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At least 217 records · Page 12Linked to original sources

Preconditioned Recycling Krylov subspace methods for self-adjoint problems

The authors propose a recycling Krylov subspace method for the solution of a sequence of self-adjoint linear systems. Such problems appear, for example, in the Newton process for solving nonlinear equations. Ritz vectors are automatically extracted from one MINRES run and then used for self-adjoint deflation in the next. The method is designed to work with arbitrary inner products and arbitrary self-adjoint positive-definite preconditioners whose inverse can be computed with high accuracy. Numerical experiments with nonlinear Schrödinger equations indicate a substantial decrease in computation time when recycling is used.

math.NA↗

Derivation of Radiation from a Dipole immersed in a Homogenous Magnetized Plasma

We are considering a dipole antenna immersed in cold plasma and investigate its radiation patterns. We are solving Maxwell's equations using (1) analytic solutions for the case when the antenna is parallel to the magnetic field $B_0$ and (2) numerical solutions for any orientation and angle $θ$ of the antenna. We investigate various phase velocities regimes as well as the effect of varying the frequency and the plasma parameters on the electromagnetic waves are presented and discussed.

physics.plasm-ph↗

A novel efficient numerical solution of Poisson equation for arbitrary shapes in two dimensions

We propose a novel efficient algorithm to solve Poisson equation in irregular two dimensional domains for electrostatics. It can handle Dirichlet, Neumann or mixed boundary problems in which the filling media can be homogeneous or inhomogeneous. The basic idea of the new method is solve the problem in three steps: (i) First solve the equation $\nabla\cdot\mathbf D=ρ$. The inverse of the divergence operator in a restricted subspace is found to yield the electric flux density $\mathbf D$ by a fast direct solver in O(N) operations. The $\mathbf D$ so obtained is nonunique with indeterminate divergence-free component. Then the electric field is found by $\mathbf E=\mathbf D/ε$. But $\nabla\times\mathbf E=0$ for electrostatic field; hence, $\mathbf E$ is curl free and orthogonal to the divergence free space. (ii) An orthogonalization process is used to purify the electric field making it curl free and unique. (iii) Then the potential $ϕ$ is obtained by solving $\nabla ϕ=-\mathbf E$ or finding the inverse of the gradient operator in a restricted subspace by a similar fast direct solver in O(N) operations. Treatments for both Dirichlet and Neumann boundary conditions are addressed. Finally, the validation and efficiency are illustrated by several numerical examples. Through these simulations, it is observed that the computational complexity of our proposed method almost scales as O(N) where N is the triangle patch number of meshes. Consequently, this new algorithm is a feasible fast Poisson solver.

math-ph↗

CuBA - a CUDA implementation of BAMPS

Using CUDA as programming language, we create a code named CuBA which is based on the CPU code "Boltzmann Approach for Many Parton Scattering (BAMPS)" developed in Frankfurt in order to study a system of many colliding particles resulting from heavy ion collisions. Furthermore, we benchmark our code with the Riemann Problem and compare the results with BAMPS. They demonstrate an improvement of the computational runtime, by one order of magitude.

hep-ph↗

Transition from ideal to viscous Mach cones in BAMPS

We investigate in a microscopical transport model the evolution of conical structures originating from the supersonic projectile moving through the matter of ultrarelativistic particles. Using different scenarios for the interaction between projectile and matter, and different transport properties of the matter, we study the formation and structure of Mach cones. Furthermore, the two-particle correlations for different viscosities are extracted from the numerical calculations and we compare them to an analytical approximation. In addition, by adjusting he cross section we investigate the influence of the viscosity to the structure of Mach cones.

hep-ph↗

Numerical Study of Geometric Multigrid Methods on CPU--GPU Heterogeneous Computers

