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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14609 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp
2016-02-15 18:04:59 +00:00
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318
examples/rigid/log.15May15.rigid.g++.1
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@ -1,318 +0,0 @@
LAMMPS (30 Apr 2015)
# 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
Neighbor list info ...
1 neighbor list requests
update every 1 steps, delay 10 steps, check yes
master list distance cutoff = 2.8
Memory usage per processor = 3.15778 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 -7.972284e-05 0 5269.5046 14.510657
2650 16733.017 1.7051479 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 7.2419352 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 1.2554429 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 7.8460621 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 -0.070934368 0 5269.4889 12.025288
3750 16737.731 0.20706558 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 -0.0002211587 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 -0.00039690666 0 5269.5189 12.011706
8500 16738.481 -0.0034646804 0 5269.5182 12.011643
8550 16738.483 -0.0045307409 0 5269.5178 12.011621
8600 16738.474 -0.00076532811 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 -0.00037652434 0 5269.5216 12.011692
9550 16738.493 -0.005315616 0 5269.5203 12.011611
9600 16738.549 -0.026814368 0 5269.5163 12.011415
9650 16738.765 -0.10191523 0 5269.5092 12.011013
9700 16735.041 1.0589885 0 5269.4979 12.062708
9750 16738.013 0.13550123 0 5269.5101 11.407245
9800 16738.512 -0.011620328 0 5269.5201 11.394974
9850 16738.489 -0.00067270523 0 5269.5237 11.395098
9900 16738.489 -0.00024984554 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 0.121942 on 1 procs for 10000 steps with 81 atoms
Pair time (%) = 0.00923467 (7.573)
Neigh time (%) = 0.0365384 (29.9637)
Comm time (%) = 0.00748825 (6.14083)
Outpt time (%) = 0.00112414 (0.921867)
Other time (%) = 0.0675566 (55.4006)
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

318
examples/rigid/log.15May15.rigid.g++.4
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@ -1,318 +0,0 @@
LAMMPS (30 Apr 2015)
# 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
Neighbor list info ...
1 neighbor list requests
update every 1 steps, delay 10 steps, check yes
master list distance cutoff = 2.8
Memory usage per processor = 3.1287 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 -7.9722832e-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 1.2554429 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 -0.070934368 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 -0.00039690663 0 5269.5189 12.011706
8500 16738.481 -0.0034646803 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 -0.00037652438 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 -0.10191523 0 5269.5092 12.011013
9700 16735.041 1.0589894 0 5269.4979 12.062708
9750 16738.013 0.13550109 0 5269.5101 11.407246
9800 16738.512 -0.011620327 0 5269.5201 11.394974
9850 16738.489 -0.00067270507 0 5269.5237 11.395098
9900 16738.489 -0.00024984555 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 0.132679 on 4 procs for 10000 steps with 81 atoms
Pair time (%) = 0.00307167 (2.31512)
Neigh time (%) = 0.0113522 (8.55614)
Comm time (%) = 0.0526423 (39.6765)
Outpt time (%) = 0.00284737 (2.14607)
Other time (%) = 0.0627652 (47.3061)
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

321
examples/rigid/log.15May15.rigid.poems.g++.1
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@ -1,321 +0,0 @@
LAMMPS (30 Apr 2015)
# 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
Neighbor list info ...
1 neighbor list requests
update every 1 steps, delay 10 steps, check yes
master list distance cutoff = 2.8
Memory usage per processor = 2.47028 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 45.317414 0 3681.1512 1.5988314
1250 18655.437 572.41453 0 3681.654 10.064078
1300 20780.781 217.36506 0 3680.8286 6.0538616
1350 20558.971 254.36482 0 3680.8601 -3.6773952
1400 21485.029 99.812921 0 3680.6511 -16.185473
1450 21771.107 52.15961 0 3680.6775 -2.4756673
1500 21520.948 93.503927 0 3680.3286 2.1023576
1550 21351.418 121.68137 0 3680.2511 5.5159947
1600 20778.805 216.92177 0 3680.0559 15.089188
1650 21477.638 100.21836 0 3679.8247 -1.1045746
1700 18501.339 596.47914 0 3680.0357 -15.679679
1750 18563.642 587.34785 0 3681.2882 33.532209
1800 19110.185 494.8234 0 3679.8543 18.024046
1850 21364.191 119.23545 0 3679.9339 2.5291103
1900 20146.626 322.14867 0 3679.9197 5.7313218
1950 20692.672 231.25325 0 3680.0319 4.2977763
2000 20943.904 189.11235 0 3679.7629 -22.645121
2050 19668.057 401.82994 0 3679.8394 3.6251916
2100 20280.442 299.76155 0 3679.8353 7.4807949
2150 19181.86 483.522 0 3680.4987 22.620507
2200 21300.161 130.70534 0 3680.7322 4.7102665
2250 20486.943 266.63931 0 3681.1299 -8.6456512
2300 18653.122 572.24819 0 3681.1018 -5.2637122
2350 21513.523 95.614901 0 3681.2021 -9.3621767
2400 21466.272 103.56446 0 3681.2765 -29.561368
2450 20100.105 332.27123 0 3682.2887 35.744287
2500 20764.395 221.6677 0 3682.4001 -12.468906
2550 20435.699 276.31055 0 3682.2603 -22.413697
2600 21466.467 104.53618 0 3682.2807 -10.078508
2650 20814.737 213.23892 0 3682.3617 5.1390411
2700 18565.761 588.3578 0 3682.6513 22.27664
2750 20772.36 220.1607 0 3682.2206 -7.9448198
2800 21018.563 179.10058 0 3682.1945 -7.0717829
2850 16789.412 884.21472 0 3682.4501 33.279015
2900 19304.363 464.75282 0 3682.1466 7.947554
2950 20513.758 263.07578 0 3682.0355 2.2361434
3000 20617.309 245.95251 0 3682.1706 -0.75213689
3050 18567.52 587.90473 0 3682.4914 -4.0112006
3100 18696.577 566.20617 0 3682.3023 -1.4814167
3150 19864.606 371.56078 0 3682.3284 8.9362836
3200 18902.643 532.04614 0 3682.4867 0.76630303
3250 21110.454 163.86212 0 3682.271 -1.6253894
3300 19369.939 454.05833 0 3682.3816 4.9066544
3350 19082.603 501.69905 0 3682.133 3.5982292
3400 19527.779 426.918 0 3681.5478 6.9612143
3450 19892.953 366.19989 0 3681.6921 3.0050426
3500 19708.981 396.84552 0 3681.6756 7.0757635
3550 20256.096 306.23937 0 3682.2554 -1.752138
3600 21289.889 133.93823 0 3682.253 -3.7462615
3650 18333.877 627.18028 0 3682.8264 -15.276791
3700 19829.133 377.33753 0 3682.1931 -6.269648
3750 20771.635 220.07171 0 3682.0109 -28.479036
3800 18373.813 619.79253 0 3682.0947 29.594781
3850 19320.99 461.92786 0 3682.0928 -5.3212101
3900 16119.825 995.68064 0 3682.3182 -8.4683118
3950 15556.948 1091.3655 0 3684.1902 20.98273
4000 20000.464 348.24891 0 3681.6596 7.1589745
4050 18870.219 536.59924 0 3681.6358 -3.7997025
4100 19889.518 367.49253 0 3682.4122 -14.091266
4150 15789.623 1051.3399 0 3682.9438 -4.4152389
4200 20548.889 256.83493 0 3681.6498 0.92234153
4250 20681.925 235.46113 0 3682.4487 -11.515773
4300 19330.404 460.80975 0 3682.5437 -22.351775
4350 19369.443 453.35405 0 3681.5945 29.418242
4400 20762.165 222.24133 0 3682.6021 2.6627047
4450 19984.657 350.71294 0 3681.4891 28.88731
4500 21167.58 154.25344 0 3682.1834 -3.0784322
4550 18133.576 660.73671 0 3682.9995 2.5305835
4600 19935.069 360.36826 0 3682.8798 2.4575034
4650 21413.76 113.86464 0 3682.8246 -5.1271547
4700 21716.333 63.609419 0 3682.9982 -2.4708049
4750 21352.947 124.36961 0 3683.1941 -0.29026265
4800 19043.788 508.8617 0 3682.8264 14.797006
4850 20516.121 263.78758 0 3683.1411 7.1348281
4900 20624.5 245.81827 0 3683.235 0.34708051
4950 20317.197 296.68937 0 3682.8889 -0.55065946
5000 18346.865 625.37246 0 3683.1832 7.3371413
5050 18867.53 538.49153 0 3683.0799 1.9249866
5100 18790.276 551.17224 0 3682.885 2.2333017
5150 20241.365 311.84683 0 3685.4076 -3.998004
5200 17685.058 739.76418 0 3687.2739 3.2835025
5250 18496.626 604.58166 0 3687.3526 -10.185776
5300 18420.042 617.82026 0 3687.8273 -16.392458
5350 18767.338 559.0349 0 3686.9246 4.5320767
5400 20423.245 284.90517 0 3688.7794 -8.6356656
5450 21080.398 176.18494 0 3689.5846 -16.450038
5500 16684.424 909.12643 0 3689.8637 49.94555
5550 20132.31 335.03663 0 3690.4216 -16.018038
5600 20430.923 285.17562 0 3690.3295 -5.0773675
5650 20479.943 276.55962 0 3689.8834 5.4334564
5700 20061.532 345.95553 0 3689.5441 -16.230658
5750 20523.759 268.92217 0 3689.5487 -4.4128812
5800 18900.356 537.65462 0 3687.7139 13.605549
5850 20280.502 310.27193 0 3690.3556 -4.7884959
5900 19050.26 515.66087 0 3690.7042 7.8864722
5950 19566.917 430.2997 0 3691.4525 31.715268
6000 18878.118 544.75449 0 3691.1076 -4.2415329
6050 19308.682 471.70734 0 3689.821 -10.561614
6100 18776.194 560.04764 0 3689.4133 -7.7286747
6150 21475.064 110.1508 0 3689.3281 -3.6506391
6200 19975 360.82675 0 3689.9934 10.282021
6250 21396.341 123.5341 0 3689.5909 -5.7215163
6300 18533.423 600.87422 0 3689.778 15.408027
6350 20653.152 247.19253 0 3689.3846 8.5607784
6400 19716.537 403.41487 0 3689.5044 13.165575
6450 21120.66 168.79838 0 3688.9084 -0.50382728
6500 19700.345 404.7155 0 3688.1064 13.941375
6550 10818.393 1892.037 0 3695.1025 38.423155
6600 18684.478 574.84755 0 3688.9273 5.9176985
6650 19219.732 486.04269 0 3689.3314 18.287659
6700 20058.587 344.88255 0 3687.9804 6.5372086
6750 21279.318 142.77333 0 3689.3264 2.498188
6800 20671.545 244.25024 0 3689.5078 -4.1356416
6850 21203.598 155.82001 0 3689.753 -0.0083061182
6900 21699.344 73.301497 0 3689.8588 -8.0309898
6950 20951.212 197.19403 0 3689.0627 0.76668303
7000 20166.275 329.02869 0 3690.0746 2.0083318
7050 21554.944 97.465792 0 3689.9564 -3.2420086
7100 20817.494 220.25476 0 3689.8372 0.17206182
7150 21481.11 109.84029 0 3690.0253 -3.6814741
7200 21266.824 145.53099 0 3690.0016 -2.060543
7250 19434.684 450.81331 0 3689.9273 9.4822765
7300 21246.525 148.96573 0 3690.0532 3.3208839
7350 19749.269 398.60049 0 3690.1454 1.0929662
7400 20354.792 297.70261 0 3690.168 1.547159
7450 19996.859 357.16723 0 3689.977 -0.68412025
7500 20179.628 326.53243 0 3689.8038 -2.4805507
7550 18765.184 561.65039 0 3689.1811 -1.7976428
7600 19457.496 447.04428 0 3689.9603 -1.9055522
7650 18206.823 655.57276 0 3690.0433 1.2797964
7700 19152.344 497.77422 0 3689.8315 18.145069
7750 21387.484 125.48654 0 3690.0673 -2.9915772
7800 18127.052 668.61425 0 3689.7896 9.044869
7850 21419.557 120.08889 0 3690.015 6.2651717
7900 21817.182 53.739819 0 3689.9368 -4.2387416
7950 18215.195 654.15494 0 3690.0208 -54.628049
8000 21523.503 102.58018 0 3689.8307 -4.84236
8050 20720.799 236.28689 0 3689.7535 -9.3725225
8100 21196.483 157.3232 0 3690.0704 -7.7222497
8150 20869.667 211.65308 0 3689.9309 -6.8438295
8200 17790.052 725.72497 0 3690.7336 -25.697688
8250 19634.94 417.71929 0 3690.2094 8.861604
8300 19135.784 500.92443 0 3690.2218 -3.1245167
8350 20191.718 324.93312 0 3690.2195 6.5736107
8400 20695.239 241.02378 0 3690.2302 -14.592221
8450 21793.857 57.609525 0 3689.9191 -11.509747
8500 21271.088 144.43102 0 3689.6124 -0.091587085
8550 20064.337 345.21754 0 3689.2737 9.5058471
8600 20282.86 308.2307 0 3688.7074 2.265529
8650 21223.055 151.24306 0 3688.419 1.7296834
8700 18875.342 542.42055 0 3688.3108 6.367148
8750 20922.65 201.55122 0 3688.6595 3.4208578
8800 21406.54 120.8539 0 3688.6106 1.8253729
8850 19868.524 377.05623 0 3688.477 16.327796
8900 20025.322 348.94892 0 3686.5025 17.063406
8950 21224.374 151.3567 0 3688.7524 -0.11028753
9000 21318.309 135.862 0 3688.9135 -0.50826819
9050 17538.618 768.00136 0 3691.1043 37.978645
9100 21247.861 147.84641 0 3689.1566 -6.7773259
9150 18455.677 613.08767 0 3689.0339 -3.4844751
9200 19486.859 441.03829 0 3688.8482 -18.602827
9250 21774.926 59.710446 0 3688.8648 -13.379919
9300 17628.877 750.72321 0 3688.8694 27.797974
9350 19827.334 383.85708 0 3688.4128 6.5459021
9400 20020.126 351.61742 0 3688.3051 -14.332562
9450 21596.338 88.904175 0 3688.2939 1.5779716
9500 18981.418 524.60141 0 3688.1711 5.4352409
9550 18652.616 579.05144 0 3687.8208 25.600729
9600 21198.037 155.23097 0 3688.2371 -3.3586596
9650 19958.317 361.32544 0 3687.7115 4.2910178
9700 19129.101 499.5993 0 3687.7828 13.267102
9750 21913.967 35.689587 0 3688.0174 -7.3222905
9800 21314.694 135.43794 0 3687.8869 -9.5613518
9850 20899.743 204.82802 0 3688.1185 -2.6321428
9900 20288.244 306.5013 0 3687.8753 3.6196618
9950 19271.015 475.88527 0 3687.7211 -1.8196764
10000 21122.24 167.82714 0 3688.2005 -3.8464842
Loop time of 3.72695 on 1 procs for 10000 steps with 81 atoms
Pair time (%) = 0.157488 (4.22567)
Neigh time (%) = 0.0999317 (2.68133)
Comm time (%) = 0.00889969 (0.238793)
Outpt time (%) = 0.00177169 (0.0475372)
Other time (%) = 3.45886 (92.8067)
Nlocal: 81 ave 81 max 81 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 95 ave 95 max 95 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 744 ave 744 max 744 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 744
Ave neighs/atom = 9.18519
Neighbor list builds = 992
Dangerous builds = 941
Please see the log.cite file for references relevant to this simulation

321
examples/rigid/log.15May15.rigid.poems.g++.4
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@ -1,321 +0,0 @@
LAMMPS (30 Apr 2015)
# Simple rigid body system
units lj
atom_style atomic
pair_style lj/cut 2.5
read_data data.rigid
orthogonal box = (-12 -12 -12) to (12 12 12)
1 by 2 by 2 MPI processor grid
reading atoms ...
