//---------------------------------------------------------------------
int IDisturbance.ReduceOrKillMarkedCohort(ICohort cohort)
{
int reduction;
if (reductions[cohort.Species.Index].TryGetValue(cohort.Age, out reduction))
{
int litter = cohort.ComputeNonWoodyBiomass(currentSite);
int woody = reduction - litter;
SiteVars.BiomassRemoved[currentSite] += reduction;
SiteVars.WoodyDebris[currentSite].Mass += woody;
SiteVars.Litter[currentSite].Mass += litter;
SiteVars.CohortsPartiallyDamaged[currentSite]++;
if (originalStand.LastPrescription.PreventEstablishment)
{
numberCohortsReduced++;
capacityReduction += (double) reduction / (double) cohort.Biomass;
}
// Record any cohort touched, not just killed:
BaseHarvest.SiteVars.Stand[currentSite].UpdateDamageTable(cohort.Species.Name);
BaseHarvest.SiteVars.Stand[currentSite].RecordBiomassRemoved(cohort.Species, reduction);
return reduction;
}
else
return 0;
}
public static void CohortDied(object sender,
DeathEventArgs eventArgs)
{
ExtensionType disturbanceType = eventArgs.DisturbanceType;
PoolPercentages cohortReductions = Module.Parameters.CohortReductions[disturbanceType];
ICohort cohort = (Landis.Library.BiomassCohorts.ICohort)eventArgs.Cohort;
ActiveSite site = eventArgs.Site;
int nonWoody = cohort.ComputeNonWoodyBiomass(site);
int woody = (cohort.Biomass - nonWoody);
int nonWoodyInput = ReduceInput(nonWoody, cohortReductions.Foliar);
int woodyInput = ReduceInput(woody, cohortReductions.Wood);
//ForestFloor.AddBiomass(woodyInput, nonWoodyInput, cohort.Species, site);
ForestFloor.AddWoody(woodyInput, cohort.Species, site);
ForestFloor.AddLitter(nonWoodyInput, cohort.Species, site);
}
public static void CohortDied(object sender,
DeathEventArgs eventArgs)
{
ExtensionType disturbanceType = eventArgs.DisturbanceType;
//PoolPercentages cohortReductions = Module.Parameters.CohortReductions[disturbanceType];
ICohort cohort = eventArgs.Cohort;
ActiveSite site = eventArgs.Site;
if (disturbanceType.IsMemberOf("disturbance:harvest")) //base harvest doesn't get here ever, but biomass harvest does.
{
return; //It has already been accounted for, however in PlugIn.CohortDied, so don't repeat here.
}
double foliar = (double)cohort.ComputeNonWoodyBiomass(site);
double wood = ((double)cohort.Biomass - foliar);
SiteVars.soilClass[site].DisturbanceImpactsBiomass(site, cohort.Species, cohort.Age, wood, foliar, disturbanceType.Name, 0);
}
//---------------------------------------------------------------------
/// <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 int ComputeChange(ICohort cohort,
ActiveSite site)
{
ecoregion = PlugIn.ModelCore.Ecoregion[site];
int siteBiomass = SiteVars.TotalBiomass[site];
//Save the pre-growth root biomass. This needs to be calculated BEFORE growth and mortality
double TotalRoots = Roots.CalculateRootBiomass(site, cohort.Species, cohort.Biomass);
SiteVars.soilClass[site].CollectRootBiomass(TotalRoots, 0);
// First, calculate age-related mortality.
// Age-related mortality will include woody and standing leaf biomass (=0 for deciduous trees).
double mortalityAge = ComputeAgeMortality(cohort);
double actualANPP = ComputeActualANPP(cohort, site, siteBiomass, SiteVars.PreviousYearMortality[site]);
// Age mortality is discounted from ANPP to prevent the over-
// estimation of mortality. ANPP cannot be negative.
actualANPP = Math.Max(1, actualANPP - mortalityAge);
// Growth-related mortality
double mortalityGrowth = ComputeGrowthMortality(cohort, site, siteBiomass);
// Age-related mortality is discounted from growth-related
// mortality to prevent the under-estimation of mortality. Cannot be negative.
