Parallel 3D Mortar Element Method for Adaptive Nonconforming Meshes
NASA Technical Reports Server (NTRS)
Feng, Huiyu; Mavriplis, Catherine; VanderWijngaart, Rob; Biswas, Rupak
2004-01-01
High order methods are frequently used in computational simulation for their high accuracy. An efficient way to avoid unnecessary computation in smooth regions of the solution is to use adaptive meshes which employ fine grids only in areas where they are needed. Nonconforming spectral elements allow the grid to be flexibly adjusted to satisfy the computational accuracy requirements. The method is suitable for computational simulations of unsteady problems with very disparate length scales or unsteady moving features, such as heat transfer, fluid dynamics or flame combustion. In this work, we select the Mark Element Method (MEM) to handle the non-conforming interfaces between elements. A new technique is introduced to efficiently implement MEM in 3-D nonconforming meshes. By introducing an "intermediate mortar", the proposed method decomposes the projection between 3-D elements and mortars into two steps. In each step, projection matrices derived in 2-D are used. The two-step method avoids explicitly forming/deriving large projection matrices for 3-D meshes, and also helps to simplify the implementation. This new technique can be used for both h- and p-type adaptation. This method is applied to an unsteady 3-D moving heat source problem. With our new MEM implementation, mesh adaptation is able to efficiently refine the grid near the heat source and coarsen the grid once the heat source passes. The savings in computational work resulting from the dynamic mesh adaptation is demonstrated by the reduction of the the number of elements used and CPU time spent. MEM and mesh adaptation, respectively, bring irregularity and dynamics to the computer memory access pattern. Hence, they provide a good way to gauge the performance of computer systems when running scientific applications whose memory access patterns are irregular and unpredictable. We select a 3-D moving heat source problem as the Unstructured Adaptive (UA) grid benchmark, a new component of the NAS Parallel
3D Finite Element Trajectory Code with Adaptive Meshing
NASA Astrophysics Data System (ADS)
Ives, Lawrence; Bui, Thuc; Vogler, William; Bauer, Andy; Shephard, Mark; Beal, Mark; Tran, Hien
2004-11-01
Beam Optics Analysis, a new, 3D charged particle program is available and in use for the design of complex, 3D electron guns and charged particle devices. The code reads files directly from most CAD and solid modeling programs, includes an intuitive Graphical User Interface (GUI), and a robust mesh generator that is fully automatic. Complex problems can be set up, and analysis initiated in minutes. The program includes a user-friendly post processor for displaying field and trajectory data using 3D plots and images. The electrostatic solver is based on the standard nodal finite element method. The magnetostatic field solver is based on the vector finite element method and is also called during the trajectory simulation process to solve for self magnetic fields. The user imports the geometry from essentially any commercial CAD program and uses the GUI to assign parameters (voltages, currents, dielectric constant) and designate emitters (including work function, emitter temperature, and number of trajectories). The the mesh is generated automatically and analysis is performed, including mesh adaptation to improve accuracy and optimize computational resources. This presentation will provide information on the basic structure of the code, its operation, and it's capabilities.
Parallel adaptive mesh refinement within the PUMAA3D Project
NASA Technical Reports Server (NTRS)
Freitag, Lori; Jones, Mark; Plassmann, Paul
1995-01-01
To enable the solution of large-scale applications on distributed memory architectures, we are designing and implementing parallel algorithms for the fundamental tasks of unstructured mesh computation. In this paper, we discuss efficient algorithms developed for two of these tasks: parallel adaptive mesh refinement and mesh partitioning. The algorithms are discussed in the context of two-dimensional finite element solution on triangular meshes, but are suitable for use with a variety of element types and with h- or p-refinement. Results demonstrating the scalability and efficiency of the refinement algorithm and the quality of the mesh partitioning are presented for several test problems on the Intel DELTA.
3D Compressible Melt Transport with Adaptive Mesh Refinement
NASA Astrophysics Data System (ADS)
Dannberg, Juliane; Heister, Timo
2015-04-01
Melt generation and migration have been the subject of numerous investigations, but their typical time and length-scales are vastly different from mantle convection, which makes it difficult to study these processes in a unified framework. The equations that describe coupled Stokes-Darcy flow have been derived a long time ago and they have been successfully implemented and applied in numerical models (Keller et al., 2013). However, modelling magma dynamics poses the challenge of highly non-linear and spatially variable material properties, in particular the viscosity. Applying adaptive mesh refinement to this type of problems is particularly advantageous, as the resolution can be increased in mesh cells where melt is present and viscosity gradients are high, whereas a lower resolution is sufficient in regions without melt. In addition, previous models neglect the compressibility of both the solid and the fluid phase. However, experiments have shown that the melt density change from the depth of melt generation to the surface leads to a volume increase of up to 20%. Considering these volume changes in both phases also ensures self-consistency of models that strive to link melt generation to processes in the deeper mantle, where the compressibility of the solid phase becomes more important. We describe our extension of the finite-element mantle convection code ASPECT (Kronbichler et al., 2012) that allows for solving additional equations describing the behaviour of silicate melt percolating through and interacting with a viscously deforming host rock. We use the original compressible formulation of the McKenzie equations, augmented by an equation for the conservation of energy. This approach includes both melt migration and melt generation with the accompanying latent heat effects. We evaluate the functionality and potential of this method using a series of simple model setups and benchmarks, comparing results of the compressible and incompressible formulation and
NASA Astrophysics Data System (ADS)
Yang, Dikun; Oldenburg, Douglas W.; Haber, Eldad
2014-03-01
Airborne electromagnetic (AEM) methods are highly efficient tools for assessing the Earth's conductivity structures in a large area at low cost. However, the configuration of AEM measurements, which typically have widely distributed transmitter-receiver pairs, makes the rigorous modelling and interpretation extremely time-consuming in 3-D. Excessive overcomputing can occur when working on a large mesh covering the entire survey area and inverting all soundings in the data set. We propose two improvements. The first is to use a locally optimized mesh for each AEM sounding for the forward modelling and calculation of sensitivity. This dedicated local mesh is small with fine cells near the sounding location and coarse cells far away in accordance with EM diffusion and the geometric decay of the signals. Once the forward problem is solved on the local meshes, the sensitivity for the inversion on the global mesh is available through quick interpolation. Using local meshes for AEM forward modelling avoids unnecessary computing on fine cells on a global mesh that are far away from the sounding location. Since local meshes are highly independent, the forward modelling can be efficiently parallelized over an array of processors. The second improvement is random and dynamic down-sampling of the soundings. Each inversion iteration only uses a random subset of the soundings, and the subset is reselected for every iteration. The number of soundings in the random subset, determined by an adaptive algorithm, is tied to the degree of model regularization. This minimizes the overcomputing caused by working with redundant soundings. Our methods are compared against conventional methods and tested with a synthetic example. We also invert a field data set that was previously considered to be too large to be practically inverted in 3-D. These examples show that our methodology can dramatically reduce the processing time of 3-D inversion to a practical level without losing resolution
Dynamic Implicit 3D Adaptive Mesh Refinement for Non-Equilibrium Radiation Diffusion
Philip, Bobby; Wang, Zhen; Berrill, Mark A; Rodriguez Rodriguez, Manuel; Pernice, Michael
2014-01-01
The time dependent non-equilibrium radiation diffusion equations are important for solving the transport of energy through radiation in optically thick regimes and find applications in several fields including astrophysics and inertial confinement fusion. The associated initial boundary value problems that are encountered exhibit a wide range of scales in space and time and are extremely challenging to solve. To efficiently and accurately simulate these systems we describe our research on combining techniques that will also find use more broadly for long term time integration of nonlinear multiphysics systems: implicit time integration for efficient long term time integration of stiff multiphysics systems, local control theory based step size control to minimize the required global number of time steps while controlling accuracy, dynamic 3D adaptive mesh refinement (AMR) to minimize memory and computational costs, Jacobian Free Newton Krylov methods on AMR grids for efficient nonlinear solution, and optimal multilevel preconditioner components that provide level independent linear solver convergence.
NASA Astrophysics Data System (ADS)
Bajc, Iztok; Hecht, Frédéric; Žumer, Slobodan
2016-09-01
This paper presents a 3D mesh adaptivity strategy on unstructured tetrahedral meshes by a posteriori error estimates based on metrics derived from the Hessian of a solution. The study is made on the case of a nonlinear finite element minimization scheme for the Landau-de Gennes free energy functional of nematic liquid crystals. Newton's iteration for tensor fields is employed with steepest descent method possibly stepping in. Aspects relating the driving of mesh adaptivity within the nonlinear scheme are considered. The algorithmic performance is found to depend on at least two factors: when to trigger each single mesh adaptation, and the precision of the correlated remeshing. Each factor is represented by a parameter, with its values possibly varying for every new mesh adaptation. We empirically show that the time of the overall algorithm convergence can vary considerably when different sequences of parameters are used, thus posing a question about optimality. The extensive testings and debugging done within this work on the simulation of systems of nematic colloids substantially contributed to the upgrade of an open source finite element-oriented programming language to its 3D meshing possibilities, as also to an outer 3D remeshing module.
Dynamic implicit 3D adaptive mesh refinement for non-equilibrium radiation diffusion
B. Philip; Z. Wang; M.A. Berrill; M. Birke; M. Pernice
2014-04-01
The time dependent non-equilibrium radiation diffusion equations are important for solving the transport of energy through radiation in optically thick regimes and find applications in several fields including astrophysics and inertial confinement fusion. The associated initial boundary value problems that are encountered often exhibit a wide range of scales in space and time and are extremely challenging to solve. To efficiently and accurately simulate these systems we describe our research on combining techniques that will also find use more broadly for long term time integration of nonlinear multi-physics systems: implicit time integration for efficient long term time integration of stiff multi-physics systems, local control theory based step size control to minimize the required global number of time steps while controlling accuracy, dynamic 3D adaptive mesh refinement (AMR) to minimize memory and computational costs, Jacobian Free Newton–Krylov methods on AMR grids for efficient nonlinear solution, and optimal multilevel preconditioner components that provide level independent solver convergence.
A 3-D adaptive mesh refinement algorithm for multimaterial gas dynamics
Puckett, E.G. ); Saltzman, J.S. )
1991-08-12
Adaptive Mesh Refinement (AMR) in conjunction with high order upwind finite difference methods has been used effectively on a variety of problems. In this paper we discuss an implementation of an AMR finite difference method that solves the equations of gas dynamics with two material species in three dimensions. An equation for the evolution of volume fractions augments the gas dynamics system. The material interface is preserved and tracked from the volume fractions using a piecewise linear reconstruction technique. 14 refs., 4 figs.
3D Adaptive Mesh Refinement Simulations of Pellet Injection in Tokamaks
R. Samtaney; S.C. Jardin; P. Colella; D.F. Martin
2003-10-20
We present results of Adaptive Mesh Refinement (AMR) simulations of the pellet injection process, a proven method of refueling tokamaks. AMR is a computationally efficient way to provide the resolution required to simulate realistic pellet sizes relative to device dimensions. The mathematical model comprises of single-fluid MHD equations with source terms in the continuity equation along with a pellet ablation rate model. The numerical method developed is an explicit unsplit upwinding treatment of the 8-wave formulation, coupled with a MAC projection method to enforce the solenoidal property of the magnetic field. The Chombo framework is used for AMR. The role of the E x B drift in mass redistribution during inside and outside pellet injections is emphasized.
3D Boltzmann Simulation of the Io's Plasma Environment with Adaptive Mesh and Particle Refinement
NASA Astrophysics Data System (ADS)
Lipatov, A. S.; Combi, M. R.
2002-12-01
The global dynamics of the ionized and neutral components in the environment of Io plays an important role in the interaction of Jupiter's corotating magnetospheric plasma with Io [Combi et al., 2002; 1998; Kabin et al., 2001]. The stationary simulation of this problem was done in the MHD [Combi et al., 1998; Linker et al, 1998; Kabin et al., 2001] and the electrodynamic [Saur et al., 1999] approaches. In this report, we develop a method of kinetic ion-neutral simulation, which is based on a multiscale adaptive mesh, particle and algorithm refinement. This method employs the fluid description for electrons whereas for ions the drift-kinetic and particle approaches are used. This method takes into account charge-exchange and photoionization processes. The first results of such simulation of the dynamics of ions in the Io's environment are discussed in this report. ~ M R Combi et al., J. Geophys. Res., 103, 9071, 1998. M R Combi, T I Gombosi, K Kabin, Atmospheres in the Solar System: Comparative\\ Aeronomy. Geophys. Monograph Series, 130, 151, 2002. K Kabin et al., Planetary and Space Sci., 49, 337, 2001. J A Linker et al., J. Geophys. Res., 103(E9), 19867, 1998. J Saur et al., J. Geophys. Res., 104, 25105, 1999.
Vertical Scan (V-SCAN) for 3-D Grid Adaptive Mesh Refinement for an atmospheric Model Dynamical Core
NASA Astrophysics Data System (ADS)
Andronova, N. G.; Vandenberg, D.; Oehmke, R.; Stout, Q. F.; Penner, J. E.
2009-12-01
One of the major building blocks of a rigorous representation of cloud evolution in global atmospheric models is a parallel adaptive grid MPI-based communication library (an Adaptive Blocks for Locally Cartesian Topologies library -- ABLCarT), which manages the block-structured data layout, handles ghost cell updates among neighboring blocks and splits a block as refinements occur. The library has several modules that provide a layer of abstraction for adaptive refinement: blocks, which contain individual cells of user data; shells - the global geometry for the problem, including a sphere, reduced sphere, and now a 3D sphere; a load balancer for placement of blocks onto processors; and a communication support layer which encapsulates all data movement. A major performance concern with adaptive mesh refinement is how to represent calculations that have need to be sequenced in a particular order in a direction, such as calculating integrals along a specific path (e.g. atmospheric pressure or geopotential in the vertical dimension). This concern is compounded if the blocks have varying levels of refinement, or are scattered across different processors, as can be the case in parallel computing. In this paper we describe an implementation in ABLCarT of a vertical scan operation, which allows computing along vertical paths in the correct order across blocks transparent to their resolution and processor location. We test this functionality on a 2D and a 3D advection problem, which tests the performance of the model’s dynamics (transport) and physics (sources and sinks) for different model resolutions needed for inclusion of cloud formation.
3-D Mesh Generation Nonlinear Systems
1994-04-07
INGRID is a general-purpose, three-dimensional mesh generator developed for use with finite element, nonlinear, structural dynamics codes. INGRID generates the large and complex input data files for DYNA3D, NIKE3D, FACET, and TOPAZ3D. One of the greatest advantages of INGRID is that virtually any shape can be described without resorting to wedge elements, tetrahedrons, triangular elements or highly distorted quadrilateral or hexahedral elements. Other capabilities available are in the areas of geometry and graphics. Exact surfacemore » equations and surface intersections considerably improve the ability to deal with accurate models, and a hidden line graphics algorithm is included which is efficient on the most complicated meshes. The primary new capability is associated with the boundary conditions, loads, and material properties required by nonlinear mechanics programs. Commands have been designed for each case to minimize user effort. This is particularly important since special processing is almost always required for each load or boundary condition.« less
Improvements to the Unstructured Mesh Generator MESH3D
NASA Technical Reports Server (NTRS)
Thomas, Scott D.; Baker, Timothy J.; Cliff, Susan E.
1999-01-01
The AIRPLANE process starts with an aircraft geometry stored in a CAD system. The surface is modeled with a mesh of triangles and then the flow solver produces pressures at surface points which may be integrated to find forces and moments. The biggest advantage is that the grid generation bottleneck of the CFD process is eliminated when an unstructured tetrahedral mesh is used. MESH3D is the key to turning around the first analysis of a CAD geometry in days instead of weeks. The flow solver part of AIRPLANE has proven to be robust and accurate over a decade of use at NASA. It has been extensively validated with experimental data and compares well with other Euler flow solvers. AIRPLANE has been applied to all the HSR geometries treated at Ames over the course of the HSR program in order to verify the accuracy of other flow solvers. The unstructured approach makes handling complete and complex geometries very simple because only the surface of the aircraft needs to be discretized, i.e. covered with triangles. The volume mesh is created automatically by MESH3D. AIRPLANE runs well on multiple platforms. Vectorization on the Cray Y-MP is reasonable for a code that uses indirect addressing. Massively parallel computers such as the IBM SP2, SGI Origin 2000, and the Cray T3E have been used with an MPI version of the flow solver and the code scales very well on these systems. AIRPLANE can run on a desktop computer as well. AIRPLANE has a future. The unstructured technologies developed as part of the HSR program are now targeting high Reynolds number viscous flow simulation. The pacing item in this effort is Navier-Stokes mesh generation.
Cubit Adaptive Meshing Algorithm Library
2004-09-01
CAMAL (Cubit adaptive meshing algorithm library) is a software component library for mesh generation. CAMAL 2.0 includes components for triangle, quad and tetrahedral meshing. A simple Application Programmers Interface (API) takes a discrete boundary definition and CAMAL computes a quality interior unstructured grid. The triangle and quad algorithms may also import a geometric definition of a surface on which to define the grid. CAMALs triangle meshing uses a 3D space advancing front method, the quadmore » meshing algorithm is based upon Sandias patented paving algorithm and the tetrahedral meshing algorithm employs the GHS3D-Tetmesh component developed by INRIA, France.« less
An efficient and robust 3D mesh compression based on 3D watermarking and wavelet transform
NASA Astrophysics Data System (ADS)
Zagrouba, Ezzeddine; Ben Jabra, Saoussen; Didi, Yosra
2011-06-01
The compression and watermarking of 3D meshes are very important in many areas of activity including digital cinematography, virtual reality as well as CAD design. However, most studies on 3D watermarking and 3D compression are done independently. To verify a good trade-off between protection and a fast transfer of 3D meshes, this paper proposes a new approach which combines 3D mesh compression with mesh watermarking. This combination is based on a wavelet transformation. In fact, the used compression method is decomposed to two stages: geometric encoding and topologic encoding. The proposed approach consists to insert a signature between these two stages. First, the wavelet transformation is applied to the original mesh to obtain two components: wavelets coefficients and a coarse mesh. Then, the geometric encoding is done on these two components. The obtained coarse mesh will be marked using a robust mesh watermarking scheme. This insertion into coarse mesh allows obtaining high robustness to several attacks. Finally, the topologic encoding is applied to the marked coarse mesh to obtain the compressed mesh. The combination of compression and watermarking permits to detect the presence of signature after a compression of the marked mesh. In plus, it allows transferring protected 3D meshes with the minimum size. The experiments and evaluations show that the proposed approach presents efficient results in terms of compression gain, invisibility and robustness of the signature against of many attacks.
NASA Technical Reports Server (NTRS)
Banks, D. W.; Hafez, M. M.
1996-01-01
Grid adaptation for structured meshes is the art of using information from an existing, but poorly resolved, solution to automatically redistribute the grid points in such a way as to improve the resolution in regions of high error, and thus the quality of the solution. This involves: (1) generate a grid vis some standard algorithm, (2) calculate a solution on this grid, (3) adapt the grid to this solution, (4) recalculate the solution on this adapted grid, and (5) repeat steps 3 and 4 to satisfaction. Steps 3 and 4 can be repeated until some 'optimal' grid is converged to but typically this is not worth the effort and just two or three repeat calculations are necessary. They also may be repeated every 5-10 time steps for unsteady calculations.
Advanced numerical methods in mesh generation and mesh adaptation
Lipnikov, Konstantine; Danilov, A; Vassilevski, Y; Agonzal, A
2010-01-01
-based error estimates. We conclude that the quasi-optimal mesh must be quasi-uniform in this metric. All numerical experiments are based on the publicly available Ani3D package, the collection of advanced numerical instruments.
3-D UNSTRUCTURED HEXAHEDRAL-MESH Sn TRANSPORT METHODS
J. MOREL; J. MCGHEE; ET AL
2000-11-01
This is the final report of a three-year, Laboratory-Directed Research and Development (LDRD) project at the Los Alamos National Laboratory (LANL). We have developed a method for solving the neutral-particle transport equation on 3-D unstructured hexahedral meshes using a S{sub n} discretization in angle in conjunction with a discontinuous finite-element discretization in space and a multigroup discretization in energy. Previous methods for solving this equation in 3-D have been limited to rectangular meshes. The unstructured-mesh method that we have developed is far more efficient for solving problems with complex 3-D geometric features than rectangular-mesh methods. In spite of having to make several compromises in our spatial discretization technique and our iterative solution technique, our method has been found to be both accurate and efficient for a broad class of problems.
Unstructured mesh generation and adaptivity
NASA Technical Reports Server (NTRS)
Mavriplis, D. J.
1995-01-01
An overview of current unstructured mesh generation and adaptivity techniques is given. Basic building blocks taken from the field of computational geometry are first described. Various practical mesh generation techniques based on these algorithms are then constructed and illustrated with examples. Issues of adaptive meshing and stretched mesh generation for anisotropic problems are treated in subsequent sections. The presentation is organized in an education manner, for readers familiar with computational fluid dynamics, wishing to learn more about current unstructured mesh techniques.
Triangular framework mesh generation of 3D geological structure
NASA Astrophysics Data System (ADS)
Meng, Xianhai; Zhou, Kun; Li, Jigang; Yang, Qin
2013-03-01
The dynamic simulation of oil migration and accumulation is an important issue on the research of petroleum exploration, and it is a numerical simulation process with special requirement on the framework mesh of 3D geological models, which means that the mesh should have same geometry and topology relation near the intersected part of geological surfaces. In this paper, basing on the conforming Delaunay triangulation algorithm to construct mesh of individual geological stratum or fault, a novel link-Delaunay-triangulation method is presented to achieve the geometric and topological consistency in the intersected line between two surfaces, also with the analysis of termination of our algorithm. Finally, some examples of the geological framework mesh are provided and the experimental result proved that the algorithm's effectiveness in engineering practice.
Parallel Adaptive Mesh Refinement
Diachin, L; Hornung, R; Plassmann, P; WIssink, A
2005-03-04
As large-scale, parallel computers have become more widely available and numerical models and algorithms have advanced, the range of physical phenomena that can be simulated has expanded dramatically. Many important science and engineering problems exhibit solutions with localized behavior where highly-detailed salient features or large gradients appear in certain regions which are separated by much larger regions where the solution is smooth. Examples include chemically-reacting flows with radiative heat transfer, high Reynolds number flows interacting with solid objects, and combustion problems where the flame front is essentially a two-dimensional sheet occupying a small part of a three-dimensional domain. Modeling such problems numerically requires approximating the governing partial differential equations on a discrete domain, or grid. Grid spacing is an important factor in determining the accuracy and cost of a computation. A fine grid may be needed to resolve key local features while a much coarser grid may suffice elsewhere. Employing a fine grid everywhere may be inefficient at best and, at worst, may make an adequately resolved simulation impractical. Moreover, the location and resolution of fine grid required for an accurate solution is a dynamic property of a problem's transient features and may not be known a priori. Adaptive mesh refinement (AMR) is a technique that can be used with both structured and unstructured meshes to adjust local grid spacing dynamically to capture solution features with an appropriate degree of resolution. Thus, computational resources can be focused where and when they are needed most to efficiently achieve an accurate solution without incurring the cost of a globally-fine grid. Figure 1.1 shows two example computations using AMR; on the left is a structured mesh calculation of a impulsively-sheared contact surface and on the right is the fuselage and volume discretization of an RAH-66 Comanche helicopter [35]. Note the
Dynamic mesh adaption for triangular and tetrahedral grids
NASA Technical Reports Server (NTRS)
Biswas, Rupak; Strawn, Roger
1993-01-01
The following topics are discussed: requirements for dynamic mesh adaption; linked-list data structure; edge-based data structure; adaptive-grid data structure; three types of element subdivision; mesh refinement; mesh coarsening; additional constraints for coarsening; anisotropic error indicator for edges; unstructured-grid Euler solver; inviscid 3-D wing; and mesh quality for solution-adaptive grids. The discussion is presented in viewgraph form.
Mesh generation from 3D multi-material images.
Boltcheva, Dobrina; Yvinec, Mariette; Boissonnat, Jean-Daniel
2009-01-01
The problem of generating realistic computer models of objects represented by 3D segmented images is important in many biomedical applications. Labelled 3D images impose particular challenges for meshing algorithms because multi-material junctions form features such as surface pacthes, edges and corners which need to be preserved into the output mesh. In this paper, we propose a feature preserving Delaunay refinement algorithm which can be used to generate high-quality tetrahedral meshes from segmented images. The idea is to explicitly sample corners and edges from the input image and to constrain the Delaunay refinement algorithm to preserve these features in addition to the surface patches. Our experimental results on segmented medical images have shown that, within a few seconds, the algorithm outputs a tetrahedral mesh in which each material is represented as a consistent submesh without gaps and overlaps. The optimization property of the Delaunay triangulation makes these meshes suitable for the purpose of realistic visualization or finite element simulations. PMID:20426123
3D unstructured mesh discontinuous finite element hydro
Prasad, M.K.; Kershaw, D.S.; Shaw, M.J.
1995-07-01
The authors present detailed features of the ICF3D hydrodynamics code used for inertial fusion simulations. This code is intended to be a state-of-the-art upgrade of the well-known fluid code, LASNEX. ICF3D employs discontinuous finite elements on a discrete unstructured mesh consisting of a variety of 3D polyhedra including tetrahedra, prisms, and hexahedra. The authors discussed details of how the ROE-averaged second-order convection was applied on the discrete elements, and how the C++ coding interface has helped to simplify implementing the many physics and numerics modules within the code package. The author emphasized the virtues of object-oriented design in large scale projects such as ICF3D.
Conservative Patch Algorithm and Mesh Sequencing for PAB3D
NASA Technical Reports Server (NTRS)
Pao, S. P.; Abdol-Hamid, K. S.
2005-01-01
A mesh-sequencing algorithm and a conservative patched-grid-interface algorithm (hereafter Patch Algorithm ) have been incorporated into the PAB3D code, which is a computer program that solves the Navier-Stokes equations for the simulation of subsonic, transonic, or supersonic flows surrounding an aircraft or other complex aerodynamic shapes. These algorithms are efficient, flexible, and have added tremendously to the capabilities of PAB3D. The mesh-sequencing algorithm makes it possible to perform preliminary computations using only a fraction of the grid cells (provided the original cell count is divisible by an integer) along any grid coordinate axis, independently of the other axes. The patch algorithm addresses another critical need in multi-block grid situation where the cell faces of adjacent grid blocks may not coincide, leading to errors in calculating fluxes of conserved physical quantities across interfaces between the blocks. The patch algorithm, based on the Stokes integral formulation of the applicable conservation laws, effectively matches each of the interfacial cells on one side of the block interface to the corresponding fractional cell area pieces on the other side. This approach is comprehensive and unified such that all interface topology is automatically processed without user intervention. This algorithm is implemented in a preprocessing code that creates a cell-by-cell database that will maintain flux conservation at any level of full or reduced grid density as the user may choose by way of the mesh-sequencing algorithm. These two algorithms have enhanced the numerical accuracy of the code, reduced the time and effort for grid preprocessing, and provided users with the flexibility of performing computations at any desired full or reduced grid resolution to suit their specific computational requirements.
Parallel Adaptive Mesh Refinement Library
NASA Technical Reports Server (NTRS)
Mac-Neice, Peter; Olson, Kevin
2005-01-01
Parallel Adaptive Mesh Refinement Library (PARAMESH) is a package of Fortran 90 subroutines designed to provide a computer programmer with an easy route to extension of (1) a previously written serial code that uses a logically Cartesian structured mesh into (2) a parallel code with adaptive mesh refinement (AMR). Alternatively, in its simplest use, and with minimal effort, PARAMESH can operate as a domain-decomposition tool for users who want to parallelize their serial codes but who do not wish to utilize adaptivity. The package builds a hierarchy of sub-grids to cover the computational domain of a given application program, with spatial resolution varying to satisfy the demands of the application. The sub-grid blocks form the nodes of a tree data structure (a quad-tree in two or an oct-tree in three dimensions). Each grid block has a logically Cartesian mesh. The package supports one-, two- and three-dimensional models.
Adaptive and Unstructured Mesh Cleaving
Bronson, Jonathan R.; Sastry, Shankar P.; Levine, Joshua A.; Whitaker, Ross T.
2015-01-01
We propose a new strategy for boundary conforming meshing that decouples the problem of building tetrahedra of proper size and shape from the problem of conforming to complex, non-manifold boundaries. This approach is motivated by the observation that while several methods exist for adaptive tetrahedral meshing, they typically have difficulty at geometric boundaries. The proposed strategy avoids this conflict by extracting the boundary conforming constraint into a secondary step. We first build a background mesh having a desired set of tetrahedral properties, and then use a generalized stenciling method to divide, or “cleave”, these elements to get a set of conforming tetrahedra, while limiting the impacts cleaving has on element quality. In developing this new framework, we make several technical contributions including a new method for building graded tetrahedral meshes as well as a generalization of the isosurface stuffing and lattice cleaving algorithms to unstructured background meshes. PMID:26137171
NASA Astrophysics Data System (ADS)
Ha, Manh Hung; Cauvin, Ludovic; Rassineux, Alain
2016-04-01
We present a new numerical methodology to build a Representative Volume Element (RVE) of a wide range of 3D woven composites in order to determine the mechanical behavior of the fabric unit cell by a mesoscopic approach based on a 3D finite element analysis. Emphasis is put on the numerous difficulties of creating a mesh of these highly complex weaves embedded in a resin. A conforming mesh at the numerous interfaces between yarns is created by a multi-quadtree adaptation technique, which makes it possible thereafter to build an unstructured 3D mesh of the resin with tetrahedral elements. The technique is not linked with any specific tool, but can be carried out with the use of any 2D and 3D robust mesh generators.
3D meshes of carbon nanotubes guide functional reconnection of segregated spinal explants.
Usmani, Sadaf; Aurand, Emily Rose; Medelin, Manuela; Fabbro, Alessandra; Scaini, Denis; Laishram, Jummi; Rosselli, Federica B; Ansuini, Alessio; Zoccolan, Davide; Scarselli, Manuela; De Crescenzi, Maurizio; Bosi, Susanna; Prato, Maurizio; Ballerini, Laura
2016-07-01
In modern neuroscience, significant progress in developing structural scaffolds integrated with the brain is provided by the increasing use of nanomaterials. We show that a multiwalled carbon nanotube self-standing framework, consisting of a three-dimensional (3D) mesh of interconnected, conductive, pure carbon nanotubes, can guide the formation of neural webs in vitro where the spontaneous regrowth of neurite bundles is molded into a dense random net. This morphology of the fiber regrowth shaped by the 3D structure supports the successful reconnection of segregated spinal cord segments. We further observed in vivo the adaptability of these 3D devices in a healthy physiological environment. Our study shows that 3D artificial scaffolds may drive local rewiring in vitro and hold great potential for the development of future in vivo interfaces. PMID:27453939
3D meshes of carbon nanotubes guide functional reconnection of segregated spinal explants
Usmani, Sadaf; Aurand, Emily Rose; Medelin, Manuela; Fabbro, Alessandra; Scaini, Denis; Laishram, Jummi; Rosselli, Federica B.; Ansuini, Alessio; Zoccolan, Davide; Scarselli, Manuela; De Crescenzi, Maurizio; Bosi, Susanna; Prato, Maurizio; Ballerini, Laura
2016-01-01
In modern neuroscience, significant progress in developing structural scaffolds integrated with the brain is provided by the increasing use of nanomaterials. We show that a multiwalled carbon nanotube self-standing framework, consisting of a three-dimensional (3D) mesh of interconnected, conductive, pure carbon nanotubes, can guide the formation of neural webs in vitro where the spontaneous regrowth of neurite bundles is molded into a dense random net. This morphology of the fiber regrowth shaped by the 3D structure supports the successful reconnection of segregated spinal cord segments. We further observed in vivo the adaptability of these 3D devices in a healthy physiological environment. Our study shows that 3D artificial scaffolds may drive local rewiring in vitro and hold great potential for the development of future in vivo interfaces. PMID:27453939
Adaptive Mesh Refinement in CTH
Crawford, David
1999-05-04
This paper reports progress on implementing a new capability of adaptive mesh refinement into the Eulerian multimaterial shock- physics code CTH. The adaptivity is block-based with refinement and unrefinement occurring in an isotropic 2:1 manner. The code is designed to run on serial, multiprocessor and massive parallel platforms. An approximate factor of three in memory and performance improvements over comparable resolution non-adaptive calculations has-been demonstrated for a number of problems.
Adaptive triangular mesh generation
NASA Technical Reports Server (NTRS)
Erlebacher, G.; Eiseman, P. R.
1984-01-01
A general adaptive grid algorithm is developed on triangular grids. The adaptivity is provided by a combination of node addition, dynamic node connectivity and a simple node movement strategy. While the local restructuring process and the node addition mechanism take place in the physical plane, the nodes are displaced on a monitor surface, constructed from the salient features of the physical problem. An approximation to mean curvature detects changes in the direction of the monitor surface, and provides the pulling force on the nodes. Solutions to the axisymmetric Grad-Shafranov equation demonstrate the capturing, by triangles, of the plasma-vacuum interface in a free-boundary equilibrium configuration.
3D Mesh optimization methods for unstructured polyhedra: A progress report
Miller, D.S.; Burton, D.E.
1994-11-22
A mesh optimization scheme allows a Lagrangian code to run problems with extreme mesh distortion by reconfiguring node and zone connectivity as the problem evolves. We have developed some 3D mesh optimization operations and criteria for applying them. These are demonstrated in a 3D Free Lagrange code being developed at LLNL. In the simplest case of a mesh or mesh subregion composed purely of tetrahedra we can maintain a Delaunay tetrahedralization. For more interesting meshes, made up of general polyhedra, a suite of optimization operations and their respective application criteria have been developed.
Issues in adaptive mesh refinement
Dai, William Wenlong
2009-01-01
In this paper, we present an approach for a patch-based adaptive mesh refinement (AMR) for multi-physics simulations. The approach consists of clustering, symmetry preserving, mesh continuity, flux correction, communications, and management of patches. Among the special features of this patch-based AMR are symmetry preserving, efficiency of refinement, special implementation offlux correction, and patch management in parallel computing environments. Here, higher efficiency of refinement means less unnecessarily refined cells for a given set of cells to be refined. To demonstrate the capability of the AMR framework, hydrodynamics simulations with many levels of refinement are shown in both two- and three-dimensions.
LayTracks3D: A new approach for meshing general solids using medial axis transform
Quadros, William Roshan
2015-08-22
This study presents an extension of the all-quad meshing algorithm called LayTracks to generate high quality hex-dominant meshes of general solids. LayTracks3D uses the mapping between the Medial Axis (MA) and the boundary of the 3D domain to decompose complex 3D domains into simpler domains called Tracks. Tracks in 3D have no branches and are symmetric, non-intersecting, orthogonal to the boundary, and the shortest path from the MA to the boundary. These properties of tracks result in desired meshes with near cube shape elements at the boundary, structured mesh along the boundary normal with any irregular nodes restricted to the MA, and sharp boundary feature preservation. The algorithm has been tested on a few industrial CAD models and hex-dominant meshes are shown in the Results section. Work is underway to extend LayTracks3D to generate all-hex meshes.
DISCO: 3-D moving-mesh magnetohydrodynamics package
NASA Astrophysics Data System (ADS)
Duffell, Paul C.
2016-05-01
DISCO evolves orbital fluid motion in two and three dimensions, especially at high Mach number, for studying astrophysical disks. The software uses a moving-mesh approach with a dynamic cylindrical mesh that can shear azimuthally to follow the orbital motion of the gas, thus removing diffusive advection errors and permitting longer timesteps than a static grid. DISCO uses an HLLD Riemann solver and a constrained transport scheme compatible with the mesh motion to implement magnetohydrodynamics.
Adaptive Skin Meshes Coarsening for Biomolecular Simulation.
Shi, Xinwei; Koehl, Patrice
2011-06-01
In this paper, we present efficient algorithms for generating hierarchical molecular skin meshes with decreasing size and guaranteed quality. Our algorithms generate a sequence of coarse meshes for both the surfaces and the bounded volumes. Each coarser surface mesh is adaptive to the surface curvature and maintains the topology of the skin surface with guaranteed mesh quality. The corresponding tetrahedral mesh is conforming to the interface surface mesh and contains high quality tetrahedral that decompose both the interior of the molecule and the surrounding region (enclosed in a sphere). Our hierarchical tetrahedral meshes have a number of advantages that will facilitate fast and accurate multigrid PDE solvers. Firstly, the quality of both the surface triangulations and tetrahedral meshes is guaranteed. Secondly, the interface in the tetrahedral mesh is an accurate approximation of the molecular boundary. In particular, all the boundary points lie on the skin surface. Thirdly, our meshes are Delaunay meshes. Finally, the meshes are adaptive to the geometry. PMID:21779137
Adaptive Skin Meshes Coarsening for Biomolecular Simulation
Shi, Xinwei; Koehl, Patrice
2011-01-01
In this paper, we present efficient algorithms for generating hierarchical molecular skin meshes with decreasing size and guaranteed quality. Our algorithms generate a sequence of coarse meshes for both the surfaces and the bounded volumes. Each coarser surface mesh is adaptive to the surface curvature and maintains the topology of the skin surface with guaranteed mesh quality. The corresponding tetrahedral mesh is conforming to the interface surface mesh and contains high quality tetrahedral that decompose both the interior of the molecule and the surrounding region (enclosed in a sphere). Our hierarchical tetrahedral meshes have a number of advantages that will facilitate fast and accurate multigrid PDE solvers. Firstly, the quality of both the surface triangulations and tetrahedral meshes is guaranteed. Secondly, the interface in the tetrahedral mesh is an accurate approximation of the molecular boundary. In particular, all the boundary points lie on the skin surface. Thirdly, our meshes are Delaunay meshes. Finally, the meshes are adaptive to the geometry. PMID:21779137
A hierarchical structure for automatic meshing and adaptive FEM analysis
NASA Technical Reports Server (NTRS)
Kela, Ajay; Saxena, Mukul; Perucchio, Renato
1987-01-01
A new algorithm for generating automatically, from solid models of mechanical parts, finite element meshes that are organized as spatially addressable quaternary trees (for 2-D work) or octal trees (for 3-D work) is discussed. Because such meshes are inherently hierarchical as well as spatially addressable, they permit efficient substructuring techniques to be used for both global analysis and incremental remeshing and reanalysis. The global and incremental techniques are summarized and some results from an experimental closed loop 2-D system in which meshing, analysis, error evaluation, and remeshing and reanalysis are done automatically and adaptively are presented. The implementation of 3-D work is briefly discussed.
A Software System for Filling Complex Holes in 3D Meshes by Flexible Interacting Particles
NASA Astrophysics Data System (ADS)
Yamazaki, Daisuke; Savchenko, Vladimir
3D meshes generated by acquisition devices such as laser range scanners often contain holes due to occlusion, etc. In practice, these holes are extremely geometrically and topologically complex. We propose a heuristic hole filling technique using particle systems to fill complex holes with arbitrary topology in 3D meshes. Our approach includes the following steps: hole identification, base surface creation, particle distribution, triangulation, and mesh refinement. We demonstrate the functionality of the proposed surface retouching system on synthetic and real data.
Hex-dominant mesh generation using 3D constrained triangulation
OWEN,STEVEN J.
2000-05-30
A method for decomposing a volume with a prescribed quadrilateral surface mesh, into a hexahedral-dominated mesh is proposed. With this method, known as Hex-Morphing (H-Morph), an initial tetrahedral mesh is provided. Tetrahedral are transformed and combined starting from the boundary and working towards the interior of the volume. The quadrilateral faces of the hexahedra are treated as internal surfaces, which can be recovered using constrained triangulation techniques. Implementation details of the edge and face recovery process are included. Examples and performance of the H-Morph algorithm are also presented.
Shape design sensitivities using fully automatic 3-D mesh generation
NASA Technical Reports Server (NTRS)
Botkin, M. E.
1990-01-01
Previous work in three dimensional shape optimization involved specifying design variables by associating parameters directly with mesh points. More recent work has shown the use of fully-automatic mesh generation based upon a parameterized geometric representation. Design variables have been associated with a mathematical model of the part rather than the discretized representation. The mesh generation procedure uses a nonuniform grid intersection technique to place nodal points directly on the surface geometry. Although there exists an associativity between the mesh and the geometrical/topological entities, there is no mathematical functional relationship. This poses a problem during certain steps in the optimization process in which geometry modification is required. For the large geometrical changes which occur at the beginning of each optimization step, a completely new mesh is created. However, for gradient calculations many small changes must be made and it would be too costly to regenerate the mesh for each design variable perturbation. For that reason, a local remeshing procedure has been implemented which operates only on the specific edges and faces associated with the design variable being perturbed. Two realistic design problems are presented which show the efficiency of this process and test the accuracy of the gradient computations.
Feature edge extraction from 3D triangular meshes using a thinning algorithm
NASA Astrophysics Data System (ADS)
Nomura, Masaru; Hamada, Nozomu
2001-11-01
Highly detailed geometric models, which are represented as dense triangular meshes are becoming popular in computer graphics. Since such 3D meshes often have huge information, we require some methods to treat them efficiently in the 3D mesh processing such as, surface simplification, subdivision surface, curved surface approximation and morphing. In these applications, we often extract features of 3D meshes such as feature vertices and feature edges in preprocessing step. An automatic extraction method of feature edges is treated in this study. In order to realize the feature edge extraction method, we first introduce the concavity and convexity evaluation value. Then the histogram of the concavity and convexity evaluation value is used to separate the feature edge region. We apply a thinning algorithm, which is used in 2D binary image processing. It is shown that the proposed method can extract appropriate feature edges from 3D meshes.
A preliminary evaluation of 3D mesh animation coding techniques
NASA Astrophysics Data System (ADS)
Mamou, Khaled; Zaharia, Titus; Preteux, Francoise
2005-08-01
This paper provides an overview of the state-of-the-art techniques recently developed within the emerging field of dynamic mesh compression. Static encoders, wavelet-based schemes, PCA-based approaches, differential temporal and spatio-temporal predictive techniques, and clustering-based representations are considered, presented, analyzed, and objectively compared in terms of compression efficiency, algorithmic and computational aspects and offered functionalities (such as progressive transmission, scalable rendering, computational and algorithmic aspects, field of applicability...). The proposed comparative study reveals that: (1) clustering-based approaches offer the best compromise between compression performances and computational complexity; (2) PCA-based representations are highly efficient on long animated sequences (i.e. with number of mesh vertices much smaller than the number of frames) at the price of prohibitive computational complexity of the encoding process; (3) Spatio-temporal Dynapack predictors provides simple yet effective predictive schemes that outperforms simple predictors such as those considered within the interpolator compression node adopted by the MPEG-4 within the AFX standard; (4) Wavelet-based approaches, which provide the best compression performances for static meshes show here again good results, with the additional advantage of a fully progressive representation, but suffer from an applicability limited to large meshes with at least several thousands of vertices per connected component.
3D unstructured-mesh radiation transport codes
Morel, J.
1997-12-31
Three unstructured-mesh radiation transport codes are currently being developed at Los Alamos National Laboratory. The first code is ATTILA, which uses an unstructured tetrahedral mesh in conjunction with standard Sn (discrete-ordinates) angular discretization, standard multigroup energy discretization, and linear-discontinuous spatial differencing. ATTILA solves the standard first-order form of the transport equation using source iteration in conjunction with diffusion-synthetic acceleration of the within-group source iterations. DANTE is designed to run primarily on workstations. The second code is DANTE, which uses a hybrid finite-element mesh consisting of arbitrary combinations of hexahedra, wedges, pyramids, and tetrahedra. DANTE solves several second-order self-adjoint forms of the transport equation including the even-parity equation, the odd-parity equation, and a new equation called the self-adjoint angular flux equation. DANTE also offers three angular discretization options: $S{_}n$ (discrete-ordinates), $P{_}n$ (spherical harmonics), and $SP{_}n$ (simplified spherical harmonics). DANTE is designed to run primarily on massively parallel message-passing machines, such as the ASCI-Blue machines at LANL and LLNL. The third code is PERICLES, which uses the same hybrid finite-element mesh as DANTE, but solves the standard first-order form of the transport equation rather than a second-order self-adjoint form. DANTE uses a standard $S{_}n$ discretization in angle in conjunction with trilinear-discontinuous spatial differencing, and diffusion-synthetic acceleration of the within-group source iterations. PERICLES was initially designed to run on workstations, but a version for massively parallel message-passing machines will be built. The three codes will be described in detail and computational results will be presented.
Isoparametric 3-D Finite Element Mesh Generation Using Interactive Computer Graphics
NASA Technical Reports Server (NTRS)
Kayrak, C.; Ozsoy, T.
1985-01-01
An isoparametric 3-D finite element mesh generator was developed with direct interface to an interactive geometric modeler program called POLYGON. POLYGON defines the model geometry in terms of boundaries and mesh regions for the mesh generator. The mesh generator controls the mesh flow through the 2-dimensional spans of regions by using the topological data and defines the connectivity between regions. The program is menu driven and the user has a control of element density and biasing through the spans and can also apply boundary conditions, loads interactively.
Graphical postprocessing for 3-D mesh quality evaluation
NASA Technical Reports Server (NTRS)
Panthaki, M. J.; Abel, J. F.; Wawrzynek, P. A.
1989-01-01
An important objective of three-dimensional graphical finite-element postprocessing is to indicate to the engineer the accuracy of analysis results. The inclusion of mesh quality sensors permits a subjective evaluation of the adequacy of a single analysis being interpreted. For graphical approaches, both strain-energy-density gradients and discontinuities of unsmoothed responses and their gradients have proved to be effective sensors. Interactive graphical tools which can display discontinuity information effectively are described; these are essentially different from the ordinary methods used for the viewing of smoothed results.
Parallel automated adaptive procedures for unstructured meshes
NASA Technical Reports Server (NTRS)
Shephard, M. S.; Flaherty, J. E.; Decougny, H. L.; Ozturan, C.; Bottasso, C. L.; Beall, M. W.
1995-01-01
Consideration is given to the techniques required to support adaptive analysis of automatically generated unstructured meshes on distributed memory MIMD parallel computers. The key areas of new development are focused on the support of effective parallel computations when the structure of the numerical discretization, the mesh, is evolving, and in fact constructed, during the computation. All the procedures presented operate in parallel on already distributed mesh information. Starting from a mesh definition in terms of a topological hierarchy, techniques to support the distribution, redistribution and communication among the mesh entities over the processors is given, and algorithms to dynamically balance processor workload based on the migration of mesh entities are given. A procedure to automatically generate meshes in parallel, starting from CAD geometric models, is given. Parallel procedures to enrich the mesh through local mesh modifications are also given. Finally, the combination of these techniques to produce a parallel automated finite element analysis procedure for rotorcraft aerodynamics calculations is discussed and demonstrated.
Adaptive mesh refinement in titanium
Colella, Phillip; Wen, Tong
2005-01-21
In this paper, we evaluate Titanium's usability as a high-level parallel programming language through a case study, where we implement a subset of Chombo's functionality in Titanium. Chombo is a software package applying the Adaptive Mesh Refinement methodology to numerical Partial Differential Equations at the production level. In Chombo, the library approach is used to parallel programming (C++ and Fortran, with MPI), whereas Titanium is a Java dialect designed for high-performance scientific computing. The performance of our implementation is studied and compared with that of Chombo in solving Poisson's equation based on two grid configurations from a real application. Also provided are the counts of lines of code from both sides.
LayTracks3D: A new approach for meshing general solids using medial axis transform
Quadros, William Roshan
2015-08-22
This study presents an extension of the all-quad meshing algorithm called LayTracks to generate high quality hex-dominant meshes of general solids. LayTracks3D uses the mapping between the Medial Axis (MA) and the boundary of the 3D domain to decompose complex 3D domains into simpler domains called Tracks. Tracks in 3D have no branches and are symmetric, non-intersecting, orthogonal to the boundary, and the shortest path from the MA to the boundary. These properties of tracks result in desired meshes with near cube shape elements at the boundary, structured mesh along the boundary normal with any irregular nodes restricted to themore » MA, and sharp boundary feature preservation. The algorithm has been tested on a few industrial CAD models and hex-dominant meshes are shown in the Results section. Work is underway to extend LayTracks3D to generate all-hex meshes.« less
Auto-adaptive finite element meshes
NASA Technical Reports Server (NTRS)
Richter, Roland; Leyland, Penelope
1995-01-01
Accurate capturing of discontinuities within compressible flow computations is achieved by coupling a suitable solver with an automatic adaptive mesh algorithm for unstructured triangular meshes. The mesh adaptation procedures developed rely on non-hierarchical dynamical local refinement/derefinement techniques, which hence enable structural optimization as well as geometrical optimization. The methods described are applied for a number of the ICASE test cases are particularly interesting for unsteady flow simulations.
Parallel tetrahedral mesh adaptation with dynamic load balancing
Oliker, Leonid; Biswas, Rupak; Gabow, Harold N.
2000-06-28
The ability to dynamically adapt an unstructured grid is a powerful tool for efficiently solving computational problems with evolving physical features. In this paper, we report on our experience parallelizing an edge-based adaptation scheme, called 3D-TAG, using message passing. Results show excellent speedup when a realistic helicopter rotor mesh is randomly refined. However, performance deteriorates when the mesh is refined using a solution-based error indicator since mesh adaptation for practical problems occurs in a localized region, creating a severe load imbalance. To address this problem, we have developed PLUM, a global dynamic load balancing framework for adaptive numerical computations. Even though PLUM primarily balances processor workloads for the solution phase, it reduces the load imbalance problem within mesh adaptation by repartitioning the mesh after targeting edges for refinement but before the actual subdivision. This dramatically improves the performance of parallel 3D-TAG since refinement occurs in a more load balanced fashion. We also present optimal and heuristic algorithms that, when applied to the default mapping of a parallel repartitioner, significantly reduce the data redistribution overhead. Finally, portability is examined by comparing performance on three state-of-the-art parallel machines.
Parallel Tetrahedral Mesh Adaptation with Dynamic Load Balancing
NASA Technical Reports Server (NTRS)
Oliker, Leonid; Biswas, Rupak; Gabow, Harold N.
1999-01-01
The ability to dynamically adapt an unstructured grid is a powerful tool for efficiently solving computational problems with evolving physical features. In this paper, we report on our experience parallelizing an edge-based adaptation scheme, called 3D_TAG. using message passing. Results show excellent speedup when a realistic helicopter rotor mesh is randomly refined. However. performance deteriorates when the mesh is refined using a solution-based error indicator since mesh adaptation for practical problems occurs in a localized region., creating a severe load imbalance. To address this problem, we have developed PLUM, a global dynamic load balancing framework for adaptive numerical computations. Even though PLUM primarily balances processor workloads for the solution phase, it reduces the load imbalance problem within mesh adaptation by repartitioning the mesh after targeting edges for refinement but before the actual subdivision. This dramatically improves the performance of parallel 3D_TAG since refinement occurs in a more load balanced fashion. We also present optimal and heuristic algorithms that, when applied to the default mapping of a parallel repartitioner, significantly reduce the data redistribution overhead. Finally, portability is examined by comparing performance on three state-of-the-art parallel machines.
PARAMESH V4.1: Parallel Adaptive Mesh Refinement
NASA Astrophysics Data System (ADS)
MacNeice, Peter; Olson, Kevin M.; Mobarry, Clark; de Fainchtein, Rosalinda; Packer, Charles
2011-06-01
PARAMESH is a package of Fortran 90 subroutines designed to provide an application developer with an easy route to extend an existing serial code which uses a logically cartesian structured mesh into a parallel code with adaptive mesh refinement (AMR). Alternatively, in its simplest use, and with minimal effort, it can operate as a domain decomposition tool for users who want to parallelize their serial codes, but who do not wish to use adaptivity. The package builds a hierarchy of sub-grids to cover the computational domain, with spatial resolution varying to satisfy the demands of the application. These sub-grid blocks form the nodes of a tree data-structure (quad-tree in 2D or oct-tree in 3D). Each grid block has a logically cartesian mesh. The package supports 1, 2 and 3D models. PARAMESH is released under the NASA-wide Open-Source software license.
Floating shock fitting via Lagrangian adaptive meshes
NASA Technical Reports Server (NTRS)
Vanrosendale, John
1995-01-01
In recent work we have formulated a new approach to compressible flow simulation, combining the advantages of shock-fitting and shock-capturing. Using a cell-centered on Roe scheme discretization on unstructured meshes, we warp the mesh while marching to steady state, so that mesh edges align with shocks and other discontinuities. This new algorithm, the Shock-fitting Lagrangian Adaptive Method (SLAM), is, in effect, a reliable shock-capturing algorithm which yields shock-fitted accuracy at convergence.
Comprehensive study of numerical anisotropy and dispersion in 3-D TLM meshes
NASA Astrophysics Data System (ADS)
Berini, Pierre; Wu, Ke
1995-05-01
This paper presents a comprehensive analysis of the numerical anisotropy and dispersion of 3-D TLM meshes constructed using several generalized symmetrical condensed TLM nodes. The dispersion analysis is performed in isotropic lossless, isotropic lossy and anisotropic lossless media and yields a comparison of the simulation accuracy for the different TLM nodes. The effect of mesh grading on the numerical dispersion is also determined. The results compare meshes constructed with Johns' symmetrical condensed node (SCN), two hybrid symmetrical condensed nodes (HSCN) and two frequency domain symmetrical condensed nodes (FDSCN). It has been found that under certain circumstances, the time domain nodes may introduce numerical anisotropy when modelling isotropic media.
Novel irregular mesh tagging algorithm for wound synthesis on a 3D face.
Lee, Sangyong; Chin, Seongah
2015-01-01
Recently, advanced visualizing techniques in computer graphics have considerably enhanced the visual appearance of synthetic models. To realize enhanced visual graphics for synthetic medical effects, the first step followed by rendering techniques involves attaching albedo textures to the region where a certain graphic is to be rendered. For instance, in order to render wound textures efficiently, the first step is to recognize the area where the user wants to attach a wound. However, in general, face indices are not stored in sequential order, which makes sub-texturing difficult. In this paper, we present a novel mesh tagging algorithm that utilizes a task for mesh traversals and level extension in the general case of a wound sub-texture mapping and a selected region deformation in a three-dimensional (3D) model. This method works automatically on both regular and irregular mesh surfaces. The approach consists of mesh selection (MS), mesh leveling (ML), and mesh tagging (MT). To validate our approach, we performed experiments for synthesizing wounds on a 3D face model and on a simulated mesh. PMID:26405904
Parallel Adaptive Computation of Blood Flow in a 3D ``Whole'' Body Model
NASA Astrophysics Data System (ADS)
Zhou, M.; Figueroa, C. A.; Taylor, C. A.; Sahni, O.; Jansen, K. E.
2008-11-01
Accurate numerical simulations of vascular trauma require the consideration of a larger portion of the vasculature than previously considered, due to the systemic nature of the human body's response. A patient-specific 3D model composed of 78 connected arterial branches extending from the neck to the lower legs is constructed to effectively represent the entire body. Recently developed outflow boundary conditions that appropriately represent the downstream vasculature bed which is not included in the 3D computational domain are applied at 78 outlets. In this work, the pulsatile blood flow simulations are started on a fairly uniform, unstructured mesh that is subsequently adapted using a solution-based approach to efficiently resolve the flow features. The adapted mesh contains non-uniform, anisotropic elements resulting in resolution that conforms with the physical length scales present in the problem. The effects of the mesh resolution on the flow field are studied, specifically on relevant quantities of pressure, velocity and wall shear stress.
Hybrid Surface Mesh Adaptation for Climate Modeling
Khamayseh, Ahmed K; de Almeida, Valmor F; Hansen, Glen
2008-01-01
Solution-driven mesh adaptation is becoming quite popular for spatial error control in the numerical simulation of complex computational physics applications, such as climate modeling. Typically, spatial adaptation is achieved by element subdivision (h adaptation) with a primary goal of resolving the local length scales of interest. A second, less-popular method of spatial adaptivity is called "mesh motion" (r adaptation); the smooth repositioning of mesh node points aimed at resizing existing elements to capture the local length scales. This paper proposes an adaptation method based on a combination of both element subdivision and node point repositioning (rh adaptation). By combining these two methods using the notion of a mobility function, the proposed approach seeks to increase the flexibility and extensibility of mesh motion algorithms while providing a somewhat smoother transition between refined regions than is produced by element subdivision alone. Further, in an attempt to support the requirements of a very general class of climate simulation applications, the proposed method is designed to accommodate unstructured, polygonal mesh topologies in addition to the most popular mesh types.
Hybrid Surface Mesh Adaptation for Climate Modeling
Ahmed Khamayseh; Valmor de Almeida; Glen Hansen
2008-10-01
Solution-driven mesh adaptation is becoming quite popular for spatial error control in the numerical simulation of complex computational physics applications, such as climate modeling. Typically, spatial adaptation is achieved by element subdivision (h adaptation) with a primary goal of resolving the local length scales of interest. A second, less-popular method of spatial adaptivity is called “mesh motion” (r adaptation); the smooth repositioning of mesh node points aimed at resizing existing elements to capture the local length scales. This paper proposes an adaptation method based on a combination of both element subdivision and node point repositioning (rh adaptation). By combining these two methods using the notion of a mobility function, the proposed approach seeks to increase the flexibility and extensibility of mesh motion algorithms while providing a somewhat smoother transition between refined regions than is produced by element subdivision alone. Further, in an attempt to support the requirements of a very general class of climate simulation applications, the proposed method is designed to accommodate unstructured, polygonal mesh topologies in addition to the most popular mesh types.
A structured multi-block solution-adaptive mesh algorithm with mesh quality assessment
NASA Technical Reports Server (NTRS)
Ingram, Clint L.; Laflin, Kelly R.; Mcrae, D. Scott
1995-01-01
The dynamic solution adaptive grid algorithm, DSAGA3D, is extended to automatically adapt 2-D structured multi-block grids, including adaption of the block boundaries. The extension is general, requiring only input data concerning block structure, connectivity, and boundary conditions. Imbedded grid singular points are permitted, but must be prevented from moving in space. Solutions for workshop cases 1 and 2 are obtained on multi-block grids and illustrate both increased resolution of and alignment with the solution. A mesh quality assessment criteria is proposed to determine how well a given mesh resolves and aligns with the solution obtained upon it. The criteria is used to evaluate the grid quality for solutions of workshop case 6 obtained on both static and dynamically adapted grids. The results indicate that this criteria shows promise as a means of evaluating resolution.
Arbitrary Lagrangian Eulerian Adaptive Mesh Refinement
Koniges, A.; Eder, D.; Masters, N.; Fisher, A.; Anderson, R.; Gunney, B.; Wang, P.; Benson, D.; Dixit, P.
2009-09-29
This is a simulation code involving an ALE (arbitrary Lagrangian-Eulerian) hydrocode with AMR (adaptive mesh refinement) and pluggable physics packages for material strength, heat conduction, radiation diffusion, and laser ray tracing developed a LLNL, UCSD, and Berkeley Lab. The code is an extension of the open source SAMRAI (Structured Adaptive Mesh Refinement Application Interface) code/library. The code can be used in laser facilities such as the National Ignition Facility. The code is alsi being applied to slurry flow (landslides).
An Automatic 3D Mesh Generation Method for Domains with Multiple Materials.
Zhang, Yongjie; Hughes, Thomas J R; Bajaj, Chandrajit L
2010-01-01
This paper describes an automatic and efficient approach to construct unstructured tetrahedral and hexahedral meshes for a composite domain made up of heterogeneous materials. The boundaries of these material regions form non-manifold surfaces. In earlier papers, we developed an octree-based isocontouring method to construct unstructured 3D meshes for a single-material (homogeneous) domain with manifold boundary. In this paper, we introduce the notion of a material change edge and use it to identify the interface between two or several different materials. A novel method to calculate the minimizer point for a cell shared by more than two materials is provided, which forms a non-manifold node on the boundary. We then mesh all the material regions simultaneously and automatically while conforming to their boundaries directly from volumetric data. Both material change edges and interior edges are analyzed to construct tetrahedral meshes, and interior grid points are analyzed for proper hexahedral mesh construction. Finally, edge-contraction and smoothing methods are used to improve the quality of tetrahedral meshes, and a combination of pillowing, geometric flow and optimization techniques is used for hexahedral mesh quality improvement. The shrink set of pillowing schemes is defined automatically as the boundary of each material region. Several application results of our multi-material mesh generation method are also provided. PMID:20161555
Sampling and surface reconstruction with adaptive-size meshes
NASA Astrophysics Data System (ADS)
Huang, Wen-Chen; Goldgof, Dmitry B.
1992-03-01
This paper presents a new approach to sampling and surface reconstruction which uses the physically based models. We introduce adaptive-size meshes which automatically update the size of the meshes as the distance between the nodes changes. We have implemented the adaptive-size algorithm to the following three applications: (1) Sampling of the intensity data. (2) Surface reconstruction of the range data. (3) Surface reconstruction of the 3-D computed tomography left ventricle data. The LV data was acquired by the 3-D computed tomography (CT) scanner. It was provided by Dr. Eric Hoffman at University of Pennsylvania Medical school and consists of 16 volumetric (128 X 128 X 118) images taken through the heart cycle.
Generic remeshing of 3D triangular meshes with metric-dependent discrete voronoi diagrams.
Valette, Sebastien; Chassery, Jean Marc; Prost, Rémy
2008-01-01
In this paper, we propose a generic framework for 3D surface remeshing. Based on a metric-driven Discrete Voronoi Diagram construction, our output is an optimized 3D triangular mesh with a user defined vertex budget. Our approach can deal with a wide range of applications, from high quality mesh generation to shape approximation. By using appropriate metric constraints the method generates isotropic or anisotropic elements. Based on point-sampling, our algorithm combines the robustness and theoretical strength of Delaunay criteria with the efficiency of entirely discrete geometry processing . Besides the general described framework, we show experimental results using isotropic, quadric-enhanced isotropic and anisotropic metrics which prove the efficiency of our method on large meshes, for a low computational cost. PMID:18192716
Adaptive fuzzy system for 3-D vision
NASA Technical Reports Server (NTRS)
Mitra, Sunanda
1993-01-01
An adaptive fuzzy system using the concept of the Adaptive Resonance Theory (ART) type neural network architecture and incorporating fuzzy c-means (FCM) system equations for reclassification of cluster centers was developed. The Adaptive Fuzzy Leader Clustering (AFLC) architecture is a hybrid neural-fuzzy system which learns on-line in a stable and efficient manner. The system uses a control structure similar to that found in the Adaptive Resonance Theory (ART-1) network to identify the cluster centers initially. The initial classification of an input takes place in a two stage process; a simple competitive stage and a distance metric comparison stage. The cluster prototypes are then incrementally updated by relocating the centroid positions from Fuzzy c-Means (FCM) system equations for the centroids and the membership values. The operational characteristics of AFLC and the critical parameters involved in its operation are discussed. The performance of the AFLC algorithm is presented through application of the algorithm to the Anderson Iris data, and laser-luminescent fingerprint image data. The AFLC algorithm successfully classifies features extracted from real data, discrete or continuous, indicating the potential strength of this new clustering algorithm in analyzing complex data sets. The hybrid neuro-fuzzy AFLC algorithm will enhance analysis of a number of difficult recognition and control problems involved with Tethered Satellite Systems and on-orbit space shuttle attitude controller.
Landmark detection from 3D mesh facial models for image-based analysis of dysmorphology.
Chendeb, Marwa; Tortorici, Claudio; Al Muhairi, Hassan; Al Safar, Habiba; Linguraru, Marius; Werghi, Naoufel
2015-01-01
Facial landmark detection is a task of interest for facial dysmorphology, an important factor in the diagnosis of genetic conditions. In this paper, we propose a framework for feature points detection from 3D face images. The method is based on 3D Constrained Local Model (CLM) which learns both global variations in the 3D facial scan and local changes around every vertex landmark. Compared to state of the art methods our framework is distinguished by the following novel aspects: 1) It operates on facial surfaces, 2) It allows fusion of shape and color information on the mesh surface, 3) It introduces the use of LBP descriptors on the mesh. We showcase our landmarks detection framework on a set of scans including down syndrome and control cases. We also validate our method through a series of quantitative experiments conducted with the publicly available Bosphorus database. PMID:26736227
Moriconi, S; Scalco, E; Broggi, S; Avuzzi, B; Valdagni, R; Rizzo, G
2015-08-01
A novel approach for three-dimensional (3D) surface reconstruction of anatomical structures in radiotherapy (RT) is presented. This is obtained from manual cross-sectional contours by combining both image voxel segmentation processing and implicit surface streaming methods using wavelets. 3D meshes reconstructed with the proposed approach are compared to those obtained from traditional triangulation algorithm. Qualitative and quantitative evaluations are performed in terms of mesh quality metrics. Differences in smoothness, detail and accuracy are observed in the comparison, considering three different anatomical districts and several organs at risk in radiotherapy. Overall best performances were recorded for the proposed approach, regardless the complexity of the anatomical structure. This demonstrates the efficacy of the proposed approach for the 3D surface reconstruction in radiotherapy and allows for further specific image analyses using real biomedical data. PMID:26737226
Adaptive Mesh Refinement for Microelectronic Device Design
NASA Technical Reports Server (NTRS)
Cwik, Tom; Lou, John; Norton, Charles
1999-01-01
Finite element and finite volume methods are used in a variety of design simulations when it is necessary to compute fields throughout regions that contain varying materials or geometry. Convergence of the simulation can be assessed by uniformly increasing the mesh density until an observable quantity stabilizes. Depending on the electrical size of the problem, uniform refinement of the mesh may be computationally infeasible due to memory limitations. Similarly, depending on the geometric complexity of the object being modeled, uniform refinement can be inefficient since regions that do not need refinement add to the computational expense. In either case, convergence to the correct (measured) solution is not guaranteed. Adaptive mesh refinement methods attempt to selectively refine the region of the mesh that is estimated to contain proportionally higher solution errors. The refinement may be obtained by decreasing the element size (h-refinement), by increasing the order of the element (p-refinement) or by a combination of the two (h-p refinement). A successful adaptive strategy refines the mesh to produce an accurate solution measured against the correct fields without undue computational expense. This is accomplished by the use of a) reliable a posteriori error estimates, b) hierarchal elements, and c) automatic adaptive mesh generation. Adaptive methods are also useful when problems with multi-scale field variations are encountered. These occur in active electronic devices that have thin doped layers and also when mixed physics is used in the calculation. The mesh needs to be fine at and near the thin layer to capture rapid field or charge variations, but can coarsen away from these layers where field variations smoothen and charge densities are uniform. This poster will present an adaptive mesh refinement package that runs on parallel computers and is applied to specific microelectronic device simulations. Passive sensors that operate in the infrared portion of
Gravitational Collapse With Distributed Adaptive Mesh Refinement
NASA Astrophysics Data System (ADS)
Liebling, Steven; Lehner, Luis; Motl, Patrick; Neilsen, David; Rahman, Tanvir; Reula, Oscar
2006-04-01
Gravitational collapse is studied using distributed adaptive mesh refinement (AMR). The AMR infrastructure includes a novel treatment of adaptive boundaries which allows for high orders of accuracy. Results of the collapse of Brill waves to black holes are presented. Combining both vertex centered and cell centered fields in the same evolution is discussed.
Grid adaptation using chimera composite overlapping meshes
NASA Technical Reports Server (NTRS)
Kao, Kai-Hsiung; Liou, Meng-Sing; Chow, Chuen-Yen
1994-01-01
The objective of this paper is to perform grid adaptation using composite overlapping meshes in regions of large gradient to accurately capture the salient features during computation. The chimera grid scheme, a multiple overset mesh technique, is used in combination with a Navier-Stokes solver. The numerical solution is first converged to a steady state based on an initial coarse mesh. Solution-adaptive enhancement is then performed by using a secondary fine grid system which oversets on top of the base grid in the high-gradient region, but without requiring the mesh boundaries to join in any special way. Communications through boundary interfaces between those separated grids are carried out using trilinear interpolation. Application to the Euler equations for shock reflections and to shock wave/boundary layer interaction problem are tested. With the present method, the salient features are well-resolved.
