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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/flow/log.15Feb16.flow.couette.g++.1 → examples/flow/log.5Oct16.flow.couette.g++.1
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@ -1,4 +1,4 @@
LAMMPS (15 Feb 2016)
LAMMPS (5 Oct 2016)
# 2-d LJ flow simulation
dimension 2
@ -75,7 +75,7 @@ fix 4 all enforce2d
timestep 0.003
thermo 500
thermo_modify temp mobile
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.flow
@ -116,20 +116,20 @@ Step Temp E_pair E_mol TotEng Press Volume
9000 1 -0.402333 0 0.30957177 2.4852035 571.54286
9500 0.99889786 -0.46870263 0 0.24241751 2.3763314 571.54286
10000 1 -0.43338695 0 0.27851782 2.405424 571.54286
Loop time of 0.271851 on 1 procs for 10000 steps with 420 atoms
Loop time of 0.281614 on 1 procs for 10000 steps with 420 atoms
Performance: 9534632.580 tau/day, 36784.848 timesteps/s
100.0% CPU use with 1 MPI tasks x no OpenMP threads
Performance: 9204085.735 tau/day, 35509.590 timesteps/s
100.1% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.12448 | 0.12448 | 0.12448 | 0.0 | 45.79
Neigh | 0.054694 | 0.054694 | 0.054694 | 0.0 | 20.12
Comm | 0.0075622 | 0.0075622 | 0.0075622 | 0.0 | 2.78
Output | 0.00014329 | 0.00014329 | 0.00014329 | 0.0 | 0.05
Modify | 0.067663 | 0.067663 | 0.067663 | 0.0 | 24.89
Other | | 0.01731 | | | 6.37
Pair | 0.12437 | 0.12437 | 0.12437 | 0.0 | 44.16
Neigh | 0.062146 | 0.062146 | 0.062146 | 0.0 | 22.07
Comm | 0.0076008 | 0.0076008 | 0.0076008 | 0.0 | 2.70
Output | 0.00014687 | 0.00014687 | 0.00014687 | 0.0 | 0.05
Modify | 0.067444 | 0.067444 | 0.067444 | 0.0 | 23.95
Other | | 0.01991 | | | 7.07
Nlocal: 420 ave 420 max 420 min
Histogram: 1 0 0 0 0 0 0 0 0 0

22
examples/flow/log.15Feb16.flow.couette.g++.4 → examples/flow/log.5Oct16.flow.couette.g++.4
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@ -1,4 +1,4 @@
LAMMPS (15 Feb 2016)
LAMMPS (5 Oct 2016)
# 2-d LJ flow simulation
dimension 2
@ -75,7 +75,7 @@ fix 4 all enforce2d
timestep 0.003
thermo 500
thermo_modify temp mobile
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.flow
@ -116,20 +116,20 @@ Step Temp E_pair E_mol TotEng Press Volume
9000 1 -0.45171969 0 0.26018507 2.5525861 571.54286
9500 1.0322994 -0.40989898 0 0.32499991 2.6021234 571.54286
10000 1 -0.42489516 0 0.28700961 2.619505 571.54286
Loop time of 0.131903 on 4 procs for 10000 steps with 420 atoms
Loop time of 0.134939 on 4 procs for 10000 steps with 420 atoms
Performance: 19650813.964 tau/day, 75813.325 timesteps/s
99.5% CPU use with 4 MPI tasks x no OpenMP threads
Performance: 19208643.416 tau/day, 74107.421 timesteps/s
99.3% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.024203 | 0.030848 | 0.037153 | 3.6 | 23.39
Neigh | 0.013397 | 0.014826 | 0.016212 | 1.1 | 11.24
Comm | 0.039776 | 0.04867 | 0.05801 | 3.7 | 36.90
Output | 0.00026822 | 0.00028723 | 0.00034046 | 0.2 | 0.22
Modify | 0.018224 | 0.0192 | 0.020054 | 0.6 | 14.56
Other | | 0.01807 | | | 13.70
Pair | 0.024453 | 0.030829 | 0.036954 | 3.5 | 22.85
Neigh | 0.0152 | 0.016832 | 0.018415 | 1.2 | 12.47
Comm | 0.040894 | 0.049385 | 0.058308 | 3.7 | 36.60
Output | 0.00027037 | 0.00029039 | 0.0003438 | 0.2 | 0.22
Modify | 0.017885 | 0.018734 | 0.019774 | 0.6 | 13.88
Other | | 0.01887 | | | 13.98
Nlocal: 105 ave 113 max 97 min
Histogram: 2 0 0 0 0 0 0 0 0 2

