LAMMPS (15 Feb 2016) # 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 max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 2.8 ghost atom cutoff = 2.8 binsize = 1.4 -> bins = 45 45 45 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 6.61347 on 1 procs for 5000 steps with 5600 atoms Performance: 326606.103 tau/day, 756.033 timesteps/s 99.9% CPU use with 1 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.53158 | 0.53158 | 0.53158 | 0.0 | 8.04 Bond | 0.24987 | 0.24987 | 0.24987 | 0.0 | 3.78 Neigh | 1.8367 | 1.8367 | 1.8367 | 0.0 | 27.77 Comm | 0.17261 | 0.17261 | 0.17261 | 0.0 | 2.61 Output | 0.0035651 | 0.0035651 | 0.0035651 | 0.0 | 0.05 Modify | 3.6673 | 3.6673 | 3.6673 | 0.0 | 55.45 Other | | 0.1519 | | | 2.30 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 1.34998 on 1 procs for 1000 steps with 5600 atoms Performance: 320004.261 tau/day, 740.751 timesteps/s 99.9% CPU use with 1 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.14397 | 0.14397 | 0.14397 | 0.0 | 10.66 Bond | 0.049438 | 0.049438 | 0.049438 | 0.0 | 3.66 Neigh | 0.39013 | 0.39013 | 0.39013 | 0.0 | 28.90 Comm | 0.033965 | 0.033965 | 0.033965 | 0.0 | 2.52 Output | 0.00092816 | 0.00092816 | 0.00092816 | 0.0 | 0.07 Modify | 0.70139 | 0.70139 | 0.70139 | 0.0 | 51.96 Other | | 0.03017 | | | 2.23 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 1.36768 on 1 procs for 1000 steps with 5600 atoms Performance: 315862.242 tau/day, 731.163 timesteps/s 99.9% CPU use with 1 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.14502 | 0.14502 | 0.14502 | 0.0 | 10.60 Bond | 0.049546 | 0.049546 | 0.049546 | 0.0 | 3.62 Neigh | 0.38711 | 0.38711 | 0.38711 | 0.0 | 28.30 Comm | 0.033742 | 0.033742 | 0.033742 | 0.0 | 2.47 Output | 0.00089908 | 0.00089908 | 0.00089908 | 0.0 | 0.07 Modify | 0.72137 | 0.72137 | 0.72137 | 0.0 | 52.74 Other | | 0.03 | | | 2.19 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 3.01539 on 1 procs for 1000 steps with 5600 atoms Performance: 143265.281 tau/day, 331.633 timesteps/s 99.9% CPU use with 1 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.37256 | 0.37256 | 0.37256 | 0.0 | 12.36 Bond | 0.072008 | 0.072008 | 0.072008 | 0.0 | 2.39 Neigh | 1.3608 | 1.3608 | 1.3608 | 0.0 | 45.13 Comm | 0.073025 | 0.073025 | 0.073025 | 0.0 | 2.42 Output | 0.00085115 | 0.00085115 | 0.00085115 | 0.0 | 0.03 Modify | 1.099 | 1.099 | 1.099 | 0.0 | 36.45 Other | | 0.03715 | | | 1.23 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 3.0303 on 1 procs for 1000 steps with 5600 atoms Performance: 142560.181 tau/day, 330.000 timesteps/s 99.9% CPU use with 1 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.59848 | 0.59848 | 0.59848 | 0.0 | 19.75 Bond | 0.075771 | 0.075771 | 0.075771 | 0.0 | 2.50 Neigh | 1.0984 | 1.0984 | 1.0984 | 0.0 | 36.25 Comm | 0.055339 | 0.055339 | 0.055339 | 0.0 | 1.83 Output | 0.00087357 | 0.00087357 | 0.00087357 | 0.0 | 0.03 Modify | 1.1671 | 1.1671 | 1.1671 | 0.0 | 38.51 Other | | 0.03439 | | | 1.13 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 3.1675 on 1 procs for 1000 steps with 5600 atoms Performance: 136384.997 tau/day, 315.706 timesteps/s 99.9% CPU use with 1 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.68944 | 0.68944 | 0.68944 | 0.0 | 21.77 Bond | 0.074669 | 0.074669 | 0.074669 | 0.0 | 2.36 Neigh | 1.1761 | 1.1761 | 1.1761 | 0.0 | 37.13 Comm | 0.058399 | 0.058399 | 0.058399 | 0.0 | 1.84 Output | 0.0006671 | 0.0006671 | 0.0006671 | 0.0 | 0.02 Modify | 1.1339 | 1.1339 | 1.1339 | 0.0 | 35.80 Other | | 0.03435 | | | 1.08 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 3.24668 on 1 procs for 1000 steps with 5600 atoms Performance: 133059.040 tau/day, 308.007 timesteps/s 99.9% CPU use with 1 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.75941 | 0.75941 | 0.75941 | 0.0 | 23.39 Bond | 0.075467 | 0.075467 | 0.075467 | 0.0 | 2.32 Neigh | 1.1751 | 1.1751 | 1.1751 | 0.0 | 36.19 Comm | 0.059018 | 0.059018 | 0.059018 | 0.0 | 1.82 Output | 0.00065112 | 0.00065112 | 0.00065112 | 0.0 | 0.02 Modify | 1.1432 | 1.1432 | 1.1432 | 0.0 | 35.21 Other | | 0.03387 | | | 1.04 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 Total wall time: 0:00:21