81 atoms
velocity all create 100.0 4928459
# unconnected bodies
#group clump1 id <> 1 9
#group clump2 id <> 10 18
#group clump3 id <> 19 27
#group clump4 id <> 28 36
#group clump5 id <> 37 45
#group clump6 id <> 46 54
#group clump7 id <> 55 63
#group clump8 id <> 64 72
#group clump9 id <> 73 81
#fix 1 all rigid group 9 clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9
# 1 chain of connected bodies
group clump1 id <> 1 9
9 atoms in group clump1
group clump2 id <> 9 18
10 atoms in group clump2
group clump3 id <> 18 27
10 atoms in group clump3
group clump4 id <> 27 36
10 atoms in group clump4
group clump5 id <> 36 45
10 atoms in group clump5
group clump6 id <> 45 54
10 atoms in group clump6
group clump7 id <> 54 63
10 atoms in group clump7
group clump8 id <> 63 72
10 atoms in group clump8
group clump9 id <> 72 81
10 atoms in group clump9
fix 1 all poems group clump1 clump2 clump3 clump4 clump5 clump6 clump7 clump8 clump9
1 clusters, 9 bodies, 8 joints, 81 atoms
# 2 chains of connected bodies
#group clump1 id <> 1 9
#group clump2 id <> 9 18
#group clump3 id <> 18 27
#group clump4 id <> 27 36
#group clump5 id <> 37 45
#group clump6 id <> 45 54
#group clump7 id <> 54 63
#group clump8 id <> 63 72
#group clump9 id <> 72 81
#fix 1 all poems group clump1 clump2 clump3 clump4
#fix 2 all poems group clump5 clump6 clump7 clump8 clump9
neigh_modify exclude group clump1 clump1
neigh_modify exclude group clump2 clump2
neigh_modify exclude group clump3 clump3
neigh_modify exclude group clump4 clump4
neigh_modify exclude group clump5 clump5
neigh_modify exclude group clump6 clump6
neigh_modify exclude group clump7 clump7
neigh_modify exclude group clump8 clump8
neigh_modify exclude group clump9 clump9
thermo 100
#dump 1 all atom 50 dump.rigid.poems
#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 2 pad 5
#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 3 pad 5
timestep 0.0001
thermo 50
run 10000
Neighbor list info ...
1 neighbor list requests
update every 1 steps, delay 10 steps, check yes
master list distance cutoff = 2.8
Memory usage per processor = 2.4412 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 7.4384276
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 -1.2184718
1150 20849.582 206.01695 0 3680.9472 -0.8669916
1200 21815.003 45.317417 0 3681.1512 1.5988314
1250 18655.437 572.41453 0 3681.654 10.064076
1300 20780.781 217.36504 0 3680.8286 6.0538619
1350 20558.972 254.3648 0 3680.8601 -3.6773987
1400 21485.029 99.812949 0 3680.6511 -16.185471
1450 21771.108 52.15959 0 3680.6775 -2.4756681
1500 21520.948 93.503949 0 3680.3286 2.1023578
1550 21351.418 121.6814 0 3680.2511 5.5159978
1600 20778.805 216.92171 0 3680.0559 15.089182
1650 21477.639 100.2182 0 3679.8247 -1.1045944
1700 18501.343 596.47853 0 3680.0357 -15.67963
1750 18563.643 587.34767 0 3681.2882 33.532167
1800 19110.19 494.82264 0 3679.8543 18.024034
1850 21364.196 119.23454 0 3679.9339 2.5291491
1900 20146.643 322.14595 0 3679.9197 5.731152
1950 20692.67 231.25357 0 3680.0319 4.2977641
2000 20943.904 189.11223 0 3679.763 -22.645645
2050 19668.152 401.81407 0 3679.8394 3.6255896
2100 20280.572 299.73976 0 3679.8351 7.4809355
2150 19182.121 483.47905 0 3680.4992 22.615309
2200 21299.76 130.77281 0 3680.7327 4.7114154
2250 20487.784 266.4995 0 3681.1302 -8.6406776
2300 18655.125 571.91487 0 3681.1023 -5.2671669
2350 21512.614 95.766913 0 3681.2025 -9.3523428
2400 21467.773 103.31519 0 3681.2773 -29.600307
2450 20096.937 332.80159 0 3682.2911 35.890912
2500 20761.446 222.16118 0 3682.4022 -12.528127
2550 20409.6 280.67234 0 3682.2723 -22.277373
2600 21469.964 103.95529 0 3682.2826 -10.038267
2650 20708.138 231.00516 0 3682.3615 5.3659502
2700 18584.743 585.07862 0 3682.5357 21.785261
2750 20503.019 264.91491 0 3682.0847 -4.5583917
2800 20584.075 251.44664 0 3682.1258 -6.5084595
2850 17277.076 802.33356 0 3681.8462 15.519513
2900 19392.956 449.92915 0 3682.0885 -4.3829957
2950 18371.786 620.29835 0 3682.2626 7.2117592
3000 20412.015 280.25302 0 3682.2555 0.32492606
3050 20858.248 205.65269 0 3682.0273 4.5055715
3100 21561.094 88.438447 0 3681.9541 -3.7523733
3150 15471.278 1103.4497 0 3681.9961 -14.576367
3200 15386.973 1117.8815 0 3682.377 15.051163
3250 19741.037 392.04755 0 3682.2204 -2.6610995
3300 20870.191 203.58229 0 3681.9475 -4.7795545
3350 16648.228 907.66571 0 3682.3704 -8.9242511
3400 20104.016 331.58603 0 3682.2554 6.4783858
3450 21421.316 112.28228 0 3682.5015 -8.3484987
3500 19284.533 467.80739 0 3681.8962 -12.835452
3550 20160.125 322.4476 0 3682.4684 1.6574827
3600 16682.415 902.73752 0 3683.14 22.383296
3650 16762.19 890.14636 0 3683.8446 16.119412
3700 17858.568 707.37212 0 3683.8 -1.6582504
3750 20029.881 345.15986 0 3683.4733 -3.1415889
3800 20734 227.99158 0 3683.6582 -7.9580418
3850 20741.089 226.39408 0 3683.2423 8.3055765
3900 18671.251 571.42296 0 3683.2981 -3.7468858
3950 19547.209 423.14256 0 3681.0108 5.8312279
4000 19739.799 393.58799 0 3683.5544 18.604884
4050 20014.121 347.8176 0 3683.5044 9.93387
4100 20503.654 266.08691 0 3683.3626 8.1304118
4150 18309.702 632.29807 0 3683.9151 -0.0021480359
4200 20509.423 265.60353 0 3683.8408 -2.1658857
4250 21805.541 50.325935 0 3684.5828 1.082842
4300 21420.551 114.90431 0 3684.9962 -1.7985998
4350 20256.928 308.74187 0 3684.8966 -11.669472
4400 21633.488 79.629274 0 3685.2106 -0.96131785
4450 20793.327 219.66955 0 3685.2241 1.3752349
4500 18719.484 564.86754 0 3684.7816 2.6308699
4550 20966.335 190.68308 0 3685.0722 -18.587627
4600 19428.962 446.59618 0 3684.7565 -4.4051672
4650 18408.956 616.85009 0 3685.0095 2.777272
4700 19215.779 482.57562 0 3685.2054 19.441016
4750 20155.927 326.13401 0 3685.4553 6.1734993
4800 20918.085 199.31832 0 3685.6659 3.4407437
4850 20236.958 312.07276 0 3684.899 3.2612893
4900 21419.89 115.36879 0 3685.3505 -4.675951
4950 19707.901 401.14828 0 3685.7985 -10.730734
5000 19407.201 450.64394 0 3685.1775 17.518981
5050 21527.598 97.655186 0 3685.5882 -9.2294707
5100 21581.933 88.595517 0 3685.5843 -20.669485
5150 21161.214 158.48503 0 3685.3541 -2.7587502
5200 21166.679 157.24762 0 3685.0275 -18.180044
5250 20909.576 200.23507 0 3685.1644 -16.617303
5300 21911.746 33.236563 0 3685.1942 -5.8313967
5350 20857.303 208.87453 0 3685.0916 12.176312
5400 20958.96 191.96694 0 3685.1269 3.6116429
5450 20433.179 279.61178 0 3685.1415 13.324529
5500 19604.675 416.88499 0 3684.3308 21.536484
5550 18171.145 655.92915 0 3684.4534 -9.2269804
5600 19799.907 385.12116 0 3685.1056 22.202165
5650 19711.882 399.30581 0 3684.6194 15.93063
5700 17908.833 699.52405 0 3684.3295 0.35530356
5750 18606.518 583.538 0 3684.6243 -4.4540843
5800 21814.053 48.974627 0 3684.6501 -1.5206358
5850 18029.107 679.9357 0 3684.7868 12.137677
5900 21090.739 169.64502 0 3684.7682 -1.5051545
5950 21086.26 170.29075 0 3684.6674 -2.8164474
6000 21285.771 136.95608 0 3684.5846 -26.582739
6050 21203.994 150.87822 0 3684.8772 -2.6617226
6100 21481.553 104.57796 0 3684.8368 -16.524974
6150 20354.4 292.57675 0 3684.9767 2.7960207
6200 21326.591 130.75243 0 3685.1843 -1.5929194
6250 21505.087 101.07817 0 3685.2593 -3.7821931
6300 21296.273 135.6593 0 3685.0382 -0.55635908
6350 21295.389 135.86485 0 3685.0964 5.6614093
6400 16552.242 926.02655 0 3684.7336 14.177218
6450 20148.951 327.1151 0 3685.2736 7.4561085
6500 20962.151 191.79415 0 3685.486 -4.5436711
6550 21710.328 67.433972 0 3685.8219 -5.7678572
6600 20698.571 234.79099 0 3684.5528 -2.1984068
6650 17892.287 704.05484 0 3686.1026 11.525836
6700 21272.999 141.26589 0 3686.7657 0.44088069
6750 19558.993 426.46448 0 3686.2966 -16.907401
6800 20350.247 295.23951 0 3686.9474 1.1284348
6850 18665.05 573.5326 0 3684.3742 17.088712
6900 19769.199 392.1551 0 3687.0216 6.7562425
6950 19439.159 446.99138 0 3686.8512 -6.0105763
7000 19379.907 456.53471 0 3686.5192 -9.0505095
7050 19983.754 356.02523 0 3686.651 -5.6274314
7100 19867.737 375.47627 0 3686.7658 17.315482
7150 19258.794 477.47344 0 3687.2724 14.316676
7200 21282.428 139.96051 0 3687.0318 -0.77043459
7250 19828.603 381.98919 0 3686.7564 6.5142869
7300 20574.582 257.8245 0 3686.9215 -3.6547118
7350 21613.467 84.771568 0 3687.0161 -7.5188826
7400 21817.009 50.844944 0 3687.0131 -14.888864
7450 14937.538 1197.4257 0 3687.0154 1.7540499
7500 18326.914 632.40374 0 3686.8894 8.3397357
7550 13611.007 1418.4727 0 3686.9739 -19.379482
7600 19173.985 491.9482 0 3687.6123 17.229001
7650 16911.504 867.33649 0 3685.9204 -21.042834
7700 21752.116 61.143705 0 3686.4963 -10.344487
7750 20208.337 318.26355 0 3686.3197 13.385814
7800 21649.909 77.950987 0 3686.2692 -1.7911084
7850 20139.64 329.50319 0 3686.1098 -5.5805093
7900 21355.026 126.7642 0 3685.9352 -7.7062172
7950 21336.178 129.88925 0 3685.9188 -2.059298
8000 21047.596 177.71546 0 3685.6482 0.37963466
8050 19217.351 482.62331 0 3685.5152 6.5582595
8100 20499.057 268.7173 0 3685.2268 -1.1959737
