/// <summary>
/// Initializes the ecosystem model
/// </summary>
/// <param name="initialisation">An instance of the model initialisation class</param>
/// <param name="scenarioParameters">The parameters for the scenarios to run</param>
/// <param name="scenarioIndex">The index of the scenario being run</param>
/// <param name="outputFilesSuffix">The suffix to be applied to all outputs from this model run</param>
/// <param name="globalModelTimeStepUnit">The time step unit used in the model</param>
/// <param name="simulation">The index of the simulation being run</param>
public MadingleyModel(MadingleyModelInitialisation initialisation, ScenarioParameterInitialisation scenarioParameters, int scenarioIndex,
string outputFilesSuffix, string globalModelTimeStepUnit, int simulation)
{
// Assign the properties for this model run
AssignModelRunProperties(initialisation, scenarioParameters, scenarioIndex, outputFilesSuffix);
// Set up list of global diagnostics
SetUpGlobalDiagnosticsList();
// Set up the model grid
SetUpModelGrid(initialisation, scenarioParameters, scenarioIndex, simulation);
// Set up model outputs
SetUpOutputs(initialisation, simulation, scenarioIndex);
// Make the initial outputs
InitialOutputs(outputFilesSuffix, initialisation, CurrentMonth);
// Instance the array of process trackers
ProcessTrackers = new ProcessTracker[_CellList.Count];
// Temporary variables
Boolean varExists;
// Set up process trackers for each grid cell
for (int i = 0; i < _CellList.Count; i++)
{
ProcessTrackers[i] = new ProcessTracker(NumTimeSteps,
EcosystemModelGrid.Lats, EcosystemModelGrid.Lons,
_CellList,
initialisation.ProcessTrackingOutputs,
initialisation.TrackProcesses,
CohortFunctionalGroupDefinitions,
EcosystemModelGrid.GlobalMissingValue,
outputFilesSuffix,
initialisation.OutputPath, initialisation.ModelMassBins,
SpecificLocations, i, initialisation,
EcosystemModelGrid.GetEnviroLayer("Realm", 0, _CellList[i][0], _CellList[i][1], out varExists) == 2.0,
EcosystemModelGrid.LatCellSize,
EcosystemModelGrid.LonCellSize);
}
// Set up a cross cell process tracker
TrackCrossCellProcesses = new CrossCellProcessTracker(initialisation.TrackCrossCellProcesses, "DispersalData", initialisation.OutputPath, outputFilesSuffix);
//Set up a global process tracker
if (SpecificLocations) initialisation.TrackGlobalProcesses = false;
TrackGlobalProcesses = new GlobalProcessTracker(NumTimeSteps,
EcosystemModelGrid.Lats, EcosystemModelGrid.Lons,
_CellList,
initialisation.ProcessTrackingOutputs,
initialisation.TrackGlobalProcesses,
CohortFunctionalGroupDefinitions,
StockFunctionalGroupDefinitions,
EcosystemModelGrid.GlobalMissingValue,
outputFilesSuffix,
initialisation.OutputPath, initialisation.ModelMassBins,
SpecificLocations, initialisation,
EcosystemModelGrid.LatCellSize,
EcosystemModelGrid.LonCellSize);
//Set-up the instance of OutputModelState
WriteModelState = new OutputModelState(initialisation, outputFilesSuffix, simulation);
if (SpecificLocations) initialisation.RunRealm = "";
// Record the initial cohorts in the process trackers
RecordInitialCohorts();
// Initialise the class for cross-grid-cell ecology
MadingleyEcologyCrossGridCell = new EcologyCrossGridCell();
// Initialise the time step timer
TimeStepTimer = new StopWatch();
EcologyTimer = new StopWatch();
OutputTimer = new StopWatch();
// Set the global model time step unit
_GlobalModelTimeStepUnit = globalModelTimeStepUnit;
// Initialise the utility functions
Utilities = new UtilityFunctions();
// Initialise the climate change impacts class
ClimateChangeSimulator = new ClimateChange();
// Initialise the harvesting impacts class
HarvestingSimulator = new Harvesting(EcosystemModelGrid.Lats, EcosystemModelGrid.Lons, (float)EcosystemModelGrid.LatCellSize);
}
/// <summary>
/// Apply all updates from the ecological processes to the properties of the acting cohort and to the environment
/// </summary>
public void UpdateAllCrossGridCellEcology(ModelGrid madingleyModelGrid, ref uint dispersalCounter, CrossCellProcessTracker trackCrossCellProcesses, uint currentTimeStep)
