Reactive system

Abstract: STATEMATE is a set of tools, with a heavy graphical orientation, intended for the specification, analysis, design, and documentation of large and complex reactive systems. It enables a user to prepare, analyze, and debug diagrammatic, yet precise, descriptions of the system under development from three interrelated points of view, capturing structure, functionality, and behavior. These views are represented by three graphical languages, the most intricate of which is the language of statecharts, used to depict reactive behavior over time. In addition to the use of statecharts, the main novelty of STATEMATE is in the fact that it understands the entire descriptions perfectly, to the point of being able to analyze them for crucial dynamic properties, to carry out rigorous executions and simulations of the described system, and to create running code automatically. These features are invaluable when it comes to the quality and reliability of the final outcome. >

Abstract: Some observations are made concerning the process of developing complex systems. A broad class of systems, termed reactive, is singled out as being particularly problematic when it comes to finding satisfactory methods for behavioral description. In this paper we recommend the recently proposed statechart method for this purpose. Moreover, it is observed that most reactive systems cannot be developed in a linear stepwise fashion, but, rather, give rise to a two-dimensional development process, featuring behavioral aspects in the one dimension and implementational ones in the other. Concurrency may occur in both dimensions, as orthogonality of states in the one and as parallelism of subsystems in the other. A preliminary approach to working one’s way through this “magic square” of system development is then presented. The ideas described herein seem to be relevant to a wide variety of application areas.

Abstract: Molecular dynamics modeling has provided a powerful tool for simulating and understanding diverse systems - ranging from materials processes to biophysical phenomena. Parallel formulations of these methods have been shown to be among the most scalable scientific computing applications. Many instances of this class of methods rely on a static bond structure for molecules, rendering them infeasible for reactive systems. Recent work on reactive force fields has resulted in the development of ReaxFF, a novel bond order potential that bridges quantum-scale and classical MD approaches by explicitly modeling bond activity (reactions) and charge equilibration. These aspects of ReaxFF pose significant challenges from a computational standpoint, both in sequential and parallel contexts. Evolving bond structure requires efficient dynamic data structures. Minimizing electrostatic energy through charge equilibration requires the solution of a large sparse linear system with a shielded electrostatic kernel at each sub-femtosecond long time-step. In this context, reaching spatio-temporal scales of tens of nanometers and nanoseconds, where phenomena of interest can be observed, poses significant challenges. In this paper, we present the design and implementation details of the Purdue Reactive Molecular Dynamics code, PuReMD. PuReMD has been demonstrated to be highly efficient (in terms of processor performance) and scalable. It extends current spatio-temporal simulation capability for reactive atomistic systems by over an order of magnitude. It incorporates efficient dynamic data structures, algorithmic optimizations, and effective solvers to deliver low per-time-step simulation time, with a small memory footprint. PuReMD is comprehensively validated for performance and accuracy on up to 3375 cores on a commodity cluster (Hera at LLNL-OCF). Potential performance bottlenecks to scalability beyond our experiments have also been analyzed. PuReMD is available over the public domain and has been used to model diverse systems, ranging from strain relaxation in Si-Ge nanobars, water-silica surface interaction, and oxidative stress in lipid bilayers (bio-membranes).