We discuss the scalable parallel solution of the Poisson equation within a Particle-In-Cell (PIC) code for the simulation of electron beams in particle accelerators of irregular shape. The problem is discretized by Finite Differences. Depending on the treatment of the Dirichlet boundary the resulting system of equations is symmetric or `mildly' nonsymmetric positive definite. In all cases, the system is solved by the preconditioned conjugate gradient algorithm with smoothed aggregation (SA) based algebraic multigrid (AMG) preconditioning. We investigate variants of the implementation of SA-AMG that lead to considerable improvements in the execution times. We demonstrate good scalability of the solver on distributed memory parallel processor with up to 2048 processors. We also compare our SAAMG-PCG solver with an FFT-based solver that is more commonly used for applications in beam dynamics.
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 the Poisson equation using a spectral finite-difference method. This method uses a computational domain that contains the charged particle beam only and has a computational complexity of $O(N_u(logN_{mode}))$, where $N_u$ is the total number of unknowns and $N_{mode}$ is the maximum number of longitudinal or azimuthal modes. This saves both the computational…
Self-consistent multi-particle simulation plays an important role in studying beam-beam effects and space charge effects in high-intensity beams. The Poisson equation has to be solved at each time-step based on the particle density distribution in the multi-particle simulation. In this paper, we review a number of numerical methods that can be used to solve the Poisson equation efficiently. The computational complexity of those numerical methods will be O(N log(N)) or O(N) instead of O(N2), where N is the total number of grid points used to solve the Poisson equation.
We describe an implementation to solve Poisson's equation for an isolated system on a unigrid mesh using FFTs. The method solves the equation globally on mesh blocks distributed across multiple processes on a distributed-memory parallel computer. Test results to demonstrate the convergence and scaling properties of the implementation are presented. The solver is offered to interested users as the library PSPFFT.
A method is presented to include irregular domain boundaries in a geometric multigrid solver. Dirichlet boundary conditions can be imposed on an irregular boundary defined by a level set function. Our implementation employs quadtree/octree grids with adaptive refinement, a cell-centered discretization and pointwise smoothing. Boundary locations are determined at a subgrid resolution by performing line searches. For grid blocks near the interface, custom operator stencils are stored that take the interface into account. For grid block away from boundaries, a standard second-order accurate discr…
The computational study of chemical reactions in complex, wet environments is critical for applications in many fields. It is often essential to study chemical reactions in the presence of applied electrochemical potentials, taking into account the non-trivial electrostatic screening coming from the solvent and the electrolytes. As a consequence the electrostatic potential has to be found by solving the generalized Poisson and the Poisson-Boltzmann equation for neutral and ionic solutions, respectively. In the present work solvers for both problems have been developed. A preconditioned conjuga…
A 3-dimensional GPU Poisson solver is developed for all possible combinations of free and periodic boundary conditions (BCs) along the three directions. It is benchmarked for various grid sizes and different BCs and a significant performance gain is observed for problems including one or more free BCs. The GPU Poisson solver is also benchmarked against two different CPU implementations of the same method and a significant amount of acceleration of the computation is observed with the GPU version.
The Poisson-Boltzmann model is an effective and popular approach for modeling solvated biomolecules in continuum solvent with dissolved electrolytes. In this paper, we report our recent work in developing a Galerkin boundary integral method for solving the Poisson-Boltzmann (PB) equation. The solver has combined advantages in accuracy, efficiency, and memory usage as it applies a well-posed boundary integral formulation to circumvent many numerical difficulties associated with the PB equation and uses an O(N) Cartesian Fast Multipole Method (FMM) to accelerate the GMRES iteration. In addition,…
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 calculations are essential but computationally very demanding for molecular dynamics or continuum simulations of complex systems in molecular biophysics and electrochemistry. The graphic processing unit (GPU) with enormous arithmetic capability and streaming memory bandwidth is now a powerful engine for scientific as well as industrial computing. We propose two paralle…
Many problems in beam physics and plasma physics require the solution of Poisson's equation with free-space boundary conditions. The algorithm proposed by Hockney and Eastwood is a popular scheme to solve this problem numerically, used by many cutting-edge codes, because of its speed and its simplicity. However, the potential and its gradient obtained with this method have low accuracy, and the numerical error converges slowly with the number of grid points. We demonstrate that the closely related algorithm recently proposed by Vico, Greengard, and Ferrando is just as easy to implement, just a…
Electroconvective flow between two infinitely long parallel electrodes is investigated via a multiphysics computational model. The model solves for spatiotemporal flow properties using two-relaxation-time Lattice Boltzmann Method for fluid and charge transport coupled to Fast Fourier Transport Poisson solver for the electric potential. The segregated model agrees with the previous analytical and numerical results providing a robust approach for modeling electrohydrodynamic flows.
