Koji and Jamie suggested me to include the coupling between DoFs when I calculate the last matrix. So far, I just add all the pos-offsets of 5 DoFs and re-calculate the matrix again. However, once I add one DoF pos-offset, it could already change the LSC matrix therefore different pos-offset to the other four DoF, we must iterate this process until we get the equilibrium pos-offsets for 5 DoFs.

I also noticed an error in the optical configuration file. AM mod levels were smaller than that supposed to be because of the hald power going through the AM-EOMs in the MZI paths. Also I have put PM-Mods in the MZT path which gives the smaller mod indexes. So, smaller mod levels were applied both for PM and AM. As PM-AM ratio is still kept in this, so the matrices were not very wrong, I assume. I'll modify that and post the results again.