LAMMPS (27 Nov 2018) using 1 OpenMP thread(s) per MPI task # 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/intra 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 ... 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 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair lj/cut, perpetual attributes: half, newton on pair build: half/bin/newton stencil: half/bin/3d/newton bin: standard Per MPI rank memory allocation (min/avg/max) = 7.769 | 7.769 | 7.769 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 6.84203 on 1 procs for 5000 steps with 5600 atoms Performance: 315695.745 tau/day, 730.777 timesteps/s 99.5% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.53182 | 0.53182 | 0.53182 | 0.0 | 7.77 Bond | 0.18231 | 0.18231 | 0.18231 | 0.0 | 2.66 Neigh | 1.8709 | 1.8709 | 1.8709 | 0.0 | 27.34 Comm | 0.18452 | 0.18452 | 0.18452 | 0.0 | 2.70 Output | 0.0043087 | 0.0043087 | 0.0043087 | 0.0 | 0.06 Modify | 3.8809 | 3.8809 | 3.8809 | 0.0 | 56.72 Other | | 0.1873 | | | 2.74 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 Per MPI rank memory allocation (min/avg/max) = 7.77 | 7.77 | 7.77 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 1.40593 on 1 procs for 1000 steps with 5600 atoms Performance: 307270.224 tau/day, 711.274 timesteps/s 99.1% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.14844 | 0.14844 | 0.14844 | 0.0 | 10.56 Bond | 0.036852 | 0.036852 | 0.036852 | 0.0 | 2.62 Neigh | 0.40537 | 0.40537 | 0.40537 | 0.0 | 28.83 Comm | 0.036592 | 0.036592 | 0.036592 | 0.0 | 2.60 Output | 0.00085831 | 0.00085831 | 0.00085831 | 0.0 | 0.06 Modify | 0.74053 | 0.74053 | 0.74053 | 0.0 | 52.67 Other | | 0.03729 | | | 2.65 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 Per MPI rank memory allocation (min/avg/max) = 7.77 | 7.77 | 7.77 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 0.0054065561 7.2245364 62.244 62.244 62.244 0.009227645 0.0019623802 0.0050296432 6200 1.3976825 5.8924426 6.9902474 0.00043900876 7.0091524 62.244 62.244 62.244 -0.0023073124 -0.00049925318 0.0041235918 6300 1.4077283 5.8847362 6.9904313 0.0066398301 7.2763625 62.244 62.244 62.244 0.0058018934 0.0091933877 0.0049242093 6400 1.3749203 5.8817073 6.9616336 0.0074967162 7.2844648 62.244 62.244 62.244 0.012281887 0.0039781589 0.0062301027 6500 1.3467096 5.8881264 6.9458946 -0.00011926349 6.9407588 62.244 62.244 62.244 0.0030721967 -0.0013265863 -0.0021034009 6600 1.3646558 5.8739857 6.9458497 0.0056064043 7.1872784 62.244 62.244 62.244 0.0059660337 0.0057680048 0.0050851745 6700 1.3927251 5.883612 6.9775229 0.0025583824 7.0876946 62.244 62.244 62.244 0.0030974706 0.0018499606 0.002727716 6800 1.4016999 5.9015886 7.0025488 0.0039070678 7.1707989 62.244 62.244 62.244 0.0068320586 0.0020056859 0.002883459 6900 1.4136745 5.8914714 7.001837 0.0051755091 7.22471 62.244 62.244 62.244 0.0028467792 0.0094052519 0.0032744962 7000 1.4286639 5.893567 7.0157059 0.0062957476 7.2868198 62.244 62.244 62.244 0.0047242086 0.0093408867 0.0048221474 Loop time of 1.41045 on 1 procs for 1000 steps with 5600 atoms Performance: 306284.404 tau/day, 708.992 timesteps/s 99.6% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.1497 | 0.1497 | 0.1497 | 0.0 | 10.61 Bond | 0.036719 | 