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 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) = 2.979 | 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 723.08283 20 549.138 -2289.442 0 -2253.2413 -2444.5194 30 1047.0106 -2321.1522 0 -2252.1305 9013.2015 40 663.46143 -2294.2083 0 -2250.4711 2942.5358 50 504.74533 -2282.849 0 -2249.5748 -461.44817 60 1019.2173 -2315.5639 0 -2248.3744 7706.429 70 844.51197 -2302.5251 0 -2246.8526 3116.8313 80 814.90406 -2299.3372 0 -2245.6165 794.77536 90 1269.5635 -2327.4775 0 -2243.7845 7729.3971 100 977.61566 -2306.1118 0 -2241.6647 2969.9952 110 843.08538 -2295.6547 0 -2240.0763 1393.4046 120 1161.6968 -2314.6587 0 -2238.0766 7398.3495 130 918.19453 -2296.4321 0 -2235.9022 2537.4011 140 881.42546 -2292.2768 0 -2234.1709 1550.3345 150 1231.1005 -2313.1054 0 -2231.9479 8112.7568 160 967.01865 -2293.332 0 -2229.5836 3422.964 170 833.51246 -2282.7489 0 -2227.8015 43.99251 180 1240.8487 -2307.3633 0 -2225.5632 6557.8652 190 1126.4621 -2297.1922 0 -2222.9328 4289.0083 200 947.5957 -2283.29 0 -2220.8219 586.28203 210 1228.153 -2299.4702 0 -2218.5071 5315.0427 220 1215.4104 -2295.9407 0 -2215.8176 4870.343 230 1112.436 -2286.7552 0 -2213.4204 2527.1887 240 1300.081 -2296.6013 0 -2210.8965 5738.3711 250 1192.5739 -2286.8463 0 -2208.2286 4076.4913 260 1004.7055 -2272.1753 0 -2205.9424 359.3769 270 1241.2018 -2285.3632 0 -2203.5399 4160.5764 280 1360.1974 -2290.325 0 -2200.6572 5802.3912 290 1151.9366 -2273.9467 0 -2198.008 1418.8905 300 1174.3518 -2273.0089 0 -2195.5925 1998.2297 310 1329.2726 -2280.5049 0 -2192.8757 4721.7304 320 1284.4414 -2274.7519 0 -2190.0781 2985.4687 330 1328.3761 -2274.9545 0 -2187.3844 4543.2115 340 1446.3847 -2279.8693 0 -2184.5198 6254.4071 350 1366.2165 -2271.7475 0 -2181.6828 3637.8351 360 1358.9609 -2268.5982 0 -2179.0118 3049.5811 370 1552.2079 -2278.4802 0 -2176.1545 6334.0061 380 1562.5295 -2276.1793 0 -2173.1731 5787.5565 390 1415.5498 -2263.7823 0 -2170.4655 3438.5782 400 1323.1568 -2255.1641 0 -2167.938 2427.2311 410 1260.7186 -2248.5373 0 -2165.4273 1208.6316 420 1282.1118 -2247.3718 0 -2162.8516 462.65508 430 1451.9439 -2255.7551 0 -2160.0391 2037.8027 440 1568.9415 -2260.417 0 -2156.9882 3531.1613 450 1565.8261 -2257.2396 0 -2154.0161 2586.7896 460 1677.7143 -2261.7214 0 -2151.122 4112.976 470 1762.9071 -2264.4244 0 -2148.2089 5053.2148 480 1704.5898 -2257.8678 0 -2145.4966 4077.4649 490 1731.2619 -2257.1048 0 -2142.9753 4710.5276 500 1723.9777 -2254.161 0 -2140.5118 4760.7316 Loop time of 0.312472 on 1 procs for 500 steps with 511 atoms Performance: 138.252 ns/day, 0.174 hours/ns, 1600.143 timesteps/s 99.6% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.28525 | 0.28525 | 0.28525 | 0.0 | 91.29 Neigh | 0.013753 | 0.013753 | 0.013753 | 0.0 | 4.40 Comm | 0.0033333 | 0.0033333 | 0.0033333 | 0.0 | 1.07 Output | 0.00071096 | 0.00071096 | 0.00071096 | 0.0 | 0.23 Modify | 0.008044 | 0.008044 | 0.008044 | 0.0 | 2.57 Other | | 0.001385 | | | 0.44 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