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The hardware diversity in leadership-class computing facilities, alongside the immense performance boosts from today's GPUs when computing in lower precision, incentivizes scientific HPC workflows to adopt mixed-precision algorithms and…
Recently, a fully implicit, energy- and charge-conserving particle-in-cell method has been proposed for multi-scale, full-f kinetic simulations [G. Chen, et al., J. Comput. Phys. 230,18 (2011)]. The method employs a Jacobian-free…
The two main thrusts of computational science are more accurate predictions and faster calculations; to this end, the zeitgeist in molecular dynamics (MD) simulations is pursuing machine learned and data driven interatomic models, e.g.…
The GW method, which can describe accurately electronic excitations, is one of the most widely used ab initio electronic structure technique and allows the physics of both molecular and condensed phase materials to be studied. However, the…
Ordinary state-based peridynamic (OSB-PD) models have an unparalleled capability to simulate crack propagation phenomena in solids with arbitrary Poisson's ratio. However, their non-locality also leads to prohibitively high computational…
We present a GPU implementation of LAMMPS, a widely-used parallel molecular dynamics (MD) software package, and show 5x to 13x single node speedups versus the CPU-only version of LAMMPS. This new CUDA package for LAMMPS also enables…
These notes accompany the open-source code published in GitHub which implements a GPU-based line-segment, surface-triangle intersection algorithm in CUDA. It mentions some relevant works and discusses issues specific to this implementation.…
We report on the design, implementation, optimization, and performance of the CADISHI software package, which calculates histograms of pair-distances of ensembles of particles on CPUs and GPUs. These histograms represent 2-point spatial…
Principal component analysis (PCA) is a key statistical technique for multivariate data analysis. For large data sets the common approach to PCA computation is based on the standard NIPALS-PCA algorithm, which unfortunately suffers from…
Low-dose Proton Computed Tomography (pCT) is an evolving imaging modality that is used in proton therapy planning which addresses the range uncertainty problem. The goal of pCT is generating a 3D map of Relative Stopping Power (RSP)…
The ISO C++17 standard introduces \emph{parallel algorithms}, a parallel programming model promising portability across a wide variety of parallel hardware including multi-core CPUs, GPUs, and FPGAs. Since 2019, the NVIDIA HPC SDK compiler…
\textsc{Quantum Package} is an open-source programming environment for quantum chemistry specially designed for wave function methods. Its main goal is the development of determinant-driven selected configuration interaction (sCI) methods…
Modern atomic physics applications in science and technology pose ever higher demands on the precision of computations of properties of atoms and ions. Especially challenging is the modeling of electronic correlations within the…
We describe the use of Graphics Processing Units (GPUs) for speeding up the code NBODY6 which is widely used for direct $N$-body simulations. Over the years, the $N^2$ nature of the direct force calculation has proved a barrier for…
Accelerated computing is widely used in high-performance computing. Therefore, it is crucial to experiment and discover how to better utilize GPUGPUs latest generations on relevant applications. In this paper, we present results and share…
Matrix multiplication is a foundational operation in scientific computing and machine learning, yet its computational complexity makes it a significant bottleneck for large-scale applications. The shift to parallel architectures, primarily…
We propose a fault-tolerant quantum computer architecture for trapped-ion devices, which we call the walking cat architecture. Our blueprint includes a compiler, a detailed description of all the quantum error-correction protocols, a…
Electrostatic interactions play crucial roles in biophysical processes such as protein folding and molecular recognition. Poisson-Boltzmann equation (PBE)-based models have emerged as widely used in modeling these important processes.…
The Variational Quantum Eigensolver (VQE) is a hybrid quantum-classical algorithm for computing ground state energies of molecular systems. We implement VQE to calculate the potential energy surface of the hydrogen molecule (H$_2$) across…
Coulomb collisions in particle simulations for weakly coupled plasmas are modeled by the Landau-Fokker-Planck equation, which is typically solved by Monte-Carlo (MC) methods. One of the main disadvantages of MC is the timestep accuracy…