1D shelf sea examples and test cases

Shelf Domains and Processes

Figure 1

1D shelf configuration Domains and processes. Blue dots: tracers. Red arrows: circulation transport represented as eddy diffusivivity Kz, implmented by PALEOocean.Ocean.OceanTransportColumn.ReactionOceanTransportColumn. Black arrow: vertical transport, implemented by PALEOocean.Ocean.VerticalTransport.ReactionSinkFloat

Installation and configuration

These examples require netcdf files defining an annual cycle of physical variables:

water column eddy diffusivity Kz, temperature, density
surface windspeed

The example configurations assume a zip file (available from https://github.com/PALEOtoolkit/PALEOocean.jl/releases) with an illustrative 80m deep seasonally-stratifying shelf (50N, Celtic sea) derived from the S2P3 model has been unpacked to subfolder S2P3_transport_20240614, the script download_S2P3_files.jl provides a function to do this:

include("download_S2P3_files.jl")

download_romaniello_S2P3_files()  # download and unzip

(this is collated output from the Windows 'Physics Biology Model' (s2p3.exe), http://pcwww.liv.ac.uk/~jons/model.htm see 'Introduction to the Physical and Biological Oceanography of Shelf Seas', Simpson & Sharples (2012), CUP)

1D shelf examples

O2 and passive tracer test case

julia> include("PALEO_examples_shelf1D_O2_only.jl")

Test case demonstrating O2 air-sea exchange, and mixing of fast and slow sinking passive tracers.

Minimal phytoplankton P, O2

julia> include("PALEO_examples_shelf1D_P_O2.jl")

Minimal single-nutrient (parameterized as phosphorus) and light-limited phytoplankton population.

Sulphur and carbonate system

julia> include("PALEO_examples_shelf1D_P_O2_S_CH4_carb.jl")

Oxygenic and anoxygenic phytoplankton populations, with sulphur + methane and marine carbonate system.

1D shelf + sediment examples

Minimal phytoplankton water-column sediment

julia> include("PALEO_examples_shelf1Dsed.jl")

Coupled water-column - sediment configuration, with single phytoplankton population, sulphur + methane.

Reading output with python xarray

Test xarray netcdf.ipynb demonstrates reading PALEO netcdf output using Python xarray.