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 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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#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) = 3.854 | 3.854 | 3.854 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 15163.926 957.47585 0 3765.6103 -17.92346
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1500 19223.688 204.15177 0 3764.0939 -1.6134528
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1550 18147.996 404.12677 0 3764.8668 8.4194783
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1600 18615.043 317.42469 0 3764.6548 -2.3288917
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1650 20120.654 38.887903 0 3764.935 -8.7620301
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1700 19450.907 162.98262 0 3765.0025 2.3254748
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1750 19374.631 177.37975 0 3765.2744 8.9328771
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1800 19424.404 167.93963 0 3765.0514 0.081227378
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1850 17936.203 442.85082 0 3764.3699 6.6011902
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1900 19982.595 64.406292 0 3764.8868 -2.95296
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1950 16215.781 761.92636 0 3764.8487 13.995056
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2000 18584.444 322.1163 0 3763.6801 7.1653369
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2050 20107.965 41.025841 0 3764.723 -0.31088772
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2100 20002.324 60.594786 0 3764.7288 -6.7919989
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2150 16949.875 626.57523 0 3765.4409 3.50855
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2200 20010.954 58.808121 0 3764.5403 -10.862112
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2250 18982.734 247.00818 0 3762.3293 -0.53817452
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2300 18401.254 354.88774 0 3762.5274 1.0921595
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2350 19390.545 172.93755 0 3763.7793 -3.3523777
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2400 16080.137 786.51156 0 3764.3147 -16.202632
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2450 18870.17 268.79443 0 3763.2704 11.201845
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2500 19688.736 117.49945 0 3763.5616 4.3786781
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2550 18869.811 268.97474 0 3763.3842 -5.6659314
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2600 17021.088 611.38597 0 3763.4393 6.3051835
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2650 18743.998 292.7827 0 3763.8934 2.4233167
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2700 19745.629 106.63088 0 3763.2289 -0.34816161
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2750 19527.584 147.21131 0 3763.4306 -1.6219417
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2800 18195.354 392.99533 0 3762.5053 24.376674
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2850 18550.094 327.77867 0 3762.9812 4.2654596
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2900 20174.105 27.269108 0 3763.2144 1.7109311
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2950 17744.679 476.70478 0 3762.7564 0.46336417
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3000 19161.715 214.56545 0 3763.0311 2.3774967
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3050 18357.87 363.54089 0 3763.1465 7.5885138
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3100 18851.02 272.19735 0 3763.1269 8.0560784
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3150 19586.208 136.32381 0 3763.3995 -10.118566
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3200 19300.444 189.2076 0 3763.3639 -12.590066
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3250 18680.955 303.88073 0 3763.3168 -1.0138975
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3300 18444.612 347.49752 0 3763.1664 8.9271155
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3350 19006.554 243.54359 0 3763.2757 4.7398999
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3400 17842.797 459.11352 0 3763.3351 28.63048
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3450 19801.317 96.103613 0 3763.0141 4.0933253
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3500 18599.338 318.61343 0 3762.9353 6.3657111
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3550 19737.266 107.84071 0 3762.89 1.3861757
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3600 19002.648 244.0525 0 3763.0613 8.7615304
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3650 19154.418 215.94396 0 3763.0584 -2.6243193
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3700 19036.117 237.84014 0 3763.047 -5.6841944
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3750 20045.863 50.759281 0 3762.9562 -2.1930939
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3800 19331.877 182.69303 0 3762.6703 0.57474959
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3850 18193.947 393.70074 0 3762.9502 -4.1144639
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3900 19675.638 119.2295 0 3762.8663 0.46172332
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3950 19506.743 150.36614 0 3762.7259 5.8020668
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4000 17985.008 431.80897 0 3762.366 10.755615
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4050 19947.208 68.962683 0 3762.8902 -2.0041629
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4100 19936.06 70.997196 0 3762.8602 -6.6295574
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4150 19011.006 242.10402 0 3762.6608 -12.682711
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4200 18108.183 409.44214 0 3762.8094 -0.42654932
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4250 18734.162 293.70086 0 3762.9901 8.8549986
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4300 16619.218 686.30953 0 3763.9426 43.405681
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4350 18818.184 277.95188 0 3762.8007 20.953883
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4400 18649.616 307.93211 0 3761.5647 -3.6011031
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4450 18626.995 313.23564 0 3762.6792 -2.5430627
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4500 18133.284 405.27778 0 3763.2934 3.057056
