Ansys Employee

If the two files are producing different results despite having the same geometry then it's true that there must be some difference in a simulation setting (mesh, bandwidth, boundary conditions, etc.) that is causing the discrepancy. However, I don't think that changing the settings in the file with the pyramids to match the planar Si file is the best approach. After all, we don't know which of these files has more accurate settings. It's possible that the TiO2 pyramid file has better settings, and by matching them to the planar Si file we are actually making the settings worse. If you believe the planar Si file has better settings, on the other hand, then it would be much easier and faster to just add the pyramids to that file rather than making adjustments to the pyramid file settings until the results match.
I think a better approach to determine the improvement from the addition of the pyramids would be to first perform convergence testing with the file with the pyramids included. Once the convergence test has confirmed that the simulation settings are sufficient for the required level of accuracy, you can disable the pyramids and run the simulation again to get the results with no pyramids. For a proper comparison, all of the other simulation settings should be the same, the only difference between the two simulations should be disabling the pyramids. I don't think it would be necessary to perform convergence testing again for the simulation without the pyramids, since you are just replacing the pyramids with empty space.
If you would like to verify your simulation results by comparing them to a different simulation, it is better to use a different solver or algorithm for the second simulation. For example, you could compare your FDTD results to results from the STACK or DGTD solvers. This page has an example that compares results from the STACK solver to results from the FDTD example:
You could use the scripts from this to verify the Jsc results from the planar solar cell simulations. This wouldn't work for the simulation with the pyramids because the STACK solver requires a planar geometry, however. You might be able to replicate the FDTD simulation with the pyramids with the DGTD solver, however there isn't a solar cell analysis group in DGTD so you would have to rewrite the script from the FDTD solar cell analysis group for the Jsc calculation in DGTD.
I hope this helps. Let me know if you have any questions.