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Re: [ESPResSo-users] cell_grid $ verlet_reuse

From: Mikheil Azatov
Subject: Re: [ESPResSo-users] cell_grid $ verlet_reuse
Date: Thu, 6 Jan 2011 16:54:27 -0500

Hi, yeah the max_num_cells was set to MAX_INT = 32767. After I changed it to a bigger number everything seems to work fine. 

Do you know what is an optimal for speed number of verlet_reuse per number of integration steps in integrate command ? Also does it matter for speed how many integration steps I do during integrate command ?


On Thu, Jan 6, 2011 at 12:56 PM, Axel Arnold <address@hidden> wrote:
On Tuesday 04 January 2011, Mikheil Azatov wrote:
> Hi,
> I noticed my cell_grid size doesn't go above curtain size. Is there a limit
> on the number of cells or something like this ? I'm running the code on 2
> CPUs and the maximum cell_grid I get is 20 40 40. If I increase the
> simulation box size or decrease the skin parameter it stays the same...

There was a long time a limit, which was lifted only in the latest version.
However, the limit was 512 cells, which is less than what you get, so it seems
that for you the limit is basically infinite. To check, use "puts [setmd
max_num_cells]", or set this variable to a high value.

> Also I noticed that my verlet_reuse parameter can only be 0 or 1 which is
> obviously not good for parallel computing. If I decrease my skin to like
> 0.1 then verlet_reuse is always 1.0 and if I start increasing the skin.
> the verlet _reuse starts to become 0 more and more integration steps. At
> large skin like 2 or 3, verlet_reuse is 0 every integration step. I'm a
> little bit confused here how is that possible... Shouldn't verlet_reuse
> increase when I increase the skin ?

verlet_reuse tells you how often _during the last integrate command_ the
verlet lists where updated on average. Since you do only a single time step,
the answer can be only 0 (if no update occured) or 1 (if an update occured),
and the number of 0s should indeed increase. If you do the typicall 100 or
more time steps at once, the output will be more what you expect.


> for {set i 0} { $i < 10000000 } { incr i} {
>   integrate 1
>   #setmd time [expr $i*$time_step]
>     imd positions
>      puts "verlet_reuse =  [setmd verlet_reuse] "
>      puts [setmd cell_grid]
>      if {[expr $i%$pdbstep] == 0 } {
>      incr pdbindex
>      writepsf "$name$ident/$name$ident$pdbindex.psf"
>      writepdb "$name$ident/$name$ident$pdbindex.pdb"
>      puts " i = $i "
>      puts "verlet_reuse =  [setmd verlet_reuse] "
>      }
> }

JP Dr. Axel Arnold      Tel: +49 711 685 67609
ICP, Universität Stuttgart      Email: address@hidden
Pfaffenwaldring 27
70569 Stuttgart, Germany

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