An Interoperable, Data-Structure-Neutral Component for Mesh Query and Manipulation

Abstract

Much of the effort required to create a new simulation code goes into developing infrastructure for mesh data manipulation, adaptive refinement, design optimization, and so forth. This infrastructure is an obvious target for code reuse, except that implementations of these functionalities are typically tied to specific data structures. In this article, we describe a software component---an abstract data model and programming interface---designed to provide low-level mesh query and manipulation support for meshing and solution algorithms. The component’s data model provides a data abstraction, completely hiding all details of how mesh data is stored, while its interface defines how applications can interact with that data. Because the component has been carefully designed to be general purpose and efficient, it provides a practical platform for implementing high-level mesh operations independently of the underlying mesh data structures. After describing the data model and interface, we provide several usage examples, each of which has been used successfully with multiple implementations of the interface functionality. The overhead due to accessing mesh data through the interface rather than directly accessing the underlying mesh data is shown to be acceptably small.

Multiphysics simulations: challenges and opportunities.

“…The various ITAPS iMesh implementations (Devine et al, 2009;Chand et al, 2008;Ollivier-Gooch et al, 2010), and others, are based on such a topological abstraction of the mesh. Although it is possible to base the representations used on only the specific mesh entities and adjacencies used in the linkage of specific components, many implementations employ a complete representation in the sense that any of the desired 12 mesh adjacencies can be determined in O(1) time (i.e., are not a function of the number of mesh entities) (Beall and Shephard, 1997;Remacle and Shephard, 2003;Seol and Shephard, 2006).…”

Algorithms and data structures for massively parallel generic adaptive finite element codes

“…However, any other software that allows the well-defined and small list of queries detailed below may equally well be used in place of p4est. For example, this could include the packages that support the ITAPS iMesh interface [Ollivier-Gooch et al 2010].…”

“…Using queries to the oracle, each processor can then rebuild the rich data structures necessary for finite element computations for the "locally owned" part of the global mesh and perform the necessary computations on them. In our implementation, we use the p4est algorithms for 2d and 3d parallel mesh topology [Burstedde et al 2011b] as the oracle; however, it is entirely conceivable to connect to different oracle implementations-for example, packages that support the ITAPS iMesh interface [Ollivier-Gooch et al 2010]-provided they adhere to the query structure detailed in this article, and can respond to certain mesh modification directives discussed below.…”

Efficient Mesh Management in Firedrake Using PETSc DMPlex

“…The PUMI library provides a data model for encapsulating nonmanifold mesh geometries, complete with parallel domain decomposition, data migration capabilities, and predefined discretization definitions [13]. The iMesh component interface [22] defines a generalized data model along with a set of basic capabilities for adaptive mesh generation and manipulation. This has been implemented in MOAB [25] and integrated with mesh generation and adaptation packages [21].…”