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Michael L Norman - One of the best experts on this subject based on the ideXlab platform.
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enzo an Adaptive Mesh refinement code for astrophysics
Astrophysical Journal Supplement Series, 2014Co-Authors: G.l. Bryan, P Wang, Michael L Norman, David C Collins, Tom Abel, Brian W Oshea, John H Wise, Matthew J Turk, Daniel R ReynoldsAbstract:This paper describes the open-source code Enzo, which uses block-structured Adaptive Mesh refinement to provide high spatial and temporal resolution for modeling astrophysical fluid flows. The code is Cartesian, can be run in one, two, and three dimensions, and supports a wide variety of physics including hydrodynamics, ideal and non-ideal magnetohydrodynamics, N-body dynamics (and, more broadly, self-gravity of fluids and particles), primordial gas chemistry, optically thin radiative cooling of primordial and metal-enriched plasmas (as well as some optically-thick cooling models), radiation transport, cosmological expansion, and models for star formation and feedback in a cosmological context. In addition to explaining the algorithms implemented, we present solutions for a wide range of test problems, demonstrate the code's parallel performance, and discuss the Enzo collaboration's code development methodology.
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enzo an Adaptive Mesh refinement code for astrophysics
arXiv: Instrumentation and Methods for Astrophysics, 2013Co-Authors: G.l. Bryan, P Wang, Michael L Norman, David C Collins, Tom Abel, Brian W Oshea, John H Wise, Matthew J Turk, Daniel R Reynolds, Samuel W SkillmanAbstract:This paper describes the open-source code Enzo, which uses block-structured Adaptive Mesh refinement to provide high spatial and temporal resolution for modeling astrophysical fluid flows. The code is Cartesian, can be run in 1, 2, and 3 dimensions, and supports a wide variety of physics including hydrodynamics, ideal and non-ideal magnetohydrodynamics, N-body dynamics (and, more broadly, self-gravity of fluids and particles), primordial gas chemistry, optically-thin radiative cooling of primordial and metal-enriched plasmas (as well as some optically-thick cooling models), radiation transport, cosmological expansion, and models for star formation and feedback in a cosmological context. In addition to explaining the algorithms implemented, we present solutions for a wide range of test problems, demonstrate the code's parallel performance, and discuss the Enzo collaboration's code development methodology.
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cosmological Adaptive Mesh refinement magnetohydrodynamics with enzo
Astrophysical Journal Supplement Series, 2010Co-Authors: David C Collins, Michael L Norman, Hao Xu, Hui Li, Shengtai LiAbstract:In this work, we present EnzoMHD, the extension of the cosmological code Enzo to include the effects of magnetic fields through the ideal magnetohydrodynamics approximation. We use a higher order Godunov method for the computation of interface fluxes. We use two constrained transport methods to compute the electric field from those interface fluxes, which simultaneously advances the induction equation and maintains the divergence of the magnetic field. A second-order divergence-free reconstruction technique is used to interpolate the magnetic fields in the block-structured Adaptive Mesh refinement framework already extant in Enzo. This reconstruction also preserves the divergence of the magnetic field to machine precision. We use operator splitting to include gravity and cosmological expansion. We then present a series of cosmological and non-cosmological test problems to demonstrate the quality of solution resulting from this combination of solvers.
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cosmological shocks in Adaptive Mesh refinement simulations and the acceleration of cosmic rays
The Astrophysical Journal, 2008Co-Authors: Samuel W Skillman, Brian W Oshea, Eric J Hallman, Jack O Burns, Michael L NormanAbstract:We present new results characterizing cosmological shocks within Adaptive Mesh refinement N-body/hydrodynamic simulations that are used to predict nonthermal components of large-scale structure. This represents the first study of shocks using Adaptive Mesh refinement. We propose a modified algorithm for finding shocks from those used on unigrid simulations that reduces the shock frequency of low Mach number shocks by a factor of ~3. We then apply our new technique to a large, (512 h−1 Mpc)3, cosmological volume and study the shock Mach number () distribution as a function of preshock temperature, density, and redshift. Because of the large volume of the simulation, we have superb statistics that result from having thousands of galaxy clusters. We find that the Mach number evolution can be interpreted as a method to visualize large-scale structure formation. Shocks with 20 generally follow accretion onto filaments and galaxy clusters, respectively. By applying results from nonlinear diffusive shock acceleration models using the first-order Fermi process, we calculate the amount of kinetic energy that is converted into cosmic-ray protons. The acceleration of cosmic-ray protons is large enough that in order to use galaxy clusters as cosmological probes, the dynamic response of the gas to the cosmic rays must be included in future numerical simulations.