8150 21494.301 102.83829 0 3685.2219 -1.6427647
8200 20074.928 339.19817 0 3685.0195 6.285123
8250 17335.157 793.47566 0 3682.6685 22.877381
8300 17340.544 794.62619 0 3684.7168 3.9147755
8350 20529.345 262.51162 0 3684.0691 4.031768
8400 18884.747 537.47827 0 3684.9361 22.853404
8450 20341.86 293.10484 0 3683.4148 0.33856656
8500 19300.282 467.58127 0 3684.2949 12.35507
8550 21631.936 78.254534 0 3683.5772 -10.992959
8600 20204.913 316.83233 0 3684.3178 20.74228
8650 21018.189 181.32054 0 3684.352 1.8412068
8700 20161.304 323.97907 0 3684.1964 -2.646629
8750 19081.79 504.00155 0 3684.2998 -10.088053
8800 20834.489 211.76247 0 3684.1773 14.896336
8850 20929.355 196.18335 0 3684.4092 -1.2602398
8900 21491.074 102.47788 0 3684.3235 -1.4696758
8950 20474.735 271.69461 0 3684.1504 -6.9489258
9000 21128.641 162.40732 0 3683.8474 -7.7928168
9050 18421.801 614.46442 0 3684.7646 24.40313
9100 19301.292 466.98873 0 3683.8707 4.4687046
9150 21575.705 88.213763 0 3684.1646 -0.94696984
9200 20004.776 350.05448 0 3684.1838 -7.3466605
9250 21384.079 120.14472 0 3684.1578 -8.3773844
9300 21980.599 20.702393 0 3684.1356 -12.666293
9350 21686.606 69.517984 0 3683.9524 -8.8366533
9400 20732.704 228.46247 0 3683.9131 -6.4080307
9450 19798.859 384.34696 0 3684.1568 7.6198484
9500 20270.695 305.22664 0 3683.6758 1.5862486
9550 16496.156 935.28481 0 3684.6441 15.001468
9600 20642.429 241.08853 0 3681.4934 -9.2159382
9650 21292.587 135.4474 0 3684.2119 -0.54770976
9700 18888.158 536.60518 0 3684.6315 5.3236926
9750 18750.018 559.35922 0 3684.3623 -9.9424949
9800 20544.772 259.71076 0 3683.8394 8.732202
9850 16698.125 901.90076 0 3684.9216 9.9553329
9900 21450.963 109.58687 0 3684.7474 -4.8001999
9950 20664.461 240.66995 0 3684.7468 -3.4840781
10000 18951.367 526.45428 0 3685.0155 21.512727
Loop time of 3.82591 on 4 procs for 10000 steps with 81 atoms
Pair time (%) = 0.0397754 (1.03963)
Neigh time (%) = 0.0267723 (0.699761)
Comm time (%) = 0.182709 (4.77556)
Outpt time (%) = 0.00539947 (0.141129)
Other time (%) = 3.57126 (93.3439)
Nlocal: 20.25 ave 81 max 0 min
Histogram: 3 0 0 0 0 0 0 0 0 1
Nghost: 46.25 ave 95 max 14 min
Histogram: 2 0 0 0 0 1 0 0 0 1
Neighs: 249.25 ave 997 max 0 min
Histogram: 3 0 0 0 0 0 0 0 0 1
Total # of neighbors = 997
Ave neighs/atom = 12.3086
Neighbor list builds = 993
Dangerous builds = 943
Please see the log.cite file for references relevant to this simulation

325
examples/rigid/log.15May15.rigid.poems2.g++.1
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@ -1,325 +0,0 @@
LAMMPS (30 Apr 2015)
# Simple rigid body system
units lj
atom_style atomic
pair_style lj/cut 2.5
read_data data.rigid
orthogonal box = (-12 -12 -12) to (12 12 12)
1 by 1 by 1 MPI processor grid
reading atoms ...
81 atoms
velocity all create 100.0 4928459
# unconnected bodies
#group clump1 id <> 1 9
#group clump2 id <> 10 18
#group clump3 id <> 19 27
#group clump4 id <> 28 36
#group clump5 id <> 37 45
#group clump6 id <> 46 54
#group clump7 id <> 55 63
#group clump8 id <> 64 72
#group clump9 id <> 73 81
#fix 1 all rigid group 9 clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9
# 1 chain of connected bodies
#group clump1 id <> 1 9
#group clump2 id <> 9 18
#group clump3 id <> 18 27
#group clump4 id <> 27 36
#group clump5 id <> 36 45
#group clump6 id <> 45 54
#group clump7 id <> 54 63
#group clump8 id <> 63 72
#group clump9 id <> 72 81
#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9
# 2 chains of connected bodies
group clump1 id <> 1 9
9 atoms in group clump1
group clump2 id <> 9 18
10 atoms in group clump2
group clump3 id <> 18 27
10 atoms in group clump3
group clump4 id <> 27 36
10 atoms in group clump4
group clump5 id <> 37 45
9 atoms in group clump5
group clump6 id <> 45 54
10 atoms in group clump6
group clump7 id <> 54 63
10 atoms in group clump7
group clump8 id <> 63 72
10 atoms in group clump8
group clump9 id <> 72 81
10 atoms in group clump9
fix 1 all poems group clump1 clump2 clump3 clump4
1 clusters, 4 bodies, 3 joints, 36 atoms
fix 2 all poems group clump5 clump6 clump7 clump8 clump9
1 clusters, 5 bodies, 4 joints, 45 atoms
neigh_modify exclude group clump1 clump1
neigh_modify exclude group clump2 clump2
neigh_modify exclude group clump3 clump3
neigh_modify exclude group clump4 clump4
neigh_modify exclude group clump5 clump5
neigh_modify exclude group clump6 clump6
neigh_modify exclude group clump7 clump7
neigh_modify exclude group clump8 clump8
neigh_modify exclude group clump9 clump9
thermo 100
#dump 1 all atom 50 dump.rigid.poems2
#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 2 pad 5
#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 3 pad 5
timestep 0.0001
thermo 50
run 10000
WARNING: More than one fix poems (../fix_poems.cpp:352)
WARNING: More than one fix poems (../fix_poems.cpp:352)
WARNING: One or more atoms are time integrated more than once (../modify.cpp:264)
Neighbor list info ...
1 neighbor list requests
update every 1 steps, delay 10 steps, check yes
master list distance cutoff = 2.8
Memory usage per processor = 3.03278 Mbytes
Step Temp E_pair E_mol TotEng Press
0 196.00047 3632.2347 0 3668.5311 -2.7403788
50 12167.633 1505.5478 0 3758.8133 35.125973
100 17556.978 512.66277 0 3763.9549 11.137534
150 19579.586 138.04942 0 3763.8987 -29.953971
200 19757.51 105.30542 0 3764.1036 -0.030645317
250 18218.374 390.10747 0 3763.8804 13.711001
300 19383.039 174.40688 0 3763.8586 5.7240693
350 20125.986 36.972611 0 3764.0071 1.9559205
400 18888.816 266.10975 0 3764.0386 9.6362168
450 19307.656 188.2511 0 3763.743 1.9326206
500 16331.197 738.56392 0 3762.8597 9.1715579
550 19318.722 186.16172 0 3763.7027 3.0115336
600 19455.268 161.20621 0 3764.0336 0.55208034
650 18487.011 340.03216 0 3763.5528 -8.0359122
700 17321.201 556.32471 0 3763.9545 -13.631751
750 18979.187 249.04389 0 3763.7082 -2.6072455
800 19342.456 181.85552 0 3763.7918 8.1918726
850 19070.641 232.19342 0 3763.7936 7.3148472
900 19478.873 156.65987 0 3763.8586 2.4284987
950 19912.415 76.437437 0 3763.9216 -1.4667227
1000 16003.749 802.39753 0 3766.0548 46.642188
1050 19859.583 86.64176 0 3764.3424 -2.1961943
1100 19229.575 203.61488 0 3764.6473 -10.632365
1150 18821.6 279.15861 0 3764.64 -0.89495035
1200 19392.695 173.59744 0 3764.8373 1.8508753
1250 16459.624 717.32104 0 3765.3995 33.478127
1300 19343.863 182.59043 0 3764.7874 0.75890736
1350 20019.643 57.503573 0 3764.8448 0.31444671
1400 18549.582 329.31436 0 3764.4221 10.738303
1450 15163.926 957.47585 0 3765.6103 -17.923459
1500 19223.688 204.15175 0 3764.0939 -1.6134531
1550 18147.996 404.12677 0 3764.8668 8.4194779
1600 18615.043 317.42467 0 3764.6548 -2.3288934
1650 20120.654 38.887913 0 3764.935 -8.7620277
1700 19450.907 162.98272 0 3765.0025 2.3254731
1750 19374.632 177.37966 0 3765.2744 8.9328774
1800 19424.404 167.93966 0 3765.0514 0.081230261
1850 17936.249 442.84231 0 3764.3699 6.6010636
1900 19982.595 64.406198 0 3764.8868 -2.9529813
1950 16215.852 761.91287 0 3764.8485 13.994708
2000 18584.422 322.12049 0 3763.68 7.1654003
2050 20107.965 41.025754 0 3764.723 -0.3109069
2100 20002.333 60.593017 0 3764.7288 -6.7919784
2150 16949.762 626.59623 0 3765.441 3.508941
2200 20010.953 58.808279 0 3764.5403 -10.862172
2250 18982.73 247.00892 0 3762.3292 -0.53807815
2300 18401.298 354.87973 0 3762.5274 1.0920554
2350 19390.524 172.9415 0 3763.7793 -3.3524932
2400 16080.801 786.38838 0 3764.3146 -16.200514
2450 18870.412 268.74976 0 3763.2705 11.197736
2500 19688.29 117.58223 0 3763.5618 4.382644
2550 18870.825 268.78678 0 3763.384 -5.6623656
2600 17019.35 611.70808 0 3763.4395 6.3109641
2650 18753.285 291.0596 0 3763.8902 2.4120296
2700 19742.456 107.20901 0 3763.2193 -0.33061303
2750 19522.438 148.16759 0 3763.4339 -1.6254851
2800 18304.801 372.55152 0 3762.3295 22.6368
2850 18465.36 343.48495 0 3762.9961 4.4169272
2900 20151.999 31.372926 0 3763.2245 1.2013699
2950 15498.143 892.80071 0 3762.8272 13.263724
3000 18728.301 294.65113 0 3762.855 8.1897838
3050 18538.466 330.25223 0 3763.3015 8.5865739
3100 19081.409 229.5907 0 3763.1849 -4.8573813
3150 18498.802 337.11548 0 3762.8195 1.0555321
3200 19925.897 73.358029 0 3763.339 -7.7325108
3250 19780.108 100.23785 0 3763.2209 -5.5974972
3300 19221.043 203.82387 0 3763.2763 4.2703251
3350 19025.292 240.11329 0 3763.3156 5.7708328
3400 18153.696 401.52086 0 3763.3164 21.076943
3450 18611.375 316.50396 0 3763.0548 -3.5484945
3500 19931.319 71.969274 0 3762.9543 1.8764978
3550 19747.562 106.05439 0 3763.0103 -2.5506186
3600 18491.39 338.4134 0 3762.7449 -4.0527808
3650 19757.998 104.19207 0 3763.0806 1.4865598
3700 20108.003 39.345514 0 3763.0498 0.062827129
3750 19222.505 203.28065 0 3763.0039 0.33719277
3800 19286.383 191.08831 0 3762.6406 -0.1826802
3850 19450.083 161.09138 0 3762.9587 -0.2708263
3900 18002.304 429.25655 0 3763.0166 -4.6832439
