Dear Kevin,
sorry for the huge delay of this answer. In the past months I have been trying to study this system with different methods, and I wanted to be sure that I explored all my options before coming back to annoy you :)
The Hamiltonian that I showed in the first post can indeed be handled by QuTip by setting the option that you mentioned. In that Hamiltonian, the presence of the waveguide is described by adding an imaginary part to the frequencies of the resonators and to their mutual interaction rate.
However, I became interested in simulating numerically the full dynamic of the system, i.e. including the waveguide which acts as an excitation channel for the system. Note that I cannot use the Lindblad operator to incoherently pump the system, because I am interested in the correlations that arise between the two cavities due to the fact that they interact with the same waveguide.
Do you think that it would be possible (and/or correct) to simulate the presence of the waveguide by adding a third cavity with a very large linewidth and which couples to the first two cavities? Or do you know of any other trick that could be used for simulating a waveguide in QuTip? I was thinking about describing the waveguide by a chain of coupled cavities, but that would increase dramatically the dimension of the Hilbert space...
(I have spent quite some time addressing the problem with the analytical approach of the single-photon transport in 1D waveguide that has been described in many papers by the group of Shanhui Fan and others. While being quite an elegant method, the calculations become rather complicated and lengthy when going from a 1-excitation sector to a 2-excitation sector, so having some numerical backup could be extremely useful)
Thanks in advance for any help!
p.S. I gave a look to that book chapter - very interesting, thanks!