public InputModelState(
GridCellCohortHandler[,] gridCellCohorts,
GridCellStockHandler[,] gridCellStocks)
{
this._GridCellCohorts = gridCellCohorts;
this._GridCellStocks = gridCellStocks;
this._InputState = true;
}
/// <summary>
/// Initializes an implementation of eating
/// </summary>
/// <param name="gridCellCohorts">The cohorts in the current grid cell</param>
/// <param name="gridCellStocks">The stocks in the current grid cell</param>
/// <param name="madingleyCohortDefinitions">The definitions for cohort functional groups in the model</param>
/// <param name="madingleyStockDefinitions">The definitions for stock functional groups in the model</param>
/// <param name="implementationKey">The name of the implementation of eating to initialize</param>
/// <param name="cellEnvironment">The environment in the current grid cell</param>
/// <remarks>Eating needs to be initialized every time step</remarks>
public void InitializeEcologicalProcess(GridCellCohortHandler gridCellCohorts, GridCellStockHandler gridCellStocks,
FunctionalGroupDefinitions madingleyCohortDefinitions, FunctionalGroupDefinitions madingleyStockDefinitions,
string implementationKey, SortedList<string, double[]> cellEnvironment)
{
// Initialize the implementation of the eating process
Implementations[implementationKey].InitializeEatingPerTimeStep(gridCellCohorts, gridCellStocks,
madingleyCohortDefinitions, madingleyStockDefinitions,cellEnvironment);
}
/// <summary>
/// Convert NPP estimate into biomass of an autotroph stock
/// </summary>
/// <param name="cellEnvironment">The environment of the current grid cell</param>
/// <param name="gridCellStockHandler">The stock handler for the current stock</param>
/// <param name="actingStock">The location of the stock to add biomass to</param>
/// <param name="terrestrialNPPUnits">The units of the terrestrial NPP data</param>
/// <param name="oceanicNPPUnits">The units of the oceanic NPP data</param>
/// <param name="currentTimestep">The current model time step</param>
/// <param name="GlobalModelTimeStepUnit">The time step unit used in the model</param>
/// <param name="trackProcesses">Whether to output data describing the ecological processes</param>
/// <param name="globalTracker">Whether to output data describing the global-scale environment</param>
/// <param name="outputDetail">The level of output detail to use for the outputs</param>
/// <param name="specificLocations">Whether the model is being run for specific locations</param>
/// <param name="currentMonth">The current month in the model run</param>
public void ConvertNPPToAutotroph(SortedList<string, double[]> cellEnvironment, GridCellStockHandler gridCellStockHandler, int[]
actingStock, string terrestrialNPPUnits, string oceanicNPPUnits, uint currentTimestep, string GlobalModelTimeStepUnit,
ProcessTracker trackProcesses, GlobalProcessTracker globalTracker, string outputDetail, bool specificLocations, uint currentMonth)
{
// Get NPP from the cell environment
double NPP = cellEnvironment["NPP"][currentMonth];
// If NPP is a mssing value then set to zero
if (NPP == cellEnvironment["Missing Value"][0]) NPP = 0.0;
// Check that this is an ocean cell
if (cellEnvironment["Realm"][0] == 2.0)
{
// Check that the units of oceanic NPP are gC per m2 per day
Debug.Assert(oceanicNPPUnits == "gC/m2/day", "Oceanic NPP data are not in the correct units for this formulation of the model");
// Convert to g/cell/month
NPP *= _MsqToKmSqConversion;
// Multiply by cell area to get g/cell/day
NPP *= cellEnvironment["Cell Area"][0];
// Convert to g wet matter, assuming carbon content of phytoplankton is 10% of wet matter
NPP *= _PhytoplanktonConversionRatio;
// Finally convert to g/cell/month and add to the stock totalbiomass
NPP *= Utilities.ConvertTimeUnits(GlobalModelTimeStepUnit, "day");
gridCellStockHandler[actingStock].TotalBiomass += NPP;
if (trackProcesses.TrackProcesses && (outputDetail == "high") && specificLocations)
{
trackProcesses.TrackPrimaryProductionTrophicFlow((uint)cellEnvironment["LatIndex"][0], (uint)cellEnvironment["LonIndex"][0],
NPP);
}
if (globalTracker.TrackProcesses)
{
globalTracker.RecordNPP((uint)cellEnvironment["LatIndex"][0], (uint)cellEnvironment["LonIndex"][0], (uint)actingStock[0],
NPP / cellEnvironment["Cell Area"][0]);
}
// If the biomass of the autotroph stock has been made less than zero (i.e. because of negative NPP) then reset to zero
if (gridCellStockHandler[actingStock].TotalBiomass < 0.0)
gridCellStockHandler[actingStock].TotalBiomass = 0.0;
}
// Else if neither on land or in the ocean
else
{
Debug.Fail("This is not a marine cell!");
// Set the autotroph biomass to zero
gridCellStockHandler[actingStock].TotalBiomass = 0.0;
}
Debug.Assert(gridCellStockHandler[actingStock].TotalBiomass >= 0.0, "stock negative");
}
/// <summary>
/// Run metabolism for the acting cohort
/// </summary>
/// <param name="gridCellCohorts">The cohorts in the current grid cell</param>
/// <param name="gridCellStocks">The stocks in the current grid cell</param>
/// <param name="actingCohort">The position of the acting cohort in the jagged array of grid cell cohorts</param>
/// <param name="cellEnvironment">The environment in the current grid cell</param>
/// <param name="deltas">The sorted list to track changes in biomass and abundance of the acting cohort in this grid cell</param>
/// <param name="madingleyCohortDefinitions">The definitions for cohort functional groups in the model</param>
/// <param name="madingleyStockDefinitions">The definitions for the stock functional groups in the model</param>
/// <param name="currentTimestep">The current model time step</param>
/// <param name="currentMonth">The current model month</param>
public void RunMetabolism(GridCellCohortHandler gridCellCohorts, GridCellStockHandler gridCellStocks,
int[] actingCohort, SortedList<string, double[]> cellEnvironment, Dictionary<string, Dictionary<string, double>>
deltas, FunctionalGroupDefinitions madingleyCohortDefinitions, FunctionalGroupDefinitions madingleyStockDefinitions,
uint currentTimestep, uint currentMonth)
{
// Calculate metabolic loss for an individual and add the value to the delta biomass for metabolism
deltas["biomass"]["metabolism"] = -CalculateIndividualMetabolicRate(gridCellCohorts[actingCohort].IndividualBodyMass,
cellEnvironment["Temperature"][currentMonth] + _TemperatureUnitsConvert) * _DeltaT;
// If metabolic loss is greater than individual body mass after herbivory and predation, then set equal to individual body mass
deltas["biomass"]["metabolism"] = Math.Max(deltas["biomass"]["metabolism"],-(gridCellCohorts[actingCohort].IndividualBodyMass + deltas["biomass"]["predation"] + deltas["biomass"]["herbivory"]));
// Add total metabolic loss for all individuals in the cohort to delta biomass for metabolism in the respiratory CO2 pool
deltas["respiratoryCO2pool"]["metabolism"] = -deltas["biomass"]["metabolism"] * gridCellCohorts[actingCohort].CohortAbundance;
}
/// <summary>
/// Run reproduction
/// </summary>
/// <param name="gridCellCohorts">The cohorts in the current grid cell</param>
/// <param name="gridCellStocks">The stocks in the current grid cell</param>
/// <param name="actingCohort">The position of the acting cohort in the jagged array of grid cell cohorts</param>
/// <param name="cellEnvironment">The environment in the current grid cell</param>
/// <param name="deltas">The sorted list to track changes in biomass and abundance of the acting cohort in this grid cell</param>
/// <param name="madingleyCohortDefinitions">The definitions for cohort functional groups in the model</param>
/// <param name="madingleyStockDefinitions">The definitions for stock functional groups in the model</param>
/// <param name="currentTimeStep">The current model time step</param>
/// <param name="processTracker">An instance of ProcessTracker to hold diagnostics for eating</param>
/// <param name="partial">Thread-locked variables for the parallelised version</param>
/// <param name="specificLocations">Whether the model is being run for specific locations</param>
/// <param name="outputDetail">The level of output detail being used for this model run</param>
/// <param name="currentMonth">The current model month</param>
/// <param name="initialisation">The Madingley Model initialisation</param>
public void RunEcologicalProcess(GridCellCohortHandler gridCellCohorts, GridCellStockHandler gridCellStocks,
int[] actingCohort, SortedList<string, double[]> cellEnvironment, Dictionary<string,Dictionary<string,double>> deltas ,
FunctionalGroupDefinitions madingleyCohortDefinitions, FunctionalGroupDefinitions madingleyStockDefinitions,
uint currentTimeStep, ProcessTracker processTracker, ref ThreadLockedParallelVariables partial,
Boolean specificLocations, string outputDetail, uint currentMonth, MadingleyModelInitialisation initialisation)
{
// Holds the reproductive strategy of a cohort
bool _Iteroparous = madingleyCohortDefinitions.GetTraitNames("reproductive strategy", actingCohort[0])=="iteroparity";
// Assign mass to reproductive potential
Implementations["reproduction basic"].RunReproductiveMassAssignment(gridCellCohorts, gridCellStocks, actingCohort, cellEnvironment, deltas,
madingleyCohortDefinitions, madingleyStockDefinitions, currentTimeStep, processTracker);
// Run reproductive events. Note that we can't skip juveniles here as they could conceivably grow to adulthood and get enough biomass to reproduce in a single time step
// due to other ecological processes
Implementations["reproduction basic"].RunReproductionEvents(gridCellCohorts, gridCellStocks, actingCohort, cellEnvironment,
deltas, madingleyCohortDefinitions, madingleyStockDefinitions, currentTimeStep, processTracker, ref partial, _Iteroparous, currentMonth);
}
/// <summary>
/// Run ecological processes that operate on stocks within a single grid cell
/// </summary>
///<param name="gridCellStocks">The stocks in the current grid cell</param>
///<param name="actingStock">The acting stock</param>
///<param name="cellEnvironment">The stocks in the current grid cell</param>
///<param name="environmentalDataUnits">List of units associated with the environmental variables</param>
///<param name="humanNPPScenario">The human appropriation of NPP scenario to apply</param>
///<param name="madingleyStockDefinitions">The functional group definitions for stocks in the model</param>
///<param name="currentTimeStep">The current model time step</param>
///<param name="burninSteps">The number of time steps to spin the model up for before applying human impacts</param>
///<param name="impactSteps">The number of time steps to apply human impacts for</param>
///<param name="globalModelTimeStepUnit">The time step unit used in the model</param>
///<param name="trackProcesses">Whether to track properties of ecological processes</param>
///<param name="tracker">An instance of the ecological process tracker</param>
///<param name="globalTracker">An instance of the global process tracker</param>
///<param name="currentMonth">The current model month</param>
///<param name="outputDetail">The level of detail to use in outputs</param>
///<param name="specificLocations">Whether to run the model for specific locations</param>
///<param name="impactCell">Whether this cell should have human impacts applied</param>
public void RunWithinCellEcology(GridCellStockHandler gridCellStocks, int[] actingStock, SortedList<string, double[]> cellEnvironment,
SortedList<string, string> environmentalDataUnits, Madingley.Common.ScenarioParameter humanNPPScenario,
FunctionalGroupDefinitions madingleyStockDefinitions,
uint currentTimeStep, uint burninSteps, uint impactSteps, uint recoverySteps, uint instantStep, uint numInstantSteps, string globalModelTimeStepUnit, Boolean trackProcesses,
ProcessTracker tracker,
GlobalProcessTracker globalTracker, uint currentMonth,
string outputDetail, bool specificLocations, Boolean impactCell)
{
if (madingleyStockDefinitions.GetTraitNames("Realm", actingStock[0]) == "marine")
{
// Run the autotroph processor
MarineNPPtoAutotrophStock.ConvertNPPToAutotroph(cellEnvironment, gridCellStocks, actingStock, environmentalDataUnits["LandNPP"],
environmentalDataUnits["OceanNPP"], currentTimeStep, globalModelTimeStepUnit, tracker, globalTracker, outputDetail, specificLocations, currentMonth);
}
else if (madingleyStockDefinitions.GetTraitNames("Realm", actingStock[0]) == "terrestrial")
{
// Run the dynamic plant model to update the leaf stock for this time step
double WetMatterNPP = DynamicPlantModel.UpdateLeafStock(cellEnvironment, gridCellStocks, actingStock, currentTimeStep, madingleyStockDefinitions.
