Learning Hamiltonian Flow Maps: Mean Flow Consistency for Large-Timestep Molecular Dynamics

Learning solution operators for differential equations is a central problem in scientific machine learning. However, many neural operator methods optimize prediction accuracy without explicitly enforcing the geometric structure of the dynamics. Structure-preserving models such as SympNets and Symplectic Neural Flows address this issue for conservative Hamiltonian systems by preserving the symplectic form. In dissipative Hamiltonian systems with conformal symplectic structure, however, the symplectic form evolves according to a conformal factor determined by the dissipation. We propose CoSynFlow, a conformal symplectic neural flow for learning continuous-time solution maps of dissipative Hamiltonian dynamics. CoSynFlow composes symplectic shear maps with explicit conformal scaling, preserving the conformal symplectic structure by construction. By conditioning it on a finite-dimensional Hamiltonian descriptor and the dissipation parameter, a single trained model predicts solution maps for unseen systems without retraining. CoSynFlow keeps the structure error at machine precision, attains the lowest long-horizon error, and admits physics-informed training.

We introduce implicit machine learning force fields (I-MLFFs), which replace explicit stacks of neural network layers with self-consistent fixed-point equations. In molecular simulations, this formulation enables intermediate representations to be reused across successive timesteps, thereby warm-starting force evaluation. The resulting models effectively combine the computational footprint of a shallow, single-layer MLFF with the representational capacity and accuracy of a deep neural network. Our approach unlocks architecture-agnostic efficiency gains that are inaccessible when force prediction and trajectory integration are considered separately. We demonstrate this across three major classes of graph neural networks: invariant, equivariant Cartesian tensor, and SO(3)-equivariant spherical-tensor architectures. Each yields a two- to five-fold reduction in compute and memory footprint. Crucially, these gains are achieved while retaining full atomistic resolution and the original integration timestep, avoiding spatial or temporal coarse graining. Our contribution therefore advances the scaling frontier of quantum-mechanically faithful molecular simulation, enabling longer trajectories and larger atomistic systems within fixed GPU memory and compute budgets, and thereby opening access to new insights across biomolecular and material systems.

Hamiltonian dynamics describe a wide range of physical systems. As such, data-driven simulations of Hamiltonian systems are important for many scientific and engineering problems. In this work, we propose kernel-based methods for identifying and forecasting Hamiltonian systems directly from trajectory data. We present two approaches: a 2-step method that reconstructs trajectories before learning the Hamiltonian, and a 1-step method that jointly infers both. Across several benchmark systems, including mass-spring dynamics, a nonlinear pendulum, and the Henon-Heiles system, we demonstrate that our framework achieves accurate, data-efficient predictions and outperforms 2-step kernel-based baselines, particularly in scarce-data regimes, while preserving the Hamiltonian structure. Moreover, we prove a priori error estimates, ensuring reliability of the learned models. We also provide a more general, problem-agnostic numerical framework that goes beyond Hamiltonian systems and can be used for data-driven learning of arbitrary dynamical systems.