HTR: An ultra-high speed algorithm for cage recognition of clathrate hydrates

Abstract

Clathrate hydrates find diverse significant applications including but not limited to future energy resources, gas storage and transport, gas separation, water desalination, and refrigeration. Studies on the nucleation, growth, dissociation, and micro/nanoscale properties of clathrate hydrates that are of utmost importance for those applications are challenging by experiments but can be accessible by molecular simulations. By this method, however, identification of cage structures to extract useful insights is highly required. Herein, we introduce a hierarchical topology ring (HTR) algorithm to recognize cage structures with high efficiency and high accuracy. The HTR algorithm can identify all types of complete cages and is particularly optimized for hydrate identification in large-scale systems composed of millions of water molecules. Moreover, topological isomers of cages and n × guest@cage can be uniquely identified. Besides, we validate the use of HTR for the identification of cages of clathrate hydrates upon mechanical loads to failure.