We present a comprehensive computational framework for simulating nonadiabatic molecular dynamics with explicit inclusion of geometric phase effects. Our approach is based on a generalized two-level Hamiltonian model that can represent various electronic state crossings—conical intersections, avoided crossings, and elliptic intersections—through appropriate parametrization. A key challenge in mixed quantum-classical methods is that standard trajectory initializations place nuclear wave packets far from the crossing region with random electronic phases so that the ensemble generically undersamples the geometric phase effect and misses the coupling region entirely. Our prelooping scheme addresses this by jointly specifying the nuclear positions (near the crossing), momenta (tangential to orbits guided by the local Berry curvature), and electronic phase (set to the analytically computed Berry phase)—ensuring that trajectories begin with the full topological memory of a completed adiabatic loop. We introduce a novel prelooping trajectory initialization scheme, allowing us to encode the memory as an initial phase accumulated due to the adiabatic evolution over the potential energy surface. This is a unified framework to handle different types of level crossings by incorporating Berry curvature-based force corrections to Ehrenfest dynamics, ensuring accurate representation of topological effects. For conical intersections, our method incorporates the theoretically expected phase $\pi$, while for elliptic intersections, it yields a parametrically tunable but loop-radius- (energy) independent phase different from $\pi$. We also include an eccentricity parameter ($e$) in the diabatic coupling to model more realistic molecular systems. Numerical simulations demonstrate the consistency of our approach with theoretical predictions for mixing of states and inhibition from mixing due to geometric phase effects. This framework provides a valuable tool for studying quantum-classical interactions in molecular systems where geometric phase effects play a significant role.

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• Atomic & molecular processes in external fields
• Potential energy surfaces
• Vibrational states
• Molecules