e076e56f76e97bd788954384
Author: Pierre de Buyl <address@hidden>
Date: 2013-07-17 (Wed, 17 Jul 2013)
Changed paths:
M draft.rst
Log Message:
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Addition of id within the trajectory group.
Commit: f14a32585a36f9692561972eec79d6664f3803cb
https://github.com/h5md/h5md/commit/f14a32585a36f9692561972eec79d6664f3803cb
Author: Pierre de Buyl <address@hidden>
Date: 2013-07-17 (Wed, 17 Jul 2013)
Changed paths:
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Log Message:
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Modification of "type" to "geometry" for the box.
Addition of "boundary" to specifies the "open" or "periodic" nature of the box
in each dimension.
Commit: fcf5da84f9ea28424833b110bec7f6e710a432da
https://github.com/h5md/h5md/commit/fcf5da84f9ea28424833b110bec7f6e710a432da
Author: Pierre de Buyl <address@hidden>
Date: 2013-07-17 (Wed, 17 Jul 2013)
Changed paths:
M draft.rst
Log Message:
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Move notation section at the beginning of the document for clarity.
Commit: 08e85c574703f65a455a116072de7fecf4f54c29
https://github.com/h5md/h5md/commit/08e85c574703f65a455a116072de7fecf4f54c29
Author: Pierre de Buyl <address@hidden>
Date: 2013-07-17 (Wed, 17 Jul 2013)
Changed paths:
M draft.rst
Log Message:
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Minor rephrase in definition of "id".
Commit: d444355ed2865fdb845d279b2afaab9412dea2fd
https://github.com/h5md/h5md/commit/d444355ed2865fdb845d279b2afaab9412dea2fd
Author: Pierre de Buyl <address@hidden>
Date: 2013-07-17 (Wed, 17 Jul 2013)
Changed paths:
M draft.rst
Log Message:
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Given the addition of the box boundary information, removal of the fact that
the absence of "image" means that we have absolute positions.
Commit: 9d962459b6058f509cb2b9e1939cfba6584c233a
https://github.com/h5md/h5md/commit/9d962459b6058f509cb2b9e1939cfba6584c233a
Author: Pierre de Buyl <address@hidden>
Date: 2013-07-17 (Wed, 17 Jul 2013)
Changed paths:
M draft.rst
Log Message:
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Specified that id is of integer kind.
Commit: 645d3f5f2c7cd28a6f149c6d3d27596dfc36b8c5
https://github.com/h5md/h5md/commit/645d3f5f2c7cd28a6f149c6d3d27596dfc36b8c5
Author: Pierre de Buyl <address@hidden>
Date: 2013-07-19 (Fri, 19 Jul 2013)
Changed paths:
M draft.rst
Log Message:
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Make particle attribute/dataset optional in /observables.
Commit: 951dabd5eb5839ffc64969df2a19bf30290955ff
https://github.com/h5md/h5md/commit/951dabd5eb5839ffc64969df2a19bf30290955ff
Author: Pierre de Buyl <address@hidden>
Date: 2013-07-19 (Fri, 19 Jul 2013)
Changed paths:
M draft.rst
Log Message:
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Correct bad indentation for bullet list.
Commit: 0ab6ea2fc8d1d5b7ad0146c98fdb145f8e559650
https://github.com/h5md/h5md/commit/0ab6ea2fc8d1d5b7ad0146c98fdb145f8e559650
Author: Pierre de Buyl <address@hidden>
Date: 2013-07-21 (Sun, 21 Jul 2013)
Changed paths:
M draft.rst
Log Message:
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Changed boundary kinds to periodic/nonperiodic instead of periodic/open.
Commit: f87541201da0c9f294e73c71e0e4004893e0c647
https://github.com/h5md/h5md/commit/f87541201da0c9f294e73c71e0e4004893e0c647
Author: Pierre de Buyl <address@hidden>
Date: 2013-07-21 (Sun, 21 Jul 2013)
Changed paths:
M draft.rst
Log Message:
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Modification of time-dependent section to reflect the general change to
time-dependence agnosticity.
Commit: 9b1bd45f0c59b4434eec453cd9756463a146b5d5
https://github.com/h5md/h5md/commit/9b1bd45f0c59b4434eec453cd9756463a146b5d5
Author: Pierre de Buyl <address@hidden>
Date: 2013-07-21 (Sun, 21 Jul 2013)
Changed paths:
M draft.rst
Log Message:
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Update of Trajectory section to reflect the time-dependence agnosticity.
Commit: b0cc9e6cc578ed315ddd394d1441f074e0c126f0
https://github.com/h5md/h5md/commit/b0cc9e6cc578ed315ddd394d1441f074e0c126f0
Author: Pierre de Buyl <address@hidden>
Date: 2013-07-21 (Sun, 21 Jul 2013)
Changed paths:
M draft.rst
Log Message:
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Update of trajectory example.
Commit: 1fd1904e32ea9289186431e995df65e362ed431e
https://github.com/h5md/h5md/commit/1fd1904e32ea9289186431e995df65e362ed431e
Author: Peter Colberg <address@hidden>
Date: 2013-07-21 (Sun, 21 Jul 2013)
Changed paths:
M discussion.rst
M draft.rst
Log Message:
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Replace creation_time attribute with automatic object time tracking.
Object time tracking requires HDF5 file format version 2.
Commit: 3549ada82c4cfa8a7a55d564ca0d5ed7eb2031e5
https://github.com/h5md/h5md/commit/3549ada82c4cfa8a7a55d564ca0d5ed7eb2031e5
Author: Peter Colberg <address@hidden>
Date: 2013-07-21 (Sun, 21 Jul 2013)
Changed paths:
A implementation.rst
M index.rst
Log Message:
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Add implementation hints for the H5MD file format.