3950 17186.829 582.26502 0 3765.0111 55.816834
4000 16826.434 645.84974 0 3761.856 19.675962
4050 19227.526 202.18151 0 3762.8344 -0.2596098
4100 19908.792 76.084531 0 3762.8978 -2.796813
4150 17821.329 462.63065 0 3762.8768 13.069155
4200 19917.133 74.574998 0 3762.9329 -6.4181155
4250 19012.618 241.96787 0 3762.823 4.0847974
4300 19077.34 229.98133 0 3762.8221 4.324323
4350 19361.128 177.47406 0 3762.8681 -7.377974
4400 18565.044 324.95107 0 3762.9223 2.5229032
4450 19352.406 178.98756 0 3762.7665 0.10862717
4500 18482.218 340.15496 0 3762.788 12.518301
4550 18359.732 362.83749 0 3762.7879 3.7500902
4600 19623.618 128.71624 0 3762.7196 -1.1328521
4650 17565.707 509.99904 0 3762.9078 1.7135935
4700 19876.052 81.892814 0 3762.6431 0.32476108
4750 19022.676 239.92262 0 3762.6403 -0.24613022
4800 18862.685 269.24248 0 3762.3324 6.2733979
4850 19899.174 77.426145 0 3762.4584 0.42535238
4900 18250.865 382.72867 0 3762.5185 23.308462
4950 18895.847 263.22651 0 3762.4575 8.0634675
5000 19096.705 225.69358 0 3762.1204 3.6816481
5050 16546.294 698.91312 0 3763.0416 17.453618
5100 19501.208 151.20999 0 3762.5449 -1.1231291
5150 19479.879 155.00669 0 3762.3917 -3.983378
5200 17397.818 541.23039 0 3763.0485 6.1109992
5250 18564.869 324.10557 0 3762.0442 9.2244762
5300 16271.663 747.52374 0 3760.7947 -6.5256602
5350 19831.418 89.851887 0 3762.3367 -2.3453958
5400 18723.697 294.67435 0 3762.0256 4.6822081
5450 19547.28 142.21934 0 3762.086 -5.5243408
5500 19415.447 166.68729 0 3762.1404 -9.5658991
5550 18492.721 337.54773 0 3762.1256 6.5184903
5600 19391.389 171.14375 0 3762.1416 -0.53835361
5650 18503.465 334.62751 0 3761.1951 4.6580363
5700 18153.344 399.91064 0 3761.6409 12.851587
5750 18342.297 365.14769 0 3761.8694 2.7148176
5800 19583.241 135.64969 0 3762.1758 -1.089608
5850 15967.283 804.18382 0 3761.088 11.278762
5900 19040.271 235.35509 0 3761.3312 5.1352158
5950 17920.962 443.17951 0 3761.8762 4.9621366
6000 19100.92 224.3946 0 3761.602 -9.537589
6050 17982.119 432.3251 0 3762.3472 -2.851617
6100 16233.096 755.46191 0 3761.5908 25.113316
6150 18316.543 370.01118 0 3761.9635 -1.7445703
6200 18483.464 339.13282 0 3761.9966 -2.0857447
6250 18609.406 315.56032 0 3761.7467 -12.289208
6300 17167.919 582.68212 0 3761.9264 -3.8263397
6350 17870.329 452.58116 0 3761.9013 -3.3843134
6400 19309.717 186.11786 0 3761.9913 -4.9462739
6450 17964.073 435.39924 0 3762.0794 12.272972
6500 18772.847 285.61959 0 3762.0727 6.7928648
6550 18915.116 259.41365 0 3762.213 -4.1449761
6600 19446.628 161.18763 0 3762.415 -2.1906581
6650 16348.787 734.99282 0 3762.546 -9.9624546
6700 19066.684 231.43863 0 3762.3061 -5.362833
6750 14890.323 1004.547 0 3762.0143 37.373013
6800 18235.19 385.253 0 3762.1401 0.21012662
6850 16447.997 716.11276 0 3762.0382 -9.2095411
6900 18343.362 364.81902 0 3761.7379 10.417932
6950 16014.084 797.13348 0 3762.7046 6.7906777
7000 19120.393 221.29236 0 3762.1059 -1.3461375
7050 18055.409 418.30136 0 3761.8957 1.5772317
7100 18407.231 353.41868 0 3762.1652 0.61071769
7150 18728.136 293.64021 0 3761.8136 5.1649654
7200 17706.628 483.07628 0 3762.0815 18.000708
7250 19349.505 178.89673 0 3762.1385 2.540201
7300 20016.293 55.389159 0 3762.1101 -1.5793163
7350 19398.573 169.86661 0 3762.1949 -5.060123
7400 19466.526 157.37407 0 3762.2862 1.7158273
7450 18440.348 347.09196 0 3761.9712 12.781963
7500 19989.907 60.555934 0 3762.3906 -1.5033319
7550 19667.28 120.27403 0 3762.363 -3.3502366
7600 18497.707 336.15863 0 3761.66 1.7887539
7650 17901.957 447.17282 0 3762.3501 0.016725252
7700 19758.725 103.3129 0 3762.3361 -23.534448
7750 19443.957 161.6532 0 3762.386 -10.323924
7800 19776.178 100.1773 0 3762.4324 6.0854422
7850 19242.512 198.86705 0 3762.2952 5.2823659
7900 19499.929 151.30366 0 3762.4017 12.299911
7950 19630.317 127.19541 0 3762.4393 8.0799632
8000 19872.384 82.421129 0 3762.4923 2.2126691
8050 17747.038 476.27982 0 3762.7683 -7.7042786
8100 18832.654 274.78106 0 3762.3095 13.882157
8150 19949.814 68.09711 0 3762.5072 -0.54410896
8200 17555.866 511.02517 0 3762.1115 6.2471175
8250 17800.1 465.9992 0 3762.314 13.583485
8300 19755.224 103.89732 0 3762.2721 -1.487243
8350 17583.61 506.17539 0 3762.3995 -9.7819128
8400 18529.003 330.75623 0 3762.0532 14.731228
8450 20155.902 29.797078 0 3762.3716 -8.5711085
8500 18047.548 420.54645 0 3762.685 7.3875118
8550 19790.794 97.493375 0 3762.4553 -3.3427911
8600 19997.902 59.172074 0 3762.4874 3.3479688
8650 19987.319 61.148363 0 3762.5037 -1.889232
8700 19363.91 176.41833 0 3762.3276 -9.4291288
8750 18712.689 296.3979 0 3761.7107 5.9221369
8800 19783.17 98.860518 0 3762.4105 -3.5262066
8850 18796.049 281.60057 0 3762.3504 -8.2913002
8900 16738.277 662.62261 0 3762.3035 8.5838631
8950 17869.613 452.25006 0 3761.4377 11.561101
9000 18682.512 302.27997 0 3762.0043 3.8878724
9050 17513.759 518.50265 0 3761.7914 23.05778
9100 17500.686 521.57944 0 3762.4473 -2.8435751
9150 19645.683 124.43597 0 3762.5254 -3.0193092
9200 18898.897 262.76552 0 3762.5612 3.5891701
9250 20114.279 37.614866 0 3762.4813 -0.58120871
9300 19562.613 139.54073 0 3762.2468 -3.2630158
9350 19679.811 118.05865 0 3762.468 -3.4644363
9400 19297.384 188.84527 0 3762.4349 0.40498037
9450 18267.029 379.52581 0 3762.309 -0.13762867
9500 19951.072 67.63844 0 3762.2814 -7.575539
9550 19134.562 218.46835 0 3761.9057 -1.9626244
9600 19089.093 227.29178 0 3762.3089 -1.94158
9650 16964.603 620.71289 0 3762.3061 16.987042
9700 18846.881 271.3129 0 3761.4761 3.4458802
9750 19309.225 186.0142 0 3761.7966 9.4048627
9800 16359.704 733.51007 0 3763.0849 15.870164
9850 19958.532 66.203725 0 3762.2282 6.0043645
9900 19864.564 83.502384 0 3762.1253 -0.65360617
9950 18996.789 244.25101 0 3762.1749 -2.4961826
10000 17933.494 441.33587 0 3762.3532 -6.0731708
Loop time of 3.82367 on 1 procs for 10000 steps with 81 atoms
Pair time (%) = 0.112469 (2.9414)
Neigh time (%) = 0.0745587 (1.94993)
Comm time (%) = 0.0103831 (0.271549)
Outpt time (%) = 0.00174665 (0.0456801)
Other time (%) = 3.62451 (94.7914)
Nlocal: 81 ave 81 max 81 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 71 ave 71 max 71 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 612 ave 612 max 612 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 612
Ave neighs/atom = 7.55556
Neighbor list builds = 989
Dangerous builds = 906
Please see the log.cite file for references relevant to this simulation

325
examples/rigid/log.15May15.rigid.poems2.g++.4
View File

@ -1,325 +0,0 @@
LAMMPS (30 Apr 2015)
# Simple rigid body system
units lj
atom_style atomic
pair_style lj/cut 2.5
read_data data.rigid
orthogonal box = (-12 -12 -12) to (12 12 12)
1 by 2 by 2 MPI processor grid
reading atoms ...
81 atoms
velocity all create 100.0 4928459
# unconnected bodies
#group clump1 id <> 1 9
#group clump2 id <> 10 18
#group clump3 id <> 19 27
#group clump4 id <> 28 36
#group clump5 id <> 37 45
#group clump6 id <> 46 54
#group clump7 id <> 55 63
#group clump8 id <> 64 72
#group clump9 id <> 73 81
#fix 1 all rigid group 9 clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9
# 1 chain of connected bodies
#group clump1 id <> 1 9
#group clump2 id <> 9 18
#group clump3 id <> 18 27
#group clump4 id <> 27 36
#group clump5 id <> 36 45
#group clump6 id <> 45 54
#group clump7 id <> 54 63
#group clump8 id <> 63 72
#group clump9 id <> 72 81
#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9
# 2 chains of connected bodies
group clump1 id <> 1 9
9 atoms in group clump1
group clump2 id <> 9 18
10 atoms in group clump2
group clump3 id <> 18 27
10 atoms in group clump3
group clump4 id <> 27 36
10 atoms in group clump4
group clump5 id <> 37 45
9 atoms in group clump5
group clump6 id <> 45 54
10 atoms in group clump6
group clump7 id <> 54 63
10 atoms in group clump7
group clump8 id <> 63 72
10 atoms in group clump8
group clump9 id <> 72 81
10 atoms in group clump9
fix 1 all poems group clump1 clump2 clump3 clump4
1 clusters, 4 bodies, 3 joints, 36 atoms
fix 2 all poems group clump5 clump6 clump7 clump8 clump9
1 clusters, 5 bodies, 4 joints, 45 atoms
neigh_modify exclude group clump1 clump1
neigh_modify exclude group clump2 clump2
neigh_modify exclude group clump3 clump3
neigh_modify exclude group clump4 clump4
neigh_modify exclude group clump5 clump5
neigh_modify exclude group clump6 clump6
neigh_modify exclude group clump7 clump7
neigh_modify exclude group clump8 clump8
neigh_modify exclude group clump9 clump9
thermo 100
#dump 1 all atom 50 dump.rigid.poems2
#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 2 pad 5
#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 3 pad 5
timestep 0.0001
thermo 50
run 10000
WARNING: More than one fix poems (../fix_poems.cpp:352)
WARNING: More than one fix poems (../fix_poems.cpp:352)
WARNING: One or more atoms are time integrated more than once (../modify.cpp:264)
Neighbor list info ...
