[Date Prev][Date Next][Thread Prev][Thread Next][Date Index][Thread Index]
[h5md-user] Pre-averaged observables
From: |
Felix Höfling |
Subject: |
[h5md-user] Pre-averaged observables |
Date: |
Wed, 15 May 2013 12:10:13 +0200 |
User-agent: |
Opera Mail/12.15 (Linux) |
Hi all,
sometimes, one wants to store pre-averaged observables, i.e. accumulated
over a certain time span. For example, compute the pressure every 1000
steps and compute the mean from 10 values, i.e. writing the data only
every 10000 steps. Such a functionality is provided by LAMMPS and recently
also by HALMD.
http://lammps.sandia.gov/doc/fix_ave_time.html
http://halmd.org/modules/observables/utility/accumulator.html
Now my question: how shall such data be stored in the H5MD observables
group? Along with the mean value, one would like to store also the
standard error (or the variance) and the number of accumulated values. One
scheme would be to distribute this information over several groups under
the roof of the observable's name:
obs1
\-- mean
| +-- count
| \-- value
| \-- step
| \-- time
|
\-- error_of_mean
| +-- count
| \-- value
| \-- step
| \-- time
|
\-- count
+-- count
\-- value
\-- step
\-- time
The obvious drawback is that the structure is pretty nested and that
pre-averaged observables have a disjoint structure from plain observables,
e.g., the mean value is obs1/mean/value in one case and obs1/value in the
other. Further, the step/time fields show up repeatedly (although they may
link each other.)
A second scheme would extend the existing value/step/time triple to
include the error and the number:
obs1
+-- count
\-- value
\-- error
\-- count/number/samples ???
\-- step
\-- time
This scheme appears more natural to me and I would prefer it. In addition,
one may add "variance" and "standard_deviation". There is, however, a
naming clash between the attribute or dataset "count" for the number of
particles and the number of accumulated values/samples.
Nicolas Höft noted on the halmd-devel mailing list that "count" for the
number of particles is not very descriptive, may we change it to "size" or
"number"?
http://article.gmane.org/gmane.science.simulation.halmd.devel/292
The whole issue may be beyond the current release candidate. I mainly
would like to hear your opinion at an early stage.
Best wishes,
Felix
- [h5md-user] Pre-averaged observables,
Felix Höfling <=