LAMMPS (20 Apr 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 -0.0046216998 -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 0.0083738261 0.0090537939 0.013165402 2500 1.4153808 5.9421661 7.0538718 0.00015906308 7.0607216 62.244 62.244 62.244 0.0023516211 -0.0019814987 0.00010706678 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 0.0024268843 7.1518859 62.244 62.244 62.244 0.0052918436 0.0014960354 0.00049277379 2800 1.432192 5.9347676 7.0596777 0.0077670448 7.3941501 62.244 62.244 62.244 0.012668421 0.0059113032 0.0047214106 2900 1.3938659 5.921023 7.01583 0.0053751201 7.2472989 62.244 62.244 62.244 0.0020490372 0.0076566097 0.0064197134 3000 1.390221 5.9205014 7.0124455 -0.0010750973 6.9661486 62.244 62.244 62.244 0.0019519817 -0.0041878875 -0.0009893861 3100 1.4205722 5.9178284 7.0336117 0.0098735467 7.4587964 62.244 62.244 62.244 0.0040973349 0.012167268 0.013356037 3200 1.398418 5.9150349 7.0134173 0.0061541837 7.278435 62.244 62.244 62.244 0.0067621825 0.011952562 -0.00025219321 3300 1.4269859 5.9148727 7.0356937 0.006062387 7.2967584 62.244 62.244 62.244 0.012956233 -2.480748e-05 0.005255736 3400 1.434286 5.9356705 7.0622253 0.0002731615 7.0739885 62.244 62.244 62.244 -0.00054959543 0.0052526331 -0.0038835532 3500 1.4416808 5.9228153 7.0551783 0.0083383068 7.414251 62.244 62.244 62.244 0.0073994017 0.0030328023 0.014582716 3600 1.4136063 5.9039442 7.0142562 0.0019711852 7.0991414 62.244 62.244 62.244 -0.00032317688 0.0035029725 0.0027337599 3700 1.433382 5.91201 7.0378548 0.0071286927 7.3448378 62.244 62.244 62.244 0.0064768108 0.0046765006 0.010232767 3800 1.3659481 5.9032872 6.9761663 -0.0054034056 6.7434793 62.244 62.244 62.244 -0.007394357 -0.0082833116 -0.00053254832 3900 1.396322 5.9043001 7.0010362 0.005331024 7.2306062 62.244 62.244 62.244 0.0081855301 0.0048806234 0.0029269184 4000 1.412548 5.906066 7.0155468 0.0028450132 7.1380616 62.244 62.244 62.244 0.0052588387 0.00072412871 0.0025520721 4100 1.3943949 5.9040868 6.9993093 0.0058053193 7.2493039 62.244 62.244 62.244 0.0060583148 0.0024781972 0.0088794459 4200 1.4249768 5.8906369 7.0098798 0.0030209006 7.1399689 62.244 62.244 62.244 0.0061742017 -0.0020795681 0.0049680681 4300 1.3899827 5.8966327 6.9883897 0.0057278096 7.2350464 62.244 62.244 62.244 0.0049035059 0.0021868561 0.010093067 4400 1.4414361 5.8986386 7.0308094 0.0050941357 7.2501783 62.244 62.244 62.244 0.0057971901 0.0037941986 0.0056910185 4500 1.4093099 5.8922729 6.9992103 0.0012182325 7.0516711 62.244 62.244 62.244 0.0042896986 0.0014287789 -0.00206378 4600 1.3779677 5.892894 6.9752138 0.002057623 7.0638213 62.244 62.244 62.244 0.0029271755 -0.0031752166 0.0064209102 4700 1.4086418 5.9096898 7.0161024 -0.00052853259 6.9933422 62.244 62.244 62.244 -0.001862386 -0.0018129293 0.0020897176 4800 1.4394 5.9146102 7.0451818 0.015326441 7.7051846 62.244 62.244 62.244 0.014754936 0.017967956 0.013256431 4900 1.4496219 5.9074613 7.0460616 0.0075297868 7.370317 62.244 62.244 62.244 0.0092907193 0.0079794674 0.0053191736 5000 1.4280291 5.9106136 7.032254 -0.0013249587 6.9751972 62.244 62.244 62.244 -0.0044875103 0.0020723667 -0.0015597324 Loop time of 6.73744 on 1 procs for 5000 steps with 5600 atoms Performance: 320596.735 tau/day, 742.122 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 | 0.52635 | 0.52635 | 0.52635 | 0.0 | 7.81 Bond | 0.26628 | 0.26628 | 0.26628 | 0.0 | 3.95 Neigh | 1.5927 | 1.5927 | 1.5927 | 0.0 | 23.64 Comm | 0.16011 | 0.16011 | 0.16011 | 0.0 | 2.38 Output | 0.0040634 | 0.0040634 | 0.0040634 | 0.0 | 0.06 Modify | 4.0145 | 4.0145 | 4.0145 | 0.0 | 59.58 Other | | 0.1735 | | | 2.57 Nlocal: 5600 ave 5600 max 5600 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1352 ave 1352 max 1352 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 5257 ave 5257 max 5257 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 5257 Ave neighs/atom = 0.93875 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 1.4280291 5.9106136 7.032254 0.02814128 8.2441024 62.244 62.244 62.244 0.019873502 0.039656784 0.024893554 5100 1.4435659 5.8998386 7.0336823 0.0063929319 7.3089813 62.244 62.244 62.244 0.0089837757 0.0052773116 0.0049177085 5200 1.3970069 5.9117164 7.0089904 0.0065245686 7.289958 62.244 62.244 62.244 0.008502047 0.0043872479 0.0066844108 5300 1.433167 5.8796669 7.0053428 0.0076478538 7.3346825 62.244 62.244 62.244 0.0061384889 0.0070193789 0.0097856935 5400 1.4191626 5.8830864 6.9977626 0.0026371359 7.1113257 62.244 62.244 62.244 0.0024097043 -0.00082200506 0.0063237084 5500 1.409376 5.8753367 6.982326 0.010180815 7.4207427 62.244 62.244 62.244 0.010429709 0.0081711083 0.011941628 5600 1.4005678 5.882485 6.9825559 0.00036705268 6.9983623 62.244 62.244 62.244 -0.0034485466 0.0031079204 0.0014417843 5700 1.4116833 5.8842566 6.9930582 0.00053413233 7.0160595 62.244 62.244 62.244 0.0016669624 -0.0030741941 0.0030096286 5800 1.409035 5.894902 7.0016235 4.7080816e-05 7.003651 62.244 62.244 62.244 0.0018596854 -5.3937508e-05 -0.0016645054 5900 1.4150353 5.8928576 7.004292 0.0063467985 7.2776043 62.244 62.244 62.244 0.0055755751 0.0090839847 0.0043808358 6000 1.4374163 5.8778036 7.0068171 0.0031890481 7.1441472 62.244 62.244 62.244 0.0067647375 0.0015458579 0.0012565488 Loop time of 1.41082 on 1 procs for 1000 steps with 5600 atoms Performance: 306205.780 tau/day, 708.810 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 | 0.149 | 0.149 | 0.149 | 0.0 | 10.56 Bond | 0.053873 | 0.053873 | 0.053873 | 0.0 | 3.82 Neigh | 0.35532 | 0.35532 | 0.35532 | 0.0 | 25.19 Comm | 0.032433 | 0.032433 | 0.032433 | 0.0 | 2.30 Output | 0.00080752 | 0.00080752 | 0.00080752 | 0.0 | 0.06 Modify | 0.78447 | 0.78447 | 0.78447 | 0.0 | 55.60 Other | | 0.03491 | | | 2.47 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: 5592 ave 5592 max 5592 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 5592 Ave neighs/atom = 0.998571 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 1.4374163 5.8778036 7.0068171 -0.0020672233 6.9177963 62.244 62.244 62.244 0.034504923 -0.030001164 -0.010705429 6100 1.4393824 5.8852696 7.0158274 0.0055792227 7.2560855 62.244 62.244 62.244 0.0072602759 0.0074870643 0.0019903278 6200 1.4265711 5.8853532 7.0058484 0.0019366613 7.0892468 62.244 62.244 62.244 -0.0035411799 0.0047319741 0.0046191897 6300 1.4030198 5.8824874 6.9844843 0.0055760353 7.2246052 62.244 62.244 62.244 0.0031273033 0.0080002386 0.005600564 6400 1.3592064 5.8924876 6.9600714 0.0051450348 7.1816321 62.244 62.244 62.244 0.0042848197 0.0044005693 0.0067497155 6500 1.3946028 5.8798014 6.9751872 0.0051168754 7.1955353 62.244 62.244 62.244 0.0020473208 0.0038175566 0.0094857487 6600 1.3652122 5.8985637 6.9708648 0.0065480579 7.2528439 62.244 62.244 62.244 0.0056940621 0.0062242398 0.0077258719 6700 1.3808929 5.9047739 6.9893913 0.0074053719 7.308289 62.244 62.244 62.244 0.0049554161 