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proper handle partial initialization from infile

This commit is contained in:
Axel Kohlmeyer 2022-03-20 20:23:55 -04:00
parent 89c7d8f707
commit 550ae15dff
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GPG Key ID: D9B44E93BF0C375A
20 changed files with 3228 additions and 323 deletions
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7
examples/rigid/bodyinfo.dat Normal file
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# set fix rigid mass, COM, inertia tensor info for 4 of the 9 bodies
4
2 9.0000000000000000e+00 1.6111111111111112e+00 1.7222222222222223e+00 1.1111111111111110e-01 3.9444444444444442e+00 2.2777777777777772e+00 4.4444444444444438e+00 -2.7777777777777757e-01 1.1111111111111105e-01 2.2222222222222235e-01 4.3171479957811609e+00 -1.0618113255001780e+00 -1.8643700998325481e+00 4.5148932178264438e+00 1.0733638777335948e+01 9.1950804203772858e+00 0 0 0
3 9.0000000000000000e+00 2.8333333333333335e+00 2.7222222222222223e+00 1.1111111111111110e-01 3.9444444444444446e+00 3.3888888888888902e+00 5.5555555555555562e+00 -8.3333333333333415e-01 3.3333333333333304e-01 2.2222222222222254e-01 1.6315473697148597e-01 -7.2705885868299369e-01 5.5332911778921119e+00 -1.5846021643158503e+01 6.3829570883561679e+00 -4.3451481846875879e+01 0 0 0
5 9.0000000000000000e+00 5.1111111111111107e+00 5.0000000000000000e+00 1.1111111111111110e-01 4.3888888888888911e+00 2.7777777777777790e+00 5.3888888888888919e+00 -7.5000000000000056e-01 6.1111111111111172e-01 5.0000000000000022e-01 -5.9985136455141390e+00 3.8759047575157033e+00 -2.0802380702072480e+00 -9.6671050263449843e+00 -2.3012986946431408e+01 -2.3443650645115170e+01 0 0 0
9 9.0000000000000000e+00 9.5000000000000000e+00 9.5000000000000000e+00 1.1111111111111110e-01 2.3888888888888893e+00 2.3888888888888888e+00 3.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 -1.8008148769529069e+00 -2.6284193340862787e+00 -3.3758037136596228e+00 -1.1454679561601873e+01 2.8578517607187521e+01 -2.0466336627273300e+01 0 0 0

176
examples/rigid/data.rigid
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# LAMMPS data file for rigid bodies # LAMMPS data file for rigid bodies
81 atoms 81 atoms
1 atom types 1 atom types
-12 12 xlo xhi -12 12 xlo xhi
-12 12 ylo yhi -12 12 ylo yhi
-12 12 zlo zhi -12 12 zlo zhi
Masses Masses
1 1 1 1
Pair Coeffs Pair Coeffs
1 1 1 1 1 1
Atoms Atoms
1 1 0 0 0 1 1 0 0 0
2 1 0 1 0 2 1 0 1 0
3 1 0 0.5 0 3 1 0 0.5 0
4 1 0.5 0 0 4 1 0.5 0 0
5 1 0.5 0.5 1 5 1 0.5 0.5 1
6 1 1 0.5 0 6 1 1 0.5 0
7 1 0.5 1 0 7 1 0.5 1 0
8 1 1 0 0 8 1 1 0 0
9 1 1 1 0 9 1 1 1 0
10 1 2 1 0 10 1 2 1 0
11 1 1 2 0 11 1 1 2 0
12 1 1.5 2 0 12 1 1.5 2 0
13 1 1.5 1 0 13 1 1.5 1 0
14 1 1 1.5 0 14 1 1 1.5 0
15 1 1.5 1.5 1 15 1 1.5 1.5 1
16 1 2 1.5 0 16 1 2 1.5 0
17 1 2 2 0 17 1 2 2 0
18 1 2 3 0 18 1 2 3 0
19 1 2 2.5 0 19 1 2 2.5 0
20 1 2.5 2 0 20 1 2.5 2 0
21 1 2.5 2.5 1 21 1 2.5 2.5 1
22 1 3 2.5 0 22 1 3 2.5 0
23 1 2.5 3 0 23 1 2.5 3 0
24 1 3 2 0 24 1 3 2 0
25 1 3 3 0 25 1 3 3 0
26 1 4 3 0 26 1 4 3 0
27 1 3 4 0 27 1 3 4 0
28 1 3.5 4 0 28 1 3.5 4 0
29 1 3.5 3 0 29 1 3.5 3 0
30 1 3 3.5 0 30 1 3 3.5 0
31 1 3.5 3.5 1 31 1 3.5 3.5 1
32 1 4 3.5 0 32 1 4 3.5 0
33 1 4 4 0 33 1 4 4 0
34 1 4 5 0 34 1 4 5 0
35 1 4 4.5 0 35 1 4 4.5 0
36 1 4.5 4 0 36 1 4.5 4 0
37 1 4.5 4.5 1 37 1 4.5 4.5 1
38 1 5 4.5 0 38 1 5 4.5 0
39 1 4.5 5 0 39 1 4.5 5 0
40 1 5 4 0 40 1 5 4 0
41 1 5 5 0 41 1 5 5 0
42 1 6 5 0 42 1 6 5 0
43 1 5 6 0 43 1 5 6 0
44 1 5.5 6 0 44 1 5.5 6 0
45 1 5.5 5 0 45 1 5.5 5 0
46 1 5 5.5 0 46 1 5 5.5 0
47 1 5.5 5.5 1 47 1 5.5 5.5 1
48 1 6 5.5 0 48 1 6 5.5 0
49 1 6 6 0 49 1 6 6 0
50 1 6 7 0 50 1 6 7 0
51 1 6 6.5 0 51 1 6 6.5 0
52 1 6.5 6 0 52 1 6.5 6 0
53 1 6.5 6.5 1 53 1 6.5 6.5 1
54 1 7 6.5 0 54 1 7 6.5 0
55 1 6.5 7 0 55 1 6.5 7 0
56 1 7 6 0 56 1 7 6 0
57 1 7 7 0 57 1 7 7 0
58 1 8 7 0 58 1 8 7 0
59 1 7 8 0 59 1 7 8 0
60 1 7.5 8 0 60 1 7.5 8 0
61 1 7.5 7 0 61 1 7.5 7 0
62 1 7 7.5 0 62 1 7 7.5 0
63 1 7.5 7.5 1 63 1 7.5 7.5 1
64 1 8 7.5 0 64 1 8 7.5 0
65 1 8 8 0 65 1 8 8 0
66 1 8 9 0 66 1 8 9 0
67 1 8 8.5 0 67 1 8 8.5 0
68 1 8.5 8 0 68 1 8.5 8 0
69 1 8.5 8.5 1 69 1 8.5 8.5 1
70 1 9 8.5 0 70 1 9 8.5 0
71 1 8.5 9 0 71 1 8.5 9 0
72 1 9 8 0 72 1 9 8 0
73 1 9 9 0 73 1 9 9 0
74 1 10 9 0 74 1 10 9 0
75 1 9 10 0 75 1 9 10 0
76 1 9.5 10 0 76 1 9.5 10 0
77 1 9.5 9 0 77 1 9.5 9 0
78 1 9 9.5 0 78 1 9 9.5 0
79 1 9.5 9.5 1 79 1 9.5 9.5 1
80 1 10 9.5 0 80 1 10 9.5 0
81 1 10 10 0 81 1 10 10 0

100
examples/rigid/data.rigid.small Normal file
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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 1 0 0 0
2 1 1 0 1 0
3 1 1 0 0.5 0
4 1 1 0.5 0 0
5 1 1 0.5 0.5 1
6 1 1 1 0.5 0
7 1 1 0.5 1 0
8 1 1 1 0 0
9 1 1 1 1 0
10 2 1 2 1 0
11 2 1 1 2 0
12 2 1 1.5 2 0
13 2 1 1.5 1 0
14 2 1 1 1.5 0
15 2 1 1.5 1.5 1
16 2 1 2 1.5 0
17 2 1 2 2 0
18 2 1 2 3 0
19 3 1 2 2.5 0
20 3 1 2.5 2 0
21 3 1 2.5 2.5 1
22 3 1 3 2.5 0
23 3 1 2.5 3 0
24 3 1 3 2 0
25 3 1 3 3 0
26 3 1 4 3 0
27 3 1 3 4 0
28 4 1 3.5 4 0
29 4 1 3.5 3 0
30 4 1 3 3.5 0
31 4 1 3.5 3.5 1
32 4 1 4 3.5 0
33 4 1 4 4 0
34 4 1 4 5 0
35 4 1 4 4.5 0
36 4 1 4.5 4 0
37 5 1 4.5 4.5 1
38 5 1 5 4.5 0
39 5 1 4.5 5 0
40 5 1 5 4 0
41 5 1 5 5 0
42 5 1 6 5 0
43 5 1 5 6 0
44 5 1 5.5 6 0
45 5 1 5.5 5 0
46 6 1 5 5.5 0
47 6 1 5.5 5.5 1
48 6 1 6 5.5 0
49 6 1 6 6 0
50 6 1 6 7 0
51 6 1 6 6.5 0
52 6 1 6.5 6 0
53 6 1 6.5 6.5 1
54 6 1 7 6.5 0
55 7 1 6.5 7 0
56 7 1 7 6 0
57 7 1 7 7 0
58 7 1 8 7 0
59 7 1 7 8 0
60 7 1 7.5 8 0
61 7 1 7.5 7 0
62 7 1 7 7.5 0
63 7 1 7.5 7.5 1
64 8 1 8 7.5 0
65 8 1 8 8 0
66 8 1 8 9 0
67 8 1 8 8.5 0
68 8 1 8.5 8 0
69 8 1 8.5 8.5 1
70 8 1 9 8.5 0
71 8 1 8.5 9 0
72 8 1 9 8 0
73 9 1 9 9 0
74 9 1 10 9 0
75 9 1 9 10 0
76 9 1 9.5 10 0
77 9 1 9.5 9 0
78 9 1 9 9.5 0
79 9 1 9.5 9.5 1
80 9 1 10 9.5 0
81 9 1 10 10 0

108
examples/rigid/in.rigid
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# Simple rigid body system # Simple rigid body system
units lj units lj
atom_style atomic atom_style atomic
pair_style lj/cut 2.5 pair_style lj/cut 2.5
read_data data.rigid read_data data.rigid
velocity all create 100.0 4928459 velocity all create 100.0 4928459
# unconnected bodies # unconnected bodies
group clump1 id <> 1 9 group clump1 id <> 1 9
group clump2 id <> 10 18 group clump2 id <> 10 18
group clump3 id <> 19 27 group clump3 id <> 19 27
group clump4 id <> 28 36 group clump4 id <> 28 36
group clump5 id <> 37 45 group clump5 id <> 37 45
group clump6 id <> 46 54 group clump6 id <> 46 54
group clump7 id <> 55 63 group clump7 id <> 55 63
group clump8 id <> 64 72 group clump8 id <> 64 72
group clump9 id <> 73 81 group clump9 id <> 73 81
fix 1 all rigid group 9 clump1 clump2 clump3 clump4 clump5 & fix 1 all rigid group 9 clump1 clump2 clump3 clump4 clump5 &
clump6 clump7 clump8 clump9 clump6 clump7 clump8 clump9
# 1 chain of connected bodies # 1 chain of connected bodies
#group clump1 id <> 1 9 #group clump1 id <> 1 9
#group clump2 id <> 9 18 #group clump2 id <> 9 18
#group clump3 id <> 18 27 #group clump3 id <> 18 27
#group clump4 id <> 27 36 #group clump4 id <> 27 36
#group clump5 id <> 36 45 #group clump5 id <> 36 45
#group clump6 id <> 45 54 #group clump6 id <> 45 54
#group clump7 id <> 54 63 #group clump7 id <> 54 63
#group clump8 id <> 63 72 #group clump8 id <> 63 72
#group clump9 id <> 72 81 #group clump9 id <> 72 81
#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 & #fix 1 all poems group clump1 clump2 clump3 clump4 clump5 &
# clump6 clump7 clump8 clump9 # clump6 clump7 clump8 clump9
# 2 chains of connected bodies # 2 chains of connected bodies
#group clump1 id <> 1 9 #group clump1 id <> 1 9
#group clump2 id <> 9 18 #group clump2 id <> 9 18
#group clump3 id <> 18 27 #group clump3 id <> 18 27
#group clump4 id <> 27 36 #group clump4 id <> 27 36
#group clump5 id <> 37 45 #group clump5 id <> 37 45
#group clump6 id <> 45 54 #group clump6 id <> 45 54
#group clump7 id <> 54 63 #group clump7 id <> 54 63
#group clump8 id <> 63 72 #group clump8 id <> 63 72
#group clump9 id <> 72 81 #group clump9 id <> 72 81
#fix 1 all poems group clump1 clump2 clump3 clump4 #fix 1 all poems group clump1 clump2 clump3 clump4
#fix 2 all poems group clump5 clump6 clump7 clump8 clump9 #fix 2 all poems group clump5 clump6 clump7 clump8 clump9
neigh_modify exclude group clump1 clump1 neigh_modify exclude group clump1 clump1
neigh_modify exclude group clump2 clump2 neigh_modify exclude group clump2 clump2
neigh_modify exclude group clump3 clump3 neigh_modify exclude group clump3 clump3
neigh_modify exclude group clump4 clump4 neigh_modify exclude group clump4 clump4
neigh_modify exclude group clump5 clump5 neigh_modify exclude group clump5 clump5
neigh_modify exclude group clump6 clump6 neigh_modify exclude group clump6 clump6
neigh_modify exclude group clump7 clump7 neigh_modify exclude group clump7 clump7
neigh_modify exclude group clump8 clump8 neigh_modify exclude group clump8 clump8
neigh_modify exclude group clump9 clump9 neigh_modify exclude group clump9 clump9
thermo 100 thermo 100
#dump 1 all atom 50 dump.rigid #dump 1 all atom 50 dump.rigid
#dump 2 all image 100 image.*.jpg type type & #dump 2 all image 100 image.*.jpg type type &
# axes yes 0.8 0.02 view 60 -30 # axes yes 0.8 0.02 view 60 -30
#dump_modify 2 pad 5 #dump_modify 2 pad 5
#dump 3 all movie 100 movie.mpg type type & #dump 3 all movie 100 movie.mpg type type &
# axes yes 0.8 0.02 view 60 -30 # axes yes 0.8 0.02 view 60 -30
#dump_modify 3 pad 5 #dump_modify 3 pad 5
timestep 0.0001 timestep 0.0001
thermo 50 thermo 50
run 10000 run 10000

52
examples/rigid/in.rigid.infile Normal file
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# Simple rigid body system
units lj
atom_style atomic
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
fix 1 all rigid group 9 clump1 clump2 clump3 clump4 clump5 &
clump6 clump7 clump8 clump9 &
infile bodyinfo.dat
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

50
examples/rigid/in.rigid.molecule Normal file
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# Simple rigid body system
units lj
atom_style bond
pair_style lj/cut 2.5
read_data data.rigid.small
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
fix 1 all rigid molecule
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

50
examples/rigid/in.rigid.small Normal file
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# Simple rigid body system
units lj
atom_style bond
pair_style lj/cut 2.5
read_data data.rigid.small
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
fix 1 all rigid/small molecule
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

50
examples/rigid/in.rigid.small.infile Normal file
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# Simple rigid body system
units lj
atom_style bond
pair_style lj/cut 2.5
read_data data.rigid.small
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
fix 1 all rigid/small molecule infile bodyinfo.dat
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

