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.
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.
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.
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
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.
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 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.
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
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).
Strategies for hp-adaptive Refinement
Mitchell, William F.
2008-09-01
In the hp-adaptive version of the finite element method for solving partial differential equations, the grid is adaptively refined in both h, the size of the elements, and p, the degree of the piecewise polynomial approximation over the element. The selection of which elements to refine is determined by a local a posteriori error indicator, and is well established. But the determination of whether the element should be refined by h or p is still open. In this paper, we describe several strategies that have been proposed for making this determination. A numerical example to illustrate the effectiveness of these strategies will be presented.
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.
Arbitrary Lagrangian Eulerian Adaptive Mesh Refinement
Energy Science and Technology Software Center (ESTSC)
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
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.
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.
Adaptive refinement tools for tetrahedral unstructured grids
NASA Technical Reports Server (NTRS)
Pao, S. Paul (Inventor); Abdol-Hamid, Khaled S. (Inventor)
2011-01-01
An exemplary embodiment providing one or more improvements includes software which is robust, efficient, and has a very fast run time for user directed grid enrichment and flow solution adaptive grid refinement. All user selectable options (e.g., the choice of functions, the choice of thresholds, etc.), other than a pre-marked cell list, can be entered on the command line. The ease of application is an asset for flow physics research and preliminary design CFD analysis where fast grid modification is often needed to deal with unanticipated development of flow details.
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.
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.
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.
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.
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.
Adaptive h -refinement for reduced-order models: ADAPTIVE h -refinement for reduced-order models
Carlberg, Kevin T.
2014-11-05
Our work presents a method to adaptively refine reduced-order models a posteriori without requiring additional full-order-model solves. The technique is analogous to mesh-adaptive h-refinement: it enriches the reduced-basis space online by ‘splitting’ a given basis vector into several vectors with disjoint support. The splitting scheme is defined by a tree structure constructed offline via recursive k-means clustering of the state variables using snapshot data. This method identifies the vectors to split online using a dual-weighted-residual approach that aims to reduce error in an output quantity of interest. The resulting method generates a hierarchy of subspaces online without requiring large-scale operationsmore » or full-order-model solves. Furthermore, it enables the reduced-order model to satisfy any prescribed error tolerance regardless of its original fidelity, as a completely refined reduced-order model is mathematically equivalent to the original full-order model. Experiments on a parameterized inviscid Burgers equation highlight the ability of the method to capture phenomena (e.g., moving shocks) not contained in the span of the original reduced basis.« less
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.
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.
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.
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.
Structured Adaptive Mesh Refinement Application Infrastructure
Energy Science and Technology Software Center (ESTSC)
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 particle refinement and derefinement applied to the smoothed particle hydrodynamics method
NASA Astrophysics Data System (ADS)
Barcarolo, D. A.; Le Touzé, D.; Oger, G.; de Vuyst, F.
2014-09-01
SPH simulations are usually performed with a uniform particle distribution. New techniques have been recently proposed to enable the use of spatially varying particle distributions, which encouraged the development of automatic adaptivity and particle refinement/derefinement algorithms. All these efforts resulted in very interesting and promising procedures leading to more efficient and faster SPH simulations. In this article, a family of particle refinement techniques is reviewed and a new derefinement technique is proposed and validated through several test cases involving both free-surface and viscous flows. Besides, this new procedure allows higher resolutions in the regions requiring increased accuracy. Moreover, several levels of refinement can be used with this new technique, as often encountered in adaptive mesh refinement techniques in mesh-based methods.
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.
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.
Effects of adaptive refinement on the inverse EEG solution
NASA Astrophysics Data System (ADS)
Weinstein, David M.; Johnson, Christopher R.; Schmidt, John A.
1995-10-01
One of the fundamental problems in electroencephalography can be characterized by an inverse problem. Given a subset of electrostatic potentials measured on the surface of the scalp and the geometry and conductivity properties within the head, calculate the current vectors and potential fields within the cerebrum. Mathematically the generalized EEG problem can be stated as solving Poisson's equation of electrical conduction for the primary current sources. The resulting problem is mathematically ill-posed i.e., the solution does not depend continuously on the data, such that small errors in the measurement of the voltages on the scalp can yield unbounded errors in the solution, and, for the general treatment of a solution of Poisson's equation, the solution is non-unique. However, if accurate solutions the general treatment of a solution of Poisson's equation, the solution is non-unique. However, if accurate solutions to such problems could be obtained, neurologists would gain noninvasive accesss to patient-specific cortical activity. Access to such data would ultimately increase the number of patients who could be effectively treated for pathological cortical conditions such as temporal lobe epilepsy. In this paper, we present the effects of spatial adaptive refinement on the inverse EEG problem and show that the use of adaptive methods allow for significantly better estimates of electric and potential fileds within the brain through an inverse procedure. To test these methods, we have constructed several finite element head models from magneteic resonance images of a patient. The finite element meshes ranged in size from 2724 nodes and 12,812 elements to 5224 nodes and 29,135 tetrahedral elements, depending on the level of discretization. We show that an adaptive meshing algorithm minimizes the error in the forward problem due to spatial discretization and thus increases the accuracy of the inverse solution.
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.
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.
Procedures and computer programs for telescopic mesh refinement using MODFLOW
Leake, Stanley A.; Claar, David V.
1999-01-01
Ground-water models are commonly used to evaluate flow systems in areas that are small relative to entire aquifer systems. In many of these analyses, simulation of the entire flow system is not desirable or will not allow sufficient detail in the area of interest. The procedure of telescopic mesh refinement allows use of a small, detailed model in the area of interest by taking boundary conditions from a larger model that encompasses the model in the area of interest. Some previous studies have used telescopic mesh refinement; however, better procedures are needed in carrying out telescopic mesh refinement using the U.S. Geological Survey ground-water flow model, referred to as MODFLOW. This report presents general procedures and three computer programs for use in telescopic mesh refinement with MODFLOW. The first computer program, MODTMR, constructs MODFLOW data sets for a local or embedded model using MODFLOW data sets and simulation results from a regional or encompassing model. The second computer program, TMRDIFF, provides a means of comparing head or drawdown in the local model with head or drawdown in the corresponding area of the regional model. The third program, RIVGRID, provides a means of constructing data sets for the River Package, Drain Package, General-Head Boundary Package, and Stream Package for regional and local models using grid-independent data specifying locations of these features. RIVGRID may be needed in some applications of telescopic mesh refinement because regional-model data sets do not contain enough information on locations of head-dependent flow features to properly locate the features in local models. The program is a general utility program that can be used in constructing data sets for head-dependent flow packages for any MODFLOW model under construction.
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.
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
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.
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.
Fast transport simulation with an adaptive grid refinement.
Haefner, Frieder; Boy, Siegrun
2003-01-01
One of the main difficulties in transport modeling and calibration is the extraordinarily long computing times necessary for simulation runs. Improved execution time is a prerequisite for calibration in transport modeling. In this paper we investigate the problem of code acceleration using an adaptive grid refinement, neglecting subdomains, and devising a method by which the Courant condition can be ignored while maintaining accurate solutions. Grid refinement is based on dividing selected cells into regular subcells and including the balance equations of subcells in the equation system. The connection of coarse and refined cells satisfies the mass balance with an interpolation scheme that is implicitly included in the equation system. The refined subdomain can move with the average transport velocity of the subdomain. Very small time steps are required on a fine or a refined grid, because of the combined effect of the Courant and Peclet conditions. Therefore, we have developed a special upwind technique in small grid cells with high velocities (velocity suppression). We have neglected grid subdomains with very small concentration gradients (zero suppression). The resulting software, MODCALIF, is a three-dimensional, modularly constructed FORTRAN code. For convenience, the package names used by the well-known MODFLOW and MT3D computer programs are adopted, and the same input file structure and format is used, but the program presented here is separate and independent. Also, MODCALIF includes algorithms for variable density modeling and model calibration. The method is tested by comparison with an analytical solution, and illustrated by means of a two-dimensional theoretical example and three-dimensional simulations of the variable-density Cape Cod and SALTPOOL experiments. Crossing from fine to coarse grid produces numerical dispersion when the whole subdomain of interest is refined; however, we show that accurate solutions can be obtained using a fraction of the
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)
Fully Threaded Tree for Adaptive Refinement Fluid Dynamics Simulations
NASA Technical Reports Server (NTRS)
Khokhlov, A. M.
1997-01-01
A fully threaded tree (FTT) for adaptive refinement of regular meshes is described. By using a tree threaded at all levels, tree traversals for finding nearest neighbors are avoided. All operations on a tree including tree modifications are O(N), where N is a number of cells, and are performed in parallel. An efficient implementation of the tree is described that requires 2N words of memory. A filtering algorithm for removing high frequency noise during mesh refinement is described. A FTT can be used in various numerical applications. In this paper, it is applied to the integration of the Euler equations of fluid dynamics. An adaptive mesh time stepping algorithm is described in which different time steps are used at different l evels of the tree. Time stepping and mesh refinement are interleaved to avoid extensive buffer layers of fine mesh which were otherwise required ahead of moving shocks. Test examples are presented, and the FTT performance is evaluated. The three dimensional simulation of the interaction of a shock wave and a spherical bubble is carried out that shows the development of azimuthal perturbations on the bubble surface.
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.
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.
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.
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.
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.
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.
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.
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.
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].
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.
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
Tsunami modelling with adaptively refined finite volume methods
LeVeque, R.J.; George, D.L.; Berger, M.J.
2011-01-01
Numerical modelling of transoceanic tsunami propagation, together with the detailed modelling of inundation of small-scale coastal regions, poses a number of algorithmic challenges. The depth-averaged shallow water equations can be used to reduce this to a time-dependent problem in two space dimensions, but even so it is crucial to use adaptive mesh refinement in order to efficiently handle the vast differences in spatial scales. This must be done in a 'wellbalanced' manner that accurately captures very small perturbations to the steady state of the ocean at rest. Inundation can be modelled by allowing cells to dynamically change from dry to wet, but this must also be done carefully near refinement boundaries. We discuss these issues in the context of Riemann-solver-based finite volume methods for tsunami modelling. Several examples are presented using the GeoClaw software, and sample codes are available to accompany the paper. The techniques discussed also apply to a variety of other geophysical flows. ?? 2011 Cambridge University Press.
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.
NASA Astrophysics Data System (ADS)
D'Amato, Anthony M.
Input reconstruction is the process of using the output of a system to estimate its input. In some cases, input reconstruction can be accomplished by determining the output of the inverse of a model of the system whose input is the output of the original system. Inversion, however, requires an exact and fully known analytical model, and is limited by instabilities arising from nonminimum-phase zeros. The main contribution of this work is a novel technique for input reconstruction that does not require model inversion. This technique is based on a retrospective cost, which requires a limited number of Markov parameters. Retrospective cost input reconstruction (RCIR) does not require knowledge of nonminimum-phase zero locations or an analytical model of the system. RCIR provides a technique that can be used for model refinement, state estimation, and adaptive control. In the model refinement application, data are used to refine or improve a model of a system. It is assumed that the difference between the model output and the data is due to an unmodeled subsystem whose interconnection with the modeled system is inaccessible, that is, the interconnection signals cannot be measured and thus standard system identification techniques cannot be used. Using input reconstruction, these inaccessible signals can be estimated, and the inaccessible subsystem can be fitted. We demonstrate input reconstruction in a model refinement framework by identifying unknown physics in a space weather model and by estimating an unknown film growth in a lithium ion battery. The same technique can be used to obtain estimates of states that cannot be directly measured. Adaptive control can be formulated as a model-refinement problem, where the unknown subsystem is the idealized controller that minimizes a measured performance variable. Minimal modeling input reconstruction for adaptive control is useful for applications where modeling information may be difficult to obtain. We demonstrate
Cosmos++: Relativistic Magnetohydrodynamics on Unstructured Grids with Local Adaptive Refinement
Anninos, P; Fragile, P C; Salmonson, J D
2005-05-06
A new code and methodology are introduced for solving the fully general relativistic magnetohydrodynamic (GRMHD) equations using time-explicit, finite-volume discretization. The code has options for solving the GRMHD equations using traditional artificial-viscosity (AV) or non-oscillatory central difference (NOCD) methods, or a new extended AV (eAV) scheme using artificial-viscosity together with a dual energy-flux-conserving formulation. The dual energy approach allows for accurate modeling of highly relativistic flows at boost factors well beyond what has been achieved to date by standard artificial viscosity methods. it provides the benefit of Godunov methods in capturing high Lorentz boosted flows but without complicated Riemann solvers, and the advantages of traditional artificial viscosity methods in their speed and flexibility. Additionally, the GRMHD equations are solved on an unstructured grid that supports local adaptive mesh refinement using a fully threated oct-tree (in three dimensions) network to traverse the grid hierarchy across levels and immediate neighbors. A number of tests are presented to demonstrate robustness of the numerical algorithms and adaptive mesh framework over a wide spectrum of problems, boosts, and astrophysical applications, including relativistic shock tubes, shock collisions, magnetosonic shocks, Alfven wave propagation, blast waves, magnetized Bondi flow, and the magneto-rotational instability in Kerr black hole spacetimes.
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.
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
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.
The Stratified Ocean Model with Adaptive Refinement (SOMAR)
NASA Astrophysics Data System (ADS)
Santilli, Edward; Scotti, Alberto
2015-06-01
A computational framework for the evolution of non-hydrostatic, baroclinic flows encountered in regional and coastal ocean simulations is presented, which combines the flexibility of Adaptive Mesh Refinement (AMR) with a suite of numerical tools specifically developed to deal with the high degree of anisotropy of oceanic flows and their attendant numerical challenges. This framework introduces a semi-implicit update of the terms that give rise to buoyancy oscillations, which permits a stable integration of the Navier-Stokes equations when a background density stratification is present. The lepticity of each grid in the AMR hierarchy, which serves as a useful metric for anisotropy, is used to select one of several different efficient Poisson-solving techniques. In this way, we compute the pressure over the entire set of AMR grids without resorting to the hydrostatic approximation, which can degrade the structure of internal waves whose dynamics may have large-scale significance. We apply the modeling framework to three test cases, for which numerical or analytical solutions are known that can be used to benchmark the results. In all the cases considered, the model achieves an excellent degree of congruence with the benchmark, while at the same time achieving a substantial reduction of the computational resources needed.