GetTraitNames("leaf strategy", actingStock[0]).Equals("deciduous"), globalModelTimeStepUnit, tracker, globalTracker, currentMonth,
outputDetail, specificLocations);
/// <summary>
double fhanpp = HANPP.RemoveHumanAppropriatedMatter(WetMatterNPP, cellEnvironment, humanNPPScenario, gridCellStocks, actingStock,
currentTimeStep, burninSteps, impactSteps, recoverySteps, instantStep, numInstantSteps, impactCell, globalModelTimeStepUnit);
// Apply human appropriation of NPP
gridCellStocks[actingStock].TotalBiomass += WetMatterNPP * (1.0 - fhanpp);
if (globalTracker.TrackProcesses)
{
globalTracker.RecordHANPP((uint)cellEnvironment["LatIndex"][0], (uint)cellEnvironment["LonIndex"][0], (uint)actingStock[0],
fhanpp);
}
if (gridCellStocks[actingStock].TotalBiomass < 0.0) gridCellStocks[actingStock].TotalBiomass = 0.0;
}
else
{
Debug.Fail("Stock must be classified as belonging to either the marine or terrestrial realm");
}
}
/// <summary>
/// Generate new cohorts from reproductive potential mass
/// </summary>
/// <param name="gridCellCohorts">The cohorts in the current grid cell</param>
/// <param name="gridCellStocks">The stocks in the current grid cell</param>
/// <param name="actingCohort">The position of the acting cohort in the jagged array of grid cell cohorts</param>
/// <param name="cellEnvironment">The environment of the current grid cell</param>
/// <param name="deltas">The sorted list to track changes in biomass and abundance of the acting cohort in this grid cell</param>
/// <param name="madingleyCohortDefinitions">The definitions of cohort functional groups in the model</param>
/// <param name="madingleyStockDefinitions">The definitions of stock functional groups in the model</param>
/// <param name="currentTimestep">The current model time step</param>
/// <param name="tracker">An instance of ProcessTracker to hold diagnostics for reproduction</param>
/// <param name="partial">Thread-locked variables</param>
public void RunReproduction(GridCellCohortHandler gridCellCohorts, GridCellStockHandler gridCellStocks,
int[] actingCohort, SortedList<string, double[]> cellEnvironment, Dictionary<string, Dictionary<string, double>>
deltas, FunctionalGroupDefinitions madingleyCohortDefinitions, FunctionalGroupDefinitions madingleyStockDefinitions,
uint currentTimestep, ProcessTracker tracker, ref ThreadLockedParallelVariables partial)
{
// Check that the abundance in the cohort to produce is greater than or equal to zero
Debug.Assert(_OffspringCohortAbundance >= 0.0, "Offspring abundance < 0");
// Get the adult and juvenile masses of the cohort to produce
double[] OffspringProperties = GetOffspringCohortProperties(gridCellCohorts, actingCohort,
madingleyCohortDefinitions);
// Update cohort abundance in case juvenile mass has been altered
_OffspringCohortAbundance = (_OffspringCohortAbundance * gridCellCohorts[actingCohort].JuvenileMass) /
OffspringProperties[0];
//Create the offspring cohort
Cohort OffspringCohort = new Cohort((byte)actingCohort[0],
OffspringProperties[0],
OffspringProperties[1],
OffspringProperties[0],
_OffspringCohortAbundance,
(ushort)currentTimestep, ref partial.NextCohortIDThreadLocked);
// Add the offspring cohort to the grid cell cohorts array
gridCellCohorts[actingCohort[0]].Add(OffspringCohort);
// If the cohort has never been merged with another cohort, then add it to the tracker for output as diagnostics
if ((!gridCellCohorts[actingCohort].Merged) && tracker.TrackProcesses)
tracker.RecordNewCohort((uint)cellEnvironment["LatIndex"][0],
(uint)cellEnvironment["LonIndex"][0], currentTimestep, _OffspringCohortAbundance,
gridCellCohorts[actingCohort].AdultMass, gridCellCohorts[actingCohort].FunctionalGroupIndex);
// Subtract all of the reproductive potential mass of the parent cohort, which has been used to generate the new
// cohort, from the delta reproductive potential mass
deltas["reproductivebiomass"]["reproduction"] -= (gridCellCohorts[actingCohort].IndividualReproductivePotentialMass);
}
/// <summary>
/// Run metabolism
/// </summary>
/// <param name="gridCellCohorts">The cohorts in the current grid cell</param>
/// <param name="gridCellStocks">The stocks in the current grid cell</param>
/// <param name="actingCohort">The position of the acting cohort in the jagged array of grid cell cohorts</param>
/// <param name="cellEnvironment">The environment in the current grid cell</param>
/// <param name="deltas">The sorted list to track changes in biomass and abundance of the acting cohort in this grid cell</param>
/// <param name="madingleyCohortDefinitions">The definitions for cohort functional groups in the model</param>
/// <param name="madingleyStockDefinitions">The definitions for stock functional groups in the model</param>
/// <param name="currentTimestep">The current model time step</param>
/// <param name="trackProcesses">An instance of ProcessTracker to hold diagnostics for metabolism</param>
/// <param name="partial">Thread-locked variables</param>
/// <param name="specificLocations">Whether the model is being run for specific locations</param>
/// <param name="outputDetail">The level of output detail being used for the current model run</param>
/// <param name="currentMonth">The current model month</param>
/// <param name="initialisation">The Madingley Model initialisation</param>
public void RunEcologicalProcess(GridCellCohortHandler gridCellCohorts, GridCellStockHandler gridCellStocks,
int[] actingCohort, SortedList<string, double[]> cellEnvironment, Dictionary<string, Dictionary<string, double>> deltas,
FunctionalGroupDefinitions madingleyCohortDefinitions, FunctionalGroupDefinitions madingleyStockDefinitions,
uint currentTimestep, ProcessTracker trackProcesses, ref ThreadLockedParallelVariables partial,
Boolean specificLocations, string outputDetail, uint currentMonth, MadingleyModelInitialisation initialisation)
{
double Realm = cellEnvironment["Realm"][0];
if (madingleyCohortDefinitions.GetTraitNames("Heterotroph/Autotroph", gridCellCohorts[actingCohort].FunctionalGroupIndex) == "heterotroph")
{
if (madingleyCohortDefinitions.GetTraitNames("Endo/Ectotherm", gridCellCohorts[actingCohort].FunctionalGroupIndex) == "endotherm")
{
Implementations["basic endotherm"].RunMetabolism(gridCellCohorts, gridCellStocks, actingCohort, cellEnvironment, deltas, madingleyCohortDefinitions, madingleyStockDefinitions, currentTimestep, currentMonth);
}
else
{
Implementations["basic ectotherm"].RunMetabolism(gridCellCohorts, gridCellStocks, actingCohort, cellEnvironment, deltas, madingleyCohortDefinitions, madingleyStockDefinitions, currentTimestep, currentMonth);
}
}
// If the process tracker is on and output detail is set to high and this cohort has not been merged yet, then record
// the number of individuals that have died
if (trackProcesses.TrackProcesses && (outputDetail == "high"))
{
trackProcesses.TrackTimestepMetabolism((uint)cellEnvironment["LatIndex"][0],
(uint)cellEnvironment["LonIndex"][0],
currentTimestep,
gridCellCohorts[actingCohort].IndividualBodyMass,
actingCohort[0],
cellEnvironment["Temperature"][currentMonth],
deltas["biomass"]["metabolism"]);
}
}
private void RunWithinCellDispersalOnly(uint latCellIndex, uint lonCellIndex, ThreadLockedParallelVariables partial,
GridCellCohortHandler workingGridCellCohorts, GridCellStockHandler workingGridCellStocks)
{
// Merge cohorts. Requires cohorts to be identical, for testing purposes (remember that they don't grow etc)
// SHOULD ONLY BE RUN FOR RESPONSIVE DISPERSAL TESTING
//partial.Combinations = Merger.MergeForResponsiveDispersalOnly(workingGridCellCohorts);
// Loop over cohorts and remove any whose abundance is below the extinction threshold
for (int kk = 0; kk < CohortFunctionalGroupDefinitions.GetNumberOfFunctionalGroups(); kk++)
{
// Create a list to hold the cohorts to remove
List<int> CohortIndicesToRemove = new List<int>();
// Loop through each cohort in the functional group
for (int ll = 0; ll < workingGridCellCohorts[kk].Count; ll++)
{
// If cohort abundance is less than the extinction threshold then add to the list for extinction
if (workingGridCellCohorts[kk][ll].CohortAbundance <= _ExtinctionThreshold)
{
CohortIndicesToRemove.Add(ll);
partial.Extinctions += 1;
}
}
// Note that we don't keep track of the organic biomass pool if running dispersal only, since there are cohorts with strange biomasses
for (int ll = (CohortIndicesToRemove.Count - 1); ll >= 0; ll--)
{
// Remove the extinct cohort from the list of cohorts
workingGridCellCohorts[kk].RemoveAt(CohortIndicesToRemove[ll]);
}
}
// Write out the updated cohort numbers after all ecological processes have occured
EcosystemModelGrid.SetGridCellCohorts(workingGridCellCohorts, latCellIndex, lonCellIndex);
}
/// <summary>
/// Calculate the actual amount eaten in herbivory, apply the changes to the eaten autotroph stocks, and update deltas for the herbivore cohort
/// </summary>
/// <param name="gridCellCohorts">The cohorts in this grid cell</param>
/// <param name="gridCellStocks">The stocks in this grid cell</param>
/// <param name="actingCohort">The acting cohort</param>
/// <param name="cellEnvironment">The environmental conditions in this grid cell</param>
/// <param name="deltas">The sorted list to track changes in biomass and abundance of the acting cohort in this grid cell</param>
/// <param name="madingleyCohortDefinitions">The functional group definitions for cohorts in the model</param>
/// <param name="madingleyStockDefinitions">The functional group definitions for stocks in the model</param>
/// <param name="trackProcesses">An instance of ProcessTracker to hold diagnostics for herbivory</param>
/// <param name="currentTimestep">The current model time step</param>
/// <param name="specificLocations">Whether the model is being run for specific locations</param>
/// <param name="outputDetail">The level of output detail being used in this model run</param>
/// <param name="initialisation">The Madingley Model initialisation</param>
public void RunEating(GridCellCohortHandler gridCellCohorts, GridCellStockHandler gridCellStocks, int[] actingCohort, SortedList<string, double[]>
cellEnvironment, Dictionary<string, Dictionary<string, double>> deltas, FunctionalGroupDefinitions madingleyCohortDefinitions,
FunctionalGroupDefinitions madingleyStockDefinitions, ProcessTracker trackProcesses, uint currentTimestep, Boolean specificLocations,
string outputDetail, MadingleyModelInitialisation initialisation)
{
EdibleScaling = 1.0;
if (cellEnvironment["Realm"][0] == 1.0) EdibleScaling = 0.1;
// Loop over autotroph functional groups that can be eaten
foreach (int FunctionalGroup in _FunctionalGroupIndicesToEat)
{
// Loop over stocks within the functional groups
for (int i = 0; i < gridCellStocks[FunctionalGroup].Count; i++)
{
// Get the mass from this stock that is available for eating (assumes only 10% is edible in the terrestrial realm)
EdibleMass = gridCellStocks[FunctionalGroup][i].TotalBiomass * EdibleScaling;
// Calculate the biomass actually eaten from this stock by the acting cohort
_BiomassesEaten[FunctionalGroup][i] = CalculateBiomassesEaten(_PotentialBiomassesEaten[FunctionalGroup][i],
_TimeUnitsToHandlePotentialFoodItems, gridCellCohorts[actingCohort].CohortAbundance, EdibleMass);
gridCellCohorts[actingCohort].TrophicIndex += _BiomassesEaten[FunctionalGroup][i];
// Remove the biomass eaten from the autotroph stock
gridCellStocks[FunctionalGroup][i].TotalBiomass -= _BiomassesEaten[FunctionalGroup][i];
// If the model is being run for specific locations and if track processes has been specified, then track the mass flow between
// primary producer and herbivore
if (specificLocations && trackProcesses.TrackProcesses)
{
trackProcesses.RecordHerbivoryMassFlow(currentTimestep, _BodyMassHerbivore, _BiomassesEaten[FunctionalGroup][i]);
}
// If track processes has been specified and the output detail level is set to high and the model is being run for specific locations,
// then track the flow of mass between trophic levels
if (trackProcesses.TrackProcesses && (outputDetail == "high") && specificLocations)
{
trackProcesses.TrackHerbivoryTrophicFlow((uint)cellEnvironment["LatIndex"][0], (uint)cellEnvironment["LonIndex"][0],
gridCellCohorts[actingCohort].FunctionalGroupIndex, madingleyCohortDefinitions, _BiomassesEaten[FunctionalGroup][i], _BodyMassHerbivore, initialisation, cellEnvironment["Realm"][0] == 2.0);
}
// Check that the biomass eaten is not a negative value
// Commented out for purposes of speed
//Debug.Assert(_BiomassesEaten[FunctionalGroup][i] >= 0,
// "Herbivory negative for this herbivore cohort" + actingCohort);
// Add the biomass eaten and assimilated by an individual to the delta biomass for the acting cohort
deltas["biomass"]["herbivory"] += _BiomassesEaten[FunctionalGroup][i] * AssimilationEfficiency / gridCellCohorts[actingCohort].CohortAbundance;
// Move the biomass eaten but not assimilated by an individual into the organic matter pool
deltas["organicpool"]["herbivory"] += _BiomassesEaten[FunctionalGroup][i] * (1 - AssimilationEfficiency);
}
// Check that the delta biomass from eating for the acting cohort is not negative
// Commented out for the purposes of speed
//Debug.Assert(deltas["biomass"]["herbivory"] >= 0, "Delta biomass from herbviory is negative");
// Calculate the total biomass eaten by the acting (herbivore) cohort
_TotalBiomassEatenByCohort = deltas["biomass"]["herbivory"] * gridCellCohorts[actingCohort].CohortAbundance;
}
}
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>
/// Sets the stocks in the specified grid cell to the passed stocks
/// </summary>
/// <param name="newGridCellStocks">New stocks for the grid cell</param>
/// <param name="latIndex">Latitude index</param>
/// <param name="lonIndex">Longitude index</param>
public void SetGridCellStocks(GridCellStockHandler newGridCellStocks, uint latIndex, uint lonIndex)
{
InternalGrid[latIndex, lonIndex].GridCellStocks = newGridCellStocks;
}
/// <summary>
/// Constructor for a grid cell; creates cell and reads in environmental data
/// </summary>
/// <param name="latitude">The latitude of the grid cell</param>
/// <param name="latIndex">The latitudinal index of the grid cell</param>
/// <param name="longitude">The longitude of the grid cell</param>
/// <param name="lonIndex">The longitudinal index of the grid cell</param>
/// <param name="latCellSize">The latitudinal dimension of the grid cell</param>
/// <param name="lonCellSize">The longitudinal dimension of the grid cell</param>
/// <param name="dataLayers">A list of environmental data variables in the model</param>
/// <param name="missingValue">The missing value to be applied to all data in the grid cell</param>
/// <param name="cohortFunctionalGroups">The definitions for cohort functional groups in the model</param>
/// <param name="stockFunctionalGroups">The definitions for stock functional groups in the model</param>
/// <param name="globalDiagnostics">A list of global diagnostic variables for the model grid</param>
/// <param name="tracking">Whether process-tracking is enabled</param>
/// <param name="specificLocations">Whether the model is being run for specific locations</param>
public GridCell(float latitude, uint latIndex, float longitude, uint lonIndex, float latCellSize, float lonCellSize,
SortedList<string, EnviroData> dataLayers, double missingValue, FunctionalGroupDefinitions cohortFunctionalGroups,
FunctionalGroupDefinitions stockFunctionalGroups, SortedList<string, double> globalDiagnostics,Boolean tracking,
bool specificLocations)
{
// Boolean to track when environmental data are missing
Boolean EnviroMissingValue;
// Initialise the utility functions
Utilities = new UtilityFunctions();
// Temporary vector for holding initial values of grid cell properties
double[] tempVector;
// Initialise deltas sorted list
_Deltas = new Dictionary<string, Dictionary<string, double>>();
// Initialize delta abundance sorted list with appropriate processes
Dictionary<string, double> DeltaAbundance = new Dictionary<string, double>();
DeltaAbundance.Add("mortality", 0.0);
// Add delta abundance sorted list to deltas sorted list
_Deltas.Add("abundance", DeltaAbundance);
// Initialize delta biomass sorted list with appropriate processes
Dictionary<string, double> DeltaBiomass = new Dictionary<string, double>();
DeltaBiomass.Add("metabolism", 0.0);
DeltaBiomass.Add("predation", 0.0);
DeltaBiomass.Add("herbivory", 0.0);
DeltaBiomass.Add("reproduction", 0.0);
// Add delta biomass sorted list to deltas sorted list
_Deltas.Add("biomass", DeltaBiomass);
// Initialize delta reproductive biomass vector with appropriate processes
