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Revert "change ordering of eigenvalues in jacobi3() function. update tests."

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This reverts commit c4eadd3a59.
This commit is contained in:
Axel Kohlmeyer
2024-04-02 23:02:04 -04:00
parent dfc68fb338
commit 21745538a7
99 changed files with 13271 additions and 13772 deletions
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2
examples/micelle/in.micelle
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dimension 2
neighbor 0.33 bin
neighbor 0.3 bin
neigh_modify delay 5
atom_style bond

2
examples/micelle/in.micelle-rigid
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dimension 2
neighbor 0.33 bin
neighbor 0.3 bin
neigh_modify delay 5
atom_style bond

272
examples/micelle/log.25Mar24.micelle-rigid.g++.1
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LAMMPS (7 Feb 2024 - Development - patch_7Feb2024_update1-306-gf3391199e7-modified)
using 1 OpenMP thread(s) per MPI task
# 2d micelle simulation
dimension 2
neighbor 0.33 bin
neigh_modify delay 5
atom_style bond
# Soft potential push-off
read_data data.micelle
Reading data file ...
orthogonal box = (0 0 -0.1) to (35.85686 35.85686 0.1)
1 by 1 by 1 MPI processor grid
reading atoms ...
1200 atoms
scanning bonds ...
1 = max bonds/atom
reading bonds ...
300 bonds
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
2 = max # of 1-2 neighbors
1 = max # of 1-3 neighbors
1 = max # of 1-4 neighbors
2 = max # of special neighbors
special bonds CPU = 0.000 seconds
read_data CPU = 0.004 seconds
special_bonds fene
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 1 1
special bond factors coul: 0 1 1
2 = max # of 1-2 neighbors
2 = max # of special neighbors
special bonds CPU = 0.000 seconds
pair_style soft 1.12246
pair_coeff * * 0.0 1.12246
bond_style harmonic
bond_coeff 1 50.0 0.75
velocity all create 0.45 2349852
variable prefactor equal ramp(1.0,20.0)
fix 1 all nve
fix 2 all temp/rescale 100 0.45 0.45 0.02 1.0
fix 3 all adapt 1 pair soft a * * v_prefactor
fix 4 all enforce2d
thermo 50
run 500
Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule
WARNING: Communication cutoff 1.45246 is shorter than a bond length based estimate of 1.455. This may lead to errors. (src/comm.cpp:730)
Neighbor list info ...
update: every = 1 steps, delay = 5 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 1.45246
ghost atom cutoff = 1.45246
binsize = 0.72623, bins = 50 50 1
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair soft, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/2d
bin: standard
WARNING: Communication cutoff 1.45246 is shorter than a bond length based estimate of 1.455. This may lead to errors. (src/comm.cpp:730)
Per MPI rank memory allocation (min/avg/max) = 4.148 | 4.148 | 4.148 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0.45 0.40003481 2.2200223e-06 0.84966203 0.78952518
50 0.54981866 0.93548899 0.068440043 1.5532895 1.9232786
100 0.45 0.99659327 0.079228519 1.5254468 3.2135679
150 0.86965411 0.90456016 0.07493355 1.8484231 4.3821925
200 0.45 1.01454 0.10663502 1.5708 4.7598476
250 0.79636561 0.82567712 0.12105337 1.7424325 5.4983899
300 0.45 0.86475538 0.11819875 1.4325791 5.8554758
350 0.72135464 0.70693069 0.10912636 1.5368106 6.0388247
400 0.45 0.75067331 0.14165013 1.3419484 6.3840708
450 0.64839221 0.62402486 0.14173679 1.4136135 6.4791009
500 0.45 0.66669513 0.13695201 1.2532721 6.807146
Loop time of 0.0683956 on 1 procs for 500 steps with 1200 atoms
Performance: 3158095.858 tau/day, 7310.407 timesteps/s, 8.772 Matom-step/s
99.1% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.042818 | 0.042818 | 0.042818 | 0.0 | 62.60
Bond | 0.0026205 | 0.0026205 | 0.0026205 | 0.0 | 3.83
Neigh | 0.011794 | 0.011794 | 0.011794 | 0.0 | 17.24
Comm | 0.0014012 | 0.0014012 | 0.0014012 | 0.0 | 2.05
Output | 0.00012752 | 0.00012752 | 0.00012752 | 0.0 | 0.19
Modify | 0.0078924 | 0.0078924 | 0.0078924 | 0.0 | 11.54
Other | | 0.001743 | | | 2.55
Nlocal: 1200 ave 1200 max 1200 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 198 ave 198 max 198 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 3199 ave 3199 max 3199 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 3199
Ave neighs/atom = 2.6658333
Ave special neighs/atom = 0.5
Neighbor list builds = 48
Dangerous builds = 0
unfix 3
# Main run
pair_style lj/cut 2.5
# solvent/head - full-size and long-range
pair_coeff 1 1 1.0 1.0 2.5
pair_coeff 2 2 1.0 1.0 2.5
pair_coeff 1 2 1.0 1.0 2.5
# tail/tail - size-averaged and long-range
pair_coeff 3 3 1.0 0.75 2.5
pair_coeff 4 4 1.0 0.50 2.5
pair_coeff 3 4 1.0 0.67 2.5
# solvent/tail - full-size and repulsive
pair_coeff 1 3 1.0 1.0 1.12246
pair_coeff 1 4 1.0 1.0 1.12246
# head/tail - size-averaged and repulsive
pair_coeff 2 3 1.0 0.88 1.12246
pair_coeff 2 4 1.0 0.75 1.12246
thermo 50
#dump 1 all atom 2000 dump.micelle
#dump 2 all image 2000 image.*.jpg type type zoom 1.6
#dump_modify 2 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75
#dump 3 all movie 2000 movie.mpg type type zoom 1.6
#dump_modify 3 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75
reset_timestep 0
group solvent molecule 0
750 atoms in group solvent
group solute subtract all solvent
450 atoms in group solute
unfix 1
unfix 2
unfix 4
fix 1 solvent nve
fix 2 solvent temp/rescale 100 0.45 0.45 0.02 1.0
fix 5 solute rigid molecule langevin 0.45 0.45 0.5 112211
150 rigid bodies with 450 atoms
fix 4 all enforce2d
run 500
Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update: every = 1 steps, delay = 5 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.83
ghost atom cutoff = 2.83
binsize = 1.415, bins = 26 26 1
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/2d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 5.391 | 5.391 | 5.391 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0.45318168 -1.3753652 0.13695201 -0.8705807 1.975423
50 0.77344732 -1.6944083 0.13695201 -0.92967487 0.58657109
100 0.53530681 -1.7006195 0.13695201 -1.1291768 0.11219772
150 0.60820175 -1.8071581 0.13695201 -1.176549 1.5161796
200 0.49410558 -1.7945459 0.13695201 -1.2565449 3.7958258
250 0.52460847 -1.8528672 0.13695201 -1.290108 2.9929445
300 0.46596803 -1.8680499 0.13695201 -1.3528872 2.7958851
350 0.48831812 -1.8723486 0.13695201 -1.3390451 -4.5106818
400 0.46798432 -1.9008529 0.13695201 -1.3840536 -4.3096566
450 0.46000658 -1.9081144 0.13695201 -1.3977904 3.3360611
500 0.45822409 -1.9077531 0.13695201 -1.3988759 0.45428738
Loop time of 0.129419 on 1 procs for 500 steps with 1200 atoms
Performance: 1668996.565 tau/day, 3863.418 timesteps/s, 4.636 Matom-step/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 | 0.059482 | 0.059482 | 0.059482 | 0.0 | 45.96
Bond | 0.0027154 | 0.0027154 | 0.0027154 | 0.0 | 2.10
Neigh | 0.017086 | 0.017086 | 0.017086 | 0.0 | 13.20
Comm | 0.0019065 | 0.0019065 | 0.0019065 | 0.0 | 1.47
Output | 0.00012035 | 0.00012035 | 0.00012035 | 0.0 | 0.09
Modify | 0.046099 | 0.046099 | 0.046099 | 0.0 | 35.62
Other | | 0.002009 | | | 1.55
Nlocal: 1200 ave 1200 max 1200 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 413 ave 413 max 413 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 8944 ave 8944 max 8944 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 8944
Ave neighs/atom = 7.4533333
Ave special neighs/atom = 0.5
Neighbor list builds = 41
Dangerous builds = 1
unfix 2
unfix 4
unfix 5
fix 5 solute rigid/small molecule
create bodies CPU = 0.000 seconds
150 rigid bodies with 450 atoms
1.3043524 = max distance from body owner to body atom
fix 4 all enforce2d
run 500
Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule
Per MPI rank memory allocation (min/avg/max) = 9.306 | 9.306 | 9.306 Mbytes
Step Temp E_pair E_mol TotEng Press
500 0.45822409 -1.9077531 0.13695201 -1.3988759 2.4509752
550 0.46736204 -1.9141964 0.13695201 -1.3979022 2.1695662
600 0.47872194 -1.9232781 0.13695201 -1.3977635 2.0058379
650 0.47491575 -1.9224109 0.13695201 -1.3999857 2.0637789
700 0.44714331 -1.8990682 0.13695201 -1.3991848 2.4863082
750 0.49089274 -1.9231004 0.13695201 -1.3877071 2.123147
800 0.4753839 -1.8959698 0.13695201 -1.3731645 2.3030481
850 0.46870816 -1.8972225 0.13695201 -1.3798357 2.2464703
900 0.49610454 -1.9070748 0.13695201 -1.3674513 2.2196388
950 0.4773035 -1.8925765 0.13695201 -1.3682132 2.3534786
1000 0.50413702 -1.9292393 0.13695201 -1.383096 2.1630987
Loop time of 0.119542 on 1 procs for 500 steps with 1200 atoms
Performance: 1806900.644 tau/day, 4182.640 timesteps/s, 5.019 Matom-step/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 | 0.058715 | 0.058715 | 0.058715 | 0.0 | 49.12
Bond | 0.0028428 | 0.0028428 | 0.0028428 | 0.0 | 2.38
Neigh | 0.015212 | 0.015212 | 0.015212 | 0.0 | 12.73
Comm | 0.0019242 | 0.0019242 | 0.0019242 | 0.0 | 1.61
Output | 0.00018977 | 0.00018977 | 0.00018977 | 0.0 | 0.16
Modify | 0.038399 | 0.038399 | 0.038399 | 0.0 | 32.12
Other | | 0.002259 | | | 1.89
Nlocal: 1200 ave 1200 max 1200 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 425 ave 425 max 425 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 8846 ave 8846 max 8846 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 8846
Ave neighs/atom = 7.3716667
Ave special neighs/atom = 0.5
Neighbor list builds = 36
Dangerous builds = 0
Total wall time: 0:00:00

272
examples/micelle/log.25Mar24.micelle-rigid.g++.4
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LAMMPS (7 Feb 2024 - Development - patch_7Feb2024_update1-306-gf3391199e7-modified)
using 1 OpenMP thread(s) per MPI task
# 2d micelle simulation
dimension 2
neighbor 0.33 bin
neigh_modify delay 5
atom_style bond
# Soft potential push-off
read_data data.micelle
Reading data file ...
orthogonal box = (0 0 -0.1) to (35.85686 35.85686 0.1)
2 by 2 by 1 MPI processor grid
reading atoms ...
1200 atoms
scanning bonds ...
1 = max bonds/atom
reading bonds ...
300 bonds
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
2 = max # of 1-2 neighbors
1 = max # of 1-3 neighbors
1 = max # of 1-4 neighbors
2 = max # of special neighbors
special bonds CPU = 0.000 seconds
read_data CPU = 0.004 seconds
special_bonds fene
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 1 1
special bond factors coul: 0 1 1
2 = max # of 1-2 neighbors
2 = max # of special neighbors
special bonds CPU = 0.000 seconds
pair_style soft 1.12246
pair_coeff * * 0.0 1.12246
bond_style harmonic
bond_coeff 1 50.0 0.75
velocity all create 0.45 2349852
variable prefactor equal ramp(1.0,20.0)
fix 1 all nve
fix 2 all temp/rescale 100 0.45 0.45 0.02 1.0
fix 3 all adapt 1 pair soft a * * v_prefactor
fix 4 all enforce2d
thermo 50
run 500
Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule
WARNING: Communication cutoff 1.45246 is shorter than a bond length based estimate of 1.455. This may lead to errors. (src/comm.cpp:730)
Neighbor list info ...
update: every = 1 steps, delay = 5 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 1.45246
ghost atom cutoff = 1.45246
binsize = 0.72623, bins = 50 50 1
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair soft, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/2d
bin: standard
WARNING: Communication cutoff 1.45246 is shorter than a bond length based estimate of 1.455. This may lead to errors. (src/comm.cpp:730)
Per MPI rank memory allocation (min/avg/max) = 4.126 | 4.126 | 4.127 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0.45 0.40003481 2.2200223e-06 0.84966203 0.78952518
50 0.54981866 0.93548899 0.068440043 1.5532895 1.9232786
100 0.45 0.99659327 0.079228519 1.5254468 3.2135679
150 0.86965411 0.90456016 0.07493355 1.8484231 4.3821925
200 0.45 1.01454 0.10663502 1.5708 4.7598476
250 0.79636561 0.82567712 0.12105337 1.7424325 5.4983899
300 0.45 0.86475538 0.11819875 1.4325791 5.8554758
350 0.72135464 0.70693069 0.10912636 1.5368106 6.0388247
400 0.45 0.75067331 0.14165013 1.3419484 6.3840708
450 0.64839221 0.62402486 0.14173679 1.4136135 6.4791009
500 0.45 0.66669513 0.13695201 1.2532721 6.807146
Loop time of 0.0217401 on 4 procs for 500 steps with 1200 atoms
Performance: 9935551.276 tau/day, 22998.961 timesteps/s, 27.599 Matom-step/s
99.7% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0088539 | 0.0095602 | 0.010452 | 0.6 | 43.97
Bond | 0.00058476 | 0.00062647 | 0.00070207 | 0.0 | 2.88
Neigh | 0.0030965 | 0.0031112 | 0.0031222 | 0.0 | 14.31
Comm | 0.0040493 | 0.0050374 | 0.0057508 | 0.9 | 23.17
Output | 8.0051e-05 | 8.6079e-05 | 0.00010294 | 0.0 | 0.40
Modify | 0.0024258 | 0.0025227 | 0.0026365 | 0.2 | 11.60
Other | | 0.0007961 | | | 3.66
Nlocal: 300 ave 305 max 292 min
Histogram: 1 0 0 0 0 0 1 1 0 1
Nghost: 105.25 ave 110 max 99 min
Histogram: 1 0 0 1 0 0 0 0 0 2
Neighs: 799.75 ave 817 max 763 min
Histogram: 1 0 0 0 0 0 0 1 0 2
Total # of neighbors = 3199
Ave neighs/atom = 2.6658333
Ave special neighs/atom = 0.5
Neighbor list builds = 48
Dangerous builds = 0
unfix 3
# Main run
pair_style lj/cut 2.5
# solvent/head - full-size and long-range
pair_coeff 1 1 1.0 1.0 2.5
pair_coeff 2 2 1.0 1.0 2.5
pair_coeff 1 2 1.0 1.0 2.5
# tail/tail - size-averaged and long-range
pair_coeff 3 3 1.0 0.75 2.5
pair_coeff 4 4 1.0 0.50 2.5
pair_coeff 3 4 1.0 0.67 2.5
# solvent/tail - full-size and repulsive
pair_coeff 1 3 1.0 1.0 1.12246
pair_coeff 1 4 1.0 1.0 1.12246
# head/tail - size-averaged and repulsive
pair_coeff 2 3 1.0 0.88 1.12246
pair_coeff 2 4 1.0 0.75 1.12246
thermo 50
#dump 1 all atom 2000 dump.micelle
#dump 2 all image 2000 image.*.jpg type type zoom 1.6
#dump_modify 2 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75
#dump 3 all movie 2000 movie.mpg type type zoom 1.6
#dump_modify 3 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75
reset_timestep 0
group solvent molecule 0
750 atoms in group solvent
group solute subtract all solvent
450 atoms in group solute
unfix 1
unfix 2
unfix 4
fix 1 solvent nve
fix 2 solvent temp/rescale 100 0.45 0.45 0.02 1.0
fix 5 solute rigid molecule langevin 0.45 0.45 0.5 112211
150 rigid bodies with 450 atoms
fix 4 all enforce2d
run 500
Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update: every = 1 steps, delay = 5 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.83
ghost atom cutoff = 2.83
binsize = 1.415, bins = 26 26 1
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/2d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 5.375 | 5.375 | 5.375 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0.45318168 -1.3753652 0.13695201 -0.8705807 1.975423
50 0.77344732 -1.6944083 0.13695201 -0.92967487 0.58657109
100 0.53530681 -1.7006195 0.13695201 -1.1291768 0.11219772
150 0.60820175 -1.8071581 0.13695201 -1.176549 1.5161796
200 0.49410558 -1.7945459 0.13695201 -1.2565449 3.7958258
250 0.52460847 -1.8528672 0.13695201 -1.290108 2.9929445
300 0.46596803 -1.8680499 0.13695201 -1.3528872 2.7958851
350 0.48831812 -1.8723486 0.13695201 -1.3390451 -4.5106818
400 0.46798432 -1.9008529 0.13695201 -1.3840536 -4.3096566
450 0.46000658 -1.9081144 0.13695201 -1.3977904 3.3360611
500 0.45822409 -1.9077531 0.13695201 -1.3988759 0.45428738
Loop time of 0.0560481 on 4 procs for 500 steps with 1200 atoms
Performance: 3853834.547 tau/day, 8920.913 timesteps/s, 10.705 Matom-step/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 | 0.013556 | 0.013707 | 0.013803 | 0.1 | 24.46
Bond | 0.00063884 | 0.00066997 | 0.0007103 | 0.0 | 1.20
Neigh | 0.004707 | 0.0047121 | 0.0047151 | 0.0 | 8.41
Comm | 0.0060936 | 0.0061963 | 0.006299 | 0.1 | 11.06
Output | 9.3791e-05 | 0.00010703 | 0.00013426 | 0.0 | 0.19
Modify | 0.029359 | 0.029467 | 0.029627 | 0.1 | 52.57
Other | | 0.001189 | | | 2.12
Nlocal: 300 ave 303 max 296 min
Histogram: 1 0 0 0 1 0 0 0 1 1
Nghost: 217.75 ave 220 max 215 min
Histogram: 1 0 0 0 0 0 2 0 0 1
Neighs: 2236 ave 2264 max 2213 min
Histogram: 1 0 1 0 0 1 0 0 0 1
Total # of neighbors = 8944
Ave neighs/atom = 7.4533333
Ave special neighs/atom = 0.5
Neighbor list builds = 41
Dangerous builds = 1
unfix 2
unfix 4
unfix 5
fix 5 solute rigid/small molecule
create bodies CPU = 0.000 seconds
150 rigid bodies with 450 atoms
1.3043524 = max distance from body owner to body atom
fix 4 all enforce2d
run 500
Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule
Per MPI rank memory allocation (min/avg/max) = 9.233 | 9.233 | 9.234 Mbytes
Step Temp E_pair E_mol TotEng Press
500 0.45822409 -1.9077531 0.13695201 -1.3988759 2.4509752
550 0.46736204 -1.9141964 0.13695201 -1.3979022 2.1695662
600 0.47872194 -1.9232781 0.13695201 -1.3977635 2.0058379
650 0.47491575 -1.9224109 0.13695201 -1.3999857 2.0637789
700 0.44714331 -1.8990682 0.13695201 -1.3991848 2.4863082
750 0.49089274 -1.9231004 0.13695201 -1.3877071 2.123147
800 0.4753839 -1.8959698 0.13695201 -1.3731645 2.3030481
850 0.46870816 -1.8972225 0.13695201 -1.3798357 2.2464703
900 0.49610454 -1.9070748 0.13695201 -1.3674513 2.2196388
950 0.4773035 -1.8925765 0.13695201 -1.3682132 2.3534786
1000 0.50413702 -1.9292393 0.13695201 -1.383096 2.1630987
Loop time of 0.0401556 on 4 procs for 500 steps with 1200 atoms
Performance: 5379078.679 tau/day, 12451.571 timesteps/s, 14.942 Matom-step/s
98.8% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.013239 | 0.013488 | 0.013882 | 0.2 | 33.59
Bond | 0.00064766 | 0.00068403 | 0.00074631 | 0.0 | 1.70
Neigh | 0.0040808 | 0.0040899 | 0.0041035 | 0.0 | 10.19
Comm | 0.0056353 | 0.0060663 | 0.0063864 | 0.3 | 15.11
Output | 0.0001049 | 0.0001153 | 0.00014195 | 0.0 | 0.29
Modify | 0.014414 | 0.014559 | 0.014753 | 0.1 | 36.26
Other | | 0.001153 | | | 2.87
Nlocal: 300 ave 305 max 295 min
Histogram: 1 0 0 0 1 0 1 0 0 1
Nghost: 226 ave 231 max 220 min
Histogram: 1 0 0 0 1 0 0 1 0 1
Neighs: 2211.5 ave 2313 max 2144 min
Histogram: 1 1 0 0 1 0 0 0 0 1
Total # of neighbors = 8846
Ave neighs/atom = 7.3716667
Ave special neighs/atom = 0.5
Neighbor list builds = 36
Dangerous builds = 0
Total wall time: 0:00:00

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examples/micelle/log.25Mar24.micelle.g++.1
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LAMMPS (7 Feb 2024 - Development - patch_7Feb2024_update1-306-gf3391199e7-modified)
using 1 OpenMP thread(s) per MPI task
# 2d micelle simulation
dimension 2
neighbor 0.33 bin
neigh_modify delay 5
atom_style bond
# Soft potential push-off
read_data data.micelle
Reading data file ...
orthogonal box = (0 0 -0.1) to (35.85686 35.85686 0.1)
1 by 1 by 1 MPI processor grid
reading atoms ...
1200 atoms
scanning bonds ...
1 = max bonds/atom
reading bonds ...
300 bonds
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
2 = max # of 1-2 neighbors
1 = max # of 1-3 neighbors
1 = max # of 1-4 neighbors
2 = max # of special neighbors
special bonds CPU = 0.001 seconds
read_data CPU = 0.005 seconds
special_bonds fene
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 1 1
special bond factors coul: 0 1 1
2 = max # of 1-2 neighbors
2 = max # of special neighbors
special bonds CPU = 0.000 seconds
pair_style soft 1.12246
pair_coeff * * 0.0 1.12246
bond_style harmonic
bond_coeff 1 50.0 0.75
velocity all create 0.45 2349852
variable prefactor equal ramp(1.0,20.0)
fix 1 all nve
fix 2 all temp/rescale 100 0.45 0.45 0.02 1.0
fix 3 all adapt 1 pair soft a * * v_prefactor
fix 4 all enforce2d
thermo 50
run 1000
Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule
WARNING: Communication cutoff 1.45246 is shorter than a bond length based estimate of 1.455. This may lead to errors. (src/comm.cpp:730)
Neighbor list info ...
update: every = 1 steps, delay = 5 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 1.45246
ghost atom cutoff = 1.45246
binsize = 0.72623, bins = 50 50 1
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair soft, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/2d
bin: standard
WARNING: Communication cutoff 1.45246 is shorter than a bond length based estimate of 1.455. This may lead to errors. (src/comm.cpp:730)
Per MPI rank memory allocation (min/avg/max) = 4.148 | 4.148 | 4.148 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0.45 0.40003481 2.2200223e-06 0.84966203 0.78952518
50 0.47411013 0.67721272 0.057404514 1.2083323 1.3375852
100 0.45 0.73046745 0.054836584 1.234929 2.3196516
150 0.67521742 0.72402001 0.043490075 1.4421648 2.8744416
200 0.45 0.78481891 0.076931503 1.3113754 3.0412388
250 0.66479018 0.69790602 0.081075564 1.4432178 3.6917024
300 0.45 0.76820218 0.066727591 1.2845548 3.7861054
350 0.67619136 0.625715 0.072722727 1.3740656 4.2861621
400 0.45 0.68527759 0.090724527 1.2256271 4.4725214
450 0.56702844 0.64402767 0.080555563 1.2911391 4.7402211
500 0.45 0.64883009 0.078376672 1.1768318 4.7919294
550 0.564664 0.58260368 0.080779475 1.2275766 4.9855705
600 0.45 0.58193041 0.088386617 1.119942 5.131481
650 0.52110993 0.5415273 0.097683746 1.1598867 5.2500294
700 0.45 0.50856787 0.088471208 1.0466641 5.2550165
750 0.51510855 0.47441291 0.089429375 1.0785216 5.375763
800 0.45 0.49926696 0.085958476 1.0348504 5.4665914
850 0.50688494 0.46614429 0.088962292 1.0615691 5.556932
900 0.45 0.47785593 0.10150857 1.0289895 5.7765975
950 0.49590559 0.46050477 0.096404887 1.052402 5.8649245
1000 0.45 0.47691182 0.08808163 1.0146185 6.0177568
Loop time of 0.135036 on 1 procs for 1000 steps with 1200 atoms
Performance: 3199144.549 tau/day, 7405.427 timesteps/s, 8.887 Matom-step/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 | 0.086466 | 0.086466 | 0.086466 | 0.0 | 64.03
Bond | 0.0052524 | 0.0052524 | 0.0052524 | 0.0 | 3.89
Neigh | 0.020278 | 0.020278 | 0.020278 | 0.0 | 15.02
Comm | 0.0026978 | 0.0026978 | 0.0026978 | 0.0 | 2.00
Output | 0.00032119 | 0.00032119 | 0.00032119 | 0.0 | 0.24
Modify | 0.016117 | 0.016117 | 0.016117 | 0.0 | 11.94
Other | | 0.003904 | | | 2.89
Nlocal: 1200 ave 1200 max 1200 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 200 ave 200 max 200 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 3220 ave 3220 max 3220 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 3220
Ave neighs/atom = 2.6833333
Ave special neighs/atom = 0.5
Neighbor list builds = 84
Dangerous builds = 0
unfix 3
# Main run
pair_style lj/cut 2.5
# solvent/head - full-size and long-range
pair_coeff 1 1 1.0 1.0 2.5
pair_coeff 2 2 1.0 1.0 2.5
pair_coeff 1 2 1.0 1.0 2.5
# tail/tail - size-averaged and long-range
pair_coeff 3 3 1.0 0.75 2.5
pair_coeff 4 4 1.0 0.50 2.5
pair_coeff 3 4 1.0 0.67 2.5
# solvent/tail - full-size and repulsive
pair_coeff 1 3 1.0 1.0 1.12246
pair_coeff 1 4 1.0 1.0 1.12246
# head/tail - size-averaged and repulsive
pair_coeff 2 3 1.0 0.88 1.12246
pair_coeff 2 4 1.0 0.75 1.12246
thermo 50
#dump 1 all atom 2000 dump.micelle
#dump 2 all image 2000 image.*.jpg type type zoom 1.6
#dump_modify 2 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75
#dump 3 all movie 2000 movie.mpg type type zoom 1.6
#dump_modify 3 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75
reset_timestep 0
run 1000
Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update: every = 1 steps, delay = 5 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.83
ghost atom cutoff = 2.83
binsize = 1.415, bins = 26 26 1
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/2d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 4.141 | 4.141 | 4.141 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0.45 -1.7056163 0.08808163 -1.1679097 3.9431686
50 0.59734982 -1.8103783 0.076066922 -1.1374593 3.2770557
100 0.45 -1.8347112 0.093132329 -1.2919539 3.024661
150 0.51924311 -1.8943977 0.076004124 -1.2995832 2.5570373
200 0.45 -1.8918673 0.082422107 -1.3598201 2.5629655
250 0.50281134 -1.920406 0.074011331 -1.3440023 2.3518682
300 0.45 -1.9351047 0.075337265 -1.4101424 2.3249947
350 0.47650026 -1.9313687 0.072115118 -1.3831504 2.1987532
400 0.45 -1.9554318 0.081603939 -1.4242028 2.0787066
450 0.47220237 -1.9468502 0.065625625 -1.4094157 2.0984288
500 0.46846731 -1.9444333 0.076696281 -1.3996601 2.0528682
550 0.47683129 -1.958676 0.070589717 -1.4116523 2.0856022
600 0.46851244 -1.9338267 0.070605485 -1.3950992 2.2640498
650 0.46874143 -1.9462493 0.069134673 -1.4087638 2.1070264
700 0.46437375 -1.9309952 0.071977553 -1.3950309 2.2256927
750 0.47326219 -1.9484255 0.075435861 -1.4001218 2.0880257
800 0.45 -1.9646003 0.064159585 -1.4508158 2.0612708
850 0.46748293 -1.9705587 0.060384889 -1.4430805 1.9472917
900 0.46909505 -1.9537228 0.06246996 -1.4225487 2.0222946
950 0.45631552 -1.9387752 0.067536414 -1.4153035 2.0638412
1000 0.45 -1.9727636 0.058608205 -1.4645304 1.9982412
Loop time of 0.172925 on 1 procs for 1000 steps with 1200 atoms
Performance: 2498198.117 tau/day, 5782.866 timesteps/s, 6.939 Matom-step/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 | 0.11308 | 0.11308 | 0.11308 | 0.0 | 65.39
Bond | 0.0054036 | 0.0054036 | 0.0054036 | 0.0 | 3.12
Neigh | 0.032892 | 0.032892 | 0.032892 | 0.0 | 19.02
Comm | 0.0038268 | 0.0038268 | 0.0038268 | 0.0 | 2.21
Output | 0.00023892 | 0.00023892 | 0.00023892 | 0.0 | 0.14
Modify | 0.013461 | 0.013461 | 0.013461 | 0.0 | 7.78
Other | | 0.004027 | | | 2.33
Nlocal: 1200 ave 1200 max 1200 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 421 ave 421 max 421 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 8779 ave 8779 max 8779 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 8779
Ave neighs/atom = 7.3158333
Ave special neighs/atom = 0.5
Neighbor list builds = 77
Dangerous builds = 0
Total wall time: 0:00:00

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examples/micelle/log.25Mar24.micelle.g++.4
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LAMMPS (7 Feb 2024 - Development - patch_7Feb2024_update1-306-gf3391199e7-modified)
using 1 OpenMP thread(s) per MPI task
# 2d micelle simulation
dimension 2
neighbor 0.33 bin
neigh_modify delay 5
atom_style bond
# Soft potential push-off
read_data data.micelle
Reading data file ...
orthogonal box = (0 0 -0.1) to (35.85686 35.85686 0.1)
2 by 2 by 1 MPI processor grid
reading atoms ...
1200 atoms
scanning bonds ...
1 = max bonds/atom
reading bonds ...
300 bonds
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
2 = max # of 1-2 neighbors
1 = max # of 1-3 neighbors
1 = max # of 1-4 neighbors
2 = max # of special neighbors
special bonds CPU = 0.000 seconds
read_data CPU = 0.004 seconds
special_bonds fene
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 1 1
special bond factors coul: 0 1 1
2 = max # of 1-2 neighbors
2 = max # of special neighbors
special bonds CPU = 0.000 seconds
pair_style soft 1.12246
pair_coeff * * 0.0 1.12246
bond_style harmonic
bond_coeff 1 50.0 0.75
velocity all create 0.45 2349852
variable prefactor equal ramp(1.0,20.0)
fix 1 all nve
fix 2 all temp/rescale 100 0.45 0.45 0.02 1.0
fix 3 all adapt 1 pair soft a * * v_prefactor
fix 4 all enforce2d
thermo 50
run 1000
Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule
WARNING: Communication cutoff 1.45246 is shorter than a bond length based estimate of 1.455. This may lead to errors. (src/comm.cpp:730)
Neighbor list info ...
update: every = 1 steps, delay = 5 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 1.45246
ghost atom cutoff = 1.45246
binsize = 0.72623, bins = 50 50 1
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair soft, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/2d
bin: standard
WARNING: Communication cutoff 1.45246 is shorter than a bond length based estimate of 1.455. This may lead to errors. (src/comm.cpp:730)
Per MPI rank memory allocation (min/avg/max) = 4.126 | 4.126 | 4.127 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0.45 0.40003481 2.2200223e-06 0.84966203 0.78952518
50 0.47411013 0.67721272 0.057404514 1.2083323 1.3375852
100 0.45 0.73046745 0.054836584 1.234929 2.3196516
150 0.67521742 0.72402001 0.043490075 1.4421648 2.8744416
200 0.45 0.78481891 0.076931503 1.3113754 3.0412388
250 0.66479018 0.69790602 0.081075564 1.4432178 3.6917024
300 0.45 0.76820218 0.066727591 1.2845548 3.7861054
350 0.67619136 0.625715 0.072722727 1.3740656 4.2861621
400 0.45 0.68527759 0.090724527 1.2256271 4.4725214
450 0.56702844 0.64402767 0.080555563 1.2911391 4.7402211
500 0.45 0.64883009 0.078376672 1.1768318 4.7919294
550 0.564664 0.58260368 0.080779475 1.2275766 4.9855705
600 0.45 0.58193041 0.088386617 1.119942 5.131481
650 0.52110993 0.5415273 0.097683746 1.1598867 5.2500294
700 0.45 0.50856787 0.088471208 1.0466641 5.2550165
750 0.51510855 0.47441291 0.089429375 1.0785216 5.375763
800 0.45 0.49926696 0.085958476 1.0348504 5.4665914
850 0.50688494 0.46614429 0.088962292 1.0615691 5.556932
900 0.45 0.47785593 0.10150857 1.0289895 5.7765975
950 0.49590559 0.46050477 0.096404887 1.052402 5.8649245
1000 0.45 0.47691182 0.08808163 1.0146185 6.0177568
Loop time of 0.0430044 on 4 procs for 1000 steps with 1200 atoms
Performance: 10045485.178 tau/day, 23253.438 timesteps/s, 27.904 Matom-step/s
98.8% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.01855 | 0.019447 | 0.019916 | 0.4 | 45.22
Bond | 0.0011939 | 0.0012689 | 0.0013518 | 0.2 | 2.95
Neigh | 0.0054396 | 0.0054535 | 0.0054635 | 0.0 | 12.68
Comm | 0.0093296 | 0.0097958 | 0.010731 | 0.6 | 22.78
Output | 0.00016417 | 0.00018578 | 0.00024995 | 0.0 | 0.43
Modify | 0.0049758 | 0.0050749 | 0.005268 | 0.2 | 11.80
Other | | 0.001778 | | | 4.14
Nlocal: 300 ave 306 max 294 min
Histogram: 1 0 0 1 0 0 1 0 0 1
Nghost: 103 ave 110 max 98 min
Histogram: 2 0 0 0 0 0 1 0 0 1
Neighs: 805 ave 827 max 768 min
Histogram: 1 0 0 0 0 0 1 0 1 1
Total # of neighbors = 3220
Ave neighs/atom = 2.6833333
Ave special neighs/atom = 0.5
Neighbor list builds = 84
Dangerous builds = 0
unfix 3
# Main run
pair_style lj/cut 2.5
# solvent/head - full-size and long-range
pair_coeff 1 1 1.0 1.0 2.5
pair_coeff 2 2 1.0 1.0 2.5
pair_coeff 1 2 1.0 1.0 2.5
# tail/tail - size-averaged and long-range
pair_coeff 3 3 1.0 0.75 2.5
pair_coeff 4 4 1.0 0.50 2.5
pair_coeff 3 4 1.0 0.67 2.5
# solvent/tail - full-size and repulsive
pair_coeff 1 3 1.0 1.0 1.12246
pair_coeff 1 4 1.0 1.0 1.12246
# head/tail - size-averaged and repulsive
pair_coeff 2 3 1.0 0.88 1.12246
pair_coeff 2 4 1.0 0.75 1.12246
thermo 50
#dump 1 all atom 2000 dump.micelle
#dump 2 all image 2000 image.*.jpg type type zoom 1.6
#dump_modify 2 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75
#dump 3 all movie 2000 movie.mpg type type zoom 1.6
#dump_modify 3 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75
reset_timestep 0
run 1000
Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update: every = 1 steps, delay = 5 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.83
ghost atom cutoff = 2.83
binsize = 1.415, bins = 26 26 1
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/2d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 4.125 | 4.125 | 4.125 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0.45 -1.7056163 0.08808163 -1.1679097 3.9431686
50 0.59734982 -1.8103783 0.076066922 -1.1374593 3.2770557
100 0.45 -1.8347112 0.093132329 -1.2919539 3.024661
150 0.51924311 -1.8943977 0.076004124 -1.2995832 2.5570373
200 0.45 -1.8918673 0.082422107 -1.3598201 2.5629655
250 0.50281134 -1.920406 0.074011331 -1.3440023 2.3518682
300 0.45 -1.9351047 0.075337265 -1.4101424 2.3249947
350 0.47650026 -1.9313687 0.072115117 -1.3831504 2.1987532
400 0.45 -1.9554318 0.08160394 -1.4242028 2.0787066
450 0.47220237 -1.9468502 0.065625625 -1.4094157 2.0984288
500 0.46846732 -1.9444333 0.076696282 -1.3996601 2.0528682
550 0.47683129 -1.958676 0.070589715 -1.4116523 2.0856023
600 0.46851246 -1.9338267 0.070605474 -1.3950992 2.2640497
650 0.46874145 -1.9462493 0.069134673 -1.4087638 2.1070263
700 0.46437384 -1.9309953 0.071977538 -1.3950309 2.2256921
750 0.47326257 -1.9484258 0.075435782 -1.4001218 2.0880238
800 0.45 -1.9646002 0.064159564 -1.4508156 2.0612711
850 0.46748245 -1.9705585 0.060385282 -1.4430803 1.9472928
900 0.46909475 -1.953722 0.062469986 -1.4225482 2.0223017
950 0.45631666 -1.9387749 0.067535547 -1.415303 2.0638464
1000 0.45 -1.9727662 0.058608374 -1.4645328 1.9982544
Loop time of 0.0580559 on 4 procs for 1000 steps with 1200 atoms
Performance: 7441102.030 tau/day, 17224.773 timesteps/s, 20.670 Matom-step/s
99.5% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.025537 | 0.026849 | 0.0293 | 0.9 | 46.25
Bond | 0.0012241 | 0.0013287 | 0.0015123 | 0.3 | 2.29
Neigh | 0.0093194 | 0.0093648 | 0.0093978 | 0.0 | 16.13
Comm | 0.011992 | 0.014606 | 0.015998 | 1.3 | 25.16
Output | 0.00018318 | 0.0001963 | 0.0002352 | 0.0 | 0.34
Modify | 0.003441 | 0.0035887 | 0.0037522 | 0.2 | 6.18
Other | | 0.002122 | | | 3.66
Nlocal: 300 ave 305 max 294 min
Histogram: 1 0 0 1 0 0 0 0 1 1
Nghost: 222.25 ave 231 max 215 min
Histogram: 1 0 0 1 0 1 0 0 0 1
Neighs: 2195 ave 2233 max 2150 min
Histogram: 1 0 0 0 0 2 0 0 0 1
Total # of neighbors = 8780
Ave neighs/atom = 7.3166667
Ave special neighs/atom = 0.5
Neighbor list builds = 77
Dangerous builds = 0
Total wall time: 0:00:00

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LAMMPS (29 Mar 2019)
using 1 OpenMP thread(s) per MPI task
# 2d micelle simulation
dimension 2
neighbor 0.3 bin
neigh_modify delay 5
atom_style bond
# Soft potential push-off
read_data data.micelle
orthogonal box = (0 0 -0.1) to (35.8569 35.8569 0.1)
1 by 1 by 1 MPI processor grid
reading atoms ...
1200 atoms
scanning bonds ...
1 = max bonds/atom
reading bonds ...
300 bonds
2 = max # of 1-2 neighbors
1 = max # of 1-3 neighbors
1 = max # of 1-4 neighbors
2 = max # of special neighbors
special bonds CPU = 0.000473022 secs
read_data CPU = 0.0024147 secs
special_bonds fene
2 = max # of 1-2 neighbors
2 = max # of special neighbors
special bonds CPU = 0.00022316 secs
pair_style soft 1.12246
pair_coeff * * 0.0 1.12246
bond_style harmonic
bond_coeff 1 50.0 0.75
velocity all create 0.45 2349852
variable prefactor equal ramp(1.0,20.0)
fix 1 all nve
fix 2 all temp/rescale 100 0.45 0.45 0.02 1.0
fix 3 all adapt 1 pair soft a * * v_prefactor
fix 4 all enforce2d
thermo 50
run 500
Neighbor list info ...
update every 1 steps, delay 5 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 1.42246
ghost atom cutoff = 1.42246
binsize = 0.71123, bins = 51 51 1
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair soft, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/2d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.799 | 3.799 | 3.799 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0.45 0.40003481 2.2200223e-06 0.84966203 0.78952518
50 0.54981866 0.93548899 0.068440043 1.5532895 1.9232786
100 0.45 0.99659327 0.079228519 1.5254468 3.2135679
150 0.86965411 0.90456016 0.07493355 1.8484231 4.3821925
200 0.45 1.01454 0.10663502 1.5708 4.7598476
250 0.79636561 0.82567712 0.12105337 1.7424325 5.4983899
300 0.45 0.86475538 0.11819875 1.4325791 5.8554758
350 0.72135464 0.70693069 0.10912636 1.5368106 6.0388247
400 0.45 0.75067331 0.14165013 1.3419484 6.3840708
450 0.64839221 0.62402486 0.14173679 1.4136135 6.4791009
500 0.45 0.66669513 0.13695201 1.2532721 6.807146
Loop time of 0.103162 on 1 procs for 500 steps with 1200 atoms
Performance: 2093802.885 tau/day, 4846.766 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 | 0.068308 | 0.068308 | 0.068308 | 0.0 | 66.21
Bond | 0.004235 | 0.004235 | 0.004235 | 0.0 | 4.11
Neigh | 0.014069 | 0.014069 | 0.014069 | 0.0 | 13.64
Comm | 0.0019219 | 0.0019219 | 0.0019219 | 0.0 | 1.86
Output | 0.00017262 | 0.00017262 | 0.00017262 | 0.0 | 0.17
Modify | 0.011728 | 0.011728 | 0.011728 | 0.0 | 11.37
Other | | 0.002726 | | | 2.64
Nlocal: 1200 ave 1200 max 1200 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 197 ave 197 max 197 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 3094 ave 3094 max 3094 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 3094
Ave neighs/atom = 2.57833
Ave special neighs/atom = 0.5
Neighbor list builds = 52
Dangerous builds = 0
unfix 3
# Main run
pair_style lj/cut 2.5
# solvent/head - full-size and long-range
pair_coeff 1 1 1.0 1.0 2.5
pair_coeff 2 2 1.0 1.0 2.5
pair_coeff 1 2 1.0 1.0 2.5
# tail/tail - size-averaged and long-range
pair_coeff 3 3 1.0 0.75 2.5
pair_coeff 4 4 1.0 0.50 2.5
pair_coeff 3 4 1.0 0.67 2.5
# solvent/tail - full-size and repulsive
pair_coeff 1 3 1.0 1.0 1.12246
pair_coeff 1 4 1.0 1.0 1.12246
# head/tail - size-averaged and repulsive
pair_coeff 2 3 1.0 0.88 1.12246
pair_coeff 2 4 1.0 0.75 1.12246
thermo 50
#dump 1 all atom 2000 dump.micelle
#dump 2 all image 2000 image.*.jpg type type zoom 1.6
#dump_modify 2 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75
#dump 3 all movie 2000 movie.mpg type type zoom 1.6
#dump_modify 3 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75
reset_timestep 0
group solvent molecule 0
750 atoms in group solvent
group solute subtract all solvent
450 atoms in group solute
unfix 1
unfix 2
unfix 4
fix 1 solvent nve
fix 2 solvent temp/rescale 100 0.45 0.45 0.02 1.0
fix 5 solute rigid molecule langevin 0.45 0.45 0.5 112211
150 rigid bodies with 450 atoms
fix 4 all enforce2d
run 500
Neighbor list info ...
update every 1 steps, delay 5 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4, bins = 26 26 1
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/2d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 5.274 | 5.274 | 5.274 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0.45318168 -1.3753652 0.13695201 -0.8705807 1.975423
50 0.77871641 -1.6955252 0.13695201 -0.92651507 0.64222539
100 0.5336062 -1.7124572 0.13695201 -1.1423948 -0.11959696
150 0.58789067 -1.7926109 0.13695201 -1.1784877 1.2592743
200 0.47864796 -1.8040298 0.13695201 -1.2785752 3.6739793
250 0.51124651 -1.8614797 0.13695201 -1.309566 2.5817722
300 0.45695639 -1.8708384 0.13695201 -1.3629901 3.0833794
350 0.477504 -1.8924359 0.13695201 -1.3679098 -5.1605926
400 0.45328205 -1.87754 0.13695201 -1.372674 -4.0355858
450 0.47465031 -1.9071924 0.13695201 -1.3849826 3.1949617
500 0.45533691 -1.9072316 0.13695201 -1.4006978 0.48079061
Loop time of 0.178806 on 1 procs for 500 steps with 1200 atoms
Performance: 1208012.705 tau/day, 2796.326 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 | 0.086131 | 0.086131 | 0.086131 | 0.0 | 48.17
Bond | 0.0042472 | 0.0042472 | 0.0042472 | 0.0 | 2.38
Neigh | 0.021317 | 0.021317 | 0.021317 | 0.0 | 11.92
Comm | 0.0025985 | 0.0025985 | 0.0025985 | 0.0 | 1.45
Output | 0.000175 | 0.000175 | 0.000175 | 0.0 | 0.10
Modify | 0.061408 | 0.061408 | 0.061408 | 0.0 | 34.34
Other | | 0.00293 | | | 1.64
Nlocal: 1200 ave 1200 max 1200 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 416 ave 416 max 416 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 8769 ave 8769 max 8769 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 8769
Ave neighs/atom = 7.3075
Ave special neighs/atom = 0.5
Neighbor list builds = 47
Dangerous builds = 2
unfix 2
unfix 4
unfix 5
fix 5 solute rigid/small molecule
create bodies CPU = 0.00015378 secs
150 rigid bodies with 450 atoms
1.30435 = max distance from body owner to body atom
fix 4 all enforce2d
run 500
Per MPI rank memory allocation (min/avg/max) = 8.64 | 8.64 | 8.64 Mbytes
Step Temp E_pair E_mol TotEng Press
500 0.45533691 -1.9072316 0.13695201 -1.4006978 2.4545793
550 0.45627282 -1.912409 0.13695201 -1.4051155 2.1845065
600 0.44734553 -1.8890695 0.13695201 -1.389022 2.3458965
650 0.46444648 -1.9042462 0.13695201 -1.3903185 2.1609319
700 0.47113236 -1.8977576 0.13695201 -1.3784032 2.2420351
750 0.48554548 -1.9253545 0.13695201 -1.3943015 2.143907
800 0.46350091 -1.8865749 0.13695201 -1.3734146 2.294431
850 0.4766104 -1.9094039 0.13695201 -1.3856031 2.2077157
900 0.48988467 -1.9051538 0.13695201 -1.3705787 2.0107056
950 0.48351943 -1.9162485 0.13695201 -1.3868399 2.1891332
1000 0.49033701 -1.9115165 0.13695201 -1.3765742 2.1508141
Loop time of 0.166502 on 1 procs for 500 steps with 1200 atoms
Performance: 1297278.008 tau/day, 3002.958 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 | 0.085767 | 0.085767 | 0.085767 | 0.0 | 51.51
Bond | 0.0042562 | 0.0042562 | 0.0042562 | 0.0 | 2.56
Neigh | 0.018039 | 0.018039 | 0.018039 | 0.0 | 10.83
Comm | 0.0024002 | 0.0024002 | 0.0024002 | 0.0 | 1.44
Output | 0.00018239 | 0.00018239 | 0.00018239 | 0.0 | 0.11
Modify | 0.052717 | 0.052717 | 0.052717 | 0.0 | 31.66
Other | | 0.003141 | | | 1.89
Nlocal: 1200 ave 1200 max 1200 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 415 ave 415 max 415 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 8743 ave 8743 max 8743 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 8743
Ave neighs/atom = 7.28583
Ave special neighs/atom = 0.5
Neighbor list builds = 40
Dangerous builds = 0
Total wall time: 0:00:00

260
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LAMMPS (29 Mar 2019)
using 1 OpenMP thread(s) per MPI task
# 2d micelle simulation
dimension 2
neighbor 0.3 bin
neigh_modify delay 5
atom_style bond
# Soft potential push-off
read_data data.micelle
orthogonal box = (0 0 -0.1) to (35.8569 35.8569 0.1)
2 by 2 by 1 MPI processor grid
reading atoms ...
1200 atoms
scanning bonds ...
1 = max bonds/atom
reading bonds ...
300 bonds
2 = max # of 1-2 neighbors
1 = max # of 1-3 neighbors
1 = max # of 1-4 neighbors
2 = max # of special neighbors
special bonds CPU = 0.000422001 secs
read_data CPU = 0.00473404 secs
special_bonds fene
2 = max # of 1-2 neighbors
2 = max # of special neighbors
special bonds CPU = 0.000183344 secs
pair_style soft 1.12246
pair_coeff * * 0.0 1.12246
bond_style harmonic
bond_coeff 1 50.0 0.75
velocity all create 0.45 2349852
variable prefactor equal ramp(1.0,20.0)
fix 1 all nve
fix 2 all temp/rescale 100 0.45 0.45 0.02 1.0
fix 3 all adapt 1 pair soft a * * v_prefactor
fix 4 all enforce2d
thermo 50
run 500
Neighbor list info ...
update every 1 steps, delay 5 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 1.42246
ghost atom cutoff = 1.42246
binsize = 0.71123, bins = 51 51 1
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair soft, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/2d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.758 | 3.85 | 4.126 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0.45 0.40003481 2.2200223e-06 0.84966203 0.78952518
50 0.54981866 0.93548899 0.068440043 1.5532895 1.9232786
100 0.45 0.99659327 0.079228519 1.5254468 3.2135679
150 0.86965411 0.90456016 0.07493355 1.8484231 4.3821925
200 0.45 1.01454 0.10663502 1.5708 4.7598476
250 0.79636561 0.82567712 0.12105337 1.7424325 5.4983899
300 0.45 0.86475538 0.11819875 1.4325791 5.8554758
350 0.72135464 0.70693069 0.10912636 1.5368106 6.0388247
400 0.45 0.75067331 0.14165013 1.3419484 6.3840708
450 0.64839221 0.62402486 0.14173679 1.4136135 6.4791009
500 0.45 0.66669513 0.13695201 1.2532721 6.807146
Loop time of 0.0426326 on 4 procs for 500 steps with 1200 atoms
Performance: 5066547.720 tau/day, 11728.120 timesteps/s
98.7% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.016784 | 0.019254 | 0.022154 | 1.5 | 45.16
Bond | 0.0010612 | 0.0012558 | 0.0014153 | 0.4 | 2.95
Neigh | 0.0046048 | 0.0046697 | 0.0047245 | 0.1 | 10.95
Comm | 0.0064592 | 0.0097114 | 0.012527 | 2.4 | 22.78
Output | 0.00022507 | 0.00026393 | 0.00033951 | 0.0 | 0.62
Modify | 0.0041659 | 0.0048084 | 0.0053945 | 0.8 | 11.28
Other | | 0.002669 | | | 6.26
Nlocal: 300 ave 304 max 292 min
Histogram: 1 0 0 0 0 0 0 0 2 1
Nghost: 103.5 ave 108 max 98 min
Histogram: 1 0 0 1 0 0 0 0 0 2
Neighs: 773.5 ave 792 max 735 min
Histogram: 1 0 0 0 0 0 0 0 2 1
Total # of neighbors = 3094
Ave neighs/atom = 2.57833
Ave special neighs/atom = 0.5
Neighbor list builds = 52
Dangerous builds = 0
unfix 3
# Main run
pair_style lj/cut 2.5
# solvent/head - full-size and long-range
pair_coeff 1 1 1.0 1.0 2.5
pair_coeff 2 2 1.0 1.0 2.5
pair_coeff 1 2 1.0 1.0 2.5
# tail/tail - size-averaged and long-range
pair_coeff 3 3 1.0 0.75 2.5
pair_coeff 4 4 1.0 0.50 2.5
pair_coeff 3 4 1.0 0.67 2.5
# solvent/tail - full-size and repulsive
pair_coeff 1 3 1.0 1.0 1.12246
pair_coeff 1 4 1.0 1.0 1.12246
# head/tail - size-averaged and repulsive
pair_coeff 2 3 1.0 0.88 1.12246
pair_coeff 2 4 1.0 0.75 1.12246
thermo 50
#dump 1 all atom 2000 dump.micelle
#dump 2 all image 2000 image.*.jpg type type zoom 1.6
#dump_modify 2 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75
#dump 3 all movie 2000 movie.mpg type type zoom 1.6
#dump_modify 3 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75
reset_timestep 0
group solvent molecule 0
750 atoms in group solvent
group solute subtract all solvent
450 atoms in group solute
unfix 1
unfix 2
unfix 4
fix 1 solvent nve
fix 2 solvent temp/rescale 100 0.45 0.45 0.02 1.0
fix 5 solute rigid molecule langevin 0.45 0.45 0.5 112211
150 rigid bodies with 450 atoms
fix 4 all enforce2d
run 500
Neighbor list info ...
update every 1 steps, delay 5 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4, bins = 26 26 1
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/2d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 5.251 | 5.282 | 5.374 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0.45318168 -1.3753652 0.13695201 -0.8705807 1.975423
50 0.77871641 -1.6955252 0.13695201 -0.92651507 0.64222539
100 0.5336062 -1.7124572 0.13695201 -1.1423948 -0.11959696
150 0.58789067 -1.7926109 0.13695201 -1.1784877 1.2592743
200 0.47864796 -1.8040298 0.13695201 -1.2785752 3.6739793
250 0.51124651 -1.8614797 0.13695201 -1.309566 2.5817722
300 0.45695639 -1.8708384 0.13695201 -1.3629901 3.0833794
350 0.477504 -1.8924359 0.13695201 -1.3679098 -5.1605926
400 0.45328205 -1.87754 0.13695201 -1.372674 -4.0355858
450 0.47465031 -1.9071924 0.13695201 -1.3849826 3.1949617
500 0.45533691 -1.9072316 0.13695201 -1.4006978 0.48079061
Loop time of 0.0887392 on 4 procs for 500 steps with 1200 atoms
Performance: 2434100.210 tau/day, 5634.491 timesteps/s
98.9% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.022611 | 0.022839 | 0.023082 | 0.1 | 25.74
Bond | 0.0010793 | 0.0011569 | 0.0012515 | 0.2 | 1.30
Neigh | 0.0064609 | 0.0064996 | 0.0065265 | 0.0 | 7.32
Comm | 0.0071712 | 0.0073687 | 0.0077734 | 0.3 | 8.30
Output | 0.00023389 | 0.00025356 | 0.00030327 | 0.0 | 0.29
Modify | 0.047258 | 0.047683 | 0.048503 | 0.2 | 53.73
Other | | 0.002938 | | | 3.31
Nlocal: 300 ave 309 max 291 min
Histogram: 1 0 0 1 0 0 1 0 0 1
Nghost: 218.75 ave 223 max 216 min
Histogram: 1 0 2 0 0 0 0 0 0 1
Neighs: 2192.25 ave 2251 max 2113 min
Histogram: 1 0 0 1 0 0 0 0 0 2
Total # of neighbors = 8769
Ave neighs/atom = 7.3075
Ave special neighs/atom = 0.5
Neighbor list builds = 47
Dangerous builds = 2
unfix 2
unfix 4
unfix 5
fix 5 solute rigid/small molecule
create bodies CPU = 7.70092e-05 secs
150 rigid bodies with 450 atoms
1.30435 = max distance from body owner to body atom
fix 4 all enforce2d
run 500
Per MPI rank memory allocation (min/avg/max) = 8.565 | 8.597 | 8.69 Mbytes
Step Temp E_pair E_mol TotEng Press
500 0.45533691 -1.9072316 0.13695201 -1.4006978 2.4545793
550 0.45627282 -1.912409 0.13695201 -1.4051155 2.1845065
600 0.44734553 -1.8890695 0.13695201 -1.389022 2.3458965
650 0.46444648 -1.9042462 0.13695201 -1.3903185 2.1609319
700 0.47113236 -1.8977576 0.13695201 -1.3784032 2.2420351
750 0.48554548 -1.9253545 0.13695201 -1.3943015 2.143907
800 0.46350091 -1.8865749 0.13695201 -1.3734146 2.294431
850 0.4766104 -1.9094039 0.13695201 -1.3856031 2.2077157
900 0.48988467 -1.9051538 0.13695201 -1.3705787 2.0107056
950 0.48351942 -1.9162485 0.13695201 -1.3868399 2.1891332
1000 0.490337 -1.9115164 0.13695201 -1.3765742 2.1508141
Loop time of 0.0588261 on 4 procs for 500 steps with 1200 atoms
Performance: 3671840.233 tau/day, 8499.630 timesteps/s
98.3% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.022407 | 0.022631 | 0.0229 | 0.1 | 38.47
Bond | 0.0010669 | 0.0011355 | 0.0012124 | 0.2 | 1.93
Neigh | 0.0052333 | 0.00528 | 0.0053182 | 0.0 | 8.98
Comm | 0.0063677 | 0.0066406 | 0.0068488 | 0.2 | 11.29
Output | 0.00023055 | 0.00024778 | 0.00028086 | 0.0 | 0.42
Modify | 0.020577 | 0.020651 | 0.020834 | 0.1 | 35.11
Other | | 0.00224 | | | 3.81
Nlocal: 300 ave 303 max 295 min
Histogram: 1 0 0 0 0 0 1 0 1 1
Nghost: 219 ave 224 max 215 min
Histogram: 1 0 0 1 1 0 0 0 0 1
Neighs: 2185.75 ave 2244 max 2143 min
Histogram: 1 1 0 0 0 1 0 0 0 1
Total # of neighbors = 8743
Ave neighs/atom = 7.28583
Ave special neighs/atom = 0.5
Neighbor list builds = 40
Dangerous builds = 0
Total wall time: 0:00:00

218
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LAMMPS (29 Mar 2019)
using 1 OpenMP thread(s) per MPI task
# 2d micelle simulation
dimension 2
neighbor 0.3 bin
neigh_modify delay 5
atom_style bond
# Soft potential push-off
read_data data.micelle
orthogonal box = (0 0 -0.1) to (35.8569 35.8569 0.1)
1 by 1 by 1 MPI processor grid
reading atoms ...
1200 atoms
scanning bonds ...
1 = max bonds/atom
reading bonds ...
300 bonds
2 = max # of 1-2 neighbors
1 = max # of 1-3 neighbors
1 = max # of 1-4 neighbors
2 = max # of special neighbors
special bonds CPU = 0.00037837 secs
read_data CPU = 0.00206876 secs
special_bonds fene
2 = max # of 1-2 neighbors
2 = max # of special neighbors
special bonds CPU = 0.000177383 secs
pair_style soft 1.12246
pair_coeff * * 0.0 1.12246
bond_style harmonic
bond_coeff 1 50.0 0.75
velocity all create 0.45 2349852
variable prefactor equal ramp(1.0,20.0)
fix 1 all nve
fix 2 all temp/rescale 100 0.45 0.45 0.02 1.0
fix 3 all adapt 1 pair soft a * * v_prefactor
fix 4 all enforce2d
thermo 50
run 1000
Neighbor list info ...
update every 1 steps, delay 5 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 1.42246
ghost atom cutoff = 1.42246
binsize = 0.71123, bins = 51 51 1
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair soft, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/2d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.799 | 3.799 | 3.799 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0.45 0.40003481 2.2200223e-06 0.84966203 0.78952518
50 0.47411013 0.67721272 0.057404514 1.2083323 1.3375852
100 0.45 0.73046745 0.054836584 1.234929 2.3196516
150 0.67521742 0.72402001 0.043490075 1.4421648 2.8744416
200 0.45 0.78481891 0.076931503 1.3113754 3.0412388
250 0.66479018 0.69790602 0.081075564 1.4432178 3.6917024
300 0.45 0.76820218 0.066727591 1.2845548 3.7861054
350 0.67619136 0.625715 0.072722727 1.3740656 4.2861621
400 0.45 0.68527759 0.090724527 1.2256271 4.4725214
450 0.56702844 0.64402767 0.080555563 1.2911391 4.7402211
500 0.45 0.64883009 0.078376672 1.1768318 4.7919294
550 0.564664 0.58260368 0.080779475 1.2275766 4.9855705
600 0.45 0.58193041 0.088386617 1.119942 5.131481
650 0.52110993 0.5415273 0.097683746 1.1598867 5.2500294
700 0.45 0.50856787 0.088471208 1.0466641 5.2550165
750 0.51510855 0.47441291 0.089429375 1.0785216 5.375763
800 0.45 0.49926696 0.085958476 1.0348504 5.4665914
850 0.50688494 0.46614429 0.088962292 1.0615691 5.556932
900 0.45 0.47785593 0.10150857 1.0289895 5.7765975
950 0.49590559 0.46050477 0.096404887 1.052402 5.8649245
1000 0.45 0.47691182 0.08808163 1.0146185 6.0177568
Loop time of 0.208895 on 1 procs for 1000 steps with 1200 atoms
Performance: 2068027.282 tau/day, 4787.100 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 | 0.14142 | 0.14142 | 0.14142 | 0.0 | 67.70
Bond | 0.008441 | 0.008441 | 0.008441 | 0.0 | 4.04
Neigh | 0.025716 | 0.025716 | 0.025716 | 0.0 | 12.31
Comm | 0.0036864 | 0.0036864 | 0.0036864 | 0.0 | 1.76
Output | 0.0003562 | 0.0003562 | 0.0003562 | 0.0 | 0.17
Modify | 0.023699 | 0.023699 | 0.023699 | 0.0 | 11.35
Other | | 0.00558 | | | 2.67
Nlocal: 1200 ave 1200 max 1200 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 195 ave 195 max 195 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 3136 ave 3136 max 3136 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 3136
Ave neighs/atom = 2.61333
Ave special neighs/atom = 0.5
Neighbor list builds = 92
Dangerous builds = 0
unfix 3
# Main run
pair_style lj/cut 2.5
# solvent/head - full-size and long-range
pair_coeff 1 1 1.0 1.0 2.5
pair_coeff 2 2 1.0 1.0 2.5
pair_coeff 1 2 1.0 1.0 2.5
# tail/tail - size-averaged and long-range
pair_coeff 3 3 1.0 0.75 2.5
pair_coeff 4 4 1.0 0.50 2.5
pair_coeff 3 4 1.0 0.67 2.5
# solvent/tail - full-size and repulsive
pair_coeff 1 3 1.0 1.0 1.12246
pair_coeff 1 4 1.0 1.0 1.12246
# head/tail - size-averaged and repulsive
pair_coeff 2 3 1.0 0.88 1.12246
pair_coeff 2 4 1.0 0.75 1.12246
thermo 50
#dump 1 all atom 2000 dump.micelle
#dump 2 all image 2000 image.*.jpg type type zoom 1.6
#dump_modify 2 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75
#dump 3 all movie 2000 movie.mpg type type zoom 1.6
#dump_modify 3 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75
reset_timestep 0
run 1000
Neighbor list info ...
update every 1 steps, delay 5 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4, bins = 26 26 1
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/2d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 4.024 | 4.024 | 4.024 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0.45 -1.7056163 0.08808163 -1.1679097 3.9431686
50 0.59734982 -1.8103783 0.076066922 -1.1374593 3.2770557
100 0.45 -1.8347112 0.093132329 -1.2919539 3.024661
150 0.51924311 -1.8943977 0.076004124 -1.2995832 2.5570373
200 0.45 -1.8918672 0.082422107 -1.3598201 2.5629655
250 0.50281134 -1.920406 0.074011331 -1.3440023 2.3518682
300 0.45 -1.9351047 0.075337265 -1.4101424 2.3249947
350 0.47650026 -1.9313687 0.072115117 -1.3831504 2.1987532
400 0.45 -1.9554318 0.081603939 -1.4242028 2.0787066
450 0.47220236 -1.9468502 0.065625624 -1.4094157 2.0984288
500 0.4684673 -1.9444333 0.076696283 -1.3996601 2.0528682
550 0.47683128 -1.958676 0.070589719 -1.4116523 2.0856022
600 0.46851243 -1.9338267 0.07060548 -1.3950992 2.26405
650 0.46874142 -1.9462493 0.069134685 -1.4087638 2.1070263
700 0.46437384 -1.9309953 0.071977522 -1.3950309 2.2256923
750 0.47326225 -1.9484255 0.075435845 -1.4001218 2.0880254
800 0.45 -1.9646005 0.064159585 -1.4508159 2.0612696
850 0.46748307 -1.970559 0.060384874 -1.4430806 1.9472879
900 0.46909484 -1.953723 0.062470295 -1.4225488 2.0222909
950 0.45631531 -1.9387753 0.067536568 -1.4153037 2.0638421
1000 0.45 -1.9727646 0.058607721 -1.4645318 1.9982315
Loop time of 0.252254 on 1 procs for 1000 steps with 1200 atoms
Performance: 1712557.882 tau/day, 3964.254 timesteps/s
99.0% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.17177 | 0.17177 | 0.17177 | 0.0 | 68.09
Bond | 0.0084555 | 0.0084555 | 0.0084555 | 0.0 | 3.35
Neigh | 0.03991 | 0.03991 | 0.03991 | 0.0 | 15.82
Comm | 0.0049119 | 0.0049119 | 0.0049119 | 0.0 | 1.95
Output | 0.00039077 | 0.00039077 | 0.00039077 | 0.0 | 0.15
Modify | 0.021131 | 0.021131 | 0.021131 | 0.0 | 8.38
Other | | 0.005685 | | | 2.25
Nlocal: 1200 ave 1200 max 1200 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 415 ave 415 max 415 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 8586 ave 8586 max 8586 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 8586
Ave neighs/atom = 7.155
Ave special neighs/atom = 0.5
Neighbor list builds = 86
Dangerous builds = 0
Total wall time: 0:00:00

218
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LAMMPS (29 Mar 2019)
using 1 OpenMP thread(s) per MPI task
# 2d micelle simulation
dimension 2
neighbor 0.3 bin
neigh_modify delay 5
atom_style bond
# Soft potential push-off
read_data data.micelle
orthogonal box = (0 0 -0.1) to (35.8569 35.8569 0.1)
2 by 2 by 1 MPI processor grid
reading atoms ...
1200 atoms
scanning bonds ...
1 = max bonds/atom
reading bonds ...
300 bonds
2 = max # of 1-2 neighbors
1 = max # of 1-3 neighbors
1 = max # of 1-4 neighbors
2 = max # of special neighbors
special bonds CPU = 0.000413656 secs
read_data CPU = 0.00487924 secs
special_bonds fene
2 = max # of 1-2 neighbors
2 = max # of special neighbors
special bonds CPU = 0.000178576 secs
pair_style soft 1.12246
pair_coeff * * 0.0 1.12246
bond_style harmonic
bond_coeff 1 50.0 0.75
velocity all create 0.45 2349852
variable prefactor equal ramp(1.0,20.0)
fix 1 all nve
fix 2 all temp/rescale 100 0.45 0.45 0.02 1.0
fix 3 all adapt 1 pair soft a * * v_prefactor
fix 4 all enforce2d
thermo 50
run 1000
Neighbor list info ...
update every 1 steps, delay 5 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 1.42246
ghost atom cutoff = 1.42246
binsize = 0.71123, bins = 51 51 1
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair soft, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/2d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.758 | 3.85 | 4.126 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0.45 0.40003481 2.2200223e-06 0.84966203 0.78952518
50 0.47411013 0.67721272 0.057404514 1.2083323 1.3375852
100 0.45 0.73046745 0.054836584 1.234929 2.3196516
150 0.67521742 0.72402001 0.043490075 1.4421648 2.8744416
200 0.45 0.78481891 0.076931503 1.3113754 3.0412388
250 0.66479018 0.69790602 0.081075564 1.4432178 3.6917024
300 0.45 0.76820218 0.066727591 1.2845548 3.7861054
350 0.67619136 0.625715 0.072722727 1.3740656 4.2861621
400 0.45 0.68527759 0.090724527 1.2256271 4.4725214
450 0.56702844 0.64402767 0.080555563 1.2911391 4.7402211
500 0.45 0.64883009 0.078376672 1.1768318 4.7919294
550 0.564664 0.58260368 0.080779475 1.2275766 4.9855705
600 0.45 0.58193041 0.088386617 1.119942 5.131481
650 0.52110993 0.5415273 0.097683746 1.1598867 5.2500294
700 0.45 0.50856787 0.088471208 1.0466641 5.2550165
750 0.51510855 0.47441291 0.089429375 1.0785216 5.375763
800 0.45 0.49926696 0.085958476 1.0348504 5.4665914
850 0.50688494 0.46614429 0.088962292 1.0615691 5.556932
900 0.45 0.47785593 0.10150857 1.0289895 5.7765975
950 0.49590559 0.46050477 0.096404887 1.052402 5.8649245
1000 0.45 0.47691182 0.08808163 1.0146185 6.0177568
Loop time of 0.0906248 on 4 procs for 1000 steps with 1200 atoms
Performance: 4766906.584 tau/day, 11034.506 timesteps/s
98.9% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.036572 | 0.039266 | 0.041216 | 1.0 | 43.33
Bond | 0.0023205 | 0.0024512 | 0.0025697 | 0.2 | 2.70
Neigh | 0.0088909 | 0.0089301 | 0.0089679 | 0.0 | 9.85
Comm | 0.022308 | 0.024047 | 0.027175 | 1.3 | 26.53
Output | 0.00057411 | 0.00061274 | 0.00071025 | 0.0 | 0.68
Modify | 0.0083182 | 0.0092374 | 0.0098341 | 0.6 | 10.19
Other | | 0.006081 | | | 6.71
Nlocal: 300 ave 305 max 292 min
Histogram: 1 0 0 0 0 0 1 0 1 1
Nghost: 100.25 ave 108 max 93 min
Histogram: 1 0 1 0 0 0 1 0 0 1
Neighs: 784 ave 815 max 739 min
Histogram: 1 0 0 0 0 0 1 1 0 1
Total # of neighbors = 3136
Ave neighs/atom = 2.61333
Ave special neighs/atom = 0.5
Neighbor list builds = 92
Dangerous builds = 0
unfix 3
# Main run
pair_style lj/cut 2.5
# solvent/head - full-size and long-range
pair_coeff 1 1 1.0 1.0 2.5
pair_coeff 2 2 1.0 1.0 2.5
pair_coeff 1 2 1.0 1.0 2.5
# tail/tail - size-averaged and long-range
pair_coeff 3 3 1.0 0.75 2.5
pair_coeff 4 4 1.0 0.50 2.5
pair_coeff 3 4 1.0 0.67 2.5
# solvent/tail - full-size and repulsive
pair_coeff 1 3 1.0 1.0 1.12246
pair_coeff 1 4 1.0 1.0 1.12246
# head/tail - size-averaged and repulsive
pair_coeff 2 3 1.0 0.88 1.12246
pair_coeff 2 4 1.0 0.75 1.12246
thermo 50
#dump 1 all atom 2000 dump.micelle
#dump 2 all image 2000 image.*.jpg type type zoom 1.6
#dump_modify 2 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75
#dump 3 all movie 2000 movie.mpg type type zoom 1.6
#dump_modify 3 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75
reset_timestep 0
run 1000
Neighbor list info ...
update every 1 steps, delay 5 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4, bins = 26 26 1
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/2d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 4.001 | 4.032 | 4.124 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0.45 -1.7056163 0.08808163 -1.1679097 3.9431686
50 0.59734982 -1.8103783 0.076066922 -1.1374593 3.2770557
100 0.45 -1.8347112 0.093132329 -1.2919539 3.024661
150 0.51924311 -1.8943977 0.076004124 -1.2995832 2.5570373
200 0.45 -1.8918672 0.082422107 -1.3598201 2.5629655
250 0.50281134 -1.920406 0.074011331 -1.3440023 2.3518682
300 0.45 -1.9351047 0.075337265 -1.4101424 2.3249947
350 0.47650026 -1.9313687 0.072115117 -1.3831504 2.1987532
400 0.45 -1.9554318 0.081603939 -1.4242028 2.0787066
450 0.47220236 -1.9468502 0.065625625 -1.4094157 2.0984288
500 0.4684673 -1.9444333 0.076696285 -1.3996601 2.0528682
550 0.47683128 -1.958676 0.070589721 -1.4116523 2.0856023
600 0.46851245 -1.9338267 0.070605469 -1.3950992 2.26405
650 0.46874143 -1.9462493 0.069134686 -1.4087638 2.1070262
700 0.4643739 -1.9309953 0.071977511 -1.3950309 2.225692
750 0.47326259 -1.9484258 0.075435808 -1.4001218 2.0880235
800 0.45 -1.9646003 0.06415956 -1.4508158 2.0612703
850 0.46748278 -1.9705588 0.06038513 -1.4430804 1.9472884
900 0.46909438 -1.9537221 0.062470305 -1.4225483 2.0223008
950 0.45631508 -1.9387742 0.067536066 -1.4153033 2.063854
1000 0.45 -1.9727651 0.058608085 -1.464532 1.9982447
Loop time of 0.0878521 on 4 procs for 1000 steps with 1200 atoms
Performance: 4917357.613 tau/day, 11382.772 timesteps/s
99.0% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.043517 | 0.044455 | 0.046903 | 0.7 | 50.60
Bond | 0.0020199 | 0.0022303 | 0.0024347 | 0.4 | 2.54
Neigh | 0.012207 | 0.012335 | 0.012512 | 0.1 | 14.04
Comm | 0.014938 | 0.018265 | 0.020068 | 1.5 | 20.79
Output | 0.00061369 | 0.00064814 | 0.00073504 | 0.0 | 0.74
Modify | 0.0052264 | 0.0053691 | 0.0055039 | 0.2 | 6.11
Other | | 0.00455 | | | 5.18
Nlocal: 300 ave 305 max 296 min
Histogram: 1 1 0 0 0 0 1 0 0 1
Nghost: 219.5 ave 228 max 214 min
Histogram: 1 0 1 1 0 0 0 0 0 1
Neighs: 2146.5 ave 2201 max 2114 min
Histogram: 1 1 0 1 0 0 0 0 0 1
Total # of neighbors = 8586
Ave neighs/atom = 7.155
Ave special neighs/atom = 0.5
Neighbor list builds = 86
Dangerous builds = 0
Total wall time: 0:00:00

312
examples/rigid/log.20Mar22.rigid.infile.g++.1 Normal file
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LAMMPS (17 Feb 2022)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
# Simple rigid body system
units lj
atom_style atomic
pair_style lj/cut 2.5
read_data data.rigid
Reading data file ...
orthogonal box = (-12 -12 -12) to (12 12 12)
1 by 1 by 1 MPI processor grid
reading atoms ...
81 atoms
read_data CPU = 0.000 seconds
velocity all create 100.0 4928459
# unconnected bodies
group clump1 id <> 1 9
9 atoms in group clump1
group clump2 id <> 10 18
9 atoms in group clump2
group clump3 id <> 19 27
9 atoms in group clump3
group clump4 id <> 28 36
9 atoms in group clump4
group clump5 id <> 37 45
9 atoms in group clump5
group clump6 id <> 46 54
9 atoms in group clump6
group clump7 id <> 55 63
9 atoms in group clump7
group clump8 id <> 64 72
9 atoms in group clump8
group clump9 id <> 73 81
9 atoms in group clump9
fix 1 all rigid group 9 clump1 clump2 clump3 clump4 clump5 clump6 clump7 clump8 clump9 infile bodyinfo.dat
9 rigid bodies with 81 atoms
neigh_modify exclude group clump1 clump1
neigh_modify exclude group clump2 clump2
neigh_modify exclude group clump3 clump3
neigh_modify exclude group clump4 clump4
neigh_modify exclude group clump5 clump5
neigh_modify exclude group clump6 clump6
neigh_modify exclude group clump7 clump7
neigh_modify exclude group clump8 clump8
neigh_modify exclude group clump9 clump9
thermo 100
#dump 1 all atom 50 dump.rigid
#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 2 pad 5
#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 3 pad 5
timestep 0.0001
thermo 50
run 10000
generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Reading rigid body data for 4 bodies from file bodyinfo.dat
Reading rigid body data for 4 bodies from file bodyinfo.dat
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4, bins = 18 18 18
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 4.353 | 4.353 | 4.353 Mbytes
Step Temp E_pair E_mol TotEng Press
0 115.29439 5235.9179 0 5272.2142 -2.7403788
50 14910.685 571.71558 0 5265.82 32.006171
100 16298.442 136.66184 0 5267.653 16.444229
150 16682.606 17.490511 0 5269.4219 14.900344
200 16733.929 1.372872 0 5269.4617 14.569267
250 16738.853 -0.15252816 0 5269.4864 14.496404
300 16738.588 -0.055171335 0 5269.5002 14.496025
350 16738.492 -0.017444677 0 5269.5077 14.496446
400 16738.464 -0.0060102023 0 5269.5104 14.496618
450 16738.455 -0.0012713351 0 5269.5124 14.496701
500 16738.455 -0.00081068621 0 5269.5128 14.496709
550 16738.455 -0.00083203497 0 5269.5129 14.496707
600 16738.455 -0.00058355356 0 5269.5131 14.496709
650 16738.455 -0.00047226704 0 5269.5131 14.496708
700 16738.455 0 0 5269.5136 14.496713
750 16738.455 0 0 5269.5136 14.49671
800 16738.455 0 0 5269.5137 14.496709
850 16738.455 0 0 5269.5137 14.49671
900 16738.456 0 0 5269.5138 14.496713
950 16738.462 -0.0035323872 0 5269.5122 14.496671
1000 16738.586 -0.051135144 0 5269.5036 14.496229
1050 16737.358 0.32995057 0 5269.4981 14.525763
1100 16737.892 0.16210246 0 5269.4984 14.531983
1150 16738.703 -0.089235095 0 5269.5025 14.509899
1200 16738.466 -0.0075446243 0 5269.5096 14.510615
1250 16738.456 0 0 5269.514 14.510704
1300 16738.457 0 0 5269.5141 14.510701
1350 16738.457 0 0 5269.5141 14.510699
1400 16738.457 -0.00044736511 0 5269.5138 14.510693
1450 16738.458 -0.0010971179 0 5269.5134 14.510687
1500 16738.458 -0.00057885428 0 5269.5139 14.510698
1550 16738.457 0 0 5269.5143 14.51071
1600 16738.457 0 0 5269.5144 14.510712
1650 16738.457 0 0 5269.5144 14.510712
1700 16738.458 0 0 5269.5144 14.51071
1750 16738.458 0 0 5269.5145 14.510708
1800 16738.458 0 0 5269.5145 14.510706
1850 16738.458 0 0 5269.5146 14.510705
1900 16738.458 0 0 5269.5146 14.510706
1950 16738.465 -0.0031733615 0 5269.5134 14.510659
2000 16738.491 -0.013255268 0 5269.5117 14.510532
2050 16738.556 -0.0365811 0 5269.5087 14.51029
2100 16738.633 -0.063209659 0 5269.5065 14.510219
2150 16738.607 -0.05601761 0 5269.5055 14.510231
2200 16738.557 -0.038423032 0 5269.5072 14.510404
2250 16738.515 -0.023709918 0 5269.5088 14.510539
2300 16738.489 -0.013249035 0 5269.5111 14.510621
2350 16738.468 -0.0045563719 0 5269.5131 14.510714
2400 16738.46 -0.00052194273 0 5269.5146 14.510771
2450 16738.464 -0.0023259756 0 5269.514 14.510746
2500 16738.468 -0.0051929186 0 5269.5127 14.510731
2550 16738.581 -0.044940117 0 5269.5085 14.510315
2600 16738.427 -7.9722793e-05 0 5269.5046 14.510657
2650 16733.017 1.7051479 0 5269.5067 14.596295
2700 16738.761 -0.10614946 0 5269.5038 14.499584
2750 16733.973 1.4038179 0 5269.5064 14.598107
2800 16738.585 -0.046813448 0 5269.5076 14.511073
2850 16738.487 -0.012558719 0 5269.5111 14.510111
2900 16738.465 -0.0026252725 0 5269.514 14.510277
2950 16738.476 -0.0082220764 0 5269.512 14.510223
3000 16738.66 -0.071284779 0 5269.507 14.509758
3050 16715.332 7.2419352 0 5269.476 14.870305
3100 16653.226 26.818761 0 5269.5009 14.496764
3150 16739.351 -0.30690375 0 5269.4886 13.643904
3200 16733.238 1.6025328 0 5269.4737 12.016934
3250 16734.374 1.2554429 0 5269.4841 11.963561
3300 16732.156 1.9585967 0 5269.4893 12.234024
3350 16738.655 -0.079693236 0 5269.497 12.092757
3400 16738.543 -0.042215005 0 5269.4991 12.092809
3450 16738.591 -0.059327511 0 5269.4972 12.092536
3500 16738.759 -0.11761245 0 5269.4918 12.09203
3550 16713.405 7.8460621 0 5269.4737 12.389816
3600 16734.939 1.0821936 0 5269.4891 12.173591
3650 16738.808 -0.13663194 0 5269.4882 12.027009
3700 16738.602 -0.070934368 0 5269.4889 12.025288
3750 16737.731 0.20706558 0 5269.4927 12.061948
3800 16738.578 -0.05582043 0 5269.4965 12.035665
3850 16738.471 -0.016307928 0 5269.5024 12.035302
3900 16738.449 -0.0058182199 0 5269.5059 12.035401
3950 16738.439 -0.0012027325 0 5269.5074 12.035461
4000 16738.436 -0.00020698452 0 5269.5075 12.035469
4050 16738.437 0 0 5269.5078 12.035454
4100 16738.437 0 0 5269.508 12.035435
4150 16738.438 0 0 5269.5081 12.035426
4200 16738.438 0 0 5269.5083 12.035432
4250 16738.439 0 0 5269.5085 12.035447
4300 16738.439 0 0 5269.5086 12.035463
4350 16738.44 0 0 5269.5087 12.035474
4400 16738.44 0 0 5269.5088 12.035478
4450 16738.44 0 0 5269.5089 12.035474
4500 16738.44 0 0 5269.509 12.035462
4550 16738.441 0 0 5269.5092 12.035449
4600 16738.441 0 0 5269.5093 12.035445
4650 16738.442 0 0 5269.5095 12.035451
4700 16738.442 0 0 5269.5096 12.03546
4750 16738.443 0 0 5269.5097 12.035465
4800 16738.443 0 0 5269.5098 12.035466
4850 16738.443 0 0 5269.51 12.035463
4900 16738.444 0 0 5269.5101 12.035456
4950 16738.444 0 0 5269.5102 12.035447
5000 16738.445 0 0 5269.5104 12.03544
5050 16738.445 0 0 5269.5105 12.035442
5100 16738.446 0 0 5269.5107 12.035455
5150 16738.446 0 0 5269.5108 12.03547
5200 16738.446 0 0 5269.5109 12.035479
5250 16738.447 0 0 5269.511 12.035479
5300 16738.447 0 0 5269.5111 12.03547
5350 16738.447 0 0 5269.5112 12.035454
5400 16738.448 0 0 5269.5113 12.035434
5450 16738.448 0 0 5269.5115 12.03542
5500 16738.449 0 0 5269.5117 12.035422
5550 16738.457 -0.0030919234 0 5269.5111 12.035383
5600 16738.51 -0.021618357 0 5269.5092 12.035106
5650 16738.622 -0.059214788 0 5269.507 12.035694
5700 16395.28 108.06941 0 5269.5463 24.369038
5750 16738.544 -0.033973429 0 5269.5077 12.011261
5800 16738.456 -0.0037013529 0 5269.5102 12.011675
5850 16738.451 0 0 5269.5123 12.011709
5900 16738.451 -0.0002211587 0 5269.5122 12.011687
5950 16738.452 -0.00024253349 0 5269.5124 12.011678
6000 16738.452 0 0 5269.5128 12.011688
6050 16738.453 0 0 5269.513 12.011702
6100 16738.453 0 0 5269.5131 12.011716
6150 16738.454 0 0 5269.5132 12.011725
6200 16738.454 0 0 5269.5133 12.011728
6250 16738.454 0 0 5269.5134 12.011723
6300 16738.455 0 0 5269.5135 12.011712
6350 16738.455 0 0 5269.5137 12.0117
6400 16738.456 0 0 5269.5138 12.011697
6450 16738.456 0 0 5269.514 12.011704
6500 16738.456 0 0 5269.5141 12.011714
6550 16738.457 0 0 5269.5142 12.011719
6600 16738.457 0 0 5269.5143 12.011718
6650 16738.458 0 0 5269.5144 12.011713
6700 16738.458 0 0 5269.5146 12.011705
6750 16738.459 0 0 5269.5147 12.011696
6800 16738.459 0 0 5269.5149 12.01169
6850 16738.46 0 0 5269.515 12.011695
6900 16738.46 0 0 5269.5152 12.01171
6950 16738.46 0 0 5269.5153 12.011726
7000 16738.461 0 0 5269.5154 12.011736
7050 16738.461 0 0 5269.5155 12.011737
7100 16738.461 0 0 5269.5155 12.011728
7150 16738.461 0 0 5269.5156 12.011712
7200 16738.462 0 0 5269.5158 12.011691
7250 16738.463 0 0 5269.516 12.011676
7300 16738.463 0 0 5269.5162 12.011677
7350 16738.464 0 0 5269.5164 12.011693
7400 16738.464 0 0 5269.5165 12.011713
7450 16738.465 0 0 5269.5166 12.011729
7500 16738.465 0 0 5269.5167 12.011736
7550 16738.465 0 0 5269.5168 12.011734
7600 16738.465 0 0 5269.5168 12.011722
7650 16738.466 0 0 5269.517 12.011704
7700 16738.466 0 0 5269.5171 12.011687
7750 16738.467 0 0 5269.5173 12.011681
7800 16738.467 0 0 5269.5175 12.011687
7850 16738.468 0 0 5269.5176 12.0117
7900 16738.468 0 0 5269.5178 12.011712
7950 16738.469 0 0 5269.5179 12.011721
8000 16738.469 0 0 5269.518 12.011724
8050 16738.469 0 0 5269.5181 12.01172
8100 16738.47 0 0 5269.5182 12.011709
8150 16738.47 0 0 5269.5183 12.0117
8200 16738.47 0 0 5269.5185 12.0117
8250 16738.471 0 0 5269.5186 12.011709
8300 16738.471 0 0 5269.5187 12.011719
8350 16738.472 0 0 5269.5189 12.011723
8400 16738.472 0 0 5269.519 12.01172
8450 16738.473 -0.00039690666 0 5269.5189 12.011706
8500 16738.481 -0.0034646804 0 5269.5182 12.011643
8550 16738.483 -0.0045307409 0 5269.5178 12.011621
8600 16738.474 -0.00076532812 0 5269.5189 12.011681
8650 16738.474 0 0 5269.5197 12.011699
8700 16738.475 0 0 5269.5199 12.011715
8750 16738.475 0 0 5269.52 12.011732
8800 16738.475 0 0 5269.52 12.011743
8850 16738.476 0 0 5269.5201 12.011744
8900 16738.476 0 0 5269.5202 12.011735
8950 16738.476 0 0 5269.5203 12.011719
9000 16738.477 0 0 5269.5205 12.011698
9050 16738.477 0 0 5269.5206 12.011683
9100 16738.478 0 0 5269.5208 12.011684
9150 16738.479 0 0 5269.521 12.011701
9200 16738.479 0 0 5269.5212 12.011722
9250 16738.479 0 0 5269.5213 12.011738
9300 16738.48 0 0 5269.5214 12.011746
9350 16738.48 0 0 5269.5214 12.011744
9400 16738.48 0 0 5269.5215 12.011732
9450 16738.48 0 0 5269.5216 12.011715
9500 16738.481 -0.00037652435 0 5269.5216 12.011692
9550 16738.493 -0.0053156167 0 5269.5203 12.011611
9600 16738.549 -0.02681437 0 5269.5163 12.011415
9650 16738.765 -0.10191524 0 5269.5092 12.011013
9700 16735.041 1.0589895 0 5269.4979 12.062708
9750 16738.013 0.13550156 0 5269.5101 11.407246
9800 16738.512 -0.011620325 0 5269.5201 11.394974
9850 16738.489 -0.00067270436 0 5269.5237 11.395099
9900 16738.489 -0.0002498452 0 5269.5242 11.395085
9950 16738.49 0 0 5269.5245 11.395077
10000 16738.49 0 0 5269.5246 11.395076
Loop time of 0.0882903 on 1 procs for 10000 steps with 81 atoms
Performance: 978589.581 tau/day, 113262.683 timesteps/s
97.6% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0064583 | 0.0064583 | 0.0064583 | 0.0 | 7.31
Neigh | 0.027186 | 0.027186 | 0.027186 | 0.0 | 30.79
Comm | 0.0057041 | 0.0057041 | 0.0057041 | 0.0 | 6.46
Output | 0.0020628 | 0.0020628 | 0.0020628 | 0.0 | 2.34
Modify | 0.042816 | 0.042816 | 0.042816 | 0.0 | 48.49
Other | | 0.004063 | | | 4.60
Nlocal: 81 ave 81 max 81 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 84 ave 84 max 84 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0
Neighbor list builds = 998
Dangerous builds = 997
Total wall time: 0:00:00

312
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LAMMPS (17 Feb 2022)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
# Simple rigid body system
units lj
atom_style atomic
pair_style lj/cut 2.5
read_data data.rigid
Reading data file ...
orthogonal box = (-12 -12 -12) to (12 12 12)
1 by 2 by 2 MPI processor grid
reading atoms ...
81 atoms
read_data CPU = 0.000 seconds
velocity all create 100.0 4928459
# unconnected bodies
group clump1 id <> 1 9
9 atoms in group clump1
group clump2 id <> 10 18
9 atoms in group clump2
group clump3 id <> 19 27
9 atoms in group clump3
group clump4 id <> 28 36
9 atoms in group clump4
group clump5 id <> 37 45
9 atoms in group clump5
group clump6 id <> 46 54
9 atoms in group clump6
group clump7 id <> 55 63
9 atoms in group clump7
group clump8 id <> 64 72
9 atoms in group clump8
group clump9 id <> 73 81
9 atoms in group clump9
fix 1 all rigid group 9 clump1 clump2 clump3 clump4 clump5 clump6 clump7 clump8 clump9 infile bodyinfo.dat
9 rigid bodies with 81 atoms
neigh_modify exclude group clump1 clump1
neigh_modify exclude group clump2 clump2
neigh_modify exclude group clump3 clump3
neigh_modify exclude group clump4 clump4
neigh_modify exclude group clump5 clump5
neigh_modify exclude group clump6 clump6
neigh_modify exclude group clump7 clump7
neigh_modify exclude group clump8 clump8
neigh_modify exclude group clump9 clump9
thermo 100
#dump 1 all atom 50 dump.rigid
#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 2 pad 5
#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 3 pad 5
timestep 0.0001
thermo 50
run 10000
generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Reading rigid body data for 4 bodies from file bodyinfo.dat
Reading rigid body data for 4 bodies from file bodyinfo.dat
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4, bins = 18 18 18
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 4.201 | 4.233 | 4.327 Mbytes
Step Temp E_pair E_mol TotEng Press
0 115.29439 5235.9179 0 5272.2142 -2.7403788
50 14910.685 571.71558 0 5265.82 32.006171
100 16298.442 136.66184 0 5267.653 16.444229
150 16682.606 17.490511 0 5269.4219 14.900344
200 16733.929 1.372872 0 5269.4617 14.569267
250 16738.853 -0.15252816 0 5269.4864 14.496404
300 16738.588 -0.055171335 0 5269.5002 14.496025
350 16738.492 -0.017444677 0 5269.5077 14.496446
400 16738.464 -0.0060102023 0 5269.5104 14.496618
450 16738.455 -0.0012713351 0 5269.5124 14.496701
500 16738.455 -0.00081068621 0 5269.5128 14.496709
550 16738.455 -0.00083203497 0 5269.5129 14.496707
600 16738.455 -0.00058355356 0 5269.5131 14.496709
650 16738.455 -0.00047226704 0 5269.5131 14.496708
700 16738.455 0 0 5269.5136 14.496713
750 16738.455 0 0 5269.5136 14.49671
800 16738.455 0 0 5269.5137 14.496709
850 16738.455 0 0 5269.5137 14.49671
900 16738.456 0 0 5269.5138 14.496713
950 16738.462 -0.0035323872 0 5269.5122 14.496671
1000 16738.586 -0.051135144 0 5269.5036 14.496229
1050 16737.358 0.32995057 0 5269.4981 14.525763
1100 16737.892 0.16210246 0 5269.4984 14.531983
1150 16738.703 -0.089235095 0 5269.5025 14.509899
1200 16738.466 -0.0075446243 0 5269.5096 14.510615
1250 16738.456 0 0 5269.514 14.510704
1300 16738.457 0 0 5269.5141 14.510701
1350 16738.457 0 0 5269.5141 14.510699
1400 16738.457 -0.00044736511 0 5269.5138 14.510693
1450 16738.458 -0.0010971179 0 5269.5134 14.510687
1500 16738.458 -0.00057885428 0 5269.5139 14.510698
1550 16738.457 0 0 5269.5143 14.51071
1600 16738.457 0 0 5269.5144 14.510712
1650 16738.457 0 0 5269.5144 14.510712
1700 16738.458 0 0 5269.5144 14.51071
1750 16738.458 0 0 5269.5145 14.510708
1800 16738.458 0 0 5269.5145 14.510706
1850 16738.458 0 0 5269.5146 14.510705
1900 16738.458 0 0 5269.5146 14.510706
1950 16738.465 -0.0031733615 0 5269.5134 14.510659
2000 16738.491 -0.013255268 0 5269.5117 14.510532
2050 16738.556 -0.0365811 0 5269.5087 14.51029
2100 16738.633 -0.063209659 0 5269.5065 14.510219
2150 16738.607 -0.05601761 0 5269.5055 14.510231
2200 16738.557 -0.038423032 0 5269.5072 14.510404
2250 16738.515 -0.023709918 0 5269.5088 14.510539
2300 16738.489 -0.013249035 0 5269.5111 14.510621
2350 16738.468 -0.0045563719 0 5269.5131 14.510714
2400 16738.46 -0.00052194273 0 5269.5146 14.510771
2450 16738.464 -0.0023259756 0 5269.514 14.510746
2500 16738.468 -0.0051929186 0 5269.5127 14.510731
2550 16738.581 -0.044940117 0 5269.5085 14.510315
2600 16738.427 -7.972279e-05 0 5269.5046 14.510657
2650 16733.017 1.7051479 0 5269.5067 14.596295
2700 16738.761 -0.10614946 0 5269.5038 14.499584
2750 16733.973 1.4038179 0 5269.5064 14.598107
2800 16738.585 -0.046813448 0 5269.5076 14.511073
2850 16738.487 -0.012558719 0 5269.5111 14.510111
2900 16738.465 -0.0026252725 0 5269.514 14.510277
2950 16738.476 -0.0082220764 0 5269.512 14.510223
3000 16738.66 -0.071284779 0 5269.507 14.509758
3050 16715.332 7.2419352 0 5269.476 14.870305
3100 16653.226 26.818761 0 5269.5009 14.496764
3150 16739.351 -0.30690375 0 5269.4886 13.643904
3200 16733.238 1.6025328 0 5269.4737 12.016934
3250 16734.374 1.2554429 0 5269.4841 11.963561
3300 16732.156 1.9585967 0 5269.4893 12.234024
3350 16738.655 -0.079693236 0 5269.497 12.092757
3400 16738.543 -0.042215005 0 5269.4991 12.092809
3450 16738.591 -0.059327511 0 5269.4972 12.092536
3500 16738.759 -0.11761245 0 5269.4918 12.09203
3550 16713.405 7.8460621 0 5269.4737 12.389816
3600 16734.939 1.0821936 0 5269.4891 12.173591
3650 16738.808 -0.13663194 0 5269.4882 12.027009
3700 16738.602 -0.070934368 0 5269.4889 12.025288
3750 16737.731 0.20706557 0 5269.4927 12.061948
3800 16738.578 -0.05582043 0 5269.4965 12.035665
3850 16738.471 -0.016307928 0 5269.5024 12.035302
3900 16738.449 -0.0058182199 0 5269.5059 12.035401
3950 16738.439 -0.0012027325 0 5269.5074 12.035461
4000 16738.436 -0.00020698452 0 5269.5075 12.035469
4050 16738.437 0 0 5269.5078 12.035454
4100 16738.437 0 0 5269.508 12.035435
4150 16738.438 0 0 5269.5081 12.035426
4200 16738.438 0 0 5269.5083 12.035432
4250 16738.439 0 0 5269.5085 12.035447
4300 16738.439 0 0 5269.5086 12.035463
4350 16738.44 0 0 5269.5087 12.035474
4400 16738.44 0 0 5269.5088 12.035478
4450 16738.44 0 0 5269.5089 12.035474
4500 16738.44 0 0 5269.509 12.035462
4550 16738.441 0 0 5269.5092 12.035449
4600 16738.441 0 0 5269.5093 12.035445
4650 16738.442 0 0 5269.5095 12.035451
4700 16738.442 0 0 5269.5096 12.03546
4750 16738.443 0 0 5269.5097 12.035465
4800 16738.443 0 0 5269.5098 12.035466
4850 16738.443 0 0 5269.51 12.035463
4900 16738.444 0 0 5269.5101 12.035456
4950 16738.444 0 0 5269.5102 12.035447
5000 16738.445 0 0 5269.5104 12.03544
5050 16738.445 0 0 5269.5105 12.035442
5100 16738.446 0 0 5269.5107 12.035455
5150 16738.446 0 0 5269.5108 12.03547
5200 16738.446 0 0 5269.5109 12.035479
5250 16738.447 0 0 5269.511 12.035479
5300 16738.447 0 0 5269.5111 12.03547
5350 16738.447 0 0 5269.5112 12.035454
5400 16738.448 0 0 5269.5113 12.035434
5450 16738.448 0 0 5269.5115 12.03542
5500 16738.449 0 0 5269.5117 12.035422
5550 16738.457 -0.0030919234 0 5269.5111 12.035383
5600 16738.51 -0.021618357 0 5269.5092 12.035106
5650 16738.622 -0.059214788 0 5269.507 12.035694
5700 16395.28 108.06941 0 5269.5463 24.369038
5750 16738.544 -0.033973429 0 5269.5077 12.011261
5800 16738.456 -0.0037013529 0 5269.5102 12.011675
5850 16738.451 0 0 5269.5123 12.011709
5900 16738.451 -0.00022115871 0 5269.5122 12.011687
5950 16738.452 -0.00024253349 0 5269.5124 12.011678
6000 16738.452 0 0 5269.5128 12.011688
6050 16738.453 0 0 5269.513 12.011702
6100 16738.453 0 0 5269.5131 12.011716
6150 16738.454 0 0 5269.5132 12.011725
6200 16738.454 0 0 5269.5133 12.011728
6250 16738.454 0 0 5269.5134 12.011723
6300 16738.455 0 0 5269.5135 12.011712
6350 16738.455 0 0 5269.5137 12.0117
6400 16738.456 0 0 5269.5138 12.011697
6450 16738.456 0 0 5269.514 12.011704
6500 16738.456 0 0 5269.5141 12.011714
6550 16738.457 0 0 5269.5142 12.011719
6600 16738.457 0 0 5269.5143 12.011718
6650 16738.458 0 0 5269.5144 12.011713
6700 16738.458 0 0 5269.5146 12.011705
6750 16738.459 0 0 5269.5147 12.011696
6800 16738.459 0 0 5269.5149 12.01169
6850 16738.46 0 0 5269.515 12.011695
6900 16738.46 0 0 5269.5152 12.01171
6950 16738.46 0 0 5269.5153 12.011726
7000 16738.461 0 0 5269.5154 12.011736
7050 16738.461 0 0 5269.5155 12.011737
7100 16738.461 0 0 5269.5155 12.011728
7150 16738.461 0 0 5269.5156 12.011712
7200 16738.462 0 0 5269.5158 12.011691
7250 16738.463 0 0 5269.516 12.011676
7300 16738.463 0 0 5269.5162 12.011677
7350 16738.464 0 0 5269.5164 12.011693
7400 16738.464 0 0 5269.5165 12.011713
7450 16738.465 0 0 5269.5166 12.011729
7500 16738.465 0 0 5269.5167 12.011736
7550 16738.465 0 0 5269.5168 12.011734
7600 16738.465 0 0 5269.5168 12.011722
7650 16738.466 0 0 5269.517 12.011704
7700 16738.466 0 0 5269.5171 12.011687
7750 16738.467 0 0 5269.5173 12.011681
7800 16738.467 0 0 5269.5175 12.011687
7850 16738.468 0 0 5269.5176 12.0117
7900 16738.468 0 0 5269.5178 12.011712
7950 16738.469 0 0 5269.5179 12.011721
8000 16738.469 0 0 5269.518 12.011724
8050 16738.469 0 0 5269.5181 12.01172
8100 16738.47 0 0 5269.5182 12.011709
8150 16738.47 0 0 5269.5183 12.0117
8200 16738.47 0 0 5269.5185 12.0117
8250 16738.471 0 0 5269.5186 12.011709
8300 16738.471 0 0 5269.5187 12.011719
8350 16738.472 0 0 5269.5189 12.011723
8400 16738.472 0 0 5269.519 12.01172
8450 16738.473 -0.00039690664 0 5269.5189 12.011706
8500 16738.481 -0.0034646803 0 5269.5182 12.011643
8550 16738.483 -0.004530741 0 5269.5178 12.01162
8600 16738.474 -0.00076532813 0 5269.5189 12.011681
8650 16738.474 0 0 5269.5197 12.011699
8700 16738.475 0 0 5269.5199 12.011715
8750 16738.475 0 0 5269.52 12.011732
8800 16738.475 0 0 5269.52 12.011743
8850 16738.476 0 0 5269.5201 12.011744
8900 16738.476 0 0 5269.5202 12.011735
8950 16738.476 0 0 5269.5203 12.011719
9000 16738.477 0 0 5269.5205 12.011698
9050 16738.477 0 0 5269.5206 12.011683
9100 16738.478 0 0 5269.5208 12.011684
9150 16738.479 0 0 5269.521 12.011701
9200 16738.479 0 0 5269.5212 12.011722
9250 16738.479 0 0 5269.5213 12.011738
9300 16738.48 0 0 5269.5214 12.011746
9350 16738.48 0 0 5269.5214 12.011744
9400 16738.48 0 0 5269.5215 12.011732
9450 16738.48 0 0 5269.5216 12.011715
9500 16738.481 -0.00037652436 0 5269.5216 12.011692
9550 16738.493 -0.0053156168 0 5269.5203 12.011611
9600 16738.549 -0.026814371 0 5269.5163 12.011415
9650 16738.765 -0.10191524 0 5269.5092 12.011013
9700 16735.041 1.0589899 0 5269.4979 12.062708
9750 16738.013 0.13550149 0 5269.5101 11.407246
9800 16738.512 -0.011620325 0 5269.5201 11.394974
9850 16738.489 -0.00067270428 0 5269.5237 11.395099
9900 16738.489 -0.0002498452 0 5269.5242 11.395085
9950 16738.49 0 0 5269.5245 11.395077
10000 16738.49 0 0 5269.5246 11.395076
Loop time of 0.100422 on 4 procs for 10000 steps with 81 atoms
Performance: 860368.209 tau/day, 99579.654 timesteps/s
99.0% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0014853 | 0.0020649 | 0.0026245 | 0.9 | 2.06
Neigh | 0.0075956 | 0.0080256 | 0.0091971 | 0.8 | 7.99
Comm | 0.037221 | 0.041059 | 0.043195 | 1.2 | 40.89
Output | 0.0020995 | 0.0023594 | 0.003073 | 0.8 | 2.35
Modify | 0.041318 | 0.042855 | 0.044215 | 0.5 | 42.67
Other | | 0.004059 | | | 4.04
Nlocal: 20.25 ave 38 max 3 min
Histogram: 1 0 1 0 0 0 1 0 0 1
Nghost: 27.25 ave 48 max 13 min
Histogram: 1 0 1 1 0 0 0 0 0 1
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0
Neighbor list builds = 998
Dangerous builds = 997
Total wall time: 0:00:00

349
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LAMMPS (17 Feb 2022)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
# Simple rigid body system
units lj
atom_style bond
pair_style lj/cut 2.5
read_data data.rigid.small
Reading data file ...
orthogonal box = (-12 -12 -12) to (12 12 12)
1 by 1 by 1 MPI processor grid
reading atoms ...
81 atoms
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
0 = max # of 1-2 neighbors
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
1 = max # of special neighbors
special bonds CPU = 0.000 seconds
read_data CPU = 0.001 seconds
velocity all create 100.0 4928459
# unconnected bodies
group clump1 id <> 1 9
9 atoms in group clump1
group clump2 id <> 10 18
9 atoms in group clump2
group clump3 id <> 19 27
9 atoms in group clump3
group clump4 id <> 28 36
9 atoms in group clump4
group clump5 id <> 37 45
9 atoms in group clump5
group clump6 id <> 46 54
9 atoms in group clump6
group clump7 id <> 55 63
9 atoms in group clump7
group clump8 id <> 64 72
9 atoms in group clump8
group clump9 id <> 73 81
9 atoms in group clump9
fix 1 all rigid molecule
9 rigid bodies with 81 atoms
# 1 chain of connected bodies
#group clump1 id <> 1 9
#group clump2 id <> 9 18
#group clump3 id <> 18 27
#group clump4 id <> 27 36
#group clump5 id <> 36 45
#group clump6 id <> 45 54
#group clump7 id <> 54 63
#group clump8 id <> 63 72
#group clump9 id <> 72 81
#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9
# 2 chains of connected bodies
#group clump1 id <> 1 9
#group clump2 id <> 9 18
#group clump3 id <> 18 27
#group clump4 id <> 27 36
#group clump5 id <> 37 45
#group clump6 id <> 45 54
#group clump7 id <> 54 63
#group clump8 id <> 63 72
#group clump9 id <> 72 81
#fix 1 all poems group clump1 clump2 clump3 clump4
#fix 2 all poems group clump5 clump6 clump7 clump8 clump9
neigh_modify exclude group clump1 clump1
neigh_modify exclude group clump2 clump2
neigh_modify exclude group clump3 clump3
neigh_modify exclude group clump4 clump4
neigh_modify exclude group clump5 clump5
neigh_modify exclude group clump6 clump6
neigh_modify exclude group clump7 clump7
neigh_modify exclude group clump8 clump8
neigh_modify exclude group clump9 clump9
thermo 100
#dump 1 all atom 50 dump.rigid
#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 2 pad 5
#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 3 pad 5
timestep 0.0001
thermo 50
run 10000
generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4, bins = 18 18 18
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 5.233 | 5.233 | 5.233 Mbytes
Step Temp E_pair E_mol TotEng Press
0 115.29439 5235.9179 0 5272.2142 -2.7403788
50 14910.685 571.71558 0 5265.82 32.006171
100 16298.442 136.66184 0 5267.653 16.444229
150 16682.606 17.490511 0 5269.4219 14.900344
200 16733.929 1.372872 0 5269.4617 14.569267
250 16738.853 -0.15252816 0 5269.4864 14.496404
300 16738.588 -0.055171335 0 5269.5002 14.496025
350 16738.492 -0.017444677 0 5269.5077 14.496446
400 16738.464 -0.0060102023 0 5269.5104 14.496618
450 16738.455 -0.0012713351 0 5269.5124 14.496701
500 16738.455 -0.00081068621 0 5269.5128 14.496709
550 16738.455 -0.00083203497 0 5269.5129 14.496707
600 16738.455 -0.00058355356 0 5269.5131 14.496709
650 16738.455 -0.00047226704 0 5269.5131 14.496708
700 16738.455 0 0 5269.5136 14.496713
750 16738.455 0 0 5269.5136 14.49671
800 16738.455 0 0 5269.5137 14.496709
850 16738.455 0 0 5269.5137 14.49671
900 16738.456 0 0 5269.5138 14.496713
950 16738.462 -0.0035323872 0 5269.5122 14.496671
1000 16738.586 -0.051135144 0 5269.5036 14.496229
1050 16737.358 0.32995057 0 5269.4981 14.525763
1100 16737.892 0.16210246 0 5269.4984 14.531983
1150 16738.703 -0.089235095 0 5269.5025 14.509899
1200 16738.466 -0.0075446243 0 5269.5096 14.510615
1250 16738.456 0 0 5269.514 14.510704
1300 16738.457 0 0 5269.5141 14.510701
1350 16738.457 0 0 5269.5141 14.510699
1400 16738.457 -0.00044736511 0 5269.5138 14.510693
1450 16738.458 -0.0010971179 0 5269.5134 14.510687
1500 16738.458 -0.00057885428 0 5269.5139 14.510698
1550 16738.457 0 0 5269.5143 14.51071
1600 16738.457 0 0 5269.5144 14.510712
1650 16738.457 0 0 5269.5144 14.510712
1700 16738.458 0 0 5269.5144 14.51071
1750 16738.458 0 0 5269.5145 14.510708
1800 16738.458 0 0 5269.5145 14.510706
1850 16738.458 0 0 5269.5146 14.510705
1900 16738.458 0 0 5269.5146 14.510706
1950 16738.465 -0.0031733615 0 5269.5134 14.510659
2000 16738.491 -0.013255268 0 5269.5117 14.510532
2050 16738.556 -0.0365811 0 5269.5087 14.51029
2100 16738.633 -0.063209659 0 5269.5065 14.510219
2150 16738.607 -0.05601761 0 5269.5055 14.510231
2200 16738.557 -0.038423032 0 5269.5072 14.510404
2250 16738.515 -0.023709918 0 5269.5088 14.510539
2300 16738.489 -0.013249035 0 5269.5111 14.510621
2350 16738.468 -0.0045563719 0 5269.5131 14.510714
2400 16738.46 -0.00052194273 0 5269.5146 14.510771
2450 16738.464 -0.0023259756 0 5269.514 14.510746
2500 16738.468 -0.0051929186 0 5269.5127 14.510731
2550 16738.581 -0.044940117 0 5269.5085 14.510315
2600 16738.427 -7.97228e-05 0 5269.5046 14.510657
2650 16733.017 1.7051479 0 5269.5067 14.596295
2700 16738.761 -0.10614946 0 5269.5038 14.499584
2750 16733.973 1.4038179 0 5269.5064 14.598107
2800 16738.585 -0.046813448 0 5269.5076 14.511073
2850 16738.487 -0.012558719 0 5269.5111 14.510111
2900 16738.465 -0.0026252725 0 5269.514 14.510277
2950 16738.476 -0.0082220764 0 5269.512 14.510223
3000 16738.66 -0.071284779 0 5269.507 14.509758
3050 16715.332 7.2419352 0 5269.476 14.870305
3100 16653.226 26.818761 0 5269.5009 14.496764
3150 16739.351 -0.30690375 0 5269.4886 13.643904
3200 16733.238 1.6025328 0 5269.4737 12.016934
3250 16734.374 1.2554429 0 5269.4841 11.963561
3300 16732.156 1.9585967 0 5269.4893 12.234024
3350 16738.655 -0.079693236 0 5269.497 12.092757
3400 16738.543 -0.042215005 0 5269.4991 12.092809
3450 16738.591 -0.059327511 0 5269.4972 12.092536
3500 16738.759 -0.11761245 0 5269.4918 12.09203
3550 16713.405 7.8460621 0 5269.4737 12.389816
3600 16734.939 1.0821936 0 5269.4891 12.173591
3650 16738.808 -0.13663194 0 5269.4882 12.027009
3700 16738.602 -0.070934368 0 5269.4889 12.025288
3750 16737.731 0.20706557 0 5269.4927 12.061948
3800 16738.578 -0.05582043 0 5269.4965 12.035665
3850 16738.471 -0.016307928 0 5269.5024 12.035302
3900 16738.449 -0.0058182199 0 5269.5059 12.035401
3950 16738.439 -0.0012027325 0 5269.5074 12.035461
4000 16738.436 -0.00020698452 0 5269.5075 12.035469
4050 16738.437 0 0 5269.5078 12.035454
4100 16738.437 0 0 5269.508 12.035435
4150 16738.438 0 0 5269.5081 12.035426
4200 16738.438 0 0 5269.5083 12.035432
4250 16738.439 0 0 5269.5085 12.035447
4300 16738.439 0 0 5269.5086 12.035463
4350 16738.44 0 0 5269.5087 12.035474
4400 16738.44 0 0 5269.5088 12.035478
4450 16738.44 0 0 5269.5089 12.035474
4500 16738.44 0 0 5269.509 12.035462
4550 16738.441 0 0 5269.5092 12.035449
4600 16738.441 0 0 5269.5093 12.035445
4650 16738.442 0 0 5269.5095 12.035451
4700 16738.442 0 0 5269.5096 12.03546
4750 16738.443 0 0 5269.5097 12.035465
4800 16738.443 0 0 5269.5098 12.035466
4850 16738.443 0 0 5269.51 12.035463
4900 16738.444 0 0 5269.5101 12.035456
4950 16738.444 0 0 5269.5102 12.035447
5000 16738.445 0 0 5269.5104 12.03544
5050 16738.445 0 0 5269.5105 12.035442
5100 16738.446 0 0 5269.5107 12.035455
5150 16738.446 0 0 5269.5108 12.03547
5200 16738.446 0 0 5269.5109 12.035479
5250 16738.447 0 0 5269.511 12.035479
5300 16738.447 0 0 5269.5111 12.03547
5350 16738.447 0 0 5269.5112 12.035454
5400 16738.448 0 0 5269.5113 12.035434
5450 16738.448 0 0 5269.5115 12.03542
5500 16738.449 0 0 5269.5117 12.035422
5550 16738.457 -0.0030919234 0 5269.5111 12.035383
5600 16738.51 -0.021618357 0 5269.5092 12.035106
5650 16738.622 -0.059214788 0 5269.507 12.035694
5700 16395.28 108.06941 0 5269.5463 24.369038
5750 16738.544 -0.033973429 0 5269.5077 12.011261
5800 16738.456 -0.0037013529 0 5269.5102 12.011675
5850 16738.451 0 0 5269.5123 12.011709
5900 16738.451 -0.00022115871 0 5269.5122 12.011687
5950 16738.452 -0.00024253349 0 5269.5124 12.011678
6000 16738.452 0 0 5269.5128 12.011688
6050 16738.453 0 0 5269.513 12.011702
6100 16738.453 0 0 5269.5131 12.011716
6150 16738.454 0 0 5269.5132 12.011725
6200 16738.454 0 0 5269.5133 12.011728
6250 16738.454 0 0 5269.5134 12.011723
6300 16738.455 0 0 5269.5135 12.011712
6350 16738.455 0 0 5269.5137 12.0117
6400 16738.456 0 0 5269.5138 12.011697
6450 16738.456 0 0 5269.514 12.011704
6500 16738.456 0 0 5269.5141 12.011714
6550 16738.457 0 0 5269.5142 12.011719
6600 16738.457 0 0 5269.5143 12.011718
6650 16738.458 0 0 5269.5144 12.011713
6700 16738.458 0 0 5269.5146 12.011705
6750 16738.459 0 0 5269.5147 12.011696
6800 16738.459 0 0 5269.5149 12.01169
6850 16738.46 0 0 5269.515 12.011695
6900 16738.46 0 0 5269.5152 12.01171
6950 16738.46 0 0 5269.5153 12.011726
7000 16738.461 0 0 5269.5154 12.011736
7050 16738.461 0 0 5269.5155 12.011737
7100 16738.461 0 0 5269.5155 12.011728
7150 16738.461 0 0 5269.5156 12.011712
7200 16738.462 0 0 5269.5158 12.011691
7250 16738.463 0 0 5269.516 12.011676
7300 16738.463 0 0 5269.5162 12.011677
7350 16738.464 0 0 5269.5164 12.011693
7400 16738.464 0 0 5269.5165 12.011713
7450 16738.465 0 0 5269.5166 12.011729
7500 16738.465 0 0 5269.5167 12.011736
7550 16738.465 0 0 5269.5168 12.011734
7600 16738.465 0 0 5269.5168 12.011722
7650 16738.466 0 0 5269.517 12.011704
7700 16738.466 0 0 5269.5171 12.011687
7750 16738.467 0 0 5269.5173 12.011681
7800 16738.467 0 0 5269.5175 12.011687
7850 16738.468 0 0 5269.5176 12.0117
7900 16738.468 0 0 5269.5178 12.011712
7950 16738.469 0 0 5269.5179 12.011721
8000 16738.469 0 0 5269.518 12.011724
8050 16738.469 0 0 5269.5181 12.01172
8100 16738.47 0 0 5269.5182 12.011709
8150 16738.47 0 0 5269.5183 12.0117
8200 16738.47 0 0 5269.5185 12.0117
8250 16738.471 0 0 5269.5186 12.011709
8300 16738.471 0 0 5269.5187 12.011719
8350 16738.472 0 0 5269.5189 12.011723
8400 16738.472 0 0 5269.519 12.01172
8450 16738.473 -0.00039690664 0 5269.5189 12.011706
8500 16738.481 -0.0034646803 0 5269.5182 12.011643
8550 16738.483 -0.0045307409 0 5269.5178 12.011621
8600 16738.474 -0.00076532813 0 5269.5189 12.011681
8650 16738.474 0 0 5269.5197 12.011699
8700 16738.475 0 0 5269.5199 12.011715
8750 16738.475 0 0 5269.52 12.011732
8800 16738.475 0 0 5269.52 12.011743
8850 16738.476 0 0 5269.5201 12.011744
8900 16738.476 0 0 5269.5202 12.011735
8950 16738.476 0 0 5269.5203 12.011719
9000 16738.477 0 0 5269.5205 12.011698
9050 16738.477 0 0 5269.5206 12.011683
9100 16738.478 0 0 5269.5208 12.011684
9150 16738.479 0 0 5269.521 12.011701
9200 16738.479 0 0 5269.5212 12.011722
9250 16738.479 0 0 5269.5213 12.011738
9300 16738.48 0 0 5269.5214 12.011746
9350 16738.48 0 0 5269.5214 12.011744
9400 16738.48 0 0 5269.5215 12.011732
9450 16738.48 0 0 5269.5216 12.011715
9500 16738.481 -0.00037652436 0 5269.5216 12.011692
9550 16738.493 -0.0053156166 0 5269.5203 12.011611
9600 16738.549 -0.026814371 0 5269.5163 12.011415
9650 16738.765 -0.10191524 0 5269.5092 12.011013
9700 16735.041 1.0589897 0 5269.4979 12.062708
9750 16738.013 0.1355014 0 5269.5101 11.407246
9800 16738.512 -0.011620325 0 5269.5201 11.394974
9850 16738.489 -0.00067270449 0 5269.5237 11.395099
9900 16738.489 -0.00024984529 0 5269.5242 11.395085
9950 16738.49 0 0 5269.5245 11.395077
10000 16738.49 0 0 5269.5246 11.395076
Loop time of 0.0974108 on 1 procs for 10000 steps with 81 atoms
Performance: 886965.415 tau/day, 102658.034 timesteps/s
96.8% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0068054 | 0.0068054 | 0.0068054 | 0.0 | 6.99
Bond | 0.00034618 | 0.00034618 | 0.00034618 | 0.0 | 0.36
Neigh | 0.033076 | 0.033076 | 0.033076 | 0.0 | 33.96
Comm | 0.0067938 | 0.0067938 | 0.0067938 | 0.0 | 6.97
Output | 0.0022905 | 0.0022905 | 0.0022905 | 0.0 | 2.35
Modify | 0.044027 | 0.044027 | 0.044027 | 0.0 | 45.20
Other | | 0.004071 | | | 4.18
Nlocal: 81 ave 81 max 81 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 84 ave 84 max 84 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0
Ave special neighs/atom = 0
Neighbor list builds = 998
Dangerous builds = 997
Total wall time: 0:00:00

349
examples/rigid/log.20Mar22.rigid.molecule.g++.4 Normal file
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@ -0,0 +1,349 @@
LAMMPS (17 Feb 2022)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
# Simple rigid body system
units lj
atom_style bond
pair_style lj/cut 2.5
read_data data.rigid.small
Reading data file ...
orthogonal box = (-12 -12 -12) to (12 12 12)
1 by 2 by 2 MPI processor grid
reading atoms ...
81 atoms
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
0 = max # of 1-2 neighbors
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
1 = max # of special neighbors
special bonds CPU = 0.000 seconds
read_data CPU = 0.001 seconds
velocity all create 100.0 4928459
# unconnected bodies
group clump1 id <> 1 9
9 atoms in group clump1
group clump2 id <> 10 18
9 atoms in group clump2
group clump3 id <> 19 27
9 atoms in group clump3
group clump4 id <> 28 36
9 atoms in group clump4
group clump5 id <> 37 45
9 atoms in group clump5
group clump6 id <> 46 54
9 atoms in group clump6
group clump7 id <> 55 63
9 atoms in group clump7
group clump8 id <> 64 72
9 atoms in group clump8
group clump9 id <> 73 81
9 atoms in group clump9
fix 1 all rigid molecule
9 rigid bodies with 81 atoms
# 1 chain of connected bodies
#group clump1 id <> 1 9
#group clump2 id <> 9 18
#group clump3 id <> 18 27
#group clump4 id <> 27 36
#group clump5 id <> 36 45
#group clump6 id <> 45 54
#group clump7 id <> 54 63
#group clump8 id <> 63 72
#group clump9 id <> 72 81
#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9
# 2 chains of connected bodies
#group clump1 id <> 1 9
#group clump2 id <> 9 18
#group clump3 id <> 18 27
#group clump4 id <> 27 36
#group clump5 id <> 37 45
#group clump6 id <> 45 54
#group clump7 id <> 54 63
#group clump8 id <> 63 72
#group clump9 id <> 72 81
#fix 1 all poems group clump1 clump2 clump3 clump4
#fix 2 all poems group clump5 clump6 clump7 clump8 clump9
neigh_modify exclude group clump1 clump1
neigh_modify exclude group clump2 clump2
neigh_modify exclude group clump3 clump3
neigh_modify exclude group clump4 clump4
neigh_modify exclude group clump5 clump5
neigh_modify exclude group clump6 clump6
neigh_modify exclude group clump7 clump7
neigh_modify exclude group clump8 clump8
neigh_modify exclude group clump9 clump9
thermo 100
#dump 1 all atom 50 dump.rigid
#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 2 pad 5
#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 3 pad 5
timestep 0.0001
thermo 50
run 10000
generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4, bins = 18 18 18
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 5.08 | 5.112 | 5.206 Mbytes
Step Temp E_pair E_mol TotEng Press
0 115.29439 5235.9179 0 5272.2142 -2.7403788
50 14910.685 571.71558 0 5265.82 32.006171
100 16298.442 136.66184 0 5267.653 16.444229
150 16682.606 17.490511 0 5269.4219 14.900344
200 16733.929 1.372872 0 5269.4617 14.569267
250 16738.853 -0.15252816 0 5269.4864 14.496404
300 16738.588 -0.055171335 0 5269.5002 14.496025
350 16738.492 -0.017444677 0 5269.5077 14.496446
400 16738.464 -0.0060102023 0 5269.5104 14.496618
450 16738.455 -0.0012713351 0 5269.5124 14.496701
500 16738.455 -0.00081068621 0 5269.5128 14.496709
550 16738.455 -0.00083203497 0 5269.5129 14.496707
600 16738.455 -0.00058355356 0 5269.5131 14.496709
650 16738.455 -0.00047226704 0 5269.5131 14.496708
700 16738.455 0 0 5269.5136 14.496713
750 16738.455 0 0 5269.5136 14.49671
800 16738.455 0 0 5269.5137 14.496709
850 16738.455 0 0 5269.5137 14.49671
900 16738.456 0 0 5269.5138 14.496713
950 16738.462 -0.0035323872 0 5269.5122 14.496671
1000 16738.586 -0.051135144 0 5269.5036 14.496229
1050 16737.358 0.32995057 0 5269.4981 14.525763
1100 16737.892 0.16210246 0 5269.4984 14.531983
1150 16738.703 -0.089235095 0 5269.5025 14.509899
1200 16738.466 -0.0075446243 0 5269.5096 14.510615
1250 16738.456 0 0 5269.514 14.510704
1300 16738.457 0 0 5269.5141 14.510701
1350 16738.457 0 0 5269.5141 14.510699
1400 16738.457 -0.00044736511 0 5269.5138 14.510693
1450 16738.458 -0.0010971179 0 5269.5134 14.510687
1500 16738.458 -0.00057885428 0 5269.5139 14.510698
1550 16738.457 0 0 5269.5143 14.51071
1600 16738.457 0 0 5269.5144 14.510712
1650 16738.457 0 0 5269.5144 14.510712
1700 16738.458 0 0 5269.5144 14.51071
1750 16738.458 0 0 5269.5145 14.510708
1800 16738.458 0 0 5269.5145 14.510706
1850 16738.458 0 0 5269.5146 14.510705
1900 16738.458 0 0 5269.5146 14.510706
1950 16738.465 -0.0031733615 0 5269.5134 14.510659
2000 16738.491 -0.013255268 0 5269.5117 14.510532
2050 16738.556 -0.0365811 0 5269.5087 14.51029
2100 16738.633 -0.063209659 0 5269.5065 14.510219
2150 16738.607 -0.05601761 0 5269.5055 14.510231
2200 16738.557 -0.038423032 0 5269.5072 14.510404
2250 16738.515 -0.023709918 0 5269.5088 14.510539
2300 16738.489 -0.013249035 0 5269.5111 14.510621
2350 16738.468 -0.0045563719 0 5269.5131 14.510714
2400 16738.46 -0.00052194273 0 5269.5146 14.510771
2450 16738.464 -0.0023259756 0 5269.514 14.510746
2500 16738.468 -0.0051929186 0 5269.5127 14.510731
2550 16738.581 -0.044940117 0 5269.5085 14.510315
2600 16738.427 -7.9722775e-05 0 5269.5046 14.510657
2650 16733.017 1.705148 0 5269.5067 14.596295
2700 16738.761 -0.10614946 0 5269.5038 14.499584
2750 16733.973 1.4038179 0 5269.5064 14.598107
2800 16738.585 -0.046813448 0 5269.5076 14.511073
2850 16738.487 -0.012558719 0 5269.5111 14.510111
2900 16738.465 -0.0026252725 0 5269.514 14.510277
2950 16738.476 -0.0082220764 0 5269.512 14.510223
3000 16738.66 -0.071284779 0 5269.507 14.509758
3050 16715.332 7.2419352 0 5269.476 14.870305
3100 16653.226 26.818761 0 5269.5009 14.496764
3150 16739.351 -0.30690375 0 5269.4886 13.643904
3200 16733.238 1.6025328 0 5269.4737 12.016934
3250 16734.374 1.2554429 0 5269.4841 11.963561
3300 16732.156 1.9585967 0 5269.4893 12.234024
3350 16738.655 -0.079693236 0 5269.497 12.092757
3400 16738.543 -0.042215005 0 5269.4991 12.092809
3450 16738.591 -0.059327511 0 5269.4972 12.092536
3500 16738.759 -0.11761245 0 5269.4918 12.09203
3550 16713.405 7.8460621 0 5269.4737 12.389816
3600 16734.939 1.0821936 0 5269.4891 12.173591
3650 16738.808 -0.13663194 0 5269.4882 12.027009
3700 16738.602 -0.070934367 0 5269.4889 12.025288
3750 16737.731 0.20706556 0 5269.4927 12.061948
3800 16738.578 -0.05582043 0 5269.4965 12.035665
3850 16738.471 -0.016307928 0 5269.5024 12.035302
3900 16738.449 -0.0058182199 0 5269.5059 12.035401
3950 16738.439 -0.0012027325 0 5269.5074 12.035461
4000 16738.436 -0.00020698452 0 5269.5075 12.035469
4050 16738.437 0 0 5269.5078 12.035454
4100 16738.437 0 0 5269.508 12.035435
4150 16738.438 0 0 5269.5081 12.035426
4200 16738.438 0 0 5269.5083 12.035432
4250 16738.439 0 0 5269.5085 12.035447
4300 16738.439 0 0 5269.5086 12.035463
4350 16738.44 0 0 5269.5087 12.035474
4400 16738.44 0 0 5269.5088 12.035478
4450 16738.44 0 0 5269.5089 12.035474
4500 16738.44 0 0 5269.509 12.035462
4550 16738.441 0 0 5269.5092 12.035449
4600 16738.441 0 0 5269.5093 12.035445
4650 16738.442 0 0 5269.5095 12.035451
4700 16738.442 0 0 5269.5096 12.03546
4750 16738.443 0 0 5269.5097 12.035465
4800 16738.443 0 0 5269.5098 12.035466
4850 16738.443 0 0 5269.51 12.035463
4900 16738.444 0 0 5269.5101 12.035456
4950 16738.444 0 0 5269.5102 12.035447
5000 16738.445 0 0 5269.5104 12.03544
5050 16738.445 0 0 5269.5105 12.035442
5100 16738.446 0 0 5269.5107 12.035455
5150 16738.446 0 0 5269.5108 12.03547
5200 16738.446 0 0 5269.5109 12.035479
5250 16738.447 0 0 5269.511 12.035479
5300 16738.447 0 0 5269.5111 12.03547
5350 16738.447 0 0 5269.5112 12.035454
5400 16738.448 0 0 5269.5113 12.035434
5450 16738.448 0 0 5269.5115 12.03542
5500 16738.449 0 0 5269.5117 12.035422
5550 16738.457 -0.0030919234 0 5269.5111 12.035383
5600 16738.51 -0.021618357 0 5269.5092 12.035106
5650 16738.622 -0.059214788 0 5269.507 12.035694
5700 16395.28 108.06941 0 5269.5463 24.369038
5750 16738.544 -0.033973429 0 5269.5077 12.011261
5800 16738.456 -0.0037013529 0 5269.5102 12.011675
5850 16738.451 0 0 5269.5123 12.011709
5900 16738.451 -0.00022115871 0 5269.5122 12.011687
5950 16738.452 -0.00024253349 0 5269.5124 12.011678
6000 16738.452 0 0 5269.5128 12.011688
6050 16738.453 0 0 5269.513 12.011702
6100 16738.453 0 0 5269.5131 12.011716
6150 16738.454 0 0 5269.5132 12.011725
6200 16738.454 0 0 5269.5133 12.011728
6250 16738.454 0 0 5269.5134 12.011723
6300 16738.455 0 0 5269.5135 12.011712
6350 16738.455 0 0 5269.5137 12.0117
6400 16738.456 0 0 5269.5138 12.011697
6450 16738.456 0 0 5269.514 12.011704
6500 16738.456 0 0 5269.5141 12.011714
6550 16738.457 0 0 5269.5142 12.011719
6600 16738.457 0 0 5269.5143 12.011718
6650 16738.458 0 0 5269.5144 12.011713
6700 16738.458 0 0 5269.5146 12.011705
6750 16738.459 0 0 5269.5147 12.011696
6800 16738.459 0 0 5269.5149 12.01169
6850 16738.46 0 0 5269.515 12.011695
6900 16738.46 0 0 5269.5152 12.01171
6950 16738.46 0 0 5269.5153 12.011726
7000 16738.461 0 0 5269.5154 12.011736
7050 16738.461 0 0 5269.5155 12.011737
7100 16738.461 0 0 5269.5155 12.011728
7150 16738.461 0 0 5269.5156 12.011712
7200 16738.462 0 0 5269.5158 12.011691
7250 16738.463 0 0 5269.516 12.011676
7300 16738.463 0 0 5269.5162 12.011677
7350 16738.464 0 0 5269.5164 12.011693
7400 16738.464 0 0 5269.5165 12.011713
7450 16738.465 0 0 5269.5166 12.011729
7500 16738.465 0 0 5269.5167 12.011736
7550 16738.465 0 0 5269.5168 12.011734
7600 16738.465 0 0 5269.5168 12.011722
7650 16738.466 0 0 5269.517 12.011704
7700 16738.466 0 0 5269.5171 12.011687
7750 16738.467 0 0 5269.5173 12.011681
7800 16738.467 0 0 5269.5175 12.011687
7850 16738.468 0 0 5269.5176 12.0117
7900 16738.468 0 0 5269.5178 12.011712
7950 16738.469 0 0 5269.5179 12.011721
8000 16738.469 0 0 5269.518 12.011724
8050 16738.469 0 0 5269.5181 12.01172
8100 16738.47 0 0 5269.5182 12.011709
8150 16738.47 0 0 5269.5183 12.0117
8200 16738.47 0 0 5269.5185 12.0117
8250 16738.471 0 0 5269.5186 12.011709
8300 16738.471 0 0 5269.5187 12.011719
8350 16738.472 0 0 5269.5189 12.011723
8400 16738.472 0 0 5269.519 12.01172
8450 16738.473 -0.00039690662 0 5269.5189 12.011706
8500 16738.481 -0.0034646802 0 5269.5182 12.011643
8550 16738.483 -0.004530741 0 5269.5178 12.01162
8600 16738.474 -0.00076532815 0 5269.5189 12.011681
8650 16738.474 0 0 5269.5197 12.011699
8700 16738.475 0 0 5269.5199 12.011715
8750 16738.475 0 0 5269.52 12.011732
8800 16738.475 0 0 5269.52 12.011743
8850 16738.476 0 0 5269.5201 12.011744
8900 16738.476 0 0 5269.5202 12.011735
8950 16738.476 0 0 5269.5203 12.011719
9000 16738.477 0 0 5269.5205 12.011698
9050 16738.477 0 0 5269.5206 12.011683
9100 16738.478 0 0 5269.5208 12.011684
9150 16738.479 0 0 5269.521 12.011701
9200 16738.479 0 0 5269.5212 12.011722
9250 16738.479 0 0 5269.5213 12.011738
9300 16738.48 0 0 5269.5214 12.011746
9350 16738.48 0 0 5269.5214 12.011744
9400 16738.48 0 0 5269.5215 12.011732
9450 16738.48 0 0 5269.5216 12.011715
9500 16738.481 -0.00037652439 0 5269.5216 12.011692
9550 16738.493 -0.0053156171 0 5269.5203 12.011611
9600 16738.549 -0.026814373 0 5269.5163 12.011415
9650 16738.765 -0.10191525 0 5269.5092 12.011013
9700 16735.041 1.0589908 0 5269.4979 12.062708
9750 16738.013 0.13550139 0 5269.5101 11.407247
9800 16738.512 -0.011620323 0 5269.5201 11.394975
9850 16738.489 -0.00067270407 0 5269.5237 11.395099
9900 16738.489 -0.00024984518 0 5269.5242 11.395086
9950 16738.49 0 0 5269.5245 11.395077
10000 16738.49 0 0 5269.5246 11.395076
Loop time of 0.102079 on 4 procs for 10000 steps with 81 atoms
Performance: 846406.333 tau/day, 97963.696 timesteps/s
98.7% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0015357 | 0.0020418 | 0.0024561 | 0.7 | 2.00
Bond | 0.00030031 | 0.00031957 | 0.00034464 | 0.0 | 0.31
Neigh | 0.0091719 | 0.0094934 | 0.010243 | 0.4 | 9.30
Comm | 0.038015 | 0.041242 | 0.043481 | 1.1 | 40.40
Output | 0.002223 | 0.0024412 | 0.0030738 | 0.7 | 2.39
Modify | 0.040725 | 0.042557 | 0.043982 | 0.7 | 41.69
Other | | 0.003983 | | | 3.90
Nlocal: 20.25 ave 38 max 3 min
Histogram: 1 0 1 0 0 0 1 0 0 1
Nghost: 27.25 ave 48 max 13 min
Histogram: 1 0 1 1 0 0 0 0 0 1
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0
Ave special neighs/atom = 0
Neighbor list builds = 998
Dangerous builds = 997
Total wall time: 0:00:00

