Custom Query (1539 matches)

In SaveEcosimTimeStepData, removed the division by biomass. The tracer concentration was being divided by biomass to get the conc/biomass, but then being divided again in the graphing/output section.

For Ecosim Ecotracer calculations: CUpdate (cContaminantTracer)

• Moved to an adaptive number of sub-timesteps per ecosim timestep (used to be fixed at 3). The number of timesteps is based on how far the concentration is away from the estimated equilibrium, and the fastest loss-rate parameter. The largest timestep is 0.1 times 1/(max loss rate).
• Changed the time-integration method to explicit Adams-Bashforth multistep. Previously, a semi-analytical solution was assumed over the timestep, but this was not great at conserving tracer mass.

For Ecospace Ecotracer calcuations:

• Fixed initialization of spatial CCell array for the environment (as a function of RelCin and CZero)
• Same as Ecosim version, moved to an adaptive number of sub-timesteps per ecosapce timestep (used to be fixed at 1). Same criteria as ecosim to get the timestep.
• Changed integration method same as Ecosim. Previously this was a single-step backward Euler implicit integration. The old method performed very poorly if the loss rates were large compared to the timestep.
• Added a !SolveCellC routine that performs all the Ecotracer sections of the SolveCell code since this needs to be done multiple times per ecospace timestep (while the rest of SolveCell does not).
• Added multi-threading for the SolveCellC calculations.

For *ALL* Ecospace calculations:

• In setMovementParameters: set the Depth, width, HabCap, Xvel and Yvel variables on the boundary to inherit the values just inside the boundary. Previously, open boundaries would sometimes appear to be closed under advection/diffusion since these values were not being set properly.

As far as interface stuff goes, I think we need one more column for the tracer input: excretion or metabolism rate. This should be the rate that the contaminant is excreted from itself into the environment. Currently there is a CexcretionRate parameter, but the name should probably be changed to CexcretionFraction or something, since it is the fraction of contaminant that is assimilated into tissue, and is not a rate at all. Maybe the CexcretionRate should be used for excretion/metabolism, and a new variable made like CassimFrac or something to represent the fraction assimilated by the organism.

When I ran a model in Ecosim, when I changed the input fishing effort for all fleets, it keeps giving me the same graphical outputs no matter what the level of fishing effort I put into the model. Also, in the Ecosim results tab, there are missing figures for the Catch start and end, and value start and end, either by functional group or by fleet. I attached the model that I am working on here for your reference.Could you please let me know whether it is due to a bug in the software, or I have to do specific things to make it work.