Quadtree grid generation: Information handling, boundary fitting and CFD applications

When solving partial differential equations by numerical methods, an automatic mesh generation technique which can accommodate local mesh refinement adaptively is desirable. One efficient technique for producing such meshes in two-dimensional space is to subdivide recursively the domain into quadrants using a quadtree to store and manipulate the mesh information. Here, the quadtree grid generation technique is reviewed and its programming discussed. Three data storage methods are examined. The conversion of the quadtree grid to a triangular finite element mesh is also described, along with methods for fitting the mesh to smooth boundary contours. Results from viscous flow and standing wave simulations are used to illustrate mesh adaptivity about internal and boundary features.     

Development of adaptive mesh refinement scheme for engine spray simulations

Spray modeling is a critical component to engine combustion and emissions simulations. Accurate spray modeling often requires a fine computational mesh for better numerical resolutions. However, computations with a fine mesh will require extensive computer time. This study developed a methodology that uses a locally refined mesh in the spray region. The fine mesh virtually moves with the liquid spray. Such adaptive mesh refinement can enable greater resolution of the liquid-gas interaction while incurring only a small increase in the total number of computational cells. The present study uses an h-refinement adaptive method. A face-based approach is used for the inter-level boundary condition. The prolongation and restriction procedure preserves conservation of properties in performing grid refinement/coarsening. The refinement criterion is based on the total mass of liquid drops and fuel vapor in each cell. The efficiency and accuracy of the present adaptive mesh refinement scheme is described in the paper. Results show that the present scheme can achieve the same level of accuracy in modeling sprays with significantly lower computational cost as compared to a uniformly fine mesh.     

Finite element analysis on implicitly defined domains: An accurate representation based on arbitrary parametric surfaces

In this paper, we present some novel results and ideas for robust and accurate implicit representation of geometric surfaces in finite element analysis. The novel contributions of this paper are threefold: (1) describe and validate a method to represent arbitrary parametric surfaces implicitly; (2) represent arbitrary solids implicitly, including sharp features using level sets and boolean operations; (3) impose arbitrary Dirichlet and Neumann boundary conditions on the resulting implicitly defined boundaries. The methods proposed do not require local refinement of the finite element mesh in regions of high curvature, ensure the independence of the domain’s volume on the mesh, do not rely on boundary regularization, and are well suited to methods based on fixed grids such as the extended finite element method (XFEM). Numerical examples are presented to demonstrate the robustness and effectiveness of the proposed approach and show that it is possible to achieve optimal convergence rates using a fully implicit representation of object boundaries. This approach is one step in the desired direction of tying numerical simulations to computer aided design (CAD), similarly to the isogeometric analysis paradigm.     

A higher order numerical scheme for scalar transport

The computational principles of a numerical scheme for the solution of the two-dimensional scalar transport equation are presented. The scheme is designed for use in transient flow situations where accurate simulation of the advective process is important. Advective transport is computed by the method of characteristics in which the scalar field is represented by a Hermitian polynomial complete through the third degree in both coordinate directions, while diffusion is computed by central differencing. The superior accuracy of the new method is demonstrated by analysing its propagation characteristics and by comparing its performance on standard test problems with that of some well-known lower order methods. Finally, the method's applicability is demonstrated in several examples involving tracer releases into channel flows. Where possible the results of these simulations are compared with analytical solutions.     

Flow simulations in arbitrarily complex cardiovascular anatomies – An unstructured Cartesian grid approach

Image guided computational fluid dynamics is attracting increasing attention as a tool for refining in vivo flow measurements or predicting the outcome of different surgical scenarios. Sharp interface Cartesian/Immersed-Boundary methods constitute an attractive option for handling complex in vivo geometries but their capability to carry out fine-mesh simulations in the branching, multi-vessel configurations typically encountered in cardiovascular anatomies or pulmonary airways has yet to be demonstrated. A major computational challenge stems from the fact that when such a complex geometry is immersed in a rectangular Cartesian box the excessively large number of grid nodes in the exterior of the flow domain imposes an unnecessary burden on both memory and computational overhead of the Cartesian solver without enhancing the numerical resolution in the region of interest. For many anatomies, this added burden could be large enough to render comprehensive mesh refinement studies impossible. To remedy this situation, we recast the original structured Cartesian formulation of Gilmanov and Sotiropoulos [Gilmanov A, Sotiropoulos F. A hybrid Cartesian/immersed boundary method for simulating flows with 3D, geometrically complex, moving bodies. J Comput Phys 2005;207(2):457–92] into an unstructured Cartesian grid layout. This simple yet powerful approach retains the simplicity and computational efficiency of a Cartesian grid solver, while drastically reducing its memory footprint. The method is applied to carry out systematic mesh refinement studies for several internal flow problems ranging in complexity from flow in a 90° pipe bend to flow in an actual, patient-specific anatomy reconstructed from magnetic resonance images. Finally, we tackle the challenging clinical scenario of a single-ventricle patient with severe arterio-venous malformations, seeking to provide a fluid dynamics prospective on a clinical problem and suggestions for procedure improvements. Results from these simulations demonstrate very complex cardiovascular flow dynamics and underscore the need for high-resolution simulations prior to drawing any clinical recommendations.     