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4550 19985.929 61.792735 0 3762.8908 1.9540846
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4600 18664.305 306.02805 0 3762.3809 1.2395242
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4650 19822.408 92.030223 0 3762.8466 -1.0496216
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4700 19218.014 203.93895 0 3762.8305 0.74203538
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4750 19425.781 165.36374 0 3762.7306 4.0113982
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4800 18604.891 317.55244 0 3762.9026 16.671366
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4850 19648.156 124.29963 0 3762.8471 4.1073
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4900 18928.508 257.76023 0 3763.0394 -4.3547566
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4950 19795.841 97.135231 0 3763.0317 -10.401888
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5000 20150.671 31.452661 0 3763.0584 -3.352706
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5050 18694.789 300.8954 0 3762.8933 11.690808
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5100 16936.745 627.00902 0 3763.4434 -0.56880353
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5150 18446.99 346.49004 0 3762.5992 8.409244
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5200 18532.691 330.61677 0 3762.5966 10.358529
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5250 18342.743 366.3264 0 3763.1306 -9.5622676
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5300 20038.203 52.234825 0 3763.0131 -3.6974868
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5350 19337.092 182.06755 0 3763.0106 -0.045248915
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5400 19561.005 140.5518 0 3762.9602 1.3850963
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5450 19415.557 167.29181 0 3762.7654 2.6966013
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5500 18646.823 309.81657 0 3762.9319 7.4858844
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5550 19165.312 214.07271 0 3763.2046 1.4335924
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5600 18879.507 266.90953 0 3763.1146 7.8746695
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5650 19824.482 91.786842 0 3762.9872 -2.4395467
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5700 19699.85 114.8239 0 3762.9442 4.2779932
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5750 19535.697 145.24886 0 3762.9706 5.9452722
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5800 18275.446 378.66191 0 3763.0038 11.965062
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5850 19931.992 71.873259 0 3762.9828 -2.3097575
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5900 18528.705 331.64793 0 3762.8897 -18.312104
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5950 16535.446 701.02536 0 3763.1451 -14.797902
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6000 18678.807 303.76763 0 3762.806 -3.2732626
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6050 16661.525 677.73561 0 3763.2031 17.862761
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6100 18100.317 410.39139 0 3762.3019 -4.9765779
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6150 16487.861 707.08907 0 3760.3967 32.53899
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6200 16823.279 647.56578 0 3762.9878 -9.8237219
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6250 18418.096 351.89624 0 3762.6548 -2.0149855
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6300 18822.067 277.01314 0 3762.5811 5.3782716
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6350 19300.198 188.57243 0 3762.6832 -1.9316023
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6400 18425.789 350.70367 0 3762.8868 2.6884393
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6450 18708.506 297.50643 0 3762.0447 -13.808707
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6500 19528.099 146.10805 0 3762.4226 -1.5991505
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6550 19701.841 114.01327 0 3762.5023 4.4322487
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6600 18892.934 262.83827 0 3761.5297 10.689265
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6650 19041.669 235.52692 0 3761.7619 -1.1425512
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6700 19352.162 178.40501 0 3762.1388 -0.55130997
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6750 16177.653 765.61942 0 3761.481 4.6526477
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6800 19007.323 242.63753 0 3762.5122 3.6202242
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6850 14255.206 1125.4974 0 3765.3503 -31.10433
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6900 18481.408 340.4703 0 3762.9532 0.53246054
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6950 19227.569 202.33363 0 3762.9946 -0.94126626
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7000 18771.85 286.70279 0 3762.9714 3.151759
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7050 18689.51 301.95602 0 3762.9765 8.0511724
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7100 18599.258 318.83229 0 3763.1394 -0.86222116
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7150 17739.189 478.35458 0 3763.3896 11.976827
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7200 19492.829 153.62536 0 3763.4084 -8.6815909
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7250 18797.718 282.17319 0 3763.232 -19.897633
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7300 18353.871 364.09362 0 3762.9585 5.4538454
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7350 19040.053 237.34144 0 3763.2772 6.5600248
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7400 19452.586 160.98629 0 3763.317 -9.0542585
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7450 19033.845 238.45033 0 3763.2365 3.2654681
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7500 18137.358 404.80969 0 3763.5796 -7.2639486
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7550 16863.391 642.47654 0 3765.3267 31.248679
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7600 16374.538 731.74039 0 3764.0622 29.566291
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7650 19837.917 89.823014 0 3763.5114 -2.6605403
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7700 15593.154 876.08807 0 3763.7093 -9.7668717