Describe file format and object time tracking.
Commit: 5e7bf9f2e6ca924ec126b5f0f257ae663b8fd544
https://github.com/h5md/h5md/commit/5e7bf9f2e6ca924ec126b5f0f257ae663b8fd544
Author: Peter Colberg <address@hidden>
Date: 2013-07-21 (Sun, 21 Jul 2013)
Changed paths:
M index.rst
A software.rst
Log Message:
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Add Free/Libre software for H5MD files.
Commit: 9c0c5fc526d43ae5e31924946eeb493cbd823b55
https://github.com/h5md/h5md/commit/9c0c5fc526d43ae5e31924946eeb493cbd823b55
Author: Peter Colberg <address@hidden>
Date: 2013-07-21 (Sun, 21 Jul 2013)
Changed paths:
A _static/h5md.css
A _theme/h5md/theme.conf
M conf.py
Log Message:
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Add h5md html theme
Commit: 2497eecb7544d1d090f806156d393691535d8ece
https://github.com/h5md/h5md/commit/2497eecb7544d1d090f806156d393691535d8ece
Author: Peter Colberg <address@hidden>
Date: 2013-07-21 (Sun, 21 Jul 2013)
Changed paths:
M _static/h5md.css
Log Message:
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Reduce html body margins and sidebar width for wider text.
This provides a better reading experience for awesome users.
Commit: 23b4bd667e37c522d799eac41fd96f10cf022e6f
https://github.com/h5md/h5md/commit/23b4bd667e37c522d799eac41fd96f10cf022e6f
Author: Peter Colberg <address@hidden>
Date: 2013-07-21 (Sun, 21 Jul 2013)
Changed paths:
M conf.py
Log Message:
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Update copyright years.
Commit: a40a6d0480d9d44f64847c8f975f0a41d31e4d08
https://github.com/h5md/h5md/commit/a40a6d0480d9d44f64847c8f975f0a41d31e4d08
Author: Peter Colberg <address@hidden>
Date: 2013-07-21 (Sun, 21 Jul 2013)
Changed paths:
M implementation.rst
Log Message:
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Name implementation sections after language.
Commit: 60453af49e09c5043391d3a2f997c0e7aed185d3
https://github.com/h5md/h5md/commit/60453af49e09c5043391d3a2f997c0e7aed185d3
Author: Peter Colberg <address@hidden>
Date: 2013-07-21 (Sun, 21 Jul 2013)
Changed paths:
M draft.rst
Log Message:
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Omit duplicate word.
Commit: 11762d30ebfcc714cc3f79aedd16a764dcd7a271
https://github.com/h5md/h5md/commit/11762d30ebfcc714cc3f79aedd16a764dcd7a271
Author: Peter Colberg <address@hidden>
Date: 2013-07-21 (Sun, 21 Jul 2013)
Changed paths:
M software.rst
Log Message:
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Add simulation subsection to software.
Commit: 7b297127e23de386a8b2dc609097c7530d994c00
https://github.com/h5md/h5md/commit/7b297127e23de386a8b2dc609097c7530d994c00
Author: Pierre de Buyl <address@hidden>
Date: 2013-07-22 (Mon, 22 Jul 2013)
Changed paths:
M draft.rst
Log Message:
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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.
Commit: 392c910c8f03103c92334efbedfbe5f6e03ea7d7
https://github.com/h5md/h5md/commit/392c910c8f03103c92334efbedfbe5f6e03ea7d7
Author: Pierre de Buyl <address@hidden>
Date: 2013-07-22 (Mon, 22 Jul 2013)
Changed paths:
M draft.rst
Log Message:
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Fix typo.
Commit: 844ed727272d68c71db043b7d98424a2bb11c3d3
https://github.com/h5md/h5md/commit/844ed727272d68c71db043b7d98424a2bb11c3d3
Author: Pierre de Buyl <address@hidden>
Date: 2013-07-22 (Mon, 22 Jul 2013)
Changed paths:
M draft.rst
Log Message:
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Clarify sentence.
Commit: 95369c449fb7219574d78f8c978f13f902ff3bef
https://github.com/h5md/h5md/commit/95369c449fb7219574d78f8c978f13f902ff3bef
Author: Pierre de Buyl <address@hidden>
Date: 2013-07-22 (Mon, 22 Jul 2013)
Changed paths:
M draft.rst
Log Message:
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Moved parameters down in the general organization section.
Commit: 5a6b4621b33b099fae0c77f5681f99366c6c5d5b
https://github.com/h5md/h5md/commit/5a6b4621b33b099fae0c77f5681f99366c6c5d5b
Author: Pierre de Buyl <address@hidden>
Date: 2013-07-22 (Mon, 22 Jul 2013)
Changed paths:
M draft.rst
Log Message:
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Fix typo.
Commit: ca3396a2c4e0c383e71a68aff799ed9317edee55
https://github.com/h5md/h5md/commit/ca3396a2c4e0c383e71a68aff799ed9317edee55
Author: Pierre de Buyl <address@hidden>
Date: 2013-07-22 (Mon, 22 Jul 2013)
Changed paths:
M discussion.rst
Log Message:
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Fix typo.
Commit: 5b9da536eff563b70a72ab7132479821d3a7c3f7
https://github.com/h5md/h5md/commit/5b9da536eff563b70a72ab7132479821d3a7c3f7
Author: Pierre de Buyl <address@hidden>
Date: 2013-07-24 (Wed, 24 Jul 2013)
Changed paths:
M draft.rst
Log Message:
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Change of /trajectory to /particles
Commit: e28e307bf0d155bd1036bb64d53cdaeefed0fc2a
https://github.com/h5md/h5md/commit/e28e307bf0d155bd1036bb64d53cdaeefed0fc2a
Author: Peter Colberg <address@hidden>
Date: 2013-07-25 (Thu, 25 Jul 2013)
Changed paths:
M draft.rst
Log Message:
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Remove Draft from title
Commit: 49fd211bcdaf4e40120bf4b65a4d720c4b56d421
https://github.com/h5md/h5md/commit/49fd211bcdaf4e40120bf4b65a4d720c4b56d421
Author: Peter Colberg <address@hidden>
Date: 2013-07-25 (Thu, 25 Jul 2013)
Changed paths:
M draft.rst
Log Message:
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Update summary of parameters group.