Grid adaptation using Chimera composite overlapping meshes
NASA Technical Reports Server (NTRS)
Kao, Kai-Hsiung; Liou, Meng-Sing; Chow, Chuen-Yen
1993-01-01
The objective of this paper is to perform grid adaptation using composite over-lapping meshes in regions of large gradient to capture the salient features accurately during computation. The Chimera grid scheme, a multiple overset mesh technique, is used in combination with a Navier-Stokes solver. The numerical solution is first converged to a steady state based on an initial coarse mesh. Solution-adaptive enhancement is then performed by using a secondary fine grid system which oversets on top of the base grid in the high-gradient region, but without requiring the mesh boundaries to join in any special way. Communications through boundary interfaces between those separated grids are carried out using tri-linear interpolation. Applications to the Euler equations for shock reflections and to a shock wave/boundary layer interaction problem are tested. With the present method, the salient features are well resolved.
Grid adaption using Chimera composite overlapping meshes
NASA Technical Reports Server (NTRS)
Kao, Kai-Hsiung; Liou, Meng-Sing; Chow, Chuen-Yen
1993-01-01
The objective of this paper is to perform grid adaptation using composite over-lapping meshes in regions of large gradient to capture the salient features accurately during computation. The Chimera grid scheme, a multiple overset mesh technique, is used in combination with a Navier-Stokes solver. The numerical solution is first converged to a steady state based on an initial coarse mesh. Solution-adaptive enhancement is then performed by using a secondary fine grid system which oversets on top of the base grid in the high-gradient region, but without requiring the mesh boundaries to join in any special way. Communications through boundary interfaces between those separated grids are carried out using tri-linear interpolation. Applications to the Euler equations for shock reflections and to a shock wave/boundary layer interaction problem are tested. With the present method, the salient features are well resolved.
Polymer-Based Mesh as Supports for Multi-layered 3D Cell Culture and Assays
Simon, Karen A.; Park, Kyeng Min; Mosadegh, Bobak; Subramaniam, Anand Bala; Mazzeo, Aaron; Ngo, Phil M.; Whitesides, George M.
2013-01-01
Three-dimensional (3D) culture systems can mimic certain aspects of the cellular microenvironment found in vivo, but generation, analysis and imaging of current model systems for 3D cellular constructs and tissues remain challenging. This work demonstrates a 3D culture system – Cells-in-Gels-in-Mesh (CiGiM) – that uses stacked sheets of polymer-based mesh to support cells embedded in gels to form tissue-like constructs; the stacked sheets can be disassembled by peeling the sheets apart to analyze cultured cells—layer-by-layer—within the construct. The mesh sheets leave openings large enough for light to pass through with minimal scattering, and thus allowing multiple options for analysis—(i) using straightforward analysis by optical light microscopy, (ii) by high-resolution analysis with fluorescence microscopy, or (iii) with a fluorescence gel scanner. The sheets can be patterned into separate zones with paraffin film-based decals, in order to conduct multiple experiments in parallel; the paraffin-based decal films also block lateral diffusion of oxygen effectively. CiGiM simplifies the generation and analysis of 3D culture without compromising throughput, and quality of the data collected: it is especially useful in experiments that require control of oxygen levels, and isolation of adjacent wells in a multi-zone format. PMID:24095253
Translation, Enhancement, Filtering, and Visualization of Large 3D Triangle Mesh
1997-04-21
The runthru system consists of five programs: workcell filter, just do it, transl8g, decim8, and runthru. The workcell filter program is useful if the source of your 3D triangle mesh model is IGRIP. It will traverse a directory structure of Deneb IGRIP files and filter out any IGRIP part files that are not referenced by an accompanying IGRIP work cell file. The just do it program automates translating and/or filtering of large numbers of partsmore » that are organized in hierarchical directory structures. The transl8g program facilitates the interchange, topology generation, error checking, and enhancement of large 3D triangle meshes. Such data is frequently used to represent conceptual designs, scientific visualization volume modeling, or discrete sample data. Interchange is provided between several popular commercial and defacto standard geometry formats. Error checking is included to identify duplicate and zero area triangles. Model engancement features include common vertex joining, consistent triangle vertex ordering, vertex noemal vector averaging, and triangle strip generation. Many of the traditional O(n2) algorithms required to provide the above features have been recast and are o(nlog(n)) which support large mesh sizes. The decim8 program is based on a data filter algorithm that significantly reduces the number of triangles required to represent 3D models of geometry, scientific visualization results, and discretely sampled data. It eliminates local patches of triangles whose geometries are not appreciably different and replaces them with fewer, larger triangles. The algorithm has been used to reduce triangles in large conceptual design models to facilitate virtual walk throughs and to enable interactive viewing of large 3D iso-surface volume visualizations. The runthru program provides high performance interactive display and manipulation of 3D triangle mesh models.« less
Accurate, finite-volume methods for 3D MHD on unstructured Lagrangian meshes
Barnes, D.C.; Rousculp, C.L.
1998-10-01
Previous 2D methods for magnetohydrodynamics (MHD) have contributed both to development of core code capability and to physics applications relevant to AGEX pulsed-power experiments. This strategy is being extended to 3D by development of a modular extension of an ASCI code. Extension to 3D not only increases complexity by problem size, but also introduces new physics, such as magnetic helicity transport. The authors have developed a method which incorporates all known conservation properties into the difference scheme on a Lagrangian unstructured mesh. Because the method does not depend on the mesh structure, mesh refinement is possible during a calculation to prevent the well known problem of mesh tangling. Arbitrary polyhedral cells are decomposed into tetrahedrons. The action of the magnetic vector potential, A {center_dot} {delta}l, is centered on the edges of this extended mesh. For ideal flow, this maintains {del} {center_dot} B = 0 to round-off error. Vertex forces are derived by the variation of magnetic energy with respect to vertex positions, F = {minus}{partial_derivative}W{sub B}/{partial_derivative}r. This assures symmetry as well as magnetic flux, momentum, and energy conservation. The method is local so that parallelization by domain decomposition is natural for large meshes. In addition, a simple, ideal-gas, finite pressure term has been included. The resistive diffusion part is calculated using the support operator method, to obtain an energy conservative, symmetric method on an arbitrary mesh. Implicit time difference equations are solved by preconditioned, conjugate gradient methods. Results of convergence tests are presented. Initial results of an annular Z-pinch implosion problem illustrate the application of these methods to multi-material problems.
3D-2D Deformable Image Registration Using Feature-Based Nonuniform Meshes
Guo, Xiaohu; Cai, Yiqi; Yang, Yin; Wang, Jing; Jia, Xun
2016-01-01
By using prior information of planning CT images and feature-based nonuniform meshes, this paper demonstrates that volumetric images can be efficiently registered with a very small portion of 2D projection images of a Cone-Beam Computed Tomography (CBCT) scan. After a density field is computed based on the extracted feature edges from planning CT images, nonuniform tetrahedral meshes will be automatically generated to better characterize the image features according to the density field; that is, finer meshes are generated for features. The displacement vector fields (DVFs) are specified at the mesh vertices to drive the deformation of original CT images. Digitally reconstructed radiographs (DRRs) of the deformed anatomy are generated and compared with corresponding 2D projections. DVFs are optimized to minimize the objective function including differences between DRRs and projections and the regularity. To further accelerate the above 3D-2D registration, a procedure to obtain good initial deformations by deforming the volume surface to match 2D body boundary on projections has been developed. This complete method is evaluated quantitatively by using several digital phantoms and data from head and neck cancer patients. The feature-based nonuniform meshing method leads to better results than either uniform orthogonal grid or uniform tetrahedral meshes. PMID:27019849
A moving mesh algorithm for 3-D regional groundwater flow with water table and seepage face
NASA Astrophysics Data System (ADS)
Knupp, P.
A numerical algorithm is described for solving the free-surface groundwater flow equations in 3-D large-scale unconfined aquifers with strongly heterogeneous conductivity and surface recharge. The algorithm uses a moving mesh to track the water-table as it evolves according to kinematic and seepage face boundary conditions. Both steady-state and transient algorithms are implemented in the SECO-Flow 3-D code and demonstrated on stratigraphy based on the Delaware Basin of south-eastern New Mexico.
Metal-mesh based transparent electrode on a 3-D curved surface by electrohydrodynamic jet printing
NASA Astrophysics Data System (ADS)
Seong, Baekhoon; Yoo, Hyunwoong; Dat Nguyen, Vu; Jang, Yonghee; Ryu, Changkook; Byun, Doyoung
2014-09-01
Invisible Ag mesh transparent electrodes (TEs), with a width of 7 μm, were prepared on a curved glass surface by electrohydrodynamic (EHD) jet printing. With a 100 μm pitch, the EHD jet printed the Ag mesh on the convex glass which had a sheet resistance of 1.49 Ω/□. The printing speed was 30 cm s-1 using Ag ink, which had a 10 000 cPs viscosity and a 70 wt% Ag nanoparticle concentration. We further showed the performance of a 3-D transparent heater using the Ag mesh transparent electrode. The EHD jet printed an invisible Ag grid transparent electrode with good electrical and optical properties with promising applications on printed optoelectronic devices.
Unstructured 3D Delaunay mesh generation applied to planes, trains and automobiles
NASA Technical Reports Server (NTRS)
Blake, Kenneth R.; Spragle, Gregory S.
1993-01-01
Technical issues associated with domain-tessellation production, including initial boundary node triangulation and volume mesh refinement, are presented for the 'TGrid' 3D Delaunay unstructured grid generation program. The approach employed is noted to be capable of preserving predefined triangular surface facets in the final tessellation. The capabilities of the approach are demonstrated by generating grids about an entire fighter aircraft configuration, a train, and a wind tunnel model of an automobile.
Arbitrary Lagrangian Eulerian Adaptive Mesh Refinement
2009-09-29
This is a simulation code involving an ALE (arbitrary Lagrangian-Eulerian) hydrocode with AMR (adaptive mesh refinement) and pluggable physics packages for material strength, heat conduction, radiation diffusion, and laser ray tracing developed a LLNL, UCSD, and Berkeley Lab. The code is an extension of the open source SAMRAI (Structured Adaptive Mesh Refinement Application Interface) code/library. The code can be used in laser facilities such as the National Ignition Facility. The code is alsi being appliedmore » to slurry flow (landslides).« less
Bayesian Segmentation of Atrium Wall Using Globally-Optimal Graph Cuts on 3D Meshes
Veni, Gopalkrishna; Fu, Zhisong; Awate, Suyash P.; Whitaker, Ross T.
2014-01-01
Efficient segmentation of the left atrium (LA) wall from delayed enhancement MRI is challenging due to inconsistent contrast, combined with noise, and high variation in atrial shape and size. We present a surface-detection method that is capable of extracting the atrial wall by computing an optimal a-posteriori estimate. This estimation is done on a set of nested meshes, constructed from an ensemble of segmented training images, and graph cuts on an associated multi-column, proper-ordered graph. The graph/mesh is a part of a template/model that has an associated set of learned intensity features. When this mesh is overlaid onto a test image, it produces a set of costs which lead to an optimal segmentation. The 3D mesh has an associated weighted, directed multi-column graph with edges that encode smoothness and inter-surface penalties. Unlike previous graph-cut methods that impose hard constraints on the surface properties, the proposed method follows from a Bayesian formulation resulting in soft penalties on spatial variation of the cuts through the mesh. The novelty of this method also lies in the construction of proper-ordered graphs on complex shapes for choosing among distinct classes of base shapes for automatic LA segmentation. We evaluate the proposed segmentation framework on simulated and clinical cardiac MRI. PMID:24684007
A novel mesh processing based technique for 3D plant analysis
2012-01-01
Background In recent years, imaging based, automated, non-invasive, and non-destructive high-throughput plant phenotyping platforms have become popular tools for plant biology, underpinning the field of plant phenomics. Such platforms acquire and record large amounts of raw data that must be accurately and robustly calibrated, reconstructed, and analysed, requiring the development of sophisticated image understanding and quantification algorithms. The raw data can be processed in different ways, and the past few years have seen the emergence of two main approaches: 2D image processing and 3D mesh processing algorithms. Direct image quantification methods (usually 2D) dominate the current literature due to comparative simplicity. However, 3D mesh analysis provides the tremendous potential to accurately estimate specific morphological features cross-sectionally and monitor them over-time. Result In this paper, we present a novel 3D mesh based technique developed for temporal high-throughput plant phenomics and perform initial tests for the analysis of Gossypium hirsutum vegetative growth. Based on plant meshes previously reconstructed from multi-view images, the methodology involves several stages, including morphological mesh segmentation, phenotypic parameters estimation, and plant organs tracking over time. The initial study focuses on presenting and validating the accuracy of the methodology on dicotyledons such as cotton but we believe the approach will be more broadly applicable. This study involved applying our technique to a set of six Gossypium hirsutum (cotton) plants studied over four time-points. Manual measurements, performed for each plant at every time-point, were used to assess the accuracy of our pipeline and quantify the error on the morphological parameters estimated. Conclusion By directly comparing our automated mesh based quantitative data with manual measurements of individual stem height, leaf width and leaf length, we obtained the mean
Parallel object-oriented adaptive mesh refinement
Balsara, D.; Quinlan, D.J.
1997-04-01
In this paper we study adaptive mesh refinement (AMR) for elliptic and hyperbolic systems. We use the Asynchronous Fast Adaptive Composite Grid Method (AFACX), a parallel algorithm based upon the of Fast Adaptive Composite Grid Method (FAC) as a test case of an adaptive elliptic solver. For our hyperbolic system example we use TVD and ENO schemes for solving the Euler and MHD equations. We use the structured grid load balancer MLB as a tool for obtaining a load balanced distribution in a parallel environment. Parallel adaptive mesh refinement poses difficulties in expressing both the basic single grid solver, whether elliptic or hyperbolic, in a fashion that parallelizes seamlessly. It also requires that these basic solvers work together within the adaptive mesh refinement algorithm which uses the single grid solvers as one part of its adaptive solution process. We show that use of AMR++, an object-oriented library within the OVERTURE Framework, simplifies the development of AMR applications. Parallel support is provided and abstracted through the use of the P++ parallel array class.
Particle systems for adaptive, isotropic meshing of CAD models
Levine, Joshua A.; Whitaker, Ross T.
2012-01-01
We present a particle-based approach for generating adaptive triangular surface and tetrahedral volume meshes from computer-aided design models. Input shapes are treated as a collection of smooth, parametric surface patches that can meet non-smoothly on boundaries. Our approach uses a hierarchical sampling scheme that places particles on features in order of increasing dimensionality. These particles reach a good distribution by minimizing an energy computed in 3D world space, with movements occurring in the parametric space of each surface patch. Rather than using a pre-computed measure of feature size, our system automatically adapts to both curvature as well as a notion of topological separation. It also enforces a measure of smoothness on these constraints to construct a sizing field that acts as a proxy to piecewise-smooth feature size. We evaluate our technique with comparisons against other popular triangular meshing techniques for this domain. PMID:23162181
Dubai 3d Textuerd Mesh Using High Quality Resolution Vertical/oblique Aerial Imagery
NASA Astrophysics Data System (ADS)
Tayeb Madani, Adib; Ziad Ahmad, Abdullateef; Christoph, Lueken; Hammadi, Zamzam; Manal Abdullah Sabeal, Manal Abdullah x.
2016-06-01
Providing high quality 3D data with reasonable quality and cost were always essential, affording the core data and foundation for developing an information-based decision-making tool of urban environments with the capability of providing decision makers, stakeholders, professionals, and public users with 3D views and 3D analysis tools of spatial information that enables real-world views. Helps and assist in improving users' orientation and also increase their efficiency in performing their tasks related to city planning, Inspection, infrastructures, roads, and cadastre management. In this paper, the capability of multi-view Vexcel UltraCam Osprey camera images is examined to provide a 3D model of building façades using an efficient image-based modeling workflow adopted by commercial software's. The main steps of this work include: Specification, point cloud generation, and 3D modeling. After improving the initial values of interior and exterior parameters at first step, an efficient image matching technique such as Semi Global Matching (SGM) is applied on the images to generate point cloud. Then, a mesh model of points is calculated using and refined to obtain an accurate model of buildings. Finally, a texture is assigned to mesh in order to create a realistic 3D model. The resulting model has provided enough LoD2 details of the building based on visual assessment. The objective of this paper is neither comparing nor promoting a specific technique over the other and does not mean to promote a sensor-based system over another systems or mechanism presented in existing or previous paper. The idea is to share experience.
Adaption of unstructured meshes using node movement
Carpenter, J.G.; McRae, V.D.S.
1996-12-31
The adaption algorithm of Benson and McRae is modified for application to unstructured grids. The weight function generation was modified for application to unstructured grids and movement was limited to prevent cross over. A NACA 0012 airfoil is used as a test case to evaluate the modified algorithm when applied to unstructured grids and compared to results obtained by Warren. An adaptive mesh solution for the Sudhoo and Hall four element airfoil is included as a demonstration case.
Multigrid solution strategies for adaptive meshing problems
NASA Technical Reports Server (NTRS)
Mavriplis, Dimitri J.
1995-01-01
This paper discusses the issues which arise when combining multigrid strategies with adaptive meshing techniques for solving steady-state problems on unstructured meshes. A basic strategy is described, and demonstrated by solving several inviscid and viscous flow cases. Potential inefficiencies in this basic strategy are exposed, and various alternate approaches are discussed, some of which are demonstrated with an example. Although each particular approach exhibits certain advantages, all methods have particular drawbacks, and the formulation of a completely optimal strategy is considered to be an open problem.
Unstructured Adaptive Meshes: Bad for Your Memory?
NASA Technical Reports Server (NTRS)
Biswas, Rupak; Feng, Hui-Yu; VanderWijngaart, Rob
2003-01-01
This viewgraph presentation explores the need for a NASA Advanced Supercomputing (NAS) parallel benchmark for problems with irregular dynamical memory access. This benchmark is important and necessary because: 1) Problems with localized error source benefit from adaptive nonuniform meshes; 2) Certain machines perform poorly on such problems; 3) Parallel implementation may provide further performance improvement but is difficult. Some examples of problems which use irregular dynamical memory access include: 1) Heat transfer problem; 2) Heat source term; 3) Spectral element method; 4) Base functions; 5) Elemental discrete equations; 6) Global discrete equations. Nonconforming Mesh and Mortar Element Method are covered in greater detail in this presentation.
Virtual view adaptation for 3D multiview video streaming
NASA Astrophysics Data System (ADS)
Petrovic, Goran; Do, Luat; Zinger, Sveta; de With, Peter H. N.
2010-02-01
Virtual views in 3D-TV and multi-view video systems are reconstructed images of the scene generated synthetically from the original views. In this paper, we analyze the performance of streaming virtual views over IP-networks with a limited and time-varying available bandwidth. We show that the average video quality perceived by the user can be improved with an adaptive streaming strategy aiming at maximizing the average video quality. Our adaptive 3D multi-view streaming can provide a quality improvement of 2 dB on the average - over non-adaptive streaming. We demonstrate that an optimized virtual view adaptation algorithm needs to be view-dependent and achieve an improvement of up to 0.7 dB. We analyze our adaptation strategies under dynamic available bandwidth in the network.
TRANSL8GDECIM8. Data Translation and Filtering for Large 3D Triangle Mesh Models
Janucik, F.X.; Ross, D.M.
1993-09-01
The TRANSL8GDECIM8 system consists of two programs: TRANSL8G and DECIM8. The TRANSL8G program facilitates the interchange, topology generation, error checking, and enhancement of large 3D triangle meshes. Such data is frequently used to represent conceptual designs, scientific visualization volume modeling, or discrete sample data. Interchange is provided between several popular commercial and defacto standard geometry formats. Error checking is included to identify duplicate and zero area triangles. Model enhancement features include common vertex joining, consistent triangle vertex ordering, vertex normal vector averaging, and triangle strip generation. Many of the traditional O(n squared) algorithms required to provide the above features have been recast and are O(n) which support large mesh sizes. The DECIM8 program is based on a data filter algorithm that significantly reduces the number of triangles required to represent three dimensional (3D) models of geometry, scientific visualization results, and discretely sampled data. The algorithm uses a combined incremental and iterative strategy. It eliminates local patches of triangles whose geometries are not appreciably different and replaces them with fewer larger triangles. The algorithm has been used to reduce triangles in large conceptual design models to facilitate virtual walk throughs and to enable interactive viewing of large 3D iso-surface volume visualizations.
Curved Mesh Correction And Adaptation Tool to Improve COMPASS Electromagnetic Analyses
Luo, X.; Shephard, M.; Lee, L.Q.; Ng, C.; Ge, L.; /SLAC
2011-11-14
SLAC performs large-scale simulations for the next-generation accelerator design using higher-order finite elements. This method requires using valid curved meshes and adaptive mesh refinement in complex 3D curved domains to achieve its fast rate of convergence. ITAPS has developed a procedure to address those mesh requirements to enable petascale electromagnetic accelerator simulations by SLAC. The results demonstrate that those correct valid curvilinear meshes can not only make the simulation more reliable but also improve computational efficiency up to 30%. This paper presents a procedure to track moving adaptive mesh refinement in curved domains. The procedure is capable of generating suitable curvilinear meshes to enable large-scale accelerator simulations. The procedure can generate valid curved meshes with substantially fewer elements to improve the computational efficiency and reliability of the COMPASS electromagnetic analyses. Future work will focus on the scalable parallelization of all steps for petascale simulations.
GRChombo: Numerical relativity with adaptive mesh refinement
NASA Astrophysics Data System (ADS)
Clough, Katy; Figueras, Pau; Finkel, Hal; Kunesch, Markus; Lim, Eugene A.; Tunyasuvunakool, Saran
2015-12-01
In this work, we introduce {\\mathtt{GRChombo}}: a new numerical relativity code which incorporates full adaptive mesh refinement (AMR) using block structured Berger-Rigoutsos grid generation. The code supports non-trivial 'many-boxes-in-many-boxes' mesh hierarchies and massive parallelism through the message passing interface. {\\mathtt{GRChombo}} evolves the Einstein equation using the standard BSSN formalism, with an option to turn on CCZ4 constraint damping if required. The AMR capability permits the study of a range of new physics which has previously been computationally infeasible in a full 3 + 1 setting, while also significantly simplifying the process of setting up the mesh for these problems. We show that {\\mathtt{GRChombo}} can stably and accurately evolve standard spacetimes such as binary black hole mergers and scalar collapses into black holes, demonstrate the performance characteristics of our code, and discuss various physics problems which stand to benefit from the AMR technique.
Floating shock fitting via Lagrangian adaptive meshes
NASA Technical Reports Server (NTRS)
Vanrosendale, John
1994-01-01
In recent works we have formulated a new approach to compressible flow simulation, combining the advantages of shock-fitting and shock-capturing. Using a cell-centered Roe scheme discretization on unstructured meshes, we warp the mesh while marching to steady state, so that mesh edges align with shocks and other discontinuities. This new algorithm, the Shock-fitting Lagrangian Adaptive Method (SLAM) is, in effect, a reliable shock-capturing algorithm which yields shock-fitted accuracy at convergence. Shock-capturing algorithms like this, which warp the mesh to yield shock-fitted accuracy, are new and relatively untried. However, their potential is clear. In the context of sonic booms, accurate calculation of near-field sonic boom signatures is critical to the design of the High Speed Civil Transport (HSCT). SLAM should allow computation of accurate N-wave pressure signatures on comparatively coarse meshes, significantly enhancing our ability to design low-boom configurations for high-speed aircraft.
Generation and adaptation of 3-D unstructured grids for transient problems
NASA Technical Reports Server (NTRS)
Loehner, Rainald
1990-01-01
Grid generation and adaptive refinement techniques suitable for the simulation of strongly unsteady flows past geometrically complex bodies in 3-D are described. The grids are generated using the advancing front technique. Emphasis is placed not to generate elements that are too small, as this would severely increase the cost of simulations with explicit flow solvers. The grids are adapted to an evolving flowfield using simple h-refinement. A grid change is performed every 5 to 10 timesteps, and only one level of refinement/coarsening is allowed per mesh change.
Details of tetrahedral anisotropic mesh adaptation
NASA Astrophysics Data System (ADS)
Jensen, Kristian Ejlebjerg; Gorman, Gerard
2016-04-01
We have implemented tetrahedral anisotropic mesh adaptation using the local operations of coarsening, swapping, refinement and smoothing in MATLAB without the use of any for- N loops, i.e. the script is fully vectorised. In the process of doing so, we have made three observations related to details of the implementation: 1. restricting refinement to a single edge split per element not only simplifies the code, it also improves mesh quality, 2. face to edge swapping is unnecessary, and 3. optimising for the Vassilevski functional tends to give a little higher value for the mean condition number functional than optimising for the condition number functional directly. These observations have been made for a uniform and a radial shock metric field, both starting from a structured mesh in a cube. Finally, we compare two coarsening techniques and demonstrate the importance of applying smoothing in the mesh adaptation loop. The results pertain to a unit cube geometry, but we also show the effect of corners and edges by applying the implementation in a spherical geometry.
Adapting 3D Equilibrium Reconstruction to Reconstruct Weakly 3D H-mode Tokamaks
NASA Astrophysics Data System (ADS)
Cianciosa, M. R.; Hirshman, S. P.; Seal, S. K.; Unterberg, E. A.; Wilcox, R. S.; Wingen, A.; Hanson, J. D.
2015-11-01
The application of resonant magnetic perturbations for edge localized mode (ELM) mitigation breaks the toroidal symmetry of tokamaks. In these scenarios, the axisymmetric assumptions of the Grad-Shafranov equation no longer apply. By extension, equilibrium reconstruction tools, built around these axisymmetric assumptions, are insufficient to fully reconstruct a 3D perturbed equilibrium. 3D reconstruction tools typically work on systems where the 3D components of signals are a significant component of the input signals. In nominally axisymmetric systems, applied field perturbations can be on the order of 1% of the main field or less. To reconstruct these equilibria, the 3D component of signals must be isolated from the axisymmetric portions to provide the necessary information for reconstruction. This presentation will report on the adaptation to V3FIT for application on DIII-D H-mode discharges with applied resonant magnetic perturbations (RMPs). Newly implemented motional stark effect signals and modeling of electric field effects will also be discussed. Work supported under U.S. DOE Cooperative Agreement DE-AC05-00OR22725.
Electrostatic PIC with adaptive Cartesian mesh
NASA Astrophysics Data System (ADS)
Kolobov, Vladimir; Arslanbekov, Robert
2016-05-01
We describe an initial implementation of an electrostatic Particle-in-Cell (ES-PIC) module with adaptive Cartesian mesh in our Unified Flow Solver framework. Challenges of PIC method with cell-based adaptive mesh refinement (AMR) are related to a decrease of the particle-per-cell number in the refined cells with a corresponding increase of the numerical noise. The developed ES-PIC solver is validated for capacitively coupled plasma, its AMR capabilities are demonstrated for simulations of streamer development during high-pressure gas breakdown. It is shown that cell-based AMR provides a convenient particle management algorithm for exponential multiplications of electrons and ions in the ionization events.
Lafarge, Florent; Keriven, Renaud; Brédif, Mathieu
2010-07-01
We propose an original hybrid modeling process of urban scenes that represents 3-D models as a combination of mesh-based surfaces and geometric 3-D-primitives. Meshes describe details such as ornaments and statues, whereas 3-D-primitives code for regular shapes such as walls and columns. Starting from an 3-D-surface obtained by multiview stereo techniques, these primitives are inserted into the surface after being detected. This strategy allows the introduction of semantic knowledge, the simplification of the modeling, and even correction of errors generated by the acquisition process. We design a hierarchical approach exploring different scales of an observed scene. Each level consists first in segmenting the surface using a multilabel energy model optimized by -expansion and then in fitting 3-D-primitives such as planes, cylinders or tori on the obtained partition where relevant. Experiments on real meshes, depth maps and synthetic surfaces show good potential for the proposed approach. PMID:20236893
Robust and Blind 3D Mesh Watermarking in Spatial Domain Based on Faces Categorization and Sorting
NASA Astrophysics Data System (ADS)
Molaei, Amir Masoud; Ebrahimnezhad, Hossein; Sedaaghi, Mohammad Hossein
2016-06-01
In this paper, a 3D watermarking algorithm in spatial domain is presented with blind detection. In the proposed method, a negligible visual distortion is observed in host model. Initially, a preprocessing is applied on the 3D model to make it robust against geometric transformation attacks. Then, a number of triangle faces are determined as mark triangles using a novel systematic approach in which faces are categorized and sorted robustly. In order to enhance the capability of information retrieval by attacks, block watermarks are encoded using Reed-Solomon block error-correcting code before embedding into the mark triangles. Next, the encoded watermarks are embedded in spherical coordinates. The proposed method is robust against additive noise, mesh smoothing and quantization attacks. Also, it is stout next to geometric transformation, vertices and faces reordering attacks. Moreover, the proposed algorithm is designed so that it is robust against the cropping attack. Simulation results confirm that the watermarked models confront very low distortion if the control parameters are selected properly. Comparison with other methods demonstrates that the proposed method has good performance against the mesh smoothing attacks.
Robust Detection of Round Shaped Pits Lying on 3D Meshes: Application to Impact Crater Recognition
NASA Astrophysics Data System (ADS)
Schmidt, Martin-Pierre; Muscato, Jennifer; Viseur, Sophie; Jorda, Laurent; Bouley, Sylvain; Mari, Jean-Luc
2015-04-01
Most celestial bodies display impacts of collisions with asteroids and meteoroids. These traces are called craters. The possibility of observing and identifying these craters and their characteristics (radius, depth and morphology) is the only method available to measure the age of different units at the surface of the body, which in turn allows to constrain its conditions of formation. Interplanetary space probes always carry at least one imaging instrument on board. The visible images of the target are used to reconstruct high-resolution 3D models of its surface as a cloud of points in the case of multi-image dense stereo, or as a triangular mesh in the case of stereo and shape-from-shading. The goal of this work is to develop a methodology to automatically detect the craters lying on these 3D models. The robust extraction of feature areas on surface objects embedded in 3D, like circular pits, is a challenging problem. Classical approaches generally rely on image processing and template matching on a 2D flat projection of the 3D object (i.e.: a high-resolution photograph). In this work, we propose a full-3D method that mainly relies on curvature analysis. Mean and Gaussian curvatures are estimated on the surface. They are used to label vertices that belong to concave parts corresponding to specific pits on the surface. The surface is thus transformed into binary map distinguishing potential crater features to other types of features. Centers are located in the targeted surface regions, corresponding to potential crater features. Concentric rings are then built around the found centers. They consist in circular closed lines exclusively composed of edges of the initial mesh. The first built ring represents the nearest vertex neighborhood of the found center. The ring is then optimally expanded using a circularity constrain and the curvature values of the ring vertices. This method has been tested on a 3D model of the asteroid Lutetia observed by the ROSETTA (ESA
Parallel goal-oriented adaptive finite element modeling for 3D electromagnetic exploration
NASA Astrophysics Data System (ADS)
Zhang, Y.; Key, K.; Ovall, J.; Holst, M.
2014-12-01
We present a parallel goal-oriented adaptive finite element method for accurate and efficient electromagnetic (EM) modeling of complex 3D structures. An unstructured tetrahedral mesh allows this approach to accommodate arbitrarily complex 3D conductivity variations and a priori known boundaries. The total electric field is approximated by the lowest order linear curl-conforming shape functions and the discretized finite element equations are solved by a sparse LU factorization. Accuracy of the finite element solution is achieved through adaptive mesh refinement that is performed iteratively until the solution converges to the desired accuracy tolerance. Refinement is guided by a goal-oriented error estimator that uses a dual-weighted residual method to optimize the mesh for accurate EM responses at the locations of the EM receivers. As a result, the mesh refinement is highly efficient since it only targets the elements where the inaccuracy of the solution corrupts the response at the possibly distant locations of the EM receivers. We compare the accuracy and efficiency of two approaches for estimating the primary residual error required at the core of this method: one uses local element and inter-element residuals and the other relies on solving a global residual system using a hierarchical basis. For computational efficiency our method follows the Bank-Holst algorithm for parallelization, where solutions are computed in subdomains of the original model. To resolve the load-balancing problem, this approach applies a spectral bisection method to divide the entire model into subdomains that have approximately equal error and the same number of receivers. The finite element solutions are then computed in parallel with each subdomain carrying out goal-oriented adaptive mesh refinement independently. We validate the newly developed algorithm by comparison with controlled-source EM solutions for 1D layered models and with 2D results from our earlier 2D goal oriented
Fully implicit adaptive mesh refinement MHD algorithm
NASA Astrophysics Data System (ADS)
Philip, Bobby
2005-10-01
In the macroscopic simulation of plasmas, the numerical modeler is faced with the challenge of dealing with multiple time and length scales. The former results in stiffness due to the presence of very fast waves. The latter requires one to resolve the localized features that the system develops. Traditional approaches based on explicit time integration techniques and fixed meshes are not suitable for this challenge, as such approaches prevent the modeler from using realistic plasma parameters to keep the computation feasible. We propose here a novel approach, based on implicit methods and structured adaptive mesh refinement (SAMR). Our emphasis is on both accuracy and scalability with the number of degrees of freedom. To our knowledge, a scalable, fully implicit AMR algorithm has not been accomplished before for MHD. As a proof-of-principle, we focus on the reduced resistive MHD model as a basic MHD model paradigm, which is truly multiscale. The approach taken here is to adapt mature physics-based technologyootnotetextL. Chac'on et al., J. Comput. Phys. 178 (1), 15- 36 (2002) to AMR grids, and employ AMR-aware multilevel techniques (such as fast adaptive composite --FAC-- algorithms) for scalability. We will demonstrate that the concept is indeed feasible, featuring optimal scalability under grid refinement. Results of fully-implicit, dynamically-adaptive AMR simulations will be presented on a variety of problems.
Efficient triangular adaptive meshes for tsunami simulations
NASA Astrophysics Data System (ADS)
Behrens, J.
2012-04-01
With improving technology and increased sensor density for accurate determination of tsunamogenic earthquake source parameters and consecutively uplift distribution, real-time simulations of even near-field tsunami hazard appears feasible in the near future. In order to support such efforts a new generation of tsunami models is currently under development. These models comprise adaptively refined meshes, in order to save computational resources (in areas of low wave activity) and still represent the inherently multi-scale behavior of a tsunami approaching coastal waters. So far, these methods have been based on oct-tree quadrilateral refinement. The method introduced here is based on binary tree refinement on triangular grids. By utilizing the structure stemming from the refinement strategy, a very efficient method can be achieved, with a triangular mesh, able to accurately represent complex boundaries.
Anisotropic Mesh Adaptivity for FE-simulation of cardiovascular flow
NASA Astrophysics Data System (ADS)
Mueller, Jens; Sahni, Onkar; Jansen, Kenneth E.; Shephard, Mark S.; Taylor, Charles A.
2004-11-01
In this study we present an adaptive anisotropic finite element method and demonstrate how computational efficiency can be increased when applying the method to the simulation of blood flow in the cardiovascular system. We use the weak SUPG formulation for the transient 3D incompressible Navier-Stokes equations which are discretized by linear finite elements, both for the pressure and the velocity field. Given the pulsatile nature of the flow in blood vessels we have pursued adaptavity based on the average flow over a cardiac cycle. Error indicators are derived to define an anisotropic mesh metric field. Mesh modification algorithms are used to anisotropically adapt the mesh according to the desired size field. We demonstrate the efficiency of the method by first applying it to pulsatile flow in a straight cylindrical pipe and then to a pig artery with a stenosis bypassed by a graft. The efficiency of the method is measured in terms of computational savings when we compute the wall shear stresses, a quantity identified to be important to understanding arterial disease.
Adaptive radial basis function mesh deformation using data reduction
NASA Astrophysics Data System (ADS)
Gillebaart, T.; Blom, D. S.; van Zuijlen, A. H.; Bijl, H.
2016-09-01
Radial Basis Function (RBF) mesh deformation is one of the most robust mesh deformation methods available. Using the greedy (data reduction) method in combination with an explicit boundary correction, results in an efficient method as shown in literature. However, to ensure the method remains robust, two issues are addressed: 1) how to ensure that the set of control points remains an accurate representation of the geometry in time and 2) how to use/automate the explicit boundary correction, while ensuring a high mesh quality. In this paper, we propose an adaptive RBF mesh deformation method, which ensures the set of control points always represents the geometry/displacement up to a certain (user-specified) criteria, by keeping track of the boundary error throughout the simulation and re-selecting when needed. Opposed to the unit displacement and prescribed displacement selection methods, the adaptive method is more robust, user-independent and efficient, for the cases considered. Secondly, the analysis of a single high aspect ratio cell is used to formulate an equation for the correction radius needed, depending on the characteristics of the correction function used, maximum aspect ratio, minimum first cell height and boundary error. Based on the analysis two new radial basis correction functions are derived and proposed. This proposed automated procedure is verified while varying the correction function, Reynolds number (and thus first cell height and aspect ratio) and boundary error. Finally, the parallel efficiency is studied for the two adaptive methods, unit displacement and prescribed displacement for both the CPU as well as the memory formulation with a 2D oscillating and translating airfoil with oscillating flap, a 3D flexible locally deforming tube and deforming wind turbine blade. Generally, the memory formulation requires less work (due to the large amount of work required for evaluating RBF's), but the parallel efficiency reduces due to the limited
3DSEM++: Adaptive and intelligent 3D SEM surface reconstruction.
Tafti, Ahmad P; Holz, Jessica D; Baghaie, Ahmadreza; Owen, Heather A; He, Max M; Yu, Zeyun
2016-08-01
Structural analysis of microscopic objects is a longstanding topic in several scientific disciplines, such as biological, mechanical, and materials sciences. The scanning electron microscope (SEM), as a promising imaging equipment has been around for decades to determine the surface properties (e.g., compositions or geometries) of specimens by achieving increased magnification, contrast, and resolution greater than one nanometer. Whereas SEM micrographs still remain two-dimensional (2D), many research and educational questions truly require knowledge and facts about their three-dimensional (3D) structures. 3D surface reconstruction from SEM images leads to remarkable understanding of microscopic surfaces, allowing informative and qualitative visualization of the samples being investigated. In this contribution, we integrate several computational technologies including machine learning, contrario methodology, and epipolar geometry to design and develop a novel and efficient method called 3DSEM++ for multi-view 3D SEM surface reconstruction in an adaptive and intelligent fashion. The experiments which have been performed on real and synthetic data assert the approach is able to reach a significant precision to both SEM extrinsic calibration and its 3D surface modeling. PMID:27200484
Efficient 3D geometric and Zernike moments computation from unstructured surface meshes.
Pozo, José María; Villa-Uriol, Maria-Cruz; Frangi, Alejandro F
2011-03-01
This paper introduces and evaluates a fast exact algorithm and a series of faster approximate algorithms for the computation of 3D geometric moments from an unstructured surface mesh of triangles. Being based on the object surface reduces the computational complexity of these algorithms with respect to volumetric grid-based algorithms. In contrast, it can only be applied for the computation of geometric moments of homogeneous objects. This advantage and restriction is shared with other proposed algorithms based on the object boundary. The proposed exact algorithm reduces the computational complexity for computing geometric moments up to order N with respect to previously proposed exact algorithms, from N(9) to N(6). The approximate series algorithm appears as a power series on the rate between triangle size and object size, which can be truncated at any desired degree. The higher the number and quality of the triangles, the better the approximation. This approximate algorithm reduces the computational complexity to N(3). In addition, the paper introduces a fast algorithm for the computation of 3D Zernike moments from the computed geometric moments, with a computational complexity N(4), while the previously proposed algorithm is of order N(6). The error introduced by the proposed approximate algorithms is evaluated in different shapes and the cost-benefit ratio in terms of error, and computational time is analyzed for different moment orders. PMID:20714011
KNUPP,PATRICK; MITCHELL,SCOTT A.
1999-11-01
In an attempt to automatically produce high-quality all-hex meshes, we investigated a mesh improvement strategy: given an initial poor-quality all-hex mesh, we iteratively changed the element connectivity, adding and deleting elements and nodes, and optimized the node positions. We found a set of hex reconnection primitives. We improved the optimization algorithms so they can untangle a negative-Jacobian mesh, even considering Jacobians on the boundary, and subsequently optimize the condition number of elements in an untangled mesh. However, even after applying both the primitives and optimization we were unable to produce high-quality meshes in certain regions. Our experiences suggest that many boundary configurations of quadrilaterals admit no hexahedral mesh with positive Jacobians, although we have no proof of this.
3D Game Content Distributed Adaptation in Heterogeneous Environments
NASA Astrophysics Data System (ADS)
Morán, Francisco; Preda, Marius; Lafruit, Gauthier; Villegas, Paulo; Berretty, Robert-Paul
2007-12-01
Most current multiplayer 3D games can only be played on a single dedicated platform (a particular computer, console, or cell phone), requiring specifically designed content and communication over a predefined network. Below we show how, by using signal processing techniques such as multiresolution representation and scalable coding for all the components of a 3D graphics object (geometry, texture, and animation), we enable online dynamic content adaptation, and thus delivery of the same content over heterogeneous networks to terminals with very different profiles, and its rendering on them. We present quantitative results demonstrating how the best displayed quality versus computational complexity versus bandwidth tradeoffs have been achieved, given the distributed resources available over the end-to-end content delivery chain. Additionally, we use state-of-the-art, standardised content representation and compression formats (MPEG-4 AFX, JPEG 2000, XML), enabling deployment over existing infrastructure, while keeping hooks to well-established practices in the game industry.
Adaptive Meshing Techniques for Viscous Flow Calculations on Mixed Element Unstructured Meshes
NASA Technical Reports Server (NTRS)
Mavriplis, D. J.
1997-01-01
An adaptive refinement strategy based on hierarchical element subdivision is formulated and implemented for meshes containing arbitrary mixtures of tetrahendra, hexahendra, prisms and pyramids. Special attention is given to keeping memory overheads as low as possible. This procedure is coupled with an algebraic multigrid flow solver which operates on mixed-element meshes. Inviscid flows as well as viscous flows are computed an adaptively refined tetrahedral, hexahedral, and hybrid meshes. The efficiency of the method is demonstrated by generating an adapted hexahedral mesh containing 3 million vertices on a relatively inexpensive workstation.
NASA Astrophysics Data System (ADS)
Fang, F.; Zhang, T.; Pavlidis, D.; Pain, C. C.; Buchan, A. G.; Navon, I. M.
2014-10-01
A novel reduced order model (ROM) based on proper orthogonal decomposition (POD) has been developed for a finite-element (FE) adaptive mesh air pollution model. A quadratic expansion of the non-linear terms is employed to ensure the method remained efficient. This is the first time such an approach has been applied to air pollution LES turbulent simulation through three dimensional landscapes. The novelty of this work also includes POD's application within a FE-LES turbulence model that uses adaptive resolution. The accuracy of the reduced order model is assessed and validated for a range of 2D and 3D urban street canyon flow problems. By comparing the POD solutions against the fine detail solutions obtained from the full FE model it is shown that the accuracy is maintained, where fine details of the air flows are captured, whilst the computational requirements are reduced. In the examples presented below the size of the reduced order models is reduced by factors up to 2400 in comparison to the full FE model while the CPU time is reduced by up to 98% of that required by the full model.
Adaptive Mesh Refinement Simulations of Relativistic Binaries
NASA Astrophysics Data System (ADS)
Motl, Patrick M.; Anderson, M.; Lehner, L.; Olabarrieta, I.; Tohline, J. E.; Liebling, S. L.; Rahman, T.; Hirschman, E.; Neilsen, D.
2006-09-01
We present recent results from our efforts to evolve relativistic binaries composed of compact objects. We simultaneously solve the general relativistic hydrodynamics equations to evolve the material components of the binary and Einstein's equations to evolve the space-time. These two codes are coupled through an adaptive mesh refinement driver (had). One of the ultimate goals of this project is to address the merger of a neutron star and black hole and assess the possible observational signature of such systems as gamma ray bursts. This work has been supported in part by NSF grants AST 04-07070 and PHY 03-26311 and in part through NASA's ATP program grant NAG5-13430. The computations were performed primarily at NCSA through grant MCA98N043 and at LSU's Center for Computation & Technology.
Visualization Tools for Adaptive Mesh Refinement Data
Weber, Gunther H.; Beckner, Vincent E.; Childs, Hank; Ligocki,Terry J.; Miller, Mark C.; Van Straalen, Brian; Bethel, E. Wes
2007-05-09
Adaptive Mesh Refinement (AMR) is a highly effective method for simulations that span a large range of spatiotemporal scales, such as astrophysical simulations that must accommodate ranges from interstellar to sub-planetary. Most mainstream visualization tools still lack support for AMR as a first class data type and AMR code teams use custom built applications for AMR visualization. The Department of Energy's (DOE's) Science Discovery through Advanced Computing (SciDAC) Visualization and Analytics Center for Enabling Technologies (VACET) is currently working on extending VisIt, which is an open source visualization tool that accommodates AMR as a first-class data type. These efforts will bridge the gap between general-purpose visualization applications and highly specialized AMR visual analysis applications. Here, we give an overview of the state of the art in AMR visualization research and tools and describe how VisIt currently handles AMR data.
Visualization of Scalar Adaptive Mesh Refinement Data
VACET; Weber, Gunther; Weber, Gunther H.; Beckner, Vince E.; Childs, Hank; Ligocki, Terry J.; Miller, Mark C.; Van Straalen, Brian; Bethel, E. Wes
2007-12-06
Adaptive Mesh Refinement (AMR) is a highly effective computation method for simulations that span a large range of spatiotemporal scales, such as astrophysical simulations, which must accommodate ranges from interstellar to sub-planetary. Most mainstream visualization tools still lack support for AMR grids as a first class data type and AMR code teams use custom built applications for AMR visualization. The Department of Energy's (DOE's) Science Discovery through Advanced Computing (SciDAC) Visualization and Analytics Center for Enabling Technologies (VACET) is currently working on extending VisIt, which is an open source visualization tool that accommodates AMR as a first-class data type. These efforts will bridge the gap between general-purpose visualization applications and highly specialized AMR visual analysis applications. Here, we give an overview of the state of the art in AMR scalar data visualization research.
Simulation of nonpoint source contamination based on adaptive mesh refinement
NASA Astrophysics Data System (ADS)
Kourakos, G.; Harter, T.
2014-12-01
Contamination of groundwater aquifers from nonpoint sources is a worldwide problem. Typical agricultural groundwater basins receive contamination from a large array (in the order of ~10^5-6) of spatially and temporally heterogeneous sources such as fields, crops, dairies etc, while the received contaminants emerge at significantly uncertain time lags to a large array of discharge surfaces such as public supply, domestic and irrigation wells and streams. To support decision making in such complex regimes several approaches have been developed, which can be grouped into 3 categories: i) Index methods, ii)regression methods and iii) physically based methods. Among the three, physically based methods are considered more accurate, but at the cost of computational demand. In this work we present a physically based simulation framework which exploits the latest hardware and software developments to simulate large (>>1,000 km2) groundwater basins. First we simulate groundwater flow using a sufficiently detailed mesh to capture the spatial heterogeneity. To achieve optimal mesh quality we combine adaptive mesh refinement with the nonlinear solution for unconfined flow. Starting from a coarse grid the mesh is refined iteratively in the parts of the domain where the flow heterogeneity appears higher resulting in optimal grid. Secondly we simulate the nonpoint source pollution based on the detailed velocity field computed from the previous step. In our approach we use the streamline model where the 3D transport problem is decomposed into multiple 1D transport problems. The proposed framework is applied to simulate nonpoint source pollution in the Central Valley aquifer system, California.
Elliptic Solvers for Adaptive Mesh Refinement Grids
Quinlan, D.J.; Dendy, J.E., Jr.; Shapira, Y.
1999-06-03
We are developing multigrid methods that will efficiently solve elliptic problems with anisotropic and discontinuous coefficients on adaptive grids. The final product will be a library that provides for the simplified solution of such problems. This library will directly benefit the efforts of other Laboratory groups. The focus of this work is research on serial and parallel elliptic algorithms and the inclusion of our black-box multigrid techniques into this new setting. The approach applies the Los Alamos object-oriented class libraries that greatly simplify the development of serial and parallel adaptive mesh refinement applications. In the final year of this LDRD, we focused on putting the software together; in particular we completed the final AMR++ library, we wrote tutorials and manuals, and we built example applications. We implemented the Fast Adaptive Composite Grid method as the principal elliptic solver. We presented results at the Overset Grid Conference and other more AMR specific conferences. We worked on optimization of serial and parallel performance and published several papers on the details of this work. Performance remains an important issue and is the subject of continuing research work.
NASA Astrophysics Data System (ADS)
Lian, Y.-Y.; Hsu, K.-H.; Shao, Y.-L.; Lee, Y.-M.; Jeng, Y.-W.; Wu, J.-S.
2006-12-01
The development of a parallel three-dimensional (3-D) adaptive mesh refinement (PAMR) scheme for an unstructured tetrahedral mesh using dynamic domain decomposition on a memory-distributed machine is presented in detail. A memory-saving cell-based data structure is designed such that the resulting mesh information can be readily utilized in both node- or cell-based numerical methods. The general procedures include isotropic refinement from one parent cell into eight child cells and then followed by anisotropic refinement which effectively removes hanging nodes. A simple but effective mesh-quality control mechanism is employed to preserve the mesh quality. The resulting parallel performance of this PAMR is found to scale approximately as N for N⩽32. Two test cases, including a particle method (parallel DSMC solver for rarefied gas dynamics) and an equation-based method (parallel Poisson-Boltzmann equation solver for electrostatic field), are used to demonstrate the generality of the PAMR module. It is argued that this PAMR scheme can be applied in any numerical method if the unstructured tetrahedral mesh is adopted.
NASA Astrophysics Data System (ADS)
Gansen, A.; Hachemi, M. El; Belouettar, S.; Hassan, O.; Morgan, K.
2016-09-01
The standard Yee algorithm is widely used in computational electromagnetics because of its simplicity and divergence free nature. A generalization of the classical Yee scheme to 3D unstructured meshes is adopted, based on the use of a Delaunay primal mesh and its high quality Voronoi dual. This allows the problem of accuracy losses, which are normally associated with the use of the standard Yee scheme and a staircased representation of curved material interfaces, to be circumvented. The 3D dual mesh leapfrog-scheme which is presented has the ability to model both electric and magnetic anisotropic lossy materials. This approach enables the modelling of problems, of current practical interest, involving structured composites and metamaterials.
A parallel adaptive mesh refinement algorithm
NASA Technical Reports Server (NTRS)
Quirk, James J.; Hanebutte, Ulf R.
1993-01-01
Over recent years, Adaptive Mesh Refinement (AMR) algorithms which dynamically match the local resolution of the computational grid to the numerical solution being sought have emerged as powerful tools for solving problems that contain disparate length and time scales. In particular, several workers have demonstrated the effectiveness of employing an adaptive, block-structured hierarchical grid system for simulations of complex shock wave phenomena. Unfortunately, from the parallel algorithm developer's viewpoint, this class of scheme is quite involved; these schemes cannot be distilled down to a small kernel upon which various parallelizing strategies may be tested. However, because of their block-structured nature such schemes are inherently parallel, so all is not lost. In this paper we describe the method by which Quirk's AMR algorithm has been parallelized. This method is built upon just a few simple message passing routines and so it may be implemented across a broad class of MIMD machines. Moreover, the method of parallelization is such that the original serial code is left virtually intact, and so we are left with just a single product to support. The importance of this fact should not be underestimated given the size and complexity of the original algorithm.
Parallel, Gradient-Based Anisotropic Mesh Adaptation for Re-entry Vehicle Configurations
NASA Technical Reports Server (NTRS)
Bibb, Karen L.; Gnoffo, Peter A.; Park, Michael A.; Jones, William T.
2006-01-01
Two gradient-based adaptation methodologies have been implemented into the Fun3d refine GridEx infrastructure. A spring-analogy adaptation which provides for nodal movement to cluster mesh nodes in the vicinity of strong shocks has been extended for general use within Fun3d, and is demonstrated for a 70 sphere cone at Mach 2. A more general feature-based adaptation metric has been developed for use with the adaptation mechanics available in Fun3d, and is applicable to any unstructured, tetrahedral, flow solver. The basic functionality of general adaptation is explored through a case of flow over the forebody of a 70 sphere cone at Mach 6. A practical application of Mach 10 flow over an Apollo capsule, computed with the Felisa flow solver, is given to compare the adaptive mesh refinement with uniform mesh refinement. The examples of the paper demonstrate that the gradient-based adaptation capability as implemented can give an improvement in solution quality.
Solution of the Skyrme HF + BCS equation on a 3D mesh
NASA Astrophysics Data System (ADS)
Bonche, P.; Flocard, H.; Heenen, P. H.
2005-09-01
Over the years, the ev8 code has been a very useful tool for the study of nuclear mean-field theory. Its main characteristic is that it solves the Hartree-Fock plus BCS equations for Skyrme type functionals via a discretization of the individual wave-functions on a three-dimensional Cartesian mesh. This allows maximal flexibility in the determination of the nuclear shape by the variational process. For instance, the same mesh can be used to describe the oblate deformed, spherical, prolate deformed, superdeformed and fission configurations of a given nucleus. The quadrupole constraining operator yielding the deformation energy curve covering all these configurations is included in ev8. This version of the code is restricted to even-even nuclei. Program summaryTitle of program:ev8 Catalogue identifier:ADWA Program obtainable from: CPC Program Library, Queen's University of Belfast, N. Ireland Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADWA Licensing provisions: none Computers on which the program has been tested: HP-RX4640, Compaq-Digital Alpha GS140, has run on several other platforms Computer for which the program is designed and others on which is has been tested:Unix, Linux Operating systems or monitors under which the program has been tested:FORTRAN-90 Programming language used:depends on problem; example given requires 60 MB Memory required to execute with typical data:yes No. of lines in distributed program, including test data, etc.:11 524 No. of bytes in distributed program, including test data, etc.:89 949 Distribution format:tar.gzip file Nature of the physical problem:By means of the Hartree-Fock plus BCS method using Skyrme type functionals, ev8 allows a study of the evolution of the binding energy of even-even nuclei for various shapes determined by the most general quadrupole constraint. Solution method:The program expands the single-particle wave-functions on a 3D Cartesian mesh. The nonlinear mean-field equations are solved by the
Adaptive mesh fluid simulations on GPU
NASA Astrophysics Data System (ADS)
Wang, Peng; Abel, Tom; Kaehler, Ralf
2010-10-01
We describe an implementation of compressible inviscid fluid solvers with block-structured adaptive mesh refinement on Graphics Processing Units using NVIDIA's CUDA. We show that a class of high resolution shock capturing schemes can be mapped naturally on this architecture. Using the method of lines approach with the second order total variation diminishing Runge-Kutta time integration scheme, piecewise linear reconstruction, and a Harten-Lax-van Leer Riemann solver, we achieve an overall speedup of approximately 10 times faster execution on one graphics card as compared to a single core on the host computer. We attain this speedup in uniform grid runs as well as in problems with deep AMR hierarchies. Our framework can readily be applied to more general systems of conservation laws and extended to higher order shock capturing schemes. This is shown directly by an implementation of a magneto-hydrodynamic solver and comparing its performance to the pure hydrodynamic case. Finally, we also combined our CUDA parallel scheme with MPI to make the code run on GPU clusters. Close to ideal speedup is observed on up to four GPUs.
Anisotropic Mesh Adaptivity for Turbulent Flows with Boundary Layers
NASA Astrophysics Data System (ADS)
Chitale, Kedar C.
Turbulent flows are found everywhere in nature and are studied, analyzed and simulated using various experimental and numerical tools. For computational analysis, a variety of turbulence models are available and the accuracy of these models in capturing the phenomenon depends largely on the mesh spacings, especially near the walls, in the boundary layer region. Special semi-structured meshes called "mesh boundary layers" are widely used in the CFD community in simulations of turbulent flows, because of their graded and orthogonal layered structure. They provide an efficient way to achieve very fine and highly anisotropic mesh spacings without introducing poorly shaped elements. Since usually the required mesh spacings to accurately resolve the flow are not known a priori to the simulations, an adaptive approach based on a posteriori error indicators is used to achieve an appropriate mesh. In this study, we apply the adaptive meshing techniques to turbulent flows with a focus on boundary layers. We construct a framework to calculate the critical wall normal mesh spacings inside the boundary layers based on the flow physics and the knowledge of the turbulence model. This approach is combined with numerical error indicators to adapt the entire flow region. We illustrate the effectiveness of this hybrid approach by applying it to three aerodynamic flows and studying their superior performance in capturing the flow structures in detail. We also demonstrate the capabilities of the current developments in parallel boundary layer mesh adaptation by applying them to two internal flow problems. We also study the application of adaptive boundary layer meshes to complex geometries like multi element wings. We highlight the advantage of using such techniques for superior wake and tip region resolution by showcasing flow results. We also outline the future direction for the adaptive meshing techniques to be useful to the large scale flow computations.
DISCO: A 3D Moving-mesh Magnetohydrodynamics Code Designed for the Study of Astrophysical Disks
NASA Astrophysics Data System (ADS)
Duffell, Paul C.
2016-09-01
This work presents the publicly available moving-mesh magnetohydrodynamics (MHD) code DISCO. DISCO is efficient and accurate at evolving orbital fluid motion in two and three dimensions, especially at high Mach numbers. DISCO employs a moving-mesh approach utilizing a dynamic cylindrical mesh that can shear azimuthally to follow the orbital motion of the gas. The moving mesh removes diffusive advection errors and allows for longer time-steps than a static grid. MHD is implemented in DISCO using an HLLD Riemann solver and a novel constrained transport (CT) scheme that is compatible with the mesh motion. DISCO is tested against a wide variety of problems, which are designed to test its stability, accuracy, and scalability. In addition, several MHD tests are performed which demonstrate the accuracy and stability of the new CT approach, including two tests of the magneto-rotational instability, one testing the linear growth rate and the other following the instability into the fully turbulent regime.
Adaptive mesh refinement for stochastic reaction-diffusion processes
Bayati, Basil; Chatelain, Philippe; Koumoutsakos, Petros
2011-01-01
We present an algorithm for adaptive mesh refinement applied to mesoscopic stochastic simulations of spatially evolving reaction-diffusion processes. The transition rates for the diffusion process are derived on adaptive, locally refined structured meshes. Convergence of the diffusion process is presented and the fluctuations of the stochastic process are verified. Furthermore, a refinement criterion is proposed for the evolution of the adaptive mesh. The method is validated in simulations of reaction-diffusion processes as described by the Fisher-Kolmogorov and Gray-Scott equations.
Adaptive and Quality Quadrilateral/Hexahedral Meshing from Volumetric Data⋆
Zhang, Yongjie; Bajaj, Chandrajit
2009-01-01
This paper describes an algorithm to extract adaptive and quality quadrilateral/hexahedral meshes directly from volumetric data. First, a bottom-up surface topology preserving octree-based algorithm is applied to select a starting octree level. Then the dual contouring method is used to extract a preliminary uniform quad/hex mesh, which is decomposed into finer quads/hexes adaptively without introducing any hanging nodes. The positions of all boundary vertices are recalculated to approximate the boundary surface more accurately. Mesh adaptivity can be controlled by a feature sensitive error function, the regions that users are interested in, or finite element calculation results. Finally, a relaxation based technique is deployed to improve mesh quality. Several demonstration examples are provided from a wide variety of application domains. Some extracted meshes have been extensively used in finite element simulations. PMID:19750180
Adaptive-mesh algorithms for computational fluid dynamics
NASA Technical Reports Server (NTRS)
Powell, Kenneth G.; Roe, Philip L.; Quirk, James
1993-01-01
The basic goal of adaptive-mesh algorithms is to distribute computational resources wisely by increasing the resolution of 'important' regions of the flow and decreasing the resolution of regions that are less important. While this goal is one that is worthwhile, implementing schemes that have this degree of sophistication remains more of an art than a science. In this paper, the basic pieces of adaptive-mesh algorithms are described and some of the possible ways to implement them are discussed and compared. These basic pieces are the data structure to be used, the generation of an initial mesh, the criterion to be used to adapt the mesh to the solution, and the flow-solver algorithm on the resulting mesh. Each of these is discussed, with particular emphasis on methods suitable for the computation of compressible flows.
Numerical modeling of seismic waves using frequency-adaptive meshes
NASA Astrophysics Data System (ADS)
Hu, Jinyin; Jia, Xiaofeng
2016-08-01
An improved modeling algorithm using frequency-adaptive meshes is applied to meet the computational requirements of all seismic frequency components. It automatically adopts coarse meshes for low-frequency computations and fine meshes for high-frequency computations. The grid intervals are adaptively calculated based on a smooth inversely proportional function of grid size with respect to the frequency. In regular grid-based methods, the uniform mesh or non-uniform mesh is used for frequency-domain wave propagators and it is fixed for all frequencies. A too coarse mesh results in inaccurate high-frequency wavefields and unacceptable numerical dispersion; on the other hand, an overly fine mesh may cause storage and computational overburdens as well as invalid propagation angles of low-frequency wavefields. Experiments on the Padé generalized screen propagator indicate that the Adaptive mesh effectively solves these drawbacks of regular fixed-mesh methods, thus accurately computing the wavefield and its propagation angle in a wide frequency band. Several synthetic examples also demonstrate its feasibility for seismic modeling and migration.
Serial and parallel dynamic adaptation of general hybrid meshes
NASA Astrophysics Data System (ADS)
Kavouklis, Christos
The Navier-Stokes equations are a standard mathematical representation of viscous fluid flow. Their numerical solution in three dimensions remains a computationally intensive and challenging task, despite recent advances in computer speed and memory. A strategy to increase accuracy of Navier-Stokes simulations, while maintaining computing resources to a minimum, is local refinement of the associated computational mesh in regions of large solution gradients and coarsening in regions where the solution does not vary appreciably. In this work we consider adaptation of general hybrid meshes for Computational Fluid Dynamics (CFD) applications. Hybrid meshes are composed of four types of elements; hexahedra, prisms, pyramids and tetrahedra, and have been proven a promising technology in accurately resolving fluid flow for complex geometries. The first part of this dissertation is concerned with the design and implementation of a serial scheme for the adaptation of general three dimensional hybrid meshes. We have defined 29 refinement types, for all four kinds of elements. The core of the present adaptation scheme is an iterative algorithm that flags mesh edges for refinement, so that the adapted mesh is conformal. Of primary importance is considered the design of a suitable dynamic data structure that facilitates refinement and coarsening operations and furthermore minimizes memory requirements. A special dynamic list is defined for mesh elements, in contrast with the usual tree structures. It contains only elements of the current adaptation step and minimal information that is utilized to reconstruct parent elements when the mesh is coarsened. In the second part of this work, a new parallel dynamic mesh adaptation and load balancing algorithm for general hybrid meshes is presented. Partitioning of a hybrid mesh reduces to partitioning of the corresponding dual graph. Communication among processors is based on the faces of the interpartition boundary. The distributed
Recent Enhancements To The FUN3D Flow Solver For Moving-Mesh Applications
NASA Technical Reports Server (NTRS)
Biedron, Robert T,; Thomas, James L.
2009-01-01
An unsteady Reynolds-averaged Navier-Stokes solver for unstructured grids has been extended to handle general mesh movement involving rigid, deforming, and overset meshes. Mesh deformation is achieved through analogy to elastic media by solving the linear elasticity equations. A general method for specifying the motion of moving bodies within the mesh has been implemented that allows for inherited motion through parent-child relationships, enabling simulations involving multiple moving bodies. Several example calculations are shown to illustrate the range of potential applications. For problems in which an isolated body is rotating with a fixed rate, a noninertial reference-frame formulation is available. An example calculation for a tilt-wing rotor is used to demonstrate that the time-dependent moving grid and noninertial formulations produce the same results in the limit of zero time-step size.
PARAMESH: A Parallel Adaptive Mesh Refinement Community Toolkit
NASA Technical Reports Server (NTRS)
MacNeice, Peter; Olson, Kevin M.; Mobarry, Clark; deFainchtein, Rosalinda; Packer, Charles
1999-01-01
In this paper, we describe a community toolkit which is designed to provide parallel support with adaptive mesh capability for a large and important class of computational models, those using structured, logically cartesian meshes. The package of Fortran 90 subroutines, called PARAMESH, is designed to provide an application developer with an easy route to extend an existing serial code which uses a logically cartesian structured mesh into a parallel code with adaptive mesh refinement. Alternatively, in its simplest use, and with minimal effort, it can operate as a domain decomposition tool for users who want to parallelize their serial codes, but who do not wish to use adaptivity. The package can provide them with an incremental evolutionary path for their code, converting it first to uniformly refined parallel code, and then later if they so desire, adding adaptivity.
Adaptive mesh and algorithm refinement using direct simulation Monte Carlo
Garcia, A.L.; Bell, J.B.; Crutchfield, W.Y.; Alder, B.J.
1999-09-01
Adaptive mesh and algorithm refinement (AMAR) embeds a particle method within a continuum method at the finest level of an adaptive mesh refinement (AMR) hierarchy. The coupling between the particle region and the overlaying continuum grid is algorithmically equivalent to that between the fine and coarse levels of AMR. Direct simulation Monte Carlo (DSMC) is used as the particle algorithm embedded within a Godunov-type compressible Navier-Stokes solver. Several examples are presented and compared with purely continuum calculations.
Anisotropic adaptive mesh generation in two dimensions for CFD
Borouchaki, H.; Castro-Diaz, M.J.; George, P.L.; Hecht, F.; Mohammadi, B.
1996-12-31
This paper describes the extension of the classical Delaunay method in the case where anisotropic meshes are required such as in CFD when the modelized physic is strongly directional. The way in which such a mesh generation method can be incorporated in an adaptative loop of CFD as well as the case of multicriterium adaptation are discussed. Several concrete application examples are provided to illustrate the capabilities of the proposed method.
Parallel adaptive mesh refinement for electronic structure calculations
Kohn, S.; Weare, J.; Ong, E.; Baden, S.
1996-12-01
We have applied structured adaptive mesh refinement techniques to the solution of the LDA equations for electronic structure calculations. Local spatial refinement concentrates memory resources and numerical effort where it is most needed, near the atomic centers and in regions of rapidly varying charge density. The structured grid representation enables us to employ efficient iterative solver techniques such as conjugate gradients with multigrid preconditioning. We have parallelized our solver using an object-oriented adaptive mesh refinement framework.
Turbulent flow calculations using unstructured and adaptive meshes
NASA Technical Reports Server (NTRS)
Mavriplis, Dimitri J.
1990-01-01
A method of efficiently computing turbulent compressible flow over complex two dimensional configurations is presented. The method makes use of fully unstructured meshes throughout the entire flow-field, thus enabling the treatment of arbitrarily complex geometries and the use of adaptive meshing techniques throughout both viscous and inviscid regions of flow-field. Mesh generation is based on a locally mapped Delaunay technique in order to generate unstructured meshes with highly-stretched elements in the viscous regions. The flow equations are discretized using a finite element Navier-Stokes solver, and rapid convergence to steady-state is achieved using an unstructured multigrid algorithm. Turbulence modeling is performed using an inexpensive algebraic model, implemented for use on unstructured and adaptive meshes. Compressible turbulent flow solutions about multiple-element airfoil geometries are computed and compared with experimental data.
A fast approach for accurate content-adaptive mesh generation.
