4.19. Summary

4.19.1. Run parameters

Table 4.12 Run parameters
Parameter Description
simulation.time.nyear Number of years of the simulation
simulation.time.ndtPerYear Number of time steps in one year of simulation. For instance simulation.time.ndtPerYear = 24 means the year is divided in 24 time steps of identical length, 15 days each.
   
simulation.nsimulation Number of replicated simulations with identical set of parameters
simulation.ncpu By default OSMOSE will try to run the replicates in multi-thread environment. If you do not want OSMOSE to use all of them, assign here the number of CPUs that OSMOSE is allowed to use. If this parameter is not defined or the value is higher than the number of CPUs on your computer, OSMOSE will run on the maximum number of CPUs available on the computer. If simulation.ncpu is smaller than 1 or null, OSMOSE will only use one CPU.
simulation.nspecies Number of focal species
simulation.nplankton Number of biotic resource (read from NetCDF file)
simulation.nschool This parameter controls how many new schools will be added to the population for each species at each reproduction event. simulation.nschool=15 means that, for a given species at a given time step, the spawning stock biomass will be homogeneously split among 15 new schools. If simulation.nschool is not defined, then OSMOSE assumes that simulation.nschool=10
simulation.nschool.spX Same meaning as the parameter simulation.nschool, but at species level. This parameter has priority over simulation.nschool. If missing for one species then OSMOSE will use the parameter simulation.nschool.
   
simulation.restart.file Restarts OSMOSE from (a) restart file(s). Either file gol_snapshot_step959.nc exists and all the replicates (if any) will restart on this file. If the file does not exist, OSMOSE assumes that there is instead as many NetCDF restart files as replicates with the following names: gol_snapshot_step959.nc.0, gol_snapshot_step959.nc.1, gol_snapshot_step959.nc.#, etc. If null, no restart is used.
simulation.restart.recordfrequency.ndt Record frequency (expressed in number of time steps) for the restart file. If null then OSMOSE will write only one restart file, at the end of the simulation.
   
simulation.onestep True if only one step should be run (debugging purpose)
   
osmose.version Osmose version (format “Osmose X Update Y (YYYY/MM/DD)”)

4.19.2. Output parameters

Table 4.13 General output parameters
Parameter Description
output.abundance.byage.enabled True if abundance by age must be saved
output.abundance.enable True if abundance output must be saved
output.abundance.bysize.enabled True if abundance by size must be saved
   
output.biomass.enabled True if biomass output must be saved
output.biomass.bysize.enabled True if biomass by size must be saved
output.biomass.byage.enabled True if biomass by age must be saved
output.biomass.byTL.enabled True if biomass by trophic level must be saved
   
output.cutoff.enabled True if age class 0 (i.e. larvae) must be saved => see output.cutoff.age parameters
   
output.diet.composition.enabled True if the diet composition must be saved
output.diet.composition.byAge.enabled True if the diet composition by age must be saved
output.diet.composition.bySize.enabled True if the diet composition by size must be saved
   
output.diet.pressure.enabled True if the predation pressure must be saved
output.diet.pressure.byAge.enabled True if the predation pressure by age must be saved
output.diet.pressure.bySize.enabled True if the predation pressure by size must be saved
   
output.diet.stage.structure Structure of the diet and predator pressure matrices (‘age’ or ‘size’) => see output.diet.stage.threshold. params
output.file.prefix Simulation prefix (should contain only letters)
   
output.meanSize.byAge.enabled True if the mean size by age must be saved
output.meanTL.bySize.enabled True if the mean trophic level by size must be saved
output.meanTL.byAge.enabled True if the mean trophic level by age must be saved
   
output.mortality.enabled True if mortality output must be saved
output.mortality.perSpecies.byAge.enabled True if mortality by size must be saved
output.mortality.perSpecies.bySize.enabled True if mortality by age must be saved
   
output.ndeadschool.enabled True if the number of dead schools should be saved
output.ndeadschool.byage.enabled True if the number of dead schools per age should be saved
output.ndeadschool.bysize.enabled True if the number of dead schools per size should be saved
   
output.nschool.enabled True if the number of school should be saved
output.nschool.byage.enabled True if the number of school per age should be saved
output.nschool.bysize.enabled True if the number of school per size should be saved
   
output.recordfrequency.ndt Output frequency
output.restart.recordfrequency.ndt Restart output frequency
output.restart.enabled Whether a restart file should be saved.
output.restart.spinup Number of years before writing restart files
   
output.size.enabled True if size output must be saved
output.size.catch.enabled True if size catch output must be saved
   
output.spatial.enabled True if spatial outputs must be saved
output.spatial.ltl.enabled True of spatial outputs of biotic resource must be saved.
   
output.ssb.enabled True if spawning stock biomass should be saved
output.start.year First year of data output (0 by default)
output.step0.include True if the first time step should be saved.
   
