282,048 research outputs found
Hyperorthogonal well-folded Hilbert curves
R-trees can be used to store and query sets of point data in two or more
dimensions. An easy way to construct and maintain R-trees for two-dimensional
points, due to Kamel and Faloutsos, is to keep the points in the order in which
they appear along the Hilbert curve. The R-tree will then store bounding boxes
of points along contiguous sections of the curve, and the efficiency of the
R-tree depends on the size of the bounding boxes---smaller is better. Since
there are many different ways to generalize the Hilbert curve to higher
dimensions, this raises the question which generalization results in the
smallest bounding boxes. Familiar methods, such as the one by Butz, can result
in curve sections whose bounding boxes are a factor larger
than the volume traversed by that section of the curve. Most of the volume
bounded by such bounding boxes would not contain any data points. In this paper
we present a new way of generalizing Hilbert's curve to higher dimensions,
which results in much tighter bounding boxes: they have at most 4 times the
volume of the part of the curve covered, independent of the number of
dimensions. Moreover, we prove that a factor 4 is asymptotically optimal.Comment: Manuscript submitted to Journal of Computational Geometry. An
abstract appeared in the 31st Int Symp on Computational Geometry (SoCG 2015),
LIPIcs 34:812-82
Arbitrary-Lagrangian-Eulerian discontinuous Galerkin schemes with a posteriori subcell finite volume limiting on moving unstructured meshes
We present a new family of high order accurate fully discrete one-step
Discontinuous Galerkin (DG) finite element schemes on moving unstructured
meshes for the solution of nonlinear hyperbolic PDE in multiple space
dimensions, which may also include parabolic terms in order to model
dissipative transport processes. High order piecewise polynomials are adopted
to represent the discrete solution at each time level and within each spatial
control volume of the computational grid, while high order of accuracy in time
is achieved by the ADER approach. In our algorithm the spatial mesh
configuration can be defined in two different ways: either by an isoparametric
approach that generates curved control volumes, or by a piecewise linear
decomposition of each spatial control volume into simplex sub-elements. Our
numerical method belongs to the category of direct
Arbitrary-Lagrangian-Eulerian (ALE) schemes, where a space-time conservation
formulation of the governing PDE system is considered and which already takes
into account the new grid geometry directly during the computation of the
numerical fluxes. Our new Lagrangian-type DG scheme adopts the novel a
posteriori sub-cell finite volume limiter method, in which the validity of the
candidate solution produced in each cell by an unlimited ADER-DG scheme is
verified against a set of physical and numerical detection criteria. Those
cells which do not satisfy all of the above criteria are flagged as troubled
cells and are recomputed with a second order TVD finite volume scheme. The
numerical convergence rates of the new ALE ADER-DG schemes are studied up to
fourth order in space and time and several test problems are simulated.
Finally, an application inspired by Inertial Confinement Fusion (ICF) type
flows is considered by solving the Euler equations and the PDE of viscous and
resistive magnetohydrodynamics (VRMHD).Comment: 39 pages, 21 figure
MGOS: A library for molecular geometry and its operating system
The geometry of atomic arrangement underpins the structural understanding of molecules in many fields. However, no general framework of mathematical/computational theory for the geometry of atomic arrangement exists. Here we present "Molecular Geometry (MG)'' as a theoretical framework accompanied by "MG Operating System (MGOS)'' which consists of callable functions implementing the MG theory. MG allows researchers to model complicated molecular structure problems in terms of elementary yet standard notions of volume, area, etc. and MGOS frees them from the hard and tedious task of developing/implementing geometric algorithms so that they can focus more on their primary research issues. MG facilitates simpler modeling of molecular structure problems; MGOS functions can be conveniently embedded in application programs for the efficient and accurate solution of geometric queries involving atomic arrangements. The use of MGOS in problems involving spherical entities is akin to the use of math libraries in general purpose programming languages in science and engineering. (C) 2019 The Author(s). Published by Elsevier B.V
Mechanistic and pathological study of the genesis, growth, and rupture of abdominal aortic aneurysms
Postprint (published version
A Moving Boundary Flux Stabilization Method for Cartesian Cut-Cell Grids using Directional Operator Splitting
An explicit moving boundary method for the numerical solution of
time-dependent hyperbolic conservation laws on grids produced by the
intersection of complex geometries with a regular Cartesian grid is presented.
