SAMRAI Source Code Documentation

SAMRAI (Structured Adaptive Mesh Refinement Applications Infrastructure) is a research-oriented software development effort in the Center for Applied Scientific Computing (CASC) at Lawrence Livermore National Laboratory (LLNL). The project has two main objectives. First, SAMRAI enables the application of SAMR (Structured Adaptive Mesh Refinement) technology to computational physics problems important to the DOE and the ASCI program. Seecond, SAMRAI supports algorithm research for adaptive methods in high-performance massively-parallel computing environments.

Questions about this document or the SAMRAI library code should be addressed to samrai@llnl.gov.

The SAMRAI framework source code is partitioned into a number of software ``packages". Each package contains a collection of classes that are logically-related with respect to the role they play in structured AMR applications. Organizing the SAMRAI library in this fashion aids in understanding the overall software design and helps to maintain the integrity of the software architecture. The packages are listed here in order of their library compilation dependencies. This provides insight into the relative complexity of the classes and indicates which packages are needed when using parts of the library. Links to package contents follow the list of package descriptions.

• Toolbox: The "Toolbox" package provides basic, general utility classes that are used throughout the library and in application development. The utilities include: memory management via arena mechanisms; smart pointers, arrays and other container classes; basic MPI utilities; stream classes for packing and unpacking data during interprocessor communication and reading and writing to files; tools for managing input and restart files; and event logging, tracing, and timing.

• Hierarchy: The "Hierarchy" package supports abstract index spaces and box calculus on which most operations on a structured AMR patch hierarchy depend. Structural classes such as patch, patch level, and patch hierarchy, and base classes for managing variables and data living on the hierarchy also reside here.

• Transfer: The "Transfer" package contains classes that provide routines for transferring data between patches on an structured AMR hierarchy. This includes communication algorithms and schedules of transactions for moving data between patches on the same level as well as coarsening and refining data between different levels. The package also contains base classes for operators that refine and coarsen data spatially, interpolate data in time, and implement physical boundary conditions.

• Patchdata: The "Patchdata" package provides support for various concrete patch data types that reside on an structured AMR patch hierarchy. The data types found here include a variety of array-based quantities (cell-centered, node-centered, face-centered, etc.) as well as an "index" type for managing data associated with an arbitrary collection of cell indices (e.g., irregular structures like embedded boundaries or lists of particles). Other types may be added in the future to meet the application needs.

• Mathematical Operations: The "Math Operations" package provides basic arithmetic and other operations that are required for vector kernels, such as dot products and norms. These operations apply to patch data living on a single patch, a single level, or an entire AMR patch hierarchy. This support is provided for all array-based data types in SAMRAI.

• Mesh: The "Mesh" package contains classes for creating patches during construction and adaptive regridding of a structured AMR patch hierarchy. Routines include clustering of tagged cells into box regions (algorithm due to Berger and Rigoutsos) and load balancing based on on either spatially-uniform or nonuniform workload estimates.

• Algorithm: The "Algorithm" package houses classes that are useful for constructing solution algorithms for certain classes of PDE problems on a structured AMR patch hierarchy. For example, this package contains time integration routines, including local time cycling on hierarchy levels, method of lines, and methods for hyperbolic conservation laws. Additional algorithmic support may be introduced to meet application needs as they arise.

• Solvers: The "Solvers" package contains support for applying linear and nonlinear solver method to problems defined on an AMR patch hierarchy. Vectors for treating data defined on a structured AMR patch hierarchy are provided here. SAMRAI also provides interfaces and wrapper classes for employing the PETSc and KINSOL nonlinear solver libraries, the CVODE ODE solver library, and the hypre preconditioner library. An FAC algorithm for solving Poisson problems on an AMR hierarchy is also included.

• Geometry: The "Geometry" package provides support for specific coordinate systems on structured AMR patch hierarchies. This includes mesh spacing, locations of patches in space, as well as a variety of spatial refine/coarsen operators and time interpolation operators for array-based patch data types.

• Application Utilities: The ``Application Utilities'' package contains utilities that are useful when construction applications with SAMRAI, such as routines for setting physical boundary conditions and tools for generating Vizamrai and VisIt data files.

Using SAMRAI Doxygen-generated Documentation with your Doxygen-generated Documentation

If your project uses doxygen and you would like to have your documentation link with SAMRAI's documentation, you will need the tag file generated by SAMRAI's doxygen run.

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