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.
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
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.
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.
Refining Procedures: A Needs Analysis Project at Kuwait University.
ERIC Educational Resources Information Center
Basturkmen, Helen
1998-01-01
Outlines the procedures followed in the needs analysis (NA) project carried out in 1996 at the College of Petroleum and Engineering at Kuwait University. Focuses on the steps taken in the project and the rationale behind them. Offers an illustration of an NA project and to show the procedural steps involved. (Author/VWL)
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.
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.
JPEG 2000 coding of image data over adaptive refinement grids
NASA Astrophysics Data System (ADS)
Gamito, Manuel N.; Dias, Miguel S.
2003-06-01
An extension of the JPEG 2000 standard is presented for non-conventional images resulting from an adaptive subdivision process. Samples, generated through adaptive subdivision, can have different sizes, depending on the amount of subdivision that was locally introduced in each region of the image. The subdivision principle allows each individual sample to be recursively subdivided into sets of four progressively smaller samples. Image datasets generated through adaptive subdivision find application in Computational Physics where simulations of natural processes are often performed over adaptive grids. It is also found that compression gains can be achieved for non-natural imagery, like text or graphics, if they first undergo an adaptive subdivision process. The representation of adaptive subdivision images is performed by first coding the subdivision structure into the JPEG 2000 bitstream, ina lossless manner, followed by the entropy coded and quantized transform coefficients. Due to the irregular distribution of sample sizes across the image, the wavelet transform must be applied on irregular image subsets that are nested across all the resolution levels. Using the conventional JPEG 2000 coding standard, adaptive subdivision images would first have to be upsampled to the smallest sample size in order to attain a uniform resolution. The proposed method for coding adaptive subdivision images is shown to perform better than conventional JPEG 2000 for medium to high bitrates.
Adaptive resolution refinement for high-fidelity continuum parameterizations
Anderson, J.W.; Khamayseh, A.; Jean, B.A.
1996-10-01
This paper describes an algorithm the adaptively samples a parametric continuum so that a fidelity metric is satisfied. Using the divide-and-conquer strategy of adaptive sampling eliminates the guesswork of traditional uniform parameterization techniques. The space and time complexity of parameterization are increased in a controllable manner so that a desired fidelity is obtained.
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.
Toward Objectivity in Diagnosing Learning Disabilities: Refinement of Established Procedures.
ERIC Educational Resources Information Center
Goodman, Marvin; Mina, Elias
Variability in diagnostic procedures and a lack of valid and reliable measures led to the development of a comprehensive battery, which incorporated an operational definition of learning disabilities. The battery consisted of forms for observing these functions: intelligence, academic achievement, gross and fine motor control, visual perception,…
F-8C adaptive control law refinement and software development
NASA Technical Reports Server (NTRS)
Hartmann, G. L.; Stein, G.
1981-01-01
An explicit adaptive control algorithm based on maximum likelihood estimation of parameters was designed. To avoid iterative calculations, the algorithm uses parallel channels of Kalman filters operating at fixed locations in parameter space. This algorithm was implemented in NASA/DFRC's Remotely Augmented Vehicle (RAV) facility. Real-time sensor outputs (rate gyro, accelerometer, surface position) are telemetered to a ground computer which sends new gain values to an on-board system. Ground test data and flight records were used to establish design values of noise statistics and to verify the ground-based adaptive software.
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.
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
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.
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.
Adaptive h -refinement for reduced-order models: ADAPTIVE h -refinement for reduced-order models
Carlberg, Kevin T.
2014-11-05
Our work presents a method to adaptively refine reduced-order models a posteriori without requiring additional full-order-model solves. The technique is analogous to mesh-adaptive h-refinement: it enriches the reduced-basis space online by ‘splitting’ a given basis vector into several vectors with disjoint support. The splitting scheme is defined by a tree structure constructed offline via recursive k-means clustering of the state variables using snapshot data. This method identifies the vectors to split online using a dual-weighted-residual approach that aims to reduce error in an output quantity of interest. The resulting method generates a hierarchy of subspaces online without requiring large-scale operations or full-order-model solves. Furthermore, it enables the reduced-order model to satisfy any prescribed error tolerance regardless of its original fidelity, as a completely refined reduced-order model is mathematically equivalent to the original full-order model. Experiments on a parameterized inviscid Burgers equation highlight the ability of the method to capture phenomena (e.g., moving shocks) not contained in the span of the original reduced basis.
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.
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.
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.
40 CFR 80.133 - Agreed-upon procedures for refiners and importers.
Code of Federal Regulations, 2011 CFR
2011-07-01
... 40 Protection of Environment 16 2011-07-01 2011-07-01 false Agreed-upon procedures for refiners and importers. 80.133 Section 80.133 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) AIR PROGRAMS (CONTINUED) REGULATION OF FUELS AND FUEL ADDITIVES Attest Engagements §...
40 CFR 80.133 - Agreed-upon procedures for refiners and importers.
Code of Federal Regulations, 2013 CFR
2013-07-01
... 40 Protection of Environment 17 2013-07-01 2013-07-01 false Agreed-upon procedures for refiners and importers. 80.133 Section 80.133 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) AIR PROGRAMS (CONTINUED) REGULATION OF FUELS AND FUEL ADDITIVES Attest Engagements §...
40 CFR 80.133 - Agreed-upon procedures for refiners and importers.
Code of Federal Regulations, 2012 CFR
2012-07-01
... 40 Protection of Environment 17 2012-07-01 2012-07-01 false Agreed-upon procedures for refiners and importers. 80.133 Section 80.133 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) AIR PROGRAMS (CONTINUED) REGULATION OF FUELS AND FUEL ADDITIVES Attest Engagements §...
Refining the Measurement of Axis II: A Q-sort Procedure for Assessing Personality Pathology.
ERIC Educational Resources Information Center
Shedler, Jonathan; Westen, Drew
1998-01-01
Results from a study involving 153 clinicians who used the new Shedler-Westen Assessment Procedure (a Q-sort approach) and eight patient interviews suggest the usefulness of the SWAP to measure personality disorders and refine categories and criteria according to Axis II of the "Diagnostic and Statistical Manual of Mental Disorders" (American…
An Efficient Means of Adaptive Refinement Within Systems of Overset Grids
NASA Technical Reports Server (NTRS)
Meakin, Robert L.
1996-01-01
An efficient means of adaptive refinement within systems of overset grids is presented. Problem domains are segregated into near-body and off-body fields. Near-body fields are discretized via overlapping body-fitted grids that extend only a short distance from body surfaces. Off-body fields are discretized via systems of overlapping uniform Cartesian grids of varying levels of refinement. a novel off-body grid generation and management scheme provides the mechanism for carrying out adaptive refinement of off-body flow dynamics and solid body motion. The scheme allows for very efficient use of memory resources, and flow solvers and domain connectivity routines that can exploit the structure inherent to uniform Cartesian grids.
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
Adaptively Refined Euler and Navier-Stokes Solutions with a Cartesian-Cell Based Scheme
NASA Technical Reports Server (NTRS)
Coirier, William J.; Powell, Kenneth G.
1995-01-01
A Cartesian-cell based scheme with adaptive mesh refinement for solving the Euler and Navier-Stokes equations in two dimensions has been developed and tested. Grids about geometrically complicated bodies were generated automatically, by recursive subdivision of a single Cartesian cell encompassing the entire flow domain. Where the resulting cells intersect bodies, N-sided 'cut' cells were created using polygon-clipping algorithms. The grid was stored in a binary-tree data structure which provided a natural means of obtaining cell-to-cell connectivity and of carrying out solution-adaptive mesh refinement. The Euler and Navier-Stokes equations were solved on the resulting grids using an upwind, finite-volume formulation. The inviscid fluxes were found in an upwinded manner using a linear reconstruction of the cell primitives, providing the input states to an approximate Riemann solver. The viscous fluxes were formed using a Green-Gauss type of reconstruction upon a co-volume surrounding the cell interface. Data at the vertices of this co-volume were found in a linearly K-exact manner, which ensured linear K-exactness of the gradients. Adaptively-refined solutions for the inviscid flow about a four-element airfoil (test case 3) were compared to theory. Laminar, adaptively-refined solutions were compared to accepted computational, experimental and theoretical results.
AN OPTIMAL ADAPTIVE LOCAL GRID REFINEMENT APPROACH TO MODELING CONTAMINANT TRANSPORT
A Lagrangian-Eulerian method with an optimal adaptive local grid refinement is used to model contaminant transport equations. pplication of this approach to two bench-mark problems indicates that it completely resolves difficulties of peak clipping, numerical diffusion, and spuri...
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.
NASA Technical Reports Server (NTRS)
Brislawn, Kristi D.; Brown, David L.; Chesshire, Geoffrey S.; Saltzman, Jeffrey S.
1995-01-01
Adaptive mesh refinement (AMR) in conjunction with higher-order upwind finite-difference methods have been used effectively on a variety of problems in two and three dimensions. In this paper we introduce an approach for resolving problems that involve complex geometries in which resolution of boundary geometry is important. The complex geometry is represented by using the method of overlapping grids, while local resolution is obtained by refining each component grid with the AMR algorithm, appropriately generalized for this situation. The CMPGRD algorithm introduced by Chesshire and Henshaw is used to automatically generate the overlapping grid structure for the underlying mesh.
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
COMET-AR User's Manual: COmputational MEchanics Testbed with Adaptive Refinement
NASA Technical Reports Server (NTRS)
Moas, E. (Editor)
1997-01-01
The COMET-AR User's Manual provides a reference manual for the Computational Structural Mechanics Testbed with Adaptive Refinement (COMET-AR), a software system developed jointly by Lockheed Palo Alto Research Laboratory and NASA Langley Research Center under contract NAS1-18444. The COMET-AR system is an extended version of an earlier finite element based structural analysis system called COMET, also developed by Lockheed and NASA. The primary extensions are the adaptive mesh refinement capabilities and a new "object-like" database interface that makes COMET-AR easier to extend further. This User's Manual provides a detailed description of the user interface to COMET-AR from the viewpoint of a structural analyst.
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
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.
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.
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.
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.
Adaptive Distributed Environment for Procedure Training (ADEPT)
NASA Technical Reports Server (NTRS)
Domeshek, Eric; Ong, James; Mohammed, John
2013-01-01
ADEPT (Adaptive Distributed Environment for Procedure Training) is designed to provide more effective, flexible, and portable training for NASA systems controllers. When creating a training scenario, an exercise author can specify a representative rationale structure using the graphical user interface, annotating the results with instructional texts where needed. The author's structure may distinguish between essential and optional parts of the rationale, and may also include "red herrings" - hypotheses that are essential to consider, until evidence and reasoning allow them to be ruled out. The system is built from pre-existing components, including Stottler Henke's SimVentive? instructional simulation authoring tool and runtime. To that, a capability was added to author and exploit explicit control decision rationale representations. ADEPT uses SimVentive's Scalable Vector Graphics (SVG)- based interactive graphic display capability as the basis of the tool for quickly noting aspects of decision rationale in graph form. The ADEPT prototype is built in Java, and will run on any computer using Windows, MacOS, or Linux. No special peripheral equipment is required. The software enables a style of student/ tutor interaction focused on the reasoning behind systems control behavior that better mimics proven Socratic human tutoring behaviors for highly cognitive skills. It supports fast, easy, and convenient authoring of such tutoring behaviors, allowing specification of detailed scenario-specific, but content-sensitive, high-quality tutor hints and feedback. The system places relatively light data-entry demands on the student to enable its rationale-centered discussions, and provides a support mechanism for fostering coherence in the student/ tutor dialog by including focusing, sequencing, and utterance tuning mechanisms intended to better fit tutor hints and feedback into the ongoing context.
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.
Interactive solution-adaptive grid generation procedure
NASA Technical Reports Server (NTRS)
Henderson, Todd L.; Choo, Yung K.; Lee, Ki D.
1992-01-01
TURBO-AD is an interactive solution adaptive grid generation program under development. The program combines an interactive algebraic grid generation technique and a solution adaptive grid generation technique into a single interactive package. The control point form uses a sparse collection of control points to algebraically generate a field grid. This technique provides local grid control capability and is well suited to interactive work due to its speed and efficiency. A mapping from the physical domain to a parametric domain was used to improve difficulties encountered near outwardly concave boundaries in the control point technique. Therefore, all grid modifications are performed on the unit square in the parametric domain, and the new adapted grid is then mapped back to the physical domain. The grid adaption is achieved by adapting the control points to a numerical solution in the parametric domain using control sources obtained from the flow properties. Then a new modified grid is generated from the adapted control net. This process is efficient because the number of control points is much less than the number of grid points and the generation of the grid is an efficient algebraic process. TURBO-AD provides the user with both local and global controls.
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.
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
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.
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.
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.
NASA Astrophysics Data System (ADS)
Rosenberg, Duane; Fournier, Aimé; Fischer, Paul; Pouquet, Annick
2006-06-01
An object-oriented geophysical and astrophysical spectral-element adaptive refinement (GASpAR) code is introduced. Like most spectral-element codes, GASpAR combines finite-element efficiency with spectral-method accuracy. It is also designed to be flexible enough for a range of geophysics and astrophysics applications where turbulence or other complex multiscale problems arise. The formalism accommodates both conforming and non-conforming elements. Several aspects of this code derive from existing methods, but here are synthesized into a new formulation of dynamic adaptive refinement (DARe) of non-conforming h-type. As a demonstration of the code, several new 2D test cases are introduced that have time-dependent analytic solutions and exhibit localized flow features, including the 2D Burgers equation with straight, curved-radial and oblique-colliding fronts. These are proposed as standard test problems for comparable DARe codes. Quantitative errors are reported for 2D spatial and temporal convergence of DARe.
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.
