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[ESPResSo-devel] Cellsystem, folded position, constraints (was: Nsquare
From: |
Ulf Schiller |
Subject: |
[ESPResSo-devel] Cellsystem, folded position, constraints (was: Nsquare cellsystem and folded positions) |
Date: |
Mon, 13 Aug 2007 17:20:11 +0200 |
User-agent: |
Mozilla/5.0 (X11; U; Linux x86_64; en-US; rv:1.7.12) Gecko/20050921 |
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Hi,
Axel Arnold wrote:
> On Monday 13 August 2007 16:26, Olaf Lenz wrote:
>>Axel Arnold wrote:
>>>Why not????? For forces, energy etc. the distances are correctly folded,
>>>as far as I can remember.
>>Hmm, apparently you are not of the same opinion as Hanjo in that
>>respect. However, my tests showed that at least for constraints, the
>>force computation does not work correctly. I'll provide an example
>>script soon.
>
> Ok, to clarify that: The pair forces use the minimum image distance, both in
> domdec and nsquare. For the constraint forces, for some reason we use the
> internally folded coordinates. That can indeed cause a problem, but actually
> for both cellsystems. E.g. consider an excluded sphere close to the boundary.
> Again, the example:
>
> setmd box_l 5 5 5
> part 0 pos 0 0 0 v -0.1 0 0
>
> inter 0 0 lennard-jones 1.0 1.0 1.12246 0.25 0
>
> constraint sphere center 4 0 0 radius 1 direction outside type 0
>
> setmd time_step 0.01
> thermostat off
> setmd skin 1
> for {set i 0} {$i < 100} {incr i} {
> integrate 10
> puts [part 0 pr folded]
> }
>
> The particles goes unperturbed right into the sphere, then gets folded, and
> Espresso crashes :). And that is domaindecomposition.
>
> So, we have a bug treating constraints, but that actually applies to all
> cellsystems.
Another issue about constraints is whether they have periodic images.
E.g. in case of walls, a common tutorial example is that one can
simulate channel flow by putting a single wall into a system with
periodic boundary conditions. This is not the case in ESPResSo. This
might be a source of confusion (actually it was already).
Cheers,
Ulf
- --
Ulf D. Schiller * Room 1.404 * Phone +49 6131 379-481
Max Planck Institute for Polymer Research
Theory Group
D-55128 Mainz, Germany 50° 0' N, 008° 16' E
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- RE: [ESPResSo-devel] Nsquare cellsystem and folded positions, (continued)
Re: [ESPResSo-devel] Nsquare cellsystem and folded positions, Axel Arnold, 2007/08/13
- Re: [ESPResSo-devel] Nsquare cellsystem and folded positions, Olaf Lenz, 2007/08/13
- Re: [ESPResSo-devel] Nsquare cellsystem and folded positions, Axel Arnold, 2007/08/13
- Re: [ESPResSo-devel] Nsquare cellsystem and folded positions, Kai Grass, 2007/08/13
- Re: [ESPResSo-devel] Nsquare cellsystem and folded positions, Olaf Lenz, 2007/08/13
- Re: [ESPResSo-devel] Nsquare cellsystem and folded positions, Axel Arnold, 2007/08/13
- Re: [ESPResSo-devel] Nsquare cellsystem and folded positions, Olaf Lenz, 2007/08/13
- Re: [ESPResSo-devel] Nsquare cellsystem and folded positions, Axel Arnold, 2007/08/13
- [ESPResSo-devel] Cellsystem, folded position, constraints (was: Nsquare cellsystem and folded positions),
Ulf Schiller <=
- Re: [ESPResSo-devel] Cellsystem, folded position, constraints, Olaf Lenz, 2007/08/13
- Re: [ESPResSo-devel] Nsquare cellsystem and folded positions, Olaf Lenz, 2007/08/13
- Re: [ESPResSo-devel] Nsquare cellsystem and folded positions, Kai Grass, 2007/08/13
- Re: [ESPResSo-devel] Nsquare cellsystem and folded positions, Axel Arnold, 2007/08/13
- Re: [ESPResSo-devel] Nsquare cellsystem and folded positions, Olaf Lenz, 2007/08/13
- RE: [ESPResSo-devel] Nsquare cellsystem and folded positions, Limbach, Hans Joerg, LAUSANNE, NRC-FS, 2007/08/14