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- Log -----------------------------------------------------------------
commit 5bd007c352802a1a1e8070e004cacccf8adf818f
Author:     Felix Höfling <address@hidden>
AuthorDate: Tue Jul 31 17:27:04 2012 +0200
Commit:     Felix Höfling <address@hidden>
CommitDate: Tue Jul 31 17:27:04 2012 +0200

    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.
---
 draft.rst |   16 ++++++++++++----
 1 files changed, 12 insertions(+), 4 deletions(-)

diff --git a/draft.rst b/draft.rst
index 3376c22..9b7cf91 100644
--- a/draft.rst
+++ b/draft.rst
@@ -191,14 +191,14 @@ Cuboid box
 """"""""""
 
 * edges: A vector specifying the length of the box in the D dimensions of
-    space.
+  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.
+* 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
@@ -230,16 +230,19 @@ Observables group
 
 Macroscopic observables are stored as \[variable\] time series for scalar
 observables and as \[variable\]\[d\] time series for d-dimensional vector
-observables. The variable dimension allows to accumulate time-steps. The name 
of
+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 "value" and the step and time datasets.
+Observables representing only a subset of the particles may be stored in
+appropriate subgroups similarly to the "trajectory" tree.
 
 The following names should be obeyed for the corresponding observables:
 
 * total_energy
 * potential_energy
 * kinetic_energy
+* pressure
 * temperature
 
 The content of the observables group is the following::
@@ -253,6 +256,11 @@ The content of the observables group is the following::
      |    \-- value
      |    \-- step
      |    \-- time
+     \-- group1
+     |    \-- obs3
+     |         \-- value
+     |         \-- step
+     |         \-- time
      \-- ...
 
 Program-dependent groups

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

Summary of changes:
 draft.rst |   16 ++++++++++++----
 1 files changed, 12 insertions(+), 4 deletions(-)


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