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We study a temporal step size control of explicit Runge-Kutta (RK) methods for compressible computational fluid dynamics (CFD), including the Navier-Stokes equations and hyperbolic systems of conservation laws such as the Euler equations. We demonstrate that error-based approaches are convenient in a wide range of applications and compare them to more classical step size control based on a Courant-Friedrichs-Lewy (CFL) number. Our numerical examples show that the error-based step size control is easy to use, robust, and efficient, e.g., for (initial) transient periods, complex geometries, nonlinear shock capturing approaches, and schemes that use nonlinear entropy projections. We demonstrate these properties for problems ranging from well-understood academic test cases to industrially relevant large-scale computations with two disjoint code bases, the open source Julia packages Trixi.jl with OrdinaryDiffEq.jl and the C/Fortran code SSDC based on PETSc.

Background: Next generation sequencing (NGS) has become indispensable for diagnosis, risk stratification, prognostication, and monitoring of response in patients with myeloid neoplasias. Guidelines require bone marrow evaluations for the above, which are often not performed outside of clinical trials, indicating a need for surrogate samples. Methods: Myeloid NGS analyses (40 genes and 29 fusion drivers) of 240 consecutive, non-selected, prospectively collected, paired bone marrow/peripheral blood samples were compared. Findings: Very strong correlation (r = 0.91, p < 0.0001), high concordance (99.6%), sensitivity (98.8%), specificity (99.9%), positive predictive value (99.8%), and negative predictive value (99.6%) between NGS analyses of paired samples was observed. A total of 9/1321 (0.68%) detected mutations were discordant, 8 of which had a variant allele frequency (VAF) ≤ 3.7%. VAFs between peripheral blood and bone marrow samples were very strongly correlated in the total cohort (r = 0.93, p = 0.0001) and in subgroups without circulating blasts (r = 0.92, p < 0.0001) or with neutropenia (r = 0.88, p < 0.0001). There was a weak correlation between the VAF of a detected mutation and the blast count in either the peripheral blood (r = 0.19) or the bone marrow (r = 0.11). Interpretation: Peripheral blood samples can be used to molecularly classify and monitor myeloid neoplasms via NGS without loss of sensitivity/specificity, even in the absence of circulating blasts or in neutropenic patients.

In this paper, we show that diagonal-norm summation by parts (SBP) discretizations of general non-conservative systems of hyperbolic balance laws can be rewritten as a finite-volume-type formula, also known as flux-differencing formula, if the non-conservative terms can be written as the product of a local and a symmetric contribution. Furthermore, we show that the existence of a flux-differencing formula enables the use of recent subcell limiting strategies to improve the robustness of the high-order discretizations. To demonstrate the utility of the novel flux-differencing formula, we construct hybrid schemes that combine high-order SBP methods (the discontinuous Galerkin spectral element method and a high-order SBP finite difference method) with a compatible low-order finite volume (FV) scheme at the subcell level. We apply the hybrid schemes to solve challenging magnetohydrodynamics (MHD) problems featuring strong shocks.

High order (HO) schemes are attractive candidates for the numerical solution of multiscale problems occurring in fluid dynamics and related disciplines. Among the HO discretization variants, discontinuous Galerkin schemes offer a collection of advantageous features which have lead to a strong increase in interest in them and related formulations in the last decade. The methods have matured sufficiently to be of practical use for a range of problems, for example in direct numerical and large eddy simulation of turbulence. However, in order to take full advantage of the potential benefits of these methods, all steps in the simulation chain must be designed and executed with HO in mind. Especially in this area, many commercially available closed-source solutions fall short. In this work, we therefor present the FLEXI framework, a HO consistent, open-source simulation tool chain for solving the compressible Navier-Stokes equations in a high performance computing setting. We describe the numerical algorithms and implementation details and give an overview of the features and capabilities of all parts of the framework. Beyond these technical details, we also discuss the important, but often overlooked issues of code stability, reproducibility and user-friendliness. The benefits gained by developing an open-source framework are discussed, with a particular focus on usability for the open-source community. We close with sample applications that demonstrate the wide range of use cases and the expandability of FLEXI and an overview of current and future developments.

In this paper, we present an entropy-stable Gauss collocation discontinuous Galerkin (DG) method on 3D curvilinear meshes for the GLM-MHD equations: the single-fluid magneto-hydrodynamics (MHD) equations with a generalized Lagrange multiplier (GLM) divergence cleaning mechanism. For the continuous entropy analysis to hold and to ensure Galilean invariance in the divergence cleaning technique, the GLM-MHD system requires the use of non-conservative terms. Traditionally, entropy-stable DG discretizations have used a collocated nodal variant of the DG method, also known as the discontinuous Galerkin spectral element method (DGSEM) on Legendre-Gauss-Lobatto (LGL) points. Recently, Chan et al. ("Efficient Entropy Stable Gauss Collocation Methods". SIAM -2019) presented an entropy-stable DGSEM scheme that uses Legendre-Gauss points (instead of LGL points) for conservation laws. Our main contribution is to extend the discretization technique of Chan et al. to the non-conservative GLM-MHD system. We provide a numerical verification of the entropy behavior and convergence properties of our novel scheme on 3D curvilinear meshes. Moreover, we test the robustness and accuracy of our scheme with a magneto-hydrodynamic Kelvin-Helmholtz instability problem. The numerical experiments suggest that the entropy-stable DGSEM on Gauss points for the GLM-MHD system is more accurate than the LGL counterpart.

