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lammps/bench-nsf/wat/log.wat-omp-longhorn
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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 4 processor grid
using 2 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 4 processor grid
using 2 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/omp 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 = 2744 900 1764
Memory usage per processor = 11.1222 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 9.183384
20 -1.1179164 300 0.80326909 10.22405 1000000 29606.391 7.6934212
30 -1.5482814 300 0.45429355 10.075525 1000000 -6780.3529 5.5983388
40 -1.6615478 300 0.43793571 10.055152 1000000 16576.175 3.7942298
50 -1.8610264 300 0.35826881 9.9278023 1000000 8567.8822 4.3490592
60 -2.113159 300 0.29267303 9.7442739 1000000 6459.288 5.6146874
70 -2.2428442 300 0.27484557 9.6373795 1000000 15518.054 4.4185517
80 -2.4130941 300 0.25471857 9.4965952 1000000 3390.6028 4.5622206
84 -2.4150614 300 0.25444899 9.495168 1000000 4419.2006 2.9993689
Loop time of 16.6797 on 128 procs (64 MPI x 2 OpenMP) for 84 steps with 84000 atoms
Minimization stats:
Stopping criterion = energy tolerance
Energy initial, next-to-last, final =
656.399401959 -2.41482175132 -2.41506139116
Force two-norm initial, final = 2.24428e+07 1326.85
Force max component initial, final = 305690 14.6931
Final line search alpha, max atom move = 7.30151e-06 0.000107281
Iterations, force evaluations = 84 443
Pair time (%) = 12.2296 (73.3204)
Bond time (%) = 0.0479575 (0.28752)
Kspce time (%) = 3.86201 (23.154)
Neigh time (%) = 0 (0)
Comm time (%) = 0.458186 (2.74697)
Outpt time (%) = 0.0010033 (0.00601507)
Other time (%) = 0.0809199 (0.48514)
FFT time (% of Kspce) = 0.0816388 (2.11389)
FFT Gflps 3d (1d only) = 10.3217 85.3641
Nlocal: 1312.5 ave 1369 max 1259 min
Histogram: 8 0 16 0 0 16 8 8 0 8
Nghost: 15043 ave 15311 max 14729 min
Histogram: 8 0 8 8 0 8 16 8 0 8
Neighs: 1.03562e+06 ave 1.08657e+06 max 986357 min
Histogram: 8 0 16 0 0 16 16 0 0 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 = 2744 900 1764
SHAKE stats (type/ave/delta) on step 0
1 0.957312 0.00034842
1 104.485 0.0719648
Memory usage per processor = 10.795 Mbytes
Step PotEng Temp E_vdwl E_coul Volume Press S/CPU
0 -2.4164866 450.00268 0.25444899 9.495168 1000000 2681.6722 0
500 -3.1077046 306.86615 0.31622537 8.7480173 955952.95 -1253.8452 40.504091
1000 -3.2043239 298.82128 0.34243217 8.6257832 906184.49 -799.66713 35.748569
1500 -3.2366359 300.98592 0.34391763 8.5919507 873462.51 -550.28446 36.006766
SHAKE stats (type/ave/delta) on step 2000
1 0.957187 3.91907e-06
1 104.52 0.000412683
2000 -3.2481602 299.9884 0.34347325 8.581075 851222 -286.84643 33.562239
2500 -3.259908 298.40341 0.34255531 8.5704014 837945.2 -129.41356 34.00444
3000 -3.2617895 298.31092 0.34421476 8.5667716 832206.76 8.8400155 32.532397
3500 -3.2671504 298.90189 0.34327175 8.562567 829684.27 -28.7516 33.457689
SHAKE stats (type/ave/delta) on step 4000
1 0.957204 4.16062e-06
1 104.52 0.000602422
4000 -3.2678465 301.00602 0.34755093 8.5573175 829982.88 91.659058 32.22263
4500 -3.2601438 300.21902 0.34611689 8.5667295 831122.18 98.028758 33.367401
5000 -3.260451 300.92742 0.34095428 8.571437 830124.66 -18.557225 32.544782
5500 -3.2632413 300.54126 0.34087156 8.5688076 830512.09 -53.603898 32.944789
SHAKE stats (type/ave/delta) on step 6000
1 0.957203 4.63746e-06
1 104.52 0.000538516
6000 -3.2666689 300.46881 0.34163055 8.5645874 830685.53 -65.920436 32.327609
6500 -3.2651721 300.16077 0.3444511 8.5631291 829731.09 26.553756 33.2876
7000 -3.2675687 299.48889 0.34284613 8.5625102 830623.49 -32.091298 32.3446
7500 -3.2630105 298.52773 0.34530678 8.5644677 828805.4 81.763873 33.224521
SHAKE stats (type/ave/delta) on step 8000
1 0.957202 4.1759e-06
1 104.52 0.00053471
8000 -3.2659903 299.54359 0.34636056 8.5604593 828253.66 78.594443 32.237324
8500 -3.2624296 298.8526 0.34220114 8.5682185 831022.76 -26.695579 33.437551
9000 -3.26825 298.33793 0.3418415 8.5627666 832490.94 -131.19731 32.404516
9500 -3.2675216 299.134 0.34048302 8.5646679 828434.14 -68.260065 33.215929
SHAKE stats (type/ave/delta) on step 10000
1 0.957206 3.98311e-06
1 104.52 0.000452887
10000 -3.2663126 298.40364 0.34322539 8.5632372 830461.78 -29.899976 32.305622
Loop time of 298.593 on 128 procs (64 MPI x 2 OpenMP) for 10000 steps with 84000 atoms
Pair time (%) = 171.475 (57.4277)
Bond time (%) = 0.0159633 (0.00534617)
Kspce time (%) = 50.3823 (16.8732)
Neigh time (%) = 49.4863 (16.5732)
Comm time (%) = 12.3889 (4.14908)
Outpt time (%) = 0.00299207 (0.00100206)
Other time (%) = 14.8413 (4.97043)
FFT time (% of Kspce) = 8.58328 (17.0363)
FFT Gflps 3d (1d only) = 11.6873 85.3446
Nlocal: 1312.5 ave 1353 max 1271 min
Histogram: 3 1 9 9 9 12 6 7 4 4
Nghost: 16931.1 ave 17027 max 16825 min
Histogram: 2 2 4 12 13 7 8 10 4 2
Neighs: 1.24866e+06 ave 1.31202e+06 max 1.1902e+06 min
Histogram: 7 8 4 5 7 10 7 8 3 5
Total # of neighbors = 79914191
Ave neighs/atom = 951.359
Ave special neighs/atom = 2
Neighbor list builds = 886
Dangerous builds = 0
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