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 change_box all boundary p f p Changing box ... variable cut_inner equal 0.5 variable k_n equal 100 variable k_na equal 2 variable c_n equal 0.1 variable c_t equal 0.1 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 0.1 ${c_t} ${mu} ${delta_ua} ${cut_inner} pair_style body/rounded/polygon 0.1 0.1 ${mu} ${delta_ua} ${cut_inner} pair_style body/rounded/polygon 0.1 0.1 0.1 ${delta_ua} ${cut_inner} pair_style body/rounded/polygon 0.1 0.1 0.1 0.5 ${cut_inner} pair_style body/rounded/polygon 0.1 0.1 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 fixedpoint 0 0 0 fix 1 all npt/body temp 0.5 $T 1.0 x 0.001 $P 1.0 fixedpoint 0 0 0 fix 1 all npt/body temp 0.5 0.5 1.0 x 0.001 $P 1.0 fixedpoint 0 0 0 fix 1 all npt/body temp 0.5 0.5 1.0 x 0.001 0.1 1.0 fixedpoint 0 0 0 fix 2 all enforce2d fix 3 all wall/body/polygon 2000 50 50 yplane 0.0 48.0 #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) = 5.378 | 5.378 | 5.379 Mbytes Step KinEng PotEng TotEng Press 0 0.484375 0.25 0.734375 0.0067274306 1000 0.51464289 0.00099012638 0.51563301 0.013444625 2000 0.55653313 0.0040982283 0.56063136 0.0034505512 3000 0.75323998 0.023578898 0.77681887 0.0036652891 4000 0.70044978 0.092406287 0.79285607 0.0089262842 5000 0.54548803 0.096501313 0.64198934 0.0051379522 6000 0.48208828 0.097798868 0.57988715 0.01529805 7000 0.68219182 0.038843949 0.72103577 0.016842202 8000 0.53792445 0.01298383 0.55090828 0.0066797984 9000 0.49980358 0.029397965 0.52920155 0.0046731992 10000 0.48705755 0.10138831 0.58844586 -1.9690665e-05 11000 0.52151879 0.065897951 0.58741674 0.0049324908 12000 0.59065198 0.03929683 0.62994881 0.0014198454 13000 0.46076897 0.073363984 0.53413295 0.0057849056 14000 0.38058168 0.16336914 0.54395082 0.0099910111 15000 0.58924494 0.13219579 0.72144074 0.012781632 16000 0.65163924 0.10979538 0.76143462 0.015088945 17000 0.51431594 0.036344433 0.55066037 0.001446035 18000 0.42677394 0.093297234 0.52007117 0.00093775852 19000 0.62399853 0.13309136 0.75708989 0.0095351169 20000 0.52835966 0.085936455 0.61429611 0.013158115 21000 0.42999051 0.12857394 0.55856445 0.024369485 22000 0.56770038 0.19738636 0.76508675 0.024211788 23000 0.55137392 0.18212359 0.7334975 0.024095463 24000 0.6225794 0.13091248 0.75349189 0.032707954 25000 0.47106345 0.10241626 0.57347971 0.0059731265 26000 0.60567231 0.055894222 0.66156653 0.010614697 27000 0.49075416 0.13914345 0.62989761 0.00048442735 28000 0.48902573 0.21423204 0.70325777 0.021295043 29000 0.42728391 0.24136135 0.66864527 0.031633766 30000 0.64658635 0.15368867 0.80027502 0.0084616839 31000 0.71370199 0.18014549 0.89384748 0.02367184 32000 0.40141173 0.1833294 0.58474113 0.034918949 33000 0.55780706 0.14130843 0.69911549 0.012266172 34000 0.36544303 0.15788143 0.52332446 0.0084938225 35000 0.56844142 0.17507842 0.74351984 0.061506713 36000 0.5048707 0.15834563 0.66321633 0.0286909 37000 0.4371274 0.087735559 0.52486296 -0.0016289252 38000 0.49941117 0.22576207 0.72517324 0.059233327 39000 0.69480051 0.15465372 0.84945423 0.039061293 40000 0.52881719 0.29110071 0.8199179 0.032439208 41000 0.56931201 0.38596881 0.95528082 0.045284803 42000 0.46759969 0.21337568 0.68097537 0.086759715 43000 0.63416318 0.44687151 1.0810347 0.072272415 44000 0.43914666 0.20832735 0.64747401 0.026280272 45000 0.38329718 0.25407815 0.63737533 0.017356403 46000 0.59511045 0.32148788 0.91659833 -0.0076184601 47000 0.50635988 