BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES

LAMMPS
1

Hello,
When I was doing deposition simulations with reaxff, I started reporting errors after reading the molecular template file, what is the reason

Read molecule template dimer:
1 molecules
0 fragments
3 atoms with max type 2
2 bonds with max type 1
1 angles with max type 1
0 dihedrals with max type 0
0 impropers with max type 0
Setting up Verlet run …
Unit style : real
Current step : 10
Time step : 0.01
Per MPI rank memory allocation (min/avg/max) = 10.35 | 15.68 | 22.27 Mbytes
Step Temp PotEng KinEng TotEng Time
10 300 -104275.83 982.77307 -103293.05 0

===================================================================================
= BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
= RANK 0 PID 41335 RUNNING AT node15_gds_hpc
= KILLED BY SIGNAL: 9 (Killed)

===================================================================================
= BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
= RANK 1 PID 41336 RUNNING AT node15_gds_hpc
= KILLED BY SIGNAL: 9 (Killed)

2

Impossible to say with so little information. Most likely your batch job has timed out.

4

I tried to deposit silica on a silicon substrate with a reaction force field at a temperature of 300K, depositing a molecule every 5,000 steps, and when the molecular file was read and then added to the system, the simulation began to report an error ：
= BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
= RANK 0 PID 41335 RUNNING AT node15_gds_hpc
= KILLED BY SIGNAL: 9 (Killed)

My input file：
dimension 3
units real
atom_style full
boundary p p f

neighbor 2.0 bin
neigh_modify every 100 delay 0 check yes

read_data Si.data extra/atom/types 2 extra/bond/types 1 extra/angle/types 1 extra/special/per/atom 2 extra/dihedral/types 1 extra/bond/per/atom 2 extra/angle/per/atom 1 extra/dihedral/per/atom 1

region fix1 block INF INF INF INF INF -9.964 units box
region con_temp block INF INF INF INF -9.964 -5.891 units box
region free_layer block INF INF INF INF -5.891 0.5 units box

group fix1 region fix1
group con_temp region con_temp
group free_layer region free_layer

group Si type 1
group addatoms type 2 3

mass 1 28
mass 2 16
mass 3 1

pair_style reax/c lmp_control checkqeq yes
pair_coeff * * ffield16.reax Si O H

timestep 0.01

velocity all create 300 39849 rot yes dist gaussian

fix f1 fix1 setforce 0.0 0.0 0.0
fix nvt1 con_temp nvt temp 300 300 10
fix nvt2 addatoms nvt temp 300 300 10
fix 1 all qeq/reax 1 0.0 10.0 1.0e-6 reax/c

min_style cg
minimize 1.0e-4 1.0e-6 1000 10000

dump 1 all custom 10000 dump.xyz id type x y z
dump_modify 1 sort id

thermo 1000
thermo_style custom step temp pe ke etotal time

#run 10000

compute Si Si temp
compute add addatoms temp
compute all all temp

#compute_modify add dynamic/dof yes
#compute_modify Si dynamic/dof yes
#compute_modify all dynamic/dof yes
#fix_modify nvt2 temp add dynamic/dof yes energy yes

#thermo 1000
#thermo_style custom step pe ke etotal c_Si c_add c_all temp

molecule dimer SiO2.dimer

region slab block 2 35 2 35 38 38 units box

fix deposit1 addatoms deposit 10 0 10000 12345 region slab id next mol dimer near 2.0 vz -10 -10 units box
fix r1 all wall/reflect zhi EDGE

run 1100000

5

Could also be running out of memory and killed by Linux OOM killer with signal 9.