10.24435/MATERIALSCLOUD:2019.0008/V1
Kahle, Leonid
Musaelian, Albert
Marzari, Nicola
Kozinsky, Boris
Unsupervised landmark analysis for jump detection in molecular dynamics simulations
Materials Cloud
2019
molecular dynamics
site analysis
tracer diffusion
BIG-MAP
2019-02-12
en
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International https://creativecommons.org/licenses/by/4.0/legalcode
Molecular dynamics is a versatile and powerful method to study diffusion in solid-state ionic conductors, requiring minimal prior knowledge of equilibrium or transition states of the system's free energy surface. However, the analysis of trajectories for relevant but rare events, such as a jump of the diffusing mobile ion, is still rather cumbersome, requiring prior knowledge of the diffusive process in order to get meaningful results. In this work we present a novel approach to detect the relevant events in a diffusive system without assuming prior information regarding the underlying process. We start from a projection of the atomic coordinates into a landmark basis to identify the dominant features in a mobile ion's environment. Subsequent clustering in landmark space enables a discretization of any trajectory into a sequence of distinct states. As a final step, the use of the Smooth Overlap of Atomic Positions descriptor allows distinguishing between different environments in a straightforward way. We apply this algorithm to ten Li-ionic systems and conduct in-depth analyses of cubic Li7La3Zr2O12, tetragonal Li10GeP2S12, and the β-eucryptite LiAlSiO4. We compare our results to existing methods, underscoring strong points, weaknesses, and insights into the diffusive behavior of the ionic conduction in the materials investigated.