79 lines
1.7 KiB
Plaintext
79 lines
1.7 KiB
Plaintext
# Parallel replica dynamics model for a single vacancy in bulk Si
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# events occur when a neighboring atom diffuses to the vacant site
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# run this on multiple partitions as
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# mpirun -np 4 lmp_g++ -partition 4x1 -in in.prd
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units metal
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atom_style atomic
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atom_modify map array
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boundary p p p
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atom_modify sort 0 0.0
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# temperature
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variable t equal 1800.0
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# coordination number cutoff
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variable r equal 2.835
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# minimization parameters
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variable etol equal 1.0e-5
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variable ftol equal 1.0e-5
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variable maxiter equal 100
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variable maxeval equal 100
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variable dmax equal 1.0e-1
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# diamond unit cell
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variable a equal 5.431
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lattice custom $a &
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a1 1.0 0.0 0.0 &
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a2 0.0 1.0 0.0 &
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a3 0.0 0.0 1.0 &
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basis 0.0 0.0 0.0 &
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basis 0.0 0.5 0.5 &
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basis 0.5 0.0 0.5 &
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basis 0.5 0.5 0.0 &
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basis 0.25 0.25 0.25 &
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basis 0.25 0.75 0.75 &
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basis 0.75 0.25 0.75 &
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basis 0.75 0.75 0.25
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region myreg block 0 4 &
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0 4 &
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0 4
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create_box 1 myreg
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create_atoms 1 region myreg
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mass 1 28.06
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group Si type 1
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velocity all create $t 5287287 mom yes rot yes dist gaussian
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# make a vacancy
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group del id 300
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delete_atoms group del
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replicate 2 2 2
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pair_style tersoff
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pair_coeff * * Si.tersoff Si
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thermo 100
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fix 1 all nvt temp $t $t 0.1 tchain 1
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timestep 1.0e-3
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neighbor 1.0 bin
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neigh_modify every 1 delay 10 check yes
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# equilibrate
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run 1000
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