# Bead-spring polymer simulation

#log		log.nvt.2000
boundary	p s s 
atom_style 	bond
read_data	wall.data

neighbor	0.3 bin
neigh_modify	every 1 delay 1

bond_style	fene
bond_coeff	1 30.0 1.5 1.0 1.0

#special_bonds   0.0 1.0 1.0

# potential start-up in two stages

pair_style	hybrid lj/cut 2.5 soft 1.12246

# interactions

pair_coeff	1 2* lj/cut 1.0 1.0 2.5
pair_coeff	2* 2* lj/cut 1.0 1.0 0.0

# setting wall atoms as boundary 

group		boundary molecule 0
group		flow subtract all boundary

compute 	mobile flow temp
velocity	flow create 1.0 387093 loop geom
fix		1 all nvt 1.0 1.0 1.0
fix		2 boundary setforce 0.0 0.0 0.0

thermo		1000
timestep 	1.0e-6 
dump		1 all xyz 1000 relax.xyz
pair_coeff	1 1 soft 0.0 10.0 1.12246
run		20000
 
timestep 	1.0e-5 
pair_coeff	1 1 soft 10.0 20.0 1.12246
run		20000

timestep 	1.0e-4
pair_coeff	1 1 soft 20.0 30.0 1.12246
run		20000

timestep 	1.0e-3
pair_coeff	1 1 soft 30.0 40.0 1.12246
run		20000

timestep 	1.0e-2
pair_coeff	1 1 soft 40.0 50.0 1.12246
run		20000

# main run with LJ potentials
# interaction between polymer molecules in different regions

pair_style	lj/cut 1.12246
pair_modify	shift yes

pair_coeff	1 1 1.0 1.0 1.12246
pair_coeff	1 2* 1.0 1.0 1.12246
pair_coeff	2* 2* 1.0 1.0 0.0  

reset_timestep	0
dump		2 all custom 2001 atom_id.xyz tag
dump		3 all custom 2001 mol_id.xyz mol
dump		4 all custom 2001 x.xyz x
dump		5 all custom 2001 y.xyz y
dump		6 all custom 2001 z.xyz z
dump		7 all custom 2001 ix.xyz ix
dump		8 all custom 2001 iy.xyz iy
dump		9 all custom 2001 iz.xyz iz
dump		10 all custom 2001 atom_type.xyz type

run		2000