I'm trying to write down the bath Hamiltonian for a system of dimers and trimers. Imagine each of the monomers in the excited state can interact with several phonons with given frequencies. The bath Hamiltonian has the following form $\sum\limits_{n = 1}^N {\sum\limits_{j = 1}^M {{\omega _{nj}}} } a_{nj}^\dagger {a_{nj}}$. Here N is the number of monomers and M is the number of vibrational modes. I don't understand how the matrix of vibrational modes look like for a trimer with lets say four modes. It looks like I will have a 3-by-4 matrix, where all the rows are the same since I have the same modes for all the monomers. This doesn't make sense to me, since I'm supposed to diagonalize this matrix. Another ambiguity arises when I'm trying to figure out what values the number operator takes for each element of this matrix, since it looks to me it has to be 1 for each element. Imagine, you have two or three monomers which are all coupled to the same modes.
I will appreciate your comments!