Add topo gen workflow

README.md

@@ -1 +1,12 @@
-# make_OM3_025deg_topo
+# make_OM3_025deg_topo
+
+Make 0.25 degree topog.nc MOM bathymetry file from GEBCO 2024 dataset.
+
+./gen_topog.sh will generate topography and associated files. For 0.25deg resolution and higher this will require qsub.
+
+When the output files are to your satisfaction, commit and push your changes and add the git commit hash as metadata in the output .nc files by running finalise.sh.
+
+Use the qsub command to submit the script, passing the required input files as arguments, For example:
+
+qsub -v INPUT_HGRID="/path/to/ocean_hgrid.nc",INPUT_VGRID="/path/to/ocean_vgrid.nc",INPUT_GBCO="/path/to/GEBCO_2024.nc" gen_topo.sh
+

build.sh

@@ -0,0 +1,19 @@
+module purge
+module load intel-compiler 
+module load netcdf
+
+cd ./domain-tools/
+
+
+# Check if the build directory exists before cleaning
+if [ -d "build" ]; then
+  cmake --build build --target clean
+fi
+
+cmake -B build -DCMAKE_BUILD_TYPE=Release -DNetCDF_Fortran_LIBRARY=$NETCDF_ROOT/lib/Intel/libnetcdff.so -DNetCDF_C_LIBRARY=$NETCDF_ROOT/lib/libnetcdf.so -DNetCDF_Fortran_INCLUDE_DIRS=$NETCDF_ROOT/include/Intel  
+
+cmake --build build
+
+cmake --install build --prefix=./
+
+cd ../

edit_topog_new_fillfraction.txt

@@ -0,0 +1,11 @@
+editTopo.py edits file version 1
+#
+# This file can be used as an argument for editTopo.py --apply
+#
+# created: Fri Nov  1 12:56:59 2024
+# by: ek4684
+# via: editTopo.py /g/data/tm70/ek4684/domain-tools/C-grid-workflow/fill_fraction_0.5/topog_new_fillfraction.nc --overwrite
+#
+#    i    j  old  new
+  1235  737  0.0  65.28469848632812
+  1227  734  0.0  56.118499755859375

finalise.sh

@@ -0,0 +1,26 @@
+#!/usr/bin/env sh
+# Commit changes and push, then add metadata to note how changes were made 
+
+module load nco
+module load git
+
+echo "About to commit all changes to git repository and push to remote."
+read -p "Proceed? (y/n) " yesno
+case $yesno in
+   [Yy] ) ;;
+      * ) echo "Cancelled."; exit 0;;
+esac
+
+set -x
+set -e
+
+git commit -am "update" || true
+git push || true
+
+ncatted -O -h -a history,global,a,c," | Created on $(date) using https://github.com/ACCESS-NRI/make_OM3_025deg_topo/tree/$(git rev-parse --short HEAD)" topog.nc
+ncatted -O -h -a history,global,a,c," | Updated on $(date) using https://github.com/ACCESS-NRI/make_OM3_025deg_topo/tree/$(git rev-parse --short HEAD)" ocean_mask.nc
+ncatted -O -h -a history,global,a,c," | Created on $(date) using https://github.com/ACCESS-NRI/make_OM3_025deg_topo/tree/$(git rev-parse --short HEAD)" kmt.nc
+ncatted -O -h -a history,global,a,c," | Updated on $(date) using https://github.com/ACCESS-NRI/make_OM3_025deg_topo/tree/$(git rev-parse --short HEAD)" ocean_vgrid.nc
+
+ncatted -O -h -a history,global,a,c," and based on GEBCO_2024 topography" topog.nc
+

