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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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22
examples/rigid/log.15Feb16.rigid.g++.1 → examples/rigid/log.5Oct16.rigid.g++.1
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@ -1,4 +1,4 @@
LAMMPS (15 Feb 2016)
LAMMPS (5 Oct 2016)
# Simple rigid body system
units lj
@ -97,7 +97,7 @@ Neighbor list info ...
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4 -> bins = 18 18 18
Memory usage per processor = 3.15778 Mbytes
Memory usage per processor = 3.65531 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
@ -300,20 +300,20 @@ Step Temp E_pair E_mol TotEng Press
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 0.122539 on 1 procs for 10000 steps with 81 atoms
Loop time of 0.125672 on 1 procs for 10000 steps with 81 atoms
Performance: 705081.398 tau/day, 81606.643 timesteps/s
100.4% CPU use with 1 MPI tasks x no OpenMP threads
Performance: 687503.421 tau/day, 79572.155 timesteps/s
100.2% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0094028 | 0.0094028 | 0.0094028 | 0.0 | 7.67
Neigh | 0.03594 | 0.03594 | 0.03594 | 0.0 | 29.33
Comm | 0.00758 | 0.00758 | 0.00758 | 0.0 | 6.19
Output | 0.0011275 | 0.0011275 | 0.0011275 | 0.0 | 0.92
Modify | 0.065143 | 0.065143 | 0.065143 | 0.0 | 53.16
Other | | 0.003345 | | | 2.73
Pair | 0.0097554 | 0.0097554 | 0.0097554 | 0.0 | 7.76
Neigh | 0.038657 | 0.038657 | 0.038657 | 0.0 | 30.76
Comm | 0.0074 | 0.0074 | 0.0074 | 0.0 | 5.89
Output | 0.0010791 | 0.0010791 | 0.0010791 | 0.0 | 0.86
Modify | 0.064604 | 0.064604 | 0.064604 | 0.0 | 51.41
Other | | 0.004176 | | | 3.32
Nlocal: 81 ave 81 max 81 min
Histogram: 1 0 0 0 0 0 0 0 0 0

22
examples/rigid/log.15Feb16.rigid.g++.4 → examples/rigid/log.5Oct16.rigid.g++.4
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@ -1,4 +1,4 @@
LAMMPS (15 Feb 2016)
LAMMPS (5 Oct 2016)
# Simple rigid body system
units lj
@ -97,7 +97,7 @@ Neighbor list info ...
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4 -> bins = 18 18 18
Memory usage per processor = 3.1287 Mbytes
Memory usage per processor = 3.62803 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
@ -300,20 +300,20 @@ Step Temp E_pair E_mol TotEng Press
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 0.187163 on 4 procs for 10000 steps with 81 atoms
Loop time of 0.169479 on 4 procs for 10000 steps with 81 atoms
Performance: 461628.979 tau/day, 53429.280 timesteps/s
95.5% CPU use with 4 MPI tasks x no OpenMP threads
Performance: 509796.561 tau/day, 59004.232 timesteps/s
98.1% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0022814 | 0.0031556 | 0.0039577 | 1.1 | 1.69
Neigh | 0.010708 | 0.011337 | 0.012736 | 0.8 | 6.06
Comm | 0.084257 | 0.090435 | 0.10014 | 2.1 | 48.32
Output | 0.003355 | 0.0035859 | 0.0039752 | 0.4 | 1.92
Modify | 0.062852 | 0.072432 | 0.07759 | 2.1 | 38.70
Other | | 0.006218 | | | 3.32
Pair | 0.0024633 | 0.0031875 | 0.0039403 | 0.9 | 1.88
Neigh | 0.010975 | 0.011817 | 0.013459 | 0.9 | 6.97
Comm | 0.072126 | 0.074024 | 0.076456 | 0.7 | 43.68
Output | 0.0034711 | 0.0036327 | 0.0040615 | 0.4 | 2.14
Modify | 0.069286 | 0.070574 | 0.073233 | 0.6 | 41.64
Other | | 0.006244 | | | 3.68
Nlocal: 20.25 ave 38 max 3 min
Histogram: 1 0 1 0 0 0 1 0 0 1

20
examples/rigid/log.15Feb16.rigid.poems.g++.1 → examples/rigid/log.5Oct16.rigid.poems.g++.1
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@ -1,4 +1,4 @@
LAMMPS (15 Feb 2016)
LAMMPS (5 Oct 2016)
# Simple rigid body system
units lj
@ -97,7 +97,7 @@ Neighbor list info ...
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4 -> bins = 18 18 18
Memory usage per processor = 2.47028 Mbytes
Memory usage per processor = 2.96781 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
@ -300,20 +300,20 @@ Step Temp E_pair E_mol TotEng Press
9900 20288.244 306.5013 0 3687.8753 3.6196618
9950 19271.015 475.88527 0 3687.7211 -1.8196764
10000 21122.24 167.82714 0 3688.2005 -3.8464842
Loop time of 3.72277 on 1 procs for 10000 steps with 81 atoms
Loop time of 3.6648 on 1 procs for 10000 steps with 81 atoms
Performance: 23208.538 tau/day, 2686.173 timesteps/s
Performance: 23575.670 tau/day, 2728.665 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 | 0.16199 | 0.16199 | 0.16199 | 0.0 | 4.35
Neigh | 0.098636 | 0.098636 | 0.098636 | 0.0 | 2.65
Comm | 0.010331 | 0.010331 | 0.010331 | 0.0 | 0.28
Output | 0.0020616 | 0.0020616 | 0.0020616 | 0.0 | 0.06
Modify | 3.4423 | 3.4423 | 3.4423 | 0.0 | 92.47
Other | | 0.007444 | | | 0.20
Pair | 0.15599 | 0.15599 | 0.15599 | 0.0 | 4.26
Neigh | 0.099093 | 0.099093 | 0.099093 | 0.0 | 2.70
Comm | 0.0088665 | 0.0088665 | 0.0088665 | 0.0 | 0.24
Output | 0.0016377 | 0.0016377 | 0.0016377 | 0.0 | 0.04
Modify | 3.392 | 3.392 | 3.392 | 0.0 | 92.56
Other | | 0.007194 | | | 0.20
Nlocal: 81 ave 81 max 81 min
Histogram: 1 0 0 0 0 0 0 0 0 0

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examples/rigid/log.15Feb16.rigid.poems.g++.4 → examples/rigid/log.5Oct16.rigid.poems.g++.4
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LAMMPS (15 Feb 2016)
LAMMPS (5 Oct 2016)
# Simple rigid body system
units lj
@ -97,7 +97,7 @@ Neighbor list info ...
