Computational experiments using molecular dynamics (MD) calculations are an important approach to accessing the structures of molten and solidified glasses. Potential functions, which are explicit functional forms for distances and angles, have been developed to reproduce experimental data obtained using borate glasses to create realistic glass models. This type of MD calculations is sometimes referred to as classical MD (CMD) to contrast it with ab initio calculations. Although a certain amount of success in understanding the structures of glasses has been achieved with CMD, it is known that the unique superstructures found in borate glasses, such as boroxol rings, are not reproduced well using this approach. We investigated the reaction mechanisms in the process from glass melt to solidification using a representation based on the reaction transition matrix. A comprehensive analysis of the coordination structure of REs in the borate glass was also performed based on coordination shape and symmetry to highlight the differences in RE types.