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refactor and apply clang-format

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- replace file reader code using TextFileReader and ValueTokenizer
- replace traversing list of fixes with accessor functions
- enable and apply clang-format
- add examples for reading rigid bodies from file
This commit is contained in:
Axel Kohlmeyer
2022-03-20 15:28:31 -04:00
parent 649e8a27b3
commit adf4a23f58
24 changed files with 3950 additions and 1931 deletions
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15
examples/rigid/connected-bodies.dat Normal file
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# Body definition file for POEMS fix
# 1 chain of 9 connected bodies
# Format
# Body-ID Body-Type Atom-ID1 Atom-ID2 ...
1 1 1 2 3 4 5 6 7 8 9
2 2 9 10 11 12 13 14 15 16 17 18
3 1 18 19 20 21 22 23 24 25 26 27
4 2 27 28 29 30 31 32 33 34 35 36
5 3 36 37 38 39 40 41 42 43 44 45
6 1 45 46 47 48 49 50 51 52 53 54
7 2 54 55 56 57 58 59 60 61 62 63
8 1 63 64 65 66 67 68 69 70 71 72
9 2 72 73 74 75 76 77 78 79 80 81

17
examples/rigid/connected-bodies2.dat Normal file
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# Body definition file for POEMS fix
# 2 chains of 4 and 5 connected rigid bodies, respectively
# Format
# Body-ID Body-Type Atom-ID1 Atom-ID2 ...
# chain 1
1 1 1 2 3 4 5 6 7 8 9
2 2 9 10 11 12 13 14 15 16 17 18
3 1 18 19 20 21 22 23 24 25 26 27
4 2 27 28 29 30 31 32 33 34 35 36
# chain 2
5 3 37 38 39 40 41 42 43 44 45
6 1 45 46 47 48 49 50 51 52 53 54
7 2 54 55 56 57 58 59 60 61 62 63
8 1 63 64 65 66 67 68 69 70 71 72
9 2 72 73 74 75 76 77 78 79 80 81

100
examples/rigid/in.rigid.poems
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@ -1,81 +1,51 @@
# 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
#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
# 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 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
#group clump1 id <> 1 9 thermo 100
#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 #dump 1 all atom 50 dump.rigid.poems
#fix 2 all poems group clump5 clump6 clump7 clump8 clump9
neigh_modify exclude group clump1 clump1 #dump 2 all image 100 image.*.jpg type type &
neigh_modify exclude group clump2 clump2 # axes yes 0.8 0.02 view 60 -30
neigh_modify exclude group clump3 clump3 #dump_modify 2 pad 5
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 3 all movie 100 movie.mpg type type &
# axes yes 0.8 0.02 view 60 -30
#dump_modify 3 pad 5
#dump 1 all atom 50 dump.rigid.poems timestep 0.0001
thermo 50
#dump 2 all image 100 image.*.jpg type type & run 10000
# 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

104
examples/rigid/in.rigid.poems2
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@ -1,81 +1,53 @@
# 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
#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
# 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 # 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
fix 1 all poems group clump1 clump2 clump3 clump4 &
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.poems2 #dump 1 all atom 50 dump.rigid.poems2
#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

50
examples/rigid/in.rigid.poems3 Normal file
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@ -0,0 +1,50 @@
# 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 poems file unconnected-bodies.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.poems
#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.poems4 Normal file
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@ -0,0 +1,50 @@
# 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
# 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 file connected-bodies.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.poems
#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

51
examples/rigid/in.rigid.poems5 Normal file
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@ -0,0 +1,51 @@
# 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
# 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 file connected-bodies2.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.poems
#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

328
examples/rigid/log.20Mar22.rigid.poems.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
# 1 chain of connected bodies
group clump1 id <> 1 9
9 atoms in group clump1
group clump2 id <> 9 18
10 atoms in group clump2
group clump3 id <> 18 27
10 atoms in group clump3
group clump4 id <> 27 36
10 atoms in group clump4
group clump5 id <> 36 45
10 atoms in group clump5
group clump6 id <> 45 54
10 atoms in group clump6
group clump7 id <> 54 63
10 atoms in group clump7
group clump8 id <> 63 72
10 atoms in group clump8
group clump9 id <> 72 81
10 atoms in group clump9
fix 1 all poems group clump1 clump2 clump3 clump4 clump5 clump6 clump7 clump8 clump9
1 clusters, 9 bodies, 8 joints, 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.poems
#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
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- fix poems command:
@Article{Mukherjee08,
author = {R. M. Mukherjee, P. S. Crozier, S. J. Plimpton, K. S. Anderson},
title = {Substructured molecular dynamics using multibody dynamics algorithms},
journal = {Intl.~J.~Non-linear Mechanics},
year = 2008,
volume = 43,
pages = {1045--1055}
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
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/atomonly/newton
stencil: half/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.666 | 3.666 | 3.666 Mbytes
Step Temp E_pair E_mol TotEng Press
0 217.7783 3430.3907 0 3466.6871 -2.7403788
50 13679.637 1404.2468 0 3684.1863 12.446066
100 16777.225 888.87665 0 3685.0808 -31.828677
150 19595.365 418.45042 0 3684.3446 40.709078
200 18524.188 596.47273 0 3683.8375 -0.8159371
250 21015.789 180.96521 0 3683.5967 -10.042469
300 20785.513 219.25314 0 3683.5053 2.6452719
350 21072.46 171.2554 0 3683.3321 7.0609024
400 19956.414 356.36381 0 3682.4328 19.320259
450 20724.42 227.73284 0 3681.8028 8.1259249
500 20152.578 322.71466 0 3681.4777 5.4929878
550 20017.022 345.29701 0 3681.4673 5.4661666
600 17897.743 698.72196 0 3681.6791 3.2854742
650 17297.758 796.60256 0 3679.5623 15.191113
700 18581.934 584.29715 0 3681.2861 5.1588289
750 21774.158 52.821062 0 3681.8474 -10.775664
800 21604.055 81.188546 0 3681.8644 -3.2045742
850 17821.483 711.53827 0 3681.7854 7.438428
900 21033.292 175.98127 0 3681.5299 -16.345167
950 20968.166 186.59847 0 3681.2929 -2.330456
1000 20490.66 266.19374 0 3681.3037 11.787982
1050 20222.396 310.94072 0 3681.34 -8.3459539
1100 21321.687 127.61533 0 3681.2299 -1.2184716
1150 20849.582 206.01696 0 3680.9472 -0.86699118
1200 21815.003 45.317409 0 3681.1512 1.5988314
1250 18655.437 572.41453 0 3681.654 10.064083
1300 20780.781 217.36511 0 3680.8286 6.0538604
1350 20558.971 254.36489 0 3680.8601 -3.6773868
1400 21485.029 99.812844 0 3680.6511 -16.185479
1450 21771.107 52.159653 0 3680.6775 -2.4756655
1500 21520.949 93.503876 0 3680.3286 2.1023573
1550 21351.419 121.6813 0 3680.2511 5.5159876
1600 20778.804 216.92191 0 3680.0559 15.089203
1650 21477.636 100.21873 0 3679.8247 -1.1045277
1700 18501.33 596.4807 0 3680.0357 -15.6798
1750 18563.64 587.34824 0 3681.2882 33.532308
1800 19110.175 494.82517 0 3679.8543 18.024074
1850 21364.178 119.23765 0 3679.9339 2.5290144
1900 20146.588 322.15509 0 3679.9197 5.7317299
1950 20692.676 231.25264 0 3680.0319 4.297803
2000 20943.902 189.11251 0 3679.7629 -22.643824
2050 19667.823 401.86882 0 3679.8394 3.6241915
2100 20280.125 299.81485 0 3679.8357 7.4804047
2150 19181.201 483.6306 0 3680.4975 22.63342
2200 21301.144 130.54014 0 3680.7308 4.7074288
2250 20484.876 266.98315 0 3681.1291 -8.6578278
2300 18648.161 573.07329 0 3681.1001 -5.2550954
2350 21515.748 95.243054 0 3681.201 -9.386512
2400 21462.551 104.18267 0 3681.2745 -29.46442
2450 20107.732 330.99437 0 3682.2831 35.38497
2500 20771.509 220.47713 0 3682.3953 -12.324858
2550 20499.887 265.58494 0 3682.2327 -22.713874
2600 21462.182 105.24427 0 3682.2747 -10.175788
2650 21004.949 181.51383 0 3682.3387 4.949195
2700 18673.552 570.45017 0 3682.7089 21.201437
2750 21257.562 139.198 0 3682.1249 -7.5793039
2800 21559.645 88.844759 0 3682.119 -6.2360467
2850 20865.227 204.46262 0 3682.0004 0.39575069
2900 19428.614 443.93293 0 3682.0352 12.796676
2950 19630.1 410.18487 0 3681.8681 -0.50572623
3000 19663.218 404.06316 0 3681.2661 6.0827093
3050 19087.572 500.8452 0 3682.1073 -6.3526476
3100 18229.94 643.77681 0 3682.1001 11.453637
3150 18927.492 527.51919 0 3682.1011 -1.662863
3200 18320.514 628.55895 0 3681.978 21.176126
3250 18204.677 647.96462 0 3682.0775 11.331521
3300 19231.978 477.02117 0 3682.3509 3.8381593
3350 18153.44 656.70376 0 3682.2772 15.135615
3400 17476.768 770.0598 0 3682.8545 -3.394312
3450 21097.531 166.17241 0 3682.4276 3.74301
3500 17605.784 747.54808 0 3681.8454 3.3420627
3550 19238.34 476.00608 0 3682.3961 1.1413836
3600 18155.288 656.57434 0 3682.4557 3.4360446
3650 18735.622 559.2377 0 3681.8413 28.760363
3700 15310.261 1134.4215 0 3686.1317 44.207018
3750 15377.116 1123.4786 0 3686.3313 7.6773215
3800 18798.895 549.05928 0 3682.2084 -12.905825
3850 18322.563 628.87744 0 3682.6379 -16.067793
3900 19963.049 355.65441 0 3682.8292 3.4694064
3950 19925.48 361.2507 0 3682.1641 5.0058567
4000 19141.423 492.41081 0 3682.648 -12.782769
4050 20022.241 345.61655 0 3682.6568 -3.0149905
4100 21348.635 124.95646 0 3683.0624 -4.85779
4150 21011.812 181.1132 0 3683.0819 -3.9526196
4200 20222.276 312.63945 0 3683.0187 -23.63437
4250 20957.757 189.77152 0 3682.731 -1.3712469
4300 20070.215 337.5751 0 3682.611 -6.8816517
4350 21322.437 129.09228 0 3682.8318 -6.9442178
4400 19440.445 442.77531 0 3682.8495 -0.11606236
4450 20964.516 188.67174 0 3682.7577 4.8533525
4500 13530.08 1428.5497 0 3683.563 12.333187
4550 20461.637 272.58882 0 3682.8616 4.5111943
4600 17072.994 836.58228 0 3682.0812 5.7611617
4650 18860.748 539.82027 0 3683.2782 -2.5558958
4700 18373.927 621.04093 0 3683.3621 5.4020702
4750 20321.437 296.63662 0 3683.5428 8.9571617
4800 21083.122 169.84086 0 3683.6946 10.566368
4850 20499.669 267.7012 0 3684.3128 4.2924237
4900 20308.781 300.38168 0 3685.1785 -12.396923
4950 21043.303 178.56295 0 3685.7801 3.8923762
5000 20718.383 232.52208 0 3685.5859 -12.43234
5050 21005.749 184.4363 0 3685.3945 -7.6463487
5100 20714.133 233.27745 0 3685.6329 -1.6944135
5150 19577.452 422.73035 0 3685.639 -21.831219
5200 14044.647 1343.9545 0 3684.729 -6.8407194
5250 19089.805 504.0893 0 3685.7235 4.05641
5300 21094.745 169.94699 0 3685.7378 -0.66593212
5350 19907.559 366.77598 0 3684.7024 1.5248525
5400 20382.81 289.13263 0 3686.2676 -11.919321
5450 19593.693 420.70548 0 3686.3209 -1.1568628
5500 20906.08 202.09801 0 3686.4447 -2.4284971
5550 16315.465 965.56973 0 3684.8138 -33.178221
5600 19714.57 400.39687 0 3686.1586 19.950231
5650 20561.724 259.54797 0 3686.502 8.2074524
5700 19349.502 460.7789 0 3685.6959 16.252649
5750 21006.818 185.56805 0 3686.7044 -11.96089
5800 20268.2 307.97547 0 3686.0089 17.322311
5850 21018.322 184.16179 0 3687.2154 -14.379909
5900 19695.647 404.57094 0 3687.1787 -20.718904
5950 21021.687 183.66311 0 3687.2776 -15.206081
6000 18947.535 529.30554 0 3687.2281 17.863927
6050 15272.373 1141.012 0 3686.4075 -0.43375666
6100 17766.197 721.75792 0 3682.7908 11.378913
6150 18612.573 584.06688 0 3686.1623 17.543241
6200 19005.155 518.97146 0 3686.4973 -16.223107
6250 20997.507 187.55499 0 3687.1394 -11.613546
6300 19639.901 413.58048 0 3686.8974 14.407136
6350 19580.399 423.02818 0 3686.428 -5.5801796
6400 14134.119 1332.0662 0 3687.7527 84.864425
6450 21598.824 87.419966 0 3687.224 -5.8358352
6500 18208.216 649.29108 0 3683.9938 -8.1510884
6550 19364.586 459.59813 0 3687.0291 -12.053563
6600 20710.927 235.11914 0 3686.9403 -1.0470193
6650 21132.334 165.08091 0 3687.1366 1.0785471
6700 20217.285 317.589 0 3687.1365 0.055447462
6750 21232.279 148.57412 0 3687.2873 -2.4551657
6800 20292.683 304.76539 0 3686.8793 -0.42311295
6850 19056.291 510.49927 0 3686.5478 6.9533826
6900 20429.82 282.23764 0 3687.2076 -4.2360112
6950 21281.278 140.27361 0 3687.1533 -0.07475261
7000 17173.388 824.54446 0 3686.7758 10.753828
7050 18079.7 674.56274 0 3687.846 12.975804
7100 16433.233 950.73904 0 3689.6112 -10.5102
7150 19033.335 515.59672 0 3687.8193 0.29109447
7200 17286.428 809.02352 0 3690.0948 2.3015698
7250 16811.962 886.6645 0 3688.6582 -7.4787512
7300 15992.461 1023.4849 0 3688.895 -5.2354222
7350 19211.451 487.63129 0 3689.5398 8.4351737
7400 19065.682 511.95629 0 3689.57 -12.47448
7450 21369.265 128.10098 0 3689.6451 2.2930546
7500 16807.109 888.64602 0 3689.8308 14.761969
7550 18063.046 679.21873 0 3689.7264 3.8950434
7600 17794.987 724.55404 0 3690.3851 14.379016
7650 17904.751 706.14354 0 3690.2688 23.813776
7700 19670.09 411.3021 0 3689.6504 14.099245
7750 18082.562 675.23975 0 3689.0001 15.788521
7800 17776.135 726.91445 0 3689.6037 6.9780735
7850 17062.575 846.33412 0 3690.0966 -8.9289256
7900 19059.2 513.07737 0 3689.6107 16.992843
7950 16269.685 978.48914 0 3690.1033 11.180179
8000 20115.278 336.91405 0 3689.4604 -6.4882518
8050 21173.72 161.15229 0 3690.1056 -2.2164491
8100 19238.235 484.42784 0 3690.8004 23.412709
8150 18438.4 617.58743 0 3690.6542 0.89156316
8200 21438.764 117.12721 0 3690.2546 -1.7193227
8250 21195.806 157.66607 0 3690.3003 3.820447
8300 21177.549 161.13702 0 3690.7286 0.94938203
8350 21060.267 181.06887 0 3691.1135 2.8179025
8400 20087.113 343.46206 0 3691.3142 8.1484473
8450 19298.478 474.87133 0 3691.2843 -16.239664
8500 21654.353 82.083485 0 3691.1423 -8.1464138
8550 19920.544 371.34795 0 3691.4386 20.765144
8600 21692.293 75.655154 0 3691.0373 -13.316763
8650 21231.322 151.8989 0 3690.4526 -11.388238
8700 19530.647 434.89585 0 3690.0037 2.7433786
8750 19720.63 403.07773 0 3689.8493 -6.416414
8800 21321.378 136.04091 0 3689.604 1.3661635
8850 19811.906 387.80489 0 3689.7893 3.704143
8900 19734.167 400.92444 0 3689.9523 2.5685155
8950 21076.459 177.18119 0 3689.9244 -11.939513
9000 20967.246 195.42966 0 3689.9707 2.0092705
9050 21122.023 169.62103 0 3689.9582 2.3791301
9100 20169.346 328.27229 0 3689.8299 -3.5017988
9150 21418.641 119.84513 0 3689.6187 2.486073
9200 20876.042 210.26452 0 3689.6048 -5.3839897
9250 21572.38 93.74407 0 3689.1407 -8.3676952
9300 20944.78 197.98577 0 3688.7824 1.3278314
9350 20706.52 237.48767 0 3688.5744 4.6944204
9400 16412.314 953.47251 0 3688.8581 26.134976
9450 20461.68 277.76243 0 3688.0424 17.647445
9500 20893.994 205.64261 0 3687.9749 -10.642418
9550 20503.447 270.63504 0 3687.8761 -17.769897
9600 19677.799 408.05887 0 3687.692 -2.7938604
9650 17480.971 774.1855 0 3687.6806 0.59827043
9700 17799.126 721.50817 0 3688.0292 44.387928
9750 20443.384 280.16837 0 3687.399 3.0619324
9800 20545.255 263.40108 0 3687.6102 3.6229381
9850 20722.819 233.57142 0 3687.3745 0.86462694
9900 21128.462 165.09767 0 3686.508 -6.9636843
9950 21343.307 130.46714 0 3687.685 -9.7382705
10000 20623.887 250.37866 0 3687.6932 2.7529835
Loop time of 2.27157 on 1 procs for 10000 steps with 81 atoms
Performance: 38035.351 tau/day, 4402.240 timesteps/s
99.4% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.092926 | 0.092926 | 0.092926 | 0.0 | 4.09
Neigh | 0.076362 | 0.076362 | 0.076362 | 0.0 | 3.36
Comm | 0.0069691 | 0.0069691 | 0.0069691 | 0.0 | 0.31
Output | 0.0037444 | 0.0037444 | 0.0037444 | 0.0 | 0.16
Modify | 2.0832 | 2.0832 | 2.0832 | 0.0 | 91.71
Other | | 0.00841 | | | 0.37
Nlocal: 81 ave 81 max 81 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 62 ave 62 max 62 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 905 ave 905 max 905 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 905
Ave neighs/atom = 11.17284
Neighbor list builds = 991
Dangerous builds = 927
Total wall time: 0:00:02

328
examples/rigid/log.20Mar22.rigid.poems.g++.4 Normal file
View File

@ -0,0 +1,328 @@
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 = 0.001 seconds
velocity all create 100.0 4928459
# 1 chain of connected bodies
group clump1 id <> 1 9
9 atoms in group clump1
group clump2 id <> 9 18
10 atoms in group clump2
group clump3 id <> 18 27
10 atoms in group clump3
group clump4 id <> 27 36
10 atoms in group clump4
group clump5 id <> 36 45
10 atoms in group clump5
group clump6 id <> 45 54
10 atoms in group clump6
group clump7 id <> 54 63
10 atoms in group clump7
group clump8 id <> 63 72
10 atoms in group clump8
group clump9 id <> 72 81
10 atoms in group clump9
fix 1 all poems group clump1 clump2 clump3 clump4 clump5 clump6 clump7 clump8 clump9
1 clusters, 9 bodies, 8 joints, 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.poems
#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
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- fix poems command:
@Article{Mukherjee08,
author = {R. M. Mukherjee, P. S. Crozier, S. J. Plimpton, K. S. Anderson},
title = {Substructured molecular dynamics using multibody dynamics algorithms},
journal = {Intl.~J.~Non-linear Mechanics},
year = 2008,
volume = 43,
pages = {1045--1055}
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
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/atomonly/newton
stencil: half/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.514 | 3.545 | 3.639 Mbytes
Step Temp E_pair E_mol TotEng Press
0 217.7783 3430.3907 0 3466.6871 -2.7403788
50 13679.637 1404.2468 0 3684.1863 12.446066
100 16777.225 888.87665 0 3685.0808 -31.828677
150 19595.365 418.45042 0 3684.3446 40.709078
200 18524.188 596.47273 0 3683.8375 -0.8159371
250 21015.789 180.96521 0 3683.5967 -10.042469
300 20785.513 219.25314 0 3683.5053 2.6452719
350 21072.46 171.2554 0 3683.3321 7.0609024
400 19956.414 356.36381 0 3682.4328 19.320259
450 20724.42 227.73284 0 3681.8028 8.1259249
500 20152.578 322.71466 0 3681.4777 5.4929878
550 20017.022 345.29701 0 3681.4673 5.4661666
600 17897.743 698.72196 0 3681.6791 3.2854742
650 17297.758 796.60256 0 3679.5623 15.191113
700 18581.934 584.29715 0 3681.2861 5.1588289
750 21774.158 52.821062 0 3681.8474 -10.775664
800 21604.055 81.188546 0 3681.8644 -3.2045742
850 17821.483 711.53827 0 3681.7854 7.4384281
900 21033.292 175.98127 0 3681.5299 -16.345167
950 20968.166 186.59847 0 3681.2929 -2.330456
1000 20490.66 266.19374 0 3681.3037 11.787982
1050 20222.396 310.94072 0 3681.34 -8.3459539
1100 21321.687 127.61533 0 3681.2299 -1.2184716
1150 20849.582 206.01696 0 3680.9472 -0.86699115
1200 21815.003 45.317409 0 3681.1512 1.5988314
1250 18655.437 572.41453 0 3681.654 10.064083
1300 20780.781 217.36511 0 3680.8286 6.0538606
1350 20558.971 254.36489 0 3680.8601 -3.6773868
1400 21485.03 99.812843 0 3680.6511 -16.185479
1450 21771.107 52.159652 0 3680.6775 -2.4756656
1500 21520.949 93.503872 0 3680.3286 2.1023574
1550 21351.419 121.68131 0 3680.2511 5.5159875
1600 20778.804 216.92191 0 3680.0559 15.089203
1650 21477.636 100.21877 0 3679.8247 -1.104524
1700 18501.329 596.48084 0 3680.0357 -15.679806
1750 18563.639 587.34841 0 3681.2882 33.532316
1800 19110.174 494.82524 0 3679.8543 18.024079
1850 21364.178 119.23767 0 3679.9339 2.5290075
1900 20146.588 322.15506 0 3679.9197 5.7317368
1950 20692.674 231.25288 0 3680.0319 4.2977982
2000 20943.904 189.11229 0 3679.7629 -22.643749
2050 19667.815 401.87016 0 3679.8394 3.6240972
2100 20280.109 299.81759 0 3679.8357 7.4803647
2150 19181.146 483.63975 0 3680.4974 22.634167
2200 21301.194 130.53171 0 3680.7308 4.7072523
2250 20484.79 266.99736 0 3681.1291 -8.6583002
2300 18648.002 573.09962 0 3681.1 -5.2548835
2350 21515.851 95.225745 0 3681.2009 -9.3875216
2400 21462.37 104.21272 0 3681.2744 -29.459857
2450 20108.034 330.94394 0 3682.2829 35.37058
2500 20771.818 220.42545 0 3682.3951 -12.318936
2550 20502.815 265.09577 0 3682.2316 -22.726822
2600 21462.006 105.2733 0 3682.2744 -10.180394
2650 21009.656 180.72738 0 3682.3367 4.9580828
2700 18680.012 569.37179 0 3682.7071 21.114114
2750 21256.19 139.42201 0 3682.1203 -7.4744399
2800 21552.267 90.071446 0 3682.1159 -6.2906304
2850 20879.958 202.00905 0 3682.0021 0.57990903
2900 19018.645 512.35214 0 3682.1262 13.883084
2950 19819.365 378.55747 0 3681.785 -0.7348943
3000 20269.229 303.35149 0 3681.5563 6.3088075
3050 19236.727 475.99457 0 3682.1158 -10.703575
3100 18391.55 616.96976 0 3682.2281 9.850079
3150 20258.563 305.82076 0 3682.248 7.1951283
3200 20716.384 229.15502 0 3681.8856 2.9042294
3250 18662.237 572.0784 0 3682.4512 9.2108597
3300 19162.278 488.60646 0 3682.3195 3.3306562
3350 21235.679 142.98279 0 3682.2626 0.29397483
3400 17677.053 736.09247 0 3682.2679 32.75269
3450 20852.392 206.65618 0 3682.0548 -4.8319056
3500 21182.918 151.46754 0 3681.9539 -5.6330382
3550 20589.85 250.40724 0 3682.049 12.582133
3600 20973.659 186.28043 0 3681.8903 10.935266
3650 17838.632 707.92145 0 3681.0268 -17.200926
3700 21538.002 92.744409 0 3682.4114 -0.72124229
3750 21390.294 117.90865 0 3682.9576 -7.8431786
3800 17921.046 696.50311 0 3683.344 -9.4641531
3850 20356.471 290.22624 0 3682.9715 2.4593463
3900 20374.077 287.10249 0 3682.782 -1.9519082
3950 20563.915 255.29993 0 3682.619 -6.124649
4000 20991.467 184.76183 0 3683.3397 1.8954961
4050 17805.623 716.24698 0 3683.8509 -20.454944
4100 19916.389 363.86301 0 3683.2611 -0.27912557
4150 19221.623 480.01232 0 3683.6161 -11.562492
4200 20526.82 261.78571 0 3682.9224 -3.9522917
4250 20922.813 196.1799 0 3683.3154 0.11947446
4300 19956.66 357.78133 0 3683.8914 19.156093
4350 19735.73 394.45981 0 3683.7482 14.865775
4400 21702.656 67.099805 0 3684.2092 -13.502538
4450 18163.055 656.97231 0 3684.1482 -0.6243111
4500 17477.718 771.25976 0 3684.2127 -0.4664004
4550 20676.507 238.19814 0 3684.2827 -19.444969
4600 17322.922 796.77058 0 3683.9242 27.003966
4650 11905.158 1704.9151 0 3689.1082 15.574169
4700 18689.079 569.80982 0 3684.6563 -14.67311
4750 19821.745 381.01914 0 3684.6433 5.0436795
4800 20621.335 247.96269 0 3684.8518 -16.407263
4850 21923.814 30.965964 0 3684.935 -13.418244
4900 18840.555 544.41538 0 3684.5079 11.005357
4950 15366.601 1124.2481 0 3685.3482 17.412375
5000 18274.314 639.01311 0 3684.732 5.3261109
5050 21173.687 155.83673 0 3684.7845 5.4056809
5100 21738.219 61.75201 0 3684.7885 -2.631945
5150 16597.949 918.84841 0 3685.1732 -10.124101
5200 20752.758 225.95919 0 3684.7522 -5.2441372
5250 17652.088 741.2645 0 3683.2793 2.0080739
5300 19907.523 366.53115 0 3684.4516 8.4266792
5350 20104.189 334.14522 0 3684.8433 17.21925
5400 21499.848 101.71631 0 3685.0243 -6.1103541
5450 21203.533 151.14574 0 3685.068 -5.9468503
5500 21076.513 172.45652 0 3685.2088 5.1418181
5550 20158.398 325.56609 0 3685.2992 -1.6486034
5600 20787.836 221.19563 0 3685.835 -10.66805
5650 19687.154 404.77204 0 3685.9644 -23.49128
5700 20419.311 282.58328 0 3685.8017 -0.52808211
5750 19738.522 395.95893 0 3685.7126 1.3889817
5800 18300.025 635.66905 0 3685.6732 23.490447
5850 20585.004 255.02032 0 3685.8543 -0.20699939
5900 20373.839 290.15881 0 3685.7987 -7.9712187
5950 18163.832 659.91192 0 3687.2173 5.4494586
6000 21049.247 177.43029 0 3685.6382 2.9138342
6050 21239.803 145.77613 0 3685.7433 -1.4927769
6100 20686.361 237.86454 0 3685.5913 -0.95516297
6150 20461.754 275.31546 0 3685.6079 -3.4166412
6200 19264.208 474.73017 0 3685.4316 11.750757
6250 21180.813 155.31746 0 3685.4529 2.8188219
6300 21047.543 177.4394 0 3685.3632 1.8641486
6350 20232.576 313.17716 0 3685.2731 2.8150209
6400 20185.616 321.33454 0 3685.6038 -3.8697311
6450 18969.632 523.95865 0 3685.5639 0.6725512
6500 17592.574 753.49959 0 3685.5952 -1.2557393
6550 21279.049 138.42524 0 3684.9335 -1.208945
6600 21408.457 116.4143 0 3684.4904 -1.5332953
6650 19758.218 391.17316 0 3684.2096 1.8511312
6700 20766.943 223.44631 0 3684.6036 -2.3672623
6750 20399.631 284.09914 0 3684.0377 -5.4089876
6800 21296.628 135.14662 0 3684.5847 -3.8442549
6850 20641.481 244.4451 0 3684.692 1.4020639
6900 20852.81 209.23009 0 3684.6984 1.8512104
6950 20940.555 194.66882 0 3684.7614 -6.554676
7000 19496.988 435.28199 0 3684.78 -15.120269
7050 19796.829 385.04227 0 3684.5138 -4.1068804
7100 19945.264 360.42431 0 3684.635 -4.0629042
7150 19431.123 446.12911 0 3684.6497 -6.8321751
7200 16864.851 873.80043 0 3684.6089 14.309069
7250 20438.75 277.85982 0 3684.3181 -11.41223
7300 17688.684 734.01576 0 3682.1298 35.938373
7350 21573.419 88.63421 0 3684.204 -3.9032749
7400 21198.486 150.72249 0 3683.8034 -7.1477117
7450 20586.708 252.93928 0 3684.0572 -7.6634645
7500 21815.377 48.180377 0 3684.0765 0.97457507
7550 17791.352 718.87564 0 3684.101 28.248235
7600 21828.874 45.928597 0 3684.0742 -0.25814944
7650 20827.961 212.35674 0 3683.6835 -3.4083384
7700 21319.176 130.43547 0 3683.6315 -12.434856
7750 20127.904 328.69643 0 3683.3471 -16.975711
7800 21741.772 59.679206 0 3683.3078 3.6261863
7850 19612.334 414.37418 0 3683.0964 1.3763274
7900 20071.318 337.74624 0 3682.9658 -0.40982763
7950 17925.664 695.29582 0 3682.9065 17.104439
8000 19125.978 492.76383 0 3680.4268 10.807662
8050 20233.848 310.42681 0 3682.7347 13.386237
8100 20551.619 257.86699 0 3683.1368 -13.97515
8150 21578.323 86.88362 0 3683.2708 -9.6811587
8200 21154.833 157.72897 0 3683.5344 0.62312375
8250 21321.143 129.83967 0 3683.3636 1.9536438
8300 21041.696 176.04177 0 3682.9911 4.7475567
8350 19883.39 369.32649 0 3683.2247 -7.0959328
8400 21626.067 79.062992 0 3683.4075 -14.919059
8450 21375.201 120.86836 0 3683.4019 -5.3461514
8500 20281.059 303.10304 0 3683.2796 3.7975093
8550 21170.533 154.48432 0 3682.9065 -1.1568561
8600 17754.931 724.00158 0 3683.1568 14.15254
8650 20685.478 235.65879 0 3683.2385 -5.2694179
8700 21489.165 101.90509 0 3683.4326 -4.2510612
8750 21106.682 165.41638 0 3683.1968 -3.9186708
8800 19149.516 491.5843 0 3683.1702 -11.419849
8850 21451.865 108.1814 0 3683.4923 -7.8256219
8900 19567.4 421.81206 0 3683.0454 -0.71997056
8950 20934.097 194.48033 0 3683.4965 -7.0106879
9000 18531.559 595.25957 0 3683.8528 3.7449399
9050 18868.821 537.22549 0 3682.029 9.9926092
9100 19972.527 354.73119 0 3683.4858 -0.30871263
9150 19641.651 409.18618 0 3682.7947 -1.3036238
9200 20019.08 346.19657 0 3682.7099 6.7425386
9250 19259.286 473.04973 0 3682.9308 -24.120659
9300 21597.757 82.971857 0 3682.598 -13.748483
9350 19348.379 457.23576 0 3681.9656 3.1571402
9400 19129.588 493.35235 0 3681.617 8.6293783
9450 20337.025 291.20959 0 3680.7138 6.8590795
9500 20581.788 249.65891 0 3679.9569 -18.892836
9550 19482.069 433.0077 0 3680.0192 23.029778
9600 19182.794 482.96871 0 3680.101 -11.081731
9650 20086.771 332.5311 0 3680.3263 -18.939681
9700 20274.046 300.98818 0 3679.9959 6.7538762
9750 18743.595 555.08045 0 3679.0129 8.2757138
9800 19464.311 435.66288 0 3679.7148 7.0528759
9850 21249.848 138.27382 0 3679.9152 -10.847402
9900 21156.214 153.84621 0 3679.8819 -7.8359674
9950 21643.134 72.547515 0 3679.7365 -10.507744
10000 19587.948 414.64942 0 3679.3075 6.1173553
Loop time of 2.36879 on 4 procs for 10000 steps with 81 atoms
Performance: 36474.344 tau/day, 4221.568 timesteps/s
99.2% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.005348 | 0.024925 | 0.056071 | 12.2 | 1.05
Neigh | 0.0075012 | 0.022046 | 0.043933 | 9.3 | 0.93
Comm | 0.13135 | 0.16461 | 0.1917 | 5.9 | 6.95
Output | 0.0036298 | 0.004271 | 0.0056384 | 1.2 | 0.18
Modify | 2.1147 | 2.1322 | 2.1418 | 0.7 | 90.01
Other | | 0.02072 | | | 0.87
Nlocal: 20.25 ave 81 max 0 min
Histogram: 3 0 0 0 0 0 0 0 0 1
Nghost: 41 ave 78 max 11 min
Histogram: 2 0 0 0 0 0 0 1 0 1
Neighs: 193.5 ave 774 max 0 min
Histogram: 3 0 0 0 0 0 0 0 0 1
Total # of neighbors = 774
Ave neighs/atom = 9.5555556
Neighbor list builds = 989
Dangerous builds = 915
Total wall time: 0:00:02