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4 -> bins = 18 18 18
Memory usage per processor = 2.4412 Mbytes
Memory usage per processor = 2.94053 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
@ -300,20 +300,20 @@ Step Temp E_pair E_mol TotEng Press
9900 21450.963 109.58687 0 3684.7474 -4.8001999
9950 20664.461 240.66995 0 3684.7468 -3.4840781
10000 18951.367 526.45428 0 3685.0155 21.512727
Loop time of 3.8586 on 4 procs for 10000 steps with 81 atoms
Loop time of 3.89095 on 4 procs for 10000 steps with 81 atoms
Performance: 22391.551 tau/day, 2591.615 timesteps/s
Performance: 22205.346 tau/day, 2570.063 timesteps/s
99.6% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.014034 | 0.040794 | 0.089783 | 14.9 | 1.06
Neigh | 0.012468 | 0.027018 | 0.055093 | 10.5 | 0.70
Comm | 0.13187 | 0.18206 | 0.2474 | 11.1 | 4.72
Output | 0.0053496 | 0.0060334 | 0.0076718 | 1.2 | 0.16
Modify | 3.5463 | 3.5828 | 3.6347 | 2.0 | 92.85
Other | | 0.01995 | | | 0.52
Pair | 0.012426 | 0.039516 | 0.089301 | 15.3 | 1.02
Neigh | 0.012618 | 0.027118 | 0.055113 | 10.4 | 0.70
Comm | 0.16629 | 0.21469 | 0.26329 | 8.2 | 5.52
Output | 0.0051188 | 0.0053029 | 0.0055087 | 0.2 | 0.14
Modify | 3.5241 | 3.5783 | 3.6729 | 3.0 | 91.96
Other | | 0.02605 | | | 0.67
Nlocal: 20.25 ave 81 max 0 min
Histogram: 3 0 0 0 0 0 0 0 0 1

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examples/rigid/log.15Feb16.rigid.poems2.g++.1 → examples/rigid/log.5Oct16.rigid.poems2.g++.1
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@ -1,4 +1,4 @@
LAMMPS (15 Feb 2016)
LAMMPS (5 Oct 2016)
# Simple rigid body system
units lj
@ -93,7 +93,7 @@ thermo 50
run 10000
WARNING: More than one fix poems (../fix_poems.cpp:352)
WARNING: More than one fix poems (../fix_poems.cpp:352)
WARNING: One or more atoms are time integrated more than once (../modify.cpp:266)
WARNING: One or more atoms are time integrated more than once (../modify.cpp:269)
Neighbor list info ...
1 neighbor list requests
update every 1 steps, delay 10 steps, check yes
@ -101,7 +101,7 @@ Neighbor list info ...
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4 -> bins = 18 18 18
Memory usage per processor = 3.03278 Mbytes
Memory usage per processor = 3.53031 Mbytes
Step Temp E_pair E_mol TotEng Press
0 196.00047 3632.2347 0 3668.5311 -2.7403788
50 12167.633 1505.5478 0 3758.8133 35.125973
@ -304,20 +304,20 @@ Step Temp E_pair E_mol TotEng Press
9900 19864.564 83.502384 0 3762.1253 -0.65360617
9950 18996.789 244.25101 0 3762.1749 -2.4961826
10000 17933.494 441.33587 0 3762.3532 -6.0731708
Loop time of 3.92046 on 1 procs for 10000 steps with 81 atoms
Loop time of 3.80061 on 1 procs for 10000 steps with 81 atoms
Performance: 22038.237 tau/day, 2550.722 timesteps/s
99.9% CPU use with 1 MPI tasks x no OpenMP threads
Performance: 22733.175 tau/day, 2631.155 timesteps/s
100.0% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.11453 | 0.11453 | 0.11453 | 0.0 | 2.92
Neigh | 0.076222 | 0.076222 | 0.076222 | 0.0 | 1.94
Comm | 0.011672 | 0.011672 | 0.011672 | 0.0 | 0.30
Output | 0.0017154 | 0.0017154 | 0.0017154 | 0.0 | 0.04
Modify | 3.7089 | 3.7089 | 3.7089 | 0.0 | 94.60
Other | | 0.007422 | | | 0.19
Pair | 0.11276 | 0.11276 | 0.11276 | 0.0 | 2.97
Neigh | 0.075881 | 0.075881 | 0.075881 | 0.0 | 2.00
Comm | 0.011113 | 0.011113 | 0.011113 | 0.0 | 0.29
Output | 0.0016332 | 0.0016332 | 0.0016332 | 0.0 | 0.04
Modify | 3.5918 | 3.5918 | 3.5918 | 0.0 | 94.51
Other | | 0.007383 | | | 0.19
Nlocal: 81 ave 81 max 81 min
Histogram: 1 0 0 0 0 0 0 0 0 0

24
examples/rigid/log.15Feb16.rigid.poems2.g++.4 → examples/rigid/log.5Oct16.rigid.poems2.g++.4
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@ -1,4 +1,4 @@
LAMMPS (15 Feb 2016)
LAMMPS (5 Oct 2016)
# Simple rigid body system
units lj
@ -93,7 +93,7 @@ thermo 50
run 10000
WARNING: More than one fix poems (../fix_poems.cpp:352)
WARNING: More than one fix poems (../fix_poems.cpp:352)
WARNING: One or more atoms are time integrated more than once (../modify.cpp:266)
WARNING: One or more atoms are time integrated more than once (../modify.cpp:269)
Neighbor list info ...
