In this paper, we present a new type of Hermite weighted essentially non-oscillatory (HWENO) schemes for solving the Hamilton-Jacobi equations on the finite volume framework. The cell averages of the function and its first one (in one dimension) or two (in two dimensions) derivative values are together evolved via time approaching and used in the reconstructions. And the major advantages of the new HWENO schemes are their compactness in the spacial field, purely on the finite volume framework and only one set of small stencils is used for different type of the polynomial reconstructions. Extensive numerical tests are performed to illustrate the capability of the methodologies.

In this paper, we study an exponential time differencing method for solving the gauge system of incompressible viscous flows governed by Stokes or Navier-Stokes equations. The momentum equation is decoupled from the kinematic equation at a discrete level and is then solved by exponential time stepping multistep schemes in our approach. We analyze the stability of the proposed method and rigorously prove that the first order exponential time differencing scheme is unconditionally stable for the Stokes problem. We also present a compact representation of the algorithm for problems on rectangular domains, which makes FFT-based solvers available for the resulting fully discretized system. Various numerical experiments in two and three dimensional spaces are carried out to demonstrate the accuracy and stability of the proposed method.

It is well-known that the traditional full integral quadrilateral element fails to provide accurate results to the Helmholtz equation with large wave numbers due to the “pollution error” caused by the numerical dispersion. To overcome this deficiency, this paper proposed an element decomposition method (EDM) for analyzing 2D acoustic problems by using quadrilateral element. In the present EDM, the quadrilateral element is first subdivided into four sub-triangles, and the local acoustic gradient in each sub-triangle is obtained using linear interpolation function. The acoustic gradient field of the whole quadrilateral is then formulated through a weighted averaging operation, which means only one integration point is adopted to construct the system matrix. To cure the numerical instability of one-point integration, a variation gradient item is complemented by variance of the local gradients. The discretized system equations are derived using the generalized Galerkin weakform. Numerical examples demonstrate that the EDM can achieves better accuracy and higher computational efficiency. Besides, as no mapping or coordinate transformation is involved, restrictions on the shape elements can be easily removed, which makes the EDM works well even for severely distorted meshes.

We present a high precision frequency determination method for digitized NMR FID signals. The method employs high precision numerical integration rather than simple summation as in many other techniques. With no independent knowledge of the other parameters of a NMR FID signal (phase ф, amplitude A, and transverse relaxation time T2) this method can determine the signal frequency f0 with a precision of if the observation time T ≫ T2. The method is especially convenient when the detailed shape of the observed FT NMR spectrum is not well defined. When T2 is +∞ and the signal becomes pure sinusoidal, the precision of the method is which is one order more precise than the ±1 count error induced precision of a typical frequency counter. Analysis of this method shows that the integration reduces the noise by bandwidth narrowing as in a lock-in amplifier, and no extra signal filters are needed. For a pure sinusoidal signal we find from numerical simulations that the noise-induced error in this method reaches the Cramer-Rao Lower Band (CRLB) on frequency determination. For the damped sinusoidal case of most interest, the noise-induced error is found to be within a factor of 2 of CRLB when the measurement time T is 2 or 3 times larger than T2. We discuss possible improvements for the precision of this method.

The emission of scission neutrons from fissioning nuclei is of high practical interest. To study this process we have used the sudden approximation and also a more realistic approach that takes into account the scission dynamics. Numerically, this implies the solution of the bi-dimensional Schrödinger equation, both stationary and time-dependent. To describe axially symmetric extremely deformed nuclear shapes, we have used the Cassini parametrization. The Hamiltonian is discretized by using finite difference approximations of the derivatives. The main computational challenges are the solution of algebraic eigenvalue problems and of linear systems with large sparse matrices. We have employed appropriate procedures (Arnoldi and bi-conjugate gradients). The numerical solutions have been used to evaluate physical quantities, like the number of emitted neutrons per scission event, the primary fragments’ excitation energy and the distribution of the emission points.

