forked from lijiext/lammps
341 lines
19 KiB
Groff
341 lines
19 KiB
Groff
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LAMMPS (27 Nov 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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atom_modify map array
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pair_style lj/cut 2.5
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fix 0 all property/atom i_bodies
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read_data data.rigid-property fix 0 NULL Bodies
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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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9 atoms in group clump1
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group clump2 id <> 10 18
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9 atoms in group clump2
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group clump3 id <> 19 27
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9 atoms in group clump3
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group clump4 id <> 28 36
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9 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 <> 46 54
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9 atoms in group clump6
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group clump7 id <> 55 63
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9 atoms in group clump7
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group clump8 id <> 64 72
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9 atoms in group clump8
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group clump9 id <> 73 81
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9 atoms in group clump9
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# assemble bodies from per-atom custom integer property bodies
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fix 1 all rigid custom i_bodies
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9 rigid bodies with 81 atoms
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# 1 chain 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 <> 36 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 clump5 # clump6 clump7 clump8 clump9
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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
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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) = 4.046 | 4.046 | 4.046 Mbytes
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Step Temp E_pair E_mol TotEng Press
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0 115.29439 5235.9179 0 5272.2142 -2.7403788
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50 14910.685 571.71558 0 5265.82 32.006171
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100 16298.442 136.66184 0 5267.653 16.444229
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150 16682.606 17.490511 0 5269.4219 14.900344
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200 16733.929 1.372872 0 5269.4617 14.569267
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250 16738.853 -0.15252816 0 5269.4864 14.496404
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300 16738.588 -0.055171335 0 5269.5002 14.496025
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350 16738.492 -0.017444677 0 5269.5077 14.496446
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400 16738.464 -0.0060102023 0 5269.5104 14.496618
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450 16738.455 -0.0012713351 0 5269.5124 14.496701
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500 16738.455 -0.00081068621 0 5269.5128 14.496709
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550 16738.455 -0.00083203497 0 5269.5129 14.496707
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600 16738.455 -0.00058355356 0 5269.5131 14.496709
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650 16738.455 -0.00047226704 0 5269.5131 14.496708
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700 16738.455 0 0 5269.5136 14.496713
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750 16738.455 0 0 5269.5136 14.49671
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800 16738.455 0 0 5269.5137 14.496709
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850 16738.455 0 0 5269.5137 14.49671
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900 16738.456 0 0 5269.5138 14.496713
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950 16738.462 -0.0035323872 0 5269.5122 14.496671
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1000 16738.586 -0.051135144 0 5269.5036 14.496229
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1050 16737.358 0.32995057 0 5269.4981 14.525763
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1100 16737.892 0.16210246 0 5269.4984 14.531983
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1150 16738.703 -0.089235095 0 5269.5025 14.509899
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1200 16738.466 -0.0075446243 0 5269.5096 14.510615
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1250 16738.456 0 0 5269.514 14.510704
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1300 16738.457 0 0 5269.5141 14.510701
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1350 16738.457 0 0 5269.5141 14.510699
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1400 16738.457 -0.00044736511 0 5269.5138 14.510693
