# LAMMPS Input File

# Licensed under CC BY 4.0

# A Set of Tutorials for the LAMMPS Simulation Package (LiveCoMS, 2025)

# By Simon Gravelle, Cecilia M. S. Alvares, Jacob R. Gissinger, and Axel Kohlmeyer

# Please cite doi.org/10.33011/livecoms.6.1.3037

# Find more on GitHub: https://github.com/lammpstutorials

variable sigma equal 3.405

variable epsilon equal 0.238

variable U0 equal 10*${epsilon}

variable dlt equal 1.0

variable x0 equal 10.0

variable k equal 0.5

units real

atom_style atomic

pair_style lj/cut $(2^(1/6)*v_sigma)

pair_modify shift yes

boundary p p p

region myreg block -50 50 -15 15 -50 50

create_box 2 myreg

create_atoms 2 single 0 0 0

create_atoms 1 random 199 34134 myreg overlap 3 maxtry 50

mass * 39.948

pair_coeff * * ${epsilon} ${sigma}

group topull type 2

variable U atom ${U0}*atan((x+${x0})/${dlt})-${U0}*atan((x-${x0})/${dlt})

variable F atom ${U0}/((x-${x0})^2/${dlt}^2+1)/${dlt}-${U0}/((x+${x0})^2/${dlt}^2+1)/${dlt}

fix myadf all addforce v_F 0.0 0.0 energy v_U

fix mynve all nve

fix mylgv all langevin 119.8 119.8 500 30917

thermo 5000

dump viz all image 5000 myimage-*.ppm type type &

shiny 0.1 box yes 0.01 view 180 90 zoom 6 &

size 1600 500 fsaa yes

dump_modify viz backcolor white acolor 1 cyan &

acolor 2 red adiam 1 3 adiam 2 3 boxcolor black

timestep 2.0

run 50000

variable a loop 15

label loop

variable xdes equal 4*${a}-32

variable xave equal xcm(topull,x)

fix mytth topull spring tether ${k} ${xdes} 0 0 0

run 20000

fix myat1 all ave/time 10 10 100 v_xave v_xdes file umbrella-sampling.${a}.dat

run 200000

unfix myat1

next a

jump SELF loop