LAMMPS (29 Jun 2018) # pouring 3d rounded polyhedron bodies variable steps index 6000 units lj boundary p p fm comm_modify vel yes atom_style body rounded/polyhedron 1 8 atom_modify map array region reg block 0 50 0 50 0 50 units box create_box 4 reg Created orthogonal box = (0 0 0) to (50 50 50) 1 by 1 by 1 MPI processor grid variable cut_inner equal 0.5 variable k_n equal 100 variable k_na equal 5 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 5 neighbor 0.5 bin neigh_modify every 1 delay 0 check yes timestep 0.001 fix 1 all nve/body fix 2 all gravity 1.0 spherical 0.0 -180.0 molecule object molecule.cube molecule.tetra toff 1 molecule.rod3d toff 2 molecule.point3d toff 3 Read molecule object: 1 atoms with max type 1 0 bonds with max type 0 0 angles with max type 0 0 dihedrals with max type 0 0 impropers with max type 0 Read molecule object: 1 atoms with max type 2 0 bonds with max type 0 0 angles with max type 0 0 dihedrals with max type 0 0 impropers with max type 0 Read molecule object: 1 atoms with max type 3 0 bonds with max type 0 0 angles with max type 0 0 dihedrals with max type 0 0 impropers with max type 0 Read molecule object: 1 atoms with max type 4 0 bonds with max type 0 0 angles with max type 0 0 dihedrals with max type 0 0 impropers with max type 0 region slab block 5 45 5 45 25 35 units box fix ins all pour 500 0 4767548 vol 0.4 10 region slab mol object molfrac 0.25 0.25 0.25 0.25 Particle insertion: 134 every 4472 steps, 500 by step 13417 fix 4 all wall/body/polyhedron 2000 50 50 zplane 0.0 NULL #compute 1 all body/local type 1 2 3 #dump 1 all local 1000 dump.polyhedron index c_1[1] c_1[2] c_1[3] c_1[4] #dump 10 all custom 1000 tmp.dump id type x y z radius thermo_style custom step atoms ke pe etotal press thermo 1000 #dump 2 all image 500 image.*.jpg type type # zoom 1.5 adiam 1.5 body type 0 0 view 75 15 #dump_modify 2 pad 6 run ${steps} run 6000 Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 5 ghost atom cutoff = 5 binsize = 2.5, bins = 20 20 20 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/newton bin: standard Per MPI rank memory allocation (min/avg/max) = 0.5065 | 0.5065 | 0.5065 Mbytes Step Atoms KinEng PotEng TotEng Press 0 0 -0 0 0 0 1000 134 -0 0.00083010524 0.00083010524 -2.1515152e-06 2000 134 -0 -0.00069962476 -0.00069962476 -1.4170663e-08 3000 134 -0 -0.00069962687 -0.00069962687 -4.1478181e-11 4000 134 -0 -0.00069962687 -0.00069962687 -1.2141026e-13 5000 268 -0 0.014969705 0.014969705 3.0797164e-05 6000 268 -0 0.042467887 0.042467887 0.00056148005 Loop time of 0.634737 on 1 procs for 6000 steps with 268 atoms Performance: 816716.196 tau/day, 9452.734 timesteps/s 100.0% CPU use with 1 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.41391 | 0.41391 | 0.41391 | 0.0 | 65.21 Neigh | 0.010547 | 0.010547 | 0.010547 | 0.0 | 1.66 Comm | 0.0030921 | 0.0030921 | 0.0030921 | 0.0 | 0.49 Output | 0.00011492 | 0.00011492 | 0.00011492 | 0.0 | 0.02 Modify | 0.19736 | 0.19736 | 0.19736 | 0.0 | 31.09 Other | | 0.009719 | | | 1.53 Nlocal: 268 ave 268 max 268 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3 ave 3 max 3 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 68 ave 68 max 68 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 68 Ave neighs/atom = 0.253731 Neighbor list builds = 168 Dangerous builds = 0 Total wall time: 0:00:00