ChemNetworks: New Capabilities for High-Throughput, Real-Time Chemical Graph Construction and Analysis

A major revision of the ChemNetworks software (originally published in the \textit{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 $O(N^RT/P)$, 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.