forked from lijiext/lammps
343 lines
19 KiB
Groff
343 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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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 (src/POEMS/fix_poems.cpp:363)
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WARNING: More than one fix poems (src/POEMS/fix_poems.cpp:363)
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WARNING: One or more atoms are time integrated more than once (src/modify.cpp:283)
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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 15163.926 957.47585 0 3765.6103 -17.923459
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1500 19223.688 204.15176 0 3764.0939 -1.6134529
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1550 18147.996 404.12677 0 3764.8668 8.4194781
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1600 18615.043 317.42468 0 3764.6548 -2.3288926
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1650 20120.654 38.887908 0 3764.935 -8.7620288
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1700 19450.907 162.98267 0 3765.0025 2.3254739
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1750 19374.631 177.3797 0 3765.2744 8.9328773
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1800 19424.404 167.93965 0 3765.0514 0.081228843
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1850 17936.227 442.84645 0 3764.3699 6.6011251
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1900 19982.595 64.406244 0 3764.8868 -2.952971
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1950 16215.818 761.91942 0 3764.8486 13.994877
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2000 18584.433 322.11846 0 3763.6801 7.1653695
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2050 20107.965 41.025796 0 3764.723 -0.31089763
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2100 20002.329 60.593879 0 3764.7288 -6.7919882
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2150 16949.817 626.58598 0 3765.4409 3.5087505
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2200 20010.954 58.8082 0 3764.5403 -10.862143
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2250 18982.732 247.00854 0 3762.3293 -0.53812607
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2300 18401.276 354.88369 0 3762.5274 1.0921058
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2350 19390.535 172.93951 0 3763.7793 -3.3524354
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2400 16080.475 786.44896 0 3764.3146 -16.201558
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2450 18870.293 268.77171 0 3763.2704 11.199749
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2500 19688.508 117.54164 0 3763.5617 4.3806994
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2550 18870.328 268.87896 0 3763.3841 -5.6641099
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2600 17020.211 611.54841 0 3763.4394 6.3081434
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2650 18748.838 291.88478 0 3763.8917 2.4175163
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2700 19743.991 106.92945 0 3763.224 -0.33916964
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2750 19525.446 147.60906 0 3763.4324 -1.6251174
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2800 18257.411 381.40184 0 3762.4038 23.39495
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2850 18496.796 337.65425 0 3762.9868 4.3657735
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2900 20163.418 29.253902 0 3763.2203 1.4431917
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2950 16823.317 646.69817 0 3762.1273 4.9041552
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3000 19223.007 203.2529 0 3763.069 4.0414458
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3050 17391.02 542.93746 0 3763.4968 15.139863
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3100 19205.6 206.57791 0 3763.1705 4.8519241
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3150 19835.659 90.247763 0 3763.5179 -14.900053
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3200 18962.776 251.5838 0 3763.2089 -13.706561
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3250 19418.837 167.29058 0 3763.3716 -2.0866468
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3300 18628.291 313.69067 0 3763.3742 5.9919715
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3350 17465.974 529.14439 0 3763.5841 14.122593
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3400 18488.661 339.6186 0 3763.4448 21.526798
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3450 19163.152 214.26098 0 3762.9928 4.1888096
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3500 18000.27 429.81789 0 3763.2011 5.4734485
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3550 19582.423 136.71887 0 3763.0935 -2.5335675
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3600 19634.325 127.2219 0 3763.208 -1.9728322
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3650 19428.114 165.40707 0 3763.2059 -2.3318779
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3700 19861.116 85.356944 0 3763.3414 -3.9097609
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3750 19337.239 182.43992 0 3763.4102 -3.3559651
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3800 19493.146 153.40349 0 3763.2453 -0.71089657
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3850 18607.616 317.74889 0 3763.6037 3.475832
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3900 19719.59 111.5553 0 3763.3313 0.58876668
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3950 19756.661 104.5522 0 3763.1931 3.7526698
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4000 17904.708 447.1673 0 3762.854 12.270654
