Stochastic chemical systems with diffusion are modeled with a reaction-diffusion master equation. On a macroscopic level, the governing equation is a reaction-diffusion equation for the averages of the chemical species. On a mesoscopic level, the master equation for a well stirred chemical system is combined with Brownian motion in space to obtain the reaction-diffusion master equation. The space is covered by an unstructured mesh and the diffusion coefficients on the mesoscale are obtained from a finite element discretization of the Laplace operator on the macroscale. The resulting method is a flexible hybrid algorithm in that the diffusion can be handled either on the meso- or on the macroscale level. The accuracy and the efficiency of the method are illustrated in three numerical examples inspired by molecular biology.
A priori subcell limiting approach is developed for high-order flux reconstruction/correction procedure via reconstruction (FR/CPR) on two-dimensional unstructured quadrilateral meshes. Firstly, a modified indicator based on modal energy coefficients is proposed to detect troubled cells. Then, troubled cells are decomposed into nonuniform subcells and each subcell has one solution point. A second-order finite difference shock-capturing scheme based on nonuniform nonlinear weighted (NNW) interpolation is constructed to calculate troubled cells while smooth cells are calculated by the CPR method…
In this paper, a third order gas kinetic scheme is developed on the three dimensional hybrid unstructured meshes for the numerical simulation of compressible inviscid and viscous flows. A third-order WENO reconstruction is developed on the hybrid unstructured meshes, including tetrahedron, pyramid, prism and hexahedron. A simple strategy is adopted for the selection of big stencil and sub-stencils. Incorporate with the two-stage fourth-order temporal discretization and lower-upper symmetric Gauss-Seidel methods, both explicit and implicit high-order gas-kinetic schemes are developed. A variety…
We present a novel approach for high-order accurate numerical differentiation on unstructured meshes of quadrilateral elements. To differentiate a given function, an auxiliary function with greater smoothness properties is defined which when differentiated provides the derivatives of the original function. The method generalises traditional finite difference methods to meshes of arbitrary topology in any number of dimensions for any order of derivative and accuracy. We demonstrate the accuracy of the numerical scheme using dual quadrilateral meshes and a refinement method based on subdivision …
We present a geometric multigrid solver for the Compact Discontinuous Galerkin method through building a hierarchy of coarser meshes using a simple agglomeration method which handles arbitrary element shapes and dimensions. The method is easily extendable to other discontinuous Galerkin discretizations, including the Local DG method and the Interior Penalty method. We demonstrate excellent solver performance for Poisson's equation, provided a flux formulation is used for the operator coarsening and a suitable switch function chosen for the numerical fluxes.
Stochastic collocation on unstructured multivariate meshes
University of Massachusetts Dartmouth（马萨诸塞大学达特茅斯分校）；Institute of Computational Mathematics and Scientific/Engineering Computing, AMSS, the Chinese Academy of Sciences（中国科学院数学与系统科学研究院计算数学与科学工程计算研究所）
In this paper, we generalize the compact subcell weighted essentially non oscillatory (CSWENO) limiting strategy for Runge-Kutta discontinuous Galerkin method developed recently by us in 2021 for structured meshes to unstructured triangular meshes. The main idea of the limiting strategy is to divide the immediate neighbors of a given cell into the required stencil and to use a WENO reconstruction for limiting. This strategy can be applied for any type of WENO reconstruction. We have used the WENO reconstruction proposed by Zhu and Shu in 2019 and provided accuracy tests and results for two-dim…
This work concerns adaptive refinement procedures for meshes of polygonal virtual elements. Specifically, refinement procedures previously proposed by the authors for structured meshes are generalized for the challenging case of arbitrary element geometries arising in unstructured/Voronoi discretizations. Here, structured and unstructured meshes are considered and are created via Voronoi tessellation of sets of structured and unstructured seed points respectively. The novel mesh refinement procedures for both structured and unstructured meshes allow for accurate and efficient application of th…
A cell-centred finite volume approximation for second order partial derivative operators with full matrix on unstructured meshes in any space dimension
We present a convergence result for the finite volume method applied to a particular phase field problem suitable for simulation of pure substance solidification. The model consists of the heat equation and the phase field equation with a general form of the reaction term which encompasses a variety of existing models governing dendrite growth and elementary interface tracking problems. We apply the well known compact embedding techniques in the context of the finite volume method on admissible unstructured polyhedral meshes. We develop the necessary interpolation theory and derive an a priori…