312
examples/rigid/log.20Mar22.rigid.infile.g++.1 Normal file
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LAMMPS (17 Feb 2022)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
# Simple rigid body system
units lj
atom_style atomic
pair_style lj/cut 2.5
read_data data.rigid
Reading data file ...
orthogonal box = (-12 -12 -12) to (12 12 12)
1 by 1 by 1 MPI processor grid
reading atoms ...
81 atoms
read_data CPU = 0.000 seconds
velocity all create 100.0 4928459
# unconnected bodies
group clump1 id <> 1 9
9 atoms in group clump1
group clump2 id <> 10 18
9 atoms in group clump2
group clump3 id <> 19 27
9 atoms in group clump3
group clump4 id <> 28 36
9 atoms in group clump4
group clump5 id <> 37 45
9 atoms in group clump5
group clump6 id <> 46 54
9 atoms in group clump6
group clump7 id <> 55 63
9 atoms in group clump7
group clump8 id <> 64 72
9 atoms in group clump8
group clump9 id <> 73 81
9 atoms in group clump9
fix 1 all rigid group 9 clump1 clump2 clump3 clump4 clump5 clump6 clump7 clump8 clump9 infile bodyinfo.dat
9 rigid bodies with 81 atoms
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
generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Reading rigid body data for 4 bodies from file bodyinfo.dat
Reading rigid body data for 4 bodies from file bodyinfo.dat
Neighbor list info ...
update every 1 steps, delay 10 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 = 18 18 18
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/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 4.353 | 4.353 | 4.353 Mbytes
Step Temp E_pair E_mol TotEng Press
0 115.29439 5235.9179 0 5272.2142 -2.7403788
50 14910.685 571.71558 0 5265.82 32.006171
100 16298.442 136.66184 0 5267.653 16.444229
150 16682.606 17.490511 0 5269.4219 14.900344
200 16733.929 1.372872 0 5269.4617 14.569267
250 16738.853 -0.15252816 0 5269.4864 14.496404
300 16738.588 -0.055171335 0 5269.5002 14.496025
350 16738.492 -0.017444677 0 5269.5077 14.496446
400 16738.464 -0.0060102023 0 5269.5104 14.496618
450 16738.455 -0.0012713351 0 5269.5124 14.496701
500 16738.455 -0.00081068621 0 5269.5128 14.496709
550 16738.455 -0.00083203497 0 5269.5129 14.496707
600 16738.455 -0.00058355356 0 5269.5131 14.496709
650 16738.455 -0.00047226704 0 5269.5131 14.496708
700 16738.455 0 0 5269.5136 14.496713
750 16738.455 0 0 5269.5136 14.49671
800 16738.455 0 0 5269.5137 14.496709
850 16738.455 0 0 5269.5137 14.49671
900 16738.456 0 0 5269.5138 14.496713
950 16738.462 -0.0035323872 0 5269.5122 14.496671
1000 16738.586 -0.051135144 0 5269.5036 14.496229
1050 16737.358 0.32995057 0 5269.4981 14.525763
1100 16737.892 0.16210246 0 5269.4984 14.531983
1150 16738.703 -0.089235095 0 5269.5025 14.509899
1200 16738.466 -0.0075446243 0 5269.5096 14.510615
1250 16738.456 0 0 5269.514 14.510704
1300 16738.457 0 0 5269.5141 14.510701
1350 16738.457 0 0 5269.5141 14.510699
1400 16738.457 -0.00044736511 0 5269.5138 14.510693
1450 16738.458 -0.0010971179 0 5269.5134 14.510687
1500 16738.458 -0.00057885428 0 5269.5139 14.510698
1550 16738.457 0 0 5269.5143 14.51071
1600 16738.457 0 0 5269.5144 14.510712
1650 16738.457 0 0 5269.5144 14.510712
1700 16738.458 0 0 5269.5144 14.51071
1750 16738.458 0 0 5269.5145 14.510708
1800 16738.458 0 0 5269.5145 14.510706
1850 16738.458 0 0 5269.5146 14.510705
1900 16738.458 0 0 5269.5146 14.510706
1950 16738.465 -0.0031733615 0 5269.5134 14.510659
2000 16738.491 -0.013255268 0 5269.5117 14.510532
2050 16738.556 -0.0365811 0 5269.5087 14.51029
2100 16738.633 -0.063209659 0 5269.5065 14.510219
2150 16738.607 -0.05601761 0 5269.5055 14.510231
2200 16738.557 -0.038423032 0 5269.5072 14.510404
2250 16738.515 -0.023709918 0 5269.5088 14.510539
2300 16738.489 -0.013249035 0 5269.5111 14.510621
2350 16738.468 -0.0045563719 0 5269.5131 14.510714
2400 16738.46 -0.00052194273 0 5269.5146 14.510771
2450 16738.464 -0.0023259756 0 5269.514 14.510746
2500 16738.468 -0.0051929186 0 5269.5127 14.510731
2550 16738.581 -0.044940117 0 5269.5085 14.510315
2600 16738.427 -7.9722793e-05 0 5269.5046 14.510657
2650 16733.017 1.7051479 0 5269.5067 14.596295
2700 16738.761 -0.10614946 0 5269.5038 14.499584
2750 16733.973 1.4038179 0 5269.5064 14.598107
2800 16738.585 -0.046813448 0 5269.5076 14.511073
2850 16738.487 -0.012558719 0 5269.5111 14.510111
2900 16738.465 -0.0026252725 0 5269.514 14.510277
2950 16738.476 -0.0082220764 0 5269.512 14.510223
3000 16738.66 -0.071284779 0 5269.507 14.509758
3050 16715.332 7.2419352 0 5269.476 14.870305
3100 16653.226 26.818761 0 5269.5009 14.496764
3150 16739.351 -0.30690375 0 5269.4886 13.643904
3200 16733.238 1.6025328 0 5269.4737 12.016934
3250 16734.374 1.2554429 0 5269.4841 11.963561
3300 16732.156 1.9585967 0 5269.4893 12.234024
3350 16738.655 -0.079693236 0 5269.497 12.092757
3400 16738.543 -0.042215005 0 5269.4991 12.092809
3450 16738.591 -0.059327511 0 5269.4972 12.092536
3500 16738.759 -0.11761245 0 5269.4918 12.09203
3550 16713.405 7.8460621 0 5269.4737 12.389816
3600 16734.939 1.0821936 0 5269.4891 12.173591
3650 16738.808 -0.13663194 0 5269.4882 12.027009
3700 16738.602 -0.070934368 0 5269.4889 12.025288
3750 16737.731 0.20706558 0 5269.4927 12.061948
3800 16738.578 -0.05582043 0 5269.4965 12.035665
3850 16738.471 -0.016307928 0 5269.5024 12.035302
3900 16738.449 -0.0058182199 0 5269.5059 12.035401
3950 16738.439 -0.0012027325 0 5269.5074 12.035461
4000 16738.436 -0.00020698452 0 5269.5075 12.035469
4050 16738.437 0 0 5269.5078 12.035454
4100 16738.437 0 0 5269.508 12.035435
4150 16738.438 0 0 5269.5081 12.035426
4200 16738.438 0 0 5269.5083 12.035432
4250 16738.439 0 0 5269.5085 12.035447
4300 16738.439 0 0 5269.5086 12.035463
4350 16738.44 0 0 5269.5087 12.035474
4400 16738.44 0 0 5269.5088 12.035478
4450 16738.44 0 0 5269.5089 12.035474
4500 16738.44 0 0 5269.509 12.035462
4550 16738.441 0 0 5269.5092 12.035449
4600 16738.441 0 0 5269.5093 12.035445
4650 16738.442 0 0 5269.5095 12.035451
4700 16738.442 0 0 5269.5096 12.03546
4750 16738.443 0 0 5269.5097 12.035465
4800 16738.443 0 0 5269.5098 12.035466
4850 16738.443 0 0 5269.51 12.035463
4900 16738.444 0 0 5269.5101 12.035456
4950 16738.444 0 0 5269.5102 12.035447
5000 16738.445 0 0 5269.5104 12.03544
5050 16738.445 0 0 5269.5105 12.035442
5100 16738.446 0 0 5269.5107 12.035455
5150 16738.446 0 0 5269.5108 12.03547
5200 16738.446 0 0 5269.5109 12.035479
5250 16738.447 0 0 5269.511 12.035479
5300 16738.447 0 0 5269.5111 12.03547
5350 16738.447 0 0 5269.5112 12.035454
5400 16738.448 0 0 5269.5113 12.035434
5450 16738.448 0 0 5269.5115 12.03542
5500 16738.449 0 0 5269.5117 12.035422
5550 16738.457 -0.0030919234 0 5269.5111 12.035383
5600 16738.51 -0.021618357 0 5269.5092 12.035106
5650 16738.622 -0.059214788 0 5269.507 12.035694
5700 16395.28 108.06941 0 5269.5463 24.369038
5750 16738.544 -0.033973429 0 5269.5077 12.011261
5800 16738.456 -0.0037013529 0 5269.5102 12.011675
5850 16738.451 0 0 5269.5123 12.011709
5900 16738.451 -0.0002211587 0 5269.5122 12.011687
5950 16738.452 -0.00024253349 0 5269.5124 12.011678
6000 16738.452 0 0 5269.5128 12.011688
6050 16738.453 0 0 5269.513 12.011702
6100 16738.453 0 0 5269.5131 12.011716
6150 16738.454 0 0 5269.5132 12.011725
6200 16738.454 0 0 5269.5133 12.011728
6250 16738.454 0 0 5269.5134 12.011723
6300 16738.455 0 0 5269.5135 12.011712
6350 16738.455 0 0 5269.5137 12.0117
6400 16738.456 0 0 5269.5138 12.011697
6450 16738.456 0 0 5269.514 12.011704
6500 16738.456 0 0 5269.5141 12.011714
6550 16738.457 0 0 5269.5142 12.011719
6600 16738.457 0 0 5269.5143 12.011718
6650 16738.458 0 0 5269.5144 12.011713
6700 16738.458 0 0 5269.5146 12.011705
6750 16738.459 0 0 5269.5147 12.011696
6800 16738.459 0 0 5269.5149 12.01169
6850 16738.46 0 0 5269.515 12.011695
6900 16738.46 0 0 5269.5152 12.01171
6950 16738.46 0 0 5269.5153 12.011726
7000 16738.461 0 0 5269.5154 12.011736
7050 16738.461 0 0 5269.5155 12.011737
7100 16738.461 0 0 5269.5155 12.011728
7150 16738.461 0 0 5269.5156 12.011712
7200 16738.462 0 0 5269.5158 12.011691
7250 16738.463 0 0 5269.516 12.011676
7300 16738.463 0 0 5269.5162 12.011677
7350 16738.464 0 0 5269.5164 12.011693
7400 16738.464 0 0 5269.5165 12.011713
7450 16738.465 0 0 5269.5166 12.011729
7500 16738.465 0 0 5269.5167 12.011736
7550 16738.465 0 0 5269.5168 12.011734
7600 16738.465 0 0 5269.5168 12.011722
7650 16738.466 0 0 5269.517 12.011704
7700 16738.466 0 0 5269.5171 12.011687
7750 16738.467 0 0 5269.5173 12.011681
7800 16738.467 0 0 5269.5175 12.011687
7850 16738.468 0 0 5269.5176 12.0117
7900 16738.468 0 0 5269.5178 12.011712
7950 16738.469 0 0 5269.5179 12.011721
8000 16738.469 0 0 5269.518 12.011724
8050 16738.469 0 0 5269.5181 12.01172
8100 16738.47 0 0 5269.5182 12.011709
8150 16738.47 0 0 5269.5183 12.0117
8200 16738.47 0 0 5269.5185 12.0117
8250 16738.471 0 0 5269.5186 12.011709
8300 16738.471 0 0 5269.5187 12.011719
8350 16738.472 0 0 5269.5189 12.011723
8400 16738.472 0 0 5269.519 12.01172
8450 16738.473 -0.00039690666 0 5269.5189 12.011706
8500 16738.481 -0.0034646804 0 5269.5182 12.011643
8550 16738.483 -0.0045307409 0 5269.5178 12.011621
8600 16738.474 -0.00076532812 0 5269.5189 12.011681
8650 16738.474 0 0 5269.5197 12.011699
8700 16738.475 0 0 5269.5199 12.011715
8750 16738.475 0 0 5269.52 12.011732
8800 16738.475 0 0 5269.52 12.011743
8850 16738.476 0 0 5269.5201 12.011744
8900 16738.476 0 0 5269.5202 12.011735
8950 16738.476 0 0 5269.5203 12.011719
9000 16738.477 0 0 5269.5205 12.011698
9050 16738.477 0 0 5269.5206 12.011683
9100 16738.478 0 0 5269.5208 12.011684
9150 16738.479 0 0 5269.521 12.011701
9200 16738.479 0 0 5269.5212 12.011722
9250 16738.479 0 0 5269.5213 12.011738
9300 16738.48 0 0 5269.5214 12.011746
9350 16738.48 0 0 5269.5214 12.011744
9400 16738.48 0 0 5269.5215 12.011732
9450 16738.48 0 0 5269.5216 12.011715
9500 16738.481 -0.00037652435 0 5269.5216 12.011692
9550 16738.493 -0.0053156167 0 5269.5203 12.011611
9600 16738.549 -0.02681437 0 5269.5163 12.011415
9650 16738.765 -0.10191524 0 5269.5092 12.011013
9700 16735.041 1.0589895 0 5269.4979 12.062708
9750 16738.013 0.13550156 0 5269.5101 11.407246
9800 16738.512 -0.011620325 0 5269.5201 11.394974
9850 16738.489 -0.00067270436 0 5269.5237 11.395099
9900 16738.489 -0.0002498452 0 5269.5242 11.395085
9950 16738.49 0 0 5269.5245 11.395077
10000 16738.49 0 0 5269.5246 11.395076
Loop time of 0.0882903 on 1 procs for 10000 steps with 81 atoms
Performance: 978589.581 tau/day, 113262.683 timesteps/s
97.6% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0064583 | 0.0064583 | 0.0064583 | 0.0 | 7.31
Neigh | 0.027186 | 0.027186 | 0.027186 | 0.0 | 30.79
Comm | 0.0057041 | 0.0057041 | 0.0057041 | 0.0 | 6.46
Output | 0.0020628 | 0.0020628 | 0.0020628 | 0.0 | 2.34
Modify | 0.042816 | 0.042816 | 0.042816 | 0.0 | 48.49
Other | | 0.004063 | | | 4.60
Nlocal: 81 ave 81 max 81 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 84 ave 84 max 84 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0
Neighbor list builds = 998
Dangerous builds = 997
Total wall time: 0:00:00

312
examples/rigid/log.20Mar22.rigid.infile.g++.4 Normal file
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LAMMPS (17 Feb 2022)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
# Simple rigid body system
units lj
atom_style atomic
pair_style lj/cut 2.5
read_data data.rigid
Reading data file ...
orthogonal box = (-12 -12 -12) to (12 12 12)
1 by 2 by 2 MPI processor grid
reading atoms ...
81 atoms
read_data CPU = 0.000 seconds
velocity all create 100.0 4928459
# unconnected bodies
group clump1 id <> 1 9
9 atoms in group clump1
group clump2 id <> 10 18
9 atoms in group clump2
group clump3 id <> 19 27
9 atoms in group clump3
group clump4 id <> 28 36
9 atoms in group clump4
group clump5 id <> 37 45
9 atoms in group clump5
group clump6 id <> 46 54
9 atoms in group clump6
group clump7 id <> 55 63
9 atoms in group clump7
group clump8 id <> 64 72
9 atoms in group clump8
group clump9 id <> 73 81
9 atoms in group clump9
fix 1 all rigid group 9 clump1 clump2 clump3 clump4 clump5 clump6 clump7 clump8 clump9 infile bodyinfo.dat
9 rigid bodies with 81 atoms
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
generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Reading rigid body data for 4 bodies from file bodyinfo.dat
Reading rigid body data for 4 bodies from file bodyinfo.dat
Neighbor list info ...
update every 1 steps, delay 10 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 = 18 18 18
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/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 4.201 | 4.233 | 4.327 Mbytes
Step Temp E_pair E_mol TotEng Press
0 115.29439 5235.9179 0 5272.2142 -2.7403788
50 14910.685 571.71558 0 5265.82 32.006171
100 16298.442 136.66184 0 5267.653 16.444229
150 16682.606 17.490511 0 5269.4219 14.900344
200 16733.929 1.372872 0 5269.4617 14.569267
250 16738.853 -0.15252816 0 5269.4864 14.496404
300 16738.588 -0.055171335 0 5269.5002 14.496025
350 16738.492 -0.017444677 0 5269.5077 14.496446
400 16738.464 -0.0060102023 0 5269.5104 14.496618
450 16738.455 -0.0012713351 0 5269.5124 14.496701
500 16738.455 -0.00081068621 0 5269.5128 14.496709
550 16738.455 -0.00083203497 0 5269.5129 14.496707
600 16738.455 -0.00058355356 0 5269.5131 14.496709
650 16738.455 -0.00047226704 0 5269.5131 14.496708
700 16738.455 0 0 5269.5136 14.496713
750 16738.455 0 0 5269.5136 14.49671
800 16738.455 0 0 5269.5137 14.496709
850 16738.455 0 0 5269.5137 14.49671
900 16738.456 0 0 5269.5138 14.496713
950 16738.462 -0.0035323872 0 5269.5122 14.496671
1000 16738.586 -0.051135144 0 5269.5036 14.496229
1050 16737.358 0.32995057 0 5269.4981 14.525763
1100 16737.892 0.16210246 0 5269.4984 14.531983
1150 16738.703 -0.089235095 0 5269.5025 14.509899
1200 16738.466 -0.0075446243 0 5269.5096 14.510615
1250 16738.456 0 0 5269.514 14.510704
1300 16738.457 0 0 5269.5141 14.510701
1350 16738.457 0 0 5269.5141 14.510699
1400 16738.457 -0.00044736511 0 5269.5138 14.510693
1450 16738.458 -0.0010971179 0 5269.5134 14.510687
1500 16738.458 -0.00057885428 0 5269.5139 14.510698
1550 16738.457 0 0 5269.5143 14.51071
1600 16738.457 0 0 5269.5144 14.510712
1650 16738.457 0 0 5269.5144 14.510712
1700 16738.458 0 0 5269.5144 14.51071
1750 16738.458 0 0 5269.5145 14.510708
1800 16738.458 0 0 5269.5145 14.510706
1850 16738.458 0 0 5269.5146 14.510705
1900 16738.458 0 0 5269.5146 14.510706
1950 16738.465 -0.0031733615 0 5269.5134 14.510659
2000 16738.491 -0.013255268 0 5269.5117 14.510532
2050 16738.556 -0.0365811 0 5269.5087 14.51029
2100 16738.633 -0.063209659 0 5269.5065 14.510219
2150 16738.607 -0.05601761 0 5269.5055 14.510231
2200 16738.557 -0.038423032 0 5269.5072 14.510404
2250 16738.515 -0.023709918 0 5269.5088 14.510539
2300 16738.489 -0.013249035 0 5269.5111 14.510621
2350 16738.468 -0.0045563719 0 5269.5131 14.510714
2400 16738.46 -0.00052194273 0 5269.5146 14.510771
2450 16738.464 -0.0023259756 0 5269.514 14.510746
2500 16738.468 -0.0051929186 0 5269.5127 14.510731
2550 16738.581 -0.044940117 0 5269.5085 14.510315
2600 16738.427 -7.972279e-05 0 5269.5046 14.510657
2650 16733.017 1.7051479 0 5269.5067 14.596295
2700 16738.761 -0.10614946 0 5269.5038 14.499584
2750 16733.973 1.4038179 0 5269.5064 14.598107
2800 16738.585 -0.046813448 0 5269.5076 14.511073
2850 16738.487 -0.012558719 0 5269.5111 14.510111
2900 16738.465 -0.0026252725 0 5269.514 14.510277
2950 16738.476 -0.0082220764 0 5269.512 14.510223
3000 16738.66 -0.071284779 0 5269.507 14.509758
3050 16715.332 7.2419352 0 5269.476 14.870305
3100 16653.226 26.818761 0 5269.5009 14.496764
3150 16739.351 -0.30690375 0 5269.4886 13.643904
3200 16733.238 1.6025328 0 5269.4737 12.016934
3250 16734.374 1.2554429 0 5269.4841 11.963561
3300 16732.156 1.9585967 0 5269.4893 12.234024
3350 16738.655 -0.079693236 0 5269.497 12.092757
3400 16738.543 -0.042215005 0 5269.4991 12.092809
3450 16738.591 -0.059327511 0 5269.4972 12.092536
3500 16738.759 -0.11761245 0 5269.4918 12.09203
3550 16713.405 7.8460621 0 5269.4737 12.389816
3600 16734.939 1.0821936 0 5269.4891 12.173591
3650 16738.808 -0.13663194 0 5269.4882 12.027009
3700 16738.602 -0.070934368 0 5269.4889 12.025288
3750 16737.731 0.20706557 0 5269.4927 12.061948
3800 16738.578 -0.05582043 0 5269.4965 12.035665
3850 16738.471 -0.016307928 0 5269.5024 12.035302
3900 16738.449 -0.0058182199 0 5269.5059 12.035401
3950 16738.439 -0.0012027325 0 5269.5074 12.035461
4000 16738.436 -0.00020698452 0 5269.5075 12.035469
4050 16738.437 0 0 5269.5078 12.035454
4100 16738.437 0 0 5269.508 12.035435
4150 16738.438 0 0 5269.5081 12.035426
4200 16738.438 0 0 5269.5083 12.035432
4250 16738.439 0 0 5269.5085 12.035447
4300 16738.439 0 0 5269.5086 12.035463
4350 16738.44 0 0 5269.5087 12.035474
4400 16738.44 0 0 5269.5088 12.035478
4450 16738.44 0 0 5269.5089 12.035474
4500 16738.44 0 0 5269.509 12.035462
4550 16738.441 0 0 5269.5092 12.035449
4600 16738.441 0 0 5269.5093 12.035445
4650 16738.442 0 0 5269.5095 12.035451
4700 16738.442 0 0 5269.5096 12.03546
4750 16738.443 0 0 5269.5097 12.035465
4800 16738.443 0 0 5269.5098 12.035466
4850 16738.443 0 0 5269.51 12.035463
4900 16738.444 0 0 5269.5101 12.035456
4950 16738.444 0 0 5269.5102 12.035447
5000 16738.445 0 0 5269.5104 12.03544
5050 16738.445 0 0 5269.5105 12.035442
5100 16738.446 0 0 5269.5107 12.035455
5150 16738.446 0 0 5269.5108 12.03547
5200 16738.446 0 0 5269.5109 12.035479
5250 16738.447 0 0 5269.511 12.035479
5300 16738.447 0 0 5269.5111 12.03547
5350 16738.447 0 0 5269.5112 12.035454
5400 16738.448 0 0 5269.5113 12.035434
5450 16738.448 0 0 5269.5115 12.03542
5500 16738.449 0 0 5269.5117 12.035422
5550 16738.457 -0.0030919234 0 5269.5111 12.035383
5600 16738.51 -0.021618357 0 5269.5092 12.035106
5650 16738.622 -0.059214788 0 5269.507 12.035694
5700 16395.28 108.06941 0 5269.5463 24.369038
5750 16738.544 -0.033973429 0 5269.5077 12.011261
5800 16738.456 -0.0037013529 0 5269.5102 12.011675
5850 16738.451 0 0 5269.5123 12.011709
5900 16738.451 -0.00022115871 0 5269.5122 12.011687
5950 16738.452 -0.00024253349 0 5269.5124 12.011678
6000 16738.452 0 0 5269.5128 12.011688
6050 16738.453 0 0 5269.513 12.011702
6100 16738.453 0 0 5269.5131 12.011716
6150 16738.454 0 0 5269.5132 12.011725
6200 16738.454 0 0 5269.5133 12.011728
6250 16738.454 0 0 5269.5134 12.011723
6300 16738.455 0 0 5269.5135 12.011712
6350 16738.455 0 0 5269.5137 12.0117
6400 16738.456 0 0 5269.5138 12.011697
6450 16738.456 0 0 5269.514 12.011704
6500 16738.456 0 0 5269.5141 12.011714
6550 16738.457 0 0 5269.5142 12.011719
6600 16738.457 0 0 5269.5143 12.011718
6650 16738.458 0 0 5269.5144 12.011713
6700 16738.458 0 0 5269.5146 12.011705
6750 16738.459 0 0 5269.5147 12.011696
6800 16738.459 0 0 5269.5149 12.01169
6850 16738.46 0 0 5269.515 12.011695
6900 16738.46 0 0 5269.5152 12.01171
6950 16738.46 0 0 5269.5153 12.011726
7000 16738.461 0 0 5269.5154 12.011736
7050 16738.461 0 0 5269.5155 12.011737
7100 16738.461 0 0 5269.5155 12.011728
7150 16738.461 0 0 5269.5156 12.011712
7200 16738.462 0 0 5269.5158 12.011691
7250 16738.463 0 0 5269.516 12.011676
7300 16738.463 0 0 5269.5162 12.011677
7350 16738.464 0 0 5269.5164 12.011693
7400 16738.464 0 0 5269.5165 12.011713
7450 16738.465 0 0 5269.5166 12.011729
7500 16738.465 0 0 5269.5167 12.011736
7550 16738.465 0 0 5269.5168 12.011734
7600 16738.465 0 0 5269.5168 12.011722
7650 16738.466 0 0 5269.517 12.011704
7700 16738.466 0 0 5269.5171 12.011687
7750 16738.467 0 0 5269.5173 12.011681
7800 16738.467 0 0 5269.5175 12.011687
7850 16738.468 0 0 5269.5176 12.0117
7900 16738.468 0 0 5269.5178 12.011712
7950 16738.469 0 0 5269.5179 12.011721
8000 16738.469 0 0 5269.518 12.011724
8050 16738.469 0 0 5269.5181 12.01172
8100 16738.47 0 0 5269.5182 12.011709
8150 16738.47 0 0 5269.5183 12.0117
8200 16738.47 0 0 5269.5185 12.0117
8250 16738.471 0 0 5269.5186 12.011709
8300 16738.471 0 0 5269.5187 12.011719
8350 16738.472 0 0 5269.5189 12.011723
8400 16738.472 0 0 5269.519 12.01172
8450 16738.473 -0.00039690664 0 5269.5189 12.011706
8500 16738.481 -0.0034646803 0 5269.5182 12.011643
8550 16738.483 -0.004530741 0 5269.5178 12.01162
8600 16738.474 -0.00076532813 0 5269.5189 12.011681
8650 16738.474 0 0 5269.5197 12.011699
8700 16738.475 0 0 5269.5199 12.011715
8750 16738.475 0 0 5269.52 12.011732
8800 16738.475 0 0 5269.52 12.011743
8850 16738.476 0 0 5269.5201 12.011744
8900 16738.476 0 0 5269.5202 12.011735
8950 16738.476 0 0 5269.5203 12.011719
9000 16738.477 0 0 5269.5205 12.011698
9050 16738.477 0 0 5269.5206 12.011683
9100 16738.478 0 0 5269.5208 12.011684
9150 16738.479 0 0 5269.521 12.011701
9200 16738.479 0 0 5269.5212 12.011722
9250 16738.479 0 0 5269.5213 12.011738
9300 16738.48 0 0 5269.5214 12.011746
9350 16738.48 0 0 5269.5214 12.011744
9400 16738.48 0 0 5269.5215 12.011732
9450 16738.48 0 0 5269.5216 12.011715
9500 16738.481 -0.00037652436 0 5269.5216 12.011692
9550 16738.493 -0.0053156168 0 5269.5203 12.011611
9600 16738.549 -0.026814371 0 5269.5163 12.011415
9650 16738.765 -0.10191524 0 5269.5092 12.011013
9700 16735.041 1.0589899 0 5269.4979 12.062708
9750 16738.013 0.13550149 0 5269.5101 11.407246
9800 16738.512 -0.011620325 0 5269.5201 11.394974
9850 16738.489 -0.00067270428 0 5269.5237 11.395099
9900 16738.489 -0.0002498452 0 5269.5242 11.395085
9950 16738.49 0 0 5269.5245 11.395077
10000 16738.49 0 0 5269.5246 11.395076
Loop time of 0.100422 on 4 procs for 10000 steps with 81 atoms
Performance: 860368.209 tau/day, 99579.654 timesteps/s
99.0% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0014853 | 0.0020649 | 0.0026245 | 0.9 | 2.06
Neigh | 0.0075956 | 0.0080256 | 0.0091971 | 0.8 | 7.99
Comm | 0.037221 | 0.041059 | 0.043195 | 1.2 | 40.89
Output | 0.0020995 | 0.0023594 | 0.003073 | 0.8 | 2.35
Modify | 0.041318 | 0.042855 | 0.044215 | 0.5 | 42.67
Other | | 0.004059 | | | 4.04
Nlocal: 20.25 ave 38 max 3 min
Histogram: 1 0 1 0 0 0 1 0 0 1
Nghost: 27.25 ave 48 max 13 min
Histogram: 1 0 1 1 0 0 0 0 0 1
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0
Neighbor list builds = 998
Dangerous builds = 997
Total wall time: 0:00:00

