LAMMPS (4 May 2017) using 1 OpenMP thread(s) per MPI task 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) 1 by 2 by 2 MPI processor grid 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 pair_style edip/multi pair_coeff * * Si.edip Si Reading potential file Si.edip with DATE: 2011-09-15 thermo 10 fix 1 all nvt temp $t $t 0.1 fix 1 all nvt temp 1800 $t 0.1 fix 1 all nvt temp 1800 1800 0.1 timestep 1.0e-3 neighbor 1.0 bin neigh_modify every 1 delay 10 check yes # equilibrate run 500 Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 4.12138 ghost atom cutoff = 4.12138 binsize = 2.06069, bins = 11 11 11 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair edip/multi, perpetual attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 2.955 | 2.955 | 2.955 Mbytes Step Temp E_pair E_mol TotEng Press 0 1802.3816 -2372.6618 0 -2253.844 12260.967 10 938.75954 -2315.5185 0 -2253.6329 558.21646 20 534.27233 -2288.4721 0 -2253.2514 -2710.768 30 1043.7796 -2320.9485 0 -2252.1398 8679.4381 40 658.0916 -2293.8597 0 -2250.4765 2165.3742 50 517.93009 -2283.7238 0 -2249.5805 -1124.9373 60 1063.3594 -2318.4409 0 -2248.3414 7277.8526 70 868.14006 -2304.0134 0 -2246.7832 2050.2848 80 826.37805 -2300.0187 0 -2245.5416 91.099408 90 1289.6772 -2328.7151 0 -2243.6961 8180.7423 100 976.36208 -2305.9371 0 -2241.5727 3614.0499 110 810.81713 -2293.4705 0 -2240.0193 1359.368 120 1165.707 -2314.9026 0 -2238.056 7336.45 130 929.81245 -2297.139 0 -2235.8432 2793.8451 140 804.47874 -2287.2074 0 -2234.174 704.92455 150 1182.4141 -2310.0266 0 -2232.0787 7822.2337 160 979.92391 -2294.2969 0 -2229.6977 3206.7458 170 830.14748 -2282.6079 0 -2227.8824 -296.87377 180 1271.1133 -2309.4274 0 -2225.6322 7199.614 190 1209.6006 -2302.6407 0 -2222.9006 5528.3784 200 954.67693 -2283.6621 0 -2220.7273 47.02795 210 1260.814 -2301.5582 0 -2218.442 4829.788 220 1274.9954 -2299.7285 0 -2215.6774 5518.0597 230 1048.0074 -2282.398 0 -2213.3106 1754.4144 240 1261.7072 -2294.1108 0 -2210.9356 5233.2712 250 1272.6178 -2292.0793 0 -2208.1849 4795.9325 260 989.14205 -2271.0278 0 -2205.8209 -820.1828 270 1212.0445 -2283.4212 0 -2203.52 3395.8634 280 1391.9572 -2292.3809 0 -2200.6194 6666.2451 290 1093.1204 -2270.0421 0 -2197.9807 206.94523 300 1159.4831 -2272.102 0 -2195.6657 778.53806 310 1407.3528 -2285.6228 0 -2192.8463 5223.048 320 1236.7163 -2271.5389 0 -2190.0113 1865.3943 330 1258.8275 -2270.4611 0 -2187.4758 2333.3209 340 1507.9519 -2283.9906 0 -2184.5824 6775.5456 350 1366.5116 -2271.7287 0 -2181.6446 3432.115 360 1305.2829 -2265.1092 0 -2179.0614 1498.4073 370 1581.4335 -2280.4645 0 -2176.2122 6518.5597 380 1589.5319 -2277.9428 0 -2173.1567 6334.6506 390 1402.6781 -2262.9323 0 -2170.464 3278.3038 400 1374.9587 -2258.5717 0 -2167.9307 3608.7284 410 1295.7416 -2250.7752 0 -2165.3565 1877.5222 420 1278.6727 -2247.1099 0 -2162.8164 1599.4181 430 1508.1328 -2259.4245 0 -2160.0044 4300.2224 440 1624.2957 -2263.9806 0 -2156.9026 4432.625 450 1597.3356 -2259.263 0 -2153.9624 3370.3816 460 1772.0922 -2267.9106 0 -2151.0895 5788.3214 470 1806.4047 -2267.304 0 -2148.221 5950.1166 480 1593.0406 -2250.7469 0 -2145.7294 2518.0576 490 1660.9767 -2252.894 0 -2143.398 4282.1643 500 1714.283 -2253.9295 0 -2140.9194 5740.0247 Loop time of 0.205398 on 4 procs for 500 steps with 511 atoms Performance: 210.324 ns/day, 0.114 hours/ns, 2434.304 timesteps/s 99.0% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.16285 | 0.1688 | 0.17446 | 1.1 | 82.18 Neigh | 0.0035172 | 0.0036234 | 0.0038214 | 0.2 | 1.76 Comm | 0.018727 | 0.024851 | 0.030996 | 2.9 | 12.10 Output | 0.0013061 | 0.0014012 | 0.0015635 | 0.3 | 0.68 Modify | 0.0046582 | 0.0048603 | 0.0050988 | 0.2 | 2.37 Other | | 0.001861 | | | 0.91 Nlocal: 127.75 ave 131 max 124 min Histogram: 1 0 1 0 0 0 0 0 1 1 Nghost: 433.75 ave 441 max 426 min Histogram: 1 0 1 0 0 0 0 0 1 1 Neighs: 0 ave 0 max 0 min Histogram: 4 0 0 0 0 0 0 0 0 0 FullNghs: 1979.5 ave 2040 max 1895 min Histogram: 1 0 0 0 1 0 0 0 0 2 Total # of neighbors = 7918 Ave neighs/atom = 15.4951 Neighbor list builds = 19 Dangerous builds = 0 Total wall time: 0:00:00