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add input examples for custom rigid body definition

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This commit is contained in:
Axel Kohlmeyer
2017-10-20 13:54:45 -04:00
parent f12031f84d
commit ac6434e496
5 changed files with 519 additions and 0 deletions
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3 1
4 1
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6 1
7 1
8 1
9 1
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# LAMMPS data file for rigid bodies
81 atoms
1 atom types
-12 12 xlo xhi
-12 12 ylo yhi
-12 12 zlo zhi
Masses
1 1
Pair Coeffs
1 1 1
Atoms
1 1 0 0 0
2 1 0 1 0
3 1 0 0.5 0
4 1 0.5 0 0
5 1 0.5 0.5 1
6 1 1 0.5 0
7 1 0.5 1 0
8 1 1 0 0
9 1 1 1 0
10 1 2 1 0
11 1 1 2 0
12 1 1.5 2 0
13 1 1.5 1 0
14 1 1 1.5 0
15 1 1.5 1.5 1
16 1 2 1.5 0
17 1 2 2 0
18 1 2 3 0
19 1 2 2.5 0
20 1 2.5 2 0
21 1 2.5 2.5 1
22 1 3 2.5 0
23 1 2.5 3 0
24 1 3 2 0
25 1 3 3 0
26 1 4 3 0
27 1 3 4 0
28 1 3.5 4 0
29 1 3.5 3 0
30 1 3 3.5 0
31 1 3.5 3.5 1
32 1 4 3.5 0
33 1 4 4 0
34 1 4 5 0
35 1 4 4.5 0
36 1 4.5 4 0
37 1 4.5 4.5 1
38 1 5 4.5 0
39 1 4.5 5 0
40 1 5 4 0
41 1 5 5 0
42 1 6 5 0
43 1 5 6 0
44 1 5.5 6 0
45 1 5.5 5 0
46 1 5 5.5 0
47 1 5.5 5.5 1
48 1 6 5.5 0
49 1 6 6 0
50 1 6 7 0
51 1 6 6.5 0
52 1 6.5 6 0
53 1 6.5 6.5 1
54 1 7 6.5 0
55 1 6.5 7 0
56 1 7 6 0
57 1 7 7 0
58 1 8 7 0
59 1 7 8 0
60 1 7.5 8 0
61 1 7.5 7 0
62 1 7 7.5 0
63 1 7.5 7.5 1
64 1 8 7.5 0
65 1 8 8 0
66 1 8 9 0
67 1 8 8.5 0
68 1 8.5 8 0
69 1 8.5 8.5 1
70 1 9 8.5 0
71 1 8.5 9 0
72 1 9 8 0
73 1 9 9 0
74 1 10 9 0
75 1 9 10 0
76 1 9.5 10 0
77 1 9.5 9 0
78 1 9 9.5 0
79 1 9.5 9.5 1
80 1 10 9.5 0
81 1 10 10 0
Bodies
1 1
2 1
3 1
4 1
5 1
6 1
7 1
8 1
9 1
10 2
11 2
12 2
13 2
14 2
15 2
16 2
17 2
18 2
19 3
20 3
21 3
22 3
23 3
24 3
25 3
26 3
27 3
28 4
29 4
30 4
31 4
32 4
33 4
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69 8
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71 8
72 8
73 9
74 9
75 9
76 9
77 9
78 9
79 9
80 9
81 9

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# Simple rigid body system
units lj
atom_style atomic
atom_modify map array
pair_style lj/cut 2.5
read_data data.rigid
velocity all create 100.0 4928459
# unconnected bodies
group clump1 id <> 1 9
group clump2 id <> 10 18
group clump3 id <> 19 27
group clump4 id <> 28 36
group clump5 id <> 37 45
group clump6 id <> 46 54
group clump7 id <> 55 63
group clump8 id <> 64 72
group clump9 id <> 73 81
variable bodies atomfile bodies.txt
fix 1 all rigid custom v_bodies
# 1 chain of connected bodies
#group clump1 id <> 1 9
#group clump2 id <> 9 18
#group clump3 id <> 18 27
#group clump4 id <> 27 36
#group clump5 id <> 36 45
#group clump6 id <> 45 54
#group clump7 id <> 54 63
#group clump8 id <> 63 72
#group clump9 id <> 72 81
#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 &
# clump6 clump7 clump8 clump9
# 2 chains of connected bodies
#group clump1 id <> 1 9
#group clump2 id <> 9 18
#group clump3 id <> 18 27
#group clump4 id <> 27 36
#group clump5 id <> 37 45
#group clump6 id <> 45 54
#group clump7 id <> 54 63
#group clump8 id <> 63 72
#group clump9 id <> 72 81
#fix 1 all poems group clump1 clump2 clump3 clump4
#fix 2 all poems group clump5 clump6 clump7 clump8 clump9
neigh_modify exclude group clump1 clump1
neigh_modify exclude group clump2 clump2
neigh_modify exclude group clump3 clump3
neigh_modify exclude group clump4 clump4
neigh_modify exclude group clump5 clump5
neigh_modify exclude group clump6 clump6
neigh_modify exclude group clump7 clump7
neigh_modify exclude group clump8 clump8
neigh_modify exclude group clump9 clump9
thermo 100
#dump 1 all atom 50 dump.rigid
#dump 2 all image 100 image.*.jpg type type &
# axes yes 0.8 0.02 view 60 -30
#dump_modify 2 pad 5
#dump 3 all movie 100 movie.mpg type type &
# axes yes 0.8 0.02 view 60 -30
#dump_modify 3 pad 5
timestep 0.0001
thermo 50
run 10000