349
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LAMMPS (17 Feb 2022)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
# Simple rigid body system
units lj
atom_style bond
pair_style lj/cut 2.5
read_data data.rigid.small
Reading data file ...
orthogonal box = (-12 -12 -12) to (12 12 12)
1 by 1 by 1 MPI processor grid
reading atoms ...
81 atoms
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
0 = max # of 1-2 neighbors
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
1 = max # of special neighbors
special bonds CPU = 0.000 seconds
read_data CPU = 0.001 seconds
velocity all create 100.0 4928459
# unconnected bodies
group clump1 id <> 1 9
9 atoms in group clump1
group clump2 id <> 10 18
9 atoms in group clump2
group clump3 id <> 19 27
9 atoms in group clump3
group clump4 id <> 28 36
9 atoms in group clump4
group clump5 id <> 37 45
9 atoms in group clump5
group clump6 id <> 46 54
9 atoms in group clump6
group clump7 id <> 55 63
9 atoms in group clump7
group clump8 id <> 64 72
9 atoms in group clump8
group clump9 id <> 73 81
9 atoms in group clump9
fix 1 all rigid molecule
9 rigid bodies with 81 atoms
# 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
generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update every 1 steps, delay 10 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 = 18 18 18
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 5.233 | 5.233 | 5.233 Mbytes
Step Temp E_pair E_mol TotEng Press
0 115.29439 5235.9179 0 5272.2142 -2.7403788
50 14910.685 571.71558 0 5265.82 32.006171
100 16298.442 136.66184 0 5267.653 16.444229
150 16682.606 17.490511 0 5269.4219 14.900344
200 16733.929 1.372872 0 5269.4617 14.569267
250 16738.853 -0.15252816 0 5269.4864 14.496404
300 16738.588 -0.055171335 0 5269.5002 14.496025
350 16738.492 -0.017444677 0 5269.5077 14.496446
400 16738.464 -0.0060102023 0 5269.5104 14.496618
450 16738.455 -0.0012713351 0 5269.5124 14.496701
500 16738.455 -0.00081068621 0 5269.5128 14.496709
550 16738.455 -0.00083203497 0 5269.5129 14.496707
600 16738.455 -0.00058355356 0 5269.5131 14.496709
650 16738.455 -0.00047226704 0 5269.5131 14.496708
700 16738.455 0 0 5269.5136 14.496713
750 16738.455 0 0 5269.5136 14.49671
800 16738.455 0 0 5269.5137 14.496709
850 16738.455 0 0 5269.5137 14.49671
900 16738.456 0 0 5269.5138 14.496713
950 16738.462 -0.0035323872 0 5269.5122 14.496671
1000 16738.586 -0.051135144 0 5269.5036 14.496229
1050 16737.358 0.32995057 0 5269.4981 14.525763
1100 16737.892 0.16210246 0 5269.4984 14.531983
1150 16738.703 -0.089235095 0 5269.5025 14.509899
1200 16738.466 -0.0075446243 0 5269.5096 14.510615
1250 16738.456 0 0 5269.514 14.510704
1300 16738.457 0 0 5269.5141 14.510701
1350 16738.457 0 0 5269.5141 14.510699
1400 16738.457 -0.00044736511 0 5269.5138 14.510693
1450 16738.458 -0.0010971179 0 5269.5134 14.510687
1500 16738.458 -0.00057885428 0 5269.5139 14.510698
1550 16738.457 0 0 5269.5143 14.51071
1600 16738.457 0 0 5269.5144 14.510712
1650 16738.457 0 0 5269.5144 14.510712
1700 16738.458 0 0 5269.5144 14.51071
1750 16738.458 0 0 5269.5145 14.510708
1800 16738.458 0 0 5269.5145 14.510706
1850 16738.458 0 0 5269.5146 14.510705
1900 16738.458 0 0 5269.5146 14.510706
1950 16738.465 -0.0031733615 0 5269.5134 14.510659
2000 16738.491 -0.013255268 0 5269.5117 14.510532
2050 16738.556 -0.0365811 0 5269.5087 14.51029
2100 16738.633 -0.063209659 0 5269.5065 14.510219
2150 16738.607 -0.05601761 0 5269.5055 14.510231
2200 16738.557 -0.038423032 0 5269.5072 14.510404
2250 16738.515 -0.023709918 0 5269.5088 14.510539
2300 16738.489 -0.013249035 0 5269.5111 14.510621
2350 16738.468 -0.0045563719 0 5269.5131 14.510714
2400 16738.46 -0.00052194273 0 5269.5146 14.510771
2450 16738.464 -0.0023259756 0 5269.514 14.510746
2500 16738.468 -0.0051929186 0 5269.5127 14.510731
2550 16738.581 -0.044940117 0 5269.5085 14.510315
2600 16738.427 -7.97228e-05 0 5269.5046 14.510657
2650 16733.017 1.7051479 0 5269.5067 14.596295
2700 16738.761 -0.10614946 0 5269.5038 14.499584
2750 16733.973 1.4038179 0 5269.5064 14.598107
2800 16738.585 -0.046813448 0 5269.5076 14.511073
2850 16738.487 -0.012558719 0 5269.5111 14.510111
2900 16738.465 -0.0026252725 0 5269.514 14.510277
2950 16738.476 -0.0082220764 0 5269.512 14.510223
3000 16738.66 -0.071284779 0 5269.507 14.509758
3050 16715.332 7.2419352 0 5269.476 14.870305
3100 16653.226 26.818761 0 5269.5009 14.496764
3150 16739.351 -0.30690375 0 5269.4886 13.643904
3200 16733.238 1.6025328 0 5269.4737 12.016934
3250 16734.374 1.2554429 0 5269.4841 11.963561
3300 16732.156 1.9585967 0 5269.4893 12.234024
3350 16738.655 -0.079693236 0 5269.497 12.092757
3400 16738.543 -0.042215005 0 5269.4991 12.092809
3450 16738.591 -0.059327511 0 5269.4972 12.092536
3500 16738.759 -0.11761245 0 5269.4918 12.09203
3550 16713.405 7.8460621 0 5269.4737 12.389816
3600 16734.939 1.0821936 0 5269.4891 12.173591
3650 16738.808 -0.13663194 0 5269.4882 12.027009
3700 16738.602 -0.070934368 0 5269.4889 12.025288
3750 16737.731 0.20706557 0 5269.4927 12.061948
3800 16738.578 -0.05582043 0 5269.4965 12.035665
3850 16738.471 -0.016307928 0 5269.5024 12.035302
3900 16738.449 -0.0058182199 0 5269.5059 12.035401
3950 16738.439 -0.0012027325 0 5269.5074 12.035461
4000 16738.436 -0.00020698452 0 5269.5075 12.035469
4050 16738.437 0 0 5269.5078 12.035454
4100 16738.437 0 0 5269.508 12.035435
4150 16738.438 0 0 5269.5081 12.035426
4200 16738.438 0 0 5269.5083 12.035432
4250 16738.439 0 0 5269.5085 12.035447
4300 16738.439 0 0 5269.5086 12.035463
4350 16738.44 0 0 5269.5087 12.035474
4400 16738.44 0 0 5269.5088 12.035478
4450 16738.44 0 0 5269.5089 12.035474
4500 16738.44 0 0 5269.509 12.035462
4550 16738.441 0 0 5269.5092 12.035449
4600 16738.441 0 0 5269.5093 12.035445
4650 16738.442 0 0 5269.5095 12.035451
4700 16738.442 0 0 5269.5096 12.03546
4750 16738.443 0 0 5269.5097 12.035465
4800 16738.443 0 0 5269.5098 12.035466
4850 16738.443 0 0 5269.51 12.035463
4900 16738.444 0 0 5269.5101 12.035456
4950 16738.444 0 0 5269.5102 12.035447
5000 16738.445 0 0 5269.5104 12.03544
5050 16738.445 0 0 5269.5105 12.035442
5100 16738.446 0 0 5269.5107 12.035455
5150 16738.446 0 0 5269.5108 12.03547
5200 16738.446 0 0 5269.5109 12.035479
5250 16738.447 0 0 5269.511 12.035479
5300 16738.447 0 0 5269.5111 12.03547
5350 16738.447 0 0 5269.5112 12.035454
5400 16738.448 0 0 5269.5113 12.035434
5450 16738.448 0 0 5269.5115 12.03542
5500 16738.449 0 0 5269.5117 12.035422
5550 16738.457 -0.0030919234 0 5269.5111 12.035383
5600 16738.51 -0.021618357 0 5269.5092 12.035106
5650 16738.622 -0.059214788 0 5269.507 12.035694
5700 16395.28 108.06941 0 5269.5463 24.369038
5750 16738.544 -0.033973429 0 5269.5077 12.011261
5800 16738.456 -0.0037013529 0 5269.5102 12.011675
5850 16738.451 0 0 5269.5123 12.011709
5900 16738.451 -0.00022115871 0 5269.5122 12.011687
5950 16738.452 -0.00024253349 0 5269.5124 12.011678
6000 16738.452 0 0 5269.5128 12.011688
6050 16738.453 0 0 5269.513 12.011702
6100 16738.453 0 0 5269.5131 12.011716
6150 16738.454 0 0 5269.5132 12.011725
6200 16738.454 0 0 5269.5133 12.011728
6250 16738.454 0 0 5269.5134 12.011723
6300 16738.455 0 0 5269.5135 12.011712
6350 16738.455 0 0 5269.5137 12.0117
6400 16738.456 0 0 5269.5138 12.011697
6450 16738.456 0 0 5269.514 12.011704
6500 16738.456 0 0 5269.5141 12.011714
6550 16738.457 0 0 5269.5142 12.011719
6600 16738.457 0 0 5269.5143 12.011718
6650 16738.458 0 0 5269.5144 12.011713
6700 16738.458 0 0 5269.5146 12.011705
6750 16738.459 0 0 5269.5147 12.011696
6800 16738.459 0 0 5269.5149 12.01169
6850 16738.46 0 0 5269.515 12.011695
6900 16738.46 0 0 5269.5152 12.01171
6950 16738.46 0 0 5269.5153 12.011726
7000 16738.461 0 0 5269.5154 12.011736
7050 16738.461 0 0 5269.5155 12.011737
7100 16738.461 0 0 5269.5155 12.011728
7150 16738.461 0 0 5269.5156 12.011712
7200 16738.462 0 0 5269.5158 12.011691
7250 16738.463 0 0 5269.516 12.011676
7300 16738.463 0 0 5269.5162 12.011677
7350 16738.464 0 0 5269.5164 12.011693
7400 16738.464 0 0 5269.5165 12.011713
7450 16738.465 0 0 5269.5166 12.011729
7500 16738.465 0 0 5269.5167 12.011736
7550 16738.465 0 0 5269.5168 12.011734
7600 16738.465 0 0 5269.5168 12.011722
7650 16738.466 0 0 5269.517 12.011704
7700 16738.466 0 0 5269.5171 12.011687
7750 16738.467 0 0 5269.5173 12.011681
7800 16738.467 0 0 5269.5175 12.011687
7850 16738.468 0 0 5269.5176 12.0117
7900 16738.468 0 0 5269.5178 12.011712
7950 16738.469 0 0 5269.5179 12.011721
8000 16738.469 0 0 5269.518 12.011724
8050 16738.469 0 0 5269.5181 12.01172
8100 16738.47 0 0 5269.5182 12.011709
8150 16738.47 0 0 5269.5183 12.0117
8200 16738.47 0 0 5269.5185 12.0117
8250 16738.471 0 0 5269.5186 12.011709
8300 16738.471 0 0 5269.5187 12.011719
8350 16738.472 0 0 5269.5189 12.011723
8400 16738.472 0 0 5269.519 12.01172
8450 16738.473 -0.00039690664 0 5269.5189 12.011706
8500 16738.481 -0.0034646803 0 5269.5182 12.011643
8550 16738.483 -0.0045307409 0 5269.5178 12.011621
8600 16738.474 -0.00076532813 0 5269.5189 12.011681
8650 16738.474 0 0 5269.5197 12.011699
8700 16738.475 0 0 5269.5199 12.011715
8750 16738.475 0 0 5269.52 12.011732
8800 16738.475 0 0 5269.52 12.011743
8850 16738.476 0 0 5269.5201 12.011744
8900 16738.476 0 0 5269.5202 12.011735
8950 16738.476 0 0 5269.5203 12.011719
9000 16738.477 0 0 5269.5205 12.011698
9050 16738.477 0 0 5269.5206 12.011683
9100 16738.478 0 0 5269.5208 12.011684
9150 16738.479 0 0 5269.521 12.011701
9200 16738.479 0 0 5269.5212 12.011722
9250 16738.479 0 0 5269.5213 12.011738
9300 16738.48 0 0 5269.5214 12.011746
9350 16738.48 0 0 5269.5214 12.011744
9400 16738.48 0 0 5269.5215 12.011732
9450 16738.48 0 0 5269.5216 12.011715
9500 16738.481 -0.00037652436 0 5269.5216 12.011692
9550 16738.493 -0.0053156166 0 5269.5203 12.011611
9600 16738.549 -0.026814371 0 5269.5163 12.011415
9650 16738.765 -0.10191524 0 5269.5092 12.011013
9700 16735.041 1.0589897 0 5269.4979 12.062708
9750 16738.013 0.1355014 0 5269.5101 11.407246
9800 16738.512 -0.011620325 0 5269.5201 11.394974
9850 16738.489 -0.00067270449 0 5269.5237 11.395099
9900 16738.489 -0.00024984529 0 5269.5242 11.395085
9950 16738.49 0 0 5269.5245 11.395077
10000 16738.49 0 0 5269.5246 11.395076
Loop time of 0.0974108 on 1 procs for 10000 steps with 81 atoms
Performance: 886965.415 tau/day, 102658.034 timesteps/s
96.8% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0068054 | 0.0068054 | 0.0068054 | 0.0 | 6.99
Bond | 0.00034618 | 0.00034618 | 0.00034618 | 0.0 | 0.36
Neigh | 0.033076 | 0.033076 | 0.033076 | 0.0 | 33.96
Comm | 0.0067938 | 0.0067938 | 0.0067938 | 0.0 | 6.97
Output | 0.0022905 | 0.0022905 | 0.0022905 | 0.0 | 2.35
Modify | 0.044027 | 0.044027 | 0.044027 | 0.0 | 45.20
Other | | 0.004071 | | | 4.18
Nlocal: 81 ave 81 max 81 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 84 ave 84 max 84 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0
Ave special neighs/atom = 0
Neighbor list builds = 998
Dangerous builds = 997
Total wall time: 0:00:00

