forked from lijiext/lammps
333 lines
18 KiB
Groff
333 lines
18 KiB
Groff
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LAMMPS (15 Feb 2016)
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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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1 neighbor list requests
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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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Memory usage per processor = 2.47028 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 -0.86699149
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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 6.0538616
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1350 20558.971 254.36482 0 3680.8601 -3.6773952
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1400 21485.029 99.812921 0 3680.6511 -16.185473
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1450 21771.107 52.15961 0 3680.6775 -2.4756673
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1500 21520.948 93.503927 0 3680.3286 2.1023576
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1550 21351.418 121.68137 0 3680.2511 5.5159947
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1600 20778.805 216.92177 0 3680.0559 15.089188
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1650 21477.638 100.21836 0 3679.8247 -1.1045746
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1700 18501.339 596.47914 0 3680.0357 -15.679679
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1750 18563.642 587.34785 0 3681.2882 33.532209
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1800 19110.185 494.8234 0 3679.8543 18.024046
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1850 21364.191 119.23545 0 3679.9339 2.5291103
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1900 20146.626 322.14867 0 3679.9197 5.7313218
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1950 20692.672 231.25325 0 3680.0319 4.2977763
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2000 20943.904 189.11235 0 3679.7629 -22.645121
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2050 19668.057 401.82994 0 3679.8394 3.6251916
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2100 20280.442 299.76155 0 3679.8353 7.4807949
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2150 19181.86 483.522 0 3680.4987 22.620507
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2200 21300.161 130.70534 0 3680.7322 4.7102665
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2250 20486.943 266.63931 0 3681.1299 -8.6456512
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2300 18653.122 572.24819 0 3681.1018 -5.2637122
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2350 21513.523 95.614901 0 3681.2021 -9.3621767
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2400 21466.272 103.56446 0 3681.2765 -29.561368
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2450 20100.105 332.27123 0 3682.2887 35.744287
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2500 20764.395 221.6677 0 3682.4001 -12.468906
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2550 20435.699 276.31055 0 3682.2603 -22.413697
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2600 21466.467 104.53618 0 3682.2807 -10.078508
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2650 20814.737 213.23892 0 3682.3617 5.1390411
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2700 18565.761 588.3578 0 3682.6513 22.27664
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2750 20772.36 220.1607 0 3682.2206 -7.9448198
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2800 21018.563 179.10058 0 3682.1945 -7.0717829
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2850 16789.412 884.21472 0 3682.4501 33.279015
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2900 19304.363 464.75282 0 3682.1466 7.947554
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2950 20513.758 263.07578 0 3682.0355 2.2361434
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3000 20617.309 245.95251 0 3682.1706 -0.75213689
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3050 18567.52 587.90473 0 3682.4914 -4.0112006
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3100 18696.577 566.20617 0 3682.3023 -1.4814167
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3150 19864.606 371.56078 0 3682.3284 8.9362836
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3200 18902.643 532.04614 0 3682.4867 0.76630303
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3250 21110.454 163.86212 0 3682.271 -1.6253894
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3300 19369.939 454.05833 0 3682.3816 4.9066544
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3350 19082.603 501.69905 0 3682.133 3.5982292
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3400 19527.779 426.918 0 3681.5478 6.9612143
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3450 19892.953 366.19989 0 3681.6921 3.0050426
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3500 19708.981 396.84552 0 3681.6756 7.0757635
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3550 20256.096 306.23937 0 3682.2554 -1.752138
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3600 21289.889 133.93823 0 3682.253 -3.7462615
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3650 18333.877 627.18028 0 3682.8264 -15.276791
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3700 19829.133 377.33753 0 3682.1931 -6.269648
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3750 20771.635 220.07171 0 3682.0109 -28.479036
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3800 18373.813 619.79253 0 3682.0947 29.594781
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3850 19320.99 461.92786 0 3682.0928 -5.3212101
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3900 16119.825 995.68064 0 3682.3182 -8.4683118
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3950 15556.948 1091.3655 0 3684.1902 20.98273