328
examples/rigid/log.20Mar22.rigid.poems.g++.1 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 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
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@ -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
examples/rigid/log.20Mar22.rigid.poems2.g++.4 Normal file
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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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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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@ -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 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

328
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@ -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 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

0
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LAMMPS (17 Feb 2022)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
# Simple rigid body system
units lj
atom_style bond
pair_style lj/cut 2.5
read_data data.rigid.small
Reading data file ...
orthogonal box = (-12 -12 -12) to (12 12 12)
1 by 1 by 1 MPI processor grid
reading atoms ...
81 atoms
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
0 = max # of 1-2 neighbors
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
1 = max # of special neighbors
special bonds CPU = 0.000 seconds
read_data CPU = 0.001 seconds
velocity all create 100.0 4928459
# unconnected bodies
group clump1 id <> 1 9
9 atoms in group clump1
group clump2 id <> 10 18
9 atoms in group clump2
group clump3 id <> 19 27
9 atoms in group clump3
group clump4 id <> 28 36
9 atoms in group clump4
group clump5 id <> 37 45
9 atoms in group clump5
group clump6 id <> 46 54
9 atoms in group clump6
group clump7 id <> 55 63
9 atoms in group clump7
group clump8 id <> 64 72
9 atoms in group clump8
group clump9 id <> 73 81
9 atoms in group clump9
fix 1 all rigid/small molecule
create bodies CPU = 0.000 seconds
9 rigid bodies with 81 atoms
1.2247449 = max distance from body owner to body atom
neigh_modify exclude group clump1 clump1
neigh_modify exclude group clump2 clump2
neigh_modify exclude group clump3 clump3
neigh_modify exclude group clump4 clump4
neigh_modify exclude group clump5 clump5
neigh_modify exclude group clump6 clump6
neigh_modify exclude group clump7 clump7
neigh_modify exclude group clump8 clump8
neigh_modify exclude group clump9 clump9
thermo 100
#dump 1 all atom 50 dump.rigid
#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 2 pad 5
#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 3 pad 5
timestep 0.0001
thermo 50
run 10000
generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4, bins = 18 18 18
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 9.034 | 9.034 | 9.034 Mbytes
Step Temp E_pair E_mol TotEng Press
0 115.29439 5235.9179 0 5272.2142 -2.7403788
50 14910.685 571.71558 0 5265.82 32.006171
100 16298.442 136.66184 0 5267.653 16.444229
150 16682.606 17.490511 0 5269.4219 14.900344
200 16733.929 1.372872 0 5269.4617 14.569267
250 16738.853 -0.15252816 0 5269.4864 14.496404
300 16738.588 -0.055171335 0 5269.5002 14.496025
350 16738.492 -0.017444677 0 5269.5077 14.496446
400 16738.464 -0.0060102023 0 5269.5104 14.496618
450 16738.455 -0.0012713351 0 5269.5124 14.496701
500 16738.455 -0.00081068621 0 5269.5128 14.496709
550 16738.455 -0.00083203497 0 5269.5129 14.496707
600 16738.455 -0.00058355356 0 5269.5131 14.496709
650 16738.455 -0.00047226704 0 5269.5131 14.496708
700 16738.455 0 0 5269.5136 14.496713
750 16738.455 0 0 5269.5136 14.49671
800 16738.455 0 0 5269.5137 14.496709
850 16738.455 0 0 5269.5137 14.49671
900 16738.456 0 0 5269.5138 14.496713
950 16738.462 -0.0035323872 0 5269.5122 14.496671
1000 16738.586 -0.051135144 0 5269.5036 14.496229
1050 16737.358 0.32995057 0 5269.4981 14.525763
1100 16737.892 0.16210246 0 5269.4984 14.531983
1150 16738.703 -0.089235095 0 5269.5025 14.509899
1200 16738.466 -0.0075446243 0 5269.5096 14.510615
1250 16738.456 0 0 5269.514 14.510704
1300 16738.457 0 0 5269.5141 14.510701
1350 16738.457 0 0 5269.5141 14.510699
1400 16738.457 -0.00044736511 0 5269.5138 14.510693
1450 16738.458 -0.0010971179 0 5269.5134 14.510687
1500 16738.458 -0.00057885428 0 5269.5139 14.510698
1550 16738.457 0 0 5269.5143 14.51071
1600 16738.457 0 0 5269.5144 14.510712
1650 16738.457 0 0 5269.5144 14.510712
1700 16738.458 0 0 5269.5144 14.51071
1750 16738.458 0 0 5269.5145 14.510708
1800 16738.458 0 0 5269.5145 14.510706
1850 16738.458 0 0 5269.5146 14.510705
1900 16738.458 0 0 5269.5146 14.510706
1950 16738.465 -0.0031733615 0 5269.5134 14.510659
2000 16738.491 -0.013255268 0 5269.5117 14.510532
2050 16738.556 -0.0365811 0 5269.5087 14.51029
2100 16738.633 -0.063209659 0 5269.5065 14.510219
2150 16738.607 -0.05601761 0 5269.5055 14.510231
2200 16738.557 -0.038423032 0 5269.5072 14.510404
2250 16738.515 -0.023709918 0 5269.5088 14.510539
2300 16738.489 -0.013249035 0 5269.5111 14.510621
2350 16738.468 -0.0045563719 0 5269.5131 14.510714
2400 16738.46 -0.00052194273 0 5269.5146 14.510771
2450 16738.464 -0.0023259756 0 5269.514 14.510746
2500 16738.468 -0.0051929186 0 5269.5127 14.510731
2550 16738.581 -0.044940117 0 5269.5085 14.510315
2600 16738.427 -7.9722826e-05 0 5269.5046 14.510657
2650 16733.017 1.7051479 0 5269.5067 14.596295
2700 16738.761 -0.10614946 0 5269.5038 14.499584
2750 16733.973 1.4038179 0 5269.5064 14.598107
2800 16738.585 -0.046813448 0 5269.5076 14.511073
2850 16738.487 -0.012558719 0 5269.5111 14.510111
2900 16738.465 -0.0026252725 0 5269.514 14.510277
2950 16738.476 -0.0082220764 0 5269.512 14.510223
3000 16738.66 -0.071284779 0 5269.507 14.509758
3050 16715.332 7.2419352 0 5269.476 14.870305
3100 16653.226 26.818761 0 5269.5009 14.496764
3150 16739.351 -0.30690375 0 5269.4886 13.643904
3200 16733.238 1.6025328 0 5269.4737 12.016934
3250 16734.374 1.255443 0 5269.4841 11.963561
3300 16732.156 1.9585966 0 5269.4893 12.234024
3350 16738.655 -0.079693235 0 5269.497 12.092757
3400 16738.543 -0.042215005 0 5269.4991 12.092809
3450 16738.591 -0.05932751 0 5269.4972 12.092536
3500 16738.759 -0.11761245 0 5269.4918 12.092031
3550 16713.405 7.8460623 0 5269.4737 12.389816
3600 16734.939 1.0821936 0 5269.4891 12.173591
3650 16738.808 -0.13663192 0 5269.4882 12.027009
3700 16738.602 -0.070934371 0 5269.4889 12.025288
3750 16737.731 0.20706562 0 5269.4927 12.061948
3800 16738.578 -0.05582043 0 5269.4965 12.035665
3850 16738.471 -0.016307928 0 5269.5024 12.035302
3900 16738.449 -0.0058182199 0 5269.5059 12.035401
3950 16738.439 -0.0012027325 0 5269.5074 12.035461
4000 16738.436 -0.00020698452 0 5269.5075 12.035469
4050 16738.437 0 0 5269.5078 12.035454
4100 16738.437 0 0 5269.508 12.035435
4150 16738.438 0 0 5269.5081 12.035426
4200 16738.438 0 0 5269.5083 12.035432
4250 16738.439 0 0 5269.5085 12.035447
4300 16738.439 0 0 5269.5086 12.035463
4350 16738.44 0 0 5269.5087 12.035474
4400 16738.44 0 0 5269.5088 12.035478
4450 16738.44 0 0 5269.5089 12.035474
4500 16738.44 0 0 5269.509 12.035462
4550 16738.441 0 0 5269.5092 12.035449
4600 16738.441 0 0 5269.5093 12.035445
4650 16738.442 0 0 5269.5095 12.035451
4700 16738.442 0 0 5269.5096 12.03546
4750 16738.443 0 0 5269.5097 12.035465
4800 16738.443 0 0 5269.5098 12.035466
4850 16738.443 0 0 5269.51 12.035463
4900 16738.444 0 0 5269.5101 12.035456
4950 16738.444 0 0 5269.5102 12.035447
5000 16738.445 0 0 5269.5104 12.03544
5050 16738.445 0 0 5269.5105 12.035442
5100 16738.446 0 0 5269.5107 12.035455
5150 16738.446 0 0 5269.5108 12.03547
5200 16738.446 0 0 5269.5109 12.035479
5250 16738.447 0 0 5269.511 12.035479
5300 16738.447 0 0 5269.5111 12.03547
5350 16738.447 0 0 5269.5112 12.035454
5400 16738.448 0 0 5269.5113 12.035434
5450 16738.448 0 0 5269.5115 12.03542
5500 16738.449 0 0 5269.5117 12.035422
5550 16738.457 -0.0030919234 0 5269.5111 12.035383
5600 16738.51 -0.021618357 0 5269.5092 12.035106
5650 16738.622 -0.059214788 0 5269.507 12.035694
5700 16395.28 108.06942 0 5269.5463 24.369038
5750 16738.544 -0.033973429 0 5269.5077 12.011261
5800 16738.456 -0.0037013529 0 5269.5102 12.011675
5850 16738.451 0 0 5269.5123 12.011709
5900 16738.451 -0.0002211587 0 5269.5122 12.011687
5950 16738.452 -0.00024253348 0 5269.5124 12.011678
6000 16738.452 0 0 5269.5128 12.011688
6050 16738.453 0 0 5269.513 12.011702
6100 16738.453 0 0 5269.5131 12.011716
6150 16738.454 0 0 5269.5132 12.011725
6200 16738.454 0 0 5269.5133 12.011728
6250 16738.454 0 0 5269.5134 12.011723
6300 16738.455 0 0 5269.5135 12.011712
6350 16738.455 0 0 5269.5137 12.0117
6400 16738.456 0 0 5269.5138 12.011697
6450 16738.456 0 0 5269.514 12.011704
6500 16738.456 0 0 5269.5141 12.011714
6550 16738.457 0 0 5269.5142 12.011719
6600 16738.457 0 0 5269.5143 12.011718
6650 16738.458 0 0 5269.5144 12.011713
6700 16738.458 0 0 5269.5146 12.011705
6750 16738.459 0 0 5269.5147 12.011696
6800 16738.459 0 0 5269.5149 12.01169
6850 16738.46 0 0 5269.515 12.011695
6900 16738.46 0 0 5269.5152 12.01171
6950 16738.46 0 0 5269.5153 12.011726
7000 16738.461 0 0 5269.5154 12.011736
7050 16738.461 0 0 5269.5155 12.011737
7100 16738.461 0 0 5269.5155 12.011728
7150 16738.461 0 0 5269.5156 12.011712
7200 16738.462 0 0 5269.5158 12.011691
7250 16738.463 0 0 5269.516 12.011676
7300 16738.463 0 0 5269.5162 12.011677
7350 16738.464 0 0 5269.5164 12.011693
7400 16738.464 0 0 5269.5165 12.011713
7450 16738.465 0 0 5269.5166 12.011729
7500 16738.465 0 0 5269.5167 12.011736
7550 16738.465 0 0 5269.5168 12.011734
7600 16738.465 0 0 5269.5168 12.011722
7650 16738.466 0 0 5269.517 12.011704
7700 16738.466 0 0 5269.5171 12.011687
7750 16738.467 0 0 5269.5173 12.011681
7800 16738.467 0 0 5269.5175 12.011687
7850 16738.468 0 0 5269.5176 12.0117
7900 16738.468 0 0 5269.5178 12.011712
7950 16738.469 0 0 5269.5179 12.011721
8000 16738.469 0 0 5269.518 12.011724
8050 16738.469 0 0 5269.5181 12.01172
8100 16738.47 0 0 5269.5182 12.011709
8150 16738.47 0 0 5269.5183 12.0117
8200 16738.47 0 0 5269.5185 12.0117
8250 16738.471 0 0 5269.5186 12.011709
8300 16738.471 0 0 5269.5187 12.011719
8350 16738.472 0 0 5269.5189 12.011723
8400 16738.472 0 0 5269.519 12.01172
8450 16738.473 -0.00039690678 0 5269.5189 12.011706
8500 16738.481 -0.0034646809 0 5269.5182 12.011643
8550 16738.483 -0.0045307407 0 5269.5178 12.011621
8600 16738.474 -0.00076532803 0 5269.5189 12.011681
8650 16738.474 0 0 5269.5197 12.011699
8700 16738.475 0 0 5269.5199 12.011715
8750 16738.475 0 0 5269.52 12.011732
8800 16738.475 0 0 5269.52 12.011743
8850 16738.476 0 0 5269.5201 12.011744
8900 16738.476 0 0 5269.5202 12.011735
8950 16738.476 0 0 5269.5203 12.011719
9000 16738.477 0 0 5269.5205 12.011698
9050 16738.477 0 0 5269.5206 12.011683
9100 16738.478 0 0 5269.5208 12.011684
9150 16738.479 0 0 5269.521 12.011701
9200 16738.479 0 0 5269.5212 12.011722
9250 16738.479 0 0 5269.5213 12.011738
9300 16738.48 0 0 5269.5214 12.011746
9350 16738.48 0 0 5269.5214 12.011744
9400 16738.48 0 0 5269.5215 12.011732
9450 16738.48 0 0 5269.5216 12.011715
9500 16738.481 -0.0003765242 0 5269.5216 12.011692
9550 16738.493 -0.0053156153 0 5269.5203 12.011611
9600 16738.549 -0.026814361 0 5269.5163 12.011415
9650 16738.765 -0.1019152 0 5269.5092 12.011013
9700 16735.041 1.0589855 0 5269.4979 12.062708
9750 16738.013 0.13550223 0 5269.5101 11.407246
9800 16738.512 -0.01162033 0 5269.5201 11.394974
9850 16738.489 -0.000672705 0 5269.5237 11.395098
9900 16738.489 -0.00024984511 0 5269.5242 11.395085
9950 16738.49 0 0 5269.5245 11.395077
10000 16738.49 0 0 5269.5246 11.395075
Loop time of 0.097001 on 1 procs for 10000 steps with 81 atoms
Performance: 890712.494 tau/day, 103091.724 timesteps/s
99.6% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0064264 | 0.0064264 | 0.0064264 | 0.0 | 6.63
Bond | 0.0003385 | 0.0003385 | 0.0003385 | 0.0 | 0.35
Neigh | 0.030894 | 0.030894 | 0.030894 | 0.0 | 31.85
Comm | 0.0065732 | 0.0065732 | 0.0065732 | 0.0 | 6.78
Output | 0.0021773 | 0.0021773 | 0.0021773 | 0.0 | 2.24
Modify | 0.046477 | 0.046477 | 0.046477 | 0.0 | 47.91
Other | | 0.004115 | | | 4.24
Nlocal: 81 ave 81 max 81 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 84 ave 84 max 84 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0
Ave special neighs/atom = 0
Neighbor list builds = 998
Dangerous builds = 997
Total wall time: 0:00:00

322
examples/rigid/log.20Mar22.rigid.small.g++.4 Normal file
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@ -0,0 +1,322 @@
LAMMPS (17 Feb 2022)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
# Simple rigid body system
units lj
atom_style bond
pair_style lj/cut 2.5
read_data data.rigid.small
Reading data file ...
orthogonal box = (-12 -12 -12) to (12 12 12)
1 by 2 by 2 MPI processor grid
reading atoms ...
81 atoms
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
0 = max # of 1-2 neighbors
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
1 = max # of special neighbors
special bonds CPU = 0.000 seconds
read_data CPU = 0.001 seconds
velocity all create 100.0 4928459
# unconnected bodies
group clump1 id <> 1 9
9 atoms in group clump1
group clump2 id <> 10 18
9 atoms in group clump2
group clump3 id <> 19 27
9 atoms in group clump3
group clump4 id <> 28 36
9 atoms in group clump4
group clump5 id <> 37 45
9 atoms in group clump5
group clump6 id <> 46 54
9 atoms in group clump6
group clump7 id <> 55 63
9 atoms in group clump7
group clump8 id <> 64 72
9 atoms in group clump8
group clump9 id <> 73 81
9 atoms in group clump9
fix 1 all rigid/small molecule
create bodies CPU = 0.000 seconds
9 rigid bodies with 81 atoms
1.2247449 = max distance from body owner to body atom
neigh_modify exclude group clump1 clump1
neigh_modify exclude group clump2 clump2
neigh_modify exclude group clump3 clump3
neigh_modify exclude group clump4 clump4
neigh_modify exclude group clump5 clump5
neigh_modify exclude group clump6 clump6
neigh_modify exclude group clump7 clump7
neigh_modify exclude group clump8 clump8
neigh_modify exclude group clump9 clump9
thermo 100
#dump 1 all atom 50 dump.rigid
#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 2 pad 5
#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 3 pad 5
timestep 0.0001
thermo 50
run 10000
generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4, bins = 18 18 18
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 8.892 | 8.94 | 9.049 Mbytes
Step Temp E_pair E_mol TotEng Press
0 115.29439 5235.9179 0 5272.2142 -2.7403788
50 14910.685 571.71558 0 5265.82 32.006171
100 16298.442 136.66184 0 5267.653 16.444229
150 16682.606 17.490511 0 5269.4219 14.900344
200 16733.929 1.372872 0 5269.4617 14.569267
250 16738.853 -0.15252816 0 5269.4864 14.496404
300 16738.588 -0.055171335 0 5269.5002 14.496025
350 16738.492 -0.017444677 0 5269.5077 14.496446
400 16738.464 -0.0060102023 0 5269.5104 14.496618
450 16738.455 -0.0012713351 0 5269.5124 14.496701
500 16738.455 -0.00081068621 0 5269.5128 14.496709
550 16738.455 -0.00083203497 0 5269.5129 14.496707
600 16738.455 -0.00058355356 0 5269.5131 14.496709
650 16738.455 -0.00047226704 0 5269.5131 14.496708
700 16738.455 0 0 5269.5136 14.496713
750 16738.455 0 0 5269.5136 14.49671
800 16738.455 0 0 5269.5137 14.496709
850 16738.455 0 0 5269.5137 14.49671
900 16738.456 0 0 5269.5138 14.496713
950 16738.462 -0.0035323872 0 5269.5122 14.496671
1000 16738.586 -0.051135144 0 5269.5036 14.496229
1050 16737.358 0.32995057 0 5269.4981 14.525763
1100 16737.892 0.16210246 0 5269.4984 14.531983
1150 16738.703 -0.089235095 0 5269.5025 14.509899
1200 16738.466 -0.0075446243 0 5269.5096 14.510615
1250 16738.456 0 0 5269.514 14.510704
1300 16738.457 0 0 5269.5141 14.510701
1350 16738.457 0 0 5269.5141 14.510699
1400 16738.457 -0.00044736511 0 5269.5138 14.510693
1450 16738.458 -0.0010971179 0 5269.5134 14.510687
1500 16738.458 -0.00057885428 0 5269.5139 14.510698
1550 16738.457 0 0 5269.5143 14.51071
1600 16738.457 0 0 5269.5144 14.510712
1650 16738.457 0 0 5269.5144 14.510712
1700 16738.458 0 0 5269.5144 14.51071
1750 16738.458 0 0 5269.5145 14.510708
1800 16738.458 0 0 5269.5145 14.510706
1850 16738.458 0 0 5269.5146 14.510705
1900 16738.458 0 0 5269.5146 14.510706
1950 16738.465 -0.0031733615 0 5269.5134 14.510659
2000 16738.491 -0.013255268 0 5269.5117 14.510532
2050 16738.556 -0.0365811 0 5269.5087 14.51029
2100 16738.633 -0.063209659 0 5269.5065 14.510219
2150 16738.607 -0.05601761 0 5269.5055 14.510231
2200 16738.557 -0.038423032 0 5269.5072 14.510404
2250 16738.515 -0.023709918 0 5269.5088 14.510539
2300 16738.489 -0.013249035 0 5269.5111 14.510621
2350 16738.468 -0.0045563719 0 5269.5131 14.510714
2400 16738.46 -0.00052194273 0 5269.5146 14.510771
2450 16738.464 -0.0023259756 0 5269.514 14.510746
2500 16738.468 -0.0051929186 0 5269.5127 14.510731
2550 16738.581 -0.044940117 0 5269.5085 14.510315
2600 16738.427 -7.972281e-05 0 5269.5046 14.510657
2650 16733.017 1.7051479 0 5269.5067 14.596295
2700 16738.761 -0.10614946 0 5269.5038 14.499584
2750 16733.973 1.4038179 0 5269.5064 14.598107
2800 16738.585 -0.046813448 0 5269.5076 14.511073
2850 16738.487 -0.012558719 0 5269.5111 14.510111
2900 16738.465 -0.0026252725 0 5269.514 14.510277
2950 16738.476 -0.0082220764 0 5269.512 14.510223
3000 16738.66 -0.071284779 0 5269.507 14.509758
3050 16715.332 7.2419352 0 5269.476 14.870305
3100 16653.226 26.818761 0 5269.5009 14.496764
3150 16739.351 -0.30690375 0 5269.4886 13.643904
3200 16733.238 1.6025328 0 5269.4737 12.016934
3250 16734.374 1.2554429 0 5269.4841 11.963561
3300 16732.156 1.9585967 0 5269.4893 12.234024
3350 16738.655 -0.079693236 0 5269.497 12.092757
3400 16738.543 -0.042215005 0 5269.4991 12.092809
3450 16738.591 -0.059327511 0 5269.4972 12.092536
3500 16738.759 -0.11761245 0 5269.4918 12.09203
3550 16713.405 7.8460621 0 5269.4737 12.389816
3600 16734.939 1.0821936 0 5269.4891 12.173591
3650 16738.808 -0.13663194 0 5269.4882 12.027009
3700 16738.602 -0.070934368 0 5269.4889 12.025288
3750 16737.731 0.20706558 0 5269.4927 12.061948
3800 16738.578 -0.05582043 0 5269.4965 12.035665
3850 16738.471 -0.016307928 0 5269.5024 12.035302
3900 16738.449 -0.0058182199 0 5269.5059 12.035401
3950 16738.439 -0.0012027325 0 5269.5074 12.035461
4000 16738.436 -0.00020698452 0 5269.5075 12.035469
4050 16738.437 0 0 5269.5078 12.035454
4100 16738.437 0 0 5269.508 12.035435
4150 16738.438 0 0 5269.5081 12.035426
4200 16738.438 0 0 5269.5083 12.035432
4250 16738.439 0 0 5269.5085 12.035447
4300 16738.439 0 0 5269.5086 12.035463
4350 16738.44 0 0 5269.5087 12.035474
4400 16738.44 0 0 5269.5088 12.035478
4450 16738.44 0 0 5269.5089 12.035474
4500 16738.44 0 0 5269.509 12.035462
4550 16738.441 0 0 5269.5092 12.035449
4600 16738.441 0 0 5269.5093 12.035445
4650 16738.442 0 0 5269.5095 12.035451
4700 16738.442 0 0 5269.5096 12.03546
4750 16738.443 0 0 5269.5097 12.035465
4800 16738.443 0 0 5269.5098 12.035466
4850 16738.443 0 0 5269.51 12.035463
4900 16738.444 0 0 5269.5101 12.035456
4950 16738.444 0 0 5269.5102 12.035447
5000 16738.445 0 0 5269.5104 12.03544
5050 16738.445 0 0 5269.5105 12.035442
5100 16738.446 0 0 5269.5107 12.035455
5150 16738.446 0 0 5269.5108 12.03547
5200 16738.446 0 0 5269.5109 12.035479
5250 16738.447 0 0 5269.511 12.035479
5300 16738.447 0 0 5269.5111 12.03547
5350 16738.447 0 0 5269.5112 12.035454
5400 16738.448 0 0 5269.5113 12.035434
5450 16738.448 0 0 5269.5115 12.03542
5500 16738.449 0 0 5269.5117 12.035422
5550 16738.457 -0.0030919234 0 5269.5111 12.035383
5600 16738.51 -0.021618357 0 5269.5092 12.035106
5650 16738.622 -0.059214788 0 5269.507 12.035694
5700 16395.28 108.06942 0 5269.5463 24.369038
5750 16738.544 -0.033973429 0 5269.5077 12.011261
5800 16738.456 -0.0037013529 0 5269.5102 12.011675
5850 16738.451 0 0 5269.5123 12.011709
5900 16738.451 -0.0002211587 0 5269.5122 12.011687
5950 16738.452 -0.00024253349 0 5269.5124 12.011678
6000 16738.452 0 0 5269.5128 12.011688
6050 16738.453 0 0 5269.513 12.011702
6100 16738.453 0 0 5269.5131 12.011716
6150 16738.454 0 0 5269.5132 12.011725
6200 16738.454 0 0 5269.5133 12.011728
6250 16738.454 0 0 5269.5134 12.011723
6300 16738.455 0 0 5269.5135 12.011712
6350 16738.455 0 0 5269.5137 12.0117
6400 16738.456 0 0 5269.5138 12.011697
6450 16738.456 0 0 5269.514 12.011704
6500 16738.456 0 0 5269.5141 12.011714
6550 16738.457 0 0 5269.5142 12.011719
6600 16738.457 0 0 5269.5143 12.011718
6650 16738.458 0 0 5269.5144 12.011713
6700 16738.458 0 0 5269.5146 12.011705
6750 16738.459 0 0 5269.5147 12.011696
6800 16738.459 0 0 5269.5149 12.01169
6850 16738.46 0 0 5269.515 12.011695
6900 16738.46 0 0 5269.5152 12.01171
6950 16738.46 0 0 5269.5153 12.011726
7000 16738.461 0 0 5269.5154 12.011736
7050 16738.461 0 0 5269.5155 12.011737
7100 16738.461 0 0 5269.5155 12.011728
7150 16738.461 0 0 5269.5156 12.011712
7200 16738.462 0 0 5269.5158 12.011691
7250 16738.463 0 0 5269.516 12.011676
7300 16738.463 0 0 5269.5162 12.011677
7350 16738.464 0 0 5269.5164 12.011693
7400 16738.464 0 0 5269.5165 12.011713
7450 16738.465 0 0 5269.5166 12.011729
7500 16738.465 0 0 5269.5167 12.011736
7550 16738.465 0 0 5269.5168 12.011734
7600 16738.465 0 0 5269.5168 12.011722
7650 16738.466 0 0 5269.517 12.011704
7700 16738.466 0 0 5269.5171 12.011687
7750 16738.467 0 0 5269.5173 12.011681
7800 16738.467 0 0 5269.5175 12.011687
7850 16738.468 0 0 5269.5176 12.0117
7900 16738.468 0 0 5269.5178 12.011712
7950 16738.469 0 0 5269.5179 12.011721
8000 16738.469 0 0 5269.518 12.011724
8050 16738.469 0 0 5269.5181 12.01172
8100 16738.47 0 0 5269.5182 12.011709
8150 16738.47 0 0 5269.5183 12.0117
8200 16738.47 0 0 5269.5185 12.0117
8250 16738.471 0 0 5269.5186 12.011709
8300 16738.471 0 0 5269.5187 12.011719
8350 16738.472 0 0 5269.5189 12.011723
8400 16738.472 0 0 5269.519 12.01172
8450 16738.473 -0.00039690665 0 5269.5189 12.011706
8500 16738.481 -0.0034646804 0 5269.5182 12.011643
8550 16738.483 -0.0045307409 0 5269.5178 12.011621
8600 16738.474 -0.00076532812 0 5269.5189 12.011681
8650 16738.474 0 0 5269.5197 12.011699
8700 16738.475 0 0 5269.5199 12.011715
8750 16738.475 0 0 5269.52 12.011732
8800 16738.475 0 0 5269.52 12.011743
8850 16738.476 0 0 5269.5201 12.011744
8900 16738.476 0 0 5269.5202 12.011735
8950 16738.476 0 0 5269.5203 12.011719
9000 16738.477 0 0 5269.5205 12.011698
9050 16738.477 0 0 5269.5206 12.011683
9100 16738.478 0 0 5269.5208 12.011684
9150 16738.479 0 0 5269.521 12.011701
9200 16738.479 0 0 5269.5212 12.011722
9250 16738.479 0 0 5269.5213 12.011738
9300 16738.48 0 0 5269.5214 12.011746
9350 16738.48 0 0 5269.5214 12.011744
9400 16738.48 0 0 5269.5215 12.011732
9450 16738.48 0 0 5269.5216 12.011715
9500 16738.481 -0.00037652435 0 5269.5216 12.011692
9550 16738.493 -0.0053156165 0 5269.5203 12.011611
9600 16738.549 -0.02681437 0 5269.5163 12.011415
9650 16738.765 -0.10191523 0 5269.5092 12.011013
9700 16735.041 1.0589893 0 5269.4979 12.062708
9750 16738.013 0.1355014 0 5269.5101 11.407246
9800 16738.512 -0.011620326 0 5269.5201 11.394974
9850 16738.489 -0.00067270465 0 5269.5237 11.395099
9900 16738.489 -0.00024984533 0 5269.5242 11.395085
9950 16738.49 0 0 5269.5245 11.395077
10000 16738.49 0 0 5269.5246 11.395076
Loop time of 0.115632 on 4 procs for 10000 steps with 81 atoms
Performance: 747196.558 tau/day, 86481.083 timesteps/s
98.7% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0014528 | 0.0020376 | 0.0024938 | 0.9 | 1.76
Bond | 0.00030255 | 0.00030731 | 0.00031718 | 0.0 | 0.27
Neigh | 0.0089963 | 0.0094964 | 0.010494 | 0.6 | 8.21
Comm | 0.035947 | 0.038848 | 0.040951 | 1.0 | 33.60
Output | 0.0022924 | 0.002542 | 0.0032643 | 0.8 | 2.20
Modify | 0.056743 | 0.058255 | 0.059447 | 0.4 | 50.38
Other | | 0.004146 | | | 3.59
Nlocal: 20.25 ave 38 max 3 min
Histogram: 1 0 1 0 0 0 1 0 0 1
Nghost: 27.25 ave 48 max 13 min
Histogram: 1 0 1 1 0 0 0 0 0 1
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0
Ave special neighs/atom = 0
Neighbor list builds = 998
Dangerous builds = 997
Total wall time: 0:00:00

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LAMMPS (17 Feb 2022)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
# Simple rigid body system
units lj
atom_style bond
pair_style lj/cut 2.5
read_data data.rigid.small
Reading data file ...
orthogonal box = (-12 -12 -12) to (12 12 12)
1 by 1 by 1 MPI processor grid
reading atoms ...
81 atoms
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
0 = max # of 1-2 neighbors
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
1 = max # of special neighbors
special bonds CPU = 0.000 seconds
read_data CPU = 0.001 seconds
velocity all create 100.0 4928459
# unconnected bodies
group clump1 id <> 1 9
9 atoms in group clump1
group clump2 id <> 10 18
9 atoms in group clump2
group clump3 id <> 19 27
9 atoms in group clump3
group clump4 id <> 28 36
9 atoms in group clump4
group clump5 id <> 37 45
9 atoms in group clump5
group clump6 id <> 46 54
9 atoms in group clump6
group clump7 id <> 55 63
9 atoms in group clump7
group clump8 id <> 64 72
9 atoms in group clump8
group clump9 id <> 73 81
9 atoms in group clump9
fix 1 all rigid/small molecule infile bodyinfo.dat
create bodies CPU = 0.000 seconds
9 rigid bodies with 81 atoms
1.2247449 = max distance from body owner to body atom
neigh_modify exclude group clump1 clump1
neigh_modify exclude group clump2 clump2
neigh_modify exclude group clump3 clump3
neigh_modify exclude group clump4 clump4
neigh_modify exclude group clump5 clump5
neigh_modify exclude group clump6 clump6
neigh_modify exclude group clump7 clump7
neigh_modify exclude group clump8 clump8
neigh_modify exclude group clump9 clump9
thermo 100
#dump 1 all atom 50 dump.rigid
#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 2 pad 5
#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 3 pad 5
timestep 0.0001
thermo 50
run 10000
generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4, bins = 18 18 18
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d
bin: standard
Reading rigid body data for 4 bodies from file bodyinfo.dat
Per MPI rank memory allocation (min/avg/max) = 9.034 | 9.034 | 9.034 Mbytes
Step Temp E_pair E_mol TotEng Press
0 115.29439 5235.9179 0 5272.2142 -2.7403788
50 14910.685 571.71558 0 5265.82 32.006171
100 16298.442 136.66184 0 5267.653 16.444229
150 16682.606 17.490511 0 5269.4219 14.900344
200 16733.929 1.372872 0 5269.4617 14.569267
250 16738.853 -0.15252816 0 5269.4864 14.496404
300 16738.588 -0.055171335 0 5269.5002 14.496025
350 16738.492 -0.017444677 0 5269.5077 14.496446
400 16738.464 -0.0060102023 0 5269.5104 14.496618
450 16738.455 -0.0012713351 0 5269.5124 14.496701
500 16738.455 -0.00081068621 0 5269.5128 14.496709
550 16738.455 -0.00083203497 0 5269.5129 14.496707
600 16738.455 -0.00058355356 0 5269.5131 14.496709
650 16738.455 -0.00047226704 0 5269.5131 14.496708
700 16738.455 0 0 5269.5136 14.496713
750 16738.455 0 0 5269.5136 14.49671
800 16738.455 0 0 5269.5137 14.496709
850 16738.455 0 0 5269.5137 14.49671
900 16738.456 0 0 5269.5138 14.496713
950 16738.462 -0.0035323872 0 5269.5122 14.496671
1000 16738.586 -0.051135144 0 5269.5036 14.496229
1050 16737.358 0.32995057 0 5269.4981 14.525763
1100 16737.892 0.16210246 0 5269.4984 14.531983
1150 16738.703 -0.089235095 0 5269.5025 14.509899
1200 16738.466 -0.0075446243 0 5269.5096 14.510615
1250 16738.456 0 0 5269.514 14.510704
1300 16738.457 0 0 5269.5141 14.510701
1350 16738.457 0 0 5269.5141 14.510699
1400 16738.457 -0.00044736511 0 5269.5138 14.510693
1450 16738.458 -0.0010971179 0 5269.5134 14.510687
1500 16738.458 -0.00057885428 0 5269.5139 14.510698
1550 16738.457 0 0 5269.5143 14.51071
1600 16738.457 0 0 5269.5144 14.510712
1650 16738.457 0 0 5269.5144 14.510712
1700 16738.458 0 0 5269.5144 14.51071
1750 16738.458 0 0 5269.5145 14.510708
1800 16738.458 0 0 5269.5145 14.510706
1850 16738.458 0 0 5269.5146 14.510705
1900 16738.458 0 0 5269.5146 14.510706
1950 16738.465 -0.0031733615 0 5269.5134 14.510659
2000 16738.491 -0.013255268 0 5269.5117 14.510532
2050 16738.556 -0.0365811 0 5269.5087 14.51029
2100 16738.633 -0.063209659 0 5269.5065 14.510219
2150 16738.607 -0.05601761 0 5269.5055 14.510231
2200 16738.557 -0.038423032 0 5269.5072 14.510404
2250 16738.515 -0.023709918 0 5269.5088 14.510539
2300 16738.489 -0.013249035 0 5269.5111 14.510621
2350 16738.468 -0.0045563719 0 5269.5131 14.510714
2400 16738.46 -0.00052194273 0 5269.5146 14.510771
2450 16738.464 -0.0023259756 0 5269.514 14.510746
2500 16738.468 -0.0051929186 0 5269.5127 14.510731
2550 16738.581 -0.044940117 0 5269.5085 14.510315
2600 16738.427 -7.9722817e-05 0 5269.5046 14.510657
2650 16733.017 1.7051479 0 5269.5067 14.596295
2700 16738.761 -0.10614946 0 5269.5038 14.499584
2750 16733.973 1.4038179 0 5269.5064 14.598107
2800 16738.585 -0.046813448 0 5269.5076 14.511073
2850 16738.487 -0.012558719 0 5269.5111 14.510111
2900 16738.465 -0.0026252725 0 5269.514 14.510277
2950 16738.476 -0.0082220764 0 5269.512 14.510223
3000 16738.66 -0.071284779 0 5269.507 14.509758
3050 16715.332 7.2419352 0 5269.476 14.870305
3100 16653.226 26.818761 0 5269.5009 14.496764
3150 16739.351 -0.30690375 0 5269.4886 13.643904
3200 16733.238 1.6025328 0 5269.4737 12.016934
3250 16734.374 1.2554429 0 5269.4841 11.963561
3300 16732.156 1.9585967 0 5269.4893 12.234024
3350 16738.655 -0.079693236 0 5269.497 12.092757
3400 16738.543 -0.042215005 0 5269.4991 12.092809
3450 16738.591 -0.05932751 0 5269.4972 12.092536
3500 16738.759 -0.11761245 0 5269.4918 12.09203
3550 16713.405 7.8460621 0 5269.4737 12.389816
3600 16734.939 1.0821936 0 5269.4891 12.173591
3650 16738.808 -0.13663194 0 5269.4882 12.027009
3700 16738.602 -0.070934369 0 5269.4889 12.025288
3750 16737.731 0.20706559 0 5269.4927 12.061948
3800 16738.578 -0.05582043 0 5269.4965 12.035665
3850 16738.471 -0.016307928 0 5269.5024 12.035302
3900 16738.449 -0.0058182199 0 5269.5059 12.035401
3950 16738.439 -0.0012027325 0 5269.5074 12.035461
4000 16738.436 -0.00020698452 0 5269.5075 12.035469
4050 16738.437 0 0 5269.5078 12.035454
4100 16738.437 0 0 5269.508 12.035435
4150 16738.438 0 0 5269.5081 12.035426
4200 16738.438 0 0 5269.5083 12.035432
4250 16738.439 0 0 5269.5085 12.035447
4300 16738.439 0 0 5269.5086 12.035463
4350 16738.44 0 0 5269.5087 12.035474
4400 16738.44 0 0 5269.5088 12.035478
4450 16738.44 0 0 5269.5089 12.035474
4500 16738.44 0 0 5269.509 12.035462
4550 16738.441 0 0 5269.5092 12.035449
4600 16738.441 0 0 5269.5093 12.035445
4650 16738.442 0 0 5269.5095 12.035451
4700 16738.442 0 0 5269.5096 12.03546
4750 16738.443 0 0 5269.5097 12.035465
4800 16738.443 0 0 5269.5098 12.035466
4850 16738.443 0 0 5269.51 12.035463
4900 16738.444 0 0 5269.5101 12.035456
4950 16738.444 0 0 5269.5102 12.035447
5000 16738.445 0 0 5269.5104 12.03544
5050 16738.445 0 0 5269.5105 12.035442
5100 16738.446 0 0 5269.5107 12.035455
5150 16738.446 0 0 5269.5108 12.03547
5200 16738.446 0 0 5269.5109 12.035479
5250 16738.447 0 0 5269.511 12.035479
5300 16738.447 0 0 5269.5111 12.03547
5350 16738.447 0 0 5269.5112 12.035454
5400 16738.448 0 0 5269.5113 12.035434
5450 16738.448 0 0 5269.5115 12.03542
5500 16738.449 0 0 5269.5117 12.035422
5550 16738.457 -0.0030919234 0 5269.5111 12.035383
5600 16738.51 -0.021618357 0 5269.5092 12.035106
5650 16738.622 -0.059214788 0 5269.507 12.035694
5700 16395.28 108.06942 0 5269.5463 24.369038
5750 16738.544 -0.033973429 0 5269.5077 12.011261
5800 16738.456 -0.0037013529 0 5269.5102 12.011675
5850 16738.451 0 0 5269.5123 12.011709
5900 16738.451 -0.0002211587 0 5269.5122 12.011687
5950 16738.452 -0.00024253349 0 5269.5124 12.011678
6000 16738.452 0 0 5269.5128 12.011688
6050 16738.453 0 0 5269.513 12.011702
6100 16738.453 0 0 5269.5131 12.011716
6150 16738.454 0 0 5269.5132 12.011725
6200 16738.454 0 0 5269.5133 12.011728
6250 16738.454 0 0 5269.5134 12.011723
6300 16738.455 0 0 5269.5135 12.011712
6350 16738.455 0 0 5269.5137 12.0117
6400 16738.456 0 0 5269.5138 12.011697
6450 16738.456 0 0 5269.514 12.011704
6500 16738.456 0 0 5269.5141 12.011714
6550 16738.457 0 0 5269.5142 12.011719
6600 16738.457 0 0 5269.5143 12.011718
6650 16738.458 0 0 5269.5144 12.011713
6700 16738.458 0 0 5269.5146 12.011705
6750 16738.459 0 0 5269.5147 12.011696
6800 16738.459 0 0 5269.5149 12.01169
6850 16738.46 0 0 5269.515 12.011695
6900 16738.46 0 0 5269.5152 12.01171
6950 16738.46 0 0 5269.5153 12.011726
7000 16738.461 0 0 5269.5154 12.011736
7050 16738.461 0 0 5269.5155 12.011737
7100 16738.461 0 0 5269.5155 12.011728
7150 16738.461 0 0 5269.5156 12.011712
7200 16738.462 0 0 5269.5158 12.011691
7250 16738.463 0 0 5269.516 12.011676
7300 16738.463 0 0 5269.5162 12.011677
7350 16738.464 0 0 5269.5164 12.011693
7400 16738.464 0 0 5269.5165 12.011713
7450 16738.465 0 0 5269.5166 12.011729
7500 16738.465 0 0 5269.5167 12.011736
7550 16738.465 0 0 5269.5168 12.011734
7600 16738.465 0 0 5269.5168 12.011722
7650 16738.466 0 0 5269.517 12.011704
7700 16738.466 0 0 5269.5171 12.011687
7750 16738.467 0 0 5269.5173 12.011681
7800 16738.467 0 0 5269.5175 12.011687
7850 16738.468 0 0 5269.5176 12.0117
7900 16738.468 0 0 5269.5178 12.011712
7950 16738.469 0 0 5269.5179 12.011721
8000 16738.469 0 0 5269.518 12.011724
8050 16738.469 0 0 5269.5181 12.01172
8100 16738.47 0 0 5269.5182 12.011709
8150 16738.47 0 0 5269.5183 12.0117
8200 16738.47 0 0 5269.5185 12.0117
8250 16738.471 0 0 5269.5186 12.011709
8300 16738.471 0 0 5269.5187 12.011719
8350 16738.472 0 0 5269.5189 12.011723
8400 16738.472 0 0 5269.519 12.01172
8450 16738.473 -0.00039690668 0 5269.5189 12.011706
8500 16738.481 -0.0034646805 0 5269.5182 12.011643
8550 16738.483 -0.0045307409 0 5269.5178 12.011621
8600 16738.474 -0.0007653281 0 5269.5189 12.011681
8650 16738.474 0 0 5269.5197 12.011699
8700 16738.475 0 0 5269.5199 12.011715
8750 16738.475 0 0 5269.52 12.011732
8800 16738.475 0 0 5269.52 12.011743
8850 16738.476 0 0 5269.5201 12.011744
8900 16738.476 0 0 5269.5202 12.011735
8950 16738.476 0 0 5269.5203 12.011719
9000 16738.477 0 0 5269.5205 12.011698
9050 16738.477 0 0 5269.5206 12.011683
9100 16738.478 0 0 5269.5208 12.011684
9150 16738.479 0 0 5269.521 12.011701
9200 16738.479 0 0 5269.5212 12.011722
9250 16738.479 0 0 5269.5213 12.011738
9300 16738.48 0 0 5269.5214 12.011746
9350 16738.48 0 0 5269.5214 12.011744
9400 16738.48 0 0 5269.5215 12.011732
9450 16738.48 0 0 5269.5216 12.011715
9500 16738.481 -0.00037652432 0 5269.5216 12.011692
9550 16738.493 -0.0053156162 0 5269.5203 12.011611
9600 16738.549 -0.026814368 0 5269.5163 12.011415
9650 16738.765 -0.10191523 0 5269.5092 12.011013
9700 16735.041 1.0589884 0 5269.4979 12.062708
9750 16738.013 0.13550153 0 5269.5101 11.407246
9800 16738.512 -0.011620327 0 5269.5201 11.394974
9850 16738.489 -0.00067270481 0 5269.5237 11.395098
9900 16738.489 -0.00024984532 0 5269.5242 11.395085
9950 16738.49 0 0 5269.5245 11.395077
10000 16738.49 0 0 5269.5246 11.395075
Loop time of 0.0973982 on 1 procs for 10000 steps with 81 atoms
Performance: 887079.894 tau/day, 102671.284 timesteps/s
99.5% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0065928 | 0.0065928 | 0.0065928 | 0.0 | 6.77
Bond | 0.00033457 | 0.00033457 | 0.00033457 | 0.0 | 0.34
Neigh | 0.031245 | 0.031245 | 0.031245 | 0.0 | 32.08
Comm | 0.0065444 | 0.0065444 | 0.0065444 | 0.0 | 6.72
Output | 0.0024004 | 0.0024004 | 0.0024004 | 0.0 | 2.46
Modify | 0.045966 | 0.045966 | 0.045966 | 0.0 | 47.19
Other | | 0.004315 | | | 4.43
Nlocal: 81 ave 81 max 81 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 84 ave 84 max 84 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0
Ave special neighs/atom = 0
Neighbor list builds = 998
Dangerous builds = 997
Total wall time: 0:00:00

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LAMMPS (17 Feb 2022)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
# Simple rigid body system
units lj
atom_style bond
pair_style lj/cut 2.5
read_data data.rigid.small
Reading data file ...
orthogonal box = (-12 -12 -12) to (12 12 12)
1 by 2 by 2 MPI processor grid
reading atoms ...
81 atoms
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
0 = max # of 1-2 neighbors
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
1 = max # of special neighbors
special bonds CPU = 0.000 seconds
read_data CPU = 0.001 seconds
velocity all create 100.0 4928459
# unconnected bodies
group clump1 id <> 1 9
9 atoms in group clump1
group clump2 id <> 10 18
9 atoms in group clump2
group clump3 id <> 19 27
9 atoms in group clump3
group clump4 id <> 28 36
9 atoms in group clump4
group clump5 id <> 37 45
9 atoms in group clump5
group clump6 id <> 46 54
9 atoms in group clump6
group clump7 id <> 55 63
9 atoms in group clump7
group clump8 id <> 64 72
9 atoms in group clump8
group clump9 id <> 73 81
9 atoms in group clump9
fix 1 all rigid/small molecule infile bodyinfo.dat
create bodies CPU = 0.000 seconds
9 rigid bodies with 81 atoms
1.2247449 = max distance from body owner to body atom
neigh_modify exclude group clump1 clump1
neigh_modify exclude group clump2 clump2
neigh_modify exclude group clump3 clump3
neigh_modify exclude group clump4 clump4
neigh_modify exclude group clump5 clump5
neigh_modify exclude group clump6 clump6
neigh_modify exclude group clump7 clump7
neigh_modify exclude group clump8 clump8
neigh_modify exclude group clump9 clump9
thermo 100
#dump 1 all atom 50 dump.rigid
#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 2 pad 5
#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 3 pad 5
timestep 0.0001
thermo 50
run 10000
generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4, bins = 18 18 18
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d
bin: standard
Reading rigid body data for 4 bodies from file bodyinfo.dat
Per MPI rank memory allocation (min/avg/max) = 8.892 | 8.94 | 9.049 Mbytes
Step Temp E_pair E_mol TotEng Press
0 115.29439 5235.9179 0 5272.2142 -2.7403788
50 14910.685 571.71558 0 5265.82 32.006171
100 16298.442 136.66184 0 5267.653 16.444229
150 16682.606 17.490511 0 5269.4219 14.900344
200 16733.929 1.372872 0 5269.4617 14.569267
250 16738.853 -0.15252816 0 5269.4864 14.496404
300 16738.588 -0.055171335 0 5269.5002 14.496025
350 16738.492 -0.017444677 0 5269.5077 14.496446
400 16738.464 -0.0060102023 0 5269.5104 14.496618
450 16738.455 -0.0012713351 0 5269.5124 14.496701
500 16738.455 -0.00081068621 0 5269.5128 14.496709
550 16738.455 -0.00083203497 0 5269.5129 14.496707
600 16738.455 -0.00058355356 0 5269.5131 14.496709
650 16738.455 -0.00047226704 0 5269.5131 14.496708
700 16738.455 0 0 5269.5136 14.496713
750 16738.455 0 0 5269.5136 14.49671
800 16738.455 0 0 5269.5137 14.496709
850 16738.455 0 0 5269.5137 14.49671
900 16738.456 0 0 5269.5138 14.496713
950 16738.462 -0.0035323872 0 5269.5122 14.496671
1000 16738.586 -0.051135144 0 5269.5036 14.496229
1050 16737.358 0.32995057 0 5269.4981 14.525763
1100 16737.892 0.16210246 0 5269.4984 14.531983
1150 16738.703 -0.089235095 0 5269.5025 14.509899
1200 16738.466 -0.0075446243 0 5269.5096 14.510615
1250 16738.456 0 0 5269.514 14.510704
1300 16738.457 0 0 5269.5141 14.510701
1350 16738.457 0 0 5269.5141 14.510699
1400 16738.457 -0.00044736511 0 5269.5138 14.510693
1450 16738.458 -0.0010971179 0 5269.5134 14.510687
1500 16738.458 -0.00057885428 0 5269.5139 14.510698
1550 16738.457 0 0 5269.5143 14.51071
1600 16738.457 0 0 5269.5144 14.510712
1650 16738.457 0 0 5269.5144 14.510712
1700 16738.458 0 0 5269.5144 14.51071
1750 16738.458 0 0 5269.5145 14.510708
1800 16738.458 0 0 5269.5145 14.510706
1850 16738.458 0 0 5269.5146 14.510705
1900 16738.458 0 0 5269.5146 14.510706
1950 16738.465 -0.0031733615 0 5269.5134 14.510659
2000 16738.491 -0.013255268 0 5269.5117 14.510532
2050 16738.556 -0.0365811 0 5269.5087 14.51029
2100 16738.633 -0.063209659 0 5269.5065 14.510219
2150 16738.607 -0.05601761 0 5269.5055 14.510231
2200 16738.557 -0.038423032 0 5269.5072 14.510404
2250 16738.515 -0.023709918 0 5269.5088 14.510539
2300 16738.489 -0.013249035 0 5269.5111 14.510621
2350 16738.468 -0.0045563719 0 5269.5131 14.510714
2400 16738.46 -0.00052194273 0 5269.5146 14.510771
2450 16738.464 -0.0023259756 0 5269.514 14.510746
2500 16738.468 -0.0051929186 0 5269.5127 14.510731
2550 16738.581 -0.044940117 0 5269.5085 14.510315
2600 16738.427 -7.9722791e-05 0 5269.5046 14.510657
2650 16733.017 1.7051479 0 5269.5067 14.596295
2700 16738.761 -0.10614946 0 5269.5038 14.499584
2750 16733.973 1.4038179 0 5269.5064 14.598107
2800 16738.585 -0.046813448 0 5269.5076 14.511073
2850 16738.487 -0.012558719 0 5269.5111 14.510111
2900 16738.465 -0.0026252725 0 5269.514 14.510277
2950 16738.476 -0.0082220764 0 5269.512 14.510223
3000 16738.66 -0.071284779 0 5269.507 14.509758
3050 16715.332 7.2419352 0 5269.476 14.870305
3100 16653.226 26.818761 0 5269.5009 14.496764
3150 16739.351 -0.30690375 0 5269.4886 13.643904
3200 16733.238 1.6025328 0 5269.4737 12.016934
3250 16734.374 1.2554429 0 5269.4841 11.963561
3300 16732.156 1.9585966 0 5269.4893 12.234024
3350 16738.655 -0.079693236 0 5269.497 12.092757
3400 16738.543 -0.042215005 0 5269.4991 12.092809
3450 16738.591 -0.05932751 0 5269.4972 12.092536
3500 16738.759 -0.11761245 0 5269.4918 12.09203
3550 16713.405 7.8460622 0 5269.4737 12.389816
3600 16734.939 1.0821936 0 5269.4891 12.173591
3650 16738.808 -0.13663193 0 5269.4882 12.027009
3700 16738.602 -0.070934369 0 5269.4889 12.025288
3750 16737.731 0.20706559 0 5269.4927 12.061948
3800 16738.578 -0.05582043 0 5269.4965 12.035665
3850 16738.471 -0.016307928 0 5269.5024 12.035302
3900 16738.449 -0.0058182199 0 5269.5059 12.035401
3950 16738.439 -0.0012027325 0 5269.5074 12.035461
4000 16738.436 -0.00020698452 0 5269.5075 12.035469
4050 16738.437 0 0 5269.5078 12.035454
4100 16738.437 0 0 5269.508 12.035435
4150 16738.438 0 0 5269.5081 12.035426
4200 16738.438 0 0 5269.5083 12.035432
4250 16738.439 0 0 5269.5085 12.035447
4300 16738.439 0 0 5269.5086 12.035463
4350 16738.44 0 0 5269.5087 12.035474
4400 16738.44 0 0 5269.5088 12.035478
4450 16738.44 0 0 5269.5089 12.035474
4500 16738.44 0 0 5269.509 12.035462
4550 16738.441 0 0 5269.5092 12.035449
4600 16738.441 0 0 5269.5093 12.035445
4650 16738.442 0 0 5269.5095 12.035451
4700 16738.442 0 0 5269.5096 12.03546
4750 16738.443 0 0 5269.5097 12.035465
4800 16738.443 0 0 5269.5098 12.035466
4850 16738.443 0 0 5269.51 12.035463
4900 16738.444 0 0 5269.5101 12.035456
4950 16738.444 0 0 5269.5102 12.035447
5000 16738.445 0 0 5269.5104 12.03544
5050 16738.445 0 0 5269.5105 12.035442
5100 16738.446 0 0 5269.5107 12.035455
5150 16738.446 0 0 5269.5108 12.03547
5200 16738.446 0 0 5269.5109 12.035479
5250 16738.447 0 0 5269.511 12.035479
5300 16738.447 0 0 5269.5111 12.03547
5350 16738.447 0 0 5269.5112 12.035454
5400 16738.448 0 0 5269.5113 12.035434
5450 16738.448 0 0 5269.5115 12.03542
5500 16738.449 0 0 5269.5117 12.035422
5550 16738.457 -0.0030919234 0 5269.5111 12.035383
5600 16738.51 -0.021618357 0 5269.5092 12.035106
5650 16738.622 -0.059214788 0 5269.507 12.035694
5700 16395.28 108.06942 0 5269.5463 24.369038
5750 16738.544 -0.033973429 0 5269.5077 12.011261
5800 16738.456 -0.0037013529 0 5269.5102 12.011675
5850 16738.451 0 0 5269.5123 12.011709
5900 16738.451 -0.0002211587 0 5269.5122 12.011687
5950 16738.452 -0.00024253349 0 5269.5124 12.011678
6000 16738.452 0 0 5269.5128 12.011688
6050 16738.453 0 0 5269.513 12.011702
6100 16738.453 0 0 5269.5131 12.011716
6150 16738.454 0 0 5269.5132 12.011725
6200 16738.454 0 0 5269.5133 12.011728
6250 16738.454 0 0 5269.5134 12.011723
6300 16738.455 0 0 5269.5135 12.011712
6350 16738.455 0 0 5269.5137 12.0117
6400 16738.456 0 0 5269.5138 12.011697
6450 16738.456 0 0 5269.514 12.011704
6500 16738.456 0 0 5269.5141 12.011714
6550 16738.457 0 0 5269.5142 12.011719
6600 16738.457 0 0 5269.5143 12.011718
6650 16738.458 0 0 5269.5144 12.011713
6700 16738.458 0 0 5269.5146 12.011705
6750 16738.459 0 0 5269.5147 12.011696
6800 16738.459 0 0 5269.5149 12.01169
6850 16738.46 0 0 5269.515 12.011695
6900 16738.46 0 0 5269.5152 12.01171
6950 16738.46 0 0 5269.5153 12.011726
7000 16738.461 0 0 5269.5154 12.011736
7050 16738.461 0 0 5269.5155 12.011737
7100 16738.461 0 0 5269.5155 12.011728
7150 16738.461 0 0 5269.5156 12.011712
7200 16738.462 0 0 5269.5158 12.011691
7250 16738.463 0 0 5269.516 12.011676
7300 16738.463 0 0 5269.5162 12.011677
7350 16738.464 0 0 5269.5164 12.011693
7400 16738.464 0 0 5269.5165 12.011713
7450 16738.465 0 0 5269.5166 12.011729
7500 16738.465 0 0 5269.5167 12.011736
7550 16738.465 0 0 5269.5168 12.011734
7600 16738.465 0 0 5269.5168 12.011722
7650 16738.466 0 0 5269.517 12.011704
7700 16738.466 0 0 5269.5171 12.011687
7750 16738.467 0 0 5269.5173 12.011681
7800 16738.467 0 0 5269.5175 12.011687
7850 16738.468 0 0 5269.5176 12.0117
7900 16738.468 0 0 5269.5178 12.011712
7950 16738.469 0 0 5269.5179 12.011721
8000 16738.469 0 0 5269.518 12.011724
8050 16738.469 0 0 5269.5181 12.01172
8100 16738.47 0 0 5269.5182 12.011709
8150 16738.47 0 0 5269.5183 12.0117
8200 16738.47 0 0 5269.5185 12.0117
8250 16738.471 0 0 5269.5186 12.011709
8300 16738.471 0 0 5269.5187 12.011719
8350 16738.472 0 0 5269.5189 12.011723
8400 16738.472 0 0 5269.519 12.01172
8450 16738.473 -0.00039690669 0 5269.5189 12.011706
8500 16738.481 -0.0034646806 0 5269.5182 12.011643
8550 16738.483 -0.0045307409 0 5269.5178 12.011621
8600 16738.474 -0.00076532809 0 5269.5189 12.011681
8650 16738.474 0 0 5269.5197 12.011699
8700 16738.475 0 0 5269.5199 12.011715
8750 16738.475 0 0 5269.52 12.011732
8800 16738.475 0 0 5269.52 12.011743
8850 16738.476 0 0 5269.5201 12.011744
8900 16738.476 0 0 5269.5202 12.011735
8950 16738.476 0 0 5269.5203 12.011719
9000 16738.477 0 0 5269.5205 12.011698
9050 16738.477 0 0 5269.5206 12.011683
9100 16738.478 0 0 5269.5208 12.011684
9150 16738.479 0 0 5269.521 12.011701
9200 16738.479 0 0 5269.5212 12.011722
9250 16738.479 0 0 5269.5213 12.011738
9300 16738.48 0 0 5269.5214 12.011746
9350 16738.48 0 0 5269.5214 12.011744
9400 16738.48 0 0 5269.5215 12.011732
9450 16738.48 0 0 5269.5216 12.011715
9500 16738.481 -0.0003765243 0 5269.5216 12.011692
9550 16738.493 -0.0053156164 0 5269.5203 12.011611
9600 16738.549 -0.026814368 0 5269.5163 12.011415
9650 16738.765 -0.10191523 0 5269.5092 12.011013
9700 16735.041 1.0589884 0 5269.4979 12.062708
9750 16738.013 0.13550185 0 5269.5101 11.407246
9800 16738.512 -0.011620326 0 5269.5201 11.394974
9850 16738.489 -0.00067270434 0 5269.5237 11.395099
9900 16738.489 -0.00024984508 0 5269.5242 11.395085
9950 16738.49 0 0 5269.5245 11.395077
10000 16738.49 0 0 5269.5246 11.395076
Loop time of 0.135757 on 4 procs for 10000 steps with 81 atoms
Performance: 636433.251 tau/day, 73661.256 timesteps/s
98.4% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0020781 | 0.0024716 | 0.0032187 | 0.9 | 1.82
Bond | 0.00029013 | 0.000332 | 0.00037076 | 0.0 | 0.24
Neigh | 0.0087772 | 0.011705 | 0.014134 | 2.3 | 8.62
Comm | 0.042702 | 0.045012 | 0.048023 | 1.1 | 33.16
Output | 0.0027373 | 0.0030292 | 0.0036178 | 0.6 | 2.23
Modify | 0.067437 | 0.068617 | 0.069634 | 0.3 | 50.54
Other | | 0.004589 | | | 3.38
Nlocal: 20.25 ave 38 max 3 min
Histogram: 1 0 1 0 0 0 1 0 0 1
Nghost: 27.25 ave 48 max 13 min
Histogram: 1 0 1 1 0 0 0 0 0 1
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0
Ave special neighs/atom = 0
Neighbor list builds = 998
Dangerous builds = 997
Total wall time: 0:00:00

341
examples/rigid/log.25Mar24.rigid.atomfile.g++.1
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@ -1,341 +0,0 @@
LAMMPS (7 Feb 2024 - Development - patch_7Feb2024_update1-306-gf3391199e7-modified)
using 1 OpenMP thread(s) per MPI task
# Simple rigid body system
units lj
atom_style atomic
atom_modify map array
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 = 0.001 seconds
velocity all create 100.0 4928459
# unconnected bodies
group clump1 id <> 1 9
9 atoms in group clump1
group clump2 id <> 10 18
9 atoms in group clump2
group clump3 id <> 19 27
9 atoms in group clump3
group clump4 id <> 28 36
9 atoms in group clump4
group clump5 id <> 37 45
9 atoms in group clump5
group clump6 id <> 46 54
9 atoms in group clump6
group clump7 id <> 55 63
9 atoms in group clump7
group clump8 id <> 64 72
9 atoms in group clump8
group clump9 id <> 73 81
9 atoms in group clump9
variable bodies atomfile bodies.txt
fix 1 all rigid custom v_bodies
9 rigid bodies with 81 atoms
# 1 chain of connected bodies
#group clump1 id <> 1 9
#group clump2 id <> 9 18
#group clump3 id <> 18 27
#group clump4 id <> 27 36
#group clump5 id <> 36 45
#group clump6 id <> 45 54
#group clump7 id <> 54 63
#group clump8 id <> 63 72
#group clump9 id <> 72 81
#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9
# 2 chains of connected bodies
#group clump1 id <> 1 9
#group clump2 id <> 9 18
#group clump3 id <> 18 27
#group clump4 id <> 27 36
#group clump5 id <> 37 45
#group clump6 id <> 45 54
#group clump7 id <> 54 63
#group clump8 id <> 63 72
#group clump9 id <> 72 81
#fix 1 all poems group clump1 clump2 clump3 clump4
#fix 2 all poems group clump5 clump6 clump7 clump8 clump9
neigh_modify exclude group clump1 clump1
neigh_modify exclude group clump2 clump2
neigh_modify exclude group clump3 clump3
neigh_modify exclude group clump4 clump4
neigh_modify exclude group clump5 clump5
neigh_modify exclude group clump6 clump6
neigh_modify exclude group clump7 clump7
neigh_modify exclude group clump8 clump8
neigh_modify exclude group clump9 clump9
thermo 100
#dump 1 all atom 50 dump.rigid
#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 2 pad 5
#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 3 pad 5
timestep 0.0001
thermo 50
run 10000
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4, bins = 18 18 18
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 4.483 | 4.483 | 4.483 Mbytes
Step Temp E_pair E_mol TotEng Press
0 115.29439 5235.9179 0 5272.2142 -2.7403788
50 14910.685 571.71558 0 5265.82 32.006171
100 16298.442 136.66184 0 5267.653 16.444229
150 16682.606 17.490511 0 5269.4219 14.900344
200 16733.929 1.372872 0 5269.4617 14.569267
250 16738.853 -0.15252816 0 5269.4864 14.496404
300 16738.588 -0.055171335 0 5269.5002 14.496025
350 16738.492 -0.017444677 0 5269.5077 14.496446
400 16738.464 -0.0060102023 0 5269.5104 14.496618
450 16738.455 -0.0012713351 0 5269.5124 14.496701
500 16738.455 -0.00081068621 0 5269.5128 14.496709
550 16738.455 -0.00083203497 0 5269.5129 14.496707
600 16738.455 -0.00058355356 0 5269.5131 14.496709
650 16738.455 -0.00047226704 0 5269.5131 14.496708
700 16738.455 0 0 5269.5136 14.496713
750 16738.455 0 0 5269.5136 14.49671
800 16738.455 0 0 5269.5137 14.496709
850 16738.455 0 0 5269.5137 14.49671
900 16738.456 0 0 5269.5138 14.496713
950 16738.462 -0.0035323872 0 5269.5122 14.496671
1000 16738.586 -0.051135144 0 5269.5036 14.496229
1050 16737.358 0.32995057 0 5269.4981 14.525763
1100 16737.892 0.16210246 0 5269.4984 14.531983
1150 16738.703 -0.089235095 0 5269.5025 14.509899
1200 16738.466 -0.0075446243 0 5269.5096 14.510615
1250 16738.456 0 0 5269.514 14.510704
1300 16738.457 0 0 5269.5141 14.510701
1350 16738.457 0 0 5269.5141 14.510699
1400 16738.457 -0.00044736511 0 5269.5138 14.510693
1450 16738.458 -0.0010971179 0 5269.5134 14.510687
1500 16738.458 -0.00057885428 0 5269.5139 14.510698
1550 16738.457 0 0 5269.5143 14.51071
1600 16738.457 0 0 5269.5144 14.510712
1650 16738.457 0 0 5269.5144 14.510712
1700 16738.458 0 0 5269.5144 14.51071
1750 16738.458 0 0 5269.5145 14.510708
1800 16738.458 0 0 5269.5145 14.510706
1850 16738.458 0 0 5269.5146 14.510705
1900 16738.458 0 0 5269.5146 14.510706
1950 16738.465 -0.0031733615 0 5269.5134 14.510659
2000 16738.491 -0.013255268 0 5269.5117 14.510532
2050 16738.556 -0.0365811 0 5269.5087 14.51029
2100 16738.633 -0.063209659 0 5269.5065 14.510219
2150 16738.607 -0.05601761 0 5269.5055 14.510231
2200 16738.557 -0.038423032 0 5269.5072 14.510404
2250 16738.515 -0.023709918 0 5269.5088 14.510539
2300 16738.489 -0.013249035 0 5269.5111 14.510621
2350 16738.468 -0.0045563719 0 5269.5131 14.510714
2400 16738.46 -0.00052194273 0 5269.5146 14.510771
2450 16738.464 -0.0023259756 0 5269.514 14.510746
2500 16738.468 -0.0051929186 0 5269.5127 14.510731
2550 16738.581 -0.044940117 0 5269.5085 14.510315
2600 16738.427 -7.9722875e-05 0 5269.5046 14.510657
2650 16733.017 1.705148 0 5269.5067 14.596295
2700 16738.761 -0.10614946 0 5269.5038 14.499584
2750 16733.973 1.4038179 0 5269.5064 14.598107
2800 16738.585 -0.046813448 0 5269.5076 14.511073
2850 16738.487 -0.012558719 0 5269.5111 14.510111
2900 16738.465 -0.0026252725 0 5269.514 14.510277
2950 16738.476 -0.0082220764 0 5269.512 14.510223
3000 16738.66 -0.071284779 0 5269.507 14.509758
3050 16715.332 7.2419351 0 5269.476 14.870305
3100 16653.226 26.818761 0 5269.5009 14.496764
3150 16739.351 -0.30690375 0 5269.4886 13.643904
3200 16733.238 1.6025328 0 5269.4737 12.016934
3250 16734.374 1.2554429 0 5269.4841 11.963561
3300 16732.156 1.9585967 0 5269.4893 12.234024
3350 16738.655 -0.079693236 0 5269.497 12.092757
3400 16738.543 -0.042215005 0 5269.4991 12.092809
3450 16738.591 -0.059327511 0 5269.4972 12.092536
3500 16738.759 -0.11761245 0 5269.4918 12.09203
3550 16713.405 7.846062 0 5269.4737 12.389816
3600 16734.939 1.0821936 0 5269.4891 12.173591
3650 16738.808 -0.13663194 0 5269.4882 12.027009
3700 16738.602 -0.070934368 0 5269.4889 12.025288
3750 16737.731 0.20706558 0 5269.4927 12.061948
3800 16738.578 -0.05582043 0 5269.4965 12.035665
3850 16738.471 -0.016307928 0 5269.5024 12.035302
3900 16738.449 -0.0058182199 0 5269.5059 12.035401
3950 16738.439 -0.0012027325 0 5269.5074 12.035461
4000 16738.436 -0.00020698452 0 5269.5075 12.035469
4050 16738.437 0 0 5269.5078 12.035454
4100 16738.437 0 0 5269.508 12.035435
4150 16738.438 0 0 5269.5081 12.035426
4200 16738.438 0 0 5269.5083 12.035432
4250 16738.439 0 0 5269.5085 12.035447
4300 16738.439 0 0 5269.5086 12.035463
4350 16738.44 0 0 5269.5087 12.035474
4400 16738.44 0 0 5269.5088 12.035478
4450 16738.44 0 0 5269.5089 12.035474
4500 16738.44 0 0 5269.509 12.035462
4550 16738.441 0 0 5269.5092 12.035449
4600 16738.441 0 0 5269.5093 12.035445
4650 16738.442 0 0 5269.5095 12.035451
4700 16738.442 0 0 5269.5096 12.03546
4750 16738.443 0 0 5269.5097 12.035465
4800 16738.443 0 0 5269.5098 12.035466
4850 16738.443 0 0 5269.51 12.035463
4900 16738.444 0 0 5269.5101 12.035456
4950 16738.444 0 0 5269.5102 12.035447
5000 16738.445 0 0 5269.5104 12.03544
5050 16738.445 0 0 5269.5105 12.035442
5100 16738.446 0 0 5269.5107 12.035455
5150 16738.446 0 0 5269.5108 12.03547
5200 16738.446 0 0 5269.5109 12.035479
5250 16738.447 0 0 5269.511 12.035479
5300 16738.447 0 0 5269.5111 12.03547
5350 16738.447 0 0 5269.5112 12.035454
5400 16738.448 0 0 5269.5113 12.035434
5450 16738.448 0 0 5269.5115 12.03542
5500 16738.449 0 0 5269.5117 12.035422
5550 16738.457 -0.0030919234 0 5269.5111 12.035383
5600 16738.51 -0.021618357 0 5269.5092 12.035106
5650 16738.622 -0.059214788 0 5269.507 12.035694
5700 16395.28 108.06942 0 5269.5463 24.369038
5750 16738.544 -0.033973429 0 5269.5077 12.011261
5800 16738.456 -0.0037013529 0 5269.5102 12.011675
5850 16738.451 0 0 5269.5123 12.011709
5900 16738.451 -0.0002211587 0 5269.5122 12.011687
5950 16738.452 -0.00024253349 0 5269.5124 12.011678
6000 16738.452 0 0 5269.5128 12.011688
6050 16738.453 0 0 5269.513 12.011702
6100 16738.453 0 0 5269.5131 12.011716
6150 16738.454 0 0 5269.5132 12.011725
6200 16738.454 0 0 5269.5133 12.011728
6250 16738.454 0 0 5269.5134 12.011723
6300 16738.455 0 0 5269.5135 12.011712
6350 16738.455 0 0 5269.5137 12.0117
6400 16738.456 0 0 5269.5138 12.011697
6450 16738.456 0 0 5269.514 12.011704
6500 16738.456 0 0 5269.5141 12.011714
6550 16738.457 0 0 5269.5142 12.011719
6600 16738.457 0 0 5269.5143 12.011718
6650 16738.458 0 0 5269.5144 12.011713
6700 16738.458 0 0 5269.5146 12.011705
6750 16738.459 0 0 5269.5147 12.011696
6800 16738.459 0 0 5269.5149 12.01169
6850 16738.46 0 0 5269.515 12.011695
6900 16738.46 0 0 5269.5152 12.01171
6950 16738.46 0 0 5269.5153 12.011726
7000 16738.461 0 0 5269.5154 12.011736
7050 16738.461 0 0 5269.5155 12.011737
7100 16738.461 0 0 5269.5155 12.011728
7150 16738.461 0 0 5269.5156 12.011712
7200 16738.462 0 0 5269.5158 12.011691
7250 16738.463 0 0 5269.516 12.011676
7300 16738.463 0 0 5269.5162 12.011677
7350 16738.464 0 0 5269.5164 12.011693
7400 16738.464 0 0 5269.5165 12.011713
7450 16738.465 0 0 5269.5166 12.011729
7500 16738.465 0 0 5269.5167 12.011736
7550 16738.465 0 0 5269.5168 12.011734
7600 16738.465 0 0 5269.5168 12.011722
7650 16738.466 0 0 5269.517 12.011704
7700 16738.466 0 0 5269.5171 12.011687
7750 16738.467 0 0 5269.5173 12.011681
7800 16738.467 0 0 5269.5175 12.011687
7850 16738.468 0 0 5269.5176 12.0117
7900 16738.468 0 0 5269.5178 12.011712
7950 16738.469 0 0 5269.5179 12.011721
8000 16738.469 0 0 5269.518 12.011724
8050 16738.469 0 0 5269.5181 12.01172
8100 16738.47 0 0 5269.5182 12.011709
8150 16738.47 0 0 5269.5183 12.0117
8200 16738.47 0 0 5269.5185 12.0117
8250 16738.471 0 0 5269.5186 12.011709
8300 16738.471 0 0 5269.5187 12.011719
8350 16738.472 0 0 5269.5189 12.011723
8400 16738.472 0 0 5269.519 12.01172
8450 16738.473 -0.00039690665 0 5269.5189 12.011706
8500 16738.481 -0.0034646803 0 5269.5182 12.011643
8550 16738.483 -0.0045307408 0 5269.5178 12.011621
8600 16738.474 -0.0007653281 0 5269.5189 12.011681
8650 16738.474 0 0 5269.5197 12.011699
8700 16738.475 0 0 5269.5199 12.011715
8750 16738.475 0 0 5269.52 12.011732
8800 16738.475 0 0 5269.52 12.011743
8850 16738.476 0 0 5269.5201 12.011744
8900 16738.476 0 0 5269.5202 12.011735
8950 16738.476 0 0 5269.5203 12.011719
9000 16738.477 0 0 5269.5205 12.011698
9050 16738.477 0 0 5269.5206 12.011683
9100 16738.478 0 0 5269.5208 12.011684
9150 16738.479 0 0 5269.521 12.011701
9200 16738.479 0 0 5269.5212 12.011722
9250 16738.479 0 0 5269.5213 12.011738
9300 16738.48 0 0 5269.5214 12.011746
9350 16738.48 0 0 5269.5214 12.011744
9400 16738.48 0 0 5269.5215 12.011732
9450 16738.48 0 0 5269.5216 12.011715
9500 16738.481 -0.00037652436 0 5269.5216 12.011692
9550 16738.493 -0.0053156156 0 5269.5203 12.011611
9600 16738.549 -0.026814368 0 5269.5163 12.011415
9650 16738.765 -0.10191522 0 5269.5092 12.011013
9700 16735.041 1.0589881 0 5269.4979 12.062708
9750 16738.013 0.13550093 0 5269.5101 11.407245
9800 16738.512 -0.01162033 0 5269.5201 11.394973
9850 16738.489 -0.00067270581 0 5269.5237 11.395098
9900 16738.489 -0.0002498458 0 5269.5242 11.395084
9950 16738.49 0 0 5269.5245 11.395076
10000 16738.49 0 0 5269.5246 11.395075
Loop time of 0.119912 on 1 procs for 10000 steps with 81 atoms
Performance: 720528.892 tau/day, 83394.548 timesteps/s, 6.755 Matom-step/s
98.8% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.007138 | 0.007138 | 0.007138 | 0.0 | 5.95
Neigh | 0.04331 | 0.04331 | 0.04331 | 0.0 | 36.12
Comm | 0.0080707 | 0.0080707 | 0.0080707 | 0.0 | 6.73
Output | 0.001757 | 0.001757 | 0.001757 | 0.0 | 1.47
Modify | 0.052965 | 0.052965 | 0.052965 | 0.0 | 44.17
Other | | 0.006671 | | | 5.56
Nlocal: 81 ave 81 max 81 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 84 ave 84 max 84 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0
Neighbor list builds = 1552
Dangerous builds = 0
Total wall time: 0:00:00

341
examples/rigid/log.25Mar24.rigid.atomfile.g++.4
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@ -1,341 +0,0 @@
LAMMPS (7 Feb 2024 - Development - patch_7Feb2024_update1-306-gf3391199e7-modified)
using 1 OpenMP thread(s) per MPI task
# Simple rigid body system
units lj
atom_style atomic
atom_modify map array
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
# 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
variable bodies atomfile bodies.txt
fix 1 all rigid custom v_bodies
9 rigid bodies with 81 atoms
# 1 chain of connected bodies
#group clump1 id <> 1 9
#group clump2 id <> 9 18
#group clump3 id <> 18 27
#group clump4 id <> 27 36
#group clump5 id <> 36 45
#group clump6 id <> 45 54
#group clump7 id <> 54 63
#group clump8 id <> 63 72
#group clump9 id <> 72 81
#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9
# 2 chains of connected bodies
#group clump1 id <> 1 9
#group clump2 id <> 9 18
#group clump3 id <> 18 27
#group clump4 id <> 27 36
#group clump5 id <> 37 45
#group clump6 id <> 45 54
#group clump7 id <> 54 63
#group clump8 id <> 63 72
#group clump9 id <> 72 81
#fix 1 all poems group clump1 clump2 clump3 clump4
#fix 2 all poems group clump5 clump6 clump7 clump8 clump9
neigh_modify exclude group clump1 clump1
neigh_modify exclude group clump2 clump2
neigh_modify exclude group clump3 clump3
neigh_modify exclude group clump4 clump4
neigh_modify exclude group clump5 clump5
neigh_modify exclude group clump6 clump6
neigh_modify exclude group clump7 clump7
neigh_modify exclude group clump8 clump8
neigh_modify exclude group clump9 clump9
thermo 100
#dump 1 all atom 50 dump.rigid
#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 2 pad 5
#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 3 pad 5
timestep 0.0001
thermo 50
run 10000
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4, bins = 18 18 18
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 4.33 | 4.362 | 4.456 Mbytes
Step Temp E_pair E_mol TotEng Press
0 115.29439 5235.9179 0 5272.2142 -2.7403788
50 14910.685 571.71558 0 5265.82 32.006171
100 16298.442 136.66184 0 5267.653 16.444229
150 16682.606 17.490511 0 5269.4219 14.900344
200 16733.929 1.372872 0 5269.4617 14.569267
250 16738.853 -0.15252816 0 5269.4864 14.496404
300 16738.588 -0.055171335 0 5269.5002 14.496025
350 16738.492 -0.017444677 0 5269.5077 14.496446
400 16738.464 -0.0060102023 0 5269.5104 14.496618
450 16738.455 -0.0012713351 0 5269.5124 14.496701
500 16738.455 -0.00081068621 0 5269.5128 14.496709
550 16738.455 -0.00083203497 0 5269.5129 14.496707
600 16738.455 -0.00058355356 0 5269.5131 14.496709
650 16738.455 -0.00047226704 0 5269.5131 14.496708
700 16738.455 0 0 5269.5136 14.496713
750 16738.455 0 0 5269.5136 14.49671
800 16738.455 0 0 5269.5137 14.496709
850 16738.455 0 0 5269.5137 14.49671
900 16738.456 0 0 5269.5138 14.496713
950 16738.462 -0.0035323872 0 5269.5122 14.496671
1000 16738.586 -0.051135144 0 5269.5036 14.496229
1050 16737.358 0.32995057 0 5269.4981 14.525763
1100 16737.892 0.16210246 0 5269.4984 14.531983
1150 16738.703 -0.089235095 0 5269.5025 14.509899
1200 16738.466 -0.0075446243 0 5269.5096 14.510615
1250 16738.456 0 0 5269.514 14.510704
1300 16738.457 0 0 5269.5141 14.510701
1350 16738.457 0 0 5269.5141 14.510699
1400 16738.457 -0.00044736511 0 5269.5138 14.510693
1450 16738.458 -0.0010971179 0 5269.5134 14.510687
1500 16738.458 -0.00057885428 0 5269.5139 14.510698
1550 16738.457 0 0 5269.5143 14.51071
1600 16738.457 0 0 5269.5144 14.510712
1650 16738.457 0 0 5269.5144 14.510712
1700 16738.458 0 0 5269.5144 14.51071
1750 16738.458 0 0 5269.5145 14.510708
1800 16738.458 0 0 5269.5145 14.510706
1850 16738.458 0 0 5269.5146 14.510705
1900 16738.458 0 0 5269.5146 14.510706
1950 16738.465 -0.0031733615 0 5269.5134 14.510659
2000 16738.491 -0.013255268 0 5269.5117 14.510532
2050 16738.556 -0.0365811 0 5269.5087 14.51029
2100 16738.633 -0.063209659 0 5269.5065 14.510219
2150 16738.607 -0.05601761 0 5269.5055 14.510231
2200 16738.557 -0.038423032 0 5269.5072 14.510404
2250 16738.515 -0.023709918 0 5269.5088 14.510539
2300 16738.489 -0.013249035 0 5269.5111 14.510621
2350 16738.468 -0.0045563719 0 5269.5131 14.510714
2400 16738.46 -0.00052194273 0 5269.5146 14.510771
2450 16738.464 -0.0023259756 0 5269.514 14.510746
2500 16738.468 -0.0051929186 0 5269.5127 14.510731
2550 16738.581 -0.044940117 0 5269.5085 14.510315
2600 16738.427 -7.9722867e-05 0 5269.5046 14.510657
2650 16733.017 1.705148 0 5269.5067 14.596295
2700 16738.761 -0.10614946 0 5269.5038 14.499584
2750 16733.973 1.4038179 0 5269.5064 14.598107
2800 16738.585 -0.046813448 0 5269.5076 14.511073
2850 16738.487 -0.012558719 0 5269.5111 14.510111
2900 16738.465 -0.0026252725 0 5269.514 14.510277
2950 16738.476 -0.0082220764 0 5269.512 14.510223
3000 16738.66 -0.071284779 0 5269.507 14.509758
3050 16715.332 7.2419351 0 5269.476 14.870305
3100 16653.226 26.818761 0 5269.5009 14.496764
3150 16739.351 -0.30690375 0 5269.4886 13.643904
3200 16733.238 1.6025328 0 5269.4737 12.016934
3250 16734.374 1.2554429 0 5269.4841 11.963561
3300 16732.156 1.9585967 0 5269.4893 12.234024
3350 16738.655 -0.079693236 0 5269.497 12.092757
3400 16738.543 -0.042215005 0 5269.4991 12.092809
3450 16738.591 -0.059327511 0 5269.4972 12.092536
3500 16738.759 -0.11761245 0 5269.4918 12.09203
3550 16713.405 7.846062 0 5269.4737 12.389816
3600 16734.939 1.0821936 0 5269.4891 12.173591
3650 16738.808 -0.13663194 0 5269.4882 12.027009
3700 16738.602 -0.070934368 0 5269.4889 12.025288
3750 16737.731 0.20706558 0 5269.4927 12.061948
3800 16738.578 -0.05582043 0 5269.4965 12.035665
3850 16738.471 -0.016307928 0 5269.5024 12.035302
3900 16738.449 -0.0058182199 0 5269.5059 12.035401
3950 16738.439 -0.0012027325 0 5269.5074 12.035461
4000 16738.436 -0.00020698452 0 5269.5075 12.035469
4050 16738.437 0 0 5269.5078 12.035454
4100 16738.437 0 0 5269.508 12.035435
4150 16738.438 0 0 5269.5081 12.035426
4200 16738.438 0 0 5269.5083 12.035432
4250 16738.439 0 0 5269.5085 12.035447
4300 16738.439 0 0 5269.5086 12.035463
4350 16738.44 0 0 5269.5087 12.035474
4400 16738.44 0 0 5269.5088 12.035478
4450 16738.44 0 0 5269.5089 12.035474
4500 16738.44 0 0 5269.509 12.035462
4550 16738.441 0 0 5269.5092 12.035449
4600 16738.441 0 0 5269.5093 12.035445
4650 16738.442 0 0 5269.5095 12.035451
4700 16738.442 0 0 5269.5096 12.03546
4750 16738.443 0 0 5269.5097 12.035465
4800 16738.443 0 0 5269.5098 12.035466
4850 16738.443 0 0 5269.51 12.035463
4900 16738.444 0 0 5269.5101 12.035456
4950 16738.444 0 0 5269.5102 12.035447
5000 16738.445 0 0 5269.5104 12.03544
5050 16738.445 0 0 5269.5105 12.035442
5100 16738.446 0 0 5269.5107 12.035455
5150 16738.446 0 0 5269.5108 12.03547
5200 16738.446 0 0 5269.5109 12.035479
5250 16738.447 0 0 5269.511 12.035479
5300 16738.447 0 0 5269.5111 12.03547
5350 16738.447 0 0 5269.5112 12.035454
5400 16738.448 0 0 5269.5113 12.035434
5450 16738.448 0 0 5269.5115 12.03542
5500 16738.449 0 0 5269.5117 12.035422
5550 16738.457 -0.0030919234 0 5269.5111 12.035383
5600 16738.51 -0.021618357 0 5269.5092 12.035106
5650 16738.622 -0.059214788 0 5269.507 12.035694
5700 16395.28 108.06942 0 5269.5463 24.369038
5750 16738.544 -0.033973429 0 5269.5077 12.011261
5800 16738.456 -0.0037013529 0 5269.5102 12.011675
5850 16738.451 0 0 5269.5123 12.011709
5900 16738.451 -0.0002211587 0 5269.5122 12.011687
5950 16738.452 -0.00024253349 0 5269.5124 12.011678
6000 16738.452 0 0 5269.5128 12.011688
6050 16738.453 0 0 5269.513 12.011702
6100 16738.453 0 0 5269.5131 12.011716
6150 16738.454 0 0 5269.5132 12.011725
6200 16738.454 0 0 5269.5133 12.011728
6250 16738.454 0 0 5269.5134 12.011723
6300 16738.455 0 0 5269.5135 12.011712
6350 16738.455 0 0 5269.5137 12.0117
6400 16738.456 0 0 5269.5138 12.011697
6450 16738.456 0 0 5269.514 12.011704
6500 16738.456 0 0 5269.5141 12.011714
6550 16738.457 0 0 5269.5142 12.011719
6600 16738.457 0 0 5269.5143 12.011718
6650 16738.458 0 0 5269.5144 12.011713
6700 16738.458 0 0 5269.5146 12.011705
6750 16738.459 0 0 5269.5147 12.011696
6800 16738.459 0 0 5269.5149 12.01169
6850 16738.46 0 0 5269.515 12.011695
6900 16738.46 0 0 5269.5152 12.01171
6950 16738.46 0 0 5269.5153 12.011726
7000 16738.461 0 0 5269.5154 12.011736
7050 16738.461 0 0 5269.5155 12.011737
7100 16738.461 0 0 5269.5155 12.011728
7150 16738.461 0 0 5269.5156 12.011712
7200 16738.462 0 0 5269.5158 12.011691
7250 16738.463 0 0 5269.516 12.011676
7300 16738.463 0 0 5269.5162 12.011677
7350 16738.464 0 0 5269.5164 12.011693
7400 16738.464 0 0 5269.5165 12.011713
7450 16738.465 0 0 5269.5166 12.011729
7500 16738.465 0 0 5269.5167 12.011736
7550 16738.465 0 0 5269.5168 12.011734
7600 16738.465 0 0 5269.5168 12.011722
7650 16738.466 0 0 5269.517 12.011704
7700 16738.466 0 0 5269.5171 12.011687
7750 16738.467 0 0 5269.5173 12.011681
7800 16738.467 0 0 5269.5175 12.011687
7850 16738.468 0 0 5269.5176 12.0117
7900 16738.468 0 0 5269.5178 12.011712
7950 16738.469 0 0 5269.5179 12.011721
8000 16738.469 0 0 5269.518 12.011724
8050 16738.469 0 0 5269.5181 12.01172
8100 16738.47 0 0 5269.5182 12.011709
8150 16738.47 0 0 5269.5183 12.0117
8200 16738.47 0 0 5269.5185 12.0117
8250 16738.471 0 0 5269.5186 12.011709
8300 16738.471 0 0 5269.5187 12.011719
8350 16738.472 0 0 5269.5189 12.011723
8400 16738.472 0 0 5269.519 12.01172
8450 16738.473 -0.00039690664 0 5269.5189 12.011706
8500 16738.481 -0.0034646803 0 5269.5182 12.011643
8550 16738.483 -0.0045307409 0 5269.5178 12.011621
8600 16738.474 -0.00076532811 0 5269.5189 12.011681
8650 16738.474 0 0 5269.5197 12.011699
8700 16738.475 0 0 5269.5199 12.011715
8750 16738.475 0 0 5269.52 12.011732
8800 16738.475 0 0 5269.52 12.011743
8850 16738.476 0 0 5269.5201 12.011744
8900 16738.476 0 0 5269.5202 12.011735
8950 16738.476 0 0 5269.5203 12.011719
9000 16738.477 0 0 5269.5205 12.011698
9050 16738.477 0 0 5269.5206 12.011683
9100 16738.478 0 0 5269.5208 12.011684
9150 16738.479 0 0 5269.521 12.011701
9200 16738.479 0 0 5269.5212 12.011722
9250 16738.479 0 0 5269.5213 12.011738
9300 16738.48 0 0 5269.5214 12.011746
9350 16738.48 0 0 5269.5214 12.011744
9400 16738.48 0 0 5269.5215 12.011732
9450 16738.48 0 0 5269.5216 12.011715
9500 16738.481 -0.00037652437 0 5269.5216 12.011692
9550 16738.493 -0.0053156158 0 5269.5203 12.011611
9600 16738.549 -0.026814369 0 5269.5163 12.011415
9650 16738.765 -0.10191523 0 5269.5092 12.011013
9700 16735.041 1.0589886 0 5269.4979 12.062708
9750 16738.013 0.13550089 0 5269.5101 11.407245
9800 16738.512 -0.011620329 0 5269.5201 11.394973
9850 16738.489 -0.00067270567 0 5269.5237 11.395098
9900 16738.489 -0.00024984578 0 5269.5242 11.395084
9950 16738.49 0 0 5269.5245 11.395076
10000 16738.49 0 0 5269.5246 11.395075
Loop time of 0.135195 on 4 procs for 10000 steps with 81 atoms
Performance: 639077.466 tau/day, 73967.299 timesteps/s, 5.991 Matom-step/s
97.5% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0016842 | 0.0023498 | 0.0027328 | 0.8 | 1.74
Neigh | 0.012614 | 0.013371 | 0.014361 | 0.5 | 9.89
Comm | 0.062345 | 0.06407 | 0.065902 | 0.6 | 47.39
Output | 0.0018312 | 0.0019801 | 0.0024023 | 0.5 | 1.46
Modify | 0.038532 | 0.039713 | 0.041474 | 0.6 | 29.37
Other | | 0.01371 | | | 10.14
Nlocal: 20.25 ave 37 max 3 min
Histogram: 1 0 0 1 0 0 0 1 0 1
Nghost: 27.25 ave 48 max 13 min
Histogram: 1 0 0 2 0 0 0 0 0 1
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0
Neighbor list builds = 1552
Dangerous builds = 0
Total wall time: 0:00:00

341
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@ -1,341 +0,0 @@
LAMMPS (7 Feb 2024 - Development - patch_7Feb2024_update1-306-gf3391199e7-modified)
using 1 OpenMP thread(s) per MPI task
# Simple rigid body system
units lj
atom_style atomic
atom_modify map array
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 = 0.001 seconds
velocity all create 100.0 4928459
# unconnected bodies
group clump1 id <> 1 9
9 atoms in group clump1
group clump2 id <> 10 18
9 atoms in group clump2
group clump3 id <> 19 27
9 atoms in group clump3
group clump4 id <> 28 36
9 atoms in group clump4
group clump5 id <> 37 45
9 atoms in group clump5
group clump6 id <> 46 54
9 atoms in group clump6
group clump7 id <> 55 63
9 atoms in group clump7
group clump8 id <> 64 72
9 atoms in group clump8
group clump9 id <> 73 81
9 atoms in group clump9
variable bodies atom 1.0*gmask(clump1)+2.0*gmask(clump2)+3.0*gmask(clump3)+4.0*gmask(clump4)+5.0*gmask(clump5)+6.0*gmask(clump6)+7.0*gmask(clump7)+8.0*gmask(clump8)+9.0*gmask(clump9)
fix 1 all rigid custom v_bodies
9 rigid bodies with 81 atoms
# 1 chain of connected bodies
#group clump1 id <> 1 9
#group clump2 id <> 9 18
#group clump3 id <> 18 27
#group clump4 id <> 27 36
#group clump5 id <> 36 45
#group clump6 id <> 45 54
#group clump7 id <> 54 63
#group clump8 id <> 63 72
#group clump9 id <> 72 81
#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9
# 2 chains of connected bodies
#group clump1 id <> 1 9
#group clump2 id <> 9 18
#group clump3 id <> 18 27
#group clump4 id <> 27 36
#group clump5 id <> 37 45
#group clump6 id <> 45 54
#group clump7 id <> 54 63
#group clump8 id <> 63 72
#group clump9 id <> 72 81
#fix 1 all poems group clump1 clump2 clump3 clump4
#fix 2 all poems group clump5 clump6 clump7 clump8 clump9
neigh_modify exclude group clump1 clump1
neigh_modify exclude group clump2 clump2
neigh_modify exclude group clump3 clump3
neigh_modify exclude group clump4 clump4
neigh_modify exclude group clump5 clump5
neigh_modify exclude group clump6 clump6
neigh_modify exclude group clump7 clump7
neigh_modify exclude group clump8 clump8
neigh_modify exclude group clump9 clump9
thermo 100
#dump 1 all atom 50 dump.rigid
#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 2 pad 5
#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 3 pad 5
timestep 0.0001
thermo 50
run 10000
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4, bins = 18 18 18
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 4.358 | 4.358 | 4.358 Mbytes
Step Temp E_pair E_mol TotEng Press
0 115.29439 5235.9179 0 5272.2142 -2.7403788
50 14910.685 571.71558 0 5265.82 32.006171
100 16298.442 136.66184 0 5267.653 16.444229
150 16682.606 17.490511 0 5269.4219 14.900344
200 16733.929 1.372872 0 5269.4617 14.569267
250 16738.853 -0.15252816 0 5269.4864 14.496404
300 16738.588 -0.055171335 0 5269.5002 14.496025
350 16738.492 -0.017444677 0 5269.5077 14.496446
400 16738.464 -0.0060102023 0 5269.5104 14.496618
450 16738.455 -0.0012713351 0 5269.5124 14.496701
500 16738.455 -0.00081068621 0 5269.5128 14.496709
550 16738.455 -0.00083203497 0 5269.5129 14.496707
600 16738.455 -0.00058355356 0 5269.5131 14.496709
650 16738.455 -0.00047226704 0 5269.5131 14.496708
700 16738.455 0 0 5269.5136 14.496713
750 16738.455 0 0 5269.5136 14.49671
800 16738.455 0 0 5269.5137 14.496709
850 16738.455 0 0 5269.5137 14.49671
900 16738.456 0 0 5269.5138 14.496713
950 16738.462 -0.0035323872 0 5269.5122 14.496671
1000 16738.586 -0.051135144 0 5269.5036 14.496229
1050 16737.358 0.32995057 0 5269.4981 14.525763
1100 16737.892 0.16210246 0 5269.4984 14.531983
1150 16738.703 -0.089235095 0 5269.5025 14.509899
1200 16738.466 -0.0075446243 0 5269.5096 14.510615
1250 16738.456 0 0 5269.514 14.510704
1300 16738.457 0 0 5269.5141 14.510701
1350 16738.457 0 0 5269.5141 14.510699
1400 16738.457 -0.00044736511 0 5269.5138 14.510693
1450 16738.458 -0.0010971179 0 5269.5134 14.510687
1500 16738.458 -0.00057885428 0 5269.5139 14.510698
1550 16738.457 0 0 5269.5143 14.51071
1600 16738.457 0 0 5269.5144 14.510712
1650 16738.457 0 0 5269.5144 14.510712
1700 16738.458 0 0 5269.5144 14.51071
1750 16738.458 0 0 5269.5145 14.510708
1800 16738.458 0 0 5269.5145 14.510706
1850 16738.458 0 0 5269.5146 14.510705
1900 16738.458 0 0 5269.5146 14.510706
1950 16738.465 -0.0031733615 0 5269.5134 14.510659
2000 16738.491 -0.013255268 0 5269.5117 14.510532
2050 16738.556 -0.0365811 0 5269.5087 14.51029
2100 16738.633 -0.063209659 0 5269.5065 14.510219
2150 16738.607 -0.05601761 0 5269.5055 14.510231
2200 16738.557 -0.038423032 0 5269.5072 14.510404
2250 16738.515 -0.023709918 0 5269.5088 14.510539
2300 16738.489 -0.013249035 0 5269.5111 14.510621
2350 16738.468 -0.0045563719 0 5269.5131 14.510714
2400 16738.46 -0.00052194273 0 5269.5146 14.510771
2450 16738.464 -0.0023259756 0 5269.514 14.510746
2500 16738.468 -0.0051929186 0 5269.5127 14.510731
2550 16738.581 -0.044940117 0 5269.5085 14.510315
2600 16738.427 -7.9722875e-05 0 5269.5046 14.510657
2650 16733.017 1.705148 0 5269.5067 14.596295
2700 16738.761 -0.10614946 0 5269.5038 14.499584
2750 16733.973 1.4038179 0 5269.5064 14.598107
2800 16738.585 -0.046813448 0 5269.5076 14.511073
2850 16738.487 -0.012558719 0 5269.5111 14.510111
2900 16738.465 -0.0026252725 0 5269.514 14.510277
2950 16738.476 -0.0082220764 0 5269.512 14.510223
3000 16738.66 -0.071284779 0 5269.507 14.509758
3050 16715.332 7.2419351 0 5269.476 14.870305
3100 16653.226 26.818761 0 5269.5009 14.496764
3150 16739.351 -0.30690375 0 5269.4886 13.643904
3200 16733.238 1.6025328 0 5269.4737 12.016934
3250 16734.374 1.2554429 0 5269.4841 11.963561
3300 16732.156 1.9585967 0 5269.4893 12.234024
3350 16738.655 -0.079693236 0 5269.497 12.092757
3400 16738.543 -0.042215005 0 5269.4991 12.092809
3450 16738.591 -0.059327511 0 5269.4972 12.092536
3500 16738.759 -0.11761245 0 5269.4918 12.09203
3550 16713.405 7.846062 0 5269.4737 12.389816
3600 16734.939 1.0821936 0 5269.4891 12.173591
3650 16738.808 -0.13663194 0 5269.4882 12.027009
3700 16738.602 -0.070934368 0 5269.4889 12.025288
3750 16737.731 0.20706558 0 5269.4927 12.061948
3800 16738.578 -0.05582043 0 5269.4965 12.035665
3850 16738.471 -0.016307928 0 5269.5024 12.035302
3900 16738.449 -0.0058182199 0 5269.5059 12.035401
3950 16738.439 -0.0012027325 0 5269.5074 12.035461
4000 16738.436 -0.00020698452 0 5269.5075 12.035469
4050 16738.437 0 0 5269.5078 12.035454
4100 16738.437 0 0 5269.508 12.035435
4150 16738.438 0 0 5269.5081 12.035426
4200 16738.438 0 0 5269.5083 12.035432
4250 16738.439 0 0 5269.5085 12.035447
4300 16738.439 0 0 5269.5086 12.035463
4350 16738.44 0 0 5269.5087 12.035474
4400 16738.44 0 0 5269.5088 12.035478
4450 16738.44 0 0 5269.5089 12.035474
4500 16738.44 0 0 5269.509 12.035462
4550 16738.441 0 0 5269.5092 12.035449
4600 16738.441 0 0 5269.5093 12.035445
4650 16738.442 0 0 5269.5095 12.035451
4700 16738.442 0 0 5269.5096 12.03546
4750 16738.443 0 0 5269.5097 12.035465
4800 16738.443 0 0 5269.5098 12.035466
4850 16738.443 0 0 5269.51 12.035463
4900 16738.444 0 0 5269.5101 12.035456
4950 16738.444 0 0 5269.5102 12.035447
5000 16738.445 0 0 5269.5104 12.03544
5050 16738.445 0 0 5269.5105 12.035442
5100 16738.446 0 0 5269.5107 12.035455
5150 16738.446 0 0 5269.5108 12.03547
5200 16738.446 0 0 5269.5109 12.035479
5250 16738.447 0 0 5269.511 12.035479
5300 16738.447 0 0 5269.5111 12.03547
5350 16738.447 0 0 5269.5112 12.035454
5400 16738.448 0 0 5269.5113 12.035434
5450 16738.448 0 0 5269.5115 12.03542
5500 16738.449 0 0 5269.5117 12.035422
5550 16738.457 -0.0030919234 0 5269.5111 12.035383
5600 16738.51 -0.021618357 0 5269.5092 12.035106
5650 16738.622 -0.059214788 0 5269.507 12.035694
5700 16395.28 108.06942 0 5269.5463 24.369038
5750 16738.544 -0.033973429 0 5269.5077 12.011261
5800 16738.456 -0.0037013529 0 5269.5102 12.011675
5850 16738.451 0 0 5269.5123 12.011709
5900 16738.451 -0.0002211587 0 5269.5122 12.011687
5950 16738.452 -0.00024253349 0 5269.5124 12.011678
6000 16738.452 0 0 5269.5128 12.011688
6050 16738.453 0 0 5269.513 12.011702
6100 16738.453 0 0 5269.5131 12.011716
6150 16738.454 0 0 5269.5132 12.011725
6200 16738.454 0 0 5269.5133 12.011728
6250 16738.454 0 0 5269.5134 12.011723
6300 16738.455 0 0 5269.5135 12.011712
6350 16738.455 0 0 5269.5137 12.0117
6400 16738.456 0 0 5269.5138 12.011697
6450 16738.456 0 0 5269.514 12.011704
6500 16738.456 0 0 5269.5141 12.011714
6550 16738.457 0 0 5269.5142 12.011719
6600 16738.457 0 0 5269.5143 12.011718
6650 16738.458 0 0 5269.5144 12.011713
6700 16738.458 0 0 5269.5146 12.011705
6750 16738.459 0 0 5269.5147 12.011696
6800 16738.459 0 0 5269.5149 12.01169
6850 16738.46 0 0 5269.515 12.011695
6900 16738.46 0 0 5269.5152 12.01171
6950 16738.46 0 0 5269.5153 12.011726
7000 16738.461 0 0 5269.5154 12.011736
7050 16738.461 0 0 5269.5155 12.011737
7100 16738.461 0 0 5269.5155 12.011728
7150 16738.461 0 0 5269.5156 12.011712
7200 16738.462 0 0 5269.5158 12.011691
7250 16738.463 0 0 5269.516 12.011676
7300 16738.463 0 0 5269.5162 12.011677
7350 16738.464 0 0 5269.5164 12.011693
7400 16738.464 0 0 5269.5165 12.011713
7450 16738.465 0 0 5269.5166 12.011729
7500 16738.465 0 0 5269.5167 12.011736
7550 16738.465 0 0 5269.5168 12.011734
7600 16738.465 0 0 5269.5168 12.011722
7650 16738.466 0 0 5269.517 12.011704
7700 16738.466 0 0 5269.5171 12.011687
7750 16738.467 0 0 5269.5173 12.011681
7800 16738.467 0 0 5269.5175 12.011687
7850 16738.468 0 0 5269.5176 12.0117
7900 16738.468 0 0 5269.5178 12.011712
7950 16738.469 0 0 5269.5179 12.011721
8000 16738.469 0 0 5269.518 12.011724
8050 16738.469 0 0 5269.5181 12.01172
8100 16738.47 0 0 5269.5182 12.011709
8150 16738.47 0 0 5269.5183 12.0117
8200 16738.47 0 0 5269.5185 12.0117
8250 16738.471 0 0 5269.5186 12.011709
8300 16738.471 0 0 5269.5187 12.011719
8350 16738.472 0 0 5269.5189 12.011723
8400 16738.472 0 0 5269.519 12.01172
8450 16738.473 -0.00039690665 0 5269.5189 12.011706
8500 16738.481 -0.0034646803 0 5269.5182 12.011643
8550 16738.483 -0.0045307408 0 5269.5178 12.011621
8600 16738.474 -0.0007653281 0 5269.5189 12.011681
8650 16738.474 0 0 5269.5197 12.011699
8700 16738.475 0 0 5269.5199 12.011715
8750 16738.475 0 0 5269.52 12.011732
8800 16738.475 0 0 5269.52 12.011743
8850 16738.476 0 0 5269.5201 12.011744
8900 16738.476 0 0 5269.5202 12.011735
8950 16738.476 0 0 5269.5203 12.011719
9000 16738.477 0 0 5269.5205 12.011698
9050 16738.477 0 0 5269.5206 12.011683
9100 16738.478 0 0 5269.5208 12.011684
9150 16738.479 0 0 5269.521 12.011701
9200 16738.479 0 0 5269.5212 12.011722
9250 16738.479 0 0 5269.5213 12.011738
9300 16738.48 0 0 5269.5214 12.011746
9350 16738.48 0 0 5269.5214 12.011744
9400 16738.48 0 0 5269.5215 12.011732
9450 16738.48 0 0 5269.5216 12.011715
9500 16738.481 -0.00037652436 0 5269.5216 12.011692
9550 16738.493 -0.0053156156 0 5269.5203 12.011611
9600 16738.549 -0.026814368 0 5269.5163 12.011415
9650 16738.765 -0.10191522 0 5269.5092 12.011013
9700 16735.041 1.0589881 0 5269.4979 12.062708
9750 16738.013 0.13550093 0 5269.5101 11.407245
9800 16738.512 -0.01162033 0 5269.5201 11.394973
9850 16738.489 -0.00067270581 0 5269.5237 11.395098
9900 16738.489 -0.0002498458 0 5269.5242 11.395084
9950 16738.49 0 0 5269.5245 11.395076
10000 16738.49 0 0 5269.5246 11.395075
Loop time of 0.131374 on 1 procs for 10000 steps with 81 atoms
Performance: 657662.971 tau/day, 76118.399 timesteps/s, 6.166 Matom-step/s
99.1% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0075531 | 0.0075531 | 0.0075531 | 0.0 | 5.75
Neigh | 0.047177 | 0.047177 | 0.047177 | 0.0 | 35.91
Comm | 0.0090961 | 0.0090961 | 0.0090961 | 0.0 | 6.92
Output | 0.0018917 | 0.0018917 | 0.0018917 | 0.0 | 1.44
Modify | 0.058064 | 0.058064 | 0.058064 | 0.0 | 44.20
Other | | 0.007593 | | | 5.78
Nlocal: 81 ave 81 max 81 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 84 ave 84 max 84 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0
Neighbor list builds = 1552
Dangerous builds = 0
Total wall time: 0:00:00

341
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@ -1,341 +0,0 @@
LAMMPS (7 Feb 2024 - Development - patch_7Feb2024_update1-306-gf3391199e7-modified)
using 1 OpenMP thread(s) per MPI task
# Simple rigid body system
units lj
atom_style atomic
atom_modify map array
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
# 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
variable bodies atom 1.0*gmask(clump1)+2.0*gmask(clump2)+3.0*gmask(clump3)+4.0*gmask(clump4)+5.0*gmask(clump5)+6.0*gmask(clump6)+7.0*gmask(clump7)+8.0*gmask(clump8)+9.0*gmask(clump9)
fix 1 all rigid custom v_bodies
9 rigid bodies with 81 atoms
# 1 chain of connected bodies
#group clump1 id <> 1 9
#group clump2 id <> 9 18
#group clump3 id <> 18 27
#group clump4 id <> 27 36
#group clump5 id <> 36 45
#group clump6 id <> 45 54
#group clump7 id <> 54 63
#group clump8 id <> 63 72
#group clump9 id <> 72 81
#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9
# 2 chains of connected bodies
#group clump1 id <> 1 9
#group clump2 id <> 9 18
#group clump3 id <> 18 27
#group clump4 id <> 27 36
#group clump5 id <> 37 45
#group clump6 id <> 45 54
#group clump7 id <> 54 63
#group clump8 id <> 63 72
#group clump9 id <> 72 81
#fix 1 all poems group clump1 clump2 clump3 clump4
#fix 2 all poems group clump5 clump6 clump7 clump8 clump9
neigh_modify exclude group clump1 clump1
neigh_modify exclude group clump2 clump2
neigh_modify exclude group clump3 clump3
neigh_modify exclude group clump4 clump4
neigh_modify exclude group clump5 clump5
neigh_modify exclude group clump6 clump6
neigh_modify exclude group clump7 clump7
neigh_modify exclude group clump8 clump8
neigh_modify exclude group clump9 clump9
thermo 100
#dump 1 all atom 50 dump.rigid
#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 2 pad 5
#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 3 pad 5
timestep 0.0001
thermo 50
run 10000
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4, bins = 18 18 18
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 4.205 | 4.237 | 4.331 Mbytes
Step Temp E_pair E_mol TotEng Press
0 115.29439 5235.9179 0 5272.2142 -2.7403788
50 14910.685 571.71558 0 5265.82 32.006171
100 16298.442 136.66184 0 5267.653 16.444229
150 16682.606 17.490511 0 5269.4219 14.900344
200 16733.929 1.372872 0 5269.4617 14.569267
250 16738.853 -0.15252816 0 5269.4864 14.496404
300 16738.588 -0.055171335 0 5269.5002 14.496025
350 16738.492 -0.017444677 0 5269.5077 14.496446
400 16738.464 -0.0060102023 0 5269.5104 14.496618
450 16738.455 -0.0012713351 0 5269.5124 14.496701
500 16738.455 -0.00081068621 0 5269.5128 14.496709
550 16738.455 -0.00083203497 0 5269.5129 14.496707
600 16738.455 -0.00058355356 0 5269.5131 14.496709
650 16738.455 -0.00047226704 0 5269.5131 14.496708
700 16738.455 0 0 5269.5136 14.496713
750 16738.455 0 0 5269.5136 14.49671
800 16738.455 0 0 5269.5137 14.496709
850 16738.455 0 0 5269.5137 14.49671
900 16738.456 0 0 5269.5138 14.496713
950 16738.462 -0.0035323872 0 5269.5122 14.496671
1000 16738.586 -0.051135144 0 5269.5036 14.496229
1050 16737.358 0.32995057 0 5269.4981 14.525763
1100 16737.892 0.16210246 0 5269.4984 14.531983
1150 16738.703 -0.089235095 0 5269.5025 14.509899
1200 16738.466 -0.0075446243 0 5269.5096 14.510615
1250 16738.456 0 0 5269.514 14.510704
1300 16738.457 0 0 5269.5141 14.510701
1350 16738.457 0 0 5269.5141 14.510699
1400 16738.457 -0.00044736511 0 5269.5138 14.510693
1450 16738.458 -0.0010971179 0 5269.5134 14.510687
1500 16738.458 -0.00057885428 0 5269.5139 14.510698
1550 16738.457 0 0 5269.5143 14.51071
1600 16738.457 0 0 5269.5144 14.510712
1650 16738.457 0 0 5269.5144 14.510712
1700 16738.458 0 0 5269.5144 14.51071
1750 16738.458 0 0 5269.5145 14.510708
1800 16738.458 0 0 5269.5145 14.510706
1850 16738.458 0 0 5269.5146 14.510705
1900 16738.458 0 0 5269.5146 14.510706
1950 16738.465 -0.0031733615 0 5269.5134 14.510659
2000 16738.491 -0.013255268 0 5269.5117 14.510532
2050 16738.556 -0.0365811 0 5269.5087 14.51029
2100 16738.633 -0.063209659 0 5269.5065 14.510219
2150 16738.607 -0.05601761 0 5269.5055 14.510231
2200 16738.557 -0.038423032 0 5269.5072 14.510404
2250 16738.515 -0.023709918 0 5269.5088 14.510539
2300 16738.489 -0.013249035 0 5269.5111 14.510621
2350 16738.468 -0.0045563719 0 5269.5131 14.510714
2400 16738.46 -0.00052194273 0 5269.5146 14.510771
2450 16738.464 -0.0023259756 0 5269.514 14.510746
2500 16738.468 -0.0051929186 0 5269.5127 14.510731
2550 16738.581 -0.044940117 0 5269.5085 14.510315
2600 16738.427 -7.9722867e-05 0 5269.5046 14.510657
2650 16733.017 1.705148 0 5269.5067 14.596295
2700 16738.761 -0.10614946 0 5269.5038 14.499584
2750 16733.973 1.4038179 0 5269.5064 14.598107
2800 16738.585 -0.046813448 0 5269.5076 14.511073
2850 16738.487 -0.012558719 0 5269.5111 14.510111
2900 16738.465 -0.0026252725 0 5269.514 14.510277
2950 16738.476 -0.0082220764 0 5269.512 14.510223
3000 16738.66 -0.071284779 0 5269.507 14.509758
3050 16715.332 7.2419351 0 5269.476 14.870305
3100 16653.226 26.818761 0 5269.5009 14.496764
3150 16739.351 -0.30690375 0 5269.4886 13.643904
3200 16733.238 1.6025328 0 5269.4737 12.016934
3250 16734.374 1.2554429 0 5269.4841 11.963561
3300 16732.156 1.9585967 0 5269.4893 12.234024
3350 16738.655 -0.079693236 0 5269.497 12.092757
3400 16738.543 -0.042215005 0 5269.4991 12.092809
3450 16738.591 -0.059327511 0 5269.4972 12.092536
3500 16738.759 -0.11761245 0 5269.4918 12.09203
3550 16713.405 7.846062 0 5269.4737 12.389816
3600 16734.939 1.0821936 0 5269.4891 12.173591
3650 16738.808 -0.13663194 0 5269.4882 12.027009
3700 16738.602 -0.070934368 0 5269.4889 12.025288
3750 16737.731 0.20706558 0 5269.4927 12.061948
3800 16738.578 -0.05582043 0 5269.4965 12.035665
3850 16738.471 -0.016307928 0 5269.5024 12.035302
3900 16738.449 -0.0058182199 0 5269.5059 12.035401
3950 16738.439 -0.0012027325 0 5269.5074 12.035461
4000 16738.436 -0.00020698452 0 5269.5075 12.035469
4050 16738.437 0 0 5269.5078 12.035454
4100 16738.437 0 0 5269.508 12.035435
4150 16738.438 0 0 5269.5081 12.035426
4200 16738.438 0 0 5269.5083 12.035432
4250 16738.439 0 0 5269.5085 12.035447
4300 16738.439 0 0 5269.5086 12.035463
4350 16738.44 0 0 5269.5087 12.035474
4400 16738.44 0 0 5269.5088 12.035478
4450 16738.44 0 0 5269.5089 12.035474
4500 16738.44 0 0 5269.509 12.035462
4550 16738.441 0 0 5269.5092 12.035449
4600 16738.441 0 0 5269.5093 12.035445
4650 16738.442 0 0 5269.5095 12.035451
4700 16738.442 0 0 5269.5096 12.03546
4750 16738.443 0 0 5269.5097 12.035465
4800 16738.443 0 0 5269.5098 12.035466
4850 16738.443 0 0 5269.51 12.035463
4900 16738.444 0 0 5269.5101 12.035456
4950 16738.444 0 0 5269.5102 12.035447
5000 16738.445 0 0 5269.5104 12.03544
5050 16738.445 0 0 5269.5105 12.035442
5100 16738.446 0 0 5269.5107 12.035455
5150 16738.446 0 0 5269.5108 12.03547
5200 16738.446 0 0 5269.5109 12.035479
5250 16738.447 0 0 5269.511 12.035479
5300 16738.447 0 0 5269.5111 12.03547
5350 16738.447 0 0 5269.5112 12.035454
5400 16738.448 0 0 5269.5113 12.035434
5450 16738.448 0 0 5269.5115 12.03542
5500 16738.449 0 0 5269.5117 12.035422
5550 16738.457 -0.0030919234 0 5269.5111 12.035383
5600 16738.51 -0.021618357 0 5269.5092 12.035106
5650 16738.622 -0.059214788 0 5269.507 12.035694
5700 16395.28 108.06942 0 5269.5463 24.369038
5750 16738.544 -0.033973429 0 5269.5077 12.011261
5800 16738.456 -0.0037013529 0 5269.5102 12.011675
5850 16738.451 0 0 5269.5123 12.011709
5900 16738.451 -0.0002211587 0 5269.5122 12.011687
5950 16738.452 -0.00024253349 0 5269.5124 12.011678
6000 16738.452 0 0 5269.5128 12.011688
6050 16738.453 0 0 5269.513 12.011702
6100 16738.453 0 0 5269.5131 12.011716
6150 16738.454 0 0 5269.5132 12.011725
6200 16738.454 0 0 5269.5133 12.011728
6250 16738.454 0 0 5269.5134 12.011723
6300 16738.455 0 0 5269.5135 12.011712
6350 16738.455 0 0 5269.5137 12.0117
6400 16738.456 0 0 5269.5138 12.011697
6450 16738.456 0 0 5269.514 12.011704
6500 16738.456 0 0 5269.5141 12.011714
6550 16738.457 0 0 5269.5142 12.011719
6600 16738.457 0 0 5269.5143 12.011718
6650 16738.458 0 0 5269.5144 12.011713
6700 16738.458 0 0 5269.5146 12.011705
6750 16738.459 0 0 5269.5147 12.011696
6800 16738.459 0 0 5269.5149 12.01169
6850 16738.46 0 0 5269.515 12.011695
6900 16738.46 0 0 5269.5152 12.01171
6950 16738.46 0 0 5269.5153 12.011726
7000 16738.461 0 0 5269.5154 12.011736
7050 16738.461 0 0 5269.5155 12.011737
7100 16738.461 0 0 5269.5155 12.011728
7150 16738.461 0 0 5269.5156 12.011712
7200 16738.462 0 0 5269.5158 12.011691
7250 16738.463 0 0 5269.516 12.011676
7300 16738.463 0 0 5269.5162 12.011677
7350 16738.464 0 0 5269.5164 12.011693
7400 16738.464 0 0 5269.5165 12.011713
7450 16738.465 0 0 5269.5166 12.011729
7500 16738.465 0 0 5269.5167 12.011736
7550 16738.465 0 0 5269.5168 12.011734
7600 16738.465 0 0 5269.5168 12.011722
7650 16738.466 0 0 5269.517 12.011704
7700 16738.466 0 0 5269.5171 12.011687
7750 16738.467 0 0 5269.5173 12.011681
7800 16738.467 0 0 5269.5175 12.011687
7850 16738.468 0 0 5269.5176 12.0117
7900 16738.468 0 0 5269.5178 12.011712
7950 16738.469 0 0 5269.5179 12.011721
8000 16738.469 0 0 5269.518 12.011724
8050 16738.469 0 0 5269.5181 12.01172
8100 16738.47 0 0 5269.5182 12.011709
8150 16738.47 0 0 5269.5183 12.0117
8200 16738.47 0 0 5269.5185 12.0117
8250 16738.471 0 0 5269.5186 12.011709
8300 16738.471 0 0 5269.5187 12.011719
8350 16738.472 0 0 5269.5189 12.011723
8400 16738.472 0 0 5269.519 12.01172
8450 16738.473 -0.00039690664 0 5269.5189 12.011706
8500 16738.481 -0.0034646803 0 5269.5182 12.011643
8550 16738.483 -0.0045307409 0 5269.5178 12.011621
8600 16738.474 -0.00076532811 0 5269.5189 12.011681
8650 16738.474 0 0 5269.5197 12.011699
8700 16738.475 0 0 5269.5199 12.011715
8750 16738.475 0 0 5269.52 12.011732
8800 16738.475 0 0 5269.52 12.011743
8850 16738.476 0 0 5269.5201 12.011744
8900 16738.476 0 0 5269.5202 12.011735
8950 16738.476 0 0 5269.5203 12.011719
9000 16738.477 0 0 5269.5205 12.011698
9050 16738.477 0 0 5269.5206 12.011683
9100 16738.478 0 0 5269.5208 12.011684
9150 16738.479 0 0 5269.521 12.011701
9200 16738.479 0 0 5269.5212 12.011722
9250 16738.479 0 0 5269.5213 12.011738
9300 16738.48 0 0 5269.5214 12.011746
9350 16738.48 0 0 5269.5214 12.011744
9400 16738.48 0 0 5269.5215 12.011732
9450 16738.48 0 0 5269.5216 12.011715
9500 16738.481 -0.00037652437 0 5269.5216 12.011692
9550 16738.493 -0.0053156158 0 5269.5203 12.011611
9600 16738.549 -0.026814369 0 5269.5163 12.011415
9650 16738.765 -0.10191523 0 5269.5092 12.011013
9700 16735.041 1.0589886 0 5269.4979 12.062708
9750 16738.013 0.13550089 0 5269.5101 11.407245
9800 16738.512 -0.011620329 0 5269.5201 11.394973
9850 16738.489 -0.00067270567 0 5269.5237 11.395098
9900 16738.489 -0.00024984578 0 5269.5242 11.395084
9950 16738.49 0 0 5269.5245 11.395076
10000 16738.49 0 0 5269.5246 11.395075
Loop time of 0.135534 on 4 procs for 10000 steps with 81 atoms
Performance: 637479.927 tau/day, 73782.399 timesteps/s, 5.976 Matom-step/s
98.7% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0016589 | 0.0022805 | 0.0027973 | 0.9 | 1.68
Neigh | 0.012838 | 0.013347 | 0.014456 | 0.6 | 9.85
Comm | 0.062667 | 0.064428 | 0.066142 | 0.6 | 47.54
Output | 0.0018075 | 0.001966 | 0.0024125 | 0.6 | 1.45
Modify | 0.038219 | 0.039639 | 0.041101 | 0.6 | 29.25
Other | | 0.01387 | | | 10.24
Nlocal: 20.25 ave 37 max 3 min
Histogram: 1 0 0 1 0 0 0 1 0 1
Nghost: 27.25 ave 48 max 13 min
Histogram: 1 0 0 2 0 0 0 0 0 1
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0
Neighbor list builds = 1552
Dangerous builds = 0
Total wall time: 0:00:00

340
examples/rigid/log.25Mar24.rigid.early.g++.1
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@ -1,340 +0,0 @@
LAMMPS (7 Feb 2024 - Development - patch_7Feb2024_update1-306-gf3391199e7-modified)
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 = 0.001 seconds
velocity all create 100.0 4928459
# unconnected bodies
group clump1 id <> 1 9
9 atoms in group clump1
group clump2 id <> 10 18
9 atoms in group clump2
group clump3 id <> 19 27
9 atoms in group clump3
group clump4 id <> 28 36
9 atoms in group clump4
group clump5 id <> 37 45
9 atoms in group clump5
group clump6 id <> 46 54
9 atoms in group clump6
group clump7 id <> 55 63
9 atoms in group clump7
group clump8 id <> 64 72
9 atoms in group clump8
group clump9 id <> 73 81
9 atoms in group clump9
fix 1 all rigid group 9 clump1 clump2 clump3 clump4 clump5 clump6 clump7 clump8 clump9
9 rigid bodies with 81 atoms
fix_modify 1 bodyforces early
# 1 chain of connected bodies
#group clump1 id <> 1 9
#group clump2 id <> 9 18
#group clump3 id <> 18 27
#group clump4 id <> 27 36
#group clump5 id <> 36 45
#group clump6 id <> 45 54
#group clump7 id <> 54 63
#group clump8 id <> 63 72
#group clump9 id <> 72 81
#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9
# 2 chains of connected bodies
#group clump1 id <> 1 9
#group clump2 id <> 9 18
#group clump3 id <> 18 27
#group clump4 id <> 27 36
#group clump5 id <> 37 45
#group clump6 id <> 45 54
#group clump7 id <> 54 63
#group clump8 id <> 63 72
#group clump9 id <> 72 81
#fix 1 all poems group clump1 clump2 clump3 clump4
#fix 2 all poems group clump5 clump6 clump7 clump8 clump9
neigh_modify exclude group clump1 clump1
neigh_modify exclude group clump2 clump2
neigh_modify exclude group clump3 clump3
neigh_modify exclude group clump4 clump4
neigh_modify exclude group clump5 clump5
neigh_modify exclude group clump6 clump6
neigh_modify exclude group clump7 clump7
neigh_modify exclude group clump8 clump8
neigh_modify exclude group clump9 clump9
thermo 100
#dump 1 all atom 50 dump.rigid
#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 2 pad 5
#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 3 pad 5
timestep 0.0001
thermo 50
run 10000
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4, bins = 18 18 18
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 4.353 | 4.353 | 4.353 Mbytes
Step Temp E_pair E_mol TotEng Press
0 115.29439 5235.9179 0 5272.2142 -2.7403788
50 14910.685 571.71558 0 5265.82 32.006171
100 16298.442 136.66184 0 5267.653 16.444229
150 16682.606 17.490511 0 5269.4219 14.900344
200 16733.929 1.372872 0 5269.4617 14.569267
250 16738.853 -0.15252816 0 5269.4864 14.496404
300 16738.588 -0.055171335 0 5269.5002 14.496025
350 16738.492 -0.017444677 0 5269.5077 14.496446
400 16738.464 -0.0060102023 0 5269.5104 14.496618
450 16738.455 -0.0012713351 0 5269.5124 14.496701
500 16738.455 -0.00081068621 0 5269.5128 14.496709
550 16738.455 -0.00083203497 0 5269.5129 14.496707
600 16738.455 -0.00058355356 0 5269.5131 14.496709
650 16738.455 -0.00047226704 0 5269.5131 14.496708
700 16738.455 0 0 5269.5136 14.496713
750 16738.455 0 0 5269.5136 14.49671
800 16738.455 0 0 5269.5137 14.496709
850 16738.455 0 0 5269.5137 14.49671
900 16738.456 0 0 5269.5138 14.496713
950 16738.462 -0.0035323872 0 5269.5122 14.496671
1000 16738.586 -0.051135144 0 5269.5036 14.496229
1050 16737.358 0.32995057 0 5269.4981 14.525763
1100 16737.892 0.16210246 0 5269.4984 14.531983
1150 16738.703 -0.089235095 0 5269.5025 14.509899
1200 16738.466 -0.0075446243 0 5269.5096 14.510615
1250 16738.456 0 0 5269.514 14.510704
1300 16738.457 0 0 5269.5141 14.510701
1350 16738.457 0 0 5269.5141 14.510699
1400 16738.457 -0.00044736511 0 5269.5138 14.510693
1450 16738.458 -0.0010971179 0 5269.5134 14.510687
1500 16738.458 -0.00057885428 0 5269.5139 14.510698
1550 16738.457 0 0 5269.5143 14.51071
1600 16738.457 0 0 5269.5144 14.510712
1650 16738.457 0 0 5269.5144 14.510712
1700 16738.458 0 0 5269.5144 14.51071
1750 16738.458 0 0 5269.5145 14.510708
1800 16738.458 0 0 5269.5145 14.510706
1850 16738.458 0 0 5269.5146 14.510705
1900 16738.458 0 0 5269.5146 14.510706
1950 16738.465 -0.0031733615 0 5269.5134 14.510659
2000 16738.491 -0.013255268 0 5269.5117 14.510532
2050 16738.556 -0.0365811 0 5269.5087 14.51029
2100 16738.633 -0.063209659 0 5269.5065 14.510219
2150 16738.607 -0.05601761 0 5269.5055 14.510231
2200 16738.557 -0.038423032 0 5269.5072 14.510404
2250 16738.515 -0.023709918 0 5269.5088 14.510539
2300 16738.489 -0.013249035 0 5269.5111 14.510621
2350 16738.468 -0.0045563719 0 5269.5131 14.510714
2400 16738.46 -0.00052194273 0 5269.5146 14.510771
2450 16738.464 -0.0023259756 0 5269.514 14.510746
2500 16738.468 -0.0051929186 0 5269.5127 14.510731
2550 16738.581 -0.044940117 0 5269.5085 14.510315
2600 16738.427 -7.9722875e-05 0 5269.5046 14.510657
2650 16733.017 1.705148 0 5269.5067 14.596295
2700 16738.761 -0.10614946 0 5269.5038 14.499584
2750 16733.973 1.4038179 0 5269.5064 14.598107
2800 16738.585 -0.046813448 0 5269.5076 14.511073
2850 16738.487 -0.012558719 0 5269.5111 14.510111
2900 16738.465 -0.0026252725 0 5269.514 14.510277
2950 16738.476 -0.0082220764 0 5269.512 14.510223
3000 16738.66 -0.071284779 0 5269.507 14.509758
3050 16715.332 7.2419351 0 5269.476 14.870305
3100 16653.226 26.818761 0 5269.5009 14.496764
3150 16739.351 -0.30690375 0 5269.4886 13.643904
3200 16733.238 1.6025328 0 5269.4737 12.016934
3250 16734.374 1.2554429 0 5269.4841 11.963561
3300 16732.156 1.9585967 0 5269.4893 12.234024
3350 16738.655 -0.079693236 0 5269.497 12.092757
3400 16738.543 -0.042215005 0 5269.4991 12.092809
3450 16738.591 -0.059327511 0 5269.4972 12.092536
3500 16738.759 -0.11761245 0 5269.4918 12.09203
3550 16713.405 7.846062 0 5269.4737 12.389816
3600 16734.939 1.0821936 0 5269.4891 12.173591
3650 16738.808 -0.13663194 0 5269.4882 12.027009
3700 16738.602 -0.070934368 0 5269.4889 12.025288
3750 16737.731 0.20706558 0 5269.4927 12.061948
3800 16738.578 -0.05582043 0 5269.4965 12.035665
3850 16738.471 -0.016307928 0 5269.5024 12.035302
3900 16738.449 -0.0058182199 0 5269.5059 12.035401
3950 16738.439 -0.0012027325 0 5269.5074 12.035461
4000 16738.436 -0.00020698452 0 5269.5075 12.035469
4050 16738.437 0 0 5269.5078 12.035454
4100 16738.437 0 0 5269.508 12.035435
4150 16738.438 0 0 5269.5081 12.035426
4200 16738.438 0 0 5269.5083 12.035432
4250 16738.439 0 0 5269.5085 12.035447
4300 16738.439 0 0 5269.5086 12.035463
4350 16738.44 0 0 5269.5087 12.035474
4400 16738.44 0 0 5269.5088 12.035478
4450 16738.44 0 0 5269.5089 12.035474
4500 16738.44 0 0 5269.509 12.035462
4550 16738.441 0 0 5269.5092 12.035449
4600 16738.441 0 0 5269.5093 12.035445
4650 16738.442 0 0 5269.5095 12.035451
4700 16738.442 0 0 5269.5096 12.03546
4750 16738.443 0 0 5269.5097 12.035465
4800 16738.443 0 0 5269.5098 12.035466
4850 16738.443 0 0 5269.51 12.035463
4900 16738.444 0 0 5269.5101 12.035456
4950 16738.444 0 0 5269.5102 12.035447
5000 16738.445 0 0 5269.5104 12.03544
5050 16738.445 0 0 5269.5105 12.035442
5100 16738.446 0 0 5269.5107 12.035455
5150 16738.446 0 0 5269.5108 12.03547
5200 16738.446 0 0 5269.5109 12.035479
5250 16738.447 0 0 5269.511 12.035479
5300 16738.447 0 0 5269.5111 12.03547
5350 16738.447 0 0 5269.5112 12.035454
5400 16738.448 0 0 5269.5113 12.035434
5450 16738.448 0 0 5269.5115 12.03542
5500 16738.449 0 0 5269.5117 12.035422
5550 16738.457 -0.0030919234 0 5269.5111 12.035383
5600 16738.51 -0.021618357 0 5269.5092 12.035106
5650 16738.622 -0.059214788 0 5269.507 12.035694
5700 16395.28 108.06942 0 5269.5463 24.369038
5750 16738.544 -0.033973429 0 5269.5077 12.011261
5800 16738.456 -0.0037013529 0 5269.5102 12.011675
5850 16738.451 0 0 5269.5123 12.011709
5900 16738.451 -0.0002211587 0 5269.5122 12.011687
5950 16738.452 -0.00024253349 0 5269.5124 12.011678
6000 16738.452 0 0 5269.5128 12.011688
6050 16738.453 0 0 5269.513 12.011702
6100 16738.453 0 0 5269.5131 12.011716
6150 16738.454 0 0 5269.5132 12.011725
6200 16738.454 0 0 5269.5133 12.011728
6250 16738.454 0 0 5269.5134 12.011723
6300 16738.455 0 0 5269.5135 12.011712
6350 16738.455 0 0 5269.5137 12.0117
6400 16738.456 0 0 5269.5138 12.011697
6450 16738.456 0 0 5269.514 12.011704
6500 16738.456 0 0 5269.5141 12.011714
6550 16738.457 0 0 5269.5142 12.011719
6600 16738.457 0 0 5269.5143 12.011718
6650 16738.458 0 0 5269.5144 12.011713
6700 16738.458 0 0 5269.5146 12.011705
6750 16738.459 0 0 5269.5147 12.011696
6800 16738.459 0 0 5269.5149 12.01169
6850 16738.46 0 0 5269.515 12.011695
6900 16738.46 0 0 5269.5152 12.01171
6950 16738.46 0 0 5269.5153 12.011726
7000 16738.461 0 0 5269.5154 12.011736
7050 16738.461 0 0 5269.5155 12.011737
7100 16738.461 0 0 5269.5155 12.011728
7150 16738.461 0 0 5269.5156 12.011712
7200 16738.462 0 0 5269.5158 12.011691
7250 16738.463 0 0 5269.516 12.011676
7300 16738.463 0 0 5269.5162 12.011677
7350 16738.464 0 0 5269.5164 12.011693
7400 16738.464 0 0 5269.5165 12.011713
7450 16738.465 0 0 5269.5166 12.011729
7500 16738.465 0 0 5269.5167 12.011736
7550 16738.465 0 0 5269.5168 12.011734
7600 16738.465 0 0 5269.5168 12.011722
7650 16738.466 0 0 5269.517 12.011704
7700 16738.466 0 0 5269.5171 12.011687
7750 16738.467 0 0 5269.5173 12.011681
7800 16738.467 0 0 5269.5175 12.011687
7850 16738.468 0 0 5269.5176 12.0117
7900 16738.468 0 0 5269.5178 12.011712
7950 16738.469 0 0 5269.5179 12.011721
8000 16738.469 0 0 5269.518 12.011724
8050 16738.469 0 0 5269.5181 12.01172
8100 16738.47 0 0 5269.5182 12.011709
8150 16738.47 0 0 5269.5183 12.0117
8200 16738.47 0 0 5269.5185 12.0117
8250 16738.471 0 0 5269.5186 12.011709
8300 16738.471 0 0 5269.5187 12.011719
8350 16738.472 0 0 5269.5189 12.011723
8400 16738.472 0 0 5269.519 12.01172
8450 16738.473 -0.00039690665 0 5269.5189 12.011706
8500 16738.481 -0.0034646803 0 5269.5182 12.011643
8550 16738.483 -0.0045307408 0 5269.5178 12.011621
8600 16738.474 -0.0007653281 0 5269.5189 12.011681
8650 16738.474 0 0 5269.5197 12.011699
8700 16738.475 0 0 5269.5199 12.011715
8750 16738.475 0 0 5269.52 12.011732
8800 16738.475 0 0 5269.52 12.011743
8850 16738.476 0 0 5269.5201 12.011744
8900 16738.476 0 0 5269.5202 12.011735
8950 16738.476 0 0 5269.5203 12.011719
9000 16738.477 0 0 5269.5205 12.011698
9050 16738.477 0 0 5269.5206 12.011683
9100 16738.478 0 0 5269.5208 12.011684
9150 16738.479 0 0 5269.521 12.011701
9200 16738.479 0 0 5269.5212 12.011722
9250 16738.479 0 0 5269.5213 12.011738
9300 16738.48 0 0 5269.5214 12.011746
9350 16738.48 0 0 5269.5214 12.011744
9400 16738.48 0 0 5269.5215 12.011732
9450 16738.48 0 0 5269.5216 12.011715
9500 16738.481 -0.00037652436 0 5269.5216 12.011692
9550 16738.493 -0.0053156156 0 5269.5203 12.011611
9600 16738.549 -0.026814368 0 5269.5163 12.011415
9650 16738.765 -0.10191522 0 5269.5092 12.011013
9700 16735.041 1.0589881 0 5269.4979 12.062708
9750 16738.013 0.13550093 0 5269.5101 11.407245
9800 16738.512 -0.01162033 0 5269.5201 11.394973
9850 16738.489 -0.00067270581 0 5269.5237 11.395098
9900 16738.489 -0.0002498458 0 5269.5242 11.395084
9950 16738.49 0 0 5269.5245 11.395076
10000 16738.49 0 0 5269.5246 11.395075
Loop time of 0.127115 on 1 procs for 10000 steps with 81 atoms
Performance: 679698.303 tau/day, 78668.785 timesteps/s, 6.372 Matom-step/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 | 0.0074904 | 0.0074904 | 0.0074904 | 0.0 | 5.89
Neigh | 0.044675 | 0.044675 | 0.044675 | 0.0 | 35.15
Comm | 0.0079194 | 0.0079194 | 0.0079194 | 0.0 | 6.23
Output | 0.0018129 | 0.0018129 | 0.0018129 | 0.0 | 1.43
Modify | 0.057845 | 0.057845 | 0.057845 | 0.0 | 45.51
Other | | 0.007372 | | | 5.80
Nlocal: 81 ave 81 max 81 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 84 ave 84 max 84 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0
Neighbor list builds = 1552
Dangerous builds = 0
Total wall time: 0:00:00

