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For an overview of the Topography generation process, see the parent page: Adding support for new grids - internalRunning 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  

For "pg2" grids (E3SM v2):  dont follow this page and instead see the instructions on  Special Considerations for FV Physics Grids 

Step (a)

To begin Step (a) with a SCRIP file in hand,  interpolate the high resolution USGS data. The source topography file is the USGS high resolution topography on a 3 km cube sphere grid. This data exists on the CESM inputdata server here.  The data has also been downloaded to NERSC computing facilities and is located here:

...

#!/bin/bash

grid_name=ne4
output_root=/gscratch/bhillma/e3sm/grids/${grid_name}
atm_scrip_file="${output_root}/ne4np4b_scrip.nc"

# Set paths
e3sm_root="${HOME}/codes/e3sm/branches/master"
datestring=`date +'%y%m%d'`
cube_to_target_root=${e3sm_root}/components/cam/tools/topo_tool/cube_to_target
input_topography_file=/project/projectdirs/acme/inputdata/atm/cam/hrtopo/USGS-topo-cube3000.nc
output_topography_file=${output_root}/topo/USGS_${grid_name}_unsmoothed_${datestring}.nc

# Get machine-specific modules
${e3sm_root}/cime/tools/configure && source .env_mach_specific.sh

# build the code
cd ${cube_to_target_root}
export FC=ifort INC_NETCDF=${NETCDF_DIR}/include LIB_NETCDF=${NETCDF_DIR}/lib
make clean && make
echo "Done building cube_to_target."

# run the code
echo "Run cube_to_target to interpolate topography..."
mkdir -p `dirname ${output_topography_file}`
${cube_to_target_root}/cube_to_target \
	--target-grid ${atm_scrip_file} \
	--input-topography ${input_topography_file} \
	--output-topography ${output_topography_file}
echo "Done running cube_to_target."

Step (b)

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 Adding support for new grids - internal 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:

# 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}

...