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Welcome to the AMM75 wiki!

Initial notes

(1) Create the coordinates.nc file

A python notebook, coarsen_amm15_coordinates.ipynb, is in the repository which does the following

1. Get the AMM15 coordinates.nc file. On archer2 this is /work/n01/n01/shared/CO_AMM15/P1_INPUTS/COORDINATES/amm15.coordinates.nc
2. To get the AMM75 coordiantes we take every 5th lat/lon of AMM15
3. To get the horizontal scale factors e[1,2][t,u,v,f], which define the horizontal surface areas of the cells, we compute them manually using the definitions in the NEMO manual.
4. Save to disk

(2) Create bathy_meter.nc file

A python notebook, Coarsen_bathy.ipynb, is in the repository which does the following

1. Get the bathymetry used in AMM15. On Jasmin this is "/gws/nopw/j04/jmmp/jmmp_collab/AMM15/AMM15_BATHY/ADD_NICO_BALTIC_BDY_RIM_SMOOTH_BDY_COPY_CUTAMM15_CORRECTED_EXPANDED_MERGE_GEBCO_DEEP_TO_200-100_EMODNET_TO_10-5_GEBCO_TO_COAST_amm15.bathydepth.co7.cs3x.cs20.nc"
2. Using the AMM15 and AMM75 coordinates files we conservatively regrid the bathymetry from 1.5 km to 7.5 km. As part of the regridding, if more the half of the AMM15 grid points used to calculate the AMM75 bathymetry are land, then the resulting AMM75 point will be land. If less than half of the AMM15 points are land then the resulting AMM75 bathymetry will be calculated to conserve the volume of water.
3. Now there was a manual removal of closed bodies of water and smoothing of coastline that looked like they might cause stability issues. This step is not repeatable and is time consuming and therefore not ideal. A more automated process that preserved the fidelity of the coast lines could not be found at this stage (open to suggestions for future reference).
4. The pathways from the baltic boundary to the Kattegat sea are partially closed during the regridding and need to be openned up.
5. Set land points to -9999 (not sure this is necessary?)
6. Save to disk as bathy_meter.nc

(3) Create the domain_cfg file

1. On Archer2 download the NEMO 4.0.4 repo
2. Compile the DOMAINcfg tools
3. modify the namelist_cfg to be the same as AMM15, see namelist_cfg in repo
4. create a slurm submission script (see repo) and create the domain_cfg using the coordinates and bathy_meter netcdf files

(4) Try running unforced

1. On Archer2 compile NEMO 4.0.4.

export NEMO_DIR=$BASE_DIR/nemo_4.0.4 
export AMM75_DIR=$NEMO_DIR/cfgs/AMM75
mkdir $AMM75_DIR 
mkdir $AMM75_DIR/EXP00 

Add physics on configuration echo 'AMM75 OCE' >> $NEMO_DIR/cfgs/work_cfgs.txt

Copy the compiler flags file cpp_AMM75.fcm from repo into $AMM75_DIR

On archer2 I have used the shared cray precompiled xios2, /work/n01/shared/nemo/XIOS2_Cray/bin/xios_server.exe

With ./makenemo -m X86_ARCHER2-cray -r AMM75 -j 16

2. Set up the experiment EXP_unforced.

(5) Try running with tides only