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7750 16609.929 687.32679 0 3763.2396 1.0775966
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7800 17513.384 519.87756 0 3763.0968 3.4979836
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7850 20022.015 56.036771 0 3763.8173 -4.316185
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7900 17681.324 489.71547 0 3764.0347 5.1978443
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7950 18320.382 371.17872 0 3763.8421 6.1860655
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8000 20014.059 57.688322 0 3763.9956 -9.0623854
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8050 16203.013 762.61545 0 3763.1735 31.662714
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8100 18749.745 291.57889 0 3763.7538 -14.015057
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8150 19411.326 169.05845 0 3763.7485 -4.3392799
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8200 17994.991 431.56932 0 3763.9751 6.8158642
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8250 19325.923 185.1137 0 3763.9883 9.4923883
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8300 17354.302 550.33316 0 3764.0927 6.1636399
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8350 19900.895 78.431831 0 3763.7828 -4.5224196
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8400 17775.757 471.62915 0 3763.4361 12.949899
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8450 19909.324 76.935162 0 3763.8471 -2.950115
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8500 18601.933 318.79405 0 3763.5965 6.0173542
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8550 18685.758 303.59497 0 3763.9205 2.7277487
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8600 19297.521 190.12606 0 3763.741 4.8998933
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8650 17396.37 542.14326 0 3763.6932 39.937715
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8700 17134.714 590.99465 0 3764.0898 10.37328
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8750 14348.104 1106.7544 0 3763.8106 -3.8604659
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8800 19830.924 90.929138 0 3763.3225 0.26603444
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8850 18551.537 326.53747 0 3762.0072 -1.5369982
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8900 20040.322 52.066026 0 3763.2367 -12.667979
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8950 19314.585 186.54793 0 3763.3228 -0.64755555
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9000 19117.66 222.84553 0 3763.153 5.2990011
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9050 19072.016 231.26038 0 3763.1152 -1.6513695
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9100 19284.933 191.73976 0 3763.0237 -3.932358
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9150 17356.576 548.61808 0 3762.7988 1.3659056
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9200 18939.549 255.43703 0 3762.761 3.3037106
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9250 19621.961 129.5012 0 3763.1976 1.667
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9300 16898.033 633.79921 0 3763.0647 7.5941845
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9350 19662.75 122.10836 0 3763.3584 -3.3144828
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9400 16118.338 778.70243 0 3763.5799 9.8684537
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9450 17362.374 548.18847 0 3763.443 6.8117548
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9500 17873.057 453.37389 0 3763.1993 9.5651746
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9550 19282.305 192.593 0 3763.3901 -4.987757
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9600 18236.48 386.36263 0 3763.4886 8.8658343
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9650 17695.571 486.6517 0 3763.6093 12.471421
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9700 19044.003 237.04652 0 3763.7138 0.84430497
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9750 17937.299 442.4372 0 3764.1592 3.981475
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9800 18179.761 396.86987 0 3763.4923 -11.397273
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9850 19157.292 215.8937 0 3763.5404 -7.7648682
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9900 19719.066 111.98124 0 3763.6602 5.5378968
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9950 18103.235 410.65473 0 3763.1056 28.201374
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10000 18479.903 341.32548 0 3763.5297 -5.0581298
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Loop time of 3.14341 on 1 procs for 10000 steps with 81 atoms
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Performance: 27486.104 tau/day, 3181.262 timesteps/s
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99.3% CPU use with 1 MPI tasks x 1 OpenMP threads
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MPI task timing breakdown:
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Section | min time | avg time | max time |%varavg| %total
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---------------------------------------------------------------
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Pair | 0.12201 | 0.12201 | 0.12201 | 0.0 | 3.88
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Neigh | 0.077269 | 0.077269 | 0.077269 | 0.0 | 2.46
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Comm | 0.012246 | 0.012246 | 0.012246 | 0.0 | 0.39
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Output | 0.0032048 | 0.0032048 | 0.0032048 | 0.0 | 0.10
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Modify | 2.9172 | 2.9172 | 2.9172 | 0.0 | 92.80
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Other | | 0.01151 | | | 0.37
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Nlocal: 81 ave 81 max 81 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 67 ave 67 max 67 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 599 ave 599 max 599 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 599
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Ave neighs/atom = 7.39506
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Neighbor list builds = 993
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Dangerous builds = 945
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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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