22
examples/flow/log.15Feb16.flow.pois.g++.1 → examples/flow/log.5Oct16.flow.pois.g++.1
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@ -1,4 +1,4 @@
LAMMPS (15 Feb 2016)
LAMMPS (5 Oct 2016)
# 2-d LJ flow simulation
dimension 2
@ -75,7 +75,7 @@ fix 7 all enforce2d
timestep 0.003
thermo 500
thermo_modify temp mobile
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.flow
@ -116,20 +116,20 @@ Step Temp E_pair E_mol TotEng Press Volume
9000 1 -0.74461165 0 -0.032706889 2.574656 498.14523
9500 1.2047533 -0.75768848 0 0.09998113 2.4174997 501.8877
10000 1 -0.67361996 0 0.038284798 2.2310948 507.57444
Loop time of 0.308209 on 1 procs for 10000 steps with 420 atoms
Loop time of 0.313724 on 1 procs for 10000 steps with 420 atoms
Performance: 8409879.284 tau/day, 32445.522 timesteps/s
99.9% CPU use with 1 MPI tasks x no OpenMP threads
Performance: 8262038.165 tau/day, 31875.147 timesteps/s
100.1% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.13686 | 0.13686 | 0.13686 | 0.0 | 44.40
Neigh | 0.030894 | 0.030894 | 0.030894 | 0.0 | 10.02
Comm | 0.0063944 | 0.0063944 | 0.0063944 | 0.0 | 2.07
Output | 0.00016952 | 0.00016952 | 0.00016952 | 0.0 | 0.06
Modify | 0.11606 | 0.11606 | 0.11606 | 0.0 | 37.66
Other | | 0.01783 | | | 5.79
Pair | 0.13662 | 0.13662 | 0.13662 | 0.0 | 43.55
Neigh | 0.034956 | 0.034956 | 0.034956 | 0.0 | 11.14
Comm | 0.0064242 | 0.0064242 | 0.0064242 | 0.0 | 2.05
Output | 0.00014639 | 0.00014639 | 0.00014639 | 0.0 | 0.05
Modify | 0.11616 | 0.11616 | 0.11616 | 0.0 | 37.03
Other | | 0.01941 | | | 6.19
Nlocal: 420 ave 420 max 420 min
Histogram: 1 0 0 0 0 0 0 0 0 0

22
examples/flow/log.15Feb16.flow.pois.g++.4 → examples/flow/log.5Oct16.flow.pois.g++.4
View File

@ -1,4 +1,4 @@
LAMMPS (15 Feb 2016)
LAMMPS (5 Oct 2016)
# 2-d LJ flow simulation
dimension 2
@ -75,7 +75,7 @@ fix 7 all enforce2d
timestep 0.003
thermo 500
thermo_modify temp mobile
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.flow
@ -116,20 +116,20 @@ Step Temp E_pair E_mol TotEng Press Volume
9000 1 -0.8200207 0 -0.10811593 2.6210027 502.60511
9500 1.2167146 -0.77385956 0 0.092325373 2.5938179 500.86068
10000 1 -0.73082779 0 -0.018923029 2.735112 505.69856
Loop time of 0.196428 on 4 procs for 10000 steps with 420 atoms
Loop time of 0.225282 on 4 procs for 10000 steps with 420 atoms
Performance: 13195670.685 tau/day, 50909.223 timesteps/s
99.3% CPU use with 4 MPI tasks x no OpenMP threads
Performance: 11505578.988 tau/day, 44388.808 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 | 0.033267 | 0.034629 | 0.035398 | 0.5 | 17.63
Neigh | 0.0084751 | 0.0087134 | 0.0089035 | 0.2 | 4.44
Comm | 0.063612 | 0.066345 | 0.06988 | 0.9 | 33.78
Output | 0.00033164 | 0.00035477 | 0.00041437 | 0.2 | 0.18
Modify | 0.056999 | 0.058513 | 0.061231 | 0.7 | 29.79
Other | | 0.02787 | | | 14.19
Pair | 0.032012 | 0.033154 | 0.035252 | 0.7 | 14.72
Neigh | 0.0094411 | 0.0097138 | 0.010069 | 0.2 | 4.31
Comm | 0.080785 | 0.085431 | 0.088782 | 1.0 | 37.92
Output | 0.0003736 | 0.00039834 | 0.00046349 | 0.2 | 0.18
Modify | 0.062812 | 0.064686 | 0.066481 | 0.6 | 28.71
Other | | 0.0319 | | | 14.16
Nlocal: 105 ave 106 max 103 min
Histogram: 1 0 0 0 0 0 1 0 0 2