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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@11411 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp
2014-01-30 22:50:33 +00:00
parent abdec3cb5d
commit dd122f6a0b
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examples/rigid/log.rigid.1Feb14.linux.1 Normal file
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LAMMPS (1 Feb 2014)
# Simple rigid body system
units lj
atom_style atomic
pair_style lj/cut 2.5
read_data data.rigid
orthogonal box = (-12 -12 -12) to (12 12 12)
1 by 1 by 1 MPI processor grid
reading atoms ...
81 atoms
velocity all create 100.0 4928459
# unconnected bodies
group clump1 id <> 1 9
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
#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
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 -7.9722845e-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 -0.13663194 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 -0.00039690662 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 -0.00037652439 0 5269.5216 12.011692
9550 16738.493 -0.0053156163 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 0.13550094 0 5269.5101 11.407245
9800 16738.512 -0.011620328 0 5269.5201 11.394974
9850 16738.489 -0.00067270524 0 5269.5237 11.395098
9900 16738.489 -0.00024984565 0 5269.5242 11.395085
9950 16738.49 0 0 5269.5245 11.395076
10000 16738.49 0 0 5269.5246 11.395075
Loop time of 0.127403 on 1 procs for 10000 steps with 81 atoms
Pair time (%) = 0.00816727 (6.41058)
Neigh time (%) = 0.0309787 (24.3155)
Comm time (%) = 0.00888801 (6.97629)
Outpt time (%) = 0.00162864 (1.27833)
Other time (%) = 0.0777404 (61.0193)
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 (1 Feb 2014)
# 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
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
#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
Memory usage per processor = 1.8248 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 -7.9722856e-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 -0.13663194 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 -0.00039690662 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 -0.00037652439 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 1.0589893 0 5269.4979 12.062708
9750 16738.013 0.13550084 0 5269.5101 11.407245
9800 16738.512 -0.011620328 0 5269.5201 11.394973
9850 16738.489 -0.00067270547 0 5269.5237 11.395098
9900 16738.489 -0.00024984575 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 0.173009 on 4 procs for 10000 steps with 81 atoms
Pair time (%) = 0.00257808 (1.49014)
Neigh time (%) = 0.0103006 (5.95377)
Comm time (%) = 0.0810853 (46.8676)
Outpt time (%) = 0.00332773 (1.92344)
Other time (%) = 0.0757175 (43.765)
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

317
examples/rigid/log.rigid.poems.1Feb14.linux.1 Normal file
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@ -0,0 +1,317 @@
LAMMPS (1 Feb 2014)
# Simple rigid body system
units lj
atom_style atomic
pair_style lj/cut 2.5
read_data data.rigid
orthogonal box = (-12 -12 -12) to (12 12 12)
1 by 1 by 1 MPI processor grid
reading atoms ...
81 atoms
velocity all create 100.0 4928459
# unconnected bodies
#group clump1 id <> 1 9
#group clump2 id <> 10 18
#group clump3 id <> 19 27
#group clump4 id <> 28 36
#group clump5 id <> 37 45
#group clump6 id <> 46 54
#group clump7 id <> 55 63
#group clump8 id <> 64 72
#group clump9 id <> 73 81
#fix 1 all rigid group 9 clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9
# 1 chain of connected bodies
group clump1 id <> 1 9
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
Memory usage per processor = 1.93979 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 3.5147 on 1 procs for 10000 steps with 81 atoms
Pair time (%) = 0.153219 (4.35937)
Neigh time (%) = 0.0883856 (2.51474)
Comm time (%) = 0.00992155 (0.282288)
Outpt time (%) = 0.00212979 (0.0605968)
Other time (%) = 3.26104 (92.783)
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
Please see the log.cite file for references relevant to this simulation

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LAMMPS (1 Feb 2014)
# 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
Memory usage per processor = 1.90126 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 3.73648 on 4 procs for 10000 steps with 81 atoms
Pair time (%) = 0.0408831 (1.09416)
Neigh time (%) = 0.026132 (0.699376)
Comm time (%) = 0.239869 (6.41966)
Outpt time (%) = 0.00523436 (0.140088)
Other time (%) = 3.42436 (91.6467)
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
Please see the log.cite file for references relevant to this simulation

321
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LAMMPS (1 Feb 2014)
# Simple rigid body system
units lj
atom_style atomic
pair_style lj/cut 2.5
read_data data.rigid
orthogonal box = (-12 -12 -12) to (12 12 12)
1 by 1 by 1 MPI processor grid
reading atoms ...
81 atoms
velocity all create 100.0 4928459
# unconnected bodies
#group clump1 id <> 1 9
#group clump2 id <> 10 18
#group clump3 id <> 19 27
#group clump4 id <> 28 36
#group clump5 id <> 37 45
#group clump6 id <> 46 54
#group clump7 id <> 55 63
#group clump8 id <> 64 72
#group clump9 id <> 73 81
#fix 1 all rigid group 9 clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9
# 1 chain of connected bodies
#group clump1 id <> 1 9
#group clump2 id <> 9 18
#group clump3 id <> 18 27
#group clump4 id <> 27 36
#group clump5 id <> 36 45
#group clump6 id <> 45 54
#group clump7 id <> 54 63
#group clump8 id <> 63 72
#group clump9 id <> 72 81
#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9
# 2 chains of connected bodies
group clump1 id <> 1 9
9 atoms in group clump1
group clump2 id <> 9 18
10 atoms in group clump2
group clump3 id <> 18 27
10 atoms in group clump3
group clump4 id <> 27 36
10 atoms in group clump4
group clump5 id <> 37 45
9 atoms in group clump5
group clump6 id <> 45 54
10 atoms in group clump6
group clump7 id <> 54 63
10 atoms in group clump7
group clump8 id <> 63 72
10 atoms in group clump8
group clump9 id <> 72 81
10 atoms in group clump9
fix 1 all poems group clump1 clump2 clump3 clump4
1 clusters, 4 bodies, 3 joints, 36 atoms
fix 2 all poems group clump5 clump6 clump7 clump8 clump9
1 clusters, 5 bodies, 4 joints, 45 atoms
neigh_modify exclude group clump1 clump1
neigh_modify exclude group clump2 clump2
neigh_modify exclude group clump3 clump3
neigh_modify exclude group clump4 clump4
neigh_modify exclude group clump5 clump5
neigh_modify exclude group clump6 clump6
neigh_modify exclude group clump7 clump7
neigh_modify exclude group clump8 clump8
neigh_modify exclude group clump9 clump9
thermo 100
#dump 1 all atom 50 dump.rigid.poems2
#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 2 pad 5
#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 3 pad 5
timestep 0.0001
thermo 50
run 10000
WARNING: More than one fix poems (../fix_poems.cpp:351)
WARNING: More than one fix poems (../fix_poems.cpp:351)
WARNING: One or more atoms are time integrated more than once (../modify.cpp:245)
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 3.72182 on 1 procs for 10000 steps with 81 atoms
Pair time (%) = 0.113393 (3.0467)
Neigh time (%) = 0.0677266 (1.81972)
Comm time (%) = 0.0135663 (0.364506)
Outpt time (%) = 0.00212884 (0.0571989)
Other time (%) = 3.525 (94.7119)
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
Please see the log.cite file for references relevant to this simulation

321
examples/rigid/log.rigid.poems2.1Feb14.linux.4 Normal file
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@ -0,0 +1,321 @@
LAMMPS (1 Feb 2014)
# 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:351)
WARNING: More than one fix poems (../fix_poems.cpp:351)
WARNING: One or more atoms are time integrated more than once (../modify.cpp:245)
Memory usage per processor = 2.24534 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 3.78797 on 4 procs for 10000 steps with 81 atoms
Pair time (%) = 0.0290385 (0.766597)
Neigh time (%) = 0.0196837 (0.519638)
Comm time (%) = 0.144778 (3.82205)
Outpt time (%) = 0.0049271 (0.130072)
Other time (%) = 3.58954 (94.7616)
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
Please see the log.cite file for references relevant to this simulation

401
examples/rigid/log.rigid.tnr.1Feb14.linux.1 Normal file
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@ -0,0 +1,401 @@
LAMMPS (1 Feb 2014)
# Tethered nanorods
atom_style molecular
read_data data.rigid.tnr
orthogonal box = (-31.122 -31.122 -31.122) to (31.122 31.122 31.122)
1 by 1 by 1 MPI processor grid
reading atoms ...
