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lammps/bench-nsf/wat/log.wat-omp-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)
2 by 4 by 4 processor grid
using 4 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 4 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 = 18.4497 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 1.4651109
20 -1.1179164 300 0.8032691 10.22405 1000000 29606.38 1.0048228
30 -1.550068 300 0.45425986 10.07552 1000000 -7194.9234 0.7330491
40 -1.8056976 300 0.37185415 9.956739 1000000 26401.718 0.60681777
50 -2.0139685 300 0.31698509 9.8214529 1000000 -2147.5047 0.59620398
60 -2.1142989 300 0.29794602 9.7469688 1000000 6341.0782 0.54136256
70 -2.2379835 300 0.2785657 9.6449889 1000000 7611.2505 0.57662804
80 -2.3165759 300 0.26806491 9.5782704 1000000 4992.2914 0.52494271
89 -2.3627534 300 0.26200833 9.5389537 1000000 5189.3507 0.48696023
Loop time of 137.017 on 128 procs (32 MPI x 4 OpenMP) for 89 steps with 84000 atoms
Minimization stats:
Stopping criterion = energy tolerance
Energy initial, next-to-last, final =
656.399401958 -2.36253977921 -2.36275338231
Force two-norm initial, final = 2.24428e+07 1522.58
Force max component initial, final = 305690 15.6326
Final line search alpha, max atom move = 7.9201e-06 0.000123811
Iterations, force evaluations = 89 481
Pair time (%) = 80.8737 (59.0245)
Bond time (%) = 0.172307 (0.125756)
Kspce time (%) = 53.7669 (39.241)
Neigh time (%) = 0 (0)
Comm time (%) = 1.88835 (1.37819)
Outpt time (%) = 0.00174937 (0.00127676)
Other time (%) = 0.314185 (0.229303)
FFT time (% of Kspce) = 0.113634 (0.211346)
FFT Gflps 3d (1d only) = 7.85687 9.85394
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 0.957307 0.000395021
1 104.488 0.082611
Memory usage per processor = 17.9479 Mbytes
Step PotEng Temp E_vdwl E_coul Volume Press S/CPU
0 -2.3640272 450.00268 0.26200833 9.5389537 1000000 3192.4678 0
500 -3.0987721 305.88495 0.30645548 8.7670086 958039.49 -1431.7803 17.854701
1000 -3.1976145 298.75039 0.33534963 8.6394662 907473.13 -926.15572 15.658304
1500 -3.2340194 301.01999 0.33980021 8.5987667 872776.58 -606.36474 16.075608
SHAKE stats (type/ave/delta) on step 2000
1 0.957192 4.58865e-06
1 104.52 0.000433556
2000 -3.2525424 301.40012 0.34615747 8.5741866 850145.67 -183.85348 15.093001
2500 -3.263336 300.77269 0.34363973 8.5659094 837925.81 -143.74163 15.309719
3000 -3.2676013 298.09426 0.34490684 8.5603025 832386.01 -36.718543 14.339066
3500 -3.2688375 300.93221 0.34542384 8.5585242 829514.39 43.709407 15.140539
SHAKE stats (type/ave/delta) on step 4000
1 0.957203 4.83296e-06
1 104.52 0.000426559
4000 -3.2708293 300.59357 0.34859115 8.5533152 829235.03 107.15102 14.373868
4500 -3.2615571 298.92286 0.34220341 8.5690976 831018.66 -18.981569 14.944177
5000 -3.269589 299.18229 0.34141437 8.5618669 828636.12 -62.716029 14.275813
5500 -3.2684725 299.90287 0.34931223 8.5548429 829554.41 128.18759 14.983524
SHAKE stats (type/ave/delta) on step 6000
1 0.957197 4.45862e-06
1 104.52 0.000490763
6000 -3.2680519 298.86529 0.34438112 8.5605684 830542.96 -33.348414 14.400605
6500 -3.2629085 299.64957 0.34019545 8.5697142 832652.82 -112.5754 15.10415
7000 -3.2656569 300.03044 0.34123353 8.5660049 830364.14 -65.41323 14.428344
7500 -3.2662164 300.43814 0.34086775 8.5658232 831060 -75.166033 15.093605
SHAKE stats (type/ave/delta) on step 8000
1 0.9572 3.88085e-06
1 104.52 0.00041767
8000 -3.2664236 298.78303 0.34175702 8.5645315 830546.75 -72.844718 14.307071
8500 -3.2631404 299.93992 0.34470422 8.5649159 830624.47 28.433783 15.033573
9000 -3.2674132 299.80137 0.34410701 8.5611682 828106.77 27.787124 14.300598
9500 -3.2693403 299.93032 0.34488801 8.5585709 830366.67 -3.4231044 15.142609
SHAKE stats (type/ave/delta) on step 10000
1 0.957193 4.19643e-06
1 104.52 0.000431537
10000 -3.2664078 301.78078 0.34205558 8.5644222 828665.62 -9.153498 14.363225
Loop time of 667.963 on 128 procs (32 MPI x 4 OpenMP) for 10000 steps with 84000 atoms
Pair time (%) = 339.834 (50.8762)
Bond time (%) = 0.0512627 (0.00767449)
Kspce time (%) = 87.1782 (13.0514)
Neigh time (%) = 129.261 (19.3516)
Comm time (%) = 45.992 (6.88542)
Outpt time (%) = 0.00426503 (0.000638513)
Other time (%) = 65.6415 (9.82712)
FFT time (% of Kspce) = 12.8778 (14.7718)
FFT Gflps 3d (1d only) = 7.7898 32.7682
Nlocal: 2625 ave 2674 max 2569 min
Histogram: 1 0 1 6 7 6 5 2 3 1
Nghost: 23236.2 ave 23358 max 23103 min
Histogram: 1 1 4 4 6 3 6 4 1 2
Neighs: 2.50211e+06 ave 2.59389e+06 max 2.43562e+06 min
Histogram: 5 4 5 3 3 3 1 4 0 4
Total # of neighbors = 80067416
Ave neighs/atom = 953.184
Ave special neighs/atom = 2
Neighbor list builds = 890
Dangerous builds = 0
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