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 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/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) = 7.216 | 7.384 | 7.552 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 -0.00088278431 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 0.0001686213 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 0.00098119435 -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 0.0062444035 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 -0.00063825028 2500 1.4200762 5.9359254 7.0513193 0.002831965 7.1732722 62.244 62.244 62.244 -0.00030414188 0.0039571831 0.0048428539 2600 1.3876469 5.9249124 7.0148347 -0.0017777223 6.9382806 62.244 62.244 62.244 -0.00047616388 -0.0025484917 -0.0023085112 2700 1.4099941 5.916763 7.0242378 0.0070716262 7.3287634 62.244 62.244 62.244 0.012628756 0.0053812867 0.0032048357 2800 1.4444643 5.9283432 7.0628925 0.0019400019 7.1464348 62.244 62.244 62.244 0.0014895075 0.0046367395 -0.0003062412 2900 1.3902832 5.9152516 7.0072446 -0.0021662211 6.9139606 62.244 62.244 62.244 -0.0012374413 -0.00056403267 -0.0046971892 3000 1.3711706 5.922146 6.999127 0.011101505 7.4771914 62.244 62.244 62.244 0.011063833 0.012093025 0.010147658 3100 1.3569137 5.9171753 6.9829583 -0.0028266781 6.861233 62.244 62.244 62.244 -0.0069507246 0.001008439 -0.0025377485 3200 1.4004275 5.905939 7.0058998 0.005439464 7.2401395 62.244 62.244 62.244 0.010352181 0.0057594129 0.00020679783 3300 1.3641217 5.9145275 6.985972 -0.0027212797 6.8687855 62.244 62.244 62.244 -0.00065933477 -0.0057712994 -0.0017332048 3400 1.3868722 5.9059546 6.9952684 0.0092591181 7.3939939 62.244 62.244 62.244 0.010690872 0.01075251 0.0063339724 3500 1.3939168 5.8992292 6.9940762 0.0074340103 7.3142071 62.244 62.244 62.244 0.010137319 0.0044252681 0.0077394433 3600 1.3982507 5.921946 7.020197 0.0056794467 7.2647712 62.244 62.244 62.244 0.0023367139 0.0080592038 0.0066424225 3700 1.4019908 5.9059954 7.007184 0.0065915246 7.291035 62.244 62.244 62.244 0.0049554227 0.010827006 0.0039921455 3800 1.3960735 5.9020788 6.9986197 0.0027763543 7.1181779 62.244 62.244 62.244 -0.0015907599 0.0025861989 0.007333624 3900 1.4352827 5.8986213 7.025959 0.0034983366 7.1766079 62.244 62.244 62.244 0.0030418079 0.002773833 0.0046793689 4000 1.4121839 5.9079032 7.017098 0.0050464926 7.2344152 62.244 62.244 62.244 0.0045546986 0.0064116168 0.0041731626 4100 1.3989613 5.9082377 7.0070468 0.00042898744 7.0255203 62.244 62.244 62.244 0.0025736361 0.0025182434 -0.0038049172 4200 1.3998851 5.8998106 6.9993454 0.0042770066 7.1835262 62.244 62.244 62.244 0.0013728904 0.0064694548 0.0049886746 4300 1.4076016 5.9044534 7.0100491 0.0066777871 7.2976147 62.244 62.244 62.244 0.0073579039 0.0048129651 0.0078624924 4400 1.3948857 5.9101851 7.0057931 0.0013429373 7.063624 62.244 62.244 62.244 -0.00084288143 0.0061856571 -0.0013139638 4500 1.4356157 5.8855608 7.01316 -0.0013707942 6.9541295 62.244 62.244 62.244 -0.0018523205 -0.0050195956 0.0027595334 4600 1.4148397 