...

No change in the procedure for generating domain files except that the physgrid grid and mapping files described above need to be used because the physics grid is used when communicating with the coupler, which is primarily where the domain files are needed. 

Topography

There was much discussion about how to handle topography with the new physgrid. The dynamics requires a The dycore requires smoothed topography on the GLL grid, but and the physics parameterization for turbulent mountain stress operates on the physics grid, so the initial question was which grid should the input topography be on? PR's (FV) grid. PRs #3267 and #3406 introduced a new file format for topography and related tools that allow a better consistency between the representation of topography on both grids. Specifically, there provide consistent topography data on each grid. There are two new tools to support this new treatment of topography for the physgrid.

The tools are motivated by the following considerations: Both the dycore and the physics parameterizations require surface geopotential (topography) phi_s. Thus, there a number of address the following requirements.

1. The dycore needs these data geopotential phi_s at GLL points, and the physics needs them phi_s at FV cell centers.
2. In addition, physics Physics parameterizations need SGH, SGH30, LANDFRAC, and some other fields computed offline LANDM_COSLAT computed on the FV grid.
3. We require that the map of the GLL phi_s data be equal to the FV phi_s data.
4. We want to run HOMME's smoother on GLL phi_s.
5. We do not want to use the GLL dual grid, which requires using an unscalable tool; we want to use only the FV dual grid, which can be created straightforwardly and quickly using, e.g., TempestRemap in a matter of seconds.

To fulfill meet these requirements, we introduce a new topography file format that has all data at FV points and, in addition, phi_s at the GLL points.

...