Manipulating and engineering atom dynamics with single atom precision has long been the ultimate goal in nanoscience and nanotechnology ^[1]. Direct atom manipulation or beam induced structural evolution by scanning transmission electron microscopy (STEM) has several advantages, i.e. much faster speed of atom manipulation (a few tens of seconds) and manipulation at room temperature ^[1]. STEM has been applied in various research, such as, structural defects ^[2], phase transitions ^[3], electron beam lithography ^[4], assembly of atoms ^[5] and single-atom migration ^[6].

When electrons pass through atomically thin 2D materials, energy can be either elastically or inelastically transferred to the targeted atom. During an elastic collision, impinging electrons are scattered to high angles by the recoiling nucleus and energy and momentum are both conserved. During the inelastic scattering process, the incident electron interacts with the electronic system of the target atom resulting in electronic excitation and electrostatic charging ^[1]