Yang, Yongyi; Wernick, Miles N; Brankov, Jovan G
2003-01-01
Mesh modeling is an important problem with many applications in image processing. A key issue in mesh modeling is how to generate a mesh structure that well represents an image by adapting to its content. We propose a new approach to mesh generation, which is based on a theoretical result derived on the error bound of a mesh representation. In the proposed method, the classical Floyd-Steinberg error-diffusion algorithm is employed to place mesh nodes in the image domain so that their spatial density varies according to the local image content. Delaunay triangulation is next applied to connect the mesh nodes. The result of this approach is that fine mesh elements are placed automatically in regions of the image containing high-frequency features while coarse mesh elements are used to represent smooth areas. The proposed algorithm is noniterative, fast, and easy to implement. Numerical results demonstrate that, at very low computational cost, the proposed approach can produce mesh representations that are more accurate than those produced by several existing methods. Moreover, it is demonstrated that the proposed algorithm performs well with images of various kinds, even in the presence of noise. PMID:18237961
Numerical simulation of 3D unsteady flow in a rotating pump by dynamic mesh technique
NASA Astrophysics Data System (ADS)
Huang, S.; Guo, J.; Yang, F. X.
2013-12-01
In this paper, the numerical simulation of unsteady flow for three kinds of typical rotating pumps, roots blower, roto-jet pump and centrifugal pump, were performed using the three-dimensional Dynamic Mesh technique. In the unsteady simulation, all the computational domains, as stationary, were set in one inertial reference frame. The motions of the solid boundaries were defined by the Profile file in FLUENT commercial code, in which the rotational orientation and speed of the rotors were specified. Three methods (Spring-based Smoothing, Dynamic Layering and Local Re-meshing) were used to achieve mesh deformation and re-meshing. The unsteady solutions of flow field and pressure distribution were solved. After a start-up stage, the flow parameters exhibit time-periodic behaviour corresponding to blade passing frequency of rotor. This work shows that Dynamic Mesh technique could achieve numerical simulation of three-dimensional unsteady flow field in various kinds of rotating pumps and have a strong versatility and broad application prospects.
Large-Scale Parallel Unstructured Mesh Computations for 3D High-Lift Analysis
NASA Technical Reports Server (NTRS)
Mavriplis, D. J.; Pirzadeh, S.
1999-01-01
A complete "geometry to drag-polar" analysis capability for three-dimensional high-lift configurations is described. The approach is based on the use of unstructured meshes in order to enable rapid turnaround for complicated geometries which arise in high-lift configurations. Special attention is devoted to creating a capability for enabling analyses on highly resolved grids. Unstructured meshes of several million vertices are initially generated on a work-station, and subsequently refined on a supercomputer. The flow is solved on these refined meshes on large parallel computers using an unstructured agglomeration multigrid algorithm. Good prediction of lift and drag throughout the range of incidences is demonstrated on a transport take-off configuration using up to 24.7 million grid points. The feasibility of using this approach in a production environment on existing parallel machines is demonstrated, as well as the scalability of the solver on machines using up to 1450 processors.
Large-scale Parallel Unstructured Mesh Computations for 3D High-lift Analysis
NASA Technical Reports Server (NTRS)
Mavriplis, Dimitri J.; Pirzadeh, S.
1999-01-01
A complete "geometry to drag-polar" analysis capability for the three-dimensional high-lift configurations is described. The approach is based on the use of unstructured meshes in order to enable rapid turnaround for complicated geometries that arise in high-lift configurations. Special attention is devoted to creating a capability for enabling analyses on highly resolved grids. Unstructured meshes of several million vertices are initially generated on a work-station, and subsequently refined on a supercomputer. The flow is solved on these refined meshes on large parallel computers using an unstructured agglomeration multigrid algorithm. Good prediction of lift and drag throughout the range of incidences is demonstrated on a transport take-off configuration using up to 24.7 million grid points. The feasibility of using this approach in a production environment on existing parallel machines is demonstrated, as well as the scalability of the solver on machines using up to 1450 processors.
Large-Scale Parallel Unstructured Mesh Computations for 3D High-Lift Analysis
NASA Technical Reports Server (NTRS)
Mavriplis, D. J.; Pirzadeh, S.
1999-01-01
A complete "geometry to drag-polar" analysis capability for three-dimensional high-lift configurations is described. The approach is based on the use of unstructured meshes in order to enable rapid turnaround for complicated geometries which arise in high-lift con gurations. Special attention is devoted to creating a capability for enabling analyses on highly resolved grids. Unstructured meshes of several million vertices are initially generated on a work-station, and subsequently refined on a supercomputer. The flow is solved on these refined meshes on large parallel computers using an unstructured agglomeration multigrid algorithm. Good prediction of lift and drag throughout the range of incidences is demonstrated on a transport take-off configuration using up to 24.7 million grid points. The feasibility of using this approach in a production environment on existing parallel machines is demonstrated, as well as the scalability of the solver on machines using up to 1450 processors.
Brief communication: Impact of mesh resolution for MISMIP and MISMIP3d experiments using Elmer/Ice
NASA Astrophysics Data System (ADS)
Gagliardini, O.; Brondex, J.; Gillet-Chaulet, F.; Tavard, L.; Peyaud, V.; Durand, G.
2016-02-01
The dynamical contribution of marine ice sheets to sea level rise is largely controlled by grounding line (GL) dynamics. Two marine ice sheet model intercomparison exercises, namely MISMIP and MISMIP3d, have been proposed to the community to test and compare the ability of models to capture the GL dynamics. Both exercises are known to present a discontinuity of the friction at the GL, which is believed to increase the model sensitivity to mesh resolution. Here, using Elmer/Ice, the only Stokes model which completed both intercomparisons, the sensitivity to the mesh resolution is studied from an extended MISMIP experiment in which the friction continuously decreases over a transition distance and equals zero at the GL. Using this MISMIP-like setup, it is shown that the sensitivity to the mesh resolution is not improved for a vanishing friction at the GL. For the original MISMIP experiment, i.e. for a discontinuous friction at the GL, we further show that the results are moreover very sensitive to the way the friction is interpolated in the close vicinity of the GL. In the light of these new insights, and thanks to increased computing resources, new results for the MISMIP3d experiments obtained for higher resolutions than previously published are made available for future comparisons as the Supplement.
NASA Astrophysics Data System (ADS)
Gansen, A.; El Hachemi, M.; Belouettar, S.; Hassan, O.; Morgan, K.
2015-12-01
In computational electromagnetics, the advantages of the standard Yee algorithm are its simplicity and its low computational costs. However, because of the accuracy losses resulting from the staircased representation of curved interfaces, it is normally not the method of choice for modelling electromagnetic interactions with objects of arbitrary shape. For these problems, an unstructured mesh finite volume time domain method is often employed, although the scheme does not satisfy the divergence free condition at the discrete level. In this paper, we generalize the standard Yee algorithm for use on unstructured meshes and solve the problem concerning the loss of accuracy linked to staircasing, while preserving the divergence free nature of the algorithm. The scheme is implemented on high quality primal Delaunay and dual Voronoi meshes. The performance of the approach was validated in previous work by simulating the scattering of electromagnetic waves by spherical 3D PEC objects in free space. In this paper we demonstrate the performance of this scheme for penetration problems in lossy dielectrics using a new averaging technique for Delaunay and Voronoi edges at the interface. A detailed explanation of the implementation of the method, and a demonstration of the quality of the results obtained for transmittance and scattering simulations by 3D objects of arbitrary shapes, are presented.
Drag Prediction for the NASA CRM Wing-Body-Tail Using CFL3D and OVERFLOW on an Overset Mesh
NASA Technical Reports Server (NTRS)
Sclafani, Anthony J.; DeHaan, Mark A.; Vassberg, John C.; Rumsey, Christopher L.; Pulliam, Thomas H.
2010-01-01
In response to the fourth AIAA CFD Drag Prediction Workshop (DPW-IV), the NASA Common Research Model (CRM) wing-body and wing-body-tail configurations are analyzed using the Reynolds-averaged Navier-Stokes (RANS) flow solvers CFL3D and OVERFLOW. Two families of structured, overset grids are built for DPW-IV. Grid Family 1 (GF1) consists of a coarse (7.2 million), medium (16.9 million), fine (56.5 million), and extra-fine (189.4 million) mesh. Grid Family 2 (GF2) is an extension of the first and includes a superfine (714.2 million) and an ultra-fine (2.4 billion) mesh. The medium grid anchors both families with an established build process for accurate cruise drag prediction studies. This base mesh is coarsened and enhanced to form a set of parametrically equivalent grids that increase in size by a factor of roughly 3.4 from one level to the next denser level. Both CFL3D and OVERFLOW are run on GF1 using a consistent numerical approach. Additional OVERFLOW runs are made to study effects of differencing scheme and turbulence model on GF1 and to obtain results for GF2. All CFD results are post-processed using Richardson extrapolation, and approximate grid-converged values of drag are compared. The medium grid is also used to compute a trimmed drag polar for both codes.
3D active shape models of human brain structures: application to patient-specific mesh generation
NASA Astrophysics Data System (ADS)
Ravikumar, Nishant; Castro-Mateos, Isaac; Pozo, Jose M.; Frangi, Alejandro F.; Taylor, Zeike A.
2015-03-01
The use of biomechanics-based numerical simulations has attracted growing interest in recent years for computer-aided diagnosis and treatment planning. With this in mind, a method for automatic mesh generation of brain structures of interest, using statistical models of shape (SSM) and appearance (SAM), for personalised computational modelling is presented. SSMs are constructed as point distribution models (PDMs) while SAMs are trained using intensity profiles sampled from a training set of T1-weighted magnetic resonance images. The brain structures of interest are, the cortical surface (cerebrum, cerebellum & brainstem), lateral ventricles and falx-cerebri membrane. Two methods for establishing correspondences across the training set of shapes are investigated and compared (based on SSM quality): the Coherent Point Drift (CPD) point-set registration method and B-spline mesh-to-mesh registration method. The MNI-305 (Montreal Neurological Institute) average brain atlas is used to generate the template mesh, which is deformed and registered to each training case, to establish correspondence over the training set of shapes. 18 healthy patients' T1-weightedMRimages form the training set used to generate the SSM and SAM. Both model-training and model-fitting are performed over multiple brain structures simultaneously. Compactness and generalisation errors of the BSpline-SSM and CPD-SSM are evaluated and used to quantitatively compare the SSMs. Leave-one-out cross validation is used to evaluate SSM quality in terms of these measures. The mesh-based SSM is found to generalise better and is more compact, relative to the CPD-based SSM. Quality of the best-fit model instance from the trained SSMs, to test cases are evaluated using the Hausdorff distance (HD) and mean absolute surface distance (MASD) metrics.
PLUM: Parallel Load Balancing for Unstructured Adaptive Meshes
NASA Technical Reports Server (NTRS)
Oliker, Leonid
1998-01-01
Dynamic mesh adaption on unstructured grids is a powerful tool for computing large-scale problems that require grid modifications to efficiently resolve solution features. Unfortunately, an efficient parallel implementation is difficult to achieve, primarily due to the load imbalance created by the dynamically-changing nonuniform grid. To address this problem, we have developed PLUM, an automatic portable framework for performing adaptive large-scale numerical computations in a message-passing environment. First, we present an efficient parallel implementation of a tetrahedral mesh adaption scheme. Extremely promising parallel performance is achieved for various refinement and coarsening strategies on a realistic-sized domain. Next we describe PLUM, a novel method for dynamically balancing the processor workloads in adaptive grid computations. This research includes interfacing the parallel mesh adaption procedure based on actual flow solutions to a data remapping module, and incorporating an efficient parallel mesh repartitioner. A significant runtime improvement is achieved by observing that data movement for a refinement step should be performed after the edge-marking phase but before the actual subdivision. We also present optimal and heuristic remapping cost metrics that can accurately predict the total overhead for data redistribution. Several experiments are performed to verify the effectiveness of PLUM on sequences of dynamically adapted unstructured grids. Portability is demonstrated by presenting results on the two vastly different architectures of the SP2 and the Origin2OOO. Additionally, we evaluate the performance of five state-of-the-art partitioning algorithms that can be used within PLUM. It is shown that for certain classes of unsteady adaption, globally repartitioning the computational mesh produces higher quality results than diffusive repartitioning schemes. We also demonstrate that a coarse starting mesh produces high quality load balancing, at
NASA Astrophysics Data System (ADS)
Wendling, A.; Daniel, J. L.; Hivet, G.; Vidal-Sallé, E.; Boisse, P.
2015-12-01
Numerical simulation is a powerful tool to predict the mechanical behavior and the feasibility of composite parts. Among the available numerical approaches, as far as woven reinforced composites are concerned, 3D finite element simulation at the mesoscopic scale leads to a good compromise between realism and complexity. At this scale, the fibrous reinforcement is modeled by an interlacement of yarns assumed to be homogeneous that have to be accurately represented. Among the numerous issues induced by these simulations, the first one consists in providing a representative meshed geometrical model of the unit cell at the mesoscopic scale. The second one consists in enabling a fast data input in the finite element software (contacts definition, boundary conditions, elements reorientation, etc.) so as to obtain results within reasonable time. Based on parameterized 3D CAD modeling tool of unit-cells of dry fabrics already developed, this paper presents an efficient strategy which permits an automated meshing of the models with 3D hexahedral elements and to accelerate of several orders of magnitude the simulation data input. Finally, the overall modeling strategy is illustrated by examples of finite element simulation of the mechanical behavior of fabrics.
Progress in integrated analysis with adaptive unstructured meshing
NASA Technical Reports Server (NTRS)
Dechaumphai, Pramote
1992-01-01
Design of lightweight structures and thermal protection systems for hypersonic vehicles depend on accurate prediction of aerothermal loads, structural temperatures and their gradients, and structural deformations and stresses. Concentration is on an alternative meshing technique which generates an entirely new adaptive unstructured mesh based on the solution obtained from the earlier mesh. The technique combined with the finite element method has been shown to significantly improve the efficiency and accuracy of the fluid, thermal, and structural analyses. Current capability of the adaptive unstructured meshing technique for the integrated fluid-thermal-structural analysis is described first. The technique was extended to transient thermal analysis of structures with time-dependent adaptive meshing to capture the detailed temperature response with a minimum number of unknowns and computational cost. Both linear and higher-order finite elements are implemented to demonstrate the generality of the technique and to investigate their solution accuracy. Currently, the adaptive meshing technique is being developed for plane structures that can be modeled with membrane elements and built-up structures modeled with membrane and bending elements. The capability of the technique to these different disciplinary problems is demonstrated by several examples.
Arbitrary-level hanging nodes for adaptive hphp-FEM approximations in 3D
Pavel Kus; Pavel Solin; David Andrs
2014-11-01
In this paper we discuss constrained approximation with arbitrary-level hanging nodes in adaptive higher-order finite element methods (hphp-FEM) for three-dimensional problems. This technique enables using highly irregular meshes, and it greatly simplifies the design of adaptive algorithms as it prevents refinements from propagating recursively through the finite element mesh. The technique makes it possible to design efficient adaptive algorithms for purely hexahedral meshes. We present a detailed mathematical description of the method and illustrate it with numerical examples.
Adaptive upscaling with the dual mesh method
Guerillot, D.; Verdiere, S.
1997-08-01
The objective of this paper is to demonstrate that upscaling should be calculated during the flow simulation instead of trying to enhance the a priori upscaling methods. Hence, counter-examples are given to motivate our approach, the so-called Dual Mesh Method. The main steps of this numerical algorithm are recalled. Applications illustrate the necessity to consider different average relative permeability values depending on the direction in space. Moreover, these values could be different for the same average saturation. This proves that an a priori upscaling cannot be the answer even in homogeneous cases because of the {open_quotes}dynamical heterogeneity{close_quotes} created by the saturation profile. Other examples show the efficiency of the Dual Mesh Method applied to heterogeneous medium and to an actual field case in South America.
Structured Adaptive Mesh Refinement Application Infrastructure
2010-07-15
SAMRAI is an object-oriented support library for structured adaptice mesh refinement (SAMR) simulation of computational science problems, modeled by systems of partial differential equations (PDEs). SAMRAI is developed and maintained in the Center for Applied Scientific Computing (CASC) under ASCI ITS and PSE support. SAMRAI is used in a variety of application research efforts at LLNL and in academia. These applications are developed in collaboration with SAMRAI development team members.
Adaptive mesh generation for viscous flows using Delaunay triangulation
NASA Technical Reports Server (NTRS)
Mavriplis, Dimitri J.
1988-01-01
A method for generating an unstructured triangular mesh in two dimensions, suitable for computing high Reynolds number flows over arbitrary configurations is presented. The method is based on a Delaunay triangulation, which is performed in a locally stretched space, in order to obtain very high aspect ratio triangles in the boundary layer and the wake regions. It is shown how the method can be coupled with an unstructured Navier-Stokes solver to produce a solution adaptive mesh generation procedure for viscous flows.
Parallel adaptation of general three-dimensional hybrid meshes
NASA Astrophysics Data System (ADS)
Kavouklis, Christos; Kallinderis, Yannis
2010-05-01
A new parallel dynamic mesh adaptation and load balancing algorithm for general hybrid grids has been developed. The meshes considered in this work are composed of four kinds of elements; tetrahedra, prisms, hexahedra and pyramids, which poses a challenge to parallel mesh adaptation. Additional complexity imposed by the presence of multiple types of elements affects especially data migration, updates of local data structures and interpartition data structures. Efficient partition of hybrid meshes has been accomplished by transforming them to suitable graphs and using serial graph partitioning algorithms. Communication among processors is based on the faces of the interpartition boundary and the termination detection algorithm of Dijkstra is employed to ensure proper flagging of edges for refinement. An inexpensive dynamic load balancing strategy is introduced to redistribute work load among processors after adaptation. In particular, only the initial coarse mesh, with proper weighting, is balanced which yields savings in computation time and relatively simple implementation of mesh quality preservation rules, while facilitating coarsening of refined elements. Special algorithms are employed for (i) data migration and dynamic updates of the local data structures, (ii) determination of the resulting interpartition boundary and (iii) identification of the communication pattern of processors. Several representative applications are included to evaluate the method.
Parallel Implementation of an Adaptive Scheme for 3D Unstructured Grids on the SP2
NASA Technical Reports Server (NTRS)
Oliker, Leonid; Biswas, Rupak; Strawn, Roger C.
1996-01-01
Dynamic mesh adaption on unstructured grids is a powerful tool for computing unsteady flows that require local grid modifications to efficiently resolve solution features. For this work, we consider an edge-based adaption scheme that has shown good single-processor performance on the C90. We report on our experience parallelizing this code for the SP2. Results show a 47.OX speedup on 64 processors when 10% of the mesh is randomly refined. Performance deteriorates to 7.7X when the same number of edges are refined in a highly-localized region. This is because almost all mesh adaption is confined to a single processor. However, this problem can be remedied by repartitioning the mesh immediately after targeting edges for refinement but before the actual adaption takes place. With this change, the speedup improves dramatically to 43.6X.
Parallel implementation of an adaptive scheme for 3D unstructured grids on the SP2
NASA Technical Reports Server (NTRS)
Strawn, Roger C.; Oliker, Leonid; Biswas, Rupak
1996-01-01
Dynamic mesh adaption on unstructured grids is a powerful tool for computing unsteady flows that require local grid modifications to efficiently resolve solution features. For this work, we consider an edge-based adaption scheme that has shown good single-processor performance on the C90. We report on our experience parallelizing this code for the SP2. Results show a 47.0X speedup on 64 processors when 10 percent of the mesh is randomly refined. Performance deteriorates to 7.7X when the same number of edges are refined in a highly-localized region. This is because almost all the mesh adaption is confined to a single processor. However, this problem can be remedied by repartitioning the mesh immediately after targeting edges for refinement but before the actual adaption takes place. With this change, the speedup improves dramatically to 43.6X.
Stereo 3D vision adapter using commercial DIY goods
NASA Astrophysics Data System (ADS)
Sakamoto, Kunio; Ohara, Takashi
2009-10-01
The conventional display can show only one screen, but it is impossible to enlarge the size of a screen, for example twice. Meanwhile the mirror supplies us with the same image but this mirror image is usually upside down. Assume that the images on an original screen and a virtual screen in the mirror are completely different and both images can be displayed independently. It would be possible to enlarge a screen area twice. This extension method enables the observers to show the virtual image plane and to enlarge a screen area twice. Although the displaying region is doubled, this virtual display could not produce 3D images. In this paper, we present an extension method using a unidirectional diffusing image screen and an improvement for displaying a 3D image using orthogonal polarized image projection.
A Case Study of Communication Optimizations on 3D Mesh Interconnects
NASA Astrophysics Data System (ADS)
Bhatelé, Abhinav; Bohm, Eric; Kalé, Laxmikant V.
Optimal network performance is critical to efficient parallel scaling for communication-bound applications on large machines. With wormhole routing, no-load latencies do not increase significantly with number of hops traveled. Yet, we, and others have recently shown that in presence of contention, message latencies can grow substantially large. Hence task mapping strategies should take the topology of the machine into account on large machines. In this paper, we present topology aware mapping as a technique to optimize communication on 3-dimensional mesh interconnects and hence improve performance.
Multigrid solution of internal flows using unstructured solution adaptive meshes
NASA Astrophysics Data System (ADS)
Smith, Wayne A.; Blake, Kenneth R.
1992-11-01
This is the final report of the NASA Lewis SBIR Phase 2 Contract Number NAS3-25785, Multigrid Solution of Internal Flows Using Unstructured Solution Adaptive Meshes. The objective of this project, as described in the Statement of Work, is to develop and deliver to NASA a general three-dimensional Navier-Stokes code using unstructured solution-adaptive meshes for accuracy and multigrid techniques for convergence acceleration. The code will primarily be applied, but not necessarily limited, to high speed internal flows in turbomachinery.
MHD simulations on an unstructured mesh
Strauss, H.R.; Park, W.; Belova, E.; Fu, G.Y.; Longcope, D.W.; Sugiyama, L.E.
1998-12-31
Two reasons for using an unstructured computational mesh are adaptivity, and alignment with arbitrarily shaped boundaries. Two codes which use finite element discretization on an unstructured mesh are described. FEM3D solves 2D and 3D RMHD using an adaptive grid. MH3D++, which incorporates methods of FEM3D into the MH3D generalized MHD code, can be used with shaped boundaries, which might be 3D.
Kinetic solvers with adaptive mesh in phase space.
Arslanbekov, Robert R; Kolobov, Vladimir I; Frolova, Anna A
2013-12-01
An adaptive mesh in phase space (AMPS) methodology has been developed for solving multidimensional 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" (ToT) data structure. The r mesh is automatically generated around embedded boundaries, and is dynamically adapted to local solution properties. The v mesh is created on-the-fly in each r cell. Mappings between neighboring v-space trees is implemented for the advection operator in r space. We have developed 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 v mesh: the importance sampling, multipoint projection, and variance reduction methods. We have developed an efficient algorithm for calculating the linear Boltzmann collision integral for elastic and inelastic collisions of hot light particles in a Lorentz gas. Our 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 the computational cost and memory usage for solving challenging kinetic problems. PMID:24483578
Kinetic solvers with adaptive mesh in phase space
NASA Astrophysics Data System (ADS)
Arslanbekov, Robert R.; Kolobov, Vladimir I.; Frolova, Anna A.
2013-12-01
An adaptive mesh in phase space (AMPS) methodology has been developed for solving multidimensional 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” (ToT) data structure. The r mesh is automatically generated around embedded boundaries, and is dynamically adapted to local solution properties. The v mesh is created on-the-fly in each r cell. Mappings between neighboring v-space trees is implemented for the advection operator in r space. We have developed 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 v mesh: the importance sampling, multipoint projection, and variance reduction methods. We have developed an efficient algorithm for calculating the linear Boltzmann collision integral for elastic and inelastic collisions of hot light particles in a Lorentz gas. Our 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 the computational cost and memory usage for solving challenging kinetic problems.
Adaptive anisotropic meshing for steady convection-dominated problems
Nguyen, Hoa; Gunzburger, Max; Ju, Lili; Burkardt, John
2009-01-01
Obtaining accurate solutions for convection–diffusion equations is challenging due to the presence of layers when convection dominates the diffusion. To solve this problem, we design an adaptive meshing algorithm which optimizes the alignment of anisotropic meshes with the numerical solution. Three main ingredients are used. First, the streamline upwind Petrov–Galerkin method is used to produce a stabilized solution. Second, an adapted metric tensor is computed from the approximate solution. Third, optimized anisotropic meshes are generated from the computed metric tensor by an anisotropic centroidal Voronoi tessellation algorithm. Our algorithm is tested on a variety of two-dimensional examples and the results shows that the algorithm is robust in detecting layers and efficient in avoiding non-physical oscillations in the numerical approximation.
NASA Astrophysics Data System (ADS)
Dawes, W. N.
This paper describes some recent improvements made to an unstructed mesh, solution-adaptive three-dimensional Navier-Stokes solver aimed at extending the range of geometric complexity which can be handled in the general context of turbomachinery. The methodology involves generation of a topologically cuboidal mesh, and then the detetion of cells which are not required to allow the formation of relatively complex geometries. This comparatively simple approach permits much of the benefits of an unstructured solution environment to be achieved with minimal complication. Solutions are presented for the highly three-dimensional flows associated with a truncated cylinder in a cross flow, a periodic array of coolant ejection holes, and the overtip leakage flow in an annular cascade of turbine blades.
Amato, Giuseppe; Romano, Giorgio; Agrusa, Antonino; Marasa, Salvatore; Cocorullo, Gianfranco; Gulotta, Gaspare; Goetze, Thorsten; Puleio, Roberto
2015-01-01
Despite improvements in prosthetics and surgical techniques, the rate of complications following inguinal hernia repair remains high. Among these, discomfort and chronic pain have become a source of increasing concern among surgeons. Poor quality of tissue ingrowth, such as thin scar plates or shrinking scars-typical results with conventional static implants and plugs-may contribute to these adverse events. Recently, a new type of 3D dynamically responsive implant was introduced to the market. This device, designed to be placed fixation-free, seems to induce ingrowth of viable and structured tissue instead of regressive fibrotic scarring. To elucidate the differences in biologic response between the conventional static meshes and this 3D dynamically responsive implant, a histological comparison was planned. The aim of this study was to determine the quality of tissue incorporation in both types of implants excised after short, medium, and long periods post-implantation. The results showed large differences in the biologic responses between the two implant types. Histologically, the 3D dynamic implant showed development of tissue elements more similar to natural abdominal wall structures, such as the ingrowth of loose and well-hydrated connective tissue, well-formed vascular structures, elastic fibers, and mature nerves, with negligible or absent inflammatory response. All these characteristics were completely absent in the conventional static implants, where a persistent inflammatory reaction was associated with thin, hardened, and shrunken fibrotic scar formation. Consequently, as herniation is a degenerative process, the 3D dynamic implants, which induce regeneration of the typical groin components, seem to address its pathogenesis. PMID:25626584
Numerical simulation of immiscible viscous fingering using adaptive unstructured meshes
NASA Astrophysics Data System (ADS)
Adam, A.; Salinas, P.; Percival, J. R.; Pavlidis, D.; Pain, C.; Muggeridge, A. H.; Jackson, M.
2015-12-01
Displacement of one fluid by another in porous media occurs in various settings including hydrocarbon recovery, CO2 storage and water purification. When the invading fluid is of lower viscosity than the resident fluid, the displacement front is subject to a Saffman-Taylor instability and is unstable to transverse perturbations. These instabilities can grow, leading to fingering of the invading fluid. Numerical simulation of viscous fingering is challenging. The physics is controlled by a complex interplay of viscous and diffusive forces and it is necessary to ensure physical diffusion dominates numerical diffusion to obtain converged solutions. This typically requires the use of high mesh resolution and high order numerical methods. This is computationally expensive. We demonstrate here the use of a novel control volume - finite element (CVFE) method along with dynamic unstructured mesh adaptivity to simulate viscous fingering with higher accuracy and lower computational cost than conventional methods. Our CVFE method employs a discontinuous representation for both pressure and velocity, allowing the use of smaller control volumes (CVs). This yields higher resolution of the saturation field which is represented CV-wise. Moreover, dynamic mesh adaptivity allows high mesh resolution to be employed where it is required to resolve the fingers and lower resolution elsewhere. We use our results to re-examine the existing criteria that have been proposed to govern the onset of instability.Mesh adaptivity requires the mapping of data from one mesh to another. Conventional methods such as consistent interpolation do not readily generalise to discontinuous fields and are non-conservative. We further contribute a general framework for interpolation of CV fields by Galerkin projection. The method is conservative, higher order and yields improved results, particularly with higher order or discontinuous elements where existing approaches are often excessively diffusive.
McGhee, J.M.; Roberts, R.M.; Morel, J.E.
1997-06-01
A spherical harmonics research code (DANTE) has been developed which is compatible with parallel computer architectures. DANTE provides 3-D, multi-material, deterministic, transport capabilities using an arbitrary finite element mesh. The linearized Boltzmann transport equation is solved in a second order self-adjoint form utilizing a Galerkin finite element spatial differencing scheme. The core solver utilizes a preconditioned conjugate gradient algorithm. Other distinguishing features of the code include options for discrete-ordinates and simplified spherical harmonics angular differencing, an exact Marshak boundary treatment for arbitrarily oriented boundary faces, in-line matrix construction techniques to minimize memory consumption, and an effective diffusion based preconditioner for scattering dominated problems. Algorithm efficiency is demonstrated for a massively parallel SIMD architecture (CM-5), and compatibility with MPP multiprocessor platforms or workstation clusters is anticipated.
Narayanaswamy, Arunachalam; Dwarakapuram, Saritha; Bjornsson, Christopher S.; Cutler, Barbara M.; Shain, William
2010-01-01
This paper presents robust 3-D algorithms to segment vasculature that is imaged by labeling laminae, rather than the lumenal volume. The signal is weak, sparse, noisy, nonuniform, low-contrast, and exhibits gaps and spectral artifacts, so adaptive thresholding and Hessian filtering based methods are not effective. The structure deviates from a tubular geometry, so tracing algorithms are not effective. We propose a four step approach. The first step detects candidate voxels using a robust hypothesis test based on a model that assumes Poisson noise and locally planar geometry. The second step performs an adaptive region growth to extract weakly labeled and fine vessels while rejecting spectral artifacts. To enable interactive visualization and estimation of features such as statistical confidence, local curvature, local thickness, and local normal, we perform the third step. In the third step, we construct an accurate mesh representation using marching tetrahedra, volume-preserving smoothing, and adaptive decimation algorithms. To enable topological analysis and efficient validation, we describe a method to estimate vessel centerlines using a ray casting and vote accumulation algorithm which forms the final step of our algorithm. Our algorithm lends itself to parallel processing, and yielded an 8× speedup on a graphics processor (GPU). On synthetic data, our meshes had average error per face (EPF) values of (0.1–1.6) voxels per mesh face for peak signal-to-noise ratios from (110–28 dB). Separately, the error from decimating the mesh to less than 1% of its original size, the EPF was less than 1 voxel/face. When validated on real datasets, the average recall and precision values were found to be 94.66% and 94.84%, respectively. PMID:20199906
Adaptive mesh refinement for 1-dimensional gas dynamics
Hedstrom, G.; Rodrigue, G.; Berger, M.; Oliger, J.
1982-01-01
We consider the solution of the one-dimensional equation of gas-dynamics. Accurate numerical solutions are difficult to obtain on a given spatial mesh because of the existence of physical regions where components of the exact solution are either discontinuous or have large gradient changes. Numerical methods treat these phenomena in a variety of ways. In this paper, the method of adaptive mesh refinement is used. A thorough description of this method for general hyperbolic systems is given elsewhere and only properties of the method pertinent to the system are elaborated.
3-D Adaptive Sparsity Based Image Compression With Applications to Optical Coherence Tomography.
Fang, Leyuan; Li, Shutao; Kang, Xudong; Izatt, Joseph A; Farsiu, Sina
2015-06-01
We present a novel general-purpose compression method for tomographic images, termed 3D adaptive sparse representation based compression (3D-ASRC). In this paper, we focus on applications of 3D-ASRC for the compression of ophthalmic 3D optical coherence tomography (OCT) images. The 3D-ASRC algorithm exploits correlations among adjacent OCT images to improve compression performance, yet is sensitive to preserving their differences. Due to the inherent denoising mechanism of the sparsity based 3D-ASRC, the quality of the compressed images are often better than the raw images they are based on. Experiments on clinical-grade retinal OCT images demonstrate the superiority of the proposed 3D-ASRC over other well-known compression methods. PMID:25561591
3-D Adaptive Sparsity Based Image Compression with Applications to Optical Coherence Tomography
Fang, Leyuan; Li, Shutao; Kang, Xudong; Izatt, Joseph A.; Farsiu, Sina
2015-01-01
We present a novel general-purpose compression method for tomographic images, termed 3D adaptive sparse representation based compression (3D-ASRC). In this paper, we focus on applications of 3D-ASRC for the compression of ophthalmic 3D optical coherence tomography (OCT) images. The 3D-ASRC algorithm exploits correlations among adjacent OCT images to improve compression performance, yet is sensitive to preserving their differences. Due to the inherent denoising mechanism of the sparsity based 3D-ASRC, the quality of the compressed images are often better than the raw images they are based on. Experiments on clinical-grade retinal OCT images demonstrate the superiority of the proposed 3D-ASRC over other well-known compression methods. PMID:25561591
PLUM: Parallel Load Balancing for Adaptive Unstructured Meshes
NASA Technical Reports Server (NTRS)
Oliker, Leonid; Biswas, Rupak; Saini, Subhash (Technical Monitor)
1998-01-01
Mesh adaption is a powerful tool for efficient unstructured-grid computations but causes load imbalance among processors on a parallel machine. We present a novel method called PLUM to dynamically balance the processor workloads with a global view. This paper presents the implementation and integration of all major components within our dynamic load balancing strategy for adaptive grid calculations. Mesh adaption, repartitioning, processor assignment, and remapping are critical components of the framework that must be accomplished rapidly and efficiently so as not to cause a significant overhead to the numerical simulation. A data redistribution model is also presented that predicts the remapping cost on the SP2. This model is required to determine whether the gain from a balanced workload distribution offsets the cost of data movement. Results presented in this paper demonstrate that PLUM is an effective dynamic load balancing strategy which remains viable on a large number of processors.
New methods and astrophysical applications of adaptive mesh fluid simulations
NASA Astrophysics Data System (ADS)
Wang, Peng
cooling module, we performed the first MHD simulations of disk galaxy formation. We find that the initial magnetic fields are quickly amplified to Milky-Way strength in a self-regulated way with amplification rate roughly one e-folding per orbit. This suggests that Milky Way strength magnetic field might be common in high redshift disk galaxies. We have also developed AMR relativistic hydrodynamics code to simulate black hole relativistic jets. We discuss the coupling of the AMR framework with various relativistic solvers and conducted extensive algorithmic comparisons. Via various test problems, we emphasize the importance of resolution studies in relativistic flow simulations because extremely high resolution is required especially when shear flows are present in the problem. Then we present the results of 3D simulations of supermassive black hole jets propagation and gamma ray burst jet breakout. Resolution studies of the two 3D jets simulations further highlight the need of high resolutions to calculate accurately relativistic flow problems. Finally, to push forward the kind of simulations described above, we need faster codes with more physics included. We describe an implementation of compressible inviscid fluid solvers with AMR on Graphics Processing Units (GPU) using NVIDIA's CUDA. We show that the class of high resolution shock capturing schemes can be mapped naturally on this architecture. For both uniform and adaptive simulations, we achieve an overall speedup of approximately 10 times faster execution on one Quadro FX 5600 GPU as compared to a single 3 GHz Intel core on the host computer. Our framework can readily be applied to more general systems of conservation laws and extended to higher order shock capturing schemes. This is shown directly by an implementation of a magneto-hydrodynamic solver and comparing its performance to the pure hydrodynamic case.
Adaptive mesh strategies for the spectral element method
NASA Technical Reports Server (NTRS)
Mavriplis, Catherine
1992-01-01
An adaptive spectral method was developed for the efficient solution of time dependent partial differential equations. Adaptive mesh strategies that include resolution refinement and coarsening by three different methods are illustrated on solutions to the 1-D viscous Burger equation and the 2-D Navier-Stokes equations for driven flow in a cavity. Sharp gradients, singularities, and regions of poor resolution are resolved optimally as they develop in time using error estimators which indicate the choice of refinement to be used. The adaptive formulation presents significant increases in efficiency, flexibility, and general capabilities for high order spectral methods.
Parallel Block Structured Adaptive Mesh Refinement on Graphics Processing Units
Beckingsale, D. A.; Gaudin, W. P.; Hornung, R. D.; Gunney, B. T.; Gamblin, T.; Herdman, J. A.; Jarvis, S. A.
2014-11-17
Block-structured adaptive mesh refinement is a technique that can be used when solving partial differential equations to reduce the number of zones necessary to achieve the required accuracy in areas of interest. These areas (shock fronts, material interfaces, etc.) are recursively covered with finer mesh patches that are grouped into a hierarchy of refinement levels. Despite the potential for large savings in computational requirements and memory usage without a corresponding reduction in accuracy, AMR adds overhead in managing the mesh hierarchy, adding complex communication and data movement requirements to a simulation. In this paper, we describe the design and implementation of a native GPU-based AMR library, including: the classes used to manage data on a mesh patch, the routines used for transferring data between GPUs on different nodes, and the data-parallel operators developed to coarsen and refine mesh data. We validate the performance and accuracy of our implementation using three test problems and two architectures: an eight-node cluster, and over four thousand nodes of Oak Ridge National Laboratory’s Titan supercomputer. Our GPU-based AMR hydrodynamics code performs up to 4.87× faster than the CPU-based implementation, and has been scaled to over four thousand GPUs using a combination of MPI and CUDA.
Parallel load balancing strategy for Volume-of-Fluid methods on 3-D unstructured meshes
NASA Astrophysics Data System (ADS)
Jofre, Lluís; Borrell, Ricard; Lehmkuhl, Oriol; Oliva, Assensi
2015-02-01
Volume-of-Fluid (VOF) is one of the methods of choice to reproduce the interface motion in the simulation of multi-fluid flows. One of its main strengths is its accuracy in capturing sharp interface geometries, although requiring for it a number of geometric calculations. Under these circumstances, achieving parallel performance on current supercomputers is a must. The main obstacle for the parallelization is that the computing costs are concentrated only in the discrete elements that lie on the interface between fluids. Consequently, if the interface is not homogeneously distributed throughout the domain, standard domain decomposition (DD) strategies lead to imbalanced workload distributions. In this paper, we present a new parallelization strategy for general unstructured VOF solvers, based on a dynamic load balancing process complementary to the underlying DD. Its parallel efficiency has been analyzed and compared to the DD one using up to 1024 CPU-cores on an Intel SandyBridge based supercomputer. The results obtained on the solution of several artificially generated test cases show a speedup of up to ∼12× with respect to the standard DD, depending on the interface size, the initial distribution and the number of parallel processes engaged. Moreover, the new parallelization strategy presented is of general purpose, therefore, it could be used to parallelize any VOF solver without requiring changes on the coupled flow solver. Finally, note that although designed for the VOF method, our approach could be easily adapted to other interface-capturing methods, such as the Level-Set, which may present similar workload imbalances.
Development of a Godunov method for Maxwell's equations with Adaptive Mesh Refinement
NASA Astrophysics Data System (ADS)
Barbas, Alfonso; Velarde, Pedro
2015-11-01
In this paper we present a second order 3D method for Maxwell's equations based on a Godunov scheme with Adaptive Mesh Refinement (AMR). In order to achieve it, we apply a limiter which better preserves extrema and boundary conditions based on a characteristic fields decomposition. Despite being more complex, simplifications in the boundary conditions make the resulting method competitive in computer time consumption and accuracy compared to FDTD. AMR allows us to simulate systems with a sharp step in material properties with negligible rebounds and also large domains with accuracy in small wavelengths.
AN ADAPTIVE PARTICLE-MESH GRAVITY SOLVER FOR ENZO
Passy, Jean-Claude; Bryan, Greg L.
2014-11-01
We describe and implement an adaptive particle-mesh algorithm to solve the Poisson equation for grid-based hydrodynamics codes with nested grids. The algorithm is implemented and extensively tested within the astrophysical code Enzo against the multigrid solver available by default. We find that while both algorithms show similar accuracy for smooth mass distributions, the adaptive particle-mesh algorithm is more accurate for the case of point masses, and is generally less noisy. We also demonstrate that the two-body problem can be solved accurately in a configuration with nested grids. In addition, we discuss the effect of subcycling, and demonstrate that evolving all the levels with the same timestep yields even greater precision.
NASA Astrophysics Data System (ADS)
O'Hara, Ryan P.; Chand, Arpita; Vidiyala, Sowmya; Arechavala, Stacie M.; Mitsouras, Dimitrios; Rudin, Stephen; Ionita, Ciprian N.
2016-03-01
Complex vascular anatomies can cause the failure of image-guided endovascular procedures. 3D printed patient-specific vascular phantoms provide clinicians and medical device companies the ability to preemptively plan surgical treatments, test the likelihood of device success, and determine potential operative setbacks. This research aims to present advanced mesh manipulation techniques of stereolithographic (STL) files segmented from medical imaging and post-print surface optimization to match physiological vascular flow resistance. For phantom design, we developed three mesh manipulation techniques. The first method allows outlet 3D mesh manipulations to merge superfluous vessels into a single junction, decreasing the number of flow outlets and making it feasible to include smaller vessels. Next we introduced Boolean operations to eliminate the need to manually merge mesh layers and eliminate errors of mesh self-intersections that previously occurred. Finally we optimize support addition to preserve the patient anatomical geometry. For post-print surface optimization, we investigated various solutions and methods to remove support material and smooth the inner vessel surface. Solutions of chloroform, alcohol and sodium hydroxide were used to process various phantoms and hydraulic resistance was measured and compared with values reported in literature. The newly mesh manipulation methods decrease the phantom design time by 30 - 80% and allow for rapid development of accurate vascular models. We have created 3D printed vascular models with vessel diameters less than 0.5 mm. The methods presented in this work could lead to shorter design time for patient specific phantoms and better physiological simulations.
Boltzmann Solver with Adaptive Mesh in Velocity Space
Kolobov, Vladimir I.; Arslanbekov, Robert R.; Frolova, Anna A.
2011-05-20
We describe the implementation of direct Boltzmann solver with Adaptive Mesh in Velocity Space (AMVS) using quad/octree data structure. The benefits of the AMVS technique are demonstrated for the charged particle transport in weakly ionized plasmas where the collision integral is linear. We also describe the implementation of AMVS for the nonlinear Boltzmann collision integral. Test computations demonstrate both advantages and deficiencies of the current method for calculations of narrow-kernel distributions.
Advances in Patch-Based Adaptive Mesh Refinement Scalability
Gunney, Brian T.N.; Anderson, Robert W.
2015-12-18
Patch-based structured adaptive mesh refinement (SAMR) is widely used for high-resolution simu- lations. Combined with modern supercomputers, it could provide simulations of unprecedented size and resolution. A persistent challenge for this com- bination has been managing dynamically adaptive meshes on more and more MPI tasks. The dis- tributed mesh management scheme in SAMRAI has made some progress SAMR scalability, but early al- gorithms still had trouble scaling past the regime of 105 MPI tasks. This work provides two critical SAMR regridding algorithms, which are integrated into that scheme to ensure efficiency of the whole. The clustering algorithm is an extension of the tile- clustering approach, making it more flexible and efficient in both clustering and parallelism. The partitioner is a new algorithm designed to prevent the network congestion experienced by its prede- cessor. We evaluated performance using weak- and strong-scaling benchmarks designed to be difficult for dynamic adaptivity. Results show good scaling on up to 1.5M cores and 2M MPI tasks. Detailed timing diagnostics suggest scaling would continue well past that.
Advances in Patch-Based Adaptive Mesh Refinement Scalability
Gunney, Brian T.N.; Anderson, Robert W.
2015-12-18
Patch-based structured adaptive mesh refinement (SAMR) is widely used for high-resolution simu- lations. Combined with modern supercomputers, it could provide simulations of unprecedented size and resolution. A persistent challenge for this com- bination has been managing dynamically adaptive meshes on more and more MPI tasks. The dis- tributed mesh management scheme in SAMRAI has made some progress SAMR scalability, but early al- gorithms still had trouble scaling past the regime of 105 MPI tasks. This work provides two critical SAMR regridding algorithms, which are integrated into that scheme to ensure efficiency of the whole. The clustering algorithm is an extensionmore » of the tile- clustering approach, making it more flexible and efficient in both clustering and parallelism. The partitioner is a new algorithm designed to prevent the network congestion experienced by its prede- cessor. We evaluated performance using weak- and strong-scaling benchmarks designed to be difficult for dynamic adaptivity. Results show good scaling on up to 1.5M cores and 2M MPI tasks. Detailed timing diagnostics suggest scaling would continue well past that.« less
NASA Astrophysics Data System (ADS)
Ashir, Moniruddoza; Hahn, Lars; Kluge, Axel; Nocke, Andreas; Cherif, Chokri
2016-03-01
The industrial importance of fiber reinforced plastics (FRPs) is growing steadily in recent years, which are mostly used in different niche products, has been growing steadily in recent years. The integration of sensors and actuators in FRP is potentially valuable for creating innovative applications and therefore the market acceptance of adaptive FRP is increasing. In particular, in the field of highly stressed FRP, structural integrated systems for continuous component parts monitoring play an important role. This presented work focuses on the electro-mechanical characterization of adaptive three-dimensional (3D)FRP with integrated textile-based actuators. Here, the friction spun hybrid yarn, consisting of shape memory alloy (SMA) in wire form as core, serves as an actuator. Because of the shape memory effect, the SMA-hybrid yarn returns to its original shape upon heating that also causes the deformation of adaptive 3D FRP. In order to investigate the influences of the deformation behavior of the adaptive 3D FRP, investigations in this research are varied according to the structural parameters such as radius of curvature of the adaptive 3D FRP, fabric types and number of layers of the fabric in the composite. Results show that reproducible deformations can be realized with adaptive 3D FRP and that structural parameters have a significant impact on the deformation capability.
Block-structured adaptive mesh refinement - theory, implementation and application
Deiterding, Ralf
2011-01-01
Structured adaptive mesh refinement (SAMR) techniques can enable cutting-edge simulations of problems governed by conservation laws. Focusing on the strictly hyperbolic case, these notes explain all algorithmic and mathematical details of a technically relevant implementation tailored for distributed memory computers. An overview of the background of commonly used finite volume discretizations for gas dynamics is included and typical benchmarks to quantify accuracy and performance of the dynamically adaptive code are discussed. Large-scale simulations of shock-induced realistic combustion in non-Cartesian geometry and shock-driven fluid-structure interaction with fully coupled dynamic boundary motion demonstrate the applicability of the discussed techniques for complex scenarios.
ROAMing terrain (Real-time Optimally Adapting Meshes)
Duchaineau, M.; Wolinsky, M.; Sigeti, D.E.; Miller, M.C.; Aldrich, C.; Mineev, M.
1997-07-01
Terrain visualization is a difficult problem for applications requiring accurate images of large datasets at high frame rates, such as flight simulation and ground-based aircraft testing using synthetic sensor stimulation. On current graphics hardware, the problem is to maintain dynamic, view-dependent triangle meshes and texture maps that produce good images at the required frame rate. We present an algorithm for constructing triangle meshes that optimizes flexible view-dependent error metrics, produces guaranteed error bounds, achieves specified triangle counts directly, and uses frame-to-frame coherence to operate at high frame rates for thousands of triangles per frame. Our method, dubbed Real-time Optimally Adapting Meshes (ROAM), uses two priority queues to drive split and merge operations that maintain continuous triangulations built from pre-processed bintree triangles. We introduce two additional performance optimizations: incremental triangle stripping and priority-computation deferral lists. ROAM execution time is proportionate to the number of triangle changes per frame, which is typically a few percent of the output mesh size, hence ROAM performance is insensitive to the resolution and extent of the input terrain. Dynamic terrain and simple vertex morphing are supported.
NASA Technical Reports Server (NTRS)
Raju, I. S.
1992-01-01
A computer program that generates three-dimensional (3D) finite element models for cracked 3D solids was written. This computer program, gensurf, uses minimal input data to generate 3D finite element models for isotropic solids with elliptic or part-elliptic cracks. These models can be used with a 3D finite element program called surf3d. This report documents this mesh generator. In this manual the capabilities, limitations, and organization of gensurf are described. The procedures used to develop 3D finite element models and the input for and the output of gensurf are explained. Several examples are included to illustrate the use of this program. Several input data files are included with this manual so that the users can edit these files to conform to their crack configuration and use them with gensurf.
Elliptic Solvers with Adaptive Mesh Refinement on Complex Geometries
Phillip, B.
2000-07-24
Adaptive Mesh Refinement (AMR) is a numerical technique for locally tailoring the resolution computational grids. Multilevel algorithms for solving elliptic problems on adaptive grids include the Fast Adaptive Composite grid method (FAC) and its parallel variants (AFAC and AFACx). Theory that confirms the independence of the convergence rates of FAC and AFAC on the number of refinement levels exists under certain ellipticity and approximation property conditions. Similar theory needs to be developed for AFACx. The effectiveness of multigrid-based elliptic solvers such as FAC, AFAC, and AFACx on adaptively refined overlapping grids is not clearly understood. Finally, a non-trivial eye model problem will be solved by combining the power of using overlapping grids for complex moving geometries, AMR, and multilevel elliptic solvers.
Fully implicit adaptive mesh refinement algorithm for reduced MHD
NASA Astrophysics Data System (ADS)
Philip, Bobby; Pernice, Michael; Chacon, Luis
2006-10-01
In the macroscopic simulation of plasmas, the numerical modeler is faced with the challenge of dealing with multiple time and length scales. Traditional approaches based on explicit time integration techniques and fixed meshes are not suitable for this challenge, as such approaches prevent the modeler from using realistic plasma parameters to keep the computation feasible. We propose here a novel approach, based on implicit methods and structured adaptive mesh refinement (SAMR). Our emphasis is on both accuracy and scalability with the number of degrees of freedom. As a proof-of-principle, we focus on the reduced resistive MHD model as a basic MHD model paradigm, which is truly multiscale. The approach taken here is to adapt mature physics-based technology to AMR grids, and employ AMR-aware multilevel techniques (such as fast adaptive composite grid --FAC-- algorithms) for scalability. We demonstrate that the concept is indeed feasible, featuring near-optimal scalability under grid refinement. Results of fully-implicit, dynamically-adaptive AMR simulations in challenging dissipation regimes will be presented on a variety of problems that benefit from this capability, including tearing modes, the island coalescence instability, and the tilt mode instability. L. Chac'on et al., J. Comput. Phys. 178 (1), 15- 36 (2002) B. Philip, M. Pernice, and L. Chac'on, Lecture Notes in Computational Science and Engineering, accepted (2006)
2011-01-01
A 63 year-old male with a huge odontogenic lesion of sinus maxillaris was treated with computer-assisted surgery. After resection of the odontogenic lesion, the sinus wall was reconstructed with a prebended 3D titanium-mesh using CAD/CAM technique. This work provides a new treatment device for maxillary reconstruction via rapid prototyping procedures. PMID:22070833
Toward parallel, adaptive mesh refinement for chemically reacting flow simulations
Devine, K.D.; Shadid, J.N.; Salinger, A.G. Hutchinson, S.A.; Hennigan, G.L.
1997-12-01
Adaptive numerical methods offer greater efficiency than traditional numerical methods by concentrating computational effort in regions of the problem domain where the solution is difficult to obtain. In this paper, the authors describe progress toward adding mesh refinement to MPSalsa, a computer program developed at Sandia National laboratories to solve coupled three-dimensional fluid flow and detailed reaction chemistry systems for modeling chemically reacting flow on large-scale parallel computers. Data structures that support refinement and dynamic load-balancing are discussed. Results using uniform refinement with mesh sequencing to improve convergence to steady-state solutions are also presented. Three examples are presented: a lid driven cavity, a thermal convection flow, and a tilted chemical vapor deposition reactor.
Real-time 3D adaptive filtering for portable imaging systems
NASA Astrophysics Data System (ADS)
Bockenbach, Olivier; Ali, Murtaza; Wainwright, Ian; Nadeski, Mark
2015-03-01
Portable imaging devices have proven valuable for emergency medical services both in the field and hospital environments and are becoming more prevalent in clinical settings where the use of larger imaging machines is impractical. 3D adaptive filtering is one of the most advanced techniques aimed at noise reduction and feature enhancement, but is computationally very demanding and hence often not able to run with sufficient performance on a portable platform. In recent years, advanced multicore DSPs have been introduced that attain high processing performance while maintaining low levels of power dissipation. These processors enable the implementation of complex algorithms like 3D adaptive filtering, improving the image quality of portable medical imaging devices. In this study, the performance of a 3D adaptive filtering algorithm on a digital signal processor (DSP) is investigated. The performance is assessed by filtering a volume of size 512x256x128 voxels sampled at a pace of 10 MVoxels/sec.
The development of a solution-adaptive 3D Navier-Stokes solver for turbomachinery
NASA Astrophysics Data System (ADS)
Dawes, W. N.
1991-06-01
This paper describes the early stages in the development of a solution-adaptive fully three-dimensional Navier-Stokes solver. The compressible, Navier-Stokes equations, closed with k-epsiton turbulence modeling, are discretized on an unstructured mesh formed from tetrahedral computational control volumes. At the mesh generation stage and at stages during the solution process itself, mesh refinement is carried out by flagging cells which satisfy particular critera. These criteria include geometric features such as proximity to wetted surfaces and features associated with the particular flowfield, such as fractional variation of a flow variable over cell faces. Solutions are presented for the highly three-dimensional flows associated with a truncated cylinder in a cross flow, a three-dimensional swept transonic bump, and the corner stall and secondary flow in a transonic compressor cascade.
NASA Technical Reports Server (NTRS)
Stapleton, Scott; Gries, Thomas; Waas, Anthony M.; Pineda, Evan J.
2014-01-01
Enhanced finite elements are elements with an embedded analytical solution that can capture detailed local fields, enabling more efficient, mesh independent finite element analysis. The shape functions are determined based on the analytical model rather than prescribed. This method was applied to adhesively bonded joints to model joint behavior with one element through the thickness. This study demonstrates two methods of maintaining the fidelity of such elements during adhesive non-linearity and cracking without increasing the mesh needed for an accurate solution. The first method uses adaptive shape functions, where the shape functions are recalculated at each load step based on the softening of the adhesive. The second method is internal mesh adaption, where cracking of the adhesive within an element is captured by further discretizing the element internally to represent the partially cracked geometry. By keeping mesh adaptations within an element, a finer mesh can be used during the analysis without affecting the global finite element model mesh. Examples are shown which highlight when each method is most effective in reducing the number of elements needed to capture adhesive nonlinearity and cracking. These methods are validated against analogous finite element models utilizing cohesive zone elements.
Väänänen, Sami P; Grassi, Lorenzo; Flivik, Gunnar; Jurvelin, Jukka S; Isaksson, Hanna
2015-08-01
Areal bone mineral density (aBMD), as measured by dual-energy X-ray absorptiometry (DXA), predicts hip fracture risk only moderately. Simulation of bone mechanics based on DXA imaging of the proximal femur, may help to improve the prediction accuracy. Therefore, we collected three (1-3) image sets, including CT images and DXA images of 34 proximal cadaver femurs (set 1, including 30 males, 4 females), 35 clinical patient CT images of the hip (set 2, including 27 males, 8 females) and both CT and DXA images of clinical patients (set 3, including 12 female patients). All CT images were segmented manually and landmarks were placed on both femurs and pelvises. Two separate statistical appearance models (SAMs) were built using the CT images of the femurs and pelvises in sets 1 and 2, respectively. The 3D shape of the femur was reconstructed from the DXA image by matching the SAMs with the DXA images. The orientation and modes of variation of the SAMs were adjusted to minimize the sum of the absolute differences between the projection of the SAMs and a DXA image. The mesh quality and the location of the SAMs with respect to the manually placed control points on the DXA image were used as additional constraints. Then, finite element (FE) models were built from the reconstructed shapes. Mean point-to-surface distance between the reconstructed shape and CT image was 1.0 mm for cadaver femurs in set 1 (leave-one-out test) and 1.4 mm for clinical subjects in set 3. The reconstructed volumetric BMD showed a mean absolute difference of 140 and 185 mg/cm(3) for set 1 and set 3 respectively. The generation of the SAM and the limitation of using only one 2D image were found to be the most significant sources of errors in the shape reconstruction. The noise in the DXA images had only small effect on the accuracy of the shape reconstruction. DXA-based FE simulation was able to explain 85% of the CT-predicted strength of the femur in stance loading. The present method can be used to
3D-SoftChip: A Novel Architecture for Next-Generation Adaptive Computing Systems
NASA Astrophysics Data System (ADS)
Kim, Chul; Rassau, Alex; Lachowicz, Stefan; Lee, Mike Myung-Ok; Eshraghian, Kamran
2006-12-01
This paper introduces a novel architecture for next-generation adaptive computing systems, which we term 3D-SoftChip. The 3D-SoftChip is a 3-dimensional (3D) vertically integrated adaptive computing system combining state-of-the-art processing and 3D interconnection technology. It comprises the vertical integration of two chips (a configurable array processor and an intelligent configurable switch) through an indium bump interconnection array (IBIA). The configurable array processor (CAP) is an array of heterogeneous processing elements (PEs), while the intelligent configurable switch (ICS) comprises a switch block, 32-bit dedicated RISC processor for control, on-chip program/data memory, data frame buffer, along with a direct memory access (DMA) controller. This paper introduces the novel 3D-SoftChip architecture for real-time communication and multimedia signal processing as a next-generation computing system. The paper further describes the advanced HW/SW codesign and verification methodology, including high-level system modeling of the 3D-SoftChip using SystemC, being used to determine the optimum hardware specification in the early design stage.
Compressible Flows on Adaptive and Unstrucured Meshes with FLUIDITY
NASA Astrophysics Data System (ADS)
Nelson, R.; Piggott, M.; Wilson, C.; Kramer, S.
2011-09-01
Fluidity is an open source, general purpose, multi-phase CFD code capable of solving numerically the Navier-Stokes and accompanying field equations on arbitrary unstructured finite element meshes in one, two and three dimensions. It uses a moving finite element/control volume method which allows arbitrary movement of the mesh in time dependent problems. It has a wide range of finite element/control volume element choices including mixed formulations. Here, continuous Galerkin (CG) and control volumes (CV) solutions of the compressible Navier-Stokes (N-S) equations are presented for the stratified tests cases of the rising thermal bubble and inertia gravity waves. Results show good agreement with previously published literature and novel result presented here is the ability to dynamically adapt the mesh to increase resolution in the region of interest, thus reducing the number of degrees of freedom in the problem without decreasing the accuracy of the result. Finally, results from the case of a fully three dimensional rising thermal bubble are presented.
Thermal-chemical Mantle Convection Models With Adaptive Mesh Refinement
NASA Astrophysics Data System (ADS)
Leng, W.; Zhong, S.
2008-12-01
In numerical modeling of mantle convection, resolution is often crucial for resolving small-scale features. New techniques, adaptive mesh refinement (AMR), allow local mesh refinement wherever high resolution is needed, while leaving other regions with relatively low resolution. Both computational efficiency for large- scale simulation and accuracy for small-scale features can thus be achieved with AMR. Based on the octree data structure [Tu et al. 2005], we implement the AMR techniques into the 2-D mantle convection models. For pure thermal convection models, benchmark tests show that our code can achieve high accuracy with relatively small number of elements both for isoviscous cases (i.e. 7492 AMR elements v.s. 65536 uniform elements) and for temperature-dependent viscosity cases (i.e. 14620 AMR elements v.s. 65536 uniform elements). We further implement tracer-method into the models for simulating thermal-chemical convection. By appropriately adding and removing tracers according to the refinement of the meshes, our code successfully reproduces the benchmark results in van Keken et al. [1997] with much fewer elements and tracers compared with uniform-mesh models (i.e. 7552 AMR elements v.s. 16384 uniform elements, and ~83000 tracers v.s. ~410000 tracers). The boundaries of the chemical piles in our AMR code can be easily refined to the scales of a few kilometers for the Earth's mantle and the tracers are concentrated near the chemical boundaries to precisely trace the evolvement of the boundaries. It is thus very suitable for our AMR code to study the thermal-chemical convection problems which need high resolution to resolve the evolvement of chemical boundaries, such as the entrainment problems [Sleep, 1988].
Parallel Processing of Adaptive Meshes with Load Balancing
NASA Technical Reports Server (NTRS)
Das, Sajal K.; Harvey, Daniel J.; Biswas, Rupak; Biegel, Bryan (Technical Monitor)
2001-01-01
Many scientific applications involve grids that lack a uniform underlying structure. These applications are often also dynamic in nature in that the grid structure significantly changes between successive phases of execution. In parallel computing environments, mesh adaptation of unstructured grids through selective refinement/coarsening has proven to be an effective approach. However, achieving load balance while minimizing interprocessor communication and redistribution costs is a difficult problem. Traditional dynamic load balancers are mostly inadequate because they lack a global view of system loads across processors. In this paper, we propose a novel and general-purpose load balancer that utilizes symmetric broadcast networks (SBN) as the underlying communication topology, and compare its performance with a successful global load balancing environment, called PLUM, specifically created to handle adaptive unstructured applications. Our experimental results on an IBM SP2 demonstrate that the SBN-based load balancer achieves lower redistribution costs than that under PLUM by overlapping processing and data migration.
Dynamic Load Balancing for Adaptive Meshes using Symmetric Broadcast Networks
NASA Technical Reports Server (NTRS)
Das, Sajal K.; Harvey, Daniel J.; Biswas, Rupak; Saini, Subhash (Technical Monitor)
1998-01-01
Many scientific applications involve grids that lack a uniform underlying structure. These applications are often dynamic in the sense that the grid structure significantly changes between successive phases of execution. In parallel computing environments, mesh adaptation of grids through selective refinement/coarsening has proven to be an effective approach. However, achieving load balance while minimizing inter-processor communication and redistribution costs is a difficult problem. Traditional dynamic load balancers are mostly inadequate because they lack a global view across processors. In this paper, we compare a novel load balancer that utilizes symmetric broadcast networks (SBN) to a successful global load balancing environment (PLUM) created to handle adaptive unstructured applications. Our experimental results on the IBM SP2 demonstrate that performance of the proposed SBN load balancer is comparable to results achieved under PLUM.
A Predictive Model of Fragmentation using Adaptive Mesh Refinement and a Hierarchical Material Model
Koniges, A E; Masters, N D; Fisher, A C; Anderson, R W; Eder, D C; Benson, D; Kaiser, T B; Gunney, B T; Wang, P; Maddox, B R; Hansen, J F; Kalantar, D H; Dixit, P; Jarmakani, H; Meyers, M A
2009-03-03
Fragmentation is a fundamental material process that naturally spans spatial scales from microscopic to macroscopic. We developed a mathematical framework using an innovative combination of hierarchical material modeling (HMM) and adaptive mesh refinement (AMR) to connect the continuum to microstructural regimes. This framework has been implemented in a new multi-physics, multi-scale, 3D simulation code, NIF ALE-AMR. New multi-material volume fraction and interface reconstruction algorithms were developed for this new code, which is leading the world effort in hydrodynamic simulations that combine AMR with ALE (Arbitrary Lagrangian-Eulerian) techniques. The interface reconstruction algorithm is also used to produce fragments following material failure. In general, the material strength and failure models have history vector components that must be advected along with other properties of the mesh during remap stage of the ALE hydrodynamics. The fragmentation models are validated against an electromagnetically driven expanding ring experiment and dedicated laser-based fragmentation experiments conducted at the Jupiter Laser Facility. As part of the exit plan, the NIF ALE-AMR code was applied to a number of fragmentation problems of interest to the National Ignition Facility (NIF). One example shows the added benefit of multi-material ALE-AMR that relaxes the requirement that material boundaries must be along mesh boundaries.
Grid-Adapted FUN3D Computations for the Second High Lift Prediction Workshop
NASA Technical Reports Server (NTRS)
Lee-Rausch, E. M.; Rumsey, C. L.; Park, M. A.
2014-01-01
Contributions of the unstructured Reynolds-averaged Navier-Stokes code FUN3D to the 2nd AIAA CFD High Lift Prediction Workshop are described, and detailed comparisons are made with experimental data. Using workshop-supplied grids, results for the clean wing configuration are compared with results from the structured code CFL3D Using the same turbulence model, both codes compare reasonably well in terms of total forces and moments, and the maximum lift is similarly over-predicted for both codes compared to experiment. By including more representative geometry features such as slat and flap brackets and slat pressure tube bundles, FUN3D captures the general effects of the Reynolds number variation, but under-predicts maximum lift on workshop-supplied grids in comparison with the experimental data, due to excessive separation. However, when output-based, off-body grid adaptation in FUN3D is employed, results improve considerably. In particular, when the geometry includes both brackets and the pressure tube bundles, grid adaptation results in a more accurate prediction of lift near stall in comparison with the wind-tunnel data. Furthermore, a rotation-corrected turbulence model shows improved pressure predictions on the outboard span when using adapted grids.
NASA Astrophysics Data System (ADS)
Zheng, J.; Zhu, J.; Wang, Z.; Fang, F.; Pain, C. C.; Xiang, J.
2015-10-01
An integrated method of advanced anisotropic hr-adaptive mesh and discretization numerical techniques has been, for first time, applied to modelling of multiscale advection-diffusion problems, which is based on a discontinuous Galerkin/control volume discretization on unstructured meshes. Over existing air quality models typically based on static-structured grids using a locally nesting technique, the advantage of the anisotropic hr-adaptive model has the ability to adapt the mesh according to the evolving pollutant distribution and flow features. That is, the mesh resolution can be adjusted dynamically to simulate the pollutant transport process accurately and effectively. To illustrate the capability of the anisotropic adaptive unstructured mesh model, three benchmark numerical experiments have been set up for two-dimensional (2-D) advection phenomena. Comparisons have been made between the results obtained using uniform resolution meshes and anisotropic adaptive resolution meshes. Performance achieved in 3-D simulation of power plant plumes indicates that this new adaptive multiscale model has the potential to provide accurate air quality modelling solutions effectively.
Visualization of Octree Adaptive Mesh Refinement (AMR) in Astrophysical Simulations
NASA Astrophysics Data System (ADS)
Labadens, M.; Chapon, D.; Pomaréde, D.; Teyssier, R.
2012-09-01
Computer simulations are important in current cosmological research. Those simulations run in parallel on thousands of processors, and produce huge amount of data. Adaptive mesh refinement is used to reduce the computing cost while keeping good numerical accuracy in regions of interest. RAMSES is a cosmological code developed by the Commissariat à l'énergie atomique et aux énergies alternatives (English: Atomic Energy and Alternative Energies Commission) which uses Octree adaptive mesh refinement. Compared to grid based AMR, the Octree AMR has the advantage to fit very precisely the adaptive resolution of the grid to the local problem complexity. However, this specific octree data type need some specific software to be visualized, as generic visualization tools works on Cartesian grid data type. This is why the PYMSES software has been also developed by our team. It relies on the python scripting language to ensure a modular and easy access to explore those specific data. In order to take advantage of the High Performance Computer which runs the RAMSES simulation, it also uses MPI and multiprocessing to run some parallel code. We would like to present with more details our PYMSES software with some performance benchmarks. PYMSES has currently two visualization techniques which work directly on the AMR. The first one is a splatting technique, and the second one is a custom ray tracing technique. Both have their own advantages and drawbacks. We have also compared two parallel programming techniques with the python multiprocessing library versus the use of MPI run. The load balancing strategy has to be smartly defined in order to achieve a good speed up in our computation. Results obtained with this software are illustrated in the context of a massive, 9000-processor parallel simulation of a Milky Way-like galaxy.
An adaptive mesh-moving and refinement procedure for one-dimensional conservation laws
NASA Technical Reports Server (NTRS)
Biswas, Rupak; Flaherty, Joseph E.; Arney, David C.
