211 lines
10 KiB
Groff
211 lines
10 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.shake
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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 shake 6
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fix 5 addatoms wall/reflect zhi EDGE
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fix 6 all shake 0.0001 20 1000 b 1 mol dimer
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0 = # of size 2 clusters
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0 = # of size 3 clusters
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0 = # of size 4 clusters
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0 = # of frozen angles
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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 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 tmp.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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SHAKE stats (type/ave/delta) on step 0
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Memory usage per processor = 3.36903 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 0.84041725 -6.7834986 -6.7553282 -0.68860028
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500 360 0.84183519 -6.7432451 -6.7081686 -0.72724802
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600 362 0.84576393 -6.714465 -6.6724104 -0.66535527
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700 364 0.8717559 -6.6683922 -6.6180986 -0.65401104
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800 366 0.8972223 -6.6397054 -6.5808712 -0.6644064
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900 368 0.89269075 -6.6040689 -6.5385725 -0.6293193
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SHAKE stats (type/ave/delta) on step 1000
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1 1 1.9984e-15
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1000 370 0.8729371 -6.5843837 -6.513605 -0.66197956
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1100 372 0.93342483 -6.5845128 -6.501709 -0.66278095
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1200 374 0.91864917 -6.5632239 -6.4747977 -0.66231969
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1300 376 0.88129406 -6.5508349 -6.4594241 -0.66330811
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1400 378 0.88948953 -6.5759309 -6.4770988 -0.65591838
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1500 380 0.66619538 -6.5716683 -6.4927768 -0.59010827
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1600 382 0.64223132 -6.5753954 -6.4946962 -0.64796777
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1700 384 0.71053601 -6.5931071 -6.498739 -0.71037238
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1800 386 0.54790722 -6.5681884 -6.4915382 -0.63518672
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1900 388 0.52085896 -6.5677463 -6.4912283 -0.67745991
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SHAKE stats (type/ave/delta) on step 2000
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1 1 2.22045e-15
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2000 390 0.53994531 -6.563133 -6.4800645 -0.70555161
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2100 392 0.64094961 -6.5675869 -6.4645772 -0.61019297
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2200 394 0.50620722 -6.5592797 -6.4744836 -0.63511891
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2300 396 0.6301209 -6.5760707 -6.4662769 -0.6545461
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2400 398 0.53704268 -6.5642828 -6.4671294 -0.68416557
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2500 400 0.64625918 -6.586831 -6.4656574 -0.68064342
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2600 402 0.45719634 -6.5878773 -6.4991676 -0.72641767
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2700 404 0.45430513 -6.5902202 -6.4991343 -0.64780429
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2800 406 0.39401639 -6.5731811 -6.4916604 -0.63232952
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2900 408 0.56403499 -6.5944647 -6.4741925 -0.66065801
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SHAKE stats (type/ave/delta) on step 3000
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1 1 1.88738e-15
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3000 410 0.42366175 -6.5762728 -6.4832739 -0.58419502
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3100 412 0.46961858 -6.597044 -6.4910379 -0.72500263
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3200 414 0.45608063 -6.579384 -6.4736262 -0.66491063
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3300 416 0.41525459 -6.6061269 -6.5073043 -0.7034034
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3400 418 0.34167228 -6.5966324 -6.5132578 -0.69889479
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3500 420 0.35438956 -6.5897102 -6.5011128 -0.69191247
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3600 422 0.371945 -6.587433 -6.4922433 -0.74209613
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3700 424 0.42415073 -6.5959033 -6.4848638 -0.70963735
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3800 426 0.41039811 -6.5821598 -6.4723349 -0.77667535
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3900 428 0.49077557 -6.6168589 -6.4826982 -0.73113384
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SHAKE stats (type/ave/delta) on step 4000
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1 1 2.10942e-15
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4000 430 0.40203105 -6.6345318 -6.5223371 -0.71969376
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4100 432 0.36787594 -6.6171373 -6.5123949 -0.76807348
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4200 434 0.3261302 -6.6032025 -6.5085195 -0.74955499
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4300 436 0.38926276 -6.6029583 -6.4877865 -0.72978015
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4400 438 0.41086026 -6.621007 -6.4971861 -0.68550032
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4500 440 0.3521118 -6.6242377 -6.5162034 -0.76756664
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4600 442 0.38603968 -6.6293115 -6.5087832 -0.74258268
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4700 444 0.34056733 -6.6415895 -6.5334364 -0.65780725
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4800 446 0.37197114 -6.6416079 -6.5215096 -0.82603673
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4900 448 0.30132362 -6.6363593 -6.5374874 -0.71862716
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SHAKE stats (type/ave/delta) on step 5000
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1 1 2.33147e-15
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5000 450 0.28288619 -6.6354525 -6.5411571 -0.77201855
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5100 452 0.26546305 -6.6297974 -6.5399393 -0.71006539
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5200 454 0.30926196 -6.6267464 -6.5204801 -0.81320777
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5300 456 0.32583739 -6.6465492 -6.5329349 -0.71621457
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5400 458 0.32161442 -6.6474216 -6.5336628 -0.71056186
