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- Log -----------------------------------------------------------------
commit eff7ae6559a9fe119f5a5b7774c31aa1930e1bf8
Author:     Pierre de Buyl <address@hidden>
AuthorDate: Fri Feb 10 16:52:21 2012 +0100
Commit:     Pierre de Buyl <address@hidden>
CommitDate: Fri Feb 10 16:52:21 2012 +0100

    Changed "sample" dataset name to "value" everywhere.
---
 draft.rst |   24 ++++++++++++------------
 1 files changed, 12 insertions(+), 12 deletions(-)

diff --git a/draft.rst b/draft.rst
index 1722c56..0951cf2 100644
--- a/draft.rst
+++ b/draft.rst
@@ -94,11 +94,11 @@ As an example, here is the data for the position in a group 
of particles::
     trajectory
       \-- group1
            \-- position
-                \-- sample
+                \-- value
                 \-- step
                 \-- time
 
-where the first dimension of "sample" must match the unique dimension of "step"
+where the first dimension of "value" must match the unique dimension of "step"
 and "time".
 
 The "step" dataset must be of integer datatype to allow exact temporal matching
@@ -120,11 +120,11 @@ itself is only a container for groups that represent 
different parts of the
 system under consideration. There may be one or several groups in the 
trajectory
 group, as needed, but the trajectory group may only contain groups.
 Inside of these subgroups, for each kind of trajectory information there is a
-group that contains datasets "sample", "step", and "time".
+group that contains datasets "value", "step", and "time".
 
 * Standardised subgroups are "position", "velocity", "force" and "species".
 
-* The "sample" dataset holds the actual data and has dimensions
+* The "value" dataset holds the actual data and has dimensions
   \[variable\]\[N\]\[D\], where the variable dimension is present to accumulate
   time steps.
 
@@ -135,7 +135,7 @@ group that contains datasets "sample", "step", and "time".
 * The "time" dataset is as the "step" dataset, but contains the real value of
   the time.
 
-* The "species/sample" dataset has dimensions \[N\] if the species do not
+* The "species/value" dataset has dimensions \[N\] if the species do not
   change in the course of time, that is if there is no chemical reaction
   occurring, or of dimensions \[variable\]\[N\] if the species of particles may
   change in the course of time. The species dataset should be of an integer
@@ -157,19 +157,19 @@ The content of the trajectory group is the following::
     trajectory
      \-- group1
           \-- position
-          |    \-- sample
+          |    \-- value
           |    \-- step
           |    \-- time
           \-- velocity
-          |    \-- sample
+          |    \-- value
           |    \-- step
           |    \-- time
           \-- force
-          |    \-- sample
+          |    \-- value
           |    \-- step
           |    \-- time
           \-- species
-          |    \-- sample
+          |    \-- value
           |    \-- step
           |    \-- time
 
@@ -233,7 +233,7 @@ observables and as \[variable\]\[d\] time series for 
d-dimensional vector
 observables. The variable dimension allows to accumulate time-steps. The name 
of
 the group holding these datasets is "observables". This group has the same
 structure as "trajectory": for each observable there is a group containing 
three
-datasets: the actual data in "sample" and the step and time datasets.
+datasets: the actual data in "value" and the step and time datasets.
 
 The following names should be obeyed for the corresponding observables:
 
@@ -246,11 +246,11 @@ The content of the observables group is the following::
 
     observables
      \-- obs1
-     |    \-- sample
+     |    \-- value
      |    \-- step
      |    \-- time
      \-- obs2
-     |    \-- sample
+     |    \-- value
      |    \-- step
      |    \-- time
      \-- ...

commit 9c15daed2a30e51125161140548be198e223f7b3
Author:     Pierre de Buyl <address@hidden>
AuthorDate: Fri Feb 10 16:43:58 2012 +0100
Commit:     Pierre de Buyl <address@hidden>
CommitDate: Fri Feb 10 16:43:58 2012 +0100

    Added an example for the information found in "parameters".
---
 draft.rst |    3 ++-
 1 files changed, 2 insertions(+), 1 deletions(-)

diff --git a/draft.rst b/draft.rst
index ce55156..1722c56 100644
--- a/draft.rst
+++ b/draft.rst
@@ -265,7 +265,8 @@ Parameters
 ^^^^^^^^^^
 
 The "parameters" group may contain all parameters passed to initialize the
-simulation. Example are: temperature, random number generator seed, ...
+simulation. Example are: temperature, random number generator seed, initial box
+size, ...
 
 Profiling
 ^^^^^^^^^

commit 64800b08c248942e23709e209fb26eaf1831ba89
Author:     Pierre de Buyl <address@hidden>
AuthorDate: Fri Feb 10 16:43:17 2012 +0100
Commit:     Pierre de Buyl <address@hidden>
CommitDate: Fri Feb 10 16:43:17 2012 +0100

    Removed extraneous box information from the trajectory group.
---
 draft.rst |    8 --------
 1 files changed, 0 insertions(+), 8 deletions(-)

diff --git a/draft.rst b/draft.rst
index 9fc539b..ce55156 100644
--- a/draft.rst
+++ b/draft.rst
@@ -152,20 +152,12 @@ N atoms D dimensions system) and the hdf5 file will be 
the same.
 The "position", "velocity" and "force" datasets possess an optional attribute
 that is the unit of their respective data ("nm" for the position, for 
instance).
 
