# sample LAMMPS input script for thermal conductivity of liquid LJ
# use fix $method to add/subtract energy from 2 regions

# settings

variable	x equal 10
variable	y equal 10
variable	z equal 20

variable	rho equal 0.6
variable        t equal 1.35
variable	rc equal 2.5

#variable	rho equal 0.85
#variable        t equal 0.7
#variable	rc equal 3.0

# setup problem

units		lj
atom_style	atomic

lattice		fcc ${rho}
region		box block 0 $x 0 $y 0 $z
create_box	1 box
create_atoms	1 box
mass		1 1.0

velocity	all create $t 87287

pair_style	lj/cut ${rc}
pair_coeff	1 1 1.0 1.0

neighbor	0.3 bin
neigh_modify	delay 0 every 1

# heat layers

region          hot block INF INF INF INF 0 1
region          cold block  INF INF INF INF 10 11
compute         Thot all temp/region hot
compute         Tcold all temp/region cold

# 1st equilibration run

fix             1 all nvt temp $t $t 0.5
thermo	        100
run             1000

velocity	all scale $t

unfix		1

# 2nd equilibration run

fix		1 all nve
fix             hot all $method 1 100.0 region hot
fix             cold all $method 1 -100.0 region cold

thermo_style    custom step temp c_Thot c_Tcold
thermo	        1000
run             10000 

# thermal conductivity calculation

compute		ke all ke/atom
variable	temp atom c_ke/1.5

compute         layers all chunk/atom bin/1d z lower 0.05 units reduced
fix		2 all ave/chunk 10 100 1000 layers v_temp file profile.$method

variable        tdiff equal f_2[11][3]-f_2[1][3]
fix             ave all ave/time 1 1 1000 v_tdiff ave running start 13000
thermo_style    custom step temp c_Thot c_Tcold v_tdiff f_ave

run             20000
