forked from lijiext/lammps
336 lines
19 KiB
Groff
336 lines
19 KiB
Groff
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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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 2 by 2 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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fix 1 all rigid/nve group 9 clump1 clump2 clump3 clump4 clump5 clump6 clump7 clump8 clump9
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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) = 3.95 | 4.044 | 4.326 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 14910.69 571.70921 0 5265.8153 32.005816
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100 16298.128 136.75661 0 5267.6488 16.449029
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150 16682.532 17.504156 0 5269.4124 14.901186
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200 16733.906 1.3755079 0 5269.4571 14.571305
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250 16738.861 -0.15272039 0 5269.4886 14.498342
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300 16738.608 -0.055216883 0 5269.5066 14.498
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350 16738.5 -0.017457072 0 5269.5104 14.498392
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400 16738.451 -0.0060161309 0 5269.5063 14.49851
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450 16738.435 -0.001271965 0 5269.5059 14.498571
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500 16738.443 -0.00081074175 0 5269.509 14.498598
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550 16738.452 -0.00083208965 0 5269.5118 14.498618
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600 16738.45 -0.00058358431 0 5269.5116 14.498617
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650 16738.443 -0.00047228525 0 5269.5093 14.4986
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700 16738.444 0 0 5269.5102 14.498612
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750 16738.461 0 0 5269.5157 14.498654
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800 16738.479 0 0 5269.521 14.498697
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850 16738.473 0 0 5269.5192 14.498683
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900 16738.449 0 0 5269.5116 14.498624
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950 16738.438 -0.0035324203 0 5269.5046 14.498537
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1000 16738.562 -0.051134242 0 5269.4963 14.498093
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1050 16737.343 0.32970192 0 5269.4934 14.527634
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1100 16737.878 0.16213235 0 5269.4941 14.533864
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1150 16738.682 -0.089236256 0 5269.4959 14.511765
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1200 16738.444 -0.0075446558 0 5269.5025 14.512479
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1250 16738.45 0 0 5269.5119 14.512611
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1300 16738.475 0 0 5269.5199 14.512673
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1350 16738.484 0 0 5269.5228 14.512696
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1400 16738.469 -0.00044683992 0 5269.5175 14.512651
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1450 16738.45 -0.0010933363 0 5269.511 14.512595
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1500 16738.445 -0.00057484239 0 5269.51 14.512591
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1550 16738.451 0 0 5269.5123 14.512615
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1600 16738.452 0 0 5269.5127 14.512618
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1650 16738.443 0 0 5269.5099 14.512596
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1700 16738.433 0 0 5269.5068 14.512572
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1750 16738.438 0 0 5269.5084 14.512584
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1800 16738.459 0 0 5269.5149 14.512635
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1850 16738.473 0 0 5269.5193 14.51267
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1900 16738.462 0 0 5269.5159 14.512644
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1950 16738.446 -0.0032069962 0 5269.5076 14.512539
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2000 16738.463 -0.013425408 0 5269.5027 14.512382
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2050 16738.535 -0.036964311 0 5269.5017 14.512152
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2100 16738.621 -0.063490509 0 5269.5023 14.512108
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2150 16738.594 -0.056143934 0 5269.5012 14.512117
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2200 16738.536 -0.038486645 0 5269.5007 14.512277
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2250 16738.496 -0.023712406 0 5269.503 14.51242
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2300 16738.488 -0.013209094 0 5269.5109 14.51255
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2350 16738.486 -0.0045244524 0 5269.519 14.512693
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2400 16738.475 -0.00051678325 0 5269.5194 14.512743
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2450 16738.456 -0.0023209272 0 5269.5115 14.512659
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2500 16738.442 -0.0052101787 0 5269.5042 14.512594
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2550 16738.552 -0.04420046 0 5269.4998 14.512177
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2600 16738.42 -0.004347531 0 5269.4982 14.512783
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2650 16734.241 1.3131302 0 5269.5 14.577195
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2700 16738.737 -0.10612056 0 5269.4961 14.503874
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2750 16732.705 1.7939719 0 5269.4974 14.629294
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2800 16738.558 -0.042867033 0 5269.5032 14.519893
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2850 16738.499 -0.01271227 0 5269.5146 14.518524
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2900 16738.486 -0.0032778045 0 5269.52 14.518712
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2950 16738.482 -0.0089544631 0 5269.5133 14.518629
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3000 16738.647 -0.070862542 0 5269.5031 14.51803
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3050 16678.313 18.829038 0 5269.409 15.533426
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3100 16632.312 33.399217 0 5269.4975 14.588597
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3150 16739.318 -0.31388148 0 5269.4715 13.520782
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3200 16727.951 3.26736 0 5269.4741 12.288358
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3250 16686.364 16.353793 0 5269.4682 14.152517
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3300 16738.532 -0.031574462 0 5269.5064 13.310615
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3350 16738.454 -0.0062292918 0 5269.5071 13.308187
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3400 16738.445 -0.0049349125 0 5269.5055 13.308178