-The "position" dataset possesses two optional attributes that are the minimum
-and maximum values of the simulation box. The attributes are named "minimum" 
and
-"maximum" and are of dimension \[D\]. If they are absent, the analysis program
-may still use the bounding box of the position dataset as a fallback.
-
-
 The content of the trajectory group is the following::
 
     trajectory
      \-- group1
           \-- position
           |    \-- sample
-          |    |    +-- [minimum]
-          |    |    +-- [maximum]
           |    \-- step
           |    \-- time
           \-- velocity

commit 2b89c13f75102167f64bae8445cdbbc89f7c73b6
Author:     Pierre de Buyl <address@hidden>
AuthorDate: Fri Feb 10 16:31:02 2012 +0100
Commit:     Pierre de Buyl <address@hidden>
CommitDate: Fri Feb 10 16:31:02 2012 +0100

    Moved the "time data" information to be separated from the
    trajectory group, as it is now generalized.
---
 draft.rst |   45 ++++++++++++++++++++++++++++-----------------
 1 files changed, 28 insertions(+), 17 deletions(-)

diff --git a/draft.rst b/draft.rst
index c374ac1..9fc539b 100644
--- a/draft.rst
+++ b/draft.rst
@@ -80,6 +80,34 @@ The content of this group is::
      +-- creation_time
      +-- author
 
+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,
+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,
+real-valued).
+
+As an example, here is the data for the position in a group of particles::
+
+    trajectory
+      \-- group1
+           \-- position
+                \-- sample
+                \-- step
+                \-- time
+
+where the first dimension of "sample" must match the unique dimension of "step"
+and "time".
+
+The "step" dataset must be of integer datatype to allow exact temporal matching
+of data from one data group to another within the same file.
+
+If several datasets are dumped at equal times, "step" and "time" may be hard
+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
 --------------------------
@@ -205,23 +233,6 @@ For instance, a cubic box that changes in time would 
appear as ::
 where "type" is set to "cubic".
 
 
-Storage of the time information in the trajectory group
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
-To link data from the trajectory group datasets to a time in the simulation,
-two datasets containing the integer time step (number of simulation steps) and
-the physical time (the time in simulation or physical units, real-valued) are
-necessary. They are present in the same group as a trajectory dataset. If all
-data are dumped at equal times, "step" and "time" may be hard links to the
-"step" and "time" datasets of another subgroup. 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 subgroup.
-
-In order to read the information, the procedure is similar in both cases: the
-coordinate group contain the attributes either "step" and "time" as datasets or
-as hard links.
-
-
 Observables group
 ^^^^^^^^^^^^^^^^^
 

commit fa0467b2e6ad784d035bdb94065b89e3271e80db
Author:     Pierre de Buyl <address@hidden>
AuthorDate: Wed Jan 4 17:34:58 2012 +0100
Commit:     Pierre de Buyl <address@hidden>
CommitDate: Wed Jan 4 17:34:58 2012 +0100

    Added a sentence on the structure of time-dependent data groups in
    the intro.
---
 draft.rst |    3 +++
 1 files changed, 3 insertions(+), 0 deletions(-)

diff --git a/draft.rst b/draft.rst
index d57b88b..c374ac1 100644
--- a/draft.rst
+++ b/draft.rst
@@ -51,6 +51,9 @@ The groups that are part of the H5MD specifications are
 * observables: Group containing all time-dependent variables in the system,
   except the ones found in the "trajectory group".
 
+All time dependent data (whether in "trajectory" or "observables") is organized
+into HDF5 groups that contain time information in addition to the data.
+
 Global attributes
 -----------------
 

commit c787ebb6c08261f75a419ec2d1a8ff6a2a58551d
Author:     Pierre de Buyl <address@hidden>
AuthorDate: Fri Oct 21 15:30:21 2011 +0200
Commit:     Pierre de Buyl <address@hidden>
CommitDate: Fri Oct 21 15:30:21 2011 +0200

    Added, in "general organization", a list of all root groups.
    Updated the box information.
---
 draft.rst |   59 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
 1 files changed, 59 insertions(+), 0 deletions(-)

diff --git a/draft.rst b/draft.rst
index 785e80b..d57b88b 100644
--- a/draft.rst
+++ b/draft.rst
@@ -42,6 +42,15 @@ trajectory via dataset slicing.
 The file is allowed to possess non-conforming groups that contain other
 information such as simulation parameters.
 
+The groups that are part of the H5MD specifications are
+
+* h5md: Group containing, as attributes, information on the file itself.
+* parameters: Group containing the parameters for a simulation/dataset, such as
+  the spatial dimension of the system or simulation parameters.
+* trajectory: Group containing the trajectory of the system (positions, ...).
+* observables: Group containing all time-dependent variables in the system,
+  except the ones found in the "trajectory group".
+
 Global attributes
 -----------------
 
@@ -141,6 +150,56 @@ The content of the trajectory group is the following::
           |    \-- step
           |    \-- 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 ::
+
+  observables
+   \-- box
+        +-- type
+   ...
+
+The box type can be "cubic" or "triclinic". Depending on this information,
+additional data is stored.
+
+Cubic 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 vectors specifying the directions and
+  lengths of the sides 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
+value organization.
+
+For instance, a cubic box that changes in time would appear as ::
+
+  observables
+   \-- box
+        +-- type
+        \-- edges
+             \-- step [var]
+             \-- time [var]
+             \-- value [var][D]
+        \-- offset
+             \-- step [var]
+             \-- time [var]
+             \-- value [var][D]
+
+where "type" is set to "cubic".
 
 
 Storage of the time information in the trajectory group

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

Summary of changes:
 draft.rst |  130 ++++++++++++++++++++++++++++++++++++++++++++++---------------
 1 files changed, 98 insertions(+), 32 deletions(-)


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