LAMMPS (27 Nov 2018) using 1 OpenMP thread(s) per MPI task # 2d rounded polygon bodies variable r index 4 variable steps index 100000 variable T index 0.5 variable P index 0.1 variable seed index 980411 units lj dimension 2 atom_style body rounded/polygon 1 6 atom_modify map array read_data data.squares orthogonal box = (0 0 -0.5) to (12 12 0.5) 2 by 2 by 1 MPI processor grid reading atoms ... 2 atoms 2 bodies replicate $r $r 1 replicate 4 $r 1 replicate 4 4 1 orthogonal box = (0 0 -0.5) to (48 48 0.5) 2 by 2 by 1 MPI processor grid 32 atoms Time spent = 0.000329733 secs velocity all create $T ${seed} dist gaussian mom yes rot yes velocity all create 0.5 ${seed} dist gaussian mom yes rot yes velocity all create 0.5 980411 dist gaussian mom yes rot yes change_box all boundary p f p variable cut_inner equal 0.5 variable k_n equal 100 variable k_na equal 2 variable c_n equal 0.1 variable c_t equal 0.1 variable mu equal 0.1 variable delta_ua equal 0.5 pair_style body/rounded/polygon ${c_n} ${c_t} ${mu} ${delta_ua} ${cut_inner} pair_style body/rounded/polygon 0.1 ${c_t} ${mu} ${delta_ua} ${cut_inner} pair_style body/rounded/polygon 0.1 0.1 ${mu} ${delta_ua} ${cut_inner} pair_style body/rounded/polygon 0.1 0.1 0.1 ${delta_ua} ${cut_inner} pair_style body/rounded/polygon 0.1 0.1 0.1 0.5 ${cut_inner} pair_style body/rounded/polygon 0.1 0.1 0.1 0.5 0.5 pair_coeff * * ${k_n} ${k_na} pair_coeff * * 100 ${k_na} pair_coeff * * 100 2 comm_modify vel yes neighbor 0.5 bin neigh_modify every 1 delay 0 check yes timestep 0.001 #fix 1 all nve/body #fix 1 all nvt/body temp $T $T 1.0 fix 1 all npt/body temp $T $T 1.0 x 0.001 $P 1.0 fixedpoint 0 0 0 fix 1 all npt/body temp 0.5 $T 1.0 x 0.001 $P 1.0 fixedpoint 0 0 0 fix 1 all npt/body temp 0.5 0.5 1.0 x 0.001 $P 1.0 fixedpoint 0 0 0 fix 1 all npt/body temp 0.5 0.5 1.0 x 0.001 0.1 1.0 fixedpoint 0 0 0 fix 2 all enforce2d fix 3 all wall/body/polygon 2000 50 50 yplane 0.0 48.0 #compute 1 all body/local id 1 2 3 #dump 1 all local 100000 dump.polygon.* index c_1[1] c_1[2] c_1[3] c_1[4] thermo_style custom step ke pe etotal press thermo 1000 #dump 2 all image 10000 image.*.jpg type type zoom 2.0 # adiam 1.5 body type 0 0 #dump_modify 2 pad 6 run ${steps} run 100000 Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 6.15685 ghost atom cutoff = 6.15685 binsize = 3.07843, bins = 16 16 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair body/rounded/polygon, perpetual attributes: half, newton on pair build: half/bin/atomonly/newton stencil: half/bin/2d/newton bin: standard Per MPI rank memory allocation (min/avg/max) = 4.773 | 4.773 | 4.773 Mbytes Step KinEng PotEng TotEng Press 0 0.484375 0.25 0.734375 0.0067274306 1000 0.51467204 0.00099202506 0.51566407 0.013452386 2000 0.55674899 0.0040762275 0.56082522 0.0034529066 3000 0.7546177 0.02259362 0.77721132 