1993-01-01
We examine the performance of an adaptive mesh-moving and /or local mesh refinement procedure for the finite difference solution of one-dimensional hyperbolic systems of conservation laws. Adaptive motion of a base mesh is designed to isolate spatially distinct phenomena, and recursive local refinement of the time step and cells of the stationary or moving base mesh is performed in regions where a refinement indicator exceeds a prescribed tolerance. These adaptive procedures are incorporated into a computer code that includes a MacCormack finite difference scheme wih Davis' artificial viscosity model and a discretization error estimate based on Richardson's extrapolation. Experiments are conducted on three problems in order to qualify the advantages of adaptive techniques relative to uniform mesh computations and the relative benefits of mesh moving and refinement. Key results indicate that local mesh refinement, with and without mesh moving, can provide reliable solutions at much lower computational cost than possible on uniform meshes; that mesh motion can be used to improve the results of uniform mesh solutions for a modest computational effort; that the cost of managing the tree data structure associated with refinement is small; and that a combination of mesh motion and refinement reliably produces solutions for the least cost per unit accuracy.
Adaptive mesh refinement and adjoint methods in geophysics simulations
NASA Astrophysics Data System (ADS)
Burstedde, Carsten
2013-04-01
It is an ongoing challenge to increase the resolution that can be achieved by numerical geophysics simulations. This applies to considering sub-kilometer mesh spacings in global-scale mantle convection simulations as well as to using frequencies up to 1 Hz in seismic wave propagation simulations. One central issue is the numerical cost, since for three-dimensional space discretizations, possibly combined with time stepping schemes, a doubling of resolution can lead to an increase in storage requirements and run time by factors between 8 and 16. A related challenge lies in the fact that an increase in resolution also increases the dimensionality of the model space that is needed to fully parametrize the physical properties of the simulated object (a.k.a. earth). Systems that exhibit a multiscale structure in space are candidates for employing adaptive mesh refinement, which varies the resolution locally. An example that we found well suited is the mantle, where plate boundaries and fault zones require a resolution on the km scale, while deeper area can be treated with 50 or 100 km mesh spacings. This approach effectively reduces the number of computational variables by several orders of magnitude. While in this case it is possible to derive the local adaptation pattern from known physical parameters, it is often unclear what are the most suitable criteria for adaptation. We will present the goal-oriented error estimation procedure, where such criteria are derived from an objective functional that represents the observables to be computed most accurately. Even though this approach is well studied, it is rarely used in the geophysics community. A related strategy to make finer resolution manageable is to design methods that automate the inference of model parameters. Tweaking more than a handful of numbers and judging the quality of the simulation by adhoc comparisons to known facts and observations is a tedious task and fundamentally limited by the turnaround times
Modeling and simulating the adaptive electrical properties of stochastic polymeric 3D networks
NASA Astrophysics Data System (ADS)
Sigala, R.; Smerieri, A.; Schüz, A.; Camorani, P.; Erokhin, V.
2013-10-01
Memristors are passive two-terminal circuit elements that combine resistance and memory. Although in theory memristors are a very promising approach to fabricate hardware with adaptive properties, there are only very few implementations able to show their basic properties. We recently developed stochastic polymeric matrices with a functionality that evidences the formation of self-assembled three-dimensional (3D) networks of memristors. We demonstrated that those networks show the typical hysteretic behavior observed in the ‘one input-one output’ memristive configuration. Interestingly, using different protocols to electrically stimulate the networks, we also observed that their adaptive properties are similar to those present in the nervous system. Here, we model and simulate the electrical properties of these self-assembled polymeric networks of memristors, the topology of which is defined stochastically. First, we show that the model recreates the hysteretic behavior observed in the real experiments. Second, we demonstrate that the networks modeled indeed have a 3D instead of a planar functionality. Finally, we show that the adaptive properties of the networks depend on their connectivity pattern. Our model was able to replicate fundamental qualitative behavior of the real organic 3D memristor networks; yet, through the simulations, we also explored other interesting properties, such as the relation between connectivity patterns and adaptive properties. Our model and simulations represent an interesting tool to understand the very complex behavior of self-assembled memristor networks, which can finally help to predict and formulate hypotheses for future experiments.
A Spectral Adaptive Mesh Refinement Method for the Burgers equation
NASA Astrophysics Data System (ADS)
Nasr Azadani, Leila; Staples, Anne
2013-03-01
Adaptive mesh refinement (AMR) is a powerful technique in computational fluid dynamics (CFD). Many CFD problems have a wide range of scales which vary with time and space. In order to resolve all the scales numerically, high grid resolutions are required. The smaller the scales the higher the resolutions should be. However, small scales are usually formed in a small portion of the domain or in a special period of time. AMR is an efficient method to solve these types of problems, allowing high grid resolutions where and when they are needed and minimizing memory and CPU time. Here we formulate a spectral version of AMR in order to accelerate simulations of a 1D model for isotropic homogenous turbulence, the Burgers equation, as a first test of this method. Using pseudo spectral methods, we applied AMR in Fourier space. The spectral AMR (SAMR) method we present here is applied to the Burgers equation and the results are compared with the results obtained using standard solution methods performed using a fine mesh.
Improved Simulation of Electrodiffusion in the Node of Ranvier by Mesh Adaptation.
Dione, Ibrahima; Deteix, Jean; Briffard, Thomas; Chamberland, Eric; Doyon, Nicolas
2016-01-01
In neural structures with complex geometries, numerical resolution of the Poisson-Nernst-Planck (PNP) equations is necessary to accurately model electrodiffusion. This formalism allows one to describe ionic concentrations and the electric field (even away from the membrane) with arbitrary spatial and temporal resolution which is impossible to achieve with models relying on cable theory. However, solving the PNP equations on complex geometries involves handling intricate numerical difficulties related either to the spatial discretization, temporal discretization or the resolution of the linearized systems, often requiring large computational resources which have limited the use of this approach. In the present paper, we investigate the best ways to use the finite elements method (FEM) to solve the PNP equations on domains with discontinuous properties (such as occur at the membrane-cytoplasm interface). 1) Using a simple 2D geometry to allow comparison with analytical solution, we show that mesh adaptation is a very (if not the most) efficient way to obtain accurate solutions while limiting the computational efforts, 2) We use mesh adaptation in a 3D model of a node of Ranvier to reveal details of the solution which are nearly impossible to resolve with other modelling techniques. For instance, we exhibit a non linear distribution of the electric potential within the membrane due to the non uniform width of the myelin and investigate its impact on the spatial profile of the electric field in the Debye layer. PMID:27548674
Improved Simulation of Electrodiffusion in the Node of Ranvier by Mesh Adaptation
Dione, Ibrahima; Briffard, Thomas; Doyon, Nicolas
2016-01-01
In neural structures with complex geometries, numerical resolution of the Poisson-Nernst-Planck (PNP) equations is necessary to accurately model electrodiffusion. This formalism allows one to describe ionic concentrations and the electric field (even away from the membrane) with arbitrary spatial and temporal resolution which is impossible to achieve with models relying on cable theory. However, solving the PNP equations on complex geometries involves handling intricate numerical difficulties related either to the spatial discretization, temporal discretization or the resolution of the linearized systems, often requiring large computational resources which have limited the use of this approach. In the present paper, we investigate the best ways to use the finite elements method (FEM) to solve the PNP equations on domains with discontinuous properties (such as occur at the membrane-cytoplasm interface). 1) Using a simple 2D geometry to allow comparison with analytical solution, we show that mesh adaptation is a very (if not the most) efficient way to obtain accurate solutions while limiting the computational efforts, 2) We use mesh adaptation in a 3D model of a node of Ranvier to reveal details of the solution which are nearly impossible to resolve with other modelling techniques. For instance, we exhibit a non linear distribution of the electric potential within the membrane due to the non uniform width of the myelin and investigate its impact on the spatial profile of the electric field in the Debye layer. PMID:27548674
Pavarino, E.; Neves, L. A.; Machado, J. M.; de Godoy, M. F.; Shiyou, Y.; Momente, J. C.; Zafalon, G. F. D.; Pinto, A. R.; Valêncio, C. R.
2013-01-01
The Finite Element Method is a well-known technique, being extensively applied in different areas. Studies using the Finite Element Method (FEM) are targeted to improve cardiac ablation procedures. For such simulations, the finite element meshes should consider the size and histological features of the target structures. However, it is possible to verify that some methods or tools used to generate meshes of human body structures are still limited, due to nondetailed models, nontrivial preprocessing, or mainly limitation in the use condition. In this paper, alternatives are demonstrated to solid modeling and automatic generation of highly refined tetrahedral meshes, with quality compatible with other studies focused on mesh generation. The innovations presented here are strategies to integrate Open Source Software (OSS). The chosen techniques and strategies are presented and discussed, considering cardiac structures as a first application context. PMID:23762031
Adaptive image warping for hole prevention in 3D view synthesis.
Plath, Nils; Knorr, Sebastian; Goldmann, Lutz; Sikora, Thomas
2013-09-01
Increasing popularity of 3D videos calls for new methods to ease the conversion process of existing monocular video to stereoscopic or multi-view video. A popular way to convert video is given by depth image-based rendering methods, in which a depth map that is associated with an image frame is used to generate a virtual view. Because of the lack of knowledge about the 3D structure of a scene and its corresponding texture, the conversion of 2D video, inevitably, however, leads to holes in the resulting 3D image as a result of newly-exposed areas. The conversion process can be altered such that no holes become visible in the resulting 3D view by superimposing a regular grid over the depth map and deforming it. In this paper, an adaptive image warping approach as an improvement to the regular approach is proposed. The new algorithm exploits the smoothness of a typical depth map to reduce the complexity of the underlying optimization problem that is necessary to find the deformation, which is required to prevent holes. This is achieved by splitting a depth map into blocks of homogeneous depth using quadtrees and running the optimization on the resulting adaptive grid. The results show that this approach leads to a considerable reduction of the computational complexity while maintaining the visual quality of the synthesized views. PMID:23782807
Production-quality Tools for Adaptive Mesh RefinementVisualization
Weber, Gunther H.; Childs, Hank; Bonnell, Kathleen; Meredith,Jeremy; Miller, Mark; Whitlock, Brad; Bethel, E. Wes
2007-10-25
Adaptive Mesh Refinement (AMR) is a highly effectivesimulation method for spanning a large range of spatiotemporal scales,such as astrophysical simulations that must accommodate ranges frominterstellar to sub-planetary. Most mainstream visualization tools stilllack support for AMR as a first class data type and AMR code teams usecustom built applications for AMR visualization. The Department ofEnergy's (DOE's) Science Discovery through Advanced Computing (SciDAC)Visualization and Analytics Center for Enabling Technologies (VACET) isextending and deploying VisIt, an open source visualization tool thataccommodates AMR as a first-class data type, for use asproduction-quality, parallel-capable AMR visual data analysisinfrastructure. This effort will help science teams that use AMR-basedsimulations and who develop their own AMR visual data analysis softwareto realize cost and labor savings.
Structured adaptive mesh refinement on the connection machine
Berger, M.J. . Courant Inst. of Mathematical Sciences); Saltzman, J.S. )
1993-01-01
Adaptive mesh refinement has proven itself to be a useful tool in a large collection of applications. By refining only a small portion of the computational domain, computational savings of up to a factor of 80 in 3 dimensional calculations have been obtained on serial machines. A natural question is, can this algorithm be used on massively parallel machines and still achieve the same efficiencies We have designed a data layout scheme for mapping grid points to processors that preserves locality and minimizes global communication for the CM-200. The effect of the data layout scheme is that at the finest level nearby grid points from adjacent grids in physical space are in adjacent memory locations. Furthermore, coarse grid points are arranged in memory to be near their associated fine grid points. We show applications of the algorithm to inviscid compressible fluid flow in two space dimensions.
Unstructured and adaptive mesh generation for high Reynolds number viscous flows
NASA Technical Reports Server (NTRS)
Mavriplis, Dimitri J.
1991-01-01
A method for generating and adaptively refining a highly stretched unstructured mesh suitable for the computation of high-Reynolds-number viscous flows about arbitrary two-dimensional geometries was developed. The method is based on the Delaunay triangulation of a predetermined set of points and employs a local mapping in order to achieve the high stretching rates required in the boundary-layer and wake regions. The initial mesh-point distribution is determined in a geometry-adaptive manner which clusters points in regions of high curvature and sharp corners. Adaptive mesh refinement is achieved by adding new points in regions of large flow gradients, and locally retriangulating; thus, obviating the need for global mesh regeneration. Initial and adapted meshes about complex multi-element airfoil geometries are shown and compressible flow solutions are computed on these meshes.
NASA Technical Reports Server (NTRS)
Usab, William J., Jr.; Jiang, Yi-Tsann
1991-01-01
The objective of the present research is to develop a general solution adaptive scheme for the accurate prediction of inviscid quasi-three-dimensional flow in advanced compressor and turbine designs. The adaptive solution scheme combines an explicit finite-volume time-marching scheme for unstructured triangular meshes and an advancing front triangular mesh scheme with a remeshing procedure for adapting the mesh as the solution evolves. The unstructured flow solver has been tested on a series of two-dimensional airfoil configurations including a three-element analytic test case presented here. Mesh adapted quasi-three-dimensional Euler solutions are presented for three spanwise stations of the NASA rotor 67 transonic fan. Computed solutions are compared with available experimental data.
Implicit adaptive mesh refinement for 2D reduced resistive magnetohydrodynamics
NASA Astrophysics Data System (ADS)
Philip, Bobby; Chacón, Luis; Pernice, Michael
2008-10-01
An implicit structured adaptive mesh refinement (SAMR) solver for 2D reduced magnetohydrodynamics (MHD) is described. The time-implicit discretization is able to step over fast normal modes, while the spatial adaptivity resolves thin, dynamically evolving features. A Jacobian-free Newton-Krylov method is used for the nonlinear solver engine. For preconditioning, we have extended the optimal "physics-based" approach developed in [L. Chacón, D.A. Knoll, J.M. Finn, An implicit, nonlinear reduced resistive MHD solver, J. Comput. Phys. 178 (2002) 15-36] (which employed multigrid solver technology in the preconditioner for scalability) to SAMR grids using the well-known Fast Adaptive Composite grid (FAC) method [S. McCormick, Multilevel Adaptive Methods for Partial Differential Equations, SIAM, Philadelphia, PA, 1989]. A grid convergence study demonstrates that the solver performance is independent of the number of grid levels and only depends on the finest resolution considered, and that it scales well with grid refinement. The study of error generation and propagation in our SAMR implementation demonstrates that high-order (cubic) interpolation during regridding, combined with a robustly damping second-order temporal scheme such as BDF2, is required to minimize impact of grid errors at coarse-fine interfaces on the overall error of the computation for this MHD application. We also demonstrate that our implementation features the desired property that the overall numerical error is dependent only on the finest resolution level considered, and not on the base-grid resolution or on the number of refinement levels present during the simulation. We demonstrate the effectiveness of the tool on several challenging problems.
NASA Astrophysics Data System (ADS)
Tago, J.; Cruz-Atienza, V. M.; Etienne, V.; Virieux, J.; Benjemaa, M.; Sanchez-Sesma, F. J.
2010-12-01
Simulating any realistic seismic scenario requires incorporating physical basis into the model. Considering both the dynamics of the rupture process and the anelastic attenuation of seismic waves is essential to this purpose and, therefore, we choose to extend the hp-adaptive Discontinuous Galerkin finite-element method to integrate these physical aspects. The 3D elastodynamic equations in an unstructured tetrahedral mesh are solved with a second-order time marching approach in a high-performance computing environment. The first extension incorporates the viscoelastic rheology so that the intrinsic attenuation of the medium is considered in terms of frequency dependent quality factors (Q). On the other hand, the extension related to dynamic rupture is integrated through explicit boundary conditions over the crack surface. For this visco-elastodynamic formulation, we introduce an original discrete scheme that preserves the optimal code performance of the elastodynamic equations. A set of relaxation mechanisms describes the behavior of a generalized Maxwell body. We approximate almost constant Q in a wide frequency range by selecting both suitable relaxation frequencies and anelastic coefficients characterizing these mechanisms. In order to do so, we solve an optimization problem which is critical to minimize the amount of relaxation mechanisms. Two strategies are explored: 1) a least squares method and 2) a genetic algorithm (GA). We found that the improvement provided by the heuristic GA method is negligible. Both optimization strategies yield Q values within the 5% of the target constant Q mechanism. Anelastic functions (i.e. memory variables) are introduced to efficiently evaluate the time convolution terms involved in the constitutive equations and thus to minimize the computational cost. The incorporation of anelastic functions implies new terms with ordinary differential equations in the mathematical formulation. We solve these equations using the same order
Lopez-Camara, D.; Lazzati, Davide; Morsony, Brian J.; Begelman, Mitchell C.
2013-04-10
We present the results of special relativistic, adaptive mesh refinement, 3D simulations of gamma-ray burst jets expanding inside a realistic stellar progenitor. Our simulations confirm that relativistic jets can propagate and break out of the progenitor star while remaining relativistic. This result is independent of the resolution, even though the amount of turbulence and variability observed in the simulations is greater at higher resolutions. We find that the propagation of the jet head inside the progenitor star is slightly faster in 3D simulations compared to 2D ones at the same resolution. This behavior seems to be due to the fact that the jet head in 3D simulations can wobble around the jet axis, finding the spot of least resistance to proceed. Most of the average jet properties, such as density, pressure, and Lorentz factor, are only marginally affected by the dimensionality of the simulations and therefore results from 2D simulations can be considered reliable.
NASA Astrophysics Data System (ADS)
Papadakis, A. P.; Georghiou, G. E.; Metaxas, A. C.
2008-12-01
A new adaptive mesh generator has been developed and used in the analysis of high-pressure gas discharges, such as avalanches and streamers, reducing computational times and computer memory needs significantly. The new adaptive mesh generator developed, uses normalized error indicators, varying from 0 to 1, to guarantee optimal mesh resolution for all carriers involved in the analysis. Furthermore, it uses h- and r-refinement techniques such as mesh jiggling, edge swapping and node addition/removal to develop an element quality improvement algorithm that improves the mesh quality significantly and a fast and accurate algorithm for interpolation between meshes. Finally, the mesh generator is applied in the characterization of the transition from a single electron to the avalanche and streamer discharges in high-voltage, high-pressure gas discharges for dc 1 mm gaps, RF 1 cm point-plane gaps and parallel-plate 40 MHz configurations, in ambient atmospheric air.
NASA Technical Reports Server (NTRS)
Marvriplis, D. J.; Venkatakrishnan, V.
1995-01-01
An agglomeration multigrid strategy is developed and implemented for the solution of three-dimensional steady viscous flows. The method enables convergence acceleration with minimal additional memory overheads, and is completely automated, in that it can deal with grids of arbitrary construction. The multigrid technique is validated by comparing the delivered convergence rates with those obtained by a previously developed overset-mesh multigrid approach, and by demonstrating grid independent convergence rates for aerodynamic problems on very large grids. Prospects for further increases in multigrid efficiency for high-Reynolds number viscous flows on highly stretched meshes are discussed.
FUN3D Grid Refinement and Adaptation Studies for the Ares Launch Vehicle
NASA Technical Reports Server (NTRS)
Bartels, Robert E.; Vasta, Veer; Carlson, Jan-Renee; Park, Mike; Mineck, Raymond E.
2010-01-01
This paper presents grid refinement and adaptation studies performed in conjunction with computational aeroelastic analyses of the Ares crew launch vehicle (CLV). The unstructured grids used in this analysis were created with GridTool and VGRID while the adaptation was performed using the Computational Fluid Dynamic (CFD) code FUN3D with a feature based adaptation software tool. GridTool was developed by ViGYAN, Inc. while the last three software suites were developed by NASA Langley Research Center. The feature based adaptation software used here operates by aligning control volumes with shock and Mach line structures and by refining/de-refining where necessary. It does not redistribute node points on the surface. This paper assesses the sensitivity of the complex flow field about a launch vehicle to grid refinement. It also assesses the potential of feature based grid adaptation to improve the accuracy of CFD analysis for a complex launch vehicle configuration. The feature based adaptation shows the potential to improve the resolution of shocks and shear layers. Further development of the capability to adapt the boundary layer and surface grids of a tetrahedral grid is required for significant improvements in modeling the flow field.
High performance 3D adaptive filtering for DSP based portable medical imaging systems
NASA Astrophysics Data System (ADS)
Bockenbach, Olivier; Ali, Murtaza; Wainwright, Ian; Nadeski, Mark
2015-03-01
Portable medical imaging devices have proven valuable for emergency medical services both in the field and hospital environments and are becoming more prevalent in clinical settings where the use of larger imaging machines is impractical. Despite their constraints on power, size and cost, portable imaging devices must still deliver high quality images. 3D adaptive filtering is one of the most advanced techniques aimed at noise reduction and feature enhancement, but is computationally very demanding and hence often cannot be run with sufficient performance on a portable platform. In recent years, advanced multicore digital signal processors (DSP) have been developed that attain high processing performance while maintaining low levels of power dissipation. These processors enable the implementation of complex algorithms on a portable platform. In this study, the performance of a 3D adaptive filtering algorithm on a DSP is investigated. The performance is assessed by filtering a volume of size 512x256x128 voxels sampled at a pace of 10 MVoxels/sec with an Ultrasound 3D probe. Relative performance and power is addressed between a reference PC (Quad Core CPU) and a TMS320C6678 DSP from Texas Instruments.
Lin, Paul Tinphone; Jameson, Antony, 1934-; Baker, Timothy J.; Martinelli, Luigi
2005-01-01
An implicit multigrid-driven algorithm for two-dimensional incompressible laminar viscous flows has been coupled with a solution adaptation method and a mesh movement method for boundary movement. Time-dependent calculations are performed implicitly by regarding each time step as a steady-state problem in pseudo-time. The method of artificial compressibility is used to solve the flow equations. The solution mesh adaptation method performs local mesh refinement using an incremental Delaunay algorithm and mesh coarsening by means of edge collapse. Mesh movement is achieved by modeling the computational domain as an elastic solid and solving the equilibrium equations for the stress field. The solution adaptation method has been validated by comparison with experimental results and other computational results for low Reynolds number flow over a shedding circular cylinder. Preliminary validation of the mesh movement method has been demonstrated by a comparison with experimental results of an oscillating airfoil and with computational results for an oscillating cylinder.
NASA Astrophysics Data System (ADS)
Kaiser, Markus; John, Matthias; Borsdorf, Anja; Mountney, Peter; Ionasec, Razvan; Nöttling, Alois; Kiefer, Philipp; Seeburger, Jörg; Neumuth, Thomas
2013-03-01
For transcatheter-based minimally invasive procedures in structural heart disease ultrasound and X-ray are the two enabling imaging modalities. A live fusion of both real-time modalities can potentially improve the workflow and the catheter navigation by combining the excellent instrument imaging of X-ray with the high-quality soft tissue imaging of ultrasound. A recently published approach to fuse X-ray fluoroscopy with trans-esophageal echo (TEE) registers the ultrasound probe to X-ray images by a 2D-3D registration method which inherently provides a registration of ultrasound images to X-ray images. In this paper, we significantly accelerate the 2D-3D registration method in this context. The main novelty is to generate the projection images (DRR) of the 3D object not via volume ray-casting but instead via a fast rendering of triangular meshes. This is possible, because in the setting for TEE/X-ray fusion the 3D geometry of the ultrasound probe is known in advance and their main components can be described by triangular meshes. We show that the new approach can achieve a speedup factor up to 65 and does not affect the registration accuracy when used in conjunction with the gradient correlation similarity measure. The improvement is independent of the underlying registration optimizer. Based on the results, a TEE/X-ray fusion could be performed with a higher frame rate and a shorter time lag towards real-time registration performance. The approach could potentially accelerate other applications of 2D-3D registrations, e.g. the registration of implant models with X-ray images.
Aeroacoustic Simulation of Nose Landing Gear on Adaptive Unstructured Grids With FUN3D
NASA Technical Reports Server (NTRS)
Vatsa, Veer N.; Khorrami, Mehdi R.; Park, Michael A.; Lockhard, David P.
2013-01-01
Numerical simulations have been performed for a partially-dressed, cavity-closed nose landing gear configuration that was tested in NASA Langley s closed-wall Basic Aerodynamic Research Tunnel (BART) and in the University of Florida's open-jet acoustic facility known as the UFAFF. The unstructured-grid flow solver FUN3D, developed at NASA Langley Research center, is used to compute the unsteady flow field for this configuration. Starting with a coarse grid, a series of successively finer grids were generated using the adaptive gridding methodology available in the FUN3D code. A hybrid Reynolds-averaged Navier-Stokes/large eddy simulation (RANS/LES) turbulence model is used for these computations. Time-averaged and instantaneous solutions obtained on these grids are compared with the measured data. In general, the correlation with the experimental data improves with grid refinement. A similar trend is observed for sound pressure levels obtained by using these CFD solutions as input to a FfowcsWilliams-Hawkings noise propagation code to compute the farfield noise levels. In general, the numerical solutions obtained on adapted grids compare well with the hand-tuned enriched fine grid solutions and experimental data. In addition, the grid adaption strategy discussed here simplifies the grid generation process, and results in improved computational efficiency of CFD simulations.
An object-oriented approach for parallel self adaptive mesh refinement on block structured grids
NASA Technical Reports Server (NTRS)
Lemke, Max; Witsch, Kristian; Quinlan, Daniel
1993-01-01
Self-adaptive mesh refinement dynamically matches the computational demands of a solver for partial differential equations to the activity in the application's domain. In this paper we present two C++ class libraries, P++ and AMR++, which significantly simplify the development of sophisticated adaptive mesh refinement codes on (massively) parallel distributed memory architectures. The development is based on our previous research in this area. The C++ class libraries provide abstractions to separate the issues of developing parallel adaptive mesh refinement applications into those of parallelism, abstracted by P++, and adaptive mesh refinement, abstracted by AMR++. P++ is a parallel array class library to permit efficient development of architecture independent codes for structured grid applications, and AMR++ provides support for self-adaptive mesh refinement on block-structured grids of rectangular non-overlapping blocks. Using these libraries, the application programmers' work is greatly simplified to primarily specifying the serial single grid application and obtaining the parallel and self-adaptive mesh refinement code with minimal effort. Initial results for simple singular perturbation problems solved by self-adaptive multilevel techniques (FAC, AFAC), being implemented on the basis of prototypes of the P++/AMR++ environment, are presented. Singular perturbation problems frequently arise in large applications, e.g. in the area of computational fluid dynamics. They usually have solutions with layers which require adaptive mesh refinement and fast basic solvers in order to be resolved efficiently.
Algebraic turbulence modeling for unstructured and adaptive meshes
NASA Technical Reports Server (NTRS)
Mavriplis, Dimitri J.
1990-01-01
An algebraic turbulence model based on the Baldwin-Lomax model, has been implemented for use on unstructured grids. The implementation is based on the use of local background structured turbulence meshes. At each time-step, flow variables are interpolated from the unstructured mesh onto the background structured meshes, the turbulence model is executed on these meshes, and the resulting eddy viscosity values are interpolated back to the unstructured mesh. Modifications to the algebraic model were required to enable the treatment of more complicated flows, such as confluent boundary layers and wakes. The model is used in conjuction with an efficient unstructured multigrid finite-element Navier-Stokes solver in order to compute compressible turbulent flows on fully unstructured meshes. Solutions about single and multiple element airfoils are obtained and compared with experimental data.
Xia, Kelin; Zhan, Meng; Wan, Decheng; Wei, Guo-Wei
2012-02-01
Mesh deformation methods are a versatile strategy for solving partial differential equations (PDEs) with a vast variety of practical applications. However, these methods break down for elliptic PDEs with discontinuous coefficients, namely, elliptic interface problems. For this class of problems, the additional interface jump conditions are required to maintain the well-posedness of the governing equation. Consequently, in order to achieve high accuracy and high order convergence, additional numerical algorithms are required to enforce the interface jump conditions in solving elliptic interface problems. The present work introduces an interface technique based adaptively deformed mesh strategy for resolving elliptic interface problems. We take the advantages of the high accuracy, flexibility and robustness of the matched interface and boundary (MIB) method to construct an adaptively deformed mesh based interface method for elliptic equations with discontinuous coefficients. The proposed method generates deformed meshes in the physical domain and solves the transformed governed equations in the computational domain, which maintains regular Cartesian meshes. The mesh deformation is realized by a mesh transformation PDE, which controls the mesh redistribution by a source term. The source term consists of a monitor function, which builds in mesh contraction rules. Both interface geometry based deformed meshes and solution gradient based deformed meshes are constructed to reduce the L(∞) and L(2) errors in solving elliptic interface problems. The proposed adaptively deformed mesh based interface method is extensively validated by many numerical experiments. Numerical results indicate that the adaptively deformed mesh based interface method outperforms the original MIB method for dealing with elliptic interface problems. PMID:22586356
Xia, Kelin; Zhan, Meng; Wan, Decheng; Wei, Guo-Wei
2011-01-01
Mesh deformation methods are a versatile strategy for solving partial differential equations (PDEs) with a vast variety of practical applications. However, these methods break down for elliptic PDEs with discontinuous coefficients, namely, elliptic interface problems. For this class of problems, the additional interface jump conditions are required to maintain the well-posedness of the governing equation. Consequently, in order to achieve high accuracy and high order convergence, additional numerical algorithms are required to enforce the interface jump conditions in solving elliptic interface problems. The present work introduces an interface technique based adaptively deformed mesh strategy for resolving elliptic interface problems. We take the advantages of the high accuracy, flexibility and robustness of the matched interface and boundary (MIB) method to construct an adaptively deformed mesh based interface method for elliptic equations with discontinuous coefficients. The proposed method generates deformed meshes in the physical domain and solves the transformed governed equations in the computational domain, which maintains regular Cartesian meshes. The mesh deformation is realized by a mesh transformation PDE, which controls the mesh redistribution by a source term. The source term consists of a monitor function, which builds in mesh contraction rules. Both interface geometry based deformed meshes and solution gradient based deformed meshes are constructed to reduce the L∞ and L2 errors in solving elliptic interface problems. The proposed adaptively deformed mesh based interface method is extensively validated by many numerical experiments. Numerical results indicate that the adaptively deformed mesh based interface method outperforms the original MIB method for dealing with elliptic interface problems. PMID:22586356
Bauer, Carl A.; Werner, Gregory R.; Cary, John R.
2011-03-01
A new frequency-domain electromagnetics algorithm is developed for simulating curved interfaces between anisotropic dielectrics embedded in a Yee mesh with second-order error in resonant frequencies. The algorithm is systematically derived using the finite integration formulation of Maxwell's equations on the Yee mesh. Second-order convergence of the error in resonant frequencies is achieved by guaranteeing first-order error on dielectric boundaries and second-order error in bulk (possibly anisotropic) regions. Convergence studies, conducted for an analytically solvable problem and for a photonic crystal of ellipsoids with anisotropic dielectric constant, both show second-order convergence of frequency error; the convergence is sufficiently smooth that Richardson extrapolation yields roughly third-order convergence. The convergence of electric fields near the dielectric interface for the analytic problem is also presented.
Fast animation of lightning using an adaptive mesh.
Kim, Theodore; Lin, Ming C
2007-01-01
We present a fast method for simulating, animating, and rendering lightning using adaptive grids. The "dielectric breakdown model" is an elegant algorithm for electrical pattern formation that we extend to enable animation of lightning. The simulation can be slow, particularly in 3D, because it involves solving a large Poisson problem. Losasso et al. recently proposed an octree data structure for simulating water and smoke, and we show that this discretization can be applied to the problem of lightning simulation as well. However, implementing the incomplete Cholesky conjugate gradient (ICCG) solver for this problem can be daunting, so we provide an extensive discussion of implementation issues. ICCG solvers can usually be accelerated using "Eisenstat's trick," but the trick cannot be directly applied to the adaptive case. Fortunately, we show that an "almost incomplete Cholesky" factorization can be computed so that Eisenstat's trick can still be used. We then present a fast rendering method based on convolution that is competitive with Monte Carlo ray tracing but orders of magnitude faster, and we also show how to further improve the visual results using jittering. PMID:17218754
Single-pass GPU-raycasting for structured adaptive mesh refinement data
NASA Astrophysics Data System (ADS)
Kaehler, Ralf; Abel, Tom
2013-01-01
Structured Adaptive Mesh Refinement (SAMR) is a popular numerical technique to study processes with high spatial and temporal dynamic range. It reduces computational requirements by adapting the lattice on which the underlying differential equations are solved to most efficiently represent the solution. Particularly in astrophysics and cosmology such simulations now can capture spatial scales ten orders of magnitude apart and more. The irregular locations and extensions of the refined regions in the SAMR scheme and the fact that different resolution levels partially overlap, poses a challenge for GPU-based direct volume rendering methods. kD-trees have proven to be advantageous to subdivide the data domain into non-overlapping blocks of equally sized cells, optimal for the texture units of current graphics hardware, but previous GPU-supported raycasting approaches for SAMR data using this data structure required a separate rendering pass for each node, preventing the application of many advanced lighting schemes that require simultaneous access to more than one block of cells. In this paper we present the first single-pass GPU-raycasting algorithm for SAMR data that is based on a kD-tree. The tree is efficiently encoded by a set of 3D-textures, which allows to adaptively sample complete rays entirely on the GPU without any CPU interaction. We discuss two different data storage strategies to access the grid data on the GPU and apply them to several datasets to prove the benefits of the proposed method.
An adaptive mesh refinement algorithm for the discrete ordinates method
Jessee, J.P.; Fiveland, W.A.; Howell, L.H.; Colella, P.; Pember, R.B.
1996-03-01
The discrete ordinates form of the radiative transport equation (RTE) is spatially discretized and solved using an adaptive mesh refinement (AMR) algorithm. This technique permits the local grid refinement to minimize spatial discretization error of the RTE. An error estimator is applied to define regions for local grid refinement; overlapping refined grids are recursively placed in these regions; and the RTE is then solved over the entire domain. The procedure continues until the spatial discretization error has been reduced to a sufficient level. The following aspects of the algorithm are discussed: error estimation, grid generation, communication between refined levels, and solution sequencing. This initial formulation employs the step scheme, and is valid for absorbing and isotopically scattering media in two-dimensional enclosures. The utility of the algorithm is tested by comparing the convergence characteristics and accuracy to those of the standard single-grid algorithm for several benchmark cases. The AMR algorithm provides a reduction in memory requirements and maintains the convergence characteristics of the standard single-grid algorithm; however, the cases illustrate that efficiency gains of the AMR algorithm will not be fully realized until three-dimensional geometries are considered.
Numerical study of Taylor bubbles with adaptive unstructured meshes
NASA Astrophysics Data System (ADS)
Xie, Zhihua; Pavlidis, Dimitrios; Percival, James; Pain, Chris; Matar, Omar; Hasan, Abbas; Azzopardi, Barry
2014-11-01
The Taylor bubble is a single long bubble which nearly fills the entire cross section of a liquid-filled circular tube. This type of bubble flow regime often occurs in gas-liquid slug flows in many industrial applications, including oil-and-gas production, chemical and nuclear reactors, and heat exchangers. The objective of this study is to investigate the fluid dynamics of Taylor bubbles rising in a vertical pipe filled with oils of extremely high viscosity (mimicking the ``heavy oils'' found in the oil-and-gas industry). A modelling and simulation framework is presented here which can modify and adapt anisotropic unstructured meshes to better represent the underlying physics of bubble rise and reduce the computational effort without sacrificing accuracy. The numerical framework consists of a mixed control-volume and finite-element formulation, a ``volume of fluid''-type method for the interface capturing based on a compressive control volume advection method, and a force-balanced algorithm for the surface tension implementation. Numerical examples of some benchmark tests and the dynamics of Taylor bubbles are presented to show the capability of this method. EPSRC Programme Grant, MEMPHIS, EP/K0039761/1.
CONSTRAINED-TRANSPORT MAGNETOHYDRODYNAMICS WITH ADAPTIVE MESH REFINEMENT IN CHARM
Miniati, Francesco; Martin, Daniel F. E-mail: DFMartin@lbl.gov
2011-07-01
We present the implementation of a three-dimensional, second-order accurate Godunov-type algorithm for magnetohydrodynamics (MHD) in the adaptive-mesh-refinement (AMR) cosmological code CHARM. The algorithm is based on the full 12-solve spatially unsplit corner-transport-upwind (CTU) scheme. The fluid quantities are cell-centered and are updated using the piecewise-parabolic method (PPM), while the magnetic field variables are face-centered and are evolved through application of the Stokes theorem on cell edges via a constrained-transport (CT) method. The so-called multidimensional MHD source terms required in the predictor step for high-order accuracy are applied in a simplified form which reduces their complexity in three dimensions without loss of accuracy or robustness. The algorithm is implemented on an AMR framework which requires specific synchronization steps across refinement levels. These include face-centered restriction and prolongation operations and a reflux-curl operation, which maintains a solenoidal magnetic field across refinement boundaries. The code is tested against a large suite of test problems, including convergence tests in smooth flows, shock-tube tests, classical two- and three-dimensional MHD tests, a three-dimensional shock-cloud interaction problem, and the formation of a cluster of galaxies in a fully cosmological context. The magnetic field divergence is shown to remain negligible throughout.
Constrained-transport Magnetohydrodynamics with Adaptive Mesh Refinement in CHARM
NASA Astrophysics Data System (ADS)
Miniati, Francesco; Martin, Daniel F.
2011-07-01
We present the implementation of a three-dimensional, second-order accurate Godunov-type algorithm for magnetohydrodynamics (MHD) in the adaptive-mesh-refinement (AMR) cosmological code CHARM. The algorithm is based on the full 12-solve spatially unsplit corner-transport-upwind (CTU) scheme. The fluid quantities are cell-centered and are updated using the piecewise-parabolic method (PPM), while the magnetic field variables are face-centered and are evolved through application of the Stokes theorem on cell edges via a constrained-transport (CT) method. The so-called multidimensional MHD source terms required in the predictor step for high-order accuracy are applied in a simplified form which reduces their complexity in three dimensions without loss of accuracy or robustness. The algorithm is implemented on an AMR framework which requires specific synchronization steps across refinement levels. These include face-centered restriction and prolongation operations and a reflux-curl operation, which maintains a solenoidal magnetic field across refinement boundaries. The code is tested against a large suite of test problems, including convergence tests in smooth flows, shock-tube tests, classical two- and three-dimensional MHD tests, a three-dimensional shock-cloud interaction problem, and the formation of a cluster of galaxies in a fully cosmological context. The magnetic field divergence is shown to remain negligible throughout.
AMR++: Object-oriented design for adaptive mesh refinement
Quinlan, D.
1998-12-01
The development of object-oriented libraries for scientific computing is complicated by the wide range of applications that are targeted and the complexity and wide range of numerical methods that are used. A problem is to design a library that can be customized to handle a wide range of target applications and increasingly complex numerical methods while maintaining a sufficiently useful library for simple problems. These problems have been classically at odds with one another and have compromised the design of many object-oriented library solutions. In this paper the authors detail the mechanisms used within AMR**, and object-oriented library for Adaptive Mesh Refinement (AMR), to provide the level of extensibility that is required to make AMR++ easily customizable for the more obscure applications while remaining small and simple for less complex applications. The goal has been to have a complex applications. The goal has been to have a complexity that matches the complexity of the target application. These mechanisms are general and extend to other libraries as well.
A New Approach to Parallel Dynamic Partitioning for Adaptive Unstructured Meshes
NASA Technical Reports Server (NTRS)
Heber, Gerd; Biswas, Rupak; Gao, Guang R.
1999-01-01
Classical mesh partitioning algorithms were designed for rather static situations, and their straightforward application in a dynamical framework may lead to unsatisfactory results, e.g., excessive data migration among processors. Furthermore, special attention should be paid to their amenability to parallelization. In this paper, a novel parallel method for the dynamic partitioning of adaptive unstructured meshes is described. It is based on a linear representation of the mesh using self-avoiding walks.
Adaptive noise suppression technique for dense 3D point cloud reconstructions from monocular vision
NASA Astrophysics Data System (ADS)
Diskin, Yakov; Asari, Vijayan K.
2012-10-01
Mobile vision-based autonomous vehicles use video frames from multiple angles to construct a 3D model of their environment. In this paper, we present a post-processing adaptive noise suppression technique to enhance the quality of the computed 3D model. Our near real-time reconstruction algorithm uses each pair of frames to compute the disparities of tracked feature points to translate the distance a feature has traveled within the frame in pixels into real world depth values. As a result these tracked feature points are plotted to form a dense and colorful point cloud. Due to the inevitable small vibrations in the camera and the mismatches within the feature tracking algorithm, the point cloud model contains a significant amount of misplaced points appearing as noise. The proposed noise suppression technique utilizes the spatial information of each point to unify points of similar texture and color into objects while simultaneously removing noise dissociated with any nearby objects. The noise filter combines all the points of similar depth into 2D layers throughout the point cloud model. By applying erosion and dilation techniques we are able to eliminate the unwanted floating points while retaining points of larger objects. To reverse the compression process, we transform the 2D layer back into the 3D model allowing points to return to their original position without the attached noise components. We evaluate the resulting noiseless point cloud by utilizing an unmanned ground vehicle to perform obstacle avoidance tasks. The contribution of the noise suppression technique is measured by evaluating the accuracy of the 3D reconstruction.
Object-adaptive depth compensated inter prediction for depth video coding in 3D video system
NASA Astrophysics Data System (ADS)
Kang, Min-Koo; Lee, Jaejoon; Lim, Ilsoon; Ho, Yo-Sung
2011-01-01
Nowadays, the 3D video system using the MVD (multi-view video plus depth) data format is being actively studied. The system has many advantages with respect to virtual view synthesis such as an auto-stereoscopic functionality, but compression of huge input data remains a problem. Therefore, efficient 3D data compression is extremely important in the system, and problems of low temporal consistency and viewpoint correlation should be resolved for efficient depth video coding. In this paper, we propose an object-adaptive depth compensated inter prediction method to resolve the problems where object-adaptive mean-depth difference between a current block, to be coded, and a reference block are compensated during inter prediction. In addition, unique properties of depth video are exploited to reduce side information required for signaling decoder to conduct the same process. To evaluate the coding performance, we have implemented the proposed method into MVC (multiview video coding) reference software, JMVC 8.2. Experimental results have demonstrated that our proposed method is especially efficient for depth videos estimated by DERS (depth estimation reference software) discussed in the MPEG 3DV coding group. The coding gain was up to 11.69% bit-saving, and it was even increased when we evaluated it on synthesized views of virtual viewpoints.
Global Load Balancing with Parallel Mesh Adaption on Distributed-Memory Systems
NASA Technical Reports Server (NTRS)
Biswas, Rupak; Oliker, Leonid; Sohn, Andrew
1996-01-01
Dynamic mesh adaptation on unstructured grids is a powerful tool for efficiently computing unsteady problems to resolve solution features of interest. Unfortunately, this causes load inbalances among processors on a parallel machine. This paper described the parallel implementation of a tetrahedral mesh adaption scheme and a new global load balancing method. A heuristic remapping algorithm is presented that assigns partitions to processors such that the redistribution coast is minimized. Results indicate that the parallel performance of the mesh adaption code depends on the nature of the adaption region and show a 35.5X speedup on 64 processors of an SP2 when 35 percent of the mesh is randomly adapted. For large scale scientific computations, our load balancing strategy gives an almost sixfold reduction in solver execution times over non-balanced loads. Furthermore, our heuristic remappier yields processor assignments that are less than 3 percent of the optimal solutions, but requires only 1 percent of the computational time.
Global Load Balancing with Parallel Mesh Adaption on Distributed-Memory Systems
NASA Technical Reports Server (NTRS)
Biswas, Rupak; Oliker, Leonid; Sohn, Andrew
1996-01-01
Dynamic mesh adaption on unstructured grids is a powerful tool for efficiently computing unsteady problems to resolve solution features of interest. Unfortunately, this causes load imbalance among processors on a parallel machine. This paper describes the parallel implementation of a tetrahedral mesh adaption scheme and a new global load balancing method. A heuristic remapping algorithm is presented that assigns partitions to processors such that the redistribution cost is minimized. Results indicate that the parallel performance of the mesh adaption code depends on the nature of the adaption region and show a 35.5X speedup on 64 processors of an SP2 when 35% of the mesh is randomly adapted. For large-scale scientific computations, our load balancing strategy gives almost a sixfold reduction in solver execution times over non-balanced loads. Furthermore, our heuristic remapper yields processor assignments that are less than 3% off the optimal solutions but requires only 1% of the computational time.
A Robust and Scalable Software Library for Parallel Adaptive Refinement on Unstructured Meshes
NASA Technical Reports Server (NTRS)
Lou, John Z.; Norton, Charles D.; Cwik, Thomas A.
1999-01-01
The design and implementation of Pyramid, a software library for performing parallel adaptive mesh refinement (PAMR) on unstructured meshes, is described. This software library can be easily used in a variety of unstructured parallel computational applications, including parallel finite element, parallel finite volume, and parallel visualization applications using triangular or tetrahedral meshes. The library contains a suite of well-designed and efficiently implemented modules that perform operations in a typical PAMR process. Among these are mesh quality control during successive parallel adaptive refinement (typically guided by a local-error estimator), parallel load-balancing, and parallel mesh partitioning using the ParMeTiS partitioner. The Pyramid library is implemented in Fortran 90 with an interface to the Message-Passing Interface (MPI) library, supporting code efficiency, modularity, and portability. An EM waveguide filter application, adaptively refined using the Pyramid library, is illustrated.
NASA Astrophysics Data System (ADS)
Destrez, Raphaël.; Albouy-Kissi, Benjamin; Treuillet, Sylvie; Lucas, Yves
2015-04-01
Computer aided planning for orthodontic treatment requires knowing occlusion of separately scanned dental casts. A visual guided registration is conducted starting by extracting corresponding features in both photographs and 3D scans. To achieve this, dental neck and occlusion surface are firstly extracted by image segmentation and 3D curvature analysis. Then, an iterative registration process is conducted during which feature positions are refined, guided by previously found anatomic edges. The occlusal edge image detection is improved by an original algorithm which follows Canny's poorly detected edges using a priori knowledge of tooth shapes. Finally, the influence of feature extraction and position optimization is evaluated in terms of the quality of the induced registration. Best combination of feature detection and optimization leads to a positioning average error of 1.10 mm and 2.03°.
Patch-based Adaptive Mesh Refinement for Multimaterial Hydrodynamics
Lomov, I; Pember, R; Greenough, J; Liu, B
2005-10-18
We present a patch-based direct Eulerian adaptive mesh refinement (AMR) algorithm for modeling real equation-of-state, multimaterial compressible flow with strength. Our approach to AMR uses a hierarchical, structured grid approach first developed by (Berger and Oliger 1984), (Berger and Oliger 1984). The grid structure is dynamic in time and is composed of nested uniform rectangular grids of varying resolution. The integration scheme on the grid hierarchy is a recursive procedure in which the coarse grids are advanced, then the fine grids are advanced multiple steps to reach the same time, and finally the coarse and fine grids are synchronized to remove conservation errors during the separate advances. The methodology presented here is based on a single grid algorithm developed for multimaterial gas dynamics by (Colella et al. 1993), refined by(Greenough et al. 1995), and extended to the solution of solid mechanics problems with significant strength by (Lomov and Rubin 2003). The single grid algorithm uses a second-order Godunov scheme with an approximate single fluid Riemann solver and a volume-of-fluid treatment of material interfaces. The method also uses a non-conservative treatment of the deformation tensor and an acoustic approximation for shear waves in the Riemann solver. This departure from a strict application of the higher-order Godunov methodology to the equation of solid mechanics is justified due to the fact that highly nonlinear behavior of shear stresses is rare. This algorithm is implemented in two codes, Geodyn and Raptor, the latter of which is a coupled rad-hydro code. The present discussion will be solely concerned with hydrodynamics modeling. Results from a number of simulations for flows with and without strength will be presented.
RAM: a Relativistic Adaptive Mesh Refinement Hydrodynamics Code
Zhang, Wei-Qun; MacFadyen, Andrew I.; /Princeton, Inst. Advanced Study
2005-06-06
The authors have developed a new computer code, RAM, to solve the conservative equations of special relativistic hydrodynamics (SRHD) using adaptive mesh refinement (AMR) on parallel computers. They have implemented a characteristic-wise, finite difference, weighted essentially non-oscillatory (WENO) scheme using the full characteristic decomposition of the SRHD equations to achieve fifth-order accuracy in space. For time integration they use the method of lines with a third-order total variation diminishing (TVD) Runge-Kutta scheme. They have also implemented fourth and fifth order Runge-Kutta time integration schemes for comparison. The implementation of AMR and parallelization is based on the FLASH code. RAM is modular and includes the capability to easily swap hydrodynamics solvers, reconstruction methods and physics modules. In addition to WENO they have implemented a finite volume module with the piecewise parabolic method (PPM) for reconstruction and the modified Marquina approximate Riemann solver to work with TVD Runge-Kutta time integration. They examine the difficulty of accurately simulating shear flows in numerical relativistic hydrodynamics codes. They show that under-resolved simulations of simple test problems with transverse velocity components produce incorrect results and demonstrate the ability of RAM to correctly solve these problems. RAM has been tested in one, two and three dimensions and in Cartesian, cylindrical and spherical coordinates. they have demonstrated fifth-order accuracy for WENO in one and two dimensions and performed detailed comparison with other schemes for which they show significantly lower convergence rates. Extensive testing is presented demonstrating the ability of RAM to address challenging open questions in relativistic astrophysics.
Fonseca, T C Ferreira; Bogaerts, R; Lebacq, A L; Mihailescu, C L; Vanhavere, F
2014-04-01
A realistic computational 3D human body library, called MaMP and FeMP (Male and Female Mesh Phantoms), based on polygonal mesh surface geometry, has been created to be used for numerical calibration of the whole body counter (WBC) system of the nuclear power plant (NPP) in Doel, Belgium. The main objective was to create flexible computational models varying in gender, body height, and mass for studying the morphology-induced variation of the detector counting efficiency (CE) and reducing the measurement uncertainties. First, the counting room and an HPGe detector were modeled using MCNPX (Monte Carlo radiation transport code). The validation of the model was carried out for different sample-detector geometries with point sources and a physical phantom. Second, CE values were calculated for a total of 36 different mesh phantoms in a seated position using the validated Monte Carlo model. This paper reports on the validation process of the in vivo whole body system and the CE calculated for different body heights and weights. The results reveal that the CE is strongly dependent on the individual body shape, size, and gender and may vary by a factor of 1.5 to 3 depending on the morphology aspects of the individual to be measured. PMID:24562069
Adaptive multi-GPU Exchange Monte Carlo for the 3D Random Field Ising Model
NASA Astrophysics Data System (ADS)
Navarro, Cristóbal A.; Huang, Wei; Deng, Youjin
2016-08-01
This work presents an adaptive multi-GPU Exchange Monte Carlo approach for the simulation of the 3D Random Field Ising Model (RFIM). The design is based on a two-level parallelization. The first level, spin-level parallelism, maps the parallel computation as optimal 3D thread-blocks that simulate blocks of spins in shared memory with minimal halo surface, assuming a constant block volume. The second level, replica-level parallelism, uses multi-GPU computation to handle the simulation of an ensemble of replicas. CUDA's concurrent kernel execution feature is used in order to fill the occupancy of each GPU with many replicas, providing a performance boost that is more notorious at the smallest values of L. In addition to the two-level parallel design, the work proposes an adaptive multi-GPU approach that dynamically builds a proper temperature set free of exchange bottlenecks. The strategy is based on mid-point insertions at the temperature gaps where the exchange rate is most compromised. The extra work generated by the insertions is balanced across the GPUs independently of where the mid-point insertions were performed. Performance results show that spin-level performance is approximately two orders of magnitude faster than a single-core CPU version and one order of magnitude faster than a parallel multi-core CPU version running on 16-cores. Multi-GPU performance is highly convenient under a weak scaling setting, reaching up to 99 % efficiency as long as the number of GPUs and L increase together. The combination of the adaptive approach with the parallel multi-GPU design has extended our possibilities of simulation to sizes of L = 32 , 64 for a workstation with two GPUs. Sizes beyond L = 64 can eventually be studied using larger multi-GPU systems.
NASA Technical Reports Server (NTRS)
Barnard, Stephen T.; Simon, Horst; Lasinski, T. A. (Technical Monitor)
1994-01-01
The design of a parallel implementation of multilevel recursive spectral bisection is described. The goal is to implement a code that is fast enough to enable dynamic repartitioning of adaptive meshes.
Lober, R.R.; Tautges, T.J.; Vaughan, C.T.
1997-03-01
Paving is an automated mesh generation algorithm which produces all-quadrilateral elements. It can additionally generate these elements in varying sizes such that the resulting mesh adapts to a function distribution, such as an error function. While powerful, conventional paving is a very serial algorithm in its operation. Parallel paving is the extension of serial paving into parallel environments to perform the same meshing functions as conventional paving only on distributed, discretized models. This extension allows large, adaptive, parallel finite element simulations to take advantage of paving`s meshing capabilities for h-remap remeshing. A significantly modified version of the CUBIT mesh generation code has been developed to host the parallel paving algorithm and demonstrate its capabilities on both two dimensional and three dimensional surface geometries and compare the resulting parallel produced meshes to conventionally paved meshes for mesh quality and algorithm performance. Sandia`s {open_quotes}tiling{close_quotes} dynamic load balancing code has also been extended to work with the paving algorithm to retain parallel efficiency as subdomains undergo iterative mesh refinement.
Kohn, S.; Weare, J.; Ong, E.; Baden, S.
1997-05-01
We have applied structured adaptive mesh refinement techniques to the solution of the LDA equations for electronic structure calculations. Local spatial refinement concentrates memory resources and numerical effort where it is most needed, near the atomic centers and in regions of rapidly varying charge density. The structured grid representation enables us to employ efficient iterative solver techniques such as conjugate gradient with FAC multigrid preconditioning. We have parallelized our solver using an object- oriented adaptive mesh refinement framework.
Importance of dynamic mesh adaptivity for simulation of viscous fingering in porous media
NASA Astrophysics Data System (ADS)
Mostaghimi, P.; Jackson, M.; Pain, C.; Gorman, G.
2014-12-01
Viscous fingering is a major concern in many natural and engineered processes such as water flooding of heavy-oil reservoirs. Common reservoir simulators employ low-order finite volume/difference methods on structured grids to resolve this phenomenon. However, their approach suffers from a significant numerical dispersion error along the fingering patterns due to insufficient mesh resolution and smears out some important features of the flow. We propose use of an unstructured control volume finite element method for simulation of viscous fingering in porous media. Our approach is equipped with anisotropic mesh adaptivity where the mesh resolution is optimized based on the evolving features of flow. The adaptive algorithm uses a metric tensor field based on solution error estimates to locally control the size and shape of elements in the metric. We resolve the viscous fingering patterns accurately and reduce the numerical dispersion error significantly. The mesh optimization, generates an unstructured coarse mesh in other regions of the computational domain which significantly decreases the computational cost. The effect of grid resolution on the resolved fingers is thoroughly investigated. We analyze the computational cost of mesh adaptivty on unstructured mesh and compare it with common finite volume methods. The results of this study suggests that mesh adaptivity is an efficient and accurate approach for resolving complex behaviors and instabilities of flow in porous media such as viscous fingering.
NASA Astrophysics Data System (ADS)
Lee, W. H.; Kim, T.-S.; Cho, M. H.; Ahn, Y. B.; Lee, S. Y.
2006-12-01
In studying bioelectromagnetic problems, finite element analysis (FEA) offers several advantages over conventional methods such as the boundary element method. It allows truly volumetric analysis and incorporation of material properties such as anisotropic conductivity. For FEA, mesh generation is the first critical requirement and there exist many different approaches. However, conventional approaches offered by commercial packages and various algorithms do not generate content-adaptive meshes (cMeshes), resulting in numerous nodes and elements in modelling the conducting domain, and thereby increasing computational load and demand. In this work, we present efficient content-adaptive mesh generation schemes for complex biological volumes of MR images. The presented methodology is fully automatic and generates FE meshes that are adaptive to the geometrical contents of MR images, allowing optimal representation of conducting domain for FEA. We have also evaluated the effect of cMeshes on FEA in three dimensions by comparing the forward solutions from various cMesh head models to the solutions from the reference FE head model in which fine and equidistant FEs constitute the model. The results show that there is a significant gain in computation time with minor loss in numerical accuracy. We believe that cMeshes should be useful in the FEA of bioelectromagnetic problems.
The image adaptive method for solder paste 3D measurement system
NASA Astrophysics Data System (ADS)
Xiaohui, Li; Changku, Sun; Peng, Wang
2015-03-01
The extensive application of Surface Mount Technology (SMT) requires various measurement methods to evaluate the circuit board. The solder paste 3D measurement system utilizing laser light projecting on the printed circuit board (PCB) surface is one of the critical methods. The local oversaturation, arising from the non-consistent reflectivity of the PCB surface, will lead to inaccurate measurement. The paper reports a novel optical image adaptive method of remedying the local oversaturation for solder paste measurement. The liquid crystal on silicon (LCoS) and image sensor (CCD or CMOS) are combined as the high dynamic range image (HDRI) acquisition system. The significant characteristic of the new method is that the image after adjustment is captured by specially designed HDRI acquisition system programmed by the LCoS mask. The formation of the LCoS mask, depending on a HDRI combined with the image fusion algorithm, is based on separating the laser light from the local oversaturated region. Experimental results demonstrate that the method can significantly improve the accuracy for the solder paste 3D measurement system with local oversaturation.
A 3D approach for object recognition in illuminated scenes with adaptive correlation filters
NASA Astrophysics Data System (ADS)
Picos, Kenia; Díaz-Ramírez, Víctor H.
2015-09-01
In this paper we solve the problem of pose recognition of a 3D object in non-uniformly illuminated and noisy scenes. The recognition system employs a bank of space-variant correlation filters constructed with an adaptive approach based on local statistical parameters of the input scene. The position and orientation of the target are estimated with the help of the filter bank. For an observed input frame, the algorithm computes the correlation process between the observed image and the bank of filters using a combination of data and task parallelism by taking advantage of a graphics processing unit (GPU) architecture. The pose of the target is estimated by finding the template that better matches the current view of target within the scene. The performance of the proposed system is evaluated in terms of recognition accuracy, location and orientation errors, and computational performance.
Model-based adaptive 3D sonar reconstruction in reverberating environments.
Saucan, Augustin-Alexandru; Sintes, Christophe; Chonavel, Thierry; Caillec, Jean-Marc Le
2015-10-01
In this paper, we propose a novel model-based approach for 3D underwater scene reconstruction, i.e., bathymetry, for side scan sonar arrays in complex and highly reverberating environments like shallow water areas. The presence of multipath echoes and volume reverberation generates false depth estimates. To improve the resulting bathymetry, this paper proposes and develops an adaptive filter, based on several original geometrical models. This multimodel approach makes it possible to track and separate the direction of arrival trajectories of multiple echoes impinging the array. Echo tracking is perceived as a model-based processing stage, incorporating prior information on the temporal evolution of echoes in order to reject cluttered observations generated by interfering echoes. The results of the proposed filter on simulated and real sonar data showcase the clutter-free and regularized bathymetric reconstruction. Model validation is carried out with goodness of fit tests, and demonstrates the importance of model-based processing for bathymetry reconstruction. PMID:25974936
MMW and THz images denoising based on adaptive CBM3D
NASA Astrophysics Data System (ADS)
Dai, Li; Zhang, Yousai; Li, Yuanjiang; Wang, Haoxiang
2014-04-01
Over the past decades, millimeter wave and terahertz radiation has received a lot of interest due to advances in emission and detection technologies which allowed the widely application of the millimeter wave and terahertz imaging technology. This paper focuses on solving the problem of this sort of images existing stripe noise, block effect and other interfered information. A new kind of nonlocal average method is put forward. Suitable level Gaussian noise is added to resonate with the image. Adaptive color block-matching 3D filtering is used to denoise. Experimental results demonstrate that it improves the visual effect and removes interference at the same time, making the analysis of the image and target detection more easily.
NASA Astrophysics Data System (ADS)
Todarello, Giovanni; Vonck, Floris; Bourasseau, Sébastien; Peter, Jacques; Désidéri, Jean-Antoine
2016-05-01
A new goal-oriented mesh adaptation method for finite volume/finite difference schemes is extended from the structured mesh framework to a more suitable setting for adaptation of unstructured meshes. The method is based on the total derivative of the goal with respect to volume mesh nodes that is computable after the solution of the goal discrete adjoint equation. The asymptotic behaviour of this derivative is assessed on regularly refined unstructured meshes. A local refinement criterion is derived from the requirement of limiting the first order change in the goal that an admissible node displacement may cause. Mesh adaptations are then carried out for classical test cases of 2D Euler flows. Efficiency and local density of the adapted meshes are presented. They are compared with those obtained with a more classical mesh adaptation method in the framework of finite volume/finite difference schemes [46]. Results are very close although the present method only makes usage of the current grid.
Nava, José L; Sirés, Ignasi; Brillas, Enric
2014-01-01
This paper compares the performance of 2D (plate) and 3D (mesh) boron-doped diamond (BDD) electrodes, fitted into a filter-press reactor, during the electrochemical incineration of indigo textile dye as a model organic compound in chloride medium. The electrolyses were carried out in the FM01-LC reactor at mean fluid velocities between 0.9 ≤ u ≤ 10.4 and 1.2 ≤ u ≤ 13.9 cm s(-1) for the 2D BDD and the 3D BDD electrodes, respectively, at current densities of 5.63 and 15 mA cm(-2). The oxidation of the organic matter was promoted, on the one hand, via the physisorbed hydroxyl radicals (BDD(·OH)) formed from water oxidation at the BDD surface and, on the other hand, via active chlorine formed from the oxidation of chloride ions on BDD. The performance of 2D BDD and 3D BDD electrodes in terms of current efficiency, energy consumption, and charge passage during the treatments is discussed. PMID:24737017
Development of a scalable gas-dynamics solver with adaptive mesh refinement
NASA Astrophysics Data System (ADS)
Korkut, Burak
There are various computational physics areas in which Direct Simulation Monte Carlo (DSMC) and Particle in Cell (PIC) methods are being employed. The accuracy of results from such simulations depend on the fidelity of the physical models being used. The computationally demanding nature of these problems make them ideal candidates to make use of modern supercomputers. The software developed to run such simulations also needs special attention so that the maintainability and extendability is considered with the recent numerical methods and programming paradigms. Suited for gas-dynamics problems, a software called SUGAR (Scalable Unstructured Gas dynamics with Adaptive mesh Refinement) has recently been developed and written in C++ and MPI. Physical and numerical models were added to this framework to simulate ion thruster plumes. SUGAR is used to model the charge-exchange (CEX) reactions occurring between the neutral and ion species as well as the induced electric field effect due to ions. Multiple adaptive mesh refinement (AMR) meshes were used in order to capture different physical length scales present in the flow. A multiple-thruster configuration was run to extend the studies to cases for which there is no axial or radial symmetry present that could only be modeled with a three-dimensional simulation capability. The combined plume structure showed interactions between individual thrusters where AMR capability captured this in an automated way. The back flow for ions was found to occur when CEX and momentum-exchange (MEX) collisions are present and strongly enhanced when the induced electric field is considered. The ion energy distributions in the back flow region were obtained and it was found that the inclusion of the electric field modeling is the most important factor in determining its shape. The plume back flow structure was also examined for a triple-thruster, 3-D geometry case and it was found that the ion velocity in the back flow region appears to be
Star formation with adaptive mesh refinement and magnetohydrodynamics
NASA Astrophysics Data System (ADS)
Collins, David C.
2009-01-01
In this thesis, we develop an adaptive mesh refinement (AMR) code including magnetic fields, and use it to perform high resolution simulations of magnetized molecular clouds. The purpose of these simulations is to study present day star formation in the presence of turbulence and magnetic fields. We first present MHDEnzo, the extension of the cosmology and astrophysics code Enzo to include the effects magnetic fields. We use a higher order Godunov Riemann solver for the computation of interface fluxes; constrained transport to compute the electric field from those interface fluxes, which advances the induction equation in a divergence free manner; divergence free reconstruction technique to interpolate the magnetic fields to fine grids; operator splitting to include gravity and cosmological expansion. We present a series of test problems to demonstrate the quality of solution achieved. Additionally, we present several other solvers that were developed along the way. Finally we present the results from several AMR simulations that study isothermal turbulence in the presence of magnetic fields and self gravity. Ten simulations with initial Mach number 8.9 were studied varying several parameters; virial parameter a from 0.52 to 3.1; whether they were continuously stirred or allowed to decay; and the number of refinement levels (4 or 6). Measurements of the density probability density function (PDF) were made, showing both the expected log normal distribution and an additional power law. Measurements of the line of sight magnetic field vs. column density are done, giving excellent agreement with recent observations. The line width vs. size relationship is measured and compared with good agreement to observations, reproducing both turbulent and collapse signatures The core mass distribution is measured and agrees well with observations of Serpens and Perseus core samples, but the power-law distribution in Ophiuchus is not reproduced by our simulations. Finally we
Vortex-dominated conical-flow computations using unstructured adaptively-refined meshes
NASA Technical Reports Server (NTRS)
Batina, John T.
1989-01-01
A conical Euler/Navier-Stokes algorithm is presented for the computation of vortex-dominated flows. The flow solver involves a multistage Runge-Kutta time stepping scheme which uses a finite-volume spatial discretization on an unstructured grid made up of triangles. The algorithm also employs an adaptive mesh refinement procedure which enriches the mesh locally to more accurately resolve the vortical flow features. Results are presented for several highly-swept delta wing and circular cone cases at high angles of attack and at supersonic freestream flow conditions. Accurate solutions were obtained more efficiently when adaptive mesh refinement was used in contrast with refining the grid globally. The paper presents descriptions of the conical Euler/Navier-Stokes flow solver and adaptive mesh refinement procedures along with results which demonstrate the capability.
Zonal multigrid solution of compressible flow problems on unstructured and adaptive meshes
NASA Technical Reports Server (NTRS)
Mavriplis, Dimitri J.
1989-01-01
The simultaneous use of adaptive meshing techniques with a multigrid strategy for solving the 2-D Euler equations in the context of unstructured meshes is studied. To obtain optimal efficiency, methods capable of computing locally improved solutions without recourse to global recalculations are pursued. A method for locally refining an existing unstructured mesh, without regenerating a new global mesh is employed, and the domain is automatically partitioned into refined and unrefined regions. Two multigrid strategies are developed. In the first, time-stepping is performed on a global fine mesh covering the entire domain, and convergence acceleration is achieved through the use of zonal coarse grid accelerator meshes, which lie under the adaptively refined regions of the global fine mesh. Both schemes are shown to produce similar convergence rates to each other, and also with respect to a previously developed global multigrid algorithm, which performs time-stepping throughout the entire domain, on each mesh level. However, the present schemes exhibit higher computational efficiency due to the smaller number of operations on each level.
The adaptive GRP scheme for compressible fluid flows over unstructured meshes
NASA Astrophysics Data System (ADS)
Li, Jiequan; Zhang, Yongjin
2013-06-01
Unstructured mesh methods have attracted much attention in CFD community due to the flexibility for dealing with complex geometries and the ability to easily incorporate adaptive (moving) mesh strategies. When the finite volume framework is applied, a reliable solver is crucial for the construction of numerical fluxes, for which the generalized Riemann problem (GRP) scheme undertakes such a task in the sense of second order accuracy. Combining these techniques yields a second order accurate adaptive generalized Riemann problem (AGRP) scheme for two dimensional compressible fluid flows over unstructured triangular meshes. Besides the generation of meshes, the main process of this combination consists of two ingredients: Fluid dynamical evolution and mesh redistribution. The fluid dynamical evolution ingredient serves to evolve the compressible fluid flows on a fixed nonuniform triangular mesh with the direct Eulerian GRP solver. The role of the mesh redistribution is to redistribute mesh points on which a conservative interpolation formula is adopted to calculate the cell-averages for the conservative variables, and the gradients of primitive variables are reconstructed using the least squares method. Several examples are taken from various contexts to demonstrate the performance of such a program.