340
examples/rigid/log.25Mar24.rigid.early.g++.4
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@ -1,340 +0,0 @@
LAMMPS (7 Feb 2024 - Development - patch_7Feb2024_update1-306-gf3391199e7-modified)
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
# unconnected bodies
group clump1 id <> 1 9
9 atoms in group clump1
group clump2 id <> 10 18
9 atoms in group clump2
group clump3 id <> 19 27
9 atoms in group clump3
group clump4 id <> 28 36
9 atoms in group clump4
group clump5 id <> 37 45
9 atoms in group clump5
group clump6 id <> 46 54
9 atoms in group clump6
group clump7 id <> 55 63
9 atoms in group clump7
group clump8 id <> 64 72
9 atoms in group clump8
group clump9 id <> 73 81
9 atoms in group clump9
fix 1 all rigid group 9 clump1 clump2 clump3 clump4 clump5 clump6 clump7 clump8 clump9
9 rigid bodies with 81 atoms
fix_modify 1 bodyforces early
# 1 chain of connected bodies
#group clump1 id <> 1 9
#group clump2 id <> 9 18
#group clump3 id <> 18 27
#group clump4 id <> 27 36
#group clump5 id <> 36 45
#group clump6 id <> 45 54
#group clump7 id <> 54 63
#group clump8 id <> 63 72
#group clump9 id <> 72 81
#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9
# 2 chains of connected bodies
#group clump1 id <> 1 9
#group clump2 id <> 9 18
#group clump3 id <> 18 27
#group clump4 id <> 27 36
#group clump5 id <> 37 45
#group clump6 id <> 45 54
#group clump7 id <> 54 63
#group clump8 id <> 63 72
#group clump9 id <> 72 81
#fix 1 all poems group clump1 clump2 clump3 clump4
#fix 2 all poems group clump5 clump6 clump7 clump8 clump9
neigh_modify exclude group clump1 clump1
neigh_modify exclude group clump2 clump2
neigh_modify exclude group clump3 clump3
neigh_modify exclude group clump4 clump4
neigh_modify exclude group clump5 clump5
neigh_modify exclude group clump6 clump6
neigh_modify exclude group clump7 clump7
neigh_modify exclude group clump8 clump8
neigh_modify exclude group clump9 clump9
thermo 100
#dump 1 all atom 50 dump.rigid
#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 2 pad 5
#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 3 pad 5
timestep 0.0001
thermo 50
run 10000
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4, bins = 18 18 18
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 4.201 | 4.233 | 4.327 Mbytes
Step Temp E_pair E_mol TotEng Press
0 115.29439 5235.9179 0 5272.2142 -2.7403788
50 14910.685 571.71558 0 5265.82 32.006171
100 16298.442 136.66184 0 5267.653 16.444229
150 16682.606 17.490511 0 5269.4219 14.900344
200 16733.929 1.372872 0 5269.4617 14.569267
250 16738.853 -0.15252816 0 5269.4864 14.496404
300 16738.588 -0.055171335 0 5269.5002 14.496025
350 16738.492 -0.017444677 0 5269.5077 14.496446
400 16738.464 -0.0060102023 0 5269.5104 14.496618
450 16738.455 -0.0012713351 0 5269.5124 14.496701
500 16738.455 -0.00081068621 0 5269.5128 14.496709
550 16738.455 -0.00083203497 0 5269.5129 14.496707
600 16738.455 -0.00058355356 0 5269.5131 14.496709
650 16738.455 -0.00047226704 0 5269.5131 14.496708
700 16738.455 0 0 5269.5136 14.496713
750 16738.455 0 0 5269.5136 14.49671
800 16738.455 0 0 5269.5137 14.496709
850 16738.455 0 0 5269.5137 14.49671
900 16738.456 0 0 5269.5138 14.496713
950 16738.462 -0.0035323872 0 5269.5122 14.496671
1000 16738.586 -0.051135144 0 5269.5036 14.496229
1050 16737.358 0.32995057 0 5269.4981 14.525763
1100 16737.892 0.16210246 0 5269.4984 14.531983
1150 16738.703 -0.089235095 0 5269.5025 14.509899
1200 16738.466 -0.0075446243 0 5269.5096 14.510615
1250 16738.456 0 0 5269.514 14.510704
1300 16738.457 0 0 5269.5141 14.510701
1350 16738.457 0 0 5269.5141 14.510699
1400 16738.457 -0.00044736511 0 5269.5138 14.510693
1450 16738.458 -0.0010971179 0 5269.5134 14.510687
1500 16738.458 -0.00057885428 0 5269.5139 14.510698
1550 16738.457 0 0 5269.5143 14.51071
1600 16738.457 0 0 5269.5144 14.510712
1650 16738.457 0 0 5269.5144 14.510712
1700 16738.458 0 0 5269.5144 14.51071
1750 16738.458 0 0 5269.5145 14.510708
1800 16738.458 0 0 5269.5145 14.510706
1850 16738.458 0 0 5269.5146 14.510705
1900 16738.458 0 0 5269.5146 14.510706
1950 16738.465 -0.0031733615 0 5269.5134 14.510659
2000 16738.491 -0.013255268 0 5269.5117 14.510532
2050 16738.556 -0.0365811 0 5269.5087 14.51029
2100 16738.633 -0.063209659 0 5269.5065 14.510219
2150 16738.607 -0.05601761 0 5269.5055 14.510231
2200 16738.557 -0.038423032 0 5269.5072 14.510404
2250 16738.515 -0.023709918 0 5269.5088 14.510539
2300 16738.489 -0.013249035 0 5269.5111 14.510621
2350 16738.468 -0.0045563719 0 5269.5131 14.510714
2400 16738.46 -0.00052194273 0 5269.5146 14.510771
2450 16738.464 -0.0023259756 0 5269.514 14.510746
2500 16738.468 -0.0051929186 0 5269.5127 14.510731
2550 16738.581 -0.044940117 0 5269.5085 14.510315
2600 16738.427 -7.9722867e-05 0 5269.5046 14.510657
2650 16733.017 1.705148 0 5269.5067 14.596295
2700 16738.761 -0.10614946 0 5269.5038 14.499584
2750 16733.973 1.4038179 0 5269.5064 14.598107
2800 16738.585 -0.046813448 0 5269.5076 14.511073
2850 16738.487 -0.012558719 0 5269.5111 14.510111
2900 16738.465 -0.0026252725 0 5269.514 14.510277
2950 16738.476 -0.0082220764 0 5269.512 14.510223
3000 16738.66 -0.071284779 0 5269.507 14.509758
3050 16715.332 7.2419351 0 5269.476 14.870305
3100 16653.226 26.818761 0 5269.5009 14.496764
3150 16739.351 -0.30690375 0 5269.4886 13.643904
3200 16733.238 1.6025328 0 5269.4737 12.016934
3250 16734.374 1.2554429 0 5269.4841 11.963561
3300 16732.156 1.9585967 0 5269.4893 12.234024
3350 16738.655 -0.079693236 0 5269.497 12.092757
3400 16738.543 -0.042215005 0 5269.4991 12.092809
3450 16738.591 -0.059327511 0 5269.4972 12.092536
3500 16738.759 -0.11761245 0 5269.4918 12.09203
3550 16713.405 7.846062 0 5269.4737 12.389816
3600 16734.939 1.0821936 0 5269.4891 12.173591
3650 16738.808 -0.13663194 0 5269.4882 12.027009
3700 16738.602 -0.070934368 0 5269.4889 12.025288
3750 16737.731 0.20706558 0 5269.4927 12.061948
3800 16738.578 -0.05582043 0 5269.4965 12.035665
3850 16738.471 -0.016307928 0 5269.5024 12.035302
3900 16738.449 -0.0058182199 0 5269.5059 12.035401
3950 16738.439 -0.0012027325 0 5269.5074 12.035461
4000 16738.436 -0.00020698452 0 5269.5075 12.035469
4050 16738.437 0 0 5269.5078 12.035454
4100 16738.437 0 0 5269.508 12.035435
4150 16738.438 0 0 5269.5081 12.035426
4200 16738.438 0 0 5269.5083 12.035432
4250 16738.439 0 0 5269.5085 12.035447
4300 16738.439 0 0 5269.5086 12.035463
4350 16738.44 0 0 5269.5087 12.035474
4400 16738.44 0 0 5269.5088 12.035478
4450 16738.44 0 0 5269.5089 12.035474
4500 16738.44 0 0 5269.509 12.035462
4550 16738.441 0 0 5269.5092 12.035449
4600 16738.441 0 0 5269.5093 12.035445
4650 16738.442 0 0 5269.5095 12.035451
4700 16738.442 0 0 5269.5096 12.03546
4750 16738.443 0 0 5269.5097 12.035465
4800 16738.443 0 0 5269.5098 12.035466
4850 16738.443 0 0 5269.51 12.035463
4900 16738.444 0 0 5269.5101 12.035456
4950 16738.444 0 0 5269.5102 12.035447
5000 16738.445 0 0 5269.5104 12.03544
5050 16738.445 0 0 5269.5105 12.035442
5100 16738.446 0 0 5269.5107 12.035455
5150 16738.446 0 0 5269.5108 12.03547
5200 16738.446 0 0 5269.5109 12.035479
5250 16738.447 0 0 5269.511 12.035479
5300 16738.447 0 0 5269.5111 12.03547
5350 16738.447 0 0 5269.5112 12.035454
5400 16738.448 0 0 5269.5113 12.035434
5450 16738.448 0 0 5269.5115 12.03542
5500 16738.449 0 0 5269.5117 12.035422
5550 16738.457 -0.0030919234 0 5269.5111 12.035383
5600 16738.51 -0.021618357 0 5269.5092 12.035106
5650 16738.622 -0.059214788 0 5269.507 12.035694
5700 16395.28 108.06942 0 5269.5463 24.369038
5750 16738.544 -0.033973429 0 5269.5077 12.011261
5800 16738.456 -0.0037013529 0 5269.5102 12.011675
5850 16738.451 0 0 5269.5123 12.011709
5900 16738.451 -0.0002211587 0 5269.5122 12.011687
5950 16738.452 -0.00024253349 0 5269.5124 12.011678
6000 16738.452 0 0 5269.5128 12.011688
6050 16738.453 0 0 5269.513 12.011702
6100 16738.453 0 0 5269.5131 12.011716
6150 16738.454 0 0 5269.5132 12.011725
6200 16738.454 0 0 5269.5133 12.011728
6250 16738.454 0 0 5269.5134 12.011723
6300 16738.455 0 0 5269.5135 12.011712
6350 16738.455 0 0 5269.5137 12.0117
6400 16738.456 0 0 5269.5138 12.011697
6450 16738.456 0 0 5269.514 12.011704
6500 16738.456 0 0 5269.5141 12.011714
6550 16738.457 0 0 5269.5142 12.011719
6600 16738.457 0 0 5269.5143 12.011718
6650 16738.458 0 0 5269.5144 12.011713
6700 16738.458 0 0 5269.5146 12.011705
6750 16738.459 0 0 5269.5147 12.011696
6800 16738.459 0 0 5269.5149 12.01169
6850 16738.46 0 0 5269.515 12.011695
6900 16738.46 0 0 5269.5152 12.01171
6950 16738.46 0 0 5269.5153 12.011726
7000 16738.461 0 0 5269.5154 12.011736
7050 16738.461 0 0 5269.5155 12.011737
7100 16738.461 0 0 5269.5155 12.011728
7150 16738.461 0 0 5269.5156 12.011712
7200 16738.462 0 0 5269.5158 12.011691
7250 16738.463 0 0 5269.516 12.011676
7300 16738.463 0 0 5269.5162 12.011677
7350 16738.464 0 0 5269.5164 12.011693
7400 16738.464 0 0 5269.5165 12.011713
7450 16738.465 0 0 5269.5166 12.011729
7500 16738.465 0 0 5269.5167 12.011736
7550 16738.465 0 0 5269.5168 12.011734
7600 16738.465 0 0 5269.5168 12.011722
7650 16738.466 0 0 5269.517 12.011704
7700 16738.466 0 0 5269.5171 12.011687
7750 16738.467 0 0 5269.5173 12.011681
7800 16738.467 0 0 5269.5175 12.011687
7850 16738.468 0 0 5269.5176 12.0117
7900 16738.468 0 0 5269.5178 12.011712
7950 16738.469 0 0 5269.5179 12.011721
8000 16738.469 0 0 5269.518 12.011724
8050 16738.469 0 0 5269.5181 12.01172
8100 16738.47 0 0 5269.5182 12.011709
8150 16738.47 0 0 5269.5183 12.0117
8200 16738.47 0 0 5269.5185 12.0117
8250 16738.471 0 0 5269.5186 12.011709
8300 16738.471 0 0 5269.5187 12.011719
8350 16738.472 0 0 5269.5189 12.011723
8400 16738.472 0 0 5269.519 12.01172
8450 16738.473 -0.00039690664 0 5269.5189 12.011706
8500 16738.481 -0.0034646803 0 5269.5182 12.011643
8550 16738.483 -0.0045307409 0 5269.5178 12.011621
8600 16738.474 -0.00076532811 0 5269.5189 12.011681
8650 16738.474 0 0 5269.5197 12.011699
8700 16738.475 0 0 5269.5199 12.011715
8750 16738.475 0 0 5269.52 12.011732
8800 16738.475 0 0 5269.52 12.011743
8850 16738.476 0 0 5269.5201 12.011744
8900 16738.476 0 0 5269.5202 12.011735
8950 16738.476 0 0 5269.5203 12.011719
9000 16738.477 0 0 5269.5205 12.011698
9050 16738.477 0 0 5269.5206 12.011683
9100 16738.478 0 0 5269.5208 12.011684
9150 16738.479 0 0 5269.521 12.011701
9200 16738.479 0 0 5269.5212 12.011722
9250 16738.479 0 0 5269.5213 12.011738
9300 16738.48 0 0 5269.5214 12.011746
9350 16738.48 0 0 5269.5214 12.011744
9400 16738.48 0 0 5269.5215 12.011732
9450 16738.48 0 0 5269.5216 12.011715
9500 16738.481 -0.00037652437 0 5269.5216 12.011692
9550 16738.493 -0.0053156158 0 5269.5203 12.011611
9600 16738.549 -0.026814369 0 5269.5163 12.011415
9650 16738.765 -0.10191523 0 5269.5092 12.011013
9700 16735.041 1.0589886 0 5269.4979 12.062708
9750 16738.013 0.13550089 0 5269.5101 11.407245
9800 16738.512 -0.011620329 0 5269.5201 11.394973
9850 16738.489 -0.00067270567 0 5269.5237 11.395098
9900 16738.489 -0.00024984578 0 5269.5242 11.395084
9950 16738.49 0 0 5269.5245 11.395076
10000 16738.49 0 0 5269.5246 11.395075
Loop time of 0.133679 on 4 procs for 10000 steps with 81 atoms
Performance: 646325.439 tau/day, 74806.185 timesteps/s, 6.059 Matom-step/s
98.8% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0016629 | 0.0023406 | 0.0028762 | 0.9 | 1.75
Neigh | 0.012558 | 0.013331 | 0.015279 | 1.0 | 9.97
Comm | 0.060677 | 0.062779 | 0.0646 | 0.7 | 46.96
Output | 0.0017495 | 0.001914 | 0.0023526 | 0.6 | 1.43
Modify | 0.037566 | 0.039361 | 0.040514 | 0.6 | 29.44
Other | | 0.01395 | | | 10.44
Nlocal: 20.25 ave 37 max 3 min
Histogram: 1 0 0 1 0 0 0 1 0 1
Nghost: 27.25 ave 48 max 13 min
Histogram: 1 0 0 2 0 0 0 0 0 1
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0
Neighbor list builds = 1552
Dangerous builds = 0
Total wall time: 0:00:00

338
examples/rigid/log.25Mar24.rigid.g++.1
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LAMMPS (7 Feb 2024 - Development - patch_7Feb2024_update1-306-gf3391199e7-modified)
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 = 0.002 seconds
velocity all create 100.0 4928459
# unconnected bodies
group clump1 id <> 1 9
9 atoms in group clump1
group clump2 id <> 10 18
9 atoms in group clump2
group clump3 id <> 19 27
9 atoms in group clump3
group clump4 id <> 28 36
9 atoms in group clump4
group clump5 id <> 37 45
9 atoms in group clump5
group clump6 id <> 46 54
9 atoms in group clump6
group clump7 id <> 55 63
9 atoms in group clump7
group clump8 id <> 64 72
9 atoms in group clump8
group clump9 id <> 73 81
9 atoms in group clump9
fix 1 all rigid group 9 clump1 clump2 clump3 clump4 clump5 clump6 clump7 clump8 clump9
9 rigid bodies with 81 atoms
# 1 chain of connected bodies
#group clump1 id <> 1 9
#group clump2 id <> 9 18
#group clump3 id <> 18 27
#group clump4 id <> 27 36
#group clump5 id <> 36 45
#group clump6 id <> 45 54
#group clump7 id <> 54 63
#group clump8 id <> 63 72
#group clump9 id <> 72 81
#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9
# 2 chains of connected bodies
#group clump1 id <> 1 9
#group clump2 id <> 9 18
#group clump3 id <> 18 27
#group clump4 id <> 27 36
#group clump5 id <> 37 45
#group clump6 id <> 45 54
#group clump7 id <> 54 63
#group clump8 id <> 63 72
#group clump9 id <> 72 81
#fix 1 all poems group clump1 clump2 clump3 clump4
#fix 2 all poems group clump5 clump6 clump7 clump8 clump9
neigh_modify exclude group clump1 clump1
neigh_modify exclude group clump2 clump2
neigh_modify exclude group clump3 clump3
neigh_modify exclude group clump4 clump4
neigh_modify exclude group clump5 clump5
neigh_modify exclude group clump6 clump6
neigh_modify exclude group clump7 clump7
neigh_modify exclude group clump8 clump8
neigh_modify exclude group clump9 clump9
thermo 100
#dump 1 all atom 50 dump.rigid
#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 2 pad 5
#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 3 pad 5
timestep 0.0001
thermo 50
run 10000
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4, bins = 18 18 18
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 4.353 | 4.353 | 4.353 Mbytes
Step Temp E_pair E_mol TotEng Press
0 115.29439 5235.9179 0 5272.2142 -2.7403788
50 14910.685 571.71558 0 5265.82 32.006171
100 16298.442 136.66184 0 5267.653 16.444229
150 16682.606 17.490511 0 5269.4219 14.900344
200 16733.929 1.372872 0 5269.4617 14.569267
250 16738.853 -0.15252816 0 5269.4864 14.496404
300 16738.588 -0.055171335 0 5269.5002 14.496025
350 16738.492 -0.017444677 0 5269.5077 14.496446
400 16738.464 -0.0060102023 0 5269.5104 14.496618
450 16738.455 -0.0012713351 0 5269.5124 14.496701
500 16738.455 -0.00081068621 0 5269.5128 14.496709
550 16738.455 -0.00083203497 0 5269.5129 14.496707
600 16738.455 -0.00058355356 0 5269.5131 14.496709
650 16738.455 -0.00047226704 0 5269.5131 14.496708
700 16738.455 0 0 5269.5136 14.496713
750 16738.455 0 0 5269.5136 14.49671
800 16738.455 0 0 5269.5137 14.496709
850 16738.455 0 0 5269.5137 14.49671
900 16738.456 0 0 5269.5138 14.496713
950 16738.462 -0.0035323872 0 5269.5122 14.496671
1000 16738.586 -0.051135144 0 5269.5036 14.496229
1050 16737.358 0.32995057 0 5269.4981 14.525763
1100 16737.892 0.16210246 0 5269.4984 14.531983
1150 16738.703 -0.089235095 0 5269.5025 14.509899
1200 16738.466 -0.0075446243 0 5269.5096 14.510615
1250 16738.456 0 0 5269.514 14.510704
1300 16738.457 0 0 5269.5141 14.510701
1350 16738.457 0 0 5269.5141 14.510699
1400 16738.457 -0.00044736511 0 5269.5138 14.510693
1450 16738.458 -0.0010971179 0 5269.5134 14.510687
1500 16738.458 -0.00057885428 0 5269.5139 14.510698
1550 16738.457 0 0 5269.5143 14.51071
1600 16738.457 0 0 5269.5144 14.510712
1650 16738.457 0 0 5269.5144 14.510712
1700 16738.458 0 0 5269.5144 14.51071
1750 16738.458 0 0 5269.5145 14.510708
1800 16738.458 0 0 5269.5145 14.510706
1850 16738.458 0 0 5269.5146 14.510705
1900 16738.458 0 0 5269.5146 14.510706
1950 16738.465 -0.0031733615 0 5269.5134 14.510659
2000 16738.491 -0.013255268 0 5269.5117 14.510532
2050 16738.556 -0.0365811 0 5269.5087 14.51029
2100 16738.633 -0.063209659 0 5269.5065 14.510219
2150 16738.607 -0.05601761 0 5269.5055 14.510231
2200 16738.557 -0.038423032 0 5269.5072 14.510404
2250 16738.515 -0.023709918 0 5269.5088 14.510539
2300 16738.489 -0.013249035 0 5269.5111 14.510621
2350 16738.468 -0.0045563719 0 5269.5131 14.510714
2400 16738.46 -0.00052194273 0 5269.5146 14.510771
2450 16738.464 -0.0023259756 0 5269.514 14.510746
2500 16738.468 -0.0051929186 0 5269.5127 14.510731
2550 16738.581 -0.044940117 0 5269.5085 14.510315
2600 16738.427 -7.9722875e-05 0 5269.5046 14.510657
2650 16733.017 1.705148 0 5269.5067 14.596295
2700 16738.761 -0.10614946 0 5269.5038 14.499584
2750 16733.973 1.4038179 0 5269.5064 14.598107
2800 16738.585 -0.046813448 0 5269.5076 14.511073
2850 16738.487 -0.012558719 0 5269.5111 14.510111
2900 16738.465 -0.0026252725 0 5269.514 14.510277
2950 16738.476 -0.0082220764 0 5269.512 14.510223
3000 16738.66 -0.071284779 0 5269.507 14.509758
3050 16715.332 7.2419351 0 5269.476 14.870305
3100 16653.226 26.818761 0 5269.5009 14.496764
3150 16739.351 -0.30690375 0 5269.4886 13.643904
3200 16733.238 1.6025328 0 5269.4737 12.016934
3250 16734.374 1.2554429 0 5269.4841 11.963561
3300 16732.156 1.9585967 0 5269.4893 12.234024
3350 16738.655 -0.079693236 0 5269.497 12.092757
3400 16738.543 -0.042215005 0 5269.4991 12.092809
3450 16738.591 -0.059327511 0 5269.4972 12.092536
3500 16738.759 -0.11761245 0 5269.4918 12.09203
3550 16713.405 7.846062 0 5269.4737 12.389816
3600 16734.939 1.0821936 0 5269.4891 12.173591
3650 16738.808 -0.13663194 0 5269.4882 12.027009
3700 16738.602 -0.070934368 0 5269.4889 12.025288
3750 16737.731 0.20706558 0 5269.4927 12.061948
3800 16738.578 -0.05582043 0 5269.4965 12.035665
3850 16738.471 -0.016307928 0 5269.5024 12.035302
3900 16738.449 -0.0058182199 0 5269.5059 12.035401
3950 16738.439 -0.0012027325 0 5269.5074 12.035461
4000 16738.436 -0.00020698452 0 5269.5075 12.035469
4050 16738.437 0 0 5269.5078 12.035454
4100 16738.437 0 0 5269.508 12.035435
4150 16738.438 0 0 5269.5081 12.035426
4200 16738.438 0 0 5269.5083 12.035432
4250 16738.439 0 0 5269.5085 12.035447
4300 16738.439 0 0 5269.5086 12.035463
4350 16738.44 0 0 5269.5087 12.035474
4400 16738.44 0 0 5269.5088 12.035478
4450 16738.44 0 0 5269.5089 12.035474
4500 16738.44 0 0 5269.509 12.035462
4550 16738.441 0 0 5269.5092 12.035449
4600 16738.441 0 0 5269.5093 12.035445
4650 16738.442 0 0 5269.5095 12.035451
4700 16738.442 0 0 5269.5096 12.03546
4750 16738.443 0 0 5269.5097 12.035465
4800 16738.443 0 0 5269.5098 12.035466
4850 16738.443 0 0 5269.51 12.035463
4900 16738.444 0 0 5269.5101 12.035456
4950 16738.444 0 0 5269.5102 12.035447
5000 16738.445 0 0 5269.5104 12.03544
5050 16738.445 0 0 5269.5105 12.035442
5100 16738.446 0 0 5269.5107 12.035455
5150 16738.446 0 0 5269.5108 12.03547
5200 16738.446 0 0 5269.5109 12.035479
5250 16738.447 0 0 5269.511 12.035479
5300 16738.447 0 0 5269.5111 12.03547
5350 16738.447 0 0 5269.5112 12.035454
5400 16738.448 0 0 5269.5113 12.035434
5450 16738.448 0 0 5269.5115 12.03542
5500 16738.449 0 0 5269.5117 12.035422
5550 16738.457 -0.0030919234 0 5269.5111 12.035383
5600 16738.51 -0.021618357 0 5269.5092 12.035106
5650 16738.622 -0.059214788 0 5269.507 12.035694
5700 16395.28 108.06942 0 5269.5463 24.369038
5750 16738.544 -0.033973429 0 5269.5077 12.011261
5800 16738.456 -0.0037013529 0 5269.5102 12.011675
5850 16738.451 0 0 5269.5123 12.011709
5900 16738.451 -0.0002211587 0 5269.5122 12.011687
5950 16738.452 -0.00024253349 0 5269.5124 12.011678
6000 16738.452 0 0 5269.5128 12.011688
6050 16738.453 0 0 5269.513 12.011702
6100 16738.453 0 0 5269.5131 12.011716
6150 16738.454 0 0 5269.5132 12.011725
6200 16738.454 0 0 5269.5133 12.011728
6250 16738.454 0 0 5269.5134 12.011723
6300 16738.455 0 0 5269.5135 12.011712
6350 16738.455 0 0 5269.5137 12.0117
6400 16738.456 0 0 5269.5138 12.011697
6450 16738.456 0 0 5269.514 12.011704
6500 16738.456 0 0 5269.5141 12.011714
6550 16738.457 0 0 5269.5142 12.011719
6600 16738.457 0 0 5269.5143 12.011718
6650 16738.458 0 0 5269.5144 12.011713
6700 16738.458 0 0 5269.5146 12.011705
6750 16738.459 0 0 5269.5147 12.011696
6800 16738.459 0 0 5269.5149 12.01169
6850 16738.46 0 0 5269.515 12.011695
6900 16738.46 0 0 5269.5152 12.01171
6950 16738.46 0 0 5269.5153 12.011726
7000 16738.461 0 0 5269.5154 12.011736
7050 16738.461 0 0 5269.5155 12.011737
7100 16738.461 0 0 5269.5155 12.011728
7150 16738.461 0 0 5269.5156 12.011712
7200 16738.462 0 0 5269.5158 12.011691
7250 16738.463 0 0 5269.516 12.011676
7300 16738.463 0 0 5269.5162 12.011677
7350 16738.464 0 0 5269.5164 12.011693
7400 16738.464 0 0 5269.5165 12.011713
7450 16738.465 0 0 5269.5166 12.011729
7500 16738.465 0 0 5269.5167 12.011736
7550 16738.465 0 0 5269.5168 12.011734
7600 16738.465 0 0 5269.5168 12.011722
7650 16738.466 0 0 5269.517 12.011704
7700 16738.466 0 0 5269.5171 12.011687
7750 16738.467 0 0 5269.5173 12.011681
7800 16738.467 0 0 5269.5175 12.011687
7850 16738.468 0 0 5269.5176 12.0117
7900 16738.468 0 0 5269.5178 12.011712
7950 16738.469 0 0 5269.5179 12.011721
8000 16738.469 0 0 5269.518 12.011724
8050 16738.469 0 0 5269.5181 12.01172
8100 16738.47 0 0 5269.5182 12.011709
8150 16738.47 0 0 5269.5183 12.0117
8200 16738.47 0 0 5269.5185 12.0117
8250 16738.471 0 0 5269.5186 12.011709
8300 16738.471 0 0 5269.5187 12.011719
8350 16738.472 0 0 5269.5189 12.011723
8400 16738.472 0 0 5269.519 12.01172
8450 16738.473 -0.00039690665 0 5269.5189 12.011706
8500 16738.481 -0.0034646803 0 5269.5182 12.011643
8550 16738.483 -0.0045307408 0 5269.5178 12.011621
8600 16738.474 -0.0007653281 0 5269.5189 12.011681
8650 16738.474 0 0 5269.5197 12.011699
8700 16738.475 0 0 5269.5199 12.011715
8750 16738.475 0 0 5269.52 12.011732
8800 16738.475 0 0 5269.52 12.011743
8850 16738.476 0 0 5269.5201 12.011744
8900 16738.476 0 0 5269.5202 12.011735
8950 16738.476 0 0 5269.5203 12.011719
9000 16738.477 0 0 5269.5205 12.011698
9050 16738.477 0 0 5269.5206 12.011683
9100 16738.478 0 0 5269.5208 12.011684
9150 16738.479 0 0 5269.521 12.011701
9200 16738.479 0 0 5269.5212 12.011722
9250 16738.479 0 0 5269.5213 12.011738
9300 16738.48 0 0 5269.5214 12.011746
9350 16738.48 0 0 5269.5214 12.011744
9400 16738.48 0 0 5269.5215 12.011732
9450 16738.48 0 0 5269.5216 12.011715
9500 16738.481 -0.00037652436 0 5269.5216 12.011692
9550 16738.493 -0.0053156156 0 5269.5203 12.011611
9600 16738.549 -0.026814368 0 5269.5163 12.011415
9650 16738.765 -0.10191522 0 5269.5092 12.011013
9700 16735.041 1.0589881 0 5269.4979 12.062708
9750 16738.013 0.13550093 0 5269.5101 11.407245
9800 16738.512 -0.01162033 0 5269.5201 11.394973
9850 16738.489 -0.00067270581 0 5269.5237 11.395098
9900 16738.489 -0.0002498458 0 5269.5242 11.395084
9950 16738.49 0 0 5269.5245 11.395076
10000 16738.49 0 0 5269.5246 11.395075
Loop time of 0.136528 on 1 procs for 10000 steps with 81 atoms
Performance: 632835.120 tau/day, 73244.806 timesteps/s, 5.933 Matom-step/s
98.9% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0091674 | 0.0091674 | 0.0091674 | 0.0 | 6.71
Neigh | 0.046854 | 0.046854 | 0.046854 | 0.0 | 34.32
Comm | 0.0076933 | 0.0076933 | 0.0076933 | 0.0 | 5.63
Output | 0.001779 | 0.001779 | 0.001779 | 0.0 | 1.30
Modify | 0.063842 | 0.063842 | 0.063842 | 0.0 | 46.76
Other | | 0.007193 | | | 5.27
Nlocal: 81 ave 81 max 81 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 84 ave 84 max 84 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0
Neighbor list builds = 1552
Dangerous builds = 0
Total wall time: 0:00:00

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LAMMPS (7 Feb 2024 - Development - patch_7Feb2024_update1-306-gf3391199e7-modified)
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
# unconnected bodies
group clump1 id <> 1 9
9 atoms in group clump1
group clump2 id <> 10 18
9 atoms in group clump2
group clump3 id <> 19 27
9 atoms in group clump3
group clump4 id <> 28 36
9 atoms in group clump4
group clump5 id <> 37 45
9 atoms in group clump5
group clump6 id <> 46 54
9 atoms in group clump6
group clump7 id <> 55 63
9 atoms in group clump7
group clump8 id <> 64 72
9 atoms in group clump8
group clump9 id <> 73 81
9 atoms in group clump9
fix 1 all rigid group 9 clump1 clump2 clump3 clump4 clump5 clump6 clump7 clump8 clump9
9 rigid bodies with 81 atoms
# 1 chain of connected bodies
#group clump1 id <> 1 9
#group clump2 id <> 9 18
#group clump3 id <> 18 27
#group clump4 id <> 27 36
#group clump5 id <> 36 45
#group clump6 id <> 45 54
#group clump7 id <> 54 63
#group clump8 id <> 63 72
#group clump9 id <> 72 81
#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9
# 2 chains of connected bodies
#group clump1 id <> 1 9
#group clump2 id <> 9 18
#group clump3 id <> 18 27
#group clump4 id <> 27 36
#group clump5 id <> 37 45
#group clump6 id <> 45 54
#group clump7 id <> 54 63
#group clump8 id <> 63 72
#group clump9 id <> 72 81
#fix 1 all poems group clump1 clump2 clump3 clump4
#fix 2 all poems group clump5 clump6 clump7 clump8 clump9
neigh_modify exclude group clump1 clump1
neigh_modify exclude group clump2 clump2
neigh_modify exclude group clump3 clump3
neigh_modify exclude group clump4 clump4
neigh_modify exclude group clump5 clump5
neigh_modify exclude group clump6 clump6
neigh_modify exclude group clump7 clump7
neigh_modify exclude group clump8 clump8
neigh_modify exclude group clump9 clump9
thermo 100
#dump 1 all atom 50 dump.rigid
#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 2 pad 5
#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 3 pad 5
timestep 0.0001
thermo 50
run 10000
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4, bins = 18 18 18
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 4.201 | 4.233 | 4.327 Mbytes
Step Temp E_pair E_mol TotEng Press
0 115.29439 5235.9179 0 5272.2142 -2.7403788
50 14910.685 571.71558 0 5265.82 32.006171
100 16298.442 136.66184 0 5267.653 16.444229
150 16682.606 17.490511 0 5269.4219 14.900344
200 16733.929 1.372872 0 5269.4617 14.569267
250 16738.853 -0.15252816 0 5269.4864 14.496404
300 16738.588 -0.055171335 0 5269.5002 14.496025
350 16738.492 -0.017444677 0 5269.5077 14.496446
400 16738.464 -0.0060102023 0 5269.5104 14.496618
450 16738.455 -0.0012713351 0 5269.5124 14.496701
500 16738.455 -0.00081068621 0 5269.5128 14.496709
550 16738.455 -0.00083203497 0 5269.5129 14.496707
600 16738.455 -0.00058355356 0 5269.5131 14.496709
650 16738.455 -0.00047226704 0 5269.5131 14.496708
700 16738.455 0 0 5269.5136 14.496713
750 16738.455 0 0 5269.5136 14.49671
800 16738.455 0 0 5269.5137 14.496709
850 16738.455 0 0 5269.5137 14.49671
900 16738.456 0 0 5269.5138 14.496713
950 16738.462 -0.0035323872 0 5269.5122 14.496671
1000 16738.586 -0.051135144 0 5269.5036 14.496229
1050 16737.358 0.32995057 0 5269.4981 14.525763
1100 16737.892 0.16210246 0 5269.4984 14.531983
1150 16738.703 -0.089235095 0 5269.5025 14.509899
1200 16738.466 -0.0075446243 0 5269.5096 14.510615
1250 16738.456 0 0 5269.514 14.510704
1300 16738.457 0 0 5269.5141 14.510701
1350 16738.457 0 0 5269.5141 14.510699
1400 16738.457 -0.00044736511 0 5269.5138 14.510693
1450 16738.458 -0.0010971179 0 5269.5134 14.510687
1500 16738.458 -0.00057885428 0 5269.5139 14.510698
1550 16738.457 0 0 5269.5143 14.51071
1600 16738.457 0 0 5269.5144 14.510712
1650 16738.457 0 0 5269.5144 14.510712
1700 16738.458 0 0 5269.5144 14.51071
1750 16738.458 0 0 5269.5145 14.510708
1800 16738.458 0 0 5269.5145 14.510706
1850 16738.458 0 0 5269.5146 14.510705
1900 16738.458 0 0 5269.5146 14.510706
1950 16738.465 -0.0031733615 0 5269.5134 14.510659
2000 16738.491 -0.013255268 0 5269.5117 14.510532
2050 16738.556 -0.0365811 0 5269.5087 14.51029
2100 16738.633 -0.063209659 0 5269.5065 14.510219
2150 16738.607 -0.05601761 0 5269.5055 14.510231
2200 16738.557 -0.038423032 0 5269.5072 14.510404
2250 16738.515 -0.023709918 0 5269.5088 14.510539
2300 16738.489 -0.013249035 0 5269.5111 14.510621
2350 16738.468 -0.0045563719 0 5269.5131 14.510714
2400 16738.46 -0.00052194273 0 5269.5146 14.510771
2450 16738.464 -0.0023259756 0 5269.514 14.510746
2500 16738.468 -0.0051929186 0 5269.5127 14.510731
2550 16738.581 -0.044940117 0 5269.5085 14.510315
2600 16738.427 -7.9722867e-05 0 5269.5046 14.510657
2650 16733.017 1.705148 0 5269.5067 14.596295
2700 16738.761 -0.10614946 0 5269.5038 14.499584
2750 16733.973 1.4038179 0 5269.5064 14.598107
2800 16738.585 -0.046813448 0 5269.5076 14.511073
2850 16738.487 -0.012558719 0 5269.5111 14.510111
2900 16738.465 -0.0026252725 0 5269.514 14.510277
2950 16738.476 -0.0082220764 0 5269.512 14.510223
3000 16738.66 -0.071284779 0 5269.507 14.509758
3050 16715.332 7.2419351 0 5269.476 14.870305
3100 16653.226 26.818761 0 5269.5009 14.496764
3150 16739.351 -0.30690375 0 5269.4886 13.643904
3200 16733.238 1.6025328 0 5269.4737 12.016934
3250 16734.374 1.2554429 0 5269.4841 11.963561
3300 16732.156 1.9585967 0 5269.4893 12.234024
3350 16738.655 -0.079693236 0 5269.497 12.092757
3400 16738.543 -0.042215005 0 5269.4991 12.092809
3450 16738.591 -0.059327511 0 5269.4972 12.092536
3500 16738.759 -0.11761245 0 5269.4918 12.09203
3550 16713.405 7.846062 0 5269.4737 12.389816
3600 16734.939 1.0821936 0 5269.4891 12.173591
3650 16738.808 -0.13663194 0 5269.4882 12.027009
3700 16738.602 -0.070934368 0 5269.4889 12.025288
3750 16737.731 0.20706558 0 5269.4927 12.061948
3800 16738.578 -0.05582043 0 5269.4965 12.035665
3850 16738.471 -0.016307928 0 5269.5024 12.035302
3900 16738.449 -0.0058182199 0 5269.5059 12.035401
3950 16738.439 -0.0012027325 0 5269.5074 12.035461
4000 16738.436 -0.00020698452 0 5269.5075 12.035469
4050 16738.437 0 0 5269.5078 12.035454
4100 16738.437 0 0 5269.508 12.035435
4150 16738.438 0 0 5269.5081 12.035426
4200 16738.438 0 0 5269.5083 12.035432
4250 16738.439 0 0 5269.5085 12.035447
4300 16738.439 0 0 5269.5086 12.035463
4350 16738.44 0 0 5269.5087 12.035474
4400 16738.44 0 0 5269.5088 12.035478
4450 16738.44 0 0 5269.5089 12.035474
4500 16738.44 0 0 5269.509 12.035462
4550 16738.441 0 0 5269.5092 12.035449
4600 16738.441 0 0 5269.5093 12.035445
4650 16738.442 0 0 5269.5095 12.035451
4700 16738.442 0 0 5269.5096 12.03546
4750 16738.443 0 0 5269.5097 12.035465
4800 16738.443 0 0 5269.5098 12.035466
4850 16738.443 0 0 5269.51 12.035463
4900 16738.444 0 0 5269.5101 12.035456
4950 16738.444 0 0 5269.5102 12.035447
5000 16738.445 0 0 5269.5104 12.03544
5050 16738.445 0 0 5269.5105 12.035442
5100 16738.446 0 0 5269.5107 12.035455
5150 16738.446 0 0 5269.5108 12.03547
5200 16738.446 0 0 5269.5109 12.035479
5250 16738.447 0 0 5269.511 12.035479
5300 16738.447 0 0 5269.5111 12.03547
5350 16738.447 0 0 5269.5112 12.035454
5400 16738.448 0 0 5269.5113 12.035434
5450 16738.448 0 0 5269.5115 12.03542
5500 16738.449 0 0 5269.5117 12.035422
5550 16738.457 -0.0030919234 0 5269.5111 12.035383
5600 16738.51 -0.021618357 0 5269.5092 12.035106
5650 16738.622 -0.059214788 0 5269.507 12.035694
5700 16395.28 108.06942 0 5269.5463 24.369038
5750 16738.544 -0.033973429 0 5269.5077 12.011261
5800 16738.456 -0.0037013529 0 5269.5102 12.011675
5850 16738.451 0 0 5269.5123 12.011709
5900 16738.451 -0.0002211587 0 5269.5122 12.011687
5950 16738.452 -0.00024253349 0 5269.5124 12.011678
6000 16738.452 0 0 5269.5128 12.011688
6050 16738.453 0 0 5269.513 12.011702
6100 16738.453 0 0 5269.5131 12.011716
6150 16738.454 0 0 5269.5132 12.011725
6200 16738.454 0 0 5269.5133 12.011728
6250 16738.454 0 0 5269.5134 12.011723
6300 16738.455 0 0 5269.5135 12.011712
6350 16738.455 0 0 5269.5137 12.0117
6400 16738.456 0 0 5269.5138 12.011697
6450 16738.456 0 0 5269.514 12.011704
6500 16738.456 0 0 5269.5141 12.011714
6550 16738.457 0 0 5269.5142 12.011719
6600 16738.457 0 0 5269.5143 12.011718
6650 16738.458 0 0 5269.5144 12.011713
6700 16738.458 0 0 5269.5146 12.011705
6750 16738.459 0 0 5269.5147 12.011696
6800 16738.459 0 0 5269.5149 12.01169
6850 16738.46 0 0 5269.515 12.011695
6900 16738.46 0 0 5269.5152 12.01171
6950 16738.46 0 0 5269.5153 12.011726
7000 16738.461 0 0 5269.5154 12.011736
7050 16738.461 0 0 5269.5155 12.011737
7100 16738.461 0 0 5269.5155 12.011728
7150 16738.461 0 0 5269.5156 12.011712
7200 16738.462 0 0 5269.5158 12.011691
7250 16738.463 0 0 5269.516 12.011676
7300 16738.463 0 0 5269.5162 12.011677
7350 16738.464 0 0 5269.5164 12.011693
7400 16738.464 0 0 5269.5165 12.011713
7450 16738.465 0 0 5269.5166 12.011729
7500 16738.465 0 0 5269.5167 12.011736
7550 16738.465 0 0 5269.5168 12.011734
7600 16738.465 0 0 5269.5168 12.011722
7650 16738.466 0 0 5269.517 12.011704
7700 16738.466 0 0 5269.5171 12.011687
7750 16738.467 0 0 5269.5173 12.011681
7800 16738.467 0 0 5269.5175 12.011687
7850 16738.468 0 0 5269.5176 12.0117
7900 16738.468 0 0 5269.5178 12.011712
7950 16738.469 0 0 5269.5179 12.011721
8000 16738.469 0 0 5269.518 12.011724
8050 16738.469 0 0 5269.5181 12.01172
8100 16738.47 0 0 5269.5182 12.011709
8150 16738.47 0 0 5269.5183 12.0117
8200 16738.47 0 0 5269.5185 12.0117
8250 16738.471 0 0 5269.5186 12.011709
8300 16738.471 0 0 5269.5187 12.011719
8350 16738.472 0 0 5269.5189 12.011723
8400 16738.472 0 0 5269.519 12.01172
8450 16738.473 -0.00039690664 0 5269.5189 12.011706
8500 16738.481 -0.0034646803 0 5269.5182 12.011643
8550 16738.483 -0.0045307409 0 5269.5178 12.011621
8600 16738.474 -0.00076532811 0 5269.5189 12.011681
8650 16738.474 0 0 5269.5197 12.011699
8700 16738.475 0 0 5269.5199 12.011715
8750 16738.475 0 0 5269.52 12.011732
8800 16738.475 0 0 5269.52 12.011743
8850 16738.476 0 0 5269.5201 12.011744
8900 16738.476 0 0 5269.5202 12.011735
8950 16738.476 0 0 5269.5203 12.011719
9000 16738.477 0 0 5269.5205 12.011698
9050 16738.477 0 0 5269.5206 12.011683
9100 16738.478 0 0 5269.5208 12.011684
9150 16738.479 0 0 5269.521 12.011701
9200 16738.479 0 0 5269.5212 12.011722
9250 16738.479 0 0 5269.5213 12.011738
9300 16738.48 0 0 5269.5214 12.011746
9350 16738.48 0 0 5269.5214 12.011744
9400 16738.48 0 0 5269.5215 12.011732
9450 16738.48 0 0 5269.5216 12.011715
9500 16738.481 -0.00037652437 0 5269.5216 12.011692
9550 16738.493 -0.0053156158 0 5269.5203 12.011611
9600 16738.549 -0.026814369 0 5269.5163 12.011415
9650 16738.765 -0.10191523 0 5269.5092 12.011013
9700 16735.041 1.0589886 0 5269.4979 12.062708
9750 16738.013 0.13550089 0 5269.5101 11.407245
9800 16738.512 -0.011620329 0 5269.5201 11.394973
9850 16738.489 -0.00067270567 0 5269.5237 11.395098
9900 16738.489 -0.00024984578 0 5269.5242 11.395084
9950 16738.49 0 0 5269.5245 11.395076
10000 16738.49 0 0 5269.5246 11.395075
Loop time of 0.134503 on 4 procs for 10000 steps with 81 atoms
Performance: 642365.322 tau/day, 74347.838 timesteps/s, 6.022 Matom-step/s
96.6% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0016076 | 0.0023247 | 0.002836 | 0.9 | 1.73
Neigh | 0.012491 | 0.013229 | 0.0145 | 0.7 | 9.84
Comm | 0.062105 | 0.063666 | 0.06514 | 0.5 | 47.33
Output | 0.0017602 | 0.0019318 | 0.0024227 | 0.6 | 1.44
Modify | 0.038132 | 0.039518 | 0.040852 | 0.5 | 29.38
Other | | 0.01383 | | | 10.29
Nlocal: 20.25 ave 37 max 3 min
Histogram: 1 0 0 1 0 0 0 1 0 1
Nghost: 27.25 ave 48 max 13 min
Histogram: 1 0 0 2 0 0 0 0 0 1
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0
Neighbor list builds = 1552
Dangerous builds = 0
Total wall time: 0:00:00

228
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@ -1,228 +0,0 @@
LAMMPS (7 Feb 2024 - Development - patch_7Feb2024_update1-306-gf3391199e7-modified)
using 1 OpenMP thread(s) per MPI task
#Pour composite granular particles on flat wall
newton on
atom_style sphere
atom_modify map array sort 0 0
thermo_modify flush yes
units si
variable minrad equal 0.5
variable maxrad equal 1.4
variable skin equal 0.3*${maxrad}
variable skin equal 0.3*1.4
boundary p p f
region reg block 0 20 0 20 0 200 units box
create_box 1 reg
Created orthogonal box = (0 0 0) to (20 20 200)
1 by 1 by 1 MPI processor grid
fix prop all property/atom mol ghost yes
variable dumpfreq equal 1000
variable logfreq equal 1000
pair_style gran/hooke/history 4e5 NULL 1e2 NULL 0.5 0
pair_coeff * *
timestep 0.0001
group particles type 1
0 atoms in group particles
atom_modify first particles
neighbor ${skin} bin
neighbor 0.42 bin
group rigid type 1
0 atoms in group rigid
neigh_modify every 1 delay 0 check yes exclude molecule/intra all
thermo ${logfreq}
thermo 1000
thermo_style custom step cpu atoms ke
WARNING: New thermo_style command, previous thermo_modify settings will be lost (src/output.cpp:904)
thermo_modify flush yes lost warn
comm_modify vel yes cutoff 3
molecule mymol molecule.data
Read molecule template mymol:
LAMMPS data file created for rigid body molecule template
1 molecules
0 fragments
5 atoms with max type 1
0 bonds with max type 0
0 angles with max type 0
0 dihedrals with max type 0
0 impropers with max type 0
region pourreg block 5 15 5 15 80 100 side in units box
#Note: in versions prior to 1/2020, the 'disable' keyword to fix/gravity
# and the 'gravity' keyword to fix rigid/small were not available.
# These settings produce undesirable behavior, where gravity can induce
# torque on rigid bodies.
#fix gravfix all gravity 9.8 vector 0 0 -1 #disable
#fix rigidfix all rigid/small molecule mol mymol #gravity gravfix
#The correct behavior is recovered with the following settings:
fix gravfix all gravity 9.8 vector 0 0 -1 disable
fix rigidfix all rigid/small molecule mol mymol gravity gravfix
create bodies CPU = 0.000 seconds
0 rigid bodies with 0 atoms
1.2 = max distance from body owner to body atom
fix pourfix all pour 5 0 1234 region pourreg mol mymol rigid rigidfix
Particle insertion: 15 every 20203 steps, 5 by step 1
fix zwall all wall/gran hooke/history 4000.0 NULL 100.0 NULL 0.5 0 zplane 0.1 NULL
#dump 1 all custom 1000 molecule_pour.dump id type mass radius x y z fx fy fz
run 100000
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 1.62
ghost atom cutoff = 3
binsize = 0.81, bins = 25 25 247
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair gran/hooke/history, perpetual
attributes: half, newton on, size, history
pair build: half/size/bin/atomonly/newton
stencil: half/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 6.893 | 6.893 | 6.893 Mbytes
Step CPU Atoms KinEng
0 0 0 -0
1000 0.005385611 25 -0
2000 0.01106897 25 -0
3000 0.01569532 25 -0
4000 0.020782538 25 -0
5000 0.02656256 25 -0
6000 0.03132421 25 -0
7000 0.035996621 25 -0
8000 0.040816339 25 -0
9000 0.045911912 25 -0
10000 0.051486339 25 -0
11000 0.058049641 25 -0
12000 0.063206805 25 -0
13000 0.068374138 25 -0
14000 0.073423818 25 -0
15000 0.078890587 25 -0
16000 0.086372246 25 -0
17000 0.091912312 25 -0
18000 0.097317178 25 -0
19000 0.10284163 25 -0
20000 0.10836857 25 -0
21000 0.11476057 25 -0
22000 0.12201322 25 -0
23000 0.127963 25 -0
24000 0.13386968 25 -0
25000 0.1397396 25 -0
26000 0.14672759 25 -0
27000 0.15447534 25 -0
28000 0.16103509 25 -0
29000 0.16703686 25 -0
30000 0.17306375 25 -0
31000 0.18150464 25 -0
32000 0.1874536 25 -0
33000 0.19372953 25 -0
34000 0.19997087 25 -0
35000 0.20643521 25 -0
36000 0.21499446 25 -0
37000 0.22129475 25 -0
38000 0.2278159 25 -0
39000 0.23262556 25 -0
40000 0.23679 25 -0
41000 0.2428383 25 -0
42000 0.24757287 25 -0
43000 0.25190701 25 -0
44000 0.25617771 25 -0
45000 0.26057242 25 -0
46000 0.26469065 25 -0
47000 0.26921214 25 -0
48000 0.27502337 25 -0
49000 0.27911905 25 -0
50000 0.28338379 25 -0
51000 0.28736617 25 -0
52000 0.29127304 25 -0
53000 0.29504445 25 -0
54000 0.29898933 25 -0
55000 0.30479176 25 -0
56000 0.30893347 25 -0
57000 0.31277358 25 -0
58000 0.31658797 25 -0
59000 0.32024112 25 -0
60000 0.32373109 25 -0
61000 0.32753442 25 -0
62000 0.33123815 25 -0
63000 0.33643285 25 -0
64000 0.34036569 25 -0
65000 0.34399532 25 -0
66000 0.3475875 25 -0
67000 0.35124833 25 -0
68000 0.35503825 25 -0
69000 0.35870471 25 -0
70000 0.3624294 25 -0
71000 0.36714884 25 -0
72000 0.37082887 25 -0
73000 0.37459885 25 -0
74000 0.37835449 25 -0
75000 0.38245549 25 -0
76000 0.38681838 25 -0
77000 0.39069919 25 -0
78000 0.39460729 25 -0
79000 0.39908672 25 -0
80000 0.40266481 25 -0
81000 0.40645032 25 -0
82000 0.41005038 25 -0
83000 0.41355864 25 -0
84000 0.41741638 25 -0
85000 0.42182475 25 -0
86000 0.42614449 25 -0
87000 0.43024819 25 -0
88000 0.43389722 25 -0
89000 0.4372946 25 -0
90000 0.44097963 25 -0
91000 0.44451596 25 -0
92000 0.44800886 25 -0
93000 0.45171482 25 -0
94000 0.45568312 25 -0
95000 0.46068385 25 -0
96000 0.46423783 25 -0
97000 0.46783791 25 -0
98000 0.47132532 25 -0
99000 0.47462675 25 -0
100000 0.47811781 25 -0
Loop time of 0.478128 on 1 procs for 100000 steps with 25 atoms
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 | 0.016638 | 0.016638 | 0.016638 | 0.0 | 3.48
Neigh | 0.12338 | 0.12338 | 0.12338 | 0.0 | 25.81
Comm | 0.026212 | 0.026212 | 0.026212 | 0.0 | 5.48
Output | 0.0015672 | 0.0015672 | 0.0015672 | 0.0 | 0.33
Modify | 0.28303 | 0.28303 | 0.28303 | 0.0 | 59.20
Other | | 0.0273 | | | 5.71
Nlocal: 25 ave 25 max 25 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1 ave 1 max 1 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0
Neighbor list builds = 703
Dangerous builds = 0
Total wall time: 0:00:00

228
examples/rigid/log.25Mar24.rigid.gravity.g++.4
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@ -1,228 +0,0 @@
LAMMPS (7 Feb 2024 - Development - patch_7Feb2024_update1-306-gf3391199e7-modified)
using 1 OpenMP thread(s) per MPI task
#Pour composite granular particles on flat wall
newton on
atom_style sphere
atom_modify map array sort 0 0
thermo_modify flush yes
units si
variable minrad equal 0.5
variable maxrad equal 1.4
variable skin equal 0.3*${maxrad}
variable skin equal 0.3*1.4
boundary p p f
region reg block 0 20 0 20 0 200 units box
create_box 1 reg
Created orthogonal box = (0 0 0) to (20 20 200)
1 by 1 by 4 MPI processor grid
fix prop all property/atom mol ghost yes
variable dumpfreq equal 1000
variable logfreq equal 1000
pair_style gran/hooke/history 4e5 NULL 1e2 NULL 0.5 0
pair_coeff * *
timestep 0.0001
group particles type 1
0 atoms in group particles
atom_modify first particles
neighbor ${skin} bin
neighbor 0.42 bin
group rigid type 1
0 atoms in group rigid
neigh_modify every 1 delay 0 check yes exclude molecule/intra all
thermo ${logfreq}
thermo 1000
thermo_style custom step cpu atoms ke
WARNING: New thermo_style command, previous thermo_modify settings will be lost (src/output.cpp:904)
thermo_modify flush yes lost warn
comm_modify vel yes cutoff 3
molecule mymol molecule.data
Read molecule template mymol:
LAMMPS data file created for rigid body molecule template
1 molecules
0 fragments
5 atoms with max type 1
0 bonds with max type 0
0 angles with max type 0
0 dihedrals with max type 0
0 impropers with max type 0
region pourreg block 5 15 5 15 80 100 side in units box
#Note: in versions prior to 1/2020, the 'disable' keyword to fix/gravity
# and the 'gravity' keyword to fix rigid/small were not available.
# These settings produce undesirable behavior, where gravity can induce
# torque on rigid bodies.
#fix gravfix all gravity 9.8 vector 0 0 -1 #disable
#fix rigidfix all rigid/small molecule mol mymol #gravity gravfix
#The correct behavior is recovered with the following settings:
fix gravfix all gravity 9.8 vector 0 0 -1 disable
fix rigidfix all rigid/small molecule mol mymol gravity gravfix
create bodies CPU = 0.000 seconds
0 rigid bodies with 0 atoms
1.2 = max distance from body owner to body atom
fix pourfix all pour 5 0 1234 region pourreg mol mymol rigid rigidfix
Particle insertion: 15 every 20203 steps, 5 by step 1
fix zwall all wall/gran hooke/history 4000.0 NULL 100.0 NULL 0.5 0 zplane 0.1 NULL
#dump 1 all custom 1000 molecule_pour.dump id type mass radius x y z fx fy fz
run 100000
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 1.62
ghost atom cutoff = 3
binsize = 0.81, bins = 25 25 247
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair gran/hooke/history, perpetual
attributes: half, newton on, size, history
pair build: half/size/bin/atomonly/newton
stencil: half/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 6.09 | 6.09 | 6.09 Mbytes
Step CPU Atoms KinEng
0 0 0 -0
1000 0.007155423 25 -0
2000 0.013621411 25 -0
3000 0.018069993 25 -0
4000 0.022375597 25 -0
5000 0.027610001 25 -0
6000 0.032700728 25 -0
7000 0.036781214 25 -0
8000 0.041026343 25 -0
9000 0.045133974 25 -0
10000 0.049302504 25 -0
11000 0.053475155 25 -0
12000 0.058101552 25 -0
13000 0.063617332 25 -0
14000 0.070220865 25 -0
15000 0.079467476 25 -0
16000 0.085128592 25 -0
17000 0.088670803 25 -0
18000 0.093576466 25 -0
19000 0.096967506 25 -0
20000 0.10032704 25 -0
21000 0.1037381 25 -0
22000 0.10714647 25 -0
23000 0.11062389 25 -0
24000 0.11408744 25 -0
25000 0.12017243 25 -0
26000 0.12858759 25 -0
27000 0.13356253 25 -0
28000 0.13819667 25 -0
29000 0.14299332 25 -0
30000 0.14766723 25 -0
31000 0.15258071 25 -0
32000 0.15836989 25 -0
33000 0.16306841 25 -0
34000 0.16769723 25 -0
35000 0.172317 25 -0
36000 0.17698336 25 -0
37000 0.18173594 25 -0
38000 0.1879449 25 -0
39000 0.19236501 25 -0
40000 0.1964458 25 -0
41000 0.20045733 25 -0
42000 0.20454794 25 -0
43000 0.20872097 25 -0
44000 0.21291348 25 -0
45000 0.21780319 25 -0
46000 0.22260816 25 -0
47000 0.22686931 25 -0
48000 0.23117793 25 -0
49000 0.23535185 25 -0
50000 0.24054306 25 -0
51000 0.24463963 25 -0
52000 0.24938311 25 -0
53000 0.25348209 25 -0
54000 0.25745703 25 -0
55000 0.26145377 25 -0
56000 0.26534485 25 -0
57000 0.26928518 25 -0
58000 0.27321574 25 -0
59000 0.27791991 25 -0
60000 0.28284558 25 -0
61000 0.28673327 25 -0
62000 0.29055931 25 -0
63000 0.2945131 25 -0
64000 0.29846467 25 -0
65000 0.30238139 25 -0
66000 0.3062491 25 -0
67000 0.31026454 25 -0
68000 0.31498685 25 -0
69000 0.31887771 25 -0
70000 0.32278066 25 -0
71000 0.32658541 25 -0
72000 0.33047871 25 -0
73000 0.33441507 25 -0
74000 0.33830186 25 -0
75000 0.34298503 25 -0
76000 0.3470502 25 -0
77000 0.35093166 25 -0
78000 0.35472767 25 -0
79000 0.35858626 25 -0
80000 0.36236101 25 -0
81000 0.36621078 25 -0
82000 0.36998141 25 -0
83000 0.37417451 25 -0
84000 0.37850331 25 -0
85000 0.38230344 25 -0
86000 0.38621429 25 -0
87000 0.38998154 25 -0
88000 0.39378687 25 -0
89000 0.397529 25 -0
90000 0.40133202 25 -0
91000 0.40575097 25 -0
92000 0.41012392 25 -0
93000 0.41397633 25 -0
94000 0.41791732 25 -0
95000 0.42174915 25 -0
96000 0.42570384 25 -0
97000 0.4295687 25 -0
98000 0.43339555 25 -0
99000 0.43810319 25 -0
100000 0.44205356 25 -0
Loop time of 0.442071 on 4 procs for 100000 steps with 25 atoms
99.1% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0043596 | 0.0077919 | 0.015026 | 4.9 | 1.76
Neigh | 0.03639 | 0.037869 | 0.038842 | 0.5 | 8.57
Comm | 0.029189 | 0.034805 | 0.038937 | 2.3 | 7.87
Output | 0.00094691 | 0.0012173 | 0.0019545 | 1.2 | 0.28
Modify | 0.031085 | 0.10076 | 0.24754 | 27.5 | 22.79
Other | | 0.2596 | | | 58.73
Nlocal: 6.25 ave 25 max 0 min
Histogram: 3 0 0 0 0 0 0 0 0 1
Nghost: 0.25 ave 1 max 0 min
Histogram: 3 0 0 0 0 0 0 0 0 1
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0
Neighbor list builds = 703
Dangerous builds = 0
Total wall time: 0:00:00

310
examples/rigid/log.25Mar24.rigid.infile.g++.1
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@ -1,310 +0,0 @@
LAMMPS (7 Feb 2024 - Development - patch_7Feb2024_update1-306-gf3391199e7-modified)
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 = 0.001 seconds
velocity all create 100.0 4928459
# unconnected bodies
group clump1 id <> 1 9
9 atoms in group clump1
group clump2 id <> 10 18
9 atoms in group clump2
group clump3 id <> 19 27
9 atoms in group clump3
group clump4 id <> 28 36
9 atoms in group clump4
group clump5 id <> 37 45
9 atoms in group clump5
group clump6 id <> 46 54
9 atoms in group clump6
group clump7 id <> 55 63
9 atoms in group clump7
group clump8 id <> 64 72
9 atoms in group clump8
group clump9 id <> 73 81
9 atoms in group clump9
fix 1 all rigid group 9 clump1 clump2 clump3 clump4 clump5 clump6 clump7 clump8 clump9 infile bodyinfo.dat
9 rigid bodies with 81 atoms
neigh_modify exclude group clump1 clump1
neigh_modify exclude group clump2 clump2
neigh_modify exclude group clump3 clump3
neigh_modify exclude group clump4 clump4
neigh_modify exclude group clump5 clump5
neigh_modify exclude group clump6 clump6
neigh_modify exclude group clump7 clump7
neigh_modify exclude group clump8 clump8
neigh_modify exclude group clump9 clump9
thermo 100
#dump 1 all atom 50 dump.rigid
#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 2 pad 5
#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 3 pad 5
timestep 0.0001
thermo 50
run 10000
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Reading rigid body data for 4 bodies from file bodyinfo.dat
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4, bins = 18 18 18
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 4.353 | 4.353 | 4.353 Mbytes
Step Temp E_pair E_mol TotEng Press
0 115.29439 5235.9179 0 5272.2142 -2.7403788
50 14910.685 571.71558 0 5265.82 32.006171
100 16298.442 136.66184 0 5267.653 16.444229
150 16682.606 17.490511 0 5269.4219 14.900344
200 16733.929 1.372872 0 5269.4617 14.569267
250 16738.853 -0.15252816 0 5269.4864 14.496404
300 16738.588 -0.055171335 0 5269.5002 14.496025
350 16738.492 -0.017444677 0 5269.5077 14.496446
400 16738.464 -0.0060102023 0 5269.5104 14.496618
450 16738.455 -0.0012713351 0 5269.5124 14.496701
500 16738.455 -0.00081068621 0 5269.5128 14.496709
550 16738.455 -0.00083203497 0 5269.5129 14.496707
600 16738.455 -0.00058355356 0 5269.5131 14.496709
650 16738.455 -0.00047226704 0 5269.5131 14.496708
700 16738.455 0 0 5269.5136 14.496713
750 16738.455 0 0 5269.5136 14.49671
800 16738.455 0 0 5269.5137 14.496709
850 16738.455 0 0 5269.5137 14.49671
900 16738.456 0 0 5269.5138 14.496713
950 16738.462 -0.0035323872 0 5269.5122 14.496671
1000 16738.586 -0.051135144 0 5269.5036 14.496229
1050 16737.358 0.32995057 0 5269.4981 14.525763
1100 16737.892 0.16210246 0 5269.4984 14.531983
1150 16738.703 -0.089235095 0 5269.5025 14.509899
1200 16738.466 -0.0075446243 0 5269.5096 14.510615
1250 16738.456 0 0 5269.514 14.510704
1300 16738.457 0 0 5269.5141 14.510701
1350 16738.457 0 0 5269.5141 14.510699
1400 16738.457 -0.00044736511 0 5269.5138 14.510693
1450 16738.458 -0.0010971179 0 5269.5134 14.510687
1500 16738.458 -0.00057885428 0 5269.5139 14.510698
1550 16738.457 0 0 5269.5143 14.51071
1600 16738.457 0 0 5269.5144 14.510712
1650 16738.457 0 0 5269.5144 14.510712
1700 16738.458 0 0 5269.5144 14.51071
1750 16738.458 0 0 5269.5145 14.510708
1800 16738.458 0 0 5269.5145 14.510706
1850 16738.458 0 0 5269.5146 14.510705
1900 16738.458 0 0 5269.5146 14.510706
1950 16738.465 -0.0031733615 0 5269.5134 14.510659
2000 16738.491 -0.013255268 0 5269.5117 14.510532
2050 16738.556 -0.0365811 0 5269.5087 14.51029
2100 16738.633 -0.063209659 0 5269.5065 14.510219
2150 16738.607 -0.05601761 0 5269.5055 14.510231
2200 16738.557 -0.038423032 0 5269.5072 14.510404
2250 16738.515 -0.023709918 0 5269.5088 14.510539
2300 16738.489 -0.013249035 0 5269.5111 14.510621
2350 16738.468 -0.0045563719 0 5269.5131 14.510714
2400 16738.46 -0.00052194273 0 5269.5146 14.510771
2450 16738.464 -0.0023259756 0 5269.514 14.510746
2500 16738.468 -0.0051929186 0 5269.5127 14.510731
2550 16738.581 -0.044940117 0 5269.5085 14.510315
2600 16738.427 -7.9722859e-05 0 5269.5046 14.510657
2650 16733.017 1.7051479 0 5269.5067 14.596295
2700 16738.761 -0.10614946 0 5269.5038 14.499584
2750 16733.973 1.4038179 0 5269.5064 14.598107
2800 16738.585 -0.046813448 0 5269.5076 14.511073
2850 16738.487 -0.012558719 0 5269.5111 14.510111
2900 16738.465 -0.0026252725 0 5269.514 14.510277
2950 16738.476 -0.0082220764 0 5269.512 14.510223
3000 16738.66 -0.071284779 0 5269.507 14.509758
3050 16715.332 7.2419352 0 5269.476 14.870305
3100 16653.226 26.818761 0 5269.5009 14.496764
3150 16739.351 -0.30690375 0 5269.4886 13.643904
3200 16733.238 1.6025328 0 5269.4737 12.016934
3250 16734.374 1.2554429 0 5269.4841 11.963561
3300 16732.156 1.9585967 0 5269.4893 12.234024
3350 16738.655 -0.079693236 0 5269.497 12.092757
3400 16738.543 -0.042215005 0 5269.4991 12.092809
3450 16738.591 -0.05932751 0 5269.4972 12.092536
3500 16738.759 -0.11761245 0 5269.4918 12.09203
3550 16713.405 7.8460621 0 5269.4737 12.389816
3600 16734.939 1.0821936 0 5269.4891 12.173591
3650 16738.808 -0.13663193 0 5269.4882 12.027009
3700 16738.602 -0.070934369 0 5269.4889 12.025288
3750 16737.731 0.20706559 0 5269.4927 12.061948
3800 16738.578 -0.05582043 0 5269.4965 12.035665
3850 16738.471 -0.016307928 0 5269.5024 12.035302
3900 16738.449 -0.0058182199 0 5269.5059 12.035401
3950 16738.439 -0.0012027325 0 5269.5074 12.035461
4000 16738.436 -0.00020698452 0 5269.5075 12.035469
4050 16738.437 0 0 5269.5078 12.035454
4100 16738.437 0 0 5269.508 12.035435
4150 16738.438 0 0 5269.5081 12.035426
4200 16738.438 0 0 5269.5083 12.035432
4250 16738.439 0 0 5269.5085 12.035447
4300 16738.439 0 0 5269.5086 12.035463
4350 16738.44 0 0 5269.5087 12.035474
4400 16738.44 0 0 5269.5088 12.035478
4450 16738.44 0 0 5269.5089 12.035474
4500 16738.44 0 0 5269.509 12.035462
4550 16738.441 0 0 5269.5092 12.035449
4600 16738.441 0 0 5269.5093 12.035445
4650 16738.442 0 0 5269.5095 12.035451
4700 16738.442 0 0 5269.5096 12.03546
4750 16738.443 0 0 5269.5097 12.035465
4800 16738.443 0 0 5269.5098 12.035466
4850 16738.443 0 0 5269.51 12.035463
4900 16738.444 0 0 5269.5101 12.035456
4950 16738.444 0 0 5269.5102 12.035447
5000 16738.445 0 0 5269.5104 12.03544
5050 16738.445 0 0 5269.5105 12.035442
5100 16738.446 0 0 5269.5107 12.035455
5150 16738.446 0 0 5269.5108 12.03547
5200 16738.446 0 0 5269.5109 12.035479
5250 16738.447 0 0 5269.511 12.035479
5300 16738.447 0 0 5269.5111 12.03547
5350 16738.447 0 0 5269.5112 12.035454
5400 16738.448 0 0 5269.5113 12.035434
5450 16738.448 0 0 5269.5115 12.03542
5500 16738.449 0 0 5269.5117 12.035422
5550 16738.457 -0.0030919234 0 5269.5111 12.035383
5600 16738.51 -0.021618357 0 5269.5092 12.035106
5650 16738.622 -0.059214788 0 5269.507 12.035694
5700 16395.28 108.06942 0 5269.5463 24.369038
5750 16738.544 -0.033973429 0 5269.5077 12.011261
5800 16738.456 -0.0037013529 0 5269.5102 12.011675
5850 16738.451 0 0 5269.5123 12.011709
5900 16738.451 -0.0002211587 0 5269.5122 12.011687
5950 16738.452 -0.00024253348 0 5269.5124 12.011678
6000 16738.452 0 0 5269.5128 12.011688
6050 16738.453 0 0 5269.513 12.011702
6100 16738.453 0 0 5269.5131 12.011716
6150 16738.454 0 0 5269.5132 12.011725
6200 16738.454 0 0 5269.5133 12.011728
6250 16738.454 0 0 5269.5134 12.011723
6300 16738.455 0 0 5269.5135 12.011712
6350 16738.455 0 0 5269.5137 12.0117
6400 16738.456 0 0 5269.5138 12.011697
6450 16738.456 0 0 5269.514 12.011704
6500 16738.456 0 0 5269.5141 12.011714
6550 16738.457 0 0 5269.5142 12.011719
6600 16738.457 0 0 5269.5143 12.011718
6650 16738.458 0 0 5269.5144 12.011713
6700 16738.458 0 0 5269.5146 12.011705
6750 16738.459 0 0 5269.5147 12.011696
6800 16738.459 0 0 5269.5149 12.01169
6850 16738.46 0 0 5269.515 12.011695
6900 16738.46 0 0 5269.5152 12.01171
6950 16738.46 0 0 5269.5153 12.011726
7000 16738.461 0 0 5269.5154 12.011736
7050 16738.461 0 0 5269.5155 12.011737
7100 16738.461 0 0 5269.5155 12.011728
7150 16738.461 0 0 5269.5156 12.011712
7200 16738.462 0 0 5269.5158 12.011691
7250 16738.463 0 0 5269.516 12.011676
7300 16738.463 0 0 5269.5162 12.011677
7350 16738.464 0 0 5269.5164 12.011693
7400 16738.464 0 0 5269.5165 12.011713
7450 16738.465 0 0 5269.5166 12.011729
7500 16738.465 0 0 5269.5167 12.011736
7550 16738.465 0 0 5269.5168 12.011734
7600 16738.465 0 0 5269.5168 12.011722
7650 16738.466 0 0 5269.517 12.011704
7700 16738.466 0 0 5269.5171 12.011687
7750 16738.467 0 0 5269.5173 12.011681
7800 16738.467 0 0 5269.5175 12.011687
7850 16738.468 0 0 5269.5176 12.0117
7900 16738.468 0 0 5269.5178 12.011712
7950 16738.469 0 0 5269.5179 12.011721
8000 16738.469 0 0 5269.518 12.011724
8050 16738.469 0 0 5269.5181 12.01172
8100 16738.47 0 0 5269.5182 12.011709
8150 16738.47 0 0 5269.5183 12.0117
8200 16738.47 0 0 5269.5185 12.0117
8250 16738.471 0 0 5269.5186 12.011709
8300 16738.471 0 0 5269.5187 12.011719
8350 16738.472 0 0 5269.5189 12.011723
8400 16738.472 0 0 5269.519 12.01172
8450 16738.473 -0.00039690669 0 5269.5189 12.011706
8500 16738.481 -0.0034646805 0 5269.5182 12.011643
8550 16738.483 -0.0045307408 0 5269.5178 12.011621
8600 16738.474 -0.00076532807 0 5269.5189 12.011681
8650 16738.474 0 0 5269.5197 12.011699
8700 16738.475 0 0 5269.5199 12.011715
8750 16738.475 0 0 5269.52 12.011732
8800 16738.475 0 0 5269.52 12.011743
8850 16738.476 0 0 5269.5201 12.011744
8900 16738.476 0 0 5269.5202 12.011735
8950 16738.476 0 0 5269.5203 12.011719
9000 16738.477 0 0 5269.5205 12.011698
9050 16738.477 0 0 5269.5206 12.011683
9100 16738.478 0 0 5269.5208 12.011684
9150 16738.479 0 0 5269.521 12.011701
9200 16738.479 0 0 5269.5212 12.011722
9250 16738.479 0 0 5269.5213 12.011738
9300 16738.48 0 0 5269.5214 12.011746
9350 16738.48 0 0 5269.5214 12.011744
9400 16738.48 0 0 5269.5215 12.011732
9450 16738.48 0 0 5269.5216 12.011715
9500 16738.481 -0.0003765243 0 5269.5216 12.011692
9550 16738.493 -0.0053156155 0 5269.5203 12.011611
9600 16738.549 -0.026814365 0 5269.5163 12.011415
9650 16738.765 -0.10191521 0 5269.5092 12.011013
9700 16735.041 1.0589871 0 5269.4979 12.062708
9750 16738.013 0.13550136 0 5269.5101 11.407245
9800 16738.512 -0.01162033 0 5269.5201 11.394973
9850 16738.489 -0.00067270559 0 5269.5237 11.395098
9900 16738.489 -0.00024984558 0 5269.5242 11.395084
9950 16738.49 0 0 5269.5245 11.395076
10000 16738.49 0 0 5269.5246 11.395075
Loop time of 0.134486 on 1 procs for 10000 steps with 81 atoms
Performance: 642445.705 tau/day, 74357.142 timesteps/s, 6.023 Matom-step/s
99.0% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0076798 | 0.0076798 | 0.0076798 | 0.0 | 5.71
Neigh | 0.048776 | 0.048776 | 0.048776 | 0.0 | 36.27
Comm | 0.0085249 | 0.0085249 | 0.0085249 | 0.0 | 6.34
Output | 0.0021846 | 0.0021846 | 0.0021846 | 0.0 | 1.62
Modify | 0.059372 | 0.059372 | 0.059372 | 0.0 | 44.15
Other | | 0.007949 | | | 5.91
Nlocal: 81 ave 81 max 81 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 84 ave 84 max 84 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0
Neighbor list builds = 1552
Dangerous builds = 0
Total wall time: 0:00:00

310
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@ -1,310 +0,0 @@
LAMMPS (7 Feb 2024 - Development - patch_7Feb2024_update1-306-gf3391199e7-modified)
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
# unconnected bodies
group clump1 id <> 1 9
9 atoms in group clump1
group clump2 id <> 10 18
9 atoms in group clump2
group clump3 id <> 19 27
9 atoms in group clump3
group clump4 id <> 28 36
9 atoms in group clump4
group clump5 id <> 37 45
9 atoms in group clump5
group clump6 id <> 46 54
9 atoms in group clump6
group clump7 id <> 55 63
9 atoms in group clump7
group clump8 id <> 64 72
9 atoms in group clump8
group clump9 id <> 73 81
9 atoms in group clump9
fix 1 all rigid group 9 clump1 clump2 clump3 clump4 clump5 clump6 clump7 clump8 clump9 infile bodyinfo.dat
9 rigid bodies with 81 atoms
neigh_modify exclude group clump1 clump1
neigh_modify exclude group clump2 clump2
neigh_modify exclude group clump3 clump3
neigh_modify exclude group clump4 clump4
neigh_modify exclude group clump5 clump5
neigh_modify exclude group clump6 clump6
neigh_modify exclude group clump7 clump7
neigh_modify exclude group clump8 clump8
neigh_modify exclude group clump9 clump9
thermo 100
#dump 1 all atom 50 dump.rigid
#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 2 pad 5
#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 3 pad 5
timestep 0.0001
thermo 50
run 10000
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Reading rigid body data for 4 bodies from file bodyinfo.dat
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4, bins = 18 18 18
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 4.201 | 4.233 | 4.327 Mbytes
Step Temp E_pair E_mol TotEng Press
0 115.29439 5235.9179 0 5272.2142 -2.7403788
50 14910.685 571.71558 0 5265.82 32.006171
100 16298.442 136.66184 0 5267.653 16.444229
150 16682.606 17.490511 0 5269.4219 14.900344
200 16733.929 1.372872 0 5269.4617 14.569267
250 16738.853 -0.15252816 0 5269.4864 14.496404
300 16738.588 -0.055171335 0 5269.5002 14.496025
350 16738.492 -0.017444677 0 5269.5077 14.496446
400 16738.464 -0.0060102023 0 5269.5104 14.496618
450 16738.455 -0.0012713351 0 5269.5124 14.496701
500 16738.455 -0.00081068621 0 5269.5128 14.496709
550 16738.455 -0.00083203497 0 5269.5129 14.496707
600 16738.455 -0.00058355356 0 5269.5131 14.496709
650 16738.455 -0.00047226704 0 5269.5131 14.496708
700 16738.455 0 0 5269.5136 14.496713
750 16738.455 0 0 5269.5136 14.49671
800 16738.455 0 0 5269.5137 14.496709
850 16738.455 0 0 5269.5137 14.49671
900 16738.456 0 0 5269.5138 14.496713
950 16738.462 -0.0035323872 0 5269.5122 14.496671
1000 16738.586 -0.051135144 0 5269.5036 14.496229
1050 16737.358 0.32995057 0 5269.4981 14.525763
1100 16737.892 0.16210246 0 5269.4984 14.531983
1150 16738.703 -0.089235095 0 5269.5025 14.509899
1200 16738.466 -0.0075446243 0 5269.5096 14.510615
1250 16738.456 0 0 5269.514 14.510704
1300 16738.457 0 0 5269.5141 14.510701
1350 16738.457 0 0 5269.5141 14.510699
1400 16738.457 -0.00044736511 0 5269.5138 14.510693
1450 16738.458 -0.0010971179 0 5269.5134 14.510687
1500 16738.458 -0.00057885428 0 5269.5139 14.510698
1550 16738.457 0 0 5269.5143 14.51071
1600 16738.457 0 0 5269.5144 14.510712
1650 16738.457 0 0 5269.5144 14.510712
1700 16738.458 0 0 5269.5144 14.51071
1750 16738.458 0 0 5269.5145 14.510708
1800 16738.458 0 0 5269.5145 14.510706
1850 16738.458 0 0 5269.5146 14.510705
1900 16738.458 0 0 5269.5146 14.510706
1950 16738.465 -0.0031733615 0 5269.5134 14.510659
2000 16738.491 -0.013255268 0 5269.5117 14.510532
2050 16738.556 -0.0365811 0 5269.5087 14.51029
2100 16738.633 -0.063209659 0 5269.5065 14.510219
2150 16738.607 -0.05601761 0 5269.5055 14.510231
2200 16738.557 -0.038423032 0 5269.5072 14.510404
2250 16738.515 -0.023709918 0 5269.5088 14.510539
2300 16738.489 -0.013249035 0 5269.5111 14.510621
2350 16738.468 -0.0045563719 0 5269.5131 14.510714
2400 16738.46 -0.00052194273 0 5269.5146 14.510771
2450 16738.464 -0.0023259756 0 5269.514 14.510746
2500 16738.468 -0.0051929186 0 5269.5127 14.510731
2550 16738.581 -0.044940117 0 5269.5085 14.510315
2600 16738.427 -7.9722861e-05 0 5269.5046 14.510657
2650 16733.017 1.7051479 0 5269.5067 14.596295
2700 16738.761 -0.10614946 0 5269.5038 14.499584
2750 16733.973 1.4038179 0 5269.5064 14.598107
2800 16738.585 -0.046813448 0 5269.5076 14.511073
2850 16738.487 -0.012558719 0 5269.5111 14.510111
2900 16738.465 -0.0026252725 0 5269.514 14.510277
2950 16738.476 -0.0082220764 0 5269.512 14.510223
3000 16738.66 -0.071284779 0 5269.507 14.509758
3050 16715.332 7.2419352 0 5269.476 14.870305
3100 16653.226 26.818761 0 5269.5009 14.496764
3150 16739.351 -0.30690375 0 5269.4886 13.643904
3200 16733.238 1.6025328 0 5269.4737 12.016934
3250 16734.374 1.2554429 0 5269.4841 11.963561
3300 16732.156 1.9585967 0 5269.4893 12.234024
3350 16738.655 -0.079693236 0 5269.497 12.092757
3400 16738.543 -0.042215005 0 5269.4991 12.092809
3450 16738.591 -0.059327511 0 5269.4972 12.092536
3500 16738.759 -0.11761245 0 5269.4918 12.09203
3550 16713.405 7.8460621 0 5269.4737 12.389816
3600 16734.939 1.0821936 0 5269.4891 12.173591
3650 16738.808 -0.13663194 0 5269.4882 12.027009
3700 16738.602 -0.070934368 0 5269.4889 12.025288
3750 16737.731 0.20706559 0 5269.4927 12.061948
3800 16738.578 -0.05582043 0 5269.4965 12.035665
3850 16738.471 -0.016307928 0 5269.5024 12.035302
3900 16738.449 -0.0058182199 0 5269.5059 12.035401
3950 16738.439 -0.0012027325 0 5269.5074 12.035461
4000 16738.436 -0.00020698452 0 5269.5075 12.035469
4050 16738.437 0 0 5269.5078 12.035454
4100 16738.437 0 0 5269.508 12.035435
4150 16738.438 0 0 5269.5081 12.035426
4200 16738.438 0 0 5269.5083 12.035432
4250 16738.439 0 0 5269.5085 12.035447
4300 16738.439 0 0 5269.5086 12.035463
4350 16738.44 0 0 5269.5087 12.035474
4400 16738.44 0 0 5269.5088 12.035478
4450 16738.44 0 0 5269.5089 12.035474
4500 16738.44 0 0 5269.509 12.035462
4550 16738.441 0 0 5269.5092 12.035449
4600 16738.441 0 0 5269.5093 12.035445
4650 16738.442 0 0 5269.5095 12.035451
4700 16738.442 0 0 5269.5096 12.03546
4750 16738.443 0 0 5269.5097 12.035465
4800 16738.443 0 0 5269.5098 12.035466
4850 16738.443 0 0 5269.51 12.035463
4900 16738.444 0 0 5269.5101 12.035456
4950 16738.444 0 0 5269.5102 12.035447
5000 16738.445 0 0 5269.5104 12.03544
5050 16738.445 0 0 5269.5105 12.035442
5100 16738.446 0 0 5269.5107 12.035455
5150 16738.446 0 0 5269.5108 12.03547
5200 16738.446 0 0 5269.5109 12.035479
5250 16738.447 0 0 5269.511 12.035479
5300 16738.447 0 0 5269.5111 12.03547
5350 16738.447 0 0 5269.5112 12.035454
5400 16738.448 0 0 5269.5113 12.035434
5450 16738.448 0 0 5269.5115 12.03542
5500 16738.449 0 0 5269.5117 12.035422
5550 16738.457 -0.0030919234 0 5269.5111 12.035383
5600 16738.51 -0.021618357 0 5269.5092 12.035106
5650 16738.622 -0.059214788 0 5269.507 12.035694
5700 16395.28 108.06942 0 5269.5463 24.369038
5750 16738.544 -0.033973429 0 5269.5077 12.011261
5800 16738.456 -0.0037013529 0 5269.5102 12.011675
5850 16738.451 0 0 5269.5123 12.011709
5900 16738.451 -0.0002211587 0 5269.5122 12.011687
5950 16738.452 -0.00024253348 0 5269.5124 12.011678
6000 16738.452 0 0 5269.5128 12.011688
6050 16738.453 0 0 5269.513 12.011702
6100 16738.453 0 0 5269.5131 12.011716
6150 16738.454 0 0 5269.5132 12.011725
6200 16738.454 0 0 5269.5133 12.011728
6250 16738.454 0 0 5269.5134 12.011723
6300 16738.455 0 0 5269.5135 12.011712
6350 16738.455 0 0 5269.5137 12.0117
6400 16738.456 0 0 5269.5138 12.011697
6450 16738.456 0 0 5269.514 12.011704
6500 16738.456 0 0 5269.5141 12.011714
6550 16738.457 0 0 5269.5142 12.011719
6600 16738.457 0 0 5269.5143 12.011718
6650 16738.458 0 0 5269.5144 12.011713
6700 16738.458 0 0 5269.5146 12.011705
6750 16738.459 0 0 5269.5147 12.011696
6800 16738.459 0 0 5269.5149 12.01169
6850 16738.46 0 0 5269.515 12.011695
6900 16738.46 0 0 5269.5152 12.01171
6950 16738.46 0 0 5269.5153 12.011726
7000 16738.461 0 0 5269.5154 12.011736
7050 16738.461 0 0 5269.5155 12.011737
7100 16738.461 0 0 5269.5155 12.011728
7150 16738.461 0 0 5269.5156 12.011712
7200 16738.462 0 0 5269.5158 12.011691
7250 16738.463 0 0 5269.516 12.011676
7300 16738.463 0 0 5269.5162 12.011677
7350 16738.464 0 0 5269.5164 12.011693
7400 16738.464 0 0 5269.5165 12.011713
7450 16738.465 0 0 5269.5166 12.011729
7500 16738.465 0 0 5269.5167 12.011736
7550 16738.465 0 0 5269.5168 12.011734
7600 16738.465 0 0 5269.5168 12.011722
7650 16738.466 0 0 5269.517 12.011704
7700 16738.466 0 0 5269.5171 12.011687
7750 16738.467 0 0 5269.5173 12.011681
7800 16738.467 0 0 5269.5175 12.011687
7850 16738.468 0 0 5269.5176 12.0117
7900 16738.468 0 0 5269.5178 12.011712
7950 16738.469 0 0 5269.5179 12.011721
8000 16738.469 0 0 5269.518 12.011724
8050 16738.469 0 0 5269.5181 12.01172
8100 16738.47 0 0 5269.5182 12.011709
8150 16738.47 0 0 5269.5183 12.0117
8200 16738.47 0 0 5269.5185 12.0117
8250 16738.471 0 0 5269.5186 12.011709
8300 16738.471 0 0 5269.5187 12.011719
8350 16738.472 0 0 5269.5189 12.011723
8400 16738.472 0 0 5269.519 12.01172
8450 16738.473 -0.00039690667 0 5269.5189 12.011706
8500 16738.481 -0.0034646804 0 5269.5182 12.011643
8550 16738.483 -0.0045307408 0 5269.5178 12.011621
8600 16738.474 -0.00076532809 0 5269.5189 12.011681
8650 16738.474 0 0 5269.5197 12.011699
8700 16738.475 0 0 5269.5199 12.011715
8750 16738.475 0 0 5269.52 12.011732
8800 16738.475 0 0 5269.52 12.011743
8850 16738.476 0 0 5269.5201 12.011744
8900 16738.476 0 0 5269.5202 12.011735
8950 16738.476 0 0 5269.5203 12.011719
9000 16738.477 0 0 5269.5205 12.011698
9050 16738.477 0 0 5269.5206 12.011683
9100 16738.478 0 0 5269.5208 12.011684
9150 16738.479 0 0 5269.521 12.011701
9200 16738.479 0 0 5269.5212 12.011722
9250 16738.479 0 0 5269.5213 12.011738
9300 16738.48 0 0 5269.5214 12.011746
9350 16738.48 0 0 5269.5214 12.011744
9400 16738.48 0 0 5269.5215 12.011732
9450 16738.48 0 0 5269.5216 12.011715
9500 16738.481 -0.00037652433 0 5269.5216 12.011692
9550 16738.493 -0.0053156156 0 5269.5203 12.011611
9600 16738.549 -0.026814367 0 5269.5163 12.011415
9650 16738.765 -0.10191522 0 5269.5092 12.011013
9700 16735.041 1.0589878 0 5269.4979 12.062708
9750 16738.013 0.13550114 0 5269.5101 11.407245
9800 16738.512 -0.01162033 0 5269.5201 11.394973
9850 16738.489 -0.00067270564 0 5269.5237 11.395098
9900 16738.489 -0.00024984568 0 5269.5242 11.395084
9950 16738.49 0 0 5269.5245 11.395076
10000 16738.49 0 0 5269.5246 11.395075
Loop time of 0.135118 on 4 procs for 10000 steps with 81 atoms
Performance: 639441.862 tau/day, 74009.475 timesteps/s, 5.995 Matom-step/s
97.2% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0015919 | 0.0022753 | 0.0028384 | 0.9 | 1.68
Neigh | 0.012494 | 0.013468 | 0.015484 | 1.0 | 9.97
Comm | 0.061357 | 0.0636 | 0.06555 | 0.7 | 47.07
Output | 0.0017441 | 0.0018894 | 0.0023095 | 0.6 | 1.40
Modify | 0.037856 | 0.039816 | 0.041217 | 0.6 | 29.47
Other | | 0.01407 | | | 10.41
Nlocal: 20.25 ave 37 max 3 min
Histogram: 1 0 0 1 0 0 0 1 0 1
Nghost: 27.25 ave 48 max 13 min
Histogram: 1 0 0 2 0 0 0 0 0 1
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0
Neighbor list builds = 1552
Dangerous builds = 0
Total wall time: 0:00:00

319
examples/rigid/log.25Mar24.rigid.molecule.g++.1
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@ -1,319 +0,0 @@
LAMMPS (7 Feb 2024 - Development - patch_7Feb2024_update1-306-gf3391199e7-modified)
using 1 OpenMP thread(s) per MPI task
# Simple rigid body system
units lj
atom_style bond
pair_style lj/cut 2.5
read_data data.rigid.small
Reading data file ...
orthogonal box = (-12 -12 -12) to (12 12 12)
1 by 1 by 1 MPI processor grid
reading atoms ...
81 atoms
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
0 = max # of 1-2 neighbors
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
1 = max # of special neighbors
special bonds CPU = 0.000 seconds
read_data CPU = 0.001 seconds
velocity all create 100.0 4928459
# unconnected bodies
group clump1 id <> 1 9
9 atoms in group clump1
group clump2 id <> 10 18
9 atoms in group clump2
group clump3 id <> 19 27
9 atoms in group clump3
group clump4 id <> 28 36
9 atoms in group clump4
group clump5 id <> 37 45
9 atoms in group clump5
group clump6 id <> 46 54
9 atoms in group clump6
group clump7 id <> 55 63
9 atoms in group clump7
group clump8 id <> 64 72
9 atoms in group clump8
group clump9 id <> 73 81
9 atoms in group clump9
fix 1 all rigid molecule
9 rigid bodies with 81 atoms
neigh_modify exclude group clump1 clump1
neigh_modify exclude group clump2 clump2
neigh_modify exclude group clump3 clump3
neigh_modify exclude group clump4 clump4
neigh_modify exclude group clump5 clump5
neigh_modify exclude group clump6 clump6
neigh_modify exclude group clump7 clump7
neigh_modify exclude group clump8 clump8
neigh_modify exclude group clump9 clump9
thermo 100
#dump 1 all atom 50 dump.rigid
#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 2 pad 5
#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 3 pad 5
timestep 0.0001
thermo 50
run 10000
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4, bins = 18 18 18
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 5.233 | 5.233 | 5.233 Mbytes
Step Temp E_pair E_mol TotEng Press
0 115.29439 5235.9179 0 5272.2142 -2.7403788
50 14910.685 571.71558 0 5265.82 32.006171
100 16298.442 136.66184 0 5267.653 16.444229
150 16682.606 17.490511 0 5269.4219 14.900344
200 16733.929 1.372872 0 5269.4617 14.569267
250 16738.853 -0.15252816 0 5269.4864 14.496404
300 16738.588 -0.055171335 0 5269.5002 14.496025
350 16738.492 -0.017444677 0 5269.5077 14.496446
400 16738.464 -0.0060102023 0 5269.5104 14.496618
450 16738.455 -0.0012713351 0 5269.5124 14.496701
500 16738.455 -0.00081068621 0 5269.5128 14.496709
550 16738.455 -0.00083203497 0 5269.5129 14.496707
600 16738.455 -0.00058355356 0 5269.5131 14.496709
650 16738.455 -0.00047226704 0 5269.5131 14.496708
700 16738.455 0 0 5269.5136 14.496713
750 16738.455 0 0 5269.5136 14.49671
800 16738.455 0 0 5269.5137 14.496709
850 16738.455 0 0 5269.5137 14.49671
900 16738.456 0 0 5269.5138 14.496713
950 16738.462 -0.0035323872 0 5269.5122 14.496671
1000 16738.586 -0.051135144 0 5269.5036 14.496229
1050 16737.358 0.32995057 0 5269.4981 14.525763
1100 16737.892 0.16210246 0 5269.4984 14.531983
1150 16738.703 -0.089235095 0 5269.5025 14.509899
1200 16738.466 -0.0075446243 0 5269.5096 14.510615
1250 16738.456 0 0 5269.514 14.510704
1300 16738.457 0 0 5269.5141 14.510701
1350 16738.457 0 0 5269.5141 14.510699
1400 16738.457 -0.00044736511 0 5269.5138 14.510693
1450 16738.458 -0.0010971179 0 5269.5134 14.510687
1500 16738.458 -0.00057885428 0 5269.5139 14.510698
1550 16738.457 0 0 5269.5143 14.51071
1600 16738.457 0 0 5269.5144 14.510712
1650 16738.457 0 0 5269.5144 14.510712
1700 16738.458 0 0 5269.5144 14.51071
1750 16738.458 0 0 5269.5145 14.510708
1800 16738.458 0 0 5269.5145 14.510706
1850 16738.458 0 0 5269.5146 14.510705
1900 16738.458 0 0 5269.5146 14.510706
1950 16738.465 -0.0031733615 0 5269.5134 14.510659
2000 16738.491 -0.013255268 0 5269.5117 14.510532
2050 16738.556 -0.0365811 0 5269.5087 14.51029
2100 16738.633 -0.063209659 0 5269.5065 14.510219
2150 16738.607 -0.05601761 0 5269.5055 14.510231
2200 16738.557 -0.038423032 0 5269.5072 14.510404
2250 16738.515 -0.023709918 0 5269.5088 14.510539
2300 16738.489 -0.013249035 0 5269.5111 14.510621
2350 16738.468 -0.0045563719 0 5269.5131 14.510714
2400 16738.46 -0.00052194273 0 5269.5146 14.510771
2450 16738.464 -0.0023259756 0 5269.514 14.510746
2500 16738.468 -0.0051929186 0 5269.5127 14.510731
2550 16738.581 -0.044940117 0 5269.5085 14.510315
2600 16738.427 -7.9722875e-05 0 5269.5046 14.510657
2650 16733.017 1.705148 0 5269.5067 14.596295
2700 16738.761 -0.10614946 0 5269.5038 14.499584
2750 16733.973 1.4038179 0 5269.5064 14.598107
2800 16738.585 -0.046813448 0 5269.5076 14.511073
2850 16738.487 -0.012558719 0 5269.5111 14.510111
2900 16738.465 -0.0026252725 0 5269.514 14.510277
2950 16738.476 -0.0082220764 0 5269.512 14.510223
3000 16738.66 -0.071284779 0 5269.507 14.509758
3050 16715.332 7.2419351 0 5269.476 14.870305
3100 16653.226 26.818761 0 5269.5009 14.496764
3150 16739.351 -0.30690375 0 5269.4886 13.643904
3200 16733.238 1.6025328 0 5269.4737 12.016934
3250 16734.374 1.2554429 0 5269.4841 11.963561
3300 16732.156 1.9585967 0 5269.4893 12.234024
3350 16738.655 -0.079693236 0 5269.497 12.092757
3400 16738.543 -0.042215005 0 5269.4991 12.092809
3450 16738.591 -0.059327511 0 5269.4972 12.092536
3500 16738.759 -0.11761245 0 5269.4918 12.09203
3550 16713.405 7.846062 0 5269.4737 12.389816
3600 16734.939 1.0821936 0 5269.4891 12.173591
3650 16738.808 -0.13663194 0 5269.4882 12.027009
3700 16738.602 -0.070934368 0 5269.4889 12.025288
3750 16737.731 0.20706558 0 5269.4927 12.061948
3800 16738.578 -0.05582043 0 5269.4965 12.035665
3850 16738.471 -0.016307928 0 5269.5024 12.035302
3900 16738.449 -0.0058182199 0 5269.5059 12.035401
3950 16738.439 -0.0012027325 0 5269.5074 12.035461
4000 16738.436 -0.00020698452 0 5269.5075 12.035469
4050 16738.437 0 0 5269.5078 12.035454
4100 16738.437 0 0 5269.508 12.035435
4150 16738.438 0 0 5269.5081 12.035426
4200 16738.438 0 0 5269.5083 12.035432
4250 16738.439 0 0 5269.5085 12.035447
4300 16738.439 0 0 5269.5086 12.035463
4350 16738.44 0 0 5269.5087 12.035474
4400 16738.44 0 0 5269.5088 12.035478
4450 16738.44 0 0 5269.5089 12.035474
4500 16738.44 0 0 5269.509 12.035462
4550 16738.441 0 0 5269.5092 12.035449
4600 16738.441 0 0 5269.5093 12.035445
4650 16738.442 0 0 5269.5095 12.035451
4700 16738.442 0 0 5269.5096 12.03546
4750 16738.443 0 0 5269.5097 12.035465
4800 16738.443 0 0 5269.5098 12.035466
4850 16738.443 0 0 5269.51 12.035463
4900 16738.444 0 0 5269.5101 12.035456
4950 16738.444 0 0 5269.5102 12.035447
5000 16738.445 0 0 5269.5104 12.03544
5050 16738.445 0 0 5269.5105 12.035442
5100 16738.446 0 0 5269.5107 12.035455
5150 16738.446 0 0 5269.5108 12.03547
5200 16738.446 0 0 5269.5109 12.035479
5250 16738.447 0 0 5269.511 12.035479
5300 16738.447 0 0 5269.5111 12.03547
5350 16738.447 0 0 5269.5112 12.035454
5400 16738.448 0 0 5269.5113 12.035434
5450 16738.448 0 0 5269.5115 12.03542
5500 16738.449 0 0 5269.5117 12.035422
5550 16738.457 -0.0030919234 0 5269.5111 12.035383
5600 16738.51 -0.021618357 0 5269.5092 12.035106
5650 16738.622 -0.059214788 0 5269.507 12.035694
5700 16395.28 108.06942 0 5269.5463 24.369038
5750 16738.544 -0.033973429 0 5269.5077 12.011261
5800 16738.456 -0.0037013529 0 5269.5102 12.011675
5850 16738.451 0 0 5269.5123 12.011709
5900 16738.451 -0.0002211587 0 5269.5122 12.011687
5950 16738.452 -0.00024253349 0 5269.5124 12.011678
6000 16738.452 0 0 5269.5128 12.011688
6050 16738.453 0 0 5269.513 12.011702
6100 16738.453 0 0 5269.5131 12.011716
6150 16738.454 0 0 5269.5132 12.011725
6200 16738.454 0 0 5269.5133 12.011728
6250 16738.454 0 0 5269.5134 12.011723
6300 16738.455 0 0 5269.5135 12.011712
6350 16738.455 0 0 5269.5137 12.0117
6400 16738.456 0 0 5269.5138 12.011697
6450 16738.456 0 0 5269.514 12.011704
6500 16738.456 0 0 5269.5141 12.011714
6550 16738.457 0 0 5269.5142 12.011719
6600 16738.457 0 0 5269.5143 12.011718
6650 16738.458 0 0 5269.5144 12.011713
6700 16738.458 0 0 5269.5146 12.011705
6750 16738.459 0 0 5269.5147 12.011696
6800 16738.459 0 0 5269.5149 12.01169
6850 16738.46 0 0 5269.515 12.011695
6900 16738.46 0 0 5269.5152 12.01171
6950 16738.46 0 0 5269.5153 12.011726
7000 16738.461 0 0 5269.5154 12.011736
7050 16738.461 0 0 5269.5155 12.011737
7100 16738.461 0 0 5269.5155 12.011728
7150 16738.461 0 0 5269.5156 12.011712
7200 16738.462 0 0 5269.5158 12.011691
7250 16738.463 0 0 5269.516 12.011676
7300 16738.463 0 0 5269.5162 12.011677
7350 16738.464 0 0 5269.5164 12.011693
7400 16738.464 0 0 5269.5165 12.011713
7450 16738.465 0 0 5269.5166 12.011729
7500 16738.465 0 0 5269.5167 12.011736
7550 16738.465 0 0 5269.5168 12.011734
7600 16738.465 0 0 5269.5168 12.011722
7650 16738.466 0 0 5269.517 12.011704
7700 16738.466 0 0 5269.5171 12.011687
7750 16738.467 0 0 5269.5173 12.011681
7800 16738.467 0 0 5269.5175 12.011687
7850 16738.468 0 0 5269.5176 12.0117
7900 16738.468 0 0 5269.5178 12.011712
7950 16738.469 0 0 5269.5179 12.011721
8000 16738.469 0 0 5269.518 12.011724
8050 16738.469 0 0 5269.5181 12.01172
8100 16738.47 0 0 5269.5182 12.011709
8150 16738.47 0 0 5269.5183 12.0117
8200 16738.47 0 0 5269.5185 12.0117
8250 16738.471 0 0 5269.5186 12.011709
8300 16738.471 0 0 5269.5187 12.011719
8350 16738.472 0 0 5269.5189 12.011723
8400 16738.472 0 0 5269.519 12.01172
8450 16738.473 -0.00039690665 0 5269.5189 12.011706
8500 16738.481 -0.0034646803 0 5269.5182 12.011643
8550 16738.483 -0.0045307408 0 5269.5178 12.011621
8600 16738.474 -0.0007653281 0 5269.5189 12.011681
8650 16738.474 0 0 5269.5197 12.011699
8700 16738.475 0 0 5269.5199 12.011715
8750 16738.475 0 0 5269.52 12.011732
8800 16738.475 0 0 5269.52 12.011743
8850 16738.476 0 0 5269.5201 12.011744
8900 16738.476 0 0 5269.5202 12.011735
8950 16738.476 0 0 5269.5203 12.011719
9000 16738.477 0 0 5269.5205 12.011698
9050 16738.477 0 0 5269.5206 12.011683
9100 16738.478 0 0 5269.5208 12.011684
9150 16738.479 0 0 5269.521 12.011701
9200 16738.479 0 0 5269.5212 12.011722
9250 16738.479 0 0 5269.5213 12.011738
9300 16738.48 0 0 5269.5214 12.011746
9350 16738.48 0 0 5269.5214 12.011744
9400 16738.48 0 0 5269.5215 12.011732
9450 16738.48 0 0 5269.5216 12.011715
9500 16738.481 -0.00037652436 0 5269.5216 12.011692
9550 16738.493 -0.0053156156 0 5269.5203 12.011611
9600 16738.549 -0.026814368 0 5269.5163 12.011415
9650 16738.765 -0.10191522 0 5269.5092 12.011013
9700 16735.041 1.0589881 0 5269.4979 12.062708
9750 16738.013 0.13550093 0 5269.5101 11.407245
9800 16738.512 -0.01162033 0 5269.5201 11.394973
9850 16738.489 -0.00067270581 0 5269.5237 11.395098
9900 16738.489 -0.0002498458 0 5269.5242 11.395084
9950 16738.49 0 0 5269.5245 11.395076
10000 16738.49 0 0 5269.5246 11.395075
Loop time of 0.130618 on 1 procs for 10000 steps with 81 atoms
Performance: 661470.393 tau/day, 76559.073 timesteps/s, 6.201 Matom-step/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 | 0.0069622 | 0.0069622 | 0.0069622 | 0.0 | 5.33
Bond | 0.00033246 | 0.00033246 | 0.00033246 | 0.0 | 0.25
Neigh | 0.053402 | 0.053402 | 0.053402 | 0.0 | 40.88
Comm | 0.008192 | 0.008192 | 0.008192 | 0.0 | 6.27
Output | 0.0015884 | 0.0015884 | 0.0015884 | 0.0 | 1.22
Modify | 0.053219 | 0.053219 | 0.053219 | 0.0 | 40.74
Other | | 0.006922 | | | 5.30
Nlocal: 81 ave 81 max 81 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 84 ave 84 max 84 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0
Ave special neighs/atom = 0
Neighbor list builds = 1552
Dangerous builds = 0
Total wall time: 0:00:00

319
examples/rigid/log.25Mar24.rigid.molecule.g++.4
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@ -1,319 +0,0 @@
LAMMPS (7 Feb 2024 - Development - patch_7Feb2024_update1-306-gf3391199e7-modified)
using 1 OpenMP thread(s) per MPI task
# Simple rigid body system
units lj
atom_style bond
pair_style lj/cut 2.5
read_data data.rigid.small
Reading data file ...
orthogonal box = (-12 -12 -12) to (12 12 12)
1 by 2 by 2 MPI processor grid
reading atoms ...
81 atoms
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
0 = max # of 1-2 neighbors
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
1 = max # of special neighbors
special bonds CPU = 0.000 seconds
read_data CPU = 0.001 seconds
velocity all create 100.0 4928459
# unconnected bodies
group clump1 id <> 1 9
9 atoms in group clump1
group clump2 id <> 10 18
9 atoms in group clump2
group clump3 id <> 19 27
9 atoms in group clump3
group clump4 id <> 28 36
9 atoms in group clump4
group clump5 id <> 37 45
9 atoms in group clump5
group clump6 id <> 46 54
9 atoms in group clump6
group clump7 id <> 55 63
9 atoms in group clump7
group clump8 id <> 64 72
9 atoms in group clump8
group clump9 id <> 73 81
9 atoms in group clump9
fix 1 all rigid molecule
9 rigid bodies with 81 atoms
neigh_modify exclude group clump1 clump1
neigh_modify exclude group clump2 clump2
neigh_modify exclude group clump3 clump3
neigh_modify exclude group clump4 clump4
neigh_modify exclude group clump5 clump5
neigh_modify exclude group clump6 clump6
neigh_modify exclude group clump7 clump7
neigh_modify exclude group clump8 clump8
neigh_modify exclude group clump9 clump9
thermo 100
#dump 1 all atom 50 dump.rigid
#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 2 pad 5
#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 3 pad 5
timestep 0.0001
thermo 50
run 10000
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4, bins = 18 18 18
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 5.08 | 5.112 | 5.206 Mbytes
Step Temp E_pair E_mol TotEng Press
0 115.29439 5235.9179 0 5272.2142 -2.7403788
50 14910.685 571.71558 0 5265.82 32.006171
100 16298.442 136.66184 0 5267.653 16.444229
150 16682.606 17.490511 0 5269.4219 14.900344
200 16733.929 1.372872 0 5269.4617 14.569267
250 16738.853 -0.15252816 0 5269.4864 14.496404
300 16738.588 -0.055171335 0 5269.5002 14.496025
350 16738.492 -0.017444677 0 5269.5077 14.496446
400 16738.464 -0.0060102023 0 5269.5104 14.496618
450 16738.455 -0.0012713351 0 5269.5124 14.496701
500 16738.455 -0.00081068621 0 5269.5128 14.496709
550 16738.455 -0.00083203497 0 5269.5129 14.496707
600 16738.455 -0.00058355356 0 5269.5131 14.496709
650 16738.455 -0.00047226704 0 5269.5131 14.496708
700 16738.455 0 0 5269.5136 14.496713
750 16738.455 0 0 5269.5136 14.49671
800 16738.455 0 0 5269.5137 14.496709
850 16738.455 0 0 5269.5137 14.49671
900 16738.456 0 0 5269.5138 14.496713
950 16738.462 -0.0035323872 0 5269.5122 14.496671
1000 16738.586 -0.051135144 0 5269.5036 14.496229
1050 16737.358 0.32995057 0 5269.4981 14.525763
1100 16737.892 0.16210246 0 5269.4984 14.531983
1150 16738.703 -0.089235095 0 5269.5025 14.509899
1200 16738.466 -0.0075446243 0 5269.5096 14.510615
1250 16738.456 0 0 5269.514 14.510704
1300 16738.457 0 0 5269.5141 14.510701
1350 16738.457 0 0 5269.5141 14.510699
1400 16738.457 -0.00044736511 0 5269.5138 14.510693
1450 16738.458 -0.0010971179 0 5269.5134 14.510687
1500 16738.458 -0.00057885428 0 5269.5139 14.510698
1550 16738.457 0 0 5269.5143 14.51071
1600 16738.457 0 0 5269.5144 14.510712
1650 16738.457 0 0 5269.5144 14.510712
1700 16738.458 0 0 5269.5144 14.51071
1750 16738.458 0 0 5269.5145 14.510708
1800 16738.458 0 0 5269.5145 14.510706
1850 16738.458 0 0 5269.5146 14.510705
1900 16738.458 0 0 5269.5146 14.510706
1950 16738.465 -0.0031733615 0 5269.5134 14.510659
2000 16738.491 -0.013255268 0 5269.5117 14.510532
2050 16738.556 -0.0365811 0 5269.5087 14.51029
2100 16738.633 -0.063209659 0 5269.5065 14.510219
2150 16738.607 -0.05601761 0 5269.5055 14.510231
2200 16738.557 -0.038423032 0 5269.5072 14.510404
2250 16738.515 -0.023709918 0 5269.5088 14.510539
2300 16738.489 -0.013249035 0 5269.5111 14.510621
2350 16738.468 -0.0045563719 0 5269.5131 14.510714
2400 16738.46 -0.00052194273 0 5269.5146 14.510771
2450 16738.464 -0.0023259756 0 5269.514 14.510746
2500 16738.468 -0.0051929186 0 5269.5127 14.510731
2550 16738.581 -0.044940117 0 5269.5085 14.510315
2600 16738.427 -7.9722867e-05 0 5269.5046 14.510657
2650 16733.017 1.705148 0 5269.5067 14.596295
2700 16738.761 -0.10614946 0 5269.5038 14.499584
2750 16733.973 1.4038179 0 5269.5064 14.598107
2800 16738.585 -0.046813448 0 5269.5076 14.511073
2850 16738.487 -0.012558719 0 5269.5111 14.510111
2900 16738.465 -0.0026252725 0 5269.514 14.510277
2950 16738.476 -0.0082220764 0 5269.512 14.510223
3000 16738.66 -0.071284779 0 5269.507 14.509758
3050 16715.332 7.2419351 0 5269.476 14.870305
3100 16653.226 26.818761 0 5269.5009 14.496764
3150 16739.351 -0.30690375 0 5269.4886 13.643904
3200 16733.238 1.6025328 0 5269.4737 12.016934
3250 16734.374 1.2554429 0 5269.4841 11.963561
3300 16732.156 1.9585967 0 5269.4893 12.234024
3350 16738.655 -0.079693236 0 5269.497 12.092757
3400 16738.543 -0.042215005 0 5269.4991 12.092809
3450 16738.591 -0.059327511 0 5269.4972 12.092536
3500 16738.759 -0.11761245 0 5269.4918 12.09203
3550 16713.405 7.846062 0 5269.4737 12.389816
3600 16734.939 1.0821936 0 5269.4891 12.173591
3650 16738.808 -0.13663194 0 5269.4882 12.027009
3700 16738.602 -0.070934368 0 5269.4889 12.025288
3750 16737.731 0.20706558 0 5269.4927 12.061948
3800 16738.578 -0.05582043 0 5269.4965 12.035665
3850 16738.471 -0.016307928 0 5269.5024 12.035302
3900 16738.449 -0.0058182199 0 5269.5059 12.035401
3950 16738.439 -0.0012027325 0 5269.5074 12.035461
4000 16738.436 -0.00020698452 0 5269.5075 12.035469
4050 16738.437 0 0 5269.5078 12.035454
4100 16738.437 0 0 5269.508 12.035435
4150 16738.438 0 0 5269.5081 12.035426
4200 16738.438 0 0 5269.5083 12.035432
4250 16738.439 0 0 5269.5085 12.035447
4300 16738.439 0 0 5269.5086 12.035463
4350 16738.44 0 0 5269.5087 12.035474
4400 16738.44 0 0 5269.5088 12.035478
4450 16738.44 0 0 5269.5089 12.035474
4500 16738.44 0 0 5269.509 12.035462
4550 16738.441 0 0 5269.5092 12.035449
4600 16738.441 0 0 5269.5093 12.035445
4650 16738.442 0 0 5269.5095 12.035451
4700 16738.442 0 0 5269.5096 12.03546
4750 16738.443 0 0 5269.5097 12.035465
4800 16738.443 0 0 5269.5098 12.035466
4850 16738.443 0 0 5269.51 12.035463
4900 16738.444 0 0 5269.5101 12.035456
4950 16738.444 0 0 5269.5102 12.035447
5000 16738.445 0 0 5269.5104 12.03544
5050 16738.445 0 0 5269.5105 12.035442
5100 16738.446 0 0 5269.5107 12.035455
5150 16738.446 0 0 5269.5108 12.03547
5200 16738.446 0 0 5269.5109 12.035479
5250 16738.447 0 0 5269.511 12.035479
5300 16738.447 0 0 5269.5111 12.03547
5350 16738.447 0 0 5269.5112 12.035454
5400 16738.448 0 0 5269.5113 12.035434
5450 16738.448 0 0 5269.5115 12.03542
5500 16738.449 0 0 5269.5117 12.035422
5550 16738.457 -0.0030919234 0 5269.5111 12.035383
5600 16738.51 -0.021618357 0 5269.5092 12.035106
5650 16738.622 -0.059214788 0 5269.507 12.035694
5700 16395.28 108.06942 0 5269.5463 24.369038
5750 16738.544 -0.033973429 0 5269.5077 12.011261
5800 16738.456 -0.0037013529 0 5269.5102 12.011675
5850 16738.451 0 0 5269.5123 12.011709
5900 16738.451 -0.0002211587 0 5269.5122 12.011687
5950 16738.452 -0.00024253349 0 5269.5124 12.011678
6000 16738.452 0 0 5269.5128 12.011688
6050 16738.453 0 0 5269.513 12.011702
6100 16738.453 0 0 5269.5131 12.011716
6150 16738.454 0 0 5269.5132 12.011725
6200 16738.454 0 0 5269.5133 12.011728
6250 16738.454 0 0 5269.5134 12.011723
6300 16738.455 0 0 5269.5135 12.011712
6350 16738.455 0 0 5269.5137 12.0117
6400 16738.456 0 0 5269.5138 12.011697
6450 16738.456 0 0 5269.514 12.011704
6500 16738.456 0 0 5269.5141 12.011714
6550 16738.457 0 0 5269.5142 12.011719
6600 16738.457 0 0 5269.5143 12.011718
6650 16738.458 0 0 5269.5144 12.011713
6700 16738.458 0 0 5269.5146 12.011705
6750 16738.459 0 0 5269.5147 12.011696
6800 16738.459 0 0 5269.5149 12.01169
6850 16738.46 0 0 5269.515 12.011695
6900 16738.46 0 0 5269.5152 12.01171
6950 16738.46 0 0 5269.5153 12.011726
7000 16738.461 0 0 5269.5154 12.011736
7050 16738.461 0 0 5269.5155 12.011737
7100 16738.461 0 0 5269.5155 12.011728
7150 16738.461 0 0 5269.5156 12.011712
7200 16738.462 0 0 5269.5158 12.011691
7250 16738.463 0 0 5269.516 12.011676
7300 16738.463 0 0 5269.5162 12.011677
7350 16738.464 0 0 5269.5164 12.011693
7400 16738.464 0 0 5269.5165 12.011713
7450 16738.465 0 0 5269.5166 12.011729
7500 16738.465 0 0 5269.5167 12.011736
7550 16738.465 0 0 5269.5168 12.011734
7600 16738.465 0 0 5269.5168 12.011722
7650 16738.466 0 0 5269.517 12.011704
7700 16738.466 0 0 5269.5171 12.011687
7750 16738.467 0 0 5269.5173 12.011681
7800 16738.467 0 0 5269.5175 12.011687
7850 16738.468 0 0 5269.5176 12.0117
7900 16738.468 0 0 5269.5178 12.011712
7950 16738.469 0 0 5269.5179 12.011721
8000 16738.469 0 0 5269.518 12.011724
8050 16738.469 0 0 5269.5181 12.01172
8100 16738.47 0 0 5269.5182 12.011709
8150 16738.47 0 0 5269.5183 12.0117
8200 16738.47 0 0 5269.5185 12.0117
8250 16738.471 0 0 5269.5186 12.011709
8300 16738.471 0 0 5269.5187 12.011719
8350 16738.472 0 0 5269.5189 12.011723
8400 16738.472 0 0 5269.519 12.01172
8450 16738.473 -0.00039690664 0 5269.5189 12.011706
8500 16738.481 -0.0034646803 0 5269.5182 12.011643
8550 16738.483 -0.0045307409 0 5269.5178 12.011621
8600 16738.474 -0.00076532811 0 5269.5189 12.011681
8650 16738.474 0 0 5269.5197 12.011699
8700 16738.475 0 0 5269.5199 12.011715
8750 16738.475 0 0 5269.52 12.011732
8800 16738.475 0 0 5269.52 12.011743
8850 16738.476 0 0 5269.5201 12.011744
8900 16738.476 0 0 5269.5202 12.011735
8950 16738.476 0 0 5269.5203 12.011719
9000 16738.477 0 0 5269.5205 12.011698
9050 16738.477 0 0 5269.5206 12.011683
9100 16738.478 0 0 5269.5208 12.011684
9150 16738.479 0 0 5269.521 12.011701
9200 16738.479 0 0 5269.5212 12.011722
9250 16738.479 0 0 5269.5213 12.011738
9300 16738.48 0 0 5269.5214 12.011746
9350 16738.48 0 0 5269.5214 12.011744
9400 16738.48 0 0 5269.5215 12.011732
9450 16738.48 0 0 5269.5216 12.011715
9500 16738.481 -0.00037652437 0 5269.5216 12.011692
9550 16738.493 -0.0053156158 0 5269.5203 12.011611
9600 16738.549 -0.026814369 0 5269.5163 12.011415
9650 16738.765 -0.10191523 0 5269.5092 12.011013
9700 16735.041 1.0589886 0 5269.4979 12.062708
9750 16738.013 0.13550089 0 5269.5101 11.407245
9800 16738.512 -0.011620329 0 5269.5201 11.394973
9850 16738.489 -0.00067270567 0 5269.5237 11.395098
9900 16738.489 -0.00024984578 0 5269.5242 11.395084
9950 16738.49 0 0 5269.5245 11.395076
10000 16738.49 0 0 5269.5246 11.395075
Loop time of 0.139893 on 4 procs for 10000 steps with 81 atoms
Performance: 617616.025 tau/day, 71483.336 timesteps/s, 5.790 Matom-step/s
98.9% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0015795 | 0.0022375 | 0.0027109 | 0.9 | 1.60
Bond | 0.00031772 | 0.00032314 | 0.00032894 | 0.0 | 0.23
Neigh | 0.015169 | 0.016101 | 0.017803 | 0.8 | 11.51
Comm | 0.063065 | 0.06514 | 0.06737 | 0.7 | 46.56
Output | 0.001945 | 0.0020985 | 0.0025044 | 0.5 | 1.50
Modify | 0.03865 | 0.039853 | 0.041246 | 0.6 | 28.49
Other | | 0.01414 | | | 10.11
Nlocal: 20.25 ave 37 max 3 min
Histogram: 1 0 0 1 0 0 0 1 0 1
Nghost: 27.25 ave 48 max 13 min
Histogram: 1 0 0 2 0 0 0 0 0 1
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0
Ave special neighs/atom = 0
Neighbor list builds = 1552
Dangerous builds = 0
Total wall time: 0:00:00