0.036719 | 0.036719 | 0.0 | 2.60 Neigh | 0.40272 | 0.40272 | 0.40272 | 0.0 | 28.55 Comm | 0.036315 | 0.036315 | 0.036315 | 0.0 | 2.57 Output | 0.00085187 | 0.00085187 | 0.00085187 | 0.0 | 0.06 Modify | 0.747 | 0.747 | 0.747 | 0.0 | 52.96 Other | | 0.03715 | | | 2.63 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 Per MPI rank memory allocation (min/avg/max) = 7.77 | 7.77 | 7.77 Mbytes Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz 7000 1.4286639 5.893567 7.0157059 0.032101512 8.3980939 62.244 62.244 62.244 0.0040045405 0.040447803 0.051852194 7100 1.4709161 5.8870949 7.0424207 0.019697134 7.6953761 57.045689 57.045689 57.045689 0.012929484 0.020492532 0.025669387 7200 1.5163078 5.8421187 7.0330973 0.018916867 7.46241 50.277171 50.277171 50.277171 0.017823354 0.026688031 0.012239218 7300 1.5675309 5.7752739 7.0064855 0.022899743 7.3829781 45.154874 45.154874 45.154874 0.019324617 0.024318577 0.025056034 7400 1.5432228 5.7513096 6.9634284 0.024381819 7.272744 41.416613 41.416613 41.416613 0.032026791 0.022254425 0.018864241 7500 1.5511419 5.7072564 6.9255953 0.030632381 7.2405167 38.613262 38.613262 38.613262 0.041572196 0.012539031 0.037785916 7600 1.5437461 5.6656571 6.8781869 0.031293788 7.1486082 36.440994 36.440994 36.440994 0.036220762 0.02125772 0.036402883 7700 1.5873874 5.6134986 6.8603063 0.04807003 7.221002 34.765744 34.765744 34.765744 0.031608235 0.053442472 0.059159381 7800 1.5079648 5.601961 6.7863866 0.031128515 6.9971673 33.59594 33.59594 33.59594 0.032932226 0.015950578 0.044502741 7900 1.4737447 5.5644198 6.7219673 0.099246661 7.3415696 32.698542 32.698542 32.698542 0.071386679 0.10758014 0.11877317 8000 1.4727947 5.5161158 6.6729171 0.072190554 7.0973199 32.050043 32.050043 32.050043 0.072806068 0.06277287 0.080992723 Loop time of 3.15299 on 1 procs for 1000 steps with 5600 atoms Performance: 137012.841 tau/day, 317.159 timesteps/s 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.37069 | 0.37069 | 0.37069 | 0.0 | 11.76 Bond | 0.05046 | 0.05046 | 0.05046 | 0.0 | 1.60 Neigh | 1.4844 | 1.4844 | 1.4844 | 0.0 | 47.08 Comm | 0.081178 | 0.081178 | 0.081178 | 0.0 | 2.57 Output | 0.00083494 | 0.00083494 | 0.00083494 | 0.0 | 0.03 Modify | 1.1163 | 1.1163 | 1.1163 | 0.0 | 35.41 Other | | 0.0491 | | | 1.56 Nlocal: 5600 ave 5600 max 5600 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2954 ave 2954 max 2954 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 25585 ave 25585 max 25585 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 25585 Ave neighs/atom = 4.56875 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 Per MPI rank memory allocation (min/avg/max) = 7.785 | 7.785 | 7.785 Mbytes Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz 8000 1.4727947 5.5161158 6.6729171 0.13628586 7.4741313 32.050043 32.050043 32.050043 -0.030897367 0.27196335 0.1677916 8100 1.4522497 5.5136331 6.6542974 0.057107124 6.9895036 32.000184 32.050043 32.050043 0.049932793 0.056130194 0.065258384 8200 1.4407937 5.5014539 6.6331202 0.024119241 6.7733276 31.691157 32.050043 32.050043 0.041526366 0.022503949 0.0083274089 8300 1.4542258 5.496977 6.6391934 0.043395674 6.887667 31.215092 32.050043 32.050043 0.025407647 0.075227689 0.029551686 8400 1.4375595 