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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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46
examples/micelle/log.15Feb16.micelle.g++.1 → examples/micelle/log.5Oct16.micelle.g++.1
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@ -1,4 +1,4 @@
LAMMPS (15 Feb 2016)
LAMMPS (5 Oct 2016)
# 2d micelle simulation
dimension 2
@ -51,7 +51,7 @@ Neighbor list info ...
master list distance cutoff = 1.42246
ghost atom cutoff = 1.42246
binsize = 0.71123 -> bins = 51 51 1
Memory usage per processor = 2.98958 Mbytes
Memory usage per processor = 3.45296 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
@ -74,21 +74,21 @@ Step Temp E_pair E_mol TotEng Press
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 0.188732 on 1 procs for 1000 steps with 1200 atoms
Loop time of 0.192637 on 1 procs for 1000 steps with 1200 atoms
Performance: 2288961.113 tau/day, 5298.521 timesteps/s
100.1% CPU use with 1 MPI tasks x no OpenMP threads
Performance: 2242560.228 tau/day, 5191.112 timesteps/s
99.7% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.13192 | 0.13192 | 0.13192 | 0.0 | 69.90
Bond | 0.0065749 | 0.0065749 | 0.0065749 | 0.0 | 3.48
Neigh | 0.021622 | 0.021622 | 0.021622 | 0.0 | 11.46
Comm | 0.003341 | 0.003341 | 0.003341 | 0.0 | 1.77
Output | 0.00019431 | 0.00019431 | 0.00019431 | 0.0 | 0.10
Modify | 0.020563 | 0.020563 | 0.020563 | 0.0 | 10.90
Other | | 0.004518 | | | 2.39
Pair | 0.13348 | 0.13348 | 0.13348 | 0.0 | 69.29
Bond | 0.0066328 | 0.0066328 | 0.0066328 | 0.0 | 3.44
Neigh | 0.023894 | 0.023894 | 0.023894 | 0.0 | 12.40
Comm | 0.0032849 | 0.0032849 | 0.0032849 | 0.0 | 1.71
Output | 0.00019765 | 0.00019765 | 0.00019765 | 0.0 | 0.10
Modify | 0.020029 | 0.020029 | 0.020029 | 0.0 | 10.40
Other | | 0.005115 | | | 2.66
Nlocal: 1200 ave 1200 max 1200 min
Histogram: 1 0 0 0 0 0 0 0 0 0
@ -150,7 +150,7 @@ Neighbor list info ...
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4 -> bins = 26 26 1
Memory usage per processor = 2.98958 Mbytes
Memory usage per processor = 3.45296 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0.45 -1.7056163 0.08808163 -1.1679097 3.9431686
1000 0.45 -1.9727655 0.058608718 -1.4645318 1.9982299
@ -213,21 +213,21 @@ Step Temp E_pair E_mol TotEng Press
58000 0.437031 -2.0998724 0.051717885 -1.6114877 0.86071379
59000 0.45070454 -2.1115874 0.053721754 -1.6075367 0.62358834
60000 0.44181643 -2.1243164 0.060489492 -1.6223786 0.6992428
Loop time of 13.7021 on 1 procs for 60000 steps with 1200 atoms
Loop time of 13.6136 on 1 procs for 60000 steps with 1200 atoms
Performance: 1891674.479 tau/day, 4378.876 timesteps/s
99.9% CPU use with 1 MPI tasks x no OpenMP threads
Performance: 1903978.372 tau/day, 4407.357 timesteps/s
99.5% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 9.5222 | 9.5222 | 9.5222 | 0.0 | 69.49
Bond | 0.39977 | 0.39977 | 0.39977 | 0.0 | 2.92
Neigh | 2.1261 | 2.1261 | 2.1261 | 0.0 | 15.52
Comm | 0.26046 | 0.26046 | 0.26046 | 0.0 | 1.90
Output | 0.00084543 | 0.00084543 | 0.00084543 | 0.0 | 0.01
Modify | 1.1202 | 1.1202 | 1.1202 | 0.0 | 8.18
