forked from lijiext/lammps
185 lines
9.3 KiB
Groff
185 lines
9.3 KiB
Groff
LAMMPS (30 Dec 2013)
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# sample surface deposition script for molecules
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units lj
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atom_style bond
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boundary p p f
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lattice fcc 1.0
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Lattice spacing in x,y,z = 1.5874 1.5874 1.5874
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region box block 0 5 0 5 0 10
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create_box 3 box "bond types" 1 "extra bond per atom" 1
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Created orthogonal box = (0 0 0) to (7.93701 7.93701 15.874)
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1 by 1 by 1 MPI processor grid
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region substrate block INF INF INF INF INF 3
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create_atoms 1 region substrate
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Created 350 atoms
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pair_style lj/cut 2.5
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pair_coeff * * 1.0 1.0
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pair_coeff 1 2 1.0 1.0 5.0
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mass * 1.0
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bond_style harmonic
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bond_coeff 1 5.0 1.0
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neigh_modify delay 0
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group addatoms type 2
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0 atoms in group addatoms
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region mobile block 0 5 0 5 2 INF
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group mobile region mobile
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150 atoms in group mobile
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compute add addatoms temp
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compute_modify add dynamic yes extra 0
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fix 1 addatoms nve
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fix 2 mobile langevin 0.1 0.1 0.1 587283
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fix 3 mobile nve
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molecule dimer molecule.dimer
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region slab block 0 5 0 5 8 9
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fix 4 addatoms deposit 100 0 100 12345 region slab near 1.0 mol dimer vz -1.0 -1.0
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fix 5 addatoms wall/reflect zhi EDGE
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thermo_style custom step atoms temp epair etotal press
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thermo 100
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thermo_modify temp add lost/bond ignore lost warn
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WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:439)
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#dump 1 all atom 50 dump.deposit.atom
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#dump 1 all movie 50 image.*.jpg type type # axes yes 0.8 0.02 view 80 -30
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#dump_modify 1 pad 5
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#dump 1 all movie 50 movie.mpg type type # axes yes 0.8 0.02 view 80 -30
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#dump_modify 1 pad 5
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run 10000
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Memory usage per processor = 2.76078 Mbytes
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Step Atoms Temp E_pair TotEng Press
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0 350 0 -6.9215833 -6.9215833 -1.0052629
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100 352 0.83994737 -6.8875167 -6.8803581 -0.73353914
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200 354 0.83994737 -6.8593854 -6.845149 -0.70414703
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300 356 0.83994737 -6.8170634 -6.7958288 -0.69170868
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400 358 0.84042015 -6.7849768 -6.756806 -0.70352248
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500 360 0.84184269 -6.7489038 -6.7138265 -0.68386838
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600 362 0.84581137 -6.7098504 -6.6677911 -0.6828296
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700 364 0.87382946 -6.6715894 -6.6211265 -0.66625495
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800 366 0.87689746 -6.6396776 -6.5813408 -0.68710928
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900 368 0.89661715 -6.6072681 -6.5411455 -0.66320699
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1000 370 1.00676 -6.5947268 -6.512331 -0.68611219
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1100 372 0.86243824 -6.5866848 -6.5042223 -0.67174009
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1200 374 0.84425239 -6.5636281 -6.479445 -0.69383244
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1300 376 1.0078184 -6.550962 -6.4431087 -0.66633027
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1400 378 1.0391938 -6.5969765 -6.4778058 -0.56558987
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1500 380 0.74712353 -6.6166281 -6.5240793 -0.66003498
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1600 382 0.58302452 -6.5997567 -6.5184528 -0.67167612
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1700 384 0.56467802 -6.5776894 -6.4975516 -0.64668082
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1800 386 0.71825353 -6.5726227 -6.4691096 -0.65076646
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1900 388 0.53975986 -6.5613236 -6.4741837 -0.63639897
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2000 390 0.59341094 -6.5769909 -6.4682541 -0.65193031
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2100 392 0.68035001 -6.5827033 -6.4574143 -0.62788928
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2200 394 0.57776644 -6.589353 -6.4761586 -0.69498055
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2300 396 0.5318152 -6.5951551 -6.4885222 -0.60457555
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2400 398 0.49568196 -6.6007559 -6.4881834 -0.69316627
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2500 400 0.53409937 -6.6072399 -6.4763374 -0.69823432
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2600 402 0.45633292 -6.6332159 -6.5034387 -0.65145273
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2700 404 0.4892626 -6.6191003 -6.4911656 -0.66150699
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2800 406 0.4586448 -6.6101924 -6.4821935 -0.71952986
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2900 408 0.50133988 -6.6233932 -6.4820172 -0.69040381
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3000 410 0.49942448 -6.6353753 -6.4859797 -0.6737426
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3100 412 0.42190611 -6.6280489 -6.4885103 -0.71665975
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3200 414 0.41178932 -6.621106 -6.4868768 -0.70387051
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3300 416 0.46253061 -6.6361091 -6.4919436 -0.71264477
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3400 418 0.42181868 -6.6317908 -6.4923081 -0.66171467
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3500 420 0.41797099 -6.6287141 -6.4897821 -0.65879262
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3600 422 0.36509229 -6.6214108 -6.4915707 -0.70324811
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3700 424 0.39348534 -6.6179504 -6.4817297 -0.68426814
