SPaMD studio: An integrated platform for atomistic modeling, simulation, analysis, and visualization

An integrated platform for custom and modular atomistic modeling, high-throughput implementation of various functional simulations, robust atomic topological analysis, and high-fidelity processing and visualization was developed in this study, called the Scalable Parallel Molecular Dynamics (SPaMD) studio. The modular modeling system provides a fast and direct means of constructing specific models such as those of nanostructures, dislocations, and cracks, as well as complex models such as those of bilayers, multilayers, and nanocomposites. Further, the custom modeling system enables consecutive nested processing of selections and operations with a comprehensive workflow to obtain arbitrary models with complicated geometry. Various high-throughput schemes were designed for functional simulations through the integration of automatic modeling tools, loadbalanced task allocation systems, adaptive real-time data analysis, and visualization methods, as well as a robust logic feedback system. In addition, the atomistic analysis supports both on-the-fly and post-quantification for crystal structure, orientation, and dislocation by integrating AACSD and AADIS codes. To facilitate processing and simulation, a user-friendly graphical user interface was designed for SPaMD, which also supports highly efficient rendering for tens of millions of atoms. To demonstrate the efficiency and functionalities of this platform, it was critically validated by conducting several evaluations and tests, which provide guidance for and confidence in its potential applications in targeted atomistic simulations.