input.lammps

# This LAMMPS input script simulates neutral particles reversibly adsorbing at the surface of a cylindrical nanopore.
# Tested with the 30Jul2021 version of LAMMPS
# Written by Simon Gravelle (https://simongravelle.github.io/)
# Find more scripts here: https://github.com/simongravelle/lammps-input-files
# LAMMPS tutorials for beginners: https://lammpstutorials.github.io/

# basic parameters
units real
newton on off
dimension 3
boundary p p p
atom_style full
pair_style lj/cut 3.367386145
pair_modify shift yes

# read data, define region, import group
read_data data.lammps
region acces cylinder z 0 0 20.0535228296 INF INF
include group.lammps
include parm.lammps

# dynamics : nve + langevin = nvt
fix 1 ions nve 
fix 2 ions langevin 300.0 300.0 23.0 33414 zero yes

# bond file for tapping
include bond.lammps

# output properties
thermo 10000
compute Tion ions temp 
thermo_modify temp Tion
dump mydmp all atom 10000 dump.lammpstrj 

# wall to prevent particle to leave cylinder
fix mur ions wall/region acces lj93 10.0 1.0 1.0

# first step small timestep
timestep 0.1
run 10000

# second equilibration step
timestep 2.0
run 100000
undump mydmp
reset_timestep 0

# save adsorbed status of atoms
fix myavt all ave/time 1000 1 1000 v_Ntot file AdsorbedParticles.dat

# final run
run 1000000