Tracking explicit chain sequence in kinetic Monte Carlo simulations

The execution of individual KMC events can become a major computational bottleneck in the simulation of sequences along chains using KMC because of complex data storage schemes required to record the sequence of each chain. The execution of a KMC event can be very time-consuming because searching, moving, and modifying all the data detailing a chain to reflect the transformation as a result of a chemical reaction event can be computationally expensive. To address this issue, we developed a new data storage scheme for recording sequence, which can significantly improve calculation speed without affecting the information content of the calculations. By using the proposed data storage scheme, the computational time can be reduced significantly from 12 h to 4 min for our test reaction system. The execution of individual KMC events can become a major computational bottleneck in the simulation of sequences along chains using kinetic Monte Carlo because of the complex data storage schemes required to record sequence of each chain. Here, we report a new data storage scheme for recording sequence, which can significantly reduce calculation time from hours to minutes in our test system without affecting the information content of the calculations.