Here is my script
units lj
dimension 3
boundary p p p
atom_style hybrid bond granular
lattice diamond 1
neighbor 0.3 bin
neigh_modify delay 5
region box cylinder x 0 0 7 0 20 side in units lattice
create_box 2 box
define groups
region 1 cylinder x 0 0 6.8 0.2 19.8 side out units lattice
region 2 cylinder x 0 0 6.0 0.0 20.0 side out units lattice
region 3 cylinder x 0 0 6.2 0.0 20.0 side in units lattice
region 4 cylinder x 0 0 6.0 0.0 20.0 side in units lattice
create_atoms 1 region 2
create_atoms 1 random 1000 12481 4
group box region box
group 1 region 1
group 2 region 2
group 3 region 3
group 4 region 4
group 5 intersect box 1
group 6 intersect 2 3
#group 8 for freeze
#group 10 for bond
#group 9 for membrane
#group 4 for flow
group 7 union 5 6
group 8 subtract 7 4
group 9 intersect box 2
group 10 subtract 9 8
#group 11 subtract all 9
LJ potentials
pair_style lj/cut 1.12246
pair_coeff * * 1.0 1.0 1.12246
pair_coeff 1 2 6.0 1.0 1.12246
#here is the problem, as I add “#” to ignore bond style and coeff command, it run normally.
bond_style harmonic
bond_coeff 1 30.0 1.0
set group 9 type 1
set group 4 type 2
mass 1 1.0
mass 2 1.0
fix 1 all nve
velocity 8 set 0.0 0.0 0.0
fix 2 8 freeze
Run
timestep 0.0001
thermo 10
thermo_modify lost ignore
run 1000