Related papers: Fully Integrated On-FPGA Molecular Dynamics Simula…
The ever increasing demands placed upon machine performance have resulted in the need for more comprehensive particle accelerator modeling. Computer simulations are key to the success of particle accelerators. Many aspects of particle…
Molecular dynamics simulations have emerged as a potent tool for investigating the physical properties and kinetic behaviors of materials at the atomic scale, particularly in extreme conditions. Ab initio accuracy is now achievable with…
Particle-in-Cell (PIC) Monte Carlo (MC) simulations are central to plasma physics but face increasing challenges on heterogeneous HPC systems due to excessive data movement, synchronization overheads, and inefficient utilization of multiple…
Hybrid computational architectures based on the joint power of Central Processing Units and Graphic Processing Units (GPUs) are becoming popular and powerful hardware tools for a wide range of simulations in biology, chemistry, engineering,…
We provide a mathematically proven parallelization scheme for particle methods on distributed-memory computer systems. Particle methods are a versatile and widely used class of algorithms for computer simulations and numerical predictions…
We report on our implementation of the RHMC algorithm for the simulation of lattice QCD with two staggered flavors on Graphics Processing Units, using the NVIDIA CUDA programming language. The main feature of our code is that the GPU is not…
We describe the hardwired implementation of algorithms for Monte Carlo simulations of a large class of spin models. We have implemented these algorithms as VHDL codes and we have mapped them onto a dedicated processor based on a large FPGA…
A simple and efficient algorithm of the molecular-dynamics simulation of the hard disk system based on the Event-Driven method is developed. From the analysis of algorithm, the complexity is O(log N) per 1 event, and the constant…
With the advent of high-performance computing techniques, the data for analysis has grown significantly. Here, graphic processing unit (GPU) based program kernels are discussed to exploit parallelism in the analysis codes specific to…
A multi-scale framework was recently proposed for more realistic molecular dynamics simulations in continuum solvent models by coupling a molecular mechanics treatment of solute with a fluid mechanics treatment of solvent, where we…
FFT-based solvers are increasingly used by many researcher groups interested in modelling the mechanical behavior associated to a heterogeneous microstructure. A development is reported here that concerns the viscoelastic behavior of…
We introduce JAX MD, a software package for performing differentiable physics simulations with a focus on molecular dynamics. JAX MD includes a number of physics simulation environments, as well as interaction potentials and neural networks…
The most popular and universally predictive protein simulation models employ all-atom molecular dynamics (MD), but they come at extreme computational cost. The development of a universal, computationally efficient coarse-grained (CG) model…
We compare a newly developed hybrid simulation method which combines classical molecular dynamics (MD) and computational fluid dynamics (CFD) to a simulation consisting only of molecular dynamics. The hybrid code is composed of three…
A fluid flow in a simple dense liquid, passing an obstacle in a two-dimensional thin film geometry, is simulated by Molecular Dynamics (MD) computer simulation and compared to results of Lattice Boltzmann (LB) simulations. By the…
In this paper, we describe the algorithms we implemented in FDPS to make efficient use of accelerator hardware such as GPGPUs. We have developed FDPS to make it possible for many researchers to develop their own high-performance parallel…
We present an approach to molecular-dynamics simulations of ferrofluids on graphics processing units (GPUs). Our numerical scheme is based on a GPU-oriented modification of the Barnes-Hut (BH) algorithm designed to increase the parallelism…
The force field describing the calculated interaction between atoms or molecules is the key to the accuracy of many molecular dynamics (MD) simulation results. Compared with traditional or semi-empirical force fields, machine learning force…
The powerful molecular dynamics (MD) simulation is basically based on a picture that the atoms experience classical-like trajectories under the exertion of classical force field determined by the quantum mechanically solved electronic…
Over the last couple of years it has been realized that the vast computational power of graphics processing units (GPUs) could be harvested for purposes other than the video game industry. This power, which at least nominally exceeds that…