/// <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>
/// 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);
}
/// <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>
/// 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);
}