in.gk.2d
576c6315c7f1efficient_neuronet

in.gk.2d
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			# sample LAMMPS input script for viscosity of 2d LJ liquid
			# Green-Kubo method via fix ave/correlate

			# settings

			variable x equal 20
			variable y equal 20

			variable rho equal 0.6
			variable t equal 1.0
			variable rc equal 2.5

			variable p equal 400 # correlation length
			variable s equal 5 # sample interval
			variable d equal $p*$s # dump interval

			# problem setup

			units lj
			dimension 2
			atom_style atomic
			neigh_modify delay 0 every 1

			lattice sq2 ${rho}
			region simbox block 0 $x 0 $y -0.1 0.1
			create_box 1 simbox
			create_atoms 1 box

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

			mass * 1.0
			velocity all create $t 97287

			# equilibration run

			fix 1 all nve
			fix 2 all langevin $t $t 0.1 498094
			fix 3 all enforce2d

			thermo $d
			run 10000

			velocity all scale $t

			unfix 2

			# Green-Kubo viscosity calculation

			reset_timestep 0

			# Define distinct components of symmetric traceless stress tensor

			variable pxy equal pxy
			variable pxx equal pxx-press

			fix SS all ave/correlate $s $p $d &
			v_pxy v_pxx type auto file profile.gk.2d ave running

			# Diagonal components of SS are larger by factor 2-2/d,
			# which is 4/3 for d=3, but 1 for d=2.
			# See Daivis and Evans, J.Chem.Phys, 100, 541-547 (1994)

			variable scale equal 1.0/$tvol$s*dt
			variable diagfac equal 2-2/2
			variable vxy equal trap(f_SS[3])*${scale}
			variable vxx equal trap(f_SS[4])*${scale}/${diagfac}

			thermo_style custom step temp press pxy v_vxy v_vxx

			run 500000

			variable etaxy equal v_vxy
			variable etaxx equal v_vxx
			variable eta equal 0.5*(${etaxy}+${etaxx})
			print "running average viscosity: ${eta}"