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NERSC Directory Change Notice Due to project's name change at NERSC from 'ACME' to 'E3SM' and NERSC’s file system update, the directory ' |
For an overview of the Topography generation process, see the parent page: Adding support for new gridsRunning 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:
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#!/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 ${output_topography_file}
echo "Done running cube_to_target." |
Step (b)
The unsmoothed topography then needs to be smoothed using the smoothing operator in HOMME. This is done using the homme_tool utility. Follow the instructions in the Adding support for new grids Running E3SM on New Atmosphere Grids page, SCRIP section, to configure and build this tool. A sample namelist for the topo smoothing option is given in components/homme/test/tool/toposmooth_gll.nl
- For cubed sphere grids:
- Set resolution via
set ne = 4(for ne4 example here). - Set
smooth_phis_numcycle=16. (adjustable paramemter, lower for less smoothing) - Set smooth_phis_nudt. This is a resolution dependent parameter, recommend value for cubed sphere grids is 28e7 * ( 30/NE)**2
- Set resolution via
- For RRM grids, we use the tensor laplace operator so that the amount of smoothing is proportional to the resolution
- ne=0, mesh_file=/path/to/exodus-rrm-grid-file.g
- Set
smooth_phis_numcycle=12. (adjustable paramemter, lower for less smoothing) - smooth_phis_nudt = 4e-16.
- Set infilenames=/path/to/unsmoothed/PHISdata
After running the tool, the output will be named "geos", in the file there should be output file 'phis-smoothed1.nc, along with other unnecessary fields. To convert this file into an ' with one of the fields named "PHIS". We then extract just the variables needed for the EAM topo file:
- ncks -O -v geosPHIS,lat,lon phis-smoothed1.ncphis-smoothed2.ncncrename -v geos,PHIS phis-smoothed2.nc
Step (c)
The topography tool then needs to be re-ran to compute the subgrid surface roughness. This is done by passing an extra argument to the topography tool with the smoothed topography output from the standalone HOMME run above:
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# Get machine-specific modules
e3sm_root=${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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