forked from lijiext/lammps
343 lines
19 KiB
Groff
343 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 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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#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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#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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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 <> 37 45
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9 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
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1 clusters, 4 bodies, 3 joints, 36 atoms
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fix 2 all poems group clump5 clump6 clump7 clump8 clump9
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1 clusters, 5 bodies, 4 joints, 45 atoms
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neigh_modify exclude group clump1 clump1
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neigh_modify exclude group clump2 clump2
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neigh_modify exclude group clump3 clump3
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neigh_modify exclude group clump4 clump4
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neigh_modify exclude group clump5 clump5
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neigh_modify exclude group clump6 clump6
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neigh_modify exclude group clump7 clump7
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neigh_modify exclude group clump8 clump8
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neigh_modify exclude group clump9 clump9
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thermo 100
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#dump 1 all atom 50 dump.rigid.poems2
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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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WARNING: More than one fix poems (../fix_poems.cpp:363)
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WARNING: More than one fix poems (../fix_poems.cpp:363)
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WARNING: One or more atoms are time integrated more than once (../modify.cpp:279)
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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) = 3.825 | 3.919 | 4.201 Mbytes
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Step Temp E_pair E_mol TotEng Press
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0 196.00047 3632.2347 0 3668.5311 -2.7403788
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50 12167.633 1505.5478 0 3758.8133 35.125973
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100 17556.978 512.66277 0 3763.9549 11.137534
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150 19579.586 138.04942 0 3763.8987 -29.953971
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200 19757.51 105.30542 0 3764.1036 -0.030645317
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250 18218.374 390.10747 0 3763.8804 13.711001
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300 19383.039 174.40688 0 3763.8586 5.7240693
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350 20125.986 36.972611 0 3764.0071 1.9559205
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400 18888.816 266.10975 0 3764.0386 9.6362168
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450 19307.656 188.2511 0 3763.743 1.9326206
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500 16331.197 738.56392 0 3762.8597 9.1715579
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550 19318.722 186.16172 0 3763.7027 3.0115336
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600 19455.268 161.20621 0 3764.0336 0.55208034
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650 18487.011 340.03216 0 3763.5528 -8.0359122
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700 17321.201 556.32471 0 3763.9545 -13.631751
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750 18979.187 249.04389 0 3763.7082 -2.6072455
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800 19342.456 181.85552 0 3763.7918 8.1918726
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850 19070.641 232.19342 0 3763.7936 7.3148472
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900 19478.873 156.65987 0 3763.8586 2.4284987
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950 19912.415 76.437437 0 3763.9216 -1.4667227
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1000 16003.749 802.39753 0 3766.0548 46.642188
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1050 19859.583 86.64176 0 3764.3424 -2.1961943
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1100 19229.575 203.61488 0 3764.6473 -10.632365
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1150 18821.6 279.15861 0 3764.64 -0.89495035
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1200 19392.695 173.59744 0 3764.8373 1.8508753
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1250 16459.624 717.32104 0 3765.3995 33.478127
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1300 19343.863 182.59043 0 3764.7874 0.75890736
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1350 20019.643 57.503573 0 3764.8448 0.31444671
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1400 18549.582 329.31436 0 3764.4221 10.738303
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1450 15163.926 957.47584 0 3765.6103 -17.923459
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1500 19223.688 204.15172 0 3764.0939 -1.6134536
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1550 18147.996 404.12676 0 3764.8668 8.4194774
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1600 18615.043 317.42466 0 3764.6548 -2.3288957
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1650 20120.654 38.887927 0 3764.935 -8.7620244
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1700 19450.906 162.98284 0 3765.0025 2.3254707