340
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@ -1,340 +0,0 @@
LAMMPS (7 Feb 2024 - Development - patch_7Feb2024_update1-306-gf3391199e7-modified)
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 = 0.001 seconds
velocity all create 100.0 4928459
# unconnected bodies
group clump1 id <> 1 9
9 atoms in group clump1
group clump2 id <> 10 18
9 atoms in group clump2
group clump3 id <> 19 27
9 atoms in group clump3
group clump4 id <> 28 36
9 atoms in group clump4
group clump5 id <> 37 45
9 atoms in group clump5
group clump6 id <> 46 54
9 atoms in group clump6
group clump7 id <> 55 63
9 atoms in group clump7
group clump8 id <> 64 72
9 atoms in group clump8
group clump9 id <> 73 81
9 atoms in group clump9
fix 1 all rigid/nve group 9 clump1 clump2 clump3 clump4 clump5 clump6 clump7 clump8 clump9
9 rigid bodies with 81 atoms
fix_modify 1 bodyforces early
# 1 chain of connected bodies
#group clump1 id <> 1 9
#group clump2 id <> 9 18
#group clump3 id <> 18 27
#group clump4 id <> 27 36
#group clump5 id <> 36 45
#group clump6 id <> 45 54
#group clump7 id <> 54 63
#group clump8 id <> 63 72
#group clump9 id <> 72 81
#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9
# 2 chains of connected bodies
#group clump1 id <> 1 9
#group clump2 id <> 9 18
#group clump3 id <> 18 27
#group clump4 id <> 27 36
#group clump5 id <> 37 45
#group clump6 id <> 45 54
#group clump7 id <> 54 63
#group clump8 id <> 63 72
#group clump9 id <> 72 81
#fix 1 all poems group clump1 clump2 clump3 clump4
#fix 2 all poems group clump5 clump6 clump7 clump8 clump9
neigh_modify exclude group clump1 clump1
neigh_modify exclude group clump2 clump2
neigh_modify exclude group clump3 clump3
neigh_modify exclude group clump4 clump4
neigh_modify exclude group clump5 clump5
neigh_modify exclude group clump6 clump6
neigh_modify exclude group clump7 clump7
neigh_modify exclude group clump8 clump8
neigh_modify exclude group clump9 clump9
thermo 100
#dump 1 all atom 50 dump.rigid
#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 2 pad 5
#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 3 pad 5
timestep 0.0001
thermo 50
run 10000
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4, bins = 18 18 18
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 4.353 | 4.353 | 4.353 Mbytes
Step Temp E_pair E_mol TotEng Press
0 115.29439 5235.9179 0 5272.2142 -2.7403788
50 14910.688 571.72044 0 5265.826 32.006558
100 16298.426 136.669 0 5267.6551 16.445373
150 16682.627 17.489692 0 5269.4277 14.900277
200 16733.935 1.3740602 0 5269.4647 14.569704
250 16738.854 -0.15258528 0 5269.4868 14.496759
300 16738.584 -0.055187603 0 5269.4992 14.496371
350 16738.492 -0.017449036 0 5269.5078 14.496801
400 16738.472 -0.006012316 0 5269.513 14.496991
450 16738.469 -0.0012715314 0 5269.5169 14.497085
500 16738.471 -0.00081065611 0 5269.5177 14.497095
550 16738.47 -0.00083201064 0 5269.5175 14.497091
600 16738.469 -0.00058353965 0 5269.5174 14.497091
650 16738.467 -0.0004722653 0 5269.5169 14.497088
700 16738.462 0 0 5269.5158 14.497085
750 16738.454 0 0 5269.5134 14.497066
800 16738.449 0 0 5269.5116 14.497052
850 16738.451 0 0 5269.5123 14.497057
900 16738.46 0 0 5269.5151 14.497079
950 16738.475 -0.0035324469 0 5269.5163 14.497056
1000 16738.603 -0.05113463 0 5269.509 14.496621
1050 16737.376 0.32970882 0 5269.5037 14.526144
1100 16737.909 0.16215423 0 5269.5038 14.53237
1150 16738.719 -0.089236594 0 5269.5074 14.510282
1200 16738.477 -0.0075446521 0 5269.513 14.51099
1250 16738.458 0 0 5269.5146 14.511061
1300 16738.448 0 0 5269.5114 14.511036
1350 16738.444 0 0 5269.5102 14.511026
1400 16738.449 -0.00044714105 0 5269.5113 14.511031
1450 16738.458 -0.0010956657 0 5269.5136 14.511043
1500 16738.464 -0.00057735083 0 5269.516 14.511066
1550 16738.467 0 0 5269.5173 14.511083
1600 16738.469 0 0 5269.5179 14.511087
1650 16738.47 0 0 5269.5183 14.511091
1700 16738.469 0 0 5269.5181 14.511089
1750 16738.464 0 0 5269.5164 14.511076
1800 16738.455 0 0 5269.5137 14.511055
1850 16738.45 0 0 5269.5121 14.511042
1900 16738.453 0 0 5269.513 14.511049
1950 16738.468 -0.0031854173 0 5269.5144 14.51102
2000 16738.501 -0.01331726 0 5269.5148 14.510906
2050 16738.568 -0.036719673 0 5269.5126 14.510668
2100 16738.646 -0.063312431 0 5269.5103 14.510597
2150 16738.619 -0.05606591 0 5269.5091 14.510608
2200 16738.566 -0.038448437 0 5269.5101 14.510779
2250 16738.52 -0.023712465 0 5269.5103 14.510906
2300 16738.485 -0.01323561 0 5269.5099 14.510971
2350 16738.457 -0.0045452995 0 5269.5097 14.511049
2400 16738.449 -0.00052013007 0 5269.5113 14.511107
2450 16738.461 -0.002321933 0 5269.5132 14.511099
2500 16738.474 -0.0051804641 0 5269.5145 14.511103
2550 16738.592 -0.04492566 0 5269.5117 14.510696
2600 16738.45 -0.0038193536 0 5269.5082 14.510939
2650 16733.621 1.5177478 0 5269.5097 14.586333
2700 16738.772 -0.1064304 0 5269.5069 14.500913
2750 16733.165 1.6598389 0 5269.5082 14.616957
2800 16738.577 -0.04523598 0 5269.5068 14.51458
2850 16738.475 -0.01269037 0 5269.5073 14.513396
2900 16738.449 -0.002688737 0 5269.5089 14.513555
2950 16738.465 -0.0082345477 0 5269.5084 14.513515
3000 16738.657 -0.071197475 0 5269.5061 14.513024
3050 16706.71 9.9435728 0 5269.4634 15.021496
3100 16643.257 29.968327 0 5269.5123 14.548247
3150 16739.45 -0.33134743 0 5269.4956 13.595814
3200 16731.445 2.1723572 0 5269.4792 12.100834
3250 16612.686 39.57457 0 5269.4942 13.879807
3300 16738.601 -0.059713795 0 5269.4997 12.666612
3350 16738.587 -0.044640809 0 5269.5106 12.663574
3400 16737.995 0.14468663 0 5269.5136 12.680161
3450 16738.607 -0.050706049 0 5269.5107 12.665118
3500 16738.819 -0.12122411 0 5269.5069 12.665394
3550 16738.498 -0.021940182 0 5269.5052 12.676141
3600 16673.205 20.482364 0 5269.4544 13.525704
3650 16738.648 -0.074052044 0 5269.5003 12.817014
3700 16738.632 -0.07184695 0 5269.4975 12.810978
3750 16738.621 -0.07013081 0 5269.4958 12.811663
3800 16738.552 -0.044378799 0 5269.4998 12.811871
3850 16738.492 -0.015384402 0 5269.5099 12.811397
3900 16738.487 -0.0058199162 0 5269.518 12.811514
3950 16738.482 -0.0012032457 0 5269.521 12.811589
4000 16738.478 -0.00020707654 0 5269.5208 12.811606
4050 16738.477 0 0 5269.5207 12.811608
4100 16738.477 0 0 5269.5206 12.811607
4150 16738.475 0 0 5269.5199 12.811602
4200 16738.464 0 0 5269.5165 12.811576
4250 16738.446 0 0 5269.5109 12.811532
4300 16738.44 0 0 5269.5089 12.811516
4350 16738.454 0 0 5269.5131 12.811549
4400 16738.468 0 0 5269.5177 12.811585
4450 16738.47 0 0 5269.5184 12.811591
4500 16738.466 0 0 5269.517 12.811579
4550 16738.463 0 0 5269.5162 12.811573
4600 16738.466 0 0 5269.517 12.81158
4650 16738.471 0 0 5269.5186 12.811592
4700 16738.47 0 0 5269.5182 12.811589
4750 16738.456 0 0 5269.5139 12.811556
4800 16738.441 0 0 5269.5091 12.811518
4850 16738.444 0 0 5269.5102 12.811526
4900 16738.462 0 0 5269.5159 12.81157
4950 16738.475 0 0 5269.5201 12.811603
5000 16738.479 0 0 5269.5212 12.811612
5050 16738.479 0 0 5269.5212 12.811612
5100 16738.479 0 0 5269.5212 12.811612
5150 16738.478 0 0 5269.5209 12.81161
5200 16738.472 0 0 5269.519 12.811595
5250 16738.456 0 0 5269.5138 12.811555
5300 16738.432 0 0 5269.5064 12.811497
5350 16738.422 0 0 5269.5033 12.811472
5400 16738.438 0 0 5269.5082 12.81151
5450 16738.46 0 0 5269.515 12.811564
5500 16738.471 -0.0002100851 0 5269.5183 12.811588
5550 16738.481 -0.003484166 0 5269.5185 12.811534
5600 16738.542 -0.024500002 0 5269.5164 12.81122
5650 16738.641 -0.058023282 0 5269.5142 12.812225
5700 16384.935 111.24508 0 5269.4653 26.09278
5750 16738.555 -0.030778873 0 5269.5142 13.052328
5800 16738.462 -0.0034050629 0 5269.5125 13.052653
5850 16738.441 -0.00034406845 0 5269.5089 13.052656
5900 16738.443 0 0 5269.5098 13.052667
5950 16738.459 0 0 5269.5149 13.052707
6000 16738.468 0 0 5269.5177 13.052729
6050 16738.466 0 0 5269.5172 13.052725
6100 16738.462 0 0 5269.516 13.052715
6150 16738.463 0 0 5269.5162 13.052717
6200 16738.468 0 0 5269.5178 13.052729
6250 16738.472 0 0 5269.5189 13.052738
6300 16738.465 0 0 5269.5169 13.052723
6350 16738.448 0 0 5269.5115 13.052681
6400 16738.439 0 0 5269.5086 13.052658
6450 16738.451 0 0 5269.5124 13.052687
6500 16738.469 0 0 5269.5181 13.052732
6550 16738.478 0 0 5269.5209 13.052754
6600 16738.48 0 0 5269.5214 13.052758
6650 16738.479 0 0 5269.5213 13.052757
6700 16738.48 -0.00057913194 0 5269.521 13.052744
6750 16738.483 -0.0025329373 0 5269.5198 13.0527
6800 16738.482 -0.0065110045 0 5269.5156 13.052612
6850 16738.465 -0.0072245165 0 5269.5095 13.052574
6900 16738.436 -0.0036561206 0 5269.5039 13.052609
6950 16738.433 -0.0010530752 0 5269.5056 13.052661
7000 16738.455 -0.00056878712 0 5269.5132 13.052723
7050 16738.475 -0.0011717775 0 5269.5187 13.052755
7100 16738.48 -0.00047531448 0 5269.5209 13.052781
7150 16738.479 0 0 5269.5211 13.052788
7200 16738.478 0 0 5269.5207 13.052785
7250 16738.477 0 0 5269.5207 13.052785
7300 16738.476 0 0 5269.5201 13.052781
7350 16738.466 0 0 5269.5172 13.052758
7400 16738.448 0 0 5269.5115 13.052714
7450 16738.438 0 0 5269.5083 13.052688
7500 16738.448 0 0 5269.5115 13.052713
7550 16738.464 -0.00053504438 0 5269.5158 13.052742
7600 16738.483 -0.010043243 0 5269.5123 13.052657
7650 16738.674 -0.077543712 0 5269.5051 13.052041
7700 16736.839 0.49724664 0 5269.502 13.085872
7750 16731.931 2.0427463 0 5269.5024 13.190769
7800 16738.762 -0.10404434 0 5269.5061 13.082626
7850 16738.525 -0.024994384 0 5269.5108 13.082681
7900 16738.479 -0.008372534 0 5269.5129 13.082885
7950 16738.449 -0.0038549468 0 5269.5079 13.082917
8000 16738.441 -0.0016367618 0 5269.5074 13.082937
8050 16738.455 -0.0014865651 0 5269.5123 13.082971
8100 16738.47 -0.00072796093 0 5269.5175 13.083021
8150 16738.476 0 0 5269.5202 13.08305
8200 16738.477 0 0 5269.5204 13.083051
8250 16738.476 0 0 5269.5201 13.083049
8300 16738.474 0 0 5269.5197 13.083046
8350 16738.47 0 0 5269.5185 13.083036
8400 16738.462 -0.0017116105 0 5269.5142 13.082984
8450 16738.447 -0.003289664 0 5269.5078 13.082915
8500 16738.429 -0.00098100125 0 5269.5043 13.082918
8550 16738.435 0 0 5269.5075 13.082953
8600 16738.458 0 0 5269.5146 13.083009
8650 16738.474 0 0 5269.5195 13.083048
8700 16738.478 0 0 5269.5208 13.083058
8750 16738.477 0 0 5269.5206 13.083056
8800 16738.476 0 0 5269.5203 13.083054
8850 16738.477 0 0 5269.5206 13.083056
8900 16738.476 0 0 5269.5203 13.083054
8950 16738.468 0 0 5269.5177 13.083034
9000 16738.451 0 0 5269.5122 13.082991
9050 16738.44 0 0 5269.5089 13.082965
9100 16738.448 0 0 5269.5113 13.082984
9150 16738.46 0 0 5269.5153 13.083014
9200 16738.464 0 0 5269.5163 13.083023
9250 16738.462 0 0 5269.5158 13.083019
9300 16738.462 0 0 5269.5159 13.08302
9350 16738.467 0 0 5269.5174 13.083031
9400 16738.472 -0.00023657901 0 5269.5188 13.083039
9450 16738.472 0 0 5269.519 13.083044
9500 16738.46 0 0 5269.5153 13.083016
9550 16738.443 0 0 5269.5099 13.082974
9600 16738.441 0 0 5269.5092 13.082967
9650 16738.458 -0.00038368065 0 5269.5142 13.083
9700 16738.475 -0.00099963025 0 5269.519 13.083029
9750 16738.492 -0.0049852397 0 5269.5203 13.082953
9800 16738.483 -0.0018715252 0 5269.5204 13.083034
9850 16738.477 0 0 5269.5205 13.083063
9900 16738.477 -0.0018402419 0 5269.5186 13.083025
9950 16738.482 -0.005648013 0 5269.5164 13.082936
10000 16738.467 -0.0045058746 0 5269.5129 13.082944
Loop time of 0.13715 on 1 procs for 10000 steps with 81 atoms
Performance: 629968.103 tau/day, 72912.975 timesteps/s, 5.906 Matom-step/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 | 0.0074777 | 0.0074777 | 0.0074777 | 0.0 | 5.45
Neigh | 0.043608 | 0.043608 | 0.043608 | 0.0 | 31.80
Comm | 0.0078838 | 0.0078838 | 0.0078838 | 0.0 | 5.75
Output | 0.002002 | 0.002002 | 0.002002 | 0.0 | 1.46
Modify | 0.06884 | 0.06884 | 0.06884 | 0.0 | 50.19
Other | | 0.007339 | | | 5.35
Nlocal: 81 ave 81 max 81 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 63 ave 63 max 63 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 19 ave 19 max 19 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 19
Ave neighs/atom = 0.2345679
Neighbor list builds = 1481
Dangerous builds = 0
Total wall time: 0:00:00

340
examples/rigid/log.25Mar24.rigid.nve.early.g++.4
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@ -1,340 +0,0 @@
LAMMPS (7 Feb 2024 - Development - patch_7Feb2024_update1-306-gf3391199e7-modified)
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
# unconnected bodies
group clump1 id <> 1 9
9 atoms in group clump1
group clump2 id <> 10 18
9 atoms in group clump2
group clump3 id <> 19 27
9 atoms in group clump3
group clump4 id <> 28 36
9 atoms in group clump4
group clump5 id <> 37 45
9 atoms in group clump5
group clump6 id <> 46 54
9 atoms in group clump6
group clump7 id <> 55 63
9 atoms in group clump7
group clump8 id <> 64 72
9 atoms in group clump8
group clump9 id <> 73 81
9 atoms in group clump9
fix 1 all rigid/nve group 9 clump1 clump2 clump3 clump4 clump5 clump6 clump7 clump8 clump9
9 rigid bodies with 81 atoms
fix_modify 1 bodyforces early
# 1 chain of connected bodies
#group clump1 id <> 1 9
#group clump2 id <> 9 18
#group clump3 id <> 18 27
#group clump4 id <> 27 36
#group clump5 id <> 36 45
#group clump6 id <> 45 54
#group clump7 id <> 54 63
#group clump8 id <> 63 72
#group clump9 id <> 72 81
#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9
# 2 chains of connected bodies
#group clump1 id <> 1 9
#group clump2 id <> 9 18
#group clump3 id <> 18 27
#group clump4 id <> 27 36
#group clump5 id <> 37 45
#group clump6 id <> 45 54
#group clump7 id <> 54 63
#group clump8 id <> 63 72
#group clump9 id <> 72 81
#fix 1 all poems group clump1 clump2 clump3 clump4
#fix 2 all poems group clump5 clump6 clump7 clump8 clump9
neigh_modify exclude group clump1 clump1
neigh_modify exclude group clump2 clump2
neigh_modify exclude group clump3 clump3
neigh_modify exclude group clump4 clump4
neigh_modify exclude group clump5 clump5
neigh_modify exclude group clump6 clump6
neigh_modify exclude group clump7 clump7
neigh_modify exclude group clump8 clump8
neigh_modify exclude group clump9 clump9
thermo 100
#dump 1 all atom 50 dump.rigid
#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 2 pad 5
#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 3 pad 5
timestep 0.0001
thermo 50
run 10000
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4, bins = 18 18 18
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 4.201 | 4.233 | 4.327 Mbytes
Step Temp E_pair E_mol TotEng Press
0 115.29439 5235.9179 0 5272.2142 -2.7403788
50 14910.688 571.72044 0 5265.826 32.006558
100 16298.426 136.669 0 5267.6551 16.445373
150 16682.627 17.489692 0 5269.4277 14.900277
200 16733.935 1.3740602 0 5269.4647 14.569704
250 16738.854 -0.15258528 0 5269.4868 14.496759
300 16738.584 -0.055187603 0 5269.4992 14.496371
350 16738.492 -0.017449036 0 5269.5078 14.496801
400 16738.472 -0.006012316 0 5269.513 14.496991
450 16738.469 -0.0012715314 0 5269.5169 14.497085
500 16738.471 -0.00081065611 0 5269.5177 14.497095
550 16738.47 -0.00083201064 0 5269.5175 14.497091
600 16738.469 -0.00058353965 0 5269.5174 14.497091
650 16738.467 -0.0004722653 0 5269.5169 14.497088
700 16738.462 0 0 5269.5158 14.497085
750 16738.454 0 0 5269.5134 14.497066
800 16738.449 0 0 5269.5116 14.497052
850 16738.451 0 0 5269.5123 14.497057
900 16738.46 0 0 5269.5151 14.497079
950 16738.475 -0.0035324469 0 5269.5163 14.497056
1000 16738.603 -0.05113463 0 5269.509 14.496621
1050 16737.376 0.32970882 0 5269.5037 14.526144
1100 16737.909 0.16215423 0 5269.5038 14.53237
1150 16738.719 -0.089236594 0 5269.5074 14.510282
1200 16738.477 -0.0075446521 0 5269.513 14.51099
1250 16738.458 0 0 5269.5146 14.511061
1300 16738.448 0 0 5269.5114 14.511036
1350 16738.444 0 0 5269.5102 14.511026
1400 16738.449 -0.00044714105 0 5269.5113 14.511031
1450 16738.458 -0.0010956657 0 5269.5136 14.511043
1500 16738.464 -0.00057735083 0 5269.516 14.511066
1550 16738.467 0 0 5269.5173 14.511083
1600 16738.469 0 0 5269.5179 14.511087
1650 16738.47 0 0 5269.5183 14.511091
1700 16738.469 0 0 5269.5181 14.511089
1750 16738.464 0 0 5269.5164 14.511076
1800 16738.455 0 0 5269.5137 14.511055
1850 16738.45 0 0 5269.5121 14.511042
1900 16738.453 0 0 5269.513 14.511049
1950 16738.468 -0.0031854173 0 5269.5144 14.51102
2000 16738.501 -0.01331726 0 5269.5148 14.510906
2050 16738.568 -0.036719673 0 5269.5126 14.510668
2100 16738.646 -0.063312431 0 5269.5103 14.510597
2150 16738.619 -0.05606591 0 5269.5091 14.510608
2200 16738.566 -0.038448437 0 5269.5101 14.510779
2250 16738.52 -0.023712465 0 5269.5103 14.510906
2300 16738.485 -0.01323561 0 5269.5099 14.510971
2350 16738.457 -0.0045452995 0 5269.5097 14.511049
2400 16738.449 -0.00052013007 0 5269.5113 14.511107
2450 16738.461 -0.002321933 0 5269.5132 14.511099
2500 16738.474 -0.0051804641 0 5269.5145 14.511103
2550 16738.592 -0.04492566 0 5269.5117 14.510696
2600 16738.45 -0.0038193536 0 5269.5082 14.510939
2650 16733.621 1.5177478 0 5269.5097 14.586333
2700 16738.772 -0.1064304 0 5269.5069 14.500913
2750 16733.165 1.6598389 0 5269.5082 14.616957
2800 16738.577 -0.04523598 0 5269.5068 14.51458
2850 16738.475 -0.01269037 0 5269.5073 14.513396
2900 16738.449 -0.002688737 0 5269.5089 14.513555
2950 16738.465 -0.0082345477 0 5269.5084 14.513515
3000 16738.657 -0.071197475 0 5269.5061 14.513024
3050 16706.71 9.9435728 0 5269.4634 15.021496
3100 16643.257 29.968327 0 5269.5123 14.548247
3150 16739.45 -0.33134743 0 5269.4956 13.595814
3200 16731.445 2.1723572 0 5269.4792 12.100834
3250 16612.686 39.57457 0 5269.4942 13.879807
3300 16738.601 -0.059713795 0 5269.4997 12.666612
3350 16738.587 -0.044640809 0 5269.5106 12.663574
3400 16737.995 0.14468663 0 5269.5136 12.680161
3450 16738.607 -0.050706049 0 5269.5107 12.665118
3500 16738.819 -0.12122411 0 5269.5069 12.665394
3550 16738.498 -0.021940181 0 5269.5052 12.676141
3600 16673.205 20.482364 0 5269.4544 13.525704
3650 16738.648 -0.074052045 0 5269.5003 12.817014
3700 16738.632 -0.07184695 0 5269.4975 12.810978
3750 16738.621 -0.07013081 0 5269.4958 12.811663
3800 16738.552 -0.044378799 0 5269.4998 12.811871
3850 16738.492 -0.015384402 0 5269.5099 12.811397
3900 16738.487 -0.0058199162 0 5269.518 12.811514
3950 16738.482 -0.0012032457 0 5269.521 12.811589
4000 16738.478 -0.00020707654 0 5269.5208 12.811606
4050 16738.477 0 0 5269.5207 12.811608
4100 16738.477 0 0 5269.5206 12.811607
4150 16738.475 0 0 5269.5199 12.811602
4200 16738.464 0 0 5269.5165 12.811576
4250 16738.446 0 0 5269.5109 12.811532
4300 16738.44 0 0 5269.5089 12.811516
4350 16738.454 0 0 5269.5131 12.811549
4400 16738.468 0 0 5269.5177 12.811585
4450 16738.47 0 0 5269.5184 12.811591
4500 16738.466 0 0 5269.517 12.811579
4550 16738.463 0 0 5269.5162 12.811573
4600 16738.466 0 0 5269.517 12.81158
4650 16738.471 0 0 5269.5186 12.811592
4700 16738.47 0 0 5269.5182 12.811589
4750 16738.456 0 0 5269.5139 12.811556
4800 16738.441 0 0 5269.5091 12.811518
4850 16738.444 0 0 5269.5102 12.811526
4900 16738.462 0 0 5269.5159 12.81157
4950 16738.475 0 0 5269.5201 12.811603
5000 16738.479 0 0 5269.5212 12.811612
5050 16738.479 0 0 5269.5212 12.811612
5100 16738.479 0 0 5269.5212 12.811612
5150 16738.478 0 0 5269.5209 12.81161
5200 16738.472 0 0 5269.519 12.811595
5250 16738.456 0 0 5269.5138 12.811555
5300 16738.432 0 0 5269.5064 12.811497
5350 16738.422 0 0 5269.5033 12.811472
5400 16738.438 0 0 5269.5082 12.81151
5450 16738.46 0 0 5269.515 12.811564
5500 16738.471 -0.0002100851 0 5269.5183 12.811588
5550 16738.481 -0.003484166 0 5269.5185 12.811534
5600 16738.542 -0.024500002 0 5269.5164 12.81122
5650 16738.641 -0.058023282 0 5269.5142 12.812225
5700 16384.935 111.24508 0 5269.4653 26.09278
5750 16738.555 -0.030778873 0 5269.5142 13.052328
5800 16738.462 -0.0034050628 0 5269.5125 13.052653
5850 16738.441 -0.00034406845 0 5269.5089 13.052656
5900 16738.443 0 0 5269.5098 13.052667
5950 16738.459 0 0 5269.5149 13.052707
6000 16738.468 0 0 5269.5177 13.052729
6050 16738.466 0 0 5269.5172 13.052725
6100 16738.462 0 0 5269.516 13.052715
6150 16738.463 0 0 5269.5162 13.052717
6200 16738.468 0 0 5269.5178 13.052729
6250 16738.472 0 0 5269.5189 13.052738
6300 16738.465 0 0 5269.5169 13.052723
6350 16738.448 0 0 5269.5115 13.052681
6400 16738.439 0 0 5269.5086 13.052658
6450 16738.451 0 0 5269.5124 13.052687
6500 16738.469 0 0 5269.5181 13.052732
6550 16738.478 0 0 5269.5209 13.052754
6600 16738.48 0 0 5269.5214 13.052758
6650 16738.479 0 0 5269.5213 13.052757
6700 16738.48 -0.00057913195 0 5269.521 13.052744
6750 16738.483 -0.0025329373 0 5269.5198 13.0527
6800 16738.482 -0.0065110047 0 5269.5156 13.052612
6850 16738.465 -0.0072245166 0 5269.5095 13.052574
6900 16738.436 -0.0036561206 0 5269.5039 13.052609
6950 16738.433 -0.0010530752 0 5269.5056 13.052661
7000 16738.455 -0.00056878712 0 5269.5132 13.052723
7050 16738.475 -0.0011717775 0 5269.5187 13.052755
7100 16738.48 -0.00047531448 0 5269.5209 13.052781
7150 16738.479 0 0 5269.5211 13.052788
7200 16738.478 0 0 5269.5207 13.052785
7250 16738.477 0 0 5269.5207 13.052785
7300 16738.476 0 0 5269.5201 13.052781
7350 16738.466 0 0 5269.5172 13.052758
7400 16738.448 0 0 5269.5115 13.052714
7450 16738.438 0 0 5269.5083 13.052688
7500 16738.448 0 0 5269.5115 13.052713
7550 16738.464 -0.00053504439 0 5269.5158 13.052742
7600 16738.483 -0.010043243 0 5269.5123 13.052657
7650 16738.674 -0.077543714 0 5269.5051 13.052041
7700 16736.839 0.49724671 0 5269.502 13.085872
7750 16731.931 2.0427465 0 5269.5024 13.190769
7800 16738.762 -0.10404434 0 5269.5061 13.082626
7850 16738.525 -0.024994385 0 5269.5108 13.082681
7900 16738.479 -0.008372534 0 5269.5129 13.082885
7950 16738.449 -0.0038549468 0 5269.5079 13.082917
8000 16738.441 -0.0016367617 0 5269.5074 13.082937
8050 16738.455 -0.0014865651 0 5269.5123 13.082971
8100 16738.47 -0.00072796092 0 5269.5175 13.083021
8150 16738.476 0 0 5269.5202 13.08305
8200 16738.477 0 0 5269.5204 13.083051
8250 16738.476 0 0 5269.5201 13.083049
8300 16738.474 0 0 5269.5197 13.083046
8350 16738.47 0 0 5269.5185 13.083036
8400 16738.462 -0.0017116105 0 5269.5142 13.082984
8450 16738.447 -0.003289664 0 5269.5078 13.082915
8500 16738.429 -0.00098100125 0 5269.5043 13.082918
8550 16738.435 0 0 5269.5075 13.082953
8600 16738.458 0 0 5269.5146 13.083009
8650 16738.474 0 0 5269.5195 13.083048
8700 16738.478 0 0 5269.5208 13.083058
8750 16738.477 0 0 5269.5206 13.083056
8800 16738.476 0 0 5269.5203 13.083054
8850 16738.477 0 0 5269.5206 13.083056
8900 16738.476 0 0 5269.5203 13.083054
8950 16738.468 0 0 5269.5177 13.083034
9000 16738.451 0 0 5269.5122 13.082991
9050 16738.44 0 0 5269.5089 13.082965
9100 16738.448 0 0 5269.5113 13.082984
9150 16738.46 0 0 5269.5153 13.083014
9200 16738.464 0 0 5269.5163 13.083023
9250 16738.462 0 0 5269.5158 13.083019
9300 16738.462 0 0 5269.5159 13.08302
9350 16738.467 0 0 5269.5174 13.083031
9400 16738.472 -0.00023657902 0 5269.5188 13.083039
9450 16738.472 0 0 5269.519 13.083044
9500 16738.46 0 0 5269.5153 13.083016
9550 16738.443 0 0 5269.5099 13.082974
9600 16738.441 0 0 5269.5092 13.082967
9650 16738.458 -0.00038368067 0 5269.5142 13.083
9700 16738.475 -0.00099963027 0 5269.519 13.083029
9750 16738.492 -0.00498524 0 5269.5203 13.082953
9800 16738.483 -0.0018715253 0 5269.5204 13.083034
9850 16738.477 0 0 5269.5205 13.083063
9900 16738.477 -0.0018402419 0 5269.5186 13.083025
9950 16738.482 -0.0056480132 0 5269.5164 13.082936
10000 16738.467 -0.0045058747 0 5269.5129 13.082944
Loop time of 0.14818 on 4 procs for 10000 steps with 81 atoms
Performance: 583075.499 tau/day, 67485.590 timesteps/s, 5.466 Matom-step/s
99.0% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0018099 | 0.0023754 | 0.0030445 | 1.0 | 1.60
Neigh | 0.011989 | 0.012986 | 0.01555 | 1.3 | 8.76
Comm | 0.062426 | 0.065066 | 0.066364 | 0.6 | 43.91
Output | 0.0017674 | 0.0019257 | 0.002368 | 0.6 | 1.30
Modify | 0.050371 | 0.051161 | 0.052809 | 0.4 | 34.53
Other | | 0.01467 | | | 9.90
Nlocal: 20.25 ave 35 max 0 min
Histogram: 1 0 0 0 0 1 0 1 0 1
Nghost: 41 ave 52 max 30 min
Histogram: 1 0 0 0 1 1 0 0 0 1
Neighs: 4.75 ave 19 max 0 min
Histogram: 3 0 0 0 0 0 0 0 0 1
Total # of neighbors = 19
Ave neighs/atom = 0.2345679
Neighbor list builds = 1481
Dangerous builds = 0
Total wall time: 0:00:00

338
examples/rigid/log.25Mar24.rigid.nve.g++.1
View File

@ -1,338 +0,0 @@
LAMMPS (7 Feb 2024 - Development - patch_7Feb2024_update1-306-gf3391199e7-modified)
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 = 0.001 seconds
velocity all create 100.0 4928459
# unconnected bodies
group clump1 id <> 1 9
9 atoms in group clump1
group clump2 id <> 10 18
9 atoms in group clump2
group clump3 id <> 19 27
9 atoms in group clump3
group clump4 id <> 28 36
9 atoms in group clump4
group clump5 id <> 37 45
9 atoms in group clump5
group clump6 id <> 46 54
9 atoms in group clump6
group clump7 id <> 55 63
9 atoms in group clump7
group clump8 id <> 64 72
9 atoms in group clump8
group clump9 id <> 73 81
9 atoms in group clump9
fix 1 all rigid/nve group 9 clump1 clump2 clump3 clump4 clump5 clump6 clump7 clump8 clump9
9 rigid bodies with 81 atoms
# 1 chain of connected bodies
#group clump1 id <> 1 9
#group clump2 id <> 9 18
#group clump3 id <> 18 27
#group clump4 id <> 27 36
#group clump5 id <> 36 45
#group clump6 id <> 45 54
#group clump7 id <> 54 63
#group clump8 id <> 63 72
#group clump9 id <> 72 81
#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9
# 2 chains of connected bodies
#group clump1 id <> 1 9
#group clump2 id <> 9 18
#group clump3 id <> 18 27
#group clump4 id <> 27 36
#group clump5 id <> 37 45
#group clump6 id <> 45 54
#group clump7 id <> 54 63
#group clump8 id <> 63 72
#group clump9 id <> 72 81
#fix 1 all poems group clump1 clump2 clump3 clump4
#fix 2 all poems group clump5 clump6 clump7 clump8 clump9
neigh_modify exclude group clump1 clump1
neigh_modify exclude group clump2 clump2
neigh_modify exclude group clump3 clump3
neigh_modify exclude group clump4 clump4
neigh_modify exclude group clump5 clump5
neigh_modify exclude group clump6 clump6
neigh_modify exclude group clump7 clump7
neigh_modify exclude group clump8 clump8
neigh_modify exclude group clump9 clump9
thermo 100
#dump 1 all atom 50 dump.rigid
#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 2 pad 5
#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 3 pad 5
timestep 0.0001
thermo 50
run 10000
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4, bins = 18 18 18
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 4.353 | 4.353 | 4.353 Mbytes
Step Temp E_pair E_mol TotEng Press
0 115.29439 5235.9179 0 5272.2142 -2.7403788
50 14910.688 571.72044 0 5265.826 32.006558
100 16298.426 136.669 0 5267.6551 16.445373
150 16682.627 17.489692 0 5269.4277 14.900277
200 16733.935 1.3740602 0 5269.4647 14.569704
250 16738.854 -0.15258528 0 5269.4868 14.496759
300 16738.584 -0.055187603 0 5269.4992 14.496371
350 16738.492 -0.017449036 0 5269.5078 14.496801
400 16738.472 -0.006012316 0 5269.513 14.496991
450 16738.469 -0.0012715314 0 5269.5169 14.497085
500 16738.471 -0.00081065611 0 5269.5177 14.497095
550 16738.47 -0.00083201064 0 5269.5175 14.497091
600 16738.469 -0.00058353965 0 5269.5174 14.497091
650 16738.467 -0.0004722653 0 5269.5169 14.497088
700 16738.462 0 0 5269.5158 14.497085
750 16738.454 0 0 5269.5134 14.497066
800 16738.449 0 0 5269.5116 14.497052
850 16738.451 0 0 5269.5123 14.497057
900 16738.46 0 0 5269.5151 14.497079
950 16738.475 -0.0035324469 0 5269.5163 14.497056
1000 16738.603 -0.05113463 0 5269.509 14.496621
1050 16737.376 0.32970882 0 5269.5037 14.526144
1100 16737.909 0.16215423 0 5269.5038 14.53237
1150 16738.719 -0.089236594 0 5269.5074 14.510282
1200 16738.477 -0.0075446521 0 5269.513 14.51099
1250 16738.458 0 0 5269.5146 14.511061
1300 16738.448 0 0 5269.5114 14.511036
1350 16738.444 0 0 5269.5102 14.511026
1400 16738.449 -0.00044714105 0 5269.5113 14.511031
1450 16738.458 -0.0010956657 0 5269.5136 14.511043
1500 16738.464 -0.00057735083 0 5269.516 14.511066
1550 16738.467 0 0 5269.5173 14.511083
1600 16738.469 0 0 5269.5179 14.511087
1650 16738.47 0 0 5269.5183 14.511091
1700 16738.469 0 0 5269.5181 14.511089
1750 16738.464 0 0 5269.5164 14.511076
1800 16738.455 0 0 5269.5137 14.511055
1850 16738.45 0 0 5269.5121 14.511042
1900 16738.453 0 0 5269.513 14.511049
1950 16738.468 -0.0031854173 0 5269.5144 14.51102
2000 16738.501 -0.01331726 0 5269.5148 14.510906
2050 16738.568 -0.036719673 0 5269.5126 14.510668
2100 16738.646 -0.063312431 0 5269.5103 14.510597
2150 16738.619 -0.05606591 0 5269.5091 14.510608
2200 16738.566 -0.038448437 0 5269.5101 14.510779
2250 16738.52 -0.023712465 0 5269.5103 14.510906
2300 16738.485 -0.01323561 0 5269.5099 14.510971
2350 16738.457 -0.0045452995 0 5269.5097 14.511049
2400 16738.449 -0.00052013007 0 5269.5113 14.511107
2450 16738.461 -0.002321933 0 5269.5132 14.511099
2500 16738.474 -0.0051804641 0 5269.5145 14.511103
2550 16738.592 -0.04492566 0 5269.5117 14.510696
2600 16738.45 -0.0038193536 0 5269.5082 14.510939
2650 16733.621 1.5177478 0 5269.5097 14.586333
2700 16738.772 -0.1064304 0 5269.5069 14.500913
2750 16733.165 1.6598389 0 5269.5082 14.616957
2800 16738.577 -0.04523598 0 5269.5068 14.51458
2850 16738.475 -0.01269037 0 5269.5073 14.513396
2900 16738.449 -0.002688737 0 5269.5089 14.513555
2950 16738.465 -0.0082345477 0 5269.5084 14.513515
3000 16738.657 -0.071197475 0 5269.5061 14.513024
3050 16706.71 9.9435728 0 5269.4634 15.021496
3100 16643.257 29.968327 0 5269.5123 14.548247
3150 16739.45 -0.33134743 0 5269.4956 13.595814
3200 16731.445 2.1723572 0 5269.4792 12.100834
3250 16612.686 39.57457 0 5269.4942 13.879807
3300 16738.601 -0.059713795 0 5269.4997 12.666612
3350 16738.587 -0.044640809 0 5269.5106 12.663574
3400 16737.995 0.14468663 0 5269.5136 12.680161
3450 16738.607 -0.050706049 0 5269.5107 12.665118
3500 16738.819 -0.12122411 0 5269.5069 12.665394
3550 16738.498 -0.021940182 0 5269.5052 12.676141
3600 16673.205 20.482364 0 5269.4544 13.525704
3650 16738.648 -0.074052044 0 5269.5003 12.817014
3700 16738.632 -0.07184695 0 5269.4975 12.810978
3750 16738.621 -0.07013081 0 5269.4958 12.811663
3800 16738.552 -0.044378799 0 5269.4998 12.811871
3850 16738.492 -0.015384402 0 5269.5099 12.811397
3900 16738.487 -0.0058199162 0 5269.518 12.811514
3950 16738.482 -0.0012032457 0 5269.521 12.811589
4000 16738.478 -0.00020707654 0 5269.5208 12.811606
4050 16738.477 0 0 5269.5207 12.811608
4100 16738.477 0 0 5269.5206 12.811607
4150 16738.475 0 0 5269.5199 12.811602
4200 16738.464 0 0 5269.5165 12.811576
4250 16738.446 0 0 5269.5109 12.811532
4300 16738.44 0 0 5269.5089 12.811516
4350 16738.454 0 0 5269.5131 12.811549
4400 16738.468 0 0 5269.5177 12.811585
4450 16738.47 0 0 5269.5184 12.811591
4500 16738.466 0 0 5269.517 12.811579
4550 16738.463 0 0 5269.5162 12.811573
4600 16738.466 0 0 5269.517 12.81158
4650 16738.471 0 0 5269.5186 12.811592
4700 16738.47 0 0 5269.5182 12.811589
4750 16738.456 0 0 5269.5139 12.811556
4800 16738.441 0 0 5269.5091 12.811518
4850 16738.444 0 0 5269.5102 12.811526
4900 16738.462 0 0 5269.5159 12.81157
4950 16738.475 0 0 5269.5201 12.811603
5000 16738.479 0 0 5269.5212 12.811612
5050 16738.479 0 0 5269.5212 12.811612
5100 16738.479 0 0 5269.5212 12.811612
5150 16738.478 0 0 5269.5209 12.81161
5200 16738.472 0 0 5269.519 12.811595
5250 16738.456 0 0 5269.5138 12.811555
5300 16738.432 0 0 5269.5064 12.811497
5350 16738.422 0 0 5269.5033 12.811472
5400 16738.438 0 0 5269.5082 12.81151
5450 16738.46 0 0 5269.515 12.811564
5500 16738.471 -0.0002100851 0 5269.5183 12.811588
5550 16738.481 -0.003484166 0 5269.5185 12.811534
5600 16738.542 -0.024500002 0 5269.5164 12.81122
5650 16738.641 -0.058023282 0 5269.5142 12.812225
5700 16384.935 111.24508 0 5269.4653 26.09278
5750 16738.555 -0.030778873 0 5269.5142 13.052328
5800 16738.462 -0.0034050629 0 5269.5125 13.052653
5850 16738.441 -0.00034406845 0 5269.5089 13.052656
5900 16738.443 0 0 5269.5098 13.052667
5950 16738.459 0 0 5269.5149 13.052707
6000 16738.468 0 0 5269.5177 13.052729
6050 16738.466 0 0 5269.5172 13.052725
6100 16738.462 0 0 5269.516 13.052715
6150 16738.463 0 0 5269.5162 13.052717
6200 16738.468 0 0 5269.5178 13.052729
6250 16738.472 0 0 5269.5189 13.052738
6300 16738.465 0 0 5269.5169 13.052723
6350 16738.448 0 0 5269.5115 13.052681
6400 16738.439 0 0 5269.5086 13.052658
6450 16738.451 0 0 5269.5124 13.052687
6500 16738.469 0 0 5269.5181 13.052732
6550 16738.478 0 0 5269.5209 13.052754
6600 16738.48 0 0 5269.5214 13.052758
6650 16738.479 0 0 5269.5213 13.052757
6700 16738.48 -0.00057913194 0 5269.521 13.052744
6750 16738.483 -0.0025329373 0 5269.5198 13.0527
6800 16738.482 -0.0065110045 0 5269.5156 13.052612
6850 16738.465 -0.0072245165 0 5269.5095 13.052574
6900 16738.436 -0.0036561206 0 5269.5039 13.052609
6950 16738.433 -0.0010530752 0 5269.5056 13.052661
7000 16738.455 -0.00056878712 0 5269.5132 13.052723
7050 16738.475 -0.0011717775 0 5269.5187 13.052755
7100 16738.48 -0.00047531448 0 5269.5209 13.052781
7150 16738.479 0 0 5269.5211 13.052788
7200 16738.478 0 0 5269.5207 13.052785
7250 16738.477 0 0 5269.5207 13.052785
7300 16738.476 0 0 5269.5201 13.052781
7350 16738.466 0 0 5269.5172 13.052758
7400 16738.448 0 0 5269.5115 13.052714
7450 16738.438 0 0 5269.5083 13.052688
7500 16738.448 0 0 5269.5115 13.052713
7550 16738.464 -0.00053504438 0 5269.5158 13.052742
7600 16738.483 -0.010043243 0 5269.5123 13.052657
7650 16738.674 -0.077543712 0 5269.5051 13.052041
7700 16736.839 0.49724664 0 5269.502 13.085872
7750 16731.931 2.0427463 0 5269.5024 13.190769
7800 16738.762 -0.10404434 0 5269.5061 13.082626
7850 16738.525 -0.024994384 0 5269.5108 13.082681
7900 16738.479 -0.008372534 0 5269.5129 13.082885
7950 16738.449 -0.0038549468 0 5269.5079 13.082917
8000 16738.441 -0.0016367618 0 5269.5074 13.082937
8050 16738.455 -0.0014865651 0 5269.5123 13.082971
8100 16738.47 -0.00072796093 0 5269.5175 13.083021
8150 16738.476 0 0 5269.5202 13.08305
8200 16738.477 0 0 5269.5204 13.083051
8250 16738.476 0 0 5269.5201 13.083049
8300 16738.474 0 0 5269.5197 13.083046
8350 16738.47 0 0 5269.5185 13.083036
8400 16738.462 -0.0017116105 0 5269.5142 13.082984
8450 16738.447 -0.003289664 0 5269.5078 13.082915
8500 16738.429 -0.00098100125 0 5269.5043 13.082918
8550 16738.435 0 0 5269.5075 13.082953
8600 16738.458 0 0 5269.5146 13.083009
8650 16738.474 0 0 5269.5195 13.083048
8700 16738.478 0 0 5269.5208 13.083058
8750 16738.477 0 0 5269.5206 13.083056
8800 16738.476 0 0 5269.5203 13.083054
8850 16738.477 0 0 5269.5206 13.083056
8900 16738.476 0 0 5269.5203 13.083054
8950 16738.468 0 0 5269.5177 13.083034
9000 16738.451 0 0 5269.5122 13.082991
9050 16738.44 0 0 5269.5089 13.082965
9100 16738.448 0 0 5269.5113 13.082984
9150 16738.46 0 0 5269.5153 13.083014
9200 16738.464 0 0 5269.5163 13.083023
9250 16738.462 0 0 5269.5158 13.083019
9300 16738.462 0 0 5269.5159 13.08302
9350 16738.467 0 0 5269.5174 13.083031
9400 16738.472 -0.00023657901 0 5269.5188 13.083039
9450 16738.472 0 0 5269.519 13.083044
9500 16738.46 0 0 5269.5153 13.083016
9550 16738.443 0 0 5269.5099 13.082974
9600 16738.441 0 0 5269.5092 13.082967
9650 16738.458 -0.00038368065 0 5269.5142 13.083
9700 16738.475 -0.00099963025 0 5269.519 13.083029
9750 16738.492 -0.0049852397 0 5269.5203 13.082953
9800 16738.483 -0.0018715252 0 5269.5204 13.083034
9850 16738.477 0 0 5269.5205 13.083063
9900 16738.477 -0.0018402419 0 5269.5186 13.083025
9950 16738.482 -0.005648013 0 5269.5164 13.082936
10000 16738.467 -0.0045058746 0 5269.5129 13.082944
Loop time of 0.139287 on 1 procs for 10000 steps with 81 atoms
Performance: 620300.751 tau/day, 71794.068 timesteps/s, 5.815 Matom-step/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 | 0.0074128 | 0.0074128 | 0.0074128 | 0.0 | 5.32
Neigh | 0.045566 | 0.045566 | 0.045566 | 0.0 | 32.71
Comm | 0.007912 | 0.007912 | 0.007912 | 0.0 | 5.68
Output | 0.0015912 | 0.0015912 | 0.0015912 | 0.0 | 1.14
Modify | 0.06951 | 0.06951 | 0.06951 | 0.0 | 49.90
Other | | 0.007295 | | | 5.24
Nlocal: 81 ave 81 max 81 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 63 ave 63 max 63 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 19 ave 19 max 19 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 19
Ave neighs/atom = 0.2345679
Neighbor list builds = 1481
Dangerous builds = 0
Total wall time: 0:00:00

338
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@ -1,338 +0,0 @@
LAMMPS (7 Feb 2024 - Development - patch_7Feb2024_update1-306-gf3391199e7-modified)
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
# unconnected bodies
group clump1 id <> 1 9
9 atoms in group clump1
group clump2 id <> 10 18
9 atoms in group clump2
group clump3 id <> 19 27
9 atoms in group clump3
group clump4 id <> 28 36
9 atoms in group clump4
group clump5 id <> 37 45
9 atoms in group clump5
group clump6 id <> 46 54
9 atoms in group clump6
group clump7 id <> 55 63
9 atoms in group clump7
group clump8 id <> 64 72
9 atoms in group clump8
group clump9 id <> 73 81
9 atoms in group clump9
fix 1 all rigid/nve group 9 clump1 clump2 clump3 clump4 clump5 clump6 clump7 clump8 clump9
9 rigid bodies with 81 atoms
# 1 chain of connected bodies
#group clump1 id <> 1 9
#group clump2 id <> 9 18
#group clump3 id <> 18 27
#group clump4 id <> 27 36
#group clump5 id <> 36 45
#group clump6 id <> 45 54
#group clump7 id <> 54 63
#group clump8 id <> 63 72
#group clump9 id <> 72 81
#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9
# 2 chains of connected bodies
#group clump1 id <> 1 9
#group clump2 id <> 9 18
#group clump3 id <> 18 27
#group clump4 id <> 27 36
#group clump5 id <> 37 45
#group clump6 id <> 45 54
#group clump7 id <> 54 63
#group clump8 id <> 63 72
#group clump9 id <> 72 81
#fix 1 all poems group clump1 clump2 clump3 clump4
#fix 2 all poems group clump5 clump6 clump7 clump8 clump9
neigh_modify exclude group clump1 clump1
neigh_modify exclude group clump2 clump2
neigh_modify exclude group clump3 clump3
neigh_modify exclude group clump4 clump4
neigh_modify exclude group clump5 clump5
neigh_modify exclude group clump6 clump6
neigh_modify exclude group clump7 clump7
neigh_modify exclude group clump8 clump8
neigh_modify exclude group clump9 clump9
thermo 100
#dump 1 all atom 50 dump.rigid
#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 2 pad 5
#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 3 pad 5
timestep 0.0001
thermo 50
run 10000
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4, bins = 18 18 18
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 4.201 | 4.233 | 4.327 Mbytes
Step Temp E_pair E_mol TotEng Press
0 115.29439 5235.9179 0 5272.2142 -2.7403788
50 14910.688 571.72044 0 5265.826 32.006558
100 16298.426 136.669 0 5267.6551 16.445373
150 16682.627 17.489692 0 5269.4277 14.900277
200 16733.935 1.3740602 0 5269.4647 14.569704
250 16738.854 -0.15258528 0 5269.4868 14.496759
300 16738.584 -0.055187603 0 5269.4992 14.496371
350 16738.492 -0.017449036 0 5269.5078 14.496801
400 16738.472 -0.006012316 0 5269.513 14.496991
450 16738.469 -0.0012715314 0 5269.5169 14.497085
500 16738.471 -0.00081065611 0 5269.5177 14.497095
550 16738.47 -0.00083201064 0 5269.5175 14.497091
600 16738.469 -0.00058353965 0 5269.5174 14.497091
650 16738.467 -0.0004722653 0 5269.5169 14.497088
700 16738.462 0 0 5269.5158 14.497085
750 16738.454 0 0 5269.5134 14.497066
800 16738.449 0 0 5269.5116 14.497052
850 16738.451 0 0 5269.5123 14.497057
900 16738.46 0 0 5269.5151 14.497079
950 16738.475 -0.0035324469 0 5269.5163 14.497056
1000 16738.603 -0.05113463 0 5269.509 14.496621
1050 16737.376 0.32970882 0 5269.5037 14.526144
1100 16737.909 0.16215423 0 5269.5038 14.53237
1150 16738.719 -0.089236594 0 5269.5074 14.510282
1200 16738.477 -0.0075446521 0 5269.513 14.51099
1250 16738.458 0 0 5269.5146 14.511061
1300 16738.448 0 0 5269.5114 14.511036
1350 16738.444 0 0 5269.5102 14.511026
1400 16738.449 -0.00044714105 0 5269.5113 14.511031
1450 16738.458 -0.0010956657 0 5269.5136 14.511043
1500 16738.464 -0.00057735083 0 5269.516 14.511066
1550 16738.467 0 0 5269.5173 14.511083
1600 16738.469 0 0 5269.5179 14.511087
1650 16738.47 0 0 5269.5183 14.511091
1700 16738.469 0 0 5269.5181 14.511089
1750 16738.464 0 0 5269.5164 14.511076
1800 16738.455 0 0 5269.5137 14.511055
1850 16738.45 0 0 5269.5121 14.511042
1900 16738.453 0 0 5269.513 14.511049
1950 16738.468 -0.0031854173 0 5269.5144 14.51102
2000 16738.501 -0.01331726 0 5269.5148 14.510906
2050 16738.568 -0.036719673 0 5269.5126 14.510668
2100 16738.646 -0.063312431 0 5269.5103 14.510597
2150 16738.619 -0.05606591 0 5269.5091 14.510608
2200 16738.566 -0.038448437 0 5269.5101 14.510779
2250 16738.52 -0.023712465 0 5269.5103 14.510906
2300 16738.485 -0.01323561 0 5269.5099 14.510971
2350 16738.457 -0.0045452995 0 5269.5097 14.511049
2400 16738.449 -0.00052013007 0 5269.5113 14.511107
2450 16738.461 -0.002321933 0 5269.5132 14.511099
2500 16738.474 -0.0051804641 0 5269.5145 14.511103
2550 16738.592 -0.04492566 0 5269.5117 14.510696
2600 16738.45 -0.0038193536 0 5269.5082 14.510939
2650 16733.621 1.5177478 0 5269.5097 14.586333
2700 16738.772 -0.1064304 0 5269.5069 14.500913
2750 16733.165 1.6598389 0 5269.5082 14.616957
2800 16738.577 -0.04523598 0 5269.5068 14.51458
2850 16738.475 -0.01269037 0 5269.5073 14.513396
2900 16738.449 -0.002688737 0 5269.5089 14.513555
2950 16738.465 -0.0082345477 0 5269.5084 14.513515
3000 16738.657 -0.071197475 0 5269.5061 14.513024
3050 16706.71 9.9435728 0 5269.4634 15.021496
3100 16643.257 29.968327 0 5269.5123 14.548247
3150 16739.45 -0.33134743 0 5269.4956 13.595814
3200 16731.445 2.1723572 0 5269.4792 12.100834
3250 16612.686 39.57457 0 5269.4942 13.879807
3300 16738.601 -0.059713795 0 5269.4997 12.666612
3350 16738.587 -0.044640809 0 5269.5106 12.663574
3400 16737.995 0.14468663 0 5269.5136 12.680161
3450 16738.607 -0.050706049 0 5269.5107 12.665118
3500 16738.819 -0.12122411 0 5269.5069 12.665394
3550 16738.498 -0.021940181 0 5269.5052 12.676141
3600 16673.205 20.482364 0 5269.4544 13.525704
3650 16738.648 -0.074052045 0 5269.5003 12.817014
3700 16738.632 -0.07184695 0 5269.4975 12.810978
3750 16738.621 -0.07013081 0 5269.4958 12.811663
3800 16738.552 -0.044378799 0 5269.4998 12.811871
3850 16738.492 -0.015384402 0 5269.5099 12.811397
3900 16738.487 -0.0058199162 0 5269.518 12.811514
3950 16738.482 -0.0012032457 0 5269.521 12.811589
4000 16738.478 -0.00020707654 0 5269.5208 12.811606
4050 16738.477 0 0 5269.5207 12.811608
4100 16738.477 0 0 5269.5206 12.811607
4150 16738.475 0 0 5269.5199 12.811602
4200 16738.464 0 0 5269.5165 12.811576
4250 16738.446 0 0 5269.5109 12.811532
4300 16738.44 0 0 5269.5089 12.811516
4350 16738.454 0 0 5269.5131 12.811549
4400 16738.468 0 0 5269.5177 12.811585
4450 16738.47 0 0 5269.5184 12.811591
4500 16738.466 0 0 5269.517 12.811579
4550 16738.463 0 0 5269.5162 12.811573
4600 16738.466 0 0 5269.517 12.81158
4650 16738.471 0 0 5269.5186 12.811592
4700 16738.47 0 0 5269.5182 12.811589
4750 16738.456 0 0 5269.5139 12.811556
4800 16738.441 0 0 5269.5091 12.811518
4850 16738.444 0 0 5269.5102 12.811526
4900 16738.462 0 0 5269.5159 12.81157
4950 16738.475 0 0 5269.5201 12.811603
5000 16738.479 0 0 5269.5212 12.811612
5050 16738.479 0 0 5269.5212 12.811612
5100 16738.479 0 0 5269.5212 12.811612
5150 16738.478 0 0 5269.5209 12.81161
5200 16738.472 0 0 5269.519 12.811595
5250 16738.456 0 0 5269.5138 12.811555
5300 16738.432 0 0 5269.5064 12.811497
5350 16738.422 0 0 5269.5033 12.811472
5400 16738.438 0 0 5269.5082 12.81151
5450 16738.46 0 0 5269.515 12.811564
5500 16738.471 -0.0002100851 0 5269.5183 12.811588
5550 16738.481 -0.003484166 0 5269.5185 12.811534
5600 16738.542 -0.024500002 0 5269.5164 12.81122
5650 16738.641 -0.058023282 0 5269.5142 12.812225
5700 16384.935 111.24508 0 5269.4653 26.09278
5750 16738.555 -0.030778873 0 5269.5142 13.052328
5800 16738.462 -0.0034050628 0 5269.5125 13.052653
5850 16738.441 -0.00034406845 0 5269.5089 13.052656
5900 16738.443 0 0 5269.5098 13.052667
5950 16738.459 0 0 5269.5149 13.052707
6000 16738.468 0 0 5269.5177 13.052729
6050 16738.466 0 0 5269.5172 13.052725
6100 16738.462 0 0 5269.516 13.052715
6150 16738.463 0 0 5269.5162 13.052717
6200 16738.468 0 0 5269.5178 13.052729
6250 16738.472 0 0 5269.5189 13.052738
6300 16738.465 0 0 5269.5169 13.052723
6350 16738.448 0 0 5269.5115 13.052681
6400 16738.439 0 0 5269.5086 13.052658
6450 16738.451 0 0 5269.5124 13.052687
6500 16738.469 0 0 5269.5181 13.052732
6550 16738.478 0 0 5269.5209 13.052754
6600 16738.48 0 0 5269.5214 13.052758
6650 16738.479 0 0 5269.5213 13.052757
6700 16738.48 -0.00057913195 0 5269.521 13.052744
6750 16738.483 -0.0025329373 0 5269.5198 13.0527
6800 16738.482 -0.0065110047 0 5269.5156 13.052612
6850 16738.465 -0.0072245166 0 5269.5095 13.052574
6900 16738.436 -0.0036561206 0 5269.5039 13.052609
6950 16738.433 -0.0010530752 0 5269.5056 13.052661
7000 16738.455 -0.00056878712 0 5269.5132 13.052723
7050 16738.475 -0.0011717775 0 5269.5187 13.052755
7100 16738.48 -0.00047531448 0 5269.5209 13.052781
7150 16738.479 0 0 5269.5211 13.052788
7200 16738.478 0 0 5269.5207 13.052785
7250 16738.477 0 0 5269.5207 13.052785
7300 16738.476 0 0 5269.5201 13.052781
7350 16738.466 0 0 5269.5172 13.052758
7400 16738.448 0 0 5269.5115 13.052714
7450 16738.438 0 0 5269.5083 13.052688
7500 16738.448 0 0 5269.5115 13.052713
7550 16738.464 -0.00053504439 0 5269.5158 13.052742
7600 16738.483 -0.010043243 0 5269.5123 13.052657
7650 16738.674 -0.077543714 0 5269.5051 13.052041
7700 16736.839 0.49724671 0 5269.502 13.085872
7750 16731.931 2.0427465 0 5269.5024 13.190769
7800 16738.762 -0.10404434 0 5269.5061 13.082626
7850 16738.525 -0.024994385 0 5269.5108 13.082681
7900 16738.479 -0.008372534 0 5269.5129 13.082885
7950 16738.449 -0.0038549468 0 5269.5079 13.082917
8000 16738.441 -0.0016367617 0 5269.5074 13.082937
8050 16738.455 -0.0014865651 0 5269.5123 13.082971
8100 16738.47 -0.00072796092 0 5269.5175 13.083021
8150 16738.476 0 0 5269.5202 13.08305
8200 16738.477 0 0 5269.5204 13.083051
8250 16738.476 0 0 5269.5201 13.083049
8300 16738.474 0 0 5269.5197 13.083046
8350 16738.47 0 0 5269.5185 13.083036
8400 16738.462 -0.0017116105 0 5269.5142 13.082984
8450 16738.447 -0.003289664 0 5269.5078 13.082915
8500 16738.429 -0.00098100125 0 5269.5043 13.082918
8550 16738.435 0 0 5269.5075 13.082953
8600 16738.458 0 0 5269.5146 13.083009
8650 16738.474 0 0 5269.5195 13.083048
8700 16738.478 0 0 5269.5208 13.083058
8750 16738.477 0 0 5269.5206 13.083056
8800 16738.476 0 0 5269.5203 13.083054
8850 16738.477 0 0 5269.5206 13.083056
8900 16738.476 0 0 5269.5203 13.083054
8950 16738.468 0 0 5269.5177 13.083034
9000 16738.451 0 0 5269.5122 13.082991
9050 16738.44 0 0 5269.5089 13.082965
9100 16738.448 0 0 5269.5113 13.082984
9150 16738.46 0 0 5269.5153 13.083014
9200 16738.464 0 0 5269.5163 13.083023
9250 16738.462 0 0 5269.5158 13.083019
9300 16738.462 0 0 5269.5159 13.08302
9350 16738.467 0 0 5269.5174 13.083031
9400 16738.472 -0.00023657902 0 5269.5188 13.083039
9450 16738.472 0 0 5269.519 13.083044
9500 16738.46 0 0 5269.5153 13.083016
9550 16738.443 0 0 5269.5099 13.082974
9600 16738.441 0 0 5269.5092 13.082967
9650 16738.458 -0.00038368067 0 5269.5142 13.083
9700 16738.475 -0.00099963027 0 5269.519 13.083029
9750 16738.492 -0.00498524 0 5269.5203 13.082953
9800 16738.483 -0.0018715253 0 5269.5204 13.083034
9850 16738.477 0 0 5269.5205 13.083063
9900 16738.477 -0.0018402419 0 5269.5186 13.083025
9950 16738.482 -0.0056480132 0 5269.5164 13.082936
10000 16738.467 -0.0045058747 0 5269.5129 13.082944
Loop time of 0.147071 on 4 procs for 10000 steps with 81 atoms
Performance: 587469.667 tau/day, 67994.174 timesteps/s, 5.508 Matom-step/s
98.2% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0016588 | 0.0023518 | 0.0030017 | 1.0 | 1.60
Neigh | 0.011581 | 0.012949 | 0.014883 | 1.1 | 8.80
Comm | 0.063654 | 0.065097 | 0.066501 | 0.4 | 44.26
Output | 0.0017378 | 0.0018782 | 0.0022756 | 0.5 | 1.28
Modify | 0.049872 | 0.050432 | 0.051195 | 0.2 | 34.29
Other | | 0.01436 | | | 9.77
Nlocal: 20.25 ave 35 max 0 min
Histogram: 1 0 0 0 0 1 0 1 0 1
Nghost: 41 ave 52 max 30 min
Histogram: 1 0 0 0 1 1 0 0 0 1
Neighs: 4.75 ave 19 max 0 min
Histogram: 3 0 0 0 0 0 0 0 0 1
Total # of neighbors = 19
Ave neighs/atom = 0.2345679
Neighbor list builds = 1481
Dangerous builds = 0
Total wall time: 0:00:00

328
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@ -1,328 +0,0 @@
LAMMPS (7 Feb 2024 - Development - patch_7Feb2024_update1-306-gf3391199e7-modified)
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 = 0.001 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: doi:10.1016/j.ijnonlinmec.2008.04.003
@Article{Mukherjee08,
author = {R. M. Mukherjee and P. S. Crozier and S. J. Plimpton and K. S. Anderson},
title = {Substructured Molecular Dynamics Using Multibody Dynamics Algorithms},
journal = {Intl.\ J.\ Non-Linear Mechanics},
year = 2008,
volume = 43,
number = 10,
pages = {1040--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 = 0 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 -3.2045743
850 17821.483 711.53827 0 3681.7854 7.4384279
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 -0.86699135
1200 21815.003 45.317412 0 3681.1512 1.5988314
1250 18655.437 572.41453 0 3681.654 10.06408
1300 20780.781 217.36509 0 3680.8286 6.0538614
1350 20558.971 254.36485 0 3680.8601 -3.6773923
1400 21485.029 99.812891 0 3680.6511 -16.185475
1450 21771.107 52.159624 0 3680.6775 -2.4756668
1500 21520.948 93.503905 0 3680.3286 2.1023577
1550 21351.418 121.68136 0 3680.2511 5.5159922
1600 20778.805 216.92182 0 3680.0559 15.089193
1650 21477.637 100.21853 0 3679.8247 -1.1045536
1700 18501.335 596.47986 0 3680.0357 -15.679729
1750 18563.64 587.34819 0 3681.2882 33.532254
1800 19110.181 494.82407 0 3679.8543 18.02406
1850 21364.186 119.23625 0 3679.9339 2.5290683
1900 20146.613 322.15086 0 3679.9197 5.7314718
1950 20692.671 231.25334 0 3680.0319 4.2977791
2000 20943.905 189.11211 0 3679.7629 -22.644575
2050 19667.965 401.84519 0 3679.8394 3.6247265
2100 20280.309 299.78396 0 3679.8355 7.4806221
2150 19181.565 483.57073 0 3680.4982 22.62593
2200 21300.569 130.63684 0 3680.7316 4.7090558
2250 20486.112 266.77753 0 3681.1296 -8.6505201
2300 18651.193 572.56862 0 3681.1008 -5.2604682
2350 21514.435 95.462414 0 3681.2016 -9.3718933
2400 21464.75 103.81741 0 3681.2757 -29.521964
2450 20103.185 331.7557 0 3682.2865 35.600257
2500 20767.309 221.18002 0 3682.3981 -12.41075
2550 20461.88 271.93545 0 3682.2488 -22.542329
2600 21463.807 104.97703 0 3682.2782 -10.118749
2650 20902.135 198.66716 0 3682.3564 5.0103958
2700 18582.384 585.6465 0 3682.7106 22.212808
2750 21079.961 168.86261 0 3682.1894 -8.8401109
2800 21425.876 111.18035 0 3682.1598 -6.7933883
2850 17414.605 780.0645 0 3682.4987 28.180022
2900 19978.961 352.1845 0 3682.0113 8.4280816
2950 21189.046 150.47808 0 3681.9858 2.8898793
3000 19271.367 469.54947 0 3681.4439 -7.1530396
3050 21470.889 103.45294 0 3681.9344 -1.4975516
3100 21574.513 85.87604 0 3681.6282 7.0301554
3150 21649.42 73.506656 0 3681.7434 1.6649326
3200 20857.44 205.3704 0 3681.6104 2.9318184
3250 18573.575 585.73328 0 3681.3292 5.9394399
3300 17938.353 691.67199 0 3681.3975 9.7205454
3350 18668.795 570.23722 0 3681.7031 3.6442733
3400 16834.721 876.36804 0 3682.1548 21.869594
3450 20148.848 323.06988 0 3681.2112 3.8120475
3500 21039.942 175.06064 0 3681.7177 1.4965105
3550 21439.472 108.66655 0 3681.9119 4.192594
3600 21457.784 105.54883 0 3681.8461 -2.932673
3650 21409.999 113.49591 0 3681.829 -15.09817
3700 21380.023 118.56895 0 3681.9061 -15.461367
3750 20422.085 277.28852 0 3680.9694 19.331799
3800 18275.038 635.75951 0 3681.5992 22.413362
3850 20906.341 197.06897 0 3681.4592 2.5691289
3900 20041.032 341.11847 0 3681.2905 1.8089245
3950 18917.084 528.44677 0 3681.2941 -10.656627
4000 20425.89 276.98688 0 3681.3018 7.5960674
4050 18289.157 633.13575 0 3681.3286 6.5695895
4100 19601.884 414.64621 0 3681.6269 8.6144847
4150 20790.308 216.9575 0 3682.0088 1.6300255
4200 21043.169 174.98738 0 3682.1822 3.8942459
4250 19073.45 503.63057 0 3682.5389 -10.975988
4300 21251.971 140.63454 0 3682.6298 -7.7937426
4350 20844.867 208.08653 0 3682.2311 -10.295096
4400 20869.781 203.57469 0 3681.8716 -8.7176985
4450 20384.41 284.19751 0 3681.5992 3.9044821
4500 20002.241 346.95848 0 3680.6654 12.100678
4550 21410.259 112.40994 0 3680.7864 -6.6653767
4600 18230.418 641.88921 0 3680.2922 22.502391
4650 21319.778 127.76737 0 3681.0638 -0.50309316
4700 19429.05 441.85455 0 3680.0296 20.851722
4750 20395.967 281.13332 0 3680.4611 12.635024
4800 19405.371 446.47714 0 3680.7056 -3.0340076
4850 19935.979 358.4478 0 3681.1109 -7.9390554
4900 18822.801 543.80607 0 3680.9396 -3.1086099
4950 20569.881 252.87963 0 3681.1932 11.807076
5000 20311.182 296.63458 0 3681.8315 -4.2409472
5050 20187.672 316.83663 0 3681.4486 1.8723981
5100 17439.679 775.35516 0 3681.9684 -5.7037267
5150 20394.4 282.56755 0 3681.6342 4.3399253
5200 20294.84 299.10095 0 3681.5742 -9.9868412
5250 20396.122 282.31614 0 3681.6698 -4.9932521
5300 20617.465 245.11679 0 3681.3609 0.97429493
5350 21651.191 72.878802 0 3681.4106 2.0913693
5400 19097.721 498.69617 0 3681.6496 21.808511
5450 21856.73 38.930299 0 3681.7186 -4.0225451
5500 20087.477 334.09405 0 3682.0069 5.7109498
5550 17734.477 726.10594 0 3681.8522 16.277738
5600 21183.231 151.714 0 3682.2525 -2.1080998
5650 20832.185 210.14251 0 3682.1733 -8.0602581
5700 18879.226 535.50935 0 3682.0471 -14.351666
5750 18931.81 529.67506 0 3684.9768 4.8675164
5800 21674.979 70.259619 0 3682.7561 -14.990544
5850 21395.905 116.47471 0 3682.4588 -0.94334402
5900 18532.955 593.27143 0 3682.0973 26.072477
5950 20767.534 220.78554 0 3682.0413 -1.6468662
6000 21546.127 91.167146 0 3682.1882 -5.4664857
6050 20085.534 334.40872 0 3681.9977 -0.34825498
6100 21218.156 145.88926 0 3682.2486 2.2871905
6150 20902.857 198.59424 0 3682.4038 6.0082154
6200 21726.547 61.195607 0 3682.2868 -2.2981656
6250 17507.589 764.20763 0 3682.1392 9.4977327
6300 21687.283 67.283821 0 3681.831 -8.694756
6350 19806.474 380.24632 0 3681.3254 -0.94067379
6400 21128.461 160.65399 0 3682.0641 -4.8435757
6450 19747.214 390.89694 0 3682.0992 1.9108969
6500 20460.408 272.79545 0 3682.8634 -4.1094877
6550 16740.095 892.11547 0 3682.1313 13.20551
6600 18326.164 628.80415 0 3683.1648 -19.884336
6650 18469.284 605.36384 0 3683.5778 10.345658
6700 21086.876 168.61821 0 3683.0976 -0.036118094
6750 19924.801 361.46485 0 3682.2649 -2.1144953
6800 19812.028 380.5919 0 3682.5966 11.119936
6850 19118.501 496.38857 0 3682.8054 0.53906703
6900 19221.04 478.31879 0 3681.8255 11.13851
6950 20482.79 269.03445 0 3682.8328 2.6705981
7000 16350.403 957.96283 0 3683.03 -2.9783385
7050 20789.906 218.36242 0 3683.3467 4.2465754
7100 17718.126 730.09011 0 3683.111 15.271811
7150 19020.414 513.34591 0 3683.4149 -8.3035633
7200 21165.007 156.24494 0 3683.7461 -7.3085107
7250 20520.422 264.35574 0 3684.4261 -6.7803072
7300 19078.795 505.10953 0 3684.9087 -11.147107
7350 20529.173 263.85389 0 3685.3827 0.59881989
7400 20548.068 261.27337 0 3685.9513 -5.0067382
7450 20849.172 211.46852 0 3686.3306 -0.80175538
7500 20869.894 207.95335 0 3686.2689 0.44541197
7550 18490.583 605.63557 0 3687.3993 -11.744631
7600 19185.381 488.52218 0 3686.0857 3.0881652
7650 20520.848 265.65037 0 3685.7917 -0.28165722
7700 20599.631 251.69265 0 3684.9645 0.19835423
7750 18428.55 614.11446 0 3685.5395 5.8092563
7800 19660.337 408.61674 0 3685.3396 4.9902979
7850 19409.663 450.30454 0 3685.2483 8.8641567
7900 21307.628 133.95865 0 3685.23 -1.8297128
7950 17828.245 713.05722 0 3684.4314 5.9673166
8000 15894.788 1036.4896 0 3685.621 57.567209
8050 18588.022 587.45738 0 3685.4611 1.5643233
8100 20664.194 241.59965 0 3685.632 -4.9298687
8150 17745.538 728.43249 0 3686.0221 6.121885
8200 18433.239 612.84747 0 3685.0539 17.078623
8250 19162.628 492.52511 0 3686.2965 12.204945
8300 18507.768 602.21188 0 3686.8399 -14.003487
8350 21010.715 184.80032 0 3686.5861 -0.93351338
8400 20888.233 205.24214 0 3686.6143 -5.3433619
8450 20920.621 199.6941 0 3686.4643 -30.437742
8500 17085.22 840.80474 0 3688.3414 3.9123878
8550 20900.377 203.87077 0 3687.267 -6.7525851
8600 19771.517 392.67499 0 3687.9278 13.762684
8650 19541.099 431.09497 0 3687.9448 2.0785077
8700 21056.327 178.88314 0 3688.2709 -13.663758
8750 20109.075 336.93228 0 3688.4447 -1.0445182
8800 21821.77 51.337654 0 3688.2993 -10.263971
8850 17653.401 740.45074 0 3682.6842 49.147758
8900 20311.01 302.92663 0 3688.095 -8.1910583
8950 19745.488 396.38557 0 3687.3003 -16.948557
9000 20248.989 311.52221 0 3686.3537 -2.4158415
9050 17850.649 710.17969 0 3685.2878 25.692377
9100 19370.284 456.73812 0 3685.1187 -21.201413
9150 20452.896 276.95741 0 3685.7735 2.0316457
9200 19174.266 488.9925 0 3684.7035 10.317202
9250 20174.171 323.4614 0 3685.8232 -2.1072552
9300 21442.761 111.68542 0 3685.479 -12.303658
9350 19697.287 402.21503 0 3685.0963 8.4697153
9400 21553.763 93.03581 0 3685.3297 -6.7286485
9450 18946.935 527.04498 0 3684.8674 -6.6174191
9500 21162.915 158.64321 0 3685.7957 -3.2085936
9550 20704.844 235.41227 0 3686.2196 10.847095
9600 20664.074 242.09733 0 3686.1096 3.7301969
9650 20829.655 214.20146 0 3685.8107 7.2197609
9700 17336.625 797.22781 0 3686.6654 14.775351
9750 19978.15 356.51126 0 3686.2029 -1.1978838
9800 21150.487 162.1616 0 3687.2427 -15.596643
9850 20849.962 213.10316 0 3688.0968 -5.5443282
9900 18407.158 620.93592 0 3688.7956 10.177471
9950 20459.637 278.24203 0 3688.1815 0.0020687238
10000 21667.112 78.10938 0 3689.2948 -12.660594
Loop time of 3.06048 on 1 procs for 10000 steps with 81 atoms
Performance: 28230.843 tau/day, 3267.459 timesteps/s, 264.664 katom-step/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 | 0.11571 | 0.11571 | 0.11571 | 0.0 | 3.78
Neigh | 0.094982 | 0.094982 | 0.094982 | 0.0 | 3.10
Comm | 0.0098585 | 0.0098585 | 0.0098585 | 0.0 | 0.32
Output | 0.003355 | 0.003355 | 0.003355 | 0.0 | 0.11
Modify | 2.8226 | 2.8226 | 2.8226 | 0.0 | 92.23
Other | | 0.01395 | | | 0.46
Nlocal: 81 ave 81 max 81 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 115 ave 115 max 115 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 808 ave 808 max 808 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 808
Ave neighs/atom = 9.9753086
Neighbor list builds = 1162
Dangerous builds = 0
Total wall time: 0:00:03

328
examples/rigid/log.25Mar24.rigid.poems.g++.4
View File

@ -1,328 +0,0 @@
LAMMPS (7 Feb 2024 - Development - patch_7Feb2024_update1-306-gf3391199e7-modified)
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: doi:10.1016/j.ijnonlinmec.2008.04.003
@Article{Mukherjee08,
author = {R. M. Mukherjee and P. S. Crozier and S. J. Plimpton and K. S. Anderson},
title = {Substructured Molecular Dynamics Using Multibody Dynamics Algorithms},
journal = {Intl.\ J.\ Non-Linear Mechanics},
year = 2008,
volume = 43,
number = 10,
pages = {1040--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 = 0 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 -3.2045743
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 -1.2184718
1150 20849.582 206.01695 0 3680.9472 -0.86699156
1200 21815.003 45.317416 0 3681.1512 1.5988314
1250 18655.437 572.41453 0 3681.654 10.064076
1300 20780.781 217.36505 0 3680.8286 6.0538619
1350 20558.972 254.36481 0 3680.8601 -3.6773978
1400 21485.029 99.812941 0 3680.6511 -16.185471
1450 21771.108 52.159596 0 3680.6775 -2.4756679
1500 21520.948 93.503942 0 3680.3286 2.1023578
1550 21351.418 121.6814 0 3680.2511 5.5159969
1600 20778.805 216.92173 0 3680.0559 15.089183
1650 21477.639 100.21825 0 3679.8247 -1.1045878
1700 18501.342 596.47873 0 3680.0357 -15.679646
1750 18563.643 587.34777 0 3681.2882 33.532181
1800 19110.189 494.82286 0 3679.8543 18.024038
1850 21364.195 119.2348 0 3679.9339 2.5291365
1900 20146.638 322.1467 0 3679.9197 5.7312008
1950 20692.67 231.25355 0 3680.0319 4.297766
2000 20943.904 189.1122 0 3679.7629 -22.645478
2050 19668.123 401.81885 0 3679.8394 3.6254541
2100 20280.531 299.74669 0 3679.8352 7.4808896
2150 19182.034 483.49332 0 3680.4991 22.616956
2200 21299.885 130.75166 0 3680.7326 4.7110487
2250 20487.525 266.54254 0 3681.1301 -8.6422018
2300 18654.522 572.01515 0 3681.1021 -5.2661499
2350 21512.897 95.719565 0 3681.2024 -9.3553511
2400 21467.306 103.39279 0 3681.2771 -29.588234
2450 20097.914 332.63812 0 3682.2904 35.845886
2500 20762.362 222.00787 0 3682.4016 -12.509872
2550 20417.692 279.31982 0 3682.2685 -22.320693
2600 21468.738 104.15905 0 3682.2821 -10.050868
2650 20742.305 225.31121 0 3682.362 5.2887043
2700 18575.367 586.68141 0 3682.5759 21.990986
2750 20577.766 252.52411 0 3682.1518 -5.8697894
2800 20683.69 234.89244 0 3682.1741 -6.7464964
2850 16088.831 1001.1454 0 3682.6172 27.686908
2900 20715.565 229.46407 0 3682.0583 6.5207552
2950 19969.143 353.98595 0 3682.1765 5.3891903
3000 20429.639 277.11063 0 3682.0505 -10.302229
3050 19840.965 375.78339 0 3682.611 -6.1970263
3100 19149.859 490.69976 0 3682.3429 22.372557
3150 20421.772 278.3256 0 3681.9543 8.7381033
3200 19492.899 433.22833 0 3682.0448 4.3431162
3250 20231.034 310.12852 0 3681.9675 -3.2734265
3300 19420.155 445.8855 0 3682.578 14.157316
3350 21386.445 117.85565 0 3682.2631 1.9590216
3400 20372.28 286.91596 0 3682.296 8.2472357
3450 20870.351 203.91619 0 3682.308 7.9601676
3500 21469.401 104.14434 0 3682.3778 2.5067348
3550 21630.799 77.317219 0 3682.4504 -6.5148709
3600 21291.513 133.97558 0 3682.5611 -8.8761801
3650 19138.211 493.09199 0 3682.7937 25.075733
3700 21282.953 135.36631 0 3682.5252 -8.1163312
3750 20660.876 239.15863 0 3682.638 -24.806983
3800 20161.169 322.26065 0 3682.4555 13.204808
3850 19477.477 435.56421 0 3681.8105 31.065794
3900 21108.425 164.35492 0 3682.4258 0.37839399
3950 21195.124 150.68497 0 3683.2056 -10.098889
4000 21477.025 103.95273 0 3683.4568 -4.139886
4050 20603.58 249.35497 0 3683.2849 1.3114756
4100 19724.656 396.37166 0 3683.8144 -6.6159163
4150 20768.839 221.21034 0 3682.6835 -3.4649381
4200 19675.942 404.01538 0 3683.339 17.586922
4250 21022.927 179.12036 0 3682.9415 0.59436606
4300 20511.134 264.68208 0 3683.2044 8.8380269
4350 21038.204 177.05256 0 3683.42 -1.3698914
4400 18866.857 539.5082 0 3683.9844 10.461602
4450 21607.322 83.184316 0 3684.4046 -1.5071605
4500 20895.628 201.9445 0 3684.5492 5.7578991
4550 20210.744 316.5044 0 3684.9617 5.6678493
4600 20416.269 282.24539 0 3684.9569 -3.0067543
4650 18811.283 549.46791 0 3684.6817 7.5182454
4700 20899.462 201.92249 0 3685.1661 2.6998262
4750 20771.285 223.44307 0 3685.3239 12.165622
4800 21834.653 46.231798 0 3685.3407 2.021615
4850 21282.348 138.2858 0 3685.3437 4.2174481
4900 21892.433 36.607993 0 3685.3468 -10.208769
4950 21731.003 63.442124 0 3685.2759 -26.918841
5000 21476.967 105.69026 0 3685.1848 -10.007088
5050 20485.84 270.81814 0 3685.1248 0.65119013
5100 21485.763 104.28837 0 3685.2488 -5.3826149
5150 21485.096 104.44183 0 3685.2912 -1.274141
5200 21388.175 120.61165 0 3685.3074 -7.7953815
5250 20656.672 242.51472 0 3685.2934 -4.4067447
5300 20132.262 330.10916 0 3685.4862 -11.466755
5350 19080.054 505.63228 0 3685.6413 4.6356684
5400 21683.337 71.886529 0 3685.7761 -8.4520633
5450 20632.669 246.77173 0 3685.5499 5.5429152
5500 20896.92 202.76984 0 3685.5898 3.9762924
5550 21172.409 156.92085 0 3685.6557 2.6573146
5600 20695.91 236.255 0 3685.5733 -18.109158
5650 21741.679 61.956471 0 3685.5697 -3.7520994
5700 21164.94 157.60813 0 3685.098 2.4020734
5750 21075.393 172.84386 0 3685.4093 7.646915
5800 20638.831 245.82076 0 3685.6259 8.3009859
5850 20262.966 308.37489 0 3685.5359 7.5861941
5900 21730.418 63.97074 0 3685.7071 -6.2813552
5950 21820.659 48.990687 0 3685.7673 -5.6400713
6000 21027.051 181.2853 0 3685.7937 1.213872
6050 14422.66 1284.4174 0 3688.194 57.908667
6100 19852.685 377.0743 0 3685.8552 -5.1418207
6150 20678.783 239.10987 0 3685.5737 -11.982018
6200 19788.097 387.62127 0 3685.6375 -2.684571
6250 21611.523 83.575418 0 3685.496 1.7544019
6300 19214.109 482.45067 0 3684.8021 24.711965
6350 18800.074 553.07966 0 3686.4254 11.125791
6400 19771.53 390.40388 0 3685.659 -6.1254643
6450 20192.282 319.53713 0 3684.9175 13.959536
6500 20360.332 292.28682 0 3685.6755 4.4265274
6550 21778.739 56.056362 0 3685.8462 -4.6705452
6600 16612.689 917.96646 0 3686.748 -32.617733
6650 21068.368 174.38501 0 3685.7797 -0.84207954
6700 20749.675 227.41249 0 3685.6916 2.9235268
6750 20594.96 253.47665 0 3685.9699 -12.440843
6800 19974.133 357.05242 0 3686.0745 34.064247
6850 21802.523 52.05173 0 3685.8055 -1.4073818
6900 18644.747 577.97031 0 3685.4282 19.759245
6950 20463.441 274.90799 0 3685.4815 1.2230553
7000 20213.292 316.50714 0 3685.3892 23.9288
7050 21571.525 90.089593 0 3685.3437 -26.539261
7100 20480.036 271.77541 0 3685.1147 -0.13969301
7150 21064.842 174.4144 0 3685.2214 3.5451037
7200 21179.296 154.8514 0 3684.7341 -5.007319
7250 20714.182 232.84783 0 3685.2115 10.601943
7300 19341.561 461.91524 0 3685.5087 18.89547
7350 21011.016 183.55321 0 3685.3893 1.6481821
7400 21206.598 151.07364 0 3685.5066 1.5040526
7450 19999.404 352.83129 0 3686.0652 -18.58587
7500 21581.952 88.519362 0 3685.5114 -4.0009441
7550 21652.618 76.962392 0 3685.7321 -5.758242
7600 21207.411 150.86712 0 3685.4355 -0.023727123
7650 21756.168 59.804311 0 3685.8323 0.76768563
7700 21825.037 48.380795 0 3685.8869 -0.11098207
7750 21581.665 89.078228 0 3686.0223 -0.50220667
7800 21714.856 66.946216 0 3686.0889 4.637364
7850 21319.774 132.905 0 3686.2007 3.4663558
7900 21730.647 64.263898 0 3686.0384 1.0898763
7950 21597.663 86.255996 0 3685.8664 3.2847476
8000 21724.118 65.137632 0 3685.8239 3.7318614
8050 19672.702 406.56191 0 3685.3456 -0.37960768
8100 21696.026 69.71367 0 3685.7179 -6.2273451
8150 18869.648 540.09908 0 3685.0403 22.915669
8200 21717.002 66.01922 0 3685.5196 -4.8553801
8250 20292.502 303.3445 0 3685.4282 -13.203008
8300 21314.341 133.18215 0 3685.5724 -10.023288
8350 20992.272 186.87998 0 3685.592 -4.5538872
8400 21726.088 64.55825 0 3685.573 -5.1228188
8450 21188.98 153.93449 0 3685.4311 -6.8622554
8500 21113.87 166.54678 0 3685.5251 2.6009221
8550 20620.735 248.66776 0 3685.4569 -8.0047984
8600 19715.276 399.79648 0 3685.6758 -10.980391
8650 18898.94 535.95488 0 3685.7782 22.513752
8700 21692.841 70.067726 0 3685.5413 -3.3917479
8750 20242.909 311.87115 0 3685.6893 17.996012
8800 19253.702 476.69077 0 3685.6411 3.7170165
8850 17625.913 748.07802 0 3685.7302 11.095548
8900 21554.709 92.817998 0 3685.2696 0.30720376
8950 21585.337 87.685891 0 3685.2421 -0.22047593
9000 17454.847 776.14227 0 3685.2834 22.631913
9050 20023.106 347.35041 0 3684.5348 4.0008899
9100 21100.691 168.07199 0 3684.8539 2.9016681
9150 20307.206 299.45669 0 3683.991 2.1630277
9200 21747.579 60.245542 0 3684.8421 -15.419887
9250 21525.571 97.26157 0 3684.8567 -7.0449498
9300 15084.149 1170.5925 0 3684.6173 43.259279
9350 21198.648 151.70957 0 3684.8176 3.0716881
9400 17771.533 724.65805 0 3686.5802 -18.320033
9450 20029.819 346.23988 0 3684.543 -4.0976705
9500 19913.342 365.57743 0 3684.4677 2.4909741
9550 20594.619 252.35578 0 3684.7923 -4.4263632
9600 21013.668 182.33425 0 3684.6122 -1.9371919
9650 16915.052 865.78051 0 3684.9559 1.8697619
9700 18789.78 553.48818 0 3685.1181 15.642074
9750 21236.716 145.75801 0 3685.2107 -3.6730702
9800 20972.957 189.72849 0 3685.2214 0.85691231
9850 19658.721 408.29826 0 3684.7517 14.8446
9900 21624.401 81.484234 0 3685.5511 3.4507557
9950 21883.535 38.474607 0 3685.7304 0.3038348
10000 21355.31 126.72088 0 3685.9392 -5.5872974
Loop time of 3.32742 on 4 procs for 10000 steps with 81 atoms
Performance: 25966.084 tau/day, 3005.334 timesteps/s, 243.432 katom-step/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 | 0.0073125 | 0.031081 | 0.067049 | 13.5 | 0.93
Neigh | 0.010912 | 0.030444 | 0.058202 | 10.8 | 0.91
Comm | 0.084952 | 0.12347 | 0.18323 | 10.9 | 3.71
Output | 0.0033463 | 0.0038996 | 0.0047508 | 0.9 | 0.12
Modify | 2.8501 | 2.9361 | 3.0072 | 3.5 | 88.24
Other | | 0.2024 | | | 6.08
Nlocal: 20.25 ave 81 max 0 min
Histogram: 3 0 0 0 0 0 0 0 0 1
Nghost: 33.5 ave 66 max 2 min
Histogram: 1 1 0 0 0 0 0 1 0 1
Neighs: 212.5 ave 850 max 0 min
Histogram: 3 0 0 0 0 0 0 0 0 1
Total # of neighbors = 850
Ave neighs/atom = 10.493827
Neighbor list builds = 1246
Dangerous builds = 0
Total wall time: 0:00:03

330
examples/rigid/log.25Mar24.rigid.poems2.g++.1
View File

@ -1,330 +0,0 @@
LAMMPS (7 Feb 2024 - Development - patch_7Feb2024_update1-306-gf3391199e7-modified)
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 = 0.001 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: doi:10.1016/j.ijnonlinmec.2008.04.003
@Article{Mukherjee08,
author = {R. M. Mukherjee and P. S. Crozier and S. J. Plimpton and K. S. Anderson},
title = {Substructured Molecular Dynamics Using Multibody Dynamics Algorithms},
journal = {Intl.\ J.\ Non-Linear Mechanics},
year = 2008,
volume = 43,
number = 10,
pages = {1040--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 = 0 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 1538.7378 0 3904.434 18.086356
100 19803.641 237.21132 0 3904.5523 -3.1528278
150 20259.6 152.62072 0 3904.3985 -4.6173512
200 20705.978 69.977442 0 3904.4178 9.0928146
250 19552.211 283.50505 0 3904.2848 15.670464
300 19266.324 333.5788 0 3901.4165 7.2119173
350 20738.325 63.738945 0 3904.1694 -23.039989
400 20616.682 86.082444 0 3903.9864 -13.783584
450 19831.326 230.13818 0 3902.6059 0.42074126
500 20365.825 131.47231 0 3902.9213 0.69215475
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 18960.662 391.26028 0 3902.494 12.047308
800 20142.432 172.05197 0 3902.1319 4.6838632
850 19932.48 210.71155 0 3901.9116 3.471602
900 20243.528 153.13972 0 3901.9411 3.6490762
950 20388.132 126.88722 0 3902.4671 -4.4518463
1000 20076.333 184.61916 0 3902.4586 -2.2723139
1050 20859.506 39.696992 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 56.717093 0 3902.5839 -34.817443
1250 20625.583 82.586395 0 3902.1388 11.697328
1300 20690.013 71.006479 0 3902.4903 -29.292783
1350 20936.019 26.022787 0 3903.0634 1.0316033
1400 19753.56 244.81774 0 3902.8844 6.7138457
1450 15690.143 998.34271 0 3903.9248 48.124667
1500 20234.455 155.92517 0 3903.0465 13.172173
1550 20779.63 55.062895 0 3903.1426 -2.6390424
1600 20642.757 80.232879 0 3902.9657 -2.4687934
1650 18785.716 423.90031 0 3902.7365 -5.6468747
1700 20965.076 20.760295 0 3903.1818 -0.45382233
1750 18935.466 396.94949 0 3903.5173 25.912008
1800 20581.509 91.766145 0 3903.1567 3.8229018
1850 20616.968 85.18122 0 3903.1382 4.1907646
1900 16600.676 828.66496 0 3902.8643 -0.49197745
1950 20175.677 166.50513 0 3902.7416 5.6027746
2000 20268.078 149.2566 0 3902.6044 -1.1951453
2050 20155.388 170.16328 0 3902.6425 -0.79473147
2100 19715.497 250.63403 0 3901.652 3.6719022
2150 20677.205 73.792009 0 3902.9041 0.64246071
2200 20041.156 191.58407 0 3902.9093 7.4438342
2250 19924.453 213.0259 0 3902.7394 2.3652069
2300 20432.764 119.13103 0 3902.9763 -11.527566
2350 18265.828 520.75569 0 3903.3165 -8.9634198
2400 19574.981 277.7963 0 3902.7927 1.8085002
2450 20655.975 77.958119 0 3903.1387 3.4001031
2500 19783.143 239.3546 0 3902.8995 24.872182
2550 16660.113 818.36907 0 3903.5752 -11.766765
2600 19789.524 238.61817 0 3903.3448 3.3910931
2650 18532.96 471.8684 0 3903.898 -4.812577
2700 19081.457 369.81185 0 3903.4151 -0.49159968
2750 20370.042 131.6764 0 3903.9064 -3.3818893
2800 20727.087 65.499688 0 3903.8491 4.3537941
2850 18252.657 523.061 0 3903.1827 11.774986
2900 20780.391 55.586541 0 3903.8071 5.4415831
2950 20361.047 132.98647 0 3903.5508 -2.4847656
3000 19528.633 284.87405 0 3901.2876 14.23453
3050 20385.56 127.80448 0 3902.9081 -0.51079949
3100 19040.7 376.96613 0 3903.0216 -8.9425331
3150 20053.417 189.7312 0 3903.327 4.6695643
3200 20862.681 40.219985 0 3903.6795 1.2220199
3250 20692.32 71.660474 0 3903.5716 2.118694
3300 20560.104 95.905282 0 3903.332 5.9856809
3350 20693.236 71.35789 0 3903.4387 3.9315564
3400 19045.135 376.64379 0 3903.5206 3.9692419
3450 20354.826 134.28157 0 3903.6938 7.6208552
3500 20528.053 102.12643 0 3903.6178 7.2863414
3550 20525.13 103.01612 0 3903.9661 8.4807852
3600 19782.42 240.28031 0 3903.6914 1.0181878
3650 20519.52 104.05243 0 3903.9636 -2.36641
3700 20024.307 195.68587 0 3903.8908 -6.261818
3750 20239.643 155.72722 0 3903.8092 -20.781566
3800 20601.2 88.794605 0 3903.8317 -11.491217
3850 20973.346 19.675436 0 3903.6283 -9.0554155
3900 16212.846 902.10241 0 3904.4813 -19.773976
3950 19645.576 264.59477 0 3902.6643 16.065663
4000 17439.655 673.47397 0 3903.0398 -3.7357722
4050 19305.077 328.50056 0 3903.5148 10.43441
4100 18634.36 451.24343 0 3902.0508 3.4327844
4150 20249.11 153.64108 0 3903.4763 -2.5190604
4200 19177.928 351.81896 0 3903.2871 -5.5110274
4250 20754.898 60.189732 0 3903.6893 -3.3019026
4300 19693.307 256.31591 0 3903.2245 5.8795929
4350 18411.713 494.6957 0 3904.2722 4.2513782
4400 18499.707 474.35141 0 3900.2231 10.120914
4450 18620.543 449.98137 0 3898.2301 0.74648702
4500 18930.676 398.47668 0 3904.1573 -3.3953153
4550 18708.382 438.70363 0 3903.2188 8.478793
4600 19937.049 211.7655 0 3903.8117 4.8300368
4650 19919.169 214.98435 0 3903.7194 -1.0166319
4700 19345.329 321.18127 0 3903.6496 -23.032019
4750 18391.67 498.629 0 3904.4939 -15.40779
4800 18597.103 459.20983 0 3903.1179 9.3900723
4850 19857.892 226.27908 0 3903.6665 4.1998427
4900 20428.515 120.59483 0 3903.6532 -1.8636046
4950 18457.127 485.79992 0 3903.7864 -7.2380409
5000 20543.123 99.480661 0 3903.7627 -0.39555479
5050 18716.671 436.46735 0 3902.5175 29.395654
5100 20048.411 191.03727 0 3903.706 -0.91178091
5150 19647.675 265.24989 0 3903.7083 3.8658742
5200 20787.465 54.078505 0 3903.6091 -3.3582221
5250 20630.096 83.165593 0 3903.5538 -11.86045
5300 16598.926 830.02918 0 3903.9043 -1.8793568
5350 19114.667 363.424 0 3903.1772 11.894383
5400 19563.654 280.22257 0 3903.1215 8.8285523
5450 20012.628 197.27325 0 3903.3154 2.1981092
5500 17845.428 599.4114 0 3904.1202 20.091131
5550 20630.423 82.857857 0 3903.3065 0.93827014
5600 19675.125 259.89939 0 3903.4411 -2.4034875
5650 19932.349 212.22024 0 3903.3961 2.0064698
5700 20499.192 107.17918 0 3903.3259 2.5440649
5750 19522.335 287.94941 0 3903.1966 -0.7615272
5800 18010.242 568.31554 0 3903.5455 -6.3433889
5850 20177.497 166.64243 0 3903.2159 -0.95012013
5900 17919.358 584.40694 0 3902.8065 10.49282
5950 18390.453 498.29164 0 3903.9311 10.026285
6000 18040.232 562.71939 0 3903.5032 0.22172862
6050 19777.355 240.88597 0 3903.3592 -3.1899015
6100 19132.014 360.58765 0 3903.5531 1.6644736
6150 19780.214 240.31985 0 3903.3224 4.2403325
6200 18883.45 406.45503 0 3903.3902 -3.5422327
6250 19875.924 222.49729 0 3903.2239 3.0535292
6300 19882.454 221.4928 0 3903.4287 5.7371152
6350 19040.565 377.18193 0 3903.2124 -0.26454332
6400 19137.008 359.7025 0 3903.5929 9.5375531
6450 19655.205 263.59789 0 3903.4507 -1.8592763
6500 18385.045 499.5436 0 3904.1816 -7.8549266
6550 18823.423 417.69964 0 3903.5187 -2.8268518
6600 19414.118 308.11966 0 3903.3268 4.6627243
6650 20533.065 100.75047 0 3903.1698 3.3716972
6700 20206.283 161.18079 0 3903.085 5.6368472
6750 19517.622 288.72511 0 3903.0995 0.3337076
6800 18152.278 541.45525 0 3902.9883 -7.2734044
6850 18910.032 401.19322 0 3903.0511 6.2653128
6900 18580.612 462.26403 0 3903.1182 15.681586
6950 20459.012 114.44928 0 3903.1552 -0.82985388
7000 20866.868 38.822988 0 3903.0578 -6.2182429
7050 20460.074 114.11492 0 3903.0175 -2.1465384
7100 20553.533 96.636153 0 3902.846 -5.105486
7150 20447.915 116.30898 0 3902.9599 8.2035464
7200 20703.396 69.030336 0 3902.9926 9.1221166
7250 19652.215 263.63438 0 3902.9335 17.675447
7300 20691.205 71.094727 0 3902.7994 -1.7423404
7350 18845.785 412.74313 0 3902.7033 -2.0276584
7400 18462.131 483.73088 0 3902.6441 -0.22424322
7450 20458.641 113.96173 0 3902.599 -4.9286236
7500 17681.258 628.1576 0 3902.4647 -16.803813
7550 19149.34 356.35773 0 3902.5318 -5.3481685
7600 19723.907 249.45462 0 3902.03 7.2597963
7650 19317.18 325.01536 0 3902.271 -0.16642424
7700 19620.248 269.22043 0 3902.5996 -4.6771277
7750 17751.083 615.46827 0 3902.7058 7.3637076
7800 20724.904 64.633157 0 3902.5784 5.2079592
7850 19966.924 204.60327 0 3902.1817 6.4943932
7900 19730.339 248.88701 0 3902.6536 8.4392109
7950 19907.748 216.06587 0 3902.6859 -5.1989259
8000 18217.971 528.46486 0 3902.1632 -15.394144
8050 17868.898 592.98294 0 3902.0381 9.1139508
8100 19370.601 315.22753 0 3902.3759 7.9651368
8150 18199.01 532.43818 0 3902.6252 10.07163
8200 20646.337 79.222148 0 3902.6179 0.17396159
8250 20811.938 48.374613 0 3902.4372 -14.594973
8300 20906.571 30.626024 0 3902.2132 -12.34909
8350 19873.431 221.86861 0 3902.1335 7.1435615
8400 20374.979 127.96219 0 3901.1064 10.527044
8450 20701.502 68.073078 0 3901.6846 2.5071154
8500 20452.423 113.98399 0 3901.4698 4.2164058
8550 19695.059 253.87834 0 3901.1115 8.0656507
8600 19447.531 299.45597 0 3900.8505 -0.71982287
8650 17202.668 714.55842 0 3900.2378 -16.743518
8700 18579.153 459.20676 0 3899.7906 3.4494692
8750 20247.204 150.39086 0 3899.8731 -0.1022032
8800 18520.797 469.57224 0 3899.3494 5.7412252
8850 16011.411 934.80107 0 3899.8772 34.500452
8900 19045.914 372.92529 0 3899.9464 10.001612
8950 19798.369 233.70991 0 3900.0746 9.3270865
9000 17141.02 725.70858 0 3899.9716 -6.7470927
9050 17722.847 617.81927 0 3899.828 -10.909071
9100 20811.604 45.701413 0 3899.7021 -12.300065
9150 18066.034 554.62654 0 3900.1884 -5.7606837
9200 19259.884 332.49612 0 3899.1412 -40.231609
9250 19116.782 359.42396 0 3899.5689 0.68271469
9300 18785.022 421.1178 0 3899.8256 -20.433345
9350 19018.32 377.90289 0 3899.814 3.2963902
9400 17321.798 691.93839 0 3899.6788 24.552549
9450 18318.437 507.12661 0 3899.4297 6.1367468
9500 16431.681 857.32722 0 3900.2311 25.431389
9550 17920.939 581.45381 0 3900.1462 9.1734747
9600 16603.394 825.79291 0 3900.4954 -5.9643183
9650 17753.931 607.15019 0 3894.9151 2.2302338
9700 17452.305 668.30613 0 3900.2145 2.4635322
9750 15955.164 945.80159 0 3900.4617 20.290857
9800 17958.495 574.7055 0 3900.3526 12.218625
9850 18759.766 423.66965 0 3897.7005 -4.8999337
9900 19798.529 232.2507 0 3898.6449 0.10312101
9950 18260.87 517.50071 0 3899.1432 5.7261992
10000 19116.279 359.58291 0 3899.6345 3.2110764
Loop time of 3.11933 on 1 procs for 10000 steps with 81 atoms
Performance: 27698.233 tau/day, 3205.814 timesteps/s, 259.671 katom-step/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 | 0.063297 | 0.063297 | 0.063297 | 0.0 | 2.03
Neigh | 0.072119 | 0.072119 | 0.072119 | 0.0 | 2.31
Comm | 0.012058 | 0.012058 | 0.012058 | 0.0 | 0.39
Output | 0.0036722 | 0.0036722 | 0.0036722 | 0.0 | 0.12
Modify | 2.953 | 2.953 | 2.953 | 0.0 | 94.67
Other | | 0.01515 | | | 0.49
Nlocal: 81 ave 81 max 81 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 105 ave 105 max 105 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 498 ave 498 max 498 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 498
Ave neighs/atom = 6.1481481
Neighbor list builds = 1202
Dangerous builds = 0
Total wall time: 0:00:03

330
examples/rigid/log.25Mar24.rigid.poems2.g++.4
View File

@ -1,330 +0,0 @@
LAMMPS (7 Feb 2024 - Development - patch_7Feb2024_update1-306-gf3391199e7-modified)
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
# 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: doi:10.1016/j.ijnonlinmec.2008.04.003
@Article{Mukherjee08,
author = {R. M. Mukherjee and P. S. Crozier and S. J. Plimpton and K. S. Anderson},
title = {Substructured Molecular Dynamics Using Multibody Dynamics Algorithms},
journal = {Intl.\ J.\ Non-Linear Mechanics},
year = 2008,
volume = 43,
number = 10,
pages = {1040--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 = 0 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 1538.7378 0 3904.434 18.086356
100 19803.641 237.21132 0 3904.5523 -3.1528278
150 20259.6 152.62032 0 3904.3981 -4.6173548
200 20705.978 69.977442 0 3904.4178 9.0928146
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 20365.825 131.47271 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 20076.333 184.61916 0 3902.4586 -2.272315
1050 20859.506 39.696992 0 3902.5684 6.45166
1100 15284.661 1072.1906 0 3902.6833 21.194041
1150 19658.317 261.99809 0 3902.4272 -2.8744196
1200 20767.681 56.717093 0 3902.5839 -34.817444
1250 20625.583 82.586396 0 3902.1388 11.697328
1300 20690.013 71.006479 0 3902.4903 -29.292783
1350 20936.019 26.022787 0 3903.0634 1.0316031
1400 19753.56 244.81777 0 3902.8844 6.713847
1450 15690.145 998.34279 0 3903.9252 48.124638
1500 20234.455 155.92476 0 3903.0461 13.17218
1550 20779.631 55.063072 0 3903.1428 -2.6390427
1600 20642.756 80.233303 0 3902.9659 -2.4688077
1650 18785.71 423.90132 0 3902.7365 -5.6468182
1700 20965.076 20.760481 0 3903.182 -0.45377448
1750 18935.45 396.95247 0 3903.5173 25.912353
1800 20581.523 91.763662 0 3903.1567 3.8225817
1850 20616.962 85.182351 0 3903.1382 4.1907744
1900 16601.061 828.59343 0 3902.8639 -0.49284971
1950 20175.618 166.51633 0 3902.7419 5.6031735
2000 20266.439 149.55931 0 3902.6036 -1.1956447
2050 20159.308 169.44017 0 3902.6453 -0.7983344
2100 19743.72 245.40822 0 3901.6527 3.5301052
2150 20674.556 74.284034 0 3902.9055 0.61532081
2200 19950.784 208.30189 0 3902.8915 7.6523945
2250 19817.161 232.7485 0 3902.5932 3.4492756
2300 20459.058 114.2307 0 3902.9451 -11.066393
2350 18359.21 503.25787 0 3903.1115 -9.0741539
2400 19952.914 207.84881 0 3902.8328 -0.53972874
2450 19661.352 259.78979 0 3900.781 7.8669927
2500 20917.293 29.699201 0 3903.2719 1.1433085
2550 20763.955 57.990256 0 3903.1671 -1.1088372
2600 20640.005 80.556339 0 3902.7795 9.6127007
2650 20823.227 47.292746 0 3903.446 2.2923503
2700 20401.43 125.53141 0 3903.5739 -8.0683618
2750 20689.918 72.242212 0 3903.7084 0.22078527
2800 20783.922 54.87309 0 3903.7476 2.0668249
2850 19258.563 336.84835 0 3903.2488 4.2704683
2900 20565.694 95.184831 0 3903.6468 -0.24799068
2950 20915.041 30.344751 0 3903.5004 -2.9900907
3000 19571.964 278.74004 0 3903.1778 12.195325
3050 20356.693 133.43974 0 3903.1976 0.11608195
3100 20047.888 190.69627 0 3903.268 -4.5895546
3150 19834.363 230.59072 0 3903.6209 -1.4352632
3200 20213.412 160.25129 0 3903.4757 3.7488266
3250 19286.774 332.04497 0 3903.6699 -5.0835358
3300 20952.226 23.774103 0 3903.816 0.10019546
3350 20407.952 124.62932 0 3903.8798 0.4403531
3400 19401.716 311.03567 0 3903.9461 1.8034568
3450 20880.78 37.20558 0 3904.0167 6.3948533
3500 19529.313 287.50301 0 3904.0425 12.311168
3550 20943.604 25.677677 0 3904.1228 5.1786098
3600 20272.725 149.91697 0 3904.1254 1.196909
3650 19781.047 240.95421 0 3904.1111 -8.5091671
3700 20613.433 86.53896 0 3903.8414 -9.1622102
3750 20567.605 95.294456 0 3904.1101 -0.11887825
3800 19891.98 220.32932 0 3904.0292 6.8801146
3850 20669.735 76.407858 0 3904.1365 -7.4310509
3900 20908.711 32.197181 0 3904.1807 -4.6573356
3950 20822.78 48.03134 0 3904.1018 0.086779759
4000 20199.055 163.66262 0 3904.2283 2.0027771
4050 20072.638 187.07041 0 3904.2256 4.4103784
4100 17724.651 619.7903 0 3902.1331 11.210006
4150 20760.201 60.001382 0 3904.4831 -3.8510009
4200 19159.102 356.30472 0 3904.2865 -2.3503308
4250 19403.974 311.3497 0 3904.6783 -1.2458384
4300 20858.687 42.000734 0 3904.7206 2.1750528
4350 20486.989 110.94383 0 3904.8306 5.017245
4400 20231.073 158.28825 0 3904.7832 7.4295979
4450 16369.689 873.39361 0 3904.8175 14.371454
4500 20745.196 63.11427 0 3904.8172 -7.855609
4550 18688.003 443.85636 0 3904.5977 9.8067426
4600 17755.672 616.68475 0 3904.7721 -3.9654703
4650 19843.131 230.34486 0 3904.9988 -0.13553926
4700 18873.202 409.99341 0 3905.0308 15.912724
4750 20605.355 89.223116 0 3905.0295 2.0847611
4800 20136.483 176.1278 0 3905.1062 -1.7091113
4850 19808.073 236.83278 0 3904.9945 5.0982271
4900 19142.083 359.55764 0 3904.3878 8.2072008
4950 20539.687 101.08198 0 3904.7277 8.0469319
5000 20840.809 45.759021 0 3905.168 4.771755
5050 20009.696 199.45528 0 3904.9546 6.1191423
5100 20882.034 38.247578 0 3905.2909 -6.3068822
5150 20329.869 140.47458 0 3905.2651 -21.720979
5200 17334.411 695.67098 0 3905.7471 -9.8243617
5250 19602.025 275.17282 0 3905.1775 -3.2371379
5300 20858.74 42.630642 0 3905.3603 0.38011789
5350 20828.619 48.188698 0 3905.3403 5.7187945
5400 20978.428 20.447148 0 3905.3413 6.1168011
5450 20115.374 179.9294 0 3904.9987 8.6440563
5500 20522.744 104.7733 0 3905.2815 -2.6561664
5550 20625.724 85.600795 0 3905.1792 -1.327206
5600 19559.638 282.68742 0 3904.8426 17.893028
5650 20552.224 98.978098 0 3904.9455 2.4489071
5700 19982.142 204.09989 0 3904.4966 9.9034011
5750 20408.825 125.30875 0 3904.7209 1.2515548
5800 19773.143 243.02134 0 3904.7144 -2.6729948
5850 20781.934 56.310486 0 3904.8168 -1.659054
5900 19807.668 236.54392 0 3904.6306 0.49776361
5950 20741.237 63.921667 0 3904.8916 4.2800039
6000 20322.7 140.98125 0 3904.4442 7.4978024
6050 20858.439 42.383629 0 3905.0575 -4.6872323
6100 20212.538 162.022 0 3905.0847 -7.0796165
6150 18513.957 476.7087 0 3905.2193 7.107138
6200 20802.734 52.621638 0 3904.9797 3.7242428
6250 20818.044 49.717458 0 3904.9109 -0.91041774
6300 19987.245 203.4635 0 3904.8052 -0.86714551
6350 20806.906 51.449749 0 3904.5806 -4.0699629
6400 20530.3 103.09809 0 3905.0055 1.660177
6450 20667.085 77.715553 0 3904.9535 0.99217521
6500 20515.816 105.81762 0 3905.0428 3.0994091
6550 20548.348 99.627131 0 3904.8769 -0.77417688
6600 19827.378 232.99889 0 3904.7355 3.295082
6650 19237.199 342.94808 0 3905.3923 -6.2226637
6700 19611.621 273.139 0 3904.9206 -3.5465535
6750 20874.805 39.1893 0 3904.8939 -0.051336814
6800 19433.717 305.99952 0 3904.8361 -19.858865
6850 20119.223 179.19987 0 3904.9818 4.6466283
6900 20467.389 114.77871 0 3905.0359 10.290214
6950 20334.202 139.43289 0 3905.0259 7.5448433
7000 20504.591 107.86929 0 3905.0158 -0.10092084
7050 17969.214 576.83722 0 3904.4694 10.852897
7100 19186.398 351.80467 0 3904.8414 0.24779979
7150 20261.23 152.54684 0 3904.6265 -7.0175844
7200 20696.821 71.985154 0 3904.7298 3.9649146
7250 18456.212 487.1819 0 3904.9989 5.8280225
7300 17705.1 625.95928 0 3904.6816 6.8298215
7350 17032.039 750.96958 0 3905.051 11.833303
7400 20557.431 97.599213 0 3904.5308 0.43747863
7450 20466.847 114.5693 0 3904.7261 1.9786538
7500 20416.862 123.31643 0 3904.2168 -2.9094738
7550 18433.95 487.50767 0 3901.2022 4.0921479
7600 19950.107 209.92208 0 3904.3863 3.9114888
7650 16037.844 934.94785 0 3904.9189 -1.2183461
7700 20145.239 173.99945 0 3904.5993 3.1185554
7750 18672.579 446.35236 0 3904.2373 4.1086445
7800 19740.616 249.10395 0 3904.7737 4.6048428
7850 20801.917 52.742096 0 3904.9489 1.5978265
7900 20305.348 144.57749 0 3904.8272 2.7348725
7950 20221.086 159.31958 0 3903.9652 7.1592496
8000 20826.907 47.953835 0 3904.7884 6.2728901
8050 18646.418 452.02126 0 3905.0617 5.9716218
8100 20653.653 80.183024 0 3904.9336 -1.8274783
8150 20843.275 45.172279 0 3905.0379 -6.9445524
8200 20364.78 133.45082 0 3904.7064 -12.094533
8250 18163.745 541.08818 0 3904.7447 -2.6103997
8300 20889.664 36.793018 0 3905.2494 -9.2650749
8350 20307.367 144.33088 0 3904.9543 -0.65999546
8400 20485.202 111.41317 0 3904.9691 -0.42802224
8450 20864.395 41.146879 0 3904.9238 7.7084978
8500 20901.899 34.291267 0 3905.0132 -5.2070823
8550 20211.78 162.02611 0 3904.9484 -5.8363409
8600 19639.538 268.05291 0 3905.0044 3.8180903
8650 19919.356 216.24885 0 3905.0185 0.17130921
8700 19499.449 293.97522 0 3904.9843 -4.897872
8750 20270.687 151.1571 0 3904.9879 0.28558082
8800 18804.137 422.61651 0 3904.864 15.351015
8850 20654.443 80.110976 0 3905.0078 4.1368065
8900 19953.725 209.81046 0 3904.9447 10.71743
8950 18195.013 536.67764 0 3906.1245 21.497802
9000 20478.531 112.78923 0 3905.1098 -13.053056
9050 20866.484 40.901611 0 3905.0653 -3.6134066
9100 20322.595 141.61419 0 3905.0577 15.459697
9150 20855.456 42.94311 0 3905.0646 4.9123213
9200 20208.201 162.79363 0 3905.0531 2.5454472
9250 18394.203 498.63686 0 3904.9707 0.041811692
9300 18776.997 427.7118 0 3904.9335 -7.652483
9350 18330.751 510.07857 0 3904.6621 8.3424059
9400 17538.366 657.08623 0 3904.9319 8.5478668
9450 20309.605 143.77142 0 3904.8093 6.6831447
9500 19982.331 203.81545 0 3904.2471 -7.6711411
9550 19410.612 310.1139 0 3904.6717 5.3983286
9600 19198.225 349.06634 0 3904.2932 -4.107658
9650 19388.043 314.31566 0 3904.6939 6.1198194
9700 18849.37 414.1045 0 3904.7286 5.4468861
9750 18263.312 523.38716 0 3905.4819 -0.56480349
9800 20421.858 122.53973 0 3904.3653 -15.641399
9850 17678.959 631.15683 0 3905.0381 -1.805446
9900 19421.046 306.67446 0 3903.1644 7.0287747
9950 18460.64 483.18902 0 3901.8261 3.658774
10000 19781.151 239.38136 0 3902.5575 6.3312911
Loop time of 3.44431 on 4 procs for 10000 steps with 81 atoms
Performance: 25084.833 tau/day, 2903.337 timesteps/s, 235.170 katom-step/s
98.8% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.007256 | 0.017426 | 0.044845 | 12.0 | 0.51
Neigh | 0.010951 | 0.023139 | 0.043878 | 8.2 | 0.67
Comm | 0.070404 | 0.096764 | 0.1104 | 5.0 | 2.81
Output | 0.0039809 | 0.0074043 | 0.010167 | 2.6 | 0.21
Modify | 3.0537 | 3.0735 | 3.1272 | 1.8 | 89.23
Other | | 0.226 | | | 6.56
Nlocal: 20.25 ave 36 max 0 min
Histogram: 1 0 0 0 0 1 0 1 0 1
Nghost: 38.25 ave 50 max 28 min
Histogram: 1 0 1 0 0 1 0 0 0 1
Neighs: 126.5 ave 213 max 0 min
Histogram: 1 0 0 0 1 0 0 0 0 2
Total # of neighbors = 506
Ave neighs/atom = 6.2469136
Neighbor list builds = 1207
Dangerous builds = 0
Total wall time: 0:00:03

329
examples/rigid/log.25Mar24.rigid.poems3.g++.1
View File

@ -1,329 +0,0 @@
LAMMPS (7 Feb 2024 - Development - patch_7Feb2024_update1-306-gf3391199e7-modified)
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:1038)
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: doi:10.1016/j.ijnonlinmec.2008.04.003
@Article{Mukherjee08,
author = {R. M. Mukherjee and P. S. Crozier and S. J. Plimpton and K. S. Anderson},
title = {Substructured Molecular Dynamics Using Multibody Dynamics Algorithms},
journal = {Intl.\ J.\ Non-Linear Mechanics},
year = 2008,
volume = 43,
number = 10,
pages = {1040--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 = 0 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 0.00096754004 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 0.35071213 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 2.7475276 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 -0.00023792127 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 -0.00084974053 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 -0.00022763101 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 -0.0032567427 0 5269.522 11.911005
9500 16738.495 -0.0036645346 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 -0.00058544655 0 5269.5243 11.911032
10000 16738.493 -0.0015244935 0 5269.5242 11.911015
Loop time of 3.15773 on 1 procs for 10000 steps with 81 atoms
Performance: 27361.390 tau/day, 3166.828 timesteps/s, 256.513 katom-step/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 | 0.0090105 | 0.0090105 | 0.0090105 | 0.0 | 0.29
Neigh | 0.047552 | 0.047552 | 0.047552 | 0.0 | 1.51
Comm | 0.012213 | 0.012213 | 0.012213 | 0.0 | 0.39
Output | 0.0028666 | 0.0028666 | 0.0028666 | 0.0 | 0.09
Modify | 3.0714 | 3.0714 | 3.0714 | 0.0 | 97.27
Other | | 0.01471 | | | 0.47
Nlocal: 81 ave 81 max 81 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 66 ave 66 max 66 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 = 1576
Dangerous builds = 0
Total wall time: 0:00:03

329
examples/rigid/log.25Mar24.rigid.poems3.g++.4
View File

@ -1,329 +0,0 @@
LAMMPS (7 Feb 2024 - Development - patch_7Feb2024_update1-306-gf3391199e7-modified)
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
# 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:1038)
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: doi:10.1016/j.ijnonlinmec.2008.04.003
@Article{Mukherjee08,
author = {R. M. Mukherjee and P. S. Crozier and S. J. Plimpton and K. S. Anderson},
title = {Substructured Molecular Dynamics Using Multibody Dynamics Algorithms},
journal = {Intl.\ J.\ Non-Linear Mechanics},
year = 2008,
volume = 43,
number = 10,
pages = {1040--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 = 0 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 0.00096754006 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 0.35071213 0 5269.4974 11.918931
3300 16732.493 1.866382 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 2.7475276 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 -0.00023792127 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 -0.00033136079 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 -0.00022763102 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 -0.0016306434 0 5269.5235 11.911038
9450 16738.492 -0.0032567424 0 5269.522 11.911005
9500 16738.495 -0.0036645342 0 5269.5224 11.910982
9550 16738.49 -0.0010673909 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 -0.0005854466 0 5269.5243 11.911032
10000 16738.493 -0.0015244937 0 5269.5242 11.911015
Loop time of 3.27386 on 4 procs for 10000 steps with 81 atoms
Performance: 26390.874 tau/day, 3054.499 timesteps/s, 247.414 katom-step/s
99.5% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.003643 | 0.0042095 | 0.0048106 | 0.7 | 0.13
Neigh | 0.015047 | 0.01644 | 0.018121 | 0.9 | 0.50
Comm | 0.08923 | 0.091442 | 0.093047 | 0.5 | 2.79
Output | 0.0033998 | 0.0040485 | 0.0051625 | 1.0 | 0.12
Modify | 2.9783 | 2.9943 | 3.0343 | 1.3 | 91.46
Other | | 0.1635 | | | 4.99
Nlocal: 20.25 ave 27 max 9 min
Histogram: 1 0 0 0 0 1 0 0 0 2
Nghost: 30.5 ave 50 max 14 min
Histogram: 1 0 0 1 1 0 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 = 1576
Dangerous builds = 0
Total wall time: 0:00:03

328
examples/rigid/log.25Mar24.rigid.poems4.g++.1
View File

@ -1,328 +0,0 @@
LAMMPS (7 Feb 2024 - Development - patch_7Feb2024_update1-306-gf3391199e7-modified)
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 = 0.001 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 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: doi:10.1016/j.ijnonlinmec.2008.04.003
@Article{Mukherjee08,
author = {R. M. Mukherjee and P. S. Crozier and S. J. Plimpton and K. S. Anderson},
title = {Substructured Molecular Dynamics Using Multibody Dynamics Algorithms},
journal = {Intl.\ J.\ Non-Linear Mechanics},
year = 2008,
volume = 43,
number = 10,
pages = {1040--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 = 0 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 -3.2045743
850 17821.483 711.53827 0 3681.7854 7.4384279
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 -0.86699135
1200 21815.003 45.317412 0 3681.1512 1.5988314
1250 18655.437 572.41453 0 3681.654 10.06408
1300 20780.781 217.36509 0 3680.8286 6.0538614
1350 20558.971 254.36485 0 3680.8601 -3.6773923
1400 21485.029 99.812891 0 3680.6511 -16.185475
1450 21771.107 52.159624 0 3680.6775 -2.4756668
1500 21520.948 93.503905 0 3680.3286 2.1023577
1550 21351.418 121.68136 0 3680.2511 5.5159922
1600 20778.805 216.92182 0 3680.0559 15.089193
1650 21477.637 100.21853 0 3679.8247 -1.1045536
1700 18501.335 596.47986 0 3680.0357 -15.679729
1750 18563.64 587.34819 0 3681.2882 33.532254
1800 19110.181 494.82407 0 3679.8543 18.02406
1850 21364.186 119.23625 0 3679.9339 2.5290683
1900 20146.613 322.15086 0 3679.9197 5.7314718
1950 20692.671 231.25334 0 3680.0319 4.2977791
2000 20943.905 189.11211 0 3679.7629 -22.644575
2050 19667.965 401.84519 0 3679.8394 3.6247265
2100 20280.309 299.78396 0 3679.8355 7.4806221
2150 19181.565 483.57073 0 3680.4982 22.62593
2200 21300.569 130.63684 0 3680.7316 4.7090558
2250 20486.112 266.77753 0 3681.1296 -8.6505201
2300 18651.193 572.56862 0 3681.1008 -5.2604682
2350 21514.435 95.462414 0 3681.2016 -9.3718933
2400 21464.75 103.81741 0 3681.2757 -29.521964
2450 20103.185 331.7557 0 3682.2865 35.600257
2500 20767.309 221.18002 0 3682.3981 -12.41075
2550 20461.88 271.93545 0 3682.2488 -22.542329
2600 21463.807 104.97703 0 3682.2782 -10.118749
2650 20902.135 198.66716 0 3682.3564 5.0103958
2700 18582.384 585.6465 0 3682.7106 22.212808
2750 21079.961 168.86261 0 3682.1894 -8.8401109
2800 21425.876 111.18035 0 3682.1598 -6.7933883
2850 17414.605 780.0645 0 3682.4987 28.180022
2900 19978.961 352.1845 0 3682.0113 8.4280816
2950 21189.046 150.47808 0 3681.9858 2.8898793
3000 19271.367 469.54947 0 3681.4439 -7.1530396
3050 21470.889 103.45294 0 3681.9344 -1.4975516
3100 21574.513 85.87604 0 3681.6282 7.0301554
3150 21649.42 73.506656 0 3681.7434 1.6649326
3200 20857.44 205.3704 0 3681.6104 2.9318184
3250 18573.575 585.73328 0 3681.3292 5.9394399
3300 17938.353 691.67199 0 3681.3975 9.7205454
3350 18668.795 570.23722 0 3681.7031 3.6442733
3400 16834.721 876.36804 0 3682.1548 21.869594
3450 20148.848 323.06988 0 3681.2112 3.8120475
3500 21039.942 175.06064 0 3681.7177 1.4965105
3550 21439.472 108.66655 0 3681.9119 4.192594
3600 21457.784 105.54883 0 3681.8461 -2.932673
3650 21409.999 113.49591 0 3681.829 -15.09817
3700 21380.023 118.56895 0 3681.9061 -15.461367
3750 20422.085 277.28852 0 3680.9694 19.331799
3800 18275.038 635.75951 0 3681.5992 22.413362
3850 20906.341 197.06897 0 3681.4592 2.5691289
3900 20041.032 341.11847 0 3681.2905 1.8089245
3950 18917.084 528.44677 0 3681.2941 -10.656627
4000 20425.89 276.98688 0 3681.3018 7.5960674
4050 18289.157 633.13575 0 3681.3286 6.5695895
4100 19601.884 414.64621 0 3681.6269 8.6144847
4150 20790.308 216.9575 0 3682.0088 1.6300255
4200 21043.169 174.98738 0 3682.1822 3.8942459
4250 19073.45 503.63057 0 3682.5389 -10.975988
4300 21251.971 140.63454 0 3682.6298 -7.7937426
4350 20844.867 208.08653 0 3682.2311 -10.295096
4400 20869.781 203.57469 0 3681.8716 -8.7176985
4450 20384.41 284.19751 0 3681.5992 3.9044821
4500 20002.241 346.95848 0 3680.6654 12.100678
4550 21410.259 112.40994 0 3680.7864 -6.6653767
4600 18230.418 641.88921 0 3680.2922 22.502391
4650 21319.778 127.76737 0 3681.0638 -0.50309316
4700 19429.05 441.85455 0 3680.0296 20.851722
4750 20395.967 281.13332 0 3680.4611 12.635024
4800 19405.371 446.47714 0 3680.7056 -3.0340076
4850 19935.979 358.4478 0 3681.1109 -7.9390554
4900 18822.801 543.80607 0 3680.9396 -3.1086099
4950 20569.881 252.87963 0 3681.1932 11.807076
5000 20311.182 296.63458 0 3681.8315 -4.2409472
5050 20187.672 316.83663 0 3681.4486 1.8723981
5100 17439.679 775.35516 0 3681.9684 -5.7037267
5150 20394.4 282.56755 0 3681.6342 4.3399253
5200 20294.84 299.10095 0 3681.5742 -9.9868412
5250 20396.122 282.31614 0 3681.6698 -4.9932521
5300 20617.465 245.11679 0 3681.3609 0.97429493
5350 21651.191 72.878802 0 3681.4106 2.0913693
5400 19097.721 498.69617 0 3681.6496 21.808511
5450 21856.73 38.930299 0 3681.7186 -4.0225451
5500 20087.477 334.09405 0 3682.0069 5.7109498
5550 17734.477 726.10594 0 3681.8522 16.277738
5600 21183.231 151.714 0 3682.2525 -2.1080998
5650 20832.185 210.14251 0 3682.1733 -8.0602581
5700 18879.226 535.50935 0 3682.0471 -14.351666
5750 18931.81 529.67506 0 3684.9768 4.8675164
5800 21674.979 70.259619 0 3682.7561 -14.990544
5850 21395.905 116.47471 0 3682.4588 -0.94334402
5900 18532.955 593.27143 0 3682.0973 26.072477
5950 20767.534 220.78554 0 3682.0413 -1.6468662
6000 21546.127 91.167146 0 3682.1882 -5.4664857
6050 20085.534 334.40872 0 3681.9977 -0.34825498
6100 21218.156 145.88926 0 3682.2486 2.2871905
6150 20902.857 198.59424 0 3682.4038 6.0082154
6200 21726.547 61.195607 0 3682.2868 -2.2981656
6250 17507.589 764.20763 0 3682.1392 9.4977327
6300 21687.283 67.283821 0 3681.831 -8.694756
6350 19806.474 380.24632 0 3681.3254 -0.94067379
6400 21128.461 160.65399 0 3682.0641 -4.8435757
6450 19747.214 390.89694 0 3682.0992 1.9108969
6500 20460.408 272.79545 0 3682.8634 -4.1094877
6550 16740.095 892.11547 0 3682.1313 13.20551
6600 18326.164 628.80415 0 3683.1648 -19.884336
6650 18469.284 605.36384 0 3683.5778 10.345658
6700 21086.876 168.61821 0 3683.0976 -0.036118094
6750 19924.801 361.46485 0 3682.2649 -2.1144953
6800 19812.028 380.5919 0 3682.5966 11.119936
6850 19118.501 496.38857 0 3682.8054 0.53906703
6900 19221.04 478.31879 0 3681.8255 11.13851
6950 20482.79 269.03445 0 3682.8328 2.6705981
7000 16350.403 957.96283 0 3683.03 -2.9783385
7050 20789.906 218.36242 0 3683.3467 4.2465754
7100 17718.126 730.09011 0 3683.111 15.271811
7150 19020.414 513.34591 0 3683.4149 -8.3035633
7200 21165.007 156.24494 0 3683.7461 -7.3085107
7250 20520.422 264.35574 0 3684.4261 -6.7803072
7300 19078.795 505.10953 0 3684.9087 -11.147107
7350 20529.173 263.85389 0 3685.3827 0.59881989
7400 20548.068 261.27337 0 3685.9513 -5.0067382
7450 20849.172 211.46852 0 3686.3306 -0.80175538
7500 20869.894 207.95335 0 3686.2689 0.44541197
7550 18490.583 605.63557 0 3687.3993 -11.744631
7600 19185.381 488.52218 0 3686.0857 3.0881652
7650 20520.848 265.65037 0 3685.7917 -0.28165722
7700 20599.631 251.69265 0 3684.9645 0.19835423
7750 18428.55 614.11446 0 3685.5395 5.8092563
7800 19660.337 408.61674 0 3685.3396 4.9902979
7850 19409.663 450.30454 0 3685.2483 8.8641567
7900 21307.628 133.95865 0 3685.23 -1.8297128
7950 17828.245 713.05722 0 3684.4314 5.9673166
8000 15894.788 1036.4896 0 3685.621 57.567209
8050 18588.022 587.45738 0 3685.4611 1.5643233
8100 20664.194 241.59965 0 3685.632 -4.9298687
8150 17745.538 728.43249 0 3686.0221 6.121885
8200 18433.239 612.84747 0 3685.0539 17.078623
8250 19162.628 492.52511 0 3686.2965 12.204945
8300 18507.768 602.21188 0 3686.8399 -14.003487
8350 21010.715 184.80032 0 3686.5861 -0.93351338
8400 20888.233 205.24214 0 3686.6143 -5.3433619
8450 20920.621 199.6941 0 3686.4643 -30.437742
8500 17085.22 840.80474 0 3688.3414 3.9123878
8550 20900.377 203.87077 0 3687.267 -6.7525851
8600 19771.517 392.67499 0 3687.9278 13.762684
8650 19541.099 431.09497 0 3687.9448 2.0785077
8700 21056.327 178.88314 0 3688.2709 -13.663758
8750 20109.075 336.93228 0 3688.4447 -1.0445182
8800 21821.77 51.337654 0 3688.2993 -10.263971
8850 17653.401 740.45074 0 3682.6842 49.147758
8900 20311.01 302.92663 0 3688.095 -8.1910583
8950 19745.488 396.38557 0 3687.3003 -16.948557
9000 20248.989 311.52221 0 3686.3537 -2.4158415
9050 17850.649 710.17969 0 3685.2878 25.692377
9100 19370.284 456.73812 0 3685.1187 -21.201413
9150 20452.896 276.95741 0 3685.7735 2.0316457
9200 19174.266 488.9925 0 3684.7035 10.317202
9250 20174.171 323.4614 0 3685.8232 -2.1072552
9300 21442.761 111.68542 0 3685.479 -12.303658
9350 19697.287 402.21503 0 3685.0963 8.4697153
9400 21553.763 93.03581 0 3685.3297 -6.7286485
9450 18946.935 527.04498 0 3684.8674 -6.6174191
9500 21162.915 158.64321 0 3685.7957 -3.2085936
9550 20704.844 235.41227 0 3686.2196 10.847095
9600 20664.074 242.09733 0 3686.1096 3.7301969
9650 20829.655 214.20146 0 3685.8107 7.2197609
9700 17336.625 797.22781 0 3686.6654 14.775351
9750 19978.15 356.51126 0 3686.2029 -1.1978838
9800 21150.487 162.1616 0 3687.2427 -15.596643
9850 20849.962 213.10316 0 3688.0968 -5.5443282
9900 18407.158 620.93592 0 3688.7956 10.177471
9950 20459.637 278.24203 0 3688.1815 0.0020687238
10000 21667.112 78.10938 0 3689.2948 -12.660594
Loop time of 3.40889 on 1 procs for 10000 steps with 81 atoms
Performance: 25345.463 tau/day, 2933.503 timesteps/s, 237.614 katom-step/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 | 0.12904 | 0.12904 | 0.12904 | 0.0 | 3.79
Neigh | 0.10613 | 0.10613 | 0.10613 | 0.0 | 3.11
Comm | 0.011135 | 0.011135 | 0.011135 | 0.0 | 0.33
Output | 0.0042137 | 0.0042137 | 0.0042137 | 0.0 | 0.12
Modify | 3.142 | 3.142 | 3.142 | 0.0 | 92.17
Other | | 0.01636 | | | 0.48
Nlocal: 81 ave 81 max 81 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 115 ave 115 max 115 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 808 ave 808 max 808 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 808
Ave neighs/atom = 9.9753086
Neighbor list builds = 1162
Dangerous builds = 0
Total wall time: 0:00:03