The geometric multigrid method (GMG) is one of the most efficient solving techniques for discrete algebraic systems arising from elliptic partial differential equations. GMG utilizes a hierarchy of grids or discretizations and reduces the error at a number of frequencies simultaneously. Graphics processing units (GPUs) have recently burst onto the scientific computing scene as a technology that has yielded substantial performance and energy-efficiency improvements. A central challenge in implementing GMG on GPUs, though, is that computational work on coarse levels cannot fully utilize the capacity of a GPU. In this work, we perform numerical studies of GMG on CPU--GPU heterogeneous computers. Furthermore, we compare our implementation with an efficient CPU implementation of GMG and with the most popular fast Poisson solver, Fast Fourier Transform, in the cuFFT library developed by NVIDIA.

math.NA↗

Improved Maximum Entropy Method with an Extended Search Space

We report on an improvement to the implementation of the Maximum Entropy Method (MEM). It amounts to departing from the search space obtained through a singular value decomposition (SVD) of the Kernel. Based on the shape of the SVD basis functions we argue that the MEM spectrum for given $N_τ$ data-points $D(τ)$ and prior information $m(ω)$ does not in general lie in this $N_τ$ dimensional singular subspace. Systematically extending the search basis will eventually recover the full search space and the correct extremum. We illustrate this idea through a mock data analysis inspired by actual lattice spectra, to show where our improvement becomes essential for the success of the MEM. To remedy the shortcomings of Bryan's SVD prescription we propose to use the real Fourier basis, which consists of trigonometric functions. Not only does our approach lead to more stable numerical behavior, as the SVD is not required for the determination of the basis functions, but also the resolution of the MEM becomes independent from the position of the reconstructed peaks.

physics.comp-ph↗

A method for calculating solvation structure on a sample surface from a force curve between a probe and the sample: One-dimensional version

Recent surface force apparatus (SFA) and atomic force microscopy (AFM) can measure force curves between a probe and a sample surface in solvent. The force curve is thought as the solvation structure in some articles, because its shape is generally oscilltive and pitch of the oscillation is about the same as diameter of the solvent. However, it is not the solvation structure. It is only the force between the probe and the sample surface. Therefore, this brief paper presents a method for calculating the solvation structure from the force curve. The method is constructed by using integral equation theory, a statistical mechanics of liquid (Ornstein-Zernike equation coupled by hypernetted-chain closure). This method is considered to be important for elucidation of the solvation structure on a sample surface.

physics.chem-ph↗

A three-dimensional domain decomposition method for large-scale DFT electronic structure calculations

With tens of petaflops supercomputers already in operation and exaflops machines expected to appear within the next 10 years, efficient parallel computational methods are required to take advantage of such extreme-scale machines. In this paper, we present a three-dimensional domain decomposition scheme for enabling large-scale electronic calculations based on density functional theory (DFT) on massively parallel computers. It is composed of two methods: (i) atom decomposition method and (ii) grid decomposition method. In the former, we develop a modified recursive bisection method based on inertia tensor moment to reorder the atoms along a principal axis so that atoms that are close in real space are also close on the axis to ensure data locality. The atoms are then divided into sub-domains depending on their projections onto the principal axis in a balanced way among the processes. In the latter, we define four data structures for the partitioning of grids that are carefully constructed to make data locality consistent with that of the clustered atoms for minimizing data communications between the processes. We also propose a decomposition method for solving the Poisson equation using three-dimensional FFT in Hartree potential calculation, which is shown to be better than a previously proposed parallelization method based on a two-dimensional decomposition in terms of communication efficiency. For evaluation, we perform benchmark calculations with our open-source DFT code, OpenMX, paying particular attention to the O(N) Krylov subspace method. The results show that our scheme exhibits good strong and weak scaling properties, with the parallel efficiency at 131,072 cores being 67.7% compared to the baseline of 16,384 cores with 131,072 diamond atoms on the K computer.

cond-mat.mtrl-sci↗

A proposal to first principles electronic structure calculation: Symbolic-Numeric method

