339 lines
19 KiB
Groff
339 lines
19 KiB
Groff
LAMMPS (20 Apr 2018)
|
|
using 1 OpenMP thread(s) per MPI task
|
|
# 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 2 by 2 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
|
|
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 <> 36 45
|
|
10 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 clump5 clump6 clump7 clump8 clump9
|
|
1 clusters, 9 bodies, 8 joints, 81 atoms
|
|
|
|
# 2 chains 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 <> 37 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
|
|
#fix 2 all poems group clump5 clump6 clump7 clump8 clump9
|
|
|
|
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.poems
|
|
|
|
#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
|
|
Neighbor list info ...
|
|
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
|
|
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
|
(1) pair lj/cut, perpetual
|
|
attributes: half, newton on
|
|
pair build: half/bin/atomonly/newton
|
|
stencil: half/bin/3d/newton
|
|
bin: standard
|
|
Per MPI rank memory allocation (min/avg/max) = 3.263 | 3.357 | 3.638 Mbytes
|
|
Step Temp E_pair E_mol TotEng Press
|
|
0 217.7783 3430.3907 0 3466.6871 -2.7403788
|
|
50 13679.637 1404.2468 0 3684.1863 12.446066
|
|
100 16777.225 888.87665 0 3685.0808 -31.828677
|
|
150 19595.365 418.45042 0 3684.3446 40.709078
|
|
200 18524.188 596.47273 0 3683.8375 -0.8159371
|
|
250 21015.789 180.96521 0 3683.5967 -10.042469
|
|
300 20785.513 219.25314 0 3683.5053 2.6452719
|
|
350 21072.46 171.2554 0 3683.3321 7.0609024
|
|
400 19956.414 356.36381 0 3682.4328 19.320259
|
|
450 20724.42 227.73284 0 3681.8028 8.1259249
|
|
500 20152.578 322.71466 0 3681.4777 5.4929878
|
|
550 20017.022 345.29701 0 3681.4673 5.4661666
|
|
600 17897.743 698.72196 0 3681.6791 3.2854742
|
|
650 17297.758 796.60256 0 3679.5623 15.191113
|
|
700 18581.934 584.29715 0 3681.2861 5.1588289
|
|
750 21774.158 52.821062 0 3681.8474 -10.775664
|
|
800 21604.055 81.188546 0 3681.8644 -3.2045743
|
|
850 17821.483 711.53827 0 3681.7854 7.4384277
|
|
900 21033.292 175.98127 0 3681.5299 -16.345167
|
|
950 20968.166 186.59847 0 3681.2929 -2.330456
|
|
1000 20490.66 266.19375 0 3681.3037 11.787983
|
|
1050 20222.396 310.94072 0 3681.34 -8.3459539
|
|
1100 21321.687 127.61533 0 3681.2299 -1.2184717
|
|
1150 20849.582 206.01695 0 3680.9472 -0.86699147
|
|
1200 21815.003 45.317414 0 3681.1512 1.5988314
|
|
1250 18655.437 572.41453 0 3681.654 10.064078
|
|
1300 20780.781 217.36506 0 3680.8286 6.0538614
|
|
1350 20558.971 254.36483 0 3680.8601 -3.6773951
|
|
1400 21485.029 99.812917 0 3680.6511 -16.185473
|
|
1450 21771.107 52.15961 0 3680.6775 -2.4756673
|
|
1500 21520.948 93.503926 0 3680.3286 2.1023576
|
|
1550 21351.418 121.68137 0 3680.2511 5.5159947
|
|
1600 20778.805 216.92177 0 3680.0559 15.089188
|
|
1650 21477.638 100.21836 0 3679.8247 -1.1045741
|
|
1700 18501.339 596.4792 0 3680.0357 -15.679682
|
|
1750 18563.642 587.34785 0 3681.2882 33.53221
|
|
1800 19110.185 494.82342 0 3679.8543 18.024046
|
|
1850 21364.191 119.23548 0 3679.9339 2.5291079
|
|
1900 20146.626 322.14873 0 3679.9197 5.7313282
