An adaptive octree finite element method for PDEs posed on surfaces

The paper develops a finite element method for partial differential equations posed on hypersurfaces in $\mathbb{R}^N$, $N=2,3$. The method uses traces of bulk finite element functions on a surface embedded in a volumetric domain. The bulk finite element space is defined on an octree grid which is locally refined or coarsened depending on error indicators and estimated values of the surface curvatures. The cartesian structure of the bulk mesh leads to easy and efficient adaptation process, while the trace finite element method makes fitting the mesh to the surface unnecessary. The number of degrees of freedom involved in computations is consistent with the two-dimension nature of surface PDEs. No parametrization of the surface is required; it can be given implicitly by a level set function. In practice, a variant of the marching cubes method is used to recover the surface with the second order accuracy. We prove the optimal order of accuracy for the trace finite element method in $H^1$ and $L^2$ surface norms for a problem with smooth solution and quasi-uniform mesh refinement. Experiments with less regular problems demonstrate optimal convergence with respect to the number of degrees of freedom, if grid adaptation is based on an appropriate error indicator. The paper shows results of numerical experiments for a variety of geometries and problems, including advection-diffusion equations on surfaces. Analysis and numerical results of the paper suggest that combination of cartesian adaptive meshes and the unfitted (trace) finite elements provide simple, efficient, and reliable tool for numerical treatment of PDEs posed on surfaces

A topological comparison of surface extraction algorithms

In many application areas, it is useful to convert the discrete information stored in the nodes of a regular grid into a continuous boundary model. Isosurface extraction algorithms di er on how the discrete information in the grid is generated, on what information does the grid store and on the properties of the output surface.Preprin

A fast voxelization algorithm for trilinearly interpolated isosurfaces

International audienceIn this work we propose a new method for a fast incremental voxelization of isosurfaces obtained by the trilinear interpolation of 3D data. Our objective consists in the fast generation of subvoxelized iso-surfaces extracted by a point-based technique similar to the Dividing Cubes algorithm. Our technique involves neither an exhaustive scan search process nor a graph-based search approach when generating iso-surface points. Instead an optimized incremental approach is adopted here for a rapid isosurface extraction. With a sufficient sampling subdivision criteria around critical points, the extracted isosurface is both correct and topologically consistent with respect to the piece-wise trilinear interpolant. Furthermore, the discretiza-tion scheme used in our method ensures obtaining thin-one voxel width-isosurfaces as compared to the given by the Dividing Cubes algorithm. The resultant sub-voxelized isosurfaces are efficiently tested against all possible configurations of the trilinear interpolant and real-world datasets

Topology verification for isosurface extraction

Journal ArticleThe broad goals of verifiable visualization rely on correct algorithmic implementations. We extend a framework for verification of isosurfacing implementations to check topological properties. Specifically, we use stratified Morse theory and digital topology to design algorithms which verify topological invariants. Our extended framework reveals unexpected behavior and coding mistakes in popular publicly available isosurface codes

A topological comparison of surface extraction algorithms

In many application areas, it is useful to convert the discrete information stored in the nodes of a regular grid into a continuous boundary model. Isosurface extraction algorithms differ on how the discrete information in the grid is generated, on what information does the grid store and on the properties of the output surface. Recent algorithms offer different solutions for the disambiguation problem and for controlling the final topology. Based on a number of properties of the grid’s grey cells and of the reconstruction algorithms, a characterization of several surface extraction strategies is proposed. The classification presented shows the inherent limitations of the different algorithms concerning global topology control and reconstruction of local features like thin portions of the volume and almost non-manifold regions. These limitations can be observed and are illustrated with some practical examples. We review in light of this classification some of the relevant papers in the literature, and see that they cluster in some areas of the proposed hierarchy, making a case for where it might be more interesting to focus in future research.Preprin

Adaptive approximation of signed distance fields through piecewise continuous interpolation

In this paper, we present an adaptive structure to represent a signed distance field through trilinear or tricubic interpolation of values, and derivatives, that allows for fast querying of the field. We also provide a method to decide when to subdivide a node to achieve a provided threshold error. Both the numerical error control, and the values needed to build the interpolants, require the evaluation of the input field. Still, both are designed to minimize the total number of evaluations. C0 continuity is guaranteed for both the trilinear and tricubic version of the algorithm. Furthermore, we describe how to preserve C1 continuity between nodes of different levels when using a tricubic interpolant, and provide a proof that this property is maintained. Finally, we illustrate the usage of our approach in several applications, including direct rendering using sphere marching.This work has been partially funded by Ministeri de Ciència i Innovació (MICIN), Agencia Estatal de Investigación (AEI) and the Fons Europeu de Desenvolupament Regional (FEDER) (project PID2021-122136OB-C21 funded by MCIN/AEI/10.13039/501100011033/FEDER, UE). The first author gratefully acknowledges the Universitat Politècnica de Catalunya and Banco Santander for the financial support of his predoctoral grant FPI-UPC grant.Peer ReviewedPostprint (published version