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4000 20000.464 348.24891 0 3681.6596 7.1589745
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4050 18870.219 536.59924 0 3681.6358 -3.7997025
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4100 19889.518 367.49253 0 3682.4122 -14.091266
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4150 15789.623 1051.3399 0 3682.9438 -4.4152389
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4200 20548.889 256.83493 0 3681.6498 0.92234153
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4250 20681.925 235.46113 0 3682.4487 -11.515773
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4300 19330.404 460.80975 0 3682.5437 -22.351775
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4350 19369.443 453.35405 0 3681.5945 29.418242
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4400 20762.165 222.24133 0 3682.6021 2.6627047
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4450 19984.657 350.71294 0 3681.4891 28.88731
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4500 21167.58 154.25344 0 3682.1834 -3.0784322
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4550 18133.576 660.73671 0 3682.9995 2.5305835
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4600 19935.069 360.36826 0 3682.8798 2.4575034
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4650 21413.76 113.86464 0 3682.8246 -5.1271547
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4700 21716.333 63.609419 0 3682.9982 -2.4708049
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4750 21352.947 124.36961 0 3683.1941 -0.29026265
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4800 19043.788 508.8617 0 3682.8264 14.797006
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4850 20516.121 263.78758 0 3683.1411 7.1348281
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4900 20624.5 245.81827 0 3683.235 0.34708051
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4950 20317.197 296.68937 0 3682.8889 -0.55065946
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5000 18346.865 625.37246 0 3683.1832 7.3371413
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5050 18867.53 538.49153 0 3683.0799 1.9249866
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5100 18790.276 551.17224 0 3682.885 2.2333017
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5150 20241.365 311.84683 0 3685.4076 -3.998004
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5200 17685.058 739.76418 0 3687.2739 3.2835025
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5250 18496.626 604.58166 0 3687.3526 -10.185776
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5300 18420.042 617.82026 0 3687.8273 -16.392458
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5350 18767.338 559.0349 0 3686.9246 4.5320767
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5400 20423.245 284.90517 0 3688.7794 -8.6356656
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5450 21080.398 176.18494 0 3689.5846 -16.450038
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5500 16684.424 909.12643 0 3689.8637 49.94555
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5550 20132.31 335.03663 0 3690.4216 -16.018038
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5600 20430.923 285.17562 0 3690.3295 -5.0773675
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5650 20479.943 276.55962 0 3689.8834 5.4334564
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5700 20061.532 345.95553 0 3689.5441 -16.230658
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5750 20523.759 268.92217 0 3689.5487 -4.4128812
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5800 18900.356 537.65462 0 3687.7139 13.605549
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5850 20280.502 310.27193 0 3690.3556 -4.7884959
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5900 19050.26 515.66087 0 3690.7042 7.8864722
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5950 19566.917 430.2997 0 3691.4525 31.715268
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6000 18878.118 544.75449 0 3691.1076 -4.2415329
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6050 19308.682 471.70734 0 3689.821 -10.561614
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6100 18776.194 560.04764 0 3689.4133 -7.7286747
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6150 21475.064 110.1508 0 3689.3281 -3.6506391
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6200 19975 360.82675 0 3689.9934 10.282021
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6250 21396.341 123.5341 0 3689.5909 -5.7215163
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6300 18533.423 600.87422 0 3689.778 15.408027
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6350 20653.152 247.19253 0 3689.3846 8.5607784
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6400 19716.537 403.41487 0 3689.5044 13.165575
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6450 21120.66 168.79838 0 3688.9084 -0.50382728
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6500 19700.345 404.7155 0 3688.1064 13.941375
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6550 10818.393 1892.037 0 3695.1025 38.423155
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6600 18684.478 574.84755 0 3688.9273 5.9176985
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6650 19219.732 486.04269 0 3689.3314 18.287659
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6700 20058.587 344.88255 0 3687.9804 6.5372086
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6750 21279.318 142.77333 0 3689.3264 2.498188
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6800 20671.545 244.25024 0 3689.5078 -4.1356416
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6850 21203.598 155.82001 0 3689.753 -0.0083061182
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6900 21699.344 73.301497 0 3689.8588 -8.0309898
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6950 20951.212 197.19403 0 3689.0627 0.76668303
