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 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 #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 = 3.50303 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 19223.688 204.15176 0 3764.0939 -1.6134529 1550 18147.996 404.12677 0 3764.8668 8.4194781 1600 18615.043 317.42468 0 3764.6548 -2.3288926 1650 20120.654 38.887908 0 3764.935 -8.7620288 1700 19450.907 162.98267 0 3765.0025 2.3254739 1750 19374.631 177.3797 0 3765.2744 8.9328773 1800 19424.404 167.93965 0 3765.0514 0.081228843 1850 17936.227 442.84645 0 3764.3699 6.6011251 1900 19982.595 64.406244 0 3764.8868 -2.952971 1950 16215.818 761.91942 0 3764.8486 13.994877 2000 18584.433 322.11846 0 3763.6801 7.1653695 2050 20107.965 41.025796 0 3764.723 -0.31089763 2100 20002.329 60.593879 0 3764.7288 -6.7919882 2150 16949.817 626.58598 0 3765.4409 3.5087505 2200 20010.954 58.8082 0 3764.5403 -10.862143 2250 18982.732 247.00854 0 3762.3293 -0.53812607 2300 18401.276 354.88369 0 3762.5274 1.0921058 2350 19390.535 172.93951 0 3763.7793 -3.3524354 2400 16080.475 786.44896 0 3764.3146 -16.201558 2450 18870.293 268.77171 0 3763.2704 11.199749 2500 19688.508 117.54164 0 3763.5617 4.3806994 2550 18870.328 268.87896 0 3763.3841 -5.6641099 2600 17020.211 611.54841 0 3763.4394 6.3081434 2650 18748.838 291.88478 0 3763.8917 2.4175163 2700 19743.991 106.92945 0 3763.224 -0.33916964 2750 19525.446 147.60906 0 3763.4324 -1.6251174 2800 18257.411 381.40184 0 3762.4038 23.39495 2850 18496.796 337.65425 0 3762.9868 4.3657735 2900 20163.418 29.253902 0 3763.2203 1.4431917 2950 16823.317 646.69817 0 3762.1273 4.9041552 3000 19223.007 203.2529 0 3763.069 4.0414458 3050 17391.02 542.93746 0 3763.4968 15.139863 3100 19205.6 206.57791 0 3763.1705 4.8519241 3150 19835.659 90.247763 0 3763.5179 -14.900053 3200 18962.776 251.5838 0 3763.2089 -13.706561 3250 19418.837 167.29058 0 3763.3716 -2.0866468 3300 18628.291 313.69067 0 3763.3742 5.9919715 3350 17465.974 529.14439 0 3763.5841 14.122593 3400 18488.661 339.6186 0 3763.4448 21.526798 3450 19163.152 214.26098 0 3762.9928 4.1888096 3500 18000.27 429.81789 0 3763.2011 5.4734485 3550 19582.423 136.71887 0 3763.0935 -2.5335675 3600 19634.325 127.2219 0 3763.208 -1.9728322 3650 19428.114 165.40707 0 3763.2059 -2.3318779 3700 19861.116 85.356944 0 3763.3414 -3.9097609 3750 19337.239 182.43992 0 3763.4102 -3.3559651 3800 19493.146 153.40349 0 3763.2453 -0.71089657 3850 18607.616 317.74889 0 3763.6037 3.475832 3900 19719.59 111.5553 0 3763.3313 0.58876668 3950 19756.661 104.5522 0 3763.1931 3.7526698 4000 17904.708 447.1673 0 3762.854 12.270654 4050 19588.087 135.80435 0 3763.2279 0.94578945 4100 19065.901 232.38235 0 3763.1048 -2.7495195 4150 18775.075 286.2257 0 3763.0915 -3.7039858 4200 18800.725 281.46601 0 3763.0817 0.15619543 4250 19732.687 108.90618 0 3763.1075 3.0865861 4300 18278.151 377.63653 0 3762.4794 1.5768601 4350 17915.757 445.4804 0 3763.2133 -3.7040484 4400 15987.794 802.41575 0 3763.1183 22.252078 4450 19302.37 188.69495 0 3763.2079 0.91081327 4500 20039.32 52.304099 0 3763.2893 -2.0828905 4550 19535.953 145.4374 0 3763.2064 -3.3804255 4600 19700.723 114.79823 0 3763.0803 -1.1761163 4650 17804.641 465.85788 0 3763.0136 7.5947192 4700 19913.881 75.240289 0 3762.996 -2.1100557 4750 19982.484 62.535995 0 3762.996 -4.5821237 4800 17400.76 540.21707 0 3762.58 -5.8418778 4850 19199.88 206.90989 0 3762.4433 3.4536341 4900 19173.92 212.11327 0 