LAMMPS for beginners - Sandia National Laboratories

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Particle-mesh Methods for Coulombics• Coulomb interactions fall off as 1/r so require long-range for accuracy• Particle-mesh methods:partition into short-range and long-range contributionsshort-range via direct pairwise interactionslong-range:interpolate atomic charge to 3d meshsolve Poisson's equation on mesh (4 FFTs)interpolate E-fields back to atoms• FFTs scale as NlogN if cutoff is held fixed
Parallel FFTs• 3d FFT is 3 sets of 1d FFTsin parallel, 3d grid is distributed across procsperform 1d FFTs on-processornative library or FFTW (www.fftw.org)1d FFTs, transpose, 1d FFTs, transpose, ..."transpose” = data transfertransfer of entire grid is costly• FFTs for PPPM can scale poorlyon large # of procs and on clusters• Good news: Cost of PPPM is only ~2x more than 8-10 Angstrom cutoff
Page 2 and 3: A brief introduction to MD• MD: m
Page 4 and 5: MD in the Middle• Quantum mechani
Page 6 and 7: Classical MD in Parallel• MD is i
Page 8 and 9: A brief introduction to LAMMPSLAMMP
Page 10 and 11: How to get help with LAMMPS1. Excel
Page 12 and 13: Easily add your own LAMMPS feature
Page 16 and 17: Time Scale of Molecular Dynamics•
Page 18 and 19: Length Scale of Molecular Dynamics
Page 20 and 21: Melt Interface in NiAl• Mark Asta
Page 22 and 23: Shear Response of Cu Bicrystal• D
Page 24 and 25: 3d Membrane Self-Assembly• Mark S
Page 26 and 27: • Mike Brown (Sandia)Aspherical N
Page 28 and 29: LAMMPS’s Reactive Force Fields Ca
Page 30 and 31: [1000]MD Simulation of Shock-induce
Page 32 and 33: Rhodopsin photoisomerization simula
Page 34 and 35: Transition in retinal’s interacti
Page 36 and 37: Radiation damage simulations► Rad
Page 38 and 39: Defect analysis► How the defect a
Page 40 and 41: Future areas of LAMMPS development

LAMMPS for beginners - Sandia National Laboratories

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