/// <summary>
/// Calculate outputs associated with low-level outputs
/// </summary>
/// <param name="ecosystemModelGrid">The model grid</param>
/// <param name="cellIndices">The list of indices of active cells in the model grid</param>
/// <param name="cellIndex">The position of the current cell in the list of active cells</param>
/// <param name="globalDiagnosticVariables">The global diagnostic variables for this model run</param>
/// <param name="cohortFunctionalGroupDefinitions">The functional group definitions of cohorts in the model</param>
/// <param name="stockFunctionalGroupDefinitions">The functional group definitions of stocks in the model</param>
/// <param name="initialisation">The Madingley Model initialisation</param>
/// <param name="month">The current month in the model run</param>
/// <param name="MarineCell">Whether the current cell is a marine cell</param>
private void CalculateLowLevelOutputs(ModelGrid ecosystemModelGrid, List<uint[]> cellIndices, int cellIndex,
SortedList<string,double> globalDiagnosticVariables, FunctionalGroupDefinitions cohortFunctionalGroupDefinitions,
FunctionalGroupDefinitions stockFunctionalGroupDefinitions, MadingleyModelInitialisation initialisation, uint month,
Boolean MarineCell)
{
// Reset the total living biomass
TotalLivingBiomass = 0.0;
string[] Keys;
if (MarineCell)
{
// Get the list of cohort trait combinations to consider
Keys = CohortTraitIndicesMarine.Keys.ToArray();
// Get biomass, abundance and densities for each of the trait combinations. Note that the GetStateVariableDensity function deals with the assessment of whether cohorts contain individuals
// of low enough mass to be considered zooplankton in the marine realm
foreach (string TraitValue in Keys)
{
// Biomass density
TotalBiomassDensitiesOut[TraitValue] = ecosystemModelGrid.GetStateVariableDensity("Biomass", TraitValue, CohortTraitIndicesMarine[TraitValue], cellIndices[cellIndex][0], cellIndices[cellIndex][1], "cohort", initialisation) / 1000.0;
// Density
TotalDensitiesOut[TraitValue] = ecosystemModelGrid.GetStateVariableDensity("Abundance", TraitValue, CohortTraitIndicesMarine[TraitValue], cellIndices[cellIndex][0], cellIndices[cellIndex][1], "cohort", initialisation);
}
}
else
{
// Get the list of cohort trait combinations to consider
Keys = CohortTraitIndices.Keys.ToArray();
// Get biomass, abundance and densities for each of the trait combinations
foreach (string TraitValue in Keys)
{
// Biomass density
TotalBiomassDensitiesOut[TraitValue] = ecosystemModelGrid.GetStateVariableDensity("Biomass", TraitValue, CohortTraitIndices[TraitValue], cellIndices[cellIndex][0], cellIndices[cellIndex][1], "cohort", initialisation) / 1000.0;
// Density
TotalDensitiesOut[TraitValue] = ecosystemModelGrid.GetStateVariableDensity("Abundance", TraitValue, CohortTraitIndices[TraitValue], cellIndices[cellIndex][0], cellIndices[cellIndex][1], "cohort", initialisation);
}
}
// Add the total biomass of all cohorts to the total living biomass variable
TotalLivingBiomass += ecosystemModelGrid.GetStateVariable("Biomass", "NA", cohortFunctionalGroupDefinitions.AllFunctionalGroupsIndex,
cellIndices[cellIndex][0], cellIndices[cellIndex][1], "cohort", initialisation);
TotalLivingBiomassDensity = ecosystemModelGrid.GetStateVariableDensity("Biomass", "NA", cohortFunctionalGroupDefinitions.AllFunctionalGroupsIndex, cellIndices[cellIndex][0], cellIndices[cellIndex][1], "cohort", initialisation) / 1000.0;
TotalHeterotrophAbundanceDensity = ecosystemModelGrid.GetStateVariableDensity("Abundance", "NA", cohortFunctionalGroupDefinitions.AllFunctionalGroupsIndex, cellIndices[cellIndex][0], cellIndices[cellIndex][1], "cohort", initialisation);
TotalHeterotrophBiomassDensity = TotalLivingBiomassDensity;
if (MarineCell)
{
// Get the list of stock trait combinations to consider
Keys = StockTraitIndicesMarine.Keys.ToArray();
// Get biomass and biomass density for each of the trait combinations
foreach (string TraitValue in Keys)
{
// Density
TotalBiomassDensitiesOut[TraitValue] = ecosystemModelGrid.GetStateVariableDensity("Biomass", TraitValue, StockTraitIndicesMarine[TraitValue], cellIndices[cellIndex][0], cellIndices[cellIndex][1], "stock", initialisation) / 1000.0;
}
}
else
{
// Get the list of stock trait combinations to consider
Keys = StockTraitIndices.Keys.ToArray();
// Get biomass and biomass density for each of the trait combinations
foreach (string TraitValue in Keys)
{
// Density
TotalBiomassDensitiesOut[TraitValue] = ecosystemModelGrid.GetStateVariableDensity("Biomass", TraitValue, StockTraitIndices[TraitValue], cellIndices[cellIndex][0], cellIndices[cellIndex][1], "stock", initialisation) / 1000.0;
}
}
// Add the total biomass of all stocks to the total living biomass variable
TotalLivingBiomass += ecosystemModelGrid.GetStateVariable("Biomass", "NA", stockFunctionalGroupDefinitions.AllFunctionalGroupsIndex,
cellIndices[cellIndex][0], cellIndices[cellIndex][1], "stock", initialisation);
TotalLivingBiomassDensity += ecosystemModelGrid.GetStateVariableDensity("Biomass", "NA", stockFunctionalGroupDefinitions.AllFunctionalGroupsIndex, cellIndices[cellIndex][0], cellIndices[cellIndex][1], "stock", initialisation) / 1000.0;
if (TrackMarineSpecifics && MarineCell)
{
bool varExists;
TotalIncomingNPP = ecosystemModelGrid.GetEnviroLayer("NPP", month, cellIndices[cellIndex][0], cellIndices[cellIndex][1], out varExists);
}
}
