# sample LAMMPS input script for thermal conductivity of liquid LJ
# use fix ehex to add/subtract energy from 2 regions

# settings
units metal				# sets units to 'metal' units - Atomic units w/ ps timescale
dimension	3
boundary	p p p		# periodic BCs on x,y plane faces, z dimension fixed volume

atom_style	atomic		# default attribute style
neighbor	1.0	bin		# sets maximum neighbor search radius to cutoff+value, using bin-sort algorithm
neigh_modify delay 5 check yes 	# checks if neighbor list should be rebuilt every 5 steps

#---------- Create geometry using internal stuff ---------------------

lattice		diamond 3.567 orient x 1 0 0 orient y 0 1 0 orient z 0 0 1 #Lattice constant for carbon diamond orienting cube along crystal directions
region		box block 0 10 0 10 0 282 #changed from 0 50 0 50 0 50
create_box	1 box			# initialize box
create_atoms 	1 box 			# create atoms
#region		rPKA	sphere 5 4.9 9 .1 # changed from 25 24.5 49.5 .1 by dividing by 5
mass	1	12.0107		# type 1 = C

#--------------- FORCE FIELDS -------------------------
pair_style tersoff
pair_coeff * * SiC.tersoff C

# heat layers

region          hot block INF INF INF INF 0 1
region          cold block  INF INF INF INF 140 141
compute         Thot all temp/region hot
compute         Tcold all temp/region cold

# 1st equilibration run

fix             1 all nvt temp 500 500 1
thermo	        100
run             1000

velocity	all scale 500

unfix		1

# 2nd equilibration run

fix		1 all nve
fix             hot all ehex 1 10.0 region hot
fix             cold all ehex 1 -10.0 region cold

thermo_style    custom step temp c_Thot c_Tcold
thermo	        1000
run             110000 

# thermal conductivity calculation

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

compute         layers all chunk/atom bin/1d z lower 0.0035461 units reduced
fix		2 all ave/chunk 10 100 1000 layers v_temp file profile141F.ehex

variable        tdiff equal f_2[141][3]-f_2[1][3]
fix             ave all ave/time 1 1 1000 v_tdiff ave running start 13000
thermo_style    custom step temp c_Thot c_Tcold v_tdiff f_ave f_2[141][3] f_2[1][3]

run             70000