0.012378296 0.0048824031 6800 1.4140879 5.891133 7.0018233 0.001592636 7.070407 62.244 62.244 62.244 -9.4421917e-05 -0.00029455229 0.0051668821 6900 1.4364121 5.8904988 7.0187235 0.00647853 7.2977086 62.244 62.244 62.244 0.0024458531 0.0073279625 0.0096617742 7000 1.4370567 5.8900758 7.0188069 0.00098705898 7.0613127 62.244 62.244 62.244 0.0024436343 -0.0011032284 0.001620771 Loop time of 1.44111 on 1 procs for 1000 steps with 5600 atoms Performance: 299769.942 tau/day, 693.912 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 | 0.14928 | 0.14928 | 0.14928 | 0.0 | 10.36 Bond | 0.053511 | 0.053511 | 0.053511 | 0.0 | 3.71 Neigh | 0.35946 | 0.35946 | 0.35946 | 0.0 | 24.94 Comm | 0.033026 | 0.033026 | 0.033026 | 0.0 | 2.29 Output | 0.00081658 | 0.00081658 | 0.00081658 | 0.0 | 0.06 Modify | 0.80995 | 0.80995 | 0.80995 | 0.0 | 56.20 Other | | 0.03506 | | | 2.43 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: 5541 ave 5541 max 5541 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 5541 Ave neighs/atom = 0.989464 Ave special neighs/atom = 0.571429 Neighbor list builds = 153 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 1.4370567 5.8900758 7.0188069 -0.0033603557 6.8740999 62.244 62.244 62.244 -0.094745193 0.10894465 -0.024280521 7100 1.485379 5.864626 7.0313116 0.018625962 7.6475425 57.008236 57.008236 57.008236 0.023222208 0.015549704 0.017105973 7200 1.5367991 5.8157585 7.0228319 0.019179143 7.4580039 50.273593 50.273593 50.273593 0.019479917 0.008906575 0.029150938 7300 1.5692285 5.785208 7.0177529 0.026450106 7.4560147 45.27218 45.27218 45.27218 0.029705272 0.019989987 0.029655059 7400 1.5961415 5.7633541 7.0170377 0.049085262 7.6510208 41.665015 41.665015 41.665015 0.045248259 0.047932005 0.054075524 7500 1.5805951 5.7223115 6.9637843 0.022024393 7.1962354 38.952791 38.952791 38.952791 0.017398546 0.0097043058 0.038970326 7600 1.5679583 5.6928914 6.9244386 0.05023237 7.3717858 36.808633 36.808633 36.808633 0.029561593 0.080716323 0.040419195 7700 1.5214637 5.661404 6.8564322 0.038992847 7.1614257 35.25044 35.25044 35.25044 0.013961981 0.064676103 0.038340457 7800 1.5313649 5.6185256 6.8213307 0.053950562 7.1990319 33.971403 33.971403 33.971403 0.036690654 0.066107903 0.059053129 7900 1.5272701 5.5732963 6.7728851 0.067896988 7.2131774 33.115109 33.115109 33.115109 0.046486851 0.073976177 0.083227936 8000 1.4754162 5.5525858 6.7114461 0.036458901 6.9347086 32.48878 32.48878 32.48878 0.066065978 0.031260775 0.01204995 Loop time of 3.09124 on 1 procs for 1000 steps with 5600 atoms Performance: 139749.554 tau/day, 323.494 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 | 0.38334 | 0.38334 | 0.38334 | 0.0 | 12.40 Bond | 0.079063 | 0.079063 | 0.079063 | 0.0 | 2.56 Neigh | 1.3711 | 1.3711 | 1.3711 | 0.0 | 44.35 Comm | 0.07249 | 0.07249 | 0.07249 | 0.0 | 2.35 Output | 0.00079656 | 0.00079656 | 0.00079656 | 0.0 | 0.03 Modify | 1.1412 | 1.1412 | 1.1412 | 0.0 | 36.92 Other | | 0.04324 | | | 1.40 Nlocal: 5600 ave 5600 max 5600 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2922 ave 2922 max 2922 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 24639 ave 24639 max 24639 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 24639 Ave neighs/atom = 4.39982 Ave special neighs/atom = 0.571429 Neighbor list builds = 335 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) = 7.784 | 7.784 | 7.784 Mbytes Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz 