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Re: Seg error trying to combine Gay-Berne and dipoles

From: Rudolf Weeber
Subject: Re: Seg error trying to combine Gay-Berne and dipoles
Date: Thu, 1 Apr 2021 17:22:23 +0200

Hi Margaret,
On Thu, Apr 01, 2021 at 04:13:26PM +0200, Margaret Rosenberg wrote:
> I'm attempting to reproduce a simple Gay-Berne ferrofluid and getting some
> odd segmentation errors. I've attached an attempt at a minimal working
> example* below: any advice would be appreciated. The error message reads as
> follows:
> [cpk01:64078] *** Process received signal ***
> [cpk01:64078] Signal: Segmentation fault: 11 (11)
> [cpk01:64078] Signal code: Address not mapped (1)
> [cpk01:64078] Failing at address: 0x7f85d9bd5000
> [cpk01:64078] [ 0] 0   libsystem_platform.dylib
> 0x00007fff718535fd _sigtramp + 29
> [cpk01:64078] [ 1] 0   ???
> 0x00007f89d7c30220 0x0 + 140230007128608
> [cpk01:64078] [ 2] 0   EspressoCore.dylib
> 0x0000000109d691b6 _Z18dp3m_dipole_assignRK13ParticleRange + 326
A segfautl in the p3m dipole assignment (map dipoles onto the p3m gird) 
strongly sugges a particle position outside the domain.

Unfortunately, I can't check that, becaus I can only reproduce the segfault, if 
I run your sample outside a debugger. When running in the debugger (and build 
type=Debug set in cmake), the simulation eventually fails due to an assertion 
checking the stability of the rotational integrator 
``` assert(square > 0) ``` in propagate_omega_quat_particle() in rotation.cpp.
to mittigate this, you can try to slow the rotational time scale of your 
simulation, e.g., by increasing the rotational inertia of the Gay-Berne 
particles or the rotational friction coefficient in the Langevin thermostat.
Probably it is also a good ide to run minimum distance analysis on your dipoles 
during the simulation to make sure there are no surprises, there.

Hope that helps!
Regards, Rudolf

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