🌊 NEMO AMM12 + TOP + PISCES (p2z/p4z) Configuration

This repository documents the setup, configuration, and testing of the NEMO ocean model using the AMM12 regional configuration, extended with the TOP biogeochemical model and PISCES (both p2z and p4z). The goal is to explore biological tracers and sediment interactions on the North-West European Shelf.

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Repository Structure

Step 0: Download all_all_nemo.sh

https://forge.nemo-ocean.eu/nemo/nst/-/wikis/uploads/2780c5b794ebd76a3c6271b53c53ac89/install_all_nemo.sh Compile: Chmod u+x install_all_nemo.sh and then ./all_all_nemo.sh

Step 1: Base Configuration – AMM12 (No TOP)

Compile:

./makenemo -n AMM12_Hack -r AMM12 -m auto -j 4

Prepare input files:

cd $HOME/ALL_NEMO_default/nemo_5.0/sette/

./sette_fetch_inputs.sh

tar -xvzf AMM12_v5.0.0.tar.gz

mv AMM12_v5.0.0/* ../cfgs/AMM12_Hack/EXP00/

Run the model: example: ./nemo

Step 2: Add Biogeochemistry with PISCES (p2z)

Compile:

./makenemo -n AMM12_HackTop -r AMM12 -m auto -j 4

Add TOP to work_cfgs.txt

Copy base EXP00:

cp -r AMM12_Hack/EXP00/* AMM12_HackTop/EXP00/

Add XML config files from ORCA2_OFF_PISCES:

field_def_nemo-pisces.xml

file_def_nemo-pisces.xml

Edit context_nemo.xml to include TOP definitions

Run with and without open boundaries: ln_bdy = .true. / .false.

Step 3: Enable Sediment Model (PISCES p4z)

Compile:

./makenemo -n AMM12_HackTop4z -r AMM12 -m auto -j 4

Activate in namelist_pisces_cfg:

ln_p4z = .true.

Run without the sediment first

Copy and configure:

Sediment namelists from SHARED/

ln_sed_2way = .true in namelist_sediment_cfg and namelist_pisces_cfg

Ensure sediment outputs in XML definitions

🤝 Acknowledgements

Thanks to mentors and contributors (Julien and Renaud) involved in debugging and testing this setup.