5.8957564 7.0070372 0.0072212968 7.318008 62.244 62.244 62.244 0.011376867 0.0074399971 0.0028470263 4700 1.3695106 5.8936708 6.969348 0.0017509017 7.0447471 62.244 62.244 62.244 -0.0061975951 0.0044076775 0.0070426225 4800 1.4142735 5.8887578 6.9995939 0.0081923232 7.35238 62.244 62.244 62.244 0.013343877 0.0054560473 0.0057770449 4900 1.4300042 5.8867398 7.0099315 0.0070875112 7.3151411 62.244 62.244 62.244 0.0080416381 0.0042409901 0.0089799056 5000 1.4286039 5.8964609 7.0185527 -0.003158533 6.8825368 62.244 62.244 62.244 0.0024975808 -0.0097503027 -0.0022228771 Loop time of 3.4608 on 4 procs for 5000 steps with 5600 atoms Performance: 624133.913 tau/day, 1444.754 timesteps/s 98.0% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.083226 | 0.13336 | 0.18611 | 13.0 | 3.85 Bond | 0.045169 | 0.066142 | 0.087486 | 7.8 | 1.91 Neigh | 0.57772 | 0.57997 | 0.58211 | 0.3 | 16.76 Comm | 0.19402 | 0.26217 | 0.32776 | 12.2 | 7.58 Output | 0.0027087 | 0.0035715 | 0.0041978 | 0.9 | 0.10 Modify | 2.1223 | 2.2156 | 2.2842 | 4.2 | 64.02 Other | | 0.2 | | | 5.78 Nlocal: 1400 ave 1844 max 907 min Histogram: 1 1 0 0 0 0 0 0 0 2 Nghost: 642 ave 714 max 581 min Histogram: 1 1 0 0 0 0 1 0 0 1 Neighs: 1307.25 ave 1883 max 682 min Histogram: 2 0 0 0 0 0 0 0 0 2 Total # of neighbors = 5229 Ave neighs/atom = 0.93375 Ave special neighs/atom = 0.571429 Neighbor list builds = 762 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) = 7.217 | 7.395 | 7.573 Mbytes Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz 5000 1.4286039 5.8964609 7.0185527 -0.017900244 6.2477142 62.244 62.244 62.244 -0.017934885 -0.027283526 -0.0084823215 5100 1.4251274 5.887521 7.0068821 0.0066290394 7.2923486 62.244 62.244 62.244 0.0033173534 0.0056467845 0.01092298 5200 1.4246222 5.8928547 7.0118192 -0.00025763331 7.0007247 62.244 62.244 62.244 -0.001891953 -0.0031121381 0.0042311911 5300 1.3905023 5.9024119 6.994577 0.0026824588 7.1100918 62.244 62.244 62.244 0.003106008 0.0040692376 0.00087213068 5400 1.4139617 5.8906493 7.0012405 0.003175173 7.137973 62.244 62.244 62.244 0.0034546577 0.003858524 0.0022123373 5500 1.4160473 5.8891813 7.0014106 0.0032907848 7.1431217 62.244 62.244 62.244 0.0014909385 0.0067546452 0.0016267707 5600 1.4185962 5.8932473 7.0074786 0.013015823 7.5679792 62.244 62.244 62.244 0.011297248 0.011426835 0.016323387 5700 1.4115847 5.892193 7.0009171 0.0080660065 7.3482637 62.244 62.244 62.244 0.0096534077 0.004127271 0.010417341 5800 1.3920238 5.8874957 6.9808558 0.0087013878 7.3555639 62.244 62.244 62.244 0.0070865796 0.0093328615 0.0096847223 5900 1.389416 5.8996657 6.9909775 0.0053218583 7.2201528 62.244 62.244 62.244 0.0050547275 0.0054113274 0.0054995198 6000 1.4079053 5.8795437 6.9853779 0.0066005053 7.2696156 62.244 62.244 62.244 0.0087434104 0.0013589366 0.0096991689 Loop time of 0.793224 on 4 procs for 1000 steps with 5600 atoms Performance: 544612.641 tau/day, 1260.677 timesteps/s 98.6% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.018101 | 0.036068 | 0.051689 | 7.6 | 