349
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@ -0,0 +1,349 @@
LAMMPS (17 Feb 2022)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
# Simple rigid body system
units lj
atom_style bond
pair_style lj/cut 2.5
read_data data.rigid.small
Reading data file ...
orthogonal box = (-12 -12 -12) to (12 12 12)
1 by 2 by 2 MPI processor grid
reading atoms ...
81 atoms
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
0 = max # of 1-2 neighbors
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
1 = max # of special neighbors
special bonds CPU = 0.000 seconds
read_data CPU = 0.001 seconds
velocity all create 100.0 4928459
# unconnected bodies
group clump1 id <> 1 9
9 atoms in group clump1
group clump2 id <> 10 18
9 atoms in group clump2
group clump3 id <> 19 27
9 atoms in group clump3
group clump4 id <> 28 36
9 atoms in group clump4
group clump5 id <> 37 45
9 atoms in group clump5
group clump6 id <> 46 54
9 atoms in group clump6
group clump7 id <> 55 63
9 atoms in group clump7
group clump8 id <> 64 72
9 atoms in group clump8
group clump9 id <> 73 81
9 atoms in group clump9
fix 1 all rigid molecule
9 rigid bodies with 81 atoms
# 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
generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update every 1 steps, delay 10 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 = 18 18 18
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 5.08 | 5.112 | 5.206 Mbytes
Step Temp E_pair E_mol TotEng Press
0 115.29439 5235.9179 0 5272.2142 -2.7403788
50 14910.685 571.71558 0 5265.82 32.006171
100 16298.442 136.66184 0 5267.653 16.444229
150 16682.606 17.490511 0 5269.4219 14.900344
200 16733.929 1.372872 0 5269.4617 14.569267
250 16738.853 -0.15252816 0 5269.4864 14.496404
300 16738.588 -0.055171335 0 5269.5002 14.496025
350 16738.492 -0.017444677 0 5269.5077 14.496446
400 16738.464 -0.0060102023 0 5269.5104 14.496618
450 16738.455 -0.0012713351 0 5269.5124 14.496701
500 16738.455 -0.00081068621 0 5269.5128 14.496709
550 16738.455 -0.00083203497 0 5269.5129 14.496707
600 16738.455 -0.00058355356 0 5269.5131 14.496709
650 16738.455 -0.00047226704 0 5269.5131 14.496708
700 16738.455 0 0 5269.5136 14.496713
750 16738.455 0 0 5269.5136 14.49671
800 16738.455 0 0 5269.5137 14.496709
850 16738.455 0 0 5269.5137 14.49671
900 16738.456 0 0 5269.5138 14.496713
950 16738.462 -0.0035323872 0 5269.5122 14.496671
1000 16738.586 -0.051135144 0 5269.5036 14.496229
1050 16737.358 0.32995057 0 5269.4981 14.525763
1100 16737.892 0.16210246 0 5269.4984 14.531983
1150 16738.703 -0.089235095 0 5269.5025 14.509899
1200 16738.466 -0.0075446243 0 5269.5096 14.510615
1250 16738.456 0 0 5269.514 14.510704
1300 16738.457 0 0 5269.5141 14.510701
1350 16738.457 0 0 5269.5141 14.510699
1400 16738.457 -0.00044736511 0 5269.5138 14.510693
1450 16738.458 -0.0010971179 0 5269.5134 14.510687
1500 16738.458 -0.00057885428 0 5269.5139 14.510698
1550 16738.457 0 0 5269.5143 14.51071
1600 16738.457 0 0 5269.5144 14.510712
1650 16738.457 0 0 5269.5144 14.510712
1700 16738.458 0 0 5269.5144 14.51071
1750 16738.458 0 0 5269.5145 14.510708
1800 16738.458 0 0 5269.5145 14.510706
1850 16738.458 0 0 5269.5146 14.510705
1900 16738.458 0 0 5269.5146 14.510706
1950 16738.465 -0.0031733615 0 5269.5134 14.510659
2000 16738.491 -0.013255268 0 5269.5117 14.510532
2050 16738.556 -0.0365811 0 5269.5087 14.51029
2100 16738.633 -0.063209659 0 5269.5065 14.510219
2150 16738.607 -0.05601761 0 5269.5055 14.510231
2200 16738.557 -0.038423032 0 5269.5072 14.510404
2250 16738.515 -0.023709918 0 5269.5088 14.510539
2300 16738.489 -0.013249035 0 5269.5111 14.510621
2350 16738.468 -0.0045563719 0 5269.5131 14.510714
2400 16738.46 -0.00052194273 0 5269.5146 14.510771
2450 16738.464 -0.0023259756 0 5269.514 14.510746
2500 16738.468 -0.0051929186 0 5269.5127 14.510731
2550 16738.581 -0.044940117 0 5269.5085 14.510315
2600 16738.427 -7.9722775e-05 0 5269.5046 14.510657
2650 16733.017 1.705148 0 5269.5067 14.596295
2700 16738.761 -0.10614946 0 5269.5038 14.499584
2750 16733.973 1.4038179 0 5269.5064 14.598107
2800 16738.585 -0.046813448 0 5269.5076 14.511073
2850 16738.487 -0.012558719 0 5269.5111 14.510111
2900 16738.465 -0.0026252725 0 5269.514 14.510277
2950 16738.476 -0.0082220764 0 5269.512 14.510223
3000 16738.66 -0.071284779 0 5269.507 14.509758
3050 16715.332 7.2419352 0 5269.476 14.870305
3100 16653.226 26.818761 0 5269.5009 14.496764
3150 16739.351 -0.30690375 0 5269.4886 13.643904
3200 16733.238 1.6025328 0 5269.4737 12.016934
3250 16734.374 1.2554429 0 5269.4841 11.963561
3300 16732.156 1.9585967 0 5269.4893 12.234024
3350 16738.655 -0.079693236 0 5269.497 12.092757
3400 16738.543 -0.042215005 0 5269.4991 12.092809
3450 16738.591 -0.059327511 0 5269.4972 12.092536
3500 16738.759 -0.11761245 0 5269.4918 12.09203
3550 16713.405 7.8460621 0 5269.4737 12.389816
3600 16734.939 1.0821936 0 5269.4891 12.173591
3650 16738.808 -0.13663194 0 5269.4882 12.027009
3700 16738.602 -0.070934367 0 5269.4889 12.025288
3750 16737.731 0.20706556 0 5269.4927 12.061948
3800 16738.578 -0.05582043 0 5269.4965 12.035665
3850 16738.471 -0.016307928 0 5269.5024 12.035302
3900 16738.449 -0.0058182199 0 5269.5059 12.035401
3950 16738.439 -0.0012027325 0 5269.5074 12.035461
4000 16738.436 -0.00020698452 0 5269.5075 12.035469
4050 16738.437 0 0 5269.5078 12.035454
4100 16738.437 0 0 5269.508 12.035435
4150 16738.438 0 0 5269.5081 12.035426
4200 16738.438 0 0 5269.5083 12.035432
4250 16738.439 0 0 5269.5085 12.035447
4300 16738.439 0 0 5269.5086 12.035463
4350 16738.44 0 0 5269.5087 12.035474
4400 16738.44 0 0 5269.5088 12.035478
4450 16738.44 0 0 5269.5089 12.035474
4500 16738.44 0 0 5269.509 12.035462
4550 16738.441 0 0 5269.5092 12.035449
4600 16738.441 0 0 5269.5093 12.035445
4650 16738.442 0 0 5269.5095 12.035451
4700 16738.442 0 0 5269.5096 12.03546
4750 16738.443 0 0 5269.5097 12.035465
4800 16738.443 0 0 5269.5098 12.035466
4850 16738.443 0 0 5269.51 12.035463
4900 16738.444 0 0 5269.5101 12.035456
4950 16738.444 0 0 5269.5102 12.035447
5000 16738.445 0 0 5269.5104 12.03544
5050 16738.445 0 0 5269.5105 12.035442
5100 16738.446 0 0 5269.5107 12.035455
5150 16738.446 0 0 5269.5108 12.03547
5200 16738.446 0 0 5269.5109 12.035479
5250 16738.447 0 0 5269.511 12.035479
5300 16738.447 0 0 5269.5111 12.03547
5350 16738.447 0 0 5269.5112 12.035454
5400 16738.448 0 0 5269.5113 12.035434
5450 16738.448 0 0 5269.5115 12.03542
5500 16738.449 0 0 5269.5117 12.035422
5550 16738.457 -0.0030919234 0 5269.5111 12.035383
5600 16738.51 -0.021618357 0 5269.5092 12.035106
5650 16738.622 -0.059214788 0 5269.507 12.035694
5700 16395.28 108.06941 0 5269.5463 24.369038
5750 16738.544 -0.033973429 0 5269.5077 12.011261
5800 16738.456 -0.0037013529 0 5269.5102 12.011675
5850 16738.451 0 0 5269.5123 12.011709
5900 16738.451 -0.00022115871 0 5269.5122 12.011687
5950 16738.452 -0.00024253349 0 5269.5124 12.011678
6000 16738.452 0 0 5269.5128 12.011688
6050 16738.453 0 0 5269.513 12.011702
6100 16738.453 0 0 5269.5131 12.011716
6150 16738.454 0 0 5269.5132 12.011725
6200 16738.454 0 0 5269.5133 12.011728
6250 16738.454 0 0 5269.5134 12.011723
6300 16738.455 0 0 5269.5135 12.011712
6350 16738.455 0 0 5269.5137 12.0117
6400 16738.456 0 0 5269.5138 12.011697
6450 16738.456 0 0 5269.514 12.011704
6500 16738.456 0 0 5269.5141 12.011714
6550 16738.457 0 0 5269.5142 12.011719
6600 16738.457 0 0 5269.5143 12.011718
6650 16738.458 0 0 5269.5144 12.011713
6700 16738.458 0 0 5269.5146 12.011705
6750 16738.459 0 0 5269.5147 12.011696
6800 16738.459 0 0 5269.5149 12.01169
6850 16738.46 0 0 5269.515 12.011695
6900 16738.46 0 0 5269.5152 12.01171
6950 16738.46 0 0 5269.5153 12.011726
7000 16738.461 0 0 5269.5154 12.011736
7050 16738.461 0 0 5269.5155 12.011737
7100 16738.461 0 0 5269.5155 12.011728
7150 16738.461 0 0 5269.5156 12.011712
7200 16738.462 0 0 5269.5158 12.011691
7250 16738.463 0 0 5269.516 12.011676
7300 16738.463 0 0 5269.5162 12.011677
7350 16738.464 0 0 5269.5164 12.011693
7400 16738.464 0 0 5269.5165 12.011713
7450 16738.465 0 0 5269.5166 12.011729
7500 16738.465 0 0 5269.5167 12.011736
7550 16738.465 0 0 5269.5168 12.011734
7600 16738.465 0 0 5269.5168 12.011722
7650 16738.466 0 0 5269.517 12.011704
7700 16738.466 0 0 5269.5171 12.011687
7750 16738.467 0 0 5269.5173 12.011681
7800 16738.467 0 0 5269.5175 12.011687
7850 16738.468 0 0 5269.5176 12.0117
7900 16738.468 0 0 5269.5178 12.011712
7950 16738.469 0 0 5269.5179 12.011721
8000 16738.469 0 0 5269.518 12.011724
8050 16738.469 0 0 5269.5181 12.01172
8100 16738.47 0 0 5269.5182 12.011709
8150 16738.47 0 0 5269.5183 12.0117
8200 16738.47 0 0 5269.5185 12.0117
8250 16738.471 0 0 5269.5186 12.011709
8300 16738.471 0 0 5269.5187 12.011719
8350 16738.472 0 0 5269.5189 12.011723
8400 16738.472 0 0 5269.519 12.01172
8450 16738.473 -0.00039690662 0 5269.5189 12.011706
8500 16738.481 -0.0034646802 0 5269.5182 12.011643
8550 16738.483 -0.004530741 0 5269.5178 12.01162
8600 16738.474 -0.00076532815 0 5269.5189 12.011681
8650 16738.474 0 0 5269.5197 12.011699
8700 16738.475 0 0 5269.5199 12.011715
8750 16738.475 0 0 5269.52 12.011732
8800 16738.475 0 0 5269.52 12.011743
8850 16738.476 0 0 5269.5201 12.011744
8900 16738.476 0 0 5269.5202 12.011735
8950 16738.476 0 0 5269.5203 12.011719
9000 16738.477 0 0 5269.5205 12.011698
9050 16738.477 0 0 5269.5206 12.011683
9100 16738.478 0 0 5269.5208 12.011684
9150 16738.479 0 0 5269.521 12.011701
9200 16738.479 0 0 5269.5212 12.011722
9250 16738.479 0 0 5269.5213 12.011738
9300 16738.48 0 0 5269.5214 12.011746
9350 16738.48 0 0 5269.5214 12.011744
9400 16738.48 0 0 5269.5215 12.011732
9450 16738.48 0 0 5269.5216 12.011715
9500 16738.481 -0.00037652439 0 5269.5216 12.011692
9550 16738.493 -0.0053156171 0 5269.5203 12.011611
9600 16738.549 -0.026814373 0 5269.5163 12.011415
9650 16738.765 -0.10191525 0 5269.5092 12.011013
9700 16735.041 1.0589908 0 5269.4979 12.062708
9750 16738.013 0.13550139 0 5269.5101 11.407247
9800 16738.512 -0.011620323 0 5269.5201 11.394975
9850 16738.489 -0.00067270407 0 5269.5237 11.395099
9900 16738.489 -0.00024984518 0 5269.5242 11.395086
9950 16738.49 0 0 5269.5245 11.395077
10000 16738.49 0 0 5269.5246 11.395076
Loop time of 0.102079 on 4 procs for 10000 steps with 81 atoms
Performance: 846406.333 tau/day, 97963.696 timesteps/s
98.7% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0015357 | 0.0020418 | 0.0024561 | 0.7 | 2.00
Bond | 0.00030031 | 0.00031957 | 0.00034464 | 0.0 | 0.31
Neigh | 0.0091719 | 0.0094934 | 0.010243 | 0.4 | 9.30
Comm | 0.038015 | 0.041242 | 0.043481 | 1.1 | 40.40
Output | 0.002223 | 0.0024412 | 0.0030738 | 0.7 | 2.39
Modify | 0.040725 | 0.042557 | 0.043982 | 0.7 | 41.69
Other | | 0.003983 | | | 3.90
Nlocal: 20.25 ave 38 max 3 min
Histogram: 1 0 1 0 0 0 1 0 0 1
Nghost: 27.25 ave 48 max 13 min
Histogram: 1 0 1 1 0 0 0 0 0 1
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0
Ave special neighs/atom = 0
Neighbor list builds = 998
Dangerous builds = 997
Total wall time: 0:00:00

0
examples/rigid/log.20Mar22.rigid.rigid.molecule.g++.1 Normal file
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0
examples/rigid/log.20Mar22.rigid.rigid.molecule.g++.4 Normal file
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examples/rigid/log.20Mar22.rigid.small.g++.1 Normal file
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@ -0,0 +1,322 @@
LAMMPS (17 Feb 2022)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
# Simple rigid body system
units lj
atom_style bond
pair_style lj/cut 2.5
read_data data.rigid.small
Reading data file ...
orthogonal box = (-12 -12 -12) to (12 12 12)
1 by 1 by 1 MPI processor grid
reading atoms ...
81 atoms
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
0 = max # of 1-2 neighbors
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
1 = max # of special neighbors
special bonds CPU = 0.000 seconds
read_data CPU = 0.001 seconds
velocity all create 100.0 4928459
# unconnected bodies
group clump1 id <> 1 9
9 atoms in group clump1
group clump2 id <> 10 18
9 atoms in group clump2
group clump3 id <> 19 27
9 atoms in group clump3
group clump4 id <> 28 36
9 atoms in group clump4
group clump5 id <> 37 45
9 atoms in group clump5
group clump6 id <> 46 54
9 atoms in group clump6
group clump7 id <> 55 63
9 atoms in group clump7
group clump8 id <> 64 72
9 atoms in group clump8
group clump9 id <> 73 81
9 atoms in group clump9
fix 1 all rigid/small molecule
create bodies CPU = 0.000 seconds
9 rigid bodies with 81 atoms
1.2247449 = max distance from body owner to body atom
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
generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update every 1 steps, delay 10 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 = 18 18 18
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 9.034 | 9.034 | 9.034 Mbytes
Step Temp E_pair E_mol TotEng Press
0 115.29439 5235.9179 0 5272.2142 -2.7403788
50 14910.685 571.71558 0 5265.82 32.006171
100 16298.442 136.66184 0 5267.653 16.444229
150 16682.606 17.490511 0 5269.4219 14.900344
200 16733.929 1.372872 0 5269.4617 14.569267
250 16738.853 -0.15252816 0 5269.4864 14.496404
300 16738.588 -0.055171335 0 5269.5002 14.496025
350 16738.492 -0.017444677 0 5269.5077 14.496446
400 16738.464 -0.0060102023 0 5269.5104 14.496618
450 16738.455 -0.0012713351 0 5269.5124 14.496701
500 16738.455 -0.00081068621 0 5269.5128 14.496709
550 16738.455 -0.00083203497 0 5269.5129 14.496707
600 16738.455 -0.00058355356 0 5269.5131 14.496709
650 16738.455 -0.00047226704 0 5269.5131 14.496708
700 16738.455 0 0 5269.5136 14.496713
750 16738.455 0 0 5269.5136 14.49671
800 16738.455 0 0 5269.5137 14.496709
850 16738.455 0 0 5269.5137 14.49671
900 16738.456 0 0 5269.5138 14.496713
950 16738.462 -0.0035323872 0 5269.5122 14.496671
1000 16738.586 -0.051135144 0 5269.5036 14.496229
1050 16737.358 0.32995057 0 5269.4981 14.525763
1100 16737.892 0.16210246 0 5269.4984 14.531983
1150 16738.703 -0.089235095 0 5269.5025 14.509899
1200 16738.466 -0.0075446243 0 5269.5096 14.510615
1250 16738.456 0 0 5269.514 14.510704
1300 16738.457 0 0 5269.5141 14.510701
1350 16738.457 0 0 5269.5141 14.510699
1400 16738.457 -0.00044736511 0 5269.5138 14.510693
1450 16738.458 -0.0010971179 0 5269.5134 14.510687
1500 16738.458 -0.00057885428 0 5269.5139 14.510698
1550 16738.457 0 0 5269.5143 14.51071
1600 16738.457 0 0 5269.5144 14.510712
1650 16738.457 0 0 5269.5144 14.510712
1700 16738.458 0 0 5269.5144 14.51071
1750 16738.458 0 0 5269.5145 14.510708
1800 16738.458 0 0 5269.5145 14.510706
1850 16738.458 0 0 5269.5146 14.510705
1900 16738.458 0 0 5269.5146 14.510706
1950 16738.465 -0.0031733615 0 5269.5134 14.510659
2000 16738.491 -0.013255268 0 5269.5117 14.510532
2050 16738.556 -0.0365811 0 5269.5087 14.51029
2100 16738.633 -0.063209659 0 5269.5065 14.510219
2150 16738.607 -0.05601761 0 5269.5055 14.510231
2200 16738.557 -0.038423032 0 5269.5072 14.510404
2250 16738.515 -0.023709918 0 5269.5088 14.510539
2300 16738.489 -0.013249035 0 5269.5111 14.510621
2350 16738.468 -0.0045563719 0 5269.5131 14.510714
2400 16738.46 -0.00052194273 0 5269.5146 14.510771
2450 16738.464 -0.0023259756 0 5269.514 14.510746
2500 16738.468 -0.0051929186 0 5269.5127 14.510731
2550 16738.581 -0.044940117 0 5269.5085 14.510315
2600 16738.427 -7.9722826e-05 0 5269.5046 14.510657
2650 16733.017 1.7051479 0 5269.5067 14.596295
2700 16738.761 -0.10614946 0 5269.5038 14.499584
2750 16733.973 1.4038179 0 5269.5064 14.598107
2800 16738.585 -0.046813448 0 5269.5076 14.511073
2850 16738.487 -0.012558719 0 5269.5111 14.510111
2900 16738.465 -0.0026252725 0 5269.514 14.510277
2950 16738.476 -0.0082220764 0 5269.512 14.510223
3000 16738.66 -0.071284779 0 5269.507 14.509758
3050 16715.332 7.2419352 0 5269.476 14.870305
3100 16653.226 26.818761 0 5269.5009 14.496764
3150 16739.351 -0.30690375 0 5269.4886 13.643904
3200 16733.238 1.6025328 0 5269.4737 12.016934
3250 16734.374 1.255443 0 5269.4841 11.963561
3300 16732.156 1.9585966 0 5269.4893 12.234024
3350 16738.655 -0.079693235 0 5269.497 12.092757
3400 16738.543 -0.042215005 0 5269.4991 12.092809
3450 16738.591 -0.05932751 0 5269.4972 12.092536
3500 16738.759 -0.11761245 0 5269.4918 12.092031
3550 16713.405 7.8460623 0 5269.4737 12.389816
3600 16734.939 1.0821936 0 5269.4891 12.173591
3650 16738.808 -0.13663192 0 5269.4882 12.027009
3700 16738.602 -0.070934371 0 5269.4889 12.025288
3750 16737.731 0.20706562 0 5269.4927 12.061948
3800 16738.578 -0.05582043 0 5269.4965 12.035665
3850 16738.471 -0.016307928 0 5269.5024 12.035302
3900 16738.449 -0.0058182199 0 5269.5059 12.035401
3950 16738.439 -0.0012027325 0 5269.5074 12.035461
4000 16738.436 -0.00020698452 0 5269.5075 12.035469
4050 16738.437 0 0 5269.5078 12.035454
4100 16738.437 0 0 5269.508 12.035435
4150 16738.438 0 0 5269.5081 12.035426
4200 16738.438 0 0 5269.5083 12.035432
4250 16738.439 0 0 5269.5085 12.035447
4300 16738.439 0 0 5269.5086 12.035463
4350 16738.44 0 0 5269.5087 12.035474
4400 16738.44 0 0 5269.5088 12.035478
4450 16738.44 0 0 5269.5089 12.035474
4500 16738.44 0 0 5269.509 12.035462
4550 16738.441 0 0 5269.5092 12.035449
4600 16738.441 0 0 5269.5093 12.035445
4650 16738.442 0 0 5269.5095 12.035451
4700 16738.442 0 0 5269.5096 12.03546
4750 16738.443 0 0 5269.5097 12.035465
4800 16738.443 0 0 5269.5098 12.035466
4850 16738.443 0 0 5269.51 12.035463
4900 16738.444 0 0 5269.5101 12.035456
4950 16738.444 0 0 5269.5102 12.035447
5000 16738.445 0 0 5269.5104 12.03544
5050 16738.445 0 0 5269.5105 12.035442
5100 16738.446 0 0 5269.5107 12.035455
5150 16738.446 0 0 5269.5108 12.03547
5200 16738.446 0 0 5269.5109 12.035479
5250 16738.447 0 0 5269.511 12.035479
5300 16738.447 0 0 5269.5111 12.03547
5350 16738.447 0 0 5269.5112 12.035454
5400 16738.448 0 0 5269.5113 12.035434
5450 16738.448 0 0 5269.5115 12.03542
5500 16738.449 0 0 5269.5117 12.035422
5550 16738.457 -0.0030919234 0 5269.5111 12.035383
5600 16738.51 -0.021618357 0 5269.5092 12.035106
5650 16738.622 -0.059214788 0 5269.507 12.035694
5700 16395.28 108.06942 0 5269.5463 24.369038
5750 16738.544 -0.033973429 0 5269.5077 12.011261
5800 16738.456 -0.0037013529 0 5269.5102 12.011675
5850 16738.451 0 0 5269.5123 12.011709
5900 16738.451 -0.0002211587 0 5269.5122 12.011687
5950 16738.452 -0.00024253348 0 5269.5124 12.011678
6000 16738.452 0 0 5269.5128 12.011688
6050 16738.453 0 0 5269.513 12.011702
6100 16738.453 0 0 5269.5131 12.011716
6150 16738.454 0 0 5269.5132 12.011725
6200 16738.454 0 0 5269.5133 12.011728
6250 16738.454 0 0 5269.5134 12.011723
6300 16738.455 0 0 5269.5135 12.011712
6350 16738.455 0 0 5269.5137 12.0117
6400 16738.456 0 0 5269.5138 12.011697
6450 16738.456 0 0 5269.514 12.011704
6500 16738.456 0 0 5269.5141 12.011714
6550 16738.457 0 0 5269.5142 12.011719
6600 16738.457 0 0 5269.5143 12.011718
6650 16738.458 0 0 5269.5144 12.011713
6700 16738.458 0 0 5269.5146 12.011705
6750 16738.459 0 0 5269.5147 12.011696
6800 16738.459 0 0 5269.5149 12.01169
6850 16738.46 0 0 5269.515 12.011695
6900 16738.46 0 0 5269.5152 12.01171
6950 16738.46 0 0 5269.5153 12.011726
7000 16738.461 0 0 5269.5154 12.011736
7050 16738.461 0 0 5269.5155 12.011737
7100 16738.461 0 0 5269.5155 12.011728
7150 16738.461 0 0 5269.5156 12.011712
7200 16738.462 0 0 5269.5158 12.011691
7250 16738.463 0 0 5269.516 12.011676
7300 16738.463 0 0 5269.5162 12.011677
7350 16738.464 0 0 5269.5164 12.011693
7400 16738.464 0 0 5269.5165 12.011713
7450 16738.465 0 0 5269.5166 12.011729
7500 16738.465 0 0 5269.5167 12.011736
7550 16738.465 0 0 5269.5168 12.011734
7600 16738.465 0 0 5269.5168 12.011722
7650 16738.466 0 0 5269.517 12.011704
7700 16738.466 0 0 5269.5171 12.011687
7750 16738.467 0 0 5269.5173 12.011681
7800 16738.467 0 0 5269.5175 12.011687
7850 16738.468 0 0 5269.5176 12.0117
7900 16738.468 0 0 5269.5178 12.011712
7950 16738.469 0 0 5269.5179 12.011721
8000 16738.469 0 0 5269.518 12.011724
8050 16738.469 0 0 5269.5181 12.01172
8100 16738.47 0 0 5269.5182 12.011709
8150 16738.47 0 0 5269.5183 12.0117
8200 16738.47 0 0 5269.5185 12.0117
8250 16738.471 0 0 5269.5186 12.011709
8300 16738.471 0 0 5269.5187 12.011719
8350 16738.472 0 0 5269.5189 12.011723
8400 16738.472 0 0 5269.519 12.01172
8450 16738.473 -0.00039690678 0 5269.5189 12.011706
8500 16738.481 -0.0034646809 0 5269.5182 12.011643
8550 16738.483 -0.0045307407 0 5269.5178 12.011621
8600 16738.474 -0.00076532803 0 5269.5189 12.011681
8650 16738.474 0 0 5269.5197 12.011699
8700 16738.475 0 0 5269.5199 12.011715
8750 16738.475 0 0 5269.52 12.011732
8800 16738.475 0 0 5269.52 12.011743
8850 16738.476 0 0 5269.5201 12.011744
8900 16738.476 0 0 5269.5202 12.011735
8950 16738.476 0 0 5269.5203 12.011719
9000 16738.477 0 0 5269.5205 12.011698
9050 16738.477 0 0 5269.5206 12.011683
9100 16738.478 0 0 5269.5208 12.011684
9150 16738.479 0 0 5269.521 12.011701
9200 16738.479 0 0 5269.5212 12.011722
9250 16738.479 0 0 5269.5213 12.011738
9300 16738.48 0 0 5269.5214 12.011746
9350 16738.48 0 0 5269.5214 12.011744
9400 16738.48 0 0 5269.5215 12.011732
9450 16738.48 0 0 5269.5216 12.011715
9500 16738.481 -0.0003765242 0 5269.5216 12.011692
9550 16738.493 -0.0053156153 0 5269.5203 12.011611
9600 16738.549 -0.026814361 0 5269.5163 12.011415
9650 16738.765 -0.1019152 0 5269.5092 12.011013
9700 16735.041 1.0589855 0 5269.4979 12.062708
9750 16738.013 0.13550223 0 5269.5101 11.407246
9800 16738.512 -0.01162033 0 5269.5201 11.394974
9850 16738.489 -0.000672705 0 5269.5237 11.395098
9900 16738.489 -0.00024984511 0 5269.5242 11.395085
9950 16738.49 0 0 5269.5245 11.395077
10000 16738.49 0 0 5269.5246 11.395075
Loop time of 0.097001 on 1 procs for 10000 steps with 81 atoms
Performance: 890712.494 tau/day, 103091.724 timesteps/s
99.6% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0064264 | 0.0064264 | 0.0064264 | 0.0 | 6.63
Bond | 0.0003385 | 0.0003385 | 0.0003385 | 0.0 | 0.35
Neigh | 0.030894 | 0.030894 | 0.030894 | 0.0 | 31.85
Comm | 0.0065732 | 0.0065732 | 0.0065732 | 0.0 | 6.78
Output | 0.0021773 | 0.0021773 | 0.0021773 | 0.0 | 2.24
Modify | 0.046477 | 0.046477 | 0.046477 | 0.0 | 47.91
Other | | 0.004115 | | | 4.24
Nlocal: 81 ave 81 max 81 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 84 ave 84 max 84 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0
Ave special neighs/atom = 0
Neighbor list builds = 998
Dangerous builds = 997
Total wall time: 0:00:00

