A generalized gyrokinetic Poisson solver
Energy Technology Data Exchange (ETDEWEB)
Lin, Z.; Lee, W.W.
1995-03-01
A generalized gyrokinetic Poisson solver has been developed, which employs local operations in the configuration space to compute the polarization density response. The new technique is based on the actual physical process of gyrophase-averaging. It is useful for nonlocal simulations using general geometry equilibrium. Since it utilizes local operations rather than the global ones such as FFT, the new method is most amenable to massively parallel algorithms.
A high order multi-resolution solver for the Poisson equation with application to vortex methods
DEFF Research Database (Denmark)
Hejlesen, Mads Mølholm; Spietz, Henrik Juul; Walther, Jens Honore
A high order method is presented for solving the Poisson equation subject to mixed free-space and periodic boundary conditions by using fast Fourier transforms (FFT). The high order convergence is achieved by deriving mollified Green’s functions from a high order regularization function which...... provides a correspondingly smooth solution to the Poisson equation.The high order regularization function may be obtained analogous to the approximate deconvolution method used in turbulence models and strongly relates to deblurring algorithms used in image processing. At first we show that the regularized...... by super-positioning an inter-mesh correction. For sufficiently smooth vector fields this multi-resolution correction can be achieved without the loss of convergence rate. An implementation of the multi-resolution solver in a two-dimensional re-meshed particle-mesh based vortex method is presented...
Advanced 3D Poisson solvers and particle-in-cell methods for accelerator modeling
Energy Technology Data Exchange (ETDEWEB)
Serafini, David B; McCorquodale, Peter; Colella, Phillip [Lawrence Berkeley National Lab, Applied Numerical Algorithms Group, SciDAC Applied Differential Equations Center (United States)
2005-01-01
We seek to improve on the conventional FFT-based algorithms for solving the Poisson equation with infinite-domain (open) boundary conditions for large problems in accelerator modeling and related areas. In particular, improvements in both accuracy and performance are possible by combining several technologies: the method of local corrections (MLC); the James algorithm; and adaptive mesh refinement (AMR). The MLC enables the parallelization (by domain decomposition) of problems with large domains and many grid points. This improves on the FFT-based Poisson solvers typically used as it doesn't require the all-to-all communication pattern that parallel 3d FFT algorithms require, which tends to be a performance bottleneck on current (and foreseeable) parallel computers. In initial tests, good scalability up to 1000 processors has been demonstrated for our new MLC solver. An essential component of our approach is a new version of the James algorithm for infinite-domain boundary conditions for the case of three dimensions. By using a simplified version of the fast multipole method in the boundary-to-boundary potential calculation, we improve on the performance of the Hockney algorithm typically used by reducing the number of grid points by a factor of 8, and the CPU costs by a factor of 3. This is particularly important for large problems where computer memory limits are a consideration. The MLC allows for the use of adaptive mesh refinement, which reduces the number of grid points and increases the accuracy in the Poisson solution. This improves on the uniform grid methods typically used in PIC codes, particularly in beam problems where the halo is large. Also, the number of particles per cell can be controlled more closely with adaptivity than with a uniform grid. To use AMR with particles is more complicated than using uniform grids. It affects depositing particles on the non-uniform grid, reassigning particles when the adaptive grid changes and maintaining the
A generalized Poisson and Poisson-Boltzmann solver for electrostatic environments
Energy Technology Data Exchange (ETDEWEB)
Fisicaro, G., E-mail: giuseppe.fisicaro@unibas.ch; Goedecker, S. [Department of Physics, University of Basel, Klingelbergstrasse 82, 4056 Basel (Switzerland); Genovese, L. [University of Grenoble Alpes, CEA, INAC-SP2M, L-Sim, F-38000 Grenoble (France); Andreussi, O. [Institute of Computational Science, Università della Svizzera Italiana, Via Giuseppe Buffi 13, CH-6904 Lugano (Switzerland); Theory and Simulations of Materials (THEOS) and National Centre for Computational Design and Discovery of Novel Materials (MARVEL), École Polytechnique Fédérale de Lausanne, Station 12, CH-1015 Lausanne (Switzerland); Marzari, N. [Theory and Simulations of Materials (THEOS) and National Centre for Computational Design and Discovery of Novel Materials (MARVEL), École Polytechnique Fédérale de Lausanne, Station 12, CH-1015 Lausanne (Switzerland)
2016-01-07
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 equations for neutral and ionic solutions, respectively. In the present work, solvers for both problems have been developed. A preconditioned conjugate gradient method has been implemented for the solution of the generalized Poisson equation and the linear regime of the Poisson-Boltzmann, allowing to solve iteratively the minimization problem with some ten iterations of the ordinary Poisson equation solver. In addition, a self-consistent procedure enables us to solve the non-linear Poisson-Boltzmann problem. Both solvers exhibit very high accuracy and parallel efficiency and allow for the treatment of periodic, free, and slab boundary conditions. The solver has been integrated into the BigDFT and Quantum-ESPRESSO electronic-structure packages and will be released as an independent program, suitable for integration in other codes.
An adaptive fast multipole accelerated Poisson solver for complex geometries
Askham, T.; Cerfon, A. J.
2017-09-01
We present a fast, direct and adaptive Poisson solver for complex two-dimensional geometries based on potential theory and fast multipole acceleration. More precisely, the solver relies on the standard decomposition of the solution as the sum of a volume integral to account for the source distribution and a layer potential to enforce the desired boundary condition. The volume integral is computed by applying the FMM on a square box that encloses the domain of interest. For the sake of efficiency and convergence acceleration, we first extend the source distribution (the right-hand side in the Poisson equation) to the enclosing box as a C0 function using a fast, boundary integral-based method. We demonstrate on multiply connected domains with irregular boundaries that this continuous extension leads to high accuracy without excessive adaptive refinement near the boundary and, as a result, to an extremely efficient ;black box; fast solver.
PSH3D fast Poisson solver for petascale DNS
Adams, Darren; Dodd, Michael; Ferrante, Antonino
2016-11-01
Direct numerical simulation (DNS) of high Reynolds number, Re >= O (105) , turbulent flows requires computational meshes >= O (1012) grid points, and, thus, the use of petascale supercomputers. DNS often requires the solution of a Helmholtz (or Poisson) equation for pressure, which constitutes the bottleneck of the solver. We have developed a parallel solver of the Helmholtz equation in 3D, PSH3D. The numerical method underlying PSH3D combines a parallel 2D Fast Fourier transform in two spatial directions, and a parallel linear solver in the third direction. For computational meshes up to 81923 grid points, our numerical results show that PSH3D scales up to at least 262k cores of Cray XT5 (Blue Waters). PSH3D has a peak performance 6 × faster than 3D FFT-based methods when used with the 'partial-global' optimization, and for a 81923 mesh solves the Poisson equation in 1 sec using 128k cores. Also, we have verified that the use of PSH3D with the 'partial-global' optimization in our DNS solver does not reduce the accuracy of the numerical solution of the incompressible Navier-Stokes equations.
High order Poisson Solver for unbounded flows
DEFF Research Database (Denmark)
Hejlesen, Mads Mølholm; Rasmussen, Johannes Tophøj; Chatelain, Philippe
2015-01-01
as regularisation we document an increased convergence rate up to tenth order. The method however, can easily be extended well beyond the tenth order. To show the full extend of the method we present the special case of a spectrally ideal regularisation of the velocity formulated integration kernel, which achieves......This paper presents a high order method for solving the unbounded Poisson equation on a regular mesh using a Green’s function solution. The high order convergence was achieved by formulating mollified integration kernels, that were derived from a filter regularisation of the solution field...... or by performing the differentiation as a multiplication of the Fourier coefficients. In this way, differential operators such as the divergence or curl of the solution field could be solved to the same high order convergence without additional computational effort. The method was applied and validated using...
Accuracy analysis of a spectral Poisson solver
Energy Technology Data Exchange (ETDEWEB)
Rambaldi, S. [Dipartimento di Fisica Universita di Bologna and INFN, Bologna, Via Irnerio 46, 40126 (Italy)]. E-mail: rambaldi@bo.infn.it; Turchetti, G. [Dipartimento di Fisica Universita di Bologna and INFN, Bologna, Via Irnerio 46, 40126 (Italy); Benedetti, C. [Dipartimento di Fisica Universita di Bologna and INFN, Bologna, Via Irnerio 46, 40126 (Italy); Mattioli, F. [Dipartimento di Fisica Universita di Bologna, Bologna, Via Irnerio 46, 40126 (Italy); Franchi, A. [GSI, Darmstadt, Planckstr. 1, 64291 (Germany)
2006-06-01
We solve Poisson's equation in d=2,3 space dimensions by using a spectral method based on Fourier decomposition. The choice of the basis implies that Dirichlet boundary conditions on a box are satisfied. A Green's function-based procedure allows us to impose Dirichlet conditions on any smooth closed boundary, by doubling the computational complexity. The error introduced by the spectral truncation and the discretization of the charge distribution is evaluated by comparison with the exact solution, known in the case of elliptical symmetry. To this end boundary conditions on an equipotential ellipse (ellipsoid) are imposed on the numerical solution. Scaling laws for the error dependence on the number K of Fourier components for each space dimension and the number N of point charges used to simulate the charge distribution are presented and tested. A procedure to increase the accuracy of the method in the beam core region is briefly outlined.
A Fast Poisson Solver with Periodic Boundary Conditions for GPU Clusters in Various Configurations
Rattermann, Dale Nicholas
Fast Poisson solvers using the Fast Fourier Transform on uniform grids are especially suited for parallel implementation, making them appropriate for portability on graphical processing unit (GPU) devices. The goal of the following work was to implement, test, and evaluate a fast Poisson solver for periodic boundary conditions for use on a variety of GPU configurations. The solver used in this research was FLASH, an immersed-boundary-based method, which is well suited for complex, time-dependent geometries, has robust adaptive mesh refinement/de-refinement capabilities to capture evolving flow structures, and has been successfully implemented on conventional, parallel supercomputers. However, these solvers are still computationally costly to employ, and the total solver time is dominated by the solution of the pressure Poisson equation using state-of-the-art multigrid methods. FLASH improves the performance of its multigrid solvers by integrating a parallel FFT solver on a uniform grid during a coarse level. This hybrid solver could then be theoretically improved by replacing the highly-parallelizable FFT solver with one that utilizes GPUs, and, thus, was the motivation for my research. In the present work, the CPU-utilizing parallel FFT solver (PFFT) used in the base version of FLASH for solving the Poisson equation on uniform grids has been modified to enable parallel execution on CUDA-enabled GPU devices. New algorithms have been implemented to replace the Poisson solver that decompose the computational domain and send each new block to a GPU for parallel computation. One-dimensional (1-D) decomposition of the computational domain minimizes the amount of network traffic involved in this bandwidth-intensive computation by limiting the amount of all-to-all communication required between processes. Advanced techniques have been incorporated and implemented in a GPU-centric code design, while allowing end users the flexibility of parameter control at runtime in
Carrillo, J A; Majorana, A; Shu, C W
2003-01-01
In this paper we develop a deterministic high order accurate finite-difference WENO solver to the solution of the 1-D Boltzmann-Poisson system for semiconductor devices. We follow the work in Fatemi and Odeh and in Majorana and Pidatella to formulate the Boltzmann-Poisson system in a spherical coordinate system using the energy as one of the coordinate variables, thus reducing the computational complexity to two dimensions in phase space and dramatically simplifying the evaluations of the collision terms. The solver is accurate in time hence potentially useful for time-dependent simulations, although in this paper we only test it for steady-state devices. The high order accuracy and nonoscillatory properties of the solver allow us to use very coarse meshes to get a satisfactory resolution, thus making it feasible to develop a 2-D solver (which will be five dimensional plus time when the phase space is discretized) on today's computers. The computational results have been compared with those by a Monte Carlo s...
Parallel FFT-based Poisson Solver for Isolated Three-dimensional Systems
Budiardja, Reuben D
2011-01-01
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.
Directory of Open Access Journals (Sweden)
Khoie R.
1996-01-01
Full Text Available A self-consistent Boltzmann-Poisson-Schrödinger solver for High Electron Mobility Transistor is presented. The quantization of electrons in the quantum well normal to the heterojunction is taken into account by solving the two higher moments of Boltzmann equation along with the Schrödinger and Poisson equations, self-consistently. The Boltzmann transport equation in the form of a current continuity equation and an energy balance equation are solved to obtain the transient and steady-state transport behavior. The numerical instability problems associated with the simulator are presented, and the criteria for smooth convergence of the solutions are discussed. The current-voltage characteristics, transconductance, gate capacitance, and unity-gain frequency of a single quantum well HEMT is discussed. It has been found that a HEMT device with a gate length of 0.7 μ m , and with a gate bias voltage of 0.625 V, has a transconductance of 579.2 mS/mm, which together with the gate capacitance of 19.28 pF/cm, can operate at a maximum unity-gain frequency of 47.8 GHz.
Directory of Open Access Journals (Sweden)
R. Khoie
1996-01-01
Full Text Available A self-consistent Boltzmann-Poisson-Schrödinger solver for High Electron Mobility Transistor is presented. The quantization of electrons in the quantum well normal to the heterojunction is taken into account by solving the two higher moments of Boltzmann equation along with the Schrödinger and Poisson equations, self-consistently. The Boltzmann transport equation in the form of a current continuity equation and an energy balance equation are solved to obtain the transient and steady-state transport behavior. The numerical instability problems associated with the simulator are presented, and the criteria for smooth convergence of the solutions are discussed. The current-voltage characteristics, transconductance, gate capacitance, and unity-gain frequency of a single quantum well HEMT is discussed. It has been found that a HEMT device with a gate length of 0.7 μm, and with a gate bias voltage of 0.625 V, has a transconductance of 579.2 mS/mm, which together with the gate capacitance of 19.28 pF/cm, can operate at a maximum unity-gain frequency of 47.8 GHz.
García-Risueño, Pablo; Oliveira, Micael J T; Andrade, Xavier; Pippig, Michael; Muguerza, Javier; Arruabarrena, Agustin; Rubio, Angel
2012-01-01
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 obtained from our work.
Application of wavelets to a Poisson equation solver and its parallel processing
Energy Technology Data Exchange (ETDEWEB)
Tanaka, Nobuatsu [Toshiba Corp., Kawasaki, Kanagawa (Japan)
1998-03-01
This paper describes a powerful and simple new wavelet-based preconditioning method for the CG solvers of Poisson equation. The equation can be solved with an iterative matrix solver, however, in the absence of our method, the computing time will increase exponentially with respect to an increase in grid points. Use of our technique leads to a matrix with a bounded condition number so that computing time is reduced significantly. Results from our numerical experiments confirm the power and accuracy of our wavelet-based preconditioning method. Unlike many preconditioning methods which are not suitable for vector and parallel processing, our algorithm can take advantage of the extra processing capabilities and enhance computing performance. For example, a speed up of over 100 fold can be achieved when solving Poisson equations on a Cray T3D using 128 processors in parallel. (author)
A high order solver for the unbounded Poisson equation
DEFF Research Database (Denmark)
Hejlesen, Mads Mølholm; Rasmussen, Johannes Tophøj; Chatelain, Philippe
and the integration kernel. In this work we show an implementation of high order regularised integration kernels in the HE algorithm for the unbounded Poisson equation to formally achieve an arbitrary high order convergence. We further present a quantitative study of the convergence rate to give further insight......In mesh-free particle methods a high order solution to the unbounded Poisson equation is usually achieved by constructing regularised integration kernels for the Biot-Savart law. Here the singular, point particles are regularised using smoothed particles to obtain an accurate solution with an order...
PB-AM: An open-source, fully analytical linear poisson-boltzmann solver
Energy Technology Data Exchange (ETDEWEB)
Felberg, Lisa E. [Department of Chemical and Biomolecular Engineering, University of California Berkeley, Berkeley California 94720; Brookes, David H. [Department of Chemistry, University of California Berkeley, Berkeley California 94720; Yap, Eng-Hui [Department of Systems and Computational Biology, Albert Einstein College of Medicine, Bronx New York 10461; Jurrus, Elizabeth [Division of Computational and Statistical Analytics, Pacific Northwest National Laboratory, Richland Washington 99352; Scientific Computing and Imaging Institute, University of Utah, Salt Lake City Utah 84112; Baker, Nathan A. [Advanced Computing, Mathematics, and Data Division, Pacific Northwest National Laboratory, Richland Washington 99352; Division of Applied Mathematics, Brown University, Providence Rhode Island 02912; Head-Gordon, Teresa [Department of Chemical and Biomolecular Engineering, University of California Berkeley, Berkeley California 94720; Department of Chemistry, University of California Berkeley, Berkeley California 94720; Department of Bioengineering, University of California Berkeley, Berkeley California 94720; Chemical Sciences Division, Lawrence Berkeley National Labs, Berkeley California 94720
2016-11-02
We present the open source distributed software package Poisson-Boltzmann Analytical Method (PB-AM), a fully analytical solution to the linearized Poisson Boltzmann equation. The PB-AM software package includes the generation of outputs files appropriate for visualization using VMD, a Brownian dynamics scheme that uses periodic boundary conditions to simulate dynamics, the ability to specify docking criteria, and offers two different kinetics schemes to evaluate biomolecular association rate constants. Given that PB-AM defines mutual polarization completely and accurately, it can be refactored as a many-body expansion to explore 2- and 3-body polarization. Additionally, the software has been integrated into the Adaptive Poisson-Boltzmann Solver (APBS) software package to make it more accessible to a larger group of scientists, educators and students that are more familiar with the APBS framework.
AQUASOL: An efficient solver for the dipolar Poisson-Boltzmann-Langevin equation.
Koehl, Patrice; Delarue, Marc
2010-02-14
The Poisson-Boltzmann (PB) formalism is among the most popular approaches to modeling the solvation of molecules. It assumes a continuum model for water, leading to a dielectric permittivity that only depends on position in space. In contrast, the dipolar Poisson-Boltzmann-Langevin (DPBL) formalism represents the solvent as a collection of orientable dipoles with nonuniform concentration; this leads to a nonlinear permittivity function that depends both on the position and on the local electric field at that position. The differences in the assumptions underlying these two models lead to significant differences in the equations they generate. The PB equation is a second order, elliptic, nonlinear partial differential equation (PDE). Its response coefficients correspond to the dielectric permittivity and are therefore constant within each subdomain of the system considered (i.e., inside and outside of the molecules considered). While the DPBL equation is also a second order, elliptic, nonlinear PDE, its response coefficients are nonlinear functions of the electrostatic potential. Many solvers have been developed for the PB equation; to our knowledge, none of these can be directly applied to the DPBL equation. The methods they use may adapt to the difference; their implementations however are PBE specific. We adapted the PBE solver originally developed by Holst and Saied [J. Comput. Chem. 16, 337 (1995)] to the problem of solving the DPBL equation. This solver uses a truncated Newton method with a multigrid preconditioner. Numerical evidences suggest that it converges for the DPBL equation and that the convergence is superlinear. It is found however to be slow and greedy in memory requirement for problems commonly encountered in computational biology and computational chemistry. To circumvent these problems, we propose two variants, a quasi-Newton solver based on a simplified, inexact Jacobian and an iterative self-consistent solver that is based directly on the PBE
Progress in developing Poisson-Boltzmann equation solvers
Li, Chuan; Li, Lin; Petukh, Marharyta; Alexov, Emil
2013-01-01
This review outlines the recent progress made in developing more accurate and efficient solutions to model electrostatics in systems comprised of bio-macromolecules and nano-objects, the last one referring to objects that do not have biological function themselves but nowadays are frequently used in biophysical and medical approaches in conjunction with bio-macromolecules. The problem of modeling macromolecular electrostatics is reviewed from two different angles: as a mathematical task provided the specific definition of the system to be modeled and as a physical problem aiming to better capture the phenomena occurring in the real experiments. In addition, specific attention is paid to methods to extend the capabilities of the existing solvers to model large systems toward applications of calculations of the electrostatic potential and energies in molecular motors, mitochondria complex, photosynthetic machinery and systems involving large nano-objects. PMID:24199185
Progress in developing Poisson-Boltzmann equation solvers.
Li, Chuan; Li, Lin; Petukh, Marharyta; Alexov, Emil
2013-03-01
This review outlines the recent progress made in developing more accurate and efficient solutions to model electrostatics in systems comprised of bio-macromolecules and nano-objects, the last one referring to objects that do not have biological function themselves but nowadays are frequently used in biophysical and medical approaches in conjunction with bio-macromolecules. The problem of modeling macromolecular electrostatics is reviewed from two different angles: as a mathematical task provided the specific definition of the system to be modeled and as a physical problem aiming to better capture the phenomena occurring in the real experiments. In addition, specific attention is paid to methods to extend the capabilities of the existing solvers to model large systems toward applications of calculations of the electrostatic potential and energies in molecular motors, mitochondria complex, photosynthetic machinery and systems involving large nano-objects.
PB-AM: An open-source, fully analytical linear poisson-boltzmann solver.
Felberg, Lisa E; Brookes, David H; Yap, Eng-Hui; Jurrus, Elizabeth; Baker, Nathan A; Head-Gordon, Teresa
2017-06-05
We present the open source distributed software package Poisson-Boltzmann Analytical Method (PB-AM), a fully analytical solution to the linearized PB equation, for molecules represented as non-overlapping spherical cavities. The PB-AM software package includes the generation of outputs files appropriate for visualization using visual molecular dynamics, a Brownian dynamics scheme that uses periodic boundary conditions to simulate dynamics, the ability to specify docking criteria, and offers two different kinetics schemes to evaluate biomolecular association rate constants. Given that PB-AM defines mutual polarization completely and accurately, it can be refactored as a many-body expansion to explore 2- and 3-body polarization. Additionally, the software has been integrated into the Adaptive Poisson-Boltzmann Solver (APBS) software package to make it more accessible to a larger group of scientists, educators, and students that are more familiar with the APBS framework. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.
Features of CPB: a Poisson-Boltzmann solver that uses an adaptive Cartesian grid.
Fenley, Marcia O; Harris, Robert C; Mackoy, Travis; Boschitsch, Alexander H
2015-02-05
The capabilities of an adaptive Cartesian grid (ACG)-based Poisson-Boltzmann (PB) solver (CPB) are demonstrated. CPB solves various PB equations with an ACG, built from a hierarchical octree decomposition of the computational domain. This procedure decreases the number of points required, thereby reducing computational demands. Inside the molecule, CPB solves for the reaction-field component (ϕrf ) of the electrostatic potential (ϕ), eliminating the charge-induced singularities in ϕ. CPB can also use a least-squares reconstruction method to improve estimates of ϕ at the molecular surface. All surfaces, which include solvent excluded, Gaussians, and others, are created analytically, eliminating errors associated with triangulated surfaces. These features allow CPB to produce detailed surface maps of ϕ and compute polar solvation and binding free energies for large biomolecular assemblies, such as ribosomes and viruses, with reduced computational demands compared to other Poisson-Boltzmann equation solvers. The reader is referred to http://www.continuum-dynamics.com/solution-mm.html for how to obtain the CPB software. © 2014 Wiley Periodicals, Inc.
Quantum Monte Carlo using a Stochastic Poisson Solver
Energy Technology Data Exchange (ETDEWEB)
Das, D; Martin, R M; Kalos, M H
2005-05-06
Quantum Monte Carlo (QMC) is an extremely powerful method to treat many-body systems. Usually quantum Monte Carlo has been applied in cases where the interaction potential has a simple analytic form, like the 1/r Coulomb potential. However, in a complicated environment as in a semiconductor heterostructure, the evaluation of the interaction itself becomes a non-trivial problem. Obtaining the potential from any grid-based finite-difference method, for every walker and every step is unfeasible. We demonstrate an alternative approach of solving the Poisson equation by a classical Monte Carlo within the overall quantum Monte Carlo scheme. We have developed a modified ''Walk On Spheres'' algorithm using Green's function techniques, which can efficiently account for the interaction energy of walker configurations, typical of quantum Monte Carlo algorithms. This stochastically obtained potential can be easily incorporated within popular quantum Monte Carlo techniques like variational Monte Carlo (VMC) or diffusion Monte Carlo (DMC). We demonstrate the validity of this method by studying a simple problem, the polarization of a helium atom in the electric field of an infinite capacitor.
Lu, Benzhuo; Cheng, Xiaolin; Huang, Jingfang; McCammon, J. Andrew
2013-11-01
A Fortran program package is introduced for rapid evaluation of the electrostatic potentials and forces in biomolecular systems modeled by the linearized Poisson-Boltzmann equation. The numerical solver utilizes a well-conditioned boundary integral equation (BIE) formulation, a node-patch discretization scheme, a Krylov subspace iterative solver package with reverse communication protocols, and an adaptive new version of the fast multipole method in which the exponential expansions are used to diagonalize the multipole-to-local translations. The program and its full description, as well as several closely related libraries and utility tools are available at http://lsec.cc.ac.cn/~lubz/afmpb.html and a mirror site at http://mccammon.ucsd.edu/. This paper is a brief summary of the program: the algorithms, the implementation and the usage. Restrictions: Only three or six significant digits options are provided in this version. Unusual features: Most of the codes are in Fortran77 style. Memory allocation functions from Fortran90 and above are used in a few subroutines. Additional comments: The current version of the codes is designed and written for single core/processor desktop machines. Check http://lsec.cc.ac.cn/lubz/afmpb.html for updates and changes. Running time: The running time varies with the number of discretized elements (N) in the system and their distributions. In most cases, it scales linearly as a function of N.
A GPU-accelerated Direct-sum Boundary Integral Poisson-Boltzmann Solver
Geng, Weihua
2013-01-01
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-double device memory for a biomolecule with $N$ triangular surface elements and $N_c$ partial charges. Numerical tests of these schemes show well-maintained accuracy and fast convergence. The GPU implementation using one GPU card (Nvidia Tesla M2070) achieves 120-150X speed-up to the implementation using one CPU (Intel L5640 2.27GHz). With our approach, solving PB equations on well-discretized molecular surfaces with up ...
Qiang, Ji
2016-01-01
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 time and the memory usage by using an artificial boundary condition in a large extended computational domain.
Reimer, Ashton S.; Cheviakov, Alexei F.
2013-03-01
A Matlab-based finite-difference numerical solver for the Poisson equation for a rectangle and a disk in two dimensions, and a spherical domain in three dimensions, is presented. The solver is optimized for handling an arbitrary combination of Dirichlet and Neumann boundary conditions, and allows for full user control of mesh refinement. The solver routines utilize effective and parallelized sparse vector and matrix operations. Computations exhibit high speeds, numerical stability with respect to mesh size and mesh refinement, and acceptable error values even on desktop computers. Catalogue identifier: AENQ_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AENQ_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: GNU General Public License v3.0 No. of lines in distributed program, including test data, etc.: 102793 No. of bytes in distributed program, including test data, etc.: 369378 Distribution format: tar.gz Programming language: Matlab 2010a. Computer: PC, Macintosh. Operating system: Windows, OSX, Linux. RAM: 8 GB (8, 589, 934, 592 bytes) Classification: 4.3. Nature of problem: To solve the Poisson problem in a standard domain with “patchy surface”-type (strongly heterogeneous) Neumann/Dirichlet boundary conditions. Solution method: Finite difference with mesh refinement. Restrictions: Spherical domain in 3D; rectangular domain or a disk in 2D. Unusual features: Choice between mldivide/iterative solver for the solution of large system of linear algebraic equations that arise. Full user control of Neumann/Dirichlet boundary conditions and mesh refinement. Running time: Depending on the number of points taken and the geometry of the domain, the routine may take from less than a second to several hours to execute.
A Fast and Robust Poisson-Boltzmann Solver Based on Adaptive Cartesian Grids
Boschitsch, Alexander H.; Fenley, Marcia O.
2011-01-01
An adaptive Cartesian grid (ACG) concept is presented for the fast and robust numerical solution of the 3D Poisson-Boltzmann Equation (PBE) governing the electrostatic interactions of large-scale biomolecules and highly charged multi-biomolecular assemblies such as ribosomes and viruses. The ACG offers numerous advantages over competing grid topologies such as regular 3D lattices and unstructured grids. For very large biological molecules and multi-biomolecule assemblies, the total number of grid-points is several orders of magnitude less than that required in a conventional lattice grid used in the current PBE solvers thus allowing the end user to obtain accurate and stable nonlinear PBE solutions on a desktop computer. Compared to tetrahedral-based unstructured grids, ACG offers a simpler hierarchical grid structure, which is naturally suited to multigrid, relieves indirect addressing requirements and uses fewer neighboring nodes in the finite difference stencils. Construction of the ACG and determination of the dielectric/ionic maps are straightforward, fast and require minimal user intervention. Charge singularities are eliminated by reformulating the problem to produce the reaction field potential in the molecular interior and the total electrostatic potential in the exterior ionic solvent region. This approach minimizes grid-dependency and alleviates the need for fine grid spacing near atomic charge sites. The technical portion of this paper contains three parts. First, the ACG and its construction for general biomolecular geometries are described. Next, a discrete approximation to the PBE upon this mesh is derived. Finally, the overall solution procedure and multigrid implementation are summarized. Results obtained with the ACG-based PBE solver are presented for: (i) a low dielectric spherical cavity, containing interior point charges, embedded in a high dielectric ionic solvent – analytical solutions are available for this case, thus allowing rigorous
DEFF Research Database (Denmark)
Hejlesen, Mads Mølholm
A regularisation method for solving the Poisson equation using Green’s functions is presented.The method is shown to obtain a convergence rate which corresponds to the design of the regularised Green’s function and a spectral-like convergence rate is obtained using a spectrally ideal regularisation...... the appropriate regularised Green’s functions. Using an analogy to the particle-particle particle-mesh method, a framework for calculating multi-resolution solutions using local refinement patches is presented. The regularised Poisson solver is shown to maintain a high order converging solution for different...... configurations of the refinement patches.The regularised Poisson solver has been implemented in a high order particle-mesh based vortex method for simulating incompressible fluid flow. A re-meshing of the vortex particlesis used to ensure the convergence of the method and a re-projection of the vorticity field...
High-Order Kinetic Relaxation Schemes as High-Accuracy Poisson Solvers
Mendoza, M; Herrmann, H J
2015-01-01
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 Knudsen numbers. In order to test our kinetic approach, we discretise the Boltzmann equation and solve the Poisson equation, spending up to six order of magnitude less computational time for a given precision than standard lattice Boltzmann methods.
Xie, Yang; Ying, Jinyong; Xie, Dexuan
2017-03-30
SMPBS (Size Modified Poisson-Boltzmann Solvers) is a web server for computing biomolecular electrostatics using finite element solvers of the size modified Poisson-Boltzmann equation (SMPBE). SMPBE not only reflects ionic size effects but also includes the classic Poisson-Boltzmann equation (PBE) as a special case. Thus, its web server is expected to have a broader range of applications than a PBE web server. SMPBS is designed with a dynamic, mobile-friendly user interface, and features easily accessible help text, asynchronous data submission, and an interactive, hardware-accelerated molecular visualization viewer based on the 3Dmol.js library. In particular, the viewer allows computed electrostatics to be directly mapped onto an irregular triangular mesh of a molecular surface. Due to this functionality and the fast SMPBE finite element solvers, the web server is very efficient in the calculation and visualization of electrostatics. In addition, SMPBE is reconstructed using a new objective electrostatic free energy, clearly showing that the electrostatics and ionic concentrations predicted by SMPBE are optimal in the sense of minimizing the objective electrostatic free energy. SMPBS is available at the URL: smpbs.math.uwm.edu © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.
ColDICE: A parallel Vlasov-Poisson solver using moving adaptive simplicial tessellation
Sousbie, Thierry; Colombi, Stéphane
2016-09-01
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-space sheet at second order relying on additional tracers created when needed at runtime. In order to preserve in the best way the Hamiltonian nature of the system, refinement is anisotropic and constrained by measurements of local Poincaré invariants. Resolution of Poisson equation is performed using the fast Fourier method on a regular rectangular grid, similarly to particle in cells codes. To compute the density projected onto this grid, the intersection of the tessellation and the grid is calculated using the method of Franklin and Kankanhalli [65-67] generalised to linear order. As preliminary tests of the code, we study in four dimensional phase-space the evolution of an initially small patch in a chaotic potential and the cosmological collapse of a fluctuation composed of two sinusoidal waves. We also perform a "warm" dark matter simulation in six-dimensional phase-space that we use to check the parallel scaling of the code.
ColDICE: a parallel Vlasov-Poisson solver using moving adaptive simplicial tessellation
Sousbie, Thierry
2015-01-01
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-space sheet at second order relying on additional tracers created when needed at runtime. In order to preserve in the best way the Hamiltonian nature of the system, refinement is anisotropic and constrained by measurements of local Poincar\\'e invariants. Resolution of Poisson equation is performed using the fast Fourier method on a regular rectangular grid, similarly to particle in cells codes. To compute the density proj...
ColDICE: A parallel Vlasov–Poisson solver using moving adaptive simplicial tessellation
Energy Technology Data Exchange (ETDEWEB)
Sousbie, Thierry, E-mail: tsousbie@gmail.com [Institut d' Astrophysique de Paris, CNRS UMR 7095 and UPMC, 98bis, bd Arago, F-75014 Paris (France); Department of Physics, The University of Tokyo, Tokyo 113-0033 (Japan); Research Center for the Early Universe, School of Science, The University of Tokyo, Tokyo 113-0033 (Japan); Colombi, Stéphane, E-mail: colombi@iap.fr [Institut d' Astrophysique de Paris, CNRS UMR 7095 and UPMC, 98bis, bd Arago, F-75014 Paris (France); Yukawa Institute for Theoretical Physics, Kyoto University, Kyoto 606-8502 (Japan)
2016-09-15
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-space sheet at second order relying on additional tracers created when needed at runtime. In order to preserve in the best way the Hamiltonian nature of the system, refinement is anisotropic and constrained by measurements of local Poincaré invariants. Resolution of Poisson equation is performed using the fast Fourier method on a regular rectangular grid, similarly to particle in cells codes. To compute the density projected onto this grid, the intersection of the tessellation and the grid is calculated using the method of Franklin and Kankanhalli [65–67] generalised to linear order. As preliminary tests of the code, we study in four dimensional phase-space the evolution of an initially small patch in a chaotic potential and the cosmological collapse of a fluctuation composed of two sinusoidal waves. We also perform a “warm” dark matter simulation in six-dimensional phase-space that we use to check the parallel scaling of the code.
Ying, Jinyong
2016-01-01
The size-modified Poisson-Boltzmann equation (SMPBE) is one important variant of the popular dielectric model, the Poisson-Boltzmann equation (PBE), to reflect ionic size effects in the prediction of electrostatics for a biomolecule in an ionic solvent. In this paper, a new SMPBE hybrid solver is developed using a solution decomposition, the Schwartz's overlapped domain decomposition, finite element, and finite difference. It is then programmed as a software package in C, Fortran, and Python based on the state-of-the-art finite element library DOLFIN from the FEniCS project. This software package is well validated on a Born ball model with analytical solution and a dipole model with a known physical properties. Numerical results on six proteins with different net charges demonstrate its high performance. Finally, this new SMPBE hybrid solver is shown to be numerically stable and convergent in the calculation of electrostatic solvation free energy for 216 biomolecules and binding free energy for a DNA-drug com...
Xie, Dexuan; Jiang, Yi
2016-10-01
The nonlocal dielectric approach has been studied for more than forty years but only limited to water solvent until the recent work of Xie et al. (2013) [20]. As the development of this recent work, in this paper, a nonlocal modified Poisson-Boltzmann equation (NMPBE) is proposed to incorporate nonlocal dielectric effects into the classic Poisson-Boltzmann equation (PBE) for protein in ionic solvent. The focus of this paper is to present an efficient finite element algorithm and a related software package for solving NMPBE. Numerical results are reported to validate this new software package and demonstrate its high performance for protein molecules. They also show the potential of NMPBE as a better predictor of electrostatic solvation and binding free energies than PBE.
A QUMOND galactic N-body code I: Poisson solver and rotation curve fitting
Angus, Garry W; Famaey, Benoit; Gentile, Gianfranco; McGaugh, Stacy S; de Blok, W J G
2012-01-01
Here we present a new particle-mesh galactic N-body code that uses the full multigrid algorithm for solving the modified Poisson equation of the Quasi Linear formulation of Modified Newtonian Dynamics (QUMOND). A novel approach for handling the boundary conditions using a refinement strategy is implemented and the accuracy of the code is compared with analytical solutions of Kuzmin disks. We then employ the code to compute the predicted rotation curves for a sample of five spiral galaxies from the THINGS sample. We generated static N-body realisations of the galaxies according to their stellar and gaseous surface densities and allowed their distances, mass-to-light ratios (M/L) and both the stellar and gas scale-heights to vary in order to estimate the best fit parameters. We found that NGC 3621, NGC 3521 and DDO 154 are well fit by MOND using expected values of the distance and M/L. NGC 2403 required a moderately larger $M/L$ than expected and NGC 2903 required a substantially larger value. The surprising re...
Parallel iterative solvers and preconditioners using approximate hierarchical methods
Energy Technology Data Exchange (ETDEWEB)
Grama, A.; Kumar, V.; Sameh, A. [Univ. of Minnesota, Minneapolis, MN (United States)
1996-12-31
In this paper, we report results of the performance, convergence, and accuracy of a parallel GMRES solver for Boundary Element Methods. The solver uses a hierarchical approximate matrix-vector product based on a hybrid Barnes-Hut / Fast Multipole Method. We study the impact of various accuracy parameters on the convergence and show that with minimal loss in accuracy, our solver yields significant speedups. We demonstrate the excellent parallel efficiency and scalability of our solver. The combined speedups from approximation and parallelism represent an improvement of several orders in solution time. We also develop fast and paralellizable preconditioners for this problem. We report on the performance of an inner-outer scheme and a preconditioner based on truncated Green`s function. Experimental results on a 256 processor Cray T3D are presented.
A multiresolution method for solving the Poisson equation using high order regularization
DEFF Research Database (Denmark)
Hejlesen, Mads Mølholm; Walther, Jens Honore
2016-01-01
We present a novel high order multiresolution Poisson solver based on regularized Green's function solutions to obtain exact free-space boundary conditions while using fast Fourier transforms for computational efficiency. Multiresolution is a achieved through local refinement patches and regulari......We present a novel high order multiresolution Poisson solver based on regularized Green's function solutions to obtain exact free-space boundary conditions while using fast Fourier transforms for computational efficiency. Multiresolution is a achieved through local refinement patches...... and regularized Green's functions corresponding to the difference in the spatial resolution between the patches. The full solution is obtained utilizing the linearity of the Poisson equation enabling super-position of solutions. We show that the multiresolution Poisson solver produces convergence rates...... that correspond to the regularization order of the derived Green's functions....
Algebraic structure and Poisson method for a weakly nonholonomic system
Institute of Scientific and Technical Information of China (English)
无
2011-01-01
The algebraic structure and the Poisson method for a weakly nonholonomic system are studied.The differential equations of motion of the system can be written in a contravariant algebra form and its algebraic structure is discussed.The Poisson theory for the systems which possess Lie algebra structure is generalized to the weakly nonholonomic system.An example is given to illustrate the application of the result.
An Easy Method To Accelerate An Iterative Algebraic Equation Solver
Energy Technology Data Exchange (ETDEWEB)
Yao, Jin [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)
2014-01-06
This article proposes to add a simple term to an iterative algebraic equation solver with an order n convergence rate, and to raise the order of convergence to (2n - 1). In particular, a simple algebraic equation solver with the 5th order convergence but uses only 4 function values in each iteration, is described in details. When this scheme is applied to a Newton-Raphson method of the quadratic convergence for a system of algebraic equations, a cubic convergence can be achieved with an low overhead cost of function evaluation that can be ignored as the size of the system increases.
A new fast direct solver for the boundary element method
Huang, S.; Liu, Y. J.
2017-04-01
A new fast direct linear equation solver for the boundary element method (BEM) is presented in this paper. The idea of the new fast direct solver stems from the concept of the hierarchical off-diagonal low-rank matrix. The hierarchical off-diagonal low-rank matrix can be decomposed into the multiplication of several diagonal block matrices. The inverse of the hierarchical off-diagonal low-rank matrix can be calculated efficiently with the Sherman-Morrison-Woodbury formula. In this paper, a more general and efficient approach to approximate the coefficient matrix of the BEM with the hierarchical off-diagonal low-rank matrix is proposed. Compared to the current fast direct solver based on the hierarchical off-diagonal low-rank matrix, the proposed method is suitable for solving general 3-D boundary element models. Several numerical examples of 3-D potential problems with the total number of unknowns up to above 200,000 are presented. The results show that the new fast direct solver can be applied to solve large 3-D BEM models accurately and with better efficiency compared with the conventional BEM.
Institute of Scientific and Technical Information of China (English)
王虹宇
2016-01-01
基于Trilinos程序包中的AztecOO和ML package开发了并行Poisson求解器。在非均匀的结构化网格上实现了复杂金属/电介质几何体的建模。 Poisson方程通过有限体积方法离散形成求解矩阵，然后利用Trilinos进行并行矩阵求解。并行测试表明，求解器的收敛表现良好，在典型情况下性能满足需求。这一求解器代码可以用于从等离子体模拟到传热过程等多种任务。%A Poisson Solver based on AztecOO and ML in Trilinos is developed. The metal and dielectric ob-ject with complex geometry is modeled in a non-uniform structure grid. Poisson equation is discretized by finite volume method to build a sparse matrix. The sparse matrix is solved paralleled with Trilinos. The benchmark show good convergence rates and satisfying performance. This solver code can be used for kinds of problem as plasma simulating and heat transfer.
Pan, Zhao; Whitehead, Jared; Thomson, Scott; Truscott, Tadd
2016-08-01
Obtaining pressure field data from particle image velocimetry (PIV) is an attractive technique in fluid dynamics due to its noninvasive nature. The application of this technique generally involves integrating the pressure gradient or solving the pressure Poisson equation using a velocity field measured with PIV. However, very little research has been done to investigate the dynamics of error propagation from PIV-based velocity measurements to the pressure field calculation. Rather than measure the error through experiment, we investigate the dynamics of the error propagation by examining the Poisson equation directly. We analytically quantify the error bound in the pressure field, and are able to illustrate the mathematical roots of why and how the Poisson equation based pressure calculation propagates error from the PIV data. The results show that the error depends on the shape and type of boundary conditions, the dimensions of the flow domain, and the flow type.
Pan, Zhao; Thomson, Scott; Truscott, Tadd
2016-01-01
Obtaining pressure field data from particle image velocimetry (PIV) is an attractive technique in fluid dynamics due to its noninvasive nature. The application of this technique generally involves integrating the pressure gradient or solving the pressure Poisson equation using a velocity field measured with PIV. However, very little research has been done to investigate the dynamics of error propagation from PIV-based velocity measurements to the pressure field calculation. Rather than measure the error through experiment, we investigate the dynamics of the error propagation by examining the Poisson equation directly. We analytically quantify the error bound in the pressure field, and are able to illustrate the mathematical roots of why and how the Poisson equation based pressure calculation propagates error from the PIV data. The results show that the error depends on the shape and type of boundary conditions, the dimensions of the flow domain, and the flow type.
Pan, Zhao; Whitehead, Jared; Thomson, Scott; Truscott, Tadd
2016-08-01
Obtaining pressure field data from particle image velocimetry (PIV) is an attractive technique in fluid dynamics due to its noninvasive nature. The application of this technique generally involves integrating the pressure gradient or solving the pressure Poisson equation using a velocity field measured with PIV. However, very little research has been done to investigate the dynamics of error propagation from PIV-based velocity measurements to the pressure field calculation. Rather than measure the error through experiment, we investigate the dynamics of the error propagation by examining the Poisson equation directly. We analytically quantify the error bound in the pressure field, and are able to illustrate the mathematical roots of why and how the Poisson equation based pressure calculation propagates error from the PIV data. The results show that the error depends on the shape and type of boundary conditions, the dimensions of the flow domain, and the flow type.
Bazzani, A; Franchi, A; Rambaldi, S; Turchetti, G
2005-01-01
We analyze the accuracy of a 2D Poisson-Vlasov PIC integrator, taking the KV as a reference solution for a FODO cell. The particle evolution is symplectic and the Poisson solver is based on FFT. The numerical error, evaluated by comparing the moments of the distribution and the electric field with the exact solution, shows a linear growth. This effect can be modeled by a white noise in the envelope equations for the KV beam. In order to investigate the collisional effects we have integrated the Hamilton's equations for N charged macro-particles with a hard-core r/sub H/ reducing the computational complexity to N/sup 3/2/. In the constant focusing case we observed that a KV beam, matched or mismatched relaxes to the Maxwell-Boltzmann self consistent distribution on a time interval, which depends on r/sub H/ and has a finite limit, for r/sub H/ to 0. A fully 3D PIC code for short bunches was developed for the ADS linac design at LNL (Italy). A 3D particle-core model, based on Langevin's equations with the drift...
Optimizing tridiagonal solvers for alternating direction methods on Boolean cube multiprocessors
Energy Technology Data Exchange (ETDEWEB)
Ho, C.T. (IBM Almaden Research Center, San Jose, CA (US)); Johnsson, S.L. (Dept. of Computer Science and Electrical Engineering, Yale Univ., New Haven, CT (US))
1990-05-01
Sets of tridiagonal systems occur in many applications. Fast Poisson solvers and Alternate Direction Methods make use of tridiagonal system solvers. Network-based multiprocessors provide a cost-effective alternative to traditional supercomputer architectures. The complexity of concurrent algorithms for the solution of multiple tridiagonal systems on Boolean-cube-configured multiprocessors with distributed memory are investigated. Variations of odd-even cyclic reduction, parallel cyclic reduction, and algorithms making use of data transposition with or without substructuring and local elimination, or pipelined elimination, are considered. A simple performance model is used for algorithm comparison, and the validity of the model is verified on an Intel iPSC/1. For many combinations of machine and system parameters, pipelined elimination, or equation transposition with or without substructuring is optimum. Hybrid algorithms that at any stage choose the best algorithm among the considered ones for the remainder of the problem are presented. It is shown that the optimum partitioning of a set of independent tridiagonal systems among a set of processors yields the embarrassingly parallel case.
Poisson Downward Continuation Solution by the Jacobi Method
Kingdon, R.; Vaníček, P.
2011-03-01
Downward continuation is a continuing problem in geodesy and geophysics. Inversion of the discrete form of the Poisson integration process provides a numerical solution to the problem, but because the B matrix that defines the discrete Poisson integration is not always well conditioned the solution may be noisy in situations where the discretization step is small and in areas containing large heights. We provide two remedies, both in the context of the Jacobi iterative solution to the Poisson downward continuation problem. First, we suggest testing according to the upward continued result from each solution, rather then testing between successive solutions on the geoid, so that choice of a tolerance for the convergence of the iterative method is more meaningful and intuitive. Second, we show how a tolerance that reflects the conditioning of the B matrix can regularize the solution, and suggest an approximate way of choosing such a tolerance. Using these methods, we are able to calculate a solution that appears regular in an area of Papua New Guinea having heights over 3200 m, over a grid with 1 arc-minute spacing, based on a very poorly conditioned B matrix.
Domain decomposed preconditioners with Krylov subspace methods as subdomain solvers
Energy Technology Data Exchange (ETDEWEB)
Pernice, M. [Univ. of Utah, Salt Lake City, UT (United States)
1994-12-31
Domain decomposed preconditioners for nonsymmetric partial differential equations typically require the solution of problems on the subdomains. Most implementations employ exact solvers to obtain these solutions. Consequently work and storage requirements for the subdomain problems grow rapidly with the size of the subdomain problems. Subdomain solves constitute the single largest computational cost of a domain decomposed preconditioner, and improving the efficiency of this phase of the computation will have a significant impact on the performance of the overall method. The small local memory available on the nodes of most message-passing multicomputers motivates consideration of the use of an iterative method for solving subdomain problems. For large-scale systems of equations that are derived from three-dimensional problems, memory considerations alone may dictate the need for using iterative methods for the subdomain problems. In addition to reduced storage requirements, use of an iterative solver on the subdomains allows flexibility in specifying the accuracy of the subdomain solutions. Substantial savings in solution time is possible if the quality of the domain decomposed preconditioner is not degraded too much by relaxing the accuracy of the subdomain solutions. While some work in this direction has been conducted for symmetric problems, similar studies for nonsymmetric problems appear not to have been pursued. This work represents a first step in this direction, and explores the effectiveness of performing subdomain solves using several transpose-free Krylov subspace methods, GMRES, transpose-free QMR, CGS, and a smoothed version of CGS. Depending on the difficulty of the subdomain problem and the convergence tolerance used, a reduction in solution time is possible in addition to the reduced memory requirements. The domain decomposed preconditioner is a Schur complement method in which the interface operators are approximated using interface probing.
Intrusive Method for Uncertainty Quantification in a Multiphase Flow Solver
Turnquist, Brian; Owkes, Mark
2016-11-01
Uncertainty quantification (UQ) is a necessary, interesting, and often neglected aspect of fluid flow simulations. To determine the significance of uncertain initial and boundary conditions, a multiphase flow solver is being created which extends a single phase, intrusive, polynomial chaos scheme into multiphase flows. Reliably estimating the impact of input uncertainty on design criteria can help identify and minimize unwanted variability in critical areas, and has the potential to help advance knowledge in atomizing jets, jet engines, pharmaceuticals, and food processing. Use of an intrusive polynomial chaos method has been shown to significantly reduce computational cost over non-intrusive collocation methods such as Monte-Carlo. This method requires transforming the model equations into a weak form through substitution of stochastic (random) variables. Ultimately, the model deploys a stochastic Navier Stokes equation, a stochastic conservative level set approach including reinitialization, as well as stochastic normals and curvature. By implementing these approaches together in one framework, basic problems may be investigated which shed light on model expansion, uncertainty theory, and fluid flow in general. NSF Grant Number 1511325.
Multilevel Methods for the Poisson-Boltzmann Equation
Holst, Michael Jay
We consider the numerical solution of the Poisson -Boltzmann equation (PBE), a three-dimensional second order nonlinear elliptic partial differential equation arising in biophysics. This problem has several interesting features impacting numerical algorithms, including discontinuous coefficients representing material interfaces, rapid nonlinearities, and three spatial dimensions. Similar equations occur in various applications, including nuclear physics, semiconductor physics, population genetics, astrophysics, and combustion. In this thesis, we study the PBE, discretizations, and develop multilevel-based methods for approximating the solutions of these types of equations. We first outline the physical model and derive the PBE, which describes the electrostatic potential of a large complex biomolecule lying in a solvent. We next study the theoretical properties of the linearized and nonlinear PBE using standard function space methods; since this equation has not been previously studied theoretically, we provide existence and uniqueness proofs in both the linearized and nonlinear cases. We also analyze box-method discretizations of the PBE, establishing several properties of the discrete equations which are produced. In particular, we show that the discrete nonlinear problem is well-posed. We study and develop linear multilevel methods for interface problems, based on algebraic enforcement of Galerkin or variational conditions, and on coefficient averaging procedures. Using a stencil calculus, we show that in certain simplified cases the two approaches are equivalent, with different averaging procedures corresponding to different prolongation operators. We also develop methods for nonlinear problems based on a nonlinear multilevel method, and on linear multilevel methods combined with a globally convergent damped-inexact-Newton method. We derive a necessary and sufficient descent condition for the inexact-Newton direction, enabling the development of extremely
A 3D Unstructured Mesh Euler Solver Based on the Fourth-Order CESE Method
2013-06-01
conservation in space and time without using a one-dimensional Riemann solver, (ii) genuinely multi-dimensional treatment without dimensional splitting (iii...of the original second-order CESE method, including: (i) flux conservation in space and time without using a one-dimensional Riemann solver, (ii...treated in a unified manner. The geometry for a three-dimensional CESE method is more difficult to visualize than the one- and two-dimensional methods
Comment on: 'A Poisson resampling method for simulating reduced counts in nuclear medicine images'
DEFF Research Database (Denmark)
de Nijs, Robin
2015-01-01
methods, and compared to the theoretical values for a Poisson distribution. Statistical parameters showed the same behavior as in the original note and showed the superiority of the Poisson resampling method. Rounding off before saving of the half count image had a severe impact on counting statistics......, also in the case of rounding off of the images....
AN ACCURATE SOLUTION OF THE POISSON EQUATION BY THE FINITE DIFFERENCE-CHEBYSHEV-TAU METHOD
Institute of Scientific and Technical Information of China (English)
Hani I. Siyyam
2001-01-01
A new finite difference-Chebyshev-Tau method for the solution of the twodimensional Poisson equation is presented. Some of the numerical results are also presented which indicate that the method is satisfactory and compatible to other methods.
A parallel direct solver for the self-adaptive hp Finite Element Method
Paszyński, Maciej R.
2010-03-01
In this paper we present a new parallel multi-frontal direct solver, dedicated for the hp Finite Element Method (hp-FEM). The self-adaptive hp-FEM generates in a fully automatic mode, a sequence of hp-meshes delivering exponential convergence of the error with respect to the number of degrees of freedom (d.o.f.) as well as the CPU time, by performing a sequence of hp refinements starting from an arbitrary initial mesh. The solver constructs an initial elimination tree for an arbitrary initial mesh, and expands the elimination tree each time the mesh is refined. This allows us to keep track of the order of elimination for the solver. The solver also minimizes the memory usage, by de-allocating partial LU factorizations computed during the elimination stage of the solver, and recomputes them for the backward substitution stage, by utilizing only about 10% of the computational time necessary for the original computations. The solver has been tested on 3D Direct Current (DC) borehole resistivity measurement simulations problems. We measure the execution time and memory usage of the solver over a large regular mesh with 1.5 million degrees of freedom as well as on the highly non-regular mesh, generated by the self-adaptive h p-FEM, with finite elements of various sizes and polynomial orders of approximation varying from p = 1 to p = 9. From the presented experiments it follows that the parallel solver scales well up to the maximum number of utilized processors. The limit for the solver scalability is the maximum sequential part of the algorithm: the computations of the partial LU factorizations over the longest path, coming from the root of the elimination tree down to the deepest leaf. © 2009 Elsevier Inc. All rights reserved.
