219 lines
11 KiB
Groff
219 lines
11 KiB
Groff
LAMMPS (10 Mar 2021)
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using 1 OpenMP thread(s) per MPI task
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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 = 1.5874011 1.5874011 1.5874011
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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 = (0.0000000 0.0000000 0.0000000) to (7.9370053 7.9370053 15.874011)
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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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create_atoms CPU = 0.001 seconds
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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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molecule dimer molecule.dimer
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Read molecule template dimer:
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1 molecules
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2 atoms with max type 3
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1 bonds with max type 1
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0 angles with max type 0
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0 dihedrals with max type 0
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0 impropers with max type 0
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region slab block 0 5 0 5 8 9
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group addatoms empty
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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/dof yes extra/dof 0
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fix 1 addatoms rigid/nvt/small molecule temp 0.1 0.1 0.1 mol dimer
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create bodies CPU = 0.000 seconds
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0 rigid bodies with 0 atoms
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1.0000000 = max distance from body owner to body atom
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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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fix 4 addatoms deposit 100 0 100 12345 region slab near 1.0 mol dimer vz -1.0 -1.0 rigid 1
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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 (src/thermo.cpp:468)
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#dump 1 all atom 50 dump.deposit.atom
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#dump 2 all image 50 image.*.jpg type type # axes yes 0.8 0.02 view 80 -30
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#dump_modify 2 pad 5
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#dump 3 all movie 50 tmp.mpg type type # axes yes 0.8 0.02 view 80 -30
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#dump_modify 3 pad 5
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run 10000
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WARNING: Should not allow rigid bodies to bounce off relecting walls (src/fix_wall_reflect.cpp:182)
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Neighbor list info ...
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update every 1 steps, delay 0 steps, check yes
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 5.3
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ghost atom cutoff = 5.3
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binsize = 2.65, bins = 3 3 6
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1 neighbor lists, perpetual/occasional/extra = 1 0 0
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(1) pair lj/cut, perpetual
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attributes: half, newton on
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pair build: half/bin/newton
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stencil: half/bin/3d/newton
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bin: standard
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Per MPI rank memory allocation (min/avg/max) = 5.929 | 5.929 | 5.929 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 1.0079368 -6.8875167 -6.8803581 -0.73353914
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200 354 1.0081552 -6.8594643 -6.8452248 -0.70421276
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300 356 1.0085803 -6.8171524 -6.7959042 -0.6917826
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400 358 1.0099188 -6.7852701 -6.7570601 -0.70371699
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500 360 1.0140221 -6.7493429 -6.7141338 -0.68415307
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600 362 1.026148 -6.7105231 -6.6680032 -0.68314418
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700 364 1.0683344 -6.6725162 -6.621154 -0.65747369
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800 366 1.0958953 -6.6412275 -6.5813425 -0.68789615
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900 368 1.1250034 -6.6101882 -6.541404 -0.66674346
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1000 370 1.2326365 -6.5993719 -6.5160856 -0.69688655
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1100 372 1.1397444 -6.5912865 -6.5070312 -0.6333041
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1200 374 1.0514447 -6.5905753 -6.5062348 -0.71020272
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1300 376 1.0033284 -6.5747792 -6.4880554 -0.65459641
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1400 378 0.82996548 -6.5681806 -6.4913319 -0.60438595
