>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 MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit 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 DÃ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 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 DÃ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 -- 1.7.10.2