Interaction with atecology

Author

Unknown User (hep016)

Linkage between EwE and Atlantis

In the linkage work Mark has been doing EwE is called by Atlantis each month.
The EwE model will return mortality values for non-detritus groups and a flux value for the detritus groups.

Mark will unpack these values in a value per box, layer and cohort for each functional group affected.

These values are stored in the atEcologyModule in the following new arrays:

/The additional mortality values that are used when atlantis links to other models such as Ewe /

double ****linkageWCMortality;
double ****linkageSEDMortality;
double ***linkageEPIMortality;

/* The additional detritus flux values that are used to change the atlantis detritus biomass values
* when Atlantis links with other models such as EwE
*/

double linkageWCDetritusFlux;
double linkageSEDDetritusFlux;

These are allocated as:

bm->atEcologyModule->linkageWCDetritusFlux = AllocInit3DArrayDouble(bm->K_num_tot_sp, bm->wcnz, bm->nbox, 0.0);
bm->atEcologyModule->linkageSEDDetritusFlux = AllocInit3DArrayDouble(bm->K_num_tot_sp, bm->sednz, bm->nbox, 0.0);

bm->atEcologyModule->linkageWCMortality = AllocInit4DArrayDouble(bm->K_num_cohorts, bm->K_num_tot_sp, bm->wcnz, bm->nbox, 0.0);
bm->atEcologyModule->linkageSEDMortality = AllocInit4DArrayDouble(bm->K_num_cohorts, bm->K_num_tot_sp, bm->sednz, bm->nbox, 0.0);
bm->atEcologyModule->linkageEPIMortality = AllocInit3DArrayDouble(bm->K_num_cohorts, bm->K_num_tot_sp, bm->nbox, 0.0);

Non-Detritus Groups
The appropriate mortality value is then used in each rate of change (ROC) equation for all functional groups. These values are subtracted similar to how the mortality values are indicating a reduction in biomass.

The units of the mortality values should be mgN /m^3 for water column and sediment and mgN/m^2 for the epibenthic layer (2D).

So the standard ROC equation is:

flux = growth - naturalmortality - mortalityDueToPredator;

So we have now included an additional term in these equations:

flux = growth - naturalmortality - mortalityDueToPredator - linkageMortality.

Detritus Groups

The detritus groups are treated a bit differently. The EwE model will return a flux value for each detritus group which is then distributed through the water column and sediment layers (not sure if the sediment values are relevant here but thought i should include them now in case we need them).

So the new detritus linkage flux is added to the generate flux equation for detritus:
DetritusgroupFlux =
detritusProduction + linkageDetritus - detritusList - breakdown - uptake.

The tracer values are then multiplied by the timestep to get a change in biomass for this timestep and this is added to the actual tracer value ( this happens in IntegrateDynamicVariables());