Advances in the numerical treatment of grain-boundary migration: Coupling with mass transport and mechanics

This work is based upon a coupled, lattice-based continuum formulation that was previously applied to problems involving strong coupling between mechanics and mass transport; e.g. diffusional creep and electromigration. Here we discuss an enhancement of this formulation to account for migrating grain boundaries. The level set method is used to model grain-boundary migration in an Eulerian framework where a grain boundary is represented as the zero level set of an evolving higher-dimensional function. This approach can easily be generalized to model other problems involving migrating interfaces; e.g. void evolution and free-surface morphology evolution. The level-set equation is recast in a remarkably simple form which obviates the need for spatial stabilization techniques. This simplified level-set formulation makes use of velocity extension and field re-initialization techniques. In addition, a least-squares smoothing technique is used to compute the local curvature of a grain boundary directly from the level-set field without resorting to higher-order interpolation. A notable feature is that the coupling between mass transport, mechanics and grain-boundary migration is fully accounted for. The complexities associated with this coupling are highlighted and the operator-split algorithm used to solve the coupled equations is described.Comment: 28 pages, 9 figures, LaTeX; Accepted for publication in Computer Methods in Applied Mechanics and Engineering. [Style and formatting modifications made, references added.

A Domain-Specific Language and Editor for Parallel Particle Methods

Domain-specific languages (DSLs) are of increasing importance in scientific high-performance computing to reduce development costs, raise the level of abstraction and, thus, ease scientific programming. However, designing and implementing DSLs is not an easy task, as it requires knowledge of the application domain and experience in language engineering and compilers. Consequently, many DSLs follow a weak approach using macros or text generators, which lack many of the features that make a DSL a comfortable for programmers. Some of these features---e.g., syntax highlighting, type inference, error reporting, and code completion---are easily provided by language workbenches, which combine language engineering techniques and tools in a common ecosystem. In this paper, we present the Parallel Particle-Mesh Environment (PPME), a DSL and development environment for numerical simulations based on particle methods and hybrid particle-mesh methods. PPME uses the meta programming system (MPS), a projectional language workbench. PPME is the successor of the Parallel Particle-Mesh Language (PPML), a Fortran-based DSL that used conventional implementation strategies. We analyze and compare both languages and demonstrate how the programmer's experience can be improved using static analyses and projectional editing. Furthermore, we present an explicit domain model for particle abstractions and the first formal type system for particle methods.Comment: Submitted to ACM Transactions on Mathematical Software on Dec. 25, 201

An equation-free computational approach for extracting population-level behavior from individual-based models of biological dispersal

The movement of many organisms can be described as a random walk at either or both the individual and population level. The rules for this random walk are based on complex biological processes and it may be difficult to develop a tractable, quantitatively-accurate, individual-level model. However, important problems in areas ranging from ecology to medicine involve large collections of individuals, and a further intellectual challenge is to model population-level behavior based on a detailed individual-level model. Because of the large number of interacting individuals and because the individual-level model is complex, classical direct Monte Carlo simulations can be very slow, and often of little practical use. In this case, an equation-free approach may provide effective methods for the analysis and simulation of individual-based models. In this paper we analyze equation-free coarse projective integration. For analytical purposes, we start with known partial differential equations describing biological random walks and we study the projective integration of these equations. In particular, we illustrate how to accelerate explicit numerical methods for solving these equations. Then we present illustrative kinetic Monte Carlo simulations of these random walks and show a decrease in computational time by as much as a factor of a thousand can be obtained by exploiting the ideas developed by analysis of the closed form PDEs. The illustrative biological example here is chemotaxis, but it could be any random walker which biases its movement in response to environmental cues.Comment: 30 pages, submitted to Physica