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 1 by 1 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) = 2.979 | 2.979 | 2.979 Mbytes Step Temp E_pair E_mol TotEng Press 0 1802.5039 -2372.6618 0 -2253.8359 12261.807 10 952.62744 -2316.428 0 -2253.6283 723.08194 20 549.13801 -2289.442 0 -2253.2413 -2444.5204 30 1047.0106 -2321.1523 0 -2252.1305 9013.201 40 663.46141 -2294.2083 0 -2250.4711 2942.5348 50 504.74535 -2282.849 0 -2249.5748 -461.44909 60 1019.2173 -2315.5639 0 -2248.3744 7706.4286 70 844.51195 -2302.5251 0 -2246.8526 3116.8302 80 814.90407 -2299.3372 0 -2245.6166 794.77455 90 1269.5636 -2327.4775 0 -2243.7845 7729.3968 100 977.61563 -2306.1118 0 -2241.6647 2969.9939 110 843.08539 -2295.6547 0 -2240.0763 1393.4039 120 1161.6968 -2314.6587 0 -2238.0766 7398.3492 130 918.19451 -2296.4321 0 -2235.9022 2537.3997 140 881.42548 -2292.2768 0 -2234.1709 1550.3339 150 1231.1005 -2313.1054 0 -2231.9479 8112.7566 160 967.01862 -2293.332 0 -2229.5836 3422.9627 170 833.51248 -2282.7489 0 -2227.8015 43.991459 180 1240.8488 -2307.3633 0 -2225.5632 6557.8651 190 1126.4621 -2297.1922 0 -2222.9328 4289.0067 200 947.59571 -2283.29 0 -2220.822 586.2811 210 1228.153 -2299.4702 0 -2218.5071 5315.0425 220 1215.4104 -2295.9408 0 -2215.8176 4870.3417 230 1112.436 -2286.7552 0 -2213.4204 2527.1879 240 1300.081 -2296.6013 0 -2210.8965 5738.3708 250 1192.5738 -2286.8463 0 -2208.2286 4076.49 260 1004.7055 -2272.1753 0 -2205.9424 359.37589 270 1241.2018 -2285.3632 0 -2203.5399 4160.5763 280 1360.1974 -2290.325 0 -2200.6572 5802.3902 290 1151.9365 -2273.9467 0 -2198.008 1418.8887 300 1174.3518 -2273.0089 0 -2195.5925 1998.229 310 1329.2727 -2280.5049 0 -2192.8757 4721.7297 320 1284.4414 -2274.7519 0 -2190.0781 2985.4674 330 1328.3761 -2274.9545 0 -2187.3844 4543.2109 340 1446.3847 -2279.8693 0 -2184.5198 6254.4059 350 1366.2165 -2271.7475 0 -2181.6828 3637.8335 360 1358.9609 -2268.5982 0 -2179.0118 3049.5798 370 1552.208 -2278.4802 0 -2176.1545 6334.0058 380 1562.5295 -2276.1793 0 -2173.1732 5787.5547 390 1415.5498 -2263.7824 0 -2170.4655 3438.5766 400 1323.1568 -2255.1641 0 -2167.938 2427.2294 410 1260.7186 -2248.5373 0 -2165.4273 1208.6299 420 1282.1118 -2247.3718 0 -2162.8516 462.65374 430 1451.944 -2255.7551 0 -2160.0391 2037.8025 440 1568.9415 -2260.417 0 -2156.9882 3531.1602 450 1565.8262 -2257.2396 0 -2154.0162 2586.7886 460 1677.7143 -2261.7214 0 -2151.122 4112.9756 470 1762.9071 -2264.4244 0 -2148.2089 5053.2139 480 1704.5898 -2257.8678 0 -2145.4967 4077.4626 490 1731.2619 -2257.1048 0 -2142.9753 4710.5263 500 1723.9777 -2254.161 0 -2140.5118 4760.7295 Loop time of 0.679564 on 1 procs for 500 steps with 511 atoms Performance: 63.570 ns/day, 0.378 hours/ns, 735.765 timesteps/s 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.65181 | 0.65181 | 0.65181 | 0.0 | 95.92 Neigh | 0.013857 | 0.013857 | 0.013857 | 0.0 | 2.04 Comm | 0.0033884 | 0.0033884 | 0.0033884 | 0.0 | 0.50 Output | 0.00070739 | 0.00070739 | 0.00070739 | 0.0 | 0.10 Modify | 0.0083694 | 0.0083694 | 0.0083694 | 0.0 | 1.23 Other | | 0.001432 | | | 0.21 Nlocal: 511 ave 511 max 511 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 845 ave 845 max 845 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 7902 ave 7902 max 7902 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 7902 Ave neighs/atom = 15.4638 Neighbor list builds = 19 Dangerous builds = 0 Total wall time: 0:00:00