Visualizing microscopic structure of simulated model basalt melt

摘要

We perform a detailed visualization-based analysis of atomic-position series data for model basalt melt obtained from first-principles (quantum mechanical) molecular dynamics simulations. To gain insight into the short- and mid-range order of the melt structure, we extract and visualize the details of radial distribution function (RDF) and coordination environment. The first peaks of all partial RDFs lie in the distance range of 1.6-4 A and the corresponding mean coordination numbers vary from less than 1 to more than 9. The coordination environments involving cations and anions differ substantially from each other, each consisting of a rich set of coordination states. These states vary both spatially and temporally: The per-atom coordination information extracted on the fly is rendered instantaneously as the spheres and polyhedra as well as along the corresponding trajectories using a color-coding scheme. The information is also visualized as clusters formed by atoms that are coordinated at different time intervals during the entire simulation. The Si-0 coordination is comprised of almost all tetrahedra (4-fold) whereas the Al-O coordination includes both tetrahedra (4-fold) and pentahedra (5-fold). The animated visualization suggests that the melt structure can be viewed as a dynamic (partial) network of Al/Si-O coordination polyhedra connected via bridging oxygen in an inhomogeneous distribution of mobile magnesium and calcium atoms.