328
examples/rigid/log.25Mar24.rigid.poems4.g++.4
View File

@ -1,328 +0,0 @@
LAMMPS (7 Feb 2024 - Development - patch_7Feb2024_update1-306-gf3391199e7-modified)
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 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: doi:10.1016/j.ijnonlinmec.2008.04.003
@Article{Mukherjee08,
author = {R. M. Mukherjee and P. S. Crozier and S. J. Plimpton and K. S. Anderson},
title = {Substructured Molecular Dynamics Using Multibody Dynamics Algorithms},
journal = {Intl.\ J.\ Non-Linear Mechanics},
year = 2008,
volume = 43,
number = 10,
pages = {1040--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 = 0 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 -3.2045743
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 -1.2184718
1150 20849.582 206.01695 0 3680.9472 -0.86699156
1200 21815.003 45.317416 0 3681.1512 1.5988314
1250 18655.437 572.41453 0 3681.654 10.064076
1300 20780.781 217.36505 0 3680.8286 6.0538619
1350 20558.972 254.36481 0 3680.8601 -3.6773978
1400 21485.029 99.812941 0 3680.6511 -16.185471
1450 21771.108 52.159596 0 3680.6775 -2.4756679
1500 21520.948 93.503942 0 3680.3286 2.1023578
1550 21351.418 121.6814 0 3680.2511 5.5159969
1600 20778.805 216.92173 0 3680.0559 15.089183
1650 21477.639 100.21825 0 3679.8247 -1.1045878
1700 18501.342 596.47873 0 3680.0357 -15.679646
1750 18563.643 587.34777 0 3681.2882 33.532181
1800 19110.189 494.82286 0 3679.8543 18.024038
1850 21364.195 119.2348 0 3679.9339 2.5291365
1900 20146.638 322.1467 0 3679.9197 5.7312008
1950 20692.67 231.25355 0 3680.0319 4.297766
2000 20943.904 189.1122 0 3679.7629 -22.645478
2050 19668.123 401.81885 0 3679.8394 3.6254541
2100 20280.531 299.74669 0 3679.8352 7.4808896
2150 19182.034 483.49332 0 3680.4991 22.616956
2200 21299.885 130.75166 0 3680.7326 4.7110487
2250 20487.525 266.54254 0 3681.1301 -8.6422018
2300 18654.522 572.01515 0 3681.1021 -5.2661499
2350 21512.897 95.719565 0 3681.2024 -9.3553511
2400 21467.306 103.39279 0 3681.2771 -29.588234
2450 20097.914 332.63812 0 3682.2904 35.845886
2500 20762.362 222.00787 0 3682.4016 -12.509872
2550 20417.692 279.31982 0 3682.2685 -22.320693
2600 21468.738 104.15905 0 3682.2821 -10.050868
2650 20742.305 225.31121 0 3682.362 5.2887043
2700 18575.367 586.68141 0 3682.5759 21.990986
2750 20577.766 252.52411 0 3682.1518 -5.8697894
2800 20683.69 234.89244 0 3682.1741 -6.7464964
2850 16088.831 1001.1454 0 3682.6172 27.686908
2900 20715.565 229.46407 0 3682.0583 6.5207552
2950 19969.143 353.98595 0 3682.1765 5.3891903
3000 20429.639 277.11063 0 3682.0505 -10.302229
3050 19840.965 375.78339 0 3682.611 -6.1970263
3100 19149.859 490.69976 0 3682.3429 22.372557
3150 20421.772 278.3256 0 3681.9543 8.7381033
3200 19492.899 433.22833 0 3682.0448 4.3431162
3250 20231.034 310.12852 0 3681.9675 -3.2734265
3300 19420.155 445.8855 0 3682.578 14.157316
3350 21386.445 117.85565 0 3682.2631 1.9590216
3400 20372.28 286.91596 0 3682.296 8.2472357
3450 20870.351 203.91619 0 3682.308 7.9601676
3500 21469.401 104.14434 0 3682.3778 2.5067348
3550 21630.799 77.317219 0 3682.4504 -6.5148709
3600 21291.513 133.97558 0 3682.5611 -8.8761801
3650 19138.211 493.09199 0 3682.7937 25.075733
3700 21282.953 135.36631 0 3682.5252 -8.1163312
3750 20660.876 239.15863 0 3682.638 -24.806983
3800 20161.169 322.26065 0 3682.4555 13.204808
3850 19477.477 435.56421 0 3681.8105 31.065794
3900 21108.425 164.35492 0 3682.4258 0.37839399
3950 21195.124 150.68497 0 3683.2056 -10.098889
4000 21477.025 103.95273 0 3683.4568 -4.139886
4050 20603.58 249.35497 0 3683.2849 1.3114756
4100 19724.656 396.37166 0 3683.8144 -6.6159163
4150 20768.839 221.21034 0 3682.6835 -3.4649381
4200 19675.942 404.01538 0 3683.339 17.586922
4250 21022.927 179.12036 0 3682.9415 0.59436606
4300 20511.134 264.68208 0 3683.2044 8.8380269
4350 21038.204 177.05256 0 3683.42 -1.3698914
4400 18866.857 539.5082 0 3683.9844 10.461602
4450 21607.322 83.184316 0 3684.4046 -1.5071605
4500 20895.628 201.9445 0 3684.5492 5.7578991
4550 20210.744 316.5044 0 3684.9617 5.6678493
4600 20416.269 282.24539 0 3684.9569 -3.0067543
4650 18811.283 549.46791 0 3684.6817 7.5182454
4700 20899.462 201.92249 0 3685.1661 2.6998262
4750 20771.285 223.44307 0 3685.3239 12.165622
4800 21834.653 46.231798 0 3685.3407 2.021615
4850 21282.348 138.2858 0 3685.3437 4.2174481
4900 21892.433 36.607993 0 3685.3468 -10.208769
4950 21731.003 63.442124 0 3685.2759 -26.918841
5000 21476.967 105.69026 0 3685.1848 -10.007088
5050 20485.84 270.81814 0 3685.1248 0.65119013
5100 21485.763 104.28837 0 3685.2488 -5.3826149
5150 21485.096 104.44183 0 3685.2912 -1.274141
5200 21388.175 120.61165 0 3685.3074 -7.7953815
5250 20656.672 242.51472 0 3685.2934 -4.4067447
5300 20132.262 330.10916 0 3685.4862 -11.466755
5350 19080.054 505.63228 0 3685.6413 4.6356684
5400 21683.337 71.886529 0 3685.7761 -8.4520633
5450 20632.669 246.77173 0 3685.5499 5.5429152
5500 20896.92 202.76984 0 3685.5898 3.9762924
5550 21172.409 156.92085 0 3685.6557 2.6573146
5600 20695.91 236.255 0 3685.5733 -18.109158
5650 21741.679 61.956471 0 3685.5697 -3.7520994
5700 21164.94 157.60813 0 3685.098 2.4020734
5750 21075.393 172.84386 0 3685.4093 7.646915
5800 20638.831 245.82076 0 3685.6259 8.3009859
5850 20262.966 308.37489 0 3685.5359 7.5861941
5900 21730.418 63.97074 0 3685.7071 -6.2813552
5950 21820.659 48.990687 0 3685.7673 -5.6400713
6000 21027.051 181.2853 0 3685.7937 1.213872
6050 14422.66 1284.4174 0 3688.194 57.908667
6100 19852.685 377.0743 0 3685.8552 -5.1418207
6150 20678.783 239.10987 0 3685.5737 -11.982018
6200 19788.097 387.62127 0 3685.6375 -2.684571
6250 21611.523 83.575418 0 3685.496 1.7544019
6300 19214.109 482.45067 0 3684.8021 24.711965
6350 18800.074 553.07966 0 3686.4254 11.125791
6400 19771.53 390.40388 0 3685.659 -6.1254643
6450 20192.282 319.53713 0 3684.9175 13.959536
6500 20360.332 292.28682 0 3685.6755 4.4265274
6550 21778.739 56.056362 0 3685.8462 -4.6705452
6600 16612.689 917.96646 0 3686.748 -32.617733
6650 21068.368 174.38501 0 3685.7797 -0.84207954
6700 20749.675 227.41249 0 3685.6916 2.9235268
6750 20594.96 253.47665 0 3685.9699 -12.440843
6800 19974.133 357.05242 0 3686.0745 34.064247
6850 21802.523 52.05173 0 3685.8055 -1.4073818
6900 18644.747 577.97031 0 3685.4282 19.759245
6950 20463.441 274.90799 0 3685.4815 1.2230553
7000 20213.292 316.50714 0 3685.3892 23.9288
7050 21571.525 90.089593 0 3685.3437 -26.539261
7100 20480.036 271.77541 0 3685.1147 -0.13969301
7150 21064.842 174.4144 0 3685.2214 3.5451037
7200 21179.296 154.8514 0 3684.7341 -5.007319
7250 20714.182 232.84783 0 3685.2115 10.601943
7300 19341.561 461.91524 0 3685.5087 18.89547
7350 21011.016 183.55321 0 3685.3893 1.6481821
7400 21206.598 151.07364 0 3685.5066 1.5040526
7450 19999.404 352.83129 0 3686.0652 -18.58587
7500 21581.952 88.519362 0 3685.5114 -4.0009441
7550 21652.618 76.962392 0 3685.7321 -5.758242
7600 21207.411 150.86712 0 3685.4355 -0.023727123
7650 21756.168 59.804311 0 3685.8323 0.76768563
7700 21825.037 48.380795 0 3685.8869 -0.11098207
7750 21581.665 89.078228 0 3686.0223 -0.50220667
7800 21714.856 66.946216 0 3686.0889 4.637364
7850 21319.774 132.905 0 3686.2007 3.4663558
7900 21730.647 64.263898 0 3686.0384 1.0898763
7950 21597.663 86.255996 0 3685.8664 3.2847476
8000 21724.118 65.137632 0 3685.8239 3.7318614
8050 19672.702 406.56191 0 3685.3456 -0.37960768
8100 21696.026 69.71367 0 3685.7179 -6.2273451
8150 18869.648 540.09908 0 3685.0403 22.915669
8200 21717.002 66.01922 0 3685.5196 -4.8553801
8250 20292.502 303.3445 0 3685.4282 -13.203008
8300 21314.341 133.18215 0 3685.5724 -10.023288
8350 20992.272 186.87998 0 3685.592 -4.5538872
8400 21726.088 64.55825 0 3685.573 -5.1228188
8450 21188.98 153.93449 0 3685.4311 -6.8622554
8500 21113.87 166.54678 0 3685.5251 2.6009221
8550 20620.735 248.66776 0 3685.4569 -8.0047984
8600 19715.276 399.79648 0 3685.6758 -10.980391
8650 18898.94 535.95488 0 3685.7782 22.513752
8700 21692.841 70.067726 0 3685.5413 -3.3917479
8750 20242.909 311.87115 0 3685.6893 17.996012
8800 19253.702 476.69077 0 3685.6411 3.7170165
8850 17625.913 748.07802 0 3685.7302 11.095548
8900 21554.709 92.817998 0 3685.2696 0.30720376
8950 21585.337 87.685891 0 3685.2421 -0.22047593
9000 17454.847 776.14227 0 3685.2834 22.631913
9050 20023.106 347.35041 0 3684.5348 4.0008899
9100 21100.691 168.07199 0 3684.8539 2.9016681
9150 20307.206 299.45669 0 3683.991 2.1630277
9200 21747.579 60.245542 0 3684.8421 -15.419887
9250 21525.571 97.26157 0 3684.8567 -7.0449498
9300 15084.149 1170.5925 0 3684.6173 43.259279
9350 21198.648 151.70957 0 3684.8176 3.0716881
9400 17771.533 724.65805 0 3686.5802 -18.320033
9450 20029.819 346.23988 0 3684.543 -4.0976705
9500 19913.342 365.57743 0 3684.4677 2.4909741
9550 20594.619 252.35578 0 3684.7923 -4.4263632
9600 21013.668 182.33425 0 3684.6122 -1.9371919
9650 16915.052 865.78051 0 3684.9559 1.8697619
9700 18789.78 553.48818 0 3685.1181 15.642074
9750 21236.716 145.75801 0 3685.2107 -3.6730702
9800 20972.957 189.72849 0 3685.2214 0.85691231
9850 19658.721 408.29826 0 3684.7517 14.8446
9900 21624.401 81.484234 0 3685.5511 3.4507557
9950 21883.535 38.474607 0 3685.7304 0.3038348
10000 21355.31 126.72088 0 3685.9392 -5.5872974
Loop time of 3.23589 on 4 procs for 10000 steps with 81 atoms
Performance: 26700.576 tau/day, 3090.344 timesteps/s, 250.318 katom-step/s
99.5% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0072165 | 0.030554 | 0.065382 | 13.2 | 0.94
Neigh | 0.010707 | 0.029677 | 0.056594 | 10.6 | 0.92
Comm | 0.083225 | 0.12075 | 0.17828 | 10.6 | 3.73
Output | 0.0034779 | 0.0040163 | 0.0050814 | 1.0 | 0.12
Modify | 2.8247 | 2.8749 | 2.9245 | 2.6 | 88.85
Other | | 0.176 | | | 5.44
Nlocal: 20.25 ave 81 max 0 min
Histogram: 3 0 0 0 0 0 0 0 0 1
Nghost: 33.5 ave 66 max 2 min
Histogram: 1 1 0 0 0 0 0 1 0 1
Neighs: 212.5 ave 850 max 0 min
Histogram: 3 0 0 0 0 0 0 0 0 1
Total # of neighbors = 850
Ave neighs/atom = 10.493827
Neighbor list builds = 1246
Dangerous builds = 0
Total wall time: 0:00:03

329
examples/rigid/log.25Mar24.rigid.poems5.g++.1
View File

@ -1,329 +0,0 @@
LAMMPS (7 Feb 2024 - Development - patch_7Feb2024_update1-306-gf3391199e7-modified)
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 = 0.001 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: doi:10.1016/j.ijnonlinmec.2008.04.003
@Article{Mukherjee08,
author = {R. M. Mukherjee and P. S. Crozier and S. J. Plimpton and K. S. Anderson},
title = {Substructured Molecular Dynamics Using Multibody Dynamics Algorithms},
journal = {Intl.\ J.\ Non-Linear Mechanics},
year = 2008,
volume = 43,
number = 10,
pages = {1040--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 = 0 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 1538.7378 0 3904.434 18.086356
100 19803.641 237.21132 0 3904.5523 -3.1528278
150 20259.6 152.62072 0 3904.3985 -4.6173512
200 20705.978 69.977442 0 3904.4178 9.0928146
250 19552.211 283.50505 0 3904.2848 15.670464
300 19266.324 333.5788 0 3901.4165 7.2119173
350 20738.325 63.738945 0 3904.1694 -23.039989
400 20616.682 86.082444 0 3903.9864 -13.783584
450 19831.326 230.13818 0 3902.6059 0.42074126
500 20365.825 131.47231 0 3902.9213 0.69215475
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 18960.662 391.26028 0 3902.494 12.047308
800 20142.432 172.05197 0 3902.1319 4.6838632
850 19932.48 210.71155 0 3901.9116 3.471602
900 20243.528 153.13972 0 3901.9411 3.6490762
950 20388.132 126.88722 0 3902.4671 -4.4518463
1000 20076.333 184.61916 0 3902.4586 -2.2723139
1050 20859.506 39.696992 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 56.717093 0 3902.5839 -34.817443
1250 20625.583 82.586395 0 3902.1388 11.697328
1300 20690.013 71.006479 0 3902.4903 -29.292783
1350 20936.019 26.022787 0 3903.0634 1.0316033
1400 19753.56 244.81774 0 3902.8844 6.7138457
1450 15690.143 998.34271 0 3903.9248 48.124667
1500 20234.455 155.92517 0 3903.0465 13.172173
1550 20779.63 55.062895 0 3903.1426 -2.6390424
1600 20642.757 80.232879 0 3902.9657 -2.4687934
1650 18785.716 423.90031 0 3902.7365 -5.6468747
1700 20965.076 20.760295 0 3903.1818 -0.45382233
1750 18935.466 396.94949 0 3903.5173 25.912008
1800 20581.509 91.766145 0 3903.1567 3.8229018
1850 20616.968 85.18122 0 3903.1382 4.1907646
1900 16600.676 828.66496 0 3902.8643 -0.49197745
1950 20175.677 166.50513 0 3902.7416 5.6027746
2000 20268.078 149.2566 0 3902.6044 -1.1951453
2050 20155.388 170.16328 0 3902.6425 -0.79473147
2100 19715.497 250.63403 0 3901.652 3.6719022
2150 20677.205 73.792009 0 3902.9041 0.64246071
2200 20041.156 191.58407 0 3902.9093 7.4438342
2250 19924.453 213.0259 0 3902.7394 2.3652069
2300 20432.764 119.13103 0 3902.9763 -11.527566
2350 18265.828 520.75569 0 3903.3165 -8.9634198
2400 19574.981 277.7963 0 3902.7927 1.8085002
2450 20655.975 77.958119 0 3903.1387 3.4001031
2500 19783.143 239.3546 0 3902.8995 24.872182
2550 16660.113 818.36907 0 3903.5752 -11.766765
2600 19789.524 238.61817 0 3903.3448 3.3910931
2650 18532.96 471.8684 0 3903.898 -4.812577
2700 19081.457 369.81185 0 3903.4151 -0.49159968
2750 20370.042 131.6764 0 3903.9064 -3.3818893
2800 20727.087 65.499688 0 3903.8491 4.3537941
2850 18252.657 523.061 0 3903.1827 11.774986
2900 20780.391 55.586541 0 3903.8071 5.4415831
2950 20361.047 132.98647 0 3903.5508 -2.4847656
3000 19528.633 284.87405 0 3901.2876 14.23453
3050 20385.56 127.80448 0 3902.9081 -0.51079949
3100 19040.7 376.96613 0 3903.0216 -8.9425331
3150 20053.417 189.7312 0 3903.327 4.6695643
3200 20862.681 40.219985 0 3903.6795 1.2220199
3250 20692.32 71.660474 0 3903.5716 2.118694
3300 20560.104 95.905282 0 3903.332 5.9856809
3350 20693.236 71.35789 0 3903.4387 3.9315564
3400 19045.135 376.64379 0 3903.5206 3.9692419
3450 20354.826 134.28157 0 3903.6938 7.6208552
3500 20528.053 102.12643 0 3903.6178 7.2863414
3550 20525.13 103.01612 0 3903.9661 8.4807852
3600 19782.42 240.28031 0 3903.6914 1.0181878
3650 20519.52 104.05243 0 3903.9636 -2.36641
3700 20024.307 195.68587 0 3903.8908 -6.261818
3750 20239.643 155.72722 0 3903.8092 -20.781566
3800 20601.2 88.794605 0 3903.8317 -11.491217
3850 20973.346 19.675436 0 3903.6283 -9.0554155
3900 16212.846 902.10241 0 3904.4813 -19.773976
3950 19645.576 264.59477 0 3902.6643 16.065663
4000 17439.655 673.47397 0 3903.0398 -3.7357722
4050 19305.077 328.50056 0 3903.5148 10.43441
4100 18634.36 451.24343 0 3902.0508 3.4327844
4150 20249.11 153.64108 0 3903.4763 -2.5190604
4200 19177.928 351.81896 0 3903.2871 -5.5110274
4250 20754.898 60.189732 0 3903.6893 -3.3019026
4300 19693.307 256.31591 0 3903.2245 5.8795929
4350 18411.713 494.6957 0 3904.2722 4.2513782
4400 18499.707 474.35141 0 3900.2231 10.120914
4450 18620.543 449.98137 0 3898.2301 0.74648702
4500 18930.676 398.47668 0 3904.1573 -3.3953153
4550 18708.382 438.70363 0 3903.2188 8.478793
4600 19937.049 211.7655 0 3903.8117 4.8300368
4650 19919.169 214.98435 0 3903.7194 -1.0166319
4700 19345.329 321.18127 0 3903.6496 -23.032019
4750 18391.67 498.629 0 3904.4939 -15.40779
4800 18597.103 459.20983 0 3903.1179 9.3900723
4850 19857.892 226.27908 0 3903.6665 4.1998427
4900 20428.515 120.59483 0 3903.6532 -1.8636046
4950 18457.127 485.79992 0 3903.7864 -7.2380409
5000 20543.123 99.480661 0 3903.7627 -0.39555479
5050 18716.671 436.46735 0 3902.5175 29.395654
5100 20048.411 191.03727 0 3903.706 -0.91178091
5150 19647.675 265.24989 0 3903.7083 3.8658742
5200 20787.465 54.078505 0 3903.6091 -3.3582221
5250 20630.096 83.165593 0 3903.5538 -11.86045
5300 16598.926 830.02918 0 3903.9043 -1.8793568
5350 19114.667 363.424 0 3903.1772 11.894383
5400 19563.654 280.22257 0 3903.1215 8.8285523
5450 20012.628 197.27325 0 3903.3154 2.1981092
5500 17845.428 599.4114 0 3904.1202 20.091131
5550 20630.423 82.857857 0 3903.3065 0.93827014
5600 19675.125 259.89939 0 3903.4411 -2.4034875
5650 19932.349 212.22024 0 3903.3961 2.0064698
5700 20499.192 107.17918 0 3903.3259 2.5440649
5750 19522.335 287.94941 0 3903.1966 -0.7615272
5800 18010.242 568.31554 0 3903.5455 -6.3433889
5850 20177.497 166.64243 0 3903.2159 -0.95012013
5900 17919.358 584.40694 0 3902.8065 10.49282
5950 18390.453 498.29164 0 3903.9311 10.026285
6000 18040.232 562.71939 0 3903.5032 0.22172862
6050 19777.355 240.88597 0 3903.3592 -3.1899015
6100 19132.014 360.58765 0 3903.5531 1.6644736
6150 19780.214 240.31985 0 3903.3224 4.2403325
6200 18883.45 406.45503 0 3903.3902 -3.5422327
6250 19875.924 222.49729 0 3903.2239 3.0535292
6300 19882.454 221.4928 0 3903.4287 5.7371152
6350 19040.565 377.18193 0 3903.2124 -0.26454332
6400 19137.008 359.7025 0 3903.5929 9.5375531
6450 19655.205 263.59789 0 3903.4507 -1.8592763
6500 18385.045 499.5436 0 3904.1816 -7.8549266
6550 18823.423 417.69964 0 3903.5187 -2.8268518
6600 19414.118 308.11966 0 3903.3268 4.6627243
6650 20533.065 100.75047 0 3903.1698 3.3716972
6700 20206.283 161.18079 0 3903.085 5.6368472
6750 19517.622 288.72511 0 3903.0995 0.3337076
6800 18152.278 541.45525 0 3902.9883 -7.2734044
6850 18910.032 401.19322 0 3903.0511 6.2653128
6900 18580.612 462.26403 0 3903.1182 15.681586
6950 20459.012 114.44928 0 3903.1552 -0.82985388
7000 20866.868 38.822988 0 3903.0578 -6.2182429
7050 20460.074 114.11492 0 3903.0175 -2.1465384
7100 20553.533 96.636153 0 3902.846 -5.105486
7150 20447.915 116.30898 0 3902.9599 8.2035464
7200 20703.396 69.030336 0 3902.9926 9.1221166
7250 19652.215 263.63438 0 3902.9335 17.675447
7300 20691.205 71.094727 0 3902.7994 -1.7423404
7350 18845.785 412.74313 0 3902.7033 -2.0276584
7400 18462.131 483.73088 0 3902.6441 -0.22424322
7450 20458.641 113.96173 0 3902.599 -4.9286236
7500 17681.258 628.1576 0 3902.4647 -16.803813
7550 19149.34 356.35773 0 3902.5318 -5.3481685
7600 19723.907 249.45462 0 3902.03 7.2597963
7650 19317.18 325.01536 0 3902.271 -0.16642424
7700 19620.248 269.22043 0 3902.5996 -4.6771277
7750 17751.083 615.46827 0 3902.7058 7.3637076
7800 20724.904 64.633157 0 3902.5784 5.2079592
7850 19966.924 204.60327 0 3902.1817 6.4943932
7900 19730.339 248.88701 0 3902.6536 8.4392109
7950 19907.748 216.06587 0 3902.6859 -5.1989259
8000 18217.971 528.46486 0 3902.1632 -15.394144
8050 17868.898 592.98294 0 3902.0381 9.1139508
8100 19370.601 315.22753 0 3902.3759 7.9651368
8150 18199.01 532.43818 0 3902.6252 10.07163
8200 20646.337 79.222148 0 3902.6179 0.17396159
8250 20811.938 48.374613 0 3902.4372 -14.594973
8300 20906.571 30.626024 0 3902.2132 -12.34909
8350 19873.431 221.86861 0 3902.1335 7.1435615
8400 20374.979 127.96219 0 3901.1064 10.527044
8450 20701.502 68.073078 0 3901.6846 2.5071154
8500 20452.423 113.98399 0 3901.4698 4.2164058
8550 19695.059 253.87834 0 3901.1115 8.0656507
8600 19447.531 299.45597 0 3900.8505 -0.71982287
8650 17202.668 714.55842 0 3900.2378 -16.743518
8700 18579.153 459.20676 0 3899.7906 3.4494692
8750 20247.204 150.39086 0 3899.8731 -0.1022032
8800 18520.797 469.57224 0 3899.3494 5.7412252
8850 16011.411 934.80107 0 3899.8772 34.500452
8900 19045.914 372.92529 0 3899.9464 10.001612
8950 19798.369 233.70991 0 3900.0746 9.3270865
9000 17141.02 725.70858 0 3899.9716 -6.7470927
9050 17722.847 617.81927 0 3899.828 -10.909071
9100 20811.604 45.701413 0 3899.7021 -12.300065
9150 18066.034 554.62654 0 3900.1884 -5.7606837
9200 19259.884 332.49612 0 3899.1412 -40.231609
9250 19116.782 359.42396 0 3899.5689 0.68271469
9300 18785.022 421.1178 0 3899.8256 -20.433345
9350 19018.32 377.90289 0 3899.814 3.2963902
9400 17321.798 691.93839 0 3899.6788 24.552549
9450 18318.437 507.12661 0 3899.4297 6.1367468
9500 16431.681 857.32722 0 3900.2311 25.431389
9550 17920.939 581.45381 0 3900.1462 9.1734747
9600 16603.394 825.79291 0 3900.4954 -5.9643183
9650 17753.931 607.15019 0 3894.9151 2.2302338
9700 17452.305 668.30613 0 3900.2145 2.4635322
9750 15955.164 945.80159 0 3900.4617 20.290857
9800 17958.495 574.7055 0 3900.3526 12.218625
9850 18759.766 423.66965 0 3897.7005 -4.8999337
9900 19798.529 232.2507 0 3898.6449 0.10312101
9950 18260.87 517.50071 0 3899.1432 5.7261992
10000 19116.279 359.58291 0 3899.6345 3.2110764
Loop time of 3.40298 on 1 procs for 10000 steps with 81 atoms
Performance: 25389.516 tau/day, 2938.601 timesteps/s, 238.027 katom-step/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 | 0.068835 | 0.068835 | 0.068835 | 0.0 | 2.02
Neigh | 0.078603 | 0.078603 | 0.078603 | 0.0 | 2.31
Comm | 0.013957 | 0.013957 | 0.013957 | 0.0 | 0.41
Output | 0.0034786 | 0.0034786 | 0.0034786 | 0.0 | 0.10
Modify | 3.2212 | 3.2212 | 3.2212 | 0.0 | 94.66
Other | | 0.01692 | | | 0.50
Nlocal: 81 ave 81 max 81 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 105 ave 105 max 105 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 498 ave 498 max 498 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 498
Ave neighs/atom = 6.1481481
Neighbor list builds = 1202
Dangerous builds = 0
Total wall time: 0:00:03

329
examples/rigid/log.25Mar24.rigid.poems5.g++.4
View File

@ -1,329 +0,0 @@
LAMMPS (7 Feb 2024 - Development - patch_7Feb2024_update1-306-gf3391199e7-modified)
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
# 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: doi:10.1016/j.ijnonlinmec.2008.04.003
@Article{Mukherjee08,
author = {R. M. Mukherjee and P. S. Crozier and S. J. Plimpton and K. S. Anderson},
title = {Substructured Molecular Dynamics Using Multibody Dynamics Algorithms},
journal = {Intl.\ J.\ Non-Linear Mechanics},
year = 2008,
volume = 43,
number = 10,
pages = {1040--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 = 0 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 1538.7378 0 3904.434 18.086356
100 19803.641 237.21132 0 3904.5523 -3.1528278
150 20259.6 152.62032 0 3904.3981 -4.6173548
200 20705.978 69.977442 0 3904.4178 9.0928146
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 20365.825 131.47271 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 20076.333 184.61916 0 3902.4586 -2.272315
1050 20859.506 39.696992 0 3902.5684 6.45166
1100 15284.661 1072.1906 0 3902.6833 21.194041
1150 19658.317 261.99809 0 3902.4272 -2.8744196
1200 20767.681 56.717093 0 3902.5839 -34.817444
1250 20625.583 82.586396 0 3902.1388 11.697328
1300 20690.013 71.006479 0 3902.4903 -29.292783
1350 20936.019 26.022787 0 3903.0634 1.0316031
1400 19753.56 244.81777 0 3902.8844 6.713847
1450 15690.145 998.34279 0 3903.9252 48.124638
1500 20234.455 155.92476 0 3903.0461 13.17218
1550 20779.631 55.063072 0 3903.1428 -2.6390427
1600 20642.756 80.233303 0 3902.9659 -2.4688077
1650 18785.71 423.90132 0 3902.7365 -5.6468182
1700 20965.076 20.760481 0 3903.182 -0.45377448
1750 18935.45 396.95247 0 3903.5173 25.912353
1800 20581.523 91.763662 0 3903.1567 3.8225817
1850 20616.962 85.182351 0 3903.1382 4.1907744
1900 16601.061 828.59343 0 3902.8639 -0.49284971
1950 20175.618 166.51633 0 3902.7419 5.6031735
2000 20266.439 149.55931 0 3902.6036 -1.1956447
2050 20159.308 169.44017 0 3902.6453 -0.7983344
2100 19743.72 245.40822 0 3901.6527 3.5301052
2150 20674.556 74.284034 0 3902.9055 0.61532081
2200 19950.784 208.30189 0 3902.8915 7.6523945
2250 19817.161 232.7485 0 3902.5932 3.4492756
2300 20459.058 114.2307 0 3902.9451 -11.066393
2350 18359.21 503.25787 0 3903.1115 -9.0741539
2400 19952.914 207.84881 0 3902.8328 -0.53972874
2450 19661.352 259.78979 0 3900.781 7.8669927
2500 20917.293 29.699201 0 3903.2719 1.1433085
2550 20763.955 57.990256 0 3903.1671 -1.1088372
2600 20640.005 80.556339 0 3902.7795 9.6127007
2650 20823.227 47.292746 0 3903.446 2.2923503
2700 20401.43 125.53141 0 3903.5739 -8.0683618
2750 20689.918 72.242212 0 3903.7084 0.22078527
2800 20783.922 54.87309 0 3903.7476 2.0668249
2850 19258.563 336.84835 0 3903.2488 4.2704683
2900 20565.694 95.184831 0 3903.6468 -0.24799068
2950 20915.041 30.344751 0 3903.5004 -2.9900907
3000 19571.964 278.74004 0 3903.1778 12.195325
3050 20356.693 133.43974 0 3903.1976 0.11608195
3100 20047.888 190.69627 0 3903.268 -4.5895546
3150 19834.363 230.59072 0 3903.6209 -1.4352632
3200 20213.412 160.25129 0 3903.4757 3.7488266
3250 19286.774 332.04497 0 3903.6699 -5.0835358
3300 20952.226 23.774103 0 3903.816 0.10019546
3350 20407.952 124.62932 0 3903.8798 0.4403531
3400 19401.716 311.03567 0 3903.9461 1.8034568
3450 20880.78 37.20558 0 3904.0167 6.3948533
3500 19529.313 287.50301 0 3904.0425 12.311168
3550 20943.604 25.677677 0 3904.1228 5.1786098
3600 20272.725 149.91697 0 3904.1254 1.196909
3650 19781.047 240.95421 0 3904.1111 -8.5091671
3700 20613.433 86.53896 0 3903.8414 -9.1622102
3750 20567.605 95.294456 0 3904.1101 -0.11887825
3800 19891.98 220.32932 0 3904.0292 6.8801146
3850 20669.735 76.407858 0 3904.1365 -7.4310509
3900 20908.711 32.197181 0 3904.1807 -4.6573356
3950 20822.78 48.03134 0 3904.1018 0.086779759
4000 20199.055 163.66262 0 3904.2283 2.0027771
4050 20072.638 187.07041 0 3904.2256 4.4103784
4100 17724.651 619.7903 0 3902.1331 11.210006
4150 20760.201 60.001382 0 3904.4831 -3.8510009
4200 19159.102 356.30472 0 3904.2865 -2.3503308
4250 19403.974 311.3497 0 3904.6783 -1.2458384
4300 20858.687 42.000734 0 3904.7206 2.1750528
4350 20486.989 110.94383 0 3904.8306 5.017245
4400 20231.073 158.28825 0 3904.7832 7.4295979
4450 16369.689 873.39361 0 3904.8175 14.371454
4500 20745.196 63.11427 0 3904.8172 -7.855609
4550 18688.003 443.85636 0 3904.5977 9.8067426
4600 17755.672 616.68475 0 3904.7721 -3.9654703
4650 19843.131 230.34486 0 3904.9988 -0.13553926
4700 18873.202 409.99341 0 3905.0308 15.912724
4750 20605.355 89.223116 0 3905.0295 2.0847611
4800 20136.483 176.1278 0 3905.1062 -1.7091113
4850 19808.073 236.83278 0 3904.9945 5.0982271
4900 19142.083 359.55764 0 3904.3878 8.2072008
4950 20539.687 101.08198 0 3904.7277 8.0469319
5000 20840.809 45.759021 0 3905.168 4.771755
5050 20009.696 199.45528 0 3904.9546 6.1191423
5100 20882.034 38.247578 0 3905.2909 -6.3068822
5150 20329.869 140.47458 0 3905.2651 -21.720979
5200 17334.411 695.67098 0 3905.7471 -9.8243617
5250 19602.025 275.17282 0 3905.1775 -3.2371379
5300 20858.74 42.630642 0 3905.3603 0.38011789
5350 20828.619 48.188698 0 3905.3403 5.7187945
5400 20978.428 20.447148 0 3905.3413 6.1168011
5450 20115.374 179.9294 0 3904.9987 8.6440563
5500 20522.744 104.7733 0 3905.2815 -2.6561664
5550 20625.724 85.600795 0 3905.1792 -1.327206
5600 19559.638 282.68742 0 3904.8426 17.893028
5650 20552.224 98.978098 0 3904.9455 2.4489071
5700 19982.142 204.09989 0 3904.4966 9.9034011
5750 20408.825 125.30875 0 3904.7209 1.2515548
5800 19773.143 243.02134 0 3904.7144 -2.6729948
5850 20781.934 56.310486 0 3904.8168 -1.659054
5900 19807.668 236.54392 0 3904.6306 0.49776361
5950 20741.237 63.921667 0 3904.8916 4.2800039
6000 20322.7 140.98125 0 3904.4442 7.4978024
6050 20858.439 42.383629 0 3905.0575 -4.6872323
6100 20212.538 162.022 0 3905.0847 -7.0796165
6150 18513.957 476.7087 0 3905.2193 7.107138
6200 20802.734 52.621638 0 3904.9797 3.7242428
6250 20818.044 49.717458 0 3904.9109 -0.91041774
6300 19987.245 203.4635 0 3904.8052 -0.86714551
6350 20806.906 51.449749 0 3904.5806 -4.0699629
6400 20530.3 103.09809 0 3905.0055 1.660177
6450 20667.085 77.715553 0 3904.9535 0.99217521
6500 20515.816 105.81762 0 3905.0428 3.0994091
6550 20548.348 99.627131 0 3904.8769 -0.77417688
6600 19827.378 232.99889 0 3904.7355 3.295082
6650 19237.199 342.94808 0 3905.3923 -6.2226637
6700 19611.621 273.139 0 3904.9206 -3.5465535
6750 20874.805 39.1893 0 3904.8939 -0.051336814
6800 19433.717 305.99952 0 3904.8361 -19.858865
6850 20119.223 179.19987 0 3904.9818 4.6466283
6900 20467.389 114.77871 0 3905.0359 10.290214
6950 20334.202 139.43289 0 3905.0259 7.5448433
7000 20504.591 107.86929 0 3905.0158 -0.10092084
7050 17969.214 576.83722 0 3904.4694 10.852897
7100 19186.398 351.80467 0 3904.8414 0.24779979
7150 20261.23 152.54684 0 3904.6265 -7.0175844
7200 20696.821 71.985154 0 3904.7298 3.9649146
7250 18456.212 487.1819 0 3904.9989 5.8280225
7300 17705.1 625.95928 0 3904.6816 6.8298215
7350 17032.039 750.96958 0 3905.051 11.833303
7400 20557.431 97.599213 0 3904.5308 0.43747863
7450 20466.847 114.5693 0 3904.7261 1.9786538
7500 20416.862 123.31643 0 3904.2168 -2.9094738
7550 18433.95 487.50767 0 3901.2022 4.0921479
7600 19950.107 209.92208 0 3904.3863 3.9114888
7650 16037.844 934.94785 0 3904.9189 -1.2183461
7700 20145.239 173.99945 0 3904.5993 3.1185554
7750 18672.579 446.35236 0 3904.2373 4.1086445
7800 19740.616 249.10395 0 3904.7737 4.6048428
7850 20801.917 52.742096 0 3904.9489 1.5978265
7900 20305.348 144.57749 0 3904.8272 2.7348725
7950 20221.086 159.31958 0 3903.9652 7.1592496
8000 20826.907 47.953835 0 3904.7884 6.2728901
8050 18646.418 452.02126 0 3905.0617 5.9716218
8100 20653.653 80.183024 0 3904.9336 -1.8274783
8150 20843.275 45.172279 0 3905.0379 -6.9445524
8200 20364.78 133.45082 0 3904.7064 -12.094533
8250 18163.745 541.08818 0 3904.7447 -2.6103997
8300 20889.664 36.793018 0 3905.2494 -9.2650749
8350 20307.367 144.33088 0 3904.9543 -0.65999546
8400 20485.202 111.41317 0 3904.9691 -0.42802224
8450 20864.395 41.146879 0 3904.9238 7.7084978
8500 20901.899 34.291267 0 3905.0132 -5.2070823
8550 20211.78 162.02611 0 3904.9484 -5.8363409
8600 19639.538 268.05291 0 3905.0044 3.8180903
8650 19919.356 216.24885 0 3905.0185 0.17130921
8700 19499.449 293.97522 0 3904.9843 -4.897872
8750 20270.687 151.1571 0 3904.9879 0.28558082
8800 18804.137 422.61651 0 3904.864 15.351015
8850 20654.443 80.110976 0 3905.0078 4.1368065
8900 19953.725 209.81046 0 3904.9447 10.71743
8950 18195.013 536.67764 0 3906.1245 21.497802
9000 20478.531 112.78923 0 3905.1098 -13.053056
9050 20866.484 40.901611 0 3905.0653 -3.6134066
9100 20322.595 141.61419 0 3905.0577 15.459697
9150 20855.456 42.94311 0 3905.0646 4.9123213
9200 20208.201 162.79363 0 3905.0531 2.5454472
9250 18394.203 498.63686 0 3904.9707 0.041811692
9300 18776.997 427.7118 0 3904.9335 -7.652483
9350 18330.751 510.07857 0 3904.6621 8.3424059
9400 17538.366 657.08623 0 3904.9319 8.5478668
9450 20309.605 143.77142 0 3904.8093 6.6831447
9500 19982.331 203.81545 0 3904.2471 -7.6711411
9550 19410.612 310.1139 0 3904.6717 5.3983286
9600 19198.225 349.06634 0 3904.2932 -4.107658
9650 19388.043 314.31566 0 3904.6939 6.1198194
9700 18849.37 414.1045 0 3904.7286 5.4468861
9750 18263.312 523.38716 0 3905.4819 -0.56480349
9800 20421.858 122.53973 0 3904.3653 -15.641399
9850 17678.959 631.15683 0 3905.0381 -1.805446
9900 19421.046 306.67446 0 3903.1644 7.0287747
9950 18460.64 483.18902 0 3901.8261 3.658774
10000 19781.151 239.38136 0 3902.5575 6.3312911
Loop time of 3.21586 on 4 procs for 10000 steps with 81 atoms
Performance: 26866.868 tau/day, 3109.591 timesteps/s, 251.877 katom-step/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 | 0.0068055 | 0.017185 | 0.043838 | 11.8 | 0.53
Neigh | 0.010594 | 0.021601 | 0.042532 | 8.5 | 0.67
Comm | 0.068664 | 0.091849 | 0.10748 | 4.8 | 2.86
Output | 0.0038351 | 0.0044469 | 0.0057465 | 1.1 | 0.14
Modify | 2.8494 | 2.9033 | 2.9663 | 2.5 | 90.28
Other | | 0.1775 | | | 5.52
Nlocal: 20.25 ave 36 max 0 min
Histogram: 1 0 0 0 0 1 0 1 0 1
Nghost: 38.25 ave 50 max 28 min
Histogram: 1 0 1 0 0 1 0 0 0 1
Neighs: 126.5 ave 213 max 0 min
Histogram: 1 0 0 0 1 0 0 0 0 2
Total # of neighbors = 506
Ave neighs/atom = 6.2469136
Neighbor list builds = 1207
Dangerous builds = 0
Total wall time: 0:00:03

343
examples/rigid/log.25Mar24.rigid.property.g++.1
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@ -1,343 +0,0 @@
LAMMPS (7 Feb 2024 - Development - patch_7Feb2024_update1-306-gf3391199e7-modified)
using 1 OpenMP thread(s) per MPI task
# Simple rigid body system
units lj
atom_style atomic
atom_modify map array
pair_style lj/cut 2.5
fix 0 all property/atom i_bodies
read_data data.rigid-property fix 0 NULL Clumps
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 = 0.001 seconds
velocity all create 100.0 4928459
# unconnected bodies
group clump1 id <> 1 9
9 atoms in group clump1
group clump2 id <> 10 18
9 atoms in group clump2
group clump3 id <> 19 27
9 atoms in group clump3
group clump4 id <> 28 36
9 atoms in group clump4
group clump5 id <> 37 45
9 atoms in group clump5
group clump6 id <> 46 54
9 atoms in group clump6
group clump7 id <> 55 63
9 atoms in group clump7
group clump8 id <> 64 72
9 atoms in group clump8
group clump9 id <> 73 81
9 atoms in group clump9
# assemble bodies from per-atom custom integer property bodies
fix 1 all rigid custom i_bodies
9 rigid bodies with 81 atoms
# 1 chain of connected bodies
#group clump1 id <> 1 9
#group clump2 id <> 9 18
#group clump3 id <> 18 27
#group clump4 id <> 27 36
#group clump5 id <> 36 45
#group clump6 id <> 45 54
#group clump7 id <> 54 63
#group clump8 id <> 63 72
#group clump9 id <> 72 81
#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9
# 2 chains of connected bodies
#group clump1 id <> 1 9
#group clump2 id <> 9 18
#group clump3 id <> 18 27
#group clump4 id <> 27 36
#group clump5 id <> 37 45
#group clump6 id <> 45 54
#group clump7 id <> 54 63
#group clump8 id <> 63 72
#group clump9 id <> 72 81
#fix 1 all poems group clump1 clump2 clump3 clump4
#fix 2 all poems group clump5 clump6 clump7 clump8 clump9
neigh_modify exclude group clump1 clump1
neigh_modify exclude group clump2 clump2
neigh_modify exclude group clump3 clump3
neigh_modify exclude group clump4 clump4
neigh_modify exclude group clump5 clump5
neigh_modify exclude group clump6 clump6
neigh_modify exclude group clump7 clump7
neigh_modify exclude group clump8 clump8
neigh_modify exclude group clump9 clump9
thermo 100
#dump 1 all atom 50 dump.rigid
#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 2 pad 5
#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 3 pad 5
timestep 0.0001
thermo 50
run 10000
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4, bins = 18 18 18
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 4.42 | 4.42 | 4.42 Mbytes
Step Temp E_pair E_mol TotEng Press
0 115.29439 5235.9179 0 5272.2142 -2.7403788
50 14910.685 571.71558 0 5265.82 32.006171
100 16298.442 136.66184 0 5267.653 16.444229
150 16682.606 17.490511 0 5269.4219 14.900344
200 16733.929 1.372872 0 5269.4617 14.569267
250 16738.853 -0.15252816 0 5269.4864 14.496404
300 16738.588 -0.055171335 0 5269.5002 14.496025
350 16738.492 -0.017444677 0 5269.5077 14.496446
400 16738.464 -0.0060102023 0 5269.5104 14.496618
450 16738.455 -0.0012713351 0 5269.5124 14.496701
500 16738.455 -0.00081068621 0 5269.5128 14.496709
550 16738.455 -0.00083203497 0 5269.5129 14.496707
600 16738.455 -0.00058355356 0 5269.5131 14.496709
650 16738.455 -0.00047226704 0 5269.5131 14.496708
700 16738.455 0 0 5269.5136 14.496713
750 16738.455 0 0 5269.5136 14.49671
800 16738.455 0 0 5269.5137 14.496709
850 16738.455 0 0 5269.5137 14.49671
900 16738.456 0 0 5269.5138 14.496713
950 16738.462 -0.0035323872 0 5269.5122 14.496671
1000 16738.586 -0.051135144 0 5269.5036 14.496229
1050 16737.358 0.32995057 0 5269.4981 14.525763
1100 16737.892 0.16210246 0 5269.4984 14.531983
1150 16738.703 -0.089235095 0 5269.5025 14.509899
1200 16738.466 -0.0075446243 0 5269.5096 14.510615
1250 16738.456 0 0 5269.514 14.510704
1300 16738.457 0 0 5269.5141 14.510701
1350 16738.457 0 0 5269.5141 14.510699
1400 16738.457 -0.00044736511 0 5269.5138 14.510693
1450 16738.458 -0.0010971179 0 5269.5134 14.510687
1500 16738.458 -0.00057885428 0 5269.5139 14.510698
1550 16738.457 0 0 5269.5143 14.51071
1600 16738.457 0 0 5269.5144 14.510712
1650 16738.457 0 0 5269.5144 14.510712
1700 16738.458 0 0 5269.5144 14.51071
1750 16738.458 0 0 5269.5145 14.510708
1800 16738.458 0 0 5269.5145 14.510706
1850 16738.458 0 0 5269.5146 14.510705
1900 16738.458 0 0 5269.5146 14.510706
1950 16738.465 -0.0031733615 0 5269.5134 14.510659
2000 16738.491 -0.013255268 0 5269.5117 14.510532
2050 16738.556 -0.0365811 0 5269.5087 14.51029
2100 16738.633 -0.063209659 0 5269.5065 14.510219
2150 16738.607 -0.05601761 0 5269.5055 14.510231
2200 16738.557 -0.038423032 0 5269.5072 14.510404
2250 16738.515 -0.023709918 0 5269.5088 14.510539
2300 16738.489 -0.013249035 0 5269.5111 14.510621
2350 16738.468 -0.0045563719 0 5269.5131 14.510714
2400 16738.46 -0.00052194273 0 5269.5146 14.510771
2450 16738.464 -0.0023259756 0 5269.514 14.510746
2500 16738.468 -0.0051929186 0 5269.5127 14.510731
2550 16738.581 -0.044940117 0 5269.5085 14.510315
2600 16738.427 -7.9722875e-05 0 5269.5046 14.510657
2650 16733.017 1.705148 0 5269.5067 14.596295
2700 16738.761 -0.10614946 0 5269.5038 14.499584
2750 16733.973 1.4038179 0 5269.5064 14.598107
2800 16738.585 -0.046813448 0 5269.5076 14.511073
2850 16738.487 -0.012558719 0 5269.5111 14.510111
2900 16738.465 -0.0026252725 0 5269.514 14.510277
2950 16738.476 -0.0082220764 0 5269.512 14.510223
3000 16738.66 -0.071284779 0 5269.507 14.509758
3050 16715.332 7.2419351 0 5269.476 14.870305
3100 16653.226 26.818761 0 5269.5009 14.496764
3150 16739.351 -0.30690375 0 5269.4886 13.643904
3200 16733.238 1.6025328 0 5269.4737 12.016934
3250 16734.374 1.2554429 0 5269.4841 11.963561
3300 16732.156 1.9585967 0 5269.4893 12.234024
3350 16738.655 -0.079693236 0 5269.497 12.092757
3400 16738.543 -0.042215005 0 5269.4991 12.092809
3450 16738.591 -0.059327511 0 5269.4972 12.092536
3500 16738.759 -0.11761245 0 5269.4918 12.09203
3550 16713.405 7.846062 0 5269.4737 12.389816
3600 16734.939 1.0821936 0 5269.4891 12.173591
3650 16738.808 -0.13663194 0 5269.4882 12.027009
3700 16738.602 -0.070934368 0 5269.4889 12.025288
3750 16737.731 0.20706558 0 5269.4927 12.061948
3800 16738.578 -0.05582043 0 5269.4965 12.035665
3850 16738.471 -0.016307928 0 5269.5024 12.035302
3900 16738.449 -0.0058182199 0 5269.5059 12.035401
3950 16738.439 -0.0012027325 0 5269.5074 12.035461
4000 16738.436 -0.00020698452 0 5269.5075 12.035469
4050 16738.437 0 0 5269.5078 12.035454
4100 16738.437 0 0 5269.508 12.035435
4150 16738.438 0 0 5269.5081 12.035426
4200 16738.438 0 0 5269.5083 12.035432
4250 16738.439 0 0 5269.5085 12.035447
4300 16738.439 0 0 5269.5086 12.035463
4350 16738.44 0 0 5269.5087 12.035474
4400 16738.44 0 0 5269.5088 12.035478
4450 16738.44 0 0 5269.5089 12.035474
4500 16738.44 0 0 5269.509 12.035462
4550 16738.441 0 0 5269.5092 12.035449
4600 16738.441 0 0 5269.5093 12.035445
4650 16738.442 0 0 5269.5095 12.035451
4700 16738.442 0 0 5269.5096 12.03546
4750 16738.443 0 0 5269.5097 12.035465
4800 16738.443 0 0 5269.5098 12.035466
4850 16738.443 0 0 5269.51 12.035463
4900 16738.444 0 0 5269.5101 12.035456
4950 16738.444 0 0 5269.5102 12.035447
5000 16738.445 0 0 5269.5104 12.03544
5050 16738.445 0 0 5269.5105 12.035442
5100 16738.446 0 0 5269.5107 12.035455
5150 16738.446 0 0 5269.5108 12.03547
5200 16738.446 0 0 5269.5109 12.035479
5250 16738.447 0 0 5269.511 12.035479
5300 16738.447 0 0 5269.5111 12.03547
5350 16738.447 0 0 5269.5112 12.035454
5400 16738.448 0 0 5269.5113 12.035434
5450 16738.448 0 0 5269.5115 12.03542
5500 16738.449 0 0 5269.5117 12.035422
5550 16738.457 -0.0030919234 0 5269.5111 12.035383
5600 16738.51 -0.021618357 0 5269.5092 12.035106
5650 16738.622 -0.059214788 0 5269.507 12.035694
5700 16395.28 108.06942 0 5269.5463 24.369038
5750 16738.544 -0.033973429 0 5269.5077 12.011261
5800 16738.456 -0.0037013529 0 5269.5102 12.011675
5850 16738.451 0 0 5269.5123 12.011709
5900 16738.451 -0.0002211587 0 5269.5122 12.011687
5950 16738.452 -0.00024253349 0 5269.5124 12.011678
6000 16738.452 0 0 5269.5128 12.011688
6050 16738.453 0 0 5269.513 12.011702
6100 16738.453 0 0 5269.5131 12.011716
6150 16738.454 0 0 5269.5132 12.011725
6200 16738.454 0 0 5269.5133 12.011728
6250 16738.454 0 0 5269.5134 12.011723
6300 16738.455 0 0 5269.5135 12.011712
6350 16738.455 0 0 5269.5137 12.0117
6400 16738.456 0 0 5269.5138 12.011697
6450 16738.456 0 0 5269.514 12.011704
6500 16738.456 0 0 5269.5141 12.011714
6550 16738.457 0 0 5269.5142 12.011719
6600 16738.457 0 0 5269.5143 12.011718
6650 16738.458 0 0 5269.5144 12.011713
6700 16738.458 0 0 5269.5146 12.011705
6750 16738.459 0 0 5269.5147 12.011696
6800 16738.459 0 0 5269.5149 12.01169
6850 16738.46 0 0 5269.515 12.011695
6900 16738.46 0 0 5269.5152 12.01171
6950 16738.46 0 0 5269.5153 12.011726
7000 16738.461 0 0 5269.5154 12.011736
7050 16738.461 0 0 5269.5155 12.011737
7100 16738.461 0 0 5269.5155 12.011728
7150 16738.461 0 0 5269.5156 12.011712
7200 16738.462 0 0 5269.5158 12.011691
7250 16738.463 0 0 5269.516 12.011676
7300 16738.463 0 0 5269.5162 12.011677
7350 16738.464 0 0 5269.5164 12.011693
7400 16738.464 0 0 5269.5165 12.011713
7450 16738.465 0 0 5269.5166 12.011729
7500 16738.465 0 0 5269.5167 12.011736
7550 16738.465 0 0 5269.5168 12.011734
7600 16738.465 0 0 5269.5168 12.011722
7650 16738.466 0 0 5269.517 12.011704
7700 16738.466 0 0 5269.5171 12.011687
7750 16738.467 0 0 5269.5173 12.011681
7800 16738.467 0 0 5269.5175 12.011687
7850 16738.468 0 0 5269.5176 12.0117
7900 16738.468 0 0 5269.5178 12.011712
7950 16738.469 0 0 5269.5179 12.011721
8000 16738.469 0 0 5269.518 12.011724
8050 16738.469 0 0 5269.5181 12.01172
8100 16738.47 0 0 5269.5182 12.011709
8150 16738.47 0 0 5269.5183 12.0117
8200 16738.47 0 0 5269.5185 12.0117
8250 16738.471 0 0 5269.5186 12.011709
8300 16738.471 0 0 5269.5187 12.011719
8350 16738.472 0 0 5269.5189 12.011723
8400 16738.472 0 0 5269.519 12.01172
8450 16738.473 -0.00039690665 0 5269.5189 12.011706
8500 16738.481 -0.0034646803 0 5269.5182 12.011643
8550 16738.483 -0.0045307408 0 5269.5178 12.011621
8600 16738.474 -0.0007653281 0 5269.5189 12.011681
8650 16738.474 0 0 5269.5197 12.011699
8700 16738.475 0 0 5269.5199 12.011715
8750 16738.475 0 0 5269.52 12.011732
8800 16738.475 0 0 5269.52 12.011743
8850 16738.476 0 0 5269.5201 12.011744
8900 16738.476 0 0 5269.5202 12.011735
8950 16738.476 0 0 5269.5203 12.011719
9000 16738.477 0 0 5269.5205 12.011698
9050 16738.477 0 0 5269.5206 12.011683
9100 16738.478 0 0 5269.5208 12.011684
9150 16738.479 0 0 5269.521 12.011701
9200 16738.479 0 0 5269.5212 12.011722
9250 16738.479 0 0 5269.5213 12.011738
9300 16738.48 0 0 5269.5214 12.011746
9350 16738.48 0 0 5269.5214 12.011744
9400 16738.48 0 0 5269.5215 12.011732
9450 16738.48 0 0 5269.5216 12.011715
9500 16738.481 -0.00037652436 0 5269.5216 12.011692
9550 16738.493 -0.0053156156 0 5269.5203 12.011611
9600 16738.549 -0.026814368 0 5269.5163 12.011415
9650 16738.765 -0.10191522 0 5269.5092 12.011013
9700 16735.041 1.0589881 0 5269.4979 12.062708
9750 16738.013 0.13550093 0 5269.5101 11.407245
9800 16738.512 -0.01162033 0 5269.5201 11.394973
9850 16738.489 -0.00067270581 0 5269.5237 11.395098
9900 16738.489 -0.0002498458 0 5269.5242 11.395084
9950 16738.49 0 0 5269.5245 11.395076
10000 16738.49 0 0 5269.5246 11.395075
Loop time of 0.13897 on 1 procs for 10000 steps with 81 atoms
Performance: 621716.264 tau/day, 71957.901 timesteps/s, 5.829 Matom-step/s
98.6% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0095014 | 0.0095014 | 0.0095014 | 0.0 | 6.84
Neigh | 0.050174 | 0.050174 | 0.050174 | 0.0 | 36.10
Comm | 0.0091698 | 0.0091698 | 0.0091698 | 0.0 | 6.60
Output | 0.0016255 | 0.0016255 | 0.0016255 | 0.0 | 1.17
Modify | 0.060968 | 0.060968 | 0.060968 | 0.0 | 43.87
Other | | 0.007531 | | | 5.42
Nlocal: 81 ave 81 max 81 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 84 ave 84 max 84 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0
Neighbor list builds = 1552
Dangerous builds = 0
Total wall time: 0:00:00

343
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@ -1,343 +0,0 @@
LAMMPS (7 Feb 2024 - Development - patch_7Feb2024_update1-306-gf3391199e7-modified)
using 1 OpenMP thread(s) per MPI task
# Simple rigid body system
units lj
atom_style atomic
atom_modify map array
pair_style lj/cut 2.5
fix 0 all property/atom i_bodies
read_data data.rigid-property fix 0 NULL Clumps
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
# 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
# assemble bodies from per-atom custom integer property bodies
fix 1 all rigid custom i_bodies
9 rigid bodies with 81 atoms
# 1 chain of connected bodies
#group clump1 id <> 1 9
#group clump2 id <> 9 18
#group clump3 id <> 18 27
#group clump4 id <> 27 36
#group clump5 id <> 36 45
#group clump6 id <> 45 54
#group clump7 id <> 54 63
#group clump8 id <> 63 72
#group clump9 id <> 72 81
#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9
# 2 chains of connected bodies
#group clump1 id <> 1 9
#group clump2 id <> 9 18
#group clump3 id <> 18 27
#group clump4 id <> 27 36
#group clump5 id <> 37 45
#group clump6 id <> 45 54
#group clump7 id <> 54 63
#group clump8 id <> 63 72
#group clump9 id <> 72 81
#fix 1 all poems group clump1 clump2 clump3 clump4
#fix 2 all poems group clump5 clump6 clump7 clump8 clump9
neigh_modify exclude group clump1 clump1
neigh_modify exclude group clump2 clump2
neigh_modify exclude group clump3 clump3
neigh_modify exclude group clump4 clump4
neigh_modify exclude group clump5 clump5
neigh_modify exclude group clump6 clump6
neigh_modify exclude group clump7 clump7
neigh_modify exclude group clump8 clump8
neigh_modify exclude group clump9 clump9
thermo 100
#dump 1 all atom 50 dump.rigid
#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 2 pad 5
#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 3 pad 5
timestep 0.0001
thermo 50
run 10000
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4, bins = 18 18 18
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 4.268 | 4.3 | 4.394 Mbytes
Step Temp E_pair E_mol TotEng Press
0 115.29439 5235.9179 0 5272.2142 -2.7403788
50 14910.685 571.71558 0 5265.82 32.006171
100 16298.442 136.66184 0 5267.653 16.444229
150 16682.606 17.490511 0 5269.4219 14.900344
200 16733.929 1.372872 0 5269.4617 14.569267
250 16738.853 -0.15252816 0 5269.4864 14.496404
300 16738.588 -0.055171335 0 5269.5002 14.496025
350 16738.492 -0.017444677 0 5269.5077 14.496446
400 16738.464 -0.0060102023 0 5269.5104 14.496618
450 16738.455 -0.0012713351 0 5269.5124 14.496701
500 16738.455 -0.00081068621 0 5269.5128 14.496709
550 16738.455 -0.00083203497 0 5269.5129 14.496707
600 16738.455 -0.00058355356 0 5269.5131 14.496709
650 16738.455 -0.00047226704 0 5269.5131 14.496708
700 16738.455 0 0 5269.5136 14.496713
750 16738.455 0 0 5269.5136 14.49671
800 16738.455 0 0 5269.5137 14.496709
850 16738.455 0 0 5269.5137 14.49671
900 16738.456 0 0 5269.5138 14.496713
950 16738.462 -0.0035323872 0 5269.5122 14.496671
1000 16738.586 -0.051135144 0 5269.5036 14.496229
1050 16737.358 0.32995057 0 5269.4981 14.525763
1100 16737.892 0.16210246 0 5269.4984 14.531983
1150 16738.703 -0.089235095 0 5269.5025 14.509899
1200 16738.466 -0.0075446243 0 5269.5096 14.510615
1250 16738.456 0 0 5269.514 14.510704
1300 16738.457 0 0 5269.5141 14.510701
1350 16738.457 0 0 5269.5141 14.510699
1400 16738.457 -0.00044736511 0 5269.5138 14.510693
1450 16738.458 -0.0010971179 0 5269.5134 14.510687
1500 16738.458 -0.00057885428 0 5269.5139 14.510698
1550 16738.457 0 0 5269.5143 14.51071
1600 16738.457 0 0 5269.5144 14.510712
1650 16738.457 0 0 5269.5144 14.510712
1700 16738.458 0 0 5269.5144 14.51071
1750 16738.458 0 0 5269.5145 14.510708
1800 16738.458 0 0 5269.5145 14.510706
1850 16738.458 0 0 5269.5146 14.510705
1900 16738.458 0 0 5269.5146 14.510706
1950 16738.465 -0.0031733615 0 5269.5134 14.510659
2000 16738.491 -0.013255268 0 5269.5117 14.510532
2050 16738.556 -0.0365811 0 5269.5087 14.51029
2100 16738.633 -0.063209659 0 5269.5065 14.510219
2150 16738.607 -0.05601761 0 5269.5055 14.510231
2200 16738.557 -0.038423032 0 5269.5072 14.510404
2250 16738.515 -0.023709918 0 5269.5088 14.510539
2300 16738.489 -0.013249035 0 5269.5111 14.510621
2350 16738.468 -0.0045563719 0 5269.5131 14.510714
2400 16738.46 -0.00052194273 0 5269.5146 14.510771
2450 16738.464 -0.0023259756 0 5269.514 14.510746
2500 16738.468 -0.0051929186 0 5269.5127 14.510731
2550 16738.581 -0.044940117 0 5269.5085 14.510315
2600 16738.427 -7.9722867e-05 0 5269.5046 14.510657
2650 16733.017 1.705148 0 5269.5067 14.596295
2700 16738.761 -0.10614946 0 5269.5038 14.499584
2750 16733.973 1.4038179 0 5269.5064 14.598107
2800 16738.585 -0.046813448 0 5269.5076 14.511073
2850 16738.487 -0.012558719 0 5269.5111 14.510111
2900 16738.465 -0.0026252725 0 5269.514 14.510277
2950 16738.476 -0.0082220764 0 5269.512 14.510223
3000 16738.66 -0.071284779 0 5269.507 14.509758
3050 16715.332 7.2419351 0 5269.476 14.870305
3100 16653.226 26.818761 0 5269.5009 14.496764
3150 16739.351 -0.30690375 0 5269.4886 13.643904
3200 16733.238 1.6025328 0 5269.4737 12.016934
3250 16734.374 1.2554429 0 5269.4841 11.963561
3300 16732.156 1.9585967 0 5269.4893 12.234024
3350 16738.655 -0.079693236 0 5269.497 12.092757
3400 16738.543 -0.042215005 0 5269.4991 12.092809
3450 16738.591 -0.059327511 0 5269.4972 12.092536
3500 16738.759 -0.11761245 0 5269.4918 12.09203
3550 16713.405 7.846062 0 5269.4737 12.389816
3600 16734.939 1.0821936 0 5269.4891 12.173591
3650 16738.808 -0.13663194 0 5269.4882 12.027009
3700 16738.602 -0.070934368 0 5269.4889 12.025288
3750 16737.731 0.20706558 0 5269.4927 12.061948
3800 16738.578 -0.05582043 0 5269.4965 12.035665
3850 16738.471 -0.016307928 0 5269.5024 12.035302
3900 16738.449 -0.0058182199 0 5269.5059 12.035401
3950 16738.439 -0.0012027325 0 5269.5074 12.035461
4000 16738.436 -0.00020698452 0 5269.5075 12.035469
4050 16738.437 0 0 5269.5078 12.035454
4100 16738.437 0 0 5269.508 12.035435
4150 16738.438 0 0 5269.5081 12.035426
4200 16738.438 0 0 5269.5083 12.035432
4250 16738.439 0 0 5269.5085 12.035447
4300 16738.439 0 0 5269.5086 12.035463
4350 16738.44 0 0 5269.5087 12.035474
4400 16738.44 0 0 5269.5088 12.035478
4450 16738.44 0 0 5269.5089 12.035474
4500 16738.44 0 0 5269.509 12.035462
4550 16738.441 0 0 5269.5092 12.035449
4600 16738.441 0 0 5269.5093 12.035445
4650 16738.442 0 0 5269.5095 12.035451
4700 16738.442 0 0 5269.5096 12.03546
4750 16738.443 0 0 5269.5097 12.035465
4800 16738.443 0 0 5269.5098 12.035466
4850 16738.443 0 0 5269.51 12.035463
4900 16738.444 0 0 5269.5101 12.035456
4950 16738.444 0 0 5269.5102 12.035447
5000 16738.445 0 0 5269.5104 12.03544
5050 16738.445 0 0 5269.5105 12.035442
5100 16738.446 0 0 5269.5107 12.035455
5150 16738.446 0 0 5269.5108 12.03547
5200 16738.446 0 0 5269.5109 12.035479
5250 16738.447 0 0 5269.511 12.035479
5300 16738.447 0 0 5269.5111 12.03547
5350 16738.447 0 0 5269.5112 12.035454
5400 16738.448 0 0 5269.5113 12.035434
5450 16738.448 0 0 5269.5115 12.03542
5500 16738.449 0 0 5269.5117 12.035422
5550 16738.457 -0.0030919234 0 5269.5111 12.035383
5600 16738.51 -0.021618357 0 5269.5092 12.035106
5650 16738.622 -0.059214788 0 5269.507 12.035694
5700 16395.28 108.06942 0 5269.5463 24.369038
5750 16738.544 -0.033973429 0 5269.5077 12.011261
5800 16738.456 -0.0037013529 0 5269.5102 12.011675
5850 16738.451 0 0 5269.5123 12.011709
5900 16738.451 -0.0002211587 0 5269.5122 12.011687
5950 16738.452 -0.00024253349 0 5269.5124 12.011678
6000 16738.452 0 0 5269.5128 12.011688
6050 16738.453 0 0 5269.513 12.011702
6100 16738.453 0 0 5269.5131 12.011716
6150 16738.454 0 0 5269.5132 12.011725
6200 16738.454 0 0 5269.5133 12.011728
6250 16738.454 0 0 5269.5134 12.011723
6300 16738.455 0 0 5269.5135 12.011712
6350 16738.455 0 0 5269.5137 12.0117
6400 16738.456 0 0 5269.5138 12.011697
6450 16738.456 0 0 5269.514 12.011704
6500 16738.456 0 0 5269.5141 12.011714
6550 16738.457 0 0 5269.5142 12.011719
6600 16738.457 0 0 5269.5143 12.011718
6650 16738.458 0 0 5269.5144 12.011713
6700 16738.458 0 0 5269.5146 12.011705
6750 16738.459 0 0 5269.5147 12.011696
6800 16738.459 0 0 5269.5149 12.01169
6850 16738.46 0 0 5269.515 12.011695
6900 16738.46 0 0 5269.5152 12.01171
6950 16738.46 0 0 5269.5153 12.011726
7000 16738.461 0 0 5269.5154 12.011736
7050 16738.461 0 0 5269.5155 12.011737
7100 16738.461 0 0 5269.5155 12.011728
7150 16738.461 0 0 5269.5156 12.011712
7200 16738.462 0 0 5269.5158 12.011691
7250 16738.463 0 0 5269.516 12.011676
7300 16738.463 0 0 5269.5162 12.011677
7350 16738.464 0 0 5269.5164 12.011693
7400 16738.464 0 0 5269.5165 12.011713
7450 16738.465 0 0 5269.5166 12.011729
7500 16738.465 0 0 5269.5167 12.011736
7550 16738.465 0 0 5269.5168 12.011734
7600 16738.465 0 0 5269.5168 12.011722
7650 16738.466 0 0 5269.517 12.011704
7700 16738.466 0 0 5269.5171 12.011687
7750 16738.467 0 0 5269.5173 12.011681
7800 16738.467 0 0 5269.5175 12.011687
7850 16738.468 0 0 5269.5176 12.0117
7900 16738.468 0 0 5269.5178 12.011712
7950 16738.469 0 0 5269.5179 12.011721
8000 16738.469 0 0 5269.518 12.011724
8050 16738.469 0 0 5269.5181 12.01172
8100 16738.47 0 0 5269.5182 12.011709
8150 16738.47 0 0 5269.5183 12.0117
8200 16738.47 0 0 5269.5185 12.0117
8250 16738.471 0 0 5269.5186 12.011709
8300 16738.471 0 0 5269.5187 12.011719
8350 16738.472 0 0 5269.5189 12.011723
8400 16738.472 0 0 5269.519 12.01172
8450 16738.473 -0.00039690664 0 5269.5189 12.011706
8500 16738.481 -0.0034646803 0 5269.5182 12.011643
8550 16738.483 -0.0045307409 0 5269.5178 12.011621
8600 16738.474 -0.00076532811 0 5269.5189 12.011681
8650 16738.474 0 0 5269.5197 12.011699
8700 16738.475 0 0 5269.5199 12.011715
8750 16738.475 0 0 5269.52 12.011732
8800 16738.475 0 0 5269.52 12.011743
8850 16738.476 0 0 5269.5201 12.011744
8900 16738.476 0 0 5269.5202 12.011735
8950 16738.476 0 0 5269.5203 12.011719
9000 16738.477 0 0 5269.5205 12.011698
9050 16738.477 0 0 5269.5206 12.011683
9100 16738.478 0 0 5269.5208 12.011684
9150 16738.479 0 0 5269.521 12.011701
9200 16738.479 0 0 5269.5212 12.011722
9250 16738.479 0 0 5269.5213 12.011738
9300 16738.48 0 0 5269.5214 12.011746
9350 16738.48 0 0 5269.5214 12.011744
9400 16738.48 0 0 5269.5215 12.011732
9450 16738.48 0 0 5269.5216 12.011715
9500 16738.481 -0.00037652437 0 5269.5216 12.011692
9550 16738.493 -0.0053156158 0 5269.5203 12.011611
9600 16738.549 -0.026814369 0 5269.5163 12.011415
9650 16738.765 -0.10191523 0 5269.5092 12.011013
9700 16735.041 1.0589886 0 5269.4979 12.062708
9750 16738.013 0.13550089 0 5269.5101 11.407245
9800 16738.512 -0.011620329 0 5269.5201 11.394973
9850 16738.489 -0.00067270567 0 5269.5237 11.395098
9900 16738.489 -0.00024984578 0 5269.5242 11.395084
9950 16738.49 0 0 5269.5245 11.395076
10000 16738.49 0 0 5269.5246 11.395075
Loop time of 0.145717 on 4 procs for 10000 steps with 81 atoms
Performance: 592928.932 tau/day, 68626.034 timesteps/s, 5.559 Matom-step/s
98.1% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0017512 | 0.002579 | 0.0032423 | 1.1 | 1.77
Neigh | 0.01337 | 0.01442 | 0.016488 | 1.0 | 9.90
Comm | 0.066749 | 0.068666 | 0.070799 | 0.7 | 47.12
Output | 0.0018563 | 0.0020346 | 0.0025278 | 0.6 | 1.40
Modify | 0.040991 | 0.042542 | 0.044042 | 0.6 | 29.19
Other | | 0.01548 | | | 10.62
Nlocal: 20.25 ave 37 max 3 min
Histogram: 1 0 0 1 0 0 0 1 0 1
Nghost: 27.25 ave 48 max 13 min
Histogram: 1 0 0 2 0 0 0 0 0 1
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0
Neighbor list builds = 1552
Dangerous builds = 0
Total wall time: 0:00:00

321
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@ -1,321 +0,0 @@
LAMMPS (7 Feb 2024 - Development - patch_7Feb2024_update1-306-gf3391199e7-modified)
using 1 OpenMP thread(s) per MPI task
# Simple rigid body system
units lj
atom_style bond
pair_style lj/cut 2.5
read_data data.rigid.small
Reading data file ...
orthogonal box = (-12 -12 -12) to (12 12 12)
1 by 1 by 1 MPI processor grid
reading atoms ...
81 atoms
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
0 = max # of 1-2 neighbors
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
1 = max # of special neighbors
special bonds CPU = 0.000 seconds
read_data CPU = 0.002 seconds
velocity all create 100.0 4928459
# unconnected bodies
group clump1 id <> 1 9
9 atoms in group clump1
group clump2 id <> 10 18
9 atoms in group clump2
group clump3 id <> 19 27
9 atoms in group clump3
group clump4 id <> 28 36
9 atoms in group clump4
group clump5 id <> 37 45
9 atoms in group clump5
group clump6 id <> 46 54
9 atoms in group clump6
group clump7 id <> 55 63
9 atoms in group clump7
group clump8 id <> 64 72
9 atoms in group clump8
group clump9 id <> 73 81
9 atoms in group clump9
fix 1 all rigid/small molecule
create bodies CPU = 0.000 seconds
9 rigid bodies with 81 atoms
1.2247449 = max distance from body owner to body atom
neigh_modify exclude group clump1 clump1
neigh_modify exclude group clump2 clump2
neigh_modify exclude group clump3 clump3
neigh_modify exclude group clump4 clump4
neigh_modify exclude group clump5 clump5
neigh_modify exclude group clump6 clump6
neigh_modify exclude group clump7 clump7
neigh_modify exclude group clump8 clump8
neigh_modify exclude group clump9 clump9
thermo 100
#dump 1 all atom 50 dump.rigid
#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 2 pad 5
#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 3 pad 5
timestep 0.0001
thermo 50
run 10000
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4, bins = 18 18 18
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 9.034 | 9.034 | 9.034 Mbytes
Step Temp E_pair E_mol TotEng Press
0 115.29439 5235.9179 0 5272.2142 -2.7403788
50 14910.685 571.71558 0 5265.82 32.006171
100 16298.442 136.66184 0 5267.653 16.444229
150 16682.606 17.490511 0 5269.4219 14.900344
200 16733.929 1.372872 0 5269.4617 14.569267
250 16738.853 -0.15252816 0 5269.4864 14.496404
300 16738.588 -0.055171335 0 5269.5002 14.496025
350 16738.492 -0.017444677 0 5269.5077 14.496446
400 16738.464 -0.0060102023 0 5269.5104 14.496618
450 16738.455 -0.0012713351 0 5269.5124 14.496701
500 16738.455 -0.00081068621 0 5269.5128 14.496709
550 16738.455 -0.00083203497 0 5269.5129 14.496707
600 16738.455 -0.00058355356 0 5269.5131 14.496709
650 16738.455 -0.00047226704 0 5269.5131 14.496708
700 16738.455 0 0 5269.5136 14.496713
750 16738.455 0 0 5269.5136 14.49671
800 16738.455 0 0 5269.5137 14.496709
850 16738.455 0 0 5269.5137 14.49671
900 16738.456 0 0 5269.5138 14.496713
950 16738.462 -0.0035323872 0 5269.5122 14.496671
1000 16738.586 -0.051135144 0 5269.5036 14.496229
1050 16737.358 0.32995057 0 5269.4981 14.525763
1100 16737.892 0.16210246 0 5269.4984 14.531983
1150 16738.703 -0.089235095 0 5269.5025 14.509899
1200 16738.466 -0.0075446243 0 5269.5096 14.510615
1250 16738.456 0 0 5269.514 14.510704
1300 16738.457 0 0 5269.5141 14.510701
1350 16738.457 0 0 5269.5141 14.510699
1400 16738.457 -0.00044736511 0 5269.5138 14.510693
1450 16738.458 -0.0010971179 0 5269.5134 14.510687
1500 16738.458 -0.00057885428 0 5269.5139 14.510698
1550 16738.457 0 0 5269.5143 14.51071
1600 16738.457 0 0 5269.5144 14.510712
1650 16738.457 0 0 5269.5144 14.510712
1700 16738.458 0 0 5269.5144 14.51071
1750 16738.458 0 0 5269.5145 14.510708
1800 16738.458 0 0 5269.5145 14.510706
1850 16738.458 0 0 5269.5146 14.510705
1900 16738.458 0 0 5269.5146 14.510706
1950 16738.465 -0.0031733615 0 5269.5134 14.510659
2000 16738.491 -0.013255268 0 5269.5117 14.510532
2050 16738.556 -0.0365811 0 5269.5087 14.51029
2100 16738.633 -0.063209659 0 5269.5065 14.510219
2150 16738.607 -0.05601761 0 5269.5055 14.510231
2200 16738.557 -0.038423032 0 5269.5072 14.510404
2250 16738.515 -0.023709918 0 5269.5088 14.510539
2300 16738.489 -0.013249035 0 5269.5111 14.510621
2350 16738.468 -0.0045563719 0 5269.5131 14.510714
2400 16738.46 -0.00052194273 0 5269.5146 14.510771
2450 16738.464 -0.0023259756 0 5269.514 14.510746
2500 16738.468 -0.0051929186 0 5269.5127 14.510731
2550 16738.581 -0.044940117 0 5269.5085 14.510315
2600 16738.427 -7.9722853e-05 0 5269.5046 14.510657
2650 16733.017 1.7051479 0 5269.5067 14.596295
2700 16738.761 -0.10614946 0 5269.5038 14.499584
2750 16733.973 1.4038179 0 5269.5064 14.598107
2800 16738.585 -0.046813448 0 5269.5076 14.511073
2850 16738.487 -0.012558719 0 5269.5111 14.510111
2900 16738.465 -0.0026252725 0 5269.514 14.510277
2950 16738.476 -0.0082220764 0 5269.512 14.510223
3000 16738.66 -0.071284779 0 5269.507 14.509758
3050 16715.332 7.2419352 0 5269.476 14.870305
3100 16653.226 26.818761 0 5269.5009 14.496764
3150 16739.351 -0.30690375 0 5269.4886 13.643904
3200 16733.238 1.6025328 0 5269.4737 12.016934
3250 16734.374 1.2554429 0 5269.4841 11.963561
3300 16732.156 1.9585967 0 5269.4893 12.234024
3350 16738.655 -0.079693236 0 5269.497 12.092757
3400 16738.543 -0.042215005 0 5269.4991 12.092809
3450 16738.591 -0.05932751 0 5269.4972 12.092536
3500 16738.759 -0.11761245 0 5269.4918 12.09203
3550 16713.405 7.8460621 0 5269.4737 12.389816
3600 16734.939 1.0821936 0 5269.4891 12.173591
3650 16738.808 -0.13663194 0 5269.4882 12.027009
3700 16738.602 -0.070934369 0 5269.4889 12.025288
3750 16737.731 0.20706559 0 5269.4927 12.061948
3800 16738.578 -0.05582043 0 5269.4965 12.035665
3850 16738.471 -0.016307928 0 5269.5024 12.035302
3900 16738.449 -0.0058182199 0 5269.5059 12.035401
3950 16738.439 -0.0012027325 0 5269.5074 12.035461
4000 16738.436 -0.00020698452 0 5269.5075 12.035469
4050 16738.437 0 0 5269.5078 12.035454
4100 16738.437 0 0 5269.508 12.035435
4150 16738.438 0 0 5269.5081 12.035426
4200 16738.438 0 0 5269.5083 12.035432
4250 16738.439 0 0 5269.5085 12.035447
4300 16738.439 0 0 5269.5086 12.035463
4350 16738.44 0 0 5269.5087 12.035474
4400 16738.44 0 0 5269.5088 12.035478
4450 16738.44 0 0 5269.5089 12.035474
4500 16738.44 0 0 5269.509 12.035462
4550 16738.441 0 0 5269.5092 12.035449
4600 16738.441 0 0 5269.5093 12.035445
4650 16738.442 0 0 5269.5095 12.035451
4700 16738.442 0 0 5269.5096 12.03546
4750 16738.443 0 0 5269.5097 12.035465
4800 16738.443 0 0 5269.5098 12.035466
4850 16738.443 0 0 5269.51 12.035463
4900 16738.444 0 0 5269.5101 12.035456
4950 16738.444 0 0 5269.5102 12.035447
5000 16738.445 0 0 5269.5104 12.03544
5050 16738.445 0 0 5269.5105 12.035442
5100 16738.446 0 0 5269.5107 12.035455
5150 16738.446 0 0 5269.5108 12.03547
5200 16738.446 0 0 5269.5109 12.035479
5250 16738.447 0 0 5269.511 12.035479
5300 16738.447 0 0 5269.5111 12.03547
5350 16738.447 0 0 5269.5112 12.035454
5400 16738.448 0 0 5269.5113 12.035434
5450 16738.448 0 0 5269.5115 12.03542
5500 16738.449 0 0 5269.5117 12.035422
5550 16738.457 -0.0030919234 0 5269.5111 12.035383
5600 16738.51 -0.021618357 0 5269.5092 12.035106
5650 16738.622 -0.059214788 0 5269.507 12.035694
5700 16395.28 108.06942 0 5269.5463 24.369038
5750 16738.544 -0.033973429 0 5269.5077 12.011261
5800 16738.456 -0.0037013529 0 5269.5102 12.011675
5850 16738.451 0 0 5269.5123 12.011709
5900 16738.451 -0.0002211587 0 5269.5122 12.011687
5950 16738.452 -0.00024253348 0 5269.5124 12.011678
6000 16738.452 0 0 5269.5128 12.011688
6050 16738.453 0 0 5269.513 12.011702
6100 16738.453 0 0 5269.5131 12.011716
6150 16738.454 0 0 5269.5132 12.011725
6200 16738.454 0 0 5269.5133 12.011728
6250 16738.454 0 0 5269.5134 12.011723
6300 16738.455 0 0 5269.5135 12.011712
6350 16738.455 0 0 5269.5137 12.0117
6400 16738.456 0 0 5269.5138 12.011697
6450 16738.456 0 0 5269.514 12.011704
6500 16738.456 0 0 5269.5141 12.011714
6550 16738.457 0 0 5269.5142 12.011719
6600 16738.457 0 0 5269.5143 12.011718
6650 16738.458 0 0 5269.5144 12.011713
6700 16738.458 0 0 5269.5146 12.011705
6750 16738.459 0 0 5269.5147 12.011696
6800 16738.459 0 0 5269.5149 12.01169
6850 16738.46 0 0 5269.515 12.011695
6900 16738.46 0 0 5269.5152 12.01171
6950 16738.46 0 0 5269.5153 12.011726
7000 16738.461 0 0 5269.5154 12.011736
7050 16738.461 0 0 5269.5155 12.011737
7100 16738.461 0 0 5269.5155 12.011728
7150 16738.461 0 0 5269.5156 12.011712
7200 16738.462 0 0 5269.5158 12.011691
7250 16738.463 0 0 5269.516 12.011676
7300 16738.463 0 0 5269.5162 12.011677
7350 16738.464 0 0 5269.5164 12.011693
7400 16738.464 0 0 5269.5165 12.011713
7450 16738.465 0 0 5269.5166 12.011729
7500 16738.465 0 0 5269.5167 12.011736
7550 16738.465 0 0 5269.5168 12.011734
7600 16738.465 0 0 5269.5168 12.011722
7650 16738.466 0 0 5269.517 12.011704
7700 16738.466 0 0 5269.5171 12.011687
7750 16738.467 0 0 5269.5173 12.011681
7800 16738.467 0 0 5269.5175 12.011687
7850 16738.468 0 0 5269.5176 12.0117
7900 16738.468 0 0 5269.5178 12.011712
7950 16738.469 0 0 5269.5179 12.011721
8000 16738.469 0 0 5269.518 12.011724
8050 16738.469 0 0 5269.5181 12.01172
8100 16738.47 0 0 5269.5182 12.011709
8150 16738.47 0 0 5269.5183 12.0117
8200 16738.47 0 0 5269.5185 12.0117
8250 16738.471 0 0 5269.5186 12.011709
8300 16738.471 0 0 5269.5187 12.011719
8350 16738.472 0 0 5269.5189 12.011723
8400 16738.472 0 0 5269.519 12.01172
8450 16738.473 -0.00039690669 0 5269.5189 12.011706
8500 16738.481 -0.0034646805 0 5269.5182 12.011643
8550 16738.483 -0.0045307408 0 5269.5178 12.011621
8600 16738.474 -0.00076532808 0 5269.5189 12.011681
8650 16738.474 0 0 5269.5197 12.011699
8700 16738.475 0 0 5269.5199 12.011715
8750 16738.475 0 0 5269.52 12.011732
8800 16738.475 0 0 5269.52 12.011743
8850 16738.476 0 0 5269.5201 12.011744
8900 16738.476 0 0 5269.5202 12.011735
8950 16738.476 0 0 5269.5203 12.011719
9000 16738.477 0 0 5269.5205 12.011698
9050 16738.477 0 0 5269.5206 12.011683
9100 16738.478 0 0 5269.5208 12.011684
9150 16738.479 0 0 5269.521 12.011701
9200 16738.479 0 0 5269.5212 12.011722
9250 16738.479 0 0 5269.5213 12.011738
9300 16738.48 0 0 5269.5214 12.011746
9350 16738.48 0 0 5269.5214 12.011744
9400 16738.48 0 0 5269.5215 12.011732
9450 16738.48 0 0 5269.5216 12.011715
9500 16738.481 -0.00037652431 0 5269.5216 12.011692
9550 16738.493 -0.0053156156 0 5269.5203 12.011611
9600 16738.549 -0.026814366 0 5269.5163 12.011415
9650 16738.765 -0.10191522 0 5269.5092 12.011013
9700 16735.041 1.0589875 0 5269.4979 12.062708
9750 16738.013 0.13550135 0 5269.5101 11.407245
9800 16738.512 -0.01162033 0 5269.5201 11.394973
9850 16738.489 -0.00067270544 0 5269.5237 11.395098
9900 16738.489 -0.00024984555 0 5269.5242 11.395084
9950 16738.49 0 0 5269.5245 11.395076
10000 16738.49 0 0 5269.5246 11.395075
Loop time of 0.159025 on 1 procs for 10000 steps with 81 atoms
Performance: 543312.198 tau/day, 62883.356 timesteps/s, 5.094 Matom-step/s
98.3% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0094515 | 0.0094515 | 0.0094515 | 0.0 | 5.94
Bond | 0.00045015 | 0.00045015 | 0.00045015 | 0.0 | 0.28
Neigh | 0.066186 | 0.066186 | 0.066186 | 0.0 | 41.62
Comm | 0.0097819 | 0.0097819 | 0.0097819 | 0.0 | 6.15
Output | 0.0021947 | 0.0021947 | 0.0021947 | 0.0 | 1.38
Modify | 0.062923 | 0.062923 | 0.062923 | 0.0 | 39.57
Other | | 0.008038 | | | 5.05
Nlocal: 81 ave 81 max 81 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 84 ave 84 max 84 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0
Ave special neighs/atom = 0
Neighbor list builds = 1552
Dangerous builds = 0
Total wall time: 0:00:00

321
examples/rigid/log.25Mar24.rigid.small.g++.4
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@ -1,321 +0,0 @@
LAMMPS (7 Feb 2024 - Development - patch_7Feb2024_update1-306-gf3391199e7-modified)
using 1 OpenMP thread(s) per MPI task
# Simple rigid body system
units lj
atom_style bond
pair_style lj/cut 2.5
read_data data.rigid.small
Reading data file ...
orthogonal box = (-12 -12 -12) to (12 12 12)
1 by 2 by 2 MPI processor grid
reading atoms ...
81 atoms
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
0 = max # of 1-2 neighbors
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
1 = max # of special neighbors
special bonds CPU = 0.000 seconds
read_data CPU = 0.001 seconds
velocity all create 100.0 4928459
# unconnected bodies
group clump1 id <> 1 9
9 atoms in group clump1
group clump2 id <> 10 18
9 atoms in group clump2
group clump3 id <> 19 27
9 atoms in group clump3
group clump4 id <> 28 36
9 atoms in group clump4
group clump5 id <> 37 45
9 atoms in group clump5
group clump6 id <> 46 54
9 atoms in group clump6
group clump7 id <> 55 63
9 atoms in group clump7
group clump8 id <> 64 72
9 atoms in group clump8
group clump9 id <> 73 81
9 atoms in group clump9
fix 1 all rigid/small molecule
create bodies CPU = 0.000 seconds
9 rigid bodies with 81 atoms
1.2247449 = max distance from body owner to body atom
neigh_modify exclude group clump1 clump1
neigh_modify exclude group clump2 clump2
neigh_modify exclude group clump3 clump3
neigh_modify exclude group clump4 clump4
neigh_modify exclude group clump5 clump5
neigh_modify exclude group clump6 clump6
neigh_modify exclude group clump7 clump7
neigh_modify exclude group clump8 clump8
neigh_modify exclude group clump9 clump9
thermo 100
#dump 1 all atom 50 dump.rigid
#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 2 pad 5
#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 3 pad 5
timestep 0.0001
thermo 50
run 10000
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4, bins = 18 18 18
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 8.892 | 8.94 | 9.049 Mbytes
Step Temp E_pair E_mol TotEng Press
0 115.29439 5235.9179 0 5272.2142 -2.7403788
50 14910.685 571.71558 0 5265.82 32.006171
100 16298.442 136.66184 0 5267.653 16.444229
150 16682.606 17.490511 0 5269.4219 14.900344
200 16733.929 1.372872 0 5269.4617 14.569267
250 16738.853 -0.15252816 0 5269.4864 14.496404
300 16738.588 -0.055171335 0 5269.5002 14.496025
350 16738.492 -0.017444677 0 5269.5077 14.496446
400 16738.464 -0.0060102023 0 5269.5104 14.496618
450 16738.455 -0.0012713351 0 5269.5124 14.496701
500 16738.455 -0.00081068621 0 5269.5128 14.496709
550 16738.455 -0.00083203497 0 5269.5129 14.496707
600 16738.455 -0.00058355356 0 5269.5131 14.496709
650 16738.455 -0.00047226704 0 5269.5131 14.496708
700 16738.455 0 0 5269.5136 14.496713
750 16738.455 0 0 5269.5136 14.49671
800 16738.455 0 0 5269.5137 14.496709
850 16738.455 0 0 5269.5137 14.49671
900 16738.456 0 0 5269.5138 14.496713
950 16738.462 -0.0035323872 0 5269.5122 14.496671
1000 16738.586 -0.051135144 0 5269.5036 14.496229
1050 16737.358 0.32995057 0 5269.4981 14.525763
1100 16737.892 0.16210246 0 5269.4984 14.531983
1150 16738.703 -0.089235095 0 5269.5025 14.509899
1200 16738.466 -0.0075446243 0 5269.5096 14.510615
1250 16738.456 0 0 5269.514 14.510704
1300 16738.457 0 0 5269.5141 14.510701
1350 16738.457 0 0 5269.5141 14.510699
1400 16738.457 -0.00044736511 0 5269.5138 14.510693
1450 16738.458 -0.0010971179 0 5269.5134 14.510687
1500 16738.458 -0.00057885428 0 5269.5139 14.510698
1550 16738.457 0 0 5269.5143 14.51071
1600 16738.457 0 0 5269.5144 14.510712
1650 16738.457 0 0 5269.5144 14.510712
1700 16738.458 0 0 5269.5144 14.51071
1750 16738.458 0 0 5269.5145 14.510708
1800 16738.458 0 0 5269.5145 14.510706
1850 16738.458 0 0 5269.5146 14.510705
1900 16738.458 0 0 5269.5146 14.510706
1950 16738.465 -0.0031733615 0 5269.5134 14.510659
2000 16738.491 -0.013255268 0 5269.5117 14.510532
2050 16738.556 -0.0365811 0 5269.5087 14.51029
2100 16738.633 -0.063209659 0 5269.5065 14.510219
2150 16738.607 -0.05601761 0 5269.5055 14.510231
2200 16738.557 -0.038423032 0 5269.5072 14.510404
2250 16738.515 -0.023709918 0 5269.5088 14.510539
2300 16738.489 -0.013249035 0 5269.5111 14.510621
2350 16738.468 -0.0045563719 0 5269.5131 14.510714
2400 16738.46 -0.00052194273 0 5269.5146 14.510771
2450 16738.464 -0.0023259756 0 5269.514 14.510746
2500 16738.468 -0.0051929186 0 5269.5127 14.510731
2550 16738.581 -0.044940117 0 5269.5085 14.510315
2600 16738.427 -7.9722842e-05 0 5269.5046 14.510657
2650 16733.017 1.705148 0 5269.5067 14.596295
2700 16738.761 -0.10614946 0 5269.5038 14.499584
2750 16733.973 1.4038179 0 5269.5064 14.598107
2800 16738.585 -0.046813448 0 5269.5076 14.511073
2850 16738.487 -0.012558719 0 5269.5111 14.510111
2900 16738.465 -0.0026252725 0 5269.514 14.510277
2950 16738.476 -0.0082220764 0 5269.512 14.510223
3000 16738.66 -0.071284779 0 5269.507 14.509758
3050 16715.332 7.2419351 0 5269.476 14.870305
3100 16653.226 26.818761 0 5269.5009 14.496764
3150 16739.351 -0.30690375 0 5269.4886 13.643904
3200 16733.238 1.6025328 0 5269.4737 12.016934
3250 16734.374 1.2554428 0 5269.4841 11.963561
3300 16732.156 1.9585967 0 5269.4893 12.234024
3350 16738.655 -0.079693236 0 5269.497 12.092757
3400 16738.543 -0.042215005 0 5269.4991 12.092809
3450 16738.591 -0.059327511 0 5269.4972 12.092536
3500 16738.759 -0.11761245 0 5269.4918 12.09203
3550 16713.405 7.846062 0 5269.4737 12.389816
3600 16734.939 1.0821936 0 5269.4891 12.173591
3650 16738.808 -0.13663194 0 5269.4882 12.027009
3700 16738.602 -0.070934367 0 5269.4889 12.025288
3750 16737.731 0.20706557 0 5269.4927 12.061948
3800 16738.578 -0.05582043 0 5269.4965 12.035665
3850 16738.471 -0.016307928 0 5269.5024 12.035302
3900 16738.449 -0.0058182199 0 5269.5059 12.035401
3950 16738.439 -0.0012027325 0 5269.5074 12.035461
4000 16738.436 -0.00020698452 0 5269.5075 12.035469
4050 16738.437 0 0 5269.5078 12.035454
4100 16738.437 0 0 5269.508 12.035435
4150 16738.438 0 0 5269.5081 12.035426
4200 16738.438 0 0 5269.5083 12.035432
4250 16738.439 0 0 5269.5085 12.035447
4300 16738.439 0 0 5269.5086 12.035463
4350 16738.44 0 0 5269.5087 12.035474
4400 16738.44 0 0 5269.5088 12.035478
4450 16738.44 0 0 5269.5089 12.035474
4500 16738.44 0 0 5269.509 12.035462
4550 16738.441 0 0 5269.5092 12.035449
4600 16738.441 0 0 5269.5093 12.035445
4650 16738.442 0 0 5269.5095 12.035451
4700 16738.442 0 0 5269.5096 12.03546
4750 16738.443 0 0 5269.5097 12.035465
4800 16738.443 0 0 5269.5098 12.035466
4850 16738.443 0 0 5269.51 12.035463
4900 16738.444 0 0 5269.5101 12.035456
4950 16738.444 0 0 5269.5102 12.035447
5000 16738.445 0 0 5269.5104 12.03544
5050 16738.445 0 0 5269.5105 12.035442
5100 16738.446 0 0 5269.5107 12.035455
5150 16738.446 0 0 5269.5108 12.03547
5200 16738.446 0 0 5269.5109 12.035479
5250 16738.447 0 0 5269.511 12.035479
5300 16738.447 0 0 5269.5111 12.03547
5350 16738.447 0 0 5269.5112 12.035454
5400 16738.448 0 0 5269.5113 12.035434
5450 16738.448 0 0 5269.5115 12.03542
5500 16738.449 0 0 5269.5117 12.035422
5550 16738.457 -0.0030919234 0 5269.5111 12.035383
5600 16738.51 -0.021618357 0 5269.5092 12.035106
5650 16738.622 -0.059214788 0 5269.507 12.035694
5700 16395.28 108.06942 0 5269.5463 24.369038
5750 16738.544 -0.033973429 0 5269.5077 12.011261
5800 16738.456 -0.0037013529 0 5269.5102 12.011675
5850 16738.451 0 0 5269.5123 12.011709
5900 16738.451 -0.00022115871 0 5269.5122 12.011687
5950 16738.452 -0.00024253349 0 5269.5124 12.011678
6000 16738.452 0 0 5269.5128 12.011688
6050 16738.453 0 0 5269.513 12.011702
6100 16738.453 0 0 5269.5131 12.011716
6150 16738.454 0 0 5269.5132 12.011725
6200 16738.454 0 0 5269.5133 12.011728
6250 16738.454 0 0 5269.5134 12.011723
6300 16738.455 0 0 5269.5135 12.011712
6350 16738.455 0 0 5269.5137 12.0117
6400 16738.456 0 0 5269.5138 12.011697
6450 16738.456 0 0 5269.514 12.011704
6500 16738.456 0 0 5269.5141 12.011714
6550 16738.457 0 0 5269.5142 12.011719
6600 16738.457 0 0 5269.5143 12.011718
6650 16738.458 0 0 5269.5144 12.011713
6700 16738.458 0 0 5269.5146 12.011705
6750 16738.459 0 0 5269.5147 12.011696
6800 16738.459 0 0 5269.5149 12.01169
6850 16738.46 0 0 5269.515 12.011695
6900 16738.46 0 0 5269.5152 12.01171
6950 16738.46 0 0 5269.5153 12.011726
7000 16738.461 0 0 5269.5154 12.011736
7050 16738.461 0 0 5269.5155 12.011737
7100 16738.461 0 0 5269.5155 12.011728
7150 16738.461 0 0 5269.5156 12.011712
7200 16738.462 0 0 5269.5158 12.011691
7250 16738.463 0 0 5269.516 12.011676
7300 16738.463 0 0 5269.5162 12.011677
7350 16738.464 0 0 5269.5164 12.011693
7400 16738.464 0 0 5269.5165 12.011713
7450 16738.465 0 0 5269.5166 12.011729
7500 16738.465 0 0 5269.5167 12.011736
7550 16738.465 0 0 5269.5168 12.011734
7600 16738.465 0 0 5269.5168 12.011722
7650 16738.466 0 0 5269.517 12.011704
7700 16738.466 0 0 5269.5171 12.011687
7750 16738.467 0 0 5269.5173 12.011681
7800 16738.467 0 0 5269.5175 12.011687
7850 16738.468 0 0 5269.5176 12.0117
7900 16738.468 0 0 5269.5178 12.011712
7950 16738.469 0 0 5269.5179 12.011721
8000 16738.469 0 0 5269.518 12.011724
8050 16738.469 0 0 5269.5181 12.01172
8100 16738.47 0 0 5269.5182 12.011709
8150 16738.47 0 0 5269.5183 12.0117
8200 16738.47 0 0 5269.5185 12.0117
8250 16738.471 0 0 5269.5186 12.011709
8300 16738.471 0 0 5269.5187 12.011719
8350 16738.472 0 0 5269.5189 12.011723
8400 16738.472 0 0 5269.519 12.01172
8450 16738.473 -0.00039690662 0 5269.5189 12.011706
8500 16738.481 -0.0034646802 0 5269.5182 12.011643
8550 16738.483 -0.0045307409 0 5269.5178 12.011621
8600 16738.474 -0.00076532814 0 5269.5189 12.011681
8650 16738.474 0 0 5269.5197 12.011699
8700 16738.475 0 0 5269.5199 12.011715
8750 16738.475 0 0 5269.52 12.011732
8800 16738.475 0 0 5269.52 12.011743
8850 16738.476 0 0 5269.5201 12.011744
8900 16738.476 0 0 5269.5202 12.011735
8950 16738.476 0 0 5269.5203 12.011719
9000 16738.477 0 0 5269.5205 12.011698
9050 16738.477 0 0 5269.5206 12.011683
9100 16738.478 0 0 5269.5208 12.011684
9150 16738.479 0 0 5269.521 12.011701
9200 16738.479 0 0 5269.5212 12.011722
9250 16738.479 0 0 5269.5213 12.011738
9300 16738.48 0 0 5269.5214 12.011746
9350 16738.48 0 0 5269.5214 12.011744
9400 16738.48 0 0 5269.5215 12.011732
9450 16738.48 0 0 5269.5216 12.011715
9500 16738.481 -0.0003765244 0 5269.5216 12.011692
9550 16738.493 -0.0053156163 0 5269.5203 12.011611
9600 16738.549 -0.026814371 0 5269.5163 12.011415
9650 16738.765 -0.10191524 0 5269.5092 12.011013
9700 16735.041 1.0589896 0 5269.4979 12.062708
9750 16738.013 0.13550091 0 5269.5101 11.407245
9800 16738.512 -0.011620327 0 5269.5201 11.394974
9850 16738.489 -0.00067270523 0 5269.5237 11.395098
9900 16738.489 -0.00024984566 0 5269.5242 11.395085
9950 16738.49 0 0 5269.5245 11.395076
10000 16738.49 0 0 5269.5246 11.395075
Loop time of 0.200426 on 4 procs for 10000 steps with 81 atoms
Performance: 431082.236 tau/day, 49893.777 timesteps/s, 4.041 Matom-step/s
97.6% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.001863 | 0.0024669 | 0.0029246 | 0.8 | 1.23
Bond | 0.00033475 | 0.00034422 | 0.00035273 | 0.0 | 0.17
Neigh | 0.016097 | 0.017035 | 0.018935 | 0.9 | 8.50
Comm | 0.066051 | 0.06822 | 0.070253 | 0.7 | 34.04
Output | 0.0020466 | 0.0021927 | 0.0026005 | 0.5 | 1.09
Modify | 0.094972 | 0.096687 | 0.098173 | 0.4 | 48.24
Other | | 0.01348 | | | 6.73
Nlocal: 20.25 ave 37 max 3 min
Histogram: 1 0 0 1 0 0 0 1 0 1
Nghost: 27.25 ave 48 max 13 min
Histogram: 1 0 0 2 0 0 0 0 0 1
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0
Ave special neighs/atom = 0
Neighbor list builds = 1552
Dangerous builds = 0
Total wall time: 0:00:00

322
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@ -1,322 +0,0 @@
LAMMPS (7 Feb 2024 - Development - patch_7Feb2024_update1-306-gf3391199e7-modified)
using 1 OpenMP thread(s) per MPI task
# Simple rigid body system
units lj
atom_style bond
pair_style lj/cut 2.5
read_data data.rigid.small
Reading data file ...
orthogonal box = (-12 -12 -12) to (12 12 12)
1 by 1 by 1 MPI processor grid
reading atoms ...
81 atoms
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
0 = max # of 1-2 neighbors
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
1 = max # of special neighbors
special bonds CPU = 0.000 seconds
read_data CPU = 0.003 seconds
velocity all create 100.0 4928459
# unconnected bodies
group clump1 id <> 1 9
9 atoms in group clump1
group clump2 id <> 10 18
9 atoms in group clump2
group clump3 id <> 19 27
9 atoms in group clump3
group clump4 id <> 28 36
9 atoms in group clump4
group clump5 id <> 37 45
9 atoms in group clump5
group clump6 id <> 46 54
9 atoms in group clump6
group clump7 id <> 55 63
9 atoms in group clump7
group clump8 id <> 64 72
9 atoms in group clump8
group clump9 id <> 73 81
9 atoms in group clump9
fix 1 all rigid/small molecule infile bodyinfo.dat
create bodies CPU = 0.000 seconds
9 rigid bodies with 81 atoms
1.2247449 = max distance from body owner to body atom
neigh_modify exclude group clump1 clump1
neigh_modify exclude group clump2 clump2
neigh_modify exclude group clump3 clump3
neigh_modify exclude group clump4 clump4
neigh_modify exclude group clump5 clump5
neigh_modify exclude group clump6 clump6
neigh_modify exclude group clump7 clump7
neigh_modify exclude group clump8 clump8
neigh_modify exclude group clump9 clump9
thermo 100
#dump 1 all atom 50 dump.rigid
#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 2 pad 5
#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 3 pad 5
timestep 0.0001
thermo 50
run 10000
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4, bins = 18 18 18
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d
bin: standard
Reading rigid body data for 4 bodies from file bodyinfo.dat
Per MPI rank memory allocation (min/avg/max) = 9.034 | 9.034 | 9.034 Mbytes
Step Temp E_pair E_mol TotEng Press
0 115.29439 5235.9179 0 5272.2142 -2.7403788
50 14910.685 571.71558 0 5265.82 32.006171
100 16298.442 136.66184 0 5267.653 16.444229
150 16682.606 17.490511 0 5269.4219 14.900344
200 16733.929 1.372872 0 5269.4617 14.569267
250 16738.853 -0.15252816 0 5269.4864 14.496404
300 16738.588 -0.055171335 0 5269.5002 14.496025
350 16738.492 -0.017444677 0 5269.5077 14.496446
400 16738.464 -0.0060102023 0 5269.5104 14.496618
450 16738.455 -0.0012713351 0 5269.5124 14.496701
500 16738.455 -0.00081068621 0 5269.5128 14.496709
550 16738.455 -0.00083203497 0 5269.5129 14.496707
600 16738.455 -0.00058355356 0 5269.5131 14.496709
650 16738.455 -0.00047226704 0 5269.5131 14.496708
700 16738.455 0 0 5269.5136 14.496713
750 16738.455 0 0 5269.5136 14.49671
800 16738.455 0 0 5269.5137 14.496709
850 16738.455 0 0 5269.5137 14.49671
900 16738.456 0 0 5269.5138 14.496713
950 16738.462 -0.0035323872 0 5269.5122 14.496671
1000 16738.586 -0.051135144 0 5269.5036 14.496229
1050 16737.358 0.32995057 0 5269.4981 14.525763
1100 16737.892 0.16210246 0 5269.4984 14.531983
1150 16738.703 -0.089235095 0 5269.5025 14.509899
1200 16738.466 -0.0075446243 0 5269.5096 14.510615
1250 16738.456 0 0 5269.514 14.510704
1300 16738.457 0 0 5269.5141 14.510701
1350 16738.457 0 0 5269.5141 14.510699
1400 16738.457 -0.00044736511 0 5269.5138 14.510693
1450 16738.458 -0.0010971179 0 5269.5134 14.510687
1500 16738.458 -0.00057885428 0 5269.5139 14.510698
1550 16738.457 0 0 5269.5143 14.51071
1600 16738.457 0 0 5269.5144 14.510712
1650 16738.457 0 0 5269.5144 14.510712
1700 16738.458 0 0 5269.5144 14.51071
1750 16738.458 0 0 5269.5145 14.510708
1800 16738.458 0 0 5269.5145 14.510706
1850 16738.458 0 0 5269.5146 14.510705
1900 16738.458 0 0 5269.5146 14.510706
1950 16738.465 -0.0031733615 0 5269.5134 14.510659
2000 16738.491 -0.013255268 0 5269.5117 14.510532
2050 16738.556 -0.0365811 0 5269.5087 14.51029
2100 16738.633 -0.063209659 0 5269.5065 14.510219
2150 16738.607 -0.05601761 0 5269.5055 14.510231
2200 16738.557 -0.038423032 0 5269.5072 14.510404
2250 16738.515 -0.023709918 0 5269.5088 14.510539
2300 16738.489 -0.013249035 0 5269.5111 14.510621
2350 16738.468 -0.0045563719 0 5269.5131 14.510714
2400 16738.46 -0.00052194273 0 5269.5146 14.510771
2450 16738.464 -0.0023259756 0 5269.514 14.510746
2500 16738.468 -0.0051929186 0 5269.5127 14.510731
2550 16738.581 -0.044940117 0 5269.5085 14.510315
2600 16738.427 -7.9722875e-05 0 5269.5046 14.510657
2650 16733.017 1.7051479 0 5269.5067 14.596295
2700 16738.761 -0.10614946 0 5269.5038 14.499584
2750 16733.973 1.4038179 0 5269.5064 14.598107
2800 16738.585 -0.046813448 0 5269.5076 14.511073
2850 16738.487 -0.012558719 0 5269.5111 14.510111
2900 16738.465 -0.0026252725 0 5269.514 14.510277
2950 16738.476 -0.0082220764 0 5269.512 14.510223
3000 16738.66 -0.071284779 0 5269.507 14.509758
3050 16715.332 7.2419352 0 5269.476 14.870305
3100 16653.226 26.818761 0 5269.5009 14.496764
3150 16739.351 -0.30690375 0 5269.4886 13.643904
3200 16733.238 1.6025328 0 5269.4737 12.016934
3250 16734.374 1.2554429 0 5269.4841 11.963561
3300 16732.156 1.9585967 0 5269.4893 12.234024
3350 16738.655 -0.079693236 0 5269.497 12.092757
3400 16738.543 -0.042215005 0 5269.4991 12.092809
3450 16738.591 -0.059327511 0 5269.4972 12.092536
3500 16738.759 -0.11761245 0 5269.4918 12.09203
3550 16713.405 7.8460621 0 5269.4737 12.389816
3600 16734.939 1.0821936 0 5269.4891 12.173591
3650 16738.808 -0.13663194 0 5269.4882 12.027009
3700 16738.602 -0.070934368 0 5269.4889 12.025288
3750 16737.731 0.20706559 0 5269.4927 12.061948
3800 16738.578 -0.05582043 0 5269.4965 12.035665
3850 16738.471 -0.016307928 0 5269.5024 12.035302
3900 16738.449 -0.0058182199 0 5269.5059 12.035401
3950 16738.439 -0.0012027325 0 5269.5074 12.035461
4000 16738.436 -0.00020698452 0 5269.5075 12.035469
4050 16738.437 0 0 5269.5078 12.035454
4100 16738.437 0 0 5269.508 12.035435
4150 16738.438 0 0 5269.5081 12.035426
4200 16738.438 0 0 5269.5083 12.035432
4250 16738.439 0 0 5269.5085 12.035447
4300 16738.439 0 0 5269.5086 12.035463
4350 16738.44 0 0 5269.5087 12.035474
4400 16738.44 0 0 5269.5088 12.035478
4450 16738.44 0 0 5269.5089 12.035474
4500 16738.44 0 0 5269.509 12.035462
4550 16738.441 0 0 5269.5092 12.035449
4600 16738.441 0 0 5269.5093 12.035445
4650 16738.442 0 0 5269.5095 12.035451
4700 16738.442 0 0 5269.5096 12.03546
4750 16738.443 0 0 5269.5097 12.035465
4800 16738.443 0 0 5269.5098 12.035466
4850 16738.443 0 0 5269.51 12.035463
4900 16738.444 0 0 5269.5101 12.035456
4950 16738.444 0 0 5269.5102 12.035447
5000 16738.445 0 0 5269.5104 12.03544
5050 16738.445 0 0 5269.5105 12.035442
5100 16738.446 0 0 5269.5107 12.035455
5150 16738.446 0 0 5269.5108 12.03547
5200 16738.446 0 0 5269.5109 12.035479
5250 16738.447 0 0 5269.511 12.035479
5300 16738.447 0 0 5269.5111 12.03547
5350 16738.447 0 0 5269.5112 12.035454
5400 16738.448 0 0 5269.5113 12.035434
5450 16738.448 0 0 5269.5115 12.03542
5500 16738.449 0 0 5269.5117 12.035422
5550 16738.457 -0.0030919234 0 5269.5111 12.035383
5600 16738.51 -0.021618357 0 5269.5092 12.035106
5650 16738.622 -0.059214788 0 5269.507 12.035694
5700 16395.28 108.06942 0 5269.5463 24.369038
5750 16738.544 -0.033973429 0 5269.5077 12.011261
5800 16738.456 -0.0037013529 0 5269.5102 12.011675
5850 16738.451 0 0 5269.5123 12.011709
5900 16738.451 -0.0002211587 0 5269.5122 12.011687
5950 16738.452 -0.00024253348 0 5269.5124 12.011678
6000 16738.452 0 0 5269.5128 12.011688
6050 16738.453 0 0 5269.513 12.011702
6100 16738.453 0 0 5269.5131 12.011716
6150 16738.454 0 0 5269.5132 12.011725
6200 16738.454 0 0 5269.5133 12.011728
6250 16738.454 0 0 5269.5134 12.011723
6300 16738.455 0 0 5269.5135 12.011712
6350 16738.455 0 0 5269.5137 12.0117
6400 16738.456 0 0 5269.5138 12.011697
6450 16738.456 0 0 5269.514 12.011704
6500 16738.456 0 0 5269.5141 12.011714
6550 16738.457 0 0 5269.5142 12.011719
6600 16738.457 0 0 5269.5143 12.011718
6650 16738.458 0 0 5269.5144 12.011713
6700 16738.458 0 0 5269.5146 12.011705
6750 16738.459 0 0 5269.5147 12.011696
6800 16738.459 0 0 5269.5149 12.01169
6850 16738.46 0 0 5269.515 12.011695
6900 16738.46 0 0 5269.5152 12.01171
6950 16738.46 0 0 5269.5153 12.011726
7000 16738.461 0 0 5269.5154 12.011736
7050 16738.461 0 0 5269.5155 12.011737
7100 16738.461 0 0 5269.5155 12.011728
7150 16738.461 0 0 5269.5156 12.011712
7200 16738.462 0 0 5269.5158 12.011691
7250 16738.463 0 0 5269.516 12.011676
7300 16738.463 0 0 5269.5162 12.011677
7350 16738.464 0 0 5269.5164 12.011693
7400 16738.464 0 0 5269.5165 12.011713
7450 16738.465 0 0 5269.5166 12.011729
7500 16738.465 0 0 5269.5167 12.011736
7550 16738.465 0 0 5269.5168 12.011734
7600 16738.465 0 0 5269.5168 12.011722
7650 16738.466 0 0 5269.517 12.011704
7700 16738.466 0 0 5269.5171 12.011687
7750 16738.467 0 0 5269.5173 12.011681
7800 16738.467 0 0 5269.5175 12.011687
7850 16738.468 0 0 5269.5176 12.0117
7900 16738.468 0 0 5269.5178 12.011712
7950 16738.469 0 0 5269.5179 12.011721
8000 16738.469 0 0 5269.518 12.011724
8050 16738.469 0 0 5269.5181 12.01172
8100 16738.47 0 0 5269.5182 12.011709
8150 16738.47 0 0 5269.5183 12.0117
8200 16738.47 0 0 5269.5185 12.0117
8250 16738.471 0 0 5269.5186 12.011709
8300 16738.471 0 0 5269.5187 12.011719
8350 16738.472 0 0 5269.5189 12.011723
8400 16738.472 0 0 5269.519 12.01172
8450 16738.473 -0.00039690667 0 5269.5189 12.011706
8500 16738.481 -0.0034646804 0 5269.5182 12.011643
8550 16738.483 -0.0045307408 0 5269.5178 12.011621
8600 16738.474 -0.00076532809 0 5269.5189 12.011681
8650 16738.474 0 0 5269.5197 12.011699
8700 16738.475 0 0 5269.5199 12.011715
8750 16738.475 0 0 5269.52 12.011732
8800 16738.475 0 0 5269.52 12.011743
8850 16738.476 0 0 5269.5201 12.011744
8900 16738.476 0 0 5269.5202 12.011735
8950 16738.476 0 0 5269.5203 12.011719
9000 16738.477 0 0 5269.5205 12.011698
9050 16738.477 0 0 5269.5206 12.011683
9100 16738.478 0 0 5269.5208 12.011684
9150 16738.479 0 0 5269.521 12.011701
9200 16738.479 0 0 5269.5212 12.011722
9250 16738.479 0 0 5269.5213 12.011738
9300 16738.48 0 0 5269.5214 12.011746
9350 16738.48 0 0 5269.5214 12.011744
9400 16738.48 0 0 5269.5215 12.011732
9450 16738.48 0 0 5269.5216 12.011715
9500 16738.481 -0.00037652433 0 5269.5216 12.011692
9550 16738.493 -0.0053156155 0 5269.5203 12.011611
9600 16738.549 -0.026814367 0 5269.5163 12.011415
9650 16738.765 -0.10191522 0 5269.5092 12.011013
9700 16735.041 1.0589876 0 5269.4979 12.062708
9750 16738.013 0.13550105 0 5269.5101 11.407245
9800 16738.512 -0.011620331 0 5269.5201 11.394973
9850 16738.489 -0.00067270584 0 5269.5237 11.395098
9900 16738.489 -0.00024984576 0 5269.5242 11.395084
9950 16738.49 0 0 5269.5245 11.395076
10000 16738.49 0 0 5269.5246 11.395074
Loop time of 0.154542 on 1 procs for 10000 steps with 81 atoms
Performance: 559072.380 tau/day, 64707.451 timesteps/s, 5.241 Matom-step/s
98.6% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0094322 | 0.0094322 | 0.0094322 | 0.0 | 6.10
Bond | 0.00037544 | 0.00037544 | 0.00037544 | 0.0 | 0.24
Neigh | 0.062048 | 0.062048 | 0.062048 | 0.0 | 40.15
Comm | 0.0095533 | 0.0095533 | 0.0095533 | 0.0 | 6.18
Output | 0.0022247 | 0.0022247 | 0.0022247 | 0.0 | 1.44
Modify | 0.06281 | 0.06281 | 0.06281 | 0.0 | 40.64
Other | | 0.008098 | | | 5.24
Nlocal: 81 ave 81 max 81 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 84 ave 84 max 84 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0
Ave special neighs/atom = 0
Neighbor list builds = 1552
Dangerous builds = 0
Total wall time: 0:00:00

322
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@ -1,322 +0,0 @@
LAMMPS (7 Feb 2024 - Development - patch_7Feb2024_update1-306-gf3391199e7-modified)
using 1 OpenMP thread(s) per MPI task
# Simple rigid body system
units lj
atom_style bond
pair_style lj/cut 2.5
read_data data.rigid.small
Reading data file ...
orthogonal box = (-12 -12 -12) to (12 12 12)
1 by 2 by 2 MPI processor grid
reading atoms ...
81 atoms
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
0 = max # of 1-2 neighbors
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
1 = max # of special neighbors
special bonds CPU = 0.000 seconds
read_data CPU = 0.001 seconds
velocity all create 100.0 4928459
# unconnected bodies
group clump1 id <> 1 9
9 atoms in group clump1
group clump2 id <> 10 18
9 atoms in group clump2
group clump3 id <> 19 27
9 atoms in group clump3
group clump4 id <> 28 36
9 atoms in group clump4
group clump5 id <> 37 45
9 atoms in group clump5
group clump6 id <> 46 54
9 atoms in group clump6
group clump7 id <> 55 63
9 atoms in group clump7
group clump8 id <> 64 72
9 atoms in group clump8
group clump9 id <> 73 81
9 atoms in group clump9
fix 1 all rigid/small molecule infile bodyinfo.dat
create bodies CPU = 0.000 seconds
9 rigid bodies with 81 atoms
1.2247449 = max distance from body owner to body atom
neigh_modify exclude group clump1 clump1
neigh_modify exclude group clump2 clump2
neigh_modify exclude group clump3 clump3
neigh_modify exclude group clump4 clump4
neigh_modify exclude group clump5 clump5
neigh_modify exclude group clump6 clump6
neigh_modify exclude group clump7 clump7
neigh_modify exclude group clump8 clump8
neigh_modify exclude group clump9 clump9
thermo 100
#dump 1 all atom 50 dump.rigid
#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 2 pad 5
#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 3 pad 5
timestep 0.0001
thermo 50
run 10000
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4, bins = 18 18 18
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d
bin: standard
Reading rigid body data for 4 bodies from file bodyinfo.dat
Per MPI rank memory allocation (min/avg/max) = 8.892 | 8.94 | 9.049 Mbytes
Step Temp E_pair E_mol TotEng Press
0 115.29439 5235.9179 0 5272.2142 -2.7403788
50 14910.685 571.71558 0 5265.82 32.006171
100 16298.442 136.66184 0 5267.653 16.444229
150 16682.606 17.490511 0 5269.4219 14.900344
200 16733.929 1.372872 0 5269.4617 14.569267
250 16738.853 -0.15252816 0 5269.4864 14.496404
300 16738.588 -0.055171335 0 5269.5002 14.496025
350 16738.492 -0.017444677 0 5269.5077 14.496446
400 16738.464 -0.0060102023 0 5269.5104 14.496618
450 16738.455 -0.0012713351 0 5269.5124 14.496701
500 16738.455 -0.00081068621 0 5269.5128 14.496709
550 16738.455 -0.00083203497 0 5269.5129 14.496707
600 16738.455 -0.00058355356 0 5269.5131 14.496709
650 16738.455 -0.00047226704 0 5269.5131 14.496708
700 16738.455 0 0 5269.5136 14.496713
750 16738.455 0 0 5269.5136 14.49671
800 16738.455 0 0 5269.5137 14.496709
850 16738.455 0 0 5269.5137 14.49671
900 16738.456 0 0 5269.5138 14.496713
950 16738.462 -0.0035323872 0 5269.5122 14.496671
1000 16738.586 -0.051135144 0 5269.5036 14.496229
1050 16737.358 0.32995057 0 5269.4981 14.525763
1100 16737.892 0.16210246 0 5269.4984 14.531983
1150 16738.703 -0.089235095 0 5269.5025 14.509899
1200 16738.466 -0.0075446243 0 5269.5096 14.510615
1250 16738.456 0 0 5269.514 14.510704
1300 16738.457 0 0 5269.5141 14.510701
1350 16738.457 0 0 5269.5141 14.510699
1400 16738.457 -0.00044736511 0 5269.5138 14.510693
1450 16738.458 -0.0010971179 0 5269.5134 14.510687
1500 16738.458 -0.00057885428 0 5269.5139 14.510698
1550 16738.457 0 0 5269.5143 14.51071
1600 16738.457 0 0 5269.5144 14.510712
1650 16738.457 0 0 5269.5144 14.510712
1700 16738.458 0 0 5269.5144 14.51071
1750 16738.458 0 0 5269.5145 14.510708
1800 16738.458 0 0 5269.5145 14.510706
1850 16738.458 0 0 5269.5146 14.510705
1900 16738.458 0 0 5269.5146 14.510706
1950 16738.465 -0.0031733615 0 5269.5134 14.510659
2000 16738.491 -0.013255268 0 5269.5117 14.510532
2050 16738.556 -0.0365811 0 5269.5087 14.51029
2100 16738.633 -0.063209659 0 5269.5065 14.510219
2150 16738.607 -0.05601761 0 5269.5055 14.510231
2200 16738.557 -0.038423032 0 5269.5072 14.510404
2250 16738.515 -0.023709918 0 5269.5088 14.510539
2300 16738.489 -0.013249035 0 5269.5111 14.510621
2350 16738.468 -0.0045563719 0 5269.5131 14.510714
2400 16738.46 -0.00052194273 0 5269.5146 14.510771
2450 16738.464 -0.0023259756 0 5269.514 14.510746
2500 16738.468 -0.0051929186 0 5269.5127 14.510731
2550 16738.581 -0.044940117 0 5269.5085 14.510315
2600 16738.427 -7.9722864e-05 0 5269.5046 14.510657
2650 16733.017 1.7051479 0 5269.5067 14.596295
2700 16738.761 -0.10614946 0 5269.5038 14.499584
2750 16733.973 1.4038179 0 5269.5064 14.598107
2800 16738.585 -0.046813448 0 5269.5076 14.511073
2850 16738.487 -0.012558719 0 5269.5111 14.510111
2900 16738.465 -0.0026252725 0 5269.514 14.510277
2950 16738.476 -0.0082220764 0 5269.512 14.510223
3000 16738.66 -0.071284779 0 5269.507 14.509758
3050 16715.332 7.2419352 0 5269.476 14.870305
3100 16653.226 26.818761 0 5269.5009 14.496764
3150 16739.351 -0.30690375 0 5269.4886 13.643904
3200 16733.238 1.6025328 0 5269.4737 12.016934
3250 16734.374 1.2554429 0 5269.4841 11.963561
3300 16732.156 1.9585967 0 5269.4893 12.234024
3350 16738.655 -0.079693236 0 5269.497 12.092757
3400 16738.543 -0.042215005 0 5269.4991 12.092809
3450 16738.591 -0.05932751 0 5269.4972 12.092536
3500 16738.759 -0.11761245 0 5269.4918 12.09203
3550 16713.405 7.8460621 0 5269.4737 12.389816
3600 16734.939 1.0821936 0 5269.4891 12.173591
3650 16738.808 -0.13663194 0 5269.4882 12.027009
3700 16738.602 -0.070934369 0 5269.4889 12.025288
3750 16737.731 0.20706559 0 5269.4927 12.061948
3800 16738.578 -0.05582043 0 5269.4965 12.035665
3850 16738.471 -0.016307928 0 5269.5024 12.035302
3900 16738.449 -0.0058182199 0 5269.5059 12.035401
3950 16738.439 -0.0012027325 0 5269.5074 12.035461
4000 16738.436 -0.00020698452 0 5269.5075 12.035469
4050 16738.437 0 0 5269.5078 12.035454
4100 16738.437 0 0 5269.508 12.035435
4150 16738.438 0 0 5269.5081 12.035426
4200 16738.438 0 0 5269.5083 12.035432
4250 16738.439 0 0 5269.5085 12.035447
4300 16738.439 0 0 5269.5086 12.035463
4350 16738.44 0 0 5269.5087 12.035474
4400 16738.44 0 0 5269.5088 12.035478
4450 16738.44 0 0 5269.5089 12.035474
4500 16738.44 0 0 5269.509 12.035462
4550 16738.441 0 0 5269.5092 12.035449
4600 16738.441 0 0 5269.5093 12.035445
4650 16738.442 0 0 5269.5095 12.035451
4700 16738.442 0 0 5269.5096 12.03546
4750 16738.443 0 0 5269.5097 12.035465
4800 16738.443 0 0 5269.5098 12.035466
4850 16738.443 0 0 5269.51 12.035463
4900 16738.444 0 0 5269.5101 12.035456
4950 16738.444 0 0 5269.5102 12.035447
5000 16738.445 0 0 5269.5104 12.03544
5050 16738.445 0 0 5269.5105 12.035442
5100 16738.446 0 0 5269.5107 12.035455
5150 16738.446 0 0 5269.5108 12.03547
5200 16738.446 0 0 5269.5109 12.035479
5250 16738.447 0 0 5269.511 12.035479
5300 16738.447 0 0 5269.5111 12.03547
5350 16738.447 0 0 5269.5112 12.035454
5400 16738.448 0 0 5269.5113 12.035434
5450 16738.448 0 0 5269.5115 12.03542
5500 16738.449 0 0 5269.5117 12.035422
5550 16738.457 -0.0030919234 0 5269.5111 12.035383
5600 16738.51 -0.021618357 0 5269.5092 12.035106
5650 16738.622 -0.059214788 0 5269.507 12.035694
5700 16395.28 108.06942 0 5269.5463 24.369038
5750 16738.544 -0.033973429 0 5269.5077 12.011261
5800 16738.456 -0.0037013529 0 5269.5102 12.011675
5850 16738.451 0 0 5269.5123 12.011709
5900 16738.451 -0.0002211587 0 5269.5122 12.011687
5950 16738.452 -0.00024253348 0 5269.5124 12.011678
6000 16738.452 0 0 5269.5128 12.011688
6050 16738.453 0 0 5269.513 12.011702
6100 16738.453 0 0 5269.5131 12.011716
6150 16738.454 0 0 5269.5132 12.011725
6200 16738.454 0 0 5269.5133 12.011728
6250 16738.454 0 0 5269.5134 12.011723
6300 16738.455 0 0 5269.5135 12.011712
6350 16738.455 0 0 5269.5137 12.0117
6400 16738.456 0 0 5269.5138 12.011697
6450 16738.456 0 0 5269.514 12.011704
6500 16738.456 0 0 5269.5141 12.011714
6550 16738.457 0 0 5269.5142 12.011719
6600 16738.457 0 0 5269.5143 12.011718
6650 16738.458 0 0 5269.5144 12.011713
6700 16738.458 0 0 5269.5146 12.011705
6750 16738.459 0 0 5269.5147 12.011696
6800 16738.459 0 0 5269.5149 12.01169
6850 16738.46 0 0 5269.515 12.011695
6900 16738.46 0 0 5269.5152 12.01171
6950 16738.46 0 0 5269.5153 12.011726
7000 16738.461 0 0 5269.5154 12.011736
7050 16738.461 0 0 5269.5155 12.011737
7100 16738.461 0 0 5269.5155 12.011728
7150 16738.461 0 0 5269.5156 12.011712
7200 16738.462 0 0 5269.5158 12.011691
7250 16738.463 0 0 5269.516 12.011676
7300 16738.463 0 0 5269.5162 12.011677
7350 16738.464 0 0 5269.5164 12.011693
7400 16738.464 0 0 5269.5165 12.011713
7450 16738.465 0 0 5269.5166 12.011729
7500 16738.465 0 0 5269.5167 12.011736
7550 16738.465 0 0 5269.5168 12.011734
7600 16738.465 0 0 5269.5168 12.011722
7650 16738.466 0 0 5269.517 12.011704
7700 16738.466 0 0 5269.5171 12.011687
7750 16738.467 0 0 5269.5173 12.011681
7800 16738.467 0 0 5269.5175 12.011687
7850 16738.468 0 0 5269.5176 12.0117
7900 16738.468 0 0 5269.5178 12.011712
7950 16738.469 0 0 5269.5179 12.011721
8000 16738.469 0 0 5269.518 12.011724
8050 16738.469 0 0 5269.5181 12.01172
8100 16738.47 0 0 5269.5182 12.011709
8150 16738.47 0 0 5269.5183 12.0117
8200 16738.47 0 0 5269.5185 12.0117
8250 16738.471 0 0 5269.5186 12.011709
8300 16738.471 0 0 5269.5187 12.011719
8350 16738.472 0 0 5269.5189 12.011723
8400 16738.472 0 0 5269.519 12.01172
8450 16738.473 -0.00039690668 0 5269.5189 12.011706
8500 16738.481 -0.0034646805 0 5269.5182 12.011643
8550 16738.483 -0.0045307408 0 5269.5178 12.011621
8600 16738.474 -0.00076532808 0 5269.5189 12.011681
8650 16738.474 0 0 5269.5197 12.011699
8700 16738.475 0 0 5269.5199 12.011715
8750 16738.475 0 0 5269.52 12.011732
8800 16738.475 0 0 5269.52 12.011743
8850 16738.476 0 0 5269.5201 12.011744
8900 16738.476 0 0 5269.5202 12.011735
8950 16738.476 0 0 5269.5203 12.011719
9000 16738.477 0 0 5269.5205 12.011698
9050 16738.477 0 0 5269.5206 12.011683
9100 16738.478 0 0 5269.5208 12.011684
9150 16738.479 0 0 5269.521 12.011701
9200 16738.479 0 0 5269.5212 12.011722
9250 16738.479 0 0 5269.5213 12.011738
9300 16738.48 0 0 5269.5214 12.011746
9350 16738.48 0 0 5269.5214 12.011744
9400 16738.48 0 0 5269.5215 12.011732
9450 16738.48 0 0 5269.5216 12.011715
9500 16738.481 -0.00037652432 0 5269.5216 12.011692
9550 16738.493 -0.0053156155 0 5269.5203 12.011611
9600 16738.549 -0.026814366 0 5269.5163 12.011415
9650 16738.765 -0.10191522 0 5269.5092 12.011013
9700 16735.041 1.0589874 0 5269.4979 12.062708
9750 16738.013 0.1355012 0 5269.5101 11.407245
9800 16738.512 -0.011620331 0 5269.5201 11.394973
9850 16738.489 -0.00067270574 0 5269.5237 11.395098
9900 16738.489 -0.00024984568 0 5269.5242 11.395084
9950 16738.49 0 0 5269.5245 11.395076
10000 16738.49 0 0 5269.5246 11.395075
Loop time of 0.194899 on 4 procs for 10000 steps with 81 atoms
Performance: 443306.036 tau/day, 51308.569 timesteps/s, 4.156 Matom-step/s
98.4% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0017487 | 0.0024215 | 0.0028965 | 0.9 | 1.24
Bond | 0.00032501 | 0.00033082 | 0.0003413 | 0.0 | 0.17
Neigh | 0.015692 | 0.016603 | 0.018578 | 0.9 | 8.52
Comm | 0.063465 | 0.066081 | 0.068061 | 0.8 | 33.91
Output | 0.0019654 | 0.0021191 | 0.0025315 | 0.5 | 1.09
Modify | 0.092199 | 0.094298 | 0.096149 | 0.5 | 48.38
Other | | 0.01305 | | | 6.69
Nlocal: 20.25 ave 37 max 3 min
Histogram: 1 0 0 1 0 0 0 1 0 1
Nghost: 27.25 ave 48 max 13 min
Histogram: 1 0 0 2 0 0 0 0 0 1
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0
Ave special neighs/atom = 0
Neighbor list builds = 1552
Dangerous builds = 0
Total wall time: 0:00:00

