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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@5852 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp
2011-03-26 23:02:38 +00:00
parent 06737e36b0
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examples/rigid/log.rigid.28Mar11.linux.1 Normal file
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LAMMPS (27 Mar 2011)
# 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 processor grid
81 atoms
velocity all create 100.0 4928459
# unconnected bodies
group clump1 id <> 1 9
9 atoms in group clump1
group clump2 id <> 10 18
9 atoms in group clump2
group clump3 id <> 19 27
9 atoms in group clump3
group clump4 id <> 28 36
9 atoms in group clump4
group clump5 id <> 37 45
9 atoms in group clump5
group clump6 id <> 46 54
9 atoms in group clump6
group clump7 id <> 55 63
9 atoms in group clump7
group clump8 id <> 64 72
9 atoms in group clump8
group clump9 id <> 73 81
9 atoms in group clump9
fix 1 all rigid group 9 clump1 clump2 clump3 clump4 clump5 clump6 clump7 clump8 clump9
9 rigid bodies with 81 atoms
# 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
#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
timestep 0.0001
thermo 50
run 10000
Memory usage per processor = 1.86288 Mbytes
Step Temp E_pair E_mol TotEng Press
0 115.29439 5235.9179 0 5272.2142 -2.7403788
50 14910.685 571.71558 0 5265.82 32.006171
100 16298.442 136.66184 0 5267.653 16.444229
150 16682.606 17.490511 0 5269.4219 14.900344
200 16733.929 1.372872 0 5269.4617 14.569267
250 16738.853 -0.15252816 0 5269.4864 14.496404
300 16738.588 -0.055171335 0 5269.5002 14.496025
350 16738.492 -0.017444677 0 5269.5077 14.496446
400 16738.464 -0.0060102023 0 5269.5104 14.496618
450 16738.455 -0.0012713351 0 5269.5124 14.496701
500 16738.455 -0.00081068621 0 5269.5128 14.496709
550 16738.455 -0.00083203497 0 5269.5129 14.496707
600 16738.455 -0.00058355356 0 5269.5131 14.496709
650 16738.455 -0.00047226704 0 5269.5131 14.496708
700 16738.455 0 0 5269.5136 14.496713
750 16738.455 0 0 5269.5136 14.49671
800 16738.455 0 0 5269.5137 14.496709
850 16738.455 0 0 5269.5137 14.49671
900 16738.456 0 0 5269.5138 14.496713
950 16738.462 -0.0035323872 0 5269.5122 14.496671
1000 16738.586 -0.051135144 0 5269.5036 14.496229
1050 16737.358 0.32995057 0 5269.4981 14.525763
1100 16737.892 0.16210246 0 5269.4984 14.531983
1150 16738.703 -0.089235095 0 5269.5025 14.509899
1200 16738.466 -0.0075446243 0 5269.5096 14.510615
1250 16738.456 0 0 5269.514 14.510704
1300 16738.457 0 0 5269.5141 14.510701
1350 16738.457 0 0 5269.5141 14.510699
1400 16738.457 -0.00044736511 0 5269.5138 14.510693
1450 16738.458 -0.0010971179 0 5269.5134 14.510687
1500 16738.458 -0.00057885428 0 5269.5139 14.510698
1550 16738.457 0 0 5269.5143 14.51071
1600 16738.457 0 0 5269.5144 14.510712
1650 16738.457 0 0 5269.5144 14.510712
1700 16738.458 0 0 5269.5144 14.51071
1750 16738.458 0 0 5269.5145 14.510708
1800 16738.458 0 0 5269.5145 14.510706
1850 16738.458 0 0 5269.5146 14.510705
1900 16738.458 0 0 5269.5146 14.510706
1950 16738.465 -0.0031733615 0 5269.5134 14.510659
2000 16738.491 -0.013255268 0 5269.5117 14.510532
2050 16738.556 -0.0365811 0 5269.5087 14.51029
2100 16738.633 -0.063209659 0 5269.5065 14.510219
2150 16738.607 -0.05601761 0 5269.5055 14.510231
2200 16738.557 -0.038423032 0 5269.5072 14.510404
2250 16738.515 -0.023709918 0 5269.5088 14.510539
2300 16738.489 -0.013249035 0 5269.5111 14.510621
2350 16738.468 -0.0045563719 0 5269.5131 14.510714
2400 16738.46 -0.00052194273 0 5269.5146 14.510771
2450 16738.464 -0.0023259756 0 5269.514 14.510746
2500 16738.468 -0.0051929186 0 5269.5127 14.510731
2550 16738.581 -0.044940117 0 5269.5085 14.510315
2600 16738.427 -7.9722862e-05 0 5269.5046 14.510657
2650 16733.017 1.705148 0 5269.5067 14.596295
2700 16738.761 -0.10614946 0 5269.5038 14.499584
2750 16733.973 1.4038179 0 5269.5064 14.598107
2800 16738.585 -0.046813448 0 5269.5076 14.511073
2850 16738.487 -0.012558719 0 5269.5111 14.510111
2900 16738.465 -0.0026252725 0 5269.514 14.510277
2950 16738.476 -0.0082220764 0 5269.512 14.510223
3000 16738.66 -0.071284779 0 5269.507 14.509758
3050 16715.332 7.2419351 0 5269.476 14.870305
3100 16653.226 26.818761 0 5269.5009 14.496764
3150 16739.351 -0.30690375 0 5269.4886 13.643904
3200 16733.238 1.6025328 0 5269.4737 12.016934
3250 16734.374 1.2554428 0 5269.4841 11.963561
3300 16732.156 1.9585967 0 5269.4893 12.234024
3350 16738.655 -0.079693236 0 5269.497 12.092757
3400 16738.543 -0.042215005 0 5269.4991 12.092809
3450 16738.591 -0.059327511 0 5269.4972 12.092536
3500 16738.759 -0.11761245 0 5269.4918 12.09203
3550 16713.405 7.846062 0 5269.4737 12.389816
3600 16734.939 1.0821936 0 5269.4891 12.173591
3650 16738.808 -0.13663195 0 5269.4882 12.027009
3700 16738.602 -0.070934367 0 5269.4889 12.025288
3750 16737.731 0.20706557 0 5269.4927 12.061948
3800 16738.578 -0.05582043 0 5269.4965 12.035665
3850 16738.471 -0.016307928 0 5269.5024 12.035302
3900 16738.449 -0.0058182199 0 5269.5059 12.035401
3950 16738.439 -0.0012027325 0 5269.5074 12.035461
4000 16738.436 -0.00020698452 0 5269.5075 12.035469
4050 16738.437 0 0 5269.5078 12.035454
4100 16738.437 0 0 5269.508 12.035435
4150 16738.438 0 0 5269.5081 12.035426
4200 16738.438 0 0 5269.5083 12.035432
4250 16738.439 0 0 5269.5085 12.035447
4300 16738.439 0 0 5269.5086 12.035463
4350 16738.44 0 0 5269.5087 12.035474
4400 16738.44 0 0 5269.5088 12.035478
4450 16738.44 0 0 5269.5089 12.035474
4500 16738.44 0 0 5269.509 12.035462
4550 16738.441 0 0 5269.5092 12.035449
4600 16738.441 0 0 5269.5093 12.035445
4650 16738.442 0 0 5269.5095 12.035451
4700 16738.442 0 0 5269.5096 12.03546
4750 16738.443 0 0 5269.5097 12.035465
4800 16738.443 0 0 5269.5098 12.035466
4850 16738.443 0 0 5269.51 12.035463
4900 16738.444 0 0 5269.5101 12.035456
4950 16738.444 0 0 5269.5102 12.035447
5000 16738.445 0 0 5269.5104 12.03544
5050 16738.445 0 0 5269.5105 12.035442
5100 16738.446 0 0 5269.5107 12.035455
5150 16738.446 0 0 5269.5108 12.03547
5200 16738.446 0 0 5269.5109 12.035479
5250 16738.447 0 0 5269.511 12.035479
5300 16738.447 0 0 5269.5111 12.03547
5350 16738.447 0 0 5269.5112 12.035454
5400 16738.448 0 0 5269.5113 12.035434
5450 16738.448 0 0 5269.5115 12.03542
5500 16738.449 0 0 5269.5117 12.035422
5550 16738.457 -0.0030919234 0 5269.5111 12.035383
5600 16738.51 -0.021618357 0 5269.5092 12.035106
5650 16738.622 -0.059214788 0 5269.507 12.035694
5700 16395.28 108.06942 0 5269.5463 24.369038
5750 16738.544 -0.033973429 0 5269.5077 12.011261
5800 16738.456 -0.0037013529 0 5269.5102 12.011675
5850 16738.451 0 0 5269.5123 12.011709
5900 16738.451 -0.00022115871 0 5269.5122 12.011687
5950 16738.452 -0.00024253349 0 5269.5124 12.011678
6000 16738.452 0 0 5269.5128 12.011688
6050 16738.453 0 0 5269.513 12.011702
6100 16738.453 0 0 5269.5131 12.011716
6150 16738.454 0 0 5269.5132 12.011725
6200 16738.454 0 0 5269.5133 12.011728
6250 16738.454 0 0 5269.5134 12.011723
6300 16738.455 0 0 5269.5135 12.011712
6350 16738.455 0 0 5269.5137 12.0117
6400 16738.456 0 0 5269.5138 12.011697
6450 16738.456 0 0 5269.514 12.011704
6500 16738.456 0 0 5269.5141 12.011714
6550 16738.457 0 0 5269.5142 12.011719