Yaqi Wang; Jean C. Ragusa
2011-02-01
Standard and goal-oriented adaptive mesh refinement (AMR) techniques are presented for the linear Boltzmann transport equation. A posteriori error estimates are employed to drive the AMR process and are based on angular-moment information rather than on directional information, leading to direction-independent adapted meshes. An error estimate based on a two-mesh approach and a jump-based error indicator are compared for various test problems. In addition to the standard AMR approach, where the global error in the solution is diminished, a goal-oriented AMR procedure is devised and aims at reducing the error in user-specified quantities of interest. The quantities of interest are functionals of the solution and may include, for instance, point-wise flux values or average reaction rates in a subdomain. A high-order (up to order 4) Discontinuous Galerkin technique with standard upwinding is employed for the spatial discretization; the discrete ordinates method is used to treat the angular variable.
Multiphase flow modelling of explosive volcanic eruptions using adaptive unstructured meshes
NASA Astrophysics Data System (ADS)
Jacobs, Christian T.; Collins, Gareth S.; Piggott, Matthew D.; Kramer, Stephan C.
2014-05-01
Explosive volcanic eruptions generate highly energetic plumes of hot gas and ash particles that produce diagnostic deposits and pose an extreme environmental hazard. The formation, dispersion and collapse of these volcanic plumes are complex multiscale processes that are extremely challenging to simulate numerically. Accurate description of particle and droplet aggregation, movement and settling requires a model capable of capturing the dynamics on a range of scales (from cm to km) and a model that can correctly describe the important multiphase interactions that take place. However, even the most advanced models of eruption dynamics to date are restricted by the fixed mesh-based approaches that they employ. The research presented herein describes the development of a compressible multiphase flow model within Fluidity, a combined finite element / control volume computational fluid dynamics (CFD) code, for the study of explosive volcanic eruptions. Fluidity adopts a state-of-the-art adaptive unstructured mesh-based approach to discretise the domain and focus numerical resolution only in areas important to the dynamics, while decreasing resolution where it is not needed as a simulation progresses. This allows the accurate but economical representation of the flow dynamics throughout time, and potentially allows large multi-scale problems to become tractable in complex 3D domains. The multiphase flow model is verified with the method of manufactured solutions, and validated by simulating published gas-solid shock tube experiments and comparing the numerical results against pressure gauge data. The application of the model considers an idealised 7 km by 7 km domain in which the violent eruption of hot gas and volcanic ash high into the atmosphere is simulated. Although the simulations do not correspond to a particular eruption case study, the key flow features observed in a typical explosive eruption event are successfully captured. These include a shock wave resulting
Huang, W.; Zheng, Lingyun; Zhan, X.
2002-01-01
Accurate modelling of groundwater flow and transport with sharp moving fronts often involves high computational cost, when a fixed/uniform mesh is used. In this paper, we investigate the modelling of groundwater problems using a particular adaptive mesh method called the moving mesh partial differential equation approach. With this approach, the mesh is dynamically relocated through a partial differential equation to capture the evolving sharp fronts with a relatively small number of grid points. The mesh movement and physical system modelling are realized by solving the mesh movement and physical partial differential equations alternately. The method is applied to the modelling of a range of groundwater problems, including advection dominated chemical transport and reaction, non-linear infiltration in soil, and the coupling of density dependent flow and transport. Numerical results demonstrate that sharp moving fronts can be accurately and efficiently captured by the moving mesh approach. Also addressed are important implementation strategies, e.g. the construction of the monitor function based on the interpolation error, control of mesh concentration, and two-layer mesh movement. Copyright ?? 2002 John Wiley and Sons, Ltd.
3D segmentation of masses in DCE-MRI images using FCM and adaptive MRF
NASA Astrophysics Data System (ADS)
Zhang, Chengjie; Li, Lihua
2014-03-01
Dynamic contrast enhanced magnetic resonance imaging (DCE-MRI) is a sensitive imaging modality for the detection of breast cancer. Automated segmentation of breast lesions in DCE-MRI images is challenging due to inherent signal-to-noise ratios and high inter-patient variability. A novel 3D segmentation method based on FCM and MRF is proposed in this study. In this method, a MRI image is segmented by spatial FCM, firstly. And then MRF segmentation is conducted to refine the result. We combined with the 3D information of lesion in the MRF segmentation process by using segmentation result of contiguous slices to constraint the slice segmentation. At the same time, a membership matrix of FCM segmentation result is used for adaptive adjustment of Markov parameters in MRF segmentation process. The proposed method was applied for lesion segmentation on 145 breast DCE-MRI examinations (86 malignant and 59 benign cases). An evaluation of segmentation was taken using the traditional overlap rate method between the segmented region and hand-drawing ground truth. The average overlap rates for benign and malignant lesions are 0.764 and 0.755 respectively. Then we extracted five features based on the segmentation region, and used an artificial neural network (ANN) to classify between malignant and benign cases. The ANN had a classification performance measured by the area under the ROC curve of AUC=0.73. The positive and negative predictive values were 0.86 and 0.58, respectively. The results demonstrate the proposed method not only achieves a better segmentation performance in accuracy also has a reasonable classification performance.
Adaptive volume rendering of cardiac 3D ultrasound images: utilizing blood pool statistics
NASA Astrophysics Data System (ADS)
Åsen, Jon Petter; Steen, Erik; Kiss, Gabriel; Thorstensen, Anders; Rabben, Stein Inge
2012-03-01
In this paper we introduce and investigate an adaptive direct volume rendering (DVR) method for real-time visualization of cardiac 3D ultrasound. DVR is commonly used in cardiac ultrasound to visualize interfaces between tissue and blood. However, this is particularly challenging with ultrasound images due to variability of the signal within tissue as well as variability of noise signal within the blood pool. Standard DVR involves a global mapping of sample values to opacity by an opacity transfer function (OTF). While a global OTF may represent the interface correctly in one part of the image, it may result in tissue dropouts, or even artificial interfaces within the blood pool in other parts of the image. In order to increase correctness of the rendered image, the presented method utilizes blood pool statistics to do regional adjustments of the OTF. The regional adaptive OTF was compared with a global OTF in a dataset of apical recordings from 18 subjects. For each recording, three renderings from standard views (apical 4-chamber (A4C), inverted A4C (IA4C) and mitral valve (MV)) were generated for both methods, and each rendering was tuned to the best visual appearance by a physician echocardiographer. For each rendering we measured the mean absolute error (MAE) between the rendering depth buffer and a validated left ventricular segmentation. The difference d in MAE between the global and regional method was calculated and t-test results are reported with significant improvements for the regional adaptive method (dA4C = 1.5 +/- 0.3 mm, dIA4C = 2.5 +/- 0.4 mm, dMV = 1.7 +/- 0.2 mm, d.f. = 17, all p < 0.001). This improvement by the regional adaptive method was confirmed through qualitative visual assessment by an experienced physician echocardiographer who concluded that the regional adaptive method produced rendered images with fewer tissue dropouts and less spurious structures inside the blood pool in the vast majority of the renderings. The algorithm has been
NASA Technical Reports Server (NTRS)
Rebstock, Rainer; Lee, Edwin E., Jr.
1989-01-01
An initial wind tunnel test was made to validate a new wall adaptation method for 3-D models in test sections with two adaptive walls. First part of the adaptation strategy is an on-line assessment of wall interference at the model position. The wall induced blockage was very small at all test conditions. Lift interference occurred at higher angles of attack with the walls set aerodynamically straight. The adaptation of the top and bottom tunnel walls is aimed at achieving a correctable flow condition. The blockage was virtually zero throughout the wing planform after the wall adjustment. The lift curve measured with the walls adapted agreed very well with interference free data for Mach 0.7, regardless of the vertical position of the wing in the test section. The 2-D wall adaptation can significantly improve the correctability of 3-D model data. Nevertheless, residual spanwise variations of wall interference are inevitable.
Higher-order schemes with CIP method and adaptive Soroban grid towards mesh-free scheme
NASA Astrophysics Data System (ADS)
Yabe, Takashi; Mizoe, Hiroki; Takizawa, Kenji; Moriki, Hiroshi; Im, Hyo-Nam; Ogata, Youichi
2004-02-01
A new class of body-fitted grid system that can keep the third-order accuracy in time and space is proposed with the help of the CIP (constrained interpolation profile/cubic interpolated propagation) method. The grid system consists of the straight lines and grid points moving along these lines like abacus - Soroban in Japanese. The length of each line and the number of grid points in each line can be different. The CIP scheme is suitable to this mesh system and the calculation of large CFL (>10) at locally refined mesh is easily performed. Mesh generation and searching of upstream departure point are very simple and almost mesh-free treatment is possible. Adaptive grid movement and local mesh refinement are demonstrated.
Drag Prediction for the DLR-F6 Wing/Body and DPW Wing using CFL3D and OVERFLOW Overset Mesh
NASA Technical Reports Server (NTRS)
Sclanfani, Anthony J.; Vassberg, John C.; Harrison, Neal A.; DeHaan, Mark A.; Rumsey, Christopher L.; Rivers, S. Melissa; Morrison, Joseph H.
2007-01-01
A series of overset grids was generated in response to the 3rd AIAA CFD Drag Prediction Workshop (DPW-III) which preceded the 25th Applied Aerodynamics Conference in June 2006. DPW-III focused on accurate drag prediction for wing/body and wing-alone configurations. The grid series built for each configuration consists of a coarse, medium, fine, and extra-fine mesh. The medium mesh is first constructed using the current state of best practices for overset grid generation. The medium mesh is then coarsened and enhanced by applying a factor of 1.5 to each (I,J,K) dimension. The resulting set of parametrically equivalent grids increase in size by a factor of roughly 3.5 from one level to the next denser level. CFD simulations were performed on the overset grids using two different RANS flow solvers: CFL3D and OVERFLOW. The results were post-processed using Richardson extrapolation to approximate grid converged values of lift, drag, pitching moment, and angle-of-attack at the design condition. This technique appears to work well if the solution does not contain large regions of separated flow (similar to that seen n the DLR-F6 results) and appropriate grid densities are selected. The extra-fine grid data helped to establish asymptotic grid convergence for both the OVERFLOW FX2B wing/body results and the OVERFLOW DPW-W1/W2 wing-alone results. More CFL3D data is needed to establish grid convergence trends. The medium grid was utilized beyond the grid convergence study by running each configuration at several angles-of-attack so drag polars and lift/pitching moment curves could be evaluated. The alpha sweep results are used to compare data across configurations as well as across flow solvers. With the exception of the wing/body drag polar, the two codes compare well qualitatively showing consistent incremental trends and similar wing pressure comparisons.
Drag Prediction for the DLR-F4 Wing/Body using OVERFLOW and CFL3D on an Overset Mesh
NASA Technical Reports Server (NTRS)
Vassberg, John C.; Buning, Pieter G.; Rumsey, Christopher L.
2002-01-01
This paper reviews the importance of numerical drag prediction in an aircraft design environment. A chronicle of collaborations between the authors and colleagues is discussed. This retrospective provides a road-map which illustrates some of the actions taken in the past seven years in pursuit of accurate drag prediction. The advances made possible through these collaborations have changed the manner in which business is conducted during the design of all-new aircraft. The subject of this study is the DLR-F4 wing/body transonic model. Specifically, the work conducted herein was in support of the 1st CFD Drag Prediction Workshop, which was held in conjunction with the 19th Applied Aerodynamics Conference in Anaheim, CA during June, 2001. Comprehensive sets of OVERFLOW simulations were independently performed by several users on a variety of computational platforms. CFL3D was used on a limited basis for additional comparison on the same overset mesh. Drag polars based on this database were constructed with a CFD-to-Test correction applied and compared with test data from three facilities. These comparisons show that the predicted drag polars fall inside the scatter band of the test data, at least for pre-buffet conditions. This places the corrected drag levels within 1% of the averaged experimental values. At the design point, the OVERFLOW and CFL3D drag predictions are within 1-2% of each other. In addition, drag-rise characteristics and a boundary of drag-divergence Mach number are presented.
Wang, Lisheng; Wang, Pai; Cheng, Liuhang; Ma, Yu; Wu, Shenzhi; Wang, Yu-Ping; Xu, Zongben
2014-11-01
In this paper we propose a novel and easy to use 3D reconstruction method. With the method, users only need to specify a small boundary surface patch in a 2D section image, and then an entire continuous implicit boundary surface (CIBS) can be automatically reconstructed from a 3D image. In the method, a hierarchical tracing strategy is used to grow the known boundary surface patch gradually in the 3D image. An adaptive detection technique is applied to detect boundary surface patches from different local regions. The technique is based on both context dependence and adaptive contrast detection as in the human vision system. A recognition technique is used to distinguish true boundary surface patches from the false ones in different cubes. By integrating these different approaches, a high-resolution CIBS model can be automatically reconstructed by adaptively expanding the small boundary surface patch in the 3D image. The effectiveness of our method is demonstrated by its applications to a variety of real 3D images, where the CIBS with complex shapes/branches and with varying gray values/gradient magnitudes can be well reconstructed. Our method is easy to use, which provides a valuable tool for 3D image visualization and analysis as needed in many applications. PMID:26355329
An Adaptive Mesh Refinement Strategy for Immersed Boundary/Interface Methods.
Li, Zhilin; Song, Peng
2012-01-01
An adaptive mesh refinement strategy is proposed in this paper for the Immersed Boundary and Immersed Interface methods for two-dimensional elliptic interface problems involving singular sources. The interface is represented by the zero level set of a Lipschitz function φ(x,y). Our adaptive mesh refinement is done within a small tube of |φ(x,y)|≤ δ with finer Cartesian meshes. The discrete linear system of equations is solved by a multigrid solver. The AMR methods could obtain solutions with accuracy that is similar to those on a uniform fine grid by distributing the mesh more economically, therefore, reduce the size of the linear system of the equations. Numerical examples presented show the efficiency of the grid refinement strategy. PMID:22670155
NASA Astrophysics Data System (ADS)
Boscheri, Walter; Dumbser, Michael
2014-10-01
In this paper we present a new family of high order accurate Arbitrary-Lagrangian-Eulerian (ALE) one-step ADER-WENO finite volume schemes for the solution of nonlinear systems of conservative and non-conservative hyperbolic partial differential equations with stiff source terms on moving tetrahedral meshes in three space dimensions. A WENO reconstruction technique is used to achieve high order of accuracy in space, while an element-local space-time Discontinuous Galerkin finite element predictor on moving curved meshes is used to obtain a high order accurate one-step time discretization. Within the space-time predictor the physical element is mapped onto a reference element using a high order isoparametric approach, where the space-time basis and test functions are given by the Lagrange interpolation polynomials passing through a predefined set of space-time nodes. Since our algorithm is cell-centered, the final mesh motion is computed by using a suitable node solver algorithm. A rezoning step as well as a flattener strategy are used in some of the test problems to avoid mesh tangling or excessive element deformations that may occur when the computation involves strong shocks or shear waves. The ALE algorithm presented in this article belongs to the so-called direct ALE methods because the final Lagrangian finite volume scheme is based directly on a space-time conservation formulation of the governing PDE system, with the rezoned geometry taken already into account during the computation of the fluxes. We apply our new high order unstructured ALE schemes to the 3D Euler equations of compressible gas dynamics, for which a set of classical numerical test problems has been solved and for which convergence rates up to sixth order of accuracy in space and time have been obtained. We furthermore consider the equations of classical ideal magnetohydrodynamics (MHD) as well as the non-conservative seven-equation Baer-Nunziato model of compressible multi-phase flows with
NASA Astrophysics Data System (ADS)
He, Wenda; Juette, Arne; Denton, Erica R. E.; Zwiggelaar, Reyer
2015-03-01
Breast cancer is the most frequently diagnosed cancer in women. Early detection, precise identification of women at risk, and application of appropriate disease prevention measures are by far the most effective ways to overcome the disease. Successful mammographic density segmentation is a key aspect in deriving correct tissue composition, ensuring an accurate mammographic risk assessment. However, mammographic densities have not yet been fully incorporated with non-image based risk prediction models, (e.g. the Gail and the Tyrer-Cuzick model), because of unreliable segmentation consistency and accuracy. This paper presents a novel multiresolution mammographic density segmentation, a concept of stack representation is proposed, and 3D texture features were extracted by adapting techniques based on classic 2D first-order statistics. An unsupervised clustering technique was employed to achieve mammographic segmentation, in which two improvements were made; 1) consistent segmentation by incorporating an optimal centroids initialisation step, and 2) significantly reduced the number of missegmentation by using an adaptive cluster merging technique. A set of full field digital mammograms was used in the evaluation. Visual assessment indicated substantial improvement on segmented anatomical structures and tissue specific areas, especially in low mammographic density categories. The developed method demonstrated an ability to improve the quality of mammographic segmentation via clustering, and results indicated an improvement of 26% in segmented image with good quality when compared with the standard clustering approach. This in turn can be found useful in early breast cancer detection, risk-stratified screening, and aiding radiologists in the process of decision making prior to surgery and/or treatment.
A simple adaptive mesh generator for 2-D finite element calculations
Fernandez, F.A.; Yong, Y.C.; Ettinger, R.D. )
1993-03-01
A strategy for adaptive mesh generation is proposed. The method consists of the use of a suitably defined density function', which can either be defined by the user or be calculated from a previous approximate solution, to guide the generation of a new mesh. This new mesh is built starting from a minimal number of triangular elements which are then in several sweeps, repeatedly refined according to the density function. The Delaunay algorithm is used in each stage to keep the shape of the triangles as equilateral as possible.
Stereoscopic-3D display design: a new paradigm with Intel Adaptive Stable Image Technology [IA-SIT
NASA Astrophysics Data System (ADS)
Jain, Sunil
2012-03-01
Stereoscopic-3D (S3D) proliferation on personal computers (PC) is mired by several technical and business challenges: a) viewing discomfort due to cross-talk amongst stereo images; b) high system cost; and c) restricted content availability. Users expect S3D visual quality to be better than, or at least equal to, what they are used to enjoying on 2D in terms of resolution, pixel density, color, and interactivity. Intel Adaptive Stable Image Technology (IA-SIT) is a foundational technology, successfully developed to resolve S3D system design challenges and deliver high quality 3D visualization at PC price points. Optimizations in display driver, panel timing firmware, backlight hardware, eyewear optical stack, and synch mechanism combined can help accomplish this goal. Agnostic to refresh rate, IA-SIT will scale with shrinking of display transistors and improvements in liquid crystal and LED materials. Industry could profusely benefit from the following calls to action:- 1) Adopt 'IA-SIT S3D Mode' in panel specs (via VESA) to help panel makers monetize S3D; 2) Adopt 'IA-SIT Eyewear Universal Optical Stack' and algorithm (via CEA) to help PC peripheral makers develop stylish glasses; 3) Adopt 'IA-SIT Real Time Profile' for sub-100uS latency control (via BT Sig) to extend BT into S3D; and 4) Adopt 'IA-SIT Architecture' for Monitors and TVs to monetize via PC attach.
Yamashiro, Tsuneo; Miyara, Tetsuhiro; Honda, Osamu; Kamiya, Hisashi; Murata, Kiyoshi; Ohno, Yoshiharu; Tomiyama, Noriyuki; Moriya, Hiroshi; Koyama, Mitsuhiro; Noma, Satoshi; Kamiya, Ayano; Tanaka, Yuko; Murayama, Sadayuki
2014-01-01
Objective To assess the advantages of Adaptive Iterative Dose Reduction using Three Dimensional Processing (AIDR3D) for image quality improvement and dose reduction for chest computed tomography (CT). Methods Institutional Review Boards approved this study and informed consent was obtained. Eighty-eight subjects underwent chest CT at five institutions using identical scanners and protocols. During a single visit, each subject was scanned using different tube currents: 240, 120, and 60 mA. Scan data were converted to images using AIDR3D and a conventional reconstruction mode (without AIDR3D). Using a 5-point scale from 1 (non-diagnostic) to 5 (excellent), three blinded observers independently evaluated image quality for three lung zones, four patterns of lung disease (nodule/mass, emphysema, bronchiolitis, and diffuse lung disease), and three mediastinal measurements (small structure visibility, streak artifacts, and shoulder artifacts). Differences in these scores were assessed by Scheffe's test. Results At each tube current, scans using AIDR3D had higher scores than those without AIDR3D, which were significant for lung zones (p<0.0001) and all mediastinal measurements (p<0.01). For lung diseases, significant improvements with AIDR3D were frequently observed at 120 and 60 mA. Scans with AIDR3D at 120 mA had significantly higher scores than those without AIDR3D at 240 mA for lung zones and mediastinal streak artifacts (p<0.0001), and slightly higher or equal scores for all other measurements. Scans with AIDR3D at 60 mA were also judged superior or equivalent to those without AIDR3D at 120 mA. Conclusion For chest CT, AIDR3D provides better image quality and can reduce radiation exposure by 50%. PMID:25153797
A Numerical Study of Mesh Adaptivity in Multiphase Flows with Non-Newtonian Fluids
NASA Astrophysics Data System (ADS)
Percival, James; Pavlidis, Dimitrios; Xie, Zhihua; Alberini, Federico; Simmons, Mark; Pain, Christopher; Matar, Omar
2014-11-01
We present an investigation into the computational efficiency benefits of dynamic mesh adaptivity in the numerical simulation of transient multiphase fluid flow problems involving Non-Newtonian fluids. Such fluids appear in a range of industrial applications, from printing inks to toothpastes and introduce new challenges for mesh adaptivity due to the additional ``memory'' of viscoelastic fluids. Nevertheless, the multiscale nature of these flows implies huge potential benefits for a successful implementation. The study is performed using the open source package Fluidity, which couples an unstructured mesh control volume finite element solver for the multiphase Navier-Stokes equations to a dynamic anisotropic mesh adaptivity algorithm, based on estimated solution interpolation error criteria, and conservative mesh-to-mesh interpolation routine. The code is applied to problems involving rheologies ranging from simple Newtonian to shear-thinning to viscoelastic materials and verified against experimental data for various industrial and microfluidic flows. This work was undertaken as part of the EPSRC MEMPHIS programme grant EP/K003976/1.
Conditional entropy maximization for PET image reconstruction using adaptive mesh model.
Zhu, Hongqing; Shu, Huazhong; Zhou, Jian; Dai, Xiubin; Luo, Limin
2007-04-01
Iterative image reconstruction algorithms have been widely used in the field of positron emission tomography (PET). However, such algorithms are sensitive to noise artifacts so that the reconstruction begins to degrade when the number of iterations is high. In this paper, we propose a new algorithm to reconstruct an image from the PET emission projection data by using the conditional entropy maximization and the adaptive mesh model. In a traditional tomography reconstruction method, the reconstructed image is directly computed in the pixel domain. Unlike this kind of methods, the proposed approach is performed by estimating the nodal values from the observed projection data in a mesh domain. In our method, the initial Delaunay triangulation mesh is generated from a set of randomly selected pixel points, and it is then modified according to the pixel intensity value of the estimated image at each iteration step in which the conditional entropy maximization is used. The advantage of using the adaptive mesh model for image reconstruction is that it provides a natural spatially adaptive smoothness mechanism. In experiments using the synthetic and clinical data, it is found that the proposed algorithm is more robust to noise compared to the common pixel-based MLEM algorithm and mesh-based MLEM with a fixed mesh structure. PMID:17368841
ENZO+MORAY: radiation hydrodynamics adaptive mesh refinement simulations with adaptive ray tracing
NASA Astrophysics Data System (ADS)
Wise, John H.; Abel, Tom
2011-07-01
We describe a photon-conserving radiative transfer algorithm, using a spatially-adaptive ray-tracing scheme, and its parallel implementation into the adaptive mesh refinement cosmological hydrodynamics code ENZO. By coupling the solver with the energy equation and non-equilibrium chemistry network, our radiation hydrodynamics framework can be utilized to study a broad range of astrophysical problems, such as stellar and black hole feedback. Inaccuracies can arise from large time-steps and poor sampling; therefore, we devised an adaptive time-stepping scheme and a fast approximation of the optically-thin radiation field with multiple sources. We test the method with several radiative transfer and radiation hydrodynamics tests that are given in Iliev et al. We further test our method with more dynamical situations, for example, the propagation of an ionization front through a Rayleigh-Taylor instability, time-varying luminosities and collimated radiation. The test suite also includes an expanding H II region in a magnetized medium, utilizing the newly implemented magnetohydrodynamics module in ENZO. This method linearly scales with the number of point sources and number of grid cells. Our implementation is scalable to 512 processors on distributed memory machines and can include the radiation pressure and secondary ionizations from X-ray radiation. It is included in the newest public release of ENZO.
An adaptive mesh finite volume method for the Euler equations of gas dynamics
NASA Astrophysics Data System (ADS)
Mungkasi, Sudi
2016-06-01
The Euler equations have been used to model gas dynamics for decades. They consist of mathematical equations for the conservation of mass, momentum, and energy of the gas. For a large time value, the solution may contain discontinuities, even when the initial condition is smooth. A standard finite volume numerical method is not able to give accurate solutions to the Euler equations around discontinuities. Therefore we solve the Euler equations using an adaptive mesh finite volume method. In this paper, we present a new construction of the adaptive mesh finite volume method with an efficient computation of the refinement indicator. The adaptive method takes action automatically at around places having inaccurate solutions. Inaccurate solutions are reconstructed to reduce the error by refining the mesh locally up to a certain level. On the other hand, if the solution is already accurate, then the mesh is coarsened up to another certain level to minimize computational efforts. We implement the numerical entropy production as the mesh refinement indicator. As a test problem, we take the Sod shock tube problem. Numerical results show that the adaptive method is more promising than the standard one in solving the Euler equations of gas dynamics.
A semi-automatic 2D-to-3D video conversion with adaptive key-frame selection
NASA Astrophysics Data System (ADS)
Ju, Kuanyu; Xiong, Hongkai
2014-11-01
To compensate the deficit of 3D content, 2D to 3D video conversion (2D-to-3D) has recently attracted more attention from both industrial and academic communities. The semi-automatic 2D-to-3D conversion which estimates corresponding depth of non-key-frames through key-frames is more desirable owing to its advantage of balancing labor cost and 3D effects. The location of key-frames plays a role on quality of depth propagation. This paper proposes a semi-automatic 2D-to-3D scheme with adaptive key-frame selection to keep temporal continuity more reliable and reduce the depth propagation errors caused by occlusion. The potential key-frames would be localized in terms of clustered color variation and motion intensity. The distance of key-frame interval is also taken into account to keep the accumulated propagation errors under control and guarantee minimal user interaction. Once their depth maps are aligned with user interaction, the non-key-frames depth maps would be automatically propagated by shifted bilateral filtering. Considering that depth of objects may change due to the objects motion or camera zoom in/out effect, a bi-directional depth propagation scheme is adopted where a non-key frame is interpolated from two adjacent key frames. The experimental results show that the proposed scheme has better performance than existing 2D-to-3D scheme with fixed key-frame interval.
Locally adaptive 2D-3D registration using vascular structure model for liver catheterization.
Kim, Jihye; Lee, Jeongjin; Chung, Jin Wook; Shin, Yeong-Gil
2016-03-01
Two-dimensional-three-dimensional (2D-3D) registration between intra-operative 2D digital subtraction angiography (DSA) and pre-operative 3D computed tomography angiography (CTA) can be used for roadmapping purposes. However, through the projection of 3D vessels, incorrect intersections and overlaps between vessels are produced because of the complex vascular structure, which makes it difficult to obtain the correct solution of 2D-3D registration. To overcome these problems, we propose a registration method that selects a suitable part of a 3D vascular structure for a given DSA image and finds the optimized solution to the partial 3D structure. The proposed algorithm can reduce the registration errors because it restricts the range of the 3D vascular structure for the registration by using only the relevant 3D vessels with the given DSA. To search for the appropriate 3D partial structure, we first construct a tree model of the 3D vascular structure and divide it into several subtrees in accordance with the connectivity. Then, the best matched subtree with the given DSA image is selected using the results from the coarse registration between each subtree and the vessels in the DSA image. Finally, a fine registration is conducted to minimize the difference between the selected subtree and the vessels of the DSA image. In experimental results obtained using 10 clinical datasets, the average distance errors in the case of the proposed method were 2.34±1.94mm. The proposed algorithm converges faster and produces more correct results than the conventional method in evaluations on patient datasets. PMID:26824922
Adaptive unstructured meshing for thermal stress analysis of built-up structures
NASA Technical Reports Server (NTRS)
Dechaumphai, Pramote
1992-01-01
An adaptive unstructured meshing technique for mechanical and thermal stress analysis of built-up structures has been developed. A triangular membrane finite element and a new plate bending element are evaluated on a panel with a circular cutout and a frame stiffened panel. The adaptive unstructured meshing technique, without a priori knowledge of the solution to the problem, generates clustered elements only where needed. An improved solution accuracy is obtained at a reduced problem size and analysis computational time as compared to the results produced by the standard finite element procedure.
Using Multi-threading for the Automatic Load Balancing of 2D Adaptive Finite Element Meshes
NASA Technical Reports Server (NTRS)
Heber, Gerd; Biswas, Rupak; Thulasiraman, Parimala; Gao, Guang R.; Saini, Subhash (Technical Monitor)
1998-01-01
In this paper, we present a multi-threaded approach for the automatic load balancing of adaptive finite element (FE) meshes The platform of our choice is the EARTH multi-threaded system which offers sufficient capabilities to tackle this problem. We implement the adaption phase of FE applications oil triangular meshes and exploit the EARTH token mechanism to automatically balance the resulting irregular and highly nonuniform workload. We discuss the results of our experiments oil EARTH-SP2, on implementation of EARTH on the IBM SP2 with different load balancing strategies that are built into the runtime system.
Parallelization of Unsteady Adaptive Mesh Refinement for Unstructured Navier-Stokes Solvers
NASA Technical Reports Server (NTRS)
Schwing, Alan M.; Nompelis, Ioannis; Candler, Graham V.
2014-01-01
This paper explores the implementation of the MPI parallelization in a Navier-Stokes solver using adaptive mesh re nement. Viscous and inviscid test problems are considered for the purpose of benchmarking, as are implicit and explicit time advancement methods. The main test problem for comparison includes e ects from boundary layers and other viscous features and requires a large number of grid points for accurate computation. Ex- perimental validation against double cone experiments in hypersonic ow are shown. The adaptive mesh re nement shows promise for a staple test problem in the hypersonic com- munity. Extension to more advanced techniques for more complicated ows is described.
NASA Astrophysics Data System (ADS)
Padmanabhan, R.; Oliveira, M. C.; Baptista, A. J.; Alves, J. L.; Menezes, L. F.
2007-05-01
Springback phenomenon associated with the elastic properties of sheet metals makes the design of forming dies a complex task. Thus, to develop consistent algorithms for springback compensation an accurate prediction of the amount of springback is mandatory. The numerical simulation using the finite element method is consensually the only feasible method to predict springback. However, springback prediction is a very complicated task and highly sensitive to various numerical parameters of finite elements (FE), such as: type, order, integration scheme, shape and size, as well the time integration formulae and the unloading strategy. All these numerical parameters make numerical simulation of springback more sensitive to numerical tolerances than the forming operation. In case of an unconstrained cylindrical bending, the in-plane to thickness FE size ratio is more relevant than the number of FE layers through-thickness, for the numerical prediction of final stress and strain states, variables of paramount importance for an accurate springback prediction. The aim of the present work is to evaluate the influence of the refinement of a 3-D FE mesh, namely the in-plane mesh refinement and the number of through-thickness FE layers, in springback prediction. The selected example corresponds to the first stage of the "Numisheet'05 Benchmark♯3", which consists basically in the sheet forming of a channel section in an industrial-scale channel draw die. The physical drawbeads are accurately taken into account in the numerical model in order to accurately reproduce its influence during the forming process simulation. FEM simulations were carried out with the in-house code DD3IMP. Solid finite elements were used. They are recommended for accuracy in FE springback simulation when the ratio between the tool radius and blank thickness is lower than 5-6. In the selected example the drawbead radius is 4.0 mm. The influence of the FE mesh refinement in springback prediction is
Thickness-based adaptive mesh refinement methods for multi-phase flow simulations with thin regions
Chen, Xiaodong; Yang, Vigor
2014-07-15
In numerical simulations of multi-scale, multi-phase flows, grid refinement is required to resolve regions with small scales. A notable example is liquid-jet atomization and subsequent droplet dynamics. It is essential to characterize the detailed flow physics with variable length scales with high fidelity, in order to elucidate the underlying mechanisms. In this paper, two thickness-based mesh refinement schemes are developed based on distance- and topology-oriented criteria for thin regions with confining wall/plane of symmetry and in any situation, respectively. Both techniques are implemented in a general framework with a volume-of-fluid formulation and an adaptive-mesh-refinement capability. The distance-oriented technique compares against a critical value, the ratio of an interfacial cell size to the distance between the mass center of the cell and a reference plane. The topology-oriented technique is developed from digital topology theories to handle more general conditions. The requirement for interfacial mesh refinement can be detected swiftly, without the need of thickness information, equation solving, variable averaging or mesh repairing. The mesh refinement level increases smoothly on demand in thin regions. The schemes have been verified and validated against several benchmark cases to demonstrate their effectiveness and robustness. These include the dynamics of colliding droplets, droplet motions in a microchannel, and atomization of liquid impinging jets. Overall, the thickness-based refinement technique provides highly adaptive meshes for problems with thin regions in an efficient and fully automatic manner.
NASA Astrophysics Data System (ADS)
Tang, Qiuyan; Wang, Jing; Lv, Pin; Sun, Quan
2015-10-01
Propagation simulation method and choosing mesh grid are both very important to get the correct propagation results in wave optics simulation. A new angular spectrum propagation method with alterable mesh grid based on the traditional angular spectrum method and the direct FFT method is introduced. With this method, the sampling space after propagation is not limited to propagation methods no more, but freely alterable. However, choosing mesh grid on target board influences the validity of simulation results directly. So an adaptive mesh choosing method based on wave characteristics is proposed with the introduced propagation method. We can calculate appropriate mesh grids on target board to get satisfying results. And for complex initial wave field or propagation through inhomogeneous media, we can also calculate and set the mesh grid rationally according to above method. Finally, though comparing with theoretical results, it's shown that the simulation result with the proposed method coinciding with theory. And by comparing with the traditional angular spectrum method and the direct FFT method, it's known that the proposed method is able to adapt to a wider range of Fresnel number conditions. That is to say, the method can simulate propagation results efficiently and correctly with propagation distance of almost zero to infinity. So it can provide better support for more wave propagation applications such as atmospheric optics, laser propagation and so on.
Ma, Yingliang; Saetzler, Kurt
2008-01-01
In this paper we describe a novel 3D subdivision strategy to extract the surface of binary image data. This iterative approach generates a series of surface meshes that capture different levels of detail of the underlying structure. At the highest level of detail, the resulting surface mesh generated by our approach uses only about 10% of the triangles in comparison to the marching cube algorithm (MC) even in settings were almost no image noise is present. Our approach also eliminates the so-called "staircase effect" which voxel based algorithms like the MC are likely to show, particularly if non-uniformly sampled images are processed. Finally, we show how the presented algorithm can be parallelized by subdividing 3D image space into rectilinear blocks of subimages. As the algorithm scales very well with an increasing number of processors in a multi-threaded setting, this approach is suited to process large image data sets of several gigabytes. Although the presented work is still computationally more expensive than simple voxel-based algorithms, it produces fewer surface triangles while capturing the same level of detail, is more robust towards image noise and eliminates the above-mentioned "staircase" effect in anisotropic settings. These properties make it particularly useful for biomedical applications, where these conditions are often encountered. PMID:17993710
Klein, R.I. |; Bell, J.; Pember, R.; Kelleher, T.
1993-04-01
The authors present results for high resolution hydrodynamic calculations of the growth and development of instabilities in shock driven imploding spherical geometries in both 2D and 3D. They solve the Eulerian equations of hydrodynamics with a high order Godunov approach using local adaptive mesh refinement to study the temporal and spatial development of the turbulent mixing layer resulting from both Richtmyer Meshkov and Rayleigh Taylor instabilities. The use of a high resolution Eulerian discretization with adaptive mesh refinement permits them to study the detailed three-dimensional growth of multi-mode perturbations far into the non-linear regime for converging geometries. They discuss convergence properties of the simulations by calculating global properties of the flow. They discuss the time evolution of the turbulent mixing layer and compare its development to a simple theory for a turbulent mix model in spherical geometry based on Plesset`s equation. Their 3D calculations show that the constant found in the planar incompressible experiments of Read and Young`s may not be universal for converging compressible flow. They show the 3D time trace of transitional onset to a mixing state using the temporal evolution of volume rendered imaging. Their preliminary results suggest that the turbulent mixing layer loses memory of its initial perturbations for classical Richtmyer Meshkov and Rayleigh Taylor instabilities in spherically imploding shells. They discuss the time evolution of mixed volume fraction and the role of vorticity in converging 3D flows in enhancing the growth of a turbulent mixing layer.
The parallelization of an advancing-front, all-quadrilateral meshing algorithm for adaptive analysis
Lober, R.R.; Tautges, T.J.; Cairncross, R.A.
1995-11-01
The ability to perform effective adaptive analysis has become a critical issue in the area of physical simulation. Of the multiple technologies required to realize a parallel adaptive analysis capability, automatic mesh generation is an enabling technology, filling a critical need in the appropriate discretization of a problem domain. The paving algorithm`s unique ability to generate a function-following quadrilateral grid is a substantial advantage in Sandia`s pursuit of a modified h-method adaptive capability. This characteristic combined with a strong transitioning ability allow the paving algorithm to place elements where an error function indicates more mesh resolution is needed. Although the original paving algorithm is highly serial, a two stage approach has been designed to parallelize the algorithm but also retain the nice qualities of the serial algorithm. The authors approach also allows the subdomain decomposition used by the meshing code to be shared with the finite element physics code, eliminating the need for data transfer across the processors between the analysis and remeshing steps. In addition, the meshed subdomains are adjusted with a dynamic load balancer to improve the original decomposition and maintain load efficiency each time the mesh has been regenerated. This initial parallel implementation assumes an approach of restarting the physics problem from time zero at each interaction, with a refined mesh adapting to the previous iterations objective function. The remeshing tools are being developed to enable real time remeshing and geometry regeneration. Progress on the redesign of the paving algorithm for parallel operation is discussed including extensions allowing adaptive control and geometry regeneration.
Applications of automatic mesh generation and adaptive methods in computational medicine
Schmidt, J.A.; Macleod, R.S.; Johnson, C.R.; Eason, J.C.
1995-12-31
Important problems in Computational Medicine exist that can benefit from the implementation of adaptive mesh refinement techniques. Biological systems are so inherently complex that only efficient models running on state of the art hardware can begin to simulate reality. To tackle the complex geometries associated with medical applications we present a general purpose mesh generation scheme based upon the Delaunay tessellation algorithm and an iterative point generator. In addition, automatic, two- and three-dimensional adaptive mesh refinement methods are presented that are derived from local and global estimates of the finite element error. Mesh generation and adaptive refinement techniques are utilized to obtain accurate approximations of bioelectric fields within anatomically correct models of the heart and human thorax. Specifically, we explore the simulation of cardiac defibrillation and the general forward and inverse problems in electrocardiography (ECG). Comparisons between uniform and adaptive refinement techniques are made to highlight the computational efficiency and accuracy of adaptive methods in the solution of field problems in computational medicine.
Multilevel Error Estimation and Adaptive h-Refinement for Cartesian Meshes with Embedded Boundaries
NASA Technical Reports Server (NTRS)
Aftosmis, M. J.; Berger, M. J.; Kwak, Dochan (Technical Monitor)
2002-01-01
This paper presents the development of a mesh adaptation module for a multilevel Cartesian solver. While the module allows mesh refinement to be driven by a variety of different refinement parameters, a central feature in its design is the incorporation of a multilevel error estimator based upon direct estimates of the local truncation error using tau-extrapolation. This error indicator exploits the fact that in regions of uniform Cartesian mesh, the spatial operator is exactly the same on the fine and coarse grids, and local truncation error estimates can be constructed by evaluating the residual on the coarse grid of the restricted solution from the fine grid. A new strategy for adaptive h-refinement is also developed to prevent errors in smooth regions of the flow from being masked by shocks and other discontinuous features. For certain classes of error histograms, this strategy is optimal for achieving equidistribution of the refinement parameters on hierarchical meshes, and therefore ensures grid converged solutions will be achieved for appropriately chosen refinement parameters. The robustness and accuracy of the adaptation module is demonstrated using both simple model problems and complex three dimensional examples using meshes with from 10(exp 6), to 10(exp 7) cells.
Ibrahim, Ahmad M.; Wilson, Paul P.H.; Sawan, Mohamed E.; Mosher, Scott W.; Peplow, Douglas E.; Wagner, John C.; Evans, Thomas M.; Grove, Robert E.
2015-06-30
The CADIS and FW-CADIS hybrid Monte Carlo/deterministic techniques dramatically increase the efficiency of neutronics modeling, but their use in the accurate design analysis of very large and geometrically complex nuclear systems has been limited by the large number of processors and memory requirements for their preliminary deterministic calculations and final Monte Carlo calculation. Three mesh adaptivity algorithms were developed to reduce the memory requirements of CADIS and FW-CADIS without sacrificing their efficiency improvement. First, a macromaterial approach enhances the fidelity of the deterministic models without changing the mesh. Second, a deterministic mesh refinement algorithm generates meshes that capture as muchmore » geometric detail as possible without exceeding a specified maximum number of mesh elements. Finally, a weight window coarsening algorithm decouples the weight window mesh and energy bins from the mesh and energy group structure of the deterministic calculations in order to remove the memory constraint of the weight window map from the deterministic mesh resolution. The three algorithms were used to enhance an FW-CADIS calculation of the prompt dose rate throughout the ITER experimental facility. Using these algorithms resulted in a 23.3% increase in the number of mesh tally elements in which the dose rates were calculated in a 10-day Monte Carlo calculation and, additionally, increased the efficiency of the Monte Carlo simulation by a factor of at least 3.4. The three algorithms enabled this difficult calculation to be accurately solved using an FW-CADIS simulation on a regular computer cluster, eliminating the need for a world-class super computer.« less
Ibrahim, Ahmad M.; Wilson, Paul P.H.; Sawan, Mohamed E.; Mosher, Scott W.; Peplow, Douglas E.; Wagner, John C.; Evans, Thomas M.; Grove, Robert E.
2015-06-30
The CADIS and FW-CADIS hybrid Monte Carlo/deterministic techniques dramatically increase the efficiency of neutronics modeling, but their use in the accurate design analysis of very large and geometrically complex nuclear systems has been limited by the large number of processors and memory requirements for their preliminary deterministic calculations and final Monte Carlo calculation. Three mesh adaptivity algorithms were developed to reduce the memory requirements of CADIS and FW-CADIS without sacrificing their efficiency improvement. First, a macromaterial approach enhances the fidelity of the deterministic models without changing the mesh. Second, a deterministic mesh refinement algorithm generates meshes that capture as much geometric detail as possible without exceeding a specified maximum number of mesh elements. Finally, a weight window coarsening algorithm decouples the weight window mesh and energy bins from the mesh and energy group structure of the deterministic calculations in order to remove the memory constraint of the weight window map from the deterministic mesh resolution. The three algorithms were used to enhance an FW-CADIS calculation of the prompt dose rate throughout the ITER experimental facility. Using these algorithms resulted in a 23.3% increase in the number of mesh tally elements in which the dose rates were calculated in a 10-day Monte Carlo calculation and, additionally, increased the efficiency of the Monte Carlo simulation by a factor of at least 3.4. The three algorithms enabled this difficult calculation to be accurately solved using an FW-CADIS simulation on a regular computer cluster, eliminating the need for a world-class super computer.
Modeling, mesh generation, and adaptive numerical methods for partial differential equations
Babuska, I.; Henshaw, W.D.; Oliger, J.E.; Flaherty, J.E.; Hopcroft, J.E.; Tezduyar, T.
1995-12-31
Mesh generation is one of the most time consuming aspects of computational solutions of problems involving partial differential equations. It is, furthermore, no longer acceptable to compute solutions without proper verification that specified accuracy criteria are being satisfied. Mesh generation must be related to the solution through computable estimates of discretization errors. Thus, an iterative process of alternate mesh and solution generation evolves in an adaptive manner with the end result that the solution is computed to prescribed specifications in an optimal, or at least efficient, manner. While mesh generation and adaptive strategies are becoming available, major computational challenges remain. One, in particular, involves moving boundaries and interfaces, such as free-surface flows and fluid-structure interactions. A 3-week program was held from July 5 to July 23, 1993 with 173 participants and 66 keynote, invited, and contributed presentations. This volume represents written versions of 21 of these lectures. These proceedings are organized roughly in order of their presentation at the workshop. Thus, the initial papers are concerned with geometry and mesh generation and discuss the representation of physical objects and surfaces on a computer and techniques to use this data to generate, principally, unstructured meshes of tetrahedral or hexahedral elements. The remainder of the papers cover adaptive strategies, error estimation, and applications. Several submissions deal with high-order p- and hp-refinement methods where mesh refinement/coarsening (h-refinement) is combined with local variation of method order (p-refinement). Combinations of mathematically verified and physically motivated approaches to error estimation are represented. Applications center on fluid mechanics. Selected papers are indexed separately for inclusion in the Energy Science and Technology Database.
Vasylkiv, Oleg; Borodianska, Hanna; Badica, Petre; Grasso, Salvatore; Sakka, Yoshio; Tok, Alfred; Su, Liap Tat; Bosman, Michael; Ma, Jan
2012-02-01
Boron carbide B4C powders were subject to reactive spark plasma sintering (also known as field assisted sintering, pulsed current sintering or plasma assisted sintering) under nitrogen atmosphere. For an optimum hexagonal BN (h-BN) content estimated from X-ray diffraction measurements at approximately 0.4 wt%, the as-prepared BaCb-(BxOy/BN) ceramic shows values of Berkovich and Vickers hardness of 56.7 +/- 3.1 GPa and 39.3 +/- 7.6 GPa, respectively. These values are higher than for the vacuum SPS processed B4C pristine sample and the h-BN -mechanically-added samples. XRD and electronic microscopy data suggest that in the samples produced by reactive SPS in N2 atmosphere, and containing an estimated amount of 0.3-1.5% h-BN, the crystallite size of the boron carbide grains is decreasing with the increasing amount of N2, while for the newly formed lamellar h-BN the crystallite size is almost constant (approximately 30-50 nm). BN is located at the grain boundaries between the boron carbide grains and it is wrapped and intercalated by a thin layer of boron oxide. BxOy/BN forms a fine and continuous 3D mesh-like structure that is a possible reason for good mechanical properties. PMID:22629879
Implementation of a mesh adaptive scheme based on an element-level error indicator
NASA Technical Reports Server (NTRS)
Keating, Scott; Felippa, Carlos A.; Militello, Carmelo
1993-01-01
We investigate the formulation and application of element-level error indicators based on parametrized variational principles. The qualifier 'element-level' means that no information from adjacent elements is used for error estimation. This property is ideally suited to drive adaptive mesh refinement on parallel computers where access to neighboring elements resident on different processors may incur significant computational overhead. Furthermore, such indicators are not affected by physical jumps at junctures or interfaces. An element-level indicator has been derived from the higher-order element energy and applied to r and h mesh adaptation of meshes in plates and shell structures. We report on our initial experiments with a cylindrical shell that intersects with fist plates forming a simplified 'wing-body intersection' benchmark problem.
Adaptive mesh refinement techniques for the immersed interface method applied to flow problems.
Li, Zhilin; Song, Peng
2013-06-01
In this paper, we develop an adaptive mesh refinement strategy of the Immersed Interface Method for flow problems with a moving interface. The work is built on the AMR method developed for two-dimensional elliptic interface problems in the paper [12] (CiCP, 12(2012), 515-527). The interface is captured by the zero level set of a Lipschitz continuous function φ(x, y, t). Our adaptive mesh refinement is built within a small band of |φ(x, y, t)| ≤ δ with finer Cartesian meshes. The AMR-IIM is validated for Stokes and Navier-Stokes equations with exact solutions, moving interfaces driven by the surface tension, and classical bubble deformation problems. A new simple area preserving strategy is also proposed in this paper for the level set method. PMID:23794763
Hornung, R.D.
1996-12-31
An adaptive local mesh refinement (AMR) algorithm originally developed for unsteady gas dynamics is extended to multi-phase flow in porous media. Within the AMR framework, we combine specialized numerical methods to treat the different aspects of the partial differential equations. Multi-level iteration and domain decomposition techniques are incorporated to accommodate elliptic/parabolic behavior. High-resolution shock capturing schemes are used in the time integration of the hyperbolic mass conservation equations. When combined with AMR, these numerical schemes provide high resolution locally in a more efficient manner than if they were applied on a uniformly fine computational mesh. We will discuss the interplay of physical, mathematical, and numerical concerns in the application of adaptive mesh refinement to flow in porous media problems of practical interest.
Failure of Anisotropic Unstructured Mesh Adaption Based on Multidimensional Residual Minimization
NASA Technical Reports Server (NTRS)
Wood, William A.; Kleb, William L.
2003-01-01
An automated anisotropic unstructured mesh adaptation strategy is proposed, implemented, and assessed for the discretization of viscous flows. The adaption criteria is based upon the minimization of the residual fluctuations of a multidimensional upwind viscous flow solver. For scalar advection, this adaption strategy has been shown to use fewer grid points than gradient based adaption, naturally aligning mesh edges with discontinuities and characteristic lines. The adaption utilizes a compact stencil and is local in scope, with four fundamental operations: point insertion, point deletion, edge swapping, and nodal displacement. Evaluation of the solution-adaptive strategy is performed for a two-dimensional blunt body laminar wind tunnel case at Mach 10. The results demonstrate that the strategy suffers from a lack of robustness, particularly with regard to alignment of the bow shock in the vicinity of the stagnation streamline. In general, constraining the adaption to such a degree as to maintain robustness results in negligible improvement to the solution. Because the present method fails to consistently or significantly improve the flow solution, it is rejected in favor of simple uniform mesh refinement.
Towards a large-scale scalable adaptive heart model using shallow tree meshes
NASA Astrophysics Data System (ADS)
Krause, Dorian; Dickopf, Thomas; Potse, Mark; Krause, Rolf
2015-10-01
Electrophysiological heart models are sophisticated computational tools that place high demands on the computing hardware due to the high spatial resolution required to capture the steep depolarization front. To address this challenge, we present a novel adaptive scheme for resolving the deporalization front accurately using adaptivity in space. Our adaptive scheme is based on locally structured meshes. These tensor meshes in space are organized in a parallel forest of trees, which allows us to resolve complicated geometries and to realize high variations in the local mesh sizes with a minimal memory footprint in the adaptive scheme. We discuss both a non-conforming mortar element approximation and a conforming finite element space and present an efficient technique for the assembly of the respective stiffness matrices using matrix representations of the inclusion operators into the product space on the so-called shallow tree meshes. We analyzed the parallel performance and scalability for a two-dimensional ventricle slice as well as for a full large-scale heart model. Our results demonstrate that the method has good performance and high accuracy.
Laser ray tracing in a parallel arbitrary Lagrangian-Eulerian adaptive mesh refinement hydrocode
NASA Astrophysics Data System (ADS)
Masters, N. D.; Kaiser, T. B.; Anderson, R. W.; Eder, D. C.; Fisher, A. C.; Koniges, A. E.
2010-08-01
ALE-AMR is a new hydrocode that we are developing as a predictive modeling tool for debris and shrapnel formation in high-energy laser experiments. In this paper we present our approach to implementing laser ray tracing in ALE-AMR. We present the basic concepts of laser ray tracing and our approach to efficiently traverse the adaptive mesh hierarchy.
Cell type-specific adaptation of cellular and nuclear volume in micro-engineered 3D environments.
Greiner, Alexandra M; Klein, Franziska; Gudzenko, Tetyana; Richter, Benjamin; Striebel, Thomas; Wundari, Bayu G; Autenrieth, Tatjana J; Wegener, Martin; Franz, Clemens M; Bastmeyer, Martin
2015-11-01
Bio-functionalized three-dimensional (3D) structures fabricated by direct laser writing (DLW) are structurally and mechanically well-defined and ideal for systematically investigating the influence of three-dimensionality and substrate stiffness on cell behavior. Here, we show that different fibroblast-like and epithelial cell lines maintain normal proliferation rates and form functional cell-matrix contacts in DLW-fabricated 3D scaffolds of different mechanics and geometry. Furthermore, the molecular composition of cell-matrix contacts forming in these 3D micro-environments and under conventional 2D culture conditions is identical, based on the analysis of several marker proteins (paxillin, phospho-paxillin, phospho-focal adhesion kinase, vinculin, β1-integrin). However, fibroblast-like and epithelial cells differ markedly in the way they adapt their total cell and nuclear volumes in 3D environments. While fibroblast-like cell lines display significantly increased cell and nuclear volumes in 3D substrates compared to 2D substrates, epithelial cells retain similar cell and nuclear volumes in 2D and 3D environments. Despite differential cell volume regulation between fibroblasts and epithelial cells in 3D environments, the nucleus-to-cell (N/C) volume ratios remain constant for all cell types and culture conditions. Thus, changes in cell and nuclear volume during the transition from 2D to 3D environments are strongly cell type-dependent, but independent of scaffold stiffness, while cells maintain the N/C ratio regardless of culture conditions. PMID:26283159
The geometry of r-adaptive meshes generated using optimal transport methods
NASA Astrophysics Data System (ADS)
Budd, C. J.; Russell, R. D.; Walsh, E.
2015-02-01
The principles of mesh equidistribution and alignment play a fundamental role in the design of adaptive methods, and a metric tensor and mesh metric are useful theoretical tools for understanding a method's level of mesh alignment, or anisotropy. We consider a mesh redistribution method based on the Monge-Ampère equation which combines equidistribution of a given scalar density function with optimal transport. It does not involve explicit use of a metric tensor, although such a tensor must exist for the method, and an interesting question to ask is whether or not the alignment produced by the metric gives an anisotropic mesh. For model problems with a linear feature and with a radially symmetric feature, we derive the exact form of the metric, which involves expressions for its eigenvalues and eigenvectors. The eigenvectors are shown to be orthogonal and tangential to the feature, and the ratio of the eigenvalues (corresponding to the level of anisotropy) is shown to depend, both locally and globally, on the value of the density function and the amount of curvature. We thereby demonstrate how the optimal transport method produces an anisotropic mesh along a given feature while equidistributing a suitably chosen scalar density function. Numerical results are given to verify these results and to demonstrate how the analysis is useful for problems involving more complex features, including for a non-trivial time dependant nonlinear PDE which evolves narrow and curved reaction fronts.
Time-dependent grid adaptation for meshes of triangles and tetrahedra
NASA Technical Reports Server (NTRS)
Rausch, Russ D.
1993-01-01
This paper presents in viewgraph form a method of optimizing grid generation for unsteady CFD flow calculations that distributes the numerical error evenly throughout the mesh. Adaptive meshing is used to locally enrich in regions of relatively large errors and to locally coarsen in regions of relatively small errors. The enrichment/coarsening procedures are robust for isotropic cells; however, enrichment of high aspect ratio cells may fail near boundary surfaces with relatively large curvature. The enrichment indicator worked well for the cases shown, but in general requires user supervision for a more efficient solution.
Using Multithreading for the Automatic Load Balancing of 2D Adaptive Finite Element Meshes
NASA Technical Reports Server (NTRS)
Heber, Gerd; Biswas, Rupak; Thulasiraman, Parimala; Gao, Guang R.; Bailey, David H. (Technical Monitor)
1998-01-01
In this paper, we present a multi-threaded approach for the automatic load balancing of adaptive finite element (FE) meshes. The platform of our choice is the EARTH multi-threaded system which offers sufficient capabilities to tackle this problem. We implement the question phase of FE applications on triangular meshes, and exploit the EARTH token mechanism to automatically balance the resulting irregular and highly nonuniform workload. We discuss the results of our experiments on EARTH-SP2, an implementation of EARTH on the IBM SP2, with different load balancing strategies that are built into the runtime system.
NASA Astrophysics Data System (ADS)
Burago, N. G.; Nikitin, I. S.; Yakushev, V. L.
2016-06-01
Techniques that improve the accuracy of numerical solutions and reduce their computational costs are discussed as applied to continuum mechanics problems with complex time-varying geometry. The approach combines shock-capturing computations with the following methods: (1) overlapping meshes for specifying complex geometry; (2) elastic arbitrarily moving adaptive meshes for minimizing the approximation errors near shock waves, boundary layers, contact discontinuities, and moving boundaries; (3) matrix-free implementation of efficient iterative and explicit-implicit finite element schemes; (4) balancing viscosity (version of the stabilized Petrov-Galerkin method); (5) exponential adjustment of physical viscosity coefficients; and (6) stepwise correction of solutions for providing their monotonicity and conservativeness.
Laser Ray Tracing in a Parallel Arbitrary Lagrangian-Eulerian Adaptive Mesh Refinement Hydrocode
Masters, N D; Kaiser, T B; Anderson, R W; Eder, D C; Fisher, A C; Koniges, A E
2009-09-28
ALE-AMR is a new hydrocode that we are developing as a predictive modeling tool for debris and shrapnel formation in high-energy laser experiments. In this paper we present our approach to implementing laser ray-tracing in ALE-AMR. We present the equations of laser ray tracing, our approach to efficient traversal of the adaptive mesh hierarchy in which we propagate computational rays through a virtual composite mesh consisting of the finest resolution representation of the modeled space, and anticipate simulations that will be compared to experiments for code validation.
Adaptive Mesh Refinement in Curvilinear Body-Fitted Grid Systems
NASA Technical Reports Server (NTRS)
Steinthorsson, Erlendur; Modiano, David; Colella, Phillip
1995-01-01
To be truly compatible with structured grids, an AMR algorithm should employ a block structure for the refined grids to allow flow solvers to take advantage of the strengths of unstructured grid systems, such as efficient solution algorithms for implicit discretizations and multigrid schemes. One such algorithm, the AMR algorithm of Berger and Colella, has been applied to and adapted for use with body-fitted structured grid systems. Results are presented for a transonic flow over a NACA0012 airfoil (AGARD-03 test case) and a reflection of a shock over a double wedge.
The design of a parallel adaptive paving all-quadrilateral meshing algorithm
Tautges, T.J.; Lober, R.R.; Vaughan, C.
1995-08-01
Adaptive finite element analysis demands a great deal of computational resources, and as such is most appropriately solved in a massively parallel computer environment. This analysis will require other parallel algorithms before it can fully utilize MP computers, one of which is parallel adaptive meshing. A version of the paving algorithm is being designed which operates in parallel but which also retains the robustness and other desirable features present in the serial algorithm. Adaptive paving in a production mode is demonstrated using a Babuska-Rheinboldt error estimator on a classic linearly elastic plate problem. The design of the parallel paving algorithm is described, and is based on the decomposition of a surface into {open_quotes}virtual{close_quotes} surfaces. The topology of the virtual surface boundaries is defined using mesh entities (mesh nodes and edges) so as to allow movement of these boundaries with smoothing and other operations. This arrangement allows the use of the standard paving algorithm on subdomain interiors, after the negotiation of the boundary mesh.
Spatially adaptive bases in wavelet-based coding of semi-regular meshes
NASA Astrophysics Data System (ADS)
Denis, Leon; Florea, Ruxandra; Munteanu, Adrian; Schelkens, Peter
2010-05-01
In this paper we present a wavelet-based coding approach for semi-regular meshes, which spatially adapts the employed wavelet basis in the wavelet transformation of the mesh. The spatially-adaptive nature of the transform requires additional information to be stored in the bit-stream in order to allow the reconstruction of the transformed mesh at the decoder side. In order to limit this overhead, the mesh is first segmented into regions of approximately equal size. For each spatial region, a predictor is selected in a rate-distortion optimal manner by using a Lagrangian rate-distortion optimization technique. When compared against the classical wavelet transform employing the butterfly subdivision filter, experiments reveal that the proposed spatially-adaptive wavelet transform significantly decreases the energy of the wavelet coefficients for all subbands. Preliminary results show also that employing the proposed transform for the lowest-resolution subband systematically yields improved compression performance at low-to-medium bit-rates. For the Venus and Rabbit test models the compression improvements add up to 1.47 dB and 0.95 dB, respectively.
NASA Astrophysics Data System (ADS)
Blanco, Leonardo; Blavier, Marie; Glanc, Marie; Pouplard, Florence; Tick, Sarah; Maksimovic, Ivan; Chenegros, Guillaume; Mugnier, Laurent; Lacombe, Francois; Rousset, Gérard; Paques, Michel; Le Gargasson, Jean-François; Sahel, Jose-Alain
2008-09-01
We describe here two parts of our future 3D fundus camera coupling Adaptive Optics and full-field Optical Coherence Tomography. The first part is an Adaptive Optics flood imager installed at the Quinze-Vingts Hospital, regularly used on healthy and pathological eyes. A posteriori image reconstruction is performed, increasing the final image quality and field of view. The instrument lateral resolution is better than 2 microns. The second part is a full-field Optical Coherence Tomograph, which has demonstrated capability of performing a simple kind of "4 phases" image reconstruction of non biological samples and ex situ retinas. Final aim is to couple both parts in order to achieve 3D high resolution mapping of in vivo retinas.
NASA Astrophysics Data System (ADS)
Angelidis, Dionysios; Sotiropoulos, Fotis
2015-11-01
The geometrical details of wind turbines determine the structure of the turbulence in the near and far wake and should be taken in account when performing high fidelity calculations. Multi-resolution simulations coupled with an immersed boundary method constitutes a powerful framework for high-fidelity calculations past wind farms located over complex terrains. We develop a 3D Immersed-Boundary Adaptive Mesh Refinement flow solver (IB-AMR) which enables turbine-resolving LES of wind turbines. The idea of using a hybrid staggered/non-staggered grid layout adopted in the Curvilinear Immersed Boundary Method (CURVIB) has been successfully incorporated on unstructured meshes and the fractional step method has been employed. The overall performance and robustness of the second order accurate, parallel, unstructured solver is evaluated by comparing the numerical simulations against conforming grid calculations and experimental measurements of laminar and turbulent flows over complex geometries. We also present turbine-resolving multi-scale LES considering all the details affecting the induced flow field; including the geometry of the tower, the nacelle and especially the rotor blades of a wind tunnel scale turbine. This material is based upon work supported by the Department of Energy under Award Number DE-EE0005482 and the Sandia National Laboratories.
NASA Astrophysics Data System (ADS)
Jouan, M.; Debreu, L.; Dumas, F.
2003-04-01
In order to study the spreading of the big river discharges over the continental shelf in the bay of Biscay, a 3D model that solves the primitive equations has been developped. Following Blumberg and Mellor (1987), it is a split-implicit free-surface version for the sigma coordinates system based on a finite difference approximation. For the bay of Biscay continental shelf implementation, the domain covers the two main estuaries of Loire and Gironde with a 5km resolution. An enhancement of local resolution must significantly improve the results. As the gradients apart from thess particular areas are weaker, we focus on both areas and increase resolution up to 1.5km. For this purpose, a mesh refinement technique has been implemented in the 5km resolution configuration ; it is based on Berger-Oliger technique (i.e. domain decomposition with full overlapping). The AGRIF software library allows two computational modes : - one way : at each step on the fine grid, open boundary conditions are interpolated in time and space from the upper level - two way : in addition to the previous mode, a retroactive forcing updates some state variables on the coarser grid from the fine grid values. In one way mode, results on the fine grid can vary depending on type of prescribed variables at the interface. Results of the two way mode tend to prove the necessity to update the upper level to reproduce as fine as possible density structure and therefore improve the global solution, hence the boundary conditions of the fine grid itself. Paying attention to particular features (consistancy of the bathymetry), the system is rather stable. This configuration is then used to follow the low salinity lenses and to determine under which conditions these appear.
NASA Astrophysics Data System (ADS)
Jouan, M.; Debreu, L.; Dumas, F.
2003-04-01
In order to study the spreading of the big river discharges over the continental shelf in the bay of Biscay, a 3D model that solves the primitive equations has been developped. Following Blumberg and Mellor (1987), it is a split-implicit free-surface version for the sigma coordinates system based on a finite difference approximation. For the bay of Biscay continental shelf implementation, the domain covers the two main estuaries of Loire and Gironde with a 5km resolution. An enhancement of local resolution must significantly improve the results. As the gradients apart from thess particular areas are weaker, we focus on both areas and increase resolution up to 1.5km. For this purpose, a mesh refinement technique has been implemented in the 5km resolution configuration ; it is based on Berger-Oliger technique (i.e. domain decomposition with full overlapping). The AGRIF software library allows two computational modes : - one way : at each step on the fine grid, open boundary conditions are interpolated in time and space from the upper level - two way : in addition to the previous mode, a retroactive forcing updates some state variables on the coarser grid from the fine grid values. In one way mode, results on the fine grid can vary depending on type of prescribed variables at the interface. Results of the two way mode tend to prove the necessity to update the upper level to reproduce as fine as possible density structure and therefore improve the global solution, hence the boundary conditions of the fine grid itself. Paying attention to particular features (consistancy of the bathymetry), the system is rather stable. This configuration is then used to follow the low salinity lenses and to determine under which conditions these appear.
PLUM: Parallel Load Balancing for Unstructured Adaptive Meshes. Degree awarded by Colorado Univ.
NASA Technical Reports Server (NTRS)
Oliker, Leonid
1998-01-01
Dynamic mesh adaption on unstructured grids is a powerful tool for computing large-scale problems that require grid modifications to efficiently resolve solution features. By locally refining and coarsening the mesh to capture physical phenomena of interest, such procedures make standard computational methods more cost effective. Unfortunately, an efficient parallel implementation of these adaptive methods is rather difficult to achieve, primarily due to the load imbalance created by the dynamically-changing nonuniform grid. This requires significant communication at runtime, leading to idle processors and adversely affecting the total execution time. Nonetheless, it is generally thought that unstructured adaptive- grid techniques will constitute a significant fraction of future high-performance supercomputing. Various dynamic load balancing methods have been reported to date; however, most of them either lack a global view of loads across processors or do not apply their techniques to realistic large-scale applications.
An adaptive embedded mesh procedure for leading-edge vortex flows
NASA Technical Reports Server (NTRS)
Powell, Kenneth G.; Beer, Michael A.; Law, Glenn W.
1989-01-01
A procedure for solving the conical Euler equations on an adaptively refined mesh is presented, along with a method for determining which cells to refine. The solution procedure is a central-difference cell-vertex scheme. The adaptation procedure is made up of a parameter on which the refinement decision is based, and a method for choosing a threshold value of the parameter. The refinement parameter is a measure of mesh-convergence, constructed by comparison of locally coarse- and fine-grid solutions. The threshold for the refinement parameter is based on the curvature of the curve relating the number of cells flagged for refinement to the value of the refinement threshold. Results for three test cases are presented. The test problem is that of a delta wing at angle of attack in a supersonic free-stream. The resulting vortices and shocks are captured efficiently by the adaptive code.
Spatial adaptation procedures on tetrahedral meshes for unsteady aerodynamic flow calculations
NASA Technical Reports Server (NTRS)
Rausch, Russ D.; Batina, John T.; Yang, Henry T. Y.
1993-01-01
Spatial adaptation procedures for the accurate and efficient solution of steady and unsteady inviscid flow problems are described. The adaptation procedures were developed and implemented within a three-dimensional, unstructured-grid, upwind-type Euler code. These procedures involve mesh enrichment and mesh coarsening to either add points in high gradient regions of the flow or remove points where they are not needed, respectively, to produce solutions of high spatial accuracy at minimal computational cost. A detailed description of the enrichment and coarsening procedures are presented and comparisons with experimental data for an ONERA M6 wing and an exact solution for a shock-tube problem are presented to provide an assessment of the accuracy and efficiency of the capability. Steady and unsteady results, obtained using spatial adaptation procedures, are shown to be of high spatial accuracy, primarily in that discontinuities such as shock waves are captured very sharply.