3762.8392 5.0387071 4950 19236.635 200.57537 0 3762.9152 -1.4932783 5000 19077.616 230.04967 0 3762.9415 4.3742655 5050 19893.763 78.909747 0 3762.94 -1.5796711 5100 18884.746 265.68301 0 3762.8583 2.2767949 5150 17417.096 537.54036 0 3762.9286 -2.8632555 5200 18247.844 383.60092 0 3762.8312 10.384179 5250 19494.107 152.60532 0 3762.6251 -4.7617287 5300 18739.781 292.46206 0 3762.7919 23.210048 5350 19310.938 186.62363 0 3762.7232 14.895327 5400 19540.39 144.14287 0 3762.7336 6.094624 5450 20074.459 45.247888 0 3762.7403 -2.0871835 5500 19986.377 61.668045 0 3762.849 -2.4551918 5550 19038.904 237.07578 0 3762.7987 5.4250813 5600 19439.124 163.1438 0 3762.9816 4.1291468 5650 19480.321 155.58325 0 3763.0501 -3.5308058 5700 19869.291 83.651379 0 3763.1497 -7.8661592 5750 19991.447 61.068554 0 3763.1884 -6.8473586 5800 19454.072 160.36805 0 3762.9739 1.527662 5850 17994.409 430.95597 0 3763.2539 -5.6078082 5900 19209.794 205.74997 0 3763.1193 8.4113055 5950 19046.427 236.06321 0 3763.1793 10.463356 6000 19409.899 168.95271 0 3763.3785 2.542067 6050 18068.174 417.35443 0 3763.3125 10.498199 6100 19549.253 143.21885 0 3763.4509 2.3075797 6150 18464.719 344.0303 0 3763.4228 0.46469762 6200 19811.205 94.62725 0 3763.3689 1.2382763 6250 18715.36 297.26445 0 3763.0718 -3.4541762 6300 17115.664 594.09913 0 3763.6666 4.2065564 6350 18155.927 400.71764 0 3762.9264 1.1521258 6400 19873.093 83.169067 0 3763.3716 0.16383592 6450 19991.88 61.13218 0 3763.3321 -1.3008128 6500 19434.416 164.40698 0 3763.3728 -13.593422 6550 19855.253 86.645329 0 3763.544 -0.85704037 6600 19251.141 198.41152 0 3763.4376 4.3027745 6650 19741.815 107.69047 0 3763.582 4.994835 6700 19633.466 127.69333 0 3763.5203 6.3677145 6750 16231.353 757.83705 0 3763.6431 -1.5978692 6800 18863.396 270.1114 0 3763.3329 -11.915909 6850 19644.779 125.29421 0 3763.2163 -1.151217 6900 18883.642 266.06889 0 3763.0397 -4.3950749 6950 19042.364 236.54144 0 3762.9052 5.5718878 7000 18351.868 364.38028 0 3762.8743 7.8958273 7050 19981.031 62.840667 0 3763.0316 -5.8572298 7100 19796.372 97.073665 0 3763.0685 -3.5178361 7150 19805.385 95.235221 0 3762.899 -2.5481726 7200 18722.055 295.86113 0 3762.9084 13.826356 7250 19537.304 144.54234 0 3762.5616 1.2288666 7300 18787.328 283.49504 0 3762.6299 9.0044469 7350 18886.005 265.52121 0 3762.9295 6.6791881 7400 19891.864 79.239278 0 3762.9178 -2.3882842 7450 18164.752 399.07065 0 3762.9137 3.9400481 7500 18702.612 299.582 0 3763.0286 4.7987316 7550 19884.986 80.231665 0 3762.6365 -0.75016515 7600 19549.059 142.16243 0 3762.3586 -2.1035756 7650 18223.668 387.9047 0 3762.658 -17.064339 7700 19428.4 164.79531 0 3762.6473 -2.8342541 7750 19239.584 199.93029 0 3762.8163 3.1746033 7800 19458.005 159.46176 0 3762.7961 1.714515 7850 18320.308 369.77051 0 3762.4202 2.1422976 7900 18817.415 278.04812 0 3762.7546 0.94492621 7950 19892.761 79.115928 0 3762.9606 1.4948501 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 3.99472 on 4 procs for 10000 steps with 81 atoms Performance: 21628.565 tau/day, 2503.306 timesteps/s 99.7% CPU use with 4 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.0090363 | 0.029554 | 0.05092 | 8.8 | 0.74 Neigh | 0.0090437 | 0.021045 | 0.034359 | 6.3 | 0.53 Comm | 0.1326 | 0.17829 | 0.2132 | 7.3 | 4.46 Output | 0.0044832 | 0.0048217 | 0.0053875 | 0.5 | 0.12 Modify | 3.6632 | 3.7381 | 3.8211 | 2.9 | 93.58 Other | | 0.02291 | | | 0.57 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: 0:00:03