Online Mesh Refinement for Parallel Atmospheric Models

Forecast precisions of climatological models are limited by computing power and time available for the executions. As more and faster processors are used in the computation, the resolution of the mesh adopted to represent the Earth’s atmosphere can be increased, and consequently the numerical forecast is more accurate. However, a finer mesh resolution, able to include local phenomena in a global atmosphere integration, is still not possible due to the large number of data elements to compute in this case. To overcome this situation, different mesh refinement levels can be used at the same time for different areas of the domain. Thus, our paper evaluates how mesh refinement at run time (online) can improve performance for climatological models.The online mesh refinement (OMR) increases dynamically mesh resolution in parts of a domain,when special atmosphere conditions are registered during the execution. Experimental results show that the execution of a model improved by OMR provides better resolution for the meshes, without any significant increase of execution time. The parallel performance of the simulations is also increased through the creation of threads in order to explore different levels of parallelism.     

A cascadic geometric filtering approach to subdivision

A new approach to subdivision based on the evolution of surfaces under curvature motion is presented. Such an evolution can be understood as a natural geometric filter process where time corresponds to the filter width. Thus, subdivision can be interpreted as the application of a geometric filter on an initial surface. The concrete scheme is a model of such a filtering based on a successively improved spatial approximation starting with some initial coarse mesh and leading to a smooth limit surface.

In every subdivision step the underlying grid is refined by some regular refinement rule and a linear finite element problem is either solved exactly or, especially on fine grid levels, one confines to a small number of smoothing steps within the corresponding iterative linear solver. The approach closely connects subdivision to surface fairing concerning the geometric smoothing and to cascadic multigrid methods with respect to the actual numerical procedure. The derived method does not distinguish between different valences of nodes nor between different mesh refinement types. Furthermore, the method comes along with a new approach for the theoretical treatment of subdivision.     

Accurate shock-capturing finite volume method for advection-dominated flow and pollution transport

This paper describes an accurate shock-capturing finite volume numerical method to solve a two-dimensional flow and solute transport problem in shallow water. Hydrodynamic and advection-diffusion equations are simultaneously solved by means of a Strang operator-splitting approach. The advective part is solved in time by a third-order TDV Runge-Kutta method and in space by a second-order WAF method coupled with a fifth-order WENO reconstruction. The diffusion part is solved in time and space by a second-order accurate method. Thus the overall accuracy is second-order both in time and space. Nevertheless the Strang splitting approach allows the advective part of the equations to be solved with a reconstruction of high order, where at lower orders it shows excessive numerical diffusion and damping, especially for very long time simulations. Very good results have been obtained applying the model to standard long time numerical tests.     

A high-resolution method for the depth-integrated solute transport equation based on an unstructured mesh

This paper presents a high-resolution numerical method for solving mass transport problems involving advection and anisotropic diffusion in shallow water based on unstructured mesh. An alternating operator-splitting technique is adopted to advance the numerical solution with advection and diffusion terms solved separately in two steps. By introducing a new r-factor into the Total Variation Diminishing (TVD) limiter, an improved finite-volume method is developed to solve the advection term with significant reduction of numerical diffusion and oscillation errors. In addition, a coordinate transformation is introduced to simplify the diffusion term with the Green-Gauss theorem used to deal with the anisotropic effect based on unstructured mesh. The new scheme is validated against three benchmark cases with separated and combined advection and diffusion transport processes involved. Results show that the scheme performs better than existing methods in predicting the advective transport, particularly when a sharp concentration front is in presence. The model also provides a sound solution for the anisotropic diffusion phenomenon. Anisotropic diffusion has been largely neglected by existing flow models based on unstructured mesh, which usually treat the diffusion process as being isotropic for simplicity. Based on the flow field provided by the ELCIRC model, the developed transport model was successfully applied to simulate the transport of a hypothetical conservative tracer in a bay under the influence of tides.     

