LAMMPS (5 Oct 2016) # sample surface deposition script for molecules units lj atom_style bond boundary p p f lattice fcc 1.0 Lattice spacing in x,y,z = 1.5874 1.5874 1.5874 region box block 0 5 0 5 0 10 create_box 3 box bond/types 1 extra/bond/per/atom 1 Created orthogonal box = (0 0 0) to (7.93701 7.93701 15.874) 1 by 1 by 1 MPI processor grid region substrate block INF INF INF INF INF 3 create_atoms 1 region substrate Created 350 atoms 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 bond_style harmonic bond_coeff 1 5.0 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 yes extra 0 fix 1 addatoms nve fix 2 mobile langevin 0.1 0.1 0.1 587283 fix 3 mobile nve molecule dimer molecule.dimer Read molecule dimer: 2 atoms with 3 types 1 bonds with 1 types 0 angles with 0 types 0 dihedrals with 0 types 0 impropers with 0 types region slab block 0 5 0 5 8 9 fix 4 addatoms deposit 100 0 100 12345 region slab near 1.0 mol dimer 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 lost/bond ignore lost warn WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:474) #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 ... 1 neighbor list requests 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 Memory usage per processor = 3.56565 Mbytes Step Atoms Temp E_pair TotEng Press 0 350 0 -6.9215833 -6.9215833 -1.0052629 100 352 0.83994737 -6.8875167 -6.8803581 -0.73353914 200 354 0.83994737 -6.8593854 -6.845149 -0.70414703 300 356 0.84169616 -6.8174189 -6.7961324 -0.69200581 400 358 0.84705847 -6.785416 -6.7570071 -0.70386101 500 360 0.87562973 -6.7507562 -6.714217 -0.68491831 600 362 0.89546097 -6.7133515 -6.6684358 -0.68373096 700 364 0.86923875 -6.6724351 -6.6215093 -0.6663574 800 366 0.93007871 -6.6448092 -6.5816911 -0.68706422 900 368 1.0020611 -6.6164541 -6.540933 -0.66074734 1000 370 1.0082042 -6.5845669 -6.5014101 -0.69453732 1100 372 0.96783727 -6.5649235 -6.4753076 -0.6717256 1200 374 0.97597749 -6.5935771 -6.4925926 -0.69360182 1300 376 0.80208918 -6.5923852 -6.5033139 -0.64868248 1400 378 0.66705029 -6.582928 -6.5082634 -0.6111322 1500 380 0.67555528 -6.5640796 -6.4816473 -0.67638117 1600 382 0.65916245 -6.551728 -6.4662574 -0.62833932 1700 384 0.718469 -6.5624935 -6.4643654 -0.64737567 1800 386 0.59257091 -6.5604373 -6.4675604 -0.61982866 1900 388 0.63118529 -6.5638788 -6.467728 -0.63403973 2000 390 0.6013361 -6.571937 -6.473428 -0.62753885 2100 392 0.48508625 -6.5519559 -6.4663394 -0.66580902 2200 394 0.50266444 -6.5357335 -6.4395422 -0.71780255 2300 396 0.52557785 -6.5469569 -6.4355521 -0.65421156 2400 398 0.66055178 -6.5509266 -6.4186172 -0.65273326 2500 400 0.69210544 -6.5578062 -6.4211169 -0.68232818 2600 402 0.64576434 -6.6050398 -6.4574266 -0.64849208 2700 404 0.56298016 -6.6350083 -6.503562 -0.746185 2800 406 0.49149694 -6.6482516 -6.5155551 -0.76320999 2900 408 0.48366321 -6.6606024 -6.5257882 -0.65612432 3000 410 0.47356141 -6.6756446 -6.5312692 -0.70811639 3100 412 0.47568619 -6.6934709 -6.5474974 -0.72316681 3200 414 0.38708973 -6.6932142 -6.5659264 -0.73056797 3300 416 0.43665017 -6.6999962 -6.5567504 -0.75890315 3400 418 0.34923989 -6.7185629 -6.5909531 -0.66986444 3500 420 0.33999089 -6.6922536 -6.5729709 -0.70698979 3600 422 0.37659 -6.6827522 -6.5521249 -0.68796169 3700 424 0.34150483 -6.6973468 -6.5698573 -0.68312043 3800 426 0.41110243 -6.7043016 -6.5510735 -0.71352712 3900 428 0.40957994 -6.7172729 -6.5557011 -0.70233721 4000 430 0.42723175 -6.7170007 -6.5537357 -0.7497547 4100 432 0.37176212 -6.7218812 -6.5574518 -0.7098714 4200 434 0.33265381 -6.7082458 -6.5637164 -0.70399102 4300 436 0.43029564 -6.7142231 -6.5431037 -0.76230436 4400 438 0.38216708 -6.7315576 -6.5614315 -0.6674734 4500 440 0.35981631 -6.7496554 -6.583264 -0.73404044 4600 442 0.36073617 -6.7479258 -6.5907772 -0.71067075 4700 444 0.35705292 -6.7678184 -6.5973053 -0.75325156 4800 446 0.37426281 -6.7869581 -6.6010006 -0.67542828 4900 448 0.33524109 -6.7800476 -6.6026334 -0.66398211 5000 450 0.31770101 -6.7884069 -6.6064017 -0.74655689 5100 452 0.31791473 -6.7695361 -6.5901194 -0.77591531 5200 454 0.37320367 -6.7756559 -6.5809165 -0.76247336 5300 456 0.32228579 -6.7786007 -6.5856918 -0.67574614 5400 458 0.31274193 -6.7828483 -6.5928063 -0.72466782 5500 460 0.30708694 -6.7858555 -6.5973813 -0.76883863 5600 462 0.32849848 -6.7983978 -6.6021343 -0.76855876 5700 464 0.35124617 -6.8131288 -6.5975496 -0.78865946 5800 466 0.35055399 -6.8184367 -6.6060092 -0.70530424 5900 468 0.33326299 -6.8299034 -6.6095077 -0.68840817 6000 470 0.40104727 -6.8633145 -6.6132375 -0.77187971 6100 472 0.29105598 -6.8410097 -6.6311104 -0.7715889 6200 474 0.30288813 -6.8634336 -6.6428858 -0.78760673 6300 476 0.34293767 -6.9005784 -6.6534079 -0.74817698 6400 478 0.34963015 -6.9292987 -6.666687 -0.71175243 6500 480 0.319367 -6.9395521 -6.6743587 -0.76432283 6600 482 0.29016877 -6.9324045 -6.679475 -0.90715919 6700 484 0.35436305 -6.9551643 -6.6789059 -0.79939008 6800 486 0.327512 -6.9608693 -6.687362 -0.70392295 6900 488 0.32349315 -6.9513424 -6.6847712 -0.75205809 7000 490 0.35355467 -6.9907283 -6.7038887 -0.80881264 7100 492 0.32140685 -6.9979325 -6.7169278 -0.68673022 7200 494 0.32242041 -7.0116346 -6.728848 -0.79432529 7300 496 0.26266524 -6.9966902 -6.7334152 -0.86050198 7400 498 0.31564904 -7.0133015 -6.7158904 -0.81615792 7500 500 0.36973921 -7.0516561 -6.717083 -0.79423832 7600 502 0.33599186 -7.0516408 -6.7296713 -0.83610882 7700 504 0.29691416 -7.0495062 -6.738076 -0.83634675 7800 506 0.3244215 -7.0434148 -6.7342677 -0.7170135 7900 508 0.29167542 -7.0637209 -6.7576924 -0.78857188 8000 510 0.34198998 -7.1041546 -6.7635656 -0.83376311 8100 512 0.33068905 -7.1341746 -6.7960028 -0.78639771 8200 514 0.29688969 -7.136245 -6.8093036 -0.85753154 8300 516 0.29829676 -7.1313196 -6.8076328 -0.76960702 8400 518 0.31096049 -7.1559166 -6.8202327 -0.72775356 8500 520 0.26677854 -7.1413516 -6.8361967 -0.81908087 8600 522 0.28811568 -7.1390821 -6.8248702 -0.88515896 8700 524 0.27520272 -7.1501541 -6.8311651 -0.81462692 8800 526 0.28763152 -7.1525343 -6.8281253 -0.74124759 8900 528 0.29917883 -7.1547953 -6.8229151 -0.81440712 9000 530 0.28474306 -7.1612717 -6.8236771 -0.79150099 9100 532 0.29409713 -7.1748026 -6.8272211 -0.7916524 9200 534 0.26767862 -7.1646362 -6.8313179 -0.79362392 9300 536 0.27111075 -7.1719185 -6.8399556 -0.9578129 9400 538 0.33952348 -7.207044 -6.8368639 -0.89888939 9500 540 0.3284439 -7.2371916 -6.8625844 -0.7659201 9600 542 0.31256223 -7.2266123 -6.8655682 -0.82722861 9700 544 0.30268239 -7.2315617 -6.8705788 -0.81448482 9800 546 0.26835398 -7.2214231 -6.8757262 -0.86029096 9900 548 0.31676744 -7.264604 -6.884266 -0.74053962 10000 550 0.31368419 -7.2759575 -6.8979611 -0.76153366 Loop time of 6.51779 on 1 procs for 10000 steps with 550 atoms Performance: 662801.655 tau/day, 1534.263 timesteps/s 99.9% CPU use with 1 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.0744 | 4.0744 | 4.0744 | 0.0 | 62.51 Bond | 0.01209 | 0.01209 | 0.01209 | 0.0 | 0.19 Neigh | 2.1316 | 2.1316 | 2.1316 | 0.0 | 32.70 Comm | 0.13266 | 0.13266 | 0.13266 | 0.0 | 2.04 Output | 0.0008409 | 0.0008409 | 0.0008409 | 0.0 | 0.01 Modify | 0.12403 | 0.12403 | 0.12403 | 0.0 | 1.90 Other | | 0.04216 | | | 0.65 Nlocal: 550 ave 550 max 550 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2349 ave 2349 max 2349 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 39710 ave 39710 max 39710 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 39710 Ave neighs/atom = 72.2 Ave special neighs/atom = 0.363636 Neighbor list builds = 877 Dangerous builds = 0 Total wall time: 0:00:06