4.55 Bond | 0.0083735 | 0.013206 | 0.017318 | 3.6 | 1.66 Neigh | 0.12864 | 0.1293 | 0.13002 | 0.1 | 16.30 Comm | 0.037184 | 0.056407 | 0.077999 | 7.4 | 7.11 Output | 0.00048971 | 0.00072509 | 0.00083923 | 0.0 | 0.09 Modify | 0.49526 | 0.51293 | 0.52997 | 2.2 | 64.66 Other | | 0.04459 | | | 5.62 Nlocal: 1400 ave 1844 max 884 min Histogram: 1 1 0 0 0 0 0 0 0 2 Nghost: 713.5 ave 818 max 656 min Histogram: 1 1 1 0 0 0 0 0 0 1 Neighs: 1315 ave 1956 max 573 min Histogram: 1 0 1 0 0 0 0 0 0 2 Total # of neighbors = 5260 Ave neighs/atom = 0.939286 Ave special neighs/atom = 0.571429 Neighbor list builds = 156 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) = 7.217 | 7.395 | 7.573 Mbytes Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz 6000 1.4079053 5.8795437 6.9853779 0.010184208 7.4239406 62.244 62.244 62.244 0.0015995549 0.064769849 -0.035816779 6100 1.4031886 5.8721732 6.9743027 0.0039601 7.1448365 62.244 62.244 62.244 0.0019177243 0.0048575488 0.005105027 6200 1.4078378 5.8813987 6.9871798 -0.0019043091 6.9051745 62.244 62.244 62.244 -0.0012543967 -0.0035545317 -0.00090399881 6300 1.3898748 5.8818577 6.97353 0.0050781011 7.1922083 62.244 62.244 62.244 0.0037642013 0.0035169519 0.0079531499 6400 1.3901345 5.8620878 6.953964 -0.0013161864 6.897285 62.244 62.244 62.244 0.0024166375 -0.0023907165 -0.0039744801 6500 1.3990792 5.8647534 6.9636551 0.0025190902 7.0721348 62.244 62.244 62.244 0.003080505 -0.00072200043 0.0051987659 6600 1.3802747 5.8639204 6.9480523 0.0030906745 7.0811461 62.244 62.244 62.244 0.0041979458 0.0059358092 -0.00086173155 6700 1.392968 5.8692368 6.9633385 0.00060394401 6.9893462 62.244 62.244 62.244 0.0037955666 0.00058857296 -0.0025723075 6800 1.4139599 5.8777321 6.9883218 0.0064457022 7.2658932 62.244 62.244 62.244 0.0066202313 0.0077537688 0.0049631066 6900 1.3913822 5.8914016 6.9842578 0.0012411779 7.0377066 62.244 62.244 62.244 -0.0029791199 0.0027656154 0.0039370381 7000 1.4203244 5.8676225 6.9832112 0.0053040447 7.2116194 62.244 62.244 62.244 0.0024159021 0.0053958945 0.0081003375 Loop time of 0.812983 on 4 procs for 1000 steps with 5600 atoms Performance: 531376.713 tau/day, 1230.039 timesteps/s 98.2% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.020489 | 0.038507 | 0.054352 | 7.9 | 4.74 Bond | 0.0086164 | 0.013153 | 0.017908 | 3.5 | 1.62 Neigh | 0.13205 | 0.13275 | 0.13353 | 0.1 | 16.33 Comm | 0.039251 | 0.05774 | 0.079146 | 7.7 | 7.10 Output | 0.00057149 | 0.00076026 | 0.00087905 | 0.0 | 0.09 Modify | 0.51332 | 0.52873 | 0.54512 | 2.1 | 65.04 Other | | 0.04134 | | | 5.09 Nlocal: 1400 ave 1861 max 953 min Histogram: 2 0 0 0 0 0 0 0 1 1 Nghost: 732.5 ave 799 max 634 min Histogram: 1 0 0 0 0 1 0 0 1 1 Neighs: 1478.5 ave 2087 max 852 min Histogram: 1 1 0 0 0 0 0 0 0 2 Total # of neighbors = 5914 Ave neighs/atom = 1.05607 Ave special neighs/atom = 0.571429 Neighbor list builds = 154 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) = 7.217 | 7.395 | 7.573 Mbytes Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz 7000 