Loading examples/melt/log.5Oct16.melt.g++.1→examples/melt/log.27Nov18.melt.g++.1 +20 −13 Original line number Diff line number Diff line LAMMPS (5 Oct 2016) LAMMPS (27 Nov 2018) using 1 OpenMP thread(s) per MPI task # 3d Lennard-Jones melt units lj Loading @@ -12,6 +13,7 @@ Created orthogonal box = (0 0 0) to (16.796 16.796 16.796) 1 by 1 by 1 MPI processor grid create_atoms 1 box Created 4000 atoms Time spent = 0.000645638 secs mass 1 1.0 velocity all create 3.0 87287 Loading @@ -35,13 +37,18 @@ fix 1 all nve thermo 50 run 250 Neighbor list info ... 1 neighbor list requests update every 20 steps, delay 0 steps, check no max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 2.8 ghost atom cutoff = 2.8 binsize = 1.4 -> bins = 12 12 12 Memory usage per processor = 2.19271 Mbytes binsize = 1.4, bins = 12 12 12 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair lj/cut, perpetual attributes: half, newton on pair build: half/bin/atomonly/newton stencil: half/bin/3d/newton bin: standard Per MPI rank memory allocation (min/avg/max) = 3.221 | 3.221 | 3.221 Mbytes Step Temp E_pair E_mol TotEng Press 0 3 -6.7733681 0 -2.2744931 -3.7033504 50 1.6758903 -4.7955425 0 -2.2823355 5.670064 Loading @@ -49,20 +56,20 @@ Step Temp E_pair E_mol TotEng Press 150 1.6324555 -4.7286791 0 -2.280608 5.9589514 200 1.6630725 -4.7750988 0 -2.2811136 5.7364886 250 1.6275257 -4.7224992 0 -2.281821 5.9567365 Loop time of 0.724365 on 1 procs for 250 steps with 4000 atoms Loop time of 0.729809 on 1 procs for 250 steps with 4000 atoms Performance: 149096.106 tau/day, 345.130 timesteps/s 99.8% CPU use with 1 MPI tasks x no OpenMP threads Performance: 147983.915 tau/day, 342.555 timesteps/s 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.61654 | 0.61654 | 0.61654 | 0.0 | 85.11 Neigh | 0.081313 | 0.081313 | 0.081313 | 0.0 | 11.23 Comm | 0.010941 | 0.010941 | 0.010941 | 0.0 | 1.51 Output | 9.4891e-05 | 9.4891e-05 | 9.4891e-05 | 0.0 | 0.01 Modify | 0.012401 | 0.012401 | 0.012401 | 0.0 | 1.71 Other | | 0.003077 | | | 0.42 Pair | 0.60661 | 0.60661 | 0.60661 | 0.0 | 83.12 Neigh | 0.092198 | 0.092198 | 0.092198 | 0.0 | 12.63 Comm | 0.013581 | 0.013581 | 0.013581 | 0.0 | 1.86 Output | 0.0001452 | 0.0001452 | 0.0001452 | 0.0 | 0.02 Modify | 0.014395 | 0.014395 | 0.014395 | 0.0 | 1.97 Other | | 0.002878 | | | 0.39 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Loading examples/melt/log.5Oct16.melt.g++.4→examples/melt/log.27Nov18.melt.g++.4 +20 −13 Original line number Diff line number Diff line LAMMPS (5 Oct 2016) LAMMPS (27 Nov 2018) using 1 OpenMP thread(s) per MPI task # 3d Lennard-Jones melt units lj Loading @@ -12,6 +13,7 @@ Created orthogonal box = (0 0 0) to (16.796 16.796 16.796) 1 by 2 by 2 MPI processor grid create_atoms 1 box Created 4000 atoms Time spent = 0.00041604 secs mass 1 1.0 velocity all create 3.0 87287 Loading @@ -35,13 +37,18 @@ fix 1 all nve thermo 50 run 250 Neighbor list info ... 1 neighbor list requests update every 20 steps, delay 0 steps, check no max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 2.8 ghost atom cutoff = 2.8 binsize = 1.4 -> bins = 12 12 12 Memory usage per processor = 2.10344 Mbytes binsize = 1.4, bins = 12 12 12 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair lj/cut, perpetual attributes: half, newton on pair build: half/bin/atomonly/newton stencil: half/bin/3d/newton bin: standard Per MPI rank memory allocation (min/avg/max) = 2.705 | 2.705 | 2.705 Mbytes Step Temp E_pair E_mol TotEng Press 0 3 -6.7733681 0 -2.2744931 -3.7033504 50 1.6754119 -4.7947589 0 -2.2822693 5.6615925 Loading @@ -49,20 +56,20 @@ Step Temp E_pair E_mol TotEng Press 150 1.6596605 -4.7699432 0 -2.2810749 5.7830138 200 1.6371874 -4.7365462 0 -2.2813789 5.9246674 250 1.6323462 -4.7292021 0 -2.2812949 5.9762238 Loop time of 0.210997 on 4 procs for 250 steps with 4000 atoms Loop time of 0.223329 on 4 procs for 250 steps with 4000 atoms Performance: 511855.365 tau/day, 1184.850 timesteps/s 99.6% CPU use with 4 MPI tasks x no OpenMP threads Performance: 483592.231 tau/day, 1119.426 timesteps/s 97.3% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.15475 | 0.16099 | 0.1682 | 1.2 | 