6600 16738.457 0 0 5269.5143 12.011718
6650 16738.458 0 0 5269.5144 12.011713
6700 16738.458 0 0 5269.5146 12.011705
6750 16738.459 0 0 5269.5147 12.011696
6800 16738.459 0 0 5269.5149 12.01169
6850 16738.46 0 0 5269.515 12.011695
6900 16738.46 0 0 5269.5152 12.01171
6950 16738.46 0 0 5269.5153 12.011726
7000 16738.461 0 0 5269.5154 12.011736
7050 16738.461 0 0 5269.5155 12.011737
7100 16738.461 0 0 5269.5155 12.011728
7150 16738.461 0 0 5269.5156 12.011712
7200 16738.462 0 0 5269.5158 12.011691
7250 16738.463 0 0 5269.516 12.011676
7300 16738.463 0 0 5269.5162 12.011677
7350 16738.464 0 0 5269.5164 12.011693
7400 16738.464 0 0 5269.5165 12.011713
7450 16738.465 0 0 5269.5166 12.011729
7500 16738.465 0 0 5269.5167 12.011736
7550 16738.465 0 0 5269.5168 12.011734
7600 16738.465 0 0 5269.5168 12.011722
7650 16738.466 0 0 5269.517 12.011704
7700 16738.466 0 0 5269.5171 12.011687
7750 16738.467 0 0 5269.5173 12.011681
7800 16738.467 0 0 5269.5175 12.011687
7850 16738.468 0 0 5269.5176 12.0117
7900 16738.468 0 0 5269.5178 12.011712
7950 16738.469 0 0 5269.5179 12.011721
8000 16738.469 0 0 5269.518 12.011724
8050 16738.469 0 0 5269.5181 12.01172
8100 16738.47 0 0 5269.5182 12.011709
8150 16738.47 0 0 5269.5183 12.0117
8200 16738.47 0 0 5269.5185 12.0117
8250 16738.471 0 0 5269.5186 12.011709
8300 16738.471 0 0 5269.5187 12.011719
8350 16738.472 0 0 5269.5189 12.011723
8400 16738.472 0 0 5269.519 12.01172
8450 16738.473 -0.00039690661 0 5269.5189 12.011706
8500 16738.481 -0.0034646802 0 5269.5182 12.011643
8550 16738.483 -0.0045307409 0 5269.5178 12.011621
8600 16738.474 -0.00076532814 0 5269.5189 12.011681
8650 16738.474 0 0 5269.5197 12.011699
8700 16738.475 0 0 5269.5199 12.011715
8750 16738.475 0 0 5269.52 12.011732
8800 16738.475 0 0 5269.52 12.011743
8850 16738.476 0 0 5269.5201 12.011744
8900 16738.476 0 0 5269.5202 12.011735
8950 16738.476 0 0 5269.5203 12.011719
9000 16738.477 0 0 5269.5205 12.011698
9050 16738.477 0 0 5269.5206 12.011683
9100 16738.478 0 0 5269.5208 12.011684
9150 16738.479 0 0 5269.521 12.011701
9200 16738.479 0 0 5269.5212 12.011722
9250 16738.479 0 0 5269.5213 12.011738
9300 16738.48 0 0 5269.5214 12.011746
9350 16738.48 0 0 5269.5214 12.011744
9400 16738.48 0 0 5269.5215 12.011732
9450 16738.48 0 0 5269.5216 12.011715
9500 16738.481 -0.0003765244 0 5269.5216 12.011692
9550 16738.493 -0.0053156161 0 5269.5203 12.011611
9600 16738.549 -0.026814371 0 5269.5163 12.011415
9650 16738.765 -0.10191524 0 5269.5092 12.011013
9700 16735.041 1.0589895 0 5269.4979 12.062708
9750 16738.013 0.13550073 0 5269.5101 11.407245
9800 16738.512 -0.011620328 0 5269.5201 11.394973
9850 16738.489 -0.00067270555 0 5269.5237 11.395098
9900 16738.489 -0.00024984581 0 5269.5242 11.395084
9950 16738.49 0 0 5269.5245 11.395076
10000 16738.49 0 0 5269.5246 11.395075
Loop time of 0.240772 on 1 procs for 10000 steps with 81 atoms
Pair time (%) = 0.0153747 (6.38557)
Neigh time (%) = 0.0424147 (17.6161)
Comm time (%) = 0.0163877 (6.80631)
Outpt time (%) = 0.0295906 (12.2899)
Other time (%) = 0.137004 (56.9021)
Nlocal: 81 ave 81 max 81 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 84 ave 84 max 84 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0
Neighbor list builds = 998
Dangerous builds = 997

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LAMMPS (27 Mar 2011)
# 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 processor grid
81 atoms
velocity all create 100.0 4928459
# unconnected bodies
group clump1 id <> 1 9
9 atoms in group clump1
group clump2 id <> 10 18
9 atoms in group clump2
group clump3 id <> 19 27
9 atoms in group clump3
group clump4 id <> 28 36
9 atoms in group clump4
group clump5 id <> 37 45
9 atoms in group clump5
group clump6 id <> 46 54
9 atoms in group clump6
group clump7 id <> 55 63
9 atoms in group clump7
group clump8 id <> 64 72
9 atoms in group clump8
group clump9 id <> 73 81
9 atoms in group clump9
fix 1 all rigid group 9 clump1 clump2 clump3 clump4 clump5 clump6 clump7 clump8 clump9
9 rigid bodies with 81 atoms
# 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
#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
timestep 0.0001
thermo 50
run 10000
Memory usage per processor = 1.82479 Mbytes
Step Temp E_pair E_mol TotEng Press
0 115.29439 5235.9179 0 5272.2142 -2.7403788
50 14910.685 571.71558 0 5265.82 32.006171
100 16298.442 136.66184 0 5267.653 16.444229
150 16682.606 17.490511 0 5269.4219 14.900344
200 16733.929 1.372872 0 5269.4617 14.569267
250 16738.853 -0.15252816 0 5269.4864 14.496404
300 16738.588 -0.055171335 0 5269.5002 14.496025
350 16738.492 -0.017444677 0 5269.5077 14.496446
400 16738.464 -0.0060102023 0 5269.5104 14.496618
450 16738.455 -0.0012713351 0 5269.5124 14.496701
500 16738.455 -0.00081068621 0 5269.5128 14.496709
550 16738.455 -0.00083203497 0 5269.5129 14.496707
600 16738.455 -0.00058355356 0 5269.5131 14.496709
650 16738.455 -0.00047226704 0 5269.5131 14.496708
700 16738.455 0 0 5269.5136 14.496713
750 16738.455 0 0 5269.5136 14.49671
800 16738.455 0 0 5269.5137 14.496709
850 16738.455 0 0 5269.5137 14.49671
900 16738.456 0 0 5269.5138 14.496713
950 16738.462 -0.0035323872 0 5269.5122 14.496671
1000 16738.586 -0.051135144 0 5269.5036 14.496229
1050 16737.358 0.32995057 0 5269.4981 14.525763
1100 16737.892 0.16210246 0 5269.4984 14.531983
1150 16738.703 -0.089235095 0 5269.5025 14.509899
1200 16738.466 -0.0075446243 0 5269.5096 14.510615
1250 16738.456 0 0 5269.514 14.510704
1300 16738.457 0 0 5269.5141 14.510701
1350 16738.457 0 0 5269.5141 14.510699
1400 16738.457 -0.00044736511 0 5269.5138 14.510693
1450 16738.458 -0.0010971179 0 5269.5134 14.510687
1500 16738.458 -0.00057885428 0 5269.5139 14.510698
1550 16738.457 0 0 5269.5143 14.51071
1600 16738.457 0 0 5269.5144 14.510712
1650 16738.457 0 0 5269.5144 14.510712
1700 16738.458 0 0 5269.5144 14.51071
1750 16738.458 0 0 5269.5145 14.510708
1800 16738.458 0 0 5269.5145 14.510706
1850 16738.458 0 0 5269.5146 14.510705
1900 16738.458 0 0 5269.5146 14.510706
1950 16738.465 -0.0031733615 0 5269.5134 14.510659
2000 16738.491 -0.013255268 0 5269.5117 14.510532
2050 16738.556 -0.0365811 0 5269.5087 14.51029
2100 16738.633 -0.063209659 0 5269.5065 14.510219
2150 16738.607 -0.05601761 0 5269.5055 14.510231
2200 16738.557 -0.038423032 0 5269.5072 14.510404
2250 16738.515 -0.023709918 0 5269.5088 14.510539
2300 16738.489 -0.013249035 0 5269.5111 14.510621
2350 16738.468 -0.0045563719 0 5269.5131 14.510714
2400 16738.46 -0.00052194273 0 5269.5146 14.510771
2450 16738.464 -0.0023259756 0 5269.514 14.510746
2500 16738.468 -0.0051929186 0 5269.5127 14.510731
2550 16738.581 -0.044940117 0 5269.5085 14.510315
2600 16738.427 -7.9722858e-05 0 5269.5046 14.510657
2650 16733.017 1.705148 0 5269.5067 14.596295
2700 16738.761 -0.10614946 0 5269.5038 14.499584
2750 16733.973 1.4038179 0 5269.5064 14.598107
2800 16738.585 -0.046813448 0 5269.5076 14.511073
2850 16738.487 -0.012558719 0 5269.5111 14.510111
2900 16738.465 -0.0026252725 0 5269.514 14.510277
2950 16738.476 -0.0082220764 0 5269.512 14.510223
3000 16738.66 -0.071284779 0 5269.507 14.509758
3050 16715.332 7.2419351 0 5269.476 14.870305
3100 16653.226 26.818761 0 5269.5009 14.496764
