adf4a23f58
- replace file reader code using TextFileReader and ValueTokenizer - replace traversing list of fixes with accessor functions - enable and apply clang-format - add examples for reading rigid bodies from file
330 lines
19 KiB
Groff
330 lines
19 KiB
Groff
LAMMPS (17 Feb 2022)
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OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
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using 1 OpenMP thread(s) per MPI task
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# Simple rigid body system
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units lj
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atom_style atomic
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pair_style lj/cut 2.5
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read_data data.rigid
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Reading data file ...
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orthogonal box = (-12 -12 -12) to (12 12 12)
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1 by 2 by 2 MPI processor grid
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reading atoms ...
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81 atoms
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read_data CPU = 0.000 seconds
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velocity all create 100.0 4928459
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# 2 chains of connected bodies
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group clump1 id <> 1 9
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9 atoms in group clump1
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group clump2 id <> 9 18
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10 atoms in group clump2
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group clump3 id <> 18 27
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10 atoms in group clump3
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group clump4 id <> 27 36
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10 atoms in group clump4
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group clump5 id <> 37 45
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9 atoms in group clump5
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group clump6 id <> 45 54
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10 atoms in group clump6
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group clump7 id <> 54 63
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10 atoms in group clump7
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group clump8 id <> 63 72
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10 atoms in group clump8
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group clump9 id <> 72 81
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10 atoms in group clump9
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fix 1 all poems file connected-bodies2.dat
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2 clusters, 9 bodies, 7 joints, 81 atoms
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neigh_modify exclude group clump1 clump1
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neigh_modify exclude group clump2 clump2
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neigh_modify exclude group clump3 clump3
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neigh_modify exclude group clump4 clump4
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neigh_modify exclude group clump5 clump5
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neigh_modify exclude group clump6 clump6
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neigh_modify exclude group clump7 clump7
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neigh_modify exclude group clump8 clump8
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neigh_modify exclude group clump9 clump9
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thermo 100
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#dump 1 all atom 50 dump.rigid.poems
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#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
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#dump_modify 2 pad 5
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#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
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#dump_modify 3 pad 5
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timestep 0.0001
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thermo 50
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run 10000
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CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
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Your simulation uses code contributions which should be cited:
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- fix poems command:
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@Article{Mukherjee08,
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author = {R. M. Mukherjee, P. S. Crozier, S. J. Plimpton, K. S. Anderson},
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title = {Substructured molecular dynamics using multibody dynamics algorithms},
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journal = {Intl.~J.~Non-linear Mechanics},
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year = 2008,
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volume = 43,
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pages = {1045--1055}
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}
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CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
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generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
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Neighbor list info ...
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update every 1 steps, delay 10 steps, check yes
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 2.8
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ghost atom cutoff = 2.8
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binsize = 1.4, bins = 18 18 18
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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/atomonly/newton
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stencil: half/bin/3d
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bin: standard
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Per MPI rank memory allocation (min/avg/max) = 3.514 | 3.545 | 3.639 Mbytes
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Step Temp E_pair E_mol TotEng Press
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0 196.00047 3632.2347 0 3668.5311 -2.7403788
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50 12774.759 1538.7382 0 3904.4344 18.086358
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100 19803.641 237.21132 0 3904.5523 -3.1528278
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150 20259.6 152.62072 0 3904.3985 -4.6173524
