Related papers: A Customized 3D GPU Poisson Solver for Free Bounda…
An efficient solver for the three dimensional free-space Poisson equation is presented. The underlying numerical method is based on finite Fourier series approximation. While the error of all involved approximations can be fully controlled,…
The Poisson-Fermi model is an extension of the classical Poisson-Boltzmann model to include the steric and correlation effects of ions and water treated as nonuniform spheres in aqueous solutions. Poisson-Boltzmann electrostatic…
A three-dimensional (3D) Poisson solver with longitudinal periodic and transverse open boundary conditions can have important applications in beam physics of particle accelerators. In this paper, we present a fast efficient method to solve…
We present a method that gives highly accurate electrostatic potentials for systems where we have periodic boundary conditions in two spatial directions but free boundary conditions in the third direction. These boundary conditions are…
This paper proposes a novel Machine Learning-based approach to solve a Poisson problem with mixed boundary conditions. Leveraging Graph Neural Networks, we develop a model able to process unstructured grids with the advantage of enforcing…
It is well known since 1960s that by exploring the tensor product structure of the discrete Laplacian on Cartesian meshes, one can develop a simple direct Poisson solver with an $\mathcal O(N^{\frac{d+1}d})$ complexity in d-dimension, where…
In this paper, we present a GPU-accelerated direct-sum boundary integral method to solve the linear Poisson-Boltzmann (PB) equation. In our method, a well-posed boundary integral formulation is used to ensure the fast convergence of Krylov…
Immersed boundary methods (IBMs) facilitate the simulation of flows around stationary, moving, and deforming bodies on Cartesian grids. However, extending these simulations to the large grid sizes required for realistic flow problems…
We present an explicit solver of the three-dimensional screened and unscreened Poisson's equation which combines accuracy, computational efficiency and versatility. The solver, based on a mixed plane-wave / interpolating scaling function…
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 Radial Basis Function-generated finite differences became a popular variant of local meshless strong form methods due to its robustness regarding the position of nodes and its controllable order of accuracy. In this paper, we present a…
We present an efficient implementation for running three-dimensional numerical simulations of fluid-structure interaction problems on single GPUs, based on Nvidia CUDA through Numba and Python. The incompressible flow around moving bodies…
We present the development and benchmarking of Poisson solvers for graphics processing units (GPUs). Implemented in the Astaroth platform, the solvers feature high computational efficiency. We present novel combinations of discretizations…
In this paper, we investigate GPU based parallel triangular solvers systematically. The parallel triangular solvers are fundamental to incomplete LU factorization family preconditioners and algebraic multigrid solvers. We develop a new…
We present a fast and accurate algorithm to solve Poisson problems in complex geometries, using regular Cartesian grids. We consider a variety of configurations, including Poisson problems with interfaces across which the solution is…
GPUs have significantly accelerated first-order methods for large-scale optimization, especially in continuous optimization. However, this success has not transferred cleanly to problems with discrete variables, combinatorial structure, and…
The focus of my PhD thesis is on exploring parallel approaches to efficiently solve problems modeled by constraints and presenting a new proposal. Current solvers are very advanced; they are carefully designed to effectively manage the…
This paper proposes a GPU-accelerated optimization framework for collision avoidance problems where the controlled objects and the obstacles can be modeled as the finite union of convex polyhedra. A novel collision avoidance constraint is…
The geometric multigrid method (GMG) is one of the most efficient solving techniques for discrete algebraic systems arising from elliptic partial differential equations. GMG utilizes a hierarchy of grids or discretizations and reduces the…
In this thesis we develop techniques to efficiently solve numerical Partial Differential Equations (PDEs) using Graphical Processing Units (GPUs). Focus is put on both performance and re--usability of the methods developed, to this end a…