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Unsupervised landmark analysis for jump detection in molecular dynamics simulations

Type of publication Peer-reviewed
Publikationsform Original article (peer-reviewed)
Author Kahle Leonid, Musaelian Albert, Marzari Nicola, Kozinsky Boris,
Project The search for low temperature super protonic conductivity
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Original article (peer-reviewed)

Journal Physical Review Materials
Volume (Issue) 3(5)
Page(s) 055404 - 055404
Title of proceedings Physical Review Materials
DOI 10.1103/physrevmaterials.3.055404


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.