1 neighbor list requests
update every 1 steps, delay 10 steps, check yes
@ -101,7 +101,7 @@ Neighbor list info ...
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4 -> bins = 18 18 18
Memory usage per processor = 3.0037 Mbytes
Memory usage per processor = 3.50303 Mbytes
Step Temp E_pair E_mol TotEng Press
0 196.00047 3632.2347 0 3668.5311 -2.7403788
50 12167.633 1505.5478 0 3758.8133 35.125973
@ -304,20 +304,20 @@ Step Temp E_pair E_mol TotEng Press
9900 19447.247 161.27279 0 3762.6149 -6.4166376
9950 19807.083 95.152663 0 3763.1309 -0.88933698
10000 18972.157 249.56342 0 3762.9258 1.9189241
Loop time of 4.00036 on 4 procs for 10000 steps with 81 atoms
Loop time of 3.99472 on 4 procs for 10000 steps with 81 atoms
Performance: 21598.043 tau/day, 2499.774 timesteps/s
Performance: 21628.565 tau/day, 2503.306 timesteps/s
99.7% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0092638 | 0.031034 | 0.052506 | 8.9 | 0.78
Neigh | 0.0083086 | 0.021315 | 0.035568 | 6.7 | 0.53
Comm | 0.10259 | 0.1356 | 0.16345 | 6.8 | 3.39
Output | 0.0045969 | 0.0049881 | 0.0056102 | 0.5 | 0.12
Modify | 3.7245 | 3.7919 | 3.8593 | 2.5 | 94.79
Other | | 0.01554 | | | 0.39
Pair | 0.0090363 | 0.029554 | 0.05092 | 8.8 | 0.74
Neigh | 0.0090437 | 0.021045 | 0.034359 | 6.3 | 0.53
Comm | 0.1326 | 0.17829 | 0.2132 | 7.3 | 4.46
Output | 0.0044832 | 0.0048217 | 0.0053875 | 0.5 | 0.12
Modify | 3.6632 | 3.7381 | 3.8211 | 2.9 | 93.58
Other | | 0.02291 | | | 0.57
Nlocal: 20.25 ave 37 max 0 min
Histogram: 1 0 1 0 0 0 0 0 0 2
@ -333,4 +333,4 @@ Dangerous builds = 958
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:04
Total wall time: 0:00:03

146
examples/rigid/log.15Feb16.rigid.tnr.g++.1 → examples/rigid/log.5Oct16.rigid.tnr.g++.1
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@ -1,4 +1,4 @@
LAMMPS (15 Feb 2016)
LAMMPS (5 Oct 2016)
# Tethered nanorods
atom_style molecular
@ -67,7 +67,7 @@ Neighbor list info ...
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4 -> bins = 45 45 45
Memory usage per processor = 6.99131 Mbytes
Memory usage per processor = 7.32042 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
@ -120,21 +120,21 @@ Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
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 6.61347 on 1 procs for 5000 steps with 5600 atoms
Loop time of 6.51777 on 1 procs for 5000 steps with 5600 atoms
Performance: 326606.103 tau/day, 756.033 timesteps/s
99.9% CPU use with 1 MPI tasks x no OpenMP threads
Performance: 331401.531 tau/day, 767.133 timesteps/s
99.8% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.53158 | 0.53158 | 0.53158 | 0.0 | 8.04
Bond | 0.24987 | 0.24987 | 0.24987 | 0.0 | 3.78
Neigh | 1.8367 | 1.8367 | 1.8367 | 0.0 | 27.77
Comm | 0.17261 | 0.17261 | 0.17261 | 0.0 | 2.61
Output | 0.0035651 | 0.0035651 | 0.0035651 | 0.0 | 0.05
Modify | 3.6673 | 3.6673 | 3.6673 | 0.0 | 55.45
Other | | 0.1519 | | | 2.30
Pair | 0.51894 | 0.51894 | 0.51894 | 0.0 | 7.96
Bond | 0.24096 | 0.24096 | 0.24096 | 0.0 | 3.70
Neigh | 1.8769 | 1.8769 | 1.8769 | 0.0 | 28.80
Comm | 0.16548 | 0.16548 | 0.16548 | 0.0 | 2.54
Output | 0.0032616 | 0.0032616 | 0.0032616 | 0.0 | 0.05
Modify | 3.5349 | 3.5349 | 3.5349 | 0.0 | 54.23
Other | | 0.1774 | | | 2.72
Nlocal: 5600 ave 5600 max 5600 min
Histogram: 1 0 0 0 0 0 0 0 0 0
@ -163,7 +163,7 @@ fix 1 rods rigid/nve molecule
print "rigid/nve"
rigid/nve
run 1000
Memory usage per processor = 6.99131 Mbytes
Memory usage per processor = 7.32042 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
@ -176,21 +176,21 @@ Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
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 1.34998 on 1 procs for 1000 steps with 5600 atoms
Loop time of 1.37139 on 1 procs for 1000 steps with 5600 atoms
Performance: 320004.261 tau/day, 740.751 timesteps/s
99.9% CPU use with 1 MPI tasks x no OpenMP threads
Performance: 315008.398 tau/day, 729.186 timesteps/s
100.0% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.14397 | 0.14397 | 0.14397 | 0.0 | 10.66
Bond | 0.049438 | 0.049438 | 0.049438 | 0.0 | 3.66