1 neighbor list requests
update every 1 steps, delay 10 steps, check yes
master list distance cutoff = 2.8
Memory usage per processor = 3.0037 Mbytes
Step Temp E_pair E_mol TotEng Press
0 196.00047 3632.2347 0 3668.5311 -2.7403788
50 12167.633 1505.5478 0 3758.8133 35.125973
100 17556.978 512.66277 0 3763.9549 11.137534
150 19579.586 138.04942 0 3763.8987 -29.953971
200 19757.51 105.30542 0 3764.1036 -0.030645317
250 18218.374 390.10747 0 3763.8804 13.711001
300 19383.039 174.40688 0 3763.8586 5.7240693
350 20125.986 36.972611 0 3764.0071 1.9559205
400 18888.816 266.10975 0 3764.0386 9.6362168
450 19307.656 188.2511 0 3763.743 1.9326206
500 16331.197 738.56392 0 3762.8597 9.1715579
550 19318.722 186.16172 0 3763.7027 3.0115336
600 19455.268 161.20621 0 3764.0336 0.55208034
650 18487.011 340.03216 0 3763.5528 -8.0359122
700 17321.201 556.32471 0 3763.9545 -13.631751
750 18979.187 249.04389 0 3763.7082 -2.6072455
800 19342.456 181.85552 0 3763.7918 8.1918726
850 19070.641 232.19342 0 3763.7936 7.3148472
900 19478.873 156.65987 0 3763.8586 2.4284987
950 19912.415 76.437437 0 3763.9216 -1.4667227
1000 16003.749 802.39753 0 3766.0548 46.642188
1050 19859.583 86.64176 0 3764.3424 -2.1961943
1100 19229.575 203.61488 0 3764.6473 -10.632365
1150 18821.6 279.15861 0 3764.64 -0.89495035
1200 19392.695 173.59744 0 3764.8373 1.8508753
1250 16459.624 717.32104 0 3765.3995 33.478127
1300 19343.863 182.59043 0 3764.7874 0.75890736
1350 20019.643 57.503573 0 3764.8448 0.31444671
1400 18549.582 329.31436 0 3764.4221 10.738303
1450 15163.926 957.47585 0 3765.6103 -17.923459
1500 19223.688 204.15176 0 3764.0939 -1.6134529
1550 18147.996 404.12677 0 3764.8668 8.4194781
1600 18615.043 317.42468 0 3764.6548 -2.3288926
1650 20120.654 38.887908 0 3764.935 -8.7620288
1700 19450.907 162.98267 0 3765.0025 2.3254739
1750 19374.631 177.3797 0 3765.2744 8.9328773
1800 19424.404 167.93965 0 3765.0514 0.081228843
1850 17936.227 442.84645 0 3764.3699 6.6011251
1900 19982.595 64.406244 0 3764.8868 -2.952971
1950 16215.818 761.91942 0 3764.8486 13.994877
2000 18584.433 322.11846 0 3763.6801 7.1653695
2050 20107.965 41.025796 0 3764.723 -0.31089763
2100 20002.329 60.593879 0 3764.7288 -6.7919882
2150 16949.817 626.58598 0 3765.4409 3.5087505
2200 20010.954 58.8082 0 3764.5403 -10.862143
2250 18982.732 247.00854 0 3762.3293 -0.53812607
2300 18401.276 354.88369 0 3762.5274 1.0921058
2350 19390.535 172.93951 0 3763.7793 -3.3524354
2400 16080.475 786.44896 0 3764.3146 -16.201558
2450 18870.293 268.77171 0 3763.2704 11.199749
2500 19688.508 117.54164 0 3763.5617 4.3806994
2550 18870.328 268.87896 0 3763.3841 -5.6641099
2600 17020.211 611.54841 0 3763.4394 6.3081434
2650 18748.838 291.88478 0 3763.8917 2.4175163
2700 19743.991 106.92945 0 3763.224 -0.33916964
2750 19525.446 147.60906 0 3763.4324 -1.6251174
2800 18257.411 381.40184 0 3762.4038 23.39495
2850 18496.796 337.65425 0 3762.9868 4.3657735
2900 20163.418 29.253902 0 3763.2203 1.4431917
2950 16823.317 646.69817 0 3762.1273 4.9041552
3000 19223.007 203.2529 0 3763.069 4.0414458
3050 17391.02 542.93746 0 3763.4968 15.139863
3100 19205.6 206.57791 0 3763.1705 4.8519241
3150 19835.659 90.247763 0 3763.5179 -14.900053
3200 18962.776 251.5838 0 3763.2089 -13.706561
3250 19418.837 167.29058 0 3763.3716 -2.0866468
3300 18628.291 313.69067 0 3763.3742 5.9919715
3350 17465.974 529.14439 0 3763.5841 14.122593
3400 18488.661 339.6186 0 3763.4448 21.526798
3450 19163.152 214.26098 0 3762.9928 4.1888096
3500 18000.27 429.81789 0 3763.2011 5.4734485
3550 19582.423 136.71887 0 3763.0935 -2.5335675
3600 19634.325 127.2219 0 3763.208 -1.9728322
3650 19428.114 165.40707 0 3763.2059 -2.3318779
3700 19861.116 85.356944 0 3763.3414 -3.9097609
3750 19337.239 182.43992 0 3763.4102 -3.3559651
3800 19493.146 153.40349 0 3763.2453 -0.71089657
3850 18607.616 317.74889 0 3763.6037 3.475832
3900 19719.59 111.5553 0 3763.3313 0.58876668
3950 19756.661 104.5522 0 3763.1931 3.7526698
4000 17904.708 447.1673 0 3762.854 12.270654
4050 19588.087 135.80435 0 3763.2279 0.94578945
4100 19065.901 232.38235 0 3763.1048 -2.7495195
4150 18775.075 286.2257 0 3763.0915 -3.7039858
4200 18800.725 281.46601 0 3763.0817 0.15619543
4250 19732.687 108.90618 0 3763.1075 3.0865861
4300 18278.151 377.63653 0 3762.4794 1.5768601
4350 17915.757 445.4804 0 3763.2133 -3.7040484
4400 15987.794 802.41575 0 3763.1183 22.252078
4450 19302.37 188.69495 0 3763.2079 0.91081327
4500 20039.32 52.304099 0 3763.2893 -2.0828905
4550 19535.953 145.4374 0 3763.2064 -3.3804255
4600 19700.723 114.79823 0 3763.0803 -1.1761163
4650 17804.641 465.85788 0 3763.0136 7.5947192
4700 19913.881 75.240289 0 3762.996 -2.1100557
4750 19982.484 62.535995 0 3762.996 -4.5821237
4800 17400.76 540.21707 0 3762.58 -5.8418778
4850 19199.88 206.90989 0 3762.4433 3.4536341
4900 19173.92 212.11327 0 3762.8392 5.0387071
4950 19236.635 200.57537 0 3762.9152 -1.4932783
5000 19077.616 230.04967 0 3762.9415 4.3742655
5050 19893.763 78.909747 0 3762.94 -1.5796711
5100 18884.746 265.68301 0 3762.8583 2.2767949
5150 17417.096 537.54036 0 3762.9286 -2.8632555
5200 18247.844 383.60092 0 3762.8312 10.384179
5250 19494.107 152.60532 0 3762.6251 -4.7617287
5300 18739.781 292.46206 0 3762.7919 23.210048
5350 19310.938 186.62363 0 3762.7232 14.895327
5400 19540.39 144.14287 0 3762.7336 6.094624
5450 20074.459 45.247888 0 3762.7403 -2.0871835
5500 19986.377 61.668045 0 3762.849 -2.4551918
5550 19038.904 237.07578 0 3762.7987 5.4250813
5600 19439.124 163.1438 0 3762.9816 4.1291468
5650 19480.321 155.58325 0 3763.0501 -3.5308058
5700 19869.291 83.651379 0 3763.1497 -7.8661592
5750 19991.447 61.068554 0 3763.1884 -6.8473586
5800 19454.072 160.36805 0 3762.9739 1.527662
5850 17994.409 430.95597 0 3763.2539 -5.6078082
5900 19209.794 205.74997 0 3763.1193 8.4113055
5950 19046.427 236.06321 0 3763.1793 10.463356
6000 19409.899 168.95271 0 3763.3785 2.542067
6050 18068.174 417.35443 0 3763.3125 10.498199
6100 19549.253 143.21885 0 3763.4509 2.3075797
6150 18464.719 344.0303 0 3763.4228 0.46469762
6200 19811.205 94.62725 0 3763.3689 1.2382763
6250 18715.36 297.26445 0 3763.0718 -3.4541762
6300 17115.664 594.09913 0 3763.6666 4.2065564
6350 18155.927 400.71764 0 3762.9264 1.1521258
6400 19873.093 83.169067 0 3763.3716 0.16383592
6450 19991.88 61.13218 0 3763.3321 -1.3008128
6500 19434.416 164.40698 0 3763.3728 -13.593422
6550 19855.253 86.645329 0 3763.544 -0.85704037
6600 19251.141 198.41152 0 3763.4376 4.3027745
6650 19741.815 107.69047 0 3763.582 4.994835
6700 19633.466 127.69333 0 3763.5203 6.3677145
6750 16231.353 757.83705 0 3763.6431 -1.5978692
6800 18863.396 270.1114 0 3763.3329 -11.915909
6850 19644.779 125.29421 0 3763.2163 -1.151217
6900 18883.642 266.06889 0 3763.0397 -4.3950749
6950 19042.364 236.54144 0 3762.9052 5.5718878
7000 18351.868 364.38028 0 3762.8743 7.8958273
7050 19981.031 62.840667 0 3763.0316 -5.8572298
7100 19796.372 97.073665 0 3763.0685 -3.5178361
7150 19805.385 95.235221 0 3762.899 -2.5481726
7200 18722.055 295.86113 0 3762.9084 13.826356
7250 19537.304 144.54234 0 3762.5616 1.2288666
7300 18787.328 283.49504 0 3762.6299 9.0044469
7350 18886.005 265.52121 0 3762.9295 6.6791881
7400 19891.864 79.239278 0 3762.9178 -2.3882842
7450 18164.752 399.07065 0 3762.9137 3.9400481
7500 18702.612 299.582 0 3763.0286 4.7987316
7550 19884.986 80.231665 0 3762.6365 -0.75016515
7600 19549.059 142.16243 0 3762.3586 -2.1035756
7650 18223.668 387.9047 0 3762.658 -17.064339
7700 19428.4 164.79531 0 3762.6473 -2.8342541
7750 19239.584 199.93029 0 3762.8163 3.1746033
7800 19458.005 159.46176 0 3762.7961 1.714515
7850 18320.308 369.77051 0 3762.4202 2.1422976
7900 18817.415 278.04812 0 3762.7546 0.94492621
7950 19892.761 79.115928 0 3762.9606 1.4948501
8000 19592.344 134.7639 0 3762.9758 -1.8520224
8050 19316.109 185.70579 0 3762.7631 -4.8061205
8100 19867.017 83.850395 0 3762.9277 -3.496391
8150 19129.936 220.29802 0 3762.8789 -2.8357376
8200 18449.554 346.30415 0 3762.8883 1.4417837
8250 18405.197 354.49049 0 3762.8602 6.7020283
8300 18310.437 372.25376 0 3763.0755 3.9043508
8350 18842.702 273.55075 0 3762.94 -10.987272
8400 18574.308 323.33378 0 3763.0204 12.008785
8450 15368.628 918.21692 0 3764.2591 34.80292
8500 18432.887 349.54013 0 3763.0378 0.00064258465
8550 15777.73 841.79263 0 3763.5945 15.473699
8600 17205.381 576.4515 0 3762.6331 2.3985544
8650 19773.742 101.48276 0 3763.2869 2.3978892
8700 19059.824 232.99716 0 3762.5941 5.2611349
8750 19006.086 243.41125 0 3763.0568 4.7880403
8800 19492.691 153.0188 0 3762.7763 1.9118755
8850 19625.883 128.44474 0 3762.8675 3.4157389
8900 19916.97 74.635094 0 3762.9629 -10.157254
8950 16012.956 798.16801 0 3763.5302 16.904998
9000 19364.051 177.00354 0 3762.9389 -13.373346
9050 19133.929 219.61882 0 3762.9389 -7.3824392
9100 18657.168 307.85939 0 3762.8905 9.3071421
9150 17975.904 434.21548 0 3763.0867 6.9609506
9200 19075.282 230.41699 0 3762.8767 7.0961232
9250 20115.276 37.578674 0 3762.6298 1.8678552
9300 18195.486 393.20682 0 3762.7413 13.272552
9350 19617.155 129.85893 0 3762.6653 -2.0849447
9400 19276.325 193.03425 0 3762.724 -2.8963555
9450 18642.803 310.4759 0 3762.8467 3.407984
9500 19175.951 211.72785 0 3762.8298 -0.39025564
9550 17669.191 490.85942 0 3762.9319 5.3867954
9600 18481.199 340.29485 0 3762.7391 8.9004886
9650 20091.442 42.504743 0 3763.1422 -1.3206133
9700 19651.405 124.04835 0 3763.1975 1.4000525
9750 19138.245 219.03637 0 3763.1558 5.8352794
9800 19189.146 209.67958 0 3763.2251 6.214691
9850 19899.376 78.096337 0 3763.166 -0.75102404
9900 19447.247 161.27279 0 3762.6149 -6.4166376
9950 19807.083 95.152663 0 3763.1309 -0.88933698
10000 18972.157 249.56342 0 3762.9258 1.9189241
Loop time of 3.98302 on 4 procs for 10000 steps with 81 atoms
Pair time (%) = 0.0302114 (0.758506)
Neigh time (%) = 0.0209532 (0.526064)
Comm time (%) = 0.130531 (3.27719)
Outpt time (%) = 0.00436562 (0.109606)
Other time (%) = 3.79696 (95.3286)
Nlocal: 20.25 ave 37 max 0 min
Histogram: 1 0 1 0 0 0 0 0 0 2
Nghost: 17.75 ave 33 max 4 min
Histogram: 2 0 0 0 0 0 0 0 1 1
Neighs: 144.75 ave 356 max 0 min
Histogram: 2 0 0 0 0 0 1 0 0 1
Total # of neighbors = 579
Ave neighs/atom = 7.14815
Neighbor list builds = 994
Dangerous builds = 958
Please see the log.cite file for references relevant to this simulation

399
examples/rigid/log.15May15.rigid.tnr.g++.1
View File

@ -1,399 +0,0 @@
LAMMPS (30 Apr 2015)
# 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
Neighbor list info ...
