Inputs and Configuration Resource Forcing

LTL forcings

Vertical interpolation and regridding

Usually, LTL forcings are provided from coupled physical/biogeochemical models (for example NEMO/PISCES, NEMO/Eco3M, etc.). These models are 3D (depth, latitude and longitude), while Osmose is 2D, and are usually at a higher spatial resolution than Osmose. Aditionnally, they provide LTL forcings as concentrations (mol/L, mol/m3, mmol/L, etc.), while Osmose requires wet biomass (tons).

In the following, we provide some insights into how to prepare LTL forcing files, which will be used by Osmose as resource species (see Resource species for details).

Vertical integration

The first step is to vertically integrate the concentrations. This is done by computing the vertical weighted sum of LTL concentrations, with the weights provided by the surface volume:

$$ LTL_{2D}(x, y) = \sum_{z}\left[LTL_{3D}(z, y, x)\times V(z, y, z)\right] $$

Horizontal regridding

The second step is to regrid the LTL variables from the original grid to the Osmose grid.

It is strongly recommended to use the Python interpolation tool xESMf.

Warning

In order to conserve the original Osmose mask, the conservative or conservative_normed method should be used. For a detailed description of the methodology, see this example.

Conversion into wet weight

Once the files have been interpolated, the last step is to convert the concentrations into wet biomass (i.e. in tons).

Provided in the table below are a list of conversion factors (courtesy of Morgane Travers):

Model(s) concerned	Organisms concerned	Conversion factor used (currencies concerned and relationship with values)	References
OSMOSE-N2P2Z2D2	Phytoplankton	From mmolN to mg wet weight [phyto_in_mgWW.m-3] = 720 * [phyto_in_mmolN.m-3]	Travers et al. 2009 (Ecol.Mod 220)
OSMOSE-N2P2Z2D2	Ciliates	From mmolN to mg wet weight Conversion factor: 675 mg ww.mmol N−1	Travers et al. 2009 (Ecol.Mod 220)
OSMOSE-N2P2Z2D2	Copepods	From mmolN to mg wet weight Conversion factor: 1000 mg ww.mmol N−1	Travers et al. 2009 (Ecol.Mod 220)
ECOSMO-E2E	-	No need for conversion factor as it is an online coupled model	Daewel et al. 2019
FEISTY	-	Wet weight to carbon ratio of 9:1	Pauly & Christensen, 1995
DEB-IBM	Mesozooplankton	No need for conversion since in the DEB we use a scaled functional response (Holling Type 2)[^1]	Gatti et al., 2017 (Ecol Model) Menu et al., 2023 (Progr. Oceanogr.)
ERSEM-MIZER	Fish	Assume 10% of wet mass is carbon From mmol C to g wet weight Conversion factor: 0.12	Boundreau and Dickie, 1992
ERSEM-Fish IBM (HCMR)	Anchovy & Sardine	From mg C to mg wet weight: 6.8mg ww / mg C	Czamanski et al., 2011. Politikos et al., 2015
EcoOcean	Phytoplankton	Scaling *phyc to EcoOcean starting densities in t/km-2	Coll et al., 2020

[^1]: $f = \frac{X}{X+ KX}$, with $X$ the food and $Kx$ the half saturation coefficient. Usually we use X in $mg.m^{-3}$ or $mg.m^{-2}$. Nonetheless, as the DEB is in energy, it might be interesting to convert zooplankton mass to energy for example for calculation of daily consumption rates. In that case we use an energy density of 3.5 $kj.g^{-1}$