Neigh | 0.39013 | 0.39013 | 0.39013 | 0.0 | 28.90
Comm | 0.033965 | 0.033965 | 0.033965 | 0.0 | 2.52
Output | 0.00092816 | 0.00092816 | 0.00092816 | 0.0 | 0.07
Modify | 0.70139 | 0.70139 | 0.70139 | 0.0 | 51.96
Other | | 0.03017 | | | 2.23
Pair | 0.1443 | 0.1443 | 0.1443 | 0.0 | 10.52
Bond | 0.049211 | 0.049211 | 0.049211 | 0.0 | 3.59
Neigh | 0.40564 | 0.40564 | 0.40564 | 0.0 | 29.58
Comm | 0.033721 | 0.033721 | 0.033721 | 0.0 | 2.46
Output | 0.00065017 | 0.00065017 | 0.00065017 | 0.0 | 0.05
Modify | 0.70225 | 0.70225 | 0.70225 | 0.0 | 51.21
Other | | 0.03562 | | | 2.60
Nlocal: 5600 ave 5600 max 5600 min
Histogram: 1 0 0 0 0 0 0 0 0 0
@ -211,7 +211,7 @@ fix 1 rods rigid/nvt molecule temp 1.4 1.4 1.0
print "rigid/nvt"
rigid/nvt
run 1000
Memory usage per processor = 6.99131 Mbytes
Memory usage per processor = 7.32042 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 0.0054065567 7.2245364 62.244 62.244 62.244 0.0092276454 0.0019623806 0.005029644
@ -224,21 +224,21 @@ Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
6800 1.4017002 5.9015884 7.0025488 0.0039067256 7.1707842 62.244 62.244 62.244 0.0068315449 0.0020054024 0.0028832295
6900 1.4136756 5.8914708 7.0018372 0.005175385 7.2247049 62.244 62.244 62.244 0.0028462217 0.009405517 0.0032744161
7000 1.4286618 5.8935692 7.0157065 0.0062967875 7.2868652 62.244 62.244 62.244 0.0047257503 0.0093417536 0.0048228587
Loop time of 1.36768 on 1 procs for 1000 steps with 5600 atoms
Loop time of 1.38662 on 1 procs for 1000 steps with 5600 atoms
Performance: 315862.242 tau/day, 731.163 timesteps/s
Performance: 311550.061 tau/day, 721.181 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 | 0.14502 | 0.14502 | 0.14502 | 0.0 | 10.60
Bond | 0.049546 | 0.049546 | 0.049546 | 0.0 | 3.62
Neigh | 0.38711 | 0.38711 | 0.38711 | 0.0 | 28.30
Comm | 0.033742 | 0.033742 | 0.033742 | 0.0 | 2.47
Output | 0.00089908 | 0.00089908 | 0.00089908 | 0.0 | 0.07
Modify | 0.72137 | 0.72137 | 0.72137 | 0.0 | 52.74
Other | | 0.03 | | | 2.19
Pair | 0.14525 | 0.14525 | 0.14525 | 0.0 | 10.48
Bond | 0.048966 | 0.048966 | 0.048966 | 0.0 | 3.53
Neigh | 0.40266 | 0.40266 | 0.40266 | 0.0 | 29.04
Comm | 0.033521 | 0.033521 | 0.033521 | 0.0 | 2.42
Output | 0.00064969 | 0.00064969 | 0.00064969 | 0.0 | 0.05
Modify | 0.71998 | 0.71998 | 0.71998 | 0.0 | 51.92
Other | | 0.03559 | | | 2.57
Nlocal: 5600 ave 5600 max 5600 min
Histogram: 1 0 0 0 0 0 0 0 0 0
@ -263,7 +263,7 @@ rigid/npt iso
fix_modify 1 temp myTemp
run 1000
Memory usage per processor = 6.99131 Mbytes
Memory usage per processor = 7.32042 Mbytes
Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
7000 1.4286618 5.8935692 7.0157065 0.032107544 8.3983542 62.244 62.244 62.244 0.0040119822 0.040455544 0.051855105
7100 1.4709107 5.8870981 7.0424197 0.019698532 7.6954221 57.045709 57.045709 57.045709 0.012930036 0.020495433 0.025670125
@ -276,21 +276,21 @@ Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
7800 1.5106894 5.6005849 6.7871505 0.028896219 6.982719 33.59041 33.59041 33.59041 0.031167851 0.013090267 0.042430539
7900 1.472566 5.5634394 6.7200611 0.092340877 7.2955261 32.679168 32.679168 32.679168 0.060527481 0.10093222 0.11556293
8000 1.4805391 5.5132684 6.6761526 0.040035619 6.9105042 32.003919 32.003919 32.003919 0.04381615 0.023706176 0.052584532
Loop time of 3.01539 on 1 procs for 1000 steps with 5600 atoms
Loop time of 3.05773 on 1 procs for 1000 steps with 5600 atoms
Performance: 143265.281 tau/day, 331.633 timesteps/s
Performance: 141281.224 tau/day, 327.040 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 | 0.37256 | 0.37256 | 0.37256 | 0.0 | 12.36
Bond | 0.072008 | 0.072008 | 0.072008 | 0.0 | 2.39
Neigh | 1.3608 | 1.3608 | 1.3608 | 0.0 | 45.13
Comm | 0.073025 | 0.073025 | 0.073025 | 0.0 | 2.42
Output | 0.00085115 | 0.00085115 | 0.00085115 | 0.0 | 0.03
Modify | 1.099 | 1.099 | 1.099 | 0.0 | 36.45
Other | | 0.03715 | | | 1.23
Pair | 0.37231 | 0.37231 | 0.37231 | 0.0 | 12.18
Bond | 0.07144 | 0.07144 | 0.07144 | 0.0 | 2.34
Neigh | 1.3968 | 1.3968 | 1.3968 | 0.0 | 45.68
