forked from lijiext/lammps
107 lines
2.8 KiB
Groff
107 lines
2.8 KiB
Groff
LAMMPS (29 Jun 2012)
|
|
# SPC/E water box benchmark
|
|
|
|
units real
|
|
atom_style full
|
|
|
|
read_data data.spce
|
|
2 = max bonds/atom
|
|
1 = max angles/atom
|
|
orthogonal box = (0.02645 0.02645 0.02641) to (35.5328 35.5328 35.4736)
|
|
1 by 1 by 1 MPI processor grid
|
|
4500 atoms
|
|
3000 bonds
|
|
1500 angles
|
|
2 = max # of 1-2 neighbors
|
|
1 = max # of 1-3 neighbors
|
|
1 = max # of 1-4 neighbors
|
|
2 = max # of special neighbors
|
|
|
|
replicate 2 4 1
|
|
orthogonal box = (0.02645 0.02645 0.02641) to (71.0392 142.052 35.4736)
|
|
1 by 1 by 1 MPI processor grid
|
|
36000 atoms
|
|
24000 bonds
|
|
12000 angles
|
|
2 = max # of 1-2 neighbors
|
|
1 = max # of 1-3 neighbors
|
|
1 = max # of 1-4 neighbors
|
|
2 = max # of special neighbors
|
|
|
|
pair_style lj/cut/coul/long 9.8 9.8
|
|
kspace_style pppm 1.0e-4
|
|
|
|
pair_coeff 1 1 0.15535 3.166
|
|
pair_coeff * 2 0.0000 0.0000
|
|
|
|
bond_style harmonic
|
|
angle_style harmonic
|
|
dihedral_style none
|
|
improper_style none
|
|
|
|
bond_coeff 1 1000.00 1.000
|
|
angle_coeff 1 100.0 109.47
|
|
|
|
special_bonds lj/coul 0.0 0.0 0.5
|
|
2 = max # of 1-2 neighbors
|
|
1 = max # of 1-3 neighbors
|
|
1 = max # of 1-4 neighbors
|
|
2 = max # of special neighbors
|
|
|
|
neighbor 2.0 bin
|
|
neigh_modify every 1 delay 10 check yes
|
|
|
|
fix 1 all shake 0.0001 20 0 b 1 a 1
|
|
0 = # of size 2 clusters
|
|
0 = # of size 3 clusters
|
|
0 = # of size 4 clusters
|
|
12000 = # of frozen angles
|
|
fix 2 all nvt temp 300.0 300.0 100.0
|
|
|
|
velocity all create 300 432567 dist uniform
|
|
|
|
timestep 2.0
|
|
|
|
thermo_style one
|
|
thermo 50
|
|
|
|
run 100
|
|
PPPM initialization ...
|
|
G vector (1/distance) = 0.268811
|
|
grid = 36 64 24
|
|
stencil order = 5
|
|
estimated absolute RMS force accuracy = 0.0234088
|
|
estimated relative force accuracy = 7.0495e-05
|
|
using double precision FFTs
|
|
brick FFT buffer size/proc = 91977 55296 35604
|
|
Memory usage per processor = 102.176 Mbytes
|
|
Step Temp E_pair E_mol TotEng Press
|
|
0 300 -133281.51 0 -111820.57 -911.71286
|
|
50 256.42601 -138687.16 0 -120343.35 -931.69582
|
|
100 265.62923 -137828.91 0 -118826.74 -345.32241
|
|
Loop time of 31.5847 on 1 procs for 100 steps with 36000 atoms
|
|
|
|
Pair time (%) = 23.6339 (74.827)
|
|
Bond time (%) = 0.000171185 (0.000541985)
|
|
Kspce time (%) = 4.19505 (13.2819)
|
|
Neigh time (%) = 3.13994 (9.94134)
|
|
Comm time (%) = 0.0808184 (0.255878)
|
|
Outpt time (%) = 0.000238895 (0.000756364)
|
|
Other time (%) = 0.534611 (1.69263)
|
|
|
|
FFT time (% of Kspce) = 0.933042 (22.2415)
|
|
FFT Gflps 3d (1d only) = 1.29439 2.74331
|
|
|
|
Nlocal: 36000 ave 36000 max 36000 min
|
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
Nghost: 56916 ave 56916 max 56916 min
|
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
Neighs: 1.24624e+07 ave 1.24624e+07 max 1.24624e+07 min
|
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
|
|
Total # of neighbors = 12462366
|
|
Ave neighs/atom = 346.177
|
|
Ave special neighs/atom = 2
|
|
Neighbor list builds = 9
|
|
Dangerous builds = 8
|