mortalityGrowth = Math.Max(0, mortalityGrowth - mortalityAge);
// Also ensure that growth mortality does not exceed actualANPP.
mortalityGrowth = Math.Min(mortalityGrowth, actualANPP);
// Total mortality for the cohort
double totalMortality = mortalityAge + mortalityGrowth;
if (totalMortality > cohort.Biomass)
{
throw new ApplicationException("Error: Mortality exceeds cohort biomass");
}
// Defoliation ranges from 1.0 (total) to none (0.0).
defoliation = CohortDefoliation.Compute(cohort, site, siteBiomass);
double defoliationLoss = 0.0;
if (defoliation > 0)
{
double standing_nonwood = ComputeFractionANPPleaf(cohort.Species) * actualANPP;
defoliationLoss = standing_nonwood * defoliation;
SiteVars.soilClass[site].DisturbanceImpactsDOM(site, "defol", 0); //just soil impacts. Dist impacts are handled differently??
}
int deltaBiomass = (int)(actualANPP - totalMortality - defoliationLoss);
double newBiomass = cohort.Biomass + (double)deltaBiomass;
double totalLitter = UpdateDeadBiomass(cohort, actualANPP, totalMortality, site, newBiomass);
//if (site.Location.Row == 279 && site.Location.Column == 64 && cohort.Species.Name == "Pl")
//{
// PlugIn.ModelCore.UI.WriteLine("Yr={0}, Age={1}, mortGrow={2}, mortAge={3}, ANPP={4}, totLitter={5}", PlugIn.ModelCore.CurrentTime, cohort.Age, mortalityGrowth, mortalityAge, actualANPP, totalLitter);
// }
//if (cohort.Species.Name == "pinubank")
//{
//PlugIn.ModelCore.UI.WriteLine("Age={0}, ANPPact={1:0.0}, M={2:0.0}, litter={3:0.00}.", cohort.Age, actualANPP, totalMortality, totalLitter);
//PlugIn.ModelCore.UI.WriteLine("Name={0}, Age={1}, B={2}, ANPPact={3:0.0}, delta={4:0.0}", cohort.Species.Name, cohort.Age, cohort.Biomass, actualANPP, deltaBiomass);
// PlugIn.ModelCore.UI.WriteLine("Name={0}, Age={1}, B={2}, Mage={3:0.0}, Mgrowth={4:0.0}, ANPPact={5:0.0}, delta={6:0.0}, newbiomass={7:0.0}", cohort.Species.Name, cohort.Age, cohort.Biomass, mortalityAge, mortalityGrowth, actualANPP, deltaBiomass, newBiomass);
//}
//The KillNow flag indicates that this is the year of growth in which to kill off some cohorts in order to make snags.
if (SiteVars.soilClass[site].bKillNow && Snags.bSnagsPresent)
{
//if (SiteVars.soilClass[site].diedAt == cohort.Age && SiteVars.soilClass[site].spIndex == cohort.Species.Index)
//there could be more than one species-age combination, so we have to loop through them.
//However, the user has been asked to put the ages in order from smallest to largest, so we can stop looking
//as soon as we reach an age that is older than the cohort's age.
for (int idx = 0; idx < Snags.NUMSNAGS; idx++)
{
if (cohort.Age == Snags.DiedAt[idx] && Snags.initSpecIdx[idx] == cohort.Species.Index)
{
deltaBiomass = -cohort.Biomass; //set biomass to 0 to make core remove this from the list
//when this cohort gets passed to the cohort died event, there is no longer any biomass present, so
//we have to capture the biomass information here, while we still can.
double foliar = (double)cohort.ComputeNonWoodyBiomass(site);
double wood = ((double)cohort.Biomass - foliar);
Snags.bSnagsUsed[idx] = true;
SiteVars.soilClass[site].CollectBiomassMortality(cohort.Species, cohort.Age, wood, foliar, 5 + idx);
}
if (Snags.DiedAt[idx] > cohort.Age || Snags.DiedAt[idx] == 0)
{
break;
}
}
}
if (deltaBiomass > -cohort.Biomass)
{ //if we didn't kill this cohort to make a snag, then update the post-growth root biomass.