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4050 19588.087 135.80435 0 3763.2279 0.94578945
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4100 19065.901 232.38235 0 3763.1048 -2.7495195
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4150 18775.075 286.2257 0 3763.0915 -3.7039858
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4200 18800.725 281.46601 0 3763.0817 0.15619543
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4250 19732.687 108.90618 0 3763.1075 3.0865861
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4300 18278.151 377.63653 0 3762.4794 1.5768601
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4350 17915.757 445.4804 0 3763.2133 -3.7040484
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4400 15987.794 802.41575 0 3763.1183 22.252078
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4450 19302.37 188.69495 0 3763.2079 0.91081327
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4500 20039.32 52.304099 0 3763.2893 -2.0828905
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4550 19535.953 145.4374 0 3763.2064 -3.3804255
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4600 19700.723 114.79823 0 3763.0803 -1.1761163
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4650 17804.641 465.85788 0 3763.0136 7.5947192
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4700 19913.881 75.240289 0 3762.996 -2.1100557
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4750 19982.484 62.535995 0 3762.996 -4.5821237
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4800 17400.76 540.21707 0 3762.58 -5.8418778
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4850 19199.88 206.90989 0 3762.4433 3.4536341
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4900 19173.92 212.11327 0 3762.8392 5.0387071
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4950 19236.635 200.57537 0 3762.9152 -1.4932783
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5000 19077.616 230.04967 0 3762.9415 4.3742655
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5050 19893.763 78.909747 0 3762.94 -1.5796711
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5100 18884.746 265.68301 0 3762.8583 2.2767949
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5150 17417.096 537.54036 0 3762.9286 -2.8632555
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5200 18247.844 383.60092 0 3762.8312 10.384179
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5250 19494.107 152.60532 0 3762.6251 -4.7617287
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5300 18739.781 292.46206 0 3762.7919 23.210048
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5350 19310.938 186.62363 0 3762.7232 14.895327
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5400 19540.39 144.14287 0 3762.7336 6.094624
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5450 20074.459 45.247888 0 3762.7403 -2.0871835
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5500 19986.377 61.668045 0 3762.849 -2.4551918
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5550 19038.904 237.07578 0 3762.7987 5.4250813
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5600 19439.124 163.1438 0 3762.9816 4.1291468
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5650 19480.321 155.58325 0 3763.0501 -3.5308058
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5700 19869.291 83.651379 0 3763.1497 -7.8661592
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5750 19991.447 61.068554 0 3763.1884 -6.8473586
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5800 19454.072 160.36805 0 3762.9739 1.527662
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5850 17994.409 430.95597 0 3763.2539 -5.6078082
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5900 19209.794 205.74997 0 3763.1193 8.4113055
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5950 19046.427 236.06321 0 3763.1793 10.463356
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6000 19409.899 168.95271 0 3763.3785 2.542067
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6050 18068.174 417.35443 0 3763.3125 10.498199
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6100 19549.253 143.21885 0 3763.4509 2.3075797
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6150 18464.719 344.0303 0 3763.4228 0.46469762
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6200 19811.205 94.62725 0 3763.3689 1.2382763
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6250 18715.36 297.26445 0 3763.0718 -3.4541762
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6300 17115.664 594.09913 0 3763.6666 4.2065564
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6350 18155.927 400.71764 0 3762.9264 1.1521258
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6400 19873.093 83.169067 0 3763.3716 0.16383592
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6450 19991.88 61.13218 0 3763.3321 -1.3008128
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6500 19434.416 164.40698 0 3763.3728 -13.593422
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6550 19855.253 86.645329 0 3763.544 -0.85704037
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6600 19251.141 198.41152 0 3763.4376 4.3027745
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6650 19741.815 107.69047 0 3763.582 4.994835
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6700 19633.466 127.69333 0 3763.5203 6.3677145
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6750 16231.353 757.83705 0 3763.6431 -1.5978692
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6800 18863.396 270.1114 0 3763.3329 -11.915909
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6850 19644.779 125.29421 0 3763.2163 -1.151217
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6900 18883.642 266.06889 0 3763.0397 -4.3950749
