voFoam - A geometrical Volume of Fluid algorithm on arbitrary unstructured meshes with local dynamic adaptive mesh refinement using OpenFOAM

A new parallelized unsplit geometrical Volume of Fluid (VoF) algorithm with support for arbitrary unstructured meshes and dynamic local Adaptive Mesh Refinement (AMR), as well as for two and three dimensional computation is developed. The geometrical VoF algorithm supports arbitrary unstructured meshes in order to enable computations involving flow domains of arbitrary geometrical complexity. The implementation of the method is done within the framework of the OpenFOAM library for Computational Continuum Mechanics (CCM) using the C++ programming language with modern policy based design for high program code modularity. The development of the geometrical VoF algorithm significantly extends the method base of the OpenFOAM library by geometrical volumetric flux computation for two-phase flow simulations. For the volume fraction advection, a novel unsplit geometrical algorithm is developed, which inherently sustains volume conservation utilizing unique Lagrangian discrete trajectories located in the mesh points. This practice completely eliminates the possibility of an overlap between the flux polyhedra and hence significantly increases volume conservation. A new efficient (quadratic convergent) and accurate iterative flux correction algorithm is developed, which avoids topological changes of the flux polyhedra. Our geometrical VoF algorithm is dimension agnostic, providing automatic support for both 2D and 3D computations, following the established practice in OpenFOAM. The geometrical algorithm used for the volume fraction transport has been extended to support dynamic local AMR available in OpenFOAM. Furthermore, the existing dynamic mesh capability of OpenFOAM has been modified to support the geometrical mapping algorithm executed as a part of the dynamic local AMR cycle. The method implementation is fully parallelized using the domain decomposition approach.Comment: voFoam - geometrical unsplit VoF algorithm on unstructered meshe

MeshODE: A Robust and Scalable Framework for Mesh Deformation

We present MeshODE, a scalable and robust framework for pairwise CAD model deformation without prespecified correspondences. Given a pair of shapes, our framework provides a novel shape feature-preserving mapping function that continuously deforms one model to the other by minimizing fitting and rigidity losses based on the non-rigid iterative-closest-point (ICP) algorithm. We address two challenges in this problem, namely the design of a powerful deformation function and obtaining a feature-preserving CAD deformation. While traditional deformation directly optimizes for the coordinates of the mesh vertices or the vertices of a control cage, we introduce a deep bijective mapping that utilizes a flow model parameterized as a neural network. Our function has the capacity to handle complex deformations, produces deformations that are guaranteed free of self-intersections, and requires low rigidity constraining for geometry preservation, which leads to a better fitting quality compared with existing methods. It additionally enables continuous deformation between two arbitrary shapes without supervision for intermediate shapes. Furthermore, we propose a robust preprocessing pipeline for raw CAD meshes using feature-aware subdivision and a uniform graph template representation to address artifacts in raw CAD models including self-intersections, irregular triangles, topologically disconnected components, non-manifold edges, and nonuniformly distributed vertices. This facilitates a fast deformation optimization process that preserves global and local details. Our code is publicly available

Towards a Computational Framework for Modeling the Impact of Aortic Coarctations upon Left Ventricular Load

Computational fluid dynamics (CFD) models of blood flow in the left ventricle (LV) and aorta are important tools for analyzing the mechanistic links between myocardial deformation and flow patterns. Typically, the use of image-based kinematic CFD models prevails in applications such as predicting the acute response to interventions which alter LV afterload conditions. However, such models are limited in their ability to analyze any impacts upon LV load or key biomarkers known to be implicated in driving remodeling processes as LV function is not accounted for in a mechanistic sense. This study addresses these limitations by reporting on progress made towards a novel electro-mechano-fluidic (EMF) model that represents the entire physics of LV electromechanics (EM) based on first principles. A biophysically detailed finite element (FE) model of LV EM was coupled with a FE-based CFD solver for moving domains using an arbitrary Eulerian-Lagrangian (ALE) formulation. Two clinical cases of patients suffering from aortic coarctations (CoA) were built and parameterized based on clinical data under pre-treatment conditions. For one patient case simulations under post-treatment conditions after geometric repair of CoA by a virtual stenting procedure were compared against pre-treatment results. Numerical stability of the approach was demonstrated by analyzing mesh quality and solver performance under the significantly large deformations of the LV blood pool. Further, computational tractability and compatibility with clinical time scales were investigated by performing strong scaling benchmarks up to 1536 compute cores. The overall cost of the entire workflow for building, fitting and executing EMF simulations was comparable to those reported for image-based kinematic models, suggesting that EMF models show potential of evolving into a viable clinical research tool.Comment: This research was supported by the grants F3210-N18 and I2760-B30 from the Austrian Science Fund (FWF), the EU grant CardioProof agreement 611232 and a BioTechMed award to GP. Additionally, this project has received funding from the European Union's Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie Action H2020-MSCA-IF-2016 InsiliCardio, GA No. 75083

Cartoonish sketch-based face editing in videos using identity deformation transfer

We address the problem of using hand-drawn sketches to create exaggerated deformations to faces in videos, such as enlarging the shape or modifying the position of eyes or mouth. This task is formulated as a 3D face model reconstruction and deformation problem. We first recover the facial identity and expressions from the video by fitting a face morphable model for each frame. At the same time, user's editing intention is recognized from input sketches as a set of facial modifications. Then a novel identity deformation algorithm is proposed to transfer these facial deformations from 2D space to the 3D facial identity directly while preserving the facial expressions. After an optional stage for further refining the 3D face model, these changes are propagated to the whole video with the modified identity. Both the user study and experimental results demonstrate that our sketching framework can help users effectively edit facial identities in videos, while high consistency and fidelity are ensured at the same time.Comment: In Computers & Graphics, 2019. (12 pages, 10 figures

