  The mechanism of the vacancy ordering in metastable cubic Ge-Sb-Te (c-GST)
that underlies the ultrafast phase-change dynamics and prominent thermoelectric
properties remains elusive. Achieving a comprehensive understanding of the
vacancy-ordering process at an atomic level is challenging because of enormous
computational demands required to simulate disordered structures on large
temporal and spatial scales. In this study, we investigate the vacancy ordering
in c-GST by performing large-scale molecular dynamics simulations using machine
learning potentials. The initial c-GST structure with randomly distributed
vacancies rearranges to develop a semi-ordered cubic structure with layer-like
ordered vacancies after annealing at 700~K for 100~ns. The vacancy ordering
significantly affects the lattice dynamical properties of c-GST. In the initial
structure with fully disordered vacancies, we observe a boson peak, usually
associated with amorphous solids, that consists of localized modes at
$\sim$0.575~THz. The boson peak modes are highly localized around specific
atomic arrangements of straight vacancy-Te-vacancy trios. As vacancies become
ordered, the boson peak disappears and the Debye-Waller thermal \textit{B}
factor of Te decreases substantially. This finding indicates that the c-GST
undergoes a transition from amorphous-like to crystalline-like solid state by
thermal annealing in low-frequency dynamics.