1 neighbor list requests
update every 1 steps, delay 0 steps, check yes
master list distance cutoff = 2.8
Memory usage per processor = 6.99131 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 0.0058394292 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 0.0057709635 0.0044949165 0.0038341296
2400 1.4213285 5.9472214 7.0635988 0.010197674 7.5027414 62.244 62.244 62.244 0.008373826 0.0090537939 0.013165402
2500 1.4153808 5.9421661 7.0538718 0.00015906306 7.0607216 62.244 62.244 62.244 0.002351621 -0.0019814986 0.00010706677
2600 1.4014223 5.9431386 7.0438807 0.0070733749 7.3484816 62.244 62.244 62.244 0.0054143871 0.010055843 0.0057498948
2700 1.4138077 5.9369067 7.047377 0.0024268842 7.1518859 62.244 62.244 62.244 0.0052918436 0.0014960353 0.00049277371
2800 1.432192 5.9347676 7.0596777 0.0077670448 7.3941501 62.244 62.244 62.244 0.012668421 0.0059113033 0.0047214106
2900 1.3938659 5.921023 7.01583 0.0053751198 7.2472989 62.244 62.244 62.244 0.0020490372 0.0076566093 0.006419713
3000 1.390221 5.9205014 7.0124455 -0.0010750977 6.9661485 62.244 62.244 62.244 0.0019519817 -0.0041878885 -0.00098938611
3100 1.4205722 5.9178284 7.0336117 0.0098735475 7.4587965 62.244 62.244 62.244 0.0040973361 0.012167268 0.013356039
3200 1.398418 5.9150349 7.0134173 0.0061541841 7.2784351 62.244 62.244 62.244 0.0067621815 0.011952563 -0.00025219251
3300 1.4269859 5.9148727 7.0356937 0.0060623879 7.2967584 62.244 62.244 62.244 0.012956234 -2.4806661e-05 0.0052557362
3400 1.434286 5.9356705 7.0622253 0.00027315892 7.0739884 62.244 62.244 62.244 -0.00054959866 0.0052526278 -0.0038835524
3500 1.4416809 5.9228153 7.0551783 0.0083382977 7.4142506 62.244 62.244 62.244 0.007399393 0.0030328007 0.014582699
3600 1.4136063 5.9039442 7.0142562 0.0019712004 7.0991421 62.244 62.244 62.244 -0.00032316149 0.0035029874 0.0027337752
3700 1.4333819 5.9120101 7.0378548 0.0071287182 7.3448389 62.244 62.244 62.244 0.0064768218 0.0046765361 0.010232797
3800 1.3659481 5.9032873 6.9761663 -0.0054033416 6.7434821 62.244 62.244 62.244 -0.0073943479 -0.0082831992 -0.00053247772
3900 1.3963222 5.9042998 7.0010361 0.0053310264 7.2306062 62.244 62.244 62.244 0.0081855739 0.0048806019 0.0029269034
4000 1.4125482 5.9060665 7.0155474 0.0028450296 7.138063 62.244 62.244 62.244 0.0052588294 0.00072395285 0.0025523065
4100 1.3943951 5.9040875 6.9993102 0.0058050223 7.2492919 62.244 62.244 62.244 0.0060579697 0.0024782584 0.0088788387
4200 1.4249768 5.8906371 7.0098801 0.0030210669 7.1399763 62.244 62.244 62.244 0.006174431 -0.002079586 0.0049683557
4300 1.3899801 5.8966397 6.9883947 0.0057285402 7.2350829 62.244 62.244 62.244 0.0049048136 0.0021882328 0.010092574
4400 1.4414352 5.898628 7.0307981 0.0050932552 7.2501291 62.244 62.244 62.244 0.0057941393 0.0037951842 0.0056904421
4500 1.4092913 5.8922803 6.9992031 0.0012238869 7.0519073 62.244 62.244 62.244 0.0042907674 0.0014412643 -0.0020603711
4600 1.3779868 5.8928757 6.9752105 0.0020701322 7.0643566 62.244 62.244 62.244 0.0029283254 -0.0031683908 0.006450462
4700 1.4084635 5.9098782 7.0161508 -0.00052129502 6.9937023 62.244 62.244 62.244 -0.0018460523 -0.0018286314 0.0021107986
4800 1.4393258 5.9148464 7.0453597 0.015311954 7.7047386 62.244 62.244 62.244 0.014718813 0.01801777 0.013199278
4900 1.4500008 5.9076899 7.0465879 0.0075111779 7.3700419 62.244 62.244 62.244 0.0091865271 0.0080981174 0.0052488891
5000 1.4279632 5.9111567 7.0327453 -0.0014189553 6.9716408 62.244 62.244 62.244 -0.0046013754 0.0019937576 -0.001649248
Loop time of 6.44689 on 1 procs for 5000 steps with 5600 atoms
Pair time (%) = 0.521767 (8.09331)
Bond time (%) = 0.242588 (3.76286)
Neigh time (%) = 1.82742 (28.3457)
Comm time (%) = 0.157429 (2.44194)
Outpt time (%) = 0.00350118 (0.054308)
Other time (%) = 3.69419 (57.3018)
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: 5254 ave 5254 max 5254 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 5254
Ave neighs/atom = 0.938214
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
Memory usage per processor = 6.99131 Mbytes
Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
5000 1.4279632 5.9111567 7.0327453 0.027874409 8.2331015 62.244 62.244 62.244 0.018992956 0.039655696 0.024974575
5100 1.439608 5.9052128 7.0359478 0.0060989863 7.2985885 62.244 62.244 62.244 0.0087364157 0.004022839 0.0055377041
5200 1.4120672 5.9102569 7.01936 0.0064301432 7.2962614 62.244 62.244 62.244 0.0082738077 0.0038925667 0.0071240551
5300 1.4452434 5.8842166 7.0193778 0.008172419 7.3713068 62.244 62.244 62.244 0.0077715647 0.0068924406 0.0098532518
5400 1.4170243 5.887522 7.0005186 0.0008656658 7.0377968 62.244 62.244 62.244 -9.1800583e-05 -0.0020237513 0.0047125493
5500 1.4209082 5.8758921 6.9919394 0.0093634084 7.395156 62.244 62.244 62.244 0.0088769348 0.0087092521 0.010504038
5600 1.4132978 5.8798939 6.9899636 0.0014877766 7.0540317 62.244 62.244 62.244 -0.0023427923 0.004559371 0.002246751
5700 1.4065053 5.887541 6.9922756 0.0028083452 7.1132114 62.244 62.244 62.244 0.0025188632 0.000510969 0.0053952035
5800 1.4079051 5.8940739 6.999908 0.0015946158 7.0685769 62.244 62.244 62.244 0.0037830287 0.00021751956 0.00078329927
5900 1.4076047 5.8941577 6.9997558 0.005189853 7.2232465 62.244 62.244 62.244 -0.00093244616 0.0096403542 0.0068616509
6000 1.4322772 5.8903539 7.0153309 0.00029752476 7.0281432 62.244 62.244 62.244 0.001913333 -0.00073790796 -0.00028285075
Loop time of 1.35444 on 1 procs for 1000 steps with 5600 atoms
Pair time (%) = 0.145285 (10.7266)
Bond time (%) = 0.0492971 (3.63967)
Neigh time (%) = 0.397092 (29.3178)
Comm time (%) = 0.0317581 (2.34474)
Outpt time (%) = 0.00065136 (0.0480907)
Other time (%) = 0.730356 (53.9232)
Nlocal: 5600 ave 5600 max 5600 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1347 ave 1347 max 1347 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 5399 ave 5399 max 5399 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 5399
Ave neighs/atom = 0.964107
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
Memory usage per processor = 6.99131 Mbytes
Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
6000 1.4322772 5.8903539 7.0153309 0.012980585 7.574314 62.244 62.244 62.244 0.058317363 0.0073619377 -0.026737547
6100 1.4199699 5.8764035 6.9917138 0.0054065567 7.2245364 62.244 62.244 62.244 0.0092276454 0.0019623806 0.005029644
6200 1.3976825 5.8924426 6.9902474 0.0004390082 7.0091524 62.244 62.244 62.244 -0.0023073118 -0.00049925474 0.0041235912
6300 1.4077283 5.8847362 6.9904313 0.0066398301 7.2763625 62.244 62.244 62.244 0.0058018933 0.0091933882 0.0049242089
6400 1.3749203 5.8817073 6.9616336 0.0074967166 7.2844648 62.244 62.244 62.244 0.012281889 0.0039781604 0.0062301007
6500 1.3467096 5.8881263 6.9458946 -0.00011926206 6.9407588 62.244 62.244 62.244 0.0030721983 -0.0013265855 -0.002103399
6600 1.3646558 5.8739857 6.9458497 0.0056064173 7.1872789 62.244 62.244 62.244 0.0059660118 0.0057680329 0.0050852071
6700 1.392725 5.8836119 6.9775228 0.0025583772 7.0876942 62.244 62.244 62.244 0.0030974509 0.0018499704 0.0027277104
6800 1.4017002 5.9015884 7.0025488 0.0039067256 7.1707842 62.244 62.244 62.244 0.0068315449 0.0020054024 0.0028832295
6900 1.4136756 5.8914708 7.0018372 0.005175385 7.2247049 62.244 62.244 62.244 0.0028462217 0.009405517 0.0032744161
7000 1.4286618 5.8935692 7.0157065 0.0062967875 7.2868652 62.244 62.244 62.244 0.0047257503 0.0093417536 0.0048228587
Loop time of 1.50622 on 1 procs for 1000 steps with 5600 atoms
Pair time (%) = 0.15995 (10.6193)
Bond time (%) = 0.0535221 (3.5534)
Neigh time (%) = 0.431443 (28.6441)
Comm time (%) = 0.0377467 (2.50605)
Outpt time (%) = 0.00105238 (0.0698688)
Other time (%) = 0.822509 (54.6074)
Nlocal: 5600 ave 5600 max 5600 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1284 ave 1284 max 1284 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 5677 ave 5677 max 5677 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 5677
Ave neighs/atom = 1.01375
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
Memory usage per processor = 6.99131 Mbytes
Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
7000 1.4286618 5.8935692 7.0157065 0.032107544 8.3983542 62.244 62.244 62.244 0.0040119822 0.040455544 0.051855105
7100 1.4709107 5.8870981 7.0424197 0.019698532 7.6954221 57.045709 57.045709 57.045709 0.012930036 0.020495433 0.025670125
7200 1.5163014 5.8421234 7.0330969 0.018918793 7.4624535 50.277182 50.277182 50.277182 0.017832308 0.02668088 0.012243191
7300 1.5675512 5.7752788 7.0065063 0.02287049 7.3825189 45.15491 45.15491 45.15491 0.019317818 0.024266569 0.025027083
7400 1.5432894 5.7512252 6.9633963 0.024351591 7.2723284 41.416611 41.416611 41.416611 0.032039305 0.022247464 0.018768005
7500 1.5510339 5.7073864 6.9256404 0.030706866 7.2413185 38.612893 38.612893 38.612893 0.04157713 0.012507079 0.038036388
7600 1.5435609 5.6657445 6.8781288 0.03187398 7.1535577 36.440727 36.440727 36.440727 0.036502896 0.022097075 0.037021969
7700 1.5862733 5.6141666 6.8600993 0.053474714 7.2612259 34.762178 34.762178 34.762178 0.035691782 0.06016314 0.064569222
7800 1.5106894 5.6005849 6.7871505 0.028896219 6.982719 33.59041 33.59041 33.59041 0.031167851 0.013090267 0.042430539
7900 1.472566 5.5634394 6.7200611 0.092340877 7.2955261 32.679168 32.679168 32.679168 0.060527481 0.10093222 0.11556293
8000 1.4805391 5.5132684 6.6761526 0.040035619 6.9105042 32.003919 32.003919 32.003919 0.04381615 0.023706176 0.052584532
Loop time of 3.11801 on 1 procs for 1000 steps with 5600 atoms
Pair time (%) = 0.384178 (12.3213)
Bond time (%) = 0.0740471 (2.37482)
Neigh time (%) = 1.42301 (45.6384)
Comm time (%) = 0.0729508 (2.33966)
Outpt time (%) = 0.000980854 (0.0314577)
Other time (%) = 1.16284 (37.2944)
Nlocal: 5600 ave 5600 max 5600 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 2963 ave 2963 max 2963 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 25797 ave 25797 max 25797 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 25797
Ave neighs/atom = 4.60661
Ave special neighs/atom = 0.571429
Neighbor list builds = 334
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
Memory usage per processor = 6.99518 Mbytes
Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
8000 1.4805391 5.5132684 6.6761526 0.10591497 7.2961342 32.003919 32.003919 32.003919 -0.0085253101 0.12196602 0.20430422
8100 1.4629588 5.5087415 6.6578173 0.080159269 7.1245058 31.831354 32.003919 32.003919 0.078046473 0.088201582 0.074229751
8200 1.4061729 5.5008938 6.6053673 0.038080967 6.8240633 31.398913 32.003919 32.003919 0.041554276 0.038085252 0.034603372
8300 1.4225542 5.4730766 6.5904167 0.071241779 6.992772 30.878537 32.003919 32.003919 0.068190354 0.076631686 0.068903297
8400 1.4344356 5.4772885 6.6039608 0.044141975 6.8495696 30.421029 32.003919 32.003919 0.031058774 0.039890974 0.061476178
8500 1.4377845 5.4485066 6.5778092 0.04242205 6.8099428 29.91769 32.003919 32.003919 0.053013546 0.050003453 0.02424915
8600 1.4339418 5.4280263 6.5543108 0.0048261176 6.58031 29.453954 32.003919 32.003919 -0.0020411927 0.005967365 0.010552181
