Parallel tempering simulation is widely used in enhanced sampling of systems with complex energy surfaces. We hereby introduce generalized canonical ensemble (GCE) instead of the usual canonical ensemble into the parallel tempering to further improve abilities of the simulation technique. GCE utilizes an adapted weight function to obtain a unimodal energy distribution even in phase-coexisting region and then the parallel tempering on GCE yields the steady swap acceptance rates (SARs) instead of the fluctuated SARs in that on canonical ensemble. With the steady SARs, we can facilitate assign the parameters of the parallel tempering simulation to more efficiently reach equilibrium among different phases. We illustrate the parallel tempering simulation on GCE in the phase-coexisting region of 2-dimensional Potts model, a benchmark system for new simulation method developing. The result indicates that the new parallel tempering method is more efficient to estimate statistical quantities (i.e., to sample the conformational space) than the normal parallel tempering, specially in phase-coexisting regions of larger systems.

Lagrangian methods are widely used in many fields for multi-material compressible flow simulations such as in astrophysics and inertial confinement fusion (ICF), due to their distinguished advantage in capturing material interfaces automatically. In some of these applications, multiple internal energy equations such as those for electron, ion and radiation are involved. In the past decades, several staggered-grid based Lagrangian schemes have been developed which are designed to solve the internal energy equation directly. These schemes can be easily extended to solve problems with multiple internal energy equations. However such schemes are typically not conservative for the total energy. Recently, significant progress has been made in developing cell-centered Lagrangian schemes which have several good properties such as conservation for all the conserved variables and easiness for remapping. However, these schemes are commonly designed to solve the Euler equations in the form of the total energy, therefore they cannot be directly applied to the solution of either the single internal energy equation or the multiple internal energy equations without significant modifications. Such modifications, if not designed carefully, may lead to the loss of some of the nice properties of the original schemes such as conservation of the total energy. In this paper, we establish an equivalency relationship between the cell-centered discretizations of the Euler equations in the forms of the total energy and of the internal energy. By a carefully designed modification in the implementation, the cell-centered Lagrangian scheme can be used to solve the compressible fluid flow with one or multiple internal energy equations and meanwhile it does not lose its total energy conservation property. An advantage of this approach is that it can be easily applied to many existing large application codes which are based on the framework of solving multiple internal energy equations. Several two dimensional numerical examples for both Euler equations and three-temperature hydrodynamic equations in cylindrical coordinates are presented to demonstrate the performance of the scheme in terms of symmetry preserving, accuracy and non-oscillatory performance.

In this work the Laguerre basis for the biharmonic equation introduced by Jie Shen is employed in the spectral solution of self-similar problems of the boundary layer theory. An original Petrov-Galerkin formulation of the Falkner-Skan equation is presented which is based on a judiciously chosen special basis function to capture the asymptotic behaviour of the unknown. A spectral method of remarkable simplicity is obtained for computing Falkner-Skan-Cooke boundary layer flows. The accuracy and efficiency of the Laguerre spectral approximation is illustrated by determining the linear stability of nonseparated and separated flows according to the Orr-Sommerfeld equation. The pentadiagonal matrices representing the derivative operators are explicitly provided in an Appendix to aid an immediate implementation of the spectral solution algorithms.

An algorithm for computing wavefronts, based on the high frequency approximation to the wave equation, is presented. This technique applies the level set method to underwater acoustic wavefront propagation in the time domain. The level set method allows for computation of the acoustic phase function using established numerical techniques to solve a first order transport equation to a desired order of accuracy. Traditional methods for solving the eikonal equation directly on a fixed grid limit one to only the first arrivals, so these approaches are not useful when multi-path propagation is present. Applying the level set model to the problem allows for the time domain computation of the phase function on a fixed grid, without having to restrict to first arrival times. The implementation presented has no restrictions on range dependence or direction of travel, and offers improved efficiency over solving the full wave equation which under the high frequency assumption requires a large number of grid points to resolve the highly oscillatory solutions. Boundary conditions are discussed, and an approach is suggested for producing good results in the presence of boundary reflections. An efficient method to compute the amplitude from the level set method solutions is also presented. Comparisons to analytical solutions are presented where available, and numerical results are validated by comparing results with exact solutions where available, a full wave equation solver, and with wavefronts extracted from ray tracing software.

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.

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.

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.

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.