3150 16739.351 -0.30690375 0 5269.4886 13.643904
3200 16733.238 1.6025328 0 5269.4737 12.016934
3250 16734.374 1.2554428 0 5269.4841 11.963561
3300 16732.156 1.9585967 0 5269.4893 12.234024
3350 16738.655 -0.079693236 0 5269.497 12.092757
3400 16738.543 -0.042215005 0 5269.4991 12.092809
3450 16738.591 -0.059327511 0 5269.4972 12.092536
3500 16738.759 -0.11761245 0 5269.4918 12.09203
3550 16713.405 7.846062 0 5269.4737 12.389816
3600 16734.939 1.0821936 0 5269.4891 12.173591
3650 16738.808 -0.13663195 0 5269.4882 12.027009
3700 16738.602 -0.070934367 0 5269.4889 12.025288
3750 16737.731 0.20706557 0 5269.4927 12.061948
3800 16738.578 -0.05582043 0 5269.4965 12.035665
3850 16738.471 -0.016307928 0 5269.5024 12.035302
3900 16738.449 -0.0058182199 0 5269.5059 12.035401
3950 16738.439 -0.0012027325 0 5269.5074 12.035461
4000 16738.436 -0.00020698452 0 5269.5075 12.035469
4050 16738.437 0 0 5269.5078 12.035454
4100 16738.437 0 0 5269.508 12.035435
4150 16738.438 0 0 5269.5081 12.035426
4200 16738.438 0 0 5269.5083 12.035432
4250 16738.439 0 0 5269.5085 12.035447
4300 16738.439 0 0 5269.5086 12.035463
4350 16738.44 0 0 5269.5087 12.035474
4400 16738.44 0 0 5269.5088 12.035478
4450 16738.44 0 0 5269.5089 12.035474
4500 16738.44 0 0 5269.509 12.035462
4550 16738.441 0 0 5269.5092 12.035449
4600 16738.441 0 0 5269.5093 12.035445
4650 16738.442 0 0 5269.5095 12.035451
4700 16738.442 0 0 5269.5096 12.03546
4750 16738.443 0 0 5269.5097 12.035465
4800 16738.443 0 0 5269.5098 12.035466
4850 16738.443 0 0 5269.51 12.035463
4900 16738.444 0 0 5269.5101 12.035456
4950 16738.444 0 0 5269.5102 12.035447
5000 16738.445 0 0 5269.5104 12.03544
5050 16738.445 0 0 5269.5105 12.035442
5100 16738.446 0 0 5269.5107 12.035455
5150 16738.446 0 0 5269.5108 12.03547
5200 16738.446 0 0 5269.5109 12.035479
5250 16738.447 0 0 5269.511 12.035479
5300 16738.447 0 0 5269.5111 12.03547
5350 16738.447 0 0 5269.5112 12.035454
5400 16738.448 0 0 5269.5113 12.035434
5450 16738.448 0 0 5269.5115 12.03542
5500 16738.449 0 0 5269.5117 12.035422
5550 16738.457 -0.0030919234 0 5269.5111 12.035383
5600 16738.51 -0.021618357 0 5269.5092 12.035106
5650 16738.622 -0.059214788 0 5269.507 12.035694
5700 16395.28 108.06942 0 5269.5463 24.369038
5750 16738.544 -0.033973429 0 5269.5077 12.011261
5800 16738.456 -0.0037013529 0 5269.5102 12.011675
5850 16738.451 0 0 5269.5123 12.011709
5900 16738.451 -0.00022115871 0 5269.5122 12.011687
5950 16738.452 -0.00024253349 0 5269.5124 12.011678
6000 16738.452 0 0 5269.5128 12.011688
6050 16738.453 0 0 5269.513 12.011702
6100 16738.453 0 0 5269.5131 12.011716
6150 16738.454 0 0 5269.5132 12.011725
6200 16738.454 0 0 5269.5133 12.011728
6250 16738.454 0 0 5269.5134 12.011723
6300 16738.455 0 0 5269.5135 12.011712
6350 16738.455 0 0 5269.5137 12.0117
6400 16738.456 0 0 5269.5138 12.011697
6450 16738.456 0 0 5269.514 12.011704
6500 16738.456 0 0 5269.5141 12.011714
6550 16738.457 0 0 5269.5142 12.011719
6600 16738.457 0 0 5269.5143 12.011718
6650 16738.458 0 0 5269.5144 12.011713
6700 16738.458 0 0 5269.5146 12.011705
6750 16738.459 0 0 5269.5147 12.011696
6800 16738.459 0 0 5269.5149 12.01169
6850 16738.46 0 0 5269.515 12.011695
6900 16738.46 0 0 5269.5152 12.01171
6950 16738.46 0 0 5269.5153 12.011726
7000 16738.461 0 0 5269.5154 12.011736
7050 16738.461 0 0 5269.5155 12.011737
7100 16738.461 0 0 5269.5155 12.011728
7150 16738.461 0 0 5269.5156 12.011712
7200 16738.462 0 0 5269.5158 12.011691
7250 16738.463 0 0 5269.516 12.011676
7300 16738.463 0 0 5269.5162 12.011677
7350 16738.464 0 0 5269.5164 12.011693
7400 16738.464 0 0 5269.5165 12.011713
7450 16738.465 0 0 5269.5166 12.011729
7500 16738.465 0 0 5269.5167 12.011736
7550 16738.465 0 0 5269.5168 12.011734
7600 16738.465 0 0 5269.5168 12.011722
7650 16738.466 0 0 5269.517 12.011704
7700 16738.466 0 0 5269.5171 12.011687
7750 16738.467 0 0 5269.5173 12.011681
7800 16738.467 0 0 5269.5175 12.011687
7850 16738.468 0 0 5269.5176 12.0117
7900 16738.468 0 0 5269.5178 12.011712
7950 16738.469 0 0 5269.5179 12.011721
8000 16738.469 0 0 5269.518 12.011724
8050 16738.469 0 0 5269.5181 12.01172
8100 16738.47 0 0 5269.5182 12.011709
8150 16738.47 0 0 5269.5183 12.0117
8200 16738.47 0 0 5269.5185 12.0117
8250 16738.471 0 0 5269.5186 12.011709
8300 16738.471 0 0 5269.5187 12.011719
8350 16738.472 0 0 5269.5189 12.011723
8400 16738.472 0 0 5269.519 12.01172
8450 16738.473 -0.00039690661 0 5269.5189 12.011706
8500 16738.481 -0.0034646802 0 5269.5182 12.011643
8550 16738.483 -0.0045307409 0 5269.5178 12.011621
8600 16738.474 -0.00076532813 0 5269.5189 12.011681
8650 16738.474 0 0 5269.5197 12.011699
8700 16738.475 0 0 5269.5199 12.011715
8750 16738.475 0 0 5269.52 12.011732
8800 16738.475 0 0 5269.52 12.011743
8850 16738.476 0 0 5269.5201 12.011744
8900 16738.476 0 0 5269.5202 12.011735
8950 16738.476 0 0 5269.5203 12.011719
9000 16738.477 0 0 5269.5205 12.011698
9050 16738.477 0 0 5269.5206 12.011683
9100 16738.478 0 0 5269.5208 12.011684
9150 16738.479 0 0 5269.521 12.011701
9200 16738.479 0 0 5269.5212 12.011722
9250 16738.479 0 0 5269.5213 12.011738
9300 16738.48 0 0 5269.5214 12.011746
9350 16738.48 0 0 5269.5214 12.011744
9400 16738.48 0 0 5269.5215 12.011732
9450 16738.48 0 0 5269.5216 12.011715
9500 16738.481 -0.0003765244 0 5269.5216 12.011692
9550 16738.493 -0.0053156161 0 5269.5203 12.011611
9600 16738.549 -0.026814371 0 5269.5163 12.011415
9650 16738.765 -0.10191523 0 5269.5092 12.011013
9700 16735.041 1.0589894 0 5269.4979 12.062708
9750 16738.013 0.13550078 0 5269.5101 11.407245
9800 16738.512 -0.011620328 0 5269.5201 11.394973
9850 16738.489 -0.00067270552 0 5269.5237 11.395098
9900 16738.489 -0.00024984578 0 5269.5242 11.395084
9950 16738.49 0 0 5269.5245 11.395076
10000 16738.49 0 0 5269.5246 11.395075
Loop time of 0.374086 on 4 procs for 10000 steps with 81 atoms
Pair time (%) = 0.00579989 (1.55042)
Neigh time (%) = 0.0136012 (3.63585)
Comm time (%) = 0.171026 (45.7184)
Outpt time (%) = 0.0344212 (9.20142)
Other time (%) = 0.149238 (39.894)
Nlocal: 20.25 ave 38 max 3 min
Histogram: 1 0 1 0 0 0 1 0 0 1
Nghost: 27.25 ave 48 max 13 min
Histogram: 1 0 1 1 0 0 0 0 0 1
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0
Neighbor list builds = 998
Dangerous builds = 997

306
examples/rigid/log.rigid.poems.28Mar11.linux.1 Normal file
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LAMMPS (27 Mar 2011)
# 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 processor grid
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
timestep 0.0001
thermo 50
run 10000
Memory usage per processor = 1.9398 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 7.4384278
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 -0.86699139
1200 21815.003 45.317413 0 3681.1512 1.5988314
1250 18655.437 572.41453 0 3681.654 10.064079
1300 20780.781 217.36508 0 3680.8286 6.0538613
1350 20558.971 254.36484 0 3680.8601 -3.6773928
1400 21485.029 99.812897 0 3680.6511 -16.185475
1450 21771.107 52.159622 0 3680.6775 -2.4756668
1500 21520.948 93.50391 0 3680.3286 2.1023576
1550 21351.418 121.68135 0 3680.2511 5.5159926
1600 20778.805 216.92181 0 3680.0559 15.089192
1650 21477.637 100.21848 0 3679.8247 -1.1045589
