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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)
1 by 1 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)
1 by 1 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 = 9072 5625
PPPM/cg optimization cutoff: 1e-05
Total charged atoms: 6.5%
Min/max charged atoms/proc: 6.5% 6.5%
Memory usage per processor = 43.5393 Mbytes
Step PotEng Temp E_vdwl E_coul S/CPU
0 -495659.47 325 -499273.8 -814.32936 0
100 -492323.76 309.45577 -496520.88 -844.64029 41.326087
200 -491827.09 310.65896 -495823.68 -828.62235 39.143556
300 -490499.41 310.13273 -494545.39 -815.31482 39.385973
400 -489685.87 308.35767 -493810.79 -810.13715 40.292688
500 -489043.22 310.89958 -493093.03 -820.33527 38.539597
600 -487834.54 308.6937 -491999.3 -801.99434 39.033284
700 -486680.65 308.76345 -490812.43 -803.79045 39.434293
800 -486264.32 309.42615 -490327 -805.10312 40.652734
900 -485857.42 308.65923 -489993.19 -811.26175 40.922343
1000 -485859.25 309.68573 -489948.36 -819.90964 39.941891
Loop time of 25.095 on 1 procs (1 MPI x 1 OpenMP) for 1000 steps with 62560 atoms
Performance: 34.429 ns/day 0.697 hours/ns 39.849 timesteps/s
MPI task wallclock breakdown
Section | min time | avg time | max time |%total | %CPU
---------------------------------------------------------------
Pair | 19.462 | 19.462 | 19.462 | 77.55 | 65.9
Bond | 1.0042 | 1.0042 | 1.0042 | 4.00 | 99.8
Kspace | 1.9136 | 1.9136 | 1.9136 | 7.63 | 100.0
Neigh | 0.16131 | 0.16131 | 0.16131 | 0.64 | 100.0
Comm | 0.32112 | 0.32112 | 0.32112 | 1.28 | 96.5
Output | 0.0023868 | 0.0023868 | 0.0023868 | 0.01 | 100.0
Modify | 1.9832 | 1.9832 | 1.9832 | 7.90 | 99.5
Other | | 0.2469 | | 0.98 |
Nlocal: 62560 ave 62560 max 62560 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 20639 ave 20639 max 20639 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 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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