Comm | 0.071773 | 0.071773 | 0.071773 | 0.0 | 2.35
Output | 0.00065684 | 0.00065684 | 0.00065684 | 0.0 | 0.02
Modify | 1.0951 | 1.0951 | 1.0951 | 0.0 | 35.82
Other | | 0.04962 | | | 1.62
Nlocal: 5600 ave 5600 max 5600 min
Histogram: 1 0 0 0 0 0 0 0 0 0
@ -311,7 +311,7 @@ fix 1 rods rigid/npt molecule temp 1.4 1.4 1.0 x 0.05 0.05 1.0 dilate all
print "rigid/npt x"
rigid/npt x
run 1000
Memory usage per processor = 6.99518 Mbytes
Memory usage per processor = 7.32428 Mbytes
Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
8000 1.4805391 5.5132684 6.6761526 0.10591497 7.2961342 32.003919 32.003919 32.003919 -0.0085253101 0.12196602 0.20430422
8100 1.4629588 5.5087415 6.6578173 0.080159269 7.1245058 31.831354 32.003919 32.003919 0.078046473 0.088201582 0.074229751
@ -324,21 +324,21 @@ Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
8800 1.3993066 5.4243917 6.5234721 0.030638337 6.683965 28.639961 32.003919 32.003919 0.08972583 0.0089328704 -0.0067436909
8900 1.4429241 5.3850352 6.5183748 0.0053167016 6.5458205 28.223699 32.003919 32.003919 0.052590681 -0.031563606 -0.0050769701
9000 1.41963 5.3772308 6.4922741 0.040105311 6.6961497 27.793622 32.003919 32.003919 0.070575176 0.0044551641 0.045285594
Loop time of 3.0303 on 1 procs for 1000 steps with 5600 atoms
Loop time of 2.94424 on 1 procs for 1000 steps with 5600 atoms
Performance: 142560.181 tau/day, 330.000 timesteps/s
Performance: 146727.069 tau/day, 339.646 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 | 0.59848 | 0.59848 | 0.59848 | 0.0 | 19.75
Bond | 0.075771 | 0.075771 | 0.075771 | 0.0 | 2.50
Neigh | 1.0984 | 1.0984 | 1.0984 | 0.0 | 36.25
Comm | 0.055339 | 0.055339 | 0.055339 | 0.0 | 1.83
Output | 0.00087357 | 0.00087357 | 0.00087357 | 0.0 | 0.03
Modify | 1.1671 | 1.1671 | 1.1671 | 0.0 | 38.51
Other | | 0.03439 | | | 1.13
Pair | 0.57781 | 0.57781 | 0.57781 | 0.0 | 19.63
Bond | 0.072705 | 0.072705 | 0.072705 | 0.0 | 2.47
Neigh | 1.0768 | 1.0768 | 1.0768 | 0.0 | 36.57
Comm | 0.052799 | 0.052799 | 0.052799 | 0.0 | 1.79
Output | 0.00064921 | 0.00064921 | 0.00064921 | 0.0 | 0.02
Modify | 1.1247 | 1.1247 | 1.1247 | 0.0 | 38.20
Other | | 0.03878 | | | 1.32
Nlocal: 5600 ave 5600 max 5600 min
Histogram: 1 0 0 0 0 0 0 0 0 0
@ -359,7 +359,7 @@ fix 1 rods rigid/nph molecule iso 0.05 0.05 1.0 dilate all
print "rigid/nph iso"
rigid/nph iso
run 1000
Memory usage per processor = 6.99518 Mbytes
Memory usage per processor = 7.32428 Mbytes
Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
9000 1.41963 5.3772308 6.4922741 0.054032922 6.7669508 27.793622 32.003919 32.003919 0.36183473 -0.1011685 -0.098567468
9100 1.468276 5.3693533 6.5226054 0.062009135 6.8364521 27.753087 31.957243 31.957243 0.072952506 0.067965393 0.045109506
@ -372,21 +372,21 @@ Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
9800 1.4701089 5.2202499 6.3749417 0.055758411 6.6108197 26.142656 30.102857 30.102857 0.045171706 0.039488766 0.082614761
9900 1.4518855 5.2148116 6.3551898 0.011510897 6.4028899 25.963345 29.896384 29.896384 0.0060934464 0.010841773 0.017597473
10000 1.4445828 5.2098073 6.3444498 0.075197507 6.654918 25.931556 29.859779 29.859779 0.08350416 0.066240185 0.075848177
Loop time of 3.1675 on 1 procs for 1000 steps with 5600 atoms
Loop time of 3.13351 on 1 procs for 1000 steps with 5600 atoms
Performance: 136384.997 tau/day, 315.706 timesteps/s
Performance: 137864.384 tau/day, 319.131 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 | 0.68944 | 0.68944 | 0.68944 | 0.0 | 21.77
Bond | 0.074669 | 0.074669 | 0.074669 | 0.0 | 2.36
Neigh | 1.1761 | 1.1761 | 1.1761 | 0.0 | 37.13
Comm | 0.058399 | 0.058399 | 0.058399 | 0.0 | 1.84
Output | 0.0006671 | 0.0006671 | 0.0006671 | 0.0 | 0.02
Modify | 1.1339 | 1.1339 | 1.1339 | 0.0 | 35.80
Other | | 0.03435 | | | 1.08
Pair | 0.68 | 0.68 | 0.68 | 0.0 | 21.70
Bond | 0.073233 | 0.073233 | 0.073233 | 0.0 | 2.34
Neigh | 1.1775 | 1.1775 | 1.1775 | 0.0 | 37.58
Comm | 0.057102 | 0.057102 | 0.057102 | 0.0 | 1.82
Output | 0.00068927 | 0.00068927 | 0.00068927 | 0.0 | 0.02
