Hi @flore.h,
Sorry for the delay, it looks like we missed this discussion!
Although they use the same solver, the FDE solver of MODE Solutions and the mode source of FDTD Solutions behave a bit differently when it comes to the boundary conditions.
First, by default, both solvers are using metal boundary conditions. If in MODE, the BCs are set in the FDE objects, in FDTD, the mode source uses specific BC you can modify in the mode selection window:

In the “Boundary conditions” tab, you first need to check the “override default boundaries” box, and then you can select the BC:

Another difference is the way the solver deals with the structure when it ends where the BC starts. In your simulations, the physical structure has the same width as the FDTD and FDE region. In MODE, the structure is actually cut, as you can see in the screen capture you posted:
You can see the outline of the structure, and you can see the side limits of the structure.
In FDTD, it seems the structure is extended through the PML (like it would continue infinitely in the x direction). If you increase the size of the FDTD region and the mode source, the modes found will be similar to the ones found with MODE.
That said, this would be equivalent to a structure cut laterally, and that might not be what you want to model.
If you consider a structure where the waveguides are etched on a Si layer (the layer extends through the simulation BC), it would be useful to do some convergence testing to optimize:
- the simulation size: since the modes are quite leaky in the x direction, you may need to increase the simulation size)
- the mesh size
This could be done for individual waveguides as well as coupled waveguides, and would allow a better understanding of the modal characteristics, loss, mode profile, index and help to get an idea about how large the simulation region should be to get a physically reasonable result.
Finally, this could be done on both products so you can compare the results.