A meshless method for compressible flows with the HLLC Riemann solver
Ma, Z H; Qian, L
2014-01-01
The HLLC Riemann solver, which resolves both the shock waves and contact discontinuities, is popular to the computational fluid dynamics community studying compressible flow problems with mesh methods. Although it was reported to be used in meshless methods, the crucial information and procedure to realise this scheme within the framework of meshless methods were not clarified fully. Moreover, the capability of the meshless HLLC solver to deal with compressible liquid flows is not completely clear yet as very few related studies have been reported. Therefore, a comprehensive investigation of a dimensional non-split HLLC Riemann solver for the least-square meshless method is carried out in this study. The stiffened gas equation of state is adopted to capacitate the proposed method to deal with single-phase gases and/or liquids effectively, whilst direct applying the perfect gas equation of state for compressible liquid flows might encounter great difficulties in correlating the state variables. The spatial der...
High-performance Parallel Solver for Integral Equations of Electromagnetics Based on Galerkin Method
Kruglyakov, Mikhail
2015-01-01
A new parallel solver for the volumetric integral equations (IE) of electrodynamics is presented. The solver is based on the Galerkin method which ensures the convergent numerical solution. The main features include: 1) the reduction of the memory usage in half, compared to analogous IE based algorithms, without additional restriction on the background media; 2) accurate and stable method to compute matrix coefficients corresponding to the IE; 3) high degree of parallelism. The solver's computational efficiency is shown on a problem of magnetotelluric sounding of the high conductivity contrast media. A good agreement with the results obtained with the second order finite element method is demonstrated. Due to effective approach to parallelization and distributed data storage the program exhibits perfect scalability on different hardware platforms.
The Background Field Method and the Linearization Problem for Poisson Manifolds
Grassi, P A
2004-01-01
The background field method (BFM) for the Poisson Sigma Model (PSM) is studied as an example of the application of the BFM technique to open gauge algebras. The relationship with Seiberg-Witten maps arising in non-commutative gauge theories is clarified. It is shown that the implementation of the BFM for the PSM in the Batalin-Vilkovisky formalism is equivalent to the solution of a generalized linearization problem (in the formal sense) for Poisson structures in the presence of gauge fields. Sufficient conditions for the existence of a solution and a constructive method to derive it are presented.
Comparisons of methods for generating conditional Poisson samples and Sampford samples
Grafström, Anton
2005-01-01
Methods for conditional Poisson sampling (CP-sampling) and Sampford sampling are compared and the focus is on the efficiency of the methods. The efficiency is investigated by simulation in different sampling situations. It was of interest to compare methods since new methods for both CP-sampling and Sampford sampling were introduced by Bondesson, Traat & Lundqvist in 2004. The new methods are acceptance rejection methods that use the efficient Pareto sampling method. They are found to be ...
C1-continuous Virtual Element Method for Poisson-Kirchhoff plate problem
Energy Technology Data Exchange (ETDEWEB)
Gyrya, Vitaliy [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Mourad, Hashem Mohamed [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)
2016-09-20
We present a family of C1-continuous high-order Virtual Element Methods for Poisson-Kirchho plate bending problem. The convergence of the methods is tested on a variety of meshes including rectangular, quadrilateral, and meshes obtained by edge removal (i.e. highly irregular meshes). The convergence rates are presented for all of these tests.
Relative and Absolute Error Control in a Finite-Difference Method Solution of Poisson's Equation
Prentice, J. S. C.
2012-01-01
An algorithm for error control (absolute and relative) in the five-point finite-difference method applied to Poisson's equation is described. The algorithm is based on discretization of the domain of the problem by means of three rectilinear grids, each of different resolution. We discuss some hardware limitations associated with the algorithm,…
Wang, Xiao-Yen; Chow, Chuen-Yen; Chang, Sin-Chung
1996-01-01
The I-D, quasi I-D and 2-D Euler solvers based on the method of space-time conservation element and solution element are used to simulate various flow phenomena including shock waves, Mach stem, contact surface, expansion waves, and their intersections and reflections. Seven test problems are solved to demonstrate the capability of this method for handling unsteady compressible flows in various configurations. Numerical results so obtained are compared with exact solutions and/or numerical solutions obtained by schemes based on other established computational techniques. Comparisons show that the present Euler solvers can generate highly accurate numerical solutions to complex flow problems in a straightforward manner without using any ad hoc techniques in the scheme.
Bouleau, Nicolas
2015-01-01
A simplified approach to Malliavin calculus adapted to Poisson random measures is developed and applied in this book. Called the “lent particle method” it is based on perturbation of the position of particles. Poisson random measures describe phenomena involving random jumps (for instance in mathematical finance) or the random distribution of particles (as in statistical physics). Thanks to the theory of Dirichlet forms, the authors develop a mathematical tool for a quite general class of random Poisson measures and significantly simplify computations of Malliavin matrices of Poisson functionals. The method gives rise to a new explicit calculus that they illustrate on various examples: it consists in adding a particle and then removing it after computing the gradient. Using this method, one can establish absolute continuity of Poisson functionals such as Lévy areas, solutions of SDEs driven by Poisson measure and, by iteration, obtain regularity of laws. The authors also give applications to error calcul...
Cerroni, D.; Fancellu, L.; Manservisi, S.; Menghini, F.
2016-06-01
In this work we propose to study the behavior of a solid elastic object that interacts with a multiphase flow. Fluid structure interaction and multiphase problems are of great interest in engineering and science because of many potential applications. The study of this interaction by coupling a fluid structure interaction (FSI) solver with a multiphase problem could open a large range of possibilities in the investigation of realistic problems. We use a FSI solver based on a monolithic approach, while the two-phase interface advection and reconstruction is computed in the framework of a Volume of Fluid method which is one of the more popular algorithms for two-phase flow problems. The coupling between the FSI and VOF algorithm is efficiently handled with the use of MEDMEM libraries implemented in the computational platform Salome. The numerical results of a dam break problem over a deformable solid are reported in order to show the robustness and stability of this numerical approach.
Directory of Open Access Journals (Sweden)
Abdollah BORHANIFAR
2013-01-01
Full Text Available In this study fractional Poisson equation is scrutinized through finite difference using shifted Grünwald estimate. A novel method is proposed numerically. The existence and uniqueness of solution for the fractional Poisson equation are proved. Exact and numerical solution are constructed and compared. Then numerical result shows the efficiency of the proposed method.
DEFF Research Database (Denmark)
Harrod, Steven; Kelton, W. David
2006-01-01
Nonstationary Poisson processes are appropriate in many applications, including disease studies, transportation, finance, and social policy. The authors review the risks of ignoring nonstationarity in Poisson processes and demonstrate three algorithms for generation of Poisson processes with piec......Nonstationary Poisson processes are appropriate in many applications, including disease studies, transportation, finance, and social policy. The authors review the risks of ignoring nonstationarity in Poisson processes and demonstrate three algorithms for generation of Poisson processes...
The Closest Point Method and Multigrid Solvers for Elliptic Equations on Surfaces
Chen, Yujia
2015-01-01
© 2015 Society for Industrial and Applied Mathematics. Elliptic partial differential equations are important from both application and analysis points of view. In this paper we apply the closest point method to solve elliptic equations on general curved surfaces. Based on the closest point representation of the underlying surface, we formulate an embedding equation for the surface elliptic problem, then discretize it using standard finite differences and interpolation schemes on banded but uniform Cartesian grids. We prove the convergence of the difference scheme for the Poisson\\'s equation on a smooth closed curve. In order to solve the resulting large sparse linear systems, we propose a specific geometric multigrid method in the setting of the closest point method. Convergence studies in both the accuracy of the difference scheme and the speed of the multigrid algorithm show that our approaches are effective.
Diosady, Laslo; Murman, Scott; Blonigan, Patrick; Garai, Anirban
2017-01-01
Presented space-time adjoint solver for turbulent compressible flows. Confirmed failure of traditional sensitivity methods for chaotic flows. Assessed rate of exponential growth of adjoint for practical 3D turbulent simulation. Demonstrated failure of short-window sensitivity approximations.
Solution of Poisson's equation for finite systems using plane wave methods
Castro, A; Stott, M J; Castro, Alberto; Rubio, Angel
2003-01-01
Reciprocal space methods for solving Poisson's equation for finite charge distributions are investigated. Improvements to previous proposals are presented, and their performance is compared in the context of a real-space density functional theory code. Two basic methodologies are followed: calculation of correction terms, and imposition of a cut-off to the Coulomb potential. We conclude that these methods can be safely applied to finite or aperiodic systems with a reasonable control of speed and accuracy.
Wing aeroelasticity analysis based on an integral boundary-layer method coupled with Euler solver
Institute of Scientific and Technical Information of China (English)
Ma Yanfeng; He Erming; Zeng Xianang; Li Junjie
2016-01-01
An interactive boundary-layer method, which solves the unsteady flow, is developed for aeroelastic computation in the time domain. The coupled method combines the Euler solver with the integral boundary-layer solver (Euler/BL) in a ‘‘semi-inverse” manner to compute flows with the inviscid and viscous interaction. Unsteady boundary conditions on moving surfaces are taken into account by utilizing the approximate small-perturbation method without moving the compu-tational grids. The steady and unsteady flow calculations for the LANN wing are presented. The wing tip displacement of high Reynolds number aero-structural dynamics (HIRENASD) Project is simulated under different angles of attack. The flutter-boundary predictions for the AGARD 445.6 wing are provided. The results of the interactive boundary-layer method are compared with those of the Euler method and experimental data. The study shows that viscous effects are signif-icant for these cases and the further data analysis confirms the validity and practicability of the cou-pled method.
Wing aeroelasticity analysis based on an integral boundary-layer method coupled with Euler solver
Directory of Open Access Journals (Sweden)
Ma Yanfeng
2016-10-01
Full Text Available An interactive boundary-layer method, which solves the unsteady flow, is developed for aeroelastic computation in the time domain. The coupled method combines the Euler solver with the integral boundary-layer solver (Euler/BL in a “semi-inverse” manner to compute flows with the inviscid and viscous interaction. Unsteady boundary conditions on moving surfaces are taken into account by utilizing the approximate small-perturbation method without moving the computational grids. The steady and unsteady flow calculations for the LANN wing are presented. The wing tip displacement of high Reynolds number aero-structural dynamics (HIRENASD Project is simulated under different angles of attack. The flutter-boundary predictions for the AGARD 445.6 wing are provided. The results of the interactive boundary-layer method are compared with those of the Euler method and experimental data. The study shows that viscous effects are significant for these cases and the further data analysis confirms the validity and practicability of the coupled method.
Dry deposition model for a microscale aerosol dispersion solver based on the moment method
Šíp, Viktor
2016-01-01
A dry deposition model suitable for use in the moment method has been developed. Contributions from five main processes driving the deposition - Brownian diffusion, interception, impaction, turbulent impaction, and sedimentation - are included in the model. The deposition model was employed in the moment method solver implemented in the OpenFOAM framework. Applicability of the developed expression and the moment method solver was tested on two example problems of particle dispersion in the presence of a vegetation on small scales: a flow through a tree patch in 2D and a flow through a hedgerow in 3D. Comparison with the sectional method showed that the moment method using the developed deposition model is able to reproduce the shape of the particle size distribution well. The relative difference in terms of the third moment of the distribution was below 10\\% in both tested cases, and decreased away from the vegetation. Main source of this difference is a known overprediction of the impaction efficiency. When ...
Poisson theory and integration method for a dynamical system of relative motion
Institute of Scientific and Technical Information of China (English)
Zhang Yi; Shang Mei
2011-01-01
This paper focuses on studying the Poisson theory and the integration method of dynamics of relative motion. Equations of a dynamical system of relative motion in phase space are given. Poisson theory of the system is established. The Jacobi last multiplier of the system is defined, and the relation between the Jacobi last multiplier and the first integrals of the system is studied. Our research shows that for a dynamical system of relative motion, whose configuration is determined by n generalized coordinates, the solution of the system can be found by using the Jacobi last multiplier if (2n - 1) first integrals of the system are known. At the end of the paper, an example is given to illustrate the application of the results.
An efficient simulation method of a cyclotron sector-focusing magnet using 2D Poisson code
Energy Technology Data Exchange (ETDEWEB)
Gad Elmowla, Khaled Mohamed M; Chai, Jong Seo, E-mail: jschai@skku.edu; Yeon, Yeong H; Kim, Sangbum; Ghergherehchi, Mitra
2016-10-01
In this paper we discuss design simulations of a spiral magnet using 2D Poisson code. The Independent Layers Method (ILM) is a new technique that was developed to enable the use of two-dimensional simulation code to calculate a non-symmetric 3-dimensional magnetic field. In ILM, the magnet pole is divided into successive independent layers, and the hill and valley shape around the azimuthal direction is implemented using a reference magnet. The normalization of the magnetic field in the reference magnet produces a profile that can be multiplied by the maximum magnetic field in the hill magnet, which is a dipole magnet made of the hills at the same radius. Both magnets are then calculated using the 2D Poisson SUPERFISH code. Then a fully three-dimensional magnetic field is produced using TOSCA for the original spiral magnet, and the comparison of the 2D and 3D results shows a good agreement between both.
Directory of Open Access Journals (Sweden)
Ran Zhao
2015-01-01
Full Text Available The hybrid solvers based on integral equation domain decomposition method (HS-DDM are developed for modeling of electromagnetic radiation. Based on the philosophy of “divide and conquer,” the IE-DDM divides the original multiscale problem into many closed nonoverlapping subdomains. For adjacent subdomains, the Robin transmission conditions ensure the continuity of currents, so the meshes of different subdomains can be allowed to be nonconformal. It also allows different fast solvers to be used in different subdomains based on the property of different subdomains to reduce the time and memory consumption. Here, the multilevel fast multipole algorithm (MLFMA and hierarchical (H- matrices method are combined in the framework of IE-DDM to enhance the capability of IE-DDM and realize efficient solution of multiscale electromagnetic radiating problems. The MLFMA is used to capture propagating wave physics in large, smooth regions, while H-matrices are used to capture evanescent wave physics in small regions which are discretized with dense meshes. Numerical results demonstrate the validity of the HS-DDM.
A FORMAL SYSTEMS APPROACH TO SOLVER DESIGN-HILL CLIMBING METHOD WITH PUSH DOWN STACK
Institute of Scientific and Technical Information of China (English)
Yasuhiko TAKAHARA; Yongmei LIU; Yoshio YANO
2003-01-01
This paper presents a formal approach to design of a solver of an intelligent management information system and its implementation. The approach implies set theoretic modeling based on the general systems concepts and implementation in the extProlog. There are research efforts which attack (optimization) problems using the set theory and logics. Furthermore, they use logic programming languages for their implementation. Although their methods look quite similar to the approach of this paper, there are clear differences between them. This paper is interested in exploration of the solving system rather than algorithms. The paper first presents a design and implementation procedure of a solver. Then, classification of problems is discussed. The least structured class of the classification is the target of this paper. A data mining system is an example of the class. Formal theories are derived for the design procedure assnming the least structured case. A solving strategy, which is called a hill climbing method with a push down stack, is proposed on the theories. A data mining system is used as an example to illustrate the results. Finally, a full implementation in extProlog is presented for the data mining system.
Liu, Hailiang; Wang, Zhongming
2017-01-01
We design an arbitrary-order free energy satisfying discontinuous Galerkin (DG) method for solving time-dependent Poisson-Nernst-Planck systems. Both the semi-discrete and fully discrete DG methods are shown to satisfy the corresponding discrete free energy dissipation law for positive numerical solutions. Positivity of numerical solutions is enforced by an accuracy-preserving limiter in reference to positive cell averages. Numerical examples are presented to demonstrate the high resolution of the numerical algorithm and to illustrate the proven properties of mass conservation, free energy dissipation, as well as the preservation of steady states.
Generalized Methods and Solvers for Noise Removal from Piecewise Constant Signals
Little, Max A
2010-01-01
Removing noise from piecewise constant (PWC) signals, is a challenging signal processing problem arising in many practical contexts. For example, in exploration geosciences, noisy drill hole records need separating into stratigraphic zones, and in biophysics, jumps between molecular dwell states need extracting from noisy fluorescence microscopy signals. Many PWC denoising methods exist, including total variation regularization, mean shift clustering, stepwise jump placement, running medians, convex clustering shrinkage and bilateral filtering; conventional linear signal processing methods are fundamentally unsuited however. This paper shows that most of these methods are associated with a special case of a generalized functional, minimized to achieve PWC denoising. The minimizer can be obtained by diverse solver algorithms, including stepwise jump placement, convex programming, finite differences, iterated running medians, least angle regression, regularization path following, and coordinate descent. We intr...
Error analysis of finite element method for Poisson-Nernst-Planck equations
Energy Technology Data Exchange (ETDEWEB)
Sun, Yuzhou; Sun, Pengtao; Zheng, Bin; Lin, Guang
2016-08-01
A priori error estimates of finite element method for time-dependent Poisson-Nernst-Planck equations are studied in this work. We obtain the optimal error estimates in L∞(H1) and L2(H1) norms, and suboptimal error estimates in L∞(L2) norm, with linear element, and optimal error estimates in L∞(L2) norm with quadratic or higher-order element, for both semi- and fully discrete finite element approximations. Numerical experiments are also given to validate the theoretical results.
Directory of Open Access Journals (Sweden)
Bishnu P. Lamichhane
2013-01-01
Full Text Available We introduce two three-field mixed formulations for the Poisson equation and propose finite element methods for their approximation. Both mixed formulations are obtained by introducing a weak equation for the gradient of the solution by means of a Lagrange multiplier space. Two efficient numerical schemes are proposed based on using a pair of bases for the gradient of the solution and the Lagrange multiplier space forming biorthogonal and quasi-biorthogonal systems, respectively. We also establish an optimal a priori error estimate for both finite element approximations.
Collier, Nathaniel Oren
2014-09-17
SUMMARY: We compare the computational efficiency of isogeometric Galerkin and collocation methods for partial differential equations in the asymptotic regime. We define a metric to identify when numerical experiments have reached this regime. We then apply these ideas to analyze the performance of different isogeometric discretizations, which encompass C0 finite element spaces and higher-continuous spaces. We derive convergence and cost estimates in terms of the total number of degrees of freedom and then perform an asymptotic numerical comparison of the efficiency of these methods applied to an elliptic problem. These estimates are derived assuming that the underlying solution is smooth, the full Gauss quadrature is used in each non-zero knot span and the numerical solution of the discrete system is found using a direct multi-frontal solver. We conclude that under the assumptions detailed in this paper, higher-continuous basis functions provide marginal benefits.
Scalable, parallel poisson solvers for CFD problems
Younas, Muhammad
2012-01-01
Het grootste deel van de rekencapaciteit nodig voor het berekenen van nietsamendrukbare turbulente stromingen wordt aangewend voor het oplossen van de Poissonvergelijking voor de druk. Daarom beschouwen we de parallelle prestaties van zeer efficiënte Poissonsolvers binnen PETSc (Portable, Extensible
A parallel implementation of an EBE solver for the finite element method
Energy Technology Data Exchange (ETDEWEB)
Silva, R.P.; Las Casas, E.B.; Carvalho, M.L.B. [Federal Univ. of Minas Gerais, Belo Horizonte (Brazil)
1994-12-31
A parallel implementation using PVM on a cluster of workstations of an Element By Element (EBE) solver using the Preconditioned Conjugate Gradient (PCG) method is described, along with an application in the solution of the linear systems generated from finite element analysis of a problem in three dimensional linear elasticity. The PVM (Parallel Virtual Machine) system, developed at the Oak Ridge Laboratory, allows the construction of a parallel MIMD machine by connecting heterogeneous computers linked through a network. In this implementation, version 3.1 of PVM is used, and 11 SLC Sun workstations and a Sun SPARC-2 model are connected through Ethernet. The finite element program is based on SDP, System for Finite Element Based Software Development, developed at the Brazilian National Laboratory for Scientific Computation (LNCC). SDP provides the basic routines for a finite element application program, as well as a standard for programming and documentation, intended to allow exchanges between research groups in different centers.
Directory of Open Access Journals (Sweden)
Tsugio Fukuchi
2014-06-01
Full Text Available The finite difference method (FDM based on Cartesian coordinate systems can be applied to numerical analyses over any complex domain. A complex domain is usually taken to mean that the geometry of an immersed body in a fluid is complex; here, it means simply an analytical domain of arbitrary configuration. In such an approach, we do not need to treat the outer and inner boundaries differently in numerical calculations; both are treated in the same way. Using a method that adopts algebraic polynomial interpolations in the calculation around near-wall elements, all the calculations over irregular domains reduce to those over regular domains. Discretization of the space differential in the FDM is usually derived using the Taylor series expansion; however, if we use the polynomial interpolation systematically, exceptional advantages are gained in deriving high-order differences. In using the polynomial interpolations, we can numerically solve the Poisson equation freely over any complex domain. Only a particular type of partial differential equation, Poisson's equations, is treated; however, the arguments put forward have wider generality in numerical calculations using the FDM.
Nonparametric Inference of Doubly Stochastic Poisson Process Data via the Kernel Method.
Zhang, Tingting; Kou, S C
2010-01-01
Doubly stochastic Poisson processes, also known as the Cox processes, frequently occur in various scientific fields. In this article, motivated primarily by analyzing Cox process data in biophysics, we propose a nonparametric kernel-based inference method. We conduct a detailed study, including an asymptotic analysis, of the proposed method, and provide guidelines for its practical use, introducing a fast and stable regression method for bandwidth selection. We apply our method to real photon arrival data from recent single-molecule biophysical experiments, investigating proteins' conformational dynamics. Our result shows that conformational fluctuation is widely present in protein systems, and that the fluctuation covers a broad range of time scales, highlighting the dynamic and complex nature of proteins' structure.
Boutsikas, Michael V; 10.3150/09-BEJ201
2010-01-01
Let $X_1,X_2,...,X_n$ be a sequence of independent or locally dependent random variables taking values in $\\mathbb{Z}_+$. In this paper, we derive sharp bounds, via a new probabilistic method, for the total variation distance between the distribution of the sum $\\sum_{i=1}^nX_i$ and an appropriate Poisson or compound Poisson distribution. These bounds include a factor which depends on the smoothness of the approximating Poisson or compound Poisson distribution. This "smoothness factor" is of order $\\mathrm{O}(\\sigma ^{-2})$, according to a heuristic argument, where $\\sigma ^2$ denotes the variance of the approximating distribution. In this way, we offer sharp error estimates for a large range of values of the parameters. Finally, specific examples concerning appearances of rare runs in sequences of Bernoulli trials are presented by way of illustration.
Accurate, robust and reliable calculations of Poisson-Boltzmann solvation energies
Wang, Bao
2016-01-01
Developing accurate solvers for the Poisson Boltzmann (PB) model is the first step to make the PB model suitable for implicit solvent simulation. Reducing the grid size influence on the performance of the solver benefits to increasing the speed of solver and providing accurate electrostatics analysis for solvated molecules. In this work, we explore the accurate coarse grid PB solver based on the Green's function treatment of the singular charges, matched interface and boundary (MIB) method for treating the geometric singularities, and posterior electrostatic potential field extension for calculating the reaction field energy. We made our previous PB software, MIBPB, robust and provides almost grid size independent reaction field energy calculation. Large amount of the numerical tests verify the grid size independence merit of the MIBPB software. The advantage of MIBPB software directly make the acceleration of the PB solver from the numerical algorithm instead of utilization of advanced computer architectures...
Energy Technology Data Exchange (ETDEWEB)
Regnier, D. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); CEA, DAM, DIF, Arpajon (France); Verriere, M. [CEA, DAM, DIF, Arpajon (France); Dubray, N. [CEA, DAM, DIF, Arpajon (France); Schunck, N. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)
2015-11-30
In this study, we describe the software package FELIX that solves the equations of the time-dependent generator coordinate method (TDGCM) in NN-dimensions (N ≥ 1) under the Gaussian overlap approximation. The numerical resolution is based on the Galerkin finite element discretization of the collective space and the Crank–Nicolson scheme for time integration. The TDGCM solver is implemented entirely in C++. Several additional tools written in C++, Python or bash scripting language are also included for convenience. In this paper, the solver is tested with a series of benchmarks calculations. We also demonstrate the ability of our code to handle a realistic calculation of fission dynamics.
Regnier, D.; Verrière, M.; Dubray, N.; Schunck, N.
2016-03-01
We describe the software package FELIX that solves the equations of the time-dependent generator coordinate method (TDGCM) in N-dimensions (N ≥ 1) under the Gaussian overlap approximation. The numerical resolution is based on the Galerkin finite element discretization of the collective space and the Crank-Nicolson scheme for time integration. The TDGCM solver is implemented entirely in C++. Several additional tools written in C++, Python or bash scripting language are also included for convenience. In this paper, the solver is tested with a series of benchmarks calculations. We also demonstrate the ability of our code to handle a realistic calculation of fission dynamics.
Regnier, D; Dubray, N; Schunck, N
2015-01-01
We describe the software package FELIX that solves the equations of the time-dependent generator coordinate method (TDGCM) in N-dimensions (N $\\geq$ 1) under the Gaussian overlap approximation. The numerical resolution is based on the Galerkin finite element discretization of the collective space and the Crank-Nicolson scheme for time integration. The TDGCM solver is implemented entirely in C++. Several additional tools written in C++, Python or bash scripting language are also included for convenience. In this paper, the solver is tested with a series of benchmarks calculations. We also demonstrate the ability of our code to handle a realistic calculation of fission dynamics.
Solving the Poisson partial differential equation using vector space projection methods
Marendic, Boris
This research presents a new approach at solving the Poisson partial differential equation using Vector Space Projection (VSP) methods. The work attacks the Poisson equation as encountered in two-dimensional phase unwrapping problems, and in two-dimensional electrostatic problems. Algorithms are developed by first considering simple one-dimensional cases, and then extending them to two-dimensional problems. In the context of phase unwrapping of two-dimensional phase functions, we explore an approach to the unwrapping using a robust extrapolation-projection algorithm. The unwrapping is done iteratively by modification of the Gerchberg-Papoulis (GP) extrapolation algorithm, and the solution is refined by projecting onto the available global data. An important contribution to the extrapolation algorithm is the formulation of the algorithm with the relaxed bandwidth constraint, and the proof that such modified GP extrapolation algorithm still converges. It is also shown that the unwrapping problem is ill-posed in the VSP setting, and that the modified GP algorithm is the missing link to pushing the iterative algorithm out of the trap solution under certain conditions. Robustness of the algorithm is demonstrated through its performance in a noisy environment. Performance is demonstrated by applying it to phantom phase functions, as well as to the real phase functions. Results are compared to well known algorithms in literature. Unlike many existing unwrapping methods which perform unwrapping locally, this work approaches the unwrapping problem from a globally, and eliminates the need for guiding instruments, like quality maps. VSP algorithm also very effectively battles problems of shadowing and holes, where data is not available or is heavily corrupted. In solving the classical Poisson problems in electrostatics, we demonstrate the effectiveness and ease of implementation of the VSP methodology to solving the equation, as well as imposing of the boundary conditions
General form of the Euler-Poisson-Darboux equation and application of the transmutation method
Directory of Open Access Journals (Sweden)
Elina L. Shishkina
2017-07-01
Full Text Available In this article, we find solution representations in the compact integral form to the Cauchy problem for a general form of the Euler-Poisson-Darboux equation with Bessel operators via generalized translation and spherical mean operators for all values of the parameter k, including also not studying before exceptional odd negative values. We use a Hankel transform method to prove results in a unified way. Under additional conditions we prove that a distributional solution is a classical one too. A transmutation property for connected generalized spherical mean is proved and importance of applying transmutation methods for differential equations with Bessel operators is emphasized. The paper also contains a short historical introduction on differential equations with Bessel operators and a rather detailed reference list of monographs and papers on mathematical theory and applications of this class of differential equations.
On-the-fly Numerical Surface Integration for Finite-Difference Poisson-Boltzmann Methods.
Cai, Qin; Ye, Xiang; Wang, Jun; Luo, Ray
2011-11-01
Most implicit solvation models require the definition of a molecular surface as the interface that separates the solute in atomic detail from the solvent approximated as a continuous medium. Commonly used surface definitions include the solvent accessible surface (SAS), the solvent excluded surface (SES), and the van der Waals surface. In this study, we present an efficient numerical algorithm to compute the SES and SAS areas to facilitate the applications of finite-difference Poisson-Boltzmann methods in biomolecular simulations. Different from previous numerical approaches, our algorithm is physics-inspired and intimately coupled to the finite-difference Poisson-Boltzmann methods to fully take advantage of its existing data structures. Our analysis shows that the algorithm can achieve very good agreement with the analytical method in the calculation of the SES and SAS areas. Specifically, in our comprehensive test of 1,555 molecules, the average unsigned relative error is 0.27% in the SES area calculations and 1.05% in the SAS area calculations at the grid spacing of 1/2Å. In addition, a systematic correction analysis can be used to improve the accuracy for the coarse-grid SES area calculations, with the average unsigned relative error in the SES areas reduced to 0.13%. These validation studies indicate that the proposed algorithm can be applied to biomolecules over a broad range of sizes and structures. Finally, the numerical algorithm can also be adapted to evaluate the surface integral of either a vector field or a scalar field defined on the molecular surface for additional solvation energetics and force calculations.
Stanic, Milos; Nordlund, Markus; Kuczaj, Arkadiusz; Frederix, Edoardo; Geurts, Bernard
2014-11-01
Porous media flows can be found in a large number of fields ranging from engineering to medical applications. A volume-averaged approach to simulating porous media is often used because of its practicality and computational efficiency. Derivation of the volume-averaged porous flow equations introduces additional porous resistance terms to the momentum equation. When discretized these porous resistance terms create a body force discontinuity at the porous-fluid interface, which may lead to spurious oscillations if not accounted for properly. A variety of numerical techniques has been proposed to solve this problem, but few of them have concentrated on collocated grids and segregated solvers, which have wide applications in academia and industry. In this work we discuss the source of the spurious oscillations, quantify their amplitude and apply interface treatments methods that successfully remove the oscillations. The interface treatment methods are tested in a variety of realistic scenarios, including the porous plug and Beaver-Joseph test cases and show excellent results, minimizing or entirely removing the spurious oscillations at the porous-fluid interface. This research was financially supported by Philip Morris Products S.A.
Energy Technology Data Exchange (ETDEWEB)
Yao Yuqin [College of Sciences, Shanghai University, Shanghai 200436 (China)] e-mail: yyqinw@126.com
2005-11-01
In this paper, based on the well-known Sine-Poisson equation, a new Sine-Poisson equation expansion method with constant coefficients or variable coefficients is presented, which can be used to construct more new exact solutions of nonlinear evolution equations in mathematical physics. The KdV-mKdV equation and the typical breaking soliton equation are chosen to illustrate our method such that many types of new exact solutions are obtained, which include exponential solutions, kink-shaped solutions, singular solutions and soliton-like solutions.
Pathak, Ashish; Raessi, Mehdi
2016-04-01
We present a three-dimensional (3D) and fully Eulerian approach to capturing the interaction between two fluids and moving rigid structures by using the fictitious domain and volume-of-fluid (VOF) methods. The solid bodies can have arbitrarily complex geometry and can pierce the fluid-fluid interface, forming contact lines. The three-phase interfaces are resolved and reconstructed by using a VOF-based methodology. Then, a consistent scheme is employed for transporting mass and momentum, allowing for simulations of three-phase flows of large density ratios. The Eulerian approach significantly simplifies numerical resolution of the kinematics of rigid bodies of complex geometry and with six degrees of freedom. The fluid-structure interaction (FSI) is computed using the fictitious domain method. The methodology was developed in a message passing interface (MPI) parallel framework accelerated with graphics processing units (GPUs). The computationally intensive solution of the pressure Poisson equation is ported to GPUs, while the remaining calculations are performed on CPUs. The performance and accuracy of the methodology are assessed using an array of test cases, focusing individually on the flow solver and the FSI in surface-piercing configurations. Finally, an application of the proposed methodology in simulations of the ocean wave energy converters is presented.
A Posteriori Error Estimation for Finite Element Methods and Iterative Linear Solvers
Energy Technology Data Exchange (ETDEWEB)
Melboe, Hallgeir
2001-10-01
This thesis addresses a posteriori error estimation for finite element methods and iterative linear solvers. Adaptive finite element methods have gained a lot of popularity over the last decades due to their ability to produce accurate results with limited computer power. In these methods a posteriori error estimates play an essential role. Not only do they give information about how large the total error is, they also indicate which parts of the computational domain should be given a more sophisticated treatment in order to reduce the error. A posteriori error estimates are traditionally aimed at estimating the global error, but more recently so called goal oriented error estimators have been shown a lot of interest. The name reflects the fact that they estimate the error in user-defined local quantities. In this thesis the main focus is on global error estimators for highly stretched grids and goal oriented error estimators for flow problems on regular grids. Numerical methods for partial differential equations, such as finite element methods and other similar techniques, typically result in a linear system of equations that needs to be solved. Usually such systems are solved using some iterative procedure which due to a finite number of iterations introduces an additional error. Most such algorithms apply the residual in the stopping criterion, whereas the control of the actual error may be rather poor. A secondary focus in this thesis is on estimating the errors that are introduced during this last part of the solution procedure. The thesis contains new theoretical results regarding the behaviour of some well known, and a few new, a posteriori error estimators for finite element methods on anisotropic grids. Further, a goal oriented strategy for the computation of forces in flow problems is devised and investigated. Finally, an approach for estimating the actual errors associated with the iterative solution of linear systems of equations is suggested. (author)
Unbounded Immersed Interface solver, also for use in Vortex Particle-Mesh methods
Marichal, Yves; Chatelain, Philippe; Winckelmans, Gregoire
2012-11-01
We present a new and efficient algorithm to solve the 2-D Poisson equation in unbounded domain and with complex inner boundaries. It is based on an efficient combination of two components: the Immersed Interface method to enforce the boundary condition on each inner boundary (here using solely 1-D stencil corrections) and the James-Lackner algorithm to compute the outer boundary condition consistent with the unbounded domain solution. The algorithm is here implemented using second order finite differences and is particularized to the computation of potential flow past solid bodies. It is validated, by means of grid convergence studies, on the flow past multiple bodies (some also with circulation). The results confirm the second order accuracy everywhere. The algorithm is self consistent as ``all is done on the grid'' (thus without using a Vortex Panel boundary element method in addition to the grid). The next aim of this work is then to integrate this algorithm in the Vortex Particle-Mesh (VPM) method for the computation of unsteady viscous flows, with boundary layers, detached shear layers and wakes. Preliminary results of the combined methods will also be presented. Research Fellow (PhD student) of the F.R.S.-FNRS of Belgium.
DEFF Research Database (Denmark)
Fokianos, Konstantinos; Rahbek, Anders Christian; Tjøstheim, Dag
This paper considers geometric ergodicity and likelihood based inference for linear and nonlinear Poisson autoregressions. In the linear case the conditional mean is linked linearly to its past values as well as the observed values of the Poisson process. This also applies to the conditional...
Towards Green Multi-frontal Solver for Adaptive Finite Element Method
AbbouEisha, H.
2015-06-01
In this paper we present the optimization of the energy consumption for the multi-frontal solver algorithm executed over two dimensional grids with point singularities. The multi-frontal solver algorithm is controlled by so-called elimination tree, defining the order of elimination of rows from particular frontal matrices, as well as order of memory transfers for Schur complement matrices. For a given mesh there are many possible elimination trees resulting in different number of floating point operations (FLOPs) of the solver or different amount of data trans- ferred via memory transfers. In this paper we utilize the dynamic programming optimization procedure and we compare elimination trees optimized with respect to FLOPs with elimination trees optimized with respect to energy consumption.
A one-level FETI method for the drift–diffusion-Poisson system with discontinuities at an interface
Baumgartner, Stefan
2013-06-01
A 3d feti method for the drift-diffusion-Poisson system including discontinuities at a 2d interface is developed. The motivation for this work is to provide a parallel numerical algorithm for a system of PDEs that are the basic model equations for the simulation of semiconductor devices such as transistors and sensors. Moreover, discontinuities or jumps in the potential and its normal derivative at a 2d surface are included for the simulation of nanowire sensors based on a homogenized model. Using the feti method, these jump conditions can be included with the usual numerical properties and the original Farhat-Roux feti method is extended to the drift-diffusion-Poisson equations including discontinuities. We show two numerical examples. The first example verifies the correct implementation including the discontinuities on a 2d grid divided into eight subdomains. The second example is 3d and shows the application of the algorithm to the simulation of nanowire sensors with high aspect ratios. The Poisson-Boltzmann equation and the drift-diffusion-Poisson system with jump conditions are solved on a 3d grid with real-world boundary conditions. © 2013 Elsevier Inc..
DEFF Research Database (Denmark)
Fokianos, Konstantinos; Rahbek, Anders Christian; Tjøstheim, Dag
This paper considers geometric ergodicity and likelihood based inference for linear and nonlinear Poisson autoregressions. In the linear case the conditional mean is linked linearly to its past values as well as the observed values of the Poisson process. This also applies to the conditional...... variance, implying an interpretation as an integer valued GARCH process. In a nonlinear conditional Poisson model, the conditional mean is a nonlinear function of its past values and a nonlinear function of past observations. As a particular example an exponential autoregressive Poisson model for time...... series is considered. Under geometric ergodicity the maximum likelihood estimators of the parameters are shown to be asymptotically Gaussian in the linear model. In addition we provide a consistent estimator of the asymptotic covariance, which is used in the simulations and the analysis of some...
DEFF Research Database (Denmark)
Fokianos, Konstantinos; Rahbek, Anders Christian; Tjøstheim, Dag
2009-01-01
In this article we consider geometric ergodicity and likelihood-based inference for linear and nonlinear Poisson autoregression. In the linear case, the conditional mean is linked linearly to its past values, as well as to the observed values of the Poisson process. This also applies...... to the conditional variance, making possible interpretation as an integer-valued generalized autoregressive conditional heteroscedasticity process. In a nonlinear conditional Poisson model, the conditional mean is a nonlinear function of its past values and past observations. As a particular example, we consider...... an exponential autoregressive Poisson model for time series. Under geometric ergodicity, the maximum likelihood estimators are shown to be asymptotically Gaussian in the linear model. In addition, we provide a consistent estimator of their asymptotic covariance matrix. Our approach to verifying geometric...
DEFF Research Database (Denmark)
Fokianos, Konstantinos; Rahbæk, Anders; Tjøstheim, Dag
This paper considers geometric ergodicity and likelihood based inference for linear and nonlinear Poisson autoregressions. In the linear case the conditional mean is linked linearly to its past values as well as the observed values of the Poisson process. This also applies to the conditional...... variance, making an interpretation as an integer valued GARCH process possible. In a nonlinear conditional Poisson model, the conditional mean is a nonlinear function of its past values and a nonlinear function of past observations. As a particular example an exponential autoregressive Poisson model...... for time series is considered. Under geometric ergodicity the maximum likelihood estimators of the parameters are shown to be asymptotically Gaussian in the linear model. In addition we provide a consistent estimator of their asymptotic covariance matrix. Our approach to verifying geometric ergodicity...
Li, Xian-Ying; Hu, Shi-Min
2013-02-01
Harmonic functions are the critical points of a Dirichlet energy functional, the linear projections of conformal maps. They play an important role in computer graphics, particularly for gradient-domain image processing and shape-preserving geometric computation. We propose Poisson coordinates, a novel transfinite interpolation scheme based on the Poisson integral formula, as a rapid way to estimate a harmonic function on a certain domain with desired boundary values. Poisson coordinates are an extension of the Mean Value coordinates (MVCs) which inherit their linear precision, smoothness, and kernel positivity. We give explicit formulas for Poisson coordinates in both continuous and 2D discrete forms. Superior to MVCs, Poisson coordinates are proved to be pseudoharmonic (i.e., they reproduce harmonic functions on n-dimensional balls). Our experimental results show that Poisson coordinates have lower Dirichlet energies than MVCs on a number of typical 2D domains (particularly convex domains). As well as presenting a formula, our approach provides useful insights for further studies on coordinates-based interpolation and fast estimation of harmonic functions.
SYMPLECTIC STRUCTURE OF POISSON SYSTEM
Institute of Scientific and Technical Information of China (English)
SUN Jian-qiang; MA Zhong-qi; TIAN Yi-min; QIN Meng-zhao
2005-01-01
When the Poisson matrix of Poisson system is non-constant, classical symplectic methods, such as symplectic Runge-Kutta method, generating function method, cannot preserve the Poisson structure. The non-constant Poisson structure was transformed into the symplectic structure by the nonlinear transform.Arbitrary order symplectic method was applied to the transformed Poisson system. The Euler equation of the free rigid body problem was transformed into the symplectic structure and computed by the mid-point scheme. Numerical results show the effectiveness of the nonlinear transform.
Numerical methods for a Poisson-Nernst-Planck-Fermi model of biological ion channels.
Liu, Jinn-Liang; Eisenberg, Bob
2015-07-01
Numerical methods are proposed for an advanced Poisson-Nernst-Planck-Fermi (PNPF) model for studying ion transport through biological ion channels. PNPF contains many more correlations than most models and simulations of channels, because it includes water and calculates dielectric properties consistently as outputs. This model accounts for the steric effect of ions and water molecules with different sizes and interstitial voids, the correlation effect of crowded ions with different valences, and the screening effect of polarized water molecules in an inhomogeneous aqueous electrolyte. The steric energy is shown to be comparable to the electrical energy under physiological conditions, demonstrating the crucial role of the excluded volume of particles and the voids in the natural function of channel proteins. Water is shown to play a critical role in both correlation and steric effects in the model. We extend the classical Scharfetter-Gummel (SG) method for semiconductor devices to include the steric potential for ion channels, which is a fundamental physical property not present in semiconductors. Together with a simplified matched interface and boundary (SMIB) method for treating molecular surfaces and singular charges of channel proteins, the extended SG method is shown to exhibit important features in flow simulations such as optimal convergence, efficient nonlinear iterations, and physical conservation. The generalized SG stability condition shows why the standard discretization (without SG exponential fitting) of NP equations may fail and that divalent Ca(2+) may cause more unstable discrete Ca(2+) fluxes than that of monovalent Na(+). Two different methods-called the SMIB and multiscale methods-are proposed for two different types of channels, namely, the gramicidin A channel and an L-type calcium channel, depending on whether water is allowed to pass through the channel. Numerical methods are first validated with constructed models whose exact solutions are
Takahashi, Yusuke
2015-01-01
An analysis model of plasma flow and electromagnetic waves around a reentry vehicle for radio frequency blackout prediction during aerodynamic heating was developed in this study. The model was validated based on experimental results from the radio attenuation measurement program. The plasma flow properties, such as electron number density, in the shock layer and wake region were obtained using a newly developed unstructured grid solver that incorporated real gas effect models ...
Wolf, Eric M.; Causley, Matthew; Christlieb, Andrew; Bettencourt, Matthew
2016-12-01
We propose a new particle-in-cell (PIC) method for the simulation of plasmas based on a recently developed, unconditionally stable solver for the wave equation. This method is not subject to a CFL restriction, limiting the ratio of the time step size to the spatial step size, typical of explicit methods, while maintaining computational cost and code complexity comparable to such explicit schemes. We describe the implementation in one and two dimensions for both electrostatic and electromagnetic cases, and present the results of several standard test problems, showing good agreement with theory with time step sizes much larger than allowed by typical CFL restrictions.
Johnson, Don H
2008-01-01
We derive conditions under which alternating renewal processes can be used to construct correlated Poisson processes. The pairwise correlation function is also derived, showing that the resulting correlations can be negative. The technique and the analysis can be extended to the generation of two or more dependent renewal processes.
Energy Technology Data Exchange (ETDEWEB)
Itoh, Yoshiaki [Institute of Statistical Mathematics and the Graduate University for Advanced Studies, 4-6-7 Minami-Azabu Minatoku, Tokyo 106-8569 (Japan)], E-mail: itoh@ism.ac.jp
2009-01-16
The combinatorial method is useful to obtain conserved quantities for some nonlinear integrable systems, as an alternative to the Lax representation method. Here we extend the combinatorial method and introduce an elementary geometry to show the vanishing of the Poisson brackets of the Hamiltonian structure for a Lotka-Volterra system of competing species. We associate a set of points on a circle with a set of species of the Lotka-Volterra system, where the dominance relations between points are given by the dominance relations between the species. We associate each term of the conserved quantities with a subset of points on the circle, which simplifies to show the vanishing of the Poisson brackets.
MILAMIN: MATLAB-based finite element method solver for large problems
Dabrowski, M.; Krotkiewski, M.; Schmid, D. W.
2008-04-01
The finite element method (FEM) combined with unstructured meshes forms an elegant and versatile approach capable of dealing with the complexities of problems in Earth science. Practical applications often require high-resolution models that necessitate advanced computational strategies. We therefore developed "Million a Minute" (MILAMIN), an efficient MATLAB implementation of FEM that is capable of setting up, solving, and postprocessing two-dimensional problems with one million unknowns in one minute on a modern desktop computer. MILAMIN allows the user to achieve numerical resolutions that are necessary to resolve the heterogeneous nature of geological materials. In this paper we provide the technical knowledge required to develop such models without the need to buy a commercial FEM package, programming compiler-language code, or hiring a computer specialist. It has been our special aim that all the components of MILAMIN perform efficiently, individually and as a package. While some of the components rely on readily available routines, we develop others from scratch and make sure that all of them work together efficiently. One of the main technical focuses of this paper is the optimization of the global matrix computations. The performance bottlenecks of the standard FEM algorithm are analyzed. An alternative approach is developed that sustains high performance for any system size. Applied optimizations eliminate Basic Linear Algebra Subprograms (BLAS) drawbacks when multiplying small matrices, reduce operation count and memory requirements when dealing with symmetric matrices, and increase data transfer efficiency by maximizing cache reuse. Applying loop interchange allows us to use BLAS on large matrices. In order to avoid unnecessary data transfers between RAM and CPU cache we introduce loop blocking. The optimization techniques are useful in many areas as demonstrated with our MILAMIN applications for thermal and incompressible flow (Stokes) problems. We use
Rey, Valentine; Gosselet, Pierre
2013-01-01
This paper deals with the estimation of the distance between the solution of a static linear mechanic problem and its approximation by the finite element method solved with a non-overlapping domain decomposition method (FETI or BDD). We propose a new strict upper bound of the error which separates the contribution of the iterative solver and the contribution of the discretization. Numerical assessments show that the bound is sharp and enables us to define an objective stopping criterion for the iterative solver
Institute of Scientific and Technical Information of China (English)
舒英; 章顺; 吴文青; 黄自萍
2002-01-01
本文对分子生物物理学中产生的线性Poisson-Boltzmann方程(PBE),给出了Mortar有限元方法的计算过程,数值计算例子表明,与一般的协调有限元方法相比,用Mortar元方法求解此类有间断系数的问题是非常有效的.
Guthier, C.; Aschenbrenner, K. P.; Buergy, D.; Ehmann, M.; Wenz, F.; Hesser, J. W.
2015-03-01
This work discusses a novel strategy for inverse planning in low dose rate brachytherapy. It applies the idea of compressed sensing to the problem of inverse treatment planning and a new solver for this formulation is developed. An inverse planning algorithm was developed incorporating brachytherapy dose calculation methods as recommended by AAPM TG-43. For optimization of the functional a new variant of a matching pursuit type solver is presented. The results are compared with current state-of-the-art inverse treatment planning algorithms by means of real prostate cancer patient data. The novel strategy outperforms the best state-of-the-art methods in speed, while achieving comparable quality. It is able to find solutions with comparable values for the objective function and it achieves these results within a few microseconds, being up to 542 times faster than competing state-of-the-art strategies, allowing real-time treatment planning. The sparse solution of inverse brachytherapy planning achieved with methods from compressed sensing is a new paradigm for optimization in medical physics. Through the sparsity of required needles and seeds identified by this method, the cost of intervention may be reduced.
Lakes, R.
1991-01-01
Continuum representations of micromechanical phenomena in structured materials are described, with emphasis on cellular solids. These phenomena are interpreted in light of Cosserat elasticity, a generalized continuum theory which admits degrees of freedom not present in classical elasticity. These are the rotation of points in the material, and a couple per unit area or couple stress. Experimental work in this area is reviewed, and other interpretation schemes are discussed. The applicability of Cosserat elasticity to cellular solids and fibrous composite materials is considered as is the application of related generalized continuum theories. New experimental results are presented for foam materials with negative Poisson's ratios.
Institute of Scientific and Technical Information of China (English)
韩厚德; 郑春雄
2002-01-01
The mixed finite element method is used to solve the exterior Poisson equations with higher-order local artificial boundary conditions in 3-D space. New unknowns are introduced to reduce the order of the derivatives of the unknown to two. The result is an equivalent mixed variational problem which was solved using bilinear finite elements. The primary advantage is that special finite elements are not needed on the adjacent layer of the artificial boundary for the higher-order derivatives. Error estimates are obtained for some local artificial boundary conditions with prescibed orders. A numerical example demonstrates the effectiveness of this method.
Homogeneous systems with quadratic integrals, Lie-Poisson quasibrackets, and Kovalevskaya's method
Bizyaev, I. A.; Kozlov, V. V.
2015-12-01
We consider differential equations with quadratic right-hand sides that admit two quadratic first integrals, one of which is a positive-definite quadratic form. We indicate conditions of general nature under which a linear change of variables reduces this system to a certain 'canonical' form. Under these conditions, the system turns out to be divergenceless and can be reduced to a Hamiltonian form, but the corresponding linear Lie-Poisson bracket does not always satisfy the Jacobi identity. In the three-dimensional case, the equations can be reduced to the classical equations of the Euler top, and in four-dimensional space, the system turns out to be superintegrable and coincides with the Euler-Poincaré equations on some Lie algebra. In the five-dimensional case we find a reducing multiplier after multiplying by which the Poisson bracket satisfies the Jacobi identity. In the general case for n>5 we prove the absence of a reducing multiplier. As an example we consider a system of Lotka-Volterra type with quadratic right-hand sides that was studied by Kovalevskaya from the viewpoint of conditions of uniqueness of its solutions as functions of complex time. Bibliography: 38 titles.
A Poisson resampling method for simulating reduced counts in nuclear medicine images.
White, Duncan; Lawson, Richard S
2015-05-07
Nuclear medicine computers now commonly offer resolution recovery and other software techniques which have been developed to improve image quality for images with low counts. These techniques potentially mean that these images can give equivalent clinical information to a full-count image. Reducing the number of counts in nuclear medicine images has the benefits of either allowing reduced activity to be administered or reducing acquisition times. However, because acquisition and processing parameters vary, each user should ideally evaluate the use of images with reduced counts within their own department, and this is best done by simulating reduced-count images from the original data. Reducing the counts in an image by division and rounding off to the nearest integer value, even if additional Poisson noise is added, is inadequate because it gives incorrect counting statistics. This technical note describes how, by applying Poisson resampling to the original raw data, simulated reduced-count images can be obtained while maintaining appropriate counting statistics. The authors have developed manufacturer independent software that can retrospectively generate simulated data with reduced counts from any acquired nuclear medicine image.
M2Di: Concise and efficient MATLAB 2-D Stokes solvers using the Finite Difference Method
Räss, Ludovic; Duretz, Thibault; Podladchikov, Yury Y.; Schmalholz, Stefan M.
2017-02-01
Recent development of many multiphysics modeling tools reflects the currently growing interest for studying coupled processes in Earth Sciences. The core of such tools should rely on fast and robust mechanical solvers. Here we provide M2Di, a set of routines for 2-D linear and power law incompressible viscous flow based on Finite Difference discretizations. The 2-D codes are written in a concise vectorized MATLAB fashion and can achieve a time to solution of 22 s for linear viscous flow on 10002 grid points using a standard personal computer. We provide application examples spanning from finely resolved crystal-melt dynamics, deformation of heterogeneous power law viscous fluids to instantaneous models of mantle flow in cylindrical coordinates. The routines are validated against analytical solution for linear viscous flow with highly variable viscosity and compared against analytical and numerical solutions of power law viscous folding and necking. In the power law case, both Picard and Newton iterations schemes are implemented. For linear Stokes flow and Picard linearization, the discretization results in symmetric positive-definite matrix operators on Cartesian grids with either regular or variable grid spacing allowing for an optimized solving procedure. For Newton linearization, the matrix operator is no longer symmetric and an adequate solving procedure is provided. The reported performance of linear and power law Stokes flow is finally analyzed in terms of wall time. All MATLAB codes are provided and can readily be used for educational as well as research purposes. The M2Di routines are available from Bitbucket and the University of Lausanne Scientific Computing Group website, and are also supplementary material to this article.
Sherlock Holmes, Master Problem Solver.
Ballew, Hunter
1994-01-01
Shows the connections between Sherlock Holmes's investigative methods and mathematical problem solving, including observations, characteristics of the problem solver, importance of data, questioning the obvious, learning from experience, learning from errors, and indirect proof. (MKR)
Sherlock Holmes, Master Problem Solver.