Coupling geological and numerical models to simulate groundwater flow and contaminant transport in fractured media

A new modeling approach is presented to improve numerical simulations of groundwater flow and contaminant transport in fractured geological media. The approach couples geological and numerical models through an intermediate mesh generation phase. As a first step, a platform for 3D geological modeling is used to represent fractures as 2D surfaces with arbitrary shape and orientation in 3D space. The advantage of the geological modeling platform is that 2D triangulated fracture surfaces are modeled and visualized before building a 3D mesh. The triangulated fractures are then transferred to the mesh generation software that discretizes the 3D simulation domain with tetrahedral elements. The 2D triangular fracture elements do not cut through the 3D tetrahedral elements, but they rather form interfaces with them. The tetrahedral mesh is then used for 3D groundwater flow and contaminant transport simulations in discretely fractured porous media. The resulting mesh for the 2D fractures and 3D rock matrix is checked to ensure that there are no negative transmissibilities in the discretized flow and transport equation, to avoid unrealistic results. To test the validity of the approach, flow and transport simulations for a tetrahedral mesh are compared to simulations using a block-based mesh and with results of an analytical solution. The fluid conductance matrix for the tetrahedral mesh is also analyzed and compared with known matrix values.     

A posteriori error estimation and adaptive mesh refinement for combined thermal-stress finite element analysis

Local and global error estimators and an associated h-based adaptive mesh refinement schemes are proposed for coupled thermal-stress problems. The error estimators are based on the “flux smoothing” technique of Zienkiewicz and Zhu with important modifications to improve convergence performance and computational efficiency. Adaptive mesh refinement is based on the concept of adaptive accuracy criteria, previously presented by the authors for stress-based problems and extended here for coupled thermal-stress problems. Three methods of mesh refinement are presented and numerical results indicate that the proposed method is the most efficient in terms of number of adaptive mesh refinements required for convergence in both the thermal and stress solutions. Also, the proposed method required a smaller number of active degrees of freedom to obtain an accurate solution.     

Pseudo-transient continuation-based variable relaxation solver in nonlinear magnetohydrodynamic simulations

Efficient and robust Variable Relaxation Solver, based on pseudo-transient continuation, is developed to solve nonlinear anisotropic thermal conduction arising from fusion plasma simulations. By adding first- and/or second-order artificial time derivatives to the system, this type of method advances the resulting time-dependent nonlinear PDEs to steady state, which is the solution to be sought. In this process, only the stiffness matrix itself is involved so that the numerical complexity and errors can be greatly reduced. In fact, this work is an extension of integrating efficient linear elliptic solvers for fusion simulation on Cray X1E. Two schemes are derived in this work, first- and second-order variable relaxations. Four factors are observed to be critical for efficiency and preservation of solution's symmetric structure arising from periodic boundary condition: refining meshes in different coordinate directions, initializing nonlinear process, varying time steps in both temporal and spatial directions, and accurately generating nonlinear stiffness matrix. First finer mesh scale should be taken in strong transport direction; next the system is carefully initialized by the solution with linear conductivity; third, time step and relaxation factor are vertex-based varied and optimized at each time step; finally, the nonlinear stiffness matrix is updated by just scaling corresponding linear one with the vector generated from nonlinear thermal conductivity.     

Adaptive mixed finite element method for Reissner–Mindlin plate

Mixed finite element methods are designed to overcome shear locking phenomena observed in the numerical treatment of Reissner–Mindlin plate models. Automatic adaptive mesh-refining algorithms are an important tool to improve the approximation behavior of the finite element discretization. In this paper, a reliable and robust residual-based a posteriori error estimate is derived, which evaluates a t-depending residual norm based on results in [D. Arnold, R. Falk, R. Winther, Math. Modell. Numer. Anal. 31 (1997) 517–557]. The localized error indicators suggest an adaptive algorithm for automatic mesh refinement. Numerical examples prove that the new scheme is efficient.     

The NIRVANA code: Parallel computational MHD with adaptive mesh refinement

I report on a new version of the magnetohydrodynamics code NIRVANA¹ which is targeted at the study of astrophysical problems. The new version allows for distributed-memory simulations supporting adaptive mesh refinement. Numerical algorithms include dissipative terms (viscosity, Ohmic diffusion, thermal heat conduction) in a conservative form. Domain decomposition is preferably block-wise in case of unigrid applications but adopts space-filling curve techniques for adaptive mesh applications with a hierarchical block-structured mesh. The code architecture facilitates workload balancing among processors for arbitrary mesh refinement depths maintaining intra-level data locality via space-filling curve mappings and, at the same time, ensuring inter-level data locality by applying a novel technique called block sharing. This way, it is demonstrated that comparable performance can be achieved for problems with locally highly refined grid. The data transfer between processors extensively utilizes the coarse-granularity concept of parallel computing and makes use of the MPI library. Conservation properties of the numerical method carry over to the parallel framework. In particular, the solenoidality condition for the magnetic field is preserved to roundoff precision applying the constrained transport machinery. This paper has its focus of discussion on implementation details related to the parallelization and on a code performance analysis.     

