private void RunWithinCellCohortEcology(uint latCellIndex, uint lonCellIndex, ThreadLockedParallelVariables partial,
GridCellCohortHandler workingGridCellCohorts, GridCellStockHandler workingGridCellStocks,string outputDetail, int cellIndex, MadingleyModelInitialisation initialisation)
{
// Local instances of classes
EcologyCohort MadingleyEcologyCohort = new EcologyCohort();
Activity CohortActivity = new Activity();
CohortMerge CohortMerger = new CohortMerge(DrawRandomly);
// A list of the original cohorts inside a particular grid cell
int[] OriginalGridCellCohortsNumbers;
// A vector to hold the order in which cohorts will act
uint[] RandomCohortOrder;
// A jagged array to keep track of cohorts that are being worked on
uint[][] CohortIndices;
// The location of the acting cohort
int[] ActingCohort = new int[2];
// Temporary local variables
int EcosystemModelParallelTempval1;
int EcosystemModelParallelTempval2;
// Boolean to pass into function to get cell environmental data to check if the specified variable exists
bool VarExists;
// variable to track cohort number
uint TotalCohortNumber = 0;
// Fill in the array with the number of cohorts per functional group before ecological processes are run
OriginalGridCellCohortsNumbers = new int[workingGridCellCohorts.Count];
for (int i = 0; i < workingGridCellCohorts.Count; i++)
{
OriginalGridCellCohortsNumbers[i] = workingGridCellCohorts[i].Count;
}
// Initialize ecology for stocks and cohorts
MadingleyEcologyCohort.InitializeEcology(EcosystemModelGrid.GetCellEnvironment(latCellIndex, lonCellIndex)["Cell Area"][0],
_GlobalModelTimeStepUnit, DrawRandomly);
// Create a jagged array indexed by functional groups to hold cohort indices
CohortIndices = new uint[CohortFunctionalGroupDefinitions.GetNumberOfFunctionalGroups()][];
// Loop over functional groups
for (int ll = 0; ll < CohortFunctionalGroupDefinitions.GetNumberOfFunctionalGroups(); ll++)
{
// Dimension the number of columns in each row of the jagged array to equal number of gridCellCohorts in each functional group
if (workingGridCellCohorts[ll] == null)
{
CohortIndices[ll] = new uint[0];
}
else
{
CohortIndices[ll] = new uint[workingGridCellCohorts[ll].Count()];
}
// Loop over gridCellCohorts in the functional group
for (int kk = 0; kk < CohortIndices[ll].Count(); kk++)
{
// Fill jagged array with indices for each cohort
CohortIndices[ll][kk] = TotalCohortNumber;
TotalCohortNumber += 1;
}
}
if (DrawRandomly)
{
// Randomly order the cohort indices
RandomCohortOrder = Utilities.RandomlyOrderedIndices(TotalCohortNumber);
}
else
{
RandomCohortOrder = Utilities.NonRandomlyOrderedCohorts(TotalCohortNumber, CurrentTimeStep);
}
// Diagnostic biological variables don't need to be reset every cohort, but rather every grid cell
EcosystemModelParallelTempval2 = 0;
// Initialise eating formulations
MadingleyEcologyCohort.EatingFormulations["Basic eating"].InitializeEcologicalProcess(workingGridCellCohorts, workingGridCellStocks,
CohortFunctionalGroupDefinitions, StockFunctionalGroupDefinitions, "revised predation");
MadingleyEcologyCohort.EatingFormulations["Basic eating"].InitializeEcologicalProcess(workingGridCellCohorts, workingGridCellStocks
, CohortFunctionalGroupDefinitions, StockFunctionalGroupDefinitions, "revised herbivory");
// Loop over randomly ordered gridCellCohorts to implement biological functions
for (int ll = 0; ll < RandomCohortOrder.Length; ll++)
{
// Locate the randomly chosen cohort within the array of lists of gridCellCohorts in the grid cell
ActingCohort = Utilities.FindJaggedArrayIndex(RandomCohortOrder[ll], CohortIndices, TotalCohortNumber);
// Perform all biological functions except dispersal (which is cross grid cell)
if (workingGridCellCohorts[ActingCohort].CohortAbundance.CompareTo(_ExtinctionThreshold) > 0)
{
// Calculate number of cohorts in this functional group in this grid cell before running ecology
EcosystemModelParallelTempval1 = workingGridCellCohorts[ActingCohort[0]].Count;
CohortActivity.AssignProportionTimeActive(workingGridCellCohorts[ActingCohort], EcosystemModelGrid.GetCellEnvironment(latCellIndex, lonCellIndex), CohortFunctionalGroupDefinitions, CurrentTimeStep, CurrentMonth);
// Run ecology
MadingleyEcologyCohort.RunWithinCellEcology(workingGridCellCohorts, workingGridCellStocks,
ActingCohort, EcosystemModelGrid.GetCellEnvironment(latCellIndex, lonCellIndex),
EcosystemModelGrid.GetCellDeltas(latCellIndex, lonCellIndex),
CohortFunctionalGroupDefinitions, StockFunctionalGroupDefinitions, CurrentTimeStep,
ProcessTrackers[cellIndex], ref partial, SpecificLocations,outputDetail, CurrentMonth, initialisation);
// Update the properties of the acting cohort
MadingleyEcologyCohort.UpdateEcology(workingGridCellCohorts, workingGridCellStocks, ActingCohort,
EcosystemModelGrid.GetCellEnvironment(latCellIndex, lonCellIndex), EcosystemModelGrid.GetCellDeltas(
latCellIndex, lonCellIndex), CohortFunctionalGroupDefinitions, StockFunctionalGroupDefinitions, CurrentTimeStep,
ProcessTrackers[cellIndex]);
// Add newly produced cohorts to the tracking variable
EcosystemModelParallelTempval2 += workingGridCellCohorts[ActingCohort[0]].Count - EcosystemModelParallelTempval1;
// Check that the mass of individuals in this cohort is still >= 0 after running ecology
Debug.Assert(workingGridCellCohorts[ActingCohort].IndividualBodyMass >= 0.0, "Biomass < 0 for this cohort");
}
// Check that the mass of individuals in this cohort is still >= 0 after running ecology
Debug.Assert(workingGridCellCohorts[ActingCohort].IndividualBodyMass >= 0.0, "Biomass < 0 for this cohort");
}
// Update diagnostics of productions
partial.Productions += EcosystemModelParallelTempval2;
RunExtinction(latCellIndex, lonCellIndex, partial, workingGridCellCohorts, cellIndex);
// Merge cohorts, if necessary
if (workingGridCellCohorts.GetNumberOfCohorts() > initialisation.MaxNumberOfCohorts)
{
partial.Combinations = CohortMerger.MergeToReachThresholdFast(workingGridCellCohorts, workingGridCellCohorts.GetNumberOfCohorts(), initialisation.MaxNumberOfCohorts);
//Run extinction a second time to remove those cohorts that have been set to zero abundance when merging
RunExtinction(latCellIndex, lonCellIndex, partial, workingGridCellCohorts, cellIndex);
}
else
partial.Combinations = 0;
// Write out the updated cohort numbers after all ecological processes have occured
EcosystemModelGrid.SetGridCellCohorts(workingGridCellCohorts, latCellIndex, lonCellIndex);
}
/// <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();
}