As it employs directional operator splitting, implementation of the scheme is
rather straightforward. Extending the method for static walls from Klein et
al., Phil. Trans. Roy. Soc., A367, no. 1907, 4559-4575 (2009), the scheme
calculates fluxes needed for a conservative update of the near-wall cut-cells
as linear combinations of standard fluxes from a one-dimensional extended
stencil. Here the standard fluxes are those obtained without regard to the
small sub-cell problem, and the linear combination weights involve detailed
information regarding the cut-cell geometry. This linear combination of
standard fluxes stabilizes the updates such that the time-step yielding
marginal stability for arbitrarily small cut-cells is of the same order as that
for regular cells. Moreover, it renders the approach compatible with a wide
range of existing numerical flux-approximation methods. The scheme is extended
here to time dependent rigid boundaries by reformulating the linear combination
weights of the stabilizing flux stencil to account for the time dependence of
cut-cell volume and interface area fractions. The two-dimensional tests
discussed include advection in a channel oriented at an oblique angle to the
Cartesian computational mesh, cylinders with circular and triangular
cross-section passing through a stationary shock wave, a piston moving through
an open-ended shock tube, and the flow around an oscillating NACA 0012 aerofoil
profile.Comment: 30 pages, 27 figures, 3 table
FluSI: A novel parallel simulation tool for flapping insect flight using a Fourier method with volume penalization
FluSI, a fully parallel open source software for pseudo-spectral simulations
of three-dimensional flapping flight in viscous flows, is presented. It is
freely available for non-commercial use under
[https://github.com/pseudospectators/FLUSI]. The computational framework runs
on high performance computers with distributed memory architectures. The
discretization of the three-dimensional incompressible Navier--Stokes equations
is based on a Fourier pseudo-spectral method with adaptive time stepping. The
complex time varying geometry of insects with rigid flapping wings is handled
with the volume penalization method. The modules characterizing the insect
geometry, the flight mechanics and the wing kinematics are described.
Validation tests for different benchmarks illustrate the efficiency and
precision of the approach. Finally, computations of a model insect in the
turbulent regime demonstrate the versatility of the software
High Order Cell-Centered Lagrangian-Type Finite Volume Schemes with Time-Accurate Local Time Stepping on Unstructured Triangular Meshes
We present a novel cell-centered direct Arbitrary-Lagrangian-Eulerian (ALE)
finite volume scheme on unstructured triangular meshes that is high order
accurate in space and time and that also allows for time-accurate local time
stepping (LTS). The new scheme uses the following basic ingredients: a high
order WENO reconstruction in space on unstructured meshes, an element-local
high-order accurate space-time Galerkin predictor that performs the time
evolution of the reconstructed polynomials within each element, the computation
of numerical ALE fluxes at the moving element interfaces through approximate
Riemann solvers, and a one-step finite volume scheme for the time update which
is directly based on the integral form of the conservation equations in
space-time. The inclusion of the LTS algorithm requires a number of crucial
extensions, such as a proper scheduling criterion for the time update of each
element and for each node; a virtual projection of the elements contained in
the reconstruction stencils of the element that has to perform the WENO
reconstruction; and the proper computation of the fluxes through the space-time
boundary surfaces that will inevitably contain hanging nodes in time due to the
LTS algorithm. We have validated our new unstructured Lagrangian LTS approach
over a wide sample of test cases solving the Euler equations of compressible
gasdynamics in two space dimensions, including shock tube problems, cylindrical
explosion problems, as well as specific tests typically adopted in Lagrangian
calculations, such as the Kidder and the Saltzman problem. When compared to the
traditional global time stepping (GTS) method, the newly proposed LTS algorithm
allows to reduce the number of element updates in a given simulation by a
factor that may depend on the complexity of the dynamics, but which can be as
large as 4.7.Comment: 31 pages, 13 figure
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
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