In magnetically confined plasma research, the understandings of small and large perturbations at equilibrium are both critical for plasma controlling and steady state operation. Numerical simulations using original MHD model can hardly give clear picture for small perturbations, while non-conservative perturbed MHD model may break conservation law, and give unphysical results when perturbations grow large after long-time computation. In this paper, we present a nonlinear conservative perturbed MHD model by splitting primary variables in original MHD equations into equilibrium part and perturbed part, and apply an approach in the framework of discontinuous Galerkin (DG) spatial discretization for numerical solutions. This enables high resolution of very small perturbations, and also gives satisfactory non-smooth solutions for large perturbations, which are both broadly concerned in magnetically confined plasma research. Numerical examples demonstrate satisfactory performance of the proposed model clearly. For small perturbations, the results have higher resolution comparing with the original MHD model; for large perturbations, the non-smooth solutions match well with existing references, confirming reliability of the model for instability investigations in magnetically confined plasma numerical research.

The singularity of specific heat CV of the three-dimensional Ising model is studied based on Monte Carlo data for lattice sizes L≤1536. Fits of two data sets, one corresponding to certain value of the Binder cumulant and the other — to the maximum of CV, provide consistent values of C0 in the ansatz CV(L)=C0+ALα/ν at large L, if α/ν=0.196(6). However, a direct estimation from our data suggests that α/ν, most probably, has a smaller value (e.g., α/ν= 0.113(30)). Thus, the conventional power-law scaling ansatz can be questioned because of this inconsistency. We have found that the data are well described by certain logarithmic ansatz.

The implicit 2D3V particle-in-cell (PIC) code developed to study the interaction of ultrashort pulse lasers with matter [G. M. Petrov and J. Davis, Computer Phys. Comm. 179, 868 (2008); Phys. Plasmas 18, 073102 (2011)] has been parallelized using MPI (Message Passing Interface). The parallelization strategy is optimized for a small number of computer cores, up to about 64. Details on the algorithm implementation are given with emphasis on code optimization by overlapping computations with communications. Performance evaluation for 1D domain decomposition has been made on a small Linux cluster with 64 computer cores for two typical regimes of PIC operation: “particle dominated”, for which the bulk of the computation time is spent on pushing particles, and “field dominated”, for which computing the fields is prevalent. For a small number of computer cores, less than 32, the MPI implementation offers a significant numerical speed-up. In the “particle dominated” regime it is close to the maximum theoretical one, while in the “field dominated” regime it is about 75-80 % of the maximum speed-up. For a number of cores exceeding 32, performance degradation takes place as a result of the adopted 1D domain decomposition. The code parallelization will allow future implementation of atomic physics and extension to three dimensions.

Hierarchical bases of arbitrary order for (div)-conforming triangular and tetrahedral elements are constructed with the goal of improving the conditioning of the mass and stiffness matrices. For the basis with the triangular element, it is found numerically that the conditioning is acceptable up to the approximation of order four, and is better than a corresponding basis in the dissertation by Sabine Zaglmayr [High Order Finite Element Methods for Electromagnetic Field Computation, Johannes Kepler Universität, Linz, 2006]. The sparsity of the mass matrices from the newly constructed basis and from the one by Zaglmayr is similar for approximations up to order four. The stiffness matrix with the new basis is much sparser than that with the basis by Zaglmayr for approximations up to order four. For the tetrahedral element, it is identified numerically that the conditioning is acceptable only up to the approximation of order three. Compared with the newly constructed basis for the triangular element, the sparsity of the mass matrices from the basis for the tetrahedral element is relatively sparser.

As the numerical resolution is increased and the discretisation error decreases, the lattice Boltzmann method tends towards the discrete-velocity Boltzmann equation (DVBE). An expression for the propagation properties of plane sound waves is found for this equation. This expression is compared to similar ones from the Navier-Stokes and Burnett models, and is found to be closest to the latter. The anisotropy of sound propagation with the DVBE is examined using a two-dimensional velocity set. It is found that both the anisotropy and the deviation between the models is negligible if the Knudsen number is less than 1 by at least an order of magnitude.

