# Sample LAMMPS input script for thermal conductivity 
units       real
variable    T equal 300
variable    V equal vol
variable    dt equal 1.0
variable    p equal  5000  # correlation length (5ps)
variable    s equal  1  # sample interval (1fs)
variable    d equal $p*$s   # dump interval

log thermal_conductivity_s${s}cl${p}.log


# convert from LAMMPS real units to SI

variable    kB equal 1.3806504e-23    # [J/K] Boltzmann
variable    kCal2J equal 4186.0/6.02214e23
variable    A2m equal 1.0e-10
variable    fs2s equal 1.0e-15
variable    convert equal ${kCal2J}*${kCal2J}/${fs2s}/${A2m}

read_restart postxlink_equilibrated.restart
kspace_style pppm/cg 1.0e-4
neighbor        2.0 bin
neigh_modify    delay 0 every 1 check yes

timestep 1.0
thermo $d

# equilibration and thermalization

velocity     all create $T ${seed} mom yes rot yes dist gaussian
fix          NVT all nvt temp $T $T 10 drag 0.2
run          50000 #50ps

# thermal conductivity calculation, switch to NVE if desired

unfix       NVT
fix         NVE all nve

reset_timestep 0
compute      myKE all ke/atom
compute      myPE all pe/atom
compute      myStress all stress/atom NULL virial
compute      flux all heat/flux myKE myPE myStress
variable     Jx equal c_flux[1]/vol
variable     Jy equal c_flux[2]/vol
variable     Jz equal c_flux[3]/vol
variable     temperature equal temp
variable     volume equal vol
fix          extra all print 1 "${temperature} ${volume} ${Jx} ${Jy} ${Jz}" file heatflux.txt title "Temp Vol J[1] J[2] J[3]" screen 0
fix          JJ all ave/correlate $s $p $d &
             c_flux[1] c_flux[2] c_flux[3] type auto file J0Jt_s${s}cl${p}.dat ave running
variable     scale equal ${convert}/${kB}/$T/$T/$V*$s*${dt}
variable     k11 equal trap(f_JJ[3])*${scale}
variable     k22 equal trap(f_JJ[4])*${scale}
variable     k33 equal trap(f_JJ[5])*${scale}
thermo_style custom step temp v_Jx v_Jy v_Jz v_k11 v_k22 v_k33
run          1000000 #(1ns)
variable     k equal (v_k11+v_k22+v_k33)/3.0
variable     ndens equal count(all)/vol
print        "average conductivity: $k[W/mK] @ $T K, ${ndens} /A\^3"

unfix NVE