5600 atoms
scanning bonds ...
1 = max bonds/atom
reading bonds ...
1600 bonds
2 = max # of 1-2 neighbors
1 = max # of 1-3 neighbors
1 = max # of 1-4 neighbors
2 = max # of special neighbors
# Specify bond parameters
bond_style fene
bond_coeff 1 30.0 1.5 1.0 1.0
special_bonds fene
2 = max # of 1-2 neighbors
2 = max # of special neighbors
# Specify initial velocities
velocity all create 1.4 109345
# Specify rigid components
group rods type 2
4000 atoms in group rods
group tethers subtract all rods
1600 atoms in group tethers
neigh_modify exclude molecule rods delay 0 every 1
# Specify the pair potentials
pair_style lj/cut 2.5
pair_modify shift yes
pair_coeff * * 1.0 1.0 1.122
pair_coeff 2 2 1.0 1.0 2.5
# Specify output
thermo 100
thermo_style custom step temp pe etotal press enthalpy lx ly lz pxx pyy pzz
thermo_modify flush yes lost warn
timestep 0.005
fix 1 rods rigid molecule
800 rigid bodies with 4000 atoms
fix 2 tethers nve
fix 3 all langevin 1.4 1.4 1.0 437624
run 5000
Memory usage per processor = 6.39499 Mbytes
Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
0 1.3963219 5.9478449 7.0445809 0.048565317 9.13595 62.244 62.244 62.244 0.0091983659 0.11850113 0.017996458
100 1.3418512 5.9671777 7.0211299 0.025020362 8.0985822 62.244 62.244 62.244 0.02036076 0.038265078 0.016435248
200 1.3730638 5.9750802 7.0535483 0.0053287535 7.2830205 62.244 62.244 62.244 -0.00054924195 0.0092396988 0.0072958036
300 1.376262 5.9821642 7.0631443 0.0055536521 7.3023013 62.244 62.244 62.244 0.0033577704 0.0069111861 0.0063919998
400 1.3782954 5.9983628 7.08094 0.0020507385 7.169251 62.244 62.244 62.244 -0.0060862717 0.0098998072 0.0023386801
500 1.386863 6.0053312 7.0946377 -0.0009847031 7.0522334 62.244 62.244 62.244 -0.0038708372 0.0005697804 0.00034694745
600 1.4069849 6.0035719 7.1086832 0.0047883912 7.3148858 62.244 62.244 62.244 0.001069365 0.0078059505 0.0054898581
700 1.4423187 5.9982171 7.1310812 0.012141001 7.6539093 62.244 62.244 62.244 0.0094765272 0.011007593 0.015938883
800 1.4303878 5.9968168 7.1203098 -0.00081349095 7.0852784 62.244 62.244 62.244 0.0011153812 0.00041597298 -0.0039718271
900 1.4140538 5.9838168 7.0944803 0.00207609 7.183883 62.244 62.244 62.244 0.00043409671 0.0022778944 0.0035162788
1000 1.3906567 5.988119 7.0804053 0.0022005856 7.1751692 62.244 62.244 62.244 0.0077268425 -0.0022042977 0.0010792119
1100 1.3921992 5.9892203 7.0827181 0.0035041977 7.2336194 62.244 62.244 62.244 -0.0037576823 0.0040827951 0.01018748
1200 1.3968803 5.9795846 7.0767592 -0.0031072146 6.9429532 62.244 62.244 62.244 -0.0077387449 0.0033056124 -0.0048885115
1300 1.3755848 5.9739757 7.0544239 0.0092247106 7.4516677 62.244 62.244 62.244 0.0092788748 0.010737194 0.0076580625
1400 1.3847985 5.9703631 7.0580481 0.0071703598 7.3668254 62.244 62.244 62.244 0.0080485848 0.012260474 0.001202021
1500 1.4190051 5.956946 7.0714985 0.0035992903 7.2264948 62.244 62.244 62.244 -0.0055125437 0.01038369 0.0059267242
1600 1.3980036 5.9671666 7.0652236 0.0061819851 7.3314385 62.244 62.244 62.244 0.0062429141 0.0035120077 0.0087910334
1700 1.4276062 5.9610381 7.0823462 0.007832375 7.4196319 62.244 62.244 62.244 0.0083316819 0.0058394293 0.009326014
1800 1.4112769 5.9630595 7.0715419 0.0068032101 7.3645087 62.244 62.244 62.244 0.0065502252 0.0062317255 0.0076276797
1900 1.4276973 5.9489341 7.0703139 0.008397746 7.4319462 62.244 62.244 62.244 0.0148941 0.0032963108 0.0070028268
2000 1.4056158 5.9564624 7.0604983 0.0090470732 7.4500926 62.244 62.244 62.244 0.011871718 0.0086681344 0.0066013673
2100 1.3924778 5.9483611 7.0420778 0.0088893819 7.4248814 62.244 62.244 62.244 0.010247454 0.0097830093 0.0066376825
2200 1.3760401 5.9435877 7.0243935 -0.0042972782 6.8393397 62.244 62.244 62.244 -0.0050064436 -0.0046216999 -0.0032636911
2300 1.4191937 5.9334036 7.0481042 0.0047000032 7.2505006 62.244 62.244 62.244 0.0057709636 0.0044949165 0.0038341296
2400 1.4213285 5.9472214 7.0635988 0.010197674 7.5027414 62.244 62.244 62.244 0.0083738259 0.0090537939 0.013165402
2500 1.4153808 5.9421661 7.0538718 0.00015906304 7.0607216 62.244 62.244 62.244 0.0023516208 -0.0019814985 0.00010706681
2600 1.4014223 5.9431386 7.0438807 0.0070733748 7.3484816 62.244 62.244 62.244 0.005414387 0.010055843 0.0057498949
2700 1.4138077 5.9369067 7.047377 0.0024268844 7.1518859 62.244 62.244 62.244 0.0052918441 0.0014960354 0.00049277387
2800 1.432192 5.9347676 7.0596777 0.0077670451 7.3941501 62.244 62.244 62.244 0.012668421 0.0059113035 0.0047214114
2900 1.3938659 5.921023 7.01583 0.00537512 7.2472989 62.244 62.244 62.244 0.0020490377 0.007656609 0.0064197131
3000 1.390221 5.9205014 7.0124455 -0.0010750979 6.9661485 62.244 62.244 62.244 0.0019519824 -0.0041878903 -0.00098938592
3100 1.4205722 5.9178284 7.0336117 0.009873547 7.4587965 62.244 62.244 62.244 0.0040973363 0.012167266 0.013356039
3200 1.398418 5.9150349 7.0134173 0.0061541829 7.278435 62.244 62.244 62.244 0.0067621803 0.011952562 -0.0002521939
3300 1.4269859 5.9148726 7.0356937 0.0060623983 7.2967588 62.244 62.244 62.244 0.012956243 -2.4795615e-05 0.0052557479
3400 1.434286 5.9356705 7.0622253 0.00027314048 7.0739876 62.244 62.244 62.244 -0.00054962139 0.0052526062 -0.0038835634
3500 1.4416809 5.9228152 7.0551783 0.0083382965 7.4142505 62.244 62.244 62.244 0.0073993829 0.0030328137 0.014582693
3600 1.4136063 5.9039442 7.0142563 0.001971221 7.099143 62.244 62.244 62.244 -0.00032316217 0.003503006 0.0027338193
3700 1.433382 5.9120101 7.0378549 0.0071287089 7.3448386 62.244 62.244 62.244 0.0064768154 0.0046765426 0.010232769
3800 1.3659482 5.9032871 6.9761662 -0.0054032435 6.7434863 62.244 62.244 62.244 -0.0073942825 -0.0082831048 -0.00053234334
3900 1.3963224 5.9042995 7.0010359 0.0053310327 7.2306062 62.244 62.244 62.244 0.0081855547 0.0048807072 0.0029268363
4000 1.4125479 5.9060668 7.0155474 0.0028451204 7.1380669 62.244 62.244 62.244 0.0052588116 0.00072372172 0.0025528279
4100 1.3943956 5.9040893 6.9993123 0.0058043569 7.2492654 62.244 62.244 62.244 0.0060576276 0.002478686 0.0088767572
4200 1.4249783 5.8906355 7.0098796 0.0030213234 7.1399869 62.244 62.244 62.244 0.0061743252 -0.0020791501 0.0049687951
4300 1.3899826 5.8966344 6.9883912 0.0057294842 7.2351201 62.244 62.244 62.244 0.0049055668 0.0021899931 0.010092893
