  We present a fully three-dimensional model providing initial conditions for
energy and conserved charge density distributions in heavy ion collisions at
RHIC Beam Energy Scan (BES) collision energies. The model includes the
dynamical deceleration of participating nucleons or valence quarks. It provides
a realistic estimation of the initial baryon stopping during the early stage of
collisions. We also present the implementation of the model with 3+1
dimensional hydrodynamics, which involves the addition of source terms that
deposit energy and net-baryon densities produced by the initial state model at
proper times greater than the initial time for the hydrodynamic simulation. The
importance of this dynamical initialization stage on hadronic flow observables
at the RHIC BES is quantified.