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3450 16738.489 -0.021623738 0 5269.5026 13.308001
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3500 16737.78 0.19719043 0 5269.4983 13.325999
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3550 16658.578 25.116206 0 5269.4834 13.778249
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3600 16738.51 -0.032864725 0 5269.4981 12.392389
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3650 16738.899 -0.15952703 0 5269.4938 12.383503
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3700 16738.879 -0.16025994 0 5269.487 12.382575
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3750 16738.878 -0.16608251 0 5269.4806 12.382765
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3800 16738.591 -0.078679341 0 5269.4776 12.383227
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3850 16738.429 -0.024729409 0 5269.4807 12.382942
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3900 16738.399 -0.0062729967 0 5269.4897 12.383192
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3950 16738.428 -0.002521266 0 5269.5027 12.383324
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4000 16738.467 -0.0002068506 0 5269.5173 12.383474
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4050 16738.488 0 0 5269.5241 12.383531
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4100 16738.468 0 0 5269.5178 12.383482
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4150 16738.422 0 0 5269.5033 12.383369
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4200 16738.387 0 0 5269.4921 12.383281
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4250 16738.383 0 0 5269.4908 12.38327
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4300 16738.4 0 0 5269.4964 12.383314
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4350 16738.423 0 0 5269.5036 12.38337
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4400 16738.441 0 0 5269.5092 12.383414
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4450 16738.45 0 0 5269.5121 12.383437
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4500 16738.45 0 0 5269.5122 12.383438
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4550 16738.442 0 0 5269.5095 12.383417
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4600 16738.425 0 0 5269.5042 12.383376
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4650 16738.404 -0.0014438316 0 5269.4961 12.383299
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4700 16738.444 -0.024020551 0 5269.4862 12.382975
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4750 16738.49 -0.048521428 0 5269.4761 12.385777
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4800 16735.057 1.0347217 0 5269.4786 12.43543
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4850 16735.441 0.92650925 0 5269.4913 12.418653
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4900 16723.839 4.5908973 0 5269.5033 13.410103
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4950 16738.531 -0.02153767 0 5269.5159 13.089982
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5000 16738.45 -0.0042589696 0 5269.5077 13.090062
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5050 16738.409 -0.00024692476 0 5269.4987 13.090038
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5100 16738.404 0 0 5269.4976 13.090032
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5150 16738.421 0 0 5269.5029 13.090073
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5200 16738.44 0 0 5269.5087 13.090119
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5250 16738.448 -0.001279392 0 5269.5102 13.090114
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5300 16738.456 -0.0064376392 0 5269.5075 13.090026
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5350 16738.479 -0.020383842 0 5269.5007 13.089897
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5400 16735.845 0.79889474 0 5269.4909 13.136244
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5450 16735.558 0.87619992 0 5269.4778 12.324482
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5500 16711.494 8.4724208 0 5269.4984 12.656579
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5550 16454.525 89.074816 0 5269.2031 16.996503
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5600 16713.084 7.9801334 0 5269.5065 13.774977
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5650 16738.676 -0.079987764 0 5269.5033 13.168295
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5700 16446.281 91.866085 0 5269.399 23.764662
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5750 16738.549 -0.039869084 0 5269.5034 13.378121
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5800 16738.487 -0.014994475 0 5269.5086 13.378397
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5850 16738.466 -0.0051267556 0 5269.512 13.378559
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5900 16738.462 -0.0043690097 0 5269.5113 13.378572
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5950 16738.528 -0.03272741 0 5269.5039 13.378195
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6000 16702.774 10.969434 0 5269.2502 13.788851
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6050 16682.271 17.483158 0 5269.3092 13.3531
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6100 16738.508 -0.028838239 0 5269.5016 12.521082
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6150 16738.425 -0.0067595542 0 5269.4974 12.521221
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6200 16738.401 -0.0011499896 0 5269.4955 12.521252
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6250 16738.455 0 0 5269.5135 12.521408
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6300 16738.523 0 0 5269.5352 12.521578
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6350 16738.503 0 0 5269.5287 12.52153
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6400 16738.427 0 0 5269.5047 12.521342
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6450 16738.399 0 0 5269.496 12.521273
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6500 16738.425 0 0 5269.5042 12.521336
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6550 16738.441 0 0 5269.5093 12.521377
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6600 16738.42 0 0 5269.5025 12.521324
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6650 16738.398 0 0 5269.4957 12.52127
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6700 16738.435 0 0 5269.5074 12.52136
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6750 16738.505 0 0 5269.5293 12.521532
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6800 16738.508 0 0 5269.5303 12.521541
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6850 16738.446 0 0 5269.5108 12.521389
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6900 16738.414 0 0 5269.5009 12.521311
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6950 16738.432 0 0 5269.5063 12.521353
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7000 16738.444 0 0 5269.5102 12.521383
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7050 16738.421 0 0 5269.5029 12.521327
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7100 16738.393 0 0 5269.4941 12.521258
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7150 16738.419 0 0 5269.5022 12.52132