{
// Create an array to hold the number of cohorts dispersing in each direction from each grid cell
uint[, ,] InboundCohorts = new uint[madingleyModelGrid.DeltaFunctionalGroupDispersalArray.GetLength(0), madingleyModelGrid.DeltaFunctionalGroupDispersalArray.GetLength(1), 8];
// Create an array to hold the number of cohorts dispersing in each direction to each grid cell
uint[, ,] OutboundCohorts = new uint[madingleyModelGrid.DeltaFunctionalGroupDispersalArray.GetLength(0), madingleyModelGrid.DeltaFunctionalGroupDispersalArray.GetLength(1), 8];
// Create an list array to hold the weights of cohorts dispersing from grid cell. Dimensions are: num grid cells lon, num grid cells lat, num cohorts dispersing
List <double>[,] OutboundCohortWeights = new List <double> [madingleyModelGrid.DeltaFunctionalGroupDispersalArray.GetLength(0), madingleyModelGrid.DeltaFunctionalGroupDispersalArray.GetLength(1)];
for (uint ii = 0; ii < madingleyModelGrid.DeltaFunctionalGroupDispersalArray.GetLength(0); ii++)
{
for (uint jj = 0; jj < madingleyModelGrid.DeltaFunctionalGroupDispersalArray.GetLength(1); jj++)
{
OutboundCohortWeights[ii, jj] = new List <double>();
}
}
// Loop through the delta array that holds the grid cells of the cohorts that are flagged as needing to be moved
for (uint ii = 0; ii < madingleyModelGrid.DeltaFunctionalGroupDispersalArray.GetLength(0); ii++)
{
for (uint jj = 0; jj < madingleyModelGrid.DeltaFunctionalGroupDispersalArray.GetLength(1); jj++)
{
// No cohorts to move if there are none in the delta dispersal array
if (madingleyModelGrid.DeltaFunctionalGroupDispersalArray[ii, jj].Count == 0)
{
}
// Otherwise, loop through the cohorts and change the pointers/references to them one-by-one
else
{
for (int kk = 0; kk < madingleyModelGrid.DeltaFunctionalGroupDispersalArray[ii, jj].Count; kk++)
{
// Find out which grid cell it is going to
uint[] CellToDisperseTo = madingleyModelGrid.DeltaCellToDisperseToArray[ii, jj].ElementAt(kk);
// Functional group is identified by the first array
uint CohortToDisperseFG = madingleyModelGrid.DeltaFunctionalGroupDispersalArray[ii, jj].ElementAt(kk);
// Cohort number is identified by the second array
uint CohortToDisperseNum = madingleyModelGrid.DeltaCohortNumberDispersalArray[ii, jj].ElementAt(kk);
// If track processes is on, add this to the list of inbound and outbound cohorts
if (trackCrossCellProcesses.TrackCrossCellProcesses)
{
WriteOutCrossGridCell(madingleyModelGrid, CellToDisperseTo, InboundCohorts, OutboundCohorts, OutboundCohortWeights, ii, jj,
CohortToDisperseFG, CohortToDisperseNum, madingleyModelGrid.DeltaCellExitDirection[ii, jj].ElementAt(kk),
madingleyModelGrid.DeltaCellEntryDirection[ii, jj].ElementAt(kk));
}
// Simmply add it to the existing cohorts in that FG in the grid cell to disperse to
madingleyModelGrid.AddNewCohortToGridCell(CellToDisperseTo[0], CellToDisperseTo[1], (int)CohortToDisperseFG, madingleyModelGrid.GetGridCellIndividualCohort(ii, jj, (int)CohortToDisperseFG, (int)CohortToDisperseNum));
// Update the dispersal counter
dispersalCounter++;
// So now there is a pointer in the grid cell to which it is going. We have to delete the pointers in the original cell and in the
// delta array, but we need to do this without messing with the list structure; i.e. wait until all cohorts have been moved
}
}
}
}
// Reset the delta arrays and remove the pointers to the cohorts in the original list
for (uint ii = 0; ii < madingleyModelGrid.DeltaFunctionalGroupDispersalArray.GetLength(0); ii++)
{
for (uint jj = 0; jj < madingleyModelGrid.DeltaFunctionalGroupDispersalArray.GetLength(1); jj++)
{
// No cohorts to move if there are none in the delta dispersal array
if (madingleyModelGrid.DeltaFunctionalGroupDispersalArray[ii, jj].Count == 0)
{
}
// Otherwise, loop through the cohorts and change the pointers/references to them one-by-one
else
{
// Delete the cohorts from the original grid cell. Note that this needs to be done carefully to ensure that the correct ones
// are deleted (lists shift about when an internal element is deleted.