Ballew, Hunter
1994-01-01
Shows the connections between Sherlock Holmes's investigative methods and mathematical problem solving, including observations, characteristics of the problem solver, importance of data, questioning the obvious, learning from experience, learning from errors, and indirect proof. (MKR)
A hybrid Eulerian-Lagrangian flow solver
Palha, Artur; Ferreira, Carlos Simao; van Bussel, Gerard
2015-01-01
Currently, Eulerian flow solvers are very efficient in accurately resolving flow structures near solid boundaries. On the other hand, they tend to be diffusive and to dampen high-intensity vortical structures after a short distance away from solid boundaries. The use of high order methods and fine grids, although alleviating this problem, gives rise to large systems of equations that are expensive to solve. Lagrangian solvers, as the regularized vortex particle method, have shown to eliminate (in practice) the diffusion in the wake. As a drawback, the modelling of solid boundaries is less accurate, more complex and costly than with Eulerian solvers (due to the isotropy of its computational elements). Given the drawbacks and advantages of both Eulerian and Lagrangian solvers the combination of both methods, giving rise to a hybrid solver, is advantageous. The main idea behind the hybrid solver presented is the following. In a region close to solid boundaries the flow is solved with an Eulerian solver, where th...
Zoeteweij, P.
2005-01-01
Composing constraint solvers based on tree search and constraint propagation through generic iteration leads to efficient and flexible constraint solvers. This was demonstrated using OpenSolver, an abstract branch-and-propagate tree search engine that supports a wide range of relevant solver configu
Coupling of a 3-D vortex particle-mesh method with a finite volume near-wall solver
Marichal, Y.; Lonfils, T.; Duponcheel, M.; Chatelain, P.; Winckelmans, G.
2011-11-01
This coupling aims at improving the computational efficiency of high Reynolds number bluff body flow simulations by using two complementary methods and exploiting their respective advantages in distinct parts of the domain. Vortex particle methods are particularly well suited for free vortical flows such as wakes or jets (the computational domain -with non zero vorticity- is then compact and dispersion errors are negligible). Finite volume methods, however, can handle boundary layers much more easily due to anisotropic mesh refinement. In the present approach, the vortex method is used in the whole domain (overlapping domain technique) but its solution is highly underresolved in the vicinity of the wall. It thus has to be corrected by the near-wall finite volume solution at each time step. Conversely, the vortex method provides the outer boundary conditions for the near-wall solver. A parallel multi-resolution vortex particle-mesh approach is used here along with an Immersed Boundary method in order to take the walls into account. The near-wall flow is solved by OpenFOAM® using the PISO algorithm. We validate the methodology on the flow past a sphere at a moderate Reynolds number. F.R.S. - FNRS Research Fellow.
Poisson Spot with Magnetic Levitation
Hoover, Matthew; Everhart, Michael; D'Arruda, Jose
2010-01-01
In this paper we describe a unique method for obtaining the famous Poisson spot without adding obstacles to the light path, which could interfere with the effect. A Poisson spot is the interference effect from parallel rays of light diffracting around a solid spherical object, creating a bright spot in the center of the shadow.
An immersed interface vortex particle-mesh solver
Marichal, Yves; Chatelain, Philippe; Winckelmans, Gregoire
2014-11-01
An immersed interface-enabled vortex particle-mesh (VPM) solver is presented for the simulation of 2-D incompressible viscous flows, in the framework of external aerodynamics. Considering the simulation of free vortical flows, such as wakes and jets, vortex particle-mesh methods already provide a valuable alternative to standard CFD methods, thanks to the interesting numerical properties arising from its Lagrangian nature. Yet, accounting for solid bodies remains challenging, despite the extensive research efforts that have been made for several decades. The present immersed interface approach aims at improving the consistency and the accuracy of one very common technique (based on Lighthill's model) for the enforcement of the no-slip condition at the wall in vortex methods. Targeting a sharp treatment of the wall calls for substantial modifications at all computational levels of the VPM solver. More specifically, the solution of the underlying Poisson equation, the computation of the diffusion term and the particle-mesh interpolation are adapted accordingly and the spatial accuracy is assessed. The immersed interface VPM solver is subsequently validated on the simulation of some challenging impulsively started flows, such as the flow past a cylinder and that past an airfoil. Research Fellow (PhD student) of the F.R.S.-FNRS of Belgium.
Smoke simulation for fire engineering using a multigrid method on graphics hardware
DEFF Research Database (Denmark)
Glimberg, Stefan; Erleben, Kenny; Bennetsen, Jens
2009-01-01
We present a GPU-based Computational Fluid Dynamics solver for the purpose of fire engineering. We apply a multigrid method to the Jacobi solver when solving the Poisson pressure equation, supporting internal boundaries. Boundaries are handled on the coarse levels, ensuring that boundaries will n...
Crocker, Ryan; Desjardins, Olivier
2014-01-01
A conjugate heat transfer (CHT) immersed boundary (IB and CHTIB) method is developed for use with laminar and turbulent flows with low to moderate Reynolds numbers. The method is validated with the canonical flow of two co-annular rotating cylinders at $Re=50$ which shows second order accuracy of the $L_{2}$ and $L_{\\infty}$ error norms of the temperature field over a wide rage of solid to fluid thermal conductivities, $\\kappa_{s}/\\kappa_{f} = \\left(9-100\\right)$. To evaluate the CHTIBM with turbulent flow a fully developed, heated, turbulent channel $\\left(Re_{u_{\\tau}}=150\\text{ and } \\kappa_{s}/\\kappa_{f}=4 \\right)$ is used which shows near perfect correlation to previous direct numerical simulation (DNS) results. The CHTIB method is paired with a momentum IB method (IBM), both of which use a level set field to define the wetted boundaries of the fluid/solid interfaces and are applied to the flow solver implicitly with rescaling of the difference operators of the finite volume (FV) method (FVM).
Application of least-squares spectral element solver methods to incompressible flow problems
Proot, M.M.J.; Gerritsma, M.I.; Nool, M.
2003-01-01
Least-squares spectral element methods are based on two important and successful numerical methods: spectral /hp element methods and least-squares finite element methods. In this respect, least-squares spectral element methods are very powerfull since they combine the generality of finite element me
Augustin, Christoph M.; Neic, Aurel; Liebmann, Manfred; Prassl, Anton J.; Niederer, Steven A.; Haase, Gundolf; Plank, Gernot
2016-01-01
Electromechanical (EM) models of the heart have been used successfully to study fundamental mechanisms underlying a heart beat in health and disease. However, in all modeling studies reported so far numerous simplifications were made in terms of representing biophysical details of cellular function and its heterogeneity, gross anatomy and tissue microstructure, as well as the bidirectional coupling between electrophysiology (EP) and tissue distension. One limiting factor is the employed spatial discretization methods which are not sufficiently flexible to accommodate complex geometries or resolve heterogeneities, but, even more importantly, the limited efficiency of the prevailing solver techniques which is not sufficiently scalable to deal with the incurring increase in degrees of freedom (DOF) when modeling cardiac electromechanics at high spatio-temporal resolution. This study reports on the development of a novel methodology for solving the nonlinear equation of finite elasticity using human whole organ models of cardiac electromechanics, discretized at a high para-cellular resolution. Three patient-specific, anatomically accurate, whole heart EM models were reconstructed from magnetic resonance (MR) scans at resolutions of 220 μm, 440 μm and 880 μm, yielding meshes of approximately 184.6, 24.4 and 3.7 million tetrahedral elements and 95.9, 13.2 and 2.1 million displacement DOF, respectively. The same mesh was used for discretizing the governing equations of both electrophysiology (EP) and nonlinear elasticity. A novel algebraic multigrid (AMG) preconditioner for an iterative Krylov solver was developed to deal with the resulting computational load. The AMG preconditioner was designed under the primary objective of achieving favorable strong scaling characteristics for both setup and solution runtimes, as this is key for exploiting current high performance computing hardware. Benchmark results using the 220 μm, 440 μm and 880 μm meshes demonstrate
THE SLOP FLUX METHOD FOR NUMERICAL BALANCE IN USING ROE'S APPROXIMATE RIEMANN SOLVER
Institute of Scientific and Technical Information of China (English)
WANG Dang-wei; LIU Xiao-fang; CHEN Jian-guo; JI Zu-wen
2012-01-01
Imbalance arises when the Roe's method is directly applied in the shallow water simulation.The reasons are different for the continuity equation and the momentum equations.Based on the Roe's method,a partial surface method is proposed for a perfect balance for the continuity equation.In order to generate a mathematically hyperbolic formulation,the momentum equations are split,which causes incompatibility in the calculation of the momentum equations.In this article a numerical approach named the Slop Flux Method (SFM) is proposed to balance the source terms and the flux gradient based on the finite volume method.The method is first applied to shallow water equations.The model is verified by analytical results of classical test cases with good agreement.Finally the method is applied to a steady flow simulation over a practical complicated topography and the result shows good balance and conservation.
Evaluation of two-phase flow solvers using Level Set and Volume of Fluid methods
Bilger, C.; Aboukhedr, M.; Vogiatzaki, K.; Cant, R. S.
2017-09-01
Two principal methods have been used to simulate the evolution of two-phase immiscible flows of liquid and gas separated by an interface. These are the Level-Set (LS) method and the Volume of Fluid (VoF) method. Both methods attempt to represent the very sharp interface between the phases and to deal with the large jumps in physical properties associated with it. Both methods have their own strengths and weaknesses. For example, the VoF method is known to be prone to excessive numerical diffusion, while the basic LS method has some difficulty in conserving mass. Major progress has been made in remedying these deficiencies, and both methods have now reached a high level of physical accuracy. Nevertheless, there remains an issue, in that each of these methods has been developed by different research groups, using different codes and most importantly the implementations have been fine tuned to tackle different applications. Thus, it remains unclear what are the remaining advantages and drawbacks of each method relative to the other, and what might be the optimal way to unify them. In this paper, we address this gap by performing a direct comparison of two current state-of-the-art variations of these methods (LS: RCLSFoam and VoF: interPore) and implemented in the same code (OpenFoam). We subject both methods to a pair of benchmark test cases while using the same numerical meshes to examine a) the accuracy of curvature representation, b) the effect of tuning parameters, c) the ability to minimise spurious velocities and d) the ability to tackle fluids with very different densities. For each method, one of the test cases is chosen to be fairly benign while the other test case is expected to present a greater challenge. The results indicate that both methods can be made to work well on both test cases, while displaying different sensitivity to the relevant parameters.
AP-Cloud: Adaptive Particle-in-Cloud method for optimal solutions to Vlasov-Poisson equation
Wang, Xingyu; Samulyak, Roman; Jiao, Xiangmin; Yu, Kwangmin
2016-07-01
We propose a new adaptive Particle-in-Cloud (AP-Cloud) method for obtaining optimal numerical solutions to the Vlasov-Poisson equation. Unlike the traditional particle-in-cell (PIC) method, which is commonly used for solving this problem, the AP-Cloud adaptively selects computational nodes or particles to deliver higher accuracy and efficiency when the particle distribution is highly non-uniform. Unlike other adaptive techniques for PIC, our method balances the errors in PDE discretization and Monte Carlo integration, and discretizes the differential operators using a generalized finite difference (GFD) method based on a weighted least square formulation. As a result, AP-Cloud is independent of the geometric shapes of computational domains and is free of artificial parameters. Efficient and robust implementation is achieved through an octree data structure with 2:1 balance. We analyze the accuracy and convergence order of AP-Cloud theoretically, and verify the method using an electrostatic problem of a particle beam with halo. Simulation results show that the AP-Cloud method is substantially more accurate and faster than the traditional PIC, and it is free of artificial forces that are typical for some adaptive PIC techniques.
Landweber-Kaczmarz method in Banach spaces with inexact inner solvers
Jin, Qinian
2016-10-01
In recent years the Landweber-Kaczmarz method has been proposed for solving nonlinear ill-posed inverse problems in Banach spaces using general convex penalty functions. The implementation of this method involves solving a (nonsmooth) convex minimization problem at each iteration step and the existing theory requires its exact resolution which in general is impossible in practical applications. In this paper we propose a version of the Landweber-Kaczmarz method in Banach spaces in which the minimization problem involved in each iteration step is solved inexactly. Based on the \\varepsilon -subdifferential calculus we give a convergence analysis of our method. Furthermore, using Nesterov's strategy, we propose a possible accelerated version of the Landweber-Kaczmarz method. Numerical results on computed tomography and parameter identification in partial differential equations are provided to support our theoretical results and to demonstrate our accelerated method.
Modern solvers for Helmholtz problems
Tang, Jok; Vuik, Kees
2017-01-01
This edited volume offers a state of the art overview of fast and robust solvers for the Helmholtz equation. The book consists of three parts: new developments and analysis in Helmholtz solvers, practical methods and implementations of Helmholtz solvers, and industrial applications. The Helmholtz equation appears in a wide range of science and engineering disciplines in which wave propagation is modeled. Examples are: seismic inversion, ultrasone medical imaging, sonar detection of submarines, waves in harbours and many more. The partial differential equation looks simple but is hard to solve. In order to approximate the solution of the problem numerical methods are needed. First a discretization is done. Various methods can be used: (high order) Finite Difference Method, Finite Element Method, Discontinuous Galerkin Method and Boundary Element Method. The resulting linear system is large, where the size of the problem increases with increasing frequency. Due to higher frequencies the seismic images need to b...
A Fourier-based elliptic solver for vortical flows with periodic and unbounded directions
Chatelain, Philippe; Koumoutsakos, Petros
2010-04-01
We present a computationally efficient, adaptive solver for the solution of the Poisson and Helmholtz equation used in flow simulations in domains with combinations of unbounded and periodic directions. The method relies on using FFTs on an extended domain and it is based on the method proposed by Hockney and Eastwood for plasma simulations. The method is well-suited to problems with dynamically growing domains and in particular flow simulations using vortex particle methods. The efficiency of the method is demonstrated in simulations of trailing vortices.
A study of the efficiency of various Navier-Stokes solvers. [finite difference methods
Atias, M.; Wolfshtein, M.; Israeli, M.
1975-01-01
A comparative study of the efficiency of some finite difference methods for the solution of the Navier-Stokes equations was conducted. The study was restricted to the two-dimensional steady, uniform property vorticity-stream function equations. The comparisons were drawn by recording the CPU time required to obtain a solution as well as the accuracy of this solution using five numerical methods: central differences, first order upwind differences, second order upwind differences, exponential differences, and an ADI solution of the central difference equations. Solutions were obtained for two test cases: a recirculating eddy inside a square cavity with a moving top, and an impinging jet flow. The results show that whenever the central difference method is stable it generates results with a given accuracy for less CPU time than any other method.
Riemann solvers and numerical methods for fluid dynamics a practical introduction
Toro, Eleuterio F
2009-01-01
High resolution upwind and centred methods are a mature generation of computational techniques applicable to a range of disciplines, Computational Fluid Dynamics being the most prominent. This book gives a practical presentation of this class of techniques.
Wang, W.; Zehner, B.; Böttcher, N.; Goerke, U.; Kolditz, O.
2013-12-01
Numerical modeling of the two-phase flow process in porous media for real applications, e.g. CO2 storage processes in saline aquifers, is computationally expensive due to the complexity and the non-linearity of the observed physical processes. In such modeling, a fine discretization of the considered domain is normally needed for a high degree of accuracy, and it leads to the requirement of extremely high computational resources. This work focuses on the parallel simulation of the two-phase flow process in porous media. The Galerkin finite element method is used to solve the governing equations. Based on the overlapping domain decomposition approach, the PETSc package is employed to parallelize the global equation assembly and the linear solver, respectively. A numerical model based on the real test site Ketzin in Germany is adopted for parallel computing. The model domain is discretized with more than four million tetrahedral elements. The parallel simulations are carried out on a Linux cluster with different number of cores. The obtained speedup shows a good scalability of the current parallel finite element approach of the two-phase flow modeling in geological CO2 storage applications.
An Assessment of Linear Versus Non-linear Multigrid Methods for Unstructured Mesh Solvers
2001-05-01
problems is investigated. The first case consists of a transient radiation-diffusion problem for which an exact linearization is available, while the...to the Jacobian of a second-order accurate discretization. When an exact linearization is employed, the linear and non-linear multigrid methods
Method of Lines Transpose an Implicit Vlasov Maxwell Solver for Plasmas
2015-04-17
Numerical Analysis 52 (2014), no. 1, 220–235. 10. Roman Chapko, Rainer Kress, et al., Rothes method for the heat equation and boundary integral equations...collisionless plasma–sheath region, Physics of Fluids B: Plasma Physics (1989-1993) 2 (1990), no. 12, 3191–3205. 33. Erich Rothe , Zweidimensionale
An overlapped grid method for multigrid, finite volume/difference flow solvers: MaGGiE
Baysal, Oktay; Lessard, Victor R.
1990-01-01
The objective is to develop a domain decomposition method via overlapping/embedding the component grids, which is to be used by upwind, multi-grid, finite volume solution algorithms. A computer code, given the name MaGGiE (Multi-Geometry Grid Embedder) is developed to meet this objective. MaGGiE takes independently generated component grids as input, and automatically constructs the composite mesh and interpolation data, which can be used by the finite volume solution methods with or without multigrid convergence acceleration. Six demonstrative examples showing various aspects of the overlap technique are presented and discussed. These cases are used for developing the procedure for overlapping grids of different topologies, and to evaluate the grid connection and interpolation data for finite volume calculations on a composite mesh. Time fluxes are transferred between mesh interfaces using a trilinear interpolation procedure. Conservation losses are minimal at the interfaces using this method. The multi-grid solution algorithm, using the coaser grid connections, improves the convergence time history as compared to the solution on composite mesh without multi-gridding.
Self-correcting Multigrid Solver
Energy Technology Data Exchange (ETDEWEB)
Jerome L.V. Lewandowski
2004-06-29
A new multigrid algorithm based on the method of self-correction for the solution of elliptic problems is described. The method exploits information contained in the residual to dynamically modify the source term (right-hand side) of the elliptic problem. It is shown that the self-correcting solver is more efficient at damping the short wavelength modes of the algebraic error than its standard equivalent. When used in conjunction with a multigrid method, the resulting solver displays an improved convergence rate with no additional computational work.
Solution of Poisson's equation in electrostatic Particle-In-Cell simulations
Kahnfeld, Daniel; Schneider, Ralf; Matyash, Konstantin; Lüskow, Karl; Bandelow, Gunnar; Kalentev, Oleksandr; Duras, Julia; Kemnitz, Stefan
2016-10-01
For spacecrafts the concept of ion thrusters presents a very efficient method of propulsion. Optimization of thrusters is imperative, but experimental access is difficult. Plasma simulations offer means to understand the plasma physics within an ion thruster and can aid the design of new thruster concepts. In order to achieve best simulation performances, code optimizations and parallelization strategies need to be investigated. In this work the role of different solution strategies for Poisson's equation in electrostatic Particle-in-Cell simulations of the HEMP-DM3a ion thruster was studied. The direct solution method of LU decomposition is compared to a stationary iterative method, the successive over-relaxation solver. Results and runtime of solvers were compared, and an outlook on further improvements and developments is presented. This work was supported by the German Space Agency DLR through Project 50RS1510..
Coordination of Conditional Poisson Samples
Directory of Open Access Journals (Sweden)
Grafström Anton
2015-12-01
Full Text Available Sample coordination seeks to maximize or to minimize the overlap of two or more samples. The former is known as positive coordination, and the latter as negative coordination. Positive coordination is mainly used for estimation purposes and to reduce data collection costs. Negative coordination is mainly performed to diminish the response burden of the sampled units. Poisson sampling design with permanent random numbers provides an optimum coordination degree of two or more samples. The size of a Poisson sample is, however, random. Conditional Poisson (CP sampling is a modification of the classical Poisson sampling that produces a fixed-size πps sample. We introduce two methods to coordinate Conditional Poisson samples over time or simultaneously. The first one uses permanent random numbers and the list-sequential implementation of CP sampling. The second method uses a CP sample in the first selection and provides an approximate one in the second selection because the prescribed inclusion probabilities are not respected exactly. The methods are evaluated using the size of the expected sample overlap, and are compared with their competitors using Monte Carlo simulation. The new methods provide a good coordination degree of two samples, close to the performance of Poisson sampling with permanent random numbers.
pKa predictions with a coupled finite difference Poisson-Boltzmann and Debye-Hückel method.
Warwicker, Jim
2011-12-01
Modeling charge interactions is important for understanding many aspects of biological structure and function, and continuum methods such as Finite Difference Poisson-Boltzmann (FDPB) are commonly employed. Calculations of pH-dependence have identified separate populations; surface groups that can be modeled with a simple Debye-Hückel (DH) model, and buried groups, with stronger resultant interactions that are dependent on detailed conformation. This observation led to the development of a combined FDPB and DH method for pK(a) prediction (termed FD/DH). This study reports application of this method to ionizable groups, including engineered buried charges, in staphylococcal nuclease. The data had been made available to interested research groups before publication of mutant structures and/or pK(a) values. Overall, FD/DH calculations perform as intended with low ΔpK(a) values for surface groups (RMSD between predicted and experimental pK(a) values of 0.74), and much larger ΔpK(a) values for the engineered internal groups, with RMSD = 1.64, where mutant structures were known and RMSD = 1.80, where they were modeled. The weaker resultant interactions of the surface groups are determined mostly by charge-charge interactions. For the buried groups, R(2) for correlation between predicted and measured ΔpK(a) values is 0.74, despite the high RMSDs. Charge-charge interactions are much less important, with the R(2) value for buried group ΔpK(a) values increasing to 0.80 when the term describing charge desolvation alone is used. Engineered charge burial delivers a relatively uniform, nonspecific effect, in terms of pK(a) . How the protein environment adapts in atomic detail to deliver this resultant effect is still an open question.
Han, Song; Zhang, Wei; Zhang, Jie
2017-09-01
A fast sweeping method (FSM) determines the first arrival traveltimes of seismic waves by sweeping the velocity model in different directions meanwhile applying a local solver. It is an efficient way to numerically solve Hamilton-Jacobi equations for traveltime calculations. In this study, we develop an improved FSM to calculate the first arrival traveltimes of quasi-P (qP) waves in 2-D tilted transversely isotropic (TTI) media. A local solver utilizes the coupled slowness surface of qP and quasi-SV (qSV) waves to form a quartic equation, and solve it numerically to obtain possible traveltimes of qP-wave. The proposed quartic solver utilizes Fermat's principle to limit the range of the possible solution, then uses the bisection procedure to efficiently determine the real roots. With causality enforced during sweepings, our FSM converges fast in a few iterations, and the exact number depending on the complexity of the velocity model. To improve the accuracy, we employ high-order finite difference schemes and derive the second-order formulae. There is no weak anisotropy assumption, and no approximation is made to the complex slowness surface of qP-wave. In comparison to the traveltimes calculated by a horizontal slowness shooting method, the validity and accuracy of our FSM is demonstrated.
Electro-osmosis of non-Newtonian fluids in porous media using lattice Poisson-Boltzmann method.
Chen, Simeng; He, Xinting; Bertola, Volfango; Wang, Moran
2014-12-15
Electro-osmosis in porous media has many important applications in various areas such as oil and gas exploitation and biomedical detection. Very often, fluids relevant to these applications are non-Newtonian because of the shear-rate dependent viscosity. The purpose of this study was to investigate the behaviors and physical mechanism of electro-osmosis of non-Newtonian fluids in porous media. Model porous microstructures (granular, fibrous, and network) were created by a random generation-growth method. The nonlinear governing equations of electro-kinetic transport for a power-law fluid were solved by the lattice Poisson-Boltzmann method (LPBM). The model results indicate that: (i) the electro-osmosis of non-Newtonian fluids exhibits distinct nonlinear behaviors compared to that of Newtonian fluids; (ii) when the bulk ion concentration or zeta potential is high enough, shear-thinning fluids exhibit higher electro-osmotic permeability, while shear-thickening fluids lead to the higher electro-osmotic permeability for very low bulk ion concentration or zeta potential; (iii) the effect of the porous medium structure depends significantly on the constitutive parameters: for fluids with large constitutive coefficients strongly dependent on the power-law index, the network structure shows the highest electro-osmotic permeability while the granular structure exhibits the lowest permeability on the entire range of power law indices considered; when the dependence of the constitutive coefficient on the power law index is weaker, different behaviors can be observed especially in case of strong shear thinning.
Central simple Poisson algebras
Institute of Scientific and Technical Information of China (English)
SU Yucai; XU Xiaoping
2004-01-01
Poisson algebras are fundamental algebraic structures in physics and symplectic geometry. However, the structure theory of Poisson algebras has not been well developed. In this paper, we determine the structure of the central simple Poisson algebras related to locally finite derivations, over an algebraically closed field of characteristic zero.The Lie algebra structures of these Poisson algebras are in general not finitely-graded.
Differential equations problem solver
Arterburn, David R
2012-01-01
REA's Problem Solvers is a series of useful, practical, and informative study guides. Each title in the series is complete step-by-step solution guide. The Differential Equations Problem Solver enables students to solve difficult problems by showing them step-by-step solutions to Differential Equations problems. The Problem Solvers cover material ranging from the elementary to the advanced and make excellent review books and textbook companions. They're perfect for undergraduate and graduate studies.The Differential Equations Problem Solver is the perfect resource for any class, any exam, and
Two-dimensional Green`s function Poisson solution appropriate for cylindrical-symmetry simulations
Energy Technology Data Exchange (ETDEWEB)
Riley, M.E.
1998-04-01
This report describes the numerical procedure used to implement the Green`s function method for solving the Poisson equation in two-dimensional (r,z) cylindrical coordinates. The procedure can determine the solution to a problem with any or all of the applied voltage boundary conditions, dielectric media, floating (insulated) conducting media, dielectric surface charging, and volumetric space charge. The numerical solution is reasonably fast, and the dimension of the linear problem to be solved is that of the number of elements needed to represent the surfaces, not the whole computational volume. The method of solution is useful in the simulation of plasma particle motion in the vicinity of complex surface structures as found in microelectronics plasma processing applications. This report is a stand-alone supplement to the previous Sandia Technical Report SAND98-0537 presenting the two-dimensional Cartesian Poisson solver.
Accurate derivative evaluation for any Grad–Shafranov solver
Energy Technology Data Exchange (ETDEWEB)
Ricketson, L.F. [Courant Institute of Mathematical Sciences, New York University, New York, NY 10012 (United States); Cerfon, A.J., E-mail: cerfon@cims.nyu.edu [Courant Institute of Mathematical Sciences, New York University, New York, NY 10012 (United States); Rachh, M. [Courant Institute of Mathematical Sciences, New York University, New York, NY 10012 (United States); Freidberg, J.P. [Plasma Science and Fusion Center, Massachusetts Institute of Technology, Cambridge, MA 02139 (United States)
2016-01-15
We present a numerical scheme that can be combined with any fixed boundary finite element based Poisson or Grad–Shafranov solver to compute the first and second partial derivatives of the solution to these equations with the same order of convergence as the solution itself. At the heart of our scheme is an efficient and accurate computation of the Dirichlet to Neumann map through the evaluation of a singular volume integral and the solution to a Fredholm integral equation of the second kind. Our numerical method is particularly useful for magnetic confinement fusion simulations, since it allows the evaluation of quantities such as the magnetic field, the parallel current density and the magnetic curvature with much higher accuracy than has been previously feasible on the affordable coarse grids that are usually implemented.
基于双层位势的Poisson方程无奇异方法%A Nonsingular Method Based on Double Layer Potential for Poisson Equation
Institute of Scientific and Technical Information of China (English)
林鑫; 高发玲
2014-01-01
针对求解Poisson方程的边值问题，利用虚边界上分布的矩密度，得出基于双层位势的虚边界元方程。该方法有效地避免了奇异和强奇异积分的计算。数值算例证明了算法的有效性和精确性。%Towards the boundary problem of Poisson equation,different from the virtual boundary element equation based on the single layer potential,another virtual boundary collocation method (VBCM)is conducted based on double layer potential for Poisson problem,with the moment density distributed on the virtual boundary. The VBCM can avoid the singular,hyper-singular integral ,the numerical example presents the efficiency and accuracy of the method.
Poisson Morphisms and Reduced Affine Poisson Group Actions
Institute of Scientific and Technical Information of China (English)
YANG Qi Lin
2002-01-01
We establish the concept of a quotient affine Poisson group, and study the reduced Poisson action of the quotient of an affine Poisson group G on the quotient of an affine Poisson G-variety V. The Poisson morphisms (including equivariant cases) between Poisson affine varieties are also discussed.
Areias, P.; Rabczuk, T.; de Sá, J. César
2016-12-01
We propose an alternative crack propagation algorithm which effectively circumvents the variable transfer procedure adopted with classical mesh adaptation algorithms. The present alternative consists of two stages: a mesh-creation stage where a local damage model is employed with the objective of defining a crack-conforming mesh and a subsequent analysis stage with a localization limiter in the form of a modified screened Poisson equation which is exempt of crack path calculations. In the second stage, the crack naturally occurs within the refined region. A staggered scheme for standard equilibrium and screened Poisson equations is used in this second stage. Element subdivision is based on edge split operations using a constitutive quantity (damage). To assess the robustness and accuracy of this algorithm, we use five quasi-brittle benchmarks, all successfully solved.
George, D.L.
2011-01-01
The simulation of advancing flood waves over rugged topography, by solving the shallow-water equations with well-balanced high-resolution finite volume methods and block-structured dynamic adaptive mesh refinement (AMR), is described and validated in this paper. The efficiency of block-structured AMR makes large-scale problems tractable, and allows the use of accurate and stable methods developed for solving general hyperbolic problems on quadrilateral grids. Features indicative of flooding in rugged terrain, such as advancing wet-dry fronts and non-stationary steady states due to balanced source terms from variable topography, present unique challenges and require modifications such as special Riemann solvers. A well-balanced Riemann solver for inundation and general (non-stationary) flow over topography is tested in this context. The difficulties of modeling floods in rugged terrain, and the rationale for and efficacy of using AMR and well-balanced methods, are presented. The algorithms are validated by simulating the Malpasset dam-break flood (France, 1959), which has served as a benchmark problem previously. Historical field data, laboratory model data and other numerical simulation results (computed on static fitted meshes) are shown for comparison. The methods are implemented in GEOCLAW, a subset of the open-source CLAWPACK software. All the software is freely available at. Published in 2010 by John Wiley & Sons, Ltd.
Institute of Scientific and Technical Information of China (English)
Zhongxiao Jia; Yuquan Sun
2007-01-01
Based on the generalized minimal residual(GMRES)principle,Hu and Reichel proposed a minimal residual algorithm for the Sylvester equation.The algorithm requires the solution of a structured least squares problem.They form the normal equations of the least squares problem and then solve it by a direct solver,so it is susceptible to instability.In this paper,by exploiting the special structure of the least squares problem and working on the problem directly,a numerically stable QR decomposition based algorithm is presented for the problem.The new algorithm is more stable than the normal equations algorithm of Hu and Reichel.Numerical experiments are reported to confirm the superior stability of the new algorithm.
Crouseilles, Nicolas; Lemou, Mohammed; Méhats, Florian; Zhao, Xiaofei
2017-10-01
In this work, we focus on the numerical resolution of the four dimensional phase space Vlasov-Poisson system subject to a uniform strong external magnetic field. To do so, we consider a Particle-in-Cell based method, for which the characteristics are reformulated by means of the two-scale formalism, which is well-adapted to handle highly-oscillatory equations. Then, a numerical scheme is derived for the two-scale equations. The so-obtained scheme enjoys a uniform accuracy property, meaning that its accuracy does not depend on the small parameter. Several numerical results illustrate the capabilities of the method.
SIERRA framework version 4 : solver services.
Energy Technology Data Exchange (ETDEWEB)
Williams, Alan B.
2005-02-01
Several SIERRA applications make use of third-party libraries to solve systems of linear and nonlinear equations, and to solve eigenproblems. The classes and interfaces in the SIERRA framework that provide linear system assembly services and access to solver libraries are collectively referred to as solver services. This paper provides an overview of SIERRA's solver services including the design goals that drove the development, and relationships and interactions among the various classes. The process of assembling and manipulating linear systems will be described, as well as access to solution methods and other operations.
Rigid body dynamics on the Poisson torus
Richter, Peter H.
2008-11-01
The theory of rigid body motion with emphasis on the modifications introduced by a Cardan suspension is outlined. The configuration space is no longer SO(3) but a 3-torus; the equivalent of the Poisson sphere, after separation of an angular variable, is a Poisson torus. Iso-energy surfaces and their bifurcations are discussed. A universal Poincaré section method is proposed.
Bajaj, Chandrajit; Chen, Shun-Chuan; Rand, Alexander
2011-01-01
In order to compute polarization energy of biomolecules, we describe a boundary element approach to solving the linearized Poisson-Boltzmann equation. Our approach combines several important features including the derivative boundary formulation of the problem and a smooth approximation of the molecular surface based on the algebraic spline molecular surface. State of the art software for numerical linear algebra and the kernel independent fast multipole method is used for both simplicity and efficiency of our implementation. We perform a variety of computational experiments, testing our method on a number of actual proteins involved in molecular docking and demonstrating the effectiveness of our solver for computing molecular polarization energy. PMID:21660123
An adaptive, high-order phase-space remapping for the two-dimensional Vlasov-Poisson equations
Wang, Bei; Colella, Phil
2012-01-01
The numerical solution of high dimensional Vlasov equation is usually performed by particle-in-cell (PIC) methods. However, due to the well-known numerical noise, it is challenging to use PIC methods to get a precise description of the distribution function in phase space. To control the numerical error, we introduce an adaptive phase-space remapping which regularizes the particle distribution by periodically reconstructing the distribution function on a hierarchy of phase-space grids with high-order interpolations. The positivity of the distribution function can be preserved by using a local redistribution technique. The method has been successfully applied to a set of classical plasma problems in one dimension. In this paper, we present the algorithm for the two dimensional Vlasov-Poisson equations. An efficient Poisson solver with infinite domain boundary conditions is used. The parallel scalability of the algorithm on massively parallel computers will be discussed.
Benchmarking optimization solvers for structural topology optimization
DEFF Research Database (Denmark)
Rojas Labanda, Susana; Stolpe, Mathias
2015-01-01
The purpose of this article is to benchmark different optimization solvers when applied to various finite element based structural topology optimization problems. An extensive and representative library of minimum compliance, minimum volume, and mechanism design problem instances for different...... sizes is developed for this benchmarking. The problems are based on a material interpolation scheme combined with a density filter. Different optimization solvers including Optimality Criteria (OC), the Method of Moving Asymptotes (MMA) and its globally convergent version GCMMA, the interior point...... profiles conclude that general solvers are as efficient and reliable as classical structural topology optimization solvers. Moreover, the use of the exact Hessians in SAND formulations, generally produce designs with better objective function values. However, with the benchmarked implementations solving...
Harris, Robert C; Boschitsch, Alexander H; Fenley, Marcia O
2017-08-08
Many researchers compute surface maps of the electrostatic potential (φ) with the Poisson-Boltzmann (PB) equation to relate the structural information obtained from X-ray and NMR experiments to biomolecular functions. Here we demonstrate that the usual method of obtaining these surface maps of φ, by interpolating from neighboring grid points on the solution grid generated by a PB solver, generates large errors because of the large discontinuity in the dielectric constant (and thus in the normal derivative of φ) at the surface. The Cartesian Poisson-Boltzmann solver contains several features that reduce the numerical noise in surface maps of φ: First, CPB introduces additional mesh points at the Cartesian grid/surface intersections where the PB equation is solved. This procedure ensures that the solution for interior mesh points only references nodes on the interior or on the surfaces; similarly for exterior points. Second, for added points on the surface, a second order least-squares reconstruction (LSR) is implemented that analytically incorporates the discontinuities at the surface. LSR is used both during the solution phase to compute φ at the surface and during postprocessing to obtain φ, induced charges, and ionic pressures. Third, it uses an adaptive grid where the finest grid cells are located near the molecular surface.
Sparse Poisson noisy image deblurring.
Carlavan, Mikael; Blanc-Féraud, Laure
2012-04-01
Deblurring noisy Poisson images has recently been a subject of an increasing amount of works in many areas such as astronomy and biological imaging. In this paper, we focus on confocal microscopy, which is a very popular technique for 3-D imaging of biological living specimens that gives images with a very good resolution (several hundreds of nanometers), although degraded by both blur and Poisson noise. Deconvolution methods have been proposed to reduce these degradations, and in this paper, we focus on techniques that promote the introduction of an explicit prior on the solution. One difficulty of these techniques is to set the value of the parameter, which weights the tradeoff between the data term and the regularizing term. Only few works have been devoted to the research of an automatic selection of this regularizing parameter when considering Poisson noise; therefore, it is often set manually such that it gives the best visual results. We present here two recent methods to estimate this regularizing parameter, and we first propose an improvement of these estimators, which takes advantage of confocal images. Following these estimators, we secondly propose to express the problem of the deconvolution of Poisson noisy images as the minimization of a new constrained problem. The proposed constrained formulation is well suited to this application domain since it is directly expressed using the antilog likelihood of the Poisson distribution and therefore does not require any approximation. We show how to solve the unconstrained and constrained problems using the recent alternating-direction technique, and we present results on synthetic and real data using well-known priors, such as total variation and wavelet transforms. Among these wavelet transforms, we specially focus on the dual-tree complex wavelet transform and on the dictionary composed of curvelets and an undecimated wavelet transform.
Authorization query method for RBAC based on partial MAX-SAT solver%基于Partial MAX-SAT求解法的RBAC授权查询方法
Institute of Scientific and Technical Information of China (English)
孙伟; 李艳灵; 鲁骏
2013-01-01
In order to ensure system security and reflect availability in authorization management, a method for querying authorization was proposed based on solvers for partial maximal satisfiability problem. Static authorization descriptions and dynamic mutually exclusive constraints were translated into hard clauses. The algorithm was adopted to update hard clauses and translate requested permissions into soft clauses. Soft clauses were effectively encoded, and the recursive algorithm was utilized to satisfy all hard clauses and as many soft clauses as possible. The experimental results show that the method can ensure system security, it follows the least privilege principle, and the query efficiency outperforms solvers for maximal satisfiability problem.%为保证系统的安全性并体现授权的有效性,结合部分最大可满足性问题(Partial MAX-SAT)的研究,提出一种基于Partial MAX-SAT求解法的授权查询方法.使用转换规则将静态授权逻辑和动态互斥角色约束转化为严格子句,采用子句更新算法将满足不同匹配的请求权限转化为松弛子句,并利用子句编码及递归算法寻求真值指派,以满足所有严格子句和尽可能多的松弛子句.实验结果表明,该方法搜索的角色组合能够保证系统的安全性,并满足最小权限分配要求,且最大、精确匹配请求的查询效率优于MAX-SAT求解法.
Extended Poisson Exponential Distribution
Directory of Open Access Journals (Sweden)
Anum Fatima
2015-09-01
Full Text Available A new mixture of Modified Exponential (ME and Poisson distribution has been introduced in this paper. Taking the Maximum of Modified Exponential random variable when the sample size follows a zero truncated Poisson distribution we have derived the new distribution, named as Extended Poisson Exponential distribution. This distribution possesses increasing and decreasing failure rates. The Poisson-Exponential, Modified Exponential and Exponential distributions are special cases of this distribution. We have also investigated some mathematical properties of the distribution along with Information entropies and Order statistics of the distribution. The estimation of parameters has been obtained using the Maximum Likelihood Estimation procedure. Finally we have illustrated a real data application of our distribution.
Preconditioned CG-solvers and finite element grids
Energy Technology Data Exchange (ETDEWEB)
Bauer, R.; Selberherr, S. [Technical Univ. of Vienna (Austria)
1994-12-31
To extract parasitic capacitances in wiring structures of integrated circuits the authors developed the two- and three-dimensional finite element program SCAP (Smart Capacitance Analysis Program). The program computes the task of the electrostatic field from a solution of Poisson`s equation via finite elements and calculates the energies from which the capacitance matrix is extracted. The unknown potential vector, which has for three-dimensional applications 5000-50000 unknowns, is computed by a ICCG solver. Currently three- and six-node triangular, four- and ten-node tetrahedronal elements are supported.
Johnson, D H
2009-01-01
What constitutes jointly Poisson processes remains an unresolved issue. This report reviews the current state of the theory and indicates how the accepted but unproven model equals that resulting from the small time-interval limit of jointly Bernoulli processes. One intriguing consequence of these models is that jointly Poisson processes can only be positively correlated as measured by the correlation coefficient defined by cumulants of the probability generating functional.
Messaris, G. T.; Papastavrou, C. A.; Loukopoulos, V. C.; Karahalios, G. T.
2009-08-01
A new finite-difference method is presented for the numerical solution of the Navier-Stokes equations of motion of a viscous incompressible fluid in two (or three) dimensions and in the primitive-variable formulation. Introducing two auxiliary functions of the coordinate system and considering the form of the initial equation on lines passing through the nodal point (x0, y0) and parallel to the coordinate axes, we can separate it into two parts that are finally reduced to ordinary differential equations, one for each dimension. The final system of linear equations in n-unknowns is solved by an iterative technique and the method converges rapidly giving satisfactory results. For the pressure variable we consider a pressure Poisson equation with suitable Neumann boundary conditions. Numerical results, confirming the accuracy of the proposed method, are presented for configurations of interest, like Poiseuille flow and the flow between two parallel plates with step under the presence of a pressure gradient.
Phase Selection Heuristics for Satisfiability Solvers
Chen, Jingchao
2011-01-01
In general, a SAT Solver based on conflict-driven DPLL consists of variable selection, phase selection, Boolean Constraint Propagation, conflict analysis, clause learning and its database maintenance. Optimizing any part of these components can enhance the performance of a solver. This paper focuses on optimizing phase selection. Although the ACE (Approximation of the Combined lookahead Evaluation) weight is applied to a lookahead SAT solver such as March, so far, no conflict-driven SAT solver applies successfully the ACE weight, since computing the ACE weight is time-consuming. Here we apply the ACE weight to partial phase selection of conflict-driven SAT solvers. This can be seen as an improvement of the heuristic proposed by Jeroslow-Wang (1990). We incorporate the ACE heuristic and the existing phase selection heuristics in the new solver MPhaseSAT, and select a phase heuristic in a way similar to portfolio methods. Experimental results show that adding the ACE heuristic can improve the conflict-driven so...
Improved Stiff ODE Solvers for Combustion CFD
Imren, A.; Haworth, D. C.
2016-11-01
Increasingly large chemical mechanisms are needed to predict autoignition, heat release and pollutant emissions in computational fluid dynamics (CFD) simulations of in-cylinder processes in compression-ignition engines and other applications. Calculation of chemical source terms usually dominates the computational effort, and several strategies have been proposed to reduce the high computational cost associated with realistic chemistry in CFD. Central to most strategies is a stiff ordinary differential equation (ODE) solver to compute the change in composition due to chemical reactions over a computational time step. Most work to date on stiff ODE solvers for computational combustion has focused on backward differential formula (BDF) methods, and has not explicitly considered the implications of how the stiff ODE solver couples with the CFD algorithm. In this work, a fresh look at stiff ODE solvers is taken that includes how the solver is integrated into a turbulent combustion CFD code, and the advantages of extrapolation-based solvers in this regard are demonstrated. Benefits in CPU time and accuracy are demonstrated for homogeneous systems and compression-ignition engines, for chemical mechanisms that range in size from fewer than 50 to more than 7,000 species.
Experiments with Succinct Solvers
DEFF Research Database (Denmark)
Buchholtz, Mikael; Nielson, Hanne Riis; Nielson, Flemming
2002-01-01
time of the solver and the aim of this note is to provide some insight into which formulations are better than others. The experiments addresses three general issues: (i) the order of the parameters of relations, (ii) the order of conjuncts in preconditions and (iii) the use of memoisation....... The experiments are performed for Control Flow Analyses for Discretionary Ambients....
Leibniz Color Algebra and Leibniz Poisson Color Algebra%Leibniz Color代数和Leibniz Poisson Color代数
Institute of Scientific and Technical Information of China (English)
高齐; 王聪; 张庆成
2014-01-01
This paper presents the definition of Leibniz color algebra and Leibniz Poisson color algebra, and the method to construct the Leibniz color algebra and the Leibniz Poisson color algebra by the newly defined product.%定义了Leibniz color代数和 Leibniz Poisson color 代数，并通过新定义的乘法运算得到了构造Leibniz color代数和Leibniz Poisson color代数的方法。
Transition from Poisson to circular unitary ensemble
Indian Academy of Sciences (India)
Vinayak; Akhilesh Pandey
2009-09-01
Transitions to universality classes of random matrix ensembles have been useful in the study of weakly-broken symmetries in quantum chaotic systems. Transitions involving Poisson as the initial ensemble have been particularly interesting. The exact two-point correlation function was derived by one of the present authors for the Poisson to circular unitary ensemble (CUE) transition with uniform initial density. This is given in terms of a rescaled symmetry breaking parameter Λ. The same result was obtained for Poisson to Gaussian unitary ensemble (GUE) transition by Kunz and Shapiro, using the contour-integral method of Brezin and Hikami. We show that their method is applicable to Poisson to CUE transition with arbitrary initial density. Their method is also applicable to the more general ℓ CUE to CUE transition where CUE refers to the superposition of ℓ independent CUE spectra in arbitrary ratio.
Resolved-particle simulation by the Physalis method: Enhancements and new capabilities
Sierakowski, A.; Prosperetti, A.
2016-01-01
We present enhancements and new capabilities of the Physalis method for simulating disperse multiphase flows using particle-resolved simulation. The current work enhances the previous method by incorporating a new type of pressure-Poisson solver that couples with a new Physalis particle pressure bou
A 4th-Order Particle-in-Cell Method with Phase-Space Remapping for the Vlasov-Poisson Equation
Myers, Andrew; Van Straalen, Brian
2016-01-01
Numerical solutions to the Vlasov-Poisson system of equations have important applications to both plasma physics and cosmology. In this paper, we present a new Particle-in-Cell (PIC) method for solving this system that is 4th-order accurate in both space and time. Our method is a high-order extension of one presented previously [B. Wang, G. Miller, and P. Colella, SIAM J. Sci. Comput., 33 (2011), pp. 3509--3537]. It treats all of the stages of the standard PIC update - charge deposition, force interpolation, the field solve, and the particle push - with 4th-order accuracy, and includes a 6th-order accurate phase-space remapping step for controlling particle noise. We demonstrate the convergence of our method on a series of one- and two- dimensional electrostatic plasma test problems, comparing its accuracy to that of a 2nd-order method. As expected, the 4th-order method can achieve comparable accuracy to the 2nd-order method with many fewer resolution elements.
Generalized Poisson sigma models
Batalin, I; Batalin, Igor; Marnelius, Robert
2001-01-01
A general master action in terms of superfields is given which generates generalized Poisson sigma models by means of a natural ghost number prescription. The simplest representation is the sigma model considered by Cattaneo and Felder. For Dirac brackets considerably more general models are generated.
Matsuo, Kuniaki; Saleh, Bahaa E. A.; Teich, Malvin Carl
1982-12-01
We investigate the counting statistics for stationary and nonstationary cascaded Poisson processes. A simple equation is obtained for the variance-to-mean ratio in the limit of long counting times. Explicit expressions for the forward-recurrence and inter-event-time probability density functions are also obtained. The results are expected to be of use in a number of areas of physics.
Poisson Random Variate Generation.
1981-12-01
Poisson have been proposed. Atkinson [5] includes the approach developed in Marsaglia £15) and Norman and Cannon £16) which is based on composition...34, Naval Research Logistics Quarterly, 26, 3, 403-413. 15. Marsaglia , G. (1963). "Generating Discrete Random Variables in a Computer", Communications
Exact Dynamics via Poisson Process: a unifying Monte Carlo paradigm
Gubernatis, James
2014-03-01
A common computational task is solving a set of ordinary differential equations (o.d.e.'s). A little known theorem says that the solution of any set of o.d.e.'s is exactly solved by the expectation value over a set of arbitary Poisson processes of a particular function of the elements of the matrix that defines the o.d.e.'s. The theorem thus provides a new starting point to develop real and imaginary-time continous-time solvers for quantum Monte Carlo algorithms, and several simple observations enable various quantum Monte Carlo techniques and variance reduction methods to transfer to a new context. I will state the theorem, note a transformation to a very simple computational scheme, and illustrate the use of some techniques from the directed-loop algorithm in context of the wavefunction Monte Carlo method that is used to solve the Lindblad master equation for the dynamics of open quantum systems. I will end by noting that as the theorem does not depend on the source of the o.d.e.'s coming from quantum mechanics, it also enables the transfer of continuous-time methods from quantum Monte Carlo to the simulation of various classical equations of motion heretofore only solved deterministically.
Inductive ionospheric solver for magnetospheric MHD simulations
Directory of Open Access Journals (Sweden)
H. Vanhamäki
2011-01-01
Full Text Available We present a new scheme for solving the ionospheric boundary conditions required in magnetospheric MHD simulations. In contrast to the electrostatic ionospheric solvers currently in use, the new solver takes ionospheric induction into account by solving Faraday's law simultaneously with Ohm's law and current continuity. From the viewpoint of an MHD simulation, the new inductive solver is similar to the electrostatic solvers, as the same input data is used (field-aligned current [FAC] and ionospheric conductances and similar output is produced (ionospheric electric field. The inductive solver is tested using realistic, databased models of an omega-band and westward traveling surge. Although the tests were performed with local models and MHD simulations require a global ionospheric solution, we may nevertheless conclude that the new solution scheme is feasible also in practice. In the test cases the difference between static and electrodynamic solutions is up to ~10 V km^{−1} in certain locations, or up to 20-40% of the total electric field. This is in agreement with previous estimates. It should also be noted that if FAC is replaced by the ground magnetic field (or ionospheric equivalent current in the input data set, exactly the same formalism can be used to construct an inductive version of the KRM method originally developed by Kamide et al. (1981.
Inductive ionospheric solver for magnetospheric MHD simulations
Vanhamäki, H.
2011-01-01
We present a new scheme for solving the ionospheric boundary conditions required in magnetospheric MHD simulations. In contrast to the electrostatic ionospheric solvers currently in use, the new solver takes ionospheric induction into account by solving Faraday's law simultaneously with Ohm's law and current continuity. From the viewpoint of an MHD simulation, the new inductive solver is similar to the electrostatic solvers, as the same input data is used (field-aligned current [FAC] and ionospheric conductances) and similar output is produced (ionospheric electric field). The inductive solver is tested using realistic, databased models of an omega-band and westward traveling surge. Although the tests were performed with local models and MHD simulations require a global ionospheric solution, we may nevertheless conclude that the new solution scheme is feasible also in practice. In the test cases the difference between static and electrodynamic solutions is up to ~10 V km-1 in certain locations, or up to 20-40% of the total electric field. This is in agreement with previous estimates. It should also be noted that if FAC is replaced by the ground magnetic field (or ionospheric equivalent current) in the input data set, exactly the same formalism can be used to construct an inductive version of the KRM method originally developed by Kamide et al. (1981).
Garnier, Romain; Pascal, Olivier
2014-01-01
We present here a Finite Element Method devoted to the simulation of 3D periodic structures of arbitrary geometry. The numerical method based on ARPACK and PARDISO libraries, is discussed with the aim of extracting the eigenmodes of periodical structures and thus establishing their frequency band gaps. Simulation parameters and the computational optimization are the focus. Resolution will be used to characterize EBG (Electromagnetic Band Gap) structures, such as plasma rods and metallic cubes.
Energy Technology Data Exchange (ETDEWEB)
Alleon, G. [EADS-CCR, 31 - Blagnac (France); Carpentieri, B.; Du, I.S.; Giraud, L.; Langou, J.; Martin, E. [Cerfacs, 31 - Toulouse (France)
2003-07-01
The boundary element method has become a popular tool for the solution of Maxwell's equations in electromagnetism. It discretizes only the surface of the radiating object and gives rise to linear systems that are smaller in size compared to those arising from finite element or finite difference discretizations. However, these systems are prohibitively demanding in terms of memory for direct methods and challenging to solve by iterative methods. In this paper we address the iterative solution via preconditioned Krylov methods of electromagnetic scattering problems expressed in an integral formulation, with main focus on the design of the pre-conditioner. We consider an approximate inverse method based on the Frobenius-norm minimization with a pattern prescribed in advance. The pre-conditioner is constructed from a sparse approximation of the dense coefficient matrix, and the patterns both for the pre-conditioner and for the coefficient matrix are computed a priori using geometric information from the mesh. We describe the implementation of the approximate inverse in an out-of-core parallel code that uses multipole techniques for the matrix-vector products, and show results on the numerical scalability of our method on systems of size up to one million unknowns. We propose an embedded iterative scheme based on the GMRES method and combined with multipole techniques, aimed at improving the robustness of the approximate inverse for large problems. We prove by numerical experiments that the proposed scheme enables the solution of very large and difficult problems efficiently at reduced computational and memory cost. Finally we perform a preliminary study on a spectral two-level pre-conditioner to enhance the robustness of our method. This numerical technique exploits spectral information of the preconditioned systems to build a low rank-update of the pre-conditioner. (authors)
Lācis, Uǧis; Bagheri, Shervin
2015-01-01
Dispersion of low-density rigid particles with complex geometries is ubiquitous in both natural and industrial environments. We show that while explicit methods for coupling the incompressible Navier-Stokes equations and Newton's equations of motion are often sufficient to solve for the motion of cylindrical particles with low density ratios, for more complex particles - such as a body with a protrusion - they become unstable. We present an implicit formulation of the coupling between rigid body dynamics and fluid dynamics within the framework of the immersed boundary projection method. Similar to previous work on this method, the resulting matrix equation in the present approach is solved using a block-LU decomposition. Each step of the block-LU decomposition is modified to incorporate the rigid body dynamics. We show that our method achieves second-order accuracy in space and first-order in time (third-order for practical settings), only with a small additional computational cost to the original method. Our...
