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Seems that DFPT method in VASP has many defects. It can't include vdw interaction. Now I found it also can't include dipole correction, which leads to a large negative frequency at $\Gamma$ point. I found this problem because two different phases of my structure has almost similar large negative frequency at $\Gamma$ point. Before this I've spent days tuning precision-related parameters.

So does anyone know the reason behind this?

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I assume the problem has to do with the fact that the long-range Coulomb interaction looks different in 2D than it does in 3D. Dimensionality enters in Fourier space and yields a different asymptotic behavior for q --> 0. See Eq. (28) and (29) in https://www.nature.com/articles/s41524-022-00920-6 .

Note that this answer is for phonopy. I am not familiar with the DFPT implementation in VASP and how long-range polar corrections are included there.

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