If I choose AGL for the start height, does that mean that for the entire model run the computed heights are relative to the ground? I’m concerned about this because of the terrain in the mountains. I don’t want values to be “underground.”
The AGL only refers to the coordinate reference frame used to specify the initial starting height. The model computation is the same regardless of how the height is specified. It is a terrain following calculation. If there is no vertical motion, then the trajectory will stay at the initial AGL height regardless of the actual terrain height. By definition of the model’s vertical coordinate system, trajectories can never go below ground.