76.30 Neigh | 0.020829 | 0.021108 | 0.021522 | 0.2 | 10.00 Comm | 0.01674 | 0.024412 | 0.030987 | 3.3 | 11.57 Output | 0.00011587 | 0.0001238 | 0.00013185 | 0.1 | 0.06 Modify | 0.0031242 | 0.0031361 | 0.0031476 | 0.0 | 1.49 Other | | 0.001227 | | | 0.58 Pair | 0.15881 | 0.16314 | 0.16859 | 0.9 | 73.05 Neigh | 0.02472 | 0.025218 | 0.025828 | 0.3 | 11.29 Comm | 0.025185 | 0.030091 | 0.034351 | 1.9 | 13.47 Output | 0.00015163 | 0.00019169 | 0.00030899 | 0.0 | 0.09 Modify | 0.0037532 | 0.0038366 | 0.0040054 | 0.2 | 1.72 Other | | 0.00085 | | | 0.38 Nlocal: 1000 ave 1010 max 982 min Histogram: 1 0 0 0 0 0 1 0 0 2 Loading examples/micelle/log.5Oct16.micelle.g++.1→examples/micelle/log.27Nov18.micelle.g++.1 +255 −0 Original line number Diff line number Diff line LAMMPS (5 Oct 2016) LAMMPS (27 Nov 2018) using 1 OpenMP thread(s) per MPI task # 2d micelle simulation dimension 2 Loading Loading @@ -45,13 +46,18 @@ fix 4 all enforce2d thermo 50 run 1000 Neighbor list info ... 1 neighbor list requests update every 1 steps, delay 5 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 1.42246 ghost atom cutoff = 1.42246 binsize = 0.71123 -> bins = 51 51 1 Memory usage per processor = 3.45296 Mbytes binsize = 0.71123, bins = 51 51 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair soft, perpetual attributes: half, newton on pair build: half/bin/newton stencil: half/bin/2d/newton bin: standard Per MPI rank memory allocation (min/avg/max) = 3.799 | 3.799 | 3.799 Mbytes Step Temp E_pair E_mol TotEng Press 0 0.45 0.40003481 2.2200223e-06 0.84966203 0.78952518 50 0.47411013 0.67721272 0.057404514 1.2083323 1.3375852 Loading @@ -74,21 +80,21 @@ Step Temp E_pair E_mol TotEng Press 900 0.45 0.47785593 0.10150857 1.0289895 5.7765975 950 0.49590559 0.46050477 0.096404887 1.052402 5.8649245 1000 0.45 0.47691182 0.08808163 1.0146185 6.0177568 Loop time of 0.192637 on 1 procs for 1000 steps with 1200 atoms Loop time of 0.167265 on 1 procs for 1000 steps with 1200 atoms Performance: 2242560.228 tau/day, 5191.112 timesteps/s 99.7% CPU use with 1 MPI tasks x no OpenMP threads Performance: 2582728.958 tau/day, 5978.539 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 | 0.13348 | 0.13348 | 0.13348 | 0.0 | 69.29 Bond | 0.0066328 | 0.0066328 | 0.0066328 | 0.0 | 3.44 Neigh | 0.023894 | 0.023894 | 0.023894 | 0.0 | 12.40 Comm | 0.0032849 | 0.0032849 | 0.0032849 | 0.0 | 1.71 Output | 0.00019765 | 0.00019765 | 0.00019765 | 0.0 | 0.10 Modify | 0.020029 | 0.020029 | 0.020029 | 0.0 | 10.40 Other | | 0.005115 | | | 2.66 Pair | 0.096171 | 0.096171 | 0.096171 | 0.0 | 57.50 Bond | 0.006212 | 0.006212 | 0.006212 | 0.0 | 3.71 Neigh | 0.024826 | 0.024826 | 0.024826 | 0.0 | 14.84 Comm | 0.0047672 | 0.0047672 | 0.0047672 | 0.0 | 2.85 Output | 0.00029063 | 0.00029063 | 0.00029063 | 0.0 | 0.17 Modify | 0.028771 | 0.028771 | 0.028771 | 0.0 | 17.20 Other | | 0.006227 | | | 3.72 Nlocal: 1200 ave 1200 max 1200 min Histogram: 1 0 0 0 0 0 0 0 0 0 Loading Loading @@ -144,101 +150,106 @@ thermo 1000 reset_timestep 0 run 60000 Neighbor list info ... 1 neighbor list requests update every 1 steps, delay 5 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 = 26 26 1 Memory usage per processor = 3.45296 Mbytes binsize = 1.4, bins = 26 26 1 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/2d/newton bin: standard Per MPI rank memory allocation (min/avg/max) = 4.024 | 4.024 | 4.024 Mbytes Step Temp E_pair E_mol TotEng Press 0 0.45 -1.7056163 0.08808163 -1.1679097 3.9431686 1000 0.45 -1.9727655 0.058608718 -1.4645318 1.9982299 2000 0.4661092 -1.9963233 0.067084121 -1.4635184 1.5676107 3000 0.44946688 -2.0126501 0.070702998 -1.4928548 1.5636132 4000 0.45269674 -1.9944702 0.05825464 -1.4838961 1.6015127 5000 0.46281924 -2.0302807 0.058318349 -1.5095288 1.3929421 6000 0.45409991 -2.0339156 0.061724414 -1.5184697 1.1978692 7000 0.44058968 -2.0436374 0.060141133 -1.5432738 1.1877802 8000 0.4429781 -2.0508103 0.061300632 -1.5469007 1.1825472 9000 0.44909024 -2.0620769 0.063430248 -1.5499306 1.1841529 10000 0.44709728 -2.0337047 0.059176633 -1.5278033 1.1906481 11000 0.46222813 -2.0666276 0.053626157 -1.5511585 0.99322264 12000 0.45722371 -2.0527602 0.062728903 -1.5331886 1.1135813 13000 0.44844353 -2.0672473 0.07057216 -1.5486053 0.9416127 14000 0.44211202 -2.0804052 0.056164487 -1.5824971 0.99700319 15000 0.45659943 -2.0711771 0.059428792 -1.5555294 1.1123211 16000 0.45113626 -2.0895625 0.057848795 -1.5809534 1.0015991 17000 0.44423013 -2.0840859 0.06718595 -1.57304 0.92034012 18000 0.45279338 -2.0644167 0.058541719 -1.5534589 1.1560585 19000 0.44673847 -2.0729637 0.061474462 -1.565123 0.99627228 20000 0.44428193 -2.0937135 0.066588799 -1.583213 0.86154418 21000 0.45902797 -2.0821041 0.057286828 -1.5661718 0.76853595 22000 0.45733559 -2.0962718 0.064103239 -1.5752141 0.90967955 23000 0.44617227 -2.070896 0.061562573 -1.5635329 0.92864876 24000 0.45569898 -2.0843503 0.061015469 -1.5680156 0.90170833 25000 0.45952666 -2.0892064 0.058901296 -1.5711614 0.9123274 26000 0.44773853 -2.0896169 0.065994021 -1.5762575 0.8887526 27000 0.43541542 -2.0893237 0.060387783 -1.5938834 0.97604018 28000 0.44025187 -2.0937721 0.066174764 -1.5877124 0.98394478 29000 0.44695847 -2.0966733 0.064980967 -1.5851064 0.78278706 30000 0.44848319 -2.1017012 0.053308469 -1.6002833 0.85185298 31000 0.45215181 -2.0927324 0.057875178 -1.5830822 0.77068692 32000 0.44586981 -2.0962193 0.056970051 -1.593751 0.85672441 33000 0.43591379 -2.1069871 0.064934652 -1.6065019 0.87081371 34000 0.44153683 -2.0967535 0.061537811 -1.5940468 0.75497708 35000 0.45482946 -2.1045277 0.060250612 -1.5898266 0.80290163 36000 0.45 -2.1154856 0.052206018 -1.6136546 0.67520748 37000 0.44973679 -2.1076496 0.067371347 -1.5909163 0.83319072 38000 0.45549751 -2.1044983 0.061863351 -1.587517 0.6786145 39000 0.43927254 -2.1159446 0.057855173 -1.6191829 0.66483475 40000 0.43711657 -2.0941837 0.063039594 -1.5943918 0.90680301 41000 0.43992749 -2.0931285 0.063772204 -1.5897954 0.7538478 42000 0.44374588 -2.1029745 0.061963499 -1.5976349 0.74793466 43000 0.45 -2.0916744 0.055058096 -1.5869913 0.86069235 44000 0.45381626 -2.0984483 0.059995477 -1.5850147 0.74948091 45000 0.44547409 -2.1217483 0.058753101 -1.6178924 0.57348898 46000 0.43283033 -2.1054695 0.059343099 -1.6136567 0.77490901 47000 0.44310217 -2.1215687 0.066613901 -1.6122219 0.73014542 48000 0.44611257 -2.118313 0.05944897 -1.6131232 0.59077782 49000 0.44114725 -2.0911126 0.065639368 -1.5846936 0.78309201 50000 0.44572124 -2.0892024 0.065540869 -1.5783117 0.87647821 51000 0.4460699 -2.1142274 0.061090043 -1.6074391 0.61721581 52000 0.44799203 -2.1122931 0.056821256 -1.6078531 0.70734576 53000 0.44819437 -2.1098838 0.058117987 -1.6039449 0.71349136 54000 0.45 -2.1384776 0.051012047 -1.6378405 0.4810217 55000 0.43931842 -2.1053055 0.061275315 -1.6050778 0.58268948 56000 0.44126963 -2.1133637 0.057474037 -1.6149877 0.68063945 57000 0.45823746 -2.1205329 0.065224217 -1.5974531 0.73788456 58000 0.437031 -2.0998724 0.051717885 -1.6114877 0.86071379 59000 0.45070454 -2.1115874 0.053721754 -1.6075367 0.62358834 60000 0.44181643 -2.1243164 0.060489492 -1.6223786 0.6992428 Loop time of 13.6136 on 1 procs for 60000 steps with 1200 atoms Performance: 1903978.372 tau/day, 4407.357 timesteps/s 99.5% CPU use with 1 MPI tasks x no OpenMP threads 1000 0.45 -1.9727655 0.058608715 -1.4645318 1.9982298 2000 0.46465361 -1.9897467 0.067008449 -1.4584719 1.5873463 3000 0.46175071 -2.0129279 0.057865385 -1.4936966 1.41269 4000 0.44386154 -2.0280304 0.067167835 -1.5173709 1.4022093 5000 0.46127582 -2.0556041 0.068318674 -1.526394 1.1416711 6000 0.45354052 -2.0463246 0.05461954 -1.5385425 1.1650258 7000 0.44082313 -2.040263 0.060218047 -1.5395891 1.3258681 8000 0.44353466 -2.0423792 0.061769402 -1.5374447 1.2696989 9000 0.46192977 -2.0761348 0.064999109 -1.5495908 0.9205826 10000 0.45278646 -2.0589872 0.059623919 -1.5469542 1.075581 11000 0.45583355 -2.0661957 0.058197558 -1.5525445 1.127643 12000 0.45881198 -2.0921508 0.066937896 -1.5667833 0.98383574 13000 0.45339481 -2.079088 0.06292782 -1.5631432 1.0188637 14000 0.43601312 -2.0624084 0.057999616 -1.568759 1.1452177 15000 0.45941503 -2.0746606 0.062523373 -1.553105 0.86928343 16000 0.45 -2.0743162 0.05517924 -1.569512 0.86849848 17000 0.45603004 -2.0657683 0.058711872 -1.5514064 0.95544551 18000 