339 lines
19 KiB
Groff
339 lines
19 KiB
Groff
LAMMPS (20 Apr 2018)
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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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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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velocity all create 100.0 4928459
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# unconnected bodies
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#group clump1 id <> 1 9
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#group clump2 id <> 10 18
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#group clump3 id <> 19 27
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#group clump4 id <> 28 36
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#group clump5 id <> 37 45
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#group clump6 id <> 46 54
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#group clump7 id <> 55 63
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#group clump8 id <> 64 72
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#group clump9 id <> 73 81
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#fix 1 all rigid group 9 clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9
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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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# 2 chains of connected bodies
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#group clump1 id <> 1 9
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#group clump2 id <> 9 18
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#group clump3 id <> 18 27
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#group clump4 id <> 27 36
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#group clump5 id <> 37 45
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#group clump6 id <> 45 54
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#group clump7 id <> 54 63
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#group clump8 id <> 63 72
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#group clump9 id <> 72 81
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#fix 1 all poems group clump1 clump2 clump3 clump4
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#fix 2 all poems group clump5 clump6 clump7 clump8 clump9
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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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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/newton
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bin: standard
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Per MPI rank memory allocation (min/avg/max) = 3.292 | 3.292 | 3.292 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 -3.2045743
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850 17821.483 711.53827 0 3681.7854 7.4384277
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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 20490.66 266.19375 0 3681.3037 11.787983
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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 -1.2184717
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1150 20849.582 206.01695 0 3680.9472 -0.86699146
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1200 21815.003 45.317414 0 3681.1512 1.5988314
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1250 18655.437 572.41453 0 3681.654 10.064078
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1300 20780.781 217.36506 0 3680.8286 6.0538615
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1350 20558.971 254.36482 0 3680.8601 -3.6773954
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1400 21485.029 99.812918 0 3680.6511 -16.185473
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1450 21771.107 52.159607 0 3680.6775 -2.4756675
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1500 21520.948 93.503927 0 3680.3286 2.1023577
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1550 21351.418 121.68138 0 3680.2511 5.515995
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1600 20778.805 216.92177 0 3680.0559 15.089187
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1650 21477.638 100.21836 0 3679.8247 -1.1045739
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1700 18501.339 596.47922 0 3680.0357 -15.679682
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1750 18563.642 587.3479 0 3681.2882 33.532211
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1800 19110.186 494.82336 0 3679.8543 18.024046
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1850 21364.191 119.23543 0 3679.9339 2.5291075
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1900 20146.627 322.14849 0 3679.9197 5.7313175
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1950 20692.671 231.25345 0 3680.0319 4.297772
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2000 20943.905 189.11218 0 3679.7629 -22.64509
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2050 19668.055 401.83025 0 3679.8394 3.6251438
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2100 20280.434 299.76289 0 3679.8353 7.4807805
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2150 19181.835 483.52621 0 3680.4987 22.62081
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2200 21300.18 130.7021 0 3680.7322 4.710193
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2250 20486.914 266.64414 0 3681.1299 -8.6458025
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2300 18653.082 572.25481 0 3681.1017 -5.2636982
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2350 21513.563 95.608298 0 3681.2021 -9.3624751
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2400 21466.205 103.57569 0 3681.2765 -29.559707
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2450 20100.204 332.25468 0 3682.2886 35.739592
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2500 20764.513 221.64794 0 3682.4001 -12.46688
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2550 20436.771 276.13128 0 3682.2598 -22.419404
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2600 21466.252 104.57185 0 3682.2806 -10.080362
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2650 20817.269 212.81674 0 3682.3615 5.1374497
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2700 18565.157 588.46125 0 3682.6541 22.283866
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2750 20780.743 218.76366 0 3682.2208 -8.0046411
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2800 21032.22 176.82368 0 3682.1936 -7.078895
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2850 16817.729 879.49153 0 3682.4464 33.140849
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2900 19309.511 463.89319 0 3682.145 7.9225025
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2950 20544.978 257.86831 0 3682.0314 2.0523059
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3000 20616.438 246.0975 0 3682.1706 -0.2824889
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3050 18648.596 574.37266 0 3682.4721 -5.8677065
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3100 19147.135 490.76826 0 3681.9574 -1.9922835
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3150 18568.022 587.36965 0 3682.0399 14.694505
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3200 19720.841 395.38315 0 3682.1899 5.9162402
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3250 19008.557 514.50687 0 3682.5998 -3.4702895