We consider in this work the numerical resolution of a 2D shallow water system with a Coriolis effect and bottom friction stresses on unstructured meshes by a new Finite Volume Characteristics (FVC) scheme, which has been introduced in the preliminary works that will be cited below. Our main goal is to extend this approach to 2D unstructured formalism while preserving the physical and mathematical properties of the system, including the C-property. First, we present our extension by preserving the advantages of the finite volume discretization such as conservation property and the method of ch…
A discontinuous Galerkin method for a new class of Green-Naghdi equations on simplicial unstructured meshes
INSA Toulouse（图卢兹国立应用科学学院）；University of Montpellier, Institut Montpelliérain Alexander Grothendieck and Inria LEMON team（蒙彼利埃大学，亚历山大·格罗滕迪克蒙彼利埃研究所和Inria LEMON团队）
Easy to construct and optimally convergent generalisations of B-splines to unstructured meshes are essential for the application of isogeometric analysis to domains with non-trivial topologies. Nonetheless, especially for hexahedral meshes, the construction of smooth and optimally convergent isogeometric analysis basis functions is still an open question. We introduce a simple partition of unity construction that yields smooth blended B-splines, referred to as SB-splines, on semi-structured quadrilateral and hexahedral meshes, namely on mostly structured meshes with a few sufficiently separate…
This paper introduces a novel method for the efficient and accurate computation of volume fractions on unstructured polyhedral meshes, where the phase boundary is an orientable hypersurface, implicitly given as the iso-contour of a sufficiently smooth level-set function. Locally, i.e. in each mesh cell, we compute a principal coordinate system in which the hypersurface can be approximated as the graph of an osculating paraboloid. A recursive application of the \textsc{Gaussian} divergence theorem then allows to analytically transform the volume integrals to curve integrals associated to the po…
The accurate and efficient evaluation of potentials is of great importance for the numerical solution of partial differential equations. When the integration domain of the potential is irregular and is discretized by an unstructured mesh, the function spaces of near field and self-interactions are non-compact, and, thus, their computations cannot be easily accelerated. In this paper, we propose three novel and complementary techniques for accelerating the evaluation of potentials over unstructured meshes. Firstly, we rigorously characterize the geometry of the near field, and show that this an…
Babuška-Osborn techniques in discontinuous Galerkin methods: $L^2$-norm error estimates for unstructured meshes
University of Leicester（莱斯特大学）；National Technical University of Athens（雅典国立技术大学）；Institute for Applied and Computational Mathematics-FORTH（应用计算数学研究所-FORTH）；DMAM University of Crete（克里特大学DMAM）；University of Sussex（萨塞克斯大学）；University of Reading（雷丁大学）
Isogeometric Analysis generalizes classical finite element analysis and intends to integrate it with the field of Computer-Aided Design. A central problem in achieving this objective is the reconstruction of analysis-suitable models from Computer-Aided Design models, which is in general a non-trivial and time-consuming task. In this article, we present a novel spline construction, that enables model reconstruction as well as simulation of high-order PDEs on the reconstructed models. The proposed almost-$C^1$ are biquadratic splines on fully unstructured quadrilateral meshes (without restrictio…
We introduce new manifold-based splines that are able to exactly reproduce B-splines on unstructured surface meshes. Such splines can be used in isogeometric analysis (IGA) to represent smooth surfaces of arbitrary topology. Since prevalent computer-aided design (CAD) models are composed of tensor-product B-spline patches, any IGA suitable construction should be able to reproduce B-splines. To achieve this goal, we focus on univariate manifold-based constructions that can reproduce B-splines. The manifold-based splines are constructed by smoothly blending together polynomial interpolants defin…
An Entropy Stable Nodal Discontinuous Galerkin Method for the Two Dimensional Shallow Water Equations on Unstructured Curvilinear Meshes with Discontinuous Bathymetry
Universität zu Köln（科隆大学）；The Florida State University（佛罗里达州立大学）
We propose a new high order accurate nodal discontinuous Galerkin (DG) method for the solution of nonlinear hyperbolic systems of partial differential equations (PDE) on unstructured polygonal Voronoi meshes. Rather than using classical polynomials of degree N inside each element, in our new approach the discrete solution is represented by piecewise continuous polynomials of degree N within each Voronoi element, using a continuous finite element basis defined on a subgrid inside each polygon. We call the resulting subgrid basis an agglomerated finite element (AFE) basis for the DG method on ge…