Formal equivalence of Poisson structures around Poisson submanifolds
Marcut, I.T.
2012-01-01
Let (M,π) be a Poisson manifold. A Poisson submanifold P ⊂ M gives rise to a Lie algebroid AP → P. Formal deformations of π around P are controlled by certain cohomology groups associated to AP. Assuming that these groups vanish, we prove that π is formally rigid around P; that is, any other Poisson
Iwase, Shigeru; Hoshi, Takeo; Ono, Tomoya
2015-06-01
We propose an efficient procedure to obtain Green's functions by combining the shifted conjugate orthogonal conjugate gradient (shifted COCG) method with the nonequilibrium Green's function (NEGF) method based on a real-space finite-difference (RSFD) approach. The bottleneck of the computation in the NEGF scheme is matrix inversion of the Hamiltonian including the self-energy terms of electrodes to obtain the perturbed Green's function in the transition region. This procedure first computes unperturbed Green's functions and calculates perturbed Green's functions from the unperturbed ones using a mathematically strict relation. Since the matrices to be inverted to obtain the unperturbed Green's functions are sparse, complex-symmetric, and shifted for a given set of sampling energy points, we can use the shifted COCG method, in which once the Green's function for a reference energy point has been calculated the Green's functions for the other energy points can be obtained with a moderate computational cost. We calculate the transport properties of a C(60)@(10,10) carbon nanotube (CNT) peapod suspended by (10,10)CNTs as an example of a large-scale transport calculation. The proposed scheme opens the possibility of performing large-scale RSFD-NEGF transport calculations using massively parallel computers without the loss of accuracy originating from the incompleteness of the localized basis set.
Energy Technology Data Exchange (ETDEWEB)
Hosseini, Seyed Abolfaz [Dept. of Energy Engineering, Sharif University of Technology, Tehran (Iran, Islamic Republic of)
2017-02-15
The purpose of the present study is the presentation of the appropriate element and shape function in the solution of the neutron diffusion equation in two-dimensional (2D) geometries. To this end, the multigroup neutron diffusion equation is solved using the Galerkin finite element method in both rectangular and hexagonal reactor cores. The spatial discretization of the equation is performed using unstructured triangular and quadrilateral finite elements. Calculations are performed using both linear and quadratic approximations of shape function in the Galerkin finite element method, based on which results are compared. Using the power iteration method, the neutron flux distributions with the corresponding eigenvalue are obtained. The results are then validated against the valid results for IAEA-2D and BIBLIS-2D benchmark problems. To investigate the dependency of the results to the type and number of the elements, and shape function order, a sensitivity analysis of the calculations to the mentioned parameters is performed. It is shown that the triangular elements and second order of the shape function in each element give the best results in comparison to the other states.
Eliazar, Iddo; Klafter, Joseph
2008-05-01
Many random populations can be modeled as a countable set of points scattered randomly on the positive half-line. The points may represent magnitudes of earthquakes and tornados, masses of stars, market values of public companies, etc. In this article we explore a specific class of random such populations we coin ` Paretian Poisson processes'. This class is elemental in statistical physics—connecting together, in a deep and fundamental way, diverse issues including: the Poisson distribution of the Law of Small Numbers; Paretian tail statistics; the Fréchet distribution of Extreme Value Theory; the one-sided Lévy distribution of the Central Limit Theorem; scale-invariance, renormalization and fractality; resilience to random perturbations.
Raharjo, W.; Palupi, I. R.; Nurdian, S. W.; Giamboro, W. S.; Soesilo, J.
2016-11-01
Poisson's Ratio illustrates the elasticity properties of a rock. The value is affected by the ratio between the value of P and S wave velocity, where the high value ratio associated with partial melting while the low associated with gas saturated rock. Java which has many volcanoes as a result of the collision between the Australian and Eurasian plates also effects of earthquakes that result the P and S wave. By tomography techniques the distribution of the value of Poisson's ratio can be known. Western Java was dominated by high Poisson's Ratio until Mount Slamet and Dieng in Central Java, while the eastern part of Java is dominated by low Poisson's Ratio. The difference of Poisson's Ratio is located in Central Java that is also supported by the difference characteristic of hot water manifestation in geothermal potential area in the west and east of Central Java Province. Poisson's ratio value is also lower with increasing depth proving that the cold oceanic plate entrance under the continental plate.
Stupfel, Bruno; Lecouvez, Matthieu
2016-10-01
For the solution of the time-harmonic electromagnetic scattering problem by inhomogeneous 3-D objects, a one-way domain decomposition method (DDM) is considered: the computational domain is partitioned into concentric subdomains on the interfaces of which Robin-type transmission conditions (TCs) are prescribed; an integral representation of the electromagnetic fields on the outer boundary constitutes an exact radiation condition. The global system obtained after discretization of the finite element (FE) formulations is solved via a Krylov subspace iterative method (GMRES). It is preconditioned in such a way that, essentially, only the solution of the FE subsystems in each subdomain is required. This is made possible by a computationally cheap H (curl)- H (div) transformation performed on the interfaces that separate the two outermost subdomains. The eigenvalues of the preconditioned matrix of the system are bounded by two, and optimized values of the coefficients involved in the local TCs on the interfaces are determined so as to maximize the minimum eigenvalue. Numerical experiments are presented that illustrate the numerical accuracy of this technique, its fast convergence, and legitimate the choices made for the optimized coefficients.
Electric circuits problem solver
REA, Editors of
2012-01-01
Each Problem Solver is an insightful and essential study and solution guide chock-full of clear, concise problem-solving gems. All your questions can be found in one convenient source from one of the most trusted names in reference solution guides. More useful, more practical, and more informative, these study aids are the best review books and textbook companions available. Nothing remotely as comprehensive or as helpful exists in their subject anywhere. Perfect for undergraduate and graduate studies.Here in this highly useful reference is the finest overview of electric circuits currently av
Advanced calculus problem solver
REA, Editors of
2012-01-01
Each Problem Solver is an insightful and essential study and solution guide chock-full of clear, concise problem-solving gems. All your questions can be found in one convenient source from one of the most trusted names in reference solution guides. More useful, more practical, and more informative, these study aids are the best review books and textbook companions available. Nothing remotely as comprehensive or as helpful exists in their subject anywhere. Perfect for undergraduate and graduate studies.Here in this highly useful reference is the finest overview of advanced calculus currently av
Jin, Shi; Roche, Kenneth; Wlazłowski, Gabriel
2016-01-01
Self-consistent approaches to superfluid many-fermion systems in 3-dimensions (and subsequent time-dependent approaches) require a large number of diagonalizations of very large dimension hermitian matrices, which results in enormous computational costs. We present an approach based on the shifted conjugate-orthogonal conjugate-gradient (COCG) method for the evaluation of the Green's function, from which we subsequently extract various densities (particle number, spin, current, kinetic energy, etc.) of a nuclear system needed in self-consistent approaches. The approach eschews the construction of the quasiparticle wavefunctions and their corresponding quasiparticle energies, which are never explicitly needed in any density functional approaches. As benchmarks we present calculations for nuclei with axial symmetry, including the ground state of spherical (magic or semi-magic) and axially deformed nuclei, the saddle-point in the $^{240}$Pu constrained fission path, and a vortex in the neutron star crust.
Energy Technology Data Exchange (ETDEWEB)
Celestin, Sebastien; Bonaventura, Zdenek; Zeghondy, Barbar; Bourdon, Anne [Ecole Centrale Paris, EM2C, UPR CNRS 288, Grande voie des vignes, 92295 Chatenay-Malabry Cedex (France); Segur, Pierre, E-mail: sebastien.celestin@em2c.ecp.f, E-mail: anne.bourdon@em2c.ecp.f [Universite de Toulouse, LAPLACE, UMR CNRS 5213, INPT, UPS, 118 route de Narbonne, 31062 Toulouse Cedex 9 (France)
2009-03-21
This paper presents the application of the ghost fluid method (GFM) to solve Poisson's equation for streamer discharge simulations between electrodes of complex geometries. This approach allows one to use a simple rectilinear grid and nevertheless take into account the influence of the exact shape of the electrode on the calculation of the potential and the electric field. First, the validity of the GFM approach concerning the computation of the electric field is demonstrated by performing direct comparisons in a point-to-plane geometry of the Laplacian potential and electric field calculated with this method and given by the analytical solution. Second, the GFM is applied to the simulation of a positive streamer propagation in a hyperboloid-to-plane configuration studied by Kulikovsky (1998 Phys. Rev. E 57 7066-74). Very good agreement is obtained with the results of Kulikovsky (1998) on all positive streamer characteristics during its propagation in the interelectrode gap. Then the GFM is applied to simulate the discharge in preheated air at atmospheric pressure in point-to-point geometry. The propagation of positive and negative streamers from both point electrodes is observed. After the interaction of both discharges, the very rapid propagation of the positive streamer towards the cathode in the volume pre-ionized by the negative streamer is presented. This structure of the discharge is in qualitative agreement with the experiment.
Batty, Christopher
2017-02-01
This paper introduces a two-dimensional cell-centred finite volume discretization of the Poisson problem on adaptive Cartesian quadtree grids which exhibits second order accuracy in both the solution and its gradients, and requires no grading condition between adjacent cells. At T-junction configurations, which occur wherever resolution differs between neighboring cells, use of the standard centred difference gradient stencil requires that ghost values be constructed by interpolation. To properly recover second order accuracy in the resulting numerical gradients, prior work addressing block-structured grids and graded trees has shown that quadratic, rather than linear, interpolation is required; the gradients otherwise exhibit only first order convergence, which limits potential applications such as fluid flow. However, previous schemes fail or lose accuracy in the presence of the more complex T-junction geometries arising in the case of general non-graded quadtrees, which place no restrictions on the resolution of neighboring cells. We therefore propose novel quadratic interpolant constructions for this case that enable second order convergence by relying on stencils oriented diagonally and applied recursively as needed. The method handles complex tree topologies and large resolution jumps between neighboring cells, even along the domain boundary, and both Dirichlet and Neumann boundary conditions are supported. Numerical experiments confirm the overall second order accuracy of the method in the L∞ norm.
Implicit compressible flow solvers on unstructured meshes
Nagaoka, Makoto; Horinouchi, Nariaki
1993-09-01
An implicit solver for compressible flows using Bi-CGSTAB method is proposed. The Euler equations are discretized with the delta-form by the finite volume method on the cell-centered triangular unstructured meshes. The numerical flux is calculated by Roe's upwind scheme. The linearized simultaneous equations with the irregular nonsymmetric sparse matrix are solved by the Bi-CGSTAB method with the preconditioner of incomplete LU factorization. This method is also vectorized by the multi-colored ordering. Although the solver requires more computational memory, it shows faster and more robust convergence than the other conventional methods: three-stage Runge-Kutta method, point Gauss-Seidel method, and Jacobi method for two-dimensional inviscid steady flows.
Parallel sparse direct solver for integrated circuit simulation
Chen, Xiaoming; Yang, Huazhong
2017-01-01
This book describes algorithmic methods and parallelization techniques to design a parallel sparse direct solver which is specifically targeted at integrated circuit simulation problems. The authors describe a complete flow and detailed parallel algorithms of the sparse direct solver. They also show how to improve the performance by simple but effective numerical techniques. The sparse direct solver techniques described can be applied to any SPICE-like integrated circuit simulator and have been proven to be high-performance in actual circuit simulation. Readers will benefit from the state-of-the-art parallel integrated circuit simulation techniques described in this book, especially the latest parallel sparse matrix solution techniques. · Introduces complicated algorithms of sparse linear solvers, using concise principles and simple examples, without complex theory or lengthy derivations; · Describes a parallel sparse direct solver that can be adopted to accelerate any SPICE-like integrated circuit simulato...
Novel Scalable 3-D MT Inverse Solver
Kuvshinov, A. V.; Kruglyakov, M.; Geraskin, A.
2016-12-01
We present a new, robust and fast, three-dimensional (3-D) magnetotelluric (MT) inverse solver. As a forward modelling engine a highly-scalable solver extrEMe [1] is used. The (regularized) inversion is based on an iterative gradient-type optimization (quasi-Newton method) and exploits adjoint sources approach for fast calculation of the gradient of the misfit. The inverse solver is able to deal with highly detailed and contrasting models, allows for working (separately or jointly) with any type of MT (single-site and/or inter-site) responses, and supports massive parallelization. Different parallelization strategies implemented in the code allow for optimal usage of available computational resources for a given problem set up. To parameterize an inverse domain a mask approach is implemented, which means that one can merge any subset of forward modelling cells in order to account for (usually) irregular distribution of observation sites. We report results of 3-D numerical experiments aimed at analysing the robustness, performance and scalability of the code. In particular, our computational experiments carried out at different platforms ranging from modern laptops to high-performance clusters demonstrate practically linear scalability of the code up to thousands of nodes. 1. Kruglyakov, M., A. Geraskin, A. Kuvshinov, 2016. Novel accurate and scalable 3-D MT forward solver based on a contracting integral equation method, Computers and Geosciences, in press.
Schneider, T.; Botta, N.; Geratz, K. J.; Klein, R.
1999-11-01
When attempting to compute unsteady, variable density flows at very small or zero Mach number using a standard finite volume compressible flow solver one faces at least the following difficulties: (i) Spatial pressure variations vanish as the Mach number M→0, but they do affect the velocity field at leading order; (ii) the resulting spatial homogeneity of the leading order pressure implies an elliptic divergence constraint for the energy flux; (iii) violations of this constraint crucially affect the transport of mass, preventing a code to properly advect even a constant density distribution. We overcome these difficulties through a new algorithm for constructing numerical fluxes in the context of multi-dimensional finite volume methods in conservation form. The construction of numerical fluxes involves: (1) An explicit upwind step yielding predictions for the nonlinear convective flux components. (2) A first correction step that introduces pressure gradients which guarantee compliance of the convective fluxes with a divergence constraint. This step requires the solution of a first Poisson-type equation. (3) A second projection step which provides the yet unknown (non-convective) pressure contribution to the total flux of momentum. This second projection requires the solution of another Poisson-type equation and yields the cell centered velocity field at the new time. This velocity field exactly satisfies a divergence constraint consistent with the asymptotic limit. Step (1) can be done by any standard finite volume compressible flow solver. The input to steps (2) and (3) involves solely the fluxes from step (1) and is independent of how these were obtained. Thus, our approach allows any such solver to be extended to compute variable density incompressible flows.
Parallel Solver for H(div) Problems Using Hybridization and AMG
Energy Technology Data Exchange (ETDEWEB)
Lee, Chak S. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Vassilevski, Panayot S. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)
2016-01-15
In this paper, a scalable parallel solver is proposed for H(div) problems discretized by arbitrary order finite elements on general unstructured meshes. The solver is based on hybridization and algebraic multigrid (AMG). Unlike some previously studied H(div) solvers, the hybridization solver does not require discrete curl and gradient operators as additional input from the user. Instead, only some element information is needed in the construction of the solver. The hybridization results in a H1-equivalent symmetric positive definite system, which is then rescaled and solved by AMG solvers designed for H1 problems. Weak and strong scaling of the method are examined through several numerical tests. Our numerical results show that the proposed solver provides a promising alternative to ADS, a state-of-the-art solver [12], for H(div) problems. In fact, it outperforms ADS for higher order elements.
Bayesian regression of piecewise homogeneous Poisson processes
Directory of Open Access Journals (Sweden)
Diego Sevilla
2015-12-01
Full Text Available In this paper, a Bayesian method for piecewise regression is adapted to handle counting processes data distributed as Poisson. A numerical code in Mathematica is developed and tested analyzing simulated data. The resulting method is valuable for detecting breaking points in the count rate of time series for Poisson processes. Received: 2 November 2015, Accepted: 27 November 2015; Edited by: R. Dickman; Reviewed by: M. Hutter, Australian National University, Canberra, Australia.; DOI: http://dx.doi.org/10.4279/PIP.070018 Cite as: D J R Sevilla, Papers in Physics 7, 070018 (2015
Poisson modules and degeneracy loci
Gualtieri, Marco
2012-01-01
In this paper, we study the interplay between modules and sub-objects in holomorphic Poisson geometry. In particular, we define a new notion of "residue" for a Poisson module, analogous to the Poincar\\'e residue of a meromorphic volume form. Of particular interest is the interaction between the residues of the canonical line bundle of a Poisson manifold and its degeneracy loci---where the rank of the Poisson structure drops. As an application, we provide new evidence in favour of Bondal's conjecture that the rank \\leq 2k locus of a Fano Poisson manifold always has dimension \\geq 2k+1. In particular, we show that the conjecture holds for Fano fourfolds. We also apply our techniques to a family of Poisson structures defined by Fe\\u{\\i}gin and Odesski\\u{\\i}, where the degeneracy loci are given by the secant varieties of elliptic normal curves.
Tucker, Jordan
2008-01-01
Hypothesis tests for the presence of new sources of Poisson counts amidst background processes are frequently performed in high energy physics, gamma ray astronomy, and other branches of science. This talk brie y summarizes work in which we evaluate two classes of algorithms for dealing with uncertainty in the mean background in such tests.
DEFF Research Database (Denmark)
Hejlesen, Mads Mølholm; Spietz, Henrik J.; Walther, Jens Honore
2014-01-01
In resent work we have developed a new FFT based Poisson solver, which uses regularized Greens functions to obtain arbitrary high order convergence to the unbounded Poisson equation. The high order Poisson solver has been implemented in an unbounded particle-mesh based vortex method which uses a re......-meshing of the vortex particles to ensure the convergence of the method. Furthermore, we use a re-projection of the vorticity field to include the constraint of a divergence-free stream function which is essential for the underlying Helmholtz decomposition and ensures a divergence free vorticity field. The high order...... with the principal axis of the strain rate tensor. We find that the dynamics of the enstrophy density is dominated by the local flow deformation and axis of rotation, which is used to infer some concrete tendencies related to the topology of the vorticity field....
Eliazar, Iddo; Klafter, Joseph
2008-09-01
The Central Limit Theorem (CLT) and Extreme Value Theory (EVT) study, respectively, the stochastic limit-laws of sums and maxima of sequences of independent and identically distributed (i.i.d.) random variables via an affine scaling scheme. In this research we study the stochastic limit-laws of populations of i.i.d. random variables via nonlinear scaling schemes. The stochastic population-limits obtained are fractal Poisson processes which are statistically self-similar with respect to the scaling scheme applied, and which are characterized by two elemental structures: (i) a universal power-law structure common to all limits, and independent of the scaling scheme applied; (ii) a specific structure contingent on the scaling scheme applied. The sum-projection and the maximum-projection of the population-limits obtained are generalizations of the classic CLT and EVT results - extending them from affine to general nonlinear scaling schemes.
Nonhomogeneous fractional Poisson processes
Energy Technology Data Exchange (ETDEWEB)
Wang Xiaotian [School of Management, Tianjin University, Tianjin 300072 (China)]. E-mail: swa001@126.com; Zhang Shiying [School of Management, Tianjin University, Tianjin 300072 (China); Fan Shen [Computer and Information School, Zhejiang Wanli University, Ningbo 315100 (China)
2007-01-15
In this paper, we propose a class of non-Gaussian stationary increment processes, named nonhomogeneous fractional Poisson processes W{sub H}{sup (j)}(t), which permit the study of the effects of long-range dependance in a large number of fields including quantum physics and finance. The processes W{sub H}{sup (j)}(t) are self-similar in a wide sense, exhibit more fatter tail than Gaussian processes, and converge to the Gaussian processes in distribution in some cases. In addition, we also show that the intensity function {lambda}(t) strongly influences the existence of the highest finite moment of W{sub H}{sup (j)}(t) and the behaviour of the tail probability of W{sub H}{sup (j)}(t)
Uncertainty Quantification for Production Navier-Stokes Solvers Project
National Aeronautics and Space Administration — The uncertainty quantification methods developed under this program are designed for use with current state-of-the-art flow solvers developed by and in use at NASA....
Numerical Poisson-Boltzmann Model for Continuum Membrane Systems.
Botello-Smith, Wesley M; Liu, Xingping; Cai, Qin; Li, Zhilin; Zhao, Hongkai; Luo, Ray
2013-01-01
Membrane protein systems are important computational research topics due to their roles in rational drug design. In this study, we developed a continuum membrane model utilizing a level set formulation under the numerical Poisson-Boltzmann framework within the AMBER molecular mechanics suite for applications such as protein-ligand binding affinity and docking pose predictions. Two numerical solvers were adapted for periodic systems to alleviate possible edge effects. Validation on systems ranging from organic molecules to membrane proteins up to 200 residues, demonstrated good numerical properties. This lays foundations for sophisticated models with variable dielectric treatments and second-order accurate modeling of solvation interactions.
Energy Technology Data Exchange (ETDEWEB)
Fochesato, Ch. [CEA Bruyeres-le-Chatel, Dept. de Conception et Simulation des Armes, Service Simulation des Amorces, Lab. Logiciels de Simulation, 91 (France); Bouche, D. [CEA Bruyeres-le-Chatel, Dept. de Physique Theorique et Appliquee, Lab. de Recherche Conventionne, Centre de Mathematiques et Leurs Applications, 91 (France)
2007-07-01
The numerical solution of Maxwell equations is a challenging task. Moreover, the range of applications is very wide: microwave devices, diffraction, to cite a few. As a result, a number of methods have been proposed since the sixties. However, among all these methods, none has proved to be free of drawbacks. The finite difference scheme proposed by Yee in 1966, is well suited for Maxwell equations. However, it only works on cubical mesh. As a result, the boundaries of complex objects are not properly handled by the scheme. When classical nodal finite elements are used, spurious modes appear, which spoil the results of simulations. Edge elements overcome this problem, at the price of rather complex implementation, and computationally intensive simulations. Finite volume methods, either generalizing Yee scheme to a wider class of meshes, or applying to Maxwell equations methods initially used in the field of hyperbolic systems of conservation laws, are also used. Lastly, 'Discontinuous Galerkin' methods, generalizing to arbitrary order of accuracy finite volume methods, have recently been applied to Maxwell equations. In this report, we more specifically focus on the coupling of a Maxwell solver to a PIC (Particle-in-cell) method. We analyze advantages and drawbacks of the most widely used methods: accuracy, robustness, sensitivity to numerical artefacts, efficiency, user judgment. (authors)
Energy Technology Data Exchange (ETDEWEB)
Ruge, J.; Li, Y.; McCormick, S.F. [and others
1994-12-31
The formulation and time discretization of problems in meteorology are often tailored to the type of efficient solvers available for use on the discrete problems obtained. A common procedure is to formulate the problem so that a constant (or latitude-dependent) coefficient Poisson-like equation results at each time step, which is then solved using spectral methods. This both limits the scope of problems that can be handled and requires linearization by forward extrapolation of nonlinear terms, which, in turn, requires filtering to control noise. Multigrid methods do not suffer these limitations, and can be applied directly to systems of nonlinear equations with variable coefficients. Here, a global barotropic semi-Lagrangian model, developed by the authors, is presented which results in a system of three coupled nonlinear equations to be solved at each time step. A multigrid method for the solution of these equations is described, and results are presented.
An iterative solver for the 3D Helmholtz equation
Belonosov, Mikhail; Dmitriev, Maxim; Kostin, Victor; Neklyudov, Dmitry; Tcheverda, Vladimir
2017-09-01
We develop a frequency-domain iterative solver for numerical simulation of acoustic waves in 3D heterogeneous media. It is based on the application of a unique preconditioner to the Helmholtz equation that ensures convergence for Krylov subspace iteration methods. Effective inversion of the preconditioner involves the Fast Fourier Transform (FFT) and numerical solution of a series of boundary value problems for ordinary differential equations. Matrix-by-vector multiplication for iterative inversion of the preconditioned matrix involves inversion of the preconditioner and pointwise multiplication of grid functions. Our solver has been verified by benchmarking against exact solutions and a time-domain solver.
ISAR Imaging Algorithm Based on Focal Undetermined System Solver Method%基于欠定系统局灶解法的逆合成孔径雷达成像
Institute of Scientific and Technical Information of China (English)
江东; 童宁宁; 冯为可; 胡小伟
2016-01-01
In order to solve the problems of the existing signal reconstruction methods which have more or less defects such as big amount of calculation and needing the signal sparseness as the prior information,an improved method of ISAR imaging algorithm based on focal undetermined system solver was proposed.Of this method,conjugate gradient scheme based on QR decomposition was used to solve the linear equations in regularized focal undetermined system sol-ver (R-FOCUSS)method.Simulation results showed that it could obtain more clear imaging results and further im-proved the computing speed by using the improved method to reconstruct the received signal.%针对目前压缩感知中常用的信号重构算法普遍存在计算复杂、需要信号的稀疏度作为先验信息等缺陷的问题,提出了基于欠定系统局灶解法(Focal Undetermined System Solver,FOCUSS)的逆合成孔径雷达(Inversed Synthetic Aperture Radar,ISAR)成像方法。该方法利用 QR 分解预处理共轭梯度法求解正则化FOCUSS 算法中的线性方程组,在不需要先验信息的条件下进一步提高算法收敛速度。仿真实验表明,利用基于 QR 分解预处理共轭梯度法改进的正则化 FOCUSS 算法对回波信号进行重构,既能获得更加清晰的成像结果,又能进一步提高运算速度。
Quantum Electrodynamics vacuum polarization solver
Carneiro, Pedro; Fonseca, Ricardo; Silva, Luís
2016-01-01
The self-consistent modeling of vacuum polarization due to virtual electron-positron fluctuations is of relevance for many near term experiments associated with high intensity radiation sources and represents a milestone in describing scenarios of extreme energy density. We present a generalized finite-difference time-domain solver that can incorporate the modifications to Maxwells equations due to virtual vacuum polarization. Our multidimensional solver reproduced in one dimensional configurations the results for which an analytic treatment is possible, yielding vacuum harmonic generation and birefringence. The solver has also been tested for two-dimensional scenarios where finite laser beam spot sizes must be taken into account. We employ this solver to explore different types of counter-propagating configurations that can be relevant for future planned experiments aiming to detect quantum vacuum dynamics at ultra-high electromagnetic field intensities.
A multigrid solver for the semiconductor equations
Bachmann, Bernhard
1993-01-01
We present a multigrid solver for the exponential fitting method. The solver is applied to the current continuity equations of semiconductor device simulation in two dimensions. The exponential fitting method is based on a mixed finite element discretization using the lowest-order Raviart-Thomas triangular element. This discretization method yields a good approximation of front layers and guarantees current conservation. The corresponding stiffness matrix is an M-matrix. 'Standard' multigrid solvers, however, cannot be applied to the resulting system, as this is dominated by an unsymmetric part, which is due to the presence of strong convection in part of the domain. To overcome this difficulty, we explore the connection between Raviart-Thomas mixed methods and the nonconforming Crouzeix-Raviart finite element discretization. In this way we can construct nonstandard prolongation and restriction operators using easily computable weighted L(exp 2)-projections based on suitable quadrature rules and the upwind effects of the discretization. The resulting multigrid algorithm shows very good results, even for real-world problems and for locally refined grids.
Cousins, R D; Cousins, Robert D.; Tucker, Jordan
2007-01-01
Hypothesis tests for the presence of new sources of Poisson counts amidst background processes are frequently performed in high energy physics, gamma ray astronomy, and other branches of science. While there are conceptual issues already when the mean rate of background is precisely known, the issues are even more difficult when the mean background rate has non-negligible uncertainty, as some commonly used techniques are not on a sound foundation. In this paper, we evaluate two classes of algorithms by the criterion of how close the ensemble-average Type I error rate (rejection of the background-only hypothesis when it is true) compares with the nominal significance level given by the algorithm. Following J. Linnemann, we recommend wider use of an algorithm firmly grounded in frequentist tests of the ratio of Poisson means.
Poisson hierarchy of discrete strings
Energy Technology Data Exchange (ETDEWEB)
Ioannidou, Theodora, E-mail: ti3@auth.gr [Faculty of Civil Engineering, School of Engineering, Aristotle University of Thessaloniki, 54249, Thessaloniki (Greece); Niemi, Antti J., E-mail: Antti.Niemi@physics.uu.se [Department of Physics and Astronomy, Uppsala University, P.O. Box 803, S-75108, Uppsala (Sweden); Laboratoire de Mathematiques et Physique Theorique CNRS UMR 6083, Fédération Denis Poisson, Université de Tours, Parc de Grandmont, F37200, Tours (France); Department of Physics, Beijing Institute of Technology, Haidian District, Beijing 100081 (China)
2016-01-28
The Poisson geometry of a discrete string in three dimensional Euclidean space is investigated. For this the Frenet frames are converted into a spinorial representation, the discrete spinor Frenet equation is interpreted in terms of a transfer matrix formalism, and Poisson brackets are introduced in terms of the spinor components. The construction is then generalised, in a self-similar manner, into an infinite hierarchy of Poisson algebras. As an example, the classical Virasoro (Witt) algebra that determines reparametrisation diffeomorphism along a continuous string, is identified as a particular sub-algebra, in the hierarchy of the discrete string Poisson algebra. - Highlights: • Witt (classical Virasoro) algebra is derived in the case of discrete string. • Infinite dimensional hierarchy of Poisson bracket algebras is constructed for discrete strings. • Spinor representation of discrete Frenet equations is developed.
Canonical derivation of the Vlasov-Coulomb noncanonical Poisson structure
Energy Technology Data Exchange (ETDEWEB)
Kaufman, A.N.; Dewar, R.L.
1983-09-01
Starting from a Lagrangian formulation of the Vlasov-Coulomb system, canonical methods are used to define a Poisson structure for this system. Successive changes of representation then lead systematically to the noncanonical Lie-Poisson structure for functionals of the Vlasov distribution.
Rate-optimal Bayesian intensity smoothing for inhomogeneous Poisson processes
E. Belitser; P. Serra; H. van Zanten
2015-01-01
We apply nonparametric Bayesian methods to study the problem of estimating the intensity function of an inhomogeneous Poisson process. To motivate our results we start by analyzing count data coming from a call center which we model as a Poisson process. This analysis is carried out using a certain
Adaptive Kinetic-Fluid Solvers for Heterogeneous Computing Architectures
Zabelok, Sergey; Kolobov, Vladimir
2015-01-01
This paper describes recent progress towards porting a Unified Flow Solver (UFS) to heterogeneous parallel computing. UFS is an adaptive kinetic-fluid simulation tool, which combines Adaptive Mesh Refinement (AMR) with automatic cell-by-cell selection of kinetic or fluid solvers based on continuum breakdown criteria. The main challenge of porting UFS to graphics processing units (GPUs) comes from the dynamically adapted mesh, which causes irregular data access. We describe the implementation of CUDA kernels for three modules in UFS: the direct Boltzmann solver using discrete velocity method (DVM), the Direct Simulation Monte Carlo (DSMC) module, and the Lattice Boltzmann Method (LBM) solver, all using octree Cartesian mesh with AMR. Double digit speedups on single GPU and good scaling for multi-GPU have been demonstrated.
Mathematical programming solver based on local search
Gardi, Frédéric; Darlay, Julien; Estellon, Bertrand; Megel, Romain
2014-01-01
This book covers local search for combinatorial optimization and its extension to mixed-variable optimization. Although not yet understood from the theoretical point of view, local search is the paradigm of choice for tackling large-scale real-life optimization problems. Today's end-users demand interactivity with decision support systems. For optimization software, this means obtaining good-quality solutions quickly. Fast iterative improvement methods, like local search, are suited to satisfying such needs. Here the authors show local search in a new light, in particular presenting a new kind of mathematical programming solver, namely LocalSolver, based on neighborhood search. First, an iconoclast methodology is presented to design and engineer local search algorithms. The authors' concern about industrializing local search approaches is of particular interest for practitioners. This methodology is applied to solve two industrial problems with high economic stakes. Software based on local search induces ex...
Aleph Field Solver Challenge Problem Results Summary
Energy Technology Data Exchange (ETDEWEB)
Hooper, Russell [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Moore, Stan Gerald [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States)
2015-01-01
Aleph models continuum electrostatic and steady and transient thermal fields using a finite-element method. Much work has gone into expanding the core solver capability to support enriched modeling consisting of multiple interacting fields, special boundary conditions and two-way interfacial coupling with particles modeled using Aleph's complementary particle-in-cell capability. This report provides quantitative evidence for correct implementation of Aleph's field solver via order- of-convergence assessments on a collection of problems of increasing complexity. It is intended to provide Aleph with a pedigree and to establish a basis for confidence in results for more challenging problems important to Sandia's mission that Aleph was specifically designed to address.
Modules Over Color Hom-Poisson Algebras
2014-01-01
In this paper we introduce color Hom-Poisson algebras and show that every color Hom-associative algebra has a non-commutative Hom-Poisson algebra structure in which the Hom-Poisson bracket is the commutator bracket. Then we show that color Poisson algebras (respectively morphism of color Poisson algebras) turn to color Hom-Poisson algebras (respectively morphism of Color Hom-Poisson algebras) by twisting the color Poisson structure. Next we prove that modules over color Hom–associative algebr...
Intertime jump statistics of state-dependent Poisson processes.
Daly, Edoardo; Porporato, Amilcare
2007-01-01
A method to obtain the probability distribution of the interarrival times of jump occurrences in systems driven by state-dependent Poisson noise is proposed. Such a method uses the survivor function obtained by a modified version of the master equation associated to the stochastic process under analysis. A model for the timing of human activities shows the capability of state-dependent Poisson noise to generate power-law distributions. The application of the method to a model for neuron dynamics and to a hydrological model accounting for land-atmosphere interaction elucidates the origin of characteristic recurrence intervals and possible persistence in state-dependent Poisson models.
Intertime jump statistics of state-dependent Poisson processes
Daly, Edoardo; Porporato, Amilcare
2007-01-01
A method to obtain the probability distribution of the interarrival times of jump occurrences in systems driven by state-dependent Poisson noise is proposed. Such a method uses the survivor function obtained by a modified version of the master equation associated to the stochastic process under analysis. A model for the timing of human activities shows the capability of state-dependent Poisson noise to generate power-law distributions. The application of the method to a model for neuron dynamics and to a hydrological model accounting for land-atmosphere interaction elucidates the origin of characteristic recurrence intervals and possible persistence in state-dependent Poisson models.
A hierarchy of Poisson brackets
Pavelka, Michal; Esen, Ogul; Grmela, Miroslav
2015-01-01
The vector field generating reversible time evolution of macroscopic systems involves two ingredients: gradient of a potential (a covector) and a degenerate Poisson structure transforming the covector into a vector. The Poisson structure is conveniently expressed in Poisson brackets, its degeneracy in their Casimirs (i.e. potentials whose gradients produce no vector field). In this paper we investigate in detail hierarchies of Poisson brackets, together with their Casimirs, that arise in passages from more to less detailed (i.e. more macroscopic) descriptions. In particular, we investigate the passage from mechanics of particles (in its Liouville representation) to the reversible kinetic theory and the passage from the reversible kinetic theory to the reversible fluid mechanics. From the physical point of view, the investigation includes binary mixtures and two-point formulations suitable for describing turbulent flows. From the mathematical point of view, we reveal the Lie algebra structure involved in the p...
Gauging the Poisson sigma model
Zucchini, Roberto
2008-01-01
We show how to carry out the gauging of the Poisson sigma model in an AKSZ inspired formulation by coupling it to the a generalization of the Weil model worked out in ref. arXiv:0706.1289 [hep-th]. We call the resulting gauged field theory, Poisson--Weil sigma model. We study the BV cohomology of the model and show its relation to Hamiltonian basic and equivariant Poisson cohomology. As an application, we carry out the gauge fixing of the pure Weil model and of the Poisson--Weil model. In the first case, we obtain the 2--dimensional version of Donaldson--Witten topological gauge theory, describing the moduli space of flat connections on a closed surface. In the second case, we recover the gauged A topological sigma model worked out by Baptista describing the moduli space of solutions of the so--called vortex equations.
Nitadori, Keigo
2014-01-01
We propose an efficient algorithm for the evaluation of the potential and its gradient of gravitational/electrostatic $N$-body systems, which we call particle mesh multipole method (PMMM or PM$^3$). PMMM can be understood both as an extension of the particle mesh (PM) method and as an optimization of the fast multipole method (FMM).In the former viewpoint, the scalar density and potential held by a grid point are extended to multipole moments and local expansions in $(p+1)^2$ real numbers, where $p$ is the order of expansion. In the latter viewpoint, a hierarchical octree structure which brings its $\\mathcal O(N)$ nature, is replaced with a uniform mesh structure, and we exploit the convolution theorem with fast Fourier transform (FFT) to speed up the calculations. Hence, independent $(p+1)^2$ FFTs with the size equal to the number of grid points are performed. The fundamental idea is common to PPPM/MPE by Shimada et al. (1993) and FFTM by Ong et al. (2003). PMMM differs from them in supporting both the open ...
Preconditioners for Incompressible Navier-Stokes Solvers
Institute of Scientific and Technical Information of China (English)
A.Segal; M.ur Rehman; C.Vuik
2010-01-01
In this paper we give an overview of the present state of fast solvers for the solution of the incompressible Navier-Stokes equations discretized by the finite element method and linearized by Newton or Picard's method. It is shown that block precon- ditioners form an excellent approach for the solution, however if the grids are not to fine preconditioning with a Saddle point ILU matrix (SILU) may be an attractive al- ternative. The applicability of all methods to stabilized elements is investigated. In case of the stand-alone Stokes equations special preconditioners increase the efficiency considerably.
Scalable Parallel Algebraic Multigrid Solvers
Energy Technology Data Exchange (ETDEWEB)
Bank, R; Lu, S; Tong, C; Vassilevski, P
2005-03-23
The authors propose a parallel algebraic multilevel algorithm (AMG), which has the novel feature that the subproblem residing in each processor is defined over the entire partition domain, although the vast majority of unknowns for each subproblem are associated with the partition owned by the corresponding processor. This feature ensures that a global coarse description of the problem is contained within each of the subproblems. The advantages of this approach are that interprocessor communication is minimized in the solution process while an optimal order of convergence rate is preserved; and the speed of local subproblem solvers can be maximized using the best existing sequential algebraic solvers.
Chavez, Gustavo Ivan
2017-07-10
This dissertation introduces a novel fast direct solver and preconditioner for the solution of block tridiagonal linear systems that arise from the discretization of elliptic partial differential equations on a Cartesian product mesh, such as the variable-coefficient Poisson equation, the convection-diffusion equation, and the wave Helmholtz equation in heterogeneous media. The algorithm extends the traditional cyclic reduction method with hierarchical matrix techniques. The resulting method exposes substantial concurrency, and its arithmetic operations and memory consumption grow only log-linearly with problem size, assuming bounded rank of off-diagonal matrix blocks, even for problems with arbitrary coefficient structure. The method can be used as a standalone direct solver with tunable accuracy, or as a black-box preconditioner in conjunction with Krylov methods. The challenges that distinguish this work from other thrusts in this active field are the hybrid distributed-shared parallelism that can demonstrate the algorithm at large-scale, full three-dimensionality, and the three stressors of the current state-of-the-art multigrid technology: high wavenumber Helmholtz (indefiniteness), high Reynolds convection (nonsymmetry), and high contrast diffusion (inhomogeneity). Numerical experiments corroborate the robustness, accuracy, and complexity claims and provide a baseline of the performance and memory footprint by comparisons with competing approaches such as the multigrid solver hypre, and the STRUMPACK implementation of the multifrontal factorization with hierarchically semi-separable matrices. The companion implementation can utilize many thousands of cores of Shaheen, KAUST\\'s Haswell-based Cray XC-40 supercomputer, and compares favorably with other implementations of hierarchical solvers in terms of time-to-solution and memory consumption.
Wang, Wansheng; Chen, Long; Zhou, Jie
2016-05-01
A postprocessing technique for mixed finite element methods for the Cahn-Hilliard equation is developed and analyzed. Once the mixed finite element approximations have been computed at a fixed time on the coarser mesh, the approximations are postprocessed by solving two decoupled Poisson equations in an enriched finite element space (either on a finer grid or a higher-order space) for which many fast Poisson solvers can be applied. The nonlinear iteration is only applied to a much smaller size problem and the computational cost using Newton and direct solvers is negligible compared with the cost of the linear problem. The analysis presented here shows that this technique remains the optimal rate of convergence for both the concentration and the chemical potential approximations. The corresponding error estimate obtained in our paper, especially the negative norm error estimates, are non-trivial and different with the existing results in the literatures.
Parallel Symmetric Eigenvalue Problem Solvers
2015-05-01
Plemmons G. Golub and A. Sameh. High-speed computing : scientific appli- cations and algorithm design. University of Illinois Press, Champaign, Illinois , 1988...16. SECURITY CLASSIFICATION OF: Sparse symmetric eigenvalue problems arise in many computational science and engineering applications such as...Eigenvalue Problem Solvers Report Title Sparse symmetric eigenvalue problems arise in many computational science and engineering applications such as
Stabilities for nonisentropic Euler-Poisson equations.
Cheung, Ka Luen; Wong, Sen
2015-01-01
We establish the stabilities and blowup results for the nonisentropic Euler-Poisson equations by the energy method. By analysing the second inertia, we show that the classical solutions of the system with attractive forces blow up in finite time in some special dimensions when the energy is negative. Moreover, we obtain the stabilities results for the system in the cases of attractive and repulsive forces.
An alternative hyper-Poisson distribution
Directory of Open Access Journals (Sweden)
C. Satheesh Kumar
2013-05-01
Full Text Available An alternative form of hyper-Poisson distribution is introduced through its probability mass function and studies some of its important aspects such as mean, variance, expressions for its raw moments, factorial moments, probability generating function and recursion formulae for its probabilities, raw moments and factorial moments. The estimation of the parameters of the distribution by various methods are considered and illustrated using some real life data sets.
Free Appearance-Editing with Improved Poisson Image Cloning
Institute of Scientific and Technical Information of China (English)
Xiao-Hui Bie; Hao-Da Huang; Wen-Cheng Wang
2011-01-01
In this paper,we present a new edit tool for the user to conveniently preserve or freely edit the object appearance during seamless image composition.We observe that though Poisson image editing is effective for seamless image composition.Its color bleeding (the color of the target image is propagated into the source image) is not always desired in applications,and it provides no way to allow the user to edit the appearance of the source image.To make it more flexible and practical,we introduce new energy terms to control the appearance change,and integrate them into the Poisson image editing framework.The new energy function could still be realized using efficient sparse linear solvers,and the user can interactively refine the constraints.With the new tool,the user can enjoy not only seamless image composition,but also the flexibility to preserve or manipulate the appearance of the source image at the same time.This provides more potential for creating new images.Experimental results demonstrate the effectiveness of our new edit tool,with similar time cost to the original Poisson image editing.
On the implicit density based OpenFOAM solver for turbulent compressible flows
Fürst, Jiří
The contribution deals with the development of coupled implicit density based solver for compressible flows in the framework of open source package OpenFOAM. However the standard distribution of OpenFOAM contains several ready-made segregated solvers for compressible flows, the performance of those solvers is rather week in the case of transonic flows. Therefore we extend the work of Shen [15] and we develop an implicit semi-coupled solver. The main flow field variables are updated using lower-upper symmetric Gauss-Seidel method (LU-SGS) whereas the turbulence model variables are updated using implicit Euler method.
On the implicit density based OpenFOAM solver for turbulent compressible flows
Directory of Open Access Journals (Sweden)
Fürst Jiří
2017-01-01
Full Text Available The contribution deals with the development of coupled implicit density based solver for compressible flows in the framework of open source package OpenFOAM. However the standard distribution of OpenFOAM contains several ready-made segregated solvers for compressible flows, the performance of those solvers is rather week in the case of transonic flows. Therefore we extend the work of Shen [15] and we develop an implicit semi-coupled solver. The main flow field variables are updated using lower-upper symmetric Gauss-Seidel method (LU-SGS whereas the turbulence model variables are updated using implicit Euler method.
On the implicit density based OpenFOAM solver for turbulent compressible flows
Fürst, Jiří
2016-11-01
The contribution deals with the development of coupled implicit density based solver for compressible flows in the framework of open source package OpenFOAM. However the standard distribution of OpenFOAM contains several ready-made segregated solvers for compressible flows, the performance of those solvers is rather week in the case of transonic flows. Therefore we extend the work of Shen [15] and we develop an implicit semi-coupled solver. The main flow field variables are updated using lower-upper symmetric Gauss-Seidel method (LU-SGS) whereas the turbulence model variables are updated using implicit Euler method.
Cooper, Christopher D; Barba, L A
2013-01-01
The continuum theory applied to bimolecular electrostatics leads to an implicit-solvent model governed by the Poisson-Boltzmann equation. Solvers relying on a boundary integral representation typically do not consider features like solvent-filled cavities or ion-exclusion (Stern) layers, due to the added difficulty of treating multiple boundary surfaces. This has hindered meaningful comparisons with volume-based methods, and the effects on accuracy of including these features has remained unknown. This work presents a solver called PyGBe that uses a boundary-element formulation and can handle multiple interacting surfaces. It was used to study the effects of solvent-filled cavities and Stern layers on the accuracy of calculating solvation energy and binding energy of proteins, using the well-known APBS finite-difference code for comparison. The results suggest that if required accuracy for an application allows errors larger than about 2%, then the simpler, single-surface model can be used. When calculating b...
Absolute regularity and ergodicity of Poisson count processes
Neumann, Michael H
2012-01-01
We consider a class of observation-driven Poisson count processes where the current value of the accompanying intensity process depends on previous values of both processes. We show under a contractive condition that the bivariate process has a unique stationary distribution and that a stationary version of the count process is absolutely regular. Moreover, since the intensities can be written as measurable functionals of the count variables, we conclude that the bivariate process is ergodic. As an important application of these results, we show how a test method previously used in the case of independent Poisson data can be used in the case of Poisson count processes.
Ringe, Stefan; Oberhofer, Harald; Hille, Christoph; Matera, Sebastian; Reuter, Karsten
2016-08-01
The size-modified Poisson-Boltzmann (MPB) equation is an efficient implicit solvation model which also captures electrolytic solvent effects. It combines an account of the dielectric solvent response with a mean-field description of solvated finite-sized ions. We present a general solution scheme for the MPB equation based on a fast function-space-oriented Newton method and a Green's function preconditioned iterative linear solver. In contrast to popular multigrid solvers, this approach allows us to fully exploit specialized integration grids and optimized integration schemes. We describe a corresponding numerically efficient implementation for the full-potential density-functional theory (DFT) code FHI-aims. We show that together with an additional Stern layer correction the DFT+MPB approach can describe the mean activity coefficient of a KCl aqueous solution over a wide range of concentrations. The high sensitivity of the calculated activity coefficient on the employed ionic parameters thereby suggests to use extensively tabulated experimental activity coefficients of salt solutions for a systematic parametrization protocol.
Time-Changed Poisson Processes
Kumar, A; Vellaisamy, P
2011-01-01
We consider time-changed Poisson processes, and derive the governing difference-differential equations (DDE) these processes. In particular, we consider the time-changed Poisson processes where the the time-change is inverse Gaussian, or its hitting time process, and discuss the governing DDE's. The stable subordinator, inverse stable subordinator and their iterated versions are also considered as time-changes. DDE's corresponding to probability mass functions of these time-changed processes are obtained. Finally, we obtain a new governing partial differential equation for the tempered stable subordinator of index $0<\\beta<1,$ when $\\beta $ is a rational number. We then use this result to obtain the governing DDE for the mass function of Poisson process time-changed by tempered stable subordinator. Our results extend and complement the results in Baeumer et al. \\cite{B-M-N} and Beghin et al. \\cite{BO-1} in several directions.
DPS--a computerised diagnostic problem solver.
Bartos, P; Gyárfas, F; Popper, M
1982-01-01
The paper contains a short description of the DPS system which is a computerized diagnostic problem solver. The system is under development of the Research Institute of Medical Bionics in Bratislava, Czechoslovakia. Its underlying philosophy yields from viewing the diagnostic process as process of cognitive problem solving. The implementation of the system is based on the methods of Artificial Intelligence and utilisation of production systems and frame theory should be noted in this context. Finally a list of program modules and their characterisation is presented.
Performance of Basic Geodynamic Solvers on BG/p and on Modern Mid-sized CPU Clusters
Omlin, S.; Keller, V.; Podladchikov, Y.
2012-04-01
Nowadays, most researchers have access to computer clusters. For the community developing numerical applications in geodynamics, this constitutes a very important potential: besides that current applications can be speeded up, much bigger problems can be solved. This is particularly relevant in 3D applications. However, current practical experiments in geodynamic high-performance applications normally end with the successful demonstration of the potential by exploring the performance of the simplest example (typically the Poisson solver); more advanced practical examples are rare. For this reason, we optimize algorithms for 3D scalar problems and 3D mechanics and design concise, educational Fortran 90 templates that allow other researchers to easily plug in their own geodynamic computations: in these templates, the geodynamic computations are entirely separated from the technical programming needed for the parallelized running on a computer cluster; additionally, we develop our code with minimal syntactical differences from the MATLAB language, such that prototypes of the desired geodynamic computations can be programmed in MATLAB and then copied into the template with only minimal syntactical changes. High-performance programming requires to a big extent taking into account the specificities of the available hardware. The hardware of the world's largest CPU clusters is very different from the one of a modern mid-sized CPU cluster. In this context, we investigate the performance of basic memory-bounded geodynamic solvers on the large-sized BlueGene/P cluster, having 13 Gb/s peak memory bandwidth, and compare it with the performance of a typical modern mid-sized CPU cluster, having 100 Gb/s peak memory bandwidth. A memory-bounded solver's performance depends only on the amount of data required for its computations and on the speed this data can be read from memory (or from the CPUs' cache). In consequence, we speed up the solvers by optimizing memory access and CPU
Anisotropic Poisson Processes of Cylinders
Spiess, Malte
2010-01-01
Main characteristics of stationary anisotropic Poisson processes of cylinders (dilated k-dimensional flats) in d-dimensional Euclidean space are studied. Explicit formulae for the capacity functional, the covariance function, the contact distribution function, the volume fraction, and the intensity of the surface area measure are given which can be used directly in applications.
Berezin integrals and Poisson processes
DeAngelis, G. F.; Jona-Lasinio, G.; Sidoravicius, V.
1998-01-01
We show that the calculation of Berezin integrals over anticommuting variables can be reduced to the evaluation of expectations of functionals of Poisson processes via an appropriate Feynman-Kac formula. In this way the tools of ordinary analysis can be applied to Berezin integrals and, as an example, we prove a simple upper bound. Possible applications of our results are briefly mentioned.
Test of Poisson Failure Assumption.
1982-09-01
o. ....... 37 00/ D itlr.: DVI r TEST OF POISSON FAILURE ASSUMPTION Chapter 1. INTRODUCTION 1.1 Background. In stockage models... precipitates a regular failure pattern; it is also possible that the coding of scheduled vs unscheduled does not reflect what we would expect. Data
Advanced Algebraic Multigrid Solvers for Subsurface Flow Simulation
Chen, Meng-Huo
2015-09-13
In this research we are particularly interested in extending the robustness of multigrid solvers to encounter complex systems related to subsurface reservoir applications for flow problems in porous media. In many cases, the step for solving the pressure filed in subsurface flow simulation becomes a bottleneck for the performance of the simulator. For solving large sparse linear system arising from MPFA discretization, we choose multigrid methods as the linear solver. The possible difficulties and issues will be addressed and the corresponding remedies will be studied. As the multigrid methods are used as the linear solver, the simulator can be parallelized (although not trivial) and the high-resolution simulation become feasible, the ultimately goal which we desire to achieve.
Directory of Open Access Journals (Sweden)
A Nagasupriya
2011-01-01
Full Text Available Objective: This study is intended to analyze the predominant pattern of lip and finger prints in males and females and to correlate lip print and finger print for gender identity. Materials and Methods: The study sample comprised of 200 students of Vishnu Dental College, Bhimavaram, Andhra Pradesh, 100 males and 100 females aged between 18 to 27 years. Brown/pink colored lip stick was applied on the lips and the subject was asked to spread it uniformly over the lips. Lip prints were traced in the normal rest position of the lips with the help of cellophane tape. The imprint of the left thumb was taken on a white chart sheet and visualized using magnifying lens. While three main types of finger prints are identified, the classification of lip prints is simplified into branched, reticular, and vertical types. Association between lip prints and finger prints was statistically tested using Chi-square test. Results: This study showed that lip and finger patterns did not reveal statistically significant results within the gender. The correlation between lip and finger patterns for gender identification, was statistically significant. In males, branched type of lip pattern associated with arch, loop, and whorl type of finger pattern was most significant. In females, vertical lip pattern associated with arch finger pattern and reticular lip pattern associated with whorl finger patterns were most significant. Conclusion: We conclude that a correlative study between the lip print and finger print will be very useful in forensic science for gender identification.
Navier-Stokes Solvers and Generalizations for Reacting Flow Problems
Energy Technology Data Exchange (ETDEWEB)
Elman, Howard C
2013-01-27
This is an overview of our accomplishments during the final term of this grant (1 September 2008 -- 30 June 2012). These fall mainly into three categories: fast algorithms for linear eigenvalue problems; solution algorithms and modeling methods for partial differential equations with uncertain coefficients; and preconditioning methods and solvers for models of computational fluid dynamics (CFD).