0.003650781 4000 0.72710218 0.10284108 0.82994326 0.0059629371 5000 0.57710119 0.069052154 0.64615335 0.00053937664 6000 0.53848104 0.041891152 0.58037219 0.0018693259 7000 0.61777485 0.033380825 0.65115568 0.0027584782 8000 0.47427732 0.059553658 0.53383098 0.017087698 9000 0.46820943 0.064379697 0.53258913 0.02325702 10000 0.46605511 0.02332689 0.489382 0.013699209 11000 0.57547516 0.090133398 0.66560855 0.0083913962 12000 0.465348 0.084853345 0.55020135 0.006231552 13000 0.55340889 0.07116165 0.62457054 0.030622563 14000 0.58866362 0.052281859 0.64094548 0.0079106838 15000 0.51757672 0.12255618 0.6401329 0.014005369 16000 0.42696011 0.086987541 0.51394765 -0.0017128649 17000 0.37612579 0.13054778 0.50667357 0.0046284992 18000 0.47659682 0.14670523 0.62330205 0.02206928 19000 0.47897909 0.15540332 0.63438241 0.02544138 20000 0.59377323 0.15357757 0.7473508 0.030262926 21000 0.52781204 0.22074491 0.74855695 -0.0022170167 22000 0.44843285 0.12779345 0.5762263 0.0097268482 23000 0.60400735 0.18098124 0.78498858 0.05778325 24000 0.58254338 0.1570243 0.73956769 0.022530491 25000 0.60524318 0.23660272 0.8418459 0.062530421 26000 0.45892702 0.34294121 0.80186823 0.038657393 27000 0.58418023 0.19551937 0.7796996 -0.0055396645 28000 0.45655369 0.26718934 0.72374303 0.006593108 29000 0.50277299 0.1747088 0.67748179 0.016059369 30000 0.38640717 0.1631573 0.54956447 0.036055723 31000 0.46944541 0.22076826 0.69021367 0.014334038 32000 0.53862858 0.26867594 0.80730452 0.057406282 33000 0.45666352 0.21796554 0.67462906 0.056555205 34000 0.51644038 0.21866786 0.73510824 0.015713 35000 0.50489584 0.1596236 0.66451945 0.040400644 36000 0.41723489 0.16227853 0.57951342 0.02863261 37000 0.481638 0.28830624 0.76994424 0.038381986 38000 0.6036094 0.33479287 0.93840227 0.0032059452 39000 0.47822122 0.18876355 0.66698476 0.029252649 40000 0.54949607 0.35011086 0.89960693 0.093909148 41000 0.54876522 0.27501735 0.82378257 -0.0084167014 42000 0.67801592 0.18102522 0.85904114 -0.0058395209 43000 0.54342066 0.34322081 0.88664146 0.12263806 44000 0.46672513 0.29749157 0.76421671 0.051073701 45000 0.4679867 0.25820875 0.72619545 0.069790993 46000 0.59598501 0.22285276 0.81883777 0.050578807 47000 0.48858341 0.29811577 0.78669917 0.080971431 48000 0.41238073 0.29362937 0.7060101 0.031893588 49000 0.61516435 0.33082609 0.94599044 -0.010710982 50000 0.57576635 0.37137185 0.94713819 0.062160249 51000 0.54614001 0.36960628 0.91574629 -0.0083424769 52000 0.42232354 0.25214442 0.67446796 0.028666126 53000 0.43025129 0.24479385 0.67504514 0.030342054 54000 0.54614922 0.29602426 0.84217348 0.083070642 55000 0.60719748 0.3577285 0.96492598 0.053799744 56000 0.47073149 0.31070429 0.78143579 0.083895368 57000 0.56861582 0.33249784 0.90111366 0.032324233 58000 0.75061035 0.33313728 1.0837476 0.031039937 59000 