msd.cyl.in
e3eb61765260lammm-master-deprecated

msd.cyl.in
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			dimension 3
			units lj
			boundary f f p

			read_data msd.cyl.data
			mass 1 1.0

			pair_style none
			atom_modify sort 0 1.0

			variable R equal 5
			fix step all nve/manifold/rattle 1e-10 100 cylinder $R
			fix temp all langevin 1.0 1.0 1.0 12321 gjf yes
			velocity all create 1.0 1283
			run 25000
			compute dx2 all msd

			variable D equal "1.0"
			variable t equal time
			variable my_msd equal "2v_D(v_t-125)+ 2v_Rv_R(1.0 - exp(-(v_t-125)v_D/(v_R*v_R)) )"
			variable msd equal c_dx2[4]

			dump traj all custom 100 msd.cyl.gz id type x y zu

			fix msd_out all print 250 "$t ${msd} ${my_msd}" file msd.cyl.dat screen no

			thermo_style custom time step pe ke etotal temp c_dx2[4] v_my_msd
			thermo 1000
			run 25000