Newer
Older
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
# 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
Total # of neighbors = 14364
Ave neighs/atom = 8.33179
Neighbor list builds = 714