8000 1.4754162 5.5525858 6.7114461 -0.036273091 6.4893215 32.48878 32.48878 32.48878 -0.12886524 -0.13731772 0.15736368 8100 1.4842494 5.5359706 6.701769 0.040754696 6.9494736 32.246136 32.48878 32.48878 0.0098547221 0.069850343 0.042559024 8200 1.4385513 5.5252007 6.6551057 -0.0053954052 6.6228379 31.729684 32.48878 32.48878 0.029251386 -0.023427626 -0.022009975 8300 1.4426011 5.5073818 6.6404676 0.034683453 6.8437384 31.093797 32.48878 32.48878 0.028287259 0.027455229 0.048307871 8400 1.4194517 5.5015592 6.6164624 0.015869651 6.7074209 30.408624 32.48878 32.48878 0.020129982 0.00586219 0.021616782 8500 1.4584335 5.4424151 6.5879365 0.025786252 6.7324275 29.728548 32.48878 32.48878 0.051564744 0.0046756434 0.021118368 8600 1.4578973 5.4266016 6.5717019 0.061244725 6.9097759 29.286286 32.48878 32.48878 0.08652905 0.052448352 0.044756773 8700 1.4158345 5.4199695 6.5320317 0.076133238 6.9466617 28.894001 32.48878 32.48878 0.078560655 0.077921379 0.071917679 8800 1.4360707 5.3986549 6.5266116 0.05106059 6.7993343 28.337182 32.48878 32.48878 0.030158729 0.080651224 0.042371819 8900 1.424778 5.386975 6.5060619 0.0023828771 6.5185272 27.75397 32.48878 32.48878 -0.026562751 0.0076340254 0.026077357 9000 1.4273004 5.369067 6.490135 0.077698761 6.8879525 27.163833 32.48878 32.48878 0.056923916 0.050917329 0.12525504 Loop time of 3.05599 on 1 procs for 1000 steps with 5600 atoms Performance: 141361.930 tau/day, 327.227 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 | 0.60397 | 0.60397 | 0.60397 | 0.0 | 19.76 Bond | 0.080384 | 0.080384 | 0.080384 | 0.0 | 2.63 Neigh | 1.1078 | 1.1078 | 1.1078 | 0.0 | 36.25 Comm | 0.057267 | 0.057267 | 0.057267 | 0.0 | 1.87 Output | 0.0007937 | 0.0007937 | 0.0007937 | 0.0 | 0.03 Modify | 1.1674 | 1.1674 | 1.1674 | 0.0 | 38.20 Other | | 0.03837 | | | 1.26 Nlocal: 5600 ave 5600 max 5600 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3326 ave 3326 max 3326 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 31301 ave 31301 max 31301 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 31301 Ave neighs/atom = 5.58946 Ave special neighs/atom = 0.571429 Neighbor list builds = 168 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) = 7.787 | 7.787 | 7.787 Mbytes Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz 9000 1.4273004 5.369067 6.490135 0.075024718 6.8742614 27.163833 32.48878 32.48878 0.020257355 0.083191009 0.12162579 9100 1.425834 5.3711961 6.4911123 0.045582762 6.7236289 27.13015 32.448495 32.448495 0.047970965 0.045448278 0.043329042 9200 1.4609827 5.3288319 6.4763555 0.072880923 6.8414166 26.96611 32.252298 32.252298 0.053774659 0.093193782 0.071674329 9300 1.448717 5.3331013 6.4709909 0.048446002 6.7095138 26.811748 32.067676 32.067676 0.053340258 0.056657855 0.035339893 9400 1.441683 5.326611 6.4589758 0.014571871 6.5288665 26.578822 31.789089 31.789089 0.043939432 -0.038654064 0.038430244 9500 1.4651641 5.2943716 6.4451796 0.079668782 6.8205296 26.421077 31.600422 31.600422 0.10411792 0.075090335 0.059798087 9600 1.4617024 5.2886327 6.4367216 0.01137432 6.4894218 26.274239 31.424799 31.424799 0.023318055 0.015516795 -0.0047118896 9700 1.4381296 5.2798198 6.4093935 0.030371415 6.5484925 26.173039 31.303761 31.303761 0.05231569 0.025227191 0.013571362 9800 1.4412744 5.2674085 6.3994523 0.076731911 6.7476559 26.092768 31.207754 31.207754 0.05712947 0.077029719 0.096036545 9900 