>From 5bd007c352802a1a1e8070e004cacccf8adf818f Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Felix=20H=C3=B6fling?=
Date: Tue, 31 Jul 2012 17:27:04 +0200
Subject: [PATCH] observables: allow subgroups, add "pressure", matrix of edge
vectors
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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
DÃD 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 file 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 DÃD-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
--
1.7.10.2