330
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@ -0,0 +1,330 @@
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
# 2 chains of connected bodies
group clump1 id <> 1 9
9 atoms in group clump1
group clump2 id <> 9 18
10 atoms in group clump2
group clump3 id <> 18 27
10 atoms in group clump3
group clump4 id <> 27 36
10 atoms in group clump4
group clump5 id <> 37 45
9 atoms in group clump5
group clump6 id <> 45 54
10 atoms in group clump6
group clump7 id <> 54 63
10 atoms in group clump7
group clump8 id <> 63 72
10 atoms in group clump8
group clump9 id <> 72 81
10 atoms in group clump9
#fix 1 all poems group clump1 clump2 clump3 clump4
#fix 2 all poems group clump5 clump6 clump7 clump8 clump9
fix 1 all poems group clump1 clump2 clump3 clump4 clump5 clump6 clump7 clump8 clump9
2 clusters, 9 bodies, 7 joints, 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.poems2
#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
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- fix poems command:
@Article{Mukherjee08,
author = {R. M. Mukherjee, P. S. Crozier, S. J. Plimpton, K. S. Anderson},
title = {Substructured molecular dynamics using multibody dynamics algorithms},
journal = {Intl.~J.~Non-linear Mechanics},
year = 2008,
volume = 43,
pages = {1045--1055}
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
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/atomonly/newton
stencil: half/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.666 | 3.666 | 3.666 Mbytes
Step Temp E_pair E_mol TotEng Press
0 196.00047 3632.2347 0 3668.5311 -2.7403788
50 12774.759 1538.7382 0 3904.4344 18.086359
100 19803.641 237.21132 0 3904.5523 -3.1528278
150 20259.6 152.62072 0 3904.3985 -4.6173524
200 20705.978 69.977442 0 3904.4178 9.0928158
250 19552.211 283.50525 0 3904.285 15.670465
300 19266.324 333.5792 0 3901.4169 7.2119197
350 20738.325 63.738945 0 3904.1694 -23.03999
400 20616.682 86.082444 0 3903.9864 -13.783584
450 19831.326 230.13858 0 3902.6063 0.42074361
500 20365.825 131.47231 0 3902.9213 0.6921524
550 20794.102 52.163238 0 3902.9229 4.5895354
600 20853.873 40.899172 0 3902.7275 2.3593042
650 19255.802 336.29509 0 3902.1844 10.341742
700 18526.969 471.02462 0 3901.9448 -0.61898691
750 18960.662 391.26068 0 3902.4944 12.04731
800 20142.432 172.05177 0 3902.1317 4.6838621
850 19932.48 210.71175 0 3901.9118 3.4716043
900 20243.528 153.13972 0 3901.9411 3.6490762
950 20388.132 126.88722 0 3902.4671 -4.4518463
1000 20076.333 184.61915 0 3902.4586 -2.272315
1050 20859.506 39.696993 0 3902.5684 6.45166
1100 15284.661 1072.1908 0 3902.6836 21.194042
1150 19658.317 261.99809 0 3902.4272 -2.874422
1200 20767.681 56.717094 0 3902.5839 -34.817444
1250 20625.583 82.586399 0 3902.1388 11.697329
1300 20690.013 71.006478 0 3902.4903 -29.292777
1350 20936.019 26.022786 0 3903.0634 1.0316025
1400 19753.559 244.81785 0 3902.8844 6.7138514
1450 15690.149 998.342 0 3903.9252 48.124557
1500 20234.455 155.92516 0 3903.0465 13.17221
1550 20779.631 55.063009 0 3903.1428 -2.639045
1600 20642.753 80.233905 0 3902.9659 -2.4688467
1650 18785.696 423.90402 0 3902.7365 -5.6466663
1700 20965.076 20.760444 0 3903.182 -0.45364296
1750 18935.406 396.96067 0 3903.5173 25.913302
1800 20581.559 91.756972 0 3903.1567 3.8217234
1850 20616.946 85.184849 0 3903.1378 4.1907972
1900 16602.053 828.40949 0 3902.8637 -0.49505122
1950 20175.526 166.53362 0 3902.7421 5.603825
2000 20261.924 150.39322 0 3902.6014 -1.196958
2050 20170.339 167.40504 0 3902.6531 -0.80849882
2100 19820.132 231.26755 0 3901.6624 3.1476607
2150 20666.19 75.838461 0 3902.9106 0.53899287
2200 19873.51 222.53286 0 3902.8124 7.9310276
2250 18548.063 467.69698 0 3902.5235 16.905356
2300 20616.61 84.762399 0 3902.6531 -6.7872951
2350 18167.738 538.13635 0 3902.5322 -11.458285
2400 20120.227 177.01954 0 3902.9875 -1.2593018
2450 20436.599 118.32469 0 3902.8801 -6.5989174
2500 18919.923 400.26361 0 3903.9531 32.37476
2550 19675.809 259.77151 0 3903.4398 19.437327
2600 19739.842 247.86388 0 3903.3901 -7.519784
2650 20557.026 96.530313 0 3903.387 0.60211646
2700 20666.602 76.099892 0 3903.2484 0.16825503
2750 20924.585 28.453883 0 3903.3771 2.4227171
2800 20360.659 132.8596 0 3903.352 4.1440877
2850 20783.475 54.518625 0 3903.3102 -0.57312067
2900 20456.181 115.03745 0 3903.2191 -20.118887
2950 20779.493 55.321394 0 3903.3756 -0.26783079
3000 20011.867 197.30216 0 3903.2035 -1.4704201
3050 20741.875 62.208723 0 3903.2966 -7.5432815
3100 21001.754 14.148298 0 3903.362 2.9676438
3150 20244.086 154.44639 0 3903.3512 -1.9071213
3200 20639.615 81.136426 0 3903.2873 1.4826467
3250 20735.244 63.529571 0 3903.3895 2.1127055
3300 20142.891 173.22282 0 3903.3878 4.7739415
3350 19963.765 206.21899 0 3903.2126 5.5410771
3400 16628.667 824.13627 0 3903.519 36.087673
3450 19228.218 342.81569 0 3903.5968 3.1057274
3500 19759.293 244.57876 0 3903.707 2.2339557
3550 19853.21 227.06362 0 3903.584 -1.0882119
3600 19673.516 260.64854 0 3903.8923 -10.63775
3650 19619.238 270.5393 0 3903.7316 -6.3746003
3700 20756.865 59.790243 0 3903.6542 -8.3015766
3750 20265.025 150.47347 0 3903.2559 -5.7284695
3800 20944.683 24.669276 0 3903.3142 -0.070552298
3850 19344.831 320.59492 0 3902.971 13.040749
3900 19978.209 203.00247 0 3902.6708 0.15638133
3950 19864.118 224.19359 0 3902.734 0.453229
4000 17606.216 642.71493 0 3903.1252 -12.656002
4050 18017.895 566.54102 0 3903.1883 12.133906
4100 20092.963 182.17593 0 3903.095 7.7445947
4150 20555.337 96.395074 0 3902.939 -6.5429752
4200 20709.781 67.869199 0 3903.0138 -2.8653003
4250 18956.203 392.20748 0 3902.6155 -1.6249728
4300 17816.204 603.72704 0 3903.0241 23.089239
4350 18979.742 388.04678 0 3902.8138 3.2511108
4400 20272.085 148.82367 0 3902.9135 1.9518268
4450 18820.003 417.74789 0 3902.9337 6.3979299
4500 19991.936 200.50131 0 3902.7117 3.5118553
4550 20915.092 29.663898 0 3902.8291 -2.3174641
4600 20690.37 71.125087 0 3902.6752 -12.008575
4650 18893.76 404.50849 0 3903.3529 15.006184
4700 18611.123 456.1263 0 3902.6306 -5.3574892
4750 20497.821 106.5856 0 3902.4784 0.85039837
4800 20803.214 50.120522 0 3902.5675 3.8610873
4850 18849.598 411.72635 0 3902.3927 9.2029058
4900 18121.714 546.68042 0 3902.5533 9.4522272
4950 20377.499 128.99323 0 3902.6041 5.3825395
5000 20686.114 72.039749 0 3902.8016 -5.706271
5050 20180.449 165.51368 0 3902.634 -16.418461
5100 20274.947 148.36657 0 3902.9864 -5.6668309
5150 18042.324 560.74137 0 3901.9125 3.6791541
5200 20794.666 52.204446 0 3903.0685 -1.4517721
5250 19073.55 371.18834 0 3903.3272 -13.457439
5300 20821.412 47.364313 0 3903.1813 2.258098
5350 20583.073 91.271191 0 3902.9513 5.4323985
5400 20490.967 108.41184 0 3903.0353 4.122905
5450 18141.79 543.66874 0 3903.2594 -0.19951075
5500 20274.012 148.55528 0 3903.002 5.0489974
5550 17806.237 605.43454 0 3902.8858 43.80619
5600 20999.825 14.341937 0 3903.1983 1.0879933
5650 20930.929 27.025347 0 3903.1234 -7.0860209
5700 20677.725 73.853093 0 3903.0614 2.6864775
5750 20521.264 102.87509 0 3903.1092 2.6940548
5800 20792.571 52.596021 0 3903.0721 1.2910217
5850 20518.674 103.26595 0 3903.0204 -9.2547271
5900 18417.885 491.66696 0 3902.3865 -12.049357
5950 17243.837 709.37858 0 3902.6817 -6.2357188
6000 20262.525 149.56918 0 3901.8885 -0.28964823
6050 19883.554 219.14043 0 3901.2801 2.3071707
6100 16548.178 838.47869 0 3902.956 -11.715644
6150 19601.177 272.14674 0 3901.9944 -0.9008056
6200 20499.796 106.2363 0 3902.4949 0.79071424
6250 19601.106 272.50139 0 3902.3359 -1.9306693
6300 17210.685 712.70535 0 3899.8692 4.8890923
6350 19911.896 214.91041 0 3902.2985 12.691129
6400 18834.642 411.87123 0 3899.7678 -1.9447856
6450 20216.311 158.39781 0 3902.1591 2.6009109
6500 20452.025 114.97122 0 3902.3832 0.14644416
6550 19142.589 357.34097 0 3902.2649 2.8968485
6600 20412.915 122.08784 0 3902.2573 3.1343105
6650 17317.867 699.39994 0 3906.4123 42.25563
6700 20479.771 109.8036 0 3902.3537 1.3520625
6750 20306.902 142.12484 0 3902.6623 2.2032106
6800 20755.367 58.994834 0 3902.5814 -0.90518094
6850 20471.259 111.7197 0 3902.6936 1.5799331
6900 20702.025 69.15032 0 3902.8586 9.3910371
6950 20477.695 110.34414 0 3902.5099 1.8181164
7000 20560.727 95.057704 0 3902.5998 -15.686006
7050 20336.675 136.39386 0 3902.4448 1.3704327
7100 20757.399 58.950153 0 3902.913 -6.4250981
7150 20870.958 38.095649 0 3903.088 -4.1962169
7200 20706.869 68.489134 0 3903.0944 2.8322659
7250 20386.713 127.7432 0 3903.0604 6.0287391
7300 18391.773 497.21001 0 3903.0939 19.202343
7350 20178.898 166.4993 0 3903.3322 1.5682417
7400 16858.704 781.78682 0 3903.7691 21.317514
7450 17509.513 660.71963 0 3903.2221 -5.9456143
7500 19974.601 204.20412 0 3903.2043 -0.69202711
7550 20917.053 29.73415 0 3903.2626 -3.9962577
7600 20923.518 28.482703 0 3903.2083 -1.9016251
7650 20549.528 97.630612 0 3903.0987 3.5512257
7700 20861.441 39.903885 0 3903.1337 2.4426264
7750 18843.349 413.64461 0 3903.1537 2.677739
7800 20616.054 85.214364 0 3903.0021 3.9639004
7850 16478.851 851.93376 0 3903.5728 7.3763128
7900 20312.115 141.35103 0 3902.8539 4.6707271
7950 20389.623 127.16589 0 3903.0219 3.4414001
8000 20452.117 115.30715 0 3902.7362 -1.0162528
8050 20857.093 40.791886 0 3903.2164 -15.150068
8100 19817.543 233.4997 0 3903.415 0.89346046
8150 18649.521 449.9112 0 3903.5262 -0.40053588
8200 19619.276 270.37616 0 3903.5754 5.5161492
8250 20393.176 127.01336 0 3903.5275 2.122613
8300 19145.912 358.00424 0 3903.5435 3.863924
8350 19636.311 267.17226 0 3903.5262 -7.1496084
8400 19086.332 368.86693 0 3903.3729 7.0968952
8450 19494.416 292.89527 0 3902.9723 3.1750935
8500 20041.919 191.77756 0 3903.244 0.95215503
8550 20357.561 133.15478 0 3903.0736 -0.14020152
8600 16998.797 756.07003 0 3903.9954 -16.724408
8650 20853.26 41.386996 0 3903.1017 -3.2612965
8700 20767.768 57.360884 0 3903.2438 1.1157649
8750 20752.546 60.106518 0 3903.1705 0.39130547
8800 20574.407 92.99798 0 3903.0734 0.61728166
8850 20326.99 138.94203 0 3903.1995 -1.9434522
8900 17408.108 679.53222 0 3903.2559 21.935371
8950 20471.21 112.2721 0 3903.2368 1.8142747
9000 19129.591 360.35257 0 3902.8694 4.5786395
9050 20439.668 117.89541 0 3903.0191 2.5585685
9100 20780.375 54.788664 0 3903.0062 3.8312459
9150 19904.559 216.61504 0 3902.6445 12.150414
9200 20961.295 21.52065 0 3903.2419 -0.2120699
9250 19315.252 326.44175 0 3903.3402 -19.740867
9300 20653.002 78.77764 0 3903.4076 -7.8068233
9350 18961.572 391.20947 0 3902.6117 -12.660843
9400 16262.179 892.67633 0 3904.191 22.2435
9450 17064.394 743.33301 0 3903.406 36.139436
9500 18075.588 555.06436 0 3902.3954 24.598176
9550 20487.738 109.06287 0 3903.0884 2.6320759
9600 20358.609 133.36993 0 3903.4828 0.76449113
9650 19849.022 228.46312 0 3904.208 9.5547064
9700 20448.112 116.8757 0 3903.5632 -1.0845697
9750 20472.78 112.51661 0 3903.7722 -0.30676738
9800 19491.99 293.35361 0 3902.9814 -20.10857
9850 19895.603 218.42479 0 3902.7957 -0.18235641
9900 19704.336 254.55068 0 3903.5019 14.553184
9950 17689.462 627.9788 0 3903.805 4.9918088
10000 20184.205 165.29396 0 3903.1097 2.9472364
Loop time of 2.2898 on 1 procs for 10000 steps with 81 atoms
Performance: 37732.583 tau/day, 4367.197 timesteps/s
99.2% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.053341 | 0.053341 | 0.053341 | 0.0 | 2.33
Neigh | 0.056174 | 0.056174 | 0.056174 | 0.0 | 2.45
Comm | 0.0087028 | 0.0087028 | 0.0087028 | 0.0 | 0.38
Output | 0.0036774 | 0.0036774 | 0.0036774 | 0.0 | 0.16
Modify | 2.1598 | 2.1598 | 2.1598 | 0.0 | 94.32
Other | | 0.008128 | | | 0.35
Nlocal: 81 ave 81 max 81 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 113 ave 113 max 113 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 582 ave 582 max 582 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 582
Ave neighs/atom = 7.1851852
Neighbor list builds = 993
Dangerous builds = 950
Total wall time: 0:00:02

