1# NEB simulation of vacancy hopping in silicon crystal 2 3units metal 4 5atom_style atomic 6atom_modify map array 7boundary p p p 8atom_modify sort 0 0.0 9 10# coordination number cutoff 11 12variable r equal 2.835 13 14# diamond unit cell 15 16variable a equal 5.431 17lattice custom $a & 18 a1 1.0 0.0 0.0 & 19 a2 0.0 1.0 0.0 & 20 a3 0.0 0.0 1.0 & 21 basis 0.0 0.0 0.0 & 22 basis 0.0 0.5 0.5 & 23 basis 0.5 0.0 0.5 & 24 basis 0.5 0.5 0.0 & 25 basis 0.25 0.25 0.25 & 26 basis 0.25 0.75 0.75 & 27 basis 0.75 0.25 0.75 & 28 basis 0.75 0.75 0.25 29 30region myreg block 0 4 & 31 0 4 & 32 0 4 33 34#create_box 1 myreg 35#create_atoms 1 region myreg 36#mass 1 28.06 37#write_data initial.sivac 38 39read_data initial.sivac 40 41# make a vacancy 42 43group Si type 1 44 45group del id 300 46delete_atoms group del compress no 47group vacneigh id 174 175 301 304 306 331 337 48 49# choose potential 50 51pair_style sw 52pair_coeff * * Si.sw Si 53 54# set up neb run 55 56variable u uloop 20 57 58# only output atoms near vacancy 59 60#dump events vacneigh custom 1000 dump.neb.sivac.$u id type x y z 61 62# initial minimization to relax vacancy 63 64displace_atoms all random 0.1 0.1 0.1 123456 65minimize 1.0e-6 1.0e-4 1000 10000 66 67reset_timestep 0 68 69fix 1 all neb 1.0 70 71thermo 100 72 73# run NEB for 2000 steps or to force tolerance 74 75timestep 0.01 76min_style fire 77min_modify integrator eulerexplicit tmax 10.0 tmin 0.0 delaystep 5 & 78 dtgrow 1.1 dtshrink 0.5 alpha0 0.1 alphashrink 0.99 & 79 vdfmax 100000 halfstepback no initialdelay no 80neb 0.0 0.01 100 100 10 final final.sivac 81