# sample LAMMPS input script for thermal conductivity of liquid LJ
# Muller-Plathe method via fix thermal_conductivity 

# 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

# 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

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

fix		1 all nve
fix		2 all ave/spatial 10 100 1000 z lower 0.05 v_temp &
		  file profile.mp units reduced
fix		3 all thermal/conductivity 10 z 20

variable        tdiff equal f_2[11][3]-f_2[1][3]
thermo_style	custom step temp epair etotal f_3 v_tdiff

thermo		1000
run		20000

# thermal conductivity calculation
# reset fix thermal/conductivity to zero energy accumulation

fix		3 all thermal/conductivity 10 z 20

fix             ave all ave/time 1 1 1000 v_tdiff ave running
thermo_style	custom step temp epair etotal f_3 v_tdiff f_ave

run		20000
