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Molecular dynamics (MD) simulation with modified Brenner's reactive empirical bond order (REBO) potential is a powerful tool to investigate plasma wall interaction on divertor plates in a nuclear fusion device. However, MD simulation box's…
The Graphics Processing Unit (GPU) is a powerful tool for parallel computing. In the past years the performance and capabilities of GPUs have increased, and the Compute Unified Device Architecture (CUDA) - a parallel computing architecture…
A molecule's geometry, also known as conformation, is one of a molecule's most important properties, determining the reactions it participates in, the bonds it forms, and the interactions it has with other molecules. Conventional…
Recent progress in understanding thermal transport in complex crystals has highlighted the prominent role of heat conduction mediated by interband tunneling processes, which emerge between overlapping phonon bands (i.e. with energy…
We present an ab initio calculation of the DC conductivity of amorphous silicon and hydrogenated amorphous silicon. The Kubo-Greenwood formula is used to obtain the DC conductivity, by thermal averaging over extended dynamical simulation.…
The first non-empirical computation of lattice thermal conductivity has been performed for MgO using molecular dynamics (MD), a non-empirical ionic model (the Variationally Induced Breathing (VIB) model), and Green-Kubo theory. The…
Computer simulations can provide mechanistic insight into ionic liquids (ILs) and predict the properties of experimentally unrealized ion combinations. However, ILs suffer from a particularly large disparity in the time scales of atomistic…
Particle tracking simulations with space charge effects are very important for high-intensity proton rings. Since they include not only Hamilton mechanics of a single particle but constructing charge densities and solving Poisson equations…
Thermal conductivity of hadron matter is studied using a microscopic transport model, which will be used to simulate ultra-relativistic heavy ion collisions at different energy densities, namely the Ultra-relativistic Quantum Molecular…
Condense phase molecular systems organize in wide range of distinct molecular configurations, including amorphous melt and glass as well as crystals often exhibiting polymorphism, that originate from their intricate intra- and…
We present an algorithm named "Chamomile Scheme". The scheme is fully optimized for calculating gravitational interactions on the latest programmable Graphics Processing Unit (GPU), NVIDIA GeForce8800GTX, which has (a) small but fast shared…
Molecular dynamics (MD) simulation, which is considered an important tool for studying physical and chemical processes at the atomic scale, requires accurate calculations of energies and forces. Although reliable energies and forces can be…
As the performance of computer systems stagnates due to the end of Moore's Law, there is a need for new models that can understand and optimize the execution of general purpose code. While there is a growing body of work on using Graph…
We present an approach to molecular-dynamics simulations of ferrofluids on graphics processing units (GPUs). Our numerical scheme is based on a GPU-oriented modification of the Barnes-Hut (BH) algorithm designed to increase the parallelism…
In this study we have derived an exact framework for the calculation of the heat flux and its spectral decomposition in Molecular Dynamics (MD) for arbitrary many-body potentials. This work addresses several lacks and limitations of…
Obtaining a thermodynamically accurate phase diagram through numerical calculations is a computationally expensive problem that is crucially important to understanding the complex phenomena of solid state physics, such as superconductivity.…
In this paper, we aim to introduce a new perspective when comparing highly parallelized algorithms on GPU: the energy consumption of the GPU. We give an analysis of the performance of linear algebra operations, including addition of…
We discuss an implementation of molecular dynamics (MD) simulations on a graphic processing unit (GPU) in the NVIDIA CUDA language. We tested our code on a modern GPU, the NVIDIA GeForce 8800 GTX. Results for two MD algorithms suitable for…
Graphene foams have recently attracted a great deal of interest for their possible use in technological applications, such as electrochemical storage devices, wearable electronics, and chemical sensing. In this work, we present…
We present an implementation of all-electron density-functional theory for massively parallel GPGPU-based platforms, using localized atom-centered basis functions and real-space integration grids. Special attention is paid to domain…