#Parameters of simulation and atoms 
units metal 
dimension 3 
boundary p p p 
atom_style full
newton on off 

#Atom definition 
read_data graphene_1008atoms


#Creating Regions
region up block INF INF INF INF -5 5 units box
region down block INF INF INF INF -50 -40 units box

#Potentials
pair_style tersoff 
pair_coeff * * SiC.tersoff C 

neighbor 4.0 bin 
neigh_modify delay 0 every 1 check yes 
timestep 0.0005 
 
velocity all create 100.0 12345 mom yes rot yes dist gaussian units box 
 
# take some potential energy out of the system 

minimize 1.0e-8 1.0e-6 1000 10000 
reset_timestep 0 
 
fix thermostat all nvt temp 300.0 300.0 0.1 
 
compute alltemp all temp 


# Obtaining temperature

compute ke all ke/atom 
variable temp atom c_ke/(1.5*1.0)/8.617343*100000.0 

variable       temp atom  c_ke*1.60217e-17/(1.5*1.380654e-23)
fix temp_profile all ave/spatial 1 100000 100000 z -50 50 v_temp file temp.profile units box

fix temp_atom all ave/atom 1 100000 100000 v_temp 
compute up_temp all temp/region up 
compute down_temp all temp/region down 
variable delta_t equal c_up_temp-c_down_temp

fix delta_t all ave/time 100 5 1000 v_delta_t file delta_t.dat 

dump 1 all xyz 100000 dump.coord.* 
dump 2 all custom 100000 dump.vel.* id type mass vx vy vz fx fy fz f_temp_atom 
#Thermal conductivity calculations

fix nve all nve 
fix heat_swap all thermal/conductivity 10 z 10
fix e_exchange all ave/time 40 2500 100000 f_heat_swap file e_exchange.dat

variable thermal_conductivity equal f_heat_swap*1.60217e-19/(2*0.0005*100000*1.0e-12*50*51.77*f_delta_t*1.0e-10)*51.03

#2: To address heat flux in periodic boundary conditions
#0.0005 – Timestep
#100000 – Total number of steps in simulation
#1.0e-12: ps to second conversion
#50: Half the length of simulation box along z (i.e. heat flow direction)
#51.77: Total length of simulation box along y direction
#1.0e-10: Angstrom to metre conversion 
#51.03: Length of simulation box in x direction

fix thermal_conductivity all ave/time 100000 1 100000 v_thermal_conductivity file thermal_conductivity.dat 
thermo_style custom step atoms temp press pe ke etotal xlo xhi ylo yhi zlo zhi vol v_delta_t v_thermal_conductivity
run 9000000