475
examples/rigid/log.25Mar24.rigid.tnr.g++.1
View File

@ -1,475 +0,0 @@
LAMMPS (7 Feb 2024 - Development - patch_7Feb2024_update1-306-gf3391199e7-modified)
using 1 OpenMP thread(s) per MPI task
# Tethered nanorods
atom_style molecular
read_data data.rigid.tnr
Reading data file ...
orthogonal box = (-31.122 -31.122 -31.122) to (31.122 31.122 31.122)
1 by 1 by 1 MPI processor grid
reading atoms ...
5600 atoms
scanning bonds ...
1 = max bonds/atom
reading bonds ...
1600 bonds
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
2 = max # of 1-2 neighbors
1 = max # of 1-3 neighbors
1 = max # of 1-4 neighbors
2 = max # of special neighbors
special bonds CPU = 0.001 seconds
read_data CPU = 0.027 seconds
# Specify bond parameters
bond_style fene
bond_coeff 1 30.0 1.5 1.0 1.0
special_bonds fene
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 1 1
special bond factors coul: 0 1 1
2 = max # of 1-2 neighbors
2 = max # of special neighbors
special bonds CPU = 0.001 seconds
# Specify initial velocities
velocity all create 1.4 109345
# Specify rigid components
group rods type 2
4000 atoms in group rods
group tethers subtract all rods
1600 atoms in group tethers
neigh_modify exclude molecule/intra rods delay 0 every 1
# Specify the pair potentials
pair_style lj/cut 2.5
pair_modify shift yes
pair_coeff * * 1.0 1.0 1.122
pair_coeff 2 2 1.0 1.0 2.5
# Specify output
thermo 100
thermo_style custom step temp pe etotal press enthalpy lx ly lz pxx pyy pzz
thermo_modify flush yes lost warn
timestep 0.005
fix 1 rods rigid molecule
800 rigid bodies with 4000 atoms
fix 2 tethers nve
fix 3 all langevin 1.4 1.4 1.0 437624
run 5000
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update: every = 1 steps, delay = 0 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 = 45 45 45
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 8.017 | 8.017 | 8.017 Mbytes
Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
0 1.3963219 5.9478449 7.0445809 0.048565317 9.13595 62.244 62.244 62.244 0.0091983659 0.11850113 0.017996458
100 1.3418512 5.9671777 7.0211299 0.025020362 8.0985822 62.244 62.244 62.244 0.02036076 0.038265078 0.016435248
200 1.3730638 5.9750802 7.0535483 0.0053287535 7.2830205 62.244 62.244 62.244 -0.00054924195 0.0092396988 0.0072958036
300 1.376262 5.9821642 7.0631443 0.0055536521 7.3023013 62.244 62.244 62.244 0.0033577704 0.0069111861 0.0063919998
400 1.3782954 5.9983628 7.08094 0.0020507385 7.169251 62.244 62.244 62.244 -0.0060862717 0.0098998072 0.0023386801
500 1.386863 6.0053312 7.0946377 -0.0009847031 7.0522334 62.244 62.244 62.244 -0.0038708372 0.0005697804 0.00034694745
600 1.4069849 6.0035719 7.1086832 0.0047883912 7.3148858 62.244 62.244 62.244 0.001069365 0.0078059505 0.0054898581
700 1.4423187 5.9982171 7.1310812 0.012141001 7.6539093 62.244 62.244 62.244 0.0094765272 0.011007593 0.015938883
800 1.4303878 5.9968168 7.1203098 -0.00081349095 7.0852784 62.244 62.244 62.244 0.0011153812 0.00041597298 -0.0039718271
900 1.4140538 5.9838168 7.0944803 0.00207609 7.183883 62.244 62.244 62.244 0.00043409671 0.0022778944 0.0035162788
1000 1.3906567 5.988119 7.0804053 0.0022005856 7.1751692 62.244 62.244 62.244 0.0077268425 -0.0022042977 0.0010792119
1100 1.3921992 5.9892203 7.0827181 0.0035041977 7.2336194 62.244 62.244 62.244 -0.0037576823 0.0040827951 0.01018748
1200 1.3968803 5.9795846 7.0767592 -0.0031072146 6.9429532 62.244 62.244 62.244 -0.0077387449 0.0033056124 -0.0048885115
1300 1.3755848 5.9739757 7.0544239 0.0092247106 7.4516677 62.244 62.244 62.244 0.0092788748 0.010737194 0.0076580625
1400 1.3847985 5.9703631 7.0580481 0.0071703598 7.3668254 62.244 62.244 62.244 0.0080485848 0.012260474 0.001202021
1500 1.4190051 5.956946 7.0714985 0.0035992903 7.2264948 62.244 62.244 62.244 -0.0055125437 0.01038369 0.0059267242
1600 1.3980036 5.9671666 7.0652236 0.0061819851 7.3314385 62.244 62.244 62.244 0.0062429141 0.0035120077 0.0087910334
1700 1.4276062 5.9610381 7.0823462 0.007832375 7.4196319 62.244 62.244 62.244 0.0083316819 0.0058394292 0.009326014
1800 1.4112769 5.9630595 7.0715419 0.0068032101 7.3645087 62.244 62.244 62.244 0.0065502252 0.0062317255 0.0076276797
1900 1.4276973 5.9489341 7.0703139 0.008397746 7.4319462 62.244 62.244 62.244 0.0148941 0.0032963108 0.0070028268
2000 1.4056158 5.9564624 7.0604983 0.0090470732 7.4500926 62.244 62.244 62.244 0.011871718 0.0086681344 0.0066013673
2100 1.3924778 5.9483611 7.0420778 0.0088893819 7.4248814 62.244 62.244 62.244 0.010247454 0.0097830093 0.0066376825
2200 1.3760401 5.9435877 7.0243935 -0.0042972782 6.8393397 62.244 62.244 62.244 -0.0050064436 -0.0046216999 -0.0032636911
2300 1.4191937 5.9334036 7.0481042 0.0047000032 7.2505006 62.244 62.244 62.244 0.0057709635 0.0044949165 0.0038341296
2400 1.4213285 5.9472214 7.0635988 0.010197674 7.5027414 62.244 62.244 62.244 0.008373826 0.0090537939 0.013165402
2500 1.4153808 5.9421661 7.0538718 0.00015906306 7.0607216 62.244 62.244 62.244 0.002351621 -0.0019814986 0.00010706677
2600 1.4014223 5.9431386 7.0438807 0.0070733749 7.3484816 62.244 62.244 62.244 0.0054143871 0.010055843 0.0057498948
2700 1.4138077 5.9369067 7.047377 0.0024268842 7.1518859 62.244 62.244 62.244 0.0052918436 0.0014960353 0.00049277371
2800 1.432192 5.9347676 7.0596777 0.0077670448 7.3941501 62.244 62.244 62.244 0.012668421 0.0059113033 0.0047214106
2900 1.3938659 5.921023 7.01583 0.0053751198 7.2472989 62.244 62.244 62.244 0.0020490372 0.0076566093 0.006419713
3000 1.390221 5.9205014 7.0124455 -0.0010750977 6.9661485 62.244 62.244 62.244 0.0019519817 -0.0041878885 -0.00098938611
3100 1.4205722 5.9178284 7.0336117 0.0098735475 7.4587965 62.244 62.244 62.244 0.0040973361 0.012167268 0.013356039
3200 1.398418 5.9150349 7.0134173 0.0061541841 7.2784351 62.244 62.244 62.244 0.0067621815 0.011952563 -0.00025219251
3300 1.4269859 5.9148727 7.0356937 0.0060623879 7.2967584 62.244 62.244 62.244 0.012956234 -2.4806661e-05 0.0052557362
3400 1.434286 5.9356705 7.0622253 0.00027315892 7.0739884 62.244 62.244 62.244 -0.00054959866 0.0052526278 -0.0038835524
3500 1.4416809 5.9228153 7.0551783 0.0083382977 7.4142506 62.244 62.244 62.244 0.007399393 0.0030328007 0.014582699
3600 1.4136063 5.9039442 7.0142562 0.0019712004 7.0991421 62.244 62.244 62.244 -0.00032316149 0.0035029874 0.0027337752
3700 1.4333819 5.9120101 7.0378548 0.0071287182 7.3448389 62.244 62.244 62.244 0.0064768218 0.0046765361 0.010232797
3800 1.3659481 5.9032873 6.9761663 -0.0054033416 6.7434821 62.244 62.244 62.244 -0.0073943479 -0.0082831992 -0.00053247772
3900 1.3963222 5.9042998 7.0010361 0.0053310264 7.2306062 62.244 62.244 62.244 0.0081855739 0.0048806019 0.0029269034
4000 1.4125482 5.9060665 7.0155474 0.0028450296 7.138063 62.244 62.244 62.244 0.0052588294 0.00072395285 0.0025523065
4100 1.3943951 5.9040875 6.9993102 0.0058050223 7.2492919 62.244 62.244 62.244 0.0060579697 0.0024782584 0.0088788387
4200 1.4249768 5.8906371 7.0098801 0.0030210669 7.1399763 62.244 62.244 62.244 0.006174431 -0.002079586 0.0049683557
4300 1.3899801 5.8966397 6.9883947 0.0057285402 7.2350829 62.244 62.244 62.244 0.0049048136 0.0021882328 0.010092574
4400 1.4414352 5.898628 7.0307981 0.0050932552 7.2501291 62.244 62.244 62.244 0.0057941393 0.0037951842 0.0056904421
4500 1.4092913 5.8922803 6.9992031 0.0012238869 7.0519073 62.244 62.244 62.244 0.0042907674 0.0014412643 -0.0020603711
4600 1.3779868 5.8928757 6.9752105 0.0020701322 7.0643566 62.244 62.244 62.244 0.0029283254 -0.0031683908 0.006450462
4700 1.4084635 5.9098782 7.0161508 -0.00052129502 6.9937023 62.244 62.244 62.244 -0.0018460523 -0.0018286314 0.0021107986
4800 1.4393258 5.9148464 7.0453597 0.015311954 7.7047386 62.244 62.244 62.244 0.014718813 0.01801777 0.013199278
4900 1.4500008 5.9076899 7.0465879 0.0075111779 7.3700419 62.244 62.244 62.244 0.0091865271 0.0080981174 0.0052488891
5000 1.4279632 5.9111567 7.0327453 -0.0014189553 6.9716408 62.244 62.244 62.244 -0.0046013754 0.0019937576 -0.001649248
Loop time of 5.54157 on 1 procs for 5000 steps with 5600 atoms
Performance: 389781.415 tau/day, 902.272 timesteps/s, 5.053 Matom-step/s
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.40156 | 0.40156 | 0.40156 | 0.0 | 7.25
Bond | 0.172 | 0.172 | 0.172 | 0.0 | 3.10
Neigh | 1.6573 | 1.6573 | 1.6573 | 0.0 | 29.91
Comm | 0.10679 | 0.10679 | 0.10679 | 0.0 | 1.93
Output | 0.0033706 | 0.0033706 | 0.0033706 | 0.0 | 0.06
Modify | 3.0948 | 3.0948 | 3.0948 | 0.0 | 55.85
Other | | 0.1058 | | | 1.91
Nlocal: 5600 ave 5600 max 5600 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1351 ave 1351 max 1351 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 5254 ave 5254 max 5254 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 5254
Ave neighs/atom = 0.93821429
Ave special neighs/atom = 0.57142857
Neighbor list builds = 766
Dangerous builds = 0
# Replace fix rigid and fix langevin with new ones
unfix 1
unfix 3
fix 3 tethers langevin 1.4 1.4 1.0 198450
# Test different integrators for rods
fix 1 rods rigid/nve molecule
800 rigid bodies with 4000 atoms
print "rigid/nve"
rigid/nve
run 1000
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Per MPI rank memory allocation (min/avg/max) = 8.018 | 8.018 | 8.018 Mbytes
Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
5000 1.4279632 5.9111567 7.0327453 0.027874409 8.2331015 62.244 62.244 62.244 0.018992956 0.039655696 0.024974575
5100 1.439608 5.9052128 7.0359478 0.0060989876 7.2985886 62.244 62.244 62.244 0.0087364154 0.0040228411 0.0055377063
5200 1.4120671 5.9102569 7.01936 0.0064301456 7.2962615 62.244 62.244 62.244 0.0082738088 0.0038925707 0.0071240574
5300 1.4452434 5.8842166 7.0193778 0.0081724166 7.3713067 62.244 62.244 62.244 0.0077715644 0.0068924374 0.0098532479
5400 1.4170243 5.887522 7.0005186 0.00086566653 7.0377968 62.244 62.244 62.244 -9.179779e-05 -0.0020237494 0.0047125468
5500 1.4209084 5.875892 6.9919394 0.009363414 7.3951563 62.244 62.244 62.244 0.0088769611 0.0087092372 0.010504044
5600 1.4132978 5.8798939 6.9899636 0.0014877902 7.0540323 62.244 62.244 62.244 -0.0023427699 0.0045593956 0.0022467449
5700 1.4065055 5.8875412 6.9922759 0.002808316 7.1132105 62.244 62.244 62.244 0.0025187553 0.00051088905 0.0053953037
5800 1.4079049 5.8940749 6.9999087 0.0015946903 7.0685809 62.244 62.244 62.244 0.0037830352 0.00021762631 0.00078340928
5900 1.4076048 5.8941588 6.9997569 0.0051902121 7.2232631 62.244 62.244 62.244 -0.00093181434 0.0096405899 0.0068618607
6000 1.4322812 5.8903503 7.0153305 0.00029722379 7.0281298 62.244 62.244 62.244 0.0019139164 -0.00073870179 -0.00028354325
Loop time of 1.21399 on 1 procs for 1000 steps with 5600 atoms
Performance: 355850.342 tau/day, 823.728 timesteps/s, 4.613 Matom-step/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 | 0.12141 | 0.12141 | 0.12141 | 0.0 | 10.00
Bond | 0.038739 | 0.038739 | 0.038739 | 0.0 | 3.19
Neigh | 0.39335 | 0.39335 | 0.39335 | 0.0 | 32.40
Comm | 0.023806 | 0.023806 | 0.023806 | 0.0 | 1.96
Output | 0.00074295 | 0.00074295 | 0.00074295 | 0.0 | 0.06
Modify | 0.61212 | 0.61212 | 0.61212 | 0.0 | 50.42
Other | | 0.02383 | | | 1.96
Nlocal: 5600 ave 5600 max 5600 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1347 ave 1347 max 1347 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 5399 ave 5399 max 5399 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 5399
Ave neighs/atom = 0.96410714
Ave special neighs/atom = 0.57142857
Neighbor list builds = 153
Dangerous builds = 0
unfix 1
fix 1 rods rigid/nvt molecule temp 1.4 1.4 1.0
800 rigid bodies with 4000 atoms
print "rigid/nvt"
rigid/nvt
run 1000
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Per MPI rank memory allocation (min/avg/max) = 8.018 | 8.018 | 8.018 Mbytes
Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
6000 1.4322812 5.8903503 7.0153305 0.012984296 7.5744734 62.244 62.244 62.244 0.058323772 0.007366828 -0.026737713
6100 1.4199781 5.8764024 6.9917192 0.0054080227 7.2246049 62.244 62.244 62.244 0.0092282159 0.0019631398 0.0050327123
6200 1.3976803 5.8924474 6.9902504 0.00044474719 7.0094026 62.244 62.244 62.244 -0.0022979183 -0.0004943354 0.0041264952
6300 1.4076912 5.8847607 6.9904268 0.0066261457 7.2757686 62.244 62.244 62.244 0.0057923777 0.0091772934 0.0049087658
6400 1.3749242 5.8816641 6.9615934 0.0075045379 7.2847615 62.244 62.244 62.244 0.012318395 0.003979389 0.0062158299
6500 1.3467602 5.888001 6.945809 -6.1011018e-05 6.9431817 62.244 62.244 62.244 0.0031945051 -0.0013048764 -0.0020726618
6600 1.3638321 5.8744775 6.9456945 0.005780579 7.1946237 62.244 62.244 62.244 0.0060765968 0.0058486743 0.0054164658
6700 1.3933343 5.8833797 6.9777691 0.0026007197 7.089764 62.244 62.244 62.244 0.0029828101 0.0019631585 0.0028561905
6800 1.4025439 5.901019 7.0026421 0.0033759718 7.1480216 62.244 62.244 62.244 0.0059683617 0.0016890885 0.002470465
6900 1.4165405 5.8901618 7.0027785 0.0048537306 7.2117948 62.244 62.244 62.244 0.0031937581 0.0089194691 0.0024479647
7000 1.4256345 5.8979889 7.0177485 0.0076603683 7.347627 62.244 62.244 62.244 0.0064499957 0.0096400261 0.0068910831
Loop time of 1.16587 on 1 procs for 1000 steps with 5600 atoms
Performance: 370540.281 tau/day, 857.732 timesteps/s, 4.803 Matom-step/s
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.11675 | 0.11675 | 0.11675 | 0.0 | 10.01
Bond | 0.03628 | 0.03628 | 0.03628 | 0.0 | 3.11
Neigh | 0.36879 | 0.36879 | 0.36879 | 0.0 | 31.63
Comm | 0.022201 | 0.022201 | 0.022201 | 0.0 | 1.90
Output | 0.00070791 | 0.00070791 | 0.00070791 | 0.0 | 0.06
Modify | 0.59859 | 0.59859 | 0.59859 | 0.0 | 51.34
Other | | 0.02255 | | | 1.93
Nlocal: 5600 ave 5600 max 5600 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1284 ave 1284 max 1284 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 5691 ave 5691 max 5691 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 5691
Ave neighs/atom = 1.01625
Ave special neighs/atom = 0.57142857
Neighbor list builds = 151
Dangerous builds = 0
unfix 1
compute myTemp all temp
fix 1 rods rigid/npt molecule temp 1.4 1.4 1.0 iso 0.05 0.05 1.0 dilate all
800 rigid bodies with 4000 atoms
print "rigid/npt iso"
rigid/npt iso
fix_modify 1 temp myTemp
run 1000
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Per MPI rank memory allocation (min/avg/max) = 8.018 | 8.018 | 8.018 Mbytes
Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
7000 1.4256345 5.8979889 7.0177485 0.030670312 8.3385046 62.244 62.244 62.244 0.019152979 0.028037341 0.044820616
7100 1.4830481 5.8740667 7.0389215 0.021216954 7.7436467 57.083193 57.083193 57.083193 0.015785563 0.020078182 0.027787115
7200 1.5225973 5.8364439 7.0323626 0.015560962 7.3866118 50.329217 50.329217 50.329217 0.017379604 0.02205435 0.0072489313
7300 1.5589134 5.7874972 7.0119402 0.020613279 7.3515942 45.188285 45.188285 45.188285 0.019963793 0.02165546 0.020220585
7400 1.5629259 5.7523794 6.9799739 0.035363756 7.4299227 41.456971 41.456971 41.456971 0.030810521 0.041559103 0.033721646
7500 1.5735285 5.706087 6.9420093 0.033186427 7.2889675 38.830074 38.830074 38.830074 0.030605548 0.018770943 0.050182791
7600 1.5546074 5.6815832 6.902644 0.027297758 7.1446412 36.752801 36.752801 36.752801 0.027154479 0.030653039 0.024085757
7700 1.5396727 5.6293114 6.8386418 0.030528746 7.0744265 35.101973 35.101973 35.101973 0.022542269 0.025802901 0.043241069
7800 1.5249769 5.5826711 6.7804588 0.067321436 7.2458344 33.82824 33.82824 33.82824 0.063820368 0.072156874 0.065987065
7900 1.5017937 5.5660576 6.7456361 0.04770857 7.0497596 32.926623 32.926623 32.926623 0.035259576 0.06869573 0.039170404
8000 1.5105319 5.5459012 6.7323431 0.053301062 7.0487429 32.153588 32.153588 32.153588 0.076450314 0.07417732 0.0092755526
Loop time of 2.49405 on 1 procs for 1000 steps with 5600 atoms
Performance: 173212.568 tau/day, 400.955 timesteps/s, 2.245 Matom-step/s
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.29712 | 0.29712 | 0.29712 | 0.0 | 11.91
Bond | 0.044611 | 0.044611 | 0.044611 | 0.0 | 1.79
Neigh | 1.2735 | 1.2735 | 1.2735 | 0.0 | 51.06
Comm | 0.048469 | 0.048469 | 0.048469 | 0.0 | 1.94
Output | 0.0007418 | 0.0007418 | 0.0007418 | 0.0 | 0.03
Modify | 0.7991 | 0.7991 | 0.7991 | 0.0 | 32.04
Other | | 0.03048 | | | 1.22
Nlocal: 5600 ave 5600 max 5600 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 2993 ave 2993 max 2993 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 25312 ave 25312 max 25312 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 25312
Ave neighs/atom = 4.52
Ave special neighs/atom = 0.57142857
Neighbor list builds = 335
Dangerous builds = 0
unfix 1
fix 1 rods rigid/npt molecule temp 1.4 1.4 1.0 x 0.05 0.05 1.0 dilate all
800 rigid bodies with 4000 atoms
print "rigid/npt x"
rigid/npt x
run 1000
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Per MPI rank memory allocation (min/avg/max) = 8.033 | 8.033 | 8.033 Mbytes
Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
8000 1.5105319 5.5459012 6.7323431 -0.15611622 5.8056235 32.153588 32.153588 32.153588 -0.25823552 0.036861264 -0.24697441
8100 1.4816536 5.5214096 6.6851691 0.051659716 6.9889314 31.85012 32.153588 32.153588 0.042525917 0.079045459 0.033407772
8200 1.4364335 5.5026881 6.6309297 0.030961663 6.8100555 31.337401 32.153588 32.153588 0.062969827 0.0077436471 0.022171514
8300 1.4159126 5.504273 6.6163965 0.050231597 6.9027629 30.879771 32.153588 32.153588 0.047512875 0.071477224 0.031704693
8400 1.4479331 5.4732237 6.6104975 0.037171033 6.8195306 30.460678 32.153588 32.153588 0.016306171 0.072770628 0.022436301
8500 1.4126922 5.4616331 6.5712271 0.069137703 6.9521816 29.846079 32.153588 32.153588 0.075972518 0.063305384 0.068135208
8600 1.4129562 5.4397649 6.5495663 0.068287674 6.9190398 29.306917 32.153588 32.153588 0.077820831 0.076960087 0.050082105
8700 1.4199417 5.408767 6.5240551 0.046952367 6.7741118 28.847632 32.153588 32.153588 0.078496327 0.013710756 0.048650018
8800 1.415092 5.4082456 6.5197246 0.017068201 6.6091852 28.39051 32.153588 32.153588 0.01803734 0.0086202553 0.024547008
8900 1.4080943 5.3806524 6.486635 0.006282149 6.5189723 27.882074 32.153588 32.153588 0.023331732 0.01130818 -0.015793465
9000 1.4188356 5.3687142 6.4831335 0.078333785 6.8770321 27.237322 32.153588 32.153588 0.092873218 0.033643462 0.10848468
Loop time of 2.35076 on 1 procs for 1000 steps with 5600 atoms
Performance: 183770.370 tau/day, 425.394 timesteps/s, 2.382 Matom-step/s
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.45082 | 0.45082 | 0.45082 | 0.0 | 19.18
Bond | 0.045157 | 0.045157 | 0.045157 | 0.0 | 1.92
Neigh | 0.98655 | 0.98655 | 0.98655 | 0.0 | 41.97
Comm | 0.039968 | 0.039968 | 0.039968 | 0.0 | 1.70
Output | 0.00072296 | 0.00072296 | 0.00072296 | 0.0 | 0.03
Modify | 0.80394 | 0.80394 | 0.80394 | 0.0 | 34.20
Other | | 0.0236 | | | 1.00
Nlocal: 5600 ave 5600 max 5600 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 3422 ave 3422 max 3422 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 31084 ave 31084 max 31084 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 31084
Ave neighs/atom = 5.5507143
Ave special neighs/atom = 0.57142857
Neighbor list builds = 167
Dangerous builds = 0
unfix 1
fix 1 rods rigid/nph molecule iso 0.05 0.05 1.0 dilate all
800 rigid bodies with 4000 atoms
print "rigid/nph iso"
rigid/nph iso
run 1000
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Per MPI rank memory allocation (min/avg/max) = 8.036 | 8.036 | 8.036 Mbytes
Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
9000 1.4188356 5.3687142 6.4831335 0.066940268 6.8197402 27.237322 32.153588 32.153588 0.020750172 0.14461869 0.035451941
9100 1.418441 5.3523211 6.4664305 0.016522511 6.5489637 27.17712 32.08252 32.08252 0.01137531 0.0028933886 0.035298833
9200 1.4433401 5.3458252 6.4794915 0.038961106 6.6708176 27.023003 31.900585 31.900585 0.012667867 0.094480325 0.0097351253
9300 1.4806575 5.309105 6.4720822 0.11806636 7.0379478 26.804952 31.643176 31.643176 0.063001935 0.11667303 0.17452413
9400 1.4835179 5.3103383 6.4755622 0.098990545 6.9362503 26.543432 31.334452 31.334452 0.13023767 0.084360197 0.08237377
9500 1.4855723 5.2906327 6.4574702 -0.0012789282 6.4516456 26.352845 31.109465 31.109465 0.053813822 -0.016098782 -0.041551825
9600 1.4959395 5.2553176 6.4302979 0.036958035 6.5952607 26.176506 30.901298 30.901298 0.077457004 -0.035314705 0.068731807
9700 1.4470266 5.289874 6.4264359 0.065648447 6.7177609 26.125849 30.841497 30.841497 0.064764383 0.041383889 0.090797069
9800 1.4525327 5.2808561 6.4217428 0.0076421133 6.4554682 26.077575 30.78451 30.78451 -0.01978363 0.013568065 0.029141905
9900 1.4603761 5.269343 6.4163902 0.079488558 6.7651749 26.027767 30.725712 30.725712 0.06210239 0.062690336 0.11367295
10000 1.4437445 5.2626116 6.3965955 0.0024175103 6.4072252 26.045744 30.746933 30.746933 0.0020903338 0.023283622 -0.018121425
Loop time of 2.42718 on 1 procs for 1000 steps with 5600 atoms
Performance: 177984.690 tau/day, 412.002 timesteps/s, 2.307 Matom-step/s
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.52411 | 0.52411 | 0.52411 | 0.0 | 21.59
Bond | 0.04594 | 0.04594 | 0.04594 | 0.0 | 1.89
Neigh | 1.0079 | 1.0079 | 1.0079 | 0.0 | 41.53
Comm | 0.040182 | 0.040182 | 0.040182 | 0.0 | 1.66
Output | 0.00070663 | 0.00070663 | 0.00070663 | 0.0 | 0.03
Modify | 0.78582 | 0.78582 | 0.78582 | 0.0 | 32.38
Other | | 0.02253 | | | 0.93
Nlocal: 5600 ave 5600 max 5600 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 3638 ave 3638 max 3638 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 35778 ave 35778 max 35778 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 35778
Ave neighs/atom = 6.3889286
Ave special neighs/atom = 0.57142857
Neighbor list builds = 161
Dangerous builds = 0
unfix 1
fix 1 rods rigid/nph molecule x 0.05 0.05 1.0 y 0.05 0.05 1.0 couple xy dilate all
800 rigid bodies with 4000 atoms
print "rigid/nph xy couple"
rigid/nph xy couple
run 1000
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Per MPI rank memory allocation (min/avg/max) = 8.041 | 8.041 | 8.041 Mbytes
Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
10000 1.4437445 5.2626116 6.3965955 0.043852305 6.5894123 26.045744 30.746933 30.746933 -0.10594451 -0.016019605 0.25352103
10100 1.4544517 5.2536075 6.3960014 0.040252547 6.5723133 25.995896 30.688087 30.746933 0.036481947 0.058195014 0.026080679
10200 1.4465796 5.2533056 6.3895164 0.043103918 6.5797343 26.093233 30.802994 30.746933 0.047509548 0.023387048 0.058415158
10300 1.4703558 5.2311222 6.3860079 0.02952279 6.5179005 26.253791 30.992532 30.746933 0.067825843 -1.1742127e-05 0.020754268
10400 1.4264151 5.2426153 6.362988 0.043320767 6.5561801 26.230542 30.965087 30.746933 0.036437179 0.069318063 0.02420706
10500 1.4718495 5.213542 6.3696009 0.028876649 6.4965877 26.047535 30.749047 30.746933 0.044470994 0.03304953 0.0091094235
10600 1.4550996 5.2087392 6.3516419 0.049130073 6.5647387 25.868744 30.537985 30.746933 0.056613289 0.028555571 0.062221359
10700 1.4755834 5.1912236 6.3502153 0.0027128909 6.3617831 25.648895 30.278455 30.746933 0.035708882 0.02165412 -0.04922433
10800 1.4801906 5.1863989 6.3490092 0.030220134 6.4763468 25.497097 30.099256 30.746933 0.035963119 0.021549561 0.033147721
10900 1.4318851 5.1785312 6.3032002 0.095502071 6.7019424 25.380506 29.961622 30.746933 0.1040397 0.10708089 0.075385625
11000 1.4500789 5.1660716 6.3050309 0.072030914 6.6026703 25.249123 29.806525 30.746933 0.073199983 0.0091150749 0.13377768
Loop time of 2.55647 on 1 procs for 1000 steps with 5600 atoms
Performance: 168982.932 tau/day, 391.164 timesteps/s, 2.191 Matom-step/s
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.5683 | 0.5683 | 0.5683 | 0.0 | 22.23
Bond | 0.044877 | 0.044877 | 0.044877 | 0.0 | 1.76
Neigh | 1.0732 | 1.0732 | 1.0732 | 0.0 | 41.98
Comm | 0.041328 | 0.041328 | 0.041328 | 0.0 | 1.62
Output | 0.00078717 | 0.00078717 | 0.00078717 | 0.0 | 0.03
Modify | 0.80433 | 0.80433 | 0.80433 | 0.0 | 31.46
Other | | 0.02363 | | | 0.92
Nlocal: 5600 ave 5600 max 5600 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 3699 ave 3699 max 3699 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 39523 ave 39523 max 39523 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 39523
Ave neighs/atom = 7.0576786
Ave special neighs/atom = 0.57142857
Neighbor list builds = 163
Dangerous builds = 0
Total wall time: 0:00:17

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examples/rigid/log.25Mar24.rigid.tnr.g++.4
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LAMMPS (7 Feb 2024 - Development - patch_7Feb2024_update1-306-gf3391199e7-modified)
using 1 OpenMP thread(s) per MPI task
# Tethered nanorods
atom_style molecular
read_data data.rigid.tnr
Reading data file ...
orthogonal box = (-31.122 -31.122 -31.122) to (31.122 31.122 31.122)
1 by 2 by 2 MPI processor grid
reading atoms ...
5600 atoms
scanning bonds ...
1 = max bonds/atom
reading bonds ...
1600 bonds
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
2 = max # of 1-2 neighbors
1 = max # of 1-3 neighbors
1 = max # of 1-4 neighbors
2 = max # of special neighbors
special bonds CPU = 0.001 seconds
read_data CPU = 0.017 seconds
# Specify bond parameters
bond_style fene
bond_coeff 1 30.0 1.5 1.0 1.0
special_bonds fene
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 1 1
special bond factors coul: 0 1 1
2 = max # of 1-2 neighbors
2 = max # of special neighbors
special bonds CPU = 0.000 seconds
# Specify initial velocities
velocity all create 1.4 109345
# Specify rigid components
group rods type 2
4000 atoms in group rods
group tethers subtract all rods
1600 atoms in group tethers
neigh_modify exclude molecule/intra rods delay 0 every 1
# Specify the pair potentials
pair_style lj/cut 2.5
pair_modify shift yes
pair_coeff * * 1.0 1.0 1.122
pair_coeff 2 2 1.0 1.0 2.5
# Specify output
thermo 100
thermo_style custom step temp pe etotal press enthalpy lx ly lz pxx pyy pzz
thermo_modify flush yes lost warn
timestep 0.005
fix 1 rods rigid molecule
800 rigid bodies with 4000 atoms
fix 2 tethers nve
fix 3 all langevin 1.4 1.4 1.0 437624
run 5000
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update: every = 1 steps, delay = 0 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 = 45 45 45
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 7.552 | 7.555 | 7.559 Mbytes
Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
0 1.3963219 5.9478449 7.0445809 0.048565317 9.13595 62.244 62.244 62.244 0.0091983659 0.11850113 0.017996458
100 1.3999025 5.9707695 7.0703179 0.027293074 8.24564 62.244 62.244 62.244 0.017246307 0.04732529 0.017307624
200 1.4245544 5.9878446 7.1067558 0.0072016369 7.41688 62.244 62.244 62.244 0.0071370801 0.0084066589 0.0060611719
300 1.4212057 5.9942604 7.1105414 0.0023296933 7.210865 62.244 62.244 62.244 -0.0059197015 0.0040269953 0.008881786
400 1.4030116 5.9953214 7.0973119 0.0055751834 7.3373961 62.244 62.244 62.244 -0.0026920847 0.013323321 0.0060943141
500 1.4201338 5.9984777 7.1139168 -0.0018229523 7.035415 62.244 62.244 62.244 -0.0082217102 -0.00047319975 0.0032260529
600 1.425173 5.9902537 7.1096508 0.013367744 7.6853062 62.244 62.244 62.244 0.012971415 0.016298595 0.010833222
700 1.4181225 5.9840752 7.0979345 0.0014999758 7.1625279 62.244 62.244 62.244 -0.0015835387 0.0045967753 0.0014866907
800 1.4084205 5.9778462 7.084085 0.0063728488 7.3585191 62.244 62.244 62.244 0.0036202744 0.005593586 0.0099046859
900 1.3958301 5.9891019 7.0854517 0.0028974454 7.2102244 62.244 62.244 62.244 0.0087724642 0.0014508428 -0.001530971
1000 1.3937374 5.9794855 7.0741916 0.0087158481 7.4495223 62.244 62.244 62.244 0.014424783 0.0034958881 0.0082268735
1100 1.3729162 5.9916252 7.0699773 0.0030451966 7.2011127 62.244 62.244 62.244 0.00084635444 -0.00064448421 0.0089337195
1200 1.4427374 5.9713589 7.1045519 0.0042680608 7.2883474 62.244 62.244 62.244 0.0030884628 0.0031576538 0.0065580658
1300 1.3971469 5.9728674 7.0702514 0.0022809251 7.168475 62.244 62.244 62.244 0.00060902513 -0.00020572386 0.006439474
1400 1.4194118 5.9672631 7.082135 0.012945844 7.6396221 62.244 62.244 62.244 0.0082418827 0.016256336 0.014339314
1500 1.3866472 5.9728382 7.0619753 0.0010642438 7.1078049 62.244 62.244 62.244 0.0020316123 0.0020439035 -0.00088278432
1600 1.4184955 5.9539591 7.0681113 0.0077605409 7.4023036 62.244 62.244 62.244 0.0033721722 0.0057827512 0.014126699
1700 1.3612202 5.9676733 7.0368389 0.00016862131 7.0441002 62.244 62.244 62.244 0.0052525345 0.0007705269 -0.0055171975
1800 1.3641041 5.9521837 7.0236144 0.0057884587 7.2728829 62.244 62.244 62.244 0.0038061044 0.0044032908 0.009155981
1900 1.3594477 5.9646024 7.0323757 0.0044261926 7.2229809 62.244 62.244 62.244 0.0019417448 0.006871542 0.004465291
2000 1.3776971 5.9431816 7.0252888 -0.0012460593 6.9716298 62.244 62.244 62.244 -0.0010913822 0.00098119436 -0.0036279901
2100 1.3986245 5.9509735 7.0495181 0.007520633 7.3733792 62.244 62.244 62.244 0.008359824 0.0075919773 0.0066100978
2200 1.4033594 5.9548158 7.0570794 0.0016804284 7.1294438 62.244 62.244 62.244 -0.001842641 0.0032876741 0.0035962521
2300 1.4048926 5.9444129 7.0478808 0.0062444034 7.3167836 62.244 62.244 62.244 0.004383569 0.0065720464 0.007777595
2400 1.4044043 5.9370822 7.0401666 0.0034562836 7.1890046 62.244 62.244 62.244 0.0068959298 0.0041111713 -0.00063825026
2500 1.4200762 5.9359254 7.0513193 0.0028319649 7.1732722 62.244 62.244 62.244 -0.00030414204 0.0039571831 0.0048428538
2600 1.3876469 5.9249124 7.0148347 -0.0017777225 6.9382806 62.244 62.244 62.244 -0.00047616393 -0.0025484918 -0.0023085117
2700 1.4099941 5.916763 7.0242378 0.0070716262 7.3287634 62.244 62.244 62.244 0.012628756 0.0053812866 0.0032048359
2800 1.4444643 5.9283432 7.0628925 0.0019400023 7.1464349 62.244 62.244 62.244 0.0014895078 0.0046367397 -0.00030624049
2900 1.3902832 5.9152516 7.0072446 -0.002166221 6.9139606 62.244 62.244 62.244 -0.0012374412 -0.00056403268 -0.0046971891
3000 1.3711706 5.922146 6.9991271 0.011101505 7.4771914 62.244 62.244 62.244 0.011063833 0.012093025 0.010147657
3100 1.3569137 5.9171753 6.9829583 -0.0028266769 6.8612331 62.244 62.244 62.244 -0.0069507251 0.0010084401 -0.0025377458
3200 1.4004275 5.905939 7.0058998 0.0054394667 7.2401397 62.244 62.244 62.244 0.010352184 0.0057594139 0.00020680257
3300 1.3641217 5.9145275 6.985972 -0.0027212813 6.8687854 62.244 62.244 62.244 -0.00065933696 -0.005771301 -0.001733206
3400 1.3868722 5.9059546 6.9952684 0.0092591263 7.3939943 62.244 62.244 62.244 0.010690877 0.01075252 0.0063339817
3500 1.3939169 5.8992292 6.9940762 0.0074340014 7.3142068 62.244 62.244 62.244 0.010137307 0.0044252538 0.0077394438
3600 1.3982507 5.9219461 7.0201971 0.0056794512 7.2647714 62.244 62.244 62.244 0.0023367131 0.0080592141 0.0066424266
3700 1.4019908 5.9059957 7.0071844 0.0065915518 7.2910365 62.244 62.244 62.244 0.0049554052 0.010827013 0.0039922376
3800 1.3960736 5.902079 6.9986201 0.0027763672 7.1181788 62.244 62.244 62.244 -0.0015907142 0.0025862031 0.0073336126
3900 1.4352825 5.8986216 7.0259591 0.003498295 7.1766062 62.244 62.244 62.244 0.0030417173 0.0027739456 0.0046792221
4000 1.4121845 5.9079028 7.0170981 0.0050462581 7.2344052 62.244 62.244 62.244 0.0045543085 0.0064113637 0.0041731022
4100 1.3989579 5.9082397 7.0070461 0.00042870391 7.0255074 62.244 62.244 62.244 0.0025733986 0.0025181076 -0.0038053944
4200 1.399883 5.8998147 6.9993477 0.0042777423 7.1835602 62.244 62.244 62.244 0.0013744675 0.0064699404 0.0049888191
4300 1.4076025 5.9044509 7.0100472 0.0066788698 7.2976595 62.244 62.244 62.244 0.007361029 0.0048139331 0.0078616474
4400 1.4161078 5.9064334 7.0187102 -0.0011844913 6.9677025 62.244 62.244 62.244 -0.001908963 -0.0037556847 0.0021111739
4500 1.429225 5.8980089 7.0205885 0.0018498822 7.10025 62.244 62.244 62.244 0.0041143046 0.0010156504 0.00041969169
4600 1.3958783 5.894313 6.9907006 0.0041483111 7.1693394 62.244 62.244 62.244 0.0033996217 0.0041616835 0.004883628
4700 1.3856609 5.8886843 6.9770467 0.0013148711 7.033669 62.244 62.244 62.244 -0.00051706505 0.0030872136 0.0013744648
4800 1.4016792 5.902351 7.0032949 0.0025050908 7.1111717 62.244 62.244 62.244 0.0016540384 -0.00018095286 0.0060421869
4900 1.4466248 5.9050606 7.0413069 -0.0026620212 6.9266722 62.244 62.244 62.244 -0.00069094879 -0.0073956145 0.00010049979
5000 1.4387209 5.9077482 7.0377864 0.0049404333 7.2505363 62.244 62.244 62.244 0.0042769255 0.0046681652 0.0058762093
Loop time of 2.72962 on 4 procs for 5000 steps with 5600 atoms
Performance: 791319.942 tau/day, 1831.759 timesteps/s, 10.258 Matom-step/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 | 0.06605 | 0.10369 | 0.14557 | 11.7 | 3.80
Bond | 0.03005 | 0.045571 | 0.06035 | 6.5 | 1.67
Neigh | 0.61326 | 0.61489 | 0.61678 | 0.2 | 22.53
Comm | 0.14416 | 0.19908 | 0.25001 | 11.1 | 7.29
Output | 0.0017405 | 0.0025188 | 0.0028143 | 0.9 | 0.09
Modify | 1.522 | 1.6149 | 1.699 | 6.3 | 59.16
Other | | 0.1489 | | | 5.46
Nlocal: 1400 ave 1868 max 905 min
Histogram: 1 1 0 0 0 0 0 0 0 2
Nghost: 648.25 ave 688 max 598 min
Histogram: 1 0 0 1 0 0 0 0 1 1
Neighs: 1202.5 ave 1821 max 698 min
Histogram: 2 0 0 0 0 0 0 1 0 1
Total # of neighbors = 4810
Ave neighs/atom = 0.85892857
Ave special neighs/atom = 0.57142857
Neighbor list builds = 759
Dangerous builds = 0
# Replace fix rigid and fix langevin with new ones
unfix 1
unfix 3
fix 3 tethers langevin 1.4 1.4 1.0 198450
# Test different integrators for rods
fix 1 rods rigid/nve molecule
800 rigid bodies with 4000 atoms
print "rigid/nve"
rigid/nve
run 1000
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Per MPI rank memory allocation (min/avg/max) = 7.557 | 7.566 | 7.574 Mbytes
Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
5000 1.4387209 5.9077482 7.0377864 0.0036839327 7.1964276 62.244 62.244 62.244 0.025677952 -0.016670649 0.002044495
5100 1.4449629 5.8876265 7.0225675 0.0023125815 7.1221542 62.244 62.244 62.244 0.0045991271 0.0036872425 -0.0013486251
5200 1.4271279 5.9160281 7.0369606 0.0020315691 7.1244461 62.244 62.244 62.244 -0.0022476411 0.0039290288 0.0044133197
5300 1.4143266 5.9052803 7.0161581 0.0064093985 7.2921661 62.244 62.244 62.244 0.0090986577 0.0026397649 0.0074897729
5400 1.4426551 5.9087477 7.041876 0.0020419183 7.1298072 62.244 62.244 62.244 0.0043078454 1.5623413e-05 0.001802286
5500 1.4280605 5.9038941 7.0255591 0.00057730336 7.0504195 62.244 62.244 62.244 0.0058938228 0.00065558729 -0.0048175
5600 1.4315004 5.902394 7.0267609 0.0096531882 7.4424563 62.244 62.244 62.244 0.0054225258 0.011780272 0.011756766
5700 1.4074659 5.9076093 7.0130984 0.0052032455 7.2371658 62.244 62.244 62.244 0.0029612305 0.003678953 0.008969553
5800 1.4216898 5.9047983 7.0214595 0.0015109698 7.0865264 62.244 62.244 62.244 -6.4662019e-05 0.0023994389 0.0021981326
5900 1.4052133 5.8920187 6.9957385 0.0065755622 7.278902 62.244 62.244 62.244 0.0062703932 0.011367786 0.002088507
6000 1.3958734 5.9025061 6.9988899 0.0071783223 7.3080101 62.244 62.244 62.244 0.0088905564 0.0025533521 0.010091058
Loop time of 0.646284 on 4 procs for 1000 steps with 5600 atoms
Performance: 668436.315 tau/day, 1547.306 timesteps/s, 8.665 Matom-step/s
99.1% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.01802 | 0.028926 | 0.041262 | 6.4 | 4.48
Bond | 0.0066363 | 0.0098826 | 0.012811 | 2.9 | 1.53
Neigh | 0.14233 | 0.14273 | 0.14311 | 0.1 | 22.08
Comm | 0.029365 | 0.044453 | 0.057955 | 6.3 | 6.88
Output | 0.00034317 | 0.00049475 | 0.00055796 | 0.0 | 0.08
Modify | 0.35817 | 0.37856 | 0.40064 | 2.8 | 58.57
Other | | 0.04124 | | | 6.38
Nlocal: 1400 ave 1850 max 932 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Nghost: 642.25 ave 730 max 550 min
Histogram: 1 0 0 1 0 0 0 1 0 1
Neighs: 1267.25 ave 1805 max 729 min
Histogram: 1 1 0 0 0 0 0 0 1 1
Total # of neighbors = 5069
Ave neighs/atom = 0.90517857
Ave special neighs/atom = 0.57142857
Neighbor list builds = 154
Dangerous builds = 0
unfix 1
fix 1 rods rigid/nvt molecule temp 1.4 1.4 1.0
800 rigid bodies with 4000 atoms
print "rigid/nvt"
rigid/nvt
run 1000
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Per MPI rank memory allocation (min/avg/max) = 7.557 | 7.566 | 7.574 Mbytes
Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
6000 1.3958734 5.9025061 6.9988899 0.0021028569 7.0894453 62.244 62.244 62.244 0.013626393 0.019990521 -0.027308344
6100 1.403297 5.9008111 7.0030257 0.0034667159 7.152313 62.244 62.244 62.244 0.00094173119 0.0074633638 0.0019950526
6200 1.4025256 5.8966477 6.9982564 -0.00020483779 6.9894355 62.244 62.244 62.244 -0.0064238043 0.0010245391 0.0047847518
6300 1.4394011 5.9052004 7.0357728 0.0054604133 7.2709147 62.244 62.244 62.244 0.0096132747 0.002164465 0.0046035003
6400 1.408769 5.8824709 6.9889834 0.005608612 7.2305072 62.244 62.244 62.244 0.0042736813 0.0053311794 0.0072209755
6500 1.3956548 5.8831208 6.9793329 0.0085962528 7.3495135 62.244 62.244 62.244 0.0082055979 0.011231962 0.0063511989
6600 1.3758562 5.8829365 6.9635978 0.0065047826 7.2437134 62.244 62.244 62.244 0.005468046 0.0069917695 0.0070545323
6700 1.3804704 5.8923062 6.9765917 0.0057976076 7.2262542 62.244 62.244 62.244 0.0052851407 0.011935403 0.00017227886
6800 1.396967 5.8774293 6.974672 0.0018361999 7.0537443 62.244 62.244 62.244 1.5181397e-05 0.0031700121 0.0023234062
6900 1.3966118 5.8872183 6.9841821 0.0029553371 7.1114478 62.244 62.244 62.244 -0.0022750426 0.0055197498 0.005621304
7000 1.3992657 5.8918087 6.990857 0.0033614376 7.1356106 62.244 62.244 62.244 0.0019626838 -0.0019054573 0.010027086
Loop time of 0.627583 on 4 procs for 1000 steps with 5600 atoms
Performance: 688355.013 tau/day, 1593.414 timesteps/s, 8.923 Matom-step/s
99.5% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.017522 | 0.028358 | 0.041297 | 6.2 | 4.52
Bond | 0.0060681 | 0.0092563 | 0.012417 | 2.9 | 1.47
Neigh | 0.13625 | 0.13667 | 0.13709 | 0.1 | 21.78
Comm | 0.027966 | 0.043787 | 0.057522 | 6.2 | 6.98
Output | 0.00035478 | 0.00049121 | 0.00055892 | 0.0 | 0.08
Modify | 0.35811 | 0.37631 | 0.39333 | 2.6 | 59.96
Other | | 0.03272 | | | 5.21
Nlocal: 1400 ave 1883 max 958 min
Histogram: 2 0 0 0 0 0 0 0 1 1
Nghost: 665 ave 803 max 565 min
Histogram: 1 1 0 0 0 1 0 0 0 1
Neighs: 1272.25 ave 1895 max 762 min
Histogram: 2 0 0 0 0 0 0 1 0 1
Total # of neighbors = 5089
Ave neighs/atom = 0.90875
Ave special neighs/atom = 0.57142857
Neighbor list builds = 150
Dangerous builds = 0
unfix 1
compute myTemp all temp
fix 1 rods rigid/npt molecule temp 1.4 1.4 1.0 iso 0.05 0.05 1.0 dilate all
800 rigid bodies with 4000 atoms
print "rigid/npt iso"
rigid/npt iso
fix_modify 1 temp myTemp
run 1000
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Per MPI rank memory allocation (min/avg/max) = 7.557 | 7.566 | 7.574 Mbytes
Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
7000 1.3992657 5.8918087 6.990857 0.016459779 7.6996647 62.244 62.244 62.244 0.056781831 -0.019577361 0.012174866
7100 1.5086944 5.8706667 7.0556653 0.011656301 7.4412826 57.006966 57.006966 57.006966 0.015012728 0.015151838 0.0048043378
7200 1.5444857 5.8347072 7.047818 0.025893976 7.6357076 50.283831 50.283831 50.283831 0.021166084 0.027070838 0.029445006
7300 1.5460527 5.7950177 7.0093593 0.02162991 7.3688559 45.318555 45.318555 45.318555 0.014747735 0.037527921 0.012614075
7400 1.5613693 5.7516603 6.9780323 0.034798817 7.4279201 41.678228 41.678228 41.678228 0.041296806 0.025288632 0.037811012
7500 1.5582169 5.7359749 6.9598708 0.029878761 7.2757008 38.972622 38.972622 38.972622 0.031657651 0.020061922 0.037916711
7600 1.5578367 5.6988812 6.9224785 0.045695884 7.3351888 36.981577 36.981577 36.981577 0.040243029 0.039644927 0.057199697
7700 1.5148812 5.6528692 6.8427272 0.022439627 7.0209705 35.43196 35.43196 35.43196 0.010631952 0.017769669 0.03891726
7800 1.529109 5.6051059 6.8061392 0.054079172 7.1911354 34.161596 34.161596 34.161596 0.034939239 0.071325426 0.05597285
7900 1.5182819 5.5708546 6.7633838 0.066345571 7.1933547 33.108416 33.108416 33.108416 0.060359678 0.07068182 0.067995216
8000 1.4677372 5.5540248 6.7068537 0.033729921 6.90804 32.205032 32.205032 32.205032 0.049412183 0.016101823 0.035675755
Loop time of 1.1282 on 4 procs for 1000 steps with 5600 atoms
Performance: 382910.795 tau/day, 886.368 timesteps/s, 4.964 Matom-step/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 | 0.047245 | 0.075421 | 0.11065 | 10.1 | 6.69
Bond | 0.0077964 | 0.011056 | 0.014794 | 2.9 | 0.98
Neigh | 0.47306 | 0.4737 | 0.47434 | 0.1 | 41.99
Comm | 0.047565 | 0.086613 | 0.11788 | 10.3 | 7.68
Output | 0.00031206 | 0.00038703 | 0.00060877 | 0.0 | 0.03
Modify | 0.43174 | 0.44726 | 0.46676 | 2.3 | 39.64
Other | | 0.03376 | | | 2.99
Nlocal: 1400 ave 1845 max 1051 min
Histogram: 2 0 0 0 0 0 0 1 0 1
Nghost: 1558.25 ave 1732 max 1431 min
Histogram: 1 0 1 0 1 0 0 0 0 1
Neighs: 6210.75 ave 9543 max 3698 min
Histogram: 2 0 0 0 0 0 0 1 0 1
Total # of neighbors = 24843
Ave neighs/atom = 4.43625
Ave special neighs/atom = 0.57142857
Neighbor list builds = 335
Dangerous builds = 0
unfix 1
fix 1 rods rigid/npt molecule temp 1.4 1.4 1.0 x 0.05 0.05 1.0 dilate all
800 rigid bodies with 4000 atoms
print "rigid/npt x"
rigid/npt x
run 1000
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Per MPI rank memory allocation (min/avg/max) = 7.567 | 7.579 | 7.596 Mbytes
Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
8000 1.4677372 5.5540248 6.7068537 -0.017850632 6.6003814 32.205032 32.205032 32.205032 -0.10278017 -0.1824093 0.23163757
8100 1.4540331 5.5388671 6.6809322 0.022562574 6.8139144 31.823315 32.205032 32.205032 0.028408548 0.028883436 0.010395737
8200 1.4702497 5.4971666 6.6519689 0.031541665 6.8340274 31.164985 32.205032 32.205032 0.05198967 0.017790558 0.024844767
8300 1.4895576 5.4752966 6.6452643 0.049612462 6.9245663 30.396516 32.205032 32.205032 0.050583662 0.041684528 0.056569197
8400 1.4546023 5.4627064 6.6052185 0.014637455 6.6862795 29.901065 32.205032 32.205032 0.022874978 -0.0061332581 0.027170646
8500 1.4485789 5.4330137 6.5707949 0.06887386 6.9450276 29.337823 32.205032 32.205032 0.082103679 0.041682043 0.082835857
8600 1.4443937 5.4261726 6.5606664 0.02551672 6.6959898 28.63444 32.205032 32.205032 0.028149026 0.066325162 -0.017924027
8700 1.4329121 5.409813 6.5352887 0.028828984 6.6848753 28.015854 32.205032 32.205032 0.015384578 0.050827744 0.02027463
8800 1.4015747 5.4009279 6.5017898 0.046423411 6.7374794 27.41221 32.205032 32.205032 0.099149897 0.019633915 0.020486421
8900 1.411353 5.3728016 6.4813438 0.046095308 6.711069 26.908695 32.205032 32.205032 0.04716092 0.029778906 0.061346098
9000 1.3987178 5.3528351 6.451453 0.029891295 6.5977498 26.425959 32.205032 32.205032 0.033096258 0.039059663 0.017517965
Loop time of 1.05732 on 4 procs for 1000 steps with 5600 atoms
Performance: 408581.873 tau/day, 945.791 timesteps/s, 5.296 Matom-step/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 | 0.084017 | 0.12178 | 0.1674 | 10.7 | 11.52
Bond | 0.0087866 | 0.011339 | 0.014172 | 2.1 | 1.07
Neigh | 0.35177 | 0.35194 | 0.35221 | 0.0 | 33.29
Comm | 0.046529 | 0.094466 | 0.13331 | 12.7 | 8.93
Output | 0.00031081 | 0.00038714 | 0.00061511 | 0.0 | 0.04
Modify | 0.43779 | 0.45007 | 0.46334 | 1.8 | 42.57
Other | | 0.02734 | | | 2.59
Nlocal: 1400 ave 1718 max 1133 min
Histogram: 2 0 0 0 0 0 0 0 1 1
Nghost: 1700.75 ave 1793 max 1533 min
Histogram: 1 0 0 0 0 0 1 0 0 2
Neighs: 7936.75 ave 10967 max 5250 min
Histogram: 2 0 0 0 0 0 0 0 1 1
Total # of neighbors = 31747
Ave neighs/atom = 5.6691071
Ave special neighs/atom = 0.57142857
Neighbor list builds = 169
Dangerous builds = 0
unfix 1
fix 1 rods rigid/nph molecule iso 0.05 0.05 1.0 dilate all
800 rigid bodies with 4000 atoms
print "rigid/nph iso"
rigid/nph iso
run 1000
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Per MPI rank memory allocation (min/avg/max) = 7.568 | 7.58 | 7.597 Mbytes
Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
9000 1.3987178 5.3528351 6.451453 0.26585248 7.7526137 26.425959 32.205032 32.205032 0.02018168 0.47782722 0.29954855
9100 1.4351747 5.3304458 6.4576986 0.051746697 6.707501 26.305023 32.057649 32.057649 0.073064096 0.037508173 0.044667823
9200 1.442609 5.3185643 6.4516564 0.026933669 6.5768423 25.974904 31.655336 31.655336 0.0097800385 0.035425194 0.035595776
9300 1.4528107 5.2812305 6.4223354 0.074634951 6.7601945 25.747306 31.377965 31.377965 0.12937272 0.031196451 0.063335685
9400 1.4778194 5.2625966 6.4233445 0.0179548 6.5034822 25.626311 31.23051 31.23051 0.042627054 -0.047901197 0.059138542
9500 1.4406019 5.2661826 6.3976982 0.048963663 6.6143417 25.551982 31.139926 31.139926 0.097226703 -0.0051171725 0.054781458
9600 1.4463517 5.2420508 6.3780826 0.033338493 6.5253103 25.535743 31.120136 31.120136 0.013953126 0.066958907 0.019103444
9700 1.4040075 5.264089 6.3668617 0.075486855 6.6986983 25.496763 31.072631 31.072631 0.051974464 0.097239496 0.077246606
9800 1.4369291 5.25259 6.3812208 0.062882837 6.6532231 25.359898 30.905835 30.905835 0.088614069 0.087884794 0.012149647
9900 1.4426697 5.2270989 6.3602387 0.070910381 6.6603048 25.175015 30.68052 30.68052 0.081294501 0.056618911 0.07481773
10000 1.4714476 5.2051468 6.3608901 0.038441228 6.5234989 25.171919 30.676748 30.676748 0.021691591 0.0086967032 0.084935388
Loop time of 1.07529 on 4 procs for 1000 steps with 5600 atoms
Performance: 401751.573 tau/day, 929.980 timesteps/s, 5.208 Matom-step/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 | 0.10178 | 0.14349 | 0.18701 | 10.0 | 13.34
Bond | 0.0094369 | 0.011359 | 0.01342 | 1.5 | 1.06
Neigh | 0.35737 | 0.35764 | 0.35787 | 0.0 | 33.26
Comm | 0.048562 | 0.093503 | 0.13651 | 12.7 | 8.70
Output | 0.00029714 | 0.00035903 | 0.0005404 | 0.0 | 0.03
Modify | 0.43477 | 0.44365 | 0.45263 | 1.3 | 41.26
Other | | 0.0253 | | | 2.35
Nlocal: 1400 ave 1650 max 1148 min
Histogram: 1 0 1 0 0 0 0 1 0 1
Nghost: 1770.5 ave 1864 max 1640 min
Histogram: 1 0 0 0 0 1 0 0 1 1
Neighs: 9370.75 ave 12213 max 6410 min
Histogram: 1 1 0 0 0 0 0 0 0 2
Total # of neighbors = 37483
Ave neighs/atom = 6.6933929
Ave special neighs/atom = 0.57142857
Neighbor list builds = 162
Dangerous builds = 0
unfix 1
fix 1 rods rigid/nph molecule x 0.05 0.05 1.0 y 0.05 0.05 1.0 couple xy dilate all
800 rigid bodies with 4000 atoms
print "rigid/nph xy couple"
rigid/nph xy couple
run 1000
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Per MPI rank memory allocation (min/avg/max) = 7.569 | 7.58 | 7.597 Mbytes
Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
10000 1.4714476 5.2051468 6.3608901 -0.096738415 5.9516804 25.171919 30.676748 30.676748 -0.07465944 0.069571401 -0.28512721
10100 1.4336012 5.2129069 6.3389239 0.069305782 6.6336186 25.237381 30.756525 30.676748 0.1042358 0.062982076 0.040699467
10200 1.3850266 5.2255115 6.3133757 -0.026502584 6.1990129 25.423835 30.983755 30.676748 -0.018638813 -0.01225392 -0.048615018
10300 1.4059572 5.2273228 6.3316268 0.026841528 6.4477936 25.461278 31.029386 30.676748 0.0032748153 0.054971756 0.022278013
10400 1.4085811 5.2218002 6.3281652 0.087028058 6.7005137 25.315588 30.851835 30.676748 0.095488962 0.059423478 0.10617173
10500 1.4323046 5.1961285 6.321127 0.011963636 6.3715428 25.124329 30.61875 30.676748 0.047765438 -0.013073535 0.0011990069
10600 1.4401614 5.1744178 6.3055874 0.065577091 6.5770196 24.899891 30.345229 30.676748 0.05130409 0.11923748 0.026189709
10700 1.45262 5.1656069 6.3065622 0.019979844 6.3873914 24.616776 30.0002 30.676748 0.062077837 0.01564587 -0.017784176
10800 1.436593 5.1491998 6.2775666 0.06467682 6.5343926 24.388662 29.722201 30.676748 0.055509186 0.081686998 0.056834275
10900 1.4221057 5.1580272 6.2750151 0.10779715 6.6964287 24.198783 29.490797 30.676748 0.11821126 0.13388181 0.071298392
11000 1.4318097 5.1652839 6.2898937 0.12207839 6.7635101 24.106649 29.378514 30.676748 0.13281999 0.095712525 0.13770264
Loop time of 1.05977 on 4 procs for 1000 steps with 5600 atoms
Performance: 407635.235 tau/day, 943.600 timesteps/s, 5.284 Matom-step/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 | 0.11531 | 0.15482 | 0.18642 | 8.0 | 14.61
Bond | 0.0095915 | 0.011316 | 0.012716 | 1.2 | 1.07
Neigh | 0.34708 | 0.34732 | 0.34748 | 0.0 | 32.77
Comm | 0.050629 | 0.082561 | 0.12326 | 11.1 | 7.79
Output | 0.00029841 | 0.00036751 | 0.00057311 | 0.0 | 0.03
Modify | 0.43421 | 0.44242 | 0.45027 | 0.9 | 41.75
Other | | 0.02097 | | | 1.98
Nlocal: 1400 ave 1551 max 1205 min
Histogram: 1 0 0 1 0 0 0 0 1 1
Nghost: 1831.5 ave 1910 max 1688 min
Histogram: 1 0 0 0 0 1 0 0 0 2
Neighs: 10203.8 ave 12647 max 7619 min
Histogram: 1 0 1 0 0 0 0 1 0 1
Total # of neighbors = 40815
Ave neighs/atom = 7.2883929
Ave special neighs/atom = 0.57142857
Neighbor list builds = 161
Dangerous builds = 0
Total wall time: 0:00:08

338
examples/rigid/log.27Nov18.rigid.atomfile.g++.1 Normal file
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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
atom_modify map array
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
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
variable bodies atomfile bodies.txt
fix 1 all rigid custom v_bodies
9 rigid bodies with 81 atoms
# 1 chain of connected bodies
#group clump1 id <> 1 9
#group clump2 id <> 9 18
#group clump3 id <> 18 27
#group clump4 id <> 27 36
#group clump5 id <> 36 45
#group clump6 id <> 45 54
#group clump7 id <> 54 63
#group clump8 id <> 63 72
#group clump9 id <> 72 81
#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9
# 2 chains of connected bodies
#group clump1 id <> 1 9
#group clump2 id <> 9 18
#group clump3 id <> 18 27
#group clump4 id <> 27 36
#group clump5 id <> 37 45
#group clump6 id <> 45 54
#group clump7 id <> 54 63
#group clump8 id <> 63 72
#group clump9 id <> 72 81
#fix 1 all poems group clump1 clump2 clump3 clump4
#fix 2 all poems group clump5 clump6 clump7 clump8 clump9
neigh_modify exclude group clump1 clump1
neigh_modify exclude group clump2 clump2
neigh_modify exclude group clump3 clump3
neigh_modify exclude group clump4 clump4
neigh_modify exclude group clump5 clump5
neigh_modify exclude group clump6 clump6
neigh_modify exclude group clump7 clump7
neigh_modify exclude group clump8 clump8
neigh_modify exclude group clump9 clump9
thermo 100
#dump 1 all atom 50 dump.rigid
#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 2 pad 5
#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 3 pad 5
timestep 0.0001
thermo 50
run 10000
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) = 4.109 | 4.109 | 4.109 Mbytes
Step Temp E_pair E_mol TotEng Press
0 115.29439 5235.9179 0 5272.2142 -2.7403788
50 14910.685 571.71558 0 5265.82 32.006171
100 16298.442 136.66184 0 5267.653 16.444229
150 16682.606 17.490511 0 5269.4219 14.900344
200 16733.929 1.372872 0 5269.4617 14.569267
250 16738.853 -0.15252816 0 5269.4864 14.496404
300 16738.588 -0.055171335 0 5269.5002 14.496025
350 16738.492 -0.017444677 0 5269.5077 14.496446
400 16738.464 -0.0060102023 0 5269.5104 14.496618
450 16738.455 -0.0012713351 0 5269.5124 14.496701
500 16738.455 -0.00081068621 0 5269.5128 14.496709
550 16738.455 -0.00083203497 0 5269.5129 14.496707
600 16738.455 -0.00058355356 0 5269.5131 14.496709
650 16738.455 -0.00047226704 0 5269.5131 14.496708
700 16738.455 0 0 5269.5136 14.496713
750 16738.455 0 0 5269.5136 14.49671
800 16738.455 0 0 5269.5137 14.496709
850 16738.455 0 0 5269.5137 14.49671
900 16738.456 0 0 5269.5138 14.496713
950 16738.462 -0.0035323872 0 5269.5122 14.496671
1000 16738.586 -0.051135144 0 5269.5036 14.496229
1050 16737.358 0.32995057 0 5269.4981 14.525763
1100 16737.892 0.16210246 0 5269.4984 14.531983
1150 16738.703 -0.089235095 0 5269.5025 14.509899
1200 16738.466 -0.0075446243 0 5269.5096 14.510615
1250 16738.456 0 0 5269.514 14.510704
1300 16738.457 0 0 5269.5141 14.510701
1350 16738.457 0 0 5269.5141 14.510699
1400 16738.457 -0.00044736511 0 5269.5138 14.510693
1450 16738.458 -0.0010971179 0 5269.5134 14.510687
1500 16738.458 -0.00057885428 0 5269.5139 14.510698
1550 16738.457 0 0 5269.5143 14.51071
1600 16738.457 0 0 5269.5144 14.510712
1650 16738.457 0 0 5269.5144 14.510712
1700 16738.458 0 0 5269.5144 14.51071
1750 16738.458 0 0 5269.5145 14.510708
1800 16738.458 0 0 5269.5145 14.510706
1850 16738.458 0 0 5269.5146 14.510705
1900 16738.458 0 0 5269.5146 14.510706
1950 16738.465 -0.0031733615 0 5269.5134 14.510659
2000 16738.491 -0.013255268 0 5269.5117 14.510532
2050 16738.556 -0.0365811 0 5269.5087 14.51029
2100 16738.633 -0.063209659 0 5269.5065 14.510219
2150 16738.607 -0.05601761 0 5269.5055 14.510231
2200 16738.557 -0.038423032 0 5269.5072 14.510404
2250 16738.515 -0.023709918 0 5269.5088 14.510539
2300 16738.489 -0.013249035 0 5269.5111 14.510621
2350 16738.468 -0.0045563719 0 5269.5131 14.510714
2400 16738.46 -0.00052194273 0 5269.5146 14.510771
2450 16738.464 -0.0023259756 0 5269.514 14.510746
2500 16738.468 -0.0051929186 0 5269.5127 14.510731
2550 16738.581 -0.044940117 0 5269.5085 14.510315
2600 16738.427 -7.972284e-05 0 5269.5046 14.510657
2650 16733.017 1.7051479 0 5269.5067 14.596295
2700 16738.761 -0.10614946 0 5269.5038 14.499584
2750 16733.973 1.4038179 0 5269.5064 14.598107
2800 16738.585 -0.046813448 0 5269.5076 14.511073
2850 16738.487 -0.012558719 0 5269.5111 14.510111
2900 16738.465 -0.0026252725 0 5269.514 14.510277
2950 16738.476 -0.0082220764 0 5269.512 14.510223
3000 16738.66 -0.071284779 0 5269.507 14.509758
3050 16715.332 7.2419352 0 5269.476 14.870305
3100 16653.226 26.818761 0 5269.5009 14.496764
3150 16739.351 -0.30690375 0 5269.4886 13.643904
3200 16733.238 1.6025328 0 5269.4737 12.016934
3250 16734.374 1.2554429 0 5269.4841 11.963561
3300 16732.156 1.9585967 0 5269.4893 12.234024
3350 16738.655 -0.079693236 0 5269.497 12.092757
3400 16738.543 -0.042215005 0 5269.4991 12.092809
3450 16738.591 -0.059327511 0 5269.4972 12.092536
3500 16738.759 -0.11761245 0 5269.4918 12.09203
3550 16713.405 7.8460621 0 5269.4737 12.389816
3600 16734.939 1.0821936 0 5269.4891 12.173591
3650 16738.808 -0.13663194 0 5269.4882 12.027009
3700 16738.602 -0.070934368 0 5269.4889 12.025288
3750 16737.731 0.20706558 0 5269.4927 12.061948
3800 16738.578 -0.05582043 0 5269.4965 12.035665
3850 16738.471 -0.016307928 0 5269.5024 12.035302
3900 16738.449 -0.0058182199 0 5269.5059 12.035401
3950 16738.439 -0.0012027325 0 5269.5074 12.035461
4000 16738.436 -0.00020698452 0 5269.5075 12.035469
4050 16738.437 0 0 5269.5078 12.035454
4100 16738.437 0 0 5269.508 12.035435
4150 16738.438 0 0 5269.5081 12.035426
4200 16738.438 0 0 5269.5083 12.035432
4250 16738.439 0 0 5269.5085 12.035447
4300 16738.439 0 0 5269.5086 12.035463
4350 16738.44 0 0 5269.5087 12.035474
4400 16738.44 0 0 5269.5088 12.035478
4450 16738.44 0 0 5269.5089 12.035474
4500 16738.44 0 0 5269.509 12.035462
4550 16738.441 0 0 5269.5092 12.035449
4600 16738.441 0 0 5269.5093 12.035445
4650 16738.442 0 0 5269.5095 12.035451
4700 16738.442 0 0 5269.5096 12.03546
4750 16738.443 0 0 5269.5097 12.035465
4800 16738.443 0 0 5269.5098 12.035466
4850 16738.443 0 0 5269.51 12.035463
4900 16738.444 0 0 5269.5101 12.035456
4950 16738.444 0 0 5269.5102 12.035447
5000 16738.445 0 0 5269.5104 12.03544
5050 16738.445 0 0 5269.5105 12.035442
5100 16738.446 0 0 5269.5107 12.035455
5150 16738.446 0 0 5269.5108 12.03547
5200 16738.446 0 0 5269.5109 12.035479
5250 16738.447 0 0 5269.511 12.035479
5300 16738.447 0 0 5269.5111 12.03547
5350 16738.447 0 0 5269.5112 12.035454
5400 16738.448 0 0 5269.5113 12.035434
5450 16738.448 0 0 5269.5115 12.03542
5500 16738.449 0 0 5269.5117 12.035422
5550 16738.457 -0.0030919234 0 5269.5111 12.035383
5600 16738.51 -0.021618357 0 5269.5092 12.035106
5650 16738.622 -0.059214788 0 5269.507 12.035694
5700 16395.28 108.06942 0 5269.5463 24.369038
5750 16738.544 -0.033973429 0 5269.5077 12.011261
5800 16738.456 -0.0037013529 0 5269.5102 12.011675
5850 16738.451 0 0 5269.5123 12.011709
5900 16738.451 -0.0002211587 0 5269.5122 12.011687
5950 16738.452 -0.00024253349 0 5269.5124 12.011678
6000 16738.452 0 0 5269.5128 12.011688
6050 16738.453 0 0 5269.513 12.011702
6100 16738.453 0 0 5269.5131 12.011716
6150 16738.454 0 0 5269.5132 12.011725
6200 16738.454 0 0 5269.5133 12.011728
6250 16738.454 0 0 5269.5134 12.011723
6300 16738.455 0 0 5269.5135 12.011712
6350 16738.455 0 0 5269.5137 12.0117
6400 16738.456 0 0 5269.5138 12.011697
6450 16738.456 0 0 5269.514 12.011704
6500 16738.456 0 0 5269.5141 12.011714
6550 16738.457 0 0 5269.5142 12.011719
6600 16738.457 0 0 5269.5143 12.011718
6650 16738.458 0 0 5269.5144 12.011713
6700 16738.458 0 0 5269.5146 12.011705
6750 16738.459 0 0 5269.5147 12.011696
6800 16738.459 0 0 5269.5149 12.01169
6850 16738.46 0 0 5269.515 12.011695
6900 16738.46 0 0 5269.5152 12.01171
6950 16738.46 0 0 5269.5153 12.011726
7000 16738.461 0 0 5269.5154 12.011736
7050 16738.461 0 0 5269.5155 12.011737
7100 16738.461 0 0 5269.5155 12.011728
7150 16738.461 0 0 5269.5156 12.011712
7200 16738.462 0 0 5269.5158 12.011691
7250 16738.463 0 0 5269.516 12.011676
7300 16738.463 0 0 5269.5162 12.011677
7350 16738.464 0 0 5269.5164 12.011693
7400 16738.464 0 0 5269.5165 12.011713
7450 16738.465 0 0 5269.5166 12.011729
7500 16738.465 0 0 5269.5167 12.011736
7550 16738.465 0 0 5269.5168 12.011734
7600 16738.465 0 0 5269.5168 12.011722
7650 16738.466 0 0 5269.517 12.011704
7700 16738.466 0 0 5269.5171 12.011687
7750 16738.467 0 0 5269.5173 12.011681
7800 16738.467 0 0 5269.5175 12.011687
7850 16738.468 0 0 5269.5176 12.0117
7900 16738.468 0 0 5269.5178 12.011712
7950 16738.469 0 0 5269.5179 12.011721
8000 16738.469 0 0 5269.518 12.011724
8050 16738.469 0 0 5269.5181 12.01172
8100 16738.47 0 0 5269.5182 12.011709
8150 16738.47 0 0 5269.5183 12.0117
8200 16738.47 0 0 5269.5185 12.0117
8250 16738.471 0 0 5269.5186 12.011709
8300 16738.471 0 0 5269.5187 12.011719
8350 16738.472 0 0 5269.5189 12.011723
8400 16738.472 0 0 5269.519 12.01172
8450 16738.473 -0.00039690666 0 5269.5189 12.011706
8500 16738.481 -0.0034646804 0 5269.5182 12.011643
8550 16738.483 -0.0045307409 0 5269.5178 12.011621
8600 16738.474 -0.00076532811 0 5269.5189 12.011681
8650 16738.474 0 0 5269.5197 12.011699
8700 16738.475 0 0 5269.5199 12.011715
8750 16738.475 0 0 5269.52 12.011732
8800 16738.475 0 0 5269.52 12.011743
8850 16738.476 0 0 5269.5201 12.011744
8900 16738.476 0 0 5269.5202 12.011735
8950 16738.476 0 0 5269.5203 12.011719
9000 16738.477 0 0 5269.5205 12.011698
9050 16738.477 0 0 5269.5206 12.011683
9100 16738.478 0 0 5269.5208 12.011684
9150 16738.479 0 0 5269.521 12.011701
9200 16738.479 0 0 5269.5212 12.011722
9250 16738.479 0 0 5269.5213 12.011738
9300 16738.48 0 0 5269.5214 12.011746
9350 16738.48 0 0 5269.5214 12.011744
9400 16738.48 0 0 5269.5215 12.011732
9450 16738.48 0 0 5269.5216 12.011715
9500 16738.481 -0.00037652434 0 5269.5216 12.011692
9550 16738.493 -0.005315616 0 5269.5203 12.011611
9600 16738.549 -0.026814368 0 5269.5163 12.011415
9650 16738.765 -0.10191523 0 5269.5092 12.011013
9700 16735.041 1.0589885 0 5269.4979 12.062708
9750 16738.013 0.13550123 0 5269.5101 11.407245
9800 16738.512 -0.011620328 0 5269.5201 11.394974
9850 16738.489 -0.00067270523 0 5269.5237 11.395098
9900 16738.489 -0.00024984554 0 5269.5242 11.395085
9950 16738.49 0 0 5269.5245 11.395076
10000 16738.49 0 0 5269.5246 11.395075
Loop time of 0.153749 on 1 procs for 10000 steps with 81 atoms
Performance: 561955.786 tau/day, 65041.179 timesteps/s
98.4% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0098538 | 0.0098538 | 0.0098538 | 0.0 | 6.41
Neigh | 0.040308 | 0.040308 | 0.040308 | 0.0 | 26.22
Comm | 0.013034 | 0.013034 | 0.013034 | 0.0 | 8.48
Output | 0.0017202 | 0.0017202 | 0.0017202 | 0.0 | 1.12
Modify | 0.083709 | 0.083709 | 0.083709 | 0.0 | 54.45
Other | | 0.005123 | | | 3.33
Nlocal: 81 ave 81 max 81 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 84 ave 84 max 84 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0
Neighbor list builds = 998
Dangerous builds = 997
Total wall time: 0:00:00

338
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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
atom_modify map array
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
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
variable bodies atomfile bodies.txt
fix 1 all rigid custom v_bodies
9 rigid bodies with 81 atoms
# 1 chain of connected bodies
#group clump1 id <> 1 9
#group clump2 id <> 9 18
#group clump3 id <> 18 27
#group clump4 id <> 27 36
#group clump5 id <> 36 45
#group clump6 id <> 45 54
#group clump7 id <> 54 63
#group clump8 id <> 63 72
#group clump9 id <> 72 81
#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9
# 2 chains of connected bodies
#group clump1 id <> 1 9
#group clump2 id <> 9 18
#group clump3 id <> 18 27
#group clump4 id <> 27 36
#group clump5 id <> 37 45
#group clump6 id <> 45 54
#group clump7 id <> 54 63
#group clump8 id <> 63 72
#group clump9 id <> 72 81
#fix 1 all poems group clump1 clump2 clump3 clump4
#fix 2 all poems group clump5 clump6 clump7 clump8 clump9
neigh_modify exclude group clump1 clump1
neigh_modify exclude group clump2 clump2
neigh_modify exclude group clump3 clump3
neigh_modify exclude group clump4 clump4
neigh_modify exclude group clump5 clump5
neigh_modify exclude group clump6 clump6
neigh_modify exclude group clump7 clump7
neigh_modify exclude group clump8 clump8
neigh_modify exclude group clump9 clump9
thermo 100
#dump 1 all atom 50 dump.rigid
#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 2 pad 5
#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 3 pad 5
timestep 0.0001
thermo 50
run 10000
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) = 4.08 | 4.174 | 4.455 Mbytes
Step Temp E_pair E_mol TotEng Press
0 115.29439 5235.9179 0 5272.2142 -2.7403788
50 14910.685 571.71558 0 5265.82 32.006171
100 16298.442 136.66184 0 5267.653 16.444229
150 16682.606 17.490511 0 5269.4219 14.900344
200 16733.929 1.372872 0 5269.4617 14.569267
250 16738.853 -0.15252816 0 5269.4864 14.496404
300 16738.588 -0.055171335 0 5269.5002 14.496025
350 16738.492 -0.017444677 0 5269.5077 14.496446
400 16738.464 -0.0060102023 0 5269.5104 14.496618
450 16738.455 -0.0012713351 0 5269.5124 14.496701
500 16738.455 -0.00081068621 0 5269.5128 14.496709
550 16738.455 -0.00083203497 0 5269.5129 14.496707
600 16738.455 -0.00058355356 0 5269.5131 14.496709
650 16738.455 -0.00047226704 0 5269.5131 14.496708
700 16738.455 0 0 5269.5136 14.496713
750 16738.455 0 0 5269.5136 14.49671
800 16738.455 0 0 5269.5137 14.496709
850 16738.455 0 0 5269.5137 14.49671
900 16738.456 0 0 5269.5138 14.496713
950 16738.462 -0.0035323872 0 5269.5122 14.496671
1000 16738.586 -0.051135144 0 5269.5036 14.496229
1050 16737.358 0.32995057 0 5269.4981 14.525763
1100 16737.892 0.16210246 0 5269.4984 14.531983
1150 16738.703 -0.089235095 0 5269.5025 14.509899
1200 16738.466 -0.0075446243 0 5269.5096 14.510615
1250 16738.456 0 0 5269.514 14.510704
1300 16738.457 0 0 5269.5141 14.510701
1350 16738.457 0 0 5269.5141 14.510699
1400 16738.457 -0.00044736511 0 5269.5138 14.510693
1450 16738.458 -0.0010971179 0 5269.5134 14.510687
1500 16738.458 -0.00057885428 0 5269.5139 14.510698
1550 16738.457 0 0 5269.5143 14.51071
1600 16738.457 0 0 5269.5144 14.510712
1650 16738.457 0 0 5269.5144 14.510712
1700 16738.458 0 0 5269.5144 14.51071
1750 16738.458 0 0 5269.5145 14.510708
1800 16738.458 0 0 5269.5145 14.510706
1850 16738.458 0 0 5269.5146 14.510705
1900 16738.458 0 0 5269.5146 14.510706
1950 16738.465 -0.0031733615 0 5269.5134 14.510659
2000 16738.491 -0.013255268 0 5269.5117 14.510532
2050 16738.556 -0.0365811 0 5269.5087 14.51029
2100 16738.633 -0.063209659 0 5269.5065 14.510219
2150 16738.607 -0.05601761 0 5269.5055 14.510231
2200 16738.557 -0.038423032 0 5269.5072 14.510404
2250 16738.515 -0.023709918 0 5269.5088 14.510539
2300 16738.489 -0.013249035 0 5269.5111 14.510621
2350 16738.468 -0.0045563719 0 5269.5131 14.510714
2400 16738.46 -0.00052194273 0 5269.5146 14.510771
2450 16738.464 -0.0023259756 0 5269.514 14.510746
2500 16738.468 -0.0051929186 0 5269.5127 14.510731
2550 16738.581 -0.044940117 0 5269.5085 14.510315
2600 16738.427 -7.9722832e-05 0 5269.5046 14.510657
2650 16733.017 1.705148 0 5269.5067 14.596295
2700 16738.761 -0.10614946 0 5269.5038 14.499584
2750 16733.973 1.4038179 0 5269.5064 14.598107
2800 16738.585 -0.046813448 0 5269.5076 14.511073
2850 16738.487 -0.012558719 0 5269.5111 14.510111
2900 16738.465 -0.0026252725 0 5269.514 14.510277
2950 16738.476 -0.0082220764 0 5269.512 14.510223
3000 16738.66 -0.071284779 0 5269.507 14.509758
3050 16715.332 7.2419351 0 5269.476 14.870305
3100 16653.226 26.818761 0 5269.5009 14.496764
3150 16739.351 -0.30690375 0 5269.4886 13.643904
3200 16733.238 1.6025328 0 5269.4737 12.016934
3250 16734.374 1.2554429 0 5269.4841 11.963561
3300 16732.156 1.9585967 0 5269.4893 12.234024
3350 16738.655 -0.079693236 0 5269.497 12.092757
3400 16738.543 -0.042215005 0 5269.4991 12.092809
3450 16738.591 -0.059327511 0 5269.4972 12.092536
3500 16738.759 -0.11761245 0 5269.4918 12.09203
3550 16713.405 7.846062 0 5269.4737 12.389816
3600 16734.939 1.0821936 0 5269.4891 12.173591
3650 16738.808 -0.13663194 0 5269.4882 12.027009
3700 16738.602 -0.070934368 0 5269.4889 12.025288
3750 16737.731 0.20706557 0 5269.4927 12.061948
3800 16738.578 -0.05582043 0 5269.4965 12.035665
3850 16738.471 -0.016307928 0 5269.5024 12.035302
3900 16738.449 -0.0058182199 0 5269.5059 12.035401
3950 16738.439 -0.0012027325 0 5269.5074 12.035461
4000 16738.436 -0.00020698452 0 5269.5075 12.035469
4050 16738.437 0 0 5269.5078 12.035454
4100 16738.437 0 0 5269.508 12.035435
4150 16738.438 0 0 5269.5081 12.035426
4200 16738.438 0 0 5269.5083 12.035432
4250 16738.439 0 0 5269.5085 12.035447
4300 16738.439 0 0 5269.5086 12.035463
4350 16738.44 0 0 5269.5087 12.035474
4400 16738.44 0 0 5269.5088 12.035478
4450 16738.44 0 0 5269.5089 12.035474
4500 16738.44 0 0 5269.509 12.035462
4550 16738.441 0 0 5269.5092 12.035449
4600 16738.441 0 0 5269.5093 12.035445
4650 16738.442 0 0 5269.5095 12.035451
4700 16738.442 0 0 5269.5096 12.03546
4750 16738.443 0 0 5269.5097 12.035465
4800 16738.443 0 0 5269.5098 12.035466
4850 16738.443 0 0 5269.51 12.035463
4900 16738.444 0 0 5269.5101 12.035456
4950 16738.444 0 0 5269.5102 12.035447
5000 16738.445 0 0 5269.5104 12.03544
5050 16738.445 0 0 5269.5105 12.035442
5100 16738.446 0 0 5269.5107 12.035455
5150 16738.446 0 0 5269.5108 12.03547
5200 16738.446 0 0 5269.5109 12.035479
5250 16738.447 0 0 5269.511 12.035479
5300 16738.447 0 0 5269.5111 12.03547
5350 16738.447 0 0 5269.5112 12.035454
5400 16738.448 0 0 5269.5113 12.035434
5450 16738.448 0 0 5269.5115 12.03542
5500 16738.449 0 0 5269.5117 12.035422
5550 16738.457 -0.0030919234 0 5269.5111 12.035383
5600 16738.51 -0.021618357 0 5269.5092 12.035106
5650 16738.622 -0.059214788 0 5269.507 12.035694
5700 16395.28 108.06942 0 5269.5463 24.369038
5750 16738.544 -0.033973429 0 5269.5077 12.011261
5800 16738.456 -0.0037013529 0 5269.5102 12.011675
5850 16738.451 0 0 5269.5123 12.011709
5900 16738.451 -0.00022115871 0 5269.5122 12.011687
5950 16738.452 -0.00024253349 0 5269.5124 12.011678
6000 16738.452 0 0 5269.5128 12.011688
6050 16738.453 0 0 5269.513 12.011702
6100 16738.453 0 0 5269.5131 12.011716
6150 16738.454 0 0 5269.5132 12.011725
6200 16738.454 0 0 5269.5133 12.011728
6250 16738.454 0 0 5269.5134 12.011723
6300 16738.455 0 0 5269.5135 12.011712
6350 16738.455 0 0 5269.5137 12.0117
6400 16738.456 0 0 5269.5138 12.011697
6450 16738.456 0 0 5269.514 12.011704
6500 16738.456 0 0 5269.5141 12.011714
6550 16738.457 0 0 5269.5142 12.011719
6600 16738.457 0 0 5269.5143 12.011718
6650 16738.458 0 0 5269.5144 12.011713
6700 16738.458 0 0 5269.5146 12.011705
6750 16738.459 0 0 5269.5147 12.011696
6800 16738.459 0 0 5269.5149 12.01169
6850 16738.46 0 0 5269.515 12.011695
6900 16738.46 0 0 5269.5152 12.01171
6950 16738.46 0 0 5269.5153 12.011726
7000 16738.461 0 0 5269.5154 12.011736
7050 16738.461 0 0 5269.5155 12.011737
7100 16738.461 0 0 5269.5155 12.011728
7150 16738.461 0 0 5269.5156 12.011712
7200 16738.462 0 0 5269.5158 12.011691
7250 16738.463 0 0 5269.516 12.011676
7300 16738.463 0 0 5269.5162 12.011677
7350 16738.464 0 0 5269.5164 12.011693
7400 16738.464 0 0 5269.5165 12.011713
7450 16738.465 0 0 5269.5166 12.011729
7500 16738.465 0 0 5269.5167 12.011736
7550 16738.465 0 0 5269.5168 12.011734
7600 16738.465 0 0 5269.5168 12.011722
7650 16738.466 0 0 5269.517 12.011704
7700 16738.466 0 0 5269.5171 12.011687
7750 16738.467 0 0 5269.5173 12.011681
7800 16738.467 0 0 5269.5175 12.011687
7850 16738.468 0 0 5269.5176 12.0117
7900 16738.468 0 0 5269.5178 12.011712
7950 16738.469 0 0 5269.5179 12.011721
8000 16738.469 0 0 5269.518 12.011724
8050 16738.469 0 0 5269.5181 12.01172
8100 16738.47 0 0 5269.5182 12.011709
8150 16738.47 0 0 5269.5183 12.0117
8200 16738.47 0 0 5269.5185 12.0117
8250 16738.471 0 0 5269.5186 12.011709
8300 16738.471 0 0 5269.5187 12.011719
8350 16738.472 0 0 5269.5189 12.011723
8400 16738.472 0 0 5269.519 12.01172
8450 16738.473 -0.00039690663 0 5269.5189 12.011706
8500 16738.481 -0.0034646803 0 5269.5182 12.011643
8550 16738.483 -0.0045307409 0 5269.5178 12.011621
8600 16738.474 -0.00076532813 0 5269.5189 12.011681
8650 16738.474 0 0 5269.5197 12.011699
8700 16738.475 0 0 5269.5199 12.011715
8750 16738.475 0 0 5269.52 12.011732
8800 16738.475 0 0 5269.52 12.011743
8850 16738.476 0 0 5269.5201 12.011744
8900 16738.476 0 0 5269.5202 12.011735
8950 16738.476 0 0 5269.5203 12.011719
9000 16738.477 0 0 5269.5205 12.011698
9050 16738.477 0 0 5269.5206 12.011683
9100 16738.478 0 0 5269.5208 12.011684
9150 16738.479 0 0 5269.521 12.011701
9200 16738.479 0 0 5269.5212 12.011722
9250 16738.479 0 0 5269.5213 12.011738
9300 16738.48 0 0 5269.5214 12.011746
9350 16738.48 0 0 5269.5214 12.011744
9400 16738.48 0 0 5269.5215 12.011732
9450 16738.48 0 0 5269.5216 12.011715
9500 16738.481 -0.00037652438 0 5269.5216 12.011692
9550 16738.493 -0.0053156163 0 5269.5203 12.011611
9600 16738.549 -0.026814371 0 5269.5163 12.011415
9650 16738.765 -0.10191523 0 5269.5092 12.011013
9700 16735.041 1.0589894 0 5269.4979 12.062708
9750 16738.013 0.13550109 0 5269.5101 11.407246
9800 16738.512 -0.011620327 0 5269.5201 11.394974
9850 16738.489 -0.00067270507 0 5269.5237 11.395098
9900 16738.489 -0.00024984555 0 5269.5242 11.395085
9950 16738.49 0 0 5269.5245 11.395076
10000 16738.49 0 0 5269.5246 11.395075
Loop time of 0.202963 on 4 procs for 10000 steps with 81 atoms
Performance: 425693.239 tau/day, 49270.051 timesteps/s
89.9% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0025978 | 0.0033882 | 0.0042055 | 1.0 | 1.67
Neigh | 0.012025 | 0.013416 | 0.01623 | 1.4 | 6.61
Comm | 0.080375 | 0.087468 | 0.090782 | 1.4 | 43.10
Output | 0.0031407 | 0.0039954 | 0.0065427 | 2.3 | 1.97
Modify | 0.086613 | 0.087285 | 0.087619 | 0.1 | 43.01
Other | | 0.00741 | | | 3.65
Nlocal: 20.25 ave 38 max 3 min
Histogram: 1 0 1 0 0 0 1 0 0 1
Nghost: 27.25 ave 48 max 13 min
Histogram: 1 0 1 1 0 0 0 0 0 1
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0
Neighbor list builds = 998
Dangerous builds = 997
Total wall time: 0:00:00

338
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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
atom_modify map array
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
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
variable bodies atom 1.0*gmask(clump1)+2.0*gmask(clump2)+3.0*gmask(clump3)+4.0*gmask(clump4)+5.0*gmask(clump5)+6.0*gmask(clump6)+7.0*gmask(clump7)+8.0*gmask(clump8)+9.0*gmask(clump9)
fix 1 all rigid custom v_bodies
9 rigid bodies with 81 atoms
# 1 chain of connected bodies
#group clump1 id <> 1 9
#group clump2 id <> 9 18
#group clump3 id <> 18 27
#group clump4 id <> 27 36
#group clump5 id <> 36 45
#group clump6 id <> 45 54
#group clump7 id <> 54 63
#group clump8 id <> 63 72
#group clump9 id <> 72 81
#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9
# 2 chains of connected bodies
#group clump1 id <> 1 9
#group clump2 id <> 9 18
#group clump3 id <> 18 27
#group clump4 id <> 27 36
#group clump5 id <> 37 45
#group clump6 id <> 45 54
#group clump7 id <> 54 63
#group clump8 id <> 63 72
#group clump9 id <> 72 81
#fix 1 all poems group clump1 clump2 clump3 clump4
#fix 2 all poems group clump5 clump6 clump7 clump8 clump9
neigh_modify exclude group clump1 clump1
neigh_modify exclude group clump2 clump2
neigh_modify exclude group clump3 clump3
neigh_modify exclude group clump4 clump4
neigh_modify exclude group clump5 clump5
neigh_modify exclude group clump6 clump6
neigh_modify exclude group clump7 clump7
neigh_modify exclude group clump8 clump8
neigh_modify exclude group clump9 clump9
thermo 100
#dump 1 all atom 50 dump.rigid
#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 2 pad 5
#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 3 pad 5
timestep 0.0001
thermo 50
run 10000
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) = 3.984 | 3.984 | 3.984 Mbytes
Step Temp E_pair E_mol TotEng Press
0 115.29439 5235.9179 0 5272.2142 -2.7403788
50 14910.685 571.71558 0 5265.82 32.006171
100 16298.442 136.66184 0 5267.653 16.444229
150 16682.606 17.490511 0 5269.4219 14.900344
200 16733.929 1.372872 0 5269.4617 14.569267
250 16738.853 -0.15252816 0 5269.4864 14.496404
300 16738.588 -0.055171335 0 5269.5002 14.496025
350 16738.492 -0.017444677 0 5269.5077 14.496446
400 16738.464 -0.0060102023 0 5269.5104 14.496618
450 16738.455 -0.0012713351 0 5269.5124 14.496701
500 16738.455 -0.00081068621 0 5269.5128 14.496709
550 16738.455 -0.00083203497 0 5269.5129 14.496707
600 16738.455 -0.00058355356 0 5269.5131 14.496709
650 16738.455 -0.00047226704 0 5269.5131 14.496708
700 16738.455 0 0 5269.5136 14.496713
750 16738.455 0 0 5269.5136 14.49671
800 16738.455 0 0 5269.5137 14.496709
850 16738.455 0 0 5269.5137 14.49671
900 16738.456 0 0 5269.5138 14.496713
950 16738.462 -0.0035323872 0 5269.5122 14.496671
1000 16738.586 -0.051135144 0 5269.5036 14.496229
1050 16737.358 0.32995057 0 5269.4981 14.525763
1100 16737.892 0.16210246 0 5269.4984 14.531983
1150 16738.703 -0.089235095 0 5269.5025 14.509899
1200 16738.466 -0.0075446243 0 5269.5096 14.510615
1250 16738.456 0 0 5269.514 14.510704
1300 16738.457 0 0 5269.5141 14.510701
1350 16738.457 0 0 5269.5141 14.510699
1400 16738.457 -0.00044736511 0 5269.5138 14.510693
1450 16738.458 -0.0010971179 0 5269.5134 14.510687
1500 16738.458 -0.00057885428 0 5269.5139 14.510698
1550 16738.457 0 0 5269.5143 14.51071
1600 16738.457 0 0 5269.5144 14.510712
1650 16738.457 0 0 5269.5144 14.510712
1700 16738.458 0 0 5269.5144 14.51071
1750 16738.458 0 0 5269.5145 14.510708
1800 16738.458 0 0 5269.5145 14.510706
1850 16738.458 0 0 5269.5146 14.510705
1900 16738.458 0 0 5269.5146 14.510706
1950 16738.465 -0.0031733615 0 5269.5134 14.510659
2000 16738.491 -0.013255268 0 5269.5117 14.510532
2050 16738.556 -0.0365811 0 5269.5087 14.51029
2100 16738.633 -0.063209659 0 5269.5065 14.510219
2150 16738.607 -0.05601761 0 5269.5055 14.510231
2200 16738.557 -0.038423032 0 5269.5072 14.510404
2250 16738.515 -0.023709918 0 5269.5088 14.510539
2300 16738.489 -0.013249035 0 5269.5111 14.510621
2350 16738.468 -0.0045563719 0 5269.5131 14.510714
2400 16738.46 -0.00052194273 0 5269.5146 14.510771
2450 16738.464 -0.0023259756 0 5269.514 14.510746
2500 16738.468 -0.0051929186 0 5269.5127 14.510731
2550 16738.581 -0.044940117 0 5269.5085 14.510315
2600 16738.427 -7.972284e-05 0 5269.5046 14.510657
2650 16733.017 1.7051479 0 5269.5067 14.596295
2700 16738.761 -0.10614946 0 5269.5038 14.499584
2750 16733.973 1.4038179 0 5269.5064 14.598107
2800 16738.585 -0.046813448 0 5269.5076 14.511073
2850 16738.487 -0.012558719 0 5269.5111 14.510111
2900 16738.465 -0.0026252725 0 5269.514 14.510277
2950 16738.476 -0.0082220764 0 5269.512 14.510223
3000 16738.66 -0.071284779 0 5269.507 14.509758
3050 16715.332 7.2419352 0 5269.476 14.870305
3100 16653.226 26.818761 0 5269.5009 14.496764
3150 16739.351 -0.30690375 0 5269.4886 13.643904
3200 16733.238 1.6025328 0 5269.4737 12.016934
3250 16734.374 1.2554429 0 5269.4841 11.963561
3300 16732.156 1.9585967 0 5269.4893 12.234024
3350 16738.655 -0.079693236 0 5269.497 12.092757
3400 16738.543 -0.042215005 0 5269.4991 12.092809
3450 16738.591 -0.059327511 0 5269.4972 12.092536
3500 16738.759 -0.11761245 0 5269.4918 12.09203
3550 16713.405 7.8460621 0 5269.4737 12.389816
3600 16734.939 1.0821936 0 5269.4891 12.173591
3650 16738.808 -0.13663194 0 5269.4882 12.027009
3700 16738.602 -0.070934368 0 5269.4889 12.025288
3750 16737.731 0.20706558 0 5269.4927 12.061948
3800 16738.578 -0.05582043 0 5269.4965 12.035665
3850 16738.471 -0.016307928 0 5269.5024 12.035302
3900 16738.449 -0.0058182199 0 5269.5059 12.035401
3950 16738.439 -0.0012027325 0 5269.5074 12.035461
4000 16738.436 -0.00020698452 0 5269.5075 12.035469
4050 16738.437 0 0 5269.5078 12.035454
4100 16738.437 0 0 5269.508 12.035435
4150 16738.438 0 0 5269.5081 12.035426
4200 16738.438 0 0 5269.5083 12.035432
4250 16738.439 0 0 5269.5085 12.035447
4300 16738.439 0 0 5269.5086 12.035463
4350 16738.44 0 0 5269.5087 12.035474
4400 16738.44 0 0 5269.5088 12.035478
4450 16738.44 0 0 5269.5089 12.035474
4500 16738.44 0 0 5269.509 12.035462
4550 16738.441 0 0 5269.5092 12.035449
4600 16738.441 0 0 5269.5093 12.035445
4650 16738.442 0 0 5269.5095 12.035451
4700 16738.442 0 0 5269.5096 12.03546
4750 16738.443 0 0 5269.5097 12.035465
4800 16738.443 0 0 5269.5098 12.035466
4850 16738.443 0 0 5269.51 12.035463
4900 16738.444 0 0 5269.5101 12.035456
4950 16738.444 0 0 5269.5102 12.035447
5000 16738.445 0 0 5269.5104 12.03544
5050 16738.445 0 0 5269.5105 12.035442
5100 16738.446 0 0 5269.5107 12.035455
5150 16738.446 0 0 5269.5108 12.03547
5200 16738.446 0 0 5269.5109 12.035479
5250 16738.447 0 0 5269.511 12.035479
5300 16738.447 0 0 5269.5111 12.03547
5350 16738.447 0 0 5269.5112 12.035454
5400 16738.448 0 0 5269.5113 12.035434
5450 16738.448 0 0 5269.5115 12.03542
5500 16738.449 0 0 5269.5117 12.035422
5550 16738.457 -0.0030919234 0 5269.5111 12.035383
5600 16738.51 -0.021618357 0 5269.5092 12.035106
5650 16738.622 -0.059214788 0 5269.507 12.035694
5700 16395.28 108.06942 0 5269.5463 24.369038
5750 16738.544 -0.033973429 0 5269.5077 12.011261
5800 16738.456 -0.0037013529 0 5269.5102 12.011675
5850 16738.451 0 0 5269.5123 12.011709
5900 16738.451 -0.0002211587 0 5269.5122 12.011687
5950 16738.452 -0.00024253349 0 5269.5124 12.011678
6000 16738.452 0 0 5269.5128 12.011688
6050 16738.453 0 0 5269.513 12.011702
6100 16738.453 0 0 5269.5131 12.011716
6150 16738.454 0 0 5269.5132 12.011725
6200 16738.454 0 0 5269.5133 12.011728
6250 16738.454 0 0 5269.5134 12.011723
6300 16738.455 0 0 5269.5135 12.011712
6350 16738.455 0 0 5269.5137 12.0117
6400 16738.456 0 0 5269.5138 12.011697
6450 16738.456 0 0 5269.514 12.011704
6500 16738.456 0 0 5269.5141 12.011714
6550 16738.457 0 0 5269.5142 12.011719
6600 16738.457 0 0 5269.5143 12.011718
6650 16738.458 0 0 5269.5144 12.011713
6700 16738.458 0 0 5269.5146 12.011705
6750 16738.459 0 0 5269.5147 12.011696
6800 16738.459 0 0 5269.5149 12.01169
6850 16738.46 0 0 5269.515 12.011695
6900 16738.46 0 0 5269.5152 12.01171
6950 16738.46 0 0 5269.5153 12.011726
7000 16738.461 0 0 5269.5154 12.011736
7050 16738.461 0 0 5269.5155 12.011737
7100 16738.461 0 0 5269.5155 12.011728
7150 16738.461 0 0 5269.5156 12.011712
7200 16738.462 0 0 5269.5158 12.011691
7250 16738.463 0 0 5269.516 12.011676
7300 16738.463 0 0 5269.5162 12.011677
7350 16738.464 0 0 5269.5164 12.011693
7400 16738.464 0 0 5269.5165 12.011713
7450 16738.465 0 0 5269.5166 12.011729
7500 16738.465 0 0 5269.5167 12.011736
7550 16738.465 0 0 5269.5168 12.011734
7600 16738.465 0 0 5269.5168 12.011722
7650 16738.466 0 0 5269.517 12.011704
7700 16738.466 0 0 5269.5171 12.011687
7750 16738.467 0 0 5269.5173 12.011681
7800 16738.467 0 0 5269.5175 12.011687
7850 16738.468 0 0 5269.5176 12.0117
7900 16738.468 0 0 5269.5178 12.011712
7950 16738.469 0 0 5269.5179 12.011721
8000 16738.469 0 0 5269.518 12.011724
8050 16738.469 0 0 5269.5181 12.01172
8100 16738.47 0 0 5269.5182 12.011709
8150 16738.47 0 0 5269.5183 12.0117
8200 16738.47 0 0 5269.5185 12.0117
8250 16738.471 0 0 5269.5186 12.011709
8300 16738.471 0 0 5269.5187 12.011719
8350 16738.472 0 0 5269.5189 12.011723
8400 16738.472 0 0 5269.519 12.01172
8450 16738.473 -0.00039690666 0 5269.5189 12.011706
8500 16738.481 -0.0034646804 0 5269.5182 12.011643
8550 16738.483 -0.0045307409 0 5269.5178 12.011621
8600 16738.474 -0.00076532811 0 5269.5189 12.011681
8650 16738.474 0 0 5269.5197 12.011699
8700 16738.475 0 0 5269.5199 12.011715
8750 16738.475 0 0 5269.52 12.011732
8800 16738.475 0 0 5269.52 12.011743
8850 16738.476 0 0 5269.5201 12.011744
8900 16738.476 0 0 5269.5202 12.011735
8950 16738.476 0 0 5269.5203 12.011719
9000 16738.477 0 0 5269.5205 12.011698
9050 16738.477 0 0 5269.5206 12.011683
9100 16738.478 0 0 5269.5208 12.011684
9150 16738.479 0 0 5269.521 12.011701
9200 16738.479 0 0 5269.5212 12.011722
9250 16738.479 0 0 5269.5213 12.011738
9300 16738.48 0 0 5269.5214 12.011746
9350 16738.48 0 0 5269.5214 12.011744
9400 16738.48 0 0 5269.5215 12.011732
9450 16738.48 0 0 5269.5216 12.011715
9500 16738.481 -0.00037652434 0 5269.5216 12.011692
9550 16738.493 -0.005315616 0 5269.5203 12.011611
9600 16738.549 -0.026814368 0 5269.5163 12.011415
9650 16738.765 -0.10191523 0 5269.5092 12.011013
9700 16735.041 1.0589885 0 5269.4979 12.062708
9750 16738.013 0.13550123 0 5269.5101 11.407245
9800 16738.512 -0.011620328 0 5269.5201 11.394974
9850 16738.489 -0.00067270523 0 5269.5237 11.395098
9900 16738.489 -0.00024984554 0 5269.5242 11.395085
9950 16738.49 0 0 5269.5245 11.395076
10000 16738.49 0 0 5269.5246 11.395075
Loop time of 0.15622 on 1 procs for 10000 steps with 81 atoms
Performance: 553065.489 tau/day, 64012.209 timesteps/s
95.7% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0098181 | 0.0098181 | 0.0098181 | 0.0 | 6.28
Neigh | 0.040912 | 0.040912 | 0.040912 | 0.0 | 26.19
Comm | 0.013111 | 0.013111 | 0.013111 | 0.0 | 8.39
Output | 0.0016305 | 0.0016305 | 0.0016305 | 0.0 | 1.04
Modify | 0.085361 | 0.085361 | 0.085361 | 0.0 | 54.64
Other | | 0.005387 | | | 3.45
Nlocal: 81 ave 81 max 81 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 84 ave 84 max 84 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0
Neighbor list builds = 998
Dangerous builds = 997
Total wall time: 0:00:00

338
examples/rigid/log.27Nov18.rigid.atomvar.g++.4 Normal file
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@ -0,0 +1,338 @@
LAMMPS (27 Nov 2018)
using 1 OpenMP thread(s) per MPI task
# Simple rigid body system
units lj
atom_style atomic
atom_modify map array
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
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
variable bodies atom 1.0*gmask(clump1)+2.0*gmask(clump2)+3.0*gmask(clump3)+4.0*gmask(clump4)+5.0*gmask(clump5)+6.0*gmask(clump6)+7.0*gmask(clump7)+8.0*gmask(clump8)+9.0*gmask(clump9)
fix 1 all rigid custom v_bodies
9 rigid bodies with 81 atoms
# 1 chain of connected bodies
#group clump1 id <> 1 9
#group clump2 id <> 9 18
#group clump3 id <> 18 27
#group clump4 id <> 27 36
#group clump5 id <> 36 45
#group clump6 id <> 45 54
#group clump7 id <> 54 63
#group clump8 id <> 63 72
#group clump9 id <> 72 81
#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9
# 2 chains of connected bodies
#group clump1 id <> 1 9
#group clump2 id <> 9 18
#group clump3 id <> 18 27
#group clump4 id <> 27 36
#group clump5 id <> 37 45
#group clump6 id <> 45 54
#group clump7 id <> 54 63
#group clump8 id <> 63 72
#group clump9 id <> 72 81
#fix 1 all poems group clump1 clump2 clump3 clump4
#fix 2 all poems group clump5 clump6 clump7 clump8 clump9
neigh_modify exclude group clump1 clump1
neigh_modify exclude group clump2 clump2
neigh_modify exclude group clump3 clump3
neigh_modify exclude group clump4 clump4
neigh_modify exclude group clump5 clump5
neigh_modify exclude group clump6 clump6
neigh_modify exclude group clump7 clump7
neigh_modify exclude group clump8 clump8
neigh_modify exclude group clump9 clump9
thermo 100
#dump 1 all atom 50 dump.rigid
#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 2 pad 5
#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 3 pad 5
timestep 0.0001
thermo 50
run 10000
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) = 3.955 | 4.049 | 4.33 Mbytes
Step Temp E_pair E_mol TotEng Press
0 115.29439 5235.9179 0 5272.2142 -2.7403788
50 14910.685 571.71558 0 5265.82 32.006171
100 16298.442 136.66184 0 5267.653 16.444229
150 16682.606 17.490511 0 5269.4219 14.900344
200 16733.929 1.372872 0 5269.4617 14.569267
250 16738.853 -0.15252816 0 5269.4864 14.496404
300 16738.588 -0.055171335 0 5269.5002 14.496025
350 16738.492 -0.017444677 0 5269.5077 14.496446
400 16738.464 -0.0060102023 0 5269.5104 14.496618
450 16738.455 -0.0012713351 0 5269.5124 14.496701
500 16738.455 -0.00081068621 0 5269.5128 14.496709
550 16738.455 -0.00083203497 0 5269.5129 14.496707
600 16738.455 -0.00058355356 0 5269.5131 14.496709
650 16738.455 -0.00047226704 0 5269.5131 14.496708
700 16738.455 0 0 5269.5136 14.496713
750 16738.455 0 0 5269.5136 14.49671
800 16738.455 0 0 5269.5137 14.496709
850 16738.455 0 0 5269.5137 14.49671
900 16738.456 0 0 5269.5138 14.496713
950 16738.462 -0.0035323872 0 5269.5122 14.496671
1000 16738.586 -0.051135144 0 5269.5036 14.496229
1050 16737.358 0.32995057 0 5269.4981 14.525763
1100 16737.892 0.16210246 0 5269.4984 14.531983
1150 16738.703 -0.089235095 0 5269.5025 14.509899
1200 16738.466 -0.0075446243 0 5269.5096 14.510615
1250 16738.456 0 0 5269.514 14.510704
1300 16738.457 0 0 5269.5141 14.510701
1350 16738.457 0 0 5269.5141 14.510699
1400 16738.457 -0.00044736511 0 5269.5138 14.510693
1450 16738.458 -0.0010971179 0 5269.5134 14.510687
1500 16738.458 -0.00057885428 0 5269.5139 14.510698
1550 16738.457 0 0 5269.5143 14.51071
1600 16738.457 0 0 5269.5144 14.510712
1650 16738.457 0 0 5269.5144 14.510712
1700 16738.458 0 0 5269.5144 14.51071
1750 16738.458 0 0 5269.5145 14.510708
1800 16738.458 0 0 5269.5145 14.510706
1850 16738.458 0 0 5269.5146 14.510705
1900 16738.458 0 0 5269.5146 14.510706
1950 16738.465 -0.0031733615 0 5269.5134 14.510659
2000 16738.491 -0.013255268 0 5269.5117 14.510532
2050 16738.556 -0.0365811 0 5269.5087 14.51029
2100 16738.633 -0.063209659 0 5269.5065 14.510219
2150 16738.607 -0.05601761 0 5269.5055 14.510231
2200 16738.557 -0.038423032 0 5269.5072 14.510404
2250 16738.515 -0.023709918 0 5269.5088 14.510539
2300 16738.489 -0.013249035 0 5269.5111 14.510621
2350 16738.468 -0.0045563719 0 5269.5131 14.510714
2400 16738.46 -0.00052194273 0 5269.5146 14.510771
2450 16738.464 -0.0023259756 0 5269.514 14.510746
2500 16738.468 -0.0051929186 0 5269.5127 14.510731
2550 16738.581 -0.044940117 0 5269.5085 14.510315
2600 16738.427 -7.9722832e-05 0 5269.5046 14.510657
2650 16733.017 1.705148 0 5269.5067 14.596295
2700 16738.761 -0.10614946 0 5269.5038 14.499584
2750 16733.973 1.4038179 0 5269.5064 14.598107
2800 16738.585 -0.046813448 0 5269.5076 14.511073
2850 16738.487 -0.012558719 0 5269.5111 14.510111
2900 16738.465 -0.0026252725 0 5269.514 14.510277
2950 16738.476 -0.0082220764 0 5269.512 14.510223
3000 16738.66 -0.071284779 0 5269.507 14.509758
3050 16715.332 7.2419351 0 5269.476 14.870305
3100 16653.226 26.818761 0 5269.5009 14.496764
3150 16739.351 -0.30690375 0 5269.4886 13.643904
3200 16733.238 1.6025328 0 5269.4737 12.016934
3250 16734.374 1.2554429 0 5269.4841 11.963561
3300 16732.156 1.9585967 0 5269.4893 12.234024
3350 16738.655 -0.079693236 0 5269.497 12.092757
3400 16738.543 -0.042215005 0 5269.4991 12.092809
3450 16738.591 -0.059327511 0 5269.4972 12.092536
3500 16738.759 -0.11761245 0 5269.4918 12.09203
3550 16713.405 7.846062 0 5269.4737 12.389816
3600 16734.939 1.0821936 0 5269.4891 12.173591
3650 16738.808 -0.13663194 0 5269.4882 12.027009
3700 16738.602 -0.070934368 0 5269.4889 12.025288
3750 16737.731 0.20706557 0 5269.4927 12.061948
3800 16738.578 -0.05582043 0 5269.4965 12.035665
3850 16738.471 -0.016307928 0 5269.5024 12.035302
3900 16738.449 -0.0058182199 0 5269.5059 12.035401
3950 16738.439 -0.0012027325 0 5269.5074 12.035461
4000 16738.436 -0.00020698452 0 5269.5075 12.035469
4050 16738.437 0 0 5269.5078 12.035454
4100 16738.437 0 0 5269.508 12.035435
4150 16738.438 0 0 5269.5081 12.035426
4200 16738.438 0 0 5269.5083 12.035432
4250 16738.439 0 0 5269.5085 12.035447
4300 16738.439 0 0 5269.5086 12.035463
4350 16738.44 0 0 5269.5087 12.035474
4400 16738.44 0 0 5269.5088 12.035478
4450 16738.44 0 0 5269.5089 12.035474
4500 16738.44 0 0 5269.509 12.035462
4550 16738.441 0 0 5269.5092 12.035449
4600 16738.441 0 0 5269.5093 12.035445
4650 16738.442 0 0 5269.5095 12.035451
4700 16738.442 0 0 5269.5096 12.03546
4750 16738.443 0 0 5269.5097 12.035465
4800 16738.443 0 0 5269.5098 12.035466
4850 16738.443 0 0 5269.51 12.035463
4900 16738.444 0 0 5269.5101 12.035456
4950 16738.444 0 0 5269.5102 12.035447
5000 16738.445 0 0 5269.5104 12.03544
5050 16738.445 0 0 5269.5105 12.035442
5100 16738.446 0 0 5269.5107 12.035455
5150 16738.446 0 0 5269.5108 12.03547
5200 16738.446 0 0 5269.5109 12.035479
5250 16738.447 0 0 5269.511 12.035479
5300 16738.447 0 0 5269.5111 12.03547
5350 16738.447 0 0 5269.5112 12.035454
5400 16738.448 0 0 5269.5113 12.035434
5450 16738.448 0 0 5269.5115 12.03542
5500 16738.449 0 0 5269.5117 12.035422
5550 16738.457 -0.0030919234 0 5269.5111 12.035383
5600 16738.51 -0.021618357 0 5269.5092 12.035106
5650 16738.622 -0.059214788 0 5269.507 12.035694
5700 16395.28 108.06942 0 5269.5463 24.369038
5750 16738.544 -0.033973429 0 5269.5077 12.011261
5800 16738.456 -0.0037013529 0 5269.5102 12.011675
5850 16738.451 0 0 5269.5123 12.011709
5900 16738.451 -0.00022115871 0 5269.5122 12.011687
5950 16738.452 -0.00024253349 0 5269.5124 12.011678
6000 16738.452 0 0 5269.5128 12.011688
6050 16738.453 0 0 5269.513 12.011702
6100 16738.453 0 0 5269.5131 12.011716
6150 16738.454 0 0 5269.5132 12.011725
6200 16738.454 0 0 5269.5133 12.011728
6250 16738.454 0 0 5269.5134 12.011723
6300 16738.455 0 0 5269.5135 12.011712
6350 16738.455 0 0 5269.5137 12.0117
6400 16738.456 0 0 5269.5138 12.011697
6450 16738.456 0 0 5269.514 12.011704
6500 16738.456 0 0 5269.5141 12.011714
6550 16738.457 0 0 5269.5142 12.011719
6600 16738.457 0 0 5269.5143 12.011718
6650 16738.458 0 0 5269.5144 12.011713
6700 16738.458 0 0 5269.5146 12.011705
6750 16738.459 0 0 5269.5147 12.011696
6800 16738.459 0 0 5269.5149 12.01169
6850 16738.46 0 0 5269.515 12.011695
6900 16738.46 0 0 5269.5152 12.01171
6950 16738.46 0 0 5269.5153 12.011726
7000 16738.461 0 0 5269.5154 12.011736
7050 16738.461 0 0 5269.5155 12.011737
7100 16738.461 0 0 5269.5155 12.011728
7150 16738.461 0 0 5269.5156 12.011712
7200 16738.462 0 0 5269.5158 12.011691
7250 16738.463 0 0 5269.516 12.011676
7300 16738.463 0 0 5269.5162 12.011677
7350 16738.464 0 0 5269.5164 12.011693
7400 16738.464 0 0 5269.5165 12.011713
7450 16738.465 0 0 5269.5166 12.011729
7500 16738.465 0 0 5269.5167 12.011736
7550 16738.465 0 0 5269.5168 12.011734
7600 16738.465 0 0 5269.5168 12.011722
7650 16738.466 0 0 5269.517 12.011704
7700 16738.466 0 0 5269.5171 12.011687
7750 16738.467 0 0 5269.5173 12.011681
7800 16738.467 0 0 5269.5175 12.011687
7850 16738.468 0 0 5269.5176 12.0117
7900 16738.468 0 0 5269.5178 12.011712
7950 16738.469 0 0 5269.5179 12.011721
8000 16738.469 0 0 5269.518 12.011724
8050 16738.469 0 0 5269.5181 12.01172
8100 16738.47 0 0 5269.5182 12.011709
8150 16738.47 0 0 5269.5183 12.0117
8200 16738.47 0 0 5269.5185 12.0117
8250 16738.471 0 0 5269.5186 12.011709
8300 16738.471 0 0 5269.5187 12.011719
8350 16738.472 0 0 5269.5189 12.011723
8400 16738.472 0 0 5269.519 12.01172
8450 16738.473 -0.00039690663 0 5269.5189 12.011706
8500 16738.481 -0.0034646803 0 5269.5182 12.011643
8550 16738.483 -0.0045307409 0 5269.5178 12.011621
8600 16738.474 -0.00076532813 0 5269.5189 12.011681
8650 16738.474 0 0 5269.5197 12.011699
8700 16738.475 0 0 5269.5199 12.011715
8750 16738.475 0 0 5269.52 12.011732
8800 16738.475 0 0 5269.52 12.011743
8850 16738.476 0 0 5269.5201 12.011744
8900 16738.476 0 0 5269.5202 12.011735
8950 16738.476 0 0 5269.5203 12.011719
9000 16738.477 0 0 5269.5205 12.011698
9050 16738.477 0 0 5269.5206 12.011683
9100 16738.478 0 0 5269.5208 12.011684
9150 16738.479 0 0 5269.521 12.011701
9200 16738.479 0 0 5269.5212 12.011722
9250 16738.479 0 0 5269.5213 12.011738
9300 16738.48 0 0 5269.5214 12.011746
9350 16738.48 0 0 5269.5214 12.011744
9400 16738.48 0 0 5269.5215 12.011732
9450 16738.48 0 0 5269.5216 12.011715
9500 16738.481 -0.00037652438 0 5269.5216 12.011692
9550 16738.493 -0.0053156163 0 5269.5203 12.011611
9600 16738.549 -0.026814371 0 5269.5163 12.011415
9650 16738.765 -0.10191523 0 5269.5092 12.011013
9700 16735.041 1.0589894 0 5269.4979 12.062708
9750 16738.013 0.13550109 0 5269.5101 11.407246
9800 16738.512 -0.011620327 0 5269.5201 11.394974
9850 16738.489 -0.00067270507 0 5269.5237 11.395098
9900 16738.489 -0.00024984555 0 5269.5242 11.395085
9950 16738.49 0 0 5269.5245 11.395076
10000 16738.49 0 0 5269.5246 11.395075
Loop time of 0.199799 on 4 procs for 10000 steps with 81 atoms
Performance: 432434.078 tau/day, 50050.241 timesteps/s
91.0% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.002665 | 0.0034567 | 0.0040557 | 0.9 | 1.73
Neigh | 0.012185 | 0.013168 | 0.014083 | 0.8 | 6.59
Comm | 0.079331 | 0.082804 | 0.084927 | 0.7 | 41.44
Output | 0.0031595 | 0.0039212 | 0.0061827 | 2.1 | 1.96
Modify | 0.088465 | 0.090202 | 0.091938 | 0.4 | 45.15
Other | | 0.006247 | | | 3.13
Nlocal: 20.25 ave 38 max 3 min
Histogram: 1 0 1 0 0 0 1 0 0 1
Nghost: 27.25 ave 48 max 13 min
Histogram: 1 0 1 1 0 0 0 0 0 1
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0
Neighbor list builds = 998
Dangerous builds = 997
Total wall time: 0:00:00

337
examples/rigid/log.27Nov18.rigid.early.g++.1 Normal file
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@ -0,0 +1,337 @@
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
9 atoms in group clump1
group clump2 id <> 10 18
9 atoms in group clump2
group clump3 id <> 19 27
9 atoms in group clump3
group clump4 id <> 28 36
9 atoms in group clump4
group clump5 id <> 37 45
9 atoms in group clump5
group clump6 id <> 46 54
9 atoms in group clump6
group clump7 id <> 55 63
9 atoms in group clump7
group clump8 id <> 64 72
9 atoms in group clump8
group clump9 id <> 73 81
9 atoms in group clump9
fix 1 all rigid group 9 clump1 clump2 clump3 clump4 clump5 clump6 clump7 clump8 clump9
9 rigid bodies with 81 atoms
fix_modify 1 bodyforces early
# 1 chain of connected bodies
#group clump1 id <> 1 9
#group clump2 id <> 9 18
#group clump3 id <> 18 27
#group clump4 id <> 27 36
#group clump5 id <> 36 45
#group clump6 id <> 45 54
#group clump7 id <> 54 63
#group clump8 id <> 63 72
#group clump9 id <> 72 81
#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9
# 2 chains of connected bodies
#group clump1 id <> 1 9
#group clump2 id <> 9 18
#group clump3 id <> 18 27
#group clump4 id <> 27 36
#group clump5 id <> 37 45
#group clump6 id <> 45 54
#group clump7 id <> 54 63
#group clump8 id <> 63 72
#group clump9 id <> 72 81
#fix 1 all poems group clump1 clump2 clump3 clump4
#fix 2 all poems group clump5 clump6 clump7 clump8 clump9
neigh_modify exclude group clump1 clump1
neigh_modify exclude group clump2 clump2
neigh_modify exclude group clump3 clump3
neigh_modify exclude group clump4 clump4
neigh_modify exclude group clump5 clump5
neigh_modify exclude group clump6 clump6
neigh_modify exclude group clump7 clump7
neigh_modify exclude group clump8 clump8
neigh_modify exclude group clump9 clump9
thermo 100
#dump 1 all atom 50 dump.rigid
#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 2 pad 5
#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 3 pad 5
timestep 0.0001
thermo 50
run 10000
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) = 3.979 | 3.979 | 3.979 Mbytes
Step Temp E_pair E_mol TotEng Press
0 115.29439 5235.9179 0 5272.2142 -2.7403788
50 14910.685 571.71558 0 5265.82 32.006171
100 16298.442 136.66184 0 5267.653 16.444229
150 16682.606 17.490511 0 5269.4219 14.900344
200 16733.929 1.372872 0 5269.4617 14.569267
250 16738.853 -0.15252816 0 5269.4864 14.496404
300 16738.588 -0.055171335 0 5269.5002 14.496025
350 16738.492 -0.017444677 0 5269.5077 14.496446
400 16738.464 -0.0060102023 0 5269.5104 14.496618
450 16738.455 -0.0012713351 0 5269.5124 14.496701
500 16738.455 -0.00081068621 0 5269.5128 14.496709
550 16738.455 -0.00083203497 0 5269.5129 14.496707
600 16738.455 -0.00058355356 0 5269.5131 14.496709
650 16738.455 -0.00047226704 0 5269.5131 14.496708
700 16738.455 0 0 5269.5136 14.496713
750 16738.455 0 0 5269.5136 14.49671
800 16738.455 0 0 5269.5137 14.496709
850 16738.455 0 0 5269.5137 14.49671
900 16738.456 0 0 5269.5138 14.496713
950 16738.462 -0.0035323872 0 5269.5122 14.496671
1000 16738.586 -0.051135144 0 5269.5036 14.496229
1050 16737.358 0.32995057 0 5269.4981 14.525763
1100 16737.892 0.16210246 0 5269.4984 14.531983
1150 16738.703 -0.089235095 0 5269.5025 14.509899
1200 16738.466 -0.0075446243 0 5269.5096 14.510615
1250 16738.456 0 0 5269.514 14.510704
1300 16738.457 0 0 5269.5141 14.510701
1350 16738.457 0 0 5269.5141 14.510699
1400 16738.457 -0.00044736511 0 5269.5138 14.510693
1450 16738.458 -0.0010971179 0 5269.5134 14.510687
1500 16738.458 -0.00057885428 0 5269.5139 14.510698
1550 16738.457 0 0 5269.5143 14.51071
1600 16738.457 0 0 5269.5144 14.510712
1650 16738.457 0 0 5269.5144 14.510712
1700 16738.458 0 0 5269.5144 14.51071
1750 16738.458 0 0 5269.5145 14.510708
1800 16738.458 0 0 5269.5145 14.510706
1850 16738.458 0 0 5269.5146 14.510705
1900 16738.458 0 0 5269.5146 14.510706
1950 16738.465 -0.0031733615 0 5269.5134 14.510659
2000 16738.491 -0.013255268 0 5269.5117 14.510532
2050 16738.556 -0.0365811 0 5269.5087 14.51029
2100 16738.633 -0.063209659 0 5269.5065 14.510219
2150 16738.607 -0.05601761 0 5269.5055 14.510231
2200 16738.557 -0.038423032 0 5269.5072 14.510404
2250 16738.515 -0.023709918 0 5269.5088 14.510539
2300 16738.489 -0.013249035 0 5269.5111 14.510621
2350 16738.468 -0.0045563719 0 5269.5131 14.510714
2400 16738.46 -0.00052194273 0 5269.5146 14.510771
2450 16738.464 -0.0023259756 0 5269.514 14.510746
2500 16738.468 -0.0051929186 0 5269.5127 14.510731
2550 16738.581 -0.044940117 0 5269.5085 14.510315
2600 16738.427 -7.972284e-05 0 5269.5046 14.510657
2650 16733.017 1.7051479 0 5269.5067 14.596295
2700 16738.761 -0.10614946 0 5269.5038 14.499584
2750 16733.973 1.4038179 0 5269.5064 14.598107
2800 16738.585 -0.046813448 0 5269.5076 14.511073
2850 16738.487 -0.012558719 0 5269.5111 14.510111
2900 16738.465 -0.0026252725 0 5269.514 14.510277
2950 16738.476 -0.0082220764 0 5269.512 14.510223
3000 16738.66 -0.071284779 0 5269.507 14.509758
3050 16715.332 7.2419352 0 5269.476 14.870305
3100 16653.226 26.818761 0 5269.5009 14.496764
3150 16739.351 -0.30690375 0 5269.4886 13.643904
3200 16733.238 1.6025328 0 5269.4737 12.016934
3250 16734.374 1.2554429 0 5269.4841 11.963561
3300 16732.156 1.9585967 0 5269.4893 12.234024
3350 16738.655 -0.079693236 0 5269.497 12.092757
3400 16738.543 -0.042215005 0 5269.4991 12.092809
3450 16738.591 -0.059327511 0 5269.4972 12.092536
3500 16738.759 -0.11761245 0 5269.4918 12.09203
3550 16713.405 7.8460621 0 5269.4737 12.389816
3600 16734.939 1.0821936 0 5269.4891 12.173591
3650 16738.808 -0.13663194 0 5269.4882 12.027009
3700 16738.602 -0.070934368 0 5269.4889 12.025288
3750 16737.731 0.20706558 0 5269.4927 12.061948
3800 16738.578 -0.05582043 0 5269.4965 12.035665
3850 16738.471 -0.016307928 0 5269.5024 12.035302
3900 16738.449 -0.0058182199 0 5269.5059 12.035401
3950 16738.439 -0.0012027325 0 5269.5074 12.035461
4000 16738.436 -0.00020698452 0 5269.5075 12.035469
4050 16738.437 0 0 5269.5078 12.035454
4100 16738.437 0 0 5269.508 12.035435
4150 16738.438 0 0 5269.5081 12.035426
4200 16738.438 0 0 5269.5083 12.035432
4250 16738.439 0 0 5269.5085 12.035447
4300 16738.439 0 0 5269.5086 12.035463
4350 16738.44 0 0 5269.5087 12.035474
4400 16738.44 0 0 5269.5088 12.035478
4450 16738.44 0 0 5269.5089 12.035474
4500 16738.44 0 0 5269.509 12.035462
4550 16738.441 0 0 5269.5092 12.035449
4600 16738.441 0 0 5269.5093 12.035445
4650 16738.442 0 0 5269.5095 12.035451
4700 16738.442 0 0 5269.5096 12.03546
4750 16738.443 0 0 5269.5097 12.035465
4800 16738.443 0 0 5269.5098 12.035466
4850 16738.443 0 0 5269.51 12.035463
4900 16738.444 0 0 5269.5101 12.035456
4950 16738.444 0 0 5269.5102 12.035447
5000 16738.445 0 0 5269.5104 12.03544
5050 16738.445 0 0 5269.5105 12.035442
5100 16738.446 0 0 5269.5107 12.035455
5150 16738.446 0 0 5269.5108 12.03547
5200 16738.446 0 0 5269.5109 12.035479
5250 16738.447 0 0 5269.511 12.035479
5300 16738.447 0 0 5269.5111 12.03547
5350 16738.447 0 0 5269.5112 12.035454
5400 16738.448 0 0 5269.5113 12.035434
5450 16738.448 0 0 5269.5115 12.03542
5500 16738.449 0 0 5269.5117 12.035422
5550 16738.457 -0.0030919234 0 5269.5111 12.035383
5600 16738.51 -0.021618357 0 5269.5092 12.035106
5650 16738.622 -0.059214788 0 5269.507 12.035694
5700 16395.28 108.06942 0 5269.5463 24.369038
5750 16738.544 -0.033973429 0 5269.5077 12.011261
5800 16738.456 -0.0037013529 0 5269.5102 12.011675
5850 16738.451 0 0 5269.5123 12.011709
5900 16738.451 -0.0002211587 0 5269.5122 12.011687
5950 16738.452 -0.00024253349 0 5269.5124 12.011678
6000 16738.452 0 0 5269.5128 12.011688
6050 16738.453 0 0 5269.513 12.011702
6100 16738.453 0 0 5269.5131 12.011716
6150 16738.454 0 0 5269.5132 12.011725
6200 16738.454 0 0 5269.5133 12.011728
6250 16738.454 0 0 5269.5134 12.011723
6300 16738.455 0 0 5269.5135 12.011712
6350 16738.455 0 0 5269.5137 12.0117
6400 16738.456 0 0 5269.5138 12.011697
6450 16738.456 0 0 5269.514 12.011704
6500 16738.456 0 0 5269.5141 12.011714
6550 16738.457 0 0 5269.5142 12.011719
6600 16738.457 0 0 5269.5143 12.011718
6650 16738.458 0 0 5269.5144 12.011713
6700 16738.458 0 0 5269.5146 12.011705
6750 16738.459 0 0 5269.5147 12.011696
6800 16738.459 0 0 5269.5149 12.01169
6850 16738.46 0 0 5269.515 12.011695
6900 16738.46 0 0 5269.5152 12.01171
6950 16738.46 0 0 5269.5153 12.011726
7000 16738.461 0 0 5269.5154 12.011736
7050 16738.461 0 0 5269.5155 12.011737
7100 16738.461 0 0 5269.5155 12.011728
7150 16738.461 0 0 5269.5156 12.011712
7200 16738.462 0 0 5269.5158 12.011691
7250 16738.463 0 0 5269.516 12.011676
7300 16738.463 0 0 5269.5162 12.011677
7350 16738.464 0 0 5269.5164 12.011693
7400 16738.464 0 0 5269.5165 12.011713
7450 16738.465 0 0 5269.5166 12.011729
7500 16738.465 0 0 5269.5167 12.011736
7550 16738.465 0 0 5269.5168 12.011734
7600 16738.465 0 0 5269.5168 12.011722
7650 16738.466 0 0 5269.517 12.011704
7700 16738.466 0 0 5269.5171 12.011687
7750 16738.467 0 0 5269.5173 12.011681
7800 16738.467 0 0 5269.5175 12.011687
7850 16738.468 0 0 5269.5176 12.0117
7900 16738.468 0 0 5269.5178 12.011712
7950 16738.469 0 0 5269.5179 12.011721
8000 16738.469 0 0 5269.518 12.011724
8050 16738.469 0 0 5269.5181 12.01172
8100 16738.47 0 0 5269.5182 12.011709
8150 16738.47 0 0 5269.5183 12.0117
8200 16738.47 0 0 5269.5185 12.0117
8250 16738.471 0 0 5269.5186 12.011709
8300 16738.471 0 0 5269.5187 12.011719
8350 16738.472 0 0 5269.5189 12.011723
8400 16738.472 0 0 5269.519 12.01172
8450 16738.473 -0.00039690666 0 5269.5189 12.011706
8500 16738.481 -0.0034646804 0 5269.5182 12.011643
8550 16738.483 -0.0045307409 0 5269.5178 12.011621
8600 16738.474 -0.00076532811 0 5269.5189 12.011681
8650 16738.474 0 0 5269.5197 12.011699
8700 16738.475 0 0 5269.5199 12.011715
8750 16738.475 0 0 5269.52 12.011732
8800 16738.475 0 0 5269.52 12.011743
8850 16738.476 0 0 5269.5201 12.011744
8900 16738.476 0 0 5269.5202 12.011735
8950 16738.476 0 0 5269.5203 12.011719
9000 16738.477 0 0 5269.5205 12.011698
9050 16738.477 0 0 5269.5206 12.011683
9100 16738.478 0 0 5269.5208 12.011684
9150 16738.479 0 0 5269.521 12.011701
9200 16738.479 0 0 5269.5212 12.011722
9250 16738.479 0 0 5269.5213 12.011738
9300 16738.48 0 0 5269.5214 12.011746
9350 16738.48 0 0 5269.5214 12.011744
9400 16738.48 0 0 5269.5215 12.011732
9450 16738.48 0 0 5269.5216 12.011715
9500 16738.481 -0.00037652434 0 5269.5216 12.011692
9550 16738.493 -0.005315616 0 5269.5203 12.011611
9600 16738.549 -0.026814368 0 5269.5163 12.011415
9650 16738.765 -0.10191523 0 5269.5092 12.011013
9700 16735.041 1.0589885 0 5269.4979 12.062708
9750 16738.013 0.13550123 0 5269.5101 11.407245
9800 16738.512 -0.011620328 0 5269.5201 11.394974
9850 16738.489 -0.00067270523 0 5269.5237 11.395098
9900 16738.489 -0.00024984554 0 5269.5242 11.395085
9950 16738.49 0 0 5269.5245 11.395076
10000 16738.49 0 0 5269.5246 11.395075
Loop time of 0.152593 on 1 procs for 10000 steps with 81 atoms
Performance: 566210.692 tau/day, 65533.645 timesteps/s
96.1% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0098324 | 0.0098324 | 0.0098324 | 0.0 | 6.44
Neigh | 0.040376 | 0.040376 | 0.040376 | 0.0 | 26.46
Comm | 0.012246 | 0.012246 | 0.012246 | 0.0 | 8.03
Output | 0.0016036 | 0.0016036 | 0.0016036 | 0.0 | 1.05
Modify | 0.083605 | 0.083605 | 0.083605 | 0.0 | 54.79
Other | | 0.00493 | | | 3.23
Nlocal: 81 ave 81 max 81 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 84 ave 84 max 84 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0
Neighbor list builds = 998
Dangerous builds = 997
Total wall time: 0:00:00

