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LAMMPS (5 Oct 2016)
# Simple rigid body system
units lj
atom_style atomic
pair_style lj/cut 2.5
read_data data.rigid
orthogonal box = (-12 -12 -12) to (12 12 12)
1 by 1 by 1 MPI processor grid
reading atoms ...
81 atoms
velocity all create 100.0 4928459
# unconnected bodies
#group clump1 id <> 1 9
#group clump2 id <> 10 18
#group clump3 id <> 19 27
#group clump4 id <> 28 36
#group clump5 id <> 37 45
#group clump6 id <> 46 54
#group clump7 id <> 55 63
#group clump8 id <> 64 72
#group clump9 id <> 73 81
#fix 1 all rigid group 9 clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9
# 1 chain of connected bodies
#group clump1 id <> 1 9
#group clump2 id <> 9 18
#group clump3 id <> 18 27
#group clump4 id <> 27 36
#group clump5 id <> 36 45
#group clump6 id <> 45 54
#group clump7 id <> 54 63
#group clump8 id <> 63 72
#group clump9 id <> 72 81
#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9
# 2 chains of connected bodies
group clump1 id <> 1 9
9 atoms in group clump1
group clump2 id <> 9 18
10 atoms in group clump2
group clump3 id <> 18 27
10 atoms in group clump3
group clump4 id <> 27 36
10 atoms in group clump4
group clump5 id <> 37 45
9 atoms in group clump5
group clump6 id <> 45 54
10 atoms in group clump6
group clump7 id <> 54 63
10 atoms in group clump7
group clump8 id <> 63 72
10 atoms in group clump8
group clump9 id <> 72 81
10 atoms in group clump9
fix 1 all poems group clump1 clump2 clump3 clump4
1 clusters, 4 bodies, 3 joints, 36 atoms
fix 2 all poems group clump5 clump6 clump7 clump8 clump9
1 clusters, 5 bodies, 4 joints, 45 atoms
neigh_modify exclude group clump1 clump1
neigh_modify exclude group clump2 clump2
neigh_modify exclude group clump3 clump3
neigh_modify exclude group clump4 clump4
neigh_modify exclude group clump5 clump5
neigh_modify exclude group clump6 clump6
neigh_modify exclude group clump7 clump7
neigh_modify exclude group clump8 clump8
neigh_modify exclude group clump9 clump9
thermo 100
#dump 1 all atom 50 dump.rigid.poems2
#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 2 pad 5
#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 3 pad 5
timestep 0.0001
thermo 50
run 10000
WARNING: More than one fix poems (../fix_poems.cpp:352)
WARNING: More than one fix poems (../fix_poems.cpp:352)
WARNING: One or more atoms are time integrated more than once (../modify.cpp:269)
Neighbor list info ...
1 neighbor list requests
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4 -> bins = 18 18 18
Memory usage per processor = 3.53031 Mbytes
Step Temp E_pair E_mol TotEng Press
0 196.00047 3632.2347 0 3668.5311 -2.7403788
50 12167.633 1505.5478 0 3758.8133 35.125973
100 17556.978 512.66277 0 3763.9549 11.137534
150 19579.586 138.04942 0 3763.8987 -29.953971
200 19757.51 105.30542 0 3764.1036 -0.030645317
250 18218.374 390.10747 0 3763.8804 13.711001
300 19383.039 174.40688 0 3763.8586 5.7240693
350 20125.986 36.972611 0 3764.0071 1.9559205
400 18888.816 266.10975 0 3764.0386 9.6362168
450 19307.656 188.2511 0 3763.743 1.9326206
500 16331.197 738.56392 0 3762.8597 9.1715579
550 19318.722 186.16172 0 3763.7027 3.0115336
600 19455.268 161.20621 0 3764.0336 0.55208034
650 18487.011 340.03216 0 3763.5528 -8.0359122