0.45320383 -2.1009711 0.060716634 -1.5874283 0.8343521 19000 0.44072983 -2.0846408 0.062893297 -1.581385 0.90776246 20000 0.44452441 -2.0921415 0.060341571 -1.587646 0.98180005 21000 0.45964557 -2.0837047 0.054459432 -1.5699827 1.0213779 22000 0.46351849 -2.1053613 0.058392027 -1.5838371 0.81579487 23000 0.45576065 -2.1001888 0.057646538 -1.5871614 0.76090085 24000 0.44671746 -2.0848717 0.058192801 -1.5803337 0.77003809 25000 0.44371239 -2.0870872 0.054804981 -1.5889396 0.92295746 26000 0.45381188 -2.097021 0.057195346 -1.586392 0.7743058 27000 0.46158533 -2.1071056 0.061289644 -1.5846153 0.78981802 28000 0.46534671 -2.1056151 0.054934755 -1.5857214 0.80778664 29000 0.4505804 -2.0949318 0.065503451 -1.5792234 0.78274755 30000 0.45730883 -2.1029161 0.063461968 -1.5825264 0.82507857 31000 0.4620071 -2.1124989 0.059980378 -1.5908964 0.78583986 32000 0.46934619 -2.1107818 0.056442616 -1.5853842 0.70535653 33000 0.45800203 -2.1062502 0.054317859 -1.594312 0.726293 34000 0.44634295 -2.110401 0.057764968 -1.606665 0.85401059 35000 0.4431929 -2.1274759 0.062048133 -1.6226042 0.64243758 36000 0.46049645 -2.1300979 0.068463634 -1.6015216 0.57252544 37000 0.45366344 -2.0977407 0.053788554 -1.5906668 0.78046879 38000 0.44155077 -2.1166674 0.056888683 -1.6185959 0.53429042 39000 0.45631012 -2.096949 0.04860872 -1.5924104 0.86494908 40000 0.44684402 -2.1229137 0.067190397 -1.6092516 0.65110818 41000 0.4479377 -2.1105264 0.059375259 -1.6035867 0.79092862 42000 0.46143191 -2.1174539 0.057418393 -1.5989882 0.69762908 43000 0.4356786 -2.085826 0.056534028 -1.5939764 0.89541946 44000 0.45806826 -2.126423 0.060905733 -1.6078307 0.66389027 45000 0.44343688 -2.1116384 0.065870114 -1.602701 0.83947585 46000 0.43844672 -2.1096265 0.064158652 -1.6073865 0.77278902 47000 0.45794928 -2.1142786 0.058919562 -1.5977914 0.62611933 48000 0.45412335 -2.1106058 0.059153304 -1.5977076 0.66190677 49000 0.45927883 -2.1197656 0.068354598 -1.5925149 0.56008845 50000 0.44117285 -2.1020783 0.064763249 -1.5965099 0.85935147 51000 0.45325398 -2.1125154 0.062295387 -1.5973438 0.80951782 52000 0.43896579 -2.1039004 0.057475908 -1.6078245 0.84753768 53000 0.45180671 -2.1092446 0.063528598 -1.5942857 0.67065038 54000 0.4554341 -2.1185135 0.059603337 -1.6038556 0.76399618 55000 0.43861159 -2.0986406 0.057733879 -1.6026606 0.77334084 56000 0.45522991 -2.1207166 0.063287543 -1.6025785 0.78669598 57000 0.46125513 -2.1150202 0.06026261 -1.5938868 0.78148646 58000 0.45236938 -2.1088894 0.062678374 -1.5942186 0.75643518 59000 0.43927269 -2.1274165 0.055355076 -1.6331548 0.63495311 60000 0.45331102 -2.1336193 0.051244399 -1.6294416 0.56706921 Loop time of 13.9361 on 1 procs for 60000 steps with 1200 atoms Performance: 1859917.639 tau/day, 4305.365 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 | 9.3684 | 9.3684 | 9.3684 | 0.0 | 68.82 Bond | 0.39461 | 0.39461 | 0.39461 | 0.0 | 2.90 Neigh | 2.211 | 2.211 | 2.211 | 0.0 | 16.24 Comm | 0.2552 | 0.2552 | 0.2552 | 0.0 | 1.87 Output | 0.00065112 | 0.00065112 | 0.00065112 | 0.0 | 0.00 Modify | 1.0819 | 1.0819 | 1.0819 | 0.0 | 7.95 Other | | 0.3019 | | | 2.22 Pair | 9.2211 | 9.2211 | 9.2211 | 0.0 | 66.17 Bond | 0.33763 | 0.33763 | 0.33763 | 0.0 | 2.42 Neigh | 2.3772 | 2.3772 | 2.3772 | 0.0 | 17.06 Comm | 0.37693 | 0.37693 | 0.37693 | 0.0 | 2.70 Output | 0.0011795 | 0.0011795 | 0.0011795 | 0.0 | 0.01 Modify | 1.2727 | 1.2727 | 1.2727 | 0.0 | 9.13 Other | | 0.3493 | | | 2.51 Nlocal: 1200 ave 1200 max 1200 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 417 ave 417 max 417 min Nghost: 405 ave 405 max 405 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 9495 ave 9495 max 9495 min Neighs: 9565 ave 9565 max 9565 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 9495 Ave neighs/atom = 7.9125 Total # of neighbors = 9565 Ave neighs/atom = 7.97083 Ave special neighs/atom = 0.5 Neighbor list builds = 4885 Neighbor list builds = 4876 Dangerous builds = 0 Total wall time: 0:00:13 Total wall time: 0:00:14 examples/micelle/log.5Oct16.micelle.g++.4→examples/micelle/log.27Nov18.micelle.g++.4 +255 −0 File changed and moved.Preview size limit exceeded, changes collapsed. 