LAMMPS (29 Jun 2018) # 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 = 0.00020504 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 0.39423376 0.0017918048 0.39602557 0.0021941612 2000 0.42284177 0.01346585 0.43630762 0.0029377883 3000 0.58154405 0.011321689 0.59286574 0.003667871 4000 0.73518304 0.034603175 0.76978621 0.0018689207 5000 0.84367476 0.025292163 0.86896692 0.0089161373 6000 0.70803236 0.0085631016 0.71659546 0.0045552895 7000 0.56206452 0.10453031 0.66659483 0.010255161 8000 0.64538994 0.088817673 0.73420761 0.0037633655 9000 0.90540819 0.063696004 0.96910419 0.0077673359 10000 0.68632042 0.093265016 0.77958544 0.0057864838 11000 0.59118074 0.025654748 0.61683549 0.012518759 12000 0.67522767 0.038176401 0.71340407 0.01741153 13000 0.7644843 0.10429844 0.86878274 0.013161339 14000 0.56152694 0.067836655 0.62936359 0.016852121 15000 0.41895506 0.019513348 0.43846841 0.015225695 16000 0.55799421 0.1564559 0.71445011 0.011703561 17000 0.59391964 0.034450221 0.62836986 0.026215002 18000 0.75911858 0.030885726 0.7900043 0.018396366 19000 0.64417995 0.12110912 0.76528907 0.010247952 20000 0.57751435 0.16965651 0.74717086 0.023392323 21000 0.7613368 0.13405354 0.89539034 0.021498982 22000 0.57676692 0.18011879 0.75688571 0.024469161 23000 0.54043723 0.11842026 0.65885749 0.019799067 24000 0.62276061 0.038967924 0.66172853 0.019080086 25000 0.53157536 0.11651937 0.64809473 0.017019298 26000 0.72213293 0.039012448 0.76114538 0.015434904 27000 0.62157832 0.13697494 0.75855326 0.028711011 28000 0.41323738 0.16301101 0.57624839 0.041792632 29000 0.45774328 0.17569066 0.63343394 0.019975231 30000 0.78901796 0.099791386 0.88880934 0.024116947 31000 0.85205397 0.11977547 0.97182945 0.026667489 32000 0.37137095 0.1232622 0.49463315 0.00087637364 33000 0.26860871 0.26056381 0.52917252 0.036110517 34000 0.3018636 0.21336905 0.51523265 0.040315549 35000 0.39915129 0.28245957 0.68161085 0.034876856 36000 0.25761236 0.2352705 0.49288286 0.022772767 37000 0.1071233 0.31692858 0.42405188 0.017994666 38000 0.083729577 0.28473145 0.36846103 -0.0045370431 39000 0.070355565 0.26682083 0.33717639 0.017921556 40000 0.075894079 0.20077896 0.27667304 0.014873186 41000 0.05891028 0.15989064 0.21880092 0.025547873 42000 0.1225107 0.16583605 0.28834675 0.038842785 43000 0.17049189 0.14323991 0.3137318 0.029550161 44000 0.26823939 0.15208257 0.42032196 0.028113612 45000 0.10172203 0.1729706 0.27469264 -0.013769913 46000 0.14841355 0.19085074 0.33926429 -0.00073741985 47000 0.27654927 0.19097937 0.46752864 0.04021431 48000 0.53432331 0.080769923 0.61509323 0.029932845 49000 0.69111634 0.13064951 0.82176585 0.028985406 50000 0.24520806 0.18317453 0.42838258 0.05179746 51000 0.23541368 0.14281364 0.37822732 0.071884238 52000 0.25464996 0.095730242 0.3503802 0.034488204 53000 0.53677633 0.1058745 0.64265084 0.059932498 54000 0.32970921 0.27979128 0.60950049 0.062869716 55000 0.49094054 0.096735015 0.58767556 0.04728005 56000 0.54398249 0.2216472 