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clean up doc src

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This commit is contained in:
Steve Plimpton
2016-10-06 13:00:46 -06:00
parent 02bfa898ee
commit 493873fb93
458 changed files with 16897 additions and 11014 deletions
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72
examples/friction/log.15Feb16.friction.g++.1 → examples/friction/log.5Oct16.friction.g++.1
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@ -1,4 +1,4 @@
LAMMPS (15 Feb 2016)
LAMMPS (5 Oct 2016)
# 2d friction simulation
dimension 2
@ -94,7 +94,7 @@ fix 4 all enforce2d
timestep 0.0025
thermo 1000
thermo_modify temp new
WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:445)
WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:474)
#dump 1 all atom 500 dump.friction
@ -114,51 +114,51 @@ Neighbor list info ...
binsize = 1.4 -> bins = 41 31 1
Memory usage per processor = 2.47434 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 0.1 -3.1333672 0 -3.0921259 -1.1437867 2444.9333
1000 0.1 -3.0915465 0 -3.0503052 0.010015559 2444.9333
2000 0.1 -3.0826487 0 -3.0414074 -0.42012889 2444.9333
3000 0.089819692 -3.07584 0 -3.0387972 -0.25252108 2444.9333
4000 0.098489874 -3.0667093 0 -3.0260907 -0.25506538 2444.9333
5000 0.11379986 -3.0557087 0 -3.0087762 -0.080871179 2444.9333
6000 0.11269179 -3.04532 0 -2.9988445 -0.33381202 2444.9333
7000 0.1 -3.0380599 0 -2.9968186 -0.32423949 2444.9333
8000 0.1 -3.0346451 0 -2.9934038 -0.38015467 2444.9333
9000 0.1 -3.0328231 0 -2.9915818 -0.43229228 2444.9333
10000 0.11715901 -3.0339975 0 -2.9856796 -0.32994136 2444.9333
11000 0.11489931 -3.0347978 0 -2.9874118 -0.45189608 2444.9333
12000 0.10977417 -3.0396002 0 -2.994328 -0.18902632 2444.9333
13000 0.1 -3.0460576 0 -3.0048163 -0.30636366 2444.9333
14000 0.10650444 -3.0498066 0 -3.0058827 -0.37168966 2444.9333
15000 0.11262528 -3.053675 0 -3.0072269 -0.32295729 2444.9333
16000 0.10822084 -3.0524308 0 -3.0077991 -0.25034257 2444.9333
17000 0.10833465 -3.0487557 0 -3.0040771 -0.4048054 2444.9333
18000 0.11599608 -3.0540506 0 -3.0062123 -0.30721348 2444.9333
19000 0.11303674 -3.0521905 0 -3.0055727 -0.29399612 2444.9333
20000 0.09925739 -3.0483895 0 -3.0074545 -0.34540139 2444.9333
Loop time of 5.95865 on 1 procs for 20000 steps with 1724 atoms
0 0.1 -3.1333672 0 -3.0920969 -1.1437663 2444.9333
1000 0.1 -3.0915072 0 -3.0502369 0.0099866805 2444.9333
2000 0.1 -3.0826007 0 -3.0413304 -0.41998885 2444.9333
3000 0.08982505 -3.0757908 0 -3.0387197 -0.25244271 2444.9333
4000 0.098727892 -3.0666371 0 -3.0258918 -0.25382683 2444.9333
5000 0.11345478 -3.0506905 0 -3.0038674 -0.029177812 2444.9333
6000 0.11386723 -3.0515296 0 -3.0045363 -0.32135016 2444.9333
7000 0.11555642 -3.0379879 0 -2.9902974 -0.40431666 2444.9333
8000 0.10658282 -3.0364048 0 -2.9924178 -0.45722834 2444.9333
9000 0.11650947 -3.0271611 0 -2.9790773 -0.4588819 2444.9333
10000 0.10575546 -3.0298463 0 -2.9862007 -0.35241095 2444.9333
11000 0.10953331 -3.0352955 0 -2.9900908 -0.4622173 2444.9333
12000 0.11720787 -3.0378371 0 -2.989465 -0.27733023 2444.9333
13000 0.11492573 -3.037974 0 -2.9905438 -0.43259084 2444.9333
14000 0.11125454 -3.0413758 0 -2.9954607 -0.31244429 2444.9333
