  This paper presents a detailed computational protocol for atomistic
simulation of the formation and growth of metal-containing nanostructures
during the Focused Electron Beam Induced Deposition (FEBID) process. The
protocol is based upon the Irradiation-Driven Molecular Dynamics (IDMD) - a
novel and general methodology for computer simulations of irradiation-driven
transformations of complex molecular systems by means of the advanced software
packages MBN Explorer and MBN Studio. Atomistic simulations performed following
the formulated protocol provide valuable insights into the fundamental
mechanisms of electron-induced precursor fragmentation and the related
mechanism of nanostructure formation and growth using FEBID, which are
essential for the further advancement of FEBID-based nanofabrication. The
developed computational methodology is general and applicable to different
precursor molecules, substrate types, irradiation regimes, etc. The methodology
can also be adjusted to simulate the nanostructure formation by other
nanofabrication techniques using electron beams, such as direct electron beam
lithography. In the present study, the methodology is applied to the IDMD
simulation of the FEBID of Pt(PF$_3$)$_4$ - a widely studied precursor molecule
- on a SiO$_2$ surface. The simulations reveal the processes driving the
initial phase of nanostructure formation during FEBID, including nucleation of
Pt atoms, formation of small metal clusters on the surface, followed by their
aggregation and the formation of dendritic platinum nanostructures. The
analysis of the simulation results provides space resolved relative metal
content, height and the growth rate of the deposits which represent valuable
reference data for the experimental characterization of the nanostructures
grown by FEBID.