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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
9 atoms in group clump1
group clump2 id <> 10 18
9 atoms in group clump2
group clump3 id <> 19 27
9 atoms in group clump3
group clump4 id <> 28 36
9 atoms in group clump4
group clump5 id <> 37 45
9 atoms in group clump5
group clump6 id <> 46 54
9 atoms in group clump6
group clump7 id <> 55 63
9 atoms in group clump7
group clump8 id <> 64 72
9 atoms in group clump8
group clump9 id <> 73 81
9 atoms in group clump9
fix 1 all rigid group 9 clump1 clump2 clump3 clump4 clump5 clump6 clump7 clump8 clump9
9 rigid bodies with 81 atoms
fix_modify 1 bodyforces early
# 1 chain of connected bodies
#group clump1 id <> 1 9
#group clump2 id <> 9 18
#group clump3 id <> 18 27
#group clump4 id <> 27 36
#group clump5 id <> 36 45
#group clump6 id <> 45 54
#group clump7 id <> 54 63
#group clump8 id <> 63 72
#group clump9 id <> 72 81
#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9
# 2 chains of connected bodies
#group clump1 id <> 1 9
#group clump2 id <> 9 18
#group clump3 id <> 18 27
#group clump4 id <> 27 36
#group clump5 id <> 37 45
#group clump6 id <> 45 54
#group clump7 id <> 54 63
#group clump8 id <> 63 72
#group clump9 id <> 72 81
#fix 1 all poems group clump1 clump2 clump3 clump4
#fix 2 all poems group clump5 clump6 clump7 clump8 clump9
neigh_modify exclude group clump1 clump1
neigh_modify exclude group clump2 clump2
neigh_modify exclude group clump3 clump3
neigh_modify exclude group clump4 clump4
neigh_modify exclude group clump5 clump5
neigh_modify exclude group clump6 clump6
neigh_modify exclude group clump7 clump7
neigh_modify exclude group clump8 clump8
neigh_modify exclude group clump9 clump9
thermo 100
#dump 1 all atom 50 dump.rigid
#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 2 pad 5
#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 3 pad 5
timestep 0.0001
thermo 50
run 10000
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) = 3.95 | 4.044 | 4.326 Mbytes
Step Temp E_pair E_mol TotEng Press
0 115.29439 5235.9179 0 5272.2142 -2.7403788
50 14910.685 571.71558 0 5265.82 32.006171
100 16298.442 136.66184 0 5267.653 16.444229
150 16682.606 17.490511 0 5269.4219 14.900344
200 16733.929 1.372872 0 5269.4617 14.569267
250 16738.853 -0.15252816 0 5269.4864 14.496404
300 16738.588 -0.055171335 0 5269.5002 14.496025
350 16738.492 -0.017444677 0 5269.5077 14.496446
400 16738.464 -0.0060102023 0 5269.5104 14.496618
450 16738.455 -0.0012713351 0 5269.5124 14.496701
500 16738.455 -0.00081068621 0 5269.5128 14.496709
550 16738.455 -0.00083203497 0 5269.5129 14.496707
600 16738.455 -0.00058355356 0 5269.5131 14.496709
650 16738.455 -0.00047226704 0 5269.5131 14.496708
700 16738.455 0 0 5269.5136 14.496713
750 16738.455 0 0 5269.5136 14.49671
800 16738.455 0 0 5269.5137 14.496709
850 16738.455 0 0 5269.5137 14.49671
900 16738.456 0 0 5269.5138 14.496713
950 16738.462 -0.0035323872 0 5269.5122 14.496671
1000 16738.586 -0.051135144 0 5269.5036 14.496229
1050 16737.358 0.32995057 0 5269.4981 14.525763
1100 16737.892 0.16210246 0 5269.4984 14.531983
1150 16738.703 -0.089235095 0 5269.5025 14.509899
1200 16738.466 -0.0075446243 0 5269.5096 14.510615
1250 16738.456 0 0 5269.514 14.510704
1300 16738.457 0 0 5269.5141 14.510701
1350 16738.457 0 0 5269.5141 14.510699
1400 16738.457 -0.00044736511 0 5269.5138 14.510693
1450 16738.458 -0.0010971179 0 5269.5134 14.510687
1500 16738.458 -0.00057885428 0 5269.5139 14.510698
1550 16738.457 0 0 5269.5143 14.51071
1600 16738.457 0 0 5269.5144 14.510712
1650 16738.457 0 0 5269.5144 14.510712
1700 16738.458 0 0 5269.5144 14.51071
1750 16738.458 0 0 5269.5145 14.510708
1800 16738.458 0 0 5269.5145 14.510706
1850 16738.458 0 0 5269.5146 14.510705
1900 16738.458 0 0 5269.5146 14.510706
1950 16738.465 -0.0031733615 0 5269.5134 14.510659
2000 16738.491 -0.013255268 0 5269.5117 14.510532
2050 16738.556 -0.0365811 0 5269.5087 14.51029
2100 16738.633 -0.063209659 0 5269.5065 14.510219
2150 16738.607 -0.05601761 0 5269.5055 14.510231
2200 16738.557 -0.038423032 0 5269.5072 14.510404
2250 16738.515 -0.023709918 0 5269.5088 14.510539
2300 16738.489 -0.013249035 0 5269.5111 14.510621
2350 16738.468 -0.0045563719 0 5269.5131 14.510714
2400 16738.46 -0.00052194273 0 5269.5146 14.510771
2450 16738.464 -0.0023259756 0 5269.514 14.510746
2500 16738.468 -0.0051929186 0 5269.5127 14.510731
2550 16738.581 -0.044940117 0 5269.5085 14.510315
2600 16738.427 -7.9722832e-05 0 5269.5046 14.510657
2650 16733.017 1.705148 0 5269.5067 14.596295
2700 16738.761 -0.10614946 0 5269.5038 14.499584
2750 16733.973 1.4038179 0 5269.5064 14.598107
2800 16738.585 -0.046813448 0 5269.5076 14.511073
2850 16738.487 -0.012558719 0 5269.5111 14.510111
2900 16738.465 -0.0026252725 0 5269.514 14.510277
2950 16738.476 -0.0082220764 0 5269.512 14.510223
3000 16738.66 -0.071284779 0 5269.507 14.509758
3050 16715.332 7.2419351 0 5269.476 14.870305
3100 16653.226 26.818761 0 5269.5009 14.496764
3150 16739.351 -0.30690375 0 5269.4886 13.643904
3200 16733.238 1.6025328 0 5269.4737 12.016934
3250 16734.374 1.2554429 0 5269.4841 11.963561
3300 16732.156 1.9585967 0 5269.4893 12.234024
3350 16738.655 -0.079693236 0 5269.497 12.092757
3400 16738.543 -0.042215005 0 5269.4991 12.092809
3450 16738.591 -0.059327511 0 5269.4972 12.092536
3500 16738.759 -0.11761245 0 5269.4918 12.09203
3550 16713.405 7.846062 0 5269.4737 12.389816
3600 16734.939 1.0821936 0 5269.4891 12.173591
3650 16738.808 -0.13663194 0 5269.4882 12.027009
3700 16738.602 -0.070934368 0 5269.4889 12.025288
3750 16737.731 0.20706557 0 5269.4927 12.061948
3800 16738.578 -0.05582043 0 5269.4965 12.035665
3850 16738.471 -0.016307928 0 5269.5024 12.035302
3900 16738.449 -0.0058182199 0 5269.5059 12.035401
3950 16738.439 -0.0012027325 0 5269.5074 12.035461
4000 16738.436 -0.00020698452 0 5269.5075 12.035469
4050 16738.437 0 0 5269.5078 12.035454
4100 16738.437 0 0 5269.508 12.035435
4150 16738.438 0 0 5269.5081 12.035426
4200 16738.438 0 0 5269.5083 12.035432
4250 16738.439 0 0 5269.5085 12.035447
4300 16738.439 0 0 5269.5086 12.035463
4350 16738.44 0 0 5269.5087 12.035474
4400 16738.44 0 0 5269.5088 12.035478
4450 16738.44 0 0 5269.5089 12.035474
4500 16738.44 0 0 5269.509 12.035462
4550 16738.441 0 0 5269.5092 12.035449
4600 16738.441 0 0 5269.5093 12.035445
4650 16738.442 0 0 5269.5095 12.035451
4700 16738.442 0 0 5269.5096 12.03546
4750 16738.443 0 0 5269.5097 12.035465
4800 16738.443 0 0 5269.5098 12.035466
4850 16738.443 0 0 5269.51 12.035463
4900 16738.444 0 0 5269.5101 12.035456
4950 16738.444 0 0 5269.5102 12.035447
5000 16738.445 0 0 5269.5104 12.03544
5050 16738.445 0 0 5269.5105 12.035442
5100 16738.446 0 0 5269.5107 12.035455
5150 16738.446 0 0 5269.5108 12.03547
5200 16738.446 0 0 5269.5109 12.035479
5250 16738.447 0 0 5269.511 12.035479
5300 16738.447 0 0 5269.5111 12.03547
5350 16738.447 0 0 5269.5112 12.035454
5400 16738.448 0 0 5269.5113 12.035434
5450 16738.448 0 0 5269.5115 12.03542
5500 16738.449 0 0 5269.5117 12.035422
5550 16738.457 -0.0030919234 0 5269.5111 12.035383
5600 16738.51 -0.021618357 0 5269.5092 12.035106
5650 16738.622 -0.059214788 0 5269.507 12.035694
5700 16395.28 108.06942 0 5269.5463 24.369038
5750 16738.544 -0.033973429 0 5269.5077 12.011261
5800 16738.456 -0.0037013529 0 5269.5102 12.011675
5850 16738.451 0 0 5269.5123 12.011709
5900 16738.451 -0.00022115871 0 5269.5122 12.011687
5950 16738.452 -0.00024253349 0 5269.5124 12.011678
6000 16738.452 0 0 5269.5128 12.011688
6050 16738.453 0 0 5269.513 12.011702
6100 16738.453 0 0 5269.5131 12.011716
6150 16738.454 0 0 5269.5132 12.011725
6200 16738.454 0 0 5269.5133 12.011728
6250 16738.454 0 0 5269.5134 12.011723
6300 16738.455 0 0 5269.5135 12.011712
6350 16738.455 0 0 5269.5137 12.0117
6400 16738.456 0 0 5269.5138 12.011697
6450 16738.456 0 0 5269.514 12.011704
6500 16738.456 0 0 5269.5141 12.011714
6550 16738.457 0 0 5269.5142 12.011719
6600 16738.457 0 0 5269.5143 12.011718
6650 16738.458 0 0 5269.5144 12.011713
6700 16738.458 0 0 5269.5146 12.011705
6750 16738.459 0 0 5269.5147 12.011696
6800 16738.459 0 0 5269.5149 12.01169
6850 16738.46 0 0 5269.515 12.011695
6900 16738.46 0 0 5269.5152 12.01171
6950 16738.46 0 0 5269.5153 12.011726
7000 16738.461 0 0 5269.5154 12.011736
7050 16738.461 0 0 5269.5155 12.011737
7100 16738.461 0 0 5269.5155 12.011728
7150 16738.461 0 0 5269.5156 12.011712
7200 16738.462 0 0 5269.5158 12.011691
7250 16738.463 0 0 5269.516 12.011676
7300 16738.463 0 0 5269.5162 12.011677
7350 16738.464 0 0 5269.5164 12.011693
7400 16738.464 0 0 5269.5165 12.011713
7450 16738.465 0 0 5269.5166 12.011729
7500 16738.465 0 0 5269.5167 12.011736
7550 16738.465 0 0 5269.5168 12.011734
7600 16738.465 0 0 5269.5168 12.011722
7650 16738.466 0 0 5269.517 12.011704
7700 16738.466 0 0 5269.5171 12.011687
7750 16738.467 0 0 5269.5173 12.011681
7800 16738.467 0 0 5269.5175 12.011687
7850 16738.468 0 0 5269.5176 12.0117
7900 16738.468 0 0 5269.5178 12.011712
7950 16738.469 0 0 5269.5179 12.011721
8000 16738.469 0 0 5269.518 12.011724
8050 16738.469 0 0 5269.5181 12.01172
8100 16738.47 0 0 5269.5182 12.011709
8150 16738.47 0 0 5269.5183 12.0117
8200 16738.47 0 0 5269.5185 12.0117
8250 16738.471 0 0 5269.5186 12.011709
8300 16738.471 0 0 5269.5187 12.011719
8350 16738.472 0 0 5269.5189 12.011723
8400 16738.472 0 0 5269.519 12.01172
8450 16738.473 -0.00039690663 0 5269.5189 12.011706
8500 16738.481 -0.0034646803 0 5269.5182 12.011643
8550 16738.483 -0.0045307409 0 5269.5178 12.011621
8600 16738.474 -0.00076532813 0 5269.5189 12.011681
8650 16738.474 0 0 5269.5197 12.011699
8700 16738.475 0 0 5269.5199 12.011715
8750 16738.475 0 0 5269.52 12.011732
8800 16738.475 0 0 5269.52 12.011743
8850 16738.476 0 0 5269.5201 12.011744
8900 16738.476 0 0 5269.5202 12.011735
8950 16738.476 0 0 5269.5203 12.011719
9000 16738.477 0 0 5269.5205 12.011698
9050 16738.477 0 0 5269.5206 12.011683
9100 16738.478 0 0 5269.5208 12.011684
9150 16738.479 0 0 5269.521 12.011701
9200 16738.479 0 0 5269.5212 12.011722
9250 16738.479 0 0 5269.5213 12.011738
9300 16738.48 0 0 5269.5214 12.011746
9350 16738.48 0 0 5269.5214 12.011744
9400 16738.48 0 0 5269.5215 12.011732
9450 16738.48 0 0 5269.5216 12.011715
9500 16738.481 -0.00037652438 0 5269.5216 12.011692
9550 16738.493 -0.0053156163 0 5269.5203 12.011611
9600 16738.549 -0.026814371 0 5269.5163 12.011415
9650 16738.765 -0.10191523 0 5269.5092 12.011013
9700 16735.041 1.0589894 0 5269.4979 12.062708
9750 16738.013 0.13550109 0 5269.5101 11.407246
9800 16738.512 -0.011620327 0 5269.5201 11.394974
9850 16738.489 -0.00067270507 0 5269.5237 11.395098
9900 16738.489 -0.00024984555 0 5269.5242 11.395085
9950 16738.49 0 0 5269.5245 11.395076
10000 16738.49 0 0 5269.5246 11.395075
Loop time of 0.198859 on 4 procs for 10000 steps with 81 atoms
Performance: 434479.274 tau/day, 50286.953 timesteps/s
91.6% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.002526 | 0.0034331 | 0.0041001 | 1.0 | 1.73
Neigh | 0.012097 | 0.013092 | 0.013992 | 0.8 | 6.58
Comm | 0.075266 | 0.07972 | 0.084679 | 1.2 | 40.09
Output | 0.0030892 | 0.0043746 | 0.0081537 | 3.3 | 2.20
Modify | 0.088037 | 0.091924 | 0.095021 | 0.9 | 46.23
Other | | 0.006316 | | | 3.18
Nlocal: 20.25 ave 38 max 3 min
Histogram: 1 0 1 0 0 0 1 0 0 1
Nghost: 27.25 ave 48 max 13 min
Histogram: 1 0 1 1 0 0 0 0 0 1
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0
Neighbor list builds = 998
Dangerous builds = 997
Total wall time: 0:00:00

335
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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
9 atoms in group clump1
group clump2 id <> 10 18
9 atoms in group clump2
group clump3 id <> 19 27
9 atoms in group clump3
group clump4 id <> 28 36
9 atoms in group clump4
group clump5 id <> 37 45
9 atoms in group clump5
group clump6 id <> 46 54
9 atoms in group clump6
group clump7 id <> 55 63
9 atoms in group clump7
group clump8 id <> 64 72
9 atoms in group clump8
group clump9 id <> 73 81
9 atoms in group clump9
fix 1 all rigid group 9 clump1 clump2 clump3 clump4 clump5 clump6 clump7 clump8 clump9
9 rigid bodies with 81 atoms
# 1 chain of connected bodies
#group clump1 id <> 1 9
#group clump2 id <> 9 18
#group clump3 id <> 18 27
#group clump4 id <> 27 36
#group clump5 id <> 36 45
#group clump6 id <> 45 54
#group clump7 id <> 54 63
#group clump8 id <> 63 72
#group clump9 id <> 72 81
#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9
# 2 chains of connected bodies
#group clump1 id <> 1 9
#group clump2 id <> 9 18
#group clump3 id <> 18 27
#group clump4 id <> 27 36
#group clump5 id <> 37 45
#group clump6 id <> 45 54
#group clump7 id <> 54 63
#group clump8 id <> 63 72
#group clump9 id <> 72 81
#fix 1 all poems group clump1 clump2 clump3 clump4
#fix 2 all poems group clump5 clump6 clump7 clump8 clump9
neigh_modify exclude group clump1 clump1
neigh_modify exclude group clump2 clump2
neigh_modify exclude group clump3 clump3
neigh_modify exclude group clump4 clump4
neigh_modify exclude group clump5 clump5
neigh_modify exclude group clump6 clump6
neigh_modify exclude group clump7 clump7
neigh_modify exclude group clump8 clump8
neigh_modify exclude group clump9 clump9
thermo 100
#dump 1 all atom 50 dump.rigid
#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 2 pad 5
#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 3 pad 5
timestep 0.0001
thermo 50
run 10000
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) = 3.979 | 3.979 | 3.979 Mbytes
Step Temp E_pair E_mol TotEng Press
0 115.29439 5235.9179 0 5272.2142 -2.7403788
50 14910.685 571.71558 0 5265.82 32.006171
100 16298.442 136.66184 0 5267.653 16.444229
150 16682.606 17.490511 0 5269.4219 14.900344
200 16733.929 1.372872 0 5269.4617 14.569267
250 16738.853 -0.15252816 0 5269.4864 14.496404
300 16738.588 -0.055171335 0 5269.5002 14.496025
350 16738.492 -0.017444677 0 5269.5077 14.496446
400 16738.464 -0.0060102023 0 5269.5104 14.496618
450 16738.455 -0.0012713351 0 5269.5124 14.496701
500 16738.455 -0.00081068621 0 5269.5128 14.496709
550 16738.455 -0.00083203497 0 5269.5129 14.496707
600 16738.455 -0.00058355356 0 5269.5131 14.496709
650 16738.455 -0.00047226704 0 5269.5131 14.496708
700 16738.455 0 0 5269.5136 14.496713
750 16738.455 0 0 5269.5136 14.49671
800 16738.455 0 0 5269.5137 14.496709
850 16738.455 0 0 5269.5137 14.49671
900 16738.456 0 0 5269.5138 14.496713
950 16738.462 -0.0035323872 0 5269.5122 14.496671
1000 16738.586 -0.051135144 0 5269.5036 14.496229
1050 16737.358 0.32995057 0 5269.4981 14.525763
1100 16737.892 0.16210246 0 5269.4984 14.531983
1150 16738.703 -0.089235095 0 5269.5025 14.509899
1200 16738.466 -0.0075446243 0 5269.5096 14.510615
1250 16738.456 0 0 5269.514 14.510704
1300 16738.457 0 0 5269.5141 14.510701
1350 16738.457 0 0 5269.5141 14.510699
1400 16738.457 -0.00044736511 0 5269.5138 14.510693
1450 16738.458 -0.0010971179 0 5269.5134 14.510687
1500 16738.458 -0.00057885428 0 5269.5139 14.510698
1550 16738.457 0 0 5269.5143 14.51071
1600 16738.457 0 0 5269.5144 14.510712
1650 16738.457 0 0 5269.5144 14.510712
1700 16738.458 0 0 5269.5144 14.51071
1750 16738.458 0 0 5269.5145 14.510708
1800 16738.458 0 0 5269.5145 14.510706
1850 16738.458 0 0 5269.5146 14.510705
1900 16738.458 0 0 5269.5146 14.510706
1950 16738.465 -0.0031733615 0 5269.5134 14.510659
2000 16738.491 -0.013255268 0 5269.5117 14.510532
2050 16738.556 -0.0365811 0 5269.5087 14.51029
2100 16738.633 -0.063209659 0 5269.5065 14.510219
2150 16738.607 -0.05601761 0 5269.5055 14.510231
2200 16738.557 -0.038423032 0 5269.5072 14.510404
2250 16738.515 -0.023709918 0 5269.5088 14.510539
2300 16738.489 -0.013249035 0 5269.5111 14.510621
2350 16738.468 -0.0045563719 0 5269.5131 14.510714
2400 16738.46 -0.00052194273 0 5269.5146 14.510771
2450 16738.464 -0.0023259756 0 5269.514 14.510746
2500 16738.468 -0.0051929186 0 5269.5127 14.510731
2550 16738.581 -0.044940117 0 5269.5085 14.510315
2600 16738.427 -7.972284e-05 0 5269.5046 14.510657
2650 16733.017 1.7051479 0 5269.5067 14.596295
2700 16738.761 -0.10614946 0 5269.5038 14.499584
2750 16733.973 1.4038179 0 5269.5064 14.598107
2800 16738.585 -0.046813448 0 5269.5076 14.511073
2850 16738.487 -0.012558719 0 5269.5111 14.510111
2900 16738.465 -0.0026252725 0 5269.514 14.510277
2950 16738.476 -0.0082220764 0 5269.512 14.510223
3000 16738.66 -0.071284779 0 5269.507 14.509758
3050 16715.332 7.2419352 0 5269.476 14.870305
3100 16653.226 26.818761 0 5269.5009 14.496764
3150 16739.351 -0.30690375 0 5269.4886 13.643904
3200 16733.238 1.6025328 0 5269.4737 12.016934
3250 16734.374 1.2554429 0 5269.4841 11.963561
3300 16732.156 1.9585967 0 5269.4893 12.234024
3350 16738.655 -0.079693236 0 5269.497 12.092757
3400 16738.543 -0.042215005 0 5269.4991 12.092809
3450 16738.591 -0.059327511 0 5269.4972 12.092536
3500 16738.759 -0.11761245 0 5269.4918 12.09203
3550 16713.405 7.8460621 0 5269.4737 12.389816
3600 16734.939 1.0821936 0 5269.4891 12.173591
3650 16738.808 -0.13663194 0 5269.4882 12.027009
3700 16738.602 -0.070934368 0 5269.4889 12.025288
3750 16737.731 0.20706558 0 5269.4927 12.061948
3800 16738.578 -0.05582043 0 5269.4965 12.035665
3850 16738.471 -0.016307928 0 5269.5024 12.035302
3900 16738.449 -0.0058182199 0 5269.5059 12.035401
3950 16738.439 -0.0012027325 0 5269.5074 12.035461
4000 16738.436 -0.00020698452 0 5269.5075 12.035469
4050 16738.437 0 0 5269.5078 12.035454
4100 16738.437 0 0 5269.508 12.035435
4150 16738.438 0 0 5269.5081 12.035426
4200 16738.438 0 0 5269.5083 12.035432
4250 16738.439 0 0 5269.5085 12.035447
4300 16738.439 0 0 5269.5086 12.035463
4350 16738.44 0 0 5269.5087 12.035474
4400 16738.44 0 0 5269.5088 12.035478
4450 16738.44 0 0 5269.5089 12.035474
4500 16738.44 0 0 5269.509 12.035462
4550 16738.441 0 0 5269.5092 12.035449
4600 16738.441 0 0 5269.5093 12.035445
4650 16738.442 0 0 5269.5095 12.035451
4700 16738.442 0 0 5269.5096 12.03546
4750 16738.443 0 0 5269.5097 12.035465
4800 16738.443 0 0 5269.5098 12.035466
4850 16738.443 0 0 5269.51 12.035463
4900 16738.444 0 0 5269.5101 12.035456
4950 16738.444 0 0 5269.5102 12.035447
5000 16738.445 0 0 5269.5104 12.03544
5050 16738.445 0 0 5269.5105 12.035442
5100 16738.446 0 0 5269.5107 12.035455
5150 16738.446 0 0 5269.5108 12.03547
5200 16738.446 0 0 5269.5109 12.035479
5250 16738.447 0 0 5269.511 12.035479
5300 16738.447 0 0 5269.5111 12.03547
5350 16738.447 0 0 5269.5112 12.035454
5400 16738.448 0 0 5269.5113 12.035434
5450 16738.448 0 0 5269.5115 12.03542
5500 16738.449 0 0 5269.5117 12.035422
5550 16738.457 -0.0030919234 0 5269.5111 12.035383
5600 16738.51 -0.021618357 0 5269.5092 12.035106
5650 16738.622 -0.059214788 0 5269.507 12.035694
5700 16395.28 108.06942 0 5269.5463 24.369038
5750 16738.544 -0.033973429 0 5269.5077 12.011261
5800 16738.456 -0.0037013529 0 5269.5102 12.011675
5850 16738.451 0 0 5269.5123 12.011709
5900 16738.451 -0.0002211587 0 5269.5122 12.011687
5950 16738.452 -0.00024253349 0 5269.5124 12.011678
6000 16738.452 0 0 5269.5128 12.011688
6050 16738.453 0 0 5269.513 12.011702
6100 16738.453 0 0 5269.5131 12.011716
6150 16738.454 0 0 5269.5132 12.011725
6200 16738.454 0 0 5269.5133 12.011728
6250 16738.454 0 0 5269.5134 12.011723
6300 16738.455 0 0 5269.5135 12.011712
6350 16738.455 0 0 5269.5137 12.0117
6400 16738.456 0 0 5269.5138 12.011697
6450 16738.456 0 0 5269.514 12.011704
6500 16738.456 0 0 5269.5141 12.011714
6550 16738.457 0 0 5269.5142 12.011719
6600 16738.457 0 0 5269.5143 12.011718
6650 16738.458 0 0 5269.5144 12.011713
6700 16738.458 0 0 5269.5146 12.011705
6750 16738.459 0 0 5269.5147 12.011696
6800 16738.459 0 0 5269.5149 12.01169
6850 16738.46 0 0 5269.515 12.011695
6900 16738.46 0 0 5269.5152 12.01171
6950 16738.46 0 0 5269.5153 12.011726
7000 16738.461 0 0 5269.5154 12.011736
7050 16738.461 0 0 5269.5155 12.011737
7100 16738.461 0 0 5269.5155 12.011728
7150 16738.461 0 0 5269.5156 12.011712
7200 16738.462 0 0 5269.5158 12.011691
7250 16738.463 0 0 5269.516 12.011676
7300 16738.463 0 0 5269.5162 12.011677
7350 16738.464 0 0 5269.5164 12.011693
7400 16738.464 0 0 5269.5165 12.011713
7450 16738.465 0 0 5269.5166 12.011729
7500 16738.465 0 0 5269.5167 12.011736
7550 16738.465 0 0 5269.5168 12.011734
7600 16738.465 0 0 5269.5168 12.011722
7650 16738.466 0 0 5269.517 12.011704
7700 16738.466 0 0 5269.5171 12.011687
7750 16738.467 0 0 5269.5173 12.011681
7800 16738.467 0 0 5269.5175 12.011687
7850 16738.468 0 0 5269.5176 12.0117
7900 16738.468 0 0 5269.5178 12.011712
7950 16738.469 0 0 5269.5179 12.011721
8000 16738.469 0 0 5269.518 12.011724
8050 16738.469 0 0 5269.5181 12.01172
8100 16738.47 0 0 5269.5182 12.011709
8150 16738.47 0 0 5269.5183 12.0117
8200 16738.47 0 0 5269.5185 12.0117
8250 16738.471 0 0 5269.5186 12.011709
8300 16738.471 0 0 5269.5187 12.011719
8350 16738.472 0 0 5269.5189 12.011723
8400 16738.472 0 0 5269.519 12.01172
8450 16738.473 -0.00039690666 0 5269.5189 12.011706
8500 16738.481 -0.0034646804 0 5269.5182 12.011643
8550 16738.483 -0.0045307409 0 5269.5178 12.011621
8600 16738.474 -0.00076532811 0 5269.5189 12.011681
8650 16738.474 0 0 5269.5197 12.011699
8700 16738.475 0 0 5269.5199 12.011715
8750 16738.475 0 0 5269.52 12.011732
8800 16738.475 0 0 5269.52 12.011743
8850 16738.476 0 0 5269.5201 12.011744
8900 16738.476 0 0 5269.5202 12.011735
8950 16738.476 0 0 5269.5203 12.011719
9000 16738.477 0 0 5269.5205 12.011698
9050 16738.477 0 0 5269.5206 12.011683
9100 16738.478 0 0 5269.5208 12.011684
9150 16738.479 0 0 5269.521 12.011701
9200 16738.479 0 0 5269.5212 12.011722
9250 16738.479 0 0 5269.5213 12.011738
9300 16738.48 0 0 5269.5214 12.011746
9350 16738.48 0 0 5269.5214 12.011744
9400 16738.48 0 0 5269.5215 12.011732
9450 16738.48 0 0 5269.5216 12.011715
9500 16738.481 -0.00037652434 0 5269.5216 12.011692
9550 16738.493 -0.005315616 0 5269.5203 12.011611
9600 16738.549 -0.026814368 0 5269.5163 12.011415
9650 16738.765 -0.10191523 0 5269.5092 12.011013
9700 16735.041 1.0589885 0 5269.4979 12.062708
9750 16738.013 0.13550123 0 5269.5101 11.407245
9800 16738.512 -0.011620328 0 5269.5201 11.394974
9850 16738.489 -0.00067270523 0 5269.5237 11.395098
9900 16738.489 -0.00024984554 0 5269.5242 11.395085
9950 16738.49 0 0 5269.5245 11.395076
10000 16738.49 0 0 5269.5246 11.395075
Loop time of 0.152143 on 1 procs for 10000 steps with 81 atoms
Performance: 567885.005 tau/day, 65727.431 timesteps/s
98.9% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0097773 | 0.0097773 | 0.0097773 | 0.0 | 6.43
Neigh | 0.040602 | 0.040602 | 0.040602 | 0.0 | 26.69
Comm | 0.012049 | 0.012049 | 0.012049 | 0.0 | 7.92
Output | 0.0016172 | 0.0016172 | 0.0016172 | 0.0 | 1.06
Modify | 0.083104 | 0.083104 | 0.083104 | 0.0 | 54.62
Other | | 0.004994 | | | 3.28
Nlocal: 81 ave 81 max 81 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 84 ave 84 max 84 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0
Neighbor list builds = 998
Dangerous builds = 997
Total wall time: 0:00:00

335
examples/rigid/log.27Nov18.rigid.g++.4 Normal file
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@ -0,0 +1,335 @@
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
9 atoms in group clump1
group clump2 id <> 10 18
9 atoms in group clump2
group clump3 id <> 19 27
9 atoms in group clump3
group clump4 id <> 28 36
9 atoms in group clump4
group clump5 id <> 37 45
9 atoms in group clump5
group clump6 id <> 46 54
9 atoms in group clump6
group clump7 id <> 55 63
9 atoms in group clump7
group clump8 id <> 64 72
9 atoms in group clump8
group clump9 id <> 73 81
9 atoms in group clump9
fix 1 all rigid group 9 clump1 clump2 clump3 clump4 clump5 clump6 clump7 clump8 clump9
9 rigid bodies with 81 atoms
# 1 chain of connected bodies
#group clump1 id <> 1 9
#group clump2 id <> 9 18
#group clump3 id <> 18 27
#group clump4 id <> 27 36
#group clump5 id <> 36 45
#group clump6 id <> 45 54
#group clump7 id <> 54 63
#group clump8 id <> 63 72
#group clump9 id <> 72 81
#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9
# 2 chains of connected bodies
#group clump1 id <> 1 9
#group clump2 id <> 9 18
#group clump3 id <> 18 27
#group clump4 id <> 27 36
#group clump5 id <> 37 45
#group clump6 id <> 45 54
#group clump7 id <> 54 63
#group clump8 id <> 63 72
#group clump9 id <> 72 81
#fix 1 all poems group clump1 clump2 clump3 clump4
#fix 2 all poems group clump5 clump6 clump7 clump8 clump9
neigh_modify exclude group clump1 clump1
neigh_modify exclude group clump2 clump2
neigh_modify exclude group clump3 clump3
neigh_modify exclude group clump4 clump4
neigh_modify exclude group clump5 clump5
neigh_modify exclude group clump6 clump6
neigh_modify exclude group clump7 clump7
neigh_modify exclude group clump8 clump8
neigh_modify exclude group clump9 clump9
thermo 100
#dump 1 all atom 50 dump.rigid
#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 2 pad 5
#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 3 pad 5
timestep 0.0001
thermo 50
run 10000
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) = 3.95 | 4.044 | 4.326 Mbytes
Step Temp E_pair E_mol TotEng Press
0 115.29439 5235.9179 0 5272.2142 -2.7403788
50 14910.685 571.71558 0 5265.82 32.006171
100 16298.442 136.66184 0 5267.653 16.444229
150 16682.606 17.490511 0 5269.4219 14.900344
200 16733.929 1.372872 0 5269.4617 14.569267
250 16738.853 -0.15252816 0 5269.4864 14.496404
300 16738.588 -0.055171335 0 5269.5002 14.496025
350 16738.492 -0.017444677 0 5269.5077 14.496446
400 16738.464 -0.0060102023 0 5269.5104 14.496618
450 16738.455 -0.0012713351 0 5269.5124 14.496701
500 16738.455 -0.00081068621 0 5269.5128 14.496709
550 16738.455 -0.00083203497 0 5269.5129 14.496707
600 16738.455 -0.00058355356 0 5269.5131 14.496709
650 16738.455 -0.00047226704 0 5269.5131 14.496708
700 16738.455 0 0 5269.5136 14.496713
750 16738.455 0 0 5269.5136 14.49671
800 16738.455 0 0 5269.5137 14.496709
850 16738.455 0 0 5269.5137 14.49671
900 16738.456 0 0 5269.5138 14.496713
950 16738.462 -0.0035323872 0 5269.5122 14.496671
1000 16738.586 -0.051135144 0 5269.5036 14.496229
1050 16737.358 0.32995057 0 5269.4981 14.525763
1100 16737.892 0.16210246 0 5269.4984 14.531983
1150 16738.703 -0.089235095 0 5269.5025 14.509899
1200 16738.466 -0.0075446243 0 5269.5096 14.510615
1250 16738.456 0 0 5269.514 14.510704
1300 16738.457 0 0 5269.5141 14.510701
1350 16738.457 0 0 5269.5141 14.510699
1400 16738.457 -0.00044736511 0 5269.5138 14.510693
1450 16738.458 -0.0010971179 0 5269.5134 14.510687
1500 16738.458 -0.00057885428 0 5269.5139 14.510698
1550 16738.457 0 0 5269.5143 14.51071
1600 16738.457 0 0 5269.5144 14.510712
1650 16738.457 0 0 5269.5144 14.510712
1700 16738.458 0 0 5269.5144 14.51071
1750 16738.458 0 0 5269.5145 14.510708
1800 16738.458 0 0 5269.5145 14.510706
1850 16738.458 0 0 5269.5146 14.510705
1900 16738.458 0 0 5269.5146 14.510706
1950 16738.465 -0.0031733615 0 5269.5134 14.510659
2000 16738.491 -0.013255268 0 5269.5117 14.510532
2050 16738.556 -0.0365811 0 5269.5087 14.51029
2100 16738.633 -0.063209659 0 5269.5065 14.510219
2150 16738.607 -0.05601761 0 5269.5055 14.510231
2200 16738.557 -0.038423032 0 5269.5072 14.510404
2250 16738.515 -0.023709918 0 5269.5088 14.510539
2300 16738.489 -0.013249035 0 5269.5111 14.510621
2350 16738.468 -0.0045563719 0 5269.5131 14.510714
2400 16738.46 -0.00052194273 0 5269.5146 14.510771
2450 16738.464 -0.0023259756 0 5269.514 14.510746
2500 16738.468 -0.0051929186 0 5269.5127 14.510731
2550 16738.581 -0.044940117 0 5269.5085 14.510315
2600 16738.427 -7.9722832e-05 0 5269.5046 14.510657
2650 16733.017 1.705148 0 5269.5067 14.596295
2700 16738.761 -0.10614946 0 5269.5038 14.499584
2750 16733.973 1.4038179 0 5269.5064 14.598107
2800 16738.585 -0.046813448 0 5269.5076 14.511073
2850 16738.487 -0.012558719 0 5269.5111 14.510111
2900 16738.465 -0.0026252725 0 5269.514 14.510277
2950 16738.476 -0.0082220764 0 5269.512 14.510223
3000 16738.66 -0.071284779 0 5269.507 14.509758
3050 16715.332 7.2419351 0 5269.476 14.870305
3100 16653.226 26.818761 0 5269.5009 14.496764
3150 16739.351 -0.30690375 0 5269.4886 13.643904
3200 16733.238 1.6025328 0 5269.4737 12.016934
3250 16734.374 1.2554429 0 5269.4841 11.963561
3300 16732.156 1.9585967 0 5269.4893 12.234024
3350 16738.655 -0.079693236 0 5269.497 12.092757
3400 16738.543 -0.042215005 0 5269.4991 12.092809
3450 16738.591 -0.059327511 0 5269.4972 12.092536
3500 16738.759 -0.11761245 0 5269.4918 12.09203
3550 16713.405 7.846062 0 5269.4737 12.389816
3600 16734.939 1.0821936 0 5269.4891 12.173591
3650 16738.808 -0.13663194 0 5269.4882 12.027009
3700 16738.602 -0.070934368 0 5269.4889 12.025288
3750 16737.731 0.20706557 0 5269.4927 12.061948
3800 16738.578 -0.05582043 0 5269.4965 12.035665
3850 16738.471 -0.016307928 0 5269.5024 12.035302
3900 16738.449 -0.0058182199 0 5269.5059 12.035401
3950 16738.439 -0.0012027325 0 5269.5074 12.035461
4000 16738.436 -0.00020698452 0 5269.5075 12.035469
4050 16738.437 0 0 5269.5078 12.035454
4100 16738.437 0 0 5269.508 12.035435
4150 16738.438 0 0 5269.5081 12.035426
4200 16738.438 0 0 5269.5083 12.035432
4250 16738.439 0 0 5269.5085 12.035447
4300 16738.439 0 0 5269.5086 12.035463
4350 16738.44 0 0 5269.5087 12.035474
4400 16738.44 0 0 5269.5088 12.035478
4450 16738.44 0 0 5269.5089 12.035474
4500 16738.44 0 0 5269.509 12.035462
4550 16738.441 0 0 5269.5092 12.035449
4600 16738.441 0 0 5269.5093 12.035445
4650 16738.442 0 0 5269.5095 12.035451
4700 16738.442 0 0 5269.5096 12.03546
4750 16738.443 0 0 5269.5097 12.035465
4800 16738.443 0 0 5269.5098 12.035466
4850 16738.443 0 0 5269.51 12.035463
4900 16738.444 0 0 5269.5101 12.035456
4950 16738.444 0 0 5269.5102 12.035447
5000 16738.445 0 0 5269.5104 12.03544
5050 16738.445 0 0 5269.5105 12.035442
5100 16738.446 0 0 5269.5107 12.035455
5150 16738.446 0 0 5269.5108 12.03547
5200 16738.446 0 0 5269.5109 12.035479
5250 16738.447 0 0 5269.511 12.035479
5300 16738.447 0 0 5269.5111 12.03547
5350 16738.447 0 0 5269.5112 12.035454
5400 16738.448 0 0 5269.5113 12.035434
5450 16738.448 0 0 5269.5115 12.03542
5500 16738.449 0 0 5269.5117 12.035422
5550 16738.457 -0.0030919234 0 5269.5111 12.035383
5600 16738.51 -0.021618357 0 5269.5092 12.035106
5650 16738.622 -0.059214788 0 5269.507 12.035694
5700 16395.28 108.06942 0 5269.5463 24.369038
5750 16738.544 -0.033973429 0 5269.5077 12.011261
5800 16738.456 -0.0037013529 0 5269.5102 12.011675
5850 16738.451 0 0 5269.5123 12.011709
5900 16738.451 -0.00022115871 0 5269.5122 12.011687
5950 16738.452 -0.00024253349 0 5269.5124 12.011678
6000 16738.452 0 0 5269.5128 12.011688
6050 16738.453 0 0 5269.513 12.011702
6100 16738.453 0 0 5269.5131 12.011716
6150 16738.454 0 0 5269.5132 12.011725
6200 16738.454 0 0 5269.5133 12.011728
6250 16738.454 0 0 5269.5134 12.011723
6300 16738.455 0 0 5269.5135 12.011712
6350 16738.455 0 0 5269.5137 12.0117
6400 16738.456 0 0 5269.5138 12.011697
6450 16738.456 0 0 5269.514 12.011704
6500 16738.456 0 0 5269.5141 12.011714
6550 16738.457 0 0 5269.5142 12.011719
6600 16738.457 0 0 5269.5143 12.011718
6650 16738.458 0 0 5269.5144 12.011713
6700 16738.458 0 0 5269.5146 12.011705
6750 16738.459 0 0 5269.5147 12.011696
6800 16738.459 0 0 5269.5149 12.01169
6850 16738.46 0 0 5269.515 12.011695
6900 16738.46 0 0 5269.5152 12.01171
6950 16738.46 0 0 5269.5153 12.011726
7000 16738.461 0 0 5269.5154 12.011736
7050 16738.461 0 0 5269.5155 12.011737
7100 16738.461 0 0 5269.5155 12.011728
7150 16738.461 0 0 5269.5156 12.011712
7200 16738.462 0 0 5269.5158 12.011691
7250 16738.463 0 0 5269.516 12.011676
7300 16738.463 0 0 5269.5162 12.011677
7350 16738.464 0 0 5269.5164 12.011693
7400 16738.464 0 0 5269.5165 12.011713
7450 16738.465 0 0 5269.5166 12.011729
7500 16738.465 0 0 5269.5167 12.011736
7550 16738.465 0 0 5269.5168 12.011734
7600 16738.465 0 0 5269.5168 12.011722
7650 16738.466 0 0 5269.517 12.011704
7700 16738.466 0 0 5269.5171 12.011687
7750 16738.467 0 0 5269.5173 12.011681
7800 16738.467 0 0 5269.5175 12.011687
7850 16738.468 0 0 5269.5176 12.0117
7900 16738.468 0 0 5269.5178 12.011712
7950 16738.469 0 0 5269.5179 12.011721
8000 16738.469 0 0 5269.518 12.011724
8050 16738.469 0 0 5269.5181 12.01172
8100 16738.47 0 0 5269.5182 12.011709
8150 16738.47 0 0 5269.5183 12.0117
8200 16738.47 0 0 5269.5185 12.0117
8250 16738.471 0 0 5269.5186 12.011709
8300 16738.471 0 0 5269.5187 12.011719
8350 16738.472 0 0 5269.5189 12.011723
8400 16738.472 0 0 5269.519 12.01172
8450 16738.473 -0.00039690663 0 5269.5189 12.011706
8500 16738.481 -0.0034646803 0 5269.5182 12.011643
8550 16738.483 -0.0045307409 0 5269.5178 12.011621
8600 16738.474 -0.00076532813 0 5269.5189 12.011681
8650 16738.474 0 0 5269.5197 12.011699
8700 16738.475 0 0 5269.5199 12.011715
8750 16738.475 0 0 5269.52 12.011732
8800 16738.475 0 0 5269.52 12.011743
8850 16738.476 0 0 5269.5201 12.011744
8900 16738.476 0 0 5269.5202 12.011735
8950 16738.476 0 0 5269.5203 12.011719
9000 16738.477 0 0 5269.5205 12.011698
9050 16738.477 0 0 5269.5206 12.011683
9100 16738.478 0 0 5269.5208 12.011684
9150 16738.479 0 0 5269.521 12.011701
9200 16738.479 0 0 5269.5212 12.011722
9250 16738.479 0 0 5269.5213 12.011738
9300 16738.48 0 0 5269.5214 12.011746
9350 16738.48 0 0 5269.5214 12.011744
9400 16738.48 0 0 5269.5215 12.011732
9450 16738.48 0 0 5269.5216 12.011715
9500 16738.481 -0.00037652438 0 5269.5216 12.011692
9550 16738.493 -0.0053156163 0 5269.5203 12.011611
9600 16738.549 -0.026814371 0 5269.5163 12.011415
9650 16738.765 -0.10191523 0 5269.5092 12.011013
9700 16735.041 1.0589894 0 5269.4979 12.062708
9750 16738.013 0.13550109 0 5269.5101 11.407246
9800 16738.512 -0.011620327 0 5269.5201 11.394974
9850 16738.489 -0.00067270507 0 5269.5237 11.395098
9900 16738.489 -0.00024984555 0 5269.5242 11.395085
9950 16738.49 0 0 5269.5245 11.395076
10000 16738.49 0 0 5269.5246 11.395075
Loop time of 0.201762 on 4 procs for 10000 steps with 81 atoms
Performance: 428226.262 tau/day, 49563.225 timesteps/s
89.2% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0025356 | 0.0033935 | 0.0042305 | 1.0 | 1.68
Neigh | 0.012009 | 0.012959 | 0.015092 | 1.1 | 6.42
Comm | 0.07666 | 0.086213 | 0.092506 | 2.0 | 42.73
Output | 0.0032623 | 0.0052034 | 0.011 | 4.6 | 2.58
Modify | 0.084815 | 0.087869 | 0.089999 | 0.6 | 43.55
Other | | 0.006125 | | | 3.04
Nlocal: 20.25 ave 38 max 3 min
Histogram: 1 0 1 0 0 0 1 0 0 1
Nghost: 27.25 ave 48 max 13 min
Histogram: 1 0 1 1 0 0 0 0 0 1
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0
Neighbor list builds = 998
Dangerous builds = 997
Total wall time: 0:00:00

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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
9 atoms in group clump1
group clump2 id <> 10 18
9 atoms in group clump2
group clump3 id <> 19 27
9 atoms in group clump3
group clump4 id <> 28 36
9 atoms in group clump4
group clump5 id <> 37 45
9 atoms in group clump5
group clump6 id <> 46 54
9 atoms in group clump6
group clump7 id <> 55 63
9 atoms in group clump7
group clump8 id <> 64 72
9 atoms in group clump8
group clump9 id <> 73 81
9 atoms in group clump9
fix 1 all rigid/nve group 9 clump1 clump2 clump3 clump4 clump5 clump6 clump7 clump8 clump9
9 rigid bodies with 81 atoms
fix_modify 1 bodyforces early
# 1 chain of connected bodies
#group clump1 id <> 1 9
#group clump2 id <> 9 18
#group clump3 id <> 18 27
#group clump4 id <> 27 36
#group clump5 id <> 36 45
#group clump6 id <> 45 54
#group clump7 id <> 54 63
#group clump8 id <> 63 72
#group clump9 id <> 72 81
#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9
# 2 chains of connected bodies
#group clump1 id <> 1 9
#group clump2 id <> 9 18
#group clump3 id <> 18 27
#group clump4 id <> 27 36
#group clump5 id <> 37 45
#group clump6 id <> 45 54
#group clump7 id <> 54 63
#group clump8 id <> 63 72
#group clump9 id <> 72 81
#fix 1 all poems group clump1 clump2 clump3 clump4
#fix 2 all poems group clump5 clump6 clump7 clump8 clump9
neigh_modify exclude group clump1 clump1
neigh_modify exclude group clump2 clump2
neigh_modify exclude group clump3 clump3
neigh_modify exclude group clump4 clump4
neigh_modify exclude group clump5 clump5
neigh_modify exclude group clump6 clump6
neigh_modify exclude group clump7 clump7
neigh_modify exclude group clump8 clump8
neigh_modify exclude group clump9 clump9
thermo 100
#dump 1 all atom 50 dump.rigid
#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 2 pad 5
#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 3 pad 5
timestep 0.0001
thermo 50
run 10000
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) = 3.979 | 3.979 | 3.979 Mbytes
Step Temp E_pair E_mol TotEng Press
0 115.29439 5235.9179 0 5272.2142 -2.7403788
50 14910.69 571.70921 0 5265.8153 32.005816
100 16298.128 136.75661 0 5267.6488 16.449029
150 16682.532 17.504156 0 5269.4124 14.901186
200 16733.906 1.3755079 0 5269.4571 14.571305
250 16738.861 -0.15272039 0 5269.4886 14.498342
300 16738.608 -0.055216883 0 5269.5066 14.498
350 16738.5 -0.017457072 0 5269.5104 14.498392
400 16738.451 -0.0060161309 0 5269.5063 14.49851
450 16738.435 -0.001271965 0 5269.5059 14.498571
500 16738.443 -0.00081074175 0 5269.509 14.498598
550 16738.452 -0.00083208965 0 5269.5118 14.498618
600 16738.45 -0.00058358431 0 5269.5116 14.498617
650 16738.443 -0.00047228525 0 5269.5093 14.4986
700 16738.444 0 0 5269.5102 14.498612
750 16738.461 0 0 5269.5157 14.498654
800 16738.479 0 0 5269.521 14.498697
850 16738.473 0 0 5269.5192 14.498683
900 16738.449 0 0 5269.5116 14.498624
950 16738.438 -0.0035324203 0 5269.5046 14.498537
1000 16738.562 -0.051134242 0 5269.4963 14.498093
1050 16737.343 0.32970192 0 5269.4934 14.527634
1100 16737.878 0.16213235 0 5269.4941 14.533864
1150 16738.682 -0.089236256 0 5269.4959 14.511765
1200 16738.444 -0.0075446558 0 5269.5025 14.512479
1250 16738.45 0 0 5269.5119 14.512611
1300 16738.475 0 0 5269.5199 14.512673
1350 16738.484 0 0 5269.5228 14.512696
1400 16738.469 -0.00044683992 0 5269.5175 14.512651
1450 16738.45 -0.0010933363 0 5269.511 14.512595
1500 16738.445 -0.00057484239 0 5269.51 14.512591
1550 16738.451 0 0 5269.5123 14.512615
1600 16738.452 0 0 5269.5127 14.512618
1650 16738.443 0 0 5269.5099 14.512596
1700 16738.433 0 0 5269.5068 14.512572
1750 16738.438 0 0 5269.5084 14.512584
1800 16738.459 0 0 5269.5149 14.512635
1850 16738.473 0 0 5269.5193 14.51267
1900 16738.462 0 0 5269.5159 14.512644
1950 16738.446 -0.0032069962 0 5269.5076 14.512539
2000 16738.463 -0.013425408 0 5269.5027 14.512382
2050 16738.535 -0.036964311 0 5269.5017 14.512152
2100 16738.621 -0.063490509 0 5269.5023 14.512108
2150 16738.594 -0.056143934 0 5269.5012 14.512117
2200 16738.536 -0.038486645 0 5269.5007 14.512277
2250 16738.496 -0.023712406 0 5269.503 14.51242
2300 16738.488 -0.013209094 0 5269.5109 14.51255
2350 16738.486 -0.0045244524 0 5269.519 14.512693
2400 16738.475 -0.00051678325 0 5269.5194 14.512743
2450 16738.456 -0.0023209272 0 5269.5115 14.512659
2500 16738.442 -0.0052101787 0 5269.5042 14.512594
2550 16738.552 -0.04420046 0 5269.4998 14.512177
2600 16738.42 -0.004347531 0 5269.4982 14.512783
2650 16734.241 1.3131302 0 5269.5 14.577195
2700 16738.737 -0.10612056 0 5269.4961 14.503874
2750 16732.705 1.7939719 0 5269.4974 14.629294
2800 16738.558 -0.042867033 0 5269.5032 14.519893
2850 16738.499 -0.01271227 0 5269.5146 14.518524
2900 16738.486 -0.0032778045 0 5269.52 14.518712
2950 16738.482 -0.0089544631 0 5269.5133 14.518629
3000 16738.647 -0.070862542 0 5269.5031 14.51803
3050 16678.313 18.829038 0 5269.409 15.533426
3100 16632.312 33.399217 0 5269.4975 14.588597
3150 16739.318 -0.31388148 0 5269.4715 13.520782
3200 16727.951 3.26736 0 5269.4741 12.288358
3250 16686.364 16.353793 0 5269.4682 14.152517
3300 16738.532 -0.031574462 0 5269.5064 13.310615
3350 16738.454 -0.0062292918 0 5269.5071 13.308187
3400 16738.445 -0.0049349125 0 5269.5055 13.308178
3450 16738.489 -0.021623738 0 5269.5026 13.308001
3500 16737.78 0.19719043 0 5269.4983 13.325999
3550 16658.578 25.116206 0 5269.4834 13.778249
3600 16738.51 -0.032864725 0 5269.4981 12.392389
3650 16738.899 -0.15952703 0 5269.4938 12.383503
3700 16738.879 -0.16025994 0 5269.487 12.382575
3750 16738.878 -0.16608251 0 5269.4806 12.382765
3800 16738.591 -0.078679341 0 5269.4776 12.383227
3850 16738.429 -0.024729409 0 5269.4807 12.382942
3900 16738.399 -0.0062729967 0 5269.4897 12.383192
3950 16738.428 -0.002521266 0 5269.5027 12.383324
4000 16738.467 -0.0002068506 0 5269.5173 12.383474
4050 16738.488 0 0 5269.5241 12.383531
4100 16738.468 0 0 5269.5178 12.383482
4150 16738.422 0 0 5269.5033 12.383369
4200 16738.387 0 0 5269.4921 12.383281
4250 16738.383 0 0 5269.4908 12.38327
4300 16738.4 0 0 5269.4964 12.383314
4350 16738.423 0 0 5269.5036 12.38337
4400 16738.441 0 0 5269.5092 12.383414
4450 16738.45 0 0 5269.5121 12.383437
4500 16738.45 0 0 5269.5122 12.383438
4550 16738.442 0 0 5269.5095 12.383417
4600 16738.425 0 0 5269.5042 12.383376
4650 16738.404 -0.0014438316 0 5269.4961 12.383299
4700 16738.444 -0.024020551 0 5269.4862 12.382975
4750 16738.49 -0.04852143 0 5269.4761 12.385777
4800 16735.057 1.0347216 0 5269.4786 12.43543
4850 16735.441 0.92650925 0 5269.4913 12.418653
4900 16723.839 4.5908974 0 5269.5033 13.410103
4950 16738.531 -0.02153767 0 5269.5159 13.089982
5000 16738.45 -0.0042589697 0 5269.5077 13.090062
5050 16738.409 -0.00024692476 0 5269.4987 13.090038
5100 16738.404 0 0 5269.4976 13.090032
5150 16738.421 0 0 5269.5029 13.090073
5200 16738.44 0 0 5269.5087 13.090119
5250 16738.448 -0.001279392 0 5269.5102 13.090114
5300 16738.456 -0.0064376391 0 5269.5075 13.090026
5350 16738.479 -0.020383841 0 5269.5007 13.089897
5400 16735.845 0.7988947 0 5269.4909 13.136244
5450 16735.558 0.87620022 0 5269.4778 12.324482
5500 16711.494 8.4724178 0 5269.4984 12.656579
5550 16454.525 89.074815 0 5269.2031 16.996503
5600 16713.084 7.9801418 0 5269.5065 13.774979
5650 16738.676 -0.079987748 0 5269.5033 13.168297
5700 16446.281 91.866085 0 5269.399 23.764663
5750 16738.549 -0.039869084 0 5269.5034 13.378122
5800 16738.487 -0.014994478 0 5269.5086 13.378399
5850 16738.466 -0.0051267616 0 5269.512 13.37856
5900 16738.462 -0.0043690142 0 5269.5113 13.378573
5950 16738.528 -0.032727415 0 5269.5039 13.378197
6000 16702.774 10.969438 0 5269.2502 13.788852
6050 16682.271 17.483137 0 5269.3092 13.353101
6100 16738.508 -0.028838222 0 5269.5016 12.521084
6150 16738.425 -0.0067595536 0 5269.4974 12.521223
6200 16738.401 -0.0011499893 0 5269.4955 12.521254
6250 16738.455 0 0 5269.5135 12.52141
6300 16738.523 0 0 5269.5352 12.52158
6350 16738.503 0 0 5269.5287 12.521531
6400 16738.427 0 0 5269.5047 12.521344
6450 16738.399 0 0 5269.496 12.521274
6500 16738.425 0 0 5269.5042 12.521337
6550 16738.441 0 0 5269.5093 12.521378
6600 16738.42 0 0 5269.5025 12.521326
6650 16738.398 0 0 5269.4957 12.521272
6700 16738.435 0 0 5269.5074 12.521362
6750 16738.505 0 0 5269.5293 12.521534
6800 16738.508 0 0 5269.5303 12.521543
6850 16738.446 0 0 5269.5108 12.521391
6900 16738.414 0 0 5269.5009 12.521312
6950 16738.432 0 0 5269.5063 12.521354
7000 16738.444 0 0 5269.5102 12.521385
7050 16738.421 0 0 5269.5029 12.521329
7100 16738.393 0 0 5269.4941 12.521259
7150 16738.419 0 0 5269.5022 12.521322
7200 16738.489 0 0 5269.5244 12.521495
7250 16738.505 0 0 5269.5293 12.521535
7300 16738.443 0 0 5269.5098 12.521383
7350 16738.404 0 0 5269.4976 12.521287
7400 16738.43 0 0 5269.5058 12.52135
7450 16738.461 0 0 5269.5156 12.521427
7500 16738.447 0 0 5269.5109 12.521392
7550 16738.407 0 0 5269.4986 12.521295
7600 16738.412 0 0 5269.5002 12.521306
7650 16738.478 0 0 5269.5208 12.521467
7700 16738.51 0 0 5269.5309 12.521547
7750 16738.454 0 0 5269.5135 12.521412
7800 16738.398 0 0 5269.4958 12.521273
7850 16738.407 -0.0002118108 0 5269.4982 12.521289
7900 16738.441 -0.00021679711 0 5269.509 12.521373
7950 16738.446 -0.00023848139 0 5269.5107 12.521386
8000 16738.423 0 0 5269.5035 12.521333
8050 16738.423 0 0 5269.5034 12.521332
8100 16738.478 -0.00069622994 0 5269.52 12.521454
8150 16738.523 -0.0040058408 0 5269.531 12.521501
8200 16738.486 -0.0092298229 0 5269.5142 12.521334
8250 16738.458 -0.023189671 0 5269.4914 12.521014
8300 16738.513 -0.045845677 0 5269.4861 12.520779
8350 16723.745 4.5690412 0 5269.4516 12.849325
8400 16738.466 -0.020158442 0 5269.497 12.835773
8450 16738.437 -0.012822892 0 5269.4952 12.829936
8500 16738.408 -0.0016837088 0 5269.4972 12.830061
8550 16738.464 -0.00097379467 0 5269.5155 12.830216
8600 16738.669 -0.050578079 0 5269.5304 12.829934
8650 15917.563 250.28318 0 5261.3678 24.54572
8700 16738.445 0.0012168759 0 5269.5117 10.589499
8750 16738.473 -0.010164589 0 5269.509 10.588414
8800 16738.468 0 0 5269.5177 10.588633
8850 16738.508 0 0 5269.5304 10.588733
8900 16738.509 0 0 5269.5307 10.588736
8950 16738.496 0 0 5269.5266 10.588705
9000 16738.477 0 0 5269.5204 10.588656
9050 16738.455 0 0 5269.5135 10.588602
9100 16738.477 0 0 5269.5206 10.588656
9150 16738.512 0 0 5269.5316 10.588743
9200 16738.502 0 0 5269.5285 10.58872
9250 16738.493 0 0 5269.5255 10.588696
9300 16738.482 0 0 5269.522 10.588669
9350 16738.46 0 0 5269.5151 10.588615
9400 16738.481 0 0 5269.5217 10.588665
9450 16738.509 0 0 5269.5307 10.588736
9500 16738.491 0 0 5269.5248 10.58869
9550 16738.484 0 0 5269.5227 10.588674
9600 16738.483 0 0 5269.5223 10.588671
9650 16738.464 0 0 5269.5166 10.588626
9700 16738.484 0 0 5269.5229 10.588674
9750 16738.507 0 0 5269.5301 10.588731
9800 16738.482 0 0 5269.5221 10.588669
9850 16738.478 0 0 5269.5208 10.588659
9900 16738.487 -0.00030979474 0 5269.5233 10.588675
9950 16738.476 -0.00095968581 0 5269.5193 10.588632
10000 16738.494 -0.00062717822 0 5269.5253 10.588684
Loop time of 0.168577 on 1 procs for 10000 steps with 81 atoms
Performance: 512524.843 tau/day, 59320.005 timesteps/s
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.010812 | 0.010812 | 0.010812 | 0.0 | 6.41
Neigh | 0.04144 | 0.04144 | 0.04144 | 0.0 | 24.58
Comm | 0.012082 | 0.012082 | 0.012082 | 0.0 | 7.17
Output | 0.0016394 | 0.0016394 | 0.0016394 | 0.0 | 0.97
Modify | 0.097466 | 0.097466 | 0.097466 | 0.0 | 57.82
Other | | 0.005139 | | | 3.05
Nlocal: 81 ave 81 max 81 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 49 ave 49 max 49 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 3 ave 3 max 3 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 3
Ave neighs/atom = 0.037037
Neighbor list builds = 998
Dangerous builds = 997
Total wall time: 0:00:00

337
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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
9 atoms in group clump1
group clump2 id <> 10 18
9 atoms in group clump2
group clump3 id <> 19 27
9 atoms in group clump3
group clump4 id <> 28 36
9 atoms in group clump4
group clump5 id <> 37 45
9 atoms in group clump5
group clump6 id <> 46 54
9 atoms in group clump6
group clump7 id <> 55 63
9 atoms in group clump7
group clump8 id <> 64 72
9 atoms in group clump8
group clump9 id <> 73 81
9 atoms in group clump9
fix 1 all rigid/nve group 9 clump1 clump2 clump3 clump4 clump5 clump6 clump7 clump8 clump9
9 rigid bodies with 81 atoms
fix_modify 1 bodyforces early
# 1 chain of connected bodies
#group clump1 id <> 1 9
#group clump2 id <> 9 18
#group clump3 id <> 18 27
#group clump4 id <> 27 36
#group clump5 id <> 36 45
#group clump6 id <> 45 54
#group clump7 id <> 54 63
#group clump8 id <> 63 72
#group clump9 id <> 72 81
#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9
# 2 chains of connected bodies
#group clump1 id <> 1 9
#group clump2 id <> 9 18
#group clump3 id <> 18 27
#group clump4 id <> 27 36
#group clump5 id <> 37 45
#group clump6 id <> 45 54
#group clump7 id <> 54 63
#group clump8 id <> 63 72
#group clump9 id <> 72 81
#fix 1 all poems group clump1 clump2 clump3 clump4
#fix 2 all poems group clump5 clump6 clump7 clump8 clump9
neigh_modify exclude group clump1 clump1
neigh_modify exclude group clump2 clump2
neigh_modify exclude group clump3 clump3
neigh_modify exclude group clump4 clump4
neigh_modify exclude group clump5 clump5
neigh_modify exclude group clump6 clump6
neigh_modify exclude group clump7 clump7
neigh_modify exclude group clump8 clump8
neigh_modify exclude group clump9 clump9
thermo 100
#dump 1 all atom 50 dump.rigid
#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 2 pad 5
#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 3 pad 5
timestep 0.0001
thermo 50
run 10000
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) = 3.95 | 4.044 | 4.326 Mbytes
Step Temp E_pair E_mol TotEng Press
0 115.29439 5235.9179 0 5272.2142 -2.7403788
50 14910.69 571.70921 0 5265.8153 32.005816
100 16298.128 136.75661 0 5267.6488 16.449029
150 16682.532 17.504156 0 5269.4124 14.901186
200 16733.906 1.3755079 0 5269.4571 14.571305
250 16738.861 -0.15272039 0 5269.4886 14.498342
300 16738.608 -0.055216883 0 5269.5066 14.498
350 16738.5 -0.017457072 0 5269.5104 14.498392
400 16738.451 -0.0060161309 0 5269.5063 14.49851
450 16738.435 -0.001271965 0 5269.5059 14.498571
500 16738.443 -0.00081074175 0 5269.509 14.498598
550 16738.452 -0.00083208965 0 5269.5118 14.498618
600 16738.45 -0.00058358431 0 5269.5116 14.498617
650 16738.443 -0.00047228525 0 5269.5093 14.4986
700 16738.444 0 0 5269.5102 14.498612
750 16738.461 0 0 5269.5157 14.498654
800 16738.479 0 0 5269.521 14.498697
850 16738.473 0 0 5269.5192 14.498683
900 16738.449 0 0 5269.5116 14.498624
950 16738.438 -0.0035324203 0 5269.5046 14.498537
1000 16738.562 -0.051134242 0 5269.4963 14.498093
1050 16737.343 0.32970192 0 5269.4934 14.527634
1100 16737.878 0.16213235 0 5269.4941 14.533864
1150 16738.682 -0.089236256 0 5269.4959 14.511765
1200 16738.444 -0.0075446558 0 5269.5025 14.512479
1250 16738.45 0 0 5269.5119 14.512611
1300 16738.475 0 0 5269.5199 14.512673
1350 16738.484 0 0 5269.5228 14.512696
1400 16738.469 -0.00044683992 0 5269.5175 14.512651
1450 16738.45 -0.0010933363 0 5269.511 14.512595
1500 16738.445 -0.00057484239 0 5269.51 14.512591
1550 16738.451 0 0 5269.5123 14.512615
1600 16738.452 0 0 5269.5127 14.512618
1650 16738.443 0 0 5269.5099 14.512596
1700 16738.433 0 0 5269.5068 14.512572
1750 16738.438 0 0 5269.5084 14.512584
1800 16738.459 0 0 5269.5149 14.512635
1850 16738.473 0 0 5269.5193 14.51267
1900 16738.462 0 0 5269.5159 14.512644
1950 16738.446 -0.0032069962 0 5269.5076 14.512539
2000 16738.463 -0.013425408 0 5269.5027 14.512382
2050 16738.535 -0.036964311 0 5269.5017 14.512152
2100 16738.621 -0.063490509 0 5269.5023 14.512108
2150 16738.594 -0.056143934 0 5269.5012 14.512117
2200 16738.536 -0.038486645 0 5269.5007 14.512277
2250 16738.496 -0.023712406 0 5269.503 14.51242
2300 16738.488 -0.013209094 0 5269.5109 14.51255
2350 16738.486 -0.0045244524 0 5269.519 14.512693
2400 16738.475 -0.00051678325 0 5269.5194 14.512743
2450 16738.456 -0.0023209272 0 5269.5115 14.512659
2500 16738.442 -0.0052101787 0 5269.5042 14.512594
2550 16738.552 -0.04420046 0 5269.4998 14.512177
2600 16738.42 -0.004347531 0 5269.4982 14.512783
2650 16734.241 1.3131302 0 5269.5 14.577195
2700 16738.737 -0.10612056 0 5269.4961 14.503874
2750 16732.705 1.7939719 0 5269.4974 14.629294
2800 16738.558 -0.042867033 0 5269.5032 14.519893
2850 16738.499 -0.01271227 0 5269.5146 14.518524
2900 16738.486 -0.0032778045 0 5269.52 14.518712
2950 16738.482 -0.0089544631 0 5269.5133 14.518629
3000 16738.647 -0.070862542 0 5269.5031 14.51803
3050 16678.313 18.829038 0 5269.409 15.533426
3100 16632.312 33.399217 0 5269.4975 14.588597
3150 16739.318 -0.31388148 0 5269.4715 13.520782
3200 16727.951 3.26736 0 5269.4741 12.288358
3250 16686.364 16.353793 0 5269.4682 14.152517
3300 16738.532 -0.031574462 0 5269.5064 13.310615
3350 16738.454 -0.0062292918 0 5269.5071 13.308187
3400 16738.445 -0.0049349125 0 5269.5055 13.308178
3450 16738.489 -0.021623738 0 5269.5026 13.308001
3500 16737.78 0.19719043 0 5269.4983 13.325999
3550 16658.578 25.116206 0 5269.4834 13.778249
3600 16738.51 -0.032864725 0 5269.4981 12.392389
3650 16738.899 -0.15952703 0 5269.4938 12.383503
3700 16738.879 -0.16025994 0 5269.487 12.382575
3750 16738.878 -0.16608251 0 5269.4806 12.382765
3800 16738.591 -0.078679341 0 5269.4776 12.383227
3850 16738.429 -0.024729409 0 5269.4807 12.382942
3900 16738.399 -0.0062729967 0 5269.4897 12.383192
3950 16738.428 -0.002521266 0 5269.5027 12.383324
4000 16738.467 -0.0002068506 0 5269.5173 12.383474
4050 16738.488 0 0 5269.5241 12.383531
4100 16738.468 0 0 5269.5178 12.383482
4150 16738.422 0 0 5269.5033 12.383369
4200 16738.387 0 0 5269.4921 12.383281
4250 16738.383 0 0 5269.4908 12.38327
4300 16738.4 0 0 5269.4964 12.383314
4350 16738.423 0 0 5269.5036 12.38337
4400 16738.441 0 0 5269.5092 12.383414
4450 16738.45 0 0 5269.5121 12.383437
4500 16738.45 0 0 5269.5122 12.383438
4550 16738.442 0 0 5269.5095 12.383417
4600 16738.425 0 0 5269.5042 12.383376
4650 16738.404 -0.0014438316 0 5269.4961 12.383299
4700 16738.444 -0.024020551 0 5269.4862 12.382975
4750 16738.49 -0.048521428 0 5269.4761 12.385777
4800 16735.057 1.0347217 0 5269.4786 12.43543
4850 16735.441 0.92650925 0 5269.4913 12.418653
4900 16723.839 4.5908973 0 5269.5033 13.410103
4950 16738.531 -0.02153767 0 5269.5159 13.089982
5000 16738.45 -0.0042589696 0 5269.5077 13.090062
5050 16738.409 -0.00024692476 0 5269.4987 13.090038
5100 16738.404 0 0 5269.4976 13.090032
5150 16738.421 0 0 5269.5029 13.090073
5200 16738.44 0 0 5269.5087 13.090119
5250 16738.448 -0.001279392 0 5269.5102 13.090114
5300 16738.456 -0.0064376392 0 5269.5075 13.090026
5350 16738.479 -0.020383842 0 5269.5007 13.089897
5400 16735.845 0.79889474 0 5269.4909 13.136244
5450 16735.558 0.87619992 0 5269.4778 12.324482
5500 16711.494 8.4724208 0 5269.4984 12.656579
5550 16454.525 89.074816 0 5269.2031 16.996503
5600 16713.084 7.9801334 0 5269.5065 13.774977
5650 16738.676 -0.079987764 0 5269.5033 13.168295
5700 16446.281 91.866085 0 5269.399 23.764662
5750 16738.549 -0.039869084 0 5269.5034 13.378121
5800 16738.487 -0.014994475 0 5269.5086 13.378397
5850 16738.466 -0.0051267556 0 5269.512 13.378559
5900 16738.462 -0.0043690097 0 5269.5113 13.378572
5950 16738.528 -0.03272741 0 5269.5039 13.378195
6000 16702.774 10.969434 0 5269.2502 13.788851
6050 16682.271 17.483158 0 5269.3092 13.3531
6100 16738.508 -0.028838239 0 5269.5016 12.521082
6150 16738.425 -0.0067595542 0 5269.4974 12.521221
6200 16738.401 -0.0011499896 0 5269.4955 12.521252
6250 16738.455 0 0 5269.5135 12.521408
6300 16738.523 0 0 5269.5352 12.521578
6350 16738.503 0 0 5269.5287 12.52153
6400 16738.427 0 0 5269.5047 12.521342
6450 16738.399 0 0 5269.496 12.521273
6500 16738.425 0 0 5269.5042 12.521336
6550 16738.441 0 0 5269.5093 12.521377
6600 16738.42 0 0 5269.5025 12.521324
6650 16738.398 0 0 5269.4957 12.52127
6700 16738.435 0 0 5269.5074 12.52136
6750 16738.505 0 0 5269.5293 12.521532
6800 16738.508 0 0 5269.5303 12.521541
6850 16738.446 0 0 5269.5108 12.521389
6900 16738.414 0 0 5269.5009 12.521311
6950 16738.432 0 0 5269.5063 12.521353
7000 16738.444 0 0 5269.5102 12.521383
7050 16738.421 0 0 5269.5029 12.521327
7100 16738.393 0 0 5269.4941 12.521258
7150 16738.419 0 0 5269.5022 12.52132
7200 16738.489 0 0 5269.5244 12.521494
7250 16738.505 0 0 5269.5293 12.521533
7300 16738.443 0 0 5269.5098 12.521381
7350 16738.404 0 0 5269.4976 12.521285
7400 16738.43 0 0 5269.5058 12.521348
7450 16738.461 0 0 5269.5156 12.521425
7500 16738.447 0 0 5269.5109 12.52139
7550 16738.407 0 0 5269.4986 12.521293
7600 16738.412 0 0 5269.5002 12.521305
7650 16738.478 0 0 5269.5208 12.521465
7700 16738.51 0 0 5269.5309 12.521546
7750 16738.454 0 0 5269.5135 12.52141
7800 16738.398 0 0 5269.4958 12.521272
7850 16738.407 -0.00021180981 0 5269.4982 12.521288
7900 16738.441 -0.0002167964 0 5269.509 12.521371
7950 16738.446 -0.00023848065 0 5269.5107 12.521385
8000 16738.423 0 0 5269.5035 12.521331
8050 16738.423 0 0 5269.5034 12.52133
8100 16738.478 -0.00069623408 0 5269.52 12.521452
8150 16738.523 -0.0040058355 0 5269.531 12.521499
8200 16738.486 -0.0092298325 0 5269.5142 12.521332
8250 16738.458 -0.023189665 0 5269.4914 12.521012
8300 16738.513 -0.045846242 0 5269.4861 12.520778
8350 16723.742 4.5698786 0 5269.4516 12.849386
8400 16738.466 -0.02016972 0 5269.497 12.835784
8450 16738.437 -0.012822703 0 5269.4952 12.829948
8500 16738.408 -0.0016836132 0 5269.4972 12.830073
8550 16738.464 -0.00097380297 0 5269.5155 12.830227
8600 16738.669 -0.050578946 0 5269.5304 12.829946
8650 15917.707 250.24016 0 5261.3702 24.544744
8700 16738.445 0.0010615265 0 5269.5117 10.589987
8750 16738.473 -0.010158834 0 5269.509 10.588904
8800 16738.468 0 0 5269.5176 10.589124
8850 16738.508 0 0 5269.5304 10.589223
8900 16738.509 0 0 5269.5306 10.589226
8950 16738.496 0 0 5269.5266 10.589195
9000 16738.477 0 0 5269.5204 10.589147
9050 16738.455 0 0 5269.5135 10.589092
9100 16738.477 0 0 5269.5206 10.589146
9150 16738.512 0 0 5269.5316 10.589233
9200 16738.502 0 0 5269.5285 10.58921
9250 16738.493 0 0 5269.5255 10.589186
9300 16738.482 0 0 5269.522 10.589159
9350 16738.46 0 0 5269.5151 10.589105
9400 16738.481 0 0 5269.5217 10.589155
9450 16738.509 0 0 5269.5307 10.589226
9500 16738.491 0 0 5269.5248 10.589181
9550 16738.484 0 0 5269.5227 10.589164
9600 16738.483 0 0 5269.5223 10.589161
9650 16738.464 0 0 5269.5166 10.589116
9700 16738.484 0 0 5269.5228 10.589164
9750 16738.507 0 0 5269.5301 10.589221
9800 16738.482 0 0 5269.5221 10.589159
9850 16738.478 0 0 5269.5208 10.589149
9900 16738.487 -0.00030979591 0 5269.5233 10.589165
9950 16738.476 -0.0009596827 0 5269.5193 10.589123
10000 16738.494 -0.0006271698 0 5269.5253 10.589175
Loop time of 0.213152 on 4 procs for 10000 steps with 81 atoms
Performance: 405345.239 tau/day, 46914.958 timesteps/s
91.7% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0029514 | 0.0038354 | 0.005348 | 1.5 | 1.80
Neigh | 0.01178 | 0.013139 | 0.0167 | 1.8 | 6.16
Comm | 0.073879 | 0.078553 | 0.081131 | 1.0 | 36.85
Output | 0.0031943 | 0.0037987 | 0.0055451 | 1.6 | 1.78
Modify | 0.10553 | 0.10763 | 0.1096 | 0.4 | 50.49
Other | | 0.0062 | | | 2.91
Nlocal: 20.25 ave 34 max 9 min
Histogram: 2 0 0 0 0 0 0 1 0 1
Nghost: 38.5 ave 43 max 26 min
Histogram: 1 0 0 0 0 0 0 0 0 3
Neighs: 0.75 ave 2 max 0 min
Histogram: 2 0 0 0 0 1 0 0 0 1
Total # of neighbors = 3
Ave neighs/atom = 0.037037
Neighbor list builds = 998
Dangerous builds = 997
Total wall time: 0:00:00

335
examples/rigid/log.27Nov18.rigid.nve.g++.1 Normal file
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@ -0,0 +1,335 @@
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
9 atoms in group clump1
group clump2 id <> 10 18
9 atoms in group clump2
group clump3 id <> 19 27
9 atoms in group clump3
group clump4 id <> 28 36
9 atoms in group clump4
group clump5 id <> 37 45
9 atoms in group clump5
group clump6 id <> 46 54
9 atoms in group clump6
group clump7 id <> 55 63
9 atoms in group clump7
group clump8 id <> 64 72
9 atoms in group clump8
group clump9 id <> 73 81
9 atoms in group clump9
fix 1 all rigid/nve group 9 clump1 clump2 clump3 clump4 clump5 clump6 clump7 clump8 clump9
9 rigid bodies with 81 atoms
# 1 chain of connected bodies
#group clump1 id <> 1 9
#group clump2 id <> 9 18
#group clump3 id <> 18 27
#group clump4 id <> 27 36
#group clump5 id <> 36 45
#group clump6 id <> 45 54
#group clump7 id <> 54 63
#group clump8 id <> 63 72
#group clump9 id <> 72 81
#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9
# 2 chains of connected bodies
#group clump1 id <> 1 9
#group clump2 id <> 9 18
#group clump3 id <> 18 27
#group clump4 id <> 27 36
#group clump5 id <> 37 45
#group clump6 id <> 45 54
#group clump7 id <> 54 63
#group clump8 id <> 63 72
#group clump9 id <> 72 81
#fix 1 all poems group clump1 clump2 clump3 clump4
#fix 2 all poems group clump5 clump6 clump7 clump8 clump9
neigh_modify exclude group clump1 clump1
neigh_modify exclude group clump2 clump2
neigh_modify exclude group clump3 clump3
neigh_modify exclude group clump4 clump4
neigh_modify exclude group clump5 clump5
neigh_modify exclude group clump6 clump6
neigh_modify exclude group clump7 clump7
neigh_modify exclude group clump8 clump8
neigh_modify exclude group clump9 clump9
thermo 100
#dump 1 all atom 50 dump.rigid
#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 2 pad 5
#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 3 pad 5
timestep 0.0001
thermo 50
run 10000
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) = 3.979 | 3.979 | 3.979 Mbytes
Step Temp E_pair E_mol TotEng Press
0 115.29439 5235.9179 0 5272.2142 -2.7403788
50 14910.69 571.70921 0 5265.8153 32.005816
100 16298.128 136.75661 0 5267.6488 16.449029
150 16682.532 17.504156 0 5269.4124 14.901186
200 16733.906 1.3755079 0 5269.4571 14.571305
250 16738.861 -0.15272039 0 5269.4886 14.498342
300 16738.608 -0.055216883 0 5269.5066 14.498
350 16738.5 -0.017457072 0 5269.5104 14.498392
400 16738.451 -0.0060161309 0 5269.5063 14.49851
450 16738.435 -0.001271965 0 5269.5059 14.498571
500 16738.443 -0.00081074175 0 5269.509 14.498598
550 16738.452 -0.00083208965 0 5269.5118 14.498618
600 16738.45 -0.00058358431 0 5269.5116 14.498617
650 16738.443 -0.00047228525 0 5269.5093 14.4986
700 16738.444 0 0 5269.5102 14.498612
750 16738.461 0 0 5269.5157 14.498654
800 16738.479 0 0 5269.521 14.498697
850 16738.473 0 0 5269.5192 14.498683
900 16738.449 0 0 5269.5116 14.498624
950 16738.438 -0.0035324203 0 5269.5046 14.498537
1000 16738.562 -0.051134242 0 5269.4963 14.498093
1050 16737.343 0.32970192 0 5269.4934 14.527634
1100 16737.878 0.16213235 0 5269.4941 14.533864
1150 16738.682 -0.089236256 0 5269.4959 14.511765
1200 16738.444 -0.0075446558 0 5269.5025 14.512479
1250 16738.45 0 0 5269.5119 14.512611
1300 16738.475 0 0 5269.5199 14.512673
1350 16738.484 0 0 5269.5228 14.512696
1400 16738.469 -0.00044683992 0 5269.5175 14.512651
1450 16738.45 -0.0010933363 0 5269.511 14.512595
1500 16738.445 -0.00057484239 0 5269.51 14.512591
1550 16738.451 0 0 5269.5123 14.512615
1600 16738.452 0 0 5269.5127 14.512618
1650 16738.443 0 0 5269.5099 14.512596
1700 16738.433 0 0 5269.5068 14.512572
1750 16738.438 0 0 5269.5084 14.512584
1800 16738.459 0 0 5269.5149 14.512635
1850 16738.473 0 0 5269.5193 14.51267
1900 16738.462 0 0 5269.5159 14.512644
1950 16738.446 -0.0032069962 0 5269.5076 14.512539
2000 16738.463 -0.013425408 0 5269.5027 14.512382
2050 16738.535 -0.036964311 0 5269.5017 14.512152
2100 16738.621 -0.063490509 0 5269.5023 14.512108
2150 16738.594 -0.056143934 0 5269.5012 14.512117
2200 16738.536 -0.038486645 0 5269.5007 14.512277
2250 16738.496 -0.023712406 0 5269.503 14.51242
2300 16738.488 -0.013209094 0 5269.5109 14.51255
2350 16738.486 -0.0045244524 0 5269.519 14.512693
2400 16738.475 -0.00051678325 0 5269.5194 14.512743
2450 16738.456 -0.0023209272 0 5269.5115 14.512659
2500 16738.442 -0.0052101787 0 5269.5042 14.512594
2550 16738.552 -0.04420046 0 5269.4998 14.512177
2600 16738.42 -0.004347531 0 5269.4982 14.512783
2650 16734.241 1.3131302 0 5269.5 14.577195
2700 16738.737 -0.10612056 0 5269.4961 14.503874
2750 16732.705 1.7939719 0 5269.4974 14.629294
2800 16738.558 -0.042867033 0 5269.5032 14.519893
2850 16738.499 -0.01271227 0 5269.5146 14.518524
2900 16738.486 -0.0032778045 0 5269.52 14.518712
2950 16738.482 -0.0089544631 0 5269.5133 14.518629
3000 16738.647 -0.070862542 0 5269.5031 14.51803
3050 16678.313 18.829038 0 5269.409 15.533426
3100 16632.312 33.399217 0 5269.4975 14.588597
3150 16739.318 -0.31388148 0 5269.4715 13.520782
3200 16727.951 3.26736 0 5269.4741 12.288358
3250 16686.364 16.353793 0 5269.4682 14.152517
3300 16738.532 -0.031574462 0 5269.5064 13.310615
3350 16738.454 -0.0062292918 0 5269.5071 13.308187
3400 16738.445 -0.0049349125 0 5269.5055 13.308178
3450 16738.489 -0.021623738 0 5269.5026 13.308001
3500 16737.78 0.19719043 0 5269.4983 13.325999
3550 16658.578 25.116206 0 5269.4834 13.778249
3600 16738.51 -0.032864725 0 5269.4981 12.392389
3650 16738.899 -0.15952703 0 5269.4938 12.383503
3700 16738.879 -0.16025994 0 5269.487 12.382575
3750 16738.878 -0.16608251 0 5269.4806 12.382765
3800 16738.591 -0.078679341 0 5269.4776 12.383227
3850 16738.429 -0.024729409 0 5269.4807 12.382942
3900 16738.399 -0.0062729967 0 5269.4897 12.383192
3950 16738.428 -0.002521266 0 5269.5027 12.383324
4000 16738.467 -0.0002068506 0 5269.5173 12.383474
4050 16738.488 0 0 5269.5241 12.383531
4100 16738.468 0 0 5269.5178 12.383482
4150 16738.422 0 0 5269.5033 12.383369
4200 16738.387 0 0 5269.4921 12.383281
4250 16738.383 0 0 5269.4908 12.38327
4300 16738.4 0 0 5269.4964 12.383314
4350 16738.423 0 0 5269.5036 12.38337
4400 16738.441 0 0 5269.5092 12.383414
4450 16738.45 0 0 5269.5121 12.383437
4500 16738.45 0 0 5269.5122 12.383438
4550 16738.442 0 0 5269.5095 12.383417
4600 16738.425 0 0 5269.5042 12.383376
4650 16738.404 -0.0014438316 0 5269.4961 12.383299
4700 16738.444 -0.024020551 0 5269.4862 12.382975
4750 16738.49 -0.04852143 0 5269.4761 12.385777
4800 16735.057 1.0347216 0 5269.4786 12.43543
4850 16735.441 0.92650925 0 5269.4913 12.418653
4900 16723.839 4.5908974 0 5269.5033 13.410103
4950 16738.531 -0.02153767 0 5269.5159 13.089982
5000 16738.45 -0.0042589697 0 5269.5077 13.090062
5050 16738.409 -0.00024692476 0 5269.4987 13.090038
5100 16738.404 0 0 5269.4976 13.090032
5150 16738.421 0 0 5269.5029 13.090073
5200 16738.44 0 0 5269.5087 13.090119
5250 16738.448 -0.001279392 0 5269.5102 13.090114
5300 16738.456 -0.0064376391 0 5269.5075 13.090026
5350 16738.479 -0.020383841 0 5269.5007 13.089897
5400 16735.845 0.7988947 0 5269.4909 13.136244
5450 16735.558 0.87620022 0 5269.4778 12.324482
5500 16711.494 8.4724178 0 5269.4984 12.656579
5550 16454.525 89.074815 0 5269.2031 16.996503
5600 16713.084 7.9801418 0 5269.5065 13.774979
5650 16738.676 -0.079987748 0 5269.5033 13.168297
5700 16446.281 91.866085 0 5269.399 23.764663
5750 16738.549 -0.039869084 0 5269.5034 13.378122
5800 16738.487 -0.014994478 0 5269.5086 13.378399
5850 16738.466 -0.0051267616 0 5269.512 13.37856
5900 16738.462 -0.0043690142 0 5269.5113 13.378573
5950 16738.528 -0.032727415 0 5269.5039 13.378197
6000 16702.774 10.969438 0 5269.2502 13.788852
6050 16682.271 17.483137 0 5269.3092 13.353101
6100 16738.508 -0.028838222 0 5269.5016 12.521084
6150 16738.425 -0.0067595536 0 5269.4974 12.521223
6200 16738.401 -0.0011499893 0 5269.4955 12.521254
6250 16738.455 0 0 5269.5135 12.52141
6300 16738.523 0 0 5269.5352 12.52158
6350 16738.503 0 0 5269.5287 12.521531
6400 16738.427 0 0 5269.5047 12.521344
6450 16738.399 0 0 5269.496 12.521274
6500 16738.425 0 0 5269.5042 12.521337
6550 16738.441 0 0 5269.5093 12.521378
6600 16738.42 0 0 5269.5025 12.521326
6650 16738.398 0 0 5269.4957 12.521272
6700 16738.435 0 0 5269.5074 12.521362
6750 16738.505 0 0 5269.5293 12.521534
6800 16738.508 0 0 5269.5303 12.521543
6850 16738.446 0 0 5269.5108 12.521391
6900 16738.414 0 0 5269.5009 12.521312
6950 16738.432 0 0 5269.5063 12.521354
7000 16738.444 0 0 5269.5102 12.521385
7050 16738.421 0 0 5269.5029 12.521329
7100 16738.393 0 0 5269.4941 12.521259
7150 16738.419 0 0 5269.5022 12.521322
7200 16738.489 0 0 5269.5244 12.521495
7250 16738.505 0 0 5269.5293 12.521535
7300 16738.443 0 0 5269.5098 12.521383
7350 16738.404 0 0 5269.4976 12.521287
7400 16738.43 0 0 5269.5058 12.52135
7450 16738.461 0 0 5269.5156 12.521427
7500 16738.447 0 0 5269.5109 12.521392
7550 16738.407 0 0 5269.4986 12.521295
7600 16738.412 0 0 5269.5002 12.521306
7650 16738.478 0 0 5269.5208 12.521467
7700 16738.51 0 0 5269.5309 12.521547
7750 16738.454 0 0 5269.5135 12.521412
7800 16738.398 0 0 5269.4958 12.521273
7850 16738.407 -0.0002118108 0 5269.4982 12.521289
7900 16738.441 -0.00021679711 0 5269.509 12.521373
7950 16738.446 -0.00023848139 0 5269.5107 12.521386
8000 16738.423 0 0 5269.5035 12.521333
8050 16738.423 0 0 5269.5034 12.521332
8100 16738.478 -0.00069622994 0 5269.52 12.521454
8150 16738.523 -0.0040058408 0 5269.531 12.521501
8200 16738.486 -0.0092298229 0 5269.5142 12.521334
8250 16738.458 -0.023189671 0 5269.4914 12.521014
8300 16738.513 -0.045845677 0 5269.4861 12.520779
8350 16723.745 4.5690412 0 5269.4516 12.849325
8400 16738.466 -0.020158442 0 5269.497 12.835773
8450 16738.437 -0.012822892 0 5269.4952 12.829936
8500 16738.408 -0.0016837088 0 5269.4972 12.830061
8550 16738.464 -0.00097379467 0 5269.5155 12.830216
8600 16738.669 -0.050578079 0 5269.5304 12.829934
8650 15917.563 250.28318 0 5261.3678 24.54572
8700 16738.445 0.0012168759 0 5269.5117 10.589499
8750 16738.473 -0.010164589 0 5269.509 10.588414
8800 16738.468 0 0 5269.5177 10.588633
8850 16738.508 0 0 5269.5304 10.588733
8900 16738.509 0 0 5269.5307 10.588736
8950 16738.496 0 0 5269.5266 10.588705
9000 16738.477 0 0 5269.5204 10.588656
9050 16738.455 0 0 5269.5135 10.588602
9100 16738.477 0 0 5269.5206 10.588656
9150 16738.512 0 0 5269.5316 10.588743
9200 16738.502 0 0 5269.5285 10.58872
9250 16738.493 0 0 5269.5255 10.588696
9300 16738.482 0 0 5269.522 10.588669
9350 16738.46 0 0 5269.5151 10.588615
9400 16738.481 0 0 5269.5217 10.588665
9450 16738.509 0 0 5269.5307 10.588736
9500 16738.491 0 0 5269.5248 10.58869
9550 16738.484 0 0 5269.5227 10.588674
9600 16738.483 0 0 5269.5223 10.588671
9650 16738.464 0 0 5269.5166 10.588626
9700 16738.484 0 0 5269.5229 10.588674
9750 16738.507 0 0 5269.5301 10.588731
9800 16738.482 0 0 5269.5221 10.588669
9850 16738.478 0 0 5269.5208 10.588659
9900 16738.487 -0.00030979474 0 5269.5233 10.588675
9950 16738.476 -0.00095968581 0 5269.5193 10.588632
10000 16738.494 -0.00062717822 0 5269.5253 10.588684
Loop time of 0.171181 on 1 procs for 10000 steps with 81 atoms
Performance: 504728.317 tau/day, 58417.629 timesteps/s
97.6% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.011004 | 0.011004 | 0.011004 | 0.0 | 6.43
Neigh | 0.041984 | 0.041984 | 0.041984 | 0.0 | 24.53
Comm | 0.012262 | 0.012262 | 0.012262 | 0.0 | 7.16
Output | 0.0017002 | 0.0017002 | 0.0017002 | 0.0 | 0.99
Modify | 0.098894 | 0.098894 | 0.098894 | 0.0 | 57.77
Other | | 0.005337 | | | 3.12
Nlocal: 81 ave 81 max 81 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 49 ave 49 max 49 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 3 ave 3 max 3 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 3
Ave neighs/atom = 0.037037
Neighbor list builds = 998
Dangerous builds = 997
Total wall time: 0:00:00

335
examples/rigid/log.27Nov18.rigid.nve.g++.4 Normal file
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@ -0,0 +1,335 @@
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
9 atoms in group clump1
group clump2 id <> 10 18
9 atoms in group clump2
group clump3 id <> 19 27
9 atoms in group clump3
group clump4 id <> 28 36
9 atoms in group clump4
group clump5 id <> 37 45
9 atoms in group clump5
group clump6 id <> 46 54
9 atoms in group clump6
group clump7 id <> 55 63
9 atoms in group clump7
group clump8 id <> 64 72
9 atoms in group clump8
group clump9 id <> 73 81
9 atoms in group clump9
fix 1 all rigid/nve group 9 clump1 clump2 clump3 clump4 clump5 clump6 clump7 clump8 clump9
9 rigid bodies with 81 atoms
# 1 chain of connected bodies
#group clump1 id <> 1 9
#group clump2 id <> 9 18
#group clump3 id <> 18 27
#group clump4 id <> 27 36
#group clump5 id <> 36 45
#group clump6 id <> 45 54
#group clump7 id <> 54 63
#group clump8 id <> 63 72
#group clump9 id <> 72 81
#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9
# 2 chains of connected bodies
#group clump1 id <> 1 9
#group clump2 id <> 9 18
#group clump3 id <> 18 27
#group clump4 id <> 27 36
#group clump5 id <> 37 45
#group clump6 id <> 45 54
#group clump7 id <> 54 63
#group clump8 id <> 63 72
#group clump9 id <> 72 81
#fix 1 all poems group clump1 clump2 clump3 clump4
#fix 2 all poems group clump5 clump6 clump7 clump8 clump9
neigh_modify exclude group clump1 clump1
neigh_modify exclude group clump2 clump2
neigh_modify exclude group clump3 clump3
neigh_modify exclude group clump4 clump4
neigh_modify exclude group clump5 clump5
neigh_modify exclude group clump6 clump6
neigh_modify exclude group clump7 clump7
neigh_modify exclude group clump8 clump8
neigh_modify exclude group clump9 clump9
thermo 100
#dump 1 all atom 50 dump.rigid
#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 2 pad 5
#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 3 pad 5
timestep 0.0001
thermo 50
run 10000
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) = 3.95 | 4.044 | 4.326 Mbytes
Step Temp E_pair E_mol TotEng Press
0 115.29439 5235.9179 0 5272.2142 -2.7403788
50 14910.69 571.70921 0 5265.8153 32.005816
100 16298.128 136.75661 0 5267.6488 16.449029
150 16682.532 17.504156 0 5269.4124 14.901186
200 16733.906 1.3755079 0 5269.4571 14.571305
250 16738.861 -0.15272039 0 5269.4886 14.498342
300 16738.608 -0.055216883 0 5269.5066 14.498
350 16738.5 -0.017457072 0 5269.5104 14.498392
400 16738.451 -0.0060161309 0 5269.5063 14.49851
450 16738.435 -0.001271965 0 5269.5059 14.498571
500 16738.443 -0.00081074175 0 5269.509 14.498598
550 16738.452 -0.00083208965 0 5269.5118 14.498618
600 16738.45 -0.00058358431 0 5269.5116 14.498617
650 16738.443 -0.00047228525 0 5269.5093 14.4986
700 16738.444 0 0 5269.5102 14.498612
750 16738.461 0 0 5269.5157 14.498654
800 16738.479 0 0 5269.521 14.498697
850 16738.473 0 0 5269.5192 14.498683
900 16738.449 0 0 5269.5116 14.498624
950 16738.438 -0.0035324203 0 5269.5046 14.498537
1000 16738.562 -0.051134242 0 5269.4963 14.498093
1050 16737.343 0.32970192 0 5269.4934 14.527634
1100 16737.878 0.16213235 0 5269.4941 14.533864
1150 16738.682 -0.089236256 0 5269.4959 14.511765
1200 16738.444 -0.0075446558 0 5269.5025 14.512479
1250 16738.45 0 0 5269.5119 14.512611
1300 16738.475 0 0 5269.5199 14.512673
1350 16738.484 0 0 5269.5228 14.512696
1400 16738.469 -0.00044683992 0 5269.5175 14.512651
1450 16738.45 -0.0010933363 0 5269.511 14.512595
1500 16738.445 -0.00057484239 0 5269.51 14.512591
1550 16738.451 0 0 5269.5123 14.512615
1600 16738.452 0 0 5269.5127 14.512618
1650 16738.443 0 0 5269.5099 14.512596
1700 16738.433 0 0 5269.5068 14.512572
1750 16738.438 0 0 5269.5084 14.512584
1800 16738.459 0 0 5269.5149 14.512635
1850 16738.473 0 0 5269.5193 14.51267
1900 16738.462 0 0 5269.5159 14.512644
1950 16738.446 -0.0032069962 0 5269.5076 14.512539
2000 16738.463 -0.013425408 0 5269.5027 14.512382
2050 16738.535 -0.036964311 0 5269.5017 14.512152
2100 16738.621 -0.063490509 0 5269.5023 14.512108
2150 16738.594 -0.056143934 0 5269.5012 14.512117
2200 16738.536 -0.038486645 0 5269.5007 14.512277
2250 16738.496 -0.023712406 0 5269.503 14.51242
2300 16738.488 -0.013209094 0 5269.5109 14.51255
2350 16738.486 -0.0045244524 0 5269.519 14.512693
2400 16738.475 -0.00051678325 0 5269.5194 14.512743
2450 16738.456 -0.0023209272 0 5269.5115 14.512659
2500 16738.442 -0.0052101787 0 5269.5042 14.512594
2550 16738.552 -0.04420046 0 5269.4998 14.512177
2600 16738.42 -0.004347531 0 5269.4982 14.512783
2650 16734.241 1.3131302 0 5269.5 14.577195
2700 16738.737 -0.10612056 0 5269.4961 14.503874
2750 16732.705 1.7939719 0 5269.4974 14.629294
2800 16738.558 -0.042867033 0 5269.5032 14.519893
2850 16738.499 -0.01271227 0 5269.5146 14.518524
2900 16738.486 -0.0032778045 0 5269.52 14.518712
2950 16738.482 -0.0089544631 0 5269.5133 14.518629
3000 16738.647 -0.070862542 0 5269.5031 14.51803
3050 16678.313 18.829038 0 5269.409 15.533426
3100 16632.312 33.399217 0 5269.4975 14.588597
3150 16739.318 -0.31388148 0 5269.4715 13.520782
3200 16727.951 3.26736 0 5269.4741 12.288358
3250 16686.364 16.353793 0 5269.4682 14.152517
3300 16738.532 -0.031574462 0 5269.5064 13.310615
3350 16738.454 -0.0062292918 0 5269.5071 13.308187
3400 16738.445 -0.0049349125 0 5269.5055 13.308178
3450 16738.489 -0.021623738 0 5269.5026 13.308001
3500 16737.78 0.19719043 0 5269.4983 13.325999
3550 16658.578 25.116206 0 5269.4834 13.778249
3600 16738.51 -0.032864725 0 5269.4981 12.392389
3650 16738.899 -0.15952703 0 5269.4938 12.383503
3700 16738.879 -0.16025994 0 5269.487 12.382575
3750 16738.878 -0.16608251 0 5269.4806 12.382765
3800 16738.591 -0.078679341 0 5269.4776 12.383227
3850 16738.429 -0.024729409 0 5269.4807 12.382942
3900 16738.399 -0.0062729967 0 5269.4897 12.383192
3950 16738.428 -0.002521266 0 5269.5027 12.383324
4000 16738.467 -0.0002068506 0 5269.5173 12.383474
4050 16738.488 0 0 5269.5241 12.383531
4100 16738.468 0 0 5269.5178 12.383482
4150 16738.422 0 0 5269.5033 12.383369
4200 16738.387 0 0 5269.4921 12.383281
4250 16738.383 0 0 5269.4908 12.38327
4300 16738.4 0 0 5269.4964 12.383314
4350 16738.423 0 0 5269.5036 12.38337
4400 16738.441 0 0 5269.5092 12.383414
4450 16738.45 0 0 5269.5121 12.383437
4500 16738.45 0 0 5269.5122 12.383438
4550 16738.442 0 0 5269.5095 12.383417
4600 16738.425 0 0 5269.5042 12.383376
4650 16738.404 -0.0014438316 0 5269.4961 12.383299
4700 16738.444 -0.024020551 0 5269.4862 12.382975
4750 16738.49 -0.048521428 0 5269.4761 12.385777
4800 16735.057 1.0347217 0 5269.4786 12.43543
4850 16735.441 0.92650925 0 5269.4913 12.418653
4900 16723.839 4.5908973 0 5269.5033 13.410103
4950 16738.531 -0.02153767 0 5269.5159 13.089982
5000 16738.45 -0.0042589696 0 5269.5077 13.090062
5050 16738.409 -0.00024692476 0 5269.4987 13.090038
5100 16738.404 0 0 5269.4976 13.090032
5150 16738.421 0 0 5269.5029 13.090073
5200 16738.44 0 0 5269.5087 13.090119
5250 16738.448 -0.001279392 0 5269.5102 13.090114
5300 16738.456 -0.0064376392 0 5269.5075 13.090026
5350 16738.479 -0.020383842 0 5269.5007 13.089897
5400 16735.845 0.79889474 0 5269.4909 13.136244
5450 16735.558 0.87619992 0 5269.4778 12.324482
5500 16711.494 8.4724208 0 5269.4984 12.656579
5550 16454.525 89.074816 0 5269.2031 16.996503
5600 16713.084 7.9801334 0 5269.5065 13.774977
5650 16738.676 -0.079987764 0 5269.5033 13.168295
5700 16446.281 91.866085 0 5269.399 23.764662
5750 16738.549 -0.039869084 0 5269.5034 13.378121
5800 16738.487 -0.014994475 0 5269.5086 13.378397
5850 16738.466 -0.0051267556 0 5269.512 13.378559
5900 16738.462 -0.0043690097 0 5269.5113 13.378572
5950 16738.528 -0.03272741 0 5269.5039 13.378195
6000 16702.774 10.969434 0 5269.2502 13.788851
6050 16682.271 17.483158 0 5269.3092 13.3531
6100 16738.508 -0.028838239 0 5269.5016 12.521082
6150 16738.425 -0.0067595542 0 5269.4974 12.521221
6200 16738.401 -0.0011499896 0 5269.4955 12.521252
6250 16738.455 0 0 5269.5135 12.521408
6300 16738.523 0 0 5269.5352 12.521578
6350 16738.503 0 0 5269.5287 12.52153
6400 16738.427 0 0 5269.5047 12.521342
6450 16738.399 0 0 5269.496 12.521273
6500 16738.425 0 0 5269.5042 12.521336
6550 16738.441 0 0 5269.5093 12.521377
6600 16738.42 0 0 5269.5025 12.521324
6650 16738.398 0 0 5269.4957 12.52127
6700 16738.435 0 0 5269.5074 12.52136
6750 16738.505 0 0 5269.5293 12.521532
6800 16738.508 0 0 5269.5303 12.521541
6850 16738.446 0 0 5269.5108 12.521389
6900 16738.414 0 0 5269.5009 12.521311
6950 16738.432 0 0 5269.5063 12.521353
7000 16738.444 0 0 5269.5102 12.521383
7050 16738.421 0 0 5269.5029 12.521327
7100 16738.393 0 0 5269.4941 12.521258
7150 16738.419 0 0 5269.5022 12.52132
7200 16738.489 0 0 5269.5244 12.521494
7250 16738.505 0 0 5269.5293 12.521533
7300 16738.443 0 0 5269.5098 12.521381
7350 16738.404 0 0 5269.4976 12.521285
7400 16738.43 0 0 5269.5058 12.521348
7450 16738.461 0 0 5269.5156 12.521425
7500 16738.447 0 0 5269.5109 12.52139
7550 16738.407 0 0 5269.4986 12.521293
7600 16738.412 0 0 5269.5002 12.521305
7650 16738.478 0 0 5269.5208 12.521465
7700 16738.51 0 0 5269.5309 12.521546
7750 16738.454 0 0 5269.5135 12.52141
7800 16738.398 0 0 5269.4958 12.521272
7850 16738.407 -0.00021180981 0 5269.4982 12.521288
7900 16738.441 -0.0002167964 0 5269.509 12.521371
7950 16738.446 -0.00023848065 0 5269.5107 12.521385
8000 16738.423 0 0 5269.5035 12.521331
8050 16738.423 0 0 5269.5034 12.52133
8100 16738.478 -0.00069623408 0 5269.52 12.521452
8150 16738.523 -0.0040058355 0 5269.531 12.521499
8200 16738.486 -0.0092298325 0 5269.5142 12.521332
8250 16738.458 -0.023189665 0 5269.4914 12.521012
8300 16738.513 -0.045846242 0 5269.4861 12.520778
8350 16723.742 4.5698786 0 5269.4516 12.849386
8400 16738.466 -0.02016972 0 5269.497 12.835784
8450 16738.437 -0.012822703 0 5269.4952 12.829948
8500 16738.408 -0.0016836132 0 5269.4972 12.830073
8550 16738.464 -0.00097380297 0 5269.5155 12.830227
8600 16738.669 -0.050578946 0 5269.5304 12.829946
8650 15917.707 250.24016 0 5261.3702 24.544744
8700 16738.445 0.0010615265 0 5269.5117 10.589987
8750 16738.473 -0.010158834 0 5269.509 10.588904
8800 16738.468 0 0 5269.5176 10.589124
8850 16738.508 0 0 5269.5304 10.589223
8900 16738.509 0 0 5269.5306 10.589226
8950 16738.496 0 0 5269.5266 10.589195
9000 16738.477 0 0 5269.5204 10.589147
9050 16738.455 0 0 5269.5135 10.589092
9100 16738.477 0 0 5269.5206 10.589146
9150 16738.512 0 0 5269.5316 10.589233
9200 16738.502 0 0 5269.5285 10.58921
9250 16738.493 0 0 5269.5255 10.589186
9300 16738.482 0 0 5269.522 10.589159
9350 16738.46 0 0 5269.5151 10.589105
9400 16738.481 0 0 5269.5217 10.589155
9450 16738.509 0 0 5269.5307 10.589226
9500 16738.491 0 0 5269.5248 10.589181
9550 16738.484 0 0 5269.5227 10.589164
9600 16738.483 0 0 5269.5223 10.589161
9650 16738.464 0 0 5269.5166 10.589116
9700 16738.484 0 0 5269.5228 10.589164
9750 16738.507 0 0 5269.5301 10.589221
9800 16738.482 0 0 5269.5221 10.589159
9850 16738.478 0 0 5269.5208 10.589149
9900 16738.487 -0.00030979591 0 5269.5233 10.589165
9950 16738.476 -0.0009596827 0 5269.5193 10.589123
10000 16738.494 -0.0006271698 0 5269.5253 10.589175
Loop time of 0.212511 on 4 procs for 10000 steps with 81 atoms
Performance: 406566.385 tau/day, 47056.295 timesteps/s
91.9% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0032909 | 0.0039915 | 0.0048544 | 0.9 | 1.88
Neigh | 0.011434 | 0.01325 | 0.016991 | 1.9 | 6.24
Comm | 0.076038 | 0.082493 | 0.088069 | 1.5 | 38.82
Output | 0.0031183 | 0.0045295 | 0.0086036 | 3.5 | 2.13
Modify | 0.099662 | 0.10206 | 0.10679 | 0.9 | 48.02
Other | | 0.00619 | | | 2.91
Nlocal: 20.25 ave 34 max 9 min
Histogram: 2 0 0 0 0 0 0 1 0 1
Nghost: 38.5 ave 43 max 26 min
Histogram: 1 0 0 0 0 0 0 0 0 3
Neighs: 0.75 ave 2 max 0 min
Histogram: 2 0 0 0 0 1 0 0 0 1
Total # of neighbors = 3
Ave neighs/atom = 0.037037
Neighbor list builds = 998
Dangerous builds = 997
Total wall time: 0:00:00

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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
atom_modify map array
pair_style lj/cut 2.5
fix 0 all property/atom i_bodies
read_data data.rigid-property fix 0 NULL Bodies
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
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
# assemble bodies from per-atom custom integer property bodies
fix 1 all rigid custom i_bodies
9 rigid bodies with 81 atoms
# 1 chain of connected bodies
#group clump1 id <> 1 9
#group clump2 id <> 9 18
#group clump3 id <> 18 27
#group clump4 id <> 27 36
#group clump5 id <> 36 45
#group clump6 id <> 45 54
#group clump7 id <> 54 63
#group clump8 id <> 63 72
#group clump9 id <> 72 81
#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9
# 2 chains of connected bodies
#group clump1 id <> 1 9
#group clump2 id <> 9 18
#group clump3 id <> 18 27
#group clump4 id <> 27 36
#group clump5 id <> 37 45
#group clump6 id <> 45 54
#group clump7 id <> 54 63
#group clump8 id <> 63 72
#group clump9 id <> 72 81
#fix 1 all poems group clump1 clump2 clump3 clump4
#fix 2 all poems group clump5 clump6 clump7 clump8 clump9
neigh_modify exclude group clump1 clump1
neigh_modify exclude group clump2 clump2
neigh_modify exclude group clump3 clump3
neigh_modify exclude group clump4 clump4
neigh_modify exclude group clump5 clump5
neigh_modify exclude group clump6 clump6
neigh_modify exclude group clump7 clump7
neigh_modify exclude group clump8 clump8
neigh_modify exclude group clump9 clump9
thermo 100
#dump 1 all atom 50 dump.rigid
#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 2 pad 5
#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 3 pad 5
timestep 0.0001
thermo 50
run 10000
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) = 4.046 | 4.046 | 4.046 Mbytes
Step Temp E_pair E_mol TotEng Press
0 115.29439 5235.9179 0 5272.2142 -2.7403788
50 14910.685 571.71558 0 5265.82 32.006171
100 16298.442 136.66184 0 5267.653 16.444229
150 16682.606 17.490511 0 5269.4219 14.900344
200 16733.929 1.372872 0 5269.4617 14.569267
250 16738.853 -0.15252816 0 5269.4864 14.496404
300 16738.588 -0.055171335 0 5269.5002 14.496025
350 16738.492 -0.017444677 0 5269.5077 14.496446
400 16738.464 -0.0060102023 0 5269.5104 14.496618
450 16738.455 -0.0012713351 0 5269.5124 14.496701
500 16738.455 -0.00081068621 0 5269.5128 14.496709
550 16738.455 -0.00083203497 0 5269.5129 14.496707
600 16738.455 -0.00058355356 0 5269.5131 14.496709
650 16738.455 -0.00047226704 0 5269.5131 14.496708
700 16738.455 0 0 5269.5136 14.496713
750 16738.455 0 0 5269.5136 14.49671
800 16738.455 0 0 5269.5137 14.496709
850 16738.455 0 0 5269.5137 14.49671
900 16738.456 0 0 5269.5138 14.496713
950 16738.462 -0.0035323872 0 5269.5122 14.496671
1000 16738.586 -0.051135144 0 5269.5036 14.496229
1050 16737.358 0.32995057 0 5269.4981 14.525763
1100 16737.892 0.16210246 0 5269.4984 14.531983
1150 16738.703 -0.089235095 0 5269.5025 14.509899
1200 16738.466 -0.0075446243 0 5269.5096 14.510615
1250 16738.456 0 0 5269.514 14.510704
1300 16738.457 0 0 5269.5141 14.510701
1350 16738.457 0 0 5269.5141 14.510699
1400 16738.457 -0.00044736511 0 5269.5138 14.510693
1450 16738.458 -0.0010971179 0 5269.5134 14.510687
1500 16738.458 -0.00057885428 0 5269.5139 14.510698
1550 16738.457 0 0 5269.5143 14.51071
1600 16738.457 0 0 5269.5144 14.510712
1650 16738.457 0 0 5269.5144 14.510712
1700 16738.458 0 0 5269.5144 14.51071
1750 16738.458 0 0 5269.5145 14.510708
1800 16738.458 0 0 5269.5145 14.510706
1850 16738.458 0 0 5269.5146 14.510705
1900 16738.458 0 0 5269.5146 14.510706
1950 16738.465 -0.0031733615 0 5269.5134 14.510659
2000 16738.491 -0.013255268 0 5269.5117 14.510532
2050 16738.556 -0.0365811 0 5269.5087 14.51029
2100 16738.633 -0.063209659 0 5269.5065 14.510219
2150 16738.607 -0.05601761 0 5269.5055 14.510231
2200 16738.557 -0.038423032 0 5269.5072 14.510404
2250 16738.515 -0.023709918 0 5269.5088 14.510539
2300 16738.489 -0.013249035 0 5269.5111 14.510621
2350 16738.468 -0.0045563719 0 5269.5131 14.510714
2400 16738.46 -0.00052194273 0 5269.5146 14.510771
2450 16738.464 -0.0023259756 0 5269.514 14.510746
2500 16738.468 -0.0051929186 0 5269.5127 14.510731
2550 16738.581 -0.044940117 0 5269.5085 14.510315
2600 16738.427 -7.972284e-05 0 5269.5046 14.510657
2650 16733.017 1.7051479 0 5269.5067 14.596295
2700 16738.761 -0.10614946 0 5269.5038 14.499584
2750 16733.973 1.4038179 0 5269.5064 14.598107
2800 16738.585 -0.046813448 0 5269.5076 14.511073
2850 16738.487 -0.012558719 0 5269.5111 14.510111
2900 16738.465 -0.0026252725 0 5269.514 14.510277
2950 16738.476 -0.0082220764 0 5269.512 14.510223
3000 16738.66 -0.071284779 0 5269.507 14.509758
3050 16715.332 7.2419352 0 5269.476 14.870305
3100 16653.226 26.818761 0 5269.5009 14.496764
3150 16739.351 -0.30690375 0 5269.4886 13.643904
3200 16733.238 1.6025328 0 5269.4737 12.016934
3250 16734.374 1.2554429 0 5269.4841 11.963561
3300 16732.156 1.9585967 0 5269.4893 12.234024
3350 16738.655 -0.079693236 0 5269.497 12.092757
3400 16738.543 -0.042215005 0 5269.4991 12.092809
3450 16738.591 -0.059327511 0 5269.4972 12.092536
3500 16738.759 -0.11761245 0 5269.4918 12.09203
3550 16713.405 7.8460621 0 5269.4737 12.389816
3600 16734.939 1.0821936 0 5269.4891 12.173591
3650 16738.808 -0.13663194 0 5269.4882 12.027009
3700 16738.602 -0.070934368 0 5269.4889 12.025288
3750 16737.731 0.20706558 0 5269.4927 12.061948
3800 16738.578 -0.05582043 0 5269.4965 12.035665
3850 16738.471 -0.016307928 0 5269.5024 12.035302
3900 16738.449 -0.0058182199 0 5269.5059 12.035401
3950 16738.439 -0.0012027325 0 5269.5074 12.035461
4000 16738.436 -0.00020698452 0 5269.5075 12.035469
4050 16738.437 0 0 5269.5078 12.035454
4100 16738.437 0 0 5269.508 12.035435
4150 16738.438 0 0 5269.5081 12.035426
4200 16738.438 0 0 5269.5083 12.035432
4250 16738.439 0 0 5269.5085 12.035447
4300 16738.439 0 0 5269.5086 12.035463
4350 16738.44 0 0 5269.5087 12.035474
4400 16738.44 0 0 5269.5088 12.035478
4450 16738.44 0 0 5269.5089 12.035474
4500 16738.44 0 0 5269.509 12.035462
4550 16738.441 0 0 5269.5092 12.035449
4600 16738.441 0 0 5269.5093 12.035445
4650 16738.442 0 0 5269.5095 12.035451
4700 16738.442 0 0 5269.5096 12.03546
4750 16738.443 0 0 5269.5097 12.035465
4800 16738.443 0 0 5269.5098 12.035466
4850 16738.443 0 0 5269.51 12.035463
4900 16738.444 0 0 5269.5101 12.035456
4950 16738.444 0 0 5269.5102 12.035447
5000 16738.445 0 0 5269.5104 12.03544
5050 16738.445 0 0 5269.5105 12.035442
5100 16738.446 0 0 5269.5107 12.035455
5150 16738.446 0 0 5269.5108 12.03547
5200 16738.446 0 0 5269.5109 12.035479
5250 16738.447 0 0 5269.511 12.035479
5300 16738.447 0 0 5269.5111 12.03547
5350 16738.447 0 0 5269.5112 12.035454
5400 16738.448 0 0 5269.5113 12.035434
5450 16738.448 0 0 5269.5115 12.03542
5500 16738.449 0 0 5269.5117 12.035422
5550 16738.457 -0.0030919234 0 5269.5111 12.035383
5600 16738.51 -0.021618357 0 5269.5092 12.035106
5650 16738.622 -0.059214788 0 5269.507 12.035694
5700 16395.28 108.06942 0 5269.5463 24.369038
5750 16738.544 -0.033973429 0 5269.5077 12.011261
5800 16738.456 -0.0037013529 0 5269.5102 12.011675
5850 16738.451 0 0 5269.5123 12.011709
5900 16738.451 -0.0002211587 0 5269.5122 12.011687
5950 16738.452 -0.00024253349 0 5269.5124 12.011678
6000 16738.452 0 0 5269.5128 12.011688
6050 16738.453 0 0 5269.513 12.011702
6100 16738.453 0 0 5269.5131 12.011716
6150 16738.454 0 0 5269.5132 12.011725
6200 16738.454 0 0 5269.5133 12.011728
6250 16738.454 0 0 5269.5134 12.011723
6300 16738.455 0 0 5269.5135 12.011712
6350 16738.455 0 0 5269.5137 12.0117
6400 16738.456 0 0 5269.5138 12.011697
6450 16738.456 0 0 5269.514 12.011704
6500 16738.456 0 0 5269.5141 12.011714
6550 16738.457 0 0 5269.5142 12.011719
6600 16738.457 0 0 5269.5143 12.011718
6650 16738.458 0 0 5269.5144 12.011713
6700 16738.458 0 0 5269.5146 12.011705
6750 16738.459 0 0 5269.5147 12.011696
6800 16738.459 0 0 5269.5149 12.01169
6850 16738.46 0 0 5269.515 12.011695
6900 16738.46 0 0 5269.5152 12.01171
6950 16738.46 0 0 5269.5153 12.011726
7000 16738.461 0 0 5269.5154 12.011736
7050 16738.461 0 0 5269.5155 12.011737
7100 16738.461 0 0 5269.5155 12.011728
7150 16738.461 0 0 5269.5156 12.011712
7200 16738.462 0 0 5269.5158 12.011691
7250 16738.463 0 0 5269.516 12.011676
7300 16738.463 0 0 5269.5162 12.011677
7350 16738.464 0 0 5269.5164 12.011693
7400 16738.464 0 0 5269.5165 12.011713
7450 16738.465 0 0 5269.5166 12.011729
7500 16738.465 0 0 5269.5167 12.011736
7550 16738.465 0 0 5269.5168 12.011734
7600 16738.465 0 0 5269.5168 12.011722
7650 16738.466 0 0 5269.517 12.011704
7700 16738.466 0 0 5269.5171 12.011687
7750 16738.467 0 0 5269.5173 12.011681
7800 16738.467 0 0 5269.5175 12.011687
7850 16738.468 0 0 5269.5176 12.0117
7900 16738.468 0 0 5269.5178 12.011712
7950 16738.469 0 0 5269.5179 12.011721
8000 16738.469 0 0 5269.518 12.011724
8050 16738.469 0 0 5269.5181 12.01172
8100 16738.47 0 0 5269.5182 12.011709
8150 16738.47 0 0 5269.5183 12.0117
8200 16738.47 0 0 5269.5185 12.0117
8250 16738.471 0 0 5269.5186 12.011709
8300 16738.471 0 0 5269.5187 12.011719
8350 16738.472 0 0 5269.5189 12.011723
8400 16738.472 0 0 5269.519 12.01172
8450 16738.473 -0.00039690666 0 5269.5189 12.011706
8500 16738.481 -0.0034646804 0 5269.5182 12.011643
8550 16738.483 -0.0045307409 0 5269.5178 12.011621
8600 16738.474 -0.00076532811 0 5269.5189 12.011681
8650 16738.474 0 0 5269.5197 12.011699
8700 16738.475 0 0 5269.5199 12.011715
8750 16738.475 0 0 5269.52 12.011732
8800 16738.475 0 0 5269.52 12.011743
8850 16738.476 0 0 5269.5201 12.011744
8900 16738.476 0 0 5269.5202 12.011735
8950 16738.476 0 0 5269.5203 12.011719
9000 16738.477 0 0 5269.5205 12.011698
9050 16738.477 0 0 5269.5206 12.011683
9100 16738.478 0 0 5269.5208 12.011684
9150 16738.479 0 0 5269.521 12.011701
9200 16738.479 0 0 5269.5212 12.011722
9250 16738.479 0 0 5269.5213 12.011738
9300 16738.48 0 0 5269.5214 12.011746
9350 16738.48 0 0 5269.5214 12.011744
9400 16738.48 0 0 5269.5215 12.011732
9450 16738.48 0 0 5269.5216 12.011715
9500 16738.481 -0.00037652434 0 5269.5216 12.011692
9550 16738.493 -0.005315616 0 5269.5203 12.011611
9600 16738.549 -0.026814368 0 5269.5163 12.011415
9650 16738.765 -0.10191523 0 5269.5092 12.011013
9700 16735.041 1.0589885 0 5269.4979 12.062708
9750 16738.013 0.13550123 0 5269.5101 11.407245
9800 16738.512 -0.011620328 0 5269.5201 11.394974
9850 16738.489 -0.00067270523 0 5269.5237 11.395098
9900 16738.489 -0.00024984554 0 5269.5242 11.395085
9950 16738.49 0 0 5269.5245 11.395076
10000 16738.49 0 0 5269.5246 11.395075
Loop time of 0.156049 on 1 procs for 10000 steps with 81 atoms
Performance: 553673.043 tau/day, 64082.528 timesteps/s
97.6% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.010187 | 0.010187 | 0.010187 | 0.0 | 6.53
Neigh | 0.040601 | 0.040601 | 0.040601 | 0.0 | 26.02
Comm | 0.013221 | 0.013221 | 0.013221 | 0.0 | 8.47
Output | 0.0016611 | 0.0016611 | 0.0016611 | 0.0 | 1.06
Modify | 0.085107 | 0.085107 | 0.085107 | 0.0 | 54.54
Other | | 0.005271 | | | 3.38
Nlocal: 81 ave 81 max 81 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 84 ave 84 max 84 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0
Neighbor list builds = 998
Dangerous builds = 997
Total wall time: 0:00:00

340
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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
atom_modify map array
pair_style lj/cut 2.5
fix 0 all property/atom i_bodies
read_data data.rigid-property fix 0 NULL Bodies
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
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
# assemble bodies from per-atom custom integer property bodies
fix 1 all rigid custom i_bodies
9 rigid bodies with 81 atoms
# 1 chain of connected bodies
#group clump1 id <> 1 9
#group clump2 id <> 9 18
#group clump3 id <> 18 27
#group clump4 id <> 27 36
#group clump5 id <> 36 45
#group clump6 id <> 45 54
#group clump7 id <> 54 63
#group clump8 id <> 63 72
#group clump9 id <> 72 81
#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9
# 2 chains of connected bodies
#group clump1 id <> 1 9
#group clump2 id <> 9 18
#group clump3 id <> 18 27
#group clump4 id <> 27 36
#group clump5 id <> 37 45
#group clump6 id <> 45 54
#group clump7 id <> 54 63
#group clump8 id <> 63 72
#group clump9 id <> 72 81
#fix 1 all poems group clump1 clump2 clump3 clump4
#fix 2 all poems group clump5 clump6 clump7 clump8 clump9
neigh_modify exclude group clump1 clump1
neigh_modify exclude group clump2 clump2
neigh_modify exclude group clump3 clump3
neigh_modify exclude group clump4 clump4
neigh_modify exclude group clump5 clump5
neigh_modify exclude group clump6 clump6
neigh_modify exclude group clump7 clump7
neigh_modify exclude group clump8 clump8
neigh_modify exclude group clump9 clump9
thermo 100
#dump 1 all atom 50 dump.rigid
#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 2 pad 5
#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 3 pad 5
timestep 0.0001
thermo 50
run 10000
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) = 4.017 | 4.111 | 4.392 Mbytes
Step Temp E_pair E_mol TotEng Press
0 115.29439 5235.9179 0 5272.2142 -2.7403788
50 14910.685 571.71558 0 5265.82 32.006171
100 16298.442 136.66184 0 5267.653 16.444229
150 16682.606 17.490511 0 5269.4219 14.900344
200 16733.929 1.372872 0 5269.4617 14.569267
250 16738.853 -0.15252816 0 5269.4864 14.496404
300 16738.588 -0.055171335 0 5269.5002 14.496025
350 16738.492 -0.017444677 0 5269.5077 14.496446
400 16738.464 -0.0060102023 0 5269.5104 14.496618
450 16738.455 -0.0012713351 0 5269.5124 14.496701
500 16738.455 -0.00081068621 0 5269.5128 14.496709
550 16738.455 -0.00083203497 0 5269.5129 14.496707
600 16738.455 -0.00058355356 0 5269.5131 14.496709
650 16738.455 -0.00047226704 0 5269.5131 14.496708
700 16738.455 0 0 5269.5136 14.496713
750 16738.455 0 0 5269.5136 14.49671
800 16738.455 0 0 5269.5137 14.496709
850 16738.455 0 0 5269.5137 14.49671
900 16738.456 0 0 5269.5138 14.496713
950 16738.462 -0.0035323872 0 5269.5122 14.496671
1000 16738.586 -0.051135144 0 5269.5036 14.496229
1050 16737.358 0.32995057 0 5269.4981 14.525763
1100 16737.892 0.16210246 0 5269.4984 14.531983
1150 16738.703 -0.089235095 0 5269.5025 14.509899
1200 16738.466 -0.0075446243 0 5269.5096 14.510615
1250 16738.456 0 0 5269.514 14.510704
1300 16738.457 0 0 5269.5141 14.510701
1350 16738.457 0 0 5269.5141 14.510699
1400 16738.457 -0.00044736511 0 5269.5138 14.510693
1450 16738.458 -0.0010971179 0 5269.5134 14.510687
1500 16738.458 -0.00057885428 0 5269.5139 14.510698
1550 16738.457 0 0 5269.5143 14.51071
1600 16738.457 0 0 5269.5144 14.510712
1650 16738.457 0 0 5269.5144 14.510712
1700 16738.458 0 0 5269.5144 14.51071
1750 16738.458 0 0 5269.5145 14.510708
1800 16738.458 0 0 5269.5145 14.510706
1850 16738.458 0 0 5269.5146 14.510705
1900 16738.458 0 0 5269.5146 14.510706
1950 16738.465 -0.0031733615 0 5269.5134 14.510659
2000 16738.491 -0.013255268 0 5269.5117 14.510532
2050 16738.556 -0.0365811 0 5269.5087 14.51029
2100 16738.633 -0.063209659 0 5269.5065 14.510219
2150 16738.607 -0.05601761 0 5269.5055 14.510231
2200 16738.557 -0.038423032 0 5269.5072 14.510404
2250 16738.515 -0.023709918 0 5269.5088 14.510539
2300 16738.489 -0.013249035 0 5269.5111 14.510621
2350 16738.468 -0.0045563719 0 5269.5131 14.510714
2400 16738.46 -0.00052194273 0 5269.5146 14.510771
2450 16738.464 -0.0023259756 0 5269.514 14.510746
2500 16738.468 -0.0051929186 0 5269.5127 14.510731
2550 16738.581 -0.044940117 0 5269.5085 14.510315
2600 16738.427 -7.9722832e-05 0 5269.5046 14.510657
2650 16733.017 1.705148 0 5269.5067 14.596295
2700 16738.761 -0.10614946 0 5269.5038 14.499584
2750 16733.973 1.4038179 0 5269.5064 14.598107
2800 16738.585 -0.046813448 0 5269.5076 14.511073
2850 16738.487 -0.012558719 0 5269.5111 14.510111
2900 16738.465 -0.0026252725 0 5269.514 14.510277
2950 16738.476 -0.0082220764 0 5269.512 14.510223
3000 16738.66 -0.071284779 0 5269.507 14.509758
3050 16715.332 7.2419351 0 5269.476 14.870305
3100 16653.226 26.818761 0 5269.5009 14.496764
3150 16739.351 -0.30690375 0 5269.4886 13.643904
3200 16733.238 1.6025328 0 5269.4737 12.016934
3250 16734.374 1.2554429 0 5269.4841 11.963561
3300 16732.156 1.9585967 0 5269.4893 12.234024
3350 16738.655 -0.079693236 0 5269.497 12.092757
3400 16738.543 -0.042215005 0 5269.4991 12.092809
3450 16738.591 -0.059327511 0 5269.4972 12.092536
3500 16738.759 -0.11761245 0 5269.4918 12.09203
3550 16713.405 7.846062 0 5269.4737 12.389816
3600 16734.939 1.0821936 0 5269.4891 12.173591
3650 16738.808 -0.13663194 0 5269.4882 12.027009
3700 16738.602 -0.070934368 0 5269.4889 12.025288
3750 16737.731 0.20706557 0 5269.4927 12.061948
3800 16738.578 -0.05582043 0 5269.4965 12.035665
3850 16738.471 -0.016307928 0 5269.5024 12.035302
3900 16738.449 -0.0058182199 0 5269.5059 12.035401
3950 16738.439 -0.0012027325 0 5269.5074 12.035461
4000 16738.436 -0.00020698452 0 5269.5075 12.035469
4050 16738.437 0 0 5269.5078 12.035454
4100 16738.437 0 0 5269.508 12.035435
4150 16738.438 0 0 5269.5081 12.035426
4200 16738.438 0 0 5269.5083 12.035432
4250 16738.439 0 0 5269.5085 12.035447
4300 16738.439 0 0 5269.5086 12.035463
4350 16738.44 0 0 5269.5087 12.035474
4400 16738.44 0 0 5269.5088 12.035478
4450 16738.44 0 0 5269.5089 12.035474
4500 16738.44 0 0 5269.509 12.035462
4550 16738.441 0 0 5269.5092 12.035449
4600 16738.441 0 0 5269.5093 12.035445
4650 16738.442 0 0 5269.5095 12.035451
4700 16738.442 0 0 5269.5096 12.03546
4750 16738.443 0 0 5269.5097 12.035465
4800 16738.443 0 0 5269.5098 12.035466
4850 16738.443 0 0 5269.51 12.035463
4900 16738.444 0 0 5269.5101 12.035456
4950 16738.444 0 0 5269.5102 12.035447
5000 16738.445 0 0 5269.5104 12.03544
5050 16738.445 0 0 5269.5105 12.035442
5100 16738.446 0 0 5269.5107 12.035455
5150 16738.446 0 0 5269.5108 12.03547
5200 16738.446 0 0 5269.5109 12.035479
5250 16738.447 0 0 5269.511 12.035479
5300 16738.447 0 0 5269.5111 12.03547
5350 16738.447 0 0 5269.5112 12.035454
5400 16738.448 0 0 5269.5113 12.035434
5450 16738.448 0 0 5269.5115 12.03542
5500 16738.449 0 0 5269.5117 12.035422
5550 16738.457 -0.0030919234 0 5269.5111 12.035383
5600 16738.51 -0.021618357 0 5269.5092 12.035106
5650 16738.622 -0.059214788 0 5269.507 12.035694
5700 16395.28 108.06942 0 5269.5463 24.369038
5750 16738.544 -0.033973429 0 5269.5077 12.011261
5800 16738.456 -0.0037013529 0 5269.5102 12.011675
5850 16738.451 0 0 5269.5123 12.011709
5900 16738.451 -0.00022115871 0 5269.5122 12.011687
5950 16738.452 -0.00024253349 0 5269.5124 12.011678
6000 16738.452 0 0 5269.5128 12.011688
6050 16738.453 0 0 5269.513 12.011702
6100 16738.453 0 0 5269.5131 12.011716
6150 16738.454 0 0 5269.5132 12.011725
6200 16738.454 0 0 5269.5133 12.011728
6250 16738.454 0 0 5269.5134 12.011723
6300 16738.455 0 0 5269.5135 12.011712
6350 16738.455 0 0 5269.5137 12.0117
6400 16738.456 0 0 5269.5138 12.011697
6450 16738.456 0 0 5269.514 12.011704
6500 16738.456 0 0 5269.5141 12.011714
6550 16738.457 0 0 5269.5142 12.011719
6600 16738.457 0 0 5269.5143 12.011718
6650 16738.458 0 0 5269.5144 12.011713
6700 16738.458 0 0 5269.5146 12.011705
6750 16738.459 0 0 5269.5147 12.011696
6800 16738.459 0 0 5269.5149 12.01169
6850 16738.46 0 0 5269.515 12.011695
6900 16738.46 0 0 5269.5152 12.01171
6950 16738.46 0 0 5269.5153 12.011726
7000 16738.461 0 0 5269.5154 12.011736
7050 16738.461 0 0 5269.5155 12.011737
7100 16738.461 0 0 5269.5155 12.011728
7150 16738.461 0 0 5269.5156 12.011712
7200 16738.462 0 0 5269.5158 12.011691
7250 16738.463 0 0 5269.516 12.011676
7300 16738.463 0 0 5269.5162 12.011677
7350 16738.464 0 0 5269.5164 12.011693
7400 16738.464 0 0 5269.5165 12.011713
7450 16738.465 0 0 5269.5166 12.011729
7500 16738.465 0 0 5269.5167 12.011736
7550 16738.465 0 0 5269.5168 12.011734
7600 16738.465 0 0 5269.5168 12.011722
7650 16738.466 0 0 5269.517 12.011704
7700 16738.466 0 0 5269.5171 12.011687
7750 16738.467 0 0 5269.5173 12.011681
7800 16738.467 0 0 5269.5175 12.011687
7850 16738.468 0 0 5269.5176 12.0117
7900 16738.468 0 0 5269.5178 12.011712
7950 16738.469 0 0 5269.5179 12.011721
8000 16738.469 0 0 5269.518 12.011724
8050 16738.469 0 0 5269.5181 12.01172
8100 16738.47 0 0 5269.5182 12.011709
8150 16738.47 0 0 5269.5183 12.0117
8200 16738.47 0 0 5269.5185 12.0117
8250 16738.471 0 0 5269.5186 12.011709
8300 16738.471 0 0 5269.5187 12.011719
8350 16738.472 0 0 5269.5189 12.011723
8400 16738.472 0 0 5269.519 12.01172
8450 16738.473 -0.00039690663 0 5269.5189 12.011706
8500 16738.481 -0.0034646803 0 5269.5182 12.011643
8550 16738.483 -0.0045307409 0 5269.5178 12.011621
8600 16738.474 -0.00076532813 0 5269.5189 12.011681
8650 16738.474 0 0 5269.5197 12.011699
8700 16738.475 0 0 5269.5199 12.011715
8750 16738.475 0 0 5269.52 12.011732
8800 16738.475 0 0 5269.52 12.011743
8850 16738.476 0 0 5269.5201 12.011744
8900 16738.476 0 0 5269.5202 12.011735
8950 16738.476 0 0 5269.5203 12.011719
9000 16738.477 0 0 5269.5205 12.011698
9050 16738.477 0 0 5269.5206 12.011683
9100 16738.478 0 0 5269.5208 12.011684
9150 16738.479 0 0 5269.521 12.011701
9200 16738.479 0 0 5269.5212 12.011722
9250 16738.479 0 0 5269.5213 12.011738
9300 16738.48 0 0 5269.5214 12.011746
9350 16738.48 0 0 5269.5214 12.011744
9400 16738.48 0 0 5269.5215 12.011732
9450 16738.48 0 0 5269.5216 12.011715
9500 16738.481 -0.00037652438 0 5269.5216 12.011692
9550 16738.493 -0.0053156163 0 5269.5203 12.011611
9600 16738.549 -0.026814371 0 5269.5163 12.011415
9650 16738.765 -0.10191523 0 5269.5092 12.011013
9700 16735.041 1.0589894 0 5269.4979 12.062708
9750 16738.013 0.13550109 0 5269.5101 11.407246
9800 16738.512 -0.011620327 0 5269.5201 11.394974
9850 16738.489 -0.00067270507 0 5269.5237 11.395098
9900 16738.489 -0.00024984555 0 5269.5242 11.395085
9950 16738.49 0 0 5269.5245 11.395076
10000 16738.49 0 0 5269.5246 11.395075
Loop time of 0.198069 on 4 procs for 10000 steps with 81 atoms
Performance: 436211.675 tau/day, 50487.462 timesteps/s
91.1% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0026007 | 0.0034987 | 0.0043218 | 1.0 | 1.77
Neigh | 0.012213 | 0.013261 | 0.014237 | 0.8 | 6.70
Comm | 0.073581 | 0.082048 | 0.087982 | 2.1 | 41.42
Output | 0.0047908 | 0.0058783 | 0.009093 | 2.4 | 2.97
Modify | 0.081998 | 0.086993 | 0.09176 | 1.4 | 43.92
Other | | 0.00639 | | | 3.23
Nlocal: 20.25 ave 38 max 3 min
Histogram: 1 0 1 0 0 0 1 0 0 1
Nghost: 27.25 ave 48 max 13 min
Histogram: 1 0 1 1 0 0 0 0 0 1
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0
Neighbor list builds = 998
Dangerous builds = 997
Total wall time: 0:00:00

