LAMMPS (29 May 2010-ICMS)
# Parallel replica dynamics model for a single vacancy in bulk Si
# events occur when a neighboring atom diffuses to the vacant site
# run this on multiple partitions as
# mpirun -np 4 lmp_g++ -partition 4x1 -in in.prd
units metal
atom_style atomic
atom_modify map array
boundary p p p
atom_modify sort 0 0.0
# temperature
variable t equal 1800.0
# coordination number cutoff
variable r equal 2.835
# minimization parameters
variable etol equal 1.0e-5
variable ftol equal 1.0e-5
variable maxiter equal 100
variable maxeval equal 100
variable dmax equal 1.0e-1
# diamond unit cell
variable a equal 5.431
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
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
Lattice spacing in x,y,z = 5.431 5.431 5.431
region myreg block 0 4 0 4 0 4
create_box 1 myreg
Created orthogonal box = (0 0 0) to (21.724 21.724 21.724)
2 by 2 by 2 processor grid
using 1 OpenMP thread(s) per MPI task
create_atoms 1 region myreg
Created 512 atoms
mass 1 28.06
group Si type 1
512 atoms in group Si
velocity all create $t 5287287 mom yes rot yes dist gaussian
velocity all create 1800 5287287 mom yes rot yes dist gaussian
# make a vacancy
group del id 300
1 atoms in group del
delete_atoms group del
Deleted 1 atoms, new total = 511
replicate 2 2 2
orthogonal box = (0 0 0) to (43.448 43.448 43.448)
2 by 2 by 2 processor grid
using 1 OpenMP thread(s) per MPI task
4088 atoms
pair_style sw/omp
pair_coeff * * Si.sw Si
thermo 100
fix 1 all nvt temp $t $t 0.1 tchain 1
fix 1 all nvt temp 1800 $t 0.1 tchain 1
fix 1 all nvt temp 1800 1800 0.1 tchain 1
timestep 1.0e-3
neighbor 1.0 bin
neigh_modify every 1 delay 10 check yes
# equilibrate
run 1000
Memory usage per processor = 1.40649 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1799.4396 -17693.328 0 -16742.709 12351.85
100 1266.9031 -17157.645 0 -16488.358 14030.412
200 1737.6406 -16459.599 0 -15541.627 18555.046
300 2918.3805 -15779.611 0 -14237.87 26921.499
400 2542.842 -15682.696 0 -14339.348 14781.071
500 1779.4059 -16377.412 0 -15437.376 11997.562
600 1258.0063 -16911.29 0 -16246.703 5008.9422
700 1092.578 -17075.552 0 -16498.358 4528.9599
800 1283.6881 -16950.274 0 -16272.119 6373.2886
900 1937.2543 -16514.264 0 -15490.84 10229.344
1000 2695.0869 -15998.075 0 -14574.298 20500.358
Loop time of 3.51923 on 8 procs / 1 threads for 1000 steps with 4088 atoms
Pair time (%) = 3.3049 (93.9098)
Neigh time (%) = 0.0494682 (1.40566)
Comm time (%) = 0.135923 (3.86229)
Outpt time (%) = 0.000313759 (0.00891556)
Other time (%) = 0.028624 (0.813359)
Nlocal: 511 ave 511 max 511 min
Histogram: 8 0 0 0 0 0 0 0 0 0
Nghost: 1008 ave 1008 max 1008 min
Histogram: 8 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 8 0 0 0 0 0 0 0 0 0
FullNghs: 12842 ave 12842 max 12842 min
Histogram: 8 0 0 0 0 0 0 0 0 0
Total # of neighbors = 102736
Ave neighs/atom = 25.1311
Neighbor list builds = 51
Dangerous builds = 0