1700 18501.336 596.47967 0 3680.0357 -15.679718
1750 18563.641 587.34804 0 3681.2882 33.532242
1800 19110.182 494.82394 0 3679.8543 18.024056
1850 21364.187 119.23612 0 3679.9339 2.5290785
1900 20146.615 322.15055 0 3679.9197 5.7314455
1950 20692.672 231.25319 0 3680.0319 4.2977815
2000 20943.904 189.11228 0 3679.7629 -22.6447
2050 19667.984 401.84213 0 3679.8394 3.6248494
2100 20280.339 299.77895 0 3679.8354 7.480669
2150 19181.64 483.55835 0 3680.4983 22.624694
2200 21300.479 130.65196 0 3680.7318 4.7093384
2250 20486.287 266.74857 0 3681.1297 -8.6495123
2300 18651.575 572.50504 0 3681.1009 -5.261082
2350 21514.238 95.495372 0 3681.2017 -9.3698609
2400 21465.082 103.76223 0 3681.2758 -29.530492
2450 20102.547 331.8625 0 3682.2869 35.630207
2500 20766.689 221.28369 0 3682.3986 -12.4229
2550 20456.257 272.87511 0 3682.2513 -22.515235
2600 21464.354 104.88637 0 3682.2788 -10.110008
2650 20885.777 201.39511 0 3682.358 5.0268371
2700 18576.387 586.63809 0 3682.7026 22.269183
2750 21023.584 178.26789 0 3682.1985 -8.8172166
2800 21363.884 121.51908 0 3682.1664 -6.913586
2850 17264.155 805.16849 0 3682.5276 29.921611
2900 19751.146 390.19286 0 3682.0506 8.8575471
2950 21171.167 153.48579 0 3682.0136 1.9171651
3000 18698.646 565.2524 0 3681.6934 -16.611709
3050 19756.096 389.49951 0 3682.1822 0.79771573
3100 20716.934 229.53125 0 3682.3536 18.675629
3150 21107.033 164.26375 0 3682.1026 6.292817
3200 21194.557 149.62327 0 3682.0495 0.40762301
3250 19019.061 511.83944 0 3681.683 -1.0191767
3300 19904.232 364.91979 0 3682.2917 1.580824
3350 19383.048 452.00672 0 3682.5146 8.9939778
3400 18629.871 577.12591 0 3682.1044 19.393397
3450 20366.419 287.55662 0 3681.9598 6.7676479
3500 20957.937 189.21014 0 3682.1996 9.17515
3550 21807.252 47.635006 0 3682.1771 2.2490841
3600 21690.617 67.029898 0 3682.1327 -1.4725416
3650 21600.202 82.085085 0 3682.1188 -3.9470263
3700 19902.074 365.09934 0 3682.1117 3.5789954
3750 20669.825 237.14074 0 3682.1116 -7.992071
3800 20226.287 311.40404 0 3682.4519 -11.829103
3850 20713.814 230.18758 0 3682.4899 -11.37713
3900 19621.738 411.85323 0 3682.1428 -0.86016858
3950 20828.921 210.87742 0 3682.3643 -1.7978283
4000 21734.525 60.230547 0 3682.6513 3.0013342
4050 19859.621 371.8688 0 3681.8056 19.53421
4100 20748.845 224.82927 0 3682.9701 -0.67873587
4150 19578.269 420.02964 0 3683.0745 4.448634
4200 19142.314 492.92862 0 3683.3143 7.5300212
4250 20189.963 318.02141 0 3683.0152 2.2489634
4300 20569.793 254.7842 0 3683.0831 2.014004
4350 21505.248 99.029749 0 3683.2377 -1.8448103
4400 21795.012 50.799563 0 3683.3016 -3.3446933
4450 21630.638 78.27653 0 3683.3829 0.97935456
4500 20485.622 268.77758 0 3683.0479 9.0931688
4550 21328.202 128.77982 0 3683.4802 6.9392514
4600 20425.456 279.4671 0 3683.7097 14.657178
4650 21734.316 61.575892 0 3683.9619 -6.1228621
4700 20377.517 287.77871 0 3684.0315 -10.350636
4750 21765.762 56.481378 0 3684.1084 -13.686961
4800 21064.967 173.07588 0 3683.9038 -3.5246286
4850 21496.739 100.96272 0 3683.7525 3.4134893
4900 21387.734 118.85944 0 3683.4818 2.7545377
4950 21606.598 82.305575 0 3683.4052 2.7661083
5000 20813.389 211.50552 0 3680.4037 -1.99709
5050 21258.837 140.0257 0 3683.1652 -4.6011608
5100 18840.1 543.32464 0 3683.3413 31.178048
5150 22005.655 16.168882 0 3683.778 -4.3729594
5200 20808.086 215.87951 0 3683.8939 7.4410336
5250 18679.669 570.83153 0 3684.1098 14.191478
5300 19753.173 391.94671 0 3684.1422 -8.5241508
5350 21608.313 82.705694 0 3684.0912 -3.6094817
5400 21488.174 102.68409 0 3684.0464 4.2600964
5450 17518.356 764.26875 0 3683.9947 -0.12243804
5500 21696.071 68.069788 0 3684.0816 -1.5476526
5550 18502.148 599.7684 0 3683.4597 37.379976
5600 18128.267 662.17376 0 3683.5516 16.554047
5650 18537.13 594.3189 0 3683.8406 12.05774
5700 20851.723 208.91824 0 3684.2053 -4.3830301
5750 20941.372 194.08984 0 3684.3185 -0.1943864
5800 20194.472 318.72727 0 3684.4726 5.154744
5850 20856.188 208.56814 0 3684.5994 3.2314482
5900 21125.245 164.07233 0 3684.9465 -0.33002911
5950 20138.458 328.54345 0 3684.9532 10.557313
6000 20981.486 188.51066 0 3685.4249 -9.0163197
6050 20822.112 215.14903 0 3685.5011 -18.139995
6100 20076.859 339.70008 0 3685.8432 -3.0307257
6150 19953.615 360.46342 0 3686.066 8.3344429
6200 20903.384 202.40101 0 3686.2984 -0.39424049
6250 21134.826 163.89116 0 3686.3621 -4.1668704
6300 21258.213 143.90658 0 3686.9422 -7.391516
6350 20373.797 291.10416 0 3686.7369 -14.895748
6400 19051.752 510.8571 0 3686.1491 -0.078518196
6450 19649.32 412.61991 0 3687.5065 -1.5921483
6500 20142.923 330.66911 0 3687.8229 6.8022912
6550 19574.327 424.60137 0 3686.9891 11.82743
6600 16105.355 1002.7817 0 3687.0076 17.558797
6650 21537.744 97.953562 0 3687.5775 2.735191
6700 16808.381 887.46461 0 3688.8614 -9.3638392
6750 16391.199 958.16942 0 3690.0359 24.040757
6800 19891.18 371.95843 0 3687.1551 -25.326616
6850 19344.505 464.12314 0 3688.2073 -16.88882
6900 21489.989 106.09106 0 3687.7559 -2.7741331
6950 19023.694 517.19865 0 3687.8143 12.795625
7000 21072.663 175.47912 0 3687.5897 -4.6260178
7050 19697.946 404.85665 0 3687.8476 0.96426982
7100 20684.854 240.16243 0 3687.638 -6.9283531
7150 20888.947 205.87412 0 3687.3653 2.4592293
7200 20709.233 235.52341 0 3687.0622 1.8850608
7250 20644.676 246.05983 0 3686.8391 -1.9432958
7300 19940.501 363.58269 0 3686.9996 8.7916219
7350 20904.854 202.70884 0 3686.8511 1.1932912
7400 19794.615 388.44762 0 3687.5502 4.2494869
7450 20398.713 287.96541 0 3687.7509 1.9565661
7500 14969.907 1195.4664 0 3690.451 61.49775
7550 20048.243 346.41733 0 3687.7911 8.8637262
7600 13724.843 1400.6649 0 3688.1386 -28.102927
7650 17323.581 800.37606 0 3687.6396 17.015401
7700 20781.624 224.2726 0 3687.8767 2.5260419
7750 19629.33 416.31516 0 3687.8702 18.39744
7800 20804.173 220.99571 0 3688.3579 11.409891
7850 20756.856 228.60421 0 3688.0803 -33.84006
7900 21716.444 68.965593 0 3688.3729 -12.291272
7950 19610.154 419.14133 0 3687.5002 1.7759679
8000 18622.409 585.42868 0 3689.1635 26.686729
8050 19777.369 392.63726 0 3688.8654 -22.209128
8100 16497.521 939.24542 0 3688.8322 -42.367659
8150 19446.13 444.3108 0 3685.3324 32.613169
8200 20411.209 286.5915 0 3688.4597 -5.2887315
8250 14328.544 1302.6847 0 3690.7753 15.143982
8300 21405.234 121.47682 0 3689.0157 -4.6378296
8350 15481.055 1109.2428 0 3689.4186 57.85088
8400 14139.682 1332.356 0 3688.9697 -0.1974486
8450 15623.736 1084.5594 0 3688.5155 37.668188
8500 18872.571 543.29677 0 3688.7253 -11.622477
8550 18568.346 594.15647 0 3688.8809 -0.53198127
8600 18857.924 546.26599 0 3689.2533 6.9976522
8650 20422.926 285.18311 0 3689.0041 -2.1124395
8700 15904.428 1038.6394 0 3689.3774 11.108432
8750 17585.096 758.32272 0 3689.172 -13.175342
8800 19561.883 429.1997 0 3689.5135 31.379344
8850 21083.378 174.46783 0 3688.3642 -1.405537
8900 21922.179 35.258703 0 3688.9551 0.92994553
8950 15270.836 1145.5748 0 3690.714 59.72214
9000 21236.73 149.52929 0 3688.9843 3.6894217
9050 20391.028 289.54828 0 3688.053 -12.318301
9100 19963.6 361.58733 0 3688.854 -1.6201635
9150 20852.5 213.26173 0 3688.6783 3.4781812
9200 17559.276 763.58389 0 3690.13 23.653055
9250 20719.763 235.38861 0 3688.6825 -7.2385902
9300 20210.461 320.16875 0 3688.5789 0.71513298
