In this work, we firstly investigate how to and how well one can reproduce the Woods-Saxon density distribution of initial nuclei in the framework of the improved quantum molecular dynamics model. Then, we propose a new treatment on the initialization of nuclei. The initialization of the nuclei is correlated with the nucleonic mean-field potential with the same potential energy density functional, in which the three-body force term is accurately calculated. Based on the new version of the model, the influences of the width of wave function, calculations of three-body force, and the slope of symmetry energy on the heavy ion collision observables, such as the neutron to proton yield ratios for emitted free nucleons and for coalescence invariant nucleons, for 124 Sn+ 112 Sn at the beam energy of 200 MeV per nucleon are discussed. Our calculations show that the neutron to proton yield ratios at the high kinetic energy region can be used to probe the symmetry energy above the saturation density.