330
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@ -0,0 +1,330 @@
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
# 2 chains of connected bodies
group clump1 id <> 1 9
9 atoms in group clump1
group clump2 id <> 9 18
10 atoms in group clump2
group clump3 id <> 18 27
10 atoms in group clump3
group clump4 id <> 27 36
10 atoms in group clump4
group clump5 id <> 37 45
9 atoms in group clump5
group clump6 id <> 45 54
10 atoms in group clump6
group clump7 id <> 54 63
10 atoms in group clump7
group clump8 id <> 63 72
10 atoms in group clump8
group clump9 id <> 72 81
10 atoms in group clump9
#fix 1 all poems group clump1 clump2 clump3 clump4
#fix 2 all poems group clump5 clump6 clump7 clump8 clump9
fix 1 all poems group clump1 clump2 clump3 clump4 clump5 clump6 clump7 clump8 clump9
2 clusters, 9 bodies, 7 joints, 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.poems2
#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
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- fix poems command:
@Article{Mukherjee08,
author = {R. M. Mukherjee, P. S. Crozier, S. J. Plimpton, K. S. Anderson},
title = {Substructured molecular dynamics using multibody dynamics algorithms},
journal = {Intl.~J.~Non-linear Mechanics},
year = 2008,
volume = 43,
pages = {1045--1055}
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
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/atomonly/newton
stencil: half/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.514 | 3.545 | 3.639 Mbytes
Step Temp E_pair E_mol TotEng Press
0 196.00047 3632.2347 0 3668.5311 -2.7403788
50 12774.759 1538.7382 0 3904.4344 18.086358
100 19803.641 237.21132 0 3904.5523 -3.1528278
150 20259.6 152.62072 0 3904.3985 -4.6173524
200 20705.978 69.977039 0 3904.4174 9.0928122
250 19552.211 283.50525 0 3904.285 15.670466
300 19266.324 333.5792 0 3901.4169 7.2119197
350 20738.325 63.738945 0 3904.1694 -23.03999
400 20616.682 86.082444 0 3903.9864 -13.783584
450 19831.326 230.13858 0 3902.6063 0.42074361
500 20365.825 131.47271 0 3902.9217 0.69215592
550 20794.102 52.163238 0 3902.9229 4.5895354
600 20853.873 40.899172 0 3902.7275 2.3593042
650 19255.802 336.29509 0 3902.1844 10.341742
700 18526.969 471.02462 0 3901.9448 -0.61898691
750 18960.662 391.26068 0 3902.4944 12.04731
800 20142.432 172.05197 0 3902.1319 4.6838632
850 19932.48 210.71175 0 3901.9118 3.4716031
900 20243.528 153.13972 0 3901.9411 3.6490762
950 20388.132 126.88722 0 3902.4671 -4.4518463
1000 20076.333 184.61915 0 3902.4586 -2.272315
1050 20859.506 39.696993 0 3902.5684 6.45166
1100 15284.661 1072.1908 0 3902.6836 21.194042
1150 19658.317 261.99809 0 3902.4272 -2.8744219
1200 20767.681 56.717095 0 3902.5839 -34.817444
1250 20625.583 82.586198 0 3902.1386 11.697328
1300 20690.013 71.006478 0 3902.4903 -29.29278
1350 20936.019 26.022786 0 3903.0634 1.0316025
1400 19753.56 244.81784 0 3902.8844 6.7138497
1450 15690.149 998.34213 0 3903.9252 48.124569
1500 20234.455 155.92516 0 3903.0465 13.172207
1550 20779.631 55.063019 0 3903.1428 -2.6390455
1600 20642.753 80.233821 0 3902.9659 -2.4688431
1650 18785.698 423.90364 0 3902.7365 -5.6466892
1700 20965.076 20.760451 0 3903.182 -0.45366172
1750 18935.412 396.95958 0 3903.5173 25.913174
1800 20581.554 91.757912 0 3903.1567 3.8218442
1850 20616.949 85.184789 0 3903.1382 4.1907933
1900 16601.896 828.43849 0 3902.8638 -0.49468175
1950 20175.564 166.52646 0 3902.7421 5.6035728
2000 20262.525 150.28224 0 3902.6017 -1.1967705
2050 20168.994 167.65314 0 3902.6521 -0.80723928
2100 19810.955 232.96524 0 3901.6605 3.1936531
2150 20667.232 75.645145 0 3902.9103 0.54812734
2200 19863.772 224.34646 0 3902.8228 7.9294465
2250 18808.943 419.2084 0 3902.3461 14.344526
2300 20573.665 92.761842 0 3902.6999 -6.7671703
2350 19075.104 369.95414 0 3902.3809 -9.5353568
2400 20273.873 148.53775 0 3902.9586 -1.93796
2450 20087.769 182.30216 0 3902.2593 2.131796
2500 20711.602 67.530554 0 3903.0124 2.6280244
2550 19971.224 204.75926 0 3903.134 3.1760522
2600 20620.084 85.027145 0 3903.5612 -0.92888063
2650 19737.546 248.65474 0 3903.7559 -3.3218688
2700 20650.724 79.522243 0 3903.7303 -7.5918025
2750 19863.245 225.2505 0 3903.6292 9.2140221
2800 18992.457 386.73547 0 3903.8572 2.6244537
2850 18703.899 440.48356 0 3904.1685 14.561348
2900 17939.805 581.74599 0 3903.932 -8.0863089
2950 20867.516 39.38186 0 3903.7367 3.0985423
3000 19767.994 242.8847 0 3903.6243 1.5943109
3050 20397.448 126.31591 0 3903.6212 -0.14982775
3100 20978.114 19.126395 0 3903.9623 -9.6797253
3150 18303.556 513.8514 0 3903.3989 4.5940322
3200 19156.505 356.46608 0 3903.9671 10.071308
3250 17484.205 666.52199 0 3904.3377 -4.1641768
3300 18069.94 557.75947 0 3904.0447 11.868707
3350 20855.645 41.964632 0 3904.1212 5.4186293
3400 18011.986 568.76255 0 3904.3155 25.262783
3450 18669.69 446.92755 0 3904.2776 -4.194499
3500 20248.799 154.22147 0 3903.9991 3.9211572
3550 20226.024 158.64726 0 3904.2072 1.5299114
3600 20267.02 151.25631 0 3904.4082 -8.9821729
3650 20522.946 103.65382 0 3904.1994 -14.433796
3700 20892.319 35.294614 0 3904.2426 -21.264596
3750 19942.202 211.02993 0 3904.0304 -1.6428817
3800 20421.678 122.08118 0 3903.8734 1.7137935
3850 17899.53 588.82593 0 3903.5536 -24.450276
3900 20721.119 66.486999 0 3903.7312 -7.1772088
3950 20946.484 24.799445 0 3903.778 -0.4028037
4000 20985.362 17.608355 0 3903.7865 4.7522266
4050 19969.779 205.46466 0 3903.5719 18.941639
4100 20479.578 110.56561 0 3903.08 2.3715952
4150 18110.701 549.53348 0 3903.367 1.133321
4200 19321.098 325.58216 0 3903.5634 -3.7574942
4250 20734.436 63.87616 0 3903.5865 0.48350623
4300 19446.823 302.1727 0 3903.4362 4.0462392
4350 20494.669 108.1918 0 3903.501 2.9789077
4400 20379.244 129.61413 0 3903.5482 4.0881089
4450 19710.564 253.4251 0 3903.5295 5.3334683
4500 20744.753 61.785082 0 3903.406 4.0015409
4550 19948.024 208.76984 0 3902.8484 2.705423
4600 18367.368 502.69569 0 3904.0602 21.476471
4650 20559.367 96.133242 0 3903.4234 2.2549454
4700 20940.135 25.547808 0 3903.3505 -8.9042666
4750 20128.703 175.82088 0 3903.3584 -8.1450176
4800 20632.27 82.543887 0 3903.3347 -0.55649542
4850 19864.539 224.63792 0 3903.2563 7.1553461
4900 19332.037 323.15561 0 3903.1625 17.020214
4950 19055.575 373.68069 0 3902.4908 10.149457
5000 20219.484 159.21383 0 3903.5627 3.1806346
5050 17557.761 652.32864 0 3903.7659 10.733736
5100 20615.337 85.795304 0 3903.4503 -3.6035636
5150 20759.853 59.155843 0 3903.573 2.0152286
5200 20082.007 184.39375 0 3903.2839 -5.3745109
5250 18689.521 442.59842 0 3903.6208 -9.8911164
5300 20038.496 192.34221 0 3903.1749 -2.1437039
5350 19897.455 218.70142 0 3903.4154 0.64582116
5400 18732.385 434.21543 0 3903.1755 12.98676
5450 19831.487 230.79099 0 3903.2886 11.439958
5500 20079.89 184.6953 0 3903.1935 4.0906279
5550 20453.497 115.47128 0 3903.1559 7.8844436
5600 16673.041 815.52661 0 3903.1267 -20.17797
5650 19691.378 256.6412 0 3903.1928 3.7103317
5700 20345.743 135.29997 0 3903.0302 5.6373816
5750 20769.613 56.906603 0 3903.1312 -17.564762
5800 20713.369 67.38314 0 3903.1922 -5.340631
5850 20799.947 51.348865 0 3903.1909 -2.7827653
5900 19581.933 273.51588 0 3899.7997 12.347375
5950 20444.438 116.909 0 3902.9161 -0.74896654
6000 18970.948 389.99664 0 3903.1352 26.642912
6050 19414.753 307.13217 0 3902.4568 25.86316
6100 20780.042 54.586474 0 3902.7424 1.5387425
6150 20885.872 35.091585 0 3902.8456 -8.251884
6200 19825.81 231.40943 0 3902.8558 6.7196589
6250 20578.278 92.255994 0 3903.0481 -5.9647091
6300 20093.43 181.8699 0 3902.8754 -9.9906069
6350 20605.294 87.180289 0 3902.9755 -3.5643876
6400 19737.257 247.84828 0 3902.8958 -4.2783347
6450 19884.717 220.81633 0 3903.1714 3.8758905
6500 18719.372 436.94802 0 3903.4984 1.7865904
6550 20096.883 181.63346 0 3903.2784 2.395512
6600 20888.673 35.003062 0 3903.2758 2.7728947
6650 20437.85 118.16373 0 3902.9507 8.1456757
6700 19241.051 339.73065 0 3902.8882 13.740454
6750 20407.542 123.94326 0 3903.1177 7.6285942
6800 20536.785 99.976706 0 3903.0851 8.3496632
6850 20625.328 83.579677 0 3903.0849 6.5074992
6900 20705.37 68.944625 0 3903.2724 3.1905177
6950 18872.424 408.67134 0 3903.5647 6.2638845
7000 20072.762 186.18051 0 3903.3586 -22.780407
7050 20461.879 114.07495 0 3903.3117 -11.495523
7100 19811.566 234.50237 0 3903.3108 1.1212695
7150 20742.918 61.884088 0 3903.1651 -3.7907508
7200 20911.192 30.599903 0 3903.0429 -7.0262304
7250 20879.755 36.30274 0 3902.9241 -5.8018787
7300 20682.32 72.703261 0 3902.7626 -3.3446789
7350 19401.046 309.70672 0 3902.493 3.4836528
7400 20220.542 157.83897 0 3902.3838 2.3400031
7450 17691.193 625.47764 0 3901.6244 25.239568
7500 19745.294 245.02566 0 3901.5615 5.3622843
7550 19685.719 256.70983 0 3902.2133 3.4560563
7600 18830.192 415.10021 0 3902.1727 -0.10282681
7650 19613.136 270.18979 0 3902.2521 8.2241536
7700 20989.015 15.636879 0 3902.4915 1.2955204
7750 20301.583 142.90625 0 3902.4586 0.12548373
7800 18360.147 502.50342 0 3902.5307 17.117272
7850 20796.478 51.032537 0 3902.2321 -3.0993883
7900 20284.267 145.64296 0 3901.9887 -1.2682383
7950 20280.983 146.13471 0 3901.8723 3.5999841
8000 20915.869 28.730821 0 3902.0399 2.4987291
8050 20745.162 60.19981 0 3901.8964 4.0643481
8100 20509.039 103.70462 0 3901.6748 1.0771863
8150 20212.97 158.64893 0 3901.7916 3.0000215
8200 20323.463 138.25912 0 3901.8634 -1.2802945
8250 19997.284 198.37183 0 3901.5727 -2.6431964
8300 20138.402 171.75824 0 3901.092 1.7669897
8350 20367.568 130.22531 0 3901.9972 -1.2153731
8400 19945.534 208.35675 0 3901.9741 1.6021151
8450 20112.534 177.18642 0 3901.7298 2.2413008
8500 20686.7 71.116816 0 3901.9873 2.2888545
8550 18081.94 553.83586 0 3902.3432 7.8257937
8600 18320.081 505.67086 0 3898.2784 16.554878
8650 20235.305 154.43021 0 3901.709 3.1740823
8700 20355.413 132.22512 0 3901.746 4.3436482
8750 20087.188 182.11349 0 3901.9631 10.422134
8800 20400.795 124.09819 0 3902.0232 2.1179177
8850 20678.731 72.825797 0 3902.2204 -3.4491441
8900 20372.643 129.5072 0 3902.2189 -8.2166415
8950 20851.731 40.899364 0 3902.331 -5.8382839
9000 20318.076 139.61775 0 3902.2243 -4.1960802
9050 16879.415 776.53739 0 3902.3549 -14.429475
9100 19135.149 358.68223 0 3902.2284 -15.50479
9150 20689.556 70.939656 0 3902.339 -2.9876179
9200 19949.801 207.54882 0 3901.9564 6.4259245
9250 20207.027 160.2813 0 3902.3233 1.7402195
9300 20030.005 192.99466 0 3902.2548 5.300728
9350 19795.291 236.24003 0 3902.0347 5.8677745
9400 18232.093 526.18752 0 3902.501 19.344893
9450 18789.641 422.30568 0 3901.8687 -7.5185247
9500 16332.599 874.10423 0 3898.6597 16.241378
9550 18572.572 462.19972 0 3901.5649 -10.777359
9600 19859.645 223.32209 0 3901.0341 0.89631957
9650 19092.741 365.35768 0 3901.0504 6.7830005
9700 18391.154 495.72792 0 3901.4972 6.0683847
9750 17790.092 608.60997 0 3903.0714 8.2090184
9800 17681.783 628.99951 0 3903.4038 14.231747
9850 17804.412 605.54067 0 3902.654 22.308453
9900 19134.472 359.37911 0 3902.7999 8.5633158
9950 20099.055 180.28604 0 3902.3332 4.7905855
10000 20035.447 192.30744 0 3902.5754 1.8299201
Loop time of 2.31994 on 4 procs for 10000 steps with 81 atoms
Performance: 37242.315 tau/day, 4310.453 timesteps/s
99.4% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0052789 | 0.014781 | 0.038634 | 11.4 | 0.64
Neigh | 0.0081228 | 0.016514 | 0.033404 | 7.7 | 0.71
Comm | 0.12269 | 0.13668 | 0.14951 | 3.1 | 5.89
Output | 0.0034489 | 0.0039413 | 0.0050811 | 1.1 | 0.17
Modify | 2.1036 | 2.1312 | 2.1509 | 1.2 | 91.86
Other | | 0.01685 | | | 0.73
Nlocal: 20.25 ave 36 max 0 min
Histogram: 1 0 0 0 0 1 1 0 0 1
Nghost: 35.25 ave 47 max 24 min
Histogram: 1 0 1 0 0 0 0 1 0 1
Neighs: 137.5 ave 252 max 0 min
Histogram: 1 0 0 1 0 0 0 0 1 1
Total # of neighbors = 550
Ave neighs/atom = 6.7901235
Neighbor list builds = 994
Dangerous builds = 956
Total wall time: 0:00:02

329
examples/rigid/log.20Mar22.rigid.poems3.g++.1 Normal file
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@ -0,0 +1,329 @@
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 poems file unconnected-bodies.dat
WARNING: No joints between rigid bodies, use fix rigid instead (src/POEMS/fix_poems.cpp:1035)
9 clusters, 9 bodies, 0 joints, 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.poems
#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
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- fix poems command:
@Article{Mukherjee08,
author = {R. M. Mukherjee, P. S. Crozier, S. J. Plimpton, K. S. Anderson},
title = {Substructured molecular dynamics using multibody dynamics algorithms},
journal = {Intl.~J.~Non-linear Mechanics},
year = 2008,
volume = 43,
pages = {1045--1055}
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
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/atomonly/newton
stencil: half/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.666 | 3.666 | 3.666 Mbytes
Step Temp E_pair E_mol TotEng Press
0 115.29439 5235.9179 0 5272.2142 -2.7403788
50 14910.686 571.71596 0 5265.8207 32.006226
100 16298.5 136.65142 0 5267.6607 16.443791
150 16682.639 17.488068 0 5269.43 14.900278
200 16733.955 1.3724268 0 5269.4692 14.569123
250 16738.877 -0.15250573 0 5269.4939 14.496287
300 16738.611 -0.05516662 0 5269.5077 14.495909
350 16738.515 -0.01744351 0 5269.5152 14.496329
400 16738.488 -0.0060096677 0 5269.5178 14.496497
450 16738.479 -0.0012712918 0 5269.5199 14.496575
500 16738.479 -0.00081070354 0 5269.5203 14.49658
550 16738.479 -0.00083205205 0 5269.5203 14.496577
600 16738.479 -0.0005835658 0 5269.5206 14.49658
650 16738.479 -0.00047227225 0 5269.5206 14.496583
700 16738.479 0 0 5269.521 14.496593
750 16738.479 0 0 5269.5211 14.496595
800 16738.479 0 0 5269.5211 14.496596
850 16738.479 0 0 5269.5211 14.496595
900 16738.479 0 0 5269.5212 14.496593
950 16738.485 -0.003532391 0 5269.5196 14.496546
1000 16738.609 -0.051135033 0 5269.5109 14.496098
1050 16737.381 0.32991002 0 5269.5055 14.525627
1100 16737.915 0.16210932 0 5269.5058 14.531848
1150 16738.726 -0.089235332 0 5269.5098 14.509768
1200 16738.49 -0.0075446298 0 5269.5169 14.510489
1250 16738.48 0 0 5269.5214 14.510585
1300 16738.48 0 0 5269.5214 14.510587
1350 16738.48 0 0 5269.5215 14.510588
1400 16738.48 -0.00044742303 0 5269.5211 14.510581
1450 16738.481 -0.0010975104 0 5269.5207 14.51057
1500 16738.481 -0.00057925965 0 5269.5211 14.510575
1550 16738.48 0 0 5269.5216 14.510582
1600 16738.48 0 0 5269.5216 14.510581
1650 16738.481 0 0 5269.5216 14.510581
1700 16738.481 0 0 5269.5217 14.510582
1750 16738.481 0 0 5269.5217 14.510583
1800 16738.481 0 0 5269.5217 14.510585
1850 16738.481 0 0 5269.5218 14.510585
1900 16738.481 0 0 5269.5218 14.510585
1950 16738.487 -0.0031700155 0 5269.5206 14.510534
2000 16738.514 -0.013238802 0 5269.5188 14.510401
2050 16738.578 -0.03654435 0 5269.5158 14.510155
2100 16738.656 -0.063182323 0 5269.5137 14.510082
2150 16738.63 -0.056004395 0 5269.5127 14.510096
2200 16738.579 -0.038415873 0 5269.5143 14.510273
2250 16738.538 -0.023709094 0 5269.516 14.510414
2300 16738.512 -0.013252539 0 5269.5182 14.510501
2350 16738.491 -0.0045593284 0 5269.5203 14.510598
2400 16738.482 -0.00052242487 0 5269.5217 14.510655
2450 16738.486 -0.0023245722 0 5269.5211 14.510627
2500 16738.491 -0.005189304 0 5269.5197 14.510606
2550 16738.604 -0.044988104 0 5269.5155 14.510185
2600 16738.446 0.00096754005 0 5269.5117 14.510521
2650 16732.887 1.753125 0 5269.5138 14.598792
2700 16738.784 -0.10629556 0 5269.5107 14.499176
2750 16734.136 1.359459 0 5269.5135 14.594678
2800 16738.608 -0.047184149 0 5269.5147 14.510254
2850 16738.509 -0.012527238 0 5269.5181 14.509344
2900 16738.487 -0.0026065529 0 5269.521 14.509512
2950 16738.498 -0.0082248532 0 5269.519 14.509457
3000 16738.683 -0.071294028 0 5269.514 14.509005
3050 16717.444 6.5874862 0 5269.4864 14.834144
3100 16657.654 25.431253 0 5269.5074 14.467824
3150 16739.322 -0.28964062 0 5269.497 13.658821
3200 16733.615 1.4969789 0 5269.487 11.998304
3250 16737.289 0.35071214 0 5269.4974 11.918931
3300 16732.493 1.8663821 0 5269.503 12.109003
3350 16738.717 -0.087719164 0 5269.5085 11.979747
3400 16738.586 -0.045267897 0 5269.5095 11.97972
3450 16738.662 -0.071274216 0 5269.5076 11.979564
3500 16738.853 -0.13644992 0 5269.5026 11.979658
3550 16729.612 2.7475277 0 5269.4774 12.195939
3600 16728.659 3.0596069 0 5269.4893 12.241248
3650 16738.923 -0.15949792 0 5269.5014 11.991857
3700 16738.76 -0.10695054 0 5269.5028 11.992932
3750 16738.751 -0.10105954 0 5269.5057 11.993137
3800 16738.597 -0.048627545 0 5269.5097 11.993456
3850 16738.507 -0.016053927 0 5269.5138 11.992973
3900 16738.485 -0.0060825487 0 5269.5169 11.993052
3950 16738.475 -0.0014953722 0 5269.5183 11.993119
4000 16738.472 -0.00054315391 0 5269.5184 11.99315
4050 16738.472 -0.00023792127 0 5269.5187 11.993172
4100 16738.472 0 0 5269.5189 11.993188
4150 16738.472 0 0 5269.5189 11.993188
4200 16738.472 0 0 5269.519 11.993178
4250 16738.472 0 0 5269.519 11.993164
4300 16738.472 0 0 5269.5191 11.993152
4350 16738.473 0 0 5269.5191 11.993147
4400 16738.473 0 0 5269.5192 11.993149
4450 16738.473 0 0 5269.5192 11.993158
4500 16738.473 0 0 5269.5193 11.99317
4550 16738.473 0 0 5269.5193 11.993176
4600 16738.473 0 0 5269.5194 11.993174
4650 16738.473 0 0 5269.5194 11.993167
4700 16738.474 0 0 5269.5195 11.993162
4750 16738.474 0 0 5269.5195 11.99316
4800 16738.474 0 0 5269.5196 11.99316
4850 16738.474 0 0 5269.5196 11.993163
4900 16738.474 0 0 5269.5197 11.99317
4950 16738.474 0 0 5269.5197 11.993176
5000 16738.475 0 0 5269.5198 11.993174
5050 16738.475 0 0 5269.5198 11.993165
5100 16738.475 0 0 5269.5199 11.993155
5150 16738.475 0 0 5269.5199 11.99315
5200 16738.475 0 0 5269.52 11.993153
5250 16738.475 0 0 5269.52 11.993161
5300 16738.476 0 0 5269.5201 11.993173
5350 16738.476 0 0 5269.5201 11.993185
5400 16738.476 0 0 5269.5202 11.993189
5450 16738.476 0 0 5269.5202 11.993181
5500 16738.476 0 0 5269.5203 11.993165
5550 16738.483 -0.0030091905 0 5269.5195 11.993097
5600 16738.534 -0.020777802 0 5269.5177 11.992799
5650 16738.649 -0.059321662 0 5269.5153 11.993266
5700 16409.08 103.75288 0 5269.5745 23.626238
5750 16738.578 -0.036776519 0 5269.5155 11.910545
5800 16738.484 -0.0047306177 0 5269.518 11.911008
5850 16738.477 -0.00022082692 0 5269.5202 11.911078
5900 16738.477 -0.00033136078 0 5269.5203 11.91107
5950 16738.478 -0.00036902212 0 5269.5203 11.911052
6000 16738.477 0 0 5269.5206 11.911044
6050 16738.477 0 0 5269.5207 11.911034
6100 16738.478 0 0 5269.5207 11.911032
6150 16738.478 0 0 5269.5208 11.911037
6200 16738.478 0 0 5269.5208 11.911049
6250 16738.478 0 0 5269.5209 11.911062
6300 16738.478 0 0 5269.5209 11.911068
6350 16738.478 0 0 5269.521 11.911065
6400 16738.478 0 0 5269.521 11.911058
6450 16738.479 0 0 5269.5211 11.911052
6500 16738.479 0 0 5269.5211 11.911047
6550 16738.479 0 0 5269.5212 11.911046
6600 16738.479 0 0 5269.5212 11.911049
6650 16738.479 0 0 5269.5213 11.911056
6700 16738.479 0 0 5269.5213 11.911062
6750 16738.48 0 0 5269.5214 11.91106
6800 16738.48 0 0 5269.5214 11.911051
6850 16738.48 0 0 5269.5215 11.911044
6900 16738.48 0 0 5269.5215 11.911041
6950 16738.48 0 0 5269.5216 11.911045
7000 16738.48 0 0 5269.5216 11.911053
7050 16738.481 0 0 5269.5217 11.911063
7100 16738.481 0 0 5269.5217 11.911071
7150 16738.481 0 0 5269.5218 11.911072
7200 16738.481 0 0 5269.5218 11.911063
7250 16738.481 0 0 5269.5219 11.911048
7300 16738.481 0 0 5269.5219 11.911036
7350 16738.482 0 0 5269.522 11.911031
7400 16738.482 0 0 5269.522 11.911035
7450 16738.482 0 0 5269.5221 11.911046
7500 16738.482 0 0 5269.5221 11.911062
7550 16738.482 0 0 5269.5222 11.911077
7600 16738.482 0 0 5269.5222 11.911081
7650 16738.483 0 0 5269.5223 11.911071
7700 16738.483 0 0 5269.5223 11.911054
7750 16738.483 0 0 5269.5224 11.911039
7800 16738.483 0 0 5269.5224 11.911031
7850 16738.483 0 0 5269.5225 11.911031
7900 16738.483 0 0 5269.5226 11.911039
7950 16738.484 0 0 5269.5226 11.911052
8000 16738.484 0 0 5269.5227 11.911065
8050 16738.484 0 0 5269.5227 11.91107
8100 16738.484 0 0 5269.5228 11.911065
8150 16738.484 0 0 5269.5228 11.911056
8200 16738.484 0 0 5269.5229 11.911047
8250 16738.485 0 0 5269.5229 11.911042
8300 16738.485 0 0 5269.523 11.911041
8350 16738.485 0 0 5269.523 11.911046
8400 16738.485 0 0 5269.5231 11.911055
8450 16738.485 0 0 5269.5231 11.911062
8500 16738.485 0 0 5269.5232 11.91106
8550 16738.486 0 0 5269.5232 11.911053
8600 16738.487 -0.00084974054 0 5269.5227 11.911032
8650 16738.486 0 0 5269.5233 11.911046
8700 16738.486 0 0 5269.5234 11.91105
8750 16738.486 0 0 5269.5235 11.911056
8800 16738.486 0 0 5269.5235 11.911063
8850 16738.487 -0.000227631 0 5269.5234 11.911065
8900 16738.487 0 0 5269.5236 11.911068
8950 16738.487 0 0 5269.5237 11.911058
9000 16738.487 0 0 5269.5237 11.911045
9050 16738.487 0 0 5269.5238 11.911036
9100 16738.487 0 0 5269.5238 11.911034
9150 16738.488 0 0 5269.5239 11.91104
9200 16738.488 0 0 5269.5239 11.911052
9250 16738.488 0 0 5269.524 11.911068
9300 16738.488 0 0 5269.524 11.911079
9350 16738.488 0 0 5269.5241 11.911078
9400 16738.492 -0.0016306436 0 5269.5235 11.911038
9450 16738.492 -0.0032567429 0 5269.522 11.911005
9500 16738.495 -0.0036645351 0 5269.5224 11.910982
9550 16738.49 -0.0010673912 0 5269.5237 11.911012
9600 16738.489 0 0 5269.5244 11.911032
9650 16738.489 0 0 5269.5244 11.911043
9700 16738.49 0 0 5269.5245 11.911058
9750 16738.49 0 0 5269.5245 11.911071
9800 16738.49 0 0 5269.5246 11.911073
9850 16738.49 0 0 5269.5246 11.911065
9900 16738.49 0 0 5269.5247 11.911053
9950 16738.491 -0.00058544643 0 5269.5243 11.911032
10000 16738.493 -0.0015244931 0 5269.5242 11.911015
Loop time of 2.30195 on 1 procs for 10000 steps with 81 atoms
Performance: 37533.440 tau/day, 4344.148 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 | 0.0076839 | 0.0076839 | 0.0076839 | 0.0 | 0.33
Neigh | 0.029562 | 0.029562 | 0.029562 | 0.0 | 1.28
Comm | 0.0084877 | 0.0084877 | 0.0084877 | 0.0 | 0.37
Output | 0.0037958 | 0.0037958 | 0.0037958 | 0.0 | 0.16
Modify | 2.2446 | 2.2446 | 2.2446 | 0.0 | 97.51
Other | | 0.00785 | | | 0.34
Nlocal: 81 ave 81 max 81 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 69 ave 69 max 69 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 4 ave 4 max 4 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 4
Ave neighs/atom = 0.049382716
Neighbor list builds = 998
Dangerous builds = 997
Total wall time: 0:00:02

