FLASH is a publicly available high performance application code which has evolved into a modular, extensible software system from a collection of unconnected legacy codes. FLASH has been successful because its capabilities have been driven by the needs of scientific applications, without compromising maintainability, performance, and usability. In its newest incarnation, FLASH3 consists of inter-operable modules that can be combined to generate different applications. The FLASH architecture allows arbitrarily many alternative implementations of its components to co-exist and interchange with each other, resulting in greater flexibility. Further, a simple and elegant mechanism exists for customization of code functionality without the need to modify the core implementation of the source. A built-in unit test framework providing verifiability, combined with a rigorous software maintenance process, allow the code to operate simultaneously in the * Corresponding author dual mode of production and development. In this paper we describe the FLASH3 architecture, with emphasis on solutions to the more challenging conflicts arising from solver complexity, portable performance requirements, and legacy codes. We also include results from user surveys conducted in 2005 and 2007, which highlight the success of the code.

We have developed a three-dimensional radiative transfer method designed specifically for use with parallel adaptive mesh refinement hydrodynamics codes. This new algorithm, which we call hybrid characteristics, introduces a novel form of ray tracing that can neither be classified as long, nor as short characteristics, but which applies the underlying principles, i.e. efficient execution through interpolation and parallelizability, of both. Primary applications of the hybrid characteristics method are radiation hydrodynamics problems that take into account the effects of photoionization and heating due to point sources of radiation. The method is implemented in the hydrodynamics package FLASH. The ionization, heating, and cooling processes are modelled using the DORIC ionization package. Upon comparison with the long characteristics method, we find that our method calculates the column density with a similarly high accuracy and produces sharp and well defined shadows. We show the quality of the new algorithm in an application to the photoevaporation of multiple over-dense clumps. We present several test problems demonstrating the feasibility of our method for performing high resolution three-dimensional radiation hydrodynamics calculations that span a large range of scales. Initial performance tests show that the ray tracing part of our method takes less time to execute than other parts of the calculation (e.g. hydrodynamics and adaptive mesh refinement), and that a high degree of efficiency is obtained in parallel execution. Although the hybrid characteristics method is developed for problems involving photoionization due to point sources, and in its current implementation ignores the effects of diffuse radiation and scattering, the algorithm can be easily adapted to the case of more general radiation fields.

We investigate the miscible Rayleigh-Taylor (RT) instability in both 2 and 3 dimensions using direct numerical simulations, where the working fluid is assumed incompressible under the Boussinesq approximation. We first consider the case of randomly perturbed interfaces. With a variety of diagnostics, we develop a physical picture for the detailed temporal development of the mixed layer: We identify three distinct evolutionary phases in the development of the mixed layer, which can be related to detailed variations in the growth of the mixing zone. Our analysis provides an explanation for the observed differences between two and three-dimensional RT instability; the analysis also leads us to concentrate on the RT models which (1) work equally well for both laminar and turbulent flows, and (2) do not depend on turbulent scaling within the mixing layer between fluids. These candidate RT models are based on point sources within bubbles (or plumes) and interaction with each other (or the background flow). With this motivation, we examine the evolution of single plumes, and relate our numerical results (of single plumes) to a simple analytical model for plume evolution.

Over the last decade block-structured adaptive mesh refinement (SAMR) has found increasing use in large, publicly available codes and frameworks. SAMR frameworks have evolved along different paths. Some have stayed focused on specific domain areas, others have pursued a more general functionality, provid- ing the building blocks for a larger variety of applications. In this survey paper we examine a representative set of SAMR packages and SAMR-based codes that have been in existence for half a decade or more, have a reasonably sized and active user base outside of their home institutions, and are publicly available.The set consists of a mix of SAMR packages and application codes that cover a broad range of scientific domains. We look at their high-level frameworks, and their approach to dealing with the advent of radical changes in hardware architecture. The codes included in this survey are BoxLib, Cactus, Chombo, Enzo, FLASH, and Uintah.

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