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
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.
> 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
> 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.