An Indirect-Forcing Immersed Boundary Method for Incompressible Viscous Flows with Interfaces on Irregular Domains

An indirect-forcing immersed boundary method for solving the incompressible Navier-Stokes equations involving the interfaces and irregular domains is developed.The rigid boundaries and interfaces are represented by a number of Lagrangian control points.Stationary rigid boundaries are embedded in the Cartesian grid and singular forces at the rigid boundaries are applied to impose the prescribed velocity conditions.The singular forces at the interfaces and the rigid boundaries are then distributed to the nearby Cartesian grid points using the immersed boundary method.In the present work,the singular forces at the rigid boundaries are computed implicitly by solving a small system of equations at each time step to ensure that the prescribed velocity condition at the rigid boundary is satisfied exactly.For deformable interfaces,the forces that the interface exerts on the fluid are computed from the configuration of the elastic interface and are applied to the fluid.The Navier-Stokes equations are discretized using finite difference method on a staggered uniform Cartesian grid by a second order accurate projection method.The ability of the method to simulate viscous flows with interfaces on irregular domains is demonstrated by applying to the rotational flow problem,the relaxation of an elastic membrane and flow in a constriction with an immersed elastic membrane.

IMPLICITY LINEAR COLLOCATION METHOD AND ITERATED IMPLICITY LINEAR COLLOCATION METHOD FOR THE NUMERICAL SOLUTION OF HAMMERSTEIN FREDHOLM INTEGRAL EQUATIONS ON 2D IRREGULAR DOMAINS

In this work,we adapt and compare implicity linear collocation method and iterated implicity linear collocation method for solving nonlinear two dimensional Fredholm integral equations of Hammerstein type using IMQ-RBFs on a non-rectangular domain.IMQs show to be the most promising RBFs for this kind of equations.The proposed methods are mesh-free and they are independent of the geometry of domain.Convergence analysis of the proposed methods together with some benchmark examples are provided which support their reliability and numerical stability.

A local refinement purely meshless scheme for time fractional nonlinear Schrodinger equation in irregular geometry region

A local refinement hybrid scheme(LRCSPH-FDM)is proposed to solve the two-dimensional(2D)time fractional nonlinear Schrodinger equation(TF-NLSE)in regularly or irregularly shaped domains,and extends the scheme to predict the quantum mechanical properties governed by the time fractional Gross-Pitaevskii equation(TF-GPE)with the rotating Bose-Einstein condensate.It is the first application of the purely meshless method to the TF-NLSE to the author’s knowledge.The proposed LRCSPH-FDM(which is based on a local refinement corrected SPH method combined with FDM)is derived by using the finite difference scheme(FDM)to discretize the Caputo TF term,followed by using a corrected smoothed particle hydrodynamics(CSPH)scheme continuously without using the kernel derivative to approximate the spatial derivatives.Meanwhile,the local refinement technique is adopted to reduce the numerical error.In numerical simulations,the complex irregular geometry is considered to show the flexibility of the purely meshless particle method and its advantages over the grid-based method.The numerical convergence rate and merits of the proposed LRCSPH-FDM are illustrated by solving several 1D/2D(where 1D stands for one-dimensional)analytical TF-NLSEs in a rectangular region(with regular or irregular particle distribution)or in a region with irregular geometry.The proposed method is then used to predict the complex nonlinear dynamic characters of 2D TF-NLSE/TF-GPE in a complex irregular domain,and the results from the posed method are compared with those from the FDM.All the numerical results show that the present method has a good accuracy and flexible application capacity for the TF-NLSE/GPE in regions of a complex shape.