Dictionary<string, double> DeltaReproductiveBiomass = new Dictionary<string, double>();
DeltaReproductiveBiomass.Add("reproduction", 0.0);
// Add delta reproduction sorted list to deltas sorted list
_Deltas.Add("reproductivebiomass", DeltaReproductiveBiomass);
// Initialize organic pool delta vector with appropriate processes
Dictionary<string, double> DeltaOrganicPool = new Dictionary<string, double>();
DeltaOrganicPool.Add("herbivory", 0.0);
DeltaOrganicPool.Add("predation", 0.0);
DeltaOrganicPool.Add("mortality", 0.0);
// Add delta organic pool sorted list to deltas sorted list
_Deltas.Add("organicpool", DeltaOrganicPool);
// Initialize respiratory CO2 pool delta vector with appropriate processes
Dictionary<string, double> DeltaRespiratoryCO2Pool = new Dictionary<string, double>();
DeltaRespiratoryCO2Pool.Add("metabolism", 0.0);
// Add delta respiratory CO2 pool to deltas sorted list
_Deltas.Add("respiratoryCO2pool", DeltaRespiratoryCO2Pool);
// Set the grid cell values of latitude, longitude and missing value as specified
_Latitude = latitude;
_Longitude = longitude;
// Initialise list of environmental data layer values
_CellEnvironment = new SortedList<string, double[]>();
//Add the latitude and longitude
tempVector = new double[1];
tempVector[0] = latitude;
_CellEnvironment.Add("Latitude", tempVector);
tempVector = new double[1];
tempVector[0] = longitude;
_CellEnvironment.Add("Longitude", tempVector);
// Add an organic matter pool to the cell environment to track organic biomass not held by animals or plants with an initial value of 0
tempVector = new double[1];
tempVector[0] = 0.0;
_CellEnvironment.Add("Organic Pool", tempVector);
// Add a repsiratory CO2 pool to the cell environment with an initial value of 0
tempVector = new double[1];
tempVector[0] = 0.0;
_CellEnvironment.Add("Respiratory CO2 Pool", tempVector);
// Add the grid cell area (in km2) to the cell environment with an initial value of 0
tempVector = new double[1];
// Calculate the area of this grid cell
tempVector[0] = Utilities.CalculateGridCellArea(latitude, lonCellSize, latCellSize);
// Add it to the cell environment
_CellEnvironment.Add("Cell Area", tempVector);
//Add the latitude and longitude indices
tempVector = new double[1];
tempVector[0] = latIndex;
_CellEnvironment.Add("LatIndex", tempVector);
tempVector = new double[1];
tempVector[0] = lonIndex;
_CellEnvironment.Add("LonIndex", tempVector);
// Add the missing value of data in the grid cell to the cell environment
tempVector = new double[1];
tempVector[0] = missingValue;
_CellEnvironment.Add("Missing Value", tempVector);
// Loop through environmental data layers and extract values for this grid cell
// Also standardise missing values
// Loop over variables in the list of environmental data
foreach (string LayerName in dataLayers.Keys)
{
// Initiliase the temporary vector of values to be equal to the number of time intervals in the environmental variable
tempVector = new double[dataLayers[LayerName].NumTimes];
// Loop over the time intervals in the environmental variable
for (int hh = 0; hh < dataLayers[LayerName].NumTimes; hh++)
{
// Add the value of the environmental variable at this time interval to the temporary vector
tempVector[hh] = dataLayers[LayerName].GetValue(_Latitude, _Longitude, (uint)hh, out EnviroMissingValue,latCellSize,lonCellSize);
// If the environmental variable is a missing value, then change the value to equal the standard missing value for this cell
if (EnviroMissingValue)
tempVector[hh] = missingValue;
}
// Add the values of the environmental variables to the cell environment, with the name of the variable as the key
_CellEnvironment.Add(LayerName, tempVector);
}
if (_CellEnvironment.ContainsKey("LandSeaMask"))
{
if (_CellEnvironment["LandSeaMask"][0].CompareTo(0.0) == 0)
{
if (ContainsData(_CellEnvironment["OceanTemp"], _CellEnvironment["Missing Value"][0]))
{
//This is a marine cell
tempVector = new double[1];
tempVector[0] = 2.0;
_CellEnvironment.Add("Realm", tempVector);
_CellEnvironment.Add("NPP", _CellEnvironment["OceanNPP"]);
_CellEnvironment.Add("DiurnalTemperatureRange", _CellEnvironment["OceanDTR"]);
if (_CellEnvironment.ContainsKey("Temperature"))
{
if(_CellEnvironment.ContainsKey("SST"))
{
_CellEnvironment["Temperature"] = _CellEnvironment["SST"];
}
else
{
}
}
else
{
_CellEnvironment.Add("Temperature", _CellEnvironment["SST"]);
}
}
else
{
//This is a freshwater cell and in this model formulation is characterised as belonging to the terrestrial realm
tempVector = new double[1];
tempVector[0] = 2.0;
_CellEnvironment.Add("Realm", tempVector);
_CellEnvironment.Add("NPP", _CellEnvironment["LandNPP"]);
_CellEnvironment.Add("DiurnalTemperatureRange", _CellEnvironment["LandDTR"]);
}
}
else
{
//This is a land cell
tempVector = new double[1];
tempVector[0] = 1.0;
_CellEnvironment.Add("Realm", tempVector);
_CellEnvironment.Add("NPP", _CellEnvironment["LandNPP"]);
_CellEnvironment.Add("DiurnalTemperatureRange", _CellEnvironment["LandDTR"]);
}
}
else
{
Debug.Fail("No land sea mask defined - a mask is required to initialise appropriate ecology");
}
//Calculate and add the standard deviation of monthly temperature as a measure of seasonality
//Also calculate and add the annual mean temperature for this cell
tempVector = new double[12];
double[] sdtemp = new double[12];
double[] meantemp = new double[12];
tempVector = _CellEnvironment["Temperature"];
double Average = tempVector.Average();
meantemp[0] = Average;
double SumOfSquaresDifferences = tempVector.Select(val => (val - Average) * (val - Average)).Sum();
sdtemp[0] = Math.Sqrt(SumOfSquaresDifferences / tempVector.Length);
_CellEnvironment.Add("SDTemperature", sdtemp);
_CellEnvironment.Add("AnnualTemperature", meantemp);
//Remove unrequired cell environment layers
if (_CellEnvironment.ContainsKey("LandNPP")) _CellEnvironment.Remove("LandNPP");
if (_CellEnvironment.ContainsKey("LandDTR")) _CellEnvironment.Remove("LandDTR");
if (_CellEnvironment.ContainsKey("OceanNPP")) _CellEnvironment.Remove("OceanNPP");
if (_CellEnvironment.ContainsKey("OceanDTR")) _CellEnvironment.Remove("OceanDTR");
if (_CellEnvironment.ContainsKey("SST")) _CellEnvironment.Remove("SST");
// CREATE NPP SEASONALITY LAYER
_CellEnvironment.Add("Seasonality", CalculateNPPSeasonality(_CellEnvironment["NPP"], _CellEnvironment["Missing Value"][0]));
// Calculate other climate variables from temperature and precipitation
// Declare an instance of the climate variables calculator
ClimateVariablesCalculator CVC = new ClimateVariablesCalculator();
// Calculate the fraction of the year that experiences frost
double[] NDF = new double[1];
NDF[0] = CVC.GetNDF(_CellEnvironment["FrostDays"], _CellEnvironment["Temperature"],_CellEnvironment["Missing Value"][0]);
_CellEnvironment.Add("Fraction Year Frost", NDF);
double[] frostMonthly = new double[12];
frostMonthly[0] = Math.Min(_CellEnvironment["FrostDays"][0] / 31.0, 1.0);
frostMonthly[1] = Math.Min(_CellEnvironment["FrostDays"][1] / 28.0, 1.0);
frostMonthly[2] = Math.Min(_CellEnvironment["FrostDays"][2] / 31.0, 1.0);
frostMonthly[3] = Math.Min(_CellEnvironment["FrostDays"][3] / 30.0, 1.0);
frostMonthly[4] = Math.Min(_CellEnvironment["FrostDays"][4] / 31.0, 1.0);
frostMonthly[5] = Math.Min(_CellEnvironment["FrostDays"][5] / 30.0, 1.0);
frostMonthly[6] = Math.Min(_CellEnvironment["FrostDays"][6] / 31.0, 1.0);
frostMonthly[7] = Math.Min(_CellEnvironment["FrostDays"][7] / 31.0, 1.0);
frostMonthly[8] = Math.Min(_CellEnvironment["FrostDays"][8] / 30.0, 1.0);
frostMonthly[9] = Math.Min(_CellEnvironment["FrostDays"][9] / 31.0, 1.0);
frostMonthly[10] = Math.Min(_CellEnvironment["FrostDays"][10] / 30.0, 1.0);
frostMonthly[11] = Math.Min(_CellEnvironment["FrostDays"][11] / 31.0, 1.0);
_CellEnvironment.Add("Fraction Month Frost", frostMonthly);
_CellEnvironment.Remove("FrostDays");
// Calculate AET and the fractional length of the fire season
Tuple<double[], double, double> TempTuple = new Tuple<double[], double, double>(new double[12], new double(), new double());
TempTuple = CVC.MonthlyActualEvapotranspirationSoilMoisture(_CellEnvironment["AWC"][0], _CellEnvironment["Precipitation"], _CellEnvironment["Temperature"]);
_CellEnvironment.Add("AET", TempTuple.Item1);
_CellEnvironment.Add("Fraction Year Fire", new double[1] { TempTuple.Item3 / 360 });
// Designate a breeding season for this grid cell, where a month is considered to be part of the breeding season if its NPP is at
// least 80% of the maximum NPP throughout the whole year
double[] BreedingSeason = new double[12];
for (int i = 0; i < 12; i++)
{
if ((_CellEnvironment["Seasonality"][i] / _CellEnvironment["Seasonality"].Max()) > 0.5)
{
BreedingSeason[i] = 1.0;
}
else
{
BreedingSeason[i] = 0.0;
}
}
_CellEnvironment.Add("Breeding Season", BreedingSeason);
// Initialise the grid cell cohort and stock handlers
_GridCellCohorts = new GridCellCohortHandler(cohortFunctionalGroups.GetNumberOfFunctionalGroups());
_GridCellStocks = new GridCellStockHandler(stockFunctionalGroups.GetNumberOfFunctionalGroups());
}
/// <summary>
/// Initializes an implementation of metabolism
/// </summary>
/// <param name="gridCellCohorts">The cohorts in the current grid cell</param>
/// <param name="gridCellStocks">The stocks in the current grid cell</param>
/// <param name="madingleyCohortDefinitions">The definitions for cohort functional groups in the model</param>
/// <param name="madingleyStockDefinitions">The definitions for stock functional groups in the model</param>
/// <param name="implementationKey">The name of the implementation of metabolism to initialize</param>
public void InitializeEcologicalProcess(GridCellCohortHandler gridCellCohorts, GridCellStockHandler gridCellStocks,
FunctionalGroupDefinitions madingleyCohortDefinitions, FunctionalGroupDefinitions madingleyStockDefinitions,
string implementationKey)
{
}
/// <summary>
/// Remove human appropriated matter from the grid cell autotroph stocks
/// </summary>
/// <param name="cellEnvironment">The environment in the current grid cell</param>
/// <param name="humanNPPScenario">The type of NPP extraction to apply</param>
/// <param name="gridCellStocks">The stocks in the current grid cell</param>
/// <param name="actingStock">The position of the acting stock in the jagged array of grid cell stocks</param>
/// <param name="currentTimestep">The current model time step</param>
/// <param name="burninSteps">The number of steps to run before impact is simulated</param>
/// <param name="impactSteps">The number of time steps to apply the impact for (for 'temporary' scenarios)</param>
/// <param name="impactCell">Whether this cell should have human impacts applied</param>
/// <remarks>Scenario types are: 'no' = no removal; 'hanpp' = appropriated NPP estimate from input map; constant = constant appropriation after burn-in;
/// temporary = constant after burn-in until specified time; value = proportion of plant biomass appropriated</remarks>
public double RemoveHumanAppropriatedMatter(double wetMatterNPP, SortedList<string, double[]> cellEnvironment,
Tuple<string, double, double> humanNPPScenario, GridCellStockHandler
gridCellStocks, int[] actingStock, uint currentTimestep, uint burninSteps,
uint impactSteps, uint recoverySteps, uint instantStep, uint numInstantStep, Boolean impactCell,
string globalModelTimestepUnits)
{
double RemovalRate = 0.0;
if (impactCell)
{
// Factor to convert NPP from units per m2 to units per km2
double m2Tokm2Conversion = 1000000.0;
if (humanNPPScenario.Item1 == "hanpp")
{
if (currentTimestep > burninSteps)
{
// Loop over stocks in the grid cell and calculate the total biomass of all stocks
double TotalAutotrophBiomass = 0.0;
foreach (var stockFunctionalGroup in gridCellStocks)
{
for (int i = 0; i < stockFunctionalGroup.Count; i++)
{
TotalAutotrophBiomass += stockFunctionalGroup[i].TotalBiomass;
}
}
// Get the total amount of NPP appropriated by humans from this cell
double HANPP = cellEnvironment["HANPP"][0];
// If HANPP value is missing, then assume zero
if (HANPP == cellEnvironment["Missing Value"][0]) HANPP = 0.0;
HANPP *= cellEnvironment["Seasonality"][currentTimestep % 12];
// Allocate HANPP for this stock according to the proportion of total autotroph biomass that the stock represents
if (TotalAutotrophBiomass == 0.0)
{
HANPP = 0.0;
}
else
{
HANPP *= (gridCellStocks[actingStock].TotalBiomass / TotalAutotrophBiomass);
}
// Convert gC/m2/month to gC/km2/month
HANPP *= m2Tokm2Conversion;
// Multiply by cell area (in km2) to get g/cell/day
HANPP *= cellEnvironment["Cell Area"][0];
// Convert from gC to g dry matter
double DryMatterAppropriated = HANPP * 2;
// Convert from g dry matter to g wet matter
double WetMatterAppropriated = DryMatterAppropriated * 2;
//Calculate the rate of HANPP offtake
if (wetMatterNPP.CompareTo(0.0) == 0)
{
RemovalRate = 0.0;
}
else
{
RemovalRate = Math.Min(1.0, WetMatterAppropriated / wetMatterNPP);
}
// Remove human appropriated autotroph biomass from total autotroph biomass
//gridCellStocks[actingStock].TotalBiomass -= WetMatterAppropriated;
//if (gridCellStocks[actingStock].TotalBiomass < 0.0) gridCellStocks[actingStock].TotalBiomass = 0.0;
}
}
else if (humanNPPScenario.Item1 == "no")
{
// Do not remove any autotroph biomass
}
else if (humanNPPScenario.Item1 == "constant")
{
// If the burn-in period has been completed, then remove the specified constant
// fraction from the acting autotroph stock
if (currentTimestep > burninSteps)
{
//gridCellStocks[actingStock].TotalBiomass -= (gridCellStocks[actingStock].TotalBiomass *
// humanNPPScenario.Item2);
RemovalRate = humanNPPScenario.Item2;
}
}
else if (humanNPPScenario.Item1 == "temporary")
{
// If the spin-up period has been completed and the period of impact has not elapsed,
// then remove the specified constant fraction from the acting autotroph stock
if ((currentTimestep > burninSteps) && (currentTimestep <= (burninSteps + impactSteps)))
{
//gridCellStocks[actingStock].TotalBiomass -= (gridCellStocks[actingStock].TotalBiomass *
// humanNPPScenario.Item2);
RemovalRate = humanNPPScenario.Item2;
}
}
else if (humanNPPScenario.Item1 == "escalating")
{
// If the spin-up period has been completed, then remove a proportion of plant matter
// according to the number of time-steps that have elapsed since the spin-up ended
if (currentTimestep > burninSteps)
{
//gridCellStocks[actingStock].TotalBiomass -= gridCellStocks[actingStock].TotalBiomass *
// (Math.Min(1.0, (((currentTimestep - burninSteps) / 12.0) * humanNPPScenario.Item2)));
RemovalRate = (Math.Min(1.0, (((currentTimestep - burninSteps) / 12.0) * humanNPPScenario.Item2)));
}
}
else if (humanNPPScenario.Item1 == "temp-escalating")
{
// If the spin-up period has been completed and the period of impact has not elapsed,
// then remove a proportion of plant matter
// according to the number of time-steps that have elapsed since the spin-up ended
if ((currentTimestep > burninSteps) && (currentTimestep <= (burninSteps + impactSteps)))
{
//gridCellStocks[actingStock].TotalBiomass -= gridCellStocks[actingStock].TotalBiomass *
// (Math.Min(1.0, (((currentTimestep - burninSteps) / 12.0) * humanNPPScenario.Item2)));
RemovalRate = (Math.Min(1.0, (((currentTimestep - burninSteps) / 12.0) * humanNPPScenario.Item2)));
}
}
else if (humanNPPScenario.Item1 == "temp-escalating-const-rate")
{
// If the spin-up period has been completed and the period of impact (specified by the third scenario element
// has not elapsed,
// then remove a proportion of plant matter
// according to the number of time-steps that have elapsed since the spin-up ended
int ConstImpactSteps = Convert.ToInt32(humanNPPScenario.Item3 * _Utilities.ConvertTimeUnits("year", globalModelTimestepUnits));
if ((currentTimestep > burninSteps) && (currentTimestep <= (burninSteps + ConstImpactSteps)))
{
//gridCellStocks[actingStock].TotalBiomass -= gridCellStocks[actingStock].TotalBiomass *
// (Math.Min(1.0, (((currentTimestep - burninSteps) / 12.0) * humanNPPScenario.Item2)));
RemovalRate = (Math.Min(1.0, (((currentTimestep - burninSteps) / 12.0) * humanNPPScenario.Item2)));
}
}
else if (humanNPPScenario.Item1 == "temp-escalating-const-rate-duration")
{
// If the spin-up period has been completed and the period of impact (specified by the third scenario element
// has not elapsed,
// then remove a proportion of plant matter
// according to the number of time-steps that have elapsed since the spin-up ended
int ConstImpactSteps = Convert.ToInt32(humanNPPScenario.Item3 * _Utilities.ConvertTimeUnits("year", globalModelTimestepUnits));
if ((currentTimestep > burninSteps) && (currentTimestep <= (burninSteps + impactSteps)))
{