700 17321.201 556.32471 0 3763.9545 -13.631751
750 18979.187 249.04389 0 3763.7082 -2.6072455
800 19342.456 181.85552 0 3763.7918 8.1918726
850 19070.641 232.19342 0 3763.7936 7.3148472
900 19478.873 156.65987 0 3763.8586 2.4284987
950 19912.415 76.437437 0 3763.9216 -1.4667227
1000 16003.749 802.39753 0 3766.0548 46.642188
1050 19859.583 86.64176 0 3764.3424 -2.1961943
1100 19229.575 203.61488 0 3764.6473 -10.632365
1150 18821.6 279.15861 0 3764.64 -0.89495035
1200 19392.695 173.59744 0 3764.8373 1.8508753
1250 16459.624 717.32104 0 3765.3995 33.478127
1300 19343.863 182.59043 0 3764.7874 0.75890736
1350 20019.643 57.503573 0 3764.8448 0.31444671
1400 18549.582 329.31436 0 3764.4221 10.738303
1450 15163.926 957.47585 0 3765.6103 -17.923459
1500 19223.688 204.15175 0 3764.0939 -1.6134531
1550 18147.996 404.12677 0 3764.8668 8.4194779
1600 18615.043 317.42467 0 3764.6548 -2.3288934
1650 20120.654 38.887913 0 3764.935 -8.7620277
1700 19450.907 162.98272 0 3765.0025 2.3254731
1750 19374.632 177.37966 0 3765.2744 8.9328774
1800 19424.404 167.93966 0 3765.0514 0.081230261
1850 17936.249 442.84231 0 3764.3699 6.6010636
1900 19982.595 64.406198 0 3764.8868 -2.9529813
1950 16215.852 761.91287 0 3764.8485 13.994708
2000 18584.422 322.12049 0 3763.68 7.1654003
2050 20107.965 41.025754 0 3764.723 -0.3109069
2100 20002.333 60.593017 0 3764.7288 -6.7919784
2150 16949.762 626.59623 0 3765.441 3.508941
2200 20010.953 58.808279 0 3764.5403 -10.862172
2250 18982.73 247.00892 0 3762.3292 -0.53807815
2300 18401.298 354.87973 0 3762.5274 1.0920554
2350 19390.524 172.9415 0 3763.7793 -3.3524932
2400 16080.801 786.38838 0 3764.3146 -16.200514
2450 18870.412 268.74976 0 3763.2705 11.197736
2500 19688.29 117.58223 0 3763.5618 4.382644
2550 18870.825 268.78678 0 3763.384 -5.6623656
2600 17019.35 611.70808 0 3763.4395 6.3109641
2650 18753.285 291.0596 0 3763.8902 2.4120296
2700 19742.456 107.20901 0 3763.2193 -0.33061303
2750 19522.438 148.16759 0 3763.4339 -1.6254851
2800 18304.801 372.55152 0 3762.3295 22.6368
2850 18465.36 343.48495 0 3762.9961 4.4169272
2900 20151.999 31.372926 0 3763.2245 1.2013699
2950 15498.143 892.80071 0 3762.8272 13.263724
3000 18728.301 294.65113 0 3762.855 8.1897838
3050 18538.466 330.25223 0 3763.3015 8.5865739
3100 19081.409 229.5907 0 3763.1849 -4.8573813
3150 18498.802 337.11548 0 3762.8195 1.0555321
3200 19925.897 73.358029 0 3763.339 -7.7325108
3250 19780.108 100.23785 0 3763.2209 -5.5974972
3300 19221.043 203.82387 0 3763.2763 4.2703251
3350 19025.292 240.11329 0 3763.3156 5.7708328
3400 18153.696 401.52086 0 3763.3164 21.076943
3450 18611.375 316.50396 0 3763.0548 -3.5484945
3500 19931.319 71.969274 0 3762.9543 1.8764978
3550 19747.562 106.05439 0 3763.0103 -2.5506186
3600 18491.39 338.4134 0 3762.7449 -4.0527808
3650 19757.998 104.19207 0 3763.0806 1.4865598
3700 20108.003 39.345514 0 3763.0498 0.062827129
3750 19222.505 203.28065 0 3763.0039 0.33719277
3800 19286.383 191.08831 0 3762.6406 -0.1826802
3850 19450.083 161.09138 0 3762.9587 -0.2708263
3900 18002.304 429.25655 0 3763.0166 -4.6832439
3950 17186.829 582.26502 0 3765.0111 55.816834
4000 16826.434 645.84974 0 3761.856 19.675962
4050 19227.526 202.18151 0 3762.8344 -0.2596098