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1450 16738.458 -0.0010971179 0 5269.5134 14.510687
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1500 16738.458 -0.00057885428 0 5269.5139 14.510698
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1550 16738.457 0 0 5269.5143 14.51071
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1600 16738.457 0 0 5269.5144 14.510712
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1650 16738.457 0 0 5269.5144 14.510712
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1700 16738.458 0 0 5269.5144 14.51071
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1750 16738.458 0 0 5269.5145 14.510708
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1800 16738.458 0 0 5269.5145 14.510706
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1850 16738.458 0 0 5269.5146 14.510705
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1900 16738.458 0 0 5269.5146 14.510706
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1950 16738.465 -0.0031733615 0 5269.5134 14.510659
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2000 16738.491 -0.013255268 0 5269.5117 14.510532
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2050 16738.556 -0.0365811 0 5269.5087 14.51029
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2100 16738.633 -0.063209659 0 5269.5065 14.510219
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2150 16738.607 -0.05601761 0 5269.5055 14.510231
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2200 16738.557 -0.038423032 0 5269.5072 14.510404
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2250 16738.515 -0.023709918 0 5269.5088 14.510539
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2300 16738.489 -0.013249035 0 5269.5111 14.510621
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2350 16738.468 -0.0045563719 0 5269.5131 14.510714
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2400 16738.46 -0.00052194273 0 5269.5146 14.510771
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2450 16738.464 -0.0023259756 0 5269.514 14.510746
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2500 16738.468 -0.0051929186 0 5269.5127 14.510731
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2550 16738.581 -0.044940117 0 5269.5085 14.510315
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2600 16738.427 -7.972284e-05 0 5269.5046 14.510657
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2650 16733.017 1.7051479 0 5269.5067 14.596295
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2700 16738.761 -0.10614946 0 5269.5038 14.499584
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2750 16733.973 1.4038179 0 5269.5064 14.598107
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2800 16738.585 -0.046813448 0 5269.5076 14.511073
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2850 16738.487 -0.012558719 0 5269.5111 14.510111
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2900 16738.465 -0.0026252725 0 5269.514 14.510277
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2950 16738.476 -0.0082220764 0 5269.512 14.510223
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3000 16738.66 -0.071284779 0 5269.507 14.509758
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3050 16715.332 7.2419352 0 5269.476 14.870305
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3100 16653.226 26.818761 0 5269.5009 14.496764
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3150 16739.351 -0.30690375 0 5269.4886 13.643904
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3200 16733.238 1.6025328 0 5269.4737 12.016934
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3250 16734.374 1.2554429 0 5269.4841 11.963561
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3300 16732.156 1.9585967 0 5269.4893 12.234024
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3350 16738.655 -0.079693236 0 5269.497 12.092757
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3400 16738.543 -0.042215005 0 5269.4991 12.092809
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3450 16738.591 -0.059327511 0 5269.4972 12.092536
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3500 16738.759 -0.11761245 0 5269.4918 12.09203
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3550 16713.405 7.8460621 0 5269.4737 12.389816
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3600 16734.939 1.0821936 0 5269.4891 12.173591
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3650 16738.808 -0.13663194 0 5269.4882 12.027009
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3700 16738.602 -0.070934368 0 5269.4889 12.025288
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3750 16737.731 0.20706558 0 5269.4927 12.061948
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3800 16738.578 -0.05582043 0 5269.4965 12.035665
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3850 16738.471 -0.016307928 0 5269.5024 12.035302
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3900 16738.449 -0.0058182199 0 5269.5059 12.035401
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3950 16738.439 -0.0012027325 0 5269.5074 12.035461
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4000 16738.436 -0.00020698452 0 5269.5075 12.035469
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4050 16738.437 0 0 5269.5078 12.035454
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4100 16738.437 0 0 5269.508 12.035435
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4150 16738.438 0 0 5269.5081 12.035426
