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lammps/bench-nsf/sds/log.sds-omp-2m3t-kraken
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LAMMPS (19 Nov 2010-ICMS)
# lammps input script
units real
dimension 3
atom_style full
processors * * 1
read_data DATA.FILE
1 = max bonds/atom
1 = max angles/atom
0 = max impropers/atom
orthogonal box = (-27.713 -27.713 -200) to (27.713 27.713 200)
4 by 8 by 1 processor grid
using 3 OpenMP thread(s) per MPI task
3910 atoms
512 bonds
384 angles
0 impropers
2 = max # of 1-2 neighbors
2 = max # of 1-3 neighbors
2 = max # of 1-4 neighbors
4 = max # of special neighbors
include PARM.FILE-omp
# Generated by setup_lammps
pair_style hybrid/overlay cg/cmm/omp 15.0 coul/long/omp 25.0
bond_style harmonic
angle_style cg/cmm
special_bonds lj/coul 0.0 0.0 1.0
2 = max # of 1-2 neighbors
2 = max # of 1-3 neighbors
4 = max # of special neighbors
mass 1 96.0576 # SO4
mass 2 42.0804 # CM
mass 3 43.0883 # CT
mass 4 77.0342 # SOD
mass 5 54.0460 # W
pair_coeff 1 1 coul/long/omp # SO4 SO4
pair_coeff 1 4 coul/long/omp # SO4 SOD
pair_coeff 4 4 coul/long/omp # SOD SOD
pair_coeff 1 1 cg/cmm/omp lj9_6 0.7000 4.3210 # SO4 SO4
pair_coeff 1 2 cg/cmm/omp lj9_6 0.3830 4.4135 # SO4 CM
pair_coeff 1 3 cg/cmm/omp lj9_6 0.4050 4.4530 # SO4 CT
pair_coeff 1 4 cg/cmm/omp lj12_4 1.1000 4.1000 # SO4 SOD
pair_coeff 1 5 cg/cmm/omp lj12_4 1.1000 4.1000 # SO4 W
pair_coeff 2 2 cg/cmm/omp lj9_6 0.4200 4.5060 # CM CM
pair_coeff 2 3 cg/cmm/omp lj9_6 0.4440 4.5455 # CT CM
pair_coeff 2 4 cg/cmm/omp lj12_4 0.3400 4.4385 # SOD CM
pair_coeff 2 5 cg/cmm/omp lj12_4 0.3400 4.4385 # W CM
pair_coeff 3 3 cg/cmm/omp lj9_6 0.4690 4.5850 # CT CT
pair_coeff 3 4 cg/cmm/omp lj12_4 0.3600 4.4780 # SOD CT
pair_coeff 3 5 cg/cmm/omp lj12_4 0.3600 4.4780 # W CT
pair_coeff 4 4 cg/cmm/omp lj12_4 0.3500 4.3710 # SOD SOD
pair_coeff 4 5 cg/cmm/omp lj12_4 0.8950 4.3710 # SOD W
pair_coeff 5 5 cg/cmm/omp lj12_4 0.8950 4.3710 # W W
bond_coeff 1 11.0000 3.6300 # SO4 CM
bond_coeff 2 6.1600 3.6400 # CM CM
bond_coeff 3 6.1600 3.6500 # CM CT
angle_coeff 1 1.1000 178.0000 lj9_6 0.3830 4.4135 # SO4 CM CM
angle_coeff 2 1.1900 173.0000 lj9_6 0.4200 4.5060 # CM CM CM
angle_coeff 3 1.1900 175.0000 lj9_6 0.4440 4.5455 # CM CM CT
replicate 8 8 1
orthogonal box = (-27.713 -27.713 -200) to (415.695 415.695 200)
4 by 8 by 1 processor grid
using 3 OpenMP thread(s) per MPI task
250240 atoms
32768 bonds
24576 angles
2 = max # of 1-2 neighbors
2 = max # of 1-3 neighbors
4 = max # of special neighbors
group charged type 1 4
16384 atoms in group charged
atom_modify first charged
kspace_style pppm/cg 0.00001
kspace_modify order 3
communicate multi
neighbor 2.0 multi
neigh_modify delay 4 every 2 check yes
timestep 10.0
fix 1 all nvt temp 310.0 310.0 100.0 drag 0.1
thermo_style custom step pe temp evdwl ecoul spcpu
thermo 500
velocity all create 325.0 63443
run 10000
PPPM initialization ...
