LAMMPS (28 Mar 2023 - Development) using 1 OpenMP thread(s) per MPI task # 3d rounded cubes variable r index 3 variable steps index 10000 units lj dimension 3 atom_style body rounded/polyhedron 1 10 read_data data.cubes Reading data file ... orthogonal box = (0 0 0) to (6 6 6) 1 by 2 by 2 MPI processor grid reading atoms ... 2 atoms 2 bodies read_data CPU = 0.001 seconds replicate $r $r $r replicate 3 $r $r replicate 3 3 $r replicate 3 3 3 Replication is creating a 3x3x3 = 27 times larger system... orthogonal box = (0 0 0) to (18 18 18) 1 by 2 by 2 MPI processor grid 54 atoms replicate CPU = 0.001 seconds velocity all create 1.2 187287 dist gaussian mom yes rot yes variable cut_inner equal 0.5 variable k_n equal 100 variable k_na equal 1 variable c_n equal 20 variable c_t equal 5 variable mu equal 0 variable A_ua equal 1 pair_style body/rounded/polyhedron ${c_n} ${c_t} ${mu} ${A_ua} ${cut_inner} pair_style body/rounded/polyhedron 20 ${c_t} ${mu} ${A_ua} ${cut_inner} pair_style body/rounded/polyhedron 20 5 ${mu} ${A_ua} ${cut_inner} pair_style body/rounded/polyhedron 20 5 0 ${A_ua} ${cut_inner} pair_style body/rounded/polyhedron 20 5 0 1 ${cut_inner} pair_style body/rounded/polyhedron 20 5 0 1 0.5 pair_coeff * * ${k_n} ${k_na} pair_coeff * * 100 ${k_na} pair_coeff * * 100 1 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 1.2 1.2 0.1 #fix 1 all npt/body temp 1.2 1.2 0.1 iso 0.002 0.02 1.0 compute p2 all pressure 1_temp #compute 1 all body/local id 1 2 3 #dump 1 all local 1000 dump.* index c_1[1] c_1[2] c_1[3] c_1[4] #dump 2 all image 1000 image.*.jpg type type # zoom 1.5 adiam 1.5 body type 0 0 view 60 15 #dump_modify 2 pad 6 thermo_style custom step ke pe etotal c_p2 c_1_temp thermo 1000 run ${steps} run 10000 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 = 3.9641016 ghost atom cutoff = 3.9641016 binsize = 1.9820508, bins = 10 10 10 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair body/rounded/polyhedron, perpetual attributes: half, newton on pair build: half/bin/atomonly/newton stencil: half/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 5.901 | 5.902 | 5.904 Mbytes Step KinEng PotEng TotEng c_p2 c_1_temp 0 1.7666667 0 1.7666667 0.01090535 0.59439252 1000 3.1462962 0.17392649 3.3202227 0.02361912 1.1654694 2000 2.9311648 0.13836102 3.0695258 0.021748224 1.1950624 3000 3.090491 0.16511199 3.255603 0.018691142 1.23672 4000 2.7401565 0.17792155 2.9180781 0.015093853 1.1180839 5000 3.0880849 0.17587085 3.2639557 0.030563042 1.2831154 6000 3.2180776 0.19732251 3.4154001 0.028338151 1.258839 7000 2.9514882 0.25088882 3.202377 0.025296925 1.1746326 8000 3.0101226 0.28825968 3.2983823 0.027273454 1.2138056 9000 3.0164253 0.1901733 3.2065986 0.033228915 1.3095914 10000 2.3780401 0.34082434 2.7188644 0.031838531 1.0208679 Loop time of 16.4904 on 4 procs for 10000 steps with 54 atoms Performance: 52394.037 tau/day, 606.412 timesteps/s, 32.746 katom-step/s 95.4% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.8583 | 8.5985 | 15.966 | 145.2 | 52.14 Neigh | 0.00098311 | 0.0011219 | 0.0014163 | 0.5 | 0.01 Comm | 0.39088 | 7.7607 | 10.504 | 152.9 | 47.06 Output | 0.00016175 | 0.00044056 | 0.0012766 | 0.0 | 0.00 Modify | 0.084729 | 0.094756 | 0.10558 | 2.8 | 0.57 Other | | 0.0349 | | | 0.21 Nlocal: 13.5 ave 17 max 9 min Histogram: 1 0 0 1 0 0 0 0 1 1 Nghost: 63.5 ave 68 max 58 min Histogram: 1 0 0 1 0 0 0 0 0 2 Neighs: 25 ave 38 max 6 min Histogram: 1 0 0 0 0 1 0 0 1 1 Total # of neighbors = 100 Ave neighs/atom = 1.8518519 Neighbor list builds = 268 Dangerous builds = 0 Total wall time: 0:00:16