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 1 by 1 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) = 3.666 | 3.666 | 3.666 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 18.086359
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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 69.977442 0 3904.4178 9.0928158
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250 19552.211 283.50525 0 3904.285 15.670465
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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 20365.825 131.47231 0 3902.9213 0.6921524
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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 20142.432 172.05177 0 3902.1317 4.6838621
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850 19932.48 210.71175 0 3901.9118 3.4716043
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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 -2.874422
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1200 20767.681 56.717094 0 3902.5839 -34.817444
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1250 20625.583 82.586399 0 3902.1388 11.697329
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1300 20690.013 71.006478 0 3902.4903 -29.292777
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1350 20936.019 26.022786 0 3903.0634 1.0316025
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1400 19753.559 244.81785 0 3902.8844 6.7138514
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1450 15690.149 998.342 0 3903.9252 48.124557
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1500 20234.455 155.92516 0 3903.0465 13.17221
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1550 20779.631 55.063009 0 3903.1428 -2.639045
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1600 20642.753 80.233905 0 3902.9659 -2.4688467
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1650 18785.696 423.90402 0 3902.7365 -5.6466663
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1700 20965.076 20.760444 0 3903.182 -0.45364296
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1750 18935.406 396.96067 0 3903.5173 25.913302
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1800 20581.559 91.756972 0 3903.1567 3.8217234
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1850 20616.946 85.184849 0 3903.1378 4.1907972
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1900 16602.053 828.40949 0 3902.8637 -0.49505122
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1950 20175.526 166.53362 0 3902.7421 5.603825
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2000 20261.924 150.39322 0 3902.6014 -1.196958
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2050 20170.339 167.40504 0 3902.6531 -0.80849882
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2100 19820.132 231.26755 0 3901.6624 3.1476607
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2150 20666.19 75.838461 0 3902.9106 0.53899287
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2200 19873.51 222.53286 0 3902.8124 7.9310276
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2250 18548.063 467.69698 0 3902.5235 16.905356
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2300 20616.61 84.762399 0 3902.6531 -6.7872951
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2350 18167.738 538.13635 0 3902.5322 -11.458285
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2400 20120.227 177.01954 0 3902.9875 -1.2593018
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2450 20436.599 118.32469 0 3902.8801 -6.5989174
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2500 18919.923 400.26361 0 3903.9531 32.37476
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2550 19675.809 259.77151 0 3903.4398 19.437327
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2600 19739.842 247.86388 0 3903.3901 -7.519784
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2650 20557.026 96.530313 0 3903.387 0.60211646
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2700 20666.602 76.099892 0 3903.2484 0.16825503
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2750 20924.585 28.453883 0 3903.3771 2.4227171
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2800 20360.659 132.8596 0 3903.352 4.1440877
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2850 20783.475 54.518625 0 3903.3102 -0.57312067
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2900 20456.181 115.03745 0 3903.2191 -20.118887
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2950 20779.493 55.321394 0 3903.3756 -0.26783079
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3000 20011.867 197.30216 0 3903.2035 -1.4704201
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3050 20741.875 62.208723 0 3903.2966 -7.5432815
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3100 21001.754 14.148298 0 3903.362 2.9676438
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3150 20244.086 154.44639 0 3903.3512 -1.9071213
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3200 20639.615 81.136426 0 3903.2873 1.4826467
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3250 20735.244 63.529571 0 3903.3895 2.1127055
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3300 20142.891 173.22282 0 3903.3878 4.7739415
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3350 19963.765 206.21899 0 3903.2126 5.5410771
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3400 16628.667 824.13627 0 3903.519 36.087673
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3450 19228.218 342.81569 0 3903.5968 3.1057274
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3500 19759.293 244.57876 0 3903.707 2.2339557
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3550 19853.21 227.06362 0 3903.584 -1.0882119
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3600 19673.516 260.64854 0 3903.8923 -10.63775
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3650 19619.238 270.5393 0 3903.7316 -6.3746003
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3700 20756.865 59.790243 0 3903.6542 -8.3015766
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3750 20265.025 150.47347 0 3903.2559 -5.7284695
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3800 20944.683 24.669276 0 3903.3142 -0.070552298
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3850 19344.831 320.59492 0 3902.971 13.040749
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3900 19978.209 203.00247 0 3902.6708 0.15638133
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3950 19864.118 224.19359 0 3902.734 0.453229
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4000 17606.216 642.71493 0 3903.1252 -12.656002
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4050 18017.895 566.54102 0 3903.1883 12.133906
