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 4 MPI processor grid region substrate block INF INF INF INF INF 3 create_atoms 1 region substrate Created 350 atoms create_atoms CPU = 0.139 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 = 0.006 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) = 5.255 | 5.852 | 6.302 Mbytes Step Atoms Temp E_pair TotEng Press 0 350 0 -6.9215833 -6.9215833 -1.0052629 100 352 1.0079368 -6.8946578 -6.8874992 -0.73775337 200 354 1.0081552 -6.8645575 -6.850318 -0.69629729 300 356 1.0085803 -6.821677 -6.8004288 -0.69532657 400 358 1.0099188 -6.7837923 -6.7555822 -0.68879568 500 360 1.0140221 -6.7446709 -6.7094618 -0.72991641 600 362 1.026146 -6.7129201 -6.6704003 -0.67063836 700 364 1.0683193 -6.6776523 -6.6262908 -0.65572472 800 366 1.0958893 -6.6402029 -6.5803182 -0.66307281 900 368 1.1231768 -6.6050912 -6.5364187 -0.64076928 1000 370 1.1976283 -6.5942507 -6.5133299 -0.69249019 1100 372 1.0506263 -6.5772313 -6.499564 -0.63072939 1200 374 0.93724351 -6.5732957 -6.4981157 -0.64963897 1300 376 0.93899686 -6.5578406 -6.4766773 -0.65096289 1400 378 0.8704974 -6.5468498 -6.4662482 -0.67613931 1500 380 0.84490693 -6.5401094 -6.4567304 -0.64385968 1600 382 0.9243154 -6.5611604 -6.4643734 -0.62096869 1700 384 0.67202953 -6.5590557 -6.4846775 -0.67807465 1800 386 0.8712464 -6.5654953 -6.4639251 -0.65860236 1900 388 0.70011668 -6.5808612 -6.495151 -0.65146463 2000 390 0.64019295 -6.5652168 -6.4831408 -0.70291888 2100 392 0.67578277 -6.5596196 -6.469113 -0.63315981 2200 394 0.60785287 -6.558941 -6.4740885 -0.7133822 2300 396 0.8155086 -6.5756022 -6.4571887 -0.69176417 2400 398 0.69028748 -6.5875474 -6.483484 -0.63743938 2500 400 0.5013913 -6.5871851 -6.5088427 -0.65872179 2600 402 0.51268385 -6.5782356 -6.495339 -0.74289067 2700 404 0.57745388 -6.5815718 -6.4850912 -0.67922914 2800 406 0.47317895 -6.5974978 -6.5159152 -0.64657562 2900 408 0.50593124 -6.6019054 -6.5120034 -0.64211427 3000 410 0.44423233 -6.5956684 -6.5144064 -0.66526127 3100 412 0.40808865 -6.5949863 -6.5182221 -0.62722445 3200 414 0.40692632 -6.5866689 -6.5080358 -0.76440608 3300 416 0.43908529 -6.5851721 -6.4980939 -0.69345883 3400 418 0.53825907 -6.5880076 -6.478553 -0.69726204 3500 420 0.46363057 -6.6135193 -6.5169296 -0.58015901 3600 422 0.39262699 -6.621857 -6.5381213 -0.74921264 3700 424 0.42679205 -6.6146579 -6.5215488 -0.69040431 3800 426 0.38997492 -6.6139725 -6.5270063 -0.78237667 3900 428 0.5222531 -6.6403886 -6.5214174 -0.78298122 4000 430 0.47841128 -6.6502681 -6.5390097 -0.68125967 4100 432 0.44609186 -6.6610827 -6.5552392 -0.81157037 4200 434 0.4591431 -6.6858064 -6.5747234 -0.79000753 4300 436 0.40690573 -6.6800195 -6.579693 -0.6781696 4400 438 0.43023944 -6.6849804 -6.5769294 -0.7620548 4500 440 0.40889421 -6.6783124 -6.5737656 -0.8577593 4600 442 0.41452051 -6.6968565 -6.5890061 -0.70427746 4700 444 0.36740394 -6.6920933 -6.5948636 -0.69303162 4800 446 0.40112316 -6.6869413 -6.5790158 -0.84792822 4900 448 0.42437165 -6.6789835 -6.5629444 -0.82278531 5000 450 0.41822898 -6.6770254 -6.5608507 -0.72224472 5100 452 0.38445688 -6.6738997 -6.5654522 -0.7022418 5200 454 0.39998238 -6.6670536 -6.5525212 -0.73639959 5300 456 0.39471029 -6.6728592 -6.5581681 -0.70419927 5400 458 0.35817807 -6.6702423 -6.5646658 -0.81657219 5500 460 