An iterative discontinuous Galerkin (DG) method is proposed to solve the nonlinear Poisson Boltzmann (PB) equation. We first identify a function space in which the solution of the nonlinear PB equation is iteratively approximated through a series of linear PB equations, while an appropriate initial guess and a suitable iterative parameter are selected so that the solutions of linear PB equations are monotone within the identified solution space. For the spatial discretization we apply the direct discontinuous Galerkin method to those linear PB equations. More precisely, we use one initial guess when the Debye parameter λ = (1), and a special initial guess for λ ≫1 to ensure convergence. The iterative parameter is carefully chosen to guarantee the existence, uniqueness, and convergence of the iteration. In particular, iteration steps can be reduced for a variable iterative parameter. Both one and two-dimensional numerical results are carried out to demonstrate both accuracy and capacity of the iterative DG method for both cases of λ = (1) and λ ≪ 1. The (m + 1)th order of accuracy for L2 and mth order of accuracy for H1 for Pm elements are numerically obtained.

After setting a mixed formulation for the propagation of linearized water waves problem, we define its spectral element approximation. Then, in order to take into account unbounded domains, we construct absorbing perfectly matched layer for the problem. We approximate these perfectly matched layer by mixed spectral elements and show their stability using the “frozen coefficient” technique. Finally, numerical results will prove the efficiency of the perfectly matched layer compared to classical absorbing boundary conditions.

A new set of boundary conditions has been derived by rigorous methods for the shallow water equations in a limited domain. The aim of this article is to present these boundary conditions and to report on numerical simulations which have been performed using these boundary conditions. The new boundary conditions which are mildly dissipative let the waves move freely inside and outside the domain. The problems considered include a one-dimensional shallow water system with two layers of fluids and a two-dimensional inviscid shallow water system in a rectangle.

We present a new splitting method for time-dependent convention-dominated diffusion problems. The original convention diffusion system is split into two sub-systems: a pure convection system and a diffusion system. At each time step, a convection problem and a diffusion problem are solved successively. A few important features of the scheme lie in the facts that the convection subproblem is solved explicitly and multistep techniques can be used to essentially enlarge the stability region so that the resulting scheme behaves like an unconditionally stable scheme; while the diffusion subproblem is always self-adjoint and coercive so that they can be solved efficiently using many existing optimal preconditioned iterative solvers. The scheme can be extended for solving the Navier-Stokes equations, where the nonlinearity is resolved by a linear explicit multistep scheme at the convection step, while only a generalized Stokes problem is needed to solve at the diffusion step and the major stiffness matrix stays invariant in the time marching process. Numerical simulations are presented to demonstrate the stability, convergence and performance of the single-step and multistep variants of the new scheme.

We show that a single particle distribution for the “energy-conserving” D2Q13 lattice Boltzmann scheme can simulate coupled effects involving advection and diffusion of velocity and temperature. We consider various test cases: non-linear waves with periodic boundary conditions, a test case with buoyancy, propagation of transverse waves, Couette and Poiseuille flows. We test various boundary conditions and propose to mix bounce-back and anti-bounce-back numerical boundary conditions to take into account velocity and temperature Dirichlet conditions. We present also first results for the de Vahl Davis heated cavity. Our results are compared with the coupled D2Q9-D2Q5 lattice Boltzmann approach for the Boussinesq system and with an elementary finite differences solver for the compressible Navier-Stokes equations. Our main experimental result is the loss of symmetry in the de Vahl Davis cavity computed with the single D2Q13 lattice Boltzmann model without the Boussinesq hypothesis. This result is confirmed by a direct Navier Stokes simulation with finite differences.

Lattice-Boltzmann methods are versatile numerical modeling techniques capable of reproducing a wide variety of fluid-mechanical behavior. These methods are well suited to parallel implementation, particularly on the single-instruction multiple data (SIMD) parallel processing environments found in computer graphics processing units (GPUs).

Although recent programming tools dramatically improve the ease with which GPUbased applications can be written, the programming environment still lacks the flexibility available to more traditional CPU programs. In particular, it may be difficult to develop modular and extensible programs that require variable on-device functionality with current GPU architectures.