9350 20589.665 256.39159 0 3688.0025 11.766742
9400 21888.845 39.743204 0 3687.884 0.2325157
9450 19995.034 355.22797 0 3687.7336 -30.801824
9500 20562.534 260.81379 0 3687.9028 7.6818244
9550 20724.259 233.42976 0 3687.4729 2.5906906
9600 21156.272 161.92778 0 3687.9731 -3.6794578
9650 15407.774 1117.1504 0 3685.1127 10.296536
9700 20086.616 339.94203 0 3687.7114 6.85039
9750 21017.639 184.92766 0 3687.8675 -4.924906
9800 17788.545 723.17057 0 3687.928 19.866063
9850 21918.073 35.503859 0 3688.516 -1.9119993
9900 17765.237 727.83046 0 3688.7033 19.055502
9950 21306.635 137.72864 0 3688.8345 -5.5977574
10000 21575.787 92.853786 0 3688.8182 -4.0094168
Loop time of 5.53478 on 1 procs for 10000 steps with 81 atoms
Pair time (%) = 0.282449 (5.10317)
Neigh time (%) = 0.124412 (2.24782)
Comm time (%) = 0.0167849 (0.303262)
Outpt time (%) = 0.0310278 (0.560597)
Other time (%) = 5.08011 (91.7852)
Nlocal: 81 ave 81 max 81 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 56 ave 56 max 56 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 750 ave 750 max 750 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 750
Ave neighs/atom = 9.25926
Neighbor list builds = 990
Dangerous builds = 927

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LAMMPS (27 Mar 2011)
# 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 processor grid
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
timestep 0.0001
thermo 50
run 10000
Memory usage per processor = 1.90125 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 -0.86699149
1200 21815.003 45.317415 0 3681.1512 1.5988314
1250 18655.437 572.41453 0 3681.654 10.064078
1300 20780.781 217.36506 0 3680.8286 6.0538616
1350 20558.971 254.36482 0 3680.8601 -3.6773956
1400 21485.029 99.812922 0 3680.6511 -16.185473
1450 21771.107 52.159608 0 3680.6775 -2.4756674
1500 21520.948 93.503928 0 3680.3286 2.1023577
1550 21351.418 121.68138 0 3680.2511 5.515995
1600 20778.805 216.92177 0 3680.0559 15.089187
1650 21477.638 100.21835 0 3679.8247 -1.1045756
1700 18501.339 596.47913 0 3680.0357 -15.679677
1750 18563.642 587.34787 0 3681.2882 33.532207
1800 19110.186 494.82333 0 3679.8543 18.024046
1850 21364.191 119.23538 0 3679.9339 2.5291119
1900 20146.628 322.14841 0 3679.9197 5.7313081
1950 20692.671 231.25336 0 3680.0319 4.2977737
2000 20943.904 189.11227 0 3679.7629 -22.645146
2050 19668.063 401.82894 0 3679.8394 3.6252006
2100 20280.448 299.76054 0 3679.8353 7.4807993
2150 19181.869 483.52061 0 3680.4987 22.620257
2200 21300.14 130.70883 0 3680.7322 4.710318
2250 20486.992 266.63125 0 3681.1299 -8.6453582
2300 18653.249 572.22692 0 3681.1018 -5.2639533
2350 21513.474 95.623043 0 3681.2021 -9.3615923
2400 21466.352 103.55115 0 3681.2765 -29.563489
2450 20099.92 332.30226 0 3682.2888 35.75288
2500 20764.233 221.69469 0 3682.4003 -12.472324
2550 20434.265 276.55013 0 3682.261 -22.406554
2600 21466.593 104.51528 0 3682.2808 -10.076416
2650 20808.645 214.25423 0 3682.3618 5.1518496
2700 18565.645 588.3715 0 3682.6457 22.26312
2750 20753.062 223.37556 0 3682.2193 -7.8155982
2800 20986.776 184.39985 0 3682.1958 -7.0608776
2850 16721.211 895.59298 0 3682.4615 33.619161
2900 19294.24 466.43871 0 3682.1454 8.0033435
2950 20471.71 270.09532 0 3682.047 2.5545202
3000 20609.248 247.27073 0 3682.1453 -1.8817723
3050 18576.568 586.31423 0 3682.4089 -1.7806882
3100 19790.767 383.54865 0 3682.0099 -6.0384293
3150 20941.678 191.88039 0 3682.16 4.7195299
3200 20187.734 317.22178 0 3681.8441 7.1381064
3250 19982.327 351.80543 0 3682.1932 -10.356822
3300 19720.165 395.60482 0 3682.299 12.415019
3350 20008.047 347.27468 0 3681.9491 5.0458582
3400 20411.522 280.16521 0 3682.0855 -7.1769483
3450 20046.145 341.27051 0 3682.2947 0.22584972
3500 17937.429 692.9726 0 3682.544 16.131523
3550 18771.683 553.86993 0 3682.4837 -1.5944448
3600 19901.288 364.81878 0 3681.7001 -24.39551
3650 20746.323 224.83374 0 3682.5543 -7.6981313
3700 21681.686 68.935986 0 3682.5503 -5.7316854
3750 21130.966 160.34639 0 3682.174 2.5404231
3800 19573.729 419.87434 0 3682.1625 10.483835
3850 19672.797 403.73028 0 3682.5297 7.9092657
3900 19429.209 444.39996 0 3682.6014 4.6871663
3950 18794.538 550.12554 0 3682.5485 -3.4850598
4000 18356.499 622.71257 0 3682.1291 21.961288
4050 18499.159 599.5728 0 3682.7659 9.7197804
4100 18893.082 533.58148 0 3682.4285 7.1537738
4150 18555.438 590.46012 0 3683.0331 -5.9854705
4200 20095.772 332.86056 0 3682.1558 6.0048046
4250 21395.629 117.09714 0 3683.0352 -12.849296
4300 20642.157 242.80387 0 3683.1634 -7.1285142
4350 16782.008 886.90013 0 3683.9014 59.279202
4400 21722.722 63.477041 0 3683.9307 -6.7708918
4450 21483.705 103.77396 0 3684.3914 -14.801558
4500 18637.223 577.90593 0 3684.1097 -5.399645
4550 21501.072 101.01026 0 3684.5223 -0.2687012
4600 21419.25 114.67746 0 3684.5525 -5.1248351
4650 19532.212 428.88221 0 3684.251 -13.937733
4700 19108.648 500.22789 0 3685.0025 0.72814013
4750 21304.939 134.30984 0 3685.133 -10.419682
4800 21011.564 183.12003 0 3685.0474 -0.21596054
4850 21288.378 137.28914 0 3685.3522 -3.783224
4900 20238.761 312.44314 0 3685.57 -0.89650269
4950 20973.64 190.4195 0 3686.0262 2.3977528
5000 20982.662 188.75492 0 3685.8652 -10.898981
5050 20287.196 304.79028 0 3685.9895 7.9988821
5100 20161.046 325.98224 0 3686.1566 11.304549
5150 20768.1 224.94586 0 3686.2959 -11.679983
5200 20550.091 261.40569 0 3686.4209 -3.8503144
5250 20274.307 307.08369 0 3686.1349 3.2350203
5300 21107.734 168.31547 0 3686.2711 -2.7299125
5350 21575.088 90.511714 0 3686.3597 -23.416041
5400 19335.208 463.98466 0 3686.5193 1.1686111
5450 20334.202 297.13584 0 3686.1696 7.9612042
5500 18596.894 586.39323 0 3685.8756 19.42362
5550 16402.199 953.72484 0 3687.4247 -7.6804149
5600 19716.462 400.17421 0 3686.2512 0.73274328
5650 19794.552 387.60203 0 3686.694 7.4829917
5700 21404.995 119.38491 0 3686.884 1.1256427
5750 21737.498 64.038982 0 3686.9553 0.66497166
5800 21196.338 153.70183 0 3686.4248 -4.0562788
5850 18817.877 550.28735 0 3686.6001 15.517346
5900 20855.92 210.47881 0 3686.4654 -6.7252193
5950 18187.477 655.72108 0 3686.9673 -5.840425
6000 21574.226 91.415225 0 3687.1196 -4.1947877
6050 20647.597 245.36705 0 3686.6333 -4.2710188
6100 20195.663 320.68953 0 3686.6333 1.9183471
6150 19569.943 425.30544 0 3686.9627 -2.0191803
6200 21009.348 185.15969 0 3686.7176 -1.5383241
6250 21311.107 135.08699 0 3686.9382 -8.4198399
6300 18617.034 583.66046 0 3686.4994 11.716969
6350 19818.978 382.62883 0 3685.7919 4.9679172
6400 21403.509 119.46416 0 3686.7156 -1.3369474
6450 16394.437 955.35248 0 3687.7587 22.900909
6500 15570.429 1095.0835 0 3690.155 -24.50813
6550 20905.847 202.70205 0 3687.0099 -5.4533991
6600 20419.664 282.65592 0 3685.9333 -1.0348411
6650 16008.949 1023.4924 0 3691.6506 48.451181
6700 18929.104 531.79459 0 3686.6452 8.487112
6750 20317.67 301.1228 0 3687.4011 -9.6972866
6800 21238.238 147.54216 0 3687.2486 -4.457873
6850 19469.334 441.11845 0 3686.0075 29.322933
6900 20880.087 207.70983 0 3687.7244 -4.1197403
6950 20864.561 210.00891 0 3687.4358 -9.4014401
7000 21701.899 70.744638 0 3687.7278 2.6762921
7050 18936.455 531.70563 0 3687.7815 29.134314
7100 21418.983 118.08942 0 3687.9199 0.64845095
