The fraction of heavy vector mesons produced in a heavy ion collision, as compared to a proton proton collision, serves as an important indication of the formation of a thermal medium, the quark gluon plasma. This sort of analysis strongly depends on understanding the thermal effects of a medium like the plasma on the states of heavy mesons. In particular, it is crucial to know the temperature ranges where they undergo a thermal dissociation, or melting. AdS/QCD models are know to provide an important tool for the calculation of hadronic masses, but in general are not consistent with the observation that decay constants of heavy vector mesons decrease with excitation level. It has recently been shown that this problem can be overcome using a soft wall background and introducing an extra energy parameter, through the calculation of correlation functions at a finite position of anti-de Sitter space. This approach leads to the evaluation of masses and decay constants of S wave quarkonium states with just one flavor dependent and one flavor independent parameters. Here we extend this more realistic model to finite temperatures and analyse the thermal behavior of the states $1S, 2S$ and $ 3S$ of bottomonium and charmonium. The corresponding spectral function exhibits a consistent picture for the melting of the states where, for each flavor, the higher excitations melt at lower temperatures. We estimate for these six states, the energy ranges in which the heavy vector mesons undergo a transition from a well defined peak in the spectral function to complete melting in the thermal medium. A very clear distinction between the heavy flavors emerges, with bottomonium state $\Upsilon (1S)$ surviving deconfinemet transition at temperatures much larger than the critical deconfinement temperature of the medium.
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