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lammps/bench-nsf/wat/log.wat-cpu-ranger
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LAMMPS (19 Nov 2010-ICMS)
# TIPS water from charmm.
boundary p p p
units real
atom_style full
special_bonds lj/coul 0.0 0.0 1.0
read_data data.wat
2 = max bonds/atom
1 = max angles/atom
orthogonal box = (-5.2675 -4.985 -4.9345) to (4.7325 5.015 5.0655)
4 by 4 by 8 processor grid
using 1 OpenMP thread(s) per MPI task
84 atoms
56 bonds
28 angles
2 = max # of 1-2 neighbors
1 = max # of 1-3 neighbors
2 = max # of special neighbors
replicate ${num} ${num} ${num}
replicate 10 ${num} ${num}
replicate 10 10 ${num}
replicate 10 10 10
orthogonal box = (-5.2675 -4.985 -4.9345) to (94.7325 95.015 95.0655)
4 by 4 by 8 processor grid
using 1 OpenMP thread(s) per MPI task
84000 atoms
56000 bonds
28000 angles
2 = max # of 1-2 neighbors
1 = max # of 1-3 neighbors
2 = max # of special neighbors
pair_style lj/cut/coul/long 14.0
pair_modify mix arithmetic
pair_coeff 2 2 0.1521000000 3.15057
pair_coeff 1 1 0.046 0.400014
# 100x larger for minimize
angle_style harmonic
angle_coeff 1 5500 104.52
# 100x larger constant for minimize
bond_style harmonic
bond_coeff 1 45000 0.9572
kspace_style pppm 1.0e-4
velocity all create 300 234324 dist gaussian
neighbor 2.5 bin
neigh_modify delay 2 every 1 check yes
thermo 10
thermo_style custom step pe temp evdwl ecoul vol press spcpu
thermo_modify norm yes
minimize 1.0e-4 1.0e-6 100 1000
WARNING: Resetting reneighboring criteria during minimization
PPPM initialization ...
G vector = 0.186884
grid = 36 36 36
stencil order = 5
RMS precision = 5.73697e-05
using single precision FFTs
brick FFT buffer size/proc = 1960 540 2352
Memory usage per processor = 8.72471 Mbytes
Step PotEng Temp E_vdwl E_coul Volume Press S/CPU
0 656.3994 300 623.49127 10.7913 1000000 13052196 0
10 2.1079218 300 3.7701061 10.339662 1000000 159414.93 6.9245844
20 -1.1179163 300 0.80326896 10.22405 1000000 29606.698 4.7461476
30 -1.5664399 300 0.48485053 10.090927 1000000 -9683.2819 3.428021
40 -1.8930463 300 0.31700434 9.8662989 1000000 -41081.466 3.4293494
50 -2.1217098 300 0.28533347 9.7392883 1000000 12738.127 2.89109
60 -2.266492 300 0.26831356 9.6131442 1000000 -11980.048 2.7013579
67 -2.3750729 300 0.25729054 9.5313842 1000000 3603.9241 2.530497
Loop time of 19.3115 on 128 procs (128 MPI x 1 OpenMP) for 67 steps with 84000 atoms
Minimization stats:
Stopping criterion = energy tolerance
Energy initial, next-to-last, final =
656.399401959 -2.37484669318 -2.37507286045
Force two-norm initial, final = 2.24428e+07 1472
Force max component initial, final = 305690 16.3999
Final line search alpha, max atom move = 8.60293e-06 0.000141087
Iterations, force evaluations = 67 322
Pair time (%) = 10.5467 (54.6139)
Bond time (%) = 0.0299561 (0.155121)
Kspce time (%) = 7.05581 (36.5369)
Neigh time (%) = 0 (0)
Comm time (%) = 1.46951 (7.60953)
Outpt time (%) = 0.0016795 (0.00869691)
Other time (%) = 0.207772 (1.0759)
FFT time (% of Kspce) = 0.857227 (12.1492)
FFT Gflps 3d (1d only) = 0.784057 42.8436
Nlocal: 656.25 ave 699 max 608 min
Histogram: 8 0 16 0 40 24 16 8 8 8
Nghost: 12144.8 ave 12548 max 11847 min
Histogram: 8 24 16 16 24 16 0 8 8 8
Neighs: 517812 ave 586277 max 471216 min
Histogram: 16 24 24 8 8 0 24 8 8 8
Total # of neighbors = 66280000
Ave neighs/atom = 789.048
Ave special neighs/atom = 2
Neighbor list builds = 0
Dangerous builds = 0
reset_timestep 0
thermo 500
fix 1 all shake 0.0001 20 2000 b 1 a 1
0 = # of size 2 clusters
0 = # of size 3 clusters
0 = # of size 4 clusters
28000 = # of frozen angles
fix 2 all npt temp 300.0 300.0 100.0 iso 0.0 0.0 1000.0
timestep 2.0
run 10000
PPPM initialization ...
