Initialisation Appendix Direct school based example

Direct school-based initialisation uses a restart-like netCDF file as the initial condition itself. The corresponding configuration is minimal:

population.initialization.file = input/initial_conditions/humboldt-n_1992.nc

In this workflow, the file referenced by population.initialization.file already contains the initial schools explicitly. No population-level reconstruction is required before the OSMOSE core simulator reads the starting state.

This route is particularly suitable for restart workflows, coupling applications, or cases where a school-based state has already been prepared from a previous run.

The following example illustrates the expected structure of a direct school-based initialisation file:

File peru-initial_conditions-1992.nc (NC_FORMAT_CLASSIC):

     8 variables (excluding dimension variables):
        int species[nschool]
            units: scalar
            description: index of the species
        float x[nschool]
            units: scalar
            description: y-grid index of the school
        float y[nschool]
        double abundance[nschool]
            units: scalar
            description: number of fish in the school
        float age[nschool]
            units: year
            description: age of the school in year
        float length[nschool]
            units: cm
            description: length of the fish in the school in centimeter
        float weight[nschool]
            units: g
            description: weight of the fish in the school in gram
        float trophiclevel[nschool]
            units: scalar
            description: trophiclevel of the fish in the school

     1 dimensions:
        nschool  Size:20287 (no dimvar)

     2 global attributes:
        step: -1
        species: 0=anchovy 1=hake 2=sardine 3=jurel 4=caballa
        5=meso 6=munida 7=pota 8=euphausidos

This example shows the essential characteristics of the direct school-based format:

• one record per school;
• explicit spatial position through x and y;
• abundance, age, length, weight, and trophic level provided for each school;
• step = -1, indicating that the file is intended to be used as an initial-condition file rather than as a restart associated with a later simulation step.