//gridCellStocks[actingStock].TotalBiomass -= gridCellStocks[actingStock].TotalBiomass *
// (Math.Min(1.0, (((currentTimestep - burninSteps) / 12.0) * humanNPPScenario.Item2)));
RemovalRate = (Math.Min(1.0,
Math.Min(((ConstImpactSteps / 12.0) * humanNPPScenario.Item2),
(((currentTimestep - burninSteps) / 12.0) * humanNPPScenario.Item2))));
}
}
else if (humanNPPScenario.Item1 == "temp-escalating-declining")
{
// If the spin-up period has been completed, then apply a level of harvesting
// according to the number of time-steps that have elapsed since the spin-up ended
if ((currentTimestep > burninSteps) && (currentTimestep <= (burninSteps + impactSteps)))
{
//gridCellStocks[actingStock].TotalBiomass -= gridCellStocks[actingStock].TotalBiomass *
// (Math.Min(1.0, (((currentTimestep - burninSteps) / 12.0) * humanNPPScenario.Item2)));
RemovalRate = Math.Max(0.0, (Math.Min(1.0, (((currentTimestep - burninSteps) / 12.0) * humanNPPScenario.Item2))));
}
else if ((currentTimestep > (burninSteps + impactSteps)) & (currentTimestep <= (burninSteps + impactSteps + recoverySteps)))
{
//gridCellStocks[actingStock].TotalBiomass -= gridCellStocks[actingStock].TotalBiomass *
// (Math.Min(1.0, (((burninSteps + impactSteps + recoverySteps - currentTimestep) / 12.0) * humanNPPScenario.Item2)));
//RemovalRate = (Math.Min(1.0, (((burninSteps + impactSteps + recoverySteps - currentTimestep) / 12.0) * humanNPPScenario.Item2)));
RemovalRate = Math.Max(0.0, Math.Min(1.0, ((int)((impactSteps) - (currentTimestep - (burninSteps + impactSteps))) / 12.0) * humanNPPScenario.Item2));
}
}
else
{
Debug.Fail("There is no method for the human extraction of NPP scenario specified");
}
}
return(RemovalRate);
}
/// <summary>
/// Initialises predation implementation each time step
/// </summary>
/// <param name="gridCellCohorts">The cohorts in the current grid cell</param>
/// <param name="gridCellStocks">The stocks in the current grid cell</param>
/// <param name="madingleyCohortDefinitions">The definitions for cohorts in the model</param>
/// <param name="madingleyStockDefinitions">The definitions for stocks in the model</param>
/// <param name="cellEnvironment">The environment in the current grid cell</param>
/// <remarks>This only works if: a) predation is initialised in every grid cell; and b) if parallelisation is done by latitudinal strips
/// It is critical to run this every time step</remarks>
public void InitializeEatingPerTimeStep(GridCellCohortHandler gridCellCohorts, GridCellStockHandler gridCellStocks, FunctionalGroupDefinitions madingleyCohortDefinitions, FunctionalGroupDefinitions madingleyStockDefinitions, SortedList<string, double[]>
cellEnvironment)
{
// Get the functional group indices of all heterotroph cohorts (i.e. potential prey)
// _FunctionalGroupIndicesToEat = madingleyCohortDefinitions.GetFunctionalGroupIndex("Heterotroph/Autotroph", "heterotroph", false);
string [] realm = { "Terrestrial", "Marine" };
int realm_index = (int)cellEnvironment["Realm"][0] - 1;
string Current_realm = realm[realm_index];
_FunctionalGroupIndicesToEat = madingleyCohortDefinitions.GetFunctionalGroupIndex("realm", Current_realm, false);
// Initialise the vector to hold the number of cohorts in each functional group at the start of the time step
NumberCohortsPerFunctionalGroupNoNewCohorts = new int[gridCellCohorts.Count];
// Initialise the jagged arrays to hold the potential and actual numbers of prey eaten in each of the grid cell cohorts
_AbundancesEaten = new double[gridCellCohorts.Count][];
_PotentialAbundanceEaten = new double[gridCellCohorts.Count][];
// Initialise the vector to identify carnivore cohorts
_CarnivoreFunctionalGroups = new Boolean[_FunctionalGroupIndicesToEat.Length];
_OmnivoreFunctionalGroups = new Boolean[_FunctionalGroupIndicesToEat.Length];
_PlanktonFunctionalGroups = new Boolean[_FunctionalGroupIndicesToEat.Length];
// Loop over rows in the jagged arrays, initialise each vector within the jagged arrays, and calculate the current number of cohorts in
// each functional group
for (int i = 0; i < gridCellCohorts.Count; i++)
{
// Calculate the current number of cohorts in this functional group
int NumCohortsThisFG = gridCellCohorts[i].Count;
NumberCohortsPerFunctionalGroupNoNewCohorts[i] = NumCohortsThisFG;
// Initialise the jagged arrays
_AbundancesEaten[i] = new double[NumberCohortsPerFunctionalGroupNoNewCohorts[i]];
_PotentialAbundanceEaten[i] = new double[NumberCohortsPerFunctionalGroupNoNewCohorts[i]];
}
// Loop over functional groups that are potential prey and determine which are carnivores THIS IS COMMENTED OUT AS IT'S NOT USED
//foreach (int FunctionalGroup in FunctionalGroupIndicesToEat)
// _CarnivoreFunctionalGroups[FunctionalGroup] = madingleyCohortDefinitions.GetTraitNames("Nutrition source", FunctionalGroup) == "carnivore";
//foreach (int FunctionalGroup in FunctionalGroupIndicesToEat)
// _OmnivoreFunctionalGroups[FunctionalGroup] = madingleyCohortDefinitions.GetTraitNames("Nutrition source", FunctionalGroup) == "omnivore";
//foreach (int FunctionalGroup in FunctionalGroupIndicesToEat)
// _PlanktonFunctionalGroups[FunctionalGroup] = madingleyCohortDefinitions.GetTraitNames("Mobility", FunctionalGroup) == "planktonic";
}
/// <summary>
/// Assigns biomass from body mass to reproductive potential mass
/// </summary>
/// <param name="gridCellCohorts">The cohorts in the current grid cell</param>
/// <param name="gridCellStocks">The stocks in the current grid cell</param>
/// <param name="actingCohort">The position of the acting cohort in the jagged array of grid cell cohorts</param>
/// <param name="cellEnvironment">The environment in the current grid cell</param>
/// <param name="deltas">The sorted list to track changes in biomass and abundance of the acting cohort in this grid cell</param>
/// <param name="madingleyCohortDefinitions">The definitions of cohort functional groups in the model</param>
/// <param name="madingleyStockDefinitions">The definitions of stock functional groups in the model</param>
/// <param name="currentTimestep">The current model time step</param>
/// <param name="tracker">An instance of ProcessTracker to hold diagnostics for reproduction</param>
public void AssignMassToReproductivePotential(GridCellCohortHandler gridCellCohorts, GridCellStockHandler gridCellStocks,
int[] actingCohort, SortedList<string, double[]> cellEnvironment, Dictionary<string, Dictionary<string, double>> deltas,
FunctionalGroupDefinitions madingleyCohortDefinitions, FunctionalGroupDefinitions madingleyStockDefinitions,
uint currentTimestep, ProcessTracker tracker)
{
// If this is the first time reproductive potential mass has been assigned for this cohort,
// then set the maturity time step for this cohort as the current model time step
if (gridCellCohorts[actingCohort].MaturityTimeStep == uint.MaxValue)
{
gridCellCohorts[actingCohort].MaturityTimeStep = currentTimestep;
// Track the generation length for this cohort
if ((!gridCellCohorts[actingCohort].Merged) && tracker.TrackProcesses)
tracker.TrackMaturity((uint)cellEnvironment["LatIndex"][0], (uint)cellEnvironment["LonIndex"][0],
currentTimestep, gridCellCohorts[actingCohort].BirthTimeStep, gridCellCohorts[actingCohort].JuvenileMass,
gridCellCohorts[actingCohort].AdultMass, gridCellCohorts[actingCohort].FunctionalGroupIndex);
}
// Assign the specified mass to reproductive potential mass and remove it from individual biomass
deltas["reproductivebiomass"]["reproduction"] += _BiomassToAssignToReproductivePotential;
deltas["biomass"]["reproduction"] -= _BiomassToAssignToReproductivePotential;
}
/// <summary>
/// Calculate the potential number of prey that could be gained through predation on each cohort in the grid cell
/// </summary>
/// <param name="gridCellCohorts">The cohorts in the current grid cell</param>
/// <param name="gridCellStocks">The stocks in the current grid cell</param>
/// <param name="actingCohort">The acting cohort</param>
/// <param name="cellEnvironment">The environment in the current grid cell</param>
/// <param name="madingleyCohortDefinitions">The functional group definitions for cohorts in the model</param>
/// <param name="madingleyStockDefinitions">The functional group definitions for stocks in the model</param>
public void GetEatingPotentialMarine(GridCellCohortHandler gridCellCohorts, GridCellStockHandler gridCellStocks, int[] actingCohort,
SortedList<string, double[]> cellEnvironment, FunctionalGroupDefinitions madingleyCohortDefinitions, FunctionalGroupDefinitions
madingleyStockDefinitions)
{
BinnedPreyDensities = new double[gridCellCohorts.Count, NumberOfBins];
// Set the total eaten by the acting cohort to zero
_TotalBiomassEatenByCohort = 0.0;
// Set the total number of units to handle all potential prey individuals eaten to zero
_TimeUnitsToHandlePotentialFoodItems = 0.0;
// Get the individual body mass of the acting (predator) cohort
_BodyMassPredator = gridCellCohorts[actingCohort].IndividualBodyMass;
// Get the abundance of the acting (predator) cohort
_AbundancePredator = gridCellCohorts[actingCohort].CohortAbundance;
// Pre-calculate individual values for this predator to speed things up
_SpecificPredatorKillRateConstant = _KillRateConstant * Math.Pow(_BodyMassPredator, (_KillRateConstantMassExponent));
_SpecificPredatorTimeUnitsEatingPerGlobalTimeStep = _DeltaT * _ProportionOfTimeEating;
_PredatorAssimilationEfficiency = _AssimilationEfficiency;
_PredatorNonAssimilation = (1 - _AssimilationEfficiency);
_DietIsAllSpecial = madingleyCohortDefinitions.GetTraitNames("Diet", actingCohort[0]) == "allspecial";
_PredatorLogOptimalPreyBodySizeRatio = gridCellCohorts[actingCohort[0]][actingCohort[1]].LogOptimalPreyBodySizeRatio;
// If a filter feeder, then optimal body size is a value not a ratio: convert it to a ratio to ensure that all calculations work correctly
if (_DietIsAllSpecial)
{
// Optimal body size is actually a value, not a ratio, so convert it to a ratio based on the present body size
_PredatorLogOptimalPreyBodySizeRatio = Math.Log(
Math.Exp(gridCellCohorts[actingCohort[0]][actingCohort[1]].LogOptimalPreyBodySizeRatio) / gridCellCohorts[actingCohort[0]][actingCohort[1]].IndividualBodyMass);
}
// Calculate the reference mass scaling ratio
_ReferenceMassRatioScalingMarine = HandlingTimeScalarMarine * Math.Pow(_ReferenceMass / _BodyMassPredator, _HandlingTimeExponentMarine);
_PredatorAbundanceMultipliedByTimeEating = _AbundancePredator * _SpecificPredatorTimeUnitsEatingPerGlobalTimeStep;
LogPredatorMassPlusPredatorLogOptimalPreyBodySizeRatio = Math.Log(_BodyMassPredator) + _PredatorLogOptimalPreyBodySizeRatio;
// Calculate the abundance of prey in each of the prey mass bins
PopulateBinnedPreyAbundance(gridCellCohorts, actingCohort, FunctionalGroupIndicesToEat, LogPredatorMassPlusPredatorLogOptimalPreyBodySizeRatio);
// Loop over potential prey functional groups
foreach (int FunctionalGroup in FunctionalGroupIndicesToEat)
{
// Eating operates differently for planktivores
// This can certainly be sped up
if (_DietIsAllSpecial)
{
// Loop over cohorts within the functional group
for (int i = 0; i < NumberCohortsPerFunctionalGroupNoNewCohorts[FunctionalGroup]; i++)
{
// Get the body mass of individuals in this cohort
_BodyMassPrey = gridCellCohorts[FunctionalGroup][i].IndividualBodyMass;
// Get the bin number of this prey cohort
PreyMassBinNumber = GetBinNumber(_BodyMassPrey, LogPredatorMassPlusPredatorLogOptimalPreyBodySizeRatio);
// Check whether
// The prey cohort is within the feeding range of the predator
// the prey cohort still exists in the model (i.e. body mass > 0)
// Currently having whales etc eat everything, but preferentially feed on very small things (i.e. filter feeders)
if ((_PlanktonFunctionalGroups[FunctionalGroup]) && (0 < PreyMassBinNumber) &&
(PreyMassBinNumber < NumberOfBins) && (_BodyMassPrey > 0))
{
// Calculate the potential abundance from this cohort eaten by the acting cohort
_PotentialAbundanceEaten[FunctionalGroup][i] = CalculateExpectedNumberKilledMarine(
gridCellCohorts[FunctionalGroup][i].CohortAbundance, _BodyMassPrey, PreyMassBinNumber, FunctionalGroup,
_BodyMassPredator, _CarnivoreFunctionalGroups[FunctionalGroup], _OmnivoreFunctionalGroups[FunctionalGroup],
_OmnivoreFunctionalGroups[actingCohort[0]], _PredatorLogOptimalPreyBodySizeRatio);
// Add the time required to handle the potential abundance eaten from this cohort to the cumulative total for all cohorts
_TimeUnitsToHandlePotentialFoodItems += _PotentialAbundanceEaten[FunctionalGroup][i] *
CalculateHandlingTimeMarine(_BodyMassPrey);
}
else
{
// Assign a potential abundance eaten of zero
_PotentialAbundanceEaten[FunctionalGroup][i] = 0.0;
}
}
}
else
{
// Loop over cohorts within the functional group
for (int i = 0; i < NumberCohortsPerFunctionalGroupNoNewCohorts[FunctionalGroup]; i++)
{
// Get the body mass of individuals in this cohort
_BodyMassPrey = gridCellCohorts[FunctionalGroup][i].IndividualBodyMass;
// Get the bin number of this prey cohort
PreyMassBinNumber = GetBinNumber(_BodyMassPrey, LogPredatorMassPlusPredatorLogOptimalPreyBodySizeRatio);
// Check whether
// The prey cohort is within the feeding range of the predator
// the prey cohort still exists in the model (i.e. body mass > 0)
if ((0 < PreyMassBinNumber) && (PreyMassBinNumber < NumberOfBins) && (_BodyMassPrey > 0))
{
// Calculate the potential abundance from this cohort eaten by the acting cohort
_PotentialAbundanceEaten[FunctionalGroup][i] = CalculateExpectedNumberKilledMarine(
gridCellCohorts[FunctionalGroup][i].CohortAbundance, _BodyMassPrey, PreyMassBinNumber, FunctionalGroup,
_BodyMassPredator, _CarnivoreFunctionalGroups[FunctionalGroup], _OmnivoreFunctionalGroups[FunctionalGroup],
_OmnivoreFunctionalGroups[actingCohort[0]], _PredatorLogOptimalPreyBodySizeRatio);
// Add the time required to handle the potential abundance eaten from this cohort to the cumulative total for all cohorts
_TimeUnitsToHandlePotentialFoodItems += _PotentialAbundanceEaten[FunctionalGroup][i] *
CalculateHandlingTimeMarine(_BodyMassPrey);
}
else
{
// Assign a potential abundance eaten of zero
_PotentialAbundanceEaten[FunctionalGroup][i] = 0.0;
}
}
}
}
// No cannibalism; do this outside the loop to speed up the calculations
_TimeUnitsToHandlePotentialFoodItems -= PotentialAbundanceEaten[actingCohort[0]][actingCohort[1]] *
CalculateHandlingTimeMarine(_BodyMassPredator);
PotentialAbundanceEaten[actingCohort[0]][actingCohort[1]] = 0.0;
}
/// <summary>
/// Initialises predation implementation each time step
/// </summary>
/// <param name="gridCellCohorts">The cohorts in the current grid cell</param>
/// <param name="gridCellStocks">The stocks in the current grid cell</param>
/// <param name="madingleyCohortDefinitions">The definitions for cohorts in the model</param>
/// <param name="madingleyStockDefinitions">The definitions for stocks in the model</param>
/// <remarks>This only works if: a) predation is initialised in every grid cell; and b) if parallelisation is done by latitudinal strips
/// It is critical to run this every time step</remarks>
public void InitializeEatingPerTimeStep(GridCellCohortHandler gridCellCohorts, GridCellStockHandler gridCellStocks, FunctionalGroupDefinitions madingleyCohortDefinitions, FunctionalGroupDefinitions madingleyStockDefinitions)
{
// Get the functional group indices of all heterotroph cohorts (i.e. potential prey)
_FunctionalGroupIndicesToEat = madingleyCohortDefinitions.GetFunctionalGroupIndex("Heterotroph/Autotroph", "heterotroph", false);
// Initialise the vector to hold the number of cohorts in each functional group at the start of the time step
NumberCohortsPerFunctionalGroupNoNewCohorts = new int[gridCellCohorts.Count];
// Initialise the jagged arrays to hold the potential and actual numbers of prey eaten in each of the grid cell cohorts
_AbundancesEaten = new double[gridCellCohorts.Count][];
_PotentialAbundanceEaten = new double[gridCellCohorts.Count][];
// Initialise the vector to identify carnivore cohorts
_CarnivoreFunctionalGroups = new Boolean[_FunctionalGroupIndicesToEat.Length];
_OmnivoreFunctionalGroups = new Boolean[_FunctionalGroupIndicesToEat.Length];
_PlanktonFunctionalGroups = new Boolean[_FunctionalGroupIndicesToEat.Length];
// Loop over rows in the jagged arrays, initialise each vector within the jagged arrays, and calculate the current number of cohorts in
// each functional group
for (int i = 0; i < gridCellCohorts.Count; i++)
{
// Calculate the current number of cohorts in this functional group
int NumCohortsThisFG = gridCellCohorts[i].Count;
NumberCohortsPerFunctionalGroupNoNewCohorts[i] = NumCohortsThisFG;
// Initialise the jagged arrays
