LAMMPS (6 Oct 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 = 13.2993 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 1.14845 on 4 procs for 100 steps with 128000 atoms
Performance: 90277.919 tau/day, 87.074 timesteps/s
99.9% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.2203 | 0.22207 | 0.22386 | 0.3 | 19.34
Bond | 0.094861 | 0.095302 | 0.095988 | 0.1 | 8.30
Neigh | 0.52127 | 0.5216 | 0.52189 | 0.0 | 45.42
Comm | 0.079585 | 0.082159 | 0.084366 | 0.7 | 7.15
Output | 0.00013304 | 0.00015306 | 0.00018501 | 0.2 | 0.01
Modify | 0.18351 | 0.18419 | 0.1856 | 0.2 | 16.04
Other | | 0.04298 | | | 3.74
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