G vector = 0.0449352
grid = 15 15 15
stencil order = 3
RMS precision = 5.22732e-06
using single precision FFTs
WARNING: Reducing PPPM order b/c stencil extends beyond neighbor processor
G vector = 0.0443745
grid = 15 15 15
stencil order = 2
RMS precision = 5.39734e-06
using single precision FFTs
WARNING: Reducing PPPM order b/c stencil extends beyond neighbor processor
G vector = 0.0327087
grid = 16 16 16
stencil order = 1
RMS precision = 9.46139e-06
using single precision FFTs
brick FFT buffer size/proc = 255 128 255
Using pppm/cg optimization. Cutoff: 1e-05.
Total charged: 6.5%. Max. charged / proc: 6.5%.
Memory usage per processor = 9.53856 Mbytes
Step PotEng Temp E_vdwl E_coul S/CPU
0 -1981859.4 325 -1997095.2 -4150.0182 0
500 -1954697.5 309.90836 -1971647.5 -4139.1468 45.386866
1000 -1943697.3 310.41752 -1960744.3 -4110.2578 44.341902
1500 -1953760.7 310.88834 -1970500.5 -4131.4641 44.183744
2000 -1954151.9 309.95944 -1970702.9 -4172.8645 43.090503
2500 -1948533.6 310.68282 -1965182 -4171.7933 42.732734
3000 -1950689.4 310.22726 -1967406.4 -4214.8182 42.302176
3500 -1952440.9 310.63722 -1969152.1 -4198.3893 41.111098
4000 -1951638.6 310.11911 -1968158 -4142.7944 41.795579
4500 -1951064.8 310.47789 -1967799 -4170.2511 41.175681
5000 -1951550.2 310.12137 -1968187 -4181.2885 40.091633
5500 -1950678.7 309.90537 -1967296.7 -4185.5982 41.283415
6000 -1951293.1 310.07527 -1967990.3 -4120.5143 41.090621
6500 -1951377 309.11178 -1968065.2 -4143.7684 41.107387
7000 -1951153 311.03652 -1967880.2 -4179.4063 40.69033
7500 -1951794.5 309.50491 -1968450 -4218.3402 40.680831
8000 -1950539.7 309.72845 -1967246.6 -4185.3063 40.150497
8500 -1950440.2 310.03799 -1967169.2 -4201.4744 39.462028
9000 -1952821.3 310.04396 -1969384.7 -4246.1391 39.315034
9500 -1952039.8 310.36855 -1968749.9 -4232.4807 39.744803
10000 -1950404.9 310.66648 -1967118.2 -4191.5492 39.151318
Loop time of 241.685 on 96 procs (32 MPI x 3 OpenMP) for 10000 steps with 250240 atoms
Pair time (%) = 112.963 (46.7396)
Bond time (%) = 2.82083 (1.16715)
Kspce time (%) = 25.4351 (10.5241)
Neigh time (%) = 79.1081 (32.7318)
Comm time (%) = 13.6006 (5.62741)
Outpt time (%) = 0.00603206 (0.00249583)
Other time (%) = 7.75183 (3.20741)
FFT time (% of Kspce) = 13.3741 (52.5814)
FFT Gflps 3d (1d only) = 0.509484 55.5956
Nlocal: 7820 ave 7964 max 7697 min
Histogram: 2 3 4 4 6 4 2 3 1 3
Nghost: 9103.47 ave 9249 max 8938 min
Histogram: 1 1 1 3 8 7 6 2 2 1
Neighs: 849882 ave 874104 max 833323 min
Histogram: 4 1 5 9 5 0 3 3 1 1
Total # of neighbors = 27196227
Ave neighs/atom = 108.681
Ave special neighs/atom = 0.458312
Neighbor list builds = 1049
Dangerous builds = 0
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