[h5md-commit] H5MD branch master updated. 862ef3dda1bf627f9bfae06549b3b5bd5c6436d4

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- Log -----------------------------------------------------------------
commit 862ef3dda1bf627f9bfae06549b3b5bd5c6436d4
Author:     Pierre de Buyl <address@hidden>
AuthorDate: Mon Nov 19 16:11:51 2012 +0100
Commit:     Pierre de Buyl <address@hidden>
CommitDate: Mon Nov 19 16:11:51 2012 +0100

    Converted two only single quoted words to double quoted words;
---
 draft.rst |    4 ++--
 1 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/draft.rst b/draft.rst
index 2850d03..030ce40 100644
--- a/draft.rst
+++ b/draft.rst
@@ -73,13 +73,13 @@ Global attributes
 -----------------
 
 A few global attributes (in the HDF5 sense) are defined for convenience. These 
attributes are given
-to the 'h5md' group.
+to the "h5md" group.
 
 * creator: The name of the program that created the file.
 * creator_version: The version of the program that created the file, as a 
string
   containing proper identification for the given program.
 * version: The version of the H5MD specification that the file conforms
-  to. 'version' is a dimension \[2\] integer dataset. The first element is the
+  to. "version" is a dimension \[2\] integer dataset. The first element is the
   major version number and the second element the minor version number.
 * creation_time: The creation time of the file. It is an integer scalar dataset
   representing the number of seconds since the Epoch.

commit 02be5edff9f2152175cd5b4a064c7b88e425afde
Author:     Pierre de Buyl <address@hidden>
AuthorDate: Mon Nov 19 16:10:15 2012 +0100
Commit:     Pierre de Buyl <address@hidden>
CommitDate: Mon Nov 19 16:10:15 2012 +0100

    Added HDF5 detail.
---
 draft.rst |    4 ++--
 1 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/draft.rst b/draft.rst
index f8c1e77..2850d03 100644
--- a/draft.rst
+++ b/draft.rst
@@ -35,7 +35,7 @@ H5MD defines a HDF5 group structure. Inside a group, a number 
of required
 fields exist and should possess a conforming name and shape.
 
 Several groups may exist in a file, allowing the description of several
-subsystems. Multiple time steps are found inside a single dataset. One can then
+subsystems. Multiple time steps are found inside a single HDF5 dataset. One 
can then
 obtain either a snapshot of the system at a given time or extract a single
 trajectory via dataset slicing.
 
@@ -72,7 +72,7 @@ level, omitting to display ``file root``.
 Global attributes
 -----------------
 
-A few global attributes are defined for convenience. These attributes are given
+A few global attributes (in the HDF5 sense) are defined for convenience. These 
attributes are given
 to the 'h5md' group.
 
 * creator: The name of the program that created the file.

commit 23e87cf9a2b067666beac652a9aaeaddd8638f87
Author:     Pierre de Buyl <address@hidden>
AuthorDate: Mon Nov 19 14:57:08 2012 +0100
Commit:     Pierre de Buyl <address@hidden>
CommitDate: Mon Nov 19 14:57:08 2012 +0100

    Added example of fixed-in-time triclinic box.
---
 draft.rst |    9 +++++++++
 1 files changed, 9 insertions(+), 0 deletions(-)

diff --git a/draft.rst b/draft.rst
index b77fea0..f8c1e77 100644
--- a/draft.rst
+++ b/draft.rst
@@ -237,6 +237,15 @@ For instance, a cuboid box that changes in time would 
appear as ::
 
 where "type" is set to "cuboid".
 
+A fixed-in-time triclinic box would appear as ::
+
+  observables
+   \-- box
+        +-- type
+        \-- edges [D][D]
+        \-- offset [D]
+
+where "type" is set to "triclinic"
 
 Observables group
 -----------------

commit 6fba3944c0f682b957940eccddeaa1357a634cd3
Author:     Pierre de Buyl <address@hidden>
AuthorDate: Mon Nov 19 13:02:28 2012 +0100
Commit:     Pierre de Buyl <address@hidden>
CommitDate: Mon Nov 19 13:02:28 2012 +0100

    Fixed typos.
---
 draft.rst |    4 ++--
 1 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/draft.rst b/draft.rst
index 484632a..b77fea0 100644
--- a/draft.rst
+++ b/draft.rst
@@ -98,7 +98,7 @@ The content of this group is::
 Storage of the time information for time-dependent datasets
 -----------------------------------------------------------
 
-To link data the data of a time dependent dataset to a time in the simulation,
+To link the data of a time dependent dataset to a time in the simulation,
 H5MD defines a group structure containing, in addition to the data, the
 corresponding integer time step information (number of simulation steps) and
 physical time information (the time in simulation or physical units,
@@ -159,7 +159,7 @@ All arrays are stored in C-order as enforced by the HDF5 
file format (see `§
 3.2.5 <http://www.hdfgroup.org/HDF5/doc/UG/12_Dataspaces.html#ProgModel>`_). A 
C
 or C++ program may thus declare r\[N\]\[D\] for the coordinates array while the
 Fortran program will declare a r(D,N) array (appropriate index ordering for a
-N atoms D dimensions system) and the hdf5 file will be the same.
+N atoms D dimensions system) and the HDF5 file will be the same.
 