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structured Adaptive Mesh refinement samr grid methods
1999Co-Authors: Scott B Baden, Dennis Gannon, Michael L Norman, Nikos P ChrisochoidesAbstract:Foreword * Preface * Part I: Programming Complexity of SAMR Algorithms. Systems engineering for high-performance computing software: The HDDA/DAGH infrastructure for implementation of parallel structured Adaptive Mesh. HAMR: The hierarchical Adaptive Mesh refinement system. AMR++: A design for parallel object-oriented Adaptive Mesh refinement. RSL: A parallel runtime system library for regional atmospheric models with nesting. Software abstractions and computational issues in parallel structured Adaptive Mesh methods for electronic structure calculations. Structured Adaptive Mesh refinement using high performance fortran * Part II: Applicability and Numerical Challenges of SAMR Methods. The dynamics of localized coherent structures and the role of Adaptive software in multiscale modeling. Progress, results, and experiences in developing an Adaptive solver for steady state turbulent reacting flows in industrial boilers and furnaces. Making arbitrarily small black holes: Experiences with AMR in numerical relativity. A hybrid AMR application for cosmology and astrophysics * List of Participants
Soheil Soghrati - One of the best experts on this subject based on the ideXlab platform.
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conforming to interface structured Adaptive Mesh refinement 3d algorithm and implementation
Computational Mechanics, 2018Co-Authors: Anand Nagarajan, Soheil SoghratiAbstract:A new non-iterative Mesh generation algorithm named conforming to interface structured Adaptive Mesh refinement (CISAMR) is introduced for creating 3D finite element models of problems with complex geometries. CISAMR transforms a structured Mesh composed of tetrahedral elements into a conforming Mesh with low element aspect ratios. The construction of the Mesh begins with the structured Adaptive Mesh refinement of elements in the vicinity of material interfaces. An r-adaptivity algorithm is then employed to relocate selected nodes of nonconforming elements, followed by face-swapping a small fraction of them to eliminate tetrahedrons with high aspect ratios. The final conforming Mesh is constructed by sub-tetrahedralizing remaining nonconforming elements, as well as tetrahedrons with hanging nodes. In addition to studying the convergence and analyzing element-wise errors in Meshes generated using CISAMR, several example problems are presented to show the ability of this method for modeling 3D problems with intricate morphologies.
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a conforming to interface structured Adaptive Mesh refinement technique for modeling fracture problems
Computational Mechanics, 2017Co-Authors: Soheil Soghrati, Fei Xiao, Anand NagarajanAbstract:A Conforming to Interface Structured Adaptive Mesh Refinement (CISAMR) technique is introduced for the automated transformation of a structured grid into a conforming Mesh with appropriate element aspect ratios. The CISAMR algorithm is composed of three main phases: (i) Structured Adaptive Mesh Refinement (SAMR) of the background grid; (ii) r-adaptivity of the nodes of elements cut by the crack; (iii) sub-triangulation of the elements deformed during the r-adaptivity process and those with hanging nodes generated during the SAMR process. The required considerations for the treatment of crack tips and branching cracks are also discussed in this manuscript. Regardless of the complexity of the problem geometry and without using iterative smoothing or optimization techniques, CISAMR ensures that aspect ratios of conforming elements are lower than three. Multiple numerical examples are presented to demonstrate the application of CISAMR for modeling linear elastic fracture problems with intricate morphologies.
