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Re: [lammps-users] [EXTERNAL] Re: GCMC with Reax
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Re: [lammps-users] [EXTERNAL] Re: GCMC with Reax


From: Axel Kohlmeyer <akohlmey@...24...>
Date: Tue, 18 Jul 2017 11:41:20 -0400

On Tue, Jul 18, 2017 at 9:47 AM, Sencer Selcuk <sselcuk@...1683...> wrote:
> Axel & Stan,
>
> Thank you for responding. Compiling with Kokkos (OMP) solved the problem at
> least when I run without `overlap_cutoff`. This option still causes a seg
> fault immediately - both with dev and stable versions.

not here. i can add the flag to any of the existing gcmc input
examples and it works fine.

>
> Perhaps I should open another thread but: I cannot use threading with Kokkos
> even a simple `fix nve` run. I add `-k on t 2 -sf kk` to the command line
> arguments, and it hangs indefinitely. I was able to run only with `-k on t 1
> -sf kk`. Do I need anything else to do so?

please prefix your command line with: gdb --args
and when gdb has launched, type: run
let it run for a bit until you are certain it is hung, then hit CTRL-C
and type: where
and send us the screen output. that will tell in which subroutine it hangs.

for the segfault, please do the same thing. after lammps has
segfaulted, type where and e-mail us the stack trace.

axel.

> I will try to reproduce the two problems with a smaller system and send the
> data files etc. I just wanted to give a heads up.
>
> Best,
> Sencer
>
>
> On Mon, Jul 17, 2017 at 10:23 AM, Moore, Stan <stamoor@...3...> wrote:
>
> There are known problems with using GCMC with USER-REAXC. You should try
> Kokkos ReaxFF instead, it is more memory robust and others have had success
> with that. Stan ________________________________________ From: Axel
> Kohlmeyer <akohlmey@...24...> Sent: Sunday, July 16, 2017 9:34 PM To:
> Sencer Selcuk Cc: LAMMPS Users Mailing List Subject: [EXTERNAL] Re:
> [lammps-users] GCMC with Reax On Sun, Jul 16, 2017 at 10:38 PM, Sencer
> Selcuk <sselcuk@...1683...> wrote:
>
> Dear LAMMPS users, I am trying to set up a GCMC, and eventually a GCMC/NVT
> grand-canonical calculation. I am using ReaxFF with USER/ReaxC on a graphene
> oxide system with large defects, and trying to insert C atoms into system
> with `fix gcmc' to model healing of the defects. I understand that this is
> not the typical use case of this fix, all the examples I have seen are
> prepared to study adsorption of gas molecules etc. So, my first -or perhaps
> zeroth- question is, do you think it wouldn't be wise to try using GCMC to
> study a problem like this? I use the following input file, and my system
> (read by read_data data.in command) has no obvious problems as it runs well
> with fix nvt. However, when I try to run the appended input for GCMC
> calculation just hangs for hours. It creates the dump file writing out the
> initial coordinates, it prints outs the thermo line only for the first step,
> but does nothing else. Am I doing anything wrong here? Finally, when I
> uncomment the overlap_cutoff 0.6 part, calculation immediately crashes with
> a segmentation fault. My feeling is that the two problems are related, but I
> don't have any clues - as such, I would appreciate any help! I am using the
> latest stable LAMMPS version on a supercomputer, and running the job on a
> single node, full 16 processors.
>
> first step you need to do, is to try the same input with the latest
> development version in order to verify that your issue is not already
> solved. if the issue persists, please also provide the data file and the
> potential file, so that a developer can try to reproduce it and track down
> the origin of the segfault/hang. axel.
>
> Best, Sencer Postdoctoral Fellow Department of Chemistry Princeton
> University units real atom_style charge boundary p p p read_data data.in
> timestep 0.10 pair_style reax/c lmp_control lgvdw yes safezone 1.6 mincap
> 150 pair_coeff * * reax.fgs C H O fix reax all qeq/reax 1 0.0 10.0 1e-6
> reax/c thermo 1000 thermo_style custom step time temp press vol pe etotal
> enthalpy thermo_modify flush yes dump 1 all custom 1000 fgs.lammpstrj
> element xu yu zu dump_modify 1 sort id element C H O append yes fix mc all
> gcmc 1 100 100 1 1824 1500.0 -1.0 1.0 # overlap_cutoff 0.6 run 1000000
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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.
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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.