Three-dimensional matched interface and boundary (MIB) method for treating geometric singularities

This paper reports the three-dimensional (3D) generalization of our previous 2D higher-order matched interface and boundary (MIB) method for solving elliptic equations with discontinuous coefficients and non-smooth interfaces. New MIB algorithms that make use of two sets of interface jump conditions are proposed to remove the critical acute angle constraint of our earlier MIB scheme for treating interfaces with sharp geometric singularities, such as sharp edges, sharp wedges and sharp tips. The resulting 3D MIB schemes are of second-order accuracy for arbitrarily complex interfaces with sharp geometric singularities, of fourth-order accuracy for complex interfaces with moderate geometric singularities, and of sixth-order accuracy for curved smooth interfaces. A systematical procedure is introduced to make the MIB matrix optimally symmetric and banded by appropriately choosing auxiliary grid points. Consequently, the new MIB linear algebraic equations can be solved with fewer number of iterations. The proposed MIB method makes use of Cartesian grids, standard finite difference schemes, lowest order interface jump conditions and fictitious values. The interface jump conditions are enforced at each intersecting point of the interface and mesh lines to overcome the staircase phenomena in finite difference approximation. While a pair of fictitious values are determined along a mesh at a time, an iterative procedure is proposed to determine all the required fictitious values for higher-order schemes by repeatedly using the lowest order jump conditions. A variety of MIB techniques are developed to overcome geometric constraints. The essential strategy of the MIB method is to locally reduce a 2D or a 3D interface problem into 1D-like ones. The proposed MIB method is extensively validated in terms of the order of accuracy, the speed of convergence, the number of iterations and CPU time. Numerical experiments are carried out to complex interfaces, including the molecular surfaces of a protein, a missile interface, and van der Waals surfaces of intersecting spheres.     

Adaptively deformed mesh based interface method for elliptic equations with discontinuous coefficients

Mesh deformation methods are a versatile strategy for solving partial differential equations (PDEs) with a vast variety of practical applications. However, these methods break down for elliptic PDEs with discontinuous coefficients, namely, elliptic interface problems. For this class of problems, the additional interface jump conditions are required to maintain the well-posedness of the governing equation. Consequently, in order to achieve high accuracy and high order convergence, additional numerical algorithms are required to enforce the interface jump conditions in solving elliptic interface problems. The present work introduces an interface technique based adaptively deformed mesh strategy for resolving elliptic interface problems. We take the advantages of the high accuracy, flexibility and robustness of the matched interface and boundary (MIB) method to construct an adaptively deformed mesh based interface method for elliptic equations with discontinuous coefficients. The proposed method generates deformed meshes in the physical domain and solves the transformed governed equations in the computational domain, which maintains regular Cartesian meshes. The mesh deformation is realized by a mesh transformation PDE, which controls the mesh redistribution by a source term. The source term consists of a monitor function, which builds in mesh contraction rules. Both interface geometry based deformed meshes and solution gradient based deformed meshes are constructed to reduce the L(∞) and L(2) errors in solving elliptic interface problems. The proposed adaptively deformed mesh based interface method is extensively validated by many numerical experiments. Numerical results indicate that the adaptively deformed mesh based interface method outperforms the original MIB method for dealing with elliptic interface problems.     

Second-order Poisson Nernst-Planck solver for ion channel transport

The Poisson Nernst-Planck (PNP) theory is a simplified continuum model for a wide variety of chemical, physical and biological applications. Its ability of providing quantitative explanation and increasingly qualitative predictions of experimental measurements has earned itself much recognition in the research community. Numerous computational algorithms have been constructed for the solution of the PNP equations. However, in the realistic ion-channel context, no second order convergent PNP algorithm has ever been reported in the literature, due to many numerical obstacles, including discontinuous coefficients, singular charges, geometric singularities, and nonlinear couplings. The present work introduces a number of numerical algorithms to overcome the abovementioned numerical challenges and constructs the first second-order convergent PNP solver in the ion-channel context. First, a Dirichlet to Neumann mapping (DNM) algorithm is designed to alleviate the charge singularity due to the protein structure. Additionally, the matched interface and boundary (MIB) method is reformulated for solving the PNP equations. The MIB method systematically enforces the interface jump conditions and achieves the second order accuracy in the presence of complex geometry and geometric singularities of molecular surfaces. Moreover, two iterative schemes are utilized to deal with the coupled nonlinear equations. Furthermore, extensive and rigorous numerical validations are carried out over a number of geometries, including a sphere, two proteins and an ion channel, to examine the numerical accuracy and convergence order of the present numerical algorithms. Finally, application is considered to a real transmembrane protein, the Gramicidin A channel protein. The performance of the proposed numerical techniques is tested against a number of factors, including mesh sizes, diffusion coefficient profiles, iterative schemes, ion concentrations, and applied voltages. Numerical predictions are compared with experimental measurements.     

