Dear Axel
Thanks to your reply.
Based on your advice, I have installed lammps new version (lammps-31Mar17) and I have run same script.
However, I’m faced with same problems.
Exactly speaking, the simulation is normally finished, but the calculation does not proceed.
I checked following message in my log file.
486.933u 3.011s 0:17.77 2757.1% 0+0k 8512+38960io 883pf+0w
I am looking for your reply.
Regards.
Hyein
ffield.reax (23.6 KB)
in.sm (3.2 KB)
data.sm (250 KB)
This doesn’t look like LAMMPS output at all.
Michal
Dear Axel
Thanks to your reply.
Based on your advice, I have installed lammps new version (lammps-31Mar17)
and I have run same script.However, I’m faced with same problems.
Exactly speaking, the simulation is normally finished, but the calculation
does not proceed.I checked following message in my log file.
*486.933u 3.011s 0:17.77 2757.1% 0+0k 8512+38960io 883pf+0w*
the attached input cannot be run in parallel (with 28 CPUs) as you
claimed. it errors out immediately (see below), suggesting, that there is
something wrong with your restrain fixes. most likely you are
misunderstanding how they work, as your input seems to be hinting at that
you are assuming those are based on atom types, while fix restrain works on
atom ids.
it can be easily seen that atoms 1 and 5 are more than 12 \AA (the master
communication cutoff) apart and thus causing the error. increasing that
cutoff to make the simulation continue results in a non-physical structure.
axel.
[[email protected]... sm]$ mpirun -np 28 ~/compile/lammps/src/lmp_omp -in in.sm
LAMMPS (23 Oct 2017)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread.
(../comm.cpp:90)
using 1 OpenMP thread(s) per MPI task
Reading data file ...
orthogonal box = (0 0 0) to (31.8535 31.8535 31.8535)
2 by 2 by 7 MPI processor grid
reading atoms ...
3328 atoms
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
0 = max # of 1-2 neighbors
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
1 = max # of special neighbors
Warning: changed valency_val to valency_boc for X
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12
ghost atom cutoff = 12
binsize = 6, bins = 6 6 6
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair reax/c, perpetual
attributes: half, newton off, ghost
pair build: half/bin/newtoff/ghost
stencil: half/ghost/bin/3d/newtoff
bin: standard
(2) fix qeq/reax, perpetual, copy from (1)
attributes: half, newton off, ghost
pair build: copy
stencil: none
bin: none
Setting up Verlet run ...
Unit style : real
Current step : 0
Time step : 1
ERROR on proc 14: Restrain atoms 1 5 missing on proc 14 at step 0
(../fix_restrain.cpp:235)
Last command: run 10000
application called MPI_Abort(MPI_COMM_WORLD, 1) - process 14