322
examples/rigid/log.20Mar22.rigid.small.g++.4 Normal file
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LAMMPS (17 Feb 2022)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
# Simple rigid body system
units lj
atom_style bond
pair_style lj/cut 2.5
read_data data.rigid.small
Reading data file ...
orthogonal box = (-12 -12 -12) to (12 12 12)
1 by 2 by 2 MPI processor grid
reading atoms ...
81 atoms
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
0 = max # of 1-2 neighbors
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
1 = max # of special neighbors
special bonds CPU = 0.000 seconds
read_data CPU = 0.001 seconds
velocity all create 100.0 4928459
# unconnected bodies
group clump1 id <> 1 9
9 atoms in group clump1
group clump2 id <> 10 18
9 atoms in group clump2
group clump3 id <> 19 27
9 atoms in group clump3
group clump4 id <> 28 36
9 atoms in group clump4
group clump5 id <> 37 45
9 atoms in group clump5
group clump6 id <> 46 54
9 atoms in group clump6
group clump7 id <> 55 63
9 atoms in group clump7
group clump8 id <> 64 72
9 atoms in group clump8
group clump9 id <> 73 81
9 atoms in group clump9
fix 1 all rigid/small molecule
create bodies CPU = 0.000 seconds
9 rigid bodies with 81 atoms
1.2247449 = max distance from body owner to body atom
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
generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update every 1 steps, delay 10 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 = 18 18 18
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 8.892 | 8.94 | 9.049 Mbytes
Step Temp E_pair E_mol TotEng Press
0 115.29439 5235.9179 0 5272.2142 -2.7403788
50 14910.685 571.71558 0 5265.82 32.006171
100 16298.442 136.66184 0 5267.653 16.444229
150 16682.606 17.490511 0 5269.4219 14.900344
200 16733.929 1.372872 0 5269.4617 14.569267
250 16738.853 -0.15252816 0 5269.4864 14.496404
300 16738.588 -0.055171335 0 5269.5002 14.496025
350 16738.492 -0.017444677 0 5269.5077 14.496446
400 16738.464 -0.0060102023 0 5269.5104 14.496618
450 16738.455 -0.0012713351 0 5269.5124 14.496701
500 16738.455 -0.00081068621 0 5269.5128 14.496709
550 16738.455 -0.00083203497 0 5269.5129 14.496707
600 16738.455 -0.00058355356 0 5269.5131 14.496709
650 16738.455 -0.00047226704 0 5269.5131 14.496708
700 16738.455 0 0 5269.5136 14.496713
750 16738.455 0 0 5269.5136 14.49671
800 16738.455 0 0 5269.5137 14.496709
850 16738.455 0 0 5269.5137 14.49671
900 16738.456 0 0 5269.5138 14.496713
950 16738.462 -0.0035323872 0 5269.5122 14.496671
1000 16738.586 -0.051135144 0 5269.5036 14.496229
1050 16737.358 0.32995057 0 5269.4981 14.525763
1100 16737.892 0.16210246 0 5269.4984 14.531983
1150 16738.703 -0.089235095 0 5269.5025 14.509899
1200 16738.466 -0.0075446243 0 5269.5096 14.510615
1250 16738.456 0 0 5269.514 14.510704
1300 16738.457 0 0 5269.5141 14.510701
1350 16738.457 0 0 5269.5141 14.510699
1400 16738.457 -0.00044736511 0 5269.5138 14.510693
1450 16738.458 -0.0010971179 0 5269.5134 14.510687
1500 16738.458 -0.00057885428 0 5269.5139 14.510698
1550 16738.457 0 0 5269.5143 14.51071
1600 16738.457 0 0 5269.5144 14.510712
1650 16738.457 0 0 5269.5144 14.510712
1700 16738.458 0 0 5269.5144 14.51071
1750 16738.458 0 0 5269.5145 14.510708
1800 16738.458 0 0 5269.5145 14.510706
1850 16738.458 0 0 5269.5146 14.510705
1900 16738.458 0 0 5269.5146 14.510706
1950 16738.465 -0.0031733615 0 5269.5134 14.510659
2000 16738.491 -0.013255268 0 5269.5117 14.510532
2050 16738.556 -0.0365811 0 5269.5087 14.51029
2100 16738.633 -0.063209659 0 5269.5065 14.510219
2150 16738.607 -0.05601761 0 5269.5055 14.510231
2200 16738.557 -0.038423032 0 5269.5072 14.510404
2250 16738.515 -0.023709918 0 5269.5088 14.510539
2300 16738.489 -0.013249035 0 5269.5111 14.510621
2350 16738.468 -0.0045563719 0 5269.5131 14.510714
2400 16738.46 -0.00052194273 0 5269.5146 14.510771
2450 16738.464 -0.0023259756 0 5269.514 14.510746
2500 16738.468 -0.0051929186 0 5269.5127 14.510731
2550 16738.581 -0.044940117 0 5269.5085 14.510315
2600 16738.427 -7.972281e-05 0 5269.5046 14.510657
2650 16733.017 1.7051479 0 5269.5067 14.596295
2700 16738.761 -0.10614946 0 5269.5038 14.499584
2750 16733.973 1.4038179 0 5269.5064 14.598107
2800 16738.585 -0.046813448 0 5269.5076 14.511073
2850 16738.487 -0.012558719 0 5269.5111 14.510111
2900 16738.465 -0.0026252725 0 5269.514 14.510277
2950 16738.476 -0.0082220764 0 5269.512 14.510223
3000 16738.66 -0.071284779 0 5269.507 14.509758
3050 16715.332 7.2419352 0 5269.476 14.870305
3100 16653.226 26.818761 0 5269.5009 14.496764
3150 16739.351 -0.30690375 0 5269.4886 13.643904
3200 16733.238 1.6025328 0 5269.4737 12.016934
3250 16734.374 1.2554429 0 5269.4841 11.963561
3300 16732.156 1.9585967 0 5269.4893 12.234024
3350 16738.655 -0.079693236 0 5269.497 12.092757
3400 16738.543 -0.042215005 0 5269.4991 12.092809
3450 16738.591 -0.059327511 0 5269.4972 12.092536
3500 16738.759 -0.11761245 0 5269.4918 12.09203
3550 16713.405 7.8460621 0 5269.4737 12.389816
3600 16734.939 1.0821936 0 5269.4891 12.173591
3650 16738.808 -0.13663194 0 5269.4882 12.027009
3700 16738.602 -0.070934368 0 5269.4889 12.025288
3750 16737.731 0.20706558 0 5269.4927 12.061948
3800 16738.578 -0.05582043 0 5269.4965 12.035665
3850 16738.471 -0.016307928 0 5269.5024 12.035302
3900 16738.449 -0.0058182199 0 5269.5059 12.035401
3950 16738.439 -0.0012027325 0 5269.5074 12.035461
4000 16738.436 -0.00020698452 0 5269.5075 12.035469
4050 16738.437 0 0 5269.5078 12.035454
4100 16738.437 0 0 5269.508 12.035435
4150 16738.438 0 0 5269.5081 12.035426
4200 16738.438 0 0 5269.5083 12.035432
4250 16738.439 0 0 5269.5085 12.035447
4300 16738.439 0 0 5269.5086 12.035463
4350 16738.44 0 0 5269.5087 12.035474
4400 16738.44 0 0 5269.5088 12.035478
4450 16738.44 0 0 5269.5089 12.035474
4500 16738.44 0 0 5269.509 12.035462
4550 16738.441 0 0 5269.5092 12.035449
4600 16738.441 0 0 5269.5093 12.035445
4650 16738.442 0 0 5269.5095 12.035451
4700 16738.442 0 0 5269.5096 12.03546
4750 16738.443 0 0 5269.5097 12.035465
4800 16738.443 0 0 5269.5098 12.035466
4850 16738.443 0 0 5269.51 12.035463
4900 16738.444 0 0 5269.5101 12.035456
4950 16738.444 0 0 5269.5102 12.035447
5000 16738.445 0 0 5269.5104 12.03544
5050 16738.445 0 0 5269.5105 12.035442
5100 16738.446 0 0 5269.5107 12.035455
5150 16738.446 0 0 5269.5108 12.03547
5200 16738.446 0 0 5269.5109 12.035479
5250 16738.447 0 0 5269.511 12.035479
5300 16738.447 0 0 5269.5111 12.03547
5350 16738.447 0 0 5269.5112 12.035454
5400 16738.448 0 0 5269.5113 12.035434
5450 16738.448 0 0 5269.5115 12.03542
5500 16738.449 0 0 5269.5117 12.035422
5550 16738.457 -0.0030919234 0 5269.5111 12.035383
5600 16738.51 -0.021618357 0 5269.5092 12.035106
5650 16738.622 -0.059214788 0 5269.507 12.035694
5700 16395.28 108.06942 0 5269.5463 24.369038
5750 16738.544 -0.033973429 0 5269.5077 12.011261
5800 16738.456 -0.0037013529 0 5269.5102 12.011675
5850 16738.451 0 0 5269.5123 12.011709
5900 16738.451 -0.0002211587 0 5269.5122 12.011687
5950 16738.452 -0.00024253349 0 5269.5124 12.011678
6000 16738.452 0 0 5269.5128 12.011688
6050 16738.453 0 0 5269.513 12.011702
6100 16738.453 0 0 5269.5131 12.011716
6150 16738.454 0 0 5269.5132 12.011725
6200 16738.454 0 0 5269.5133 12.011728
6250 16738.454 0 0 5269.5134 12.011723
6300 16738.455 0 0 5269.5135 12.011712
6350 16738.455 0 0 5269.5137 12.0117
6400 16738.456 0 0 5269.5138 12.011697
6450 16738.456 0 0 5269.514 12.011704
6500 16738.456 0 0 5269.5141 12.011714
6550 16738.457 0 0 5269.5142 12.011719
6600 16738.457 0 0 5269.5143 12.011718
6650 16738.458 0 0 5269.5144 12.011713
6700 16738.458 0 0 5269.5146 12.011705
6750 16738.459 0 0 5269.5147 12.011696
6800 16738.459 0 0 5269.5149 12.01169
6850 16738.46 0 0 5269.515 12.011695
6900 16738.46 0 0 5269.5152 12.01171
6950 16738.46 0 0 5269.5153 12.011726
7000 16738.461 0 0 5269.5154 12.011736
7050 16738.461 0 0 5269.5155 12.011737
7100 16738.461 0 0 5269.5155 12.011728
7150 16738.461 0 0 5269.5156 12.011712
7200 16738.462 0 0 5269.5158 12.011691
7250 16738.463 0 0 5269.516 12.011676
7300 16738.463 0 0 5269.5162 12.011677
7350 16738.464 0 0 5269.5164 12.011693
7400 16738.464 0 0 5269.5165 12.011713
7450 16738.465 0 0 5269.5166 12.011729
7500 16738.465 0 0 5269.5167 12.011736
7550 16738.465 0 0 5269.5168 12.011734
7600 16738.465 0 0 5269.5168 12.011722
7650 16738.466 0 0 5269.517 12.011704
7700 16738.466 0 0 5269.5171 12.011687
7750 16738.467 0 0 5269.5173 12.011681
7800 16738.467 0 0 5269.5175 12.011687
7850 16738.468 0 0 5269.5176 12.0117
7900 16738.468 0 0 5269.5178 12.011712
7950 16738.469 0 0 5269.5179 12.011721
8000 16738.469 0 0 5269.518 12.011724
8050 16738.469 0 0 5269.5181 12.01172
8100 16738.47 0 0 5269.5182 12.011709
8150 16738.47 0 0 5269.5183 12.0117
8200 16738.47 0 0 5269.5185 12.0117
8250 16738.471 0 0 5269.5186 12.011709
8300 16738.471 0 0 5269.5187 12.011719
8350 16738.472 0 0 5269.5189 12.011723
8400 16738.472 0 0 5269.519 12.01172
8450 16738.473 -0.00039690665 0 5269.5189 12.011706
8500 16738.481 -0.0034646804 0 5269.5182 12.011643
8550 16738.483 -0.0045307409 0 5269.5178 12.011621
8600 16738.474 -0.00076532812 0 5269.5189 12.011681
8650 16738.474 0 0 5269.5197 12.011699
8700 16738.475 0 0 5269.5199 12.011715
8750 16738.475 0 0 5269.52 12.011732
8800 16738.475 0 0 5269.52 12.011743
8850 16738.476 0 0 5269.5201 12.011744
8900 16738.476 0 0 5269.5202 12.011735
8950 16738.476 0 0 5269.5203 12.011719
9000 16738.477 0 0 5269.5205 12.011698
9050 16738.477 0 0 5269.5206 12.011683
9100 16738.478 0 0 5269.5208 12.011684
9150 16738.479 0 0 5269.521 12.011701
9200 16738.479 0 0 5269.5212 12.011722
9250 16738.479 0 0 5269.5213 12.011738
9300 16738.48 0 0 5269.5214 12.011746
9350 16738.48 0 0 5269.5214 12.011744
9400 16738.48 0 0 5269.5215 12.011732
9450 16738.48 0 0 5269.5216 12.011715
9500 16738.481 -0.00037652435 0 5269.5216 12.011692
9550 16738.493 -0.0053156165 0 5269.5203 12.011611
9600 16738.549 -0.02681437 0 5269.5163 12.011415
9650 16738.765 -0.10191523 0 5269.5092 12.011013
9700 16735.041 1.0589893 0 5269.4979 12.062708
9750 16738.013 0.1355014 0 5269.5101 11.407246
9800 16738.512 -0.011620326 0 5269.5201 11.394974
9850 16738.489 -0.00067270465 0 5269.5237 11.395099
9900 16738.489 -0.00024984533 0 5269.5242 11.395085
9950 16738.49 0 0 5269.5245 11.395077
10000 16738.49 0 0 5269.5246 11.395076
Loop time of 0.115632 on 4 procs for 10000 steps with 81 atoms
Performance: 747196.558 tau/day, 86481.083 timesteps/s
98.7% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0014528 | 0.0020376 | 0.0024938 | 0.9 | 1.76
Bond | 0.00030255 | 0.00030731 | 0.00031718 | 0.0 | 0.27
Neigh | 0.0089963 | 0.0094964 | 0.010494 | 0.6 | 8.21
Comm | 0.035947 | 0.038848 | 0.040951 | 1.0 | 33.60
Output | 0.0022924 | 0.002542 | 0.0032643 | 0.8 | 2.20
Modify | 0.056743 | 0.058255 | 0.059447 | 0.4 | 50.38
Other | | 0.004146 | | | 3.59
Nlocal: 20.25 ave 38 max 3 min
Histogram: 1 0 1 0 0 0 1 0 0 1
Nghost: 27.25 ave 48 max 13 min
Histogram: 1 0 1 1 0 0 0 0 0 1
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0
Ave special neighs/atom = 0
Neighbor list builds = 998
Dangerous builds = 997
Total wall time: 0:00:00

