The code which I used is given below:
units real
dimension 3
boundary p p m
atom_style atomic
neighbor 2.0 bin
neigh_modify delay 5
create geometry
lattice diamond 3.57
region diamondBox block 0 40 0 40 0 32 units box
create_box 5 diamondBox
create_atoms 1 region diamondBox
group matrix region diamondBox
mass * 12.0107
LJ potentials
pair_style lj/cut 2.5
pair_coeff * * 1.0 1.0 2.5
#region
region 1 cylinder z 20 20 13.1 0 32 units box
delete_atoms region 1 compress no
read_data dat.ninefift add merge shift 20 20 2
group CNT region 1
region 2 block 0 40 0 40 2 16
group lower region 2
region 3 block 0 40 0 40 16 30
group upper region 3
region 4 block 0 40 0 40 0 2
group lowerb region 4
region 5 block 0 40 0 40 30 32
group upperb region 5
group lower subtract lower CNT
group upper subtract upper CNT
group lowerb subtract lowerb CNT
group upperb subtract upperb CNT
group boundary union lowerb upperb
group mobile subtract all boundary
set group CNT type 1
set group lower type 2
set group upper type 3
set group lowerb type 4
set group upperb type 5
velocity upper set 0.0 0.0 0.3
velocity mobile ramp vz 0.0 0.3 z 27 28 sum yes
fix 1 all nvt temp 0.05 0.05 500
run 200
fix 2 boundary setforce 0.0 0.0 NULL
run 500
timestep 0.003
thermo 200
neigh_modify exclude type 2 3
dump 1 all atom 500 dump.end
dump 2 all custom 100 dump.end_carb id type x y z fx fy fz
run 5000
print “WORKING”
Please someone point out the mistakes in it.
Thanks