4.18. Biotic ressources

Low trophic level (LTL hereafter) organisms such as phytoplankton and zooplankton are not explicitly modelled in Osmose but are essential to take into account are they constitute the base of the trophic chain. They are considered as an input of the model, spatially explicit and varying with time.

First one must define the LTL groups that are included in the configuration. In a second time, Osmose needs to know how the LTL data will be delivered.

4.18.1. Plankton groups

plankton.accessibility2fish.plk# is the fraction of the plankton biomass that are accessible to the fish, ranging from zero to one. This parameter accounts for many biological processes that are not explicitly represented in Osmose and basically says that only a small fraction of the plankton in the water column is effectively available to the fish for preying upon. Plankton accessibility is generally completely unknown and, just like larval mortality, it should be estimated in the calibration process.

plankton.conversion2tons.plk# is the factor for converting biomass from plankton unit (as provided in the LTL input file) to wet weight in \(ton/km^2\) (e.g. \(mmolN/m^2\) to \(tonne/km^2\))

plankton.name.plk# is the name of the plankton group.

plankton.size.max.plk# and plankton.size.min.plk# are the minimum and maximum size of the organisms in the plankton group, in centimeters.

plankton.TL.plk# is the trophic level of the plankton group.

The plankton.multiplier.plk# is used for multiplying plankton biomass, in order to run different scenarios of plankton forcing in relation to a reference state (plankton.multiplier.plk0 = 1 by default for the reference state). For instance plankton.multiplier.plk0=2 means that Osmose will multiply by two the biomass of the plankton group zero of the LTL dataset.

4.18.2. LTL dataset

OSMOSE expects the LTL dataset to be spatially explicit and varying with time. The plankton biomass must be provided as time series (with same time step than OSMOSE configuration) on the OSMOSE grid, in a NetCDF file (cf. Section 3.2).

The ltl.java.classname parameter indicates which Java class in Osmose should handle the reading of the LTL dataset. LTLFastForcing is the default plugin.

Danger

Do not change the default value of the ltl.java.classname parameter.

ltl.netcdf.file is the path of the NetCDF file that stores the plankton biomass for every LTL group. Here is an example of the NetCDF header for the OSMOSE default configuration:

ltl.nstep is the number of time steps in the LTL dataset file. The parameter must be a multiple of the number of time step per year. OSMOSE will loop over the LTL data through time.

4.18.3. Constant LTL values

LTL variables can be initialized by providing a total biomass in ton through the plankton.biomass.total.plk# parameter. Note that this value is the total biomass within the domain. The value within a cell is recovered by dividing by the total number of ocean cells.

Danger

The constant LTL groups must be defined last, after the other LTL groups whose biomass is provided in the NetCDF file