329
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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 poems file unconnected-bodies.dat
WARNING: No joints between rigid bodies, use fix rigid instead (src/POEMS/fix_poems.cpp:1035)
9 clusters, 9 bodies, 0 joints, 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.poems
#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
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- fix poems command:
@Article{Mukherjee08,
author = {R. M. Mukherjee, P. S. Crozier, S. J. Plimpton, K. S. Anderson},
title = {Substructured molecular dynamics using multibody dynamics algorithms},
journal = {Intl.~J.~Non-linear Mechanics},
year = 2008,
volume = 43,
pages = {1045--1055}
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
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/atomonly/newton
stencil: half/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.514 | 3.545 | 3.639 Mbytes
Step Temp E_pair E_mol TotEng Press
0 115.29439 5235.9179 0 5272.2142 -2.7403788
50 14910.686 571.71596 0 5265.8207 32.006226
100 16298.5 136.65142 0 5267.6607 16.443791
150 16682.639 17.488068 0 5269.43 14.900278
200 16733.955 1.3724268 0 5269.4692 14.569123
250 16738.877 -0.15250573 0 5269.4939 14.496287
300 16738.611 -0.05516662 0 5269.5077 14.495909
350 16738.515 -0.01744351 0 5269.5152 14.496329
400 16738.488 -0.0060096677 0 5269.5178 14.496497
450 16738.479 -0.0012712918 0 5269.5199 14.496575
500 16738.479 -0.00081070354 0 5269.5203 14.49658
550 16738.479 -0.00083205205 0 5269.5203 14.496577
600 16738.479 -0.0005835658 0 5269.5206 14.49658
650 16738.479 -0.00047227225 0 5269.5206 14.496583
700 16738.479 0 0 5269.521 14.496593
750 16738.479 0 0 5269.5211 14.496595
800 16738.479 0 0 5269.5211 14.496596
850 16738.479 0 0 5269.5211 14.496595
900 16738.479 0 0 5269.5212 14.496593
950 16738.485 -0.003532391 0 5269.5196 14.496546
1000 16738.609 -0.051135033 0 5269.5109 14.496098
1050 16737.381 0.32991002 0 5269.5055 14.525627
1100 16737.915 0.16210932 0 5269.5058 14.531848
1150 16738.726 -0.089235332 0 5269.5098 14.509768
1200 16738.49 -0.0075446298 0 5269.5169 14.510489
1250 16738.48 0 0 5269.5214 14.510585
1300 16738.48 0 0 5269.5214 14.510587
1350 16738.48 0 0 5269.5215 14.510588
1400 16738.48 -0.00044742303 0 5269.5211 14.510581
1450 16738.481 -0.0010975104 0 5269.5207 14.51057
1500 16738.481 -0.00057925965 0 5269.5211 14.510575
1550 16738.48 0 0 5269.5216 14.510582
1600 16738.48 0 0 5269.5216 14.510581
1650 16738.481 0 0 5269.5216 14.510581
1700 16738.481 0 0 5269.5217 14.510582
1750 16738.481 0 0 5269.5217 14.510583
1800 16738.481 0 0 5269.5217 14.510585
1850 16738.481 0 0 5269.5218 14.510585
1900 16738.481 0 0 5269.5218 14.510585
1950 16738.487 -0.0031700155 0 5269.5206 14.510534
2000 16738.514 -0.013238802 0 5269.5188 14.510401
2050 16738.578 -0.03654435 0 5269.5158 14.510155
2100 16738.656 -0.063182323 0 5269.5137 14.510082
2150 16738.63 -0.056004395 0 5269.5127 14.510096
2200 16738.579 -0.038415873 0 5269.5143 14.510273
2250 16738.538 -0.023709094 0 5269.516 14.510414
2300 16738.512 -0.013252539 0 5269.5182 14.510501
2350 16738.491 -0.0045593284 0 5269.5203 14.510598
2400 16738.482 -0.00052242487 0 5269.5217 14.510655
2450 16738.486 -0.0023245722 0 5269.5211 14.510627
2500 16738.491 -0.005189304 0 5269.5197 14.510606
2550 16738.604 -0.044988104 0 5269.5155 14.510185
2600 16738.446 0.0009675401 0 5269.5117 14.510521
2650 16732.887 1.753125 0 5269.5138 14.598792
2700 16738.784 -0.10629556 0 5269.5107 14.499176
2750 16734.136 1.359459 0 5269.5135 14.594678
2800 16738.608 -0.047184149 0 5269.5147 14.510254
2850 16738.509 -0.012527238 0 5269.5181 14.509344
2900 16738.487 -0.0026065529 0 5269.521 14.509512
2950 16738.498 -0.0082248532 0 5269.519 14.509457
3000 16738.683 -0.071294028 0 5269.514 14.509005
3050 16717.444 6.5874862 0 5269.4864 14.834144
3100 16657.654 25.431253 0 5269.5074 14.467824
3150 16739.322 -0.28964062 0 5269.497 13.658821
3200 16733.615 1.4969789 0 5269.487 11.998304
3250 16737.289 0.35071214 0 5269.4974 11.918931
3300 16732.493 1.8663821 0 5269.503 12.109003
3350 16738.717 -0.087719164 0 5269.5085 11.979747
3400 16738.586 -0.045267897 0 5269.5095 11.97972
3450 16738.662 -0.071274216 0 5269.5076 11.979564
3500 16738.853 -0.13644992 0 5269.5026 11.979658
3550 16729.612 2.7475277 0 5269.4774 12.195939
3600 16728.659 3.059607 0 5269.4893 12.241248
3650 16738.923 -0.15949792 0 5269.5014 11.991857
3700 16738.76 -0.10695054 0 5269.5028 11.992932
3750 16738.751 -0.10105954 0 5269.5057 11.993137
3800 16738.597 -0.048627545 0 5269.5097 11.993456
3850 16738.507 -0.016053927 0 5269.5138 11.992973
3900 16738.485 -0.0060825487 0 5269.5169 11.993052
3950 16738.475 -0.0014953722 0 5269.5183 11.993119
4000 16738.472 -0.00054315391 0 5269.5184 11.99315
4050 16738.472 -0.00023792126 0 5269.5187 11.993172
4100 16738.472 0 0 5269.5189 11.993188
4150 16738.472 0 0 5269.5189 11.993188
4200 16738.472 0 0 5269.519 11.993178
4250 16738.472 0 0 5269.519 11.993164
4300 16738.472 0 0 5269.5191 11.993152
4350 16738.473 0 0 5269.5191 11.993147
4400 16738.473 0 0 5269.5192 11.993149
4450 16738.473 0 0 5269.5192 11.993158
4500 16738.473 0 0 5269.5193 11.99317
4550 16738.473 0 0 5269.5193 11.993176
4600 16738.473 0 0 5269.5194 11.993174
4650 16738.473 0 0 5269.5194 11.993167
4700 16738.474 0 0 5269.5195 11.993162
4750 16738.474 0 0 5269.5195 11.99316
4800 16738.474 0 0 5269.5196 11.99316
4850 16738.474 0 0 5269.5196 11.993163
4900 16738.474 0 0 5269.5197 11.99317
4950 16738.474 0 0 5269.5197 11.993176
5000 16738.475 0 0 5269.5198 11.993174
5050 16738.475 0 0 5269.5198 11.993165
5100 16738.475 0 0 5269.5199 11.993155
5150 16738.475 0 0 5269.5199 11.99315
5200 16738.475 0 0 5269.52 11.993153
5250 16738.475 0 0 5269.52 11.993161
5300 16738.476 0 0 5269.5201 11.993173
5350 16738.476 0 0 5269.5201 11.993185
5400 16738.476 0 0 5269.5202 11.993189
5450 16738.476 0 0 5269.5202 11.993181
5500 16738.476 0 0 5269.5203 11.993165
5550 16738.483 -0.0030091905 0 5269.5195 11.993097
5600 16738.534 -0.020777802 0 5269.5177 11.992799
5650 16738.649 -0.059321662 0 5269.5153 11.993266
5700 16409.08 103.75288 0 5269.5745 23.626238
5750 16738.578 -0.036776519 0 5269.5155 11.910545
5800 16738.484 -0.0047306177 0 5269.518 11.911008
5850 16738.477 -0.00022082692 0 5269.5202 11.911078
5900 16738.477 -0.00033136078 0 5269.5203 11.91107
5950 16738.478 -0.00036902212 0 5269.5203 11.911052
6000 16738.477 0 0 5269.5206 11.911044
6050 16738.477 0 0 5269.5207 11.911034
6100 16738.478 0 0 5269.5207 11.911032
6150 16738.478 0 0 5269.5208 11.911037
6200 16738.478 0 0 5269.5208 11.911049
6250 16738.478 0 0 5269.5209 11.911062
6300 16738.478 0 0 5269.5209 11.911068
6350 16738.478 0 0 5269.521 11.911065
6400 16738.478 0 0 5269.521 11.911058
6450 16738.479 0 0 5269.5211 11.911052
6500 16738.479 0 0 5269.5211 11.911047
6550 16738.479 0 0 5269.5212 11.911046
6600 16738.479 0 0 5269.5212 11.911049
6650 16738.479 0 0 5269.5213 11.911056
6700 16738.479 0 0 5269.5213 11.911062
6750 16738.48 0 0 5269.5214 11.91106
6800 16738.48 0 0 5269.5214 11.911051
6850 16738.48 0 0 5269.5215 11.911044
6900 16738.48 0 0 5269.5215 11.911041
6950 16738.48 0 0 5269.5216 11.911045
7000 16738.48 0 0 5269.5216 11.911053
7050 16738.481 0 0 5269.5217 11.911063
7100 16738.481 0 0 5269.5217 11.911071
7150 16738.481 0 0 5269.5218 11.911072
7200 16738.481 0 0 5269.5218 11.911063
7250 16738.481 0 0 5269.5219 11.911048
7300 16738.481 0 0 5269.5219 11.911036
7350 16738.482 0 0 5269.522 11.911031
7400 16738.482 0 0 5269.522 11.911035
7450 16738.482 0 0 5269.5221 11.911046
7500 16738.482 0 0 5269.5221 11.911062
7550 16738.482 0 0 5269.5222 11.911077
7600 16738.482 0 0 5269.5222 11.911081
7650 16738.483 0 0 5269.5223 11.911071
7700 16738.483 0 0 5269.5223 11.911054
7750 16738.483 0 0 5269.5224 11.911039
7800 16738.483 0 0 5269.5224 11.911031
7850 16738.483 0 0 5269.5225 11.911031
7900 16738.483 0 0 5269.5226 11.911039
7950 16738.484 0 0 5269.5226 11.911052
8000 16738.484 0 0 5269.5227 11.911065
8050 16738.484 0 0 5269.5227 11.91107
8100 16738.484 0 0 5269.5228 11.911065
8150 16738.484 0 0 5269.5228 11.911056
8200 16738.484 0 0 5269.5229 11.911047
8250 16738.485 0 0 5269.5229 11.911042
8300 16738.485 0 0 5269.523 11.911041
8350 16738.485 0 0 5269.523 11.911046
8400 16738.485 0 0 5269.5231 11.911055
8450 16738.485 0 0 5269.5231 11.911062
8500 16738.485 0 0 5269.5232 11.91106
8550 16738.486 0 0 5269.5232 11.911053
8600 16738.487 -0.00084974055 0 5269.5227 11.911032
8650 16738.486 0 0 5269.5233 11.911046
8700 16738.486 0 0 5269.5234 11.91105
8750 16738.486 0 0 5269.5235 11.911056
8800 16738.486 0 0 5269.5235 11.911063
8850 16738.487 -0.000227631 0 5269.5234 11.911065
8900 16738.487 0 0 5269.5236 11.911068
8950 16738.487 0 0 5269.5237 11.911058
9000 16738.487 0 0 5269.5237 11.911045
9050 16738.487 0 0 5269.5238 11.911036
9100 16738.487 0 0 5269.5238 11.911034
9150 16738.488 0 0 5269.5239 11.91104
9200 16738.488 0 0 5269.5239 11.911052
9250 16738.488 0 0 5269.524 11.911068
9300 16738.488 0 0 5269.524 11.911079
9350 16738.488 0 0 5269.5241 11.911078
9400 16738.492 -0.0016306433 0 5269.5235 11.911038
9450 16738.492 -0.0032567425 0 5269.522 11.911005
9500 16738.495 -0.0036645345 0 5269.5224 11.910982
9550 16738.49 -0.001067391 0 5269.5237 11.911012
9600 16738.489 0 0 5269.5244 11.911032
9650 16738.489 0 0 5269.5244 11.911043
9700 16738.49 0 0 5269.5245 11.911058
9750 16738.49 0 0 5269.5245 11.911071
9800 16738.49 0 0 5269.5246 11.911073
9850 16738.49 0 0 5269.5246 11.911065
9900 16738.49 0 0 5269.5247 11.911053
9950 16738.491 -0.00058544648 0 5269.5243 11.911032
10000 16738.493 -0.0015244933 0 5269.5242 11.911015
Loop time of 2.36483 on 4 procs for 10000 steps with 81 atoms
Performance: 36535.358 tau/day, 4228.629 timesteps/s
99.4% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0030635 | 0.0035263 | 0.0040903 | 0.7 | 0.15
Neigh | 0.0093439 | 0.01002 | 0.010976 | 0.6 | 0.42
Comm | 0.11912 | 0.12509 | 0.13346 | 1.5 | 5.29
Output | 0.003411 | 0.0038449 | 0.0050123 | 1.1 | 0.16
Modify | 2.1961 | 2.2052 | 2.2137 | 0.5 | 93.25
Other | | 0.01717 | | | 0.73
Nlocal: 20.25 ave 27 max 9 min
Histogram: 1 0 0 0 0 1 0 0 0 2
Nghost: 31.5 ave 51 max 15 min
Histogram: 1 0 0 1 0 1 0 0 0 1
Neighs: 1 ave 4 max 0 min
Histogram: 3 0 0 0 0 0 0 0 0 1
Total # of neighbors = 4
Ave neighs/atom = 0.049382716
Neighbor list builds = 998
Dangerous builds = 997
Total wall time: 0:00:02

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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
# 1 chain of connected bodies
group clump1 id <> 1 9
9 atoms in group clump1
group clump2 id <> 9 18
10 atoms in group clump2
group clump3 id <> 18 27
10 atoms in group clump3
group clump4 id <> 27 36
10 atoms in group clump4
group clump5 id <> 36 45
10 atoms in group clump5
group clump6 id <> 45 54
10 atoms in group clump6
group clump7 id <> 54 63
10 atoms in group clump7
group clump8 id <> 63 72
10 atoms in group clump8
group clump9 id <> 72 81
10 atoms in group clump9
fix 1 all poems file connected-bodies.dat
1 clusters, 9 bodies, 8 joints, 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.poems
#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
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- fix poems command:
@Article{Mukherjee08,
author = {R. M. Mukherjee, P. S. Crozier, S. J. Plimpton, K. S. Anderson},
title = {Substructured molecular dynamics using multibody dynamics algorithms},
journal = {Intl.~J.~Non-linear Mechanics},
year = 2008,
volume = 43,
pages = {1045--1055}
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
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/atomonly/newton
stencil: half/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.666 | 3.666 | 3.666 Mbytes
Step Temp E_pair E_mol TotEng Press
0 217.7783 3430.3907 0 3466.6871 -2.7403788
50 13679.637 1404.2468 0 3684.1863 12.446066
100 16777.225 888.87665 0 3685.0808 -31.828677
150 19595.365 418.45042 0 3684.3446 40.709078
200 18524.188 596.47273 0 3683.8375 -0.8159371
250 21015.789 180.96521 0 3683.5967 -10.042469
300 20785.513 219.25314 0 3683.5053 2.6452719
350 21072.46 171.2554 0 3683.3321 7.0609024
400 19956.414 356.36381 0 3682.4328 19.320259
450 20724.42 227.73284 0 3681.8028 8.1259249
500 20152.578 322.71466 0 3681.4777 5.4929878
550 20017.022 345.29701 0 3681.4673 5.4661666
600 17897.743 698.72196 0 3681.6791 3.2854742
650 17297.758 796.60256 0 3679.5623 15.191113
700 18581.934 584.29715 0 3681.2861 5.1588289
750 21774.158 52.821062 0 3681.8474 -10.775664
800 21604.055 81.188546 0 3681.8644 -3.2045742
850 17821.483 711.53827 0 3681.7854 7.438428
900 21033.292 175.98127 0 3681.5299 -16.345167
950 20968.166 186.59847 0 3681.2929 -2.330456
1000 20490.66 266.19374 0 3681.3037 11.787982
1050 20222.396 310.94072 0 3681.34 -8.3459539
1100 21321.687 127.61533 0 3681.2299 -1.2184716
1150 20849.582 206.01696 0 3680.9472 -0.86699118
1200 21815.003 45.317409 0 3681.1512 1.5988314
1250 18655.437 572.41453 0 3681.654 10.064083
1300 20780.781 217.36511 0 3680.8286 6.0538604
1350 20558.971 254.36489 0 3680.8601 -3.6773868
1400 21485.029 99.812844 0 3680.6511 -16.185479
1450 21771.107 52.159653 0 3680.6775 -2.4756655
1500 21520.949 93.503876 0 3680.3286 2.1023573
1550 21351.419 121.6813 0 3680.2511 5.5159876
1600 20778.804 216.92191 0 3680.0559 15.089203
1650 21477.636 100.21873 0 3679.8247 -1.1045277
1700 18501.33 596.4807 0 3680.0357 -15.6798
1750 18563.64 587.34824 0 3681.2882 33.532308
1800 19110.175 494.82517 0 3679.8543 18.024074
1850 21364.178 119.23765 0 3679.9339 2.5290144
1900 20146.588 322.15509 0 3679.9197 5.7317299
1950 20692.676 231.25264 0 3680.0319 4.297803
2000 20943.902 189.11251 0 3679.7629 -22.643824
2050 19667.823 401.86882 0 3679.8394 3.6241915
2100 20280.125 299.81485 0 3679.8357 7.4804047
2150 19181.201 483.6306 0 3680.4975 22.63342
2200 21301.144 130.54014 0 3680.7308 4.7074288
2250 20484.876 266.98315 0 3681.1291 -8.6578278
2300 18648.161 573.07329 0 3681.1001 -5.2550954
2350 21515.748 95.243054 0 3681.201 -9.386512
2400 21462.551 104.18267 0 3681.2745 -29.46442
2450 20107.732 330.99437 0 3682.2831 35.38497
2500 20771.509 220.47713 0 3682.3953 -12.324858
2550 20499.887 265.58494 0 3682.2327 -22.713874
2600 21462.182 105.24427 0 3682.2747 -10.175788
2650 21004.949 181.51383 0 3682.3387 4.949195
2700 18673.552 570.45017 0 3682.7089 21.201437
2750 21257.562 139.198 0 3682.1249 -7.5793039
2800 21559.645 88.844759 0 3682.119 -6.2360467
2850 20865.227 204.46262 0 3682.0004 0.39575069
2900 19428.614 443.93293 0 3682.0352 12.796676
2950 19630.1 410.18487 0 3681.8681 -0.50572623
3000 19663.218 404.06316 0 3681.2661 6.0827093
3050 19087.572 500.8452 0 3682.1073 -6.3526476
3100 18229.94 643.77681 0 3682.1001 11.453637
3150 18927.492 527.51919 0 3682.1011 -1.662863
3200 18320.514 628.55895 0 3681.978 21.176126
3250 18204.677 647.96462 0 3682.0775 11.331521
3300 19231.978 477.02117 0 3682.3509 3.8381593
3350 18153.44 656.70376 0 3682.2772 15.135615
3400 17476.768 770.0598 0 3682.8545 -3.394312
3450 21097.531 166.17241 0 3682.4276 3.74301
3500 17605.784 747.54808 0 3681.8454 3.3420627
3550 19238.34 476.00608 0 3682.3961 1.1413836
3600 18155.288 656.57434 0 3682.4557 3.4360446
3650 18735.622 559.2377 0 3681.8413 28.760363
3700 15310.261 1134.4215 0 3686.1317 44.207018
3750 15377.116 1123.4786 0 3686.3313 7.6773215
3800 18798.895 549.05928 0 3682.2084 -12.905825
3850 18322.563 628.87744 0 3682.6379 -16.067793
3900 19963.049 355.65441 0 3682.8292 3.4694064
3950 19925.48 361.2507 0 3682.1641 5.0058567
4000 19141.423 492.41081 0 3682.648 -12.782769
4050 20022.241 345.61655 0 3682.6568 -3.0149905
4100 21348.635 124.95646 0 3683.0624 -4.85779
4150 21011.812 181.1132 0 3683.0819 -3.9526196
4200 20222.276 312.63945 0 3683.0187 -23.63437
4250 20957.757 189.77152 0 3682.731 -1.3712469
4300 20070.215 337.5751 0 3682.611 -6.8816517
4350 21322.437 129.09228 0 3682.8318 -6.9442178
4400 19440.445 442.77531 0 3682.8495 -0.11606236
4450 20964.516 188.67174 0 3682.7577 4.8533525
4500 13530.08 1428.5497 0 3683.563 12.333187
4550 20461.637 272.58882 0 3682.8616 4.5111943
4600 17072.994 836.58228 0 3682.0812 5.7611617
4650 18860.748 539.82027 0 3683.2782 -2.5558958
4700 18373.927 621.04093 0 3683.3621 5.4020702
4750 20321.437 296.63662 0 3683.5428 8.9571617
4800 21083.122 169.84086 0 3683.6946 10.566368
4850 20499.669 267.7012 0 3684.3128 4.2924237
4900 20308.781 300.38168 0 3685.1785 -12.396923
4950 21043.303 178.56295 0 3685.7801 3.8923762
5000 20718.383 232.52208 0 3685.5859 -12.43234
5050 21005.749 184.4363 0 3685.3945 -7.6463487
5100 20714.133 233.27745 0 3685.6329 -1.6944135
5150 19577.452 422.73035 0 3685.639 -21.831219
5200 14044.647 1343.9545 0 3684.729 -6.8407194
5250 19089.805 504.0893 0 3685.7235 4.05641
5300 21094.745 169.94699 0 3685.7378 -0.66593212
5350 19907.559 366.77598 0 3684.7024 1.5248525
5400 20382.81 289.13263 0 3686.2676 -11.919321
5450 19593.693 420.70548 0 3686.3209 -1.1568628
5500 20906.08 202.09801 0 3686.4447 -2.4284971
5550 16315.465 965.56973 0 3684.8138 -33.178221
5600 19714.57 400.39687 0 3686.1586 19.950231
5650 20561.724 259.54797 0 3686.502 8.2074524
5700 19349.502 460.7789 0 3685.6959 16.252649
5750 21006.818 185.56805 0 3686.7044 -11.96089
5800 20268.2 307.97547 0 3686.0089 17.322311
5850 21018.322 184.16179 0 3687.2154 -14.379909
5900 19695.647 404.57094 0 3687.1787 -20.718904
5950 21021.687 183.66311 0 3687.2776 -15.206081
6000 18947.535 529.30554 0 3687.2281 17.863927
6050 15272.373 1141.012 0 3686.4075 -0.43375666
6100 17766.197 721.75792 0 3682.7908 11.378913
6150 18612.573 584.06688 0 3686.1623 17.543241
6200 19005.155 518.97146 0 3686.4973 -16.223107
6250 20997.507 187.55499 0 3687.1394 -11.613546
6300 19639.901 413.58048 0 3686.8974 14.407136
6350 19580.399 423.02818 0 3686.428 -5.5801796
6400 14134.119 1332.0662 0 3687.7527 84.864425
6450 21598.824 87.419966 0 3687.224 -5.8358352
6500 18208.216 649.29108 0 3683.9938 -8.1510884
6550 19364.586 459.59813 0 3687.0291 -12.053563
6600 20710.927 235.11914 0 3686.9403 -1.0470193
6650 21132.334 165.08091 0 3687.1366 1.0785471
6700 20217.285 317.589 0 3687.1365 0.055447462
6750 21232.279 148.57412 0 3687.2873 -2.4551657
6800 20292.683 304.76539 0 3686.8793 -0.42311295
6850 19056.291 510.49927 0 3686.5478 6.9533826
6900 20429.82 282.23764 0 3687.2076 -4.2360112
6950 21281.278 140.27361 0 3687.1533 -0.07475261
7000 17173.388 824.54446 0 3686.7758 10.753828
7050 18079.7 674.56274 0 3687.846 12.975804
7100 16433.233 950.73904 0 3689.6112 -10.5102
7150 19033.335 515.59672 0 3687.8193 0.29109447
7200 17286.428 809.02352 0 3690.0948 2.3015698
7250 16811.962 886.6645 0 3688.6582 -7.4787512
7300 15992.461 1023.4849 0 3688.895 -5.2354222
7350 19211.451 487.63129 0 3689.5398 8.4351737
7400 19065.682 511.95629 0 3689.57 -12.47448
7450 21369.265 128.10098 0 3689.6451 2.2930546
7500 16807.109 888.64602 0 3689.8308 14.761969
7550 18063.046 679.21873 0 3689.7264 3.8950434
7600 17794.987 724.55404 0 3690.3851 14.379016
7650 17904.751 706.14354 0 3690.2688 23.813776
7700 19670.09 411.3021 0 3689.6504 14.099245
7750 18082.562 675.23975 0 3689.0001 15.788521
7800 17776.135 726.91445 0 3689.6037 6.9780735
7850 17062.575 846.33412 0 3690.0966 -8.9289256
7900 19059.2 513.07737 0 3689.6107 16.992843
7950 16269.685 978.48914 0 3690.1033 11.180179
8000 20115.278 336.91405 0 3689.4604 -6.4882518
8050 21173.72 161.15229 0 3690.1056 -2.2164491
8100 19238.235 484.42784 0 3690.8004 23.412709
8150 18438.4 617.58743 0 3690.6542 0.89156316
8200 21438.764 117.12721 0 3690.2546 -1.7193227
8250 21195.806 157.66607 0 3690.3003 3.820447
8300 21177.549 161.13702 0 3690.7286 0.94938203
8350 21060.267 181.06887 0 3691.1135 2.8179025
8400 20087.113 343.46206 0 3691.3142 8.1484473
8450 19298.478 474.87133 0 3691.2843 -16.239664
8500 21654.353 82.083485 0 3691.1423 -8.1464138
8550 19920.544 371.34795 0 3691.4386 20.765144
8600 21692.293 75.655154 0 3691.0373 -13.316763
8650 21231.322 151.8989 0 3690.4526 -11.388238
8700 19530.647 434.89585 0 3690.0037 2.7433786
8750 19720.63 403.07773 0 3689.8493 -6.416414
8800 21321.378 136.04091 0 3689.604 1.3661635
8850 19811.906 387.80489 0 3689.7893 3.704143
8900 19734.167 400.92444 0 3689.9523 2.5685155
8950 21076.459 177.18119 0 3689.9244 -11.939513
9000 20967.246 195.42966 0 3689.9707 2.0092705
9050 21122.023 169.62103 0 3689.9582 2.3791301
9100 20169.346 328.27229 0 3689.8299 -3.5017988
9150 21418.641 119.84513 0 3689.6187 2.486073
9200 20876.042 210.26452 0 3689.6048 -5.3839897
9250 21572.38 93.74407 0 3689.1407 -8.3676952
9300 20944.78 197.98577 0 3688.7824 1.3278314
9350 20706.52 237.48767 0 3688.5744 4.6944204
9400 16412.314 953.47251 0 3688.8581 26.134976
9450 20461.68 277.76243 0 3688.0424 17.647445
9500 20893.994 205.64261 0 3687.9749 -10.642418
9550 20503.447 270.63504 0 3687.8761 -17.769897
9600 19677.799 408.05887 0 3687.692 -2.7938604
9650 17480.971 774.1855 0 3687.6806 0.59827043
9700 17799.126 721.50817 0 3688.0292 44.387928
9750 20443.384 280.16837 0 3687.399 3.0619324
9800 20545.255 263.40108 0 3687.6102 3.6229381
9850 20722.819 233.57142 0 3687.3745 0.86462694
9900 21128.462 165.09767 0 3686.508 -6.9636843
9950 21343.307 130.46714 0 3687.685 -9.7382705
10000 20623.887 250.37866 0 3687.6932 2.7529835
Loop time of 2.28812 on 1 procs for 10000 steps with 81 atoms
Performance: 37760.318 tau/day, 4370.407 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 | 0.094122 | 0.094122 | 0.094122 | 0.0 | 4.11
Neigh | 0.076427 | 0.076427 | 0.076427 | 0.0 | 3.34
Comm | 0.0066867 | 0.0066867 | 0.0066867 | 0.0 | 0.29
Output | 0.003606 | 0.003606 | 0.003606 | 0.0 | 0.16
Modify | 2.0986 | 2.0986 | 2.0986 | 0.0 | 91.72
Other | | 0.008698 | | | 0.38
Nlocal: 81 ave 81 max 81 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 62 ave 62 max 62 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 905 ave 905 max 905 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 905
Ave neighs/atom = 11.17284
Neighbor list builds = 991
Dangerous builds = 927
Total wall time: 0:00:02

