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lammps/bench-nsf/wat/log.wat-omp-6m1t-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)
4 by 6 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 6 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/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 = 1540 324 1848
Memory usage per processor = 7.75757 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 10.775757
20 -1.1179164 300 0.80326907 10.22405 1000000 29606.435 7.4098826
30 -1.541312 300 0.45440055 10.075508 1000000 -5658.4713 5.4482851
40 -1.883827 300 0.34602581 9.9153825 1000000 25422.216 4.4986903
50 -2.061189 300 0.30376874 9.7862507 1000000 20401.93 4.2102072
60 -2.1011319 300 0.29764208 9.7540907 1000000 -6423.5 3.6852054
70 -2.2660352 300 0.27172836 9.6081359 1000000 14975.089 4.2046681
80 -2.3056374 300 0.26834141 9.5885637 1000000 7398.013 3.4654141
90 -2.4814838 300 0.24650441 9.436118 1000000 4745.6516 4.8269029
100 -2.5820556 300 0.2350563 9.3507893 1000000 3567.3218 4.3387241
Loop time of 21.0654 on 192 procs (192 MPI x 1 OpenMP) for 100 steps with 84000 atoms
Minimization stats:
Stopping criterion = energy tolerance
Energy initial, next-to-last, final =
656.399401958 -2.58185497425 -2.58205561146
Force two-norm initial, final = 2.24428e+07 1829.26
Force max component initial, final = 305690 23.4696
Final line search alpha, max atom move = 1.91763e-05 0.000450061
Iterations, force evaluations = 100 544
Pair time (%) = 9.18869 (43.6198)
Bond time (%) = 0.0296899 (0.140942)
Kspce time (%) = 10.1678 (48.2677)
Neigh time (%) = 0 (0)
Comm time (%) = 1.47011 (6.9788)
Outpt time (%) = 0.00338993 (0.0160924)
Other time (%) = 0.205759 (0.976759)
FFT time (% of Kspce) = 1.29568 (12.743)
FFT Gflps 3d (1d only) = 0.77423 198.244
Nlocal: 437.5 ave 487 max 387 min
Histogram: 8 16 8 32 16 48 16 32 8 8
Nghost: 10499.7 ave 10873 max 10263 min
Histogram: 8 40 48 16 16 16 16 16 8 8
Neighs: 345208 ave 411558 max 294959 min
Histogram: 16 16 24 32 32 24 16 24 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 = 1540 324 1848
SHAKE stats (type/ave/delta) on step 0
1 0.957312 0.000618498
1 104.484 0.0888215
Memory usage per processor = 7.44505 Mbytes
Step PotEng Temp E_vdwl E_coul Volume Press S/CPU
0 -2.5835685 450.00268 0.2350563 9.3507893 1000000 1130.7596 0
500 -3.1311461 302.70257 0.3198182 8.7214274 946662.07 -1240.1082 25.319998
1000 -3.2086024 300.15448 0.34183657 8.6222047 899679.07 -754.57214 24.761747
1500 -3.2383769 300.97119 0.34002834 8.5943533 866738.9 -519.62412 24.294012
SHAKE stats (type/ave/delta) on step 2000
1 0.957191 4.07217e-06
1 104.52 0.000526575
2000 -3.2527924 299.07346 0.34576864 8.5742445 847121.84 -159.38553 23.337789
2500 -3.2571914 298.38823 0.34083601 8.5747466 836318.81 -125.32821 23.728078
3000 -3.2682801 299.55934 0.34590992 8.5585594 830524.8 39.079003 23.449503
3500 -3.2662926 298.2148 0.34416894 8.5623542 829475.05 13.516353 23.434069
SHAKE stats (type/ave/delta) on step 4000
1 0.957203 4.14227e-06
1 104.52 0.000451551
4000 -3.2693029 300.86397 0.34518112 8.5582556 829188.12 53.116032 22.429218
4500 -3.2651602 300.9431 0.34421976 8.5634559 828957.72 54.696493 22.653545
5000 -3.2708325 300.87877 0.34157941 8.5603822 828562.73 -34.890205 23.0548
5500 -3.267119 300.22783 0.35109588 8.5546953 829874.04 171.67408 23.48617
SHAKE stats (type/ave/delta) on step 6000
1 0.957204 4.12842e-06
1 104.52 0.000491438
6000 -3.2633145 299.02224 0.34749948 8.5620523 830361.87 97.308269 23.170876
6500 -3.2644215 299.95008 0.34015489 8.5682277 827990.77 -32.795962 23.652879
7000 -3.2693546 300.22269 0.34255203 8.5609601 831241.23 -88.654862 23.464589
7500 -3.2679802 301.05849 0.34093113 8.5639847 828895.41 -39.363238 23.311321
SHAKE stats (type/ave/delta) on step 8000
1 0.957198 4.49512e-06
1 104.52 0.000529856
8000 -3.2660703 298.96131 0.34309323 8.5637643 829262.78 -0.1047861 22.149295
8500 -3.2652172 300.02764 0.34795002 8.5596259 828881.9 151.81509 23.524729
9000 -3.2675977 300.44654 0.34513707 8.560125 828155.8 69.245537 23.079097
9500 -3.2640156 299.21328 0.34247556 8.5662312 830913.61 -27.537829 23.075565
SHAKE stats (type/ave/delta) on step 10000
1 0.957196 4.55017e-06
1 104.52 0.000465493
10000 -3.2679089 301.61621 0.34431706 8.560617 827187.38 74.215793 22.28717
Loop time of 428.088 on 192 procs (192 MPI x 1 OpenMP) for 10000 steps with 84000 atoms
Pair time (%) = 161.614 (37.7526)
Bond time (%) = 0.0262945 (0.00614231)
Kspce time (%) = 181.337 (42.3599)
Neigh time (%) = 18.7438 (4.37851)
Comm time (%) = 35.7621 (8.35391)
Outpt time (%) = 0.00797678 (0.00186335)
Other time (%) = 30.596 (7.14713)
FFT time (% of Kspce) = 129.118 (71.2032)
FFT Gflps 3d (1d only) = 0.776929 201.262
Nlocal: 437.5 ave 478 max 408 min
Histogram: 6 14 27 47 29 43 16 8 1 1
Nghost: 12040.1 ave 12180 max 11928 min
Histogram: 5 18 29 26 37 33 22 13 7 2
Neighs: 417811 ave 487303 max 370812 min
Histogram: 8 11 31 48 41 27 18 4 3 1
Total # of neighbors = 80219658
Ave neighs/atom = 954.996
Ave special neighs/atom = 2
Neighbor list builds = 888
Dangerous builds = 0
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