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 = 0.000400782 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) = 4.774 | 4.774 | 4.774 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 0.12783367 0.85436581 0.023907185 9000 0.87685728 0.12398193 1.0008392 0.0064591005 10000 0.72509641 0.097241969 0.82233837 0.0012418726 11000 0.62314955 0.056042914 0.67919247 0.0018880786 12000 0.57157436 0.18187429 0.75344865 0.0096135623 13000 0.7489742 0.08262775 0.83160195 0.009183917 14000 0.78835138 0.18761048 0.97596186 0.023684357 15000 0.40408761 0.079431327 0.48351893 0.025285348 16000 0.4071013 0.13207058 0.53917188 0.02015488 17000 0.48417067 0.16699781 0.65116848 0.059188189 18000 0.60038567 0.18317457 0.78356024 -0.046456387 19000 0.73796958 0.064271521 0.8022411 0.090257204 20000 0.62508659 0.14486336 0.76994994 0.04948543 21000 0.5596837 0.10018831 0.65987201 0.044961962 22000 0.30731517 0.1386103 0.44592547 0.015096596 23000 0.34371843 0.1486761 0.49239453 0.026100892 24000 0.33484204 0.25428479 0.58912683 0.01974393 25000 0.48714744 0.32743616 0.8145836 0.037925893 26000 0.33255994 0.29851422 0.63107417 0.049419529 27000 0.21735889 0.18816203 0.40552093 0.050622152 28000 0.31911317 0.12559898 0.44471215 -0.0036236361 29000 0.53280161 0.055185441 0.58798705 0.083856225 30000 0.52916941 0.28697284 0.81614225 0.055873213 31000 0.47861645 0.21932568 0.69794214 0.02762301 32000 0.46786314 0.041856438 0.50971958 0.029923804 33000 0.69944716 0.039356744 0.7388039 0.028174645 34000 0.39964317 0.1027175 0.50236068 0.039495865 35000 0.70199237 0.10421859 0.80621095 0.015943417 36000 0.45053533 0.078626602 0.52916193 0.0073950287 37000 0.41587918 0.056551665 0.47243084 0.034091318 38000 0.58663473 0.039228671 0.6258634 0.033093641 39000 0.72480658 0.14792564 0.87273222 0.030903741 40000 0.51163285 0.13445292 0.64608577 -0.03114559 41000 0.56273761 0.16720374 0.72994135 0.027968528 42000 0.61850184 0.10584389 0.72434573 -0.036301799 43000 0.60039772 0.11984289 0.72024062 0.080894236 44000 0.57499839 0.068211092 0.64320948 0.049726122 45000 0.69937239 0.16287141 0.8622438 0.044921114 46000 0.23303785 0.2391726 0.47221045 0.021668935 47000 0.27051781 0.10690378 0.37742159 0.11963476 48000 0.408895 0.079919688 0.48881469 0.087484004 49000 0.74363181 0.040819422 0.78445123 0.011937456 50000 0.84482316 0.10205256 0.94687572 0.064133262 51000 0.84923574 0.089882984 0.93911872 0.062696388 52000 0.66278324 0.0331554 0.69593864 0.035150337 53000 0.64737251 0.039608076 0.68698058 0.057687461 54000 0.68931435 0.042661403 0.73197576 0.069664795 55000 0.84523308 0.10293275 0.94816583 0.047343755 56000 0.80033937 0.1534797 0.95381907 0.070206074 57000 0.6214799 0.1174575 0.7389374 0.078530452 58000 0.64228495 0.088089896 0.73037485 0.060245994 59000 0.89376363 0.065171887 0.95893552 0.071658895 60000 0.90162992 0.016564761 0.91819468 0.089245946 61000 0.72439995 0.0076508835 0.73205083 0.031430213 62000 0.71590702 0.0046728326 0.72057986 0.10153514 63000 0.74491219 0.0046757926 0.74958798 0.077145851 64000 0.77173614 0.008265632 0.78000178 -0.049932265 65000 0.72789092 0.0053605745 0.73325149 0.27060389 66000 0.63001101 0.013871945 0.64388296 -0.17766692 67000 0.65887071 0.0069105692 0.66578128 0.31632918 68000 0.89042862 0.0026334652 0.89306209 -0.050495873 69000 0.83442374 0.0059232957 0.84034703 -0.21871692 70000 0.65149642 0.004885383 0.65638181 0.50428108 71000 0.66888808 0.01125057 0.68013865 -0.29575772 72000 0.74941609 0.0026616299 0.75207772 0.34800716 73000 0.7898844 0.0048982026 0.7947826 -0.096872644 74000 0.68823538 0.0021467794 0.69038216 0.12272852 75000 0.5238808 0.0046112795 0.52849208 0.25760316 76000 0.65512889 0.014567969 0.66969686 -0.24622674 77000 0.82292373 0.0092471048 0.83217083 0.4002304 78000 0.76305221 0.01101937 0.77407158 -0.10704945 79000 0.66279814 0.0090486405 0.67184678 0.037466134 80000 0.65808885 0.010000569 0.66808942 0.31742291 81000 0.91357798 0.046226814 0.95980479 -0.20945693 82000 0.87611859 -0.016794871 0.85932372 0.31759733 83000 0.66285455 -0.017921021 0.64493353 0.27065273 84000 0.67460715 -0.0076174891 0.66698966 -0.024772659 85000 0.77786135 0.0014316505 0.779293 -0.21635327 86000 0.83246393 0.087489797 0.91995372 -0.13431455 87000 0.62935573 0.045088823 0.67444455 0.037766395 88000 0.55264538 -0.024625272 0.52802011 0.18121213 89000 0.74171392 -0.012629926 0.729084 -0.27666424 90000 0.82542165 -0.02296567 0.80245598 -0.30497174 91000 0.72958657 -0.026275093 0.70331147 -0.27624518 92000 0.6319558 0.022568297 0.65452409 -0.33539318 93000 0.66685301 0.021889807 0.68874282 -0.39890762 94000 0.91243243 0.0078218509 0.92025428 -0.27213648 95000 0.81125179 -0.0096756295 0.80157616 -0.099802335 96000 0.63354907 -0.018329423 0.61521965 0.18199604 97000 0.66812347 -0.016650228 0.65147324 0.49878257 98000 0.81490013 -0.0049164866 0.80998365 -0.13473106 99000 0.82131147 0.0043198846 0.82563136 -0.3083957 100000 0.50880983 -0.010467027 0.4983428 0.060606332 Loop time of 4.3169 on 4 procs for 100000 steps with 32 atoms Performance: 2001435.573 tau/day, 23164.764 timesteps/s 95.1% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.2078 | 1.3972 | 1.6653 | 15.1 | 32.36 Neigh | 0.0030954 | 0.003284 | 0.0034814 | 0.3 | 0.08 Comm | 1.074 | 1.3595 | 1.6003 | 16.2 | 31.49 Output | 0.001703 | 0.0030067 | 0.0068843 | 4.1 | 0.07 Modify | 1.2071 | 1.2647 | 1.3062 | 3.6 | 29.30 Other | | 0.2893 | | | 6.70 Nlocal: 8 ave 9 max 6 min Histogram: 1 0 0 0 0 0 1 0 0 2 Nghost: 17.75 ave 20 max 16 min Histogram: 1 0 1 0 0 1 0 0 0 1 Neighs: 14 ave 18 max 7 min Histogram: 1 0 0 0 0 0 0 1 1 1 Total # of neighbors = 56 Ave neighs/atom = 1.75 Neighbor list builds = 1566 Dangerous builds = 0 Total wall time: 0:00:04