Commit: 8f221b1b0175084f1e8c47dabf77b8239b9f89e8
https://github.com/h5md/h5md/commit/8f221b1b0175084f1e8c47dabf77b8239b9f89e8
Author: Peter Colberg <address@hidden>
Date: 2013-07-25 (Thu, 25 Jul 2013)
Changed paths:
M draft.rst
Log Message:
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Typeset HDF5 names and string values in typewriter font.
Omit leading slashes from names of root groups, to avoid a mixture of
slash and non-slash variants. The set of root groups is introduced
at the beginning of the specification.
Commit: a28ee9bd63714efcad8ef33db1cbcffed305debd
https://github.com/h5md/h5md/commit/a28ee9bd63714efcad8ef33db1cbcffed305debd
Author: Peter Colberg <address@hidden>
Date: 2013-07-25 (Thu, 25 Jul 2013)
Changed paths:
M draft.rst
Log Message:
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Reflow overlong lines.
Commit: 25959d40583aeab51aca2399cf2cdae9ffc82a64
https://github.com/h5md/h5md/commit/25959d40583aeab51aca2399cf2cdae9ffc82a64
Author: Peter Colberg <address@hidden>
Date: 2013-07-25 (Thu, 25 Jul 2013)
Changed paths:
M index.rst
Log Message:
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Place semantic links to project page and mailing list.
Commit: 41d7540eab75c9e49f7d4fb0e14a87d78c2bcce0
https://github.com/h5md/h5md/commit/41d7540eab75c9e49f7d4fb0e14a87d78c2bcce0
Author: Peter Colberg <address@hidden>
Date: 2013-07-25 (Thu, 25 Jul 2013)
Changed paths:
M index.rst
Log Message:
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Mention a few computational methods.
Commit: ad9b6ccf6af8665d289d5a273ba9c9fd2eb7850f
https://github.com/h5md/h5md/commit/ad9b6ccf6af8665d289d5a273ba9c9fd2eb7850f
Author: Peter Colberg <address@hidden>
Date: 2013-07-28 (Sun, 28 Jul 2013)
Changed paths:
M draft.rst
Log Message:
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Reorder sections.
Commit: 609c1d9cf8628a013ffb9d267b78b2144b96a9f0
https://github.com/h5md/h5md/commit/609c1d9cf8628a013ffb9d267b78b2144b96a9f0
Author: Peter Colberg <address@hidden>
Date: 2013-07-28 (Sun, 28 Jul 2013)
Changed paths:
M draft.rst
Log Message:
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Consistently order group diagrams and descriptions.
Commit: ca708c531f58a1fea9b4c95c155ef141d14c8699
https://github.com/h5md/h5md/commit/ca708c531f58a1fea9b4c95c155ef141d14c8699
Author: Peter Colberg <address@hidden>
Date: 2013-07-28 (Sun, 28 Jul 2013)
Changed paths:
M draft.rst
Log Message:
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Consistently use [variable] for dimension.
Commit: 8dc99b2e5a84ef1d82ff819bd1d40c083f5050fc
https://github.com/h5md/h5md/commit/8dc99b2e5a84ef1d82ff819bd1d40c083f5050fc
Author: Peter Colberg <address@hidden>
Date: 2013-07-28 (Sun, 28 Jul 2013)
Changed paths:
M draft.rst
Log Message:
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Avoid repeated definitions of box group.
Commit: 88b259cc46986498323481721a7957367b6dab3b
https://github.com/h5md/h5md/commit/88b259cc46986498323481721a7957367b6dab3b
Author: Peter Colberg <address@hidden>
Date: 2013-07-28 (Sun, 28 Jul 2013)
Changed paths:
M draft.rst
Log Message:
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Split author attribute into ``author`` and ``author_email``.
This avoids the necessity of string formatting and parsing.
Commit: db7da5374addd5fb70a77896f12ce2196ab78099
https://github.com/h5md/h5md/commit/db7da5374addd5fb70a77896f12ce2196ab78099
Author: Peter Colberg <address@hidden>
Date: 2013-07-28 (Sun, 28 Jul 2013)
Changed paths:
M draft.rst
Log Message:
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Revise grammar and formatting.
Commit: fca7e3c63b25b585236455f1d5f594c23b694424
https://github.com/h5md/h5md/commit/fca7e3c63b25b585236455f1d5f594c23b694424
Author: Peter Colberg <address@hidden>
Date: 2013-07-29 (Mon, 29 Jul 2013)
Changed paths:
M index.rst
Log Message:
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State full license.
Commit: 0f547fc6097515984b7695fbacd2e8731edb688b
https://github.com/h5md/h5md/commit/0f547fc6097515984b7695fbacd2e8731edb688b
Author: Peter Colberg <address@hidden>
Date: 2013-07-29 (Mon, 29 Jul 2013)
Changed paths:
M draft.rst
Log Message:
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Include H5MD version.
Commit: 5bdca032192905e072864bff96fdc2f2c8d9c7ac
https://github.com/h5md/h5md/commit/5bdca032192905e072864bff96fdc2f2c8d9c7ac
Author: Peter Colberg <address@hidden>
Date: 2013-07-29 (Mon, 29 Jul 2013)
Changed paths:
M draft.rst
Log Message:
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Use unabbreviated observable group names.
