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We present our recent code modernizations of the of the ab initio molecular dynamics program CPMD (www.cpmd.org) with a special focus on the ultra-soft pseudopotential (USPP) code path. Following the internal instrumentation of CPMD, all…
Micro-macro models provide a powerful tool to study the relationship between microscale mechanisms and emergent macroscopic behavior. However, the detailed microscopic modeling may require tracking and evolving a high-dimensional…
We describe a numerical scheme for studying time-dependent, multifluid, magnetohydrodynamic shock waves in weakly ionized interstellar clouds and cores. Shocks are modeled as propagating perpendicular to the magnetic field and consist of a…
Numerical solution of reaction-diffusion equations in three dimensions is one of the most challenging applied mathematical problems. Since these simulations are very time consuming, any ideas and strategies aiming at the reduction of CPU…
The objective of this study is to develop a fully compressible magnetohydrodynamic solver for fast simulations of the global dynamo of the Sun using unstructured grids and GPUs. Accurate modeling of the Sun's convective layers is vital to…
Magnetohydrodynamic (MHD) simulations of the solar corona have become more popular with the increased availability of computational power. Modern computational plasma codes, relying upon Computational Fluid Dynamics (CFD) methods, allow for…
Concurrently coupled numerical simulations using heterogeneous solvers are powerful tools for modeling multiscale phenomena. However, major modifications to existing codes are often required to enable such simulations, posing significant…
The trend towards highly parallel multi-processing is ubiquitous in all modern computer architectures, ranging from handheld devices to large-scale HPC systems; yet many applications are struggling to fully utilise the multiple levels of…
MDMP is a new parallel programming approach that aims to provide users with an easy way to add parallelism to programs, optimise the message passing costs of traditional scientific simulation algorithms, and enable existing MPI-based…
This paper introduces a fast Central Processing Unit (CPU) implementation of geodesic morphological operations using stream processing. In contrast to the current state-of-the-art, that focuses on achieving insensitivity to the filter sizes…
Simulation of the cosmic clustering of massive neutrinos is a daunting task, due both to their large velocity dispersion and to their weak clustering power becoming swamped by Poisson shot noise. We present a new approach, the multi-fluid…
FISH is a fast and simple ideal magneto-hydrodynamics code that scales to ~10 000 processes for a Cartesian computational domain of ~1000^3 cells. The simplicity of FISH has been achieved by the rigorous application of the operator…
The Magneto-hydrodynamic (MHD) equations in the presence of a guiding magnetic field are investigated by means of direct numerical simulations. The basis of the investigation consists of 9 runs forced at the small scales. The results…
Computational intensity and sequential nature of estimation techniques for Bayesian methods in statistics and machine learning, combined with their increasing applications for big data analytics, necessitate both the identification of…
The separation between molecular and mesoscopic length and time scales poses a severe limit to molecular simulations of mesoscale phenomena. We describe a hybrid multiscale computational technique which address this problem by keeping the…
The paper describes an explicit multi-dimensional numerical scheme for Special Relativistic Two-Fluid Magnetohydrodynamics of electron-positron plasma and a suit of test problems. The scheme utilizes Cartesian grid and the third order WENO…
Massively parallel Fourier transforms are widely used in computational sciences, and specifically in computational fluid dynamics which involves unbounded Poisson problems. In practice the latter is usually the most time-consuming operation…
We present a scalable dissipative particle dynamics simulation code, fully implemented on the Graphics Processing Units (GPUs) using a hybrid CUDA/MPI programming model, which achieves 10-30 times speedup on a single GPU over 16 CPU cores…
This article condenses current endeavors and improvements in the expansion of applications of the DualSPHysics code to analyze heat transfer in a nuclear reactor core. This includes the essential conservation equations and certain physical…
This paper presents a low-communication-overhead parallel method for solving the 3D incompressible Navier-Stokes equations. A fully-explicit projection method with second-order space-time accuracy is adopted. Combined with fast Fourier…