In this paper, we study a class of contact smoothed particle hydrodynamics (SPH) by introducing Riemann solvers and using high-order limiters. In particular, a promising concept of WENO interpolation as limiter is presented in the reconstruction process. The physical values relating interactional particles used as the initial values of the Riemann problem can be reconstructed by the Taylor series expansion. The contact solvers of the Riemann problem at contact points are incorporated in SPH approximations. In order to keep the fluid density at the wall rows to be consistent with that of the inner fluid wall boundaries, several lines of dummy particles are placed outside of the solid walls, which are assigned according to the initial configuration. At last, the method is applied to compressible flows with sharp discontinuities such as the collision of two strong shocks and the interaction of two blast waves and so on. The numerical results indicate that the method is capable of handling sharp discontinuity and efficiently reducing unphysical oscillations.

This paper summarizes the mathematical and numerical theories and computational elements of the adaptive fast multipole Poisson-Boltzmann (AFMPB) solver. We introduce and discuss the following components in order: the Poisson-Boltzmann model, boundary integral equation reformulation, surface mesh generation, the nodepatch discretization approach, Krylov iterative methods, the new version of fast multipole methods (FMMs), and a dynamic prioritization technique for scheduling parallel operations. For each component, we also remark on feasible approaches for further improvements in efficiency, accuracy and applicability of the AFMPB solver to large-scale long-time molecular dynamics simulations. The potential of the solver is demonstrated with preliminary numerical results.

Stochastic walk-on-spheres (WOS) algorithms for solving the linearized Poisson-Boltzmann equation (LPBE) provide several attractive features not available in traditional deterministic solvers: Gaussian error bars can be computed easily, the algorithm is readily parallelized and requires minimal memory and multiple solvent environments can be accounted for by reweighting trajectories. However, previously-reported computational times of these Monte Carlo methods were not competitive with existing deterministic numerical methods. The present paper demonstrates a series of numerical optimizations that collectively make the computational time of these Monte Carlo LPBE solvers competitive with deterministic methods. The optimization techniques used are to ensure that each atom’s contribution to the variance of the electrostatic solvation free energy is the same, to optimize the bias-generating parameters in the algorithm and to use an epsilon-approximate rather than exact nearest-neighbor search when determining the size of the next step in the Brownian motion when outside the molecule.

We consider constraint preserving multidimensional evolution equations. A prototypical example is provided by the magnetic induction equation of plasma physics. The constraint of interest is the divergence of the magnetic field. We design finite volume schemes which approximate these equations in a stable manner and preserve a discrete version of the constraint. The schemes are based on reformulating standard edge centered finite volume fluxes in terms of vertex centered potentials. The potential-based approach provides a general framework for faithful discretizations of constraint transport and we apply it to both divergence preserving as well as curl preserving equations. We present benchmark numerical tests which confirm that our potential-based schemes achieve high resolution, while being constraint preserving.

Feynman’s path integral reformulates the quantum Schrödinger differential equation to be an integral equation. It has been being widely used to compute internuclear quantum-statistical effects on many-body molecular systems. In this Review, the molecular Schrödinger equation will first be introduced, together with the Born-Oppenheimer approximation that decouples electronic and internuclear motions. Some effective semiclassical potentials, e.g., centroid potential, which are all formulated in terms of Feynman’s path integral, will be discussed and compared. These semiclassical potentials can be used to directly calculate the quantum canonical partition function without individual Schrödinger’s energy eigenvalues. As a result, path integrations are conventionally performed with Monte Carlo and molecular dynamics sampling techniques. To complement these techniques, we will examine how Kleinert’s variational perturbation (KP) theory can provide a complete theoretical foundation for developing non-sampling/non-stochastic methods to systematically calculate centroid potential. To enable the powerful KP theory to be practical for many-body molecular systems, we have proposed a new path-integral method: automated integration-free path-integral (AIF-PI) method. Due to the integration-free and computationally inexpensive characteristics of our AIF-PI method, we have used it to perform ab initio path-integral calculations of kinetic isotope effects on proton-transfer and RNA-related phosphoryl-transfer chemical reactions. The computational procedure of using our AIF-PI method, along with the features of our new centroid path-integral theory at the minimum of the absolute-zero energy (AMAZE), are also highlighted in this review.

The level set method is one of the most successful methods for the simulation of multi-phase flows. To keep the level set function close the signed distance function, the level set function is constantly reinitialized by solving a Hamilton-Jacobi type of equation during the simulation. When the fluid interface intersects with a solid wall, a moving contact line forms and the reinitialization of the level set function requires a boundary condition in certain regions on the wall. In this work, we propose to use the dynamic contact angle, which is extended from the contact line, as the boundary condition for the reinitialization of the level set function. The reinitialization equation and the equation for the normal extension of the dynamic contact angle form a coupled system and are solved simultaneously. The extension equation is solved on the wall and it provides the boundary condition for the reinitialization equation; the level set function provides the directions along which the contact angle is extended from the contact line. The coupled system is solved using the 3rd order TVD Runge-Kutta method and the Godunov scheme. The Godunov scheme automatically identifies the regions where the angle condition needs to be imposed. The numerical method is illustrated by examples in three dimensions.