gen_topo.sh

@@ -0,0 +1,88 @@
+#!/usr/bin/env sh
+#PBS -q normal
+#PBS -l walltime=4:00:00,mem=4GB
+#PBS -l wd
+#PBS -lstorage=gdata/hh5+gdata/ik11
+
+# Ensure build.sh is executable
+if [ ! -x "./build.sh" ]; then
+  chmod +x ./build.sh
+fi
+
+# Build domain-tools
+./build.sh
+
+module use /g/data/hh5/public/modules
+module load conda/analysis3
+module load nco
+
+set -x
+set -e
+
+# Using the environment variables passed via -v
+INPUT_HGRID=$INPUT_HGRID
+INPUT_VGRID=$INPUT_VGRID
+INPUT_GBCO=$INPUT_GBCO
+
+# Copy and link input files
+cp -L --preserve=timestamps "$INPUT_HGRID" ./ocean_hgrid.nc
+cp -L --preserve=timestamps "$INPUT_VGRID" ./ocean_vgrid.nc
+ln -sf "$INPUT_GBCO" ./GEBCO_2024.nc
+
+# Convert double precision vgrid to single
+./domain-tools/bin/float_vgrid --vgrid ocean_vgrid.nc --vgrid_type mom6
+
+# Interpolate topography on horizontal grid:
+./domain-tools/bin/topogtools gen_topo -i GEBCO_2024.nc -o topog_new.nc --hgrid ocean_hgrid.nc --tripolar --longitude-offset -100 
+
+# Cut off T cells of size less than 6kms (6000 m)
+./domain-tools/bin/topogtools min_dy -i topog_new.nc -o topog_new_min_dy.nc --cutoff 6000 --hgrid ocean_hgrid.nc
+
+# Fill cells that have a sea area fraction smaller than 0.5:
+./domain-tools/bin/topogtools fill_fraction -i topog_new_min_dy.nc -o topog_new_fillfraction.nc  --fraction 0.5
+
+# edit_topo.py
+python ./topogtools/editTopo.py --overwrite --nogui --apply edit_topog_new_fillfraction.txt --output topog_new_fillfraction_edited.nc topog_new_fillfraction.nc
+
+# Remove seas:
+./domain-tools/bin/topogtools deseas -i topog_new_fillfraction_edited.nc -o topog_new_fillfraction_edited_deseas.nc --grid_type C
+
+# Set maximum/minimum depth
+./domain-tools/bin/topogtools min_max_depth -i topog_new_fillfraction_edited_deseas.nc -o topog_new_fillfraction_edited_deseas_mindepth.nc --level 4 --vgrid ocean_vgrid.nc --vgrid_type mom6
+
+# Create land/sea mask
+cp topog_new_fillfraction_edited_deseas_mindepth.nc topog.nc
+./domain-tools/bin/topogtools mask -i topog.nc -o ocean_mask.nc
+
+# Calculate MD5 checksum for topog.nc
+MD5SUM_topog=$(md5sum topog.nc | awk '{print $1}')
+
+# Add MD5 checksum as a global attribute to topog.nc
+ncatted -O -h -a md5_checksum,global,a,c,"$MD5SUM_topog" topog.nc
+
+# Calculate MD5 checksum for ocean_mask.nc
+MD5SUM_mask=$(md5sum ocean_mask.nc | awk '{print $1}')
+
+# Add MD5 checksum as a global attribute to ocean_mask.nc
+ncatted -O -h -a md5_checksum,global,a,c,"$MD5SUM_mask" ocean_mask.nc
+
+# Make CICE mask file (`kmt.nc`) 
+ncrename -O -v mask,kmt ocean_mask.nc kmt.nc 
+
+#Move intermediate files to a separate directory
+OUTPUT_DIR="topography_output"
+mkdir -p $OUTPUT_DIR
+
+# Move all intermediate files to topography_output directory
+mv topog_new.nc $OUTPUT_DIR/
+mv topog_new_min_dy.nc $OUTPUT_DIR/
+mv topog_new_fillfraction.nc $OUTPUT_DIR/
+mv topog_new_fillfraction_edited.nc $OUTPUT_DIR/
+mv topog_new_fillfraction_edited_deseas.nc $OUTPUT_DIR/
+mv topog_new_fillfraction_edited_deseas_mindepth.nc $OUTPUT_DIR/
+
+# Create ESMF mesh from hgrid and ocean_mask.nc
+python3 ./om3-scripts/mesh_generation/generate_mesh.py --grid-type=mom --grid-filename=ocean_hgrid.nc --mesh-filename=access-om3-025deg-ESMFmesh.nc --mask-filename=ocean_mask.nc --wrap-lons
+
+# Create ESMF mesh without mask
+python3 ./om3-scripts/mesh_generation/generate_mesh.py --grid-type=mom --grid-filename=ocean_hgrid.nc --mesh-filename=access-om3-025deg-nomask-ESMFmesh.nc --wrap-lons