5.4901345 6.6192605 0.013578023 6.6952098 30.494249 32.050043 32.050043 -0.0045150608 0.033500673 0.011748456 8500 1.4410736 5.4540565 6.5859426 0.017121222 6.679397 29.757445 32.050043 32.050043 0.035675932 -0.032105 0.047792733 8600 1.4372413 5.4150437 6.5439197 0.084045699 6.9949237 29.254706 32.050043 32.050043 0.10347392 0.073148157 0.075515024 8700 1.4299119 5.3982284 6.5213476 0.00045273296 6.5237411 28.822481 32.050043 32.050043 0.0093093459 0.0081538479 -0.016104995 8800 1.4677947 5.3637715 6.5166456 0.028621833 6.6651924 28.294159 32.050043 32.050043 0.033527613 0.036046563 0.016291323 8900 1.4625499 5.3483914 6.4971459 0.032843022 6.6649394 27.852402 32.050043 32.050043 0.040751528 0.055865445 0.0019120942 9000 1.4488382 5.3486741 6.4866589 0.087522574 6.9279711 27.488856 32.050043 32.050043 0.059432129 0.10936517 0.093770421 Loop time of 3.09429 on 1 procs for 1000 steps with 5600 atoms Performance: 139611.779 tau/day, 323.175 timesteps/s 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.57714 | 0.57714 | 0.57714 | 0.0 | 18.65 Bond | 0.051715 | 0.051715 | 0.051715 | 0.0 | 1.67 Neigh | 1.223 | 1.223 | 1.223 | 0.0 | 39.52 Comm | 0.066183 | 0.066183 | 0.066183 | 0.0 | 2.14 Output | 0.00086594 | 0.00086594 | 0.00086594 | 0.0 | 0.03 Modify | 1.1355 | 1.1355 | 1.1355 | 0.0 | 36.70 Other | | 0.03994 | | | 1.29 Nlocal: 5600 ave 5600 max 5600 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3381 ave 3381 max 3381 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 31737 ave 31737 max 31737 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 31737 Ave neighs/atom = 5.66732 Ave special neighs/atom = 0.571429 Neighbor list builds = 169 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 Per MPI rank memory allocation (min/avg/max) = 7.788 | 7.788 | 7.788 Mbytes Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz 9000 1.4488382 5.3486741 6.4866589 0.20124138 7.5013717 27.488856 32.050043 32.050043 0.22160189 0.42145658 -0.039334342 9100 1.4408457 5.3612674 6.4929746 0.076331412 6.8758499 27.440968 31.994208 31.994208 0.083838068 0.041724506 0.10343166 9200 1.4870445 5.3340546 6.5020483 0.01010773 6.5521592 27.334266 31.869802 31.869802 0.024563803 -0.0068003493 0.012559737 9300 1.4376808 5.3295183 6.4587396 0.10720051 6.9752889 27.076116 31.568817 31.568817 0.11844426 0.10444301 0.09871425 9400 1.4621325 5.3011274 6.4495541 0.071127232 6.7846388 26.873295 31.332342 31.332342 0.091608834 0.02680694 0.094965923 9500 1.4463444 5.3005044 6.4365304 0.0011545049 6.4418432 26.664 31.088319 31.088319 -0.030551889 0.036011952 -0.0019965484 9600 1.4473406 5.2912939 6.4281024 0.066132857 6.7281169 26.537276 30.940568 30.940568 0.12276096 0.013455525 0.06218208 9700 1.4520445 5.2707214 6.4112246 0.077219765 6.757956 26.446587 30.834832 30.834832 0.073829267 0.11047347 0.047356559 9800 1.4825713 5.246644 6.4111243 0.061402527 6.6831281 26.327581 30.696078 30.696078 0.091860222 0.022619578 0.06972778 9900 1.4795219 5.2344495 6.3965347 0.086345107 6.7729623 26.187615 30.532888 30.532888 0.077396265 0.11142542 0.07021363 10000 1.4527053 5.2126819 6.3537041 0.045117764 6.5474705 26.057038 30.380645 30.380645 0.011087188 0.058029185 0.066236921 Loop time of 3.25046 on 