LAMMPS (28 Mar 2023 - Development)
  using 1 OpenMP thread(s) per MPI task
# 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 2 by 2 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 template object:
  1 molecules
  0 fragments
  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 template object:
  1 molecules
  0 fragments
  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 template object:
  1 molecules
  0 fragments
  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 template object:
  1 molecules
  0 fragments
  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
Generated 0 of 6 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 = 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
      bin: standard
Per MPI rank memory allocation (min/avg/max) = 0.4666 | 0.4666 | 0.4666 Mbytes
   Step        Atoms        KinEng         PotEng         TotEng         Press     
         0           0  -0              0              0              0            
      1000         134  -0              0.0038737172   0.0038737172  -3.395325e-06 
      2000         134  -0             -0.0009235483  -0.0009235483  -6.5977025e-07
      3000         134  -0              0.004338364    0.004338364   -1.4565607e-05
      4000         134  -0              0.0028464278   0.0028464278  -7.6723299e-06
      5000         268  -0              0.017425002    0.017425002    0.000175191  
      6000         268  -0              0.035730061    0.035730061    0.00019697961
Loop time of 0.266391 on 4 procs for 6000 steps with 268 atoms

Performance: 1946012.521 tau/day, 22523.293 timesteps/s, 6.036 Matom-step/s
92.6% CPU use with 4 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 0.024599   | 0.072944   | 0.14627    |  18.6 | 27.38
Neigh   | 0.0011942  | 0.0013474  | 0.0014323  |   0.3 |  0.51
Comm    | 0.047438   | 0.11992    | 0.17106    |  14.8 | 45.02
Output  | 7.6297e-05 | 0.00017637 | 0.00044875 |   0.0 |  0.07
Modify  | 0.029377   | 0.035972   | 0.040396   |   2.4 | 13.50
Other   |            | 0.03603    |            |       | 13.52

Nlocal:             67 ave          89 max          43 min
Histogram: 1 1 0 0 0 0 0 0 1 1
Nghost:             38 ave          53 max          25 min
Histogram: 1 1 0 0 0 0 0 1 0 1
Neighs:          23.75 ave          42 max           7 min
Histogram: 1 0 1 0 0 0 0 1 0 1

Total # of neighbors = 95
Ave neighs/atom = 0.35447761
Neighbor list builds = 167
Dangerous builds = 0


Total wall time: 0:00:00
