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
329 lines
19 KiB
Groff
329 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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# 1 chain 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 <> 36 45
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10 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 group clump1 clump2 clump3 clump4 clump5 clump6 clump7 clump8 clump9
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1 clusters, 9 bodies, 8 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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0 217.7783 3430.3907 0 3466.6871 -2.7403788
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50 13679.637 1404.2468 0 3684.1863 12.446066
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100 16777.225 888.87665 0 3685.0808 -31.828677
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150 19595.365 418.45042 0 3684.3446 40.709078
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200 18524.188 596.47273 0 3683.8375 -0.8159371
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250 21015.789 180.96521 0 3683.5967 -10.042469
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300 20785.513 219.25314 0 3683.5053 2.6452719
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350 21072.46 171.2554 0 3683.3321 7.0609024
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400 19956.414 356.36381 0 3682.4328 19.320259
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450 20724.42 227.73284 0 3681.8028 8.1259249
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500 20152.578 322.71466 0 3681.4777 5.4929878
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550 20017.022 345.29701 0 3681.4673 5.4661666
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600 17897.743 698.72196 0 3681.6791 3.2854742
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650 17297.758 796.60256 0 3679.5623 15.191113
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700 18581.934 584.29715 0 3681.2861 5.1588289
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750 21774.158 52.821062 0 3681.8474 -10.775664
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800 21604.055 81.188546 0 3681.8644 -3.2045742
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850 17821.483 711.53827 0 3681.7854 7.438428
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900 21033.292 175.98127 0 3681.5299 -16.345167
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950 20968.166 186.59847 0 3681.2929 -2.330456
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1000 20490.66 266.19374 0 3681.3037 11.787982
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1050 20222.396 310.94072 0 3681.34 -8.3459539
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1100 21321.687 127.61533 0 3681.2299 -1.2184716
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1150 20849.582 206.01696 0 3680.9472 -0.86699118
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1200 21815.003 45.317409 0 3681.1512 1.5988314
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1250 18655.437 572.41453 0 3681.654 10.064083
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1300 20780.781 217.36511 0 3680.8286 6.0538604
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1350 20558.971 254.36489 0 3680.8601 -3.6773868
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1400 21485.029 99.812844 0 3680.6511 -16.185479
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1450 21771.107 52.159653 0 3680.6775 -2.4756655
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1500 21520.949 93.503876 0 3680.3286 2.1023573
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1550 21351.419 121.6813 0 3680.2511 5.5159876
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1600 20778.804 216.92191 0 3680.0559 15.089203
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1650 21477.636 100.21873 0 3679.8247 -1.1045277
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1700 18501.33 596.4807 0 3680.0357 -15.6798
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1750 18563.64 587.34824 0 3681.2882 33.532308
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1800 19110.175 494.82517 0 3679.8543 18.024074
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1850 21364.178 119.23765 0 3679.9339 2.5290144
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1900 20146.588 322.15509 0 3679.9197 5.7317299
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1950 20692.676 231.25264 0 3680.0319 4.297803
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2000 20943.902 189.11251 0 3679.7629 -22.643824
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2050 19667.823 401.86882 0 3679.8394 3.6241915
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2100 20280.125 299.81485 0 3679.8357 7.4804047
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2150 19181.201 483.6306 0 3680.4975 22.63342
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2200 21301.144 130.54014 0 3680.7308 4.7074288
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2250 20484.876 266.98315 0 3681.1291 -8.6578278
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2300 18648.161 573.07329 0 3681.1001 -5.2550954
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2350 21515.748 95.243054 0 3681.201 -9.386512
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2400 21462.551 104.18267 0 3681.2745 -29.46442
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2450 20107.732 330.99437 0 3682.2831 35.38497
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2500 20771.509 220.47713 0 3682.3953 -12.324858
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2550 20499.887 265.58494 0 3682.2327 -22.713874
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2600 21462.182 105.24427 0 3682.2747 -10.175788
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2650 21004.949 181.51383 0 3682.3387 4.949195
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2700 18673.552 570.45017 0 3682.7089 21.201437
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2750 21257.562 139.198 0 3682.1249 -7.5793039
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2800 21559.645 88.844759 0 3682.119 -6.2360467
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2850 20865.227 204.46262 0 3682.0004 0.39575069
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2900 19428.614 443.93293 0 3682.0352 12.796676
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2950 19630.1 410.18487 0 3681.8681 -0.50572623
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3000 19663.218 404.06316 0 3681.2661 6.0827093
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3050 19087.572 500.8452 0 3682.1073 -6.3526476
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3100 18229.94 643.77681 0 3682.1001 11.453637
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3150 18927.492 527.51919 0 3682.1011 -1.662863
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3200 18320.514 628.55895 0 3681.978 21.176126
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3250 18204.677 647.96462 0 3682.0775 11.331521
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3300 19231.978 477.02117 0 3682.3509 3.8381593
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3350 18153.44 656.70376 0 3682.2772 15.135615