We present a general family of subcell limiting strategies to construct robust high-order accurate nodal discontinuous Galerkin (DG) schemes. The main strategy is to construct compatible low order finite volume (FV) type discretizations that allow for convex blending with the high-order variant with the goal of guaranteeing additional properties, such as bounds on physical quantities and/or guaranteed entropy dissipation. For an implementation of this main strategy, four main ingredients are identified that may be combined in a flexible manner: (i) a nodal high-order DG method on Legendre-Gauss-Lobatto nodes, (ii) a compatible robust subcell FV scheme, (iii) a convex combination strategy for the two schemes, which can be element-wise or subcell-wise, and (iv) a strategy to compute the convex blending factors, which can be either based on heuristic troubled-cell indicators, or using ideas from flux-corrected transport methods. By carefully designing the metric terms of the subcell FV method, the resulting methods can be used on unstructured curvilinear meshes, are locally conservative, can handle strong shocks efficiently while directly guaranteeing physical bounds on quantities such as density, pressure or entropy. We further show that it is possible to choose the four ingredients to recover existing methods such as a provably entropy dissipative subcell shock-capturing approach or a sparse invariant domain preserving approach. We test the versatility of the presented strategies and mix and match the four ingredients to solve challenging simulation setups, such as the KPP problem (a hyperbolic conservation law with non-convex flux function), turbulent and hypersonic Euler simulations, and MHD problems featuring shocks and turbulence., 26 pages, 11 figures

The focus of the present research is on the analysis of local energy stability of high-order (including split-form) summation-by-parts methods, with e.g. two-point entropy-conserving fluxes, approximating non-linear conservation laws. Our main finding is that local energy stability, i.e., the numerical growth rate does not exceed the growth rate of the continuous problem, is not guaranteed even when the scheme is non-linearly stable and that this may have adverse implications for simulation results. We show that entropy-conserving two-point fluxes are inherently locally energy unstable, as they can be dissipative or anti-dissipative. Unfortunately, these fluxes are at the core of many commonly used high-order entropy-stable extensions, including split-form summation-by-parts discontinuous Galerkin spectral element methods (or spectral collocation methods). For the non-linear Burgers equation, we further demonstrate numerically that such schemes cause exponential growth of errors during the simulation. Furthermore, we encounter a similar abnormal behaviour for the compressible Euler equations, for a smooth exact solution of a density wave. Finally, for the same case, we demonstrate numerically that other commonly known split-forms, such as the Kennedy and Gruber splitting, are also locally energy unstable.

We use the energy method to study the well-posedness of initial-boundary value problems approximated by overset mesh methods in one and two space dimensions for linear constant-coefficient hyperbolic systems. We show that in one space dimension, for both scalar equations and systems of equations, the problem where one domain partially oversets another is well-posed when characteristic coupling conditions are used. If a system cannot be diagonalized, as is usually the case in multiple space dimensions, then the energy method does not give proper bounds in terms of initial and boundary data. For those problems, we propose a novel penalty approach. We show, by using a global energy that accounts for the energy in the overlap region of the domains, that under well-defined conditions on the coupling matrices the penalized overset domain problems are energy bounded, conservative, well-posed and have solutions equivalent to the original single domain problem. Funding: Simons Foundation [426393]; Vetenskapsradet, SwedenSwedish Research Council [2018-05084 VR]; Swedish e-Science Research Center (SeRC); Klaus-Tschira Stiftung; European Research CouncilEuropean Research Council (ERC)European Commission [71448]

We present a hybrid continuous and discontinuous Galerkin spectral element approximation that leverages the advantages of each approach. The continuous Galerkin approximation is used on interior element faces where the equation properties are continuous. A discontinuous Galerkin approximation is used at physical boundaries and if there is a jump in properties at a face. The approximation uses a split form of the equations and two-point fluxes to ensure stability for unstructured quadrilateral/hexahedral meshes with curved elements. The approximation is also conservative and constant state preserving on such meshes. Spectral accuracy is obtained for all examples, which include wave scattering at a discontinuous medium boundary.

In this paper we will review a recent emerging paradigm shift in the construction and analysis of high order Discontinuous Galerkin methods applied to approximate solutions of hyperbolic or mixed hyperbolic-parabolic partial differential equations (PDEs) in computational physics. There is a long history using DG methods to approximate the solution of partial differential equations in computational physics with successful applications in linear wave propagation, like those governed by Maxwell’s equations, incompressible and compressible fluid and plasma dynamics governed by the Navier-Stokes and the Magnetohydrodynamics equations, or as a solver for ordinary differential equations (ODEs), e.g., in structural mechanics. The DG method amalgamates ideas from several existing methods such as the Finite Element Galerkin method (FEM) and the Finite Volume method (FVM) and is specifically applied to problems with advection dominated properties, such as fast moving fluids or wave propagation. In the numerics community, DG methods are infamous for being computationally complex and, due to their high order nature, as having issues with robustness, i.e., these methods are sometimes prone to crashing easily. In this article we will focus on efficient nodal versions of the DG scheme and present recent ideas to restore its robustness, its connections to and influence by other sectors of the numerical community, such as the finite difference community, and further discuss this young, but rapidly developing research topic by highlighting the main contributions and a closing discussion about possible next lines of research.

