HlightReaxMD: A Machine Learning-Augmented Multiscale Analysis Framework for Radiation Chemistry Dynamics and Damage...

Molecular dynamics (MD) simulations are currently widely used to study large-scale displacement cascades based on massive simulation trajectories. However, when the irradiation process involves the complex chemical reactions, effectively analyzing and extracting features from these data becomes a challenge. Here, we introduce a new cross-platform toolkit, HlightReaxMD, designed to directly obtain information about the irradiation damage process and chemical reactions from MD trajectories and further achieve the prediction of irradiation damage. The analysis tools in HlightReaxMD include chemical reaction analysis and calculation of reaction kinetic parameters, analysis of the collision cascade process, and calculation of necessary physicochemical properties. HlightReaxMD supports the analysis of all elements used in reactive force fields by reading ReaxFF potential file parameters and provides an automated solution for tracking atomic-scale collision events and analyzing chemical reaction mechanisms through constructing cascade trees and reaction network paths. A machine learning-driven model using the analysis results has been included in HlightReaxMD, which can predict irradiation damage by considering various factors, rather than relying solely on the Norgett-Robinson-Torrens displacements per atom (NRT-dpa) model. It enables researchers to automatically obtain dynamic processes and reaction information from atomic to microscale defects from terabyte-level trajectory data. Thus, HlightReaxMD can promote systematic research on irradiation effects in materials science.