|
|
1950 20692.672 231.2533 0 3680.0319 4.2977759
|
|
2000 20943.904 189.11231 0 3679.7629 -22.645089
|
|
2050 19668.052 401.83077 0 3679.8394 3.6251598
|
|
2100 20280.434 299.76292 0 3679.8353 7.4807838
|
|
2150 19181.841 483.52513 0 3680.4987 22.620829
|
|
2200 21300.185 130.70136 0 3680.7321 4.7101928
|
|
2250 20486.897 266.64698 0 3681.1299 -8.6459184
|
|
2300 18653.018 572.26538 0 3681.1017 -5.2635489
|
|
2350 21513.576 95.606125 0 3681.202 -9.3627078
|
|
2400 21466.185 103.579 0 3681.2764 -29.55912
|
|
2450 20100.274 332.24291 0 3682.2886 35.736349
|
|
2500 20764.562 221.63964 0 3682.4 -12.465656
|
|
2550 20437.187 276.06174 0 3682.2596 -22.421308
|
|
2600 21466.269 104.56898 0 3682.2805 -10.080867
|
|
2650 20819.865 212.38395 0 3682.3615 5.1305357
|
|
2700 18565.57 588.39438 0 3682.656 22.28768
|
|
2750 20789.153 217.36229 0 3682.2211 -8.051962
|
|
2800 21045.639 174.58656 0 3682.193 -7.0803377
|
|
2850 16845.227 874.90505 0 3682.4429 32.992098
|
|
2900 19319.232 462.27119 0 3682.1432 7.9276373
|
|
2950 20558.495 255.61185 0 3682.0277 1.9151653
|
|
3000 20615.868 246.18886 0 3682.1668 -0.016805532
|
|
3050 18695.136 566.5914 0 3682.4474 -7.3528355
|
|
3100 19381.554 451.57712 0 3681.8361 -2.0887636
|
|
3150 19080.633 502.00742 0 3682.1129 5.2518182
|
|
3200 20969.083 187.13559 0 3681.9828 12.156446
|
|
3250 20474.81 269.6876 0 3682.156 1.4067779
|
|
3300 18836.313 542.79266 0 3682.1781 -9.1497216
|
|
3350 21397.694 116.27473 0 3682.557 -6.4412585
|
|
3400 20886.812 201.52507 0 3682.6604 6.3038335
|
|
3450 21604.639 81.93055 0 3682.7038 2.3769444
|
|
3500 20847.621 207.85705 0 3682.4605 -2.758021
|
|
3550 20627.979 244.69999 0 3682.6964 -0.33497747
|
|
3600 19265.519 471.27582 0 3682.1956 2.3506222
|
|
3650 20351.848 290.65727 0 3682.6319 3.5445062
|
|
3700 18507.473 597.72931 0 3682.3082 -21.283074
|
|
3750 20344.017 291.60622 0 3682.2757 6.5366987
|
|
3800 20672.372 237.18966 0 3682.585 6.7310703
|
|
3850 21366.943 122.07461 0 3683.2318 -3.5870721
|
|
3900 20890.294 201.69901 0 3683.4147 -9.5644117
|
|
3950 20684.181 235.91733 0 3683.2809 -4.8913079
|
|
4000 21499.086 100.67563 0 3683.8566 1.1969651
|
|
4050 18549.152 590.04529 0 3681.5707 -9.1914883
|
|
4100 18436.457 604.2601 0 3677.003 3.6486137
|
|
4150 19332.655 462.03124 0 3684.1404 -11.280758
|
|
4200 21199.837 150.66602 0 3683.9722 0.14505208
|
|
4250 19088.228 501.77395 0 3683.1453 1.6869973
|
|
4300 16617.942 913.86736 0 3683.5244 9.1792322
|
|
4350 19765.761 388.52744 0 3682.821 -4.1982973
|
|
4400 20181.964 320.06096 0 3683.7216 5.3685715
|
|
4450 20132.04 328.29106 0 3683.631 6.3340995
|
|
4500 21026.359 179.13858 0 3683.5317 -15.365253
|
|
4550 19273.765 471.36221 0 3683.6564 -0.71397595
|
|
4600 20064.71 339.29348 0 3683.4117 -4.8121056
|
|
4650 19821.01 380.27685 0 3683.7784 11.857115
|
|
4700 18724.367 563.42963 0 3684.1575 13.250333
|
|
4750 20467.467 273.2046 0 3684.449 -1.8076823
|
|
4800 19630.315 412.48507 0 3684.2042 -9.0412254
|
|
4850 19483.424 437.0206 0 3684.258 11.22465
|
|
4900 18504.179 600.28485 0 3684.3146 -5.2345686
|
|
4950 21436.13 111.62139 0 3684.3098 -5.8197915
|
|
