Scott M. Stark

Computer generated reaction modelling: Decomposition and encoding algorithms for determining species uniqueness

Abstract The concept of computer generated reaction modelling was broadened through the development of a general planar graph algorithm for determination of isomorphism. The previous capability was limited by its inability to determine the uniqueness of ring-containing species unambiguously, restricting the application of automatic network generation to non-cyclic species or cyclic species where the ring was not involved in the chemical transformation. In this work, the systematic identification of both noncyclic and cyclic species was carried out by constructing the structurally explicit decomposition tree, an assembly of the biconnected components of the graph, from which a graph invariant unique string code was obtained by iteratively encoding and ordering the subtrees of the decomposition tree. A lexicographical comparison of the unique string code of the candidate species with the string codes of all previously generated species with the same empirical formula allowed unambiguous determination of species uniqueness.

Computer generated reaction networks: on-the-fly calculation of species properties using computational quantum chemistry

Abstract An algorithm for the translation of the chemically rich two-dimensional molecular graph into a three-dimensional internal coordinate representation of the relative positions of the atoms in space is described. This enables on-the-fly calculations of species properties during the computer generation of reaction networks. The algorithm systematically species bond distances, bond angles and dihedral angles. Geometric parameters for atoms belonging to cycles required the specification of predefined geometrical templates. Templates for six-membered rings of the types aromatic, cyclohexadienyl, cyclohexenyl and cyclohexyl were therefore developed and optimized. An algorithm was also developed for the identification of tight cycles and their member atoms. This was critical to categorize atoms as noncyclic or cyclic.

LU decomposition optimized for a parallel computer with a hierarchical distributed memory

Abstract The implementation of an efficient hybrid parallel block LU decomposition procedure for dense systems on a BBN TC2000 parallel computer is discussed. The TC2000 is of the MIMD architecture with distributed memory. The key characteristic of this architecture is a hierarchical memory structure (register, cache, local, shared). This study shows that efficient memory use, both in terms of shared memory and cache utilization, is the key to optimal performance when dealing with memory hierarchies such as in the TC2000. Although for a system of equations of fixed size, the Mflops per processor rate decreases as the number of processors increases, almost constant performance has been obtained when the number of equations is increased simultaneously to the number of processors used.

Strategies for modelling kinetic interactions in complex mixtures: Monte Carlo algorithms for MIMD parallel architectures

Abstract The parallel implementation of Monte Carlo reaction models for kinetically coupled reaction systems is discussed in the context of a BBN TC2000 MIMD architecture. A comparatively simple Rice—Herzfeld co-pyrolysis reaction scheme is utilized to develop four modelling strategies encompassing “full system”, “partial system”, “fixed-time”, and “variable-time” simulation approaches. The parallel efficiency of the partial system approaches was good. The partial system variable-time algorithm was then applied to simulate the pyrolysis of a complex petroleum resid to demonstrate the scale-up characteristics of the parallel algorithms. The resulting parallel efficiency was excellent (> 90%). These results indicate that the Monte Carlo modelling approach is sufficiently robust to handle kinetically coupled systems, and that the approach is highly parallel.