After applying Eq. 7, in which the periodic boundary conditions (PBCs) of the supercell box are not taken into account, the Cartesian coordinates of each supercell (r) are guaranteed to exist on a 3(N -1) dimensional hyperplane specified by the fixed center of mass. In other words, Eq. 7 always creates three singular DOFs in r. These three redundant dimensions were reliably removed from the flow using a PCA whitening layer, initialized on Cartesian coordinates of the oxygen atoms from the entire MD dataset (after applying Eq. 7). The whitening transformation was adopted following the approach of Ref. .