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200 20705.978 69.977039 0 3904.4174 9.0928122
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250 19552.211 283.50525 0 3904.285 15.670466
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300 19266.324 333.5792 0 3901.4169 7.2119197
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350 20738.325 63.738945 0 3904.1694 -23.03999
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400 20616.682 86.082444 0 3903.9864 -13.783584
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450 19831.326 230.13858 0 3902.6063 0.42074361
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500 20365.825 131.47271 0 3902.9217 0.69215592
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550 20794.102 52.163238 0 3902.9229 4.5895354
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600 20853.873 40.899172 0 3902.7275 2.3593042
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650 19255.802 336.29509 0 3902.1844 10.341742
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700 18526.969 471.02462 0 3901.9448 -0.61898691
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750 18960.662 391.26068 0 3902.4944 12.04731
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800 20142.432 172.05197 0 3902.1319 4.6838632
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850 19932.48 210.71175 0 3901.9118 3.4716031
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900 20243.528 153.13972 0 3901.9411 3.6490762
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950 20388.132 126.88722 0 3902.4671 -4.4518463
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1000 20076.333 184.61915 0 3902.4586 -2.272315
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1050 20859.506 39.696993 0 3902.5684 6.45166
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1100 15284.661 1072.1908 0 3902.6836 21.194042
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1150 19658.317 261.99809 0 3902.4272 -2.8744219
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1200 20767.681 56.717095 0 3902.5839 -34.817444
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1250 20625.583 82.586198 0 3902.1386 11.697328
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1300 20690.013 71.006478 0 3902.4903 -29.29278
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1350 20936.019 26.022786 0 3903.0634 1.0316025
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1400 19753.56 244.81784 0 3902.8844 6.7138497
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1450 15690.149 998.34213 0 3903.9252 48.124569
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1500 20234.455 155.92516 0 3903.0465 13.172207
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1550 20779.631 55.063019 0 3903.1428 -2.6390455
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1600 20642.753 80.233821 0 3902.9659 -2.4688431
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1650 18785.698 423.90364 0 3902.7365 -5.6466892
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1700 20965.076 20.760451 0 3903.182 -0.45366172
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1750 18935.412 396.95958 0 3903.5173 25.913174
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1800 20581.554 91.757912 0 3903.1567 3.8218442
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1850 20616.949 85.184789 0 3903.1382 4.1907933
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1900 16601.896 828.43849 0 3902.8638 -0.49468175
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1950 20175.564 166.52646 0 3902.7421 5.6035728
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2000 20262.525 150.28224 0 3902.6017 -1.1967705
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2050 20168.994 167.65314 0 3902.6521 -0.80723928
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2100 19810.955 232.96524 0 3901.6605 3.1936531
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2150 20667.232 75.645145 0 3902.9103 0.54812734
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2200 19863.772 224.34646 0 3902.8228 7.9294465
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2250 18808.943 419.2084 0 3902.3461 14.344526
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2300 20573.665 92.761842 0 3902.6999 -6.7671703
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2350 19075.104 369.95414 0 3902.3809 -9.5353568
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2400 20273.873 148.53775 0 3902.9586 -1.93796
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2450 20087.769 182.30216 0 3902.2593 2.131796
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2500 20711.602 67.530554 0 3903.0124 2.6280244
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2550 19971.224 204.75926 0 3903.134 3.1760522
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2600 20620.084 85.027145 0 3903.5612 -0.92888063
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2650 19737.546 248.65474 0 3903.7559 -3.3218688
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2700 20650.724 79.522243 0 3903.7303 -7.5918025
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2750 19863.245 225.2505 0 3903.6292 9.2140221
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2800 18992.457 386.73547 0 3903.8572 2.6244537
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2850 18703.899 440.48356 0 3904.1685 14.561348
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2900 17939.805 581.74599 0 3903.932 -8.0863089
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2950 20867.516 39.38186 0 3903.7367 3.0985423
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3000 19767.994 242.8847 0 3903.6243 1.5943109
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3050 20397.448 126.31591 0 3903.6212 -0.14982775
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3100 20978.114 19.126395 0 3903.9623 -9.6797253
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3150 18303.556 513.8514 0 3903.3989 4.5940322
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3200 19156.505 356.46608 0 3903.9671 10.071308
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3250 17484.205 666.52199 0 3904.3377 -4.1641768
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3300 18069.94 557.75947 0 3904.0447 11.868707
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3350 20855.645 41.964632 0 3904.1212 5.4186293
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3400 18011.986 568.76255 0 3904.3155 25.262783
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3450 18669.69 446.92755 0 3904.2776 -4.194499
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3500 20248.799 154.22147 0 3903.9991 3.9211572
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3550 20226.024 158.64726 0 3904.2072 1.5299114
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3600 20267.02 151.25631 0 3904.4082 -8.9821729
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3650 20522.946 103.65382 0 3904.1994 -14.433796
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3700 20892.319 35.294614 0 3904.2426 -21.264596
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3750 19942.202 211.02993 0 3904.0304 -1.6428817