8700 1.4284879 5.4273043 6.549305 0.058717611 6.8609844 29.021604 32.003919 32.003919 0.09927212 0.02309782 0.053782894
8800 1.3993066 5.4243917 6.5234721 0.030638337 6.683965 28.639961 32.003919 32.003919 0.08972583 0.0089328704 -0.0067436909
8900 1.4429241 5.3850352 6.5183748 0.0053167016 6.5458205 28.223699 32.003919 32.003919 0.052590681 -0.031563606 -0.0050769701
9000 1.41963 5.3772308 6.4922741 0.040105311 6.6961497 27.793622 32.003919 32.003919 0.070575176 0.0044551641 0.045285594
Loop time of 2.92265 on 1 procs for 1000 steps with 5600 atoms
Pair time (%) = 0.579087 (19.8137)
Bond time (%) = 0.0733221 (2.50875)
Neigh time (%) = 1.06745 (36.5233)
Comm time (%) = 0.0534718 (1.82956)
Outpt time (%) = 0.000686407 (0.0234857)
Other time (%) = 1.14864 (39.3012)
Nlocal: 5600 ave 5600 max 5600 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 3244 ave 3244 max 3244 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 30929 ave 30929 max 30929 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 30929
Ave neighs/atom = 5.52304
Ave special neighs/atom = 0.571429
Neighbor list builds = 165
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
Memory usage per processor = 6.99518 Mbytes
Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
9000 1.41963 5.3772308 6.4922741 0.054032922 6.7669508 27.793622 32.003919 32.003919 0.36183473 -0.1011685 -0.098567468
9100 1.468276 5.3693533 6.5226054 0.062009135 6.8364521 27.753087 31.957243 31.957243 0.072952506 0.067965393 0.045109506
9200 1.4790176 5.3498933 6.5115824 0.068306349 6.8531758 27.642255 31.829623 31.829623 0.057719204 0.083928825 0.063271019
9300 1.4685339 5.3439444 6.4973991 0.012381058 6.5578428 27.421331 31.575232 31.575232 0.018937907 0.0065076203 0.011697646
9400 1.4675871 5.3321417 6.4848528 0.056515448 6.7525582 27.146928 31.259261 31.259261 0.035834387 0.047161137 0.086550819
9500 1.4464119 5.3137665 6.4498455 0.043906827 6.6517871 26.881604 30.953745 30.953745 0.031891513 0.065507153 0.034321816
9600 1.4541889 5.284445 6.4266325 0.046471589 6.6332098 26.578003 30.604153 30.604153 0.0041035598 0.071274602 0.064036606
9700 1.4577034 5.2493866 6.3943346 0.045073503 6.5909605 26.41175 30.412715 30.412715 0.018293408 0.069031147 0.047895953
9800 1.4701089 5.2202499 6.3749417 0.055758411 6.6108197 26.142656 30.102857 30.102857 0.045171706 0.039488766 0.082614761
9900 1.4518855 5.2148116 6.3551898 0.011510897 6.4028899 25.963345 29.896384 29.896384 0.0060934464 0.010841773 0.017597473
10000 1.4445828 5.2098073 6.3444498 0.075197507 6.654918 25.931556 29.859779 29.859779 0.08350416 0.066240185 0.075848177
Loop time of 3.17816 on 1 procs for 1000 steps with 5600 atoms
Pair time (%) = 0.696246 (21.9072)
Bond time (%) = 0.0757198 (2.3825)
Neigh time (%) = 1.18728 (37.3574)
Comm time (%) = 0.059092 (1.85932)
Outpt time (%) = 0.000643969 (0.0202623)
Other time (%) = 1.15918 (36.4733)
Nlocal: 5600 ave 5600 max 5600 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 3635 ave 3635 max 3635 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 38235 ave 38235 max 38235 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 38235
Ave neighs/atom = 6.82768
Ave special neighs/atom = 0.571429
Neighbor list builds = 165
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
Memory usage per processor = 6.999 Mbytes
Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
10000 1.4445828 5.2098073 6.3444498 0.001962567 6.3525526 25.931556 29.859779 29.859779 0.18484796 -0.22902272 0.050062455
10100 1.4368894 5.2096239 6.3382235 0.10403552 6.7662753 25.886842 29.808292 29.859779 0.12565247 0.094955776 0.091498324
10200 1.4231669 5.2080497 6.3258711 0.086173671 6.682435 25.959905 29.892423 29.859779 0.11480457 0.12471881 0.018997629
10300 1.4334516 5.1992954 6.3251949 -0.0076414301 6.2932457 26.095439 30.048488 29.859779 0.00870511 -0.0049134764 -0.026715924
10400 1.4408912 5.1980613 6.3298041 0.070774329 6.6314048 26.345108 30.335978 29.859779 0.061559356 0.075929557 0.074834076
10500 1.4299517 5.1990298 6.3221802 0.077553868 6.6569567 26.515356 30.532016 29.859779 0.11568876 0.063812738 0.053160106
10600 1.439113 5.1937953 6.3241415 0.024333431 6.4286629 26.449816 30.456548 29.859779 0.035925567 0.023132021 0.013942706
10700 1.4379108 5.1704548 6.2998567 0.06126476 6.5597578 26.285754 30.267632 29.859779 0.074214186 0.040233796 0.069346299
10800 1.4358912 5.1798018 6.3076174 0.10549358 6.747456 26.058856 30.006363 29.859779 0.1992503 0.046346044 0.070884395
10900 1.4470038 5.1528383 6.2893823 0.045720444 6.4780533 25.92502 29.852253 29.859779 0.041394051 0.026837211 0.068930071
11000 1.437397 5.1841678 6.3131661 0.070020768 6.6023557 25.935798 29.864664 29.859779 0.11790932 0.072745235 0.019407746
Loop time of 3.17023 on 1 procs for 1000 steps with 5600 atoms
Pair time (%) = 0.745401 (23.5125)
Bond time (%) = 0.0734169 (2.31582)
Neigh time (%) = 1.15738 (36.5077)
Comm time (%) = 0.0571702 (1.80334)
Outpt time (%) = 0.000647068 (0.0204108)
Other time (%) = 1.13622 (35.8402)
Nlocal: 5600 ave 5600 max 5600 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 3799 ave 3799 max 3799 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 39646 ave 39646 max 39646 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 39646
Ave neighs/atom = 7.07964
Ave special neighs/atom = 0.571429
Neighbor list builds = 158
Dangerous builds = 0

399
examples/rigid/log.15May15.rigid.tnr.g++.4
View File

@ -1,399 +0,0 @@
LAMMPS (30 Apr 2015)
# 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
Neighbor list info ...
1 neighbor list requests
update every 1 steps, delay 0 steps, check yes
master list distance cutoff = 2.8
Memory usage per processor = 6.96454 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 0.00016862131 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 -0.00063825026
2500 1.4200762 5.9359254 7.0513193 0.0028319649 7.1732722 62.244 62.244 62.244 -0.00030414203 0.0039571831 0.0048428538
2600 1.3876469 5.9249124 7.0148347 -0.0017777224 6.9382806 62.244 62.244 62.244 -0.00047616392 -0.0025484917 -0.0023085116
2700 1.4099941 5.916763 7.0242378 0.0070716263 7.3287634 62.244 62.244 62.244 0.012628756 0.0053812867 0.0032048359
2800 1.4444643 5.9283432 7.0628925 0.0019400024 7.1464349 62.244 62.244 62.244 0.0014895079 0.0046367397 -0.00030624055
2900 1.3902832 5.9152516 7.0072446 -0.002166221 6.9139606 62.244 62.244 62.244 -0.0012374412 -0.00056403267 -0.004697189
3000 1.3711706 5.922146 6.9991271 0.011101505 7.4771914 62.244 62.244 62.244 0.011063833 0.012093026 0.010147657
3100 1.3569137 5.9171753 6.9829583 -0.002826677 6.8612331 62.244 62.244 62.244 -0.0069507252 0.0010084399 -0.0025377458
3200 1.4004275 5.905939 7.0058998 0.005439467 7.2401397 62.244 62.244 62.244 0.010352184 0.0057594148 0.00020680265
3300 1.3641217 5.9145275 6.985972 -0.0027212811 6.8687855 62.244 62.244 62.244 -0.00065933677 -0.0057713008 -0.0017332057
3400 1.3868722 5.9059546 6.9952684 0.0092591256 7.3939943 62.244 62.244 62.244 0.010690877 0.010752519 0.006333981
3500 1.3939169 5.8992292 6.9940762 0.0074340028 7.3142068 62.244 62.244 62.244 0.010137307 0.0044252569 0.0077394447
3600 1.3982507 5.9219461 7.0201971 0.005679459 7.2647718 62.244 62.244 62.244 0.0023367243 0.008059221 0.0066424317
3700 1.4019908 5.9059957 7.0071843 0.0065915477 7.2910363 62.244 62.244 62.244 0.0049554109 0.010827005 0.0039922268
3800 1.3960736 5.902079 6.99862 0.0027763588 7.1181784 62.244 62.244 62.244 -0.0015907217 0.0025862003 0.0073335977
3900 1.4352825 5.8986215 7.025959 0.003498268 7.176605 62.244 62.244 62.244 0.0030416681 0.0027739509 0.0046791851
4000 1.4121845 5.907903 7.0170983 0.005046232 7.2344043 62.244 62.244 62.244 0.0045542682 0.0064113499 0.0041730779
4100 1.3989578 5.9082397 7.0070461 0.00042880001 7.0255115 62.244 62.244 62.244 0.0025735184 0.0025181486 -0.003805267
4200 1.3998829 5.8998147 6.9993477 0.0042777376 7.18356 62.244 62.244 62.244 0.0013744091 0.00646996 0.0049888436
4300 1.4076022 5.9044509 7.010047 0.0066789366 7.2976622 62.244 62.244 62.244 0.0073610616 0.0048139129 0.0078618353
4400 1.4161075 5.9064331 7.0187096 -0.0011844267 6.9677046 62.244 62.244 62.244 -0.0019088313 -0.0037556503 0.0021112015
4500 1.4292243 5.8980093 7.0205884 0.0018500416 7.1002567 62.244 62.244 62.244 0.0041144085 0.0010160497 0.00041966655
4600 1.3958775 5.8943133 6.9907003 0.0041485723 7.1693504 62.244 62.244 62.244 0.0033999287 0.0041620406 0.0048837475
4700 1.3856614 5.8886847 6.9770475 0.0013150314 7.0336767 62.244 62.244 62.244 -0.00051753674 0.0030875481 0.0013750828
4800 1.401683 5.9023505 7.0032974 0.002504877 7.1111649 62.244 62.244 62.244 0.0016543718 -0.0001813413 0.0060416007
4900 1.446628 5.9050553 7.0413042 -0.0026645902 6.9265589 62.244 62.244 62.244 -0.00069368076 -0.0073984763 9.8386402e-05
5000 1.4387091 5.9077604 7.0377893 0.0049468048 7.2508137 62.244 62.244 62.244 0.0042902506 0.0046715523 0.0058786114
Loop time of 3.20601 on 4 procs for 5000 steps with 5600 atoms
Pair time (%) = 0.128921 (4.02124)
Bond time (%) = 0.0596074 (1.85924)
Neigh time (%) = 0.646461 (20.164)
Comm time (%) = 0.247998 (7.73541)
Outpt time (%) = 0.00292659 (0.0912844)
Other time (%) = 2.1201 (66.1288)
Nlocal: 1400 ave 1868 max 905 min
Histogram: 1 1 0 0 0 0 0 0 0 2
Nghost: 648.25 ave 688 max 598 min
Histogram: 1 0 0 1 0 0 0 0 1 1
Neighs: 1202.5 ave 1821 max 698 min
Histogram: 2 0 0 0 0 0 0 1 0 1
Total # of neighbors = 4810
Ave neighs/atom = 0.858929
Ave special neighs/atom = 0.571429
Neighbor list builds = 759
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
Memory usage per processor = 6.98553 Mbytes
Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
5000 1.4387091 5.9077604 7.0377893 0.0035977871 7.1927209 62.244 62.244 62.244 0.025518192 -0.016769871 0.0020450407
5100 1.4449405 5.8876257 7.022549 0.0023104502 7.122044 62.244 62.244 62.244 0.0045960664 0.0036845954 -0.0013493113
5200 1.4271652 5.9160022 7.036964 0.0020238904 7.1241189 62.244 62.244 62.244 -0.0022546188 0.00392213 0.0044041599
5300 1.4143299 5.9052666 7.016147 0.0064054214 7.2919838 62.244 62.244 62.244 0.0090997079 0.0026363579 0.0074801984
5400 1.4426441 5.9087558 7.0418754 0.0020465683 7.1300068 62.244 62.244 62.244 0.0043188307 3.0314417e-06 0.0018178427
5500 1.4281065 5.9038871 7.0255883 0.00058665945 7.0508516 62.244 62.244 62.244 0.005898925 0.00066013177 -0.0047990784
5600 1.4315628 5.902373 7.0267888 0.0096475978 7.4422435 62.244 62.244 62.244 0.0054175405 0.011780025 0.011745228
5700 1.4075482 5.9075587 7.0131124 0.0052150708 7.2376891 62.244 62.244 62.244 0.0030069124 0.0036690785 0.0089692215
5800 1.4215681 5.9048555 7.0214211 0.0015070444 7.086319 62.244 62.244 62.244 -5.6858344e-05 0.0023644208 0.0022135708
5900 1.3992461 5.8949367 6.9939696 0.0062425817 7.262794 62.244 62.244 62.244 0.0056972212 0.0095293238 0.0035012003
6000 1.385289 5.8972105 6.9852808 0.0043255163 7.1715506 62.244 62.244 62.244 0.0040215567 0.0026330714 0.0063219208
