In this work, we firstly investigate how to reproduce 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 for the initialization of nuclei which is correlated with the nucleonic mean-field potential by using the same potential energy density functional. In the mean field potential, the three-body force term is accurately calculated. Based on the new version of the model, the influences of precise calculations of the three-body force term, the slope of symmetry energy, the neutron-proton effective mass splitting, and the width of the wave packet on heavy ion collision observables, such as the neutron to proton yield ratios for emitted free nucleons [$R(n/p)$] and for coalescence invariant nucleons [$R_{ci}(n/p)$] for $^{124}$Sn+$^{112}$Sn at the beam energy of 200 MeV per nucleon, are discussed. Our calculations show that the spectra of neutron to proton yield ratios [$R(n/p)$] can be used to probe the slope of symmetry energy ($L$) and the neutron-proton effective mass splitting. In detail, the $R(n/p)$ in the low kinetic energy region can be used to probe the slope of symmetry energy ($L$). With a given $L$, the inclination of $R(n/p)$ to kinetic energy ($E_k$) can be used to probe the effective mass splitting. In the case where the neutron-proton effective mass splitting is fixed, $R(n/p)$ at high kinetic energy can also be used to learn the symmetry energy at suprasaturation density.
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