Modify | 1.1058 | 1.1058 | 1.1058 | 0.0 | 35.29
Other | | 0.03924 | | | 1.25
Nlocal: 5600 ave 5600 max 5600 min
Histogram: 1 0 0 0 0 0 0 0 0 0
@ -407,7 +407,7 @@ fix 1 rods rigid/nph molecule x 0.05 0.05 1.0 y 0.05 0.05 1.0 couple xy
print "rigid/nph xy couple"
rigid/nph xy couple
run 1000
Memory usage per processor = 6.999 Mbytes
Memory usage per processor = 7.32811 Mbytes
Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
10000 1.4445828 5.2098073 6.3444498 0.001962567 6.3525526 25.931556 29.859779 29.859779 0.18484796 -0.22902272 0.050062455
10100 1.4368894 5.2096239 6.3382235 0.10403552 6.7662753 25.886842 29.808292 29.859779 0.12565247 0.094955776 0.091498324
@ -420,21 +420,21 @@ Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
10800 1.4358912 5.1798018 6.3076174 0.10549358 6.747456 26.058856 30.006363 29.859779 0.1992503 0.046346044 0.070884395
10900 1.4470038 5.1528383 6.2893823 0.045720444 6.4780533 25.92502 29.852253 29.859779 0.041394051 0.026837211 0.068930071
11000 1.437397 5.1841678 6.3131661 0.070020768 6.6023557 25.935798 29.864664 29.859779 0.11790932 0.072745235 0.019407746
Loop time of 3.24668 on 1 procs for 1000 steps with 5600 atoms
Loop time of 3.22377 on 1 procs for 1000 steps with 5600 atoms
Performance: 133059.040 tau/day, 308.007 timesteps/s
Performance: 134004.591 tau/day, 310.196 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 | 0.75941 | 0.75941 | 0.75941 | 0.0 | 23.39
Bond | 0.075467 | 0.075467 | 0.075467 | 0.0 | 2.32
Neigh | 1.1751 | 1.1751 | 1.1751 | 0.0 | 36.19
Comm | 0.059018 | 0.059018 | 0.059018 | 0.0 | 1.82
Output | 0.00065112 | 0.00065112 | 0.00065112 | 0.0 | 0.02
Modify | 1.1432 | 1.1432 | 1.1432 | 0.0 | 35.21
Other | | 0.03387 | | | 1.04
Pair | 0.74959 | 0.74959 | 0.74959 | 0.0 | 23.25
Bond | 0.073572 | 0.073572 | 0.073572 | 0.0 | 2.28
Neigh | 1.1793 | 1.1793 | 1.1793 | 0.0 | 36.58
Comm | 0.057446 | 0.057446 | 0.057446 | 0.0 | 1.78
Output | 0.00065088 | 0.00065088 | 0.00065088 | 0.0 | 0.02
Modify | 1.1241 | 1.1241 | 1.1241 | 0.0 | 34.87
Other | | 0.03903 | | | 1.21
Nlocal: 5600 ave 5600 max 5600 min
Histogram: 1 0 0 0 0 0 0 0 0 0

138
examples/rigid/log.15Feb16.rigid.tnr.g++.4 → examples/rigid/log.5Oct16.rigid.tnr.g++.4
View File

@ -1,4 +1,4 @@
LAMMPS (15 Feb 2016)
LAMMPS (5 Oct 2016)
# Tethered nanorods
atom_style molecular
@ -120,21 +120,21 @@ Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
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 3.13958 on 4 procs for 5000 steps with 5600 atoms
Loop time of 3.14543 on 4 procs for 5000 steps with 5600 atoms
Performance: 687990.006 tau/day, 1592.569 timesteps/s
99.1% CPU use with 4 MPI tasks x no OpenMP threads
Performance: 686709.553 tau/day, 1589.605 timesteps/s
99.2% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.079872 | 0.12791 | 0.18245 | 13.2 | 4.07
Bond | 0.038984 | 0.058535 | 0.077727 | 7.4 | 1.86
Neigh | 0.63649 | 0.63904 | 0.64148 | 0.2 | 20.35
Comm | 0.15118 | 0.22089 | 0.28197 | 13.0 | 7.04
Output | 0.0019264 | 0.0028899 | 0.0034878 | 1.1 | 0.09
Modify | 1.8465 | 1.9323 | 2.0081 | 5.4 | 61.55
Other | | 0.158 | | | 5.03
Pair | 0.081628 | 0.12747 | 0.17984 | 12.8 | 4.05
Bond | 0.037502 | 0.057149 | 0.076595 | 7.6 | 1.82
Neigh | 0.65705 | 0.6588 | 0.66084 | 0.2 | 20.94
Comm | 0.1653 | 0.23616 | 0.29975 | 12.9 | 7.51
Output | 0.0021076 | 0.0028133 | 0.003227 | 0.9 | 0.09
Modify | 1.8231 | 1.8972 | 1.9713 | 5.2 | 60.32
Other | | 0.1658 | | | 5.27
Nlocal: 1400 ave 1868 max 905 min
Histogram: 1 1 0 0 0 0 0 0 0 2
@ -176,21 +176,21 @@ Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
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 0.745001 on 4 procs for 1000 steps with 5600 atoms
Loop time of 0.74555 on 4 procs for 1000 steps with 5600 atoms
Performance: 579865.026 tau/day, 1342.280 timesteps/s
Performance: 579437.739 tau/day, 1341.291 timesteps/s
99.6% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.020505 | 0.033631 | 0.048735 | 7.0 | 4.51
Bond | 0.0078509 | 0.011774 | 0.015532 | 3.2 | 1.58
Neigh | 0.13791 | 0.13834 | 0.13874 | 0.1 | 18.57