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7200 16738.489 0 0 5269.5244 12.521494
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7250 16738.505 0 0 5269.5293 12.521533
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7300 16738.443 0 0 5269.5098 12.521381
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7350 16738.404 0 0 5269.4976 12.521285
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7400 16738.43 0 0 5269.5058 12.521348
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7450 16738.461 0 0 5269.5156 12.521425
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7500 16738.447 0 0 5269.5109 12.52139
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7550 16738.407 0 0 5269.4986 12.521293
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7600 16738.412 0 0 5269.5002 12.521305
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7650 16738.478 0 0 5269.5208 12.521465
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7700 16738.51 0 0 5269.5309 12.521546
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7750 16738.454 0 0 5269.5135 12.52141
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7800 16738.398 0 0 5269.4958 12.521272
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7850 16738.407 -0.00021180981 0 5269.4982 12.521288
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7900 16738.441 -0.0002167964 0 5269.509 12.521371
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7950 16738.446 -0.00023848065 0 5269.5107 12.521385
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8000 16738.423 0 0 5269.5035 12.521331
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8050 16738.423 0 0 5269.5034 12.52133
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8100 16738.478 -0.00069623408 0 5269.52 12.521452
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8150 16738.523 -0.0040058355 0 5269.531 12.521499
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8200 16738.486 -0.0092298325 0 5269.5142 12.521332
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8250 16738.458 -0.023189665 0 5269.4914 12.521012
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8300 16738.513 -0.045846242 0 5269.4861 12.520778
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8350 16723.742 4.5698786 0 5269.4516 12.849386
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8400 16738.466 -0.02016972 0 5269.497 12.835784
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8450 16738.437 -0.012822703 0 5269.4952 12.829948
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8500 16738.408 -0.0016836132 0 5269.4972 12.830073
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8550 16738.464 -0.00097380297 0 5269.5155 12.830227
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8600 16738.669 -0.050578946 0 5269.5304 12.829946
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8650 15917.707 250.24016 0 5261.3702 24.544744
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8700 16738.445 0.0010615265 0 5269.5117 10.589987
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8750 16738.473 -0.010158834 0 5269.509 10.588904
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8800 16738.468 0 0 5269.5176 10.589124
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8850 16738.508 0 0 5269.5304 10.589223
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8900 16738.509 0 0 5269.5306 10.589226
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8950 16738.496 0 0 5269.5266 10.589195
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9000 16738.477 0 0 5269.5204 10.589147
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9050 16738.455 0 0 5269.5135 10.589092
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9100 16738.477 0 0 5269.5206 10.589146
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9150 16738.512 0 0 5269.5316 10.589233
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9200 16738.502 0 0 5269.5285 10.58921
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9250 16738.493 0 0 5269.5255 10.589186
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9300 16738.482 0 0 5269.522 10.589159
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9350 16738.46 0 0 5269.5151 10.589105
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9400 16738.481 0 0 5269.5217 10.589155
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9450 16738.509 0 0 5269.5307 10.589226
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9500 16738.491 0 0 5269.5248 10.589181
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9550 16738.484 0 0 5269.5227 10.589164
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9600 16738.483 0 0 5269.5223 10.589161
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9650 16738.464 0 0 5269.5166 10.589116
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9700 16738.484 0 0 5269.5228 10.589164
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9750 16738.507 0 0 5269.5301 10.589221
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9800 16738.482 0 0 5269.5221 10.589159
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9850 16738.478 0 0 5269.5208 10.589149
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9900 16738.487 -0.00030979591 0 5269.5233 10.589165
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9950 16738.476 -0.0009596827 0 5269.5193 10.589123
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10000 16738.494 -0.0006271698 0 5269.5253 10.589175
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Loop time of 0.212511 on 4 procs for 10000 steps with 81 atoms
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Performance: 406566.385 tau/day, 47056.295 timesteps/s
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91.9% CPU use with 4 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 | 0.0032909 | 0.0039915 | 0.0048544 | 0.9 | 1.88
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Neigh | 0.011434 | 0.01325 | 0.016991 | 1.9 | 6.24
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Comm | 0.076038 | 0.082493 | 0.088069 | 1.5 | 38.82
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Output | 0.0031183 | 0.0045295 | 0.0086036 | 3.5 | 2.13
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Modify | 0.099662 | 0.10206 | 0.10679 | 0.9 | 48.02
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Other | | 0.00619 | | | 2.91
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Nlocal: 20.25 ave 34 max 9 min
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Histogram: 2 0 0 0 0 0 0 1 0 1
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Nghost: 38.5 ave 43 max 26 min
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Histogram: 1 0 0 0 0 0 0 0 0 3
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Neighs: 0.75 ave 2 max 0 min
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Histogram: 2 0 0 0 0 1 0 0 0 1
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Total # of neighbors = 3
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Ave neighs/atom = 0.037037
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Neighbor list builds = 998
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Dangerous builds = 997
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Total wall time: 0:00:00
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