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examples/melt/log.5Oct16.melt.g++.1→examples/melt/log.27Nov18.melt.g++.1 +20 −13 Original line number Diff line number Diff line LAMMPS (5 Oct 2016) LAMMPS (27 Nov 2018) using 1 OpenMP thread(s) per MPI task # 3d Lennard-Jones melt units lj Loading @@ -12,6 +13,7 @@ Created orthogonal box = (0 0 0) to (16.796 16.796 16.796) 1 by 1 by 1 MPI processor grid create_atoms 1 box Created 4000 atoms Time spent = 0.000645638 secs mass 1 1.0 velocity all create 3.0 87287 Loading @@ -35,13 +37,18 @@ fix 1 all nve thermo 50 run 250 Neighbor list info ... 1 neighbor list requests update every 20 steps, delay 0 steps, check no max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 2.8 ghost atom cutoff = 2.8 binsize = 1.4 -> bins = 12 12 12 Memory usage per processor = 2.19271 Mbytes binsize = 1.4, bins = 12 12 12 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair lj/cut, perpetual attributes: half, newton on pair build: half/bin/atomonly/newton stencil: half/bin/3d/newton bin: standard Per MPI rank memory allocation (min/avg/max) = 3.221 | 3.221 | 3.221 Mbytes Step Temp E_pair E_mol TotEng Press 0 3 -6.7733681 0 -2.2744931 -3.7033504 50 1.6758903 -4.7955425 0 -2.2823355 5.670064 Loading @@ -49,20 +56,20 @@ Step Temp E_pair E_mol TotEng Press 150 1.6324555 -4.7286791 0 -2.280608 5.9589514 200 1.6630725 -4.7750988 0 -2.2811136 5.7364886 250 1.6275257 -4.7224992 0 -2.281821 5.9567365 Loop time of 0.724365 on 1 procs for 250 steps with 4000 atoms Loop time of 0.729809 on 1 procs for 250 steps with 4000 atoms Performance: 149096.106 tau/day, 345.130 timesteps/s 99.8% CPU use with 1 MPI tasks x no OpenMP threads Performance: 147983.915 tau/day, 342.555 timesteps/s 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.61654 | 0.61654 | 0.61654 | 0.0 | 85.11 Neigh | 0.081313 | 0.081313 | 0.081313 | 0.0 | 11.23 Comm | 0.010941 | 0.010941 | 0.010941 | 0.0 | 1.51 Output | 9.4891e-05 | 9.4891e-05 | 9.4891e-05 | 0.0 | 0.01 Modify | 0.012401 | 0.012401 | 0.012401 | 0.0 | 1.71 Other | | 0.003077 | | | 0.42 Pair | 0.60661 | 0.60661 | 0.60661 | 0.0 | 83.12 Neigh | 0.092198 | 0.092198 | 0.092198 | 0.0 | 12.63 Comm | 0.013581 | 0.013581 | 0.013581 | 0.0 | 1.86 Output | 0.0001452 | 0.0001452 | 0.0001452 | 0.0 | 0.02 Modify | 0.014395 | 0.014395 | 0.014395 | 0.0 | 1.97 Other | | 0.002878 | | | 0.39 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Loading
examples/melt/log.5Oct16.melt.g++.4→examples/melt/log.27Nov18.melt.g++.4 +20 −13 Original line number Diff line number Diff line LAMMPS (5 Oct 2016) LAMMPS (27 Nov 2018) using 1 OpenMP thread(s) per MPI task # 3d Lennard-Jones melt units lj Loading @@ -12,6 +13,7 @@ Created orthogonal box = (0 0 0) to (16.796 16.796 16.796) 1 by 2 by 2 MPI processor grid create_atoms 1 box Created 4000 atoms Time spent = 0.00041604 secs mass 1 1.0 velocity all create 3.0 87287 Loading @@ -35,13 +37,18 @@ fix 1 all nve thermo 50 run 250 Neighbor list info ... 1 neighbor list requests update every 20 steps, delay 0 steps, check no max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 2.8 ghost atom cutoff = 2.8 binsize = 1.4 -> bins = 12 12 12 Memory usage per processor = 2.10344 Mbytes binsize = 1.4, bins = 12 12 12 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair lj/cut, perpetual attributes: half, newton on pair build: half/bin/atomonly/newton stencil: half/bin/3d/newton bin: standard Per MPI rank memory allocation (min/avg/max) = 2.705 | 2.705 | 2.705 Mbytes Step Temp E_pair E_mol TotEng Press 0 3 -6.7733681 0 -2.2744931 -3.7033504 50 1.6754119 -4.7947589 0 -2.2822693 5.6615925 Loading @@ -49,20 +56,20 @@ Step Temp E_pair E_mol TotEng Press 150 1.6596605 -4.7699432 0 -2.2810749 5.7830138 200 1.6371874 -4.7365462 0 -2.2813789 5.9246674 250 1.6323462 -4.7292021 0 -2.2812949 5.9762238 Loop time of 0.210997 on 4 procs for 250 steps with 4000 atoms Loop time of 0.223329 on 4 procs for 250 steps with 4000 atoms Performance: 511855.365 tau/day, 1184.850 timesteps/s 99.6% CPU use with 4 MPI tasks x no OpenMP threads Performance: 483592.231 tau/day, 1119.426 timesteps/s 97.3% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.15475 | 0.16099 | 