Homec4science
Diffusion lammps (efficient_neuronet) Browse

lammps/test-user-omp/bench_sdk-coul/log.sdk-coul.4
e3eb61765260efficient_neuronet

Last Change
Raw File

log.sdk-coul.4
View Options

LAMMPS (1 Feb 2012-ICMS)
using 1 OpenMP thread(s) per MPI task
# coarse grained SDS surfactant monolayer
units real
dimension 3
atom_style full
processors * * 1
read_data data.sdk-coul
1 = max bonds/atom
1 = max angles/atom
orthogonal box = (-27.713 -27.713 -200) to (193.991 83.139 200)
4 by 1 by 1 MPI processor grid
31280 atoms
31280 velocities
4096 bonds
3072 angles
2 = max # of 1-2 neighbors
2 = max # of 1-3 neighbors
2 = max # of 1-4 neighbors
4 = max # of special neighbors
pair_style hybrid/overlay lj/sdk 15.0 coul/long 25.0
bond_style harmonic
angle_style sdk
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 # SO4 SO4
pair_coeff 1 4 coul/long # SO4 SOD
pair_coeff 4 4 coul/long # SOD SOD
pair_coeff 1 1 lj/sdk lj9_6 0.7000 4.3210 # SO4 SO4
pair_coeff 1 2 lj/sdk lj9_6 0.3830 4.4135 # SO4 CM
pair_coeff 1 3 lj/sdk lj9_6 0.4050 4.4530 # SO4 CT
pair_coeff 1 4 lj/sdk lj12_4 1.1000 4.1000 # SO4 SOD
pair_coeff 1 5 lj/sdk lj12_4 1.1000 4.1000 # SO4 W
pair_coeff 2 2 lj/sdk lj9_6 0.4200 4.5060 # CM CM
pair_coeff 2 3 lj/sdk lj9_6 0.4440 4.5455 # CT CM
pair_coeff 2 4 lj/sdk lj12_4 0.3400 4.4385 # SOD CM
pair_coeff 2 5 lj/sdk lj12_4 0.3400 4.4385 # W CM
pair_coeff 3 3 lj/sdk lj9_6 0.4690 4.5850 # CT CT
pair_coeff 3 4 lj/sdk lj12_4 0.3600 4.4780 # SOD CT
pair_coeff 3 5 lj/sdk lj12_4 0.3600 4.4780 # W CT
pair_coeff 4 4 lj/sdk lj12_4 0.3500 4.3710 # SOD SOD
pair_coeff 4 5 lj/sdk lj12_4 0.8950 4.3710 # SOD W
pair_coeff 5 5 lj/sdk 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 # SO4 CM CM
angle_coeff 2 1.1900 173.0000 # CM CM CM
angle_coeff 3 1.1900 175.0000 # CM CM CT
group charged type 1 4
2048 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
thermo 10
run 100
PPPM initialization ...
G vector = 0.0428753
grid = 8 4 15
stencil order = 3
RMS precision = 5.85298e-06
using single precision FFTs
brick FFT buffer size/proc = 630 128 756
PPPM/cg optimization cutoff: 1e-05
Total charged atoms: 6.5%
Min/max charged atoms/proc: 6.4% 6.7%
Memory usage per processor = 11.708 Mbytes
Step Temp E_pair E_mol TotEng Press
0 310.0934 -247028.33 2566.2036 -215550.03 -14.564874
10 310.8909 -247060.61 2549.5104 -215524.64 -18.063059
20 310.29495 -247016.32 2542.4915 -215542.93 -19.150562
30 308.136 -247022 2602.2787 -215690.12 -17.36493
40 309.40258 -247054.33 2559.0404 -215647.6 -15.39733
50 309.11598 -246751.69 2571.2255 -215359.49 -7.4039591
60 312.52518 -246963.1 2619.2856 -215204.98 -15.226968
70 310.11487 -246939.89 2591.9175 -215433.87 -16.132276
80 310.48392 -247086.98 2595.4468 -215543.02 -18.074376
90 309.59594 -247062.3 2604.9206 -215591.66 -14.562971
100 309.74689 -247001.01 2604.4215 -215516.8 -12.793708
Loop time of 2.97498 on 4 procs (4 MPI x 1 OpenMP) for 100 steps with 31280 atoms
Performance: 29.042 ns/day 0.826 hours/ns 33.614 timesteps/s
Section | min time | avg time | max time |%total | #Thr
--------------------------------------------------------------
Pair | 2.131 | 2.185 | 2.307 | 73.44 | 1.0x
Bond | 0.01661 | 0.01731 | 0.01783 | 0.58 | 1.0x
Kspace | 0.02436 | 0.17 | 0.2293 | 5.71 | 1.0x
Neigh | 0.5261 | 0.5372 | 0.5597 | 18.06 | 1.0x
Comm | 0.03092 | 0.03134 | 0.03169 | 1.05 | 0.9x
Output | 0.0006406 | 0.0007225 | 0.0008225 | 0.02 | 1.0x
Modify | 0.02674 | 0.02713 | 0.02768 | 0.91 | 1.1x
Other | | 0.006486 | | 0.22 |
FFT time (% of Kspce) = 0.00330567 (1.94489)
FFT Gflps 3d (1d only) = 1.79293 3.03899
Nlocal: 7820 ave 7865 max 7775 min
Histogram: 1 0 1 0 0 0 0 0 1 1
Nghost: 9115.5 ave 9137 max 9099 min
Histogram: 1 1 0 0 0 0 1 0 0 1
Neighs: 851928 ave 855085 max 848655 min
Histogram: 1 1 0 0 0 0 0 0 1 1
Total # of neighbors = 3407714
Ave neighs/atom = 108.942
Ave special neighs/atom = 0.458312
Neighbor list builds = 10
Dangerous builds = 0
c4science · Help