in.neb.hop2
b956107fc6f1lammm-master

in.neb.hop2
View Options

			# 2d NEB surface simulation, hop of adatom on surface

			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 adatom

			lattice hex 0.9
			region box block 0 20 0 11 -0.25 0.25
			region box1 block 0 20 0 10 -0.25 0.25
			create_box 3 box
			create_atoms 1 region box1
			create_atoms 1 single 11.5 10.5 0

			mass * 1.0

			# LJ potentials

			pair_style lj/cut 2.5
			pair_coeff * * 1.0 1.0 2.5

			# initial minimization to relax surface

			minimize 1.0e-6 0.001 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 421

			region surround block 10 18 17 21 0 0 units box
			group one region surround
			#group one id 421
			set group one type 3

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

			thermo 10

			dump 1 all atom 10 tmp.dump.$u
			dump_modify 1 scale no

			# run NEB for 2000 steps or to force tolerance

			min_style fire

			#neb 0.0 1000 1000 100 final.hop2
			neb 0.01 1000 1000 100 final.hop2