# sample LAMMPS input script for thermal conductivity of liquid LJ
# thermostatting 2 regions via fix langevin

# 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        tlo equal 1.0
variable        thi equal 1.70

#variable       rho equal 0.85
#variable        t equal 0.7
#variable       rc equal 3.0
#variable        tlo equal 0.3
#variable        thi equal 1.0

# 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 langevin ${thi} ${thi} 1.0 59804 tally yes
fix             cold all langevin ${tlo} ${tlo} 1.0 287859 tally yes
fix_modify      hot temp Thot
fix_modify      cold temp Tcold

variable        tdiff equal c_Thot-c_Tcold
thermo_style    custom step temp c_Thot c_Tcold f_hot f_cold v_tdiff
thermo_modify   colname c_Thot Temp_hot colname c_Tcold Temp_cold &
                colname f_hot E_hot colname f_cold E_cold &
                colname v_tdiff dTemp_step
thermo          1000
run             10000

# thermal conductivity calculation
# reset langevin thermostats to zero energy accumulation

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

fix             hot all langevin ${thi} ${thi} 1.0 59804 tally yes
fix             cold all langevin ${tlo} ${tlo} 1.0 287859 tally yes
fix_modify      hot temp Thot
fix_modify      cold temp Tcold

fix             ave all ave/time 10 100 1000 v_tdiff ave running
thermo_style    custom step temp c_Thot c_Tcold f_hot f_cold v_tdiff f_ave
thermo_modify   colname c_Thot Temp_hot colname c_Tcold Temp_cold &
                colname f_hot E_hot colname f_cold E_cold &
                colname v_tdiff dTemp_step colname f_ave dTemp

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.langevin

variable start_time equal time
variable kappa equal (0.5*(abs(f_hot)+abs(f_cold))/(time-${start_time})/(lx*ly)/2.0)*(lz/2.0)/f_ave

run             20000
print           "Running average thermal conductivity: $(v_kappa:%.2f)"