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4200 16738.438 0 0 5269.5083 12.035432
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4250 16738.439 0 0 5269.5085 12.035447
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4300 16738.439 0 0 5269.5086 12.035463
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4350 16738.44 0 0 5269.5087 12.035474
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4400 16738.44 0 0 5269.5088 12.035478
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4450 16738.44 0 0 5269.5089 12.035474
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4500 16738.44 0 0 5269.509 12.035462
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4550 16738.441 0 0 5269.5092 12.035449
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4600 16738.441 0 0 5269.5093 12.035445
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4650 16738.442 0 0 5269.5095 12.035451
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4700 16738.442 0 0 5269.5096 12.03546
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4750 16738.443 0 0 5269.5097 12.035465
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4800 16738.443 0 0 5269.5098 12.035466
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4850 16738.443 0 0 5269.51 12.035463
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4900 16738.444 0 0 5269.5101 12.035456
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4950 16738.444 0 0 5269.5102 12.035447
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5000 16738.445 0 0 5269.5104 12.03544
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5050 16738.445 0 0 5269.5105 12.035442
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5100 16738.446 0 0 5269.5107 12.035455
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5150 16738.446 0 0 5269.5108 12.03547
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5200 16738.446 0 0 5269.5109 12.035479
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5250 16738.447 0 0 5269.511 12.035479
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5300 16738.447 0 0 5269.5111 12.03547
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5350 16738.447 0 0 5269.5112 12.035454
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5400 16738.448 0 0 5269.5113 12.035434
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5450 16738.448 0 0 5269.5115 12.03542
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5500 16738.449 0 0 5269.5117 12.035422
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5550 16738.457 -0.0030919234 0 5269.5111 12.035383
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5600 16738.51 -0.021618357 0 5269.5092 12.035106
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5650 16738.622 -0.059214788 0 5269.507 12.035694
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5700 16395.28 108.06942 0 5269.5463 24.369038
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5750 16738.544 -0.033973429 0 5269.5077 12.011261
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5800 16738.456 -0.0037013529 0 5269.5102 12.011675
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5850 16738.451 0 0 5269.5123 12.011709
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5900 16738.451 -0.0002211587 0 5269.5122 12.011687
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5950 16738.452 -0.00024253349 0 5269.5124 12.011678
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6000 16738.452 0 0 5269.5128 12.011688
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6050 16738.453 0 0 5269.513 12.011702
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6100 16738.453 0 0 5269.5131 12.011716
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6150 16738.454 0 0 5269.5132 12.011725
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6200 16738.454 0 0 5269.5133 12.011728
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6250 16738.454 0 0 5269.5134 12.011723
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6300 16738.455 0 0 5269.5135 12.011712
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6350 16738.455 0 0 5269.5137 12.0117
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6400 16738.456 0 0 5269.5138 12.011697
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6450 16738.456 0 0 5269.514 12.011704
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6500 16738.456 0 0 5269.5141 12.011714
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6550 16738.457 0 0 5269.5142 12.011719
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6600 16738.457 0 0 5269.5143 12.011718
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6650 16738.458 0 0 5269.5144 12.011713
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6700 16738.458 0 0 5269.5146 12.011705
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6750 16738.459 0 0 5269.5147 12.011696
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6800 16738.459 0 0 5269.5149 12.01169
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6850 16738.46 0 0 5269.515 12.011695
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6900 16738.46 0 0 5269.5152 12.01171
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6950 16738.46 0 0 5269.5153 12.011726
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7000 16738.461 0 0 5269.5154 12.011736
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7050 16738.461 0 0 5269.5155 12.011737