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LAMMPS (17 Feb 2022)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
# Simple rigid body system
units lj
atom_style bond
pair_style lj/cut 2.5
read_data data.rigid.small
Reading data file ...
orthogonal box = (-12 -12 -12) to (12 12 12)
1 by 1 by 1 MPI processor grid
reading atoms ...
81 atoms
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
0 = max # of 1-2 neighbors
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
1 = max # of special neighbors
special bonds CPU = 0.000 seconds
read_data CPU = 0.001 seconds
velocity all create 100.0 4928459
# unconnected bodies
group clump1 id <> 1 9
9 atoms in group clump1
group clump2 id <> 10 18
9 atoms in group clump2
group clump3 id <> 19 27
9 atoms in group clump3
group clump4 id <> 28 36
9 atoms in group clump4
group clump5 id <> 37 45
9 atoms in group clump5
group clump6 id <> 46 54
9 atoms in group clump6
group clump7 id <> 55 63
9 atoms in group clump7
group clump8 id <> 64 72
9 atoms in group clump8
group clump9 id <> 73 81
9 atoms in group clump9
fix 1 all rigid/small molecule infile bodyinfo.dat
create bodies CPU = 0.000 seconds
9 rigid bodies with 81 atoms
1.2247449 = max distance from body owner to body atom
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
generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update every 1 steps, delay 10 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 = 18 18 18
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d
bin: standard
Reading rigid body data for 4 bodies from file bodyinfo.dat
Per MPI rank memory allocation (min/avg/max) = 9.034 | 9.034 | 9.034 Mbytes
Step Temp E_pair E_mol TotEng Press
0 115.29439 5235.9179 0 5272.2142 -2.7403788
50 14910.685 571.71558 0 5265.82 32.006171
100 16298.442 136.66184 0 5267.653 16.444229
150 16682.606 17.490511 0 5269.4219 14.900344
200 16733.929 1.372872 0 5269.4617 14.569267
250 16738.853 -0.15252816 0 5269.4864 14.496404
300 16738.588 -0.055171335 0 5269.5002 14.496025
350 16738.492 -0.017444677 0 5269.5077 14.496446
400 16738.464 -0.0060102023 0 5269.5104 14.496618
450 16738.455 -0.0012713351 0 5269.5124 14.496701
500 16738.455 -0.00081068621 0 5269.5128 14.496709
550 16738.455 -0.00083203497 0 5269.5129 14.496707
600 16738.455 -0.00058355356 0 5269.5131 14.496709
650 16738.455 -0.00047226704 0 5269.5131 14.496708
700 16738.455 0 0 5269.5136 14.496713
750 16738.455 0 0 5269.5136 14.49671
800 16738.455 0 0 5269.5137 14.496709
850 16738.455 0 0 5269.5137 14.49671
900 16738.456 0 0 5269.5138 14.496713
950 16738.462 -0.0035323872 0 5269.5122 14.496671
1000 16738.586 -0.051135144 0 5269.5036 14.496229
1050 16737.358 0.32995057 0 5269.4981 14.525763
1100 16737.892 0.16210246 0 5269.4984 14.531983
1150 16738.703 -0.089235095 0 5269.5025 14.509899
1200 16738.466 -0.0075446243 0 5269.5096 14.510615
1250 16738.456 0 0 5269.514 14.510704
1300 16738.457 0 0 5269.5141 14.510701
1350 16738.457 0 0 5269.5141 14.510699
1400 16738.457 -0.00044736511 0 5269.5138 14.510693
1450 16738.458 -0.0010971179 0 5269.5134 14.510687
1500 16738.458 -0.00057885428 0 5269.5139 14.510698
1550 16738.457 0 0 5269.5143 14.51071
1600 16738.457 0 0 5269.5144 14.510712
1650 16738.457 0 0 5269.5144 14.510712
1700 16738.458 0 0 5269.5144 14.51071
1750 16738.458 0 0 5269.5145 14.510708
1800 16738.458 0 0 5269.5145 14.510706
1850 16738.458 0 0 5269.5146 14.510705
1900 16738.458 0 0 5269.5146 14.510706
1950 16738.465 -0.0031733615 0 5269.5134 14.510659
2000 16738.491 -0.013255268 0 5269.5117 14.510532
2050 16738.556 -0.0365811 0 5269.5087 14.51029
2100 16738.633 -0.063209659 0 5269.5065 14.510219
2150 16738.607 -0.05601761 0 5269.5055 14.510231
2200 16738.557 -0.038423032 0 5269.5072 14.510404
2250 16738.515 -0.023709918 0 5269.5088 14.510539
2300 16738.489 -0.013249035 0 5269.5111 14.510621
2350 16738.468 -0.0045563719 0 5269.5131 14.510714
2400 16738.46 -0.00052194273 0 5269.5146 14.510771
2450 16738.464 -0.0023259756 0 5269.514 14.510746
2500 16738.468 -0.0051929186 0 5269.5127 14.510731
2550 16738.581 -0.044940117 0 5269.5085 14.510315
2600 16738.427 -7.9722817e-05 0 5269.5046 14.510657
2650 16733.017 1.7051479 0 5269.5067 14.596295
2700 16738.761 -0.10614946 0 5269.5038 14.499584
2750 16733.973 1.4038179 0 5269.5064 14.598107
2800 16738.585 -0.046813448 0 5269.5076 14.511073
2850 16738.487 -0.012558719 0 5269.5111 14.510111
2900 16738.465 -0.0026252725 0 5269.514 14.510277
2950 16738.476 -0.0082220764 0 5269.512 14.510223
3000 16738.66 -0.071284779 0 5269.507 14.509758
3050 16715.332 7.2419352 0 5269.476 14.870305
3100 16653.226 26.818761 0 5269.5009 14.496764
3150 16739.351 -0.30690375 0 5269.4886 13.643904
3200 16733.238 1.6025328 0 5269.4737 12.016934
3250 16734.374 1.2554429 0 5269.4841 11.963561
3300 16732.156 1.9585967 0 5269.4893 12.234024
3350 16738.655 -0.079693236 0 5269.497 12.092757
3400 16738.543 -0.042215005 0 5269.4991 12.092809
3450 16738.591 -0.05932751 0 5269.4972 12.092536
3500 16738.759 -0.11761245 0 5269.4918 12.09203
3550 16713.405 7.8460621 0 5269.4737 12.389816
3600 16734.939 1.0821936 0 5269.4891 12.173591
3650 16738.808 -0.13663194 0 5269.4882 12.027009
3700 16738.602 -0.070934369 0 5269.4889 12.025288
3750 16737.731 0.20706559 0 5269.4927 12.061948
3800 16738.578 -0.05582043 0 5269.4965 12.035665
3850 16738.471 -0.016307928 0 5269.5024 12.035302
3900 16738.449 -0.0058182199 0 5269.5059 12.035401
3950 16738.439 -0.0012027325 0 5269.5074 12.035461
4000 16738.436 -0.00020698452 0 5269.5075 12.035469
4050 16738.437 0 0 5269.5078 12.035454
4100 16738.437 0 0 5269.508 12.035435
4150 16738.438 0 0 5269.5081 12.035426
4200 16738.438 0 0 5269.5083 12.035432
4250 16738.439 0 0 5269.5085 12.035447
4300 16738.439 0 0 5269.5086 12.035463
4350 16738.44 0 0 5269.5087 12.035474
4400 16738.44 0 0 5269.5088 12.035478
4450 16738.44 0 0 5269.5089 12.035474
4500 16738.44 0 0 5269.509 12.035462
4550 16738.441 0 0 5269.5092 12.035449
4600 16738.441 0 0 5269.5093 12.035445
4650 16738.442 0 0 5269.5095 12.035451
4700 16738.442 0 0 5269.5096 12.03546
4750 16738.443 0 0 5269.5097 12.035465
4800 16738.443 0 0 5269.5098 12.035466
4850 16738.443 0 0 5269.51 12.035463
4900 16738.444 0 0 5269.5101 12.035456
4950 16738.444 0 0 5269.5102 12.035447
5000 16738.445 0 0 5269.5104 12.03544
5050 16738.445 0 0 5269.5105 12.035442
5100 16738.446 0 0 5269.5107 12.035455
5150 16738.446 0 0 5269.5108 12.03547
5200 16738.446 0 0 5269.5109 12.035479
5250 16738.447 0 0 5269.511 12.035479
5300 16738.447 0 0 5269.5111 12.03547
5350 16738.447 0 0 5269.5112 12.035454
5400 16738.448 0 0 5269.5113 12.035434
5450 16738.448 0 0 5269.5115 12.03542
5500 16738.449 0 0 5269.5117 12.035422
5550 16738.457 -0.0030919234 0 5269.5111 12.035383
5600 16738.51 -0.021618357 0 5269.5092 12.035106
5650 16738.622 -0.059214788 0 5269.507 12.035694
5700 16395.28 108.06942 0 5269.5463 24.369038
5750 16738.544 -0.033973429 0 5269.5077 12.011261
5800 16738.456 -0.0037013529 0 5269.5102 12.011675
5850 16738.451 0 0 5269.5123 12.011709
5900 16738.451 -0.0002211587 0 5269.5122 12.011687
5950 16738.452 -0.00024253349 0 5269.5124 12.011678
6000 16738.452 0 0 5269.5128 12.011688
6050 16738.453 0 0 5269.513 12.011702
6100 16738.453 0 0 5269.5131 12.011716
6150 16738.454 0 0 5269.5132 12.011725
6200 16738.454 0 0 5269.5133 12.011728
6250 16738.454 0 0 5269.5134 12.011723
6300 16738.455 0 0 5269.5135 12.011712
6350 16738.455 0 0 5269.5137 12.0117
6400 16738.456 0 0 5269.5138 12.011697
6450 16738.456 0 0 5269.514 12.011704
6500 16738.456 0 0 5269.5141 12.011714
6550 16738.457 0 0 5269.5142 12.011719
6600 16738.457 0 0 5269.5143 12.011718
6650 16738.458 0 0 5269.5144 12.011713
6700 16738.458 0 0 5269.5146 12.011705
6750 16738.459 0 0 5269.5147 12.011696
6800 16738.459 0 0 5269.5149 12.01169
6850 16738.46 0 0 5269.515 12.011695
6900 16738.46 0 0 5269.5152 12.01171
6950 16738.46 0 0 5269.5153 12.011726
7000 16738.461 0 0 5269.5154 12.011736
7050 16738.461 0 0 5269.5155 12.011737
7100 16738.461 0 0 5269.5155 12.011728
7150 16738.461 0 0 5269.5156 12.011712
7200 16738.462 0 0 5269.5158 12.011691
7250 16738.463 0 0 5269.516 12.011676
7300 16738.463 0 0 5269.5162 12.011677
7350 16738.464 0 0 5269.5164 12.011693
7400 16738.464 0 0 5269.5165 12.011713
7450 16738.465 0 0 5269.5166 12.011729
7500 16738.465 0 0 5269.5167 12.011736
7550 16738.465 0 0 5269.5168 12.011734
7600 16738.465 0 0 5269.5168 12.011722
7650 16738.466 0 0 5269.517 12.011704
7700 16738.466 0 0 5269.5171 12.011687
7750 16738.467 0 0 5269.5173 12.011681
7800 16738.467 0 0 5269.5175 12.011687
7850 16738.468 0 0 5269.5176 12.0117
7900 16738.468 0 0 5269.5178 12.011712
7950 16738.469 0 0 5269.5179 12.011721
8000 16738.469 0 0 5269.518 12.011724
8050 16738.469 0 0 5269.5181 12.01172
8100 16738.47 0 0 5269.5182 12.011709
8150 16738.47 0 0 5269.5183 12.0117
8200 16738.47 0 0 5269.5185 12.0117
8250 16738.471 0 0 5269.5186 12.011709
8300 16738.471 0 0 5269.5187 12.011719
8350 16738.472 0 0 5269.5189 12.011723
8400 16738.472 0 0 5269.519 12.01172
8450 16738.473 -0.00039690668 0 5269.5189 12.011706
8500 16738.481 -0.0034646805 0 5269.5182 12.011643
8550 16738.483 -0.0045307409 0 5269.5178 12.011621
8600 16738.474 -0.0007653281 0 5269.5189 12.011681
8650 16738.474 0 0 5269.5197 12.011699
8700 16738.475 0 0 5269.5199 12.011715
8750 16738.475 0 0 5269.52 12.011732
8800 16738.475 0 0 5269.52 12.011743
8850 16738.476 0 0 5269.5201 12.011744
8900 16738.476 0 0 5269.5202 12.011735
8950 16738.476 0 0 5269.5203 12.011719
9000 16738.477 0 0 5269.5205 12.011698
9050 16738.477 0 0 5269.5206 12.011683
9100 16738.478 0 0 5269.5208 12.011684
9150 16738.479 0 0 5269.521 12.011701
9200 16738.479 0 0 5269.5212 12.011722
9250 16738.479 0 0 5269.5213 12.011738
9300 16738.48 0 0 5269.5214 12.011746
9350 16738.48 0 0 5269.5214 12.011744
9400 16738.48 0 0 5269.5215 12.011732
9450 16738.48 0 0 5269.5216 12.011715
9500 16738.481 -0.00037652432 0 5269.5216 12.011692
9550 16738.493 -0.0053156162 0 5269.5203 12.011611
9600 16738.549 -0.026814368 0 5269.5163 12.011415
9650 16738.765 -0.10191523 0 5269.5092 12.011013
9700 16735.041 1.0589884 0 5269.4979 12.062708
9750 16738.013 0.13550153 0 5269.5101 11.407246
9800 16738.512 -0.011620327 0 5269.5201 11.394974
9850 16738.489 -0.00067270481 0 5269.5237 11.395098
9900 16738.489 -0.00024984532 0 5269.5242 11.395085
9950 16738.49 0 0 5269.5245 11.395077
10000 16738.49 0 0 5269.5246 11.395075
Loop time of 0.0973982 on 1 procs for 10000 steps with 81 atoms
Performance: 887079.894 tau/day, 102671.284 timesteps/s
99.5% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0065928 | 0.0065928 | 0.0065928 | 0.0 | 6.77
Bond | 0.00033457 | 0.00033457 | 0.00033457 | 0.0 | 0.34
Neigh | 0.031245 | 0.031245 | 0.031245 | 0.0 | 32.08
Comm | 0.0065444 | 0.0065444 | 0.0065444 | 0.0 | 6.72
Output | 0.0024004 | 0.0024004 | 0.0024004 | 0.0 | 2.46
Modify | 0.045966 | 0.045966 | 0.045966 | 0.0 | 47.19
Other | | 0.004315 | | | 4.43
Nlocal: 81 ave 81 max 81 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 84 ave 84 max 84 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0
Ave special neighs/atom = 0
Neighbor list builds = 998
Dangerous builds = 997
Total wall time: 0:00:00

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LAMMPS (17 Feb 2022)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
# Simple rigid body system
units lj
atom_style bond
pair_style lj/cut 2.5
read_data data.rigid.small
Reading data file ...
orthogonal box = (-12 -12 -12) to (12 12 12)
1 by 2 by 2 MPI processor grid
reading atoms ...
81 atoms
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
0 = max # of 1-2 neighbors
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
1 = max # of special neighbors
special bonds CPU = 0.000 seconds
read_data CPU = 0.001 seconds
velocity all create 100.0 4928459
# unconnected bodies
group clump1 id <> 1 9
9 atoms in group clump1
group clump2 id <> 10 18
9 atoms in group clump2
group clump3 id <> 19 27
9 atoms in group clump3
group clump4 id <> 28 36
9 atoms in group clump4
group clump5 id <> 37 45
9 atoms in group clump5
group clump6 id <> 46 54
9 atoms in group clump6
group clump7 id <> 55 63
9 atoms in group clump7
group clump8 id <> 64 72
9 atoms in group clump8
group clump9 id <> 73 81
9 atoms in group clump9
fix 1 all rigid/small molecule infile bodyinfo.dat
create bodies CPU = 0.000 seconds
9 rigid bodies with 81 atoms
1.2247449 = max distance from body owner to body atom
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
generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update every 1 steps, delay 10 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 = 18 18 18
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d
bin: standard
Reading rigid body data for 4 bodies from file bodyinfo.dat
Per MPI rank memory allocation (min/avg/max) = 8.892 | 8.94 | 9.049 Mbytes
Step Temp E_pair E_mol TotEng Press
0 115.29439 5235.9179 0 5272.2142 -2.7403788
50 14910.685 571.71558 0 5265.82 32.006171
100 16298.442 136.66184 0 5267.653 16.444229
150 16682.606 17.490511 0 5269.4219 14.900344
200 16733.929 1.372872 0 5269.4617 14.569267
250 16738.853 -0.15252816 0 5269.4864 14.496404
300 16738.588 -0.055171335 0 5269.5002 14.496025
350 16738.492 -0.017444677 0 5269.5077 14.496446
400 16738.464 -0.0060102023 0 5269.5104 14.496618
450 16738.455 -0.0012713351 0 5269.5124 14.496701
500 16738.455 -0.00081068621 0 5269.5128 14.496709
550 16738.455 -0.00083203497 0 5269.5129 14.496707
600 16738.455 -0.00058355356 0 5269.5131 14.496709
650 16738.455 -0.00047226704 0 5269.5131 14.496708
700 16738.455 0 0 5269.5136 14.496713
750 16738.455 0 0 5269.5136 14.49671
800 16738.455 0 0 5269.5137 14.496709
850 16738.455 0 0 5269.5137 14.49671
900 16738.456 0 0 5269.5138 14.496713
950 16738.462 -0.0035323872 0 5269.5122 14.496671
1000 16738.586 -0.051135144 0 5269.5036 14.496229
1050 16737.358 0.32995057 0 5269.4981 14.525763
1100 16737.892 0.16210246 0 5269.4984 14.531983
1150 16738.703 -0.089235095 0 5269.5025 14.509899
1200 16738.466 -0.0075446243 0 5269.5096 14.510615
1250 16738.456 0 0 5269.514 14.510704
1300 16738.457 0 0 5269.5141 14.510701
1350 16738.457 0 0 5269.5141 14.510699
1400 16738.457 -0.00044736511 0 5269.5138 14.510693
1450 16738.458 -0.0010971179 0 5269.5134 14.510687
1500 16738.458 -0.00057885428 0 5269.5139 14.510698
1550 16738.457 0 0 5269.5143 14.51071
1600 16738.457 0 0 5269.5144 14.510712
1650 16738.457 0 0 5269.5144 14.510712
1700 16738.458 0 0 5269.5144 14.51071
1750 16738.458 0 0 5269.5145 14.510708
1800 16738.458 0 0 5269.5145 14.510706
1850 16738.458 0 0 5269.5146 14.510705
1900 16738.458 0 0 5269.5146 14.510706
1950 16738.465 -0.0031733615 0 5269.5134 14.510659
2000 16738.491 -0.013255268 0 5269.5117 14.510532
2050 16738.556 -0.0365811 0 5269.5087 14.51029
2100 16738.633 -0.063209659 0 5269.5065 14.510219
2150 16738.607 -0.05601761 0 5269.5055 14.510231
2200 16738.557 -0.038423032 0 5269.5072 14.510404
2250 16738.515 -0.023709918 0 5269.5088 14.510539
2300 16738.489 -0.013249035 0 5269.5111 14.510621
2350 16738.468 -0.0045563719 0 5269.5131 14.510714
2400 16738.46 -0.00052194273 0 5269.5146 14.510771
2450 16738.464 -0.0023259756 0 5269.514 14.510746
2500 16738.468 -0.0051929186 0 5269.5127 14.510731
2550 16738.581 -0.044940117 0 5269.5085 14.510315
2600 16738.427 -7.9722791e-05 0 5269.5046 14.510657
2650 16733.017 1.7051479 0 5269.5067 14.596295
2700 16738.761 -0.10614946 0 5269.5038 14.499584
2750 16733.973 1.4038179 0 5269.5064 14.598107
2800 16738.585 -0.046813448 0 5269.5076 14.511073
2850 16738.487 -0.012558719 0 5269.5111 14.510111
2900 16738.465 -0.0026252725 0 5269.514 14.510277
2950 16738.476 -0.0082220764 0 5269.512 14.510223
3000 16738.66 -0.071284779 0 5269.507 14.509758
3050 16715.332 7.2419352 0 5269.476 14.870305
3100 16653.226 26.818761 0 5269.5009 14.496764
3150 16739.351 -0.30690375 0 5269.4886 13.643904
3200 16733.238 1.6025328 0 5269.4737 12.016934
3250 16734.374 1.2554429 0 5269.4841 11.963561
3300 16732.156 1.9585966 0 5269.4893 12.234024
3350 16738.655 -0.079693236 0 5269.497 12.092757
3400 16738.543 -0.042215005 0 5269.4991 12.092809
3450 16738.591 -0.05932751 0 5269.4972 12.092536
3500 16738.759 -0.11761245 0 5269.4918 12.09203
3550 16713.405 7.8460622 0 5269.4737 12.389816
3600 16734.939 1.0821936 0 5269.4891 12.173591
3650 16738.808 -0.13663193 0 5269.4882 12.027009
3700 16738.602 -0.070934369 0 5269.4889 12.025288
3750 16737.731 0.20706559 0 5269.4927 12.061948
3800 16738.578 -0.05582043 0 5269.4965 12.035665
3850 16738.471 -0.016307928 0 5269.5024 12.035302
3900 16738.449 -0.0058182199 0 5269.5059 12.035401
3950 16738.439 -0.0012027325 0 5269.5074 12.035461
4000 16738.436 -0.00020698452 0 5269.5075 12.035469
4050 16738.437 0 0 5269.5078 12.035454
4100 16738.437 0 0 5269.508 12.035435
4150 16738.438 0 0 5269.5081 12.035426
4200 16738.438 0 0 5269.5083 12.035432
4250 16738.439 0 0 5269.5085 12.035447
4300 16738.439 0 0 5269.5086 12.035463
4350 16738.44 0 0 5269.5087 12.035474
4400 16738.44 0 0 5269.5088 12.035478
4450 16738.44 0 0 5269.5089 12.035474
4500 16738.44 0 0 5269.509 12.035462
4550 16738.441 0 0 5269.5092 12.035449
4600 16738.441 0 0 5269.5093 12.035445
4650 16738.442 0 0 5269.5095 12.035451
4700 16738.442 0 0 5269.5096 12.03546
4750 16738.443 0 0 5269.5097 12.035465
4800 16738.443 0 0 5269.5098 12.035466
4850 16738.443 0 0 5269.51 12.035463
4900 16738.444 0 0 5269.5101 12.035456
4950 16738.444 0 0 5269.5102 12.035447
5000 16738.445 0 0 5269.5104 12.03544
5050 16738.445 0 0 5269.5105 12.035442
5100 16738.446 0 0 5269.5107 12.035455
5150 16738.446 0 0 5269.5108 12.03547
5200 16738.446 0 0 5269.5109 12.035479
5250 16738.447 0 0 5269.511 12.035479
5300 16738.447 0 0 5269.5111 12.03547
5350 16738.447 0 0 5269.5112 12.035454
5400 16738.448 0 0 5269.5113 12.035434
5450 16738.448 0 0 5269.5115 12.03542
5500 16738.449 0 0 5269.5117 12.035422
5550 16738.457 -0.0030919234 0 5269.5111 12.035383
5600 16738.51 -0.021618357 0 5269.5092 12.035106
5650 16738.622 -0.059214788 0 5269.507 12.035694
5700 16395.28 108.06942 0 5269.5463 24.369038
5750 16738.544 -0.033973429 0 5269.5077 12.011261
5800 16738.456 -0.0037013529 0 5269.5102 12.011675
5850 16738.451 0 0 5269.5123 12.011709
5900 16738.451 -0.0002211587 0 5269.5122 12.011687
5950 16738.452 -0.00024253349 0 5269.5124 12.011678
6000 16738.452 0 0 5269.5128 12.011688
6050 16738.453 0 0 5269.513 12.011702
6100 16738.453 0 0 5269.5131 12.011716
6150 16738.454 0 0 5269.5132 12.011725
6200 16738.454 0 0 5269.5133 12.011728
6250 16738.454 0 0 5269.5134 12.011723
6300 16738.455 0 0 5269.5135 12.011712
6350 16738.455 0 0 5269.5137 12.0117
6400 16738.456 0 0 5269.5138 12.011697
6450 16738.456 0 0 5269.514 12.011704
6500 16738.456 0 0 5269.5141 12.011714
6550 16738.457 0 0 5269.5142 12.011719
6600 16738.457 0 0 5269.5143 12.011718
6650 16738.458 0 0 5269.5144 12.011713
6700 16738.458 0 0 5269.5146 12.011705
6750 16738.459 0 0 5269.5147 12.011696
6800 16738.459 0 0 5269.5149 12.01169
6850 16738.46 0 0 5269.515 12.011695
6900 16738.46 0 0 5269.5152 12.01171
6950 16738.46 0 0 5269.5153 12.011726
7000 16738.461 0 0 5269.5154 12.011736
7050 16738.461 0 0 5269.5155 12.011737
7100 16738.461 0 0 5269.5155 12.011728
7150 16738.461 0 0 5269.5156 12.011712
7200 16738.462 0 0 5269.5158 12.011691
7250 16738.463 0 0 5269.516 12.011676
7300 16738.463 0 0 5269.5162 12.011677
7350 16738.464 0 0 5269.5164 12.011693
7400 16738.464 0 0 5269.5165 12.011713
7450 16738.465 0 0 5269.5166 12.011729
7500 16738.465 0 0 5269.5167 12.011736
7550 16738.465 0 0 5269.5168 12.011734
7600 16738.465 0 0 5269.5168 12.011722
7650 16738.466 0 0 5269.517 12.011704
7700 16738.466 0 0 5269.5171 12.011687
7750 16738.467 0 0 5269.5173 12.011681
7800 16738.467 0 0 5269.5175 12.011687
7850 16738.468 0 0 5269.5176 12.0117
7900 16738.468 0 0 5269.5178 12.011712
7950 16738.469 0 0 5269.5179 12.011721
8000 16738.469 0 0 5269.518 12.011724
8050 16738.469 0 0 5269.5181 12.01172
8100 16738.47 0 0 5269.5182 12.011709
8150 16738.47 0 0 5269.5183 12.0117
8200 16738.47 0 0 5269.5185 12.0117
8250 16738.471 0 0 5269.5186 12.011709
8300 16738.471 0 0 5269.5187 12.011719
8350 16738.472 0 0 5269.5189 12.011723
8400 16738.472 0 0 5269.519 12.01172
8450 16738.473 -0.00039690669 0 5269.5189 12.011706
8500 16738.481 -0.0034646806 0 5269.5182 12.011643
8550 16738.483 -0.0045307409 0 5269.5178 12.011621
8600 16738.474 -0.00076532809 0 5269.5189 12.011681
8650 16738.474 0 0 5269.5197 12.011699
8700 16738.475 0 0 5269.5199 12.011715
8750 16738.475 0 0 5269.52 12.011732
8800 16738.475 0 0 5269.52 12.011743
8850 16738.476 0 0 5269.5201 12.011744
8900 16738.476 0 0 5269.5202 12.011735
8950 16738.476 0 0 5269.5203 12.011719
9000 16738.477 0 0 5269.5205 12.011698
9050 16738.477 0 0 5269.5206 12.011683
9100 16738.478 0 0 5269.5208 12.011684
9150 16738.479 0 0 5269.521 12.011701
9200 16738.479 0 0 5269.5212 12.011722
9250 16738.479 0 0 5269.5213 12.011738
9300 16738.48 0 0 5269.5214 12.011746
9350 16738.48 0 0 5269.5214 12.011744
9400 16738.48 0 0 5269.5215 12.011732
9450 16738.48 0 0 5269.5216 12.011715
9500 16738.481 -0.0003765243 0 5269.5216 12.011692
9550 16738.493 -0.0053156164 0 5269.5203 12.011611
9600 16738.549 -0.026814368 0 5269.5163 12.011415
9650 16738.765 -0.10191523 0 5269.5092 12.011013
9700 16735.041 1.0589884 0 5269.4979 12.062708
9750 16738.013 0.13550185 0 5269.5101 11.407246
9800 16738.512 -0.011620326 0 5269.5201 11.394974
9850 16738.489 -0.00067270434 0 5269.5237 11.395099
9900 16738.489 -0.00024984508 0 5269.5242 11.395085
9950 16738.49 0 0 5269.5245 11.395077
10000 16738.49 0 0 5269.5246 11.395076
Loop time of 0.135757 on 4 procs for 10000 steps with 81 atoms
Performance: 636433.251 tau/day, 73661.256 timesteps/s
98.4% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0020781 | 0.0024716 | 0.0032187 | 0.9 | 1.82
Bond | 0.00029013 | 0.000332 | 0.00037076 | 0.0 | 0.24
Neigh | 0.0087772 | 0.011705 | 0.014134 | 2.3 | 8.62
Comm | 0.042702 | 0.045012 | 0.048023 | 1.1 | 33.16
Output | 0.0027373 | 0.0030292 | 0.0036178 | 0.6 | 2.23
Modify | 0.067437 | 0.068617 | 0.069634 | 0.3 | 50.54
Other | | 0.004589 | | | 3.38
Nlocal: 20.25 ave 38 max 3 min
Histogram: 1 0 1 0 0 0 1 0 0 1
Nghost: 27.25 ave 48 max 13 min
Histogram: 1 0 1 1 0 0 0 0 0 1
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0
Ave special neighs/atom = 0
Neighbor list builds = 998
Dangerous builds = 997
Total wall time: 0:00:00