_AbundancesEaten[i] = new double[NumberCohortsPerFunctionalGroupNoNewCohorts[i]];
_PotentialAbundanceEaten[i] = new double[NumberCohortsPerFunctionalGroupNoNewCohorts[i]];
}
// Loop over functional groups that are potential prey and determine which are carnivores
foreach (int FunctionalGroup in FunctionalGroupIndicesToEat)
_CarnivoreFunctionalGroups[FunctionalGroup] = madingleyCohortDefinitions.GetTraitNames("Nutrition source", FunctionalGroup) == "carnivore";
foreach (int FunctionalGroup in FunctionalGroupIndicesToEat)
_OmnivoreFunctionalGroups[FunctionalGroup] = madingleyCohortDefinitions.GetTraitNames("Nutrition source", FunctionalGroup) == "omnivore";
foreach (int FunctionalGroup in FunctionalGroupIndicesToEat)
_PlanktonFunctionalGroups[FunctionalGroup] = madingleyCohortDefinitions.GetTraitNames("Mobility", FunctionalGroup) == "planktonic";
}
/// <summary>
/// Generate new cohorts from reproductive potential mass
/// </summary>
/// <param name="gridCellCohorts">The cohorts in the current grid cell</param>
/// <param name="gridCellStocks">The stocks in the current grid cell</param>
/// <param name="actingCohort">The position of the acting cohort in the jagged array of grid cell cohorts</param>
/// <param name="cellEnvironment">The environment of the current grid cell</param>
/// <param name="deltas">The sorted list to track changes in biomass and abundance of the acting cohort in this grid cell</param>
/// <param name="madingleyCohortDefinitions">The definitions of cohort functional groups in the model</param>
/// <param name="madingleyStockDefinitions">The definitions of stock functional groups in the model</param>
/// <param name="currentTimestep">The current model time step</param>
/// <param name="tracker">An instance of ProcessTracker to hold diagnostics for reproduction</param>
/// <param name="partial">Thread-locked variables</param>
/// <param name="iteroparous">Whether the acting cohort is iteroparous, as opposed to semelparous</param>
/// <param name="currentMonth">The current model month</param>
public void RunReproductionEvents(GridCellCohortHandler gridCellCohorts, GridCellStockHandler gridCellStocks,
int[] actingCohort, SortedList<string, double[]> cellEnvironment, Dictionary<string, Dictionary<string, double>>
deltas, FunctionalGroupDefinitions madingleyCohortDefinitions, FunctionalGroupDefinitions madingleyStockDefinitions,
uint currentTimestep, ProcessTracker tracker, ref ThreadLockedParallelVariables partial, bool iteroparous, uint currentMonth)
{
// Adult non-reproductive biomass lost by semelparous organisms
double AdultMassLost;
// Offspring cohort abundance
double _OffspringCohortAbundance;
// Mass ratio of body mass + reproductive mass to adult body mass
double CurrentMassRatio;
// Individual body mass including change this time step as a result of other ecological processes
double BodyMassIncludingChangeThisTimeStep;
// Offspring juvenile and adult body masses
double[] OffspringJuvenileAndAdultBodyMasses = new double[2];
// Offspring cohort
Cohort OffspringCohort;
// Individual reproductive mass including change this time step as a result of other ecological processes
double ReproductiveMassIncludingChangeThisTimeStep;
// Calculate the biomass of an individual in this cohort including changes this time step from other ecological processes
BodyMassIncludingChangeThisTimeStep = 0.0;
foreach (var Biomass in deltas["biomass"])
{
// Add the delta biomass to net biomass
BodyMassIncludingChangeThisTimeStep += Biomass.Value;
}
BodyMassIncludingChangeThisTimeStep += gridCellCohorts[actingCohort].IndividualBodyMass;
// Calculate the reproductive biomass of an individual in this cohort including changes this time step from other ecological processes
ReproductiveMassIncludingChangeThisTimeStep = 0.0;
foreach (var ReproBiomass in deltas["reproductivebiomass"])
{
// Add the delta reproductive biomass to net biomass
ReproductiveMassIncludingChangeThisTimeStep += ReproBiomass.Value;
}
ReproductiveMassIncludingChangeThisTimeStep += gridCellCohorts[actingCohort].IndividualReproductivePotentialMass;
// Get the current ratio of total individual mass (including reproductive potential) to adult body mass
CurrentMassRatio = (BodyMassIncludingChangeThisTimeStep + ReproductiveMassIncludingChangeThisTimeStep) / gridCellCohorts[actingCohort].AdultMass;
// Must have enough mass to hit reproduction threshold criterion, and either (1) be in breeding season, or (2) be a marine cell (no breeding season in marine cells)
if ((CurrentMassRatio > _MassRatioThreshold) && ((cellEnvironment["Breeding Season"][currentMonth] == 1.0) || ((cellEnvironment["Realm"][0] == 2.0))))
{
// Iteroparous and semelparous organisms have different strategies
if (iteroparous)
{
// Iteroparous organisms do not allocate any of their current non-reproductive biomass to reproduction
AdultMassLost = 0.0;
// Calculate the number of offspring that could be produced given the reproductive potential mass of individuals
_OffspringCohortAbundance = gridCellCohorts[actingCohort].CohortAbundance * ReproductiveMassIncludingChangeThisTimeStep /
gridCellCohorts[actingCohort].JuvenileMass;
}
else
{
// Semelparous organisms allocate a proportion of their current non-reproductive biomass (including the effects of other ecological processes) to reproduction
AdultMassLost = _SemelparityAdultMassAllocation * BodyMassIncludingChangeThisTimeStep;
// Calculate the number of offspring that could be produced given the reproductive potential mass of individuals
_OffspringCohortAbundance = gridCellCohorts[actingCohort].CohortAbundance * (AdultMassLost + ReproductiveMassIncludingChangeThisTimeStep) /
gridCellCohorts[actingCohort].JuvenileMass;
}
// Check that the abundance in the cohort to produce is greater than or equal to zero
Debug.Assert(_OffspringCohortAbundance >= 0.0, "Offspring abundance < 0");
// Get the adult and juvenile masses of the offspring cohort
OffspringJuvenileAndAdultBodyMasses = GetOffspringCohortProperties(gridCellCohorts, actingCohort, madingleyCohortDefinitions);
// Update cohort abundance in case juvenile mass has been altered through 'evolution'
_OffspringCohortAbundance = (_OffspringCohortAbundance * gridCellCohorts[actingCohort].JuvenileMass) / OffspringJuvenileAndAdultBodyMasses[0];
double TrophicIndex;
switch (madingleyCohortDefinitions.GetTraitNames("nutrition source", actingCohort[0]))
{
case "herbivore":
TrophicIndex = 2;
break;
case "omnivore":
TrophicIndex = 2.5;
break;
case "carnivore":
TrophicIndex = 3;
break;
default:
Debug.Fail("Unexpected nutrition source trait value when assigning trophic index");
TrophicIndex = 0.0;
break;
}
// Create the offspring cohort
OffspringCohort = new Cohort((byte)actingCohort[0], OffspringJuvenileAndAdultBodyMasses[0], OffspringJuvenileAndAdultBodyMasses[1], OffspringJuvenileAndAdultBodyMasses[0],
_OffspringCohortAbundance, Math.Exp(gridCellCohorts[actingCohort].LogOptimalPreyBodySizeRatio),
(ushort)currentTimestep, gridCellCohorts[actingCohort].ProportionTimeActive, ref partial.NextCohortIDThreadLocked, TrophicIndex, tracker.TrackProcesses);
// Add the offspring cohort to the grid cell cohorts array
gridCellCohorts[actingCohort[0]].Add(OffspringCohort);
// If track processes has been specified then add the new cohort to the process tracker
if (tracker.TrackProcesses)
tracker.RecordNewCohort((uint)cellEnvironment["LatIndex"][0], (uint)cellEnvironment["LonIndex"][0],
currentTimestep, _OffspringCohortAbundance, gridCellCohorts[actingCohort].AdultMass, gridCellCohorts[actingCohort].FunctionalGroupIndex,
gridCellCohorts[actingCohort].CohortID, (uint)partial.NextCohortIDThreadLocked);
// Subtract all of the reproductive potential mass of the parent cohort, which has been used to generate the new
// cohort, from the delta reproductive potential mass and delta adult body mass
deltas["reproductivebiomass"]["reproduction"] -= ReproductiveMassIncludingChangeThisTimeStep;
deltas["biomass"]["reproduction"] -= AdultMassLost;
}
else
{
// Organism is not large enough, or it is not the breeding season, so take no action
}
}
/// <summary>
/// Assigns ingested biomass from other ecological processes to reproductive potential mass
/// </summary>
/// <param name="gridCellCohorts">The cohorts in the current grid cell</param>
/// <param name="gridCellStocks">The stocks in the current grid cell</param>
/// <param name="actingCohort">The position of the acting cohort in the jagged array of grid cell cohorts</param>
/// <param name="cellEnvironment">The environment in the current grid cell</param>
/// <param name="deltas">The sorted list to track changes in biomass and abundance of the acting cohort in this grid cell</param>
/// <param name="madingleyCohortDefinitions">The definitions of cohort functional groups in the model</param>
/// <param name="madingleyStockDefinitions">The definitions of stock functional groups in the model</param>
/// <param name="currentTimestep">The current model time step</param>
/// <param name="tracker">An instance of ProcessTracker to hold diagnostics for reproduction</param>
public void RunReproductiveMassAssignment(GridCellCohortHandler gridCellCohorts, GridCellStockHandler gridCellStocks,
int[] actingCohort, SortedList<string, double[]> cellEnvironment, Dictionary<string, Dictionary<string, double>> deltas,
FunctionalGroupDefinitions madingleyCohortDefinitions, FunctionalGroupDefinitions madingleyStockDefinitions,
uint currentTimestep, ProcessTracker tracker)
{
// Biomass per individual in each cohort to be assigned to reproductive potential
double _BiomassToAssignToReproductivePotential;
// Net biomass change from other ecological functions this time step
double NetBiomassFromOtherEcologicalFunctionsThisTimeStep;
// Reset variable holding net biomass change of individuals in this cohort as a result of other ecological processes
NetBiomassFromOtherEcologicalFunctionsThisTimeStep = 0.0;
// Loop over all items in the biomass deltas
foreach (var Biomass in deltas["biomass"])
{
// Add the delta biomass to net biomass
NetBiomassFromOtherEcologicalFunctionsThisTimeStep += Biomass.Value;
}
// If individual body mass after the addition of the net biomass from processes this time step will yield a body mass
// greater than the adult body mass for this cohort, then assign the surplus to reproductive potential
if ((gridCellCohorts[actingCohort].IndividualBodyMass + NetBiomassFromOtherEcologicalFunctionsThisTimeStep) > gridCellCohorts[actingCohort].AdultMass)
{
// Calculate the biomass for each individual in this cohort to be assigned to reproductive potential
_BiomassToAssignToReproductivePotential = gridCellCohorts[actingCohort].IndividualBodyMass + NetBiomassFromOtherEcologicalFunctionsThisTimeStep -
gridCellCohorts[actingCohort].AdultMass;
// Check that a positive biomass is to be assigned to reproductive potential
Debug.Assert(_BiomassToAssignToReproductivePotential >= 0.0, "Assignment of negative reproductive potential mass");
// If this is the first time reproductive potential mass has been assigned for this cohort,
// then set the maturity time step for this cohort as the current model time step
if (gridCellCohorts[actingCohort].MaturityTimeStep == uint.MaxValue)
{
gridCellCohorts[actingCohort].MaturityTimeStep = currentTimestep;
// Track the generation length for this cohort
if (tracker.TrackProcesses && (!gridCellCohorts[actingCohort].Merged))
tracker.TrackMaturity((uint)cellEnvironment["LatIndex"][0], (uint)cellEnvironment["LonIndex"][0],
currentTimestep, gridCellCohorts[actingCohort].BirthTimeStep, gridCellCohorts[actingCohort].JuvenileMass,
gridCellCohorts[actingCohort].AdultMass, gridCellCohorts[actingCohort].FunctionalGroupIndex);
}
// Assign the specified mass to reproductive potential mass and remove it from individual biomass
deltas["reproductivebiomass"]["reproduction"] += _BiomassToAssignToReproductivePotential;
deltas["biomass"]["reproduction"] -= _BiomassToAssignToReproductivePotential;
}
else
{
// Cohort has not gained sufficient biomass to assign any to reproductive potential, so take no action
}
}
/// <summary>
/// Run ecological processes that operate on cohorts within a single grid cell
/// </summary>
/// <param name="gridCellCohorts">The cohorts in the current grid cell</param>
/// <param name="gridCellStocks">The stocks in the current grid cell</param>
/// <param name="actingCohort">The acting cohort</param>
/// <param name="cellEnvironment">The environment in the current grid cell</param>
/// <param name="deltas">A sorted list of deltas to track changes in abundances and biomasses during the ecological processes</param>
/// <param name="madingleyCohortDefinitions">The definitions for cohort functional groups in the model</param>
/// <param name="madingleyStockDefinitions">The definitions for stock functional groups in the model</param>
/// <param name="currentTimestep">The current model time step</param>
/// <param name="trackProcesses">An instance of the process tracker</param>
/// <param name="partial">Thread-locked local variables</param>
/// <param name="specificLocations">Whether the model is being run for specific locations</param>
/// <param name="outputDetail">The level of output detail being used for this model run</param>
/// <param name="currentMonth">The current model month</param>
/// <param name="initialisation">The Madingley Model initialisation</param>
public void RunWithinCellEcology(GridCellCohortHandler gridCellCohorts, GridCellStockHandler gridCellStocks, int[] actingCohort,
SortedList<string, double[]> cellEnvironment, Dictionary<string, Dictionary<string, double>> deltas, FunctionalGroupDefinitions
madingleyCohortDefinitions, FunctionalGroupDefinitions madingleyStockDefinitions, uint currentTimestep, ProcessTracker trackProcesses,
ref ThreadLockedParallelVariables partial, Boolean specificLocations,string outputDetail, uint currentMonth,
MadingleyModelInitialisation initialisation)
{
// RUN EATING
_EatingFormulations["Basic eating"].RunEcologicalProcess(gridCellCohorts, gridCellStocks, actingCohort, cellEnvironment,
deltas, madingleyCohortDefinitions, madingleyStockDefinitions, currentTimestep, trackProcesses, ref partial,
specificLocations, outputDetail, currentMonth, initialisation);
// RUN METABOLISM - THIS TIME TAKE THE METABOLIC LOSS TAKING INTO ACCOUNT WHAT HAS BEEN INGESTED THROUGH EATING
_MetabolismFormulations["Basic metabolism"].RunEcologicalProcess(gridCellCohorts, gridCellStocks, actingCohort,
cellEnvironment, deltas, madingleyCohortDefinitions, madingleyStockDefinitions, currentTimestep, trackProcesses, ref partial,
specificLocations, outputDetail, currentMonth, initialisation);
// RUN REPRODUCTION - TAKING INTO ACCOUNT NET BIOMASS CHANGES RESULTING FROM EATING AND METABOLISING
_ReproductionFormulations["Basic reproduction"].RunEcologicalProcess(gridCellCohorts, gridCellStocks, actingCohort,
cellEnvironment, deltas, madingleyCohortDefinitions, madingleyStockDefinitions, currentTimestep, trackProcesses, ref partial,
specificLocations, outputDetail, currentMonth, initialisation);
// RUN MORTALITY - TAKING INTO ACCOUNT NET BIOMASS CHANGES RESULTING FROM EATING, METABOLISM AND REPRODUCTION
_MortalityFormulations["Basic mortality"].RunEcologicalProcess(gridCellCohorts, gridCellStocks, actingCohort,
cellEnvironment, deltas, madingleyCohortDefinitions, madingleyStockDefinitions, currentTimestep, trackProcesses, ref partial,
specificLocations, outputDetail, currentMonth, initialisation);
}
/// <summary>
/// Run ecological processes for stocks in a specified grid cell
/// </summary>
/// <param name="latCellIndex">The latitudinal index of the cell to run stock ecology for</param>
/// <param name="lonCellIndex">The longitudinal index of the cell to run stock ecology for</param>
/// <param name="workingGridCellStocks">A copy of the cohorts in the current grid cell</param>
/// <param name="cellIndex">The index of the current cell in the list of all cells to run the model for</param>
/// <param name="initialisation">The Madingley Model initialisation</param>
private void RunWithinCellStockEcology(uint latCellIndex, uint lonCellIndex,
GridCellStockHandler workingGridCellStocks, int cellIndex, MadingleyModelInitialisation initialisation)
{
// Create a local instance of the stock ecology class
EcologyStock MadingleyEcologyStock = new EcologyStock();
// Initialise stock ecology
MadingleyEcologyStock.InitializeEcology();
//The location of the acting stock
int[] ActingStock = new int[2];
// Get the list of functional group indices for autotroph stocks
int[] AutotrophStockFunctionalGroups = StockFunctionalGroupDefinitions.GetFunctionalGroupIndex("Heterotroph/Autotroph", "Autotroph", false).