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1500 380 0.90239071 -6.5752982 -6.4862465 -0.66528503
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1600 382 0.86403681 -6.5692212 -6.4787461 -0.65027922
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1700 384 0.64748046 -6.5644242 -6.4927629 -0.63046709
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1800 386 0.74288742 -6.5515741 -6.4649681 -0.67770665
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1900 388 0.72584537 -6.5565195 -6.4676596 -0.66175025
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2000 390 0.73351281 -6.5631154 -6.4690753 -0.64686647
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2100 392 0.76490681 -6.5573734 -6.4549305 -0.68861526
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2200 394 0.65926638 -6.5511574 -6.4591279 -0.71726284
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2300 396 0.70267414 -6.5728555 -6.4708258 -0.64360436
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2400 398 0.60523691 -6.5845973 -6.4933555 -0.63956839
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2500 400 0.5103586 -6.5812006 -6.5014571 -0.68698448
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2600 402 0.52401744 -6.6003358 -6.5156066 -0.68987222
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2700 404 0.46421291 -6.5662747 -6.4887143 -0.72872856
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2800 406 0.48254258 -6.5724266 -6.4892296 -0.75447872
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2900 408 0.53073083 -6.5809842 -6.4866754 -0.67592283
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3000 410 0.55314547 -6.5922077 -6.4910226 -0.74646953
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3100 412 0.47150308 -6.5907273 -6.5020344 -0.64994935
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3200 414 0.43047803 -6.5836315 -6.5004473 -0.79764713
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3300 416 0.46289353 -6.5739439 -6.4821441 -0.76441674
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3400 418 0.59724106 -6.5980575 -6.4766089 -0.73735626
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3500 420 0.43571285 -6.5955972 -6.5048237 -0.64145941
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3600 422 0.42461639 -6.6060271 -6.5154691 -0.70124484
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3700 424 0.44323254 -6.6059723 -6.5092766 -0.74498147
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3800 426 0.4037907 -6.592043 -6.5019958 -0.72171799
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3900 428 0.41668443 -6.5975302 -6.5026079 -0.68327878
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4000 430 0.44895183 -6.5958671 -6.4914597 -0.73939433
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4100 432 0.39798052 -6.5952115 -6.5007833 -0.74871822
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4200 434 0.45156734 -6.6237274 -6.5144772 -0.75111778
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4300 436 0.48297356 -6.6395283 -6.5204465 -0.76105913
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4400 438 0.43595234 -6.6347133 -6.5252276 -0.72858275
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4500 440 0.44683726 -6.6385398 -6.5242916 -0.74280051
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4600 442 0.47875512 -6.6419903 -6.5174274 -0.75579572
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4700 444 0.43972605 -6.6406078 -6.5242388 -0.72196509
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4800 446 0.43572615 -6.6495404 -6.5323047 -0.7135049
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4900 448 0.38063437 -6.6432385 -6.5391588 -0.77087429
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5000 450 0.4239223 -6.6617795 -6.5440233 -0.784531
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5100 452 0.37201988 -6.6581813 -6.5532421 -0.74611403
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5200 454 0.41765777 -6.6661321 -6.5465385 -0.75422239
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5300 456 0.38015287 -6.6606624 -6.5502013 -0.78866702
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5400 458 0.40549607 -6.6807118 -6.5611878 -0.78932883
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5500 460 0.34444407 -6.6720564 -6.5690976 -0.77859171
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5600 462 0.36572308 -6.6730078 -6.5621827 -0.85672419
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5700 464 0.40055073 -6.6976989 -6.574685 -0.74251563
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5800 466 0.36037213 -6.7022014 -6.5900685 -0.66239625
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5900 468 0.32810921 -6.6952135 -6.591803 -0.83981757
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6000 470 0.35110886 -6.6986862 -6.5866302 -0.82474047
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6100 472 0.29965884 -6.6839503 -6.5871326 -0.7864913
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6200 474 0.32402637 -6.6902745 -6.5843165 -0.74531083
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6300 476 0.35042653 -6.6990084 -6.5830585 -0.74839967
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6400 478 0.32695511 -6.6909459 -6.5815048 -0.76549489
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6500 480 0.35209088 -6.6902987 -6.5711013 -0.71281516
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6600 482 0.354106 -6.6890268 -6.567808 -0.81897158
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6700 484 0.3504816 -6.681739 -6.5604463 -0.811609
