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 4 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 = 2.83497 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 -6.8946578 -6.8874992 -0.73775337
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200 354 0.83994737 -6.8644786 -6.8502422 -0.69623155
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300 356 0.83994737 -6.821588 -6.8003534 -0.69525265
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400 358 0.84042015 -6.783499 -6.7553282 -0.68860116
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500 360 0.84184269 -6.7432459 -6.7081686 -0.72724605
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600 362 0.8458127 -6.7144697 -6.6724104 -0.66535013
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700 364 0.87383242 -6.6725197 -6.6220566 -0.66071708
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800 366 0.87696132 -6.6413623 -6.5830213 -0.66927232
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900 368 0.89744792 -6.6071502 -6.5409657 -0.62868608
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1000 370 0.99832562 -6.591423 -6.509704 -0.68145874
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1100 372 0.83690497 -6.5836533 -6.5010396 -0.63926628
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1200 374 0.88380837 -6.5576129 -6.4700582 -0.6448691
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1300 376 0.93920197 -6.5480148 -6.4485844 -0.67509018
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1400 378 1.0819467 -6.5984857 -6.4753138 -0.62854894
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1500 380 0.72832384 -6.6161872 -6.5284826 -0.63429953
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1600 382 0.63213539 -6.5990997 -6.5150252 -0.67037851
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1700 384 0.5824052 -6.588541 -6.5069607 -0.69907025
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1800 386 0.72529167 -6.5843125 -6.478207 -0.62283149
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1900 388 0.57664201 -6.5677387 -6.4698656 -0.65451624
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2000 390 0.65546977 -6.5676639 -6.4578769 -0.67432025
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2100 392 0.69516646 -6.5858998 -6.4683877 -0.62289901
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2200 394 0.56654159 -6.583766 -6.4770207 -0.70102083
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2300 396 0.64110841 -6.598494 -6.4743096 -0.66950817
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2400 398 0.52329199 -6.6104218 -6.4917721 -0.69664414
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2500 400 0.55744613 -6.6221319 -6.4934736 -0.67790032
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2600 402 0.46920185 -6.6192179 -6.5005058 -0.6830418
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2700 404 0.56776413 -6.6299774 -6.4918044 -0.68598379
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2800 406 0.44695801 -6.6053321 -6.4845111 -0.60979234
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2900 408 0.51785351 -6.610722 -6.4741891 -0.62751234
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3000 410 0.58665518 -6.6389279 -6.4792835 -0.64022876
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3100 412 0.423824 -6.6194712 -6.4927699 -0.66450673
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3200 414 0.45133153 -6.6230652 -6.4839389 -0.74364185
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3300 416 0.51641116 -6.6567861 -6.49277 -0.64795831
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3400 418 0.47621669 -6.6912734 -6.531463 -0.71160352
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3500 420 0.38209486 -6.6823272 -6.5355428 -0.69351964
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3600 422 0.44576071 -6.6807448 -6.5147154 -0.74737153
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3700 424 0.41694154 -6.6822051 -6.5174366 -0.68130033
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3800 426 0.40975915 -6.7048899 -6.5360548 -0.72002151
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3900 428 0.48398461 -6.7282377 -6.5350708 -0.74439115
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4000 430 0.36367577 -6.7208528 -6.5534139 -0.63650412
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4100 432 0.34028562 -6.7242165 -6.5649615 -0.70137882
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4200 434 0.33582497 -6.722058 -6.5514851 -0.76135001
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4300 436 0.3825237 -6.7180169 -6.5381019 -0.70786373
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4400 438 0.52062671 -6.7481686 -6.5135064 -0.73624603
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4500 440 0.40436975 -6.7359486 -6.5304443 -0.79135494
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4600 442 0.44491445 -6.7486865 -6.5249583 -0.76722101
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4700 444 0.42190093 -6.7620999 -6.5568957 -0.68635283
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4800 446 0.43599741 -6.7597134 -6.5440627 -0.77969628
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4900 448 0.47851973 -6.7786447 -6.5458666 -0.74770553
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5000 450 0.36262781 -6.8254599 -6.6092673 -0.71317359
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5100 452 0.33856471 -6.8140502 -6.6072777 -0.70403037
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5200 454 0.39260588 -6.835737 -6.6062808 -0.79831143
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5300 456 0.31209864 -6.8230791 -6.6185118 -0.70136268
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5400 458 0.31219166 -6.8170389 -6.6118122 -0.75454291
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5500 460 0.33107044 -6.8102616 -6.5929746 -0.75347113
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5600 462 0.40659306 -6.8413513 -6.5940668 -0.71199073
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5700 464 0.35864173 -6.8618978 -6.6302942 -0.68000488