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3400 17476.768 770.0598 0 3682.8545 -3.394312
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3450 21097.531 166.17241 0 3682.4276 3.74301
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3500 17605.784 747.54808 0 3681.8454 3.3420627
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3550 19238.34 476.00608 0 3682.3961 1.1413836
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3600 18155.288 656.57434 0 3682.4557 3.4360446
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3650 18735.622 559.2377 0 3681.8413 28.760363
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3700 15310.261 1134.4215 0 3686.1317 44.207018
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3750 15377.116 1123.4786 0 3686.3313 7.6773215
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3800 18798.895 549.05928 0 3682.2084 -12.905825
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3850 18322.563 628.87744 0 3682.6379 -16.067793
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3900 19963.049 355.65441 0 3682.8292 3.4694064
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3950 19925.48 361.2507 0 3682.1641 5.0058567
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4000 19141.423 492.41081 0 3682.648 -12.782769
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4050 20022.241 345.61655 0 3682.6568 -3.0149905
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4100 21348.635 124.95646 0 3683.0624 -4.85779
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4150 21011.812 181.1132 0 3683.0819 -3.9526196
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4200 20222.276 312.63945 0 3683.0187 -23.63437
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4250 20957.757 189.77152 0 3682.731 -1.3712469
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4300 20070.215 337.5751 0 3682.611 -6.8816517
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4350 21322.437 129.09228 0 3682.8318 -6.9442178
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4400 19440.445 442.77531 0 3682.8495 -0.11606236
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4450 20964.516 188.67174 0 3682.7577 4.8533525
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4500 13530.08 1428.5497 0 3683.563 12.333187
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4550 20461.637 272.58882 0 3682.8616 4.5111943
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4600 17072.994 836.58228 0 3682.0812 5.7611617
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4650 18860.748 539.82027 0 3683.2782 -2.5558958
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4700 18373.927 621.04093 0 3683.3621 5.4020702
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4750 20321.437 296.63662 0 3683.5428 8.9571617
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4800 21083.122 169.84086 0 3683.6946 10.566368
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4850 20499.669 267.7012 0 3684.3128 4.2924237
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4900 20308.781 300.38168 0 3685.1785 -12.396923
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4950 21043.303 178.56295 0 3685.7801 3.8923762
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5000 20718.383 232.52208 0 3685.5859 -12.43234
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5050 21005.749 184.4363 0 3685.3945 -7.6463487
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5100 20714.133 233.27745 0 3685.6329 -1.6944135
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5150 19577.452 422.73035 0 3685.639 -21.831219
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5200 14044.647 1343.9545 0 3684.729 -6.8407194
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5250 19089.805 504.0893 0 3685.7235 4.05641
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5300 21094.745 169.94699 0 3685.7378 -0.66593212
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5350 19907.559 366.77598 0 3684.7024 1.5248525
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5400 20382.81 289.13263 0 3686.2676 -11.919321
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5450 19593.693 420.70548 0 3686.3209 -1.1568628
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5500 20906.08 202.09801 0 3686.4447 -2.4284971
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5550 16315.465 965.56973 0 3684.8138 -33.178221
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5600 19714.57 400.39687 0 3686.1586 19.950231
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5650 20561.724 259.54797 0 3686.502 8.2074524
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5700 19349.502 460.7789 0 3685.6959 16.252649
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5750 21006.818 185.56805 0 3686.7044 -11.96089
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5800 20268.2 307.97547 0 3686.0089 17.322311
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5850 21018.322 184.16179 0 3687.2154 -14.379909
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5900 19695.647 404.57094 0 3687.1787 -20.718904
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5950 21021.687 183.66311 0 3687.2776 -15.206081
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6000 18947.535 529.30554 0 3687.2281 17.863927
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6050 15272.373 1141.012 0 3686.4075 -0.43375666
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6100 17766.197 721.75792 0 3682.7908 11.378913
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6150 18612.573 584.06688 0 3686.1623 17.543241
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6200 19005.155 518.97146 0 3686.4973 -16.223107
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6250 20997.507 187.55499 0 3687.1394 -11.613546
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6300 19639.901 413.58048 0 3686.8974 14.407136
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6350 19580.399 423.02818 0 3686.428 -5.5801796
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6400 14134.119 1332.0662 0 3687.7527 84.864425
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6450 21598.824 87.419966 0 3687.224 -5.8358352
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6500 18208.216 649.29108 0 3683.9938 -8.1510884
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6550 19364.586 459.59813 0 3687.0291 -12.053563
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6600 20710.927 235.11914 0 3686.9403 -1.0470193
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6650 21132.334 165.08091 0 3687.1366 1.0785471
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6700 20217.285 317.589 0 3687.1365 0.055447462
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6750 21232.279 148.57412 0 3687.2873 -2.4551657
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6800 20292.683 304.76539 0 3686.8793 -0.42311295
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6850 19056.291 510.49927 0 3686.5478 6.9533826
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6900 20429.82 282.23764 0 3687.2076 -4.2360112
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6950 21281.278 140.27361 0 3687.1533 -0.07475261
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7000 17173.388 824.54446 0 3686.7758 10.753828
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7050 18079.7 674.56274 0 3687.846 12.975804
