1st, you should not increase the number of unit cells. Since it is peridoic, you will need to offset the phases of the dipole sources doing so. Please refer the example for hexagonal PhC exmaples.
Second, you cannot use PML without Bloch BCs. The findamental principle is to use the periodicity to find the band structure. Without it you will not be able to get the regular bands.
I am not aware of L3 band structure. Please find some related papers on this subject. Usually it is done from the band structure without defects. However, you can find resonance and stop bands for cavity. Please refer this exmple https://optics.ansys.com/hc/en-us/articles/360041567754-Photonic-crystal-cavity
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