4100 19908.792 76.084531 0 3762.8978 -2.796813
4150 17821.329 462.63065 0 3762.8768 13.069155
4200 19917.133 74.574998 0 3762.9329 -6.4181155
4250 19012.618 241.96787 0 3762.823 4.0847974
4300 19077.34 229.98133 0 3762.8221 4.324323
4350 19361.128 177.47406 0 3762.8681 -7.377974
4400 18565.044 324.95107 0 3762.9223 2.5229032
4450 19352.406 178.98756 0 3762.7665 0.10862717
4500 18482.218 340.15496 0 3762.788 12.518301
4550 18359.732 362.83749 0 3762.7879 3.7500902
4600 19623.618 128.71624 0 3762.7196 -1.1328521
4650 17565.707 509.99904 0 3762.9078 1.7135935
4700 19876.052 81.892814 0 3762.6431 0.32476108
4750 19022.676 239.92262 0 3762.6403 -0.24613022
4800 18862.685 269.24248 0 3762.3324 6.2733979
4850 19899.174 77.426145 0 3762.4584 0.42535238
4900 18250.865 382.72867 0 3762.5185 23.308462
4950 18895.847 263.22651 0 3762.4575 8.0634675
5000 19096.705 225.69358 0 3762.1204 3.6816481
5050 16546.294 698.91312 0 3763.0416 17.453618
5100 19501.208 151.20999 0 3762.5449 -1.1231291
5150 19479.879 155.00669 0 3762.3917 -3.983378
5200 17397.818 541.23039 0 3763.0485 6.1109992
5250 18564.869 324.10557 0 3762.0442 9.2244762
5300 16271.663 747.52374 0 3760.7947 -6.5256602
5350 19831.418 89.851887 0 3762.3367 -2.3453958
5400 18723.697 294.67435 0 3762.0256 4.6822081
5450 19547.28 142.21934 0 3762.086 -5.5243408
5500 19415.447 166.68729 0 3762.1404 -9.5658991
5550 18492.721 337.54773 0 3762.1256 6.5184903
5600 19391.389 171.14375 0 3762.1416 -0.53835361
5650 18503.465 334.62751 0 3761.1951 4.6580363
5700 18153.344 399.91064 0 3761.6409 12.851587
5750 18342.297 365.14769 0 3761.8694 2.7148176
5800 19583.241 135.64969 0 3762.1758 -1.089608
5850 15967.283 804.18382 0 3761.088 11.278762
5900 19040.271 235.35509 0 3761.3312 5.1352158
5950 17920.962 443.17951 0 3761.8762 4.9621366
6000 19100.92 224.3946 0 3761.602 -9.537589
6050 17982.119 432.3251 0 3762.3472 -2.851617
6100 16233.096 755.46191 0 3761.5908 25.113316
6150 18316.543 370.01118 0 3761.9635 -1.7445703
6200 18483.464 339.13282 0 3761.9966 -2.0857447
6250 18609.406 315.56032 0 3761.7467 -12.289208
6300 17167.919 582.68212 0 3761.9264 -3.8263397
6350 17870.329 452.58116 0 3761.9013 -3.3843134
6400 19309.717 186.11786 0 3761.9913 -4.9462739
6450 17964.073 435.39924 0 3762.0794 12.272972
6500 18772.847 285.61959 0 3762.0727 6.7928648
6550 18915.116 259.41365 0 3762.213 -4.1449761
6600 19446.628 161.18763 0 3762.415 -2.1906581
6650 16348.787 734.99282 0 3762.546 -9.9624546
6700 19066.684 231.43863 0 3762.3061 -5.362833
6750 14890.323 1004.547 0 3762.0143 37.373013
6800 18235.19 385.253 0 3762.1401 0.21012662
6850 16447.997 716.11276 0 3762.0382 -9.2095411
6900 18343.362 364.81902 0 3761.7379 10.417932
6950 16014.084 797.13348 0 3762.7046 6.7906777
7000 19120.393 221.29236 0 3762.1059 -1.3461375
7050 18055.409 418.30136 0 3761.8957 1.5772317
7100 18407.231 353.41868 0 3762.1652 0.61071769
7150 18728.136 293.64021 0 3761.8136 5.1649654
7200 17706.628 483.07628 0 3762.0815 18.000708
7250 19349.505 178.89673 0 3762.1385 2.540201
7300 20016.293 55.389159 0 3762.1101 -1.5793163
7350 19398.573 169.86661 0 3762.1949 -5.060123
7400 19466.526 157.37407 0 3762.2862 1.7158273
7450 18440.348 347.09196 0 3761.9712 12.781963
7500 19989.907 60.555934 0 3762.3906 -1.5033319