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4100 20092.963 182.17593 0 3903.095 7.7445947
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4150 20555.337 96.395074 0 3902.939 -6.5429752
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4200 20709.781 67.869199 0 3903.0138 -2.8653003
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4250 18956.203 392.20748 0 3902.6155 -1.6249728
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4300 17816.204 603.72704 0 3903.0241 23.089239
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4350 18979.742 388.04678 0 3902.8138 3.2511108
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4400 20272.085 148.82367 0 3902.9135 1.9518268
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4450 18820.003 417.74789 0 3902.9337 6.3979299
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4500 19991.936 200.50131 0 3902.7117 3.5118553
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4550 20915.092 29.663898 0 3902.8291 -2.3174641
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4600 20690.37 71.125087 0 3902.6752 -12.008575
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4650 18893.76 404.50849 0 3903.3529 15.006184
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4700 18611.123 456.1263 0 3902.6306 -5.3574892
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4750 20497.821 106.5856 0 3902.4784 0.85039837
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4800 20803.214 50.120522 0 3902.5675 3.8610873
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4850 18849.598 411.72635 0 3902.3927 9.2029058
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4900 18121.714 546.68042 0 3902.5533 9.4522272
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4950 20377.499 128.99323 0 3902.6041 5.3825395
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5000 20686.114 72.039749 0 3902.8016 -5.706271
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5050 20180.449 165.51368 0 3902.634 -16.418461
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5100 20274.947 148.36657 0 3902.9864 -5.6668309
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5150 18042.324 560.74137 0 3901.9125 3.6791541
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5200 20794.666 52.204446 0 3903.0685 -1.4517721
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5250 19073.55 371.18834 0 3903.3272 -13.457439
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5300 20821.412 47.364313 0 3903.1813 2.258098
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5350 20583.073 91.271191 0 3902.9513 5.4323985
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5400 20490.967 108.41184 0 3903.0353 4.122905
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5450 18141.79 543.66874 0 3903.2594 -0.19951075
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5500 20274.012 148.55528 0 3903.002 5.0489974
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5550 17806.237 605.43454 0 3902.8858 43.80619
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5600 20999.825 14.341937 0 3903.1983 1.0879933
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5650 20930.929 27.025347 0 3903.1234 -7.0860209
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5700 20677.725 73.853093 0 3903.0614 2.6864775
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5750 20521.264 102.87509 0 3903.1092 2.6940548
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5800 20792.571 52.596021 0 3903.0721 1.2910217
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5850 20518.674 103.26595 0 3903.0204 -9.2547271
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5900 18417.885 491.66696 0 3902.3865 -12.049357
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5950 17243.837 709.37858 0 3902.6817 -6.2357188
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6000 20262.525 149.56918 0 3901.8885 -0.28964823
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6050 19883.554 219.14043 0 3901.2801 2.3071707
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6100 16548.178 838.47869 0 3902.956 -11.715644
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6150 19601.177 272.14674 0 3901.9944 -0.9008056
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6200 20499.796 106.2363 0 3902.4949 0.79071424
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6250 19601.106 272.50139 0 3902.3359 -1.9306693
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6300 17210.685 712.70535 0 3899.8692 4.8890923
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6350 19911.896 214.91041 0 3902.2985 12.691129
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6400 18834.642 411.87123 0 3899.7678 -1.9447856
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6450 20216.311 158.39781 0 3902.1591 2.6009109
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6500 20452.025 114.97122 0 3902.3832 0.14644416
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6550 19142.589 357.34097 0 3902.2649 2.8968485
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6600 20412.915 122.08784 0 3902.2573 3.1343105
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6650 17317.867 699.39994 0 3906.4123 42.25563
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6700 20479.771 109.8036 0 3902.3537 1.3520625
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6750 20306.902 142.12484 0 3902.6623 2.2032106
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6800 20755.367 58.994834 0 3902.5814 -0.90518094
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6850 20471.259 111.7197 0 3902.6936 1.5799331
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6900 20702.025 69.15032 0 3902.8586 9.3910371
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6950 20477.695 110.34414 0 3902.5099 1.8181164
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7000 20560.727 95.057704 0 3902.5998 -15.686006
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7050 20336.675 136.39386 0 3902.4448 1.3704327
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7100 20757.399 58.950153 0 3902.913 -6.4250981
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7150 20870.958 38.095649 0 3903.088 -4.1962169
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7200 20706.869 68.489134 0 3903.0944 2.8322659
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7250 20386.713 127.7432 0 3903.0604 6.0287391
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7300 18391.773 497.21001 0 3903.0939 19.202343
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7350 20178.898 166.4993 0 3903.3322 1.5682417
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7400 16858.704 781.78682 0 3903.7691 21.317514