Fast and Exact Fiber Surfaces for Tetrahedral Meshes

Isosurfaces are fundamental geometrical objects for the analysis and visualization of volumetric scalar fields. Recent work has generalized them to bivariate volumetric fields with fiber surfaces, the pre-image of polygons in range space. However, the existing algorithm for their computation is approximate, and is limited to closed polygons. Moreover, its runtime performance does not allow instantaneous updates of the fiber surfaces upon user edits of the polygons. Overall, these limitations prevent a reliable and interactive exploration of the space of fiber surfaces. This paper introduces the first algorithm for the exact computation of fiber surfaces in tetrahedral meshes. It assumes no restriction on the topology of the input polygon, handles degenerate cases and better captures sharp features induced by polygon bends. The algorithm also allows visualization of individual fibers on the output surface, better illustrating their relationship with data features in range space. To enable truly interactive exploration sessions, we further improve the runtime performance of this algorithm. In particular, we show that it is trivially parallelizable and that it scales nearly linearly with the number of cores. Further, we study acceleration data-structures both in geometrical domain and range space and we show how to generalize interval trees used in isosurface extraction to fiber surface extraction. Experiments demonstrate the superiority of our algorithm over previous work, both in terms of accuracy and running time, with up to two orders of magnitude speedups. This improvement enables interactive edits of range polygons with instantaneous updates of the fiber surface for exploration purpose. A VTK-based reference implementation is provided as additional material to reproduce our results

On atomistic-to-continuum couplings without ghost forces in three dimensions

In this paper we construct energy based numerical methods free of ghost forces in three dimen- sional lattices arising in crystalline materials. The analysis hinges on establishing a connection of the coupled system to conforming finite elements. Key ingredients are: (i) a new representation of discrete derivatives related to long range interactions of atoms as volume integrals of gradients of piecewise linear functions over bond volumes, and (ii) the construction of an underlying globally continuous function representing the coupled modeling method

Doctor of Philosophy

dissertationIn this dissertation, we advance the theory and practice of verifying visualization algorithms. We present techniques to assess visualization correctness through testing of important mathematical properties. Where applicable, these techniques allow us to distinguish whether anomalies in visualization features can be attributed to the underlying physical process or to artifacts from the implementation under verification. Such scientific scrutiny is at the heart of verifiable visualization - subjecting visualization algorithms to the same verification process that is used in other components of the scientific pipeline. The contributions of this dissertation are manifold. We derive the mathematical framework for the expected behavior of several visualization algorithms, and compare them to experimentally observed results in the selected codes. In the Computational Science & Engineering community CS&E, this technique is know as the Method of Manufactured Solution (MMS). We apply MMS to the verification of geometrical and topological properties of isosurface extraction algorithms, and direct volume rendering. We derive the convergence of geometrical properties of isosurface extraction techniques, such as function value and normals. For the verification of topological properties, we use stratified Morse theory and digital topology to design algorithms that verify topological invariants. In the case of volume rendering algorithms, we provide the expected discretization errors for three different error sources. The results of applying the MMS is another important contribution of this dissertation. We report unexpected behavior for almost all implementations tested. In some cases, we were able to find and fix bugs that prevented the correctness of the visualization algorithm. In particular, we address an almost 2 0 -year-old bug with the core disambiguation procedure of Marching Cubes 33, one of the first algorithms intended to preserve the topology of the trilinear interpolant. Finally, an important by-product of this work is a range of responses practitioners can expect to encounter with the visualization technique under verification

Visualization of higher order finite elements.

Finite element meshes are used to approximate the solution to some differential equation when no exact solution exists. A finite element mesh consists of many small (but finite, not infinitesimal or differential) regions of space that partition the problem domain, {Omega}. Each region, or element, or cell has an associated polynomial map, {Phi}, that converts the coordinates of any point, x = ( x y z ), in the element into another value, f(x), that is an approximate solution to the differential equation, as in Figure 1(a). This representation works quite well for axis-aligned regions of space, but when there are curved boundaries on the problem domain, {Omega}, it becomes algorithmically much more difficult to define {Phi} in terms of x. Rather, we define an archetypal element in a new coordinate space, r = ( r s t ), which has a simple, axis-aligned boundary (see Figure 1(b)) and place two maps onto our archetypal element