An Eulerian method for multi-component problems in non-linear elasticity with sliding interfaces

This paper is devoted to developing a multi-material numerical scheme for non-linear elastic solids, with emphasis on the inclusion of interfacial boundary conditions. In particular for colliding solid objects it is desirable to allow large deformations and relative slide, whilst employing fixed grids and maintaining sharp interfaces. Existing schemes utilising interface tracking methods such as volume-of-fluid typically introduce erroneous transport of tangential momentum across material boundaries. Aside from combatting these difficulties one can also make improvements in a numerical scheme for multiple compressible solids by utilising governing models that facilitate application of high-order shock capturing methods developed for hydrodynamics. A numerical scheme that simultaneously allows for sliding boundaries and utilises such high-order shock capturing methods has not yet been demonstrated. A scheme is proposed here that directly addresses these challenges by extending a ghost cell method for gas-dynamics to solid mechanics, by using a first-order model for elastic materials in conservative form. Interface interactions are captured using the solution of a multi-material Riemann problem which is derived in detail. Several different boundary conditions are considered including solid/solid and solid/vacuum contact problems. Interfaces are tracked using level-set functions. The underlying single material numerical method includes a characteristic based Riemann solver and high-order WENO reconstruction. Numerical solutions of example multi-material problems are provided in comparison to exact solutions for the one-dimensional augmented system, and for a two-dimensional friction experiment.     

Multiscale molecular dynamics using the matched interface and boundary method

The Poisson-Boltzmann (PB) equation is an established multiscale model for electrostatic analysis of biomolecules and other dielectric systems. PB based molecular dynamics (MD) approach has a potential to tackle large biological systems. Obstacles that hinder the current development of PB based MD methods are concerns in accuracy, stability, efficiency and reliability. The presence of complex solvent-solute interface, geometric singularities and charge singularities leads to challenges in the numerical solution of the PB equation and electrostatic force evaluation in PB based MD methods. Recently, the matched interface and boundary (MIB) method has been utilized to develop the first second order accurate PB solver that is numerically stable in dealing with discontinuous dielectric coefficients, complex geometric singularities and singular source charges. The present work develops the PB based MD approach using the MIB method. New formulation of electrostatic forces is derived to allow the use of sharp molecular surfaces. Accurate reaction field forces are obtained by directly differentiating the electrostatic potential. Dielectric boundary forces are evaluated at the solvent-solute interface using an accurate Cartesian-grid surface integration method. The electrostatic forces located at reentrant surfaces are appropriately assigned to related atoms. Extensive numerical tests are carried out to validate the accuracy and stability of the present electrostatic force calculation. The new PB based MD method is implemented in conjunction with the AMBER package. MIB based MD simulations of biomolecules are demonstrated via a few example systems.     

Numerical method for solving matrix coefficient elliptic equation with sharp-edged interfaces

Solving elliptic equations with sharp-edged interfaces is a challenging problem for most existing methods, especially when the solution is highly oscillatory. Nonetheless, it has wide applications in engineering and science. An accurate and efficient method is desired. We propose an efficient non-traditional finite element method with non-body-fitting grids to solve the matrix coefficient elliptic equations with sharp-edged interfaces. Extensive numerical experiments show that this method is second order accurate in the L^∞ norm and that it can handle both sharp-edged interface and oscillatory solutions.     

Numerical simulations of instabilities in the implosion process of inertial confined fusion in 2D cylindrical coordinates

In this paper, we introduce a multi-material arbitrary Lagrangian and Eulerian method for the hydrodynamic radiative multi-group diffusion model in 2D cylindrical coordinates. The basic idea in the construction of the method is the following: In the Lagrangian step, a closure model of radiation-hydrodynamics is used to give the states of equations for materials in mixed cells. In the mesh rezoning step, we couple the rezoning principle with the Lagrangian interface tracking method and an Eulerian interface capturing scheme to compute interfaces sharply according to their deformation and to keep cells in good geometric quality. In the interface reconstruction step, a dual-material Moment-of-Fluid method is introduced to obtain the unique interface in mixed cells. In the remapping step, a conservative remapping algorithm of conserved quantities is presented. A number of numerical tests are carried out and the numerical results show that the new method can simulate instabilities in complex fluid field under large deformation,and are accurate and robust.     