 The "position", "velocity" and "force" datasets possess an optional attribute
 "units" that gives the units of their respective data ("nm" for the position,

commit 54654b76a1a5bdf96aaa5de7d2b8bab622419611
Author:     Pierre de Buyl <address@hidden>
AuthorDate: Mon Nov 19 13:00:44 2012 +0100
Commit:     Pierre de Buyl <address@hidden>
CommitDate: Mon Nov 19 13:00:44 2012 +0100

    Added structure display for the root of the file.
---
 draft.rst |   11 +++++++++++
 1 files changed, 11 insertions(+), 0 deletions(-)

diff --git a/draft.rst b/draft.rst
index b45036e..484632a 100644
--- a/draft.rst
+++ b/draft.rst
@@ -58,6 +58,17 @@ The groups that are part of the H5MD specifications are
 All time dependent data (whether in "trajectory" or "observables") is organized
 into HDF5 groups that contain time information in addition to the data.
 
+The root of the HDF5 file is organized as follows::
+
+    file root
+     \-- h5md
+     \-- trajectory
+     \-- observables
+     \-- parameters
+
+In the following, the examples of HDF5 organization may start at the group
+level, omitting to display ``file root``.
+
 Global attributes
 -----------------
 

commit 96323ee12149046e6a95c282f88381d56e27905a
Author:     Pierre de Buyl <address@hidden>
AuthorDate: Mon Nov 19 12:52:16 2012 +0100
Commit:     Pierre de Buyl <address@hidden>
CommitDate: Mon Nov 19 12:52:16 2012 +0100

    Promoted 'trajectory group', 'box specification' and 'observables group' so 
that they appear in the toc.
---
 draft.rst |   15 ++++++---------
 1 files changed, 6 insertions(+), 9 deletions(-)

diff --git a/draft.rst b/draft.rst
index d7357fb..b45036e 100644
--- a/draft.rst
+++ b/draft.rst
@@ -113,11 +113,8 @@ links to the "step" and "time" datasets of one data group. 
If data are sampled
 at different times (for instance, one needs the positions more frequently than
 the velocities), "step" and "time" are unique to each data group.
 
-Standardized data elements
---------------------------
-
 Trajectory group
-^^^^^^^^^^^^^^^^
+----------------
 
 The trajectories are stored in the "trajectory" group. The trajectory group
 itself is only a container for groups that represent different parts of the
@@ -179,7 +176,7 @@ The content of the trajectory group is the following::
           |    \-- time
 
 Box specification
-^^^^^^^^^^^^^^^^^
+-----------------
 
 The box specification is stored in the observables group, as a group. The type
 of box is stored as an attribute to this box group ::
@@ -193,21 +190,21 @@ The box type can be "cuboid" or "triclinic". Depending on 
this information,
 additional data is stored.
 
 Cuboid box
-""""""""""
+^^^^^^^^^^
 
 * edges: A vector specifying the length of the box in the D dimensions of
   space.
 * offset: A vector specifying the lower coordinate for all directions.
 
 Triclinic box
-"""""""""""""
+^^^^^^^^^^^^^
 
 * edges: A set of D×D-dimensional matrices with the rows specifying the
   directions and lengths of the edges of the box.
 * offset: A vector specifying the lower coordinate for all directions.
 
 Time dependence
-"""""""""""""""
+^^^^^^^^^^^^^^^
 
 For all box kinds, if the data for edges,offset is stored as a single dataset,
 it is considered fixed in time. Else, it should comply to the step, time and
@@ -231,7 +228,7 @@ where "type" is set to "cuboid".
 
 
 Observables group
-^^^^^^^^^^^^^^^^^
+-----------------
 
 Macroscopic observables are stored as \[variable\] time series for scalar
 observables and as \[variable\]\[d\] time series for d-dimensional vector

-----------------------------------------------------------------------

Summary of changes:
 draft.rst |   47 ++++++++++++++++++++++++++++++++---------------
 1 files changed, 32 insertions(+), 15 deletions(-)


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