Kolobov, Vladimir; Arslanbekov, Robert; Frolova, Anna
2014-12-09
The paper describes an Adaptive Mesh in Phase Space (AMPS) technique for solving kinetic equations with deterministic mesh-based methods. The AMPS technique allows automatic generation of adaptive Cartesian mesh in both physical and velocity spaces using a Tree-of-Trees data structure. We illustrate advantages of AMPS for simulations of rarefied gas dynamics and electron kinetics on low temperature plasmas. In particular, we consider formation of the velocity distribution functions in hypersonic flows, particle kinetics near oscillating boundaries, and electron kinetics in a radio-frequency sheath. AMPS provide substantial savings in computational cost and increased efficiency of the mesh-based kinetic solvers.
NASA Astrophysics Data System (ADS)
Kolobov, Vladimir; Arslanbekov, Robert; Frolova, Anna
2014-12-01
The paper describes an Adaptive Mesh in Phase Space (AMPS) technique for solving kinetic equations with deterministic mesh-based methods. The AMPS technique allows automatic generation of adaptive Cartesian mesh in both physical and velocity spaces using a Tree-of-Trees data structure. We illustrate advantages of AMPS for simulations of rarefied gas dynamics and electron kinetics on low temperature plasmas. In particular, we consider formation of the velocity distribution functions in hypersonic flows, particle kinetics near oscillating boundaries, and electron kinetics in a radio-frequency sheath. AMPS provide substantial savings in computational cost and increased efficiency of the mesh-based kinetic solvers.
Practical improvements of multi-grid iteration for adaptive mesh refinement method
NASA Astrophysics Data System (ADS)
Miyashita, Hisashi; Yamada, Yoshiyuki
2005-03-01
Adaptive mesh refinement(AMR) is a powerful tool to efficiently solve multi-scaled problems. However, the vanilla AMR method has a well-known critical demerit, i.e., it cannot be applied to non-local problems. Although multi-grid iteration (MGI) can be regarded as a good remedy for a non-local problem such as the Poisson equation, we observed fundamental difficulties in applying the MGI technique in AMR to realistic problems under complicated mesh layouts because it does not converge or it requires too many iterations even if it does converge. To cope with the problem, when updating the next approximation in the MGI process, we calculate the precise total corrections that are relatively accurate to the current residual by introducing a new iteration for such a total correction. This procedure greatly accelerates the MGI convergence speed especially under complicated mesh layouts.
Adaptive optofluidic lens(es) for switchable 2D and 3D imaging
NASA Astrophysics Data System (ADS)
Huang, Hanyang; Wei, Kang; Zhao, Yi
2016-03-01
The stereoscopic image is often captured using dual cameras arranged side-by-side and optical path switching systems such as two separate solid lenses or biprism/mirrors. The miniaturization of the overall size of current stereoscopic devices down to several millimeters is at a sacrifice of further device size shrinkage. The limited light entry worsens the final image resolution and brightness. It is known that optofluidics offer good re-configurability for imaging systems. Leveraging this technique, we report a reconfigurable optofluidic system whose optical layout can be swapped between a singlet lens with 10 mm in diameter and a pair of binocular lenses with each lens of 3 mm in diameter for switchable two-dimensional (2D) and three-dimensional (3D) imaging. The singlet and the binoculars share the same optical path and the same imaging sensor. The singlet acquires a 3D image with better resolution and brightness, while the binoculars capture stereoscopic image pairs for 3D vision and depth perception. The focusing power tuning capability of the singlet and the binoculars enable image acquisition at varied object planes by adjusting the hydrostatic pressure across the lens membrane. The vari-focal singlet and binoculars thus work interchangeably and complementarily. The device is thus expected to have applications in robotic vision, stereoscopy, laparoendoscopy and miniaturized zoom lens system.
Ray, Jaideep; Lefantzi, Sophia; Najm, Habib N.; Kennedy, Christopher A.
2006-01-01
Block-structured adaptively refined meshes (SAMR) strive for efficient resolution of partial differential equations (PDEs) solved on large computational domains by clustering mesh points only where required by large gradients. Previous work has indicated that fourth-order convergence can be achieved on such meshes by using a suitable combination of high-order discretizations, interpolations, and filters and can deliver significant computational savings over conventional second-order methods at engineering error tolerances. In this paper, we explore the interactions between the errors introduced by discretizations, interpolations and filters. We develop general expressions for high-order discretizations, interpolations, and filters, in multiple dimensions, using a Fourier approach, facilitating the high-order SAMR implementation. We derive a formulation for the necessary interpolation order for given discretization and derivative orders. We also illustrate this order relationship empirically using one and two-dimensional model problems on refined meshes. We study the observed increase in accuracy with increasing interpolation order. We also examine the empirically observed order of convergence, as the effective resolution of the mesh is increased by successively adding levels of refinement, with different orders of discretization, interpolation, or filtering.
Parallel Implementation and Scaling of an Adaptive Mesh Discrete Ordinates Algorithm for Transport
Howell, L H
2004-11-29
Block-structured adaptive mesh refinement (AMR) uses a mesh structure built up out of locally-uniform rectangular grids. In the BoxLib parallel framework used by the Raptor code, each processor operates on one or more of these grids at each refinement level. The decomposition of the mesh into grids and the distribution of these grids among processors may change every few timesteps as a calculation proceeds. Finer grids use smaller timesteps than coarser grids, requiring additional work to keep the system synchronized and ensure conservation between different refinement levels. In a paper for NECDC 2002 I presented preliminary results on implementation of parallel transport sweeps on the AMR mesh, conjugate gradient acceleration, accuracy of the AMR solution, and scalar speedup of the AMR algorithm compared to a uniform fully-refined mesh. This paper continues with a more in-depth examination of the parallel scaling properties of the scheme, both in single-level and multi-level calculations. Both sweeping and setup costs are considered. The algorithm scales with acceptable performance to several hundred processors. Trends suggest, however, that this is the limit for efficient calculations with traditional transport sweeps, and that modifications to the sweep algorithm will be increasingly needed as job sizes in the thousands of processors become common.
NASA Astrophysics Data System (ADS)
Foks, Nathan Leon
The interpretation of geophysical data plays an important role in the analysis of potential field data in resource exploration industries. Two categories of interpretation techniques are discussed in this thesis; boundary detection and geophysical inversion. Fault or boundary detection is a method to interpret the locations of subsurface boundaries from measured data, while inversion is a computationally intensive method that provides 3D information about subsurface structure. My research focuses on these two aspects of interpretation techniques. First, I develop a method to aid in the interpretation of faults and boundaries from magnetic data. These processes are traditionally carried out using raster grid and image processing techniques. Instead, I use unstructured meshes of triangular facets that can extract inferred boundaries using mesh edges. Next, to address the computational issues of geophysical inversion, I develop an approach to reduce the number of data in a data set. The approach selects the data points according to a user specified proxy for its signal content. The approach is performed in the data domain and requires no modification to existing inversion codes. This technique adds to the existing suite of compressive inversion algorithms. Finally, I develop an algorithm to invert gravity data for an interfacing surface using an unstructured mesh of triangular facets. A pertinent property of unstructured meshes is their flexibility at representing oblique, or arbitrarily oriented structures. This flexibility makes unstructured meshes an ideal candidate for geometry based interface inversions. The approaches I have developed provide a suite of algorithms geared towards large-scale interpretation of potential field data, by using an unstructured representation of both the data and model parameters.
NASA Astrophysics Data System (ADS)
Calder, A. C.; Curtis, B. C.; Dursi, L. J.; Fryxell, B.; Henry, G.; MacNeice, P.; Olson, K.; Ricker, P.; Rosner, R.; Timmes, F. X.; Tufo, H. M.; Truran, J. W.; Zingale, M.
We present simulations and performance results of nuclear burning fronts in supernovae on the largest domain and at the finest spatial resolution studied to date. These simulations were performed on the Intel ASCI-Red machine at Sandia National Laboratories using FLASH, a code developed at the Center for Astrophysical Thermonuclear Flashes at the University of Chicago. FLASH is a modular, adaptive mesh, parallel simulation code capable of handling compressible, reactive fluid flows in astrophysical environments. FLASH is written primarily in Fortran 90, uses the Message-Passing Interface library for inter-processor communication and portability, and employs the PARAMESH package to manage a block-structured adaptive mesh that places blocks only where the resolution is required and tracks rapidly changing flow features, such as detonation fronts, with ease. We describe the key algorithms and their implementation as well as the optimizations required to achieve sustained performance of 238 GLOPS on 6420 processors of ASCI-Red in 64-bit arithmetic.
Implementation of Implicit Adaptive Mesh Refinement in an Unstructured Finite-Volume Flow Solver
NASA Technical Reports Server (NTRS)
Schwing, Alan M.; Nompelis, Ioannis; Candler, Graham V.
2013-01-01
This paper explores the implementation of adaptive mesh refinement in an unstructured, finite-volume solver. Unsteady and steady problems are considered. The effect on the recovery of high-order numerics is explored and the results are favorable. Important to this work is the ability to provide a path for efficient, implicit time advancement. A method using a simple refinement sensor based on undivided differences is discussed and applied to a practical problem: a shock-shock interaction on a hypersonic, inviscid double-wedge. Cases are compared to uniform grids without the use of adapted meshes in order to assess error and computational expense. Discussion of difficulties, advances, and future work prepare this method for additional research. The potential for this method in more complicated flows is described.
Anderson, R W; Pember, R B; Elliott, N S
2001-10-22
A new method that combines staggered grid Arbitrary Lagrangian-Eulerian (ALE) techniques with structured local adaptive mesh refinement (AMR) has been developed for solution of the Euler equations. This method facilitates the solution of problems currently at and beyond the boundary of soluble problems by traditional ALE methods by focusing computational resources where they are required through dynamic adaption. Many of the core issues involved in the development of the combined ALEAMR method hinge upon the integration of AMR with a staggered grid Lagrangian integration method. The novel components of the method are mainly driven by the need to reconcile traditional AMR techniques, which are typically employed on stationary meshes with cell-centered quantities, with the staggered grids and grid motion employed by Lagrangian methods. Numerical examples are presented which demonstrate the accuracy and efficiency of the method.
Adaptation of video game UVW mapping to 3D visualization of gene expression patterns
NASA Astrophysics Data System (ADS)
Vize, Peter D.; Gerth, Victor E.
2007-01-01
Analysis of gene expression patterns within an organism plays a critical role in associating genes with biological processes in both health and disease. During embryonic development the analysis and comparison of different gene expression patterns allows biologists to identify candidate genes that may regulate the formation of normal tissues and organs and to search for genes associated with congenital diseases. No two individual embryos, or organs, are exactly the same shape or size so comparing spatial gene expression in one embryo to that in another is difficult. We will present our efforts in comparing gene expression data collected using both volumetric and projection approaches. Volumetric data is highly accurate but difficult to process and compare. Projection methods use UV mapping to align texture maps to standardized spatial frameworks. This approach is less accurate but is very rapid and requires very little processing. We have built a database of over 180 3D models depicting gene expression patterns mapped onto the surface of spline based embryo models. Gene expression data in different models can easily be compared to determine common regions of activity. Visualization software, both Java and OpenGL optimized for viewing 3D gene expression data will also be demonstrated.
Turner, C. David; Kotulski, Joseph Daniel; Pasik, Michael Francis
2005-12-01
This report investigates the feasibility of applying Adaptive Mesh Refinement (AMR) techniques to a vector finite element formulation for the wave equation in three dimensions. Possible error estimators are considered first. Next, approaches for refining tetrahedral elements are reviewed. AMR capabilities within the Nevada framework are then evaluated. We summarize our conclusions on the feasibility of AMR for time-domain vector finite elements and identify a path forward.
TRIM: A finite-volume MHD algorithm for an unstructured adaptive mesh
Schnack, D.D.; Lottati, I.; Mikic, Z.
1995-07-01
The authors describe TRIM, a MHD code which uses finite volume discretization of the MHD equations on an unstructured adaptive grid of triangles in the poloidal plane. They apply it to problems related to modeling tokamak toroidal plasmas. The toroidal direction is treated by a pseudospectral method. Care was taken to center variables appropriately on the mesh and to construct a self adjoint diffusion operator for cell centered variables.
Reid, John A; Mollica, Peter A; Johnson, Garett D; Ogle, Roy C; Bruno, Robert D; Sachs, Patrick C
2016-01-01
The precision and repeatability offered by computer-aided design and computer-numerically controlled techniques in biofabrication processes is quickly becoming an industry standard. However, many hurdles still exist before these techniques can be used in research laboratories for cellular and molecular biology applications. Extrusion-based bioprinting systems have been characterized by high development costs, injector clogging, difficulty achieving small cell number deposits, decreased cell viability, and altered cell function post-printing. To circumvent the high-price barrier to entry of conventional bioprinters, we designed and 3D printed components for the adaptation of an inexpensive 'off-the-shelf' commercially available 3D printer. We also demonstrate via goal based computer simulations that the needle geometries of conventional commercially standardized, 'luer-lock' syringe-needle systems cause many of the issues plaguing conventional bioprinters. To address these performance limitations we optimized flow within several microneedle geometries, which revealed a short tapered injector design with minimal cylindrical needle length was ideal to minimize cell strain and accretion. We then experimentally quantified these geometries using pulled glass microcapillary pipettes and our modified, low-cost 3D printer. This systems performance validated our models exhibiting: reduced clogging, single cell print resolution, and maintenance of cell viability without the use of a sacrificial vehicle. Using this system we show the successful printing of human induced pluripotent stem cells (hiPSCs) into Geltrex and note their retention of a pluripotent state 7 d post printing. We also show embryoid body differentiation of hiPSC by injection into differentiation conducive environments, wherein we observed continuous growth, emergence of various evaginations, and post-printing gene expression indicative of the presence of all three germ layers. These data demonstrate an
Tatsugami, Fuminari; Higaki, Toru; Fukumoto, Wataru; Kaichi, Yoko; Fujioka, Chikako; Kiguchi, Masao; Yamamoto, Hideya; Kihara, Yasuki; Awai, Kazuo
2015-06-01
To assess the possibility of reducing the radiation dose for coronary artery calcium (CAC) scoring by using adaptive iterative dose reduction 3D (AIDR 3D) on a 320-detector CT scanner. Fifty-four patients underwent routine- and low-dose CT for CAC scoring. Low-dose CT was performed at one-third of the tube current used for routine-dose CT. Routine-dose CT was reconstructed with filtered back projection (FBP) and low-dose CT was reconstructed with AIDR 3D. We compared the calculated Agatston-, volume-, and mass scores of these images. The overall percentage difference in the Agatston-, volume-, and mass scores between routine- and low-dose CT studies was 15.9, 11.6, and 12.6%, respectively. There were no significant differences in the routine- and low-dose CT studies irrespective of the scoring algorithms applied. The CAC measurements of both imaging modalities were highly correlated with respect to the Agatston- (r = 0.996), volume- (r = 0.996), and mass score (r = 0.997; p < 0.001, all); the Bland-Altman limits of agreement scores were -37.4 to 51.4, -31.2 to 36.4 and -30.3 to 40.9%, respectively, suggesting that AIDR 3D was a good alternative for FBP. The mean effective radiation dose for routine- and low-dose CT was 2.2 and 0.7 mSv, respectively. The use of AIDR 3D made it possible to reduce the radiation dose by 67% for CAC scoring without impairing the quantification of coronary calcification. PMID:25754302
Amoeboid migration mode adaption in quasi-3D spatial density gradients of varying lattice geometry
NASA Astrophysics Data System (ADS)
Gorelashvili, Mari; Emmert, Martin; Hodeck, Kai F.; Heinrich, Doris
2014-07-01
Cell migration processes are controlled by sensitive interaction with external cues such as topographic structures of the cell’s environment. Here, we present systematically controlled assays to investigate the specific effects of spatial density and local geometry of topographic structure on amoeboid migration of Dictyostelium discoideum cells. This is realized by well-controlled fabrication of quasi-3D pillar fields exhibiting a systematic variation of inter-pillar distance and pillar lattice geometry. By time-resolved local mean-squared displacement analysis of amoeboid migration, we can extract motility parameters in order to elucidate the details of amoeboid migration mechanisms and consolidate them in a two-state contact-controlled motility model, distinguishing directed and random phases. Specifically, we find that directed pillar-to-pillar runs are found preferably in high pillar density regions, and cells in directed motion states sense pillars as attractive topographic stimuli. In contrast, cell motion in random probing states is inhibited by high pillar density, where pillars act as obstacles for cell motion. In a gradient spatial density, these mechanisms lead to topographic guidance of cells, with a general trend towards a regime of inter-pillar spacing close to the cell diameter. In locally anisotropic pillar environments, cell migration is often found to be damped due to competing attraction by different pillars in close proximity and due to lack of other potential stimuli in the vicinity of the cell. Further, we demonstrate topographic cell guidance reflecting the lattice geometry of the quasi-3D environment by distinct preferences in migration direction. Our findings allow to specifically control amoeboid cell migration by purely topographic effects and thus, to induce active cell guidance. These tools hold prospects for medical applications like improved wound treatment, or invasion assays for immune cells.
Impact of space-time mesh adaptation on solute transport modeling in porous media
NASA Astrophysics Data System (ADS)
Esfandiar, Bahman; Porta, Giovanni; Perotto, Simona; Guadagnini, Alberto
2015-02-01
We implement a space-time grid adaptation procedure to efficiently improve the accuracy of numerical simulations of solute transport in porous media in the context of model parameter estimation. We focus on the Advection Dispersion Equation (ADE) for the interpretation of nonreactive transport experiments in laboratory-scale heterogeneous porous media. When compared to a numerical approximation based on a fixed space-time discretization, our approach is grounded on a joint automatic selection of the spatial grid and the time step to capture the main (space-time) system dynamics. Spatial mesh adaptation is driven by an anisotropic recovery-based error estimator which enables us to properly select the size, shape, and orientation of the mesh elements. Adaptation of the time step is performed through an ad hoc local reconstruction of the temporal derivative of the solution via a recovery-based approach. The impact of the proposed adaptation strategy on the ability to provide reliable estimates of the key parameters of an ADE model is assessed on the basis of experimental solute breakthrough data measured following tracer injection in a nonuniform porous system. Model calibration is performed in a Maximum Likelihood (ML) framework upon relying on the representation of the ADE solution through a generalized Polynomial Chaos Expansion (gPCE). Our results show that the proposed anisotropic space-time grid adaptation leads to ML parameter estimates and to model results of markedly improved quality when compared to classical inversion approaches based on a uniform space-time discretization.
Wavelet-based adaptive numerical simulation of unsteady 3D flow around a bluff body
NASA Astrophysics Data System (ADS)
de Stefano, Giuliano; Vasilyev, Oleg
2012-11-01
The unsteady three-dimensional flow past a two-dimensional bluff body is numerically simulated using a wavelet-based method. The body is modeled by exploiting the Brinkman volume-penalization method, which results in modifying the governing equations with the addition of an appropriate forcing term inside the spatial region occupied by the obstacle. The volume-penalized incompressible Navier-Stokes equations are numerically solved by means of the adaptive wavelet collocation method, where the non-uniform spatial grid is dynamically adapted to the flow evolution. The combined approach is successfully applied to the simulation of vortex shedding flow behind a stationary prism with square cross-section. The computation is conducted at transitional Reynolds numbers, where fundamental unstable three-dimensional vortical structures exist, by well-predicting the unsteady forces arising from fluid-structure interaction.
McKinnon, Daniel D.; Domaille, Dylan W.; Cha, Jennifer N.; Anseth, Kristi S.
2015-01-01
Presented here is a cytocompatible covalently adaptable hydrogel uniquely capable of mimicking the complex biophysical properties of native tissue and enabling natural cell functions without matrix degradation. Demonstrated is both the ability to control elastic modulus and stress relaxation time constants by more than an order of magnitude while predicting these values based on fundamental theoretical understanding and the simulation of muscle tissue and the encapsulation of myoblasts. PMID:24127293
Electrowetting-based adaptive vari-focal liquid lens array for 3D display
NASA Astrophysics Data System (ADS)
Won, Yong Hyub
2014-10-01
Electrowetting is a phenomenon that can control the surface tension of liquid when a voltage is applied. This paper introduces the fabrication method of liquid lens array by the electrowetting phenomenon. The fabricated 23 by 23 lens array has 1mm diameter size with 1.6 mm interval distance between adjacent lenses. The diopter of each lens was - 24~27 operated at 0V to 50V. The lens array chamber fabricated by Deep Reactive-Ion Etching (DRIE) is deposited with IZO and parylene C and tantalum oxide. To prevent water penetration and achieve high dielectric constant, parylene C and tantalum oxide (ɛ = 23 ~ 25) are used respectively. Hydrophobic surface which enables the range of contact angle from 60 to 160 degree is coated to maximize the effect of electrowetting causing wide band of dioptric power. Liquid is injected into each lens chamber by two different ways. First way was self water-oil dosing that uses cosolvent and diffusion effect, while the second way was micro-syringe by the hydrophobic surface properties. To complete the whole process of the lens array fabrication, underwater sealing was performed using UV adhesive that does not dissolve in water. The transient time for changing from concave to convex lens was measured <33ms (at frequency of 1kHz AC voltage.). The liquid lens array was tested unprecedentedly for integral imaging to achieve more advanced depth information of 3D image.
Adaptive enhancement and visualization techniques for 3D THz images of breast cancer tumors
NASA Astrophysics Data System (ADS)
Wu, Yuhao; Bowman, Tyler; Gauch, John; El-Shenawee, Magda
2016-03-01
This paper evaluates image enhancement and visualization techniques for pulsed terahertz (THz) images of tissue samples. Specifically, our research objective is to effectively differentiate between heterogeneous regions of breast tissues that contain tumors diagnosed as triple negative infiltrating ductal carcinoma (IDC). Tissue slices and blocks of varying thicknesses were prepared and scanned using our lab's THz pulsed imaging system. One of the challenges we have encountered in visualizing the obtained images and differentiating between healthy and cancerous regions of the tissues is that most THz images have a low level of details and narrow contrast, making it difficult to accurately identify and visualize the margins around the IDC. To overcome this problem, we have applied and evaluated a number of image processing techniques to the scanned 3D THz images. In particular, we employed various spatial filtering and intensity transformation techniques to emphasize the small details in the images and adjust the image contrast. For each of these methods, we investigated how varying filter sizes and parameters affect the amount of enhancement applied to the images. Our experimentation shows that several image processing techniques are effective in producing THz images of breast tissue samples that contain distinguishable details, making further segmentation of the different image regions promising.
NASA Astrophysics Data System (ADS)
Nishino, Toshimasa; Fujitani, Yasuhiro; Kato, Norihiko; Tsuda, Naoaki; Nomura, Yoshihiko; Matsui, Hirokazu
2012-01-01
The objective of this paper is to establish a technique that levitates and conveys a hand, a kind of micro-robot, by applying magnetic forces: the hand is assumed to have a function of holding and detaching the objects. The equipment to be used in our experiments consists of four pole-pieces of electromagnets, and is expected to work as a 4DOF drive unit within some restricted range of 3D space: the three DOF are corresponding to 3D positional control and the remaining one DOF, rotational oscillation damping control. Having used the same equipment, Khamesee et al. had manipulated the impressed voltages on the four electric magnetics by a PID controller by the use of the feedback signal of the hand's 3D position, the controlled variable. However, in this system, there were some problems remaining: in the horizontal direction, when translating the hand out of restricted region, positional control performance was suddenly degraded. The authors propose a method to apply an adaptive control to the horizontal directional control. It is expected that the technique to be presented in this paper contributes not only to the improvement of the response characteristic but also to widening the applicable range in the horizontal directional control.
Patched based methods for adaptive mesh refinement solutions of partial differential equations
Saltzman, J.
1997-09-02
This manuscript contains the lecture notes for a course taught from July 7th through July 11th at the 1997 Numerical Analysis Summer School sponsored by C.E.A., I.N.R.I.A., and E.D.F. The subject area was chosen to support the general theme of that year`s school which is ``Multiscale Methods and Wavelets in Numerical Simulation.`` The first topic covered in these notes is a description of the problem domain. This coverage is limited to classical PDEs with a heavier emphasis on hyperbolic systems and constrained hyperbolic systems. The next topic is difference schemes. These schemes are the foundation for the adaptive methods. After the background material is covered, attention is focused on a simple patched based adaptive algorithm and its associated data structures for square grids and hyperbolic conservation laws. Embellishments include curvilinear meshes, embedded boundary and overset meshes. Next, several strategies for parallel implementations are examined. The remainder of the notes contains descriptions of elliptic solutions on the mesh hierarchy, elliptically constrained flow solution methods and elliptically constrained flow solution methods with diffusion.
Error estimation and adaptive mesh refinement for parallel analysis of shell structures
NASA Technical Reports Server (NTRS)
Keating, Scott C.; Felippa, Carlos A.; Park, K. C.
1994-01-01
The formulation and application of element-level, element-independent error indicators is investigated. This research culminates in the development of an error indicator formulation which is derived based on the projection of element deformation onto the intrinsic element displacement modes. The qualifier 'element-level' means that no information from adjacent elements is used for error estimation. This property is ideally suited for obtaining error values and driving adaptive mesh refinements on parallel computers where access to neighboring elements residing on different processors may incur significant overhead. In addition such estimators are insensitive to the presence of physical interfaces and junctures. An error indicator qualifies as 'element-independent' when only visible quantities such as element stiffness and nodal displacements are used to quantify error. Error evaluation at the element level and element independence for the error indicator are highly desired properties for computing error in production-level finite element codes. Four element-level error indicators have been constructed. Two of the indicators are based on variational formulation of the element stiffness and are element-dependent. Their derivations are retained for developmental purposes. The second two indicators mimic and exceed the first two in performance but require no special formulation of the element stiffness mesh refinement which we demonstrate for two dimensional plane stress problems. The parallelizing of substructures and adaptive mesh refinement is discussed and the final error indicator using two-dimensional plane-stress and three-dimensional shell problems is demonstrated.
Kallinderis, Yannis; Vitsas, Panagiotis A.; Menounou, Penelope
2012-07-15
A low-order flow/acoustics interaction method for the prediction of sound propagation and diffraction in unsteady subsonic compressible flow using adaptive 3-D hybrid grids is investigated. The total field is decomposed into the flow field described by the Euler equations, and the acoustics part described by the Nonlinear Perturbation Equations. The method is shown capable of predicting monopole sound propagation, while employment of acoustics-guided adapted grid refinement improves the accuracy of capturing the acoustic field. Interaction of sound with solid boundaries is also examined in terms of reflection, and diffraction. Sound propagation through an unsteady flow field is examined using static and dynamic flow/acoustics coupling demonstrating the importance of the latter.
Numerical modelling of tsunami generation by deformable submarine slides using mesh adaptivity
NASA Astrophysics Data System (ADS)
Smith, Rebecca; Parkinson, Samuel; Hill, Jon; Collins, Gareth; Piggott, Matthew
2014-05-01
Tsunamis generated by submarine slides are often under considered in comparison to earthquake generated tsunami, despite several recent examples. Tsunamigenic slides have generated waves that have caused significant damage and loss of life, for example the 1998 Papua New Guinea submarine mass failure resulted in a tsunami that devastated coastal villages and killed over 2,100 people. Numerical simulations of submarine slide generated waves can help us understand the nature of the waves that are generated, and identify the important factors in determining wave characteristics. There have not been many studies of tsunami generation by deformable submarine slides, largely because of the complexities and computational expense involved in modelling these large scale events. At large, real world, scales modelling of tsunami waves by the generation of slides is computationally challenging. Fluidity is an open source finite element code that is ideally suited to tackle this type of problem as it uses unstructured, adaptive meshes, which help to reduce the computational expense without losing accuracy in the results. Adaptive meshes change topology and resolution based on the current simulation state and as such can focus or reduce resolution when and where it is required. The model also allows a number of different numerical approaches to be taken to simulate the same problem within the same numerical framework. In this example we use multi-material approach, with both two materials (slide and water) and three materials (slide, water and air), alongside a density-driven sediment model approach. We will present results of validating Fluidity against benchmarks from experimental and other numerical studies, at different scales, for deformable underwater slides, and consider the utility of mesh adaptivity. We show good agreement to both laboratory results and other numerical models, both with a fixed mesh and a dynamically adaptive mesh, tracking important features of the
Adaptive multi-resolution 3D Hartree-Fock-Bogoliubov solver for nuclear structure
NASA Astrophysics Data System (ADS)
Pei, J. C.; Fann, G. I.; Harrison, R. J.; Nazarewicz, W.; Shi, Yue; Thornton, S.
2014-08-01
Background: Complex many-body systems, such as triaxial and reflection-asymmetric nuclei, weakly bound halo states, cluster configurations, nuclear fragments produced in heavy-ion fusion reactions, cold Fermi gases, and pasta phases in neutron star crust, are all characterized by large sizes and complex topologies in which many geometrical symmetries characteristic of ground-state configurations are broken. A tool of choice to study such complex forms of matter is an adaptive multi-resolution wavelet analysis. This method has generated much excitement since it provides a common framework linking many diversified methodologies across different fields, including signal processing, data compression, harmonic analysis and operator theory, fractals, and quantum field theory. Purpose: To describe complex superfluid many-fermion systems, we introduce an adaptive pseudospectral method for solving self-consistent equations of nuclear density functional theory in three dimensions, without symmetry restrictions. Methods: The numerical method is based on the multi-resolution and computational harmonic analysis techniques with a multi-wavelet basis. The application of state-of-the-art parallel programming techniques include sophisticated object-oriented templates which parse the high-level code into distributed parallel tasks with a multi-thread task queue scheduler for each multi-core node. The internode communications are asynchronous. The algorithm is variational and is capable of solving coupled complex-geometric systems of equations adaptively, with functional and boundary constraints, in a finite spatial domain of very large size, limited by existing parallel computer memory. For smooth functions, user-defined finite precision is guaranteed. Results: The new adaptive multi-resolution Hartree-Fock-Bogoliubov (HFB) solver madness-hfb is benchmarked against a two-dimensional coordinate-space solver hfb-ax that is based on the B-spline technique and a three-dimensional solver
Delanaye, M.; Essers, J.A.
1997-04-01
This paper presents a new finite volume cell-centered scheme for solving the two-dimensional Euler equations. The technique for computing the advective derivatives is based on a high-order Gauss quadrature and an original quadratic reconstruction of the conservative variables for each control volume. A very sensitive detector identifying discontinuity regions switches the scheme to a TVD scheme, and ensures the monotonicity of the solution. The code uses unstructured meshes whose cells are polygons with any number of edges. A mesh adaptation based on cell division is performed in order to increase the resolution of shocks. The accuracy, insensitivity to grid distortions, and shock capturing properties of the scheme are demonstrated for different cascade flow computations.
Chen, Hu; Wang, Han; Lv, Peijun; Wang, Yong; Sun, Yuchun
2015-01-01
Objective. To quantitatively evaluate the tissue surface adaption of a maxillary complete denture wax pattern produced by CAD and 3DP. Methods. A standard edentulous maxilla plaster cast model was used, for which a wax pattern of complete denture was designed using CAD software developed in our previous study and printed using a 3D wax printer, while another wax pattern was manufactured by the traditional manual method. The cast model and the two wax patterns were scanned in the 3D scanner as “DataModel,” “DataWaxRP,” and “DataWaxManual.” After setting each wax pattern on the plaster cast, the whole model was scanned for registration. After registration, the deviations of tissue surface between “DataModel” and “DataWaxRP” and between “DataModel” and “DataWaxManual” were measured. The data was analyzed by paired t-test. Results. For both wax patterns produced by the CAD&RP method and the manual method, scanning data of tissue surface and cast surface showed a good fit in the majority. No statistically significant (P > 0.05) difference was observed between the CAD&RP method and the manual method. Conclusions. Wax pattern of maxillary complete denture produced by the CAD&3DP method is comparable with traditional manual method in the adaption to the edentulous cast model. PMID:26583108
Adaptive optics SLO/OCT for 3D imaging of human photoreceptors in vivo
Felberer, Franz; Kroisamer, Julia-Sophie; Baumann, Bernhard; Zotter, Stefan; Schmidt-Erfurth, Ursula; Hitzenberger, Christoph K.; Pircher, Michael
2014-01-01
We present a new instrument that is capable of imaging human photoreceptors in three dimensions. To achieve high lateral resolution, the system incorporates an adaptive optics system. The high axial resolution is achieved through the implementation of optical coherence tomography (OCT). The instrument records simultaneously both, scanning laser ophthalmoscope (SLO) and OCT en-face images, with a pixel to pixel correspondence. The information provided by the SLO is used to correct for transverse eye motion in post-processing. In order to correct for axial eye motion, the instrument is equipped with a high speed axial eye tracker. In vivo images of foveal cones as well as images recorded at an eccentricity from the fovea showing cones and rods are presented. PMID:24575339
A parallel dynamic load balancing algorithm for 3-D adaptive unstructured grids
NASA Technical Reports Server (NTRS)
Vidwans, A.; Kallinderis, Y.; Venkatakrishnan, V.
1993-01-01
Adaptive local grid refinement and coarsening results in unequal distribution of workload among the processors of a parallel system. A novel method for balancing the load in cases of dynamically changing tetrahedral grids is developed. The approach employs local exchange of cells among processors in order to redistribute the load equally. An important part of the load balancing algorithm is the method employed by a processor to determine which cells within its subdomain are to be exchanged. Two such methods are presented and compared. The strategy for load balancing is based on the Divide-and-Conquer approach which leads to an efficient parallel algorithm. This method is implemented on a distributed-memory MIMD system.
Adaptive model based pulmonary artery segmentation in 3D chest CT
NASA Astrophysics Data System (ADS)
Feuerstein, Marco; Kitasaka, Takayuki; Mori, Kensaku
2010-03-01
The extraction and analysis of the pulmonary artery in computed tomography (CT) of the chest can be an important, but time-consuming step for the diagnosis and treatment of lung disease, in particular in non-contrast data, where the pulmonary artery has low contrast and frequently merges with adjacent tissue of similar intensity. We here present a new method for the automatic segmentation of the pulmonary artery based on an adaptive model, Hough and Euclidean distance transforms, and spline fitting, which works equally well on non-contrast and contrast enhanced data. An evaluation on 40 patient data sets and a comparison to manual segmentations in terms of Jaccard index, sensitivity, specificity, and minimum mean distance shows its overall robustness.
NASA Astrophysics Data System (ADS)
Fernandez, Sergio; Gdeisat, Munther A.; Salvi, Joaquim; Burton, David
2011-06-01
Fringe pattern analysis in coded structured light constitutes an active field of research. Techniques based on first projecting a sinusoidal pattern and then recovering the phase deviation permit the computation of the phase map and its corresponding depth map, leading to a dense acquisition of the measuring object. Among these techniques, the ones based on time-frequency analysis permit to extract the depth map from a single image, thus having potential applications measuring moving objects. The main techniques are Fourier Transform (FT), Windowed Fourier Transform (WFT) and Wavelet Transform (WT). This paper first analyzes the pros and cons of these three techniques, then a new algorithm for the automatic selection of the window size in WFT is proposed. This algorithm is compared to the traditional WT using adapted mother wavelet signals both with simulated and real objects, showing the performance results for quantitative and qualitative evaluations of the new method.
Data-adapted moving least squares method for 3-D image interpolation
NASA Astrophysics Data System (ADS)
Jang, Sumi; Nam, Haewon; Lee, Yeon Ju; Jeong, Byeongseon; Lee, Rena; Yoon, Jungho
2013-12-01
In this paper, we present a nonlinear three-dimensional interpolation scheme for gray-level medical images. The scheme is based on the moving least squares method but introduces a fundamental modification. For a given evaluation point, the proposed method finds the local best approximation by reproducing polynomials of a certain degree. In particular, in order to obtain a better match to the local structures of the given image, we employ locally data-adapted least squares methods that can improve the classical one. Some numerical experiments are presented to demonstrate the performance of the proposed method. Five types of data sets are used: MR brain, MR foot, MR abdomen, CT head, and CT foot. From each of the five types, we choose five volumes. The scheme is compared with some well-known linear methods and other recently developed nonlinear methods. For quantitative comparison, we follow the paradigm proposed by Grevera and Udupa (1998). (Each slice is first assumed to be unknown then interpolated by each method. The performance of each interpolation method is assessed statistically.) The PSNR results for the estimated volumes are also provided. We observe that the new method generates better results in both quantitative and visual quality comparisons.
NASA Astrophysics Data System (ADS)
Winnett, James; Mallick, Kajal K.
2014-04-01
Commercially pure titanium (Ti) and its alloys, in particular, titanium-vanadium-aluminium (Ti-6Al-4V), have been used as biomaterials due to their mechanical similarities to bone, good biocompatibility, and inertness in vivo. The introduction of porosity to the scaffolds leads to optimized mechanical properties and enhanced biological activity. The adaptive foam reticulation (AFR) technique has been previously used to generate hydroxyapatite bioscaffolds with enhanced cell behavior due to the generation of macroporous structures with microporous struts that provided routes for cell infiltration as well as attachment sites. Sacrificial polyurethane templates of 45 ppi and 90 ppi were coated in biomaterial-based slurries containing either Ti or Ti-6Al-4V as the biomaterial and camphene as the porogen. The resultant macropore sizes of 100-550 μm corresponded well with the initial template pore sizes while camphene produced micropores of 1-10 μm, with the level of microporosity related to the amount of porogen inclusion.
HIFI-C: a robust and fast method for determining NMR couplings from adaptive 3D to 2D projections.
Cornilescu, Gabriel; Bahrami, Arash; Tonelli, Marco; Markley, John L; Eghbalnia, Hamid R
2007-08-01
We describe a novel method for the robust, rapid, and reliable determination of J couplings in multi-dimensional NMR coupling data, including small couplings from larger proteins. The method, "High-resolution Iterative Frequency Identification of Couplings" (HIFI-C) is an extension of the adaptive and intelligent data collection approach introduced earlier in HIFI-NMR. HIFI-C collects one or more optimally tilted two-dimensional (2D) planes of a 3D experiment, identifies peaks, and determines couplings with high resolution and precision. The HIFI-C approach, demonstrated here for the 3D quantitative J method, offers vital features that advance the goal of rapid and robust collection of NMR coupling data. (1) Tilted plane residual dipolar couplings (RDC) data are collected adaptively in order to offer an intelligent trade off between data collection time and accuracy. (2) Data from independent planes can provide a statistical measure of reliability for each measured coupling. (3) Fast data collection enables measurements in cases where sample stability is a limiting factor (for example in the presence of an orienting medium required for residual dipolar coupling measurements). (4) For samples that are stable, or in experiments involving relatively stronger couplings, robust data collection enables more reliable determinations of couplings in shorter time, particularly for larger biomolecules. As a proof of principle, we have applied the HIFI-C approach to the 3D quantitative J experiment to determine N-C' RDC values for three proteins ranging from 56 to 159 residues (including a homodimer with 111 residues in each subunit). A number of factors influence the robustness and speed of data collection. These factors include the size of the protein, the experimental set up, and the coupling being measured, among others. To exhibit a lower bound on robustness and the potential for time saving, the measurement of dipolar couplings for the N-C' vector represents a realistic
NASA Astrophysics Data System (ADS)
Narayanan, R.; Werahera, P. N.; Barqawi, A.; Crawford, E. D.; Shinohara, K.; Simoneau, A. R.; Suri, J. S.
2008-10-01
when TRUS guided biopsies are assisted by the 3D prostate cancer atlas compared to the current standard of care. The fast registration algorithm we have developed can easily be adapted for clinical applications for the improved diagnosis of prostate cancer.
Numerical modeling of landslide-generated tsunami using adaptive unstructured meshes
NASA Astrophysics Data System (ADS)
Wilson, Cian; Collins, Gareth; Desousa Costa, Patrick; Piggott, Matthew
2010-05-01
Landslides impacting into or occurring under water generate waves, which can have devastating environmental consequences. Depending on the characteristics of the landslide the waves can have significant amplitude and potentially propagate over large distances. Linear models of classical earthquake-generated tsunamis cannot reproduce the highly nonlinear generation mechanisms required to accurately predict the consequences of landslide-generated tsunamis. Also, laboratory-scale experimental investigation is limited to simple geometries and short time-scales before wave reflections contaminate the data. Computational fluid dynamics models based on the nonlinear Navier-Stokes equations can simulate landslide-tsunami generation at realistic scales. However, traditional chessboard-like structured meshes introduce superfluous resolution and hence the computing power required for such a simulation can be prohibitively high, especially in three dimensions. Unstructured meshes allow the grid spacing to vary rapidly from high resolution in the vicinity of small scale features to much coarser, lower resolution in other areas. Combining this variable resolution with dynamic mesh adaptivity allows such high resolution zones to follow features like the interface between the landslide and the water whilst minimising the computational costs. Unstructured meshes are also better suited to representing complex geometries and bathymetries allowing more realistic domains to be simulated. Modelling multiple materials, like water, air and a landslide, on an unstructured adaptive mesh poses significant numerical challenges. Novel methods of interface preservation must be considered and coupled to a flow model in such a way that ensures conservation of the different materials. Furthermore this conservation property must be maintained during successive stages of mesh optimisation and interpolation. In this paper we validate a new multi-material adaptive unstructured fluid dynamics model
NASA Astrophysics Data System (ADS)
Shi, Lei; Wang, Z. J.
2015-08-01
Adjoint-based mesh adaptive methods are capable of distributing computational resources to areas which are important for predicting an engineering output. In this paper, we develop an adjoint-based h-adaptation approach based on the high-order correction procedure via reconstruction formulation (CPR) to minimize the output or functional error. A dual-consistent CPR formulation of hyperbolic conservation laws is developed and its dual consistency is analyzed. Super-convergent functional and error estimate for the output with the CPR method are obtained. Factors affecting the dual consistency, such as the solution point distribution, correction functions, boundary conditions and the discretization approach for the non-linear flux divergence term, are studied. The presented method is then used to perform simulations for the 2D Euler and Navier-Stokes equations with mesh adaptation driven by the adjoint-based error estimate. Several numerical examples demonstrate the ability of the presented method to dramatically reduce the computational cost comparing with uniform grid refinement.
A new adaptive mesh refinement data structure with an application to detonation
NASA Astrophysics Data System (ADS)
Ji, Hua; Lien, Fue-Sang; Yee, Eugene
2010-11-01
A new Cell-based Structured Adaptive Mesh Refinement (CSAMR) data structure is developed. In our CSAMR data structure, Cartesian-like indices are used to identify each cell. With these stored indices, the information on the parent, children and neighbors of a given cell can be accessed simply and efficiently. Owing to the usage of these indices, the computer memory required for storage of the proposed AMR data structure is only {5}/{8} word per cell, in contrast to the conventional oct-tree [P. MacNeice, K.M. Olson, C. Mobary, R. deFainchtein, C. Packer, PARAMESH: a parallel adaptive mesh refinement community toolkit, Comput. Phys. Commun. 330 (2000) 126] and the fully threaded tree (FTT) [A.M. Khokhlov, Fully threaded tree algorithms for adaptive mesh fluid dynamics simulations, J. Comput. Phys. 143 (1998) 519] data structures which require, respectively, 19 and 2{3}/{8} words per cell for storage of the connectivity information. Because the connectivity information (e.g., parent, children and neighbors) of a cell in our proposed AMR data structure can be accessed using only the cell indices, a tree structure which was required in previous approaches for the organization of the AMR data is no longer needed for this new data structure. Instead, a much simpler hash table structure is used to maintain the AMR data, with the entry keys in the hash table obtained directly from the explicitly stored cell indices. The proposed AMR data structure simplifies the implementation and parallelization of an AMR code. Two three-dimensional test cases are used to illustrate and evaluate the computational performance of the new CSAMR data structure.
A region-appearance-based adaptive variational model for 3D liver segmentation
Peng, Jialin; Dong, Fangfang; Chen, Yunmei; Kong, Dexing
2014-04-15
Purpose: Liver segmentation from computed tomography images is a challenging task owing to pixel intensity overlapping, ambiguous edges, and complex backgrounds. The authors address this problem with a novel active surface scheme, which minimizes an energy functional combining both edge- and region-based information. Methods: In this semiautomatic method, the evolving surface is principally attracted to strong edges but is facilitated by the region-based information where edge information is missing. As avoiding oversegmentation is the primary challenge, the authors take into account multiple features and appearance context information. Discriminative cues, such as multilayer consecutiveness and local organ deformation are also implicitly incorporated. Case-specific intensity and appearance constraints are included to cope with the typically large appearance variations over multiple images. Spatially adaptive balancing weights are employed to handle the nonuniformity of image features. Results: Comparisons and validations on difficult cases showed that the authors’ model can effectively discriminate the liver from adhering background tissues. Boundaries weak in gradient or with no local evidence (e.g., small edge gaps or parts with similar intensity to the background) were delineated without additional user constraint. With an average surface distance of 0.9 mm and an average volume overlap of 93.9% on the MICCAI data set, the authors’ model outperformed most state-of-the-art methods. Validations on eight volumes with different initial conditions had segmentation score variances mostly less than unity. Conclusions: The proposed model can efficiently delineate ambiguous liver edges from complex tissue backgrounds with reproducibility. Quantitative validations and comparative results demonstrate the accuracy and efficacy of the model.
An adaptive mesh method for phase-field simulation of alloy solidification in three dimensions
NASA Astrophysics Data System (ADS)
Bollada, P. C.; Jimack, P. K.; Mullis, A. M.
2015-06-01
We present our computational method for binary alloy solidification which takes advantage of high performance computing where up to 1024 cores are employed. Much of the simulation at a sufficiently fine resolution is possible on a modern 12 core PC and the 1024 core simulation is only necessary for very mature dendrite and convergence testing where high resolution puts extreme demands on memory. In outline, the method uses implicit time stepping in conjunction with an iterative solver, adaptive meshing and a scheme for dividing the work load across processors. We include three dimensional results for a Lewis number of 100 and a snapshot for a mature dendrite for a Lewis number of 40.
Compact integration factor methods for complex domains and adaptive mesh refinement
Liu, Xinfeng; Nie, Qing
2010-01-01
Implicit integration factor (IIF) method, a class of efficient semi-implicit temporal scheme, was introduced recently for stiff reaction-diffusion equations. To reduce cost of IIF, compact implicit integration factor (cIIF) method was later developed for efficient storage and calculation of exponential matrices associated with the diffusion operators in two and three spatial dimensions for Cartesian coordinates with regular meshes. Unlike IIF, cIIF cannot be directly extended to other curvilinear coordinates, such as polar and spherical coordinate, due to the compact representation for the diffusion terms in cIIF. In this paper, we present a method to generalize cIIF for other curvilinear coordinates through examples of polar and spherical coordinates. The new cIIF method in polar and spherical coordinates has similar computational efficiency and stability properties as the cIIF in Cartesian coordinate. In addition, we present a method for integrating cIIF with adaptive mesh refinement (AMR) to take advantage of the excellent stability condition for cIIF. Because the second order cIIF is unconditionally stable, it allows large time steps for AMR, unlike a typical explicit temporal scheme whose time step is severely restricted by the smallest mesh size in the entire spatial domain. Finally, we apply those methods to simulating a cell signaling system described by a system of stiff reaction-diffusion equations in both two and three spatial dimensions using AMR, curvilinear and Cartesian coordinates. Excellent performance of the new methods is observed. PMID:20543883
Earthquake Rupture Dynamics using Adaptive Mesh Refinement and High-Order Accurate Numerical Methods
NASA Astrophysics Data System (ADS)
Kozdon, J. E.; Wilcox, L.
2013-12-01
Our goal is to develop scalable and adaptive (spatial and temporal) numerical methods for coupled, multiphysics problems using high-order accurate numerical methods. To do so, we are developing an opensource, parallel library known as bfam (available at http://bfam.in). The first application to be developed on top of bfam is an earthquake rupture dynamics solver using high-order discontinuous Galerkin methods and summation-by-parts finite difference methods. In earthquake rupture dynamics, wave propagation in the Earth's crust is coupled to frictional sliding on fault interfaces. This coupling is two-way, required the simultaneous simulation of both processes. The use of laboratory-measured friction parameters requires near-fault resolution that is 4-5 orders of magnitude higher than that needed to resolve the frequencies of interest in the volume. This, along with earlier simulations using a low-order, finite volume based adaptive mesh refinement framework, suggest that adaptive mesh refinement is ideally suited for this problem. The use of high-order methods is motivated by the high level of resolution required off the fault in earlier the low-order finite volume simulations; we believe this need for resolution is a result of the excessive numerical dissipation of low-order methods. In bfam spatial adaptivity is handled using the p4est library and temporal adaptivity will be accomplished through local time stepping. In this presentation we will present the guiding principles behind the library as well as verification of code against the Southern California Earthquake Center dynamic rupture code validation test problems.
NASA Technical Reports Server (NTRS)
Langmore, Ian; Davis, Anthony B.; Bal, Guillaume; Marzouk, Youssef M.
2012-01-01
We describe a method for accelerating a 3D Monte Carlo forward radiative transfer model to the point where it can be used in a new kind of Bayesian retrieval framework. The remote sensing challenge is to detect and quantify a chemical effluent of a known absorbing gas produced by an industrial facility in a deep valley. The available data is a single low resolution noisy image of the scene in the near IR at an absorbing wavelength for the gas of interest. The detected sunlight has been multiply reflected by the variable terrain and/or scattered by an aerosol that is assumed partially known and partially unknown. We thus introduce a new class of remote sensing algorithms best described as "multi-pixel" techniques that call necessarily for a 3D radaitive transfer model (but demonstrated here in 2D); they can be added to conventional ones that exploit typically multi- or hyper-spectral data, sometimes with multi-angle capability, with or without information about polarization. The novel Bayesian inference methodology uses adaptively, with efficiency in mind, the fact that a Monte Carlo forward model has a known and controllable uncertainty depending on the number of sun-to-detector paths used.
NASA Astrophysics Data System (ADS)
Liu, Jiaqi; Han, Jing; Zhang, Yi; Bai, Lianfa
2015-10-01
Locally adaptive regression kernels model can describe the edge shape of images accurately and graphic trend of images integrally, but it did not consider images' color information while the color is an important element of an image. Therefore, we present a novel method of target recognition based on 3-D-color-space locally adaptive regression kernels model. Different from the general additional color information, this method directly calculate the local similarity features of 3-D data from the color image. The proposed method uses a few examples of an object as a query to detect generic objects with incompact, complex and changeable shapes. Our method involves three phases: First, calculating the novel color-space descriptors from the RGB color space of query image which measure the likeness of a voxel to its surroundings. Salient features which include spatial- dimensional and color -dimensional information are extracted from said descriptors, and simplifying them to construct a non-similar local structure feature set of the object class by principal components analysis (PCA). Second, we compare the salient features with analogous features from the target image. This comparison is done using a matrix generalization of the cosine similarity measure. Then the similar structures in the target image are obtained using local similarity structure statistical matching. Finally, we use the method of non-maxima suppression in the similarity image to extract the object position and mark the object in the test image. Experimental results demonstrate that our approach is effective and accurate in improving the ability to identify targets.
NASA Astrophysics Data System (ADS)
Grosges, T.; Borouchaki, H.; Barchiesi, D.
2010-12-01
We present an improved adaptive mesh process based on Riemannian transformation to control the accuracy in high field gradient representation for diffraction problems. Such an adaptive meshing is applied in representing the electromagnetic intensity around a metallic submicronic spherical particle, which is known to present high gradients in limited zones of space including the interference pattern of the electromagnetic field. We show that, the precision of the field variation being controlled, this improved scheme permits drastically decreasing the computational time as well as the memory requirements by adapting the number and the position of nodes where the electromagnetic field must be computed and represented.
Ragusa, Jean C.
2015-01-01
In this paper, we propose a piece-wise linear discontinuous (PWLD) finite element discretization of the diffusion equation for arbitrary polygonal meshes. It is based on the standard diffusion form and uses the symmetric interior penalty technique, which yields a symmetric positive definite linear system matrix. A preconditioned conjugate gradient algorithm is employed to solve the linear system. Piece-wise linear approximations also allow a straightforward implementation of local mesh adaptation by allowing unrefined cells to be interpreted as polygons with an increased number of vertices. Several test cases, taken from the literature on the discretization of the radiation diffusion equation, are presented: random, sinusoidal, Shestakov, and Z meshes are used. The last numerical example demonstrates the application of the PWLD discretization to adaptive mesh refinement.
NASA Astrophysics Data System (ADS)
Cherry, Matthew R.; Aldrin, John C.; Boehnlein, Thomas; Blackshire, James L.
2013-01-01
In this work, a combined grid/FEM method that is capable of using parallelepiped or tetragonal mesh elements, as well as a combination of the two, is investigated. A formulation was developed that leverages the architecture of GPUs with irregular grids to efficiently address complex structures and heterogeneous materials. Benchmark studies are presented comparing the computational time, memory requirements, and simulation accuracy for GPU and CPU solvers with several challenge NDE problems.
Three-dimensional numerical simulations of falling films using an adaptive unstructured mesh
NASA Astrophysics Data System (ADS)
Pain, Chris; Xie, Zhihua; Matar, Omar
2015-11-01
Falling liquid films have rich wave dynamics, often occurring in many industrial applications, such as condensers, evaporators and chemical reactors. A number of numerical studies featuring falling liquid films are available in the literature; the majority of them, however, have focused on two-dimensional falling films. Far fewer studies have considered three-dimensional falling films, and those that have only studied the flow in a periodic domain. The objective of this study is to investigate flow dynamics of developing three-dimensional falling films using the Navier-Stokes equations coupled with interface capturing approach over extended domains. An adaptive, unstructured mesh modelling framework is employed here to study this problem, which can modify and adapt three-dimensional meshes to better represent the underlying physics of multiphase problems and reduce computational effort without sacrificing accuracy. Numerical examples of three-dimensional falling films in a long domain are presented and discussed. EPSRC Programme Grant, MEMPHIS, EP/K0039761/1.
Adaptive Mesh Expansion Model (AMEM) for Liver Segmentation from CT Image
Wang, Xuehu; Yang, Jian; Ai, Danni; Zheng, Yongchang; Tang, Songyuan; Wang, Yongtian
2015-01-01
This study proposes a novel adaptive mesh expansion model (AMEM) for liver segmentation from computed tomography images. The virtual deformable simplex model (DSM) is introduced to represent the mesh, in which the motion of each vertex can be easily manipulated. The balloon, edge, and gradient forces are combined with the binary image to construct the external force of the deformable model, which can rapidly drive the DSM to approach the target liver boundaries. Moreover, tangential and normal forces are combined with the gradient image to control the internal force, such that the DSM degree of smoothness can be precisely controlled. The triangular facet of the DSM is adaptively decomposed into smaller triangular components, which can significantly improve the segmentation accuracy of the irregularly sharp corners of the liver. The proposed method is evaluated on the basis of different criteria applied to 10 clinical data sets. Experiments demonstrate that the proposed AMEM algorithm is effective and robust and thus outperforms six other up-to-date algorithms. Moreover, AMEM can achieve a mean overlap error of 6.8% and a mean volume difference of 2.7%, whereas the average symmetric surface distance and the root mean square symmetric surface distance can reach 1.3 mm and 2.7 mm, respectively. PMID:25769030
NASA Astrophysics Data System (ADS)
Fromang, S.; Hennebelle, P.; Teyssier, R.
2006-10-01
Aims. In this paper, we present a new method to perform numerical simulations of astrophysical MHD flows using the Adaptive Mesh Refinement framework and Constrained Transport. Methods: . The algorithm is based on a previous work in which the MUSCL-Hancock scheme was used to evolve the induction equation. In this paper, we detail the extension of this scheme to the full MHD equations and discuss its properties. Results: . Through a series of test problems, we illustrate the performances of this new code using two different MHD Riemann solvers (Lax-Friedrich and Roe) and the need of the Adaptive Mesh Refinement capabilities in some cases. Finally, we show its versatility by applying it to two completely different astrophysical situations well studied in the past years: the growth of the magnetorotational instability in the shearing box and the collapse of magnetized cloud cores. Conclusions: . We have implemented a new Godunov scheme to solve the ideal MHD equations in the AMR code RAMSES. We have shown that it results in a powerful tool that can be applied to a great variety of astrophysical problems, ranging from galaxies formation in the early universe to high resolution studies of molecular cloud collapse in our galaxy.
Multi-dimensional upwind fluctuation splitting scheme with mesh adaption for hypersonic viscous flow
NASA Astrophysics Data System (ADS)
Wood, William Alfred, III
production is shown relative to DMFDSFV. Remarkably the fluctuation splitting scheme shows grid converged skin friction coefficients with only five points in the boundary layer for this case. A viscous Mach 17.6 (perfect gas) cylinder case demonstrates solution monotonicity and heat transfer capability with the fluctuation splitting scheme. While fluctuation splitting is recommended over DMFDSFV, the difference in performance between the schemes is not so great as to obsolete DMFDSFV. The second half of the dissertation develops a local, compact, anisotropic unstructured mesh adaption scheme in conjunction with the multi-dimensional upwind solver, exhibiting a characteristic alignment behavior for scalar problems. This alignment behavior stands in contrast to the curvature clustering nature of the local, anisotropic unstructured adaption strategy based upon a posteriori error estimation that is used for comparison. The characteristic alignment is most pronounced for linear advection, with reduced improvement seen for the more complex non-linear advection and advection-diffusion cases. The adaption strategy is extended to the two-dimensional and axisymmetric Navier-Stokes equations of motion through the concept of fluctuation minimization. The system test case for the adaption strategy is a sting mounted capsule at Mach-10 wind tunnel conditions, considered in both two-dimensional and axisymmetric configurations. For this complex flowfield the adaption results are disappointing since feature alignment does not emerge from the local operations. Aggressive adaption is shown to result in a loss of robustness for the solver, particularly in the bow shock/stagnation point interaction region. Reducing the adaption strength maintains solution robustness but fails to produce significant improvement in the surface heat transfer predictions.
Goffin, Mark A.; Baker, Christopher M.J.; Buchan, Andrew G.; Pain, Christopher C.; Eaton, Matthew D.; Smith, Paul N.
2013-06-01
This article presents a method for goal-based anisotropic adaptive methods for the finite element method applied to the Boltzmann transport equation. The neutron multiplication factor, k{sub eff}, is used as the goal of the adaptive procedure. The anisotropic adaptive algorithm requires error measures for k{sub eff} with directional dependence. General error estimators are derived for any given functional of the flux and applied to k{sub eff} to acquire the driving force for the adaptive procedure. The error estimators require the solution of an appropriately formed dual equation. Forward and dual error indicators are calculated by weighting the Hessian of each solution with the dual and forward residual respectively. The Hessian is used as an approximation of the interpolation error in the solution which gives rise to the directional dependence. The two indicators are combined to form a single error metric that is used to adapt the finite element mesh. The residual is approximated using a novel technique arising from the sub-grid scale finite element discretisation. Two adaptive routes are demonstrated: (i) a single mesh is used to solve all energy groups, and (ii) a different mesh is used to solve each energy group. The second method aims to capture the benefit from representing the flux from each energy group on a specifically optimised mesh. The k{sub eff} goal-based adaptive method was applied to three examples which illustrate the superior accuracy in criticality problems that can be obtained.
Ying, Wenjun; Henriquez, Craig S.
2015-01-01
A both space and time adaptive algorithm is presented for simulating electrical wave propagation in the Purkinje system of the heart. The equations governing the distribution of electric potential over the system are solved in time with the method of lines. At each timestep, by an operator splitting technique, the space-dependent but linear diffusion part and the nonlinear but space-independent reactions part in the partial differential equations are integrated separately with implicit schemes, which have better stability and allow larger timesteps than explicit ones. The linear diffusion equation on each edge of the system is spatially discretized with the continuous piecewise linear finite element method. The adaptive algorithm can automatically recognize when and where the electrical wave starts to leave or enter the computational domain due to external current/voltage stimulation, self-excitation, or local change of membrane properties. Numerical examples demonstrating efficiency and accuracy of the adaptive algorithm are presented. PMID:26581455
Savkovic, Vuk; Flämig, Franziska; Schneider, Marie; Sülflow, Katharina; Loth, Tina; Lohrenz, Andrea; Hacker, Michael Christian; Schulz-Siegmund, Michaela; Simon, Jan-Christoph
2016-01-01
Melanocytes differentiated from the stem cells of human hair follicle outer root sheath (ORS) have the potential for developing non-invasive treatments for skin disorders out of a minimal sample: of hair root. With a robust procedure for melanocyte cultivation from the ORS of human hair follicle at hand, this study focused on the identification of a suitable biocompatible, biodegradable carrier as the next step toward their clinical implementation. Polycaprolactone (PCL) is a known biocompatible material used for a number of medical devices. In this study, we have populated electrospun PCL fiber meshes with normal human epidermal melanocytes (NHEM) as well as with hair-follicle-derived human melanocytes from the outer root sheath (HUMORS) and tested their functionality in vitro. PCL fiber meshes evidently provided a niche for melanocytes and supported their melanotic properties. The cells were tested for gene expression of PAX3, PMEL, TYR and MITF, as well as for proliferation, expression of melanocyte marker proteins tyrosinase and glycoprotein 100 (gp100), L-DOPA-tautomerase enzymatic activity and melanin content. Reduced mitochondrial activity and PAX-3 gene expression indicated that the three-dimensional PCL scaffold supported differentiation rather than proliferation of melanocytes. The monitored melanotic features of both the NHEM and HUMORS cultivated on PCL scaffolds significantly exceeded those of two-dimensional adherent cultures. PMID:26126647
White Dwarf Mergers on Adaptive Meshes. I. Methodology and Code Verification
NASA Astrophysics Data System (ADS)
Katz, Max P.; Zingale, Michael; Calder, Alan C.; Swesty, F. Douglas; Almgren, Ann S.; Zhang, Weiqun
2016-03-01
The Type Ia supernova (SN Ia) progenitor problem is one of the most perplexing and exciting problems in astrophysics, requiring detailed numerical modeling to complement observations of these explosions. One possible progenitor that has merited recent theoretical attention is the white dwarf (WD) merger scenario, which has the potential to naturally explain many of the observed characteristics of SNe Ia. To date there have been relatively few self-consistent simulations of merging WD systems using mesh-based hydrodynamics. This is the first paper in a series describing simulations of these systems using a hydrodynamics code with adaptive mesh refinement. In this paper we describe our numerical methodology and discuss our implementation in the compressible hydrodynamics code CASTRO, which solves the Euler equations, and the Poisson equation for self-gravity, and couples the gravitational and rotation forces to the hydrodynamics. Standard techniques for coupling gravitation and rotation forces to the hydrodynamics do not adequately conserve the total energy of the system for our problem, but recent advances in the literature allow progress and we discuss our implementation here. We present a set of test problems demonstrating the extent to which our software sufficiently models a system where large amounts of mass are advected on the computational domain over long timescales. Future papers in this series will describe our treatment of the initial conditions of these systems and will examine the early phases of the merger to determine its viability for triggering a thermonuclear detonation.
NASA Technical Reports Server (NTRS)
Ashford, Gregory A.; Powell, Kenneth G.
1995-01-01
A method for generating high quality unstructured triangular grids for high Reynolds number Navier-Stokes calculations about complex geometries is described. Careful attention is paid in the mesh generation process to resolving efficiently the disparate length scales which arise in these flows. First the surface mesh is constructed in a way which ensures that the geometry is faithfully represented. The volume mesh generation then proceeds in two phases thus allowing the viscous and inviscid regions of the flow to be meshed optimally. A solution-adaptive remeshing procedure which allows the mesh to adapt itself to flow features is also described. The procedure for tracking wakes and refinement criteria appropriate for shock detection are described. Although at present it has only been implemented in two dimensions, the grid generation process has been designed with the extension to three dimensions in mind. An implicit, higher-order, upwind method is also presented for computing compressible turbulent flows on these meshes. Two recently developed one-equation turbulence models have been implemented to simulate the effects of the fluid turbulence. Results for flow about a RAE 2822 airfoil and a Douglas three-element airfoil are presented which clearly show the improved resolution obtainable.
NASA Astrophysics Data System (ADS)
Ashford, Gregory A.; Powell, Kenneth G.
1995-10-01
A method for generating high quality unstructured triangular grids for high Reynolds number Navier-Stokes calculations about complex geometries is described. Careful attention is paid in the mesh generation process to resolving efficiently the disparate length scales which arise in these flows. First the surface mesh is constructed in a way which ensures that the geometry is faithfully represented. The volume mesh generation then proceeds in two phases thus allowing the viscous and inviscid regions of the flow to be meshed optimally. A solution-adaptive remeshing procedure which allows the mesh to adapt itself to flow features is also described. The procedure for tracking wakes and refinement criteria appropriate for shock detection are described. Although at present it has only been implemented in two dimensions, the grid generation process has been designed with the extension to three dimensions in mind. An implicit, higher-order, upwind method is also presented for computing compressible turbulent flows on these meshes. Two recently developed one-equation turbulence models have been implemented to simulate the effects of the fluid turbulence. Results for flow about a RAE 2822 airfoil and a Douglas three-element airfoil are presented which clearly show the improved resolution obtainable.
Multifluid adaptive-mesh simulation of the solar wind interaction with the local interstellar medium
Kryukov, I. A.; Borovikov, S. N.; Pogorelov, N. V.; Zank, G. P.
2006-09-26
DOE's SciDAC adaptive mesh refinement code Chombo has been modified for solution of compressible MHD flows with the application of high resolution, shock-capturing numerical schemes. The code developed is further extended to involve multiple fluids and applied to the problem of the solar wind interaction with the local interstellar medium. For this purpose, a set of MHD equations is solved together with a few sets of the Euler gas dynamics equations, depending on the number of neutral fluids included in the model. Our first results are presented that were obtained in the framework of an axially symmetric multifluid model which is applicable to magnetic-field-aligned flows. Details are shown of the generation and development of Rayleigh-Taylor and Kelvin-Helmholtz instabilities of the heliopause. A comparison is given of the results obtained with a two- and four-fluid models.
Goal functional evaluations for phase-field fracture using PU-based DWR mesh adaptivity
NASA Astrophysics Data System (ADS)
Wick, Thomas
2016-03-01
In this study, a posteriori error estimation and goal-oriented mesh adaptivity are developed for phase-field fracture propagation. Goal functionals are computed with the dual-weighted residual (DWR) method, which is realized by a recently introduced novel localization technique based on a partition-of-unity (PU). This technique is straightforward to apply since the weak residual is used. The influence of neighboring cells is gathered by the PU. Consequently, neither strong residuals nor jumps over element edges are required. Therefore, this approach facilitates the application of the DWR method to coupled (nonlinear) multiphysics problems such as fracture propagation. These developments then allow for a systematic investigation of the discretization error for certain quantities of interest. Specifically, our focus on the relationship between the phase-field regularization and the spatial discretization parameter in terms of goal functional evaluations is novel.
Detached Eddy Simulation of the UH-60 Rotor Wake Using Adaptive Mesh Refinement
NASA Technical Reports Server (NTRS)
Chaderjian, Neal M.; Ahmad, Jasim U.
2012-01-01
Time-dependent Navier-Stokes flow simulations have been carried out for a UH-60 rotor with simplified hub in forward flight and hover flight conditions. Flexible rotor blades and flight trim conditions are modeled and established by loosely coupling the OVERFLOW Computational Fluid Dynamics (CFD) code with the CAMRAD II helicopter comprehensive code. High order spatial differences, Adaptive Mesh Refinement (AMR), and Detached Eddy Simulation (DES) are used to obtain highly resolved vortex wakes, where the largest turbulent structures are captured. Special attention is directed towards ensuring the dual time accuracy is within the asymptotic range, and verifying the loose coupling convergence process using AMR. The AMR/DES simulation produced vortical worms for forward flight and hover conditions, similar to previous results obtained for the TRAM rotor in hover. AMR proved to be an efficient means to capture a rotor wake without a priori knowledge of the wake shape.
