Population initialisation

4.6. Seeding approach

This initialisation process is controlled by two parameters, the seeding biomass and the seeding duration. population.seeding.biomass.sp# is the SSB that Osmose guarantees during the initialisation process when there are no mature adults to ensure the reproduction process. The number of eggs to be released in the reproduction process are computed the following way neggs = sex_ratio * alpha * season * SSB with SSB = sum(biomass of mature individuals) or population.seeding.biomass.sp# if sum(biomass of mature individuals) is equal to zero.

This parameter could be calibrated.

population.seeding.year.max is the number of years for running the seeding process. From year 0 to year seeding max, Osmose will guarantee that some eggs will be release even though there are no mature individuals in the system. From year seeding max to the end of the simulation, the seeding ceases completely. If the parameter does not exist, Osmose will set it by default to the lifespan of the longest lived species of the system.

4.7. Initialisation from NetCDF file

Another way to initialize population is to use a NetCDF file. The population.initialization.file parameter is the path of the NetCDF initialisation file. It contains the details of every school (from every species) that must be created at the beginning of the simulation. Here is an example of the NetCDF format:

    nschool = ##### ;
int species(nschool) ;
    species:units = "scalar" ;
    species:description = "index of the species" ;
float x(nschool) ;
    x:units = "scalar" ;
    x:description = "y-grid index of the school" ;
float y(nschool) ;
double abundance(nschool) ;
    abundance:units = "scalar" ;
    abundance:description = "number of fish in the school" ;
float age(nschool) ;
age:units = "year" ;
age:description = "age of the school in year" ;
float length(nschool) ;
    length:units = "cm" ;
    length:description = "length of the fish in the school in centimeter" ;
float weight(nschool) ;
    weight:units = "g" ;
    weight:description = "weight of the fish in the school in gram" ;
float trophiclevel(nschool) ;
    trophiclevel:units = "scalar" ;
    trophiclevel:description = "trophiclevel of the fish in the school" ;

// global attributes:
    :species = "0=smallpelagic1 1=macrozooplankton 2=demersal1 3=demersal2 4=demersal3
                5=mesopelagic 6=smallpelagic2 7=smallpelagic3 8=largepelagic1
                9=largepelagic2 " ;

The file has the same format than the NetCDF restart file that is generated by Osmose at the end of a run.


Be aware that initialisation from NetCDF file and seeding mechanism are independent one from another and they may interfere if set up inconsistently. If one initialises the simulation from a NetCDF file, then the seeding process should be disabled (by setting seeding biomass or seeding maximal year to zero).