Invariantization of the Crank-Nicolson method for Burgers’ equation

In this article, a geometric technique to construct numerical schemes for partial differential equations (PDEs) that inherit Lie symmetries is proposed. The moving frame method enables one to adjust the numerical schemes in a geometric manner and systematically construct proper invariant versions of them. To illustrate the method, we study invariantization of the Crank-Nicolson scheme for Burgers’ equation. With careful choice of normalization equations, the invariantized schemes are shown to surpass the standard scheme, successfully removing numerical oscillation around sharp transition layers.     

The adaptive immersed interface finite element method for elliptic and Maxwell interface problems

We propose self-adaptive finite element methods with error control for solving elliptic and electromagnetic problems with discontinuous coefficients. The meshes in the methods do not need to fit the interfaces. New error indicators are introduced to control the error due to non-body-fitted meshes. Flexible h-adaptive strategies are developed, which can be systematically extended to a large class of interface problems. Extensive numerical experiments are performed to support the theoretical results and to show the competitive behavior of the adaptive algorithm even for interfaces involving corner or tip singularities.     

Time-Domain Numerical Solutions of Maxwell Interface Problems with Discontinuous Electromagnetic Waves

This paper is devoted to time domain numerical solutions of two-dimensional (2D) material interface problems governed by the transverse magnetic (TM) and transverse electric (TE) Maxwell's equations with discontinuous electromagnetic solutions. Due to the discontinuity in wave solutions across the interface, the usual numerical methods will converge slowly or even fail to converge. This calls for the development of advanced interface treatments for popular Maxwell solvers. We will investigate such interface treatments by considering two typical Maxwell solvers – one based on collocation formulation and the other based on Galerkin formulation. To restore the accuracy reduction of the collocation finite-difference time-domain (FDTD) algorithm near an interface, the physical jump conditions relating discontinuous wave solutions on both sides of the interface must be rigorously enforced. For this purpose, a novel matched interface and boundary (MIB) scheme is proposed in this work, in which new jump conditions are derived so that the discontinuous and staggered features of electric and magnetic field components can be accommodated. The resulting MIB time-domain (MIBTD) scheme satisfies the jump conditions locally and suppresses the staircase approximation errors completely over the Yee lattices. In the discontinuous Galerkin time-domain (DGTD) algorithm – a popular Galerkin Maxwell solver, a proper numerical flux can be designed to accurately capture the jumps in the electromagnetic waves across the interface and automatically preserves the discontinuity in the explicit time integration. The DGTD solution to Maxwell interface problems is explored in this work, by considering a nodal based high order discontinuous Galerkin method. In benchmark TM and TE tests with analytical solutions, both MIBTD and DGTD schemes achieve the second order of accuracy in solving circular interfaces. In comparison, the numerical convergence of the MIBTD method is slightly more uniform, while the DGTD method is more flexible and robust.     

An interface capturing method for the simulation of multi-phase compressible flows

A novel finite-volume interface (contact) capturing method is presented for simulation of multi-component compressible flows with high density ratios and strong shocks. In addition, the materials on the two sides of interfaces can have significantly different equations of state. Material boundaries are identified through an interface function, which is solved in concert with the governing equations on the same mesh. For long simulations, the method relies on an interface compression technique that constrains the thickness of the diffused interface to a few grid cells throughout the simulation. This is done in the spirit of shock-capturing schemes, for which numerical dissipation effectively preserves a sharp but mesh-representable shock profile. For contact capturing, the formulation is modified so that interface representations remain sharp like captured shocks, countering their tendency to diffuse via the same numerical diffusion needed for shock-capturing. Special techniques for accurate and robust computation of interface normals and derivatives of the interface function are developed. The interface compression method is coupled to a shock-capturing compressible flow solver in a way that avoids the spurious oscillations that typically develop at material boundaries. Convergence to weak solutions of the governing equations is proved for the new contact capturing approach. Comparisons with exact Riemann problems for model one-dimensional multi-material flows show that the interface compression technique is accurate. The method employs Cartesian product stencils and, therefore, there is no inherent obstacles in multiple dimensions. Examples of two- and three-dimensional flows are also presented, including a demonstration with significantly disparate equations of state: a shock induced collapse of three-dimensional van der Waal’s bubbles (air) in a stiffened equation of state liquid (water) adjacent to a Mie-Grüneisen equation of state wall (copper).     