madingleyModelGrid.DeleteGridCellIndividualCohorts(ii, jj, madingleyModelGrid.DeltaFunctionalGroupDispersalArray[ii, jj], madingleyModelGrid.DeltaCohortNumberDispersalArray[ii, jj]);
// Reset the lists in the delta dispersal arrays
madingleyModelGrid.DeltaFunctionalGroupDispersalArray[ii, jj] = new List <uint>();
madingleyModelGrid.DeltaCohortNumberDispersalArray[ii, jj] = new List <uint>();
// Reset the list in the grid cells to disperse to array
madingleyModelGrid.DeltaCellToDisperseToArray[ii, jj] = new List <uint[]>();
// Reset the lists in the delta dispersal arrays
madingleyModelGrid.DeltaCellExitDirection[ii, jj] = new List <uint>();
madingleyModelGrid.DeltaCellEntryDirection[ii, jj] = new List <uint>();
}
}
}
if (trackCrossCellProcesses.TrackCrossCellProcesses)
{
// If we are tracking dispersal, then write out how many cohorts have moved to a file
trackCrossCellProcesses.RecordDispersalForACell(InboundCohorts, OutboundCohorts, OutboundCohortWeights, currentTimeStep, madingleyModelGrid);
}
}
/// <summary>
/// Apply all updates from the ecological processes to the properties of the acting cohort and to the environment
/// </summary>
public void UpdateAllCrossGridCellEcology(ModelGrid madingleyModelGrid, ref uint dispersalCounter, CrossCellProcessTracker trackCrossCellProcesses, uint currentTimeStep)
{
// Create an array to hold the number of cohorts dispersing in each direction from each grid cell
uint[, ,] InboundCohorts = new uint[madingleyModelGrid.DeltaFunctionalGroupDispersalArray.GetLength(0), madingleyModelGrid.DeltaFunctionalGroupDispersalArray.GetLength(1), 8];
// Create an array to hold the number of cohorts dispersing in each direction to each grid cell
uint[, ,] OutboundCohorts = new uint[madingleyModelGrid.DeltaFunctionalGroupDispersalArray.GetLength(0), madingleyModelGrid.DeltaFunctionalGroupDispersalArray.GetLength(1), 8];
// Create an list array to hold the weights of cohorts dispersing from grid cell. Dimensions are: num grid cells lon, num grid cells lat, num cohorts dispersing
List<double>[,] OutboundCohortWeights = new List<double>[madingleyModelGrid.DeltaFunctionalGroupDispersalArray.GetLength(0), madingleyModelGrid.DeltaFunctionalGroupDispersalArray.GetLength(1)];
for (uint ii = 0; ii < madingleyModelGrid.DeltaFunctionalGroupDispersalArray.GetLength(0); ii++)
{
for (uint jj = 0; jj < madingleyModelGrid.DeltaFunctionalGroupDispersalArray.GetLength(1); jj++)
{
OutboundCohortWeights[ii,jj] = new List<double>();
}
}
// Loop through the delta array that holds the grid cells of the cohorts that are flagged as needing to be moved
for (uint ii = 0; ii < madingleyModelGrid.DeltaFunctionalGroupDispersalArray.GetLength(0) ; ii++)
{
for (uint jj = 0; jj < madingleyModelGrid.DeltaFunctionalGroupDispersalArray.GetLength(1); jj++)
{
if (madingleyModelGrid.DeltaFunctionalGroupDispersalArray[ii, jj] != null)
{
// No cohorts to move if there are none in the delta dispersal array
if (madingleyModelGrid.DeltaFunctionalGroupDispersalArray[ii, jj].Count == 0)
{
}
// Otherwise, loop through the cohorts and change the pointers/references to them one-by-one
else
{
for (int kk = 0; kk < madingleyModelGrid.DeltaFunctionalGroupDispersalArray[ii, jj].Count; kk++)
{
// Find out which grid cell it is going to
uint[] CellToDisperseTo = madingleyModelGrid.DeltaCellToDisperseToArray[ii, jj].ElementAt(kk);
// Functional group is identified by the first array
uint CohortToDisperseFG = madingleyModelGrid.DeltaFunctionalGroupDispersalArray[ii, jj].ElementAt(kk);
