/// <summary>
/// Calculates the variables to output
/// </summary>
/// <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="ecosystemModelGrid">The model grid</param>
/// <param name="cellIndices">The list of indices of active cells in the model grid</param>
/// <param name="globalDiagnosticVariables">Global diagnostic variables</param>
/// <param name="initialisation">The Madingley Model initialisation</param>
public void CalculateOutputs(FunctionalGroupDefinitions cohortFunctionalGroupDefinitions, FunctionalGroupDefinitions
stockFunctionalGroupDefinitions, ModelGrid ecosystemModelGrid, List <uint[]> cellIndices, SortedList <string, double>
globalDiagnosticVariables, MadingleyModelInitialisation initialisation)
{
// Get all cohort functional group indices in the model
int[] CohortFunctionalGroupIndices = cohortFunctionalGroupDefinitions.AllFunctionalGroupsIndex;
// Get all stock functional group indices in the model
int[] StockFunctionalGroupIndices = stockFunctionalGroupDefinitions.AllFunctionalGroupsIndex;
// Reset total abundance, biomass and pool biomasses
TotalAbundance = 0.0;
TotalBiomass = 0.0;
TotalLivingBiomass = 0.0;
OrganicPoolOut = 0.0;
RespiratoryPoolOut = 0.0;
// Add total cohort biomass and total stock biomass to the total biomass tracker
TotalLivingBiomass += ecosystemModelGrid.StateVariableGridTotal("Biomass", "NA", CohortFunctionalGroupIndices, cellIndices, "cohort", initialisation);
TotalLivingBiomass += ecosystemModelGrid.StateVariableGridTotal("Biomass", "NA", StockFunctionalGroupIndices, cellIndices, "stock", initialisation);
// Add total cohort abundance to the total abundance tracker
TotalAbundance += ecosystemModelGrid.StateVariableGridTotal("Abundance", "NA", CohortFunctionalGroupIndices, cellIndices, "cohort", initialisation);
// Get total organic pool biomass
OrganicPoolOut = ecosystemModelGrid.GetEnviroGridTotal("Organic Pool", 0, cellIndices);
// Get total respiratory pool biomass
RespiratoryPoolOut = ecosystemModelGrid.GetEnviroGridTotal("Respiratory CO2 Pool", 0, cellIndices);
// Get total of all biomass
TotalBiomass = TotalLivingBiomass + RespiratoryPoolOut + OrganicPoolOut;
// Get number of cohorts and stocks
TotalNumberOfCohorts = globalDiagnosticVariables["NumberOfCohortsInModel"];
TotalNumberOfStocks = globalDiagnosticVariables["NumberOfStocksInModel"];
// Get numbers of cohort extinctions and productions
NumberOfCohortsExtinct = globalDiagnosticVariables["NumberOfCohortsExtinct"];
NumberOfCohortsProduced = globalDiagnosticVariables["NumberOfCohortsProduced"];
NumberOfCohortsCombined = globalDiagnosticVariables["NumberOfCohortsCombined"];
}
/// <summary>
/// Calculates the variables to output
/// </summary>
/// <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="ecosystemModelGrid">The model grid</param>
/// <param name="cellIndices">The list of indices of active cells in the model grid</param>
/// <param name="globalDiagnosticVariables">Global diagnostic variables</param>
/// <param name="initialisation">The Madingley Model initialisation</param>
public void CalculateOutputs(FunctionalGroupDefinitions cohortFunctionalGroupDefinitions, FunctionalGroupDefinitions
stockFunctionalGroupDefinitions, ModelGrid ecosystemModelGrid, List<uint[]> cellIndices, SortedList<string, double>
globalDiagnosticVariables, MadingleyModelInitialisation initialisation)
{
// Get all cohort functional group indices in the model
int[] CohortFunctionalGroupIndices = cohortFunctionalGroupDefinitions.AllFunctionalGroupsIndex;
// Get all stock functional group indices in the model
int[] StockFunctionalGroupIndices = stockFunctionalGroupDefinitions.AllFunctionalGroupsIndex;
// Reset total abundance, biomass and pool biomasses
TotalAbundance = 0.0;
TotalBiomass = 0.0;
TotalLivingBiomass = 0.0;
OrganicPoolOut = 0.0;
RespiratoryPoolOut = 0.0;
// Add total cohort biomass and total stock biomass to the total biomass tracker
TotalLivingBiomass += ecosystemModelGrid.StateVariableGridTotal("Biomass", "NA", CohortFunctionalGroupIndices, cellIndices, "cohort", initialisation);
TotalLivingBiomass += ecosystemModelGrid.StateVariableGridTotal("Biomass", "NA", StockFunctionalGroupIndices, cellIndices, "stock", initialisation);
// Add total cohort abundance to the total abundance tracker
TotalAbundance += ecosystemModelGrid.StateVariableGridTotal("Abundance", "NA", CohortFunctionalGroupIndices, cellIndices, "cohort", initialisation);
// Get total organic pool biomass
OrganicPoolOut = ecosystemModelGrid.GetEnviroGridTotal("Organic Pool", 0, cellIndices);
// Get total respiratory pool biomass
RespiratoryPoolOut = ecosystemModelGrid.GetEnviroGridTotal("Respiratory CO2 Pool", 0, cellIndices);
// Get total of all biomass
TotalBiomass = TotalLivingBiomass + RespiratoryPoolOut + OrganicPoolOut;
// Get number of cohorts and stocks
TotalNumberOfCohorts = globalDiagnosticVariables["NumberOfCohortsInModel"];
TotalNumberOfStocks = globalDiagnosticVariables["NumberOfStocksInModel"];
// Get numbers of cohort extinctions and productions
NumberOfCohortsExtinct = globalDiagnosticVariables["NumberOfCohortsExtinct"];
NumberOfCohortsProduced = globalDiagnosticVariables["NumberOfCohortsProduced"];
NumberOfCohortsCombined = globalDiagnosticVariables["NumberOfCohortsCombined"];
}
