LAMMPS (27 Nov 2018) using 1 OpenMP thread(s) per MPI task # Simple rigid body system units lj atom_style atomic pair_style lj/cut 2.5 read_data data.rigid orthogonal box = (-12 -12 -12) to (12 12 12) 1 by 2 by 2 MPI processor grid reading atoms ... 81 atoms velocity all create 100.0 4928459 # unconnected bodies group clump1 id <> 1 9 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/nve group 9 clump1 clump2 clump3 clump4 clump5 clump6 clump7 clump8 clump9 9 rigid bodies with 81 atoms fix_modify 1 bodyforces early # 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 ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 2.8 ghost atom cutoff = 2.8 binsize = 1.4, bins = 18 18 18 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair lj/cut, perpetual attributes: half, newton on pair build: half/bin/atomonly/newton stencil: half/bin/3d/newton bin: standard Per MPI rank memory allocation (min/avg/max) = 3.95 | 4.044 | 4.326 Mbytes Step Temp E_pair E_mol TotEng Press 0 115.29439 5235.9179 0 5272.2142 -2.7403788 50 14910.69 571.70921 0 5265.8153 32.005816 100 16298.128 136.75661 0 5267.6488 16.449029 150 16682.532 17.504156 0 5269.4124 14.901186 200 16733.906 1.3755079 0 5269.4571 14.571305 250 16738.861 -0.15272039 0 5269.4886 14.498342 300 16738.608 -0.055216883 0 5269.5066 14.498 350 16738.5 -0.017457072 0 5269.5104 14.498392 400 16738.451 -0.0060161309 0 5269.5063 14.49851 450 16738.435 -0.001271965 0 5269.5059 14.498571 500 16738.443 -0.00081074175 0 5269.509 14.498598 550 16738.452 -0.00083208965 0 5269.5118 14.498618 600 16738.45 -0.00058358431 0 5269.5116 14.498617 650 16738.443 -0.00047228525 0 5269.5093 14.4986 700 16738.444 0 0 5269.5102 14.498612 750 16738.461 0 0 5269.5157 14.498654 800 16738.479 0 0 5269.521 14.498697 850 16738.473 0 0 5269.5192 14.498683 900 16738.449 0 0 5269.5116 14.498624 950 16738.438 -0.0035324203 0 5269.5046 14.498537 1000 16738.562 -0.051134242 0 5269.4963 14.498093 1050 16737.343 0.32970192 0 5269.4934 14.527634 1100 16737.878 0.16213235 0 5269.4941 14.533864 1150 16738.682 -0.089236256 0 5269.4959 14.511765 1200 16738.444 -0.0075446558 0 5269.5025 14.512479 1250 16738.45 0 0 5269.5119 14.512611 1300 16738.475 0 0 5269.5199 14.512673 1350 16738.484 0 0 5269.5228 14.512696 1400 16738.469 -0.00044683992 0 5269.5175 14.512651 1450 16738.45 -0.0010933363 0 5269.511 14.512595 1500 16738.445 -0.00057484239 0 5269.51 14.512591 1550 16738.451 0 0 5269.5123 14.512615 1600 16738.452 0 0 5269.5127 14.512618 1650 16738.443 0 0 5269.5099 14.512596 1700 16738.433 0 0 5269.5068 14.512572 1750 16738.438 0 0 5269.5084 14.512584 1800 16738.459 0 0 5269.5149 14.512635 1850 16738.473 0 0 5269.5193 14.51267 1900 16738.462 0 0 5269.5159 14.512644 1950 16738.446 -0.0032069962 0 5269.5076 14.512539 2000 16738.463 -0.013425408 0 5269.5027 14.512382 2050 16738.535 -0.036964311 0 5269.5017 14.512152 2100 16738.621 -0.063490509 0 5269.5023 14.512108 2150 16738.594 -0.056143934 0 5269.5012 14.512117 2200 16738.536 -0.038486645 0 5269.5007 14.512277 2250 16738.496 -0.023712406 0 5269.503 14.51242 2300 16738.488 -0.013209094 0 5269.5109 14.51255 2350 16738.486 -0.0045244524 0 5269.519 14.512693 2400 16738.475 -0.00051678325 0 5269.5194 14.512743 2450 16738.456 -0.0023209272 0 5269.5115 14.512659 2500 16738.442 -0.0052101787 0 5269.5042 14.512594 2550 16738.552 -0.04420046 0 5269.4998 14.512177 2600 16738.42 -0.004347531 0 5269.4982 14.512783 2650 16734.241 1.3131302 0 5269.5 14.577195 2700 16738.737 -0.10612056 0 5269.4961 14.503874 2750 16732.705 1.7939719 0 5269.4974 14.629294 2800 16738.558 -0.042867033 0 5269.5032 14.519893 2850 16738.499 -0.01271227 0 5269.5146 14.518524 2900 16738.486 -0.0032778045 0 5269.52 14.518712 2950 16738.482 -0.0089544631 0 5269.5133 14.518629 3000 16738.647 -0.070862542 0 5269.5031 14.51803 3050 16678.313 18.829038 0 5269.409 15.533426 3100 16632.312 33.399217 0 5269.4975 14.588597 3150 16739.318 -0.31388148 0 5269.4715 13.520782 3200 16727.951 3.26736 0 5269.4741 12.288358 3250 16686.364 16.353793 0 5269.4682 14.152517 3300 16738.532 -0.031574462 0 5269.5064 13.310615 3350 16738.454 -0.0062292918 0 5269.5071 13.308187 3400 16738.445 -0.0049349125 0 5269.5055 13.308178 3450 16738.489 -0.021623738 0 5269.5026 13.308001 3500 16737.78 0.19719043 0 5269.4983 13.325999 3550 16658.578 25.116206 0 5269.4834 13.778249 3600 16738.51 -0.032864725 0 5269.4981 12.392389 3650 16738.899 -0.15952703 0 5269.4938 12.383503 3700 16738.879 -0.16025994 0 5269.487 12.382575 3750 16738.878 -0.16608251 0 5269.4806 12.382765 3800 16738.591 -0.078679341 0 5269.4776 12.383227 3850 16738.429 -0.024729409 0 5269.4807 12.382942 3900 16738.399 -0.0062729967 0 5269.4897 12.383192 3950 16738.428 -0.002521266 0 5269.5027 12.383324 4000 16738.467 -0.0002068506 0 5269.5173 12.383474 4050 16738.488 0 0 5269.5241 12.383531 4100 16738.468 0 0 5269.5178 12.383482 4150 16738.422 0 0 5269.5033 12.383369 4200 16738.387 0 0 5269.4921 12.383281 4250 16738.383 0 0 5269.4908 12.38327 4300 16738.4 0 0 5269.4964 12.383314 4350 16738.423 0 0 5269.5036 12.38337 4400 16738.441 0 0 5269.5092 12.383414 4450 16738.45 0 0 5269.5121 12.383437 4500 16738.45 0 0 5269.5122 12.383438 4550 16738.442 0 0 5269.5095 12.383417 4600 16738.425 0 0 5269.5042 12.383376 4650 16738.404 -0.0014438316 0 5269.4961 12.383299 4700 16738.444 -0.024020551 0 5269.4862 12.382975 4750 16738.49 -0.048521428 0 5269.4761 12.385777 4800 16735.057 1.0347217 0 5269.4786 12.43543 4850 16735.441 0.92650925 0 5269.4913 12.418653 4900 16723.839 4.5908973 0 5269.5033 13.410103 4950 16738.531 -0.02153767 0 5269.5159 13.089982 5000 16738.45 -0.0042589696 0 5269.5077 13.090062 5050 16738.409 -0.00024692476 0 5269.4987 13.090038 5100 16738.404 0 0 5269.4976 13.090032 5150 16738.421 0 0 5269.5029 13.090073 5200 16738.44 0 0 5269.5087 13.090119 5250 16738.448 -0.001279392 0 5269.5102 13.090114 5300 16738.456 -0.0064376392 0 5269.5075 13.090026 5350 16738.479 -0.020383842 0 5269.5007 13.089897 5400 16735.845 0.79889474 0 5269.4909 13.136244 5450 16735.558 0.87619992 0 5269.4778 12.324482 5500 16711.494 8.4724208 0 5269.4984 12.656579 5550 16454.525 89.074816 0 5269.2031 16.996503 5600 16713.084 7.9801334 0 5269.5065 13.774977 5650 16738.676 -0.079987764 0 5269.5033 13.168295 5700 16446.281 91.866085 0 5269.399 23.764662 5750 16738.549 -0.039869084 0 5269.5034 13.378121 5800 16738.487 -0.014994475 0 5269.5086 13.378397 5850 16738.466 -0.0051267556 0 5269.512 13.378559 5900 16738.462 -0.0043690097 0 5269.5113 13.378572 5950 16738.528 -0.03272741 0 5269.5039 13.378195 6000 16702.774 10.969434 0 5269.2502 13.788851 6050 16682.271 17.483158 0 5269.3092 13.3531 6100 16738.508 -0.028838239 0 5269.5016 12.521082 6150 16738.425 -0.0067595542 0 5269.4974 12.521221 6200 16738.401 -0.0011499896 0 5269.4955 12.521252 6250 16738.455 0 0 5269.5135 12.521408 6300 16738.523 0 0 5269.5352 12.521578 6350 16738.503 0 0 5269.5287 12.52153 6400 16738.427 0 0 5269.5047 12.521342 6450 16738.399 0 0 5269.496 12.521273 6500 16738.425 0 0 5269.5042 12.521336 6550 16738.441 0 0 5269.5093 12.521377 6600 16738.42 0 0 5269.5025 12.521324 6650 16738.398 0 0 5269.4957 12.52127 6700 16738.435 0 0 