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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 smoothed topography on the GLL grid, but 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 #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 are two new topography tools to support this new treatment of topography for the physgrid.

The first is a simple converter. The input is an old GLL topography file. The output is a topography file in the new GLL-physgrid format. SGH, SGH30, LANDFRAC, and LANDM_COSLAT are not quite as good as with second tool, but this converter works in one step:

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