An entropy stable discontinuous Galerkin method for the shallow water equations on curvilinear meshes with wet/dry fronts accelerated by GPUs

We extend the entropy stable high order nodal discontinuous Galerkin spectral element approximation for the non-linear two dimensional shallow water equations presented by Wintermeyer et al. [N. Wintermeyer, A. R. Winters, G. J. Gassner, and D. A. Kopriva. An entropy stable nodal discontinuous Galerkin method for the two dimensional shallow water equations on unstructured curvilinear meshes with discontinuous bathymetry. Journal of Computational Physics, 340:200-242, 2017] with a shock capturing technique and a positivity preservation capability to handle dry areas. The scheme preserves the entropy inequality, is well-balanced and works on unstructured, possibly curved, quadrilateral meshes. For the shock capturing, we introduce an artificial viscosity to the equations and prove that the numerical scheme remains entropy stable. We add a positivity preserving limiter to guarantee non-negative water heights as long as the mean water height is non-negative. We prove that non-negative mean water heights are guaranteed under a certain additional time step restriction for the entropy stable numerical interface flux. We implement the method on GPU architectures using the abstract language OCCA, a unified approach to multi-threading languages. We show that the entropy stable scheme is well suited to GPUs as the necessary extra calculations do not negatively impact the runtime up to reasonably high polynomial degrees (around $N=7$). We provide numerical examples that challenge the shock capturing and positivity properties of our scheme to verify our theoretical findings

3D mesh processing using GAMer 2 to enable reaction-diffusion simulations in realistic cellular geometries

Recent advances in electron microscopy have enabled the imaging of single cells in 3D at nanometer length scale resolutions. An uncharted frontier for in silico biology is the ability to simulate cellular processes using these observed geometries. Enabling such simulations requires watertight meshing of electron micrograph images into 3D volume meshes, which can then form the basis of computer simulations of such processes using numerical techniques such as the Finite Element Method. In this paper, we describe the use of our recently rewritten mesh processing software, GAMer 2, to bridge the gap between poorly conditioned meshes generated from segmented micrographs and boundary marked tetrahedral meshes which are compatible with simulation. We demonstrate the application of a workflow using GAMer 2 to a series of electron micrographs of neuronal dendrite morphology explored at three different length scales and show that the resulting meshes are suitable for finite element simulations. This work is an important step towards making physical simulations of biological processes in realistic geometries routine. Innovations in algorithms to reconstruct and simulate cellular length scale phenomena based on emerging structural data will enable realistic physical models and advance discovery at the interface of geometry and cellular processes. We posit that a new frontier at the intersection of computational technologies and single cell biology is now open.Comment: 39 pages, 14 figures. High resolution figures and supplemental movies available upon reques