1.4427959 5.2666411 6.39988 0.034570225 6.5551479 26.003248 31.100686 31.100686 0.020955217 0.019879252 0.062876207 10000 1.4337411 5.258442 6.3845688 0.011619021 6.4367617 26.004486 31.102166 31.102166 0.018666906 0.01076669 0.005423467 Loop time of 3.23963 on 1 procs for 1000 steps with 5600 atoms Performance: 133348.758 tau/day, 308.678 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 | 0.71266 | 0.71266 | 0.71266 | 0.0 | 22.00 Bond | 0.0805 | 0.0805 | 0.0805 | 0.0 | 2.48 Neigh | 1.2019 | 1.2019 | 1.2019 | 0.0 | 37.10 Comm | 0.061646 | 0.061646 | 0.061646 | 0.0 | 1.90 Output | 0.00080585 | 0.00080585 | 0.00080585 | 0.0 | 0.02 Modify | 1.1436 | 1.1436 | 1.1436 | 0.0 | 35.30 Other | | 0.03849 | | | 1.19 Nlocal: 5600 ave 5600 max 5600 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3617 ave 3617 max 3617 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 35834 ave 35834 max 35834 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 35834 Ave neighs/atom = 6.39893 Ave special neighs/atom = 0.571429 Neighbor list builds = 162 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) = 7.793 | 7.793 | 7.793 Mbytes Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz 10000 1.4337411 5.258442 6.3845688 0.26156311 7.559515 26.004486 31.102166 31.102166 0.31569183 0.56043401 -0.091436513 10100 1.4450694 5.2429626 6.3779872 0.026397674 6.4966895 26.018016 31.118349 31.102166 0.012890725 0.035887426 0.030414871 10200 1.4603735 5.2471262 6.3941713 0.041496848 6.5804213 25.993694 31.089259 31.102166 0.043043384 0.031851909 0.04959525 10300 1.4434562 5.2268279 6.3605855 0.073867581 6.6874051 25.808018 30.867184 31.102166 0.049265569 0.084151743 0.08818543 10400 1.4391471 5.209772 6.3401449 0.010656841 6.3865593 25.605881 30.625422 31.102166 -0.012411333 -0.014743822 0.059125677 10500 1.4239127 5.2146206 6.3330277 0.08346505 6.689122 25.342982 30.310987 31.102166 0.15420896 0.040839126 0.055347067 10600 1.4524651 5.1794989 6.3203324 -0.025909515 6.2120807 25.079294 29.995608 31.102166 -0.014573849 -0.056558124 -0.0065965719 10700 1.4455577 5.1721256 6.3075337 0.084888991 6.6555495 24.842844 29.712806 31.102166 0.10063515 0.067972312 0.08605951 10800 1.4598996 5.15251 6.2991829 0.11430526 6.7624231 24.700034 29.542001 31.102166 0.12408423 0.12316195 0.095669606 10900 1.4149128 5.1641212 6.2754594 0.045495923 6.4584246 24.605124 29.428485 31.102166 0.10001213 0.053235051 -0.016759411 11000 1.3909637 5.1566933 6.2492208 0.046382806 6.433354 24.446408 29.238657 31.102166 0.091440494 0.0046064525 0.043101472 Loop time of 3.41971 on 1 procs for 1000 steps with 5600 atoms Performance: 126326.531 tau/day, 292.423 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 | 0.78521 | 0.78521 | 0.78521 | 0.0 | 22.96 Bond | 0.080655 | 0.080655 | 0.080655 | 0.0 | 2.36 Neigh | 1.2846 | 1.2846 | 1.2846 | 0.0 | 37.57 Comm | 0.064334 | 0.064334 | 0.064334 | 0.0 | 1.88 Output | 0.00080228 | 0.00080228 | 0.00080228 | 0.0 | 0.02 Modify | 1.1651 | 1.1651 | 1.1651 | 0.0 | 34.07 Other | | 0.03903 | | | 1.14 Nlocal: 5600 ave 5600 max 5600 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3805 ave 3805 max 3805 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 40038 ave 40038 max 40038 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 40038 Ave neighs/atom = 7.14964 Ave special neighs/atom = 0.571429 Neighbor list builds = 162 Dangerous builds = 0 Total wall time: 0:00:22