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lammps/examples/deposit/log.deposit.molecule.17Dec13.linux.1
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LAMMPS (16 Dec 2013)
# 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
region slab block 0 5 0 5 8 9
fix 4 addatoms deposit 100 2 100 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:439)
#dump 1 all atom 50 dump.deposit.atom
#dump 1 all movie 50 image.*.jpg type type # axes yes 0.8 0.02 view 80 -30
#dump_modify 1 pad 5
#dump 1 all movie 50 movie.mpg type type # axes yes 0.8 0.02 view 80 -30
#dump_modify 1 pad 5
run 10000
Memory usage per processor = 2.761 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 0.83994737 -6.8170634 -6.7958288 -0.69170868
400 358 0.84042015 -6.7849768 -6.756806 -0.70352248
500 360 0.84184269 -6.7489038 -6.7138265 -0.68386838
600 362 0.84581252 -6.7098504 -6.667791 -0.68282962
700 364 0.87383402 -6.6715895 -6.6211263 -0.66625521
800 366 0.87700584 -6.6397294 -6.5813855 -0.68714738
900 368 0.89799284 -6.6074178 -6.5411933 -0.6633197
1000 370 0.95083484 -6.5900376 -6.5110576 -0.69572146
1100 372 0.82985799 -6.5796732 -6.5020171 -0.64680951
1200 374 0.85651845 -6.569056 -6.4832041 -0.68799376
1300 376 0.95704327 -6.5541436 -6.446087 -0.68860769
1400 378 0.99164463 -6.5980098 -6.4811236 -0.57034819
1500 380 0.77250737 -6.6076789 -6.5065665 -0.6404344
1600 382 0.64450542 -6.5925431 -6.4979083 -0.67080474
1700 384 0.59174558 -6.570604 -6.4836042 -0.63920736
1800 386 0.68425339 -6.570226 -6.4656269 -0.65233974
1900 388 0.62329345 -6.5635189 -6.4650127 -0.63792408
2000 390 0.68456891 -6.5689788 -6.4521732 -0.65509823
2100 392 0.67321061 -6.5811717 -6.4500318 -0.65425662
2200 394 0.54478143 -6.5824499 -6.4589679 -0.69489133
2300 396 0.7025569 -6.6028441 -6.4506792 -0.64336994
2400 398 0.52296791 -6.5865304 -6.4590029 -0.66244621
2500 400 0.51361748 -6.5952192 -6.4571287 -0.73142772
2600 402 0.56909773 -6.6329678 -6.4745546 -0.68833191
2700 404 0.47316324 -6.6191013 -6.4797191 -0.68529766
2800 406 0.4024784 -6.5932129 -6.4753576 -0.72859927
2900 408 0.47244328 -6.5871757 -6.453229 -0.70781408
3000 410 0.46719857 -6.5875097 -6.4597457 -0.72630704
3100 412 0.53920664 -6.6146383 -6.4453004 -0.71086513
3200 414 0.48131175 -6.6451928 -6.4749523 -0.69309105
3300 416 0.41250886 -6.6284687 -6.4822569 -0.74495454
3400 418 0.4434617 -6.6469432 -6.4852748 -0.67332297
3500 420 0.41557109 -6.6594512 -6.4906766 -0.67511353
3600 422 0.42683402 -6.6822906 -6.5032101 -0.71730208
3700 424 0.40725472 -6.6999266 -6.5091665 -0.66350769
3800 426 0.46233068 -6.6939398 -6.4972405 -0.77367408
3900 428 0.46559823 -6.7209898 -6.5128889 -0.65590187
4000 430 0.40285904 -6.7463651 -6.5425884 -0.69952343
4100 432 0.41660438 -6.7760035 -6.5559126 -0.76829413
4200 434 0.3629958 -6.7769429 -6.5539205 -0.71514525
4300 436 0.43292832 -6.7723248 -6.5349078 -0.72086327
4400 438 0.48031456 -6.7909542 -6.5399856 -0.69055364
4500 440 0.43514381 -6.816345 -6.5668484 -0.64504209
4600 442 0.42216902 -6.8369302 -6.5912992 -0.64124177
4700 444 0.35593175 -6.8269085 -6.5961629 -0.75319222
4800 446 0.37281022 -6.8544574 -6.608371 -0.74800751
4900 448 0.38378226 -6.8650757 -6.6074728 -0.71830366
5000 450 0.35692176 -6.8758194 -6.6221425 -0.7445901
5100 452 0.4095119 -6.8844748 -6.6209625 -0.72430291