Discontinuous Galerkin (DG) methods have a long history in computational physics and engineering to approximate solutions of partial differential equations due to their high-order accuracy and geometric flexibility. However, DG is not perfect and there remain some issues. Concerning robustness, DG has undergone an extensive transformation over the past seven years into its modern form that provides statements on solution boundedness for linear and nonlinear problems. This chapter takes a constructive approach to introduce a modern incarnation of the DG spectral element method for the compressible Navier-Stokes equations in a three-dimensional curvilinear context. The groundwork of the numerical scheme comes from classic principles of spectral methods including polynomial approximations and Gauss-type quadratures. We identify aliasing as one underlying cause of the robustness issues for classical DG spectral methods. Removing said aliasing errors requires a particular differentiation matrix and careful discretization of the advective flux terms in the governing equations.

The second paper of this series presents two robust entropy stable shock-capturing methods for discontinuous Galerkin spectral element (DGSEM) discretizations of the compressible magneto-hydrodynamics (MHD) equations. Specifically, we use the resistive GLM-MHD equations, which include a divergence cleaning mechanism that is based on a generalized Lagrange multiplier (GLM). For the continuous entropy analysis to hold, and due to the divergence-free constraint on the magnetic field, the GLM-MHD system requires the use of non-conservative terms, which need special treatment. Hennemann et al. (2020) [25] recently presented an entropy stable shock-capturing strategy for DGSEM discretizations of the Euler equations that blends the DGSEM scheme with a subcell first-order finite volume (FV) method. Our first contribution is the extension of the method of Hennemann et al. to systems with non-conservative terms, such as the GLM-MHD equations. In our approach, the advective and non-conservative terms of the equations are discretized with a hybrid FV/DGSEM scheme, whereas the visco-resistive terms are discretized only with the high-order DGSEM method. We prove that the extended method is semi-discretely entropy stable on three-dimensional unstructured curvilinear meshes. Our second contribution is the derivation and analysis of a second entropy stable shock-capturing method that provides enhanced resolution by using a subcell reconstruction procedure that is carefully built to ensure entropy stability. We provide a numerical verification of the properties of the hybrid FV/DGSEM schemes on curvilinear meshes and show their robustness and accuracy with common benchmark cases, such as the Orszag-Tang vortex and the GEM (Geospace Environmental Modeling) reconnection challenge. Finally, we simulate a space physics application: the interaction of Jupiter's magnetic field with the plasma torus generated by the moon Io.

We use the behavior of the $$L_{2}$$ L 2 norm of the solutions of linear hyperbolic equations with discontinuous coefficient matrices as a surrogate to infer stability of discontinuous Galerkin spectral element methods (DGSEM). Although the $$L_{2}$$ L 2 norm is not bounded in terms of the initial data for homogeneous and dissipative boundary conditions for such systems, the $$L_{2}$$ L 2 norm is easier to work with than a norm that discounts growth due to the discontinuities. We show that the DGSEM with an upwind numerical flux that satisfies the Rankine–Hugoniot (or conservation) condition has the same energy bound as the partial differential equation does in the $$L_{2}$$ L 2 norm, plus an added dissipation that depends on how much the approximate solution fails to satisfy the Rankine–Hugoniot jump.

Recently, it was discovered that the entropy-conserving/dissipative high-order split-form discontinuous Galerkin discretizations have robustness issues when trying to solve the simple density wave propagation example for the compressible Euler equations. The issue is related to missing local linear stability, i.e., the stability of the discretization towards perturbations added to a stable base flow. This is strongly related to an anti-diffusion mechanism, that is inherent in entropy-conserving two-point fluxes, which are a key ingredient for the high-order discontinuous Galerkin extension. In this paper, we investigate if pressure equilibrium preservation is a remedy to these recently found local linear stability issues of entropy-conservative/dissipative high-order split-form discontinuous Galerkin methods for the compressible Euler equations. Pressure equilibrium preservation describes the property of a discretization to keep pressure and velocity constant for pure density wave propagation. We present the full theoretical derivation, analysis, and show corresponding numerical results to underline our findings. In addition, we characterize numerical fluxes for the Euler equations that are entropy-conservative, kinetic-energy-preserving, pressure-equilibrium-preserving, and have a density flux that does not depend on the pressure. The source code to reproduce all numerical experiments presented in this article is available online (https://doi.org/10.5281/zenodo.4054366).

The main result in this paper is a provably entropy stable shock capturing approach for the high order entropy stable DGSEM based on a hybrid blending with a subcell low order variant. Since it is possible to rewrite a high order SBP operator into an equivalent conservative finite volume form, we were able to design a low order scheme directly with the LGL nodes that is compatible to the discrete entropy analysis used for the proof of the entropy stable DGSEM. Furthermore, we present a hybrid low order/high order discretisation where it is possible to seamlessly blend between the two approaches, while still being provably entropy stable. We are able to extend the approach to three spatial dimensions on unstructured curvilinear hexahedral meshes. We validate our theoretical findings and demonstrate convergence order for smooth problems, conservation of the primary quantities and discrete entropy stability for an arbitrary blending on curvilinear grids. In practical simulations, we connect the blending factor to a local troubled element indicator that provides the control of the amount of low order dissipation injected into the high order scheme. We modified an existing shock indicator, which is based on the modal polynomial representation, to our provably stable hybrid scheme. The aim is to reduce the impact of the parameters as good as possible. We describe our indicator in detail and demonstrate its robustness in combination with the hybrid scheme, as it is possible to compute all the different test cases without changing the indicator. The test cases include e.g. the double Mach reflection setup, forward and backward facing steps with shock Mach numbers up to 100. The proposed approach is relatively straight forward to implement in an existing entropy stable DGSEM code as only modifications local to an element are necessary., 35 pages, 10 figures

