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lammps/examples/deposit/log.5Oct16.deposit.molecule.g++.4
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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 4 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 = 3.63985 Mbytes
Step Atoms Temp E_pair TotEng Press
0 350 0 -6.9215833 -6.9215833 -1.0052629
100 352 0.83994737 -6.8946578 -6.8874992 -0.73775337
200 354 0.83994737 -6.8644786 -6.8502422 -0.69623155
300 356 0.84169616 -6.8219435 -6.800657 -0.69554978
400 358 0.84705847 -6.7754627 -6.7470538 -0.67243811
500 360 0.87562973 -6.7314753 -6.6949361 -0.6950742
600 362 0.89546097 -6.710162 -6.6652463 -0.65981803
700 364 0.86924248 -6.6786002 -6.6276742 -0.66815906
800 366 0.93005193 -6.6524743 -6.5893578 -0.67112658
900 368 1.0019234 -6.6197846 -6.5442728 -0.63787501
1000 370 1.0088277 -6.5761382 -6.4929294 -0.68476387
1100 372 0.95920389 -6.5674754 -6.4791094 -0.6514881
1200 374 1.0580798 -6.5939034 -6.4854936 -0.64868897
1300 376 0.86424162 -6.5983754 -6.5057565 -0.63699331
1400 378 0.67483283 -6.5902961 -6.5114402 -0.65492911
1500 380 0.75360589 -6.5780719 -6.4817845 -0.68120797
1600 382 0.72620352 -6.569806 -6.4764019 -0.66989877
1700 384 0.70645024 -6.5716163 -6.4726668 -0.6613115
1800 386 0.69881235 -6.5763765 -6.4705405 -0.63092971
1900 388 0.55849097 -6.5759885 -6.4828798 -0.66382981
2000 390 0.61872265 -6.5695935 -6.4699984 -0.71796632
2100 392 0.5081592 -6.5617458 -6.4722443 -0.63479779
2200 394 0.48384274 -6.549079 -6.4615149 -0.66946296
2300 396 0.58288701 -6.5480033 -6.4412303 -0.71651424
2400 398 0.64008255 -6.5601944 -6.435487 -0.69102232
2500 400 0.69425764 -6.5828171 -6.4479527 -0.69066043
2600 402 0.64360746 -6.6331402 -6.4757801 -0.69090309
2700 404 0.49461099 -6.6579388 -6.5307976 -0.64409671
2800 406 0.55547146 -6.6714068 -6.5241964 -0.68541724
2900 408 0.50073205 -6.686261 -6.5339011 -0.62669192
3000 410 0.53038544 -6.6912316 -6.5383759 -0.66969696
3100 412 0.50129241 -6.7018519 -6.5548588 -0.68883024
3200 414 0.38030632 -6.6977772 -6.566269 -0.71750777
3300 416 0.46068514 -6.727184 -6.5662475 -0.68188023
3400 418 0.33822772 -6.7360772 -6.6016113 -0.72454552
3500 420 0.36453111 -6.724924 -6.5850647 -0.64608093
3600 422 0.36002968 -6.7121585 -6.5780413 -0.72223399
3700 424 0.36475294 -6.7260042 -6.5866143 -0.67031145
3800 426 0.36718557 -6.7217602 -6.5750235 -0.72937729
3900 428 0.37814959 -6.7263989 -6.5726951 -0.71591892
4000 430 0.40806996 -6.7375374 -6.5678266 -0.72678943
4100 432 0.38045271 -6.7361841 -6.568644 -0.73821367
4200 434 0.33066806 -6.7299457 -6.57638 -0.73722947
4300 436 0.41794011 -6.7644169 -6.579351 -0.73641289
4400 438 0.37024397 -6.7629482 -6.5884866 -0.71240322
4500 440 0.40320567 -6.7752853 -6.5850469 -0.77279245
4600 442 0.35772381 -6.7835099 -6.6013018 -0.73636644
4700 444 0.3651311 -6.7990539 -6.6175275 -0.66854139
4800 446 0.35091135 -6.802215 -6.6224615 -0.76162889
4900 448 0.36081012 -6.7989512 -6.6125569 -0.76016221
5000 450 0.31623339 -6.8039093 -6.6262913 -0.69115281
5100 452 0.31543867 -6.7941532 -6.6159299 -0.72205584
5200 454 0.36158004 -6.8038417 -6.5978895 -0.76776475
5300 456 0.32434144 -6.793123 -6.6082355 -0.72624243
5400 458 0.32124677 -6.793797 -6.6010261 -0.67741044
5500 460 0.32879658 -6.8125027 -6.6145418 -0.77045881
