//---------------------------------------------------------------------
// This method does not trigger reproduction
public void CohortPartialMortality(object sender, Landis.Library.BiomassCohorts.PartialDeathEventArgs eventArgs)
{
//PlugIn.ModelCore.UI.WriteLine("Cohort Partial Mortality: {0}", eventArgs.Site);
ExtensionType disturbanceType = eventArgs.DisturbanceType;
ActiveSite site = eventArgs.Site;
ICohort cohort = (Landis.Library.LeafBiomassCohorts.ICohort)eventArgs.Cohort;
float fractionPartialMortality = (float)eventArgs.Reduction;
float foliarInput = cohort.LeafBiomass * fractionPartialMortality;
float woodInput = cohort.WoodBiomass * fractionPartialMortality;
if (disturbanceType.IsMemberOf("disturbance:harvest"))
{
SiteVars.HarvestPrescriptionName = PlugIn.ModelCore.GetSiteVar <string>("Harvest.PrescriptionName");
if (!Disturbed[site]) // this is the first cohort killed/damaged
{
HarvestEffects.ReduceLayers(SiteVars.HarvestPrescriptionName[site], site);
}
woodInput -= woodInput * (float)HarvestEffects.GetCohortWoodRemoval(site);
foliarInput -= foliarInput * (float)HarvestEffects.GetCohortLeafRemoval(site);
}
if (disturbanceType.IsMemberOf("disturbance:fire"))
{
SiteVars.FireSeverity = PlugIn.ModelCore.GetSiteVar <byte>("Fire.Severity");
if (!Disturbed[site]) // this is the first cohort killed/damaged
{
SiteVars.SmolderConsumption[site] = 0.0;
SiteVars.FlamingConsumption[site] = 0.0;
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;
SiteVars.SmolderConsumption[site] += woodFireConsumption;
SiteVars.FlamingConsumption[site] += foliarFireConsumption;
woodInput -= (float)woodFireConsumption;
foliarInput -= (float)foliarFireConsumption;
}
ForestFloor.AddWoodLitter(woodInput, cohort.Species, site);
ForestFloor.AddFoliageLitter(foliarInput, cohort.Species, site);
Roots.AddCoarseRootLitter(Roots.CalculateCoarseRoot(cohort, cohort.WoodBiomass * fractionPartialMortality), cohort, cohort.Species, site);
Roots.AddFineRootLitter(Roots.CalculateFineRoot(cohort, cohort.LeafBiomass * fractionPartialMortality), 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}.", HarvestEffects.GetCohortLeafRemoval(site), HarvestEffects.GetCohortLeafRemoval(site));
//PlugIn.ModelCore.UI.WriteLine(" InputB/TotalB: Foliar={0:0.00}/{1:0.00}, Wood={2:0.0}/{3:0.0}.", foliarInput, cohort.LeafBiomass, woodInput, cohort.WoodBiomass);
Disturbed[site] = true;
return;
}
//---------------------------------------------------------------------
// Outmoded but required?
public static void SiteDisturbed(object sender,
Landis.Library.BiomassCohorts.DisturbanceEventArgs eventArgs)
{
PlugIn.ModelCore.UI.WriteLine(" Calculating Fire or Harvest Effects.");
ExtensionType disturbanceType = eventArgs.DisturbanceType;
ActiveSite site = eventArgs.Site;
if (disturbanceType.IsMemberOf("disturbance:fire"))
{
SiteVars.FireSeverity = PlugIn.ModelCore.GetSiteVar <byte>("Fire.Severity");
if (SiteVars.FireSeverity != null && SiteVars.FireSeverity[site] > 0)
{
FireEffects.ReduceLayers(SiteVars.FireSeverity[site], site);
}
}
if (disturbanceType.IsMemberOf("disturbance:harvest"))
{
HarvestEffects.ReduceLayers(SiteVars.HarvestPrescriptionName[site], 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)
{
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, Main.Month + 1, ecoregion.Index, cohort.Species.Name, cohort.Age, cohort.WoodBiomass, cohort.LeafBiomass);
}
double siteBiomass = Main.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 *******
double[] actualANPP = ComputeActualANPP(cohort, site, siteBiomass, mortalityAge);
// Growth-related mortality
double[] mortalityGrowth = ComputeGrowthMortality(cohort, site, siteBiomass, actualANPP);
double[] totalMortality = new double[2] {
Math.Min(cohort.WoodBiomass, mortalityAge[0] + mortalityGrowth[0]), Math.Min(cohort.LeafBiomass, mortalityAge[1] + mortalityGrowth[1])
};
double nonDisturbanceLeafFall = totalMortality[1];
double scorch = 0.0;
defoliatedLeafBiomass = 0.0;
if (Main.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
{
//defoliation = Landis.Library.LeafBiomassCohorts.CohortDefoliation.Compute(cohort, site, (int)siteBiomass);
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];
}
//PlugIn.ModelCore.UI.WriteLine("Defoliation.Month={0:0.0}, LeafBiomass={1:0.00}, DefoliatedLeafBiomass={2:0.00}, TotalLeafMort={2:0.00}", Main.Month, cohort.LeafBiomass, defoliatedLeafBiomass , mortalityAge[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
};
//if((totalMortality[1] + defoliatedLeafBiomass) > cohort.LeafBiomass)
// PlugIn.ModelCore.UI.WriteLine("Warning: Leaf Mortality exceeds cohort leaf biomass. M={0:0.0}, B={1:0.0}, DefoLeafBiomass={2:0.0}, defoliationIndex={3:0.0}", totalMortality[1], cohort.LeafBiomass, defoliatedLeafBiomass, defoliation);
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]);
//Outputs.CalibrateLog.WriteLine("{0:0.00}, {1:0.00}, {2:0.00}", resorbedNused, mineralNused, totalNdemand);
}
return(deltas);
}
//---------------------------------------------------------------------
public override void Initialize()
{
PlugIn.ModelCore.UI.WriteLine("Initializing {0} ...", ExtensionName);
Timestep = Parameters.Timestep;
SuccessionTimeStep = Timestep;
sufficientLight = Parameters.LightClassProbabilities;
ProbEstablishAdjust = Parameters.ProbEstablishAdjustment;
MetadataHandler.InitializeMetadata(Timestep, modelCore, SoilCarbonMapNames, SoilNitrogenMapNames, ANPPMapNames, ANEEMapNames, TotalCMapNames); //,LAIMapNames, ShadeClassMapNames);
//Initialize climate.
