in.heat
c40fdd35b65alammm-master-deprecated

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

			# settings

			variable x equal 10
			variable y equal 10
			variable z equal 20

			variable rho equal 0.6
			variable t equal 1.35
			variable rc equal 2.5

			#variable rho equal 0.85
			#variable t equal 0.7
			#variable rc equal 3.0

			# setup problem

			units lj
			atom_style atomic

			lattice fcc ${rho}
			region box block 0 $x 0 $y 0 $z
			create_box 1 box
			create_atoms 1 box
			mass 1 1.0

			velocity all create $t 87287

			pair_style lj/cut ${rc}
			pair_coeff 1 1 1.0 1.0

			neighbor 0.3 bin
			neigh_modify delay 0 every 1

			# heat layers

			region hot block INF INF INF INF 0 1
			region cold block INF INF INF INF 10 11
			compute Thot all temp/region hot
			compute Tcold all temp/region cold

			# 1st equilibration run

			fix 1 all nvt temp $t $t 0.5
			thermo 100
			run 1000

			velocity all scale $t

			unfix 1

			# 2nd equilibration run

			fix 1 all nve
			fix hot all heat 1 100.0 region hot
			fix cold all heat 1 -100.0 region cold

			thermo_style custom step temp c_Thot c_Tcold
			thermo 1000
			run 10000

			# thermal conductivity calculation

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

			compute layers all chunk/atom bin/1d z lower 0.05 units reduced
			fix 2 all ave/chunk 10 100 1000 layers v_temp file profile.heat

			variable tdiff equal f_2[11][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

			run 20000