Within the context of the European Horizon 2020 project ACDC, we intend to develop a probabilistic chemical compiler, to aid the construction of three-dimensional agglomerations of artificial hierarchical cellular constructs. These programmable discrete units offer a wide variety of technical innovations, like a portable biochemical laboratory that e.g. produces macromolecular medicine on demand. For this purpose, we have to investigate the agglomeration process of droplets and vesicles under proposed constraints, like confinement. This paper focuses on the influence of the geometry of the initialization and of the container on the agglomeration.