ToArray();
// Loop over autotroph functional groups
foreach (int FunctionalGroup in AutotrophStockFunctionalGroups)
{
for (int ll = 0; ll < workingGridCellStocks[FunctionalGroup].Count; ll++)
{
// Get the position of the acting stock
ActingStock[0] = FunctionalGroup;
ActingStock[1] = ll;
// Run stock ecology
MadingleyEcologyStock.RunWithinCellEcology(workingGridCellStocks, ActingStock, EcosystemModelGrid.GetCellEnvironment(
latCellIndex, lonCellIndex), EnvironmentalDataUnits, _HumanNPPScenario, StockFunctionalGroupDefinitions,
CurrentTimeStep, NumBurninSteps, NumImpactSteps, initialisation.RecoveryTimeSteps, initialisation.InstantaneousTimeStep, initialisation.NumInstantaneousTimeStep, _GlobalModelTimeStepUnit, ProcessTrackers[cellIndex].TrackProcesses, ProcessTrackers[cellIndex],
TrackGlobalProcesses, CurrentMonth,
InitialisationFileStrings["OutputDetail"],SpecificLocations,((initialisation.ImpactCellIndices.Contains((uint)cellIndex) || (initialisation.ImpactAll))));
}
}
}
/// <summary>
/// Run mortality
/// </summary>
/// <param name="gridCellCohorts">The cohorts in the current grid cell</param>
/// <param name="gridCellStocks">The stocks in the current grid cell</param>
/// <param name="actingCohort">The position of the acting cohort in the jagged array of grid cell cohorts</param>
/// <param name="cellEnvironment">The environment in the current grid cell</param>
/// <param name="deltas">The sorted list to track changes in biomass and abundance of the acting cohort in this grid cell</param>
/// <param name="madingleyCohortDefinitions">The definitions for cohort functional groups in the model</param>
/// <param name="madingleyStockDefinitions">The definitions for stock functional groups in the model</param>
/// <param name="currentTimestep">The current model time step</param>
/// <param name="trackProcesses">An instance of ProcessTracker to hold diagnostics for mortality</param>
/// <param name="partial">Thread-locked variables</param>
/// <param name="specificLocations">Whether the model is being run for specific locations</param>
/// <param name="outputDetail">The level output detail being used for the current model run</param>
/// <param name="currentMonth">The current model month</param>
/// <param name="initialisation">The Madingley Model initialisation</param>
public void RunEcologicalProcess(GridCellCohortHandler gridCellCohorts, GridCellStockHandler gridCellStocks,
int[] actingCohort, SortedList<string, double[]> cellEnvironment, Dictionary<string, Dictionary<string, double>> deltas,
FunctionalGroupDefinitions madingleyCohortDefinitions, FunctionalGroupDefinitions madingleyStockDefinitions,
uint currentTimestep, ProcessTracker trackProcesses, ref ThreadLockedParallelVariables partial,
Boolean specificLocations, string outputDetail, uint currentMonth, MadingleyModelInitialisation initialisation)
{
// Variables to hold the mortality rates
double MortalityRateBackground;
double MortalityRateSenescence;
double MortalityRateStarvation;
// Variable to hold the total abundance lost to all forms of mortality
double MortalityTotal;
// Individual body mass including change this time step as a result of other ecological processes
double BodyMassIncludingChangeThisTimeStep;
// Individual reproductive mass including change this time step as a result of other ecological processes
double ReproductiveMassIncludingChangeThisTimeStep;
// Calculate the body mass of individuals in this cohort including mass gained through eating this time step, up to but not exceeding adult body mass for this cohort.
// Should be fine because these deductions are made in the reproduction implementation, but use Math.Min to double check.
BodyMassIncludingChangeThisTimeStep = 0.0;
// Loop over all items in the biomass deltas
foreach (var Biomass in deltas["biomass"])
{
// Add the delta biomass to net biomass
BodyMassIncludingChangeThisTimeStep += Biomass.Value;
}
BodyMassIncludingChangeThisTimeStep = Math.Min(gridCellCohorts[actingCohort].AdultMass, BodyMassIncludingChangeThisTimeStep + gridCellCohorts[actingCohort].IndividualBodyMass);
// Temporary variable to hold net reproductive biomass change of individuals in this cohort as a result of other ecological processes
ReproductiveMassIncludingChangeThisTimeStep = 0.0;
// Loop over all items in the biomass deltas
foreach (var Biomass in deltas["reproductivebiomass"])
{
// Add the delta biomass to net biomass
ReproductiveMassIncludingChangeThisTimeStep += Biomass.Value;
}
ReproductiveMassIncludingChangeThisTimeStep += gridCellCohorts[actingCohort].IndividualReproductivePotentialMass;
// Check to see if the cohort has already been killed by predation etc
if ((BodyMassIncludingChangeThisTimeStep).CompareTo(0.0) <= 0)
{
// If individual body mass is not greater than zero, then all individuals become extinct
MortalityTotal = gridCellCohorts[actingCohort].CohortAbundance;
}
else
{
// Calculate background mortality rate
MortalityRateBackground = Implementations["basic background mortality"].CalculateMortalityRate(gridCellCohorts,
actingCohort, BodyMassIncludingChangeThisTimeStep, deltas, currentTimestep);
// If the cohort has matured, then calculate senescence mortality rate, otherwise set rate to zero
if (gridCellCohorts[actingCohort].MaturityTimeStep != uint.MaxValue)
{
MortalityRateSenescence = Implementations["basic senescence mortality"].CalculateMortalityRate(gridCellCohorts,
actingCohort, BodyMassIncludingChangeThisTimeStep, deltas, currentTimestep);
}
else
{
MortalityRateSenescence = 0.0;
}
// Calculate the starvation mortality rate based on individual body mass and maximum body mass ever
// achieved by this cohort
MortalityRateStarvation = Implementations["basic starvation mortality"].CalculateMortalityRate(gridCellCohorts, actingCohort, BodyMassIncludingChangeThisTimeStep, deltas, currentTimestep);
// Calculate the number of individuals that suffer mortality this time step from all sources of mortality
MortalityTotal = (1 - Math.Exp(-MortalityRateBackground - MortalityRateSenescence -
MortalityRateStarvation)) * gridCellCohorts[actingCohort].CohortAbundance;
}
// If the process tracker is on and output detail is set to high and this cohort has not been merged yet, then record
// the number of individuals that have died
if (trackProcesses.TrackProcesses && (outputDetail == "high") && (!gridCellCohorts[actingCohort].Merged))
{
trackProcesses.RecordMortality((uint)cellEnvironment["LatIndex"][0], (uint)cellEnvironment["LonIndex"][0], gridCellCohorts[actingCohort].BirthTimeStep,
currentTimestep, gridCellCohorts[actingCohort].IndividualBodyMass, gridCellCohorts[actingCohort].AdultMass,
gridCellCohorts[actingCohort].FunctionalGroupIndex,
gridCellCohorts[actingCohort].CohortID[0], MortalityTotal, "sen/bg/starv");
}
// Remove individuals that have died from the delta abundance for this cohort
deltas["abundance"]["mortality"] = -MortalityTotal;
// Add the biomass of individuals that have died to the delta biomass in the organic pool (including reproductive
// potential mass, and mass gained through eating, and excluding mass lost through metabolism)
deltas["organicpool"]["mortality"] = MortalityTotal * (BodyMassIncludingChangeThisTimeStep + ReproductiveMassIncludingChangeThisTimeStep);
}
/// <summary>
/// Update the properties of the acting cohort and of the environmental biomass pools after running the ecological processes for a cohort
/// </summary>
/// <param name="gridCellCohorts">The cohorts in the current grid cell</param>
/// <param name="gridCellStocks">The stocks in the current grid cell</param>
/// <param name="actingCohort">The acting cohort</param>
/// <param name="cellEnvironment">The environment of the current grid cell</param>
/// <param name="deltas">The sorted list of deltas for the current grid cell</param>
/// <param name="madingleyCohortDefinitions">The definitions for cohort functional groups in the model</param>
/// <param name="madingleyStockDefinitions">The definitions for stock functional groups in the model</param>
/// <param name="currentTimestep">The current model time step</param>
/// <param name="tracker">A process tracker</param>
public void UpdateEcology(GridCellCohortHandler gridCellCohorts, GridCellStockHandler gridCellStocks, int[] actingCohort,
SortedList<string, double[]> cellEnvironment, Dictionary<string, Dictionary<string, double>> deltas, FunctionalGroupDefinitions
madingleyCohortDefinitions, FunctionalGroupDefinitions madingleyStockDefinitions, uint currentTimestep, ProcessTracker tracker)
{
// Apply the results of within-cell ecological processes
ApplyEcologicalProcessResults.UpdateAllEcology(gridCellCohorts, actingCohort, cellEnvironment, deltas, currentTimestep, tracker);
}
public InputModelState(string outputPath, string filename, ModelGrid ecosystemModelGrid, List<uint[]> cellList)
{
//Set the input state flag to be true
_InputState = true;
// Construct the string required to access the file using Scientific Dataset
string _ReadFileString = "msds:nc?file=input/ModelStates/" + filename +".nc&openMode=readOnly";
// Open the data file using Scientific Dataset
DataSet StateDataSet = DataSet.Open(_ReadFileString);
float[] Latitude = StateDataSet.GetData<float[]>("Latitude");
float[] Longitude = StateDataSet.GetData<float[]>("Longitude");
float[] CohortFunctionalGroup = StateDataSet.GetData<float[]>("Cohort Functional Group");
float[] Cohort = StateDataSet.GetData<float[]>("Cohort");
float[] StockFunctionalGroup = StateDataSet.GetData<float[]>("Stock Functional Group");
float[] Stock = StateDataSet.GetData<float[]>("Stock");
// Check that the longitudes and latitudes in the input state match the cell environment
for (int la = 0; la < Latitude.Length; la++)
{
Debug.Assert(ecosystemModelGrid.GetCellEnvironment((uint)la, 0)["Latitude"][0] == Latitude[la],
"Error: input-state grid doesn't match current model grid");
}
for (int lo = 0; lo < Longitude.Length; lo++)
{
Debug.Assert(ecosystemModelGrid.GetCellEnvironment(0, (uint)lo)["Longitude"][0] == Longitude[lo],
"Error: input-state grid doesn't match current model grid");
}
List<double[,,]> CohortJuvenileMass = new List<double[,,]>();
List<double[,,]> CohortAdultMass = new List<double[,,]>();
List<double[,,]> CohortIndividualBodyMass = new List<double[,,]>();
List<double[,,]> CohortCohortAbundance = new List<double[,,]>();
List<double[,,]> CohortLogOptimalPreyBodySizeRatio = new List<double[,,]>();
List<double[,,]> CohortBirthTimeStep = new List<double[,,]>();
List<double[,,]> CohortProportionTimeActive = new List<double[,,]>();
List<double[,,]> CohortTrophicIndex = new List<double[,,]>();
double[,,,] tempData = new double[Latitude.Length, Longitude.Length,
CohortFunctionalGroup.Length, Cohort.Length];
tempData = StateDataSet.GetData<double[,,,]>("CohortJuvenileMass");
for (int la = 0; la < Latitude.Length; la++)
{
CohortJuvenileMass.Add(new double[Longitude.Length, CohortFunctionalGroup.Length, Cohort.Length]);
}
foreach (uint[] cell in cellList)
{
for (int fg = 0; fg < CohortFunctionalGroup.Length; fg++)
{
for (int c = 0; c < Cohort.Length; c++)
{
CohortJuvenileMass[(int)cell[0]][cell[1], fg, c] = tempData[
cell[0], cell[1], fg, c];
}
}
}
tempData = StateDataSet.GetData<double[,,,]>("CohortAdultMass");
for (int la = 0; la < Latitude.Length; la++)
{
CohortAdultMass.Add(new double[Longitude.Length, CohortFunctionalGroup.Length, Cohort.Length]);
}
foreach (uint[] cell in cellList)
{
for (int fg = 0; fg < CohortFunctionalGroup.Length; fg++)
{
for (int c = 0; c < Cohort.Length; c++)
{
CohortAdultMass[(int)cell[0]][cell[1], fg, c] = tempData[
cell[0], cell[1], fg, c];
}
}
}
tempData = StateDataSet.GetData<double[,,,]>("CohortIndividualBodyMass");
for (int la = 0; la < Latitude.Length; la++)
{
CohortIndividualBodyMass.Add(new double[Longitude.Length, CohortFunctionalGroup.Length, Cohort.Length]);
}
foreach (uint[] cell in cellList)
{
for (int fg = 0; fg < CohortFunctionalGroup.Length; fg++)
{
for (int c = 0; c < Cohort.Length; c++)
{
CohortIndividualBodyMass[(int)cell[0]][cell[1], fg, c] = tempData[
cell[0], cell[1], fg, c];
}
}
}
tempData = StateDataSet.GetData<double[,,,]>("CohortCohortAbundance");
for (int la = 0; la < Latitude.Length; la++)
{
CohortCohortAbundance.Add(new double[Longitude.Length, CohortFunctionalGroup.Length, Cohort.Length]);
}
foreach (uint[] cell in cellList)
{
for (int fg = 0; fg < CohortFunctionalGroup.Length; fg++)
{
for (int c = 0; c < Cohort.Length; c++)
{
CohortCohortAbundance[(int)cell[0]][cell[1], fg, c] = tempData[
cell[0], cell[1], fg, c];
}
}
}
tempData = StateDataSet.GetData<double[,,,]>("CohortLogOptimalPreyBodySizeRatio");
for (int la = 0; la < Latitude.Length; la++)
{
CohortLogOptimalPreyBodySizeRatio.Add(new double[Longitude.Length, CohortFunctionalGroup.Length, Cohort.Length]);
}
foreach (uint[] cell in cellList)
{
for (int fg = 0; fg < CohortFunctionalGroup.Length; fg++)
{
for (int c = 0; c < Cohort.Length; c++)
{
CohortLogOptimalPreyBodySizeRatio[(int)cell[0]][cell[1], fg, c] = tempData[
cell[0], cell[1], fg, c];
}
}
}
tempData = StateDataSet.GetData<double[,,,]>("CohortBirthTimeStep");
for (int la = 0; la < Latitude.Length; la++)
{
CohortBirthTimeStep.Add(new double[Longitude.Length, CohortFunctionalGroup.Length, Cohort.Length]);
}
foreach (uint[] cell in cellList)
{
for (int fg = 0; fg < CohortFunctionalGroup.Length; fg++)
{
for (int c = 0; c < Cohort.Length; c++)
{
CohortBirthTimeStep[(int)cell[0]][cell[1], fg, c] = tempData[
cell[0], cell[1], fg, c];
}
}
}
tempData = StateDataSet.GetData<double[,,,]>("CohortProportionTimeActive");
for (int la = 0; la < Latitude.Length; la++)
{
CohortProportionTimeActive.Add(new double[Longitude.Length, CohortFunctionalGroup.Length, Cohort.Length]);
}
foreach (uint[] cell in cellList)
{
for (int fg = 0; fg < CohortFunctionalGroup.Length; fg++)
{
for (int c = 0; c < Cohort.Length; c++)
{
CohortProportionTimeActive[(int)cell[0]][cell[1], fg, c] = tempData[
cell[0], cell[1], fg, c];
}
}
}
tempData = StateDataSet.GetData<double[,,,]>("CohortTrophicIndex");
for (int la = 0; la < Latitude.Length; la++)
{
CohortTrophicIndex.Add(new double[Longitude.Length, CohortFunctionalGroup.Length, Cohort.Length]);
}
foreach (uint[] cell in cellList)
{
for (int fg = 0; fg < CohortFunctionalGroup.Length; fg++)
{
for (int c = 0; c < Cohort.Length; c++)
{
CohortTrophicIndex[(int)cell[0]][cell[1], fg, c] = tempData[
cell[0], cell[1], fg, c];
}
}
}
_GridCellCohorts = new GridCellCohortHandler[Latitude.Length, Longitude.Length];
long temp = 0;
for (int cell = 0; cell < cellList.Count; cell++)
{
_GridCellCohorts[cellList[cell][0], cellList[cell][1]] = new GridCellCohortHandler(CohortFunctionalGroup.Length);
for (int fg = 0; fg < CohortFunctionalGroup.Length; fg++)
{
_GridCellCohorts[cellList[cell][0], cellList[cell][1]][fg] = new List<Cohort>();
for (int c = 0; c < Cohort.Length; c++)
{
if (CohortCohortAbundance[(int)cellList[cell][0]][cellList[cell][1],fg,c] > 0.0)
