input.min.lammps

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

# 2) System definition
region simulation_box block -20 20 -20 20 -20 20
#Create a region named simulation_box
create_box 2 simulation_box
#Create a simulation box based on the region simulation_box with 2 types of atoms
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
#The side in and side out keywords are used to define regions that are respectively inside and outside of the cylinder of radius 10.
create_atoms 1 random 1000 341341 region_cylinder_out
#Create 1000 atoms of type 1 randomly within region_cylinder_out
create_atoms 2 random 150 127569 region_cylinder_in

# 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

# 4) Visualization
thermo 10
thermo_style custom step temp pe ke etotal press
dump mydmp all atom 10 dump.min.lammpstrj

# 5) Run
minimize 1.0e-4 1.0e-6 1000 10000
write_data minimized_coordinate.data
#used to print the final state of the simulation in a file named minimized_coordinate.data. Note that the write_data command is placed
#after the minimize command. This .data file will be used later to restart the simulation from the final state of the energy minimization
#step.