3,262 research outputs found
An anisotropic mesh adaptation method for the finite element solution of heterogeneous anisotropic diffusion problems
Heterogeneous anisotropic diffusion problems arise in the various areas of
science and engineering including plasma physics, petroleum engineering, and
image processing. Standard numerical methods can produce spurious oscillations
when they are used to solve those problems. A common approach to avoid this
difficulty is to design a proper numerical scheme and/or a proper mesh so that
the numerical solution validates the discrete counterpart (DMP) of the maximum
principle satisfied by the continuous solution. A well known mesh condition for
the DMP satisfaction by the linear finite element solution of isotropic
diffusion problems is the non-obtuse angle condition that requires the dihedral
angles of mesh elements to be non-obtuse. In this paper, a generalization of
the condition, the so-called anisotropic non-obtuse angle condition, is
developed for the finite element solution of heterogeneous anisotropic
diffusion problems. The new condition is essentially the same as the existing
one except that the dihedral angles are now measured in a metric depending on
the diffusion matrix of the underlying problem. Several variants of the new
condition are obtained. Based on one of them, two metric tensors for use in
anisotropic mesh generation are developed to account for DMP satisfaction and
the combination of DMP satisfaction and mesh adaptivity. Numerical examples are
given to demonstrate the features of the linear finite element method for
anisotropic meshes generated with the metric tensors.Comment: 34 page
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
A feature-based mesh adaptation for the unsteady high speed compressible flows in complex three-dimensional domains
We propose an unstructured mesh adaptation approach for unsteady high speed compressible Navier–Stokes applications involving blasts and explosions with the presence of strong shock waves propagating in three dimensional complex domains. The idea is to identify the locations of critical physics locally and then re-mesh these regions based on solution derived metrics. The approach ensures both geometry fidelity and mesh validity, especially for areas near complex geometries, a task that is always a challenge in mesh adaptation. The proposed adaptivity is applied for simulations of blast wave propagations and compared with available data in literature. The results show that the proposed method is fully robust and efficient for computational fluid dynamics (CFD) problems in complex three-dimensional domains
Kinetic Solvers with Adaptive Mesh in Phase Space
An Adaptive Mesh in Phase Space (AMPS) methodology has been developed for
solving multi-dimensional kinetic equations by the discrete velocity method. A
Cartesian mesh for both configuration (r) and velocity (v) spaces is produced
using a tree of trees data structure. The mesh in r-space is automatically
generated around embedded boundaries and dynamically adapted to local solution
properties. The mesh in v-space is created on-the-fly for each cell in r-space.
Mappings between neighboring v-space trees implemented for the advection
operator in configuration space. We have developed new algorithms for solving
the full Boltzmann and linear Boltzmann equations with AMPS. Several recent
innovations were used to calculate the discrete Boltzmann collision integral
with dynamically adaptive mesh in velocity space: importance sampling,
multi-point projection method, and the variance reduction method. We have
developed an efficient algorithm for calculating the linear Boltzmann collision
integral for elastic and inelastic collisions in a Lorentz gas. New AMPS
technique has been demonstrated for simulations of hypersonic rarefied gas
flows, ion and electron kinetics in weakly ionized plasma, radiation and light
particle transport through thin films, and electron streaming in
semiconductors. We have shown that AMPS allows minimizing the number of cells
in phase space to reduce computational cost and memory usage for solving
challenging kinetic problems
Patient-specific anisotropic model of human trunk based on MR data
There are many ways to generate geometrical models for numerical simulation, and most of them start with a segmentation step to extract the boundaries of the regions of interest. This paper presents an algorithm to generate a patient-specific three-dimensional geometric model, based on a tetrahedral mesh, without an initial extraction of contours from the volumetric data. Using the information directly available in the data, such as gray levels, we built a metric to drive a mesh adaptation process. The metric is used to specify the size and orientation of the tetrahedral elements everywhere in the mesh. Our method, which produces anisotropic meshes, gives good results with synthetic and real MRI data. The resulting model quality has been evaluated qualitatively and quantitatively by comparing it with an analytical solution and with a segmentation made by an expert. Results show that our method gives, in 90% of the cases, as good or better meshes as a similar isotropic method, based on the accuracy of the volume reconstruction for a given mesh size. Moreover, a comparison of the Hausdorff distances between adapted meshes of both methods and ground-truth volumes shows that our method decreases reconstruction errors faster. Copyright © 2015 John Wiley & Sons, Ltd.Natural
Sciences and Engineering Research Council (NSERC) of Canada and the MEDITIS training program (´Ecole Polytechnique de Montreal and NSERC)
Adaptive Mesh Refinement for Electromagnetic Simulation
We consider problems related to initial meshing and adaptive mesh refinement
for the electromagnetic simulation of various structures. The quality of the
initial mesh and the performance of the adaptive refinement are of great
importance for the finite element solution of the Maxwell equations, since they
directly affect the accuracy and the computational time. In this paper, we
describe the complete meshing workflow, which allows the simulation of
arbitrary structures. Test simulations confirm that the presented approach
allows to reach the quality of the industrial simulation software
Optimizing the geometrical accuracy of curvilinear meshes
This paper presents a method to generate valid high order meshes with
optimized geometrical accuracy. The high order meshing procedure starts with a
linear mesh, that is subsequently curved without taking care of the validity of
the high order elements. An optimization procedure is then used to both
untangle invalid elements and optimize the geometrical accuracy of the mesh.
Standard measures of the distance between curves are considered to evaluate the
geometrical accuracy in planar two-dimensional meshes, but they prove
computationally too costly for optimization purposes. A fast estimate of the
geometrical accuracy, based on Taylor expansions of the curves, is introduced.
An unconstrained optimization procedure based on this estimate is shown to
yield significant improvements in the geometrical accuracy of high order
meshes, as measured by the standard Haudorff distance between the geometrical
model and the mesh. Several examples illustrate the beneficial impact of this
method on CFD solutions, with a particular role of the enhanced mesh boundary
smoothness.Comment: Submitted to JC
EIT Reconstruction Algorithms: Pitfalls, Challenges and Recent Developments
We review developments, issues and challenges in Electrical Impedance
Tomography (EIT), for the 4th Workshop on Biomedical Applications of EIT,
Manchester 2003. We focus on the necessity for three dimensional data
collection and reconstruction, efficient solution of the forward problem and
present and future reconstruction algorithms. We also suggest common pitfalls
or ``inverse crimes'' to avoid.Comment: A review paper for the 4th Workshop on Biomedical Applications of
EIT, Manchester, UK, 200
Three-dimensional CFD simulations with large displacement of the geometries using a connectivity-change moving mesh approach
This paper deals with three-dimensional (3D) numerical simulations involving 3D moving geometries with large displacements on unstructured meshes. Such simulations are of great value to industry, but remain very time-consuming. A robust moving mesh algorithm coupling an elasticity-like mesh deformation solution and mesh optimizations was proposed in previous works, which removes the need for global remeshing when performing large displacements. The optimizations, and in particular generalized edge/face swapping, preserve the initial quality of the mesh throughout the simulation. We propose to integrate an Arbitrary Lagrangian Eulerian compressible flow solver into this process to demonstrate its capabilities in a full CFD computation context. This solver relies on a local enforcement of the discrete geometric conservation law to preserve the order of accuracy of the time integration. The displacement of the geometries is either imposed, or driven by fluid–structure interaction (FSI). In the latter case, the six degrees of freedom approach for rigid bodies is considered. Finally, several 3D imposed-motion and FSI examples are given to validate the proposed approach, both in academic and industrial configurations
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