相关论文: Parallel TREE code for two-component ultracold pla…
Distributed algorithms for solving coupled semidefinite programs (SDPs) commonly require many iterations to converge. They also put high computational demand on the computational agents. In this paper we show that in case the coupled…
Current high-performance computer systems used for scientific computing typically combine shared memory computational nodes in a distributed memory environment. Extracting high performance from these complex systems requires tailored…
The ALLIANCE code is developed to solve a new set of four-dimensional electromagnetic drift-kinetic equations in slab geometry [J. Plasma Phys. 88 905880117 (2022)]. The nonlinear equations are useful for the study of magnetized plasma…
An efficient numerical algorithm for the laser driven multi-level ionization of high-atomic-number gases is proposed and implemented in an electromagnetic particle-in-cell code SPACE. The algorithm is based on analytical solutions to the…
Topologically constrained genome-like polymers often double-fold into tree-like configurations, which can be modelled on the level of folded (ring) polymers or on the level of the underlying random trees. For both descriptions, we have…
Identifying intersections among a set of d-dimensional rectangular regions (d-rectangles) is a common problem in many simulation and modeling applications. Since algorithms for computing intersections over a large number of regions can be…
The dynamic trees problem is to maintain a forest subject to edge insertions and deletions while facilitating queries such as connectivity, path weights, and subtree weights. Dynamic trees are a fundamental building block of a large number…
The paper deals with the developing of the methodological backgrounds for the modeling and simulation of complex dynamical objects. Such backgrounds allow us to perform coordinate transformation and formulate the algorithm of its usage for…
Important computational physics problems are often large-scale in nature, and it is highly desirable to have robust and high performing computational frameworks that can quickly address these problems. However, it is no trivial task to…
In this paper, we present a parallel computing method for the coupled-cluster singles and doubles (CCSD) in periodic systems. The CCSD in periodic systems solves simultaneous equations for single-excitation and double-excitation amplitudes.…
A new parallel algorithm utilizing partitioned global address space (PGAS) programming model to achieve high scalability is reported for particle tracking in direct numerical simulations of turbulent flow. The work is motivated by the…
Exploring and understanding the protein-folding problem has been a long-standing challenge in molecular biology. Here, using molecular dynamics simulation, we reveal how parallel distributed adjacent planar peptide groups of unfolded…
Modeling plasma accelerators is a computationally challenging task and the quasi-static particle-in-cell algorithm is a method of choice in a wide range of situations. In this work, we present the first performance-portable, quasi-static,…
In this article, we present a parallel recursive algorithm based on multi-level domain decomposition that can be used as a precondtioner to a Krylov subspace method to solve sparse linear systems of equations arising from the discretization…
The dynamic trees problem is to maintain a tree under edge updates while supporting queries like connectivity queries or path queries. Despite the first data structure for this fundamental problem -- the link-cut tree -- being invented 40…
We introduce an algorithm that performs a one-directional mesh overset of a parallel forest of octrees with another distributed mesh of unrelated partition. The forest mesh consists of several adaptively refined octrees. Individual smooth…
This paper presents an octree construction method, called Cornerstone, that facilitates global domain decomposition and interactions between particles in mesh-free numerical simulations. Our method is based on algorithms developed for 3D…
The electrical and electronic engineering has used parallel programming to solve its large scale complex problems for performance reasons. However, as parallel programming requires a non-trivial distribution of tasks and data, developers…
A field theory is presented for particles which interact via Coulomb and hard-core potentials. We apply the method to the one-component plasma (OCP) with hard cores, consisting of identical particles of fixed charge and diameter in a…
Multiscale methods for second order elliptic equations based on non-overlapping domain decomposition schemes have great potential to take advantage of multi-core, state-of-the-art parallel computers. These methods typically involve solving…