#---------------------NiCNT kappa----------------------------

units			metal
dimension		3
boundary		s s s
atom_style		atomic
newton		on
neigh_modify	delay 5

#------------------creating structure---------------------------------

read_data		5_Ni.data

#-------------------potentials-----------------------------------------

pair_style		hybrid airebo 3.0 eam/alloy morse 3.0
pair_coeff		* * airebo CH.airebo C NULL
pair_coeff		* * eam/alloy Ni99.eam.alloy NULL Ni
pair_coeff		1 2 morse 0.234 1.975 2.27 3.0

mass 			1 12.0111
mass 			2 58.6934

#-------------------------initial setting---------------------------------

variable 	T equal 300        	# temperature 10 Kelvin
variable 	dt equal 0.0005      	# timestep(0.5fs)
variable 	p equal 1        	# Nevery
variable 	s equal 50000            # Nrepeat
variable 	d equal $p*$s       	# Nfreq
variable 	Tlo equal 250		#cold region@250K
variable 	Thi equal 350		#hot region@350K
#variable 	tdiff1 equal c_Thot-c_Tcold
#variable 	tdiff2 equal c_TempHOT-c_TempCOLD

thermo_style 		custom step vol temp pe ke etotal
thermo_modify 		flush yes
timestep			${dt}
thermo			$d

#------------------equilibration & Nose-Hoover thermostat-----------------

compute			PE all pe/atom

dump			PEtotal all custom 20000 3WCNT.pe id type x y z c_PE

minimize 	1.0e-10 1.0e-10 10000 10000

velocity 	all create $T 5000 mom yes rot yes dist gaussian

variable 	grid equal 100
variable 	gridsize equal lx/${grid}

variable	f1lo equal xlo
variable	f1hi equal xlo+1.0*${gridsize}

variable	f2lo equal xhi-1.0*${gridsize}
variable	f2hi equal xhi

variable 	hlo equal xlo+2.0*${gridsize}
variable 	hhi equal xlo+3.0*${gridsize}

variable 	chi equal xhi-2.0*${gridsize}
variable 	clo equal xhi-3.0*${gridsize}

region	hot block ${hlo} ${hhi} INF INF INF INF units box
region	cold block ${clo} ${chi} INF INF INF INF units box	

region	F1 block ${f1lo} ${f1hi} INF INF INF INF units box	
region	F2 block ${f2lo} ${f2hi} INF INF INF INF units box

group			CNT type 1
group			METAL type 2

group		HOT region hot
group		COLD region cold

group		FE1 region F1
group		FE2 region F2

group		MODEL subtract all FE1 FE2
group		CNTmodel intersect MODEL CNT
group		METALmodel intersect MODEL METAL

fix			FIX1 FE1 setforce 0.0 0.0 0.0 region F1
fix			FIX2 FE2 setforce 0.0 0.0 0.0 region F2

#---creating heat bath separately----#

group 	HOTCNT intersect CNTmodel HOT
group		COLDCNT intersect CNTmodel COLD
group		HOTNICKEL intersect METALmodel HOT
group		COLDNICKEL intersect METALmodel COLD


fix		MUCAN MODEL nve
run		200000

fix		EQUIL MODEL langevin 300 300 0.05 1234567 zero yes

thermo_style	custom step vol temp pe ke etotal f_EQUIL

run		100000

unfix		EQUIL
unfix		MUCAN

thermo_style	custom step vol temp pe ke etotal

fix		MUCAN2 MODEL nve
run		50000
unfix		MUCAN2

dump_modify 	PEtotal every 50000
thermo	 	50000

#-------------------Temperature setting at either ends--------------------

fix 			NVEmodel MODEL nve

fix	KEin HOTCNT langevin ${Thi} ${Thi} 0.05 1234567 tally yes
fix	KEout COLDCNT langevin ${Tlo} ${Tlo} 0.05 1234567 tally yes

fix	KEinNi HOTNICKEL langevin ${Thi} ${Thi} 0.05 1234567 tally yes

fix	KEoutNi COLDNICKEL langevin ${Tlo} ${Tlo} 0.05 1234567 tally yes

#----------------------mttm--------------------------------------------------

variable 	C_e equal 21.82938e-6 #2.16117e-6
variable 	rho_e equal 0.18298 #8.49e-2
variable 	kep equal 0.0575155 #0.2503042
variable 	gmp equal 5.575921 #4.69781640
variable 	gms equal 0
variable 	v_0 equal 0
variable 	Nx equal 100
variable 	Ny equal 1
variable 	Nz equal 1

fix   		METALmttm METALmodel mttm 699489 ${C_e} ${rho_e} ${kep}  ${gmp} ${gms} ${v_0} ${Nx} ${Ny} ${Nz} inputx.txt 50000 Nimttmout.txt 1 1

compute		TempHOT HOTCNT temp
compute		TempCOLD COLDCNT temp

compute		TempHOTNi HOTNICKEL temp
compute 		TempColdNi COLDNICKEL temp

compute		KE all ke/atom
compute		KEHOT HOTCNT ke
compute		KECOLD COLDCNT ke

compute		KECNT CNTmodel ke
compute		KEMETAL METALmodel ke

variable	kB equal 8.6173324e-5      # Maxwell-Boltzmann constant in eV/K

variable	TEMP atom c_KE/(${kB}*1.5)

#fix	AVE1 CNT ave/time $p $s $d v_tdiff1 ave running
#fix	AVE2 CNT ave/time $p $s $d v_tdiff2 ave running

thermo_style	custom step temp f_KEin f_KEout f_KEinNi f_KEoutNi c_KEHOT c_KECOLD c_TempHOT c_TempCOLD ke pe etotal

compute		CC1 CNT chunk/atom bin/1d x lower 0.01 units reduced

compute		CC2 METAL chunk/atom bin/1d x lower 0.01 units reduced

fix		AVECHUNKCNT CNT ave/chunk $p $s $d CC1 v_TEMP file Temp_CNT.txt

fix		AVECHUNKNi METAL ave/chunk $p $s $d CC2 v_TEMP file Temp_Ni.txt

run             200