Other | | 0.2726 | | | 1.99
Pair | 9.3684 | 9.3684 | 9.3684 | 0.0 | 68.82
Bond | 0.39461 | 0.39461 | 0.39461 | 0.0 | 2.90
Neigh | 2.211 | 2.211 | 2.211 | 0.0 | 16.24
Comm | 0.2552 | 0.2552 | 0.2552 | 0.0 | 1.87
Output | 0.00065112 | 0.00065112 | 0.00065112 | 0.0 | 0.00
Modify | 1.0819 | 1.0819 | 1.0819 | 0.0 | 7.95
Other | | 0.3019 | | | 2.22
Nlocal: 1200 ave 1200 max 1200 min
Histogram: 1 0 0 0 0 0 0 0 0 0

40
examples/micelle/log.15Feb16.micelle.g++.4 → examples/micelle/log.5Oct16.micelle.g++.4
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@ -1,4 +1,4 @@
LAMMPS (15 Feb 2016)
LAMMPS (5 Oct 2016)
# 2d micelle simulation
dimension 2
@ -74,21 +74,21 @@ Step Temp E_pair E_mol TotEng Press
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 0.0662177 on 4 procs for 1000 steps with 1200 atoms
Loop time of 0.0670803 on 4 procs for 1000 steps with 1200 atoms
Performance: 6523939.295 tau/day, 15101.711 timesteps/s
98.9% CPU use with 4 MPI tasks x no OpenMP threads
Performance: 6440046.660 tau/day, 14907.515 timesteps/s
98.4% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.03338 | 0.034415 | 0.035278 | 0.4 | 51.97
Bond | 0.0016546 | 0.0017538 | 0.001863 | 0.2 | 2.65
Neigh | 0.0062997 | 0.0064718 | 0.0066252 | 0.2 | 9.77
Comm | 0.011654 | 0.012875 | 0.013857 | 0.8 | 19.44
Output | 0.00039363 | 0.00041753 | 0.00046754 | 0.1 | 0.63
Modify | 0.0067155 | 0.0069018 | 0.0072353 | 0.3 | 10.42
Other | | 0.003383 | | | 5.11
Pair | 0.033971 | 0.034628 | 0.036162 | 0.5 | 51.62
Bond | 0.001687 | 0.0017596 | 0.0018852 | 0.2 | 2.62
Neigh | 0.0068789 | 0.0069902 | 0.0070932 | 0.1 | 10.42
Comm | 0.011152 | 0.012883 | 0.013872 | 0.9 | 19.20
Output | 0.00035501 | 0.00038034 | 0.00044274 | 0.2 | 0.57
Modify | 0.0065997 | 0.0067009 | 0.0068605 | 0.1 | 9.99
Other | | 0.003738 | | | 5.57
Nlocal: 300 ave 305 max 292 min
Histogram: 1 0 0 0 0 0 1 0 1 1
@ -213,21 +213,21 @@ Step Temp E_pair E_mol TotEng Press
58000 0.43621486 -2.1097172 0.056706821 -1.617159 0.80497906
59000 0.44446312 -2.1103931 0.055606397 -1.610694 0.79904859
60000 0.43177211 -2.0985468 0.049687241 -1.6174473 0.81094066
Loop time of 4.44409 on 4 procs for 60000 steps with 1200 atoms
Loop time of 4.56204 on 4 procs for 60000 steps with 1200 atoms
Performance: 5832469.978 tau/day, 13501.088 timesteps/s
Performance: 5681665.051 tau/day, 13152.002 timesteps/s
99.5% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 2.3453 | 2.4228 | 2.4713 | 3.0 | 54.52
Bond | 0.084212 | 0.10413 | 0.11722 | 3.8 | 2.34
Neigh | 0.61098 | 0.61843 | 0.62485 | 0.7 | 13.92
Comm | 0.72832 | 0.81507 | 0.94114 | 9.7 | 18.34
Output | 0.0012789 | 0.0013777 | 0.0016506 | 0.4 | 0.03
Modify | 0.2745 | 0.28888 | 0.31551 | 3.0 | 6.50
Other | | 0.1934 | | | 4.35
Pair | 2.3705 | 2.4423 | 2.4948 | 2.9 | 53.54
Bond | 0.084795 | 0.10292 | 0.11359 | 3.4 | 2.26
Neigh | 0.63938 | 0.64418 | 0.64857 | 0.4 | 14.12
Comm | 0.81947 | 0.8785 | 0.9618 | 5.7 | 19.26
Output | 0.0012863 | 0.0013551 | 0.0015438 | 0.3 | 0.03
Modify | 0.26717 | 0.27596 | 0.28816 | 1.5 | 6.05
Other | | 0.2168 | | | 4.75
Nlocal: 300 ave 305 max 293 min
Histogram: 1 0 0 0 0 1 0 0 1 1