A GPU-based Multi-level Algorithm for Boundary Value Problems

A novel and scalable geometric multi-level algorithm is presented for the numerical solution of elliptic partial differential equations, specially designed to run with high occupancy of streaming processors inside Graphics Processing Units(GPUs). The algorithm consists of iterative, superposed operations on a single grid, and it is composed of two simple full-grid routines: a restriction and a coarsened interpolation-relaxation. The restriction is used to collect sources using recursive coarsened averages, and the interpolation-relaxation simultaneously applies coarsened finite-difference operators and interpolations. The routines are scheduled in a saw-like refining cycle. Convergence to machine precision is achieved repeating the full cycle using accumulated residuals and successively collecting the solution. Its total number of operations scale linearly with the number of nodes. It provides an attractive fast solver for Boundary Value Problems (BVPs), specially for simulations running entirely in the GPU. Applications shown in this work include the deformation of two-dimensional grids, the computation of three-dimensional streamlines for a singular trifoil-knot vortex and the calculation of three-dimensional electric potentials in heterogeneous dielectric media.Comment: 14 pages, 7 figure

Pixel2Mesh: Generating 3D Mesh Models from Single RGB Images

We propose an end-to-end deep learning architecture that produces a 3D shape in triangular mesh from a single color image. Limited by the nature of deep neural network, previous methods usually represent a 3D shape in volume or point cloud, and it is non-trivial to convert them to the more ready-to-use mesh model. Unlike the existing methods, our network represents 3D mesh in a graph-based convolutional neural network and produces correct geometry by progressively deforming an ellipsoid, leveraging perceptual features extracted from the input image. We adopt a coarse-to-fine strategy to make the whole deformation procedure stable, and define various of mesh related losses to capture properties of different levels to guarantee visually appealing and physically accurate 3D geometry. Extensive experiments show that our method not only qualitatively produces mesh model with better details, but also achieves higher 3D shape estimation accuracy compared to the state-of-the-art

Uniqueness of Transformation based on Jacobian Determinant and curl-Vector

Numerical examples demonstrated that a prescribed positive Jacobian determinant alone can not uniquely determine a diffeomorphism. It is conjectured that the uniqueness of a transformation can be assured by its Jacobian determinant and the curl-vector. In this work, we study the uniqueness problem analytically and propose an approach to the proof of the uniqueness of a transformation with prescribed Jacobian determinant and curl-vector.Comment: 11 pages, 8 figure

Towards realistic HPC models of the neuromuscular system

Realistic simulations of detailed, biophysics-based, multi-scale models require very high resolution and, thus, large-scale compute facilities. Existing simulation environments, especially for biomedical applications, are designed to allow for a high flexibility and generality in model development. Flexibility and model development, however, are often a limiting factor for large-scale simulations. Therefore, new models are typically tested and run on small-scale compute facilities. By using a detailed biophysics-based, chemo-electromechanical skeletal muscle model and the international open-source software library OpenCMISS as an example, we present an approach to upgrade an existing muscle simulation framework from a moderately parallel version towards a massively parallel one that scales both in terms of problem size and in terms of the number of parallel processes. For this purpose, we investigate different modeling, algorithmic and implementational aspects. We present improvements addressing both numerical and parallel scalability. In addition, our approach includes a novel visualization environment, which is based on the MegaMol environment capable of handling large amounts of simulated data. It offers a platform for fast visualization prototyping, distributed rendering, and advanced visualization techniques. We present results of a variety of scaling studies at the Tier-1 supercomputer HazelHen at the High Performance Computing Center Stuttgart (HLRS). We improve the overall runtime by a factor of up to 2.6 and achieved good scalability on up to 768 cores, where the previous implementation used only 4 cores

A unified continuum and variational multiscale formulation for fluids, solids, and fluid-structure interaction

We develop a unified continuum modeling framework for viscous fluids and hyperelastic solids using the Gibbs free energy as the thermodynamic potential. This framework naturally leads to a pressure primitive variable formulation for the continuum body, which is well-behaved in both compressible and incompressible regimes. Our derivation also provides a rational justification of the isochoric-volumetric additive split of free energies in nonlinear continuum mechanics. The variational multiscale analysis is performed for the continuum model to construct a foundation for numerical discretization. We first consider the continuum body instantiated as a hyperelastic material and develop a variational multiscale formulation for the hyper-elastodynamic problem. The generalized-alpha method is applied for temporal discretization. A segregated algorithm for the nonlinear solver is designed and carefully analyzed. Second, we apply the new formulation to construct a novel unified formulation for fluid-solid coupled problems. The variational multiscale formulation is utilized for spatial discretization in both fluid and solid subdomains. The generalized-alpha method is applied for the whole continuum body, and optimal high-frequency dissipation is achieved in both fluid and solid subproblems. A new predictor multi-corrector algorithm is developed based on the segregated algorithm to attain a good balance between robustness and efficiency. The efficacy of the new formulations is examined in several benchmark problems. The results indicate that the proposed modeling and numerical methodologies constitute a promising technology for biomedical and engineering applications, particularly those necessitating incompressible models

A curved-element unstructured discontinuous Galerkin method on GPUs for the Euler equations

In this work we consider Runge-Kutta discontinuous Galerkin methods (RKDG) for the solution of hyperbolic equations enabling high order discretization in space and time. We aim at an efficient implementation of DG for Euler equations on GPUs. A mesh curvature approach is presented for the proper resolution of the domain boundary. This approach is based on the linear elasticity equations and enables a boundary approximation with arbitrary, high order. In order to demonstrate the performance of the boundary curvature a massively parallel solver on graphics processors is implemented and utilized for the solution of the Euler equations of gas-dynamics