HOOMD-blue version 3.0 A Modern, Extensible, Flexible, Object-Oriented API for Molecular Simulations

HOOMD-blue is a library for running molecular dynamics and hard particle Monte Carlo simulations that uses pybind11 to provide a Python interface to fast C++ internals. The package is designed to scale from a single CPU core to thousands of NVIDIA or AMD GPUs. In developing HOOMD-blue version 3.0, we significantly improve the application protocol interface (API) by making it more flexible, extensible, and Pythonic. We have also striven to provide simpler and more performant entry points to the internal C++ classes and data structures. With these updates, we show how HOOMD-blue users will be able to write completely custom Python classes which integrate directly into the simulation run loop and analyze previously inaccessible data. Throughout this paper, we focus on how these goals have been achieved and explain design decisions through examples of the newly developed API.