4400 1.4414357 5.8986162 7.0307867 0.0050933157 7.2501203 62.244 62.244 62.244 0.0057939021 0.0037947176 0.0056913275
4500 1.4092608 5.892298 6.9991969 0.0012247406 7.0519379 62.244 62.244 62.244 0.0042876402 0.0014588188 -0.0020722372
4600 1.3779488 5.8928773 6.9751823 0.0020733584 7.0644674 62.244 62.244 62.244 0.0029285418 -0.0031642229 0.0064557564
4700 1.4084742 5.909909 7.0161901 -0.00053850548 6.9930004 62.244 62.244 62.244 -0.0018600331 -0.0018359559 0.0020804726
4800 1.4391588 5.9150069 7.0453891 0.015310705 7.7047142 62.244 62.244 62.244 0.014756643 0.018034492 0.013140978
4900 1.4496016 5.907877 7.0464614 0.0075305556 7.3707499 62.244 62.244 62.244 0.0091920128 0.0081340187 0.0052656353
5000 1.4293045 5.9102892 7.0329313 -0.0015935867 6.9643067 62.244 62.244 62.244 -0.0049858888 0.001820566 -0.0016154373
Loop time of 6.35156 on 1 procs for 5000 steps with 5600 atoms
Pair time (%) = 0.478212 (7.52904)
Bond time (%) = 0.222193 (3.49824)
Neigh time (%) = 1.2401 (19.5243)
Comm time (%) = 0.172963 (2.72315)
Outpt time (%) = 0.00360727 (0.0567935)
Other time (%) = 4.23449 (66.6685)
Nlocal: 5600 ave 5600 max 5600 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1351 ave 1351 max 1351 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 5255 ave 5255 max 5255 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 5255
Ave neighs/atom = 0.938393
Ave special neighs/atom = 0.571429
Neighbor list builds = 766
Dangerous builds = 0
# Replace fix rigid and fix langevin with new ones
unfix 1
unfix 3
fix 3 tethers langevin 1.4 1.4 1.0 198450
# Test different integrators for rods
fix 1 rods rigid/nve molecule
800 rigid bodies with 4000 atoms
print "rigid/nve"
rigid/nve
run 1000
WARNING: Inconsistent image flags (../domain.cpp:645)
Memory usage per processor = 6.39499 Mbytes
Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
5000 1.4293045 5.9102892 7.0329313 0.028061066 8.2413255 62.244 62.244 62.244 0.017765452 0.040562905 0.02585484
5100 1.4400998 5.9022414 7.0333627 0.0061821009 7.2995826 62.244 62.244 62.244 0.009770998 0.0030836918 0.0056916129
5200 1.4082657 5.9104139 7.0165312 0.0064210573 7.2930413 62.244 62.244 62.244 0.0080770492 0.0051169375 0.0060691852
5300 1.45649 5.8801752 7.0241701 0.0069092534 7.3217034 62.244 62.244 62.244 0.0065768895 0.0056877656 0.0084631052
5400 1.4233427 5.8824466 7.000406 0.0035507414 7.1533117 62.244 62.244 62.244 0.0033649256 -0.00080481231 0.0080921109
5500 1.4203908 5.8713513 6.9869921 0.0082802387 7.3435642 62.244 62.244 62.244 0.0073789675 0.0076306312 0.0098311173
5600 1.4100524 5.8744301 6.9819507 0.0025993542 7.0938867 62.244 62.244 62.244 -0.002226516 0.005551312 0.0044732667
5700 1.4094008 5.8740942 6.981103 0.001858876 7.0611518 62.244 62.244 62.244 -0.00080782471 -0.00061623499 0.0070006878
5800 1.4017129 5.8875092 6.9884795 0.0010380104 7.0331794 62.244 62.244 62.244 0.0043974934 -0.0033700586 0.0020865964
5900 1.3979088 5.8861057 6.9840882 0.0019969425 7.0700826 62.244 62.244 62.244 -0.002580911 0.0061245675 0.0024471709
6000 1.4274747 5.8829671 7.004172 0.00018898098 7.0123101 62.244 62.244 62.244 0.0019071211 -0.0011893793 -0.00015079887
Loop time of 1.27908 on 1 procs for 1000 steps with 5600 atoms
Pair time (%) = 0.137631 (10.7602)
Bond time (%) = 0.0451553 (3.53029)
Neigh time (%) = 0.276716 (21.634)
Comm time (%) = 0.0356052 (2.78366)
Outpt time (%) = 0.000710726 (0.0555654)
Other time (%) = 0.783261 (61.2363)
Nlocal: 5600 ave 5600 max 5600 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1380 ave 1380 max 1380 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 5416 ave 5416 max 5416 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 5416
Ave neighs/atom = 0.967143
Ave special neighs/atom = 0.571429
Neighbor list builds = 153
Dangerous builds = 0
unfix 1
fix 1 rods rigid/nvt molecule temp 1.4 1.4 1.0
800 rigid bodies with 4000 atoms
print "rigid/nvt"
rigid/nvt
run 1000
WARNING: Inconsistent image flags (../domain.cpp:645)
Memory usage per processor = 6.39499 Mbytes
Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
6000 1.4274747 5.8829671 7.004172 -0.02124798 6.0891699 62.244 62.244 62.244 -0.0035029341 -0.035545622 -0.024695385
6100 1.4047816 5.8827162 6.9860969 0.0039973389 7.1582344 62.244 62.244 62.244 0.0038546201 0.0038745986 0.0042627978
6200 1.4013195 5.8723518 6.9730132 0.0055794243 7.21328 62.244 62.244 62.244 0.0052298684 0.006566317 0.0049420874
6300 1.4164814 5.8699858 6.982556 0.0046834632 7.18424 62.244 62.244 62.244 0.0042595662 0.0075687542 0.0022220694
6400 1.4008382 5.8754385 6.9757219 0.0057855428 7.2248648 62.244 62.244 62.244 0.011229504 0.0035917167 0.0025354077
6500 1.3961747 5.8821344 6.9787548 0.0054798914 7.2147355 62.244 62.244 62.244 0.0079746581 0.0012807952 0.007184221
6600 1.3989989 5.8839851 6.9828238 0.0078068029 7.3190083 62.244 62.244 62.244 0.0075737438 0.01001737 0.0058292953
6700 1.3944424 5.8846079 6.9798678 0.0025837202 7.0911306 62.244 62.244 62.244 0.001801077 0.0043727527 0.0015773308
6800 1.3886249 5.8876899 6.9783804 0.0083096819 7.3362204 62.244 62.244 62.244 0.0057252172 0.0080731664 0.011130662
6900 1.4128008 5.8873288 6.9970082 -0.0017879625 6.9200131 62.244 62.244 62.244 0.0032920311 -0.0044843856 -0.004171533
7000 1.4296767 5.8776376 7.0005721 0.0028980535 7.125371 62.244 62.244 62.244 0.0020944649 0.002732346 0.0038673497
Loop time of 1.30653 on 1 procs for 1000 steps with 5600 atoms
Pair time (%) = 0.140375 (10.7442)
Bond time (%) = 0.0453455 (3.47069)
Neigh time (%) = 0.278969 (21.3519)
Comm time (%) = 0.0354125 (2.71043)
Outpt time (%) = 0.000714064 (0.0546535)
Other time (%) = 0.805712 (61.6681)
Nlocal: 5600 ave 5600 max 5600 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1365 ave 1365 max 1365 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 5888 ave 5888 max 5888 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 5888
Ave neighs/atom = 1.05143
Ave special neighs/atom = 0.571429
Neighbor list builds = 151
Dangerous builds = 0
unfix 1
compute myTemp all temp
fix 1 rods rigid/npt molecule temp 1.4 1.4 1.0 iso 0.05 0.05 1.0 dilate all
800 rigid bodies with 4000 atoms
print "rigid/npt iso"
