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lammps/bench-nsf/wat/log.wat-omp-1m6t-kraken
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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)
2 by 4 by 4 processor grid
using 6 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)
2 by 4 by 4 processor grid
using 6 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 = 4508 2592 2898
Memory usage per processor = 18.4498 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 159414.92 3.2442136
20 -1.1179165 300 0.80326914 10.22405 1000000 29606.271 2.267402
30 -1.5639686 300 0.45384911 10.075243 1000000 -13191.14 1.0719415
40 -1.6852376 300 0.4261297 10.043494 1000000 16498.33 0.73878017
50 -2.0779265 300 0.28870032 9.7911791 1000000 1555.8564 1.660448
60 -2.1298458 300 0.28189046 9.7352655 1000000 -21833.865 1.0819386
70 -2.2972265 300 0.26359566 9.5740581 1000000 14818.112 1.1216859
77 -2.3655048 300 0.25920911 9.5389261 1000000 3454.8032 1.0147197
Loop time of 61.4362 on 192 procs (32 MPI x 6 OpenMP) for 77 steps with 84000 atoms
Minimization stats:
Stopping criterion = energy tolerance
Energy initial, next-to-last, final =
656.399401959 -2.36531325198 -2.36550479556
Force two-norm initial, final = 2.24428e+07 1533.54
Force max component initial, final = 305690 14.1482
Final line search alpha, max atom move = 1.35901e-05 0.000192276
Iterations, force evaluations = 77 402
Pair time (%) = 44.0378 (71.6805)
Bond time (%) = 0.1229 (0.200045)
Kspce time (%) = 12.4179 (20.2127)
Neigh time (%) = 0 (0)
Comm time (%) = 4.38916 (7.14425)
Outpt time (%) = 0.00312095 (0.00507999)
Other time (%) = 0.465304 (0.757377)
FFT time (% of Kspce) = 0.964052 (7.76338)
FFT Gflps 3d (1d only) = 0.801233 39.9186
Nlocal: 2625 ave 2655 max 2595 min
Histogram: 8 8 0 0 0 0 0 0 8 8
Nghost: 21035.8 ave 21338 max 20699 min
Histogram: 8 0 0 0 0 16 0 0 0 8
Neighs: 2.07125e+06 ave 2.10053e+06 max 2.0368e+06 min
Histogram: 8 0 8 0 0 0 0 0 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 = 4508 2592 2898
SHAKE stats (type/ave/delta) on step 0
1 0.957322 0.000356004
1 104.487 0.0506388
Memory usage per processor = 17.948 Mbytes
Step PotEng Temp E_vdwl E_coul Volume Press S/CPU
0 -2.3668301 450.00268 0.25920911 9.5389261 1000000 3095.6739 0
500 -3.0972283 306.49397 0.31216832 8.762622 958027.05 -1293.6433 24.120304
1000 -3.2010541 298.45685 0.3390283 8.632231 907925.15 -853.1804 21.293804
1500 -3.2299247 300.288 0.34455776 8.5980318 873883.75 -478.49572 18.063812
SHAKE stats (type/ave/delta) on step 2000
1 0.957188 4.23856e-06
1 104.52 0.000524286
2000 -3.2491286 299.51907 0.34385105 8.5797688 852963.81 -280.64889 20.639415
2500 -3.2648468 298.12315 0.34315346 8.5649065 838450.94 -161.2679 17.479711
3000 -3.2660704 301.71691 0.34237703 8.5641791 833413.87 -99.174536 16.805819
3500 -3.2648593 299.12048 0.34651278 8.5615793 830328.95 73.273564 20.225352
SHAKE stats (type/ave/delta) on step 4000
1 0.957201 4.32387e-06
1 104.52 0.000483356
4000 -3.2659834 299.77839 0.34471457 8.5621973 829341.95 64.979394 17.276783
4500 -3.2687287 298.87602 0.34363532 8.5602414 828408.3 7.0867566 21.457598
5000 -3.2670469 301.50152 0.34305729 8.562665 828214.95 38.481991 18.189636
5500 -3.2658635 301.08395 0.34021426 8.5669004 830488.06 -85.929734 18.265004
SHAKE stats (type/ave/delta) on step 6000
1 0.957201 4.16211e-06
1 104.52 0.000513388
6000 -3.2663989 299.40906 0.34451896 8.5617587 829960.79 10.394152 18.197058
6500 -3.2670736 301.5868 0.34480753 8.5609649 829199.23 32.934559 16.350225
7000 -3.2703535 301.17272 0.34090329 8.5615538 829901.77 -82.524107 21.295094
7500 -3.2678903 300.26241 0.3422692 8.5625371 829358.85 -23.114079 21.550473
SHAKE stats (type/ave/delta) on step 8000
1 0.957199 3.99987e-06
1 104.52 0.000476334
8000 -3.2673426 300.25942 0.34234314 8.562955 828882.85 -29.700566 20.939228
8500 -3.265462 299.63005 0.34620036 8.5611578 832423.48 8.1221413 21.948678
9000 -3.266206 300.52544 0.3442258 8.562571 829829.09 18.94273 21.195348
9500 -3.2660267 300.14672 0.33853924 8.5683144 832019.96 -175.59062 21.671755
SHAKE stats (type/ave/delta) on step 10000
1 0.957204 3.91254e-06
1 104.52 0.000458072
10000 -3.2680365 300.1219 0.34065359 8.5642014 827108.61 -22.00076 21.045047
Loop time of 508.116 on 192 procs (32 MPI x 6 OpenMP) for 10000 steps with 84000 atoms
Pair time (%) = 176.739 (34.7831)
Bond time (%) = 0.0249199 (0.00490436)
Kspce time (%) = 106.119 (20.8847)
Neigh time (%) = 114.88 (22.609)
Comm time (%) = 40.2467 (7.92076)
Outpt time (%) = 0.0082835 (0.00163024)
Other time (%) = 70.0988 (13.7958)
FFT time (% of Kspce) = 23.3863 (22.0379)
FFT Gflps 3d (1d only) = 4.2895 39.0367
Nlocal: 2625 ave 2672 max 2573 min
Histogram: 1 2 4 3 5 2 6 5 3 1
Nghost: 23246.7 ave 23334 max 23167 min
Histogram: 3 2 2 5 6 5 2 2 3 2
Neighs: 2.50711e+06 ave 2.62335e+06 max 2.40804e+06 min
Histogram: 3 5 0 5 6 4 3 2 3 1
Total # of neighbors = 80227422
Ave neighs/atom = 955.088
Ave special neighs/atom = 2
Neighbor list builds = 888
Dangerous builds = 0
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