LAMMPS (5 Oct 2016)
# 2d friction simulation

dimension	2
boundary	p s p

atom_style	atomic
neighbor	0.3 bin
neigh_modify	delay 5

# create geometry

lattice		hex 0.9
Lattice spacing in x,y,z = 1.1327 1.96189 1.1327
region		box block 0 50 0 22 -0.25 0.25
create_box	4 box
Created orthogonal box = (0 0 -0.283174) to (56.6348 43.1615 0.283174)
  2 by 2 by 1 MPI processor grid

mass		1 1.0
mass		2 1.0
mass		3 1.0
mass		4 1.0

# atom regions

region          lo-fixed block INF INF INF 1.1 INF INF
region          lo-slab block INF INF INF 7 INF INF
region          above-lo block INF INF INF 7 INF INF side out
region          hi-fixed block INF INF 20.9 INF INF INF
region          hi-slab block INF INF 15 INF INF INF
region          below-hi block INF INF 15 INF INF INF side out
region		lo-asperity sphere 32 7 0 8
region		hi-asperity sphere 18 15 0 8
region		lo-half-sphere intersect 2 lo-asperity above-lo
region		hi-half-sphere intersect 2 hi-asperity below-hi

# create 2 surfaces with asperities

create_atoms	1 region lo-slab
Created 750 atoms
create_atoms	1 region hi-slab
Created 750 atoms
create_atoms	2 region lo-half-sphere
Created 112 atoms
create_atoms	3 region hi-half-sphere
Created 112 atoms

# LJ potentials

pair_style	lj/cut 2.5
pair_coeff	* * 1.0 1.0 2.5

# define groups

group	        lo region lo-slab
750 atoms in group lo
group		lo type 2
862 atoms in group lo
group		hi region hi-slab
750 atoms in group hi
group		hi type 3
862 atoms in group hi
group		lo-fixed region lo-fixed
150 atoms in group lo-fixed
group		hi-fixed region hi-fixed
150 atoms in group hi-fixed
group		boundary union lo-fixed hi-fixed
300 atoms in group boundary
group		mobile subtract all boundary
1424 atoms in group mobile

set		group lo-fixed type 4
  150 settings made for type
set		group hi-fixed type 4
  150 settings made for type

# initial velocities

compute         new mobile temp/partial 0 1 0
velocity	mobile create 0.1 482748 temp new
velocity	hi set 1.0 0.0 0.0 sum yes

# fixes

fix		1 all nve
fix		2 boundary setforce 0.0 0.0 0.0
fix		3 mobile temp/rescale 200 0.1 0.1 0.02 1.0
fix_modify	3 temp new
fix             4 all enforce2d

# Run

timestep	0.0025
thermo		1000
thermo_modify	temp new
WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:474)

#dump		1 all atom 500 dump.friction

#dump		2 all image 500 image.*.jpg type type #		zoom 1.6 adiam 1.5
#dump_modify	2 pad 5

#dump		3 all movie 500 movie.mpg type type #		zoom 1.6 adiam 1.5
#dump_modify	3 pad 5

run		20000
Neighbor list info ...
  1 neighbor list requests
  update every 1 steps, delay 5 steps, check yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 2.8
  ghost atom cutoff = 2.8
  binsize = 1.4 -> bins = 41 31 1
Memory usage per processor = 2.47775 Mbytes
Step Temp E_pair E_mol TotEng Press Volume 
       0          0.1   -3.1333672            0   -3.0920969   -1.1437663    2444.9333 
    1000  0.081947197   -3.0926906            0   -3.0588707 -0.021905504    2444.9333 
    2000  0.082643627   -3.0850391            0   -3.0509318  -0.44951926    2444.9333 
    3000   0.09228068   -3.0747307            0   -3.0366461  -0.25332113    2444.9333 
    4000  0.096009906   -3.0564001            0   -3.0167765 -0.026756079    2444.9333 
    5000   0.11991393   -3.0463606            0   -2.9968718 -0.095571711    2444.9333 
    6000   0.11344201   -3.0428779            0   -2.9960601  -0.28750906    2444.9333 
    7000   0.11932053   -3.0297394            0   -2.9804955  -0.44411602    2444.9333 
    8000   0.11472412   -3.0260173            0   -2.9786703  -0.45505281    2444.9333 
    9000    0.1153823   -3.0172996            0    -2.969681  -0.54699367    2444.9333 
   10000    0.1110096   -3.0180324            0   -2.9722184  -0.28712224    2444.9333 
   11000   0.10553488   -3.0281386            0    -2.984584  -0.40414683    2444.9333 
   12000   0.10913279   -3.0339553            0   -2.9889159  -0.23876138    2444.9333 
   13000   0.10791089    -3.036479            0   -2.9919439   -0.4066437    2444.9333 
   14000   0.11089726   -3.0434547            0   -2.9976871  -0.25931118    2444.9333 
   15000   0.10791244   -3.0452052            0   -3.0006694  -0.31309363    2444.9333 
   16000   0.11451836   -3.0490643            0   -3.0018023  -0.28317436    2444.9333 
   17000   0.10861713    -3.044417            0   -2.9995904  -0.39120148    2444.9333 
   18000   0.11086121   -3.0462098            0   -3.0004571  -0.19272619    2444.9333 
   19000   0.11407977    -3.046791            0     -2.99971  -0.29824356    2444.9333 
   20000   0.11532037   -3.0463959            0   -2.9988028   -0.3435294    2444.9333 
Loop time of 1.90668 on 4 procs for 20000 steps with 1724 atoms

Performance: 2265719.994 tau/day, 10489.444 timesteps/s
99.4% CPU use with 4 MPI tasks x no OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 1.0349     | 1.1944     | 1.3574     |  10.5 | 62.64
Neigh   | 0.070767   | 0.082252   | 0.094675   |   3.0 |  4.31
Comm    | 0.19432    | 0.3776     | 0.54764    |  20.4 | 19.80
Output  | 0.00043559 | 0.00045842 | 0.00052333 |   0.2 |  0.02
Modify  | 0.12252    | 0.14002    | 0.15438    |   3.1 |  7.34
Other   |            | 0.112      |            |       |  5.87

Nlocal:    431 ave 479 max 377 min
Histogram: 1 1 0 0 0 0 0 0 0 2
Nghost:    99.25 ave 120 max 81 min
Histogram: 1 1 0 0 0 0 1 0 0 1
Neighs:    3597 ave 4064 max 3146 min
Histogram: 2 0 0 0 0 0 0 0 0 2

Total # of neighbors = 14388
Ave neighs/atom = 8.34571
Neighbor list builds = 717
Dangerous builds = 0
Total wall time: 0:00:01
