Related papers: Kroneckerised Particle Mesh Ewald

Standard Ewald sums, which calculate e.g. the electrostatic energy or the force in periodically closed systems of charged particles, can be efficiently speeded up by the use of the Fast Fourier Transformation (FFT). In this article we…

To evaluate electrostatics interactions, Molecular dynamics (MD) simulations rely on Particle Mesh Ewald (PME), an O(Nlog(N)) algorithm that uses Fast Fourier Transforms (FFTs) or, alternatively, on O(N) Fast Multipole Methods (FMM)…

The fast Fourier transform (FFT) is one of the most successful numerical algorithms of the 20th century and has found numerous applications in many branches of computational science and engineering. The FFT algorithm can be derived from a…

The smooth particle mesh Ewald (SPME) method is an FFT based method for the fast evaluation of electrostatic interactions under periodic boundary conditions. A highly optimized implementation of this method is available in GROMACS, a widely…

Molecular Dynamics (MD) simulations play a central role in physics-driven drug discovery. MD applications often use the Particle Mesh Ewald (PME) algorithm to accelerate electrostatic force computations, but efficient parallelization has…

The evaluation of long-range Coulomb interactions is a significant cost in molecular dynamics (MD), even when using Particle Mesh Ewald (PME) or Particle-Particle-Particle-Mesh (PPPM) methods, which rely on Ewald splitting and the fast…

This paper introduces a parallel directional fast multipole method (FMM) for solving N-body problems with highly oscillatory kernels, with a focus on the Helmholtz kernel in three dimensions. This class of oscillatory kernels requires a…

In this work, the fast-convolving reproducing kernel particle method (FC-RKPM) is introduced. This method is hundreds to millions of times faster than the traditional RKPM for 3D meshfree simulations. In this approach, the meshfree…

Fourier solvers have become efficient tools to establish structure-property relations in heterogeneous materials. Introduced as an alternative to the Finite Element (FE) method, they are based on fixed-point solutions of the…

Numeric modeling of electromagnetics and acoustics frequently entails matrix-vector multiplication with block Toeplitz structure. When the corresponding block Toeplitz matrix is not highly sparse, e.g. when considering the electromagnetic…

In this paper we demonstrate the methodology for parallelizing the computation of large one-dimensional discrete fast Fourier transforms (DFFTs) on multi-core Intel Xeon processors. DFFTs based on the recursive Cooley-Tukey method have to…

Kernel methods are extensively employed for nonlinear data clustering, yet their effectiveness heavily relies on selecting suitable kernels and associated parameters, posing challenges in advance determination. In response, Multiple Kernel…

Boundary value problems involving elliptic PDEs such as the Laplace and the Helmholtz equations are ubiquitous in mathematical physics and engineering. Many such problems can be alternatively formulated as integral equations that are…

Kronecker-sparse (KS) matrices -- whose supports are Kronecker products of identity and all-ones blocks -- underpin the structure of Butterfly and Monarch matrices and offer the promise of more efficient models. However, existing GPU…

Reducing the test time resource requirements of a neural network while preserving test accuracy is crucial for running inference on resource-constrained devices. To achieve this goal, we introduce a novel network reparameterization based on…

We describe a methodology for designing efficient parallel and distributed scientific software. This methodology utilizes sequences of mechanizable algebra--based optimizing transformations. In this study, we apply our methodology to the…

The kernel-independent fast multipole method (KIFMM) proposed in [1] is of almost linear complexity. In the original KIFMM the time-consuming M2L translations are accelerated by FFT. However, when more equivalent points are used to achieve…

We derive and implement an alternative formulation of the Stochastic Lanczos algorithm to be employed in connection with the Many-Body Dispersion model (MBD). Indeed, this formulation, which is only possible due to the Stochastic Lanczos'…

We present an NPT extension of Ewald summation with prolates (ESP), a spectrally accurate and scalable particle-mesh method for molecular dynamics simulations of periodic, charged systems. Building on the recently introduced ESP framework,…

Multi-task learning is useful in NLP because it is often practically desirable to have a single model that works across a range of tasks. In the medical domain, sequential training on tasks may sometimes be the only way to train models,…