rigid/npt iso
fix_modify 1 temp myTemp
run 1000
WARNING: Inconsistent image flags (../domain.cpp:645)
Memory usage per processor = 6.39499 Mbytes
Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
7000 1.4296767 5.8776376 7.0005721 0.012931516 7.5574422 62.244 62.244 62.244 -0.033811545 0.071351891 0.0012542007
7100 1.4257807 5.8661379 6.9860122 0.0063203866 7.2286059 59.901999 59.901999 59.901999 0.0075682964 0.0028831604 0.0085097032
7200 1.407746 5.857124 6.962833 0.0084753318 7.2534913 57.694979 57.694979 57.694979 0.010202527 0.0094388943 0.005784574
7300 1.3925246 5.8467137 6.9404672 0.014254002 7.3803203 55.699712 55.699712 55.699712 0.010958166 0.015538449 0.01626539
7400 1.3876126 5.8261824 6.9160778 0.011565854 7.238709 53.8566 53.8566 53.8566 0.010074234 0.013288968 0.011334359
7500 1.4080244 5.8243986 6.9303263 0.013237792 7.2665719 52.200705 52.200705 52.200705 0.014684708 0.015549417 0.0094792517
7600 1.4024992 5.8202266 6.9218146 0.0087754412 7.1257639 50.677331 50.677331 50.677331 0.012762778 0.0046632388 0.0089003068
7700 1.4053227 5.79557 6.8993757 0.017894387 7.2814436 49.264862 49.264862 49.264862 0.017455799 0.011081333 0.02514603
7800 1.3626299 5.7913047 6.8615775 -0.0027715764 6.8070755 47.931898 47.931898 47.931898 -0.00096112659 -0.00022698058 -0.0071266219
7900 1.3811061 5.7611338 6.8459187 0.022417792 7.2542129 46.722152 46.722152 46.722152 0.017429453 0.023217068 0.026606854
8000 1.3909989 5.7527072 6.8452623 0.0050901754 6.9314891 45.607102 45.607102 45.607102 0.0033084213 0.0050773514 0.0068847534
Loop time of 2.1421 on 1 procs for 1000 steps with 5600 atoms
Pair time (%) = 0.243607 (11.3723)
Bond time (%) = 0.067399 (3.1464)
Neigh time (%) = 0.578037 (26.9846)
Comm time (%) = 0.0550971 (2.5721)
Outpt time (%) = 0.000721693 (0.0336909)
Other time (%) = 1.19724 (55.8909)
Nlocal: 5600 ave 5600 max 5600 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1964 ave 1964 max 1964 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 11395 ave 11395 max 11395 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 11395
Ave neighs/atom = 2.03482
Ave special neighs/atom = 0.571429
Neighbor list builds = 263
Dangerous builds = 0
unfix 1
fix 1 rods rigid/npt molecule temp 1.4 1.4 1.0 x 0.05 0.05 1.0 dilate all
800 rigid bodies with 4000 atoms
print "rigid/npt x"
rigid/npt x
run 1000
WARNING: Inconsistent image flags (../domain.cpp:645)
Memory usage per processor = 6.39499 Mbytes
Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
8000 1.3909989 5.7527072 6.8452623 -0.013693646 6.6132941 45.607102 45.607102 45.607102 -0.043122633 -0.045235911 0.047277607
8100 1.3859992 5.7541236 6.8427517 0.025001526 7.2534745 44.228819 45.607102 45.607102 0.034466544 0.018726978 0.021811058
8200 1.3854121 5.741923 6.83009 0.00064570832 6.8403853 42.926629 45.607102 45.607102 0.0027453757 0.0012726672 -0.002080918
8300 1.4154816 5.7503811 6.8621661 0.0142623 7.0833894 41.760381 45.607102 45.607102 0.011045171 0.01999352 0.011748208
8400 1.3809342 5.7526615 6.8373114 0.010034961 6.9882285 40.489828 45.607102 45.607102 0.013514677 0.009127176 0.0074630301
8500 1.377763 5.7274882 6.8096473 0.010601881 6.9645838 39.345393 45.607102 45.607102 0.011511215 0.00061614599 0.019678283
8600 1.431011 5.716086 6.8400685 0.0082177641 6.9567982 38.242914 45.607102 45.607102 0.017556217 0.0072745279 -0.00017745274
8700 1.4088268 5.7023605 6.8089185 0.014325516 7.006943 37.216169 45.607102 45.607102 0.030284184 0.0090717286 0.0036206352
8800 1.4053586 5.7019319 6.8057658 0.004331614 6.8641135 36.265817 45.607102 45.607102 0.0075148755 0.012823387 -0.0073434199
8900 1.4159123 5.7005178 6.812641 0.013485111 6.9893826 35.286383 45.607102 45.607102 0.025461313 0.0051541371 0.0098398833
9000 1.4232531 5.6865082 6.8043973 0.014588857 6.9910378 34.44354 45.607102 45.607102 0.016849826 0.025113792 0.0018029545
Loop time of 2.23572 on 1 procs for 1000 steps with 5600 atoms
Pair time (%) = 0.329728 (14.7482)
Bond time (%) = 0.0679741 (3.04037)
Neigh time (%) = 0.547063 (24.4692)
Comm time (%) = 0.0531805 (2.37867)
Outpt time (%) = 0.000710964 (0.0318003)
Other time (%) = 1.23706 (55.3317)
Nlocal: 5600 ave 5600 max 5600 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 2374 ave 2374 max 2374 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 14730 ave 14730 max 14730 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 14730
Ave neighs/atom = 2.63036
Ave special neighs/atom = 0.571429
Neighbor list builds = 190
Dangerous builds = 0
unfix 1
fix 1 rods rigid/nph molecule iso 0.05 0.05 1.0 dilate all
800 rigid bodies with 4000 atoms
print "rigid/nph iso"
rigid/nph iso
run 1000
WARNING: Inconsistent image flags (../domain.cpp:645)
Memory usage per processor = 6.39499 Mbytes
Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
9000 1.4232531 5.6865082 6.8043973 -0.045897712 6.2172112 34.44354 45.607102 45.607102 -0.13827955 -0.060145768 0.060732183
9100 1.4046189 5.689947 6.7931999 0.025063166 7.0966586 33.816926 44.777394 44.777394 0.026506621 0.026941055 0.021741822
9200 1.4514944 5.6439353 6.7840064 0.010043669 6.8992028 33.212004 43.97641 43.97641 0.013456849 0.016567864 0.00010629292
9300 1.4577939 5.655083 6.800102 0.010672001 6.9162857 32.639692 43.218605 43.218605 0.026259683 -0.0039439335 0.0097002517
9400 1.4990612 5.6382783 6.8157106 0.0044191075 6.8615643 32.121265 42.53215 42.53215 -0.0025936629 0.022212724 -0.0063617388
9500 1.4578238 5.6474926 6.7925351 0.011187763 6.9033093 31.623599 41.873184 41.873184 0.026402116 0.012016515 -0.0048553414
9600 1.4618782 5.6455953 6.7938223 0.040647445 7.17882 31.159311 41.258416 41.258416 0.030007882 0.037188739 0.054745715
9700 1.472894 5.6140659 6.7709452 0.031213864 7.0543129 30.721834 40.679146 40.679146 0.030150709 0.023805303 0.03968558
9800 1.4853035 5.5879969 6.7546233 0.019089748 6.920651 30.285846 40.101849 40.101849 -0.001882924 0.030361407 0.02879076
9900 1.4922807 5.5739043 6.7460109 0.034454036 7.033471 29.869325 39.55033 39.55033 0.037756787 0.037488603 0.028116717
10000 1.4702912 5.5609742 6.7158092 0.02974948 6.9548436 29.496685 39.056912 39.056912 0.048495581 0.026126614 0.014626246
Loop time of 2.46339 on 1 procs for 1000 steps with 5600 atoms
