Abstract
Clays are a broad class of ubiquitous layered materials. Their specific chemophysical properties are intimately connected to their molecular structure, featuring repeating patterns broken by substitutions. Molecular dynamics simulations can provide insight into the mechanisms leading to the emergent properties of these layered materials; however, up to now, idealized clay structures have been simulated to make the modeling process tractable. We present ClayCode, a software facilitating the modeling of clay systems closely resembling experimentally determined structures. By comparing a realistic model to a commonly used montmorillonite clay model, we demonstrate that idealized models feature noticeably different ionic adsorption patterns. We then present an application of ClayCode to the study the competitive barium and sodium adsorption on Wyoming montmorillonite, Georgia kaolinite, and Montana Illite, of interest in the context of nuclear waste disposal.