Related papers: Parallel implementation of three-dimensional molec…
Although event-driven algorithms have been shown to be far more efficient than time-driven methods such as conventional molecular dynamics, they have not become as popular. The main obstacle seems to be the difficulty of parallelizing…
Molecular dynamics simulations are an important tool for describing the evolution of a chemical system with time. However, these simulations are inherently held back either by the prohibitive cost of accurate electronic structure theory…
We present a simple and efficient method to simulate three-dimensional, complex-shaped, interacting bodies. The particle shape is represented by Minkowski operators. A time-continuous interaction between these bodies is derived using simple…
In this dissertation, a fully object-oriented, fully relativistic, multi-dimensional Particle-In-Cell code was developed and applied to answer key questions in plasma-based accelerator research. The simulations increase the understanding of…
We provide a mathematically proven parallelization scheme for particle methods on distributed-memory computer systems. Particle methods are a versatile and widely used class of algorithms for computer simulations and numerical predictions…
Particle tracking in large-scale numerical simulations of turbulent flows presents one of the major bottlenecks in parallel performance and scaling efficiency. Here, we describe a particle tracking algorithm for large-scale parallel…
iPIC3D is a widely used massively parallel Particle-in-Cell code for the simulation of space plasmas. However, its current implementation does not support execution on multiple GPUs. In this paper, we describe the porting of iPIC3D particle…
Recent advances in computing architectures and networking are bringing parallel computing systems to the masses so increasing the number of potential users of these kinds of systems. In particular, two important technological evolutions are…
We report the results of intensive numerical calculations for four atomic H2+H2 energy transfer collision. A parallel computing technique based on LAM/MPI functions is used. In this algorithm, the data is distributed to the processors…
A fully parallel version of the contact dynamics (CD) method is presented in this paper. For large enough systems, 100% efficiency has been demonstrated for up to 256 processors using a hierarchical domain decomposition with dynamic load…
Simulations of electrochemical double layer capacitors based on porous carbon electrodes, energy storage systems which accumulate and release energy through reversible ion adsorption at electrode/electrolyte interfaces, are often performed…
Simulating liquid water to an accuracy that matches its wealth of available experimental data requires both precise electronic structure methods and reliable sampling of nuclear (quantum) motion. This is challenging because applying the…
The physics goals of the next Large Hadron Collider run include high precision tests of the Standard Model and searches for new physics. These goals require detailed comparison of data with computational models simulating the expected data…
We give an overview of the theoretical results for matrix block-recursive algorithms in commutative domains and present the results of experiments that we conducted with new parallel programs based on these algorithms on a supercomputer…
This study presents an enhanced method for analyzing cluster dynamics, with a particular focus on tracking clusters' continuity over time using time-series data from molecular dynamics (MD) simulation. The proposed method was applied to…
Particle-in-cell (PIC) simulations with Monte-Carlo collisions are used in plasma science to explore a variety of kinetic effects. One major problem is the long run-time of such simulations. Even on modern computer systems, PIC codes take a…
The introduction of accelerator devices such as graphics processing units (GPUs) has had profound impact on molecular dynamics simulations and has enabled order-of-magnitude performance advances using commodity hardware. To fully reap these…
Advances in ultra-intense laser technology are enabling, for the first time, relativistic intensities at mid-infrared (mid-IR) wavelengths. Anticipating further experimental research in this domain, we present high-resolution two…
The Massive Parallel Computing (MPC) model gained popularity during the last decade and it is now seen as the standard model for processing large scale data. One significant shortcoming of the model is that it assumes to work on static…
With the advent of high-performance computing techniques, the data for analysis has grown significantly. Here, graphic processing unit (GPU) based program kernels are discussed to exploit parallelism in the analysis codes specific to…