5000 18022.817 680.57727 0 3684.38 19.238942
|
|
5050 20750.212 226.15635 0 3684.525 -0.73974419
|
|
5100 20569.533 255.21358 0 3683.4691 -18.332775
|
|
5150 21447.046 109.3048 0 3683.8124 -2.5745966
|
|
5200 18985.753 519.77191 0 3684.0641 9.7821968
|
|
5250 21334.568 128.16597 0 3683.9273 -0.61310451
|
|
5300 18836.476 544.54018 0 3683.9528 -17.979429
|
|
5350 18574.391 587.20088 0 3682.9327 40.990206
|
|
5400 21003.047 183.40176 0 3683.9096 6.1115776
|
|
5450 20693.875 234.62783 0 3683.607 5.4472209
|
|
5500 17673.479 738.99306 0 3684.5729 -28.621738
|
|
5550 19265.837 472.34663 0 3683.3195 -6.609151
|
|
5600 20800.947 217.12409 0 3683.9486 2.6477049
|
|
5650 21746.371 59.453265 0 3683.8485 1.5272163
|
|
5700 20448.97 275.57425 0 3683.736 -7.9864104
|
|
5750 19776.152 387.64417 0 3683.6695 -16.604848
|
|
5800 15779.293 1055.4995 0 3685.3817 20.365883
|
|
5850 21008.009 182.52093 0 3683.8557 -6.6727217
|
|
5900 21566.123 89.588216 0 3683.9421 -7.8944316
|
|
5950 21591.695 85.284975 0 3683.9009 -2.4895203
|
|
6000 17737.17 726.79112 0 3682.9861 1.5643841
|
|
6050 16648.524 907.73295 0 3682.487 3.0853478
|
|
6100 19917.439 363.6324 0 3683.2056 4.358303
|
|
6150 21767.004 56.152017 0 3683.986 -8.8722559
|
|
6200 17654.098 742.15421 0 3684.5039 9.7673482
|
|
6250 20125.754 329.65218 0 3683.9445 5.5050658
|
|
6300 20160.047 323.44453 0 3683.4524 4.852504
|
|
6350 20509.459 264.29515 0 3682.5383 2.5335834
|
|
6400 17199.686 817.09171 0 3683.7061 8.3428304
|
|
6450 18748.366 558.82243 0 3683.5501 0.23782614
|
|
6500 19133.519 494.28383 0 3683.2037 8.1586096
|
|
6550 20311.228 297.30741 0 3682.5122 -1.7015056
|
|
6600 18879.49 536.62652 0 3683.2082 5.0874769
|
|
6650 18189.35 651.42447 0 3682.9828 -15.223564
|
|
6700 19925.861 361.90598 0 3682.8828 0.26811015
|
|
6750 19420.312 445.30915 0 3682.0278 5.5725626
|
|
6800 19925.024 361.87412 0 3682.7114 -3.9763013
|
|
6850 16196.938 985.7242 0 3685.2138 2.8265047
|
|
6900 19779.752 386.51634 0 3683.1416 16.798629
|
|
6950 21043.144 176.83133 0 3684.0221 -4.193188
|
|
7000 18555.362 589.47043 0 3682.0307 14.516315
|
|
7050 21225.883 147.54974 0 3685.1969 -13.466586
|
|
7100 21234.667 145.92615 0 3685.0373 -5.1951121
|
|
7150 21483.472 104.62556 0 3685.2042 -5.6904048
|
|
7200 21014.278 182.97687 0 3685.3566 1.044649
|
|
7250 18588.789 587.96259 0 3686.094 22.707132
|
|
7300 20202.932 318.14401 0 3685.2994 -10.795766
|
|
7350 18304.22 634.7344 0 3685.4377 -1.6801482
|
|
7400 20967.579 190.67822 0 3685.2747 -0.94800692
|
|
7450 20991.588 186.07163 0 3684.6696 -1.411476
|
|
7500 19056.583 507.18197 0 3683.2791 3.2026014
|
|
7550 18542.455 594.92944 0 3685.3386 -27.908724
|
|
7600 19895.73 367.08589 0 3683.0409 4.1334366
|
|
7650 20384.942 285.88041 0 3683.3707 -7.515362
|
|
7700 20683.189 235.46294 0 3682.6611 10.876437
|
|
7750 20729.325 228.204 0 3683.0915 3.8844308
|
|
7800 21667.475 71.752748 0 3682.9985 -15.457992
|
|
7850 19043.652 508.96807 0 3682.9101 -5.8335792
|
|
7900 21079.827 169.61123 0 3682.9158 -1.3216223
|
|
7950 20713.266 230.43917 0 3682.6502 -0.20026535
|
|
8000 20606.41 248.06357 0 3682.4652 4.2844844
|
|