MGGHAT: Elliptic PDE software with adaptive refinement, multigrid and high order finite elements
NASA Technical Reports Server (NTRS)
Mitchell, William F.
1993-01-01
MGGHAT (MultiGrid Galerkin Hierarchical Adaptive Triangles) is a program for the solution of linear second order elliptic partial differential equations in two dimensional polygonal domains. This program is now available for public use. It is a finite element method with linear, quadratic or cubic elements over triangles. The adaptive refinement via newest vertex bisection and the multigrid iteration are both based on a hierarchical basis formulation. Visualization is available at run time through an X Window display, and a posteriori through output files that can be used as GNUPLOT input. In this paper, we describe the methods used by MGGHAT, define the problem domain for which it is appropriate, illustrate use of the program, show numerical and graphical examples, and explain how to obtain the software.
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.
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 Technical Reports Server (NTRS)
Aftosmis, M. J.; Berger, M. J.; Adomavicius, G.
2000-01-01
Preliminary verification and validation of an efficient Euler solver for adaptively refined Cartesian meshes with embedded boundaries is presented. The parallel, multilevel method makes use of a new on-the-fly parallel domain decomposition strategy based upon the use of space-filling curves, and automatically generates a sequence of coarse meshes for processing by the multigrid smoother. The coarse mesh generation algorithm produces grids which completely cover the computational domain at every level in the mesh hierarchy. A series of examples on realistically complex three-dimensional configurations demonstrate that this new coarsening algorithm reliably achieves mesh coarsening ratios in excess of 7 on adaptively refined meshes. Numerical investigations of the scheme's local truncation error demonstrate an achieved order of accuracy between 1.82 and 1.88. Convergence results for the multigrid scheme are presented for both subsonic and transonic test cases and demonstrate W-cycle multigrid convergence rates between 0.84 and 0.94. Preliminary parallel scalability tests on both simple wing and complex complete aircraft geometries shows a computational speedup of 52 on 64 processors using the run-time mesh partitioner.
Pascucci, V
2004-02-18
This paper presents a simple approach for rendering isosurfaces of a scalar field. Using the vertex programming capability of commodity graphics cards, we transfer the cost of computing an isosurface from the Central Processing Unit (CPU), running the main application, to the Graphics Processing Unit (GPU), rendering the images. We consider a tetrahedral decomposition of the domain and draw one quadrangle (quad) primitive per tetrahedron. A vertex program transforms the quad into the piece of isosurface within the tetrahedron (see Figure 2). In this way, the main application is only devoted to streaming the vertices of the tetrahedra from main memory to the graphics card. For adaptively refined rectilinear grids, the optimization of this streaming process leads to the definition of a new 3D space-filling curve, which generalizes the 2D Sierpinski curve used for efficient rendering of triangulated terrains. We maintain the simplicity of the scheme when constructing view-dependent adaptive refinements of the domain mesh. In particular, we guarantee the absence of T-junctions by satisfying local bounds in our nested error basis. The expensive stage of fixing cracks in the mesh is completely avoided. We discuss practical tradeoffs in the distribution of the workload between the application and the graphics hardware. With current GPU's it is convenient to perform certain computations on the main CPU. Beyond the performance considerations that will change with the new generations of GPU's this approach has the major advantage of avoiding completely the storage in memory of the isosurface vertices and triangles.
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.
Axisymmetric modeling of cometary mass loading on an adaptively refined grid: MHD results
NASA Technical Reports Server (NTRS)
Gombosi, Tamas I.; Powell, Kenneth G.; De Zeeuw, Darren L.
1994-01-01
The first results of an axisymmetric magnetohydrodynamic (MHD) model of the interaction of an expanding cometary atmosphere with the solar wind are presented. The model assumes that far upstream the plasma flow lines are parallel to the magnetic field vector. The effects of mass loading and ion-neutral friction are taken into account by the governing equations, whcih are solved on an adaptively refined unstructured grid using a Monotone Upstream Centered Schemes for Conservative Laws (MUSCL)-type numerical technique. The combination of the adaptive refinement with the MUSCL-scheme allows the entire cometary atmosphere to be modeled, while still resolving both the shock and the near nucleus of the comet. The main findingsare the following: (1) A shock is formed approximately = 0.45 Mkm upstream of the comet (its location is controlled by the sonic and Alfvenic Mach numbers of the ambient solar wind flow and by the cometary mass addition rate). (2) A contact surface is formed approximately = 5,600 km upstream of the nucleus separating an outward expanding cometary ionosphere from the nearly stagnating solar wind flow. The location of the contact surface is controlled by the upstream flow conditions, the mass loading rate and the ion-neutral drag. The contact surface is also the boundary of the diamagnetic cavity. (3) A closed inner shock terminates the supersonic expansion of the cometary ionosphere. This inner shock is closer to the nucleus on dayside than on the nightside.
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.
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.
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.
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.
A new procedure for dynamic adaption of three-dimensional unstructured grids
NASA Technical Reports Server (NTRS)
Biswas, Rupak; Strawn, Roger
1993-01-01
A new procedure is presented for the simultaneous coarsening and refinement of three-dimensional unstructured tetrahedral meshes. This algorithm allows for localized grid adaption that is used to capture aerodynamic flow features such as vortices and shock waves in helicopter flowfield simulations. The mesh-adaption algorithm is implemented in the C programming language and uses a data structure consisting of a series of dynamically-allocated linked lists. These lists allow the mesh connectivity to be rapidly reconstructed when individual mesh points are added and/or deleted. The algorithm allows the mesh to change in an anisotropic manner in order to efficiently resolve directional flow features. The procedure has been successfully implemented on a single processor of a Cray Y-MP computer. Two sample cases are presented involving three-dimensional transonic flow. Computed results show good agreement with conventional structured-grid solutions for the Euler equations.
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.
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.
The GeoClaw software for depth-averaged flows with adaptive refinement
NASA Astrophysics Data System (ADS)
Berger, Marsha J.; George, David L.; LeVeque, Randall J.; Mandli, Kyle T.
2011-09-01
Many geophysical flow or wave propagation problems can be modeled with two-dimensional depth-averaged equations, of which the shallow water equations are the simplest example. We describe the GeoClaw software that has been designed to solve problems of this nature, consisting of open source Fortran programs together with Python tools for the user interface and flow visualization. This software uses high-resolution shock-capturing finite volume methods on logically rectangular grids, including latitude-longitude grids on the sphere. Dry states are handled automatically to model inundation. The code incorporates adaptive mesh refinement to allow the efficient solution of large-scale geophysical problems. Examples are given illustrating its use for modeling tsunamis and dam-break flooding problems. Documentation and download information is available at www.clawpack.org/geoclaw.
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.
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.
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.
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.
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.
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.
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.
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
An Upgrading Procedure for Adaptive Assessment of Knowledge.
Anselmi, Pasquale; Robusto, Egidio; Stefanutti, Luca; de Chiusole, Debora
2016-06-01
In knowledge space theory, existing adaptive assessment procedures can only be applied when suitable estimates of their parameters are available. In this paper, an iterative procedure is proposed, which upgrades its parameters with the increasing number of assessments. The first assessments are run using parameter values that favor accuracy over efficiency. Subsequent assessments are run using new parameter values estimated on the incomplete response patterns from previous assessments. Parameter estimation is carried out through a new probabilistic model for missing-at-random data. Two simulation studies show that, with the increasing number of assessments, the performance of the proposed procedure approaches that of gold standards. PMID:27071952
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.
2014-01-01
Background Developing suitable methods for the identification of protein complexes remains an active research area. It is important since it allows better understanding of cellular functions as well as malfunctions and it consequently leads to producing more effective cures for diseases. In this context, various computational approaches were introduced to complement high-throughput experimental methods which typically involve large datasets, are expensive in terms of time and cost, and are usually subject to spurious interactions. Results In this paper, we propose ProRank+, a method which detects protein complexes in protein interaction networks. The presented approach is mainly based on a ranking algorithm which sorts proteins according to their importance in the interaction network, and a merging procedure which refines the detected complexes in terms of their protein members. ProRank + was compared to several state-of-the-art approaches in order to show its effectiveness. It was able to detect more protein complexes with higher quality scores. Conclusions The experimental results achieved by ProRank + show its ability to detect protein complexes in protein interaction networks. Eventually, the method could potentially identify previously-undiscovered protein complexes. The datasets and source codes are freely available for academic purposes at http://faculty.uaeu.ac.ae/nzaki/Research.htm. PMID:24944073
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
NASA Technical Reports Server (NTRS)
Coirier, William John
1994-01-01
A Cartesian, cell-based scheme for solving the Euler and Navier-Stokes equations in two dimensions is developed and tested. Grids about geometrically complicated bodies are generated automatically, by recursive subdivision of a single Cartesian cell encompassing the entire flow domain. Where the resulting cells intersect bodies, polygonal 'cut' cells are created. The geometry of the cut cells is computed using polygon-clipping algorithms. The grid is stored in a binary-tree data structure which provides a natural means of obtaining cell-to-cell connectivity and of carrying out solution-adaptive refinement. The Euler and Navier-Stokes equations are solved on the resulting grids using a finite-volume formulation. The convective terms are upwinded, with a limited linear reconstruction of the primitive variables used to provide input states to an approximate Riemann solver for computing the fluxes between neighboring cells. A multi-stage time-stepping scheme is used to reach a steady-state solution. Validation of the Euler solver with benchmark numerical and exact solutions is presented. An assessment of the accuracy of the approach is made by uniform and adaptive grid refinements for a steady, transonic, exact solution to the Euler equations. The error of the approach is directly compared to a structured solver formulation. A non smooth flow is also assessed for grid convergence, comparing uniform and adaptively refined results. Several formulations of the viscous terms are assessed analytically, both for accuracy and positivity. The two best formulations are used to compute adaptively refined solutions of the Navier-Stokes equations. These solutions are compared to each other, to experimental results and/or theory for a series of low and moderate Reynolds numbers flow fields. The most suitable viscous discretization is demonstrated for geometrically-complicated internal flows. For flows at high Reynolds numbers, both an altered grid-generation procedure and a
40 CFR 80.128 - Alternative agreed upon procedures for refiners and importers.
Code of Federal Regulations, 2010 CFR
2010-07-01
... inventory reconciliation analysis for the current year from the refiner or importer which includes... mathematical accuracy of the calculations contained in the analysis. (2) Agree the beginning and ending... imported. Obtain refiner's or importer's internal lab analysis for each batch and agree the consistency...
NASA Astrophysics Data System (ADS)
Hahn, Oliver; Angulo, Raul E.
2016-01-01
N-body simulations are essential for understanding the formation and evolution of structure in the Universe. However, the discrete nature of these simulations affects their accuracy when modelling collisionless systems. We introduce a new approach to simulate the gravitational evolution of cold collisionless fluids by solving the Vlasov-Poisson equations in terms of adaptively refineable `Lagrangian phase-space elements'. These geometrical elements are piecewise smooth maps between Lagrangian space and Eulerian phase-space and approximate the continuum structure of the distribution function. They allow for dynamical adaptive splitting to accurately follow the evolution even in regions of very strong mixing. We discuss in detail various one-, two- and three-dimensional test problems to demonstrate the performance of our method. Its advantages compared to N-body algorithms are: (i) explicit tracking of the fine-grained distribution function, (ii) natural representation of caustics, (iii) intrinsically smooth gravitational potential fields, thus (iv) eliminating the need for any type of ad hoc force softening. We show the potential of our method by simulating structure formation in a warm dark matter scenario. We discuss how spurious collisionality and large-scale discreteness noise of N-body methods are both strongly suppressed, which eliminates the artificial fragmentation of filaments. Therefore, we argue that our new approach improves on the N-body method when simulating self-gravitating cold and collisionless fluids, and is the first method that allows us to explicitly follow the fine-grained evolution in six-dimensional phase-space.
Effect of cooling procedure on final denture base adaptation.
Ganzarolli, S M; Rached, R N; Garcia, R C M R; Del Bel Cury, A A
2002-08-01
Well-fitted dentures prevent hyperplasic lesions, provide chewing efficiency and promote patient's comfort. Several factors may affect final adaptation of dentures, as the type of the acrylic resin, the flask cooling procedure and the water uptake. This investigation evaluated the effect of water storage and two different cooling procedures [bench cooling (BC) for 2 h; running water (RW) at 20 degrees C for 45 min] on the final adaptation of denture bases. A heat-cured acrylic resin (CL, Clássico, Clássico Artigos Odontológicos) and two microwave-cured acrylic resins [Acron MC, (AC) GC Dent. Ind. Corp.; Onda Cryl (OC), Clássico Artigos Odontológicos] were used to make the bases. Adaptation was assessed by measuring the weight of an intervening layer of silicone impression material between the base and the master die. Data was submitted to ANOVA and Tukey's test (0.05). The following means were found: (BC) CL=0.72 +/- 0.03 a; AC=0.70 +/- 0.03 b; OC=0.76 +/- 0.04 c//(RW) CL= 1.00 +/- 0.11 a; AC=1.00 +/- 0.12 a; OC=0.95 +/- 0.10 a. Different labels join groups that are not statistically different (P > 0.05). Comparisons are made among groups submitted to the same cooling procedure (BC or RW). The conclusions are: interaction of type of material and cooling procedure had a statistically significant effect on the final adaptation of the denture bases (P < 0.05); water storage was not detected as a source of variance (P > 0.05) on the final adaptation. PMID:12220348
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.
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.
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.
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.
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.
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.
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.
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
DMM assessments of attachment and adaptation: Procedures, validity and utility.
Farnfield, Steve; Hautamäki, Airi; Nørbech, Peder; Sahhar, Nicola
2010-07-01
This article gives a brief over view of the Dynamic-Maturational Model of attachment and adaptation (DMM; Crittenden, 2008) together with the various DMM assessments of attachment that have been developed for specific stages of development. Each assessment is discussed in terms of procedure, outcomes, validity, advantages and limitations, comparable procedures and areas for further research and validation. The aims are twofold: to provide an introduction to DMM theory and its application that underlie the articles in this issue of CCPP; and to provide researchers and clinicians with a guide to DMM assessments. PMID:20603420
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.