In this paper we consider a level set reinitialization technique based on a high-order, local discontinuous Galerkin method on unstructured triangular meshes. A finite volume based subcell stabilization is used to improve the nonlinear stability of the method. Instead of the standard hyperbolic level set reinitialization, the flow of time Eikonal equation is discretized to construct an approximate signed distance function. Using the Eikonal equation removes the regularization parameter in the standard approach which allows more predictable behavior and faster convergence speeds around the inte…
We present an adaptive refinement algorithm for T-splines on unstructured 2D meshes. While for structured 2D meshes, one can refine elements alternatingly in horizontal and vertical direction, such an approach cannot be generalized directly to unstructured meshes, where no two unique global mesh directions can be assigned. To resolve this issue, we introduce the concept of direction indices, i.e., integers associated to each edge, which are inspired by theory on higher-dimensional structured T-splines. Together with refinement levels of edges, these indices essentially drive the refinement sch…
In this paper we present a conservative cell-centered Lagrangian finite volume scheme for the solution of the hyper-elasticity equations on unstructured multidimensional grids. The starting point of the new method is the Eucclhyd scheme, which is here combined with the a posteriori Multidimensional Optimal Order Detection (MOOD) limiting strategy to ensure robustness and stability at shock waves with piece-wise linear spatial reconstruction. The ADER (Arbitrary high order schemes using DERivatives) approach is adopted to obtain second-order of accuracy in time as well. This method has been tes…
We present an advection-pressure flux-vector splitting method for the one and two- dimensional shallow water equations following the approach first proposed by Toro and Vázquez for the compressible Euler equations. The resulting first-order schemes turn out to be exceedingly simple, with accuracy and robustness comparable to that of the sophisticated Godunov upwind method used in conjunction with complete non- linear Riemann solvers. The technique splits the full system into two subsystems, namely an advection system and a pressure system. The sought numerical flux results from fluxes for each…
The recently proposed high-order TENO scheme [Fu et al., Journal of Computational Physics, 305, pp.333-359] has shown great potential in predicting complex fluids owing to the novel weighting strategy, which ensures the high-order accuracy, the low numerical dissipation, and the sharp shock-capturing capability. However, the applications are still restricted to simple geometries with Cartesian or curvilinear meshes. In this work, a new class of high-order shock-capturing TENO schemes for unstructured meshes are proposed. Similar to the standard TENO schemes and some variants of WENO schemes, t…
Applying Convolutional Neural Networks to Data on Unstructured Meshes with Space-Filling Curves
Imperial College London（帝国理工学院）；Department of Chemical Engineering, Imperial College London（帝国理工学院化学工程系）；Data Science Institute, Imperial College London（帝国理工学院数据科学研究所）
This work describes a concise algorithm for the generation of triangular meshes with the help of standard adaptive finite element methods. We demonstrate that a generic adaptive finite element solver can be repurposed into a triangular mesh generator if a robust mesh smoothing algorithm is applied between the mesh refinement steps. We present an implementation of the mesh generator and demonstrate the resulting meshes via examples.
We present a novel second-order semi-implicit hybrid finite volume / finite element (FV/FE) scheme for the numerical solution of the incompressible and weakly compressible Navier-Stokes equations on moving unstructured meshes using an Arbitrary-Lagrangian-Eulerian (ALE) formulation. The scheme is based on a suitable splitting of the governing PDE into subsystems and employs staggered grids, where the pressure is defined on the primal simplex mesh, while the velocity and the remaining flow quantities are defined on an edge-based staggered dual mesh. The key idea of the scheme is to discretize t…
Isogeometric analysis with $C^1$ functions on unstructured quadrilateral meshes
Johann Radon Institute for Computational and Applied Mathematics, Austrian Academy of Sciences（奥地利科学院约翰·拉顿计算与应用数学研究所）；Dipartimento di Matematica “F. Casorati”, Università degli Studi di Pavia, and IMATI-CNR（帕维亚大学F. Casorati数学系及中国科学院应用数学研究所）；Institute of Applied Geometry, Johannes Kepler University Linz（林茨约翰开普勒大学应用几何研究所）
Algebraically stabilized finite element discretizations of scalar steady-state convection-diffusion-reaction equations often provide accurate approximate solutions satisfying the discrete maximum principle (DMP). However, it was observed that a deterioration of the accuracy and convergence rates may occur for some problems if meshes without local symmetries are used. The paper investigates these phenomena both numerically and analytically and the findings are used to design a new algebraic stabilization called Symmetrized Monotone Upwind-type Algebraically Stabilized (SMUAS) method. It is prov…