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6950 19042.364 236.54144 0 3762.9052 5.5718878
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7000 18351.868 364.38028 0 3762.8743 7.8958273
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7050 19981.031 62.840667 0 3763.0316 -5.8572298
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7100 19796.372 97.073665 0 3763.0685 -3.5178361
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7150 19805.385 95.235221 0 3762.899 -2.5481726
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7200 18722.055 295.86113 0 3762.9084 13.826356
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7250 19537.304 144.54234 0 3762.5616 1.2288666
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7300 18787.328 283.49504 0 3762.6299 9.0044469
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7350 18886.005 265.52121 0 3762.9295 6.6791881
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7400 19891.864 79.239278 0 3762.9178 -2.3882842
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7450 18164.752 399.07065 0 3762.9137 3.9400481
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7500 18702.612 299.582 0 3763.0286 4.7987316
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7550 19884.986 80.231665 0 3762.6365 -0.75016515
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7600 19549.059 142.16243 0 3762.3586 -2.1035756
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7650 18223.668 387.9047 0 3762.658 -17.064339
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7700 19428.4 164.79531 0 3762.6473 -2.8342541
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7750 19239.584 199.93029 0 3762.8163 3.1746033
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7800 19458.005 159.46176 0 3762.7961 1.714515
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7850 18320.308 369.77051 0 3762.4202 2.1422976
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7900 18817.415 278.04812 0 3762.7546 0.94492621
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7950 19892.761 79.115928 0 3762.9606 1.4948501
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8000 19592.344 134.7639 0 3762.9758 -1.8520224
|
||
|
|
8050 19316.109 185.70579 0 3762.7631 -4.8061205
|
||
|
|
8100 19867.017 83.850395 0 3762.9277 -3.496391
|
||
|
|
8150 19129.936 220.29802 0 3762.8789 -2.8357376
|
||
|
|
8200 18449.554 346.30415 0 3762.8883 1.4417837
|
||
|
|
8250 18405.197 354.49049 0 3762.8602 6.7020283
|
||
|
|
8300 18310.437 372.25376 0 3763.0755 3.9043508
|
||
|
|
8350 18842.702 273.55075 0 3762.94 -10.987272
|
||
|
|
8400 18574.308 323.33378 0 3763.0204 12.008785
|
||
|
|
8450 15368.628 918.21692 0 3764.2591 34.80292
|
||
|
|
8500 18432.887 349.54013 0 3763.0378 0.00064258465
|
||
|
|
8550 15777.73 841.79263 0 3763.5945 15.473699
|
||
|
|
8600 17205.381 576.4515 0 3762.6331 2.3985544
|
||
|
|
8650 19773.742 101.48276 0 3763.2869 2.3978892
|
||
|
|
8700 19059.824 232.99716 0 3762.5941 5.2611349
|
||
|
|
8750 19006.086 243.41125 0 3763.0568 4.7880403
|
||
|
|
8800 19492.691 153.0188 0 3762.7763 1.9118755
|
||
|
|
8850 19625.883 128.44474 0 3762.8675 3.4157389
|
||
|
|
8900 19916.97 74.635094 0 3762.9629 -10.157254
|
||
|
|
8950 16012.956 798.16801 0 3763.5302 16.904998
|
||
|
|
9000 19364.051 177.00354 0 3762.9389 -13.373346
|
||
|
|
9050 19133.929 219.61882 0 3762.9389 -7.3824392
|
||
|
|
9100 18657.168 307.85939 0 3762.8905 9.3071421
|
||
|
|
9150 17975.904 434.21548 0 3763.0867 6.9609506
|
||
|
|
9200 19075.282 230.41699 0 3762.8767 7.0961232
|
||
|
|
9250 20115.276 37.578674 0 3762.6298 1.8678552
|
||
|
|
9300 18195.486 393.20682 0 3762.7413 13.272552
|
||
|
|
9350 19617.155 129.85893 0 3762.6653 -2.0849447
|
||
|
|
9400 19276.325 193.03425 0 3762.724 -2.8963555
|
||
|
|
9450 18642.803 310.4759 0 3762.8467 3.407984
|
||
|
|
9500 19175.951 211.72785 0 3762.8298 -0.39025564
|
||
|
|
9550 17669.191 490.85942 0 3762.9319 5.3867954
|
||
|
|
9600 18481.199 340.29485 0 3762.7391 8.9004886
|
||
|
|
9650 20091.442 42.504743 0 3763.1422 -1.3206133
|
||
|
|
9700 19651.405 124.04835 0 3763.1975 1.4000525
|
||
|
|
9750 19138.245 219.03637 0 3763.1558 5.8352794
|
||
|
|
9800 19189.146 209.67958 0 3763.2251 6.214691
|
||
|
|
9850 19899.376 78.096337 0 3763.166 -0.75102404
|
||
|
|
9900 19447.247 161.27279 0 3762.6149 -6.4166376
|
||
|
|
9950 19807.083 95.152663 0 3763.1309 -0.88933698
|
||
|
|
10000 18972.157 249.56342 0 3762.9258 1.9189241
|
||
|
|
Loop time of 9.05599 on 4 procs for 10000 steps with 81 atoms
|
||
|
|
|
||
|
|
Performance: 9540.646 tau/day, 1104.241 timesteps/s
|
||
|
|
94.6% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||
|
|
|
||
|
|
MPI task timing breakdown:
|
||
|
|
Section | min time | avg time | max time |%varavg| %total
|
||
|
|
---------------------------------------------------------------
|
||
|
|
Pair | 0.009043 | 0.030098 | 0.048276 | 8.1 | 0.33
|
||
|
|
Neigh | 0.012702 | 0.02622 | 0.04009 | 6.1 | 0.29
|
||
|
|
Comm | 0.99902 | 1.2924 | 1.6008 | 24.3 | 14.27
|
||
|
|
Output | 0.0057414 | 0.010684 | 0.024912 | 7.9 | 0.12
|
||
|
|
Modify | 7.2674 | 7.5881 | 7.9123 | 10.6 | 83.79
|
||
|
|
Other | | 0.1085 | | | 1.20
|
||
|
|
|
||
|
|
Nlocal: 20.25 ave 37 max 0 min
|
||
|
|
Histogram: 1 0 1 0 0 0 0 0 0 2
|
||
|
|
Nghost: 17.75 ave 33 max 4 min
|
||
|
|
Histogram: 2 0 0 0 0 0 0 0 1 1
|
||
|
|
Neighs: 144.75 ave 356 max 0 min
|
||
|
|
Histogram: 2 0 0 0 0 0 1 0 0 1
|
||
|
|
|
||
|
|
Total # of neighbors = 579
|
||
|
|
Ave neighs/atom = 7.14815
|
||
|
|
Neighbor list builds = 994
|
||
|
|
Dangerous builds = 958
|
||
|
|
|
||
|
|
Please see the log.cite file for references relevant to this simulation
|
||
|
|
|
||
|
|
Total wall time: 0:00:09
|