A novel hyperbolic grid generation procedure with inherent adaptive dissipation
Tai, C.H.; Yin, S.L.; Soong, C.Y.
1995-01-01
This paper reports a novel hyperbolic grid-generation with an inherent adaptive dissipation (HGAD), which is capable of improving the oscillation and overlapping of grid lines. In the present work upwinding differencing is applied to discretize the hyperbolic system and, thereby, to develop the adaptive dissipation coefficient. Complex configurations with the features of geometric discontinuity, exceptional concavity and convexity are used as the test cases for comparison of the present HGAD procedure with the conventional hyerbolic and elliptic ones. The results reveal that the HGAD method is superior in orthogonality and smoothness of the grid system. In addition, the computational efficiency of the flow solver may be improved by using the present HGAD procedure. 15 refs., 8 figs.
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
40 CFR 80.133 - Agreed-upon procedures for refiners and importers.
Code of Federal Regulations, 2014 CFR
2014-07-01
... (CONTINUED) AIR PROGRAMS (CONTINUED) REGULATION OF FUELS AND FUEL ADDITIVES Attest Engagements § 80.133..., obtain the refinery-specific volume and property information that was used by the refiner to prepare...
Initiating technical refinements in high-level golfers: Evidence for contradictory procedures.
Carson, Howie J; Collins, Dave; Richards, Jim
2016-06-01
When developing motor skills there are several outcomes available to an athlete depending on their skill status and needs. Whereas the skill acquisition and performance literature is abundant, an under-researched outcome relates to the refinement of already acquired and well-established skills. Contrary to current recommendations for athletes to employ an external focus of attention and a representative practice design, Carson and Collins' (2011) [Refining and regaining skills in fixation/diversification stage performers: The Five-A Model. International Review of Sport and Exercise Psychology, 4, 146-167. doi: 10.1080/1750984x.2011.613682 ] Five-A Model requires an initial narrowed internal focus on the technical aspect needing refinement: the implication being that environments which limit external sources of information would be beneficial to achieving this task. Therefore, the purpose of this paper was to (1) provide a literature-based explanation for why techniques counter to current recommendations may be (temporarily) appropriate within the skill refinement process and (2) provide empirical evidence for such efficacy. Kinematic data and self-perception reports are provided from high-level golfers attempting to consciously initiate technical refinements while executing shots onto a driving range and into a close proximity net (i.e. with limited knowledge of results). It was hypothesised that greater control over intended refinements would occur when environmental stimuli were reduced in the most unrepresentative practice condition (i.e. hitting into a net). Results confirmed this, as evidenced by reduced intra-individual movement variability for all participants' individual refinements, despite little or no difference in mental effort reported. This research offers coaches guidance when working with performers who may find conscious recall difficult during the skill refinement process. PMID:26428876
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.
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.
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.
Guzik, S; McCorquodale, P; Colella, P
2011-12-16
A fourth-order accurate finite-volume method is presented for solving time-dependent hyperbolic systems of conservation laws on mapped grids that are adaptively refined in space and time. Novel considerations for formulating the semi-discrete system of equations in computational space combined with detailed mechanisms for accommodating the adapting grids ensure that conservation is maintained and that the divergence of a constant vector field is always zero (freestream-preservation property). Advancement in time is achieved with a fourth-order Runge-Kutta method.
NASA Technical Reports Server (NTRS)
Coirier, William J.; Powell, Kenneth G.
1994-01-01
A Cartesian, cell-based approach for adaptively-refined solutions of the Euler and Navier-Stokes equations in two dimensions is developed and tested. Grids about geometrically complicated bodies are generated automatically, by recursive subdivision of a single Cartesian cell encompassing the entire flow domain. Where the resulting cells intersect bodies, N-sided 'cut' cells are created using polygon-clipping algorithms. The grid is stored in a binary-tree structure which provides a natural means of obtaining cell-to-cell connectivity and of carrying out solution-adaptive mesh refinement. The Euler and Navier-Stokes equations are solved on the resulting grids using a finite-volume formulation. The convective terms are upwinded: a gradient-limited, linear reconstruction of the primitive variables is performed, providing input states to an approximate Riemann solver for computing the fluxes between neighboring cells. The more robust of a series of viscous flux functions is used to provide the viscous fluxes at the cell interfaces. Adaptively-refined solutions of the Navier-Stokes equations using the Cartesian, cell-based approach are obtained and compared to theory, experiment, and other accepted computational results for a series of low and moderate Reynolds number flows.
NASA Technical Reports Server (NTRS)
Coirier, William J.; Powell, Kenneth G.
1995-01-01
A Cartesian, cell-based approach for adaptively-refined solutions of the Euler and Navier-Stokes equations in two dimensions is developed and tested. Grids about geometrically complicated bodies are generated automatically, by recursive subdivision of a single Cartesian cell encompassing the entire flow domain. Where the resulting cells intersect bodies, N-sided 'cut' cells are created using polygon-clipping algorithms. The grid is stored in a binary-tree data structure which provides a natural means of obtaining cell-to-cell connectivity and of carrying out solution-adaptive mesh refinement. The Euler and Navier-Stokes equations are solved on the resulting grids using a finite-volume formulation. The convective terms are upwinded: A gradient-limited, linear reconstruction of the primitive variables is performed, providing input states to an approximate Riemann solver for computing the fluxes between neighboring cells. The more robust of a series of viscous flux functions is used to provide the viscous fluxes at the cell interfaces. Adaptively-refined solutions of the Navier-Stokes equations using the Cartesian, cell-based approach are obtained and compared to theory, experiment and other accepted computational results for a series of low and moderate Reynolds number flows.
Gutowski, William J.; Prusa, Joseph M.; Smolarkiewicz, Piotr K.
2012-05-08
This project had goals of advancing the performance capabilities of the numerical general circulation model EULAG and using it to produce a fully operational atmospheric global climate model (AGCM) that can employ either static or dynamic grid stretching for targeted phenomena. The resulting AGCM combined EULAG's advanced dynamics core with the "physics" of the NCAR Community Atmospheric Model (CAM). Effort discussed below shows how we improved model performance and tested both EULAG and the coupled CAM-EULAG in several ways to demonstrate the grid stretching and ability to simulate very well a wide range of scales, that is, multi-scale capability. We leveraged our effort through interaction with an international EULAG community that has collectively developed new features and applications of EULAG, which we exploited for our own work summarized here. Overall, the work contributed to over 40 peer-reviewed publications and over 70 conference/workshop/seminar presentations, many of them invited. 3a. EULAG Advances EULAG is a non-hydrostatic, parallel computational model for all-scale geophysical flows. EULAG's name derives from its two computational options: EULerian (flux form) or semi-LAGrangian (advective form). The model combines nonoscillatory forward-in-time (NFT) numerical algorithms with a robust elliptic Krylov solver. A signature feature of EULAG is that it is formulated in generalized time-dependent curvilinear coordinates. In particular, this enables grid adaptivity. In total, these features give EULAG novel advantages over many existing dynamical cores. For EULAG itself, numerical advances included refining boundary conditions and filters for optimizing model performance in polar regions. We also added flexibility to the model's underlying formulation, allowing it to work with the pseudo-compressible equation set of Durran in addition to EULAG's standard anelastic formulation. Work in collaboration with others also extended the demonstrated range of
40 CFR 80.133 - Agreed-upon procedures for refiners and importers.
Code of Federal Regulations, 2010 CFR
2010-07-01
... each refinery. (3) Obtain a written representation from a company representative that the report copies... (B) Allowed the company to sample and test the reformulated gasoline made by the blender. (ii) Obtain... person other than the refiner or importer, as represented by management of the refinery or...
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
An Adaptive Ridge Procedure for L0 Regularization
Frommlet, Florian; Nuel, Grégory
2016-01-01
Penalized selection criteria like AIC or BIC are among the most popular methods for variable selection. Their theoretical properties have been studied intensively and are well understood, but making use of them in case of high-dimensional data is difficult due to the non-convex optimization problem induced by L0 penalties. In this paper we introduce an adaptive ridge procedure (AR), where iteratively weighted ridge problems are solved whose weights are updated in such a way that the procedure converges towards selection with L0 penalties. After introducing AR its specific shrinkage properties are studied in the particular case of orthogonal linear regression. Based on extensive simulations for the non-orthogonal case as well as for Poisson regression the performance of AR is studied and compared with SCAD and adaptive LASSO. Furthermore an efficient implementation of AR in the context of least-squares segmentation is presented. The paper ends with an illustrative example of applying AR to analyze GWAS data. PMID:26849123
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.
pH-zone-refining counter-current chromatography: Origin, mechanism, procedure and applications✩
Ito, Yoichiro
2012-01-01
Since 1980, high-speed counter-current chromatography (HSCCC) has been used for separation and purification of natural and synthetic products in a standard elution mode. In 1991, a novel elution mode called pH-zone refining CCC was introduced from an incidental discovery that an organic acid in the sample solution formed the sharp peak of an acid analyte. The cause of this sharp peak formation was found to be bromoacetic acid present in the sample solution which formed a sharp trailing border to trap the acidic analyte. Further studies on the separation of DNP-amino acids with three spacer acids in the stationary phase revealed that increased sample size resulted in the formation of fused rectangular peaks, each preserving high purity and zone pH with sharp boundaries. The mechanism of this phenomenon was found to be the formation of a sharp trailing border of an acid (retainer) in the column which moves at a lower rate than that of the mobile phase. In order to facilitate the application of the method, a new method was devised using a set of retainer and eluter to form a sharp retainer rear border which moves through the column at a desired rate regardless of the composition of the two-phase solvent system. This was achieved by adding the retainer in the stationary phase and the eluter in the mobile phase at a given molar ratio. Using this new method the hydrodynamics of pH-zone-refining CCC was diagrammatically illustrated by three acidic samples. In this review paper, typical pH-zone-refining CCC separations were presented, including affinity separations with a ligand and a separation of a racemic mixture using a chiral selector in the stationary phase. Major characteristics of pH-zone-refining CCC over conventional HSCCC are as follows: the sample loading capacity is increased over 10 times; fractions are highly concentrated near saturation level; yield is improved by increasing the sample size; minute charged compounds are concentrated and detected at the peak
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)
Development of Adaptive Model Refinement (AMoR) for Multiphysics and Multifidelity Problems
Turinsky, Paul
2015-02-09
This project investigated the development and utilization of Adaptive Model Refinement (AMoR) for nuclear systems simulation applications. AMoR refers to utilization of several models of physical phenomena which differ in prediction fidelity. If the highest fidelity model is judged to always provide or exceeded the desired fidelity, than if one can determine the difference in a Quantity of Interest (QoI) between the highest fidelity model and lower fidelity models, one could utilize the fidelity model that would just provide the magnitude of the QoI desired. Assuming lower fidelity models require less computational resources, in this manner computational efficiency can be realized provided the QoI value can be accurately and efficiently evaluated. This work utilized Generalized Perturbation Theory (GPT) to evaluate the QoI, by convoluting the GPT solution with the residual of the highest fidelity model determined using the solution from lower fidelity models. Specifically, a reactor core neutronics problem and thermal-hydraulics problem were studied to develop and utilize AMoR. The highest fidelity neutronics model was based upon the 3D space-time, two-group, nodal diffusion equations as solved in the NESTLE computer code. Added to the NESTLE code was the ability to determine the time-dependent GPT neutron flux. The lower fidelity neutronics model was based upon the point kinetics equations along with utilization of a prolongation operator to determine the 3D space-time, two-group flux. The highest fidelity thermal-hydraulics model was based upon the space-time equations governing fluid flow in a closed channel around a heat generating fuel rod. The Homogenous Equilibrium Mixture (HEM) model was used for the fluid and Finite Difference Method was applied to both the coolant and fuel pin energy conservation equations. The lower fidelity thermal-hydraulic model was based upon the same equations as used for the highest fidelity model but now with coarse spatial
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.
Constrained-Transport Magnetohydrodynamics with Adaptive-Mesh-Refinement in CHARM
Miniatii, Francesco; Martin, Daniel
2011-05-24
We present the implementation of a three-dimensional, second order accurate Godunov-type algorithm for magneto-hydrodynamic (MHD), in the adaptivemesh-refinement (AMR) cosmological code CHARM. The algorithm is based on the full 12-solve spatially unsplit Corner-Transport-Upwind (CTU) scheme. Thefluid quantities are cell-centered and are updated using the Piecewise-Parabolic- Method (PPM), while the magnetic field variables are face-centered and areevolved 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 accuracyor robustness. The algorithm is implemented on an AMR framework which requires specific synchronization steps across refinement levels. These includeface-centered restriction and prolongation operations and a reflux-curl operation, which maintains a solenoidal magnetic field across refinement boundaries. Thecode 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 isshown to remain negligible throughout. Subject headings: cosmology: theory - methods: numerical
Radiographic skills learning: procedure simulation using adaptive hypermedia.
Costaridou, L; Panayiotakis, G; Pallikarakis, N; Proimos, B
1996-10-01
The design and development of a simulation tool supporting learning of radiographic skills is reported. This tool has by textual, graphical and iconic resources, organized according to a building-block, adaptive hypermedia approach, which is described and supported by an image base of radiographs. It offers interactive user-controlled simulation of radiographic imaging procedures. The development is based on a commercially available environment (Toolbook 3.0, Asymetrix Corporation). The core of the system is an attributed precedence (priority) graph, which represents a task outline (concept and resources structure), which is dynamically adjusted to selected procedures. The user interface imitates a conventional radiography system, i.e. operating console, tube, table, patient and cassette. System parameters, such as patient positioning, focus-to-patient distance, magnification, field dimensions, tube voltage and mAs are under user control. Their effects on image quality are presented, by means of an image base acquired under controlled exposure conditions. Innovative use of hypermedia, computer based learning and simulation principles and technology in the development of this tool resulted in an enhanced interactive environment providing radiographic parameter control and visualization of parameter effects on image quality. PMID:9038530
Jakeman, J. D.; Wildey, T.
