input.md.lammps

# 1) Initialization
units lj
dimension 3
atom_style atomic
pair_style lj/cut 2.5
boundary p p p

# 2) System definition
read_data minimized_coordinate.data
region region_cylinder_in cylinder z 0 0 10 INF INF side in
region region_cylinder_out cylinder z 0 0 10 INF INF side out
group group_type_1 type 1
group group_type_2 type 2
group group_region_in region region_cylinder_in
group group_region_out region region_cylinder_out
group group_type_1_in intersect group_type_1 group_region_in
group group_type_2_out intersect group_type_2 group_region_out
delete_atoms group group_type_1_in
delete_atoms group group_type_2_out

#3) Simulation Settings is read from the data file

# 4) Visualization
thermo 1000
dump mydmp all atom 1000 dump.md.lammpstrj


variable n_type1_in equal count(group_type_1,region_cylinder_in)
variable n_type2_in equal count(group_type_2,region_cylinder_in)
fix myat1 all ave/time 10 200 2000 v_n_type1_in &
    file output-population1vstime.dat
fix myat2 all ave/time 10 200 2000 v_n_type2_in &
    file output-population2vstime.dat

compute coor12 group_type_1 coord/atom cutoff 2.0 group group_type_2
compute sumcoor12 all reduce ave c_coor12
fix myat3 all ave/time 10 200 2000 &
    c_sumcoor12 file coordinationnumber12.dat

compute pcf11 all rdf 100 1 1
fix mypcf11 all ave/time 10 200 2000 c_pcf11[*] file pcf11.dat mode vector
compute pcf22 all rdf 100 2 2
fix mypcf22 all ave/time 10 200 2000 c_pcf22[*] file pcf22.dat mode vector
compute pcf12 all rdf 100 1 2
fix mypcf12 all ave/time 10 200 2000 c_pcf12[*] file pcf12.dat mode vector
compute pcf all rdf 100
fix mypcf all ave/time 10 200 2000 c_pcf[*] file pcf.dat mode vector

compute peatom all pe/atom
compute keatom all ke/atom

# 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
timestep 0.005



run 300000
write_data mixed.data

dump final_dump all custom 300000 final_dump.data c_keatom c_peatom