PumpKin: A tool to find principal pathways in plasma chemical models

PumpKin is a software package to find all principal pathways, i.e. the dominant reaction sequences, in chemical reaction systems. Although many tools are available to integrate numerically arbitrarily complex chemical reaction systems, few tools exist in order to analyze the results and interpret them in relatively simple terms. In particular, due to the large disparity in the lifetimes of the interacting components, it is often useful to group reactions into pathways that recycle the fastest species. This allows a researcher to focus on the slow chemical dynamics, eliminating the shortest timescales. Based on the algorithm described by Lehmann (2004), PumpKin automates the process of finding such pathways, allowing the user to analyze complex kinetics and to understand the consumption and production of a certain species of interest. We designed PumpKin with an emphasis on plasma chemical systems but it can also be applied to atmospheric modeling and to industrial applications such as plasma medicine and plasma-assisted combustion. Program title: PumpKin Catalogue identifier: AETG_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AETG_v1_0.html Program obtainable from: CPC Program Library, Queen’s University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 18753 No. of bytes in distributed program, including test data, etc.: 7011133 Distribution format: tar.gz Programming language: C++. Computer: All computers with a C/C++ compiler. Operating system: All platforms with a C/C++ compiler. Classification: 16.12, 16.14, 19.11, 19.8. External routines: GLPK (GNU linear programming kit) Nature of problem: Analyzing complex chemical models. Solution method: Combining reactions into pathways that recycle short-lived species Running time: Runtime depends on the input files sizes and user’s configuration. For typical use cases we estimate runtime in the order of minutes.