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5500 460 0.34683164 -6.6587332 -6.5343262 -0.81507876
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5600 462 0.33207554 -6.6707235 -6.5499688 -0.76405763
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5700 464 0.30990462 -6.6765987 -6.5623882 -0.74469148
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5800 466 0.38115342 -6.7114459 -6.5691268 -0.76594753
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5900 468 0.3045191 -6.7224056 -6.6072349 -0.8010673
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SHAKE stats (type/ave/delta) on step 6000
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1 1 3.9968e-15
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6000 470 0.29295042 -6.7112692 -6.5990754 -0.87488246
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6100 472 0.28821962 -6.7201644 -6.6084183 -0.77836483
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6200 474 0.27856084 -6.7228536 -6.6135449 -0.84000894
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6300 476 0.27590056 -6.7303516 -6.6208028 -0.78812565
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6400 478 0.25075258 -6.7209969 -6.6202762 -0.78937406
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6500 480 0.2420497 -6.7100555 -6.6117228 -0.84935998
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6600 482 0.24559955 -6.7058717 -6.6049822 -0.73869936
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6700 484 0.26670092 -6.7106888 -6.5999308 -0.74058907
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6800 486 0.27972148 -6.7095837 -6.5921698 -0.85599188
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6900 488 0.27556092 -6.7181144 -6.6012268 -0.78080334
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SHAKE stats (type/ave/delta) on step 7000
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1 1 3.66374e-15
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7000 490 0.31988812 -6.7171565 -6.5800616 -0.79439098
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7100 492 0.28768419 -6.7050741 -6.5805279 -0.75103962
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7200 494 0.27446382 -6.6965124 -6.5765039 -0.7254846
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7300 496 0.27613579 -6.6951364 -6.5732136 -0.81917256
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7400 498 0.28716597 -6.6931216 -6.5651078 -0.83063101
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7500 500 0.29991456 -6.7065993 -6.5716377 -0.84995417
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7600 502 0.30054942 -6.7057164 -6.5692119 -0.82453964
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7700 504 0.33779908 -6.7355443 -6.5807197 -0.79378799
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7800 506 0.27918017 -6.7440838 -6.6149767 -0.80343537
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7900 508 0.27474528 -6.757924 -6.6297456 -0.9146801
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SHAKE stats (type/ave/delta) on step 8000
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1 1 3.21965e-15
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8000 510 0.27352726 -6.7606902 -6.6319715 -0.83056014
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8100 512 0.24483334 -6.7656728 -6.6494726 -0.81557302
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8200 514 0.26136253 -6.776203 -6.6511151 -0.93698626
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8300 516 0.22306201 -6.7512948 -6.6436544 -0.84185984
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8400 518 0.23781328 -6.7617152 -6.6460223 -0.92614518
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8500 520 0.26396807 -6.7687306 -6.6392847 -0.88122061
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8600 522 0.27813101 -6.7722102 -6.6347431 -0.86382754
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8700 524 0.28109538 -6.7747951 -6.6347838 -0.73669838
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8800 526 0.25374762 -6.7712592 -6.643903 -0.81383179
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8900 528 0.26572288 -6.7804903 -6.6461191 -0.88882544
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SHAKE stats (type/ave/delta) on step 9000
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1 1 2.55351e-15
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9000 530 0.23242437 -6.7530647 -6.6346599 -0.82067326
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9100 532 0.24597332 -6.7582807 -6.6320576 -0.89921536
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9200 534 0.23307655 -6.7540042 -6.6335377 -0.94279835
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9300 536 0.2252299 -6.7483888 -6.6311516 -0.72691575
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9400 538 0.24036406 -6.7561763 -6.6301862 -0.79108419
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9500 540 0.24443282 -6.7448693 -6.6158631 -0.89759125
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9600 542 0.21936118 -6.725477 -6.6089161 -0.81388326
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9700 544 0.24527855 -6.7404349 -6.6092289 -0.88469799
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9800 546 0.26358125 -6.746269 -6.6043407 -0.94325913
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9900 548 0.30133107 -6.7564789 -6.5931662 -0.95797751
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SHAKE stats (type/ave/delta) on step 10000
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1 1 2.77556e-15
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10000 550 0.24849941 -6.7407813 -6.6052361 -0.88843235
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Loop time of 6.0445 on 4 procs for 10000 steps with 550 atoms
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Pair time (%) = 1.0029 (16.5919)
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Bond time (%) = 0.0037064 (0.0613185)
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Neigh time (%) = 0.542864 (8.98112)
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Comm time (%) = 2.92824 (48.4448)
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Outpt time (%) = 0.00355923 (0.0588838)
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Other time (%) = 1.56323 (25.862)
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Nlocal: 137.5 ave 298 max 4 min
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Histogram: 2 0 0 0 0 0 0 1 0 1
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Nghost: 1913.75 ave 2692 max 538 min
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Histogram: 1 0 0 0 0 0 1 0 0 2
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Neighs: 9179.5 ave 22892 max 1 min
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Histogram: 2 0 0 0 0 1 0 0 0 1
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Total # of neighbors = 36718
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Ave neighs/atom = 66.76
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Ave special neighs/atom = 0.363636
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Neighbor list builds = 848
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Dangerous builds = 0
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