in.neb.hop1
29e25bd1267elammm-master-deprecated

in.neb.hop1
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			# 2d NEB surface simulation, hop from surface to become adatom

			dimension 2
			boundary p s p

			atom_style atomic
			neighbor 0.3 bin
			neigh_modify delay 5
			atom_modify map array sort 0 0.0

			variable u uloop 20

			# create geometry with flat surface

			lattice hex 0.9
			region box block 0 20 0 10 -0.25 0.25
			create_box 3 box
			create_atoms 1 box

			mass * 1.0

			# LJ potentials

			pair_style lj/cut 2.5
			pair_coeff * * 1.0 1.0 2.5
			pair_modify shift yes

			# initial minimization to relax surface

			minimize 1.0e-6 1.0e-4 1000 10000
			reset_timestep 0

			# define groups

			region 1 block INF INF INF 1.25 INF INF
			group lower region 1
			group mobile subtract all lower
			set group lower type 2

			timestep 0.005

			# group of NEB atoms - either block or single atom ID 412

			region surround block 10 18 17 20 0 0 units box
			group nebatoms region surround
			#group nebatoms id 412
			set group nebatoms type 3
			group nonneb subtract all nebatoms

			fix 1 lower setforce 0.0 0.0 0.0
			fix 2 nebatoms neb 1.0
			fix 3 all enforce2d

			thermo 100

			dump 1 nebatoms atom 10 dump.neb.$u
			dump 2 nonneb atom 10 dump.nonneb.$u

			# run NEB for 2000 steps or to force tolerance

			min_style quickmin

			neb 0.0 0.1 1000 1000 100 final.hop1