A robust HLLC-type Riemann solver for strong shock
Shen, Zhijun; Yan, Wei; Yuan, Guangwei
2016-03-01
It is well known that for the Eulerian equations the numerical schemes that can accurately capture contact discontinuity usually suffer from some disastrous carbuncle phenomenon, while some more dissipative schemes, such as the HLL scheme, are free from this kind of shock instability. Hybrid schemes to combine a dissipative flux with a less dissipative flux can cure the shock instability, but also may lead to other problems, such as certain arbitrariness of choosing switching parameters or contact interface becoming smeared. In order to overcome these drawbacks, this paper proposes a simple and robust HLLC-type Riemann solver for inviscid, compressible gas flows, which is capable of preserving sharp contact surface and is free from instability. The main work is to construct a HLL-type Riemann solver and a HLLC-type Riemann solver by modifying the shear viscosity of the original HLL and HLLC methods. Both of the two new schemes are positively conservative under some typical wavespeed estimations. Moreover, a linear matrix stability analysis for the proposed schemes is accomplished, which illustrates the HLLC-type solver with shear viscosity is stable whereas the HLL-type solver with vorticity wave is unstable. Our arguments and numerical experiments demonstrate that the inadequate dissipation associated to the shear wave may be a unique reason to cause the instability.
Scalable Adaptive Multilevel Solvers for Multiphysics Problems
Energy Technology Data Exchange (ETDEWEB)
Xu, Jinchao
2014-12-01
In this project, we investigated adaptive, parallel, and multilevel methods for numerical modeling of various real-world applications, including Magnetohydrodynamics (MHD), complex fluids, Electromagnetism, Navier-Stokes equations, and reservoir simulation. First, we have designed improved mathematical models and numerical discretizaitons for viscoelastic fluids and MHD. Second, we have derived new a posteriori error estimators and extended the applicability of adaptivity to various problems. Third, we have developed multilevel solvers for solving scalar partial differential equations (PDEs) as well as coupled systems of PDEs, especially on unstructured grids. Moreover, we have integrated the study between adaptive method and multilevel methods, and made significant efforts and advances in adaptive multilevel methods of the multi-physics problems.
Gpu Implementation of a Viscous Flow Solver on Unstructured Grids
Xu, Tianhao; Chen, Long
2016-06-01
Graphics processing units have gained popularities in scientific computing over past several years due to their outstanding parallel computing capability. Computational fluid dynamics applications involve large amounts of calculations, therefore a latest GPU card is preferable of which the peak computing performance and memory bandwidth are much better than a contemporary high-end CPU. We herein focus on the detailed implementation of our GPU targeting Reynolds-averaged Navier-Stokes equations solver based on finite-volume method. The solver employs a vertex-centered scheme on unstructured grids for the sake of being capable of handling complex topologies. Multiple optimizations are carried out to improve the memory accessing performance and kernel utilization. Both steady and unsteady flow simulation cases are carried out using explicit Runge-Kutta scheme. The solver with GPU acceleration in this paper is demonstrated to have competitive advantages over the CPU targeting one.
Vortex methods with immersed lifting lines applied to LES of wind turbine wakes
Chatelain, Philippe; Bricteux, Laurent; Winckelmans, Gregoire; Koumoutsakos, Petros
2010-11-01
We present the coupling of a vortex particle-mesh method with immersed lifting lines. The method relies on the Lagrangian discretization of the Navier-Stokes equations in vorticity-velocity formulation. Advection is handled by the particles while the mesh allows the evaluation of the differential operators and the use of fast Poisson solvers. We use a Fourier-based fast Poisson solver which simultaneously allows unbounded directions and inlet/outlet boundaries. A lifting line approach models the vorticity sources in the flow. Its immersed treatment efficiently captures the development of vorticity from thin sheets into a three-dimensional field. We apply this approach to the simulation of a wind turbine wake at very high Reynolds number. The combined use of particles and multiscale subgrid models allows the capture of wake dynamics with minimal spurious diffusion and dispersion.
Parallel Sparse Linear System and Eigenvalue Problem Solvers: From Multicore to Petascale Computing
2015-06-01
problems that achieve high performance on a single multicore node and clusters of many multicore nodes. Further, we demonstrate both the superior ...the superior robustness and parallel scalability of our solvers compared to other publicly available parallel solvers for these two fundamental...LU‐ and algebraic multigrid‐preconditioned Krylov subspace methods. This has been demonstrated in previous annual reports of this
An implementation of a parallel MOL solver on the Intel gamma parallel computer
Energy Technology Data Exchange (ETDEWEB)
Lawkins, W.F.; Payne, J.S.
1992-06-17
A implicit parallel method-of-lines solver that has been implemented on the MIMD Intel Gamma prototype supercomputer is discussed. The strategy for implementation is to execute the ODE solver sequentially and to do the numerical linear algebra in parallel. Performance studies for this implementation are presented.
Poisson vs. Long-Tailed Internet traffic
2005-01-01
In this thesis, we reexamine the long discussion on which model is suitable for studying Internet traffic: Poisson or Long-tailed Internet traffic. Poisson model, adapted from telephone network, has been used since the beginning of World Wide Web, while long-tailed distribution gradually takes over with believable evidence. Instead of using Superposition of Point Processes to explain why traffic that is not Poisson tends towards Poisson traffic as the load increases, as it is recent...
Krank, Benjamin; Wall, Wolfgang A; Kronbichler, Martin
2016-01-01
We present an efficient discontinuous Galerkin scheme for simulation of the incompressible Navier-Stokes equations including laminar and turbulent flow. We consider a semi-explicit high-order velocity-correction method for time integration as well as nodal equal-order discretizations for velocity and pressure. The non-linear convective term is treated explicitly while a linear system is solved for the pressure Poisson equation and the viscous term. The key feature of our solver is a consistent penalty term reducing the local divergence error in order to overcome recently reported instabilities in spatially under-resolved high-Reynolds-number flows as well as small time steps. This penalty method is similar to the grad-div stabilization widely used in continuous finite elements. We further review and compare our method to several other techniques recently proposed in literature to stabilize the method for such flow configurations. The solver is specifically designed for large-scale computations through matrix-...
Hindman, R. G.
1985-09-01
Theoretical background and several basic test cases are presented for a new, time dependent Navier-Stokes solver for two-dimensional and axisymmetric flows. The goal of the effort is to invoke state-of-the-art computational fluid dynamics (CFD) technology to improve modeling of viscous phenomenal and to increase the robustness of CFD analysis. The original motivation was inadequate representation of supersonic ramp-induced separation by existing CFD codes. The present work addresses that inadequacy by using modern numerical methods which accurately model signal propagation in high-speed fluid flow. This technique solves the Navier-Stokes equations in general curvilinear coordinates in a four-sided domain bounded by a wall, and upper boundary opposite the wall, an inflow boundary, and an outflow boundary. The interior algorithm is a flux-difference splitting method similar to that of Yang, Lombard, and Bershader, but is blended into a second order, implicit factored delta form. With implicitly treated boundary conditions, the solution is performed using a block tridiagonal method followed by an explicit updating of the boundaries. The resulting scheme satisfies the global conversation requirement to within the order of accuracy of the algorithm. The grid is generated using a relaxation Poisson solver. A systematic and rigorous development of the complete method is presented. Initial steps in code validation include successful reproduction of Couette and Blasius solutions.
The Degraded Poisson Wiretap Channel
Laourine, Amine
2010-01-01
Providing security guarantees for wireless communication is critically important for today's applications. While previous work in this area has concentrated on radio frequency (RF) channels, providing security guarantees for RF channels is inherently difficult because they are prone to rapid variations due small scale fading. Wireless optical communication, on the other hand, is inherently more secure than RF communication due to the intrinsic aspects of the signal propagation in the optical and near-optical frequency range. In this paper, secure communication over wireless optical links is examined by studying the secrecy capacity of a direct detection system. For the degraded Poisson wiretap channel, a closed-form expression of the secrecy capacity is given. A complete characterization of the general rate-equivocation region is also presented. For achievability, an optimal code is explicitly constructed by using the structured code designed by Wyner for the Poisson channel. The converse is proved in two dif...
Perturbation analysis of Poisson processes
Last, Günter
2012-01-01
We consider a Poisson process $\\Phi$ on a general phase space. The expectation of a function of $\\Phi$ can be considered as a functional of the intensity measure $\\lambda$ of $\\Phi$. Extending ealier results of Molchanov and Zuyev (2000) on finite Poisson processes, we study the behaviour of this functional under signed (possibly infinite) perturbations of $\\lambda$. In particular we obtain general Margulis--Russo type formulas for the derivative with respect to non-linear transformations of the intensity measure depending on some parameter. As an application we study the behaviour of expectations of functions of multivariate pure jump L\\'evy processes under perturbations of the L\\'evy measure. A key ingredient of our approach is the explicit Fock space representation obtained in Last and Penrose (2011).
Gong, Weiwei; Zhou, Xu
2017-06-01
In Computer Science, the Boolean Satisfiability Problem(SAT) is the problem of determining if there exists an interpretation that satisfies a given Boolean formula. SAT is one of the first problems that was proven to be NP-complete, which is also fundamental to artificial intelligence, algorithm and hardware design. This paper reviews the main algorithms of the SAT solver in recent years, including serial SAT algorithms, parallel SAT algorithms, SAT algorithms based on GPU, and SAT algorithms based on FPGA. The development of SAT is analyzed comprehensively in this paper. Finally, several possible directions for the development of the SAT problem are proposed.
An Energy Conserving Parallel Hybrid Plasma Solver
Holmstrom, M
2010-01-01
We investigate the performance of a hybrid plasma solver on the test problem of an ion beam. The parallel solver is based on cell centered finite differences in space, and a predictor-corrector leapfrog scheme in time. The implementation is done in the FLASH software framework. It is shown that the solver conserves energy well over time, and that the parallelization is efficient (it exhibits weak scaling).
An HLLC Solver for Relativistic Flows
Mignone, A
2005-01-01
We present an extension of the HLLC approximate Riemann solver by Toro, Spruce and Speares to the relativistic equations of fluid dynamics. The solver retains the simplicity of the original two-wave formulation proposed by Harten, Lax and van Leer (HLL) but it restores the missing contact wave in the solution of the Riemann problem. The resulting numerical scheme is computationally efficient, robust and positively conservative. The performance of the new solver is evaluated through numerical testing in one and two dimensions.
Predicting SMT Solver Performance for Software Verification
Directory of Open Access Journals (Sweden)
Andrew Healy
2017-01-01
Full Text Available The Why3 IDE and verification system facilitates the use of a wide range of Satisfiability Modulo Theories (SMT solvers through a driver-based architecture. We present Where4: a portfolio-based approach to discharge Why3 proof obligations. We use data analysis and machine learning techniques on static metrics derived from program source code. Our approach benefits software engineers by providing a single utility to delegate proof obligations to the solvers most likely to return a useful result. It does this in a time-efficient way using existing Why3 and solver installations - without requiring low-level knowledge about SMT solver operation from the user.
Integrating advanced reasoning into a SAT solver
Institute of Scientific and Technical Information of China (English)
DING Min; TANG Pushan; ZHOU Dian
2005-01-01
In this paper, we present a SAT solver based on the combination of DPLL (Davis Putnam Logemann and Loveland) algorithm and Failed Literal Detection (FLD), one of the advanced reasoning techniques. We propose a Dynamic Filtering method that consists of two restriction rules for FLD: internal and external filtering. The method reduces the number of tested literals in FLD and its computational time while maintaining the ability to find most of the failed literals in each decision level. Unlike the pre-defined criteria, literals are removed dynamically in our approach. In this way, our FLD can adapt itself to different real-life benchmarks. Many useless tests are therefore avoided and as a consequence it makes FLD fast. Some other static restrictions are also added to further improve the efficiency of FLD. Experiments show that our optimized FLD is much more efficient than other advanced reasoning techniques.
Asynchronous Parallelization of a CFD Solver
Directory of Open Access Journals (Sweden)
Daniel S. Abdi
2015-01-01
Full Text Available A Navier-Stokes equations solver is parallelized to run on a cluster of computers using the domain decomposition method. Two approaches of communication and computation are investigated, namely, synchronous and asynchronous methods. Asynchronous communication between subdomains is not commonly used in CFD codes; however, it has a potential to alleviate scaling bottlenecks incurred due to processors having to wait for each other at designated synchronization points. A common way to avoid this idle time is to overlap asynchronous communication with computation. For this to work, however, there must be something useful and independent a processor can do while waiting for messages to arrive. We investigate an alternative approach of computation, namely, conducting asynchronous iterations to improve local subdomain solution while communication is in progress. An in-house CFD code is parallelized using message passing interface (MPI, and scalability tests are conducted that suggest asynchronous iterations are a viable way of parallelizing CFD code.
Poisson-Boltzmann versus Size-Modified Poisson-Boltzmann Electrostatics Applied to Lipid Bilayers.
Wang, Nuo; Zhou, Shenggao; Kekenes-Huskey, Peter M; Li, Bo; McCammon, J Andrew
2014-12-26
Mean-field methods, such as the Poisson-Boltzmann equation (PBE), are often used to calculate the electrostatic properties of molecular systems. In the past two decades, an enhancement of the PBE, the size-modified Poisson-Boltzmann equation (SMPBE), has been reported. Here, the PBE and the SMPBE are reevaluated for realistic molecular systems, namely, lipid bilayers, under eight different sets of input parameters. The SMPBE appears to reproduce the molecular dynamics simulation results better than the PBE only under specific parameter sets, but in general, it performs no better than the Stern layer correction of the PBE. These results emphasize the need for careful discussions of the accuracy of mean-field calculations on realistic systems with respect to the choice of parameters and call for reconsideration of the cost-efficiency and the significance of the current SMPBE formulation.
General second order complete active space self-consistent-field solver for large-scale systems
Sun, Qiming
2016-01-01
One challenge of the complete active space self-consistent field (CASSCF) program is to solve the transition metal complexes which are typically medium or large-size molecular systems with large active space. We present an AO-driven second order CASSCF solver to efficiently handle systems which have a large number of AO functions and many active orbitals. This solver allows user to replace the active space Full CI solver with any multiconfigurational solver without breaking the quadratic convergence feature. We demonstrate the capability of the CASSCF solver with the study of Fe(ii)-porphine ground state using DMRG-CASSCF method for 22 electrons in 27 active orbitals and 3000 basis functions.
Segmentation algorithm for non-stationary compound Poisson processes
Toth, Bence; Farmer, J Doyne
2010-01-01
We introduce an algorithm for the segmentation of a class of regime switching processes. The segmentation algorithm is a non parametric statistical method able to identify the regimes (patches) of the time series. The process is composed of consecutive patches of variable length, each patch being described by a stationary compound Poisson process, i.e. a Poisson process where each count is associated to a fluctuating signal. The parameters of the process are different in each patch and therefore the time series is non stationary. Our method is a generalization of the algorithm introduced by Bernaola-Galvan, et al., Phys. Rev. Lett., 87, 168105 (2001). We show that the new algorithm outperforms the original one for regime switching compound Poisson processes. As an application we use the algorithm to segment the time series of the inventory of market members of the London Stock Exchange and we observe that our method finds almost three times more patches than the original one.
Multiscale Universal Interface: A concurrent framework for coupling heterogeneous solvers
Tang, Yu-Hang; Kudo, Shuhei; Bian, Xin; Li, Zhen; Karniadakis, George Em
2015-09-01
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 difficulties in practice. In this paper we present a C++ library, i.e. the Multiscale Universal Interface (MUI), which is capable of facilitating the coupling effort for a wide range of multiscale simulations. The library adopts a header-only form with minimal external dependency and hence can be easily dropped into existing codes. A data sampler concept is introduced, combined with a hybrid dynamic/static typing mechanism, to create an easily customizable framework for solver-independent data interpretation. The library integrates MPI MPMD support and an asynchronous communication protocol to handle inter-solver information exchange irrespective of the solvers' own MPI awareness. Template metaprogramming is heavily employed to simultaneously improve runtime performance and code flexibility. We validated the library by solving three different multiscale problems, which also serve to demonstrate the flexibility of the framework in handling heterogeneous models and solvers. In the first example, a Couette flow was simulated using two concurrently coupled Smoothed Particle Hydrodynamics (SPH) simulations of different spatial resolutions. In the second example, we coupled the deterministic SPH method with the stochastic Dissipative Particle Dynamics (DPD) method to study the effect of surface grafting on the hydrodynamics properties on the surface. In the third example, we consider conjugate heat transfer between a solid domain and a fluid domain by coupling the particle-based energy-conserving DPD (eDPD) method with the Finite Element Method (FEM).
Multiscale Universal Interface: A concurrent framework for coupling heterogeneous solvers
Energy Technology Data Exchange (ETDEWEB)
Tang, Yu-Hang, E-mail: yuhang_tang@brown.edu [Division of Applied Mathematics, Brown University, Providence, RI (United States); Kudo, Shuhei, E-mail: shuhei-kudo@outlook.jp [Graduate School of System Informatics, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe, 657-8501 (Japan); Bian, Xin, E-mail: xin_bian@brown.edu [Division of Applied Mathematics, Brown University, Providence, RI (United States); Li, Zhen, E-mail: zhen_li@brown.edu [Division of Applied Mathematics, Brown University, Providence, RI (United States); Karniadakis, George Em, E-mail: george_karniadakis@brown.edu [Division of Applied Mathematics, Brown University, Providence, RI (United States); Collaboratory on Mathematics for Mesoscopic Modeling of Materials, Pacific Northwest National Laboratory, Richland, WA 99354 (United States)
2015-09-15
Graphical abstract: - Abstract: 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 difficulties in practice. In this paper we present a C++ library, i.e. the Multiscale Universal Interface (MUI), which is capable of facilitating the coupling effort for a wide range of multiscale simulations. The library adopts a header-only form with minimal external dependency and hence can be easily dropped into existing codes. A data sampler concept is introduced, combined with a hybrid dynamic/static typing mechanism, to create an easily customizable framework for solver-independent data interpretation. The library integrates MPI MPMD support and an asynchronous communication protocol to handle inter-solver information exchange irrespective of the solvers' own MPI awareness. Template metaprogramming is heavily employed to simultaneously improve runtime performance and code flexibility. We validated the library by solving three different multiscale problems, which also serve to demonstrate the flexibility of the framework in handling heterogeneous models and solvers. In the first example, a Couette flow was simulated using two concurrently coupled Smoothed Particle Hydrodynamics (SPH) simulations of different spatial resolutions. In the second example, we coupled the deterministic SPH method with the stochastic Dissipative Particle Dynamics (DPD) method to study the effect of surface grafting on the hydrodynamics properties on the surface. In the third example, we consider conjugate heat transfer between a solid domain and a fluid domain by coupling the particle-based energy-conserving DPD (eDPD) method with the Finite Element Method (FEM)
Generalized Hamiltonian Systems on a Poisson Product Manifold%泊松流形中的一般哈密尔顿系统
Institute of Scientific and Technical Information of China (English)
王红
2005-01-01
We firstly intoruduced a kind of special functions and a kind of special Poisson bracket on a product manifold,then give a kind of special generalized Hamiltonian vector fields by using the special Poisson bracket.Moreover,we give a method to compose a new generalized Hamiltonian system on the Poisson product manifold by using two known generalized Hamitonian systems on the factor Poisson manifolds.We also discuss the conservative properties of the new composed generalized Hamiltonian systems as well as the relation between the Poisson mapping on the Poisson product manifold and that on the factor Poisson manifolds.
Poisson Manifolds, Lie Algebroids, Modular Classes: a Survey
Directory of Open Access Journals (Sweden)
Yvette Kosmann-Schwarzbach
2008-01-01
Full Text Available After a brief summary of the main properties of Poisson manifolds and Lie algebroids in general, we survey recent work on the modular classes of Poisson and twisted Poisson manifolds, of Lie algebroids with a Poisson or twisted Poisson structure, and of Poisson-Nijenhuis manifolds. A review of the spinor approach to the modular class concludes the paper.
NHPoisson: An R Package for Fitting and Validating Nonhomogeneous Poisson Processes
Directory of Open Access Journals (Sweden)
Ana C. Cebrián
2015-03-01
Full Text Available NHPoisson is an R package for the modeling of nonhomogeneous Poisson processes in one dimension. It includes functions for data preparation, maximum likelihood estimation, covariate selection and inference based on asymptotic distributions and simulation methods. It also provides specific methods for the estimation of Poisson processes resulting from a peak over threshold approach. In addition, the package supports a wide range of model validation tools and functions for generating nonhomogenous Poisson process trajectories. This paper is a description of the package and aims to help those interested in modeling data using nonhomogeneous Poisson processes.
Suppressing Background Radiation Using Poisson Principal Component Analysis
Tandon, P; Dubrawski, A; Labov, S; Nelson, K
2016-01-01
Performance of nuclear threat detection systems based on gamma-ray spectrometry often strongly depends on the ability to identify the part of measured signal that can be attributed to background radiation. We have successfully applied a method based on Principal Component Analysis (PCA) to obtain a compact null-space model of background spectra using PCA projection residuals to derive a source detection score. We have shown the method's utility in a threat detection system using mobile spectrometers in urban scenes (Tandon et al 2012). While it is commonly assumed that measured photon counts follow a Poisson process, standard PCA makes a Gaussian assumption about the data distribution, which may be a poor approximation when photon counts are low. This paper studies whether and in what conditions PCA with a Poisson-based loss function (Poisson PCA) can outperform standard Gaussian PCA in modeling background radiation to enable more sensitive and specific nuclear threat detection.
On some Aitken-like acceleration of the Schwarz method
Garbey, M.; Tromeur-Dervout, D.
2002-12-01
In this paper we present a family of domain decomposition based on Aitken-like acceleration of the Schwarz method seen as an iterative procedure with a linear rate of convergence. We first present the so-called Aitken-Schwarz procedure for linear differential operators. The solver can be a direct solver when applied to the Helmholtz problem with five-point finite difference scheme on regular grids. We then introduce the Steffensen-Schwarz variant which is an iterative domain decomposition solver that can be applied to linear and nonlinear problems. We show that these solvers have reasonable numerical efficiency compared to classical fast solvers for the Poisson problem or multigrids for more general linear and nonlinear elliptic problems. However, the salient feature of our method is that our algorithm has high tolerance to slow network in the context of distributed parallel computing and is attractive, generally speaking, to use with computer architecture for which performance is limited by the memory bandwidth rather than the flop performance of the CPU. This is nowadays the case for most parallel. computer using the RISC processor architecture. We will illustrate this highly desirable property of our algorithm with large-scale computing experiments.
Hypersonic simulations using open-source CFD and DSMC solvers
Casseau, V.; Scanlon, T. J.; John, B.; Emerson, D. R.; Brown, R. E.
2016-11-01
Hypersonic hybrid hydrodynamic-molecular gas flow solvers are required to satisfy the two essential requirements of any high-speed reacting code, these being physical accuracy and computational efficiency. The James Weir Fluids Laboratory at the University of Strathclyde is currently developing an open-source hybrid code which will eventually reconcile the direct simulation Monte-Carlo method, making use of the OpenFOAM application called dsmcFoam, and the newly coded open-source two-temperature computational fluid dynamics solver named hy2Foam. In conjunction with employing the CVDV chemistry-vibration model in hy2Foam, novel use is made of the QK rates in a CFD solver. In this paper, further testing is performed, in particular with the CFD solver, to ensure its efficacy before considering more advanced test cases. The hy2Foam and dsmcFoam codes have shown to compare reasonably well, thus providing a useful basis for other codes to compare against.
Advances in three-dimensional geoelectric forward solver techniques
Blome, M.; Maurer, H. R.; Schmidt, K.
2009-03-01
Modern geoelectrical data acquisition systems allow large amounts of data to be collected in a short time. Inversions of such data sets require powerful forward solvers for predicting the electrical potentials. State-of-the-art solvers are typically based on finite elements. Recent developments in numerical mathematics led to direct matrix solvers that allow the equation systems arising from such finite element problems to be solved very efficiently. They are particularly useful for 3-D geoelectrical problems, where many electrodes are involved. Although modern direct matrix solvers include optimized memory saving strategies, their application to realistic, large-scale 3-D problems is still somewhat limited. Therefore, we present two novel techniques that allow the number of gridpoints to be reduced considerably, while maintaining a high solution accuracy. In the areas surrounding an electrode array we attach infinite elements that continue the electrical potentials to infinity. This does not only reduce the number of gridpoints, but also avoids the artificial Dirichlet or mixed boundary conditions that are well known to be the cause of numerical inaccuracies. Our second development concerns the singularity removal in the presence of significant surface topography. We employ a fast multipole boundary element method for computing the singular potentials. This renders unnecessary mesh refinements near the electrodes, which results in substantial savings of gridpoints of up to more than 50 per cent. By means of extensive numerical tests we demonstrate that combined application of infinite elements and singularity removal allows the number of gridpoints to be reduced by a factor of ~6-10 compared with traditional finite element methods. This will be key for applying finite elements and direct matrix solver techniques to realistic 3-D inversion problems.
Migration of vectorized iterative solvers to distributed memory architectures
Energy Technology Data Exchange (ETDEWEB)
Pommerell, C. [AT& T Bell Labs., Murray Hill, NJ (United States); Ruehl, R. [CSCS-ETH, Manno (Switzerland)
1994-12-31
Both necessity and opportunity motivate the use of high-performance computers for iterative linear solvers. Necessity results from the size of the problems being solved-smaller problems are often better handled by direct methods. Opportunity arises from the formulation of the iterative methods in terms of simple linear algebra operations, even if this {open_quote}natural{close_quotes} parallelism is not easy to exploit in irregularly structured sparse matrices and with good preconditioners. As a result, high-performance implementations of iterative solvers have attracted a lot of interest in recent years. Most efforts are geared to vectorize or parallelize the dominating operation-structured or unstructured sparse matrix-vector multiplication, or to increase locality and parallelism by reformulating the algorithm-reducing global synchronization in inner products or local data exchange in preconditioners. Target architectures for iterative solvers currently include mostly vector supercomputers and architectures with one or few optimized (e.g., super-scalar and/or super-pipelined RISC) processors and hierarchical memory systems. More recently, parallel computers with physically distributed memory and a better price/performance ratio have been offered by vendors as a very interesting alternative to vector supercomputers. However, programming comfort on such distributed memory parallel processors (DMPPs) still lags behind. Here the authors are concerned with iterative solvers and their changing computing environment. In particular, they are considering migration from traditional vector supercomputers to DMPPs. Application requirements force one to use flexible and portable libraries. They want to extend the portability of iterative solvers rather than reimplementing everything for each new machine, or even for each new architecture.
Large deviations for fractional Poisson processes
Beghin, Luisa
2012-01-01
We present large deviation results for two versions of fractional Poisson processes: the main version which is a renewal process, and the alternative version where all the random variables are weighted Poisson distributed. We also present a sample path large deviation result for suitably normalized counting processes; finally we show how this result can be applied to the two versions of fractional Poisson processes considered in this paper.
Surface reconstruction through poisson disk sampling.
Directory of Open Access Journals (Sweden)
Wenguang Hou
Full Text Available This paper intends to generate the approximate Voronoi diagram in the geodesic metric for some unbiased samples selected from original points. The mesh model of seeds is then constructed on basis of the Voronoi diagram. Rather than constructing the Voronoi diagram for all original points, the proposed strategy is to run around the obstacle that the geodesic distances among neighboring points are sensitive to nearest neighbor definition. It is obvious that the reconstructed model is the level of detail of original points. Hence, our main motivation is to deal with the redundant scattered points. In implementation, Poisson disk sampling is taken to select seeds and helps to produce the Voronoi diagram. Adaptive reconstructions can be achieved by slightly changing the uniform strategy in selecting seeds. Behaviors of this method are investigated and accuracy evaluations are done. Experimental results show the proposed method is reliable and effective.
Energy Technology Data Exchange (ETDEWEB)
GARDNER, P.R.
2006-04-01
Sudoku, also known as Number Place, is a logic-based placement puzzle. The aim of the puzzle is to enter a numerical digit from 1 through 9 in each cell of a 9 x 9 grid made up of 3 x 3 subgrids (called ''regions''), starting with various digits given in some cells (the ''givens''). Each row, column, and region must contain only one instance of each numeral. Completing the puzzle requires patience and logical ability. Although first published in a U.S. puzzle magazine in 1979, Sudoku initially caught on in Japan in 1986 and attained international popularity in 2005. Last fall, after noticing Sudoku puzzles in some newspapers and magazines, I attempted a few just to see how hard they were. Of course, the difficulties varied considerably. ''Obviously'' one could use Trial and Error but all the advice was to ''Use Logic''. Thinking to flex, and strengthen, those powers, I began to tackle the puzzles systematically. That is, when I discovered a new tactical rule, I would write it down, eventually generating a list of ten or so, with some having overlap. They served pretty well except for the more difficult puzzles, but even then I managed to develop an additional three rules that covered all of them until I hit the Oregonian puzzle shown. With all of my rules, I could not seem to solve that puzzle. Initially putting my failure down to rapid mental fatigue (being unable to hold a sufficient quantity of information in my mind at one time), I decided to write a program to implement my rules and see what I had failed to notice earlier. The solver, too, failed. That is, my rules were insufficient to solve that particular puzzle. I happened across a book written by a fellow who constructs such puzzles and who claimed that, sometimes, the only tactic left was trial and error. With a trial and error routine implemented, my solver successfully completed the Oregonian puzzle, and has successfully
Parallel Nonnegative Least Squares Solvers for Model Order Reduction
2016-03-01
not for the PQN method. For the latter method the size of the active set is controlled to promote sparse solutions. This is described in Section 3.2.1...or any other aspect of this collection of information, including suggestions for reducing the burden, to Department of Defense, Washington...21005-5066 primary author’s email: <james.p.collins106.civ@mail.mil>. Parallel nonnegative least squares (NNLS) solvers are developed specifically for
Decision Engines for Software Analysis Using Satisfiability Modulo Theories Solvers
Bjorner, Nikolaj
2010-01-01
The area of software analysis, testing and verification is now undergoing a revolution thanks to the use of automated and scalable support for logical methods. A well-recognized premise is that at the core of software analysis engines is invariably a component using logical formulas for describing states and transformations between system states. The process of using this information for discovering and checking program properties (including such important properties as safety and security) amounts to automatic theorem proving. In particular, theorem provers that directly support common software constructs offer a compelling basis. Such provers are commonly called satisfiability modulo theories (SMT) solvers. Z3 is a state-of-the-art SMT solver. It is developed at Microsoft Research. It can be used to check the satisfiability of logical formulas over one or more theories such as arithmetic, bit-vectors, lists, records and arrays. The talk describes some of the technology behind modern SMT solvers, including the solver Z3. Z3 is currently mainly targeted at solving problems that arise in software analysis and verification. It has been applied to various contexts, such as systems for dynamic symbolic simulation (Pex, SAGE, Vigilante), for program verification and extended static checking (Spec#/Boggie, VCC, HAVOC), for software model checking (Yogi, SLAM), model-based design (FORMULA), security protocol code (F7), program run-time analysis and invariant generation (VS3). We will describe how it integrates support for a variety of theories that arise naturally in the context of the applications. There are several new promising avenues and the talk will touch on some of these and the challenges related to SMT solvers. Proceedings
Conditioned Poisson distributions and the concentration of chromatic numbers
Hartigan, John; Tatikonda, Sekhar
2011-01-01
The paper provides a simpler method for proving a delicate inequality that was used by Achlioptis and Naor to establish asymptotic concentration for chromatic numbers of Erdos-Renyi random graphs. The simplifications come from two new ideas. The first involves a sharpened form of a piece of statistical folklore regarding goodness-of-fit tests for two-way tables of Poisson counts under linear conditioning constraints. The second idea takes the form of a new inequality that controls the extreme tails of the distribution of a quadratic form in independent Poissons random variables.
NITSOL: A Newton iterative solver for nonlinear systems
Energy Technology Data Exchange (ETDEWEB)
Pernice, M. [Univ. of Utah, Salt Lake City, UT (United States); Walker, H.F. [Utah State Univ., Logan, UT (United States)
1996-12-31
Newton iterative methods, also known as truncated Newton methods, are implementations of Newton`s method in which the linear systems that characterize Newton steps are solved approximately using iterative linear algebra methods. Here, we outline a well-developed Newton iterative algorithm together with a Fortran implementation called NITSOL. The basic algorithm is an inexact Newton method globalized by backtracking, in which each initial trial step is determined by applying an iterative linear solver until an inexact Newton criterion is satisfied. In the implementation, the user can specify inexact Newton criteria in several ways and select an iterative linear solver from among several popular {open_quotes}transpose-free{close_quotes} Krylov subspace methods. Jacobian-vector products used by the Krylov solver can be either evaluated analytically with a user-supplied routine or approximated using finite differences of function values. A flexible interface permits a wide variety of preconditioning strategies and allows the user to define a preconditioner and optionally update it periodically. We give details of these and other features and demonstrate the performance of the implementation on a representative set of test problems.
A 2-D/3-D cartesian geometry non-conforming spherical harmonic neutron transport solver
Energy Technology Data Exchange (ETDEWEB)
Van Criekingen, S. [Laboratoire J.-L. Lions, Universite Pierre et Marie Curie, 175 rue du Chevaleret, 75013 Paris (France)]. E-mail: vancriekingen@ann.jussieu.fr
2007-03-15
A new 2-D/3-D transport core solver for the time-independent Boltzmann transport equation is presented. This solver, named FIESTA, is based on the second-order even-parity form of the transport equation. The angular discretization is performed through the expansion of the angular neutron flux into spherical harmonics (P {sub N} method). The novelty of this solver is the use of non-conforming finite elements for the spatial discretization. Such elements lead to a discontinuous scalar flux approximation. This interface continuity requirement relaxation property is shared with mixed-dual formulations discretized using Raviart-Thomas finite elements. Encouraging numerical results are presented.
Classical covariant Poisson structures and Deformation Quantization
Berra-Montiel, Jasel; Palacios-García, César D
2014-01-01
Starting with the well-defined product of quantum fields at two spacetime points, we explore an associated Poisson structure for classical field theories within the deformation quantization formalism. We realize that the induced star-product is naturally related to the standard Moyal product through the causal Green functions connecting points in the space of classical solutions to the equations of motion. Our results resemble the Peierls-DeWitt bracket analyzed in the multisymplectic context. Once our star-product is defined we are able to apply the Wigner-Weyl map in order to introduce a generalized version of Wick's theorem. Finally, we include a couple of examples to explicitly test our method: the real scalar field and the bosonic string. For both models we have encountered generalizations of the creation/annihilation relations, and also a generalization of the Virasoro algebra in the bosonic string case.
Stability of Schr(o)dinger-Poisson type equations
Institute of Scientific and Technical Information of China (English)
Juan HUANG; Jian ZHANG; Guang-gan CHEN
2009-01-01
Variational methods are used to study the nonlinear Schr(o)dinger-Poisson type equations which model the electromagnetic wave propagating in the plasma in physics. By analyzing the Halniltonian property to construct a constrained variational problem, the existence of the ground state of the system is obtained. Furthermore, it is shown that the ground state is orbitally stable.
Optimality of Poisson Processes Intensity Learning with Gaussian Processes
Kirichenko, A.; van Zanten, H.
2015-01-01
In this paper we provide theoretical support for the so-called "Sigmoidal Gaussian Cox Process" approach to learning the intensity of an inhomogeneous Poisson process on a d-dimensional domain. This method was proposed by Adams, Murray and MacKay (ICML, 2009), who developed a tractable computational
On global solutions for the Vlasov-Poisson system
Directory of Open Access Journals (Sweden)
Peter E. Zhidkov
2004-04-01
Full Text Available In this article we show that the Vlasov-Poisson system has a unique weak solution in the space $L_1cap L_infty$. For this purpose, we use the method of characteristics, unlike the approach in [12].
Optimality of Poisson Processes Intensity Learning with Gaussian Processes
A. Kirichenko; H. van Zanten
2015-01-01
In this paper we provide theoretical support for the so-called "Sigmoidal Gaussian Cox Process" approach to learning the intensity of an inhomogeneous Poisson process on a d-dimensional domain. This method was proposed by Adams, Murray and MacKay (ICML, 2009), who developed a tractable computational
Poisson Geometry from a Dirac perspective
Meinrenken, Eckhard
2016-01-01
We present proofs of classical results in Poisson geometry using techniques from Dirac geometry. This article is based on mini-courses at the Poisson summer school in Geneva, June 2016, and at the workshop "Quantum Groups and Gravity" at the University of Waterloo, April 2016.
Error Control of Iterative Linear Solvers for Integrated Groundwater Models
Dixon, Matthew; Brush, Charles; Chung, Francis; Dogrul, Emin; Kadir, Tariq
2010-01-01
An open problem that arises when using modern iterative linear solvers, such as the preconditioned conjugate gradient (PCG) method or Generalized Minimum RESidual method (GMRES) is how to choose the residual tolerance in the linear solver to be consistent with the tolerance on the solution error. This problem is especially acute for integrated groundwater models which are implicitly coupled to another model, such as surface water models, and resolve both multiple scales of flow and temporal interaction terms, giving rise to linear systems with variable scaling. This article uses the theory of 'forward error bound estimation' to show how rescaling the linear system affects the correspondence between the residual error in the preconditioned linear system and the solution error. Using examples of linear systems from models developed using the USGS GSFLOW package and the California State Department of Water Resources' Integrated Water Flow Model (IWFM), we observe that this error bound guides the choice of a prac...
A parallel PCG solver for MODFLOW.
Dong, Yanhui; Li, Guomin
2009-01-01
In order to simulate large-scale ground water flow problems more efficiently with MODFLOW, the OpenMP programming paradigm was used to parallelize the preconditioned conjugate-gradient (PCG) solver with in this study. Incremental parallelization, the significant advantage supported by OpenMP on a shared-memory computer, made the solver transit to a parallel program smoothly one block of code at a time. The parallel PCG solver, suitable for both MODFLOW-2000 and MODFLOW-2005, is verified using an 8-processor computer. Both the impact of compilers and different model domain sizes were considered in the numerical experiments. Based on the timing results, execution times using the parallel PCG solver are typically about 1.40 to 5.31 times faster than those using the serial one. In addition, the simulation results are the exact same as the original PCG solver, because the majority of serial codes were not changed. It is worth noting that this parallelizing approach reduces cost in terms of software maintenance because only a single source PCG solver code needs to be maintained in the MODFLOW source tree.
A contribution to the great Riemann solver debate
Quirk, James J.
1992-01-01
The aims of this paper are threefold: to increase the level of awareness within the shock capturing community to the fact that many Godunov-type methods contain subtle flaws that can cause spurious solutions to be computed; to identify one mechanism that might thwart attempts to produce very high resolution simulations; and to proffer a simple strategy for overcoming the specific failings of individual Riemann solvers.
An Investigation of the Performance of the Colored Gauss-Seidel Solver on CPU and GPU
Energy Technology Data Exchange (ETDEWEB)
Yoon, Jong Seon; Choi, Hyoung Gwon [Seoul Nat’l Univ. of Science and Technology, Seoul (Korea, Republic of); Jeon, Byoung Jin [Yonsei Univ., Seoul (Korea, Republic of)
2017-02-15
The performance of the colored Gauss–Seidel solver on CPU and GPU was investigated for the two- and three-dimensional heat conduction problems by using different mesh sizes. The heat conduction equation was discretized by the finite difference method and finite element method. The CPU yielded good performance for small problems but deteriorated when the total memory required for computing was larger than the cache memory for large problems. In contrast, the GPU performed better as the mesh size increased because of the latency hiding technique. Further, GPU computation by the colored Gauss–Siedel solver was approximately 7 times that by the single CPU. Furthermore, the colored Gauss–Seidel solver was found to be approximately twice that of the Jacobi solver when parallel computing was conducted on the GPU.
A Solver for Massively Parallel Direct Numerical Simulation of Three-Dimensional Multiphase Flows
Shin, S; Juric, D
2014-01-01
We present a new solver for massively parallel simulations of fully three-dimensional multiphase flows. The solver runs on a variety of computer architectures from laptops to supercomputers and on 65536 threads or more (limited only by the availability to us of more threads). The code is wholly written by the authors in Fortran 2003 and uses a domain decomposition strategy for parallelization with MPI. The fluid interface solver is based on a parallel implementation of the LCRM hybrid Front Tracking/Level Set method designed to handle highly deforming interfaces with complex topology changes. We discuss the implementation of this interface method and its particular suitability to distributed processing where all operations are carried out locally on distributed subdomains. We have developed parallel GMRES and Multigrid iterative solvers suited to the linear systems arising from the implicit solution of the fluid velocities and pressure in the presence of strong density and viscosity discontinuities across flu...
Speech parts as Poisson processes.
Badalamenti, A F
2001-09-01
This paper presents evidence that six of the seven parts of speech occur in written text as Poisson processes, simple or recurring. The six major parts are nouns, verbs, adjectives, adverbs, prepositions, and conjunctions, with the interjection occurring too infrequently to support a model. The data consist of more than the first 5000 words of works by four major authors coded to label the parts of speech, as well as periods (sentence terminators). Sentence length is measured via the period and found to be normally distributed with no stochastic model identified for its occurrence. The models for all six speech parts but the noun significantly distinguish some pairs of authors and likewise for the joint use of all words types. Any one author is significantly distinguished from any other by at least one word type and sentence length very significantly distinguishes each from all others. The variety of word type use, measured by Shannon entropy, builds to about 90% of its maximum possible value. The rate constants for nouns are close to the fractions of maximum entropy achieved. This finding together with the stochastic models and the relations among them suggest that the noun may be a primitive organizer of written text.
NONLINEAR MULTIGRID SOLVER EXPLOITING AMGe COARSE SPACES WITH APPROXIMATION PROPERTIES
Energy Technology Data Exchange (ETDEWEB)
Christensen, Max La Cour [Technical Univ. of Denmark, Lyngby (Denmark); Villa, Umberto E. [Univ. of Texas, Austin, TX (United States); Engsig-Karup, Allan P. [Technical Univ. of Denmark, Lyngby (Denmark); Vassilevski, Panayot S. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)
2016-01-22
The paper introduces a nonlinear multigrid solver for mixed nite element discretizations based on the Full Approximation Scheme (FAS) and element-based Algebraic Multigrid (AMGe). The main motivation to use FAS for unstruc- tured problems is the guaranteed approximation property of the AMGe coarse spaces that were developed recently at Lawrence Livermore National Laboratory. These give the ability to derive stable and accurate coarse nonlinear discretization problems. The previous attempts (including ones with the original AMGe method, [5, 11]), were less successful due to lack of such good approximation properties of the coarse spaces. With coarse spaces with approximation properties, our FAS approach on un- structured meshes should be as powerful/successful as FAS on geometrically re ned meshes. For comparison, Newton's method and Picard iterations with an inner state-of-the-art linear solver is compared to FAS on a nonlinear saddle point problem with applications to porous media ow. It is demonstrated that FAS is faster than Newton's method and Picard iterations for the experiments considered here. Due to the guaranteed approximation properties of our AMGe, the coarse spaces are very accurate, providing a solver with the potential for mesh-independent convergence on general unstructured meshes.
Elliptic Solvers for Adaptive Mesh Refinement Grids
Energy Technology Data Exchange (ETDEWEB)
Quinlan, D.J.; Dendy, J.E., Jr.; Shapira, Y.
1999-06-03
We are developing multigrid methods that will efficiently solve elliptic problems with anisotropic and discontinuous coefficients on adaptive grids. The final product will be a library that provides for the simplified solution of such problems. This library will directly benefit the efforts of other Laboratory groups. The focus of this work is research on serial and parallel elliptic algorithms and the inclusion of our black-box multigrid techniques into this new setting. The approach applies the Los Alamos object-oriented class libraries that greatly simplify the development of serial and parallel adaptive mesh refinement applications. In the final year of this LDRD, we focused on putting the software together; in particular we completed the final AMR++ library, we wrote tutorials and manuals, and we built example applications. We implemented the Fast Adaptive Composite Grid method as the principal elliptic solver. We presented results at the Overset Grid Conference and other more AMR specific conferences. We worked on optimization of serial and parallel performance and published several papers on the details of this work. Performance remains an important issue and is the subject of continuing research work.
Direct linear programming solver in C for structural applications
Damkilde, L.; Hoyer, O.; Krenk, S.
1994-08-01
An optimization problem can be characterized by an object-function, which is maximized, and restrictions, which limit the variation of the variables. A subclass of optimization is Linear Programming (LP), where both the object-function and the restrictions are linear functions of the variables. The traditional solution methods for LP problems are based on the simplex method, and it is customary to allow only non-negative variables. Compared to other optimization routines the LP solvers are more robust and the optimum is reached in a finite number of steps and is not sensitive to the starting point. For structural applications many optimization problems can be linearized and solved by LP routines. However, the structural variables are not always non-negative, and this requires a reformation, where a variable x is substituted by the difference of two non-negative variables, x(sup + ) and x(sup - ). The transformation causes a doubling of the number of variables, and in a computer implementation the memory allocation doubles and for a typical problem the execution time at least doubles. This paper describes a LP solver written in C, which can handle a combination of non-negative variables and unlimited variables. The LP solver also allows restart, and this may reduce the computational costs if the solution to a similar LP problem is known a priori. The algorithm is based on the simplex method, and differs only in the logical choices. Application of the new LP solver will at the same time give both a more direct problem formulation and a more efficient program.
Poisson Regression Analysis of Illness and Injury Surveillance Data
Energy Technology Data Exchange (ETDEWEB)
Frome E.L., Watkins J.P., Ellis E.D.
2012-12-12
The Department of Energy (DOE) uses illness and injury surveillance to monitor morbidity and assess the overall health of the work force. Data collected from each participating site include health events and a roster file with demographic information. The source data files are maintained in a relational data base, and are used to obtain stratified tables of health event counts and person time at risk that serve as the starting point for Poisson regression analysis. The explanatory variables that define these tables are age, gender, occupational group, and time. Typical response variables of interest are the number of absences due to illness or injury, i.e., the response variable is a count. Poisson regression methods are used to describe the effect of the explanatory variables on the health event rates using a log-linear main effects model. Results of fitting the main effects model are summarized in a tabular and graphical form and interpretation of model parameters is provided. An analysis of deviance table is used to evaluate the importance of each of the explanatory variables on the event rate of interest and to determine if interaction terms should be considered in the analysis. Although Poisson regression methods are widely used in the analysis of count data, there are situations in which over-dispersion occurs. This could be due to lack-of-fit of the regression model, extra-Poisson variation, or both. A score test statistic and regression diagnostics are used to identify over-dispersion. A quasi-likelihood method of moments procedure is used to evaluate and adjust for extra-Poisson variation when necessary. Two examples are presented using respiratory disease absence rates at two DOE sites to illustrate the methods and interpretation of the results. In the first example the Poisson main effects model is adequate. In the second example the score test indicates considerable over-dispersion and a more detailed analysis attributes the over-dispersion to extra-Poisson
Energy Technology Data Exchange (ETDEWEB)
Fisher, A. C. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Bailey, D. S. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Kaiser, T. B. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Eder, D. C. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Gunney, B. T. N. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Masters, N. D. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Koniges, A. E. [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Anderson, R. W. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)
2015-02-01
Here, we present a novel method for the solution of the diffusion equation on a composite AMR mesh. This approach is suitable for including diffusion based physics modules to hydrocodes that support ALE and AMR capabilities. To illustrate, we proffer our implementations of diffusion based radiation transport and heat conduction in a hydrocode called ALE-AMR. Numerical experiments conducted with the diffusion solver and associated physics packages yield 2nd order convergence in the L_{2} norm.
Experimental validation of a boundary element solver for exterior acoustic radiation problems
Visser, Rene; Nilsson, A; Boden, H.
2003-01-01
The relation between harmonic structural vibrations and the corresponding acoustic radiation is given by the Helmholtz integral equation (HIE). To solve this integral equation a new solver (BEMSYS) based on the boundary element method (BEM) has been implemented. This numerical tool can be used for both sound radiation and nearfield acoustic source localization purposes. After validation of the solver with analytic solutions of simple test problems, a well-defined experimental setup has been d...
An exact solver for the DCJ median problem.
Zhang, Meng; Arndt, William; Tang, Jijun
2009-01-01
The "double-cut-and-join" (DCJ) model of genome rearrangement proposed by Yancopoulos et al. uses the single DCJ operation to account for all genome rearrangement events. Given three signed permutations, the DCJ median problem is to find a fourth permutation that minimizes the sum of the pairwise DCJ distances between it and the three others. In this paper, we present a branch-and-bound method that provides accurate solution to the multichromosomal DCJ median problems. We conduct extensive simulations and the results show that the DCJ median solver performs better than other median solvers for most of the test cases. These experiments also suggest that DCJ model is more suitable for real datasets where both reversals and transpositions occur.
On improving linear solver performance: a block variant of GMRES
Energy Technology Data Exchange (ETDEWEB)
Baker, A H; Dennis, J M; Jessup, E R
2004-05-10
The increasing gap between processor performance and memory access time warrants the re-examination of data movement in iterative linear solver algorithms. For this reason, we explore and establish the feasibility of modifying a standard iterative linear solver algorithm in a manner that reduces the movement of data through memory. In particular, we present an alternative to the restarted GMRES algorithm for solving a single right-hand side linear system Ax = b based on solving the block linear system AX = B. Algorithm performance, i.e. time to solution, is improved by using the matrix A in operations on groups of vectors. Experimental results demonstrate the importance of implementation choices on data movement as well as the effectiveness of the new method on a variety of problems from different application areas.
LDRD report : parallel repartitioning for optimal solver performance.
Energy Technology Data Exchange (ETDEWEB)
Heaphy, Robert; Devine, Karen Dragon; Preis, Robert (University of Paderborn, Paderborn, Germany); Hendrickson, Bruce Alan; Heroux, Michael Allen; Boman, Erik Gunnar
2004-02-01
We have developed infrastructure, utilities and partitioning methods to improve data partitioning in linear solvers and preconditioners. Our efforts included incorporation of data repartitioning capabilities from the Zoltan toolkit into the Trilinos solver framework, (allowing dynamic repartitioning of Trilinos matrices); implementation of efficient distributed data directories and unstructured communication utilities in Zoltan and Trilinos; development of a new multi-constraint geometric partitioning algorithm (which can generate one decomposition that is good with respect to multiple criteria); and research into hypergraph partitioning algorithms (which provide up to 56% reduction of communication volume compared to graph partitioning for a number of emerging applications). This report includes descriptions of the infrastructure and algorithms developed, along with results demonstrating the effectiveness of our approaches.
Parallel Auxiliary Space AMG Solver for $H(div)$ Problems
Energy Technology Data Exchange (ETDEWEB)
Kolev, Tzanio V. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Vassilevski, Panayot S. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)
2012-12-18
We present a family of scalable preconditioners for matrices arising in the discretization of $H(div)$ problems using the lowest order Raviart--Thomas finite elements. Our approach belongs to the class of “auxiliary space''--based methods and requires only the finite element stiffness matrix plus some minimal additional discretization information about the topology and orientation of mesh entities. Also, we provide a detailed algebraic description of the theory, parallel implementation, and different variants of this parallel auxiliary space divergence solver (ADS) and discuss its relations to the Hiptmair--Xu (HX) auxiliary space decomposition of $H(div)$ [SIAM J. Numer. Anal., 45 (2007), pp. 2483--2509] and to the auxiliary space Maxwell solver AMS [J. Comput. Math., 27 (2009), pp. 604--623]. Finally, an extensive set of numerical experiments demonstrates the robustness and scalability of our implementation on large-scale $H(div)$ problems with large jumps in the material coefficients.
Elliptic Solvers with Adaptive Mesh Refinement on Complex Geometries
Energy Technology Data Exchange (ETDEWEB)
Phillip, B.
2000-07-24
Adaptive Mesh Refinement (AMR) is a numerical technique for locally tailoring the resolution computational grids. Multilevel algorithms for solving elliptic problems on adaptive grids include the Fast Adaptive Composite grid method (FAC) and its parallel variants (AFAC and AFACx). Theory that confirms the independence of the convergence rates of FAC and AFAC on the number of refinement levels exists under certain ellipticity and approximation property conditions. Similar theory needs to be developed for AFACx. The effectiveness of multigrid-based elliptic solvers such as FAC, AFAC, and AFACx on adaptively refined overlapping grids is not clearly understood. Finally, a non-trivial eye model problem will be solved by combining the power of using overlapping grids for complex moving geometries, AMR, and multilevel elliptic solvers.
Poisson's ratio and Young's modulus of lipid bilayers in different phases
Directory of Open Access Journals (Sweden)
Tayebeh eJadidi
2014-04-01
Full Text Available A general computational method is introduced to estimate the Poisson's ratio for membranes with small thickness.In this method, the Poisson's ratio is calculated by utilizing a rescaling of inter-particle distancesin one lateral direction under periodic boundary conditions. As an example for the coarse grained lipid model introduced by Lenz and Schmid, we calculate the Poisson's ratio in the gel, fluid, and interdigitated phases. Having the Poisson's ratio, enable us to obtain the Young's modulus for the membranes in different phases. The approach may be applied to other membranes such as graphene and tethered membranes in orderto predict the temperature dependence of its Poisson's ratio and Young's modulus.