output.TL.catch.enabled True if the catch trophic level must be saved
output.TL.enabled True if the trophic level must be saved
   
output.yield.biomass.enabled True if yield biomass output must be saved
output.yield.perSpecies.byAge.enabled True if yield biomass by size must be saved
output.yield.perSpecies.bySize.enabled True if yield biomass by age must be saved
   
output.yield.abundance.enabled True if yield abundance output must be saved
output.yieldN.bySize.enabled True if yield abundance by size must be saved
output.yieldN.byAge.enabled True if yield abundance by age must be saved
   
output.dir.path Output path
output.csv.separator CSV separator (COMA, SEMICOLON, EQUALS, COLON, TAB)
   
output.distrib.bySize.min Size distribution minimum common to all species
output.distrib.bySize.max Size distribution maximum common to all species
output.distrib.bySize.incr Size distribution increment common to all species
   
output.distrib.byAge.min Age distribution minimum common to all species
output.distrib.byAge.max Age distribution maximum common to all species
output.distrib.byAge.incr Age distribution increment common to all species
   
output.mortality.perSpecies.bysize.enabled True if mortality per species and per size should be saved
output.mortality.perSpecies.byage.enabled True if mortality per species and per age should be saved
   
   

4.19.3. Grid parameters

Table 4.14 Grid parameters
Parameter Description
grid.java.classname Java class used to define the Osmose grid
grid.mask.file CSV file with the land-sea mask (land = -99, sea = 0)
   
grid.ncolumn Number of longitudes
grid.nline Number of latitudes
   
grid.upleft.lat Latitude of the upper left grid corner
grid.lowright.lat Latitude of the lower right grid corner
grid.upleft.lon Longitude of the upper left grid corner
grid.lowright.lon Longitude of the lower right grid corner

4.19.4. Population parameters

Table 4.15 Population parameters
Parameter Description
population.seeding.biomass.spX Seeding biomass (in tons) for collapsed species.
population.seeding.year.max Number of year where seeding on collapse species is applied. If null, maximum lifespan is used.
   
population.initialization.file NetCDF file used in population initialisation.

4.19.5. Biotic ressource parameters

Table 4.16 General biotic ressource parameters
Parameter Description
ltl.java.classname Java class used to process biotic resource
ltl.netcdf.file NetCDF file name
ltl.nstep Number of time step in the LTL time series inputed to Osmose (multiple of ndt). Osmose will loop over it (if necessary) until the end of the simulation.
Table 4.17 Specific biotic ressource parameters
Parameter Description
plankton.name.plkX Name of the biotic ressource (i.e. name in the NetCDF file)
plankton.accessibility2fish.plkX Accessibility to fish (if not defined from file)
plankton.accessibility2fish.file.plkX File containing the time series of accessibility (if not defined, constant values are used)
plankton.conversion2tons.plkX Factor to convert data into tonne/km2
plankton.size.min.plkX Minimum size of the biotic resource
plankton.size.max.plkX Maximum size of the biotic resource
   
plankton.multiplier.plkX Data multiplier (if not defined, set to 1)
plankton.TL.plkX Trophc level of the biotic resource
plankton.biomass.total.plkX Total biomass if uniform distribution is used (in tonne)

4.19.6. Mortality parameters

Table 4.18 General mortality parameters
Parameter Description
mortality.algorithm Mortality algorithm (stochastic or iterative)
mortality.subdt Number of mortality time-step within one model time-step
   
mortality.out.rate.spX Annual mortality rate for schools that are temporarily outside the simulated domain.
mortality.starvation.rate.max.spX Maximum mortality rate due to starvation (year-1)
Table 4.19 Natural mortality parameters
Parameter Description
mortality.natural.larva.rate.spX Constant mortality rate of larvae
mortality.natural.larva.rate.bytDt.file.spX File containing the time series of larvae mortality rates for each time step
   
mortality.natural.rate.spX Constant annual mortality rate
mortality.natural.rate.bytDt.file.spX File containing the time series of natural mortality rates for each time step
mortality.natural.rate.byDt.byAge.file.spX File containing the time series of natural mortality rates by age for each time step
mortality.natural.rate.byDt.bySize.file.spX File containing the time series of natural mortality rates by size for each time step
   
mortality.natural.spatial.distrib.file.spX Map file containing a spatial map of natural mortality multiplication factor. If null, no factor is applied.
Table 4.20 Fishing mortality parameters
Parameter Description
mortality.fishing.rate.spX Constant annual fishing rate
mortality.fishing.rate.byYear.file.spX File containing the time-series of yearly fishing rates
mortality.fishing.rate.byDt.byAge.file.spX File containing the fishing rate by age and by time-step
mortality.fishing.rate.byDt.bySize.file.spX File containing the fishing rate by size and by time-step
   
mortality.fishing.catches.spX Constant annual catch
mortality.fishing.catches.byYear.file.spX File containing the time-series of yearly catchs
mortality.fishing.catches.byDt.byAge.file.spX File containing the catches by age and by time-step
mortality.fishing.catches.byDt.bySize.file.spX File containing the catches by size and by time-step
   
mortality.fishing.recruitment.age.spX Age at which a fish can be recruited.
mortality.fishing.recruitment.size.spX Size at which a fish can be recruited.
mortality.fishing.season.distrib.file.spX File containing the seasonal distribution of the fishing mortality or catches (the sum of all values must equal one)

