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Software review
CKS: Chemical Kinetics Simulator
Principal authors: William Hinsberg and Frances Houle
IBM Almaden Research Centre
San Jose, California, USA
Keywords Stochastic dynamic, Collectives computational chemistry, Simulation of collectives
Abstract A reader is introduced to a chemical kinetics simulator working on principles of stochastic imitation. Mechanics of simulation and advantages of the software are highlighted. Several toy examples are provided to make nonchemists appreciate a value of the program. Some real life applications are brought up.
There are quite few software packages for chemical simulations. Even fewer packages handle physics of the processes in a reasonably realistic way. Usually dynamic of a simulated systems is abstracted down to systems of differential equations, which are numerically integrated. Such models are difficult to control and process of their verification is painful. Every applied scientist dreams about modelling techniques that can describe physical behaviour of each system's component. In case of chemical systems direct, soft- or hardware, imitation of motion, collision and transformation of molecules would be an ideal approach. These ideas of physics oriented simulation of spatially distributed systems were implemented in cellular automata and lattice gas models (see, e.g. Doolen, 1991; Lawniczak and Kapral, 1995; Rothman and Zaleski, 1997; Chopard and Droz, 1999). A Chemical Kinetics Simulator (CKS) uses the same approach to tackle a kinetic of chemical systems.
In CKS, instead of approximation, which is necessary to integrate differential equations, interaction of molecules is directly executed in a computer. Looking at the problem from a very naive point of view we could portray a simulation of the chemical reaction
One can update array's entries probabilistically, with probability made dependent on the reaction rate constant.
We could say, behaviour of molecular ensembles is imitated rather than dynamic of a single molecule (just to decrease costs of computation). Thus, the CKS simulator relies on the following approach:
A chemical reactor is simulated as a system of discrete particles, where each particle represents a certain amount of reagents. Interaction of reagent pools is represented via interaction of particles.
How it works?
It is very simple to design a sophisticated model in CKS. Friendly and intuitive interface, concise help and cautious control of model's consistency contribute to the ease of designing.
When creating a new reaction...