#------------------------------------------------------------
#	Prepared by Manish
#
#	Model : Silica -682 Atoms
#	        Water  -900 atoms
#			Epoxy  -43 Atoms
#-------------------------Initialization---------------------
processors			1 1 1
units				real
atom_style			full
boundary			p p p  

#-----------------Force Fields and interactions--------------
bond_style			harmonic
angle_style			harmonic
dihedral_style		harmonic
improper_style		cvff
#kspace_style 		pppm/cg 1.0e-5 1.0e-6
#pair_style			lj/cut/coul/long 10.0 8.0
pair_style			lj/cut/coul/cut 10.0 8.0
#special_bonds 		lj/coul 1.0 1.0 1.0 angle no dihedral no

#-------------Atom definition--Input Geometry File-----------
read_data			WetMod.data
pair_modify			mix geometric

#-----------------------Neighbor Setting---------------------
neighbor			2.0 bin #default value for real units
#neigh_modify		delay 5
neigh_modify		delay 1
timestep			1.0
fix					e0 all nve/limit 0.0005

#----------Silica Epoxy Group/ Boundary Conditions-----------
region				1 block	-2.0 40.0 -2.0 50.0 -1.0 25.0 units box
group				hold_substrate region 1
group				Epoxy id <> 683 725
group				water id > 725
group				substrate subtract all Epoxy water
dump 				positions all atom 100 filename.lammpstrj

#------------------Step 1: Optimization----------------------
thermo_style		custom step temp fmax etotal epair press vol
thermo				100
min_style			cg
minimize			0.0 1.0e-8 1000 100000
min_modify			dmax 0.2
velocity			all create 300.00 375689
velocity			hold_substrate set 0.0 0.0 0.0 units box
fix					bc1 hold_substrate setforce 0.0 0.0 0.0
run					500
unfix				e0
fix					e1 all nve
fix					tempcontrol all temp/berendsen 300.0 300.0 100.0
run					500
minimize			0.0 1.0e-8 1000 100000
run					500
minimize			0.0 1.0e-8 1000 100000
run					500
minimize			0.0 1.0e-8 1000 100000
run					500

#------------------------------------------------------------------------
#			END OF BASICSET-UP
#------------------------------------------------------------------------
reset_timestep		0
group 				vis subtract all water
group 				carbon id 706
unfix				bc1
fix					bc2 substrate setforce 0.0 0.0 0.0
#fix 				force Epoxy spring/self 10 
fix                 pull carbon smd cvel 20.0 -0.001 tether 0.0 0.0 25.0 0.0
dump 				positions2 all atom 100 filename2.lammpstrj
#dump 				d1 vis movie 10 movie1.m4v type type zoom 2 size 1280 720
#dump 				d2 Epoxy movie 10 movie2.m4v type type zoom 2 size 1280 720
#dump 				d3 all movie 10 movie3.m4v type type zoom 2 size 1280 720
thermo_style		custom step temp fmax etotal epair press vol
thermo				100
run                	2000
print 				"All done!"