15000 0.10882772 -3.0406062 0 -2.9956927 -0.30403665 2444.9333
16000 0.1152685 -3.0433936 0 -2.9958219 -0.26659294 2444.9333
17000 0.10840025 -3.0414208 0 -2.9966837 -0.36183887 2444.9333
18000 0.11159326 -3.0416392 0 -2.9955843 -0.22725121 2444.9333
19000 0.11530974 -3.0457005 0 -2.9981118 -0.36488457 2444.9333
20000 0.1131733 -3.0417814 0 -2.9950744 -0.27902539 2444.9333
Loop time of 5.78572 on 1 procs for 20000 steps with 1724 atoms
Performance: 724995.927 tau/day, 3356.463 timesteps/s
Performance: 746665.546 tau/day, 3456.785 timesteps/s
99.9% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 4.8617 | 4.8617 | 4.8617 | 0.0 | 81.59
Neigh | 0.33399 | 0.33399 | 0.33399 | 0.0 | 5.61
Comm | 0.036682 | 0.036682 | 0.036682 | 0.0 | 0.62
Output | 0.00041318 | 0.00041318 | 0.00041318 | 0.0 | 0.01
Modify | 0.57978 | 0.57978 | 0.57978 | 0.0 | 9.73
Other | | 0.1461 | | | 2.45
Pair | 4.7167 | 4.7167 | 4.7167 | 0.0 | 81.52
Neigh | 0.30734 | 0.30734 | 0.30734 | 0.0 | 5.31
Comm | 0.036082 | 0.036082 | 0.036082 | 0.0 | 0.62
Output | 0.00039339 | 0.00039339 | 0.00039339 | 0.0 | 0.01
Modify | 0.57194 | 0.57194 | 0.57194 | 0.0 | 9.89
Other | | 0.1533 | | | 2.65
Nlocal: 1724 ave 1724 max 1724 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 145 ave 145 max 145 min
Nghost: 144 ave 144 max 144 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 14387 ave 14387 max 14387 min
Neighs: 14364 ave 14364 max 14364 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 14387
Ave neighs/atom = 8.34513
Neighbor list builds = 726
Total # of neighbors = 14364
Ave neighs/atom = 8.33179
Neighbor list builds = 714
Dangerous builds = 0
Total wall time: 0:00:05

82
examples/friction/log.15Feb16.friction.g++.4 → examples/friction/log.5Oct16.friction.g++.4
View File

@ -1,4 +1,4 @@
LAMMPS (15 Feb 2016)
LAMMPS (5 Oct 2016)
# 2d friction simulation
dimension 2
@ -94,7 +94,7 @@ fix 4 all enforce2d
timestep 0.0025
thermo 1000
thermo_modify temp new
WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:445)
WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:474)
#dump 1 all atom 500 dump.friction
@ -114,51 +114,51 @@ Neighbor list info ...
binsize = 1.4 -> bins = 41 31 1
Memory usage per processor = 2.47775 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 0.1 -3.1333672 0 -3.0921259 -1.1437867 2444.9333
1000 0.081958665 -3.0927273 0 -3.0589265 -0.021846131 2444.9333
2000 0.082641883 -3.0850764 0 -3.0509938 -0.44960195 2444.9333
3000 0.092293442 -3.0748001 0 -3.0367371 -0.25353161 2444.9333
4000 0.096012911 -3.0565129 0 -3.0169159 -0.027669541 2444.9333
5000 0.1 -3.0465555 0 -3.0053142 -0.099323956 2444.9333
6000 0.11642983 -3.0390782 0 -2.991061 -0.21034609 2444.9333
7000 0.11597774 -3.0331763 0 -2.9853456 -0.46345898 2444.9333
8000 0.11937908 -3.0305561 0 -2.9813227 -0.3077312 2444.9333
9000 0.11110633 -3.0274042 0 -2.9815825 -0.52435329 2444.9333
10000 0.11593138 -3.0164989 0 -2.9686873 -0.36943466 2444.9333
11000 0.11066412 -3.0156369 0 -2.9699976 -0.46759658 2444.9333
12000 0.10383247 -3.0199664 0 -2.9771445 -0.27390498 2444.9333
13000 0.11288647 -3.027191 0 -2.9806352 -0.38261516 2444.9333
14000 0.10587004 -3.0302799 0 -2.9866177 -0.20888958 2444.9333
