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)
  1 by 1 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 = 2.47434 Mbytes
Step Temp E_pair E_mol TotEng Press Volume 
       0          0.1   -3.1333672            0   -3.0920969   -1.1437663    2444.9333 
    1000          0.1   -3.0915072            0   -3.0502369 0.0099866805    2444.9333 
    2000          0.1   -3.0826007            0   -3.0413304  -0.41998885    2444.9333 
    3000   0.08982505   -3.0757908            0   -3.0387197  -0.25244271    2444.9333 
    4000  0.098727892   -3.0666371            0   -3.0258918  -0.25382683    2444.9333 
    5000   0.11345478   -3.0506905            0   -3.0038674 -0.029177812    2444.9333 
    6000   0.11386723   -3.0515296            0   -3.0045363  -0.32135016    2444.9333 
    7000   0.11555642   -3.0379879            0   -2.9902974  -0.40431666    2444.9333 
    8000   0.10658282   -3.0364048            0   -2.9924178  -0.45722834    2444.9333 
    9000   0.11650947   -3.0271611            0   -2.9790773   -0.4588819    2444.9333 
   10000   0.10575546   -3.0298463            0   -2.9862007  -0.35241095    2444.9333 
   11000   0.10953331   -3.0352955            0   -2.9900908   -0.4622173    2444.9333 
   12000   0.11720787   -3.0378371            0    -2.989465  -0.27733023    2444.9333 
   13000   0.11492573    -3.037974            0   -2.9905438  -0.43259084    2444.9333 
   14000   0.11125454   -3.0413758            0   -2.9954607  -0.31244429    2444.9333 
   15000   0.10882772   -3.0406062            0   -2.9956927  -0.30403665    2444.9333 
   16000    0.1152685   -3.0433936            0   -2.9958219  -0.26659294    2444.9333 
   17000   0.10840025   -3.0414208            0   -2.9966837  -0.36183887    2444.9333 
   18000   0.11159326   -3.0416392            0   -2.9955843  -0.22725121    2444.9333 
   19000   0.11530974   -3.0457005            0   -2.9981118  -0.36488457    2444.9333 
   20000    0.1131733   -3.0417814            0   -2.9950744  -0.27902539    2444.9333 
Loop time of 5.78572 on 1 procs for 20000 steps with 1724 atoms

Performance: 746665.546 tau/day, 3456.785 timesteps/s
99.9% CPU use with 1 MPI tasks x no OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 4.7167     | 4.7167     | 4.7167     |   0.0 | 81.52
Neigh   | 0.30734    | 0.30734    | 0.30734    |   0.0 |  5.31
Comm    | 0.036082   | 0.036082   | 0.036082   |   0.0 |  0.62
Output  | 0.00039339 | 0.00039339 | 0.00039339 |   0.0 |  0.01
Modify  | 0.57194    | 0.57194    | 0.57194    |   0.0 |  9.89
Other   |            | 0.1533     |            |       |  2.65

Nlocal:    1724 ave 1724 max 1724 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:    144 ave 144 max 144 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:    14364 ave 14364 max 14364 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 14364
Ave neighs/atom = 8.33179
Neighbor list builds = 714
Dangerous builds = 0
Total wall time: 0:00:05
