LAMMPS (27 Oct 2021) using 2 OpenMP thread(s) per MPI task # sample surface deposition script for atoms units lj atom_style atomic boundary p p f lattice fcc 1.0 Lattice spacing in x,y,z = 1.5874011 1.5874011 1.5874011 region box block 0 5 0 5 0 10 create_box 2 box Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (7.9370053 7.9370053 15.874011) 1 by 1 by 4 MPI processor grid region substrate block INF INF INF INF INF 3 create_atoms 1 region substrate Created 350 atoms using lattice units in orthogonal box = (0.0000000 0.0000000 0.0000000) to (7.9370053 7.9370053 15.874011) create_atoms CPU = 0.001 seconds pair_style lj/cut 2.5 pair_coeff * * 1.0 1.0 pair_coeff 1 2 1.0 1.0 5.0 mass * 1.0 neigh_modify delay 0 group addatoms type 2 0 atoms in group addatoms region mobile block 0 5 0 5 2 INF group mobile region mobile 150 atoms in group mobile compute add addatoms temp compute_modify add dynamic/dof yes extra/dof 0 fix 1 addatoms nve fix 2 mobile langevin 1.0 1.0 0.1 587283 fix 3 mobile nve region slab block 0 5 0 5 8 9 fix 4 addatoms deposit 100 2 100 12345 region slab near 1.0 vz -1.0 -1.0 fix 5 addatoms wall/reflect zhi EDGE thermo_style custom step atoms temp epair etotal press thermo 100 thermo_modify temp add WARNING: Temperature for thermo pressure is not for group all (src/thermo.cpp:482) #dump 1 all atom 50 dump.deposit.atom #dump 2 all image 50 image.*.jpg type type # axes yes 0.8 0.02 view 80 -30 #dump_modify 2 pad 5 #dump 3 all movie 50 movie.mpg type type # axes yes 0.8 0.02 view 80 -30 #dump_modify 3 pad 5 run 10000 Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 5.3 ghost atom cutoff = 5.3 binsize = 2.65, bins = 3 3 6 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair lj/cut, perpetual attributes: half, newton on pair build: half/bin/atomonly/newton stencil: half/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 3.822 | 3.959 | 4.075 Mbytes Step Atoms Temp E_pair TotEng Press 0 350 0 -6.9215833 -6.9215833 -1.0052629 100 351 0.83994737 -6.3596932 -6.3561037 -0.10696131 200 352 0.83994737 -6.3044678 -6.2973092 -0.38494392 300 353 0.83994737 -6.1647603 -6.1540527 -0.41215681 400 354 0.83994737 -6.0387266 -6.0244902 -0.31486801 500 355 0.84001073 -6.0081645 -5.9904178 -0.37468524 600 356 0.84087385 -6.0279004 -6.0066423 -0.54835292 700 357 0.84502761 -5.9533148 -5.928461 -0.48676527 800 358 0.87411744 -5.8498967 -5.8205967 -0.4215397 900 359 0.98978155 -5.8132165 -5.7759963 -0.42726645 1000 360 1.2132922 -5.7674897 -5.7169358 -0.36020237 1100 361 1.2002163 -5.864774 -5.8099165 -0.64618132 1200 362 1.3179582 -5.7382778 -5.6727439 -0.409247 1300 363 1.1308619 -5.7080724 -5.6473236 -0.4796297 1400 364 1.2201701 -5.6479837 -5.5775893 -0.51091275 1500 365 0.89869673 -5.6348706 -5.5794715 -0.49944155 1600 366 0.98530113 -5.6565278 -5.5919178 -0.47433998 1700 367 1.0935161 -5.6469823 -5.5710023 -0.42689433 1800 368 0.95516281 -5.6192229 -5.5491431 -0.44742326 1900 369 0.88657339 -5.626031 -5.5575558 -0.60336611 2000 370 1.1603027 -5.6214282 -5.5273497 -0.55319204 2100 371 0.86358624 -5.6256457 -5.5523223 -0.64735589 2200 372 0.89270826 -5.5203036 -5.4411118 -0.47301948 2300 373 0.79241466 -5.5525073 -5.4792142 -0.55521524 2400 374 1.2309636 -5.5758787 -5.4573903 -0.61493706 2500 375 1.0221162 -5.5165897 -5.414378 -0.53617081 2600 376 1.091529 -5.5411574 -5.4279402 -0.56743732 2700 377 1.154038 -5.482838 -5.3588631 -0.44480529 2800 378 1.0267703 -5.5235222 -5.4094366 -0.63062643 2900 379 1.0667941 -5.506043 -5.3836009 -0.64129272 3000 380 0.97112701 -5.4554386 -5.3404367 -0.54281095 3100 381 1.045192 -5.491329 -5.3637662 -0.63668512 3200 382 1.2114593 -5.3993835 -5.2471582 -0.46955023 3300 383 1.1353491 -5.3603017 -5.2135659 -0.52719178 3400 384 1.1041804 -5.3970575 -5.2504085 -0.72610175 3500 385 1.0813653 -5.3201368 -5.1726779 -0.51624087 3600 386 1.1525827 -5.3750492 -5.213807 -0.63008946 3700 387 1.1018804 -5.3865282 -5.2285066 -0.70467814 3800 388 1.0905011 -5.3813582 -5.2211558 -0.73956169 3900 389 0.96473641 -5.2735645 -5.128482 -0.43328142 