Efficient implementation of atom-density representations

Abstract

Physically motivated and mathematically robust atom-centered representations of molecular structures are key to the success of modern atomistic machine learning. They lie at the foundation of a wide range of methods to predict the properties of both materials and molecules and to explore and visualize their chemical structures and compositions. Recently, it has become clear that many of the most effective representations share a fundamental formal connection. They can all be expressed as a discretization of n-body correlation functions of the local atom density, suggesting the opportunity of standardizing and, more importantly, optimizing their evaluation. We present an implementation, named librascal, whose modular design lends itself both to developing refinements to the density-based formalism and to rapid prototyping for new developments of rotationally equivariant atomistic representations. As an example, we discuss smooth overlap of atomic position (SOAP) features, perhaps the most widely used member of this family of representations, to show how the expansion of the local density can be optimized for any choice of radial basis sets. We discuss the representation in the context of a kernel ridge regression model, commonly used with SOAP features, and analyze how the computational effort scales for each of the individual steps of the calculation. By applying data reduction techniques in feature space, we show how to reduce the total computational cost by a factor of up to 4 without affecting the model’s symmetry properties and without significantly impacting its accuracy.