7150 21271.75 142.65664 0 3687.9482 -6.1860835
7200 21584.017 90.531714 0 3687.8679 -15.915843
7250 20478.212 274.65055 0 3687.6858 3.5293379
7300 20787.975 223.07914 0 3687.7416 8.3746157
7350 21169.849 159.84727 0 3688.1554 4.806229
7400 18050.739 679.46766 0 3687.9242 0.1356599
7450 21759.344 61.894907 0 3688.4523 -6.0686382
7500 20115.323 334.36139 0 3686.9153 -3.9834726
7550 21513.687 103.04204 0 3688.6565 -3.6546291
7600 20396.612 289.44922 0 3688.8845 8.3149013
7650 19954.93 363.06299 0 3688.8846 6.7857536
7700 20579.453 259.44475 0 3689.3535 -13.300779
7750 21435.784 117.44734 0 3690.078 -3.5454036
7800 19676.963 410.82634 0 3690.3202 16.17995
7850 22001.763 23.427845 0 3690.3883 -3.2253193
7900 21367.244 128.97238 0 3690.1797 -10.139451
7950 21835.619 51.102569 0 3690.3723 -6.9113133
8000 21081.866 176.87472 0 3690.519 -3.400648
8050 17587.847 759.00567 0 3690.3134 42.149831
8100 20622.874 253.16935 0 3690.3149 -1.0529121
8150 18826.468 552.8081 0 3690.5528 -26.78369
8200 19639.531 417.23576 0 3690.491 11.18475
8250 18736.82 568.57113 0 3691.3744 6.4120512
8300 21628.735 86.117146 0 3690.9062 -15.136564
8350 21300.133 140.75663 0 3690.7788 -1.3028295
8400 20100.75 340.28553 0 3690.4105 2.3621868
8450 20330.628 301.64835 0 3690.0863 -6.9035421
8500 21379.743 126.87873 0 3690.1693 -0.67103323
8550 21693.455 74.592469 0 3690.1683 -6.6175553
8600 20824.252 219.41263 0 3690.1212 1.7682173
8650 20289.679 308.59538 0 3690.2085 11.354028
8700 21803.688 56.071063 0 3690.0191 -2.6145414
8750 21111.316 171.22439 0 3689.777 6.7898851
8800 20775.535 227.17109 0 3689.7603 9.4162984
8850 19043.442 515.72721 0 3689.6343 5.3736614
8900 21157.163 163.34868 0 3689.5426 1.4354174
8950 20978.891 192.95509 0 3689.437 0.96560879
9000 21292.787 140.85118 0 3689.6489 -8.9387525
9050 20239.076 316.1505 0 3689.3299 8.0442974
9100 19869.892 377.60414 0 3689.2529 -7.7929877
9150 21454.531 113.72022 0 3689.4753 -13.322839
9200 17967.414 695.13611 0 3689.705 5.5120587
9250 20511.881 271.10991 0 3689.7567 7.4880289
9300 19920.611 369.49427 0 3689.5961 20.373053
9350 20461.102 279.43877 0 3689.6224 10.339057
9400 20099.827 339.51057 0 3689.4817 6.7892922
9450 19918.317 369.41224 0 3689.1318 10.326641
9500 21020.607 186.56179 0 3689.9963 7.3622937
9550 21179.796 160.20422 0 3690.1702 -1.0782427
9600 21518.982 104.08914 0 3690.5861 -5.3790399
9650 21206.19 156.4724 0 3690.8374 1.6109043
9700 21452.317 115.4785 0 3690.8646 -6.2719599
9750 19577.709 427.73595 0 3690.6875 -5.943044
9800 15600.07 1090.9222 0 3690.9338 12.384319
9850 18256.931 647.85044 0 3690.6723 3.3325276
9900 20351.693 298.44268 0 3690.3914 1.2947227
9950 21085.505 176.1557 0 3690.4065 -6.3748251
10000 18801.541 557.05356 0 3690.6438 -8.7522263
Loop time of 6.27886 on 4 procs for 10000 steps with 81 atoms
Pair time (%) = 0.0720805 (1.14799)
Neigh time (%) = 0.034766 (0.553699)
Comm time (%) = 0.425238 (6.77253)
Outpt time (%) = 0.666104 (10.6087)
Other time (%) = 5.08067 (80.9171)
Nlocal: 20.25 ave 79 max 0 min
Histogram: 3 0 0 0 0 0 0 0 0 1
Nghost: 46.25 ave 68 max 12 min
Histogram: 1 0 0 0 0 1 0 0 0 2
Neighs: 181.5 ave 722 max 0 min
Histogram: 3 0 0 0 0 0 0 0 0 1
Total # of neighbors = 726
Ave neighs/atom = 8.96296
Neighbor list builds = 990
Dangerous builds = 920

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LAMMPS (27 Mar 2011)
# 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 processor grid
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
timestep 0.0001
thermo 50
run 10000
WARNING: More than one fix poems
WARNING: More than one fix poems
WARNING: One or more atoms are time integrated more than once
Memory usage per processor = 2.2859 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 0.31444672
1400 18549.582 329.31436 0 3764.4221 10.738303
1450 15163.926 957.47584 0 3765.6103 -17.923459
1500 19223.688 204.15169 0 3764.0939 -1.613454
1550 18147.996 404.12676 0 3764.8668 8.4194769
1600 18615.043 317.42464 0 3764.6548 -2.328898
1650 20120.654 38.887941 0 3764.935 -8.7620212
1700 19450.906 162.98296 0 3765.0025 2.3254683
1750 19374.633 177.37942 0 3765.2744 8.9328782
1800 19424.403 167.93976 0 3765.0514 0.081237835
1850 17936.373 442.81943 0 3764.3699 6.6007243
1900 19982.597 64.405942 0 3764.8868 -2.953039
1950 16216.047 761.87633 0 3764.848 13.993767
2000 18584.36 322.1319 0 3763.68 7.1655723
2050 20107.967 41.025515 0 3764.723 -0.31095875
2100 20002.359 60.588285 0 3764.7288 -6.7919218
2150 16949.463 626.65155 0 3765.4411 3.5099746
2200 20010.951 58.808709 0 3764.5403 -10.862337
2250 18982.724 247.0099 0 3762.3292 -0.53785372
2300 18401.404 354.86011 0 3762.5276 1.0917872
2350 19390.477 172.95029 0 3763.7793 -3.3527625
2400 16082.495 786.07427 0 3764.3141 -16.195237
2450 18871.033 268.63511 0 3763.2709 11.187102
2500 19687.13 117.79738 0 3763.5622 4.3929264
2550 18873.431 268.30382 0 3763.3836 -5.6531376
2600 17014.989 612.51599 0 3763.44 6.3265978
2650 18779.234 286.24534 0 3763.8812 2.3814839
2700 19733.494 108.84054 0 3763.1912 -0.28455721
2750 19487.299 154.68388 0 3763.4429 -1.5938513
2800 18419.252 351.12627 0 3762.0988 20.847774
2850 18788.886 283.58089 0 3763.0043 3.0280372
2900 20110.801 39.005938 0 3763.2284 0.0030136934
2950 15582.268 877.76573 0 3763.3708 16.827059
3000 17927.524 442.93443 0 3762.8463 4.0702273
3050 19054.272 234.78929 0 3763.3582 7.6784952
3100 19318.656 185.86832 0 3763.3972 3.4909968
3150 19336.244 182.13325 0 3762.9192 -19.24283
3200 18983.457 247.36835 0 3762.8233 -5.7526831
3250 19674.232 119.66794 0 3763.0442 1.9423166
3300 16157.209 769.95841 0 3762.0342 2.80189
3350 19030.029 239.07461 0 3763.1541 7.0444034
3400 15352.517 920.23705 0 3763.2957 26.469475
3450 19113.998 223.38478 0 3763.0139 5.4622379
3500 15355.047 921.10005 0 3764.6272 12.744088
3550 18453.302 345.84221 0 3763.1203 4.3303151
3600 15805.132 835.73363 0 3762.6098 -19.192108
3650 19366.655 176.75046 0 3763.168 3.6029674
3700 17926.815 443.58998 0 3763.3705 6.3106911
3750 18145.089 402.96409 0 3763.1657 -1.4495144
3800 17128.054 590.66146 0 3762.5233 1.3740587
3850 19650.661 123.98432 0 3762.9956 -3.6403709
3900 13651.635 1236.4269 0 3764.5075 1.8197344
3950 19607.542 131.80571 0 3762.8321 -5.2300693
4000 15976.222 803.9711 0 3762.5308 5.8844711
4050 17251.262 568.38221 0 3763.0604 -27.565001
4100 18718.869 296.1222 0 3762.5795 0.24957933
4150 18981.941 247.56533 0 3762.7396 8.9334676
4200 18058.249 418.65815 0 3762.7784 -9.7406053
4250 17840.27 458.9852 0 3762.7389 -1.2566229
4300 16801.487 651.25038 0 3762.6368 20.311604
4350 19284.648 191.5548 0 3762.786 3.8849247
4400 18089.637 412.4593 0 3762.392 -0.16156227
4450 18109.553 409.19646 0 3762.8174 -6.6744782
4500 18559.157 325.84529 0 3762.7262 -3.7834397
4550 19417.817 167.1903 0 3763.0824 -1.9438809
4600 19940.102 70.544215 0 3763.1558 -6.5714777
4650 17531.219 516.03395 0 3762.5561 16.825376
4700 18330.28 368.15762 0 3762.6539 -5.8154827
4750 18059.26 418.88115 0 3763.1886 6.9154907
4800 18230.172 387.09769 0 3763.0554 -5.8764301
4850 15352.316 920.35111 0 3763.3726 -14.150721
4900 17901.178 447.18401 0 3762.217 12.995669
4950 17096.795 596.75363 0 3762.8268 6.9584988
5000 18233.348 386.97511 0 3763.521 -8.6953829
