# 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

units metal
atom_style molecular
boundary f f f
pair_style lj/cut 14
bond_style harmonic
angle_style harmonic
dihedral_style opls
improper_style harmonic
read_data unbreakable.data extra/bond/per/atom 10 extra/special/per/atom 10
include parameters.inc

pair_style airebo 3.0 1 1
pair_coeff * * CH.airebo C
bond_style zero
bond_coeff 1 1.4
delete_bonds all angle 1
delete_bonds all dihedral 1
delete_bonds all improper 1 remove special

angle_style none
dihedral_style none
improper_style none

special_bonds lj/coul 1.0 1.0 1.0
group carbon_atoms type 1

variable xmax equal bound(carbon_atoms,xmax)-0.5
variable xmin equal bound(carbon_atoms,xmin)+0.5
region rtop block ${xmax} INF INF INF INF INF
region rbot block INF ${xmin} INF INF INF INF
region rmid block ${xmin} ${xmax} INF INF INF INF

group cnt_top region rtop
group cnt_bot region rbot
group cnt_mid region rmid

velocity cnt_mid create 300 48455 mom yes rot yes

fix mynve1 cnt_top nve
fix mynve2 cnt_bot nve
fix mynvt cnt_mid nvt temp 300 300 0.1

fix mysf1 cnt_bot setforce 0 0 0
fix mysf2 cnt_top setforce 0 0 0
velocity cnt_bot set 0 0 0
velocity cnt_top set 0 0 0

variable Lcnt equal xcm(cnt_top,x)-xcm(cnt_bot,x)
variable Fcnt equal f_mysf1[1]-f_mysf2[1]

dump viz all image 500 myimage-*.ppm element type size 1000 400 zoom 4 shiny 0.3  fsaa yes bond atom 0.8 view 0 90 box no 0.0 axes no 0.0 0.0
dump_modify viz pad 9 backcolor white element C adiam 1 0.85 bdiam 1 1.0

fix break all bond/break 1000 1 2.5
fix form all bond/create/angle 1000 1 1 2.0 1 aconstrain 90.0 180 

compute Tmid cnt_mid temp
thermo 100
thermo_style custom step temp etotal v_Lcnt v_Fcnt
thermo_modify temp Tmid line yaml

timestep 0.0005
run 10000

velocity cnt_top set 0.75 0 0
velocity cnt_bot set -0.75 0 0

run 30000