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3300 21708.937 64.231264 0 3682.3874 -5.4808611
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3350 20548.477 257.62974 0 3682.3759 9.7818301
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3400 20508.84 264.0153 0 3682.1553 -12.578182
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3450 18736.579 559.11222 0 3681.8754 21.920437
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3500 21444.82 107.82706 0 3681.9638 0.093050651
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3550 20439.241 275.31015 0 3681.8503 -3.0785302
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3600 21547.1 90.778361 0 3681.9617 -5.9189729
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3650 15623.305 1079.996 0 3683.8802 36.064752
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3700 19912.452 363.09483 0 3681.8368 5.4802367
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3750 21289.7 133.2258 0 3681.5091 -10.884642
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3800 20214.875 312.09245 0 3681.2382 8.6419893
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3850 19853.031 372.13835 0 3680.9769 2.6229234
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3900 17863.409 703.8716 0 3681.1064 -1.4250404
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3950 19926.351 359.87227 0 3680.9307 -14.60997
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4000 17595.665 747.85423 0 3680.4651 24.228859
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4050 18408.194 611.80934 0 3679.8416 4.4236034
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4100 17506.503 762.1286 0 3679.8792 5.0526379
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4150 18479.134 600.76034 0 3680.6159 -6.6523095
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4200 18475.322 601.95797 0 3681.1783 1.3292995
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4250 18301.378 630.34119 0 3680.5709 2.5387332
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4300 19384.541 449.98455 0 3680.7414 5.8750989
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4350 18717.888 561.31715 0 3680.9651 3.7948584
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4400 18893.773 532.20993 0 3681.172 10.963539
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4450 20269.613 302.15984 0 3680.4286 -10.145642
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4500 19151.762 489.32407 0 3681.2845 21.695364
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4550 19914.708 361.54065 0 3680.6587 -4.2298372
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4600 21153.44 154.99598 0 3680.5693 2.3172078
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4650 21021.611 176.81454 0 3680.4164 1.9128023
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4700 21707.966 62.767734 0 3680.762 -5.2080189
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4750 16517.674 927.53839 0 3680.484 17.329608
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4800 21654.604 71.574174 0 3680.6749 -6.0650166
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4850 18135.978 657.28622 0 3679.9493 5.4803307
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4900 20389.048 282.49215 0 3680.6668 -2.8570431
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4950 17159.074 820.81472 0 3680.6604 31.273877
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5000 20788.159 215.88415 0 3680.5773 4.6345196
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5050 21366.767 119.68693 0 3680.8148 -9.9482889
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5100 20668.21 236.17655 0 3680.8782 3.8118334
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5150 20468.573 269.83696 0 3681.2657 -26.625943
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5200 19493.142 432.49135 0 3681.3483 -7.6677112
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5250 19626.594 410.09767 0 3681.1967 7.3622341
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5300 20771.914 219.12484 0 3681.1105 -7.0871793
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5350 21152.459 155.26401 0 3680.6738 5.9030557
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5400 21376.189 117.91075 0 3680.6088 -1.2004513
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5450 21455.06 105.15166 0 3680.995 -9.1675471
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5500 21227.896 143.35739 0 3681.3401 -6.646305
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5550 21149.831 156.61404 0 3681.5858 -12.953136
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5600 21364.198 120.94695 0 3681.6466 1.0372254
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5650 20219.777 311.34588 0 3681.3088 6.5026316
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5700 21163.024 154.3001 0 3681.4708 -0.47587262
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5750 19583.077 418.40745 0 3682.2535 24.609517
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5800 18801.324 548.79742 0 3682.3515 -12.082631
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5850 20875.4 203.07604 0 3682.3093 -8.1191161
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5900 20737.053 226.2734 0 3682.4489 -7.6845943
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5950 21260.028 139.21888 0 3682.5568 -2.2977046
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6000 19823.84 378.71803 0 3682.6914 -1.1163373
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6050 20487.214 268.03474 0 3682.5704 4.313979
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6100 17853.211 707.10918 0 3682.6443 16.762322
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6150 21322.705 129.06 0 3682.8441 2.7500936
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6200 21609.008 81.580972 0 3683.0823 0.37062555
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6250 20364.115 289.30707 0 3683.3262 13.176034
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6300 20201.9 316.16558 0 3683.149 -1.6318339
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6350 21151.879 157.75018 0 3683.0634 -23.337621
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6400 21453.129 107.45563 0 3682.9772 -0.60776225
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6450 21105.382 165.1926 0 3682.7562 4.244932
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6500 20746.748 224.6945 0 3682.4859 0.2929158
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6550 20913.725 197.29847 0 3682.9194 -15.792862
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6600 17956.374 690.52623 0 3683.2552 15.445255
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6650 20270.609 303.60078 0 3682.0357 -0.26503277
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6700 21442.931 109.08904 0 3682.9109 -2.8409166
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6750 20907.994 198.30695 0 3682.9726 0.91664072
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6800 20431.208 277.98326 0 3683.1845 -1.8537161
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6850 20312.052 297.88656 0 3683.2285 3.1028547
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6900 19458.401 439.97157 0 3683.0385 -4.1856293
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6950 20507.759 264.99217 0 3682.952 -1.4597973
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7000 20782.356 219.47456 0 3683.2006 -7.1967021