4.19.7. Species parameters

Table 4.21 Specific focal species parameters
Parameter Description
species.name.sp# Name of the focal specie. Do not use space or any special character.
   
species.lifespan.sp# Lifespan of the species expressed in years. Lifespan =1 year means that the species will live one year. Lifespan = 5 years means that the species will live 5 years. The age of the schools is such that 0 <= age < lifespan. For example, if lifespan = 1 year, age will vary from zero included to 1 excluded ([0, 1[). If lifespan = 5 years, age will vary from zero included to 5 excluded ([0, 5[)
   
species.maturity.age.sp# Age at sexual maturity (in years) of focal functional group #
species.maturity.size.sp# Size at sexual maturity (in cm) of focal functional group #
   
species.relativefecundity.sp# Annual number of eggs per gram of mature female (in eggs.g-1) for focal functional group
species.sexratio.sp# Proportion of females for focal functional group #
   
species.k.sp# Von Bertalanffy instantaneous growth rate at small size (in year-1) of focal functional group #
species.linf.sp# Von Bertalanffy maximum size (size at infinity, in cm) of focal functional group #
species.t0.sp# Von Bertalanffy theoretical age of zero length (in years) of focal functional group #
species.vonbertalanffy.threshold.age.sp# Threshold age (in years) below which a linear growth model is used to calculate mean length increase for focal functional group #
   
species.length2weight.allometric.power.sp# Exponent of the allometric length-weight relationship of focal functional group #
species.length2weight.condition.factor.sp# Constant of proportionality of the allometric length-weight relationship of focal functional group #
   
species.egg.size.sp# Size (in cm) of the eggs of focal functional group #
species.egg.weight.sp# Weight (in g) of the eggs of focal functional group #
   
species.lmax.sp# Species maximum length (in cm). Default is infinity.
   
species.delta.lmax.factor.sp# Maximum growth rate factor (default=2)

4.19.8. Predation parameters

Table 4.22 Predation parameters
Parameter Description
predation.accessibility.file Name of the .csv file containing estimates of accessibility coefficients for focal functional groups and theoretical accessibility coefficients for biotic resources
predation.accessibility.stage.structure Parameter indicating whether accessibility coefficients are defined for age classes or size classes of the focal functional groups
predation.predPrey.stage.structure Parameter indicating whether the predator/prey size ratios of focal functional groups are defined for age classes or size classes
   
predation.efficiency.critical.spX Critical predation efficiency of focal functional group X
predation.ingestion.rate.max.spX Maximum annual ingestion rate (in year-1) of focal functional group X
predation.predPrey.sizeRatio.max.spX Minimum predator/prey size ratio of the juveniles and adults of focal functional group X
predation.predPrey.sizeRatio.min.spX Maximum predator/prey size ratio of the juveniles and adults of focal functional group X
   
predation.predPrey.stage.threshold.spX Array of body size (in cm) or age (in years) delineating the classes of focal functional group X for which minimum and maximum predator/prey size ratios are defined
   
predation.accessibility.stage.threshold.spX Array of body size (in cm) or age (in years) delineating the classes of focal functional group X for which accessibility coefficients are defined

4.19.9. Movement parameters

Table 4.23 Movement parameters
Parameter Description
movement.randomseed.fixed True if the random seed should be fixed
movement.distribution.method.sp# Type of spatial distribution. Either ‘random’ or ‘maps’. If ‘random’ OSMOSE will look for the parameter ‘movement.distribution.ncell.sp#’. If ‘maps’ OSMOSE will use the maps parameters. See below how to define a map.
movement.distribution.ncell.sp# Number of adjacent cells where the species is allowed to move around. OSMOSE will select randomly n adjacent cells on the grid at the beginning of the simulation and it will assume it is the area of distribution of this species for the rest of the simulation. Within this randomly created area, the school will move around following a random walk. See the parameter ‘movement.randomwalk.range.sp#’ for explanation about the random walk process.
movement.randomwalk.range.sp# Range of the random walk expressed in number of cells. If range = zero, the school remains in the current cell. If range = 1, the school can either stay in the current cell or move in any of the 8 immediately adjacent cells (as long as the destination cell is not land). If range=2, the school can either stay in the current cell or move in any of the 24 immediately adjacent cells (as long as the destination cell is not land). Etc.
Table 4.24 Map parameters
Parameter Description
movement.file.map# Name of distribution map #
movement.species.map# Focal functional group for which distribution map # was produced
movement.age.min.map# Minimum age (in years) of the individuals affected by distribution map #
movement.age.max.map# Maximum age (in years) of the individuals affected by distribution map #
movement.season.map# Time steps within a year for which distribution map # was produced
movement.year.min.map# Minimum year affected by distribution map #
movement.year.max.map# Maximum year affected by distribution map #