//---------------------------------------------------------------------
public void CohortPartialMortality(object sender, Landis.Library.BiomassCohorts.PartialDeathEventArgs eventArgs)
{
ExtensionType disturbanceType = eventArgs.DisturbanceType;
ActiveSite site = eventArgs.Site;
double reduction = eventArgs.Reduction;
ICohort cohort = (Landis.Library.LeafBiomassCohorts.ICohort)eventArgs.Cohort;
float fractionPartialMortality = (float)eventArgs.Reduction;
//PlugIn.ModelCore.UI.WriteLine("Cohort experienced partial mortality: species={0}, age={1}, wood_biomass={2}, fraction_mortality={3:0.0}.", cohort.Species.Name, cohort.Age, cohort.WoodBiomass, fractionPartialMortality);
AgeOnlyDisturbances.PoolPercentages cohortReductions = AgeOnlyDisturbances.Module.Parameters.CohortReductions[disturbanceType];
float foliar = cohort.LeafBiomass * fractionPartialMortality;
float wood = cohort.WoodBiomass * fractionPartialMortality;
float foliarInput = AgeOnlyDisturbances.Events.ReduceInput(foliar, cohortReductions.Foliar, site);
float woodInput = AgeOnlyDisturbances.Events.ReduceInput(wood, cohortReductions.Wood, site);
ForestFloor.AddWoodLitter(woodInput, cohort.Species, site);
ForestFloor.AddFoliageLitter(foliarInput, cohort.Species, site);
Roots.AddCoarseRootLitter(woodInput, cohort, cohort.Species, site); // All of cohorts roots are killed.
Roots.AddFineRootLitter(foliarInput, cohort, cohort.Species, site);
//PlugIn.ModelCore.UI.WriteLine("EVENT: Cohort Partial Mortality: species={0}, age={1}, disturbance={2}.", cohort.Species.Name, cohort.Age, disturbanceType);
//PlugIn.ModelCore.UI.WriteLine(" Cohort Reductions: Foliar={0:0.00}. Wood={1:0.00}.", cohortReductions.Foliar, cohortReductions.Wood);
//PlugIn.ModelCore.UI.WriteLine(" InputB/TotalB: Foliar={0:0.00}/{1:0.00}, Wood={2:0.0}/{3:0.0}.", foliarInput, foliar, woodInput, wood);
return;
}
/// <summary>
/// Summarize cohort C&N for output.
/// </summary>
private static void CalculateCohortCN(ActiveSite site, ICohort cohort)
{
ISpecies species = cohort.Species;
double leafC = cohort.LeafBiomass * 0.47;
double woodC = cohort.WoodBiomass * 0.47;
double fRootC = Roots.CalculateFineRoot(cohort, leafC);
double cRootC = Roots.CalculateCoarseRoot(cohort, woodC);
double totalC = leafC + woodC + fRootC + cRootC;
double leafN = leafC / (double)SpeciesData.LeafCN[species];
double woodN = woodC / (double)SpeciesData.WoodCN[species];
double cRootN = cRootC / (double)SpeciesData.CoarseRootCN[species];
double fRootN = fRootC / (double)SpeciesData.FineRootCN[species];
//double totalN = woodN + cRootN + leafN + fRootN;
//PlugIn.ModelCore.UI.WriteLine("month={0}, species={1}, leafB={2:0.0}, leafC={3:0.00}, leafN={4:0.0}, woodB={5:0.0}, woodC={6:0.000}, woodN={7:0.0}", Month, cohort.Species.Name, cohort.LeafBiomass, leafC, leafN, cohort.WoodBiomass, woodC, woodN);
SiteVars.CohortLeafC[site] += leafC;
SiteVars.CohortFRootC[site] += fRootC;
SiteVars.CohortLeafN[site] += leafN;
SiteVars.CohortFRootN[site] += fRootN;
SiteVars.CohortWoodC[site] += woodC;
SiteVars.CohortCRootC[site] += cRootC;
SiteVars.CohortWoodN[site] += woodN;
SiteVars.CohortCRootN[site] += cRootN;
return;
}
//---------------------------------------------------------------------
// Method for calculating Mineral N allocation, called from Century.cs Run method before calling Grow
// Iterates through cohorts, assigning each a portion of mineral N based on coarse root biomass. Uses an exponential function to "distribute"
// the N more evenly between spp. so that the ones with the most woody biomass don't get all the N (L122).