Galaxy Mergers with Adaptive Mesh Refinement: Star Formation and Hot Gas Outflow
Kim, Ji-hoon; Wise, John H.; Abel, Tom; /KIPAC, Menlo Park /Stanford U., Phys. Dept.
2011-06-22
In hierarchical structure formation, merging of galaxies is frequent and known to dramatically affect their properties. To comprehend these interactions high-resolution simulations are indispensable because of the nonlinear coupling between pc and Mpc scales. To this end, we present the first adaptive mesh refinement (AMR) simulation of two merging, low mass, initially gas-rich galaxies (1.8 x 10{sup 10} M{sub {circle_dot}} each), including star formation and feedback. With galaxies resolved by {approx} 2 x 10{sup 7} total computational elements, we achieve unprecedented resolution of the multiphase interstellar medium, finding a widespread starburst in the merging galaxies via shock-induced star formation. The high dynamic range of AMR also allows us to follow the interplay between the galaxies and their embedding medium depicting how galactic outflows and a hot metal-rich halo form. These results demonstrate that AMR provides a powerful tool in understanding interacting galaxies.
A consistent approach to large eddy simulation using adaptive mesh refinement
Cook, A.W.
1999-09-01
The large eddy simulation of turbulent flows is discussed with particular attention paid to the issue of commutation of differentiation and filtering. Multi-level adaptive mesh refinement is proposed as a means of mostly avoiding commutation errors where increased grid resolution is required to capture key flow features. The strategy is to employ multiple uniform grids in a nested hierarchy using a constant-width filter for each grid. It is shown that commutivity of fine and coarse grid filters must be enforced in order to consistently relate variables at different refinement levels. Methods for treating fine grid boundaries and walls are also discussed. It is shown that errors associated with boundary treatments are small and localized.
NASA Astrophysics Data System (ADS)
Zanotti, O.; Dumbser, M.; Fambri, F.
2016-05-01
We describe a new method for the solution of the ideal MHD equations in special relativity which adopts the following strategy: (i) the main scheme is based on Discontinuous Galerkin (DG) methods, allowing for an arbitrary accuracy of order N+1, where N is the degree of the basis polynomials; (ii) in order to cope with oscillations at discontinuities, an ”a-posteriori” sub-cell limiter is activated, which scatters the DG polynomials of the previous time-step onto a set of 2N+1 sub-cells, over which the solution is recomputed by means of a robust finite volume scheme; (iii) a local spacetime Discontinuous-Galerkin predictor is applied both on the main grid of the DG scheme and on the sub-grid of the finite volume scheme; (iv) adaptive mesh refinement (AMR) with local time-stepping is used. We validate the new scheme and comment on its potential applications in high energy astrophysics.
AstroBEAR: Adaptive Mesh Refinement Code for Ideal Hydrodynamics & Magnetohydrodynamics
NASA Astrophysics Data System (ADS)
Cunningham, Andrew J.; Frank, Adam; Varniere, Peggy; Mitran, Sorin; Jones, Thomas W.
2011-04-01
AstroBEAR is a modular hydrodynamic & magnetohydrodynamic code environment designed for a variety of astrophysical applications. It uses the BEARCLAW package, a multidimensional, Eulerian computational code used to solve hyperbolic systems of equations. AstroBEAR allows adaptive-mesh-refinment (AMR) simulations in 2, 2.5 (i.e., cylindrical), and 3 dimensions, in either cartesian or curvilinear coordinates. Parallel applications are supported through the MPI architecture. AstroBEAR is written in Fortran 90/95 using standard libraries. AstroBEAR supports hydrodynamic (HD) and magnetohydrodynamic (MHD) applications using a variety of spatial and temporal methods. MHD simulations are kept divergence-free via the constrained transport (CT) methods of Balsara & Spicer. Three different equation of state environments are available: ideal gas, gas with differing isentropic γ, and the analytic Thomas-Fermi formulation of A.R. Bell [2]. Current work is being done to develop a more advanced real gas equation of state.
On the Computation of Integral Curves in Adaptive Mesh Refinement Vector Fields
Deines, Eduard; Weber, Gunther H.; Garth, Christoph; Van Straalen, Brian; Borovikov, Sergey; Martin, Daniel F.; Joy, Kenneth I.
2011-06-27
Integral curves, such as streamlines, streaklines, pathlines, and timelines, are an essential tool in the analysis of vector field structures, offering straightforward and intuitive interpretation of visualization results. While such curves have a long-standing tradition in vector field visualization, their application to Adaptive Mesh Refinement (AMR) simulation results poses unique problems. AMR is a highly effective discretization method for a variety of physical simulation problems and has recently been applied to the study of vector fields in flow and magnetohydrodynamic applications. The cell-centered nature of AMR data and discontinuities in the vector field representation arising from AMR level boundaries complicate the application of numerical integration methods to compute integral curves. In this paper, we propose a novel approach to alleviate these problems and show its application to streamline visualization in an AMR model of the magnetic field of the solar system as well as to a simulation of two incompressible viscous vortex rings merging.
Goal functional evaluations for phase-field fracture using PU-based DWR mesh adaptivity
NASA Astrophysics Data System (ADS)
Wick, Thomas
2016-06-01
In this study, a posteriori error estimation and goal-oriented mesh adaptivity are developed for phase-field fracture propagation. Goal functionals are computed with the dual-weighted residual (DWR) method, which is realized by a recently introduced novel localization technique based on a partition-of-unity (PU). This technique is straightforward to apply since the weak residual is used. The influence of neighboring cells is gathered by the PU. Consequently, neither strong residuals nor jumps over element edges are required. Therefore, this approach facilitates the application of the DWR method to coupled (nonlinear) multiphysics problems such as fracture propagation. These developments then allow for a systematic investigation of the discretization error for certain quantities of interest. Specifically, our focus on the relationship between the phase-field regularization and the spatial discretization parameter in terms of goal functional evaluations is novel.
Block structured adaptive mesh and time refinement for hybrid, hyperbolic + N-body systems
NASA Astrophysics Data System (ADS)
Miniati, Francesco; Colella, Phillip
2007-11-01
We present a new numerical algorithm for the solution of coupled collisional and collisionless systems, based on the block structured adaptive mesh and time refinement strategy (AMR). We describe the issues associated with the discretization of the system equations and the synchronization of the numerical solution on the hierarchy of grid levels. We implement a code based on a higher order, conservative and directionally unsplit Godunov’s method for hydrodynamics; a symmetric, time centered modified symplectic scheme for collisionless component; and a multilevel, multigrid relaxation algorithm for the elliptic equation coupling the two components. Numerical results that illustrate the accuracy of the code and the relative merit of various implemented schemes are also presented.
Radiation hydrodynamics including irradiation and adaptive mesh refinement with AZEuS. I. Methods
NASA Astrophysics Data System (ADS)
Ramsey, J. P.; Dullemond, C. P.
2015-02-01
Aims: The importance of radiation to the physical structure of protoplanetary disks cannot be understated. However, protoplanetary disks evolve with time, and so to understand disk evolution and by association, disk structure, one should solve the combined and time-dependent equations of radiation hydrodynamics. Methods: We implement a new implicit radiation solver in the AZEuS adaptive mesh refinement magnetohydrodynamics fluid code. Based on a hybrid approach that combines frequency-dependent ray-tracing for stellar irradiation with non-equilibrium flux limited diffusion, we solve the equations of radiation hydrodynamics while preserving the directionality of the stellar irradiation. The implementation permits simulations in Cartesian, cylindrical, and spherical coordinates, on both uniform and adaptive grids. Results: We present several hydrostatic and hydrodynamic radiation tests which validate our implementation on uniform and adaptive grids as appropriate, including benchmarks specifically designed for protoplanetary disks. Our results demonstrate that the combination of a hybrid radiation algorithm with AZEuS is an effective tool for radiation hydrodynamics studies, and produces results which are competitive with other astrophysical radiation hydrodynamics codes.
The PLUTO Code for Adaptive Mesh Computations in Astrophysical Fluid Dynamics
NASA Astrophysics Data System (ADS)
Mignone, A.; Zanni, C.; Tzeferacos, P.; van Straalen, B.; Colella, P.; Bodo, G.
2012-01-01
We present a description of the adaptive mesh refinement (AMR) implementation of the PLUTO code for solving the equations of classical and special relativistic magnetohydrodynamics (MHD and RMHD). The current release exploits, in addition to the static grid version of the code, the distributed infrastructure of the CHOMBO library for multidimensional parallel computations over block-structured, adaptively refined grids. We employ a conservative finite-volume approach where primary flow quantities are discretized at the cell center in a dimensionally unsplit fashion using the Corner Transport Upwind method. Time stepping relies on a characteristic tracing step where piecewise parabolic method, weighted essentially non-oscillatory, or slope-limited linear interpolation schemes can be handily adopted. A characteristic decomposition-free version of the scheme is also illustrated. The solenoidal condition of the magnetic field is enforced by augmenting the equations with a generalized Lagrange multiplier providing propagation and damping of divergence errors through a mixed hyperbolic/parabolic explicit cleaning step. Among the novel features, we describe an extension of the scheme to include non-ideal dissipative processes, such as viscosity, resistivity, and anisotropic thermal conduction without operator splitting. Finally, we illustrate an efficient treatment of point-local, potentially stiff source terms over hierarchical nested grids by taking advantage of the adaptivity in time. Several multidimensional benchmarks and applications to problems of astrophysical relevance assess the potentiality of the AMR version of PLUTO in resolving flow features separated by large spatial and temporal disparities.
THE PLUTO CODE FOR ADAPTIVE MESH COMPUTATIONS IN ASTROPHYSICAL FLUID DYNAMICS
Mignone, A.; Tzeferacos, P.; Zanni, C.; Bodo, G.; Van Straalen, B.; Colella, P.
2012-01-01
We present a description of the adaptive mesh refinement (AMR) implementation of the PLUTO code for solving the equations of classical and special relativistic magnetohydrodynamics (MHD and RMHD). The current release exploits, in addition to the static grid version of the code, the distributed infrastructure of the CHOMBO library for multidimensional parallel computations over block-structured, adaptively refined grids. We employ a conservative finite-volume approach where primary flow quantities are discretized at the cell center in a dimensionally unsplit fashion using the Corner Transport Upwind method. Time stepping relies on a characteristic tracing step where piecewise parabolic method, weighted essentially non-oscillatory, or slope-limited linear interpolation schemes can be handily adopted. A characteristic decomposition-free version of the scheme is also illustrated. The solenoidal condition of the magnetic field is enforced by augmenting the equations with a generalized Lagrange multiplier providing propagation and damping of divergence errors through a mixed hyperbolic/parabolic explicit cleaning step. Among the novel features, we describe an extension of the scheme to include non-ideal dissipative processes, such as viscosity, resistivity, and anisotropic thermal conduction without operator splitting. Finally, we illustrate an efficient treatment of point-local, potentially stiff source terms over hierarchical nested grids by taking advantage of the adaptivity in time. Several multidimensional benchmarks and applications to problems of astrophysical relevance assess the potentiality of the AMR version of PLUTO in resolving flow features separated by large spatial and temporal disparities.
Adaptive mesh refinement with spectral accuracy for magnetohydrodynamics in two space dimensions
NASA Astrophysics Data System (ADS)
Rosenberg, D.; Pouquet, A.; Mininni, P. D.
2007-08-01
We examine the effect of accuracy of high-order spectral element methods, with or without adaptive mesh refinement (AMR), in the context of a classical configuration of magnetic reconnection in two space dimensions, the so-called Orszag-Tang (OT) vortex made up of a magnetic X-point centred on a stagnation point of the velocity. A recently developed spectral-element adaptive refinement incompressible magnetohydrodynamic (MHD) code is applied to simulate this problem. The MHD solver is explicit, and uses the Elsässer formulation on high-order elements. It automatically takes advantage of the adaptive grid mechanics that have been described elsewhere in the fluid context (Rosenberg et al 2006 J. Comput. Phys. 215 59-80) the code allows both statically refined and dynamically refined grids. Tests of the algorithm using analytic solutions are described, and comparisons of the OT solutions with pseudo-spectral computations are performed. We demonstrate for moderate Reynolds numbers that the algorithms using both static and refined grids reproduce the pseudo-spectral solutions quite well. We show that low-order truncation—even with a comparable number of global degrees of freedom—fails to correctly model some strong (sup-norm) quantities in this problem, even though it satisfies adequately the weak (integrated) balance diagnostics.
A Parallel Ocean Model With Adaptive Mesh Refinement Capability For Global Ocean Prediction
Herrnstein, A
2005-09-08
An ocean model with adaptive mesh refinement (AMR) capability is presented for simulating ocean circulation on decade time scales. The model closely resembles the LLNL ocean general circulation model with some components incorporated from other well known ocean models when appropriate. Spatial components are discretized using finite differences on a staggered grid where tracer and pressure variables are defined at cell centers and velocities at cell vertices (B-grid). Horizontal motion is modeled explicitly with leapfrog and Euler forward-backward time integration, and vertical motion is modeled semi-implicitly. New AMR strategies are presented for horizontal refinement on a B-grid, leapfrog time integration, and time integration of coupled systems with unequal time steps. These AMR capabilities are added to the LLNL software package SAMRAI (Structured Adaptive Mesh Refinement Application Infrastructure) and validated with standard benchmark tests. The ocean model is built on top of the amended SAMRAI library. The resulting model has the capability to dynamically increase resolution in localized areas of the domain. Limited basin tests are conducted using various refinement criteria and produce convergence trends in the model solution as refinement is increased. Carbon sequestration simulations are performed on decade time scales in domains the size of the North Atlantic and the global ocean. A suggestion is given for refinement criteria in such simulations. AMR predicts maximum pH changes and increases in CO{sub 2} concentration near the injection sites that are virtually unattainable with a uniform high resolution due to extremely long run times. Fine scale details near the injection sites are achieved by AMR with shorter run times than the finest uniform resolution tested despite the need for enhanced parallel performance. The North Atlantic simulations show a reduction in passive tracer errors when AMR is applied instead of a uniform coarse resolution. No
NASA Astrophysics Data System (ADS)
Farooq, Umar; Myler, Peter
2014-09-01
This work is concerned with physical testing and numerical simulations of flat and round nose drop-weight impact of carbon fibre-reinforced laminate composite panels to predict ply level failure. Majority of the existing studies on impact of composites by spherical nose impactors are experimental, computational models are simplified, and based on classical laminated plate theories where contributions of through-thickness stresses are neglected. Present work considers flat nose impact and contributions from through-thickness stresses and is mainly simulation based. A computational model was developed in ABAQUS™ software using adaptive meshing techniques. Simulation produced (2D model) stresses were numerically integrated using MATALB™ code to predict through-thickness (3D) stresses. Through-the-thickness stresses were then utilised in advanced failure criteria coded in MATLAB™ software to predict ply level failures. Simulation produced results demonstrate that the computational model can efficiently and effectively predict ply-by-ply failure status of relatively thick laminates.
NASA Astrophysics Data System (ADS)
Northrup, Scott A.
A new parallel implicit adaptive mesh refinement (AMR) algorithm is developed for the prediction of unsteady behaviour of laminar flames. The scheme is applied to the solution of the system of partial-differential equations governing time-dependent, two- and three-dimensional, compressible laminar flows for reactive thermally perfect gaseous mixtures. A high-resolution finite-volume spatial discretization procedure is used to solve the conservation form of these equations on body-fitted multi-block hexahedral meshes. A local preconditioning technique is used to remove numerical stiffness and maintain solution accuracy for low-Mach-number, nearly incompressible flows. A flexible block-based octree data structure has been developed and is used to facilitate automatic solution-directed mesh adaptation according to physics-based refinement criteria. The data structure also enables an efficient and scalable parallel implementation via domain decomposition. The parallel implicit formulation makes use of a dual-time-stepping like approach with an implicit second-order backward discretization of the physical time, in which a Jacobian-free inexact Newton method with a preconditioned generalized minimal residual (GMRES) algorithm is used to solve the system of nonlinear algebraic equations arising from the temporal and spatial discretization procedures. An additive Schwarz global preconditioner is used in conjunction with block incomplete LU type local preconditioners for each sub-domain. The Schwarz preconditioning and block-based data structure readily allow efficient and scalable parallel implementations of the implicit AMR approach on distributed-memory multi-processor architectures. The scheme was applied to solutions of steady and unsteady laminar diffusion and premixed methane-air combustion and was found to accurately predict key flame characteristics. For a premixed flame under terrestrial gravity, the scheme accurately predicted the frequency of the natural
Feasibility of electrical impedance tomography in haemorrhagic stroke treatment using adaptive mesh
NASA Astrophysics Data System (ADS)
Nasehi Tehrani, J.; Anderson, C.; Jin, C.; van Schaik, A.; Holder, D.; McEwan, A.
2010-04-01
EIT has been proposed for acute stroke differentiation, specifically to determine the type of stroke, either ischaemia (clot) or haemorrhage (bleed) to allow the rapid use of clot-busting drugs in the former (Romsauerova et al 2006) . This addresses an important medical need, although there is little treatment offered in the case of haemorrhage. Also the demands on EIT are high with usually no availability to take a 'before' measurement, ruling out time difference imaging. Recently a new treatment option for haemorrhage has been proposed and is being studied in international randomised controlled trial: the early reduction of elevated blood pressure to attenuate the haematoma. This has been shown via CT to reduce bleeds by up to 1mL by Anderson et al 2008. The use of EIT as a continuous measure is desirable here to monitor the effect of blood pressure reduction. A 1mL increase of haemorrhagic lesion located near scalp on the right side of head caused a boundary voltage change of less than 0.05% at 50 kHz. This could be visually observed in a time difference 3D reconstruction with no change in electrode positions, mesh, background conductivity or drift when baseline noise was less than 0.005% but not when noise was increased to 0.01%. This useful result informs us that the EIT system must have noise of less than 0.005% at 50 kHz including instrumentation, physiological and other biases.
NASA Astrophysics Data System (ADS)
Kocaoglu, Omer P.; Lee, Sangyeol; Jonnal, Ravi S.; Wang, Qiang; Herde, Ashley E.; Besecker, Jason; Gao, Weihua; Miller, Donald T.
2011-03-01
Optical coherence tomography with adaptive optics (AO-OCT) is a highly sensitive, noninvasive method for 3D imaging of the microscopic retina. The purpose of this study is to advance AO-OCT technology by enabling repeated imaging of cone photoreceptors over extended periods of time (days). This sort of longitudinal imaging permits monitoring of 3D cone dynamics in both normal and diseased eyes, in particular the physiological processes of disc renewal and phagocytosis, which are disrupted by retinal diseases such as age related macular degeneration and retinitis pigmentosa. For this study, the existing AO-OCT system at Indiana underwent several major hardware and software improvements to optimize system performance for 4D cone imaging. First, ultrahigh speed imaging was realized using a Basler Sprint camera. Second, a light source with adjustable spectrum was realized by integration of an Integral laser (Femto Lasers, λc=800nm, ▵λ=160nm) and spectral filters in the source arm. For cone imaging, we used a bandpass filter with λc=809nm and ▵λ=81nm (2.6 μm nominal axial resolution in tissue, and 167 KHz A-line rate using 1,408 px), which reduced the impact of eye motion compared to previous AO-OCT implementations. Third, eye motion artifacts were further reduced by custom ImageJ plugins that registered (axially and laterally) the volume videos. In two subjects, cone photoreceptors were imaged and tracked over a ten day period and their reflectance and outer segment (OS) lengths measured. High-speed imaging and image registration/dewarping were found to reduce eye motion to a fraction of a cone width (1 μm root mean square). The pattern of reflections in the cones was found to change dramatically and occurred on a spatial scale well below the resolution of clinical instruments. Normalized reflectance of connecting cilia (CC) and OS posterior tip (PT) of an exemplary cone was 54+/-4, 47+/-4, 48+/-6, 50+/-5, 56+/-1% and 46+/-4, 53+/-4, 52+/-6, 50+/-5, 44
Shen, Hesong; Dai, Guochao; Luo, Mingyue; Duan, Chaijie; Cai, Wenli; Liang, Dan; Wang, Xinhua; Zhu, Dongyun; Li, Wenru; Qiu, Jianping
2015-01-01
Purpose To investigate image quality and radiation dose of CT coronary angiography (CTCA) scanned using automatic tube current modulation (ATCM) and reconstructed by strong adaptive iterative dose reduction three-dimensional (AIDR3D). Methods Eighty-four consecutive CTCA patients were collected for the study. All patients were scanned using ATCM and reconstructed with strong AIDR3D, standard AIDR3D and filtered back-projection (FBP) respectively. Two radiologists who were blinded to the patients' clinical data and reconstruction methods evaluated image quality. Quantitative image quality evaluation included image noise, signal-to-noise ratio (SNR), and contrast-to-noise ratio (CNR). To evaluate image quality qualitatively, coronary artery is classified into 15 segments based on the modified guidelines of the American Heart Association. Qualitative image quality was evaluated using a 4-point scale. Radiation dose was calculated based on dose-length product. Results Compared with standard AIDR3D, strong AIDR3D had lower image noise, higher SNR and CNR, their differences were all statistically significant (P<0.05); compared with FBP, strong AIDR3D decreased image noise by 46.1%, increased SNR by 84.7%, and improved CNR by 82.2%, their differences were all statistically significant (P<0.05 or 0.001). Segments with diagnostic image quality for strong AIDR3D were 336 (100.0%), 486 (96.4%), and 394 (93.8%) in proximal, middle, and distal part respectively; whereas those for standard AIDR3D were 332 (98.8%), 472 (93.7%), 378 (90.0%), respectively; those for FBP were 217 (64.6%), 173 (34.3%), 114 (27.1%), respectively; total segments with diagnostic image quality in strong AIDR3D (1216, 96.5%) were higher than those of standard AIDR3D (1182, 93.8%) and FBP (504, 40.0%); the differences between strong AIDR3D and standard AIDR3D, strong AIDR3D and FBP were all statistically significant (P<0.05 or 0.001). The mean effective radiation dose was (2.55±1.21) mSv. Conclusion
CRASH: A BLOCK-ADAPTIVE-MESH CODE FOR RADIATIVE SHOCK HYDRODYNAMICS-IMPLEMENTATION AND VERIFICATION
Van der Holst, B.; Toth, G.; Sokolov, I. V.; Myra, E. S.; Fryxell, B.; Drake, R. P.; Powell, K. G.; Holloway, J. P.; Stout, Q.; Adams, M. L.; Morel, J. E.; Karni, S.
2011-06-01
We describe the Center for Radiative Shock Hydrodynamics (CRASH) code, a block-adaptive-mesh code for multi-material radiation hydrodynamics. The implementation solves the radiation diffusion model with a gray or multi-group method and uses a flux-limited diffusion approximation to recover the free-streaming limit. Electrons and ions are allowed to have different temperatures and we include flux-limited electron heat conduction. The radiation hydrodynamic equations are solved in the Eulerian frame by means of a conservative finite-volume discretization in either one-, two-, or three-dimensional slab geometry or in two-dimensional cylindrical symmetry. An operator-split method is used to solve these equations in three substeps: (1) an explicit step of a shock-capturing hydrodynamic solver; (2) a linear advection of the radiation in frequency-logarithm space; and (3) an implicit solution of the stiff radiation diffusion, heat conduction, and energy exchange. We present a suite of verification test problems to demonstrate the accuracy and performance of the algorithms. The applications are for astrophysics and laboratory astrophysics. The CRASH code is an extension of the Block-Adaptive Tree Solarwind Roe Upwind Scheme (BATS-R-US) code with a new radiation transfer and heat conduction library and equation-of-state and multi-group opacity solvers. Both CRASH and BATS-R-US are part of the publicly available Space Weather Modeling Framework.
CRASH: A Block-adaptive-mesh Code for Radiative Shock Hydrodynamics—Implementation and Verification
NASA Astrophysics Data System (ADS)
van der Holst, B.; Tóth, G.; Sokolov, I. V.; Powell, K. G.; Holloway, J. P.; Myra, E. S.; Stout, Q.; Adams, M. L.; Morel, J. E.; Karni, S.; Fryxell, B.; Drake, R. P.
2011-06-01
We describe the Center for Radiative Shock Hydrodynamics (CRASH) code, a block-adaptive-mesh code for multi-material radiation hydrodynamics. The implementation solves the radiation diffusion model with a gray or multi-group method and uses a flux-limited diffusion approximation to recover the free-streaming limit. Electrons and ions are allowed to have different temperatures and we include flux-limited electron heat conduction. The radiation hydrodynamic equations are solved in the Eulerian frame by means of a conservative finite-volume discretization in either one-, two-, or three-dimensional slab geometry or in two-dimensional cylindrical symmetry. An operator-split method is used to solve these equations in three substeps: (1) an explicit step of a shock-capturing hydrodynamic solver; (2) a linear advection of the radiation in frequency-logarithm space; and (3) an implicit solution of the stiff radiation diffusion, heat conduction, and energy exchange. We present a suite of verification test problems to demonstrate the accuracy and performance of the algorithms. The applications are for astrophysics and laboratory astrophysics. The CRASH code is an extension of the Block-Adaptive Tree Solarwind Roe Upwind Scheme (BATS-R-US) code with a new radiation transfer and heat conduction library and equation-of-state and multi-group opacity solvers. Both CRASH and BATS-R-US are part of the publicly available Space Weather Modeling Framework.
CRASH: A Block-Adaptive-Mesh Code for Radiative Shock Hydrodynamics
NASA Astrophysics Data System (ADS)
van der Holst, B.; Toth, G.; Sokolov, I. V.; Powell, K. G.; Holloway, J. P.; Myra, E. S.; Stout, Q.; Adams, M. L.; Morel, J. E.; Drake, R. P.
2011-01-01
We describe the CRASH (Center for Radiative Shock Hydrodynamics) code, a block adaptive mesh code for multi-material radiation hydrodynamics. The implementation solves the radiation diffusion model with the gray or multigroup method and uses a flux limited diffusion approximation to recover the free-streaming limit. The electrons and ions are allowed to have different temperatures and we include a flux limited electron heat conduction. The radiation hydrodynamic equations are solved in the Eulerian frame by means of a conservative finite volume discretization in either one, two, or three-dimensional slab geometry or in two-dimensional cylindrical symmetry. An operator split method is used to solve these equations in three substeps: (1) solve the hydrodynamic equations with shock-capturing schemes, (2) a linear advection of the radiation in frequency-logarithm space, and (3) an implicit solve of the stiff radiation diffusion, heat conduction, and energy exchange. We present a suite of verification test problems to demonstrate the accuracy and performance of the algorithms. The CRASH code is an extension of the Block-Adaptive Tree Solarwind Roe Upwind Scheme (BATS-R-US) code with this new radiation transfer and heat conduction library and equation-of-state and multigroup opacity solvers. Both CRASH and BATS-R-US are part of the publicly available Space Weather Modeling Framework (SWMF).
Performance Characteristics of an Adaptive Mesh RefinementCalculation on Scalar and Vector Platforms
Welcome, Michael; Rendleman, Charles; Oliker, Leonid; Biswas, Rupak
2006-01-31
Adaptive mesh refinement (AMR) is a powerful technique thatreduces the resources necessary to solve otherwise in-tractable problemsin computational science. The AMR strategy solves the problem on arelatively coarse grid, and dynamically refines it in regions requiringhigher resolution. However, AMR codes tend to be far more complicatedthan their uniform grid counterparts due to the software infrastructurenecessary to dynamically manage the hierarchical grid framework. Despitethis complexity, it is generally believed that future multi-scaleapplications will increasingly rely on adaptive methods to study problemsat unprecedented scale and resolution. Recently, a new generation ofparallel-vector architectures have become available that promise toachieve extremely high sustained performance for a wide range ofapplications, and are the foundation of many leadership-class computingsystems worldwide. It is therefore imperative to understand the tradeoffsbetween conventional scalar and parallel-vector platforms for solvingAMR-based calculations. In this paper, we examine the HyperCLaw AMRframework to compare and contrast performance on the Cray X1E, IBM Power3and Power5, and SGI Altix. To the best of our knowledge, this is thefirst work that investigates and characterizes the performance of an AMRcalculation on modern parallel-vector systems.
NASA Astrophysics Data System (ADS)
Hatori, Tomoharu; Ito, Atsushi M.; Nunami, Masanori; Usui, Hideyuki; Miura, Hideaki
2016-08-01
We propose a numerical method to determine the artificial viscosity in magnetohydrodynamics (MHD) simulations with adaptive mesh refinement (AMR) method, where the artificial viscosity is adaptively changed due to the resolution level of the AMR hierarchy. Although the suitable value of the artificial viscosity depends on the governing equations and the model of target problem, it can be determined by von Neumann stability analysis. By means of the new method, "level-by-level artificial viscosity method," MHD simulations of Rayleigh-Taylor instability (RTI) are carried out with the AMR method. The validity of the level-by-level artificial viscosity method is confirmed by the comparison of the linear growth rates of RTI between the AMR simulations and the simple simulations with uniform grid and uniform artificial viscosity whose resolution is the same as that in the highest level of the AMR simulation. Moreover, in the nonlinear phase of RTI, the secondary instability is clearly observed where the hierarchical data structure of AMR calculation is visualized as high resolution region floats up like terraced fields. In the applications of the method to general fluid simulations, the growth of small structures can be sufficiently reproduced, while the divergence of numerical solutions can be suppressed.
Feger, Sarah; Rief, Matthias; Zimmermann, Elke; Martus, Peter; Schuijf, Joanne Désirée; Blobel, Jörg; Richter, Felicitas; Dewey, Marc
2015-01-01
Purpose The aim of this study was the systematic image quality evaluation of coronary CT angiography (CTA), reconstructed with the 3 different levels of adaptive iterative dose reduction (AIDR 3D) and compared to filtered back projection (FBP) with quantum denoising software (QDS). Methods Standard-dose CTA raw data of 30 patients with mean radiation dose of 3.2 ± 2.6 mSv were reconstructed using AIDR 3D mild, standard, strong and compared to FBP/QDS. Objective image quality comparison (signal, noise, signal-to-noise ratio (SNR), contrast-to-noise ratio (CNR), contour sharpness) was performed using 21 measurement points per patient, including measurements in each coronary artery from proximal to distal. Results Objective image quality parameters improved with increasing levels of AIDR 3D. Noise was lowest in AIDR 3D strong (p≤0.001 at 20/21 measurement points; compared with FBP/QDS). Signal and contour sharpness analysis showed no significant difference between the reconstruction algorithms for most measurement points. Best coronary SNR and CNR were achieved with AIDR 3D strong. No loss of SNR or CNR in distal segments was seen with AIDR 3D as compared to FBP. Conclusions On standard-dose coronary CTA images, AIDR 3D strong showed higher objective image quality than FBP/QDS without reducing contour sharpness. Trial Registration Clinicaltrials.gov NCT00967876 PMID:25945924
NASA Technical Reports Server (NTRS)
Steger, J. L.; Dougherty, F. C.; Benek, J. A.
1983-01-01
A mesh system composed of multiple overset body-conforming grids is described for adapting finite-difference procedures to complex aircraft configurations. In this so-called 'chimera mesh,' a major grid is generated about a main component of the configuration and overset minor grids are used to resolve all other features. Methods for connecting overset multiple grids and modifications of flow-simulation algorithms are discussed. Computational tests in two dimensions indicate that the use of multiple overset grids can simplify the task of grid generation without an adverse effect on flow-field algorithms and computer code complexity.
NASA Astrophysics Data System (ADS)
Rastigejev, Y.; Semakin, A. N.
2012-12-01
In this work we present a multilevel Wavelet-based Adaptive Mesh Refinement (WAMR) method for numerical modeling of global atmospheric chemical transport problems. An accurate numerical simulation of such problems presents an enormous challenge. Atmospheric Chemical Transport Models (CTMs) combine chemical reactions with meteorologically predicted atmospheric advection and turbulent mixing. The resulting system of multi-scale advection-reaction-diffusion equations is extremely stiff, nonlinear and involves a large number of chemically interacting species. As a consequence, the need for enormous computational resources for solving these equations imposes severe limitations on the spatial resolution of the CTMs implemented on uniform or quasi-uniform grids. In turn, this relatively crude spatial resolution results in significant numerical diffusion introduced into the system. This numerical diffusion is shown to noticeably distort the pollutant mixing and transport dynamics for typically used grid resolutions. The developed WAMR method for numerical modeling of atmospheric chemical evolution equations presented in this work provides a significant reduction in the computational cost, without upsetting numerical accuracy, therefore it addresses the numerical difficulties described above. WAMR method introduces a fine grid in the regions where sharp transitions occur and cruder grid in the regions of smooth solution behavior. Therefore WAMR results in much more accurate solutions than conventional numerical methods implemented on uniform or quasi-uniform grids. The algorithm allows one to provide error estimates of the solution that are used in conjunction with appropriate threshold criteria to adapt the non-uniform grid. The method has been tested for a variety of problems including numerical simulation of traveling pollution plumes. It was shown that pollution plumes in the remote troposphere can propagate as well-defined layered structures for two weeks or more as
NASA Astrophysics Data System (ADS)
Rastigejev, Y.; Semakin, A. N.
2013-12-01
Accurate numerical simulations of global scale three-dimensional atmospheric chemical transport models (CTMs) are essential for studies of many important atmospheric chemistry problems such as adverse effect of air pollutants on human health, ecosystems and the Earth's climate. These simulations usually require large CPU time due to numerical difficulties associated with a wide range of spatial and temporal scales, nonlinearity and large number of reacting species. In our previous work we have shown that in order to achieve adequate convergence rate and accuracy, the mesh spacing in numerical simulation of global synoptic-scale pollution plume transport must be decreased to a few kilometers. This resolution is difficult to achieve for global CTMs on uniform or quasi-uniform grids. To address the described above difficulty we developed a three-dimensional Wavelet-based Adaptive Mesh Refinement (WAMR) algorithm. The method employs a highly non-uniform adaptive grid with fine resolution over the areas of interest without requiring small grid-spacing throughout the entire domain. The method uses multi-grid iterative solver that naturally takes advantage of a multilevel structure of the adaptive grid. In order to represent the multilevel adaptive grid efficiently, a dynamic data structure based on indirect memory addressing has been developed. The data structure allows rapid access to individual points, fast inter-grid operations and re-gridding. The WAMR method has been implemented on parallel computer architectures. The parallel algorithm is based on run-time partitioning and load-balancing scheme for the adaptive grid. The partitioning scheme maintains locality to reduce communications between computing nodes. The parallel scheme was found to be cost-effective. Specifically we obtained an order of magnitude increase in computational speed for numerical simulations performed on a twelve-core single processor workstation. We have applied the WAMR method for numerical
AMR++: A design for parallel object-oriented adaptive mesh refinement
Quinlan, D.
1997-11-01
Adaptive mesh refinement computations are complicated by their dynamic nature. In the serial environment they require substantial infrastructures to support the regridding processes, intergrid operations, and local bookkeeping of positions of grids relative to one another. In the parallel environment the dynamic behavior is more problematic because it requires dynamic distribution support and load balancing. Parallel AMR is further complicated by the substantial task parallelism, in addition to the obvious data parallelism, this task parallelism requires additional infrastructure to support efficiently. The degree of parallelism is typically dependent upon the algorithms in use and the equations being solved. Different algorithms have significant compromises between computation and communication. Substantial research work is often required to define efficient methods and suitable infrastructure. The purpose of this paper is to introduce AMR++ as an object-oriented library which forms a part of the OVERTURE framework, a much larger object-oriented numerical framework developed and supported at Los Alamos National Laboratory and distributed on the Web for the last several years.
Advances in Rotor Performance and Turbulent Wake Simulation Using DES and Adaptive Mesh Refinement
NASA Technical Reports Server (NTRS)
Chaderjian, Neal M.
2012-01-01
Time-dependent Navier-Stokes simulations have been carried out for a rigid V22 rotor in hover, and a flexible UH-60A rotor in forward flight. Emphasis is placed on understanding and characterizing the effects of high-order spatial differencing, grid resolution, and Spalart-Allmaras (SA) detached eddy simulation (DES) in predicting the rotor figure of merit (FM) and resolving the turbulent rotor wake. The FM was accurately predicted within experimental error using SA-DES. Moreover, a new adaptive mesh refinement (AMR) procedure revealed a complex and more realistic turbulent rotor wake, including the formation of turbulent structures resembling vortical worms. Time-dependent flow visualization played a crucial role in understanding the physical mechanisms involved in these complex viscous flows. The predicted vortex core growth with wake age was in good agreement with experiment. High-resolution wakes for the UH-60A in forward flight exhibited complex turbulent interactions and turbulent worms, similar to the V22. The normal force and pitching moment coefficients were in good agreement with flight-test data.
Operator splitting and adaptive mesh refinement for the Luo-Rudy I model
NASA Astrophysics Data System (ADS)
Trangenstein, John A.; Kim, Chisup
2004-05-01
We apply second-order operator splitting to the Luo-Rudy I model for electrical wave propagation in the heart. The purpose of the operator splitting is to separate the nonlinear but local reaction computations from the linear but globally coupled diffusion computations. This approach allows us to use local nonlinear iterations for the stiff nonlinear reactions and to solve global linear systems for the implicit treatment of diffusion. For computational efficiency, we use dynamically adaptive mesh refinement (AMR), involving hierarchies of unions of grid patches on distinct levels of refinement. The linear system for the discretization of the diffusion on the composite AMR grid is formulated via standard conforming finite elements on unions grid patches within a level of refinement and aligned mortar elements along interfaces between levels of refinement. The linear systems are solved iteratively by preconditioned conjugate gradients. Our preconditioner uses multiplicative domain decomposition between levels of refinement; the smoother involves algebraic additive domain decomposition between patches within a level of refinement, and Gauss-Seidel iteration within grid patches. Numerical results are presented in 1D and 2D, including spiral waves.
Relativistic Flows Using Spatial And Temporal Adaptive Structured Mesh Refinement. I. Hydrodynamics
Wang, Peng; Abel, Tom; Zhang, Weiqun; /KIPAC, Menlo Park
2007-04-02
Astrophysical relativistic flow problems require high resolution three-dimensional numerical simulations. In this paper, we describe a new parallel three-dimensional code for simulations of special relativistic hydrodynamics (SRHD) using both spatially and temporally structured adaptive mesh refinement (AMR). We used method of lines to discrete SRHD equations spatially and used a total variation diminishing (TVD) Runge-Kutta scheme for time integration. For spatial reconstruction, we have implemented piecewise linear method (PLM), piecewise parabolic method (PPM), third order convex essentially non-oscillatory (CENO) and third and fifth order weighted essentially non-oscillatory (WENO) schemes. Flux is computed using either direct flux reconstruction or approximate Riemann solvers including HLL, modified Marquina flux, local Lax-Friedrichs flux formulas and HLLC. The AMR part of the code is built on top of the cosmological Eulerian AMR code enzo, which uses the Berger-Colella AMR algorithm and is parallel with dynamical load balancing using the widely available Message Passing Interface library. We discuss the coupling of the AMR framework with the relativistic solvers and show its performance on eleven test problems.
EMMA: an adaptive mesh refinement cosmological simulation code with radiative transfer
NASA Astrophysics Data System (ADS)
Aubert, Dominique; Deparis, Nicolas; Ocvirk, Pierre
2015-11-01
EMMA is a cosmological simulation code aimed at investigating the reionization epoch. It handles simultaneously collisionless and gas dynamics, as well as radiative transfer physics using a moment-based description with the M1 approximation. Field quantities are stored and computed on an adaptive three-dimensional mesh and the spatial resolution can be dynamically modified based on physically motivated criteria. Physical processes can be coupled at all spatial and temporal scales. We also introduce a new and optional approximation to handle radiation: the light is transported at the resolution of the non-refined grid and only once the dynamics has been fully updated, whereas thermo-chemical processes are still tracked on the refined elements. Such an approximation reduces the overheads induced by the treatment of radiation physics. A suite of standard tests are presented and passed by EMMA, providing a validation for its future use in studies of the reionization epoch. The code is parallel and is able to use graphics processing units (GPUs) to accelerate hydrodynamics and radiative transfer calculations. Depending on the optimizations and the compilers used to generate the CPU reference, global GPU acceleration factors between ×3.9 and ×16.9 can be obtained. Vectorization and transfer operations currently prevent better GPU performance and we expect that future optimizations and hardware evolution will lead to greater accelerations.
NASA Astrophysics Data System (ADS)
Teyssier, Romain; Fromang, Sébastien; Dormy, Emmanuel
2006-10-01
We propose to extend the well-known MUSCL-Hancock scheme for Euler equations to the induction equation modeling the magnetic field evolution in kinematic dynamo problems. The scheme is based on an integral form of the underlying conservation law which, in our formulation, results in a “finite-surface” scheme for the induction equation. This naturally leads to the well-known “constrained transport” method, with additional continuity requirement on the magnetic field representation. The second ingredient in the MUSCL scheme is the predictor step that ensures second order accuracy both in space and time. We explore specific constraints that the mathematical properties of the induction equations place on this predictor step, showing that three possible variants can be considered. We show that the most aggressive formulations (referred to as C-MUSCL and U-MUSCL) reach the same level of accuracy as the other one (referred to as Runge Kutta), at a lower computational cost. More interestingly, these two schemes are compatible with the adaptive mesh refinement (AMR) framework. It has been implemented in the AMR code RAMSES. It offers a novel and efficient implementation of a second order scheme for the induction equation. We have tested it by solving two kinematic dynamo problems in the low diffusion limit. The construction of this scheme for the induction equation constitutes a step towards solving the full MHD set of equations using an extension of our current methodology.
NASA Astrophysics Data System (ADS)
Wang, Cheng; Dong, XinZhuang; Shu, Chi-Wang
2015-10-01
For numerical simulation of detonation, computational cost using uniform meshes is large due to the vast separation in both time and space scales. Adaptive mesh refinement (AMR) is advantageous for problems with vastly different scales. This paper aims to propose an AMR method with high order accuracy for numerical investigation of multi-dimensional detonation. A well-designed AMR method based on finite difference weighted essentially non-oscillatory (WENO) scheme, named as AMR&WENO is proposed. A new cell-based data structure is used to organize the adaptive meshes. The new data structure makes it possible for cells to communicate with each other quickly and easily. In order to develop an AMR method with high order accuracy, high order prolongations in both space and time are utilized in the data prolongation procedure. Based on the message passing interface (MPI) platform, we have developed a workload balancing parallel AMR&WENO code using the Hilbert space-filling curve algorithm. Our numerical experiments with detonation simulations indicate that the AMR&WENO is accurate and has a high resolution. Moreover, we evaluate and compare the performance of the uniform mesh WENO scheme and the parallel AMR&WENO method. The comparison results provide us further insight into the high performance of the parallel AMR&WENO method.
Finite-element 3D simulation tools for high-current relativistic electron beams
NASA Astrophysics Data System (ADS)
Humphries, Stanley; Ekdahl, Carl
2002-08-01
The DARHT second-axis injector is a challenge for computer simulations. Electrons are subject to strong beam-generated forces. The fields are fully three-dimensional and accurate calculations at surfaces are critical. We describe methods applied in OmniTrak, a 3D finite-element code suite that can address DARHT and the full range of charged-particle devices. The system handles mesh generation, electrostatics, magnetostatics and self-consistent particle orbits. The MetaMesh program generates meshes of conformal hexahedrons to fit any user geometry. The code has the unique ability to create structured conformal meshes with cubic logic. Organized meshes offer advantages in speed and memory utilization in the orbit and field solutions. OmniTrak is a versatile charged-particle code that handles 3D electric and magnetic field solutions on independent meshes. The program can update both 3D field solutions from the calculated beam space-charge and current-density. We shall describe numerical methods for orbit tracking on a hexahedron mesh. Topics include: 1) identification of elements along the particle trajectory, 2) fast searches and adaptive field calculations, 3) interpolation methods to terminate orbits on material surfaces, 4) automatic particle generation on multiple emission surfaces to model space-charge-limited emission and field emission, 5) flexible Child law algorithms, 6) implementation of the dual potential model for 3D magnetostatics, and 7) assignment of charge and current from model particle orbits for self-consistent fields.
NASA Technical Reports Server (NTRS)
Kleb, William L.; Williams, Marc H.; Batina, John T.
1990-01-01
A temporal adaptive algorithm for the time-integration of the two-dimensional Euler or Navier-Stokes equations is presented. The flow solver involves an upwind flux-split spatial discretization for the convective terms and central differencing for the shear-stress and heat flux terms on an unstructured mesh of triangles. The temporal adaptive algorithm is a time-accurate integration procedure which allows flows with high spatial and temporal gradients to be computed efficiently by advancing each grid cell near its maximum allowable time step. Results indicate that an appreciable computational savings can be achieved for both inviscid and viscous unsteady airfoil problems using unstructured meshes without degrading spatial or temporal accuracy.
NASA Astrophysics Data System (ADS)
Adam, A.; Pavlidis, D.; Percival, J. R.; Salinas, P.; Xie, Z.; Fang, F.; Pain, C. C.; Muggeridge, A. H.; Jackson, M. D.
2016-09-01
A general, higher-order, conservative and bounded interpolation for the dynamic and adaptive meshing of control-volume fields dual to continuous and discontinuous finite element representations is presented. Existing techniques such as node-wise interpolation are not conservative and do not readily generalise to discontinuous fields, whilst conservative methods such as Grandy interpolation are often too diffusive. The new method uses control-volume Galerkin projection to interpolate between control-volume fields. Bounded solutions are ensured by using a post-interpolation diffusive correction. Example applications of the method to interface capturing during advection and also to the modelling of multiphase porous media flow are presented to demonstrate the generality and robustness of the approach.
SU-D-207-04: GPU-Based 4D Cone-Beam CT Reconstruction Using Adaptive Meshing Method
Zhong, Z; Gu, X; Iyengar, P; Mao, W; Wang, J; Guo, X
2015-06-15
Purpose: Due to the limited number of projections at each phase, the image quality of a four-dimensional cone-beam CT (4D-CBCT) is often degraded, which decreases the accuracy of subsequent motion modeling. One of the promising methods is the simultaneous motion estimation and image reconstruction (SMEIR) approach. The objective of this work is to enhance the computational speed of the SMEIR algorithm using adaptive feature-based tetrahedral meshing and GPU-based parallelization. Methods: The first step is to generate the tetrahedral mesh based on the features of a reference phase 4D-CBCT, so that the deformation can be well captured and accurately diffused from the mesh vertices to voxels of the image volume. After the mesh generation, the updated motion model and other phases of 4D-CBCT can be obtained by matching the 4D-CBCT projection images at each phase with the corresponding forward projections of the deformed reference phase of 4D-CBCT. The entire process of this 4D-CBCT reconstruction method is implemented on GPU, resulting in significantly increasing the computational efficiency due to its tremendous parallel computing ability. Results: A 4D XCAT digital phantom was used to test the proposed mesh-based image reconstruction algorithm. The image Result shows both bone structures and inside of the lung are well-preserved and the tumor position can be well captured. Compared to the previous voxel-based CPU implementation of SMEIR, the proposed method is about 157 times faster for reconstructing a 10 -phase 4D-CBCT with dimension 256×256×150. Conclusion: The GPU-based parallel 4D CBCT reconstruction method uses the feature-based mesh for estimating motion model and demonstrates equivalent image Result with previous voxel-based SMEIR approach, with significantly improved computational speed.
Parallel adaptive simplical re-meshing for deforming domain CFD computations
NASA Astrophysics Data System (ADS)
Menon, Sandeep; Mooney, Kyle G.; Stapf, K. G.; Schmidt, David P.
2015-10-01
Deforming domains occur in many fields of computational fluid dynamics (CFD), such as interface tracking, simulation of pumps and engines, and fluid/structure interaction. The deformation of the domain presents a challenge to the integrity of the computational mesh; substantial motion of the domain boundaries requires vertex motion and changes in mesh connectivity. For cases of simple boundary motion or structured meshes, predetermined changes to the mesh structure can be sufficient. However, without a priori knowledge of how the domain will change, a more robust solution is required. The present work offers a parallelized solution for simplical meshes that is well-suited to extremely complex geometry. The mesh continuously evolves without user intervention or the use of target meshes. Varying length scales imposed by evolving boundary curvatures and narrow gaps are resolved with a fast length-scale algorithm. The set of algorithms are incorporated into an object-oriented code structure that permits broad application to a range of CFD problems. The robustness and versatility of the algorithm is demonstrated in several examples, representing motion of internal and external boundaries, where the boundary motion may or may not be known a priori.
NASA Astrophysics Data System (ADS)
Ravindran, Prashaanth
The unstable nature of detonation waves is a result of the critical relationship between the hydrodynamic shock and the chemical reactions sustaining the shock. A perturbative analysis of the critical point is quite challenging due to the multiple spatio-temporal scales involved along with the non-linear nature of the shock-reaction mechanism. The author's research attempts to provide detailed resolution of the instabilities at the shock front. Another key aspect of the present research is to develop an understanding of the causality between the non-linear dynamics of the front and the eventual breakdown of the sub-structures. An accurate numerical simulation of detonation waves requires a very efficient solution of the Euler equations in conservation form with detailed, non-equilibrium chemistry. The difference in the flow and reaction length scales results in very stiff source terms, requiring the problem to be solved with adaptive mesh refinement. For this purpose, Berger-Colella's block-structured adaptive mesh refinement (AMR) strategy has been developed and applied to time-explicit finite volume methods. The block-structured technique uses a hierarchy of parent-child sub-grids, integrated recursively over time. One novel approach to partition the problem within a large supercomputer was the use of modified Peano-Hilbert space filling curves. The AMR framework was merged with CLAWPACK, a package providing finite volume numerical methods tailored for wave-propagation problems. The stiffness problem is bypassed by using a 1st order Godunov or a 2nd order Strang splitting technique, where the flow variables and source terms are integrated independently. A linearly explicit fourth-order Runge-Kutta integrator is used for the flow, and an ODE solver was used to overcome the numerical stiffness. Second-order spatial resolution is obtained by using a second-order Roe-HLL scheme with the inclusion of numerical viscosity to stabilize the solution near the discontinuity
NASA Astrophysics Data System (ADS)
De Colle, Fabio; Granot, Jonathan; López-Cámara, Diego; Ramirez-Ruiz, Enrico
2012-02-01
We report on the development of Mezcal-SRHD, a new adaptive mesh refinement, special relativistic hydrodynamics (SRHD) code, developed with the aim of studying the highly relativistic flows in gamma-ray burst sources. The SRHD equations are solved using finite-volume conservative solvers, with second-order interpolation in space and time. The correct implementation of the algorithms is verified by one-dimensional (1D) and multi-dimensional tests. The code is then applied to study the propagation of 1D spherical impulsive blast waves expanding in a stratified medium with ρvpropr -k , bridging between the relativistic and Newtonian phases (which are described by the Blandford-McKee and Sedov-Taylor self-similar solutions, respectively), as well as to a two-dimensional (2D) cylindrically symmetric impulsive jet propagating in a constant density medium. It is shown that the deceleration to nonrelativistic speeds in one dimension occurs on scales significantly larger than the Sedov length. This transition is further delayed with respect to the Sedov length as the degree of stratification of the ambient medium is increased. This result, together with the scaling of position, Lorentz factor, and the shock velocity as a function of time and shock radius, is explained here using a simple analytical model based on energy conservation. The method used for calculating the afterglow radiation by post-processing the results of the simulations is described in detail. The light curves computed using the results of 1D numerical simulations during the relativistic stage correctly reproduce those calculated assuming the self-similar Blandford-McKee solution for the evolution of the flow. The jet dynamics from our 2D simulations and the resulting afterglow light curves, including the jet break, are in good agreement with those presented in previous works. Finally, we show how the details of the dynamics critically depend on properly resolving the structure of the relativistic flow.
Projections of grounding line retreat in West Antarctica carried out with an adaptive mesh model
NASA Astrophysics Data System (ADS)
Cornford, Stephen; Payne, Antony; Martin, Daniel; Le Brocq, Anne
2013-04-01
Present and future sea level rise associated with mass loss from West Antarctica is typically attributed to marine glaciers retreating in response to a warming ocean. Warmer waters melt the floating ice shelves that restrain some, if not all, marine glaciers, and the glaciers themselves respond by speeding up. That leads to thinning and in turn grounding line retreat. Satellite observations indicate that Amundsen Sea Embayment and, in particular, Pine Island Glacier, are undergoing this kind of dynamic change today. Numerical models, however, struggle to reproduce the observed behavior because either high resolution or some other kind special treatment is required at the grounding line. We present 200-year projections of three major glacier systems of West Antarctica: those that drain into the Amundsen Sea , the Filchner-Ronne Ice Shelf and the Ross Ice shelf. We do so using the newly developed BISICLES ice sheet model, which employs adaptive mesh refinement to maintain sub-kilometer resolution close to the grounding line and coarser resolution elsewhere. Ice accumulation and ice shelf melt-rate are derived from a range of models of the Antarctic atmosphere and ocean forced by the SRES A1B and E1 scenarios. We find that a substantial proportion of the grounding line in West Antarctica retreats, however the total sea level rise is less than 50 mm by 2100, and less than 100 mm by 2200. The lion's share of the mass loss is attributed to Pine Island Glacier, while its immediate neighbor Thwaites Glacier does not retreat until the end of the simulations.
Henshaw, W; Schwendeman, D
2007-11-15
This paper describes an approach for the numerical solution of time-dependent partial differential equations in complex three-dimensional domains. The domains are represented by overlapping structured grids, and block-structured adaptive mesh refinement (AMR) is employed to locally increase the grid resolution. In addition, the numerical method is implemented on parallel distributed-memory computers using a domain-decomposition approach. The implementation is flexible so that each base grid within the overlapping grid structure and its associated refinement grids can be independently partitioned over a chosen set of processors. A modified bin-packing algorithm is used to specify the partition for each grid so that the computational work is evenly distributed amongst the processors. All components of the AMR algorithm such as error estimation, regridding, and interpolation are performed in parallel. The parallel time-stepping algorithm is illustrated for initial-boundary-value problems involving a linear advection-diffusion equation and the (nonlinear) reactive Euler equations. Numerical results are presented for both equations to demonstrate the accuracy and correctness of the parallel approach. Exact solutions of the advection-diffusion equation are constructed, and these are used to check the corresponding numerical solutions for a variety of tests involving different overlapping grids, different numbers of refinement levels and refinement ratios, and different numbers of processors. The problem of planar shock diffraction by a sphere is considered as an illustration of the numerical approach for the Euler equations, and a problem involving the initiation of a detonation from a hot spot in a T-shaped pipe is considered to demonstrate the numerical approach for the reactive case. For both problems, the solutions are shown to be well resolved on the finest grid. The parallel performance of the approach is examined in detail for the shock diffraction problem.
NASA Astrophysics Data System (ADS)
Schaal, Kevin; Bauer, Andreas; Chandrashekar, Praveen; Pakmor, Rüdiger; Klingenberg, Christian; Springel, Volker
2015-11-01
Solving the Euler equations of ideal hydrodynamics as accurately and efficiently as possible is a key requirement in many astrophysical simulations. It is therefore important to continuously advance the numerical methods implemented in current astrophysical codes, especially also in light of evolving computer technology, which favours certain computational approaches over others. Here we introduce the new adaptive mesh refinement (AMR) code TENET, which employs a high-order discontinuous Galerkin (DG) scheme for hydrodynamics. The Euler equations in this method are solved in a weak formulation with a polynomial basis by means of explicit Runge-Kutta time integration and Gauss-Legendre quadrature. This approach offers significant advantages over commonly employed second-order finite-volume (FV) solvers. In particular, the higher order capability renders it computationally more efficient, in the sense that the same precision can be obtained at significantly less computational cost. Also, the DG scheme inherently conserves angular momentum in regions where no limiting takes place, and it typically produces much smaller numerical diffusion and advection errors than an FV approach. A further advantage lies in a more natural handling of AMR refinement boundaries, where a fall-back to first order can be avoided. Finally, DG requires no wide stencils at high order, and offers an improved data locality and a focus on local computations, which is favourable for current and upcoming highly parallel supercomputers. We describe the formulation and implementation details of our new code, and demonstrate its performance and accuracy with a set of two- and three-dimensional test problems. The results confirm that DG schemes have a high potential for astrophysical applications.
MR image denoising method for brain surface 3D modeling
NASA Astrophysics Data System (ADS)
Zhao, De-xin; Liu, Peng-jie; Zhang, De-gan
2014-11-01
Three-dimensional (3D) modeling of medical images is a critical part of surgical simulation. In this paper, we focus on the magnetic resonance (MR) images denoising for brain modeling reconstruction, and exploit a practical solution. We attempt to remove the noise existing in the MR imaging signal and preserve the image characteristics. A wavelet-based adaptive curve shrinkage function is presented in spherical coordinates system. The comparative experiments show that the denoising method can preserve better image details and enhance the coefficients of contours. Using these denoised images, the brain 3D visualization is given through surface triangle mesh model, which demonstrates the effectiveness of the proposed method.
NASA Astrophysics Data System (ADS)
Sui, Yi; Spelt, Peter D. M.; Ding, Hang
2010-11-01
Diffuse Interface (DI) methods are employed widely for the numerical simulation of two-phase flows, even with moving contact lines. In a DI method, the interface thickness should be as thin as possible to simulate spreading phenomena under realistic flow conditions, so a fine grid is required, beyond the reach of current methods that employ a uniform grid. Here we have integrated a DI method based on a uniform mesh, to a block-based adaptive mesh refinement method, so that only the regions near the interface are resolved by a fine mesh. The performance of the present method is tested by simulations including drop deformation in shear flow, Rayleigh-Taylor instability and drop spreading on a flat surface, et al. The results show that the present method can give accurate results with much smaller computational cost, compared to the original DI method based on a uniform mesh. Based on the present method, simulation of drop spreading is carried out with Cahn number of 0.001 and the contact line region is well resolved. The flow field near the contact line, the contact line speed as well as the apparent contact angle are investigated in detail and compared with previous analytical work.
NASA Astrophysics Data System (ADS)
Zheng, H. W.; Shu, C.; Chew, Y. T.
2008-07-01
In this paper, an object-oriented and quadrilateral-mesh based solution adaptive algorithm for the simulation of compressible multi-fluid flows is presented. The HLLC scheme (Harten, Lax and van Leer approximate Riemann solver with the Contact wave restored) is extended to adaptively solve the compressible multi-fluid flows under complex geometry on unstructured mesh. It is also extended to the second-order of accuracy by using MUSCL extrapolation. The node, edge and cell are arranged in such an object-oriented manner that each of them inherits from a basic object. A home-made double link list is designed to manage these objects so that the inserting of new objects and removing of the existing objects (nodes, edges and cells) are independent of the number of objects and only of the complexity of O( 1). In addition, the cells with different levels are further stored in different lists. This avoids the recursive calculation of solution of mother (non-leaf) cells. Thus, high efficiency is obtained due to these features. Besides, as compared to other cell-edge adaptive methods, the separation of nodes would reduce the memory requirement of redundant nodes, especially in the cases where the level number is large or the space dimension is three. Five two-dimensional examples are used to examine its performance. These examples include vortex evolution problem, interface only problem under structured mesh and unstructured mesh, bubble explosion under the water, bubble-shock interaction, and shock-interface interaction inside the cylindrical vessel. Numerical results indicate that there is no oscillation of pressure and velocity across the interface and it is feasible to apply it to solve compressible multi-fluid flows with large density ratio (1000) and strong shock wave (the pressure ratio is 10,000) interaction with the interface.
Garcia-Molla, V M; Liberos, A; Vidal, A; Guillem, M S; Millet, J; Gonzalez, A; Martinez-Zaldivar, F J; Climent, A M
2014-01-01
In this paper we studied the implementation and performance of adaptive step methods for large systems of ordinary differential equations systems in graphics processing units, focusing on the simulation of three-dimensional electric cardiac activity. The Rush-Larsen method was applied in all the implemented solvers to improve efficiency. We compared the adaptive methods with the fixed step methods, and we found that the fixed step methods can be faster while the adaptive step methods are better in terms of accuracy and robustness. PMID:24377685
NASA Astrophysics Data System (ADS)
Danilov, A. A.; Salamatova, V. Yu; Vassilevski, Yu V.
2012-12-01
Here, a workflow for high-resolution efficient numerical modeling of bioimpedance measurements is suggested that includes 3D image segmentation, adaptive mesh generation, finite-element discretization, and the analysis of simulation results. Using the adaptive unstructured tetrahedral meshes enables to decrease significantly a number of mesh elements while keeping model accuracy. The numerical results illustrate current, potential, and sensitivity field distributions for a conventional Kubicek-like scheme of bioimpedance measurements using segmented geometric model of human torso based on Visible Human Project data. The whole body VHP man computational mesh is constructed that contains 574 thousand vertices and 3.3 million tetrahedrons.
NASA Astrophysics Data System (ADS)
Pantano, Carlos
2005-11-01
We describe a hybrid finite difference method for large-eddy simulation (LES) of compressible flows with a low-numerical dissipation scheme and structured adaptive mesh refinement (SAMR). Numerical experiments and validation calculations are presented including a turbulent jet and the strongly shock-driven mixing of a Richtmyer-Meshkov instability. The approach is a conservative flux-based SAMR formulation and as such, it utilizes refinement to computational advantage. The numerical method for the resolved scale terms encompasses the cases of scheme alternation and internal mesh interfaces resulting from SAMR. An explicit centered scheme that is consistent with a skew-symmetric finite difference formulation is used in turbulent flow regions while a weighted essentially non-oscillatory (WENO) scheme is employed to capture shocks. The subgrid stresses and transports are calculated by means of the streched-vortex model, Misra & Pullin (1997)
NASA Astrophysics Data System (ADS)
Pantano, C.; Deiterding, R.; Hill, D. J.; Pullin, D. I.
2007-01-01
We present a methodology for the large-eddy simulation of compressible flows with a low-numerical dissipation scheme and structured adaptive mesh refinement (SAMR). A description of a conservative, flux-based hybrid numerical method that uses both centered finite-difference and a weighted essentially non-oscillatory (WENO) scheme is given, encompassing the cases of scheme alternation and internal mesh interfaces resulting from SAMR. In this method, the centered scheme is used in turbulent flow regions while WENO is employed to capture shocks. One-, two- and three-dimensional numerical experiments and example simulations are presented including homogeneous shock-free turbulence, a turbulent jet and the strongly shock-driven mixing of a Richtmyer-Meshkov instability.
NASA Technical Reports Server (NTRS)
Steinthorsson, E.; Modiano, David; Colella, Phillip
1994-01-01
A methodology for accurate and efficient simulation of unsteady, compressible flows is presented. The cornerstones of the methodology are a special discretization of the Navier-Stokes equations on structured body-fitted grid systems and an efficient solution-adaptive mesh refinement technique for structured grids. The discretization employs an explicit multidimensional upwind scheme for the inviscid fluxes and an implicit treatment of the viscous terms. The mesh refinement technique is based on the AMR algorithm of Berger and Colella. In this approach, cells on each level of refinement are organized into a small number of topologically rectangular blocks, each containing several thousand cells. The small number of blocks leads to small overhead in managing data, while their size and regular topology means that a high degree of optimization can be achieved on computers with vector processors.
A 3D front tracking method on a CPU/GPU system
Bo, Wurigen; Grove, John
2011-01-21
We describe the method to port a sequential 3D interface tracking code to a GPU with CUDA. The interface is represented as a triangular mesh. Interface geometry properties and point propagation are performed on a GPU. Interface mesh adaptation is performed on a CPU. The convergence of the method is assessed from the test problems with given velocity fields. Performance results show overall speedups from 11 to 14 for the test problems under mesh refinement. We also briefly describe our ongoing work to couple the interface tracking method with a hydro solver.
Adaptive Mesh Refinement Cosmological Simulations of Cosmic Rays in Galaxy Clusters
NASA Astrophysics Data System (ADS)
Skillman, Samuel William
2013-12-01
Galaxy clusters are unique astrophysical laboratories that contain many thermal and non-thermal phenomena. In particular, they are hosts to cosmic shocks, which propagate through the intracluster medium as a by-product of structure formation. It is believed that at these shock fronts, magnetic field inhomogeneities in a compressing flow may lead to the acceleration of cosmic ray electrons and ions. These relativistic particles decay and radiate through a variety of mechanisms, and have observational signatures in radio, hard X-ray, and Gamma-ray wavelengths. We begin this dissertation by developing a method to find shocks in cosmological adaptive mesh refinement simulations of structure formation. After describing the evolution of shock properties through cosmic time, we make estimates for the amount of kinetic energy processed and the total number of cosmic ray protons that could be accelerated at these shocks. We then use this method of shock finding and a model for the acceleration of and radio synchrotron emission from cosmic ray electrons to estimate the radio emission properties in large scale structures. By examining the time-evolution of the radio emission with respect to the X-ray emission during a galaxy cluster merger, we find that the relative timing of the enhancements in each are important consequences of the shock dynamics. By calculating the radio emission expected from a given mass galaxy cluster, we make estimates for future large-area radio surveys. Next, we use a state-of-the-art magnetohydrodynamic simulation to follow the electron acceleration in a massive merging galaxy cluster. We use the magnetic field information to calculate not only the total radio emission, but also create radio polarization maps that are compared to recent observations. We find that we can naturally reproduce Mpc-scale radio emission that resemble many of the known double radio relic systems. Finally, motivated by our previous studies, we develop and introduce a
NASA Astrophysics Data System (ADS)
Otis, Collin; Ferrero, Pietro; Candler, Graham; Givi, Peyman
2013-11-01
The scalar filtered mass density function (SFMDF) methodology is implemented into the computer code US3D. This is an unstructured Eulerian finite volume hydrodynamic solver and has proven very effective for simulation of compressible turbulent flows. The resulting SFMDF-US3D code is employed for large eddy simulation (LES) on unstructured meshes. Simulations are conducted of subsonic and supersonic flows under non-reacting and reacting conditions. The consistency and the accuracy of the simulated results are assessed along with appraisal of the overall performance of the methodology. The SFMDF-US3D is now capable of simulating high speed flows in complex configurations.
Lipnikov, Konstantin; Agouzal, Abdellatif; Vassilevski, Yuri
2009-01-01
We present a new technology for generating meshes minimizing the interpolation and discretization errors or their gradients. The key element of this methodology is construction of a space metric from edge-based error estimates. For a mesh with N{sub h} triangles, the error is proportional to N{sub h}{sup -1} and the gradient of error is proportional to N{sub h}{sup -1/2} which are optimal asymptotics. The methodology is verified with numerical experiments.
NASA Astrophysics Data System (ADS)
Weller, Hilary; Browne, Philip; Budd, Chris; Cullen, Mike
2016-03-01
An equation of Monge-Ampère type has, for the first time, been solved numerically on the surface of the sphere in order to generate optimally transported (OT) meshes, equidistributed with respect to a monitor function. Optimal transport generates meshes that keep the same connectivity as the original mesh, making them suitable for r-adaptive simulations, in which the equations of motion can be solved in a moving frame of reference in order to avoid mapping the solution between old and new meshes and to avoid load balancing problems on parallel computers. The semi-implicit solution of the Monge-Ampère type equation involves a new linearisation of the Hessian term, and exponential maps are used to map from old to new meshes on the sphere. The determinant of the Hessian is evaluated as the change in volume between old and new mesh cells, rather than using numerical approximations to the gradients. OT meshes are generated to compare with centroidal Voronoi tessellations on the sphere and are found to have advantages and disadvantages; OT equidistribution is more accurate, the number of iterations to convergence is independent of the mesh size, face skewness is reduced and the connectivity does not change. However anisotropy is higher and the OT meshes are non-orthogonal. It is shown that optimal transport on the sphere leads to meshes that do not tangle. However, tangling can be introduced by numerical errors in calculating the gradient of the mesh potential. Methods for alleviating this problem are explored. Finally, OT meshes are generated using observed precipitation as a monitor function, in order to demonstrate the potential power of the technique.
