Related papers: Molecular dynamics for long-range interacting syst…
Efficient implementations of the classical molecular dynamics (MD) method for Lennard-Jones particle systems are considered. Not only general algorithms but also techniques that are efficient for some specific CPU architectures are also…
The latest Graphics Processing Units (GPUs) are reported to reach up to 200 billion floating point operations per second (200 Gflops) and to have price performance of 0.1 cents per M flop. These facts raise great interest in the…
We present and discuss the characteristics and performances, both in term of computational speed and precision, of a numerical code which numerically integrates the equation of motions of N 'particles' interacting via Newtonian gravitation…
The introduction of accelerator devices such as graphics processing units (GPUs) has had profound impact on molecular dynamics simulations and has enabled order-of-magnitude performance advances using commodity hardware. To fully reap these…
Due to the very long timescales involved (us-s), theoretical modeling of fundamental biological processes including folding, misfolding, and mechanical unraveling of biomolecules, under physiologically relevant conditions, is challenging…
We introduce a class of fourth order symplectic algorithms that are ideal for doing long time integration of gravitational few-body problems. These algorithms have only positive time steps, but require computing the force gradient in…
Particle-in-cell (PIC) simulations with Monte-Carlo collisions are used in plasma science to explore a variety of kinetic effects. One major problem is the long run-time of such simulations. Even on modern computer systems, PIC codes take a…
Path integral Monte Carlo (PIMC) and path integral molecular dynamics (PIMD) provide the golden standard for the ab initio simulations of identical particles. In this work, we achieved significant GPU acceleration based on PIMD, which is…
The Graphics Processing Unit (GPU) is a powerful tool for parallel computing. In the past years the performance and capabilities of GPUs have increased, and the Compute Unified Device Architecture (CUDA) - a parallel computing architecture…
This article presents new algorithms for massively parallel granular dynamics simulations on distributed memory architectures using a domain partitioning approach. Collisions are modelled with hard contacts in order to hide their…
The Kernel Polynomial Method (KPM) is one of the fast diagonalization methods used for simulations of quantum systems in research fields of condensed matter physics and chemistry. The algorithm has a difficulty to be parallelized on a…
This paper presents a novel, high-performance, graphical processing unit-based algorithm for efficiently solving two-dimensional linear programs in batches. The domain of two-dimensional linear programs is particularly useful due to the…
This article presents an optimized algorithm and implementation for calculating resolution-of-the-identity Hartree-Fock (RI-HF) energies and analytic gradients using multiple Graphics Processing Units (GPUs). The algorithm is especially…
Stochastic simulation techniques employed for the analysis of portfolios of insurance/reinsurance risk, often referred to as `Aggregate Risk Analysis', can benefit from exploiting state-of-the-art high-performance computing platforms. In…
We present an algorithm named "Chamomile Scheme". The scheme is fully optimized for calculating gravitational interactions on the latest programmable Graphics Processing Unit (GPU), NVIDIA GeForce8800GTX, which has (a) small but fast shared…
Computational fluid dynamics and fluid-structure interaction simulations involving moving and deforming bodies is extremely hard. In this work, we present a graphical processing unit (GPU) optimized implementation of the sharp-interface…
We propose explicit symplectic integrators of molecular dynamics (MD) algorithms for rigid-body molecules in the canonical and isothermal-isobaric ensembles. We also present a symplectic algorithm in the constant normal pressure and lateral…
Graphics Processing Units (GPUs) have become a de facto solution for accelerating high-performance computing (HPC) applications. Understanding their memory error behavior is an essential step toward achieving efficient and reliable HPC…
The conductor-like polarization model (C-PCM) with switching/Gaussian smooth discretization is a widely used implicit solvation model in chemical simulations. However, its application in quantum mechanical calculations of large-scale…
We present the results of gravitational direct $N$-body simulations using the Graphics Processing Unit (GPU) on a commercial NVIDIA GeForce 8800GTX designed for gaming computers. The force evaluation of the $N$-body problem is implemented…