An adaptive multilevel multigrid formulation for Cartesian hierarchical grid methods

A Cartesian grid method with adaptive mesh refinement and multigrid acceleration is presented for the compressible Navier-Stokes equations. Cut cells are used to represent boundaries on the Cartesian grid, while ghost cells are introduced to facilitate the implementation of boundary conditions. A cell-tree data structure is used to organize the grid cells in a hierarchical manner. Cells of all refinement levels are present in this data structure such that grid level changes as they are required in a multigrid context do not have to be carried out explicitly. Adaptive mesh refinement is introduced using phenomenon-based sensors. The application of the multilevel method in conjunction with the Cartesian cut-cell method to problems with curved boundaries is described in detail. A 5-step Runge-Kutta multigrid scheme with local time stepping is used for steady problems and also for the inner integration within a dual time-stepping method for unsteady problems. The inefficiency of customary multigrid methods on Cartesian grids with embedded boundaries requires a new multilevel concept for this application, which is introduced in this paper. This new concept is based on the following novelties: a formulation of a multigrid method for Cartesian hierarchical grid methods, the concept of averaged control volumes, and a mesh adaptation strategy allowing to directly control the number of refined and coarsened cells.     

An application-centric characterization of domain-based SFC partitioners for parallel SAMR

Structured adaptive mesh refinement (SAMR) methods for the numerical solution of partial differential equations yield highly advantageous ratios for cost/accuracy as compared to methods based on static uniform approximations. These techniques are being effectively used in many domains including computational fluid dynamics, numerical relativity, astrophysics, subsurface modeling, and oil reservoir simulation. Distributed implementations of these methods, however, lead to significant challenges in dynamic data-distribution, load-balancing, and runtime management. This paper presents an application-centric characterization of a suite of dynamic domain-based inverse space-filling curve partitioning techniques for the distributed adaptive grid hierarchies that underlie SAMR applications. The overall goal of this research is to formulate policies required to drive a dynamically adaptive metapartitioner for SAMR grid hierarchies capable of selecting the most appropriate partitioning strategy at runtime based on current application and system state. Such a metapartitioner can significantly reduce the execution time of SAMR applications.     

The unconditionally positive-convergent implicit time integration scheme for two-equation turbulence models: Revisited

The unconditionally positive-convergent implicit scheme for two-equation turbulence models, originally developed by Mor-Yossef and Levy, is revisited. A compact, simple, and uniform reformulation of the method for the use of both structured and unstructured grid based flow solvers is presented. An analytical proof of the scheme revision is given showing that positivity of the turbulence model solutions and convergence of the turbulence model equations are guaranteed for any time step. Numerical experiments are conducted, simulating two test cases of three-dimensional complex flow fields using structured and hybrid unstructured grids. To demonstrate the overall scheme’s robustness, it is applied to non-linear k-ω and non-linear k- turbulence models. Results from the numerical simulations show that the scheme exhibits very good convergence characteristics, is robust, and it always preserves the positivity of the turbulence model dependent variables, even for an infinite time step.     

Adaptive mesh refinement in stress-constrained topology optimization

We present a topology structural optimization framework with adaptive mesh refinement and stress-constraints. Finite element approximation and geometry representation benefit from such refinement by enabling more accurate stress field predictions and greater resolution of the optimal structural boundaries. We combine a volume fraction filter to impose a minimum design feature size, the RAMP penalization to generate “black-and-white designs” and a RAMP-like stress definition to resolve the “stress singularity problem.” Regions with stress concentrations dominate the optimized design. As such, rigorous simulations are required to accurately approximate the stress field. To achieve this goal, we invoke a threshold operation and mesh refinement during the optimization. We do so in an optimal fashion, by applying adaptive mesh refinement techniques that use error indicators to refine and coarsen the mesh as needed. In this way, we obtain more accurate simulations and greater resolution of the design domain. We present results in two dimensions to demonstrate the efficiency of our method.     

Flux-based methods of characteristics for coupled transport equations in porous media

Mathematical models of transport of radioactive contaminants in flowing groundwater involve large systems of coupled advection dominated transport equations. High-resolution explicit finite volume methods, if applied to advective part of model and combined with appropriate numerical methods for diffusion-dispersion-reaction part, can offer precise and monotone numerical solutions, but they require small time steps. This paper describes Flux-Based Methods Of Characteristics that are extension of explicit finite volume methods, that have no restriction on time steps and that produce numerical solutions with valid discrete minimum and maximum principle. Such particular method was implemented in software package R³T (Retardation, Reaction, Radionuclides and Transport) and it was used successfully to solve large systems of coupled transport equations with different retardation factors for transport.