0.76562969 0.056712022 57000 0.60869068 0.2338422 0.84253288 0.077143302 58000 0.72175509 0.18687368 0.90862877 0.019357656 59000 0.79442757 0.092502981 0.88693055 0.066882632 60000 0.6810555 0.077699385 0.75875488 0.095975173 61000 0.63178834 0.05071143 0.68249977 0.043586668 62000 0.76589344 0.044615704 0.81050914 0.085718411 63000 0.84815889 0.030527848 0.87868674 0.053072795 64000 0.7309043 0.051938637 0.78284294 0.058887766 65000 0.62498816 0.034474465 0.65946262 0.068446407 66000 0.69817494 0.068546004 0.76672094 0.062634433 67000 0.86444275 0.010184259 0.87462701 0.073635055 68000 0.77820319 0.0079319524 0.78613515 0.090330925 69000 0.56938919 0.0092629332 0.57865213 0.061838729 70000 0.61870712 0.010047381 0.6287545 0.066501338 71000 0.71651803 0.0088366199 0.72535465 0.079136316 72000 0.76278925 0.008828151 0.77161741 0.063672771 73000 0.75447428 0.0083985526 0.76287283 0.078256913 74000 0.66185251 0.0091910052 0.67104351 0.069840511 75000 0.58458829 0.0097671568 0.59435544 0.076123422 76000 0.7487564 0.0100022 0.7587586 0.076171741 77000 0.89505465 0.009250681 0.90430533 0.074921699 78000 0.73738164 0.0092029279 0.74658457 0.078835344 79000 0.65735281 0.010099528 0.66745233 0.077940627 80000 0.70247542 0.010306464 0.71278189 0.079560093 81000 0.74839505 0.010199092 0.75859415 0.080835104 82000 0.75193767 0.010274058 0.76221173 0.081086684 83000 0.71392598 0.010495573 0.72442156 0.082746145 84000 0.58498928 0.011027388 0.59601667 0.08356465 85000 0.59022869 0.011729474 0.60195817 0.084519397 86000 0.81753578 0.011208964 0.82874475 0.085490261 87000 0.83480682 0.010542579 0.8453494 0.086268527 88000 0.67322538 0.011170734 0.68439611 0.08751623 89000 0.62637389 0.012033316 0.6384072 0.088548094 90000 0.92828557 0.011750388 0.94003596 0.089199823 91000 0.96072564 0.010324509 0.97105015 0.090204803 92000 0.72105071 0.011484152 0.73253486 0.09140819 93000 0.65762527 0.012558219 0.67018349 0.092453474 94000 0.73991591 0.01261909 0.752535 0.093373477 95000 0.91791653 0.011980455 0.92989699 0.094182136 96000 0.76562561 0.011807085 0.7774327 0.095323684 97000 0.57292104 0.013610205 0.58653124 0.096505977 98000 0.68141076 0.013863204 0.69527396 0.097380069 99000 0.82390969 0.013002341 0.83691203 0.098235926 100000 0.77639728 0.012989342 0.78938662 0.099274147 Loop time of 3.88899 on 1 procs for 100000 steps with 32 atoms Performance: 2221655.884 tau/day, 25713.610 timesteps/s 99.9% CPU use with 1 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.056 | 3.056 | 3.056 | 0.0 | 78.58 Neigh | 0.0051048 | 0.0051048 | 0.0051048 | 0.0 | 0.13 Comm | 0.091444 | 0.091444 | 0.091444 | 0.0 | 2.35 Output | 0.0011995 | 0.0011995 | 0.0011995 | 0.0 | 0.03 Modify | 0.69909 | 0.69909 | 0.69909 | 0.0 | 17.98 Other | | 0.03616 | | | 0.93 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: 57 ave 57 max 57 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 57 Ave neighs/atom = 1.78125 Neighbor list builds = 1445 Dangerous builds = 0 Total wall time: 0:00:03