1.4203244 5.8676225 6.9832112 -0.040722281 5.2295869 62.244 62.244 62.244 -0.12474488 0.041369653 -0.038791619 7100 1.4820526 5.8454198 7.0094927 0.013935005 7.4687465 56.934813 56.934813 56.934813 0.011753675 0.011015866 0.019035475 7200 1.5504398 5.8024995 7.0202869 0.023075447 7.5454178 50.323226 50.323226 50.323226 0.02128889 0.024383628 0.023553823 7300 1.5422614 5.7803177 6.9916814 0.022398755 7.3670099 45.442117 45.442117 45.442117 0.011815608 0.027421849 0.027958808 7400 1.5762224 5.7500188 6.988057 0.044637382 7.5673845 41.732187 41.732187 41.732187 0.045858714 0.035776277 0.052277154 7500 1.5734284 5.7222605 6.9581042 0.029862564 7.2743396 38.996336 38.996336 38.996336 0.024440229 0.034455527 0.030691934 7600 1.5572312 5.6929606 6.9160823 0.050216724 7.366563 36.898208 36.898208 36.898208 0.059366814 0.056376093 0.034907266 7700 1.5225653 5.659289 6.8551824 0.042054552 7.1814902 35.15611 35.15611 35.15611 0.043735305 0.039349247 0.043079104 7800 1.5081978 5.629903 6.8145116 0.057013188 7.2106251 33.885255 33.885255 33.885255 0.055017894 0.053733429 0.062288242 7900 1.4721367 5.5821237 6.7384082 0.067262555 7.1645957 32.860322 32.860322 32.860322 0.097134972 0.066643481 0.03800921 8000 1.4710105 5.5302806 6.6856805 0.054118027 7.0029681 32.020862 32.020862 32.020862 0.039052412 0.059044234 0.064257435 Loop time of 1.47728 on 4 procs for 1000 steps with 5600 atoms Performance: 292430.022 tau/day, 676.921 timesteps/s 98.1% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.064968 | 0.10073 | 0.1395 | 10.5 | 6.82 Bond | 0.014031 | 0.019927 | 0.02572 | 3.7 | 1.35 Neigh | 0.52043 | 0.52145 | 0.52214 | 0.1 | 35.30 Comm | 0.069327 | 0.11344 | 0.15499 | 11.3 | 7.68 Output | 0.00045276 | 0.00050163 | 0.00058174 | 0.0 | 0.03 Modify | 0.65598 | 0.67559 | 0.69898 | 2.4 | 45.73 Other | | 0.04563 | | | 3.09 Nlocal: 1400 ave 1711 max 1074 min Histogram: 2 0 0 0 0 0 0 0 0 2 Nghost: 1617 ave 1748 max 1514 min Histogram: 1 0 0 2 0 0 0 0 0 1 Neighs: 6221.75 ave 8875 max 3829 min Histogram: 2 0 0 0 0 0 0 0 1 1 Total # of neighbors = 24887 Ave neighs/atom = 4.44411 Ave special neighs/atom = 0.571429 Neighbor list builds = 340 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) = 7.227 | 7.408 | 7.596 Mbytes Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz 8000 1.4710105 5.5302806 6.6856805 0.19181859 7.81029 32.020862 32.020862 32.020862 0.26866704 0.14123342 0.16555531 8100 1.47531 5.5300767 6.6888537 0.072844262 7.1138998 31.868578 32.020862 32.020862 0.090224787 0.062332105 0.065975895 8200 1.448408 5.51143 6.6490768 0.069870568 7.0519422 31.491082 32.020862 32.020862 0.087940256 0.058037199 0.063634249 8300 1.4057002 5.4923673 6.5964694 0.065508742 6.9688194 31.043742 32.020862 32.020862 0.079268242 0.048811269 0.068446714 8400 1.3991297 5.4626242 6.5615657 -0.017027709 6.4660067 30.650474 32.020862 32.020862 0.0088006578 -0.001632039 -0.058251747 8500 1.4126457 5.4676374 6.5771949 0.012615987 6.6471389 30.279686 32.020862 32.020862 0.010145607 0.017449486 0.010252867 