Integer lattice dynamics for Vlasov-Poisson
Mocz, Philip; Succi, Sauro
2017-03-01
We revisit the integer lattice (IL) method to numerically solve the Vlasov-Poisson equations, and show that a slight variant of the method is a very easy, viable, and efficient numerical approach to study the dynamics of self-gravitating, collisionless systems. The distribution function lives in a discretized lattice phase-space, and each time-step in the simulation corresponds to a simple permutation of the lattice sites. Hence, the method is Lagrangian, conservative, and fully time-reversible. IL complements other existing methods, such as N-body/particle mesh (computationally efficient, but affected by Monte Carlo sampling noise and two-body relaxation) and finite volume (FV) direct integration schemes (expensive, accurate but diffusive). We also present improvements to the FV scheme, using a moving-mesh approach inspired by IL, to reduce numerical diffusion and the time-step criterion. Being a direct integration scheme like FV, IL is memory limited (memory requirement for a full 3D problem scales as N6, where N is the resolution per linear phase-space dimension). However, we describe a new technique for achieving N4 scaling. The method offers promise for investigating the full 6D phase-space of collisionless systems of stars and dark matter.
A chemical reaction network solver for the astrophysics code NIRVANA
Ziegler, U.
2016-02-01
Context. Chemistry often plays an important role in astrophysical gases. It regulates thermal properties by changing species abundances and via ionization processes. This way, time-dependent cooling mechanisms and other chemistry-related energy sources can have a profound influence on the dynamical evolution of an astrophysical system. Modeling those effects with the underlying chemical kinetics in realistic magneto-gasdynamical simulations provide the basis for a better link to observations. Aims: The present work describes the implementation of a chemical reaction network solver into the magneto-gasdynamical code NIRVANA. For this purpose a multispecies structure is installed, and a new module for evolving the rate equations of chemical kinetics is developed and coupled to the dynamical part of the code. A small chemical network for a hydrogen-helium plasma was constructed including associated thermal processes which is used in test problems. Methods: Evolving a chemical network within time-dependent simulations requires the additional solution of a set of coupled advection-reaction equations for species and gas temperature. Second-order Strang-splitting is used to separate the advection part from the reaction part. The ordinary differential equation (ODE) system representing the reaction part is solved with a fourth-order generalized Runge-Kutta method applicable for stiff systems inherent to astrochemistry. Results: A series of tests was performed in order to check the correctness of numerical and technical implementation. Tests include well-known stiff ODE problems from the mathematical literature in order to confirm accuracy properties of the solver used as well as problems combining gasdynamics and chemistry. Overall, very satisfactory results are achieved. Conclusions: The NIRVANA code is now ready to handle astrochemical processes in time-dependent simulations. An easy-to-use interface allows implementation of complex networks including thermal processes
Full characterization of the fractional Poisson process
Politi, Mauro; Scalas, Enrico
2011-01-01
The fractional Poisson process (FPP) is a counting process with independent and identically distributed inter-event times following the Mittag-Leffler distribution. This process is very useful in several fields of applied and theoretical physics including models for anomalous diffusion. Contrary to the well-known Poisson process, the fractional Poisson process does not have stationary and independent increments. It is not a L\\'evy process and it is not a Markov process. In this letter, we present formulae for its finite-dimensional distribution functions, fully characterizing the process. These exact analytical results are compared to Monte Carlo simulations.
Integer Lattice Dynamics for Vlasov-Poisson
Mocz, Philip
2016-01-01
We revisit the integer lattice (IL) method to numerically solve the Vlasov-Poisson equations, and show that a slight variant of the method is a very easy, viable, and efficient numerical approach to study the dynamics of self-gravitating, collisionless systems. The distribution function lives in a discretized lattice phase-space, and each time-step in the simulation corresponds to a simple permutation of the lattice sites. Hence, the method is Lagrangian, conservative, and fully time-reversible. IL complements other existing methods, such as N-body/particle mesh (computationally efficient, but affected by Monte-Carlo sampling noise and two-body relaxation) and finite volume (FV) direct integration schemes (expensive, accurate but diffusive). We also present improvements to the FV scheme, using a moving mesh approach inspired by IL, to reduce numerical diffusion and the time-step criterion. Being a direct integration scheme like FV, IL is memory limited (memory requirement for a full 3D problem scales as N^6, ...
A Novel High-Order, Entropy Stable, 3D AMR MHD Solver with Guaranteed Positive Pressure
Derigs, Dominik; Gassner, Gregor J; Walch, Stefanie
2016-01-01
We describe a high-order numerical magnetohydrodynamics (MHD) solver built upon a novel non-linear entropy stable numerical flux function that supports eight travelling wave solutions. By construction the solver conserves mass, momentum, and energy and is entropy stable. The method is designed to treat the divergence-free constraint on the magnetic field in a similar fashion to a hyperbolic divergence cleaning technique. The solver described herein is especially well-suited for flows involving strong discontinuities. Furthermore, we present a new formulation to guarantee positivity of the pressure. We present the underlying theory and implementation of the new solver into the multi-physics, multi-scale adaptive mesh refinement (AMR) simulation code $\\texttt{FLASH}$ (http://flash.uchicago.edu). The accuracy, robustness and computational efficiency is demonstrated with a number of tests, including comparisons to available MHD implementations in $\\texttt{FLASH}$.
Advanced field-solver techniques for RC extraction of integrated circuits
Yu, Wenjian
2014-01-01
Resistance and capacitance (RC) extraction is an essential step in modeling the interconnection wires and substrate coupling effect in nanometer-technology integrated circuits (IC). The field-solver techniques for RC extraction guarantee the accuracy of modeling, and are becoming increasingly important in meeting the demand for accurate modeling and simulation of VLSI designs. Advanced Field-Solver Techniques for RC Extraction of Integrated Circuits presents a systematic introduction to, and treatment of, the key field-solver methods for RC extraction of VLSI interconnects and substrate coupling in mixed-signal ICs. Various field-solver techniques are explained in detail, with real-world examples to illustrate the advantages and disadvantages of each algorithm. This book will benefit graduate students and researchers in the field of electrical and computer engineering, as well as engineers working in the IC design and design automation industries. Dr. Wenjian Yu is an Associate Professor at the Department of ...
A novel high-order, entropy stable, 3D AMR MHD solver with guaranteed positive pressure
Derigs, Dominik; Winters, Andrew R.; Gassner, Gregor J.; Walch, Stefanie
2016-07-01
We describe a high-order numerical magnetohydrodynamics (MHD) solver built upon a novel non-linear entropy stable numerical flux function that supports eight travelling wave solutions. By construction the solver conserves mass, momentum, and energy and is entropy stable. The method is designed to treat the divergence-free constraint on the magnetic field in a similar fashion to a hyperbolic divergence cleaning technique. The solver described herein is especially well-suited for flows involving strong discontinuities. Furthermore, we present a new formulation to guarantee positivity of the pressure. We present the underlying theory and implementation of the new solver into the multi-physics, multi-scale adaptive mesh refinement (AMR) simulation code FLASH (http://flash.uchicago.edu)
Wavelet-based Poisson rate estimation using the Skellam distribution
Hirakawa, Keigo; Baqai, Farhan; Wolfe, Patrick J.
2009-02-01
Owing to the stochastic nature of discrete processes such as photon counts in imaging, real-world data measurements often exhibit heteroscedastic behavior. In particular, time series components and other measurements may frequently be assumed to be non-iid Poisson random variables, whose rate parameter is proportional to the underlying signal of interest-witness literature in digital communications, signal processing, astronomy, and magnetic resonance imaging applications. In this work, we show that certain wavelet and filterbank transform coefficients corresponding to vector-valued measurements of this type are distributed as sums and differences of independent Poisson counts, taking the so-called Skellam distribution. While exact estimates rarely admit analytical forms, we present Skellam mean estimators under both frequentist and Bayes models, as well as computationally efficient approximations and shrinkage rules, that may be interpreted as Poisson rate estimation method performed in certain wavelet/filterbank transform domains. This indicates a promising potential approach for denoising of Poisson counts in the above-mentioned applications.
dftatom: A robust and general Schrödinger and Dirac solver for atomic structure calculations
Čertík, Ondřej; Pask, John E.; Vackář, Jiří
2013-07-01
A robust and general solver for the radial Schrödinger, Dirac, and Kohn-Sham equations is presented. The formulation admits general potentials and meshes: uniform, exponential, or other defined by nodal distribution and derivative functions. For a given mesh type, convergence can be controlled systematically by increasing the number of grid points. Radial integrations are carried out using a combination of asymptotic forms, Runge-Kutta, and implicit Adams methods. Eigenfunctions are determined by a combination of bisection and perturbation methods for robustness and speed. An outward Poisson integration is employed to increase accuracy in the core region, allowing absolute accuracies of 10-8 Hartree to be attained for total energies of heavy atoms such as uranium. Detailed convergence studies are presented and computational parameters are provided to achieve accuracies commonly required in practice. Comparisons to analytic and current-benchmark density-functional results for atomic number Z=1-92 are presented, verifying and providing a refinement to current benchmarks. An efficient, modular Fortran 95 implementation, dftatom, is provided as open source, including examples, tests, and wrappers for interface to other languages; wherein particular emphasis is placed on the independence (no global variables), reusability, and generality of the individual routines. Program summaryProgram title:dftatom Catalogue identifier: AEPA_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEPA_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: MIT license No. of lines in distributed program, including test data, etc.: 14122 No. of bytes in distributed program, including test data, etc.: 157453 Distribution format: tar.gz Programming language: Fortran 95 with interfaces to Python and C. Computer: Any computer with a Fortran 95 compiler. Operating system: Any OS with a Fortran 95 compiler. RAM: 500 MB
Noncommutative Poisson brackets on Loday algebras and related deformation quantization
UCHINO, Kyousuke
2010-01-01
We introduce a new type of algebra which is called a Loday-Poisson algebra. The class of the Loday-Poisson algebras forms a special subclass of Aguiar's dual-prePoisson algebas (\\cite{A}). We will prove that there exists a unique Loday-Poisson algebra over a Loday algebra, like the Lie-Poisson algebra over a Lie algebra. Thus, Loday-Poisson algebras are regarded as noncommutative analogues of Lie-Poisson algebras. We will show that the polinomial Loday-Poisson algebra is deformation quantizable and that the associated quantum algebra is Loday's associative dialgebra.
IGA-ADS: Isogeometric analysis FEM using ADS solver
Łoś, Marcin M.; Woźniak, Maciej; Paszyński, Maciej; Lenharth, Andrew; Hassaan, Muhamm Amber; Pingali, Keshav
2017-08-01
In this paper we present a fast explicit solver for solution of non-stationary problems using L2 projections with isogeometric finite element method. The solver has been implemented within GALOIS framework. It enables parallel multi-core simulations of different time-dependent problems, in 1D, 2D, or 3D. We have prepared the solver framework in a way that enables direct implementation of the selected PDE and corresponding boundary conditions. In this paper we describe the installation, implementation of exemplary three PDEs, and execution of the simulations on multi-core Linux cluster nodes. We consider three case studies, including heat transfer, linear elasticity, as well as non-linear flow in heterogeneous media. The presented package generates output suitable for interfacing with Gnuplot and ParaView visualization software. The exemplary simulations show near perfect scalability on Gilbert shared-memory node with four Intel® Xeon® CPU E7-4860 processors, each possessing 10 physical cores (for a total of 40 cores).
Newton-Krylov-BDDC solvers for nonlinear cardiac mechanics
Pavarino, L.F.
2015-07-18
The aim of this work is to design and study a Balancing Domain Decomposition by Constraints (BDDC) solver for the nonlinear elasticity system modeling the mechanical deformation of cardiac tissue. The contraction–relaxation process in the myocardium is induced by the generation and spread of the bioelectrical excitation throughout the tissue and it is mathematically described by the coupling of cardiac electro-mechanical models consisting of systems of partial and ordinary differential equations. In this study, the discretization of the electro-mechanical models is performed by Q1 finite elements in space and semi-implicit finite difference schemes in time, leading to the solution of a large-scale linear system for the bioelectrical potentials and a nonlinear system for the mechanical deformation at each time step of the simulation. The parallel mechanical solver proposed in this paper consists in solving the nonlinear system with a Newton-Krylov-BDDC method, based on the parallel solution of local mechanical problems and a coarse problem for the so-called primal unknowns. Three-dimensional parallel numerical tests on different machines show that the proposed parallel solver is scalable in the number of subdomains, quasi-optimal in the ratio of subdomain to mesh sizes, and robust with respect to tissue anisotropy.
Vlasov-Poisson in 1D: waterbags
Colombi, Stéphane
2014-01-01
We revisit in one dimension the waterbag method to solve numerically Vlasov-Poisson equations. In this approach, the phase-space distribution function $f(x,v)$ is initially sampled by an ensemble of patches, the waterbags, where $f$ is assumed to be constant. As a consequence of Liouville theorem it is only needed to follow the evolution of the border of these waterbags, which can be done by employing an orientated, self-adaptive polygon tracing isocontours of $f$. This method, which is entropy conserving in essence, is very accurate and can trace very well non linear instabilities as illustrated by specific examples. As an application of the method, we generate an ensemble of single waterbag simulations with decreasing thickness, to perform a convergence study to the cold case. Our measurements show that the system relaxes to a steady state where the gravitational potential profile is a power-law of slowly varying index $\\beta$, with $\\beta$ close to $3/2$ as found in the literature. However, detailed analys...
Negative Poisson's Ratio in Modern Functional Materials.
Huang, Chuanwei; Chen, Lang
2016-10-01
Materials with negative Poisson's ratio attract considerable attention due to their underlying intriguing physical properties and numerous promising applications, particularly in stringent environments such as aerospace and defense areas, because of their unconventional mechanical enhancements. Recent progress in materials with a negative Poisson's ratio are reviewed here, with the current state of research regarding both theory and experiment. The inter-relationship between the underlying structure and a negative Poisson's ratio is discussed in functional materials, including macroscopic bulk, low-dimensional nanoscale particles, films, sheets, or tubes. The coexistence and correlations with other negative indexes (such as negative compressibility and negative thermal expansion) are also addressed. Finally, open questions and future research opportunities are proposed for functional materials with negative Poisson's ratios.
Poisson point processes imaging, tracking, and sensing
Streit, Roy L
2010-01-01
This overview of non-homogeneous and multidimensional Poisson point processes and their applications features mathematical tools and applications from emission- and transmission-computed tomography to multiple target tracking and distributed sensor detection.
Some Characterizations of Mixed Poisson Processes
Lyberopoulos, D P
2011-01-01
A characterization of mixed Poisson processes in terms of disintegrations is proven. As a consequence some further characterizations of such processes via claim interarrival processes, martingales and claim measures are obtained.
A Novel Preconditioner for Electromagnetic Solvers
Institute of Scientific and Technical Information of China (English)
无
2006-01-01
A novel preconditioning scheme for electromagnetic scattering solver is presented to improve the convergence of the iterative solver for the linear system resulted by the integral quations. Its kernel idea is the selection of the main contribution of the matrix elements, which affect the matrix condition number the most. We employ the important part similar to the near-field to build the preconditioning matrix. A parameter delta is given to control the balance between the computational expense to get the preconditioner and the effectiveness of the preconditioner. A practical selection of the control parameter delta of the preconditioner is discussed, which indicates the preconditioner is effective in conjunction with a BiCGstab(l) solver.
New iterative solvers for the NAG Libraries
Energy Technology Data Exchange (ETDEWEB)
Salvini, S.; Shaw, G. [Numerical Algorithms Group Ltd., Oxford (United Kingdom)
1996-12-31
The purpose of this paper is to introduce the work which has been carried out at NAG Ltd to update the iterative solvers for sparse systems of linear equations, both symmetric and unsymmetric, in the NAG Fortran 77 Library. Our current plans to extend this work and include it in our other numerical libraries in our range are also briefly mentioned. We have added to the Library the new Chapter F11, entirely dedicated to sparse linear algebra. At Mark 17, the F11 Chapter includes sparse iterative solvers, preconditioners, utilities and black-box routines for sparse symmetric (both positive-definite and indefinite) linear systems. Mark 18 will add solvers, preconditioners, utilities and black-boxes for sparse unsymmetric systems: the development of these has already been completed.
Modeling Events with Cascades of Poisson Processes
Simma, Aleksandr
2012-01-01
We present a probabilistic model of events in continuous time in which each event triggers a Poisson process of successor events. The ensemble of observed events is thereby modeled as a superposition of Poisson processes. Efficient inference is feasible under this model with an EM algorithm. Moreover, the EM algorithm can be implemented as a distributed algorithm, permitting the model to be applied to very large datasets. We apply these techniques to the modeling of Twitter messages and the revision history of Wikipedia.
Poisson׳s ratio of arterial wall - Inconsistency of constitutive models with experimental data.
Skacel, Pavel; Bursa, Jiri
2016-02-01
Poisson׳s ratio of fibrous soft tissues is analyzed in this paper on the basis of constitutive models and experimental data. Three different up-to-date constitutive models accounting for the dispersion of fibre orientations are analyzed. Their predictions of the anisotropic Poisson׳s ratios are investigated under finite strain conditions together with the effects of specific orientation distribution functions and of other parameters. The applied constitutive models predict the tendency to lower (or even negative) out-of-plane Poisson׳s ratio. New experimental data of porcine arterial layer under uniaxial tension in orthogonal directions are also presented and compared with the theoretical predictions and other literature data. The results point out the typical features of recent constitutive models with fibres concentrated in circumferential-axial plane of arterial layers and their potential inconsistence with some experimental data. The volumetric (in)compressibility of arterial tissues is also discussed as an eventual and significant factor influencing this inconsistency.
GEMPIC: Geometric ElectroMagnetic Particle-In-Cell Methods
Kraus, Michael; Morrison, Philip J; Sonnendrücker, Eric
2016-01-01
We present a novel framework for Finite Element Particle-in-Cell methods based on the discretization of the underlying Hamiltonian structure of the Vlasov-Maxwell system. We derive a semi-discrete Poisson bracket, which satisfies the Jacobi identity , and apply Hamiltonian splitting schemes for time integration. Techniques from Finite Element Exterior Calculus ensure conservation of the divergence of the magnetic field and Gauss' law as well as stability of the field solver. The resulting methods are gauge-invariant, feature exact charge conservation and show excellent long-time energy and momentum behavior.
Modification of Ordinary Differential Equations MATLAB Solver
Directory of Open Access Journals (Sweden)
E. Cocherova
2003-12-01
Full Text Available Various linear or nonlinear electronic circuits can be described bythe set of ordinary differential equations (ODEs. The ordinarydifferential equations can be solved in the MATLAB environment inanalytical (symbolic toolbox or numerical way. The set of nonlinearODEs with high complexity can be usually solved only by use ofnumerical integrator (solver. The modification of ode23 MATLABnumerical solver has been suggested in this article for the applicationin solution of some special cases of ODEs. The main feature of thismodification is that the solution is found at every prescribed point,in which the special behavior of system is anticipated. Theextrapolation of solution is not allowed in those points.
Differential expression analysis for RNAseq using Poisson mixed models.
Sun, Shiquan; Hood, Michelle; Scott, Laura; Peng, Qinke; Mukherjee, Sayan; Tung, Jenny; Zhou, Xiang
2017-06-20
Identifying differentially expressed (DE) genes from RNA sequencing (RNAseq) studies is among the most common analyses in genomics. However, RNAseq DE analysis presents several statistical and computational challenges, including over-dispersed read counts and, in some settings, sample non-independence. Previous count-based methods rely on simple hierarchical Poisson models (e.g. negative binomial) to model independent over-dispersion, but do not account for sample non-independence due to relatedness, population structure and/or hidden confounders. Here, we present a Poisson mixed model with two random effects terms that account for both independent over-dispersion and sample non-independence. We also develop a scalable sampling-based inference algorithm using a latent variable representation of the Poisson distribution. With simulations, we show that our method properly controls for type I error and is generally more powerful than other widely used approaches, except in small samples (n <15) with other unfavorable properties (e.g. small effect sizes). We also apply our method to three real datasets that contain related individuals, population stratification or hidden confounders. Our results show that our method increases power in all three data compared to other approaches, though the power gain is smallest in the smallest sample (n = 6). Our method is implemented in MACAU, freely available at www.xzlab.org/software.html. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.
Yosui, Kuniaki; Iwashita, Takeshi; Mori, Michiya; Kobayashi, Eiichi
Finite element analyses of electromagnetic field are commonly used for designing of various electronic devices. The scale of the analyses becomes larger and larger, therefore, a fast linear solver is needed to solve linear equations arising from the finite element method. Since a multigrid solver is the fastest linear solver for these problems, parallelization of a multigrid solver is a quite useful approach. From the viewpoint of industrial applications, an effective usage of a small-scale PC cluster is important due to initial cost for introducing parallel computers. In this paper, a distributed parallel multigrid solver for a small-scale PC cluster is developed. In high frequency electromagnetic field analyses, a special block Gauss-Seidel smoother is used for the multigrid solver instead of general smoothers such as Gauss-Seidel smoother or Jacobi smoother in order to improve a convergence rate. The block multicolor ordering technique is applied to parallelize the smoother. A numerical exsample shows that a 3.7-fold speed-up in computational time and a 3.0-fold increase in the scale of the analysis were attained when the number of CPU was increased from one to five.
Energy Technology Data Exchange (ETDEWEB)
Abu Saleem, Rabie A., E-mail: raabusaleem@just.edu.jo [Nuclear Engineering Department, Jordan University of Science and Technology, P.O. Box 3030, Irbid 22110 (Jordan); Kozlowski, Tomasz, E-mail: txk@illinois.edu [Department of Nuclear, Plasma and Radiological Engineering, University of Illinois at Urbana-Champaign, 216 Talbot Laboratory, 104 S. Wright St., Urbana, IL 61801 (United States); Shrestha, Rijan, E-mail: rijan.shrestha@intel.com [Portland Technology Development, Intel Corporation, 2501 NW 229th Ave Hillsboro OR 97124 (United States)
2016-05-15
Highlights: • The two-fluid model and the challenges associated with its numerical modeling are investigated. • A high-order solver based on flux limiter schemes and the theta method was developed. • The solver was compared to existing thermal hydraulics codes used in nuclear industry. • The solver was shown to handle fast transients with discontinuities and phase change. - Abstract: Finite volume techniques with staggered mesh are used to develop a new numerical solver for the one-dimensional two-phase two-fluid model using a high-resolution, Total Variation Diminishing (TVD) scheme. The solver is implemented to analyze numerical benchmark problems for verification and testing its abilities to handle discontinuities and fast transients with phase change. Convergence rates are investigated by comparing numerical results to analytical solutions available in literature for the case of the faucet flow problem. The solver based on a new TVD scheme is shown to exhibit higher-order of accuracy compared to other numerical schemes. Mass errors are also examined when phase change occurs for the shock tube problem, and compared to those of the 1st-order upwind scheme implemented in the nuclear thermal-hydraulics code TRACE. The solver is shown to exhibit numerical stability when applied to problems with discontinuous solutions and results of the new solver are free of spurious oscillations.
WAKES: Wavelet Adaptive Kinetic Evolution Solvers
Mardirian, Marine; Afeyan, Bedros; Larson, David
2016-10-01
We are developing a general capability to adaptively solve phase space evolution equations mixing particle and continuum techniques in an adaptive manner. The multi-scale approach is achieved using wavelet decompositions which allow phase space density estimation to occur with scale dependent increased accuracy and variable time stepping. Possible improvements on the SFK method of Larson are discussed, including the use of multiresolution analysis based Richardson-Lucy Iteration, adaptive step size control in explicit vs implicit approaches. Examples will be shown with KEEN waves and KEEPN (Kinetic Electrostatic Electron Positron Nonlinear) waves, which are the pair plasma generalization of the former, and have a much richer span of dynamical behavior. WAKES techniques are well suited for the study of driven and released nonlinear, non-stationary, self-organized structures in phase space which have no fluid, limit nor a linear limit, and yet remain undamped and coherent well past the drive period. The work reported here is based on the Vlasov-Poisson model of plasma dynamics. Work supported by a Grant from the AFOSR.
A modified global Newton solver for viscous-plastic sea ice models
Mehlmann, C.; Richter, T.
2017-08-01
We present and analyze a modified Newton solver, the so called operator-related damped Jacobian method, with a line search globalization for the solution of the strongly nonlinear momentum equation in a viscous-plastic (VP) sea ice model.Due to large variations in the viscosities, the resulting nonlinear problem is very difficult to solve. The development of fast, robust and converging solvers is subject to present research. There are mainly three approaches for solving the nonlinear momentum equation of the VP model, a fixed-point method denoted as Picard solver, an inexact Newton method and a subcycling procedure based on an elastic-viscous-plastic model approximation. All methods tend to have problems on fine meshes by sharp structures in the solution. Convergence rates deteriorate such that either too many iterations are required to reach sufficient accuracy or convergence is not obtained at all.To improve robustness globalization and acceleration approaches, which increase the area of fast convergence, are needed. We develop an implicit scheme with improved convergence properties by combining an inexact Newton method with a Picard solver. We derive the full Jacobian of the viscous-plastic sea ice momentum equation and show that the Jacobian is a positive definite matrix, guaranteeing global convergence of a properly damped Newton iteration. We compare our modified Newton solver with line search damping to an inexact Newton method with established globalization and acceleration techniques. We present a test case that shows improved robustness of our new approach, in particular on fine meshes.
Histogram bin width selection for time-dependent Poisson processes
Energy Technology Data Exchange (ETDEWEB)
Koyama, Shinsuke; Shinomoto, Shigeru [Department of Physics, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502 (Japan)
2004-07-23
In constructing a time histogram of the event sequences derived from a nonstationary point process, we wish to determine the bin width such that the mean squared error of the histogram from the underlying rate of occurrence is minimized. We find that the optimal bin widths obtained for a doubly stochastic Poisson process and a sinusoidally regulated Poisson process exhibit different scaling relations with respect to the number of sequences, time scale and amplitude of rate modulation, but both diverge under similar parametric conditions. This implies that under these conditions, no determination of the time-dependent rate can be made. We also apply the kernel method to these point processes, and find that the optimal kernels do not exhibit any critical phenomena, unlike the time histogram method.
Histogram bin width selection for time-dependent Poisson processes
Koyama, Shinsuke; Shinomoto, Shigeru
2004-07-01
In constructing a time histogram of the event sequences derived from a nonstationary point process, we wish to determine the bin width such that the mean squared error of the histogram from the underlying rate of occurrence is minimized. We find that the optimal bin widths obtained for a doubly stochastic Poisson process and a sinusoidally regulated Poisson process exhibit different scaling relations with respect to the number of sequences, time scale and amplitude of rate modulation, but both diverge under similar parametric conditions. This implies that under these conditions, no determination of the time-dependent rate can be made. We also apply the kernel method to these point processes, and find that the optimal kernels do not exhibit any critical phenomena, unlike the time histogram method.
Advances in the hydrodynamics solver of CO5BOLD
Freytag, Bernd
Many features of the Roe solver used in the hydrodynamics module of CO5BOLD have recently been added or overhauled, including the reconstruction methods (by adding the new second-order ``Frankenstein's method''), the treatment of transversal velocities, energy-flux averaging and entropy-wave treatment at small Mach numbers, the CTU scheme to combine the one-dimensional fluxes, and additional safety measures. All this results in a significantly better behavior at low Mach number flows, and an improved stability at larger Mach numbers requiring less (or no) additional tensor viscosity, which then leads to a noticeable increase in effective resolution.
DEFF Research Database (Denmark)
Bjørner, Nikolaj; Dung, Phan Anh; Fleckenstein, Lars
2015-01-01
vZ is a part of the SMT solver Z3. It allows users to pose and solve optimization problems modulo theories. Many SMT applications use models to provide satisfying assignments, and a growing number of these build on top of Z3 to get optimal assignments with respect to objective functions. vZ provi...
Causal Poisson bracket via deformation quantization
Berra-Montiel, Jasel; Molgado, Alberto; Palacios-García, César D.
2016-06-01
Starting with the well-defined product of quantum fields at two spacetime points, we explore an associated Poisson structure for classical field theories within the deformation quantization formalism. We realize that the induced star-product is naturally related to the standard Moyal product through an appropriate causal Green’s functions connecting points in the space of classical solutions to the equations of motion. Our results resemble the Peierls-DeWitt bracket that has been analyzed in the multisymplectic context. Once our star-product is defined, we are able to apply the Wigner-Weyl map in order to introduce a generalized version of Wick’s theorem. Finally, we include some examples to explicitly test our method: the real scalar field, the bosonic string and a physically motivated nonlinear particle model. For the field theoretic models, we have encountered causal generalizations of the creation/annihilation relations, and also a causal generalization of the Virasoro algebra for the bosonic string. For the nonlinear particle case, we use the approximate solution in terms of the Green’s function, in order to construct a well-behaved causal bracket.
Events in time: Basic analysis of Poisson data
Energy Technology Data Exchange (ETDEWEB)
Engelhardt, M.E.
1994-09-01
The report presents basic statistical methods for analyzing Poisson data, such as the member of events in some period of time. It gives point estimates, confidence intervals, and Bayesian intervals for the rate of occurrence per unit of time. It shows how to compare subsets of the data, both graphically and by statistical tests, and how to look for trends in time. It presents a compound model when the rate of occurrence varies randomly. Examples and SAS programs are given.
Statistical Tests of the PTHA Poisson Assumption for Submarine Landslides
Geist, E. L.; Chaytor, J. D.; Parsons, T.; Ten Brink, U. S.
2012-12-01
We demonstrate that a sequence of dated mass transport deposits (MTDs) can provide information to statistically test whether or not submarine landslides associated with these deposits conform to a Poisson model of occurrence. Probabilistic tsunami hazard analysis (PTHA) most often assumes Poissonian occurrence for all sources, with an exponential distribution of return times. Using dates that define the bounds of individual MTDs, we first describe likelihood and Monte Carlo methods of parameter estimation for a suite of candidate occurrence models (Poisson, lognormal, gamma, Brownian Passage Time). In addition to age-dating uncertainty, both methods incorporate uncertainty caused by the open time intervals: i.e., before the first and after the last event to the present. Accounting for these open intervals is critical when there are a small number of observed events. The optimal occurrence model is selected according to both the Akaike Information Criteria (AIC) and Akaike's Bayesian Information Criterion (ABIC). In addition, the likelihood ratio test can be performed on occurrence models from the same family: e.g., the gamma model relative to the exponential model of return time distribution. Parameter estimation, model selection, and hypothesis testing are performed on data from two IODP holes in the northern Gulf of Mexico that penetrated a total of 14 MTDs, some of which are correlated between the two holes. Each of these events has been assigned an age based on microfossil zonations and magnetostratigraphic datums. Results from these sites indicate that the Poisson assumption is likely valid. However, parameter estimation results using the likelihood method for one of the sites suggest that the events may have occurred quasi-periodically. Methods developed in this study provide tools with which one can determine both the rate of occurrence and the statistical validity of the Poisson assumption when submarine landslides are included in PTHA.
An advanced implicit solver for MHD
Udrea, Bogdan
A new implicit algorithm has been developed for the solution of the time-dependent, viscous and resistive single fluid magnetohydrodynamic (MHD) equations. The algorithm is based on an approximate Riemann solver for the hyperbolic fluxes and central differencing applied on a staggered grid for the parabolic fluxes. The algorithm employs a locally aligned coordinate system that allows the solution to the Riemann problems to be solved in a natural direction, normal to cell interfaces. The result is an original scheme that is robust and reduces the complexity of the flux formulas. The evaluation of the parabolic fluxes is also implemented using a locally aligned coordinate system, this time on the staggered grid. The implicit formulation employed by WARP3 is a two level scheme that was applied for the first time to the single fluid MHD model. The flux Jacobians that appear in the implicit scheme are evaluated numerically. The linear system that results from the implicit discretization is solved using a robust symmetric Gauss-Seidel method. The code has an explicit mode capability so that implementation and test of new algorithms or new physics can be performed in this simpler mode. Last but not least the code was designed and written to run on parallel computers so that complex, high resolution runs can be per formed in hours rather than days. The code has been benchmarked against analytical and experimental gas dynamics and MHD results. The benchmarks consisted of one-dimensional Riemann problems and diffusion dominated problems, two-dimensional supersonic flow over a wedge, axisymmetric magnetoplasmadynamic (MPD) thruster simulation and three-dimensional supersonic flow over intersecting wedges and spheromak stability simulation. The code has been proven to be robust and the results of the simulations showed excellent agreement with analytical and experimental results. Parallel performance studies showed that the code performs as expected when run on parallel
Probability Measure of Navigation pattern predition using Poisson Distribution Analysis
Directory of Open Access Journals (Sweden)
Dr.V.Valli Mayil
2012-06-01
Full Text Available The World Wide Web has become one of the most important media to store, share and distribute information. The rapid expansion of the web has provided a great opportunity to study user and system behavior by exploring web access logs. Web Usage Mining is the application of data mining techniques to large web data repositories in order to extract usage patterns. Every web server keeps a log of all transactions between the server and the clients. The log data which are collected by web servers contains information about every click of user to the web documents of the site. The useful log information needs to be analyzed and interpreted in order to obtainknowledge about actual user preferences in accessing web pages. In recent years several methods have been proposed for mining web log data. This paper addresses the statistical method of Poisson distribution analysis to find out the higher probability session sequences which is then used to test the web application performance.The analysis of large volumes of click stream data demands the employment of data mining methods. Conducting data mining on logs of web servers involves the determination of frequently occurring access sequences. A statistical poisson distribution shows the frequency probability of specific events when the average probability of a single occurrence is known. The Poisson distribution is a discrete function wich is used in this paper to find out the probability frequency of particular page is visited by the user.
Parallel Symmetric Eigenvalue Problem Solvers
2015-05-01
Jacobi - Davidson, and FEAST), establishing the competitiveness of my methods . Graduate School Form 30 Updated 1/15/2015 PURDUE UNIVERSITY GRADUATE...LOBPCG, Jacobi -Davidson, and FEAST), establishing the competitiveness of our methods . 1 1 INTRODUCTION Many applications in science and engineering give...though SLEPc’s Jacobi -Davidson is the fastest method ; it is roughly twice as fast as TraceMin-Davidson. However, since it uses a block size 90 of 1
Joe, Harry; Zhu, Rong
2005-04-01
We prove that the generalized Poisson distribution GP(theta, eta) (eta > or = 0) is a mixture of Poisson distributions; this is a new property for a distribution which is the topic of the book by Consul (1989). Because we find that the fits to count data of the generalized Poisson and negative binomial distributions are often similar, to understand their differences, we compare the probability mass functions and skewnesses of the generalized Poisson and negative binomial distributions with the first two moments fixed. They have slight differences in many situations, but their zero-inflated distributions, with masses at zero, means and variances fixed, can differ more. These probabilistic comparisons are helpful in selecting a better fitting distribution for modelling count data with long right tails. Through a real example of count data with large zero fraction, we illustrate how the generalized Poisson and negative binomial distributions as well as their zero-inflated distributions can be discriminated.
A Hybrid Riemann Solver for Large Hyperbolic Systems of Conservation Laws
Schmidtmann, Birte
2016-01-01
We are interested in the numerical solution of large systems of hyperbolic conservation laws or systems in which the characteristic decomposition is expensive to compute. Solving such equations using finite volumes or Discontinuous Galerkin requires a numerical flux function which solves local Riemann problems at cell interfaces. There are various methods to express the numerical flux function. On the one end, there is the robust but very diffusive Lax-Friedrichs solver; on the other end the upwind Godunov solver which respects all resulting waves. The drawback of the latter method is the costly computation of the eigensystem. This work presents a family of simple first order Riemann solvers, named HLLX$\\omega$, which avoid solving the eigensystem. The new method reproduces all waves of the system with less dissipation than other solvers with similar input and effort, such as HLL and FORCE. The family of Riemann solvers can be seen as an extension or generalization of the methods introduced by Degond et al. \\...
Poisson-weighted Lindley distribution and its application on insurance claim data
Manesh, Somayeh Nik; Hamzah, Nor Aishah; Zamani, Hossein
2014-07-01
This paper introduces a new two-parameter mixed Poisson distribution, namely the Poisson-weighted Lindley (P-WL), which is obtained by mixing the Poisson with a new class of weighted Lindley distributions. The closed form, the moment generating function and the probability generating function are derived. The parameter estimations methods of moments and the maximum likelihood procedure are provided. Some simulation studies are conducted to investigate the performance of P-WL distribution. In addition, the compound P-WL distribution is derived and some applications to insurance area based on observations of the number of claims and on observations of the total amount of claims incurred will be illustrated.
Mohr, M; Vanrumste, B
2003-01-01
Model-based reconstruction of electrical brain activity from electro-encephalographic measurements is of growing importance in neurology and neurosurgery. Algorithms for this task involve the solution of a 3D Poisson problem on a realistic head geometry obtained from medical imaging. In the model, several compartments with different conductivities have to be distinguished, leading to a problem with jumping coefficients. Furthermore, the Poisson problem needs to be solved repeatedly for different source contributions. Thus efficient solvers for this subtask are required. Experience with different iterative solvers is reported, i.e. successive over-relaxation, (preconditioned) conjugate gradients and algebraic multigrid, for a discretisation based on cell-centred finite differences. It was found that: first, the multigrid-based solver performed the task 1.8-3.5 times faster, depending on the platform, than the second-best contender; secondly, there was no need to introduce a reference potential that forced a unique solution; and, thirdly, neither the grid- nor matrix-based implementation of the solvers consistently gave a smaller run time.
Fast Multipole-Based Elliptic PDE Solver and Preconditioner
Ibeid, Huda
2016-12-07
Exascale systems are predicted to have approximately one billion cores, assuming Gigahertz cores. Limitations on affordable network topologies for distributed memory systems of such massive scale bring new challenges to the currently dominant parallel programing model. Currently, there are many efforts to evaluate the hardware and software bottlenecks of exascale designs. It is therefore of interest to model application performance and to understand what changes need to be made to ensure extrapolated scalability. Fast multipole methods (FMM) were originally developed for accelerating N-body problems for particle-based methods in astrophysics and molecular dynamics. FMM is more than an N-body solver, however. Recent efforts to view the FMM as an elliptic PDE solver have opened the possibility to use it as a preconditioner for even a broader range of applications. In this thesis, we (i) discuss the challenges for FMM on current parallel computers and future exascale architectures, with a focus on inter-node communication, and develop a performance model that considers the communication patterns of the FMM for spatially quasi-uniform distributions, (ii) employ this performance model to guide performance and scaling improvement of FMM for all-atom molecular dynamics simulations of uniformly distributed particles, and (iii) demonstrate that, beyond its traditional use as a solver in problems for which explicit free-space kernel representations are available, the FMM has applicability as a preconditioner in finite domain elliptic boundary value problems, by equipping it with boundary integral capability for satisfying conditions at finite boundaries and by wrapping it in a Krylov method for extensibility to more general operators. Compared with multilevel methods, FMM is capable of comparable algebraic convergence rates down to the truncation error of the discretized PDE, and it has superior multicore and distributed memory scalability properties on commodity
A Poisson-based adaptive affinity propagation clustering for SAGE data.
Tang, DongMing; Zhu, QingXin; Yang, Fan
2010-02-01
Serial analysis of gene expression (SAGE) is a powerful tool to obtain gene expression profiles. Clustering analysis is a valuable technique for analyzing SAGE data. In this paper, we propose an adaptive clustering method for SAGE data analysis, namely, PoissonAPS. The method incorporates a novel clustering algorithm, Affinity Propagation (AP). While AP algorithm has demonstrated good performance on many different data sets, it also faces several limitations. PoissonAPS overcomes the limitations of AP using the clustering validation measure as a cost function of merging and splitting, and as a result, it can automatically cluster SAGE data without user-specified parameters. We evaluated PoissonAPS and compared its performance with other methods on several real life SAGE datasets. The experimental results show that PoissonAPS can produce meaningful and interpretable clusters for SAGE data.
Probability distributions for Poisson processes with pile-up
Sevilla, Diego J R
2013-01-01
In this paper, two parametric probability distributions capable to describe the statistics of X-ray photon detection by a CCD are presented. They are formulated from simple models that account for the pile-up phenomenon, in which two or more photons are counted as one. These models are based on the Poisson process, but they have an extra parameter which includes all the detailed mechanisms of the pile-up process that must be fitted to the data statistics simultaneously with the rate parameter. The new probability distributions, one for number of counts per time bins (Poisson-like), and the other for waiting times (exponential-like) are tested fitting them to statistics of real data, and between them through numerical simulations, and their results are analyzed and compared. The probability distributions presented here can be used as background statistical models to derive likelihood functions for statistical methods in signal analysis.
Compressed sensing performance bounds under Poisson noise
Raginsky, Maxim; Marcia, Roummel F; Willett, Rebecca M
2009-01-01
This paper describes performance bounds for compressed sensing (CS) where the underlying sparse or compressible (sparsely approximable) signal is a vector of nonnegative intensities whose measurements are corrupted by Poisson noise. In this setting, standard CS techniques cannot be applied directly for several reasons. First, the usual signal-independent and/or bounded noise models do not apply to Poisson noise, which is non-additive and signal-dependent. Second, the CS matrices typically considered are not feasible in real optical systems because they do not adhere to important constraints, such as nonnegativity and photon flux preservation. Third, the typical $\\ell_2$--$\\ell_1$ minimization leads to overfitting in the high-intensity regions and oversmoothing in the low-intensity areas. In this paper, we describe how a feasible positivity- and flux-preserving sensing matrix can be constructed, and then analyze the performance of a CS reconstruction approach for Poisson data that minimizes an objective functi...
The oligarchic structure of Paretian Poisson processes
Eliazar, I.; Klafter, J.
2008-08-01
Paretian Poisson processes are a mathematical model of random fractal populations governed by Paretian power law tail statistics, and connect together and underlie elemental issues in statistical physics. Considering Paretian Poisson processes to represent the wealth of individuals in human populations, we explore their oligarchic structure via the analysis of the following random ratios: the aggregate wealth of the oligarchs ranked from m+1 to n, measured relative to the wealth of the m-th oligarch (n> m). A mean analysis and a stochastic-limit analysis (as n→∞) of these ratios are conducted. We obtain closed-form results which turn out to be highly contingent on the fractal exponent of the Paretian Poisson process considered.
The Space-Fractional Poisson Process
Orsingher, Enzo
2011-01-01
In this paper we introduce the space-fractional Poisson process whose state probabilities $p_k^\\alpha(t)$, $t>0$, $\\alpha \\in (0,1]$, are governed by the equations $(\\mathrm d/\\mathrm dt)p_k(t) = -\\lambda^\\alpha (1-B)p_k^\\alpha(t)$, where $(1-B)^\\alpha$ is the fractional difference operator found in the study of time series analysis. We explicitly obtain the distributions $p_k^\\alpha(t)$, the probability generating functions $G_\\alpha(u,t)$, which are also expressed as distributions of the minimum of i.i.d.\\ uniform random variables. The comparison with the time-fractional Poisson process is investigated and finally, we arrive at the more general space-time fractional Poisson process of which we give the explicit distribution.
The Isolation Time of Poisson Brownian motions
Peres, Yuval; Stauffer, Alexandre
2011-01-01
Let the nodes of a Poisson point process move independently in $\\R^d$ according to Brownian motions. We study the isolation time for a target particle that is placed at the origin, namely how long it takes until there is no node of the Poisson point process within distance $r$ of it. We obtain asymptotics for the tail probability which are tight up to constants in the exponent in dimension $d\\geq 3$ and tight up to logarithmic factors in the exponent for dimensions $d=1,2$.
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M ARRIE KUNILASARI ELYNA
2012-09-01
Full Text Available Alpha In this study the used method of Geographically Weighted Poisson Regression (GWPR is a statistical method to analyze the data to account for spatial factors. GWPR is a local form of Poisson regression with respect to the location of the assumption that the data is Poisson distributed. There are factors that are used in this study is the number of health facilities and midwives, the average length of breastfeeding, the percentage of deliveries performed by non-medical assistance, and the average length of schooling a woman is married. The research results showed that factors significantly influence the number of infant deaths in sluruh districts / municipalities in Bali is the average length of schooling a woman is married. Then the results of hypothesis test obtained the results that there was no difference who significant between the regression model poisson and GWPR in Bali.
Integrating Standard Dependency Schemes in QCSP Solvers
Institute of Scientific and Technical Information of China (English)
Ji-Wei Jin; Fei-Fei Ma; Jian Zhang
2012-01-01
Quantified constraint satisfaction problems (QCSPs) are an extension to constraint satisfaction problems (CSPs) with both universal quantifiers and existential quantifiers.In this paper we apply variable ordering heuristics and integrate standard dependency schemes in QCSP solvers.The technique can help to decide the next variable to be assigned in QCSP solving.We also introduce a new factor into the variable ordering heuristics:a variable's dep is the number of variables depending on it.This factor represents the probability of getting more candidates for the next variable to be assigned.Experimental results show that variable ordering heuristics with standard dependency schemes and the new factor dep can improve the performance of QCSP solvers.
Brain, music, and non-Poisson renewal processes
Bianco, Simone; Ignaccolo, Massimiliano; Rider, Mark S.; Ross, Mary J.; Winsor, Phil; Grigolini, Paolo
2007-06-01
In this paper we show that both music composition and brain function, as revealed by the electroencephalogram (EEG) analysis, are renewal non-Poisson processes living in the nonergodic dominion. To reach this important conclusion we process the data with the minimum spanning tree method, so as to detect significant events, thereby building a sequence of times, which is the time series to analyze. Then we show that in both cases, EEG and music composition, these significant events are the signature of a non-Poisson renewal process. This conclusion is reached using a technique of statistical analysis recently developed by our group, the aging experiment (AE). First, we find that in both cases the distances between two consecutive events are described by nonexponential histograms, thereby proving the non-Poisson nature of these processes. The corresponding survival probabilities Ψ(t) are well fitted by stretched exponentials [ Ψ(t)∝exp (-(γt)α) , with 0.5music composition yield μmusic on the human brain.
Fork Tensor-Product States: Efficient Multiorbital Real-Time DMFT Solver
Bauernfeind, Daniel; Zingl, Manuel; Triebl, Robert; Aichhorn, Markus; Evertz, Hans Gerd
2017-07-01
We present a tensor network especially suited for multi-orbital Anderson impurity models and as an impurity solver for multi-orbital dynamical mean-field theory (DMFT). The solver works directly on the real-frequency axis and yields high spectral resolution at all frequencies. We use a large number (O (100 )) of bath sites and therefore achieve an accurate representation of the bath. The solver can treat full rotationally invariant interactions with reasonable numerical effort. We show the efficiency and accuracy of the method by a benchmark for the three-orbital test-bed material SrVO3 . There we observe multiplet structures in the high-energy spectrum, which are almost impossible to resolve by other multi-orbital methods. The resulting structure of the Hubbard bands can be described as a broadened atomic spectrum with rescaled interaction parameters. Additional features emerge when U is increased. Finally, we show that our solver can be applied even to models with five orbitals. This impurity solver offers a new route to the calculation of precise real-frequency spectral functions of correlated materials.
A class of CTRWs: Compound fractional Poisson processes
Scalas, Enrico
2011-01-01
This chapter is an attempt to present a mathematical theory of compound fractional Poisson processes. The chapter begins with the characterization of a well-known L\\'evy process: The compound Poisson process. The semi-Markov extension of the compound Poisson process naturally leads to the compound fractional Poisson process, where the Poisson counting process is replaced by the Mittag-Leffler counting process also known as fractional Poisson process. This process is no longer Markovian and L\\'evy. However, several analytical results are available and some of them are discussed here. The functional limit of the compound Poisson process is an $\\alpha$-stable L\\'evy process, whereas in the case of the compound fractional Poisson process, one gets an $\\alpha$-stable L\\'evy process subordinated to the fractional Poisson process.
Frickenhaus, Stephan; Hiller, Wolfgang; Best, Meike
The portable software FoSSI is introduced that—in combination with additional free solver software packages—allows for an efficient and scalable parallel solution of large sparse linear equations systems arising in finite element model codes. FoSSI is intended to support rapid model code development, completely hiding the complexity of the underlying solver packages. In particular, the model developer need not be an expert in parallelization and is yet free to switch between different solver packages by simple modifications of the interface call. FoSSI offers an efficient and easy, yet flexible interface to several parallel solvers, most of them available on the web, such as PETSC, AZTEC, MUMPS, PILUT and HYPRE. FoSSI makes use of the concept of handles for vectors, matrices, preconditioners and solvers, that is frequently used in solver libraries. Hence, FoSSI allows for a flexible treatment of several linear equations systems and associated preconditioners at the same time, even in parallel on separate MPI-communicators. The second special feature in FoSSI is the task specifier, being a combination of keywords, each configuring a certain phase in the solver setup. This enables the user to control a solver over one unique subroutine. Furthermore, FoSSI has rather similar features for all solvers, making a fast solver intercomparison or exchange an easy task. FoSSI is a community software, proven in an adaptive 2D-atmosphere model and a 3D-primitive equation ocean model, both formulated in finite elements. The present paper discusses perspectives of an OpenMP-implementation of parallel iterative solvers based on domain decomposition methods. This approach to OpenMP solvers is rather attractive, as the code for domain-local operations of factorization, preconditioning and matrix-vector product can be readily taken from a sequential implementation that is also suitable to be used in an MPI-variant. Code development in this direction is in an advanced state under
Chemical Mechanism Solvers in Air Quality Models
Directory of Open Access Journals (Sweden)
John C. Linford
2011-09-01
Full Text Available The solution of chemical kinetics is one of the most computationally intensivetasks in atmospheric chemical transport simulations. Due to the stiff nature of the system,implicit time stepping algorithms which repeatedly solve linear systems of equations arenecessary. This paper reviews the issues and challenges associated with the construction ofefficient chemical solvers, discusses several families of algorithms, presents strategies forincreasing computational efficiency, and gives insight into implementing chemical solverson accelerated computer architectures.
Institute of Scientific and Technical Information of China (English)
无
2010-01-01
Saddlepoint approximations for the studentized compound Poisson sums with no moment conditions in audit sampling are derived. This result not only provides a very accurate approximation for studentized compound Poisson sums, but also can be applied much more widely in statistical inference of the error amount in an audit population of accounts to check the validity of financial statements of a firm. Some numerical illustrations and comparison with the normal approximation method are presented.
Affine Poisson Groups and WZW Model
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Ctirad Klimcík
2008-01-01
Full Text Available We give a detailed description of a dynamical system which enjoys a Poisson-Lie symmetry with two non-isomorphic dual groups. The system is obtained by taking the q → ∞ limit of the q-deformed WZW model and the understanding of its symmetry structure results in uncovering an interesting duality of its exchange relations.
Transportation inequalities: From Poisson to Gibbs measures
Ma, Yutao; Wang, Xinyu; Wu, Liming; 10.3150/00-BEJ268
2011-01-01
We establish an optimal transportation inequality for the Poisson measure on the configuration space. Furthermore, under the Dobrushin uniqueness condition, we obtain a sharp transportation inequality for the Gibbs measure on $\\mathbb{N}^{\\Lambda}$ or the continuum Gibbs measure on the configuration space.
Poisson boundaries over locally compact quantum groups
Kalantar, Mehrdad; Ruan, Zhong-Jin
2011-01-01
We present versions of several classical results on harmonic functions and Poisson boundaries in the setting of locally compact quantum groups $\\mathbb{G}$. In particular, the Choquet-Deny theorem holds for compact quantum groups; also, the result of Kaimanovich-Vershik and Rosenblatt, which characterizes group amenability in terms of harmonic functions, answering a conjecture by Furstenberg, admits a non-commutative analogue in the separable case. We also explore the relation between classical and quantum Poisson boundaries by investigating the spectrum of the quantum group. We apply this machinery to find a concrete realization of the Poisson boundaries of the compact quantum group $SU_{q}(2)$ arising from measures on its spectrum. We further show that the Poisson boundary of the natural Markov operator extension of the convolution action of a quantum probability measure $\\mu$ on $L_\\infty(\\mathbb{G})$ to $B(L_2(\\mathbb{G}))$, as introduced and studied - for general completely bounded multipliers on $L_1(\\m...
Continental moisture recycling as a Poisson process
Directory of Open Access Journals (Sweden)
H. F. Goessling
2013-04-01
Full Text Available On their journey across large land masses, water molecules experience a number of precipitation-evaporation cycles (recycling events. We derive analytically the frequency distributions of recycling events for the water molecules contained in a given air parcel. Given the validity of certain simplifying assumptions, continental moisture recycling is shown to develop either into a Poisson distribution or a geometric distribution. We distinguish two cases: in case (A recycling events are counted since the water molecules were last advected across the ocean-land boundary. In case (B recycling events are counted since the water molecules were last evaporated from the ocean. For case B we show by means of a simple scale analysis that, given the conditions on Earth, realistic frequency distributions may be regarded as a mixture of a Poisson distribution and a geometric distribution. By contrast, in case A the Poisson distribution generally appears as a reasonable approximation. This conclusion is consistent with the simulation results of an earlier study where an atmospheric general circulation model equipped with water vapor tracers was used. Our results demonstrate that continental moisture recycling can be interpreted as a Poisson process.
Bayesian credible interval construction for Poisson statistics
Institute of Scientific and Technical Information of China (English)
ZHU Yong-Sheng
2008-01-01
The construction of the Bayesian credible (confidence) interval for a Poisson observable including both the signal and background with and without systematic uncertainties is presented.Introducing the conditional probability satisfying the requirement of the background not larger than the observed events to construct the Bayesian credible interval is also discussed.A Fortran routine,BPOCI,has been developed to implement the calculation.