5269.5074 12.52136 6750 16738.505 0 0 5269.5293 12.521532 6800 16738.508 0 0 5269.5303 12.521541 6850 16738.446 0 0 5269.5108 12.521389 6900 16738.414 0 0 5269.5009 12.521311 6950 16738.432 0 0 5269.5063 12.521353 7000 16738.444 0 0 5269.5102 12.521383 7050 16738.421 0 0 5269.5029 12.521327 7100 16738.393 0 0 5269.4941 12.521258 7150 16738.419 0 0 5269.5022 12.52132 7200 16738.489 0 0 5269.5244 12.521494 7250 16738.505 0 0 5269.5293 12.521533 7300 16738.443 0 0 5269.5098 12.521381 7350 16738.404 0 0 5269.4976 12.521285 7400 16738.43 0 0 5269.5058 12.521348 7450 16738.461 0 0 5269.5156 12.521425 7500 16738.447 0 0 5269.5109 12.52139 7550 16738.407 0 0 5269.4986 12.521293 7600 16738.412 0 0 5269.5002 12.521305 7650 16738.478 0 0 5269.5208 12.521465 7700 16738.51 0 0 5269.5309 12.521546 7750 16738.454 0 0 5269.5135 12.52141 7800 16738.398 0 0 5269.4958 12.521272 7850 16738.407 -0.00021180981 0 5269.4982 12.521288 7900 16738.441 -0.0002167964 0 5269.509 12.521371 7950 16738.446 -0.00023848065 0 5269.5107 12.521385 8000 16738.423 0 0 5269.5035 12.521331 8050 16738.423 0 0 5269.5034 12.52133 8100 16738.478 -0.00069623408 0 5269.52 12.521452 8150 16738.523 -0.0040058355 0 5269.531 12.521499 8200 16738.486 -0.0092298325 0 5269.5142 12.521332 8250 16738.458 -0.023189665 0 5269.4914 12.521012 8300 16738.513 -0.045846242 0 5269.4861 12.520778 8350 16723.742 4.5698786 0 5269.4516 12.849386 8400 16738.466 -0.02016972 0 5269.497 12.835784 8450 16738.437 -0.012822703 0 5269.4952 12.829948 8500 16738.408 -0.0016836132 0 5269.4972 12.830073 8550 16738.464 -0.00097380297 0 5269.5155 12.830227 8600 16738.669 -0.050578946 0 5269.5304 12.829946 8650 15917.707 250.24016 0 5261.3702 24.544744 8700 16738.445 0.0010615265 0 5269.5117 10.589987 8750 16738.473 -0.010158834 0 5269.509 10.588904 8800 16738.468 0 0 5269.5176 10.589124 8850 16738.508 0 0 5269.5304 10.589223 8900 16738.509 0 0 5269.5306 10.589226 8950 16738.496 0 0 5269.5266 10.589195 9000 16738.477 0 0 5269.5204 10.589147 9050 16738.455 0 0 5269.5135 10.589092 9100 16738.477 0 0 5269.5206 10.589146 9150 16738.512 0 0 5269.5316 10.589233 9200 16738.502 0 0 5269.5285 10.58921 9250 16738.493 0 0 5269.5255 10.589186 9300 16738.482 0 0 5269.522 10.589159 9350 16738.46 0 0 5269.5151 10.589105 9400 16738.481 0 0 5269.5217 10.589155 9450 16738.509 0 0 5269.5307 10.589226 9500 16738.491 0 0 5269.5248 10.589181 9550 16738.484 0 0 5269.5227 10.589164 9600 16738.483 0 0 5269.5223 10.589161 9650 16738.464 0 0 5269.5166 10.589116 9700 16738.484 0 0 5269.5228 10.589164 9750 16738.507 0 0 5269.5301 10.589221 9800 16738.482 0 0 5269.5221 10.589159 9850 16738.478 0 0 5269.5208 10.589149 9900 16738.487 -0.00030979591 0 5269.5233 10.589165 9950 16738.476 -0.0009596827 0 5269.5193 10.589123 10000 16738.494 -0.0006271698 0 5269.5253 10.589175 Loop time of 0.213152 on 4 procs for 10000 steps with 81 atoms Performance: 405345.239 tau/day, 46914.958 timesteps/s 91.7% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.0029514 | 0.0038354 | 0.005348 | 1.5 | 1.80 Neigh | 0.01178 | 0.013139 | 0.0167 | 1.8 | 6.16 Comm | 0.073879 | 0.078553 | 0.081131 | 1.0 | 36.85 Output | 0.0031943 | 0.0037987 | 0.0055451 | 1.6 | 1.78 Modify | 0.10553 | 0.10763 | 0.1096 | 0.4 | 50.49 Other | | 0.0062 | | | 2.91 Nlocal: 20.25 ave 34 max 9 min Histogram: 2 0 0 0 0 0 0 1 0 1 Nghost: 38.5 ave 43 max 26 min Histogram: 1 0 0 0 0 0 0 0 0 3 Neighs: 0.75 ave 2 max 0 min Histogram: 2 0 0 0 0 1 0 0 0 1 Total # of neighbors = 3 Ave neighs/atom = 0.037037 Neighbor list builds = 998 Dangerous builds = 997 Total wall time: 0:00:00