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conforming to interface structured Adaptive Mesh refinement
Finite Elements in Analysis and Design, 2017Co-Authors: Soheil Soghrati, Anand Nagarajan, Bowen LiangAbstract:This manuscript introduces a new method named Conforming to Interface Structured Adaptive Mesh Refinement (CISAMR) for the automated finite element modeling of problems with complex morphologies. The CISAMR transforms a simple structured Mesh of quadrilateral elements into a conforming hybrid Mesh composed of quadrilateral and triangular elements with low aspect ratios using a non-iterative algorithm. The automated construction of the Mesh begins with implementing a customized Structured Adaptive Mesh Refinement (SAMR) algorithm to achieve the desired element size along materials interfaces. A new r-adaptivity algorithm is then employed to move selected nodes of nonconforming elements to intersection points of their edges with the interface, followed by the diagonal sub-triangulation of all elements deformed during this process into conforming sub-triangles. CISAMR does not require relocating the nodes of the background Mesh or creating any new node away from materials interfaces after the completion of the SAMR phase. Further, this method can easily handle special cases such as intersecting boundaries/interfaces, while ensuring that aspect ratios of resulting sub-elements are lower than three. A comprehensive discussion is provided on different aspects of the implementation of CISAMR, followed by several example problems to show its application for modeling materials with complex microstructures. HighlightsNew non-iterative algorithm (CISAMR) for the automated transformation of structured grids into conforming Meshes.Ensuring that aspect ratios of resulting elements are lower than three.Preserving the hierarchy of element in the refined background Mesh.Demonstrating the application of CISAMR for modeling heterogeneous and fiber reinforced composites with intricate microstructures.
P Wang - One of the best experts on this subject based on the ideXlab platform.
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enzo an Adaptive Mesh refinement code for astrophysics
Astrophysical Journal Supplement Series, 2014Co-Authors: G.l. Bryan, P Wang, Michael L Norman, David C Collins, Tom Abel, Brian W Oshea, John H Wise, Matthew J Turk, Daniel R ReynoldsAbstract:This paper describes the open-source code Enzo, which uses block-structured Adaptive Mesh refinement to provide high spatial and temporal resolution for modeling astrophysical fluid flows. The code is Cartesian, can be run in one, two, and three dimensions, and supports a wide variety of physics including hydrodynamics, ideal and non-ideal magnetohydrodynamics, N-body dynamics (and, more broadly, self-gravity of fluids and particles), primordial gas chemistry, optically thin radiative cooling of primordial and metal-enriched plasmas (as well as some optically-thick cooling models), radiation transport, cosmological expansion, and models for star formation and feedback in a cosmological context. In addition to explaining the algorithms implemented, we present solutions for a wide range of test problems, demonstrate the code's parallel performance, and discuss the Enzo collaboration's code development methodology.
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enzo an Adaptive Mesh refinement code for astrophysics
arXiv: Instrumentation and Methods for Astrophysics, 2013Co-Authors: G.l. Bryan, P Wang, Michael L Norman, David C Collins, Tom Abel, Brian W Oshea, John H Wise, Matthew J Turk, Daniel R Reynolds, Samuel W SkillmanAbstract:This paper describes the open-source code Enzo, which uses block-structured Adaptive Mesh refinement to provide high spatial and temporal resolution for modeling astrophysical fluid flows. The code is Cartesian, can be run in 1, 2, and 3 dimensions, and supports a wide variety of physics including hydrodynamics, ideal and non-ideal magnetohydrodynamics, N-body dynamics (and, more broadly, self-gravity of fluids and particles), primordial gas chemistry, optically-thin radiative cooling of primordial and metal-enriched plasmas (as well as some optically-thick cooling models), radiation transport, cosmological expansion, and models for star formation and feedback in a cosmological context. In addition to explaining the algorithms implemented, we present solutions for a wide range of test problems, demonstrate the code's parallel performance, and discuss the Enzo collaboration's code development methodology.
