3. ``Theoretical Models of H$_2$ and CO Emission From Optically Thick Disks'' U. Gorti and D. Hollenbach (ApJ, 2004), high commitment, medium duration. This paper is completely analogous to paper 1, except the disks are optically thick in dust opacity at IR wavelengths. We will treat the heating and colling of the gas in the surface layers, where the gas temperature may differ significantly from the dust temperature. For stars producing large amounts of X-rays and/or UV, we anticipate that the gas will be hotter than the dust. Conversely, for cool stars with little X-ray emission, the gas might be somewhat cooler than the dust. We note that an interesting by product (not related to SIRTF observations) of this research will be the determination of the photoevaporation rate of the disk cause by the FUV and X ray fluxes from the central star.