Chronic lymphocytic leukemia (CLL) is a high incidence B cell leukemia with a highly variable clinical course, leading to survival times ranging from months to several decades. MicroRNAs (miRNAs) are small non-coding RNAs that regulate the expression levels of genes by binding to the untranslated regions of transcripts. Although miRNAs have been previously shown to play a crucial role in CLL development, progression and treatment resistance, their further processing and diversification by RNA editing (specifically adenosine to inosine or cytosine to uracil deamination) has not been addressed so far. In this study, we analyzed next generation sequencing data to provide a detailed map of adenosine to inosine and cytosine to uracil changes in miRNAs from CLL and normal B cells. Our results reveal that in addition to a CLL-specific expression pattern, there is also specific RNA editing of many miRNAs, particularly miR-3157 and miR-6503, in CLL. Our data draw further light on how miRNAs and miRNA editing might be implicated in the pathogenesis of the disease.

The construction of discontinuous Galerkin (DG) methods for the compressible Euler or Navier-Stokes equations (NSE) includes the approximation of non-linear flux terms in the volume integrals. The terms can lead to aliasing and stability issues in turbulence simulations with moderate Mach numbers (Ma < 0.3), e.g. due to under-resolution of vortical dominated structures typical in large eddy simulations (LES). The kinetic energy or entropy are elevated in smooth, but under-resolved parts of the solution which are affected by aliasing. It is known that the kinetic energy is not a conserved quantity for compressible flows, but for small Mach numbers minor deviations from a conserved evolution can be expected. While it is formally possible to construct kinetic energy preserving (KEP) and entropy conserving (EC) DG methods for the Euler equations, due to the viscous terms in case of the NSE, we aim to construct kinetic energy dissipative (KED) or entropy stable (ES) DG methods on moving curved hexahedral meshes. The Arbitrary Lagrangian-Eulerian (ALE) approach is used to include the effect of mesh motion in the split form DG methods. First, we use the three dimensional Taylor-Green vortex to investigate and analyze our theoretical findings and the behavior of the novel split form ALE DG schemes for a turbulent vortical dominated flow. Second, we apply the framework to a complex aerodynamics application. An implicit LES split form ALE DG approach is used to simulate the transitional flow around a plunging SD7003 airfoil at Reynolds number Re = 40, 000 and Mach number Ma = 0.1. We compare the standard nodal ALE DG scheme, the ALE DG variant with consistent overintegration of the non-linear terms and the novel KED and ES split form ALE DG methods in terms of robustness, accuracy and computational efficiency., Submitted to Journal of Computational Physics

One of the challenges when simulating astrophysical flows with self-gravity is to compute the gravitational forces. In contrast to the hyperbolic hydrodynamic equations, the gravity field is described by an elliptic Poisson equation. We present a purely hyperbolic approach by reformulating the elliptic problem into a hyperbolic diffusion problem, which is solved in pseudotime using the same explicit high-order discontinuous Galerkin method we use for the flow solution. The flow and the gravity solvers operate on a joint hierarchical Cartesian mesh and are two-way coupled via the source terms. A key benefit of our approach is that it allows the reuse of existing explicit hyperbolic solvers without modifications, while retaining their advanced features such as non-conforming and solution-adaptive grids. By updating the gravitational field in each Runge-Kutta stage of the hydrodynamics solver, high-order convergence is achieved even in coupled multi-physics simulations. After verifying the expected order of convergence for single-physics and multi-physics setups, we validate our approach by a simulation of the Jeans gravitational instability. Furthermore, we demonstrate the full capabilities of our numerical framework by computing a self-gravitating Sedov blast with shock capturing in the flow solver and adaptive mesh refinement for the entire coupled system., Comment: 30 pages, 7 figures, second revision

