in.msd.2d
c1aebdd391f3lammm-master-deprecated

in.msd.2d
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			# sample LAMMPS input script for diffusion of 2d LJ liquid
			# mean-squared displacement via compute msd

			# settings

			variable x equal 40
			variable y equal 40

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

			# 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

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

			# equilibration run

			thermo 1000
			run 5000

			unfix 2

			# data gathering run

			reset_timestep 0

			# factor of 4 in 2 variables is for 2d

			compute msd all msd com yes
			variable twopoint equal c_msd[4]/4/(step*dt+1.0e-6)
			fix 9 all vector 10 c_msd[4]
			variable fitslope equal slope(f_9)/4/(10*dt)

			thermo_style custom step temp c_msd[4] v_twopoint v_fitslope

			# only need to run for 10K steps to make a good 100-frame movie

			#dump 1 all custom 1 tmp.dump id type vx vy vz

			#dump 2 all image 100 image.*.jpg type type zoom 1.6 adiam 1.2

			thermo 1000
			run 100000