The immersed boundary method has been extensively used to simulate the motion of elastic structures immersed in a viscous fluid. For some applications, such as modeling biological materials, capturing internal boundary viscosity is important. We present numerical methods for simulating Kelvin-Voigt and standard linear viscoelastic structures immersed in zero Reynolds number flow. We find that the explicit time immersed boundary update is unconditionally unstable above a critical boundary to fluid viscosity ratio for a Kelvin-Voigt material. We also show there is a severe time step restriction when simulating a standard linear boundary with a small relaxation time scale using the same explicit update. A stable implicit method is presented to overcome these computation challenges.

Simulation of elastic wave propagation has important applications in many areas such as inverse problem and geophysical exploration. In this paper, stability conditions for wave simulation in 3-D anisotropic media with the pseudospectral method are investigated. They can be expressed explicitly by elasticity constants which are easy to be applied in computations. The 3-D wave simulation for two typical anisotropic media, transversely isotropic media and orthorhombic media, are carried out. The results demonstrate some satisfactory behaviors of the pseudospectral method.

This study shows a new way to implement terrain-following σ-coordinate in a numerical model, which does not lead to the well-known “pressure gradient force (PGF)” problem. First, the causes of the PGF problem are analyzed with existing methods that are categorized into two different types based on the causes. Then, the new method that bypasses the PGF problem all together is proposed. By comparing these three methods and analyzing the expression of the scalar gradient in a curvilinear coordinate system, this study finds out that only when using the covariant scalar equations of σ-coordinate will the PGF computational form have one term in each momentum component equation, thereby avoiding the PGF problem completely. A convenient way of implementing the covariant scalar equations of σ-coordinate in a numerical atmospheric model is illustrated, which is to set corresponding parameters in the scalar equations of the Cartesian coordinate. Finally, two idealized experiments manifest that the PGF calculated with the new method is more accurate than using the classic one. This method can be used for oceanic models as well, and needs to be tested in both the atmospheric and oceanic models.

We consider a non-standard mixed method for the Stokes problem in ℝn, n Є {2,3}, with Dirichlet boundary conditions, in which, after using the incompressibility condition to eliminate the pressure, the pseudostress tensor σ and the velocity vector u become the only unknowns. Then, we apply the Babuška-Brezzi theory to prove the well-posedness of the corresponding continuous and discrete formulations. In particular, we show that Raviart-Thomas elements of order k≥0 for σ and piecewise polynomials of degree k for u ensure unique solvability and stability of the associated Galerkin scheme. In addition, we introduce and analyze an augmented approach for our pseudostress-velocity formulation. The methodology employed is based on the introduction of the Galerkin least-squares type terms arising from the constitutive and equilibrium equations, and the Dirichlet boundary condition for the velocity, all of them multiplied by suitable stabilization parameters. We show that these parameters can be chosen so that the resulting augmented variational formulation is defined by a strongly coercive bilinear form, whence the associated Galerkin scheme becomes well posed for any choice of finite element subspaces. For instance, Raviart-Thomas elements of order k≥0 for σ and continuous piecewise polynomials of degree k+1 for u become a feasible choice in this case. Finally, extensive numerical experiments illustrating the good performance of the methods and comparing them with other procedures available in the literature, are provided.

In this paper, we present the use of the orthogonal spline collocation method for the semi-discretization scheme of the one-dimensional coupled nonlinear Schrödinger equations. This method uses the Hermite basis functions, by which physical quantities are approximated with their values and derivatives associated with Gaussian points. The convergence rate with order and the stability of the scheme are proved. Conservation properties are shown in both theory and practice. Extensive numerical experiments are presented to validate the numerical study under consideration.

Orbital-free density functional theory (OFDFT) is a quantum mechanical method in which the energy of a material depends only on the electron density and ionic positions. We examine some popular algorithms for optimizing the electron density distribution in OFDFT, explaining their suitability, benchmarking their performance, and suggesting some improvements. We start by describing the constrained optimization problem that encompasses electron density optimization. Next, we discuss the line search (including Wolfe conditions) and the nonlinear conjugate gradient and truncated Newton algorithms, as implemented in our open source OFDFT code. We finally focus on preconditioners derived from OFDFT energy functionals. Newly-derived preconditioners are successful for simulation cells of all sizes without regions of low electron-density and for small simulation cells with such regions.

In this article, we present two new novel finite difference approximations of order two and four, respectively, for the three dimensional non-linear triharmonic partial differential equations on a compact stencil where the values of u, ∂2u/∂n2 and ∂4u/∂n4 are prescribed on the boundary. We introduce new ideas to handle the boundary conditions and there is no need to discretize the derivative boundary conditions. We require only 7- and 19-grid points on the compact cell for the second and fourth order approximation, respectively. The Laplacian and the biharmonic of the solution are obtained as by-product of the methods. We require only system of three equations to obtain the solution. Numerical results are provided to illustrate the usefulness of the proposed methods.