15000 0.11092262 -3.0308702 0 -2.9851243 -0.37310523 2444.9333
16000 0.11258624 -3.0421958 0 -2.9957638 -0.27895709 2444.9333
17000 0.10980848 -3.0388353 0 -2.9935488 -0.31492687 2444.9333
18000 0.11125763 -3.0392991 0 -2.993415 -0.30414022 2444.9333
19000 0.11673298 -3.0405242 0 -2.992382 -0.34902574 2444.9333
20000 0.11753441 -3.0437232 0 -2.9952505 -0.31244935 2444.9333
Loop time of 1.96189 on 4 procs for 20000 steps with 1724 atoms
0 0.1 -3.1333672 0 -3.0920969 -1.1437663 2444.9333
1000 0.081947197 -3.0926906 0 -3.0588707 -0.021905504 2444.9333
2000 0.082643627 -3.0850391 0 -3.0509318 -0.44951926 2444.9333
3000 0.09228068 -3.0747307 0 -3.0366461 -0.25332113 2444.9333
4000 0.096009906 -3.0564001 0 -3.0167765 -0.026756079 2444.9333
5000 0.11991393 -3.0463606 0 -2.9968718 -0.095571711 2444.9333
6000 0.11344201 -3.0428779 0 -2.9960601 -0.28750906 2444.9333
7000 0.11932053 -3.0297394 0 -2.9804955 -0.44411602 2444.9333
8000 0.11472412 -3.0260173 0 -2.9786703 -0.45505281 2444.9333
9000 0.1153823 -3.0172996 0 -2.969681 -0.54699367 2444.9333
10000 0.1110096 -3.0180324 0 -2.9722184 -0.28712224 2444.9333
11000 0.10553488 -3.0281386 0 -2.984584 -0.40414683 2444.9333
12000 0.10913279 -3.0339553 0 -2.9889159 -0.23876138 2444.9333
13000 0.10791089 -3.036479 0 -2.9919439 -0.4066437 2444.9333
14000 0.11089726 -3.0434547 0 -2.9976871 -0.25931118 2444.9333
15000 0.10791244 -3.0452052 0 -3.0006694 -0.31309363 2444.9333
16000 0.11451836 -3.0490643 0 -3.0018023 -0.28317436 2444.9333
17000 0.10861713 -3.044417 0 -2.9995904 -0.39120148 2444.9333
18000 0.11086121 -3.0462098 0 -3.0004571 -0.19272619 2444.9333
19000 0.11407977 -3.046791 0 -2.99971 -0.29824356 2444.9333
20000 0.11532037 -3.0463959 0 -2.9988028 -0.3435294 2444.9333
Loop time of 1.90668 on 4 procs for 20000 steps with 1724 atoms
Performance: 2201963.286 tau/day, 10194.274 timesteps/s
99.3% CPU use with 4 MPI tasks x no OpenMP threads
Performance: 2265719.994 tau/day, 10489.444 timesteps/s
99.4% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 1.0666 | 1.2376 | 1.4382 | 12.1 | 63.08
Neigh | 0.072524 | 0.085115 | 0.099557 | 3.4 | 4.34
Comm | 0.16011 | 0.38337 | 0.56903 | 24.0 | 19.54
Output | 0.00041413 | 0.00043744 | 0.0005033 | 0.2 | 0.02
Modify | 0.12679 | 0.14438 | 0.15946 | 3.2 | 7.36
Other | | 0.111 | | | 5.66
Pair | 1.0349 | 1.1944 | 1.3574 | 10.5 | 62.64
Neigh | 0.070767 | 0.082252 | 0.094675 | 3.0 | 4.31
Comm | 0.19432 | 0.3776 | 0.54764 | 20.4 | 19.80
Output | 0.00043559 | 0.00045842 | 0.00052333 | 0.2 | 0.02
Modify | 0.12252 | 0.14002 | 0.15438 | 3.1 | 7.34
Other | | 0.112 | | | 5.87
Nlocal: 431 ave 495 max 377 min
Histogram: 1 0 1 0 0 1 0 0 0 1
Nghost: 96 ave 125 max 74 min
Histogram: 1 1 0 0 0 1 0 0 0 1
Neighs: 3597.75 ave 4233 max 3149 min
Histogram: 1 1 0 0 0 1 0 0 0 1
Nlocal: 431 ave 479 max 377 min
Histogram: 1 1 0 0 0 0 0 0 0 2
Nghost: 99.25 ave 120 max 81 min
Histogram: 1 1 0 0 0 0 1 0 0 1
Neighs: 3597 ave 4064 max 3146 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Total # of neighbors = 14391
Ave neighs/atom = 8.34745
Neighbor list builds = 704
Total # of neighbors = 14388
Ave neighs/atom = 8.34571
Neighbor list builds = 717
Dangerous builds = 0
Total wall time: 0:00:01