1 procs for 1000 steps with 5600 atoms Performance: 132904.162 tau/day, 307.649 timesteps/s 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.68223 | 0.68223 | 0.68223 | 0.0 | 20.99 Bond | 0.05211 | 0.05211 | 0.05211 | 0.0 | 1.60 Neigh | 1.2617 | 1.2617 | 1.2617 | 0.0 | 38.82 Comm | 0.069407 | 0.069407 | 0.069407 | 0.0 | 2.14 Output | 0.00085688 | 0.00085688 | 0.00085688 | 0.0 | 0.03 Modify | 1.1438 | 1.1438 | 1.1438 | 0.0 | 35.19 Other | | 0.04037 | | | 1.24 Nlocal: 5600 ave 5600 max 5600 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3756 ave 3756 max 3756 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 37360 ave 37360 max 37360 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 37360 Ave neighs/atom = 6.67143 Ave special neighs/atom = 0.571429 Neighbor list builds = 158 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 Per MPI rank memory allocation (min/avg/max) = 7.795 | 7.795 | 7.795 Mbytes Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz 10000 1.4527053 5.2126819 6.3537041 0.056937886 6.5982342 26.057038 30.380645 30.380645 -0.37001102 0.18554825 0.35527643 10100 1.4606958 5.2220088 6.3693071 0.10308269 6.8132489 26.093341 30.422971 30.380645 0.12567436 0.057087258 0.12648646 10200 1.4429187 5.2134399 6.3467753 0.022637194 6.4450326 26.195743 30.542365 30.380645 0.010739012 0.071921542 -0.014748971 10300 1.4559104 5.2293511 6.3728908 0.0079467818 6.4073504 26.182966 30.527467 30.380645 -0.014274944 0.032205181 0.0059101087 10400 1.4741126 5.2072221 6.3650586 0.095611559 6.7814715 26.240156 30.594148 30.380645 0.073579289 0.092441893 0.12081349 10500 1.4411698 5.2173262 6.3492878 0.010458046 6.3947259 26.208633 30.557393 30.380645 0.036794882 -0.0051462954 -0.00027444949 10600 1.4492728 5.1940541 6.3323802 0.042602534 6.5163992 26.132032 30.468083 30.380645 0.090116773 0.0022769844 0.035413845 10700 1.4599974 5.1895935 6.3363432 0.05533717 6.573197 26.013045 30.329352 30.380645 0.070180878 0.08084881 0.014981824 10800 1.4781084 5.1724704 6.3334454 0.031843587 6.4690539 25.947295 30.252692 30.380645 0.0041524129 0.077618702 0.013759645 10900 1.4410507 5.1708846 6.3027527 0.020221033 6.3881531 25.839719 30.127267 30.380645 -0.0014092876 0.014833141 0.047239245 11000 1.4150286 5.1756927 6.2871219 0.039768792 6.45242 25.63435 29.887821 30.380645 0.034930907 0.032278926 0.052096542 Loop time of 3.43774 on 1 procs for 1000 steps with 5600 atoms Performance: 125663.855 tau/day, 290.889 timesteps/s 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.75066 | 0.75066 | 0.75066 | 0.0 | 21.84 Bond | 0.053177 | 0.053177 | 0.053177 | 0.0 | 1.55 Neigh | 1.3577 | 1.3577 | 1.3577 | 0.0 | 39.49 Comm | 0.07294 | 0.07294 | 0.07294 | 0.0 | 2.12 Output | 0.00086403 | 0.00086403 | 0.00086403 | 0.0 | 0.03 Modify | 1.1612 | 1.1612 | 1.1612 | 0.0 | 33.78 Other | | 0.0412 | | | 1.20 Nlocal: 5600 ave 5600 max 5600 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3904 ave 3904 max 3904 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 39666 ave 39666 max 39666 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 39666 Ave neighs/atom = 7.08321 Ave special neighs/atom = 0.571429 Neighbor list builds = 159 Dangerous builds = 0 Total wall time: 0:00:22