Power-law distributions and other skew distributions, observed in various models and real systems, are considered. A model, describing evolving systems with increasing number of elements, is considered to study the distribution over element sizes. Stationary power-law distributions are found. Certain non-stationary skew distributions are obtained and analyzed, based on exact solutions and numerical simulations.

Quasi-Monte Carlo methods and stochastic collocation methods based on sparse grids have become popular with solving stochastic partial differential equations. These methods use deterministic points for multi-dimensional integration or interpolation without suffering from the curse of dimensionality. It is not evident which method is best, specially on random models of physical phenomena. We numerically study the error of quasi-Monte Carlo and sparse grid methods in the context of ground-water flow in heterogeneous media. In particular, we consider the dependence of the variance error on the stochastic dimension and the number of samples/collocation points for steady flow problems in which the hydraulic conductivity is a lognormal process. The suitability of each technique is identified in terms of computational cost and error tolerance.

We extend the immersed boundary (IB) method to simulate the dynamics of a 2D dry foam by including the topological changes of the bubble network. In the article [Y. Kim, M.-C. Lai, and C. S. Peskin, J. Comput. Phys. 229:5194-5207,2010], we implemented an IB method for the foam problem in the two-dimensional case, and tested it by verifying the von Neumann relation which governs the coarsening of a two-dimensional dry foam. However, the method implemented in that article had an important limitation; we did not allow for the resolution of quadruple or higher order junctions into triple junctions. A total shrinkage of a bubble with more than four edges generates a quadruple or higher order junction. In reality, a higher order junction is unstable and resolves itself into triple junctions. We here extend the methodology previously introduced by allowing topological changes, and we illustrate the significance of such topological changes by comparing the behaviors of foams in which topological changes are allowed to those in which they are not.

We present a systematic derivation of a model based on the central moment lattice Boltzmann equation that rigorously maintains Galilean invariance of forces to simulate inertial frame independent flow fields. In this regard, the central moments, i.e. moments shifted by the local fluid velocity, of the discrete source terms of the lattice Boltzmann equation are obtained by matching those of the continuous full Boltzmann equation of various orders. This results in an exact hierarchical identity between the central moments of the source terms of a given order and the components of the central moments of the distribution functions and sources of lower orders. The corresponding source terms in velocity space are then obtained from an exact inverse transformation due to a suitable choice of orthogonal basis for moments. Furthermore, such a central moment based kinetic model is further extended by incorporating reduced compressibility effects to represent incompressible flow. Moreover, the description and simulation of fluid turbulence for full or any subset of scales or their averaged behavior should remain independent of any inertial frame of reference. Thus, based on the above formulation, a new approach in lattice Boltzmann framework to incorporate turbulence models for simulation of Galilean invariant statistical averaged or filtered turbulent fluid motion is discussed.

The paper is devoted to the development of an efficient deterministic framework for modelling of three-dimensional rarefied gas flows on the basis of the numerical solution of the Boltzmann kinetic equation with the model collision integrals. The framework consists of a high-order accurate implicit advection scheme on arbitrary unstructured meshes, the conservative procedure for the calculation of the model collision integral and efficient implementation on parallel machines. The main application area of the suggested methods is micro-scale flows. Performance of the proposed approach is demonstrated on a rarefied gas flow through the finite-length circular pipe. The results show good accuracy of the proposed algorithm across all flow regimes and its high efficiency and excellent parallel scalability for up to 512 cores.

Consider the inverse diffraction problem to determine a two-dimensional periodic structure from scattered elastic waves measured above the structure. We formulate the inverse problem as a least squares optimization problem, following the two-step algorithm by G. Bruckner and J. Elschner [Inverse Probl., 19 (2003), 315-329] for electromagnetic diffraction gratings. Such a method is based on the Kirsch-Kress optimization scheme and consists of two parts: a linear severely ill-posed problem and a nonlinear well-posed one. We apply this method to both smooth (C2) and piecewise linear gratings for the Dirichlet boundary value problem of the Navier equation. Numerical reconstructions from exact and noisy data illustrate the feasibility of the method.

The space-time conservation element and solution element (CE/SE) method is proposed for solving a conservative interface-capturing reduced model of compressible two-fluid flows. The flow equations are the bulk equations, combined with mass and energy equations for one of the two fluids. The latter equation contains a source term for accounting the energy exchange. The one and two-dimensional flow models are numerically investigated in this manuscript. The CE/SE method is capable to accurately capture the sharp propagating wavefronts of the fluids without excessive numerical diffusion or spurious oscillations. In contrast to the existing upwind finite volume schemes, the Riemann solver and reconstruction procedure are not the building block of the suggested method. The method differs from the previous techniques because of global and local flux conservation in a space-time domain without resorting to interpolation or extrapolation. In order to reveal the efficiency and performance of the approach, several numerical test cases are presented. For validation, the results of the current method are compared with other finite volume schemes.