Pair time (%) = 0.418965 (17.0077)
Bond time (%) = 0.0689692 (2.79977)
Neigh time (%) = 0.69069 (28.0382)
Comm time (%) = 0.0612285 (2.48554)
Outpt time (%) = 0.00073576 (0.0298677)
Other time (%) = 1.2228 (49.639)
Nlocal: 5600 ave 5600 max 5600 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 2884 ave 2884 max 2884 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 21437 ave 21437 max 21437 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 21437
Ave neighs/atom = 3.82804
Ave special neighs/atom = 0.571429
Neighbor list builds = 190
Dangerous builds = 0
unfix 1
fix 1 rods rigid/nph molecule x 0.05 0.05 1.0 y 0.05 0.05 1.0 couple xy dilate all
800 rigid bodies with 4000 atoms
print "rigid/nph xy couple"
rigid/nph xy couple
run 1000
WARNING: Inconsistent image flags (../domain.cpp:645)
Memory usage per processor = 6.39881 Mbytes
Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
10000 1.4702912 5.5609742 6.7158092 0.072285735 7.2966186 29.496685 39.056912 39.056912 0.0517015 0.12420995 0.040945755
10100 1.4573097 5.5587677 6.7034064 0.044500854 7.0509833 29.081982 38.507799 39.056912 0.044350384 0.023335488 0.06581669
10200 1.4979402 5.529745 6.7062968 0.020491404 6.8628393 28.761597 38.083573 39.056912 0.027897265 0.011514546 0.0220624
10300 1.5172843 5.5187731 6.7105187 0.02641776 6.9082543 28.469328 37.696576 39.056912 0.036912371 0.030960772 0.011380138
10400 1.4760818 5.5254938 6.684877 0.0091876447 6.7521031 28.14814 37.271288 39.056912 0.015300105 0.02827069 -0.016007861
10500 1.5146302 5.5026001 6.692261 0.021789385 6.8479527 27.815895 36.831359 39.056912 0.015592969 0.032547229 0.017227956
10600 1.4679788 5.4885912 6.64161 0.011753224 6.7237238 27.505044 36.419757 39.056912 0.010721153 0.010926592 0.013611926
10700 1.4667245 5.4720863 6.6241198 0.0043905713 6.6539747 27.135001 35.929779 39.056912 -0.03606819 0.013643937 0.035595967
10800 1.4647544 5.4559859 6.606472 0.036718423 6.8501768 26.80851 35.497468 39.056912 0.044497798 0.031324763 0.034332708
10900 1.4580432 5.4564769 6.6016918 0.065478135 7.0263115 26.499317 35.088061 39.056912 0.08229008 0.052793688 0.061350637
11000 1.4700915 5.4471801 6.6018582 -0.016382922 6.4976429 26.245381 34.751822 39.056912 -0.0093025128 -0.034580288 -0.005265964
Loop time of 2.65811 on 1 procs for 1000 steps with 5600 atoms
Pair time (%) = 0.524128 (19.7181)
Bond time (%) = 0.068589 (2.58037)
Neigh time (%) = 0.759783 (28.5836)
Comm time (%) = 0.0634546 (2.38721)
Outpt time (%) = 0.000737429 (0.0277426)
Other time (%) = 1.24142 (46.7031)
Nlocal: 5600 ave 5600 max 5600 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 3289 ave 3289 max 3289 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 27077 ave 27077 max 27077 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 27077
Ave neighs/atom = 4.83518
Ave special neighs/atom = 0.571429
Neighbor list builds = 170
Dangerous builds = 0

401
examples/rigid/log.rigid.tnr.1Feb14.linux.4 Normal file
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LAMMPS (1 Feb 2014)
# Tethered nanorods
atom_style molecular
read_data data.rigid.tnr
orthogonal box = (-31.122 -31.122 -31.122) to (31.122 31.122 31.122)
1 by 2 by 2 MPI processor grid
reading atoms ...
5600 atoms
scanning bonds ...
1 = max bonds/atom
reading bonds ...
1600 bonds
2 = max # of 1-2 neighbors
1 = max # of 1-3 neighbors
1 = max # of 1-4 neighbors
2 = max # of special neighbors
# Specify bond parameters
bond_style fene
bond_coeff 1 30.0 1.5 1.0 1.0
special_bonds fene
2 = max # of 1-2 neighbors
2 = max # of special neighbors
# Specify initial velocities
velocity all create 1.4 109345
# Specify rigid components
group rods type 2
4000 atoms in group rods
group tethers subtract all rods
1600 atoms in group tethers
neigh_modify exclude molecule rods delay 0 every 1
# Specify the pair potentials
pair_style lj/cut 2.5
pair_modify shift yes
pair_coeff * * 1.0 1.0 1.122
pair_coeff 2 2 1.0 1.0 2.5
# Specify output
thermo 100
thermo_style custom step temp pe etotal press enthalpy lx ly lz pxx pyy pzz
thermo_modify flush yes lost warn
timestep 0.005
fix 1 rods rigid molecule
800 rigid bodies with 4000 atoms
fix 2 tethers nve
fix 3 all langevin 1.4 1.4 1.0 437624
run 5000
Memory usage per processor = 4.9731 Mbytes
Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
0 1.3963219 5.9478449 7.0445809 0.048565317 9.13595 62.244 62.244 62.244 0.0091983659 0.11850113 0.017996458
100 1.3999025 5.9707695 7.0703179 0.027293074 8.24564 62.244 62.244 62.244 0.017246307 0.04732529 0.017307624
200 1.4245544 5.9878446 7.1067558 0.0072016369 7.41688 62.244 62.244 62.244 0.0071370801 0.0084066589 0.0060611719
300 1.4212057 5.9942604 7.1105414 0.0023296933 7.210865 62.244 62.244 62.244 -0.0059197015 0.0040269953 0.008881786
400 1.4030116 5.9953214 7.0973119 0.0055751834 7.3373961 62.244 62.244 62.244 -0.0026920847 0.013323321 0.0060943141
500 1.4201338 5.9984777 7.1139168 -0.0018229523 7.035415 62.244 62.244 62.244 -0.0082217102 -0.00047319975 0.0032260529
600 1.425173 5.9902537 7.1096508 0.013367744 7.6853062 62.244 62.244 62.244 0.012971415 0.016298595 0.010833222
700 1.4181225 5.9840752 7.0979345 0.0014999758 7.1625279 62.244 62.244 62.244 -0.0015835387 0.0045967753 0.0014866907
800 1.4084205 5.9778462 7.084085 0.0063728488 7.3585191 62.244 62.244 62.244 0.0036202744 0.005593586 0.0099046859
900 1.3958301 5.9891019 7.0854517 0.0028974454 7.2102244 62.244 62.244 62.244 0.0087724642 0.0014508428 -0.001530971
1000 1.3937374 5.9794855 7.0741916 0.0087158481 7.4495223 62.244 62.244 62.244 0.014424783 0.0034958881 0.0082268735
1100 1.3729162 5.9916252 7.0699773 0.0030451966 7.2011127 62.244 62.244 62.244 0.00084635444 -0.00064448421 0.0089337195
1200 1.4427374 5.9713589 7.1045519 0.0042680608 7.2883474 62.244 62.244 62.244 0.0030884628 0.0031576538 0.0065580658
1300 1.3971469 5.9728674 7.0702514 0.0022809251 7.168475 62.244 62.244 62.244 0.00060902513 -0.00020572386 0.006439474
1400 1.4194118 5.9672631 7.082135 0.012945844 7.6396221 62.244 62.244 62.244 0.0082418827 0.016256336 0.014339314
1500 1.3866472 5.9728382 7.0619753 0.0010642438 7.1078049 62.244 62.244 62.244 0.0020316123 0.0020439035 -0.00088278432