Commit: d01063ae84266f443b542963d6381ab01462ae36
https://github.com/h5md/h5md/commit/d01063ae84266f443b542963d6381ab01462ae36
Author: Felix Höfling <address@hidden>
Date: 2013-07-30 (Tue, 30 Jul 2013)
Changed paths:
M draft.rst
Log Message:
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slightly rephrase objective and notation
Add a sentence to notation introducing the elements of an HDF5 file. The
reader is most likely not familiar with HDF5.
Commit: 8a6832d04fb9ce65382d6b75e2a628d9e9b62f7c
https://github.com/h5md/h5md/commit/8a6832d04fb9ce65382d6b75e2a628d9e9b62f7c
Author: Felix Höfling <address@hidden>
Date: 2013-07-30 (Tue, 30 Jul 2013)
Changed paths:
M draft.rst
Log Message:
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move spec of root groups after time-dependent data
Let's do all the generic stuff before we go into the details. The
specification of the root group is then followed by the specification of
the h5md group.
Rename the heading "Global attributes" to "H5MD metadata"
Commit: 503a99858d72660366c3fb82b642a05e3b62cbcd
https://github.com/h5md/h5md/commit/503a99858d72660366c3fb82b642a05e3b62cbcd
Author: Felix Höfling <address@hidden>
Date: 2013-07-30 (Tue, 30 Jul 2013)
Changed paths:
M draft.rst
Log Message:
-----------
Reword general organization and data layout
Mention the general aspects on optional and mandatory elements first.
Introduce the distinction between time-independent and time-dependent
data.
Merge the two sections, but introduce subsections for time-dependent and
time-independent data. The latter has been added for completeness.
Mention that there is a choice between HDF5 datasets and attributes.
Commit: 0d93f1a557c5de9e11a7ec468b8d548c5d4a7d01
https://github.com/h5md/h5md/commit/0d93f1a557c5de9e11a7ec468b8d548c5d4a7d01
Author: Felix Höfling <address@hidden>
Date: 2013-07-30 (Tue, 30 Jul 2013)
Changed paths:
M draft.rst
Log Message:
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revise spec of root level
Rephrase explanations to form proper sentences.
Make the content of the observables group less restrictive.
Add comments on the scaling of the size of stored data.
Indicate that all groups except h5md are optional.
Commit: 907a8383ca17ca3f8df27b7405537e3d00f4edae
https://github.com/h5md/h5md/commit/907a8383ca17ca3f8df27b7405537e3d00f4edae
Author: Felix Höfling <address@hidden>
Date: 2013-07-30 (Tue, 30 Jul 2013)
Changed paths:
M draft.rst
Log Message:
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reword spec of h5md group
Sort the attributes alphabetically and form proper sentences to be
coherent in style. Mention for each attribute that it is of string type.
Commit: 56f840cc6bb926f182bc98b817ac7511c5ffb4d1
https://github.com/h5md/h5md/commit/56f840cc6bb926f182bc98b817ac7511c5ffb4d1
Author: Felix Höfling <address@hidden>
Date: 2013-07-30 (Tue, 30 Jul 2013)
Changed paths:
M draft.rst
Log Message:
-----------
fix level of subsection headlines
Commit: 26190130c52599e0afbf4bffc1b4fbc4ebdc94b1
https://github.com/h5md/h5md/commit/26190130c52599e0afbf4bffc1b4fbc4ebdc94b1
Author: Felix Höfling <address@hidden>
Date: 2013-07-30 (Tue, 30 Jul 2013)
Changed paths:
M draft.rst
Log Message:
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move note on storage order to general section
This paragraph is not specific to the particles group.
Commit: 52d67407c0e5c5920cd8f4139452868b3a3d22f2
https://github.com/h5md/h5md/commit/52d67407c0e5c5920cd8f4139452868b3a3d22f2
Author: Felix Höfling <address@hidden>
Date: 2013-07-30 (Tue, 30 Jul 2013)
Changed paths:
M draft.rst
Log Message:
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revise particles group
Mention that the box is mandatory in each subgroup, re-add the box group
(without its children) to the example tree.
Note that the particle index is the second index, i.e., that the
indexing is [N][D] and not [D][N].
Distinguish between scalar- and vector-valued data sets.
Commit: 884f4cbafe86474294a4971606f4843bc36cf8e0
https://github.com/h5md/h5md/commit/884f4cbafe86474294a4971606f4843bc36cf8e0
Author: Felix Höfling <address@hidden>
Date: 2013-07-30 (Tue, 30 Jul 2013)
Changed paths:
M draft.rst
Log Message:
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cleanup observables group
Move specification of array dimension to the general layout section.
Mention that box is mandatory and put "box" back in the tree graph.
Omit bullet list for specified observable identifiers. Mention that they
are understood as 'per particle'.
Commit: 92fd38c024420d87e9309064217551598daef72d
https://github.com/h5md/h5md/commit/92fd38c024420d87e9309064217551598daef72d
Author: Felix Höfling <address@hidden>
Date: 2013-07-30 (Tue, 30 Jul 2013)
Changed paths:
M draft.rst
Log Message:
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box spec: minor rewording
Commit: 843fc3468d592162b71c455aa29af48d0c3b256d
https://github.com/h5md/h5md/commit/843fc3468d592162b71c455aa29af48d0c3b256d
Author: Felix Höfling <address@hidden>
Date: 2013-07-30 (Tue, 30 Jul 2013)
Changed paths:
M draft.rst
Log Message:
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add a bit more explanation to the parameters group
Commit: f569d81b10e6ae99efcb6e4977592e27ce641c1f
https://github.com/h5md/h5md/commit/f569d81b10e6ae99efcb6e4977592e27ce641c1f
Author: Felix Höfling <address@hidden>
Date: 2013-07-30 (Tue, 30 Jul 2013)
Changed paths:
M draft.rst
Log Message:
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replace content by contents
http://oald8.oxfordlearnersdictionaries.com/dictionary/content
Commit: cec61a1b2bb6bc8fa51579dac435fe70eb7206df
https://github.com/h5md/h5md/commit/cec61a1b2bb6bc8fa51579dac435fe70eb7206df
Author: Felix Höfling <address@hidden>
Date: 2013-07-30 (Tue, 30 Jul 2013)
Changed paths:
M draft.rst
Log Message:
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fix spelling
The spell checker complained further about "nonperiodic". The preferred
(British) spelling of the non-prefix is with a hyphen: "non-periodic".
