in.neb.sivac
42ff3a7abaffefficient_neuronet

in.neb.sivac
View Options

			# NEB simulation of vacancy hopping in silicon crystal

			units metal

			atom_style atomic
			atom_modify map array
			boundary p p p
			atom_modify sort 0 0.0

			# coordination number cutoff

			variable r equal 2.835

			# diamond unit cell

			variable a equal 5.431
			lattice custom $a &
			a1 1.0 0.0 0.0 &
			a2 0.0 1.0 0.0 &
			a3 0.0 0.0 1.0 &
			basis 0.0 0.0 0.0 &
			basis 0.0 0.5 0.5 &
			basis 0.5 0.0 0.5 &
			basis 0.5 0.5 0.0 &
			basis 0.25 0.25 0.25 &
			basis 0.25 0.75 0.75 &
			basis 0.75 0.25 0.75 &
			basis 0.75 0.75 0.25

			region myreg block 0 4 &
			0 4 &
			0 4
			create_box 1 myreg
			create_atoms 1 region myreg

			mass 1 28.06

			group Si type 1

			# make a vacancy

			group del id 300
			delete_atoms group del
			group vacneigh id 174 175 301 304 306 331 337

			# choose potential

			pair_style sw
			pair_coeff * * Si.sw Si

			# set up neb run

			variable u uloop 20

			# only output atoms near vacancy

			dump events vacneigh custom 1000 dump.neb.sivac.$u id type x y z

			# initial minimization to relax vacancy

			displace_atoms all random 0.1 0.1 0.1 123456
			minimize 1.0e-6 1.0e-4 1000 10000

			reset_timestep 0

			fix 1 all neb 1.0

			thermo 100

			# run NEB for 2000 steps or to force tolerance

			timestep 0.01
			min_style quickmin

			neb 0.0 0.01 50 100 10 final final.sivac