328
examples/rigid/log.20Mar22.rigid.poems4.g++.4 Normal file
View File

@ -0,0 +1,328 @@
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
# 1 chain of connected bodies
group clump1 id <> 1 9
9 atoms in group clump1
group clump2 id <> 9 18
10 atoms in group clump2
group clump3 id <> 18 27
10 atoms in group clump3
group clump4 id <> 27 36
10 atoms in group clump4
group clump5 id <> 36 45
10 atoms in group clump5
group clump6 id <> 45 54
10 atoms in group clump6
group clump7 id <> 54 63
10 atoms in group clump7
group clump8 id <> 63 72
10 atoms in group clump8
group clump9 id <> 72 81
10 atoms in group clump9
fix 1 all poems file connected-bodies.dat
1 clusters, 9 bodies, 8 joints, 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.poems
#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
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- fix poems command:
@Article{Mukherjee08,
author = {R. M. Mukherjee, P. S. Crozier, S. J. Plimpton, K. S. Anderson},
title = {Substructured molecular dynamics using multibody dynamics algorithms},
journal = {Intl.~J.~Non-linear Mechanics},
year = 2008,
volume = 43,
pages = {1045--1055}
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
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/atomonly/newton
stencil: half/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.514 | 3.545 | 3.639 Mbytes
Step Temp E_pair E_mol TotEng Press
0 217.7783 3430.3907 0 3466.6871 -2.7403788
50 13679.637 1404.2468 0 3684.1863 12.446066
100 16777.225 888.87665 0 3685.0808 -31.828677
150 19595.365 418.45042 0 3684.3446 40.709078
200 18524.188 596.47273 0 3683.8375 -0.8159371
250 21015.789 180.96521 0 3683.5967 -10.042469
300 20785.513 219.25314 0 3683.5053 2.6452719
350 21072.46 171.2554 0 3683.3321 7.0609024
400 19956.414 356.36381 0 3682.4328 19.320259
450 20724.42 227.73284 0 3681.8028 8.1259249
500 20152.578 322.71466 0 3681.4777 5.4929878
550 20017.022 345.29701 0 3681.4673 5.4661666
600 17897.743 698.72196 0 3681.6791 3.2854742
650 17297.758 796.60256 0 3679.5623 15.191113
700 18581.934 584.29715 0 3681.2861 5.1588289
750 21774.158 52.821062 0 3681.8474 -10.775664
800 21604.055 81.188546 0 3681.8644 -3.2045742
850 17821.483 711.53827 0 3681.7854 7.4384281
900 21033.292 175.98127 0 3681.5299 -16.345167
950 20968.166 186.59847 0 3681.2929 -2.330456
1000 20490.66 266.19374 0 3681.3037 11.787982
1050 20222.396 310.94072 0 3681.34 -8.3459539
1100 21321.687 127.61533 0 3681.2299 -1.2184716
1150 20849.582 206.01696 0 3680.9472 -0.86699115
1200 21815.003 45.317409 0 3681.1512 1.5988314
1250 18655.437 572.41453 0 3681.654 10.064083
1300 20780.781 217.36511 0 3680.8286 6.0538606
1350 20558.971 254.36489 0 3680.8601 -3.6773868
1400 21485.03 99.812843 0 3680.6511 -16.185479
1450 21771.107 52.159652 0 3680.6775 -2.4756656
1500 21520.949 93.503872 0 3680.3286 2.1023574
1550 21351.419 121.68131 0 3680.2511 5.5159875
1600 20778.804 216.92191 0 3680.0559 15.089203
1650 21477.636 100.21877 0 3679.8247 -1.104524
1700 18501.329 596.48084 0 3680.0357 -15.679806
1750 18563.639 587.34841 0 3681.2882 33.532316
1800 19110.174 494.82524 0 3679.8543 18.024079
1850 21364.178 119.23767 0 3679.9339 2.5290075
1900 20146.588 322.15506 0 3679.9197 5.7317368
1950 20692.674 231.25288 0 3680.0319 4.2977982
2000 20943.904 189.11229 0 3679.7629 -22.643749
2050 19667.815 401.87016 0 3679.8394 3.6240972
2100 20280.109 299.81759 0 3679.8357 7.4803647
2150 19181.146 483.63975 0 3680.4974 22.634167
2200 21301.194 130.53171 0 3680.7308 4.7072523
2250 20484.79 266.99736 0 3681.1291 -8.6583002
2300 18648.002 573.09962 0 3681.1 -5.2548835
2350 21515.851 95.225745 0 3681.2009 -9.3875216
2400 21462.37 104.21272 0 3681.2744 -29.459857
2450 20108.034 330.94394 0 3682.2829 35.37058
2500 20771.818 220.42545 0 3682.3951 -12.318936
2550 20502.815 265.09577 0 3682.2316 -22.726822
2600 21462.006 105.2733 0 3682.2744 -10.180394
2650 21009.656 180.72738 0 3682.3367 4.9580828
2700 18680.012 569.37179 0 3682.7071 21.114114
2750 21256.19 139.42201 0 3682.1203 -7.4744399
2800 21552.267 90.071446 0 3682.1159 -6.2906304
2850 20879.958 202.00905 0 3682.0021 0.57990903
2900 19018.645 512.35214 0 3682.1262 13.883084
2950 19819.365 378.55747 0 3681.785 -0.7348943
3000 20269.229 303.35149 0 3681.5563 6.3088075
3050 19236.727 475.99457 0 3682.1158 -10.703575
3100 18391.55 616.96976 0 3682.2281 9.850079
3150 20258.563 305.82076 0 3682.248 7.1951283
3200 20716.384 229.15502 0 3681.8856 2.9042294
3250 18662.237 572.0784 0 3682.4512 9.2108597
3300 19162.278 488.60646 0 3682.3195 3.3306562
3350 21235.679 142.98279 0 3682.2626 0.29397483
3400 17677.053 736.09247 0 3682.2679 32.75269
3450 20852.392 206.65618 0 3682.0548 -4.8319056
3500 21182.918 151.46754 0 3681.9539 -5.6330382
3550 20589.85 250.40724 0 3682.049 12.582133
3600 20973.659 186.28043 0 3681.8903 10.935266
3650 17838.632 707.92145 0 3681.0268 -17.200926
3700 21538.002 92.744409 0 3682.4114 -0.72124229
3750 21390.294 117.90865 0 3682.9576 -7.8431786
3800 17921.046 696.50311 0 3683.344 -9.4641531
3850 20356.471 290.22624 0 3682.9715 2.4593463
3900 20374.077 287.10249 0 3682.782 -1.9519082
3950 20563.915 255.29993 0 3682.619 -6.124649
4000 20991.467 184.76183 0 3683.3397 1.8954961
4050 17805.623 716.24698 0 3683.8509 -20.454944
4100 19916.389 363.86301 0 3683.2611 -0.27912557
4150 19221.623 480.01232 0 3683.6161 -11.562492
4200 20526.82 261.78571 0 3682.9224 -3.9522917
4250 20922.813 196.1799 0 3683.3154 0.11947446
4300 19956.66 357.78133 0 3683.8914 19.156093
4350 19735.73 394.45981 0 3683.7482 14.865775
4400 21702.656 67.099805 0 3684.2092 -13.502538
4450 18163.055 656.97231 0 3684.1482 -0.6243111
4500 17477.718 771.25976 0 3684.2127 -0.4664004
4550 20676.507 238.19814 0 3684.2827 -19.444969
4600 17322.922 796.77058 0 3683.9242 27.003966
4650 11905.158 1704.9151 0 3689.1082 15.574169
4700 18689.079 569.80982 0 3684.6563 -14.67311
4750 19821.745 381.01914 0 3684.6433 5.0436795
4800 20621.335 247.96269 0 3684.8518 -16.407263
4850 21923.814 30.965964 0 3684.935 -13.418244
4900 18840.555 544.41538 0 3684.5079 11.005357
4950 15366.601 1124.2481 0 3685.3482 17.412375
5000 18274.314 639.01311 0 3684.732 5.3261109
5050 21173.687 155.83673 0 3684.7845 5.4056809
5100 21738.219 61.75201 0 3684.7885 -2.631945
5150 16597.949 918.84841 0 3685.1732 -10.124101
5200 20752.758 225.95919 0 3684.7522 -5.2441372
5250 17652.088 741.2645 0 3683.2793 2.0080739
5300 19907.523 366.53115 0 3684.4516 8.4266792
5350 20104.189 334.14522 0 3684.8433 17.21925
5400 21499.848 101.71631 0 3685.0243 -6.1103541
5450 21203.533 151.14574 0 3685.068 -5.9468503
5500 21076.513 172.45652 0 3685.2088 5.1418181
5550 20158.398 325.56609 0 3685.2992 -1.6486034
5600 20787.836 221.19563 0 3685.835 -10.66805
5650 19687.154 404.77204 0 3685.9644 -23.49128
5700 20419.311 282.58328 0 3685.8017 -0.52808211
5750 19738.522 395.95893 0 3685.7126 1.3889817
5800 18300.025 635.66905 0 3685.6732 23.490447
5850 20585.004 255.02032 0 3685.8543 -0.20699939
5900 20373.839 290.15881 0 3685.7987 -7.9712187
5950 18163.832 659.91192 0 3687.2173 5.4494586
6000 21049.247 177.43029 0 3685.6382 2.9138342
6050 21239.803 145.77613 0 3685.7433 -1.4927769
6100 20686.361 237.86454 0 3685.5913 -0.95516297
6150 20461.754 275.31546 0 3685.6079 -3.4166412
6200 19264.208 474.73017 0 3685.4316 11.750757
6250 21180.813 155.31746 0 3685.4529 2.8188219
6300 21047.543 177.4394 0 3685.3632 1.8641486
6350 20232.576 313.17716 0 3685.2731 2.8150209
6400 20185.616 321.33454 0 3685.6038 -3.8697311
6450 18969.632 523.95865 0 3685.5639 0.6725512
6500 17592.574 753.49959 0 3685.5952 -1.2557393
6550 21279.049 138.42524 0 3684.9335 -1.208945
6600 21408.457 116.4143 0 3684.4904 -1.5332953
6650 19758.218 391.17316 0 3684.2096 1.8511312
6700 20766.943 223.44631 0 3684.6036 -2.3672623
6750 20399.631 284.09914 0 3684.0377 -5.4089876
6800 21296.628 135.14662 0 3684.5847 -3.8442549
6850 20641.481 244.4451 0 3684.692 1.4020639
6900 20852.81 209.23009 0 3684.6984 1.8512104
6950 20940.555 194.66882 0 3684.7614 -6.554676
7000 19496.988 435.28199 0 3684.78 -15.120269
7050 19796.829 385.04227 0 3684.5138 -4.1068804
7100 19945.264 360.42431 0 3684.635 -4.0629042
7150 19431.123 446.12911 0 3684.6497 -6.8321751
7200 16864.851 873.80043 0 3684.6089 14.309069
7250 20438.75 277.85982 0 3684.3181 -11.41223
7300 17688.684 734.01576 0 3682.1298 35.938373
7350 21573.419 88.63421 0 3684.204 -3.9032749
7400 21198.486 150.72249 0 3683.8034 -7.1477117
7450 20586.708 252.93928 0 3684.0572 -7.6634645
7500 21815.377 48.180377 0 3684.0765 0.97457507
7550 17791.352 718.87564 0 3684.101 28.248235
7600 21828.874 45.928597 0 3684.0742 -0.25814944
7650 20827.961 212.35674 0 3683.6835 -3.4083384
7700 21319.176 130.43547 0 3683.6315 -12.434856
7750 20127.904 328.69643 0 3683.3471 -16.975711
7800 21741.772 59.679206 0 3683.3078 3.6261863
7850 19612.334 414.37418 0 3683.0964 1.3763274
7900 20071.318 337.74624 0 3682.9658 -0.40982763
7950 17925.664 695.29582 0 3682.9065 17.104439
8000 19125.978 492.76383 0 3680.4268 10.807662
8050 20233.848 310.42681 0 3682.7347 13.386237
8100 20551.619 257.86699 0 3683.1368 -13.97515
8150 21578.323 86.88362 0 3683.2708 -9.6811587
8200 21154.833 157.72897 0 3683.5344 0.62312375
8250 21321.143 129.83967 0 3683.3636 1.9536438
8300 21041.696 176.04177 0 3682.9911 4.7475567
8350 19883.39 369.32649 0 3683.2247 -7.0959328
8400 21626.067 79.062992 0 3683.4075 -14.919059
8450 21375.201 120.86836 0 3683.4019 -5.3461514
8500 20281.059 303.10304 0 3683.2796 3.7975093
8550 21170.533 154.48432 0 3682.9065 -1.1568561
8600 17754.931 724.00158 0 3683.1568 14.15254
8650 20685.478 235.65879 0 3683.2385 -5.2694179
8700 21489.165 101.90509 0 3683.4326 -4.2510612
8750 21106.682 165.41638 0 3683.1968 -3.9186708
8800 19149.516 491.5843 0 3683.1702 -11.419849
8850 21451.865 108.1814 0 3683.4923 -7.8256219
8900 19567.4 421.81206 0 3683.0454 -0.71997056
8950 20934.097 194.48033 0 3683.4965 -7.0106879
9000 18531.559 595.25957 0 3683.8528 3.7449399
9050 18868.821 537.22549 0 3682.029 9.9926092
9100 19972.527 354.73119 0 3683.4858 -0.30871263
9150 19641.651 409.18618 0 3682.7947 -1.3036238
9200 20019.08 346.19657 0 3682.7099 6.7425386
9250 19259.286 473.04973 0 3682.9308 -24.120659
9300 21597.757 82.971857 0 3682.598 -13.748483
9350 19348.379 457.23576 0 3681.9656 3.1571402
9400 19129.588 493.35235 0 3681.617 8.6293783
9450 20337.025 291.20959 0 3680.7138 6.8590795
9500 20581.788 249.65891 0 3679.9569 -18.892836
9550 19482.069 433.0077 0 3680.0192 23.029778
9600 19182.794 482.96871 0 3680.101 -11.081731
9650 20086.771 332.5311 0 3680.3263 -18.939681
9700 20274.046 300.98818 0 3679.9959 6.7538762
9750 18743.595 555.08045 0 3679.0129 8.2757138
9800 19464.311 435.66288 0 3679.7148 7.0528759
9850 21249.848 138.27382 0 3679.9152 -10.847402
9900 21156.214 153.84621 0 3679.8819 -7.8359674
9950 21643.134 72.547515 0 3679.7365 -10.507744
10000 19587.948 414.64942 0 3679.3075 6.1173553
Loop time of 2.35562 on 4 procs for 10000 steps with 81 atoms
Performance: 36678.236 tau/day, 4245.166 timesteps/s
99.3% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0055581 | 0.024882 | 0.055326 | 12.0 | 1.06
Neigh | 0.0073809 | 0.022107 | 0.043683 | 9.2 | 0.94
Comm | 0.12484 | 0.14528 | 0.1833 | 6.2 | 6.17
Output | 0.0035526 | 0.0041048 | 0.0055462 | 1.3 | 0.17
Modify | 2.1078 | 2.1414 | 2.162 | 1.5 | 90.91
Other | | 0.0178 | | | 0.76
Nlocal: 20.25 ave 81 max 0 min
Histogram: 3 0 0 0 0 0 0 0 0 1
Nghost: 41 ave 78 max 11 min
Histogram: 2 0 0 0 0 0 0 1 0 1
Neighs: 193.5 ave 774 max 0 min
Histogram: 3 0 0 0 0 0 0 0 0 1
Total # of neighbors = 774
Ave neighs/atom = 9.5555556
Neighbor list builds = 989
Dangerous builds = 915
Total wall time: 0:00:02

329
examples/rigid/log.20Mar22.rigid.poems5.g++.1 Normal file
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@ -0,0 +1,329 @@
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
# 2 chains of connected bodies
group clump1 id <> 1 9
9 atoms in group clump1
group clump2 id <> 9 18
10 atoms in group clump2
group clump3 id <> 18 27
10 atoms in group clump3
group clump4 id <> 27 36
10 atoms in group clump4
group clump5 id <> 37 45
9 atoms in group clump5
group clump6 id <> 45 54
10 atoms in group clump6
group clump7 id <> 54 63
10 atoms in group clump7
group clump8 id <> 63 72
10 atoms in group clump8
group clump9 id <> 72 81
10 atoms in group clump9
fix 1 all poems file connected-bodies2.dat
2 clusters, 9 bodies, 7 joints, 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.poems
#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
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- fix poems command:
@Article{Mukherjee08,
author = {R. M. Mukherjee, P. S. Crozier, S. J. Plimpton, K. S. Anderson},
title = {Substructured molecular dynamics using multibody dynamics algorithms},
journal = {Intl.~J.~Non-linear Mechanics},
year = 2008,
volume = 43,
pages = {1045--1055}
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
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/atomonly/newton
stencil: half/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.666 | 3.666 | 3.666 Mbytes
Step Temp E_pair E_mol TotEng Press
0 196.00047 3632.2347 0 3668.5311 -2.7403788
50 12774.759 1538.7382 0 3904.4344 18.086359
100 19803.641 237.21132 0 3904.5523 -3.1528278
150 20259.6 152.62072 0 3904.3985 -4.6173524
200 20705.978 69.977442 0 3904.4178 9.0928158
250 19552.211 283.50525 0 3904.285 15.670465
300 19266.324 333.5792 0 3901.4169 7.2119197
350 20738.325 63.738945 0 3904.1694 -23.03999
400 20616.682 86.082444 0 3903.9864 -13.783584
450 19831.326 230.13858 0 3902.6063 0.42074361
500 20365.825 131.47231 0 3902.9213 0.6921524
550 20794.102 52.163238 0 3902.9229 4.5895354
600 20853.873 40.899172 0 3902.7275 2.3593042
650 19255.802 336.29509 0 3902.1844 10.341742
700 18526.969 471.02462 0 3901.9448 -0.61898691
750 18960.662 391.26068 0 3902.4944 12.04731
800 20142.432 172.05177 0 3902.1317 4.6838621
850 19932.48 210.71175 0 3901.9118 3.4716043
900 20243.528 153.13972 0 3901.9411 3.6490762
950 20388.132 126.88722 0 3902.4671 -4.4518463
1000 20076.333 184.61915 0 3902.4586 -2.272315
1050 20859.506 39.696993 0 3902.5684 6.45166
1100 15284.661 1072.1908 0 3902.6836 21.194042
1150 19658.317 261.99809 0 3902.4272 -2.874422
1200 20767.681 56.717094 0 3902.5839 -34.817444
1250 20625.583 82.586399 0 3902.1388 11.697329
1300 20690.013 71.006478 0 3902.4903 -29.292777
1350 20936.019 26.022786 0 3903.0634 1.0316025
1400 19753.559 244.81785 0 3902.8844 6.7138514
1450 15690.149 998.342 0 3903.9252 48.124557
1500 20234.455 155.92516 0 3903.0465 13.17221
1550 20779.631 55.063009 0 3903.1428 -2.639045
1600 20642.753 80.233905 0 3902.9659 -2.4688467
1650 18785.696 423.90402 0 3902.7365 -5.6466663
1700 20965.076 20.760444 0 3903.182 -0.45364296
1750 18935.406 396.96067 0 3903.5173 25.913302
1800 20581.559 91.756972 0 3903.1567 3.8217234
1850 20616.946 85.184849 0 3903.1378 4.1907972
1900 16602.053 828.40949 0 3902.8637 -0.49505122
1950 20175.526 166.53362 0 3902.7421 5.603825
2000 20261.924 150.39322 0 3902.6014 -1.196958
2050 20170.339 167.40504 0 3902.6531 -0.80849882
2100 19820.132 231.26755 0 3901.6624 3.1476607
2150 20666.19 75.838461 0 3902.9106 0.53899287
2200 19873.51 222.53286 0 3902.8124 7.9310276
2250 18548.063 467.69698 0 3902.5235 16.905356
2300 20616.61 84.762399 0 3902.6531 -6.7872951
2350 18167.738 538.13635 0 3902.5322 -11.458285
2400 20120.227 177.01954 0 3902.9875 -1.2593018
2450 20436.599 118.32469 0 3902.8801 -6.5989174
2500 18919.923 400.26361 0 3903.9531 32.37476
2550 19675.809 259.77151 0 3903.4398 19.437327
2600 19739.842 247.86388 0 3903.3901 -7.519784
2650 20557.026 96.530313 0 3903.387 0.60211646
2700 20666.602 76.099892 0 3903.2484 0.16825503
2750 20924.585 28.453883 0 3903.3771 2.4227171
2800 20360.659 132.8596 0 3903.352 4.1440877
2850 20783.475 54.518625 0 3903.3102 -0.57312067
2900 20456.181 115.03745 0 3903.2191 -20.118887
2950 20779.493 55.321394 0 3903.3756 -0.26783079
3000 20011.867 197.30216 0 3903.2035 -1.4704201
3050 20741.875 62.208723 0 3903.2966 -7.5432815
3100 21001.754 14.148298 0 3903.362 2.9676438
3150 20244.086 154.44639 0 3903.3512 -1.9071213
3200 20639.615 81.136426 0 3903.2873 1.4826467
3250 20735.244 63.529571 0 3903.3895 2.1127055
3300 20142.891 173.22282 0 3903.3878 4.7739415
3350 19963.765 206.21899 0 3903.2126 5.5410771
3400 16628.667 824.13627 0 3903.519 36.087673
3450 19228.218 342.81569 0 3903.5968 3.1057274
3500 19759.293 244.57876 0 3903.707 2.2339557
3550 19853.21 227.06362 0 3903.584 -1.0882119
3600 19673.516 260.64854 0 3903.8923 -10.63775
3650 19619.238 270.5393 0 3903.7316 -6.3746003
3700 20756.865 59.790243 0 3903.6542 -8.3015766
3750 20265.025 150.47347 0 3903.2559 -5.7284695
3800 20944.683 24.669276 0 3903.3142 -0.070552298
3850 19344.831 320.59492 0 3902.971 13.040749
3900 19978.209 203.00247 0 3902.6708 0.15638133
3950 19864.118 224.19359 0 3902.734 0.453229
4000 17606.216 642.71493 0 3903.1252 -12.656002
4050 18017.895 566.54102 0 3903.1883 12.133906
4100 20092.963 182.17593 0 3903.095 7.7445947
4150 20555.337 96.395074 0 3902.939 -6.5429752
4200 20709.781 67.869199 0 3903.0138 -2.8653003
4250 18956.203 392.20748 0 3902.6155 -1.6249728
4300 17816.204 603.72704 0 3903.0241 23.089239
4350 18979.742 388.04678 0 3902.8138 3.2511108
4400 20272.085 148.82367 0 3902.9135 1.9518268
4450 18820.003 417.74789 0 3902.9337 6.3979299
4500 19991.936 200.50131 0 3902.7117 3.5118553
4550 20915.092 29.663898 0 3902.8291 -2.3174641
4600 20690.37 71.125087 0 3902.6752 -12.008575
4650 18893.76 404.50849 0 3903.3529 15.006184
4700 18611.123 456.1263 0 3902.6306 -5.3574892
4750 20497.821 106.5856 0 3902.4784 0.85039837
4800 20803.214 50.120522 0 3902.5675 3.8610873
4850 18849.598 411.72635 0 3902.3927 9.2029058
4900 18121.714 546.68042 0 3902.5533 9.4522272
4950 20377.499 128.99323 0 3902.6041 5.3825395
5000 20686.114 72.039749 0 3902.8016 -5.706271
5050 20180.449 165.51368 0 3902.634 -16.418461
5100 20274.947 148.36657 0 3902.9864 -5.6668309
5150 18042.324 560.74137 0 3901.9125 3.6791541
5200 20794.666 52.204446 0 3903.0685 -1.4517721
5250 19073.55 371.18834 0 3903.3272 -13.457439
5300 20821.412 47.364313 0 3903.1813 2.258098
5350 20583.073 91.271191 0 3902.9513 5.4323985
5400 20490.967 108.41184 0 3903.0353 4.122905
5450 18141.79 543.66874 0 3903.2594 -0.19951075
5500 20274.012 148.55528 0 3903.002 5.0489974
5550 17806.237 605.43454 0 3902.8858 43.80619
5600 20999.825 14.341937 0 3903.1983 1.0879933
5650 20930.929 27.025347 0 3903.1234 -7.0860209
5700 20677.725 73.853093 0 3903.0614 2.6864775
5750 20521.264 102.87509 0 3903.1092 2.6940548
5800 20792.571 52.596021 0 3903.0721 1.2910217
5850 20518.674 103.26595 0 3903.0204 -9.2547271
5900 18417.885 491.66696 0 3902.3865 -12.049357
5950 17243.837 709.37858 0 3902.6817 -6.2357188
6000 20262.525 149.56918 0 3901.8885 -0.28964823
6050 19883.554 219.14043 0 3901.2801 2.3071707
6100 16548.178 838.47869 0 3902.956 -11.715644
6150 19601.177 272.14674 0 3901.9944 -0.9008056
6200 20499.796 106.2363 0 3902.4949 0.79071424
6250 19601.106 272.50139 0 3902.3359 -1.9306693
6300 17210.685 712.70535 0 3899.8692 4.8890923
6350 19911.896 214.91041 0 3902.2985 12.691129
6400 18834.642 411.87123 0 3899.7678 -1.9447856
6450 20216.311 158.39781 0 3902.1591 2.6009109
6500 20452.025 114.97122 0 3902.3832 0.14644416
6550 19142.589 357.34097 0 3902.2649 2.8968485
6600 20412.915 122.08784 0 3902.2573 3.1343105
6650 17317.867 699.39994 0 3906.4123 42.25563
6700 20479.771 109.8036 0 3902.3537 1.3520625
6750 20306.902 142.12484 0 3902.6623 2.2032106
6800 20755.367 58.994834 0 3902.5814 -0.90518094
6850 20471.259 111.7197 0 3902.6936 1.5799331
6900 20702.025 69.15032 0 3902.8586 9.3910371
6950 20477.695 110.34414 0 3902.5099 1.8181164
7000 20560.727 95.057704 0 3902.5998 -15.686006
7050 20336.675 136.39386 0 3902.4448 1.3704327
7100 20757.399 58.950153 0 3902.913 -6.4250981
7150 20870.958 38.095649 0 3903.088 -4.1962169
7200 20706.869 68.489134 0 3903.0944 2.8322659
7250 20386.713 127.7432 0 3903.0604 6.0287391
7300 18391.773 497.21001 0 3903.0939 19.202343
7350 20178.898 166.4993 0 3903.3322 1.5682417
7400 16858.704 781.78682 0 3903.7691 21.317514
7450 17509.513 660.71963 0 3903.2221 -5.9456143
7500 19974.601 204.20412 0 3903.2043 -0.69202711
7550 20917.053 29.73415 0 3903.2626 -3.9962577
7600 20923.518 28.482703 0 3903.2083 -1.9016251
7650 20549.528 97.630612 0 3903.0987 3.5512257
7700 20861.441 39.903885 0 3903.1337 2.4426264
7750 18843.349 413.64461 0 3903.1537 2.677739
7800 20616.054 85.214364 0 3903.0021 3.9639004
7850 16478.851 851.93376 0 3903.5728 7.3763128
7900 20312.115 141.35103 0 3902.8539 4.6707271
7950 20389.623 127.16589 0 3903.0219 3.4414001
8000 20452.117 115.30715 0 3902.7362 -1.0162528
8050 20857.093 40.791886 0 3903.2164 -15.150068
8100 19817.543 233.4997 0 3903.415 0.89346046
8150 18649.521 449.9112 0 3903.5262 -0.40053588
8200 19619.276 270.37616 0 3903.5754 5.5161492
8250 20393.176 127.01336 0 3903.5275 2.122613
8300 19145.912 358.00424 0 3903.5435 3.863924
8350 19636.311 267.17226 0 3903.5262 -7.1496084
8400 19086.332 368.86693 0 3903.3729 7.0968952
8450 19494.416 292.89527 0 3902.9723 3.1750935
8500 20041.919 191.77756 0 3903.244 0.95215503
8550 20357.561 133.15478 0 3903.0736 -0.14020152
8600 16998.797 756.07003 0 3903.9954 -16.724408
8650 20853.26 41.386996 0 3903.1017 -3.2612965
8700 20767.768 57.360884 0 3903.2438 1.1157649
8750 20752.546 60.106518 0 3903.1705 0.39130547
8800 20574.407 92.99798 0 3903.0734 0.61728166
8850 20326.99 138.94203 0 3903.1995 -1.9434522
8900 17408.108 679.53222 0 3903.2559 21.935371
8950 20471.21 112.2721 0 3903.2368 1.8142747
9000 19129.591 360.35257 0 3902.8694 4.5786395
9050 20439.668 117.89541 0 3903.0191 2.5585685
9100 20780.375 54.788664 0 3903.0062 3.8312459
9150 19904.559 216.61504 0 3902.6445 12.150414
9200 20961.295 21.52065 0 3903.2419 -0.2120699
9250 19315.252 326.44175 0 3903.3402 -19.740867
9300 20653.002 78.77764 0 3903.4076 -7.8068233
9350 18961.572 391.20947 0 3902.6117 -12.660843
9400 16262.179 892.67633 0 3904.191 22.2435
9450 17064.394 743.33301 0 3903.406 36.139436
9500 18075.588 555.06436 0 3902.3954 24.598176
9550 20487.738 109.06287 0 3903.0884 2.6320759
9600 20358.609 133.36993 0 3903.4828 0.76449113
9650 19849.022 228.46312 0 3904.208 9.5547064
9700 20448.112 116.8757 0 3903.5632 -1.0845697
9750 20472.78 112.51661 0 3903.7722 -0.30676738
9800 19491.99 293.35361 0 3902.9814 -20.10857
9850 19895.603 218.42479 0 3902.7957 -0.18235641
9900 19704.336 254.55068 0 3903.5019 14.553184
9950 17689.462 627.9788 0 3903.805 4.9918088
10000 20184.205 165.29396 0 3903.1097 2.9472364
Loop time of 2.28393 on 1 procs for 10000 steps with 81 atoms
Performance: 37829.498 tau/day, 4378.414 timesteps/s
99.3% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.052911 | 0.052911 | 0.052911 | 0.0 | 2.32
Neigh | 0.056658 | 0.056658 | 0.056658 | 0.0 | 2.48
Comm | 0.0087389 | 0.0087389 | 0.0087389 | 0.0 | 0.38
Output | 0.0037996 | 0.0037996 | 0.0037996 | 0.0 | 0.17
Modify | 2.1537 | 2.1537 | 2.1537 | 0.0 | 94.30
Other | | 0.008147 | | | 0.36
Nlocal: 81 ave 81 max 81 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 113 ave 113 max 113 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 582 ave 582 max 582 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 582
Ave neighs/atom = 7.1851852
Neighbor list builds = 993
Dangerous builds = 950
Total wall time: 0:00:02

