LAMMPS (27 Nov 2018) 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 = 1.5874 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 4 MPI processor grid region substrate block INF INF INF INF INF 3 create_atoms 1 region substrate Created 350 atoms Time spent = 0.000810623 secs 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/dof yes extra/dof 0 fix 1 addatoms nve fix 2 mobile langevin 0.1 0.1 0.1 587283 fix 3 mobile nve molecule dimer molecule.dimer.shake Read molecule dimer: 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 fix 4 addatoms deposit 100 0 100 12345 region slab near 1.0 mol dimer vz -1.0 -1.0 shake 6 fix 5 addatoms wall/reflect zhi EDGE fix 6 all shake 0.0001 20 1000 b 1 mol dimer 0 = # of size 2 clusters 0 = # of size 3 clusters 0 = # of size 4 clusters 0 = # of frozen angles 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:488) #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 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 SHAKE stats (type/ave/delta) on step 0 Per MPI rank memory allocation (min/avg/max) = 0.4411 | 3.816 | 5.101 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 1.0079368 -6.8644786 -6.8502422 -0.69623155 300 356 1.0098741 -6.8219324 -6.800657 -0.69552497 400 358 1.015821 -6.775427 -6.7470521 -0.67240912 500 360 1.0431742 -6.7311558 -6.6949345 -0.69505765 600 362 1.0978772 -6.7107816 -6.6652895 -0.66124338 700 364 1.0536993 -6.6818292 -6.6311706 -0.67789771 800 366 1.0615655 -6.6354474 -6.5774383 -0.64710621 900 368 1.1688557 -6.614281 -6.5428156 -0.64842218 SHAKE stats (type/ave/delta) on step 1000 1 1 1.22125e-15 1000 370 1.2172009 -6.5772424 -6.4949991 -0.67942188 1100 372 1.1031034 -6.55895 -6.4774034 -0.65896897 1200 374 1.040192 -6.5874108 -6.503973 -0.62919433 1300 376 0.94890463 -6.5897148 -6.5076952 -0.63346087 1400 378 0.78945672 -6.5952649 -6.522167 -0.67613271 1500 380 0.82876461 -6.5798609 -6.4980749 -0.65306056 1600 382 0.73883758 -6.5591084 -6.4817432 -0.62749488 1700 384 0.73539709 -6.5556021 -6.4742105 -0.66817567 1800 386 0.67455206 -6.5535874 -6.474948 -0.57721026 1900 388 0.66352723 -6.5469905 -6.4657597 -0.69276627 SHAKE stats (type/ave/delta) on step 2000 1 1 2.22045e-15 2000 390 0.81013116 -6.5567994 -6.4529364 -0.71579948 2100 392 0.72889872 -6.5689128 -6.4712924 -0.65504494 2200 394 0.57901901 -6.552299 -6.4714715 -0.67723953 2300 396 0.59157803 -6.5485081 -6.4626098 -0.66397554 2400 398 0.70712699 -6.5593644 -6.4527623 -0.70641253 2500 400 0.7569242 -6.576119 -6.4578496 -0.69907756 2600 402 0.6662505 -6.6038869 -6.4961599 -0.66941055 2700 404 0.51455113 -6.6038412 -6.5178704 -0.69578494 2800 406 0.58401979 -6.6058664 -6.5051733 -0.70647457 2900 408 0.50129416 -6.6138934 -6.5248154 -0.64390758 SHAKE stats (type/ave/delta) on step 3000 1 1 2.66454e-15 3000 410 0.44807689 -6.6222658 -6.5403005 -0.68340233 3100 412 0.45962393 -6.6204312 -6.5339728 -0.66309459 3200 414 0.50182826 -6.6295842 -6.5326126 -0.74122586 3300 416 0.48471205 -6.6424495 -6.5463227 -0.69764601 3400 418 0.36856546 -6.6251783 -6.5502308 -0.76543921 3500 420 0.4203509 -6.6198957 -6.5323226 -0.64154608 3600 422 0.54795097 -6.6410801 -6.5242185 -0.7463818 3700 424 0.51183952 -6.6521145 -6.5404514 -0.70304908 3800 426 0.39414561 -6.6456807 -6.5577844 -0.74178922 3900 428 0.40589341 -6.6564647 -6.5640007 -0.78327027 SHAKE stats (type/ave/delta) on step 4000 1 1 1.88738e-15 4000 430 0.43166847 -6.6566443 -6.5562563 -0.73290988 4100 432 0.40408931 -6.6500622 -6.5541845 -0.73057986 4200 434 0.35377187 -6.6356255 -6.5500355 -0.76557381 4300 436 0.4291929 -6.657321 -6.5514993 -0.78608144 4400 438 0.43151668 -6.6494979 -6.5411262 -0.70820395 4500 440 0.44315446 -6.6596739 -6.5463674 -0.82000058 4600 442 0.41285261 -6.6553044 -6.547888 -0.76115447 4700 444 0.38354616 -6.6502515 -6.54875 -0.6954286 4800 446 0.39108666 -6.648355 -6.5431299 -0.72779836 4900 448 0.3799768 -6.6517925 -6.5478926 -0.79771549 SHAKE stats (type/ave/delta) on step 5000 1 1 3.10862e-15 5000 450 0.39260452 -6.6598567 -6.5507999 -0.76677324 5100 452 0.41475009 -6.6627963 -6.5458038 -0.70468384 5200 454 0.4115583 -6.6658575 -6.5480104 -0.78115993 5300 456 0.3753641 -6.6631393 -6.5540696 -0.78711192 5400 458 0.36565536 -6.6545908 -6.5468103 -0.74549556 5500 460 0.33271655 -6.6418893 -6.542436 -0.76780862 5600 462 0.36832168 -6.6440805 -6.5324679 -0.75143503 5700 464 0.39059076 -6.6481163 -6.5281612 -0.78380485 5800 466 0.36650802 -6.6430337 -6.5289916 -0.75502025 5900 468 0.35914314 -6.6418801 -6.5286886 -0.67704807 SHAKE stats (type/ave/delta) on step 6000 1 1 2.22045e-15 6000 470 0.39116517 -6.6612874 -6.5364474 -0.84800605 6100 472 0.38421704 -6.6693489 -6.545211 -0.78734456 6200 474 0.38216918 -6.6812774 -6.5563065 -0.81814647 6300 476 0.34722048 -6.6730701 -6.5581809 -0.77616674 6400 478 0.32907391 -6.6719973 -6.5618471 -0.7458085 6500 480 0.31094699 -6.6715976 -6.566329 -0.83282406 6600 482 0.35169592 -6.6680323 -6.5476384 -0.85138473 6700 484 0.36350925 -6.6706468 -6.5448456 -0.71970784 6800 486 0.38133383 -6.6922722 -6.5588839 -0.77339402 6900 488 0.34810579 -6.6746177 -6.551568 -0.77360649 SHAKE stats (type/ave/delta) on step 7000 1 1 3.66374e-15 7000 490 0.3590117 -6.683101 -6.5548825 -0.80004574 7100 492 0.38269726 -6.688913 -6.5508464 -0.81445922 7200 494 0.31934554 -6.6944357 -6.578075 -0.74069497 7300 496 0.32758627 -6.6955862 -6.5750529 -0.78679117 7400 498 0.3660502 -6.7111626 -6.5751801 -0.78104263 7500 500 0.32569889 -6.6953555 -6.5732185 -0.74496853 7600 502 0.33737271 -6.6971694 -6.5694785 -0.90240288 7700 504 0.35222518 -6.7006509 -6.5661204 -0.86220892 7800 506 0.31834385 -6.6988433 -6.5761614 -0.78723443 7900 508 0.35977076 -6.7264843 -6.5866128 -0.8568963 SHAKE stats (type/ave/delta) on step 8000 1 1 2.22045e-15 8000 510 0.35931856 -6.7266146 -6.5857054 -0.85544232 8100 512 0.36797798 -6.739034 -6.5934958 -0.82062699 8200 514 0.40277035 -6.7571847 -6.5965467 -0.82121365 8300 516 0.32568144 -6.7419653 -6.6109984 -0.78580816 8400 518 0.33705466 -6.7532799 -6.6166361 -0.83332745 8500 520 0.30158673 -6.7342587 -6.6110142 -0.8578352 8600 522 0.32525112 -6.7446972 -6.6107336 -0.96759 8700 524 0.32985772 -6.7480971 -6.611181 -0.78464535 8800 526 0.32397396 -6.7465569 -6.6110545 -0.81041129 8900 528 0.33669589 -6.7543874 -6.6125032 -0.87866197 SHAKE stats (type/ave/delta) on step 9000 1 1 3.88578e-15 9000 530 0.32538398 -6.7436298 -6.6054951 -0.79985713 9100 532 0.3336509 -6.7541485 -6.6114688 -0.84449566 9200 534 0.31516122 -6.7553334 -6.6195898 -0.88997909 9300 536 0.30963064 -6.7627673 -6.6284593 -0.75349544 9400 538 0.34228518 -6.7754099 -6.6258988 -0.77001741 9500 540 0.29032769 -6.7737667 -6.6460763 -0.85854407 9600 542 0.31033087 -6.7764458 -6.63903 -0.8553105 9700 544 0.33657054 -6.7798228 -6.629789 -0.91356823 9800 546 0.30235172 -6.7634263 -6.6277557 -0.92787364 9900 548 0.3446797 -6.7794717 -6.6237998 -0.88766558 SHAKE stats (type/ave/delta) on step 10000 1 1 2.55351e-15 10000 550 0.30296128 -6.7756768 -6.6379672 -0.84420968 Loop time of 6.71355 on 4 procs for 10000 steps with 550 atoms Performance: 643474.692 tau/day, 1489.525 timesteps/s 95.0% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.0023715 | 1.0684 | 3.1403 | 123.9 | 15.91 Bond | 0.0018587 | 0.0045958 | 0.011149 | 5.6 | 0.07 Neigh | 0.0059454 | 0.74298 | 2.4218 | 114.9 | 11.07 Comm | 0.53191 | 3.1926 | 5.7443 | 113.9 | 47.55 Output | 0.0028977 | 0.0060919 | 0.010627 | 4.2 | 0.09 Modify | 0.47242 | 1.5021 | 4.1679 | 126.1 | 22.37 Other | | 0.1969 | | | 2.93 Nlocal: 137.5 ave 300 max 2 min Histogram: 2 0 0 0 0 0 0 1 0 1 Nghost: 1874.5 ave 2648 max 509 min Histogram: 1 0 0 0 0 0 1 0 0 2 Neighs: 9185.75 ave 23231 max 0 min Histogram: 2 0 0 0 0 1 0 0 0 1 Total # of neighbors = 36743 Ave neighs/atom = 66.8055 Ave special neighs/atom = 0.363636 Neighbor list builds = 833 Dangerous builds = 0 Total wall time: 0:00:06