Thinning spatial point processes into Poisson processes
DEFF Research Database (Denmark)
Møller, Jesper; Schoenberg, Frederic Paik
2010-01-01
are identified, and where we simulate backwards and forwards in order to obtain the thinned process. In the case of a Cox process, a simple independent thinning technique is proposed. In both cases, the thinning results in a Poisson process if and only if the true Papangelou conditional intensity is used, and...
Thinning spatial point processes into Poisson processes
DEFF Research Database (Denmark)
Møller, Jesper; Schoenberg, Frederic Paik
, and where one simulates backwards and forwards in order to obtain the thinned process. In the case of a Cox process, a simple independent thinning technique is proposed. In both cases, the thinning results in a Poisson process if and only if the true Papangelou conditional intensity is used, and thus can...
Evolutionary inference via the Poisson Indel Process.
Bouchard-Côté, Alexandre; Jordan, Michael I
2013-01-22
We address the problem of the joint statistical inference of phylogenetic trees and multiple sequence alignments from unaligned molecular sequences. This problem is generally formulated in terms of string-valued evolutionary processes along the branches of a phylogenetic tree. The classic evolutionary process, the TKF91 model [Thorne JL, Kishino H, Felsenstein J (1991) J Mol Evol 33(2):114-124] is a continuous-time Markov chain model composed of insertion, deletion, and substitution events. Unfortunately, this model gives rise to an intractable computational problem: The computation of the marginal likelihood under the TKF91 model is exponential in the number of taxa. In this work, we present a stochastic process, the Poisson Indel Process (PIP), in which the complexity of this computation is reduced to linear. The Poisson Indel Process is closely related to the TKF91 model, differing only in its treatment of insertions, but it has a global characterization as a Poisson process on the phylogeny. Standard results for Poisson processes allow key computations to be decoupled, which yields the favorable computational profile of inference under the PIP model. We present illustrative experiments in which Bayesian inference under the PIP model is compared with separate inference of phylogenies and alignments.
Computation of confidence intervals for Poisson processes
Aguilar-Saavedra, J. A.
2000-07-01
We present an algorithm which allows a fast numerical computation of Feldman-Cousins confidence intervals for Poisson processes, even when the number of background events is relatively large. This algorithm incorporates an appropriate treatment of the singularities that arise as a consequence of the discreteness of the variable.
Computation of confidence intervals for Poisson processes
Aguilar-Saavedra, J A
2000-01-01
We present an algorithm which allows a fast numerical computation of Feldman-Cousins confidence intervals for Poisson processes, even when the number of background events is relatively large. This algorithm incorporates an appropriate treatment of the singularities that arise as a consequence of the discreteness of the variable.
Exit problems for oscillating compound Poisson process
Kadankova, Tetyana
2011-01-01
In this article we determine the Laplace transforms of the main boundary functionals of the oscillating compound Poisson process. These are the first passage time of the level, the joint distribution of the first exit time from the interval and the value of the overshoot through the boundary. Under certain conditions we establish the asymptotic behaviour of the mentioned functionals.
An accurate predictor-corrector HOC solver for the two dimensional Riemann problem of gas dynamics
Gogoi, Bidyut B.
2016-10-01
The work in the present manuscript is concerned with the simulation of twodimensional (2D) Riemann problem of gas dynamics. We extend our recently developed higher order compact (HOC) method from one-dimensional (1D) to 2D solver and simulate the problem on a square geometry with different initial conditions. The method is fourth order accurate in space and second order accurate in time. We then compare our results with the available benchmark results. The comparison shows an excellent agreement of our results with the existing ones in the literature. Being a finite difference solver, it is quite straight-forward and simple.
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Jeng Hei Chow
2016-07-01
Full Text Available An implicit method of solving the six degree-of-freedom rigid body motion equations based on the second order Adams-Bashforth-Moulten method was utilised as an improvement over the leapfrog scheme by making modifications to the rigid body motion solver libraries directly. The implementation will depend on predictor-corrector steps still residing within the hybrid Pressure Implicit with Splitting of Operators - Semi-Implicit Method for Pressure Linked Equations (PIMPLE outer corrector loops to ensure strong coupling between fluid and motion. Aitken's under-relaxation is also introduced in this study to optimise the convergence rate and stability of the coupled solver. The resulting coupled solver ran on a free floating object tutorial test case when converged matches the original solver. It further allows a varying 70%–80% reduction in simulation times compared using a fixed under-relaxation to achieve the required stability.
A Direct Elliptic Solver Based on Hierarchically Low-Rank Schur Complements
Chávez, Gustavo
2017-03-17
A parallel fast direct solver for rank-compressible block tridiagonal linear systems is presented. Algorithmic synergies between Cyclic Reduction and Hierarchical matrix arithmetic operations result in a solver with O(Nlog2N) arithmetic complexity and O(NlogN) memory footprint. We provide a baseline for performance and applicability by comparing with well-known implementations of the $$\\\\mathcal{H}$$ -LU factorization and algebraic multigrid within a shared-memory parallel environment that leverages the concurrency features of the method. Numerical experiments reveal that this method is comparable with other fast direct solvers based on Hierarchical Matrices such as $$\\\\mathcal{H}$$ -LU and that it can tackle problems where algebraic multigrid fails to converge.
Homological unimodularity and Calabi-Yau condition for Poisson algebras
Lü, Jiafeng; Wang, Xingting; Zhuang, Guangbin
2017-09-01
In this paper, we show that the twisted Poincaré duality between Poisson homology and cohomology can be derived from the Serre invertible bimodule. This gives another definition of a unimodular Poisson algebra in terms of its Poisson Picard group. We also achieve twisted Poincaré duality for Hochschild (co)homology of Poisson bimodules using rigid dualizing complex. For a smooth Poisson affine variety with the trivial canonical bundle, we prove that its enveloping algebra is a Calabi-Yau algebra if the Poisson structure is unimodular.
Cooper, Christopher D.; Barba, Lorena A.
2016-05-01
Interactions between surfaces and proteins occur in many vital processes and are crucial in biotechnology: the ability to control specific interactions is essential in fields like biomaterials, biomedical implants and biosensors. In the latter case, biosensor sensitivity hinges on ligand proteins adsorbing on bioactive surfaces with a favorable orientation, exposing reaction sites to target molecules. Protein adsorption, being a free-energy-driven process, is difficult to study experimentally. This paper develops and evaluates a computational model to study electrostatic interactions of proteins and charged nanosurfaces, via the Poisson-Boltzmann equation. We extended the implicit-solvent model used in the open-source code PyGBe to include surfaces of imposed charge or potential. This code solves the boundary integral formulation of the Poisson-Boltzmann equation, discretized with surface elements. PyGBe has at its core a treecode-accelerated Krylov iterative solver, resulting in O(N log N) scaling, with further acceleration on hardware via multi-threaded execution on GPUs. It computes solvation and surface free energies, providing a framework for studying the effect of electrostatics on adsorption. We derived an analytical solution for a spherical charged surface interacting with a spherical dielectric cavity, and used it in a grid-convergence study to build evidence on the correctness of our approach. The study showed the error decaying with the average area of the boundary elements, i.e., the method is O(1 / N) , which is consistent with our previous verification studies using PyGBe. We also studied grid-convergence using a real molecular geometry (protein G B1 D4‧), in this case using Richardson extrapolation (in the absence of an analytical solution) and confirmed the O(1 / N) scaling. With this work, we can now access a completely new family of problems, which no other major bioelectrostatics solver, e.g. APBS, is capable of dealing with. PyGBe is open
Application of alternating decision trees in selecting sparse linear solvers
Bhowmick, Sanjukta
2010-01-01
The solution of sparse linear systems, a fundamental and resource-intensive task in scientific computing, can be approached through multiple algorithms. Using an algorithm well adapted to characteristics of the task can significantly enhance the performance, such as reducing the time required for the operation, without compromising the quality of the result. However, the best solution method can vary even across linear systems generated in course of the same PDE-based simulation, thereby making solver selection a very challenging problem. In this paper, we use a machine learning technique, Alternating Decision Trees (ADT), to select efficient solvers based on the properties of sparse linear systems and runtime-dependent features, such as the stages of simulation. We demonstrate the effectiveness of this method through empirical results over linear systems drawn from computational fluid dynamics and magnetohydrodynamics applications. The results also demonstrate that using ADT can resolve the problem of over-fitting, which occurs when limited amount of data is available. © 2010 Springer Science+Business Media LLC.
WIENER-HOPF SOLVER WITH SMOOTH PROBABILITY DISTRIBUTIONS OF ITS COMPONENTS
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Mr. Vladimir A. Smagin
2016-12-01
Full Text Available The Wiener – Hopf solver with smooth probability distributions of its component is presented. The method is based on hyper delta approximations of initial distributions. The use of Fourier series transformation and characteristic function allows working with the random variable method concentrated in transversal axis of absc.
Fu, X.; Waters, T.; Gary, S. P.
2014-12-01
Collisionless space plasmas often deviate from Maxwellian-like velocity distributions. To study kinetic waves and instabilities in such plasmas, the dispersion relation, which depends on the velocity distribution, needs to be solved numerically. Most current dispersion solvers (e.g. WHAMP) take advantage of mathematical properties of the Gaussian (or generalized Lorentzian) function, and assume that the velocity distributions can be modeled by a combination of several drift-Maxwellian (or drift-Lorentzian) components. In this study we are developing a kinetic dispersion solver that admits nearly arbitrary non-relativistic parallel velocity distributions. A key part of any dispersion solver is the evaluation of a Hilbert transform of the velocity distribution function and its derivative along Landau contours. Our new solver builds upon a recent method to compute the Hilbert transform accurately and efficiently using the fast Fourier transform, while simultaneously treating the singularities arising from resonances analytically. We have benchmarked our new solver against other codes dealing with Maxwellian distributions. As an example usage of our code, we will show results for several instabilities that occur for electron velocity distributions observed in the solar wind.
Pressure Decimation and Interpolation (PDI) method for a baroclinic non-hydrostatic model
Shi, Jian; Shi, Fengyan; Kirby, James T.; Ma, Gangfeng; Wu, Guoxiang; Tong, Chaofeng; Zheng, Jinhai
2015-12-01
Non-hydrostatic models are computationally expensive in simulating density flows and mass transport problems due to the requirement of sufficient grid resolution to resolve density and flow structures. Numerical tests based on the Non-Hydrostatic Wave Model, NHWAVE (Ma et al., 2012), indicated that up to 70% of the total computational cost may be born by the pressure Poisson solver in cases with high grid resolution in both vertical and horizontal directions. However, recent studies using Poisson solver-based non-hydrostatic models have shown that an accurate prediction of wave dispersion does not require a large number of vertical layers if the dynamic pressure is properly discretized. In this study, we explore the possibility that the solution for the dynamic pressure field may, in general, be decimated to a resolution far coarser than that used in representing velocities and other transported quantities, without sacrificing accuracy of solutions. Following van Reeuwijk (2002), we determine the dynamic pressure field by solving the Poisson equation on a coarser grid and then interpolate the pressure field onto a finer grid used for solving for the remaining dynamic variables. With the Pressure Decimation and Interpolation (PDI) method, computational efficiency is greatly improved. We use three test cases to demonstrate the model's accuracy and efficiency in modeling density flows.
Maslov indices, Poisson brackets, and singular differential forms
Esterlis, I.; Haggard, H. M.; Hedeman, A.; Littlejohn, R. G.
2014-06-01
Maslov indices are integers that appear in semiclassical wave functions and quantization conditions. They are often notoriously difficult to compute. We present methods of computing the Maslov index that rely only on typically elementary Poisson brackets and simple linear algebra. We also present a singular differential form, whose integral along a curve gives the Maslov index of that curve. The form is closed but not exact, and transforms by an exact differential under canonical transformations. We illustrate the method with the 6j-symbol, which is important in angular-momentum theory and in quantum gravity.
Localization of Point Sources for Poisson Equation using State Observers
Majeed, M. U.
2016-08-09
A method based On iterative observer design is presented to solve point source localization problem for Poisson equation with riven boundary data. The procedure involves solution of multiple boundary estimation sub problems using the available Dirichlet and Neumann data from different parts of the boundary. A weighted sum of these solution profiles of sub-problems localizes point sources inside the domain. Method to compute these weights is also provided. Numerical results are presented using finite differences in a rectangular domain. (C) 2016, IFAC (International Federation of Automatic Control) Hosting by Elsevier Ltd. All rights reserved.
An intrinsic algorithm for parallel Poisson disk sampling on arbitrary surfaces.
Ying, Xiang; Xin, Shi-Qing; Sun, Qian; He, Ying
2013-09-01
Poisson disk sampling has excellent spatial and spectral properties, and plays an important role in a variety of visual computing. Although many promising algorithms have been proposed for multidimensional sampling in euclidean space, very few studies have been reported with regard to the problem of generating Poisson disks on surfaces due to the complicated nature of the surface. This paper presents an intrinsic algorithm for parallel Poisson disk sampling on arbitrary surfaces. In sharp contrast to the conventional parallel approaches, our method neither partitions the given surface into small patches nor uses any spatial data structure to maintain the voids in the sampling domain. Instead, our approach assigns each sample candidate a random and unique priority that is unbiased with regard to the distribution. Hence, multiple threads can process the candidates simultaneously and resolve conflicts by checking the given priority values. Our algorithm guarantees that the generated Poisson disks are uniformly and randomly distributed without bias. It is worth noting that our method is intrinsic and independent of the embedding space. This intrinsic feature allows us to generate Poisson disk patterns on arbitrary surfaces in IR(n). To our knowledge, this is the first intrinsic, parallel, and accurate algorithm for surface Poisson disk sampling. Furthermore, by manipulating the spatially varying density function, we can obtain adaptive sampling easily.
Institute of Scientific and Technical Information of China (English)
LIU Zhi; ZHANG Xian-kang; WANG Fu-yun; DUAN Yong-hong; LAI Xiao-ling
2005-01-01
Based on the inversion method of 2D velocity structure and interface, the crustal velocity structures of P-wave and S-wave along the profile L1 are determined simultaneously with deep seismic sounding data in Changbaishan Tianchi volcanic region, and then its Poisson's ratio is obtained. Calculated results show that this technique overcomes some defects of traditional forward calculation method, and it is also very effective to determine Poisson's ratio distribution of deep seismic sounding profile, especially useful for study on volcanic magma and crustal fault zone. Study result indicates that there is an abnormally high Poisson's ratio body that is about 30 km wide and 12 km high in the low velocity region under Tianchi crater. Its value of Poisson's ratio is 8% higher than that of surrounding medium and it should be the magma chamber formed from melted rock with high temperature. There is a high Poisson's ratio zone ranging from magma chamber to the top of crust, which may be the uprise passage of hot substance. The lower part with high Poisson's ratio, which stretches downward to Moho, is possibly the extrusion way of hot substance from the uppermost mantle. The conclusions above are consistent with the study results of both tomographic determination of 3D crustal structure and magnetotelluric survey in this region.
The role and status of Euler solvers in impulsive rotor noise computations
Baeder, James D.
1995-01-01
Several recent applications (in the last five years) of Euler solvers in the computation of impulsive noise from rotor blades emphasize their emerging role in complementing other methods and experimental work. In the area of high-speed impulsive noise the use of Euler solvers as research tools has become fairly mature with very favorable comparisons with experimental data, especially in hover. The grid sizes and resulting computational times are reasonable when compared to those required for accurate surface aerodynamics alone. Furthermore, Euler solvers have provided a rich database with the resolution and accuracy needed for input to Kirchhoff and acoustic analogy methods for predicting the far-field noise. On the other hand, the application of Euler solvers to calculate blade-vortex interaction noise is still far from mature. The computational resources required for accurate calculations away from the blade are much larger than for high-speed impulsive noise. Current calculations help improve the basic understanding of the phenomena involved, but to date no comparisons with experiment have been made. Fortunately, the use of coupled Euler solver/Kirchhoff methods seems to offer promise for a robust and efficient technique for predicting both high-speed impulsive noise and blade-vortex interaction noise. Finally, a simple model problem of an isolated vortex interacting with an arbitrarily prescribed pitching airfoil demonstrates the feasibility of using Euler solvers to examine noise reduction techniques. The use of simple aerodynamic quasi-static theory and the computed lift time history as feedback to determine the required pitching motion appears sufficient to significantly dampen the unsteady loading and subsequent acoustics by an order of magnitude within a few blade passages.
A Generic High-performance GPU-based Library for PDE solvers
DEFF Research Database (Denmark)
Glimberg, Stefan Lemvig; Engsig-Karup, Allan Peter
legacy codes are not always easily parallelized and the time spent on conversion might not pay o in the end. We present a highly generic C++ library for fast assembling of partial differential equation (PDE) solvers, aiming at utilizing the computational resources of GPUs. The library requires a minimum......, two important features for ecient GPU utilization and for enabling solution of large problems. In order to solve the large linear systems of equations, arising from the discretization of PDEs, the library includes a set of common iterative solvers. All iterative solvers are based on template arguments...... of fully nonlinear free surface water waves over uneven depths[1, 2, 3]. The wave model is based on the potential ow formulation, with the computational bottleneck of solving a fully three dimensional Laplace problem eciently. A robust h- or p-multigrid preconditioned defect correction method is applied...
Gomez-Sousa, Hipolito; Martinez-Lorenzo, Jose Angel
2015-01-01
The electromagnetic behavior of plasmonic structures can be predicted after discretizing and solving a linear system of equations, derived from a continuous surface integral equation (SIE) and the appropriate boundary conditions, using a method of moments (MoM) methodology. In realistic large-scale optical problems, a direct inversion of the SIE-MoM matrix cannot be performed due to its large size, and an iterative solver must be used instead. This paper investigates the performance of four iterative solvers (GMRES, TFQMR, CGS, and BICGSTAB) for five different SIE-MoM formulations (PMCHWT, JMCFIE, CTF, CNF, and MNMF). Moreover, under this plasmonic context, a set of suggested guidelines are provided to choose a suitable SIE formulation and iterative solver depending on the desired simulation error and available runtime resources.
Deriving all minimal consistency-based diagnosis sets using SAT solvers
Institute of Scientific and Technical Information of China (English)
Xiangfu Zhao; Liming Zhang; Dantong Ouyang; Yu Jiao
2009-01-01
In this paper,a novel method is proposed for judging whether a component set is a consistency-based diagnostic set,using SAT solvers.Firstly,the model of the system to be diagnosed and all the observations are described with conjunctive normal forms (CNF).Then,all the related clauses in the CNF files to the components other than the considered ones are extracted,to be used for satisfiability checking by SAT solvers.Next,all the minimal consistency-based diagnostic sets are derived by the CSSE-tree or by other similar algorithms.We have implemented four related algorithms,by calling the gold medal SAT solver in SAT07 competition - RSAT.Experimental results show that all the minimal consistency-based diagnostic sets can be quickly computed.Especially our CSSE-tree has the best efficiency for the single-or double-fault diagnosis.
A Gaussian Belief Propagation Solver for Large Scale Support Vector Machines
Bickson, Danny; Dolev, Danny
2008-01-01
Support vector machines (SVMs) are an extremely successful type of classification and regression algorithms. Building an SVM entails solving a constrained convex quadratic programming problem, which is quadratic in the number of training samples. We introduce an efficient parallel implementation of an support vector regression solver, based on the Gaussian Belief Propagation algorithm (GaBP). In this paper, we demonstrate that methods from the complex system domain could be utilized for performing efficient distributed computation. We compare the proposed algorithm to previously proposed distributed and single-node SVM solvers. Our comparison shows that the proposed algorithm is just as accurate as these solvers, while being significantly faster, especially for large datasets. We demonstrate scalability of the proposed algorithm to up to 1,024 computing nodes and hundreds of thousands of data points using an IBM Blue Gene supercomputer. As far as we know, our work is the largest parallel implementation of bel...
Gao, Hao; Phan, Lan; Lin, Yuting
2012-09-01
A graphics processing unit-based parallel multigrid solver for a radiative transfer equation with vacuum boundary condition or reflection boundary condition is presented for heterogeneous media with complex geometry based on two-dimensional triangular meshes or three-dimensional tetrahedral meshes. The computational complexity of this parallel solver is linearly proportional to the degrees of freedom in both angular and spatial variables, while the full multigrid method is utilized to minimize the number of iterations. The overall gain of speed is roughly 30 to 300 fold with respect to our prior multigrid solver, which depends on the underlying regime and the parallelization. The numerical validations are presented with the MATLAB codes at https://sites.google.com/site/rtefastsolver/.
On higher Poisson and Koszul--Schouten brackets
Bruce, Andrew James
2009-01-01
In this note we show how to construct a homotopy BV-algebra on the algebra of differential forms over a higher Poisson manifold. The Lie derivative along the higher Poisson structure provides the generating operator.
On the Confidence Interval for the parameter of Poisson Distribution
Bityukov, S I; Taperechkina, V A
2000-01-01
In present paper the possibility of construction of continuous analogue of Poisson distribution with the search of bounds of confidence intervals for parameter of Poisson distribution is discussed and the results of numerical construction of confidence intervals are presented.
Parallel H1-based auxiliary space AMG solver for H(curl) problems
Energy Technology Data Exchange (ETDEWEB)
Kolev, T V; Vassilevski, P S
2006-06-30
This report describes a parallel implementation of the auxiliary space methods for definite Maxwell problems proposed in [4]. The solver, named AMS, extends our previous study [7]. AMS uses ParCSR sparse matrix storage and the parallel AMG (algebraic multigrid) solver BoomerAMG [1] from the hypre library. It is designed for general unstructured finite element discretizations of (semi)definite H(curl) problems discretized by Nedelec elements. We document the usage of AMS and illustrate its parallel scalability and overall performance.
Poisson Bracket on the Space of Histories
Marolf, D
1994-01-01
We extend the Poisson bracket from a Lie bracket of phase space functions to a Lie bracket of functions on the space of canonical histories and investigate the resulting algebras. Typically, such extensions define corresponding Lie algebras on the space of Lagrangian histories via pull back to a space of partial solutions. These are the same spaces of histories studied with regard to path integration and decoherence. Such spaces of histories are familiar from path integration and some studies of decoherence. For gauge systems, we extend both the canonical and reduced Poisson brackets to the full space of histories. We then comment on the use of such algebras in time reparameterization invariant systems and systems with a Gribov ambiguity, though our main goal is to introduce concepts and techniques for use in a companion paper.
Model selection for Poisson processes with covariates
Sart, Mathieu
2011-01-01
We observe $n$ inhomogeneous Poisson processes with covariates and aim at estimating their intensities. To handle this problem, we assume that the intensity of each Poisson process is of the form $s (\\cdot, x)$ where $x$ is the covariate and where $s$ is an unknown function. We propose a model selection approach where the models are used to approximate the multivariate function $s$. We show that our estimator satisfies an oracle-type inequality under very weak assumptions both on the intensities and the models. By using an Hellinger-type loss, we establish non-asymptotic risk bounds and specify them under various kind of assumptions on the target function $s$ such as being smooth or composite. Besides, we show that our estimation procedure is robust with respect to these assumptions.
The local Poisson hypothesis for solar flares
Wheatland, M S
2001-01-01
The question of whether flares occur as a Poisson process has important consequences for flare physics. Recently Lepreti et al. presented evidence for local departure from Poisson statistics in the Geostationary Operational Environmental Satellite (GOES) X-ray flare catalog. Here it is argued that this effect arises from a selection effect inherent in the soft X-ray observations; namely that the slow decay of enhanced flux following a large flare makes detection of subsequent flares less likely. It is also shown that the power-law tail of the GOES waiting-time distribution varies with the solar cycle. This counts against any intrinsic significance to the appearance of a power law, or to the value of its index.
A General Symbolic PDE Solver Generator: Beyond Explicit Schemes
Directory of Open Access Journals (Sweden)
K. Sheshadri
2003-01-01
Full Text Available This paper presents an extension of our Mathematica- and MathCode-based symbolic-numeric framework for solving a variety of partial differential equation (PDE problems. The main features of our earlier work, which implemented explicit finite-difference schemes, include the ability to handle (1 arbitrary number of dependent variables, (2 arbitrary dimensionality, and (3 arbitrary geometry, as well as (4 developing finite-difference schemes to any desired order of approximation. In the present paper, extensions of this framework to implicit schemes and the method of lines are discussed. While C++ code is generated, using the MathCode system for the implicit method, Modelica code is generated for the method of lines. The latter provides a preliminary PDE support for the Modelica language. Examples illustrating the various aspects of the solver generator are presented.
Fast Multipole-Based Preconditioner for Sparse Iterative Solvers
Ibeid, Huda
2014-05-04
Among optimal hierarchical algorithms for the computational solution of elliptic problems, the Fast Multipole Method (FMM) stands out for its adaptability to emerging architectures, having high arithmetic intensity, tunable accuracy, and relaxed global synchronization requirements. We demonstrate that, beyond its traditional use as a solver in problems for which explicit free-space kernel representations are available, the FMM has applicability as a preconditioner in finite domain elliptic boundary value problems, by equipping it with boundary integral capability for finite boundaries and by wrapping it in a Krylov method for extensibility to more general operators. Compared with multilevel methods, it is capable of comparable algebraic convergence rates down to the truncation error of the discretized PDE, and it has superior multicore and distributed memory scalability properties on commodity architecture supercomputers.
Modeling animal-vehicle collisions using diagonal inflated bivariate Poisson regression.
Lao, Yunteng; Wu, Yao-Jan; Corey, Jonathan; Wang, Yinhai
2011-01-01
Two types of animal-vehicle collision (AVC) data are commonly adopted for AVC-related risk analysis research: reported AVC data and carcass removal data. One issue with these two data sets is that they were found to have significant discrepancies by previous studies. In order to model these two types of data together and provide a better understanding of highway AVCs, this study adopts a diagonal inflated bivariate Poisson regression method, an inflated version of bivariate Poisson regression model, to fit the reported AVC and carcass removal data sets collected in Washington State during 2002-2006. The diagonal inflated bivariate Poisson model not only can model paired data with correlation, but also handle under- or over-dispersed data sets as well. Compared with three other types of models, double Poisson, bivariate Poisson, and zero-inflated double Poisson, the diagonal inflated bivariate Poisson model demonstrates its capability of fitting two data sets with remarkable overlapping portions resulting from the same stochastic process. Therefore, the diagonal inflated bivariate Poisson model provides researchers a new approach to investigating AVCs from a different perspective involving the three distribution parameters (λ(1), λ(2) and λ(3)). The modeling results show the impacts of traffic elements, geometric design and geographic characteristics on the occurrences of both reported AVC and carcass removal data. It is found that the increase of some associated factors, such as speed limit, annual average daily traffic, and shoulder width, will increase the numbers of reported AVCs and carcass removals. Conversely, the presence of some geometric factors, such as rolling and mountainous terrain, will decrease the number of reported AVCs.
Continental moisture recycling as a Poisson process
2013-01-01
On their journey across large land masses, water molecules experience a number of precipitation-evaporation cycles (recycling events). We derive analytically the frequency distributions of recycling events for the water molecules contained in a given air parcel. Given the validity of certain simplifying assumptions, continental moisture recycling is shown to develop either into a Poisson distribution or a geometric distribution. We distinguish two cases: in case (A) recycling events a...
Continental moisture recycling as a Poisson process
2013-01-01
On their journey over large land masses, water molecules experience a number of precipitation–evaporation cycles (recycling events). We derive analytically the frequency distributions of recycling events for the water molecules contained in a given air parcel. Given the validity of certain simplifying assumptions, the frequency distribution of recycling events is shown to develop either into a Poisson distribution or a geometric distribution. We distingu...
A New Echeloned Poisson Series Processor (EPSP)
Ivanova, Tamara
2001-07-01
A specialized Echeloned Poisson Series Processor (EPSP) is proposed. It is a typical software for the implementation of analytical algorithms of Celestial Mechanics. EPSP is designed for manipulating long polynomial-trigonometric series with literal divisors. The coefficients of these echeloned series are the rational or floating-point numbers. The Keplerian processor and analytical generator of special celestial mechanics functions based on the EPSP are also developed.
Irreversible thermodynamics of Poisson processes with reaction.
Méndez, V; Fort, J
1999-11-01
A kinetic model is derived to study the successive movements of particles, described by a Poisson process, as well as their generation. The irreversible thermodynamics of this system is also studied from the kinetic model. This makes it possible to evaluate the differences between thermodynamical quantities computed exactly and up to second-order. Such differences determine the range of validity of the second-order approximation to extended irreversible thermodynamics.
Irreversible thermodynamics of Poisson processes with reaction
Méndez, Vicenç; Fort, Joaquim
1999-11-01
A kinetic model is derived to study the successive movements of particles, described by a Poisson process, as well as their generation. The irreversible thermodynamics of this system is also studied from the kinetic model. This makes it possible to evaluate the differences between thermodynamical quantities computed exactly and up to second-order. Such differences determine the range of validity of the second-order approximation to extended irreversible thermodynamics.
Lefkimmiatis, Stamatios; Maragos, Petros; Papandreou, George
2009-08-01
We present an improved statistical model for analyzing Poisson processes, with applications to photon-limited imaging. We build on previous work, adopting a multiscale representation of the Poisson process in which the ratios of the underlying Poisson intensities (rates) in adjacent scales are modeled as mixtures of conjugate parametric distributions. Our main contributions include: 1) a rigorous and robust regularized expectation-maximization (EM) algorithm for maximum-likelihood estimation of the rate-ratio density parameters directly from the noisy observed Poisson data (counts); 2) extension of the method to work under a multiscale hidden Markov tree model (HMT) which couples the mixture label assignments in consecutive scales, thus modeling interscale coefficient dependencies in the vicinity of image edges; 3) exploration of a 2-D recursive quad-tree image representation, involving Dirichlet-mixture rate-ratio densities, instead of the conventional separable binary-tree image representation involving beta-mixture rate-ratio densities; and 4) a novel multiscale image representation, which we term Poisson-Haar decomposition, that better models the image edge structure, thus yielding improved performance. Experimental results on standard images with artificially simulated Poisson noise and on real photon-limited images demonstrate the effectiveness of the proposed techniques.
On the verification of polynomial system solvers
Institute of Scientific and Technical Information of China (English)
Changbo CHEN; Marc MORENO MAZA; Wei PAN; Yuzhen XI
2008-01-01
We discuss the verification of mathematical software solving polynomial systems symbolically by way of triangular decomposition. Standard verification techniques are highly resource consuming and apply only to polynomial systems which are easy to solve. We exhibit a new approach which manipulates constructible sets represented by regular systems. We provide comparative benchmarks of different verification procedures applied to four solvers on a large set of well-known polynomial systems. Our experimental results illustrate the high effi-ciency of our new approach. In particular, we are able to verify triangular decompositions of polynomial systems which are not easy to solve.
Some topics of Navier-Stokes solvers
Honma, H.; Nishikawa, N.
1990-03-01
The process of numerical simulation consists of selection of some items: a mathematical model, a numerical scheme, the level of the computer, and post processing. From this point of view, recent numerical studies of viscous flows are described especially for the fluid engineering laboratories in the Chiba University. The examples of simulations are Mach reflection on a wedge using a kinetic model equation and a cylinder-plate juncture flow using incompressible Navier Stokes equation. Some attempts at graphic monitoring of fluid mechanical calculations are also shown for some combinations of computers with Computational Fluid Dynamics (CFD) solvers.
Input-output-controlled nonlinear equation solvers
Padovan, Joseph
1988-01-01
To upgrade the efficiency and stability of the successive substitution (SS) and Newton-Raphson (NR) schemes, the concept of input-output-controlled solvers (IOCS) is introduced. By employing the formal properties of the constrained version of the SS and NR schemes, the IOCS algorithm can handle indefiniteness of the system Jacobian, can maintain iterate monotonicity, and provide for separate control of load incrementation and iterate excursions, as well as having other features. To illustrate the algorithmic properties, the results for several benchmark examples are presented. These define the associated numerical efficiency and stability of the IOCS.
Metaheuristics progress as real problem solvers
Nonobe, Koji; Yagiura, Mutsunori
2005-01-01
Metaheuristics: Progress as Real Problem Solvers is a peer-reviewed volume of eighteen current, cutting-edge papers by leading researchers in the field. Included are an invited paper by F. Glover and G. Kochenberger, which discusses the concept of Metaheuristic agent processes, and a tutorial paper by M.G.C. Resende and C.C. Ribeiro discussing GRASP with path-relinking. Other papers discuss problem-solving approaches to timetabling, automated planograms, elevators, space allocation, shift design, cutting stock, flexible shop scheduling, colorectal cancer and cartography. A final group of methodology papers clarify various aspects of Metaheuristics from the computational view point.
Three-dimensional nanoelectronic device simulation using spectral element methods
Cheng, Candong
The purpose of this thesis is to develop an efficient 3-Dimensional (3-D) nanoelectronic device simulator. Specifically, the self-consistent Schrodinger-Poisson model was implemented in this simulator to simulate band structures and quantum transport properties. Also, an efficient fast algorithm, spectral element method (SEM), was used in this simulator to achieve spectral accuracy where the error decreases exponentially with the increase of sampling densities and the basis order of the polynomial functions, thus significantly reducing the CPU time and memory usage. Moreover, within this simulator, a perfectly matched layer (PML) boundary condition method was used for the Schrodinger solver, which significantly simplifies the problem and reduces the computational time. Furthermore, the effective mass in semiconductor devices was treated as a full anisotropic mass tensor, which provides an excellent tool to study the anisotropy characteristics along arbitrary orientation of the device. Nanoelectronic devices usually involve the simulations of energy band and quantum transport properties. One of the models to perform these simulations is by solving a self-consistent Schrodinger-Poisson system. Two efficient fast algorithms, spectral grid method (SGM) and SEM, are investigated and implemented in this thesis. The spectral accuracy is achieved in both algorithms, whose errors decrease exponentially with the increase of the sampling density and basis orders. The spectral grid method is a pseudospectral method to achieve a high-accuracy result by choosing special nonuniform grid set and high-order Lagrange interpolants for a partial differential equation. Spectral element method is a high-order finite element method which uses the Gauss-Lobatto-Legendre (GLL) polynomials to represent the field variables in the Schrodinger-Poisson system and, therefore, to achieve spectral accuracy. We have implemented the SGM in the Schrodinger equation to solve the energy band structures
Xie, Dexuan; Volkmer, Hans W.; Ying, Jinyong
2016-04-01
The nonlocal dielectric approach has led to new models and solvers for predicting electrostatics of proteins (or other biomolecules), but how to validate and compare them remains a challenge. To promote such a study, in this paper, two typical nonlocal dielectric models are revisited. Their analytical solutions are then found in the expressions of simple series for a dielectric sphere containing any number of point charges. As a special case, the analytical solution of the corresponding Poisson dielectric model is also derived in simple series, which significantly improves the well known Kirkwood's double series expansion. Furthermore, a convolution of one nonlocal dielectric solution with a commonly used nonlocal kernel function is obtained, along with the reaction parts of these local and nonlocal solutions. To turn these new series solutions into a valuable research tool, they are programed as a free fortran software package, which can input point charge data directly from a protein data bank file. Consequently, different validation tests can be quickly done on different proteins. Finally, a test example for a protein with 488 atomic charges is reported to demonstrate the differences between the local and nonlocal models as well as the importance of using the reaction parts to develop local and nonlocal dielectric solvers.
Xie, Dexuan; Volkmer, Hans W; Ying, Jinyong
2016-04-01
The nonlocal dielectric approach has led to new models and solvers for predicting electrostatics of proteins (or other biomolecules), but how to validate and compare them remains a challenge. To promote such a study, in this paper, two typical nonlocal dielectric models are revisited. Their analytical solutions are then found in the expressions of simple series for a dielectric sphere containing any number of point charges. As a special case, the analytical solution of the corresponding Poisson dielectric model is also derived in simple series, which significantly improves the well known Kirkwood's double series expansion. Furthermore, a convolution of one nonlocal dielectric solution with a commonly used nonlocal kernel function is obtained, along with the reaction parts of these local and nonlocal solutions. To turn these new series solutions into a valuable research tool, they are programed as a free fortran software package, which can input point charge data directly from a protein data bank file. Consequently, different validation tests can be quickly done on different proteins. Finally, a test example for a protein with 488 atomic charges is reported to demonstrate the differences between the local and nonlocal models as well as the importance of using the reaction parts to develop local and nonlocal dielectric solvers.
Alternative Forms of Compound Fractional Poisson Processes
Directory of Open Access Journals (Sweden)
Luisa Beghin
2012-01-01
Full Text Available We study here different fractional versions of the compound Poisson process. The fractionality is introduced in the counting process representing the number of jumps as well as in the density of the jumps themselves. The corresponding distributions are obtained explicitly and proved to be solution of fractional equations of order less than one. Only in the final case treated in this paper, where the number of jumps is given by the fractional-difference Poisson process defined in Orsingher and Polito (2012, we have a fractional driving equation, with respect to the time argument, with order greater than one. Moreover, in this case, the compound Poisson process is Markovian and this is also true for the corresponding limiting process. All the processes considered here are proved to be compositions of continuous time random walks with stable processes (or inverse stable subordinators. These subordinating relationships hold, not only in the limit, but also in the finite domain. In some cases the densities satisfy master equations which are the fractional analogues of the well-known Kolmogorov one.
Differential Poisson Sigma Models with Extended Supersymmetry
Arias, Cesar; Torres-Gomez, Alexander
2016-01-01
The induced two-dimensional topological N=1 supersymmetric sigma model on a differential Poisson manifold M presented in arXiv:1503.05625 is shown to be a special case of the induced Poisson sigma model on the bi-graded supermanifold T[0,1]M. The bi-degree comprises the standard N-valued target space degree, corresponding to the form degree on the worldsheet, and an additional Z-valued fermion number, corresponding to the degree in the differential graded algebra of forms on M. The N=1 supersymmetry stems from the compatibility between the (extended) differential Poisson bracket and the de Rham differential on M. The latter is mapped to a nilpotent vector field Q of bi-degree (0,1) on T*[1,0](T[0,1]M), and the covariant Hamiltonian action is Q-exact. New extended supersymmetries arise as inner derivatives along special bosonic Killing vectors on M that induce Killing supervector fields of bi-degree (0,-1) on T*[1,0](T[0,1]M).
Connectivity in Sub-Poisson Networks
Blaszczyszyn, Bartlomiej
2010-01-01
We consider a class of point processes (pp), which we call {\\em sub-Poisson}; these are pp that can be directionally-convexly ($dcx$) dominated by some Poisson pp. The $dcx$ order has already been shown useful in comparing various point process characteristics, including Ripley's and correlation functions as well as shot-noise fields generated by pp, indicating in particular that smaller in the $dcx$ order processes exhibit more regularity (less clustering, less voids) in the repartition of their points. Using these results, in this paper we study the impact of the $dcx$ ordering of pp on the properties of two continuum percolation models, which have been proposed in the literature to address macroscopic connectivity properties of large wireless networks. As the first main result of this paper, we extend the classical result on the existence of phase transition in the percolation of the Gilbert's graph (called also the Boolean model), generated by a homogeneous Poisson pp, to the class of homogeneous sub-Pois...
Finite Horizon Decision Timing with Partially Observable Poisson Processes
Ludkovski, Michael
2011-01-01
We study decision timing problems on finite horizon with Poissonian information arrivals. In our model, a decision maker wishes to optimally time her action in order to maximize her expected reward. The reward depends on an unobservable Markovian environment, and information about the environment is collected through a (compound) Poisson observation process. Examples of such systems arise in investment timing, reliability theory, Bayesian regime detection and technology adoption models. We solve the problem by studying an optimal stopping problem for a piecewise-deterministic process which gives the posterior likelihoods of the unobservable environment. Our method lends itself to simple numerical implementation and we present several illustrative numerical examples.
Fission meter and neutron detection using poisson distribution comparison
Energy Technology Data Exchange (ETDEWEB)
Rowland, Mark S; Snyderman, Neal J
2014-11-18
A neutron detector system and method for discriminating fissile material from non-fissile material wherein a digital data acquisition unit collects data at high rate, and in real-time processes large volumes of data directly into information that a first responder can use to discriminate materials. The system comprises counting neutrons from the unknown source and detecting excess grouped neutrons to identify fission in the unknown source. Comparison of the observed neutron count distribution with a Poisson distribution is performed to distinguish fissile material from non-fissile material.
Energy Technology Data Exchange (ETDEWEB)
Bordner, J.; Saied, F. [Univ. of Illinois, Urbana, IL (United States)
1996-12-31
GLab3D is an enhancement of an interactive environment (MGLab) for experimenting with iterative solvers and multigrid algorithms. It is implemented in MATLAB. The new version has built-in 3D elliptic pde`s and several iterative methods and preconditioners that were not available in the original version. A sparse direct solver option has also been included. The multigrid solvers have also been extended to 3D. The discretization and pde domains are restricted to standard finite differences on the unit square/cube. The power of this software studies in the fact that no programming is needed to solve, for example, the convection-diffusion equation in 3D with TFQMR and a customized V-cycle preconditioner, for a variety of problem sizes and mesh Reynolds, numbers. In addition to the graphical user interface, some sample drivers are included to show how experiments can be composed using the underlying suite of problems and solvers.
Robust large-scale parallel nonlinear solvers for simulations.
Energy Technology Data Exchange (ETDEWEB)
Bader, Brett William; Pawlowski, Roger Patrick; Kolda, Tamara Gibson (Sandia National Laboratories, Livermore, CA)
2005-11-01
This report documents research to develop robust and efficient solution techniques for solving large-scale systems of nonlinear equations. The most widely used method for solving systems of nonlinear equations is Newton's method. While much research has been devoted to augmenting Newton-based solvers (usually with globalization techniques), little has been devoted to exploring the application of different models. Our research has been directed at evaluating techniques using different models than Newton's method: a lower order model, Broyden's method, and a higher order model, the tensor method. We have developed large-scale versions of each of these models and have demonstrated their use in important applications at Sandia. Broyden's method replaces the Jacobian with an approximation, allowing codes that cannot evaluate a Jacobian or have an inaccurate Jacobian to converge to a solution. Limited-memory methods, which have been successful in optimization, allow us to extend this approach to large-scale problems. We compare the robustness and efficiency of Newton's method, modified Newton's method, Jacobian-free Newton-Krylov method, and our limited-memory Broyden method. Comparisons are carried out for large-scale applications of fluid flow simulations and electronic circuit simulations. Results show that, in cases where the Jacobian was inaccurate or could not be computed, Broyden's method converged in some cases where Newton's method failed to converge. We identify conditions where Broyden's method can be more efficient than Newton's method. We also present modifications to a large-scale tensor method, originally proposed by Bouaricha, for greater efficiency, better robustness, and wider applicability. Tensor methods are an alternative to Newton-based methods and are based on computing a step based on a local quadratic model rather than a linear model. The advantage of Bouaricha's method is that it can use any
Experimental validation of a boundary element solver for exterior acoustic radiation problems
Visser, Rene; Nilsson, A.; Boden, H.
2003-01-01
The relation between harmonic structural vibrations and the corresponding acoustic radiation is given by the Helmholtz integral equation (HIE). To solve this integral equation a new solver (BEMSYS) based on the boundary element method (BEM) has been implemented. This numerical tool can be used for b
ROS3P : an accurate third-order Rosenbrock solver designed for parabolic problems
Lang, J.; Verwer, J.G.
2000-01-01
In this note we present a new Rosenbrock solver which is third--order accurate for nonlinear parabolic problems. Since Rosenbrock methods suffer from order reductions when they are applied to partial differential equations, additional order conditions have to be satisfied. Although these conditions
Newton-Raphson preconditioner for Krylov type solvers on GPU devices.
Kushida, Noriyuki
2016-01-01
A new Newton-Raphson method based preconditioner for Krylov type linear equation solvers for GPGPU is developed, and the performance is investigated. Conventional preconditioners improve the convergence of Krylov type solvers, and perform well on CPUs. However, they do not perform well on GPGPUs, because of the complexity of implementing powerful preconditioners. The developed preconditioner is based on the BFGS Hessian matrix approximation technique, which is well known as a robust and fast nonlinear equation solver. Because the Hessian matrix in the BFGS represents the coefficient matrix of a system of linear equations in some sense, the approximated Hessian matrix can be a preconditioner. On the other hand, BFGS is required to store dense matrices and to invert them, which should be avoided on modern computers and supercomputers. To overcome these disadvantages, we therefore introduce a limited memory BFGS, which requires less memory space and less computational effort than the BFGS. In addition, a limited memory BFGS can be implemented with BLAS libraries, which are well optimized for target architectures. There are advantages and disadvantages to the Hessian matrix approximation becoming better as the Krylov solver iteration continues. The preconditioning matrix varies through Krylov solver iterations, and only flexible Krylov solvers can work well with the developed preconditioner. The GCR method, which is a flexible Krylov solver, is employed because of the prevalence of GCR as a Krylov solver with a variable preconditioner. As a result of the performance investigation, the new preconditioner indicates the following benefits: (1) The new preconditioner is robust; i.e., it converges while conventional preconditioners (the diagonal scaling, and the SSOR preconditioners) fail. (2) In the best case scenarios, it is over 10 times faster than conventional preconditioners on a CPU. (3) Because it requries only simple operations, it performs well on a GPGPU. In
Reflection-free finite volume Maxwell's solver for adaptive grids
Elkina, Nina
2015-01-01
We present a non-staggered method for the Maxwell equations in adaptively refined grids. The code is based on finite volume central scheme that preserves in a discrete form both divergence-free property of magnetic field and the Gauss law. High spatial accuracy is achieved with help of non-oscillatory extrema preserving piece-wise or piece-wise-quadratic reconstructions. The semi-discrete equations are solved by implicit-explicit Runge-Kutta method. The new adaptive grid Maxwell's solver is examined based on several 1d examples, including the an propagation of a Gaussian pulse through vacuum and partially ionised gas. Two-dimensional extension is tested with a Gaussian pulse incident on dielectric disc. Additionally, we focus on testing computational accuracy and efficiency.
Nonlinear Multigrid solver exploiting AMGe Coarse Spaces with Approximation Properties
DEFF Research Database (Denmark)
Christensen, Max la Cour; Villa, Umberto; Engsig-Karup, Allan Peter;
The paper introduces a nonlinear multigrid solver for mixed finite element discretizations based on the Full Approximation Scheme (FAS) and element-based Algebraic Multigrid (AMGe). The main motivation to use FAS for unstructured problems is the guaranteed approximation property of the AMGe coarse...... spaces that were developed recently at Lawrence Livermore National Laboratory. These give the ability to derive stable and accurate coarse nonlinear discretization problems. The previous attempts (including ones with the original AMGe method), were less successful due to lack of such good approximation...... are compared to FAS on a nonlinear saddle point problem with applications to porous media flow. It is demonstrated that FAS is faster than Newton’s method and Picard iterations for the experiments considered here. Due to the guaranteed approximation properties of our AMGe, the coarse spaces are very accurate...
Compositions, Random Sums and Continued Random Fractions of Poisson and Fractional Poisson Processes
Orsingher, Enzo; Polito, Federico
2012-08-01
In this paper we consider the relation between random sums and compositions of different processes. In particular, for independent Poisson processes N α ( t), N β ( t), t>0, we have that N_{α}(N_{β}(t)) stackrel{d}{=} sum_{j=1}^{N_{β}(t)} Xj, where the X j s are Poisson random variables. We present a series of similar cases, where the outer process is Poisson with different inner processes. We highlight generalisations of these results where the external process is infinitely divisible. A section of the paper concerns compositions of the form N_{α}(tauk^{ν}), ν∈(0,1], where tauk^{ν} is the inverse of the fractional Poisson process, and we show how these compositions can be represented as random sums. Furthermore we study compositions of the form Θ( N( t)), t>0, which can be represented as random products. The last section is devoted to studying continued fractions of Cauchy random variables with a Poisson number of levels. We evaluate the exact distribution and derive the scale parameter in terms of ratios of Fibonacci numbers.
A Combined MPI-CUDA Parallel Solution of Linear and Nonlinear Poisson-Boltzmann Equation
Colmenares, José; Galizia, Antonella; Ortiz, Jesús; Clematis, Andrea; Rocchia, Walter
2014-01-01
The Poisson-Boltzmann equation models the electrostatic potential generated by fixed charges on a polarizable solute immersed in an ionic solution. This approach is often used in computational structural biology to estimate the electrostatic energetic component of the assembly of molecular biological systems. In the last decades, the amount of data concerning proteins and other biological macromolecules has remarkably increased. To fruitfully exploit these data, a huge computational power is needed as well as software tools capable of exploiting it. It is therefore necessary to move towards high performance computing and to develop proper parallel implementations of already existing and of novel algorithms. Nowadays, workstations can provide an amazing computational power: up to 10 TFLOPS on a single machine equipped with multiple CPUs and accelerators such as Intel Xeon Phi or GPU devices. The actual obstacle to the full exploitation of modern heterogeneous resources is efficient parallel coding and porting of software on such architectures. In this paper, we propose the implementation of a full Poisson-Boltzmann solver based on a finite-difference scheme using different and combined parallel schemes and in particular a mixed MPI-CUDA implementation. Results show great speedups when using the two schemes, achieving an 18.9x speedup using three GPUs. PMID:25013789
A combined MPI-CUDA parallel solution of linear and nonlinear Poisson-Boltzmann equation.
Colmenares, José; Galizia, Antonella; Ortiz, Jesús; Clematis, Andrea; Rocchia, Walter
2014-01-01
The Poisson-Boltzmann equation models the electrostatic potential generated by fixed charges on a polarizable solute immersed in an ionic solution. This approach is often used in computational structural biology to estimate the electrostatic energetic component of the assembly of molecular biological systems. In the last decades, the amount of data concerning proteins and other biological macromolecules has remarkably increased. To fruitfully exploit these data, a huge computational power is needed as well as software tools capable of exploiting it. It is therefore necessary to move towards high performance computing and to develop proper parallel implementations of already existing and of novel algorithms. Nowadays, workstations can provide an amazing computational power: up to 10 TFLOPS on a single machine equipped with multiple CPUs and accelerators such as Intel Xeon Phi or GPU devices. The actual obstacle to the full exploitation of modern heterogeneous resources is efficient parallel coding and porting of software on such architectures. In this paper, we propose the implementation of a full Poisson-Boltzmann solver based on a finite-difference scheme using different and combined parallel schemes and in particular a mixed MPI-CUDA implementation. Results show great speedups when using the two schemes, achieving an 18.9x speedup using three GPUs.
A Combined MPI-CUDA Parallel Solution of Linear and Nonlinear Poisson-Boltzmann Equation
Directory of Open Access Journals (Sweden)
José Colmenares
2014-01-01
Full Text Available The Poisson-Boltzmann equation models the electrostatic potential generated by fixed charges on a polarizable solute immersed in an ionic solution. This approach is often used in computational structural biology to estimate the electrostatic energetic component of the assembly of molecular biological systems. In the last decades, the amount of data concerning proteins and other biological macromolecules has remarkably increased. To fruitfully exploit these data, a huge computational power is needed as well as software tools capable of exploiting it. It is therefore necessary to move towards high performance computing and to develop proper parallel implementations of already existing and of novel algorithms. Nowadays, workstations can provide an amazing computational power: up to 10 TFLOPS on a single machine equipped with multiple CPUs and accelerators such as Intel Xeon Phi or GPU devices. The actual obstacle to the full exploitation of modern heterogeneous resources is efficient parallel coding and porting of software on such architectures. In this paper, we propose the implementation of a full Poisson-Boltzmann solver based on a finite-difference scheme using different and combined parallel schemes and in particular a mixed MPI-CUDA implementation. Results show great speedups when using the two schemes, achieving an 18.9x speedup using three GPUs.
A Nonlocal Poisson-Fermi Model for Ionic Solvent
Xie, Dexuan; Eisenberg, Bob; Scott, L Ridgway
2016-01-01
We propose a nonlocal Poisson-Fermi model for ionic solvent that includes ion size effects and polarization correlations among water molecules in the calculation of electrostatic potential. It includes the previous Poisson-Fermi models as special cases, and its solution is the convolution of a solution of the corresponding nonlocal Poisson dielectric model with a Yukawa-type kernel function. Moreover, the Fermi distribution is shown to be a set of optimal ionic concentration functions in the sense of minimizing an electrostatic potential free energy. Finally, numerical results are reported to show the difference between a Poisson-Fermi solution and a corresponding Poisson solution.
Nonlocal Poisson-Fermi model for ionic solvent.
Xie, Dexuan; Liu, Jinn-Liang; Eisenberg, Bob
2016-07-01
We propose a nonlocal Poisson-Fermi model for ionic solvent that includes ion size effects and polarization correlations among water molecules in the calculation of electrostatic potential. It includes the previous Poisson-Fermi models as special cases, and its solution is the convolution of a solution of the corresponding nonlocal Poisson dielectric model with a Yukawa-like kernel function. The Fermi distribution is shown to be a set of optimal ionic concentration functions in the sense of minimizing an electrostatic potential free energy. Numerical results are reported to show the difference between a Poisson-Fermi solution and a corresponding Poisson solution.
Zhu, Feng; Feng, Weiyue; Wang, Huajian; Huang, Shaosen; Lv, Yisong; Chen, Yong
2013-01-01
X-ray spectral imaging provides quantitative imaging of trace elements in biological sample with high sensitivity. We propose a novel algorithm to promote the signal-to-noise ratio (SNR) of X-ray spectral images that have low photon counts. Firstly, we estimate the image data area that belongs to the homogeneous parts through confidence interval testing. Then, we apply the Poisson regression through its maximum likelihood estimation on this area to estimate the true photon counts from the Poisson noise corrupted data. Unlike other denoising methods based on regression analysis, we use the bootstrap resampling methods to ensure the accuracy of regression estimation. Finally, we use a robust local nonparametric regression method to estimate the baseline and subsequently subtract it from the X-ray spectral data to further improve the SNR of the data. Experiments on several real samples show that the proposed method performs better than some state-of-the-art approaches to ensure accuracy and precision for quantit...
