Related papers: Parallel implementation of three-dimensional molec…
A parallel 2D+1 split-step Fourier method with Crank-Nicholson scheme running on multi-core shared memory architectures is developed to study the propagation of ultra-short high-intensity laser pulses in air. The parallel method achieves a…
Cluster identification tasks occur in a multitude of contexts in physics and engineering such as, for instance, cluster algorithms for simulating spin models, percolation simulations, segmentation problems in image processing, or network…
Scientific applications are often irregular and characterized by large computationally-intensive parallel loops. Dynamic loop scheduling (DLS) techniques improve the performance of computationally-intensive scientific applications via load…
Multiscale and inhomogeneous molecular systems are challenging topics in the field of molecular simulation. In particular, modeling biological systems in the context of multiscale simulations and exploring material properties are driving a…
In finite-size scaling analyses of Monte Carlo simulations of second-order phase transitions one often needs an extended temperature range around the critical point. By combining the parallel tempering algorithm with cluster updates and an…
Much of our mechanistic understanding of the functions of biological macromolecules is based on static structural experiments, which can be modelled either as single structures or conformational ensembles. While these provide us with…
Particle-in-cell methods with stochastic collision models are commonly used to simulate collisional plasma dynamics, with applications ranging from hypersonic flight to semiconductor manufacturing. Code verification of such methods is…
Tingkat kompleksitas dari program simulasi dinamika molekular membutuhkan mesin pemroses dengan kemampuan yang sangat besar. Mesin-mesin paralel terbukti memiliki potensi untuk menjawab tantangan komputasi ini. Untuk memanfaatkan potensi…
The main theoretical tools used in the physics of cluster-laser interaction are discussed starting from the basic principles of Quantum Mechanics and ending with purely classical methods. The schematic overview of the theory is complemented…
We review a family of local algorithms that permit the simulation of charged particles with purely local dynamics. Molecular dynamics formulations lead to discretizations similar to those of ``particle in cell'' methods in plasma physics.…
Particle-in-cell methods couple mesh-based methods for the solution of continuum mechanics problems, with the ability to advect and evolve particles. They have a long history and many applications in scientific computing. However, they have…
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…
The acceleration of sparse matrix computations on modern many-core processors, such as the graphics processing units (GPUs), has been recognized and studied over a decade. Significant performance enhancements have been achieved for many…
We have developed molecular dynamics codes for a short-range interaction potential that adopt both the flat-MPI and MPI/OpenMP hybrid parallelizations on the basis of a full domain decomposition strategy. Benchmark simulations involving up…
We propose and theoretically analyse an experimental configuration in which lasers induce 3-spin interactions between trapped ions.By properly choosing the intensities and frequencies of the lasers, 3-spin couplings may be dominant or…
In this paper we deal with the impact of multi and many-core processor architectures on simulation. Despite the fact that modern CPUs have an increasingly large number of cores, most softwares are still unable to take advantage of them. In…
A version of the time-parallel algorithm parareal is analyzed and applied to stochastic models in chemical kinetics. A fast predictor at the macroscopic scale (evaluated in serial) is available in the form of the usual reaction rate…
This article presents the parallel implementation of the coupled harmonic oscillator. From the analytical solution of the coupled harmonic oscillator, the design parameters are obtained. After that, a numerical integration of the system…
Particle-in-cell codes are the most widely used simulation tools for kinetic studies of ultra-intense laser-plasma interactions. Using the motion of a single electron in a plane electromagnetic wave as a benchmark problem, we show…
Context. The magnetic field in the solar atmosphere continually reconnects and accelerates charged particles to high energies. Simulations of the atmosphere in three dimensions that include the effects of accelerated particles can aid our…