LAMMPS (28 Mar 2023 - Development) 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 Reading data file ... 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 read_data CPU = 0.001 seconds replicate $r $r 1 replicate 4 $r 1 replicate 4 4 1 Replication is creating a 4x4x1 = 16 times larger system... orthogonal box = (0 0 -0.5) to (48 48 0.5) 1 by 1 by 1 MPI processor grid 32 atoms replicate CPU = 0.001 seconds 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 Changing box ... 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 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 6.1568542 ghost atom cutoff = 6.1568542 binsize = 3.0784271, 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 bin: standard Per MPI rank memory allocation (min/avg/max) = 5.376 | 5.376 | 5.376 Mbytes Step KinEng PotEng TotEng Press 0 0.484375 0.25 0.734375 0.0067274306 1000 0.51464289 0.00099012638 0.51563301 0.013444625 2000 0.55653313 0.0040982283 0.56063136 0.0034505512 3000 0.75323998 0.023578898 0.77681887 0.0036652891 4000 0.70044978 0.092406287 0.79285607 0.0089262842 5000 0.54548803 0.096501313 0.64198934 0.0051379523 6000 0.48208829 0.097798861 0.57988715 0.015298049 7000 0.68219182 0.038843941 0.72103576 0.016842202 8000 0.53792445 0.012983807 0.55090825 0.0066797902 9000 0.49980359 0.029397948 0.52920154 0.0046731993 10000 0.48705779 0.10138799 0.58844578 -1.9696743e-05 11000 0.52151792 0.065893508 0.58741142 0.0049365175 12000 0.59066419 0.039261015 0.62992521 0.001420608 13000 0.46059009 0.07386532 0.53445541 0.005654565 14000 0.37899234 0.13421331 0.51320565 0.0097199047 15000 0.49566894 0.052006844 0.54767578 0.00053157628 16000 0.59294062 0.028393451 0.62133407 0.0057809461 17000 0.51260882 0.1266054 0.63921422 0.0021637817 18000 0.45603179 0.15710959 0.61314138 0.017707488 19000 0.52137969 0.1123825 0.63376219 0.015894031 20000 0.64553686 0.11579772 0.76133459 0.013239309 21000 0.38581837 0.17867419 0.56449256 0.0048572535 22000 0.42776514 0.12979071 0.55755585 0.008093469 23000 0.490055 0.14197765 0.63203265 -0.003575896 24000 0.57689881 0.10164831 0.67854712 0.022418321 25000 0.45630031 0.057905852 0.51420616 0.007959034 26000 0.59497685 0.193113 0.78808985 0.0076331679 27000 0.40943362 0.098595954 0.50802958 0.0016863757 28000 0.34512273 0.15696637 0.50208909 0.037435926 29000 0.59187862 0.1845377 0.77641632 0.014563665 30000 0.69204623 0.16392147 0.8559677 0.031708423 31000 0.40436029 0.34429435 0.74865464 0.073818847 32000 0.47580383 0.22708448 0.70288831 0.015795198 33000 0.48923447 0.23636413 0.72559861 0.025932606 34000 0.51960128 0.15145893 0.67106021 -0.00079607564 35000 0.44792834 0.19927109 0.64719943 -0.0063461505 36000 0.54265821 0.17924788 0.72190609 0.017916439 37000 0.56020344 0.24977507 0.80997851 0.057844411 38000 0.28874871 0.21399353 0.50274224 0.022675277 39000 0.39030236 0.30170176 0.69200411 0.037482614 40000 0.4699469 0.20663643 0.67658333 -0.014082215 41000 0.50202447 0.21510708 0.71713155 -0.0063284222 42000 0.43029593 0.23511818 0.6654141 0.046478372 43000 0.41628842 0.21031596 0.62660438 -0.0053073644 44000 0.51101573 0.15862165 0.66963738 0.010251868 45000 0.56984114 0.18071709 0.75055823 0.021333409 46000 0.45510513 0.15385488 0.60896001 0.048441048 47000 0.41229547 0.20577222 0.61806769 0.027485704 48000 0.64114797 0.33672519 0.97787315 0.13522091 49000 0.44298056 0.27708867 