0.37243112 0.878791 0.025435347 48000 0.42316224 0.29368731 0.71684954 0.00067040329 49000 0.40194259 0.26659105 0.66853364 0.069225504 50000 0.4740342 0.305674 0.77970819 0.014813566 51000 0.57279011 0.32080139 0.8935915 0.0091332017 52000 0.54543481 0.34482955 0.89026435 -0.021131696 53000 0.39241519 0.36432403 0.75673922 0.0077163816 54000 0.62021406 0.32010094 0.940315 0.044477965 55000 0.45160485 0.29442122 0.74602607 0.02563201 56000 0.41737028 0.31207675 0.72944704 0.050342936 57000 0.53454189 0.29192181 0.8264637 0.068452573 58000 0.65449932 0.33567481 0.99017413 0.055352019 59000 0.58742699 0.37317432 0.96060131 0.012805462 60000 0.42430458 0.33744246 0.76174704 0.018744436 61000 0.65433333 0.40723506 1.0615684 0.019757611 62000 0.64472397 0.34658649 0.99131047 0.090688735 63000 0.65381774 0.47452792 1.1283457 0.2090513 64000 0.44107995 0.60507044 1.0461504 0.03144844 65000 0.38159186 0.45527276 0.83686462 0.090856608 66000 0.48842595 0.49445721 0.98288316 0.08753844 67000 0.65088575 0.4611542 1.11204 0.066602605 68000 0.5155131 0.38693864 0.90245174 0.0062596909 69000 0.41477899 0.45120406 0.86598306 0.037396561 70000 0.60305022 0.47624271 1.0792929 0.040607751 71000 0.67077877 0.51044906 1.1812278 0.029084971 72000 0.50912034 0.34340114 0.85252148 0.055767674 73000 0.55167778 0.43795801 0.98963579 0.083371911 74000 0.53603549 0.37357862 0.90961411 0.058762722 75000 0.47521522 0.529749 1.0049642 0.12419171 76000 0.48952134 0.63953611 1.1290574 0.09709472 77000 0.63445283 0.57542295 1.2098758 0.11868116 78000 0.62184463 0.60025138 1.222096 0.079417229 79000 0.52715665 0.54847579 1.0756324 0.033981154 80000 0.6264593 0.39323366 1.019693 0.05627332 81000 0.78582235 0.47541992 1.2612423 0.031287815 82000 0.69665491 0.58355423 1.2802091 -0.04433392 83000 0.4994351 0.40089694 0.90033204 -0.0019687817 84000 0.50932093 0.62716285 1.1364838 0.095177695 85000 0.56251638 0.56010929 1.1226257 0.013989132 86000 0.67155822 0.51326814 1.1848264 0.10616402 87000 0.61317511 0.52704394 1.140219 0.076578899 88000 0.57436568 0.60641096 1.1807766 0.042050421 89000 0.62350614 0.65896923 1.2824754 0.15949038 90000 0.57445242 0.65085438 1.2253068 0.034123951 91000 0.50043488 0.69213026 1.1925651 -0.076403957 92000 0.57345231 0.74801993 1.3214722 0.033715387 93000 0.63056204 0.64474627 1.2753083 0.051205732 94000 0.70948937 0.61081243 1.3203018 -0.0069457836 95000 0.66048722 0.61001641 1.2705036 0.16072266 96000 0.48720026 0.64888522 1.1360855 0.12573765 97000 0.41570988 0.68810987 1.1038198 -0.033070846 98000 0.53689925 0.83787736 1.3747766 0.098173219 99000 0.5147061 0.92360546 1.4383116 0.12155736 100000 0.5793939 0.63393822 1.2133321 0.090967465 Loop time of 2.08698 on 4 procs for 100000 steps with 32 atoms Performance: 4139957.491 tau/day, 47916.175 timesteps/s, 1.533 Matom-step/s 92.1% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.31 | 0.33594 | 0.35254 | 2.8 | 16.10 Neigh | 0.001991 | 0.0021241 | 0.0022581 | 0.2 | 0.10 Comm | 0.40717 | 0.43106 | 0.46731 | 3.4 | 20.65 Output | 0.00076842 | 0.002908 | 0.0092082 | 6.7 | 0.14 Modify | 1.1389 | 1.1624 | 1.1753 | 1.3 | 55.70 Other | | 0.1525 | | | 7.31 Nlocal: 8 ave 9 max 7 min Histogram: 2 0 0 0 0 0 0 0 0 2 Nghost: 14 ave 16 max 12 min Histogram: 1 0 1 0 0 0 0 1 0 1 Neighs: 13.25 ave 17 max 11 min Histogram: 1 1 0 1 0 0 0 0 0 1 Total # of neighbors = 53 Ave neighs/atom = 1.65625 Neighbor list builds = 3000 Dangerous builds = 0 Total wall time: 0:00:02