forked from lijiext/lammps
96 lines
2.2 KiB
Plaintext
96 lines
2.2 KiB
Plaintext
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# 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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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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# 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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pair_style sw
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pair_coeff * * si.sw Si
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thermo 10
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fix 1 all nvt $t $t 0.1
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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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# output settings
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# only output atoms near vacancy
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compute coord all coord/atom $r
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dump events all custom 1 dump.events id type x y z
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dump_modify events thresh c_coord != 4
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restart 1 tmp.restart
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compute patom all pe/atom
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compute pe all reduce sum c_patom
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compute satom all stress/atom
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compute str all reduce sum c_satom[1] c_satom[2] c_satom[3]
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variable press equal (c_str[1]+c_str[2]+c_str[3])/(3*vol)
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thermo_style custom step temp pe c_pe press v_press
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compute 1 all event/displace 0.5
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prd 2000 100 10 10 100 1 54985 temp $t &
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min ${etol} ${ftol} ${maxiter} ${maxeval} vel all uniform
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