[h5md-commit] H5MD branch master updated. 9d7ee050b56a321ffd7fc32f72e90396af1306ca

[h5md-commit]

This is an automated email from the git hooks/post-receive script. It was
generated because a ref change was pushed to the repository containing
the project "H5MD".

The branch, master has been updated
       via  9d7ee050b56a321ffd7fc32f72e90396af1306ca (commit)
      from  74a28be0e82d4babfadbb92429636753b1f849fd (commit)

Those revisions listed above that are new to this repository have
not appeared on any other notification email; so we list those
revisions in full, below.

- Log -----------------------------------------------------------------
commit 9d7ee050b56a321ffd7fc32f72e90396af1306ca
Author:     Felix Höfling <address@hidden>
AuthorDate: Mon Aug 29 09:11:37 2011 +0200
Commit:     Felix Höfling <address@hidden>
CommitDate: Mon Aug 29 09:24:21 2011 +0200

    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.
---
 draft.rst |   41 ++++++++++++++++++++---------------------
 1 files changed, 20 insertions(+), 21 deletions(-)

diff --git a/draft.rst b/draft.rst
index 6b742e7..7dc6594 100644
--- a/draft.rst
+++ b/draft.rst
@@ -80,11 +80,13 @@ 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 a "coordinates" dataset, a "step" dataset and a "time"
-dataset.
+group that contains datasets "sample", "step", and "time".
 
-* The "coordinates" dataset has dimensions \[variable\]\[N\]\[D\] where the
-  variable dimension is present to accumulate time steps.
+* Standardised subgroups are "position", "velocity", "force" and "species".
+
+* The "sample" dataset holds the actual data and has dimensions
+  \[variable\]\[N\]\[D\], where the variable dimension is present to accumulate
+  time steps.
 
 * The "step" dataset has dimensions \[variable\] and contains the integer step
   corresponding to the time step at which the corresponding data has been
@@ -93,9 +95,7 @@ dataset.
 * The "time" dataset is as the "step" dataset, but contains the real value of
   the time.
 
-* The coordinates are "position", "velocity", "force" and "species".
-
-* The "species/coordinates" dataset has dimensions \[N\] if the species do not
+* The "species/sample" 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
@@ -123,21 +123,21 @@ The content of the trajectory group is the following::
     trajectory
      \-- group1
           \-- position
-          |    \-- coordinates
+          |    \-- sample
           |    |    \-- minimum
           |    |    \-- maximum
           |    \-- step
           |    \-- time
           \-- velocity
-          |    \-- coordinates
+          |    \-- sample
           |    \-- step
           |    \-- time
           \-- force
-          |    \-- coordinates
+          |    \-- sample
           |    \-- step
           |    \-- time
           \-- species
-          |    \-- coordinates
+          |    \-- sample
           |    \-- step
           |    \-- time
 
@@ -146,14 +146,14 @@ The content of the trajectory group is the following::
 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
+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 coordinates variable. 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 coordinates variable.
+"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
@@ -168,7 +168,7 @@ 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 "samples" and the step and time datasets.
+datasets: the actual data in "sample" and the step and time datasets.
 
 The following names should be obeyed for the corresponding observables:
 
@@ -181,11 +181,11 @@ The content of the observables group is the following::
 
     observables
      \-- obs1
-     |    \-- samples
+     |    \-- sample
      |    \-- step
      |    \-- time
      \-- obs2
-     |    \-- samples
+     |    \-- sample
      |    \-- step
      |    \-- time
      \-- ...
@@ -217,7 +217,6 @@ names should be kept concise but worded fully.
 
 The present list of reserved names is:
 
-* coordinates
 * creator
 * datetime
 * force

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

Summary of changes:
 draft.rst |   41 ++++++++++++++++++++---------------------
 1 files changed, 20 insertions(+), 21 deletions(-)


hooks/post-receive
-- 
H5MD