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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: Sencer Selcuk <sselcuk@...1683...>
Date: Tue, 18 Jul 2017 09:47:47 -0400

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.

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?

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 ------------------------------------------------------------------------------ Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot _______________________________________________ lammps-users mailing list lammps-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/lammps-users
-- 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. ------------------------------------------------------------------------------ Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot _______________________________________________ lammps-users mailing list lammps-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/lammps-users