But see:
http://oald8.oxfordlearnersdictionaries.com/dictionary/non
Commit: 284d8b533f04c44af0abd8223a18e33ac447eb2f
https://github.com/h5md/h5md/commit/284d8b533f04c44af0abd8223a18e33ac447eb2f
Author: Felix Höfling <address@hidden>
Date: 2013-07-30 (Tue, 30 Jul 2013)
Changed paths:
M draft.rst
Log Message:
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parameters: fix notation in tree graph
Attributes have a '+' while datasets have a '\'.
Commit: 6420bff72985f031ab3ec01a2f4e28b1fb93444f
https://github.com/h5md/h5md/commit/6420bff72985f031ab3ec01a2f4e28b1fb93444f
Author: Peter Colberg <address@hidden>
Date: 2013-07-30 (Tue, 30 Jul 2013)
Changed paths:
M draft.rst
Log Message:
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Avoid overlong line with ``..., temperature``.
Commit: 6881645dcb5025f490a505715a86add967f452e4
https://github.com/h5md/h5md/commit/6881645dcb5025f490a505715a86add967f452e4
Author: Peter Colberg <address@hidden>
Date: 2013-07-30 (Tue, 30 Jul 2013)
Changed paths:
M draft.rst
Log Message:
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Remove verbatim escape sequences.
Commit: 8b27fe9b5c3c97f2db4f6ba608f35b3cd9b1a306
https://github.com/h5md/h5md/commit/8b27fe9b5c3c97f2db4f6ba608f35b3cd9b1a306
Author: Peter Colberg <address@hidden>
Date: 2013-07-30 (Tue, 30 Jul 2013)
Changed paths:
M draft.rst
Log Message:
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Use definition lists in place of bullet lists.
This allows for fast recognition of names, both in the HTML output,
and the LaTeX output created using pandoc. Definition lists eliminate
inconsistencies of the form “The X group” versus “The group X” versus
“X: A group”.
http://docutils.sourceforge.net/docs/ref/rst/restructuredtext.html#definition-lists
Commit: 52f1e6676b2d76f4cd0ee00c8d1953680768a0ad
https://github.com/h5md/h5md/commit/52f1e6676b2d76f4cd0ee00c8d1953680768a0ad
Author: Peter Colberg <address@hidden>
Date: 2013-07-30 (Tue, 30 Jul 2013)
Changed paths:
M draft.rst
Log Message:
-----------
Use “must” to emphasize mandatory presences of box specification.
Commit: 95e47c1605456fdbf81af56609ea39c362030cf9
https://github.com/h5md/h5md/commit/95e47c1605456fdbf81af56609ea39c362030cf9
Author: Peter Colberg <address@hidden>
Date: 2013-07-30 (Tue, 30 Jul 2013)
Changed paths:
M draft.rst
Log Message:
-----------
Avoid overlong line for ``author_email``.
Commit: 5ad4e13b140f520d4776bd269445a0834e6f22d9
https://github.com/h5md/h5md/commit/5ad4e13b140f520d4776bd269445a0834e6f22d9
Author: Peter Colberg <address@hidden>
Date: 2013-07-30 (Tue, 30 Jul 2013)
Changed paths:
M draft.rst
Log Message:
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Non-specified elements include attributes.
Commit: 50342b63c761679c6d43b944b35e9cf02988f025
https://github.com/h5md/h5md/commit/50342b63c761679c6d43b944b35e9cf02988f025
Author: Peter Colberg <address@hidden>
Date: 2013-07-30 (Tue, 30 Jul 2013)
Changed paths:
M draft.rst
Log Message:
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Use definition of group, dataset and attribute from HDF5.
Omit the repeated prefix “HDF5”, since the terms “group”, “dataset” and
“attribute” are equivalent to the definition of the HDF5 specification.
Commit: 6e40f224c64d7439ffbd6d93a06f8a7d2f75637c
https://github.com/h5md/h5md/commit/6e40f224c64d7439ffbd6d93a06f8a7d2f75637c
Author: Peter Colberg <address@hidden>
Date: 2013-07-30 (Tue, 30 Jul 2013)
Changed paths:
M draft.rst
Log Message:
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Explicitly define and use the term "data-group".
Commit: d15f8306f6be367041fb8ad5ebe271922d5c9cd3
https://github.com/h5md/h5md/commit/d15f8306f6be367041fb8ad5ebe271922d5c9cd3
Author: Peter Colberg <address@hidden>
Date: 2013-07-30 (Tue, 30 Jul 2013)
Changed paths:
M draft.rst
Log Message:
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Describe optional root groups as optional.
Commit: 4c6e6711d2c58214048d437348cc52cc7741f981
https://github.com/h5md/h5md/commit/4c6e6711d2c58214048d437348cc52cc7741f981
Author: Peter Colberg <address@hidden>
Date: 2013-07-30 (Tue, 30 Jul 2013)
Changed paths:
M draft.rst
Log Message:
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Define <identifier> to distinguish between unspecified and specified names.