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1750 19374.632 177.37954 0 3765.2744 8.9328778
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1800 19424.403 167.93971 0 3765.0514 0.081234023
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1850 17936.311 442.83087 0 3764.3699 6.600894
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1900 19982.596 64.40607 0 3764.8868 -2.9530102
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1950 16215.95 761.89459 0 3764.8482 13.994238
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2000 18584.39 322.12621 0 3763.68 7.1654863
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2050 20107.966 41.025634 0 3764.723 -0.31093298
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2100 20002.346 60.590652 0 3764.7288 -6.7919499
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2150 16949.612 626.62391 0 3765.441 3.5094585
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2200 20010.952 58.808492 0 3764.5403 -10.862255
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2250 18982.727 247.00941 0 3762.3292 -0.53796622
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2300 18401.351 354.86992 0 3762.5275 1.0919209
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2350 19390.5 172.94589 0 3763.7793 -3.3526281
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2400 16081.648 786.23133 0 3764.3143 -16.197875
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2450 18870.722 268.69249 0 3763.2707 11.192419
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2500 19687.71 117.6898 0 3763.562 4.387789
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2550 18872.129 268.54506 0 3763.3838 -5.6577428
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2600 17017.179 612.11028 0 3763.4397 6.3187623
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2650 18766.343 288.63699 0 3763.8856 2.3968008
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2700 19737.998 108.02069 0 3763.2054 -0.30752024
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2750 19508.797 150.69812 0 3763.4384 -1.6171126
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2800 18394.822 355.73011 0 3762.1787 21.193311
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2850 18561.108 325.76417 0 3763.0065 3.9331499
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2900 20124.042 36.554163 0 3763.2286 0.54133121
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2950 15727.607 849.90471 0 3762.4245 13.885323
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3000 17991.206 431.32693 0 3763.0317 9.9953567
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3050 18834.86 275.34241 0 3763.2795 9.1519305
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3100 18986.272 247.38123 0 3763.3575 -1.8754521
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3150 19979.145 63.575968 0 3763.4177 -11.800026
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3200 19953.846 68.376593 0 3763.5332 -6.7719573
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3250 15646.02 867.19502 0 3764.6062 16.433911
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3300 16946.252 625.14854 0 3763.3433 4.3975456
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3350 19006.567 243.97026 0 3763.7048 5.3392405
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3400 18082.133 414.87059 0 3763.4138 15.143954
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3450 18273.719 379.36162 0 3763.3836 5.4465204
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3500 19783.17 100.06678 0 3763.6167 1.9588505
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3550 19794.99 97.904519 0 3763.6435 -3.0349395
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3600 18357.708 363.98291 0 3763.5585 -2.1229788
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3650 19647.179 125.48949 0 3763.8559 1.2967845
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3700 18806.632 281.78709 0 3764.4967 5.125718
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3750 18982.747 248.97053 0 3764.294 -0.72036085
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3800 19597.926 135.04805 0 3764.2935 -3.2129291
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3850 18914.042 261.7133 0 3764.3136 -12.163282
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3900 18646.326 311.16482 0 3764.1881 5.1808943
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3950 18589.554 321.36256 0 3763.8726 4.9554103
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4000 17877.615 453.02456 0 3763.694 9.8457113
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4050 19440.059 164.15739 0 3764.1684 -5.4054486
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4100 18505.545 337.36023 0 3764.313 4.8468985
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4150 19220.307 204.85944 0 3764.1755 -6.5040818
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4200 19058.915 234.79578 0 3764.2245 3.1852011
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4250 19867.025 85.136186 0 3764.2149 5.6156236
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4300 16989.857 616.86564 0 3763.1355 -3.4041875
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4350 19782.09 100.85847 0 3764.2085 3.2531098
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4400 19879.56 82.559198 0 3763.9593 1.6340828
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4450 19409.95 169.46676 0 3763.9019 -1.824265
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4500 19742.977 107.72786 0 3763.8347 -0.72711698
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4550 17166.529 585.04113 0 3764.028 -0.38806102
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4600 19604.596 133.61426 0 3764.0949 -5.2712214
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4650 18865.608 270.23956 0 3763.8707 1.5751363
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4700 20190.139 25.270932 0 3764.1855 -10.159924
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4750 20043.487 52.56327 0 3764.3201 -4.713579
