Analysis of Trajectory Similarity and Configuration Similarity in On-the-Fly Surface-Hopping Simulation on Multi-Channel Nonadiabatic Photoisomerization Dynamics

TL;DR

This paper introduces an automatic analysis method for classifying and understanding trajectories in multi-channel nonadiabatic photoisomerization simulations, revealing reaction pathways and dominant molecular motions without prior knowledge.

Contribution

The study presents a novel protocol combining trajectory similarity measures and clustering to analyze complex photoisomerization dynamics automatically.

Findings

Successfully classifies trajectories into distinct reaction channels.

Identifies major geometric evolution features in each channel.

Extracts representative trajectories for each reaction pathway.

Abstract

We propose an 'automatic' approach to analyze the results of the on-the-fly trajectory surface hopping simulation on the multi-channel nonadiabatic photoisomerization dynamics by considering the trajectory similarity and the configuration similarity. We choose a representative system phytochromobilin chromophore model to illustrate the analysis protocol. After a large number of trajectories are obtained, it is possible to define the similarity of different trajectories by the Fr\'echet distance and to employ the trajectory clustering analysis to divide all trajectories into several clusters. Each cluster in principle represents a photoinduced isomerization reaction channel. This idea provides an effective approach to understand the branching ratio of the multi-channel photoisomerization dynamics. For each cluster the dimensionality reduction is employed to understand the configuration similarity in the trajectory propagation, which provides the understanding of the major geometry evolution features in each reaction channel. The results show that this analysis protocol not only assigns all trajectories into different photoisomerization reaction channels, but also extracts the major molecular motion without the requirement of the pre-known knowledge of the active photoisomerization site. As a side product of this analysis tool, we can also easily to find the so-called 'typical' or 'representative' trajectory for each reaction channel.