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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:

# Get machine-specific modules
e3sm_root=${HOME}/codes/e3sm/branches/update-topo-tool
${e3sm_root}/cime/tools/configure && source .env_mach_specific.sh

# Set paths; datestring will probably be different if the workflow takes multiple days!
datestring=`date +'%y%m%d'`
atm_scrip_file="${output_root}/templates/ne4np4b_scrip_${datestring}.nc"
input_topography_file="${inputdata_root}/atm/cam/hrtopo/USGS-topo-cube3000.nc"
output_topography_file="${output_root}/topo/USGS_ne4np4_consistentSGH_${datestring}.nc"
smoothed_topography_file="${output_root}/topo/USGS_ne4np4_smoothed_${datestring}.nc"phis-smoothed2.nc"   # output of step(b) above

# Run the code
${cube_to_target_root}/cube_to_target \
	--target-grid ${atm_scrip_file} \
	--input-topography ${input_topography_file} \
	--output-topography ${output_topography_file} \
	--smoothed-topography ${smoothed_topography_file}

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