Comm | 0.029133 | 0.04799 | 0.064085 | 7.4 | 6.44
Output | 0.0004046 | 0.00066173 | 0.00084162 | 0.6 | 0.09
Modify | 0.46937 | 0.48315 | 0.4976 | 1.9 | 64.85
Other | | 0.02945 | | | 3.95
Pair | 0.020915 | 0.033416 | 0.047822 | 6.7 | 4.48
Bond | 0.0076883 | 0.011506 | 0.015239 | 3.3 | 1.54
Neigh | 0.14225 | 0.14262 | 0.14297 | 0.1 | 19.13
Comm | 0.030192 | 0.0485 | 0.064376 | 7.2 | 6.51
Output | 0.00039148 | 0.0005275 | 0.00062299 | 0.4 | 0.07
Modify | 0.46557 | 0.47773 | 0.49051 | 1.7 | 64.08
Other | | 0.03125 | | | 4.19
Nlocal: 1400 ave 1868 max 935 min
Histogram: 2 0 0 0 0 0 0 0 0 2
@ -224,21 +224,21 @@ Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
6800 1.3816731 5.8909305 6.9761607 -9.1110394e-05 6.9722372 62.244 62.244 62.244 -0.0048195881 -0.00080983527 0.0053560922
6900 1.4011479 5.8881921 6.9887187 0.0010084642 7.0321462 62.244 62.244 62.244 0.0012132523 -0.0025918018 0.0044039422
7000 1.3973667 5.8867951 6.9843517 0.0070023833 7.2858955 62.244 62.244 62.244 0.0058928565 0.0076813429 0.0074329504
Loop time of 0.760565 on 4 procs for 1000 steps with 5600 atoms
Loop time of 0.761012 on 4 procs for 1000 steps with 5600 atoms
Performance: 567998.937 tau/day, 1314.812 timesteps/s
99.5% CPU use with 4 MPI tasks x no OpenMP threads
Performance: 567665.504 tau/day, 1314.041 timesteps/s
99.6% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.021564 | 0.034813 | 0.049583 | 6.9 | 4.58
Bond | 0.0080154 | 0.011744 | 0.015375 | 3.2 | 1.54
Neigh | 0.13546 | 0.13583 | 0.13616 | 0.1 | 17.86
Comm | 0.029489 | 0.047668 | 0.06437 | 7.4 | 6.27
Output | 0.00040579 | 0.00063974 | 0.00079918 | 0.6 | 0.08
Modify | 0.48726 | 0.50088 | 0.51473 | 1.7 | 65.86
Other | | 0.02899 | | | 3.81
Pair | 0.022122 | 0.034862 | 0.048912 | 6.6 | 4.58
Bond | 0.0078702 | 0.011574 | 0.015191 | 3.2 | 1.52
Neigh | 0.1398 | 0.14013 | 0.14044 | 0.1 | 18.41
Comm | 0.029736 | 0.047586 | 0.064077 | 7.3 | 6.25
Output | 0.00039291 | 0.00053465 | 0.00063396 | 0.4 | 0.07
Modify | 0.48838 | 0.49907 | 0.50959 | 1.4 | 65.58
Other | | 0.02726 | | | 3.58
Nlocal: 1400 ave 1832 max 970 min
Histogram: 2 0 0 0 0 0 0 0 0 2
@ -276,21 +276,21 @@ Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
7800 1.4922447 5.6135845 6.7856627 0.066398531 7.2467615 33.879827 33.879827 33.879827 0.05766722 0.07643975 0.065088623
7900 1.5126099 5.5498409 6.7379149 0.060758513 7.1190044 32.749346 32.749346 32.749346 0.045401188 0.069519167 0.067355184
8000 1.498932 5.5307653 6.708096 0.0068958389 6.7481394 31.918601 31.918601 31.918601 0.004934357 -0.0067897493 0.022542909
Loop time of 1.41333 on 4 procs for 1000 steps with 5600 atoms
Loop time of 1.40621 on 4 procs for 1000 steps with 5600 atoms
Performance: 305661.545 tau/day, 707.550 timesteps/s
99.2% CPU use with 4 MPI tasks x no OpenMP threads
Performance: 307209.818 tau/day, 711.134 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 | 0.057705 | 0.096282 | 0.13813 | 11.4 | 6.81
Bond | 0.012531 | 0.01785 | 0.023392 | 3.7 | 1.26
Neigh | 0.50189 | 0.5024 | 0.50294 | 0.1 | 35.55
Comm | 0.058384 | 0.10518 | 0.14841 | 12.2 | 7.44
Output | 0.00038195 | 0.00049835 | 0.0007689 | 0.7 | 0.04
Modify | 0.62292 | 0.64876 | 0.67248 | 2.8 | 45.90
Other | | 0.04236 | | | 3.00
Pair | 0.057011 | 0.094542 | 0.13471 | 11.0 | 6.72
Bond | 0.012043 | 0.017356 | 0.022935 | 3.8 | 1.23
Neigh | 0.50655 | 0.50716 | 0.50781 | 0.1 | 36.07
Comm | 0.060325 | 0.10627 | 0.14985 | 12.0 | 7.56
Output | 0.0003705 | 0.00040978 | 0.00051475 | 0.3 | 0.03
Modify | 0.60798 | 0.63453 | 0.65863 | 2.9 | 45.12
Other | | 0.04594 | | | 3.27
Nlocal: 1400 ave 1820 max 1010 min
Histogram: 1 1 0 0 0 0 0 0 1 1
@ -324,21 +324,21 @@ Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
8800 1.4272224 5.3956531 6.5166598 0.051937078 6.7855855 28.46133 31.918601 31.918601 0.038718856 0.054121272 0.062971108
8900 1.430201 5.3881483 6.5114945 0.042705385 6.728515 27.933053 31.918601 31.918601 0.053090216 0.033892798 0.04113314
9000 1.4147254 5.3571794 6.4683705 0.015474623 6.5454193 27.368213 31.918601 31.918601 0.018517547 0.023668345 0.0042379783