The governing equations for heat transfer and fluid flow are often formulated in a general form for the simplification of discretization and programming, which has achieved great success in thermal science and engineering. Based on the analysis of the popular general form of governing equations, we found that energy conservation cannot be guaranteed when specific heat capacity is not constant, which may lead to unreliable results. A new concept of generalized density is put forward, based on which a new general form of governing equations is proposed to guarantee energy conservation. A number of calculation examples have been employed to verify validation and feasibility.

A reconstruction-based discontinuous Galerkin (RDG(P1P2)) method, a variant of P1P2 method, is presented for the solution of the compressible Euler equations on arbitrary grids. In this method, an in-cell reconstruction, designed to enhance the accuracy of the discontinuous Galerkin method, is used to obtain a quadratic polynomial solution (P2) from the underlying linear polynomial (P1) discontinuous Galerkin solution using a least-squares method. The stencils used in the reconstruction involve only the von Neumann neighborhood (face-neighboring cells) and are compact and consistent with the underlying DG method. The developed RDG method is used to compute a variety of flow problems on arbitrary meshes to demonstrate its accuracy, efficiency, robustness, and versatility. The numerical results indicate that this RDG(P1P2) method is third-order accurate, and outperforms the third-order DG method (DG(P2)) in terms of both computing costs and storage requirements.

Optimal Replacement Variables (ORV) is a method for approximating a large system of ODEs by one with fewer equations, while attempting to preserve the essential dynamics of a reduced set of variables of interest. An earlier version of ORV [1] had some issues, including limited accuracy and in some rare cases, instability. Here we present a new version of ORV, inspired by the linear quadratic regulator problem of control theory, which provides better accuracy, a guarantee of stability and is in some ways easier to use.

We construct an efficient numerical scheme for the quantum Fokker-Planck- Landau (FPL) equation that works uniformly from kinetic to fluid regimes. Such a scheme inevitably needs an implicit discretization of the nonlinear collision operator, which is difficult to invert. Inspired by work [9] we seek a linear operator to penalize the quantum FPL collision term QqFPL in order to remove the stiffness induced by the small Knudsen number. However, there is no suitable simple quantum operator serving the purpose and for this kind of operators one has to solve the complicated quantum Maxwellians (Bose-Einstein or Fermi-Dirac distribution). In this paper, we propose to penalize QqFPL by the "classical" linear Fokker-Planck operator. It is based on the observation that the classical Maxwellian, with the temperature replaced by the internal energy, has the same first five moments as the quantum Maxwellian. Numerical results for Bose and Fermi gases are presented to illustrate the efficiency of the scheme in both fluid and kinetic regimes.

We present a parallel Cartesian method to solve elliptic problems with complex immersed interfaces. This method is based on a finite-difference scheme and is second-order accurate in the whole domain. The originality of the method lies in the use of additional unknowns located on the interface, allowing to express straightforwardly the interface transmission conditions. We describe the method and the details of its parallelization performed with the PETSc library. Then we present numerical validations in two dimensions, assorted with comparisons to other related methods, and a numerical study of the parallelized method.

The Cubic-Polynomial Interpolation scheme has been developed and applied to many practical simulations. However, it seems the existing Cubic-Polynomial Interpolation scheme are restricted to uniform rectangular meshes. Consequently, this scheme has some limitations to problems in irregular domains. This paper will extend the Cubic-Polynomial Interpolation scheme to triangular meshes by using some spline interpolation techniques. Numerical examples are provided to demonstrate the accuracy of the proposed schemes.

Three high order shock-capturing schemes are compared for large eddy simulations (LES) of temporally evolving mixing layers for different convective Mach numbers ranging from the quasi-incompressible regime to highly compressible supersonic regime. The considered high order schemes are fifth-order WENO (WENO5), seventh-order WENO (WENO7) and the associated eighth-order central spatial base scheme with the dissipative portion of WENO7 as a nonlinear post-processing filter step (WENO7fi). This high order nonlinear filter method of Yee & Sjögreen is designed for accurate and efficient simulations of shock-free compressible turbulence, turbulence with shocklets and turbulence with strong shocks with minimum tuning of scheme parameters. The LES results by WENO7fi using the same scheme parameter agree well with experimental results compiled by Barone et al., and published direct numerical simulations (DNS) work of Rogers & Moser and Pantano & Sarkar, whereas results by WENO5 and WENO7 compare poorly with experimental data and DNS computations.