4000 390 1.1121248 -5.2834113 -5.1123151 -0.63719094 4100 391 1.3151019 -5.283931 -5.07708 -0.58888706 4200 392 1.0716499 -5.2550936 -5.0828641 -0.63470197 4300 393 1.0244216 -5.2759168 -5.1077865 -0.68883175 4400 394 1.1459695 -5.2389871 -5.0470226 -0.63122765 4500 395 0.93083182 -5.2383093 -5.0792431 -0.66379481 4600 396 0.98860239 -5.1803046 -5.0080482 -0.52055537 4700 397 1.0938236 -5.1770388 -4.9827956 -0.50289656 4800 398 1.181808 -5.2545743 -5.0407799 -0.65125211 4900 399 1.1296795 -5.2545323 -5.0464334 -0.59232589 5000 400 1.0489126 -5.2453822 -5.048711 -0.58862017 5100 401 1.0104059 -5.2152161 -5.0224579 -0.56264189 5200 402 1.0526307 -5.2132196 -5.0089778 -0.59367674 5300 403 1.1090937 -5.2444963 -5.0257049 -0.69279272 5400 404 1.127955 -5.1641029 -4.9379536 -0.57759926 5500 405 0.94717919 -5.1170818 -4.9241379 -0.4377215 5600 406 1.0078519 -5.1199852 -4.9114642 -0.51817347 5700 407 1.1001677 -5.1793462 -4.9482299 -0.56901692 5800 408 0.93457135 -5.1108347 -4.9115511 -0.4620485 5900 409 1.0953467 -5.1510514 -4.9140387 -0.6377434 6000 410 0.94237584 -5.1670713 -4.9602083 -0.67810879 6100 411 1.0057435 -5.1477983 -4.9238919 -0.52662569 6200 412 1.1444077 -5.2486496 -4.9903246 -0.66344162 6300 413 1.2051124 -5.2291952 -4.9534492 -0.60437798 6400 414 1.0076362 -5.1965116 -4.9628568 -0.56358298 6500 415 1.0575299 -5.1659177 -4.9174619 -0.56024897 6600 416 1.0751437 -5.1737857 -4.9179221 -0.65448665 6700 417 0.9884531 -5.2283778 -4.9901535 -0.67700234 6800 418 0.94489506 -5.2550471 -5.0244746 -0.75060775 6900 419 0.92756432 -5.2169199 -4.987796 -0.57497441 7000 420 1.0134284 -5.200205 -4.9468479 -0.70074051 7100 421 0.90313447 -5.2089841 -4.980519 -0.77657764 7200 422 1.0994014 -5.1875996 -4.9062363 -0.62482061 7300 423 0.96741934 -5.18159 -4.9311587 -0.63443686 7400 424 1.1714845 -5.2258315 -4.9191457 -0.5307891 7500 425 0.96546127 -5.1255898 -4.8700265 -0.41650813 7600 426 0.98282222 -5.1567215 -4.8937127 -0.50760346 7700 427 0.94172105 -5.227297 -4.9725692 -0.70658326 7800 428 0.99138416 -5.1151947 -4.8441855 -0.4999804 7900 429 1.0441712 -5.1804201 -4.8919952 -0.60334472 8000 430 1.0693556 -5.1948944 -4.8964696 -0.67057662 8100 431 1.0723576 -5.2113271 -4.9090268 -0.74142348 8200 432 1.1802182 -5.1685761 -4.8325417 -0.58857331 8300 433 1.0698731 -5.2010993 -4.8934799 -0.58858482 8400 434 1.0748997 -5.1928141 -4.8807465 -0.53670469 8500 435 1.0967683 -5.2206806 -4.899214 -0.61641735 8600 436 1.1373277 -5.27361 -4.937107 -0.71560014 8700 437 1.0904858 -5.2109473 -4.8852988 -0.55017079 8800 438 0.97086248 -5.2488756 -4.9562869 -0.55559263 8900 439 0.95391235 -5.2417746 -4.9516896 -0.55416294 9000 440 1.1646258 -5.293388 -4.9360597 -0.73593866 9100 441 0.99548137 -5.2636578 -4.9555326 -0.61040255 9200 442 0.98184595 -5.1995669 -4.8930177 -0.490599 9300 443 0.97121595 -5.1791409 -4.8733065 -0.44155484 9400 444 1.0788651 -5.1799748 -4.8373622 -0.38488651 9500 445 1.1165553 -5.1887305 -4.8311818 -0.32221277 9600 446 0.9743981 -5.192753 -4.8781491 -0.46443549 9700 447 1.0748698 -5.1605212 -4.8106474 -0.44935739 9800 448 1.0570711 -5.2067449 -4.8598935 -0.62362658 9900 449 0.95863234 -5.2464765 -4.9294233 -0.63248376 10000 450 1.0776374 -5.252114 -4.8929015 -0.42769982 Loop time of 5.07006 on 8 procs for 10000 steps with 450 atoms Performance: 852060.192 tau/day, 1972.362 timesteps/s 130.6% CPU use with 4 MPI tasks x 2 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.0082156 | 0.88976 | 2.232 | 98.5 | 17.55 Neigh | 0.008378 | 0.57608 | 1.7675 | 94.1 | 11.36 Comm | 0.83087 | 3.2213 | 4.5616 | 83.6 | 63.54 Output | 0.003745 | 0.0062651 | 0.0078307 | 2.0 | 0.12 Modify | 0.023693 | 0.06017 | 0.11519 | 15.0 | 1.19 Other | | 0.3165 | | | 6.24 Nlocal: 112.500 ave 250 max 10 min Histogram: 2 0 0 0 0 0 1 0 0 1 Nghost: 1515.00 ave 2233 max 427 min Histogram: 1 0 0 0 0 1 0 0 0 2 Neighs: 7473.75 ave 17229 max 14 min Histogram: 2 0 0 0 0 0 0 1 0 1 Total # of neighbors = 29895 Ave neighs/atom = 66.433333 Neighbor list builds = 1146 Dangerous builds = 0 Total wall time: 0:00:05