相关论文: Optimization and Parallelization of a force field …

The increasing number of processing elements and decreas- ing memory to core ratio in modern high-performance platforms makes efficient strong scaling a key requirement for numerical algorithms. In order to achieve efficient scalability on…

The accuracy of atomistic simulations depends on the precision of force fields. Traditional numerical methods often struggle to optimize the empirical force field parameters for reproducing target properties. Recent approaches rely on…

In this Chapter we review our works on force fields for molecular simulations of protein systems. We first discuss the functional forms of the force fields and present some extensions of the conventional ones. We then present various…

Finite field multiplier is mainly used in error-correcting codes and signal processing. Finite field multiplier is regarded as the bottleneck arithmetic unit for such applications and it is the most complicated operation over finite field…

Nowadays, latency-critical, high-performance applications are parallelized even on power-constrained client systems to improve performance. However, an important scenario of fine-grained tasking on simultaneous multithreading CPU cores in…

Writing efficient hybrid parallel code is tedious, error-prone, and requires good knowledge of both parallel programming and multithreading such as MPI and OpenMP, resp. Therefore, we present a framework which is based on a job model that…

This article introduces a highly parallel algorithm for molecular dynamics simulations with short-range forces on single node multi- and many-core systems. The algorithm is designed to achieve high parallel speedups for strongly…

Fast Multipole Methods (FMM) are a fundamental operation for the simulation of many physical problems. The high performance design of such methods usually requires to carefully tune the algorithm for both the targeted physics and the…

As fusion energy devices advance, plasma simulations are crucial for reactor design. Our work extends BIT1 hybrid parallelization by integrating MPI with OpenMP and OpenACC, focusing on asynchronous multi-GPU programming. Results show…

A novel method combining the ensemble refinement by maximum entropy principle and the force field fitting approach is presented. Its formulation allows to continuously interpolate in between these two methods, which can thus be interpreted…

The One Sided Crossing Minimization (OSCM) problem is an optimization problem in graph drawing that aims to minimize the number of edge crossings in bipartite graph layouts. It has practical applications in areas such as network…

Scalable and efficient numerical simulations continue to gain importance, as computation is firmly established as the third pillar of discovery, alongside theory and experiment. Meanwhile, the performance of computing hardware grows through…

Machine-learned coarse-grained (CG) models have the potential for simulating large molecular complexes beyond what is possible with atomistic molecular dynamics. However, training accurate CG models remains a challenge. A widely used…

The implicit 2D3V particle-in-cell (PIC) code developed to study the interaction of ultrashort pulse lasers with matter [G. M. Petrov and J. Davis, Computer Phys. Comm. 179, 868 (2008); Phys. Plasmas 18, 073102 (2011)] has been parallelized…

We describe a parallelised version of the MOLDY molecular dynamics program. This Fortran code is aimed at systems which may be described by short-range potentials and specifically those which may be addressed with the embedded atom method.…

We present an algorithm for parallelising the TreePM code. We use both functional and domain decompositions. Functional decomposition is used to separate the computation of long range and short range forces, as well as the task of…

Balkanski and Singer [5] recently initiated the study of adaptivity (or parallelism) for constrained submodular function maximization, and studied the setting of a cardinality constraint. Very recent improvements for this problem by…

The aim of parallel computing is to increase an application performance by executing the application on multiple processors. OpenMP is an API that supports multi platform shared memory programming model and shared-memory programs are…

We present a technique designed for parallelizing large rigid body simulations, capable of exploiting multiple CPU cores within a computer and across a network. Our approach can be applied to simulate both unilateral and bilateral…

The trend towards highly parallel multi-processing is ubiquitous in all modern computer architectures, ranging from handheld devices to large-scale HPC systems; yet many applications are struggling to fully utilise the multiple levels of…