{
Cohort TempCohort = new Cohort(
(byte)fg,
CohortJuvenileMass[(int)cellList[cell][0]][cellList[cell][1], fg, c],
CohortAdultMass[(int)cellList[cell][0]][cellList[cell][1], fg, c],
CohortIndividualBodyMass[(int)cellList[cell][0]][cellList[cell][1], fg, c],
CohortCohortAbundance[(int)cellList[cell][0]][cellList[cell][1], fg, c],
Math.Exp(CohortLogOptimalPreyBodySizeRatio[(int)cellList[cell][0]][cellList[cell][1], fg, c]),
Convert.ToUInt16(CohortBirthTimeStep[(int)cellList[cell][0]][cellList[cell][1], fg, c]),
CohortProportionTimeActive[(int)cellList[cell][0]][cellList[cell][1], fg, c], ref temp,
CohortTrophicIndex[(int)cellList[cell][0]][cellList[cell][1], fg, c],
false);
_GridCellCohorts[cellList[cell][0], cellList[cell][1]][fg].Add(TempCohort);
}
}
}
}
CohortJuvenileMass.RemoveRange(0, CohortJuvenileMass.Count);
CohortAdultMass.RemoveRange(0, CohortAdultMass.Count);
CohortIndividualBodyMass.RemoveRange(0, CohortIndividualBodyMass.Count);
CohortCohortAbundance.RemoveRange(0, CohortCohortAbundance.Count);
CohortLogOptimalPreyBodySizeRatio.RemoveRange(0, CohortLogOptimalPreyBodySizeRatio.Count);
CohortBirthTimeStep.RemoveRange(0, CohortBirthTimeStep.Count);
CohortProportionTimeActive.RemoveRange(0, CohortProportionTimeActive.Count);
CohortTrophicIndex.RemoveRange(0, CohortTrophicIndex.Count);
List<double[,,]> StockIndividualBodyMass = new List<double[,,]>();
List<double[,,]> StockTotalBiomass = new List<double[,,]>();
double[,,,] tempData2 = new double[Latitude.Length, Longitude.Length,
StockFunctionalGroup.Length,Stock.Length];
tempData2 = StateDataSet.GetData<double[,,,]>("StockIndividualBodyMass");
for (int la = 0; la < Latitude.Length; la++)
{
StockIndividualBodyMass.Add(new double[Longitude.Length, StockFunctionalGroup.Length, Stock.Length]);
}
foreach (uint[] cell in cellList)
{
for (int fg = 0; fg < StockFunctionalGroup.Length; fg++)
{
for (int c = 0; c < Stock.Length; c++)
{
StockIndividualBodyMass[(int)cell[0]][cell[1], fg, c] = tempData2[
cell[0], cell[1], fg, c];
}
}
}
tempData2 = StateDataSet.GetData<double[,,,]>("StockTotalBiomass");
for (int la = 0; la < Latitude.Length; la++)
{
StockTotalBiomass.Add(new double[Longitude.Length, StockFunctionalGroup.Length, Stock.Length]);
}
foreach (uint[] cell in cellList)
{
for (int fg = 0; fg < StockFunctionalGroup.Length; fg++)
{
for (int c = 0; c < Stock.Length; c++)
{
StockTotalBiomass[(int)cell[0]][cell[1], fg, c] = tempData2[
cell[0], cell[1], fg, c];
}
}
}
_GridCellStocks = new GridCellStockHandler[Latitude.Length, Longitude.Length];
for (int cell = 0; cell < cellList.Count; cell++)
{
_GridCellStocks[cellList[cell][0], cellList[cell][1]] = new GridCellStockHandler(StockFunctionalGroup.Length);
for (int fg = 0; fg < StockFunctionalGroup.Length; fg++)
{
_GridCellStocks[cellList[cell][0], cellList[cell][1]][fg] = new List<Stock>();
for (int c = 0; c < Stock.Length; c++)
{
if (StockTotalBiomass[(int)cellList[cell][0]][cellList[cell][1], fg, c] > 0.0)
{
Stock TempStock = new Stock(
(byte)fg,
StockIndividualBodyMass[(int)cellList[cell][0]][cellList[cell][1], fg, c],
StockTotalBiomass[(int)cellList[cell][0]][cellList[cell][1], fg, c]);
_GridCellStocks[cellList[cell][0], cellList[cell][1]][fg].Add(TempStock);
}
}
}
}
}
/// <summary>
/// Calculate the potential number of prey that could be gained through predation on each cohort in the grid cell
/// </summary>
/// <param name="gridCellCohorts">The cohorts in the current grid cell</param>
/// <param name="gridCellStocks">The stocks in the current grid cell</param>
/// <param name="actingCohort">The acting cohort</param>
/// <param name="cellEnvironment">The environment in the current grid cell</param>
/// <param name="madingleyCohortDefinitions">The functional group definitions for cohorts in the model</param>
/// <param name="madingleyStockDefinitions">The functional group definitions for stocks in the model</param>
public void GetEatingPotentialTerrestrial(GridCellCohortHandler gridCellCohorts, GridCellStockHandler gridCellStocks, int[] actingCohort,
SortedList<string, double[]> cellEnvironment, FunctionalGroupDefinitions madingleyCohortDefinitions, FunctionalGroupDefinitions
madingleyStockDefinitions)
{
BinnedPreyDensities = new double[gridCellCohorts.Count, NumberOfBins];
// Set the total eaten by the acting cohort to zero
_TotalBiomassEatenByCohort = 0.0;
// Set the total number of units to handle all potential prey individuals eaten to zero
_TimeUnitsToHandlePotentialFoodItems = 0.0;
// Get the individual body mass of the acting (predator) cohort
_BodyMassPredator = gridCellCohorts[actingCohort].IndividualBodyMass;
// Get the abundance of the acting (predator) cohort
_AbundancePredator = gridCellCohorts[actingCohort].CohortAbundance;
// Pre-calculate individual values for this predator
_SpecificPredatorKillRateConstant = _KillRateConstant * Math.Pow(_BodyMassPredator, (_KillRateConstantMassExponent));
_SpecificPredatorTimeUnitsEatingPerGlobalTimeStep = _DeltaT * _ProportionOfTimeEating;
_PredatorAssimilationEfficiency = _AssimilationEfficiency;
_PredatorNonAssimilation = (1 - _AssimilationEfficiency);
// When body sizes are less than one gram, we have a flat handling time relationship to stop small things have extraordinarily short handling times
// if (_BodyMassPredator > 1.0)
// {
_ReferenceMassRatioScalingTerrestrial = HandlingTimeScalarTerrestrial * Math.Pow(_ReferenceMass / _BodyMassPredator, _HandlingTimeExponentTerrestrial);
// }
// else
// {
// _ReferenceMassRatioScalingTerrestrial = HandlingTimeScalarTerrestrial * _ReferenceMass / _BodyMassPredator;
// }
_PredatorAbundanceMultipliedByTimeEating = _AbundancePredator * _SpecificPredatorTimeUnitsEatingPerGlobalTimeStep;
_PredatorLogOptimalPreyBodySizeRatio = gridCellCohorts[actingCohort[0]][actingCohort[1]].LogOptimalPreyBodySizeRatio;
LogPredatorMassPlusPredatorLogOptimalPreyBodySizeRatio = Math.Log(_BodyMassPredator) + _PredatorLogOptimalPreyBodySizeRatio;
// Calculate the abundance of prey in each of the prey mass bins
PopulateBinnedPreyAbundance(gridCellCohorts, actingCohort, FunctionalGroupIndicesToEat, LogPredatorMassPlusPredatorLogOptimalPreyBodySizeRatio);
// Loop over potential prey functional groups
foreach (int FunctionalGroup in FunctionalGroupIndicesToEat)
{
// Loop over cohorts within the functional group
for (int i = 0; i < NumberCohortsPerFunctionalGroupNoNewCohorts[FunctionalGroup]; i++)
{
// Get the body mass of individuals in this cohort
_BodyMassPrey = gridCellCohorts[FunctionalGroup][i].IndividualBodyMass;
// Get the bin number of this prey cohort
PreyMassBinNumber = GetBinNumber(_BodyMassPrey, LogPredatorMassPlusPredatorLogOptimalPreyBodySizeRatio);
// Check whether the prey cohort still exists in the model (i.e. body mass > 0)
if ((0 < PreyMassBinNumber) && (PreyMassBinNumber < NumberOfBins) && (_BodyMassPrey > 0))
{
// Calculate the potential abundance from this cohort eaten by the acting cohort
_PotentialAbundanceEaten[FunctionalGroup][i] = CalculateExpectedNumberKilledTerrestrial(
gridCellCohorts[FunctionalGroup][i].CohortAbundance, _BodyMassPrey, PreyMassBinNumber, FunctionalGroup,
_BodyMassPredator, _CarnivoreFunctionalGroups[FunctionalGroup], _OmnivoreFunctionalGroups[FunctionalGroup],
_OmnivoreFunctionalGroups[actingCohort[0]], _PredatorLogOptimalPreyBodySizeRatio);
// Add the time required to handle the potential abundance eaten from this cohort to the cumulative total for all cohorts
_TimeUnitsToHandlePotentialFoodItems += _PotentialAbundanceEaten[FunctionalGroup][i] *
CalculateHandlingTimeTerrestrial(_BodyMassPrey);
}
else
{
// Assign a potential abundance eaten of zero
_PotentialAbundanceEaten[FunctionalGroup][i] = 0.0;
}
}
}
// No cannibalism; do this outside the loop to speed up the calculations
_TimeUnitsToHandlePotentialFoodItems -= PotentialAbundanceEaten[actingCohort[0]][actingCohort[1]] *
CalculateHandlingTimeTerrestrial(_BodyMassPredator);
PotentialAbundanceEaten[actingCohort[0]][actingCohort[1]] = 0.0;
}
/// <summary>
/// Run eating
/// </summary>
/// <param name="gridCellCohorts">The cohorts in the current grid cell</param>
/// <param name="gridCellStocks">The stocks in the current grid cell</param>
/// <param name="actingCohort">The position of the acting cohort in the jagged array of grid cell cohorts</param>
/// <param name="cellEnvironment">The environment in the current grid cell</param>
/// <param name="deltas">The sorted list to track changes in biomass and abundance of the acting cohort in this grid cell</param>
/// <param name="madingleyCohortDefinitions">The definitions for cohort functional groups in the model</param>
/// <param name="madingleyStockDefinitions">The definitions for stock functional groups in the model</param>
/// <param name="currentTimestep">The current model time step</param>
/// <param name="trackProcesses">An instance of ProcessTracker to hold diagnostics for eating</param>
/// <param name="partial">Thread-locked variables</param>
/// <param name="specificLocations">Whether the model is being run for specific locations</param>
/// <param name="outputDetail">The level of output detail being used for the current model run</param>
/// <param name="currentMonth">The current model month</param>
/// <param name="initialisation">The Madingley Model initialisation</param>
public void RunEcologicalProcess(GridCellCohortHandler gridCellCohorts,
GridCellStockHandler gridCellStocks, int[] actingCohort,
SortedList<string, double[]> cellEnvironment,
Dictionary<string, Dictionary<string, double>> deltas,
FunctionalGroupDefinitions madingleyCohortDefinitions,
FunctionalGroupDefinitions madingleyStockDefinitions,
uint currentTimestep, ProcessTracker trackProcesses,
ref ThreadLockedParallelVariables partial, Boolean specificLocations,
string outputDetail, uint currentMonth, MadingleyModelInitialisation initialisation)
{
PreviousTrophicIndex = gridCellCohorts[actingCohort].TrophicIndex;
//Reset this cohort's trohic index ready for calculation across its feeding this timetsstep
gridCellCohorts[actingCohort].TrophicIndex = 0.0;
// Get the nutrition source (herbivory, carnivory or omnivory) of the acting cohort
string NutritionSource = madingleyCohortDefinitions.GetTraitNames("Nutrition source", gridCellCohorts[actingCohort].FunctionalGroupIndex);
// Switch to the appropriate eating process(es) given the cohort's nutrition source
switch (NutritionSource)
{
case "herbivore":
// Get the assimilation efficiency for herbivory for this cohort from the functional group definitions
Implementations["revised herbivory"].AssimilationEfficiency =
madingleyCohortDefinitions.GetBiologicalPropertyOneFunctionalGroup
("herbivory assimilation", gridCellCohorts[actingCohort].FunctionalGroupIndex);
// Get the proportion of time spent eating for this cohort from the functional group definitions
Implementations["revised herbivory"].ProportionTimeEating = gridCellCohorts[actingCohort].ProportionTimeActive;
// Calculate the potential biomass available from herbivory
if (cellEnvironment["Realm"][0] == 2.0)
Implementations["revised herbivory"].GetEatingPotentialMarine
(gridCellCohorts, gridCellStocks, actingCohort,
cellEnvironment, madingleyCohortDefinitions, madingleyStockDefinitions);
else
Implementations["revised herbivory"].GetEatingPotentialTerrestrial
(gridCellCohorts, gridCellStocks, actingCohort,
cellEnvironment, madingleyCohortDefinitions, madingleyStockDefinitions);
// Run herbivory to apply changes in autotroph biomass from herbivory and add biomass eaten to the delta arrays
Implementations["revised herbivory"].RunEating
(gridCellCohorts, gridCellStocks, actingCohort,
cellEnvironment, deltas, madingleyCohortDefinitions,
madingleyStockDefinitions, trackProcesses,
currentTimestep, specificLocations,outputDetail, initialisation);
break;
case "carnivore":
// Get the assimilation efficiency for predation for this cohort from the functional group definitions
Implementations["revised predation"].AssimilationEfficiency =
madingleyCohortDefinitions.GetBiologicalPropertyOneFunctionalGroup
("carnivory assimilation", gridCellCohorts[actingCohort].FunctionalGroupIndex);
Implementations["revised predation"].ProportionTimeEating = gridCellCohorts[actingCohort].ProportionTimeActive;
// Calculate the potential biomass available from predation
if (cellEnvironment["Realm"][0] == 2.0)
Implementations["revised predation"].GetEatingPotentialMarine
(gridCellCohorts, gridCellStocks, actingCohort,
cellEnvironment, madingleyCohortDefinitions, madingleyStockDefinitions);
else
Implementations["revised predation"].GetEatingPotentialTerrestrial
(gridCellCohorts, gridCellStocks, actingCohort,
cellEnvironment, madingleyCohortDefinitions, madingleyStockDefinitions);
// Run predation to apply changes in prey biomass from predation and add biomass eaten to the delta arrays
Implementations["revised predation"].RunEating
(gridCellCohorts, gridCellStocks, actingCohort, cellEnvironment, deltas,
madingleyCohortDefinitions, madingleyStockDefinitions, trackProcesses,
currentTimestep, specificLocations,outputDetail, initialisation);
break;
case "omnivore":
// Get the assimilation efficiency for predation for this cohort from the functional group definitions
Implementations["revised predation"].AssimilationEfficiency =
madingleyCohortDefinitions.GetBiologicalPropertyOneFunctionalGroup
("carnivory assimilation", gridCellCohorts[actingCohort].FunctionalGroupIndex);
// Get the assimilation efficiency for herbivory for this cohort from the functional group definitions
Implementations["revised herbivory"].AssimilationEfficiency =
madingleyCohortDefinitions.GetBiologicalPropertyOneFunctionalGroup
("herbivory assimilation", gridCellCohorts[actingCohort].FunctionalGroupIndex);
// Get the proportion of time spent eating and assign to both the herbivory and predation implementations
double ProportionTimeEating = gridCellCohorts[actingCohort].ProportionTimeActive;
Implementations["revised predation"].ProportionTimeEating = ProportionTimeEating;
Implementations["revised herbivory"].ProportionTimeEating = ProportionTimeEating;
// Calculate the potential biomass available from herbivory
if (cellEnvironment["Realm"][0] == 2.0)
Implementations["revised herbivory"].GetEatingPotentialMarine
(gridCellCohorts, gridCellStocks, actingCohort,
cellEnvironment, madingleyCohortDefinitions,
madingleyStockDefinitions);
else
Implementations["revised herbivory"].GetEatingPotentialTerrestrial
(gridCellCohorts, gridCellStocks, actingCohort,
cellEnvironment, madingleyCohortDefinitions,
madingleyStockDefinitions);
// Calculate the potential biomass available from predation
if (cellEnvironment["Realm"][0] == 2.0)
Implementations["revised predation"].GetEatingPotentialMarine
(gridCellCohorts, gridCellStocks, actingCohort,
cellEnvironment, madingleyCohortDefinitions,
madingleyStockDefinitions);
else
Implementations["revised predation"].GetEatingPotentialTerrestrial
(gridCellCohorts, gridCellStocks, actingCohort,
