in.si-vacancy
0ddcd03c13d5lammm-devel

in.si-vacancy
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			# Parallel replica dynamics model for a single vacancy in bulk Si
			# events occur when a neighboring atom diffuses to the vacant site
			# run this on multiple partitions as
			# mpirun -np 4 lmp_g++ -partition 4x1 -in in.prd

			units metal

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

			# temperature

			variable t equal 1800.0

			# coordination number cutoff

			variable r equal 2.835

			# minimization parameters

			variable etol equal 1.0e-5
			variable ftol equal 1.0e-5
			variable maxiter equal 100
			variable maxeval equal 100
			variable dmax equal 1.0e-1

			# 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

			velocity all create $t 5287287 mom yes rot yes dist gaussian

			# make a vacancy

			group del id 300
			delete_atoms group del

			replicate 2 2 2

			pair_style sw
			pair_coeff * * Si.sw Si

			thermo 100

			fix 1 all nvt temp $t $t 0.1 tchain 1

			timestep 1.0e-3
			neighbor 1.0 bin
			neigh_modify every 1 delay 10 check yes

			# equilibrate

			run 1000