This work is focused on the entropy analysis of a semi-discrete nodal discontinuous Galerkin spectral element method (DGSEM) on moving meshes for hyperbolic conservation laws. The DGSEM is constructed with a local tensor-product Lagrange-polynomial basis computed from Legendre-Gauss-Lobatto points. Furthermore, the collocation of interpolation and quadrature nodes is used in the spatial discretization. This approach leads to discrete derivative approximations in space that are summation-by-parts (SBP) operators. On a static mesh, the SBP property and suitable two-point flux functions, which satisfy the entropy condition from Tadmor, allow to mimic results from the continuous entropy analysis, if it is ensured that properties such as positivity preservation (of the water height, density or pressure) are satisfied on the discrete level. In this paper, Tadmor’s condition is extended to the moving mesh framework. We show that the volume terms in the semi-discrete moving mesh DGSEM do not contribute to the discrete entropy evolution when a two-point flux function that satisfies the moving mesh entropy condition is applied in the split form DG framework. The discrete entropy behavior then depends solely on the interface contributions and on the domain boundary contribution. The interface contributions are directly controlled by proper choice of the numerical element interface fluxes. If an entropy conserving two-point flux is chosen, the interface contributions vanish. To increase the robustness of the discretization we use so-called entropy stable two-point fluxes at the interfaces that are guaranteed entropy dissipative and thus give a bound on the interface contributions in the discrete entropy balance. The remaining boundary condition contributions depend on the type of the considered boundary condition. E.g. for periodic boundary conditions that are of entropy conserving type, our methodology with the entropy conserving interface fluxes is fully entropy conservative and with the entropy stable interface fluxes is guaranteed entropy stable. The presented proof does not require any exactness of quadrature in the spatial integrals of the variational forms. As it is the case for static meshes, these results rely on the assumption that additional properties like positivity preservation are satisfied on the discrete level. Besides the entropy stability, the time discretization of the moving mesh DGSEM will be investigated and it will be proven that the moving mesh DGSEM satisfies the free stream preservation property for an arbitrary s-stage Runge–Kutta method, when periodic boundary conditions are used. The theoretical properties of the moving mesh DGSEM will be validated by numerical experiments for the compressible Euler equations with periodic boundary conditions., H2020 European Research Council, Projekt DEAL

We perform a linear and entropy stability analysis for wall boundary condition procedures for discontinuous Galerkin spectral element approximations of the compressible Euler equations. Two types of boundary procedures are examined. The first defines a special wall boundary flux that incorporates the boundary condition. The other is the commonly used reflection condition where an external state is specified that has an equal and opposite normal velocity. The internal and external states are then combined through an approximate Riemann solver to weakly impose the boundary condition. We show that with the exact upwind and Lax-Friedrichs solvers the approximations are energy dissipative, with the amount of dissipation proportional to the square of the normal Mach number. Standard approximate Riemann solvers, namely Lax-Friedrichs, HLL, HLLC are entropy stable. The Roe flux is entropy stable under certain conditions. An entropy conserving flux with an entropy stable dissipation term (EC-ES) is also presented. The analysis gives insight into why these boundary conditions are robust in that they introduce large amounts of energy or entropy dissipation when the boundary condition is not accurately satisfied, e.g. due to an impulsive start or under resolution., Comment: ICOSAHOM 2018 conference proceedings, 14 pages, 2 Figures

In this paper, a new strategy for a sub-element based shock capturing for discontinuous Galerkin (DG) approximations is presented. The idea is to interpret a DG element as a collection of data and construct a hierarchy of low to high order discretizations on this set of data, including a first order finite volume scheme up to the full order DG scheme. The different DG discretizations are then blended according to sub-element troubled cell indicators, resulting in a final discretization that adaptively blends from low to high order within a single DG element. The goal is to retain as much high order accuracy as possible, even in simulations with very strong shocks, as e.g. presented in the Sedov test. The framework retains the locality of the standard DG scheme and is hence well suited for a combination with adaptive mesh refinement and parallel computing. The numerical tests demonstrate the sub-element adaptive behavior of the new shock capturing approach and its high accuracy., Comment: 40 pages in total: 30 pages of main text and 7 pages of appendix

Recently, element based high order methods such as Discontinuous Galerkin (DG) methods and the closely related flux reconstruction (FR) schemes have become popular for compressible large eddy simulation (LES). Element based high order methods with Riemann solver based interface numerical flux functions offer an interesting dispersion dissipation behavior for multi-scale problems: dispersion errors are very low for a broad range of scales, while dissipation errors are very low for well resolved scales and are very high for scales close to the Nyquist cutoff. In some sense, the inherent numerical dissipation caused by the interface Riemann solver acts as a filter of high frequency solution components. This observation motivates the trend that element based high order methods with Riemann solvers are used without an explicit LES model added. Only the high frequency type inherent dissipation caused by the Riemann solver at the element interfaces is used to account for the missing sub-grid scale dissipation. Due to under-resolution of vortical dominated structures typical for LES type setups, element based high order methods suffer from stability issues caused by aliasing errors of the non-linear flux terms. A very common strategy to fight these aliasing issues (and instabilities) is so-called polynomial de-aliasing, where interpolation is exchanged with projection based on an increased number of quadrature points. In this paper, we start with this common no-model or implicit LES (iLES) DG approach with polynomial de-aliasing and Riemann solver dissipation and review its capabilities and limitations. We find that the strategy gives excellent results, but only when the resolution is such, that about 40% of the dissipation is resolved. For more realistic, coarser resolutions used in classical LES e.g. of industrial applications, the iLES DG strategy becomes quite inaccurate. We show that there is no obvious fix to this strategy, as adding for instance a sub-grid-scale models on top doesn't change much or in worst case decreases the fidelity even more. Finally, the core of this work is a novel LES strategy based on split form DG methods that are kinetic energy preserving. The scheme offers excellent stability with full control over the amount and shape of the added artificial dissipation. This premise is the main idea of the work and we will assess the LES capabilities of the novel split form DG approach when applied to shock-free, moderate Mach number turbulence. We will demonstrate that the novel DG LES strategy offers similar accuracy as the iLES methodology for well resolved cases, but strongly increases fidelity in case of more realistic coarse resolutions.