public static void CalculateMineralNfraction(Site site)
{
AvailableN.CohortMineralNfraction = new Dictionary <int, Dictionary <int, double> >();
double NAllocTotal = 0.0;
foreach (ISpeciesCohorts speciesCohorts in SiteVars.Cohorts[site])
{
foreach (ICohort cohort in speciesCohorts)
{
int cohortAddYear = GetAddYear(cohort);
//PlugIn.ModelCore.UI.WriteLine("CALCMineralNfraction: year={0}, mo={1}, species={2}, cohortAge={3}, cohortAddYear={4}.", PlugIn.ModelCore.CurrentTime, Century.Month, cohort.Species.Name, cohort.Age, cohortAddYear);
//Nallocation is a measure of how much N a cohort can gather relative to other cohorts
//double Nallocation = Roots.CalculateFineRoot(cohort.LeafBiomass);
double Nallocation = 1 - Math.Exp((-Roots.CalculateCoarseRoot(cohort, cohort.WoodBiomass) * 0.02));
if (Nallocation <= 0.0)
{
Nallocation = Math.Max(Nallocation, cohort.WoodBiomass * 0.01);
}
NAllocTotal += Nallocation;
Dictionary <int, double> newEntry = new Dictionary <int, double>();
newEntry.Add(cohortAddYear, Nallocation);
if (CohortMineralNfraction.ContainsKey(cohort.Species.Index))
{
if (!CohortMineralNfraction[cohort.Species.Index].ContainsKey(cohortAddYear))
{
CohortMineralNfraction[cohort.Species.Index][cohortAddYear] = Nallocation;
}
}
else
{
CohortMineralNfraction.Add(cohort.Species.Index, newEntry);
}
}
}
// Next relativize
foreach (ISpeciesCohorts speciesCohorts in SiteVars.Cohorts[site])
{
//PlugIn.ModelCore.UI.WriteLine(" SpeciesCohorts = {0}", speciesCohorts.Species.Name);
foreach (ICohort cohort in speciesCohorts)
{
int cohortAddYear = GetAddYear(cohort);
double Nallocation = CohortMineralNfraction[cohort.Species.Index][cohortAddYear];
double relativeNallocation = Nallocation / NAllocTotal;
CohortMineralNfraction[cohort.Species.Index][cohortAddYear] = relativeNallocation;
if (Double.IsNaN(relativeNallocation) || Double.IsNaN(Nallocation) || Double.IsNaN(NAllocTotal))
{
PlugIn.ModelCore.UI.WriteLine(" N ALLOCATION CALCULATION = NaN! ");
PlugIn.ModelCore.UI.WriteLine(" Site_Row={0:0}, Site_Column={1:0}.", site.Location.Row, site.Location.Column);
PlugIn.ModelCore.UI.WriteLine(" Nallocation={0:0.00}, NAllocTotal={1:0.00}, relativeNallocation={2:0.00}.", Nallocation, NAllocTotal, relativeNallocation);
PlugIn.ModelCore.UI.WriteLine(" Wood={0:0.00}, Leaf={1:0.00}.", cohort.WoodBiomass, cohort.LeafBiomass);
}
}
}
}
//---------------------------------------------------------------------
public void CohortDied(object sender,
Landis.Library.BiomassCohorts.DeathEventArgs eventArgs)
{
//PlugIn.ModelCore.UI.WriteLine("Cohort Died! :-(");
ExtensionType disturbanceType = eventArgs.DisturbanceType;
ActiveSite site = eventArgs.Site;
ICohort cohort = (Landis.Library.LeafBiomassCohorts.ICohort)eventArgs.Cohort;
double foliar = (double)cohort.LeafBiomass;
double wood = (double)cohort.WoodBiomass;
if (disturbanceType == null)
{
ForestFloor.AddWoodLitter(wood, cohort.Species, eventArgs.Site);
ForestFloor.AddFoliageLitter(foliar, cohort.Species, eventArgs.Site);
Roots.AddCoarseRootLitter(wood, cohort, cohort.Species, eventArgs.Site);
Roots.AddFineRootLitter(foliar, cohort, cohort.Species, eventArgs.Site);
}
if (disturbanceType != null)
{
Disturbed[site] = true;
if (disturbanceType.IsMemberOf("disturbance:fire"))
{
