117 lines
4.2 KiB
Plaintext
117 lines
4.2 KiB
Plaintext
LAMMPS (29 May 2010-ICMS)
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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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# 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 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
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lattice custom 5.431 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
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Lattice spacing in x,y,z = 5.431 5.431 5.431
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region myreg block 0 4 0 4 0 4
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create_box 1 myreg
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Created orthogonal box = (0 0 0) to (21.724 21.724 21.724)
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2 by 2 by 2 processor grid
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using 1 OpenMP thread(s) per MPI task
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create_atoms 1 region myreg
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Created 512 atoms
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mass 1 28.06
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group Si type 1
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512 atoms in group Si
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velocity all create $t 5287287 mom yes rot yes dist gaussian
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velocity all create 1800 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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1 atoms in group del
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delete_atoms group del
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Deleted 1 atoms, new total = 511
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replicate 2 2 2
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orthogonal box = (0 0 0) to (43.448 43.448 43.448)
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2 by 2 by 2 processor grid
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using 1 OpenMP thread(s) per MPI task
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4088 atoms
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pair_style sw/omp
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pair_coeff * * Si.sw 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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fix 1 all nvt temp 1800 $t 0.1 tchain 1
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fix 1 all nvt temp 1800 1800 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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Memory usage per processor = 1.40649 Mbytes
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Step Temp E_pair E_mol TotEng Press
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0 1799.4396 -17693.328 0 -16742.709 12351.85
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100 1266.9031 -17157.645 0 -16488.358 14030.412
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200 1737.6406 -16459.599 0 -15541.627 18555.046
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300 2918.3805 -15779.611 0 -14237.87 26921.499
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400 2542.842 -15682.696 0 -14339.348 14781.071
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500 1779.4059 -16377.412 0 -15437.376 11997.562
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600 1258.0063 -16911.29 0 -16246.703 5008.9422
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700 1092.578 -17075.552 0 -16498.358 4528.9599
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800 1283.6881 -16950.274 0 -16272.119 6373.2886
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900 1937.2543 -16514.264 0 -15490.84 10229.344
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1000 2695.0869 -15998.075 0 -14574.298 20500.358
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Loop time of 3.51923 on 8 procs / 1 threads for 1000 steps with 4088 atoms
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Pair time (%) = 3.3049 (93.9098)
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Neigh time (%) = 0.0494682 (1.40566)
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Comm time (%) = 0.135923 (3.86229)
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Outpt time (%) = 0.000313759 (0.00891556)
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Other time (%) = 0.028624 (0.813359)
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Nlocal: 511 ave 511 max 511 min
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Histogram: 8 0 0 0 0 0 0 0 0 0
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Nghost: 1008 ave 1008 max 1008 min
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Histogram: 8 0 0 0 0 0 0 0 0 0
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Neighs: 0 ave 0 max 0 min
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Histogram: 8 0 0 0 0 0 0 0 0 0
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FullNghs: 12842 ave 12842 max 12842 min
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Histogram: 8 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 102736
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Ave neighs/atom = 25.1311
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Neighbor list builds = 51
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Dangerous builds = 0
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