NASA Astrophysics Data System (ADS)
Wilson, C. R.; Kramer, S. C.; Collins, G. S.
2010-12-01
Linear wave models cannot reproduce the highly nonlinear generation mechanisms required to accurately predict the consequences of landslide-generated tsunamis. Models based on the nonlinear Navier-Stokes equations can simulate complex landslide-water interactions at realistic scales; however, the computing power required for such a simulation can be prohibitively high for large domains with realistic bathymetries. The variable resolution available with the use of unstructured adaptive meshes allows larger domains to be modeled at the same resolution for a lower computational cost than on structured meshes; they are also better at representing complex geometries and bathymetries. However, unstructured meshes introduce extra numerical challenges requiring the use of novel interface preservation techniques coupled with velocity-pressure discretisations that ensure the conservation and boundedness of all materials in the simulation. In this study we describe some of the challenges encountered extending the finite element, finite volume multiple-material fluid dynamics model Fluidity to large-scale landslide-generated tsunami simulations. In particular, we focus on the ability of the model to preserve the balance between the buoyancy and pressure gradient forces. Failure to discretely satisfy this relationship is shown to result in spurious waves that contaminate any physical tsunami signal. However, ensuring that balance is preserved in a computationally efficient manner imposes extra constraints on the dynamic mesh optimisation process. Incorporating these restrictions allows us to validate our model against multi-scale experimental simulations of landslide generated tsunami (see figure). Experimental (top, taken from Di Risio et. al. 2009, doi:10.1029/2008JC004858) and equivalent numerical simulation (bottom) of a subaerial landslide impacting into water. In the experiment the 80cm long landslide produces waves of amplitude 1-2cm around a 9m diameter island in a 50x
Application of adaptive mesh refinement to particle-in-cell simulations of plasmas and beams
Vay, J.-L.; Colella, P.; Kwan, J.W.; McCorquodale, P.; Serafini, D.B.; Friedman, A.; Grote, D.P.; Westenskow, G.; Adam, J.-C.; Heron, A.; Haber, I.
2003-11-04
Plasma simulations are often rendered challenging by the disparity of scales in time and in space which must be resolved. When these disparities are in distinctive zones of the simulation domain, a method which has proven to be effective in other areas (e.g. fluid dynamics simulations) is the mesh refinement technique. We briefly discuss the challenges posed by coupling this technique with plasma Particle-In-Cell simulations, and present examples of application in Heavy Ion Fusion and related fields which illustrate the effectiveness of the approach. We also report on the status of a collaboration under way at Lawrence Berkeley National Laboratory between the Applied Numerical Algorithms Group (ANAG) and the Heavy Ion Fusion group to upgrade ANAG's mesh refinement library Chombo to include the tools needed by Particle-In-Cell simulation codes.
NASA Astrophysics Data System (ADS)
Ghattas, O.; Burstedde, C.; Stadler, G.; Wilcox, L. C.; Tu, T.; Issac, T.; Gurnis, M.; Alisic, L.; Tan, E.; Zhong, S.
2009-12-01
Many problems in solid earth geophysics are characterized by dynamics occurring on a wide range of length and time scales, placing the solution of the governing partial differential equations (PDEs) for such problems among the grand challenges of computational geophysics. One approach to overcoming the tyranny of scales is adaptive mesh refinement (AMR), which locally and dynamically adapts the mesh to resolve spatio-temporal scales and features of interest. For example, we are interested in modeling global mantle convection with nonlinear rheology and kilometer-scale resolution at faulted plate boundaries. Another problem of interest is modeling the dynamics of polar ice sheets with fine resolution in the vicinity of stick-slip transitions. Geophysical inverse problems characterized by a wide range of medium properties can also benefit from AMR as the earth model is updated. While AMR promises to help overcome the challenges inherent in modeling multiscale problems, the benefits are difficult to achieve in practice, particularly on petascale computers that are essential for frontier problems. Due to the complex dynamic data structures and communication patterns, and frequent data exchange and redistribution, scaling dynamic AMR to tens of thousands of processors has long been considered a challenge. Another difficulty is extending parallel AMR techniques to high-order-accurate, complex-geometry-conforming finite element methods that are favored for many classes of solid earth geophysical problems. Here, we present the ALPS (Adaptive Large-scale Parallel Simulations) framework for parallel adaptive solution of PDEs. ALPS includes the octor and p4est libraries for parallel dynamic mesh adaptivity on single-octree-based and forest-of-octree-based geometries, respectively, and the mangll library for arbitrary-order hexahedral continuous and discontinuous finite/spectral element discretizations on general multi-octree geometries. ALPS has been shown to scale well
Cunningham, Andrew J.; Frank, Adam; Varniere, Peggy; Mitran, Sorin; Jones, Thomas W.
2009-06-15
A description is given of the algorithms implemented in the AstroBEAR adaptive mesh-refinement code for ideal magnetohydrodynamics. The code provides several high-resolution shock-capturing schemes which are constructed to maintain conserved quantities of the flow in a finite-volume sense. Divergence-free magnetic field topologies are maintained to machine precision by collating the components of the magnetic field on a cell-interface staggered grid and utilizing the constrained transport approach for integrating the induction equations. The maintenance of magnetic field topologies on adaptive grids is achieved using prolongation and restriction operators which preserve the divergence and curl of the magnetic field across collocated grids of different resolutions. The robustness and correctness of the code is demonstrated by comparing the numerical solution of various tests with analytical solutions or previously published numerical solutions obtained by other codes.
XML3D and Xflow: combining declarative 3D for the Web with generic data flows.
Klein, Felix; Sons, Kristian; Rubinstein, Dmitri; Slusallek, Philipp
2013-01-01
Researchers have combined XML3D, which provides declarative, interactive 3D scene descriptions based on HTML5, with Xflow, a language for declarative, high-performance data processing. The result lets Web developers combine a 3D scene graph with data flows for dynamic meshes, animations, image processing, and postprocessing. PMID:24808080
Jeong, Jeho; Chen, Qing; Febo, Robert; Yang, Jie; Pham, Hai; Xiong, Jian-Ping; Zanzonico, Pat B; Deasy, Joseph O; Humm, John L; Mageras, Gig S
2016-06-01
Although spatially precise systems are now available for small-animal irradiations, there are currently limited software tools available for treatment planning for such irradiations. We report on the adaptation, commissioning, and evaluation of a 3-dimensional treatment planning system for use with a small-animal irradiation system. The 225-kV X-ray beam of the X-RAD 225Cx microirradiator (Precision X-Ray) was commissioned using both ion-chamber and radiochromic film for 10 different collimators ranging in field size from 1 mm in diameter to 40 × 40 mm(2) A clinical 3-dimensional treatment planning system (Metropolis) developed at our institution was adapted to small-animal irradiation by making it compatible with the dimensions of mice and rats, modeling the microirradiator beam orientations and collimators, and incorporating the measured beam data for dose calculation. Dose calculations in Metropolis were verified by comparison with measurements in phantoms. Treatment plans for irradiation of a tumor-bearing mouse were generated with both the Metropolis and the vendor-supplied software. The calculated beam-on times and the plan evaluation tools were compared. The dose rate at the central axis ranges from 74 to 365 cGy/min depending on the collimator size. Doses calculated with Metropolis agreed with phantom measurements within 3% for all collimators. The beam-on times calculated by Metropolis and the vendor-supplied software agreed within 1% at the isocenter. The modified 3-dimensional treatment planning system provides better visualization of the relationship between the X-ray beams and the small-animal anatomy as well as more complete dosimetric information on target tissues and organs at risk. It thereby enhances the potential of image-guided microirradiator systems for evaluation of dose-response relationships and for preclinical experimentation generally. PMID:25948321
Potentially singular solutions of the 3D axisymmetric Euler equations
Luo, Guo; Hou, Thomas Y.
2014-01-01
The question of finite-time blowup of the 3D incompressible Euler equations is numerically investigated in a periodic cylinder with solid boundaries. Using rotational symmetry, the equations are discretized in the (2D) meridian plane on an adaptive (moving) mesh and is integrated in time with adaptively chosen time steps. The vorticity is observed to develop a ring-singularity on the solid boundary with a growth proportional to ∼(ts − t)−2.46, where ts ∼ 0.0035056 is the estimated singularity time. A local analysis also suggests the existence of a self-similar blowup. The simulations stop at τ2 = 0.003505 at which time the vorticity amplifies by more than (3 × 108)-fold and the maximum mesh resolution exceeds (3 × 1012)2. The vorticity vector is observed to maintain four significant digits throughout the computations. PMID:25157172
NASA Astrophysics Data System (ADS)
Fraser, Danielle; Fava, Palma; Cury, Fabio; Vuong, Te; Falco, Tony; Verhaegen, Frank
2007-03-01
Sonography has good topographic accuracy for superficial lymph node assessment in patients with head and neck cancers. It is therefore an ideal non-invasive tool for precise inter-fraction volumetric analysis of enlarged cervical nodes. In addition, when registered with computed tomography (CT) images, ultrasound information may improve target volume delineation and facilitate image-guided adaptive radiation therapy. A feasibility study was developed to evaluate the use of a prototype ultrasound system capable of three dimensional visualization and multi-modality image fusion for cervical node geometry. A ceiling-mounted optical tracking camera recorded the position and orientation of a transducer in order to synchronize the transducer's position with respect to the room's coordinate system. Tracking systems were installed in both the CT-simulator and radiation therapy treatment rooms. Serial images were collected at the time of treatment planning and at subsequent treatment fractions. Volume reconstruction was performed by generating surfaces around contours. The quality of the spatial reconstruction and semi-automatic segmentation was highly dependent on the system's ability to track the transducer throughout each scan procedure. The ultrasound information provided enhanced soft tissue contrast and facilitated node delineation. Manual segmentation was the preferred method to contour structures due to their sonographic topography.
Postprocessing of compressed 3D graphic data by using subdivision
NASA Astrophysics Data System (ADS)
Cheang, Ka Man; Li, Jiankun; Kuo, C.-C. Jay
1998-10-01
In this work, we present a postprocessing technique applied to a 3D graphic model of a lower resolution to obtain a visually more pleasant representation. Our method is an improved version of the Butterfly subdivision scheme developed by Zorin et al. Our main contribution is to exploit the flatness information of local areas of a 3D graphic model for adaptive refinement. Consequently, we can avoid unnecessary subdivision in regions which are relatively flat. The proposed new algorithm not only reduces the computational complexity but also saves the storage space. With the hierarchical mesh compression method developed by Li and Kuo as the baseline coding method, we show that the postprocessing technique can greatly improve the visual quality of the decoded 3D graphic model.
Evaluation of discretization procedures for transition elements in adaptive mesh refinement
NASA Technical Reports Server (NTRS)
Park, K. C.; Levit, Itzak; Stanley, Gary M.
1991-01-01
Three transition interpolation schemes for use in h-or r-refinement have been analyzed in terms of accuracy, implementation ease and extendability. They include blending-function interpolation, displacement averaging, and strain matching at discrete points along the transition edge lines. The results suggest that the choice of matching depends strongly on the element formulations, (viz. displacement or assumed strain, etc.) and mesh refinement criteria employed, and to a lesser extent the choice of computer architecture (serial vs. parallel) and the equation solution procedures. A recommended pairing of some of the elements with the choice factors is suggested.
An adaptive-mesh finite-difference solution method for the Navier-Stokes equations
NASA Astrophysics Data System (ADS)
Luchini, Paolo
1987-02-01
An adjustable variable-spacing grid is presented which permits the addition or deletion of single points during iterative solutions of the Navier-Stokes equations by finite difference methods. The grid is designed for application to two-dimensional steady-flow problems which can be described by partial differential equations whose second derivatives are constrained to the Laplacian operator. An explicit Navier-Stokes equations solution technique defined for use with the grid incorporates a hybrid form of the convective terms. Three methods are developed for automatic modifications of the mesh during calculations.
NASA Astrophysics Data System (ADS)
Berchtold, Waldemar; Schäfer, Marcel; Rettig, Michael; Steinebach, Martin
2014-02-01
3D models and applications are of utmost interest in both science and industry. With the increment of their usage, their number and thereby the challenge to correctly identify them increases. Content identification is commonly done by cryptographic hashes. However, they fail as a solution in application scenarios such as computer aided design (CAD), scientific visualization or video games, because even the smallest alteration of the 3D model, e.g. conversion or compression operations, massively changes the cryptographic hash as well. Therefore, this work presents a robust hashing algorithm for 3D mesh data. The algorithm applies several different bit extraction methods. They are built to resist desired alterations of the model as well as malicious attacks intending to prevent correct allocation. The different bit extraction methods are tested against each other and, as far as possible, the hashing algorithm is compared to the state of the art. The parameters tested are robustness, security and runtime performance as well as False Acceptance Rate (FAR) and False Rejection Rate (FRR), also the probability calculation of hash collision is included. The introduced hashing algorithm is kept adaptive e.g. in hash length, to serve as a proper tool for all applications in practice.
NASA Astrophysics Data System (ADS)
Kimura, Satoshi; Candy, Adam S.; Holland, Paul R.; Piggott, Matthew D.; Jenkins, Adrian
2013-07-01
Several different classes of ocean model are capable of representing floating glacial ice shelves. We describe the incorporation of ice shelves into Fluidity-ICOM, a nonhydrostatic finite-element ocean model with the capacity to utilize meshes that are unstructured and adaptive in three dimensions. This geometric flexibility offers several advantages over previous approaches. The model represents melting and freezing on all ice-shelf surfaces including vertical faces, treats the ice shelf topography as continuous rather than stepped, and does not require any smoothing of the ice topography or any of the additional parameterisations of the ocean mixed layer used in isopycnal or z-coordinate models. The model can also represent a water column that decreases to zero thickness at the 'grounding line', where the floating ice shelf is joined to its tributary ice streams. The model is applied to idealised ice-shelf geometries in order to demonstrate these capabilities. In these simple experiments, arbitrarily coarsening the mesh outside the ice-shelf cavity has little effect on the ice-shelf melt rate, while the mesh resolution within the cavity is found to be highly influential. Smoothing the vertical ice front results in faster flow along the smoothed ice front, allowing greater exchange with the ocean than in simulations with a realistic ice front. A vanishing water-column thickness at the grounding line has little effect in the simulations studied. We also investigate the response of ice shelf basal melting to variations in deep water temperature in the presence of salt stratification.
NASA Astrophysics Data System (ADS)
Mammadov, Ramiz
2013-04-01
coastal areas at hydraulic engineering projects the sea level should be considered as multistage process, what we have considered by development of adaptation of a coastal zone The exact three-dimensional map of a coastal zone has been created. For different scenario sea levels, or example, -30.0; -29.0; -28.0; -27.0; -26.0; -25.0 and -24.0 exact coastal lines have been certain. Further maps of a vegetative cover, ground, social and economic and ecological conditions have been developed for different level and respective alterations are certain. More vulnerable coastal zone, flooded area and socio-economic damage were estimated.
2012-01-04
GEN3D is a three-dimensional mesh generation program. The three-dimensional mesh is generated by mapping a two-dimensional mesh into threedimensions according to one of four types of transformations: translating, rotating, mapping onto a spherical surface, and mapping onto a cylindrical surface. The generated three-dimensional mesh can then be reoriented by offsetting, reflecting about an axis, and revolving about an axis. GEN3D can be used to mesh geometries that are axisymmetric or planar, but, due to three-dimensionalmore » loading or boundary conditions, require a three-dimensional finite element mesh and analysis. More importantly, it can be used to mesh complex three-dimensional geometries composed of several sections when the sections can be defined in terms of transformations of two dimensional geometries. The code GJOIN is then used to join the separate sections into a single body. GEN3D reads and writes twodimensional and threedimensional mesh databases in the GENESIS database format; therefore, it is compatible with the preprocessing, postprocessing, and analysis codes used by the Engineering Analysis Department at Sandia National Laboratories, Albuquerque, NM.« less
Armstrong, Jerawan C.; Favorite, Jeffrey A.
2012-06-20
The Levenberg-Marquardt (or simply Marquardt) and differential evolution (DE) optimization methods were recently applied to solve inverse transport problems. The Marquardt method is fast but convergence of the method is dependent on the initial guess. While it has been shown to work extremely well at finding an optimum independent of the initial guess, the DE method does not provide a global optimal solution in some problems. In this paper, we apply the Mesh Adaptive Direct Search (MADS) algorithm to solve the inverse problem of material interface location identification in one-dimensional spherical radiation source/shield systems, and we compare the results obtained by MADS to those obtained by Levenberg-Marquardt and DE.
NASA Astrophysics Data System (ADS)
Kerimoglu, Onur; Hofmeister, Richard; Wirtz, Kai
2016-04-01
Adaptation and acclimation processes are often ignored in ecosystem-scale model implementations, despite the long-standing recognition of their importance. Here we present a novel adaptive phytoplankton growth model where acclimation of the community to the changes in external resource ratios is accounted for, using optimality principles and dynamic physiological traits. We show that the model can reproduce the internal stoichiometries obtained at marginal supply ratios in chemostat experiments. The model is applied in a decadal hindcast simulation of the southern North Sea, where it is coupled to a 2-D benthic model and a 3-D hydrodynamic model in an approximately 1.5km horizontal resolution at the German Bight coast. The model is shown to have good skill in capturing the steep, coastal gradients in the German Bight, suggested by the match between the estimated and observed dissolved nutrient and chlorophyll concentrations. We then analyze the differential sensitivity of the coastal and off-shore zones to major drivers of the system, such as riverine nutrient loads. We demonstrate that the relevance of phytoplankton acclimation varies across coastal gradients and can become particularly significant in terms of summer nutrient depletion.
NASA Astrophysics Data System (ADS)
Ferreira, F.; Dehmeshki, J.; Amin, H.; Dehkordi, M. E.; Belli, A.; Jouannic, A.; Qanadli, S.
2010-03-01
Thoracic Aortic Aneurysm (TAA) is a localized swelling of the thoracic aorta. The progressive growth of an aneurysm may eventually cause a rupture if not diagnosed or treated. This necessitates the need for an accurate measurement which in turn calls for the accurate segmentation of the aneurysm regions. Computer Aided Detection (CAD) is a tool to automatically detect and segment the TAA in the Computer tomography angiography (CTA) images. The fundamental major step of developing such a system is to develop a robust method for the detection of main vessel and measuring its diameters. In this paper we propose a novel adaptive method to simultaneously segment the thoracic aorta and to indentify its center line. For this purpose, an adaptive parametric 3D region growing is proposed in which its seed will be automatically selected through the detection of the celiac artery and the parameters of the method will be re-estimated while the region is growing thorough the aorta. At each phase of region growing the initial center line of aorta will also be identified and modified through the process. Thus the proposed method simultaneously detect aorta and identify its centerline. The method has been applied on CT images from 20 patients with good agreement with the visual assessment by two radiologists.
NASA Astrophysics Data System (ADS)
Guo, Zhikui; Chen, Chao; Tao, Chunhui
2016-04-01
Since 2007, there are four China Da yang cruises (CDCs), which have been carried out to investigate polymetallic sulfides in the southwest Indian ridge (SWIR) and have acquired both gravity data and bathymetry data on the corresponding survey lines(Tao et al., 2014). Sandwell et al. (2014) published a new global marine gravity model including the free air gravity data and its first order vertical gradient (Vzz). Gravity data and its gradient can be used to extract unknown density structure information(e.g. crust thickness) under surface of the earth, but they contain all the mass effect under the observation point. Therefore, how to get accurate gravity and its gradient effect of the existing density structure (e.g. terrain) has been a key issue. Using the bathymetry data or ETOPO1 (http://www.ngdc.noaa.gov/mgg/global/global.html) model at a full resolution to calculate the terrain effect could spend too much computation time. We expect to develop an effective method that takes less time but can still yield the desired accuracy. In this study, a constant-density polyhedral model is used to calculate the gravity field and its vertical gradient, which is based on the work of Tsoulis (2012). According to gravity field attenuation with distance and variance of bathymetry, we present an adaptive mesh refinement and coarsening strategies to merge both global topography data and multi-beam bathymetry data. The local coarsening or size of mesh depends on user-defined accuracy and terrain variation (Davis et al., 2011). To depict terrain better, triangular surface element and rectangular surface element are used in fine and coarse mesh respectively. This strategy can also be applied to spherical coordinate in large region and global scale. Finally, we applied this method to calculate Bouguer gravity anomaly (BGA), mantle Bouguer anomaly(MBA) and their vertical gradient in SWIR. Further, we compared the result with previous results in the literature. Both synthetic model
NASA Astrophysics Data System (ADS)
Moura, R. C.; Silva, A. F. C.; Bigarella, E. D. V.; Fazenda, A. L.; Ortega, M. A.
2016-08-01
This paper proposes two important improvements to shock-capturing strategies using a discontinuous Galerkin scheme, namely, accurate shock identification via finite-time Lyapunov exponent (FTLE) operators and efficient shock treatment through a point-implicit discretization of a PDE-based artificial viscosity technique. The advocated approach is based on the FTLE operator, originally developed in the context of dynamical systems theory to identify certain types of coherent structures in a flow. We propose the application of FTLEs in the detection of shock waves and demonstrate the operator's ability to identify strong and weak shocks equally well. The detection algorithm is coupled with a mesh refinement procedure and applied to transonic and supersonic flows. While the proposed strategy can be used potentially with any numerical method, a high-order discontinuous Galerkin solver is used in this study. In this context, two artificial viscosity approaches are employed to regularize the solution near shocks: an element-wise constant viscosity technique and a PDE-based smooth viscosity model. As the latter approach is more sophisticated and preferable for complex problems, a point-implicit discretization in time is proposed to reduce the extra stiffness introduced by the PDE-based technique, making it more competitive in terms of computational cost.
Interactive 3d Landscapes on Line
NASA Astrophysics Data System (ADS)
Fanini, B.; Calori, L.; Ferdani, D.; Pescarin, S.
2011-09-01
The paper describes challenges identified while developing browser embedded 3D landscape rendering applications, our current approach and work-flow and how recent development in browser technologies could affect. All the data, even if processed by optimization and decimation tools, result in very huge databases that require paging, streaming and Level-of-Detail techniques to be implemented to allow remote web based real time fruition. Our approach has been to select an open source scene-graph based visual simulation library with sufficient performance and flexibility and adapt it to the web by providing a browser plug-in. Within the current Montegrotto VR Project, content produced with new pipelines has been integrated. The whole Montegrotto Town has been generated procedurally by CityEngine. We used this procedural approach, based on algorithms and procedures because it is particularly functional to create extensive and credible urban reconstructions. To create the archaeological sites we used optimized mesh acquired with laser scanning and photogrammetry techniques whereas to realize the 3D reconstructions of the main historical buildings we adopted computer-graphic software like blender and 3ds Max. At the final stage, semi-automatic tools have been developed and used up to prepare and clusterise 3D models and scene graph routes for web publishing. Vegetation generators have also been used with the goal of populating the virtual scene to enhance the user perceived realism during the navigation experience. After the description of 3D modelling and optimization techniques, the paper will focus and discuss its results and expectations.
3-D transient analysis of pebble-bed HTGR by TORT-TD/ATTICA3D
Seubert, A.; Sureda, A.; Lapins, J.; Buck, M.; Bader, J.; Laurien, E.
2012-07-01
As most of the acceptance criteria are local core parameters, application of transient 3-D fine mesh neutron transport and thermal hydraulics coupled codes is mandatory for best estimate evaluations of safety margins. This also applies to high-temperature gas cooled reactors (HTGR). Application of 3-D fine-mesh transient transport codes using few energy groups coupled with 3-D thermal hydraulics codes becomes feasible in view of increasing computing power. This paper describes the discrete ordinates based coupled code system TORT-TD/ATTICA3D that has recently been extended by a fine-mesh diffusion solver. Based on transient analyses for the PBMR-400 design, the transport/diffusion capabilities are demonstrated and 3-D local flux and power redistribution effects during a partial control rod withdrawal are shown. (authors)
3D reconstruction of SEM images by use of optical photogrammetry software.
Eulitz, Mona; Reiss, Gebhard
2015-08-01
Reconstruction of the three-dimensional (3D) surface of an object to be examined is widely used for structure analysis in science and many biological questions require information about their true 3D structure. For Scanning Electron Microscopy (SEM) there has been no efficient non-destructive solution for reconstruction of the surface morphology to date. The well-known method of recording stereo pair images generates a 3D stereoscope reconstruction of a section, but not of the complete sample surface. We present a simple and non-destructive method of 3D surface reconstruction from SEM samples based on the principles of optical close range photogrammetry. In optical close range photogrammetry a series of overlapping photos is used to generate a 3D model of the surface of an object. We adapted this method to the special SEM requirements. Instead of moving a detector around the object, the object itself was rotated. A series of overlapping photos was stitched and converted into a 3D model using the software commonly used for optical photogrammetry. A rabbit kidney glomerulus was used to demonstrate the workflow of this adaption. The reconstruction produced a realistic and high-resolution 3D mesh model of the glomerular surface. The study showed that SEM micrographs are suitable for 3D reconstruction by optical photogrammetry. This new approach is a simple and useful method of 3D surface reconstruction and suitable for various applications in research and teaching. PMID:26073969
Zawadzki, Robert J.; Zhang, Pengfei; Zam, Azhar; Miller, Eric B.; Goswami, Mayank; Wang, Xinlei; Jonnal, Ravi S.; Lee, Sang-Hyuck; Kim, Dae Yu; Flannery, John G.; Werner, John S.; Burns, Marie E.; Pugh, Edward N.
2015-01-01
Adaptive optics scanning laser ophthalmoscopy (AO-SLO) has recently been used to achieve exquisite subcellular resolution imaging of the mouse retina. Wavefront sensing-based AO typically restricts the field of view to a few degrees of visual angle. As a consequence the relationship between AO-SLO data and larger scale retinal structures and cellular patterns can be difficult to assess. The retinal vasculature affords a large-scale 3D map on which cells and structures can be located during in vivo imaging. Phase-variance OCT (pv-OCT) can efficiently image the vasculature with near-infrared light in a label-free manner, allowing 3D vascular reconstruction with high precision. We combined widefield pv-OCT and SLO imaging with AO-SLO reflection and fluorescence imaging to localize two types of fluorescent cells within the retinal layers: GFP-expressing microglia, the resident macrophages of the retina, and GFP-expressing cone photoreceptor cells. We describe in detail a reflective afocal AO-SLO retinal imaging system designed for high resolution retinal imaging in mice. The optical performance of this instrument is compared to other state-of-the-art AO-based mouse retinal imaging systems. The spatial and temporal resolution of the new AO instrumentation was characterized with angiography of retinal capillaries, including blood-flow velocity analysis. Depth-resolved AO-SLO fluorescent images of microglia and cone photoreceptors are visualized in parallel with 469 nm and 663 nm reflectance images of the microvasculature and other structures. Additional applications of the new instrumentation are discussed. PMID:26114038
Medical case-based retrieval: integrating query MeSH terms for query-adaptive multi-modal fusion
NASA Astrophysics Data System (ADS)
Seco de Herrera, Alba G.; Foncubierta-Rodríguez, Antonio; Müller, Henning
2015-03-01
Advances in medical knowledge give clinicians more objective information for a diagnosis. Therefore, there is an increasing need for bibliographic search engines that can provide services helping to facilitate faster information search. The ImageCLEFmed benchmark proposes a medical case-based retrieval task. This task aims at retrieving articles from the biomedical literature that are relevant for differential diagnosis of query cases including a textual description and several images. In the context of this campaign many approaches have been investigated showing that the fusion of visual and text information can improve the precision of the retrieval. However, fusion does not always lead to better results. In this paper, a new query-adaptive fusion criterion to decide when to use multi-modal (text and visual) or only text approaches is presented. The proposed method integrates text information contained in MeSH (Medical Subject Headings) terms extracted and visual features of the images to find synonym relations between them. Given a text query, the query-adaptive fusion criterion decides when it is suitable to also use visual information for the retrieval. Results show that this approach can decide if a text or multi{modal approach should be used with 77.15% of accuracy.
NASA Astrophysics Data System (ADS)
Huang, Rongzong; Wu, Huiying
2016-06-01
A total enthalpy-based lattice Boltzmann (LB) method with adaptive mesh refinement (AMR) is developed in this paper to efficiently simulate solid-liquid phase change problem where variables vary significantly near the phase interface and thus finer grid is required. For the total enthalpy-based LB method, the velocity field is solved by an incompressible LB model with multiple-relaxation-time (MRT) collision scheme, and the temperature field is solved by a total enthalpy-based MRT LB model with the phase interface effects considered and the deviation term eliminated. With a kinetic assumption that the density distribution function for solid phase is at equilibrium state, a volumetric LB scheme is proposed to accurately realize the nonslip velocity condition on the diffusive phase interface and in the solid phase. As compared with the previous schemes, this scheme can avoid nonphysical flow in the solid phase. As for the AMR approach, it is developed based on multiblock grids. An indicator function is introduced to control the adaptive generation of multiblock grids, which can guarantee the existence of overlap area between adjacent blocks for information exchange. Since MRT collision schemes are used, the information exchange is directly carried out in the moment space. Numerical tests are firstly performed to validate the strict satisfaction of the nonslip velocity condition, and then melting problems in a square cavity with different Prandtl numbers and Rayleigh numbers are simulated, which demonstrate that the present method can handle solid-liquid phase change problem with high efficiency and accuracy.
woptic: Optical conductivity with Wannier functions and adaptive k-mesh refinement
NASA Astrophysics Data System (ADS)
Assmann, E.; Wissgott, P.; Kuneš, J.; Toschi, A.; Blaha, P.; Held, K.
2016-05-01
We present an algorithm for the adaptive tetrahedral integration over the Brillouin zone of crystalline materials, and apply it to compute the optical conductivity, dc conductivity, and thermopower. For these quantities, whose contributions are often localized in small portions of the Brillouin zone, adaptive integration is especially relevant. Our implementation, the woptic package, is tied into the WIEN2WANNIER framework and allows including a local many-body self energy, e.g. from dynamical mean-field theory (DMFT). Wannier functions and dipole matrix elements are computed with the DFT package WIEN2k and Wannier90. For illustration, we show DFT results for fcc-Al and DMFT results for the correlated metal SrVO3.
A parallel second-order adaptive mesh algorithm for incompressible flow in porous media.
Pau, George S H; Almgren, Ann S; Bell, John B; Lijewski, Michael J
2009-11-28
In this paper, we present a second-order accurate adaptive algorithm for solving multi-phase, incompressible flow in porous media. We assume a multi-phase form of Darcy's law with relative permeabilities given as a function of the phase saturation. The remaining equations express conservation of mass for the fluid constituents. In this setting, the total velocity, defined to be the sum of the phase velocities, is divergence free. The basic integration method is based on a total-velocity splitting approach in which we solve a second-order elliptic pressure equation to obtain a total velocity. This total velocity is then used to recast component conservation equations as nonlinear hyperbolic equations. Our approach to adaptive refinement uses a nested hierarchy of logically rectangular grids with simultaneous refinement of the grids in both space and time. The integration algorithm on the grid hierarchy is a recursive procedure in which coarse grids are advanced in time, fine grids are advanced multiple steps to reach the same time as the coarse grids and the data at different levels are then synchronized. The single-grid algorithm is described briefly, but the emphasis here is on the time-stepping procedure for the adaptive hierarchy. Numerical examples are presented to demonstrate the algorithm's accuracy and convergence properties and to illustrate the behaviour of the method. PMID:19840985
A Parallel Second-Order Adaptive Mesh Algorithm for Incompressible Flow in Porous Media
Pau, George Shu Heng; Almgren, Ann S.; Bell, John B.; Lijewski, Michael J.
2008-04-01
In this paper we present a second-order accurate adaptive algorithm for solving multiphase, incompressible flows in porous media. We assume a multiphase form of Darcy's law with relative permeabilities given as a function of the phase saturation. The remaining equations express conservation of mass for the fluid constituents. In this setting the total velocity, defined to be the sum of the phase velocities, is divergence-free. The basic integration method is based on a total-velocity splitting approach in which we solve a second-order elliptic pressure equation to obtain a total velocity. This total velocity is then used to recast component conservation equations as nonlinear hyperbolic equations. Our approach to adaptive refinement uses a nested hierarchy of logically rectangular grids with simultaneous refinement of the grids in both space and time. The integration algorithm on the grid hierarchy is a recursive procedure in which coarse grids are advanced in time, fine grids areadvanced multiple steps to reach the same time as the coarse grids and the data atdifferent levels are then synchronized. The single grid algorithm is described briefly,but the emphasis here is on the time-stepping procedure for the adaptive hierarchy. Numerical examples are presented to demonstrate the algorithm's accuracy and convergence properties and to illustrate the behavior of the method.
TACO3D. 3-D Finite Element Heat Transfer Code
Mason, W.E.
1992-03-04
TACO3D is a three-dimensional, finite-element program for heat transfer analysis. An extension of the two-dimensional TACO program, it can perform linear and nonlinear analyses and can be used to solve either transient or steady-state problems. The program accepts time-dependent or temperature-dependent material properties, and materials may be isotropic or orthotropic. A variety of time-dependent and temperature-dependent boundary conditions and loadings are available including temperature, flux, convection, and radiation boundary conditions and internal heat generation. Additional specialized features treat enclosure radiation, bulk nodes, and master/slave internal surface conditions (e.g., contact resistance). Data input via a free-field format is provided. A user subprogram feature allows for any type of functional representation of any independent variable. A profile (bandwidth) minimization option is available. The code is limited to implicit time integration for transient solutions. TACO3D has no general mesh generation capability. Rows of evenly-spaced nodes and rows of sequential elements may be generated, but the program relies on separate mesh generators for complex zoning. TACO3D does not have the ability to calculate view factors internally. Graphical representation of data in the form of time history and spatial plots is provided through links to the POSTACO and GRAPE postprocessor codes.
3D Hydrodynamic Simulations of Relativistic Jets
NASA Astrophysics Data System (ADS)
Hughes, P. A.; Miller, M. A.; Duncan, G. C.; Swift, C. M.
1998-12-01
We present the results of validation runs and the first extragalactic jet simulations performed with a 3D relativistic numerical hydrodynamic code employing a solver of the RHLLE type and using adaptive mesh refinement (AMR; Duncan & Hughes, 1994, Ap. J., 436, L119). Test problems include the shock tube, blast wave and spherical shock reflection (implosion). Trials with the code show that as a consequence of AMR it is viable to perform exploratory runs on workstation class machines (with no more than 128Mb of memory) prior to production runs. In the former case we achieve a resolution not much less than that normally regarded as the minimum needed to capture the essential physics of a problem, which means that such runs can provide valuable guidance allowing the optimum use of supercomputer resources. We present initial results from a program to explore the 3D stability properties of flows previously studied using a 2D axisymmetric code, and our first attempt to explore the structure and morphology of a relativistic jet encountering an ambient density gradient that mimics an ambient inhomogeneity or cloud.
Beam Optics Analysis - An Advanced 3D Trajectory Code
Ives, R. Lawrence; Bui, Thuc; Vogler, William; Neilson, Jeff; Read, Mike; Shephard, Mark; Bauer, Andrew; Datta, Dibyendu; Beal, Mark
2006-01-03
Calabazas Creek Research, Inc. has completed initial development of an advanced, 3D program for modeling electron trajectories in electromagnetic fields. The code is being used to design complex guns and collectors. Beam Optics Analysis (BOA) is a fully relativistic, charged particle code using adaptive, finite element meshing. Geometrical input is imported from CAD programs generating ACIS-formatted files. Parametric data is inputted using an intuitive, graphical user interface (GUI), which also provides control of convergence, accuracy, and post processing. The program includes a magnetic field solver, and magnetic information can be imported from Maxwell 2D/3D and other programs. The program supports thermionic emission and injected beams. Secondary electron emission is also supported, including multiple generations. Work on field emission is in progress as well as implementation of computer optimization of both the geometry and operating parameters. The principle features of the program and its capabilities are presented.
Beam Optics Analysis — An Advanced 3D Trajectory Code
NASA Astrophysics Data System (ADS)
Ives, R. Lawrence; Bui, Thuc; Vogler, William; Neilson, Jeff; Read, Mike; Shephard, Mark; Bauer, Andrew; Datta, Dibyendu; Beal, Mark
2006-01-01
Calabazas Creek Research, Inc. has completed initial development of an advanced, 3D program for modeling electron trajectories in electromagnetic fields. The code is being used to design complex guns and collectors. Beam Optics Analysis (BOA) is a fully relativistic, charged particle code using adaptive, finite element meshing. Geometrical input is imported from CAD programs generating ACIS-formatted files. Parametric data is inputted using an intuitive, graphical user interface (GUI), which also provides control of convergence, accuracy, and post processing. The program includes a magnetic field solver, and magnetic information can be imported from Maxwell 2D/3D and other programs. The program supports thermionic emission and injected beams. Secondary electron emission is also supported, including multiple generations. Work on field emission is in progress as well as implementation of computer optimization of both the geometry and operating parameters. The principle features of the program and its capabilities are presented.
NASA Astrophysics Data System (ADS)
Power, C.; Read, J. I.; Hobbs, A.
2014-06-01
We simulate cosmological galaxy cluster formation using three different approaches to solving the equations of non-radiative hydrodynamics - classic smoothed particle hydrodynamics (SPH), novel SPH with a higher order dissipation switch (SPHS), and an adaptive mesh refinement (AMR) method. Comparing spherically averaged entropy profiles, we find that SPHS and AMR approaches result in a well-defined entropy core that converges rapidly with increasing mass and force resolution. In contrast, the central entropy profile in the SPH approach is sensitive to the cluster's assembly history and shows poor numerical convergence. We trace this disagreement to the known artificial surface tension in SPH that appears at phase boundaries. Varying systematically numerical dissipation in SPHS, we study the contributions of numerical and physical dissipation to the entropy core and argue that numerical dissipation is required to ensure single-valued fluid quantities in converging flows. However, provided it occurs only at the resolution limit and does not propagate errors to larger scales, its effect is benign - there is no requirement to build `sub-grid' models of unresolved turbulence for galaxy cluster simulations. We conclude that entropy cores in non-radiative galaxy cluster simulations are physical, resulting from entropy generation in shocked gas during cluster assembly.
NASA Astrophysics Data System (ADS)
Rasia, Elena; Lau, Erwin T.; Borgani, Stefano; Nagai, Daisuke; Dolag, Klaus; Avestruz, Camille; Granato, Gian Luigi; Mazzotta, Pasquale; Murante, Giuseppe; Nelson, Kaylea; Ragone-Figueroa, Cinthia
2014-08-01
Analyses of cosmological hydrodynamic simulations of galaxy clusters suggest that X-ray masses can be underestimated by 10%-30%. The largest bias originates from both violation of hydrostatic equilibrium (HE) and an additional temperature bias caused by inhomogeneities in the X-ray-emitting intracluster medium (ICM). To elucidate this large dispersion among theoretical predictions, we evaluate the degree of temperature structures in cluster sets simulated either with smoothed-particle hydrodynamics (SPH) or adaptive-mesh refinement (AMR) codes. We find that the SPH simulations produce larger temperature variations connected to the persistence of both substructures and their stripped cold gas. This difference is more evident in nonradiative simulations, whereas it is reduced in the presence of radiative cooling. We also find that the temperature variation in radiative cluster simulations is generally in agreement with that observed in the central regions of clusters. Around R 500 the temperature inhomogeneities of the SPH simulations can generate twice the typical HE mass bias of the AMR sample. We emphasize that a detailed understanding of the physical processes responsible for the complex thermal structure in ICM requires improved resolution and high-sensitivity observations in order to extend the analysis to higher temperature systems and larger cluster-centric radii.
Zhang, S.; Yuen, D.A.; Zhu, A.; Song, S.; George, D.L.
2011-01-01
We parallelized the GeoClaw code on one-level grid using OpenMP in March, 2011 to meet the urgent need of simulating tsunami waves at near-shore from Tohoku 2011 and achieved over 75% of the potential speed-up on an eight core Dell Precision T7500 workstation [1]. After submitting that work to SC11 - the International Conference for High Performance Computing, we obtained an unreleased OpenMP version of GeoClaw from David George, who developed the GeoClaw code as part of his PH.D thesis. In this paper, we will show the complementary characteristics of the two approaches used in parallelizing GeoClaw and the speed-up obtained by combining the advantage of each of the two individual approaches with adaptive mesh refinement (AMR), demonstrating the capabilities of running GeoClaw efficiently on many-core systems. We will also show a novel simulation of the Tohoku 2011 Tsunami waves inundating the Sendai airport and Fukushima Nuclear Power Plants, over which the finest grid distance of 20 meters is achieved through a 4-level AMR. This simulation yields quite good predictions about the wave-heights and travel time of the tsunami waves. ?? 2011 IEEE.
Rasia, Elena; Lau, Erwin T.; Nagai, Daisuke; Avestruz, Camille; Borgani, Stefano; Dolag, Klaus; Granato, Gian Luigi; Murante, Giuseppe; Ragone-Figueroa, Cinthia; Mazzotta, Pasquale; Nelson, Kaylea
2014-08-20
Analyses of cosmological hydrodynamic simulations of galaxy clusters suggest that X-ray masses can be underestimated by 10%-30%. The largest bias originates from both violation of hydrostatic equilibrium (HE) and an additional temperature bias caused by inhomogeneities in the X-ray-emitting intracluster medium (ICM). To elucidate this large dispersion among theoretical predictions, we evaluate the degree of temperature structures in cluster sets simulated either with smoothed-particle hydrodynamics (SPH) or adaptive-mesh refinement (AMR) codes. We find that the SPH simulations produce larger temperature variations connected to the persistence of both substructures and their stripped cold gas. This difference is more evident in nonradiative simulations, whereas it is reduced in the presence of radiative cooling. We also find that the temperature variation in radiative cluster simulations is generally in agreement with that observed in the central regions of clusters. Around R {sub 500} the temperature inhomogeneities of the SPH simulations can generate twice the typical HE mass bias of the AMR sample. We emphasize that a detailed understanding of the physical processes responsible for the complex thermal structure in ICM requires improved resolution and high-sensitivity observations in order to extend the analysis to higher temperature systems and larger cluster-centric radii.
Ly{alpha} RADIATIVE TRANSFER IN COSMOLOGICAL SIMULATIONS USING ADAPTIVE MESH REFINEMENT
Laursen, Peter; Razoumov, Alexei O.; Sommer-Larsen, Jesper E-mail: razoumov@ap.smu.ca
2009-05-01
A numerical code for solving various Ly{alpha} radiative transfer (RT) problems is presented. The code is suitable for an arbitrary, three-dimensional distribution of Ly{alpha} emissivity, gas temperature, density, and velocity field. Capable of handling Ly{alpha} RT in an adaptively refined grid-based structure, it enables detailed investigation of the effects of clumpiness of the interstellar (or intergalactic) medium. The code is tested against various geometrically and physically idealized configurations for which analytical solutions exist, and subsequently applied to three different simulated high-resolution 'Lyman-break galaxies', extracted from high-resolution cosmological simulations at redshift z = 3.6. Proper treatment of the Ly{alpha} scattering reveals a diversity of surface brightness (SB) and line profiles. Specifically, for a given galaxy the maximum observed SB can vary by an order of magnitude, and the total flux by a factor of 3-6, depending on the viewing angle. This may provide an explanation for differences in observed properties of high-redshift galaxies, and in particular a possible physical link between Lyman-break galaxies and regular Ly{alpha} emitters.
Freud, Erez; Ganel, Tzvi; Avidan, Galia
2015-11-15
fMRI adaptation (fMRIa), the attenuation of fMRI signal which follows repeated presentation of a stimulus, is a well-documented phenomenon. Yet, the underlying neural mechanisms supporting this effect are not fully understood. Recently, short-term perceptual expectations, induced by specific experimental settings, were shown to play an important modulating role in fMRIa. Here we examined the role of long-term expectations, based on 3D structural statistical regularities, in the modulation of fMRIa. To this end, human participants underwent fMRI scanning while performing a same-different task on pairs of possible (regular, expected) objects and spatially impossible (irregular, unexpected) objects. We hypothesized that given the spatial irregularity of impossible objects in relation to real-world visual experience, the visual system would always generate a prediction which is biased to the possible version of the objects. Consistently, fMRIa effects in the lateral occipital cortex (LOC) were found for possible, but not for impossible objects. Additionally, in alternating trials the order of stimulus presentation modulated LOC activity. That is, reduced activation was observed in trials in which the impossible version of the object served as the prime object (i.e. first object) and was followed by the possible version compared to the reverse order. These results were also supported by the behavioral advantage observed for trials that were primed by possible objects. Together, these findings strongly emphasize the importance of perceptual expectations in object representation and provide novel evidence for the role of real-world statistical regularities in eliciting fMRIa. PMID:26254586
Documentation for MeshKit - Reactor Geometry (&mesh) Generator
Jain, Rajeev; Mahadevan, Vijay
2015-09-30
This report gives documentation for using MeshKit’s Reactor Geometry (and mesh) Generator (RGG) GUI and also briefly documents other algorithms and tools available in MeshKit. RGG is a program designed to aid in modeling and meshing of complex/large hexagonal and rectilinear reactor cores. RGG uses Argonne’s SIGMA interfaces, Qt and VTK to produce an intuitive user interface. By integrating a 3D view of the reactor with the meshing tools and combining them into one user interface, RGG streamlines the task of preparing a simulation mesh and enables real-time feedback that reduces accidental scripting mistakes that could waste hours of meshing. RGG interfaces with MeshKit tools to consolidate the meshing process, meaning that going from model to mesh is as easy as a button click. This report is designed to explain RGG v 2.0 interface and provide users with the knowledge and skills to pilot RGG successfully. Brief documentation of MeshKit source code, tools and other algorithms available are also presented for developers to extend and add new algorithms to MeshKit. RGG tools work in serial and parallel and have been used to model complex reactor core models consisting of conical pins, load pads, several thousands of axially varying material properties of instrumentation pins and other interstices meshes.
PMESH: A parallel mesh generator
Hardin, D.D.
1994-10-21
The Parallel Mesh Generation (PMESH) Project is a joint LDRD effort by A Division and Engineering to develop a unique mesh generation system that can construct large calculational meshes (of up to 10{sup 9} elements) on massively parallel computers. Such a capability will remove a critical roadblock to unleashing the power of massively parallel processors (MPPs) for physical analysis. PMESH will support a variety of LLNL 3-D physics codes in the areas of electromagnetics, structural mechanics, thermal analysis, and hydrodynamics.
NASA Astrophysics Data System (ADS)
Pantano, C.; Deiterding, R.; Hill, D. J.; Pullin, D. I.
2006-09-01
This paper describes a hybrid finite-difference method for the large-eddy simulation of compressible flows with low-numerical dissipation and structured adaptive mesh refinement (SAMR). A conservative flux-based approach is described with an explicit centered scheme used in turbulent flow regions while a weighted essentially non-oscillatory (WENO) scheme is employed to capture shocks. Three-dimensional numerical simulations of a Richtmyer-Meshkov instability are presented.
NASA Astrophysics Data System (ADS)
Sarkis, C.; Silva, L.; Gandin, Ch-A.; Plapp, M.
2016-03-01
Dendritic growth is computed with automatic adaptation of an anisotropic and unstructured finite element mesh. The energy conservation equation is formulated for solid and liquid phases considering an interface balance that includes the Gibbs-Thomson effect. An equation for a diffuse interface is also developed by considering a phase field function with constant negative value in the liquid and constant positive value in the solid. Unknowns are the phase field function and a dimensionless temperature, as proposed by [1]. Linear finite element interpolation is used for both variables, and discretization stabilization techniques ensure convergence towards a correct non-oscillating solution. In order to perform quantitative computations of dendritic growth on a large domain, two additional numerical ingredients are necessary: automatic anisotropic unstructured adaptive meshing [2,[3] and parallel implementations [4], both made available with the numerical platform used (CimLib) based on C++ developments. Mesh adaptation is found to greatly reduce the number of degrees of freedom. Results of phase field simulations for dendritic solidification of a pure material in two and three dimensions are shown and compared with reference work [1]. Discussion on algorithm details and the CPU time will be outlined.
NASA Astrophysics Data System (ADS)
Skutnik, Steven E.; Davis, David R.
2016-05-01
The use of passive gamma and neutron signatures from fission indicators is a common means of estimating used fuel burnup, enrichment, and cooling time. However, while characteristic fission product signatures such as 134Cs, 137Cs, 154Eu, and others are generally reliable estimators for used fuel burnup within the context where the assembly initial enrichment and the discharge time are known, in the absence of initial enrichment and/or cooling time information (such as when applying NDA measurements in a safeguards/verification context), these fission product indicators no longer yield a unique solution for assembly enrichment, burnup, and cooling time after discharge. Through the use of a new Mesh-Adaptive Direct Search (MADS) algorithm, it is possible to directly probe the shape of this "degeneracy space" characteristic of individual nuclides (and combinations thereof), both as a function of constrained parameters (such as the assembly irradiation history) and unconstrained parameters (e.g., the cooling time before measurement and the measurement precision for particular indicator nuclides). In doing so, this affords the identification of potential means of narrowing the uncertainty space of potential assembly enrichment, burnup, and cooling time combinations, thereby bounding estimates of assembly plutonium content. In particular, combinations of gamma-emitting nuclides with distinct half-lives (e.g., 134Cs with 137Cs and 154Eu) in conjunction with gross neutron counting (via 244Cm) are able to reasonably constrain the degeneracy space of possible solutions to a space small enough to perform useful discrimination and verification of fuel assemblies based on their irradiation history.
Moving Overlapping Grids with Adaptive Mesh Refinement for High-Speed Reactive and Non-reactive Flow
Henshaw, W D; Schwendeman, D W
2005-08-30
We consider the solution of the reactive and non-reactive Euler equations on two-dimensional domains that evolve in time. The domains are discretized using moving overlapping grids. In a typical grid construction, boundary-fitted grids are used to represent moving boundaries, and these grids overlap with stationary background Cartesian grids. Block-structured adaptive mesh refinement (AMR) is used to resolve fine-scale features in the flow such as shocks and detonations. Refinement grids are added to base-level grids according to an estimate of the error, and these refinement grids move with their corresponding base-level grids. The numerical approximation of the governing equations takes place in the parameter space of each component grid which is defined by a mapping from (fixed) parameter space to (moving) physical space. The mapped equations are solved numerically using a second-order extension of Godunov's method. The stiff source term in the reactive case is handled using a Runge-Kutta error-control scheme. We consider cases when the boundaries move according to a prescribed function of time and when the boundaries of embedded bodies move according to the surface stress exerted by the fluid. In the latter case, the Newton-Euler equations describe the motion of the center of mass of the each body and the rotation about it, and these equations are integrated numerically using a second-order predictor-corrector scheme. Numerical boundary conditions at slip walls are described, and numerical results are presented for both reactive and non-reactive flows in order to demonstrate the use and accuracy of the numerical approach.
NASA Astrophysics Data System (ADS)
Pletinckx, D.
2011-09-01
The current 3D hype creates a lot of interest in 3D. People go to 3D movies, but are we ready to use 3D in our homes, in our offices, in our communication? Are we ready to deliver real 3D to a general public and use interactive 3D in a meaningful way to enjoy, learn, communicate? The CARARE project is realising this for the moment in the domain of monuments and archaeology, so that real 3D of archaeological sites and European monuments will be available to the general public by 2012. There are several aspects to this endeavour. First of all is the technical aspect of flawlessly delivering 3D content over all platforms and operating systems, without installing software. We have currently a working solution in PDF, but HTML5 will probably be the future. Secondly, there is still little knowledge on how to create 3D learning objects, 3D tourist information or 3D scholarly communication. We are still in a prototype phase when it comes to integrate 3D objects in physical or virtual museums. Nevertheless, Europeana has a tremendous potential as a multi-facetted virtual museum. Finally, 3D has a large potential to act as a hub of information, linking to related 2D imagery, texts, video, sound. We describe how to create such rich, explorable 3D objects that can be used intuitively by the generic Europeana user and what metadata is needed to support the semantic linking.
An Improved Version of TOPAZ 3D
Krasnykh, Anatoly
2003-07-29
An improved version of the TOPAZ 3D gun code is presented as a powerful tool for beam optics simulation. In contrast to the previous version of TOPAZ 3D, the geometry of the device under test is introduced into TOPAZ 3D directly from a CAD program, such as Solid Edge or AutoCAD. In order to have this new feature, an interface was developed, using the GiD software package as a meshing code. The article describes this method with two models to illustrate the results.
PLOT3D/AMES, APOLLO UNIX VERSION USING GMR3D (WITH TURB3D)
NASA Technical Reports Server (NTRS)
Buning, P.
1994-01-01
PLOT3D is an interactive graphics program designed to help scientists visualize computational fluid dynamics (CFD) grids and solutions. Today, supercomputers and CFD algorithms can provide scientists with simulations of such highly complex phenomena that obtaining an understanding of the simulations has become a major problem. Tools which help the scientist visualize the simulations can be of tremendous aid. PLOT3D/AMES offers more functions and features, and has been adapted for more types of computers than any other CFD graphics program. Version 3.6b+ is supported for five computers and graphic libraries. Using PLOT3D, CFD physicists can view their computational models from any angle, observing the physics of problems and the quality of solutions. As an aid in designing aircraft, for example, PLOT3D's interactive computer graphics can show vortices, temperature, reverse flow, pressure, and dozens of other characteristics of air flow during flight. As critical areas become obvious, they can easily be studied more closely using a finer grid. PLOT3D is part of a computational fluid dynamics software cycle. First, a program such as 3DGRAPE (ARC-12620) helps the scientist generate computational grids to model an object and its surrounding space. Once the grids have been designed and parameters such as the angle of attack, Mach number, and Reynolds number have been specified, a "flow-solver" program such as INS3D (ARC-11794 or COS-10019) solves the system of equations governing fluid flow, usually on a supercomputer. Grids sometimes have as many as two million points, and the "flow-solver" produces a solution file which contains density, x- y- and z-momentum, and stagnation energy for each grid point. With such a solution file and a grid file containing up to 50 grids as input, PLOT3D can calculate and graphically display any one of 74 functions, including shock waves, surface pressure, velocity vectors, and particle traces. PLOT3D's 74 functions are organized into
PLOT3D/AMES, APOLLO UNIX VERSION USING GMR3D (WITHOUT TURB3D)
NASA Technical Reports Server (NTRS)
Buning, P.
1994-01-01
PLOT3D is an interactive graphics program designed to help scientists visualize computational fluid dynamics (CFD) grids and solutions. Today, supercomputers and CFD algorithms can provide scientists with simulations of such highly complex phenomena that obtaining an understanding of the simulations has become a major problem. Tools which help the scientist visualize the simulations can be of tremendous aid. PLOT3D/AMES offers more functions and features, and has been adapted for more types of computers than any other CFD graphics program. Version 3.6b+ is supported for five computers and graphic libraries. Using PLOT3D, CFD physicists can view their computational models from any angle, observing the physics of problems and the quality of solutions. As an aid in designing aircraft, for example, PLOT3D's interactive computer graphics can show vortices, temperature, reverse flow, pressure, and dozens of other characteristics of air flow during flight. As critical areas become obvious, they can easily be studied more closely using a finer grid. PLOT3D is part of a computational fluid dynamics software cycle. First, a program such as 3DGRAPE (ARC-12620) helps the scientist generate computational grids to model an object and its surrounding space. Once the grids have been designed and parameters such as the angle of attack, Mach number, and Reynolds number have been specified, a "flow-solver" program such as INS3D (ARC-11794 or COS-10019) solves the system of equations governing fluid flow, usually on a supercomputer. Grids sometimes have as many as two million points, and the "flow-solver" produces a solution file which contains density, x- y- and z-momentum, and stagnation energy for each grid point. With such a solution file and a grid file containing up to 50 grids as input, PLOT3D can calculate and graphically display any one of 74 functions, including shock waves, surface pressure, velocity vectors, and particle traces. PLOT3D's 74 functions are organized into
Robust, multidimensional mesh motion based on Monge-Kantorovich equidistribution
Delzanno, G L; Finn, J M
2009-01-01
Mesh-motion (r-refinement) grid adaptivity schemes are attractive due to their potential to minimize the numerical error for a prescribed number of degrees of freedom. However, a key roadblock to a widespread deployment of the technique has been the formulation of robust, reliable mesh motion governing principles, which (1) guarantee a solution in multiple dimensions (2D and 3D), (2) avoid grid tangling (or folding of the mesh, whereby edges of a grid cell cross somewhere in the domain), and (3) can be solved effectively and efficiently. In this study, we formulate such a mesh-motion governing principle, based on volume equidistribution via Monge-Kantorovich optimization (MK). In earlier publications [1, 2], the advantages of this approach in regards to these points have been demonstrated for the time-independent case. In this study, demonstrate that Monge-Kantorovich equidistribution can in fact be used effectively in a time stepping context, and delivers an elegant solution to the otherwise pervasive problem of grid tangling in mesh motion approaches, without resorting to ad-hoc time-dependent terms (as in moving-mesh PDEs, or MMPDEs [3, 4]). We explore two distinct r-refinement implementations of MK: direct, where the current mesh relates to an initial, unchanging mesh, and sequential, where the current mesh is related to the previous one in time. We demonstrate that the direct approach is superior in regards to mesh distortion and robustness. The properties of the approach are illustrated with a paradigmatic hyperbolic PDE, the advection of a passive scalar. Imposed velocity flow fields or varying vorticity levels and flow shears are considered.
NASA Technical Reports Server (NTRS)
Wood, William A., III
2002-01-01
A multi-dimensional upwind fluctuation splitting scheme is developed and implemented for two-dimensional and axisymmetric formulations of the Navier-Stokes equations on unstructured meshes. Key features of the scheme are the compact stencil, full upwinding, and non-linear discretization which allow for second-order accuracy with enforced positivity. Throughout, the fluctuation splitting scheme is compared to a current state-of-the-art finite volume approach, a second-order, dual mesh upwind flux difference splitting scheme (DMFDSFV), and is shown to produce more accurate results using fewer computer resources for a wide range of test cases. A Blasius flat plate viscous validation case reveals a more accurate upsilon-velocity profile for fluctuation splitting, and the reduced artificial dissipation production is shown relative to DMFDSFV. Remarkably, the fluctuation splitting scheme shows grid converged skin friction coefficients with only five points in the boundary layer for this case. The second half of the report develops a local, compact, anisotropic unstructured mesh adaptation scheme in conjunction with the multi-dimensional upwind solver, exhibiting a characteristic alignment behavior for scalar problems. The adaptation strategy is extended to the two-dimensional and axisymmetric Navier-Stokes equations of motion through the concept of fluctuation minimization.
3d-3d correspondence revisited
NASA Astrophysics Data System (ADS)
Chung, Hee-Joong; Dimofte, Tudor; Gukov, Sergei; Sułkowski, Piotr
2016-04-01
In fivebrane compactifications on 3-manifolds, we point out the importance of all flat connections in the proper definition of the effective 3d {N}=2 theory. The Lagrangians of some theories with the desired properties can be constructed with the help of homological knot invariants that categorify colored Jones polynomials. Higgsing the full 3d theories constructed this way recovers theories found previously by Dimofte-Gaiotto-Gukov. We also consider the cutting and gluing of 3-manifolds along smooth boundaries and the role played by all flat connections in this operation.
THE GENERATION OF TETRAHEDRAL MESH MODELS FOR NEUROANATOMICAL MRI
Lederman, Carl; Joshi, Anand; Dinov, Ivo; Vese, Luminita; Toga, Arthur; Van Horn, John Darrell
2010-01-01
In this article, we describe a detailed method for automatically generating tetrahedral meshes from 3D images having multiple region labels. An adaptively sized tetrahedral mesh modeling approach is described that is capable of producing meshes conforming precisely to the voxelized regions in the image. Efficient tetrahedral construction is performed minimizing an energy function containing three terms: a smoothing term to remove the voxelization, a fidelity term to maintain continuity with the image data, and a novel elasticity term to prevent the tetrahedra from becoming flattened or inverted as the mesh deforms while allowing the voxelization to be removed entirely. The meshing algorithm is applied to structural MR image data that has been automatically segmented into 56 neuroanatomical sub-divisions as well as on two other examples. The resulting tetrahedral representation has several desirable properties such as tetrahedra with dihedral angles away from 0 and 180 degrees, smoothness, and a high resolution. Tetrahedral modeling via the approach described here has applications in modeling brain structure in normal as well as diseased brain in human and non-human data and facilitates examination of 3D object deformations resulting from neurological illness (e.g. Alzheimer’s Disease), development, and/or aging. PMID:21073968
Koch, M.
1995-12-31
A new mesh-adaptive 1D collocation technique has been developed to efficiently solve transient advection-dominated transport problems in porous media that are governed by a hyperbolic/parabolic (singularly perturbed) PDE. After spatial discretization a singularly perturbed ODE is obtained which is solved by a modification of the COLNEW ODE-collocation code. The latter also contains an adaptive mesh procedure that has been enhanced here to resolve linear and nonlinear transport flow problems with steep fronts where regular FD and FE methods often fail. An implicit first-order backward Euler and a third-order Taylor-Donea technique are employed for the time integration. Numerical simulations on a variety of high Peclet-number transport phenomena as they occur in realistic porous media flow situations are presented. Examples include classical linear advection-diffusion, nonlinear adsorption, two-phase Buckley-Leverett flow without and with capillary forces (Rapoport-Leas equation) and Burgers` equation for inviscid fluid flow. In most of these examples sharp fronts and/or shocks develop which are resolved in an oscillation-free manner by the present adaptive collocation method. The backward Euler method has some amount of numerical dissipation is observed when the time-steps are too large. The third-order Taylor-Donea technique is less dissipative but is more prone to numerical oscillations. The simulations show that for the efficient solution of nonlinear singularly perturbed PDE`s governing flow transport a careful balance must be struck between the optimal mesh adaptation, the nonlinear iteration method and the time-stepping procedure. More theoretical research is needed with this regard.
NASA Astrophysics Data System (ADS)
Gill, Stuart P. D.; Knebe, Alexander; Gibson, Brad K.; Flynn, Chris; Ibata, Rodrigo A.; Lewis, Geraint F.
2003-04-01
An adaptive multi grid approach to simulating the formation of structure from collisionless dark matter is described. MLAPM (Multi-Level Adaptive Particle Mesh) is one of the most efficient serial codes available on the cosmological "market" today. As part of Swinburne University's role in the development of the Square Kilometer Array, we are implementing hydrodynamics, feedback, and radiative transfer within the MLAPM adaptive mesh, in order to simulate baryonic processes relevant to the interstellar and intergalactic media at high redshift. We will outline our progress to date in applying the existing MLAPM to a study of the decay of satellite galaxies within massive host potentials.
YouDash3D: exploring stereoscopic 3D gaming for 3D movie theaters
NASA Astrophysics Data System (ADS)
Schild, Jonas; Seele, Sven; Masuch, Maic
2012-03-01
Along with the success of the digitally revived stereoscopic cinema, events beyond 3D movies become attractive for movie theater operators, i.e. interactive 3D games. In this paper, we present a case that explores possible challenges and solutions for interactive 3D games to be played by a movie theater audience. We analyze the setting and showcase current issues related to lighting and interaction. Our second focus is to provide gameplay mechanics that make special use of stereoscopy, especially depth-based game design. Based on these results, we present YouDash3D, a game prototype that explores public stereoscopic gameplay in a reduced kiosk setup. It features live 3D HD video stream of a professional stereo camera rig rendered in a real-time game scene. We use the effect to place the stereoscopic effigies of players into the digital game. The game showcases how stereoscopic vision can provide for a novel depth-based game mechanic. Projected trigger zones and distributed clusters of the audience video allow for easy adaptation to larger audiences and 3D movie theater gaming.
ATHENA 3D: A finite element code for ultrasonic wave propagation
NASA Astrophysics Data System (ADS)
Rose, C.; Rupin, F.; Fouquet, T.; Chassignole, B.
2014-04-01
The understanding of wave propagation phenomena requires use of robust numerical models. 3D finite element (FE) models are generally prohibitively time consuming. However, advances in computing processor speed and memory allow them to be more and more competitive. In this context, EDF R&D developed the 3D version of the well-validated FE code ATHENA2D. The code is dedicated to the simulation of wave propagation in all kinds of elastic media and in particular, heterogeneous and anisotropic materials like welds. It is based on solving elastodynamic equations in the calculation zone expressed in terms of stress and particle velocities. The particularity of the code relies on the fact that the discretization of the calculation domain uses a Cartesian regular 3D mesh while the defect of complex geometry can be described using a separate (2D) mesh using the fictitious domains method. This allows combining the rapidity of regular meshes computation with the capability of modelling arbitrary shaped defects. Furthermore, the calculation domain is discretized with a quasi-explicit time evolution scheme. Thereby only local linear systems of small size have to be solved. The final step to reduce the computation time relies on the fact that ATHENA3D has been parallelized and adapted to the use of HPC resources. In this paper, the validation of the 3D FE model is discussed. A cross-validation of ATHENA 3D and CIVA is proposed for several inspection configurations. The performances in terms of calculation time are also presented in the cases of both local computer and computation cluster use.
Design, Implementation and Applications of 3d Web-Services in DB4GEO
NASA Astrophysics Data System (ADS)
Breunig, M.; Kuper, P. V.; Dittrich, A.; Wild, P.; Butwilowski, E.; Al-Doori, M.
2013-09-01
The object-oriented database architecture DB4GeO was originally designed to support sub-surface applications in the geo-sciences. This is reflected in DB4GeO's geometric data model as well as in its import and export functions. Initially, these functions were designed for communication with 3D geological modeling and visualization tools such as GOCAD or MeshLab. However, it soon became clear that DB4GeO was suitable for a much wider range of applications. Therefore it is natural to move away from a standalone solution and to open the access to DB4GeO data by standardized OGC web-services. Though REST and OGC services seem incompatible at first sight, the implementation in DB4GeO shows that OGC-based implementation of web-services may use parts of the DB4GeO-REST implementation. Starting with initial solutions in the history of DB4GeO, this paper will introduce the design, adaptation (i.e. model transformation), and first steps in the implementation of OGC Web Feature (WFS) and Web Processing Services (WPS), as new interfaces to DB4GeO data and operations. Among its capabilities, DB4GeO can provide data in different data formats like GML, GOCAD, or DB3D XML through a WFS, as well as its ability to run operations like a 3D-to-2D service, or mesh-simplification (Progressive Meshes) through a WPS. We then demonstrate, an Android-based mobile 3D augmented reality viewer for DB4GeO that uses the Web Feature Service to visualize 3D geo-database query results. Finally, we explore future research work considering DB4GeO in the framework of the research group "Computer-Aided Collaborative Subway Track Planning in Multi-Scale 3D City and Building Models".
NASA Astrophysics Data System (ADS)
Meulien Ohlmann, Odile
2013-02-01
Today the industry offers a chain of 3D products. Learning to "read" and to "create in 3D" becomes an issue of education of primary importance. 25 years professional experience in France, the United States and Germany, Odile Meulien set up a personal method of initiation to 3D creation that entails the spatial/temporal experience of the holographic visual. She will present some different tools and techniques used for this learning, their advantages and disadvantages, programs and issues of educational policies, constraints and expectations related to the development of new techniques for 3D imaging. Although the creation of display holograms is very much reduced compared to the creation of the 90ies, the holographic concept is spreading in all scientific, social, and artistic activities of our present time. She will also raise many questions: What means 3D? Is it communication? Is it perception? How the seeing and none seeing is interferes? What else has to be taken in consideration to communicate in 3D? How to handle the non visible relations of moving objects with subjects? Does this transform our model of exchange with others? What kind of interaction this has with our everyday life? Then come more practical questions: How to learn creating 3D visualization, to learn 3D grammar, 3D language, 3D thinking? What for? At what level? In which matter? for whom?