//---------------------------------------------------------------------
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);
CohortBiomass.SpinupMortalityFraction = parameters.SpinupMortalityFraction;
//Initialize climate.
Climate.Initialize(parameters.ClimateConfigFile, false, modelCore);
FutureClimateBaseYear = Climate.Future_MonthlyData.Keys.Min();
EcoregionData.Initialize(parameters);
SpeciesData.Initialize(parameters);
EcoregionData.ChangeParameters(parameters);
OtherData.Initialize(parameters);
FunctionalType.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);
InitialBiomass.Initialize(Timestep);
Landis.Library.BiomassCohorts.Cohort.DeathEvent += CohortDied;
Landis.Library.LeafBiomassCohorts.Cohort.PartialDeathEvent += CohortPartialMortality;
AgeOnlyDisturbances.Module.Initialize(parameters.AgeOnlyDisturbanceParms);
Dynamic.Module.Initialize(parameters.DynamicUpdates);
FireEffects.Initialize(parameters);
InitializeSites(parameters.InitialCommunities, parameters.InitialCommunitiesMap, modelCore); //the spinup is heppend within this fucntion
if (parameters.CalibrateMode)
{
Outputs.CreateCalibrateLogFile();
}
Outputs.WritePrimaryLogFile(0);
Outputs.WriteShortPrimaryLogFile(0);
}
/// <summary>
/// Grows all cohorts at a site for a specified number of years.
/// Litter is decomposed following growth.
/// </summary>
public static ISiteCohorts Run(ActiveSite site,
int years,
bool isSuccessionTimeStep)
{
ISiteCohorts siteCohorts = SiteVars.Cohorts[site];
IEcoregion ecoregion = PlugIn.ModelCore.Ecoregion[site];
for (int y = 0; y < years; ++y)
{
Year = y + 1;
if (PlugIn.ModelCore.CurrentTime > 0 && Climate.Future_MonthlyData.ContainsKey(PlugIn.FutureClimateBaseYear + y + PlugIn.ModelCore.CurrentTime - years))
{
EcoregionData.AnnualWeather[ecoregion] = Climate.Future_MonthlyData[PlugIn.FutureClimateBaseYear + y - years + PlugIn.ModelCore.CurrentTime][ecoregion.Index];
}
SiteVars.ResetAnnualValues(site);
if (y == 0 && SiteVars.FireSeverity != null && SiteVars.FireSeverity[site] > 0)
{
FireEffects.ReduceLayers(SiteVars.FireSeverity[site], site);
}
// Next, Grow and Decompose each month
int[] months = new int[12] {
6, 7, 8, 9, 10, 11, 0, 1, 2, 3, 4, 5
};
if (OtherData.CalibrateMode)
{
months = new int[12] {
6, 7, 8, 9, 10, 11, 0, 1, 2, 3, 4, 5
}
}
;
for (MonthCnt = 0; MonthCnt < 12; MonthCnt++)
{
// Calculate mineral N fractions based on coarse root biomass
if (MonthCnt == 0)
{
AvailableN.CalculateMineralNfraction(site);
}
//PlugIn.ModelCore.UI.WriteLine("SiteVars.MineralN = {0:0.00}, month = {1}.", SiteVars.MineralN[site], i);
Month = months[MonthCnt];
SiteVars.MonthlyAGNPPcarbon[site][Month] = 0.0;
SiteVars.MonthlyBGNPPcarbon[site][Month] = 0.0;
SiteVars.MonthlyNEE[site][Month] = 0.0;
SiteVars.MonthlyResp[site][Month] = 0.0;
SiteVars.MonthlyStreamN[site][Month] = 0.0;
SiteVars.SourceSink[site].Carbon = 0.0;
SiteVars.TotalWoodBiomass[site] = Main.ComputeWoodBiomass((ActiveSite)site);
//SiteVars.LAI[site] = Main.ComputeLAI((ActiveSite)site);
double ppt = EcoregionData.AnnualWeather[ecoregion].MonthlyPrecip[Main.Month];
double monthlyNdeposition;
if (EcoregionData.AtmosNintercept[ecoregion] != -1 && EcoregionData.AtmosNslope[ecoregion] != -1)
{
monthlyNdeposition = EcoregionData.AtmosNintercept[ecoregion] + (EcoregionData.AtmosNslope[ecoregion] * ppt);
}
else
{
monthlyNdeposition = EcoregionData.AnnualWeather[ecoregion].MonthlyNDeposition[Main.Month];
}
if (monthlyNdeposition < 0)
{
throw new System.ApplicationException("Error: Nitrogen deposition input data are not present in climate library");
}
EcoregionData.MonthlyNDeposition[ecoregion][Month] = monthlyNdeposition;
EcoregionData.AnnualNDeposition[ecoregion] += monthlyNdeposition;
SiteVars.MineralN[site] += monthlyNdeposition;
//PlugIn.ModelCore.UI.WriteLine("Ndeposition={0},MineralN={1:0.00}.", monthlyNdeposition, SiteVars.MineralN[site]);
double liveBiomass = (double)ComputeLivingBiomass(siteCohorts);
double baseFlow, stormFlow;
SoilWater.Run(y, Month, liveBiomass, site, out baseFlow, out stormFlow);
// Calculate N allocation for each cohort
AvailableN.SetMineralNallocation(site);
if (MonthCnt == 11)
{
siteCohorts.Grow(site, (y == years && isSuccessionTimeStep), true);
}
else
{
siteCohorts.Grow(site, (y == years && isSuccessionTimeStep), false);
}
WoodLayer.Decompose(site);
LitterLayer.Decompose(site);
SoilLayer.Decompose(site);
//...Volatilization loss as a function of the mineral n which
// remains after uptake by plants. ML added a correction factor for wetlands since their denitrification rate is double that of wetlands
//based on a review paper by Seitziner 2006.
double volatilize = (SiteVars.MineralN[site] * EcoregionData.Denitrif[ecoregion]); // monthly value
//PlugIn.ModelCore.UI.WriteLine("BeforeVol. MineralN={0:0.00}.", SiteVars.MineralN[site]);
SiteVars.MineralN[site] -= volatilize;
SiteVars.SourceSink[site].Nitrogen += volatilize;
SiteVars.Nvol[site] += volatilize;
SoilWater.Leach(site, baseFlow, stormFlow);
SiteVars.MonthlyNEE[site][Month] -= SiteVars.MonthlyAGNPPcarbon[site][Month];
SiteVars.MonthlyNEE[site][Month] -= SiteVars.MonthlyBGNPPcarbon[site][Month];
SiteVars.MonthlyNEE[site][Month] += SiteVars.SourceSink[site].Carbon;
}
}
ComputeTotalCohortCN(site, siteCohorts);
return(siteCohorts);
}
//---------------------------------------------------------------------
/// <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-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])
};
double nonDisturbanceLeafFall = totalMortality[1];
// ****** Growth *******
double[] actualANPP = ComputeActualANPP(cohort, site, siteBiomass, mortalityAge);
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
{
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);
}