# ------------- initialisation ---------------- 

atom_style  full
units   real
dimension 3
boundary p p p

# ------------- variables ---------------- 
variable T equal 300
variable Ctype equal  	 	1
variable Htype equal            2
variable seed equal 		1
variable pressure equal 		0.0001
variable 1atm equal 		-0.000033

# ------------- potential types ----------------
pair_style airebo 2.5 1 1
pair_modify tail yes
bond_style harmonic
angle_style harmonic
dihedral_style none

# ------------- Data ----------------

read_data dataMem.data

variable natoms equal "count(all)"

# ------------- Groups and regions ----------------

group carbon    type ${Ctype}
variable ymax equal bound(carbon,ymax)-4.5
variable ymin equal bound(carbon,ymin)+4.5
region rtop block  INF INF ${ymax} INF INF INF
region rbot block  INF INF INF ${ymin} INF INF
region rmid block  INF INF ${ymin} ${ymax} INF INF

group gtop region rtop
group gbot region rbot
group gmid region rmid

# ------------- Coefficients ---------------- 
pair_coeff * * CH.airebo_real C H
bond_coeff * 0.0 0.0 
angle_coeff * 0.0 0.0 
# ------------- neighboring ---------------- 

neighbor        4.0 bin
neigh_modify	every 1 delay 0 check yes

velocity gmid create ${T} 48455 mom yes rot yes
fix mynve all nve
compute Tmid gmid temp
fix myber gmid temp/berendsen ${T} ${T} 0.1
fix_modify myber temp Tmid

# ------------- Minimization ----------------     

fix relax all box/relax x 0.0 y 0.0
minimize 1.0e-4 1.0e-6 100 1000
unfix relax

# ------------- Mechanical test ----------------

fix mysf1 gtop setforce 0 NULL 0
fix mysf2 gbot setforce 0 NULL 0
velocity gtop set 0 NULL 0
velocity gbot set 0 NULL 0


variable pos equal xcm(gtop,y)
fix at1 all ave/time 10 100 1000 v_pos file cnt_deflection.dat
fix at2 all ave/time 10 100 1000 f_mysf1[1] f_mysf2[1] file force.dat
dump mydmp all atom 1000 dump.lammpstrj

thermo 100
thermo_modify temp Tmid
# Run
timestep 0.0005
run 5000


variable var loop 50
label loop

displace_atoms gtop move 0 0.1 0
displace_atoms gbot move 0 -0.1 0
run 1000
next var
jump input1.in loop