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 = 0.000279665 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 variable cut_inner equal 0.5 variable k_n equal 100 variable k_na equal 2 variable c_n equal 1 variable c_t equal 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 1 ${c_t} ${mu} ${delta_ua} ${cut_inner} pair_style body/rounded/polygon 1 1 ${mu} ${delta_ua} ${cut_inner} pair_style body/rounded/polygon 1 1 0.1 ${delta_ua} ${cut_inner} pair_style body/rounded/polygon 1 1 0.1 0.5 ${cut_inner} pair_style body/rounded/polygon 1 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 y 0.001 $P 1.0 couple xy fixedpoint 0 0 0 fix 1 all npt/body temp 0.5 $T 1.0 x 0.001 $P 1.0 y 0.001 $P 1.0 couple xy fixedpoint 0 0 0 fix 1 all npt/body temp 0.5 0.5 1.0 x 0.001 $P 1.0 y 0.001 $P 1.0 couple xy fixedpoint 0 0 0 fix 1 all npt/body temp 0.5 0.5 1.0 x 0.001 0.1 1.0 y 0.001 $P 1.0 couple xy fixedpoint 0 0 0 fix 1 all npt/body temp 0.5 0.5 1.0 x 0.001 0.1 1.0 y 0.001 0.1 1.0 couple xy fixedpoint 0 0 0 fix 2 all enforce2d #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) = 4.781 | 4.781 | 4.781 Mbytes Step KinEng PotEng TotEng Press 0 0.484375 0.25 0.734375 0.0067274306 1000 0.38428256 0.0014168922 0.38569945 0.0020468171 2000 0.41372193 0.015263236 0.42898517 0.0029343462 3000 0.54844547 0.014870378 0.56331585 0.001978353 4000 0.73816048 0.031668204 0.76982869 0.0025939718 5000 0.84536165 0.011504649 0.8568663 0.0037990517 6000 0.73776478 0.14445932 0.8822241 0.0086538113 7000 0.52022565 0.069507637 0.58973329 0.0072098694 8000 0.72653213 0.12783368 0.85436581 0.023907183 9000 0.87685727 0.1239819 1.0008392 0.0064590959 10000 0.7250918 0.097243508 0.82233531 0.0012448267 11000 0.62302234 0.05597557 0.67899791 0.00080239872 12000 0.57159363 0.18199602 0.75358965 0.01033626 13000 0.7505295 0.071545266 0.82207477 0.011480236 14000 0.84703598 0.15914379 1.0061798 0.032814039 15000 0.41905013 0.090552572 0.5096027 0.015717153 16000 0.41805189 0.042916881 0.46096877 0.020702707 17000 0.59966233 0.05285043 0.65251275 0.016526024 18000 0.54282285 0.20835047 0.75117332 0.036414059 19000 0.777922 0.034754101 0.8126761 0.036467537 20000 0.54703924 0.14633506 0.6933743 0.012917248 21000 0.49337931 0.1858754 0.67925471 0.037890735 22000 0.64916623 0.19281344 0.84197967 0.011996773 23000 0.66958738 0.20459682 0.8741842 0.023639466 24000 0.63729755 0.1111959 0.74849345 0.025049919 25000 0.60094316 0.13375799 0.73470115 0.035286376 26000 0.35419589 0.22049451 0.5746904 0.0024215291 27000 0.33789786 0.18494942 0.52284728 0.0066457643 28000 0.32376056 0.13151726 0.45527782 0.010773856 29000 0.36198203 0.11044834 0.47243037 0.063012638 30000 0.22624436 0.19690087 0.42314523 0.037422734 31000 0.32284312 0.059623656 0.38246677 0.0287682 32000 0.4457193 0.042396136 0.48811544 0.022025252 33000 0.61078662 0.059447221 0.67023384 0.030335089 34000 0.63157762 0.062056279 0.6936339 0.044624352 35000 0.69577644 0.086216204 0.78199264 0.0319995 36000 0.76814336 0.062105963 0.83024933 0.044316891 37000 0.58641664 0.095034548 0.68145119 0.03234133 38000 0.48772813 0.12911854 0.61684667 0.038732146 39000 0.74957742 0.09823432 0.84781174 0.053181162 40000 0.57881374 0.2932491 0.87206284 0.065740126 41000 0.4415176 0.22899179 0.67050939 0.026159841 42000 0.5260339 0.2048105 0.7308444 0.046294432 43000 0.33493572 0.32500572 0.65994144 -0.01250241 44000 0.46467243 0.07907132 0.54374375 0.13386238 45000 0.48135518 0.2618908 0.74324598 -0.016767159 46000 0.27223209 0.24562643 0.51785852 0.052118439 