5600 462 0.33544185 -6.8282158 -6.6181936 -0.82298638
5700 464 0.31929648 -6.8312019 -6.617542 -0.77506457
5800 466 0.38513813 -6.8569307 -6.6094667 -0.72432147
5900 468 0.36275508 -6.8784065 -6.6183826 -0.71794686
6000 470 0.36550412 -6.8913174 -6.6280912 -0.73323549
6100 472 0.31989948 -6.8850192 -6.653122 -0.770755
6200 474 0.31533478 -6.8764261 -6.6470078 -0.81602846
6300 476 0.33764472 -6.9058038 -6.6574918 -0.70233823
6400 478 0.33629492 -6.9384728 -6.6676899 -0.750356
6500 480 0.329134 -6.9539905 -6.6660118 -0.76780643
6600 482 0.35893902 -6.9727388 -6.6687914 -0.79588633
6700 484 0.35256839 -6.980576 -6.6800042 -0.67119736
6800 486 0.3498406 -6.9854977 -6.6867156 -0.78135658
6900 488 0.31757914 -6.9609817 -6.6859771 -0.78048643
7000 490 0.40129918 -6.9903536 -6.6713072 -0.75727925
7100 492 0.33833658 -7.0145206 -6.6977622 -0.7587661
7200 494 0.35160231 -7.0237931 -6.7095634 -0.67933941
7300 496 0.28084778 -7.024433 -6.7195845 -0.82825025
7400 498 0.32213221 -7.0527945 -6.7230557 -0.84919299
7500 500 0.40905237 -7.1021905 -6.7203497 -0.93185466
7600 502 0.3609358 -7.1596615 -6.7690359 -0.64194099
7700 504 0.29253629 -7.1428432 -6.796613 -0.6976599
7800 506 0.31731365 -7.176045 -6.8068169 -0.87636485
7900 508 0.2905957 -7.1788367 -6.8119013 -0.75756081
8000 510 0.28404368 -7.1870361 -6.824287 -0.79842667
8100 512 0.34219804 -7.222691 -6.8386818 -0.75369138
8200 514 0.32055193 -7.2353127 -6.8551345 -0.78172901
8300 516 0.30120879 -7.2446887 -6.8672024 -0.83621194
8400 518 0.30883515 -7.2596909 -6.8762796 -0.71183282
8500 520 0.26204254 -7.2431895 -6.8834311 -0.83712537
8600 522 0.29103293 -7.2694658 -6.8867581 -0.82744948
8700 524 0.26753583 -7.2593959 -6.889244 -0.78004892
8800 526 0.26521096 -7.2599673 -6.8902608 -0.79408301
8900 528 0.28003646 -7.2530274 -6.8808417 -0.8606495
9000 530 0.26313192 -7.2628164 -6.8855381 -0.7707451
9100 532 0.2646514 -7.2830171 -6.893178 -0.76585646
9200 534 0.27846656 -7.2721664 -6.8861564 -0.89816607
9300 536 0.30560594 -7.2964254 -6.8845198 -0.72034116
9400 538 0.29262217 -7.3023252 -6.8913192 -0.62961985
9500 540 0.29718418 -7.3048523 -6.8949946 -0.87394403
9600 542 0.34146099 -7.349026 -6.9092212 -0.76789895
9700 544 0.28703519 -7.3161372 -6.9121067 -0.84885733
9800 546 0.28129876 -7.3140275 -6.9098746 -0.82726219
9900 548 0.28891495 -7.3235633 -6.9092268 -0.88128702
10000 550 0.29861445 -7.3507915 -6.9161229 -0.73192335
Loop time of 5.59197 on 4 procs for 10000 steps with 550 atoms
Performance: 772536.289 tau/day, 1788.278 timesteps/s
98.4% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0012441 | 1.0454 | 2.9987 | 119.8 | 18.70
Bond | 0.0012348 | 0.0039268 | 0.010973 | 6.5 | 0.07
Neigh | 0.0049584 | 0.57381 | 1.8059 | 96.8 | 10.26
Comm | 0.62167 | 2.892 | 5.0562 | 98.9 | 51.72
Output | 0.0021472 | 0.014835 | 0.048822 | 16.2 | 0.27
Modify | 0.0069871 | 0.038206 | 0.074167 | 15.4 | 0.68
Other | | 1.024 | | | 18.31
Nlocal: 137.5 ave 299 max 2 min
Histogram: 2 0 0 0 0 0 0 1 0 1
Nghost: 1866.25 ave 2673 max 377 min
Histogram: 1 0 0 0 0 0 1 0 0 2
Neighs: 9891 ave 24535 max 0 min
Histogram: 2 0 0 0 0 0 1 0 0 1
Total # of neighbors = 39564
Ave neighs/atom = 71.9345
Ave special neighs/atom = 0.363636
Neighbor list builds = 884
Dangerous builds = 0
Total wall time: 0:00:05
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