Homec4science
Diffusion lammps (efficient_neuronet) Browse

lammps/bench-nsf/sds/log.sds-cpu-ranger
909931539d6defficient_neuronet

Last Change
Raw File

log.sds-cpu-ranger
View Options

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)
8 by 16 by 1 processor grid
using 1 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
# Generated by setup_lammps
pair_style cg/cmm/coul/long 15.0
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 lj9_6 0.7000 4.3210 # SO4 SO4
pair_coeff 1 2 lj9_6 0.3830 4.4135 # SO4 CM
pair_coeff 1 3 lj9_6 0.4050 4.4530 # SO4 CT
pair_coeff 1 4 lj12_4 1.1000 4.1000 # SO4 SOD
pair_coeff 1 5 lj12_4 1.1000 4.1000 # SO4 W
pair_coeff 2 2 lj9_6 0.4200 4.5060 # CM CM
pair_coeff 2 3 lj9_6 0.4440 4.5455 # CT CM
pair_coeff 2 4 lj12_4 0.3400 4.4385 # SOD CM
pair_coeff 2 5 lj12_4 0.3400 4.4385 # W CM
pair_coeff 3 3 lj9_6 0.4690 4.5850 # CT CT
pair_coeff 3 4 lj12_4 0.3600 4.4780 # SOD CT
pair_coeff 3 5 lj12_4 0.3600 4.4780 # W CT
pair_coeff 4 4 lj12_4 0.3500 4.3710 # SOD SOD
pair_coeff 4 5 lj12_4 0.8950 4.3710 # SOD W
pair_coeff 5 5 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)
8 by 16 by 1 processor grid
using 1 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
kspace_style pppm/cg 0.00001
kspace_modify order 3
neighbor 2.0 bin
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 = 0.079973
grid = 30 30 25
stencil order = 3
RMS precision = 5.65346e-06
using single precision FFTs
WARNING: Reducing PPPM order b/c stencil extends beyond neighbor processor
G vector = 0.0777637
grid = 30 30 25
stencil order = 2
RMS precision = 6.11594e-06
using single precision FFTs
WARNING: Reducing PPPM order b/c stencil extends beyond neighbor processor
G vector = 0.0630598
grid = 40 40 45
stencil order = 1
RMS precision = 9.74324e-06
using single precision FFTs
brick FFT buffer size/proc = 1104 675 1656
Using pppm/cg optimization. Cutoff: 1e-05.
Total charged: 6.5%. Max. charged / proc: 6.7%.
Memory usage per processor = 4.94242 Mbytes
Step PotEng Temp E_vdwl E_coul S/CPU
0 -1982521.9 325 -1997095.2 -3580.9623 0
500 -1954651.7 309.48015 -1970868.5 -3688.9586 34.321342
1000 -1944467.9 308.91013 -1960838.5 -3589.5387 34.058124
1500 -1953098.8 309.34819 -1969476.9 -3615.146 34.347699
2000 -1954231.1 310.08373 -1970380.2 -3622.6716 33.628638
2500 -1949715.7 309.80632 -1966085.8 -3607.6604 34.324699
3000 -1951705.4 310.21655 -1968279.9 -3626.0547 33.758009
3500 -1952444.6 310.59802 -1968735.2 -3658.0707 34.152872
4000 -1951594.1 310.39146 -1967847.5 -3623.4761 33.808795
4500 -1951159.9 309.67168 -1967541.8 -3602.4953 34.148739
5000 -1952097 310.27581 -1968601.4 -3597.6746 32.848408
5500 -1951356 310.23571 -1967801.8 -3618.4793 34.256925
6000 -1951278 310.33658 -1967650.5 -3582.5806 33.700021
6500 -1952161.2 309.96699 -1968459.6 -3600.2763 34.081834
7000 -1951235.4 309.52763 -1967565.6 -3609.6763 33.565357
7500 -1951375.4 309.47181 -1967627.1 -3678.9352 34.226009
8000 -1951420.8 309.15519 -1967556.4 -3654.0091 33.545097
8500 -1951999.9 309.48396 -1968103.4 -3684.1784 34.261704
9000 -1951390.5 310.20105 -1967507.6 -3682.7611 33.64065
9500 -1951848.6 310.84965 -1968050.6 -3714.906 34.161565
10000 -1951846.6 310.54596 -1967898.6 -3659.7021 33.864537
Loop time of 294.715 on 128 procs (128 MPI x 1 OpenMP) for 10000 steps with 250240 atoms
Pair time (%) = 108.292 (36.7445)
Bond time (%) = 0.966651 (0.327995)
Kspce time (%) = 144.101 (48.8951)
Neigh time (%) = 12.5745 (4.26665)
Comm time (%) = 23.7368 (8.05415)
Outpt time (%) = 0.00461355 (0.00156542)
Other time (%) = 5.03985 (1.71007)
FFT time (% of Kspce) = 88.6284 (61.5042)
FFT Gflps 3d (1d only) = 1.8172 5.17395
Nlocal: 1955 ave 2043 max 1875 min
Histogram: 2 2 15 28 26 22 20 8 3 2
Nghost: 5070.19 ave 5233 max 4967 min
Histogram: 4 20 23 19 29 15 9 5 3 1
Neighs: 209121 ave 221093 max 199778 min
Histogram: 3 5 15 33 30 20 15 4 2 1
Total # of neighbors = 26767496
Ave neighs/atom = 106.967
Ave special neighs/atom = 0.458312
Neighbor list builds = 1046
Dangerous builds = 0
c4science · Help