7550 19667.28 120.27403 0 3762.363 -3.3502366
7600 18497.707 336.15863 0 3761.66 1.7887539
7650 17901.957 447.17282 0 3762.3501 0.016725252
7700 19758.725 103.3129 0 3762.3361 -23.534448
7750 19443.957 161.6532 0 3762.386 -10.323924
7800 19776.178 100.1773 0 3762.4324 6.0854422
7850 19242.512 198.86705 0 3762.2952 5.2823659
7900 19499.929 151.30366 0 3762.4017 12.299911
7950 19630.317 127.19541 0 3762.4393 8.0799632
8000 19872.384 82.421129 0 3762.4923 2.2126691
8050 17747.038 476.27982 0 3762.7683 -7.7042786
8100 18832.654 274.78106 0 3762.3095 13.882157
8150 19949.814 68.09711 0 3762.5072 -0.54410896
8200 17555.866 511.02517 0 3762.1115 6.2471175
8250 17800.1 465.9992 0 3762.314 13.583485
8300 19755.224 103.89732 0 3762.2721 -1.487243
8350 17583.61 506.17539 0 3762.3995 -9.7819128
8400 18529.003 330.75623 0 3762.0532 14.731228
8450 20155.902 29.797078 0 3762.3716 -8.5711085
8500 18047.548 420.54645 0 3762.685 7.3875118
8550 19790.794 97.493375 0 3762.4553 -3.3427911
8600 19997.902 59.172074 0 3762.4874 3.3479688
8650 19987.319 61.148363 0 3762.5037 -1.889232
8700 19363.91 176.41833 0 3762.3276 -9.4291288
8750 18712.689 296.3979 0 3761.7107 5.9221369
8800 19783.17 98.860518 0 3762.4105 -3.5262066
8850 18796.049 281.60057 0 3762.3504 -8.2913002
8900 16738.277 662.62261 0 3762.3035 8.5838631
8950 17869.613 452.25006 0 3761.4377 11.561101
9000 18682.512 302.27997 0 3762.0043 3.8878724
9050 17513.759 518.50265 0 3761.7914 23.05778
9100 17500.686 521.57944 0 3762.4473 -2.8435751
9150 19645.683 124.43597 0 3762.5254 -3.0193092
9200 18898.897 262.76552 0 3762.5612 3.5891701
9250 20114.279 37.614866 0 3762.4813 -0.58120871
9300 19562.613 139.54073 0 3762.2468 -3.2630158
9350 19679.811 118.05865 0 3762.468 -3.4644363
9400 19297.384 188.84527 0 3762.4349 0.40498037
9450 18267.029 379.52581 0 3762.309 -0.13762867
9500 19951.072 67.63844 0 3762.2814 -7.575539
9550 19134.562 218.46835 0 3761.9057 -1.9626244
9600 19089.093 227.29178 0 3762.3089 -1.94158
9650 16964.603 620.71289 0 3762.3061 16.987042
9700 18846.881 271.3129 0 3761.4761 3.4458802
9750 19309.225 186.0142 0 3761.7966 9.4048627
9800 16359.704 733.51007 0 3763.0849 15.870164
9850 19958.532 66.203725 0 3762.2282 6.0043645
9900 19864.564 83.502384 0 3762.1253 -0.65360617
9950 18996.789 244.25101 0 3762.1749 -2.4961826
10000 17933.494 441.33587 0 3762.3532 -6.0731708
Loop time of 3.80061 on 1 procs for 10000 steps with 81 atoms
Performance: 22733.175 tau/day, 2631.155 timesteps/s
100.0% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.11276 | 0.11276 | 0.11276 | 0.0 | 2.97
Neigh | 0.075881 | 0.075881 | 0.075881 | 0.0 | 2.00
Comm | 0.011113 | 0.011113 | 0.011113 | 0.0 | 0.29
Output | 0.0016332 | 0.0016332 | 0.0016332 | 0.0 | 0.04
Modify | 3.5918 | 3.5918 | 3.5918 | 0.0 | 94.51
Other | | 0.007383 | | | 0.19
Nlocal: 81 ave 81 max 81 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 71 ave 71 max 71 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 612 ave 612 max 612 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 612
Ave neighs/atom = 7.55556
Neighbor list builds = 989
Dangerous builds = 906
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:03
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