forked from lijiext/lammps
79 lines
1.7 KiB
Plaintext
79 lines
1.7 KiB
Plaintext
# NEB simulation of vacancy hopping in silicon crystal
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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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# coordination number cutoff
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variable r equal 2.835
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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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#write_data initial.sivac
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read_data initial.sivac
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# make a vacancy
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group Si type 1
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group del id 300
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delete_atoms group del compress no
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group vacneigh id 174 175 301 304 306 331 337
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# choose potential
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pair_style sw
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pair_coeff * * Si.sw Si
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# set up neb run
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variable u uloop 20
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# only output atoms near vacancy
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#dump events vacneigh custom 1000 dump.neb.sivac.$u id type x y z
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# initial minimization to relax vacancy
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displace_atoms all random 0.1 0.1 0.1 123456
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minimize 1.0e-6 1.0e-4 1000 10000
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reset_timestep 0
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fix 1 all neb 1.0
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thermo 100
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# run NEB for 2000 steps or to force tolerance
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timestep 0.01
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min_style fire
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min_modify integrator verlet
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neb 0.0 0.01 100 100 10 final final.sivac
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