Zacros (http://zacros.org) is a Graph-Theoretical Kinetic Monte Carlo software application for simulating molecular phenomena on catalytic surfaces. The implemented method for listing and randomly choosing a process is based on the idea that the next event to occur has to be the one with the smallest waiting time. The main task is, therefore, reduced to creating a “catalogue” containing the waiting time of all realizable events, finding their minimum and updating the time values of the involved processes. A Skip List based data structure was implemented in Zacros and further extended to provide us with an almost constant time removal operation. Benchmarks have shown that the new algorithm outperforms the existing one, the “Binary Heap”, in a special class of problems. The “bottlenecks”, namely the operations that potentially hinder performance were clearly identified and discussed along with possible performance improvements.