Due to α radioactive decay Pu is vulnerable to aging. The behavior of He in Pu is the foundation for understanding Pu self-radiation damage aging. Molecular dynamics technique is performed to investigate the behavior of defects, the interaction between He and defects, the processes of initial nucleation and growth of He bubble and the dependence of He bubble on the macroscopical properties of Pu. Modified embedded atom method, Morse pair potential and the Lennard-Jones pair potential are used for describing the interactions of Pu-Pu, Pu-He and He-He, respectively. The main calculated results show that He atoms can combine with vacancies to form Hevacancy cluster (i.e., the precursor of He bubble) during the process of self-radiation as a result of high binding energy of an interstitial He atom to vacancy; He bubble’s growth can be dominated by the mechanism of punching out of dislocation loop; the swelling induced by He bubble is very small; grain boundaries give rise to an energetically more favorable zone for the interstitial He atom and self-interstitial atom accumulation than for vacancy accumulation; the process of He release can be identified as the formation of release channel induced by the cracking of He bubble and surface structure.

A concept of “static reconstruction” and “dynamic reconstruction” was introduced for higher-order (third-order or more) numerical methods in our previous work. Based on this concept, a class of hybrid DG/FV methods had been developed for one-dimensional conservation law using a “hybrid reconstruction” approach, and extended to two-dimensional scalar equations on triangular and Cartesian/triangular hybrid grids. In the hybrid DG/FV schemes, the lower-order derivatives of the piece-wise polynomial are computed locally in a cell by the traditional DG method (called as “dynamic reconstruction”), while the higher-order derivatives are re-constructed by the “static reconstruction” of the FV method, using the known lower-order derivatives in the cell itself and in its adjacent neighboring cells. In this paper, the hybrid DG/FV schemes are extended to two-dimensional Euler equations on triangular and Cartesian/triangular hybrid grids. Some typical test cases are presented to demonstrate the performance of the hybrid DG/FV methods, including the standard vortex evolution problem with exact solution, isentropic vortex/weak shock wave interaction, subsonic flows past a circular cylinder and a three-element airfoil (30P30N), transonic flow past a NACA0012 airfoil. The accuracy study shows that the hybrid DG/FV method achieves the desired third-order accuracy, and the applications demonstrate that they can capture the flow structure accurately, and can reduce the CPU time and memory requirement greatly than the traditional DG method with the same order of accuracy.

The rotational incremental pressure-correction (RIPC) scheme, described in Timmermans et al. [Int. J. Numer. Methods. Fluids., 22 (1996)] and Shen et al. [Math. Comput., 73 (2003)] for non-rotational Navier-Stokes equations, is extended to rotating incompressible flows. The method is implemented in the context of a pseudo Fourier-spectral code and applied to several rotating laminar and turbulent flows. The performance of the scheme and the computational results are compared to the so-called diagonalization method (DM) developed by Morinishi et al. [Int. J. Heat. Fluid. Flow., 22 (2001)]. The RIPC predictions are in excellent agreement with the DM predictions, while being simpler to implement and computationally more efficient. The RIPC scheme is not in anyway limited to implementation in a pseudo-spectral code or periodic boundary conditions, and can be used in complex geometries and with other suitable boundary conditions.

We critically compare the practicality and accuracy of numerical approximations of phase field models and sharp interface models of solidification. Here we focus on Stefan problems, and their quasi-static variants, with applications to crystal growth. New approaches with a high mesh quality for the parametric approximations of the resulting free boundary problems and new stable discretizations of the anisotropic phase field system are taken into account in a comparison involving benchmark problems based on exact solutions of the free boundary problem.

This paper is the second part of a two part sequence on multiphysics algorithms and software. The first [1] focused on the algorithms; this part treats the multiphysics software framework and applications based on it. Tight coupling is typically designed into the analysis application at inception, as such an application is strongly tied to a composite nonlinear solver that arrives at the final solution by treating all equations simultaneously. The application must also take care to minimize both time and space error between the physics, particularly if more than one mesh representation is needed in the solution process. This paper presents an application framework that was specifically designed to support tightly coupled multiphysics analysis. The Multiphysics Object Oriented Simulation Environment (MOOSE) is based on the Jacobian-free Newton-Krylov (JFNK) method combined with physics-based preconditioning to provide the underlying mathematical structure for applications. The report concludes with the presentation of a host of nuclear, energy and environmental applications that demonstrate the efficacy of the approach and the utility of a well-designed multiphysics framework.

We report about a numerical algorithm based on the lattice Boltzmann method and its applications for simulations of turbulent convection in multi-phase flows. We discuss the issue of ’latent heat’ definition using a thermodynamically consistent pseudo-potential on the lattice. We present results of numerical simulations in 3D with and without boiling, showing the distribution of pressure, density and temperature fluctuations inside a convective cell.