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4800 19361.931 178.70311 0 3764.246 4.2460799
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4850 19460.365 160.29083 0 3764.0621 3.5079181
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4900 18252.89 384.16194 0 3764.3268 4.1870604
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4950 19516.947 150.07365 0 3764.3231 4.0238527
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5000 19041.145 238.27335 0 3764.4113 8.2280019
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5050 19519.408 149.66793 0 3764.3731 -0.088904966
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5100 18087.848 415.34004 0 3764.9416 8.9482852
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5150 19392.463 173.43121 0 3764.628 -6.6722716
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5200 19683.968 119.46663 0 3764.6458 -2.0330852
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5250 19675.404 121.09497 0 3764.6884 3.0627309
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5300 18627.53 314.96107 0 3764.5038 5.2692141
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5350 20022.616 56.725346 0 3764.6172 -7.7034469
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5400 19353.4 180.6482 0 3764.6112 -2.3897589
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5450 16966.649 622.29693 0 3764.2689 6.3601638
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5500 17584.292 508.42495 0 3764.7753 5.949219
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5550 19169.69 214.76864 0 3764.7113 3.3778997
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5600 19491.814 155.19149 0 3764.7866 -0.20031164
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5650 19079.585 231.70394 0 3764.9605 7.3017226
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5700 19686.564 119.34 0 3765 0.98980357
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5750 19639.909 127.89886 0 3764.919 2.3982612
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5800 19474.109 158.55418 0 3764.8706 3.4940447
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5850 16957.663 624.72623 0 3765.0342 10.739819
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5900 19950.579 70.027987 0 3764.5796 4.6925057
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5950 19759.601 105.38621 0 3764.5716 3.0958319
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6000 19129.749 221.96406 0 3764.5102 -1.0612997
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6050 16087.951 785.36134 0 3764.6115 -15.255986
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6100 18851.976 272.98306 0 3764.0896 4.9341766
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6150 19532.23 147.4113 0 3764.4909 1.3206073
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6200 18051.604 421.79367 0 3764.6833 2.587863
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6250 18922.77 259.81211 0 3764.0287 10.363589
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6300 18402.504 356.81518 0 3764.6864 8.3589218
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6350 19315.369 187.64457 0 3764.5647 1.0716382
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6400 19700.59 116.50438 0 3764.7618 2.165408
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6450 19596.362 135.79675 0 3764.7527 1.6466783
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6500 20217.677 20.884953 0 3764.8993 -3.5893732
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6550 18278.991 379.95981 0 3764.9582 7.0433091
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6600 20142.999 34.761283 0 3764.9462 1.7083655
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6650 20185.488 26.899017 0 3764.9524 -0.65741058
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6700 17942.962 441.72909 0 3764.4999 -3.691039
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6750 16435.681 720.9581 0 3764.6028 -9.4583249
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6800 17825.95 463.58979 0 3764.6916 6.1557503
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6850 19440.75 164.52796 0 3764.6669 -11.921703
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6900 18824.905 278.4897 0 3764.5832 -1.4668322
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6950 19069.14 233.25502 0 3764.5772 6.8149838
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7000 18983.209 249.29193 0 3764.701 15.140158
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7050 15623.103 872.33684 0 3765.5041 7.3268767
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7100 20090.283 44.006184 0 3764.429 2.6959947
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7150 15535.27 888.39683 0 3765.2987 -4.1285644
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7200 19425.575 167.19079 0 3764.5195 4.9190857
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7250 18684.497 304.24754 0 3764.3396 7.3927682
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7300 17632.518 498.82765 0 3764.1087 5.1101854
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7350 18969.793 251.66375 0 3764.5884 -3.7865508
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7400 17700.626 486.89931 0 3764.7931 -8.8531288
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7450 17897.361 450.31562 0 3764.6417 -3.6095062
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7500 18795.228 284.03842 0 3764.6361 8.3567203
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7550 18658.285 309.34015 0 3764.5781 0.4306691
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7600 19230.039 203.5385 0 3764.6567 0.80253549
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7650 19513.551 150.86999 0 3764.4906 0.32848159
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7700 19494.849 154.28788 0 3764.4452 -4.2498631
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7750 20011.058 58.832118 0 3764.5835 0.54896615
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7800 19241.055 201.57548 0 3764.7338 -0.26200786