2015-01-01
In this paper we present an algorithm for adaptive sparse grid approximations of quantities of interest computed from discretized partial differential equations. We use adjoint-based a posteriori error estimates of the interpolation error in the sparse grid to enhance the sparse grid approximation and to drive adaptivity. We show that utilizing these error estimates provides significantly more accurate functional values for random samples of the sparse grid approximation. We also demonstrate that alternative refinement strategies based upon a posteriori error estimates can lead to further increases in accuracy in the approximation over traditional hierarchical surplus based strategies. Throughout this papermore » we also provide and test a framework for balancing the physical discretization error with the stochastic interpolation error of the enhanced sparse grid approximation.« less
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.
Jakeman, J. D.; Wildey, T.
2015-01-01
In this paper we present an algorithm for adaptive sparse grid approximations of quantities of interest computed from discretized partial differential equations. We use adjoint-based a posteriori error estimates of the interpolation error in the sparse grid to enhance the sparse grid approximation and to drive adaptivity. We show that utilizing these error estimates provides significantly more accurate functional values for random samples of the sparse grid approximation. We also demonstrate that alternative refinement strategies based upon a posteriori error estimates can lead to further increases in accuracy in the approximation over traditional hierarchical surplus based strategies. Throughout this paper we also provide and test a framework for balancing the physical discretization error with the stochastic interpolation error of the enhanced sparse grid approximation.
Refinement procedure for the image alignment in high-resolution electron tomography.
Houben, L; Bar Sadan, M
2011-01-01
High-resolution electron tomography from a tilt series of transmission electron microscopy images requires an accurate image alignment procedure in order to maximise the resolution of the tomogram. This is the case in particular for ultra-high resolution where even very small misalignments between individual images can dramatically reduce the fidelity of the resultant reconstruction. A tomographic-reconstruction based and marker-free method is proposed, which uses an iterative optimisation of the tomogram resolution. The method utilises a search algorithm that maximises the contrast in tomogram sub-volumes. Unlike conventional cross-correlation analysis it provides the required correlation over a large tilt angle separation and guarantees a consistent alignment of images for the full range of object tilt angles. An assessment based on experimental reconstructions shows that the marker-free procedure is competitive to the reference of marker-based procedures at lower resolution and yields sub-pixel accuracy even for simulated high-resolution data. PMID:21930024
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.
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.
Eça, L.; Hoekstra, M.
2014-04-01
This paper offers a procedure for the estimation of the numerical uncertainty of any integral or local flow quantity as a result of a fluid flow computation; the procedure requires solutions on systematically refined grids. The error is estimated with power series expansions as a function of the typical cell size. These expansions, of which four types are used, are fitted to the data in the least-squares sense. The selection of the best error estimate is based on the standard deviation of the fits. The error estimate is converted into an uncertainty with a safety factor that depends on the observed order of grid convergence and on the standard deviation of the fit. For well-behaved data sets, i.e. monotonic convergence with the expected observed order of grid convergence and no scatter in the data, the method reduces to the well known Grid Convergence Index. Examples of application of the procedure are included. - Highlights: • Estimation of the numerical uncertainty of any integral or local flow quantity. • Least squares fits to power series expansions to handle noisy data. • Excellent results obtained for manufactured solutions. • Consistent results obtained for practical CFD calculations. • Reduces to the well known Grid Convergence Index for well-behaved data sets.
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.
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.
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.
Maltby, John; Day, Liz; Hall, Sophie
2015-01-01
The current paper presents a new measure of trait resilience derived from three common mechanisms identified in ecological theory: Engineering, Ecological and Adaptive (EEA) resilience. Exploratory and confirmatory factor analyses of five existing resilience scales suggest that the three trait resilience facets emerge, and can be reduced to a 12-item scale. The conceptualization and value of EEA resilience within the wider trait and well-being psychology is illustrated in terms of differing relationships with adaptive expressions of the traits of the five-factor personality model and the contribution to well-being after controlling for personality and coping, or over time. The current findings suggest that EEA resilience is a useful and parsimonious model and measure of trait resilience that can readily be placed within wider trait psychology and that is found to contribute to individual well-being. PMID:26132197
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.
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.
Maier, A.; Schmidt, W.; Iapichino, L.; Niemeyer, J. C.
2009-12-10
We present a numerical scheme for modeling unresolved turbulence in cosmological adaptive mesh refinement codes. As a first application, we study the evolution of turbulence in the intracluster medium (ICM) and in the core of a galaxy cluster. Simulations with and without subgrid scale (SGS) model are compared in detail. Since the flow in the ICM is subsonic, the global turbulent energy contribution at the unresolved length scales is smaller than 1% of the internal energy. We find that the production of turbulence is closely correlated with merger events occurring in the cluster environment, and its dissipation locally affects the cluster energy budget. Because of this additional source of dissipation, the core temperature is larger and the density is smaller in the presence of SGS turbulence than in the standard adiabatic run, resulting in a higher entropy core value.
GeoClawSed: A Model with Finite Volume and Adaptive Refinement Method for Tsunami Sediment Transport
NASA Astrophysics Data System (ADS)
Tang, H.; Weiss, R.
2015-12-01
The shallow-water and advection-diffusion equations are commonly used for tsunami sediment-transport modeling. GeoClawSed is based on GeoClaw and adds a bed updating and avalanching scheme to the two-dimensional coupled system combining the shallow- water and advection-diffusion equations, which is a set of hyperbolic integral conservation laws. The modeling system consists of three coupled model components: (1) the shallow-water equations for hydrodynamics; (2) advection-diffusion equation for sediment transport; and (3) an equation for morphodynamics. For the hydrodynamic part, the finite-volume wave propagation methods (high resolution Godunov-type methods) are applied to the shallow-water equations. The well-known Riemann solver in GeoClaw is capable of dealing with diverse flow regimes present during tsunami flows. For the sediment-transport part, the advection-diffusion equation is employed to calculate the distribution of sediment in the water column. In the fully-coupled version, the advection-diffusion equation is also included in the Riemann solver. The Van Leer method is applied for calculating sediment flux in each direction. The bed updating and avalanching scheme (morphodynamics) is used for updating topography during tsunami wave propagation. Adaptive refinement method is extended to hydrodynamic part, sediment transport model and topography. GeoClawSed can evolve different resolution and accurately capture discontinuities in both flow dynamic and sediment transport. Together, GeoClawSed is designed for modeling tsunami propagation, inundation, sediment transport as well as topography change. Finally, GeoClawSed is applied for studying marine and terrestrial deposit distribution after tsunami wave. Keywords: Tsunami; Sediment Transport; Shallow Water Equations; Advection-Diffusion Equation; Adaptive Refinement Method
Type 2 immunity and wound healing: evolutionary refinement of adaptive immunity by helminths
Gause, William C.; Wynn, Thomas A.; Allen, Judith E.
2013-01-01
Helminth-induced type 2 immune responses, which are characterized by the T helper 2 cell-associated cytokines interleukin-4 (IL-4) and IL-13, mediate host protection through enhanced tissue repair, the control of inflammation and worm expulsion. In this Opinion article, we consider type 2 immunity in the context of helminth-mediated tissue damage. We examine the relationship between the control of helminth infection and the mechanisms of wound repair, and we provide a new understanding of the adaptive type 2 immune response and its contribution to both host tolerance and resistance. PMID:23827958
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.
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.
Refined Adaptive Optics simulation with wide field of view for the ELT.
NASA Astrophysics Data System (ADS)
Chebbo, M.; Fusco, T.; Sauvage, J.-F.; Conan, J.-M.; Meimon, S.; Le Roux, B.
2011-09-01
Refined simulation tools for wide field AO systems (such as MOAO, MCAO or LTAO) on ELTs present new challenges. Increasing the number of degrees of freedom (scales as the square of the telescope diameter) makes the standard codes useless due to the huge number of operations to be performed at each step of the AO loop process. This computational burden requires new approaches in the computation of the DM voltages from WFS data. The classical matrix inversion and the matrix vector multiplication have to be replaced by a cleverer iterative resolution of the Least Square or Minimum Mean Square Error criterion (based on sparse matrices approaches). Moreover, for this new generation of AO systems, concepts themselves will become more complex: data fusion coming from multiple Laser and natural guide stars will have to be optimized, mirrors covering all the field of view associated to dedicated mirrors inside the scientific instrument itself will have to be coupled with split or integrated tomography schemes, differential pupil or/and field rotations will have to be considered, etc ... All these new entries should be carefully simulated, analysed and quantified in terms of performance before any implementation in AO systems. In this paper we present a new E2E simulator, developed to deal with all these specific ELT challenges. It is based on an iterative resolution of the linear model with high number of degrees of freedom (using the sparse matrix) and includes new concepts of filtering and coupling between LGS and NGS to effectively manage modes such as tip / tilt and defocus in the entire process of tomographic reconstruction. The first application of this tool in the frame of the EAGLE project, a flagship instrument of the future E-ELT combining all these issues, is presented.
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.
NASA Technical Reports Server (NTRS)
Aftosmis, M. J.; Berger, M. J.; Adomavicius, G.; Nixon, David (Technical Monitor)
1998-01-01
The work presents a new method for on-the-fly domain decomposition technique for mapping grids and solution algorithms to parallel machines, and is applicable to both shared-memory and message-passing architectures. It will be demonstrated on the Cray T3E, HP Exemplar, and SGI Origin 2000. Computing time has been secured on all these platforms. The decomposition technique is an outgrowth of techniques used in computational physics for simulations of N-body problems and the event horizons of black holes, and has not been previously used by the CFD community. Since the technique offers on-the-fly partitioning, it offers a substantial increase in flexibility for computing in heterogeneous environments, where the number of available processors may not be known at the time of job submission. In addition, since it is dynamic it permits the job to be repartitioned without global communication in cases where additional processors become available after the simulation has begun, or in cases where dynamic mesh adaptation changes the mesh size during the course of a simulation. The platform for this partitioning strategy is a completely new Cartesian Euler solver tarcreted at parallel machines which may be used in conjunction with Ames' "Cart3D" arbitrary geometry simulation package.
NASA Technical Reports Server (NTRS)
Davis, M. W.
1984-01-01
A Real-Time Self-Adaptive (RTSA) active vibration controller was used as the framework in developing a computer program for a generic controller that can be used to alleviate helicopter vibration. Based upon on-line identification of system parameters, the generic controller minimizes vibration in the fuselage by closed-loop implementation of higher harmonic control in the main rotor system. The new generic controller incorporates a set of improved algorithms that gives the capability to readily define many different configurations by selecting one of three different controller types (deterministic, cautious, and dual), one of two linear system models (local and global), and one or more of several methods of applying limits on control inputs (external and/or internal limits on higher harmonic pitch amplitude and rate). A helicopter rotor simulation analysis was used to evaluate the algorithms associated with the alternative controller types as applied to the four-bladed H-34 rotor mounted on the NASA Ames Rotor Test Apparatus (RTA) which represents the fuselage. After proper tuning all three controllers provide more effective vibration reduction and converge more quickly and smoothly with smaller control inputs than the initial RTSA controller (deterministic with external pitch-rate limiting). It is demonstrated that internal limiting of the control inputs a significantly improves the overall performance of the deterministic controller.
Adapting Assessment Procedures for Delivery via an Automated Format.
ERIC Educational Resources Information Center
Kelly, Karen L.; And Others
The Office of Personnel Management (OPM) decided to explore alternative examining procedures for positions covered by the Administrative Careers with America (ACWA) examination. One requirement for new procedures was that they be automated for use with OPM's recently developed Microcomputer Assisted Rating System (MARS), a highly efficient system…
NASA Astrophysics Data System (ADS)
Novoselov, V. B.; Shekhter, M. V.
2012-12-01
A refined procedure for estimating the effect the flashing of condensate in a steam turbine's regenerative and delivery-water heaters on the increase of rotor rotation frequency during rejection of electric load is presented. The results of calculations carried out according to the proposed procedure as applied to the delivery-water and regenerative heaters of a T-110/120-12.8 turbine are given.
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)
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.
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.
Sheth, Saumil; Lanzetta, Paolo; Veritti, Daniele; Zucchiatti, Ilaria; Savorgnani, Carola; Bandello, Francesco
2011-01-01
Aim: To systematically refine and recommend parameter settings of spot size, power, and treatment duration using the Pascal® photocoagulator, a multi-spot, semi-automated, short-duration laser system. Materials and Methods: A retrospective consecutive series with 752 Caucasian eyes and 1242 laser procedures over two years were grouped into, (1) 374 macular focal / grid photocoagulation (FP), (2), 666 panretinal photocoagulation (PRP), and (3) 202 barrage photocoagulation (BP). Parameters for power, duration, spot number, and spot size were recorded for every group. Results: Power parameters for all groups showed a non-gaussian distribution; FP group, median 190 mW, range 100 – 950 mW, and PRP group, median 800 mW, range 100 – 2000 mW. On subgroup comparison, for similar spot size, as treatment duration decreased, the power required increased, albeit in a much lesser proportion than that given by energy = power × time. Most frequently used patterns were single spot (89% of cases) in FP, 5 × 5 box (72%) in PRP, and 2 × 2 box (78%) in BP. Spot diameters as high as ≈ 700 μm on retina were given in the PRP group. Single session PRP was attempted in six eyes with a median spot count of 3500. Conclusion: Overall, due to the small duration of its pulse, the Pascal® photocoagulator tends to use higher powers, although much lower cumulative energies, than those used in a conventional laser. The consequent lesser heat dissipation, especially lateral, can allow one to use relatively larger spot sizes and give more closely spaced burns, without incurring significant side effects. PMID:21350276
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.
Mesh quality control for multiply-refined tetrahedral grids
NASA Technical Reports Server (NTRS)
Biswas, Rupak; Strawn, Roger
1994-01-01
A new algorithm for controlling the quality of multiply-refined tetrahedral meshes is presented in this paper. The basic dynamic mesh adaption procedure allows localized grid refinement and coarsening to efficiently capture aerodynamic flow features in computational fluid dynamics problems; however, repeated application of the procedure may significantly deteriorate the quality of the mesh. Results presented show the effectiveness of this mesh quality algorithm and its potential in the area of helicopter aerodynamics and acoustics.
