[ESPResSo-devel] Cell lists vs. domain decomposition

[Olaf Lenz]

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Hi Despressies!

In context of the thread on diffusion, I noticed that in the docs (i.e.
the UG) two things seem to be intermixed that are related but not really
the same:
1. To my understanding, "domain decomposition" is related to
parallelization. It means that the simulation box is decomposed into
domains, each of which can be computed on another processor. The size
and shape of the domains is completely arbitrary. However, it is
favourable to minimise the interface with neighbouring domains to reduce
the communication overhead required to communicate the particles that
interact with neighbouring domains.
2. "Cell lists" on the other hand are needed to speed up the algorithm
on a single processor: the domain is decomposed into cells with a
minimal side length of the interaction range. When it is necessary to
loop over the interaction partners of a particle, it is only necessary
to consider those particles that are in the 26 neighbouring cells and
the cell itself. This algorithm in combination with Verlet lists is the
fastest option for many systems.

Both of these points can be related, and one can think of choosing the
domains from item 1 from the cells of item 2, but in theory they are
completely independent, are they not?
To my understanding, the "cellsystem" command of ES refers to item 2,
doesn't it? However, in the documentation of the command, the notion
"domain decomposition" is used. This bugs me.

I would propose to remove the term "domain decomposition" from the docs
on the cellsystem command, or else describe how they are interrelated in
the case of ESPResSo.

Olaf
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