Multiresolution method for bending of plates with complex shapes

A high-accuracy multiresolution method is proposed to solve mechanics problems subject to complex shapes or irregular domains.To realize this method,we design a new wavelet basis function,by which we construct a fifth-order numerical scheme for the approximation of multi-dimensional functions and their multiple integrals defined in complex domains.In the solution of differential equations,various derivatives of the unknown function are denoted as new functions.Then,the integral relations between these functions are applied in terms of wavelet approximation of multiple integrals.Therefore,the original equation with derivatives of various orders can be converted to a system of algebraic equations with discrete nodal values of the highest-order derivative.During the application of the proposed method,boundary conditions can be automatically included in the integration operations,and relevant matrices can be assured to exhibit perfect sparse patterns.As examples,we consider several second-order mathematics problems defined on regular and irregular domains and the fourth-order bending problems of plates with various shapes.By comparing the solutions obtained by the proposed method with the exact solutions,the new multiresolution method is found to have a convergence rate of fifth order.The solution accuracy of this method with only a few hundreds of nodes can be much higher than that of the finite element method(FEM)with tens of thousands of elements.In addition,because the accuracy order for direct approximation of a function using the proposed basis function is also fifth order,we may conclude that the accuracy of the proposed method is almost independent of the equation order and domain complexity.

High efficient parallel numerical surface wave model based on an irregular quasi-rectangular domain decomposition scheme

To achieve high parallel efficiency for the global MASNUM surface wave model, the algorithm of an irregular quasirectangular domain decomposition and related serializing of calculating points and data exchanging schemes are developed and conducted, based on the environment of Message Passing Interface(MPI). The new parallel version of the surface wave model is tested for parallel computing on the platform of the Sunway BlueLight supercomputer in the National Supercomputing Center in Jinan. The testing involves four horizontal resolutions, which are 1°×1°,(1/2)°×(1/2)°,(1/4)°×(1/4)°, and(1/8)°×(1/8)°. These tests are performed without data Input/Output(IO) and the maximum amount of processors used in these tests reaches to 131072. The testing results show that the computing speeds of the model with different resolutions are all increased with the increasing of numbers of processors. When the number of processors is four times that of the base processor number, the parallel efficiencies of all resolutions are greater than 80%. When the number of processors is eight times that of the base processor number, the parallel efficiency of tests with resolutions of 1°×1°,(1/2)°×(1/2)° and(1/4)°×(1/4)° is greater than 80%, and it is 62% for the test with a resolution of(1/8)°×(1/8)° using 131072 processors, which is the nearly all processors of Sunway BlueLight. When the processor's number is 24 times that of the base processor number, the parallel efficiencies for tests with resolutions of 1°×1°,(1/2)°×(1/2)°, and(1/4)°×(1/4)° are 72%, 62%, and 38%, respectively. The speedup and parallel efficiency indicate that the irregular quasi-rectangular domain decomposition and serialization schemes lead to high parallel efficiency and good scalability for a global numerical wave model.

PIMOL: The Finite Difference Method of Lines Based on the Precise Integration Method for an Arbitrary Irregular Domain

The aim of this paper is to introduce a new semi-analytical method named precise integration method of lines(PIMOL),which is developed and used to solve the ordinary differential equation(ODE)systems based on the finite difference method of lines and the precise integration method.The irregular domain problem is mainly discussed in this paper.Three classical examples of Poisson^equation problems are given,including one regular and two irregular domain examples.The PIMOL reduces a semi-discrete ODE problem to a linear algebraic matrix equation and does not require domain mapping for treating the irregular domain problem.Numerical results show that the PIMOL is a powerful method.

Numerical Solution of Partial Differential Equations in Arbitrary Shaped Domains Using Cartesian Cut-Stencil Finite Difference Method.Part II:Higher-Order Schemes

Compact higher-order(HO)schemes for a new finite difference method,referred to as the Cartesian cut-stencil FD method,for the numerical solution of the convection-diffusion equation in complex shaped domains have been addressed in this paper.The Cartesian cut-stencil FD method,which employs 1-D quadratic transformation functions to map a non-uniform(uncut or cut)physical stencil to a uniform computational stencil,can be combined with compact HO Pad´e-Hermitian formulations to produce HO cut-stencil schemes.The modified partial differential equation technique is used to develop formulas for the local truncation error for the cut-stencil HO formulations.The effect of various HO approximations for Neumann boundary conditions on the solution accuracy and global order of convergence are discussed.The numerical results for second-order and compact HO formulations of the Cartesian cut-stencil FD method have been compared for test problems using the method of manufactured solutions.

