forked from lijiext/lammps
179 lines
9.0 KiB
Groff
179 lines
9.0 KiB
Groff
LAMMPS (16 Dec 2013)
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# sample surface deposition script for atoms
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units lj
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atom_style atomic
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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 2 box
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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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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 1.0 1.0 0.1 587283
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fix 3 mobile nve
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region slab block 0 5 0 5 8 9
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fix 4 addatoms deposit 100 2 100 12345 region slab near 1.0 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
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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 image 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 = 2.19138 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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100 351 0.83994737 -6.3596932 -6.3561037 -0.10696131
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200 352 0.83994737 -6.3044678 -6.2973092 -0.38494392
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300 353 0.84063802 -6.164881 -6.1541646 -0.41223901
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400 354 0.84248131 -6.0388811 -6.0246018 -0.31496573
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500 355 0.84688124 -6.0084178 -5.990526 -0.37482638
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600 356 0.86681079 -6.0286531 -6.0067393 -0.54868509
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700 357 0.93465165 -5.9564751 -5.9289854 -0.48728319
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800 358 0.86905333 -5.8498868 -5.8207565 -0.4146325
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900 359 0.90267243 -5.7844092 -5.7504647 -0.38165702
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1000 360 0.92357983 -5.777549 -5.7390665 -0.38381524
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1100 361 1.3481334 -5.7713272 -5.7097089 -0.44738093
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1200 362 1.15494 -5.7155857 -5.6581577 -0.38961524
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1300 363 0.97329529 -5.6445379 -5.5922534 -0.37655267
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1400 364 1.2187161 -5.6818221 -5.6115115 -0.60238965
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1500 365 1.2026123 -5.66813 -5.5939963 -0.56317155
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1600 366 1.4012284 -5.6764268 -5.584543 -0.49098723
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1700 367 1.3618781 -5.6121414 -5.517515 -0.47893702
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1800 368 0.9670811 -5.5551479 -5.4841935 -0.3409573
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1900 369 1.002089 -5.6037307 -5.5263336 -0.45325785
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2000 370 1.3599868 -5.5793818 -5.4691126 -0.44566809
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2100 371 1.0007794 -5.585692 -5.5007201 -0.54221497
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2200 372 1.1061186 -5.5172266 -5.4191031 -0.46551394
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2300 373 0.99747295 -5.556485 -5.4642255 -0.55670261
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2400 374 1.0990417 -5.5538565 -5.4480664 -0.63197286
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2500 375 1.1415126 -5.5118583 -5.3977071 -0.515634
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2600 376 1.0106197 -5.5221131 -5.4172882 -0.54958102
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2700 377 1.0964027 -5.4985654 -5.3807821 -0.54044665
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2800 378 0.93035607 -5.4391662 -5.3357933 -0.52401636
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2900 379 0.93052107 -5.5146104 -5.4078092 -0.69426617
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3000 380 1.0256715 -5.4314645 -5.3100034 -0.55807748
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3100 381 1.1165704 -5.441198 -5.3049236 -0.67260986
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3200 382 1.0516479 -5.3743543 -5.2422101 -0.55726796
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3300 383 1.3015716 -5.393488 -5.2252692 -0.55526352
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3400 384 1.2021373 -5.4152522 -5.2555933 -0.63254327
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3500 385 1.0712229 -5.3875667 -5.2414908 -0.53868713
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3600 386 0.83109486 -5.3651207 -5.2488536 -0.65516002
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3700 387 0.91939065 -5.3500756 -5.218225 -0.6090015
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3800 388 1.1887187 -5.4422838 -5.2676524 -0.69893677
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3900 389 1.0816342 -5.3817634 -5.2191012 -0.58777145
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4000 390 0.85854697 -5.3988171 -5.2667329 -0.68550599
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4100 391 1.0028015 -5.3760402 -5.2183106 -0.61280389
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4200 392 1.1063074 -5.373048 -5.1952486 -0.69264824
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4300 393 0.94803569 -5.2768075 -5.1212139 -0.4968846
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4400 394 1.0358207 -5.2313016 -5.0577885 -0.47759843
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4500 395 0.99463555 -5.2840763 -5.1141069 -0.65377832
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4600 396 1.1336626 -5.2732108 -5.0756787 -0.68505207
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4700 397 1.043989 -5.3177843 -5.1323907 -0.66352488
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4800 398 1.1880124 -5.2919552 -5.0770384 -0.5760075
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4900 399 1.03793 -5.2870595 -5.0958618 -0.42225723
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5000 400 0.94525219 -5.3621262 -5.1848915 -0.57578045
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5100 401 1.0012033 -5.2951115 -5.1041089 -0.49619424