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7100 16433.233 950.73904 0 3689.6112 -10.5102
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7150 19033.335 515.59672 0 3687.8193 0.29109447
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7200 17286.428 809.02352 0 3690.0948 2.3015698
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7250 16811.962 886.6645 0 3688.6582 -7.4787512
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7300 15992.461 1023.4849 0 3688.895 -5.2354222
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7350 19211.451 487.63129 0 3689.5398 8.4351737
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7400 19065.682 511.95629 0 3689.57 -12.47448
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7450 21369.265 128.10098 0 3689.6451 2.2930546
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7500 16807.109 888.64602 0 3689.8308 14.761969
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7550 18063.046 679.21873 0 3689.7264 3.8950434
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7600 17794.987 724.55404 0 3690.3851 14.379016
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7650 17904.751 706.14354 0 3690.2688 23.813776
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7700 19670.09 411.3021 0 3689.6504 14.099245
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7750 18082.562 675.23975 0 3689.0001 15.788521
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7800 17776.135 726.91445 0 3689.6037 6.9780735
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7850 17062.575 846.33412 0 3690.0966 -8.9289256
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7900 19059.2 513.07737 0 3689.6107 16.992843
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7950 16269.685 978.48914 0 3690.1033 11.180179
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8000 20115.278 336.91405 0 3689.4604 -6.4882518
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8050 21173.72 161.15229 0 3690.1056 -2.2164491
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8100 19238.235 484.42784 0 3690.8004 23.412709
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8150 18438.4 617.58743 0 3690.6542 0.89156316
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8200 21438.764 117.12721 0 3690.2546 -1.7193227
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8250 21195.806 157.66607 0 3690.3003 3.820447
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8300 21177.549 161.13702 0 3690.7286 0.94938203
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8350 21060.267 181.06887 0 3691.1135 2.8179025
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8400 20087.113 343.46206 0 3691.3142 8.1484473
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8450 19298.478 474.87133 0 3691.2843 -16.239664
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8500 21654.353 82.083485 0 3691.1423 -8.1464138
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8550 19920.544 371.34795 0 3691.4386 20.765144
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8600 21692.293 75.655154 0 3691.0373 -13.316763
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8650 21231.322 151.8989 0 3690.4526 -11.388238
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8700 19530.647 434.89585 0 3690.0037 2.7433786
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8750 19720.63 403.07773 0 3689.8493 -6.416414
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8800 21321.378 136.04091 0 3689.604 1.3661635
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8850 19811.906 387.80489 0 3689.7893 3.704143
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8900 19734.167 400.92444 0 3689.9523 2.5685155
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8950 21076.459 177.18119 0 3689.9244 -11.939513
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9000 20967.246 195.42966 0 3689.9707 2.0092705
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9050 21122.023 169.62103 0 3689.9582 2.3791301
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9100 20169.346 328.27229 0 3689.8299 -3.5017988
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9150 21418.641 119.84513 0 3689.6187 2.486073
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9200 20876.042 210.26452 0 3689.6048 -5.3839897
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9250 21572.38 93.74407 0 3689.1407 -8.3676952
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9300 20944.78 197.98577 0 3688.7824 1.3278314
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9350 20706.52 237.48767 0 3688.5744 4.6944204
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9400 16412.314 953.47251 0 3688.8581 26.134976
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9450 20461.68 277.76243 0 3688.0424 17.647445
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9500 20893.994 205.64261 0 3687.9749 -10.642418
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9550 20503.447 270.63504 0 3687.8761 -17.769897
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9600 19677.799 408.05887 0 3687.692 -2.7938604
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9650 17480.971 774.1855 0 3687.6806 0.59827043
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9700 17799.126 721.50817 0 3688.0292 44.387928
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9750 20443.384 280.16837 0 3687.399 3.0619324
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9800 20545.255 263.40108 0 3687.6102 3.6229381
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9850 20722.819 233.57142 0 3687.3745 0.86462694
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9900 21128.462 165.09767 0 3686.508 -6.9636843
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9950 21343.307 130.46714 0 3687.685 -9.7382705
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10000 20623.887 250.37866 0 3687.6932 2.7529835
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Loop time of 2.27157 on 1 procs for 10000 steps with 81 atoms
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Performance: 38035.351 tau/day, 4402.240 timesteps/s
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99.4% 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 | 0.092926 | 0.092926 | 0.092926 | 0.0 | 4.09
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Neigh | 0.076362 | 0.076362 | 0.076362 | 0.0 | 3.36
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Comm | 0.0069691 | 0.0069691 | 0.0069691 | 0.0 | 0.31
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Output | 0.0037444 | 0.0037444 | 0.0037444 | 0.0 | 0.16
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Modify | 2.0832 | 2.0832 | 2.0832 | 0.0 | 91.71
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Other | | 0.00841 | | | 0.37
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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: 62 ave 62 max 62 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 905 ave 905 max 905 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 905
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Ave neighs/atom = 11.17284
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Neighbor list builds = 991
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Dangerous builds = 927
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Total wall time: 0:00:02
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