At any given time t of the MD simulation the amount X i (t) of a species i can be computed from the results of the bond analysis. The chemical state of the system can then be represented by the vector X(t), containing the amount of each species at a given time t. The species that are considered here are either one atom with one specific atomic fingerprint or a cluster of two or three bonded atoms with their specific atomic fingerprint. The species with one atom can only create a bond, while the species with two or three bonded atoms can undergo the breaking of their bonds. The probability of occurrence of a unique reaction j in the time interval [t, t + ∆t] is equal to the product a j (X(t))∆t, with a j (X(t)) being the propensity function of the reaction j given the state of the system X(t). The propensity function is a j (X(t)) = k j h j (X(t)), where k j is the reaction rate coefficient of the reaction j and h j (X(t)) is the number of times that the reaction j can take place given the system state X(t). This function h j (X(t)) is the product of the number of the reactant species of the reaction j.