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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
# 2 chains of connected bodies
group clump1 id <> 1 9
9 atoms in group clump1
group clump2 id <> 9 18
10 atoms in group clump2
group clump3 id <> 18 27
10 atoms in group clump3
group clump4 id <> 27 36
10 atoms in group clump4
group clump5 id <> 37 45
9 atoms in group clump5
group clump6 id <> 45 54
10 atoms in group clump6
group clump7 id <> 54 63
10 atoms in group clump7
group clump8 id <> 63 72
10 atoms in group clump8
group clump9 id <> 72 81
10 atoms in group clump9
fix 1 all poems file connected-bodies2.dat
2 clusters, 9 bodies, 7 joints, 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.poems
#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
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- fix poems command:
@Article{Mukherjee08,
author = {R. M. Mukherjee, P. S. Crozier, S. J. Plimpton, K. S. Anderson},
title = {Substructured molecular dynamics using multibody dynamics algorithms},
journal = {Intl.~J.~Non-linear Mechanics},
year = 2008,
volume = 43,
pages = {1045--1055}
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
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/atomonly/newton
stencil: half/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.514 | 3.545 | 3.639 Mbytes
Step Temp E_pair E_mol TotEng Press
0 196.00047 3632.2347 0 3668.5311 -2.7403788
50 12774.759 1538.7382 0 3904.4344 18.086358
100 19803.641 237.21132 0 3904.5523 -3.1528278
150 20259.6 152.62072 0 3904.3985 -4.6173524
200 20705.978 69.977039 0 3904.4174 9.0928122
250 19552.211 283.50525 0 3904.285 15.670466
300 19266.324 333.5792 0 3901.4169 7.2119197
350 20738.325 63.738945 0 3904.1694 -23.03999
400 20616.682 86.082444 0 3903.9864 -13.783584
450 19831.326 230.13858 0 3902.6063 0.42074361
500 20365.825 131.47271 0 3902.9217 0.69215592
550 20794.102 52.163238 0 3902.9229 4.5895354
600 20853.873 40.899172 0 3902.7275 2.3593042
650 19255.802 336.29509 0 3902.1844 10.341742
700 18526.969 471.02462 0 3901.9448 -0.61898691
750 18960.662 391.26068 0 3902.4944 12.04731
800 20142.432 172.05197 0 3902.1319 4.6838632
850 19932.48 210.71175 0 3901.9118 3.4716031
900 20243.528 153.13972 0 3901.9411 3.6490762
950 20388.132 126.88722 0 3902.4671 -4.4518463
1000 20076.333 184.61915 0 3902.4586 -2.272315
1050 20859.506 39.696993 0 3902.5684 6.45166
1100 15284.661 1072.1908 0 3902.6836 21.194042
1150 19658.317 261.99809 0 3902.4272 -2.8744219
1200 20767.681 56.717095 0 3902.5839 -34.817444
1250 20625.583 82.586198 0 3902.1386 11.697328
1300 20690.013 71.006478 0 3902.4903 -29.29278
1350 20936.019 26.022786 0 3903.0634 1.0316025
1400 19753.56 244.81784 0 3902.8844 6.7138497
1450 15690.149 998.34213 0 3903.9252 48.124569
1500 20234.455 155.92516 0 3903.0465 13.172207
1550 20779.631 55.063019 0 3903.1428 -2.6390455
1600 20642.753 80.233821 0 3902.9659 -2.4688431
1650 18785.698 423.90364 0 3902.7365 -5.6466892
1700 20965.076 20.760451 0 3903.182 -0.45366172
1750 18935.412 396.95958 0 3903.5173 25.913174
1800 20581.554 91.757912 0 3903.1567 3.8218442
1850 20616.949 85.184789 0 3903.1382 4.1907933
1900 16601.896 828.43849 0 3902.8638 -0.49468175
1950 20175.564 166.52646 0 3902.7421 5.6035728
2000 20262.525 150.28224 0 3902.6017 -1.1967705
2050 20168.994 167.65314 0 3902.6521 -0.80723928
2100 19810.955 232.96524 0 3901.6605 3.1936531
2150 20667.232 75.645145 0 3902.9103 0.54812734
2200 19863.772 224.34646 0 3902.8228 7.9294465
2250 18808.943 419.2084 0 3902.3461 14.344526
2300 20573.665 92.761842 0 3902.6999 -6.7671703
2350 19075.104 369.95414 0 3902.3809 -9.5353568
2400 20273.873 148.53775 0 3902.9586 -1.93796
2450 20087.769 182.30216 0 3902.2593 2.131796
2500 20711.602 67.530554 0 3903.0124 2.6280244
2550 19971.224 204.75926 0 3903.134 3.1760522
2600 20620.084 85.027145 0 3903.5612 -0.92888063
2650 19737.546 248.65474 0 3903.7559 -3.3218688
2700 20650.724 79.522243 0 3903.7303 -7.5918025
2750 19863.245 225.2505 0 3903.6292 9.2140221
2800 18992.457 386.73547 0 3903.8572 2.6244537
2850 18703.899 440.48356 0 3904.1685 14.561348
2900 17939.805 581.74599 0 3903.932 -8.0863089
2950 20867.516 39.38186 0 3903.7367 3.0985423
3000 19767.994 242.8847 0 3903.6243 1.5943109
3050 20397.448 126.31591 0 3903.6212 -0.14982775
3100 20978.114 19.126395 0 3903.9623 -9.6797253
3150 18303.556 513.8514 0 3903.3989 4.5940322
3200 19156.505 356.46608 0 3903.9671 10.071308
3250 17484.205 666.52199 0 3904.3377 -4.1641768
3300 18069.94 557.75947 0 3904.0447 11.868707
3350 20855.645 41.964632 0 3904.1212 5.4186293
3400 18011.986 568.76255 0 3904.3155 25.262783
3450 18669.69 446.92755 0 3904.2776 -4.194499
3500 20248.799 154.22147 0 3903.9991 3.9211572
3550 20226.024 158.64726 0 3904.2072 1.5299114
3600 20267.02 151.25631 0 3904.4082 -8.9821729
3650 20522.946 103.65382 0 3904.1994 -14.433796
3700 20892.319 35.294614 0 3904.2426 -21.264596
3750 19942.202 211.02993 0 3904.0304 -1.6428817
3800 20421.678 122.08118 0 3903.8734 1.7137935
3850 17899.53 588.82593 0 3903.5536 -24.450276
3900 20721.119 66.486999 0 3903.7312 -7.1772088
3950 20946.484 24.799445 0 3903.778 -0.4028037
4000 20985.362 17.608355 0 3903.7865 4.7522266
4050 19969.779 205.46466 0 3903.5719 18.941639
4100 20479.578 110.56561 0 3903.08 2.3715952
4150 18110.701 549.53348 0 3903.367 1.133321
4200 19321.098 325.58216 0 3903.5634 -3.7574942
4250 20734.436 63.87616 0 3903.5865 0.48350623
4300 19446.823 302.1727 0 3903.4362 4.0462392
4350 20494.669 108.1918 0 3903.501 2.9789077
4400 20379.244 129.61413 0 3903.5482 4.0881089
4450 19710.564 253.4251 0 3903.5295 5.3334683
4500 20744.753 61.785082 0 3903.406 4.0015409
4550 19948.024 208.76984 0 3902.8484 2.705423
4600 18367.368 502.69569 0 3904.0602 21.476471
4650 20559.367 96.133242 0 3903.4234 2.2549454
4700 20940.135 25.547808 0 3903.3505 -8.9042666
4750 20128.703 175.82088 0 3903.3584 -8.1450176
4800 20632.27 82.543887 0 3903.3347 -0.55649542
4850 19864.539 224.63792 0 3903.2563 7.1553461
4900 19332.037 323.15561 0 3903.1625 17.020214
4950 19055.575 373.68069 0 3902.4908 10.149457
5000 20219.484 159.21383 0 3903.5627 3.1806346
5050 17557.761 652.32864 0 3903.7659 10.733736
5100 20615.337 85.795304 0 3903.4503 -3.6035636
5150 20759.853 59.155843 0 3903.573 2.0152286
5200 20082.007 184.39375 0 3903.2839 -5.3745109
5250 18689.521 442.59842 0 3903.6208 -9.8911164
5300 20038.496 192.34221 0 3903.1749 -2.1437039
5350 19897.455 218.70142 0 3903.4154 0.64582116
5400 18732.385 434.21543 0 3903.1755 12.98676
5450 19831.487 230.79099 0 3903.2886 11.439958
5500 20079.89 184.6953 0 3903.1935 4.0906279
5550 20453.497 115.47128 0 3903.1559 7.8844436
5600 16673.041 815.52661 0 3903.1267 -20.17797
5650 19691.378 256.6412 0 3903.1928 3.7103317
5700 20345.743 135.29997 0 3903.0302 5.6373816
5750 20769.613 56.906603 0 3903.1312 -17.564762
5800 20713.369 67.38314 0 3903.1922 -5.340631
5850 20799.947 51.348865 0 3903.1909 -2.7827653
5900 19581.933 273.51588 0 3899.7997 12.347375
5950 20444.438 116.909 0 3902.9161 -0.74896654
6000 18970.948 389.99664 0 3903.1352 26.642912
6050 19414.753 307.13217 0 3902.4568 25.86316
6100 20780.042 54.586474 0 3902.7424 1.5387425
6150 20885.872 35.091585 0 3902.8456 -8.251884
6200 19825.81 231.40943 0 3902.8558 6.7196589
6250 20578.278 92.255994 0 3903.0481 -5.9647091
6300 20093.43 181.8699 0 3902.8754 -9.9906069
6350 20605.294 87.180289 0 3902.9755 -3.5643876
6400 19737.257 247.84828 0 3902.8958 -4.2783347
6450 19884.717 220.81633 0 3903.1714 3.8758905
6500 18719.372 436.94802 0 3903.4984 1.7865904
6550 20096.883 181.63346 0 3903.2784 2.395512
6600 20888.673 35.003062 0 3903.2758 2.7728947
6650 20437.85 118.16373 0 3902.9507 8.1456757
6700 19241.051 339.73065 0 3902.8882 13.740454
6750 20407.542 123.94326 0 3903.1177 7.6285942
6800 20536.785 99.976706 0 3903.0851 8.3496632
6850 20625.328 83.579677 0 3903.0849 6.5074992
6900 20705.37 68.944625 0 3903.2724 3.1905177
6950 18872.424 408.67134 0 3903.5647 6.2638845
7000 20072.762 186.18051 0 3903.3586 -22.780407
7050 20461.879 114.07495 0 3903.3117 -11.495523
7100 19811.566 234.50237 0 3903.3108 1.1212695
7150 20742.918 61.884088 0 3903.1651 -3.7907508
7200 20911.192 30.599903 0 3903.0429 -7.0262304
7250 20879.755 36.30274 0 3902.9241 -5.8018787
7300 20682.32 72.703261 0 3902.7626 -3.3446789
7350 19401.046 309.70672 0 3902.493 3.4836528
7400 20220.542 157.83897 0 3902.3838 2.3400031
7450 17691.193 625.47764 0 3901.6244 25.239568
7500 19745.294 245.02566 0 3901.5615 5.3622843
7550 19685.719 256.70983 0 3902.2133 3.4560563
7600 18830.192 415.10021 0 3902.1727 -0.10282681
7650 19613.136 270.18979 0 3902.2521 8.2241536
7700 20989.015 15.636879 0 3902.4915 1.2955204
7750 20301.583 142.90625 0 3902.4586 0.12548373
7800 18360.147 502.50342 0 3902.5307 17.117272
7850 20796.478 51.032537 0 3902.2321 -3.0993883
7900 20284.267 145.64296 0 3901.9887 -1.2682383
7950 20280.983 146.13471 0 3901.8723 3.5999841
8000 20915.869 28.730821 0 3902.0399 2.4987291
8050 20745.162 60.19981 0 3901.8964 4.0643481
8100 20509.039 103.70462 0 3901.6748 1.0771863
8150 20212.97 158.64893 0 3901.7916 3.0000215
8200 20323.463 138.25912 0 3901.8634 -1.2802945
8250 19997.284 198.37183 0 3901.5727 -2.6431964
8300 20138.402 171.75824 0 3901.092 1.7669897
8350 20367.568 130.22531 0 3901.9972 -1.2153731
8400 19945.534 208.35675 0 3901.9741 1.6021151
8450 20112.534 177.18642 0 3901.7298 2.2413008
8500 20686.7 71.116816 0 3901.9873 2.2888545
8550 18081.94 553.83586 0 3902.3432 7.8257937
8600 18320.081 505.67086 0 3898.2784 16.554878
8650 20235.305 154.43021 0 3901.709 3.1740823
8700 20355.413 132.22512 0 3901.746 4.3436482
8750 20087.188 182.11349 0 3901.9631 10.422134
8800 20400.795 124.09819 0 3902.0232 2.1179177
8850 20678.731 72.825797 0 3902.2204 -3.4491441
8900 20372.643 129.5072 0 3902.2189 -8.2166415
8950 20851.731 40.899364 0 3902.331 -5.8382839
9000 20318.076 139.61775 0 3902.2243 -4.1960802
9050 16879.415 776.53739 0 3902.3549 -14.429475
9100 19135.149 358.68223 0 3902.2284 -15.50479
9150 20689.556 70.939656 0 3902.339 -2.9876179
9200 19949.801 207.54882 0 3901.9564 6.4259245
9250 20207.027 160.2813 0 3902.3233 1.7402195
9300 20030.005 192.99466 0 3902.2548 5.300728
9350 19795.291 236.24003 0 3902.0347 5.8677745
9400 18232.093 526.18752 0 3902.501 19.344893
9450 18789.641 422.30568 0 3901.8687 -7.5185247
9500 16332.599 874.10423 0 3898.6597 16.241378
9550 18572.572 462.19972 0 3901.5649 -10.777359
9600 19859.645 223.32209 0 3901.0341 0.89631957
9650 19092.741 365.35768 0 3901.0504 6.7830005
9700 18391.154 495.72792 0 3901.4972 6.0683847
9750 17790.092 608.60997 0 3903.0714 8.2090184
9800 17681.783 628.99951 0 3903.4038 14.231747
9850 17804.412 605.54067 0 3902.654 22.308453
9900 19134.472 359.37911 0 3902.7999 8.5633158
9950 20099.055 180.28604 0 3902.3332 4.7905855
10000 20035.447 192.30744 0 3902.5754 1.8299201
Loop time of 2.34062 on 4 procs for 10000 steps with 81 atoms
Performance: 36913.309 tau/day, 4272.374 timesteps/s
99.3% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0052865 | 0.014915 | 0.039366 | 11.6 | 0.64
Neigh | 0.0080708 | 0.016504 | 0.03345 | 7.7 | 0.71
Comm | 0.1357 | 0.14237 | 0.15111 | 1.5 | 6.08
Output | 0.0033429 | 0.0037922 | 0.0050931 | 1.2 | 0.16
Modify | 2.1033 | 2.1433 | 2.1609 | 1.6 | 91.57
Other | | 0.01973 | | | 0.84
Nlocal: 20.25 ave 36 max 0 min
Histogram: 1 0 0 0 0 1 1 0 0 1
Nghost: 35.25 ave 47 max 24 min
Histogram: 1 0 1 0 0 0 0 1 0 1
Neighs: 137.5 ave 252 max 0 min
Histogram: 1 0 0 1 0 0 0 0 1 1
Total # of neighbors = 550
Ave neighs/atom = 6.7901235
Neighbor list builds = 994
Dangerous builds = 956
Total wall time: 0:00:02

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LAMMPS (27 Nov 2018)
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
orthogonal box = (-12 -12 -12) to (12 12 12)
1 by 1 by 1 MPI processor grid
reading atoms ...
81 atoms
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
# 1 chain of connected bodies
group clump1 id <> 1 9
9 atoms in group clump1
group clump2 id <> 9 18
10 atoms in group clump2
group clump3 id <> 18 27
10 atoms in group clump3
group clump4 id <> 27 36
10 atoms in group clump4
group clump5 id <> 36 45
10 atoms in group clump5
group clump6 id <> 45 54
10 atoms in group clump6
group clump7 id <> 54 63
10 atoms in group clump7
group clump8 id <> 63 72
10 atoms in group clump8
group clump9 id <> 72 81
10 atoms in group clump9
fix 1 all poems group clump1 clump2 clump3 clump4 clump5 clump6 clump7 clump8 clump9
1 clusters, 9 bodies, 8 joints, 81 atoms
# 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.poems
#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
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/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.292 | 3.292 | 3.292 Mbytes
Step Temp E_pair E_mol TotEng Press
0 217.7783 3430.3907 0 3466.6871 -2.7403788
50 13679.637 1404.2468 0 3684.1863 12.446066
100 16777.225 888.87665 0 3685.0808 -31.828677
150 19595.365 418.45042 0 3684.3446 40.709078
200 18524.188 596.47273 0 3683.8375 -0.8159371
250 21015.789 180.96521 0 3683.5967 -10.042469
300 20785.513 219.25314 0 3683.5053 2.6452719
350 21072.46 171.2554 0 3683.3321 7.0609024
400 19956.414 356.36381 0 3682.4328 19.320259
450 20724.42 227.73284 0 3681.8028 8.1259249
500 20152.578 322.71466 0 3681.4777 5.4929878
550 20017.022 345.29701 0 3681.4673 5.4661666
600 17897.743 698.72196 0 3681.6791 3.2854742
650 17297.758 796.60256 0 3679.5623 15.191113
700 18581.934 584.29715 0 3681.2861 5.1588289
750 21774.158 52.821062 0 3681.8474 -10.775664
800 21604.055 81.188546 0 3681.8644 -3.2045743
850 17821.483 711.53827 0 3681.7854 7.4384277
900 21033.292 175.98127 0 3681.5299 -16.345167
950 20968.166 186.59847 0 3681.2929 -2.330456
1000 20490.66 266.19375 0 3681.3037 11.787983
1050 20222.396 310.94072 0 3681.34 -8.3459539
1100 21321.687 127.61533 0 3681.2299 -1.2184717
1150 20849.582 206.01695 0 3680.9472 -0.86699149
1200 21815.003 45.317414 0 3681.1512 1.5988314
1250 18655.437 572.41453 0 3681.654 10.064078
1300 20780.781 217.36506 0 3680.8286 6.0538616
1350 20558.971 254.36482 0 3680.8601 -3.6773952
1400 21485.029 99.812921 0 3680.6511 -16.185473
1450 21771.107 52.15961 0 3680.6775 -2.4756673
1500 21520.948 93.503927 0 3680.3286 2.1023576
1550 21351.418 121.68137 0 3680.2511 5.5159947
1600 20778.805 216.92177 0 3680.0559 15.089188
1650 21477.638 100.21836 0 3679.8247 -1.1045746
1700 18501.339 596.47914 0 3680.0357 -15.679679
1750 18563.642 587.34785 0 3681.2882 33.532209
1800 19110.185 494.8234 0 3679.8543 18.024046
1850 21364.191 119.23545 0 3679.9339 2.5291103
1900 20146.626 322.14867 0 3679.9197 5.7313218
1950 20692.672 231.25325 0 3680.0319 4.2977763
2000 20943.904 189.11235 0 3679.7629 -22.645121
2050 19668.057 401.82994 0 3679.8394 3.6251916
2100 20280.442 299.76155 0 3679.8353 7.4807949
2150 19181.86 483.522 0 3680.4987 22.620507
2200 21300.161 130.70534 0 3680.7322 4.7102665
2250 20486.943 266.63931 0 3681.1299 -8.6456512
2300 18653.122 572.24819 0 3681.1018 -5.2637122
2350 21513.523 95.614901 0 3681.2021 -9.3621767
2400 21466.272 103.56446 0 3681.2765 -29.561368
2450 20100.105 332.27123 0 3682.2887 35.744287
2500 20764.395 221.6677 0 3682.4001 -12.468906
2550 20435.699 276.31055 0 3682.2603 -22.413697
2600 21466.467 104.53618 0 3682.2807 -10.078508
2650 20814.737 213.23892 0 3682.3617 5.1390411
2700 18565.761 588.3578 0 3682.6513 22.27664
2750 20772.36 220.1607 0 3682.2206 -7.9448198
2800 21018.563 179.10058 0 3682.1945 -7.0717829
2850 16789.412 884.21472 0 3682.4501 33.279015
2900 19304.363 464.75282 0 3682.1466 7.947554
2950 20513.758 263.07578 0 3682.0355 2.2361434
3000 20617.309 245.95251 0 3682.1706 -0.75213689
3050 18567.52 587.90473 0 3682.4914 -4.0112006
3100 18696.577 566.20617 0 3682.3023 -1.4814167
3150 19864.606 371.56078 0 3682.3284 8.9362836
3200 18902.643 532.04614 0 3682.4867 0.76630303
3250 21110.454 163.86212 0 3682.271 -1.6253894
3300 19369.939 454.05833 0 3682.3816 4.9066544
3350 19082.603 501.69905 0 3682.133 3.5982292
3400 19527.779 426.918 0 3681.5478 6.9612143
3450 19892.953 366.19989 0 3681.6921 3.0050426
3500 19708.981 396.84552 0 3681.6756 7.0757635
3550 20256.096 306.23937 0 3682.2554 -1.752138
3600 21289.889 133.93823 0 3682.253 -3.7462615
3650 18333.877 627.18028 0 3682.8264 -15.276791
3700 19829.133 377.33753 0 3682.1931 -6.269648
3750 20771.635 220.07171 0 3682.0109 -28.479036
3800 18373.813 619.79253 0 3682.0947 29.594781
3850 19320.99 461.92786 0 3682.0928 -5.3212101
3900 16119.825 995.68064 0 3682.3182 -8.4683118
3950 15556.948 1091.3655 0 3684.1902 20.98273
4000 20000.464 348.24891 0 3681.6596 7.1589745
4050 18870.219 536.59924 0 3681.6358 -3.7997025
4100 19889.518 367.49253 0 3682.4122 -14.091266
4150 15789.623 1051.3399 0 3682.9438 -4.4152389
4200 20548.889 256.83493 0 3681.6498 0.92234153
4250 20681.925 235.46113 0 3682.4487 -11.515773
4300 19330.404 460.80975 0 3682.5437 -22.351775
4350 19369.443 453.35405 0 3681.5945 29.418242
4400 20762.165 222.24133 0 3682.6021 2.6627047
4450 19984.657 350.71294 0 3681.4891 28.88731
4500 21167.58 154.25344 0 3682.1834 -3.0784322
4550 18133.576 660.73671 0 3682.9995 2.5305835
4600 19935.069 360.36826 0 3682.8798 2.4575034
4650 21413.76 113.86464 0 3682.8246 -5.1271547
4700 21716.333 63.609419 0 3682.9982 -2.4708049
4750 21352.947 124.36961 0 3683.1941 -0.29026265
4800 19043.788 508.8617 0 3682.8264 14.797006
4850 20516.121 263.78758 0 3683.1411 7.1348281
4900 20624.5 245.81827 0 3683.235 0.34708051
4950 20317.197 296.68937 0 3682.8889 -0.55065946
5000 18346.865 625.37246 0 3683.1832 7.3371413
5050 18867.53 538.49153 0 3683.0799 1.9249866
5100 18790.276 551.17224 0 3682.885 2.2333017
5150 20241.365 311.84683 0 3685.4076 -3.998004
5200 17685.058 739.76418 0 3687.2739 3.2835025
5250 18496.626 604.58166 0 3687.3526 -10.185776
5300 18420.042 617.82026 0 3687.8273 -16.392458
5350 18767.338 559.0349 0 3686.9246 4.5320767
5400 20423.245 284.90517 0 3688.7794 -8.6356656
5450 21080.398 176.18494 0 3689.5846 -16.450038
5500 16684.424 909.12643 0 3689.8637 49.94555
5550 20132.31 335.03663 0 3690.4216 -16.018038
5600 20430.923 285.17562 0 3690.3295 -5.0773675
5650 20479.943 276.55962 0 3689.8834 5.4334564
5700 20061.532 345.95553 0 3689.5441 -16.230658
5750 20523.759 268.92217 0 3689.5487 -4.4128812
5800 18900.356 537.65462 0 3687.7139 13.605549
5850 20280.502 310.27193 0 3690.3556 -4.7884959
5900 19050.26 515.66087 0 3690.7042 7.8864722
5950 19566.917 430.2997 0 3691.4525 31.715268
6000 18878.118 544.75449 0 3691.1076 -4.2415329
6050 19308.682 471.70734 0 3689.821 -10.561614
6100 18776.194 560.04764 0 3689.4133 -7.7286747
6150 21475.064 110.1508 0 3689.3281 -3.6506391
6200 19975 360.82675 0 3689.9934 10.282021
6250 21396.341 123.5341 0 3689.5909 -5.7215163
6300 18533.423 600.87422 0 3689.778 15.408027
6350 20653.152 247.19253 0 3689.3846 8.5607784
6400 19716.537 403.41487 0 3689.5044 13.165575
6450 21120.66 168.79838 0 3688.9084 -0.50382728
6500 19700.345 404.7155 0 3688.1064 13.941375
6550 10818.393 1892.037 0 3695.1025 38.423155
6600 18684.478 574.84755 0 3688.9273 5.9176985
6650 19219.732 486.04269 0 3689.3314 18.287659
6700 20058.587 344.88255 0 3687.9804 6.5372086
6750 21279.318 142.77333 0 3689.3264 2.498188
6800 20671.545 244.25024 0 3689.5078 -4.1356416
6850 21203.598 155.82001 0 3689.753 -0.0083061182
6900 21699.344 73.301497 0 3689.8588 -8.0309898
6950 20951.212 197.19403 0 3689.0627 0.76668303
7000 20166.275 329.02869 0 3690.0746 2.0083318
7050 21554.944 97.465792 0 3689.9564 -3.2420086
7100 20817.494 220.25476 0 3689.8372 0.17206182
7150 21481.11 109.84029 0 3690.0253 -3.6814741
7200 21266.824 145.53099 0 3690.0016 -2.060543
7250 19434.684 450.81331 0 3689.9273 9.4822765
7300 21246.525 148.96573 0 3690.0532 3.3208839
7350 19749.269 398.60049 0 3690.1454 1.0929662
7400 20354.792 297.70261 0 3690.168 1.547159
7450 19996.859 357.16723 0 3689.977 -0.68412025
7500 20179.628 326.53243 0 3689.8038 -2.4805507
7550 18765.184 561.65039 0 3689.1811 -1.7976428
7600 19457.496 447.04428 0 3689.9603 -1.9055522
7650 18206.823 655.57276 0 3690.0433 1.2797964
7700 19152.344 497.77422 0 3689.8315 18.145069
7750 21387.484 125.48654 0 3690.0673 -2.9915772
7800 18127.052 668.61425 0 3689.7896 9.044869
7850 21419.557 120.08889 0 3690.015 6.2651717
7900 21817.182 53.739819 0 3689.9368 -4.2387416
7950 18215.195 654.15494 0 3690.0208 -54.628049
8000 21523.503 102.58018 0 3689.8307 -4.84236
8050 20720.799 236.28689 0 3689.7535 -9.3725225
8100 21196.483 157.3232 0 3690.0704 -7.7222497
8150 20869.667 211.65308 0 3689.9309 -6.8438295
8200 17790.052 725.72497 0 3690.7336 -25.697688
8250 19634.94 417.71929 0 3690.2094 8.861604
8300 19135.784 500.92443 0 3690.2218 -3.1245167
8350 20191.718 324.93312 0 3690.2195 6.5736107
8400 20695.239 241.02378 0 3690.2302 -14.592221
8450 21793.857 57.609525 0 3689.9191 -11.509747
8500 21271.088 144.43102 0 3689.6124 -0.091587085
8550 20064.337 345.21754 0 3689.2737 9.5058471
8600 20282.86 308.2307 0 3688.7074 2.265529
8650 21223.055 151.24306 0 3688.419 1.7296834
8700 18875.342 542.42055 0 3688.3108 6.367148
8750 20922.65 201.55122 0 3688.6595 3.4208578
8800 21406.54 120.8539 0 3688.6106 1.8253729
8850 19868.524 377.05623 0 3688.477 16.327796
8900 20025.322 348.94892 0 3686.5025 17.063406
8950 21224.374 151.3567 0 3688.7524 -0.11028753
9000 21318.309 135.862 0 3688.9135 -0.50826819
9050 17538.618 768.00136 0 3691.1043 37.978645
9100 21247.861 147.84641 0 3689.1566 -6.7773259
9150 18455.677 613.08767 0 3689.0339 -3.4844751
9200 19486.859 441.03829 0 3688.8482 -18.602827
9250 21774.926 59.710446 0 3688.8648 -13.379919
9300 17628.877 750.72321 0 3688.8694 27.797974
9350 19827.334 383.85708 0 3688.4128 6.5459021
9400 20020.126 351.61742 0 3688.3051 -14.332562
9450 21596.338 88.904175 0 3688.2939 1.5779716
9500 18981.418 524.60141 0 3688.1711 5.4352409
9550 18652.616 579.05144 0 3687.8208 25.600729
9600 21198.037 155.23097 0 3688.2371 -3.3586596
9650 19958.317 361.32544 0 3687.7115 4.2910178
9700 19129.101 499.5993 0 3687.7828 13.267102
9750 21913.967 35.689587 0 3688.0174 -7.3222905
9800 21314.694 135.43794 0 3687.8869 -9.5613518
9850 20899.743 204.82802 0 3688.1185 -2.6321428
9900 20288.244 306.5013 0 3687.8753 3.6196618
9950 19271.015 475.88527 0 3687.7211 -1.8196764
10000 21122.24 167.82714 0 3688.2005 -3.8464842
Loop time of 6.61148 on 1 procs for 10000 steps with 81 atoms
Performance: 13068.179 tau/day, 1512.521 timesteps/s
97.7% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.14595 | 0.14595 | 0.14595 | 0.0 | 2.21
Neigh | 0.10704 | 0.10704 | 0.10704 | 0.0 | 1.62
Comm | 0.013317 | 0.013317 | 0.013317 | 0.0 | 0.20
Output | 0.0047956 | 0.0047956 | 0.0047956 | 0.0 | 0.07
Modify | 6.3318 | 6.3318 | 6.3318 | 0.0 | 95.77
Other | | 0.008603 | | | 0.13
Nlocal: 81 ave 81 max 81 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 95 ave 95 max 95 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 744 ave 744 max 744 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 744
Ave neighs/atom = 9.18519
Neighbor list builds = 992
Dangerous builds = 941
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:06