We present an analysis of different methods to calculate the classical electrostatic Hartree potential created by charge distributions. Our goal is to provide the reader with an estimation on the performance ---in terms of both numerical complexity and accuracy--- of popular Poisson solvers, and to give an intuitive idea on the way these solvers operate. Highly parallelisable routines have been implemented in the first-principle simulation code Octopus to be used in our tests, so that reliable conclusions about the capability of methods to tackle large systems in cluster computing can be obtai…
We present an accurate and efficient method to calculate the gravitational potential of an isolated system in three-dimensional Cartesian and cylindrical coordinates subject to vacuum (open) boundary conditions. Our method consists of two parts: an interior solver and a boundary solver. The interior solver adopts an eigenfunction expansion method together with a tridiagonal matrix solver to solve the Poisson equation subject to the zero boundary condition. The boundary solver employs James's method to calculate the boundary potential due to the screening charges required to keep the zero bound…
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 overall computation error is driven by the convergence of the finite Fourier series of the density. For smooth and fast-decaying densities the proposed method will be spectral accurate. The method scales with $\mathcal{O}(N\log N)$ operations, where $N$ is the total number of discretization points in the Cartesian grid. The majority of the computational…
A novel approach to unstructured quadrilateral mesh generation for planar domains is presented. Away from irregular vertices, the resulting meshes have the properties of nearly conformal grids. The technique is based on a theoretical relation between the present problem, and the inverse Poisson (IP) problem with point sources. An IP algorithm is described, which constructs a point-source distribution, whose sources correspond to the irregular vertices of the mesh. Both the background theory and the IP algorithm address the global nature of the mesh generation problem. The IP algorithm is incor…
We present a novel physics-informed deep learning framework for solving steady-state incompressible flow on multiple sets of irregular geometries by incorporating two main elements: using a point-cloud based neural network to capture geometric features of computational domains, and using the mean squared residuals of the governing partial differential equations, boundary conditions, and sparse observations as the loss function of the network to capture the physics. While the solution of the continuity and Navier-Stokes equations is a function of the geometry of the computational domain, curren…
The Poisson-Boltzmann (PB) implicit solvent model is a popular framework for studying the electrostatics of biomolecules immersed in water with dissolved salt. In this model the dielectric interface between the biomolecule and solvent is often taken to be the molecular surface or solvent-excluded surface (SES), and the quality of the SES triangulation is critical in boundary element simulations of the PB model. In this work we compare the MSMS and NanoShaper surface triangulation codes for a set of 38 biomolecules. While MSMS produces triangles of exceedingly small area and large aspect ratio,…
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 representation, can deal with any kind of periodicity (along one, two, or three spatial axes) as well as with fully isolated boundary conditions. It can seamlessly accommodate a finite screening length, non-orthorhombic lattices and charged systems. This approach is particularly advantageous because convergence is attained by simply refining the real space gri…
This paper presents an optimized and scalable semi-Lagrangian solver for the Vlasov-Poisson system in six-dimensional phase space. Grid-based solvers of the Vlasov equation are known to give accurate results. At the same time, these solvers are challenged by the curse of dimensionality resulting in very high memory requirements, and moreover, requiring highly efficient parallelization schemes. In this paper, we consider the 6d Vlasov-Poisson problem discretized by a split-step semi-Lagrangian scheme, using successive 1d interpolations on 1d stripes of the 6d domain. Two parallelization paradig…
Study on a Poisson's Equation Solver Based On Deep Learning Technique
Tsinghua National Laboratory for Information Science and Technology (TNList), Department Of Electronic Engineering, Tsinghua University（清华大学电子工程系，清华大学信息科学技术国家重点实验室）
A parallel, relativistic, three-dimensional particle-in-cell code SPACE has been developed for the simulation of electromagnetic fields, relativistic particle beams, and plasmas. In addition to the standard second-order Particle-in-Cell (PIC) algorithm, SPACE includes efficient novel algorithms to resolve atomic physics processes such as multi-level ionization of plasma atoms, recombination, and electron attachment to dopants in dense neutral gases. SPACE also contains a highly adaptive particle-based method, called Adaptive Particle-in-Cloud (AP-Cloud), for solving the Vlasov-Poisson problems…
A Fourier-based Library of Unbounded Poisson Solvers (FLUPS) for 2D and 3D homogeneous distributed grids is presented. It is designed to handle every possible combination of periodic, symmetric, semi-unbounded and fully unbounded boundary conditions for the Poisson equation on rectangular domains with uniform resolution. FLUPS leverages a dedicated implementation of 3D Fourier transforms to solve the Poisson equation using Green's functions, in a fast and memory-efficient way. Several Green's functions are available, optionally with explicit regularization, spectral truncation, or using lattic…
