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Parallel algorithms on CPU and GPU are implemented for the Unified Gas-Kinetic Scheme and their performances are investigated and compared by a two dimensional channel flow case. The parallel CPU algorithm has a one dimensional block…
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…
Computationally-intensive loops are the primary source of parallelism in scientific applications. Such loops are often irregular and a balanced execution of their loop iterations is critical for achieving high performance. However, several…
This paper introduces the model, numerical methods, algorithms and parallel implementation of a thermal reservoir simulator that designed for numerical simulations of thermal reservoir with multiple components in three dimensional domain…
This paper proposes a new multiple-scattering frequency-time hybrid (FTH-MS) integral equation solver for problems of wave scattering by obstacles in two dimensional space, including interior problems in closed cavities and problems…
We provide a thorough comparison of the GMHD3D code and the PLUTO4.4 code for both two and three-dimensional hydrodynamic and magnetohydrodynamic problems. The open-source finite-volume solver PLUTO4.4 and the in-house developed…
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…
A modern graphics processing unit (GPU) is able to perform massively parallel scientific computations at low cost. We extend our implementation of the checkerboard algorithm for the two dimensional Ising model [T. Preis et al., J. Comp.…
This paper presents a comprehensive numerical framework for simulating radiation-plasma systems. The radiative transfer process spans multiple flow regimes due to varying fluid opacity across different regions, necessitating a robust…
Axisymmetric magnetohydrodynamics (MHD) can be invoked for describing astrophysical magnetized flows and formulated to model stellar magnetospheres including main sequence stars (e.g. the Sun), compact stellar objects [e.g. magnetic white…
The freud Python package is a powerful library for analyzing simulation data. Written with modern simulation and data analysis workflows in mind, freud provides a Python interface to fast, parallelized C++ routines that run efficiently on…
Molecular dynamics (MD) simulation is one of the past decade's most important tools for enabling biology scientists and researchers to explore human health and diseases. However, due to the computation complexity of the MD algorithm, it…
In this paper, we contribute operator-splitting methods improved by the Zassenhaus product for the numerical solution of linear partial differential equations. We address iterative splitting methods, that can be improved by means of the…
We compare the statistical properties of J=1-0 13CO spectra observed in the Perseus Molecular Cloud with synthetic J=1-0 13CO spectra from a 5 pc model cloud. The synthetic spectra are computed solving the non-LTE radiative transfer problem…
The main features of a three dimensional, high-resolution special relativistic hydro code based on relativistic Riemann solvers are described. The capabilities and performance of the code are discussed. In particular, we present the results…
We investigate the parallel performance of Parallel Spectral Deferred corrections, a numerical approach that provides small-scale parallelism for the numerical solution of initial value problems. The scheme is applied to the shallow-water…
We describe an extension of the Enzo code to enable fully-coupled radiation hydrodynamical simulation of inhomogeneous reionization in large $\sim (100 Mpc)^3$ cosmological volumes with thousands to millions of point sources. We solve all…
Magnetized turbulence is ubiquitous in many astrophysical and terrestrial plasmas but no universal theory exists. Even the detailed energy dynamics in magnetohydrodynamic (MHD) turbulence are still not well understood. We present a suite of…
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…
Modeling and direct numerical simulation of particle-laden flows have a tremendous variety of applications in science and engineering across a vast spectrum of scales from pollution dispersion in the atmosphere, to fluidization in the…