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3800 426 0.39474314 -6.6086782 -6.4636684 -0.71591333
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3900 428 0.45542305 -6.635636 -6.4706661 -0.68175206
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4000 430 0.39042908 -6.6488343 -6.500435 -0.66366199
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4100 432 0.39468368 -6.6585928 -6.49931 -0.76227835
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4200 434 0.41142379 -6.6557126 -6.4903949 -0.73380042
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4300 436 0.48160084 -6.6588571 -6.4749235 -0.71948887
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4400 438 0.55431951 -6.698039 -6.4754774 -0.68067319
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4500 440 0.4585125 -6.7096071 -6.5073393 -0.68190471
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4600 442 0.44221158 -6.7238275 -6.5235013 -0.72486537
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4700 444 0.3530253 -6.7116222 -6.5326725 -0.78475189
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4800 446 0.39053263 -6.7192087 -6.5305763 -0.7500161
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4900 448 0.39195928 -6.7304752 -6.5391648 -0.7414609
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5000 450 0.39808899 -6.7364876 -6.5449794 -0.68624334
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5100 452 0.40415767 -6.7520155 -6.5566586 -0.77799849
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5200 454 0.32066094 -6.7478767 -6.5677968 -0.70955786
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5300 456 0.3189586 -6.7748028 -6.5774312 -0.76013414
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5400 458 0.28680679 -6.754829 -6.57373 -0.75077874
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5500 460 0.3229394 -6.7693127 -6.565559 -0.76453959
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5600 462 0.39545678 -6.7962985 -6.5645492 -0.75110236
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5700 464 0.41518466 -6.8618036 -6.6026038 -0.79792247
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5800 466 0.41117489 -6.8979481 -6.6272973 -0.68505301
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5900 468 0.34391673 -6.8959897 -6.6377009 -0.67914717
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6000 470 0.30168814 -6.8907915 -6.643955 -0.79643615
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6100 472 0.30916205 -6.8885557 -6.6360589 -0.81599518
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6200 474 0.35424257 -6.8990909 -6.6305161 -0.75613637
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6300 476 0.35703296 -6.9174766 -6.6367178 -0.72950736
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6400 478 0.37445271 -6.9445085 -6.6442671 -0.69659454
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6500 480 0.329543 -6.9458858 -6.6609468 -0.75534893
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6600 482 0.33963739 -6.947355 -6.6559786 -0.86232494
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6700 484 0.34574376 -6.9518517 -6.6559314 -0.78159338
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6800 486 0.38169407 -6.9787425 -6.6545343 -0.69654215
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6900 488 0.36970486 -6.9727516 -6.6668784 -0.73296306
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7000 490 0.32030483 -6.9604688 -6.6704554 -0.79884199
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7100 492 0.34751955 -6.9885857 -6.6859115 -0.72531587
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7200 494 0.34236112 -7.0019964 -6.700804 -0.81526247
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7300 496 0.27559869 -7.0056964 -6.7192826 -0.77309778
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7400 498 0.31846741 -7.0236162 -6.7200064 -0.84787873
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7500 500 0.321674 -7.0382328 -6.7191195 -0.75690059
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7600 502 0.31379969 -7.0541204 -6.7245415 -0.84134932
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7700 504 0.33442098 -7.0824103 -6.7379709 -0.77808299
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7800 506 0.31650445 -7.1121677 -6.7680346 -0.78541215
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7900 508 0.30347752 -7.1100388 -6.7724658 -0.89260888
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8000 510 0.31695084 -7.121996 -6.7701485 -0.80026292
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8100 512 0.29991827 -7.133499 -6.779965 -0.77547985
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8200 514 0.32128068 -7.1588222 -6.7891361 -0.85855005
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8300 516 0.28103196 -7.1423077 -6.7970623 -0.76011418
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8400 518 0.27077784 -7.150974 -6.8102547 -0.8189845
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8500 520 0.29179445 -7.1717624 -6.8140245 -0.81319487
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8600 522 0.29543603 -7.1666027 -6.8067797 -0.87228723
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8700 524 0.27449088 -7.1899692 -6.824729 -0.86748792
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8800 526 0.28192057 -7.1737434 -6.8131045 -0.80681355
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8900 528 0.29164865 -7.1791336 -6.8042773 -0.83580175
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9000 530 0.3473538 -7.2167575 -6.8110439 -0.84061628
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9100 532 0.29792019 -7.211711 -6.8136015 -0.7023788
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9200 534 0.2856865 -7.2088408 -6.8221795 -0.89143929
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9300 536 0.27649993 -7.2299192 -6.8337365 -0.95862494
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9400 538 0.29410309 -7.243419 -6.8486336 -0.91099619
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9500 540 0.29981454 -7.2655451 -6.8556167 -0.79314135
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9600 542 0.2972807 -7.2726656 -6.8578775 -0.77556553
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9700 544 0.27946124 -7.2703884 -6.8622493 -0.78651169
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9800 546 0.29668633 -7.2869601 -6.8663987 -0.86233713
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9900 548 0.27596387 -7.2922319 -6.8749679 -0.78008994
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10000 550 0.29155875 -7.2941724 -6.8764764 -0.76577583
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Loop time of 6.55461 on 1 procs for 10000 steps with 550 atoms
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Pair time (%) = 4.01151 (61.2013)
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Bond time (%) = 0.0117879 (0.179841)
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Neigh time (%) = 2.16259 (32.9935)
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Comm time (%) = 0.187663 (2.86307)
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Outpt time (%) = 0.000994444 (0.0151717)
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Other time (%) = 0.18006 (2.74707)
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Nlocal: 550 ave 550 max 550 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 2375 ave 2375 max 2375 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 39585 ave 39585 max 39585 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 39585
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Ave neighs/atom = 71.9727
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Ave special neighs/atom = 0.363636
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Neighbor list builds = 885
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Dangerous builds = 0
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