Layher, Georg; Schrodt, Fabian; Butz, Martin V.; Neumann, Heiko
2014-01-01
The categorization of real world objects is often reflected in the similarity of their visual appearances. Such categories of objects do not necessarily form disjunct sets of objects, neither semantically nor visually. The relationship between categories can often be described in terms of a hierarchical structure. For instance, tigers and leopards build two separate mammalian categories, both of which are subcategories of the category Felidae. In the last decades, the unsupervised learning of categories of visual input stimuli has been addressed by numerous approaches in machine learning as well as in computational neuroscience. However, the question of what kind of mechanisms might be involved in the process of subcategory learning, or category refinement, remains a topic of active investigation. We propose a recurrent computational network architecture for the unsupervised learning of categorial and subcategorial visual input representations. During learning, the connection strengths of bottom-up weights from input to higher-level category representations are adapted according to the input activity distribution. In a similar manner, top-down weights learn to encode the characteristics of a specific stimulus category. Feedforward and feedback learning in combination realize an associative memory mechanism, enabling the selective top-down propagation of a category's feedback weight distribution. We suggest that the difference between the expected input encoded in the projective field of a category node and the current input pattern controls the amplification of feedforward-driven representations. Large enough differences trigger the recruitment of new representational resources and the establishment of additional (sub-) category representations. We demonstrate the temporal evolution of such learning and show how the proposed combination of an associative memory with a modulatory feedback integration successfully establishes category and subcategory representations
Differential Effects of Two Spelling Procedures on Acquisition, Maintenance and Adaption to Reading
ERIC Educational Resources Information Center
Cates, Gary L.; Dunne, Megan; Erkfritz, Karyn N.; Kivisto, Aaron; Lee, Nicole; Wierzbicki, Jennifer
2007-01-01
An alternating treatments design was used to assess the effects of a constant time delay (CTD) procedure and a cover-copy-compare (CCC) procedure on three students' acquisition, subsequent maintenance, and adaptation (i.e., application) of acquired spelling words to reading passages. Students were randomly presented two trials of word lists from…
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.
Kim, D.; Ghanem, R.
1994-12-31
Multigrid solution technique to solve a material nonlinear problem in a visual programming environment using the finite element method is discussed. The nonlinear equation of equilibrium is linearized to incremental form using Newton-Rapson technique, then multigrid solution technique is used to solve linear equations at each Newton-Rapson step. In the process, adaptive mesh refinement, which is based on the bisection of a pair of triangles, is used to form grid hierarchy for multigrid iteration. The solution process is implemented in a visual programming environment with distributed computing capability, which enables more intuitive understanding of solution process, and more effective use of resources.
A Procedure for Controlling General Test Overlap in Computerized Adaptive Testing
ERIC Educational Resources Information Center
Chen, Shu-Ying
2010-01-01
To date, exposure control procedures that are designed to control test overlap in computerized adaptive tests (CATs) are based on the assumption of item sharing between pairs of examinees. However, in practice, examinees may obtain test information from more than one previous test taker. This larger scope of information sharing needs to be…
Greenough, Jeffrey A.; de Supinski, Bronis R.; Yates, Robert K.; Rendleman, Charles A.; Skinner, David; Beckner, Vince; Lijewski, Mike; Bell, John; Sexton, James C.
2005-04-25
We describe the performance of the block-structured Adaptive Mesh Refinement (AMR) code Raptor on the 32k node IBM BlueGene/L computer. This machine represents a significant step forward towards petascale computing. As such, it presents Raptor with many challenges for utilizing the hardware efficiently. In terms of performance, Raptor shows excellent weak and strong scaling when running in single level mode (no adaptivity). Hardware performance monitors show Raptor achieves an aggregate performance of 3:0 Tflops in the main integration kernel on the 32k system. Results from preliminary AMR runs on a prototype astrophysical problem demonstrate the efficiency of the current software when running at large scale. The BG/L system is enabling a physics problem to be considered that represents a factor of 64 increase in overall size compared to the largest ones of this type computed to date. Finally, we provide a description of the development work currently underway to address our inefficiencies.
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.
SAXO, the eXtreme Adaptive Optics System of SPHERE: overview and calibration procedure
NASA Astrophysics Data System (ADS)
Sauvage, J.-F.; Fusco, T.; Petit, C.; Meimon, S.; Fedrigo, E.; Suarez Valles, M.; Kasper, M.; Hubin, N.; Beuzit, J.-L.; Charton, J.; Costille, A.; Rabou, P., .; Mouillet, D.; Baudoz, P.; Buey, T.; Sevin, A.; Wildi, F.; Dohlen, K.
2010-07-01
The direct imaging of exoplanet is a challenging goal of todays astronomy. The light transmitted by exoplanet atmosphere is of a great interest as it may witness for life sign. SPHERE is a second generation instrument for the VLT, dedicated to exoplanet imaging, detection, and characterisation. SPHERE is a global project of an European consortium of 11 institutes from 5 countries. We present here the state of the art of the AIT of the Adaptive Optics part of the instrument. In addition we present fine calibration procedures dedicated to eXtreme Adaptive Optics systems. First we emphasized on vibration and turbulence identification for optimization of the control law. Then, we describe a procedure able to measure and compensate for NCPA with a coronagraphic system.
Refined numerical solution of the transonic flow past a wedge
NASA Technical Reports Server (NTRS)
Liang, S.-M.; Fung, K.-Y.
1985-01-01
A numerical procedure combining the ideas of solving a modified difference equation and of adaptive mesh refinement is introduced. The numerical solution on a fixed grid is improved by using better approximations of the truncation error computed from local subdomain grid refinements. This technique is used to obtain refined solutions of steady, inviscid, transonic flow past a wedge. The effects of truncation error on the pressure distribution, wave drag, sonic line, and shock position are investigated. By comparing the pressure drag on the wedge and wave drag due to the shocks, a supersonic-to-supersonic shock originating from the wedge shoulder is confirmed.
NASA Astrophysics Data System (ADS)
Shih, Chihhsiong; Yang, Yuanfan
2012-02-01
A novel three-dimensional (3-D) photorealistic texturing process is presented that applies a view-planning and view-sequencing algorithm to the 3-D coarse model to determine a set of best viewing angles for capturing the individual real-world objects/building's images. The best sequence of views will generate sets of visible edges in each view to serve as a guide for camera field shots by either manual adjustment or equipment alignment. The best view tries to cover as many objects/building surfaces as possible in one shot. This will lead to a smaller total number of shots taken for a complete model reconstruction requiring texturing with photo-realistic effects. The direct linear transformation method (DLT) is used for reprojection of 3-D model vertices onto a two-dimensional (2-D) images plane for actual texture mapping. Given this method, the actual camera orientations do not have to be unique and can be set arbitrarily without heavy and expensive positioning equipment. We also present results of a study on the texture-mapping precision as a function of the level of visible mesh subdivision. In addition, the control points selection for the DLT method used for reprojection of 3-D model vertices onto 2-D textured images is also investigated for its effects on mapping precision. By using DLT and perspective projection theories on a coarse model feature points, this technique will allow accurate 3-D texture mapping of refined model meshes of real-world buildings. The novel integration flow of this research not only greatly reduces the human labor and intensive equipment requirements of traditional methods, but also generates a more appealing photo-realistic appearance of reconstructed models, which is useful in many multimedia applications. The roles of view planning (VP) are multifold. VP can (1) reduce the repetitive texture-mapping computation load, (2) can present a set of visible model wireframe edges that can serve as a guide for images with sharp edges and
Prism Adaptation and Aftereffect: Specifying the Properties of a Procedural Memory System
Fernández-Ruiz, Juan; Díaz, Rosalinda
1999-01-01
Prism adaptation, a form of procedural learning, is a phenomenon in which the motor system adapts to new visuospatial coordinates imposed by prisms that displace the visual field. Once the prisms are withdrawn, the degree and strength of the adaptation can be measured by the spatial deviation of the motor actions in the direction opposite to the visual displacement imposed by the prisms, a phenomenon known as aftereffect. This study was designed to define the variables that affect the acquisition and retention of the aftereffect. Subjects were required to throw balls to a target in front of them before, during, and after lateral displacement of the visual field with prismatic spectacles. The diopters of the prisms and the number of throws were varied among different groups of subjects. The results show that the adaptation process is dependent on the number of interactions between the visual and motor system, and not on the time spent wearing the prisms. The results also show that the magnitude of the aftereffect is highly correlated with the magnitude of the adaptation, regardless of the diopters of the prisms or the number of throws. Finally, the results suggest that persistence of the aftereffect depends on the number of throws after the adaptation is complete. On the basis of these results, we propose that the system underlying this kind of learning stores at least two different parameters, the contents (measured as the magnitude of displacement) and the persistence (measured as the number of throws to return to the baseline) of the learned information. PMID:10355523
General tuning procedure for the nonlinear balance-based adaptive controller
NASA Astrophysics Data System (ADS)
Stebel, Krzysztof; Czeczot, Jacek; Laszczyk, Piotr
2014-01-01
This paper presents the intuitive and ready-to-use, general procedure for tuning the balance-based adaptive controller (B-BAC) based on its equivalence to the controller with PI term and with additional improvements shown for the linearised approximation of the dynamics of the nonlinear controlled process. The simple formulas are suggested to calculate the B-BAC tunings based on the PI tunings determined by any PI tuning procedure chosen accordingly to the desired closed-loop performance. This methodology is verified by comparing the closed-loop performance of the equivalently tuned B-BAC and PI/PI+feedforward controllers under the same scenario, both by the simulation and practical experiments.
An adaptive procedure for the numerical parameters of a particle simulation
NASA Astrophysics Data System (ADS)
Galitzine, Cyril; Boyd, Iain D.
2015-01-01
In this article, a computational procedure that automatically determines the optimum time step, cell weight and species weights for steady-state multi-species DSMC (direct simulation Monte Carlo) simulations is presented. The time step is required to satisfy the basic requirements of the DSMC method while the weight and relative weights fields are chosen so as to obtain a user-specified average number of particles in all cells of the domain. The procedure allows the conduct of efficient DSMC simulations with minimal user input and is integrable into existing DSMC codes. The adaptive method is used to simulate a test case consisting of two counterflowing jets at a Knudsen number of 0.015. Large accuracy gains for sampled number densities and velocities over a standard simulation approach for the same number of particles are observed.
An adaptive gating approach for x-ray dose reduction during cardiac interventional procedures
Abdel-Malek, A.; Yassa, F.; Bloomer, J. )
1994-03-01
The increasing number of cardiac interventional procedures has resulted in a tremendous increase in the absorbed x-ray dose by radiologists as well as patients. A new method is presented for x-ray dose reduction which utilizes adaptive tube pulse-rate scheduling in pulsed fluoroscopic systems. In the proposed system, pulse-rate scheduling depends on the heart muscle activity phase determined through continuous guided segmentation of the patient's electrocardiogram (ECG). Displaying images generated at the proposed adaptive nonuniform rate is visually unacceptable; therefore, a frame-filling approach is devised to ensure a 30 frame/sec display rate. The authors adopted two approaches for the frame-filling portion of the system depending on the imaging mode used in the procedure. During cine-mode imaging (high x-ray dose), collected image frame-to-frame pixel motion is estimated using a pel-recursive algorithm followed by motion-based pixel interpolation to estimate the frames necessary to increase the rate to 30 frames/sec. The other frame-filling approach is adopted during fluoro-mode imaging (low x-ray dose), characterized by low signal-to-noise ratio images. This approach consists of simply holding the last collected frame for as many frames as necessary to maintain the real-time display rate.
qPR: An adaptive partial-report procedure based on Bayesian inference
Baek, Jongsoo; Lesmes, Luis Andres; Lu, Zhong-Lin
2016-01-01
Iconic memory is best assessed with the partial report procedure in which an array of letters appears briefly on the screen and a poststimulus cue directs the observer to report the identity of the cued letter(s). Typically, 6–8 cue delays or 600–800 trials are tested to measure the iconic memory decay function. Here we develop a quick partial report, or qPR, procedure based on a Bayesian adaptive framework to estimate the iconic memory decay function with much reduced testing time. The iconic memory decay function is characterized by an exponential function and a joint probability distribution of its three parameters. Starting with a prior of the parameters, the method selects the stimulus to maximize the expected information gain in the next test trial. It then updates the posterior probability distribution of the parameters based on the observer's response using Bayesian inference. The procedure is reiterated until either the total number of trials or the precision of the parameter estimates reaches a certain criterion. Simulation studies showed that only 100 trials were necessary to reach an average absolute bias of 0.026 and a precision of 0.070 (both in terms of probability correct). A psychophysical validation experiment showed that estimates of the iconic memory decay function obtained with 100 qPR trials exhibited good precision (the half width of the 68.2% credible interval = 0.055) and excellent agreement with those obtained with 1,600 trials of the conventional method of constant stimuli procedure (RMSE = 0.063). Quick partial-report relieves the data collection burden in characterizing iconic memory and makes it possible to assess iconic memory in clinical populations. PMID:27580045
Adaptive remapping procedure for electronic cleansing of fecal tagging CT colonography images
NASA Astrophysics Data System (ADS)
Morra, Lia; Delsanto, Silvia; Campanella, Delia; Regge, Daniele; Bert, Alberto
2009-02-01
Fecal tagging preparations are attracting notable interest as a way to increase patients' compliance to virtual colonoscopy. Patient-friendly preparations, however, often result in less homogeneous tagging. Electronic cleansing algorithms should be capable of dealing with such preparations and yield good quality 2D and 3D images; moreover, successful electronic cleansing lays the basis for the application of Computer Aided Detection schemes. In this work, we present a cleansing algorithm based on an adaptive remapping procedure, which is based on a model of how partial volume affects both the air-tissue and the soft-tissue interfaces. Partial volume at the stool-soft tissue interface is characterized in terms of the local characteristics of tagged regions, in order to account for variations in tagging intensity throughout the colon. The two models are then combined in order to obtain a remapping equation relating the observed intensity to the that of the cleansed colon. The electronic cleansed datasets were then processed by a CAD scheme composed of three main steps: colon surface extraction, polyp candidate segmentation through curvature-based features, and linear classifier-based discrimination between true polyps and false alarms. Results obtained were compared with a previous version of the cleansing algorithm, in which a simpler remapping procedure was used. Performances are increased both in terms of the visual quality of the 2D cleansed images and 3D rendered volumes, and of CAD performances on a sameday FT virtual colonoscopy dataset.