Parallel Molecular Dynamics with Irregular Domain Decomposition

The spatial domain of Molecular Dynamics simulations is usually a regular box that can be easily divided in subdomains for parallel processing.Recent efforts aimed at simulating complex biological systems,like the blood flow inside arteries,require the execution of Parallel Molecular Dynamics(PMD)in vessels that have,by nature,an irregular shape.In those cases,the geometry of the domain becomes an additional input parameter that directly influences the outcome of the simulation.In this paper we discuss the problems due to the parallelization of MD in complex geometries and show an efficient and general method to perform MD in irregular domains.

HIGH ORDER NUMERICAL METHODS TO TWO DIMENSIONAL HEAVISIDE FUNCTION INTEGRALS

In this paper we design and analyze a class of high order numerical methods to two dimensional Heaviside function integrals. Inspired by our high order numerical methods to two dimensional delta function integrals [19], the methods comprise approximating the mesh cell restrictions of the Heaviside function integral. In each mesh cell the two dimen- sional Heaviside function integral can be rewritten as a one dimensional ordinary integral with the integrand being a one dimensional Heaviside function integral which is smooth on several subsets of the integral interval. Thus the two dimensional Heaviside function inte- gral is approximated by applying standard one dimensional high order numerical quadra- tures and high order numerical methods to one dimensional Heaviside function integrals. We establish error estimates for the method which show that the method can achieve any desired accuracy by assigning the corresponding accuracy to the sub-algorithms. Numerical examples are presented showing that the in this paper achieve or exceed the expected second to fourth-order methods implemented accuracy.

The Sensitivity Analysis for the Flow Past Obstacles Problem with Respect to the Reynolds Number

In this paper,numerical sensitivity analysis with respect to the Reynolds number for the flow past obstacle problem is presented.To carry out such analysis,at each time step,we need to solve the incompressible Navier-Stokes equations on irregular domains twice,one for the primary variables;the other is for the sensitivity variables with homogeneous boundary conditions.The Navier-Stokes solver is the augmented immersed interface method for Navier-Stokes equations on irregular domains.One of the most important contribution of this paper is that our analysis can predict the critical Reynolds number at which the vortex shading begins to develop in the wake of the obstacle.Some interesting experiments are shown to illustrate how the critical Reynolds number varies with different geometric settings.

An Adaptive,Finite Difference Solver for the Nonlinear Poisson-Boltzmann Equation with Applications to Biomolecular Computations

We present a solver for the Poisson-Boltzmann equation and demonstrate its applicability for biomolecular electrostatics computation.The solver uses a level set framework to represent sharp,complex interfaces in a simple and robust manner.It also uses non-graded,adaptive octree grids which,in comparison to uniform grids,drastically decrease memory usage and runtime without sacrificing accuracy.The basic solver was introduced in earlier works[16,27],and here is extended to address biomolecular systems.First,a novel approach of calculating the solvent excluded and the solvent accessible surfaces is explained;this allows to accurately represent the location of the molecule’s surface.Next,a hybrid finite difference/finite volume approach is presented for discretizing the nonlinear Poisson-Boltzmann equation and enforcing the jump boundary conditions at the interface.Since the interface is implicitly represented by a level set function,imposing the jump boundary conditions is straightforward and efficient.

Multiscale Hemodynamics Using GPU Clusters

The parallel implementation of MUPHY,a concurrent multiscale code for large-scale hemodynamic simulations in anatomically realistic geometries,for multi-GPU platforms is presented.Performance tests show excellent results,with a nearly linear parallel speed-up on up to 32GPUs and a more than tenfold GPU/CPU acceleration,all across the range of GPUs.The basic MUPHY scheme combines a hydrokinetic(Lattice Boltzmann)representation of the blood plasma,with a Particle Dynamics treatment of suspended biological bodies,such as red blood cells.To the best of our knowledge,this represents the first effort in the direction of laying down general design principles for multiscale/physics parallel Particle Dynamics applications in non-ideal geometries.This configures the present multi-GPU version of MUPHY as one of the first examples of a high-performance parallel code for multiscale/physics biofluidic applications in realistically complex geometries.