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 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) = 5.386 | 5.386 | 5.386 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 0.0054997323 9000 0.93104065 0.071628784 1.0026694 0.011330629 10000 0.75494389 0.15204106 0.90698495 0.021702117 11000 0.72349154 0.11102332 0.83451486 0.019264158 12000 0.56216531 0.117059 0.67922431 -0.028295891 13000 0.63793498 0.11701868 0.75495366 0.029470631 14000 0.62996509 0.020871971 0.65083706 0.0086224023 15000 0.6403927 0.0091092209 0.64950192 0.016897685 16000 0.70288045 0.046856749 0.7497372 0.02312871 17000 0.6820593 0.038994474 0.72105377 0.0068705173 18000 0.75623543 0.0069908315 0.76322626 0.025170959 19000 0.85962145 0.059005169 0.91862661 0.012725758 20000 0.73334823 0.033043489 0.76639172 0.023661433 21000 0.60850654 0.081277767 0.68978431 0.021031136 22000 0.38251144 0.27624263 0.65875407 0.047336318 23000 0.4288127 0.30632792 0.73514062 0.034108416 24000 0.4452138 0.13179024 0.57700404 0.010303821 25000 0.48091107 0.1816109 0.66252197 0.021201342 26000 0.67970784 0.088616708 0.76832455 0.034997245 27000 0.8223642 0.08699442 0.90935862 0.023508839 28000 0.60062179 0.1119578 0.71257959 -0.0010008016 29000 0.54629437 0.1202995 0.66659387 0.040613547 30000 0.28102412 0.38657163 0.66759575 -0.0086538064 31000 0.12433474 0.18824131 0.31257605 0.049899211 32000 0.089510322 0.20890679 0.29841711 0.045555094 33000 0.12657665 0.17720119 0.30377784 0.028306214 34000 0.18400652 0.17677189 0.36077841 0.034628531 35000 0.24048631 0.11010844 0.35059475 0.029848365 36000 0.33435006 0.077341882 0.41169194 0.055963098 37000 0.46088842 0.1210638 0.58195222 0.072006022 38000 0.76551752 0.07037755 0.83589507 0.018204686 39000 0.89388464 0.080990198 0.97487484 0.038361105 40000 0.65618718 0.078644754 0.73483193 0.040567246 41000 0.47284043 0.16391389 0.63675432 0.027523843 42000 0.52454668 0.057988616 0.58253529 0.03122996 43000 0.78769394 0.08405077 0.87174471 0.044743697 44000 0.92932837 0.093922981 1.0232514 0.042510479 45000 0.5722596 0.17607834 0.74833794 0.034646914 46000 0.54352389 0.085652886 0.62917677 0.033203865 47000 0.45608912 0.25183842 0.70792754 0.08370224 48000 0.47530886 0.10106466 0.57637352 0.046113986 49000 0.67945305 0.0065249477 0.68597799 0.054743491 50000 0.49661922 0.097381596 0.59400082 0.006998965 51000 0.60992235 0.059017331 0.66893968 0.09445106 52000 0.69563455 0.18702969 0.88266424 0.034154598 53000 0.87598532 0.18260917 1.0585945 0.065734536 54000 0.58822846 0.27562038 0.86384884 0.0764045 55000 0.43454899 0.17174441 0.6062934 0.026434052 56000 0.4004495 0.12778644 0.52823594 0.065986005 57000 0.36272102 0.09849578 0.4612168 0.064217596 58000 0.40987214 0.21777618 0.62764832 0.058625636 59000 0.64813089 0.1479689 0.79609979 0.033378701 60000 0.90328265 0.11049926 1.0137819 0.055828397 61000 0.82921839 0.074638688 0.90385707 0.062488824 62000 0.63223087 0.094386302 0.72661718 0.054784559 63000 0.62946839 0.087807829 0.71727622 0.058398323 64000 0.79784108 0.094756776 0.89259786 0.065765914 65000 0.87500942 0.13514078 1.0101502 0.068123475 66000 0.66961949 0.19942965 0.86904914 0.065587832 67000 0.61612396 0.11436282 0.73048678 0.061233427 68000 0.74149449 0.03129016 0.77278465 0.072517897 69000 0.84060202 0.027261803 0.86786382 0.063374451 70000 0.78182528 0.023528774 0.80535405 0.07431822 71000 0.71611101 0.023512727 0.73962374 0.069575276 72000 0.68437263 0.023941199 0.70831382 0.069821154 73000 0.75652323 0.023580324 0.78010355 0.075046425 74000 0.92077658 0.023272419 0.944049 0.070992373 75000 0.75277766 0.023186631 0.77596429 0.074859227 76000 0.59333539 0.024276648 0.61761204 0.076132037 77000 0.68243436 0.024600726 0.70703508 0.075525977 78000 0.79699751 0.024238959 0.82123647 0.078255526 79000 0.77318109 0.024249895 0.79743099 0.078223339 80000 0.72004911 0.024522473 0.74457159 0.079009398 81000 0.71732947 0.024702988 0.74203245 0.080902007 82000 0.73395391 0.024817681 0.75877159 0.081203115 83000 0.74389794 0.02487774 0.76877568 0.082273058 84000 0.73219737 0.024967311 0.75716468 0.08359401 85000 0.66523255 0.025299293 0.69053184 0.084260931 86000 0.67031201 0.02564609 0.6959581 0.085495986 87000 0.81345283 0.025297963 0.8387508 0.086292085 88000 0.85008513 0.024879647 0.87496478 0.087116741 89000 0.62893149 0.025674927 0.65460642 0.088514693 90000 0.58336052 0.026632218 0.60999274 0.089459637 91000 0.72615388 0.026181899 0.75233578 0.090289473 92000 0.76593408 0.025893082 0.79182717 0.091294308 93000 0.73475998 0.026113022 0.76087301 0.092256366 94000 0.68995562 0.026409704 0.71636532 0.093332419 95000 0.69491284 0.026726159 0.721639 0.094314615 96000 0.83274635 0.026420125 0.85916648 0.09513317 97000 0.85486073 0.025941089 0.88080181 0.096122793 98000 0.63095894 0.027021709 0.65798064 0.097348373 99000 0.60847495 0.027908563 0.63638351 0.098362493 100000 0.75867487 0.027331375 0.78600625 0.099184572 Loop time of 3.87848 on 1 procs for 100000 steps with 32 atoms Performance: 2227674.150 tau/day, 25783.266 timesteps/s, 825.065 katom-step/s 97.7% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.9048 | 2.9048 | 2.9048 | 0.0 | 74.90 Neigh | 0.0027304 | 0.0027304 | 0.0027304 | 0.0 | 0.07 Comm | 0.071653 | 0.071653 | 0.071653 | 0.0 | 1.85 Output | 0.00069287 | 0.00069287 | 0.00069287 | 0.0 | 0.02 Modify | 0.85771 | 0.85771 | 0.85771 | 0.0 | 22.11 Other | | 0.04088 | | | 1.05 Nlocal: 32 ave 32 max 32 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 32 ave 32 max 32 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 = 1379 Dangerous builds = 0 Total wall time: 0:00:03