# ------------------------------------------
# LAMMPS script created by Kasra Momeni
# The goal to run the MD simulations of 
# MoS2 on Al2O3
# ------------------------------------------
dimension  3
boundary   p p p
units      metal
atom_style atomic

#---------------Atom Defination--------------------------

read_data Al2O3.lmp extra/atom/types 2
read_data MoS2.lmp add append offset 2 0 0 0 0 shift 0.0 0.0 10.0


#--------------Forcefield setup--------------------------

pair_style hybrid/overlay eam/alloy sw lj/cut 8.5 lj/cut 8.5 lj/cut 8.5 lj/cut 8.5
#pair_style hybrid/overlay eam/alloy sw
pair_coeff * * eam/alloy AlO.eam.alloy Al O NULL NULL
pair_coeff * * sw mos2.sw NULL NULL Mo S
pair_coeff 1 3 lj/cut 1 .00058595 2.75 8.5  
pair_coeff 1 4 lj/cut 2 0.0202033 3.268 8.5 
pair_coeff 2 3 lj/cut 3 0.07502 2.858 8.5 
pair_coeff 2 4 lj/cut 4 0.020 2.065 8.5 

mass 1 27.94 	# Al
mass 2 15.99 	# O
mass 3 95.94 	# Mo
mass 4 32.065	# S

#--------------Group setup--------------------------
group substrate type 1 2
group layer type 3 4

#--------------variable--------------------------


variable V equal 1.0
variable z equal vdisplace(0.0,$V)
variable ecoh equal "etotal"
variable evw equal "evdwl"

#---------------Energy Equilibriation--------------------------

neighbor     0.3 bin
neigh_modify delay 10
thermo 1
thermo_style custom  step temp pe etotal evdwl press vol
velocity all create 0.01 12824

fix 7 all nve
fix 8 all temp/rescale 10 0.01 0.01 0.02 1
#dump DUMP1 all atom 1 dump_Al2O3.lammpstrj

run 1000

unfix 7
unfix 8

#-----------------Pressure Equilibriation-----------------------
reset_timestep 0
fix 3 all npt temp 0.01 0.01 10.0 aniso 0.0 0.0 10 drag 0.3
run 1000
unfix 3

#-----------------Moving the Boundary-----------------------
#fix 1 layer deform 1 x final 20.29 75.94 y final -2.25 43.177 units box
#reset_timestep 0

fix 4 layer move variable NULL NULL v_z NULL NULL v_V
reset_timestep	0
dump	2 all atom 1 dump.AlNiIndent1.lammpstrj
run		1000
#reset_timestep	0

dump DUMP1 all atom 1 dump_Al2O3.lammpstrj
#run 1000

print "All done!"