5050 19238.643 200.76564 0 3763.4773 -0.95923788
5100 18851.592 272.21836 0 3763.2539 6.6015785
5150 17618.203 500.9924 0 3763.6226 6.4089848
5200 19510.809 150.29265 0 3763.4053 -1.138488
5250 17991.038 431.73878 0 3763.4124 0.9206177
5300 16496.992 709.42568 0 3764.4241 8.328767
5350 16683.15 674.66196 0 3764.1342 -12.119189
5400 19197.624 208.27759 0 3763.3932 1.8895925
5450 16776.936 656.25236 0 3763.0923 8.3324322
5500 18314.437 372.39317 0 3763.9556 0.87158511
5550 18678.675 304.31808 0 3763.3319 8.1494425
5600 18772.959 286.93218 0 3763.406 -1.3023432
5650 15494.947 894.36223 0 3763.7968 -10.336527
5700 18507.481 336.45923 0 3763.7704 -3.8746687
5750 17082.667 600.40729 0 3763.8641 42.148906
5800 19845.873 88.449333 0 3763.611 1.7380604
5850 17992.679 431.95872 0 3763.9363 -12.928704
5900 19680.707 119.00911 0 3763.5844 -0.79613571
5950 19914.393 75.816066 0 3763.6667 5.5342994
6000 19142.271 218.80112 0 3763.6661 7.4018805
6050 17025.724 611.14107 0 3764.053 -6.1043602
6100 18966.612 250.76138 0 3763.0969 1.1322144
6150 17451.81 531.32734 0 3763.144 -6.5894955
6200 16334.478 739.3296 0 3764.233 -27.518822
6250 18790.228 283.56338 0 3763.2353 -7.8911412
6300 18163.654 399.45237 0 3763.092 -0.20584174
6350 18674.03 305.36153 0 3763.5151 -10.44952
6400 19677.482 119.8165 0 3763.7947 4.767842
6450 19606.353 133.20697 0 3764.0132 3.1402747
6500 18685.174 303.25291 0 3763.4703 1.219211
6550 18842.997 274.29542 0 3763.7394 -3.0675196
6600 18984.844 247.94633 0 3763.6582 3.2871433
6650 19270.874 194.75275 0 3763.4332 2.0520948
6700 16730.98 665.42234 0 3763.752 24.63305
6750 18240.959 385.54575 0 3763.5012 9.3542656
6800 19212.072 205.42671 0 3763.2178 -4.7707967
6850 19428.264 165.41827 0 3763.2449 -5.9896144
6900 16510.385 705.90782 0 3763.3866 -4.5120114
6950 18469.724 342.72852 0 3763.0477 1.5930349
7000 19023.531 240.06714 0 3762.9432 0.97630625
7050 19981.38 63.051871 0 3763.3075 1.1975773
7100 18884.497 266.0407 0 3763.1698 5.014732
7150 20007.363 58.305336 0 3763.3725 -3.8475432
7200 19060.008 233.74726 0 3763.3784 -7.355987
7250 19587.118 136.14609 0 3763.3902 -0.071525055
7300 18255.08 382.9175 0 3763.4878 8.3070642
7350 19840.127 89.391828 0 3763.4894 3.0925365
7400 19081.218 229.96717 0 3763.5261 -0.088491483
7450 19495.919 153.12566 0 3763.481 7.3486168
7500 18103.878 410.89471 0 3763.4647 8.253657
7550 18818.034 278.46924 0 3763.2904 -6.6529064
7600 16900.909 634.03412 0 3763.8321 24.447016
7650 19309.193 187.4356 0 3763.2121 5.0831969
7700 17040.81 608.00812 0 3763.7136 -4.5789647
7750 19420.333 167.12363 0 3763.4815 4.3678178
7800 19164.248 214.10676 0 3763.0416 0.12405627
7850 19137.03 219.31269 0 3763.2071 -6.7131335
7900 19606.78 132.67382 0 3763.5591 -4.5096484
7950 18593.444 319.64585 0 3762.8763 -4.9001288
8000 19288.423 191.51728 0 3763.4475 3.8370068
8050 19132.57 220.46289 0 3763.5314 -1.3284232
8100 17510.857 520.52922 0 3763.2806 -4.6183989
8150 18356.887 364.17504 0 3763.5986 4.3938444
8200 19553.346 142.51623 0 3763.5063 0.93248057
8250 17919.922 444.70362 0 3763.2076 7.3984984
8300 17268.822 564.38824 0 3762.3182 24.155843
8350 19389.272 172.63516 0 3763.241 5.9225389
8400 17896.652 449.19012 0 3763.3849 0.63394353
8450 18315.977 371.4271 0 3763.2746 -33.234548
8500 16047.998 796.54623 0 3768.3978 51.901492
8550 19188.248 210.03454 0 3763.4138 -1.5401941
8600 17951.392 433.85317 0 3758.185 26.657038
8650 18678.909 304.65925 0 3763.7164 -0.5735548
8700 18473.965 342.61835 0 3763.7231 -0.39588258
8750 17278.537 562.78121 0 3762.5102 16.884408
8800 19997.623 60.585822 0 3763.8494 -2.7220886
8850 17720.683 482.98842 0 3764.5963 13.298184
8900 19450.503 162.05753 0 3764.0025 -5.0266355
8950 20065.748 48.178324 0 3764.0575 -3.298456
9000 18411.075 354.70332 0 3764.1617 2.5439463
9050 19835.128 90.878715 0 3764.0505 -2.4322016
9100 19486.363 155.54042 0 3764.1261 -5.332552
9150 19203.984 207.95102 0 3764.2443 3.1640673
9200 18048.222 421.26909 0 3763.5324 23.881772
9250 19682.985 119.25528 0 3764.2524 1.533906
9300 19857.159 86.947891 0 3764.1996 -4.5024234
9350 20060.359 49.452616 0 3764.3338 -1.493574
9400 19561.395 141.85818 0 3764.3387 -3.1573118
9450 19134.008 221.07861 0 3764.4133 -0.60832086
9500 18369.624 362.74228 0 3764.5244 -0.37049085
9550 18146.354 404.01981 0 3764.4558 10.150467
9600 15002.89 991.64237 0 3769.9553 51.550272
9650 18607.005 318.66284 0 3764.4045 3.3985276
9700 18489.496 340.51647 0 3764.4972 2.941698
9750 19635.157 128.29122 0 3764.4315 -14.101437
9800 18284.554 378.61 0 3764.6385 -7.2125841
9850 17756.297 476.00442 0 3764.2076 -4.4238573
9900 18996.512 246.68301 0 3764.5557 -5.0986512
9950 19432.438 165.78467 0 3764.3843 -3.7163888
10000 19336.629 183.60921 0 3764.4664 -0.93973872
Loop time of 5.96365 on 1 procs for 10000 steps with 81 atoms
Pair time (%) = 0.209019 (3.50489)
Neigh time (%) = 0.095875 (1.60766)
Comm time (%) = 0.0209796 (0.351792)
Outpt time (%) = 0.0316613 (0.530904)
Other time (%) = 5.60612 (94.0048)
Nlocal: 81 ave 81 max 81 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 69 ave 69 max 69 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 636 ave 636 max 636 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 636
Ave neighs/atom = 7.85185
Neighbor list builds = 991
Dangerous builds = 933

310
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LAMMPS (27 Mar 2011)
# 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 processor grid
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
timestep 0.0001
thermo 50
run 10000
WARNING: More than one fix poems
WARNING: More than one fix poems
WARNING: One or more atoms are time integrated more than once
Memory usage per processor = 2.24533 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 15163.926 957.47586 0 3765.6103 -17.92346
1500 19223.687 204.15182 0 3764.0939 -1.613452
1550 18147.996 404.12678 0 3764.8668 8.4194792
1600 18615.043 317.42471 0 3764.6548 -2.3288881
1650 20120.654 38.887882 0 3764.935 -8.7620352
1700 19450.908 162.98242 0 3765.0025 2.3254787
1750 19374.63 177.37994 0 3765.2744 8.9328764
1800 19424.404 167.93955 0 3765.0514 0.081221207
1850 17936.104 442.8692 0 3764.3699 6.6014634
1900 19982.594 64.406495 0 3764.8868 -2.9529141
1950 16215.626 761.95548 0 3764.8491 13.995806
2000 18584.494 322.10724 0 3763.6801 7.1652003
2050 20107.964 41.026031 0 3764.723 -0.31084595
2100 20002.303 60.598606 0 3764.7288 -6.7920431
2150 16950.12 626.52975 0 3765.4408 3.5077027
2200 20010.956 58.807784 0 3764.5404 -10.861982
2250 18982.743 247.00649 0 3762.3293 -0.53838506
2300 18401.159 354.90522 0 3762.5273 1.0923853
2350 19390.592 172.92882 0 3763.7792 -3.3521232
2400 16078.693 786.77936 0 3764.3151 -16.207246
2450 18869.645 268.89132 0 3763.27 11.210758
2500 19689.703 117.31993 0 3763.5612 4.3700595
2550 18867.605 269.38371 0 3763.3847 -5.673697
2600 17024.852 610.68855 0 3763.4389 6.2927269
2650 18723.802 296.52976 0 3763.9005 2.4475504
2700 19752.355 105.40597 0 3763.2494 -0.38635488
2750 19524.414 147.78984 0 3763.4221 -1.5733395
2800 17840.968 459.3254 0 3763.2085 29.661669
2850 18887.52 265.43414 0 3763.1231 3.7534553
2900 20160.325 29.79531 0 3763.1888 2.8076367
2950 17931.673 442.25832 0 3762.9386 4.1038365