Commit: 8085ad128e2b67b40f3c2c8da5410b28a105945d
https://github.com/h5md/h5md/commit/8085ad128e2b67b40f3c2c8da5410b28a105945d
Author: Peter Colberg <address@hidden>
Date: 2013-07-30 (Tue, 30 Jul 2013)
Changed paths:
M draft.rst
Log Message:
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Spell out attribute.
Commit: 1e6c0bb3a7948fcd3306570c3c0c5b4d5028871d
https://github.com/h5md/h5md/commit/1e6c0bb3a7948fcd3306570c3c0c5b4d5028871d
Author: Peter Colberg <address@hidden>
Date: 2013-07-30 (Tue, 30 Jul 2013)
Changed paths:
M draft.rst
Log Message:
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Revert to “data group” instead of “data-group”.
This is consistent with the use of “data type”.
Commit: c1e094975c6166ed422272af6de6f23d823d1384
https://github.com/h5md/h5md/commit/c1e094975c6166ed422272af6de6f23d823d1384
Author: Felix Höfling <address@hidden>
Date: 2013-07-31 (Wed, 31 Jul 2013)
Changed paths:
M draft.rst
Log Message:
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put the definition of "data group" in italics
This emphasises that "data group" is part of the H5MD terminology.
Commit: 3ff8ba57aa90d4f8c6b26e4c1c81f77044473091
https://github.com/h5md/h5md/commit/3ff8ba57aa90d4f8c6b26e4c1c81f77044473091
Author: Felix Höfling <address@hidden>
Date: 2013-07-31 (Wed, 31 Jul 2013)
Changed paths:
M draft.rst
Log Message:
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replace "like" by "as"
"Like" is a preposition, but "as" is a conjuction.
http://oald8.oxfordlearnersdictionaries.com/dictionary/like
Commit: a32d72757222f517fed674c69678fc01a8244297
https://github.com/h5md/h5md/commit/a32d72757222f517fed674c69678fc01a8244297
Author: Pierre de Buyl <address@hidden>
Date: 2013-07-31 (Wed, 31 Jul 2013)
Changed paths:
M draft.rst
Log Message:
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Remove dataset confusion in definition of h5md version attribute.
Commit: 373691c9890d51629c546f3626e96ecdf86f8ddf
https://github.com/h5md/h5md/commit/373691c9890d51629c546f3626e96ecdf86f8ddf
Author: Peter Colberg <address@hidden>
Date: 2013-07-31 (Wed, 31 Jul 2013)
Changed paths:
M draft.rst
Log Message:
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Organize meta-data of author and creator into subgroups.
http://thread.gmane.org/gmane.science.simulation.h5md.user/206/focus=209
Commit: 73f6ca4ac2e7c0ae0b076b19628f9b9a8d918212
https://github.com/h5md/h5md/commit/73f6ca4ac2e7c0ae0b076b19628f9b9a8d918212
Author: Peter Colberg <address@hidden>
Date: 2013-08-01 (Thu, 01 Aug 2013)
Changed paths:
M discussion.rst
M draft.rst
Log Message:
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Move attribute “unit” to discussion section.
A data stored in an attribute cannot have a unit attribute.
http://thread.gmane.org/gmane.science.simulation.h5md.user/208
Commit: 001aa36271c934d8ebdf578adea62d2ca766b53b
https://github.com/h5md/h5md/commit/001aa36271c934d8ebdf578adea62d2ca766b53b
Author: Felix Höfling <address@hidden>
Date: 2013-08-01 (Thu, 01 Aug 2013)
Changed paths:
M draft.rst
Log Message:
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box: drop geometry attribute, change "nonperiodic" to "none"
The geometry attribute is not needed since it can be inferred from the
shape of "edges".
Shorten the specification of time-dependent vs. -independent and drop
the subsection headlines. The issue has been specified in the general
part already, and the two examples should clarify this again.
http://article.gmane.org/gmane.science.simulation.h5md.user/218
Commit: fd05315bf0f53a2b079d3219d109d58690378ced
https://github.com/h5md/h5md/commit/fd05315bf0f53a2b079d3219d109d58690378ced
Author: Peter Colberg <address@hidden>
Date: 2013-08-01 (Thu, 01 Aug 2013)
Changed paths:
M draft.rst
Log Message:
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Avoid duplicate specification of particles data groups.
Commit: a9a5e24d2a82e1ea2f1929b9c6327eabd02dbd3e
https://github.com/h5md/h5md/commit/a9a5e24d2a82e1ea2f1929b9c6327eabd02dbd3e
Author: Peter Colberg <address@hidden>
Date: 2013-08-01 (Thu, 01 Aug 2013)
Changed paths:
M draft.rst
Log Message:
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Format data_group as unspecified identifier.
Commit: 2303495bf6c5f5836be4ae861ee04830bc961dfb
https://github.com/h5md/h5md/commit/2303495bf6c5f5836be4ae861ee04830bc961dfb
Author: Peter Colberg <address@hidden>
Date: 2013-08-01 (Thu, 01 Aug 2013)
Changed paths:
M draft.rst
Log Message:
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Consistently use “metadata”.
Commit: 7c9eb2ccad9d98fb2e2c5b2bc8adabf47a147f75
https://github.com/h5md/h5md/commit/7c9eb2ccad9d98fb2e2c5b2bc8adabf47a147f75
Author: Felix Höfling <address@hidden>
Date: 2013-08-02 (Fri, 02 Aug 2013)
Changed paths:
M draft.rst
Log Message:
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particles: Mention that some identifiers are part of the specification
This aspect got lost in commit:fd05315.
Commit: 79384510c164b9e6428536f07b16579607bf6151
https://github.com/h5md/h5md/commit/79384510c164b9e6428536f07b16579607bf6151
Author: Peter Colberg <address@hidden>
Date: 2013-08-09 (Fri, 09 Aug 2013)
Changed paths:
M software.rst
Log Message:
-----------
Link to VMD-h5mdplugin repository.