// Cohort number is identified by the second array
uint CohortToDisperseNum = madingleyModelGrid.DeltaCohortNumberDispersalArray[ii, jj].ElementAt(kk);
// If track processes is on, add this to the list of inbound and outbound cohorts
if (trackCrossCellProcesses.TrackCrossCellProcesses)
{
WriteOutCrossGridCell(madingleyModelGrid, CellToDisperseTo, InboundCohorts, OutboundCohorts, OutboundCohortWeights, ii, jj,
CohortToDisperseFG, CohortToDisperseNum, madingleyModelGrid.DeltaCellExitDirection[ii, jj].ElementAt(kk),
madingleyModelGrid.DeltaCellEntryDirection[ii, jj].ElementAt(kk));
}
// Simmply add it to the existing cohorts in that FG in the grid cell to disperse to
madingleyModelGrid.AddNewCohortToGridCell(CellToDisperseTo[0], CellToDisperseTo[1], (int)CohortToDisperseFG, madingleyModelGrid.GetGridCellIndividualCohort(ii, jj, (int)CohortToDisperseFG, (int)CohortToDisperseNum));
// Update the dispersal counter
dispersalCounter++;
// So now there is a pointer in the grid cell to which it is going. We have to delete the pointers in the original cell and in the
// delta array, but we need to do this without messing with the list structure; i.e. wait until all cohorts have been moved
}
}
}
}
}
// Reset the delta arrays and remove the pointers to the cohorts in the original list
for (uint ii = 0; ii < madingleyModelGrid.DeltaFunctionalGroupDispersalArray.GetLength(0); ii++)
{
for (uint jj = 0; jj < madingleyModelGrid.DeltaFunctionalGroupDispersalArray.GetLength(1); jj++)
{
if (madingleyModelGrid.DeltaFunctionalGroupDispersalArray[ii, jj] != null)
{
// No cohorts to move if there are none in the delta dispersal array
if (madingleyModelGrid.DeltaFunctionalGroupDispersalArray[ii, jj].Count == 0)
{
}
// Otherwise, loop through the cohorts and change the pointers/references to them one-by-one
else
{
// Delete the cohorts from the original grid cell. Note that this needs to be done carefully to ensure that the correct ones
// are deleted (lists shift about when an internal element is deleted.
madingleyModelGrid.DeleteGridCellIndividualCohorts(ii, jj, madingleyModelGrid.DeltaFunctionalGroupDispersalArray[ii, jj], madingleyModelGrid.DeltaCohortNumberDispersalArray[ii, jj]);
// Reset the lists in the delta dispersal arrays
madingleyModelGrid.DeltaFunctionalGroupDispersalArray[ii, jj] = new List<uint>();
madingleyModelGrid.DeltaCohortNumberDispersalArray[ii, jj] = new List<uint>();
// Reset the list in the grid cells to disperse to array
madingleyModelGrid.DeltaCellToDisperseToArray[ii, jj] = new List<uint[]>();
// Reset the lists in the delta dispersal arrays
madingleyModelGrid.DeltaCellExitDirection[ii, jj] = new List<uint>();
madingleyModelGrid.DeltaCellEntryDirection[ii, jj] = new List<uint>();
}
}
}
}
if (trackCrossCellProcesses.TrackCrossCellProcesses)
{
// If we are tracking dispersal, then write out how many cohorts have moved to a file
trackCrossCellProcesses.RecordDispersalForACell(InboundCohorts, OutboundCohorts, OutboundCohortWeights, currentTimeStep, madingleyModelGrid);
}
}
/// <summary>
/// Initializes the ecosystem model
/// </summary>
/// <param name="initialisation">An instance of the model initialisation class</param>
/// <param name="scenarioParameters">The parameters for the scenarios to run</param>
/// <param name="scenarioIndex">The index of the scenario being run</param>
/// <param name="outputFilesSuffix">The suffix to be applied to all outputs from this model run</param>
