Managing complex data and geometry in parallel structured AMR applications

Adaptive mesh refinement (AMR) is an increasingly important simulation methodology for many science and engineering problems. AMR has the potential to generate highly resolved simulations efficiently by dynamically refining the computational mesh near key numerical solution features. AMR requires more complex numerical algorithms and programming than uniform fixed mesh approaches. Software libraries that provide general AMR functionality can ease these burdens significantly. A major challenge for library developers is to achieve adequate flexibility to meet diverse and evolving application requirements. In this paper, we describe the design of software abstractions for general AMR data management and parallel communication operations in SAMRAI, an object-oriented C++ structured AMR (SAMR) library developed at Lawrence Livermore National Laboratory (LLNL). The SAMRAI infrastructure provides the foundation for a variety of diverse application codes at LLNL and elsewhere. We illustrate SAMRAI functionality by describing how its unique features are used in these codes which employ complex data structures and geometry. We highlight capabilities for moving and deforming meshes, coupling multiple SAMR mesh hierarchies, and immersed and embedded boundary methods for modeling complex geometrical features. We also describe how irregular data structures, such as particles and internal mesh boundaries, may be implemented using SAMRAI tools without excessive application programmer effort. This work was performed under the auspices of the US Department of Energy by University of California Lawrence Livermore National Laboratory under contract number W-7405-Eng-48 and is released under UCRL-JRNL-214559.