Landis.Library.Succession.Reproduction.CheckForPostFireRegen(eventArgs.Cohort, site);
}
else
{
Landis.Library.Succession.Reproduction.CheckForResprouting(eventArgs.Cohort, site);
}
}
}
//---------------------------------------------------------------------
public void CohortPartialMortality(object sender, Landis.Library.BiomassCohorts.PartialDeathEventArgs eventArgs)
{
ExtensionType disturbanceType = eventArgs.DisturbanceType;
ActiveSite site = eventArgs.Site;
double reduction = eventArgs.Reduction;
ICohort cohort = (Landis.Library.LeafBiomassCohorts.ICohort)eventArgs.Cohort;
float fractionPartialMortality = (float)eventArgs.Reduction;
AgeOnlyDisturbances.PoolPercentages cohortReductions = AgeOnlyDisturbances.Module.Parameters.CohortReductions[disturbanceType];
float foliar = cohort.LeafBiomass * fractionPartialMortality;
float wood = cohort.WoodBiomass * fractionPartialMortality;
float foliarInput = AgeOnlyDisturbances.Events.ReduceInput(foliar, cohortReductions.Foliar, site);
float woodInput = AgeOnlyDisturbances.Events.ReduceInput(wood, cohortReductions.Wood, site);
ForestFloor.AddWoodLitter(woodInput, cohort.Species, site);
ForestFloor.AddFoliageLitter(foliarInput, cohort.Species, site);
Roots.AddCoarseRootLitter(woodInput, cohort, cohort.Species, site); // All of cohorts roots are killed.
Roots.AddFineRootLitter(foliarInput, cohort, cohort.Species, site);
return;
}
//---------------------------------------------------------------------
/// <summary>
/// Calculates cohort N demand depending upon how much N would be removed through growth (ANPP) of leaves, wood, coarse roots and fine roots.
/// Demand is then used to determine the amount of N that a cohort "wants".
/// </summary>
public static double CalculateCohortNDemand(ISpecies species, ActiveSite site, ICohort cohort, double[] ANPP)
{
if (ANPP[1] <= 0.0)
{
return(0.0);
}
//return 0.01;
if (SpeciesData.NFixer[species]) // We fix our own N!
{
return(0.0);
}
double ANPPwood = 0.0;
double ANPPleaf = 0.0;
double ANPPcoarseRoot = 0.0;
double ANPPfineRoot = 0.0;
double woodN = 0.0;
double coarseRootN = 0.0;
double leafN = 0.0;
double fineRootN = 0.0;
if (ANPP[0] > 0.0) // Wood
{
ANPPwood = ANPP[0];
ANPPcoarseRoot = Roots.CalculateCoarseRoot(cohort, ANPPwood);
woodN = ANPPwood * 0.47 / SpeciesData.WoodCN[species];
coarseRootN = ANPPcoarseRoot * 0.47 / SpeciesData.CoarseRootCN[species];
}
if (ANPP[1] > 0.0) // Leaf
{
ANPPleaf = ANPP[1];
ANPPfineRoot = Roots.CalculateFineRoot(cohort, ANPPleaf);
leafN = ANPPleaf * 0.47 / SpeciesData.LeafCN[species];
fineRootN = ANPPfineRoot * 0.47 / SpeciesData.FineRootCN[species];
}
double totalANPP_C = (ANPPleaf + ANPPwood + ANPPcoarseRoot + ANPPfineRoot) * 0.47;
double Ndemand = leafN + woodN + coarseRootN + fineRootN;
if (Ndemand < 0.0)
{
PlugIn.ModelCore.UI.WriteLine(" ERROR: TotalANPP-C={0:0.00} Nreduction={1:0.00}.", totalANPP_C, Ndemand);
throw new ApplicationException("Error: N Reduction is < 0. See AvailableN.cs");
}
return(Ndemand);
}
//---------------------------------------------------------------------
/// <summary>
/// Summarize NPP
/// </summary>
private static void CalculateNPPcarbon(ActiveSite site, ICohort cohort, double[] AGNPP)
{
double NPPwood = AGNPP[0] * 0.47;
double NPPleaf = AGNPP[1] * 0.47;
double NPPcoarseRoot = Roots.CalculateCoarseRoot(cohort, NPPwood);