cellEnvironment, madingleyCohortDefinitions,
madingleyStockDefinitions);
// Calculate the total handling time for all expected kills from predation and expected plant matter eaten in herbivory
TotalTimeToEatForOmnivores =
Implementations["revised herbivory"].TimeUnitsToHandlePotentialFoodItems +
Implementations["revised predation"].TimeUnitsToHandlePotentialFoodItems;
// Assign this total time to the relevant variables in both herbviory and predation, so that actual amounts eaten are calculated correctly
Implementations["revised herbivory"].TimeUnitsToHandlePotentialFoodItems = TotalTimeToEatForOmnivores;
Implementations["revised predation"].TimeUnitsToHandlePotentialFoodItems = TotalTimeToEatForOmnivores;
// Run predation to update prey cohorts and delta biomasses for the acting cohort
Implementations["revised predation"].RunEating
(gridCellCohorts, gridCellStocks, actingCohort,
cellEnvironment, deltas, madingleyCohortDefinitions,
madingleyStockDefinitions, trackProcesses,
currentTimestep, specificLocations,outputDetail, initialisation);
// Run herbivory to update autotroph biomass and delta biomasses for the acting cohort
Implementations["revised herbivory"].RunEating
(gridCellCohorts, gridCellStocks, actingCohort,
cellEnvironment, deltas, madingleyCohortDefinitions,
madingleyStockDefinitions, trackProcesses,
currentTimestep, specificLocations,outputDetail, initialisation);
break;
default:
// For nutrition source that are not supported, throw an error
Debug.Fail("The model currently does not contain an eating model for nutrition source:" + NutritionSource);
break;
}
// Check that the biomasses from predation and herbivory in the deltas is a number
Debug.Assert(!double.IsNaN(deltas["biomass"]["predation"]), "BiomassFromEating is NaN");
Debug.Assert(!double.IsNaN(deltas["biomass"]["herbivory"]), "BiomassFromEating is NaN");
double biomassEaten = 0.0;
if (madingleyCohortDefinitions.GetBiologicalPropertyOneFunctionalGroup("carnivory assimilation",
gridCellCohorts[actingCohort].FunctionalGroupIndex) > 0)
{
biomassEaten += (deltas["biomass"]["predation"] / madingleyCohortDefinitions.GetBiologicalPropertyOneFunctionalGroup("carnivory assimilation",
gridCellCohorts[actingCohort].FunctionalGroupIndex));
}
if (madingleyCohortDefinitions.GetBiologicalPropertyOneFunctionalGroup("herbivory assimilation",
gridCellCohorts[actingCohort].FunctionalGroupIndex) > 0)
{
biomassEaten += (deltas["biomass"]["herbivory"]/madingleyCohortDefinitions.GetBiologicalPropertyOneFunctionalGroup("herbivory assimilation",
gridCellCohorts[actingCohort].FunctionalGroupIndex));
}
if (biomassEaten > 0.0)
{
gridCellCohorts[actingCohort].TrophicIndex = 1 +
(gridCellCohorts[actingCohort].TrophicIndex / (biomassEaten * gridCellCohorts[actingCohort].CohortAbundance));
}
else
{
gridCellCohorts[actingCohort].TrophicIndex = PreviousTrophicIndex;
}
}
/// <summary>
/// Apply the changes from predation to prey cohorts, and update deltas for the predator cohort
/// </summary>
/// <param name="gridCellCohorts">The cohorts in the current grid cell</param>
/// <param name="gridCellStocks">The stocks in the current grid cell</param>
/// <param name="actingCohort">The acting cohort</param>
/// <param name="cellEnvironment">The environment in the current grid cell</param>
/// <param name="deltas">The sorted list to track changes in biomass and abundance of the acting cohort in this grid cell</param>
/// <param name="madingleyCohortDefinitions">The functional group definitions for cohorts in the model</param>
/// <param name="madingleyStockDefinitions">The functional group definitions for stocks in the model</param>
/// <param name="trackProcesses">An instance of ProcessTracker to hold diagnostics for predation</param>
/// <param name="currentTimestep">The current model time step</param>
/// <param name="specificLocations">Whether the model is being run for specific locations</param>
/// <param name="outputDetail">The level of output detail used in this model run</param>
/// <param name="initialisation">The Madingley Model initialisation</param>
public void RunEating(GridCellCohortHandler gridCellCohorts, GridCellStockHandler gridCellStocks, int[] actingCohort, SortedList<string, double[]>
cellEnvironment, Dictionary<string, Dictionary<string, double>> deltas, FunctionalGroupDefinitions madingleyCohortDefinitions,
FunctionalGroupDefinitions madingleyStockDefinitions, ProcessTracker trackProcesses, uint currentTimestep, Boolean specificLocations,
string outputDetail, MadingleyModelInitialisation initialisation)
{
if (trackProcesses.TrackProcesses)
{
Track = (RandomNumberGenerator.GetUniform() > 0.975) ? true : false;
}
TempDouble = 0.0;
// Temporary variable to hold the total time spent eating + 1. Saves an extra calculation in CalculateAbundanceEaten
double TotalTimeUnitsToHandlePlusOne = TimeUnitsToHandlePotentialFoodItems + 1;
// Loop over potential prey functional groups
foreach (int FunctionalGroup in _FunctionalGroupIndicesToEat)
{
// Loop over cohorts within the functional group
for (int i = 0; i < NumberCohortsPerFunctionalGroupNoNewCohorts[FunctionalGroup]; i++)
{
// Get the individual body mass of this cohort
_BodyMassPrey = gridCellCohorts[FunctionalGroup][i].IndividualBodyMass;
// Calculate the actual abundance of prey eaten from this cohort
if (gridCellCohorts[FunctionalGroup][i].CohortAbundance > 0)
{
// Calculate the actual abundance of prey eaten from this cohort
_AbundancesEaten[FunctionalGroup][i] = CalculateAbundanceEaten(_PotentialAbundanceEaten[FunctionalGroup][i], _PredatorAbundanceMultipliedByTimeEating,
TotalTimeUnitsToHandlePlusOne, gridCellCohorts[FunctionalGroup][i].CohortAbundance);
}
else
_AbundancesEaten[FunctionalGroup][i] = 0;
// Remove number of prey eaten from the prey cohort
gridCellCohorts[FunctionalGroup][i].CohortAbundance -= _AbundancesEaten[FunctionalGroup][i];
gridCellCohorts[actingCohort].TrophicIndex += (_BodyMassPrey + gridCellCohorts[FunctionalGroup][i].IndividualReproductivePotentialMass) * _AbundancesEaten[FunctionalGroup][i] * gridCellCohorts[FunctionalGroup][i].TrophicIndex;
// If the process tracker is set and output detail is set to high and the prey cohort has never been merged,
// then track its mortality owing to predation
if (trackProcesses.TrackProcesses)
{
if ((outputDetail == "high") && (gridCellCohorts[FunctionalGroup][i].CohortID.Count == 1)
&& AbundancesEaten[FunctionalGroup][i] > 0)
{
trackProcesses.RecordMortality((uint)cellEnvironment["LatIndex"][0], (uint)cellEnvironment["LonIndex"][0], gridCellCohorts
[FunctionalGroup][i].BirthTimeStep, currentTimestep, gridCellCohorts[FunctionalGroup][i].IndividualBodyMass,
gridCellCohorts[FunctionalGroup][i].AdultMass, gridCellCohorts[FunctionalGroup][i].FunctionalGroupIndex,
gridCellCohorts[FunctionalGroup][i].CohortID[0], AbundancesEaten[FunctionalGroup][i], "predation");
}
// If the model is being run for specific locations and if track processes has been specified, then track the mass flow between
// prey and predator
if (specificLocations)
{
trackProcesses.RecordPredationMassFlow(currentTimestep, _BodyMassPrey, _BodyMassPredator, _BodyMassPrey *
_AbundancesEaten[FunctionalGroup][i]);
if (outputDetail == "high")
trackProcesses.TrackPredationTrophicFlow((uint)cellEnvironment["LatIndex"][0], (uint)cellEnvironment["LonIndex"][0],
gridCellCohorts[FunctionalGroup][i].FunctionalGroupIndex, gridCellCohorts[actingCohort].FunctionalGroupIndex,
madingleyCohortDefinitions, (_AbundancesEaten[FunctionalGroup][i] * _BodyMassPrey), _BodyMassPredator, _BodyMassPrey,
initialisation, cellEnvironment["Realm"][0] == 2.0);
}
}
// Check that the abundance eaten from this cohort is not negative
// Commented out for the purposes of speed
//Debug.Assert( _AbundancesEaten[FunctionalGroup][i].CompareTo(0.0) >= 0,
// "Predation negative for this prey cohort" + actingCohort);
// Create a temporary value to speed up the predation function
// This is equivalent to the body mass of the prey cohort including reproductive potential mass, times the abundance eaten of the prey cohort,
// divided by the abundance of the predator
TempDouble += (_BodyMassPrey + gridCellCohorts[FunctionalGroup][i].IndividualReproductivePotentialMass) * _AbundancesEaten[FunctionalGroup][i] / _AbundancePredator;
}
}
// Add the biomass eaten and assimilated by an individual to the delta biomass for the acting (predator) cohort
deltas["biomass"]["predation"] = TempDouble * _PredatorAssimilationEfficiency;
// Move the biomass eaten but not assimilated by an individual into the organic matter pool
deltas["organicpool"]["predation"] = TempDouble * _PredatorNonAssimilation * _AbundancePredator;
// Check that the delta biomass from eating for the acting cohort is not negative
//Debug.Assert(deltas["biomass"]["predation"] >= 0, "Predation yields negative biomass");
// Calculate the total biomass eaten by the acting (predator) cohort
_TotalBiomassEatenByCohort = deltas["biomass"]["predation"] * _AbundancePredator;
}
/// <summary>
/// Update the leaf stock during a time step given the environmental conditions in the grid cell
/// </summary>
/// <param name="cellEnvironment">The environment in the current grid cell</param>
/// <param name="gridCellStocks">The stocks in the current grid cell</param>
/// <param name="actingStock">The position of the acting stock in the array of grid cell stocks</param>
/// <param name="currentTimeStep">The current model time step</param>
/// <param name="deciduous">Whether the acting stock consists of deciduous leaves</param>
/// <param name="GlobalModelTimeStepUnit">The time step unit used in the model</param>
/// <param name="tracker">Whether to track properties of the ecological processes</param>
/// <param name="globalTracker">Whether to output data describing the global environment</param>
/// <param name="currentMonth">The current model month</param>
/// <param name="outputDetail">The level of detail to use in model outputs</param>
/// <param name="specificLocations">Whether the model is being run for specific locations</param>
public double UpdateLeafStock(SortedList<string, double[]> cellEnvironment, GridCellStockHandler gridCellStocks, int[] actingStock,
uint currentTimeStep, bool deciduous, string GlobalModelTimeStepUnit, ProcessTracker tracker, GlobalProcessTracker globalTracker,
uint currentMonth, string outputDetail, bool specificLocations)
{
// ESTIMATE ANNUAL LEAF CARBON FIXATION ASSUMING ENVIRONMENT THROUGHOUT THE YEAR IS THE SAME AS IN THIS MONTH
// Calculate annual NPP
double NPP = this.CalculateMiamiNPP(cellEnvironment["Temperature"].Average(), cellEnvironment["Precipitation"].Sum());
// Calculate fractional allocation to structural tissue
double FracStruct = this.CalculateFracStruct(NPP);
// Estimate monthly NPP based on seasonality layer
NPP *= cellEnvironment["Seasonality"][currentMonth];
// Calculate leaf mortality rates
double AnnualLeafMortRate;
double MonthlyLeafMortRate;
double TimeStepLeafMortRate;
if (deciduous)
{
// Calculate annual deciduous leaf mortality
AnnualLeafMortRate = this.CalculateDeciduousAnnualLeafMortality(cellEnvironment["Temperature"].Average());
// For deciduous plants monthly leaf mortality is weighted by temperature deviance from the average, to capture seasonal patterns
double[] ExpTempDev = new double[12];
double SumExpTempDev = 0.0;
double[] TempDev = new double[12];
double Weight;
for (int i = 0; i < 12; i++)
{
TempDev[i] = cellEnvironment["Temperature"][i] - cellEnvironment["Temperature"].Average();
ExpTempDev[i] = Math.Exp(-TempDev[i] / 3);
SumExpTempDev += ExpTempDev[i];
}
Weight = ExpTempDev[currentMonth] / SumExpTempDev;
MonthlyLeafMortRate = AnnualLeafMortRate * Weight;
TimeStepLeafMortRate = MonthlyLeafMortRate * Utilities.ConvertTimeUnits(GlobalModelTimeStepUnit, "month");
}
else
{
// Calculate annual evergreen leaf mortality
AnnualLeafMortRate = this.CalculateEvergreenAnnualLeafMortality(cellEnvironment["Temperature"].Average());
// For evergreen plants, leaf mortality is assumed to be equal throughout the year
MonthlyLeafMortRate = AnnualLeafMortRate * (1.0 / 12.0);
TimeStepLeafMortRate = MonthlyLeafMortRate * Utilities.ConvertTimeUnits(GlobalModelTimeStepUnit, "month");
}
// Calculate fine root mortality rate
double AnnualFRootMort = this.CalculateFineRootMortalityRate(cellEnvironment["Temperature"][currentMonth]);
// Calculate the NPP allocated to non-structural tissues
double FracNonStruct = (1 - FracStruct);
// Calculate the fractional allocation to leaves
double FracLeaves = FracNonStruct * this.CalculateLeafFracAllocation(AnnualLeafMortRate, AnnualFRootMort);
// Calculate the fractional allocation of NPP to evergreen plant matter
double FracEvergreen = this.CalculateFracEvergreen(cellEnvironment["Fraction Year Frost"][0]);
// Update NPP depending on whether the acting stock is deciduous or evergreen
if (deciduous)
{
NPP *= (1 - FracEvergreen);
}
else
{
NPP *= FracEvergreen;
}
// Calculate the fire mortality rate
double FireMortRate = this.CalculateFireMortalityRate(NPP, cellEnvironment["Fraction Year Fire"][0]);
// Calculate the structural mortality rate
double StMort = this.CalculateStructuralMortality(cellEnvironment["AET"][currentMonth] * 12);
// Calculate leaf C fixation
double LeafCFixation = NPP * FracLeaves;
// Convert from carbon to leaf wet matter
double WetMatterIncrement = this.ConvertToLeafWetMass(LeafCFixation, cellEnvironment["Cell Area"][0]);
// Convert from the monthly time step used for this process to the global model time step unit
WetMatterIncrement *= Utilities.ConvertTimeUnits(GlobalModelTimeStepUnit, "month");
// Add the leaf wet matter to the acting stock
//gridCellStocks[actingStock].TotalBiomass += Math.Max(-gridCellStocks[actingStock].TotalBiomass, WetMatterIncrement);
double NPPWetMatter = Math.Max(-gridCellStocks[actingStock].TotalBiomass, WetMatterIncrement);
// If the processer tracker is enabled and output detail is high and the model is being run for specific locations, then track the biomass gained through primary production
if (tracker.TrackProcesses && (outputDetail == "high") && specificLocations)
{
tracker.TrackPrimaryProductionTrophicFlow((uint)cellEnvironment["LatIndex"][0], (uint)cellEnvironment["LonIndex"][0],
Math.Max(-gridCellStocks[actingStock].TotalBiomass, WetMatterIncrement));
}
if (globalTracker.TrackProcesses)
{
globalTracker.RecordNPP((uint)cellEnvironment["LatIndex"][0], (uint)cellEnvironment["LonIndex"][0],(uint)actingStock[0],
this.ConvertToLeafWetMass(NPP, cellEnvironment["Cell Area"][0]) *
Utilities.ConvertTimeUnits(GlobalModelTimeStepUnit, "month")/cellEnvironment["Cell Area"][0]);
}
// Calculate fractional leaf mortality
double LeafMortFrac = 1 - Math.Exp(-TimeStepLeafMortRate);
// Update the leaf stock biomass owing to the leaf mortality
gridCellStocks[actingStock].TotalBiomass *= (1 - LeafMortFrac);
NPPWetMatter *= (1 - LeafMortFrac);
return (NPPWetMatter);
}