0.72006923 0.026660315 50000 0.43250082 0.17778506 0.61028588 0.02714938 51000 0.59697891 0.25460003 0.85157894 0.026959715 52000 0.63110331 0.21528376 0.84638707 0.023157155 53000 0.46085491 0.25375607 0.71461099 0.024933391 54000 0.50772891 0.29280628 0.80053519 0.010621547 55000 0.67213557 0.2071375 0.87927307 0.061770903 56000 0.61184167 0.34686662 0.95870829 0.095262009 57000 0.42364554 0.29899934 0.72264488 -0.0080865129 58000 0.5033641 0.39810693 0.90147103 0.081474225 59000 0.61363438 0.25296035 0.86659472 0.041921315 60000 0.64600872 0.36997737 1.0159861 0.053833686 61000 0.43392277 0.29276613 0.7266889 0.054911225 62000 0.38910577 0.27714798 0.66625375 -0.0141031 63000 0.42343097 0.21637816 0.63980913 -1.6862315e-05 64000 0.52512516 0.38797726 0.91310242 0.03170217 65000 0.48930994 0.4863269 0.97563684 0.025108671 66000 0.68354817 0.3629732 1.0465214 0.066714362 67000 0.5361863 0.44003399 0.97622029 0.1063525 68000 0.3605148 0.40138904 0.76190383 0.03287684 69000 0.62747502 0.49229352 1.1197685 0.053648724 70000 0.51326037 0.36561885 0.87887922 0.070871008 71000 0.45429341 0.38458357 0.83887698 0.010485881 72000 0.55377877 0.36434231 0.91812107 0.10507819 73000 0.6857324 0.45242968 1.1381621 0.022470322 74000 0.46349397 0.39082798 0.85432196 0.067650912 75000 0.59216869 0.32893138 0.92110008 0.0196582 76000 0.42985327 0.40674342 0.83659669 0.025700762 77000 0.54319568 0.55627833 1.099474 0.067233159 78000 0.59244798 0.5121155 1.1045635 0.12063624 79000 0.61140864 0.45505083 1.0664595 0.088578795 80000 0.64308346 0.4143502 1.0574337 0.038537249 81000 0.55053046 0.43357659 0.98410705 0.053930256 82000 0.54049882 0.41354335 0.95404217 -0.036458392 83000 0.47517728 0.30128468 0.77646196 0.0019488841 84000 0.57452781 0.1949493 0.76947711 0.039244382 85000 0.7907368 0.51406164 1.3047984 0.12766082 86000 0.59488507 0.50084726 1.0957323 0.080232158 87000 0.43071262 0.4682738 0.89898642 0.1266876 88000 0.53305256 0.55941308 1.0924656 0.17062068 89000 0.60672487 0.64951209 1.256237 0.17194524 90000 0.7134227 0.57323404 1.2866567 0.074617282 91000 0.65670871 0.58567381 1.2423825 0.025281565 92000 0.72364891 0.59755693 1.3212058 0.092201188 93000 0.69254418 0.75766186 1.450206 0.16036111 94000 0.56326058 0.6398442 1.2031048 0.26280736 95000 0.47480145 0.57734551 1.052147 0.039940021 96000 0.56909151 0.73081903 1.2999105 0.030223516 97000 0.53198039 0.71808155 1.2500619 0.033191485 98000 0.63572731 0.86931519 1.5050425 0.20901135 99000 0.64477038 0.76771721 1.4124876 0.059732095 100000 0.71275398 0.66613673 1.3788907 0.020038364 Loop time of 2.21223 on 1 procs for 100000 steps with 32 atoms Performance: 3905566.671 tau/day, 45203.318 timesteps/s, 1.447 Matom-step/s 96.4% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.1162 | 1.1162 | 1.1162 | 0.0 | 50.45 Neigh | 0.0049629 | 0.0049629 | 0.0049629 | 0.0 | 0.22 Comm | 0.045069 | 0.045069 | 0.045069 | 0.0 | 2.04 Output | 0.00060169 | 0.00060169 | 0.00060169 | 0.0 | 0.03 Modify | 1.0017 | 1.0017 | 1.0017 | 0.0 | 45.28 Other | | 0.04368 | | | 1.97 Nlocal: 32 ave 32 max 32 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 19 ave 19 max 19 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 59 ave 59 max 59 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 59 Ave neighs/atom = 1.84375 Neighbor list builds = 3214 Dangerous builds = 0 Total wall time: 0:00:02