public void InitializeEcology()
{
//Initialize the autotrophprocessor
MarineNPPtoAutotrophStock = new AutotrophProcessor();
// Initialise the plant model
DynamicPlantModel = new RevisedTerrestrialPlantModel();
// Initialise the human NPP appropriation class
HANPP = new HumanAutotrophMatterAppropriation();
}
public void InitializeEcology()
{
//Initialize the autotrophprocessor
MarineNPPtoAutotrophStock = new AutotrophProcessor();
// Initialise the plant model
DynamicPlantModel = new RevisedTerrestrialPlantModel();
// Initialise the human NPP appropriation class
HANPP = new HumanAutotrophMatterAppropriation();
}
/// <summary>
/// Seed grid cell with stocks, as specified in the model input files
/// </summary>
/// <param name="functionalGroups">A reference to the stock functional group handler</param>
/// <param name="cellEnvironment">The environment in the grid cell</param>
/// <param name="globalDiagnostics">A list of global diagnostic variables for the model grid</param>
private void SeedGridCellStocks(ref FunctionalGroupDefinitions functionalGroups, ref SortedList<string, double[]>
cellEnvironment, SortedList<string, double> globalDiagnostics)
{
// Set the seed for the random number generator from the system time
RandomNumberGenerator.SetSeedFromSystemTime();
Stock NewStock;
// Define local variables
int[] FunctionalGroupsToUse;
// Get the individual body masses for organisms in each stock functional group
double[] IndividualMass = functionalGroups.GetBiologicalPropertyAllFunctionalGroups("individual mass");
// Check which realm the cell is in
if (cellEnvironment["Realm"][0] == 1.0 && _CellEnvironment["Precipitation"][0] != _CellEnvironment["Missing Value"][0] && _CellEnvironment["Temperature"][0] != _CellEnvironment["Missing Value"][0])
{
// Get the indices of all terrestrial functional groups
FunctionalGroupsToUse = functionalGroups.GetFunctionalGroupIndex("realm", "terrestrial", true);
}
else if (cellEnvironment["Realm"][0] == 2.0 && _CellEnvironment["NPP"][0] != _CellEnvironment["Missing Value"][0])
{
// Get the indices of all marine functional groups
FunctionalGroupsToUse = functionalGroups.GetFunctionalGroupIndex("realm", "marine", true);
}
else
{
// For cells without a realm designation, no functional groups will be used
FunctionalGroupsToUse = new int[0];
}
// Loop over all functional groups in the model
for (int FunctionalGroup = 0; FunctionalGroup < functionalGroups.GetNumberOfFunctionalGroups(); FunctionalGroup++)
{
// Create a new list to hold the stocks in the grid cell
_GridCellStocks[FunctionalGroup] = new List<Stock>();
// If it is a functional group that corresponds to the current realm, then seed the stock
if (FunctionalGroupsToUse.Contains(FunctionalGroup))
{
if (_CellEnvironment["Realm"][0] == 1.0)
{
// An instance of the terrestrial carbon model class
RevisedTerrestrialPlantModel PlantModel = new RevisedTerrestrialPlantModel();
// Calculate predicted leaf mass at equilibrium for this stock
double LeafMass = PlantModel.CalculateEquilibriumLeafMass(_CellEnvironment, functionalGroups.GetTraitNames("leaf strategy", FunctionalGroup) == "deciduous");
// Initialise the new stock with the relevant properties
NewStock = new Stock((byte)FunctionalGroup, IndividualMass[FunctionalGroup], LeafMass);
// Add the new stock to the list of grid cell stocks
_GridCellStocks[FunctionalGroup].Add(NewStock);
// Increment the variable tracking the total number of stocks in the model
globalDiagnostics["NumberOfStocksInModel"]++;
}
else if (FunctionalGroupsToUse.Contains(FunctionalGroup))
{
// Initialise the new stock with the relevant properties
NewStock = new Stock((byte)FunctionalGroup, IndividualMass[FunctionalGroup], 1e12);
// Add the new stock to the list of grid cell stocks
_GridCellStocks[FunctionalGroup].Add(NewStock);
// Increment the variable tracking the total number of stocks in the model
globalDiagnostics["NumberOfStocksInModel"]++;
}
else
{
}
}
}
}
/// <summary>
/// Copy parameter values to a text file in the specified output directory
/// </summary>
/// <param name="outputDirectory">THe directory for outputs</param>
public void CopyParameterValues(string outputDirectory)
{
// Create a stream write object to write the parameter values to
StreamWriter sw = new StreamWriter(outputDirectory + "Parameters.txt");
// Write out the column headings
sw.WriteLine("Ecological process\tParameter name\tParameter value");
// Create dummy instances of the ecological processes
RevisedHerbivory DummyHerbivory = new RevisedHerbivory(0.0, _GlobalModelTimeStepUnit);
RevisedPredation DummyPredation = new RevisedPredation(0.0, _GlobalModelTimeStepUnit);
MetabolismEndotherm DummyEndoMetabolism = new MetabolismEndotherm(_GlobalModelTimeStepUnit);
MetabolismEctotherm DummyEctoMetabolism = new MetabolismEctotherm(_GlobalModelTimeStepUnit);
BackgroundMortality DummyBackgroundMortality = new BackgroundMortality(_GlobalModelTimeStepUnit);
SenescenceMortality DummySenescenceMortality = new SenescenceMortality(_GlobalModelTimeStepUnit);
StarvationMortality DummyStarvationMortality = new StarvationMortality(_GlobalModelTimeStepUnit);
ReproductionBasic DummyReproduction = new ReproductionBasic(_GlobalModelTimeStepUnit, _DrawRandomly);
DiffusiveDispersal DummyDiffusiveDispersal = new DiffusiveDispersal(_GlobalModelTimeStepUnit, _DrawRandomly);
RevisedTerrestrialPlantModel DummyPlantModel = new RevisedTerrestrialPlantModel();
Activity DummyActivityModel = new Activity();
// Call the methods in these processes that write the parameter values out
DummyHerbivory.WriteOutParameterValues(sw);
DummyPredation.WriteOutParameterValues(sw);
DummyEndoMetabolism.WriteOutParameterValues(sw);
DummyEctoMetabolism.WriteOutParameterValues(sw);
DummyBackgroundMortality.WriteOutParameterValues(sw);
DummySenescenceMortality.WriteOutParameterValues(sw);
DummyStarvationMortality.WriteOutParameterValues(sw);
DummyReproduction.WriteOutParameterValues(sw);
DummyDiffusiveDispersal.WriteOutParameterValues(sw);
DummyPlantModel.WriteOutParameterValues(sw);
DummyActivityModel.WriteOutParameterValues(sw);
sw.Dispose();
}