1600 1.4184955 5.9539591 7.0681113 0.0077605409 7.4023036 62.244 62.244 62.244 0.0033721722 0.0057827512 0.014126699
1700 1.3612202 5.9676733 7.0368389 0.0001686213 7.0441002 62.244 62.244 62.244 0.0052525345 0.0007705269 -0.0055171975
1800 1.3641041 5.9521837 7.0236144 0.0057884587 7.2728829 62.244 62.244 62.244 0.0038061044 0.0044032908 0.009155981
1900 1.3594477 5.9646024 7.0323757 0.0044261926 7.2229809 62.244 62.244 62.244 0.0019417448 0.006871542 0.004465291
2000 1.3776971 5.9431816 7.0252888 -0.0012460593 6.9716298 62.244 62.244 62.244 -0.0010913822 0.00098119436 -0.0036279901
2100 1.3986245 5.9509735 7.0495181 0.007520633 7.3733792 62.244 62.244 62.244 0.008359824 0.0075919773 0.0066100978
2200 1.4033594 5.9548158 7.0570794 0.0016804284 7.1294438 62.244 62.244 62.244 -0.001842641 0.0032876741 0.0035962521
2300 1.4048926 5.9444129 7.0478808 0.0062444034 7.3167836 62.244 62.244 62.244 0.004383569 0.0065720464 0.007777595
2400 1.4044043 5.9370822 7.0401666 0.0034562836 7.1890046 62.244 62.244 62.244 0.0068959298 0.0041111713 -0.0006382503
2500 1.4200762 5.9359254 7.0513193 0.002831965 7.1732722 62.244 62.244 62.244 -0.00030414197 0.0039571832 0.0048428539
2600 1.3876469 5.9249124 7.0148347 -0.0017777225 6.9382806 62.244 62.244 62.244 -0.00047616391 -0.0025484918 -0.0023085117
2700 1.4099941 5.916763 7.0242378 0.0070716263 7.3287634 62.244 62.244 62.244 0.012628756 0.0053812868 0.0032048357
2800 1.4444643 5.9283432 7.0628925 0.0019400021 7.1464349 62.244 62.244 62.244 0.0014895075 0.0046367395 -0.00030624082
2900 1.3902832 5.9152516 7.0072446 -0.0021662209 6.9139606 62.244 62.244 62.244 -0.0012374413 -0.00056403252 -0.0046971889
3000 1.3711706 5.922146 6.9991271 0.011101505 7.4771914 62.244 62.244 62.244 0.011063833 0.012093025 0.010147657
3100 1.3569137 5.9171753 6.9829583 -0.0028266776 6.8612331 62.244 62.244 62.244 -0.0069507251 0.0010084389 -0.0025377465
3200 1.4004275 5.905939 7.0058998 0.0054394662 7.2401396 62.244 62.244 62.244 0.010352182 0.0057594147 0.00020680221
3300 1.3641217 5.9145275 6.985972 -0.0027212879 6.8687852 62.244 62.244 62.244 -0.00065934268 -0.0057713101 -0.0017332109
3400 1.3868722 5.9059546 6.9952684 0.0092591224 7.3939941 62.244 62.244 62.244 0.010690868 0.010752519 0.00633398
3500 1.3939168 5.8992292 6.9940762 0.0074340081 7.314207 62.244 62.244 62.244 0.010137313 0.0044252684 0.007739443
3600 1.3982508 5.921946 7.0201971 0.0056794461 7.2647712 62.244 62.244 62.244 0.0023367067 0.0080592062 0.0066424255
3700 1.4019908 5.9059956 7.0071842 0.0065915632 7.2910368 62.244 62.244 62.244 0.0049554575 0.010826968 0.0039922641
3800 1.3960735 5.9020789 6.9986199 0.0027763383 7.1181774 62.244 62.244 62.244 -0.0015907441 0.0025861872 0.0073335719
3900 1.4352827 5.8986212 7.0259589 0.0034983551 7.1766087 62.244 62.244 62.244 0.0030418441 0.0027739 0.0046793211
4000 1.4121841 5.9079029 7.0170979 0.0050462456 7.2344045 62.244 62.244 62.244 0.004554319 0.0064113582 0.0041730596
4100 1.3989603 5.9082373 7.0070457 0.00042910949 7.0255244 62.244 62.244 62.244 0.0025742152 0.0025182507 -0.0038051374
4200 1.3998831 5.8998111 6.9993443 0.0042773229 7.1835387 62.244 62.244 62.244 0.0013730326 0.0064696933 0.0049892428
4300 1.4076053 5.904453 7.0100516 0.0066772664 7.2975948 62.244 62.244 62.244 0.0073577056 0.0048125374 0.0078615562
4400 1.4161358 5.9064223 7.0187211 -0.0011881346 6.9675565 62.244 62.244 62.244 -0.0019130158 -0.003763749 0.002112361
4500 1.4292267 5.8980407 7.0206217 0.0018482653 7.1002136 62.244 62.244 62.244 0.0041030608 0.0010365485 0.00040518656
4600 1.4160092 5.9019877 7.0141871 0.0050227685 7.2304827 62.244 62.244 62.244 0.0041611202 0.005764734 0.0051424512
4700 1.37861 5.8826208 6.9654451 0.0035124303 7.116701 62.244 62.244 62.244 0.0079436662 0.00069676038 0.0018968642
4800 1.3775582 5.8917844 6.9737825 0.00067406862 7.00281 62.244 62.244 62.244 0.0010058199 0.00035582238 0.00066056358
4900 1.4215964 5.8938211 7.0104089 -0.00048994747 6.9893103 62.244 62.244 62.244 -0.00067798345 0.0053757544 -0.0061676133
5000 1.4066006 5.8998845 7.0046939 0.0033843577 7.1504345 62.244 62.244 62.244 0.011284317 -0.0049851816 0.0038539381
Loop time of 3.20721 on 4 procs for 5000 steps with 5600 atoms
Pair time (%) = 0.116136 (3.62109)
Bond time (%) = 0.0531921 (1.65852)
Neigh time (%) = 0.438128 (13.6607)
Comm time (%) = 0.246661 (7.69083)
Outpt time (%) = 0.00308365 (0.0961474)
Other time (%) = 2.35001 (73.2727)
Nlocal: 1400 ave 1889 max 911 min
Histogram: 1 1 0 0 0 0 0 0 1 1
Nghost: 650.75 ave 723 max 584 min
Histogram: 1 1 0 0 0 0 0 1 0 1
Neighs: 1275.5 ave 1907 max 726 min
Histogram: 2 0 0 0 0 0 0 0 1 1
Total # of neighbors = 5102
Ave neighs/atom = 0.911071
Ave special neighs/atom = 0.571429
Neighbor list builds = 757
Dangerous builds = 0
# Replace fix rigid and fix langevin with new ones
unfix 1
unfix 3
fix 3 tethers langevin 1.4 1.4 1.0 198450
# Test different integrators for rods
fix 1 rods rigid/nve molecule
800 rigid bodies with 4000 atoms
print "rigid/nve"
rigid/nve
run 1000
WARNING: Inconsistent image flags (../domain.cpp:645)
Memory usage per processor = 4.9921 Mbytes
Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
5000 1.4066006 5.8998845 7.0046939 0.032740437 8.4145959 62.244 62.244 62.244 0.045650084 0.034743967 0.017827261
5100 1.4217949 5.8923804 7.0091242 0.0086289093 7.380711 62.244 62.244 62.244 0.0055651416 0.01368451 0.0066370762
5200 1.4108746 5.9047641 7.0129305 0.0049647851 7.2267292 62.244 62.244 62.244 0.0046376956 0.0086302594 0.0016264003
5300 1.4067621 5.8876234 6.9925597 0.0027189828 7.1096473 62.244 62.244 62.244 0.0020158207 -0.00063477598 0.0067759036
5400 1.4293632 5.8838403 7.0065285 0.0092204598 7.4035893 62.244 62.244 62.244 0.0084019091 0.0099425199 0.0093169505
5500 1.4221951 5.8868259 7.003884 0.0078308214 7.3411028 62.244 62.244 62.244 0.0073406766 0.0097916953 0.0063600922
5600 1.4031432 5.8858207 6.9879145 0.001239457 7.0412893 62.244 62.244 62.244 0.0011109965 0.0023197155 0.00028765886
5700 1.4000575 5.883162 6.9828322 0.010499133 7.4349566 62.244 62.244 62.244 0.01198025 0.012641441 0.0068757094
5800 1.3722465 5.8848443 6.9626704 -0.00035914741 6.9472044 62.244 62.244 62.244 -0.0028690389 -0.00088916453 0.0026807612
