input_03 for lammps

input_03.lammps

# 1) Initialization
units lj
dimension 2
atom_style atomic
pair_style lj/cut 2.5
boundary p p p

# 2) System definition
read_data minimized_coordinate.data

region mycylin cylinder z 0 0 15 INF INF side in
region mycylou cylinder z 0 0 15 INF INF side out
group mytype1 type 1
group mytype2 type 2
group incyl region mycylin
group oucyl region mycylou
group type1in intersect mytype1 incyl
group type2ou intersect mytype2 oucyl
delete_atoms group type1in
delete_atoms group type2ou

# 3) Simulation settings
mass 1 1
mass 2 1
pair_coeff 1 1 1.0 1.0
pair_coeff 2 2 0.5 3.0
neigh_modify every 1 delay 5 check yes
group type1 type 1
group type2 type 2

# 4) Visualization
thermo 50000
dump mydmp all atom 5000 dump.RUN.lammpstrj

variable Ntype1in equal count(mytype1,mycylin)
variable Ntype1ou equal count(mytype1,mycylou)
variable Ntype2in equal count(mytype2,mycylin)
variable Ntype2ou equal count(mytype2,mycylou)
fix myat1 all ave/time 1000 10 10000 v_Ntype1in v_Ntype1ou file population1vstime.dat
fix myat2 all ave/time 1000 10 10000 v_Ntype2in v_Ntype2ou file population2vstime.dat
compute coor12 type1 coord/atom cutoff 2.0 group type2
compute sumcoor12 all reduce ave c_coor12
fix myat3 all ave/time 1000 10 10000 c_sumcoor12 file coordinationnumber12.dat

# 5) Run
velocity all create 1.0 4928459 mom yes rot yes dist gaussian
fix mynve all nve
fix mylgv all langevin 1.0 1.0 0.1 1530917 zero yes
fix myefn all enforce2d
timestep 0.005
run 3000000
write_data data.mixed.lammps