ChemNetworks: New capabilities for high-throughput, real-time chemical graph construction and analysis

A major revision of the ChemNetworks software (originally published in the Journal of Computational Chemistry, 2014, 35, 495–505) is presented. While the original ChemNetworks provided foundational graph construction capabilities for chemical systems, it was limited to simple distance and 3-body angular edge criteria, was not designed for high-performance computing environments or real-time operation alongside running simulations. This release addresses these limitations through three core contributions. First, a recursive Z-matrix-based search algorithm is introduced that enables chemically intuitive, arbitrarily descriptive three-dimensional structure searches, supporting geometric, energetic, and logical criteria. Second, the DataSpaces data staging framework is incorporated as an optional I/O engine, enabling in-memory data exchange between ChemNetworks and running simulations that eliminates persistent storage bottlenecks and supports real-time graph construction and analysis. Third, a modular analysis framework leveraging the igraph library is introduced, providing a straightforward plugin architecture for community-contributed workflows. Benchmark results demonstrate linear scaling with system size and efficient MPI parallelization across up to 64 cores, with total computational complexity of O(N^R T/P), where N is the number of atoms, R is the Z-matrix depth, T is the number of timesteps, and P is the number of MPI processes.