We present a new approach to find accurate solutions to the Poisson equation, as obtained from the steady-state limit of a diffusion equation with strong source terms. For this purpose, we start from Boltzmann's kinetic theory and investigate the influence of higher order terms on the resulting macroscopic equations. By performing an appropriate expansion of the equilibrium distribution, we provide a method to remove the unnecessary terms up to a desired order and show that it is possible to find, with high level of accuracy, the steady-state solution of the diffusion equation for sizeable Knu…
We explore the use of field solvers as approximations of classical Vlasov-Poisson systems. This correspondence is investigated in both electrostatic and gravitational contexts. We demonstrate the ability of field solvers to be excellent approximations of problems with cold initial condition into the non linear regime. We also investigate extensions of the Schrödinger-Poisson system that employ multiple stacked cold streams, and the von Neumann-Poisson equation as methods that can successfully reproduce the classical evolution of warm initial conditions. We then discuss how appropriate simulati…
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 subspace based linear algebraic solver such as the GMRES. The molecular surfaces are discretized with flat triangles and centroid collocation. To speed up our method, we take advantage of the parallel nature of the boundary integral formulation and parallelize the schemes within CUDA shared memory architecture on GPU. The schemes use only $11N+6N_c$ size-of-…
We present a multi-block finite-difference solver for massively parallel Direct Numerical Simulations (DNS) of incompressible flows. The algorithm combines the versatility of a multi-block solver with the method of eigenfunctions expansions, to speedup the solution of the pressure Poisson equation. This is achieved by employing FFT-based transforms along one homogeneous direction, which effectively reduce the problem complexity at a low cost. These FFT-based expansions are implemented in a framework that unifies all valid combinations of boundary conditions for this type of method. Subsequentl…
Several different approaches are proposed for solving fully implicit discretizations of a simplified Boltzmann-Poisson system with a linear relaxation-type collision kernel. This system models the evolution of free electrons in semiconductor devices under a low-density assumption. At each implicit time step, the discretized system is formulated as a fixed-point problem, which can then be solved with a variety of methods. A key algorithmic component in all the approaches considered here is a recently developed sweeping algorithm for Vlasov-Poisson systems. A synthetic acceleration scheme has be…
We present a parallel implementation of a direct solver for the Poisson's equation on extreme-scale supercomputers with accelerators. We introduce a chunked-pencil decomposition as the domain-decomposition strategy to distribute work among processing elements to achieve superior scalability at large number of accelerators. Chunked-pencil decomposition enables overlapping nodal communication and data transfer between the central processing units (CPUs) and the graphics processing units (GPUs). Second, it improves data locality by keeping neighboring elements in adjacent memory locations. Third,…
Implicit-solvent models are widely used to study the electrostatics in dissolved biomolecules, which are parameterized using force fields. Standard force fields treat the charge distribution with point charges, however, other force fields have emerged which offer a more realistic description by considering polarizability. In this work, we present the implementation of the polarizable and multipolar force field AMOEBA, in the boundary integral Poisson-Boltzmann solver \texttt{PyGBe}. Previous work from other researchers coupled AMOEBA with the finite-difference solver APBS, and found difficulti…
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. Though great efforts have been put into developing efficient PBE numerical models, challenges still remain due to the high dimensionality of typical biomolecular systems. In this study, we implemented and analyzed commonly used linear PBE solvers for the ever-improving graphics processing units (GPU) for biomolecular simulations, including both standard and preco…
We propose a new semi-Lagrangian Vlasov-Poisson solver. It employs elements of metric to follow locally the flow and its deformation, allowing one to find quickly and accurately the initial phase-space position $Q(P)$ of any test particle $P$, by expanding at second order the geometry of the motion in the vicinity of the closest element. It is thus possible to reconstruct accurately the phase-space distribution function at any time $t$ and position $P$ by proper interpolation of initial conditions, following Liouville theorem. When distorsion of the elements of metric becomes too large, it is …
This article presents a hardware architecture independent implementation of an adaptive mesh refinement Poisson solver that is integrated into the electrostatic Particle-In-Cell beam dynamics code OPAL. The Poisson solver is solely based on second generation Trilinos packages to ensure the desired hardware portability. Based on the massively parallel framework AMReX, formerly known as BoxLib, the new adaptive mesh refinement interface provides several refinement policies in order to enable precise large-scale neighbouring bunch simulations in high intensity cyclotrons. The solver is validated …