We present a three dimensional model of an open elastic tube immersed in fluid to understand valveless pumping mechanism. A fluid-tube interaction problem is simulated by the volume conserved immersed boundary method which prevents the generation of spurious velocity field near the tube and local cluster of the tube surface. In order to explain pumping phenomena without valves, average net flow is measured by changing parameter values such as pumping frequency, compression duration, and pumping amplitude. Some frequencies that make the system reach maximal or minimal net flow are selected to study case by case. We also study the effectiveness of fluid mixing using the Shannon entropy increase rate.

In this paper we demonstrate the accuracy and robustness of combining the advection upwind splitting method (AUSM), specifically AUSM+-UP, with high-order upwind-biased interpolation procedures, the weighted essentially non-oscillatory (WENO-JS) scheme and its variations, and the monotonicity preserving (MP) scheme, for solving the Euler equations. MP is found to be more effective than the three WENO variations studied. AUSM+-UP is also shown to be free of the so-called “carbuncle” phenomenon with the high-order interpolation. The characteristic variables are preferred for interpolation after comparing the results using primitive and conservative variables, even though they require additional matrix-vector operations. Results using the Roe flux with an entropy fix and the Lax-Friedrichs approximate Riemann solvers are also included for comparison. In addition, four reflective boundary condition implementations are compared for their effects on residual convergence and solution accuracy. Finally, a measure for quantifying the efficiency of obtaining high order solutions is proposed; the measure reveals that a maximum return is reached after which no improvement in accuracy is possible for a given grid size.

In this paper, the second in a series, we improve the discretization of the higher spatial derivative terms in a spectral volume (SV) context. The motivation for the above comes from [J. Sci. Comput., 46(2), 314-328], wherein the authors developed a variant of the LDG (Local Discontinuous Galerkin) flux discretization method. This variant (aptly named LDG2), not only displayed higher accuracy than the LDG approach, but also vastly reduced its unsymmetrical nature. In this paper, we adapt the LDG2 formulation for discretizing third derivative terms. A linear Fourier analysis was performed to compare the dispersion and the dissipation properties of the LDG2 and the LDG formulations. The results of the analysis showed that the LDG2 scheme (i) is stable for 2nd and 3rd orders and (ii) generates smaller dissipation and dispersion errors than the LDG formulation for all the orders. The 4th order LDG2 scheme is however mildly unstable: as the real component of the principal eigen value briefly becomes positive. In order to circumvent the above, a weighted average of the LDG and the LDG2 fluxes was used as the final numerical flux. Even a weight of 1.5% for the LDG (i.e., 98.5% for the LDG2) was sufficient to make the scheme stable. This weighted scheme is still predominantly LDG2 and hence generated smaller dissipation and dispersion errors than the LDG formulation. Numerical experiments are performed to validate the analysis. In general, the numerical results are very promising and indicate that the approach has a great potential for higher dimension Kortewegde Vries (KdV) type problems.

Internal waves arise in a wide array of oceanographic problems of both theoretical and engineering interest. In this contribution we present a new model, valid in the weakly nonlinear regime, for the propagation of disturbances along the interface between two ideal fluid layers of infinite extent and different densities. Additionally, we present a novel high-order/spectral algorithm for its accurate and stable simulation. Numerical validation results and simulations of wave-packet evolution are provided.

We develop a stable finite difference approximation of the three-dimensional viscoelastic wave equation. The material model is a super-imposition of N standard linear solid mechanisms, which commonly is used in seismology to model a material with constant quality factor Q. The proposed scheme discretizes the governing equations in second order displacement formulation using 3N memory variables, making it significantly more memory efficient than the commonly used first order velocity-stress formulation. The new scheme is a generalization of our energy conserving finite difference scheme for the elastic wave equation in second order formulation [SIAM J. Numer. Anal., 45 (2007), pp. 1902-1936]. Our main result is a proof that the proposed discretization is energy stable, even in the case of variable material properties. The proof relies on the summation-by-parts property of the discretization. The new scheme is implemented with grid refinement with hanging nodes on the interface. Numerical experiments verify the accuracy and stability of the new scheme. Semi-analytical solutions for a half-space problem and the LOH.3 layer over half-space problem are used to demonstrate how the number of viscoelastic mechanisms and the grid resolution influence the accuracy. We find that three standard linear solid mechanisms usually are sufficient to make the modeling error smaller than the discretization error.

An adaptive mesh refinement strategy is proposed in this paper for the Immersed Boundary and Immersed Interface methods for two-dimensional elliptic interface problems involving singular sources. The interface is represented by the zero level set of a Lipschitz function ϕ(x,y). Our adaptive mesh refinement is done within a small tube of |ϕ(x,y)|≤δ with finer Cartesian meshes. The discrete linear system of equations is solved by a multigrid solver. The AMR methods could obtain solutions with accuracy that is similar to those on a uniform fine grid by distributing the mesh more economically, therefore, reduce the size of the linear system of the equations. Numerical examples presented show the efficiency of the grid refinement strategy.