The numerical simulation of non conservative system is a difficult challenge for two reasons at least. The first one is that it is not possible to derive jump relations directly from conservation principles, so that in general, if the model description is non ambiguous for smooth solutions, this is no longer the case for discontinuous solutions. From the numerical view point, this leads to the following situation: if a scheme is stable, its limit for mesh convergence will depend on its dissipative structure. This is well known since at least [1]. In this paper we are interested in the “dual” problem: given a system in non conservative form and consistent jump relations, how can we construct a numerical scheme that will, for mesh convergence, provide limit solutions that are the exact solution of the problem. In order to investigate this problem, we consider a multiphase flow model for which jump relations are known. Our scheme is an hybridation of Glimm scheme and Roe scheme.

In this paper, we develop a novel energy-preserving wavelet collocation method for solving general multi-symplectic formulations of Hamiltonian PDEs. Based on the autocorrelation functions of Daubechies compactly supported scaling functions, the wavelet collocation method is conducted for spatial discretization. The obtained semi-discrete system is shown to be a finite-dimensional Hamiltonian system, which has an energy conservation law. Then, the average vector field method is used for time integration, which leads to an energy-preserving method for multi-symplectic Hamiltonian PDEs. The proposed method is illustrated by the nonlinear Schrödinger equation and the Camassa-Holm equation. Since differentiation matrix obtained by the wavelet collocation method is a cyclic matrix, we can apply Fast Fourier transform to solve equations in numerical calculation. Numerical experiments show the high accuracy, effectiveness and conservation properties of the proposed method.

In this paper, a newly developed second order temporally and spatially accurate finite difference scheme for biharmonic semi linear equations has been employed in simulating the time evolution of viscous flows past an impulsively started circular cylinder for Reynolds number (Re) up to 9,500. The robustness of the scheme and the effectiveness of the formulation can be gauged by the fact that it very accurately captures complex flow structures such as the von Kármán vortex street through streakline simulation and the α and β-phenomena in the range 3,000≤Re≤9,500 among others. The main focus here is the application of the technique which enables the use of the discretized version of a single semi linear biharmonic equation in order to efficiently simulate different fluid structures associated with flows around a bluff body. We compare our results, both qualitatively and quantitatively, with established numerical and more so with experimental results. Excellent comparison is obtained in all the cases.

There is a growing trend within energy and environmental simulation to consider tightly coupled solutions to multiphysics problems. This can be seen in nuclear reactor analysis where analysts are interested in coupled flow, heat transfer and neutronics, and in nuclear fuel performance simulation where analysts are interested in thermomechanics with contact coupled to species transport and chemistry. In energy and environmental applications, energy extraction involves geomechanics, flow through porous media and fractured formations, adding heat transport for enhanced oil recovery and geothermal applications, and adding reactive transport in the case of applications modeling the underground flow of contaminants. These more ambitious simulations usually motivate some level of parallel computing. Many of the physics coupling efforts to date utilize simple code coupling or first-order operator splitting, often referred to as loose coupling. While these approaches can produce answers, they usually leave questions of accuracy and stability unanswered. Additionally the different physics often reside on distinct meshes and data are coupled via simple interpolation, again leaving open questions of stability and accuracy.

In this paper, we study the numerical solution of singularly perturbed time-dependent convection-diffusion problems. To solve these problems, the backward Euler method is first applied to discretize the time derivative on a uniform mesh, and the classical upwind finite difference scheme is used to approximate the spatial derivative on an arbitrary nonuniform grid. Then, in order to obtain an adaptive grid for all temporal levels, we construct a positive monitor function, which is similar to the arc-length monitor function. Furthermore, the ε-uniform convergence of the fully discrete scheme is derived for the numerical solution. Finally, some numerical results are given to support our theoretical results.

We present a novel adaptive finite element method (AFEM) for elliptic equations which is based upon the Centroidal Voronoi Tessellation (CVT) and superconvergent gradient recovery. The constructions of CVT and its dual Centroidal Voronoi Delaunay Triangulation (CVDT) are facilitated by a localized Lloyd iteration to produce almost equilateral two dimensional meshes. Working with finite element solutions on such high quality triangulations, superconvergent recovery methods become particularly effective so that asymptotically exact a posteriori error estimations can be obtained. Through a seamless integration of these techniques, a convergent adaptive procedure is developed. As demonstrated by the numerical examples, the new AFEM is capable of solving a variety of model problems and has great potential in practical applications.

We consider scattering of a time harmonic incident plane wave by a convex polygon with piecewise constant impedance boundary conditions. Standard finite or boundary element methods require the number of degrees of freedom to grow at least linearly with respect to the frequency of the incident wave in order to maintain accuracy. Extending earlier work by Chandler-Wilde and Langdon for the sound soft problem, we propose a novel Galerkin boundary element method, with the approximation space consisting of the products of plane waves with piecewise polynomials supported on a graded mesh with smaller elements closer to the corners of the polygon. Theoretical analysis and numerical results suggest that the number of degrees of freedom required to achieve a prescribed level of accuracy grows only logarithmically with respect to the frequency of the incident wave.

In this paper, we highlight the benefits resulting from imposing energy-conserving equilibria in entropic lattice Boltzmann models for isothermal flows. The advantages are documented through a series of numerical simulations, such as Taylor-Green vortices, cavity flow and flow past a sphere.