相关论文: RPYFMM: Parallel Adaptive Fast Multipole Method fo…

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…

This paper introduces a random-batch molecular dynamics (RBMD) package for fast simulations of particle systems at the nano/micro scale. Different from existing packages, the RBMD uses random batch methods for nonbonded interactions of…

Reactive molecular dynamics simulations are computationally demanding. Reaching spatial and temporal scales where interesting scientific phenomena can be observed requires efficient and scalable implementations on modern hardware. In this…

We present teraflop-scale calculations of biomolecular electrostatics enabled by the combination of algorithmic and hardware acceleration. The algorithmic acceleration is achieved with the fast multipole method (FMM) in conjunction with a…

Generative models have emerged as a powerful paradigm for solving physics systems and modeling complex spatiotemporal dynamics. However, achieving high physical accuracy without incurring high computational cost remains a fundamental…

Fast algorithms for the computation of $N$-body problems can be broadly classified into mesh-based interpolation methods, and hierarchical or multiresolution methods. To this last class belongs the well-known fast multipole method (FMM),…

It is well known that the number of particles should be scaled up to enable industrial scale simulation. The calculations are more computationally intensive when the motion of the surrounding fluid is considered. Besides the advances in…

Exascale systems are predicted to have approximately one billion cores, assuming Gigahertz cores. Limitations on affordable network topologies for distributed memory systems of such massive scale bring new challenges to the current parallel…

Among the algorithms that are likely to play a major role in future exascale computing, the fast multipole method (FMM) appears as a rising star. Our previous recent work showed scaling of an FMM on GPU clusters, with problem sizes in the…

We present GridFF, an efficient method for simulating molecules on rigid substrates, derived from techniques used in protein-ligand docking in biochemistry. By projecting molecule-substrate interactions onto precomputed spatial grids with…

Developing an efficient code for large, multiscale astrophysical simulations is crucial in preparing the upcoming era of exascale computing. RAMSES is an astrophysical simulation code that employs parallel processing based on the Message…

The Fast Multipole Method (FMM) offers an acceleration for pairwise interaction calculation, known as $N$-body problems, from $\mathcal{O}(N^2)$ to $\mathcal{O}(N)$ with $N$ particles. This has brought dramatic increase in the capability of…

We propose a new method for molecular dynamics and Monte Carlo simulations, which is referred to as the replica-permutation method (RPM), to realize more efficient sampling than the replica-exchange method (REM).In RPM not only exchanges…

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…

Universal machine-learning interatomic potentials (uMLIPs) enable reactive molecular simulations with near-DFT accuracy, yet applying them efficiently to large, realistic condensed-phase systems remains computationally demanding. Here we…

The approximate computation of all gravitational forces between $N$ interacting particles via the fast multipole method (FMM) can be made as accurate as direct summation, but requires less than $\mathcal{O}(N)$ operations. FMM groups…

We present an updated version of the AFMPB package for fast calculation of molecular solvation-free energy. The main feature of the new version is the successful adoption of the DASHMM library, which enables AFMPB to operate on distributed…

When solving compressible multi-material flow problems, an unresolved challenge is the computation of advective fluxes across material interfaces that separate drastically different thermodynamic states and relations. A popular idea in this…

Recent results on supercomputers show that beyond 65K cores, the efficiency of molecular dynamics simulations of interfacial systems decreases significantly. In this paper, we introduce a dynamic cutoff method (DCM) for interfacial systems…

We introduce ppsim, a software package for efficiently simulating population protocols, a widely-studied subclass of chemical reaction networks (CRNs) in which all reactions have two reactants and two products. Each step in the dynamics…