0.1682 | 1.2 | 76.30 Neigh | 0.020829 | 0.021108 | 0.021522 | 0.2 | 10.00 Comm | 0.01674 | 0.024412 | 0.030987 | 3.3 | 11.57 Output | 0.00011587 | 0.0001238 | 0.00013185 | 0.1 | 0.06 Modify | 0.0031242 | 0.0031361 | 0.0031476 | 0.0 | 1.49 Other | | 0.001227 | | | 0.58 Pair | 0.15881 | 0.16314 | 0.16859 | 0.9 | 73.05 Neigh | 0.02472 | 0.025218 | 0.025828 | 0.3 | 11.29 Comm | 0.025185 | 0.030091 | 0.034351 | 1.9 | 13.47 Output | 0.00015163 | 0.00019169 | 0.00030899 | 0.0 | 0.09 Modify | 0.0037532 | 0.0038366 | 0.0040054 | 0.2 | 1.72 Other | | 0.00085 | | | 0.38 Nlocal: 1000 ave 1010 max 982 min Histogram: 1 0 0 0 0 0 1 0 0 2 Loading
examples/micelle/log.5Oct16.micelle.g++.1→examples/micelle/log.27Nov18.micelle.g++.1 +255 −0 Original line number Diff line number Diff line LAMMPS (5 Oct 2016) LAMMPS (27 Nov 2018) using 1 OpenMP thread(s) per MPI task # 2d micelle simulation dimension 2 Loading Loading @@ -45,13 +46,18 @@ fix 4 all enforce2d thermo 50 run 1000 Neighbor list info ... 1 neighbor list requests update every 1 steps, delay 5 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 1.42246 ghost atom cutoff = 1.42246 binsize = 0.71123 -> bins = 51 51 1 Memory usage per processor = 3.45296 Mbytes binsize = 0.71123, bins = 51 51 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair soft, perpetual attributes: half, newton on pair build: half/bin/newton stencil: half/bin/2d/newton bin: standard Per MPI rank memory allocation (min/avg/max) = 3.799 | 3.799 | 3.799 Mbytes Step Temp E_pair E_mol TotEng Press 0 0.45 0.40003481 2.2200223e-06 0.84966203 0.78952518 50 0.47411013 0.67721272 0.057404514 1.2083323 1.3375852 Loading @@ -74,21 +80,21 @@ Step Temp E_pair E_mol TotEng Press 900 0.45 0.47785593 0.10150857 1.0289895 5.7765975 950 0.49590559 0.46050477 0.096404887 1.052402 5.8649245 1000 0.45 0.47691182 0.08808163 1.0146185 6.0177568 Loop time of 0.192637 on 1 procs for 1000 steps with 1200 atoms Loop time of 0.167265 on 1 procs for 1000 steps with 1200 atoms Performance: 2242560.228 tau/day, 5191.112 timesteps/s 99.7% CPU use with 1 MPI tasks x no OpenMP threads Performance: 2582728.958 tau/day, 5978.539 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 | 0.13348 | 0.13348 | 0.13348 | 0.0 | 69.29 Bond | 0.0066328 | 0.0066328 | 0.0066328 | 0.0 | 3.44 Neigh | 0.023894 | 0.023894 | 0.023894 | 0.0 | 12.40 Comm | 0.0032849 | 0.0032849 | 0.0032849 | 0.0 | 1.71 Output | 0.00019765 | 0.00019765 | 0.00019765 | 0.0 | 0.10 Modify | 0.020029 | 0.020029 | 0.020029 | 0.0 | 10.40 Other | | 0.005115 | | | 2.66 Pair | 0.096171 | 0.096171 | 0.096171 | 0.0 | 57.50 Bond | 0.006212 | 0.006212 | 0.006212 | 0.0 | 3.71 Neigh | 0.024826 | 0.024826 | 0.024826 | 0.0 | 14.84 Comm | 0.0047672 | 0.0047672 | 0.0047672 | 0.0 | 2.85 Output | 0.00029063 | 0.00029063 | 0.00029063 | 0.0 | 0.17 Modify | 0.028771 | 0.028771 | 0.028771 | 0.0 | 17.20 Other | | 0.006227 | | | 3.72 Nlocal: 1200 ave 1200 max 1200 min Histogram: 1 0 0 0 0 0 0 0 0 0 Loading Loading @@ -144,101 +150,106 @@ thermo 1000 reset_timestep 0 run 60000 Neighbor list info ... 1 neighbor list requests update every 1 steps, delay 5 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 = 26 26 1 Memory usage per processor = 3.45296 Mbytes binsize = 1.4, bins = 26 26 1 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/2d/newton bin: standard Per MPI rank memory allocation (min/avg/max) = 4.024 | 4.024 | 4.024 Mbytes Step Temp E_pair E_mol TotEng Press 0 0.45 -1.7056163 0.08808163 -1.1679097 3.9431686 1000 0.45 -1.9727655 0.058608718 -1.4645318 1.9982299 2000 0.4661092 -1.9963233 0.067084121 -1.4635184 1.5676107 3000 0.44946688 -2.0126501 0.070702998 -1.4928548 1.5636132 4000 0.45269674 -1.9944702 0.05825464 -1.4838961 1.6015127 5000 0.46281924 -2.0302807 0.058318349 -1.5095288 1.3929421 6000 0.45409991 -2.0339156 0.061724414 -1.5184697 1.1978692 7000 0.44058968 -2.0436374 0.060141133 -1.5432738 1.1877802 8000 0.4429781 -2.0508103 0.061300632 -1.5469007 1.1825472 9000 0.44909024 -2.0620769 0.063430248 -1.5499306 1.1841529 10000 0.44709728 -2.0337047 0.059176633 -1.5278033 1.1906481 11000 0.46222813 -2.0666276 0.053626157 -1.5511585 0.99322264 12000 