LAMMPS (27 Nov 2018)
  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
  orthogonal box = (0 0 0) to (6 6 6)
  1 by 1 by 1 MPI processor grid
  reading atoms ...
  2 atoms
  2 bodies

replicate   $r $r $r
replicate   3 $r $r
replicate   3 3 $r
replicate   3 3 3
  orthogonal box = (0 0 0) to (18 18 18)
  1 by 1 by 1 MPI processor grid
  54 atoms
  Time spent = 0.000426769 secs

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
Neighbor list info ...
  update every 1 steps, delay 0 steps, check yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 3.9641
  ghost atom cutoff = 3.9641
  binsize = 1.98205, 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/newton
      bin: standard
Per MPI rank memory allocation (min/avg/max) = 4.953 | 4.953 | 4.953 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 51.5779 on 1 procs for 10000 steps with 54 atoms

Performance: 16751.376 tau/day, 193.882 timesteps/s
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 51.377     | 51.377     | 51.377     |   0.0 | 99.61
Neigh   | 0.0063686  | 0.0063686  | 0.0063686  |   0.0 |  0.01
Comm    | 0.072127   | 0.072127   | 0.072127   |   0.0 |  0.14
Output  | 0.0002768  | 0.0002768  | 0.0002768  |   0.0 |  0.00
Modify  | 0.10849    | 0.10849    | 0.10849    |   0.0 |  0.21
Other   |            | 0.01404    |            |       |  0.03

Nlocal:    54 ave 54 max 54 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:    96 ave 96 max 96 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:    100 ave 100 max 100 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 100
Ave neighs/atom = 1.85185
Neighbor list builds = 268
Dangerous builds = 0

Total wall time: 0:00:51
