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ABSTRACT Fragment‐based quantum chemistry offers a means to circumvent the nonlinear computational scaling of conventional electronic structure calculations, by partitioning a large calculation into smaller subsystems then considering the many‐body interactions between them. Variants of this approach have been used to parameterize classical force fields and machine learning potentials, applications that benefit from interoperability between quantum chemistry codes. However, there is a dearth of software that provides interoperability yet is purpose‐built to handle the combinatorial complexity of fragment‐based calculations. To fill this void we introduce “Fragme∩t”, an open‐source software application that provides a tool for community validation of fragment‐based methods, a platform for developing new approximations, and a framework for analyzing many‐body interactions.Fragme∩tincludes algorithms for automatic fragment generation and structure modification, and for distance‐ and energy‐based screening of the requisite subsystems. Checkpointing, database management, and parallelization are handled internally and results are archived in a portable database. Interfaces to various quantum chemistry engines are easy to write and exist already for Q‐Chem, PySCF, xTB, Orca, CP2K, MRCC, Psi4, NWChem, GAMESS, and MOPAC. Applications reported here demonstrate parallel efficiencies around 96% on more than 1000 processors but also showcase that the code can handle large‐scale protein fragmentation using only workstation hardware, all with a codebase that is designed to be usable by non‐experts.Fragme∩tconforms to modern software engineering best practices and is built upon well established technologies including Python, SQLite, and Ray. The source code is available under the Apache 2.0 license. This article is categorized under:Electronic Structure Theory > Ab Initio Electronic Structure MethodsTheoretical and Physical Chemistry > ThermochemistrySoftware > Quantum Chemistry