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7850 19512.742 151.11436 0 3764.5851 2.7308876
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7900 19688.007 118.68023 0 3764.6075 0.80454178
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7950 16891.645 636.56823 0 3764.6507 -25.839253
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8000 19425.572 167.33746 0 3764.6657 -2.8744687
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8050 19444.916 163.57779 0 3764.4882 8.5388183
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8100 19540.338 145.77731 0 3764.3585 5.5606379
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8150 17997.991 429.85951 0 3762.8208 20.179487
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8200 19463.886 159.50302 0 3763.9264 0.19577123
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8250 19517.733 149.53457 0 3763.9295 2.3294314
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8300 19236.221 201.66041 0 3763.9236 5.8204747
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8350 18662.608 308.25544 0 3764.2939 5.4422482
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8400 19030.046 239.38211 0 3763.4647 3.7940188
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8450 18058.148 419.70672 0 3763.8081 4.4010713
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8500 16866.001 641.00564 0 3764.3392 -19.894815
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8550 19484.364 155.35821 0 3763.5737 4.2635496
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8600 18562.912 326.16323 0 3763.7395 11.288271
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8650 19256.188 197.67578 0 3763.6365 -4.1872666
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8700 19653.945 124.27148 0 3763.8909 -7.4888761
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8750 19590.834 136.12748 0 3764.0596 1.0605539
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8800 19065.424 233.46882 0 3764.1029 1.8432113
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8850 18961.297 252.69734 0 3764.0486 6.7414134
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8900 19879.711 82.777822 0 3764.2058 0.12631864
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8950 18689.712 302.80546 0 3763.8632 5.1584036
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9000 19114.403 224.23511 0 3763.9393 -4.5856366
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9050 17626.3 500.49518 0 3764.6248 -3.9436947
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9100 18552.501 328.86032 0 3764.5087 -0.32810034
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9150 15039.846 979.12961 0 3764.2862 16.571104
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9200 19146.923 218.64681 0 3764.3733 -4.6264398
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9250 17606.161 503.14852 0 3763.5487 13.13675
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9300 18002.328 430.47362 0 3764.2381 4.9326117
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9350 19980.452 64.168644 0 3764.2524 -5.6111349
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9400 18953.798 254.44926 0 3764.4118 2.3662302
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9450 17151.075 588.59472 0 3764.7197 4.3116983
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9500 19128.858 221.38199 0 3763.763 3.6641306
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9550 18217.322 390.53199 0 3764.1101 1.8537154
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9600 19094.478 227.98925 0 3764.0038 3.972665
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9650 19577.649 138.55507 0 3764.0456 4.0408247
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9700 19331.361 184.31942 0 3764.2011 -4.7996733
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9750 18999.798 245.87295 0 3764.3541 -0.26741334
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9800 18987.181 248.37105 0 3764.5157 6.1717595
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9850 20094.73 43.013036 0 3764.2593 -8.9770288
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9900 18988.815 247.63984 0 3764.087 -6.3990966
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9950 18290.808 377.34967 0 3764.5363 7.7453525
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10000 19558.326 142.47047 0 3764.3828 3.4110829
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Loop time of 3.53831 on 4 procs for 10000 steps with 81 atoms
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Performance: 24418.438 tau/day, 2826.208 timesteps/s
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98.7% 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 | 0.0096724 | 0.035349 | 0.063574 | 10.3 | 1.00
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Neigh | 0.0091243 | 0.022333 | 0.037608 | 6.9 | 0.63
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Comm | 0.18063 | 0.2494 | 0.33202 | 12.6 | 7.05
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Output | 0.0060797 | 0.0065744 | 0.0074706 | 0.7 | 0.19
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Modify | 3.0943 | 3.1895 | 3.2828 | 4.0 | 90.14
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Other | | 0.0352 | | | 0.99
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Nlocal: 20.25 ave 36 max 0 min
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Histogram: 1 0 1 0 0 0 0 0 0 2
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Nghost: 17.5 ave 37 max 1 min
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Histogram: 2 0 0 0 0 0 0 0 1 1
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Neighs: 154.25 ave 393 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 = 617
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Ave neighs/atom = 7.61728
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Neighbor list builds = 993
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Dangerous builds = 948
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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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