//---------------------------------------------------------------------
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;
//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;
}
//---------------------------------------------------------------------
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;
}
//---------------------------------------------------------------------
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>
/// Computes the change in a cohort's biomass due to Annual Net Primary
/// Productivity (ANPP), age-related mortality (M_AGE), and development-
/// related mortality (M_BIO).
/// </summary>
public float[] ComputeChange(ICohort cohort, ActiveSite site)
{
double defoliatedLeafBiomass;
ecoregion = PlugIn.ModelCore.Ecoregion[site];
// First call to the Calibrate Log:
if (PlugIn.ModelCore.CurrentTime > 0 && OtherData.CalibrateMode)
{
Outputs.CalibrateLog.Write("{0},{1},{2},{3},{4},{5:0.0},{6:0.0},", PlugIn.ModelCore.CurrentTime, Century.Month + 1, ecoregion.Index, cohort.Species.Name, cohort.Age, cohort.WoodBiomass, cohort.LeafBiomass);
}
double siteBiomass = Century.ComputeLivingBiomass(SiteVars.Cohorts[site]);
if (siteBiomass < 0)
{
throw new ApplicationException("Error: Site biomass < 0");
}
// ****** Mortality *******
// Age-related mortality includes woody and standing leaf biomass.
double[] mortalityAge = ComputeAgeMortality(cohort, site);
// Growth-related mortality
double[] mortalityGrowth = ComputeGrowthMortality(cohort, site);
double[] totalMortality = new double[2] {
Math.Min(cohort.WoodBiomass, mortalityAge[0] + mortalityGrowth[0]), Math.Min(cohort.LeafBiomass, mortalityAge[1] + mortalityGrowth[1])
};
// ****** Growth *******
double[] actualANPP = ComputeActualANPP(cohort, site, siteBiomass, mortalityAge);
double scorch = 0.0;
defoliatedLeafBiomass = 0.0;
if (Century.Month == 6) //July = 6
{
if (SiteVars.FireSeverity != null && SiteVars.FireSeverity[site] > 0)
{
scorch = FireEffects.CrownScorching(cohort, SiteVars.FireSeverity[site]);
}
if (scorch > 0.0) // NEED TO DOUBLE CHECK WHAT CROWN SCORCHING RETURNS
{
totalMortality[1] = Math.Min(cohort.LeafBiomass, scorch + totalMortality[1]);
}
// Defoliation (index) ranges from 1.0 (total) to none (0.0).
if (PlugIn.ModelCore.CurrentTime > 0) //Skip this during initialization
{
int cohortBiomass = (int)(cohort.LeafBiomass + cohort.WoodBiomass);
defoliation = Landis.Library.Biomass.CohortDefoliation.Compute(site, cohort.Species, cohortBiomass, (int)siteBiomass);
}
if (defoliation > 1.0)
{
defoliation = 1.0;
}
if (defoliation > 0.0)
{
defoliatedLeafBiomass = (cohort.LeafBiomass) * defoliation;
if (totalMortality[1] + defoliatedLeafBiomass - cohort.LeafBiomass > 0.001)
{
defoliatedLeafBiomass = cohort.LeafBiomass - totalMortality[1];
}
ForestFloor.AddFrassLitter(defoliatedLeafBiomass, cohort.Species, site);
}
}
else
{
defoliation = 0.0;
defoliatedLeafBiomass = 0.0;
}
// RMS 03/2016: Additional mortality as reaching capacity limit: SAVE FOR NEXT RELEASE
//double maxBiomass = SpeciesData.B_MAX_Spp[cohort.Species][ecoregion];
//double limitCapacity = Math.Min(1.0, Math.Exp(siteBiomass / maxBiomass * 5.0) / Math.Exp(5.0)); // 1.0 = total limit; 0.0 = No limit
//totalMortality[0] += (actualANPP[0] * limitCapacity); // totalMortality not to exceed ANPP allocation
if (totalMortality[0] <= 0.0 || cohort.WoodBiomass <= 0.0)
{
totalMortality[0] = 0.0;
}
if (totalMortality[1] <= 0.0 || cohort.LeafBiomass <= 0.0)
{
totalMortality[1] = 0.0;
}
if ((totalMortality[0]) > cohort.WoodBiomass)
{
PlugIn.ModelCore.UI.WriteLine("Warning: WOOD Mortality exceeds cohort wood biomass. M={0:0.0}, B={1:0.0}", (totalMortality[0]), cohort.WoodBiomass);
PlugIn.ModelCore.UI.WriteLine("Warning: If M>B, then list mortality. Mage={0:0.0}, Mgrow={1:0.0},", mortalityAge[0], mortalityGrowth[0]);
throw new ApplicationException("Error: WOOD Mortality exceeds cohort biomass");
}
if ((totalMortality[1] + defoliatedLeafBiomass - cohort.LeafBiomass) > 0.01)
{
PlugIn.ModelCore.UI.WriteLine("Warning: LEAF Mortality exceeds cohort biomass. Mortality={0:0.000}, Leafbiomass={1:0.000}", (totalMortality[1] + defoliatedLeafBiomass), cohort.LeafBiomass);
PlugIn.ModelCore.UI.WriteLine("Warning: If M>B, then list mortality. Mage={0:0.00}, Mgrow={1:0.00}, Mdefo={2:0.000},", mortalityAge[1], mortalityGrowth[1], defoliatedLeafBiomass);
throw new ApplicationException("Error: LEAF Mortality exceeds cohort biomass");
}
float deltaWood = (float)(actualANPP[0] - totalMortality[0]);
float deltaLeaf = (float)(actualANPP[1] - totalMortality[1] - defoliatedLeafBiomass);
float[] deltas = new float[2] {
deltaWood, deltaLeaf
};
UpdateDeadBiomass(cohort, site, totalMortality);
CalculateNPPcarbon(site, cohort, actualANPP);
AvailableN.AdjustAvailableN(cohort, site, actualANPP);
if (OtherData.CalibrateMode && PlugIn.ModelCore.CurrentTime > 0)
{
Outputs.CalibrateLog.WriteLine("{0:0.00},{1:0.00},{2:0.00},{3:0.00},", deltaWood, deltaLeaf, totalMortality[0], totalMortality[1]);
}
return(deltas);
}