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Adaptive Mesh fluid simulations on gpu
New Astronomy, 2010Co-Authors: P Wang, Tom Abel, Ralf KaehlerAbstract:Abstract We describe an implementation of compressible inviscid fluid solvers with block-structured Adaptive Mesh refinement on Graphics Processing Units using NVIDIA’s CUDA. We show that a class of high resolution shock capturing schemes can be mapped naturally on this architecture. Using the method of lines approach with the second order total variation diminishing Runge–Kutta time integration scheme, piecewise linear reconstruction, and a Harten–Lax–van Leer Riemann solver, we achieve an overall speedup of approximately 10 times faster execution on one graphics card as compared to a single core on the host computer. We attain this speedup in uniform grid runs as well as in problems with deep AMR hierarchies. Our framework can readily be applied to more general systems of conservation laws and extended to higher order shock capturing schemes. This is shown directly by an implementation of a magneto-hydrodynamic solver and comparing its performance to the pure hydrodynamic case. Finally, we also combined our CUDA parallel scheme with MPI to make the code run on GPU clusters. Close to ideal speedup is observed on up to four GPUs.
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arbitrary lagrangian eulerian Adaptive Mesh refinement
2009Co-Authors: A E Koniges, D Eder, N Masters, R W Anderson, B Gunney, David J. Benson, P Wang, A. Fisher, P DixitAbstract: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).
Anand Nagarajan - One of the best experts on this subject based on the ideXlab platform.
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conforming to interface structured Adaptive Mesh refinement 3d algorithm and implementation
Computational Mechanics, 2018Co-Authors: Anand Nagarajan, Soheil SoghratiAbstract:A new non-iterative Mesh generation algorithm named conforming to interface structured Adaptive Mesh refinement (CISAMR) is introduced for creating 3D finite element models of problems with complex geometries. CISAMR transforms a structured Mesh composed of tetrahedral elements into a conforming Mesh with low element aspect ratios. The construction of the Mesh begins with the structured Adaptive Mesh refinement of elements in the vicinity of material interfaces. An r-adaptivity algorithm is then employed to relocate selected nodes of nonconforming elements, followed by face-swapping a small fraction of them to eliminate tetrahedrons with high aspect ratios. The final conforming Mesh is constructed by sub-tetrahedralizing remaining nonconforming elements, as well as tetrahedrons with hanging nodes. In addition to studying the convergence and analyzing element-wise errors in Meshes generated using CISAMR, several example problems are presented to show the ability of this method for modeling 3D problems with intricate morphologies.
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a conforming to interface structured Adaptive Mesh refinement technique for modeling fracture problems
Computational Mechanics, 2017Co-Authors: Soheil Soghrati, Fei Xiao, Anand NagarajanAbstract:A Conforming to Interface Structured Adaptive Mesh Refinement (CISAMR) technique is introduced for the automated transformation of a structured grid into a conforming Mesh with appropriate element aspect ratios. The CISAMR algorithm is composed of three main phases: (i) Structured Adaptive Mesh Refinement (SAMR) of the background grid; (ii) r-adaptivity of the nodes of elements cut by the crack; (iii) sub-triangulation of the elements deformed during the r-adaptivity process and those with hanging nodes generated during the SAMR process. The required considerations for the treatment of crack tips and branching cracks are also discussed in this manuscript. Regardless of the complexity of the problem geometry and without using iterative smoothing or optimization techniques, CISAMR ensures that aspect ratios of conforming elements are lower than three. Multiple numerical examples are presented to demonstrate the application of CISAMR for modeling linear elastic fracture problems with intricate morphologies.