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5800 466 0.35595504 -6.8739057 -6.637045 -0.72726368
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5900 468 0.30133562 -6.8629749 -6.6404473 -0.79721111
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6000 470 0.32080099 -6.860886 -6.631765 -0.79848812
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6100 472 0.27961391 -6.8709022 -6.6465395 -0.71256878
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6200 474 0.31406154 -6.8829903 -6.6410549 -0.7089865
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6300 476 0.36004409 -6.9012979 -6.6442205 -0.77551843
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6400 478 0.32635204 -6.8936662 -6.6413458 -0.6682556
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6500 480 0.32068722 -6.8935855 -6.6453583 -0.7254097
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6600 482 0.32713469 -6.9215037 -6.6558734 -0.76984099
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6700 484 0.36721979 -6.9207471 -6.6473085 -0.75359037
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6800 486 0.38350491 -6.9354455 -6.6470817 -0.79067926
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6900 488 0.3250273 -6.9458853 -6.6769931 -0.67224329
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7000 490 0.32830721 -6.9469844 -6.6778539 -0.7619618
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7100 492 0.33730308 -6.9374197 -6.6588506 -0.78689069
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7200 494 0.30775449 -6.9609022 -6.6952452 -0.67621108
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7300 496 0.28573367 -6.9569147 -6.7028926 -0.67991253
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7400 498 0.28191768 -6.988469 -6.7220227 -0.87179721
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7500 500 0.31351279 -6.9987024 -6.7160563 -0.82937872
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7600 502 0.28969341 -7.0254266 -6.7316544 -0.77890838
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7700 504 0.28407599 -7.0337382 -6.7311947 -0.80238049
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7800 506 0.29761165 -7.0326028 -6.731669 -0.8371957
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7900 508 0.34677565 -7.0523551 -6.7260518 -0.8740631
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8000 510 0.3118165 -7.0626608 -6.7450993 -0.77834874
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8100 512 0.29761479 -7.0754729 -6.7620945 -0.74405688
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8200 514 0.30483577 -7.0905149 -6.7644188 -0.85441065
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8300 516 0.33684783 -7.1137001 -6.7534121 -0.82965734
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8400 518 0.27961357 -7.0957286 -6.7677311 -0.78630354
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8500 520 0.30612337 -7.1335883 -6.7809001 -0.83422091
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8600 522 0.29624122 -7.1270458 -6.7835376 -0.84386217
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8700 524 0.29657024 -7.1402335 -6.7844074 -0.69683349
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8800 526 0.3086498 -7.137074 -6.7768455 -0.80569969
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8900 528 0.26822775 -7.1262968 -6.7891397 -0.78344768
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9000 530 0.29595187 -7.1836398 -6.8037091 -0.80740794
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9100 532 0.27991165 -7.178976 -6.8079248 -0.71421566
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9200 534 0.27664216 -7.1784888 -6.8037579 -0.84396547
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9300 536 0.27879865 -7.2033389 -6.8100683 -0.64262205
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9400 538 0.28514769 -7.1987974 -6.8126137 -0.7018808
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9500 540 0.32951622 -7.2371185 -6.8151986 -0.88679168
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9600 542 0.35683108 -7.2746833 -6.821215 -0.81047037
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9700 544 0.29775774 -7.2584568 -6.8336125 -0.85576789
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9800 546 0.29002392 -7.2763888 -6.8501209 -0.81455861
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9900 548 0.31009857 -7.2950962 -6.852398 -0.93711055
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10000 550 0.28745157 -7.3035265 -6.8657121 -0.90926429
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Loop time of 5.64819 on 4 procs for 10000 steps with 550 atoms
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Pair time (%) = 1.02706 (18.1839)
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Bond time (%) = 0.00374371 (0.0662816)
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Neigh time (%) = 0.562528 (9.95945)
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Comm time (%) = 2.94816 (52.1966)
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Outpt time (%) = 0.0134226 (0.237645)
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Other time (%) = 1.09327 (19.3561)
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Nlocal: 137.5 ave 298 max 3 min
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Histogram: 2 0 0 0 0 0 0 1 0 1
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Nghost: 1917.25 ave 2722 max 455 min
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Histogram: 1 0 0 0 0 0 1 0 0 2
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Neighs: 9881.5 ave 24370 max 1 min
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Histogram: 2 0 0 0 0 0 1 0 0 1
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Total # of neighbors = 39526
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Ave neighs/atom = 71.8655
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Ave special neighs/atom = 0.363636
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Neighbor list builds = 879
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Dangerous builds = 0
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