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) 2 by 2 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) 2 by 2 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 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 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) = 5.379 | 5.379 | 5.379 Mbytes Step KinEng PotEng TotEng Press 0 0.484375 0.25 0.734375 0.0067274306 1000 0.39720235 0.0015845731 0.39878692 0.00223489 2000 0.42893425 0.011718891 0.44065314 0.0027413224 3000 0.57823511 0.012407489 0.5906426 0.0025306081 4000 0.71610647 0.028149437 0.74425591 0.0016504948 5000 0.84027279 0.018917017 0.8591898 0.0037451875 6000 0.72410001 0.073495378 0.79759539 0.00018672875 7000 0.53886484 0.077723366 0.61658821 0.004729216 8000 0.66196054 0.05502242 0.71698296 0.0054997327 9000 0.93104065 0.071628784 1.0026694 0.011330629 10000 0.75494389 0.15204106 0.90698496 0.021702127 11000 0.72349155 0.11102332 0.83451487 0.019264192 12000 0.56216536 0.11705898 0.67922434 -0.028296196 13000 0.63793556 0.11701866 0.75495421 0.029469295 14000 0.62999448 0.020866813 0.65086129 0.008609569 15000 0.6404504 0.0090011224 0.64945152 0.01706906 16000 0.70195749 0.044735201 0.74669269 0.0179597 17000 0.69097976 0.03894214 0.72992191 0.015704476 18000 0.75303457 0.0019263825 0.75496095 0.021536711 19000 0.6459718 0.10419136 0.75016317 0.033861092 20000 0.73026363 0.13023974 0.86050337 0.022207497 21000 0.77107035 0.30464112 1.0757115 0.013967631 22000 0.44134768 0.22883887 0.67018655 0.014202518 23000 0.53410601 0.16702381 0.70112983 0.009305779 24000 0.5144312 0.19041122 0.70484242 -0.0059836303 25000 0.60922681 0.15475207 0.76397888 0.016370526 26000 0.70922367 0.25374443 0.9629681 0.027301754 27000 0.67289133 0.39287626 1.0657676 0.025562031 28000 0.62112601 0.017177715 0.63830372 0.018556767 29000 0.56492546 0.087573524 0.65249898 0.025132036 30000 0.62612507 -0.01835118 0.60777389 0.050139664 31000 0.69157641 0.064849873 0.75642628 0.033954585 32000 0.72648211 0.08597545 0.81245756 0.038082388 33000 0.58608821 0.13013111 0.71621932 0.054766043 34000 0.49330983 0.080490598 0.57380043 0.034154681 35000 0.54570666 0.075020466 0.62072713 0.03879264 36000 0.60305736 0.10717781 0.71023516 0.030701059 37000 0.52801767 0.12516316 0.65318083 0.007411688 38000 0.5838277 0.12569072 0.70951842 0.03272916 39000 0.53999819 0.043261294 0.58325949 0.084115917 40000 0.64957099 0.040023268 0.68959426 0.027021958 41000 0.59235949 0.10449793 0.69685742 0.045773377 42000 0.71752786 0.043289363 0.76081722 0.040926021 43000 0.78581005 0.024363927 0.81017398 0.034694164 44000 0.6396541 0.06004252 0.69969662 0.037227348 45000 0.35753293 0.11456039 0.47209332 0.033569048 46000 0.11031158 0.11831834 0.22862991 0.076545681 47000 0.11720754 0.035471414 0.15267896 0.022093929 48000 0.13370328 0.031802339 0.16550562 0.053298269 49000 0.2700883 0.15584422 0.42593252 0.057108168 50000 0.53837779 0.13398219 0.67235998 0.047704986 51000 0.38133073 0.011372933 0.39270366 0.04696367 52000 0.32448241 0.009137008 0.33361942 0.033573259 53000 0.25798301 -0.016530605 0.2414524 0.04623663 54000 0.2842707 0.054504088 0.33877479 0.03751156 55000 0.28895106 