double NPPfineRoot = Roots.CalculateFineRoot(cohort, NPPleaf);
if (Double.IsNaN(NPPwood) || Double.IsNaN(NPPleaf) || Double.IsNaN(NPPcoarseRoot) || Double.IsNaN(NPPfineRoot))
{
PlugIn.ModelCore.UI.WriteLine(" EITHER WOOD or LEAF NPP or COARSE ROOT or FINE ROOT = NaN! Will set to zero.");
PlugIn.ModelCore.UI.WriteLine(" Yr={0},Mo={1}. WoodNPP={0}, LeafNPP={1}, CRootNPP={2}, FRootNPP={3}.", NPPwood, NPPleaf, NPPcoarseRoot, NPPfineRoot);
if (Double.IsNaN(NPPleaf))
{
NPPleaf = 0.0;
}
if (Double.IsNaN(NPPwood))
{
NPPwood = 0.0;
}
if (Double.IsNaN(NPPcoarseRoot))
{
NPPcoarseRoot = 0.0;
}
if (Double.IsNaN(NPPfineRoot))
{
NPPfineRoot = 0.0;
}
}
SiteVars.AGNPPcarbon[site] += NPPwood + NPPleaf;
SiteVars.BGNPPcarbon[site] += NPPcoarseRoot + NPPfineRoot;
SiteVars.MonthlyAGNPPcarbon[site][Century.Month] += NPPwood + NPPleaf;
SiteVars.MonthlyBGNPPcarbon[site][Century.Month] += NPPcoarseRoot + NPPfineRoot;
if (PlugIn.ModelCore.CurrentTime > 0 && OtherData.CalibrateMode)
{
Outputs.CalibrateLog.Write("{0:0.00},{1:0.00},", NPPwood, NPPleaf);
}
}
//---------------------------------------------------------------------
private void UpdateDeadBiomass(ICohort cohort, ActiveSite site, double[] totalMortality)
{
double mortality_wood = totalMortality[0];
double mortality_nonwood = totalMortality[1];
// Add mortality to dead biomass pools.
// Coarse root mortality is assumed proportional to aboveground woody mortality
// mass is assumed 25% of aboveground wood (White et al. 2000, Niklas & Enquist 2002)
if (mortality_wood > 0.0)
{
ForestFloor.AddWoodLitter(mortality_wood, cohort.Species, site);
Roots.AddCoarseRootLitter(mortality_wood, cohort, cohort.Species, site);
}
if (mortality_nonwood > 0.0)
{
AvailableN.AddResorbedN(cohort, totalMortality[1], site); //ignoring input from scorching, which is rare, but not resorbed.
ForestFloor.AddResorbedFoliageLitter(mortality_nonwood, cohort.Species, site);
Roots.AddFineRootLitter(mortality_nonwood, cohort, cohort.Species, site);
}
}
/// <summary>
/// Summarize cohort C&N for output.
/// </summary>
private static void CalculateCohortCN(ActiveSite site, ICohort cohort)
{
ISpecies species = cohort.Species;
double leafC = cohort.LeafBiomass * 0.47;
double woodC = cohort.WoodBiomass * 0.47;
double fRootC = Roots.CalculateFineRoot(cohort, leafC);
double cRootC = Roots.CalculateCoarseRoot(cohort, woodC);
double leafN = leafC / SpeciesData.LeafCN[species];
double woodN = woodC / SpeciesData.WoodCN[species];
double cRootN = cRootC / SpeciesData.CoarseRootCN[species];
double fRootN = fRootC / SpeciesData.FineRootCN[species];
SiteVars.CohortLeafC[site] += leafC;
SiteVars.CohortFRootC[site] += fRootC;
SiteVars.CohortLeafN[site] += leafN;
SiteVars.CohortFRootN[site] += fRootN;
SiteVars.CohortWoodC[site] += woodC;
SiteVars.CohortCRootC[site] += cRootC;
SiteVars.CohortWoodN[site] += woodN;
SiteVars.CohortCRootN[site] += cRootN;
}
//---------------------------------------------------------------------
// Method for calculating Mineral N allocation, called from Century.cs Run method before calling Grow
// Iterates through cohorts, assigning each a portion of mineral N based on coarse root biomass. Uses an exponential function to "distribute"
// the N more evenly between spp. so that the ones with the most woody biomass don't get all the N (L122).
