Conceptual CTR model

A CTR structural model usually consists of at least three components, bulk structure, surface slab and interfacial structure. The bulk structure is an infinit stacking of unitcells, and the atoms in the bulk structure are not subject to change during model fitting. The surface slab (one or two surface unitcell high) is a physical continuation of the bulk structure. The surface slab is subject to structure change due to interfacial physiochemical processes, such as relaxation/contraction of surface functional groups, surface complexation reactions and surface reconstruction. Interfacial structure include ordering or semi-ordering structural feature that could extend far away from the substrate surface. One good example is the nanoparticle sorption at the solid-fluid interface. The other important structure is water layering structure, which typically form on a charged surface (e.g. muscovite). CTR modeling is actually to solve the interfacial structure to understand the chemical identity of surface complex species as well as their binding configuration on the substrate surface. In the process of designing the sample module in SuPerRod for manipulation of surface structure with any complexity, we introduce the concept of multi-domain for constructing CTR structure model, as shown in the following figure. The class object of interfacial structure (the sorbate species) is decoupled from the definition of surface slab. This way, you can freely assign a same sorbate slab to different surface slab. Very much like building objects with Lego blocks.