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3800 20421.678 122.08118 0 3903.8734 1.7137935
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3850 17899.53 588.82593 0 3903.5536 -24.450276
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3900 20721.119 66.486999 0 3903.7312 -7.1772088
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3950 20946.484 24.799445 0 3903.778 -0.4028037
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4000 20985.362 17.608355 0 3903.7865 4.7522266
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4050 19969.779 205.46466 0 3903.5719 18.941639
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4100 20479.578 110.56561 0 3903.08 2.3715952
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4150 18110.701 549.53348 0 3903.367 1.133321
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4200 19321.098 325.58216 0 3903.5634 -3.7574942
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4250 20734.436 63.87616 0 3903.5865 0.48350623
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4300 19446.823 302.1727 0 3903.4362 4.0462392
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4350 20494.669 108.1918 0 3903.501 2.9789077
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4400 20379.244 129.61413 0 3903.5482 4.0881089
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4450 19710.564 253.4251 0 3903.5295 5.3334683
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4500 20744.753 61.785082 0 3903.406 4.0015409
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4550 19948.024 208.76984 0 3902.8484 2.705423
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4600 18367.368 502.69569 0 3904.0602 21.476471
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4650 20559.367 96.133242 0 3903.4234 2.2549454
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4700 20940.135 25.547808 0 3903.3505 -8.9042666
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4750 20128.703 175.82088 0 3903.3584 -8.1450176
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4800 20632.27 82.543887 0 3903.3347 -0.55649542
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4850 19864.539 224.63792 0 3903.2563 7.1553461
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4900 19332.037 323.15561 0 3903.1625 17.020214
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4950 19055.575 373.68069 0 3902.4908 10.149457
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5000 20219.484 159.21383 0 3903.5627 3.1806346
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5050 17557.761 652.32864 0 3903.7659 10.733736
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5100 20615.337 85.795304 0 3903.4503 -3.6035636
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5150 20759.853 59.155843 0 3903.573 2.0152286
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5200 20082.007 184.39375 0 3903.2839 -5.3745109
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5250 18689.521 442.59842 0 3903.6208 -9.8911164
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5300 20038.496 192.34221 0 3903.1749 -2.1437039
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5350 19897.455 218.70142 0 3903.4154 0.64582116
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5400 18732.385 434.21543 0 3903.1755 12.98676
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5450 19831.487 230.79099 0 3903.2886 11.439958
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5500 20079.89 184.6953 0 3903.1935 4.0906279
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5550 20453.497 115.47128 0 3903.1559 7.8844436
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5600 16673.041 815.52661 0 3903.1267 -20.17797
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5650 19691.378 256.6412 0 3903.1928 3.7103317
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5700 20345.743 135.29997 0 3903.0302 5.6373816
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5750 20769.613 56.906603 0 3903.1312 -17.564762
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5800 20713.369 67.38314 0 3903.1922 -5.340631
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5850 20799.947 51.348865 0 3903.1909 -2.7827653
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5900 19581.933 273.51588 0 3899.7997 12.347375
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5950 20444.438 116.909 0 3902.9161 -0.74896654
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6000 18970.948 389.99664 0 3903.1352 26.642912
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6050 19414.753 307.13217 0 3902.4568 25.86316
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6100 20780.042 54.586474 0 3902.7424 1.5387425
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6150 20885.872 35.091585 0 3902.8456 -8.251884
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6200 19825.81 231.40943 0 3902.8558 6.7196589
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6250 20578.278 92.255994 0 3903.0481 -5.9647091
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6300 20093.43 181.8699 0 3902.8754 -9.9906069
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6350 20605.294 87.180289 0 3902.9755 -3.5643876
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6400 19737.257 247.84828 0 3902.8958 -4.2783347
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6450 19884.717 220.81633 0 3903.1714 3.8758905
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6500 18719.372 436.94802 0 3903.4984 1.7865904
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6550 20096.883 181.63346 0 3903.2784 2.395512
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6600 20888.673 35.003062 0 3903.2758 2.7728947
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6650 20437.85 118.16373 0 3902.9507 8.1456757
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6700 19241.051 339.73065 0 3902.8882 13.740454
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6750 20407.542 123.94326 0 3903.1177 7.6285942
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6800 20536.785 99.976706 0 3903.0851 8.3496632
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6850 20625.328 83.579677 0 3903.0849 6.5074992
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6900 20705.37 68.944625 0 3903.2724 3.1905177
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6950 18872.424 408.67134 0 3903.5647 6.2638845
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7000 20072.762 186.18051 0 3903.3586 -22.780407
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7050 20461.879 114.07495 0 3903.3117 -11.495523
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7100 19811.566 234.50237 0 3903.3108 1.1212695
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7150 20742.918 61.884088 0 3903.1651 -3.7907508
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7200 20911.192 30.599903 0 3903.0429 -7.0262304
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7250 20879.755 36.30274 0 3902.9241 -5.8018787
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7300 20682.32 72.703261 0 3902.7626 -3.3446789
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7350 19401.046 309.70672 0 3902.493 3.4836528