Is the experimental order of convergence lower when using the entropy stable DGSEM-LGL variant? Recently, a debate on the question of the convergence behavior of the entropy stable nodal collocation discontinuous Galerkin spectral element method (DGSEM) with Legendre-Gauss-Lobatto nodes has emerged. Whereas it is well documented that the entropy conservative variant with no additional interface dissipation shows an odd-even behavior when testing its experimental convergence order, the results in the literature are less clear regarding the entropy stable version of the DGSEM-LGL, where explicit Riemann solver type dissipation is added at the element interfaces. We contribute to the ongoing discussion and present numerical experiments for the compressible Euler equations, where we investigate the effect of the choice of the numerical surface flux function. In our experiments, it turns out that the choice of the numerical surface flux has an impact on the convergence order. Penalty type numerical fluxes with high dissipation in all waves, such as the LLF and the HLL flux, appear to affect the convergence order negatively for odd polynomial degrees $N$, in contrast to the entropy conserving variant, where even polynomial degrees $N$ are negatively affected. This behavior is more pronounced in low Mach number settings. In contrast, for numerical surface fluxes with less dissipative behavior in the contact wave such as e.g. Roe's flux, the HLLC flux and the entropy conservative flux augmented with 5-wave matrix dissipation, optimal convergence rate of $N+1$ independent of the Mach number is observed., ICOSAHOM 2018 conference proceedings, 13 pages

In this work we analyze the entropic properties of the Euler equations when the system is closed with the assumption of a polytropic gas. In this case, the pressure solely depends upon the density of the fluid and the energy equation is not necessary anymore as the mass conservation and momentum conservation then form a closed system. Further, the total energy acts as a convex mathematical entropy function for the polytropic Euler equations. The polytropic equation of state gives the pressure as a scaled power law of the density in terms of the adiabatic index $$\gamma $$ γ . As such, there are important limiting cases contained within the polytropic model like the isothermal Euler equations ($$\gamma {=}1$$ γ = 1 ) and the shallow water equations ($$\gamma {=}2$$ γ = 2 ). We first mimic the continuous entropy analysis on the discrete level in a finite volume context to get special numerical flux functions. Next, these numerical fluxes are incorporated into a particular discontinuous Galerkin (DG) spectral element framework where derivatives are approximated with summation-by-parts operators. This guarantees a high-order accurate DG numerical approximation to the polytropic Euler equations that is also consistent to its auxiliary total energy behavior. Numerical examples are provided to verify the theoretical derivations, i.e., the entropic properties of the high order DG scheme.

The under integration of the volume terms in the discontinuous Galerkin spectral element approximation introduces errors at non-conforming element faces that do not cancel and lead to free-stream preservation errors. We derive volume and face conditions on the geometry under which a constant state is preserved. From those, we catalog six special cases on the geometry that preserve a constant state, the most general being to approximate the geometry sub-parametrically to one half the order of the solution. Numerical examples are presented to illustrate the results.

In this work we investigate the interplay of polynomial de-aliasing and sub-grid scale models for large eddy simulations based on discontinuous Galerkin discretizations. It is known that stability is a major concern when simulating underresolved turbulent flows with high order nodal collocation type discretizations. By changing the interpolatory character of the nodal collocation type discretization to a projection based discretization by increasing the number of quadrature points (polynomial de-aliasing), one is able to remove the aliasing induced stability problems. We focus on this effect and on the consequence for large eddy simulations with explicit subgrid scale models. Often, subgrid scale models have to achieve two possibly conflicting tasks in a single simulation: firstly stabilizing the numerics and secondly modeling the physical effect of the missing scales. Within a discontinuous Galerkin approach, it is possible to use either a fast (but potentially aliasing afflicted) nodal collocation discretization or a projection-based (but computationally costly) variant in combination with an explicit subgrid scale model. We use this framework to investigate the effect on the appropriate model parameter of a standard Smagorinsky subgrid scale model and of a Variational Multiscale Smagorinsky formulation. For this we first consider the 3-D viscous Taylor-Green vortex example to investigate the impact on the stability of the method and second the turbulent flow past a circular cylinder to investigate and compare the accuracy of the results. We show that the aliasing instabilities of collocative discretizations severely limit the choice of the model constant, in particular for high order schemes, while for de-aliased DG schemes, the closure model parameters can be chosen independently from the numerical scheme. For the cylinder flow, we also find that for the same model settings, the projection-based results are in better agreement with the reference DNS than those of the collocative scheme.

In this work, we design an arbitrary high order accurate nodal discontinuous Galerkin spectral element type method for the one dimensional shallow water equations. The novel method uses a skew-symmetric formulation of the continuous problem. We prove that this discretisation exactly preserves the local mass and momentum. Furthermore, we show that combined with a special numerical interface flux function, the method exactly preserves the entropy, which is also the total energy for the shallow water equations. Finally, we prove that the surface fluxes, the skew-symmetric volume integrals, and the source term are well balanced. Numerical tests are performed to demonstrate the theoretical findings.