Commit: 9812310977ed5ec3aa34c316230a371570f55c4d
https://github.com/h5md/h5md/commit/9812310977ed5ec3aa34c316230a371570f55c4d
Author: Pierre de Buyl <address@hidden>
Date: 2013-08-27 (Tue, 27 Aug 2013)
Changed paths:
M implementation.rst
Log Message:
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Add hint on the use of the enum datatype for the species. Idea taken from
http://article.gmane.org/gmane.science.simulation.h5md.user/244 with additional
info from http://article.gmane.org/gmane.science.simulation.h5md.user/248
Commit: a3987f4777666f9ebb184f3c4ba95c1d72bce1ec
https://github.com/h5md/h5md/commit/a3987f4777666f9ebb184f3c4ba95c1d72bce1ec
Author: Pierre de Buyl <address@hidden>
Date: 2013-08-27 (Tue, 27 Aug 2013)
Changed paths:
M draft.rst
Log Message:
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Allow to omit edges and offset when all elements of boundary are none.
http://article.gmane.org/gmane.science.simulation.h5md.user/214
Commit: b68c3a1442f97c3d224c110745242aa8347189f0
https://github.com/h5md/h5md/commit/b68c3a1442f97c3d224c110745242aa8347189f0
Author: Felix Höfling <address@hidden>
Date: 2013-08-28 (Wed, 28 Aug 2013)
Changed paths:
M draft.rst
Log Message:
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box: define boundary conditions 'periodic' and 'none'
This change follows a suggestion by Olaf Lenz.
In addition, shorten the section title.
Commit: a2b4d04d6ee6a051f9a73dec7b7f39abd8da5012
https://github.com/h5md/h5md/commit/a2b4d04d6ee6a051f9a73dec7b7f39abd8da5012
Author: Olaf Lenz <address@hidden>
Date: 2013-08-28 (Wed, 28 Aug 2013)
Changed paths:
M draft.rst
Log Message:
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explain the interpretation of "particles/id"
The specs should specify exactly how the groups are to be interpreted,
and how it is to be interpreted if a group is missing. A general
disclaimer that any group that is missing is simply unspecified would
solve most cases. In the case of the "id", however, it is not.
Commit: 550d70223cea53957df90923dd42adbb30f1eb0c
https://github.com/h5md/h5md/commit/550d70223cea53957df90923dd42adbb30f1eb0c
Author: Felix Höfling <address@hidden>
Date: 2013-08-28 (Wed, 28 Aug 2013)
Changed paths:
M draft.rst
Log Message:
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tree graph for particles group: make all data optional
Make it explicit in the graph that the fields "position" etc. are all
optional (in contrast to "box"). Drop "example of" since the graph now
gives the general structure.
This change follows a suggestion by Olaf Lenz that optional elements are
marked consistently throughout all tree graphs.
Commit: a11788208aec1df34869927cdb20f22465cd201a
https://github.com/h5md/h5md/commit/a11788208aec1df34869927cdb20f22465cd201a
Author: Olaf Lenz <address@hidden>
Date: 2013-08-28 (Wed, 28 Aug 2013)
Changed paths:
M conf.py
M discussion.rst
Log Message:
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Small fixes.
Commit: 7b0159336df98e47e087db11db10a660199b3231
https://github.com/h5md/h5md/commit/7b0159336df98e47e087db11db10a660199b3231
Author: Peter Colberg <address@hidden>
Date: 2013-09-09 (Mon, 09 Sep 2013)
Changed paths:
M implementation.rst
Log Message:
-----------
Move Language-independent before language-specific hints
Commit: 1c2b873ab78446adf7ff6f68fc0d75408060f7a8
https://github.com/h5md/h5md/commit/1c2b873ab78446adf7ff6f68fc0d75408060f7a8
Author: Peter Colberg <address@hidden>
Date: 2013-09-09 (Mon, 09 Sep 2013)
Changed paths:
M draft.rst
M implementation.rst
Log Message:
-----------
Store time-independent data as compact datasets
http://thread.gmane.org/gmane.science.simulation.h5md.user/236/focus=293
Commit: 0f3b97425b231bb168d4ae657a052520c4b2c76c
https://github.com/h5md/h5md/commit/0f3b97425b231bb168d4ae657a052520c4b2c76c
Author: Peter Colberg <address@hidden>
Date: 2013-09-09 (Mon, 09 Sep 2013)
Changed paths:
M discussion.rst
M draft.rst
Log Message:
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Revert "Move attribute “unit” to discussion section."
This reverts commit 73f6ca4ac2e7c0ae0b076b19628f9b9a8d918212.
Commit: 27df819c3f03e2ec1890f58200d1f29c4b94c3d7
https://github.com/h5md/h5md/commit/27df819c3f03e2ec1890f58200d1f29c4b94c3d7
Author: Peter Colberg <address@hidden>
Date: 2013-09-09 (Mon, 09 Sep 2013)
Changed paths:
M draft.rst
Log Message:
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Add optional unit attribute to dimensional data
Commit: 047d5bbd1f8dc7ecc363ca1cbe6481d86898c410
https://github.com/h5md/h5md/commit/047d5bbd1f8dc7ecc363ca1cbe6481d86898c410
Author: Peter Colberg <address@hidden>
Date: 2013-09-19 (Thu, 19 Sep 2013)
Changed paths:
M draft.rst
Log Message:
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Use single number for H5MD file format version.
The H5MD specification version retains a major and a minor version
number, which allows for modifications of the text that do not affect
the file format.
