//---------------------------------------------------------------------
/// <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);
}
//---------------------------------------------------------------------
private double UpdateDeadBiomass(ICohort cohort, double actualANPP, double totalMortality, ActiveSite site, double newBiomass)
{
ISpecies species = cohort.Species;
double leafLongevity = SpeciesData.LeafLongevity[species];
double cohortBiomass = newBiomass; // Mortality is for the current year's biomass.
double leafFraction = ComputeFractionANPPleaf(species);
// First, deposit the a portion of the leaf mass directly onto the forest floor.
// In this way, the actual amount of leaf biomass is added for the year.
// In addition, add the equivalent portion of fine roots to the surface layer.
// 0.8 was used to calibrate the model to steady-state Nitrogen. Without this reduction, total N
// increases by 0.038% each year.
// Remove jan 2020 to more closely match code with the current Biomass succession model
//double annualLeafANPP = actualANPP * leafFraction * 0.8;
double annualLeafANPP = actualANPP * leafFraction;
// --------------------------------------------------------------------------------
// The next section allocates mortality from standing (wood and leaf) biomass, i.e.,
// biomass that has accrued from previous years' growth.
// Subtract annual leaf growth as that was taken care of above.
totalMortality -= annualLeafANPP;
// Assume that standing foliage is equal to this years annualLeafANPP * leaf longevity
// minus this years leaf ANPP. This assumes that actual ANPP has been relatively constant
// over the past 2 or 3 years (if coniferous).
double standing_nonwood = (annualLeafANPP * leafLongevity) - annualLeafANPP;
double standing_wood = Math.Max(0, cohortBiomass - standing_nonwood);
double fractionStandingNonwood = standing_nonwood / cohortBiomass;
// Assume that the remaining mortality is divided proportionally
// between the woody mass and non-woody mass (Niklaus & Enquist,
// 2002). Do not include current years growth.
double mortality_nonwood = Math.Max(0.0, totalMortality * fractionStandingNonwood);
double mortality_wood = Math.Max(0.0, totalMortality - mortality_nonwood);
if (mortality_wood < 0 || mortality_nonwood < 0)
{
throw new ApplicationException("Error: Woody input is < 0");
}
// Total mortality not including annual leaf litter
M_noLeafLitter = (int)mortality_wood;
SiteVars.soilClass[site].CollectBiomassMortality(species, cohort.Age, mortality_wood, (mortality_nonwood + annualLeafANPP), 0);
//add root biomass information - now calculated based on both woody and non-woody biomass
Roots.CalculateRootTurnover(site, species, cohortBiomass);
SiteVars.soilClass[site].CollectBiomassMortality(species, cohort.Age, Roots.CoarseRootTurnover, Roots.FineRootTurnover, 1);
//if biomass is going down, then we need to capture a decrease in the roots as well.
if (cohortBiomass < cohort.Biomass)
{
double preMortRoots = Roots.CalculateRootBiomass(site, species, cohort.Biomass);
double preMortCoarse = Roots.CoarseRoot;
double preMortFine = Roots.FineRoot;
double TotRoots = Roots.CalculateRootBiomass(site, species, cohortBiomass);
if (preMortRoots > TotRoots) //if the root biomass went down, then we need to allocate that difference.
{ //We will allocate the total root decline to the different pools based on the relative proportions
//prior to the decline. (Note that we are not calculating actual declines for each type because
//sometimes if we are changing calculation methods, we may change the allocation and may cause a large
//decrease in one pool and an increase in the other.)
double diffFine = (preMortFine / preMortRoots) * (preMortRoots - TotRoots);
double diffCoarse = (preMortRoots - TotRoots) - diffFine;
SiteVars.soilClass[site].CollectBiomassMortality(species, cohort.Age, diffCoarse, diffFine, 1);
//write a note to the file if the allocation changes unexpectedly, but not during spin-up
if (((preMortCoarse - Roots.CoarseRoot) < 0 || (preMortFine - Roots.FineRoot) < 0) && PlugIn.ModelCore.CurrentTime > 0)
{
string strCombo = "from: " + preMortCoarse;
strCombo += " to: " + Roots.CoarseRoot;
string strCombo2 = "from: " + preMortFine;
strCombo2 += " to: " + Roots.FineRoot;
PlugIn.ModelCore.UI.WriteLine("Root Dynamics: Overall root biomass declined but note change in coarse root allocation " + strCombo + " and fine root allocation" + strCombo2);
}
}
else if (PlugIn.ModelCore.CurrentTime > 0)
{
//write a note to the file if the root biomass increases while abio decreases, but not during spin-up
string strCombo = "from: " + cohort.Biomass;
strCombo += " to: " + cohortBiomass;
string strCombo2 = "from: " + preMortRoots;
strCombo2 += " to: " + TotRoots;
PlugIn.ModelCore.UI.WriteLine("Root Dynamics: Note that aboveground biomass decreased " + strCombo + " but root biomass increased " + strCombo2);
}
}
if (PlugIn.ModelCore.CurrentTime == 0)
{
SiteVars.soilClass[site].CollectBiomassMortality(species, cohort.Age, standing_wood, standing_nonwood, 3);
Roots.CalculateRootTurnover(site, species, (standing_wood + standing_nonwood));
SiteVars.soilClass[site].CollectBiomassMortality(species, cohort.Age, Roots.CoarseRootTurnover, Roots.FineRootTurnover, 4);
}
return(annualLeafANPP + mortality_nonwood + mortality_wood);
}