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7000 20166.275 329.02869 0 3690.0746 2.0083318
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7050 21554.944 97.465792 0 3689.9564 -3.2420086
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7100 20817.494 220.25476 0 3689.8372 0.17206182
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7150 21481.11 109.84029 0 3690.0253 -3.6814741
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7200 21266.824 145.53099 0 3690.0016 -2.060543
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7250 19434.684 450.81331 0 3689.9273 9.4822765
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7300 21246.525 148.96573 0 3690.0532 3.3208839
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7350 19749.269 398.60049 0 3690.1454 1.0929662
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7400 20354.792 297.70261 0 3690.168 1.547159
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7450 19996.859 357.16723 0 3689.977 -0.68412025
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7500 20179.628 326.53243 0 3689.8038 -2.4805507
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7550 18765.184 561.65039 0 3689.1811 -1.7976428
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7600 19457.496 447.04428 0 3689.9603 -1.9055522
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7650 18206.823 655.57276 0 3690.0433 1.2797964
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7700 19152.344 497.77422 0 3689.8315 18.145069
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7750 21387.484 125.48654 0 3690.0673 -2.9915772
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7800 18127.052 668.61425 0 3689.7896 9.044869
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7850 21419.557 120.08889 0 3690.015 6.2651717
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7900 21817.182 53.739819 0 3689.9368 -4.2387416
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7950 18215.195 654.15494 0 3690.0208 -54.628049
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8000 21523.503 102.58018 0 3689.8307 -4.84236
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8050 20720.799 236.28689 0 3689.7535 -9.3725225
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8100 21196.483 157.3232 0 3690.0704 -7.7222497
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8150 20869.667 211.65308 0 3689.9309 -6.8438295
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8200 17790.052 725.72497 0 3690.7336 -25.697688
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8250 19634.94 417.71929 0 3690.2094 8.861604
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8300 19135.784 500.92443 0 3690.2218 -3.1245167
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8350 20191.718 324.93312 0 3690.2195 6.5736107
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8400 20695.239 241.02378 0 3690.2302 -14.592221
|
||
|
|
8450 21793.857 57.609525 0 3689.9191 -11.509747
|
||
|
|
8500 21271.088 144.43102 0 3689.6124 -0.091587085
|
||
|
|
8550 20064.337 345.21754 0 3689.2737 9.5058471
|
||
|
|
8600 20282.86 308.2307 0 3688.7074 2.265529
|
||
|
|
8650 21223.055 151.24306 0 3688.419 1.7296834
|
||
|
|
8700 18875.342 542.42055 0 3688.3108 6.367148
|
||
|
|
8750 20922.65 201.55122 0 3688.6595 3.4208578
|
||
|
|
8800 21406.54 120.8539 0 3688.6106 1.8253729
|
||
|
|
8850 19868.524 377.05623 0 3688.477 16.327796
|
||
|
|
8900 20025.322 348.94892 0 3686.5025 17.063406
|
||
|
|
8950 21224.374 151.3567 0 3688.7524 -0.11028753
|
||
|
|
9000 21318.309 135.862 0 3688.9135 -0.50826819
|
||
|
|
9050 17538.618 768.00136 0 3691.1043 37.978645
|
||
|
|
9100 21247.861 147.84641 0 3689.1566 -6.7773259
|
||
|
|
9150 18455.677 613.08767 0 3689.0339 -3.4844751
|
||
|
|
9200 19486.859 441.03829 0 3688.8482 -18.602827
|
||
|
|
9250 21774.926 59.710446 0 3688.8648 -13.379919
|
||
|
|
9300 17628.877 750.72321 0 3688.8694 27.797974
|
||
|
|
9350 19827.334 383.85708 0 3688.4128 6.5459021
|
||
|
|
9400 20020.126 351.61742 0 3688.3051 -14.332562
|
||
|
|
9450 21596.338 88.904175 0 3688.2939 1.5779716
|
||
|
|
9500 18981.418 524.60141 0 3688.1711 5.4352409
|
||
|
|
9550 18652.616 579.05144 0 3687.8208 25.600729
|
||
|
|
9600 21198.037 155.23097 0 3688.2371 -3.3586596
|
||
|
|
9650 19958.317 361.32544 0 3687.7115 4.2910178
|
||
|
|
9700 19129.101 499.5993 0 3687.7828 13.267102
|
||
|
|
9750 21913.967 35.689587 0 3688.0174 -7.3222905
|
||
|
|
9800 21314.694 135.43794 0 3687.8869 -9.5613518
|
||
|
|
9850 20899.743 204.82802 0 3688.1185 -2.6321428
|
||
|
|
9900 20288.244 306.5013 0 3687.8753 3.6196618
|
||
|
|
9950 19271.015 475.88527 0 3687.7211 -1.8196764
|
||
|
|
10000 21122.24 167.82714 0 3688.2005 -3.8464842
|
||
|
|
Loop time of 3.72277 on 1 procs for 10000 steps with 81 atoms
|
||
|
|
|
||
|
|
Performance: 23208.538 tau/day, 2686.173 timesteps/s
|
||
|
|
99.9% CPU use with 1 MPI tasks x no OpenMP threads
|
||
|
|
|
||
|
|
MPI task timing breakdown:
|
||
|
|
Section | min time | avg time | max time |%varavg| %total
|
||
|
|
---------------------------------------------------------------
|
||
|
|
Pair | 0.16199 | 0.16199 | 0.16199 | 0.0 | 4.35
|
||
|
|
Neigh | 0.098636 | 0.098636 | 0.098636 | 0.0 | 2.65
|
||
|
|
Comm | 0.010331 | 0.010331 | 0.010331 | 0.0 | 0.28
|
||
|
|
Output | 0.0020616 | 0.0020616 | 0.0020616 | 0.0 | 0.06
|
||
|
|
Modify | 3.4423 | 3.4423 | 3.4423 | 0.0 | 92.47
|
||
|
|
Other | | 0.007444 | | | 0.20
|
||
|
|
|
||
|
|
Nlocal: 81 ave 81 max 81 min
|
||
|
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||
|
|
Nghost: 95 ave 95 max 95 min
|
||
|
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||
|
|
Neighs: 744 ave 744 max 744 min
|
||
|
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||
|
|
|
||
|
|
Total # of neighbors = 744
|
||
|
|
Ave neighs/atom = 9.18519
|
||
|
|
Neighbor list builds = 992
|
||
|
|
Dangerous builds = 941
|
||
|
|
|
||
|
|
Please see the log.cite file for references relevant to this simulation
|
||
|
|
|
||
|
|
Total wall time: 0:00:03
|