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examples/rigid/log.27Nov18.rigid.poems.g++.4
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LAMMPS (27 Nov 2018)
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
orthogonal box = (-12 -12 -12) to (12 12 12)
1 by 2 by 2 MPI processor grid
reading atoms ...
81 atoms
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
# 1 chain of connected bodies
group clump1 id <> 1 9
9 atoms in group clump1
group clump2 id <> 9 18
10 atoms in group clump2
group clump3 id <> 18 27
10 atoms in group clump3
group clump4 id <> 27 36
10 atoms in group clump4
group clump5 id <> 36 45
10 atoms in group clump5
group clump6 id <> 45 54
10 atoms in group clump6
group clump7 id <> 54 63
10 atoms in group clump7
group clump8 id <> 63 72
10 atoms in group clump8
group clump9 id <> 72 81
10 atoms in group clump9
fix 1 all poems group clump1 clump2 clump3 clump4 clump5 clump6 clump7 clump8 clump9
1 clusters, 9 bodies, 8 joints, 81 atoms
# 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.poems
#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
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/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.263 | 3.357 | 3.638 Mbytes
Step Temp E_pair E_mol TotEng Press
0 217.7783 3430.3907 0 3466.6871 -2.7403788
50 13679.637 1404.2468 0 3684.1863 12.446066
100 16777.225 888.87665 0 3685.0808 -31.828677
150 19595.365 418.45042 0 3684.3446 40.709078
200 18524.188 596.47273 0 3683.8375 -0.8159371
250 21015.789 180.96521 0 3683.5967 -10.042469
300 20785.513 219.25314 0 3683.5053 2.6452719
350 21072.46 171.2554 0 3683.3321 7.0609024
400 19956.414 356.36381 0 3682.4328 19.320259
450 20724.42 227.73284 0 3681.8028 8.1259249
500 20152.578 322.71466 0 3681.4777 5.4929878
550 20017.022 345.29701 0 3681.4673 5.4661666
600 17897.743 698.72196 0 3681.6791 3.2854742
650 17297.758 796.60256 0 3679.5623 15.191113
700 18581.934 584.29715 0 3681.2861 5.1588289
750 21774.158 52.821062 0 3681.8474 -10.775664
800 21604.055 81.188546 0 3681.8644 -3.2045743
850 17821.483 711.53827 0 3681.7854 7.4384276
900 21033.292 175.98127 0 3681.5299 -16.345167
950 20968.166 186.59847 0 3681.2929 -2.330456
1000 20490.66 266.19375 0 3681.3037 11.787983
1050 20222.396 310.94072 0 3681.34 -8.3459539
1100 21321.687 127.61533 0 3681.2299 -1.2184718
1150 20849.582 206.01695 0 3680.9472 -0.8669916
1200 21815.003 45.317417 0 3681.1512 1.5988314
1250 18655.437 572.41453 0 3681.654 10.064076
1300 20780.781 217.36504 0 3680.8286 6.0538619
1350 20558.972 254.3648 0 3680.8601 -3.6773987
1400 21485.029 99.812949 0 3680.6511 -16.185471
1450 21771.108 52.15959 0 3680.6775 -2.4756681
1500 21520.948 93.503949 0 3680.3286 2.1023578
1550 21351.418 121.6814 0 3680.2511 5.5159978
1600 20778.805 216.92171 0 3680.0559 15.089182
1650 21477.639 100.2182 0 3679.8247 -1.1045944
1700 18501.343 596.47853 0 3680.0357 -15.67963
1750 18563.643 587.34767 0 3681.2882 33.532167
1800 19110.19 494.82264 0 3679.8543 18.024034
1850 21364.196 119.23454 0 3679.9339 2.5291491
1900 20146.643 322.14595 0 3679.9197 5.731152
1950 20692.67 231.25357 0 3680.0319 4.2977641
2000 20943.904 189.11223 0 3679.763 -22.645645
2050 19668.152 401.81407 0 3679.8394 3.6255896
2100 20280.572 299.73976 0 3679.8351 7.4809355
2150 19182.121 483.47905 0 3680.4992 22.615309
2200 21299.76 130.77281 0 3680.7327 4.7114154
2250 20487.784 266.4995 0 3681.1302 -8.6406776
2300 18655.125 571.91487 0 3681.1023 -5.2671669
2350 21512.614 95.766913 0 3681.2025 -9.3523428
2400 21467.773 103.31519 0 3681.2773 -29.600307
2450 20096.937 332.80159 0 3682.2911 35.890912
2500 20761.446 222.16118 0 3682.4022 -12.528127
2550 20409.6 280.67234 0 3682.2723 -22.277373
2600 21469.964 103.95529 0 3682.2826 -10.038267
2650 20708.138 231.00516 0 3682.3615 5.3659502
2700 18584.743 585.07862 0 3682.5357 21.785261
2750 20503.019 264.91491 0 3682.0847 -4.5583917
2800 20584.075 251.44664 0 3682.1258 -6.5084595
2850 17277.076 802.33356 0 3681.8462 15.519513
2900 19392.956 449.92915 0 3682.0885 -4.3829957
2950 18371.786 620.29835 0 3682.2626 7.2117592
3000 20412.015 280.25302 0 3682.2555 0.32492606
3050 20858.248 205.65269 0 3682.0273 4.5055715
3100 21561.094 88.438447 0 3681.9541 -3.7523733
3150 15471.278 1103.4497 0 3681.9961 -14.576367
3200 15386.973 1117.8815 0 3682.377 15.051163
3250 19741.037 392.04755 0 3682.2204 -2.6610995
3300 20870.191 203.58229 0 3681.9475 -4.7795545
3350 16648.228 907.66571 0 3682.3704 -8.9242511
3400 20104.016 331.58603 0 3682.2554 6.4783858
3450 21421.316 112.28228 0 3682.5015 -8.3484987
3500 19284.533 467.80739 0 3681.8962 -12.835452
3550 20160.125 322.4476 0 3682.4684 1.6574827
3600 16682.415 902.73752 0 3683.14 22.383296
3650 16762.19 890.14636 0 3683.8446 16.119412
3700 17858.568 707.37212 0 3683.8 -1.6582504
3750 20029.881 345.15986 0 3683.4733 -3.1415889
3800 20734 227.99158 0 3683.6582 -7.9580418
3850 20741.089 226.39408 0 3683.2423 8.3055765
3900 18671.251 571.42296 0 3683.2981 -3.7468858
3950 19547.209 423.14256 0 3681.0108 5.8312279
4000 19739.799 393.58799 0 3683.5544 18.604884
4050 20014.121 347.8176 0 3683.5044 9.93387
4100 20503.654 266.08691 0 3683.3626 8.1304118
4150 18309.702 632.29807 0 3683.9151 -0.0021480359
4200 20509.423 265.60353 0 3683.8408 -2.1658857
4250 21805.541 50.325935 0 3684.5828 1.082842
4300 21420.551 114.90431 0 3684.9962 -1.7985998
4350 20256.928 308.74187 0 3684.8966 -11.669472
4400 21633.488 79.629274 0 3685.2106 -0.96131785
4450 20793.327 219.66955 0 3685.2241 1.3752349
4500 18719.484 564.86754 0 3684.7816 2.6308699
4550 20966.335 190.68308 0 3685.0722 -18.587627
4600 19428.962 446.59618 0 3684.7565 -4.4051672
4650 18408.956 616.85009 0 3685.0095 2.777272
4700 19215.779 482.57562 0 3685.2054 19.441016
4750 20155.927 326.13401 0 3685.4553 6.1734993
4800 20918.085 199.31832 0 3685.6659 3.4407437
4850 20236.958 312.07276 0 3684.899 3.2612893
4900 21419.89 115.36879 0 3685.3505 -4.675951
4950 19707.901 401.14828 0 3685.7985 -10.730734
5000 19407.201 450.64394 0 3685.1775 17.518981
5050 21527.598 97.655186 0 3685.5882 -9.2294707
5100 21581.933 88.595517 0 3685.5843 -20.669485
5150 21161.214 158.48503 0 3685.3541 -2.7587502
5200 21166.679 157.24762 0 3685.0275 -18.180044
5250 20909.576 200.23507 0 3685.1644 -16.617303
5300 21911.746 33.236563 0 3685.1942 -5.8313967
5350 20857.303 208.87453 0 3685.0916 12.176312
5400 20958.96 191.96694 0 3685.1269 3.6116429
5450 20433.179 279.61178 0 3685.1415 13.324529
5500 19604.675 416.88499 0 3684.3308 21.536484
5550 18171.145 655.92915 0 3684.4534 -9.2269804
5600 19799.907 385.12116 0 3685.1056 22.202165
5650 19711.882 399.30581 0 3684.6194 15.93063
5700 17908.833 699.52405 0 3684.3295 0.35530356
5750 18606.518 583.538 0 3684.6243 -4.4540843
5800 21814.053 48.974627 0 3684.6501 -1.5206358
5850 18029.107 679.9357 0 3684.7868 12.137677
5900 21090.739 169.64502 0 3684.7682 -1.5051545
5950 21086.26 170.29075 0 3684.6674 -2.8164474
6000 21285.771 136.95608 0 3684.5846 -26.582739
6050 21203.994 150.87822 0 3684.8772 -2.6617226
6100 21481.553 104.57796 0 3684.8368 -16.524974
6150 20354.4 292.57675 0 3684.9767 2.7960207
6200 21326.591 130.75243 0 3685.1843 -1.5929194
6250 21505.087 101.07817 0 3685.2593 -3.7821931
6300 21296.273 135.6593 0 3685.0382 -0.55635908
6350 21295.389 135.86485 0 3685.0964 5.6614093
6400 16552.242 926.02655 0 3684.7336 14.177218
6450 20148.951 327.1151 0 3685.2736 7.4561085
6500 20962.151 191.79415 0 3685.486 -4.5436711
6550 21710.328 67.433972 0 3685.8219 -5.7678572
6600 20698.571 234.79099 0 3684.5528 -2.1984068
6650 17892.287 704.05484 0 3686.1026 11.525836
6700 21272.999 141.26589 0 3686.7657 0.44088069
6750 19558.993 426.46448 0 3686.2966 -16.907401
6800 20350.247 295.23951 0 3686.9474 1.1284348
6850 18665.05 573.5326 0 3684.3742 17.088712
6900 19769.199 392.1551 0 3687.0216 6.7562425
6950 19439.159 446.99138 0 3686.8512 -6.0105763
7000 19379.907 456.53471 0 3686.5192 -9.0505095
7050 19983.754 356.02523 0 3686.651 -5.6274314
7100 19867.737 375.47627 0 3686.7658 17.315482
7150 19258.794 477.47344 0 3687.2724 14.316676
7200 21282.428 139.96051 0 3687.0318 -0.77043459
7250 19828.603 381.98919 0 3686.7564 6.5142869
7300 20574.582 257.8245 0 3686.9215 -3.6547118
7350 21613.467 84.771568 0 3687.0161 -7.5188826
7400 21817.009 50.844944 0 3687.0131 -14.888864
7450 14937.538 1197.4257 0 3687.0154 1.7540499
7500 18326.914 632.40374 0 3686.8894 8.3397357
7550 13611.007 1418.4727 0 3686.9739 -19.379482
7600 19173.985 491.9482 0 3687.6123 17.229001
7650 16911.504 867.33649 0 3685.9204 -21.042834
7700 21752.116 61.143705 0 3686.4963 -10.344487
7750 20208.337 318.26355 0 3686.3197 13.385814
7800 21649.909 77.950987 0 3686.2692 -1.7911084
7850 20139.64 329.50319 0 3686.1098 -5.5805093
7900 21355.026 126.7642 0 3685.9352 -7.7062172
7950 21336.178 129.88925 0 3685.9188 -2.059298
8000 21047.596 177.71546 0 3685.6482 0.37963466
8050 19217.351 482.62331 0 3685.5152 6.5582595
8100 20499.057 268.7173 0 3685.2268 -1.1959737
8150 21494.301 102.83829 0 3685.2219 -1.6427647
8200 20074.928 339.19817 0 3685.0195 6.285123
8250 17335.157 793.47566 0 3682.6685 22.877381
8300 17340.544 794.62619 0 3684.7168 3.9147755
8350 20529.345 262.51162 0 3684.0691 4.031768
8400 18884.747 537.47827 0 3684.9361 22.853404
8450 20341.86 293.10484 0 3683.4148 0.33856656
8500 19300.282 467.58127 0 3684.2949 12.35507
8550 21631.936 78.254534 0 3683.5772 -10.992959
8600 20204.913 316.83233 0 3684.3178 20.74228
8650 21018.189 181.32054 0 3684.352 1.8412068
8700 20161.304 323.97907 0 3684.1964 -2.646629
8750 19081.79 504.00155 0 3684.2998 -10.088053
8800 20834.489 211.76247 0 3684.1773 14.896336
8850 20929.355 196.18335 0 3684.4092 -1.2602398
8900 21491.074 102.47788 0 3684.3235 -1.4696758
8950 20474.735 271.69461 0 3684.1504 -6.9489258
9000 21128.641 162.40732 0 3683.8474 -7.7928168
9050 18421.801 614.46442 0 3684.7646 24.40313
9100 19301.292 466.98873 0 3683.8707 4.4687046
9150 21575.705 88.213763 0 3684.1646 -0.94696984
9200 20004.776 350.05448 0 3684.1838 -7.3466605
9250 21384.079 120.14472 0 3684.1578 -8.3773844
9300 21980.599 20.702393 0 3684.1356 -12.666293
9350 21686.606 69.517984 0 3683.9524 -8.8366533
9400 20732.704 228.46247 0 3683.9131 -6.4080307
9450 19798.859 384.34696 0 3684.1568 7.6198484
9500 20270.695 305.22664 0 3683.6758 1.5862486
9550 16496.156 935.28481 0 3684.6441 15.001468
9600 20642.429 241.08853 0 3681.4934 -9.2159382
9650 21292.587 135.4474 0 3684.2119 -0.54770976
9700 18888.158 536.60518 0 3684.6315 5.3236926
9750 18750.018 559.35922 0 3684.3623 -9.9424949
9800 20544.772 259.71076 0 3683.8394 8.732202
9850 16698.125 901.90076 0 3684.9216 9.9553329
9900 21450.963 109.58687 0 3684.7474 -4.8001999
9950 20664.461 240.66995 0 3684.7468 -3.4840781
10000 18951.367 526.45428 0 3685.0155 21.512727
Loop time of 8.99246 on 4 procs for 10000 steps with 81 atoms
Performance: 9608.051 tau/day, 1112.043 timesteps/s
93.8% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.01308 | 0.038162 | 0.084123 | 14.4 | 0.42
Neigh | 0.017227 | 0.032774 | 0.061983 | 10.0 | 0.36
Comm | 1.329 | 1.5822 | 1.8017 | 13.5 | 17.60
Output | 0.014984 | 0.029676 | 0.046035 | 6.6 | 0.33
Modify | 6.8022 | 7.1104 | 7.4356 | 8.6 | 79.07
Other | | 0.1992 | | | 2.22
Nlocal: 20.25 ave 81 max 0 min
Histogram: 3 0 0 0 0 0 0 0 0 1
Nghost: 46.25 ave 95 max 14 min
Histogram: 2 0 0 0 0 1 0 0 0 1
Neighs: 249.25 ave 997 max 0 min
Histogram: 3 0 0 0 0 0 0 0 0 1
Total # of neighbors = 997
Ave neighs/atom = 12.3086
Neighbor list builds = 993
Dangerous builds = 943
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:09