In this work, we design an entropy stable, finite volume approximation for the ideal magnetohydrodynamics (MHD) equations. The method is novel as we design an affordable analytical expression of the numerical interface flux function that discretely preserves the entropy of the system. To guarantee the discrete conservation of entropy requires the addition of a particular source term to the ideal MHD system. Exact entropy conserving schemes cannot dissipate energy at shocks, thus to compute accurate solutions to problems that may develop shocks, we determine a dissipation term to guarantee entropy stability for the numerical scheme. Numerical tests are performed to demonstrate the theoretical findings of entropy conservation and robustness., arXiv admin note: substantial text overlap with arXiv:1509.06902; text overlap with arXiv:1007.2606 by other authors

We investigate three effects of the variable geometric terms that arise when approximating linear conservation laws on curved elements with a provably stable skew-symmetric variant of the discontinuous Galerkin spectral element method (DGSEM). We show for a constant coefficient system that the non-constant coefficient problem generated by mapping a curved element to the reference element is stable and has energy bounded by the initial value as long as the discrete metric identities are satisfied. Under those same conditions, the skew-symmetric approximation is also constant state preserving and discretely conservative, just like the original DGSEM.

In this paper, we extend the entropy conservative/stable algorithms presented by Del Rey Fernandez et al. (2019) for the compressible Euler and Navier–Stokes equations on nonconforming p-refined/coarsened curvilinear grids to h/p refinement/coarsening. The main difficulty in developing nonconforming algorithms is the construction of appropriate coupling procedures across nonconforming interfaces. Here, we utilize a computationally simple and efficient approach based upon using decoupled interpolation operators. The resulting scheme is entropy conservative/stable and element-wise conservative. Numerical simulations of the isentropic vortex and viscous shock propagation confirm the entropy conservation/stability and accuracy properties of the method (achieving $$\sim p+1$$ convergence), which are comparable to those of the original conforming scheme (Carpenter et al. in SIAM J Sci Comput 36(5):B835–B867, 2014; Parsani et al. in SIAM J Sci Comput 38(5):A3129–A3162, 2016). Simulations of the Taylor–Green vortex at $$\hbox {Re}=1600$$ and turbulent flow past a sphere at $$\hbox {Re}_{\infty }=2000$$ show the robustness and stability properties of the overall spatial discretization for unstructured grids. Finally, to demonstrate the entropy conservation property of a fully-discrete explicit entropy stable algorithm with h/p refinement/coarsening, we present the time evolution of the entropy function obtained by simulating the propagation of the isentropic vortex using a relaxation Runge–Kutta scheme.

This work presents an entropy stable discontinuous Galerkin (DG) spectral element approximation for systems of non-linear conservation laws with general geometric (h) and polynomial order (p) non-conforming rectangular meshes. The crux of the proofs presented is that the nodal DG method is constructed with the collocated Legendre–Gauss–Lobatto nodes. This choice ensures that the derivative/mass matrix pair is a summation-by-parts (SBP) operator such that entropy stability proofs from the continuous analysis are discretely mimicked. Special attention is given to the coupling between non-conforming elements as we demonstrate that the standard mortar approach for DG methods does not guarantee entropy stability for non-linear problems, which can lead to instabilities. As such, we describe a precise procedure and modify the mortar method to guarantee entropy stability for general non-linear hyperbolic systems on h / p non-conforming meshes. We verify the high-order accuracy and the entropy conservation/stability of fully non-conforming approximation with numerical examples.

This work examines the development of an entropy conservative (for smooth solutions) or entropy stable (for discontinuous solutions) space-time discontinuous Galerkin (DG) method for systems of nonlinear hyperbolic conservation laws. The resulting numerical scheme is fully discrete and provides a bound on the mathematical entropy at any time according to its initial condition and boundary conditions. The crux of the method is that discrete derivative approximations in space and time are summation-by-parts (SBP) operators. This allows the discrete method to mimic results from the continuous entropy analysis and ensures that the complete numerical scheme obeys the second law of thermodynamics. Importantly, the novel method described herein does not assume any exactness of quadrature in the variational forms that naturally arise in the context of DG methods. Typically, the development of entropy stable schemes is done on the semidiscrete level ignoring the temporal dependence. In this work, we demonstrate that creating an entropy stable DG method in time is similar to the spatial discrete entropy analysis, but there are important (and subtle) differences. Therefore, we highlight the temporal entropy analysis throughout this work. For the compressible Euler equations, the preservation of kinetic energy is of interest besides entropy stability. The construction of kinetic energy preserving (KEP) schemes is, again, typically done on the semidiscrete level similar to the construction of entropy stable schemes. We present a generalization of the KEP condition from Jameson to the space-time framework and provide the temporal components for both entropy stability and kinetic energy preservation. The properties of the space-time DG method derived herein are validated through numerical tests for the compressible Euler equations. Additionally, we provide, in appendices, how to construct the temporal entropy stable components for the shallow water or ideal magnetohydrodynamic (MHD) equations.

An open-source code that implements the entropy stable discontinuous Galerkin scheme with Legendere–Gauss–Lobatto collocation (DGSEM) on curved unstructured hexahedral grids for compressible Navier–Stokes equations (NSE) is available at github.com/project-fluxo.

