2,645 research outputs found
Tetrahedral mesh improvement using moving mesh smoothing, lazy searching flips, and RBF surface reconstruction
Given a tetrahedral mesh and objective functionals measuring the mesh quality
which take into account the shape, size, and orientation of the mesh elements,
our aim is to improve the mesh quality as much as possible. In this paper, we
combine the moving mesh smoothing, based on the integration of an ordinary
differential equation coming from a given functional, with the lazy flip
technique, a reversible edge removal algorithm to modify the mesh connectivity.
Moreover, we utilize radial basis function (RBF) surface reconstruction to
improve tetrahedral meshes with curved boundary surfaces. Numerical tests show
that the combination of these techniques into a mesh improvement framework
achieves results which are comparable and even better than the previously
reported ones.Comment: Revised and improved versio
Phase-field boundary conditions for the voxel finite cell method: surface-free stress analysis of CT-based bone structures
The voxel finite cell method employs unfitted finite element meshes and voxel quadrature rules to seamlessly
transfer CT data into patient-specific bone discretizations. The method, however, still requires the explicit
parametrization of boundary surfaces to impose traction and displacement boundary conditions, which
constitutes a potential roadblock to automation. We explore a phase-field based formulation for imposing
traction and displacement constraints in a diffuse sense. Its essential component is a diffuse geometry model
generated from metastable phase-field solutions of the Allen-Cahn problem that assumes the imaging data as
initial condition. Phase-field approximations of the boundary and its gradient are then employed to transfer
all boundary terms in the variational formulation into volumetric terms. We show that in the context of the
voxel finite cell method, diffuse boundary conditions achieve the same accuracy as boundary conditions
defined over explicit sharp surfaces, if the inherent length scales, i.e., the interface width of the phase-field,
the voxel spacing and the mesh size, are properly related. We demonstrate the flexibility of the new method
by analyzing stresses in a human femur and a vertebral body
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
The diffuse Nitsche method: Dirichlet constraints on phase-field boundaries
We explore diffuse formulations of Nitsche's method for consistently imposing Dirichlet boundary conditions on phase-field approximations of sharp domains. Leveraging the properties of the phase-field gradient, we derive the variational formulation of the diffuse Nitsche method by transferring all integrals associated with the Dirichlet boundary from a geometrically sharp surface format in the standard Nitsche method to a geometrically diffuse volumetric format. We also derive conditions for the stability of the discrete system and formulate a diffuse local eigenvalue problem, from which the stabilization parameter can be estimated automatically in each element. We advertise metastable phase-field solutions of the Allen-Cahn problem for transferring complex imaging data into diffuse geometric models. In particular, we discuss the use of mixed meshes, that is, an adaptively refined mesh for the phase-field in the diffuse boundary region and a uniform mesh for the representation of the physics-based solution fields. We illustrate accuracy and convergence properties of the diffuse Nitsche method and demonstrate its advantages over diffuse penalty-type methods. In the context of imaging based analysis, we show that the diffuse Nitsche method achieves the same accuracy as the standard Nitsche method with sharp surfaces, if the inherent length scales, i.e., the interface width of the phase-field, the voxel spacing and the mesh size, are properly related. We demonstrate the flexibility of the new method by analyzing stresses in a human vertebral body
GPU-accelerated discontinuous Galerkin methods on hybrid meshes
We present a time-explicit discontinuous Galerkin (DG) solver for the
time-domain acoustic wave equation on hybrid meshes containing vertex-mapped
hexahedral, wedge, pyramidal and tetrahedral elements. Discretely energy-stable
formulations are presented for both Gauss-Legendre and Gauss-Legendre-Lobatto
(Spectral Element) nodal bases for the hexahedron. Stable timestep restrictions
for hybrid meshes are derived by bounding the spectral radius of the DG
operator using order-dependent constants in trace and Markov inequalities.
Computational efficiency is achieved under a combination of element-specific
kernels (including new quadrature-free operators for the pyramid), multi-rate
timestepping, and acceleration using Graphics Processing Units.Comment: Submitted to CMAM
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