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Monthly Layers

The Monthly Layers files contain monthly aggregated two-dimensional fields derived from model outputs at native horizontal resolution.

Purposes

Monthly Layers address three main purposes:

  1. Support the scientific analyses and research questions of the CodeBlue project.
  2. Provide the information required to develop and evaluate candidate HELCOM and OSPAR indicators.
  3. Enable the reconstruction of harmonized pan-European data layers across all participating modelling systems.

Compared with the annual indicators, monthly layers retain a lower level of aggregation and preserve the full horizontal resolution of each model. This allows detailed analyses while maintaining manageable storage requirements.

Format

Monthly Layers are NetCDF files containing monthly mean values of vertically aggregated variables.

The native horizontal grid of each model is retained. To ensure interoperability between modelling systems, all files should follow common CF conventions and metadata standards.

Recommended filenames are structured as:

MONTHLY_<SCENARIO>_<YEAR>_<MODEL>.nc

Variables

The monthly output files contain a predefined set of two-dimensional variables obtained through vertical averaging or integration procedures.

The current list includes:

ID Name Unit Depth range Depth operation Time range Time operation
M1 surface salinity psu 0-10 m mean monthly mean
M2 avg salinity psu whole water column mean monthly mean
M3 bottom salinity psu 0-10 m above seabed mean monthly mean
M4 surface temperature celsius 0-10 m mean monthly mean
M5 average temperature celsius whole column mean monthly mean
M6 bottom temperature celsius 0-10 m above seabed mean monthly mean
M7 potential energy anomaly - thermal component J/m³ * / monthly mean
M8 potential energy anomaly - haline component J/m³ * / monthly mean
M9 mixed layer depth m * / monthly mean
M10 surface DIN mmol.N/m³ 0-10 m mean monthly mean
M11 surface DIP mmol.P/m³ 0-10 m mean monthly mean
M12 surface Si mmol.Si/m³ 0-10 m mean monthly mean
M13 total N mmol.N/m³ 0-10 m mean monthly mean
M14 total P mmol.P/m³ 0-10 m mean monthly mean
M15 Chl mg.Chl/m³ 0-10 m mean monthly mean
M16 total phyto biomass mmol.C/m² whole column integrated monthly mean
M16a Total Phy1 biomass mmol.C/m² whole column integrated monthly mean
M16b Total Phy2 biomass mmol.C/m² whole column integrated monthly mean
.. .. etc, for all PFTs mmol.C/m² whole column integrated monthly mean
M17 total zooplankton biomass mmol.C/m² whole column integrated monthly mean
M18 Pelagic detritic OC mmol.C/m² whole column integrated monthly mean
M19 DIC mmol.C/m² whole column integrated monthly mean
M20 Benthic detritic OC mmol.C/m² / / monthly mean
M21 net primary production mmol.C/m²/d whole column integrated monthly mean
M22 benthic C fluxes (part.) mmol.C/m²/d / / monthly mean
M23 benthic C fluxes (diss.) mmol.C/m²/d / / monthly mean
M24 atmospheric C fluxes mmol.C/m²/d / / monthly mean
M25 O2 mmol.O2/m³ 0-10 m above seabed mean monthly mean
M26 benthic O2 fluxes mmol.O2/m2/d / / monthly mean
M27 atmospheric O2 fluxes mmol.O2/m2/d / / monthly mean
M28 secchi depth m * / monthly mean
M29 Suspended particulate matter mg/l whole column integrated monthly mean
M30 Surface pH Total Scale Surface layer / monthly mean
M31 Surface DIC mol/m³ Surface layer / monthly mean
M32 Surface Alkalinity mol/m³ Surface layer / monthly mean
M33 Bottom pH Total Scale Bottom Layer / monthly mean
M34 Bottom DIC mol/m³ Bottom Layer / monthly mean
M35 Bottom Alkalinity mol/m³ Bottom Layer / monthly mean

Specific diagnsotics marked with an asterisk '*' in the table are detailed below.

Aggregation procedures

All variables are reported as monthly means after applying the prescribed vertical aggregation.

Typical vertical aggregation methods include:

  • Mean concentration within the upper 10 m.
  • Mean concentration within the lower 10 m above the seabed.
  • Mean concentration over the entire water column.
  • Vertical integration over the entire water column.

Monthly averaging is applied after the vertical aggregation step.

Vertical integration

Differences in vertical discretization between models can complicate the calculation of vertically integrated quantities.

To ensure consistency across modelling systems, the recommended procedure is:

  1. Interpolate model outputs from the native vertical grid onto a regular 1 m vertical grid using linear interpolation.
  2. Apply the required vertical averaging or integration on the interpolated profiles.
  3. Compute the monthly mean from the resulting daily or instantaneous values.

Specific diagnostics

Potential energy anomaly

Potential Energy Anomaly (PEA, \(\Phi\)) is used as a measure of water column stratification.

Following Holt et al. (2005), PEA is defined such that:

\[ \Phi = - \frac{g}{H} \int\limits_{z=-H}^{0} z\cdot (\rho(T,S) - \rho(\overline{T},\overline{S})) dz \]

, where :

  • \(g\) is gravitional accelaration,
  • \(H\) is the water depth,
  • \(\rho(T,S)\) is the seawater density deriving from TEOS-10 standard formulaes.
  • \(\overline{T}\) represents the depth-averaged temperature.

\(\Phi\) is defined such that it is positive under stably stratified conditions and approach zero under vertically mixed conditions.

Both thermal and haline components should be reported separately:

\[ \Phi_T = - \frac{g}{H} \int\limits_{z=-H}^{0} z\cdot (\rho(T,\overline{S}) - \rho(\overline{T},\overline{S})) dz \]
\[ \Phi_S = \Phi - \Phi_T \]

Mixed layer depth

Mixed Layer Depth (MLD) follows the density-based definition commonly used in NEMO.

The mixed layer depth is defined as the shallowest depth at which the density difference relative to a reference depth exceeds a specified threshold.

The recommended parameters are:

  • \(z_{ref}\) : Reference depth: 3 m
  • \(\Delta \rho_{ref}\) : Density difference threshold, 0.03 kg m⁻³

This corresponds to the depth where:

\[ z_{MLD} = min(z) | \rho(z)- \rho(z_{ref}) > \Delta \rho_{ref} \]

Secchi depth

Secchi depth is derived from the photosynthetically active radiation (PAR) attenuation coefficient.

The recommended definition is:

\[ z_{secchi} = \frac{1}{K_d} \]

where:

  • \(z_{secchi}\) is the Secchi depth.
  • \(K_d\) is the PAR attenuation coefficient.

Output structure

Each file contains monthly fields for all requested variables on the native horizontal grid of the model.

The files should include all metadata necessary to ensure compliance with CF conventions and facilitate automated processing by downstream workflows.

Example file

..TO BE COMPLETED..