Climate.Initialize(Parameters.ClimateConfigFile, false, modelCore);
FutureClimateBaseYear = Climate.Future_MonthlyData.Keys.Min();
ClimateRegionData.Initialize(Parameters);
FunctionalType.Initialize(Parameters);
SpeciesData.Initialize(Parameters);
Util.ReadSoilDepthMap(Parameters.SoilDepthMapName);
Util.ReadSoilDrainMap(Parameters.SoilDrainMapName);
Util.ReadSoilBaseFlowMap(Parameters.SoilBaseFlowMapName);
Util.ReadSoilStormFlowMap(Parameters.SoilStormFlowMapName);
Util.ReadFieldCapacityMap(Parameters.SoilFieldCapacityMapName);
Util.ReadWiltingPointMap(Parameters.SoilWiltingPointMapName);
Util.ReadPercentSandMap(Parameters.SoilPercentSandMapName);
Util.ReadPercentClayMap(Parameters.SoilPercentClayMapName);
Util.ReadSoilCNMaps(Parameters.InitialSOM1CSurfaceMapName,
Parameters.InitialSOM1NSurfaceMapName,
Parameters.InitialSOM1CSoilMapName,
Parameters.InitialSOM1NSoilMapName,
Parameters.InitialSOM2CMapName,
Parameters.InitialSOM2NMapName,
Parameters.InitialSOM3CMapName,
Parameters.InitialSOM3NMapName);
Util.ReadDeadWoodMaps(Parameters.InitialDeadSurfaceMapName, Parameters.InitialDeadSoilMapName);
ShadeLAI = Parameters.MaximumShadeLAI;
OtherData.Initialize(Parameters);
FireEffects.Initialize(Parameters);
// Cohorts must be created before the base class is initialized
// because the base class' reproduction module uses the core's
// SuccessionCohorts property in its Initialization method.
Library.LeafBiomassCohorts.Cohorts.Initialize(Timestep, new CohortBiomass());
// Initialize Reproduction routines:
Reproduction.SufficientResources = SufficientLight;
Reproduction.Establish = Establish;
Reproduction.AddNewCohort = AddNewCohort;
Reproduction.MaturePresent = MaturePresent;
base.Initialize(modelCore, Parameters.SeedAlgorithm);
// Delegate mortality routines:
Landis.Library.LeafBiomassCohorts.Cohort.PartialDeathEvent += CohortPartialMortality;
Landis.Library.LeafBiomassCohorts.Cohort.DeathEvent += CohortTotalMortality;
InitializeSites(Parameters.InitialCommunities, Parameters.InitialCommunitiesMap, modelCore);
if (Parameters.CalibrateMode)
{
Outputs.CreateCalibrateLogFile();
}
Establishment.InitializeLogFile();
B_MAX = 0;
foreach (ISpecies species in ModelCore.Species)
{
if (SpeciesData.Max_Biomass[species] > B_MAX)
{
B_MAX = SpeciesData.Max_Biomass[species];
}
}
foreach (ActiveSite site in PlugIn.ModelCore.Landscape)
{
Main.ComputeTotalCohortCN(site, SiteVars.Cohorts[site]);
}
Outputs.WritePrimaryLogFile(0);
Outputs.WriteShortPrimaryLogFile(0);
}
//---------------------------------------------------------------------
// Total mortality, including from disturbance or senescence.
public void CohortTotalMortality(object sender, Landis.Library.BiomassCohorts.DeathEventArgs eventArgs)
{
//PlugIn.ModelCore.UI.WriteLine("Cohort Total Mortality: {0}", eventArgs.Site);
ExtensionType disturbanceType = eventArgs.DisturbanceType;
ActiveSite site = eventArgs.Site;
ICohort cohort = (Landis.Library.LeafBiomassCohorts.ICohort)eventArgs.Cohort;
double foliarInput = (double)cohort.LeafBiomass;
double woodInput = (double)cohort.WoodBiomass;
if (disturbanceType != null)
{
//PlugIn.ModelCore.UI.WriteLine("DISTURBANCE EVENT: Cohort Died: species={0}, age={1}, disturbance={2}.", cohort.Species.Name, cohort.Age, eventArgs.DisturbanceType);
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
{
SiteVars.SmolderConsumption[site] = 0.0;
SiteVars.FlamingConsumption[site] = 0.0;
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;
SiteVars.SmolderConsumption[site] += woodFireConsumption;
SiteVars.FlamingConsumption[site] += foliarFireConsumption;
woodInput -= (float)woodFireConsumption;
foliarInput -= (float)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 -= woodInput * (float)HarvestEffects.GetCohortWoodRemoval(site);
foliarInput -= 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.AddWoodLitter(woodInput, cohort.Species, eventArgs.Site);
ForestFloor.AddFoliageLitter(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;
}
