Recipes for reproducible analysis of NEMO ocean general circulation model outputs using xarray.

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About

NEMO Cookbook is a collection of recipes for performing reproducible analyses of the Nucleus for European Modelling of the Ocean (NEMO) ocean general circulation model outputs.

Our aim is to provide Python implementations of the post-processing & analysis functions available in CDFTOOLS alongside new diagnostics (e.g., surface-forced water mass transformation), which are compatible with generalised vertical coordinate systems (e.g., MES).

NEMODataTree

NEMO Cookbook introduces the NEMODataTree structure, which is an extension of the xarray.DataTree object and an alternative to the xgcm grid object.

NEMODataTree enables users to:

• Store output variables defined on NEMO T/U/V/W grids using the model’s native (i, j, k) curvilinear coordinate system.
• Analyse parent, child and grandchild domains of nested configurations using a single DataTree.
• Pre-process model outputs (i.e., removing ghost points and generating t/u/v/f masks without needing a mesh_mask file).
• Perform scalar (e.g., gradient) and vector (e.g., divergence, curl) operations as formulated in NEMO.
• Calculate grid-aware diagnostics, including masked & binned statistics.
• Perform vertical grid coordinate transformations via conservative interpolation.

Each recipe uses NEMODataTree to leverage xarray, flox & dask libraries (think of these are your cooking utensils) to calculate a diagnostic with NEMO ocean model outputs (the raw ingredients - that's where you come in!).

Getting Started

Installation

Users are recommended to installing NEMO Cookbook into a new virtual environment via GitHub:

pip install git+https://github.com/NOC-MSM/nemo_cookbook.git

Alternatively, users can clone the latest version of the nemo_cookbook repository using Git:

git clone [email protected]:NOC-MSM/nemo_cookbook.git

Then, install the dependencies in a new conda virtual environment and pip install NEMO Cookbook in editable mode:

cd nemo_cookbook

conda env create -f environment.yml
conda activate env_nemo_cookbook

pip install -e .

Documentation

To learn more about NEMO Cookbook & to start exploring our current recipes, visit our documentation here.

Recipes

Available:

The following recipes are available here:

• Meridional overturning stream function in an arbitrary tracer coordinates.

• Meridional overturning stream function in depth coordinates (z/z*).

• Meridional heat & salt transports.

• Surface-forced water mass transformation in potential density coordinates.

• Volume census in T-S coordinates.

• Masked statistics using bounding boxes and polygons.

• Extracting volume transports and properties along the Overturning in the Subpolar North Atlantic array.

• Vertical coordinate transformations.

• Barotropic stream functions.

In Development:

• Meridional overturning stream functions in depth coordinates (MES).

• Ocean heat content & mixed layer heat content.

• Sea ice diagnostics.

• Vorticity diagnostics.

Contact

Ollie Tooth ([email protected])