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[lammps-users] GCMC with Reax
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[lammps-users] GCMC with Reax


From: Sencer Selcuk <sselcuk@...1683...>
Date: Sun, 16 Jul 2017 22:38:51 -0400

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.

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