342
examples/rigid/log.27Nov18.rigid.poems2.g++.1
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@ -1,342 +0,0 @@
LAMMPS (27 Nov 2018)
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
orthogonal box = (-12 -12 -12) to (12 12 12)
1 by 1 by 1 MPI processor grid
reading atoms ...
81 atoms
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
# 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
9 atoms in group clump1
group clump2 id <> 9 18
10 atoms in group clump2
group clump3 id <> 18 27
10 atoms in group clump3
group clump4 id <> 27 36
10 atoms in group clump4
group clump5 id <> 37 45
9 atoms in group clump5
group clump6 id <> 45 54
10 atoms in group clump6
group clump7 id <> 54 63
10 atoms in group clump7
group clump8 id <> 63 72
10 atoms in group clump8
group clump9 id <> 72 81
10 atoms in group clump9
fix 1 all poems group clump1 clump2 clump3 clump4
1 clusters, 4 bodies, 3 joints, 36 atoms
fix 2 all poems group clump5 clump6 clump7 clump8 clump9
1 clusters, 5 bodies, 4 joints, 45 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.poems2
#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
WARNING: More than one fix poems (src/POEMS/fix_poems.cpp:363)
WARNING: More than one fix poems (src/POEMS/fix_poems.cpp:363)
WARNING: One or more atoms are time integrated more than once (src/modify.cpp:283)
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/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.854 | 3.854 | 3.854 Mbytes
Step Temp E_pair E_mol TotEng Press
0 196.00047 3632.2347 0 3668.5311 -2.7403788
50 12167.633 1505.5478 0 3758.8133 35.125973
100 17556.978 512.66277 0 3763.9549 11.137534
150 19579.586 138.04942 0 3763.8987 -29.953971
200 19757.51 105.30542 0 3764.1036 -0.030645317
250 18218.374 390.10747 0 3763.8804 13.711001
300 19383.039 174.40688 0 3763.8586 5.7240693
350 20125.986 36.972611 0 3764.0071 1.9559205
400 18888.816 266.10975 0 3764.0386 9.6362168
450 19307.656 188.2511 0 3763.743 1.9326206
500 16331.197 738.56392 0 3762.8597 9.1715579
550 19318.722 186.16172 0 3763.7027 3.0115336
600 19455.268 161.20621 0 3764.0336 0.55208034
650 18487.011 340.03216 0 3763.5528 -8.0359122
700 17321.201 556.32471 0 3763.9545 -13.631751
750 18979.187 249.04389 0 3763.7082 -2.6072455
800 19342.456 181.85552 0 3763.7918 8.1918726
850 19070.641 232.19342 0 3763.7936 7.3148472
900 19478.873 156.65987 0 3763.8586 2.4284987
950 19912.415 76.437437 0 3763.9216 -1.4667227
1000 16003.749 802.39753 0 3766.0548 46.642188
1050 19859.583 86.64176 0 3764.3424 -2.1961943
1100 19229.575 203.61488 0 3764.6473 -10.632365
1150 18821.6 279.15861 0 3764.64 -0.89495035
1200 19392.695 173.59744 0 3764.8373 1.8508753
1250 16459.624 717.32104 0 3765.3995 33.478127
1300 19343.863 182.59043 0 3764.7874 0.75890736
1350 20019.643 57.503573 0 3764.8448 0.31444671
1400 18549.582 329.31436 0 3764.4221 10.738303
1450 15163.926 957.47585 0 3765.6103 -17.923459
1500 19223.688 204.15175 0 3764.0939 -1.6134531
1550 18147.996 404.12677 0 3764.8668 8.4194779
1600 18615.043 317.42467 0 3764.6548 -2.3288934
1650 20120.654 38.887913 0 3764.935 -8.7620277
1700 19450.907 162.98272 0 3765.0025 2.3254731
1750 19374.632 177.37966 0 3765.2744 8.9328774
1800 19424.404 167.93966 0 3765.0514 0.081230261
1850 17936.249 442.84231 0 3764.3699 6.6010636
1900 19982.595 64.406198 0 3764.8868 -2.9529813
1950 16215.852 761.91287 0 3764.8485 13.994708
2000 18584.422 322.12049 0 3763.68 7.1654003
2050 20107.965 41.025754 0 3764.723 -0.3109069
2100 20002.333 60.593017 0 3764.7288 -6.7919784
2150 16949.762 626.59623 0 3765.441 3.508941
2200 20010.953 58.808279 0 3764.5403 -10.862172
2250 18982.73 247.00892 0 3762.3292 -0.53807815
2300 18401.298 354.87973 0 3762.5274 1.0920554
2350 19390.524 172.9415 0 3763.7793 -3.3524932
2400 16080.801 786.38838 0 3764.3146 -16.200514
2450 18870.412 268.74976 0 3763.2705 11.197736
2500 19688.29 117.58223 0 3763.5618 4.382644
2550 18870.825 268.78678 0 3763.384 -5.6623656
2600 17019.35 611.70808 0 3763.4395 6.3109641
2650 18753.285 291.0596 0 3763.8902 2.4120296
2700 19742.456 107.20901 0 3763.2193 -0.33061303
2750 19522.438 148.16759 0 3763.4339 -1.6254851
2800 18304.801 372.55152 0 3762.3295 22.6368
2850 18465.36 343.48495 0 3762.9961 4.4169272
2900 20151.999 31.372926 0 3763.2245 1.2013699
2950 15498.143 892.80071 0 3762.8272 13.263724
3000 18728.301 294.65113 0 3762.855 8.1897838
3050 18538.466 330.25223 0 3763.3015 8.5865739
3100 19081.409 229.5907 0 3763.1849 -4.8573813
3150 18498.802 337.11548 0 3762.8195 1.0555321
3200 19925.897 73.358029 0 3763.339 -7.7325108
3250 19780.108 100.23785 0 3763.2209 -5.5974972
3300 19221.043 203.82387 0 3763.2763 4.2703251
3350 19025.292 240.11329 0 3763.3156 5.7708328
3400 18153.696 401.52086 0 3763.3164 21.076943
3450 18611.375 316.50396 0 3763.0548 -3.5484945
3500 19931.319 71.969274 0 3762.9543 1.8764978
3550 19747.562 106.05439 0 3763.0103 -2.5506186
3600 18491.39 338.4134 0 3762.7449 -4.0527808
3650 19757.998 104.19207 0 3763.0806 1.4865598
3700 20108.003 39.345514 0 3763.0498 0.062827129
3750 19222.505 203.28065 0 3763.0039 0.33719277
3800 19286.383 191.08831 0 3762.6406 -0.1826802
3850 19450.083 161.09138 0 3762.9587 -0.2708263
3900 18002.304 429.25655 0 3763.0166 -4.6832439
3950 17186.829 582.26502 0 3765.0111 55.816834
4000 16826.434 645.84974 0 3761.856 19.675962
4050 19227.526 202.18151 0 3762.8344 -0.2596098
4100 19908.792 76.084531 0 3762.8978 -2.796813
4150 17821.329 462.63065 0 3762.8768 13.069155
4200 19917.133 74.574998 0 3762.9329 -6.4181155
4250 19012.618 241.96787 0 3762.823 4.0847974
4300 19077.34 229.98133 0 3762.8221 4.324323
4350 19361.128 177.47406 0 3762.8681 -7.377974
4400 18565.044 324.95107 0 3762.9223 2.5229032
4450 19352.406 178.98756 0 3762.7665 0.10862717
4500 18482.218 340.15496 0 3762.788 12.518301
4550 18359.732 362.83749 0 3762.7879 3.7500902
4600 19623.618 128.71624 0 3762.7196 -1.1328521
4650 17565.707 509.99904 0 3762.9078 1.7135935
4700 19876.052 81.892814 0 3762.6431 0.32476108
4750 19022.676 239.92262 0 3762.6403 -0.24613022
4800 18862.685 269.24248 0 3762.3324 6.2733979
4850 19899.174 77.426145 0 3762.4584 0.42535238
4900 18250.865 382.72867 0 3762.5185 23.308462
4950 18895.847 263.22651 0 3762.4575 8.0634675
5000 19096.705 225.69358 0 3762.1204 3.6816481
5050 16546.294 698.91312 0 3763.0416 17.453618
5100 19501.208 151.20999 0 3762.5449 -1.1231291
5150 19479.879 155.00669 0 3762.3917 -3.983378
5200 17397.818 541.23039 0 3763.0485 6.1109992
5250 18564.869 324.10557 0 3762.0442 9.2244762
5300 16271.663 747.52374 0 3760.7947 -6.5256602
5350 19831.418 89.851887 0 3762.3367 -2.3453958
5400 18723.697 294.67435 0 3762.0256 4.6822081
5450 19547.28 142.21934 0 3762.086 -5.5243408
5500 19415.447 166.68729 0 3762.1404 -9.5658991
5550 18492.721 337.54773 0 3762.1256 6.5184903
5600 19391.389 171.14375 0 3762.1416 -0.53835361
5650 18503.465 334.62751 0 3761.1951 4.6580363
5700 18153.344 399.91064 0 3761.6409 12.851587
5750 18342.297 365.14769 0 3761.8694 2.7148176
5800 19583.241 135.64969 0 3762.1758 -1.089608
5850 15967.283 804.18382 0 3761.088 11.278762
5900 19040.271 235.35509 0 3761.3312 5.1352158
5950 17920.962 443.17951 0 3761.8762 4.9621366
6000 19100.92 224.3946 0 3761.602 -9.537589
6050 17982.119 432.3251 0 3762.3472 -2.851617
6100 16233.096 755.46191 0 3761.5908 25.113316
6150 18316.543 370.01118 0 3761.9635 -1.7445703
6200 18483.464 339.13282 0 3761.9966 -2.0857447
6250 18609.406 315.56032 0 3761.7467 -12.289208
6300 17167.919 582.68212 0 3761.9264 -3.8263397
6350 17870.329 452.58116 0 3761.9013 -3.3843134
6400 19309.717 186.11786 0 3761.9913 -4.9462739
6450 17964.073 435.39924 0 3762.0794 12.272972
6500 18772.847 285.61959 0 3762.0727 6.7928648
6550 18915.116 259.41365 0 3762.213 -4.1449761
6600 19446.628 161.18763 0 3762.415 -2.1906581
6650 16348.787 734.99282 0 3762.546 -9.9624546
6700 19066.684 231.43863 0 3762.3061 -5.362833
6750 14890.323 1004.547 0 3762.0143 37.373013
6800 18235.19 385.253 0 3762.1401 0.21012662
6850 16447.997 716.11276 0 3762.0382 -9.2095411
6900 18343.362 364.81902 0 3761.7379 10.417932
6950 16014.084 797.13348 0 3762.7046 6.7906777
7000 19120.393 221.29236 0 3762.1059 -1.3461375
7050 18055.409 418.30136 0 3761.8957 1.5772317
7100 18407.231 353.41868 0 3762.1652 0.61071769
7150 18728.136 293.64021 0 3761.8136 5.1649654
7200 17706.628 483.07628 0 3762.0815 18.000708
7250 19349.505 178.89673 0 3762.1385 2.540201
7300 20016.293 55.389159 0 3762.1101 -1.5793163
7350 19398.573 169.86661 0 3762.1949 -5.060123
7400 19466.526 157.37407 0 3762.2862 1.7158273
7450 18440.348 347.09196 0 3761.9712 12.781963
7500 19989.907 60.555934 0 3762.3906 -1.5033319
7550 19667.28 120.27403 0 3762.363 -3.3502366
7600 18497.707 336.15863 0 3761.66 1.7887539
7650 17901.957 447.17282 0 3762.3501 0.016725252
7700 19758.725 103.3129 0 3762.3361 -23.534448
7750 19443.957 161.6532 0 3762.386 -10.323924
7800 19776.178 100.1773 0 3762.4324 6.0854422
7850 19242.512 198.86705 0 3762.2952 5.2823659
7900 19499.929 151.30366 0 3762.4017 12.299911
7950 19630.317 127.19541 0 3762.4393 8.0799632
8000 19872.384 82.421129 0 3762.4923 2.2126691
8050 17747.038 476.27982 0 3762.7683 -7.7042786
8100 18832.654 274.78106 0 3762.3095 13.882157
8150 19949.814 68.09711 0 3762.5072 -0.54410896
8200 17555.866 511.02517 0 3762.1115 6.2471175
8250 17800.1 465.9992 0 3762.314 13.583485
8300 19755.224 103.89732 0 3762.2721 -1.487243
8350 17583.61 506.17539 0 3762.3995 -9.7819128
8400 18529.003 330.75623 0 3762.0532 14.731228
8450 20155.902 29.797078 0 3762.3716 -8.5711085
8500 18047.548 420.54645 0 3762.685 7.3875118
8550 19790.794 97.493375 0 3762.4553 -3.3427911
8600 19997.902 59.172074 0 3762.4874 3.3479688
8650 19987.319 61.148363 0 3762.5037 -1.889232
8700 19363.91 176.41833 0 3762.3276 -9.4291288
8750 18712.689 296.3979 0 3761.7107 5.9221369
8800 19783.17 98.860518 0 3762.4105 -3.5262066
8850 18796.049 281.60057 0 3762.3504 -8.2913002
8900 16738.277 662.62261 0 3762.3035 8.5838631
8950 17869.613 452.25006 0 3761.4377 11.561101
9000 18682.512 302.27997 0 3762.0043 3.8878724
9050 17513.759 518.50265 0 3761.7914 23.05778
9100 17500.686 521.57944 0 3762.4473 -2.8435751
9150 19645.683 124.43597 0 3762.5254 -3.0193092
9200 18898.897 262.76552 0 3762.5612 3.5891701
9250 20114.279 37.614866 0 3762.4813 -0.58120871
9300 19562.613 139.54073 0 3762.2468 -3.2630158
9350 19679.811 118.05865 0 3762.468 -3.4644363
9400 19297.384 188.84527 0 3762.4349 0.40498037
9450 18267.029 379.52581 0 3762.309 -0.13762867
9500 19951.072 67.63844 0 3762.2814 -7.575539
9550 19134.562 218.46835 0 3761.9057 -1.9626244
9600 19089.093 227.29178 0 3762.3089 -1.94158
9650 16964.603 620.71289 0 3762.3061 16.987042
9700 18846.881 271.3129 0 3761.4761 3.4458802
9750 19309.225 186.0142 0 3761.7966 9.4048627
9800 16359.704 733.51007 0 3763.0849 15.870164
9850 19958.532 66.203725 0 3762.2282 6.0043645
9900 19864.564 83.502384 0 3762.1253 -0.65360617
9950 18996.789 244.25101 0 3762.1749 -2.4961826
10000 17933.494 441.33587 0 3762.3532 -6.0731708
Loop time of 6.84978 on 1 procs for 10000 steps with 81 atoms
Performance: 12613.550 tau/day, 1459.902 timesteps/s
96.9% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.1054 | 0.1054 | 0.1054 | 0.0 | 1.54
Neigh | 0.081336 | 0.081336 | 0.081336 | 0.0 | 1.19
Comm | 0.017124 | 0.017124 | 0.017124 | 0.0 | 0.25
Output | 0.0050254 | 0.0050254 | 0.0050254 | 0.0 | 0.07
Modify | 6.6313 | 6.6313 | 6.6313 | 0.0 | 96.81
Other | | 0.00962 | | | 0.14
Nlocal: 81 ave 81 max 81 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 71 ave 71 max 71 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 612 ave 612 max 612 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 612
Ave neighs/atom = 7.55556
Neighbor list builds = 989
Dangerous builds = 906
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:06

342
examples/rigid/log.27Nov18.rigid.poems2.g++.4
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@ -1,342 +0,0 @@
LAMMPS (27 Nov 2018)
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
orthogonal box = (-12 -12 -12) to (12 12 12)
1 by 2 by 2 MPI processor grid
reading atoms ...
81 atoms
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
# 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
9 atoms in group clump1
group clump2 id <> 9 18
10 atoms in group clump2
group clump3 id <> 18 27
10 atoms in group clump3
group clump4 id <> 27 36
10 atoms in group clump4
group clump5 id <> 37 45
9 atoms in group clump5
group clump6 id <> 45 54
10 atoms in group clump6
group clump7 id <> 54 63
10 atoms in group clump7
group clump8 id <> 63 72
10 atoms in group clump8
group clump9 id <> 72 81
10 atoms in group clump9
fix 1 all poems group clump1 clump2 clump3 clump4
1 clusters, 4 bodies, 3 joints, 36 atoms
fix 2 all poems group clump5 clump6 clump7 clump8 clump9
1 clusters, 5 bodies, 4 joints, 45 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.poems2
#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
WARNING: More than one fix poems (src/POEMS/fix_poems.cpp:363)
WARNING: More than one fix poems (src/POEMS/fix_poems.cpp:363)
WARNING: One or more atoms are time integrated more than once (src/modify.cpp:283)
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/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.825 | 3.919 | 4.201 Mbytes
Step Temp E_pair E_mol TotEng Press
0 196.00047 3632.2347 0 3668.5311 -2.7403788
50 12167.633 1505.5478 0 3758.8133 35.125973
100 17556.978 512.66277 0 3763.9549 11.137534
150 19579.586 138.04942 0 3763.8987 -29.953971
200 19757.51 105.30542 0 3764.1036 -0.030645317
250 18218.374 390.10747 0 3763.8804 13.711001
300 19383.039 174.40688 0 3763.8586 5.7240693
350 20125.986 36.972611 0 3764.0071 1.9559205
400 18888.816 266.10975 0 3764.0386 9.6362168
450 19307.656 188.2511 0 3763.743 1.9326206
500 16331.197 738.56392 0 3762.8597 9.1715579
550 19318.722 186.16172 0 3763.7027 3.0115336
600 19455.268 161.20621 0 3764.0336 0.55208034
650 18487.011 340.03216 0 3763.5528 -8.0359122
700 17321.201 556.32471 0 3763.9545 -13.631751
750 18979.187 249.04389 0 3763.7082 -2.6072455
800 19342.456 181.85552 0 3763.7918 8.1918726
850 19070.641 232.19342 0 3763.7936 7.3148472
900 19478.873 156.65987 0 3763.8586 2.4284987
950 19912.415 76.437437 0 3763.9216 -1.4667227
1000 16003.749 802.39753 0 3766.0548 46.642188
1050 19859.583 86.64176 0 3764.3424 -2.1961943
1100 19229.575 203.61488 0 3764.6473 -10.632365
1150 18821.6 279.15861 0 3764.64 -0.89495035
1200 19392.695 173.59744 0 3764.8373 1.8508753
1250 16459.624 717.32104 0 3765.3995 33.478127
1300 19343.863 182.59043 0 3764.7874 0.75890736
1350 20019.643 57.503573 0 3764.8448 0.31444671
1400 18549.582 329.31436 0 3764.4221 10.738303
1450 15163.926 957.47585 0 3765.6103 -17.923459
1500 19223.688 204.15176 0 3764.0939 -1.6134529
1550 18147.996 404.12677 0 3764.8668 8.4194781
1600 18615.043 317.42468 0 3764.6548 -2.3288926
1650 20120.654 38.887908 0 3764.935 -8.7620288
1700 19450.907 162.98267 0 3765.0025 2.3254739
1750 19374.631 177.3797 0 3765.2744 8.9328773
1800 19424.404 167.93965 0 3765.0514 0.081228843
1850 17936.227 442.84645 0 3764.3699 6.6011251
1900 19982.595 64.406244 0 3764.8868 -2.952971
1950 16215.818 761.91942 0 3764.8486 13.994877
2000 18584.433 322.11846 0 3763.6801 7.1653695
2050 20107.965 41.025796 0 3764.723 -0.31089763
2100 20002.329 60.593879 0 3764.7288 -6.7919882
2150 16949.817 626.58598 0 3765.4409 3.5087505
2200 20010.954 58.8082 0 3764.5403 -10.862143
2250 18982.732 247.00854 0 3762.3293 -0.53812607
2300 18401.276 354.88369 0 3762.5274 1.0921058
2350 19390.535 172.93951 0 3763.7793 -3.3524354
2400 16080.475 786.44896 0 3764.3146 -16.201558
2450 18870.293 268.77171 0 3763.2704 11.199749
2500 19688.508 117.54164 0 3763.5617 4.3806994
2550 18870.328 268.87896 0 3763.3841 -5.6641099
2600 17020.211 611.54841 0 3763.4394 6.3081434
2650 18748.838 291.88478 0 3763.8917 2.4175163
2700 19743.991 106.92945 0 3763.224 -0.33916964
2750 19525.446 147.60906 0 3763.4324 -1.6251174
2800 18257.411 381.40184 0 3762.4038 23.39495
2850 18496.796 337.65425 0 3762.9868 4.3657735
2900 20163.418 29.253902 0 3763.2203 1.4431917
2950 16823.317 646.69817 0 3762.1273 4.9041552
3000 19223.007 203.2529 0 3763.069 4.0414458
3050 17391.02 542.93746 0 3763.4968 15.139863
3100 19205.6 206.57791 0 3763.1705 4.8519241
3150 19835.659 90.247763 0 3763.5179 -14.900053
3200 18962.776 251.5838 0 3763.2089 -13.706561
3250 19418.837 167.29058 0 3763.3716 -2.0866468
3300 18628.291 313.69067 0 3763.3742 5.9919715
3350 17465.974 529.14439 0 3763.5841 14.122593
3400 18488.661 339.6186 0 3763.4448 21.526798
3450 19163.152 214.26098 0 3762.9928 4.1888096
3500 18000.27 429.81789 0 3763.2011 5.4734485
3550 19582.423 136.71887 0 3763.0935 -2.5335675
3600 19634.325 127.2219 0 3763.208 -1.9728322
3650 19428.114 165.40707 0 3763.2059 -2.3318779
3700 19861.116 85.356944 0 3763.3414 -3.9097609
3750 19337.239 182.43992 0 3763.4102 -3.3559651
3800 19493.146 153.40349 0 3763.2453 -0.71089657
3850 18607.616 317.74889 0 3763.6037 3.475832
3900 19719.59 111.5553 0 3763.3313 0.58876668
3950 19756.661 104.5522 0 3763.1931 3.7526698
4000 17904.708 447.1673 0 3762.854 12.270654
4050 19588.087 135.80435 0 3763.2279 0.94578945
4100 19065.901 232.38235 0 3763.1048 -2.7495195
4150 18775.075 286.2257 0 3763.0915 -3.7039858
4200 18800.725 281.46601 0 3763.0817 0.15619543
4250 19732.687 108.90618 0 3763.1075 3.0865861
4300 18278.151 377.63653 0 3762.4794 1.5768601
4350 17915.757 445.4804 0 3763.2133 -3.7040484
4400 15987.794 802.41575 0 3763.1183 22.252078
4450 19302.37 188.69495 0 3763.2079 0.91081327
4500 20039.32 52.304099 0 3763.2893 -2.0828905
4550 19535.953 145.4374 0 3763.2064 -3.3804255
4600 19700.723 114.79823 0 3763.0803 -1.1761163
4650 17804.641 465.85788 0 3763.0136 7.5947192
4700 19913.881 75.240289 0 3762.996 -2.1100557
4750 19982.484 62.535995 0 3762.996 -4.5821237
4800 17400.76 540.21707 0 3762.58 -5.8418778
4850 19199.88 206.90989 0 3762.4433 3.4536341
4900 19173.92 212.11327 0 3762.8392 5.0387071
4950 19236.635 200.57537 0 3762.9152 -1.4932783
5000 19077.616 230.04967 0 3762.9415 4.3742655
5050 19893.763 78.909747 0 3762.94 -1.5796711
5100 18884.746 265.68301 0 3762.8583 2.2767949
5150 17417.096 537.54036 0 3762.9286 -2.8632555
5200 18247.844 383.60092 0 3762.8312 10.384179
5250 19494.107 152.60532 0 3762.6251 -4.7617287
5300 18739.781 292.46206 0 3762.7919 23.210048
5350 19310.938 186.62363 0 3762.7232 14.895327
5400 19540.39 144.14287 0 3762.7336 6.094624
5450 20074.459 45.247888 0 3762.7403 -2.0871835
5500 19986.377 61.668045 0 3762.849 -2.4551918
5550 19038.904 237.07578 0 3762.7987 5.4250813
5600 19439.124 163.1438 0 3762.9816 4.1291468
5650 19480.321 155.58325 0 3763.0501 -3.5308058
5700 19869.291 83.651379 0 3763.1497 -7.8661592
5750 19991.447 61.068554 0 3763.1884 -6.8473586
5800 19454.072 160.36805 0 3762.9739 1.527662
5850 17994.409 430.95597 0 3763.2539 -5.6078082
5900 19209.794 205.74997 0 3763.1193 8.4113055
5950 19046.427 236.06321 0 3763.1793 10.463356
6000 19409.899 168.95271 0 3763.3785 2.542067
6050 18068.174 417.35443 0 3763.3125 10.498199
6100 19549.253 143.21885 0 3763.4509 2.3075797
6150 18464.719 344.0303 0 3763.4228 0.46469762
6200 19811.205 94.62725 0 3763.3689 1.2382763
6250 18715.36 297.26445 0 3763.0718 -3.4541762
6300 17115.664 594.09913 0 3763.6666 4.2065564
6350 18155.927 400.71764 0 3762.9264 1.1521258
6400 19873.093 83.169067 0 3763.3716 0.16383592
6450 19991.88 61.13218 0 3763.3321 -1.3008128
6500 19434.416 164.40698 0 3763.3728 -13.593422
6550 19855.253 86.645329 0 3763.544 -0.85704037
6600 19251.141 198.41152 0 3763.4376 4.3027745
6650 19741.815 107.69047 0 3763.582 4.994835
6700 19633.466 127.69333 0 3763.5203 6.3677145
6750 16231.353 757.83705 0 3763.6431 -1.5978692
6800 18863.396 270.1114 0 3763.3329 -11.915909
6850 19644.779 125.29421 0 3763.2163 -1.151217
6900 18883.642 266.06889 0 3763.0397 -4.3950749
6950 19042.364 236.54144 0 3762.9052 5.5718878
7000 18351.868 364.38028 0 3762.8743 7.8958273
7050 19981.031 62.840667 0 3763.0316 -5.8572298
7100 19796.372 97.073665 0 3763.0685 -3.5178361
7150 19805.385 95.235221 0 3762.899 -2.5481726
7200 18722.055 295.86113 0 3762.9084 13.826356
7250 19537.304 144.54234 0 3762.5616 1.2288666
7300 18787.328 283.49504 0 3762.6299 9.0044469
7350 18886.005 265.52121 0 3762.9295 6.6791881
7400 19891.864 79.239278 0 3762.9178 -2.3882842
7450 18164.752 399.07065 0 3762.9137 3.9400481
7500 18702.612 299.582 0 3763.0286 4.7987316
7550 19884.986 80.231665 0 3762.6365 -0.75016515
7600 19549.059 142.16243 0 3762.3586 -2.1035756
7650 18223.668 387.9047 0 3762.658 -17.064339
7700 19428.4 164.79531 0 3762.6473 -2.8342541
7750 19239.584 199.93029 0 3762.8163 3.1746033
7800 19458.005 159.46176 0 3762.7961 1.714515
7850 18320.308 369.77051 0 3762.4202 2.1422976
7900 18817.415 278.04812 0 3762.7546 0.94492621
7950 19892.761 79.115928 0 3762.9606 1.4948501
8000 19592.344 134.7639 0 3762.9758 -1.8520224
8050 19316.109 185.70579 0 3762.7631 -4.8061205
8100 19867.017 83.850395 0 3762.9277 -3.496391
8150 19129.936 220.29802 0 3762.8789 -2.8357376
8200 18449.554 346.30415 0 3762.8883 1.4417837
8250 18405.197 354.49049 0 3762.8602 6.7020283
8300 18310.437 372.25376 0 3763.0755 3.9043508
8350 18842.702 273.55075 0 3762.94 -10.987272
8400 18574.308 323.33378 0 3763.0204 12.008785
8450 15368.628 918.21692 0 3764.2591 34.80292
8500 18432.887 349.54013 0 3763.0378 0.00064258465
8550 15777.73 841.79263 0 3763.5945 15.473699
8600 17205.381 576.4515 0 3762.6331 2.3985544
8650 19773.742 101.48276 0 3763.2869 2.3978892
8700 19059.824 232.99716 0 3762.5941 5.2611349
8750 19006.086 243.41125 0 3763.0568 4.7880403
8800 19492.691 153.0188 0 3762.7763 1.9118755
8850 19625.883 128.44474 0 3762.8675 3.4157389
8900 19916.97 74.635094 0 3762.9629 -10.157254
8950 16012.956 798.16801 0 3763.5302 16.904998
9000 19364.051 177.00354 0 3762.9389 -13.373346
9050 19133.929 219.61882 0 3762.9389 -7.3824392
9100 18657.168 307.85939 0 3762.8905 9.3071421
9150 17975.904 434.21548 0 3763.0867 6.9609506
9200 19075.282 230.41699 0 3762.8767 7.0961232
9250 20115.276 37.578674 0 3762.6298 1.8678552
9300 18195.486 393.20682 0 3762.7413 13.272552
9350 19617.155 129.85893 0 3762.6653 -2.0849447
9400 19276.325 193.03425 0 3762.724 -2.8963555
9450 18642.803 310.4759 0 3762.8467 3.407984
9500 19175.951 211.72785 0 3762.8298 -0.39025564
9550 17669.191 490.85942 0 3762.9319 5.3867954
9600 18481.199 340.29485 0 3762.7391 8.9004886
9650 20091.442 42.504743 0 3763.1422 -1.3206133
9700 19651.405 124.04835 0 3763.1975 1.4000525
9750 19138.245 219.03637 0 3763.1558 5.8352794
9800 19189.146 209.67958 0 3763.2251 6.214691
9850 19899.376 78.096337 0 3763.166 -0.75102404
9900 19447.247 161.27279 0 3762.6149 -6.4166376
9950 19807.083 95.152663 0 3763.1309 -0.88933698
10000 18972.157 249.56342 0 3762.9258 1.9189241
Loop time of 9.05599 on 4 procs for 10000 steps with 81 atoms
Performance: 9540.646 tau/day, 1104.241 timesteps/s
94.6% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.009043 | 0.030098 | 0.048276 | 8.1 | 0.33
Neigh | 0.012702 | 0.02622 | 0.04009 | 6.1 | 0.29
Comm | 0.99902 | 1.2924 | 1.6008 | 24.3 | 14.27
Output | 0.0057414 | 0.010684 | 0.024912 | 7.9 | 0.12
Modify | 7.2674 | 7.5881 | 7.9123 | 10.6 | 83.79
Other | | 0.1085 | | | 1.20
Nlocal: 20.25 ave 37 max 0 min
Histogram: 1 0 1 0 0 0 0 0 0 2
Nghost: 17.75 ave 33 max 4 min
Histogram: 2 0 0 0 0 0 0 0 1 1
Neighs: 144.75 ave 356 max 0 min
Histogram: 2 0 0 0 0 0 1 0 0 1
Total # of neighbors = 579
Ave neighs/atom = 7.14815
Neighbor list builds = 994
Dangerous builds = 958
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:09

14
examples/rigid/unconnected-bodies.dat Normal file
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@ -0,0 +1,14 @@
# Body definition file for POEMS fix
# 9 individual rigid bodies
# Format
# Body-ID Body-Type Atom-ID1 Atom-ID2 ...
1 1 1 2 3 4 5 6 7 8 9
2 2 10 11 12 13 14 15 16 17 18
3 1 19 20 21 22 23 24 25 26 27
4 2 28 29 30 31 32 33 34 35 36
5 3 37 38 39 40 41 42 43 44 45
6 1 46 47 48 49 50 51 52 53 54
7 2 55 56 57 58 59 60 61 62 63
8 1 64 65 66 67 68 69 70 71 72
9 2 73 74 75 76 77 78 79 80 81

828
src/POEMS/fix_poems.cpp
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File diff suppressed because it is too large Load Diff

4
src/POEMS/fix_poems.h
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@ -53,7 +53,6 @@ class FixPOEMS : public Fix {
void reset_dt() override; void reset_dt() override;
private: private:
int me;
double dtv, dtf, dthalf; double dtv, dtf, dthalf;
double *step_respa; double *step_respa;
int nlevels_respa; int nlevels_respa;
@ -101,8 +100,7 @@ class FixPOEMS : public Fix {
// internal class functions // internal class functions
void compute_forces_and_torques(); void compute_forces_and_torques();
void readfile(char *); void readfile(const char *);
int readline(FILE *, char **, int *);
void jointbuild(); void jointbuild();
void sortlist(int, tagint **); void sortlist(int, tagint **);
int loopcheck(int, int, tagint **); int loopcheck(int, int, tagint **);