LAMMPS (5 Oct 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 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 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 = 6.96454 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 3.14543 on 4 procs for 5000 steps with 5600 atoms Performance: 686709.553 tau/day, 1589.605 timesteps/s 99.2% CPU use with 4 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.081628 | 0.12747 | 0.17984 | 12.8 | 4.05 Bond | 0.037502 | 0.057149 | 0.076595 | 7.6 | 1.82 Neigh | 0.65705 | 0.6588 | 0.66084 | 0.2 | 20.94 Comm | 0.1653 | 0.23616 | 0.29975 | 12.9 | 7.51 Output | 0.0021076 | 0.0028133 | 0.003227 | 0.9 | 0.09 Modify | 1.8231 | 1.8972 | 1.9713 | 5.2 | 60.32 Other | | 0.1658 | | | 5.27 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 0.74555 on 4 procs for 1000 steps with 5600 atoms Performance: 579437.739 tau/day, 1341.291 timesteps/s 99.6% CPU use with 4 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.020915 | 0.033416 | 0.047822 | 6.7 | 4.48 Bond | 0.0076883 | 0.011506 | 0.015239 | 3.3 | 1.54 Neigh | 0.14225 | 0.14262 | 0.14297 | 0.1 | 19.13 Comm | 0.030192 | 0.0485 | 0.064376 | 7.2 | 6.51 Output | 0.00039148 | 0.0005275 | 0.00062299 | 0.4 | 0.07 Modify | 0.46557 | 0.47773 | 0.49051 | 1.7 | 64.08 Other | | 0.03125 | | | 4.19 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 0.761012 on 4 procs for 1000 steps with 5600 atoms Performance: 567665.504 tau/day, 1314.041 timesteps/s 99.6% CPU use with 4 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.022122 | 0.034862 | 0.048912 | 6.6 | 4.58 Bond | 0.0078702 | 0.011574 | 0.015191 | 3.2 | 1.52 Neigh | 0.1398 | 0.14013 | 0.14044 | 0.1 | 18.41 Comm | 0.029736 | 0.047586 | 0.064077 | 7.3 | 6.25 Output | 0.00039291 | 0.00053465 | 0.00063396 | 0.4 | 0.07 Modify | 0.48838 | 0.49907 | 0.50959 | 1.4 | 65.58 Other | | 0.02726 | | | 3.58 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 1.40621 on 4 procs for 1000 steps with 5600 atoms Performance: 307209.818 tau/day, 711.134 timesteps/s 99.5% CPU use with 4 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.057011 | 0.094542 | 0.13471 | 11.0 | 6.72 Bond | 0.012043 | 0.017356 | 0.022935 | 3.8 | 1.23 Neigh | 0.50655 | 0.50716 | 0.50781 | 0.1 | 36.07 Comm | 0.060325 | 0.10627 | 0.14985 | 12.0 | 7.56 Output | 0.0003705 | 0.00040978 | 0.00051475 | 0.3 | 0.03 Modify | 0.60798 | 0.63453 | 0.65863 | 2.9 | 45.12 Other | | 0.04594 | | | 3.27 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 1.3981 on 4 procs for 1000 steps with 5600 atoms Performance: 308990.110 tau/day, 715.255 timesteps/s 99.4% CPU use with 4 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.090644 | 0.15054 | 0.22186 | 13.5 | 10.77 Bond | 0.013196 | 0.017756 | 0.022439 | 2.9 | 1.27 Neigh | 0.40253 | 0.40269 | 0.40288 | 0.0 | 28.80 Comm | 0.057128 | 0.13282 | 0.1979 | 15.4 | 9.50 Output | 0.00036597 | 0.00040632 | 0.0004673 | 0.2 | 0.03 Modify | 0.62613 | 0.65125 | 0.67228 | 2.1 | 46.58 Other | | 0.04265 | | | 3.05 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 1.38185 on 4 procs for 1000 steps with 5600 atoms Performance: 312625.215 tau/day, 723.669 timesteps/s 99.4% CPU use with 4 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.11291 | 0.17289 | 0.23942 | 12.0 | 12.51 Bond | 0.013814 | 0.017709 | 0.022031 | 2.5 | 1.28 Neigh | 0.40444 | 0.4048 | 0.40511 | 0.0 | 29.29 Comm | 0.055045 | 0.12527 | 0.18875 | 14.9 | 9.07 Output | 0.0003531 | 0.00038058 | 0.00045681 | 0.2 | 0.03 Modify | 0.60769 | 0.62523 | 0.64283 | 1.7 | 45.25 Other | | 0.03557 | | | 2.57 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 1.36647 on 4 procs for 1000 steps with 5600 atoms Performance: 316143.197 tau/day, 731.813 timesteps/s 99.4% CPU use with 4 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.13847 | 0.19365 | 0.24916 | 9.9 | 14.17 Bond | 0.014236 | 0.017841 | 0.02132 | 2.2 | 1.31 Neigh | 0.37634 | 0.37662 | 0.37685 | 0.0 | 27.56 Comm | 0.057297 | 0.11588 | 0.17429 | 13.5 | 8.48 Output | 0.00035167 | 0.00037664 | 0.00044203 | 0.2 | 0.03 Modify | 0.61282 | 0.62929 | 0.64128 | 1.4 | 46.05 Other | | 0.03282 | | | 2.40 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 Total wall time: 0:00:10