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 #