public static void CalculateMineralNfraction(Site site)
{
AvailableN.CohortMineralNfraction = new Dictionary <int, Dictionary <int, double> >();
double NAllocTotal = 0.0;
foreach (ISpeciesCohorts speciesCohorts in SiteVars.Cohorts[site])
{
foreach (ICohort cohort in speciesCohorts)
{
int cohortAddYear = GetAddYear(cohort);
//PlugIn.ModelCore.UI.WriteLine("CALCMineralNfraction: year={0}, mo={1}, species={2}, cohortAge={3}, cohortAddYear={4}.", PlugIn.ModelCore.CurrentTime, Century.Month, cohort.Species.Name, cohort.Age, cohortAddYear);
//Nallocation is a measure of how much N a cohort can gather relative to other cohorts
//double Nallocation = Roots.CalculateFineRoot(cohort.LeafBiomass);
double Nallocation = 1 - Math.Exp((-Roots.CalculateCoarseRoot(cohort, cohort.WoodBiomass) * 0.02));
if (Nallocation <= 0.0) //PlugIn.ModelCore.CurrentTime == 0)
{
Nallocation = Math.Max(Nallocation, cohort.WoodBiomass * 0.01);
}
NAllocTotal += Nallocation;
Dictionary <int, double> newEntry = new Dictionary <int, double>();
newEntry.Add(cohortAddYear, Nallocation);
if (CohortMineralNfraction.ContainsKey(cohort.Species.Index))
{
//CohortMineralNfraction[cohort.Species.Index].Add(cohortAddYear, Nallocation);
// option 1: regardless of whether cohortAddYear already exists, create (or replace) the new value
//CohortMineralNfraction[cohort.Species.Index][cohortAddYear] = Nallocation;
// end of option 1
// option 2: if the cohortAddYear already exists, add the new value to the existing one
//double currentNallocation;
//CohortMineralNfraction[cohort.Species.Index].TryGetValue(cohortAddYear, out currentNallocation); // currentNallocation will be set to 0.0 if the cohortAddYear key does not exist
//CohortMineralNfraction[cohort.Species.Index][cohortAddYear] = currentNallocation + Nallocation;
// end of option 2
//if key is already present, then don't trigger an error.
if (!CohortMineralNfraction[cohort.Species.Index].ContainsKey(cohortAddYear))
{
CohortMineralNfraction[cohort.Species.Index][cohortAddYear] = Nallocation;
}
}
else
{
CohortMineralNfraction.Add(cohort.Species.Index, newEntry);
}
}
}
// Next relativize
foreach (ISpeciesCohorts speciesCohorts in SiteVars.Cohorts[site])
{
//PlugIn.ModelCore.UI.WriteLine(" SpeciesCohorts = {0}", speciesCohorts.Species.Name);
foreach (ICohort cohort in speciesCohorts)
{
int cohortAddYear = GetAddYear(cohort);
double Nallocation = CohortMineralNfraction[cohort.Species.Index][cohortAddYear];
double relativeNallocation = Nallocation / NAllocTotal;
CohortMineralNfraction[cohort.Species.Index][cohortAddYear] = relativeNallocation;
if (Double.IsNaN(relativeNallocation) || Double.IsNaN(Nallocation) || Double.IsNaN(NAllocTotal))
{
PlugIn.ModelCore.UI.WriteLine(" N ALLOCATION CALCULATION = NaN! ");
PlugIn.ModelCore.UI.WriteLine(" Nallocation={0:0.00}, NAllocTotal={1:0.00}, relativeNallocation={2:0.00}.", Nallocation, NAllocTotal, relativeNallocation);
PlugIn.ModelCore.UI.WriteLine(" Wood={0:0.00}, Leaf={1:0.00}.", cohort.WoodBiomass, cohort.LeafBiomass);
}
}
}
}