5900 1.3734578 5.8841178 6.9628953 0.0065044666 7.2429973 62.244 62.244 62.244 0.0068963214 0.0094261457 0.0031909327
6000 1.3754553 5.8937449 6.9740914 0.0035762742 7.1280965 62.244 62.244 62.244 0.0028555765 0.0033314156 0.0045418303
Loop time of 0.71103 on 4 procs for 1000 steps with 5600 atoms
Pair time (%) = 0.0324474 (4.56343)
Bond time (%) = 0.0106753 (1.50138)
Neigh time (%) = 0.100071 (14.0741)
Comm time (%) = 0.0545349 (7.66984)
Outpt time (%) = 0.000602841 (0.0847842)
Other time (%) = 0.512699 (72.1065)
Nlocal: 1400 ave 1881 max 915 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Nghost: 668 ave 762 max 600 min
Histogram: 2 0 0 0 0 0 1 0 0 1
Neighs: 1269 ave 1827 max 647 min
Histogram: 1 1 0 0 0 0 0 0 0 2
Total # of neighbors = 5076
Ave neighs/atom = 0.906429
Ave special neighs/atom = 0.571429
Neighbor list builds = 154
Dangerous builds = 0
unfix 1
fix 1 rods rigid/nvt molecule temp 1.4 1.4 1.0
800 rigid bodies with 4000 atoms
print "rigid/nvt"
rigid/nvt
run 1000
WARNING: Inconsistent image flags (../domain.cpp:645)
Memory usage per processor = 4.9921 Mbytes
Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
6000 1.3754553 5.8937449 6.9740914 0.049674573 9.1132283 62.244 62.244 62.244 0.056393855 0.044956749 0.047673114
6100 1.3818996 5.8984681 6.9838762 0.00058645322 7.0091306 62.244 62.244 62.244 0.0029282001 -0.0010828799 -8.596054e-05
6200 1.4315931 5.8945239 7.0189637 0.0034484132 7.1674627 62.244 62.244 62.244 0.0058150828 0.00034494103 0.0041852159
6300 1.4553306 5.904541 7.0476252 0.0010038355 7.0908534 62.244 62.244 62.244 0.0018558228 -0.0024096116 0.0035652954
6400 1.4684339 5.8903917 7.0437678 0.0050340074 7.2605473 62.244 62.244 62.244 0.0081274355 0.0060258489 0.0009487377
6500 1.397466 5.8957046 6.9933393 0.0026494888 7.1074343 62.244 62.244 62.244 0.0025578255 0.0017879539 0.0036026871
6600 1.4017782 5.8966082 6.9976299 0.0059660342 7.2545454 62.244 62.244 62.244 0.0052881291 0.0059401179 0.0066698556
6700 1.4147355 5.8899121 7.001111 0.00034372887 7.015913 62.244 62.244 62.244 -0.00039811564 0.0042903128 -0.0028610106
6800 1.4026154 5.8846134 6.9862927 0.0058210004 7.2369625 62.244 62.244 62.244 0.0066928038 0.0053938331 0.0053763642
6900 1.4334896 5.8930688 7.0189981 0.00096971534 7.0607569 62.244 62.244 62.244 0.0014759985 0.005380295 -0.0039471475
7000 1.4183184 5.8899892 7.0040023 0.0065331422 7.2853391 62.244 62.244 62.244 0.0087688941 0.0045715326 0.0062589999
Loop time of 0.724545 on 4 procs for 1000 steps with 5600 atoms
Pair time (%) = 0.0333842 (4.60761)
Bond time (%) = 0.0107084 (1.47795)
Neigh time (%) = 0.0995998 (13.7465)
Comm time (%) = 0.0522026 (7.20488)
Outpt time (%) = 0.000613034 (0.0846095)
Other time (%) = 0.528037 (72.8784)
Nlocal: 1400 ave 1835 max 890 min
Histogram: 1 1 0 0 0 0 0 0 0 2
Nghost: 702.5 ave 810 max 574 min
Histogram: 1 0 0 0 1 0 0 1 0 1
Neighs: 1381.5 ave 1991 max 716 min
Histogram: 1 1 0 0 0 0 0 0 0 2
Total # of neighbors = 5526
Ave neighs/atom = 0.986786
Ave special neighs/atom = 0.571429
Neighbor list builds = 155
Dangerous builds = 0
unfix 1
compute myTemp all temp
fix 1 rods rigid/npt molecule temp 1.4 1.4 1.0 iso 0.05 0.05 1.0 dilate all
800 rigid bodies with 4000 atoms
print "rigid/npt iso"
rigid/npt iso
fix_modify 1 temp myTemp
run 1000
WARNING: Inconsistent image flags (../domain.cpp:645)
Memory usage per processor = 4.9921 Mbytes
Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
7000 1.4183184 5.8899892 7.0040023 0.0050486391 7.2214119 62.244 62.244 62.244 0.043816651 -0.087155941 0.058485207
7100 1.4038983 5.8814774 6.9841642 0.009993125 7.3679901 59.915655 59.915655 59.915655 0.0070735055 0.010976068 0.011929801
7200 1.4312073 5.8606903 6.984827 0.0089330912 7.2912768 57.700805 57.700805 57.700805 0.01156272 0.0074893368 0.0077472167
7300 1.4407415 5.8415009 6.9731262 0.011035789 7.313692 55.700862 55.700862 55.700862 0.010519024 0.0067474464 0.015840899
7400 1.4196359 5.8415108 6.9565587 0.0025417019 7.0274842 53.862756 53.862756 53.862756 0.0043954525 0.004824396 -0.0015947429
7500 1.4156145 5.8327435 6.9446329 0.010433473 7.2089087 52.152148 52.152148 52.152148 0.01179134 0.0055857749 0.013923305
7600 1.4180615 5.8188658 6.9326772 0.015609218 7.2939723 50.608446 50.608446 50.608446 0.0028724549 0.022210059 0.02174514
7700 1.4259294 5.8098966 6.9298877 0.0030559519 6.9948575 49.194626 49.194626 49.194626 0.0046696448 0.00055793026 0.0039402805
7800 1.411295 5.7988715 6.9073681 0.0092006473 7.0879075 47.897612 47.897612 47.897612 0.017128448 0.0054472316 0.0050262622
7900 1.4108742 5.7752582 6.8834242 0.00087414641 6.8993415 46.718678 46.718678 46.718678 0.0044372502 -0.00052897293 -0.001285838
8000 1.3910325 5.7775053 6.8700867 0.019735394 7.2031692 45.551007 45.551007 45.551007 0.012397847 0.021690086 0.02511825
Loop time of 1.04095 on 4 procs for 1000 steps with 5600 atoms
Pair time (%) = 0.0613976 (5.89824)
Bond time (%) = 0.0165009 (1.58518)
Neigh time (%) = 0.201774 (19.3837)
Comm time (%) = 0.0760022 (7.30125)
Outpt time (%) = 0.000428915 (0.0412043)
Other time (%) = 0.684844 (65.7904)
Nlocal: 1400 ave 1797 max 1000 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Nghost: 1040 ave 1186 max 930 min
Histogram: 1 0 1 0 1 0 0 0 0 1
Neighs: 2652 ave 3792 max 1522 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Total # of neighbors = 10608
Ave neighs/atom = 1.89429
Ave special neighs/atom = 0.571429
Neighbor list builds = 262
Dangerous builds = 0
unfix 1
fix 1 rods rigid/npt molecule temp 1.4 1.4 1.0 x 0.05 0.05 1.0 dilate all
800 rigid bodies with 4000 atoms
print "rigid/npt x"
rigid/npt x
run 1000
WARNING: Inconsistent image flags (../domain.cpp:645)
Memory usage per processor = 4.99592 Mbytes
Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
8000 1.3910325 5.7775053 6.8700867 0.068684018 8.0292954 45.551007 45.551007 45.551007 0.0075744454 0.11785739 0.080620215
8100 1.4160395 5.7676429 6.8798661 0.0065100016 6.9864766 44.198871 45.551007 45.551007 0.011695272 0.0040404036 0.0037943293
8200 1.4429338 5.7597227 6.8930699 0.0044623039 6.9639774 42.886955 45.551007 45.551007 0.015037624 -0.0047943681 0.0031436559
8300 1.4413276 5.7513302 6.8834158 0.010009783 7.0380516 41.694377 45.551007 45.551007 0.014564125 0.012896809 0.0025684155