5200 454 0.36077122 -6.8707148 -6.6227241 -0.71794836
5300 456 0.32219928 -6.8715464 -6.6320277 -0.72291054
5400 458 0.31616802 -6.8698226 -6.6333157 -0.74720215
5500 460 0.31786106 -6.872068 -6.6308287 -0.80360394
5600 462 0.37015248 -6.8956604 -6.6240251 -0.73210594
5700 464 0.3534065 -6.9088566 -6.6327609 -0.71453932
5800 466 0.33251725 -6.9070782 -6.641467 -0.68201092
5900 468 0.30410425 -6.9075384 -6.6426114 -0.72551088
6000 470 0.30851479 -6.8970992 -6.6383198 -0.79668941
6100 472 0.31983822 -6.8935456 -6.6343679 -0.80093887
6200 474 0.34046679 -6.9033232 -6.6366444 -0.60584348
6300 476 0.34341 -6.9228112 -6.6519685 -0.71926688
6400 478 0.34850659 -6.9401172 -6.654428 -0.67959231
6500 480 0.32905065 -6.9511765 -6.6672014 -0.75953777
6600 482 0.34907767 -6.9596072 -6.6681567 -0.88241294
6700 484 0.35028194 -6.9653815 -6.6710713 -0.78275064
6800 486 0.35051323 -6.969352 -6.6763765 -0.66893758
6900 488 0.36217701 -6.9868033 -6.6759619 -0.72513293
7000 490 0.32291745 -6.9917249 -6.6925637 -0.74768371
7100 492 0.30809063 -6.9870686 -6.7043983 -0.73169721
7200 494 0.29851506 -6.9982183 -6.7077915 -0.8299932
7300 496 0.26179616 -6.9846023 -6.7127008 -0.77318
7400 498 0.29514008 -7.0132716 -6.7075934 -0.75316322
7500 500 0.3135944 -7.0285572 -6.7115419 -0.78914193
7600 502 0.30198119 -7.0431055 -6.7121603 -0.7265163
7700 504 0.32873608 -7.0693396 -6.7082228 -0.81872378
7800 506 0.32477424 -7.0818561 -6.7212948 -0.75793697
7900 508 0.31922052 -7.1059386 -6.7389868 -0.8543698
8000 510 0.28136655 -7.1067254 -6.7459867 -0.83979756
8100 512 0.29278742 -7.1165141 -6.7510805 -0.8241496
8200 514 0.33282329 -7.1327987 -6.7472492 -0.84438285
8300 516 0.31127854 -7.1410039 -6.7529902 -0.75630712
8400 518 0.28319374 -7.1327512 -6.7707492 -0.77390852
8500 520 0.32016512 -7.1697563 -6.7823027 -0.82592367
8600 522 0.32447805 -7.1674565 -6.7749588 -0.84309705
8700 524 0.2887839 -7.1818676 -6.7859966 -0.7609437
8800 526 0.30555242 -7.2166233 -6.8001973 -0.70067115
8900 528 0.3443468 -7.2376029 -6.7979364 -0.82279495
9000 530 0.30995579 -7.2506269 -6.8126325 -0.78972208
9100 532 0.30548349 -7.2637762 -6.80996 -0.7147236
9200 534 0.27799866 -7.2455264 -6.8191946 -0.87999072
9300 536 0.31062978 -7.2754833 -6.8217503 -0.84995092
9400 538 0.3169359 -7.2912363 -6.8367367 -0.87666495
9500 540 0.29095311 -7.302781 -6.8411527 -0.7819709
9600 542 0.31893318 -7.3077289 -6.8358361 -0.78035337
9700 544 0.33737303 -7.3293865 -6.8465864 -0.8238632
9800 546 0.31835531 -7.3291308 -6.8519745 -0.77631405
9900 548 0.31244715 -7.3722703 -6.8756185 -0.82478125
10000 550 0.3025952 -7.3985931 -6.8904785 -0.88208948
Loop time of 6.59022 on 1 procs for 10000 steps with 550 atoms
Pair time (%) = 4.02228 (61.0341)
Bond time (%) = 0.0115879 (0.175834)
Neigh time (%) = 2.18644 (33.177)
Comm time (%) = 0.188319 (2.85755)
Outpt time (%) = 0.00100374 (0.0152308)
Other time (%) = 0.180595 (2.74034)
Nlocal: 550 ave 550 max 550 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 2357 ave 2357 max 2357 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 39728 ave 39728 max 39728 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 39728
Ave neighs/atom = 72.2327
Ave special neighs/atom = 0.363636
Neighbor list builds = 893
Dangerous builds = 0
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