Commit: 05190f0afdbe69d150b63c1ffa0fe524890f6223
https://github.com/h5md/h5md/commit/05190f0afdbe69d150b63c1ffa0fe524890f6223
Author: Felix Höfling <address@hidden>
Date: 2013-09-23 (Mon, 23 Sep 2013)
Changed paths:
M draft.rst
Log Message:
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replace "H5MD file" by "H5MD structure"
The H5MD root level does not need to coincide with the root of the HDF5
file. Thereby, multiple H5MD structures may be found within one file and
H5MD may become part of a superstructure.
Rename "H5MD file format" to "H5MD format".
Commit: efcf705cb1b1d17b765f766abca5d01e1dbee8a5
https://github.com/h5md/h5md/commit/efcf705cb1b1d17b765f766abca5d01e1dbee8a5
Author: Peter Colberg <address@hidden>
Date: 2013-09-23 (Mon, 23 Sep 2013)
Changed paths:
M draft.rst
Log Message:
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Specify variable-length string datatype for specified attributes.
State the dataspace of the box boundary attribute, which in the previous
version may as well be interpreted as an attribute of scalar dataspace,
and array datatype.
http://article.gmane.org/gmane.science.simulation.h5md.user/326
http://article.gmane.org/gmane.science.simulation.h5md.user/328
http://article.gmane.org/gmane.science.simulation.h5md.user/332
Commit: e9465087fa6c9a966ddedcb57f402ec6f8d3a0d0
https://github.com/h5md/h5md/commit/e9465087fa6c9a966ddedcb57f402ec6f8d3a0d0
Author: Peter Colberg <address@hidden>
Date: 2013-09-23 (Mon, 23 Sep 2013)
Changed paths:
M draft.rst
Log Message:
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Define H5MD modules
http://article.gmane.org/gmane.science.simulation.h5md.user/295
http://article.gmane.org/gmane.science.simulation.h5md.user/321
http://article.gmane.org/gmane.science.simulation.h5md.user/323
This is a prerequisite for the addition of a "units" module, which
itself is a prerequisite for a peer-reviewed publication of the H5MD
specification.
Commit: 40359cd9fc271f94b6e0d8cf2c37882fadd236ce
https://github.com/h5md/h5md/commit/40359cd9fc271f94b6e0d8cf2c37882fadd236ce
Author: Peter Colberg <address@hidden>
Date: 2013-09-23 (Mon, 23 Sep 2013)
Changed paths:
M draft.rst
Log Message:
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Fix verbatim block
Commit: 27d56803b7d99d28427c6529db04e6ed9afe4999
https://github.com/h5md/h5md/commit/27d56803b7d99d28427c6529db04e6ed9afe4999
Author: Peter Colberg <address@hidden>
Date: 2013-09-23 (Mon, 23 Sep 2013)
Changed paths:
M draft.rst
M implementation.rst
Log Message:
-----------
Specify monotonically increasing order of step and time
Commit: 38a7efc301330e96b8efe108a71943c895e70c00
https://github.com/h5md/h5md/commit/38a7efc301330e96b8efe108a71943c895e70c00
Author: Peter Colberg <address@hidden>
Date: 2013-09-23 (Mon, 23 Sep 2013)
Changed paths:
M draft.rst
Log Message:
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Move modules to H5MD metadata
Commit: 7f06862c1c2759be2e3f123aa490f2bc5cda7111
https://github.com/h5md/h5md/commit/7f06862c1c2759be2e3f123aa490f2bc5cda7111
Author: Peter Colberg <address@hidden>
Date: 2013-09-23 (Mon, 23 Sep 2013)
Changed paths:
A COPYING
M conf.py
A contents.rst
A discussion.mdwn
R discussion.rst
A draft.mdwn
R draft.rst
A implementation.mdwn
R implementation.rst
A index.mdwn
R index.rst
A software.mdwn
R software.rst
Log Message:
-----------
Switch source format to Pandoc's Markdown
http://johnmacfarlane.net/pandoc/README.html#pandocs-markdown
Commit: 1edd85ddfa75851840a87553f4d798cec51a5b09
https://github.com/h5md/h5md/commit/1edd85ddfa75851840a87553f4d798cec51a5b09
Author: Peter Colberg <address@hidden>
Date: 2013-09-23 (Mon, 23 Sep 2013)
Changed paths:
M implementation.mdwn
Log Message:
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Revise markdown following automatic conversion
Commit: 1ac5f6b0a98cb6b57c97d4457b13688c5330362a
https://github.com/h5md/h5md/commit/1ac5f6b0a98cb6b57c97d4457b13688c5330362a
Author: Peter Colberg <address@hidden>
Date: 2013-09-23 (Mon, 23 Sep 2013)
Changed paths:
M README
R index.mdwn
A index.mdwn
Log Message:
-----------
Deduplicate README and index
Commit: 8684e71579b36ee4ce2a99bcc8e350b09468b59a
https://github.com/h5md/h5md/commit/8684e71579b36ee4ce2a99bcc8e350b09468b59a
Author: Peter Colberg <address@hidden>
Date: 2013-09-23 (Mon, 23 Sep 2013)
Changed paths:
R README
A README.mdwn
M conf.py
R index.mdwn
Log Message:
-----------
Remove symbolic link from repository
Manually rename README to index for the Savannah website.
Commit: f0b20e684d064a96698529cd15343b744fccb6e0
https://github.com/h5md/h5md/commit/f0b20e684d064a96698529cd15343b744fccb6e0
Author: Felix Höfling <address@hidden>
Date: 2013-09-25 (Wed, 25 Sep 2013)
Changed paths:
M draft.mdwn
Log Message:
-----------
fix missing vertical bars in tree graphs
The leaves of a tree are a connected to the root or they fall down ...
Compare: https://github.com/h5md/h5md/compare/1ff24ac41fc0^...f0b20e684d06
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