I am facing problems in calculating phonon band structure for bilayer 2D systems. While the band structure mostly show positive frequencies for 1L system, but going to 2L make some frequencies negative. Moreover, choice of van der Waals interactions also come into account for bilayer system and for some, phonon calculations are not properly implemented. Can someone share thoughts on calculating phonon band structure for bilayer or perhaps multilayered 2D systems and which approach should be adopted to tackle this problem? T

I am facing problems in calculating the phonon band structure for bilayer 2D systems. While the band structure mostly shows positive frequencies for the 1 layer system, going to 2 layers makes some frequencies imaginary. Moreover, the choice of van der Waals interaction also comes into account for the bilayer system and for some van der Waals functionals, phonon calculations are not properly implemented.

Can someone share thoughts on calculating the phonon band structure for bilayer or perhaps multilayered 2D systems and which approach should be adopted to tackle this problem?