8400 1.4343217 5.7515313 6.8781141 0.0072223957 6.986466 40.489955 45.551007 45.551007 0.0091249482 0.0056233713 0.0069188677
8500 1.4136692 5.751692 6.8620534 0.0096235568 7.0024139 39.364181 45.551007 45.551007 0.011711119 0.013318118 0.0038414335
8600 1.3994641 5.7464082 6.8456122 0.025028488 7.2002905 38.246529 45.551007 45.551007 0.021265819 0.025439388 0.028380257
8700 1.4138866 5.7179769 6.8285091 0.014028521 7.021982 37.222055 45.551007 45.551007 0.019904996 0.022260772 -8.0204045e-05
8800 1.3697378 5.7168466 6.7927023 0.02231094 7.092514 36.267933 45.551007 45.551007 0.02769865 0.012576894 0.026657276
8900 1.402393 5.7128653 6.8143699 0.02837253 7.1862185 35.372046 45.551007 45.551007 0.02762235 0.040370216 0.017125023
9000 1.431654 5.6938727 6.8183602 0.016130352 7.0241345 34.430181 45.551007 45.551007 0.0088192249 0.0091663636 0.030405467
Loop time of 1.08382 on 4 procs for 1000 steps with 5600 atoms
Pair time (%) = 0.0826703 (7.62768)
Bond time (%) = 0.0164793 (1.52048)
Neigh time (%) = 0.202493 (18.6832)
Comm time (%) = 0.0888866 (8.20123)
Outpt time (%) = 0.000417709 (0.0385405)
Other time (%) = 0.692874 (63.9288)
Nlocal: 1400 ave 1816 max 1003 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Nghost: 1106.75 ave 1237 max 962 min
Histogram: 1 0 0 0 0 2 0 0 0 1
Neighs: 3609 ave 5743 max 1869 min
Histogram: 2 0 0 0 0 0 0 1 0 1
Total # of neighbors = 14436
Ave neighs/atom = 2.57786
Ave special neighs/atom = 0.571429
Neighbor list builds = 192
Dangerous builds = 0
unfix 1
fix 1 rods rigid/nph molecule iso 0.05 0.05 1.0 dilate all
800 rigid bodies with 4000 atoms
print "rigid/nph iso"
rigid/nph iso
run 1000
WARNING: Inconsistent image flags (../domain.cpp:645)
Memory usage per processor = 4.99592 Mbytes
Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
9000 1.431654 5.6938727 6.8183602 0.01143345 6.9642163 34.430181 45.551007 45.551007 0.087625543 -0.18424224 0.13091705
9100 1.4696353 5.669441 6.8237607 0.02683122 7.1482512 33.82289 44.747564 44.747564 0.038188706 0.021753624 0.020551331
9200 1.4503489 5.6757074 6.8148788 0.021148084 7.0572895 33.223889 43.955088 43.955088 0.028893061 0.023573367 0.010977824
9300 1.4890502 5.6551355 6.8247047 0.032005229 7.1730611 32.655613 43.20326 43.20326 0.027960938 0.047252183 0.020802567
9400 1.4974788 5.6550122 6.8312016 0.022789713 7.0672131 32.118481 42.492636 42.492636 0.014186376 0.02731245 0.026870315
9500 1.4861129 5.6301004 6.7973625 0.056540979 7.3532565 31.566986 41.763011 41.763011 0.070975879 0.039997167 0.058649893
9600 1.4882551 5.6046579 6.7736025 0.013643963 6.9021339 31.120487 41.172295 41.172295 0.0054708323 0.017134071 0.018326985
9700 1.4721961 5.5861689 6.7425 0.046847392 7.1653218 30.679447 40.5888 40.5888 0.033912637 0.065035347 0.041594191
9800 1.4827559 5.5716195 6.7362449 0.032095321 7.0144242 30.268062 40.044538 40.044538 0.048655332 0.025995432 0.021635198
9900 1.476568 5.5566339 6.716399 0.037796165 7.0309954 29.862457 39.507925 39.507925 0.034991254 0.044450492 0.033946749
10000 1.4606684 5.5590139 6.7062906 0.011771017 6.8005705 29.482105 39.00472 39.00472 -0.0066083806 0.012698228 0.029223204
Loop time of 1.14607 on 4 procs for 1000 steps with 5600 atoms
Pair time (%) = 0.107624 (9.39068)
Bond time (%) = 0.0165663 (1.44549)
Neigh time (%) = 0.246527 (21.5107)
Comm time (%) = 0.0994916 (8.68113)
Outpt time (%) = 0.000405192 (0.035355)
Other time (%) = 0.675454 (58.9367)
Nlocal: 1400 ave 1725 max 1072 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Nghost: 1286.75 ave 1414 max 1166 min
Histogram: 1 0 0 1 0 0 1 0 0 1
Neighs: 5461 ave 7932 max 3039 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Total # of neighbors = 21844
Ave neighs/atom = 3.90071
Ave special neighs/atom = 0.571429
Neighbor list builds = 190
Dangerous builds = 0
unfix 1
fix 1 rods rigid/nph molecule x 0.05 0.05 1.0 y 0.05 0.05 1.0 couple xy dilate all
800 rigid bodies with 4000 atoms
print "rigid/nph xy couple"
rigid/nph xy couple
run 1000
WARNING: Inconsistent image flags (../domain.cpp:645)
Memory usage per processor = 4.99592 Mbytes
Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
10000 1.4606684 5.5590139 6.7062906 -0.054323908 6.2711839 29.482105 39.00472 39.00472 -0.13889514 0.022522203 -0.046598788
10100 1.4657219 5.5658034 6.7170494 0.046191264 7.078621 29.145622 38.559555 39.00472 0.041993444 0.057731099 0.038849248
10200 1.5086998 5.5537733 6.7387762 0.037571227 7.0249318 28.749452 38.035423 39.00472 0.059943553 0.01714367 0.035626459
10300 1.4942525 5.5348006 6.7084559 0.035441685 6.9720943 28.412097 37.589104 39.00472 0.058842839 0.029199467 0.01828275
10400 1.4835714 5.5161809 6.6814467 0.011614772 6.7654283 28.011918 37.059668 39.00472 0.0020323206 0.044104517 -0.011292523
10500 1.4822309 5.5103173 6.6745303 0.057714827 7.0812115 27.652821 36.584584 39.00472 0.080057627 0.041550212 0.051536644
10600 1.4815153 5.4966675 6.6603185 0.033053113 6.8888568 27.392359 36.239994 39.00472 0.042895505 0.034396997 0.021866837
10700 1.4777966 5.4994576 6.6601877 0.011268502 6.7364448 27.099624 35.852707 39.00472 0.019713922 -0.0036266081 0.017718191
10800 1.4876859 5.4727622 6.6412597 0.036949917 6.8864907 26.83719 35.505507 39.00472 0.040563603 0.044972283 0.025313864
10900 1.4960872 5.4500779 6.6251742 0.0012247499 6.6331413 26.569303 35.151093 39.00472 0.0023049747 0.01451802 -0.013148745
11000 1.4608347 5.4589178 6.6063252 -0.00321258 6.5857748 26.347448 34.857581 39.00472 0.0066852906 -0.0045030316 -0.011819999
Loop time of 1.19108 on 4 procs for 1000 steps with 5600 atoms
Pair time (%) = 0.133478 (11.2065)
Bond time (%) = 0.0166689 (1.39948)
Neigh time (%) = 0.258172 (21.6755)
Comm time (%) = 0.104376 (8.76311)
Outpt time (%) = 0.000403106 (0.0338438)
Other time (%) = 0.677981 (56.9216)
Nlocal: 1400 ave 1661 max 1127 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Nghost: 1414.25 ave 1494 max 1312 min
Histogram: 1 0 1 0 0 0 0 0 0 2
Neighs: 6643.25 ave 9132 max 4197 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Total # of neighbors = 26573
Ave neighs/atom = 4.74518
Ave special neighs/atom = 0.571429
Neighbor list builds = 169
Dangerous builds = 0