Ocean Modelling Overview#

The ocean component of ICON consists of three parts:

  1. The ocean model itself (referred to as ICON-O)

  2. The sea-ice module

  3. and the bio-geochemistry module HAMOCC.

Ocean model components#

Ocean model#

The ocean model ICON-O (Korn 2018; Korn et al. 2022) solves the hydrostatic Boussinesq equations, the classical set of dynamical equations for global ocean dynamics. ICON-O uses, as the atmosphere, an icosahedral–triangular C grid. The global grid of ICON-O can be locally refined to create a “computational telescope” that zooms into a region of interest. The numerics of ICON-O share similarities to the atmosphere component but also have important differences. Both components use a mimetic discretization of discrete differential operators, but ICON-O uses the novel concept of Hilbert-space compatible reconstructions to calculate volume and tracer fluxes on the staggered ICON grid (see Korn 2018). The numerical scheme of ICON-O allows for generalized vertical coordinates: of particular importance here are the depth-based z-level coordinate and the so-called z-star coordinate where all water levels are stretched locally according to a factor depending on the sea-surface elevation and the water depth.

Several parameterizations for sub-grid processes are available in ICON-O. Upper-ocean vertical mixing is realized by a turbulent kinetic energy scheme following Gaspar et al. 1990. Deep-ocean mixing can be either approximated by constant background values of a vertical diffusivity or a constant value for turbulent kinetic energy. Furthermore, ICON-O has the option of applying the novel energetically consistent parameterization IDEMIX (Olbers and Eden 2013) for internal-wave driven mixing (see Brüggemann et al. 2024 for details). Horizontal dissipation of momentum is achieved by harmonic and biharmonic operators where Smagorinsky and Leith closures can be applied to specify the horizontal viscosities. In ICON-O simulations that are too coarse to resolve mesoscale eddies, a structure-preserving formulation of the Gent and McWilliams parameterization can be applied (see Korn 2018 for details).

Sea-ice model#

The sea ice model is part of ICON-O. It consists of a dynamic and a thermodynamic component. Sea ice thermodynamics describe freezing and melting by a single-category, zero-layer formulation (Semtner 1976). The current sea ice dynamics are based on the sea ice dynamics component of the Finite-Element Sea Ice Model (FESIM) (Danilov et al. 2015). The sea ice model solves the momentum equation for sea ice with an elastic–viscous–plastic (EVP) rheology. Since ICON-O and FESIM use different variable staggering, a wrapper is needed to transfer variables between the ICON-O grid and the sea ice dynamics component (see Korn et al. 2022). A new sea ice dynamics model has been developed to bypass these limitations (see Mehlmann and Korn 2021) and will be employed in the future.

Ocean biogeochemistry model#

The ocean biogeochemistry component is provided by HAMOCC6 (Ilyina et al. 2013). It simulates at least 20 biogeochemical tracers in the water column, following an ex- tended nutrient, phytoplankton, zooplankton, and detritus approach, also including dissolved organic matter, as described in Six and Maier-Reimer 1996. It also simulates the upper sediment by 12 biologically active layers and a burial layer to represent the dissolution and decomposition of inorganic and organic matter as well as the diffusion of pore water constituents. The co-limiting nutrients consist of phosphate, nitrate, silicate, and iron. A fixed stoichiometry for all organic compounds is assumed.

Model configurations#

Configuring ICON-O on Levante (DKRZ)#

To set up an ICON-O model simulation, it is recommended to use the tool make_target_runscript. Before, this script can be applied, a template for an ocean simulation needs to be copied into ./run. We suggest to begin with the exp.ocean_omip template:

cd run/
cp checksuite.ocean_internal/omip/exp.ocean_omip .
./make_target_runscript in_script=exp.ocean_omip \
                        in_script=exec.iconrun \
                        EXPNAME=exp.ocean_omip \
                        cpu_time=00:10:00 \
                        no_of_nodes=1 \
                        openmp_threads=4 \
                        account_no=<your-project-number>

This generate the run/exp.ocean_omip.run. In this run script several replacements need to be done:

RXBY -> Replace with desired grid type, there are templates for certain configurations like R2B4, R2B6, and R2B8
ZZZ  -> Replace with desired vertical grid, e.g. L72
NNN  -> Replace with desired vertical coordinate type: 0 for zlev and 1 for zstar

After this basic configuration, a first simulation can be started by:

sbatch exp.ocean_omip.run

Once the model is running, a directory is generated ./experiments/exp.ocean_omip, where the model output is saved.

Configuring HAMOCC#

to be added

Ocean diagnostics#

With ICON-O not only the prognostic variables but also a multitude of other diagnostic variables can be saved. In general, the output is configured within the output_nml namelist sections by blocks similar to this example:

&output_nml
  filetype                        = 5
  output_filename                 = "${EXPNAME}_P1M_3d"
  output_start                    = "${start_date}"
  output_end                      = "${end_date}"
  output_interval                 = "P1M"
  filename_format                 = "<output_filename>_<datetime2>"
  operation                       = "mean"
  file_interval                   = "${file_interval}"
  mode                            = 1
  include_last                    = .FALSE.
  output_grid                     = .TRUE.
  ml_varlist                      = 'to','so','u','v','w','A_veloc_v','A_tracer_v_to','A_tracer_v_so',
                                    'normal_velocity','rho','rhopot','mass_flux',
                                    'heat_content_liquid_water','swrab','rsdoabsorb',
                                    'group:oce_eddy'
/

Here, the following definitions apply:

filetype: 5 for netcdf
output_filename: first part of the filename, e.g."${EXPNAME}_P1M_3d" 
filename_format: structure of the filename, e.g. "<output_filename>_<datetime2>" 
output_start: ???
output_end: ???
output_interval: Specify how often an output should be written. "P1M" means every month an output will be written.
file_interval: Specify the interval once a new file will be opened. "P1Y" means every year a new file will be created.
operation: Specify if a snapshot (delete the line) or a time average ("mean") will be written.
mode: ????
include_lat: ????
output_grid: If .TRUE. the grid will be written to the file
ml_varlist: a list of variable names specified by `add_var` in the model, please use single quotes (') to encapsulate each variable.

Most output variables are structured in groups. The most important groups are:

oce_default         -> default model output
oce_essentials      -> ???
ice_default         -> default ice output
ocean_monitor       -> globally integrated quantities
ocean_moc           -> diagnostics regarding meridional overturning and heat transport
oce_eddy            -> diagnostics for products of eddy quantities like eddy kinetic energy
oce_layers          -> diagnostics for analysis in isopycnal space
oce_vmix_tke        -> diagnostics of the TKE mixing scheme
oce_vmix_iwe        -> diagnostics of the internal wave mixing scheme
oce_ts_budget       -> diagnostics for temperature and salinity budgets

Within the post-processing toolbox pyicon there are several example python notebooks that illustrate how different diagnostics can be applied to study ocean dynamics.

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