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) 1 by 1 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) 1 by 1 by 1 MPI processor grid 32 atoms Time spent = 0.000318766 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) = 4.771 | 4.771 | 4.771 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 0.5771012 0.069052145 0.64615335 0.00053937622 6000 0.53848154 0.041891239 0.58037277 0.0018693312 7000 0.61777556 0.033379829 0.65115538 0.0027584418 8000 0.47427227 0.059558934 0.5338312 0.017087187 9000 0.46822364 0.064382578 0.53260622 0.023258465 10000 0.46511051 0.027799371 0.49290988 0.015319493 11000 0.58686703 0.088016891 0.67488392 0.0088428936 12000 0.49962603 0.09879099 0.59841702 0.00074311497 13000 0.53160049 0.069625775 0.60122626 0.017019775 14000 0.49574902 0.041214164 0.53696318 0.0060355978 15000 0.56620415 0.13621516 0.70241931 0.045583297 16000 0.40942564 0.11469877 0.52412441 0.029905784 17000 0.608066 0.096938921 0.70500493 0.018509814 18000 0.45622168 0.057018077 0.51323975 0.0034035281 19000 0.48763322 0.057832224 0.54546545 0.0022972169 20000 0.41577025 0.14480819 0.56057844 0.023882542 21000 0.58565738 0.1601676 0.74582498 0.01702799 22000 0.60430354 0.16740706 0.7717106 -0.0047632836 23000 0.45659601 0.13740896 0.59400497 0.0191143 24000 0.42741367 0.25490516 0.68231884 0.051459175 25000 0.40851048 0.077823072 0.48633355 0.024392284 26000 0.53392894 0.14504323 0.67897217 0.028964572 27000 0.39775205 0.13101153 0.52876358 0.0080564916 28000 0.63138106 0.17706612 0.80844718 0.017594524 29000 0.57897788 0.26855503 0.84753292 0.019310624 30000 0.37401002 0.2274666 0.60147663 0.0044804008 31000 0.60924323 0.23142663 0.84066986 0.088271242 32000 0.60310397 0.35719837 0.96030234 0.0096762289 33000 0.47468105 0.17727177 0.65195282 0.0078486602 34000 0.42270829 0.20131235 0.62402064 0.090216203 35000 0.49578606 0.1697981 0.66558416 0.079099134 36000 0.50744538 0.29600416 0.80344954 0.018819487 37000 0.66728184 0.28166655 0.94894838 -0.01679437 38000 0.38972905 0.25798163 0.64771068 0.040442456 39000 0.38292839 0.21774389 0.60067228 0.016754932 40000 0.61770336 0.34202184 0.9597252 0.10986262 41000 0.42252651 0.13424708 0.5567736 0.040987711 42000 0.67513868 0.29515562 0.9702943 0.0013757417 43000 0.36768915 0.20349753 0.57118668 0.031443504 44000 0.49371025 0.095615653 0.5893259 0.032289477 45000 0.42144079 0.28894639 0.71038718 0.040302569 46000 0.36360136 0.33117431 0.69477567 0.010881881 47000 0.4206309 0.19557595 0.61620685 0.051137535 48000 0.4131465 0.37027912 0.78342561 0.11903042 49000 0.544703 0.38013565 0.92483865 0.054939742 50000 0.47394272 0.32384493 0.79778764 0.088363602 51000 0.55377533 0.38103395 0.93480927 0.097981664 52000 0.60648433 0.30877364 0.91525797 0.088877781 53000 0.62933509 0.33187159 0.96120668 0.10275954 54000 0.55077522 0.39050008 0.94127529 0.066721412 55000 0.41646397 0.34545572 0.76191969 0.011056796 56000 0.44244954 0.39274744 0.83519698 0.039963853 57000 0.41963092 0.33483982 0.75447073 0.032555938 58000 0.37941475 0.36905323 0.74846798 0.043952263 59000 0.53008564 0.32843795 0.85852359 0.080787301 60000 0.43408908 0.19840268 0.63249176 0.06421165 61000 0.56287814 0.31500577 0.87788391 0.12031895 62000 0.5185192 0.18275672 0.70127592 -0.0086212356 63000 0.57275413 0.45147395 1.0242281 0.054617465 64000 0.28322907 0.33687722 0.62010629 0.07268947 65000 0.40230876 0.37989067 0.78219943 -0.029604066 66000 0.58601209 0.52721274 1.1132248 -0.00037054404 67000 0.52669356 0.44276199 0.96945554 0.18969356 68000 0.41566831 0.47320489 0.8888732 0.040635264 69000 0.52140574 0.4261935 0.94759923 0.016566201 70000 0.42034133 0.55867009 0.97901142 0.047465899 71000 0.48720036 0.43749264 0.924693 0.15984789 72000 0.5244238 0.55854139 1.0829652 0.10155994 73000 0.69990219 0.57313852 1.2730407 0.11108648 74000 0.38274347 0.23359664 0.61634011 0.027968087 75000 0.47493369 0.49472607 0.96965976 0.10961568 76000 0.57064727 0.37996383 0.9506111 0.034746271 77000 0.50401727 0.34437588 0.84839315 0.015116686 78000 0.59504118 0.44154772 1.0365889 0.059341875 79000 0.4920801 0.58935767 1.0814378 0.12139906 80000 0.56992818 0.38916606 0.95909424 0.073618074 81000 0.38446945 0.77314417 1.1576136 0.12173381 82000 0.48734531 0.56198203 1.0493273 0.1080115 83000 0.5516933 0.56743096 1.1191243 0.13936805 84000 0.53336893 0.62914863 1.1625176 0.0084970895 85000 0.46456977 0.77446084 1.2390306 0.18024688 86000 0.58067599 0.53109608 1.1117721 0.012492021 87000 0.55096446 0.61715622 1.1681207 0.13264723 88000 0.56548774 0.74463701 1.3101247 0.14491188 89000 0.52492634 0.58482194 1.1097483 0.21155245 90000 0.64973565 0.85514474 1.5048804 0.036911953 91000 0.55367722 0.74046971 1.2941469 0.23918851 92000 0.44863249 0.56773761 1.0163701 0.00042860088 93000 0.64728356 0.66594086 1.3132244 0.0022850006 94000 0.65255497 0.82136644 1.4739214 0.10037643 95000 0.62266654 0.82642147 1.449088 0.11964602 96000 0.50656004 0.83312844 1.3396885 0.078491084 97000 0.47126712 0.70469684 1.175964 0.12956056 98000 0.48661103 1.0121726 1.4987837 0.043537851 99000 0.48379797 0.9520931 1.4358911 0.082047522 100000 0.54266361 1.0959698 1.6386334 -0.13092175 Loop time of 3.8532 on 1 procs for 100000 steps with 32 atoms Performance: 2242290.202 tau/day, 25952.433 timesteps/s 98.8% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.3917 | 2.3917 | 2.3917 | 0.0 | 62.07 Neigh | 0.012386 | 0.012386 | 0.012386 | 0.0 | 0.32 Comm | 0.11307 | 0.11307 | 0.11307 | 0.0 | 2.93 Output | 0.0010369 | 0.0010369 | 0.0010369 | 0.0 | 0.03 Modify | 1.246 | 1.246 | 1.246 | 0.0 | 32.34 Other | | 0.08895 | | | 2.31 Nlocal: 32 ave 32 max 32 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 21 ave 21 max 21 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 55 ave 55 max 55 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 55 Ave neighs/atom = 1.71875 Neighbor list builds = 2886 Dangerous builds = 0 Total wall time: 0:00:03