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7450 17509.513 660.71963 0 3903.2221 -5.9456143
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7500 19974.601 204.20412 0 3903.2043 -0.69202711
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7550 20917.053 29.73415 0 3903.2626 -3.9962577
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7600 20923.518 28.482703 0 3903.2083 -1.9016251
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7650 20549.528 97.630612 0 3903.0987 3.5512257
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7700 20861.441 39.903885 0 3903.1337 2.4426264
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7750 18843.349 413.64461 0 3903.1537 2.677739
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7800 20616.054 85.214364 0 3903.0021 3.9639004
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7850 16478.851 851.93376 0 3903.5728 7.3763128
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7900 20312.115 141.35103 0 3902.8539 4.6707271
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7950 20389.623 127.16589 0 3903.0219 3.4414001
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8000 20452.117 115.30715 0 3902.7362 -1.0162528
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8050 20857.093 40.791886 0 3903.2164 -15.150068
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8100 19817.543 233.4997 0 3903.415 0.89346046
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8150 18649.521 449.9112 0 3903.5262 -0.40053588
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8200 19619.276 270.37616 0 3903.5754 5.5161492
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8250 20393.176 127.01336 0 3903.5275 2.122613
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8300 19145.912 358.00424 0 3903.5435 3.863924
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8350 19636.311 267.17226 0 3903.5262 -7.1496084
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8400 19086.332 368.86693 0 3903.3729 7.0968952
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8450 19494.416 292.89527 0 3902.9723 3.1750935
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8500 20041.919 191.77756 0 3903.244 0.95215503
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8550 20357.561 133.15478 0 3903.0736 -0.14020152
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8600 16998.797 756.07003 0 3903.9954 -16.724408
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8650 20853.26 41.386996 0 3903.1017 -3.2612965
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8700 20767.768 57.360884 0 3903.2438 1.1157649
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8750 20752.546 60.106518 0 3903.1705 0.39130547
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8800 20574.407 92.99798 0 3903.0734 0.61728166
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8850 20326.99 138.94203 0 3903.1995 -1.9434522
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8900 17408.108 679.53222 0 3903.2559 21.935371
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8950 20471.21 112.2721 0 3903.2368 1.8142747
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9000 19129.591 360.35257 0 3902.8694 4.5786395
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9050 20439.668 117.89541 0 3903.0191 2.5585685
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9100 20780.375 54.788664 0 3903.0062 3.8312459
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9150 19904.559 216.61504 0 3902.6445 12.150414
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9200 20961.295 21.52065 0 3903.2419 -0.2120699
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9250 19315.252 326.44175 0 3903.3402 -19.740867
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9300 20653.002 78.77764 0 3903.4076 -7.8068233
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9350 18961.572 391.20947 0 3902.6117 -12.660843
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9400 16262.179 892.67633 0 3904.191 22.2435
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9450 17064.394 743.33301 0 3903.406 36.139436
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9500 18075.588 555.06436 0 3902.3954 24.598176
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9550 20487.738 109.06287 0 3903.0884 2.6320759
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9600 20358.609 133.36993 0 3903.4828 0.76449113
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9650 19849.022 228.46312 0 3904.208 9.5547064
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9700 20448.112 116.8757 0 3903.5632 -1.0845697
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9750 20472.78 112.51661 0 3903.7722 -0.30676738
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9800 19491.99 293.35361 0 3902.9814 -20.10857
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9850 19895.603 218.42479 0 3902.7957 -0.18235641
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9900 19704.336 254.55068 0 3903.5019 14.553184
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9950 17689.462 627.9788 0 3903.805 4.9918088
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10000 20184.205 165.29396 0 3903.1097 2.9472364
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Loop time of 2.28393 on 1 procs for 10000 steps with 81 atoms
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Performance: 37829.498 tau/day, 4378.414 timesteps/s
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99.3% 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 | 0.052911 | 0.052911 | 0.052911 | 0.0 | 2.32
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Neigh | 0.056658 | 0.056658 | 0.056658 | 0.0 | 2.48
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Comm | 0.0087389 | 0.0087389 | 0.0087389 | 0.0 | 0.38
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Output | 0.0037996 | 0.0037996 | 0.0037996 | 0.0 | 0.17
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Modify | 2.1537 | 2.1537 | 2.1537 | 0.0 | 94.30
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Other | | 0.008147 | | | 0.36
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Nlocal: 81 ave 81 max 81 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 113 ave 113 max 113 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 582 ave 582 max 582 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 582
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Ave neighs/atom = 7.1851852
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Neighbor list builds = 993
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Dangerous builds = 950
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Total wall time: 0:00:02
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