458
examples/rigid/log.27Nov18.rigid.tnr.g++.1 Normal file
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@ -0,0 +1,458 @@
LAMMPS (27 Nov 2018)
using 1 OpenMP thread(s) per MPI task
# Tethered nanorods
atom_style molecular
read_data data.rigid.tnr
orthogonal box = (-31.122 -31.122 -31.122) to (31.122 31.122 31.122)
1 by 1 by 1 MPI processor grid
reading atoms ...
5600 atoms
scanning bonds ...
1 = max bonds/atom
reading bonds ...
1600 bonds
2 = max # of 1-2 neighbors
1 = max # of 1-3 neighbors
1 = max # of 1-4 neighbors
2 = max # of special neighbors
# Specify bond parameters
bond_style fene
bond_coeff 1 30.0 1.5 1.0 1.0
special_bonds fene
2 = max # of 1-2 neighbors
2 = max # of special neighbors
# Specify initial velocities
velocity all create 1.4 109345
# Specify rigid components
group rods type 2
4000 atoms in group rods
group tethers subtract all rods
1600 atoms in group tethers
neigh_modify exclude molecule/intra rods delay 0 every 1
# Specify the pair potentials
pair_style lj/cut 2.5
pair_modify shift yes
pair_coeff * * 1.0 1.0 1.122
pair_coeff 2 2 1.0 1.0 2.5
# Specify output
thermo 100
thermo_style custom step temp pe etotal press enthalpy lx ly lz pxx pyy pzz
thermo_modify flush yes lost warn
timestep 0.005
fix 1 rods rigid molecule
800 rigid bodies with 4000 atoms
fix 2 tethers nve
fix 3 all langevin 1.4 1.4 1.0 437624
run 5000
Neighbor list info ...
update every 1 steps, delay 0 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 = 45 45 45
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 7.769 | 7.769 | 7.769 Mbytes
Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
0 1.3963219 5.9478449 7.0445809 0.048565317 9.13595 62.244 62.244 62.244 0.0091983659 0.11850113 0.017996458
100 1.3418512 5.9671777 7.0211299 0.025020362 8.0985822 62.244 62.244 62.244 0.02036076 0.038265078 0.016435248
200 1.3730638 5.9750802 7.0535483 0.0053287535 7.2830205 62.244 62.244 62.244 -0.00054924195 0.0092396988 0.0072958036
300 1.376262 5.9821642 7.0631443 0.0055536521 7.3023013 62.244 62.244 62.244 0.0033577704 0.0069111861 0.0063919998
400 1.3782954 5.9983628 7.08094 0.0020507385 7.169251 62.244 62.244 62.244 -0.0060862717 0.0098998072 0.0023386801
500 1.386863 6.0053312 7.0946377 -0.0009847031 7.0522334 62.244 62.244 62.244 -0.0038708372 0.0005697804 0.00034694745
600 1.4069849 6.0035719 7.1086832 0.0047883912 7.3148858 62.244 62.244 62.244 0.001069365 0.0078059505 0.0054898581
700 1.4423187 5.9982171 7.1310812 0.012141001 7.6539093 62.244 62.244 62.244 0.0094765272 0.011007593 0.015938883
800 1.4303878 5.9968168 7.1203098 -0.00081349095 7.0852784 62.244 62.244 62.244 0.0011153812 0.00041597298 -0.0039718271
900 1.4140538 5.9838168 7.0944803 0.00207609 7.183883 62.244 62.244 62.244 0.00043409671 0.0022778944 0.0035162788
1000 1.3906567 5.988119 7.0804053 0.0022005856 7.1751692 62.244 62.244 62.244 0.0077268425 -0.0022042977 0.0010792119
1100 1.3921992 5.9892203 7.0827181 0.0035041977 7.2336194 62.244 62.244 62.244 -0.0037576823 0.0040827951 0.01018748
1200 1.3968803 5.9795846 7.0767592 -0.0031072146 6.9429532 62.244 62.244 62.244 -0.0077387449 0.0033056124 -0.0048885115
1300 1.3755848 5.9739757 7.0544239 0.0092247106 7.4516677 62.244 62.244 62.244 0.0092788748 0.010737194 0.0076580625
1400 1.3847985 5.9703631 7.0580481 0.0071703598 7.3668254 62.244 62.244 62.244 0.0080485848 0.012260474 0.001202021
1500 1.4190051 5.956946 7.0714985 0.0035992903 7.2264948 62.244 62.244 62.244 -0.0055125437 0.01038369 0.0059267242
1600 1.3980036 5.9671666 7.0652236 0.0061819851 7.3314385 62.244 62.244 62.244 0.0062429141 0.0035120077 0.0087910334
1700 1.4276062 5.9610381 7.0823462 0.007832375 7.4196319 62.244 62.244 62.244 0.0083316819 0.0058394292 0.009326014
1800 1.4112769 5.9630595 7.0715419 0.0068032101 7.3645087 62.244 62.244 62.244 0.0065502252 0.0062317255 0.0076276797
1900 1.4276973 5.9489341 7.0703139 0.008397746 7.4319462 62.244 62.244 62.244 0.0148941 0.0032963108 0.0070028268
2000 1.4056158 5.9564624 7.0604983 0.0090470732 7.4500926 62.244 62.244 62.244 0.011871718 0.0086681344 0.0066013673
2100 1.3924778 5.9483611 7.0420778 0.0088893819 7.4248814 62.244 62.244 62.244 0.010247454 0.0097830093 0.0066376825
2200 1.3760401 5.9435877 7.0243935 -0.0042972782 6.8393397 62.244 62.244 62.244 -0.0050064436 -0.0046216999 -0.0032636911
2300 1.4191937 5.9334036 7.0481042 0.0047000032 7.2505006 62.244 62.244 62.244 0.0057709635 0.0044949165 0.0038341296
2400 1.4213285 5.9472214 7.0635988 0.010197674 7.5027414 62.244 62.244 62.244 0.008373826 0.0090537939 0.013165402
2500 1.4153808 5.9421661 7.0538718 0.00015906306 7.0607216 62.244 62.244 62.244 0.002351621 -0.0019814986 0.00010706677
2600 1.4014223 5.9431386 7.0438807 0.0070733749 7.3484816 62.244 62.244 62.244 0.0054143871 0.010055843 0.0057498948
2700 1.4138077 5.9369067 7.047377 0.0024268842 7.1518859 62.244 62.244 62.244 0.0052918436 0.0014960353 0.00049277371
2800 1.432192 5.9347676 7.0596777 0.0077670448 7.3941501 62.244 62.244 62.244 0.012668421 0.0059113033 0.0047214106
2900 1.3938659 5.921023 7.01583 0.0053751198 7.2472989 62.244 62.244 62.244 0.0020490372 0.0076566093 0.006419713
3000 1.390221 5.9205014 7.0124455 -0.0010750977 6.9661485 62.244 62.244 62.244 0.0019519817 -0.0041878885 -0.00098938611
3100 1.4205722 5.9178284 7.0336117 0.0098735475 7.4587965 62.244 62.244 62.244 0.0040973361 0.012167268 0.013356039
3200 1.398418 5.9150349 7.0134173 0.0061541841 7.2784351 62.244 62.244 62.244 0.0067621815 0.011952563 -0.00025219251
3300 1.4269859 5.9148727 7.0356937 0.0060623879 7.2967584 62.244 62.244 62.244 0.012956234 -2.4806661e-05 0.0052557362
3400 1.434286 5.9356705 7.0622253 0.00027315892 7.0739884 62.244 62.244 62.244 -0.00054959866 0.0052526278 -0.0038835524
3500 1.4416809 5.9228153 7.0551783 0.0083382977 7.4142506 62.244 62.244 62.244 0.007399393 0.0030328007 0.014582699
3600 1.4136063 5.9039442 7.0142562 0.0019712004 7.0991421 62.244 62.244 62.244 -0.00032316149 0.0035029874 0.0027337752
3700 1.4333819 5.9120101 7.0378548 0.0071287182 7.3448389 62.244 62.244 62.244 0.0064768218 0.0046765361 0.010232797
3800 1.3659481 5.9032873 6.9761663 -0.0054033416 6.7434821 62.244 62.244 62.244 -0.0073943479 -0.0082831992 -0.00053247772
3900 1.3963222 5.9042998 7.0010361 0.0053310264 7.2306062 62.244 62.244 62.244 0.0081855739 0.0048806019 0.0029269034
4000 1.4125482 5.9060665 7.0155474 0.0028450296 7.138063 62.244 62.244 62.244 0.0052588294 0.00072395285 0.0025523065
4100 1.3943951 5.9040875 6.9993102 0.0058050223 7.2492919 62.244 62.244 62.244 0.0060579697 0.0024782584 0.0088788387
4200 1.4249768 5.8906371 7.0098801 0.0030210669 7.1399763 62.244 62.244 62.244 0.006174431 -0.002079586 0.0049683557
4300 1.3899801 5.8966397 6.9883947 0.0057285402 7.2350829 62.244 62.244 62.244 0.0049048136 0.0021882328 0.010092574
4400 1.4414352 5.898628 7.0307981 0.0050932552 7.2501291 62.244 62.244 62.244 0.0057941393 0.0037951842 0.0056904421
4500 1.4092913 5.8922803 6.9992031 0.0012238869 7.0519073 62.244 62.244 62.244 0.0042907674 0.0014412643 -0.0020603711
4600 1.3779868 5.8928757 6.9752105 0.0020701322 7.0643566 62.244 62.244 62.244 0.0029283254 -0.0031683908 0.006450462
4700 1.4084635 5.9098782 7.0161508 -0.00052129502 6.9937023 62.244 62.244 62.244 -0.0018460523 -0.0018286314 0.0021107986
4800 1.4393258 5.9148464 7.0453597 0.015311954 7.7047386 62.244 62.244 62.244 0.014718813 0.01801777 0.013199278
4900 1.4500008 5.9076899 7.0465879 0.0075111779 7.3700419 62.244 62.244 62.244 0.0091865271 0.0080981174 0.0052488891
5000 1.4279632 5.9111567 7.0327453 -0.0014189553 6.9716408 62.244 62.244 62.244 -0.0046013754 0.0019937576 -0.001649248
Loop time of 6.84203 on 1 procs for 5000 steps with 5600 atoms
Performance: 315695.745 tau/day, 730.777 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 | 0.53182 | 0.53182 | 0.53182 | 0.0 | 7.77
Bond | 0.18231 | 0.18231 | 0.18231 | 0.0 | 2.66
Neigh | 1.8709 | 1.8709 | 1.8709 | 0.0 | 27.34
Comm | 0.18452 | 0.18452 | 0.18452 | 0.0 | 2.70
Output | 0.0043087 | 0.0043087 | 0.0043087 | 0.0 | 0.06
Modify | 3.8809 | 3.8809 | 3.8809 | 0.0 | 56.72
Other | | 0.1873 | | | 2.74
Nlocal: 5600 ave 5600 max 5600 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1351 ave 1351 max 1351 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 5254 ave 5254 max 5254 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 5254
Ave neighs/atom = 0.938214
Ave special neighs/atom = 0.571429
Neighbor list builds = 766
Dangerous builds = 0
# Replace fix rigid and fix langevin with new ones
unfix 1
unfix 3
fix 3 tethers langevin 1.4 1.4 1.0 198450
# Test different integrators for rods
fix 1 rods rigid/nve molecule
800 rigid bodies with 4000 atoms
print "rigid/nve"
rigid/nve
run 1000
Per MPI rank memory allocation (min/avg/max) = 7.77 | 7.77 | 7.77 Mbytes
Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
5000 1.4279632 5.9111567 7.0327453 0.027874409 8.2331015 62.244 62.244 62.244 0.018992956 0.039655696 0.024974575
5100 1.439608 5.9052128 7.0359478 0.0060989863 7.2985885 62.244 62.244 62.244 0.0087364157 0.004022839 0.0055377041
5200 1.4120672 5.9102569 7.01936 0.0064301432 7.2962614 62.244 62.244 62.244 0.0082738077 0.0038925667 0.0071240551
5300 1.4452434 5.8842166 7.0193778 0.008172419 7.3713068 62.244 62.244 62.244 0.0077715647 0.0068924406 0.0098532518
5400 1.4170243 5.887522 7.0005186 0.0008656658 7.0377968 62.244 62.244 62.244 -9.1800583e-05 -0.0020237513 0.0047125493
5500 1.4209082 5.8758921 6.9919394 0.0093634084 7.395156 62.244 62.244 62.244 0.0088769348 0.0087092521 0.010504038
5600 1.4132978 5.8798939 6.9899636 0.0014877766 7.0540317 62.244 62.244 62.244 -0.0023427923 0.004559371 0.002246751
5700 1.4065053 5.887541 6.9922756 0.0028083452 7.1132114 62.244 62.244 62.244 0.0025188632 0.000510969 0.0053952035
5800 1.4079051 5.8940739 6.999908 0.0015946158 7.0685769 62.244 62.244 62.244 0.0037830287 0.00021751956 0.00078329927
5900 1.4076047 5.8941577 6.9997558 0.005189853 7.2232465 62.244 62.244 62.244 -0.00093244616 0.0096403542 0.0068616509
6000 1.4322772 5.8903539 7.0153309 0.00029752476 7.0281432 62.244 62.244 62.244 0.001913333 -0.00073790796 -0.00028285075
Loop time of 1.40593 on 1 procs for 1000 steps with 5600 atoms
Performance: 307270.224 tau/day, 711.274 timesteps/s
99.1% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.14844 | 0.14844 | 0.14844 | 0.0 | 10.56
Bond | 0.036852 | 0.036852 | 0.036852 | 0.0 | 2.62
Neigh | 0.40537 | 0.40537 | 0.40537 | 0.0 | 28.83
Comm | 0.036592 | 0.036592 | 0.036592 | 0.0 | 2.60
Output | 0.00085831 | 0.00085831 | 0.00085831 | 0.0 | 0.06
Modify | 0.74053 | 0.74053 | 0.74053 | 0.0 | 52.67
Other | | 0.03729 | | | 2.65
Nlocal: 5600 ave 5600 max 5600 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1347 ave 1347 max 1347 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 5399 ave 5399 max 5399 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 5399
Ave neighs/atom = 0.964107
Ave special neighs/atom = 0.571429
Neighbor list builds = 153
Dangerous builds = 0
unfix 1
fix 1 rods rigid/nvt molecule temp 1.4 1.4 1.0
800 rigid bodies with 4000 atoms
print "rigid/nvt"
rigid/nvt
run 1000
Per MPI rank memory allocation (min/avg/max) = 7.77 | 7.77 | 7.77 Mbytes
Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
6000 1.4322772 5.8903539 7.0153309 0.012980585 7.574314 62.244 62.244 62.244 0.058317363 0.0073619377 -0.026737547
6100 1.4199699 5.8764035 6.9917138 0.0054065561 7.2245364 62.244 62.244 62.244 0.009227645 0.0019623802 0.0050296432
6200 1.3976825 5.8924426 6.9902474 0.00043900876 7.0091524 62.244 62.244 62.244 -0.0023073124 -0.00049925318 0.0041235918
6300 1.4077283 5.8847362 6.9904313 0.0066398301 7.2763625 62.244 62.244 62.244 0.0058018934 0.0091933877 0.0049242093
6400 1.3749203 5.8817073 6.9616336 0.0074967162 7.2844648 62.244 62.244 62.244 0.012281887 0.0039781589 0.0062301027
6500 1.3467096 5.8881264 6.9458946 -0.00011926349 6.9407588 62.244 62.244 62.244 0.0030721967 -0.0013265863 -0.0021034009
6600 1.3646558 5.8739857 6.9458497 0.0056064043 7.1872784 62.244 62.244 62.244 0.0059660337 0.0057680048 0.0050851745
6700 1.3927251 5.883612 6.9775229 0.0025583824 7.0876946 62.244 62.244 62.244 0.0030974706 0.0018499606 0.002727716
6800 1.4016999 5.9015886 7.0025488 0.0039070678 7.1707989 62.244 62.244 62.244 0.0068320586 0.0020056859 0.002883459
6900 1.4136745 5.8914714 7.001837 0.0051755091 7.22471 62.244 62.244 62.244 0.0028467792 0.0094052519 0.0032744962
7000 1.4286639 5.893567 7.0157059 0.0062957476 7.2868198 62.244 62.244 62.244 0.0047242086 0.0093408867 0.0048221474
Loop time of 1.41045 on 1 procs for 1000 steps with 5600 atoms
Performance: 306284.404 tau/day, 708.992 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 | 0.1497 | 0.1497 | 0.1497 | 0.0 | 10.61
Bond | 0.036719 | 0.036719 | 0.036719 | 0.0 | 2.60
Neigh | 0.40272 | 0.40272 | 0.40272 | 0.0 | 28.55
Comm | 0.036315 | 0.036315 | 0.036315 | 0.0 | 2.57
Output | 0.00085187 | 0.00085187 | 0.00085187 | 0.0 | 0.06
Modify | 0.747 | 0.747 | 0.747 | 0.0 | 52.96
Other | | 0.03715 | | | 2.63
Nlocal: 5600 ave 5600 max 5600 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1284 ave 1284 max 1284 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 5677 ave 5677 max 5677 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 5677
Ave neighs/atom = 1.01375
Ave special neighs/atom = 0.571429
Neighbor list builds = 151
Dangerous builds = 0
unfix 1
compute myTemp all temp
fix 1 rods rigid/npt molecule temp 1.4 1.4 1.0 iso 0.05 0.05 1.0 dilate all
800 rigid bodies with 4000 atoms
print "rigid/npt iso"
rigid/npt iso
fix_modify 1 temp myTemp
run 1000
Per MPI rank memory allocation (min/avg/max) = 7.77 | 7.77 | 7.77 Mbytes
Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
7000 1.4286639 5.893567 7.0157059 0.032101512 8.3980939 62.244 62.244 62.244 0.0040045405 0.040447803 0.051852194
7100 1.4709161 5.8870949 7.0424207 0.019697134 7.6953761 57.045689 57.045689 57.045689 0.012929484 0.020492532 0.025669387
7200 1.5163078 5.8421187 7.0330973 0.018916867 7.46241 50.277171 50.277171 50.277171 0.017823354 0.026688031 0.012239218
7300 1.5675309 5.7752739 7.0064855 0.022899743 7.3829781 45.154874 45.154874 45.154874 0.019324617 0.024318577 0.025056034
7400 1.5432228 5.7513096 6.9634284 0.024381819 7.272744 41.416613 41.416613 41.416613 0.032026791 0.022254425 0.018864241
7500 1.5511419 5.7072564 6.9255953 0.030632381 7.2405167 38.613262 38.613262 38.613262 0.041572196 0.012539031 0.037785916
7600 1.5437461 5.6656571 6.8781869 0.031293788 7.1486082 36.440994 36.440994 36.440994 0.036220762 0.02125772 0.036402883
7700 1.5873874 5.6134986 6.8603063 0.04807003 7.221002 34.765744 34.765744 34.765744 0.031608235 0.053442472 0.059159381
7800 1.5079648 5.601961 6.7863866 0.031128515 6.9971673 33.59594 33.59594 33.59594 0.032932226 0.015950578 0.044502741
7900 1.4737447 5.5644198 6.7219673 0.099246661 7.3415696 32.698542 32.698542 32.698542 0.071386679 0.10758014 0.11877317
8000 1.4727947 5.5161158 6.6729171 0.072190554 7.0973199 32.050043 32.050043 32.050043 0.072806068 0.06277287 0.080992723
Loop time of 3.15299 on 1 procs for 1000 steps with 5600 atoms
Performance: 137012.841 tau/day, 317.159 timesteps/s
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.37069 | 0.37069 | 0.37069 | 0.0 | 11.76
Bond | 0.05046 | 0.05046 | 0.05046 | 0.0 | 1.60
Neigh | 1.4844 | 1.4844 | 1.4844 | 0.0 | 47.08
Comm | 0.081178 | 0.081178 | 0.081178 | 0.0 | 2.57
Output | 0.00083494 | 0.00083494 | 0.00083494 | 0.0 | 0.03
Modify | 1.1163 | 1.1163 | 1.1163 | 0.0 | 35.41
Other | | 0.0491 | | | 1.56
Nlocal: 5600 ave 5600 max 5600 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 2954 ave 2954 max 2954 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 25585 ave 25585 max 25585 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 25585
Ave neighs/atom = 4.56875
Ave special neighs/atom = 0.571429
Neighbor list builds = 334
Dangerous builds = 0
unfix 1
fix 1 rods rigid/npt molecule temp 1.4 1.4 1.0 x 0.05 0.05 1.0 dilate all
800 rigid bodies with 4000 atoms
print "rigid/npt x"
rigid/npt x
run 1000
Per MPI rank memory allocation (min/avg/max) = 7.785 | 7.785 | 7.785 Mbytes
Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
8000 1.4727947 5.5161158 6.6729171 0.13628586 7.4741313 32.050043 32.050043 32.050043 -0.030897367 0.27196335 0.1677916
8100 1.4522497 5.5136331 6.6542974 0.057107124 6.9895036 32.000184 32.050043 32.050043 0.049932793 0.056130194 0.065258384
8200 1.4407937 5.5014539 6.6331202 0.024119241 6.7733276 31.691157 32.050043 32.050043 0.041526366 0.022503949 0.0083274089
8300 1.4542258 5.496977 6.6391934 0.043395674 6.887667 31.215092 32.050043 32.050043 0.025407647 0.075227689 0.029551686
8400 1.4375595 5.4901345 6.6192605 0.013578023 6.6952098 30.494249 32.050043 32.050043 -0.0045150608 0.033500673 0.011748456
8500 1.4410736 5.4540565 6.5859426 0.017121222 6.679397 29.757445 32.050043 32.050043 0.035675932 -0.032105 0.047792733
8600 1.4372413 5.4150437 6.5439197 0.084045699 6.9949237 29.254706 32.050043 32.050043 0.10347392 0.073148157 0.075515024
8700 1.4299119 5.3982284 6.5213476 0.00045273296 6.5237411 28.822481 32.050043 32.050043 0.0093093459 0.0081538479 -0.016104995
8800 1.4677947 5.3637715 6.5166456 0.028621833 6.6651924 28.294159 32.050043 32.050043 0.033527613 0.036046563 0.016291323
8900 1.4625499 5.3483914 6.4971459 0.032843022 6.6649394 27.852402 32.050043 32.050043 0.040751528 0.055865445 0.0019120942
9000 1.4488382 5.3486741 6.4866589 0.087522574 6.9279711 27.488856 32.050043 32.050043 0.059432129 0.10936517 0.093770421
Loop time of 3.09429 on 1 procs for 1000 steps with 5600 atoms
Performance: 139611.779 tau/day, 323.175 timesteps/s
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.57714 | 0.57714 | 0.57714 | 0.0 | 18.65
Bond | 0.051715 | 0.051715 | 0.051715 | 0.0 | 1.67
Neigh | 1.223 | 1.223 | 1.223 | 0.0 | 39.52
Comm | 0.066183 | 0.066183 | 0.066183 | 0.0 | 2.14
Output | 0.00086594 | 0.00086594 | 0.00086594 | 0.0 | 0.03
Modify | 1.1355 | 1.1355 | 1.1355 | 0.0 | 36.70
Other | | 0.03994 | | | 1.29
Nlocal: 5600 ave 5600 max 5600 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 3381 ave 3381 max 3381 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 31737 ave 31737 max 31737 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 31737
Ave neighs/atom = 5.66732
Ave special neighs/atom = 0.571429
Neighbor list builds = 169
Dangerous builds = 0
unfix 1
fix 1 rods rigid/nph molecule iso 0.05 0.05 1.0 dilate all
800 rigid bodies with 4000 atoms
print "rigid/nph iso"
rigid/nph iso
run 1000
Per MPI rank memory allocation (min/avg/max) = 7.788 | 7.788 | 7.788 Mbytes
Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
9000 1.4488382 5.3486741 6.4866589 0.20124138 7.5013717 27.488856 32.050043 32.050043 0.22160189 0.42145658 -0.039334342
9100 1.4408457 5.3612674 6.4929746 0.076331412 6.8758499 27.440968 31.994208 31.994208 0.083838068 0.041724506 0.10343166
9200 1.4870445 5.3340546 6.5020483 0.01010773 6.5521592 27.334266 31.869802 31.869802 0.024563803 -0.0068003493 0.012559737
9300 1.4376808 5.3295183 6.4587396 0.10720051 6.9752889 27.076116 31.568817 31.568817 0.11844426 0.10444301 0.09871425
9400 1.4621325 5.3011274 6.4495541 0.071127232 6.7846388 26.873295 31.332342 31.332342 0.091608834 0.02680694 0.094965923
9500 1.4463444 5.3005044 6.4365304 0.0011545049 6.4418432 26.664 31.088319 31.088319 -0.030551889 0.036011952 -0.0019965484
9600 1.4473406 5.2912939 6.4281024 0.066132857 6.7281169 26.537276 30.940568 30.940568 0.12276096 0.013455525 0.06218208
9700 1.4520445 5.2707214 6.4112246 0.077219765 6.757956 26.446587 30.834832 30.834832 0.073829267 0.11047347 0.047356559
9800 1.4825713 5.246644 6.4111243 0.061402527 6.6831281 26.327581 30.696078 30.696078 0.091860222 0.022619578 0.06972778
9900 1.4795219 5.2344495 6.3965347 0.086345107 6.7729623 26.187615 30.532888 30.532888 0.077396265 0.11142542 0.07021363
10000 1.4527053 5.2126819 6.3537041 0.045117764 6.5474705 26.057038 30.380645 30.380645 0.011087188 0.058029185 0.066236921
Loop time of 3.25046 on 1 procs for 1000 steps with 5600 atoms
Performance: 132904.162 tau/day, 307.649 timesteps/s
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.68223 | 0.68223 | 0.68223 | 0.0 | 20.99
Bond | 0.05211 | 0.05211 | 0.05211 | 0.0 | 1.60
Neigh | 1.2617 | 1.2617 | 1.2617 | 0.0 | 38.82
Comm | 0.069407 | 0.069407 | 0.069407 | 0.0 | 2.14
Output | 0.00085688 | 0.00085688 | 0.00085688 | 0.0 | 0.03
Modify | 1.1438 | 1.1438 | 1.1438 | 0.0 | 35.19
Other | | 0.04037 | | | 1.24
Nlocal: 5600 ave 5600 max 5600 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 3756 ave 3756 max 3756 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 37360 ave 37360 max 37360 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 37360
Ave neighs/atom = 6.67143
Ave special neighs/atom = 0.571429
Neighbor list builds = 158
Dangerous builds = 0
unfix 1
fix 1 rods rigid/nph molecule x 0.05 0.05 1.0 y 0.05 0.05 1.0 couple xy dilate all
800 rigid bodies with 4000 atoms
print "rigid/nph xy couple"
rigid/nph xy couple
run 1000
Per MPI rank memory allocation (min/avg/max) = 7.795 | 7.795 | 7.795 Mbytes
Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
10000 1.4527053 5.2126819 6.3537041 0.056937886 6.5982342 26.057038 30.380645 30.380645 -0.37001102 0.18554825 0.35527643
10100 1.4606958 5.2220088 6.3693071 0.10308269 6.8132489 26.093341 30.422971 30.380645 0.12567436 0.057087258 0.12648646
10200 1.4429187 5.2134399 6.3467753 0.022637194 6.4450326 26.195743 30.542365 30.380645 0.010739012 0.071921542 -0.014748971
10300 1.4559104 5.2293511 6.3728908 0.0079467818 6.4073504 26.182966 30.527467 30.380645 -0.014274944 0.032205181 0.0059101087
10400 1.4741126 5.2072221 6.3650586 0.095611559 6.7814715 26.240156 30.594148 30.380645 0.073579289 0.092441893 0.12081349
10500 1.4411698 5.2173262 6.3492878 0.010458046 6.3947259 26.208633 30.557393 30.380645 0.036794882 -0.0051462954 -0.00027444949
10600 1.4492728 5.1940541 6.3323802 0.042602534 6.5163992 26.132032 30.468083 30.380645 0.090116773 0.0022769844 0.035413845
10700 1.4599974 5.1895935 6.3363432 0.05533717 6.573197 26.013045 30.329352 30.380645 0.070180878 0.08084881 0.014981824
10800 1.4781084 5.1724704 6.3334454 0.031843587 6.4690539 25.947295 30.252692 30.380645 0.0041524129 0.077618702 0.013759645
10900 1.4410507 5.1708846 6.3027527 0.020221033 6.3881531 25.839719 30.127267 30.380645 -0.0014092876 0.014833141 0.047239245
11000 1.4150286 5.1756927 6.2871219 0.039768792 6.45242 25.63435 29.887821 30.380645 0.034930907 0.032278926 0.052096542
Loop time of 3.43774 on 1 procs for 1000 steps with 5600 atoms
Performance: 125663.855 tau/day, 290.889 timesteps/s
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.75066 | 0.75066 | 0.75066 | 0.0 | 21.84
Bond | 0.053177 | 0.053177 | 0.053177 | 0.0 | 1.55
Neigh | 1.3577 | 1.3577 | 1.3577 | 0.0 | 39.49
Comm | 0.07294 | 0.07294 | 0.07294 | 0.0 | 2.12
Output | 0.00086403 | 0.00086403 | 0.00086403 | 0.0 | 0.03
Modify | 1.1612 | 1.1612 | 1.1612 | 0.0 | 33.78
Other | | 0.0412 | | | 1.20
Nlocal: 5600 ave 5600 max 5600 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 3904 ave 3904 max 3904 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 39666 ave 39666 max 39666 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 39666
Ave neighs/atom = 7.08321
Ave special neighs/atom = 0.571429
Neighbor list builds = 159
Dangerous builds = 0
Total wall time: 0:00:22

458
examples/rigid/log.27Nov18.rigid.tnr.g++.4 Normal file
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LAMMPS (27 Nov 2018)
using 1 OpenMP thread(s) per MPI task
# Tethered nanorods
atom_style molecular
read_data data.rigid.tnr
orthogonal box = (-31.122 -31.122 -31.122) to (31.122 31.122 31.122)
1 by 2 by 2 MPI processor grid
reading atoms ...
5600 atoms
scanning bonds ...
1 = max bonds/atom
reading bonds ...
1600 bonds
2 = max # of 1-2 neighbors
1 = max # of 1-3 neighbors
1 = max # of 1-4 neighbors
2 = max # of special neighbors
# Specify bond parameters
bond_style fene
bond_coeff 1 30.0 1.5 1.0 1.0
special_bonds fene
2 = max # of 1-2 neighbors
2 = max # of special neighbors
# Specify initial velocities
velocity all create 1.4 109345
# Specify rigid components
group rods type 2
4000 atoms in group rods
group tethers subtract all rods
1600 atoms in group tethers
neigh_modify exclude molecule/intra rods delay 0 every 1
# Specify the pair potentials
pair_style lj/cut 2.5
pair_modify shift yes
pair_coeff * * 1.0 1.0 1.122
pair_coeff 2 2 1.0 1.0 2.5
# Specify output
thermo 100
thermo_style custom step temp pe etotal press enthalpy lx ly lz pxx pyy pzz
thermo_modify flush yes lost warn
timestep 0.005
fix 1 rods rigid molecule
800 rigid bodies with 4000 atoms
fix 2 tethers nve
fix 3 all langevin 1.4 1.4 1.0 437624
run 5000
Neighbor list info ...
update every 1 steps, delay 0 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 = 45 45 45
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 7.216 | 7.384 | 7.552 Mbytes
Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
0 1.3963219 5.9478449 7.0445809 0.048565317 9.13595 62.244 62.244 62.244 0.0091983659 0.11850113 0.017996458
100 1.3999025 5.9707695 7.0703179 0.027293074 8.24564 62.244 62.244 62.244 0.017246307 0.04732529 0.017307624
200 1.4245544 5.9878446 7.1067558 0.0072016369 7.41688 62.244 62.244 62.244 0.0071370801 0.0084066589 0.0060611719
300 1.4212057 5.9942604 7.1105414 0.0023296933 7.210865 62.244 62.244 62.244 -0.0059197015 0.0040269953 0.008881786
400 1.4030116 5.9953214 7.0973119 0.0055751834 7.3373961 62.244 62.244 62.244 -0.0026920847 0.013323321 0.0060943141
500 1.4201338 5.9984777 7.1139168 -0.0018229523 7.035415 62.244 62.244 62.244 -0.0082217102 -0.00047319975 0.0032260529
600 1.425173 5.9902537 7.1096508 0.013367744 7.6853062 62.244 62.244 62.244 0.012971415 0.016298595 0.010833222
700 1.4181225 5.9840752 7.0979345 0.0014999758 7.1625279 62.244 62.244 62.244 -0.0015835387 0.0045967753 0.0014866907
800 1.4084205 5.9778462 7.084085 0.0063728488 7.3585191 62.244 62.244 62.244 0.0036202744 0.005593586 0.0099046859
900 1.3958301 5.9891019 7.0854517 0.0028974454 7.2102244 62.244 62.244 62.244 0.0087724642 0.0014508428 -0.001530971
1000 1.3937374 5.9794855 7.0741916 0.0087158481 7.4495223 62.244 62.244 62.244 0.014424783 0.0034958881 0.0082268735
1100 1.3729162 5.9916252 7.0699773 0.0030451966 7.2011127 62.244 62.244 62.244 0.00084635444 -0.00064448421 0.0089337195
1200 1.4427374 5.9713589 7.1045519 0.0042680608 7.2883474 62.244 62.244 62.244 0.0030884628 0.0031576538 0.0065580658
1300 1.3971469 5.9728674 7.0702514 0.0022809251 7.168475 62.244 62.244 62.244 0.00060902513 -0.00020572386 0.006439474
1400 1.4194118 5.9672631 7.082135 0.012945844 7.6396221 62.244 62.244 62.244 0.0082418827 0.016256336 0.014339314
1500 1.3866472 5.9728382 7.0619753 0.0010642438 7.1078049 62.244 62.244 62.244 0.0020316123 0.0020439035 -0.00088278432
1600 1.4184955 5.9539591 7.0681113 0.0077605409 7.4023036 62.244 62.244 62.244 0.0033721722 0.0057827512 0.014126699
1700 1.3612202 5.9676733 7.0368389 0.00016862131 7.0441002 62.244 62.244 62.244 0.0052525345 0.0007705269 -0.0055171975
1800 1.3641041 5.9521837 7.0236144 0.0057884587 7.2728829 62.244 62.244 62.244 0.0038061044 0.0044032908 0.009155981
1900 1.3594477 5.9646024 7.0323757 0.0044261926 7.2229809 62.244 62.244 62.244 0.0019417448 0.006871542 0.004465291
2000 1.3776971 5.9431816 7.0252888 -0.0012460593 6.9716298 62.244 62.244 62.244 -0.0010913822 0.00098119436 -0.0036279901
2100 1.3986245 5.9509735 7.0495181 0.007520633 7.3733792 62.244 62.244 62.244 0.008359824 0.0075919773 0.0066100978
2200 1.4033594 5.9548158 7.0570794 0.0016804284 7.1294438 62.244 62.244 62.244 -0.001842641 0.0032876741 0.0035962521
2300 1.4048926 5.9444129 7.0478808 0.0062444034 7.3167836 62.244 62.244 62.244 0.004383569 0.0065720464 0.007777595
2400 1.4044043 5.9370822 7.0401666 0.0034562836 7.1890046 62.244 62.244 62.244 0.0068959298 0.0041111713 -0.00063825026
2500 1.4200762 5.9359254 7.0513193 0.0028319649 7.1732722 62.244 62.244 62.244 -0.00030414203 0.0039571831 0.0048428538
2600 1.3876469 5.9249124 7.0148347 -0.0017777224 6.9382806 62.244 62.244 62.244 -0.00047616392 -0.0025484917 -0.0023085116
2700 1.4099941 5.916763 7.0242378 0.0070716263 7.3287634 62.244 62.244 62.244 0.012628756 0.0053812867 0.0032048359
2800 1.4444643 5.9283432 7.0628925 0.0019400024 7.1464349 62.244 62.244 62.244 0.0014895079 0.0046367397 -0.00030624055
2900 1.3902832 5.9152516 7.0072446 -0.002166221 6.9139606 62.244 62.244 62.244 -0.0012374412 -0.00056403267 -0.004697189
3000 1.3711706 5.922146 6.9991271 0.011101505 7.4771914 62.244 62.244 62.244 0.011063833 0.012093026 0.010147657
3100 1.3569137 5.9171753 6.9829583 -0.002826677 6.8612331 62.244 62.244 62.244 -0.0069507252 0.0010084399 -0.0025377458
3200 1.4004275 5.905939 7.0058998 0.005439467 7.2401397 62.244 62.244 62.244 0.010352184 0.0057594148 0.00020680265
3300 1.3641217 5.9145275 6.985972 -0.0027212811 6.8687855 62.244 62.244 62.244 -0.00065933677 -0.0057713008 -0.0017332057
3400 1.3868722 5.9059546 6.9952684 0.0092591256 7.3939943 62.244 62.244 62.244 0.010690877 0.010752519 0.006333981
3500 1.3939169 5.8992292 6.9940762 0.0074340028 7.3142068 62.244 62.244 62.244 0.010137307 0.0044252569 0.0077394447
3600 1.3982507 5.9219461 7.0201971 0.005679459 7.2647718 62.244 62.244 62.244 0.0023367243 0.008059221 0.0066424317
3700 1.4019908 5.9059957 7.0071843 0.0065915477 7.2910363 62.244 62.244 62.244 0.0049554109 0.010827005 0.0039922268
3800 1.3960736 5.902079 6.99862 0.0027763588 7.1181784 62.244 62.244 62.244 -0.0015907217 0.0025862003 0.0073335977
3900 1.4352825 5.8986215 7.025959 0.003498268 7.176605 62.244 62.244 62.244 0.0030416681 0.0027739509 0.0046791851
4000 1.4121845 5.907903 7.0170983 0.005046232 7.2344043 62.244 62.244 62.244 0.0045542682 0.0064113499 0.0041730779
4100 1.3989578 5.9082397 7.0070461 0.00042880001 7.0255115 62.244 62.244 62.244 0.0025735184 0.0025181486 -0.003805267
4200 1.3998829 5.8998147 6.9993477 0.0042777376 7.18356 62.244 62.244 62.244 0.0013744091 0.00646996 0.0049888436
4300 1.4076022 5.9044509 7.010047 0.0066789366 7.2976622 62.244 62.244 62.244 0.0073610616 0.0048139129 0.0078618353
4400 1.4161075 5.9064331 7.0187096 -0.0011844267 6.9677046 62.244 62.244 62.244 -0.0019088313 -0.0037556503 0.0021112015
4500 1.4292243 5.8980093 7.0205884 0.0018500416 7.1002567 62.244 62.244 62.244 0.0041144085 0.0010160497 0.00041966655
4600 1.3958775 5.8943133 6.9907003 0.0041485723 7.1693504 62.244 62.244 62.244 0.0033999287 0.0041620406 0.0048837475
4700 1.3856614 5.8886847 6.9770475 0.0013150314 7.0336767 62.244 62.244 62.244 -0.00051753674 0.0030875481 0.0013750828
4800 1.401683 5.9023505 7.0032974 0.002504877 7.1111649 62.244 62.244 62.244 0.0016543718 -0.0001813413 0.0060416007
4900 1.446628 5.9050553 7.0413042 -0.0026645902 6.9265589 62.244 62.244 62.244 -0.00069368076 -0.0073984763 9.8386402e-05
5000 1.4387091 5.9077604 7.0377893 0.0049468048 7.2508137 62.244 62.244 62.244 0.0042902506 0.0046715523 0.0058786114
Loop time of 3.70354 on 4 procs for 5000 steps with 5600 atoms
Performance: 583225.455 tau/day, 1350.059 timesteps/s
92.9% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.081073 | 0.13498 | 0.20108 | 14.4 | 3.64
Bond | 0.032352 | 0.048566 | 0.066671 | 7.0 | 1.31
Neigh | 0.71345 | 0.72477 | 0.73658 | 1.3 | 19.57
Comm | 0.29998 | 0.37027 | 0.42722 | 8.9 | 10.00
Output | 0.0026417 | 0.0048325 | 0.0085185 | 3.2 | 0.13
Modify | 1.9807 | 2.1035 | 2.263 | 8.1 | 56.80
Other | | 0.3166 | | | 8.55
Nlocal: 1400 ave 1868 max 905 min
Histogram: 1 1 0 0 0 0 0 0 0 2
Nghost: 648.25 ave 688 max 598 min
Histogram: 1 0 0 1 0 0 0 0 1 1
Neighs: 1202.5 ave 1821 max 698 min
Histogram: 2 0 0 0 0 0 0 1 0 1
Total # of neighbors = 4810
Ave neighs/atom = 0.858929
Ave special neighs/atom = 0.571429
Neighbor list builds = 759
Dangerous builds = 0
# Replace fix rigid and fix langevin with new ones
unfix 1
unfix 3
fix 3 tethers langevin 1.4 1.4 1.0 198450
# Test different integrators for rods
fix 1 rods rigid/nve molecule
800 rigid bodies with 4000 atoms
print "rigid/nve"
rigid/nve
run 1000
Per MPI rank memory allocation (min/avg/max) = 7.217 | 7.395 | 7.573 Mbytes
Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
5000 1.4387091 5.9077604 7.0377893 0.0035977871 7.1927209 62.244 62.244 62.244 0.025518192 -0.016769871 0.0020450407
5100 1.4449405 5.8876257 7.022549 0.0023104502 7.122044 62.244 62.244 62.244 0.0045960664 0.0036845954 -0.0013493113
5200 1.4271652 5.9160022 7.036964 0.0020238904 7.1241189 62.244 62.244 62.244 -0.0022546188 0.00392213 0.0044041599
5300 1.4143299 5.9052666 7.016147 0.0064054214 7.2919838 62.244 62.244 62.244 0.0090997079 0.0026363579 0.0074801984
5400 1.4426441 5.9087558 7.0418754 0.0020465683 7.1300068 62.244 62.244 62.244 0.0043188307 3.0314417e-06 0.0018178427
5500 1.4281065 5.9038871 7.0255883 0.00058665945 7.0508516 62.244 62.244 62.244 0.005898925 0.00066013177 -0.0047990784
5600 1.4315628 5.902373 7.0267888 0.0096475978 7.4422435 62.244 62.244 62.244 0.0054175405 0.011780025 0.011745228
5700 1.4075482 5.9075587 7.0131124 0.0052150708 7.2376891 62.244 62.244 62.244 0.0030069124 0.0036690785 0.0089692215
5800 1.4215681 5.9048555 7.0214211 0.0015070444 7.086319 62.244 62.244 62.244 -5.6858344e-05 0.0023644208 0.0022135708
5900 1.3992461 5.8949367 6.9939696 0.0062425817 7.262794 62.244 62.244 62.244 0.0056972212 0.0095293238 0.0035012003
6000 1.385289 5.8972105 6.9852808 0.0043255163 7.1715506 62.244 62.244 62.244 0.0040215567 0.0026330714 0.0063219208
Loop time of 0.84847 on 4 procs for 1000 steps with 5600 atoms
Performance: 509151.820 tau/day, 1178.592 timesteps/s
94.3% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.020741 | 0.03547 | 0.053064 | 7.5 | 4.18
Bond | 0.0064373 | 0.0096895 | 0.013065 | 3.0 | 1.14
Neigh | 0.14992 | 0.15174 | 0.15392 | 0.4 | 17.88
Comm | 0.068751 | 0.081259 | 0.10084 | 4.2 | 9.58
Output | 0.00054288 | 0.00096381 | 0.0017593 | 0.0 | 0.11
Modify | 0.45914 | 0.48587 | 0.51316 | 2.8 | 57.26
Other | | 0.08348 | | | 9.84
Nlocal: 1400 ave 1868 max 935 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Nghost: 633.75 ave 695 max 541 min
Histogram: 1 0 0 0 1 0 0 0 0 2
Neighs: 1263 ave 1799 max 710 min
Histogram: 1 1 0 0 0 0 0 0 0 2
Total # of neighbors = 5052
Ave neighs/atom = 0.902143
Ave special neighs/atom = 0.571429
Neighbor list builds = 153
Dangerous builds = 0
unfix 1
fix 1 rods rigid/nvt molecule temp 1.4 1.4 1.0
800 rigid bodies with 4000 atoms
print "rigid/nvt"
rigid/nvt
run 1000
Per MPI rank memory allocation (min/avg/max) = 7.217 | 7.395 | 7.573 Mbytes
Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
6000 1.385289 5.8972105 6.9852808 0.0029190017 7.1109818 62.244 62.244 62.244 0.026575922 -0.075631452 0.057812535
6100 1.3829575 5.9055308 6.9917699 0.0022904842 7.090405 62.244 62.244 62.244 -0.00045870123 0.0040556461 0.0032745076
6200 1.3942692 5.90506 7.0001838 0.0046406766 7.2000253 62.244 62.244 62.244 0.0042263485 0.0051632793 0.0045324021
6300 1.4009885 5.902399 7.0028005 0.0077682466 7.3373246 62.244 62.244 62.244 0.0071636876 0.0098268446 0.0063142075
6400 1.3627532 5.9075588 6.9779284 0.0093180831 7.3791932 62.244 62.244 62.244 0.0062401458 0.01302262 0.0086914833
6500 1.3341203 5.9012967 6.9491767 0.01010805 7.3844599 62.244 62.244 62.244 0.0031876185 0.011099561 0.01603697
6600 1.3572847 5.8915298 6.9576042 -0.00034416901 6.9427833 62.244 62.244 62.244 0.0025579012 -0.0011308802 -0.0024595281
6700 1.366374 5.8985277 6.9717413 0.0029472772 7.0986599 62.244 62.244 62.244 0.0022469424 -0.00042869772 0.0070235868
6800 1.381673 5.8909304 6.9761606 -9.1063397e-05 6.9722391 62.244 62.244 62.244 -0.0048194377 -0.00080972169 0.0053559692
6900 1.4011472 5.8881927 6.9887188 0.0010086058 7.0321524 62.244 62.244 62.244 0.0012132619 -0.0025916747 0.0044042301
7000 1.3973658 5.8867938 6.9843498 0.0070015187 7.2858563 62.244 62.244 62.244 0.0058913402 0.0076802028 0.0074330131
Loop time of 0.902266 on 4 procs for 1000 steps with 5600 atoms
Performance: 478794.425 tau/day, 1108.320 timesteps/s
92.5% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.022644 | 0.037091 | 0.054025 | 7.4 | 4.11
Bond | 0.0066526 | 0.0098482 | 0.012934 | 2.8 | 1.09
Neigh | 0.15815 | 0.16028 | 0.16242 | 0.5 | 17.76
Comm | 0.086046 | 0.10069 | 0.11568 | 3.7 | 11.16
Output | 0.00047731 | 0.00090772 | 0.0016732 | 0.0 | 0.10
Modify | 0.46692 | 0.49338 | 0.52973 | 3.5 | 54.68
Other | | 0.1001 | | | 11.09
Nlocal: 1400 ave 1832 max 970 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Nghost: 652.5 ave 749 max 561 min
Histogram: 1 0 0 1 0 0 1 0 0 1
Neighs: 1407.5 ave 2071 max 748 min
Histogram: 1 1 0 0 0 0 0 0 1 1
Total # of neighbors = 5630
Ave neighs/atom = 1.00536
Ave special neighs/atom = 0.571429
Neighbor list builds = 149
Dangerous builds = 0
unfix 1
compute myTemp all temp
fix 1 rods rigid/npt molecule temp 1.4 1.4 1.0 iso 0.05 0.05 1.0 dilate all
800 rigid bodies with 4000 atoms
print "rigid/npt iso"
rigid/npt iso
fix_modify 1 temp myTemp
run 1000
Per MPI rank memory allocation (min/avg/max) = 7.217 | 7.395 | 7.573 Mbytes
Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
7000 1.3973658 5.8867938 6.9843498 0.0026564535 7.0987447 62.244 62.244 62.244 0.033711862 -0.0068580786 -0.018884423
7100 1.463906 5.861189 7.0110088 0.011521299 7.3924648 57.022165 57.022165 57.022165 0.010788399 0.0093706759 0.014404821
7200 1.4950346 5.817724 6.9919936 0.023104537 7.516484 50.28164 50.28164 50.28164 0.023252537 0.018108267 0.027952807
7300 1.5103539 5.7757334 6.9620355 0.02265972 7.3367664 45.242961 45.242961 45.242961 0.023588139 0.022279352 0.022111669
7400 1.5583184 5.7576833 6.9816589 0.028383162 7.3460731 41.582206 41.582206 41.582206 0.027312172 0.029876235 0.027961079
7500 1.5988886 5.6930714 6.9489127 0.046500933 7.4415595 39.00204 39.00204 39.00204 0.057497139 0.031007247 0.050998413
7600 1.5458926 5.6844397 6.8986555 0.034168406 7.2068206 36.96428 36.96428 36.96428 0.037874991 0.027247969 0.037382258
7700 1.5179913 5.6416448 6.8339457 0.070322183 7.3856048 35.284894 35.284894 35.284894 0.054248771 0.10402305 0.052694729
7800 1.4797888 5.6045532 6.7668481 0.07801402 7.3126319 33.963465 33.963465 33.963465 0.096058241 0.061172194 0.076811627
7900 1.4846305 5.54982 6.7159177 0.065303374 7.1325712 32.936376 32.936376 32.936376 0.089117046 0.06069295 0.046100127
8000 1.4352665 5.5157472 6.6430722 0.065962965 7.0326574 32.099391 32.099391 32.099391 0.032126133 0.070109418 0.095653344
Loop time of 1.72334 on 4 procs for 1000 steps with 5600 atoms
Performance: 250675.661 tau/day, 580.268 timesteps/s
92.5% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.060282 | 0.099801 | 0.13824 | 10.8 | 5.79
Bond | 0.0095227 | 0.013491 | 0.017217 | 3.2 | 0.78
Neigh | 0.58793 | 0.59546 | 0.60654 | 1.0 | 34.55
Comm | 0.17903 | 0.21403 | 0.24615 | 6.5 | 12.42
Output | 0.00045562 | 0.00076783 | 0.0017018 | 0.0 | 0.04
Modify | 0.64959 | 0.68513 | 0.70671 | 2.8 | 39.76
Other | | 0.1147 | | | 6.65
Nlocal: 1400 ave 1768 max 981 min
Histogram: 1 0 1 0 0 0 0 0 0 2
Nghost: 1574 ave 1663 max 1447 min
Histogram: 1 0 0 1 0 0 0 0 0 2
Neighs: 6338 ave 9521 max 3068 min
Histogram: 1 0 1 0 0 0 0 0 1 1
Total # of neighbors = 25352
Ave neighs/atom = 4.52714
Ave special neighs/atom = 0.571429
Neighbor list builds = 337
Dangerous builds = 0
unfix 1
fix 1 rods rigid/npt molecule temp 1.4 1.4 1.0 x 0.05 0.05 1.0 dilate all
800 rigid bodies with 4000 atoms
print "rigid/npt x"
rigid/npt x
run 1000
Per MPI rank memory allocation (min/avg/max) = 7.226 | 7.412 | 7.597 Mbytes
Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
8000 1.4352665 5.5157472 6.6430722 0.073641793 7.0780095 32.099391 32.099391 32.099391 0.13359913 0.13991003 -0.052583787
8100 1.4385682 5.5149882 6.6449064 0.092621097 7.1894426 31.952972 32.099391 32.099391 0.10729401 0.11619987 0.054369411
8200 1.42735 5.5149024 6.6360094 0.023903894 6.7756304 31.745099 32.099391 32.099391 0.051524189 0.013370811 0.006816681
8300 1.4335369 5.5031396 6.629106 0.024536474 6.7705237 31.324638 32.099391 32.099391 0.042356568 -0.0039258365 0.035178692
8400 1.4502714 5.4659017 6.6050122 0.06575457 6.9774701 30.785462 32.099391 32.099391 0.056998298 0.084852971 0.055412441
8500 1.4432366 5.4541505 6.5877355 0.03322226 6.7725932 30.241461 32.099391 32.099391 0.045871758 0.024443739 0.029351281
8600 1.436491 5.4272043 6.5554911 0.039811655 6.7732608 29.729098 32.099391 32.099391 0.037709456 0.060942551 0.020782958
8700 1.4099251 5.4106713 6.5180919 0.013490442 6.590596 29.209958 32.099391 32.099391 0.025833003 -0.0021161354 0.016754458
8800 1.3801478 5.3926425 6.4766747 0.028808964 6.6280205 28.552039 32.099391 32.099391 0.012603549 0.018713073 0.055110271
8900 1.4411695 5.3583474 6.4903088 0.053464468 6.7655624 27.980937 32.099391 32.099391 0.055084927 0.073292013 0.032016464
9000 1.4264395 5.3680298 6.4884216 0.066557314 6.8276318 27.69922 32.099391 32.099391 0.05380086 0.069450871 0.076420212
Loop time of 1.45936 on 4 procs for 1000 steps with 5600 atoms
Performance: 296020.704 tau/day, 685.233 timesteps/s
96.3% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.097855 | 0.1563 | 0.20542 | 12.5 | 10.71
Bond | 0.010222 | 0.01371 | 0.016844 | 2.6 | 0.94
Neigh | 0.43646 | 0.44419 | 0.4668 | 2.0 | 30.44
Comm | 0.10136 | 0.14589 | 0.19563 | 11.6 | 10.00
Output | 0.00046229 | 0.00076181 | 0.0016556 | 0.0 | 0.05
Modify | 0.59971 | 0.62524 | 0.65776 | 2.9 | 42.84
Other | | 0.07327 | | | 5.02
Nlocal: 1400 ave 1680 max 1049 min
Histogram: 1 0 1 0 0 0 0 0 0 2
Nghost: 1627.25 ave 1775 max 1488 min
Histogram: 1 1 0 0 0 0 0 1 0 1
Neighs: 7842 ave 10600 max 4326 min
Histogram: 1 0 1 0 0 0 0 0 0 2
Total # of neighbors = 31368
Ave neighs/atom = 5.60143
Ave special neighs/atom = 0.571429
Neighbor list builds = 166
Dangerous builds = 0
unfix 1
fix 1 rods rigid/nph molecule iso 0.05 0.05 1.0 dilate all
800 rigid bodies with 4000 atoms
print "rigid/nph iso"
rigid/nph iso
run 1000
Per MPI rank memory allocation (min/avg/max) = 7.227 | 7.412 | 7.597 Mbytes
Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
9000 1.4264395 5.3680298 6.4884216 0.0098629166 6.5386881 27.69922 32.099391 32.099391 -0.32352455 -0.020288613 0.37340191
9100 1.4501008 5.3468478 6.4858243 0.059250929 6.7846766 27.60347 31.988431 31.988431 0.076039445 0.051409059 0.050304282
9200 1.4635102 5.3406895 6.4901983 0.035210102 6.6656151 27.490192 31.857158 31.857158 0.0079484246 0.066653954 0.031027926
9300 1.4503713 5.3595734 6.4987624 0.020794 6.6013231 27.398334 31.750708 31.750708 0.053098983 0.0019379163 0.0073450997
9400 1.4701421 5.3186993 6.4734172 0.039118143 6.6618027 27.181055 31.498913 31.498913 0.076457868 -0.0028405762 0.043737137
9500 1.4495442 5.323167 6.4617063 0.073591495 6.8091096 27.000921 31.290164 31.290164 0.037777789 0.097624306 0.085372389
9600 1.4668438 5.3002222 6.4523494 0.06758294 6.7648428 26.814997 31.074705 31.074705 0.057941415 0.09775976 0.047047645
9700 1.4926839 5.2883964 6.4608196 0.059125916 6.7288224 26.637713 30.869258 30.869258 0.049817515 0.032285203 0.095275031
9800 1.4644558 5.2702597 6.4205112 0.0076221617 6.4543756 26.460515 30.663911 30.663911 -0.0060723629 0.010616271 0.018322577
9900 1.4669549 5.2511861 6.4034006 0.044167302 6.5961243 26.30195 30.480157 30.480157 0.026274163 0.013826125 0.092401618
10000 1.460983 5.2470476 6.3945715 0.10536479 6.8483021 26.186495 30.346361 30.346361 0.088951294 0.11273872 0.11440435
Loop time of 1.61361 on 4 procs for 1000 steps with 5600 atoms
Performance: 267722.758 tau/day, 619.729 timesteps/s
93.9% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.13322 | 0.18643 | 0.259 | 12.5 | 11.55
Bond | 0.012367 | 0.014462 | 0.016771 | 1.6 | 0.90
Neigh | 0.46284 | 0.46471 | 0.46675 | 0.3 | 28.80
Comm | 0.10183 | 0.17241 | 0.22246 | 12.4 | 10.68
Output | 0.00044584 | 0.00074542 | 0.0016396 | 0.0 | 0.05
Modify | 0.691 | 0.7057 | 0.72761 | 1.8 | 43.73
Other | | 0.06915 | | | 4.29
Nlocal: 1400 ave 1633 max 1183 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Nghost: 1747.75 ave 1847 max 1624 min
Histogram: 1 0 1 0 0 0 0 0 0 2
Neighs: 9290.75 ave 12454 max 6621 min
Histogram: 2 0 0 0 0 0 0 1 0 1
Total # of neighbors = 37163
Ave neighs/atom = 6.63625
Ave special neighs/atom = 0.571429
Neighbor list builds = 162
Dangerous builds = 0
unfix 1
fix 1 rods rigid/nph molecule x 0.05 0.05 1.0 y 0.05 0.05 1.0 couple xy dilate all
800 rigid bodies with 4000 atoms
print "rigid/nph xy couple"
rigid/nph xy couple
run 1000
Per MPI rank memory allocation (min/avg/max) = 7.229 | 7.413 | 7.597 Mbytes
Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
10000 1.460983 5.2470476 6.3945715 0.18376191 7.1859023 26.186495 30.346361 30.346361 0.015959435 0.68341409 -0.14808778
10100 1.4487259 5.2485513 6.3864479 0.060157728 6.6465409 26.238844 30.407026 30.346361 0.10289596 0.022823411 0.05475381
10200 1.4335646 5.2420513 6.3680395 0.013676852 6.4271554 26.235255 30.402867 30.346361 -0.017328522 0.040786509 0.017572569
10300 1.4334952 5.2377534 6.3636871 0.030978458 6.4967192 26.150168 30.304264 30.346361 0.044154015 0.036133394 0.012647966
10400 1.4209473 5.2242736 6.3403516 -0.00094467594 6.3363148 26.085773 30.22964 30.346361 0.030664991 0.018005544 -0.051504563
10500 1.4262805 5.2044624 6.3247294 0.045042501 6.5149748 25.934148 30.053928 30.346361 0.031103656 0.045410964 0.058612885
10600 1.4516048 5.2017459 6.3419036 0.069565209 6.6313867 25.741959 29.831208 30.346361 0.021768778 0.11302833 0.073898515
10700 1.4841074 5.1911212 6.356808 0.046866825 6.5493087 25.574636 29.637306 30.346361 0.073969059 0.064901506 0.0017299084
10800 1.4646257 5.1958815 6.3462665 0.050747116 6.5534926 25.500146 29.550982 30.346361 0.076646556 0.070734108 0.004860682
10900 1.461356 5.1821605 6.3299773 0.069060447 6.610166 25.417723 29.455466 30.346361 0.051399011 0.065631311 0.090151019
11000 1.4395386 5.1786243 6.3093047 -0.0087983274 6.2737059 25.383039 29.415273 30.346361 -0.060891892 0.037235898 -0.0027389884
Loop time of 1.56065 on 4 procs for 1000 steps with 5600 atoms
Performance: 276807.605 tau/day, 640.758 timesteps/s
94.5% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.15892 | 0.20364 | 0.2564 | 9.2 | 13.05
Bond | 0.011486 | 0.014652 | 0.01918 | 2.6 | 0.94
Neigh | 0.43915 | 0.43981 | 0.44125 | 0.1 | 28.18
Comm | 0.093711 | 0.14431 | 0.18183 | 9.9 | 9.25
Output | 0.00044441 | 0.00073904 | 0.0016198 | 0.0 | 0.05
Modify | 0.66889 | 0.68497 | 0.70418 | 1.5 | 43.89
Other | | 0.07254 | | | 4.65
Nlocal: 1400 ave 1610 max 1237 min
Histogram: 2 0 0 0 0 0 0 1 0 1
Nghost: 1832 ave 1919 max 1765 min
Histogram: 1 1 0 0 0 0 1 0 0 1
Neighs: 10008.2 ave 12428 max 7982 min
Histogram: 2 0 0 0 0 0 0 1 0 1
Total # of neighbors = 40033
Ave neighs/atom = 7.14875
Ave special neighs/atom = 0.571429
Neighbor list builds = 157
Dangerous builds = 0
Total wall time: 0:00:11

4
src/math_eigen.cpp
View File

@ -44,7 +44,7 @@ int MathEigen::jacobi3(double const mat[3][3], double *eval, double evec[3][3])
// create instance of generic Jacobi class and get eigenvalues and -vectors
Jacobi_v1 ecalc3(3, M, midx);
int ierror = ecalc3.Diagonalize(mat, eval, evec, Jacobi_v1::SORT_INCREASING_EVALS);
int ierror = ecalc3.Diagonalize(mat, eval, evec, Jacobi_v1::SORT_DECREASING_EVALS);
// transpose the evec matrix
@ -67,7 +67,7 @@ int MathEigen::jacobi3(double const *const *mat, double *eval, double **evec)
// create instance of generic Jacobi class and get eigenvalues and -vectors
Jacobi_v2 ecalc3(3, M, midx);
int ierror = ecalc3.Diagonalize(mat, eval, evec, Jacobi_v2::SORT_INCREASING_EVALS);
int ierror = ecalc3.Diagonalize(mat, eval, evec, Jacobi_v2::SORT_DECREASING_EVALS);
// transpose the evec matrix

113
unittest/force-styles/tests/fix-timestep-rigid_group.yaml
View File

@ -1,7 +1,6 @@
---
lammps_version: 7 Feb 2024
tags:
date_generated: Mon Mar 25 20:00:59 2024
lammps_version: 17 Feb 2022
date_generated: Fri Mar 18 22:18:00 2022
epsilon: 5e-13
skip_tests:
prerequisites: ! |
@ -15,65 +14,65 @@ post_commands: ! |
input_file: in.fourmol
natoms: 29
run_stress: ! |-
-1.4245356937318909e+03 -1.4496493315649632e+03 -3.6144360984225123e+03 8.4840626828644361e+02 2.0318336761612773e+02 -6.0622397707969583e+02
global_scalar: 15.711521423178084
-1.4245356937318884e+03 -1.4496493315649691e+03 -3.6144360984224995e+03 8.4840626828644076e+02 2.0318336761611761e+02 -6.0622397707970140e+02
global_scalar: 15.711521423178082
run_pos: ! |2
1 -2.7899546863891755e-01 2.4731857340328198e+00 -1.7290667740241461e-01
2 3.0296221610263996e-01 2.9517129916957550e+00 -8.5798904387772190e-01
3 -6.9368802364134963e-01 1.2445115421754176e+00 -6.2281111198650141e-01
4 -1.5764879647103172e+00 1.4919714415841279e+00 -1.2492069414674598e+00
5 -8.9434512967430235e-01 9.3651699743510453e-01 4.0191726558261442e-01
6 2.9454439634451712e-01 2.2724545792544146e-01 -1.2845195053960266e+00
7 3.4049112903270240e-01 -9.4655678322404235e-03 -2.4634480020857055e+00
8 1.1644354555804877e+00 -4.8367776650961403e-01 -6.7663643940735962e-01
9 1.3781717822696455e+00 -2.5332509530011083e-01 2.6864954436590072e-01
10 2.0186368606041905e+00 -1.4285861423625785e+00 -9.6712491252780486e-01
11 1.7929137227577487e+00 -1.9875455388407386e+00 -1.8836565352266592e+00
12 3.0032775230399622e+00 -4.8983022415173583e-01 -1.6190248017343625e+00
13 4.0448964162125964e+00 -9.0213155122390454e-01 -1.6385398399479547e+00
14 2.6035151245015857e+00 -4.0874995493218413e-01 -2.6555999074786598e+00
15 2.9761196776172323e+00 5.6287237454109007e-01 -1.2442626196083335e+00
16 2.6517373021566182e+00 -2.3957035508393734e+00 3.3389262100686046e-02
17 2.2311114924744961e+00 -2.1018393228798584e+00 1.1496088522377494e+00
18 2.1390642573201792e+00 3.0164773560693803e+00 -3.5143984803853883e+00
19 1.5353246655146293e+00 2.6305911186316160e+00 -4.2455871034737100e+00
20 2.7649421538938399e+00 3.6818603528430875e+00 -3.9364115785985545e+00
21 4.9043112657298966e+00 -4.0774268210397882e+00 -3.6200836396129850e+00
22 4.3665322424283417e+00 -4.2075138112953612e+00 -4.4636587264885925e+00
23 5.7355405581985277e+00 -3.5789558641908901e+00 -3.8805763324089995e+00
24 2.0692780332810012e+00 3.1504920436415969e+00 3.1571131300668829e+00
25 1.3007297593168976e+00 3.2745259354179459e+00 2.5110163874103693e+00
26 2.5819416446099637e+00 4.0104903120756576e+00 3.2150249624526102e+00
1 -2.7899546863891400e-01 2.4731857340328229e+00 -1.7290667740242271e-01
2 3.0296221610264262e-01 2.9517129916957545e+00 -8.5798904387773245e-01
3 -6.9368802364134741e-01 1.2445115421754194e+00 -6.2281111198650418e-01
4 -1.5764879647103154e+00 1.4919714415841279e+00 -1.2492069414674623e+00
5 -8.9434512967429969e-01 9.3651699743511030e-01 4.0191726558261276e-01
6 2.9454439634451712e-01 2.2724545792544038e-01 -1.2845195053960268e+00
7 3.4049112903270051e-01 -9.4655678322458359e-03 -2.4634480020857055e+00
8 1.1644354555804874e+00 -4.8367776650961336e-01 -6.7663643940735863e-01
9 1.3781717822696469e+00 -2.5332509530010694e-01 2.6864954436590061e-01
10 2.0186368606041896e+00 -1.4285861423625796e+00 -9.6712491252780131e-01
11 1.7929137227577452e+00 -1.9875455388407426e+00 -1.8836565352266534e+00
12 3.0032775230399604e+00 -4.8983022415174027e-01 -1.6190248017343642e+00
13 4.0448964162125947e+00 -9.0213155122391020e-01 -1.6385398399479558e+00
14 2.6035151245015822e+00 -4.0874995493219213e-01 -2.6555999074786607e+00
15 2.9761196776172318e+00 5.6287237454108674e-01 -1.2442626196083388e+00
16 2.6517373021566168e+00 -2.3957035508393707e+00 3.3389262100692263e-02
17 2.2311114924744970e+00 -2.1018393228798513e+00 1.1496088522377543e+00
18 2.1390642573201784e+00 3.0164773560693781e+00 -3.5143984803853878e+00
19 1.5353246655146278e+00 2.6305911186316133e+00 -4.2455871034737074e+00
20 2.7649421538938390e+00 3.6818603528430849e+00 -3.9364115785985550e+00
21 4.9043112657298877e+00 -4.0774268210397882e+00 -3.6200836396129836e+00
22 4.3665322424283310e+00 -4.2075138112953594e+00 -4.4636587264885881e+00
23 5.7355405581985188e+00 -3.5789558641908918e+00 -3.8805763324089981e+00
24 2.0692780332810115e+00 3.1504920436416004e+00 3.1571131300668789e+00
25 1.3007297593169076e+00 3.2745259354179481e+00 2.5110163874103675e+00
26 2.5819416446099739e+00 4.0104903120756576e+00 3.2150249624526035e+00
27 -1.9613581876744359e+00 -4.3556300596085160e+00 2.1101467673534788e+00
28 -2.7406520384725965e+00 -4.0207251278130975e+00 1.5828689861678511e+00
29 -1.3108232656499081e+00 -3.5992986322410760e+00 2.2680459788743503e+00
run_vel: ! |2
1 4.7093289825842437e-04 2.6351122778447999e-04 -4.4905093064114823e-04
2 4.9594625316470473e-04 9.4561370489632928e-05 -5.4581359894047732e-04
3 3.3306085115756054e-04 2.3224943880673362e-04 -2.3659455671746045e-04
4 3.3692327392261130e-04 2.1926810694051292e-04 -2.4716631558862576e-04
5 3.3642542694185899e-04 4.1797578013265770e-04 -1.8011341766657654e-04
6 2.0926869754934769e-04 2.6449308951579106e-05 -1.0508938983871929e-04
7 1.4629043007908003e-04 -1.6873376665349995e-04 -6.8354048774352968e-05
8 1.5844101624224859e-04 3.7728761274000288e-05 -1.9162715667092141e-05
9 2.1299362072601887e-04 1.6917140529157517e-04 -6.3528165037845917e-05
10 5.4261629412254576e-05 -9.4655528376811157e-05 1.0511362869146505e-04
11 -3.2194160796502236e-05 -2.2025095264758700e-04 2.0300202946212152e-04
12 1.2640586304750429e-04 -2.9851080445664956e-04 -7.9476371818247574e-05
13 8.4523575162143312e-05 -4.0583135407330399e-04 -4.7551111331702557e-05
14 9.9954050381271961e-05 -4.2610816481298121e-04 -7.9255633594381943e-05
15 2.4417481119789894e-04 -2.3521002264677784e-04 -2.4875318161049020e-04
16 -9.0958138549668516e-06 3.7774817121217089e-06 2.4035199548834928e-04
17 5.7507224523611227e-05 2.2629217444843685e-04 2.0686920072684740e-04
18 2.9220264989359860e-04 -6.2478376436796244e-04 8.4222594596602409e-04
19 2.0572616567799204e-04 -5.0334424271726607e-04 8.4953929443210702e-04
20 4.1224811789513060e-04 -7.4115205416011543e-04 8.3678612337507964e-04
21 -1.0671858777656406e-03 -1.1531171045499533e-03 7.3720674900162007e-04
22 -1.1066511338291734e-03 -1.0433933757600477e-03 7.4544544325708432e-04
23 -9.7629260480941644e-04 -1.3100872491594124e-03 7.2687284219704641e-04
24 4.3308126651259382e-04 -6.6527658087322671e-04 8.4451298670663671e-04
25 4.4565811905442982e-04 -5.1298436273584133e-04 8.5878867884521635e-04
26 5.9865972692022961e-04 -7.6385263287080262e-04 8.4259943226842242e-04
1 4.7093289825842508e-04 2.6351122778447809e-04 -4.4905093064114883e-04
2 4.9594625316470506e-04 9.4561370489630299e-05 -5.4581359894047775e-04
3 3.3306085115756103e-04 2.3224943880673259e-04 -2.3659455671746018e-04
4 3.3692327392261152e-04 2.1926810694051179e-04 -2.4716631558862516e-04
5 3.3642542694186002e-04 4.1797578013265738e-04 -1.8011341766657675e-04
6 2.0926869754934769e-04 2.6449308951578185e-05 -1.0508938983871811e-04
7 1.4629043007907940e-04 -1.6873376665350122e-04 -6.8354048774350921e-05
8 1.5844101624224881e-04 3.7728761273999780e-05 -1.9162715667090996e-05
9 2.1299362072601952e-04 1.6917140529157474e-04 -6.3528165037845483e-05
10 5.4261629412254495e-05 -9.4655528376811482e-05 1.0511362869146690e-04
11 -3.2194160796502724e-05 -2.2025095264758716e-04 2.0300202946212429e-04
12 1.2640586304750378e-04 -2.9851080445665107e-04 -7.9476371818245798e-05
13 8.4523575162142608e-05 -4.0583135407330561e-04 -4.7551111331700511e-05
14 9.9954050381270972e-05 -4.2610816481298294e-04 -7.9255633594379530e-05
15 2.4417481119789862e-04 -2.3521002264677992e-04 -2.4875318161048917e-04
16 -9.0958138549664992e-06 3.7774817121222391e-06 2.4035199548835096e-04
17 5.7507224523612230e-05 2.2629217444843764e-04 2.0686920072684822e-04
18 2.9220264989359833e-04 -6.2478376436796265e-04 8.4222594596602366e-04
19 2.0572616567799188e-04 -5.0334424271726639e-04 8.4953929443210648e-04
20 4.1224811789513022e-04 -7.4115205416011554e-04 8.3678612337507920e-04
21 -1.0671858777656393e-03 -1.1531171045499515e-03 7.3720674900162159e-04
22 -1.1066511338291710e-03 -1.0433933757600460e-03 7.4544544325708573e-04
23 -9.7629260480941525e-04 -1.3100872491594103e-03 7.2687284219704804e-04
24 4.3308126651259312e-04 -6.6527658087322801e-04 8.4451298670663606e-04
25 4.4565811905442889e-04 -5.1298436273584285e-04 8.5878867884521559e-04
26 5.9865972692022765e-04 -7.6385263287080381e-04 8.4259943226842166e-04
27 -2.6510179146429716e-04 3.6306203629019116e-04 -5.6235585400647747e-04
28 -2.3068708109787484e-04 -8.5663070212203200e-04 2.1302563179109169e-03
29 -2.5054744388303732e-03 -1.6773997805290820e-04 2.8436699761004796e-03

43
unittest/force-styles/tests/fix-timestep-rigid_molecule.yaml
View File

@ -1,7 +1,6 @@
---
lammps_version: 7 Feb 2024
tags:
date_generated: Mon Mar 25 20:00:59 2024
lammps_version: 17 Feb 2022
date_generated: Fri Mar 18 22:18:00 2022
epsilon: 5e-13
skip_tests:
prerequisites: ! |
@ -15,8 +14,8 @@ post_commands: ! |
input_file: in.fourmol
natoms: 29
run_stress: ! |-
-4.9200116134788615e+01 -2.6907707565987401e+01 -6.0080860422276308e+00 -2.5620423972100241e+01 -1.3450224059984270e+01 -1.4947288487006070e+00
global_scalar: 18.340560167414402
-4.9200116134789873e+01 -2.6907707565987707e+01 -6.0080860422278581e+00 -2.5620423972101300e+01 -1.3450224059983967e+01 -1.4947288487003760e+00
global_scalar: 18.3405601674144
run_pos: ! |2
1 -2.7993683669226832e-01 2.4726588069312840e+00 -1.7200860244148433e-01
2 3.0197083955402204e-01 2.9515239068888608e+00 -8.5689735572907566e-01
@ -35,15 +34,15 @@ run_pos: ! |2
15 2.9756315249791303e+00 5.6334269722969288e-01 -1.2437650754599008e+00
16 2.6517554244980306e+00 -2.3957110424978438e+00 3.2908335999178327e-02
17 2.2309964792710639e+00 -2.1022918943319384e+00 1.1491948328949437e+00
18 2.1392027588271301e+00 3.0171068018412783e+00 -3.5144628518856353e+00
19 1.5366124997074575e+00 2.6286809834111740e+00 -4.2452547844370221e+00
20 2.7628161763455852e+00 3.6842251687634775e+00 -3.9370881219352558e+00
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37
unittest/force-styles/tests/fix-timestep-rigid_molecule_tri.yaml
View File

@ -1,7 +1,6 @@
---
lammps_version: 7 Feb 2024
tags:
date_generated: Mon Mar 25 20:01:00 2024
lammps_version: 17 Feb 2022
date_generated: Fri Mar 18 22:18:00 2022
epsilon: 5e-12
skip_tests:
prerequisites: ! |
@ -16,8 +15,8 @@ post_commands: ! |
input_file: in.fourmol
natoms: 29
run_stress: ! |-
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@ -37,14 +36,14 @@ run_pos: ! |2
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85
unittest/force-styles/tests/fix-timestep-rigid_nph.yaml
View File

@ -1,7 +1,6 @@
---
lammps_version: 7 Feb 2024
tags:
date_generated: Mon Mar 25 20:01:00 2024
lammps_version: 17 Feb 2022
date_generated: Fri Mar 18 22:18:00 2022
epsilon: 5e-13
skip_tests:
prerequisites: ! |
@ -15,38 +14,38 @@ post_commands: ! |
input_file: in.fourmol
natoms: 29
run_stress: ! |2-
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global_scalar: 29.023636439584656
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global_scalar: 29.023636440847998
run_pos: ! |2
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85
unittest/force-styles/tests/fix-timestep-rigid_nph_small.yaml
View File

@ -1,7 +1,6 @@
---
lammps_version: 7 Feb 2024
tags:
date_generated: Mon Mar 25 20:01:00 2024
lammps_version: 17 Feb 2022
date_generated: Fri Mar 18 22:18:00 2022
epsilon: 6.5e-13
skip_tests:
prerequisites: ! |
@ -15,38 +14,38 @@ post_commands: ! |
input_file: in.fourmol
natoms: 29
run_stress: ! |2-
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@ -65,15 +64,15 @@ run_vel: ! |2
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119
unittest/force-styles/tests/fix-timestep-rigid_npt.yaml
View File

@ -1,7 +1,6 @@
---
lammps_version: 7 Feb 2024
tags:
date_generated: Mon Mar 25 20:01:01 2024
lammps_version: 17 Feb 2022
date_generated: Fri Mar 18 22:18:00 2022
epsilon: 5e-13
skip_tests:
prerequisites: ! |
@ -14,65 +13,65 @@ post_commands: ! |
input_file: in.fourmol
natoms: 29
run_stress: ! |-
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global_scalar: 106.86683072474244
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global_scalar: 106.86683072474125
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85
unittest/force-styles/tests/fix-timestep-rigid_npt_small.yaml
View File

@ -1,7 +1,6 @@
---
lammps_version: 7 Feb 2024
tags:
date_generated: Mon Mar 25 20:01:01 2024
lammps_version: 17 Feb 2022
date_generated: Fri Mar 18 22:18:00 2022
epsilon: 5e-13
skip_tests:
prerequisites: ! |
@ -14,38 +13,38 @@ post_commands: ! |
input_file: in.fourmol
natoms: 29
run_stress: ! |-
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global_scalar: 77.78983430422252
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global_scalar: 77.78983430293286
run_pos: ! |2
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@ -64,15 +63,15 @@ run_vel: ! |2
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113
unittest/force-styles/tests/fix-timestep-rigid_nve_group.yaml
View File

@ -1,7 +1,6 @@
---
lammps_version: 7 Feb 2024
tags:
date_generated: Mon Mar 25 20:01:02 2024
lammps_version: 17 Feb 2022
date_generated: Fri Mar 18 22:18:00 2022
epsilon: 5e-13
skip_tests:
prerequisites: ! |
@ -15,65 +14,65 @@ post_commands: ! |
input_file: in.fourmol
natoms: 29
run_stress: ! |-
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global_scalar: 15.711521423178162
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global_scalar: 15.711521423178128
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45
unittest/force-styles/tests/fix-timestep-rigid_nve_molecule.yaml
View File

@ -1,7 +1,6 @@
---
lammps_version: 7 Feb 2024
tags:
date_generated: Mon Mar 25 20:01:02 2024
lammps_version: 17 Feb 2022
date_generated: Fri Mar 18 22:18:00 2022
epsilon: 5e-13
skip_tests:
prerequisites: ! |
@ -15,8 +14,8 @@ post_commands: ! |
input_file: in.fourmol
natoms: 29
run_stress: ! |-
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global_scalar: 18.340560165889197
-4.9200114774918006e+01 -2.6907707694141354e+01 -6.0080872444875970e+00 -2.5620425756344780e+01 -1.3450222538011893e+01 -1.4947348732785031e+00
global_scalar: 18.340560167364448
run_pos: ! |2
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2 3.0197083955402204e-01 2.9515239068888608e+00 -8.5689735572907566e-01
@ -35,15 +34,15 @@ run_pos: ! |2
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29 -1.3108232656499081e+00 -3.5992986322410760e+00 2.2680459788743503e+00
@ -65,15 +64,15 @@ run_vel: ! |2
15 -4.3301707382721859e-03 -3.1802661664634938e-03 3.2037919043360571e-03
16 -9.6715751018414326e-05 -5.0016572678960377e-04 1.4945658875149626e-03
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26 -1.5679561733890424e-03 3.5146224505578228e-04 2.4446924196328459e-03
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29 -2.5054744388303732e-03 -1.6773997805290820e-04 2.8436699761004796e-03

77
unittest/force-styles/tests/fix-timestep-rigid_nve_single.yaml
View File

@ -1,7 +1,6 @@
---
lammps_version: 7 Feb 2024
tags:
date_generated: Mon Mar 25 20:01:03 2024
lammps_version: 17 Feb 2022
date_generated: Fri Mar 18 22:18:00 2022
epsilon: 5e-13
skip_tests:
prerequisites: ! |
@ -15,26 +14,26 @@ post_commands: ! |
input_file: in.fourmol
natoms: 29
run_stress: ! |-
-1.3754817467882813e+03 -1.4228425246442055e+03 -3.6087196200592184e+03 8.7407043142559792e+02 2.1665316510417179e+02 -6.0480791467761571e+02
global_scalar: 4.531423038570381
-1.3754817467882767e+03 -1.4228425246441275e+03 -3.6087196200592489e+03 8.7407043142559303e+02 2.1665316510426268e+02 -6.0480791467747542e+02
global_scalar: 4.531423038570333
run_pos: ! |2
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7 3.4049112905316026e-01 -9.4655677385761805e-03 -2.4634480019885459e+00
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9 1.3781717822376380e+00 -2.5332509534948033e-01 2.6864954447021760e-01
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8 1.1644354555589707e+00 -4.8367776651303718e-01 -6.7663643931662931e-01
9 1.3781717822376129e+00 -2.5332509534954067e-01 2.6864954447021949e-01
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20 2.7641167828863153e+00 3.6833419064000221e+00 -3.9380850623312638e+00
@ -48,23 +47,23 @@ run_pos: ! |2
28 -2.7406520384725965e+00 -4.0207251278130975e+00 1.5828689861678511e+00
29 -1.3108232656499081e+00 -3.5992986322410760e+00 2.2680459788743503e+00
run_vel: ! |2
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45
unittest/force-styles/tests/fix-timestep-rigid_nve_small.yaml
View File

@ -1,7 +1,6 @@
---
lammps_version: 7 Feb 2024
tags:
date_generated: Mon Mar 25 20:01:03 2024
lammps_version: 17 Feb 2022
date_generated: Fri Mar 18 22:18:00 2022
epsilon: 5e-13
skip_tests:
prerequisites: ! |
@ -15,8 +14,8 @@ post_commands: ! |
input_file: in.fourmol
natoms: 29
run_stress: ! |-
-4.9200114760030708e+01 -2.6907707699312748e+01 -6.0080872440179061e+00 -2.5620425767600064e+01 -1.3450222535184853e+01 -1.4947348700253382e+00
global_scalar: 0.5007318719399354
-4.9200114774918006e+01 -2.6907707694141354e+01 -6.0080872444875970e+00 -2.5620425756344780e+01 -1.3450222538011893e+01 -1.4947348732785031e+00
global_scalar: 0.5007318719663203
run_pos: ! |2
1 -2.7993683669226832e-01 2.4726588069312840e+00 -1.7200860244148433e-01
2 3.0197083955402204e-01 2.9515239068888608e+00 -8.5689735572907566e-01
@ -35,15 +34,15 @@ run_pos: ! |2
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29 -1.3108232656499081e+00 -3.5992986322410760e+00 2.2680459788743503e+00
@ -65,15 +64,15 @@ run_vel: ! |2
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79
unittest/force-styles/tests/fix-timestep-rigid_nvt.yaml
View File

@ -1,8 +1,7 @@
---
lammps_version: 7 Feb 2024
tags:
date_generated: Mon Mar 25 20:01:03 2024
epsilon: 1e-12
lammps_version: 17 Feb 2022
date_generated: Fri Mar 18 22:18:00 2022
epsilon: 5e-13
skip_tests:
prerequisites: ! |
atom full
@ -14,26 +13,26 @@ post_commands: ! |
input_file: in.fourmol
natoms: 29
run_stress: ! |-
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global_scalar: 68.08659647424867
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global_scalar: 68.08659647423171
run_pos: ! |2
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20 2.7641167828863153e+00 3.6833419064000221e+00 -3.9380850623312638e+00
@ -47,23 +46,23 @@ run_pos: ! |2
28 -2.7406520384725965e+00 -4.0207251278130975e+00 1.5828689861678511e+00
29 -1.3108232656499081e+00 -3.5992986322410760e+00 2.2680459788743503e+00
run_vel: ! |2
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20 4.7777805013736515e-03 5.1003745845520452e-03 1.8002873923729241e-03

45
unittest/force-styles/tests/fix-timestep-rigid_nvt_small.yaml
View File

@ -1,7 +1,6 @@
---
lammps_version: 7 Feb 2024
tags:
date_generated: Mon Mar 25 20:01:04 2024
lammps_version: 17 Feb 2022
date_generated: Fri Mar 18 22:18:00 2022
epsilon: 5e-13
skip_tests:
prerequisites: ! |
@ -14,8 +13,8 @@ post_commands: ! |
input_file: in.fourmol
natoms: 29
run_stress: ! |-
-1.4827261099624999e+02 -1.8411194282828326e+01 -1.0752762861573947e+02 -2.1814511471949461e+02 1.7027764305079162e+02 2.1058942246396320e+01
global_scalar: 0.9532609552151339
-1.4827261116680472e+02 -1.8411194349753309e+01 -1.0752762859308649e+02 -2.1814511477016276e+02 1.7027764307147623e+02 2.1058942244057214e+01
global_scalar: 0.9532609554739606
run_pos: ! |2
1 -2.7993683669226832e-01 2.4726588069312840e+00 -1.7200860244148433e-01
2 3.0197083955402204e-01 2.9515239068888608e+00 -8.5689735572907566e-01
@ -34,15 +33,15 @@ run_pos: ! |2
15 2.9756315249791303e+00 5.6334269722969288e-01 -1.2437650754599008e+00
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29 -1.3108232656499081e+00 -3.5992986322410760e+00 2.2680459788743503e+00
@ -64,15 +63,15 @@ run_vel: ! |2
15 -4.3301707382721859e-03 -3.1802661664634938e-03 3.2037919043360571e-03
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77
unittest/force-styles/tests/fix-timestep-rigid_single.yaml
View File

@ -1,7 +1,6 @@
---
lammps_version: 7 Feb 2024
tags:
date_generated: Mon Mar 25 20:01:04 2024
lammps_version: 17 Feb 2022
date_generated: Fri Mar 18 22:18:00 2022
epsilon: 7.5e-13
skip_tests:
prerequisites: ! |
@ -15,26 +14,26 @@ post_commands: ! |
input_file: in.fourmol
natoms: 29
run_stress: ! |-
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global_scalar: 4.531423038570312
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global_scalar: 4.531423038570297
run_pos: ! |2
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11 1.7929137227200918e+00 -1.9875455388074483e+00 -1.8836565351900385e+00
12 3.0032775230343125e+00 -4.8983022415935312e-01 -1.6190248016126132e+00
13 4.0448964161972283e+00 -9.0213155125606947e-01 -1.6385398398262669e+00
14 2.6035151245155355e+00 -4.0874995488538129e-01 -2.6555999073602123e+00
15 2.9761196776308694e+00 5.6287237451798222e-01 -1.2442626194416753e+00
16 2.6517373020764219e+00 -2.3957035509096407e+00 3.3389262134315700e-02
17 2.2311114923824857e+00 -2.1018393229879817e+00 1.1496088522768926e+00
18 2.1384791188033843e+00 3.0177261773770208e+00 -3.5160827596876225e+00
19 1.5349125211132961e+00 2.6315969880333707e+00 -4.2472859440220647e+00
20 2.7641167828863153e+00 3.6833419064000221e+00 -3.9380850623312638e+00
@ -48,23 +47,23 @@ run_pos: ! |2
28 -2.7406520384725965e+00 -4.0207251278130975e+00 1.5828689861678511e+00
29 -1.3108232656499081e+00 -3.5992986322410760e+00 2.2680459788743503e+00
run_vel: ! |2
1 4.7093296226165726e-04 2.6351124312057366e-04 -4.4905063547614750e-04
2 4.9594635271877263e-04 9.4561409237139244e-05 -5.4581325723053519e-04
3 3.3306088119083079e-04 2.3224949911015511e-04 -2.3659435306900900e-04
4 3.3692332940286722e-04 2.1926824120529738e-04 -2.4716611858556574e-04
5 3.3642541894624012e-04 4.1797578053943767e-04 -1.8011323945929113e-04
6 2.0926870695908297e-04 2.6449376032441903e-05 -1.0508922741401427e-04
7 1.4629046128362941e-04 -1.6873362379723111e-04 -6.8353900724071745e-05
8 1.5844098346817935e-04 3.7728756087619165e-05 -1.9162577392849147e-05
9 2.1299357198252962e-04 1.6917133003966793e-04 -6.3528006071199972e-05
10 5.4261569071245965e-05 -9.4655546204698774e-05 1.0511372702289789e-04
11 -3.2194218121522970e-05 -2.2025090185602350e-04 2.0300208519292848e-04
12 1.2640585449263589e-04 -2.9851081600946756e-04 -7.9476186245575178e-05
13 8.4523551795102697e-05 -4.0583140303608210e-04 -4.7550925831930561e-05
14 9.9954071734164248e-05 -4.2610809338913878e-04 -7.9255453072661758e-05
15 2.4417483202630007e-04 -2.3521005781669015e-04 -2.4875292755151984e-04
16 -9.0959360838839976e-06 3.7773746063194848e-06 2.4035204669042588e-04
17 5.7507084250806896e-05 2.2629200960629374e-04 2.0686926033794661e-04
1 4.7093296226165759e-04 2.6351124312057290e-04 -4.4905063547614669e-04
2 4.9594635271877263e-04 9.4561409237138512e-05 -5.4581325723053421e-04
3 3.3306088119083101e-04 2.3224949911015481e-04 -2.3659435306900835e-04
4 3.3692332940286717e-04 2.1926824120529722e-04 -2.4716611858556465e-04
5 3.3642541894624077e-04 4.1797578053943724e-04 -1.8011323945929064e-04
6 2.0926870695908283e-04 2.6449376032441855e-05 -1.0508922741401397e-04
7 1.4629046128362884e-04 -1.6873362379723068e-04 -6.8353900724071325e-05
8 1.5844098346817943e-04 3.7728756087619084e-05 -1.9162577392849316e-05
9 2.1299357198253002e-04 1.6917133003966749e-04 -6.3528006071200284e-05
10 5.4261569071245856e-05 -9.4655546204698666e-05 1.0511372702289738e-04
11 -3.2194218121523431e-05 -2.2025090185602293e-04 2.0300208519292805e-04
12 1.2640585449263546e-04 -2.9851081600946745e-04 -7.9476186245575585e-05
13 8.4523551795102263e-05 -4.0583140303608199e-04 -4.7550925831931374e-05
14 9.9954071734163435e-05 -4.2610809338913835e-04 -7.9255453072661880e-05
15 2.4417483202629980e-04 -2.3521005781669047e-04 -2.4875292755152005e-04
16 -9.0959360838836724e-06 3.7773746063194780e-06 2.4035204669042463e-04
17 5.7507084250807628e-05 2.2629200960629336e-04 2.0686926033794547e-04
18 -6.0936815808025862e-04 -9.3774557532468582e-04 -3.3558072507805731e-04
19 -6.9919768291957119e-04 -3.6060777270430031e-03 4.2833405289822791e-03
20 4.7777805013736515e-03 5.1003745845520452e-03 1.8002873923729241e-03

43
unittest/force-styles/tests/fix-timestep-rigid_small.yaml
View File

@ -1,7 +1,6 @@
---
lammps_version: 7 Feb 2024
tags:
date_generated: Mon Mar 25 20:01:05 2024
lammps_version: 17 Feb 2022
date_generated: Fri Mar 18 22:18:00 2022
epsilon: 5e-13
skip_tests:
prerequisites: ! |
@ -15,8 +14,8 @@ post_commands: ! |
input_file: in.fourmol
natoms: 29
run_stress: ! |-
-4.9200116134788615e+01 -2.6907707565987401e+01 -6.0080860422276308e+00 -2.5620423972100241e+01 -1.3450224059984270e+01 -1.4947288487006070e+00
global_scalar: 18.340560167414402
-4.9200116134789873e+01 -2.6907707565987707e+01 -6.0080860422278581e+00 -2.5620423972101300e+01 -1.3450224059983967e+01 -1.4947288487003760e+00
global_scalar: 18.3405601674144
run_pos: ! |2
1 -2.7993683669226832e-01 2.4726588069312840e+00 -1.7200860244148433e-01
2 3.0197083955402204e-01 2.9515239068888608e+00 -8.5689735572907566e-01
@ -35,15 +34,15 @@ run_pos: ! |2
15 2.9756315249791303e+00 5.6334269722969288e-01 -1.2437650754599008e+00
16 2.6517554244980306e+00 -2.3957110424978438e+00 3.2908335999178327e-02
17 2.2309964792710639e+00 -2.1022918943319384e+00 1.1491948328949437e+00
18 2.1392027588271301e+00 3.0171068018412783e+00 -3.5144628518856353e+00
19 1.5366124997074575e+00 2.6286809834111740e+00 -4.2452547844370221e+00
20 2.7628161763455852e+00 3.6842251687634775e+00 -3.9370881219352558e+00
21 4.9036621347791236e+00 -4.0757648442838548e+00 -3.6192617654515908e+00
22 4.3655322291888474e+00 -4.2084949965552561e+00 -4.4622011117402343e+00
23 5.7380414793463110e+00 -3.5841969195032672e+00 -3.8827839830470219e+00
18 2.1392027588271301e+00 3.0171068018412779e+00 -3.5144628518856349e+00
19 1.5366124997074571e+00 2.6286809834111748e+00 -4.2452547844370221e+00
20 2.7628161763455852e+00 3.6842251687634775e+00 -3.9370881219352554e+00
21 4.9036621347791245e+00 -4.0757648442838548e+00 -3.6192617654515904e+00
22 4.3655322291888483e+00 -4.2084949965552561e+00 -4.4622011117402334e+00
23 5.7380414793463101e+00 -3.5841969195032672e+00 -3.8827839830470219e+00
24 2.0701314765323930e+00 3.1499370533342330e+00 3.1565324852522938e+00
25 1.3030170721374787e+00 3.2711173927682244e+00 2.5081940917429759e+00
26 2.5776230782480041e+00 4.0127347068243884e+00 3.2182355138709284e+00
25 1.3030170721374779e+00 3.2711173927682249e+00 2.5081940917429768e+00
26 2.5776230782480045e+00 4.0127347068243875e+00 3.2182355138709275e+00
27 -1.9613581876744359e+00 -4.3556300596085160e+00 2.1101467673534788e+00
28 -2.7406520384725965e+00 -4.0207251278130975e+00 1.5828689861678511e+00
29 -1.3108232656499081e+00 -3.5992986322410760e+00 2.2680459788743503e+00
@ -65,15 +64,15 @@ run_vel: ! |2
15 -4.3301707382721859e-03 -3.1802661664634938e-03 3.2037919043360571e-03
16 -9.6715751018414326e-05 -5.0016572678960377e-04 1.4945658875149626e-03
17 6.5692180538157174e-04 3.6635779995305095e-04 8.3495414466050911e-04
18 3.6149625095704849e-04 -3.1032459262908286e-04 8.1043030117346052e-04
19 8.5103884665345473e-04 -1.4572280596788095e-03 1.0163621287634121e-03
20 -6.5204659278590661e-04 4.3989037444289755e-04 4.9909839028507901e-04
21 -1.3888125881903906e-03 -3.1978049143082342e-04 1.1455681499836646e-03
22 -1.6084223477729526e-03 -1.5355394240821163e-03 1.4772010826232394e-03
23 2.6392672378804821e-04 -3.9375414431174795e-03 -3.6991583139728377e-04
24 8.6062827067890269e-04 -9.4179873474469291e-04 5.5396395550012388e-04
25 1.5933645477487551e-03 -2.2139156625681673e-03 -5.5078029695647250e-04
26 -1.5679561743998888e-03 3.5146224354726068e-04 2.4446924193334487e-03
18 3.6149625095704914e-04 -3.1032459262908286e-04 8.1043030117346052e-04
19 8.5103884665345452e-04 -1.4572280596788108e-03 1.0163621287634116e-03
20 -6.5204659278590683e-04 4.3989037444289853e-04 4.9909839028507901e-04
21 -1.3888125881903923e-03 -3.1978049143082385e-04 1.1455681499836646e-03
22 -1.6084223477729510e-03 -1.5355394240821117e-03 1.4772010826232375e-03
23 2.6392672378805124e-04 -3.9375414431174821e-03 -3.6991583139728095e-04
24 8.6062827067890247e-04 -9.4179873474469237e-04 5.5396395550012453e-04
25 1.5933645477487538e-03 -2.2139156625681695e-03 -5.5078029695647401e-04
26 -1.5679561743998840e-03 3.5146224354726100e-04 2.4446924193334478e-03
27 -2.6510179146429716e-04 3.6306203629019116e-04 -5.6235585400647747e-04
28 -2.3068708109787484e-04 -8.5663070212203200e-04 2.1302563179109169e-03
29 -2.5054744388303732e-03 -1.6773997805290820e-04 2.8436699761004796e-03

288
unittest/formats/test_atom_styles.cpp
View File

@ -1922,58 +1922,70 @@ TEST_F(AtomStyleTest, tri)
EXPECT_NEAR(radius[GETIDX(5)], 0.5, EPSILON);
EXPECT_NEAR(radius[GETIDX(6)], 0.5, EPSILON);
EXPECT_NEAR(bonus[0].inertia[2], 14.017974903242481, EPSILON);
EXPECT_NEAR(bonus[0].inertia[0], 14.017974903242481, EPSILON);
EXPECT_NEAR(bonus[0].inertia[1], 13.94589575227541, EPSILON);
EXPECT_NEAR(bonus[0].inertia[0], 0.072258416330334363, EPSILON);
EXPECT_NEAR(bonus[1].inertia[2], 13.982119044342252, EPSILON);
EXPECT_NEAR(bonus[0].inertia[2], 0.072258416330334363, EPSILON);
EXPECT_NEAR(bonus[1].inertia[0], 13.982119044342252, EPSILON);
EXPECT_NEAR(bonus[1].inertia[1], 13.945895752275419, EPSILON);
EXPECT_NEAR(bonus[1].inertia[0], 0.10811427523057447, EPSILON);
EXPECT_NEAR(bonus[2].inertia[2], 19.15175691481879, EPSILON);
EXPECT_NEAR(bonus[1].inertia[2], 0.10811427523057447, EPSILON);
EXPECT_NEAR(bonus[2].inertia[0], 19.15175691481879, EPSILON);
EXPECT_NEAR(bonus[2].inertia[1], 18.948744087979005, EPSILON);
EXPECT_NEAR(bonus[2].inertia[0], 0.23541253382609079, EPSILON);
EXPECT_NEAR(bonus[3].inertia[2], 19.018309360029388, EPSILON);
EXPECT_NEAR(bonus[2].inertia[2], 0.23541253382609079, EPSILON);
EXPECT_NEAR(bonus[3].inertia[0], 19.018309360029388, EPSILON);
EXPECT_NEAR(bonus[3].inertia[1], 18.948744087979012, EPSILON);
EXPECT_NEAR(bonus[3].inertia[0], 0.36886008861549813, EPSILON);
EXPECT_NEAR(bonus[0].quat[0], 0.92373678792937974, EPSILON);
EXPECT_NEAR(bonus[0].quat[1], 0.0067268233964605136, EPSILON);
EXPECT_NEAR(bonus[0].quat[2], 0.016239988275423622, EPSILON);
EXPECT_NEAR(bonus[0].quat[3], -0.38262430562330857, EPSILON);
EXPECT_NEAR(bonus[1].quat[0], 0.63633478678991862, EPSILON);
EXPECT_NEAR(bonus[1].quat[1], 0.66894644809679971, EPSILON);
EXPECT_NEAR(bonus[1].quat[2], 0.26478147716387457, EPSILON);
EXPECT_NEAR(bonus[1].quat[3], 0.27835132126616718, EPSILON);
EXPECT_NEAR(bonus[2].quat[0], 0.90191325590647375, EPSILON);
EXPECT_NEAR(bonus[2].quat[1], 0.2009681312851252, EPSILON);
EXPECT_NEAR(bonus[2].quat[2], 0.1002758475123109, EPSILON);
EXPECT_NEAR(bonus[2].quat[3], 0.36892959143125958, EPSILON);
EXPECT_NEAR(bonus[3].quat[0], 0.34503278332913523, EPSILON);
EXPECT_NEAR(bonus[3].quat[1], 0.17090845404750615, EPSILON);
EXPECT_NEAR(bonus[3].quat[2], 0.44689296000042461, EPSILON);
EXPECT_NEAR(bonus[3].quat[3], 0.80748335033318219, EPSILON);
EXPECT_NEAR(bonus[0].c1[0], -0.14933690186163626, EPSILON);
EXPECT_NEAR(bonus[0].c1[2], -0.0052525338293288879, EPSILON);
EXPECT_NEAR(bonus[1].c1[0], -0.18681344121910512, EPSILON);
EXPECT_NEAR(bonus[1].c1[2], 0.18561232929671317, EPSILON);
EXPECT_NEAR(bonus[2].c1[0], -0.78775285695558628, EPSILON);
EXPECT_NEAR(bonus[2].c1[2], -0.22123552085772158, EPSILON);
EXPECT_NEAR(bonus[3].c1[0], -0.47901475403318072, EPSILON);
EXPECT_NEAR(bonus[3].c1[2], -0.69845793336676587, EPSILON);
EXPECT_NEAR(bonus[0].c2[0], 0.55733290519255363, EPSILON);
EXPECT_NEAR(bonus[0].c2[2], 0.019602723119529656, EPSILON);
EXPECT_NEAR(bonus[1].c2[0], -0.22223836695322477, EPSILON);
EXPECT_NEAR(bonus[1].c2[2], 0.22080949143752887, EPSILON);
EXPECT_NEAR(bonus[2].c2[0], 0.63043795621810073, EPSILON);
EXPECT_NEAR(bonus[2].c2[2], 0.17705460333259254, EPSILON);
EXPECT_NEAR(bonus[3].c2[0], 0.15093208974463557, EPSILON);
EXPECT_NEAR(bonus[3].c2[2], 0.22007613459534847, EPSILON);
EXPECT_NEAR(bonus[0].c3[0], -0.4079960033309174, EPSILON);
EXPECT_NEAR(bonus[0].c3[2], -0.014350189290200809, EPSILON);
EXPECT_NEAR(bonus[1].c3[0], 0.40905180817232961, EPSILON);
EXPECT_NEAR(bonus[1].c3[2], -0.40642182073424171, EPSILON);
EXPECT_NEAR(bonus[2].c3[0], 0.15731490073748589, EPSILON);
EXPECT_NEAR(bonus[2].c3[2], 0.044180917525128927, EPSILON);
EXPECT_NEAR(bonus[3].c3[0], 0.32808266428854477, EPSILON);
EXPECT_NEAR(bonus[3].c3[2], 0.4783817987714174, EPSILON);
EXPECT_NEAR(bonus[3].inertia[2], 0.36886008861549813, EPSILON);
EXPECT_NEAR(bonus[0].quat[0], 0.66466395261228639, EPSILON);
EXPECT_NEAR(bonus[0].quat[1], -0.26579965871355399, EPSILON);
EXPECT_NEAR(bonus[0].quat[2], -0.64169714094040209, EPSILON);
EXPECT_NEAR(bonus[0].quat[3], -0.27531282359251713, EPSILON);
EXPECT_NEAR(bonus[1].quat[0], 0.63718542087921404, EPSILON);
EXPECT_NEAR(bonus[1].quat[1], 0.66984067651944412, EPSILON);
EXPECT_NEAR(bonus[1].quat[2], -0.26272786480888066, EPSILON);
EXPECT_NEAR(bonus[1].quat[3], -0.27619246288035992, EPSILON);
EXPECT_NEAR(bonus[2].quat[0], 0.70865471105868871, EPSILON);
EXPECT_NEAR(bonus[2].quat[1], 0.40297854431552654, EPSILON);
EXPECT_NEAR(bonus[2].quat[2], -0.56684324752832238, EPSILON);
EXPECT_NEAR(bonus[2].quat[3], 0.11876668744732566, EPSILON);
EXPECT_NEAR(bonus[3].quat[0], 0.55997606330452898, EPSILON);
EXPECT_NEAR(bonus[3].quat[1], 0.69182747953492685, EPSILON);
EXPECT_NEAR(bonus[3].quat[2], 0.072026021657128514, EPSILON);
EXPECT_NEAR(bonus[3].quat[3], 0.45012642589672475, EPSILON);
EXPECT_NEAR(bonus[0].c1[0], -0.0052525338293288905, EPSILON);
EXPECT_NEAR(bonus[0].c1[1], -0.55767753582520529, EPSILON);
EXPECT_NEAR(bonus[0].c1[2], 0.14933690186163631, EPSILON);
EXPECT_NEAR(bonus[1].c1[0], 0.18561232929671426, EPSILON);
EXPECT_NEAR(bonus[1].c1[1], 0.51379191773154387, EPSILON);
EXPECT_NEAR(bonus[1].c1[2], 0.18681344121910506, EPSILON);
EXPECT_NEAR(bonus[2].c1[0], -0.22123552085772166, EPSILON);
EXPECT_NEAR(bonus[2].c1[1], -0.28372571379613187, EPSILON);
EXPECT_NEAR(bonus[2].c1[2], 0.78775285695558617, EPSILON);
EXPECT_NEAR(bonus[3].c1[0], -0.69845793336676587, EPSILON);
EXPECT_NEAR(bonus[3].c1[1], 0.18083523090249506, EPSILON);
EXPECT_NEAR(bonus[3].c1[2], 0.47901475403318056, EPSILON);
EXPECT_NEAR(bonus[0].c2[0], 0.019602723119529659, EPSILON);
EXPECT_NEAR(bonus[0].c2[1], 0.14942924536134222, EPSILON);
EXPECT_NEAR(bonus[0].c2[2], -0.55733290519255385, EPSILON);
EXPECT_NEAR(bonus[1].c2[0], 0.2208094914375279, EPSILON);
EXPECT_NEAR(bonus[1].c2[1], -0.4849604211463005, EPSILON);
EXPECT_NEAR(bonus[1].c2[2], 0.22223836695322477, EPSILON);
EXPECT_NEAR(bonus[2].c2[0], 0.17705460333259249, EPSILON);
EXPECT_NEAR(bonus[2].c2[1], -0.56674478453558153, EPSILON);
EXPECT_NEAR(bonus[2].c2[2], -0.6304379562181005, EPSILON);
EXPECT_NEAR(bonus[3].c2[0], 0.22007613459534958, EPSILON);
EXPECT_NEAR(bonus[3].c2[1], -0.82388470022624394, EPSILON);
EXPECT_NEAR(bonus[3].c2[2], -0.15093208974463557, EPSILON);
EXPECT_NEAR(bonus[0].c3[0], -0.014350189290200811, EPSILON);
EXPECT_NEAR(bonus[0].c3[1], 0.40824829046386302, EPSILON);
EXPECT_NEAR(bonus[0].c3[2], 0.40799600333091751, EPSILON);
EXPECT_NEAR(bonus[1].c3[0], -0.40642182073424188, EPSILON);
EXPECT_NEAR(bonus[1].c3[1], -0.028831496585242929, EPSILON);
EXPECT_NEAR(bonus[1].c3[2], -0.40905180817232945, EPSILON);
EXPECT_NEAR(bonus[2].c3[0], 0.044180917525129149, EPSILON);
EXPECT_NEAR(bonus[2].c3[1], 0.85047049833171351, EPSILON);
EXPECT_NEAR(bonus[2].c3[2], -0.15731490073748589, EPSILON);
EXPECT_NEAR(bonus[3].c3[0], 0.47838179877141634, EPSILON);
EXPECT_NEAR(bonus[3].c3[1], 0.64304946932374796, EPSILON);
EXPECT_NEAR(bonus[3].c3[2], -0.32808266428854477, EPSILON);
BEGIN_HIDE_OUTPUT();
command("group two id 2:4:2");
@ -2036,58 +2048,70 @@ TEST_F(AtomStyleTest, tri)
EXPECT_NEAR(radius[GETIDX(11)], 0.5, EPSILON);
EXPECT_NEAR(radius[GETIDX(12)], 0.5, EPSILON);
EXPECT_NEAR(bonus[0].inertia[2], 14.017974903242481, EPSILON);
EXPECT_NEAR(bonus[0].inertia[0], 14.017974903242481, EPSILON);
EXPECT_NEAR(bonus[0].inertia[1], 13.94589575227541, EPSILON);
EXPECT_NEAR(bonus[0].inertia[0], 0.072258416330334363, EPSILON);
EXPECT_NEAR(bonus[1].inertia[2], 19.15175691481879, EPSILON);
EXPECT_NEAR(bonus[0].inertia[2], 0.072258416330334363, EPSILON);
EXPECT_NEAR(bonus[1].inertia[0], 19.15175691481879, EPSILON);
EXPECT_NEAR(bonus[1].inertia[1], 18.948744087979005, EPSILON);
EXPECT_NEAR(bonus[1].inertia[0], 0.23541253382609079, EPSILON);
EXPECT_NEAR(bonus[2].inertia[2], 14.017974903242481, EPSILON);
EXPECT_NEAR(bonus[1].inertia[2], 0.23541253382609079, EPSILON);
EXPECT_NEAR(bonus[2].inertia[0], 14.017974903242481, EPSILON);
EXPECT_NEAR(bonus[2].inertia[1], 13.94589575227541, EPSILON);
EXPECT_NEAR(bonus[2].inertia[0], 0.072258416330334363, EPSILON);
EXPECT_NEAR(bonus[3].inertia[2], 19.15175691481879, EPSILON);
EXPECT_NEAR(bonus[2].inertia[2], 0.072258416330334363, EPSILON);
EXPECT_NEAR(bonus[3].inertia[0], 19.15175691481879, EPSILON);
EXPECT_NEAR(bonus[3].inertia[1], 18.948744087979005, EPSILON);
EXPECT_NEAR(bonus[3].inertia[0], 0.23541253382609079, EPSILON);
EXPECT_NEAR(bonus[0].quat[0], 0.92373678792937974, EPSILON);
EXPECT_NEAR(bonus[0].quat[1], 0.0067268233964605136, EPSILON);
EXPECT_NEAR(bonus[0].quat[2], 0.016239988275423622, EPSILON);
EXPECT_NEAR(bonus[0].quat[3], -0.38262430562330857, EPSILON);
EXPECT_NEAR(bonus[1].quat[0], 0.90191325590647375, EPSILON);
EXPECT_NEAR(bonus[1].quat[1], 0.2009681312851252, EPSILON);
EXPECT_NEAR(bonus[1].quat[2], 0.1002758475123109, EPSILON);
EXPECT_NEAR(bonus[1].quat[3], 0.36892959143125958, EPSILON);
EXPECT_NEAR(bonus[2].quat[0], 0.92373678792937974, EPSILON);
EXPECT_NEAR(bonus[2].quat[1], 0.0067268233964605136, EPSILON);
EXPECT_NEAR(bonus[2].quat[2], 0.016239988275423622, EPSILON);
EXPECT_NEAR(bonus[2].quat[3], -0.38262430562330857, EPSILON);
EXPECT_NEAR(bonus[3].quat[0], 0.90191325590647375, EPSILON);
EXPECT_NEAR(bonus[3].quat[1], 0.2009681312851252, EPSILON);
EXPECT_NEAR(bonus[3].quat[2], 0.1002758475123109, EPSILON);
EXPECT_NEAR(bonus[3].quat[3], 0.36892959143125958, EPSILON);
EXPECT_NEAR(bonus[0].c1[0], -0.14933690186163626, EPSILON);
EXPECT_NEAR(bonus[0].c1[2], -0.0052525338293288879, EPSILON);
EXPECT_NEAR(bonus[1].c1[0], -0.78775285695558628, EPSILON);
EXPECT_NEAR(bonus[1].c1[2], -0.22123552085772158, EPSILON);
EXPECT_NEAR(bonus[2].c1[0], -0.14933690186163626, EPSILON);
EXPECT_NEAR(bonus[2].c1[2], -0.0052525338293288879, EPSILON);
EXPECT_NEAR(bonus[3].c1[0], -0.78775285695558628, EPSILON);
EXPECT_NEAR(bonus[3].c1[2], -0.22123552085772158, EPSILON);
EXPECT_NEAR(bonus[0].c2[0], 0.55733290519255363, EPSILON);
EXPECT_NEAR(bonus[0].c2[2], 0.019602723119529656, EPSILON);
EXPECT_NEAR(bonus[1].c2[0], 0.63043795621810073, EPSILON);
EXPECT_NEAR(bonus[1].c2[2], 0.17705460333259254, EPSILON);
EXPECT_NEAR(bonus[2].c2[0], 0.55733290519255363, EPSILON);
EXPECT_NEAR(bonus[2].c2[2], 0.019602723119529656, EPSILON);
EXPECT_NEAR(bonus[3].c2[0], 0.63043795621810073, EPSILON);
EXPECT_NEAR(bonus[3].c2[2], 0.17705460333259254, EPSILON);
EXPECT_NEAR(bonus[0].c3[0], -0.4079960033309174, EPSILON);
EXPECT_NEAR(bonus[0].c3[2], -0.014350189290200809, EPSILON);
EXPECT_NEAR(bonus[1].c3[0], 0.15731490073748589, EPSILON);
EXPECT_NEAR(bonus[1].c3[2], 0.044180917525128927, EPSILON);
EXPECT_NEAR(bonus[2].c3[0], -0.4079960033309174, EPSILON);
EXPECT_NEAR(bonus[2].c3[2], -0.014350189290200809, EPSILON);
EXPECT_NEAR(bonus[3].c3[0], 0.15731490073748589, EPSILON);
EXPECT_NEAR(bonus[3].c3[2], 0.044180917525128927, EPSILON);
EXPECT_NEAR(bonus[3].inertia[2], 0.23541253382609079, EPSILON);
EXPECT_NEAR(bonus[0].quat[0], 0.66466395261228639, EPSILON);
EXPECT_NEAR(bonus[0].quat[1], -0.26579965871355399, EPSILON);
EXPECT_NEAR(bonus[0].quat[2], -0.64169714094040209, EPSILON);
EXPECT_NEAR(bonus[0].quat[3], -0.27531282359251713, EPSILON);
EXPECT_NEAR(bonus[1].quat[0], 0.70865471105868871, EPSILON);
EXPECT_NEAR(bonus[1].quat[1], 0.40297854431552654, EPSILON);
EXPECT_NEAR(bonus[1].quat[2], -0.56684324752832238, EPSILON);
EXPECT_NEAR(bonus[1].quat[3], 0.11876668744732566, EPSILON);
EXPECT_NEAR(bonus[2].quat[0], 0.66466395261228639, EPSILON);
EXPECT_NEAR(bonus[2].quat[1], -0.26579965871355399, EPSILON);
EXPECT_NEAR(bonus[2].quat[2], -0.64169714094040209, EPSILON);
EXPECT_NEAR(bonus[2].quat[3], -0.27531282359251713, EPSILON);
EXPECT_NEAR(bonus[3].quat[0], 0.70865471105868871, EPSILON);
EXPECT_NEAR(bonus[3].quat[1], 0.40297854431552654, EPSILON);
EXPECT_NEAR(bonus[3].quat[2], -0.56684324752832238, EPSILON);
EXPECT_NEAR(bonus[3].quat[3], 0.11876668744732566, EPSILON);
EXPECT_NEAR(bonus[0].c1[0], -0.0052525338293288879, EPSILON);
EXPECT_NEAR(bonus[0].c1[1], -0.55767753582520529, EPSILON);
EXPECT_NEAR(bonus[0].c1[2], 0.14933690186163626, EPSILON);
EXPECT_NEAR(bonus[1].c1[0], -0.22123552085772158, EPSILON);
EXPECT_NEAR(bonus[1].c1[1], -0.28372571379613187, EPSILON);
EXPECT_NEAR(bonus[1].c1[2], 0.78775285695558628, EPSILON);
EXPECT_NEAR(bonus[2].c1[0], -0.0052525338293288905, EPSILON);
EXPECT_NEAR(bonus[2].c1[1], -0.55767753582520529, EPSILON);
EXPECT_NEAR(bonus[2].c1[2], 0.14933690186163631, EPSILON);
EXPECT_NEAR(bonus[3].c1[0], -0.22123552085772166, EPSILON);
EXPECT_NEAR(bonus[3].c1[1], -0.28372571379613187, EPSILON);
EXPECT_NEAR(bonus[3].c1[2], 0.78775285695558617, EPSILON);
EXPECT_NEAR(bonus[0].c2[0], 0.019602723119529659, EPSILON);
EXPECT_NEAR(bonus[0].c2[1], 0.14942924536134222, EPSILON);
EXPECT_NEAR(bonus[0].c2[2], -0.55733290519255385, EPSILON);
EXPECT_NEAR(bonus[1].c2[0], 0.17705460333259249, EPSILON);
EXPECT_NEAR(bonus[1].c2[1], -0.56674478453558153, EPSILON);
EXPECT_NEAR(bonus[1].c2[2], -0.6304379562181005, EPSILON);
EXPECT_NEAR(bonus[2].c2[0], 0.019602723119529659, EPSILON);
EXPECT_NEAR(bonus[2].c2[1], 0.14942924536134222, EPSILON);
EXPECT_NEAR(bonus[2].c2[2], -0.55733290519255385, EPSILON);
EXPECT_NEAR(bonus[3].c2[0], 0.17705460333259249, EPSILON);
EXPECT_NEAR(bonus[3].c2[1], -0.56674478453558153, EPSILON);
EXPECT_NEAR(bonus[3].c2[2], -0.6304379562181005, EPSILON);
EXPECT_NEAR(bonus[0].c3[0], -0.014350189290200811, EPSILON);
EXPECT_NEAR(bonus[0].c3[1], 0.40824829046386302, EPSILON);
EXPECT_NEAR(bonus[0].c3[2], 0.40799600333091751, EPSILON);
EXPECT_NEAR(bonus[1].c3[0], 0.044180917525129149, EPSILON);
EXPECT_NEAR(bonus[1].c3[1], 0.85047049833171351, EPSILON);
EXPECT_NEAR(bonus[1].c3[2], -0.15731490073748589, EPSILON);
EXPECT_NEAR(bonus[2].c3[0], -0.014350189290200811, EPSILON);
EXPECT_NEAR(bonus[2].c3[1], 0.40824829046386302, EPSILON);
EXPECT_NEAR(bonus[2].c3[2], 0.40799600333091751, EPSILON);
EXPECT_NEAR(bonus[3].c3[0], 0.044180917525129149, EPSILON);
EXPECT_NEAR(bonus[3].c3[1], 0.85047049833171351, EPSILON);
EXPECT_NEAR(bonus[3].c3[2], -0.15731490073748589, EPSILON);
BEGIN_HIDE_OUTPUT();
command("reset_atoms id");
@ -2116,18 +2140,18 @@ TEST_F(AtomStyleTest, tri)
ASSERT_EQ(tri[GETIDX(6)], -1);
ASSERT_EQ(tri[GETIDX(7)], 3);
ASSERT_EQ(tri[GETIDX(8)], -1);
EXPECT_NEAR(bonus[0].inertia[2], 14.017974903242481, EPSILON);
EXPECT_NEAR(bonus[0].inertia[0], 14.017974903242481, EPSILON);
EXPECT_NEAR(bonus[0].inertia[1], 13.94589575227541, EPSILON);
EXPECT_NEAR(bonus[0].inertia[0], 0.072258416330334363, EPSILON);
EXPECT_NEAR(bonus[1].inertia[2], 19.15175691481879, EPSILON);
EXPECT_NEAR(bonus[0].inertia[2], 0.072258416330334363, EPSILON);
EXPECT_NEAR(bonus[1].inertia[0], 19.15175691481879, EPSILON);
EXPECT_NEAR(bonus[1].inertia[1], 18.948744087979005, EPSILON);
EXPECT_NEAR(bonus[1].inertia[0], 0.23541253382609079, EPSILON);
EXPECT_NEAR(bonus[2].inertia[2], 14.017974903242481, EPSILON);
EXPECT_NEAR(bonus[1].inertia[2], 0.23541253382609079, EPSILON);
EXPECT_NEAR(bonus[2].inertia[0], 14.017974903242481, EPSILON);
EXPECT_NEAR(bonus[2].inertia[1], 13.94589575227541, EPSILON);
EXPECT_NEAR(bonus[2].inertia[0], 0.072258416330334363, EPSILON);
EXPECT_NEAR(bonus[3].inertia[2], 19.15175691481879, EPSILON);
EXPECT_NEAR(bonus[2].inertia[2], 0.072258416330334363, EPSILON);
EXPECT_NEAR(bonus[3].inertia[0], 19.15175691481879, EPSILON);
EXPECT_NEAR(bonus[3].inertia[1], 18.948744087979005, EPSILON);
EXPECT_NEAR(bonus[3].inertia[0], 0.23541253382609079, EPSILON);
EXPECT_NEAR(bonus[3].inertia[2], 0.23541253382609079, EPSILON);
}
TEST_F(AtomStyleTest, body_nparticle)
@ -2323,18 +2347,18 @@ TEST_F(AtomStyleTest, body_nparticle)
EXPECT_NEAR(radius[GETIDX(5)], 0.5, EPSILON);
EXPECT_NEAR(radius[GETIDX(6)], 0.5, EPSILON);
EXPECT_NEAR(bonus[0].inertia[2], 2.0, EPSILON);
EXPECT_NEAR(bonus[0].inertia[0], 2.0, EPSILON);
EXPECT_NEAR(bonus[0].inertia[1], 2.0, EPSILON);
EXPECT_NEAR(bonus[0].inertia[0], 0.0, EPSILON);
EXPECT_NEAR(bonus[1].inertia[2], 4.5, EPSILON);
EXPECT_NEAR(bonus[0].inertia[2], 0.0, EPSILON);
EXPECT_NEAR(bonus[1].inertia[0], 4.5, EPSILON);
EXPECT_NEAR(bonus[1].inertia[1], 4.0, EPSILON);
EXPECT_NEAR(bonus[1].inertia[0], 0.5, EPSILON);
EXPECT_NEAR(bonus[2].inertia[2], 1.7746273249544022, EPSILON);
EXPECT_NEAR(bonus[1].inertia[2], 0.5, EPSILON);
EXPECT_NEAR(bonus[2].inertia[0], 1.7746273249544022, EPSILON);
EXPECT_NEAR(bonus[2].inertia[1], 1.67188, EPSILON);
EXPECT_NEAR(bonus[2].inertia[0], 0.49099767504559777, EPSILON);
EXPECT_NEAR(bonus[3].inertia[2], 12.0, EPSILON);
EXPECT_NEAR(bonus[2].inertia[2], 0.49099767504559777, EPSILON);
EXPECT_NEAR(bonus[3].inertia[0], 12.0, EPSILON);
EXPECT_NEAR(bonus[3].inertia[1], 12.0, EPSILON);
EXPECT_NEAR(bonus[3].inertia[0], 0.0, EPSILON);
EXPECT_NEAR(bonus[3].inertia[2], 0.0, EPSILON);
EXPECT_NEAR(bonus[0].quat[0], 1.0, EPSILON);
EXPECT_NEAR(bonus[0].quat[1], 0.0, EPSILON);
EXPECT_NEAR(bonus[0].quat[2], 0.0, EPSILON);
@ -2495,18 +2519,18 @@ TEST_F(AtomStyleTest, body_nparticle)
EXPECT_NEAR(radius[GETIDX(5)], 0.5, EPSILON);
EXPECT_NEAR(radius[GETIDX(6)], 0.5, EPSILON);
EXPECT_NEAR(bonus[0].inertia[2], 2.0, EPSILON);
EXPECT_NEAR(bonus[0].inertia[0], 2.0, EPSILON);
EXPECT_NEAR(bonus[0].inertia[1], 2.0, EPSILON);
EXPECT_NEAR(bonus[0].inertia[0], 0.0, EPSILON);
EXPECT_NEAR(bonus[1].inertia[2], 4.5, EPSILON);
EXPECT_NEAR(bonus[0].inertia[2], 0.0, EPSILON);
EXPECT_NEAR(bonus[1].inertia[0], 4.5, EPSILON);
EXPECT_NEAR(bonus[1].inertia[1], 4.0, EPSILON);
EXPECT_NEAR(bonus[1].inertia[0], 0.5, EPSILON);
EXPECT_NEAR(bonus[2].inertia[2], 1.7746273249544022, EPSILON);
EXPECT_NEAR(bonus[1].inertia[2], 0.5, EPSILON);
EXPECT_NEAR(bonus[2].inertia[0], 1.7746273249544022, EPSILON);
EXPECT_NEAR(bonus[2].inertia[1], 1.67188, EPSILON);
EXPECT_NEAR(bonus[2].inertia[0], 0.49099767504559777, EPSILON);
EXPECT_NEAR(bonus[3].inertia[2], 12.0, EPSILON);
EXPECT_NEAR(bonus[2].inertia[2], 0.49099767504559777, EPSILON);
EXPECT_NEAR(bonus[3].inertia[0], 12.0, EPSILON);
EXPECT_NEAR(bonus[3].inertia[1], 12.0, EPSILON);
EXPECT_NEAR(bonus[3].inertia[0], 0.0, EPSILON);
EXPECT_NEAR(bonus[3].inertia[2], 0.0, EPSILON);
EXPECT_NEAR(bonus[0].quat[0], 1.0, EPSILON);
EXPECT_NEAR(bonus[0].quat[1], 0.0, EPSILON);
EXPECT_NEAR(bonus[0].quat[2], 0.0, EPSILON);
@ -2519,10 +2543,10 @@ TEST_F(AtomStyleTest, body_nparticle)
EXPECT_NEAR(bonus[2].quat[1], 0.25056280708573159, EPSILON);
EXPECT_NEAR(bonus[2].quat[2], 0.0, EPSILON);
EXPECT_NEAR(bonus[2].quat[3], 0.25056280708573148, EPSILON);
EXPECT_NEAR(bonus[3].quat[0], 0.070424771223903379, EPSILON);
EXPECT_NEAR(bonus[3].quat[1], 0.81345375914352225, EPSILON);
EXPECT_NEAR(bonus[3].quat[2], 0.56848787755882768, EPSILON);
EXPECT_NEAR(bonus[3].quat[3], -0.10077135705145905, EPSILON);
EXPECT_NEAR(bonus[3].quat[0], 0.62499650256800654, EPSILON);
EXPECT_NEAR(bonus[3].quat[1], 0.47323774316465234, EPSILON);
EXPECT_NEAR(bonus[3].quat[2], 0.33072552332373728, EPSILON);
EXPECT_NEAR(bonus[3].quat[3], 0.52540083597613996, EPSILON);
ASSERT_EQ(bonus[0].ilocal, 0);
ASSERT_EQ(bonus[1].ilocal, 1);
ASSERT_EQ(bonus[2].ilocal, 2);
@ -2610,18 +2634,18 @@ TEST_F(AtomStyleTest, body_nparticle)
EXPECT_NEAR(radius[GETIDX(9)], 0.5, EPSILON);
EXPECT_NEAR(radius[GETIDX(11)], 0.5, EPSILON);
EXPECT_NEAR(radius[GETIDX(12)], 0.5, EPSILON);
EXPECT_NEAR(bonus[0].inertia[2], 2.0, EPSILON);
EXPECT_NEAR(bonus[0].inertia[0], 2.0, EPSILON);
EXPECT_NEAR(bonus[0].inertia[1], 2.0, EPSILON);
EXPECT_NEAR(bonus[0].inertia[0], 0.0, EPSILON);
EXPECT_NEAR(bonus[1].inertia[2], 1.7746273249544022, EPSILON);
EXPECT_NEAR(bonus[0].inertia[2], 0.0, EPSILON);
EXPECT_NEAR(bonus[1].inertia[0], 1.7746273249544022, EPSILON);
EXPECT_NEAR(bonus[1].inertia[1], 1.67188, EPSILON);
EXPECT_NEAR(bonus[1].inertia[0], 0.49099767504559777, EPSILON);
EXPECT_NEAR(bonus[2].inertia[2], 2.0, EPSILON);
EXPECT_NEAR(bonus[1].inertia[2], 0.49099767504559777, EPSILON);
EXPECT_NEAR(bonus[2].inertia[0], 2.0, EPSILON);
EXPECT_NEAR(bonus[2].inertia[1], 2.0, EPSILON);
EXPECT_NEAR(bonus[2].inertia[0], 0.0, EPSILON);
EXPECT_NEAR(bonus[3].inertia[2], 1.7746273249544022, EPSILON);
EXPECT_NEAR(bonus[2].inertia[2], 0.0, EPSILON);
EXPECT_NEAR(bonus[3].inertia[0], 1.7746273249544022, EPSILON);
EXPECT_NEAR(bonus[3].inertia[1], 1.67188, EPSILON);
EXPECT_NEAR(bonus[3].inertia[0], 0.49099767504559777, EPSILON);
EXPECT_NEAR(bonus[3].inertia[2], 0.49099767504559777, EPSILON);
EXPECT_NEAR(bonus[0].quat[0], 1.0, EPSILON);
EXPECT_NEAR(bonus[0].quat[1], 0.0, EPSILON);
EXPECT_NEAR(bonus[0].quat[2], 0.0, EPSILON);