This paper describes a process of automatic code generation that overcomes these difficulties for lattice-Boltzmann simulations. It details the development of GPU-based modules for an extensible lattice-Boltzmann simulation package – LBHydra. The performance of the automatically generated code is compared to equivalent purposewritten codes for both single-phase,multiphase, andmulticomponent flows. The flexibility of the new method is demonstrated by simulating a rising, dissolving droplet moving through a porous medium with user generated lattice-Boltzmann models and subroutines.

The Lattice Boltzmann Method (LBM) has established itself as a popular numerical method in computational fluid dynamics. Several advancements have been recently made in LBM, which include multiple-relaxation-time LBM to simulate anisotropic advection-diffusion processes. Because of the importance of LBM simulations for transport problems in subsurface and reactive flows, one needs to study the accuracy and structure preserving properties of numerical solutions under the LBM. The solutions to advective-diffusive systems are known to satisfy maximum principles, comparison principles, the non-negative constraint, and the decay property. In this paper, using several numerical experiments, it will be shown that current single- and multiple-relaxation-time lattice Boltzmann methods fail to preserve these mathematical properties for transient diffusion-type equations. We will also show that these violations may not be removed by simply refining the discretization parameters. More importantly, it will be shown that meeting stability conditions alone does not guarantee the preservation of the aforementioned mathematical principles and physical constraints in the discrete setting. A discussion on the source of these violations and possible approaches to avoid them is included. A condition to guarantee the non-negativity of concentration under LBM in the case of isotropic diffusion is also derived. The impact of this research is twofold. First, the study poses several outstanding research problems, which should guide researchers to develop LBM-based formulations for transport problems that respect important mathematical properties and physical constraints in the discrete setting. This paper can also serve as a good source of benchmark problems for such future research endeavors. Second, this study cautions the practitioners of the LBM for transport problems with the associated numerical deficiencies of the LBM, and provides guidelines for performing predictive simulations of advective-diffusive processes using the LBM.

In this paper, we study the selectivity of the potassium channel KcsA by a recently developed image-charge solvation method (ICSM) combined with molecular dynamics simulations. The hybrid solvation model in the ICSM is able to demonstrate atomistically the function of the selectivity filter of the KcsA channel when potassium and sodium ions are considered and their distributions inside the filter are simulated. Our study also shows that the reaction field effect, explicitly accounted for through image charge approximation in the ICSM model, is necessary in reproducing the correct selectivity property of the potassium channels.

This paper focuses on the development of an efficient, three-dimensional, thermo-mechanical, nonlinear-Stokes flow computational model for ice sheet simulation. The model is based on the parallel finite element model developed in [14] which features high-order accurate finite element discretizations on variable resolution grids. Here, we add an improved iterative solution method for treating the nonlinearity of the Stokes problem, a new high-order accurate finite element solver for the temperature equation, and a new conservative finite volume solver for handling mass conservation. The result is an accurate and efficient numerical model for thermo-mechanical glacier and ice-sheet simulations. We demonstrate the improved efficiency of the Stokes solver using the ISMIP-HOM Benchmark experiments and a realistic test case for the Greenland ice-sheet. We also apply our model to the EISMINT-II benchmark experiments and demonstrate stable thermo-mechanical ice sheet evolution on both structured and unstructured meshes. Notably, we find no evidence for the “cold spoke” instabilities observed for these same experiments when using finite difference, shallow-ice approximation models on structured grids.

The radiative transfer equation (RTE) arises in many different areas of science and engineering. In this paper, we propose and investigate a discrete-ordinate discontinuous-streamline diffusion (DODSD) method for solving the RTE, which is a combination of the discrete-ordinate technique and the discontinuous-streamline diffusion method. Different from the discrete-ordinate discontinuous Galerkin (DODG) method for the RTE, an artificial diffusion parameter is added to the test functions in the spatial discretization. Stability and error estimates in certain norms are proved. Numerical results show that the proposed method can lead to a more accurate approximation in comparison with the DODG method.