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7400 20220.542 157.83897 0 3902.3838 2.3400031
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7450 17691.193 625.47764 0 3901.6244 25.239568
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7500 19745.294 245.02566 0 3901.5615 5.3622843
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7550 19685.719 256.70983 0 3902.2133 3.4560563
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7600 18830.192 415.10021 0 3902.1727 -0.10282681
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7650 19613.136 270.18979 0 3902.2521 8.2241536
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7700 20989.015 15.636879 0 3902.4915 1.2955204
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7750 20301.583 142.90625 0 3902.4586 0.12548373
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7800 18360.147 502.50342 0 3902.5307 17.117272
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7850 20796.478 51.032537 0 3902.2321 -3.0993883
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7900 20284.267 145.64296 0 3901.9887 -1.2682383
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7950 20280.983 146.13471 0 3901.8723 3.5999841
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8000 20915.869 28.730821 0 3902.0399 2.4987291
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8050 20745.162 60.19981 0 3901.8964 4.0643481
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8100 20509.039 103.70462 0 3901.6748 1.0771863
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8150 20212.97 158.64893 0 3901.7916 3.0000215
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8200 20323.463 138.25912 0 3901.8634 -1.2802945
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8250 19997.284 198.37183 0 3901.5727 -2.6431964
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8300 20138.402 171.75824 0 3901.092 1.7669897
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8350 20367.568 130.22531 0 3901.9972 -1.2153731
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8400 19945.534 208.35675 0 3901.9741 1.6021151
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8450 20112.534 177.18642 0 3901.7298 2.2413008
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8500 20686.7 71.116816 0 3901.9873 2.2888545
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8550 18081.94 553.83586 0 3902.3432 7.8257937
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8600 18320.081 505.67086 0 3898.2784 16.554878
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8650 20235.305 154.43021 0 3901.709 3.1740823
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8700 20355.413 132.22512 0 3901.746 4.3436482
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8750 20087.188 182.11349 0 3901.9631 10.422134
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8800 20400.795 124.09819 0 3902.0232 2.1179177
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8850 20678.731 72.825797 0 3902.2204 -3.4491441
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8900 20372.643 129.5072 0 3902.2189 -8.2166415
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8950 20851.731 40.899364 0 3902.331 -5.8382839
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9000 20318.076 139.61775 0 3902.2243 -4.1960802
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9050 16879.415 776.53739 0 3902.3549 -14.429475
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9100 19135.149 358.68223 0 3902.2284 -15.50479
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9150 20689.556 70.939656 0 3902.339 -2.9876179
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9200 19949.801 207.54882 0 3901.9564 6.4259245
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9250 20207.027 160.2813 0 3902.3233 1.7402195
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9300 20030.005 192.99466 0 3902.2548 5.300728
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9350 19795.291 236.24003 0 3902.0347 5.8677745
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9400 18232.093 526.18752 0 3902.501 19.344893
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9450 18789.641 422.30568 0 3901.8687 -7.5185247
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9500 16332.599 874.10423 0 3898.6597 16.241378
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9550 18572.572 462.19972 0 3901.5649 -10.777359
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9600 19859.645 223.32209 0 3901.0341 0.89631957
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9650 19092.741 365.35768 0 3901.0504 6.7830005
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9700 18391.154 495.72792 0 3901.4972 6.0683847
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9750 17790.092 608.60997 0 3903.0714 8.2090184
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9800 17681.783 628.99951 0 3903.4038 14.231747
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9850 17804.412 605.54067 0 3902.654 22.308453
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9900 19134.472 359.37911 0 3902.7999 8.5633158
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9950 20099.055 180.28604 0 3902.3332 4.7905855
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10000 20035.447 192.30744 0 3902.5754 1.8299201
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Loop time of 2.34062 on 4 procs for 10000 steps with 81 atoms
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Performance: 36913.309 tau/day, 4272.374 timesteps/s
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99.3% CPU use with 4 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 | 0.0052865 | 0.014915 | 0.039366 | 11.6 | 0.64
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Neigh | 0.0080708 | 0.016504 | 0.03345 | 7.7 | 0.71
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Comm | 0.1357 | 0.14237 | 0.15111 | 1.5 | 6.08
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Output | 0.0033429 | 0.0037922 | 0.0050931 | 1.2 | 0.16
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Modify | 2.1033 | 2.1433 | 2.1609 | 1.6 | 91.57
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Other | | 0.01973 | | | 0.84
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Nlocal: 20.25 ave 36 max 0 min
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Histogram: 1 0 0 0 0 1 1 0 0 1
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Nghost: 35.25 ave 47 max 24 min
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Histogram: 1 0 1 0 0 0 0 1 0 1
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Neighs: 137.5 ave 252 max 0 min
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Histogram: 1 0 0 1 0 0 0 0 1 1
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Total # of neighbors = 550
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Ave neighs/atom = 6.7901235
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Neighbor list builds = 994
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Dangerous builds = 956
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Total wall time: 0:00:02
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