水中金属丝电爆炸拉氏磁流体动力学模拟方法

基于拉格朗日描述,建立了水中金属丝电爆炸的单温磁流体动力学模型,并给出一种高阶混合有限元离散求解方法。拉氏可压缩流体方程组中,速度定义在H1连续有限元空间,内能定义在L2间断有限元空间实现物质界面的精确捕捉,存在激波的区域引入张量人工粘性抑制数值振荡。磁扩散方程仅考虑周向磁通量密度,简化为标量方程,使用H1连续有限元方法离散求解。焦耳热和洛伦兹力作为源项引入实现磁流体方程的耦合。数值算例表明:磁扩散求解器能够求解存在不同电导率的多介质磁扩散问题;拉氏流体求解器能够精确追踪物质界面,具有较好的激波分辨能力;耦合RLC电路的磁流体求解器能够复现水中金属丝电爆炸加热相变、冲击波的产生与传播、放电模式转变等物理过程。     

A high-order cell-centered Lagrangian scheme for compressible fluid flows in two-dimensional cylindrical geometry

The goal of this paper is to present high-order cell-centered schemes for solving the equations of Lagrangian gas dynamics written in cylindrical geometry. A node-based discretization of the numerical fluxes is obtained through the computation of the time rate of change of the cell volume. It allows to derive finite volume numerical schemes that are compatible with the geometric conservation law (GCL). Two discretizations of the momentum equations are proposed depending on the form of the discrete gradient operator. The first one corresponds to the control volume scheme while the second one corresponds to the so-called area-weighted scheme. Both formulations share the same discretization for the total energy equation. In both schemes, fluxes are computed using the same nodal solver which can be viewed as a two-dimensional extension of an approximate Riemann solver. The control volume scheme is conservative for momentum, total energy and satisfies a local entropy inequality in its first-order semi-discrete form. However, it does not preserve spherical symmetry. On the other hand, the area-weighted scheme is conservative for total energy and preserves spherical symmetry for one-dimensional spherical flow on equi-angular polar grid. The two-dimensional high-order extensions of these two schemes are constructed employing the generalized Riemann problem (GRP) in the acoustic approximation. Many numerical tests are presented in order to assess these new schemes. The results obtained for various representative configurations of one and two-dimensional compressible fluid flows show the robustness and the accuracy of our new schemes.     

激波和单列水柱、气水固多界面相互作用的数值模拟

研究可压缩多介质流场的激波和多介质界面相互作用问题.在Descartes固定网格采用level-set方法追踪界面,气/气界面边界条件处理采用OGFM方法,采用修正的rGFM方法提高气/水和气/固界面处构造Riemann问题精度,将Riemann近似解得到的界面参数外推到两侧真实和虚拟流体,采用五阶WENO方法求解流场Euler方程和界面level-set方程,给出不同时刻流场数值纹影图像.结果表明：在可压缩流场嵌入固体和水、气体等目标,本文方法可较精确地分辨平面运动激波和单列水柱及包含气/气、气/水和气/固等界面作用后产生的复杂激波结构.和传统的分区与贴体变换方法不同,为Descartes网格包含多介质界面复杂流场计算提供新途径.     

A Well-Posed Numerical Method to Track Isolated Conformal Map Singularities in Hele-Shaw Flow

We present a new numerical method for calculating an evolving 2D Hele-Shaw interface when surface tension effects are neglected. In the case where the flow is directed from the less viscous fluid into the more viscous fluid, the motion of the interface is ill-posed; small deviations in the initial condition will produce significant changes in the ensuing motion. This situation is disastrous for numerical computation, as small roundoff errors can quickly lead to large inaccuracies in the computed solution. Our method of computation is most easily formulated using a conformal map from the fluid domain into a unit disk. The method relies on analytically continuing the initial data and equations of motion into the region exterior to the disk, where the evolution problem becomes well-posed. The equations are then numerically solved in the extended domain. The presence of singularities in the conformal map outside of the disk introduces specific structures along the fluid interface. Our method can explicitly track the location of isolated pole and branch point singularities, allowing us to draw connections between the development of interfacial patterns and the motion of singularities as they approach the unit disk. In particular, we are able to relate physical features such as finger shape, side-branch formation, and competition between fingers to the nature and location of the singularities. The usefulness of this method in studying the formation of topological singularities (self intersections of the interface) is also pointed out.     

