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For an overview of the Topography generation process, see the parent page: Running E3SM on New Atmosphere Grids

Requirements:

• High resolution USGS topography file named USGS-topo-cube3000.nc (located in the CESM inputdata server here; note this is on a 3 km cubed sphere grid)
• SCRIP-format atmosphere grid file
• topography tool (components/cam/tools/topo_tool/cube_to_target)
• homme_tool  

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The unsmoothed topography then needs to be smoothed using the smoothing operator in HOMME. This is done using the homme_tool utility.  Follow the instructions in the Running E3SM on New Atmosphere Grids page, SCRIP section, to configure and build this tool.  A sample namelist for the topo smoothing option is given in components/homme/test/tool/toposmooth_gll.nl

1. For cubed sphere grids:
   1. Set resolution via set ne = 4  (for ne4 example here).
   2. Set  smooth_phis_numcycle=16.    (adjustable paramemter, lower for less smoothing)
   3. Set smooth_phis_nudt.  This is a resolution dependent parameter, recommend value for cubed sphere grids is 28e7 * ( 30/NE)**2
2. For RRM grids, we use the tensor laplace operator so that the amount of smoothing is proportional to the resolution
   1. ne=0, mesh_file=/path/to/exodus-rrm-grid-file.g
   2. Set  smooth_phis_numcycle=12.    (adjustable paramemter, lower for less smoothing)
   3. smooth_phis_nudt = 4e-16.  
3. Set infilenames=/path/to/unsmoothed/PHISdata

After running the tool, there should be output file 'phis-smoothed1.nc' with one of the fields named "PHIS".  We then extract just the variables needed for the EAM topo file:

• ncks -O -v PHIS,lat,lon phis-smoothed1.nc phis-smoothed2.nc

Step (c)

The topography tool then needs to be re-ran to compute the subgrid surface roughness. This is done by passing an extra argument to the topography tool with the smoothed topography output from the standalone HOMME run above:

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