1. In.

friction_P1
# 2d friction simulation

dimension 2

boundary psp

atom_style atomic

neighbor 0.3 bin

neigh_modify delay 5

# create geometry

lattice hex 0.9

region box block 0 100 0 22 -0.25 0.25

create_box 4 box

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

create_atoms 1 region hi-slab

create_atoms 2 region lo-half-sphere

create_atoms 3 region hi-half-sphere

# LJ potentials

pair_style lj/cut 2.5

pair_coeff * * 1.0 1.0 2.5

# define groups

group lo region lo-slab

group lo type 2

group hi region hi-slab

group hi type 3

group lo-fixed region lo-fixed

group hi-fixed region hi-fixed

group boundary union lo-fixed hi-fixed

group mobile subtract all boundary

set group lo-fixed type 4

set group hi-fixed type 4

# 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

dump 1 all atom 500 dump.friction_P1

#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 30000

2. In.friction_P2
# 2d friction simulation

dimension 2

boundary psp

atom_style atomic

neighbor 0.3 bin

neigh_modify delay 5

# create geometry

lattice hex 0.9

region box block 0 200 0 22 -0.25 0.25

create_box 4 box

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 30 7 0 8

region lo-asperity2 sphere 120 7 0 8

region hi-asperity sphere 60 15 0 8

region hi-asperity2 sphere 160 15 0 8

region hi-half-sphere2 intersect 2 below-hi hi-asperity2

region lo-half-sphere intersect 2 lo-asperity above-lo

region lo-half-sphere2 intersect 2 lo-asperity2 above-lo

region hi-half-sphere intersect 2 hi-asperity below-hi

# create 2 surfaces with asperities

create_atoms 1 region lo-slab

create_atoms 1 region hi-slab

create_atoms 3 region hi-half-sphere2

create_atoms 2 region lo-half-sphere

create_atoms 2 region lo-half-sphere2

create_atoms 3 region hi-half-sphere

# LJ potentials

pair_style lj/cut 2.5

pair_coeff * * 1.0 1.0 2.5

# define groups

group lo region lo-slab

group lo type 2

group hi region hi-slab

group hi type 3

group lo-fixed region lo-fixed

group hi-fixed region hi-fixed

group boundary union lo-fixed hi-fixed

group mobile subtract all boundary

set group lo-fixed type 4

set group hi-fixed type 4

# 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

dump 1 all atom 500 dump.friction_P2

#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 100000

Snapshot of simulation for P2

 3. Log.in.friction_P2

#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

Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule

Neighbor list info ...

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 = 162 31 1

 1 neighbor lists, perpetual/occasional/extra = 1 0 0

(1) pair lj/cut, perpetual

attributes: half, newton on

pair build: half/bin/atomonly/newton

stencil: half/bin/2d

bin: standard

Per MPI rank memory allocation (min/avg/max) = 3.111 | 3.111 | 3.111 Mbytes

Step Temp E_pair E_mol TotEng Press Volume

0 0.1 -3.1305352 0 -3.0898482 -1.0680329 9779.7333

1000 0.1 -3.0895772 0 -3.0488902 0.066193511 9779.7333

2000 0.1 -3.0784919 0 -3.0378049 -0.58892101 9779.7333

3000 0.085125174 -3.0760412 0 -3.0414063 -0.21270751 9779.7333

4000 0.087302026 -3.0770452 0 -3.0415246 -0.52154352 9779.7333

5000 0.092660384 -3.0811622 0 -3.0434615 -0.088853689 9779.7333

6000 0.087204993 -3.0769307 0 -3.0414496 -0.5466044 9779.7333

7000 0.1027515 -3.0763231 0 -3.0345166 -0.35360692 9779.7333

8000 0.10263526 -3.0773115 0 -3.0355522 -0.21404319 9779.7333

9000 0.096910479 -3.0737901 0 -3.0343601 -0.46128572 9779.7333

10000 0.095307671 -3.0738845 0 -3.0351066 -0.2770988 9779.7333

11000 0.088429556 -3.0711267 0 -3.0351474 -0.43429333 9779.7333

12000 0.096347782 -3.0761677 0 -3.0369667 -0.11289558 9779.7333

13000 0.083551466 -3.0678001 0 -3.0338055 -0.62454967 9779.7333

14000 0.092134215 -3.0749774 0 -3.0374907 -0.053882095 9779.7333

15000 0.085941584 -3.0700847 0 -3.0351176 -0.50583355 9779.7333

16000 0.086804306 -3.0736304 0 -3.0383123 -0.18394745 9779.7333

17000 0.089006799 -3.0705946 0 -3.0343803 -0.50198219 9779.7333

18000 0.09329154 -3.0739154 0 -3.0359579 -0.15906299 9779.7333

19000 0.095003168 -3.0738777 0 -3.0352237 -0.44214125 9779.7333

20000 0.099089203 -3.0759052 0 -3.0355888 -0.3622748 9779.7333

Loop time of 17.7807 on 1 procs for 20000 steps with 6448 atoms

Performance: 242959.886 tau/day, 1124.814 timesteps/s, 7.253 Matom-step/s

72.7% CPU use with 1 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:

Section | min time | avg time | max time |%varavg| %total

---------------------------------------------------------------

Pair | 13.709 | 13.709 | 13.709 | 0.0 | 77.10

Neigh | 0.7772 | 0.7772 | 0.7772 | 0.0 | 4.37

Comm | 0.070999 | 0.070999 | 0.070999 | 0.0 | 0.40

Output | 0.58592 | 0.58592 | 0.58592 | 0.0 | 3.30

Modify | 2.0092 | 2.0092 | 2.0092 | 0.0 | 11.30

Other | | 0.6281 | | | 3.53

Nlocal: 6448 ave 6448 max 6448 min

Histogram: 1 0 0 0 0 0 0 0 0 0

Nghost: 145 ave 145 max 145 min

Histogram: 1 0 0 0 0 0 0 0 0 0

Neighs: 53854 ave 53854 max 53854 min

Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 53854

Ave neighs/atom = 8.3520471

Neighbor list builds = 698

Dangerous builds = 0

Total wall time: 0:00:17

Log.lammps_P3_a(for the same source code as P2 but different

frequency output)
#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

Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule

Neighbor list info ...

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 = 162 31 1

1 neighbor lists, perpetual/occasional/extra = 1 0 0

(1) pair lj/cut, perpetual

attributes: half, newton on

pair build: half/bin/atomonly/newton

stencil: half/bin/2d

bin: standard

Per MPI rank memory allocation (min/avg/max) = 3.111 | 3.111 | 3.111 Mbytes

Step Temp E_pair E_mol TotEng Press Volume

0 0.1 -3.1305352 0 -3.0898482 -1.0680329 9779.7333

1000 0.1 -3.0895772 0 -3.0488902 0.066193511 9779.7333

2000 0.1 -3.0784919 0 -3.0378049 -0.58892101 9779.7333

3000 0.085125174 -3.0760412 0 -3.0414063 -0.21270751 9779.7333

4000 0.087302026 -3.0770452 0 -3.0415246 -0.52154352 9779.7333

5000 0.092660384 -3.0811622 0 -3.0434615 -0.088853689 9779.7333

6000 0.087204993 -3.0769307 0 -3.0414496 -0.5466044 9779.7333

 7000 0.1027515 -3.0763231 0 -3.0345166 -0.35360692 9779.7333

8000 0.10263526 -3.0773115 0 -3.0355522 -0.21404319 9779.7333

9000 0.096910479 -3.0737901 0 -3.0343601 -0.46128572 9779.7333

10000 0.095307671 -3.0738845 0 -3.0351066 -0.2770988 9779.7333

11000 0.088429556 -3.0711267 0 -3.0351474 -0.43429333 9779.7333

12000 0.096347782 -3.0761677 0 -3.0369667 -0.11289558 9779.7333

13000 0.083551466 -3.0678001 0 -3.0338055 -0.62454967 9779.7333

14000 0.092134215 -3.0749774 0 -3.0374907 -0.053882095 9779.7333

15000 0.085941584 -3.0700847 0 -3.0351176 -0.50583355 9779.7333

16000 0.086804306 -3.0736304 0 -3.0383123 -0.18394745 9779.7333

17000 0.089006799 -3.0705946 0 -3.0343803 -0.50198219 9779.7333

18000 0.09329154 -3.0739154 0 -3.0359579 -0.15906299 9779.7333

19000 0.095003168 -3.0738777 0 -3.0352237 -0.44214125 9779.7333

20000 0.099089203 -3.0759052 0 -3.0355888 -0.3622748 9779.7333

Loop time of 24.2068 on 1 procs for 20000 steps with 6448 atoms

Performance: 178462.059 tau/day, 826.213 timesteps/s, 5.327 Matom-step/s

58.9% CPU use with 1 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:

Section | min time | avg time | max time |%varavg| %total

---------------------------------------------------------------

Pair | 15.141 | 15.141 | 15.141 | 0.0 | 62.55

Neigh | 0.8352 | 0.8352 | 0.8352 | 0.0 | 3.45

Comm | 0.080786 | 0.080786 | 0.080786 | 0.0 | 0.33

Output | 5.3147 | 5.3147 | 5.3147 | 0.0 | 21.96

Modify | 2.1698 | 2.1698 | 2.1698 | 0.0 | 8.96

Other | | 0.6654 | | | 2.75

Nlocal: 6448 ave 6448 max 6448 min

Histogram: 1 0 0 0 0 0 0 0 0 0

Nghost: 145 ave 145 max 145 min

Histogram: 1 0 0 0 0 0 0 0 0 0

Neighs: 53854 ave 53854 max 53854 min

Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 53854

Ave neighs/atom = 8.3520471

Neighbor list builds = 698

Dangerous builds = 0

Total wall time: 0:00:24