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5200 402 0.9093106 -5.323038 -5.1466046 -0.63808588
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5300 403 1.0780126 -5.3297725 -5.1171125 -0.54697182
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5400 404 1.1821134 -5.3408341 -5.1038263 -0.54142347
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5500 405 1.0861151 -5.3794714 -5.1582257 -0.62078287
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5600 406 0.99813873 -5.2575404 -5.051029 -0.46334991
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5700 407 1.0024386 -5.3416556 -5.1310696 -0.67522177
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5800 408 1.0499128 -5.2805967 -5.0567182 -0.51745165
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5900 409 1.0175995 -5.2346622 -5.0144725 -0.56525137
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6000 410 1.0580253 -5.3059195 -5.0736701 -0.72405837
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6100 411 1.0301092 -5.2456791 -5.0163483 -0.63734034
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6200 412 1.0936687 -5.2986069 -5.0517351 -0.65680297
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6300 413 1.1588036 -5.2889356 -5.0237856 -0.68692669
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6400 414 1.0738578 -5.2626417 -5.0136312 -0.61945759
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6500 415 1.0799598 -5.2267416 -4.9730161 -0.54000165
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6600 416 1.0654575 -5.2904664 -5.036908 -0.79867075
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6700 417 1.1409741 -5.2288709 -4.953888 -0.61287225
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6800 418 0.91721071 -5.2193327 -4.9955158 -0.67288058
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6900 419 0.99562084 -5.2164082 -4.9704732 -0.59995412
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7000 420 0.98493772 -5.1472091 -4.9009747 -0.5672666
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7100 421 1.1650853 -5.1686492 -4.8739186 -0.65830934
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7200 422 1.1058038 -5.1915304 -4.9085285 -0.71319305
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7300 423 1.0695793 -5.1082351 -4.8313581 -0.47793146
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7400 424 1.0205032 -5.1187042 -4.8515441 -0.45596744
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7500 425 1.0509541 -5.119854 -4.8416602 -0.53998089
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7600 426 0.94300051 -5.1572926 -4.9049403 -0.6117655
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7700 427 0.97832544 -5.1763299 -4.9117009 -0.76832421
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7800 428 0.99162405 -5.1076903 -4.8366155 -0.53958966
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7900 429 1.0777105 -5.1240548 -4.8263655 -0.63632393
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8000 430 1.0810155 -5.1582004 -4.8565216 -0.58803291
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8100 431 1.0168798 -5.1415512 -4.8548902 -0.59356121
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8200 432 1.1324612 -5.1323524 -4.8099155 -0.51666326
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8300 433 1.0225017 -5.1357067 -4.841708 -0.53308683
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8400 434 1.0938048 -5.1370091 -4.8194529 -0.50683321
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8500 435 0.98749809 -5.1760393 -4.8866002 -0.63777967
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8600 436 0.9696005 -5.1684071 -4.8815299 -0.60457804
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8700 437 1.1714664 -5.2563529 -4.9065214 -0.64901375
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8800 438 1.1068684 -5.1834342 -4.8498574 -0.448558
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8900 439 1.048918 -5.2496241 -4.9306479 -0.51509876
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9000 440 1.3045868 -5.2790483 -4.8787774 -0.63054863
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9100 441 1.1505177 -5.2631527 -4.90704 -0.60158373
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9200 442 1.0838443 -5.2358506 -4.8974558 -0.66026866
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9300 443 0.99074033 -5.1267153 -4.8147328 -0.36508529
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9400 444 1.120907 -5.2081858 -4.8522221 -0.70153485
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9500 445 1.1571034 -5.2002705 -4.8297374 -0.39376803
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9600 446 1.1427182 -5.1948759 -4.8259266 -0.50433867
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9700 447 1.1386351 -5.1960248 -4.8253953 -0.55647471
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9800 448 0.94339428 -5.1379682 -4.828417 -0.49931715
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9900 449 0.9187318 -5.1851142 -4.8812575 -0.5929999
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10000 450 1.1185411 -5.2444214 -4.8715743 -0.61322449
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Loop time of 4.76332 on 4 procs for 10000 steps with 450 atoms
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Pair time (%) = 0.82251 (17.2676)
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Neigh time (%) = 0.589647 (12.3789)
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Comm time (%) = 2.44321 (51.2921)
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Outpt time (%) = 0.011445 (0.240274)
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Other time (%) = 0.89651 (18.8211)
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Nlocal: 112.5 ave 250 max 5 min
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Histogram: 1 1 0 0 0 0 1 0 0 1
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Nghost: 1496 ave 2221 max 416 min
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Histogram: 1 0 0 0 1 0 0 0 1 1
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Neighs: 7344.75 ave 16734 max 4 min
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Histogram: 2 0 0 0 0 0 0 1 0 1
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Total # of neighbors = 29379
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Ave neighs/atom = 65.2867
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Neighbor list builds = 1150
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Dangerous builds = 0
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