G vector = 0.186884
grid = 36 36 36
stencil order = 5
RMS precision = 5.73697e-05
using single precision FFTs
brick FFT buffer size/proc = 1960 540 2352
SHAKE stats (type/ave/delta) on step 0
1 0.95732 0.000384565
1 104.487 0.0943643
Memory usage per processor = 8.40853 Mbytes
Step PotEng Temp E_vdwl E_coul Volume Press S/CPU
0 -2.3765508 450.00268 0.25729054 9.5313842 1000000 2996.9127 0
500 -3.1011864 306.55751 0.30918854 8.7618359 957112.54 -1380.9601 16.635268
1000 -3.195244 298.43071 0.3364505 8.6406576 907593.85 -877.96481 15.649414
1500 -3.2345766 299.89407 0.3434364 8.5946989 873604.6 -552.98265 15.280934
SHAKE stats (type/ave/delta) on step 2000
1 0.957188 3.99367e-06
1 104.52 0.000509805
2000 -3.2506315 299.09443 0.34453874 8.5775323 850999.12 -258.62861 14.854428
2500 -3.2604117 301.0183 0.34216943 8.5701541 837699.59 -120.8097 14.790922
3000 -3.2679344 300.73556 0.33990979 8.5650157 831237.34 -124.39486 14.186107
3500 -3.2610816 300.87323 0.33802576 8.5736763 830727.16 -106.7518 14.225469
SHAKE stats (type/ave/delta) on step 4000
1 0.957203 4.47027e-06
1 104.52 0.00044063
4000 -3.2639197 297.9293 0.34053848 8.5681342 829520.66 -45.525313 14.362088
4500 -3.2645709 298.34476 0.34916755 8.5591568 829949.21 132.39972 14.560406
5000 -3.2652645 300.25558 0.34588886 8.5616269 830509.67 58.99994 14.091744
5500 -3.2648925 301.68291 0.34078175 8.5672087 828620.05 11.045024 14.57765
SHAKE stats (type/ave/delta) on step 6000
1 0.957204 4.60683e-06
1 104.52 0.000486571
6000 -3.2724966 300.47687 0.33844906 8.5619922 829257.21 -175.32304 14.268107
6500 -3.2777223 300.8476 0.34733176 8.5479323 827138.06 78.496833 14.389753
7000 -3.2663813 299.50408 0.34110542 8.5653987 830774.84 -90.743769 14.09017
7500 -3.2644079 300.22327 0.3393885 8.5691277 830360.89 -94.547508 14.752899
SHAKE stats (type/ave/delta) on step 8000
1 0.957202 4.23872e-06
1 104.52 0.000581169
8000 -3.2626269 299.08967 0.33873342 8.571535 829645.17 -105.09656 14.596437
8500 -3.2643522 299.66505 0.34784563 8.5605392 829993.89 137.90485 14.633171
9000 -3.26637 301.44112 0.34865722 8.5579152 829507.25 139.91304 14.593958
9500 -3.2660964 299.5782 0.34127242 8.5653338 829463.93 -55.543943 14.630302
SHAKE stats (type/ave/delta) on step 10000
1 0.957205 6.18875e-06
1 104.52 0.000590098
10000 -3.2660677 298.59756 0.34406882 8.5627449 832141.71 -45.997706 14.637769
Loop time of 681.707 on 128 procs (128 MPI x 1 OpenMP) for 10000 steps with 84000 atoms
Pair time (%) = 337.606 (49.5236)
Bond time (%) = 0.0482105 (0.00707203)
Kspce time (%) = 217.342 (31.882)
Neigh time (%) = 30.0619 (4.4098)
Comm time (%) = 53.9413 (7.91268)
Outpt time (%) = 0.00499905 (0.000733315)
Other time (%) = 42.7026 (6.26407)
FFT time (% of Kspce) = 130.158 (59.8865)
FFT Gflps 3d (1d only) = 0.770719 110.992
Nlocal: 656.25 ave 696 max 629 min
Histogram: 7 11 21 28 19 22 7 6 6 1
Nghost: 13773.4 ave 13893 max 13615 min
Histogram: 1 2 6 18 14 27 32 13 10 5
Neighs: 623038 ave 681853 max 571320 min
Histogram: 5 9 16 19 23 22 14 10 7 3
Total # of neighbors = 79748807
Ave neighs/atom = 949.391
Ave special neighs/atom = 2
Neighbor list builds = 889
Dangerous builds = 0
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