0.45722371 -2.0527602 0.062728903 -1.5331886 1.1135813 13000 0.44844353 -2.0672473 0.07057216 -1.5486053 0.9416127 14000 0.44211202 -2.0804052 0.056164487 -1.5824971 0.99700319 15000 0.45659943 -2.0711771 0.059428792 -1.5555294 1.1123211 16000 0.45113626 -2.0895625 0.057848795 -1.5809534 1.0015991 17000 0.44423013 -2.0840859 0.06718595 -1.57304 0.92034012 18000 0.45279338 -2.0644167 0.058541719 -1.5534589 1.1560585 19000 0.44673847 -2.0729637 0.061474462 -1.565123 0.99627228 20000 0.44428193 -2.0937135 0.066588799 -1.583213 0.86154418 21000 0.45902797 -2.0821041 0.057286828 -1.5661718 0.76853595 22000 0.45733559 -2.0962718 0.064103239 -1.5752141 0.90967955 23000 0.44617227 -2.070896 0.061562573 -1.5635329 0.92864876 24000 0.45569898 -2.0843503 0.061015469 -1.5680156 0.90170833 25000 0.45952666 -2.0892064 0.058901296 -1.5711614 0.9123274 26000 0.44773853 -2.0896169 0.065994021 -1.5762575 0.8887526 27000 0.43541542 -2.0893237 0.060387783 -1.5938834 0.97604018 28000 0.44025187 -2.0937721 0.066174764 -1.5877124 0.98394478 29000 0.44695847 -2.0966733 0.064980967 -1.5851064 0.78278706 30000 0.44848319 -2.1017012 0.053308469 -1.6002833 0.85185298 31000 0.45215181 -2.0927324 0.057875178 -1.5830822 0.77068692 32000 0.44586981 -2.0962193 0.056970051 -1.593751 0.85672441 33000 0.43591379 -2.1069871 0.064934652 -1.6065019 0.87081371 34000 0.44153683 -2.0967535 0.061537811 -1.5940468 0.75497708 35000 0.45482946 -2.1045277 0.060250612 -1.5898266 0.80290163 36000 0.45 -2.1154856 0.052206018 -1.6136546 0.67520748 37000 0.44973679 -2.1076496 0.067371347 -1.5909163 0.83319072 38000 0.45549751 -2.1044983 0.061863351 -1.587517 0.6786145 39000 0.43927254 -2.1159446 0.057855173 -1.6191829 0.66483475 40000 0.43711657 -2.0941837 0.063039594 -1.5943918 0.90680301 41000 0.43992749 -2.0931285 0.063772204 -1.5897954 0.7538478 42000 0.44374588 -2.1029745 0.061963499 -1.5976349 0.74793466 43000 0.45 -2.0916744 0.055058096 -1.5869913 0.86069235 44000 0.45381626 -2.0984483 0.059995477 -1.5850147 0.74948091 45000 0.44547409 -2.1217483 0.058753101 -1.6178924 0.57348898 46000 0.43283033 -2.1054695 0.059343099 -1.6136567 0.77490901 47000 0.44310217 -2.1215687 0.066613901 -1.6122219 0.73014542 48000 0.44611257 -2.118313 0.05944897 -1.6131232 0.59077782 49000 0.44114725 -2.0911126 0.065639368 -1.5846936 0.78309201 50000 0.44572124 -2.0892024 0.065540869 -1.5783117 0.87647821 51000 0.4460699 -2.1142274 0.061090043 -1.6074391 0.61721581 52000 0.44799203 -2.1122931 0.056821256 -1.6078531 0.70734576 53000 0.44819437 -2.1098838 0.058117987 -1.6039449 0.71349136 54000 0.45 -2.1384776 0.051012047 -1.6378405 0.4810217 55000 0.43931842 -2.1053055 0.061275315 -1.6050778 0.58268948 56000 0.44126963 -2.1133637 0.057474037 -1.6149877 0.68063945 57000 0.45823746 -2.1205329 0.065224217 -1.5974531 0.73788456 58000 0.437031 -2.0998724 0.051717885 -1.6114877 0.86071379 59000 0.45070454 -2.1115874 0.053721754 -1.6075367 0.62358834 60000 0.44181643 -2.1243164 0.060489492 -1.6223786 0.6992428 Loop time of 13.6136 on 1 procs for 60000 steps with 1200 atoms Performance: 1903978.372 tau/day, 4407.357 timesteps/s 99.5% CPU use with 1 MPI tasks x no OpenMP threads 1000 0.45 -1.9727655 0.058608715 -1.4645318 1.9982298 2000 0.46465361 -1.9897467 0.067008449 -1.4584719 1.5873463 3000 0.46175071 -2.0129279 0.057865385 -1.4936966 1.41269 4000 0.44386154 -2.0280304 0.067167835 -1.5173709 1.4022093 5000 0.46127582 -2.0556041 0.068318674 -1.526394 1.1416711 6000 0.45354052 -2.0463246 0.05461954 -1.5385425 1.1650258 7000 0.44082313 -2.040263 0.060218047 -1.5395891 1.3258681 8000 0.44353466 -2.0423792 0.061769402 -1.5374447 1.2696989 9000 0.46192977 -2.0761348 0.064999109 -1.5495908 0.9205826 10000 0.45278646 -2.0589872 0.059623919 -1.5469542 1.075581 11000 0.45583355 -2.0661957 0.058197558 -1.5525445 1.127643 12000 0.45881198 -2.0921508 0.066937896 -1.5667833 0.98383574 13000 0.45339481 -2.079088 0.06292782 -1.5631432 1.0188637 14000 0.43601312 -2.0624084 0.057999616 -1.568759 1.1452177 15000 0.45941503 -2.0746606 0.062523373 -1.553105 0.86928343 16000 0.45 -2.0743162 0.05517924 -1.569512 0.86849848 17000 0.45603004 -2.0657683 0.058711872 -1.5514064 0.95544551 