3000 19003.992 243.57426 0 3762.832 3.5213285
3050 18907.933 261.70341 0 3763.1725 6.1845639
3100 19086.668 229.05632 0 3763.6245 -1.7059047
3150 19524.328 148.10446 0 3763.7208 -13.257029
3200 19888.015 80.720451 0 3763.6863 -5.9850932
3250 18329.653 367.80596 0 3762.1862 2.5356842
3300 17774.857 472.07926 0 3763.7194 26.05786
3350 18586.91 322.11111 0 3764.1316 5.7227572
3400 18142.722 404.27409 0 3764.0373 22.972948
3450 19641.028 126.721 0 3763.9484 4.4124099
3500 19716.345 112.83226 0 3764.0073 3.0970704
3550 19750.966 106.4596 0 3764.0458 -1.2020093
3600 19385.115 174.22116 0 3764.0572 -0.30312978
3650 19806.188 96.296016 0 3764.1086 1.3884533
3700 19632.503 128.4744 0 3764.1231 5.4783086
3750 19984.029 63.34637 0 3764.0924 -7.6169503
3800 19391.726 173.11834 0 3764.1788 -5.5199774
3850 19701.864 115.6328 0 3764.1262 -4.613059
3900 19071.277 232.53842 0 3764.2563 0.60414949
3950 19543.806 144.70463 0 3763.9279 3.9673805
4000 17072.153 601.63639 0 3763.1462 14.038181
4050 19472.634 157.9704 0 3764.0138 0.075484598
4100 19458.162 160.55562 0 3763.919 1.7856979
4150 19028.89 239.83121 0 3763.6997 11.420854
4200 20109.582 39.912078 0 3763.9088 -2.4825779
4250 19501.856 151.85318 0 3763.308 4.4374703
4300 19953.632 68.83941 0 3763.9565 -1.9144758
4350 19109.358 225.03756 0 3763.8075 0.43487388
4400 19762.511 104.29295 0 3764.0171 2.7984598
4450 19722.718 111.70804 0 3764.0632 2.2845927
4500 19915.846 75.911584 0 3764.0312 4.1625614
4550 19884.847 81.607953 0 3763.987 2.0252211
4600 18612.632 317.21746 0 3764.0011 5.1726513
4650 19078.336 230.90268 0 3763.9279 5.205472
4700 19715.75 112.95427 0 3764.019 4.3237781
4750 19742.684 107.93515 0 3763.9878 2.1485577
4800 19197.053 208.91261 0 3763.9225 -2.943785
4850 19760.387 104.71117 0 3764.0421 -4.0934577
4900 17998.47 431.02848 0 3764.0784 13.811824
4950 19604.398 133.53703 0 3763.9811 -5.5636088
5000 19232.029 202.51843 0 3764.0053 -1.8269075
5050 19715.235 112.97181 0 3763.9412 1.7390053
5100 19398.744 171.53062 0 3763.8906 3.3491974
5150 19314.84 187.15985 0 3763.982 2.8628327
5200 19694.326 116.88381 0 3763.9813 0.87055141
5250 19863.902 85.505146 0 3764.0056 -0.59127781
5300 18854.279 272.69199 0 3764.2251 0.97585642
5350 20102.125 41.375281 0 3763.9911 3.4442258
5400 18613.294 317.12781 0 3764.0342 9.5393349
5450 19559.083 141.5345 0 3763.5869 3.6962703
5500 17569.068 510.18672 0 3763.7179 13.24936
5550 19270.914 194.90196 0 3763.5898 3.8986118
5600 19498.122 153.15583 0 3763.9191 -3.4776966
5650 19777.463 101.36242 0 3763.8555 -11.848632
5700 19084.468 229.69625 0 3763.8569 1.2585904
5750 18724.734 296.2904 0 3763.8337 2.6582121
5800 19386.427 173.81408 0 3763.8932 4.2211994
5850 19803.648 96.837994 0 3764.1802 1.3140639
5900 19673.781 120.82275 0 3764.1155 -2.5154465
5950 19736.953 109.09143 0 3764.0827 -2.2181212
6000 19790.274 99.158109 0 3764.0237 -3.68098
6050 19545.34 144.53706 0 3764.0444 0.39182955
6100 17986.935 433.2002 0 3764.114 10.030916
6150 19723.117 111.58597 0 3764.015 2.7481914
6200 19196.262 209.2757 0 3764.139 -4.1838898
6250 19595.664 135.40327 0 3764.2299 -4.9572417
6300 20066.143 48.26479 0 3764.2173 -2.0440702
6350 19658.915 123.66551 0 3764.2054 6.3983302
6400 16099.375 783.30808 0 3764.6738 10.626182
6450 18777.763 287.09552 0 3764.4591 -4.455207
6500 16707.737 670.37041 0 3764.3958 13.941367
6550 19762.607 104.62762 0 3764.3696 0.16306805
6600 19257.046 198.21098 0 3764.3305 -5.4407238
6650 19832.195 91.712241 0 3764.3409 -1.9458256
6700 19850.998 88.250674 0 3764.3614 5.8183659
6750 19413.067 169.26039 0 3764.2728 6.1295075
6800 19765.494 103.96165 0 3764.2383 -3.7688435
6850 16858.457 642.54223 0 3764.4787 4.5079169
6900 19982.921 63.847652 0 3764.3885 -9.1345046
6950 19913.352 76.606013 0 3764.2639 -2.5724183
7000 19224.043 204.40946 0 3764.4174 8.8267535
7050 19611.945 132.75353 0 3764.5952 -1.2121033
7100 18439.385 350.13652 0 3764.8375 -10.124288
7150 19682.442 120.04202 0 3764.9386 -3.6256683
7200 19422.224 168.10408 0 3764.8122 0.82487728
7250 18329.588 370.25204 0 3764.6202 11.648525
7300 19708.59 114.99145 0 3764.7304 0.046523759
7350 19816.323 95.213196 0 3764.9026 -0.47763944
7400 17665.439 493.59617 0 3764.9737 -0.91038002
7450 19566.729 141.55672 0 3765.0251 -5.4595222
7500 19814.753 95.678399 0 3765.077 2.7766353
7550 18372.821 362.40112 0 3764.7753 14.250033
7600 19501.443 153.75428 0 3765.1326 7.1710143
7650 19668.707 122.7639 0 3765.117 -7.9237216
7700 19679.165 120.74844 0 3765.0382 -2.2087708
7750 19318.592 187.36213 0 3764.8791 5.2470406
7800 18421.715 352.99021 0 3764.419 9.1913905
7850 18895.708 265.3653 0 3764.5705 5.549395
7900 19577.99 139.06024 0 3764.614 -9.4076317
7950 19740.609 109.09893 0 3764.7672 -9.8961255
8000 18940.832 256.98999 0 3764.5514 3.9687427
8050 18969.072 252.07733 0 3764.8685 -4.0865115
8100 18105.878 411.85769 0 3764.798 6.9985575
8150 17720.026 483.41227 0 3764.8985 -9.9691828
8200 19228.141 204.22365 0 3764.9906 4.5129102
8250 18208.089 392.95005 0 3764.8183 -1.1095191
8300 17975.092 435.94429 0 3764.665 17.753982
8350 18763.356 290.24792 0 3764.9434 2.4934075
8400 20081.591 46.079041 0 3764.8922 -1.2146918
8450 19112.458 225.50295 0 3764.847 -4.35039
8500 19307.507 189.3956 0 3764.86 5.0874862
8550 19181.088 212.75782 0 3764.8111 0.25341129
8600 18801.701 282.9206 0 3764.7171 -11.907333
8650 18881.312 268.25685 0 3764.7961 7.0176888
8700 15686.277 860.48983 0 3765.356 21.424289
8750 18618.866 316.47733 0 3764.4154 -4.6552691
8800 18339.56 368.23406 0 3764.4489 2.6401219
8850 19445.679 163.71793 0 3764.7697 -2.4895575
8900 19121.794 223.5113 0 3764.5842 -5.0630299
8950 14402.118 1099.2335 0 3766.2923 -7.4933486
9000 19175.071 213.69795 0 3764.637 -5.6657242
9050 19412.386 169.60603 0 3764.4924 -12.723782
9100 18455.972 346.68851 0 3764.4611 9.1721288
9150 19954.848 69.041959 0 3764.3841 -0.91356236
9200 19613.768 132.03036 0 3764.2097 4.9013519
9250 15254.687 939.82439 0 3764.7665 11.510878
9300 19048.696 236.62627 0 3764.1625 0.67464829
9350 18952.271 254.3769 0 3764.0568 8.2625973
9400 17082.985 600.49483 0 3764.0105 -9.9046787
9450 16757.345 660.90075 0 3764.1128 21.116304
9500 19841.884 89.284407 0 3763.7073 -0.64193305
9550 19304.212 189.00596 0 3763.86 -12.873723
9600 16227.696 759.23524 0 3764.3641 11.721944
9650 17820.924 463.01451 0 3763.1857 3.9496789
9700 19354.393 179.78068 0 3763.9275 -2.6872013
9750 13935.985 1183.7739 0 3764.5119 10.647433
9800 19587.907 136.31855 0 3763.7087 5.5549859
9850 19080.946 230.80379 0 3764.3124 -4.0577518
9900 19455.883 161.42232 0 3764.3637 -1.6117009
9950 18749.317 292.29982 0 3764.3955 3.9849608
10000 18721.798 297.49023 0 3764.4899 1.6710415
Loop time of 6.08953 on 4 procs for 10000 steps with 81 atoms
Pair time (%) = 0.0539414 (0.885805)
Neigh time (%) = 0.0267847 (0.439848)
Comm time (%) = 0.356341 (5.8517)
Outpt time (%) = 0.039064 (0.641494)
Other time (%) = 5.6134 (92.1811)
Nlocal: 20.25 ave 36 max 0 min
Histogram: 1 0 1 0 0 0 0 0 0 2
Nghost: 16 ave 33 max 2 min
Histogram: 2 0 0 0 0 0 0 1 0 1
Neighs: 162.75 ave 371 max 0 min
Histogram: 2 0 0 0 0 0 0 1 0 1
Total # of neighbors = 651
Ave neighs/atom = 8.03704
Neighbor list builds = 993
Dangerous builds = 949