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6800 486 0.37396733 -6.7018369 -6.5710253 -0.80383296
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6900 488 0.36435774 -6.7010114 -6.5722169 -0.72063651
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7000 490 0.35631012 -6.7089806 -6.581727 -0.74152078
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7100 492 0.37646659 -6.719154 -6.5833352 -0.77739001
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7200 494 0.36546269 -6.7223269 -6.5891623 -0.8288767
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7300 496 0.37688206 -6.7457243 -6.607053 -0.80062121
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7400 498 0.30331409 -6.7284953 -6.6158184 -0.79894584
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7500 500 0.30382936 -6.7333804 -6.6194444 -0.86924602
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7600 502 0.30163143 -6.7294737 -6.6153104 -0.7689497
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7700 504 0.30281215 -6.7233976 -6.6077402 -0.8557548
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7800 506 0.33378009 -6.7244958 -6.5958651 -0.82584084
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7900 508 0.31843128 -6.7250998 -6.6013002 -0.82424684
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8000 510 0.35912946 -6.7399052 -6.5990701 -0.81879575
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8100 512 0.31405017 -6.733487 -6.6092777 -0.72940457
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8200 514 0.30475 -6.7271485 -6.6056043 -0.87958287
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8300 516 0.30717434 -6.7277574 -6.6042329 -0.81700937
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8400 518 0.33032462 -6.7382165 -6.6043011 -0.75436496
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8500 520 0.32218568 -6.7351971 -6.6035347 -0.77661738
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8600 522 0.30922651 -6.7275431 -6.6001797 -0.85334327
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8700 524 0.30728021 -6.7237477 -6.5962029 -0.94977016
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8800 526 0.31061903 -6.7181672 -6.5882505 -0.86132456
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8900 528 0.33543344 -6.728929 -6.5875768 -0.87545919
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9000 530 0.31887735 -6.7265066 -6.5911341 -0.76892061
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9100 532 0.31888326 -6.7216274 -6.5852629 -0.83190298
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9200 534 0.33310892 -6.7111349 -6.567661 -0.94282671
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9300 536 0.34737171 -6.722515 -6.5718361 -0.95235602
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9400 538 0.32752858 -6.7246204 -6.5815549 -0.86227131
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9500 540 0.30665764 -6.7225391 -6.5876665 -0.87144326
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9600 542 0.32747382 -6.7149245 -6.5699176 -0.86863105
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9700 544 0.32463079 -6.7205757 -6.5758643 -0.85393932
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9800 546 0.31517825 -6.7178961 -6.5764699 -0.81017759
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9900 548 0.33649933 -6.7380644 -6.5860871 -0.80769312
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10000 550 0.37394555 -6.7612874 -6.5913121 -0.82102213
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Loop time of 16.6615 on 1 procs for 10000 steps with 550 atoms
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Performance: 259279.806 tau/day, 600.185 timesteps/s
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99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
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MPI task timing breakdown:
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Section | min time | avg time | max time |%varavg| %total
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---------------------------------------------------------------
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Pair | 9.2639 | 9.2639 | 9.2639 | 0.0 | 55.60
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Bond | 0.021559 | 0.021559 | 0.021559 | 0.0 | 0.13
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Neigh | 4.544 | 4.544 | 4.544 | 0.0 | 27.27
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Comm | 0.62792 | 0.62792 | 0.62792 | 0.0 | 3.77
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Output | 0.0069666 | 0.0069666 | 0.0069666 | 0.0 | 0.04
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Modify | 2.1282 | 2.1282 | 2.1282 | 0.0 | 12.77
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Other | | 0.06897 | | | 0.41
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Nlocal: 550.000 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: 2344.00 ave 2344 max 2344 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 36607.0 ave 36607 max 36607 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 36607
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Ave neighs/atom = 66.558182
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Ave special neighs/atom = 0.36363636
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Neighbor list builds = 847
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Dangerous builds = 0
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Total wall time: 0:00:16
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