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RE: [ESPResSo] Diffusion of a probe particle
From: |
Limbach, Hans Joerg, LAUSANNE, NRC-FS |
Subject: |
RE: [ESPResSo] Diffusion of a probe particle |
Date: |
Fri, 10 Aug 2007 17:17:19 +0200 |
> -----Original Message-----
> From: address@hidden
> [mailto:address@hidden On Behalf Of Olaf Lenz
> Sent: lundi, 6. août 2007 16:13
> To: ESPResSo users' mailing list
> Subject: [ESPResSo] Diffusion of a probe particle
>
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>
> Hello!
>
> I'm currently computing diffusion constants of probe
> particles in systems with different obstacles. For a start, I
> just want to simulate free diffusion of non-interacting
> particles without any obstacles and measure the mean-square
> deviation (MSD).
>
> Using ESPResSo, this yields a number of problems which render
> the simulation pretty inefficient. I want to ask whether any
> of you has some more ideas on how to treat the problem efficiently.
>
> The main problem seems to originate from the following:
> On the one hand, when I set up a single probe particle and
> let it diffuse, the script needs to return control to the Tcl
> level very often, so that I get a very significant time
> overhead. The only solution to this that I see would be to
> implement the measurement of the MSD in C so that the
> simulation does not have to return to the Tcl level. This
> would however neither be simple nor in the spirit of
> ESPResSo, so I would like to avoid this.
>
> On the other hand, when I set up a larger number of probe
> particles (e.g. 10000), this also seems to create a time
> overhead, even though the particles do not interact, and the
> memory requirements are still far from any hard memory limits
> (approx 10 MB). Apparently, the particles are somehow
> included in the Verlet-list of the other particles, even
> though they do not interact. To get rid of this problem, I
> tried to make the box length as large as possible (e.g.
> box_l=1000). This should cause the particles to be far from
> each other so that they do not occur in each other's Verlet
> lists any more. This did indeed reduce the problem, but still
> a large number of particles significantly slows down the
> simulation. Also, changing the Verlet skin affected the timing.
> Where, exactly, does this overhead for larger particle
> numbers come from?
>
I guess the best choice is to set max_num_cells to roughly the number of
particles (balance running through cells and running through particles, I even
think Bernward wrote a command to optimize this) and set a dummy interaction
with 0 interaction range and skin to (box/(n_part)^1/3)=size of the cells. This
makes roughly one particle per box and a maximally large skin which reduces the
number of times Espresso tries to setup new verlet lists (which of course will
be empty all the time). This should be rather fast.
> Furthermore, making the box size very large will not work any
> more as soon as obstacles of a certain density are
> introduced. Either it is necessary to create lots of replicas
> of the obstacles, or I have to make the box relatively small
> - both methods would make the simulation slow again. Does
> anyone have an idea how to handle this?
>
> Using a large box length, I have also tried to disable the
> Verlet lists.
I guess then Espresso does try to find interaction partners at every step (Also
maximale Entschleunigung, sozusagen die Berner Variante ;-))
> - From my understanding, this should speed up the simulation,
> as no Verlet list update would ever be required and the size
> of the default cell lists should be small enough not to
> contain any neighboring particles.
> However, this did not seem to be the case. Instead, the
> simulation was significantly slower (factor 3 or so). Can
> anybody explain this to me?
See above
Greetings,
Hanjo
>
> Best regards
> Olaf
>
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