TotalRoots = Roots.CalculateRootBiomass(site, cohort.Species, newBiomass);
SiteVars.soilClass[site].CollectRootBiomass(TotalRoots, 1);
}
return(deltaBiomass);
}
public void CohortTotalMortality(object sender, DeathEventArgs eventArgs)
{
ExtensionType disturbanceType = eventArgs.DisturbanceType;
ActiveSite site = eventArgs.Site;
ICohort cohort = (Landis.Library.BiomassCohorts.ICohort)eventArgs.Cohort;
int foliarInput = cohort.ComputeNonWoodyBiomass(site);
int woodInput = (cohort.Biomass - foliarInput);
if (disturbanceType != null)
{
if (PlugIn.CalibrateMode && PlugIn.ModelCore.CurrentTime > 0)
{
PlugIn.ModelCore.UI.WriteLine(" BIOMASS SUCCESSION TOTAL MORTALITY: species={0}, age={1}, woodInput={2}, foliarInputs={3}.", cohort.Species.Name, cohort.Age, woodInput, foliarInput);
}
if (disturbanceType.IsMemberOf("disturbance:fire"))
{
SiteVars.FireSeverity = PlugIn.ModelCore.GetSiteVar <byte>("Fire.Severity");
Landis.Library.Succession.Reproduction.CheckForPostFireRegen(eventArgs.Cohort, site);
if (!Disturbed[site]) // the first cohort killed/damaged
{
if (SiteVars.FireSeverity != null && SiteVars.FireSeverity[site] > 0)
{
FireEffects.ReduceLayers(SiteVars.FireSeverity[site], site);
}
}
double woodFireConsumption = woodInput * (float)FireEffects.ReductionsTable[(int)SiteVars.FireSeverity[site]].CoarseLitterReduction;
double foliarFireConsumption = foliarInput * (float)FireEffects.ReductionsTable[(int)SiteVars.FireSeverity[site]].FineLitterReduction;
woodInput -= (int)woodFireConsumption;
foliarInput -= (int)foliarFireConsumption;
}
else
{
if (disturbanceType.IsMemberOf("disturbance:harvest"))
{
SiteVars.HarvestPrescriptionName = PlugIn.ModelCore.GetSiteVar <string>("Harvest.PrescriptionName");
if (!Disturbed[site]) // the first cohort killed/damaged
{
HarvestEffects.ReduceLayers(SiteVars.HarvestPrescriptionName[site], site);
}
woodInput -= (int)(woodInput * (float)HarvestEffects.GetCohortWoodRemoval(site));
foliarInput -= (int)(foliarInput * (float)HarvestEffects.GetCohortLeafRemoval(site));
}
// If not fire, check for resprouting:
Landis.Library.Succession.Reproduction.CheckForResprouting(eventArgs.Cohort, site);
}
}
//PlugIn.ModelCore.UI.WriteLine("Cohort Died: species={0}, age={1}, wood={2:0.00}, foliage={3:0.00}.", cohort.Species.Name, cohort.Age, wood, foliar);
ForestFloor.AddWoody(woodInput, cohort.Species, eventArgs.Site);
ForestFloor.AddLitter(foliarInput, cohort.Species, eventArgs.Site);
// Assume that ALL dead root biomass stays on site.
//Roots.AddCoarseRootLitter(Roots.CalculateCoarseRoot(cohort, cohort.WoodBiomass), cohort, cohort.Species, eventArgs.Site);
//Roots.AddFineRootLitter(Roots.CalculateFineRoot(cohort, cohort.LeafBiomass), cohort, cohort.Species, eventArgs.Site);
if (disturbanceType != null)
{
Disturbed[site] = true;
}
return;
//ExtensionType disturbanceType = eventArgs.DisturbanceType;
//if (disturbanceType != null)
//{
// ActiveSite site = eventArgs.Site;
// Disturbed[site] = true;
// if (disturbanceType.IsMemberOf("disturbance:fire"))
// Reproduction.CheckForPostFireRegen(eventArgs.Cohort, site);
// else
// Reproduction.CheckForResprouting(eventArgs.Cohort, site);
//}
}