Related papers: Parallel implementation of three-dimensional molec…
We consider the implementation of a parallel Monte Carlo code for high-performance simulations on PC clusters with MPI. We carry out tests of speedup and efficiency. The code is used for numerical simulations of pure SU(2) lattice gauge…
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.…
Skin modeling is an ongoing research area that highly benefits from modern parallel algorithms. This article aims at applying shape optimization to compute cell size and arrangement for elastic energy minimization of a cellular composite…
Recently, task-based programming models have emerged as a prominent alternative among shared-memory parallel programming paradigms. Inherently asynchronous, these models provide native support for dynamic load balancing and incorporate data…
As the Large Hadron Collider (LHC) continues its upward progression in energy and luminosity towards the planned High-Luminosity LHC (HL-LHC) in 2025, the challenges of the experiments in processing increasingly complex events will also…
Author developed the parallel fully kinetic particle-in-cell (PIC) code JPIC based on updated and advanced algorithms (e.g. numerical-dispersion-free electromagnetic field solver) for simulating laser plasma interactions. Basic technical…
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…
We have developed a parallel Particle-Particle, Particle-Mesh (P3M) simulation code for the Cray T3E parallel supercomputer that is well suited to studying the time evolution of systems of particles interacting via gravity and gas forces in…
There are now more Particle-in-Cell (PIC) codes than ever before that researchers use to simulate intense laser-plasma interactions. To date, there have been relatively few direct comparisons of these codes in the literature, especially for…
We review the status of, and prospects for, real-time data processing for collider experiments in experimental High Energy Physics. We discuss the historical evolution of data rates and volumes in the field and place them in the context of…
A technique for the enhancement of point targets in clutter is described. The local 3-D spectrum at each pixel is estimated recursively. An optical flow-field for the textured background is then generated using the 3-D autocorrelation…
Maximizing the performance potential of the modern day GPU architecture requires judicious utilization of available parallel resources. Although dramatic reductions can often be obtained through straightforward mappings, further performance…
The molecular simulations solve the equation of motion of molecular systems, making 3D shapes of molecules four-dimensional by adding the time coordinate. These methods have a great potential in drug discovery because they can realistically…
In this article we introduce a novel coupled algorithm for massively parallel direct numerical simulations of electrophoresis in microfluidic flows. This multiphysics algorithm employs an Eulerian description of fluid and ions, combined…
Molecular dynamics simulations are used to study structure formation in simple model polymer chains that are subject to excluded volume and torsional interactions. The changing conformations exhibited by chains of different lengths under…
In this paper we solve on GPUs massive problems with large amount of data, which are not appropriate for solution with the SIMD technology. For the given problem we consider a three-level parallelization. The multithreading of CPU is used…
We describe a framework for interactive molecular dynamics in a multiuser virtual reality environment, combining rigorous cloud-mounted physical atomistic simulation with commodity virtual reality hardware, which we have made accessible to…
In this study, we have developed a parallel version of the random time simulation algorithm. Firstly, we gave a rigorous basis of the random time description of the stochastic process of chemical reaction network time evolution. And then we…
In this work, we have developed a multiscale computational algorithm to couple finite element method with an open source molecular dynamics code --- the Large scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) --- to perform…
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…