We know that for a 3D system with $N$ atoms has to have exactly $3N$ phonon modes.
$$
\begin{align}
...
...
@@ -340,7 +340,7 @@ which gives us
$$
\omega_D = v_s (6\pi^2 N)^{1/3} / L.
$$
Both $N$ and $L$ are arbitrary, however we are considering an $L×L×L$ cube with $N$ atoms, so $L / N^{1/3}$ is the distance between neighboring atoms, and therefore $\omega_D$ does not depend on the box size.
Both $N$ and $L$ are arbitrary, however we are considering an $L×L×L$ box with $N$ atoms, so $L / N^{1/3}$ is the distance between neighboring atoms, and therefore $\omega_D$ does not depend on the box size.
Using the corrected expression for the total energy that includes the high frequency cut-off, the total energy without the zero-point motion part is