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lammps/bench-nsf/wat/log.wat-omp-3m2t-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 4 by 6 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 6 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 = 2156 540 1764
Memory usage per processor = 9.39809 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 6.3199733
20 -1.1179165 300 0.80326921 10.22405 1000000 29606.126 4.6002816
30 -1.5741496 300 0.45296414 10.074197 1000000 -26781.22 3.3126886
40 -1.7896319 300 0.36165722 9.9951426 1000000 -5363.4765 2.7495363
50 -2.1724128 300 0.26794176 9.7196457 1000000 9194.9241 3.5328898
60 -2.328528 300 0.2613013 9.5721096 1000000 4894.1388 2.7587281
70 -2.4167895 300 0.25155043 9.4960076 1000000 3851.5355 2.4133527
Loop time of 21.0111 on 192 procs (96 MPI x 2 OpenMP) for 70 steps with 84000 atoms
Minimization stats:
Stopping criterion = energy tolerance
Energy initial, next-to-last, final =
656.399401959 -2.41655866725 -2.41678952051
Force two-norm initial, final = 2.24428e+07 1338.05
Force max component initial, final = 305690 11.0303
Final line search alpha, max atom move = 7.51918e-06 8.29387e-05
Iterations, force evaluations = 70 337
Pair time (%) = 13.2823 (63.2156)
Bond time (%) = 0.0369634 (0.175923)
Kspce time (%) = 6.82542 (32.4848)
Neigh time (%) = 0 (0)
Comm time (%) = 0.719516 (3.42445)
Outpt time (%) = 0.00216058 (0.010283)
Other time (%) = 0.144752 (0.688932)
FFT time (% of Kspce) = 0.353133 (5.17379)
FFT Gflps 3d (1d only) = 1.98851 126.589
Nlocal: 875 ave 916 max 841 min
Histogram: 8 16 8 16 0 24 0 8 0 16
Nghost: 13101.3 ave 13284 max 12893 min
Histogram: 8 16 0 8 8 16 0 24 0 16
Neighs: 690417 ave 728833 max 660280 min
Histogram: 16 0 24 8 8 16 0 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 = 2156 540 1764
SHAKE stats (type/ave/delta) on step 0
1 0.957316 0.000353399
1 104.484 0.0714221
Memory usage per processor = 9.07824 Mbytes
Step PotEng Temp E_vdwl E_coul Volume Press S/CPU
0 -2.4183177 450.00268 0.25155043 9.4960076 1000000 2597.7791 0
500 -3.1049119 305.37018 0.31188408 8.7552767 955776.94 -1351.8233 32.747742
1000 -3.2018242 296.7355 0.33970935 8.6308075 905771.96 -853.64868 30.606375
1500 -3.2312961 299.73006 0.34270631 8.5987131 872111.84 -496.23801 30.176947
SHAKE stats (type/ave/delta) on step 2000
1 0.957188 4.81404e-06
1 104.52 0.000467538
2000 -3.2496502 299.31993 0.34061786 8.5824684 850719.66 -343.97838 29.527612
2500 -3.2547933 300.97566 0.34458147 8.5733747 837946.66 -21.644141 29.452535
3000 -3.2655593 298.88685 0.33833199 8.5688842 833145.43 -192.91825 28.728394
3500 -3.2642289 299.2309 0.34211932 8.5666091 830799.14 -37.41139 27.732352
SHAKE stats (type/ave/delta) on step 4000
1 0.957205 4.09692e-06
1 104.52 0.000432899
4000 -3.266937 300.34524 0.34494909 8.5609938 828715.76 66.32214 28.215182
4500 -3.2639609 300.28757 0.33856348 8.5702871 829516.62 -84.160146 28.326192
5000 -3.2650703 299.93134 0.3463779 8.5614361 829063.05 94.912402 28.265753
5500 -3.2671478 299.20845 0.33773389 8.5680075 829737.9 -144.59145 28.687129
SHAKE stats (type/ave/delta) on step 6000
1 0.957204 4.66488e-06
1 104.52 0.000416775
6000 -3.2667487 298.86544 0.34134698 8.5646086 828541.6 -50.398763 28.193675
6500 -3.2612559 299.40511 0.34328773 8.5684198 829597.29 42.301694 27.17959
7000 -3.2627221 300.19766 0.34278327 8.5673848 831541.01 -24.047157 27.975421
7500 -3.2687914 299.80014 0.34205326 8.5618881 829295.32 -62.135933 28.338597
SHAKE stats (type/ave/delta) on step 8000
1 0.9572 4.0524e-06
1 104.52 0.000506043
8000 -3.2654881 300.01035 0.34341403 8.5639644 830712.21 -37.194142 28.244051
8500 -3.2621471 299.20478 0.34271569 8.5680785 830777.21 -7.2654416 28.738044
9000 -3.2681417 298.85613 0.3443648 8.5602675 829463.96 0.30906245 28.510282
9500 -3.2589874 298.8676 0.33660739 8.5771556 830568.68 -118.04455 28.884373
SHAKE stats (type/ave/delta) on step 10000
1 0.957202 5.23857e-06
1 104.52 0.000643792
10000 -3.2670999 301.55361 0.34334141 8.5623377 828034.99 23.798493 27.418606
Loop time of 347.841 on 192 procs (96 MPI x 2 OpenMP) for 10000 steps with 84000 atoms
Pair time (%) = 167.067 (48.0296)
Bond time (%) = 0.0254148 (0.00730646)
Kspce time (%) = 88.8077 (25.5311)
Neigh time (%) = 37.6125 (10.8131)
Comm time (%) = 25.4734 (7.32328)
Outpt time (%) = 0.00827703 (0.00237954)
Other time (%) = 28.8472 (8.29321)
FFT time (% of Kspce) = 50.8844 (57.2973)
FFT Gflps 3d (1d only) = 1.97144 118.633
Nlocal: 875 ave 920 max 827 min
Histogram: 2 3 7 13 15 25 21 5 3 2
Nghost: 14865.2 ave 14997 max 14737 min
Histogram: 5 6 8 12 19 11 17 11 4 3
Neighs: 834802 ave 909518 max 745617 min
Histogram: 1 2 4 10 24 18 21 12 1 3
Total # of neighbors = 80141013
Ave neighs/atom = 954.06
Ave special neighs/atom = 2
Neighbor list builds = 889
Dangerous builds = 0
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