157
src/RIGID/fix_rigid.cpp
View File

@ -134,11 +134,9 @@ FixRigid::FixRigid(LAMMPS *lmp, int narg, char **arg) :
int is_double,cols; int is_double,cols;
int custom_index = atom->find_custom(arg[4]+2,is_double,cols); int custom_index = atom->find_custom(arg[4]+2,is_double,cols);
if (custom_index == -1) if (custom_index == -1)
error->all(FLERR,"Fix rigid custom requires " error->all(FLERR,"Fix rigid custom requires previously defined property/atom");
"previously defined property/atom");
else if (is_double) else if (is_double)
error->all(FLERR,"Fix rigid custom requires " error->all(FLERR,"Fix rigid custom requires integer-valued property/atom vector");
"integer-valued property/atom vector");
int minval = INT_MAX; int minval = INT_MAX;
int *value = atom->ivector[custom_index]; int *value = atom->ivector[custom_index];
for (i = 0; i < nlocal; i++) for (i = 0; i < nlocal; i++)
@ -155,9 +153,9 @@ FixRigid::FixRigid(LAMMPS *lmp, int narg, char **arg) :
} else if (utils::strmatch(arg[4],"^v_")) { } else if (utils::strmatch(arg[4],"^v_")) {
int ivariable = input->variable->find(arg[4]+2); int ivariable = input->variable->find(arg[4]+2);
if (ivariable < 0) if (ivariable < 0)
error->all(FLERR,"Variable name for fix rigid custom does not exist"); error->all(FLERR,"Variable {} for fix rigid/small custom does not exist", arg[4]+2);
if (input->variable->atomstyle(ivariable) == 0) if (input->variable->atomstyle(ivariable) == 0)
error->all(FLERR,"Fix rigid custom variable is no atom-style variable"); error->all(FLERR,"Fix rigid custom variable {} is not atom-style variable", arg[4]+2);
double *value = new double[nlocal]; double *value = new double[nlocal];
input->variable->compute_atom(ivariable,0,value,1,0); input->variable->compute_atom(ivariable,0,value,1,0);
int minval = INT_MAX; int minval = INT_MAX;
@ -218,7 +216,7 @@ FixRigid::FixRigid(LAMMPS *lmp, int narg, char **arg) :
} }
memory->destroy(ncount); memory->destroy(ncount);
if (custom_flag) delete [] molecule; if (custom_flag) delete[] molecule;
// each listed group is a rigid body // each listed group is a rigid body
// check if all listed groups exist // check if all listed groups exist
@ -259,7 +257,7 @@ FixRigid::FixRigid(LAMMPS *lmp, int narg, char **arg) :
if (flagall) if (flagall)
error->all(FLERR,"One or more atoms belong to multiple rigid bodies"); error->all(FLERR,"One or more atoms belong to multiple rigid bodies");
delete [] igroups; delete[] igroups;
} else error->all(FLERR,"Illegal fix rigid command"); } else error->all(FLERR,"Illegal fix rigid command");
@ -502,7 +500,7 @@ FixRigid::FixRigid(LAMMPS *lmp, int narg, char **arg) :
if (strcmp(arg[iarg+1],"all") == 0) allremap = 1; if (strcmp(arg[iarg+1],"all") == 0) allremap = 1;
else { else {
allremap = 0; allremap = 0;
delete [] id_dilate; delete[] id_dilate;
id_dilate = utils::strdup(arg[iarg+1]); id_dilate = utils::strdup(arg[iarg+1]);
int idilate = group->find(id_dilate); int idilate = group->find(id_dilate);
if (idilate == -1) if (idilate == -1)
@ -529,7 +527,7 @@ FixRigid::FixRigid(LAMMPS *lmp, int narg, char **arg) :
} else if (strcmp(arg[iarg],"infile") == 0) { } else if (strcmp(arg[iarg],"infile") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix rigid command"); if (iarg+2 > narg) error->all(FLERR,"Illegal fix rigid command");
delete [] inpfile; delete[] inpfile;
inpfile = utils::strdup(arg[iarg+1]); inpfile = utils::strdup(arg[iarg+1]);
restart_file = 1; restart_file = 1;
reinitflag = 0; reinitflag = 0;
@ -542,7 +540,7 @@ FixRigid::FixRigid(LAMMPS *lmp, int narg, char **arg) :
} else if (strcmp(arg[iarg],"gravity") == 0) { } else if (strcmp(arg[iarg],"gravity") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix rigid command"); if (iarg+2 > narg) error->all(FLERR,"Illegal fix rigid command");
delete [] id_gravity; delete[] id_gravity;
id_gravity = utils::strdup(arg[iarg+1]); id_gravity = utils::strdup(arg[iarg+1]);
iarg += 2; iarg += 2;
@ -584,7 +582,7 @@ FixRigid::FixRigid(LAMMPS *lmp, int narg, char **arg) :
if (body[i] >= 0) ncount[body[i]]++; if (body[i] >= 0) ncount[body[i]]++;
MPI_Allreduce(ncount,nrigid,nbody,MPI_INT,MPI_SUM,world); MPI_Allreduce(ncount,nrigid,nbody,MPI_INT,MPI_SUM,world);
delete [] ncount; delete[] ncount;
for (ibody = 0; ibody < nbody; ibody++) for (ibody = 0; ibody < nbody; ibody++)
if (nrigid[ibody] <= 1) error->all(FLERR,"One or zero atoms in rigid body"); if (nrigid[ibody] <= 1) error->all(FLERR,"One or zero atoms in rigid body");
@ -615,9 +613,9 @@ FixRigid::~FixRigid()
atom->delete_callback(id,Atom::GROW); atom->delete_callback(id,Atom::GROW);
delete random; delete random;
delete [] inpfile; delete[] inpfile;
delete [] id_dilate; delete[] id_dilate;
delete [] id_gravity; delete[] id_gravity;
memory->destroy(mol2body); memory->destroy(mol2body);
memory->destroy(body2mol); memory->destroy(body2mol);
@ -674,8 +672,6 @@ int FixRigid::setmask()
void FixRigid::init() void FixRigid::init()
{ {
int i,ibody;
triclinic = domain->triclinic; triclinic = domain->triclinic;
// atom style pointers to particles that store extra info // atom style pointers to particles that store extra info
@ -688,18 +684,16 @@ void FixRigid::init()
// if earlyflag, warn if any post-force fixes come after a rigid fix // if earlyflag, warn if any post-force fixes come after a rigid fix
int count = 0; int count = 0;
for (i = 0; i < modify->nfix; i++) for (auto ifix : modify->get_fix_list())
if (modify->fix[i]->rigid_flag) count++; if (ifix->rigid_flag) count++;
if (count > 1 && me == 0) error->warning(FLERR,"More than one fix rigid"); if (count > 1 && me == 0) error->warning(FLERR,"More than one fix rigid");
if (earlyflag) { if (earlyflag) {
int rflag = 0; bool rflag = false;
for (i = 0; i < modify->nfix; i++) { for (auto ifix : modify->get_fix_list()) {
if (modify->fix[i]->rigid_flag) rflag = 1; if (ifix->rigid_flag) rflag = true;
if (rflag && (modify->fmask[i] & POST_FORCE) && if ((comm->me == 0) && rflag && (ifix->setmask() & POST_FORCE) && !ifix->rigid_flag)
!modify->fix[i]->rigid_flag) error->warning(FLERR,"Fix {} alters forces after fix rigid", ifix->id);
error->warning(FLERR,"Fix {} alters forces after fix rigid",
modify->fix[i]->id);
} }
} }
@ -709,36 +703,30 @@ void FixRigid::init()
// and gravity is not applied correctly // and gravity is not applied correctly
if (inpfile && !id_gravity) { if (inpfile && !id_gravity) {
for (i = 0; i < modify->nfix; i++) { if (modify->get_fix_by_style("^gravity").size() > 0)
if (strcmp(modify->fix[i]->style,"gravity") == 0) { if (comm->me == 0)
if (comm->me == 0) error->warning(FLERR,"Gravity may not be correctly applied to rigid "
error->warning(FLERR,"Gravity may not be correctly applied " "bodies if they consist of overlapped particles");
"to rigid bodies if they consist of "
"overlapped particles");
break;
}
}
} }
// error if a fix changing the box comes before rigid fix // error if a fix changing the box comes before rigid fix
for (i = 0; i < modify->nfix; i++) bool boxflag = false;
if (modify->fix[i]->box_change) break; for (auto ifix : modify->get_fix_list()) {
if (i < modify->nfix) { if (ifix->box_change) boxflag = true;
for (int j = i+1; j < modify->nfix; j++) if (boxflag && utils::strmatch(ifix->style,"^rigid"))
if (utils::strmatch(modify->fix[j]->style,"^rigid"))
error->all(FLERR,"Rigid fixes must come before any box changing fix"); error->all(FLERR,"Rigid fixes must come before any box changing fix");
} }
// add gravity forces based on gravity vector from fix // add gravity forces based on gravity vector from fix
if (id_gravity) { if (id_gravity) {
int ifix = modify->find_fix(id_gravity); auto ifix = modify->get_fix_by_id(id_gravity);
if (ifix < 0) error->all(FLERR,"Fix rigid cannot find fix gravity ID"); if (!ifix) error->all(FLERR,"Fix rigid cannot find fix gravity ID {}", id_gravity);
if (!utils::strmatch(modify->fix[ifix]->style,"^gravity")) if (!utils::strmatch(ifix->style,"^gravity"))
error->all(FLERR,"Fix rigid gravity fix ID is not a gravity fix style"); error->all(FLERR,"Fix rigid gravity fix ID {} is not a gravity fix style", id_gravity);
int tmp; int tmp;
gvec = (double *) modify->fix[ifix]->extract("gvec",tmp); gvec = (double *) ifix->extract("gvec", tmp);
} }
// timestep info // timestep info
@ -767,7 +755,7 @@ void FixRigid::init()
// temperature scale factor // temperature scale factor
double ndof = 0.0; double ndof = 0.0;
for (ibody = 0; ibody < nbody; ibody++) { for (int ibody = 0; ibody < nbody; ibody++) {
ndof += fflag[ibody][0] + fflag[ibody][1] + fflag[ibody][2]; ndof += fflag[ibody][0] + fflag[ibody][1] + fflag[ibody][2];
ndof += tflag[ibody][0] + tflag[ibody][1] + tflag[ibody][2]; ndof += tflag[ibody][0] + tflag[ibody][1] + tflag[ibody][2];
} }
@ -1237,7 +1225,7 @@ int FixRigid::dof(int tgroup)
if (!setupflag) { if (!setupflag) {
if (comm->me == 0) if (comm->me == 0)
error->warning(FLERR,"Cannot count rigid body degrees-of-freedom " error->warning(FLERR,"Cannot count rigid body degrees-of-freedom "
"before bodies are initialized"); "before bodies are fully initialized");
return 0; return 0;
} }
@ -1307,10 +1295,10 @@ int FixRigid::dof(int tgroup)
n += 2*nall[ibody] + 3*mall[ibody] - 3; n += 2*nall[ibody] + 3*mall[ibody] - 3;
} }
delete [] ncount; delete[] ncount;
delete [] mcount; delete[] mcount;
delete [] nall; delete[] nall;
delete [] mall; delete[] mall;
return n; return n;
} }
@ -1397,12 +1385,9 @@ void FixRigid::set_xv()
MathExtra::matvec(ex_space[ibody],ey_space[ibody], MathExtra::matvec(ex_space[ibody],ey_space[ibody],
ez_space[ibody],displace[i],x[i]); ez_space[ibody],displace[i],x[i]);
v[i][0] = omega[ibody][1]*x[i][2] - omega[ibody][2]*x[i][1] + v[i][0] = omega[ibody][1]*x[i][2] - omega[ibody][2]*x[i][1] + vcm[ibody][0];
vcm[ibody][0]; v[i][1] = omega[ibody][2]*x[i][0] - omega[ibody][0]*x[i][2] + vcm[ibody][1];
v[i][1] = omega[ibody][2]*x[i][0] - omega[ibody][0]*x[i][2] + v[i][2] = omega[ibody][0]*x[i][1] - omega[ibody][1]*x[i][0] + vcm[ibody][2];
vcm[ibody][1];
v[i][2] = omega[ibody][0]*x[i][1] - omega[ibody][1]*x[i][0] +
vcm[ibody][2];
// add center of mass to displacement // add center of mass to displacement
// map back into periodic box via xbox,ybox,zbox // map back into periodic box via xbox,ybox,zbox
@ -1555,12 +1540,9 @@ void FixRigid::set_v()
v2 = v[i][2]; v2 = v[i][2];
} }
v[i][0] = omega[ibody][1]*delta[2] - omega[ibody][2]*delta[1] + v[i][0] = omega[ibody][1]*delta[2] - omega[ibody][2]*delta[1] + vcm[ibody][0];
vcm[ibody][0]; v[i][1] = omega[ibody][2]*delta[0] - omega[ibody][0]*delta[2] + vcm[ibody][1];
v[i][1] = omega[ibody][2]*delta[0] - omega[ibody][0]*delta[2] + v[i][2] = omega[ibody][0]*delta[1] - omega[ibody][1]*delta[0] + vcm[ibody][2];
vcm[ibody][1];
v[i][2] = omega[ibody][0]*delta[1] - omega[ibody][1]*delta[0] +
vcm[ibody][2];
// virial = unwrapped coords dotted into body constraint force // virial = unwrapped coords dotted into body constraint force
// body constraint force = implied force due to v change minus f external // body constraint force = implied force due to v change minus f external
@ -1658,8 +1640,7 @@ void FixRigid::setup_bodies_static()
{ {
int i,ibody; int i,ibody;
// extended = 1 if any particle in a rigid body is finite size // extended = 1 if any particle in a rigid body is finite size or has a dipole moment
// or has a dipole moment
extended = orientflag = dorientflag = 0; extended = orientflag = dorientflag = 0;
@ -1822,6 +1803,11 @@ void FixRigid::setup_bodies_static()
int *inbody; int *inbody;
if (inpfile) { if (inpfile) {
// must call it here so it doesn't override read in data but
// initialize bodies whose dynamic settings not set in inpfile
setup_bodies_dynamic();
memory->create(inbody,nbody,"rigid:inbody"); memory->create(inbody,nbody,"rigid:inbody");
for (ibody = 0; ibody < nbody; ibody++) inbody[ibody] = 0; for (ibody = 0; ibody < nbody; ibody++) inbody[ibody] = 0;
readfile(0,masstotal,xcm,vcm,angmom,imagebody,inbody); readfile(0,masstotal,xcm,vcm,angmom,imagebody,inbody);
@ -2268,8 +2254,7 @@ void FixRigid::setup_bodies_dynamic()
vxcm vycm vzcm lx ly lz ix iy iz vxcm vycm vzcm lx ly lz ix iy iz
------------------------------------------------------------------------- */ ------------------------------------------------------------------------- */
void FixRigid::readfile(int which, double *vec, void FixRigid::readfile(int which, double *vec, double **array1, double **array2, double **array3,
double **array1, double **array2, double **array3,
imageint *ivec, int *inbody) imageint *ivec, int *inbody)
{ {
int nchunk,id,eofflag,xbox,ybox,zbox; int nchunk,id,eofflag,xbox,ybox,zbox;
@ -2278,30 +2263,36 @@ void FixRigid::readfile(int which, double *vec,
char *eof,*start,*next,*buf; char *eof,*start,*next,*buf;
char line[MAXLINE]; char line[MAXLINE];
// open file and read and parse first non-empty, non-comment line containing the number of bodies
if (me == 0) { if (me == 0) {
fp = fopen(inpfile,"r"); fp = fopen(inpfile,"r");
if (fp == nullptr) if (fp == nullptr)
error->one(FLERR,"Cannot open fix rigid file {}: {}", inpfile,utils::getsyserror()); error->one(FLERR,"Cannot open fix rigid infile {}: {}", inpfile, utils::getsyserror());
while (true) { while (true) {
eof = fgets(line,MAXLINE,fp); eof = fgets(line,MAXLINE,fp);
if (eof == nullptr) error->one(FLERR,"Unexpected end of fix rigid file"); if (eof == nullptr) error->one(FLERR,"Unexpected end of fix rigid infile");
start = &line[strspn(line," \t\n\v\f\r")]; start = &line[strspn(line," \t\n\v\f\r")];
if (*start != '\0' && *start != '#') break; if (*start != '\0' && *start != '#') break;
} }
nlines = utils::inumeric(FLERR, utils::trim(line), true, lmp); nlines = utils::inumeric(FLERR, utils::trim(line), true, lmp);
if (which == 0)
utils::logmesg(lmp, "Reading rigid body data for {} bodies from file {}\n", nlines, inpfile);
if (nlines == 0) fclose(fp);
} }
MPI_Bcast(&nlines,1,MPI_INT,0,world); MPI_Bcast(&nlines,1,MPI_INT,0,world);
// empty file with 0 lines is needed to trigger initial restart file generation // empty file with 0 lines is needed to trigger initial restart file
if (nlines == 0) return; //error->all(FLERR,"Fix rigid file has no lines"); // generation when no infile was previously used.
if (nlines == 0) return;
else if (nlines < 0) error->all(FLERR,"Fix rigid infile has incorrect format");
char *buffer = new char[CHUNK*MAXLINE]; char *buffer = new char[CHUNK*MAXLINE];
int nread = 0; int nread = 0;
while (nread < nlines) { while (nread < nlines) {
nchunk = MIN(nlines-nread,CHUNK); nchunk = MIN(nlines-nread,CHUNK);
eofflag = utils::read_lines_from_file(fp,nchunk,MAXLINE,buffer,me,world); eofflag = utils::read_lines_from_file(fp,nchunk,MAXLINE,buffer,me,world);
if (eofflag) error->all(FLERR,"Unexpected end of fix rigid file"); if (eofflag) error->all(FLERR,"Unexpected end of fix rigid infile");
buf = buffer; buf = buffer;
next = strchr(buf,'\n'); next = strchr(buf,'\n');
@ -2328,7 +2319,7 @@ void FixRigid::readfile(int which, double *vec,
id = values.next_int(); id = values.next_int();
if (rstyle == MOLECULE) { if (rstyle == MOLECULE) {
if (id <= 0 || id > maxmol) if (id <= 0 || id > maxmol)
throw TokenizerException("invalid rigid body ID ", std::to_string(id)); throw TokenizerException("invalid rigid molecule ID ", std::to_string(id));
id = mol2body[id]; id = mol2body[id];
} else id--; } else id--;
@ -2365,7 +2356,7 @@ void FixRigid::readfile(int which, double *vec,
array1[id][3] = values.next_double(); array1[id][3] = values.next_double();
} }
} catch (TokenizerException &e) { } catch (TokenizerException &e) {
error->all(FLERR, "Invalid fix rigid file: {}", e.what()); error->all(FLERR, "Invalid fix rigid infile: {}", e.what());
} }
buf = next + 1; buf = next + 1;
} }
@ -2384,7 +2375,7 @@ void FixRigid::readfile(int which, double *vec,
void FixRigid::write_restart_file(const char *file) void FixRigid::write_restart_file(const char *file)
{ {
if (me) return; if (comm->me) return;
auto outfile = std::string(file) + ".rigid"; auto outfile = std::string(file) + ".rigid";
FILE *fp = fopen(outfile.c_str(),"w"); FILE *fp = fopen(outfile.c_str(),"w");
@ -2414,14 +2405,11 @@ void FixRigid::write_restart_file(const char *file)
ybox = (imagebody[i] >> IMGBITS & IMGMASK) - IMGMAX; ybox = (imagebody[i] >> IMGBITS & IMGMASK) - IMGMAX;
zbox = (imagebody[i] >> IMG2BITS) - IMGMAX; zbox = (imagebody[i] >> IMG2BITS) - IMGMAX;
fprintf(fp,"%d %.16g %.16g %.16g %.16g %.16g %.16g %.16g %.16g %.16g %.16g " fprintf(fp,"%d %-1.16e %-1.16e %-1.16e %-1.16e %-1.16e %-1.16e %-1.16e %-1.16e %-1.16e "
"%.16g %.16g %.16g %.16g %.16g %.16g %d %d %d\n", "%-1.16e %-1.16e %-1.16e %-1.16e %-1.16e %-1.16e %-1.16e %d %d %d\n",
id,masstotal[i],xcm[i][0],xcm[i][1],xcm[i][2], id,masstotal[i],xcm[i][0],xcm[i][1],xcm[i][2],ispace[0][0],ispace[1][1],ispace[2][2],
ispace[0][0],ispace[1][1],ispace[2][2], ispace[0][1],ispace[0][2],ispace[1][2],vcm[i][0],vcm[i][1],vcm[i][2],
ispace[0][1],ispace[0][2],ispace[1][2], angmom[i][0],angmom[i][1],angmom[i][2],xbox,ybox,zbox);
vcm[i][0],vcm[i][1],vcm[i][2],
angmom[i][0],angmom[i][1],angmom[i][2],
xbox,ybox,zbox);
} }
fclose(fp); fclose(fp);
@ -2483,6 +2471,7 @@ void FixRigid::copy_arrays(int i, int j, int /*delflag*/)
displace[j][0] = displace[i][0]; displace[j][0] = displace[i][0];
displace[j][1] = displace[i][1]; displace[j][1] = displace[i][1];
displace[j][2] = displace[i][2]; displace[j][2] = displace[i][2];
if (extended) { if (extended) {
eflags[j] = eflags[i]; eflags[j] = eflags[i];
for (int k = 0; k < orientflag; k++) for (int k = 0; k < orientflag; k++)