On the fractal characterization of Paretian Poisson processes
Eliazar, Iddo I.; Sokolov, Igor M.
2012-06-01
Paretian Poisson processes are Poisson processes which are defined on the positive half-line, have maximal points, and are quantified by power-law intensities. Paretian Poisson processes are elemental in statistical physics, and are the bedrock of a host of power-law statistics ranging from Pareto's law to anomalous diffusion. In this paper we establish evenness-based fractal characterizations of Paretian Poisson processes. Considering an array of socioeconomic evenness-based measures of statistical heterogeneity, we show that: amongst the realm of Poisson processes which are defined on the positive half-line, and have maximal points, Paretian Poisson processes are the unique class of 'fractal processes' exhibiting scale-invariance. The results established in this paper are diametric to previous results asserting that the scale-invariance of Poisson processes-with respect to physical randomness-based measures of statistical heterogeneity-is characterized by exponential Poissonian intensities.
Compositions, Random Sums and Continued Random Fractions of Poisson and Fractional Poisson Processes
Orsingher, Enzo
2011-01-01
In this paper we consider the relation between random sums and compositions of different processes. In particular, for independent Poisson processes $N_\\alpha(t)$, $N_\\beta(t)$, $t>0$, we show that $N_\\alpha(N_\\beta(t)) \\overset{\\text{d}}{=} \\sum_{j=1}^{N_\\beta(t)} X_j$, where the $X_j$s are Poisson random variables. We present a series of similar cases, the most general of which is the one in which the outer process is Poisson and the inner one is a nonlinear fractional birth process. We highlight generalisations of these results where the external process is infinitely divisible. A section of the paper concerns compositions of the form $N_\\alpha(\\tau_k^\
Adaptive and Iterative Methods for Simulations of Nanopores with the PNP-Stokes Equations
Mitscha-Baude, Gregor; Tulzer, Gerhard; Heitzinger, Clemens
2016-01-01
We present a 3D finite element solver for the nonlinear Poisson-Nernst-Planck (PNP) equations for electrodiffusion, coupled to the Stokes system of fluid dynamics. The model serves as a building block for the simulation of macromolecule dynamics inside nanopore sensors. We add to existing numerical approaches by deploying goal-oriented adaptive mesh refinement. To reduce the computation overhead of mesh adaptivity, our error estimator uses the much cheaper Poisson-Boltzmann equation as a simplified model, which is justified on heuristic grounds but shown to work well in practice. To address the nonlinearity in the full PNP-Stokes system, three different linearization schemes are proposed and investigated, with two segregated iterative approaches both outperforming a naive application of Newton's method. Numerical experiments are reported on a real-world nanopore sensor geometry. We also investigate two different models for the interaction of target molecules with the nanopore sensor through the PNP-Stokes equ...
Polarizable Atomic Multipole Solutes in a Poisson-Boltzmann Continuum
Schnieders, Michael J.; Baker, Nathan A.; Ren, Pengyu; Ponder, Jay W.
2008-01-01
Modeling the change in the electrostatics of organic molecules upon moving from vacuum into solvent, due to polarization, has long been an interesting problem. In vacuum, experimental values for the dipole moments and polarizabilities of small, rigid molecules are known to high accuracy; however, it has generally been difficult to determine these quantities for a polar molecule in water. A theoretical approach introduced by Onsager used vacuum properties of small molecules, including polarizability, dipole moment and size, to predict experimentally known permittivities of neat liquids via the Poisson equation. Since this important advance in understanding the condensed phase, a large number of computational methods have been developed to study solutes embedded in a continuum via numerical solutions to the Poisson-Boltzmann equation (PBE). Only recently have the classical force fields used for studying biomolecules begun to include explicit polarization in their functional forms. Here we describe the theory underlying a newly developed Polarizable Multipole Poisson-Boltzmann (PMPB) continuum electrostatics model, which builds on the Atomic Multipole Optimized Energetics for Biomolecular Applications (AMOEBA) force field. As an application of the PMPB methodology, results are presented for several small folded proteins studied by molecular dynamics in explicit water as well as embedded in the PMPB continuum. The dipole moment of each protein increased on average by a factor of 1.27 in explicit water and 1.26 in continuum solvent. The essentially identical electrostatic response in both models suggests that PMPB electrostatics offers an efficient alternative to sampling explicit solvent molecules for a variety of interesting applications, including binding energies, conformational analysis, and pKa prediction. Introduction of 150 mM salt lowered the electrostatic solvation energy between 2–13 kcal/mole, depending on the formal charge of the protein, but had only a
Analysis of overdispersed count data by mixtures of Poisson variables and Poisson processes.
Hougaard, P; Lee, M L; Whitmore, G A
1997-12-01
Count data often show overdispersion compared to the Poisson distribution. Overdispersion is typically modeled by a random effect for the mean, based on the gamma distribution, leading to the negative binomial distribution for the count. This paper considers a larger family of mixture distributions, including the inverse Gaussian mixture distribution. It is demonstrated that it gives a significantly better fit for a data set on the frequency of epileptic seizures. The same approach can be used to generate counting processes from Poisson processes, where the rate or the time is random. A random rate corresponds to variation between patients, whereas a random time corresponds to variation within patients.
Energy Technology Data Exchange (ETDEWEB)
Fujii, Y. [Japan National Oil Corp., Tokyo (Japan)
1998-04-01
This paper discusses the relationship between elastic wave velocities and physical properties of reservoir rocks. For sandstones, the elastic wave velocity decreases with increasing the porosity and the content of clay minerals. For rocks containing heavy oil, the P-wave velocity decreases with increasing the temperature. The P-wave velocity under dry condition is much more lower than that under water saturated condition. When there are a few percent of gas in pores against the water saturated condition, the P-wave velocity decreases rapidly. It is almost constant under the lower water saturation factor. The S-wave velocity is almost constant independent of the water saturation factor. Accordingly, the water saturation factor can not be estimated from the elastic wave velocity at the water saturation factor between 0% and 96%. The Poisson`s ratio also greatly decreases at the water saturation factor between 96% and 100%, but it is almost constant under the lower water saturation factor. The elastic wave velocity increases with increasing the pressure or increasing the depth. Since closure of cracks by pressure is inhibited due to high pore pressure, degree of increase in the elastic wave velocity is reduced. 14 refs., 6 figs.
High-order Hamiltonian splitting for Vlasov-Poisson equations
Casas, Fernando; Faou, Erwan; Mehrenberger, Michel
2015-01-01
We consider the Vlasov-Poisson equation in a Hamiltonian framework and derive new time splitting methods based on the decomposition of the Hamiltonian functional between the kinetic and electric energy. Assuming smoothness of the solutions, we study the order conditions of such methods. It appears that these conditions are of Runge-Kutta-Nystr{\\"o}m type. In the one dimensional case, the order conditions can be further simplified, and efficient methods of order 6 with a reduced number of stages can be constructed. In the general case, high-order methods can also be constructed using explicit computations of commutators. Numerical results are performed and show the benefit of using high-order splitting schemes in that context. Complete and self-contained proofs of convergence results and rigorous error estimates are also given.
A Novel Interactive MINLP Solver for CAPE Applications
DEFF Research Database (Denmark)
Henriksen, Jens Peter; Støy, S.; Russel, Boris Mariboe;
2000-01-01
This paper presents an interactive MINLP solver that is particularly suitable for solution of process synthesis, design and analysis problems. The interactive MINLP solver is based on the decomposition based MINLP algorithms, where a NLP sub-problem is solved in the innerloop and a MILP master...
Efficient use of iterative solvers in nested topology optimization
DEFF Research Database (Denmark)
Amir, Oded; Stolpe, Mathias; Sigmund, Ole
2009-01-01
by a Krylov subspace iterative solver. By choosing convergence criteria for the iterative solver that are strongly related to the optimization objective and to the design sensitivities, it is possible to terminate the iterative solution of the nested equations earlier compared to traditional convergence...
Experiences with linear solvers for oil reservoir simulation problems
Energy Technology Data Exchange (ETDEWEB)
Joubert, W.; Janardhan, R. [Los Alamos National Lab., NM (United States); Biswas, D.; Carey, G.
1996-12-31
This talk will focus on practical experiences with iterative linear solver algorithms used in conjunction with Amoco Production Company`s Falcon oil reservoir simulation code. The goal of this study is to determine the best linear solver algorithms for these types of problems. The results of numerical experiments will be presented.
Analogues of Euler and Poisson Summation Formulae
Indian Academy of Sciences (India)
Vivek V Rane
2003-08-01
Euler–Maclaurin and Poisson analogues of the summations $\\sum_{a < n ≤ b}(n)f(n), \\sum_{a < n ≤ b}d(n) f(n), \\sum_{a < n ≤ b}d(n)(n) f(n)$ have been obtained in a unified manner, where (()) is a periodic complex sequence; () is the divisor function and () is a sufficiently smooth function on [, ]. We also state a generalised Abel's summation formula, generalised Euler's summation formula and Euler's summation formula in several variables.
The Poisson ratio of crystalline surfaces
Falcioni, Marco; Bowick, Mark; Guitter, Emmanuel; Thorleifsson, Gudmar
1996-01-01
A remarkable theoretical prediction for a crystalline (polymerized) surface is that its Poisson ratio (\\sigma) is negative. Using a large scale Monte Carlo simulation of a simple model of such surfaces we show that this is indeed true. The precise numerical value we find is (\\sigma \\simeq -0.32) on a (128^2) lattice at bending rigidity (kappa = 1.1). This is in excellent agreement with the prediction (\\sigma = -1/3) following from the self-consistent screening approximation of Le Doussal and ...
Poisson sigma models and deformation quantization
Cattaneo, A S; Cattaneo, Alberto S.; Felder, Giovanni
2001-01-01
This is a review aimed at a physics audience on the relation between Poisson sigma models on surfaces with boundary and deformation quantization. These models are topological open string theories. In the classical Hamiltonian approach, we describe the reduced phase space and its structures (symplectic groupoid), explaining in particular the classical origin of the non-commutativity of the string end-point coordinates. We also review the perturbative Lagrangian approach and its connection with Kontsevich's star product. Finally we comment on the relation between the two approaches.
Deterministic Thinning of Finite Poisson Processes
Angel, Omer; Soo, Terry
2009-01-01
Let Pi and Gamma be homogeneous Poisson point processes on a fixed set of finite volume. We prove a necessary and sufficient condition on the two intensities for the existence of a coupling of Pi and Gamma such that Gamma is a deterministic function of Pi, and all points of Gamma are points of Pi. The condition exhibits a surprising lack of monotonicity. However, in the limit of large intensities, the coupling exists if and only if the expected number of points is at least one greater in Pi than in Gamma.
Preconditioned fully implicit PDE solvers for monument conservation
Semplice, Matteo
2010-01-01
Mathematical models for the description, in a quantitative way, of the damages induced on the monuments by the action of specific pollutants are often systems of nonlinear, possibly degenerate, parabolic equations. Although some the asymptotic properties of the solutions are known, for a short window of time, one needs a numerical approximation scheme in order to have a quantitative forecast at any time of interest. In this paper a fully implicit numerical method is proposed, analyzed and numerically tested for parabolic equations of porous media type and on a systems of two PDEs that models the sulfation of marble in monuments. Due to the nonlinear nature of the underlying mathematical model, the use of a fixed point scheme is required and every step implies the solution of large, locally structured, linear systems. A special effort is devoted to the spectral analysis of the relevant matrices and to the design of appropriate iterative or multi-iterative solvers, with special attention to preconditioned Krylo...
Domain Decomposition Solvers for Frequency-Domain Finite Element Equations
Copeland, Dylan
2010-10-05
The paper is devoted to fast iterative solvers for frequency-domain finite element equations approximating linear and nonlinear parabolic initial boundary value problems with time-harmonic excitations. Switching from the time domain to the frequency domain allows us to replace the expensive time-integration procedure by the solution of a simple linear elliptic system for the amplitudes belonging to the sine- and to the cosine-excitation or a large nonlinear elliptic system for the Fourier coefficients in the linear and nonlinear case, respectively. The fast solution of the corresponding linear and nonlinear system of finite element equations is crucial for the competitiveness of this method. © 2011 Springer-Verlag Berlin Heidelberg.
AQUASOL: An efficient solver for the dipolar Poisson–Boltzmann–Langevin equation
Koehl, Patrice; Delarue, Marc
2010-01-01
The Poisson–Boltzmann (PB) formalism is among the most popular approaches to modeling the solvation of molecules. It assumes a continuum model for water, leading to a dielectric permittivity that only depends on position in space. In contrast, the dipolar Poisson–Boltzmann–Langevin (DPBL) formalism represents the solvent as a collection of orientable dipoles with nonuniform concentration; this leads to a nonlinear permittivity function that depends both on the position and on the local electric field at that position. The differences in the assumptions underlying these two models lead to significant differences in the equations they generate. The PB equation is a second order, elliptic, nonlinear partial differential equation (PDE). Its response coefficients correspond to the dielectric permittivity and are therefore constant within each subdomain of the system considered (i.e., inside and outside of the molecules considered). While the DPBL equation is also a second order, elliptic, nonlinear PDE, its response coefficients are nonlinear functions of the electrostatic potential. Many solvers have been developed for the PB equation; to our knowledge, none of these can be directly applied to the DPBL equation. The methods they use may adapt to the difference; their implementations however are PBE specific. We adapted the PBE solver originally developed by Holst and Saied [J. Comput. Chem. 16, 337 (1995)] to the problem of solving the DPBL equation. This solver uses a truncated Newton method with a multigrid preconditioner. Numerical evidences suggest that it converges for the DPBL equation and that the convergence is superlinear. It is found however to be slow and greedy in memory requirement for problems commonly encountered in computational biology and computational chemistry. To circumvent these problems, we propose two variants, a quasi-Newton solver based on a simplified, inexact Jacobian and an iterative self-consistent solver that is based directly on
Chatelin, Robin; Poncet, Philippe
2014-07-01
Particle methods are very convenient to compute transport equations in fluid mechanics as their computational cost is linear and they are not limited by convection stability conditions. To achieve large 3D computations the method must be coupled to efficient algorithms for velocity computations, including a good treatment of non-homogeneities and complex moving geometries. The Penalization method enables to consider moving bodies interaction by adding a term in the conservation of momentum equation. This work introduces a new computational algorithm to solve implicitly in the same step the Penalization term and the Laplace operators, since explicit computations are limited by stability issues, especially at low Reynolds number. This computational algorithm is based on the Sherman-Morrison-Woodbury formula coupled to a GMRES iterative method to reduce the computations to a sequence of Poisson problems: this allows to formulate a penalized Poisson equation as a large perturbation of a standard Poisson, by means of algebraic relations. A direct consequence is the possibility to use fast solvers based on Fast Fourier Transforms for this problem with good efficiency from both the computational and the memory consumption point of views, since these solvers are recursive and they do not perform any matrix assembling. The resulting fluid mechanics computations are very fast and they consume a small amount of memory, compared to a reference solver or a linear system resolution. The present applications focus mainly on a coupling between transport equation and 3D Stokes equations, for studying biological organisms motion in a highly viscous flows with variable viscosity.
Optimising a parallel conjugate gradient solver
Energy Technology Data Exchange (ETDEWEB)
Field, M.R. [O`Reilly Institute, Dublin (Ireland)
1996-12-31
This work arises from the introduction of a parallel iterative solver to a large structural analysis finite element code. The code is called FEX and it was developed at Hitachi`s Mechanical Engineering Laboratory. The FEX package can deal with a large range of structural analysis problems using a large number of finite element techniques. FEX can solve either stress or thermal analysis problems of a range of different types from plane stress to a full three-dimensional model. These problems can consist of a number of different materials which can be modelled by a range of material models. The structure being modelled can have the load applied at either a point or a surface, or by a pressure, a centrifugal force or just gravity. Alternatively a thermal load can be applied with a given initial temperature. The displacement of the structure can be constrained by having a fixed boundary or by prescribing the displacement at a boundary.
Energy Technology Data Exchange (ETDEWEB)
Na, Y. W.; Park, C. E.; Lee, S. Y. [KOPEC, Daejeon (Korea, Republic of)
2009-10-15
As a part of the Ministry of Knowledge Economy (MKE) project, 'Development of safety analysis codes for nuclear power plants', KOPEC has been developing the hydraulic solver code package applicable to the safety analyses of nuclear power plants (NPP's). The matrices of the hydraulic solver are usually sparse and may be asymmetric. In the earlier stage of this project, typical direct matrix solver packages MA48 and MA28 had been tested as matrix solver for the hydraulic solver code, SPACE. The selection was based on the reasonably reliable performance experience from their former version MA18 in RELAP computer code. In the later stage of this project, the iterative methodologies have been being tested in the SPACE code. Among a few candidate iterative solution methodologies tested so far, the biconjugate gradient stabilization methodology (BICGSTAB) has shown the best performance in the applicability test and in the application to the SPACE code. Regardless of all the merits of using the direct solver packages, there are some other aspects of tackling the iterative solution methodologies. The algorithm is much simpler and easier to handle. The potential problems related to the robustness of the iterative solution methodologies have been resolved by applying pre-conditioning methods adjusted and modified as appropriate to the application in the SPACE code. The application strategy of conjugate gradient method was introduced in detail by Schewchuk, Golub and Saad in the middle of 1990's. The application of his methodology to nuclear engineering in Korea started about the same time and is still going on and there are quite a few examples of application to neutronics. Besides, Yang introduced a conjugate gradient method programmed in C++ language. The purpose of this study is to assess the performance and behavior of the iterative solution methodology compared to those of the direct solution methodology still being preferred due to its robustness and
Around Poisson--Mehler summation formula
Szabłowski, Paweł J
2011-01-01
We study some simple generalizations of the Poisson-Mehler summation formula (PM). In particular we exploit farther, the recently obtained equality {\\gamma}_{m,n}(x,y|t,q) = {\\gamma}_{0,0}(x,y|t,q)Q_{m,n}(x,y|t,q) where {\\gamma}_{m,n}(x,y|t,q) = \\Sigma_{i\\geq0}((t^{i})/([i]_{q}!))H_{i+n}(x|q)H_{m+i}(y|q), {H_{n}(x|q)}_{n\\geq-1} are the so called q-Hermite polynomials and {Q_{m,n}(x,y|t,q)}_{n,m\\geq0} are certain polynomials in x,y of order m+n being rational functions in t and q. We study properties of polynomials Q_{m,n}(x,y|t,q) expressing them with the help the so called Al-Salam--Chihara (ASC) polynomials and using them in expansion of the reciprocal of the right hand side of the Poisson-Mehler formula. We prove also some similar in nature equalities like e.g. the following \\Sigma_{i\\geq0}((t^{i})/([i]_{q}!))H_{n+i}(x|q) = H_{n}(x|t,q)\\Sigma_{i\\geq0}((t^{i})/([i]_{q}!))H_{i}(x|q), where H_{n}(x|t,q) is the so called big q-Hermite polynomial. We prove similar equalities involving big q-Hermite and ASC poly...
Renewal characterization of Markov modulated Poisson processes
Directory of Open Access Journals (Sweden)
Marcel F. Neuts
1989-01-01
Full Text Available A Markov Modulated Poisson Process (MMPP M(t defined on a Markov chain J(t is a pure jump process where jumps of M(t occur according to a Poisson process with intensity λi whenever the Markov chain J(t is in state i. M(t is called strongly renewal (SR if M(t is a renewal process for an arbitrary initial probability vector of J(t with full support on P={i:λi>0}. M(t is called weakly renewal (WR if there exists an initial probability vector of J(t such that the resulting MMPP is a renewal process. The purpose of this paper is to develop general characterization theorems for the class SR and some sufficiency theorems for the class WR in terms of the first passage times of the bivariate Markov chain [J(t,M(t]. Relevance to the lumpability of J(t is also studied.
Ground states for Schrodinger-Poisson systems with three growth terms
Directory of Open Access Journals (Sweden)
Hui Zhang
2014-12-01
Full Text Available In this article we study the existence and nonexistence of ground states of the Schrodinger-Poisson system $$\\displaylines{ -\\Delta u+V(xu+K(x\\phi u=Q(xu^3,\\quad x\\in \\mathbb{R}^3,\\cr -\\Delta\\phi=K(xu^2, \\quad x\\in \\mathbb{R}^3, }$$ where V, K, and Q are asymptotically periodic in the variable x. The proof is based on the the method of Nehari manifold and concentration compactness principle. In particular, we develop the method of Nehari manifold for Schrodinger-Poisson systems with three times growth.
Ion-Conserving Modified Poisson-Boltzmann Theory Considering a Steric Effect in an Electrolyte
Sugioka, Hideyuki
2016-12-01
The modified Poisson-Nernst-Planck (MPNP) and modified Poisson-Boltzmann (MPB) equations are well known as fundamental equations that consider a steric effect, which prevents unphysical ion concentrations. However, it is unclear whether they are equivalent or not. To clarify this problem, we propose an improved free energy formulation that considers a steric limit with an ion-conserving condition and successfully derive the ion-conserving modified Poisson-Boltzmann (IC-MPB) equations that are equivalent to the MPNP equations. Furthermore, we numerically examine the equivalence by comparing between the IC-MPB solutions obtained by the Newton method and the steady MPNP solutions obtained by the finite-element finite-volume method. A surprising aspect of our finding is that the MPB solutions are much different from the MPNP (IC-MPB) solutions in a confined space. We consider that our findings will significantly contribute to understanding the surface science between solids and liquids.
Prescription-induced jump distributions in multiplicative Poisson processes
Suweis, Samir; Porporato, Amilcare; Rinaldo, Andrea; Maritan, Amos
2011-06-01
Generalized Langevin equations (GLE) with multiplicative white Poisson noise pose the usual prescription dilemma leading to different evolution equations (master equations) for the probability distribution. Contrary to the case of multiplicative Gaussian white noise, the Stratonovich prescription does not correspond to the well-known midpoint (or any other intermediate) prescription. By introducing an inertial term in the GLE, we show that the Itô and Stratonovich prescriptions naturally arise depending on two time scales, one induced by the inertial term and the other determined by the jump event. We also show that, when the multiplicative noise is linear in the random variable, one prescription can be made equivalent to the other by a suitable transformation in the jump probability distribution. We apply these results to a recently proposed stochastic model describing the dynamics of primary soil salinization, in which the salt mass balance within the soil root zone requires the analysis of different prescriptions arising from the resulting stochastic differential equation forced by multiplicative white Poisson noise, the features of which are tailored to the characters of the daily precipitation. A method is finally suggested to infer the most appropriate prescription from the data.
Heil, Matthias; Hazel, Andrew L.; Boyle, Jonathan
2008-12-01
We compare the relative performance of monolithic and segregated (partitioned) solvers for large- displacement fluid structure interaction (FSI) problems within the framework of oomph-lib, the object-oriented multi-physics finite-element library, available as open-source software at http://www.oomph-lib.org . Monolithic solvers are widely acknowledged to be more robust than their segregated counterparts, but are believed to be too expensive for use in large-scale problems. We demonstrate that monolithic solvers are competitive even for problems in which the fluid solid coupling is weak and, hence, the segregated solvers converge within a moderate number of iterations. The efficient monolithic solution of large-scale FSI problems requires the development of preconditioners for the iterative solution of the linear systems that arise during the solution of the monolithically coupled fluid and solid equations by Newton’s method. We demonstrate that recent improvements to oomph-lib’s FSI preconditioner result in mesh-independent convergence rates under uniform and non-uniform (adaptive) mesh refinement, and explore its performance in a number of two- and three-dimensional test problems involving the interaction of finite-Reynolds-number flows with shell and beam structures, as well as finite-thickness solids.
A Tensor-Train accelerated solver for integral equations in complex geometries
Corona, Eduardo; Rahimian, Abtin; Zorin, Denis
2017-04-01
We present a framework using the Quantized Tensor Train (QTT) decomposition to accurately and efficiently solve volume and boundary integral equations in three dimensions. We describe how the QTT decomposition can be used as a hierarchical compression and inversion scheme for matrices arising from the discretization of integral equations. For a broad range of problems, computational and storage costs of the inversion scheme are extremely modest O (log N) and once the inverse is computed, it can be applied in O (Nlog N) . We analyze the QTT ranks for hierarchically low rank matrices and discuss its relationship to commonly used hierarchical compression techniques such as FMM and HSS. We prove that the QTT ranks are bounded for translation-invariant systems and argue that this behavior extends to non-translation invariant volume and boundary integrals. For volume integrals, the QTT decomposition provides an efficient direct solver requiring significantly less memory compared to other fast direct solvers. We present results demonstrating the remarkable performance of the QTT-based solver when applied to both translation and non-translation invariant volume integrals in 3D. For boundary integral equations, we demonstrate that using a QTT decomposition to construct preconditioners for a Krylov subspace method leads to an efficient and robust solver with a small memory footprint. We test the QTT preconditioners in the iterative solution of an exterior elliptic boundary value problem (Laplace) formulated as a boundary integral equation in complex, multiply connected geometries.
Graph Grammar-Based Multi-Frontal Parallel Direct Solver for Two-Dimensional Isogeometric Analysis
Kuźnik, Krzysztof
2012-06-02
This paper introduces the graph grammar based model for developing multi-thread multi-frontal parallel direct solver for two dimensional isogeometric finite element method. Execution of the solver algorithm has been expressed as the sequence of graph grammar productions. At the beginning productions construct the elimination tree with leaves corresponding to finite elements. Following sequence of graph grammar productions generates element frontal matri-ces at leaf nodes, merges matrices at parent nodes and eliminates rows corresponding to fully assembled degrees of freedom. Finally, there are graph grammar productions responsible for root problem solution and recursive backward substitutions. Expressing the solver algorithm by graph grammar productions allows us to explore the concurrency of the algorithm. The graph grammar productions are grouped into sets of independent tasks that can be executed concurrently. The resulting concurrent multi-frontal solver algorithm is implemented and tested on NVIDIA GPU, providing O(NlogN) execution time complexity where N is the number of degrees of freedom. We have confirmed this complexity by solving up to 1 million of degrees of freedom with 448 cores GPU.
VDJSeq-Solver: in silico V(DJ recombination detection tool.
Directory of Open Access Journals (Sweden)
Giulia Paciello
Full Text Available In this paper we present VDJSeq-Solver, a methodology and tool to identify clonal lymphocyte populations from paired-end RNA Sequencing reads derived from the sequencing of mRNA neoplastic cells. The tool detects the main clone that characterises the tissue of interest by recognizing the most abundant V(DJ rearrangement among the existing ones in the sample under study. The exact sequence of the clone identified is capable of accounting for the modifications introduced by the enzymatic processes. The proposed tool overcomes limitations of currently available lymphocyte rearrangements recognition methods, working on a single sequence at a time, that are not applicable to high-throughput sequencing data. In this work, VDJSeq-Solver has been applied to correctly detect the main clone and identify its sequence on five Mantle Cell Lymphoma samples; then the tool has been tested on twelve Diffuse Large B-Cell Lymphoma samples. In order to comply with the privacy, ethics and intellectual property policies of the University Hospital and the University of Verona, data is available upon request to supporto.utenti@ateneo.univr.it after signing a mandatory Materials Transfer Agreement. VDJSeq-Solver JAVA/Perl/Bash software implementation is free and available at http://eda.polito.it/VDJSeq-Solver/.
On two-echelon inventory systems with Poisson demand and lost sales
Alvarez, Elisa; van der Heijden, Matthijs C.
2011-01-01
We derive approximations for the service levels of two-echelon inventory systems with lost sales and Poisson demand. Our method is simple and accurate for a very broad range of problem instances, including cases with both high and low service levels. In contrast, existing methods only perform well
Uysal, Ismail Enes
2016-10-01
Plasmonic structures are utilized in many applications ranging from bio-medicine to solar energy generation and transfer. Numerical schemes capable of solving equations of classical electrodynamics have been the method of choice for characterizing scattering properties of such structures. However, as dimensions of these plasmonic structures reduce to nanometer scale, quantum mechanical effects start to appear. These effects cannot be accurately modeled by available classical numerical methods. One of these quantum effects is the tunneling, which is observed when two structures are located within a sub-nanometer distance of each other. At these small distances electrons “jump" from one structure to another and introduce a path for electric current to flow. Classical equations of electrodynamics and the schemes used for solving them do not account for this additional current path. This limitation can be lifted by introducing an auxiliary tunnel with material properties obtained using quantum models and applying a classical solver to the structures connected by this auxiliary tunnel. Early work on this topic focused on quantum models that are generated using a simple one-dimensional wave function to find the tunneling probability and assume a simple Drude model for the permittivity of the tunnel. These tunnel models are then used together with a classical frequency domain solver. In this thesis, a time domain surface integral equation solver for quantum corrected analysis of transient plasmonic interactions is proposed. This solver has several advantages: (i) As opposed to frequency domain solvers, it provides results at a broad band of frequencies with a single simulation. (ii) As opposed to differential equation solvers, it only discretizes surfaces (reducing number of unknowns), enforces the radiation condition implicitly (increasing the accuracy), and allows for time step selection independent of spatial discretization (increasing efficiency). The quantum model
A Conway-Maxwell-Poisson (CMP) model to address data dispersion on positron emission tomography.
Santarelli, Maria Filomena; Della Latta, Daniele; Scipioni, Michele; Positano, Vincenzo; Landini, Luigi
2016-10-01
Positron emission tomography (PET) in medicine exploits the properties of positron-emitting unstable nuclei. The pairs of γ- rays emitted after annihilation are revealed by coincidence detectors and stored as projections in a sinogram. It is well known that radioactive decay follows a Poisson distribution; however, deviation from Poisson statistics occurs on PET projection data prior to reconstruction due to physical effects, measurement errors, correction of deadtime, scatter, and random coincidences. A model that describes the statistical behavior of measured and corrected PET data can aid in understanding the statistical nature of the data: it is a prerequisite to develop efficient reconstruction and processing methods and to reduce noise. The deviation from Poisson statistics in PET data could be described by the Conway-Maxwell-Poisson (CMP) distribution model, which is characterized by the centring parameter λ and the dispersion parameter ν, the latter quantifying the deviation from a Poisson distribution model. In particular, the parameter ν allows quantifying over-dispersion (νdispersion (ν>1) of data. A simple and efficient method for λ and ν parameters estimation is introduced and assessed using Monte Carlo simulation for a wide range of activity values. The application of the method to simulated and experimental PET phantom data demonstrated that the CMP distribution parameters could detect deviation from the Poisson distribution both in raw and corrected PET data. It may be usefully implemented in image reconstruction algorithms and quantitative PET data analysis, especially in low counting emission data, as in dynamic PET data, where the method demonstrated the best accuracy.
PENERAPAN REGRESI BINOMIAL NEGATIF UNTUK MENGATASI OVERDISPERSI PADA REGRESI POISSON
Directory of Open Access Journals (Sweden)
PUTU SUSAN PRADAWATI
2013-09-01
Full Text Available Poisson regression was used to analyze the count data which Poisson distributed. Poisson regression analysis requires state equidispersion, in which the mean value of the response variable is equal to the value of the variance. However, there are deviations in which the value of the response variable variance is greater than the mean. This is called overdispersion. If overdispersion happens and Poisson Regression analysis is being used, then underestimated standard errors will be obtained. Negative Binomial Regression can handle overdispersion because it contains a dispersion parameter. From the simulation data which experienced overdispersion in the Poisson Regression model it was found that the Negative Binomial Regression was better than the Poisson Regression model.
PENERAPAN REGRESI BINOMIAL NEGATIF UNTUK MENGATASI OVERDISPERSI PADA REGRESI POISSON
Directory of Open Access Journals (Sweden)
PUTU SUSAN PRADAWATI
2013-09-01
Full Text Available Poisson regression was used to analyze the count data which Poisson distributed. Poisson regression analysis requires state equidispersion, in which the mean value of the response variable is equal to the value of the variance. However, there are deviations in which the value of the response variable variance is greater than the mean. This is called overdispersion. If overdispersion happens and Poisson Regression analysis is being used, then underestimated standard errors will be obtained. Negative Binomial Regression can handle overdispersion because it contains a dispersion parameter. From the simulation data which experienced overdispersion in the Poisson Regression model it was found that the Negative Binomial Regression was better than the Poisson Regression model.
Jeng Hong, Eng; Saudi, Azali; Sulaiman, Jumat
2017-09-01
The demand for image editing in the field of image processing has been increased throughout the world. One of the most famous equations for solving image editing problem is Poisson equation. Due to the advantages of the Successive Over Relaxation (SOR) iterative method with one weighted parameter, this paper examined the efficiency of the Modified Successive Over Relaxation (MSOR) iterative method for solving Poisson image blending problem. As we know, this iterative method requires two weighted parameters by considering the Red-Black ordering strategy, thus comparison of Jacobi, Gauss-Seidel and MSOR iterative methods in solving Poisson image blending problem is carried out in this study. The performance of these iterative methods to solve the problem is examined through assessing the number of iterations and computational time taken. Based on the numerical assessment over several experiments, the findings had shown that MSOR iterative method is able to solve Poisson image blending problem effectively than the other two methods which it requires fewer number of iterations and lesser computational time.
Species Abundance in a Forest Community in South China: A Case of Poisson Lognormal Distribution
Institute of Scientific and Technical Information of China (English)
Zuo-Yun YIN; Hai REN; Qian-Mei ZHANG; Shao-Lin PENG; Qin-Feng GUO; Guo-Yi ZHOU
2005-01-01
Case studies on Poisson lognormal distribution of species abundance have been rare, especially in forest communities. We propose a numerical method to fit the Poisson lognormal to the species abundance data at an evergreen mixed forest in the Dinghushan Biosphere Reserve, South China. Plants in the tree, shrub and herb layers in 25 quadrats of 20 m×20 m, 5 m×5 m, and 1 m×1 m were surveyed. Results indicated that: (i) for each layer, the observed species abundance with a similarly small median, mode, and a variance larger than the mean was reverse J-shaped and followed well the zero-truncated Poisson lognormal;(ii) the coefficient of variation, skewness and kurtosis of abundance, and two Poisson lognormal parameters (σ andμ) for shrub layer were closer to those for the herb layer than those for the tree layer; and (iii) from the tree to the shrub to the herb layer, the σ and the coefficient of variation decreased, whereas diversity increased. We suggest that: (i) the species abundance distributions in the three layers reflects the overall community characteristics; (ii) the Poisson lognormal can describe the species abundance distribution in diverse communities with a few abundant species but many rare species; and (iii) 1/σ should be an alternative measure of diversity.
High-Performance Solvers for Dense Hermitian Eigenproblems
Petschow, Matthias; Bientinesi, Paolo
2012-01-01
We introduce a new collection of solvers - subsequently called EleMRRR - for large-scale dense Hermitian eigenproblems. EleMRRR solves various types of problems: generalized, standard, and tridiagonal eigenproblems. Among these, the last is of particular importance as it is a solver on its own right, as well as the computational kernel for the first two; we present a fast and scalable tridiagonal solver based on the Algorithm of Multiple Relatively Robust Representations - referred to as PMRRR. Like the other EleMRRR solvers, PMRRR is part of the freely available Elemental library, and is designed to fully support both message-passing (MPI) and multithreading parallelism (SMP). As a result, the solvers can equally be used in pure MPI or in hybrid MPI-SMP fashion. We conducted a thorough performance study of EleMRRR and ScaLAPACK's solvers on two supercomputers. Such a study, performed with up to 8,192 cores, provides precise guidelines to assemble the fastest solver within the ScaLAPACK framework; it also ind...
Comparison of open-source linear programming solvers.
Energy Technology Data Exchange (ETDEWEB)
Gearhart, Jared Lee; Adair, Kristin Lynn; Durfee, Justin David.; Jones, Katherine A.; Martin, Nathaniel; Detry, Richard Joseph
2013-10-01
When developing linear programming models, issues such as budget limitations, customer requirements, or licensing may preclude the use of commercial linear programming solvers. In such cases, one option is to use an open-source linear programming solver. A survey of linear programming tools was conducted to identify potential open-source solvers. From this survey, four open-source solvers were tested using a collection of linear programming test problems and the results were compared to IBM ILOG CPLEX Optimizer (CPLEX) [1], an industry standard. The solvers considered were: COIN-OR Linear Programming (CLP) [2], [3], GNU Linear Programming Kit (GLPK) [4], lp_solve [5] and Modular In-core Nonlinear Optimization System (MINOS) [6]. As no open-source solver outperforms CPLEX, this study demonstrates the power of commercial linear programming software. CLP was found to be the top performing open-source solver considered in terms of capability and speed. GLPK also performed well but cannot match the speed of CLP or CPLEX. lp_solve and MINOS were considerably slower and encountered issues when solving several test problems.
Asymptotic Preserving schemes for highly oscillatory Vlasov–Poisson equations
Energy Technology Data Exchange (ETDEWEB)
Crouseilles, Nicolas [INRIA-Rennes Bretagne Atlantique, IPSO Project (France); Lemou, Mohammed [CNRS and IRMAR, Université de Rennes 1 and INRIA-Rennes Bretagne Atlantique, IPSO Project (France); Méhats, Florian, E-mail: florian.mehats@univ-rennes1.fr [IRMAR, Université de Rennes 1 and INRIA-Rennes Bretagne Atlantique, IPSO Project (France)
2013-09-01
This work is devoted to the numerical simulation of a Vlasov–Poisson model describing a charged particle beam under the action of a rapidly oscillating external field. We construct an Asymptotic Preserving numerical scheme for this kinetic equation in the highly oscillatory limit. This scheme enables to simulate the problem without using any time step refinement technique. Moreover, since our numerical method is not based on the derivation of the simulation of asymptotic models, it works in the regime where the solution does not oscillate rapidly, and in the highly oscillatory regime as well. Our method is based on a “two scale” reformulation of the initial equation, with the introduction of an additional periodic variable.
Gauge Poisson representations for birth/death master equations
Drummond, P D
2002-01-01
Poisson representation techniques provide a powerful method for mapping master equations for birth/death processes - found in many fields of physics, chemistry and biology - into more tractable stochastic differential equations. However, the usual expansion is not exact in the presence of boundary terms, which commonly occur when the differential equations are nonlinear. In this paper, a stochastic gauge technique is introduced that eliminates boundary terms, to give an exact representation as a weighted rate equation with stochastic terms. These methods provide novel techniques for calculating and understanding the effects of number correlations in systems that have a master equation description. As examples, correlations induced by strong mutations in genetics, and the astrophysical problem of molecule formation on microscopic grain surfaces are analyzed. Exact analytic results are obtained that can be compared with numerical simulations, demonstrating that stochastic gauge techniques can give exact results...
Poisson brackets of normal-ordered Wilson loops
Lee, C.-W. H.; Rajeev, S. G.
1999-04-01
We formulate Yang-Mills theory in terms of the large-N limit, viewed as a classical limit, of gauge-invariant dynamical variables, which are closely related to Wilson loops, via deformation quantization. We obtain a Poisson algebra of these dynamical variables corresponding to normal-ordered quantum (at a finite value of ℏ) operators. Comparing with a Poisson algebra one of us introduced in the past for Weyl-ordered quantum operators, we find, using ideas closely related to topological graph theory, that these two Poisson algebras are, roughly speaking, the same. More precisely speaking, there exists an invertible Poisson morphism between them.
Poisson process Fock space representation, chaos expansion and covariance inequalities
Last, Guenter
2009-01-01
We consider a Poisson process $\\eta$ on an arbitrary measurable space with an arbitrary sigma-finite intensity measure. We establish an explicit Fock space representation of square integrable functions of $\\eta$. As a consequence we identify explicitly, in terms of iterated difference operators, the integrands in the Wiener-Ito chaos expansion. We apply these results to extend well-known variance inequalities for homogeneous Poisson processes on the line to the general Poisson case. The Poincare inequality is a special case. Further applications are covariance identities for Poisson processes on (strictly) ordered spaces and Harris-FKG-inequalities for monotone functions of $\\eta$.
The fractional Poisson process and the inverse stable subordinator
Meerschaert, Mark M; Vellaisamy, P
2010-01-01
The fractional Poisson process is a renewal process with Mittag-Leffler waiting times. Its distributions solve a time-fractional analogue of the Kolmogorov forward equation for a Poisson process. This paper shows that a traditional Poisson process, with the time variable replaced by an independent inverse stable subordinator, is also a fractional Poisson process. This result unifies the two main approaches in the stochastic theory of time-fractional diffusion equations. The equivalence extends to a broad class of renewal processes that include models for tempered fractional diffusion, and distributed-order (e.g., ultraslow) fractional diffusion.
A Hybrid Method with Deviational Particles for Spatial Inhomogeneous Plasma
Yan, Bokai
2015-01-01
In this work we propose a Hybrid method with Deviational Particles (HDP) for a plasma modeled by the inhomogeneous Vlasov-Poisson-Landau system. We split the distribution into a Maxwellian part evolved by a grid based fluid solver and a deviation part simulated by numerical particles. These particles, named deviational particles, could be both positive and negative. We combine the Monte Carlo method proposed in \\cite{YC15}, a Particle in Cell method and a Macro-Micro decomposition method \\cite{BLM08} to design an efficient hybrid method. Furthermore, coarse particles are employed to accelerate the simulation. A particle resampling technique on both deviational particles and coarse particles is also investigated and improved. The efficiency is significantly improved compared to a PIC-MCC method, especially near the fluid regime.
Parareal in time 3D numerical solver for the LWR Benchmark neutron diffusion transient model
Baudron, Anne-Marie A -M; Maday, Yvon; Riahi, Mohamed Kamel; Salomon, Julien
2014-01-01
We present a parareal in time algorithm for the simulation of neutron diffusion transient model. The method is made efficient by means of a coarse solver defined with large time steps and steady control rods model. Using finite element for the space discretization, our implementation provides a good scalability of the algorithm. Numerical results show the efficiency of the parareal method on large light water reactor transient model corresponding to the Langenbuch-Maurer-Werner (LMW) benchmark [1].
Large-scale 3-D EM modelling with a Block Low-Rank multifrontal direct solver
Shantsev, Daniil V.; Jaysaval, Piyoosh; de la Kethulle de Ryhove, Sébastien; Amestoy, Patrick R.; Buttari, Alfredo; L'Excellent, Jean-Yves; Mary, Theo
2017-06-01
We put forward the idea of using a Block Low-Rank (BLR) multifrontal direct solver to efficiently solve the linear systems of equations arising from a finite-difference discretization of the frequency-domain Maxwell equations for 3-D electromagnetic (EM) problems. The solver uses a low-rank representation for the off-diagonal blocks of the intermediate dense matrices arising in the multifrontal method to reduce the computational load. A numerical threshold, the so-called BLR threshold, controlling the accuracy of low-rank representations was optimized by balancing errors in the computed EM fields against savings in floating point operations (flops). Simulations were carried out over large-scale 3-D resistivity models representing typical scenarios for marine controlled-source EM surveys, and in particular the SEG SEAM model which contains an irregular salt body. The flop count, size of factor matrices and elapsed run time for matrix factorization are reduced dramatically by using BLR representations and can go down to, respectively, 10, 30 and 40 per cent of their full-rank values for our largest system with N = 20.6 million unknowns. The reductions are almost independent of the number of MPI tasks and threads at least up to 90 × 10 = 900 cores. The BLR savings increase for larger systems, which reduces the factorization flop complexity from O(N2) for the full-rank solver to O(Nm) with m = 1.4-1.6. The BLR savings are significantly larger for deep-water environments that exclude the highly resistive air layer from the computational domain. A study in a scenario where simulations are required at multiple source locations shows that the BLR solver can become competitive in comparison to iterative solvers as an engine for 3-D controlled-source electromagnetic Gauss-Newton inversion that requires forward modelling for a few thousand right-hand sides.
An exact representation of the fermion dynamics in terms of Poisson processes
Beccaria, M; De Angelis, G F; Jona-Lasinio, G; Beccaria, Matteo; Presilla, Carlo; Angelis, Gian Fabrizio De; Jona-Lasinio, Giovanni
1999-01-01
We present a simple derivation of a Feynman-Kac type formula to study fermionic systems. In this approach the real time or the imaginary time dynamics is expressed in terms of the evolution of a collection of Poisson processes. A computer implementation of this formula leads to a family of algorithms parametrized by the values of the jump rates of the Poisson processes. From these an optimal algorithm can be chosen which coincides with the Green Function Monte Carlo (GFMC) method in the limit when the latter becomes exact.
A steady-state solver and stability calculator for nonlinear internal wave flows
Viner, Kevin C.; Epifanio, Craig C.; Doyle, James D.
2013-10-01
A steady solver and stability calculator is presented for the problem of nonlinear internal gravity waves forced by topography. Steady-state solutions are obtained using Newton's method, as applied to a finite-difference discretization in terrain-following coordinates. The iteration is initialized using a boundary-inflation scheme, in which the nonlinearity of the flow is gradually increased over the first few Newton steps. The resulting method is shown to be robust over the full range of nonhydrostatic and rotating parameter space. Examples are given for both nonhydrostatic and rotating flows, as well as flows with realistic upstream shear and static stability profiles. With a modest extension, the solver also allows for a linear stability analysis of the steady-state wave fields. Unstable modes are computed using a shifted-inverse method, combined with a parameter-space search over a set of realistic target values. An example is given showing resonant instability in a nonhydrostatic mountain wave.
Gauss-Seidel Accelerated: Implementing Flow Solvers on Field Programmable Gate Arrays
Energy Technology Data Exchange (ETDEWEB)
Chassin, David P.; Armstrong, Peter R.; Chavarría-Miranda, Daniel; Guttromson, Ross T.
2006-06-01
Non-linear steady-state power flow solvers have typically relied on the Newton-Raphson method to efficiently compute solutions on today's computer systems. Field Programmable Gate Array (FPGA) devices, which have recently been integrated into high-performance computers by major computer system vendors, offer an opportunity to significantly increase the performance of power flow solvers. However, only some algorithms are suitable for an FPGA implementation. The Gauss-Seidel method of solving the AC power flow problem is an excellent example of such an opportunity. In this paper we discuss algorithmic design considerations, optimization, implementation, and performance results of the implementation of the Gauss-Seidel method running on a Silicon Graphics Inc. Altix-350 computer equipped with a Xilinx Virtex II 6000 FPGA.
Anisotropic norm-oriented mesh adaptation for a Poisson problem
Brèthes, Gautier; Dervieux, Alain
2016-10-01
We present a novel formulation for the mesh adaptation of the approximation of a Partial Differential Equation (PDE). The discussion is restricted to a Poisson problem. The proposed norm-oriented formulation extends the goal-oriented formulation since it is equation-based and uses an adjoint. At the same time, the norm-oriented formulation somewhat supersedes the goal-oriented one since it is basically a solution-convergent method. Indeed, goal-oriented methods rely on the reduction of the error in evaluating a chosen scalar output with the consequence that, as mesh size is increased (more degrees of freedom), only this output is proven to tend to its continuous analog while the solution field itself may not converge. A remarkable quality of goal-oriented metric-based adaptation is the mathematical formulation of the mesh adaptation problem under the form of the optimization, in the well-identified set of metrics, of a well-defined functional. In the new proposed formulation, we amplify this advantage. We search, in the same well-identified set of metrics, the minimum of a norm of the approximation error. The norm is prescribed by the user and the method allows addressing the case of multi-objective adaptation like, for example in aerodynamics, adaptating the mesh for drag, lift and moment in one shot. In this work, we consider the basic linear finite-element approximation and restrict our study to L2 norm in order to enjoy second-order convergence. Numerical examples for the Poisson problem are computed.
Institute of Scientific and Technical Information of China (English)
Shen Chun; Sun Fengxian; Xia Xinlin
2013-01-01
Open source field operation and manipulation (OpenFOAM) is one of the most preva-lent open source computational fluid dynamics (CFD) software. It is very convenient for researchers to develop their own codes based on the class library toolbox within OpenFOAM. In recent years, several density-based solvers within OpenFOAM for supersonic/hypersonic compressible flow are coming up. Although the capabilities of these solvers to capture shock wave have already been ver-ified by some researchers, these solvers still need to be validated comprehensively as commercial CFD software. In boundary layer where diffusion is the dominant transportation manner, the con-vective discrete schemes’ capability to capture aerothermal variables, such as temperature and heat flux, is different from each other due to their own numerical dissipative characteristics and from viewpoint of this capability, these compressible solvers within OpenFOAM can be validated further. In this paper, firstly, the organizational architecture of density-based solvers within OpenFOAM is analyzed. Then, from the viewpoint of the capability to capture aerothermal vari-ables, the numerical results of several typical geometrical fields predicted by these solvers are com-pared with both the outcome obtained from the commercial software Fastran and the experimental data. During the computing process, the Roe, AUSM+(Advection Upstream Splitting Method), and HLLC(Harten-Lax-van Leer-Contact) convective discrete schemes of which the spatial accu-racy is 1st and 2nd order are utilized, respectively. The compared results show that the aerothermal variables are in agreement with results generated by Fastran and the experimental data even if the 1st order spatial precision is implemented. Overall, the accuracy of these density-based solvers can meet the requirement of engineering and scientific problems to capture aerothermal variables in diffusion boundary layer.
Steijl, R.; Hoeijmakers, H. W. M.
2004-09-01
A fourth-order accurate solution method for the three-dimensional Helmholtz equations is described that is based on a compact finite-difference stencil for the Laplace operator. Similar discretization methods for the Poisson equation have been presented by various researchers for Dirichlet boundary conditions. Here, the complicated issue of imposing Neumann boundary conditions is described in detail. The method is then applied to model Helmholtz problems to verify the accuracy of the discretization method. The implementation of the solution method is also described. The Helmholtz solver is used as the basis for a fourth-order accurate solver for the incompressible Navier-Stokes equations. Numerical results obtained with this Navier-Stokes solver for the temporal evolution of a three-dimensional instability in a counter-rotating vortex pair are discussed. The time-accurate Navier-Stokes simulations show the resolving properties of the developed discretization method and the correct prediction of the initial growth rate of the three-dimensional instability in the vortex pair.
Cooper, Christopher D
2015-01-01
Interactions between surfaces and proteins occur in many vital processes and are crucial in biotechnology: the ability to control specific interactions is essential in fields like biomaterials, biomedical implants and biosensors. In the latter case, biosensor sensitivity hinges on ligand proteins adsorbing on bioactive surfaces with a favorable orientation, exposing reaction sites to target molecules. Protein adsorption, being a free-energy-driven process, is difficult to study experimentally. This paper develops and evaluates a computational model to study electrostatic interactions of proteins and charged nanosurfaces, via the Poisson-Boltzmann equation. We extended the implicit-solvent model used in the open-source code PyGBe to include surfaces of imposed charge or potential. This code solves the boundary integral formulation of the Poisson-Boltzmann equation, discretized with surface elements. PyGBe has at its core a treecode-accelerated Krylov iterative solver, resulting in O(N log N) scaling, with furt...
Tetrahedral meshing via maximal Poisson-disk sampling
Guo, Jianwei
2016-02-15
In this paper, we propose a simple yet effective method to generate 3D-conforming tetrahedral meshes from closed 2-manifold surfaces. Our approach is inspired by recent work on maximal Poisson-disk sampling (MPS), which can generate well-distributed point sets in arbitrary domains. We first perform MPS on the boundary of the input domain, we then sample the interior of the domain, and we finally extract the tetrahedral mesh from the samples by using 3D Delaunay or regular triangulation for uniform or adaptive sampling, respectively. We also propose an efficient optimization strategy to protect the domain boundaries and to remove slivers to improve the meshing quality. We present various experimental results to illustrate the efficiency and the robustness of our proposed approach. We demonstrate that the performance and quality (e.g., minimal dihedral angle) of our approach are superior to current state-of-the-art optimization-based approaches.
Modeling the number of car theft using Poisson regression
Zulkifli, Malina; Ling, Agnes Beh Yen; Kasim, Maznah Mat; Ismail, Noriszura
2016-10-01
Regression analysis is the most popular statistical methods used to express the relationship between the variables of response with the covariates. The aim of this paper is to evaluate the factors that influence the number of car theft using Poisson regression model. This paper will focus on the number of car thefts that occurred in districts in Peninsular Malaysia. There are two groups of factor that have been considered, namely district descriptive factors and socio and demographic factors. The result of the study showed that Bumiputera composition, Chinese composition, Other ethnic composition, foreign migration, number of residence with the age between 25 to 64, number of employed person and number of unemployed person are the most influence factors that affect the car theft cases. These information are very useful for the law enforcement department, insurance company and car owners in order to reduce and limiting the car theft cases in Peninsular Malaysia.
Nonhomogeneous poisson process for reverberant and semi-reverberant environment characterization
Serra, Ramiro; Leferink, Frank Bernardus Johannes; Canavero, Flavio
2011-01-01
Abstract—We develop and evaluate a method to estimate the cumulative intensity function of nonhomogeneous Poisson processes (NHPP) observed in different configurations of a reverberation chamber. The counting data collects the number of different anomalous statistics occurrences as a function of the
Convergence of the Vlasov-Poisson-Fokker- Planck system to the incompressible Euler equations
Institute of Scientific and Technical Information of China (English)
无
2006-01-01
We establish the convergence of the Vlasov-Poisson-Fokker-Planck system to the incompressible Euler equations in this paper. The convergence is rigorously proved on the time interval where the smooth solution to the incompressible Euler equations exists. The proof relies on the compactness argument and the so-called relative-entropy method.