LAMMPS (10 Mar 2021) using 1 OpenMP thread(s) per MPI task # 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 = 1.5874011 1.5874011 1.5874011 region box block 0 5 0 5 0 10 create_box 3 box bond/types 1 extra/bond/per/atom 1 Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (7.9370053 7.9370053 15.874011) 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 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 bond_style harmonic bond_coeff 1 5.0 1.0 neigh_modify delay 0 molecule dimer molecule.dimer Read molecule template dimer: 1 molecules 2 atoms with max type 3 1 bonds with max type 1 0 angles with max type 0 0 dihedrals with max type 0 0 impropers with max type 0 region slab block 0 5 0 5 8 9 group addatoms empty 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 rigid/small molecule mol dimer create bodies CPU = 0.000 seconds 0 rigid bodies with 0 atoms 1.0000000 = max distance from body owner to body atom fix 2 mobile langevin 0.1 0.1 0.1 587283 fix 3 mobile nve fix 4 addatoms deposit 100 0 100 12345 region slab near 1.0 mol dimer vz -1.0 -1.0 rigid 1 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 (src/thermo.cpp:468) #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 tmp.mpg type type # axes yes 0.8 0.02 view 80 -30 #dump_modify 3 pad 5 run 10000 WARNING: Should not allow rigid bodies to bounce off relecting walls (src/fix_wall_reflect.cpp:182) 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/newton stencil: half/bin/3d/newton bin: standard Per MPI rank memory allocation (min/avg/max) = 5.929 | 5.929 | 5.929 Mbytes Step Atoms Temp E_pair TotEng Press 0 350 0 -6.9215833 -6.9215833 -1.0052629 100 352 1.0079368 -6.8875167 -6.8803581 -0.73353914 200 354 1.0081552 -6.8594643 -6.8452248 -0.70421276 300 356 1.0085803 -6.8171524 -6.7959042 -0.6917826 400 358 1.0099188 -6.7852701 -6.7570601 -0.70371699 500 360 1.0140221 -6.7493429 -6.7141338 -0.68415307 600 362 1.026148 -6.7105231 -6.6680032 -0.68314418 700 364 1.0683344 -6.6725162 -6.621154 -0.65747369 800 366 1.0958952 -6.6412275 -6.5813425 -0.68789614 900 368 1.1250033 -6.6101882 -6.541404 -0.66674346 1000 370 1.2326373 -6.5993719 -6.5160856 -0.6968868 1100 372 1.1397426 -6.5912861 -6.5070309 -0.63330356 1200 374 1.0514292 -6.5905747 -6.5062354 -0.71020362 1300 376 1.003296 -6.5747765 -6.4880555 -0.65459732 1400 378 0.82999289 -6.5681797 -6.4913285 -0.60438126 1500 380 0.90239175 -6.575298 -6.4862461 -0.66528725 1600 382 0.86399799 -6.5692206 -6.4787496 -0.65027781 1700 384 0.64747231 -6.5644237 -6.4927634 -0.6304614 1800 386 0.74288971 -6.5515735 -6.4649672 -0.67772325 1900 388 0.7257202 -6.5565091 -6.4676644 -0.66173549 2000 390 0.73381036 -6.5631515 -6.4690733 -0.64685916 2100 392 0.76476562 -6.5574124 -6.4549885 -0.68866192 2200 394 0.65932468 -6.5511557 -6.459118 -0.71728829 2300 396 0.70269509 -6.5728146 -6.4707819 -0.64362081 2400 398 0.60528919 -6.5845991 -6.4933494 -0.63956327 2500 400 0.51025744 -6.5812452 -6.5015175 -0.68706961 2600 402 0.5245131 -6.6003894 -6.5155801 -0.68972215 2700 404 0.46330251 -6.5659175 -6.4885092 -0.72870942 2800 406 0.48039778 -6.5715192 -6.488692 -0.753758 2900 408 0.53698616 -6.5813154 -6.4858951 -0.67117541 3000 410 0.50231419 -6.5886963 -6.4968096 -0.71905351 3100 412 0.49420225 -6.596733 -6.5037702 -0.65947518 3200 414 0.42703699 -6.5879338 -6.5054146 -0.80033546 3300 416 0.44306009 -6.580249 -6.4923825 -0.76503083 3400 418 0.55620672 -6.5923388 -6.4792346 -0.69367877 3500 420 0.39815033 -6.5911154 -6.5081674 -0.65569211 3600 422 0.44197847 -6.6026382 -6.5083774 -0.73299102 3700 424 0.45049389 -6.6060616 -6.5077817 -0.7552914 3800 426 0.43047295 -6.6079275 -6.51193 -0.71501328 3900 428 0.43779129 -6.6099306 -6.5102001 -0.71539515 4000 430 0.41113503 -6.6123009 -6.5166881 -0.74177096 4100 432 0.32800011 -6.5983566 -6.5205325 -0.71688103 4200 434 0.39168203 -6.6110342 -6.5162724 -0.78927697 4300 436 0.48151013 -6.6183315 -6.4996106 -0.70523035 4400 438 0.45391027 -6.6331732 -6.5191775 -0.7270855 4500 440 0.349126 -6.6091657 -6.5199006 -0.76974115 4600 442 0.43375023 -6.6219188 -6.5090653 -0.74576212 4700 444 0.40071749 -6.6184164 -6.5123707 -0.71919052 4800 446 0.414292 -6.6298132 -6.5183445 -0.76237313 4900 448 0.44210681 -6.6364174 -6.5155288 -0.78753121 5000 450 0.36101771 -6.6232703 -6.5229876 -0.73927083 5100 452 0.41481171 -6.6442404 -6.5272305 -0.76316209 5200 454 0.40283527 -6.6512252 -6.5358759 -0.79645689 5300 456 0.3642061 -6.6530346 -6.5472072 -0.77458364 5400 458 0.38449826 -6.6514864 -6.5381518 -0.73083784 5500 460 0.42559408 -6.6769326 -6.5497169 -0.78932279 5600 462 0.38905756 -6.6698705 -6.5519743 -0.77118812 5700 464 0.38354955 -6.6706904 -6.5528977 -0.75067129 5800 466 0.36760943 -6.6942519 -6.5798669 -0.685487 5900 468 0.30783118 -6.6838159 -6.5867965 -0.79233808 6000 470 0.33145368 -6.6733504 -6.5675673 -0.84390449 6100 472 0.39252324 -6.6912189 -6.5643973 -0.83342022 6200 474 0.32342144 -6.6906083 -6.5848481 -0.71262158 6300 476 0.34445238 -6.7008453 -6.5868721 -0.76650756 6400 478 0.38152782 -6.7017838 -6.5740758 -0.77113022 6500 480 0.37540166 -6.7119996 -6.5849105 -0.79907635 6600 482 0.3579419 -6.7034721 -6.5809401 -0.8141269 6700 484 0.33538235 -6.6916682 -6.575601 -0.83265486 6800 486 0.34081871 -6.6931924 -6.573976 -0.80582583 6900 488 0.3555283 -6.6939997 -6.5683263 -0.74771423 7000 490 0.3543769 -6.7093364 -6.5827732 -0.77643516 7100 492 0.31263107 -6.698361 -6.5855723 -0.73108333 7200 494 0.32107 -6.6959056 -6.5789166 -0.7575478 7300 496 0.32908165 -6.7137605 -6.592677 -0.86538023 7400 498 0.32539571 -6.7030353 -6.5821554 -0.79337428 7500 500 0.33902577 -6.7078178 -6.5806832 -0.85408988 7600 502 0.35530921 -6.707507 -6.5730274 -0.79914613 7700 504 0.32391812 -6.6978823 -6.5741635 -0.78603595 7800 506 0.36390015 -6.7151325 -6.5748943 -0.83164222 7900 508 0.3372561 -6.7086718 -6.5775535 -0.7949992 8000 510 0.36612946 -6.7225238 -6.5789437 -0.80322866 8100 512 0.34622305 -6.7229825 -6.5860486 -0.70478659 8200 514 0.3212233 -6.7202524 -6.5921381 -0.91836713 8300 516 0.3402461 -6.721488 -6.5846642 -0.88273592 8400 518 0.34070258 -6.7268378 -6.5887152 -0.76057264 8500 520 0.36267747 -6.744602 -6.5963924 -0.81051317 8600 522 0.3439948 -6.7376267 -6.595943 -0.84600203 8700 524 0.30960289 -6.7276471 -6.5991382 -0.90965986 8800 526 0.28868972 -6.7159628 -6.595218 -0.876093 8900 528 0.31020216 -6.7162903 -6.5855707 -0.83193125 9000 530 0.31836275 -6.7171479 -6.5819939 -0.82093897 9100 532 0.32543293 -6.724167 -6.5850016 -0.7690143 9200 534 0.32644265 -6.7139575 -6.5733549 -0.86903096 9300 536 0.33050759 -6.7254715 -6.5821077 -0.94504522 9400 538 0.30372582 -6.7139931 -6.5813247 -0.91128612 9500 540 0.32943659 -6.7206223 -6.5757312 -0.87818439 9600 542 0.30911968 -6.708091 -6.5712114 -0.79092372 9700 544 0.33909826 -6.7222948 -6.5711342 -0.80266151 9800 546 0.29015141 -6.7086869 -6.5784908 -0.87763769 9900 548 0.33838474 -6.7384955 -6.5856667 -0.85630604 10000 550 0.30213198 -6.7338924 -6.5965597 -0.75738882 Loop time of 17.2852 on 1 procs for 10000 steps with 550 atoms Performance: 249924.414 tau/day, 578.529 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 | 9.637 | 9.637 | 9.637 | 0.0 | 55.75 Bond | 0.025444 | 0.025444 | 0.025444 | 0.0 | 0.15 Neigh | 4.6852 | 4.6852 | 4.6852 | 0.0 | 27.11 Comm | 0.65556 | 0.65556 | 0.65556 | 0.0 | 3.79 Output | 0.0099883 | 0.0099883 | 0.0099883 | 0.0 | 0.06 Modify | 2.1895 | 2.1895 | 2.1895 | 0.0 | 12.67 Other | | 0.08248 | | | 0.48 Nlocal: 550.000 ave 550 max 550 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2367.00 ave 2367 max 2367 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 36781.0 ave 36781 max 36781 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 36781 Ave neighs/atom = 66.874545 Ave special neighs/atom = 0.36363636 Neighbor list builds = 840 Dangerous builds = 0 Total wall time: 0:00:17