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7050 20560.324 256.07109 0 3682.7917 -10.720013
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7100 21652.145 74.086415 0 3682.7772 -0.61455054
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7150 20134.823 326.40272 0 3682.2065 11.689827
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7200 20778.071 219.16459 0 3682.1765 -1.796567
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7250 20153.065 323.13721 0 3681.9814 -0.1215538
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7300 19524.938 427.99711 0 3682.1534 -3.1139903
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7350 20554.595 256.63855 0 3682.4044 10.023083
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7400 18778.53 552.29852 0 3682.0534 -1.7145222
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7450 18972.509 520.15393 0 3682.2388 1.4489874
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7500 17680.668 736.20139 0 3682.9794 15.096954
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7550 19070.785 504.65403 0 3683.1182 2.2707533
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7600 20805.541 214.54957 0 3682.1398 -3.4306308
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7650 18473.262 604.25322 0 3683.1301 2.2083367
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7700 19294.016 466.99211 0 3682.6615 2.2666382
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7750 20995.664 183.47108 0 3682.7484 -13.935938
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7800 21042.433 175.06619 0 3682.1384 0.49855811
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7850 19343.054 459.21955 0 3683.0618 7.9049312
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7900 18382.898 619.01969 0 3682.8361 1.7996366
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7950 16092.435 1000.6563 0 3682.7287 29.993154
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8000 17551.635 757.47719 0 3682.7498 8.1753011
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8050 20309.875 298.25877 0 3683.2379 -1.9545317
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8100 21746.174 59.002125 0 3683.3645 -2.6980678
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8150 21478.427 103.44202 0 3683.1799 -10.930392
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8200 20986.729 185.46995 0 3683.2581 -14.298403
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8250 20744.064 225.47546 0 3682.8194 -6.4982356
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8300 19887.982 368.35069 0 3683.0143 1.5899179
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8350 21871.414 37.899202 0 3683.1348 -2.0554107
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8400 20002.858 348.98887 0 3682.7985 8.2963084
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8450 21553.861 90.985193 0 3683.2953 2.8575186
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8500 21605.143 82.347635 0 3683.2048 -4.711565
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8550 20151.76 324.4703 0 3683.097 -8.5109459
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8600 20564.158 255.77814 0 3683.1378 -1.3815408
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8650 19316.602 463.61706 0 3683.0507 -2.6895635
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8700 18157.859 656.69518 0 3683.0051 19.428927
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8750 18752.43 557.67555 0 3683.0805 1.9765973
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8800 20903.812 199.07408 0 3683.0428 1.9011523
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8850 20132.963 327.56826 0 3683.0621 3.0389961
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8900 21667.171 71.80023 0 3682.9954 -2.0042246
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8950 20346.973 292.00907 0 3683.1712 7.5582361
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9000 17889.448 695.59406 0 3677.1688 7.5315391
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9050 19446.144 441.90609 0 3682.9302 5.9819228
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9100 20384.34 285.05862 0 3682.4486 9.8610378
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9150 20023.515 344.98587 0 3682.2384 -0.40175043
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9200 17786.795 718.76166 0 3683.2275 10.984317
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9250 20843.023 208.42263 0 3682.2597 -7.4709344
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9300 21670.622 70.503925 0 3682.2742 -6.2303366
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9350 20642.313 241.21277 0 3681.5983 4.7423898
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9400 19228.566 476.44753 0 3681.2085 10.836639
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9450 21215.705 146.40003 0 3682.3509 -9.091421
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9500 21543.685 91.725901 0 3682.3401 -1.0608492
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9550 20143.22 324.98532 0 3682.1887 -5.995164
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9600 21234.294 142.96512 0 3682.0142 0.004838125
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9650 21025.207 177.8801 0 3682.0813 -5.4857701
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9700 20638.235 242.46577 0 3682.1716 -1.6014085
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9750 18374.191 620.54322 0 3682.9084 13.864712
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9800 19730.262 393.89083 0 3682.2679 5.7601754
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9850 21547.855 91.283379 0 3682.5926 2.1989329
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9900 20959.935 189.28821 0 3682.6108 2.1174676
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9950 21191.026 150.79441 0 3682.6321 8.3829825
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10000 20776.574 220.03769 0 3682.8 -1.8404787
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Loop time of 3.0852 on 1 procs for 10000 steps with 81 atoms
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Performance: 28004.636 tau/day, 3241.277 timesteps/s
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99.5% 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 | 0.17336 | 0.17336 | 0.17336 | 0.0 | 5.62
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Neigh | 0.1094 | 0.1094 | 0.1094 | 0.0 | 3.55
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Comm | 0.010163 | 0.010163 | 0.010163 | 0.0 | 0.33
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Output | 0.0030687 | 0.0030687 | 0.0030687 | 0.0 | 0.10
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Modify | 2.7782 | 2.7782 | 2.7782 | 0.0 | 90.05
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Other | | 0.01105 | | | 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: 82 ave 82 max 82 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 887 ave 887 max 887 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 887
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Ave neighs/atom = 10.9506
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Neighbor list builds = 992
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Dangerous builds = 939
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Please see the log.cite file for references relevant to this simulation
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Total wall time: 0:00:03
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