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 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, 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 -2253.8439 12260.967 10 938.75954 -2315.5185 0 -2253.6329 558.21736 20 534.27232 -2288.4721 0 -2253.2514 -2710.767 30 1043.7796 -2320.9485 0 -2252.1398 8679.4385 40 658.09162 -2293.8597 0 -2250.4765 2165.3752 50 517.93008 -2283.7238 0 -2249.5805 -1124.9362 60 1063.3594 -2318.4409 0 -2248.3414 7277.853 70 868.14007 -2304.0133 0 -2246.7832 2050.2859 80 826.37803 -2300.0187 0 -2245.5416 91.100098 90 1289.6772 -2328.7151 0 -2243.6961 8180.7427 100 976.36211 -2305.9371 0 -2241.5727 3614.0511 110 810.81711 -2293.4705 0 -2240.0193 1359.3687 120 1165.707 -2314.9026 0 -2238.056 7336.4505 130 929.81248 -2297.139 0 -2235.8432 2793.8463 140 804.47872 -2287.2074 0 -2234.174 704.92524 150 1182.414 -2310.0266 0 -2232.0787 7822.2339 160 979.92395 -2294.2969 0 -2229.6977 3206.7474 170 830.14746 -2282.6079 0 -2227.8824 -296.87288 180 1271.1133 -2309.4274 0 -2225.6322 7199.614 190 1209.6006 -2302.6407 0 -2222.9006 5528.3799 200 954.67692 -2283.6621 0 -2220.7272 47.02925 210 1260.814 -2301.5582 0 -2218.442 4829.7879 220 1274.9954 -2299.7285 0 -2215.6774 5518.0611 230 1048.0074 -2282.398 0 -2213.3106 1754.4157 240 1261.7071 -2294.1107 0 -2210.9356 5233.2714 250 1272.6179 -2292.0793 0 -2208.1849 4795.934 260 989.14207 -2271.0278 0 -2205.8209 -820.18098 270 1212.0444 -2283.4212 0 -2203.52 3395.8631 280 1391.9572 -2292.3809 0 -2200.6194 6666.2464 290 1093.1205 -2270.0421 0 -2197.9807 206.94752 300 1159.483 -2272.102 0 -2195.6657 778.53823 310 1407.3528 -2285.6227 0 -2192.8463 5223.0487 320 1236.7164 -2271.5389 0 -2190.0112 1865.3963 330 1258.8275 -2270.4611 0 -2187.4758 2333.321 340 1507.9519 -2283.9906 0 -2184.5824 6775.546 350 1366.5116 -2271.7287 0 -2181.6446 3432.1175 360 1305.2828 -2265.1091 0 -2179.0614 1498.4079 370 1581.4334 -2280.4645 0 -2176.2122 6518.5598 380 1589.5319 -2277.9428 0 -2173.1566 6334.6527 390 1402.6782 -2262.9323 0 -2170.464 3278.3048 400 1374.9587 -2258.5717 0 -2167.9307 3608.7293 410 1295.7416 -2250.7752 0 -2165.3565 1877.5245 420 1278.6727 -2247.1099 0 -2162.8164 1599.4189 430 1508.1328 -2259.4245 0 -2160.0044 4300.2235 440 1624.2957 -2263.9806 0 -2156.9026 4432.6267 450 1597.3356 -2259.263 0 -2153.9623 3370.3829 460 1772.0921 -2267.9105 0 -2151.0895 5788.3219 470 1806.4047 -2267.304 0 -2148.221 5950.1188 480 1593.0406 -2250.7469 0 -2145.7294 2518.0601 490 1660.9766 -2252.894 0 -2143.398 4282.1654 500 1714.2831 -2253.9295 0 -2140.9194 5740.0268 Loop time of 0.109584 on 4 procs for 500 steps with 511 atoms Performance: 394.220 ns/day, 0.061 hours/ns, 4562.726 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 | 0.074678 | 0.077817 | 0.084705 | 1.4 | 71.01 Neigh | 0.0036662 | 0.0037943 | 0.0039661 | 0.2 | 3.46 Comm | 0.013665 | 0.020312 | 0.023178 | 2.7 | 18.54 Output | 0.0010247 | 0.0010931 | 0.0012922 | 0.3 | 1.00 Modify | 0.0043213 | 0.0047521 | 0.0051889 | 0.6 | 4.34 Other | | 0.001814 | | | 1.66 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