This study proposes an approach toward the first principles electronic structure calculation with the aid of symbolic-numeric solving. The symbolic computation enables us to express the Hartree-Fock-Roothaan equation and the molecular integrals in analytic forms and approximate them as a set of polynomial equations. By use of the Grobner bases technique, the polynomial equations are transformed into other ones which have identical roots. The converted equations take more convenient forms which will simplify numerical procedures, from which we can derive necessary physical properties in order, in an a la carte way. This method enables us to solve the electronic structure calculation, the optimization of any kind, or the inverse problem as a forward problem in a unified way, in which there is no need for iterative self-consistent procedures with trials and errors.

cs.SC↗

Simplification of QPLDA: A practical method to the correction for the LDA band gap problem

It is necessary to employ quasi-particle calculations to correct band gap problems in LDA. As an expedient way for the reliable but massive GWA, Quasi-Particle-LDA (QPLDA) is proposed by several authors, where the total computational cost scales with N. Historically, Sham and Kohn introduced the idea of the local mass operator based on local wavenumber similar to WKB, but did not execute actual numerical calculations. They took into account exchange interaction only, from which we could not expect precise treatments anyway. Later, Pickett and Wang had proposed a more qualitative method and had shown its potentiality in examples of semiconductors, such as silicon, diamond and GaP. They used a model analytic formula for the dialectic function and adopted a model energy dispersion, which is free-electron like one, except that, being accompanied with an artificial band-gap discontinuity. The latter method has two shortcomings. First, to execute the calculation, several parameters are needed, such as the macroscopic dielectric constant and the band gap, which should be evaluated by the calculation itself, rather than being prepared as parameters. Second, in their computation of the mass operator, two or three dimensional numerical integrations are needed on each point of the direct space mesh, which demand large computational costs in iterative procedures in determining local wavenumbers and quasi-particle energies. This may be the reason why QPLDA has not been widely used until now. The present work proposes a qualitative way of QPLDA which does not need any experimental parameters, being much speedier than the formalism of Picket and Wang, and more precise than that of Sham and Kohn. The computational method adopted by the present work is a modification of the original proposal by Sham and Kohn, rather than that of Picket and Wang.

physics.comp-ph↗

Efficient determination of the energy landscape of nonlinear Schrödinger-type equations

We describe a systematic approach for the efficient numerical solution of nonlinear Schrödinger-type partial differential equations of the form $(K +V + g|ψ|^2)ψ=0$, with an energy operator $K$, a scalar potential $V$, and a scalar parameter $g$. Instrumental to the approach are developments in numerical linear and nonlinear algebra, specifically numerical parameter continuation. We demonstrate how a continuous sequence of solutions can be obtained regardless of their stability, so that finally the spectrum of stable and unstable solutions in the specified parameter range is fully revealed. The method is demonstrated for the GL equation in a three-dimensional superconducting domain with an inhomogeneous magnetic field, a numerically demanding problem known to have an involved solution landscape.

physics.comp-ph↗

Mellin Transform and Image Charge Method for Dielectric Sphere in an Electrolyte

We revisit the image charge method for the Green's function problem of the Poisson-Boltzmann equation for a dielectric sphere immersed in ionic solutions. Using finite Mellin transformation, we represent the reaction potential due to a source charge inside the sphere in terms of one dimensional distribution of image charges. The image charges are generically composed of a point image at the Kelvin point and a line image extending from the Kelvin point to infinity with an oscillatory line charge strength. We further develop an efficient and accurate algorithm for discretization of the line image using Padé approximation and finite fraction expansion. Finally we illustrate the power of our method by applying it in a multiscale reaction-field Monte Carlo simulation of monovalent electrolytes.

physics.comp-ph↗

Enhanced Community Structure Detection in Complex Networks with Partial Background Information

Community structure detection in complex networks is important since it can help better understand the network topology and how the network works. However, there is still not a clear and widely-accepted definition of community structure, and in practice, different models may give very different results of communities, making it hard to explain the results. In this paper, different from the traditional methodologies, we design an enhanced semi-supervised learning framework for community detection, which can effectively incorporate the available prior information to guide the detection process and can make the results more explainable. By logical inference, the prior information is more fully utilized. The experiments on both the synthetic and the real-world networks confirm the effectiveness of the framework.