Modeling merging and breakup in the moving mesh interface tracking method for multiphase flow simulations

The three-dimensional, moving mesh interface tracking (MMIT) method coupled with local mesh adaptations by Quan and Schmidt [S.P. Quan, D.P. Schmidt, A moving mesh interface tracking method for 3D incompressible two-phase flows, J. Comput. Phys. 221 (2007) 761–780] demonstrated the capability to accurately simulate multiphase flows, to handle large deformation, and also to perform interface pinch-off for some specific cases. However, another challenge, i.e. how to handle interface merging (such as droplet coalescence) has not been addressed. In this paper, we present a mesh combination scheme for interface connection and a more general mesh separation algorithm for interface breakup. These two schemes are based on the conversion of liquid cells in one phase to another fluid by changing the fluid properties of the cells in the combination or separation region. After the conversion, the newly created interface is usually ragged, and a local projection method is employed to smooth the interface. Extra mesh adaptation criteria are introduced to handle colliding interfaces with almost zero curvatures as the distance between the interfaces diminishes. Simulations of droplet pair collisions including both head-on and off-center coalescences show that the mesh adaptations are capable of resolving very small length scales, and the mesh combination and mesh separation schemes can handle the topological transitions in multiphase flows. The potential of our method to perform detailed investigations of droplet coalescence and breakup is also displayed.     

High order matched interface and boundary methods for the Helmholtz equation in media with arbitrarily curved interfaces

This work overcomes the difficulty of the previous matched interface and boundary (MIB) method in dealing with interfaces with non-constant curvatures for optical waveguide analysis. This difficulty is essentially bypassed by avoiding the use of local cylindrical coordinates in the improved MIB method. Instead, novel jump conditions are derived along global Cartesian directions for the transverse magnetic field components. Effective interface treatments are proposed to rigorously impose jump conditions across arbitrarily curved interfaces based on a simple Cartesian grid. Even though each field component satisfies the scalar Helmholtz equation, the enforcement of jump conditions couples two transverse magnetic field components, so that the resulting MIB method is a full-vectorial approach for the modal analysis of optical waveguides. The numerical performance of the proposed MIB method is investigated by considering interface problems with both constant and general curvatures. The MIB method is shown to be able to deliver a fourth order of accuracy in all cases, even when a high frequency solution is involved.     

High-order non-uniform grid schemes for numerical simulation of hypersonic boundary-layer stability and transition

The direct numerical simulation of receptivity, instability and transition of hypersonic boundary layers requires high-order accurate schemes because lower-order schemes do not have an adequate accuracy level to compute the large range of time and length scales in such flow fields. The main limiting factor in the application of high-order schemes to practical boundary-layer flow problems is the numerical instability of high-order boundary closure schemes on the wall. This paper presents a family of high-order non-uniform grid finite difference schemes with stable boundary closures for the direct numerical simulation of hypersonic boundary-layer transition. By using an appropriate grid stretching, and clustering grid points near the boundary, high-order schemes with stable boundary closures can be obtained. The order of the schemes ranges from first-order at the lowest, to the global spectral collocation method at the highest. The accuracy and stability of the new high-order numerical schemes is tested by numerical simulations of the linear wave equation and two-dimensional incompressible flat plate boundary layer flows. The high-order non-uniform-grid schemes (up to the 11th-order) are subsequently applied for the simulation of the receptivity of a hypersonic boundary layer to free stream disturbances over a blunt leading edge. The steady and unsteady results show that the new high-order schemes are stable and are able to produce high accuracy for computations of the nonlinear two-dimensional Navier–Stokes equations for the wall bounded supersonic flow.     

Approach for simulating gas–liquid-like flows under supercritical pressures using a high-order central differencing scheme

This study proposes an approach for simulations of cryogenic fluid mixing under supercritical pressures using high-order schemes. In this approach, we introduce a pressure evolution equation and consistently construct numerical diffusion terms to maintain the velocity and pressure equilibriums at fluid interfaces. The interfaces with high density and temperature ratio are successfully captured without the generation of spurious oscillations, while a high-order central differencing scheme resolves the flow fields. The present method preserves the mass and momentum conservation properties, while the poor energy conservation property is recognized. The one-dimensional single and multi-species interface advection and two-dimensional cryogenic jet mixing problems demonstrate the superiority and robustness of the present method over a conventional fully conservative method.     

应用多介质PPM方法计算斜激波与物质交界面的相互作用

利用多介质PPM方法研究斜激波与物质交界面的相互作用.采用与体积分数耦合的Euler方程组作为计算模型,用双波近似来求解一般刚性气体状态方程Riemann问题.通过体积分数的计算来获得界面的位置,在整个流场采用统一的高阶PPM格式进行计算.文中对斜激波与不同物质界面相互作用进行了数值模拟,并给出了交界面上由于斜压效应产生的涡列的演化过程,特别是强斜激波与不同物质界面的相互作用的情况.