I am not sure you are correct on that. The Global Security website states that HAARP [in Alaska]: could allow earth- penetrating tomography over most of the northern hemisphere. Such a capability would permit the detection and precise location of tunnels, shelters, and other underground shelters. The absence of such a capability has been noted as a serious weakness in the Department of Defense plans for precision attacks on hardened targets and for counterproliferation...
It would seem there are hopes for more than atmospheric research with HAARP.