read_restart    Si_500K.STA.76000000

variable T equal 500
variable V equal vol

variable    dt equal 0.001

variable p equal 100 # correlation length
variable s equal 50 # sample interval
variable d equal $p*$s # dump interval

#convert from LAMMPS real units to SI

variable kB equal 1.3806504e-23 # [J/K] Boltzmann
variable eV2J equal 1.6e-19
variable A2m equal 1.0e-10
variable ps2s equal 1.0e-12
variable convert equal ${eV2J}*${eV2J}/${ps2s}/${A2m}

# setup problem


lattice         diamond 5.43 orient x 1 0 0 orient y 0 1 0 orient z 0 0 1 


region box block 0 6 0 6 0 6

mass 1 28.0855

pair_style sw
pair_coeff * * Si.sw Si

timestep     ${dt}



thermo $d

# equilibration and thermalization

compute		perpe all pe/atom
compute		perke all ke/atom

# 

fix nvt1 all nvt temp 500 500  0.01 

run  10000

unfix nvt1

fix         NVE all nve


reset_timestep 0 
compute      myKE all ke/atom
compute      myPE all pe/atom
compute      myStress all stress/atom 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

fix          JJ all ave/correlate $s $p $d &
             c_flux[1] c_flux[2] c_flux[3] type auto file J0Jt.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          2000000

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"