8050 20284.503 302.0469 0 3682.7973 6.3402329
|
|
8100 21859.537 39.514865 0 3682.7711 -13.302141
|
|
8150 18495.181 600.26329 0 3682.7934 9.9318242
|
|
8200 21458.549 105.63828 0 3682.0631 -7.7419285
|
|
8250 18704.511 564.30958 0 3681.728 14.680489
|
|
8300 20689.366 233.57049 0 3681.7982 2.3067527
|
|
8350 20692.974 232.67005 0 3681.499 4.2743386
|
|
8400 20240.086 307.5395 0 3680.8872 1.9694217
|
|
8450 19075.969 501.34689 0 3680.6751 11.056078
|
|
8500 21456.727 103.36067 0 3679.4818 -3.4512371
|
|
8550 20393.16 279.84781 0 3678.7078 6.3282998
|
|
8600 20898.88 195.43751 0 3678.5842 -14.393947
|
|
8650 20297.482 295.3169 0 3678.2306 -0.96829147
|
|
8700 21079.56 164.72934 0 3677.9893 -8.339122
|
|
8750 21142.519 154.18527 0 3677.9384 -4.6169442
|
|
8800 20143.871 320.23161 0 3677.5435 6.5710426
|
|
8850 21030.065 172.88831 0 3677.8992 1.3973883
|
|
8900 19814.648 375.22097 0 3677.6624 2.6996208
|
|
8950 17392.382 778.87517 0 3677.6055 11.963975
|
|
9000 19209.163 476.44659 0 3677.9738 8.7050034
|
|
9050 20143.824 320.17051 0 3677.4745 -5.8044332
|
|
9100 21400.78 110.99404 0 3677.7908 -3.0027429
|
|
9150 21834.471 38.970732 0 3678.0493 -2.5838117
|
|
9200 21344.715 120.55831 0 3678.0108 4.8187829
|
|
9250 20998.277 178.31959 0 3678.0324 -1.2009012
|
|
9300 21141.788 154.4658 0 3678.0971 -21.693564
|
|
9350 21439.398 105.00432 0 3678.2374 -16.113694
|
|
9400 21296.282 128.83877 0 3678.2191 -2.9990284
|
|
9450 19050.623 503.10319 0 3678.207 15.622525
|
|
9500 20845.847 203.77117 0 3678.079 -1.7504827
|
|
9550 18808.956 543.38757 0 3678.2135 -2.6611868
|
|
9600 20612.559 242.57373 0 3678.0002 -0.1650541
|
|
9650 20522.637 257.28926 0 3677.7288 6.8876074
|
|
9700 20970.074 182.75754 0 3677.7699 -4.5350279
|
|
9750 18297.505 625.06808 0 3674.6522 32.429153
|
|
9800 21042.472 170.78969 0 3677.8684 5.4901963
|
|
9850 20444.092 270.84839 0 3678.197 6.9444494
|
|
9900 21597.787 78.901871 0 3678.533 2.3445932
|
|
9950 18376.854 616.35469 0 3679.1636 -8.55063
|
|
10000 21490.054 97.234379 0 3678.9101 -0.36115606
|
|
Loop time of 3.38095 on 4 procs for 10000 steps with 81 atoms
|
|
|
|
Performance: 25554.943 tau/day, 2957.748 timesteps/s
|
|
98.7% CPU use with 4 MPI tasks x 1 OpenMP threads
|
|
|
|
MPI task timing breakdown:
|
|
Section | min time | avg time | max time |%varavg| %total
|
|
---------------------------------------------------------------
|
|
Pair | 0.015775 | 0.043664 | 0.1024 | 16.8 | 1.29
|
|
Neigh | 0.012822 | 0.029038 | 0.061576 | 11.5 | 0.86
|
|
Comm | 0.18256 | 0.2516 | 0.30898 | 10.5 | 7.44
|
|
Output | 0.0063725 | 0.0069898 | 0.0081069 | 0.8 | 0.21
|
|
Modify | 2.9608 | 3.0171 | 3.0947 | 2.8 | 89.24
|
|
Other | | 0.03255 | | | 0.96
|
|
|
|
Nlocal: 20.25 ave 81 max 0 min
|
|
Histogram: 3 0 0 0 0 0 0 0 0 1
|
|
Nghost: 45.5 ave 82 max 12 min
|
|
Histogram: 2 0 0 0 0 0 0 0 1 1
|
|
Neighs: 218.75 ave 875 max 0 min
|
|
Histogram: 3 0 0 0 0 0 0 0 0 1
|
|
|
|
Total # of neighbors = 875
|
|
Ave neighs/atom = 10.8025
|
|
Neighbor list builds = 993
|
|
Dangerous builds = 945
|
|
|
|
Please see the log.cite file for references relevant to this simulation
|
|
|
|
Total wall time: 0:00:03
|