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lammps/bench-nsf/wat/log.wat-cpu-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 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 4 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 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 = 1960 540 2352
Memory usage per processor = 8.72471 Mbytes
Step PotEng Temp E_vdwl E_coul Volume Press S/CPU
0 656.3994 300 623.49127 10.7913 1000000 13052196 0
10 2.1079217 300 3.7701061 10.339662 1000000 159414.93 14.043902
20 -1.1179163 300 0.80326894 10.22405 1000000 29606.74 9.7251669
30 -1.5655692 300 0.48499927 10.091069 1000000 -9731.6391 6.9538322
40 -1.9463355 300 0.28516018 9.9194312 1000000 12954.493 10.307312
50 -2.0893851 300 0.24669742 9.7762412 1000000 -47892.348 5.4059603
60 -2.2889247 300 0.24527081 9.5871513 1000000 -46841.883 5.7471595
70 -2.376128 300 0.24645026 9.5407759 1000000 1822.4845 4.5957466
80 -2.4435302 300 0.2387176 9.4655479 1000000 -1702.9602 5.4155983
90 -2.5919177 300 0.22334347 9.3432737 1000000 -1627.152 5.96772
94 -2.6028222 300 0.2225795 9.3426266 1000000 2342.2348 4.0236586
Loop time of 14.4307 on 128 procs (128 MPI x 1 OpenMP) for 94 steps with 84000 atoms
Minimization stats:
Stopping criterion = energy tolerance
Energy initial, next-to-last, final =
656.399401959 -2.60267863594 -2.60282224851
Force two-norm initial, final = 2.24428e+07 1157.47
Force max component initial, final = 305690 9.74209
Final line search alpha, max atom move = 8.75884e-06 8.53294e-05
Iterations, force evaluations = 94 490
Pair time (%) = 9.2735 (64.2621)
Bond time (%) = 0.0265173 (0.183756)
Kspce time (%) = 4.40731 (30.5412)
Neigh time (%) = 0 (0)
Comm time (%) = 0.614191 (4.25613)
Outpt time (%) = 0.00151546 (0.0105016)
Other time (%) = 0.107701 (0.746329)
FFT time (% of Kspce) = 0.470208 (10.6688)
FFT Gflps 3d (1d only) = 2.00542 135.648
Nlocal: 656.25 ave 699 max 608 min
Histogram: 8 0 16 0 40 24 16 8 8 8
Nghost: 12144.8 ave 12548 max 11847 min
Histogram: 8 24 16 16 24 16 0 8 8 8
Neighs: 517812 ave 586277 max 471216 min
Histogram: 16 24 24 8 8 0 24 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 = 1960 540 2352
SHAKE stats (type/ave/delta) on step 0
1 0.95732 0.000311943
1 104.485 0.0645909
Memory usage per processor = 8.40853 Mbytes
Step PotEng Temp E_vdwl E_coul Volume Press S/CPU
0 -2.6042277 450.00268 0.2225795 9.3426266 1000000 726.25323 0
500 -3.1314835 301.89146 0.32072464 8.7198987 945347.48 -1209.0957 35.606203
1000 -3.2160372 299.69147 0.34547913 8.6110434 897995.17 -694.0596 32.809919
1500 -3.2401904 301.16723 0.34383553 8.5886738 865855.37 -437.58481 32.466676
SHAKE stats (type/ave/delta) on step 2000
1 0.957188 4.5822e-06
1 104.52 0.000479264
2000 -3.2543225 300.80315 0.33785051 8.5806795 846642.28 -353.53589 31.211078
2500 -3.2595886 300.92277 0.34758977 8.5655909 835052.69 68.894418 31.271026
3000 -3.2720021 300.96347 0.34977871 8.5511808 831696.2 73.965048 30.138116
3500 -3.2716958 300.41343 0.34401821 8.55704 831185.86 -60.531436 30.667456
SHAKE stats (type/ave/delta) on step 4000
1 0.957199 4.28848e-06
1 104.52 0.000435217
4000 -3.2657 300.074 0.34440315 8.5625672 830457.06 -2.7616726 29.94667
4500 -3.2665861 298.02166 0.34564465 8.5605798 830192.69 39.562868 30.708325
5000 -3.2627888 298.21304 0.34425097 8.5658722 829019.12 83.61901 29.927892
5500 -3.2660258 299.67422 0.34317174 8.5636332 827747.27 55.96567 30.591424
SHAKE stats (type/ave/delta) on step 6000
1 0.9572 4.20651e-06
1 104.52 0.000479431
6000 -3.2684017 300.2124 0.34091422 8.5634509 828101.57 -37.241208 30.094675
6500 -3.2667746 300.53523 0.34749862 8.5586903 830320.65 85.996138 30.54824
7000 -3.2658356 300.15203 0.34351953 8.5635026 831070.35 -13.571725 30.207765
7500 -3.2685767 302.08742 0.34192962 8.5624215 830476.31 -64.821888 30.754321
SHAKE stats (type/ave/delta) on step 8000
1 0.95721 4.3199e-06
1 104.52 0.000515818
8000 -3.264386 300.80542 0.34289207 8.5657084 829371.18 12.79446 29.963432
8500 -3.2676874 299.34649 0.34586025 8.5593872 829250.25 63.952124 30.820803
9000 -3.2647005 301.30774 0.34558608 8.5625929 831568.92 44.795656 30.021934
9500 -3.2718936 300.59427 0.3380024 8.5629262 828423.13 -157.39155 30.566609
SHAKE stats (type/ave/delta) on step 10000
1 0.957199 4.58319e-06
1 104.52 0.000474237
10000 -3.2681228 300.38195 0.34115339 8.5634076 827690.94 -23.428348 30.196503
Loop time of 323.888 on 128 procs (128 MPI x 1 OpenMP) for 10000 steps with 84000 atoms
Pair time (%) = 187.066 (57.7565)
Bond time (%) = 0.0137312 (0.0042395)
Kspce time (%) = 84.266 (26.0171)
Neigh time (%) = 23.6017 (7.28701)
Comm time (%) = 14.8946 (4.59871)
Outpt time (%) = 0.00302201 (0.000933042)
Other time (%) = 14.0422 (4.33552)
FFT time (% of Kspce) = 46.8281 (55.5717)
FFT Gflps 3d (1d only) = 2.14221 124.929
Nlocal: 656.25 ave 687 max 625 min
Histogram: 5 7 11 16 21 22 21 13 9 3
Nghost: 13810.3 ave 13986 max 13706 min
Histogram: 8 19 17 30 23 16 7 3 3 2
Neighs: 626292 ave 691393 max 561652 min
Histogram: 1 5 16 22 23 23 16 13 3 6
Total # of neighbors = 80165351
Ave neighs/atom = 954.349
Ave special neighs/atom = 2
Neighbor list builds = 886
Dangerous builds = 0
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