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conforming to interface structured Adaptive Mesh refinement
Finite Elements in Analysis and Design, 2017Co-Authors: Soheil Soghrati, Anand Nagarajan, Bowen LiangAbstract:This manuscript introduces a new method named Conforming to Interface Structured Adaptive Mesh Refinement (CISAMR) for the automated finite element modeling of problems with complex morphologies. The CISAMR transforms a simple structured Mesh of quadrilateral elements into a conforming hybrid Mesh composed of quadrilateral and triangular elements with low aspect ratios using a non-iterative algorithm. The automated construction of the Mesh begins with implementing a customized Structured Adaptive Mesh Refinement (SAMR) algorithm to achieve the desired element size along materials interfaces. A new r-adaptivity algorithm is then employed to move selected nodes of nonconforming elements to intersection points of their edges with the interface, followed by the diagonal sub-triangulation of all elements deformed during this process into conforming sub-triangles. CISAMR does not require relocating the nodes of the background Mesh or creating any new node away from materials interfaces after the completion of the SAMR phase. Further, this method can easily handle special cases such as intersecting boundaries/interfaces, while ensuring that aspect ratios of resulting sub-elements are lower than three. A comprehensive discussion is provided on different aspects of the implementation of CISAMR, followed by several example problems to show its application for modeling materials with complex microstructures. HighlightsNew non-iterative algorithm (CISAMR) for the automated transformation of structured grids into conforming Meshes.Ensuring that aspect ratios of resulting elements are lower than three.Preserving the hierarchy of element in the refined background Mesh.Demonstrating the application of CISAMR for modeling heterogeneous and fiber reinforced composites with intricate microstructures.
Phillip Colella - One of the best experts on this subject based on the ideXlab platform.
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damping of spurious wave reflections from coarse fine Adaptive Mesh refinement grid boundaries
International Conference on Plasma Science, 2010Co-Authors: Sven H Chilton, Phillip ColellaAbstract:Adaptive Mesh refinement (AMR) is an efficient technique for solving systems of partial differential equations numerically. The underlying algorithm determines where and when a base spatial and temporal grid must be resolved further in order to achieve the desired precision and accuracy in the numerical solution. However, propagating wave solutions prove problematic for AMR. A wave traveling from a finely resolved region into a coarsely resolved region encounters a numerical impedance mismatch, resulting in spurious reflections off of the coarse-fine grid boundary. These reflected waves then become trapped inside the fine region.
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block structured Adaptive Mesh and time refinement for hybrid hyperbolic n body systems
Journal of Computational Physics, 2007Co-Authors: Francesco Miniati, Phillip ColellaAbstract: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.
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An Adaptive Mesh refinement benchmark for modern parallel programming languages
SC '07: Proceedings of the 2007 ACM IEEE Conference on Supercomputing, 2007Co-Authors: Jimmy Su, Katherine Yelick, Phillip Colella, Noel KeenAbstract:We present an Adaptive Mesh Refinement benchmark for evaluating programmability and performance of modern parallel programming languages. Benchmarks employed today by language developing teams, originally designed for performance evaluation of computer architectures, do not fully capture the complexity of state-of-the-art computational software systems running on today's parallel machines or to be run on the emerging ones from the multi-cores to the peta-scale High Productivity Computer Systems. This benchmark, extracted from a real application framework, presents challenges for a programming language in both expressiveness and performance. It consists of an infrastructure for finite difference calculations on block-structured Adaptive Meshes and a solver for elliptic Partial Differential Equations built on this infrastructure. Adaptive Mesh Refinement algorithms are challenging to implement due to the irregularity introduced by local Mesh refinement. We describe those challenges posed by this benchmark through two reference implementations (C++ /Fortran/MPI and Titanium) and in the context of three programming models.
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a fourth order accurate Adaptive Mesh refinement method forpoisson s equation
Journal of Computational Physics, 2004Co-Authors: Michael F Barad, Phillip ColellaAbstract:We present a block-structured Adaptive Mesh refinement (AMR) method for computing solutions to Poisson's equation in two and three dimensions. It is based on a conservative, finite-volume formulation of the classical Mehrstellen methods. This is combined with finite volume AMR discretizations to obtain a method that is fourth-order accurate in solution error, and with easily verifiable solvability conditions for Neumann and periodic boundary conditions.
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a fourth order accurate Adaptive Mesh refinement method for poisson s equation 1 2
Lawrence Berkeley National Laboratory, 2004Co-Authors: Michael F Barad, Phillip ColellaAbstract:We present a block-structured Adaptive Mesh refinement (AMR) method for computing solutions to Poisson’s equation in two and three dimensions. It is based on a conservative, finite-volume formulation of the classical Mehrstellen methods. This is combined with finite volume AMR discretizations to obtain a method that is fourthorder accurate in solution error, and with easily verifiable solvability conditions for Neumann and periodic boundary conditions.