forked from lijiext/lammps
338 lines
19 KiB
Groff
338 lines
19 KiB
Groff
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
|