Hi all,
I’m new to lammps and I’m trying to see the trajectory of a pfoa molecular on a single layer of polymer. And I guess after one step, the logfile shows: srun: error: bc11u27n3: task 11: Segmentation fault.
Here is my input file:
REAX input file
…
units real
atom_style charge
boundary p p p
read_data data.in
pair_style reax/c NULL
pair_coeff * * ffield C H N S F O
#Neighbor list
neighbor 2.5 bin
neigh_modify delay 0 every 5 check no
#Regions and Groups
#group COF id 1:31:1
region s block 0 25.9808 0 20 0 3 units box
group freeze_bottom region s
group mobile subtract all freeze_bottom
#Emin
Variable for minimization
variable etol equal 1.0e-10
variable ftol equal 1.0e-10
variable maxiter equal 50000
variable maxeval equal 10000
variable dmax equal 1.0e-1
Energy Minimization and equilibration
fix 1 all qeq/reax 1 0.0 10.0 1.0e-6 reax/c
fix freeze_bottom2 freeze_bottom setforce 0.0 0.0 0.0
minimize {etol} {ftol} {maxiter} {maxeval}
min_style cg
dump 1 all atom 1 dump.reax1
dump_modify 1 scale no
run 0
undump 1
#Initial temp
velocity mobile create 300 12345
timestep 0.25
reset_timestep 0
restart 1000 refile1 refile2
#NVT MD Nose-Hoover thermostat
fix 1 all qeq/reax 1 0.0 10.0 1.0e-6 reax/c
fix 5 all reax/c/bonds 10000 bonds.out
fix 6 all reax/c/species 1 10 10000 mol.out position 10000 mol.pos
dump 1 all custom 1000 dump.reax id type x y z vx vy vz
dump other all custom 1000 dump.txt id x y z
dump d_trajectory all custom 1000 trajectory.dat id type x y z vx vy vz
#variables
variable stp equal “step”
variable tt equal “time”
variable Temp equal “temp”
thermo 1000
fix 2 all nvt temp 300.0 300.0 100.0
thermo_style custom step temp time pe etotal press
run 400000
write_restart refile.*
I’m also trying to fix the bottom of the polymer layer. I really appreciate if anyone can help with the problem!