Hi LAMMPS users,
I recently was stuck by problems using LAMMPS with reax/reaxc pair style for parallel simulation. Any help is greatly appreciated!
I tried to simulate a process of CNT growth on Ni nanocatalyst. Below is the input file (Current one is for reaxc, if substitute the corresponding line with the comment, it will be the input for reax pair style.)
CNT growth on Ni nanocatalyst
boundary p p p
pair_style reax/c NULL safezone 16.0 mincap 1000
lattice fcc 1.0
region sim block -30. 30. -30. 30. -30. 30. units box
region dep1 block -30. 30. -30. 30. 20. 30. units box
region dep2 block -30. 30. -30. 30. -30. -20. units box
region dep3 block 20. 30. -30. 30. -30. 30. units box
region dep4 block -30. -20. -30. 30. -30. 30. units box
region dep5 block -30. 30. -30. -20. -30. 30. units box
region dep6 block -30. 30. 20. 30. -30. 30. units box
region deps union 6 dep1 dep2 dep3 dep4 dep5 dep6
group puf id > 126
pair_coeff * * ffield.reax.NiCH Ni C
#pair_coeff * * ffield.reax 4 1
neighbor 2 bin
neigh_modify every 10 check no
fix 1 all qeq/reax 1 0.0 10.0 1.0e-6 reax/c
Above line will be commented for reax style
fix ins puf deposit 200 2 5 12345 region deps
delete_atoms overlap 1.0 puf puf
fix trmout all nve
fix tom all langevin 1500. 1500.0 100 248158
thermo_modify lost ignore flush yes
compute_modify thermo_temp dynamic yes
dump 2 all xyz 10000 imp.xyz
dump 3 all custom 10000 imp.dat id type q x y z vx vy vz
Problem for reaxc pair style:
Every time I run the code in one node(16 cores) on cluster, it works well. But when I tried to run in multiple nodes (even 2), I will get either of the two errors running within 10s. This problem is not related to the machine, because I tried it on computing clusters of several places, and the problem is the same.
1)Segmentation fault (signal 11)
2)not enough space for bonds! total=… allocated=… (former is several orders of magnitude larger than latter)
I even tried to run the examples in tarball, they all failed when using multiple nodes. And the error is Segmentation fault.
I also tried to increase the safezone and mincap parameter, but still not working.
Problem for reax pair style:
I encountered the error: “Too many bonds on atom. Increase MBONDDEF” even with one node. So I changed the MBONDDEF from 20 to 40, and recompiled lammps. It worked, but here come two new problems:
- The benchmark speed for multiple nodes is the same or even worse than one nodes.
- The trajectory of simulation makes no physical sense (No carbon hexagons or pentagons formed. At least for reaxc with one node I can find carbon rings on Ni after some time).
On my school cluster, I used LAMMPS 10Aug15 version, compiled with mpiicpc (reax library compiled with mpiifort). I don’t know the environment of LAMMPS on other clusters, but the problems are all the same.
My data file is also included. The reaxFF file is obtained from Adri van Duin, which I don’t know if it’s proper to put here directly.
Thank you so much!
Dept. of Materials Science and Engineering
Institute for Advanced Computational Science
Stony Brook University
ni_ann.lammps (8.88 KB)