forked from lijiext/lammps
95 lines
2.6 KiB
Groff
95 lines
2.6 KiB
Groff
LAMMPS (15 Feb 2016)
|
|
# FENE beadspring benchmark
|
|
|
|
variable x index 1
|
|
variable y index 1
|
|
variable z index 1
|
|
|
|
units lj
|
|
atom_style bond
|
|
atom_modify map hash
|
|
special_bonds fene
|
|
|
|
read_data data.chain
|
|
orthogonal box = (-16.796 -16.796 -16.796) to (16.796 16.796 16.796)
|
|
1 by 2 by 2 MPI processor grid
|
|
reading atoms ...
|
|
32000 atoms
|
|
reading velocities ...
|
|
32000 velocities
|
|
scanning bonds ...
|
|
1 = max bonds/atom
|
|
reading bonds ...
|
|
31680 bonds
|
|
2 = max # of 1-2 neighbors
|
|
2 = max # of special neighbors
|
|
|
|
replicate $x $y $z
|
|
replicate 2 $y $z
|
|
replicate 2 2 $z
|
|
replicate 2 2 1
|
|
orthogonal box = (-16.796 -16.796 -16.796) to (50.388 50.388 16.796)
|
|
2 by 2 by 1 MPI processor grid
|
|
128000 atoms
|
|
126720 bonds
|
|
2 = max # of 1-2 neighbors
|
|
2 = max # of special neighbors
|
|
|
|
neighbor 0.4 bin
|
|
neigh_modify every 1 delay 1
|
|
|
|
bond_style fene
|
|
bond_coeff 1 30.0 1.5 1.0 1.0
|
|
|
|
pair_style lj/cut 1.12
|
|
pair_modify shift yes
|
|
pair_coeff 1 1 1.0 1.0 1.12
|
|
|
|
fix 1 all nve
|
|
fix 2 all langevin 1.0 1.0 10.0 904297
|
|
|
|
thermo 100
|
|
timestep 0.012
|
|
|
|
run 100
|
|
Neighbor list info ...
|
|
1 neighbor list requests
|
|
update every 1 steps, delay 1 steps, check yes
|
|
max neighbors/atom: 2000, page size: 100000
|
|
master list distance cutoff = 1.52
|
|
ghost atom cutoff = 1.52
|
|
binsize = 0.76 -> bins = 89 89 45
|
|
Memory usage per processor = 12.8735 Mbytes
|
|
Step Temp E_pair E_mol TotEng Press
|
|
0 0.97027498 0.44484087 20.494523 22.394765 4.6721833
|
|
100 0.97682955 0.44239968 20.500229 22.407862 4.6527025
|
|
Loop time of 1.20889 on 4 procs for 100 steps with 128000 atoms
|
|
|
|
Performance: 85764.410 tau/day, 82.720 timesteps/s
|
|
99.8% CPU use with 4 MPI tasks x no OpenMP threads
|
|
|
|
MPI task timing breakdown:
|
|
Section | min time | avg time | max time |%varavg| %total
|
|
---------------------------------------------------------------
|
|
Pair | 0.21738 | 0.23306 | 0.23926 | 1.9 | 19.28
|
|
Bond | 0.094536 | 0.10196 | 0.10534 | 1.4 | 8.43
|
|
Neigh | 0.52311 | 0.52392 | 0.52519 | 0.1 | 43.34
|
|
Comm | 0.090161 | 0.10022 | 0.12557 | 4.7 | 8.29
|
|
Output | 0.00012207 | 0.00017327 | 0.00019598 | 0.2 | 0.01
|
|
Modify | 0.19662 | 0.20262 | 0.20672 | 0.8 | 16.76
|
|
Other | | 0.04694 | | | 3.88
|
|
|
|
Nlocal: 32000 ave 32015 max 31983 min
|
|
Histogram: 1 0 1 0 0 0 0 0 1 1
|
|
Nghost: 9492 ave 9522 max 9432 min
|
|
Histogram: 1 0 0 0 0 0 1 0 0 2
|
|
Neighs: 155837 ave 156079 max 155506 min
|
|
Histogram: 1 0 0 0 0 1 0 0 1 1
|
|
|
|
Total # of neighbors = 623349
|
|
Ave neighs/atom = 4.86991
|
|
Ave special neighs/atom = 1.98
|
|
Neighbor list builds = 25
|
|
Dangerous builds = 0
|
|
Total wall time: 0:00:01
|