Conformal refinement of unstructured quadrilateral meshes
Garmella, Rao
2009-01-01
We present a multilevel adaptive refinement technique for unstructured quadrilateral meshes in which the mesh is kept conformal at all times. This means that the refined mesh, like the original, is formed of only quadrilateral elements that intersect strictly along edges or at vertices, i.e., vertices of one quadrilateral element do not lie in an edge of another quadrilateral. Elements are refined using templates based on 1:3 refinement of edges. We demonstrate that by careful design of the refinement and coarsening strategy, we can maintain high quality elements in the refined mesh. We demonstrate the method on a number of examples with dynamically changing refinement regions.
Sewell, Fiona; Ragan, Ian; Marczylo, Tim; Anderson, Brian; Braun, Anne; Casey, Warren; Dennison, Ngaire; Griffiths, David; Guest, Robert; Holmes, Tom; van Huygevoort, Ton; Indans, Ian; Kenny, Terry; Kojima, Hajime; Lee, Kyuhong; Prieto, Pilar; Smith, Paul; Smedley, Jason; Stokes, William S; Wnorowski, Gary; Horgan, Graham
2015-12-01
Acute inhalation studies are conducted in animals as part of chemical hazard identification and characterisation, including for classification and labelling purposes. Current accepted methods use death as an endpoint (OECD TG403 and TG436), whereas the fixed concentration procedure (FCP) (draft OECD TG433) uses fewer animals and replaces lethality as an endpoint with 'evident toxicity.' Evident toxicity is defined as clear signs of toxicity that predict exposure to the next highest concentration will cause severe toxicity or death in most animals. A global initiative including 20 organisations, led by the National Centre for the Replacement, Refinement and Reduction of Animals in Research (NC3Rs) has shared data on the clinical signs recorded during acute inhalation studies for 172 substances (primarily dusts or mists) with the aim of making evident toxicity more objective and transferable between laboratories. Pairs of studies (5 male or 5 female rats) with at least a two-fold change in concentration were analysed to determine if there are any signs at the lower dose that could have predicted severe toxicity or death at the higher concentration. The results show that signs such as body weight loss (>10% pre-dosing weight), irregular respiration, tremors and hypoactivity, seen at least once in at least one animal after the day of dosing are highly predictive (positive predictive value > 90%) of severe toxicity or death at the next highest concentration. The working group has used these data to propose changes to TG433 that incorporate a clear indication of the clinical signs that define evident toxicity. PMID:26505531
NASA Technical Reports Server (NTRS)
Rebstock, Rainer
1987-01-01
Numerical methods are developed for control of three dimensional adaptive test sections. The physical properties of the design problem occurring in the external field computation are analyzed, and a design procedure suited for solution of the problem is worked out. To do this, the desired wall shape is determined by stepwise modification of an initial contour. The necessary changes in geometry are determined with the aid of a panel procedure, or, with incident flow near the sonic range, with a transonic small perturbation (TSP) procedure. The designed wall shape, together with the wall deflections set during the tunnel run, are the input to a newly derived one-step formula which immediately yields the adapted wall contour. This is particularly important since the classical iterative adaptation scheme is shown to converge poorly for 3D flows. Experimental results obtained in the adaptive test section with eight flexible walls are presented to demonstrate the potential of the procedure. Finally, a method is described to minimize wall interference in 3D flows by adapting only the top and bottom wind tunnel walls.
NASA Astrophysics Data System (ADS)
Malgarinos, Ilias; Nikolopoulos, Nikolaos; Gavaises, Manolis
2015-11-01
This study presents the implementation of an interface sharpening scheme on the basis of the Volume of Fluid (VOF) method, as well as its application in a number of theoretical and real cases usually modelled in literature. More specifically, the solution of an additional sharpening equation along with the standard VOF model equations is proposed, offering the advantage of "restraining" interface numerical diffusion, while also keeping a quite smooth induced velocity field around the interface. This sharpening equation is solved right after volume fraction advection; however a novel method for its coupling with the momentum equation has been applied in order to save computational time. The advantages of the proposed sharpening scheme lie on the facts that a) it is mass conservative thus its application does not have a negative impact on one of the most important benefits of VOF method and b) it can be used in coarser grids as now the suppression of the numerical diffusion is grid independent. The coupling of the solved equation with an adaptive local grid refinement technique is used for further decrease of computational time, while keeping high levels of accuracy at the area of maximum interest (interface). The numerical algorithm is initially tested against two theoretical benchmark cases for interface tracking methodologies followed by its validation for the case of a free-falling water droplet accelerated by gravity, as well as the normal liquid droplet impingement onto a flat substrate. Results indicate that the coupling of the interface sharpening equation with the HRIC discretization scheme used for volume fraction flux term, not only decreases the interface numerical diffusion, but also allows the induced velocity field to be less perturbed owed to spurious velocities across the liquid-gas interface. With the use of the proposed algorithmic flow path, coarser grids can replace finer ones at the slight expense of accuracy.
An Adaptive Landscape Classification Procedure using Geoinformatics and Artificial Neural Networks
Coleman, Andre Michael
2008-06-01
The Adaptive Landscape Classification Procedure (ALCP), which links the advanced geospatial analysis capabilities of Geographic Information Systems (GISs) and Artificial Neural Networks (ANNs) and particularly Self-Organizing Maps (SOMs), is proposed as a method for establishing and reducing complex data relationships. Its adaptive and evolutionary capability is evaluated for situations where varying types of data can be combined to address different prediction and/or management needs such as hydrologic response, water quality, aquatic habitat, groundwater recharge, land use, instrumentation placement, and forecast scenarios. The research presented here documents and presents favorable results of a procedure that aims to be a powerful and flexible spatial data classifier that fuses the strengths of geoinformatics and the intelligence of SOMs to provide data patterns and spatial information for environmental managers and researchers. This research shows how evaluation and analysis of spatial and/or temporal patterns in the landscape can provide insight into complex ecological, hydrological, climatic, and other natural and anthropogenic-influenced processes. Certainly, environmental management and research within heterogeneous watersheds provide challenges for consistent evaluation and understanding of system functions. For instance, watersheds over a range of scales are likely to exhibit varying levels of diversity in their characteristics of climate, hydrology, physiography, ecology, and anthropogenic influence. Furthermore, it has become evident that understanding and analyzing these diverse systems can be difficult not only because of varying natural characteristics, but also because of the availability, quality, and variability of spatial and temporal data. Developments in geospatial technologies, however, are providing a wide range of relevant data, and in many cases, at a high temporal and spatial resolution. Such data resources can take the form of high
Karmali, Faisal; Chaudhuri, Shomesh E; Yi, Yongwoo; Merfeld, Daniel M
2016-03-01
When measuring thresholds, careful selection of stimulus amplitude can increase efficiency by increasing the precision of psychometric fit parameters (e.g., decreasing the fit parameter error bars). To find efficient adaptive algorithms for psychometric threshold ("sigma") estimation, we combined analytic approaches, Monte Carlo simulations, and human experiments for a one-interval, binary forced-choice, direction-recognition task. To our knowledge, this is the first time analytic results have been combined and compared with either simulation or human results. Human performance was consistent with theory and not significantly different from simulation predictions. Our analytic approach provides a bound on efficiency, which we compared against the efficiency of standard staircase algorithms, a modified staircase algorithm with asymmetric step sizes, and a maximum likelihood estimation (MLE) procedure. Simulation results suggest that optimal efficiency at determining threshold is provided by the MLE procedure targeting a fraction correct level of 0.92, an asymmetric 4-down, 1-up staircase targeting between 0.86 and 0.92 or a standard 6-down, 1-up staircase. Psychometric test efficiency, computed by comparing simulation and analytic results, was between 41 and 58% for 50 trials for these three algorithms, reaching up to 84% for 200 trials. These approaches were 13-21% more efficient than the commonly used 3-down, 1-up symmetric staircase. We also applied recent advances to reduce accuracy errors using a bias-reduced fitting approach. Taken together, the results lend confidence that the assumptions underlying each approach are reasonable and that human threshold forced-choice decision making is modeled well by detection theory models and mimics simulations based on detection theory models. PMID:26645306
Adaptive correction procedure for TVL1 image deblurring under impulse noise
NASA Astrophysics Data System (ADS)
Bai, Minru; Zhang, Xiongjun; Shao, Qianqian
2016-08-01
For the problem of image restoration of observed images corrupted by blur and impulse noise, the widely used TVL1 model may deviate from both the data-acquisition model and the prior model, especially for high noise levels. In order to seek a solution of high recovery quality beyond the reach of the TVL1 model, we propose an adaptive correction procedure for TVL1 image deblurring under impulse noise. Then, a proximal alternating direction method of multipliers (ADMM) is presented to solve the corrected TVL1 model and its convergence is also established under very mild conditions. It is verified by numerical experiments that our proposed approach outperforms the TVL1 model in terms of signal-to-noise ratio (SNR) values and visual quality, especially for high noise levels: it can handle salt-and-pepper noise as high as 90% and random-valued noise as high as 70%. In addition, a comparison with a state-of-the-art method, the two-phase method, demonstrates the superiority of the proposed approach.
ERIC Educational Resources Information Center
Yang, Xiangdong; Poggio, John C.; Glasnapp, Douglas R.
2006-01-01
The effects of five ability estimators, that is, maximum likelihood estimator, weighted likelihood estimator, maximum a posteriori, expected a posteriori, and Owen's sequential estimator, on the performances of the item response theory-based adaptive classification procedure on multiple categories were studied via simulations. The following…
Hawkins, P; Dennison, N; Goodman, G; Hetherington, S; Llywelyn-Jones, S; Ryder, K; Smith, A J
2011-01-01
The severity classification of procedures using animals is an important tool to help focus the implementation of refinement and to assist in reporting the application of the 3Rs (replacement, reduction and refinement). The recently revised Directive that regulates animal research and testing within the European Union requires Member States to ensure that all procedures are classified as ‘non-recovery’, ‘mild’, ‘moderate’ or ‘severe’, using assignment criteria set out by the European Commission (EC). However, these are focused upon terrestrial species, so are of limited relevance to fish users. A Working Group set up by the Norwegian Consensus-Platform for the 3Rs (Norecopa) has produced guidance on the classification of severity in scientific procedures involving fish, including examples of ‘subthreshold’, ‘mild’, ‘moderate’, ‘severe’ and ‘upper threshold’ procedures. The aims are to complement the EC guidelines and help to ensure that suffering in fish is effectively predicted and minimized. Norecopa has established a website (www.norecopa.no/categories) where more information on severity classification for procedures using fish, including field research, will be made available. PMID:21558168
Hawkins, P; Dennison, N; Goodman, G; Hetherington, S; Llywelyn-Jones, S; Ryder, K; Smith, A J
2011-10-01
The severity classification of procedures using animals is an important tool to help focus the implementation of refinement and to assist in reporting the application of the 3Rs (replacement, reduction and refinement). The recently revised Directive that regulates animal research and testing within the European Union requires Member States to ensure that all procedures are classified as 'non-recovery', 'mild', 'moderate' or 'severe', using assignment criteria set out by the European Commission (EC). However, these are focused upon terrestrial species, so are of limited relevance to fish users. A Working Group set up by the Norwegian Consensus-Platform for the 3Rs (Norecopa) has produced guidance on the classification of severity in scientific procedures involving fish, including examples of 'subthreshold', 'mild', 'moderate', 'severe' and 'upper threshold' procedures. The aims are to complement the EC guidelines and help to ensure that suffering in fish is effectively predicted and minimized. Norecopa has established a website (www.norecopa.no/categories) where more information on severity classification for procedures using fish, including field research, will be made available. PMID:21558168
NASA Astrophysics Data System (ADS)
Valdivia, Valeska; Hennebelle, Patrick
2014-11-01
Context. Ultraviolet radiation plays a crucial role in molecular clouds. Radiation and matter are tightly coupled and their interplay influences the physical and chemical properties of gas. In particular, modeling the radiation propagation requires calculating column densities, which can be numerically expensive in high-resolution multidimensional simulations. Aims: Developing fast methods for estimating column densities is mandatory if we are interested in the dynamical influence of the radiative transfer. In particular, we focus on the effect of the UV screening on the dynamics and on the statistical properties of molecular clouds. Methods: We have developed a tree-based method for a fast estimate of column densities, implemented in the adaptive mesh refinement code RAMSES. We performed numerical simulations using this method in order to analyze the influence of the screening on the clump formation. Results: We find that the accuracy for the extinction of the tree-based method is better than 10%, while the relative error for the column density can be much more. We describe the implementation of a method based on precalculating the geometrical terms that noticeably reduces the calculation time. To study the influence of the screening on the statistical properties of molecular clouds we present the probability distribution function of gas and the associated temperature per density bin and the mass spectra for different density thresholds. Conclusions: The tree-based method is fast and accurate enough to be used during numerical simulations since no communication is needed between CPUs when using a fully threaded tree. It is then suitable to parallel computing. We show that the screening for far UV radiation mainly affects the dense gas, thereby favoring low temperatures and affecting the fragmentation. We show that when we include the screening, more structures are formed with higher densities in comparison to the case that does not include this effect. We
Parallel Adaptive Multi-Mechanics Simulations using Diablo
Parsons, D; Solberg, J
2004-12-03
Coupled multi-mechanics simulations (such as thermal-stress and fluidstructure interaction problems) are of substantial interest to engineering analysts. In addition, adaptive mesh refinement techniques present an attractive alternative to current mesh generation procedures and provide quantitative error bounds that can be used for model verification. This paper discusses spatially adaptive multi-mechanics implicit simulations using the Diablo computer code. (U)
Broom, Donald M
2006-01-01
The term adaptation is used in biology in three different ways. It may refer to changes which occur at the cell and organ level, or at the individual level, or at the level of gene action and evolutionary processes. Adaptation by cells, especially nerve cells helps in: communication within the body, the distinguishing of stimuli, the avoidance of overload and the conservation of energy. The time course and complexity of these mechanisms varies. Adaptive characters of organisms, including adaptive behaviours, increase fitness so this adaptation is evolutionary. The major part of this paper concerns adaptation by individuals and its relationships to welfare. In complex animals, feed forward control is widely used. Individuals predict problems and adapt by acting before the environmental effect is substantial. Much of adaptation involves brain control and animals have a set of needs, located in the brain and acting largely via motivational mechanisms, to regulate life. Needs may be for resources but are also for actions and stimuli which are part of the mechanism which has evolved to obtain the resources. Hence pigs do not just need food but need to be able to carry out actions like rooting in earth or manipulating materials which are part of foraging behaviour. The welfare of an individual is its state as regards its attempts to cope with its environment. This state includes various adaptive mechanisms including feelings and those which cope with disease. The part of welfare which is concerned with coping with pathology is health. Disease, which implies some significant effect of pathology, always results in poor welfare. Welfare varies over a range from very good, when adaptation is effective and there are feelings of pleasure or contentment, to very poor. A key point concerning the concept of individual adaptation in relation to welfare is that welfare may be good or poor while adaptation is occurring. Some adaptation is very easy and energetically cheap and
Sukkay, Sasicha
2016-01-01
Based on a 2013 statistic published by Thai with Disability foundation, five percent of Thailand's population are disabled people. Six hundred thousand of them have mobility disability, and the number is increasing every year. To support them, the Thai government has implemented a number of disability laws and policies. One of the policies is to better disabled people's quality of life by adapting their houses to facilitate their activities. However, the policy has not been fully realized yet-there is still no specific guideline for housing adaptation for people with disabilities. This study is an attempt to address the lack of standardized criteria for such adaptation by developing a number of effective ones. Our development had 3 objectives: first, to identify the body functioning of a group of people with mobility disability according to the international classification functioning concept (ICF); second, to perform post-occupancy evaluation of this group and their houses; and third, with the collected data, to have a group of multidisciplinary experts cooperatively develop criteria for housing adaptation. The major findings were that room dimensions and furniture materials really had an impact on accessibility and toilet as well as bed room were the most difficult areas to access. PMID:27534326
EEG-Based BCI System Using Adaptive Features Extraction and Classification Procedures
Mangia, Anna Lisa; Cappello, Angelo
2016-01-01
Motor imagery is a common control strategy in EEG-based brain-computer interfaces (BCIs). However, voluntary control of sensorimotor (SMR) rhythms by imagining a movement can be skilful and unintuitive and usually requires a varying amount of user training. To boost the training process, a whole class of BCI systems have been proposed, providing feedback as early as possible while continuously adapting the underlying classifier model. The present work describes a cue-paced, EEG-based BCI system using motor imagery that falls within the category of the previously mentioned ones. Specifically, our adaptive strategy includes a simple scheme based on a common spatial pattern (CSP) method and support vector machine (SVM) classification. The system's efficacy was proved by online testing on 10 healthy participants. In addition, we suggest some features we implemented to improve a system's “flexibility” and “customizability,” namely, (i) a flexible training session, (ii) an unbalancing in the training conditions, and (iii) the use of adaptive thresholds when giving feedback.