0.025307766 0.31425882 0.03935955 56000 0.19130753 0.099678989 0.29098652 0.051888728 57000 0.12237303 0.057536458 0.17990949 0.09984021 58000 0.17962003 0.012450682 0.19207072 0.028644351 59000 0.21667262 -0.013693164 0.20297945 0.048086277 60000 0.4298123 -0.012970819 0.41684148 0.019347498 61000 0.69591654 -0.027048452 0.66886809 0.069793861 62000 1.0040382 -0.044228622 0.95980957 0.056563167 63000 0.78189663 -0.053045577 0.72885106 0.059491526 64000 0.57051419 -0.050757181 0.51975701 0.061863162 65000 0.62584243 -0.050616328 0.5752261 0.068924362 66000 0.85558894 -0.051396155 0.80419278 0.059309337 67000 0.86314978 -0.052635701 0.81051408 0.071855924 68000 0.65427495 -0.05147951 0.60279544 0.064001735 69000 0.60658011 -0.050623824 0.55595629 0.0715805 70000 0.76353932 -0.050863795 0.71267553 0.06771349 71000 0.87559332 -0.051720153 0.82387317 0.071884106 72000 0.71924774 -0.051167456 0.66808029 0.071010747 73000 0.6100998 -0.050025233 0.56007457 0.073319802 74000 0.71838075 -0.049907287 0.66847346 0.07314982 75000 0.91863251 -0.051069435 0.86756308 0.07493433 76000 0.78459189 -0.050803207 0.73378868 0.075397431 77000 0.70827012 -0.049701237 0.65856888 0.076901086 78000 0.72333497 -0.04940986 0.67392511 0.077456938 79000 0.76543474 -0.049588137 0.7158466 0.078792278 80000 0.77759003 -0.049596899 0.72799313 0.079470668 81000 0.67474562 -0.048929658 0.62581596 0.080740407 82000 0.60162355 -0.047698966 0.55392459 0.081758686 83000 0.7602675 -0.047827179 0.71244032 0.082547083 84000 0.9061851 -0.049481366 0.85670374 0.083443845 85000 0.74071256 -0.048645397 0.69206717 0.084605474 86000 0.67634638 -0.046894309 0.62945207 0.085608904 87000 0.71669859 -0.046524067 0.67017453 0.086561551 88000 0.77025498 -0.047090994 0.72316398 0.087515495 89000 0.76590655 -0.047083362 0.71882319 0.088522842 90000 0.61372503 -0.045529779 0.56819526 0.08963777 91000 0.58583927 -0.043777544 0.54206173 0.093090208 92000 0.80507421 -0.04423346 0.76084075 0.093861418 93000 0.84631942 -0.046878171 0.79944125 0.093279847 94000 0.70915593 -0.04570489 0.66345104 0.092425564 95000 0.66813988 -0.043460537 0.62467934 0.093467021 96000 0.71739316 -0.042402374 0.67499079 0.095183179 97000 0.74132854 -0.042457291 0.69887124 0.096665917 98000 0.74033914 -0.042269007 0.69807013 0.097869908 99000 0.72447372 -0.041519159 0.68295457 0.098825459 100000 0.6968193 -0.040321034 0.65649827 0.099797629 Loop time of 2.55809 on 4 procs for 100000 steps with 32 atoms Performance: 3377521.712 tau/day, 39091.686 timesteps/s, 1.251 Matom-step/s 91.9% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.53547 | 0.78258 | 1.0169 | 21.0 | 30.59 Neigh | 0.0010868 | 0.0011973 | 0.0013608 | 0.3 | 0.05 Comm | 0.57019 | 0.78963 | 1.0091 | 19.2 | 30.87 Output | 0.00075581 | 0.0030547 | 0.0098741 | 7.1 | 0.12 Modify | 0.80723 | 0.81855 | 0.83849 | 1.3 | 32.00 Other | | 0.1631 | | | 6.37 Nlocal: 8 ave 12 max 2 min Histogram: 1 0 0 0 0 0 1 0 1 1 Nghost: 15.25 ave 19 max 13 min Histogram: 1 1 0 1 0 0 0 0 0 1 Neighs: 12 ave 18 max 1 min Histogram: 1 0 0 0 0 0 0 1 1 1 Total # of neighbors = 48 Ave neighs/atom = 1.5 Neighbor list builds = 1420 Dangerous builds = 0 Total wall time: 0:00:02