8600 1.4250925 5.4367644 6.5560982 0.057260287 6.8682646 29.775194 32.020862 32.020862 0.05660339 0.10551068 0.0096667873 8700 1.4259617 5.431439 6.5514555 0.060058224 6.8743509 29.36374 32.020862 32.020862 0.059243843 0.040552126 0.080378702 8800 1.4336545 5.3949149 6.5209738 0.052324111 6.7965365 28.763424 32.020862 32.020862 0.02607362 0.067534725 0.063363987 8900 1.4228767 5.3718196 6.489413 0.04039784 6.6975045 28.133143 32.020862 32.020862 0.038493401 0.059136317 0.023563801 9000 1.3840335 5.3851579 6.4722421 0.055356171 6.7513156 27.534332 32.020862 32.020862 0.067391117 0.061540537 0.03713686 Loop time of 1.41644 on 4 procs for 1000 steps with 5600 atoms Performance: 304989.819 tau/day, 705.995 timesteps/s 98.1% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.111 | 0.15928 | 0.20768 | 11.1 | 11.25 Bond | 0.014816 | 0.020169 | 0.024592 | 3.1 | 1.42 Neigh | 0.40146 | 0.40175 | 0.40221 | 0.0 | 28.36 Comm | 0.063586 | 0.11635 | 0.16698 | 14.1 | 8.21 Output | 0.00045538 | 0.00050312 | 0.00063586 | 0.0 | 0.04 Modify | 0.66405 | 0.67875 | 0.69575 | 1.6 | 47.92 Other | | 0.03963 | | | 2.80 Nlocal: 1400 ave 1641 max 1120 min Histogram: 1 0 1 0 0 0 0 0 0 2 Nghost: 1593.5 ave 1674 max 1480 min Histogram: 1 0 0 1 0 0 0 0 0 2 Neighs: 7766.25 ave 10004 max 5618 min Histogram: 2 0 0 0 0 0 0 0 0 2 Total # of neighbors = 31065 Ave neighs/atom = 5.54732 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) = 7.228 | 7.409 | 7.596 Mbytes Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz 9000 1.3840335 5.3851579 6.4722421 0.16503405 7.3042475 27.534332 32.020862 32.020862 0.18505216 0.10781406 0.20223595 9100 1.3884253 5.3614209 6.4519546 -0.00091586458 6.4474179 27.373411 31.83372 31.83372 0.022761165 -0.0041100422 -0.021398716 9200 1.420492 5.3303864 6.4461068 0.059143817 6.7274082 27.005021 31.405303 31.405303 0.083033013 0.062389471 0.032008967 9300 1.4715513 5.2993502 6.4551749 -0.0012173753 6.4496031 26.66115 31.005402 31.005402 3.6757409e-05 -0.035942133 0.03225325 9400 1.446323 5.2997487 6.4357579 0.089723486 6.8324557 26.355721 30.650205 30.650205 0.074549411 0.091827859 0.10279319 9500 1.4429552 5.2778071 6.4111711 0.074185245 6.7328342 26.184941 30.451597 30.451597 0.081909739 0.072238574 0.068407422 9600 1.4570864 5.2601352 6.4045984 0.0580315 6.6544318 26.122769 30.379295 30.379295 0.060115487 0.027228888 0.086750125 9700 1.4421488 5.2741205 6.4068511 0.044711738 6.5981759 26.069954 30.317874 30.317874 0.093367845 0.025219144 0.015548226 9800 1.4305027 5.2831767 6.4067599 0.064007051 6.6787519 26.009567 30.247648 30.247648 0.1207317 0.021857174 0.049432283 9900 1.4457473 5.2513943 6.3869514 0.016264617 6.4551575 25.895064 30.114487 30.114487 0.055652525 0.015908352 -0.022767026 10000 1.4739193 5.2108898 6.3685744 0.066079547 6.6416503 25.768894 29.967759 29.967759 0.059174033 0.048716715 0.090347892 Loop time of 1.47405 on 4 procs for 1000 steps with 5600 atoms Performance: 293069.938 tau/day, 678.403 timesteps/s 98.3% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.14109 | 0.19261 | 0.2429 | 10.7 | 13.07 Bond | 0.015511 | 0.020164 | 0.023957 | 2.5 | 1.37 Neigh | 0.43698 | 0.43723 | 0.43759 | 0.0 | 29.66 Comm | 0.064379 | 0.1184 | 0.17429 | 14.5 | 8.03 Output | 0.00053048 | 0.00056964 | 0.00067139 | 0.0 | 0.04 Modify | 0.65413 | 0.66598 | 0.68039 | 1.3 | 45.18 Other | | 0.0391 | | | 2.65 Nlocal: 1400 ave 1629 max 1159 min Histogram: 1 1 0 0 0 0 0 0 0 2 Nghost: 1760.25 ave 1871 max 1635 min Histogram: 1 0 0 1 0 0 0 1 0 1 Neighs: 9467.75 ave 11967 max 6712 min Histogram: 1 1 0 0 0 0 0 0 0 2 Total # of neighbors = 37871 Ave neighs/atom = 6.76268 Ave special neighs/atom = 0.571429 Neighbor list builds = 163 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) = 7.229 | 7.413 | 7.597 Mbytes Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz 10000 1.4739193 5.2108898 6.3685744 0.15675952 7.0163882 25.768894 29.967759 29.967759 0.15485552 -0.045372029 0.36079506 10100 1.450711 5.2108741 6.3503298 0.0083383764 6.3849239 25.819477 30.026584 29.967759 0.0025039775 -0.0028716599 0.025382812 10200 1.4627819 5.2187046 6.3676414 0.031215755 6.4961258 25.717327 29.907789 29.967759 0.04657158 0.0023172248 0.044758461 10300 1.4689915 5.2231223 6.3769364 0.094530779 6.7645053 25.667024 29.84929 29.967759 0.10402187 0.089461211 0.090109255 10400 1.465366 5.211321 6.3622875 0.057765151 6.5976168 25.585426 29.754396 29.967759 0.025724468 0.03148259 0.1160884 10500 1.4206144 5.2096595 6.325476 0.029618225 6.4439115 25.348314 29.478648 29.967759 0.016757876 -0.021974627 0.094071428 10600 1.4490516 5.1686358 6.3067882 0.10186675 6.705618 25.082174 29.169143 29.967759 0.13985672 0.13649813 0.029245401 10700 1.42637 5.1516578 6.271995 0.12577606 6.7554051 24.851151 28.900476 29.967759 0.099699897 0.11678127 0.16084703 10800 1.4675204 5.1334029 6.2860615 0.054610838 6.494291 24.752517 28.78577 29.967759 0.018006539 0.090588468 0.055237507 10900 1.4312627 5.1332052 6.2573854 -0.0020120377 6.2496947 24.782913 28.821119 29.967759 -0.0035770106 0.047436898 -0.049896 11000 1.3986074 5.1272068 6.225738 0.045641244 6.3993661 24.72401 28.752618 29.967759 0.052336235 0.073561738 0.011025759 Loop time of 1.50406 on 4 procs for 1000 steps with 5600 atoms Performance: 287222.965 tau/day, 664.868 timesteps/s 98.3% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.16856 | 0.21287 | 0.26569 | 9.4 | 14.15 Bond | 0.016815 | 0.020397 | 0.023304 | 1.9 | 1.36 Neigh | 0.44152 | 0.44161 | 0.44172 | 0.0 | 29.36 Comm | 0.067729 | 0.1232 | 0.16886 | 13.0 | 8.19 Output | 0.00045419 | 0.00048572 | 0.0005734 | 0.0 | 0.03 Modify | 0.6568 | 0.66799 | 0.6841 | 1.3 | 44.41 Other | | 0.0375 | | | 2.49 Nlocal: 1400 ave 1605 max 1229 min Histogram: 1 1 0 0 0 0 0 1 0 1 Nghost: 1859 ave 1964 max 1718 min Histogram: 1 0 0 0 0 1 0 1 0 1 Neighs: 10208.2 ave 13091 max 7670 min Histogram: 1 1 0 0 0 0 1 0 0 1 Total # of neighbors = 40833 Ave neighs/atom = 7.29161 Ave special neighs/atom = 0.571429 Neighbor list builds = 160 Dangerous builds = 0 Total wall time: 0:00:10