There is, I think, something ethereal about i —the square root of minus one. I remember first hearing about it at school. It seemed an odd beast at that time—an intruder hovering on the edge of reality.

Usually familiarity dulls this sense of the bizarre, but in the case of i it was the reverse: over the years the sense of its surreal nature intensified. It seemed that it was impossible to write mathematics that described the real world in …

I and i

https://www.sandia.gov/~sjplimp/papers/jcompphys95.pdf

Fast parallel algorithms for short-range molecular dynamics

Three parallel algorithms for classical molecular dynamics are presented. The first assigns each processor a fixed subset of atoms; the second assigns each a fixed subset of inter-atomic forces to compute; the third assigns each a fixed spatial region. The algorithms are suitable for molecular dynamics models which can be difficult to parallelize efficiently—those with short-range forces where the neighbors of each atom change rapidly. They can be implemented on any distributed-memory parallel machine which allows for message-passing of data between independently executing processors. The algorithms are tested on a standard Lennard-Jones benchmark problem for system sizes ranging from 500 to 100,000,000 atoms on several parallel supercomputers--the nCUBE 2, Intel iPSC/860 and Paragon, and Cray T3D. Comparing the results to the fastest reported vectorized Cray Y-MP and C90 algorithm shows that the current generation of parallel machines is competitive with conventional vector supercomputers even for small problems. For large problems, the spatial algorithm achieves parallel efficiencies of 90% and a 1840-node Intel Paragon performs up to 165 faster than a single Cray C9O processor. Trade-offs between the three algorithms and guidelines for adapting them to more complex molecular dynamics simulations are also discussed.

An N⋅log(N) method for evaluating electrostatic energies and forces of large periodic systems is presented. The method is based on interpolation of the reciprocal space Ewald sums and evaluation of the resulting convolutions using fast Fourier transforms. Timings and accuracies are presented for three large crystalline ionic systems.

Particle mesh Ewald: An N⋅log(N) method for Ewald sums in large systems

The previously developed particle mesh Ewald method is reformulated in terms of efficient B‐spline interpolation of the structure factors This reformulation allows a natural extension of the method to potentials of the form 1/rp with p≥1 Furthermore, efficient calculation of the virial tensor follows Use of B‐splines in place of Lagrange interpolation leads to analytic gradients as well as a significant improvement in the accuracy We demonstrate that arbitrary accuracy can be achieved, independent of system size N, at a cost that scales as N log(N) For biomolecular systems with many thousands of atoms this method permits the use of Ewald summation at a computational cost comparable to that of a simple truncation method of 10 A or less

A smooth particle mesh Ewald method

A common task in computational physics is the convolution of a translation invariant, free-space Green's function with a smooth and compactly supported source density. Fourier methods are natural i...

https://par.nsf.gov/servlets/purl/10100023

The Anisotropic Truncated Kernel Method for Convolution with Free-Space Green's Functions

We describe a fast, stable algorithm for the solution of the inverse acoustic scattering problem in two dimensions. Given full aperture far field measurements of the scattered field for multiple angles of incidence, we use Chen's method of recursive linearization to reconstruct an unknown sound speed at resolutions of thousands of square wavelengths in a fully nonlinear regime. Despite the fact that the underlying optimization problem is formally ill-posed and non-convex, recursive linearization requires only the solution of a sequence of linear least squares problems at successively higher frequencies. By seeking a suitably band-limited approximation of the sound speed profile, each least squares calculation is well-conditioned and involves the solution of a large number of forward scattering problems, for which we employ a recently developed, spectrally accurate, fast direct solver. For the largest problems considered, involving 19,600 unknowns, approximately one million partial differential equations were solved, requiring approximately two days to compute using a parallel MATLAB implementation on a multi-core workstation.

High resolution inverse scattering in two dimensions using recursive linearization

We derive new formulas for the fundamental solutions of slow, viscous flow, governed by the Stokes equations, in a half-space. They are simpler than the classical representations obtained by Blake and collaborators, and can be efficiently implemented using existing fast solvers libraries. We show, for example, that the velocity field induced by a Stokeslet can be annihilated on the boundary (to establish a zero slip condition) using a single reflected Stokeslet combined with a single Papkovich-Neuber potential that involves only a scalar harmonic function. The new representation has a physically intuitive interpretation.

Simple and efficient representations for the fundamental solutions of Stokes flow in a half-space

Photonic crystal fibers are well-known to offer a number of unusual properties, including supercontinuum generation, large mode-areas and controllable dispersion behavior. Their manufacturability would be enhanced by a more detailed understanding of how small perturbations in the fiber’s geometric structure cause variations in the fiber’s fundamental modes. In this paper, we demonstrate that such sensitivity analysis is feasible using highly accurate boundary integral techniques.

Leslie Greengard

Papers

The Anisotropic Truncated Kernel Method for Convolution with Free-Space Green's Functions

High resolution inverse scattering in two dimensions using recursive linearization

Simple and efficient representations for the fundamental solutions of Stokes flow in a half-space

Sensitivity analysis of photonic crystal fiber.

A high-order wideband direct solver for electromagnetic scattering from bodies of revolution