/// <param name="globalModelTimeStepUnit">The time step unit used in the model</param>
/// <param name="simulation">The index of the simulation being run</param>
public MadingleyModel(MadingleyModelInitialisation initialisation, ScenarioParameterInitialisation scenarioParameters, int scenarioIndex,
string outputFilesSuffix, string globalModelTimeStepUnit, int simulation)
{
// Assign the properties for this model run
AssignModelRunProperties(initialisation, scenarioParameters, scenarioIndex, outputFilesSuffix);
#endif
// Set up the model grid
#if true
this._CellList = initialisation.CellList.ToList();
SetUpModelGrid(initialisation);
EcosystemModelGrid.SetGridCells(gridCells, this._CellList);
#else
SetUpModelGrid(initialisation, scenarioParameters, scenarioIndex, simulation);
#endif
// Set up model outputs
SetUpOutputs(initialisation, simulation, scenarioIndex);
// Make the initial outputs
InitialOutputs(outputFilesSuffix, initialisation, CurrentMonth);
// Instance the array of process trackers
ProcessTrackers = new ProcessTracker[_CellList.Count];
// Temporary variables
Boolean varExists;
// Set up process trackers for each grid cell
for (int i = 0; i < _CellList.Count; i++)
{
ProcessTrackers[i] = new ProcessTracker(NumTimeSteps,
EcosystemModelGrid.Lats, EcosystemModelGrid.Lons,
_CellList,
initialisation.ProcessTrackingOutputs,
initialisation.TrackProcesses,
CohortFunctionalGroupDefinitions,
EcosystemModelGrid.GlobalMissingValue,
outputFilesSuffix,
initialisation.OutputPath, initialisation.ModelMassBins,
SpecificLocations, i, initialisation,
EcosystemModelGrid.GetEnviroLayer("Realm", 0, _CellList[i][0], _CellList[i][1], out varExists) == 2.0,
EcosystemModelGrid.LatCellSize,
EcosystemModelGrid.LonCellSize);
}
// Set up a cross cell process tracker
TrackCrossCellProcesses = new CrossCellProcessTracker(initialisation.TrackCrossCellProcesses, "DispersalData", initialisation.OutputPath, outputFilesSuffix);
//Set up a global process tracker
if (SpecificLocations) initialisation.TrackGlobalProcesses = false;
TrackGlobalProcesses = new GlobalProcessTracker(NumTimeSteps,
EcosystemModelGrid.Lats, EcosystemModelGrid.Lons,
_CellList,
initialisation.ProcessTrackingOutputs,
initialisation.TrackGlobalProcesses,
CohortFunctionalGroupDefinitions,
StockFunctionalGroupDefinitions,
EcosystemModelGrid.GlobalMissingValue,
outputFilesSuffix,
initialisation.OutputPath, initialisation.ModelMassBins,
SpecificLocations, initialisation,
EcosystemModelGrid.LatCellSize,
EcosystemModelGrid.LonCellSize);
//Set-up the instance of OutputModelState
WriteModelState = new OutputModelState(initialisation, outputFilesSuffix, simulation);
if (SpecificLocations) initialisation.RunRealm = "";
// Record the initial cohorts in the process trackers
RecordInitialCohorts();
// Initialise the time step timer
TimeStepTimer = new StopWatch();
EcologyTimer = new StopWatch();
OutputTimer = new StopWatch();
// Set the global model time step unit
_GlobalModelTimeStepUnit = globalModelTimeStepUnit;
}
/// <summary>
/// Update the properties of all cohorts across all grid cells
/// </summary>
public void UpdateCrossGridCellEcology(ModelGrid madingleyModelGrid, ref uint dispersalCounter, CrossCellProcessTracker trackCrossCellProcesses, uint currentTimeStep)
{
// Apply the results of cross-cell ecological processes
ApplyCrossGridCellEcologicalProcessResults.UpdateAllCrossGridCellEcology(madingleyModelGrid, ref dispersalCounter, trackCrossCellProcesses, currentTimeStep);
}