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7100 16738.461 0 0 5269.5155 12.011728
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7150 16738.461 0 0 5269.5156 12.011712
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7200 16738.462 0 0 5269.5158 12.011691
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7250 16738.463 0 0 5269.516 12.011676
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7300 16738.463 0 0 5269.5162 12.011677
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7350 16738.464 0 0 5269.5164 12.011693
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7400 16738.464 0 0 5269.5165 12.011713
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7450 16738.465 0 0 5269.5166 12.011729
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7500 16738.465 0 0 5269.5167 12.011736
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7550 16738.465 0 0 5269.5168 12.011734
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7600 16738.465 0 0 5269.5168 12.011722
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7650 16738.466 0 0 5269.517 12.011704
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7700 16738.466 0 0 5269.5171 12.011687
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7750 16738.467 0 0 5269.5173 12.011681
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7800 16738.467 0 0 5269.5175 12.011687
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7850 16738.468 0 0 5269.5176 12.0117
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7900 16738.468 0 0 5269.5178 12.011712
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7950 16738.469 0 0 5269.5179 12.011721
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8000 16738.469 0 0 5269.518 12.011724
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8050 16738.469 0 0 5269.5181 12.01172
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8100 16738.47 0 0 5269.5182 12.011709
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8150 16738.47 0 0 5269.5183 12.0117
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8200 16738.47 0 0 5269.5185 12.0117
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8250 16738.471 0 0 5269.5186 12.011709
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8300 16738.471 0 0 5269.5187 12.011719
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8350 16738.472 0 0 5269.5189 12.011723
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8400 16738.472 0 0 5269.519 12.01172
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8450 16738.473 -0.00039690666 0 5269.5189 12.011706
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8500 16738.481 -0.0034646804 0 5269.5182 12.011643
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8550 16738.483 -0.0045307409 0 5269.5178 12.011621
|
||
|
|
8600 16738.474 -0.00076532811 0 5269.5189 12.011681
|
||
|
|
8650 16738.474 0 0 5269.5197 12.011699
|
||
|
|
8700 16738.475 0 0 5269.5199 12.011715
|
||
|
|
8750 16738.475 0 0 5269.52 12.011732
|
||
|
|
8800 16738.475 0 0 5269.52 12.011743
|
||
|
|
8850 16738.476 0 0 5269.5201 12.011744
|
||
|
|
8900 16738.476 0 0 5269.5202 12.011735
|
||
|
|
8950 16738.476 0 0 5269.5203 12.011719
|
||
|
|
9000 16738.477 0 0 5269.5205 12.011698
|
||
|
|
9050 16738.477 0 0 5269.5206 12.011683
|
||
|
|
9100 16738.478 0 0 5269.5208 12.011684
|
||
|
|
9150 16738.479 0 0 5269.521 12.011701
|
||
|
|
9200 16738.479 0 0 5269.5212 12.011722
|
||
|
|
9250 16738.479 0 0 5269.5213 12.011738
|
||
|
|
9300 16738.48 0 0 5269.5214 12.011746
|
||
|
|
9350 16738.48 0 0 5269.5214 12.011744
|
||
|
|
9400 16738.48 0 0 5269.5215 12.011732
|
||
|
|
9450 16738.48 0 0 5269.5216 12.011715
|
||
|
|
9500 16738.481 -0.00037652434 0 5269.5216 12.011692
|
||
|
|
9550 16738.493 -0.005315616 0 5269.5203 12.011611
|
||
|
|
9600 16738.549 -0.026814368 0 5269.5163 12.011415
|
||
|
|
9650 16738.765 -0.10191523 0 5269.5092 12.011013
|
||
|
|
9700 16735.041 1.0589885 0 5269.4979 12.062708
|
||
|
|
9750 16738.013 0.13550123 0 5269.5101 11.407245
|
||
|
|
9800 16738.512 -0.011620328 0 5269.5201 11.394974
|
||
|
|
9850 16738.489 -0.00067270523 0 5269.5237 11.395098
|
||
|
|
9900 16738.489 -0.00024984554 0 5269.5242 11.395085
|
||
|
|
9950 16738.49 0 0 5269.5245 11.395076
|
||
|
|
10000 16738.49 0 0 5269.5246 11.395075
|
||
|
|
Loop time of 0.156049 on 1 procs for 10000 steps with 81 atoms
|
||
|
|
|
||
|
|
Performance: 553673.043 tau/day, 64082.528 timesteps/s
|
||
|
|
97.6% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||
|
|
|
||
|
|
MPI task timing breakdown:
|
||
|
|
Section | min time | avg time | max time |%varavg| %total
|
||
|
|
---------------------------------------------------------------
|
||
|
|
Pair | 0.010187 | 0.010187 | 0.010187 | 0.0 | 6.53
|
||
|
|
Neigh | 0.040601 | 0.040601 | 0.040601 | 0.0 | 26.02
|
||
|
|
Comm | 0.013221 | 0.013221 | 0.013221 | 0.0 | 8.47
|
||
|
|
Output | 0.0016611 | 0.0016611 | 0.0016611 | 0.0 | 1.06
|
||
|
|
Modify | 0.085107 | 0.085107 | 0.085107 | 0.0 | 54.54
|
||
|
|
Other | | 0.005271 | | | 3.38
|
||
|
|
|
||
|
|
Nlocal: 81 ave 81 max 81 min
|
||
|
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||
|
|
Nghost: 84 ave 84 max 84 min
|
||
|
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||
|
|
Neighs: 0 ave 0 max 0 min
|
||
|
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||
|
|
|
||
|
|
Total # of neighbors = 0
|
||
|
|
Ave neighs/atom = 0
|
||
|
|
Neighbor list builds = 998
|
||
|
|
Dangerous builds = 997
|
||
|
|
Total wall time: 0:00:00
|