Heterogeneous relational message passing networks for molecular dynamics simulations

With many frameworks based on message passing neural networks proposed to predict molecular and bulk properties, machine learning methods have tremendously shifted the paradigms of computational sciences underpinning physics, material science, chemistry, and biology. While existing machine learning models have yielded superior performances in many occasions, most of them model and process molecular systems in terms of homogeneous graph, which severely limits the expressive power for representing diverse interactions. In practice, graph data with multiple node and edge types is ubiquitous and more appropriate for molecular systems. Thus, we propose the heterogeneous relational message passing network (HermNet), an end-to-end heterogeneous graph neural networks, to efficiently express multiple interactions in a single model with {it ab initio} accuracy. HermNet performs impressively against many top-performing models on both molecular and extended systems. Specifically, HermNet outperforms other tested models in nearly 75%, 83% and 94% of tasks on MD17, QM9 and extended systems datasets, respectively. Finally, we elucidate how the design of HermNet is compatible with quantum mechanics from the perspective of the density functional theory. Besides, HermNet is a universal framework, whose sub-networks could be replaced by other advanced models.

Deep Neural Network Representation of Density Functional Theory Hamiltonian

The marriage of density functional theory (DFT) and deep learning methods has the potential to revolutionize modern research of material science. Here we study the crucial problem of representing DFT Hamiltonian for crystalline materials of arbitrary configurations via deep neural network. A general framework is proposed to deal with the infinite dimensionality and covariance transformation of DFT Hamiltonian matrix in virtue of locality and use message passing neural network together with graph representation for deep learning. Our example study on graphene-based systems demonstrates that high accuracy ($sim$meV) and good transferability can be obtained for DFT Hamiltonian, ensuring accurate predictions of materials properties without DFT. The Deep Hamiltonian method provides a solution to the accuracy-efficiency dilemma of DFT and opens new opportunities to explore large-scale materials and physics.

Symmetry-adapted graph neural networks for constructing molecular dynamics force fields

Molecular dynamics is a powerful simulation tool to explore material properties. Most of the realistic material systems are too large to be simulated with first-principles molecular dynamics. Classical molecular dynamics has lower computational cost but requires accurate force fields to achieve chemical accuracy. In this work, we develop a symmetry-adapted graph neural networks framework, named molecular dynamics graph neural networks (MDGNN), to construct force fields automatically for molecular dynamics simulations for both molecules and crystals. This architecture consistently preserves the translation, rotation and permutation invariance in the simulations. We propose a new feature engineering method including higher order contributions and show that MDGNN accurately reproduces the results of both classical and first-principles molecular dynamics. We also demonstrate that force fields constructed by the model has good transferability. Therefore, MDGNN provides an efficient and promising option for molecular dynamics simulations of large scale systems with high accuracy.