[h5md-commit] branch master updated. 44c9bcefc258e31f4043edfd2ebaa815a69644ce

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- Log -----------------------------------------------------------------
commit 44c9bcefc258e31f4043edfd2ebaa815a69644ce
Author:     Pierre de Buyl <address@hidden>
AuthorDate: Sun Jul 22 05:56:05 2012 +0200
Commit:     Pierre de Buyl <address@hidden>
CommitDate: Sun Jul 22 05:56:05 2012 +0200

    Modified discussion to take into account latest updates of the draft.
---
 discussion.rst |   17 +++--------------
 1 files changed, 3 insertions(+), 14 deletions(-)

diff --git a/discussion.rst b/discussion.rst
index 76b30f4..f82247f 100644
--- a/discussion.rst
+++ b/discussion.rst
@@ -18,32 +18,21 @@
 Data elements in discussion
 ---------------------------
 
-* Reserved names
-
-  At this time, position, velocity and force are reserved. How far should we
-  specify? Other elements seem appropriate for reserved names: temperature, 
time
-  step - DT, ...
-
 * Simulation box information
 
-  Some information on the simulation box geometry could be included. The lower
-  and upper coordinates of the box are already found as attributes to the
-  position/coordinates dataset. More ?
+  Some information on the simulation box geometry could be included. For now,
+  the box size is included in the observables group. Symmetry groups could be
+  included in the future.
 
 * Topology
 
   There is the need to store topology for rigid bodies, elastic networks or
   proteins. The topology may be a connectivity table, contain bond lengths, ...
 
-* Simulation parameters
-
-  Box size, time step, used force field, per species mass, ...
-
 * Scalar and vector fields
 
   May be used to store coarse grained or cell-based physical quantities.
 
-
 * The "density" dataset has dimensions \[variable\]\[Nx\]\[Ny\]\[Nz\] where the
   variable dimension allows to accumulate steps, and Nx, Ny and Nz are the
   number of data points in each dimension. This dataset possesses the 
attributes

commit a39257fe2b702c6e7dcd15ffbf8fbb22f4c75b7e
Author:     Pierre de Buyl <address@hidden>
AuthorDate: Mon Jul 16 03:24:52 2012 +0200
Commit:     Pierre de Buyl <address@hidden>
CommitDate: Mon Jul 16 03:24:52 2012 +0200

    Removed the reserved names section.
---
 draft.rst |   23 -----------------------
 1 files changed, 0 insertions(+), 23 deletions(-)

diff --git a/draft.rst b/draft.rst
index ce2b829..3376c22 100644
--- a/draft.rst
+++ b/draft.rst
@@ -274,26 +274,3 @@ Profiling
 The "profiling" group may contain information related to the timing of various
 parts of the simulation.
 
-Reserved names
---------------
-
-Part of the H5MD specification is a number of reserved names. This allows a 
data
-analysis package to handle adequately the datasets with reserved names. Future
-names should be kept concise but worded fully.
-
-The present list of reserved names is:
-
-* creator
-* datetime
-* force
-* version
-* interaction_energy
-* kinetic_energy
-* observables
-* parameters
-* position
-* profiling
-* temperature
-* total_energy
-* velocity
-

commit 3092738fbe0687ec60ec8a6b1c244ab83447c111
Author:     Pierre de Buyl <address@hidden>
AuthorDate: Mon Jul 16 03:19:03 2012 +0200
Commit:     Pierre de Buyl <address@hidden>
CommitDate: Mon Jul 16 03:19:03 2012 +0200

    Corrected cuboid subtitle underlining.
---
 draft.rst |    2 +-
 1 files changed, 1 insertions(+), 1 deletions(-)

diff --git a/draft.rst b/draft.rst
index 47652ff..ce2b829 100644
--- a/draft.rst
+++ b/draft.rst
@@ -188,7 +188,7 @@ 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.

commit aff1f2f567b231933eb55854784b84c0654c4eea
Author:     Pierre de Buyl <address@hidden>
AuthorDate: Mon Jul 16 03:17:26 2012 +0200
Commit:     Pierre de Buyl <address@hidden>
CommitDate: Mon Jul 16 03:17:26 2012 +0200

    Changed cubic to cuboid.
---
 draft.rst |    8 ++++----
 1 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/draft.rst b/draft.rst
index 0951cf2..47652ff 100644
--- a/draft.rst
+++ b/draft.rst
@@ -184,10 +184,10 @@ of box is stored as an attribute to this box group ::
         +-- type
    ...
 
-The box type can be "cubic" or "triclinic". Depending on this information,
+The box type can be "cuboid" or "triclinic". Depending on this information,
 additional data is stored.
 
-Cubic box
+Cuboid box
 """""""""
 
 * edges: A vector specifying the length of the box in the D dimensions of
@@ -208,7 +208,7 @@ 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 ::
+For instance, a cuboid box that changes in time would appear as ::
 
   observables
    \-- box
@@ -222,7 +222,7 @@ For instance, a cubic box that changes in time would appear 
as ::
              \-- time [var]
              \-- value [var][D]
 
-where "type" is set to "cubic".
+where "type" is set to "cuboid".
 
 
 Observables group

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

Summary of changes:
 discussion.rst |   17 +++--------------
 draft.rst      |   33 +++++----------------------------
 2 files changed, 8 insertions(+), 42 deletions(-)


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