189
src/RIGID/fix_rigid_small.cpp
View File

@ -35,6 +35,7 @@
#include "random_mars.h" #include "random_mars.h"
#include "respa.h" #include "respa.h"
#include "rigid_const.h" #include "rigid_const.h"
#include "tokenizer.h"
#include "update.h" #include "update.h"
#include "variable.h" #include "variable.h"
@ -116,11 +117,9 @@ FixRigidSmall::FixRigidSmall(LAMMPS *lmp, int narg, char **arg) :
int is_double,cols; int is_double,cols;
int custom_index = atom->find_custom(arg[4]+2,is_double,cols); int custom_index = atom->find_custom(arg[4]+2,is_double,cols);
if (custom_index == -1) if (custom_index == -1)
error->all(FLERR,"Fix rigid/small custom requires " error->all(FLERR,"Fix rigid/small custom requires previously defined property/atom");
"previously defined property/atom");
else if (is_double || cols) else if (is_double || cols)
error->all(FLERR,"Fix rigid/small custom requires " error->all(FLERR,"Fix rigid/small custom requires integer-valued property/atom vector");
"integer-valued property/atom vector");
int minval = INT_MAX; int minval = INT_MAX;
int *value = atom->ivector[custom_index]; int *value = atom->ivector[custom_index];
for (i = 0; i < nlocal; i++) for (i = 0; i < nlocal; i++)
@ -136,11 +135,10 @@ FixRigidSmall::FixRigidSmall(LAMMPS *lmp, int narg, char **arg) :
} else if (utils::strmatch(arg[4],"^v_")) { } else if (utils::strmatch(arg[4],"^v_")) {
int ivariable = input->variable->find(arg[4]+2); int ivariable = input->variable->find(arg[4]+2);
if (ivariable < 0) if (ivariable < 0)
error->all(FLERR,"Variable name for fix rigid/small custom " error->all(FLERR,"Variable {} for fix rigid/small custom does not exist", arg[4]+2);
"does not exist");
if (input->variable->atomstyle(ivariable) == 0) if (input->variable->atomstyle(ivariable) == 0)
error->all(FLERR,"Fix rigid/small custom variable is not " error->all(FLERR,"Fix rigid/small custom variable {} is not atom-style variable",
"atom-style variable"); arg[4]+2);
double *value = new double[nlocal]; double *value = new double[nlocal];
input->variable->compute_atom(ivariable,0,value,1,0); input->variable->compute_atom(ivariable,0,value,1,0);
int minval = INT_MAX; int minval = INT_MAX;
@ -398,8 +396,7 @@ FixRigidSmall::FixRigidSmall(LAMMPS *lmp, int narg, char **arg) :
if (customflag) delete[] bodyID; if (customflag) delete[] bodyID;
if (comm->me == 0) if (comm->me == 0)
utils::logmesg(lmp," create bodies CPU = {:.3f} seconds\n", utils::logmesg(lmp," create bodies CPU = {:.3f} seconds\n", platform::walltime()-time1);
platform::walltime()-time1);
// set nlocal_body and allocate bodies I own // set nlocal_body and allocate bodies I own
@ -411,8 +408,7 @@ FixRigidSmall::FixRigidSmall(LAMMPS *lmp, int narg, char **arg) :
nmax_body = 0; nmax_body = 0;
while (nmax_body < nlocal_body) nmax_body += DELTA_BODY; while (nmax_body < nlocal_body) nmax_body += DELTA_BODY;
body = (Body *) memory->smalloc(nmax_body*sizeof(Body), body = (Body *) memory->smalloc(nmax_body*sizeof(Body), "rigid/small:body");
"rigid/small:body");
// set bodyown for owned atoms // set bodyown for owned atoms
@ -527,26 +523,22 @@ int FixRigidSmall::setmask()
void FixRigidSmall::init() void FixRigidSmall::init()
{ {
int i;
triclinic = domain->triclinic; triclinic = domain->triclinic;
// warn if more than one rigid fix // warn if more than one rigid fix
// if earlyflag, warn if any post-force fixes come after a rigid fix // if earlyflag, warn if any post-force fixes come after a rigid fix
int count = 0; int count = 0;
for (i = 0; i < modify->nfix; i++) for (auto ifix : modify->get_fix_list())
if (modify->fix[i]->rigid_flag) count++; if (ifix->rigid_flag) count++;
if (count > 1 && me == 0) error->warning(FLERR,"More than one fix rigid"); if (count > 1 && me == 0) error->warning(FLERR,"More than one fix rigid");
if (earlyflag) { if (earlyflag) {
int rflag = 0; bool rflag = false;
for (i = 0; i < modify->nfix; i++) { for (auto ifix : modify->get_fix_list()) {
if (modify->fix[i]->rigid_flag) rflag = 1; if (ifix->rigid_flag) rflag = true;
if (rflag && (modify->fmask[i] & POST_FORCE) && if ((comm->me == 0) && rflag && (ifix->setmask() & POST_FORCE) && !ifix->rigid_flag)
!modify->fix[i]->rigid_flag) error->warning(FLERR,"Fix {} alters forces after fix rigid", ifix->id);
error->warning(FLERR,"Fix {} alters forces after fix rigid",
modify->fix[i]->id);
} }
} }
@ -556,36 +548,30 @@ void FixRigidSmall::init()
// and gravity is not applied correctly // and gravity is not applied correctly
if ((inpfile || onemols) && !id_gravity) { if ((inpfile || onemols) && !id_gravity) {
for (i = 0; i < modify->nfix; i++) { if (modify->get_fix_by_style("^gravity").size() > 0)
if (strcmp(modify->fix[i]->style,"gravity") == 0) { if (comm->me == 0)
if (comm->me == 0) error->warning(FLERR,"Gravity may not be correctly applied to rigid "
error->warning(FLERR,"Gravity may not be correctly applied " "bodies if they consist of overlapped particles");
"to rigid bodies if they consist of "
"overlapped particles");
break;
}
}
} }
// error if a fix changing the box comes before rigid fix // error if a fix changing the box comes before rigid fix
for (i = 0; i < modify->nfix; i++) bool boxflag = false;
if (modify->fix[i]->box_change) break; for (auto ifix : modify->get_fix_list()) {
if (i < modify->nfix) { if (ifix->box_change) boxflag = true;
for (int j = i+1; j < modify->nfix; j++) if (boxflag && utils::strmatch(ifix->style,"^rigid"))
if (utils::strmatch(modify->fix[j]->style,"^rigid"))
error->all(FLERR,"Rigid fixes must come before any box changing fix"); error->all(FLERR,"Rigid fixes must come before any box changing fix");
} }
// add gravity forces based on gravity vector from fix // add gravity forces based on gravity vector from fix
if (id_gravity) { if (id_gravity) {
int ifix = modify->find_fix(id_gravity); auto ifix = modify->get_fix_by_id(id_gravity);
if (ifix < 0) error->all(FLERR,"Fix rigid/small cannot find fix gravity ID"); if (!ifix) error->all(FLERR,"Fix rigid/small cannot find fix gravity ID {}", id_gravity);
if (!utils::strmatch(modify->fix[ifix]->style,"^gravity")) if (!utils::strmatch(ifix->style,"^gravity"))
error->all(FLERR,"Fix rigid gravity fix ID is not a gravity fix style"); error->all(FLERR,"Fix rigid/small gravity fix ID {} is not a gravity fix style", id_gravity);
int tmp; int tmp;
gvec = (double *) modify->fix[ifix]->extract("gvec",tmp); gvec = (double *) ifix->extract("gvec", tmp);
} }
// timestep info // timestep info
@ -1995,6 +1981,11 @@ void FixRigidSmall::setup_bodies_static()
int *inbody; int *inbody;
if (inpfile) { if (inpfile) {
// must call it here so it doesn't override read in data but
// initialize bodies whose dynamic settings not set in inpfile
setup_bodies_dynamic();
memory->create(inbody,nlocal_body,"rigid/small:inbody"); memory->create(inbody,nlocal_body,"rigid/small:inbody");
for (ibody = 0; ibody < nlocal_body; ibody++) inbody[ibody] = 0; for (ibody = 0; ibody < nlocal_body; ibody++) inbody[ibody] = 0;
readfile(0,nullptr,inbody); readfile(0,nullptr,inbody);
@ -2467,8 +2458,7 @@ void FixRigidSmall::setup_bodies_dynamic()
void FixRigidSmall::readfile(int which, double **array, int *inbody) void FixRigidSmall::readfile(int which, double **array, int *inbody)
{ {
int i,j,m,nchunk,eofflag,nlines,xbox,ybox,zbox; int nchunk,eofflag,nlines,xbox,ybox,zbox;
tagint id;
FILE *fp; FILE *fp;
char *eof,*start,*next,*buf; char *eof,*start,*next,*buf;
char line[MAXLINE]; char line[MAXLINE];
@ -2480,7 +2470,7 @@ void FixRigidSmall::readfile(int which, double **array, int *inbody)
int nlocal = atom->nlocal; int nlocal = atom->nlocal;
std::map<tagint,int> hash; std::map<tagint,int> hash;
for (i = 0; i < nlocal; i++) for (int i = 0; i < nlocal; i++)
if (bodyown[i] >= 0) hash[atom->molecule[i]] = bodyown[i]; if (bodyown[i] >= 0) hash[atom->molecule[i]] = bodyown[i];
// open file and read header // open file and read header
@ -2488,24 +2478,27 @@ void FixRigidSmall::readfile(int which, double **array, int *inbody)
if (me == 0) { if (me == 0) {
fp = fopen(inpfile,"r"); fp = fopen(inpfile,"r");
if (fp == nullptr) if (fp == nullptr)
error->one(FLERR,"Cannot open fix rigid/small file {}: {}", error->one(FLERR,"Cannot open fix rigid/small file {}: {}", inpfile, utils::getsyserror());
inpfile,utils::getsyserror());
while (true) { while (true) {
eof = fgets(line,MAXLINE,fp); eof = fgets(line,MAXLINE,fp);
if (eof == nullptr) if (eof == nullptr) error->one(FLERR,"Unexpected end of fix rigid/small file");
error->one(FLERR,"Unexpected end of fix rigid/small file");
start = &line[strspn(line," \t\n\v\f\r")]; start = &line[strspn(line," \t\n\v\f\r")];
if (*start != '\0' && *start != '#') break; if (*start != '\0' && *start != '#') break;
} }
nlines = utils::inumeric(FLERR, utils::trim(line), true, lmp);
sscanf(line,"%d",&nlines); if (which == 0)
utils::logmesg(lmp, "Reading rigid body data for {} bodies from file {}\n", nlines, inpfile);
if (nlines == 0) fclose(fp);
} }
MPI_Bcast(&nlines,1,MPI_INT,0,world); MPI_Bcast(&nlines,1,MPI_INT,0,world);
char *buffer = new char[CHUNK*MAXLINE]; // empty file with 0 lines is needed to trigger initial restart file
char **values = new char*[ATTRIBUTE_PERBODY]; // generation when no infile was previously used.
if (nlines == 0) return;
else if (nlines < 0) error->all(FLERR,"Fix rigid infile has incorrect format");
char *buffer = new char[CHUNK*MAXLINE];
int nread = 0; int nread = 0;
while (nread < nlines) { while (nread < nlines) {
nchunk = MIN(nlines-nread,CHUNK); nchunk = MIN(nlines-nread,CHUNK);
@ -2515,7 +2508,7 @@ void FixRigidSmall::readfile(int which, double **array, int *inbody)
buf = buffer; buf = buffer;
next = strchr(buf,'\n'); next = strchr(buf,'\n');
*next = '\0'; *next = '\0';
int nwords = utils::trim_and_count_words(buf); int nwords = utils::count_words(utils::trim_comment(buf));
*next = '\n'; *next = '\n';
if (nwords != ATTRIBUTE_PERBODY) if (nwords != ATTRIBUTE_PERBODY)
@ -2527,59 +2520,61 @@ void FixRigidSmall::readfile(int which, double **array, int *inbody)
// for which = 0, store all but inertia directly in body struct // for which = 0, store all but inertia directly in body struct
// for which = 1, store inertia tensor array, invert 3,4,5 values to Voigt // for which = 1, store inertia tensor array, invert 3,4,5 values to Voigt
for (i = 0; i < nchunk; i++) { for (int i = 0; i < nchunk; i++) {
next = strchr(buf,'\n'); next = strchr(buf,'\n');
*next = '\0';
values[0] = strtok(buf," \t\n\r\f"); try {
for (j = 1; j < nwords; j++) ValueTokenizer values(buf);
values[j] = strtok(nullptr," \t\n\r\f"); tagint id = values.next_tagint();
id = ATOTAGINT(values[0]); if (id <= 0 || id > maxmol)
if (id <= 0 || id > maxmol) error->all(FLERR,"Invalid rigid body molecude ID {} in fix rigid/small file", id);
error->all(FLERR,"Invalid rigid body ID in fix rigid/small file");
if (hash.find(id) == hash.end()) { if (hash.find(id) == hash.end()) {
buf = next + 1; buf = next + 1;
continue; continue;
}
int m = hash[id];
inbody[m] = 1;
if (which == 0) {
body[m].mass = values.next_double();
body[m].xcm[0] = values.next_double();
body[m].xcm[1] = values.next_double();
body[m].xcm[2] = values.next_double();
values.skip(6);
body[m].vcm[0] = values.next_double();
body[m].vcm[1] = values.next_double();
body[m].vcm[2] = values.next_double();
body[m].angmom[0] = values.next_double();
body[m].angmom[1] = values.next_double();
body[m].angmom[2] = values.next_double();
xbox = values.next_int();
ybox = values.next_int();
zbox = values.next_int();
body[m].image = ((imageint) (xbox + IMGMAX) & IMGMASK) |
(((imageint) (ybox + IMGMAX) & IMGMASK) << IMGBITS) |
(((imageint) (zbox + IMGMAX) & IMGMASK) << IMG2BITS);
} else {
values.skip(4);
array[m][0] = values.next_double();
array[m][1] = values.next_double();
array[m][2] = values.next_double();
array[m][5] = values.next_double();
array[m][4] = values.next_double();
array[m][3] = values.next_double();
}
} catch (TokenizerException &e) {
error->all(FLERR, "Invalid fix rigid/small infile: {}", e.what());
} }
m = hash[id];
inbody[m] = 1;
if (which == 0) {
body[m].mass = atof(values[1]);
body[m].xcm[0] = atof(values[2]);
body[m].xcm[1] = atof(values[3]);
body[m].xcm[2] = atof(values[4]);
body[m].vcm[0] = atof(values[11]);
body[m].vcm[1] = atof(values[12]);
body[m].vcm[2] = atof(values[13]);
body[m].angmom[0] = atof(values[14]);
body[m].angmom[1] = atof(values[15]);
body[m].angmom[2] = atof(values[16]);
xbox = atoi(values[17]);
ybox = atoi(values[18]);
zbox = atoi(values[19]);
body[m].image = ((imageint) (xbox + IMGMAX) & IMGMASK) |
(((imageint) (ybox + IMGMAX) & IMGMASK) << IMGBITS) |
(((imageint) (zbox + IMGMAX) & IMGMASK) << IMG2BITS);
} else {
array[m][0] = atof(values[5]);
array[m][1] = atof(values[6]);
array[m][2] = atof(values[7]);
array[m][3] = atof(values[10]);
array[m][4] = atof(values[9]);
array[m][5] = atof(values[8]);
}
buf = next + 1; buf = next + 1;
} }
nread += nchunk; nread += nchunk;
} }
if (me == 0) fclose(fp); if (me == 0) fclose(fp);
delete[] buffer; delete[] buffer;
delete[] values;
} }
/* ---------------------------------------------------------------------- /* ----------------------------------------------------------------------