# 2-d LJ flow simulation

dimension	3
boundary	p s p

atom_style	atomic
neighbor	0.3 bin
neigh_modify	delay 5

# create geometry

lattice		fcc 0.81
region		box block 0 20 0 10 0 20 


atom_modify map array # !!!!!!!!!!!!!!!!
create_box	2 box

region		1 block INF INF INF  1.00 INF INF	# Define region for lower boundary
region		2 block INF INF 8.7 INF INF INF		# Define region for upper boundary
region		3 block INF INF 1.1 8.6 INF INF		# The region between the boundaries



mass		1 1.0 # Fluid
mass		2 2.0 # walls


# Create atoms

create_atoms	1 region 3

lattice 	fcc 4.2	# Use denser lattice for boundaries and nanoparticle

create_atoms	2 region 1	# Create attoms of lower boundary
create_atoms	2 region 2	# Create atoms of upper boundary


# Define groups

group		lower region 1				# Define group "lower" for lower boundary
group 		upper region 2				# Define group "upper" for upper boundary
group 		flow type 1



# LJ potentials

pair_style	hybrid lj/cut 2.2
pair_coeff	1 1 lj/cut 1.0 1.0  2.2
#pair_coeff	1 1 lj/cut 0.317 0.65 2.2
pair_coeff	1 2 lj/cut 1.0 1.0  2.2
pair_coeff	2 2 none



# Initial velocities
compute	     mobile flow temp		# Compute the temperature of the flow
compute	     compute_lower_temp lower temp			# Compute the temperature of the lower wall
compute	     compute_upper_temp upper temp			# Compute the temperature of the upper wall


velocity     flow create l.0 482748 temp mobile
velocity     lower create 1.0 482748 temp compute_lower_temp 	# Set the initial velocity of the lower wall
velocity     upper create 2.0 482748 temp compute_upper_temp	# Set the initial velocity of the upper wall

fix 	     10 lower spring/self 200.0
fix 	     11 upper spring/self 200.0



fix	     4 lower temp/rescale 1 1.0 1.1 0.02 1.0	# Re-adjust the temperature of the lower wall every time-step
fix	     3 upper temp/rescale 1 1.9 2.0 0.02 1.0	# Re-adjust the temperature of the upper wall every time-step
#fix	     6 flow temp/rescale 1 1.0 2.0 0.02 1.0	# Re-adjust the temperature of the fluid  every time-step



compute   ke flow ke/atom		# Compute the kinetic energy of the atoms of the fluid
variable  temp_profile atom c_ke/1.5	# Create a variable

fix           c9n  flow ave/spatial 1  200000 200000  y lower   0.025 density/number  vx v_temp_profile units reduced file temp_profile.dat


fix	5 all nve	# Adjust positions and velocities of all atoms every time-step

# Run

timestep	0.001
thermo		500
thermo_modify	temp mobile
dump		1 all atom 500 dump2.lammpstrj



run		1200000