The paper presents two contributions in the context of the numerical simulation of magnetized fluid dynamics. First, we show how to extend the ideal magnetohydrodynamics (MHD) equations with an inbuilt magnetic field divergence cleaning mechanism in such a way that the resulting model is consistent with the second law of thermodynamics. As a byproduct of these derivations, we show that not all of the commonly used divergence cleaning extensions of the ideal MHD equations are thermodynamically consistent. Secondly, we present a numerical scheme obtained by constructing a specific finite volume discretization that is consistent with the discrete thermodynamic entropy. It includes a mechanism to control the discrete divergence error of the magnetic field by construction and is Galilean invariant. We implement the new high-order MHD solver in the adaptive mesh refinement code FLASH where we compare the divergence cleaning efficiency to the constrained transport solver available in FLASH (unsplit staggered mesh scheme)., Comment: 54 pages

A discontinuous Galerkin scheme for unsteady fluid flows is described that allows a very high level of adaptive control in the space–time domain. The scheme is based on an explicit space–time predictor, which operates locally and takes the time evolution of the data within the grid cell into account. The predictor establishes a local space–time approximate solution in a whole space–time grid cell. This enables a time-consistent local time-stepping, by which the approximate solution is advanced in time in every grid cell with its own time step, only restricted by the local explicit stability condition. The coupling of the grid cells is solely accomplished by the corrector which is determined by the numerical fluxes. The considered discontinuous Galerkin scheme allows non-conforming meshes, together with p -adaptivity in 3 dimensions and h / p -adaptivity in 2 dimensions. Hence, we combine in this scheme all the flexibility that the discontinuous Galerkin approach provides. In this work, we investigate the combination of the local time-stepping with h - and p -adaptivity. Complex unsteady flow problems are presented to demonstrate the advantages of such an adaptive framework for simulations with strongly varying resolution requirements, e.g. shock waves, boundary layers or turbulence.

We describe a unique averaging procedure to design an entropy stable dissipation operator for the ideal magnetohydrodynamic (MHD) and compressible Euler equations. Often in the derivation of an entropy conservative numerical flux function much care is taken in the design and averaging of the entropy conservative numerical flux. We demonstrate in this work that if the discrete dissipation operator is not carefully chosen as well it can have deleterious effects on the numerical approximation. This is particularly true for very strong shocks or high Mach number flows present, for example, in astrophysical simulations. We present the underlying technique of how to construct a unique averaging technique for the discrete dissipation operator. We also demonstrate numerically the increased robustness of the approximation.

We examine the long time error behavior of discontinuous Galerkin spectral element approximations to hyperbolic equations. We show that the choice of numerical flux at interior element boundaries affects the growth rate and asymptotic value of the error. Using the upwind flux, the error reaches the asymptotic value faster, and to a lower value than a central flux gives, especially for low resolution computations. The differences in the error caused by the numerical flux choice decrease as the solution becomes better resolved.

SUMMARY In this work, we discuss the construction of a skew-symmetric discontinuous Galerkin (DG) collocation spectral element approximation for the compressible Euler equations. Starting from the skew-symmetric formulation of Morinishi, we mimic the continuous derivations on a discrete level to find a formulation for the conserved variables. In contrast to finite difference methods, DG formulations naturally have inter-domain surface flux contributions due to the discontinuous nature of the approximation space. Thus, throughout the derivations we accurately track the influence of the surface fluxes to arrive at a consistent formulation also for the surface terms. The resulting novel skew-symmetric method differs from the standard DG scheme by additional volume terms. Those volume terms have a special structure and basically represent the discretization error of the different product rules. We use the summation-by-parts (SBP) property of the Gauss–Lobatto-based DG operator and show that the novel formulation is exactly conservative for the mass, momentum, and energy. Finally, an analysis of the kinetic energy balance of the standard DG discretization shows that because of aliasing errors, a nonzero transport source term in the evolution of the discrete kinetic energy mean value may lead to an inconsistent increase or decrease in contrast to the skew-symmetric formulation. Furthermore, we derive a suitable interface flux that guarantees kinetic energy preservation in combination with the skew-symmetric DG formulation. As all derivations require only the SBP property of the Gauss–Lobatto-based DG collocation spectral element method operator and that the mass matrix is diagonal, all results for the surface terms can be directly applied in the context of multi-domain diagonal norm SBP finite difference methods. Numerical experiments are conducted to demonstrate the theoretical findings. Copyright © 2014 John Wiley & Sons, Ltd.

SUMMARY The resolution of boundary layers typically requires fine grids in the wall normal direction, which leads to anisotropic elements being refined towards the wall. Best practice guidelines for the mesh generation of stretched boundary layer grids exist for the finite volume or finite difference discretizations. A similar resolution of boundary layers with DG schemes can be achieved with a coarser grid because of the subgrid resolution of the DG scheme. High order schemes incorporate the possibility of high order element mappings, resulting in different resolution properties inside the element. In this paper, we show that the use of an internal element mapping in combination with a stretched grid can be used to reduce the error of the boundary layer approximation by an order of magnitude in comparison with the classical linear internal element mapping. The boundary layer is modeled by a one-dimensional singular perturbation problem. In addition, we discuss the construction of the element mappings by interpolation and investigate the limits of the stretching function such that the resulting element Jacobian remains positive. A parameter study shows the influence of the element mapping for different polynomial degrees on the solution. Copyright © 2014 John Wiley & Sons, Ltd.

We develop a stable split-form discontinuous Galerkin spectral element method for the solution of variable coefficient linear hyperbolic systems of conservation laws. In our presentation, we start with the simplest problem and introduce complexity as we progress. We begin with the approximation of scalar conservation laws in one space dimension. We then extend the derivation to hyperbolic systems. Finally, we approximate the two-dimensional problem. Numerical experiments are performed to compare the approximations.