cs.SI↗

Computer Models Design for Teaching and Learning using Easy Java Simulation

We are teachers who have benefited from the Open Source Physics (Brown, 2012; Christian, 2010; Esquembre, 2012) community's work and we would like to share some of the computer models and lesson packages that we have designed and implemented in five schools grade 11 to 12 classes. In a ground-up teacher-leadership (MOE, 2010) approach, we came together to learn, advancing the professionalism (MOE, 2009) of physics educators and improve students' learning experiences through suitable blend (Jaakkola, 2012) of real equipment and computer models where appropriate . We will share computer models that we have remixed from existing library of computer models into suitable learning environments for inquiry of physics customized (Wee & Mak, 2009) for the Advanced Level Physics syllabus (SEAB, 2010, 2012). We hope other teachers would find these computer models useful and remix them to suit their own context, design better learning activities and share them to benefit all humankind, becoming citizens for the world. This is an eduLab (MOE, 2012b; Wee, 2010) project funded by the National Research Fund (NRF) Singapore and Ministry of Education (MOE) Singapore.

physics.ed-ph↗

Everything you wanted to know about Data Analysis and Fitting but were afraid to ask

These notes discuss, in a style intended for physicists, how to average data and fit it to some functional form. I try to make clear what is being calculated, what assumptions are being made, and to give a derivation of results rather than just quote them. The aim is put a lot useful pedagogical material together in a convenient place. This manuscript is a substantial enlargement of lecture notes I prepared for the Bad Honnef School on "Efficient Algorithms in Computational Physics", September 10-14, 2012.

physics.data-an↗

Molecular dissipation in the nonlinear eddy viscosity in the Navier-Stokes equations: modelling of accretion discs

Physical damping, regarding the nonlinear Navier-Stokes viscous flow dynamics, refers to a tensorial turbulent dissipation term, attributed to adjacent moving macroscopic flow components. Mutual dissipation among these parts of fluid is described by a braking term in the momentum equation together with a heating term in the energy equation, both responsible of the damping of the momentum variation and of the viscous conversion of mechanical energy into heat. A macroscopic mixing scale length is currently the only characteristic length needed in the nonlinear modelling of viscous fluid dynamics describing the nonlinear eddy viscosity through the kinematic viscosity coefficient in the viscous stress tensor, without any reference to the chemical composition and to the atomic dimensions. Therefore, in this paper, we write a new formulation for the kinematic viscosity coefficient to the turbulent viscous physical dissipation in the Navier-Stokes equations, where molecular parameters are also included. Results of 2D tests are shown, where comparisons among flow structures are made on 2D shockless radial viscous transport and on 2D damping of collisional chaotic turbulence. An application to the 3D accretion disc modelling in low mass cataclysmic variables is also discussed. Consequences of the kinematic viscosity coefficient reformulation in a more strictly physical terms on the thermal conductivity coefficient for dilute gases are also discussed. The physical nature of the discussion here reported excludes any dependence by the pure mathematical aspect of the numerical modelling.

physics.flu-dyn↗

Tidal Tails of Interacting Galaxies

This paper has been withdrawn by the author. A computer simulation of two galaxies, passing in parabolic orbits, was made to show their interaction and the tidal patterns formed. The galaxies were modelled as a point masses surrounded by 5 densely packed, concentric rings of test masses in circular motion, which represented the outer disk of the galaxy. Several features were noticeable in the simulations, including: a bridge forming between the two galaxies during the interaction, mass being lost to the perturbing galaxy and universe, and an arching counterarm emanating away from the bridge. The results suggest the process was primarily kinematic. Quantitative analysis was made on the counterarm length dependence on galaxy separation and mass ratio. In both cases linear relationships were found with arm length increasing for smaller separations and for larger perturbing masses. The effects were greatly reduced in a retrograde interaction. The images were compared to astrophysical observations and qualitative features matched.

astro-ph.GA↗