0.37151428 -6.6690855 -6.558035 -0.78076653 5600 462 0.32642513 -6.6622352 -6.5633185 -0.69118644 5700 464 0.43665879 -6.6811227 -6.5470195 -0.77500043 5800 466 0.40704721 -6.6858874 -6.5592311 -0.72683597 5900 468 0.3861903 -6.6896953 -6.5679794 -0.78001958 6000 470 0.34073346 -6.6833717 -6.574627 -0.78170837 6100 472 0.39953874 -6.7083668 -6.5792785 -0.81791744 6200 474 0.36685189 -6.7114648 -6.5915027 -0.80545451 6300 476 0.35851799 -6.7261023 -6.607475 -0.77350495 6400 478 0.41771823 -6.7427425 -6.6029205 -0.85319003 6500 480 0.36519478 -6.732662 -6.6090284 -0.78712805 6600 482 0.30669571 -6.7269784 -6.6219892 -0.76698134 6700 484 0.3384344 -6.7261448 -6.6090213 -0.79935239 6800 486 0.36420902 -6.7320259 -6.6046277 -0.84650552 6900 488 0.40181215 -6.7490619 -6.6070279 -0.75753238 7000 490 0.30536068 -6.7398924 -6.6308351 -0.73210162 7100 492 0.28813004 -6.7257287 -6.6217794 -0.92178435 7200 494 0.30956277 -6.7342688 -6.6214727 -0.77532949 7300 496 0.36625115 -6.7528159 -6.6180561 -0.76247835 7400 498 0.30935271 -6.7401433 -6.6252231 -0.82809158 7500 500 0.33222282 -6.7410421 -6.6164585 -0.81948236 7600 502 0.33318693 -6.7488106 -6.622704 -0.82395904 7700 504 0.34570598 -6.7547394 -6.6226989 -0.85644369 7800 506 0.34587242 -6.7446006 -6.6113099 -0.82476511 7900 508 0.2969166 -6.7305429 -6.6151078 -0.8210214 8000 510 0.32355758 -6.7437629 -6.6168776 -0.81719054 8100 512 0.33784479 -6.7545537 -6.6209335 -0.78082067 8200 514 0.32351289 -6.7525032 -6.6234757 -0.87093587 8300 516 0.31900134 -6.7550972 -6.6268166 -0.79928704 8400 518 0.3338521 -6.7588757 -6.6235302 -0.81699503 8500 520 0.33115184 -6.7614854 -6.6261589 -0.79958489 8600 522 0.29478929 -6.7490188 -6.6276018 -0.81954456 8700 524 0.267993 -6.7467764 -6.6355389 -0.76642994 8800 526 0.28792085 -6.7527118 -6.6322887 -0.86911619 8900 528 0.32430992 -6.75901 -6.6223453 -0.87087898 9000 530 0.33151321 -6.7534845 -6.6127478 -0.79309499 9100 532 0.32760982 -6.7599992 -6.6199028 -0.7506309 9200 534 0.32579101 -6.7671489 -6.6268269 -0.94238755 9300 536 0.35144354 -6.7782581 -6.625813 -0.77952234 9400 538 0.33689976 -6.7804455 -6.6332867 -0.75768501 9500 540 0.3052486 -6.7745436 -6.6402908 -0.89621525 9600 542 0.30617581 -6.7648172 -6.6292412 -0.90623541 9700 544 0.30097715 -6.7714379 -6.6372707 -0.85534149 9800 546 0.31297479 -6.7814978 -6.6410604 -0.88651064 9900 548 0.31832347 -6.790661 -6.6468926 -1.006 10000 550 0.29239559 -6.7823137 -6.6494066 -1.0337518 Loop time of 34.7661 on 4 procs for 10000 steps with 550 atoms Performance: 124259.065 tau/day, 287.637 timesteps/s 73.4% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.0076709 | 3.1286 | 9.1834 | 211.7 | 9.00 Bond | 0.0040276 | 0.010416 | 0.022169 | 7.0 | 0.03 Neigh | 0.052413 | 1.5948 | 4.885 | 155.3 | 4.59 Comm | 4.9736 | 12.242 | 20.073 | 166.2 | 35.21 Output | 0.053549 | 0.10104 | 0.21642 | 21.0 | 0.29 Modify | 13.435 | 16.191 | 23.851 | 110.0 | 46.57 Other | | 1.499 | | | 4.31 Nlocal: 137.500 ave 299 max 2 min Histogram: 2 0 0 0 0 0 0 1 0 1 Nghost: 1898.75 ave 2679 max 524 min Histogram: 1 0 0 0 0 0 1 0 0 2 Neighs: 9204.00 ave 23014 max 0 min Histogram: 2 0 0 0 0 1 0 0 0 1 Total # of neighbors = 36816 Ave neighs/atom = 66.938182 Ave special neighs/atom = 0.36363636 Neighbor list builds = 832 Dangerous builds = 0 Total wall time: 0:00:34