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lammps/bench-nsf/sds/log.sds-omp-3m2t-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)
6 by 8 by 1 processor grid
using 2 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)
6 by 8 by 1 processor grid
using 2 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 = 204 96 306
Using pppm/cg optimization. Cutoff: 1e-05.
Total charged: 6.5%. Max. charged / proc: 6.6%.
Memory usage per processor = 7.51773 Mbytes
Step PotEng Temp E_vdwl E_coul S/CPU
0 -1981519.5 325 -1997095.2 -4150.0182 0
500 -1953554.3 309.76392 -1971036.9 -4131.2881 46.732911
1000 -1943529.3 309.98447 -1960924 -4125.6203 45.656176
1500 -1953049.3 310.18681 -1970287.4 -4121.0158 45.632079
2000 -1954286.9 309.94189 -1971375.7 -4138.8282 45.971199
2500 -1948338.5 309.3461 -1965593.5 -4147.0304 45.731893
3000 -1950287.8 309.75266 -1967402 -4218.0361 45.011571
3500 -1952751.7 309.03431 -1969806.2 -4180.6701 45.343774
4000 -1949816.9 309.94268 -1967205.9 -4176.4718 45.772733
4500 -1950162.1 310.41252 -1967369.8 -4177.5894 44.097645
5000 -1950795.1 310.54192 -1967781.3 -4251.752 43.537415
5500 -1948878.3 310.39728 -1967892.2 -4245.932 43.437671
6000 -1941741.3 309.80863 -1967974 -4223.8275 42.921572
6500 -1942230.9 310.2562 -1968444.3 -4185.2708 42.662691
7000 -1942767.6 309.99425 -1968830.3 -4171.8858 43.365638
7500 -1942458.4 310.01322 -1968506.1 -4201.2367 42.004385
8000 -1940498 309.98985 -1967019.1 -4210.992 43.604673
8500 -1922795.1 309.27509 -1967450.6 -4245.3316 43.7942
9000 -1913263 310.87435 -1966835.9 -4224.3214 43.80319
9500 -1904931.1 309.46917 -1966801.9 -4191.8725 41.329152
10000 -1896862.9 310.35157 -1967166.7 -4064.864 40.726724
Loop time of 227.284 on 96 procs (48 MPI x 2 OpenMP) for 10000 steps with 250240 atoms
Pair time (%) = 107.535 (47.3131)
Bond time (%) = 1.87672 (0.825716)
Kspce time (%) = 41.6071 (18.3062)
Neigh time (%) = 51.9616 (22.8619)
Comm time (%) = 17.6449 (7.76337)
Outpt time (%) = 0.00537522 (0.00236498)
Other time (%) = 6.65334 (2.92732)
FFT time (% of Kspce) = 21.247 (51.0658)
FFT Gflps 3d (1d only) = 0.320701 64.1518
Nlocal: 5213.33 ave 5430 max 5038 min
Histogram: 1 1 9 11 11 7 3 2 2 1
Nghost: 7434.38 ave 7560 max 7249 min
Histogram: 1 1 2 8 5 6 6 8 7 4
Neighs: 566213 ave 588941 max 546692 min
Histogram: 1 5 3 8 13 8 3 5 0 2
Total # of neighbors = 27178209
Ave neighs/atom = 108.609
Ave special neighs/atom = 0.458312
Neighbor list builds = 1080
Dangerous builds = 0
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