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LAMMPS (22 Jul 2013-ICMS)
using 1 OpenMP thread(s) per MPI task
2 = max bonds/atom
3 = max angles/atom
0 = max impropers/atom
orthogonal box = (-27.713 -27.713 -200) to (27.713 27.713 200)
2 by 2 by 1 MPI processor grid
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
2 = max # of 1-2 neighbors
2 = max # of 1-3 neighbors
4 = max # of special neighbors
orthogonal box = (-27.713 -27.713 -200) to (193.991 193.991 200)
2 by 2 by 1 MPI processor grid
62560 atoms
8192 bonds
6144 angles
2 = max # of 1-2 neighbors
2 = max # of 1-3 neighbors
4 = max # of special neighbors
PPPM initialization ...
G vector (1/distance) = 0.0800658
grid = 15 15 25
stencil order = 3
estimated absolute RMS force accuracy = 0.00264607
estimated relative force accuracy = 7.96856e-06
using double precision FFTs
3d grid and FFT values/proc = 3388 1600
PPPM/cg optimization cutoff: 1e-05
Total charged atoms: 6.5%
Min/max charged atoms/proc: 6.5% 6.5%
Memory usage per processor = 13.114 Mbytes
Step PotEng Temp E_vdwl E_coul S/CPU
0 -495659.47 325 -499273.8 -814.32935 0
100 -492323.76 309.45576 -496520.87 -844.6403 45.816475
200 -491827.02 310.65902 -495823.61 -828.62224 43.741927
300 -490499.53 310.13281 -494545.52 -815.28961 43.671024
400 -489685.83 308.35554 -493810.7 -810.13075 43.369592
500 -489038.14 310.89654 -493087.45 -820.32925 42.364067
600 -487864.07 308.7615 -492028.21 -801.64708 42.74189
700 -486576.79 307.96306 -490711.19 -801.71978 43.560973
800 -486522.62 311.06965 -490632.11 -809.94729 43.408579
900 -486029.05 311.67387 -490113.69 -804.70093 43.564823
1000 -485994.6 311.03755 -490063.73 -799.16758 43.97141
Loop time of 22.9335 on 4 procs (4 MPI x 1 OpenMP) for 1000 steps with 62560 atoms
Performance: 37.674 ns/day 0.637 hours/ns 43.604 timesteps/s
MPI task wallclock breakdown
Section | min time | avg time | max time |%total | %CPU
---------------------------------------------------------------
Pair | 13.774 | 15.18 | 17.613 | 66.19 | 62.5
Bond | 0.2764 | 0.28171 | 0.29424 | 1.23 | 97.7
Kspace | 0.80397 | 0.81834 | 0.83411 | 3.57 | 96.7
Neigh | 0.05154 | 0.05358 | 0.054629 | 0.23 | 90.0
Comm | 0.30951 | 0.31666 | 0.32181 | 1.38 | 90.0
Output | 0.00083828 | 0.00088561 | 0.00097728 | 0.00 | 100.0
Modify | 3.7534 | 6.1714 | 7.5721 | 26.91 | 98.0
Other | | 0.1106 | | 0.48 |
Nlocal: 15640 ave 15679 max 15606 min
Histogram: 1 0 0 1 0 1 0 0 0 1
Nghost: 11071.2 ave 11108 max 11051 min
Histogram: 2 0 0 0 1 0 0 0 0 1
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0
Ave special neighs/atom = 0.458312
Neighbor list builds = 100
Dangerous builds = 0
------------------------------------------------------------------------
This simulation made use of algorithms and methodologies described
in the following references:
The LAMMPS Molecular Dynamics Simulator, Version 22 Jul 2013
http://lammps.sandia.gov
S.J. Plimpton,
Fast Parallel Algorithms for Short-Range Molecular Dynamics,
J. Comp. Phys., 117, 1-19 (1995)
S.J. Plimpton, R. Pollock, M. Stevens,
Particle-Mesh Ewald and r-RESPA for Parallel Molecular Dynamics Simulations,
Proc. of the 8th SIAM Conference on Parallel Processing for Scientific Computing,
Minneapolis, MN (March 1997).
A.P. Thompson, S.J. Plimpton, W. Mattson,
General formulation of pressure and stress tensor for arbitrary many-body
interaction potentials under periodic boundary conditions,
J. Chem. Phys., 131, 154107 (2009)
W.M. Brown, P. Wang, S.J. Plimpton, A.N. Tharrington,
Implementing Molecular Dynamics on Hybrid High Performance Computers
- Short Range Forces,
Comp. Phys. Comm., 182, 898-911, (2011)
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