Loop time of 0.741772 on 4 procs for 1000 steps with 5600 atoms
Pair time (%) = 0.0337995 (4.55659)
Bond time (%) = 0.0119883 (1.61618)
Neigh time (%) = 0.140019 (18.8763)
Comm time (%) = 0.0468359 (6.31406)
Outpt time (%) = 0.00055021 (0.0741752)
Other time (%) = 0.508579 (68.5627)
Nlocal: 1400 ave 1868 max 935 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Nghost: 633.75 ave 695 max 541 min
Histogram: 1 0 0 0 1 0 0 0 0 2
Neighs: 1263 ave 1799 max 710 min
Histogram: 1 1 0 0 0 0 0 0 0 2
Total # of neighbors = 5052
Ave neighs/atom = 0.902143
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
Memory usage per processor = 6.98553 Mbytes
Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
6000 1.385289 5.8972105 6.9852808 0.0029190017 7.1109818 62.244 62.244 62.244 0.026575922 -0.075631452 0.057812535
6100 1.3829575 5.9055308 6.9917699 0.0022904847 7.0904051 62.244 62.244 62.244 -0.00045870152 0.004055647 0.0032745086
6200 1.3942692 5.90506 7.0001838 0.0046406767 7.2000253 62.244 62.244 62.244 0.0042263478 0.0051632788 0.0045324035
6300 1.4009885 5.902399 7.0028005 0.0077682485 7.3373247 62.244 62.244 62.244 0.0071636925 0.0098268465 0.0063142066
6400 1.3627532 5.9075587 6.9779284 0.0093180812 7.3791931 62.244 62.244 62.244 0.0062401482 0.013022619 0.0086914761
6500 1.3341203 5.9012967 6.9491767 0.010108056 7.3844601 62.244 62.244 62.244 0.0031876333 0.011099549 0.016036984
6600 1.3572847 5.8915298 6.9576041 -0.00034416741 6.9427833 62.244 62.244 62.244 0.0025578983 -0.0011308804 -0.0024595201
6700 1.3663741 5.8985276 6.9717412 0.002947281 7.09866 62.244 62.244 62.244 0.0022469396 -0.00042872124 0.0070236245
6800 1.3816731 5.8909305 6.9761607 -9.1110394e-05 6.9722372 62.244 62.244 62.244 -0.0048195881 -0.00080983527 0.0053560922
6900 1.4011479 5.8881921 6.9887187 0.0010084642 7.0321462 62.244 62.244 62.244 0.0012132523 -0.0025918018 0.0044039422
7000 1.3973667 5.8867951 6.9843517 0.0070023833 7.2858955 62.244 62.244 62.244 0.0058928565 0.0076813429 0.0074329504
Loop time of 0.757287 on 4 procs for 1000 steps with 5600 atoms
Pair time (%) = 0.0350551 (4.62904)
Bond time (%) = 0.0119646 (1.57993)
Neigh time (%) = 0.137299 (18.1304)
Comm time (%) = 0.0465308 (6.1444)
Outpt time (%) = 0.000546932 (0.0722226)
Other time (%) = 0.525891 (69.444)
Nlocal: 1400 ave 1832 max 970 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Nghost: 652.5 ave 749 max 561 min
Histogram: 1 0 0 1 0 0 1 0 0 1
Neighs: 1407.5 ave 2071 max 748 min
Histogram: 1 1 0 0 0 0 0 0 1 1
Total # of neighbors = 5630
Ave neighs/atom = 1.00536
Ave special neighs/atom = 0.571429
Neighbor list builds = 149
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
Memory usage per processor = 6.98553 Mbytes
Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
7000 1.3973667 5.8867951 6.9843517 0.0026559416 7.0987246 62.244 62.244 62.244 0.033713637 -0.0068647989 -0.018881013
7100 1.4639139 5.8611823 7.0110083 0.011521251 7.3924625 57.022152 57.022152 57.022152 0.010787531 0.0093708984 0.014405322
7200 1.4950463 5.8177011 6.9919798 0.023101297 7.5163969 50.281647 50.281647 50.281647 0.023242216 0.018105116 0.02795656
7300 1.5103331 5.7757714 6.9620571 0.022650056 7.3366292 45.243 45.243 45.243 0.023573421 0.022300241 0.022076507
7400 1.5582095 5.7578511 6.9817412 0.028508467 7.3477691 41.582392 41.582392 41.582392 0.02740467 0.030003113 0.028117619
7500 1.5992723 5.6927269 6.9488696 0.046538335 7.4419099 39.001967 39.001967 39.001967 0.057728057 0.030859627 0.05102732
7600 1.5572154 5.6717168 6.894826 0.032055597 7.184009 36.967405 36.967405 36.967405 0.034785798 0.033408508 0.027972486
7700 1.541013 5.6302838 6.840667 0.046629681 7.2052858 35.246953 35.246953 35.246953 0.051145184 0.022437926 0.066305932
7800 1.4922447 5.6135845 6.7856627 0.066398531 7.2467615 33.879827 33.879827 33.879827 0.05766722 0.07643975 0.065088623
7900 1.5126099 5.5498409 6.7379149 0.060758513 7.1190044 32.749346 32.749346 32.749346 0.045401188 0.069519167 0.067355184
8000 1.498932 5.5307653 6.708096 0.0068958389 6.7481394 31.918601 31.918601 31.918601 0.004934357 -0.0067897493 0.022542909
Loop time of 1.41462 on 4 procs for 1000 steps with 5600 atoms
Pair time (%) = 0.0971823 (6.86986)
Bond time (%) = 0.0180002 (1.27244)
Neigh time (%) = 0.508159 (35.922)
Comm time (%) = 0.108228 (7.65071)
Outpt time (%) = 0.000414193 (0.0292795)
Other time (%) = 0.682634 (48.2557)
Nlocal: 1400 ave 1820 max 1010 min
Histogram: 1 1 0 0 0 0 0 0 1 1
Nghost: 1576 ave 1694 max 1470 min
Histogram: 1 1 0 0 0 0 0 1 0 1
Neighs: 6543 ave 9989 max 3497 min
Histogram: 1 1 0 0 0 0 0 1 0 1
Total # of neighbors = 26172
Ave neighs/atom = 4.67357
Ave special neighs/atom = 0.571429
Neighbor list builds = 337
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
Memory usage per processor = 7.00192 Mbytes
Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
8000 1.498932 5.5307653 6.708096 0.044418732 6.9660307 31.918601 31.918601 31.918601 0.033240642 0.090981355 0.0090341992
8100 1.4932748 5.5104122 6.6832996 0.078824127 7.1379335 31.703188 31.918601 31.918601 0.046668046 0.090499077 0.099305258
8200 1.4783774 5.4958482 6.6570345 0.024180825 6.7956092 31.500184 31.918601 31.918601 -0.01991799 0.022036912 0.070423554
8300 1.4699766 5.468569 6.6231569 0.050331767 6.9062762 30.919162 31.918601 31.918601 0.030889484 0.091318073 0.028787743
8400 1.4423945 5.4591749 6.5920985 0.034769472 6.7835475 30.266023 31.918601 31.918601 0.031838545 0.067297532 0.0051723374
8500 1.4478469 5.4405027 6.5777089 0.061608005 6.9111775 29.752136 31.918601 31.918601 0.056987338 0.064105062 0.063731616
8600 1.4216004 5.443144 6.5597349 0.031739807 6.7291722 29.343028 31.918601 31.918601 0.047008356 0.040197385 0.0080136813
8700 1.3993468 5.4199487 6.5190607 0.055753353 6.8130189 28.981104 31.918601 31.918601 0.038071725 0.050746074 0.078442261
8800 1.4272224 5.3956531 6.5166598 0.051937078 6.7855855 28.46133 31.918601 31.918601 0.038718856 0.054121272 0.062971108
8900 1.430201 5.3881483 6.5114945 0.042705385 6.728515 27.933053 31.918601 31.918601 0.053090216 0.033892798 0.04113314
9000 1.4147254 5.3571794 6.4683705 0.015474623 6.5454193 27.368213 31.918601 31.918601 0.018517547 0.023668345 0.0042379783
Loop time of 1.41135 on 4 procs for 1000 steps with 5600 atoms
Pair time (%) = 0.154745 (10.9643)
Bond time (%) = 0.0182955 (1.29631)
Neigh time (%) = 0.406235 (28.7833)
Comm time (%) = 0.136895 (9.69955)
Outpt time (%) = 0.000399649 (0.0283167)
Other time (%) = 0.694785 (49.2282)
Nlocal: 1400 ave 1770 max 1095 min
Histogram: 1 1 0 0 0 0 1 0 0 1
Nghost: 1578.5 ave 1693 max 1493 min
Histogram: 2 0 0 0 0 0 0 1 0 1
Neighs: 7868 ave 12041 max 4579 min
Histogram: 1 1 0 0 0 0 1 0 0 1
Total # of neighbors = 31472
Ave neighs/atom = 5.62
Ave special neighs/atom = 0.571429
Neighbor list builds = 167
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
Memory usage per processor = 7.00192 Mbytes
Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
9000 1.4147254 5.3571794 6.4683705 0.026540417 6.6005164 27.368213 31.918601 31.918601 -0.25291277 0.19881452 0.1337195
9100 1.4143578 5.3349724 6.4458747 0.032533861 6.6070914 27.324726 31.867884 31.867884 0.031965858 0.023737907 0.041897818
9200 1.4489265 5.3126352 6.4506893 0.020125553 6.5486389 27.161226 31.6772 31.6772 0.024138053 0.045983015 -0.0097444101
9300 1.4434983 5.3100314 6.4438219 0.071722015 6.7864703 26.993744 31.481872 31.481872 0.081599435 0.059208723 0.074357889
9400 1.4179009 5.3170886 6.4307738 0.020348306 6.5262516 26.832169 31.293432 31.293432 0.070733237 -0.0042808269 -0.0054074919
9500 1.455947 5.2941589 6.4377273 0.0066330065 6.4680826 26.60963 31.033892 31.033892 -0.026145193 -0.017478757 0.06352297
9600 1.4322198 5.2747171 6.399649 0.079157317 6.755508 26.452091 30.85016 30.85016 0.09770091 0.095143096 0.044627945
9700 1.4366074 5.2650795 6.3934576 0.052444405 6.6264505 26.347873 30.728614 30.728614 0.043301655 0.043720535 0.070311026
9800 1.4311568 5.268838 6.392935 0.056161789 6.637248 26.163729 30.513853 30.513853 0.071096045 0.048086199 0.049303122
9900 1.4437347 5.2369801 6.3709564 0.11335968 6.8497267 25.907207 30.214681 30.214681 0.1259046 0.10149135 0.11268308
10000 1.4627878 5.2272205 6.376162 0.082077049 6.7164073 25.746677 30.02746 30.02746 0.060839015 0.13885619 0.046535946
Loop time of 1.41497 on 4 procs for 1000 steps with 5600 atoms
Pair time (%) = 0.178246 (12.5972)
Bond time (%) = 0.0182433 (1.2893)
Neigh time (%) = 0.410838 (29.0351)
Comm time (%) = 0.131719 (9.30895)
Outpt time (%) = 0.000414371 (0.0292848)
Other time (%) = 0.675509 (47.7402)
Nlocal: 1400 ave 1669 max 1139 min
Histogram: 1 0 1 0 0 0 0 1 0 1
Nghost: 1761.5 ave 1898 max 1632 min
Histogram: 2 0 0 0 0 0 0 0 1 1
Neighs: 9311.75 ave 12525 max 5959 min
Histogram: 1 0 1 0 0 0 0 1 0 1
Total # of neighbors = 37247
Ave neighs/atom = 6.65125
Ave special neighs/atom = 0.571429
Neighbor list builds = 165
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
Memory usage per processor = 7.00192 Mbytes
Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
10000 1.4627878 5.2272205 6.376162 0.087181735 6.7375684 25.746677 30.02746 30.02746 0.01077504 0.047196696 0.20357347
10100 1.461932 5.2277217 6.3759909 0.045218386 6.5623932 25.674625 29.943429 30.02746 0.029664553 0.034940919 0.071049687
10200 1.4394425 5.2183968 6.3490017 0.064139003 6.6129181 25.651225 29.916138 30.02746 0.063541799 0.099454655 0.029420554
10300 1.445679 5.2124787 6.3479821 0.073611235 6.6513251 25.670301 29.938385 30.02746 0.09678342 0.1092442 0.01480609
10400 1.4289478 5.2082727 6.3306346 -0.00091064043 6.3268902 25.642317 29.905748 30.02746 -0.021792005 0.043173882 -0.024113799
10500 1.4138512 5.191318 6.3018224 0.051274311 6.5114152 25.566672 29.817526 30.02746 0.087657762 0.022098862 0.04406631
10600 1.4101298 5.2048433 6.3124247 0.032021085 6.442127 25.450236 29.681731 30.02746 0.032483644 0.022737859 0.040841754
10700 1.4527253 5.1827275 6.3237654 0.045295082 6.5054661 25.327296 29.53835 30.02746 0.082847312 0.0364514 0.016586533
10800 1.4661732 5.1586918 6.3102923 0.084525247 6.6478976 25.272455 29.474391 30.02746 0.10699807 0.070825674 0.075751992
10900 1.4301511 5.1743273 6.2976344 0.014007746 6.3539547 25.356203 29.572064 30.02746 -0.015258276 -0.0047253148 0.06200683
11000 1.4346828 5.1625047 6.2893712 0.034027405 6.4273459 25.463687 29.697419 30.02746 0.041309225 0.014001823 0.046771165
Loop time of 1.3879 on 4 procs for 1000 steps with 5600 atoms
Pair time (%) = 0.19872 (14.318)
Bond time (%) = 0.0184246 (1.32751)
Neigh time (%) = 0.379613 (27.3515)
Comm time (%) = 0.121657 (8.7655)
Outpt time (%) = 0.000391245 (0.0281896)
Other time (%) = 0.669099 (48.2093)
Nlocal: 1400 ave 1607 max 1199 min
Histogram: 1 0 1 0 0 0 0 1 0 1
Nghost: 1819.25 ave 1940 max 1712 min
Histogram: 1 1 0 0 0 0 0 1 0 1
Neighs: 9882 ave 12628 max 7201 min
Histogram: 1 0 1 0 0 0 0 1 0 1
Total # of neighbors = 39528
Ave neighs/atom = 7.05857
Ave special neighs/atom = 0.571429
Neighbor list builds = 156
Dangerous builds = 0