Cementor: A toolbox to generate bio-cemented soils with specific microstructures

Bio-cemented soils can exhibit various types of microstructure depending on the relative position of the carbonate crystals with respect to the host granular skeleton. Different microstructures can have different effects on the mechanical and hydraulic responses of the material, hence it is important to develop the capacity to model these microstructures. The discrete element method (DEM) is a powerful numerical method for studying the mechanical behaviour of granular materials considering grain-scale features. This paper presents a toolbox that can be used to generate 3D DEM samples of bio-cemented soils with specific microstructures. It provides the flexibility of modelling bio-cemented soils with precipitates in the form of contact cementing, grain bridging and coating, and combinations of these distribution patterns. The algorithm is described in detail in this paper, and the impact of the precipitated carbonates on the soil microstructure is evaluated. The results indicate that carbonates precipitated in different distribution patterns affect the soil microstructure differently, suggesting the importance of modelling the microstructure of bio-cemented soils.