A Fixed-Point Neural Operator for Size- and Functional-Transferable Hamiltonian Prediction

Machine-learned (ML) operator models can be trained to predict density functional theory (DFT) Hamiltonian/density matrices at significantly reduced computational cost, thus extending electronic-structure calculations to previously unfeasible scales. Here, we introduce MALOQ (Massively Accelerated Learning of Operators for Quantum Transport), an application built to train on and predict electronic-structure matrices for systems made of few to 100k atoms, described by large basis sets, and covering a wide range of atomic elements. Based on a state-of-the-art, SO(2)-equivariant backbone architecture, MALOQ provides (i) custom data-processing kernels to handle high-rank Hamiltonian matrix data and (ii) a scalable edge-wise distribution of atomic graph(s). Trained on the largest molecular Hamiltonian datasets available today, it reduces time-per-epoch by over 30% compared to a molecule-wise-distributed framework, and enables inference on material graphs of arbitrary size. We demonstrate scalable training and inference for 3,000-12,000 atoms on the Alps supercomputer, up to 192 GPUs and 256 GPUs, respectively.

The cost of Kohn-Sham density functional theory (KS-DFT) calculations scales with the number of solver iterations, which depends on the quality of the initial guess. Machine learning methods that predict initial guesses from molecular geometry can reduce this cost, but matrix-prediction models fail when extrapolating to larger molecules, degrading rather than accelerating convergence [Liu et al., 2025]. We show that this failure is a supervision problem, not an extrapolation problem: models trained on ground-state targets fit those targets well out of distribution, yet produce initial guesses that slow convergence. Solver-Aligned Initialization Learning (SAIL) resolves this for both Hamiltonian and density matrix models by differentiating through the self-consistent field (SCF) solver end-to-end. We introduce the Effective Relative Iteration Count (ERIC), a correction to the commonly used RIC that accounts for hidden Fock-build overhead. On QM40, which contains molecules up to 4$\times$ larger than the training distribution, SAIL reduces ERIC by 37% (PBE), 33% (SCAN), and 28% (B3LYP), more than doubling the previous state-of-the-art reduction on B3LYP. On QMugs molecules 10$\times$ larger than the training set, SAIL delivers a 1.35$\times$ wall-time speedup at the hybrid level of theory, extending ML SCF acceleration to large drug-like molecules.

Machine-learning interatomic potentials (MLIPs) have enabled molecular dynamics at near ab initio accuracy, yet remain limited to energies and forces by construction, leaving electronic observables such as dipole moments and polarizabilities inaccessible. We introduce DenSNet, a density-first approach to machine-learned electronic structure that learns the Hohenberg--Kohn map from nuclear configurations to the ground-state electron density. Our approach employs an SE(3)-equivariant neural network to predict density coefficients of a flexible atom-centered Gaussian basis, combined with a $Δ$-learning strategy that uses superposed atomic densities as a prior to accelerate training. A second equivariant network then maps the predicted density to the total energy, providing a unified framework for molecular dynamics and electronic structure. We validate DenSNet on ethanol, ethanethiol, and resorcinol, where infrared spectra from machine-learned trajectories show excellent agreement with experimental gas-phase measurements. To test scalability, we train on polythiophene oligomers with 1--6 monomers and extrapolate to chains of up to 12 monomers, generating stable long-time trajectories whose infrared spectra agree with reference density functional theory calculations. Here, we show that reinstating the electron density as the central learned quantity opens a practical route to transferable prediction of spectroscopic and electronic observables in large-scale molecular simulations.