0.59473893 0.48870773 1.0834467 0.039503585 60000 0.55252481 0.38350562 0.93603043 0.0027643882 61000 0.45010855 0.43945065 0.8895592 0.028168222 62000 0.63942467 0.53372899 1.1731537 0.13790959 63000 0.69407873 0.37980402 1.0738828 0.035919608 64000 0.54898275 0.39910419 0.94808693 0.0015016851 65000 0.58229838 0.42300361 1.005302 0.089787193 66000 0.53443537 0.5597136 1.094149 -0.015781756 67000 0.59212426 0.56172146 1.1538457 0.030464683 68000 0.68164926 0.48724393 1.1688932 0.071465948 69000 0.59721737 0.49476309 1.0919805 0.07575647 70000 0.52314551 0.31950477 0.84265028 0.11206672 71000 0.53230509 0.53846575 1.0707708 0.0047204701 72000 0.71341933 0.4924749 1.2058942 0.116568 73000 0.70498496 0.54121008 1.246195 0.11210249 74000 0.54188682 0.61729607 1.1591829 0.044083048 75000 0.44073609 0.42072284 0.86145893 -0.041508511 76000 0.51225567 0.36848317 0.88073884 -0.028636748 77000 0.6517329 0.5503086 1.2020415 0.049605026 78000 0.60053898 0.52760266 1.1281416 0.094361256 79000 0.51560788 0.46563043 0.98123832 -0.03336136 80000 0.53357884 0.60743981 1.1410186 0.027259883 81000 0.6256228 0.40412923 1.029752 0.083274981 82000 0.6903519 0.69599412 1.386346 0.168747 83000 0.62621394 0.50082841 1.1270424 0.12294403 84000 0.5682146 0.73827702 1.3064916 0.085884707 85000 0.48179077 0.73669563 1.2184864 0.065002035 86000 0.61101399 0.80673836 1.4177523 0.037555163 87000 0.52278725 0.71608722 1.2388745 0.020943688 88000 0.53318823 0.50916748 1.0423557 -0.01946691 89000 0.56428713 0.56042234 1.1247095 0.040998134 90000 0.58720508 0.66023073 1.2474358 0.040313529 91000 0.61509407 0.86254343 1.4776375 0.15215034 92000 0.5640475 0.57694543 1.1409929 0.10238679 93000 0.60586378 0.67978456 1.2856483 -0.043948113 94000 0.75406595 0.74795347 1.5020194 0.015341415 95000 0.4974314 0.60192267 1.0993541 -0.018173218 96000 0.50048302 0.82845218 1.3289352 0.045394283 97000 0.65335222 0.6470855 1.3004377 0.011624967 98000 0.65693072 0.45222133 1.109152 0.13763684 99000 0.60573344 0.50284289 1.1085763 0.12853674 100000 0.50677068 0.58143063 1.0882013 0.11351254 Loop time of 3.24642 on 4 procs for 100000 steps with 32 atoms Performance: 2661396.711 tau/day, 30803.203 timesteps/s 94.4% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.64148 | 0.70244 | 0.76391 | 6.5 | 21.64 Neigh | 0.0049012 | 0.0050417 | 0.0052478 | 0.2 | 0.16 Comm | 0.79447 | 0.88412 | 0.97443 | 8.1 | 27.23 Output | 0.001776 | 0.0031438 | 0.0072262 | 4.2 | 0.10 Modify | 1.325 | 1.3684 | 1.4049 | 2.4 | 42.15 Other | | 0.2833 | | | 8.73 Nlocal: 8 ave 9 max 7 min Histogram: 1 0 0 0 0 2 0 0 0 1 Nghost: 14 ave 15 max 13 min Histogram: 1 0 0 0 0 2 0 0 0 1 Neighs: 13.25 ave 16 max 11 min Histogram: 1 0 1 0 0 0 1 0 0 1 Total # of neighbors = 53 Ave neighs/atom = 1.65625 Neighbor list builds = 2654 Dangerous builds = 0 Total wall time: 0:00:03