Loop time of 1.40527 on 4 procs for 1000 steps with 5600 atoms
Loop time of 1.3981 on 4 procs for 1000 steps with 5600 atoms
Performance: 307413.312 tau/day, 711.605 timesteps/s
99.1% CPU use with 4 MPI tasks x no OpenMP threads
Performance: 308990.110 tau/day, 715.255 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 | 0.09198 | 0.15293 | 0.22726 | 14.1 | 10.88
Bond | 0.01415 | 0.01816 | 0.022801 | 2.8 | 1.29
Neigh | 0.40174 | 0.40202 | 0.40228 | 0.0 | 28.61
Comm | 0.053445 | 0.13222 | 0.19624 | 16.1 | 9.41
Output | 0.00037909 | 0.00046462 | 0.00065279 | 0.5 | 0.03
Modify | 0.6409 | 0.65867 | 0.6806 | 2.2 | 46.87
Other | | 0.04081 | | | 2.90
Pair | 0.090644 | 0.15054 | 0.22186 | 13.5 | 10.77
Bond | 0.013196 | 0.017756 | 0.022439 | 2.9 | 1.27
Neigh | 0.40253 | 0.40269 | 0.40288 | 0.0 | 28.80
Comm | 0.057128 | 0.13282 | 0.1979 | 15.4 | 9.50
Output | 0.00036597 | 0.00040632 | 0.0004673 | 0.2 | 0.03
Modify | 0.62613 | 0.65125 | 0.67228 | 2.1 | 46.58
Other | | 0.04265 | | | 3.05
Nlocal: 1400 ave 1770 max 1095 min
Histogram: 1 1 0 0 0 0 1 0 0 1
@ -372,21 +372,21 @@ Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
9800 1.4311568 5.268838 6.392935 0.056161789 6.637248 26.163729 30.513853 30.513853 0.071096045 0.048086199 0.049303122
9900 1.4437347 5.2369801 6.3709564 0.11335968 6.8497267 25.907207 30.214681 30.214681 0.1259046 0.10149135 0.11268308
10000 1.4627878 5.2272205 6.376162 0.082077049 6.7164073 25.746677 30.02746 30.02746 0.060839015 0.13885619 0.046535946
Loop time of 1.41589 on 4 procs for 1000 steps with 5600 atoms
Loop time of 1.38185 on 4 procs for 1000 steps with 5600 atoms
Performance: 305107.630 tau/day, 706.268 timesteps/s
99.1% CPU use with 4 MPI tasks x no OpenMP threads
Performance: 312625.215 tau/day, 723.669 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 | 0.11437 | 0.17662 | 0.24699 | 12.6 | 12.47
Bond | 0.014617 | 0.018159 | 0.022451 | 2.4 | 1.28
Neigh | 0.40766 | 0.40784 | 0.40799 | 0.0 | 28.80
Comm | 0.054544 | 0.12898 | 0.19363 | 15.6 | 9.11
Output | 0.00037289 | 0.00046611 | 0.00066733 | 0.6 | 0.03
Modify | 0.62801 | 0.64468 | 0.6664 | 2.1 | 45.53
Other | | 0.03915 | | | 2.76
Pair | 0.11291 | 0.17289 | 0.23942 | 12.0 | 12.51
Bond | 0.013814 | 0.017709 | 0.022031 | 2.5 | 1.28
Neigh | 0.40444 | 0.4048 | 0.40511 | 0.0 | 29.29
Comm | 0.055045 | 0.12527 | 0.18875 | 14.9 | 9.07
Output | 0.0003531 | 0.00038058 | 0.00045681 | 0.2 | 0.03
Modify | 0.60769 | 0.62523 | 0.64283 | 1.7 | 45.25
Other | | 0.03557 | | | 2.57
Nlocal: 1400 ave 1669 max 1139 min
Histogram: 1 0 1 0 0 0 0 1 0 1
@ -420,21 +420,21 @@ Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
10800 1.4661732 5.1586918 6.3102923 0.084525247 6.6478976 25.272455 29.474391 30.02746 0.10699807 0.070825674 0.075751992
10900 1.4301511 5.1743273 6.2976344 0.014007746 6.3539547 25.356203 29.572064 30.02746 -0.015258276 -0.0047253148 0.06200683
11000 1.4346828 5.1625047 6.2893712 0.034027405 6.4273459 25.463687 29.697419 30.02746 0.041309225 0.014001823 0.046771165
Loop time of 1.39005 on 4 procs for 1000 steps with 5600 atoms
Loop time of 1.36647 on 4 procs for 1000 steps with 5600 atoms
Performance: 310781.162 tau/day, 719.401 timesteps/s
Performance: 316143.197 tau/day, 731.813 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 | 0.14204 | 0.19795 | 0.25554 | 10.2 | 14.24
Bond | 0.015064 | 0.018318 | 0.021846 | 2.0 | 1.32
Neigh | 0.37625 | 0.37681 | 0.37726 | 0.1 | 27.11
Comm | 0.058424 | 0.11817 | 0.17563 | 13.6 | 8.50
Output | 0.00036097 | 0.00047255 | 0.00073051 | 0.7 | 0.03
Modify | 0.63824 | 0.64799 | 0.66001 | 1.1 | 46.62
Other | | 0.03034 | | | 2.18
Pair | 0.13847 | 0.19365 | 0.24916 | 9.9 | 14.17
Bond | 0.014236 | 0.017841 | 0.02132 | 2.2 | 1.31
Neigh | 0.37634 | 0.37662 | 0.37685 | 0.0 | 27.56
Comm | 0.057297 | 0.11588 | 0.17429 | 13.5 | 8.48
Output | 0.00035167 | 0.00037664 | 0.00044203 | 0.2 | 0.03
Modify | 0.61282 | 0.62929 | 0.64128 | 1.4 | 46.05
Other | | 0.03282 | | | 2.40
Nlocal: 1400 ave 1607 max 1199 min
Histogram: 1 0 1 0 0 0 0 1 0 1