An accurate description of 2-D quantum transport in a double-gate metal oxide semiconductor filed effect transistor (dgMOSFET) requires a high-resolution solver to a coupled system of the 4-D Wigner equation and 2-D Poisson equation. In this paper, we propose an operator splitting spectral method to evolve such Wigner-Poisson system in 4-D phase space with high accuracy. After an operator splitting of the Wigner equation, the resulting two sub-equations can be solved analytically with spectral approximation in phase space. Meanwhile, we adopt a Chebyshev spectral method to solve the Poisson eq…
This paper studies an efficient numerical method for solving modified Poisson-Boltzmann (MPB) equations with the self Green's function as a state equation to describe electrostatic correlations in ionic systems. Previously, the most expensive point of the MPB solver is the evaluation of Green's function. The evaluation of Green's function requires solving high-dimensional partial differential equations, which is the computational bottleneck for solving MPB equations. Numerically, the MPB solver only requires the evaluation of Green's function as the diagonal part of the inverse of the discrete…
The accuracy and stability of implicit CFD codes are frequently impaired by the decoupling between variables, which can ultimately lead to numerical divergence. Coupled solvers, which solve all the governing equations simultaneously, have the potential to fix this problem. In this work, we report the implementation of coupled solvers for transient and steady-state electrically-driven flow simulations in the finite-volumes framework. The numerical method, developed in OpenFOAM, is generic for Newtonian and viscoelastic fluids and is formulated for the Poisson-Nernst-Planck and Poisson-Boltzmann…
Resolving numerically Vlasov-Poisson equations for initially cold systems can be reduced to following the evolution of a three-dimensional sheet evolving in six-dimensional phase-space. We describe a public parallel numerical algorithm consisting in representing the phase-space sheet with a conforming, self-adaptive simplicial tessellation of which the vertices follow the Lagrangian equations of motion. The algorithm is implemented both in six- and four-dimensional phase-space. Refinement of the tessellation mesh is performed using the bisection method and a local representation of the phase-s…
In many problems involving particle accelerators and relativistic plasmas, the accurate modeling of relativistic particle motion is essential for accurate physical predictions. Here, we extend a charge-conserving finite element time-domain (FETD) particle-in-cell (PIC) algorithm for the time-dependent Maxwell-Vlasov equations on irregular (unstructured) meshes to the relativistic regime by implementing and comparing three particle pushers: (relativistic) Boris, Vay, and Higuera-Cary. We illustrate the application of the proposed relativistic FETD-PIC algorithm for the analysis of particle cycl…
The solution of the Poisson equation is a ubiquitous problem in computational astrophysics. Most notably, the treatment of self-gravitating flows involves the Poisson equation for the gravitational field. In hydrodynamics codes using spherical polar grids, one often resorts to a truncated spherical harmonics expansion for an approximate solution. Here we present a non-iterative method that is similar in spirit, but uses the full set of eigenfunctions of the discretized Laplacian to obtain an exact solution of the discretized Poisson equation. This allows the solver to handle density distributi…
A Self-Adjusting FEM-BEM Coupling Scheme for the Nonlinear Poisson-Boltzmann Equation
Universidad Técnica Federico Santa María（弗雷德里科·圣塔玛丽亚技术大学）；Kingston University London（金斯顿大学伦敦分校）；Centro Científico Tecnológico de Valparaíso (CCTVal)（瓦尔帕莱索科技中心）
In this paper, we propose an efficient and accurate message-passing interface (MPI)-based parallel simulator for streamer discharges in three dimensions using the fluid model. First, we propose a new second-order semi-implicit scheme for the temporal discretization of the model that relaxes the dielectric relaxation time restriction. Moreover, it requires solving the Poisson-type equation only once at each time step, while the classical second-order explicit scheme typically needs to do twice. Second, we introduce a geometric multigrid preconditioned FGMRES solver that dramatically improves th…
We propose a novel efficient algorithm to solve Poisson equation in irregular two dimensional domains for electrostatics. It can handle Dirichlet, Neumann or mixed boundary problems in which the filling media can be homogeneous or inhomogeneous. The basic idea of the new method is solve the problem in three steps: (i) First solve the equation $\nabla\cdot\mathbf D=ρ$. The inverse of the divergence operator in a restricted subspace is found to yield the electric flux density $\mathbf D$ by a fast direct solver in O(N) operations. The $\mathbf D$ so obtained is nonunique with indeterminate diver…
We present our simulation tool JCMmode for calculating propagating modes of an optical waveguide. As ansatz functions we use higher order, vectorial elements (Nedelec elements, edge elements). Further we construct transparent boundary conditions to deal with leaky modes even for problems with inhomogeneous exterior domains as for integrated hollow core Arrow waveguides. We have implemented an error estimator which steers the adaptive mesh refinement. This allows the precise computation of singularities near the metal's corner of a Plasmon-Polariton waveguide even for irregular shaped metal fil…
