It is now abundantly clear that upper atmosphere space weather, in both neutral and plasma density, is forced both by the Sun, the lower atmosphere, and a range of internal processes. Characterizing the solar drivers has been the focus historically, and is still a major challenge; so that specifying and forecasting the solar EUV flux and the solar wind velocity, density, and interplanetary magnetic field will remain a goal. In contrast, characterizing the influence from the lower atmosphere drivers is a more recent focus. The dynamics of the lower atmosphere is a source of gravity waves, planetary waves, and tides for the upper atmosphere. The planetary waves, although currently not thought to propagate directly into the upper atmosphere above about 100 km altitude, are thought to modulate the amplitude and phase of atmospheric tides, which do propagate well into the upper atmosphere. To characterize and understand the contribution and impact of this sources the variability of the neutral and plasma density a new Whole Atmosphere Model (WAM) has been developed as part of a collaborative project Integrated Dynamics in the Earth's Atmosphere (IDEA) between the National Weather Service's (NWS) Space Weather Prediction and Environmental Modeling Centers, and the University of Colorado. WAM is a 150-layer general circulation model based on the NWS operational weather prediction Global Forecast System (GFS) model, which is coupled self-consistently with a Global Ionosphere Plasmasphere (GIP) physics model. The IDEA domain covers the region from the ground to about two Earth radii. The model is driven by forcing from the Sun, including solar wind and EUV/UV radiation, and from the lower atmosphere, including the day-to-day temporal variability and longitudinal structure of planetary waves and tides. The model can be used to quantify the relative contribution of the various sources impacting upper atmosphere variability, and specify and forecast the neutral and plasma densities.