LAMMPS (8 Feb 2023)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
  using 1 OpenMP thread(s) per MPI task
# Pour 2d granular particles into container

dimension	2
atom_style	sphere
atom_modify     map array
boundary	f fm p
newton		off
comm_modify	vel yes cutoff 2.5

fix             prop all property/atom mol ghost yes

region		reg block 0 100 0 50 -0.5 0.5 units box
create_box	1 reg
Created orthogonal box = (0 0 -0.5) to (100 50 0.5)
  1 by 1 by 1 MPI processor grid

neighbor	0.2 bin
neigh_modify	delay 0

# IMPORTANT NOTE: these values of stiffness (4000) and timestep (0.001)
# are used in this example file to produce a quick simulation and movie.
# More appropriate values for realistic simulations would be
# k = 4.0e5 and dt = 0.0001, as in bench/in.chute (if it were Hertzian).

pair_style      gran/hertz/history 4000.0 NULL 100.0 NULL 0.5 0
pair_coeff	* *

timestep	0.001

fix		2 all gravity 1.0 spherical 0.0 -180.0
fix		xwalls all wall/gran hertz/history 4000.0 NULL 100.0 NULL 0 1 		xplane 0 100
fix		ywalls all wall/gran hertz/history 4000.0 NULL 100.0 NULL 0 1 		yplane 0 NULL

molecule        object molecule.vshape
Read molecule template object:
  1 molecules
  0 fragments
  5 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
fix             3 all rigid/small molecule mol object
  create bodies CPU = 0.000 seconds
  0 rigid bodies with 0 atoms
  2.236068 = max distance from body owner to body atom

# ensure region size + molecule size does not overlap wall

region          slab block 3.0 97.0 30 34.5 -0.5 0.5 units box
fix             ins all pour 500 0 4767548 vol 0.8 10 	        region slab mol object rigid 3
Particle insertion: 26 every 3000 steps, 500 by step 57001

fix             4 all enforce2d

compute		1 all erotate/sphere
compute         Tsphere all temp/sphere
thermo_style	custom step atoms ke c_1 vol
thermo_modify	lost ignore norm no temp Tsphere
compute_modify	Tsphere dynamic/dof yes

thermo		1000

#dump		id all atom 100 tmp.dump

#variable        colors string #                "red green blue yellow white #                purple pink orange lime gray"
#variable	mol2 atom mol%10
#dump		2 all image 250 image.*.jpg v_mol2 type #		zoom 1.6 adiam 1.5
#dump_modify	2 pad 5 amap 0 10 sa 1 10 ${colors}

#variable        colors string #                "red green blue yellow white #                purple pink orange lime gray"
#variable	mol3 atom mol%10
#dump		3 all movie 250 movie.mpg v_mol3 type #		zoom 1.6 adiam 1.5
#dump_modify	3 pad 5 amap 0 10 sa 1 10 ${colors}

run	        25000
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
WARNING: Gravity may not be correctly applied to rigid bodies if they consist of overlapped particles (src/RIGID/fix_rigid_small.cpp:554)
Neighbor list info ...
  update: every = 1 steps, delay = 0 steps, check = yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 1.2
  ghost atom cutoff = 2.5
  binsize = 0.6, bins = 167 84 2
  1 neighbor lists, perpetual/occasional/extra = 1 0 0
  (1) pair gran/hertz/history, perpetual
      attributes: half, newton off, size, history
      pair build: half/size/bin/newtoff
      stencil: full/bin/2d
      bin: standard
Per MPI rank memory allocation (min/avg/max) = 5.811 | 5.811 | 5.811 Mbytes
   Step        Atoms        KinEng          c_1           Volume    
         0           0  -0              0              5000         
      1000         130   248.65568      0.002050506    5000         
      2000         130   452.01354      0.0020557556   5000         
      3000         130   720.36849      0.0021462148   5000         
      4000         260   1281.7126      0.0021462148   5000         
      5000         260   1875.9602      0.0021462148   5000         
      6000         260   1742.7747      2.0692779      5000         
      7000         390   1860.2142      1.7515066      5000         
      8000         390   1853.6219      2.3354959      5000         
      9000         390   1749.6466      5.1516327      5000         
     10000         520   1860.4314      4.2186838      5000         
     11000         520   1636.9411      4.006706       5000         
     12000         520   1454.1835      4.3341069      5000         
     13000         650   1881.6358      3.9606372      5000         
     14000         650   1648.6494      3.8239413      5000         
     15000         650   1463.0973      2.9363979      5000         
     16000         780   1571.0119      3.9061213      5000         
     17000         780   1472.941       2.0289533      5000         
     18000         780   1370.5265      3.1038747      5000         
     19000         910   1433.6728      2.7600498      5000         
     20000         910   1375.3634      2.964893       5000         
     21000         910   1184.8059      2.5050961      5000         
     22000        1040   1312.0948      1.844008       5000         
     23000        1040   1181.4208      1.7766375      5000         
     24000        1040   1263.1226      2.1430511      5000         
     25000        1170   1152.9064      2.4175531      5000         
Loop time of 3.37143 on 1 procs for 25000 steps with 1170 atoms

Performance: 640677.536 tau/day, 7415.249 timesteps/s, 8.676 Matom-step/s
99.4% CPU use with 1 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 0.91106    | 0.91106    | 0.91106    |   0.0 | 27.02
Neigh   | 0.19015    | 0.19015    | 0.19015    |   0.0 |  5.64
Comm    | 0.016916   | 0.016916   | 0.016916   |   0.0 |  0.50
Output  | 0.0011065  | 0.0011065  | 0.0011065  |   0.0 |  0.03
Modify  | 2.1372     | 2.1372     | 2.1372     |   0.0 | 63.39
Other   |            | 0.115      |            |       |  3.41

Nlocal:           1170 ave        1170 max        1170 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:              0 ave           0 max           0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:           1685 ave        1685 max        1685 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 1685
Ave neighs/atom = 1.4401709
Neighbor list builds = 1707
Dangerous builds = 0
Total wall time: 0:00:03
