Structure quantification is key to successful mining and extraction of core materials knowledge from both multiscale simulations as well as multiscale experiments. The main challenge stems from the need to transform the inherently high dimensional representations demanded by the rich hierarchical material structure into useful, high value, low dimensional representations. In this paper, we develop and demonstrate the merits of a data-driven approach for addressing this challenge at the atomic scale. The approach presented here is built on prior successes demonstrated for mesoscale representations of material internal structure, and involves three main steps: (i) digital representation of the material structure, (ii) extraction of a comprehensive set of structure measures using the framework of n-point spatial correlations, and (iii) identification of data-driven low dimensional measures using principal component analyses. These novel protocols, applied on an ensemble of structure datasets output from molecular dynamics (MD) simulations, have successfully classified the datasets based on several model input parameters such as the interatomic potential and the temperature used in the MD simulations.