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Re: [lammps-users] Bond/break causing segfaults(?)
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Re: [lammps-users] Bond/break causing segfaults(?)


From: Axel Kohlmeyer <akohlmey@...24...>
Date: Thu, 3 Aug 2017 12:15:50 -0400



On Thu, Aug 3, 2017 at 11:20 AM, Guido Ritsema van Eck <g.c.ritsemavaneck@...7037...> wrote:
Dear all,

I am trying to simulate the detachment of grafted polymers from a surface. I am currently doing this with simple bead-spring polymers, with atoms bound to each other and the surface by FENE potentials, and using the bond/break fix to break any surface-polymer bonds that exceed their equilibrium length by a small margin. All pair interactions are cut-off LJ, with interactions for directly bonded atoms set to zero via special_bonds (as required for the FENE bond type).

However, my simulations produce segfaults related to an invalid pointer, often in combination with the "fix bond/break needs ghost atoms from further away" error message (despite already using large values for the neighbor skin distance and communicate cutoff). These issues primarily occur during the run, but sometimes when writing a data file afterwards. In the latter case, an apparently valid data file is produced despite the error.

The problem shows up more quickly in large or dense systems, but it also occurs for a minimal system of 2 interacting grafted polymers. For a given system and input file, it always happens at the same time step. The simulation works fine when I take out the bond/break fix. I am working with the lammps-daily executable on Ubuntu 14.04. The problem occurs considerably faster (in terms of timesteps) when running lammps in parallel compared to serially, but working serially does not eliminate the problem.

​please provide the exact LAMMPS version that you are using. lammps-daily is obviously a moving target.
if this version is different from the current development version (24 Jul 2017 currently), then please try to compile the latest development version (or the master branch from the git repository at your preference), to confirm, that this is a genuinely new issue and not something that has already been addressed.
this page: http://lammps.sandia.gov/bug.html has a summary of recent (significant) changes.

if the issue persists, please submit a more formal bug report with suitable (minimal yet complete) input deck, so it can be reproduced by the LAMMPS developers. since we are about to release a new stable version, we are *very* eager to learn of any potential bug, so it can be fixed, if possible before the release, or at least well documented.

Any input on what might be going wrong and how to fix it would be fantastic, as I am quite baffled myself.

​that is quite difficult to do without knowing more details and specifically being able to reproduce it. please make an effort to create an input deck, that contains only the minimum number of commands and the smallest system required to reproduce the issue. please have a look at these pages:

https://github.com/lammps/lammps/blob/master/.github/CONTRIBUTING.md

​thanks in advance,
     axel.​



Thanks in advance,
Guido Ritsema van Eck

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--
Dr. Axel Kohlmeyer  akohlmey@...24...  http://goo.gl/1wk0
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.