18000 0.45320383 -2.1009711 0.060716634 -1.5874283 0.8343521 19000 0.44072983 -2.0846408 0.062893297 -1.581385 0.90776246 20000 0.44452441 -2.0921415 0.060341571 -1.587646 0.98180005 21000 0.45964557 -2.0837047 0.054459432 -1.5699827 1.0213779 22000 0.46351849 -2.1053613 0.058392027 -1.5838371 0.81579487 23000 0.45576065 -2.1001888 0.057646538 -1.5871614 0.76090085 24000 0.44671746 -2.0848717 0.058192801 -1.5803337 0.77003809 25000 0.44371239 -2.0870872 0.054804981 -1.5889396 0.92295746 26000 0.45381188 -2.097021 0.057195346 -1.586392 0.7743058 27000 0.46158533 -2.1071056 0.061289644 -1.5846153 0.78981802 28000 0.46534671 -2.1056151 0.054934755 -1.5857214 0.80778664 29000 0.4505804 -2.0949318 0.065503451 -1.5792234 0.78274755 30000 0.45730883 -2.1029161 0.063461968 -1.5825264 0.82507857 31000 0.4620071 -2.1124989 0.059980378 -1.5908964 0.78583986 32000 0.46934619 -2.1107818 0.056442616 -1.5853842 0.70535653 33000 0.45800203 -2.1062502 0.054317859 -1.594312 0.726293 34000 0.44634295 -2.110401 0.057764968 -1.606665 0.85401059 35000 0.4431929 -2.1274759 0.062048133 -1.6226042 0.64243758 36000 0.46049645 -2.1300979 0.068463634 -1.6015216 0.57252544 37000 0.45366344 -2.0977407 0.053788554 -1.5906668 0.78046879 38000 0.44155077 -2.1166674 0.056888683 -1.6185959 0.53429042 39000 0.45631012 -2.096949 0.04860872 -1.5924104 0.86494908 40000 0.44684402 -2.1229137 0.067190397 -1.6092516 0.65110818 41000 0.4479377 -2.1105264 0.059375259 -1.6035867 0.79092862 42000 0.46143191 -2.1174539 0.057418393 -1.5989882 0.69762908 43000 0.4356786 -2.085826 0.056534028 -1.5939764 0.89541946 44000 0.45806826 -2.126423 0.060905733 -1.6078307 0.66389027 45000 0.44343688 -2.1116384 0.065870114 -1.602701 0.83947585 46000 0.43844672 -2.1096265 0.064158652 -1.6073865 0.77278902 47000 0.45794928 -2.1142786 0.058919562 -1.5977914 0.62611933 48000 0.45412335 -2.1106058 0.059153304 -1.5977076 0.66190677 49000 0.45927883 -2.1197656 0.068354598 -1.5925149 0.56008845 50000 0.44117285 -2.1020783 0.064763249 -1.5965099 0.85935147 51000 0.45325398 -2.1125154 0.062295387 -1.5973438 0.80951782 52000 0.43896579 -2.1039004 0.057475908 -1.6078245 0.84753768 53000 0.45180671 -2.1092446 0.063528598 -1.5942857 0.67065038 54000 0.4554341 -2.1185135 0.059603337 -1.6038556 0.76399618 55000 0.43861159 -2.0986406 0.057733879 -1.6026606 0.77334084 56000 0.45522991 -2.1207166 0.063287543 -1.6025785 0.78669598 57000 0.46125513 -2.1150202 0.06026261 -1.5938868 0.78148646 58000 0.45236938 -2.1088894 0.062678374 -1.5942186 0.75643518 59000 0.43927269 -2.1274165 0.055355076 -1.6331548 0.63495311 60000 0.45331102 -2.1336193 0.051244399 -1.6294416 0.56706921 Loop time of 13.9361 on 1 procs for 60000 steps with 1200 atoms Performance: 1859917.639 tau/day, 4305.365 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 | 9.3684 | 9.3684 | 9.3684 | 0.0 | 68.82 Bond | 0.39461 | 0.39461 | 0.39461 | 0.0 | 2.90 Neigh | 2.211 | 2.211 | 2.211 | 0.0 | 16.24 Comm | 0.2552 | 0.2552 | 0.2552 | 0.0 | 1.87 Output | 0.00065112 | 0.00065112 | 0.00065112 | 0.0 | 0.00 Modify | 1.0819 | 1.0819 | 1.0819 | 0.0 | 7.95 Other | | 0.3019 | | | 2.22 Pair | 9.2211 | 9.2211 | 9.2211 | 0.0 | 66.17 Bond | 0.33763 | 0.33763 | 0.33763 | 0.0 | 2.42 Neigh | 2.3772 | 2.3772 | 2.3772 | 0.0 | 17.06 Comm | 0.37693 | 0.37693 | 0.37693 | 0.0 | 2.70 Output | 0.0011795 | 0.0011795 | 0.0011795 | 0.0 | 0.01 Modify | 1.2727 | 1.2727 | 1.2727 | 0.0 | 9.13 Other | | 0.3493 | | | 2.51 Nlocal: 1200 ave 1200 max 1200 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 417 ave 417 max 417 min Nghost: 405 ave 405 max 405 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 9495 ave 9495 max 9495 min Neighs: 9565 ave 9565 max 9565 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 9495 Ave neighs/atom = 7.9125 Total # of neighbors = 9565 Ave neighs/atom = 7.97083 Ave special neighs/atom = 0.5 Neighbor list builds = 4885 Neighbor list builds = 4876 Dangerous builds = 0 Total wall time: 0:00:13 Total wall time: 0:00:14
examples/micelle/log.5Oct16.micelle.g++.4→examples/micelle/log.27Nov18.micelle.g++.4 +255 −0 File changed and moved.Preview size limit exceeded, changes collapsed. Show changes