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# Simple rigid body system
units lj
atom_style atomic
atom_modify map array
pair_style lj/cut 2.5
read_data data.rigid
velocity all create 100.0 4928459
# unconnected bodies
group clump1 id <> 1 9
group clump2 id <> 10 18
group clump3 id <> 19 27
group clump4 id <> 28 36
group clump5 id <> 37 45
group clump6 id <> 46 54
group clump7 id <> 55 63
group clump8 id <> 64 72
group clump9 id <> 73 81
variable bodies atom 1.0*gmask(clump1)+2.0*gmask(clump2)+3.0*gmask(clump3)+4.0*gmask(clump4)+5.0*gmask(clump5)+6.0*gmask(clump6)+7.0*gmask(clump7)+8.0*gmask(clump8)+9.0*gmask(clump9)
fix 1 all rigid custom v_bodies
# 1 chain of connected bodies
#group clump1 id <> 1 9
#group clump2 id <> 9 18
#group clump3 id <> 18 27
#group clump4 id <> 27 36
#group clump5 id <> 36 45
#group clump6 id <> 45 54
#group clump7 id <> 54 63
#group clump8 id <> 63 72
#group clump9 id <> 72 81
#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 &
# clump6 clump7 clump8 clump9
# 2 chains of connected bodies
#group clump1 id <> 1 9
#group clump2 id <> 9 18
#group clump3 id <> 18 27
#group clump4 id <> 27 36
#group clump5 id <> 37 45
#group clump6 id <> 45 54
#group clump7 id <> 54 63
#group clump8 id <> 63 72
#group clump9 id <> 72 81
#fix 1 all poems group clump1 clump2 clump3 clump4
#fix 2 all poems group clump5 clump6 clump7 clump8 clump9
neigh_modify exclude group clump1 clump1
neigh_modify exclude group clump2 clump2
neigh_modify exclude group clump3 clump3
neigh_modify exclude group clump4 clump4
neigh_modify exclude group clump5 clump5
neigh_modify exclude group clump6 clump6
neigh_modify exclude group clump7 clump7
neigh_modify exclude group clump8 clump8
neigh_modify exclude group clump9 clump9
thermo 100
#dump 1 all atom 50 dump.rigid
#dump 2 all image 100 image.*.jpg type type &
# axes yes 0.8 0.02 view 60 -30
#dump_modify 2 pad 5
#dump 3 all movie 100 movie.mpg type type &
# axes yes 0.8 0.02 view 60 -30
#dump_modify 3 pad 5
timestep 0.0001
thermo 50
run 10000

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# Simple rigid body system
units lj
atom_style atomic
atom_modify map array
pair_style lj/cut 2.5
fix 0 all property/atom i_bodies
read_data data.rigid-property fix 0 NULL Bodies
velocity all create 100.0 4928459
# unconnected bodies
group clump1 id <> 1 9
group clump2 id <> 10 18
group clump3 id <> 19 27
group clump4 id <> 28 36
group clump5 id <> 37 45
group clump6 id <> 46 54
group clump7 id <> 55 63
group clump8 id <> 64 72
group clump9 id <> 73 81
# assemble bodies from per-atom custom integer property bodies
fix 1 all rigid custom i_bodies
# 1 chain of connected bodies
#group clump1 id <> 1 9
#group clump2 id <> 9 18
#group clump3 id <> 18 27
#group clump4 id <> 27 36
#group clump5 id <> 36 45
#group clump6 id <> 45 54
#group clump7 id <> 54 63
#group clump8 id <> 63 72
#group clump9 id <> 72 81
#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 &
# clump6 clump7 clump8 clump9
# 2 chains of connected bodies
#group clump1 id <> 1 9
#group clump2 id <> 9 18
#group clump3 id <> 18 27
#group clump4 id <> 27 36
#group clump5 id <> 37 45
#group clump6 id <> 45 54
#group clump7 id <> 54 63
#group clump8 id <> 63 72
#group clump9 id <> 72 81
#fix 1 all poems group clump1 clump2 clump3 clump4
#fix 2 all poems group clump5 clump6 clump7 clump8 clump9
neigh_modify exclude group clump1 clump1
neigh_modify exclude group clump2 clump2
neigh_modify exclude group clump3 clump3
neigh_modify exclude group clump4 clump4
neigh_modify exclude group clump5 clump5
neigh_modify exclude group clump6 clump6
neigh_modify exclude group clump7 clump7
neigh_modify exclude group clump8 clump8
neigh_modify exclude group clump9 clump9
thermo 100
#dump 1 all atom 50 dump.rigid
#dump 2 all image 100 image.*.jpg type type &
# axes yes 0.8 0.02 view 60 -30
#dump_modify 2 pad 5
#dump 3 all movie 100 movie.mpg type type &
# axes yes 0.8 0.02 view 60 -30
#dump_modify 3 pad 5
timestep 0.0001
thermo 50
run 10000