ERIC Educational Resources Information Center
Chang, Hua-Hua; And Others
Recently, R. Shealy and W. Stout (1993) proposed a procedure for detecting differential item functioning (DIF) called SIBTEST. Current versions of SIBTEST can only be used for dichotomously scored items, but this paper presents an extension to handle polytomous items. The paper presents: (1) a discussion of an appropriate definition of DIF for…
Bayesian Procedures for Identifying Aberrant Response-Time Patterns in Adaptive Testing
ERIC Educational Resources Information Center
van der Linden, Wim J.; Guo, Fanmin
2008-01-01
In order to identify aberrant response-time patterns on educational and psychological tests, it is important to be able to separate the speed at which the test taker operates from the time the items require. A lognormal model for response times with this feature was used to derive a Bayesian procedure for detecting aberrant response times.…
NASA Astrophysics Data System (ADS)
Bargatze, L. F.
2015-12-01
Active Data Archive Product Tracking (ADAPT) is a collection of software routines that permits one to generate XML metadata files to describe and register data products in support of the NASA Heliophysics Virtual Observatory VxO effort. ADAPT is also a philosophy. The ADAPT concept is to use any and all available metadata associated with scientific data to produce XML metadata descriptions in a consistent, uniform, and organized fashion to provide blanket access to the full complement of data stored on a targeted data server. In this poster, we present an application of ADAPT to describe all of the data products that are stored by using the Common Data File (CDF) format served out by the CDAWEB and SPDF data servers hosted at the NASA Goddard Space Flight Center. These data servers are the primary repositories for NASA Heliophysics data. For this purpose, the ADAPT routines have been used to generate data resource descriptions by using an XML schema named Space Physics Archive, Search, and Extract (SPASE). SPASE is the designated standard for documenting Heliophysics data products, as adopted by the Heliophysics Data and Model Consortium. The set of SPASE XML resource descriptions produced by ADAPT includes high-level descriptions of numerical data products, display data products, or catalogs and also includes low-level "Granule" descriptions. A SPASE Granule is effectively a universal access metadata resource; a Granule associates an individual data file (e.g. a CDF file) with a "parent" high-level data resource description, assigns a resource identifier to the file, and lists the corresponding assess URL(s). The CDAWEB and SPDF file systems were queried to provide the input required by the ADAPT software to create an initial set of SPASE metadata resource descriptions. Then, the CDAWEB and SPDF data repositories were queried subsequently on a nightly basis and the CDF file lists were checked for any changes such as the occurrence of new, modified, or deleted
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.
Dissociating proportion congruent and conflict adaptation effects in a Simon-Stroop procedure.
Torres-Quesada, Maryem; Funes, Maria Jesús; Lupiáñez, Juan
2013-02-01
Proportion congruent and conflict adaptation are two well known effects associated with cognitive control. A critical open question is whether they reflect the same or separate cognitive control mechanisms. In this experiment, in a training phase we introduced a proportion congruency manipulation for one conflict type (i.e. Simon), whereas in pre-training and post-training phases two conflict types (e.g. Simon and Spatial Stroop) were displayed with the same incongruent-to-congruent ratio. The results supported the sustained nature of the proportion congruent effect, as it transferred from the training to the post-training phase. Furthermore, this transfer generalized to both conflict types. By contrast, the conflict adaptation effect was specific to conflict type, as it was only observed when the same conflict type (either Simon or Stroop) was presented on two consecutive trials (no effect was observed on conflict type alternation trials). Results are interpreted as supporting the reactive and proactive control mechanisms distinction. PMID:23337083
Dynamic Load Balancing for Adaptive Unstructured Grids
NASA Technical Reports Server (NTRS)
Biswas, Rupak; Saini, Subhash (Technical Monitor)
1998-01-01
Dynamic mesh adaptation on unstructured grids is a powerful tool for computing unsteady three-dimensional problems that require grid modifications to efficiently resolve solution features. By locally refining and coarsening the mesh to capture phenomena of interest, such procedures make standard computational methods more cost effective. Highly refined meshes are required to accurately capture shock waves, contact discontinuities, vortices, and shear layers in fluid flow problems. Adaptive meshes have also proved to be useful in several other areas of computational science and engineering like computer vision and graphics, semiconductor device modeling, and structural mechanics. Local mesh adaptation provides the opportunity to obtain solutions that are comparable to those obtained on globally-refined grids but at a much lower cost. Additional information is contained in the original extended abstract.
Model Refinement Using Eigensystem Assignment
NASA Technical Reports Server (NTRS)
Maghami, Peiman G.
2000-01-01
IA novel approach for the refinement of finite-element-based analytical models of flexible structures is presented. The proposed approach models the possible refinements in the mass, damping, and stiffness matrices of the finite element model in the form of a constant gain feedback with acceleration, velocity, and displacement measurements, respectively. Once the free elements of the structural matrices have been defined, the problem of model refinement reduces to obtaining position, velocity, and acceleration gain matrices with appropriate sparsity that reassign a desired subset of the eigenvalues of the model, along with partial mode shapes, from their baseline values to those obtained from system identification test data. A sequential procedure is used to assign one conjugate pair of eigenvalues at each step using symmetric output feedback gain matrices, and the eigenvectors are partially assigned, while ensuring that the eigenvalues assigned in the previous steps are not disturbed. The procedure can also impose that gain matrices be dissipative to guarantee the stability of the refined model. A numerical example, involving finite element model refinement for a structural testbed at NASA Langley Research Center (Controls-Structures-Interaction Evolutionary model) is presented to demonstrate the feasibility of the proposed approach.
A formal protocol test procedure for the Survivable Adaptable Fiber Optic Embedded Network (SAFENET)
NASA Astrophysics Data System (ADS)
High, Wayne
1993-03-01
This thesis focuses upon a new method for verifying the correct operation of a complex, high speed fiber optic communication network. These networks are of growing importance to the military because of their increased connectivity, survivability, and reconfigurability. With the introduction and increased dependence on sophisticated software and protocols, it is essential that their operation be correct. Because of the speed and complexity of fiber optic networks being designed today, they are becoming increasingly difficult to test. Previously, testing was accomplished by application of conformance test methods which had little connection with an implementation's specification. The major goal of conformance testing is to ensure that the implementation of a profile is consistent with its specification. Formal specification is needed to ensure that the implementation performs its intended operations while exhibiting desirable behaviors. The new conformance test method presented is based upon the System of Communicating Machine model which uses a formal protocol specification to generate a test sequence. The major contribution of this thesis is the application of the System of Communicating Machine model to formal profile specifications of the Survivable Adaptable Fiber Optic Embedded Network (SAFENET) standard which results in the derivation of test sequences for a SAFENET profile. The results applying this new method to SAFENET's OSI and Lightweight profiles are presented.
Capelli, Silvia C.; Bürgi, Hans-Beat; Dittrich, Birger; Grabowsky, Simon; Jayatilaka, Dylan
2014-01-01
Hirshfeld atom refinement (HAR) is a method which determines structural parameters from single-crystal X-ray diffraction data by using an aspherical atom partitioning of tailor-made ab initio quantum mechanical molecular electron densities without any further approximation. Here the original HAR method is extended by implementing an iterative procedure of successive cycles of electron density calculations, Hirshfeld atom scattering factor calculations and structural least-squares refinements, repeated until convergence. The importance of this iterative procedure is illustrated via the example of crystalline ammonia. The new HAR method is then applied to X-ray diffraction data of the dipeptide Gly–l-Ala measured at 12, 50, 100, 150, 220 and 295 K, using Hartree–Fock and BLYP density functional theory electron densities and three different basis sets. All positions and anisotropic displacement parameters (ADPs) are freely refined without constraints or restraints – even those for hydrogen atoms. The results are systematically compared with those from neutron diffraction experiments at the temperatures 12, 50, 150 and 295 K. Although non-hydrogen-atom ADPs differ by up to three combined standard uncertainties (csu’s), all other structural parameters agree within less than 2 csu’s. Using our best calculations (BLYP/cc-pVTZ, recommended for organic molecules), the accuracy of determining bond lengths involving hydrogen atoms from HAR is better than 0.009 Å for temperatures of 150 K or below; for hydrogen-atom ADPs it is better than 0.006 Å2 as judged from the mean absolute X-ray minus neutron differences. These results are among the best ever obtained. Remarkably, the precision of determining bond lengths and ADPs for the hydrogen atoms from the HAR procedure is comparable with that from the neutron measurements – an outcome which is obtained with a routinely achievable resolution of the X-ray data of 0.65 Å. PMID:25295177
Coloured Petri Net Refinement Specification and Correctness Proof with Coq
NASA Technical Reports Server (NTRS)
Choppy, Christine; Mayero, Micaela; Petrucci, Laure
2009-01-01
In this work, we address the formalisation of symmetric nets, a subclass of coloured Petri nets, refinement in COQ. We first provide a formalisation of the net models, and of their type refinement in COQ. Then the COQ proof assistant is used to prove the refinement correctness lemma. An example adapted from a protocol example illustrates our work.
Replacement, reduction and refinement.
Flecknell, Paul
2002-01-01
In 1959, William Russell and Rex Burch published "The Principles of Humane Experimental Technique". They proposed that if animals were to be used in experiments, every effort should be made to Replace them with non-sentient alternatives, to Reduce to a minimum the number of animals used, and to Refine experiments which used animals so that they caused the minimum pain and distress. These guiding principles, the "3 Rs" of animal research, were initially given little attention. Gradually, however, they have become established as essential considerations when animals are used in research. They have influenced new legislation aimed at controlling the use of experimental animals, and in the United Kingdom they have become formally incorporated into the Animal (Scientific) Procedures Act. The three principles, of Replacement, Reduction and Refinement, have also proven to be an area of common ground for research workers who use animals, and those who oppose their use. Scientists, who accept the need to use animals in some experiments, would also agree that it would be preferable not to use animals. If animals were to be used, as few as possible should be used and they should experience a minimum of pain or distress. Many of those who oppose animal experimentation, would also agree that until animal experimentation is stopped, Russell and Burch's 3Rs provide a means to improve animal welfare. It has also been recognised that adoption of the 3Rs can improve the quality of science. Appropriately designed experiments that minimise variation, provide standardised optimum conditions of animals care and minimise unnecessary stress or pain, often yield better more reliable data. Despite the progress made as a result of attention to these principles, several major problems have been identified. When replacing animals with alternative methods, it has often proven difficult to formally validate the alternative. This has proven a particular problem in regulatory toxicology