47000 0.26402739 0.1838767 0.44790409 -0.0015878764 48000 0.10229166 0.25519169 0.35748335 -0.033927088 49000 0.24313495 0.16578185 0.40891679 0.12414926 50000 0.27400066 0.27688032 0.55088098 0.10421157 51000 0.43081855 0.18111733 0.61193587 0.16373371 52000 0.81969298 0.060995894 0.88068887 0.057285357 53000 0.99936159 0.029137886 1.0284995 0.19425015 54000 0.69750047 0.038079774 0.73558024 -0.089236384 55000 0.54823746 0.056369886 0.60460734 -0.021320579 56000 0.6752322 0.050322917 0.72555512 0.25303548 57000 0.90328009 0.061107142 0.96438723 -0.1962713 58000 0.81463148 0.050387847 0.86501933 0.35952157 59000 0.61636455 0.064910223 0.68127478 -0.27208497 60000 0.62573918 0.052264617 0.67800379 0.4493407 61000 0.81065726 0.071269668 0.88192693 -0.34643283 62000 0.86420318 0.052799365 0.91700254 0.48308047 63000 0.67848508 0.069087342 0.74757242 -0.31814526 64000 0.61430417 0.052109373 0.66641354 0.38336646 65000 0.75782937 0.063488206 0.82131757 -0.19113322 66000 0.88735857 0.051779306 0.93913787 0.29410996 67000 0.70684373 0.061786313 0.76863005 -0.16503578 68000 0.58571951 0.052402151 0.63812166 0.30173228 69000 0.64997491 0.064435462 0.71441037 -0.1920633 70000 0.75071821 0.053416991 0.8041352 0.3846747 71000 0.8124718 0.06877986 0.88125166 -0.26852566 72000 0.71352066 0.05358784 0.7671085 0.41321806 73000 0.55151827 0.066470642 0.61798891 -0.2211738 74000 0.65473635 0.061946814 0.71668316 0.29536873 75000 0.88704613 0.059476353 0.94652248 -0.0312656 76000 0.76899803 0.057351665 0.8263497 0.017885214 77000 0.65149455 0.05407174 0.70556629 0.25192449 78000 0.68614394 0.074251169 0.76039511 -0.19369404 79000 0.97451567 0.06262739 1.0371431 0.4217182 80000 0.88207775 0.070157004 0.95223476 -0.27318477 81000 0.69294455 0.062623957 0.75556851 0.40150141 82000 0.70748016 0.073924331 0.78140449 -0.17128794 83000 0.78180774 0.063513978 0.84532172 0.22033652 84000 0.80170993 0.065812223 0.86752216 0.083202913 85000 0.64788122 0.070348079 0.7182293 -0.066913668 86000 0.56575431 0.064865112 0.63061942 0.33905786 87000 0.78205358 0.07983702 0.8618906 -0.22844912 88000 0.87426443 0.065703482 0.93996791 0.448573 89000 0.73269893 0.079827385 0.81252632 -0.24183162 90000 0.66703106 0.065630146 0.73266121 0.35410109 91000 0.73107154 0.07402702 0.80509856 -0.085492997 92000 1.043635 0.067156523 1.1107915 0.14311135 93000 0.86063344 0.065607238 0.92624068 0.20750649 94000 0.68304235 0.075962239 0.75900459 -0.14594625 95000 0.7069191 0.067125732 0.77404483 0.39459759 96000 0.79860046 0.090957588 0.88955805 -0.24202125 97000 0.81366777 0.071387081 0.88505485 0.32217266 98000 0.61885746 0.041524228 0.66038169 0.31635364 99000 0.57007759 0.055438456 0.62551604 -0.21172902 100000 0.80462394 0.045542313 0.85016626 0.099207503 Loop time of 6.34495 on 1 procs for 100000 steps with 32 atoms Performance: 1361713.788 tau/day, 15760.576 timesteps/s 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.0158 | 5.0158 | 5.0158 | 0.0 | 79.05 Neigh | 0.0072868 | 0.0072868 | 0.0072868 | 0.0 | 0.11 Comm | 0.18669 | 0.18669 | 0.18669 | 0.0 | 2.94 Output | 0.00098681 | 0.00098681 | 0.00098681 | 0.0 | 0.02 Modify | 1.0417 | 1.0417 | 1.0417 | 0.0 | 16.42 Other | | 0.09245 | | | 1.46 Nlocal: 32 ave 32 max 32 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 35 ave 35 max 35 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 61 ave 61 max 61 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 61 Ave neighs/atom = 1.90625 Neighbor list builds = 1545 Dangerous builds = 0 Total wall time: 0:00:06