//--------------------------------------------------------------------- /// <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); }
/// <summary> /// Grows all cohorts at a site for a specified number of years. /// Litter is decomposed following the Century model. /// </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 (Climate.Future_MonthlyData.ContainsKey(PlugIn.FutureClimateBaseYear + y + PlugIn.ModelCore.CurrentTime - years)) { ClimateRegionData.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]{0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11}; This output will not match normal mode due to differences in initialization months = new int[12] { 6, 7, 8, 9, 10, 11, 0, 1, 2, 3, 4, 5 } } ; PlugIn.AnnualWaterBalance = 0; for (MonthCnt = 0; MonthCnt < 12; MonthCnt++) { // Calculate mineral N fractions based on coarse root biomass. Only need to do once per year. if (MonthCnt == 0) { AvailableN.CalculateMineralNfraction(site); } 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] = Century.ComputeWoodBiomass(site); double ppt = ClimateRegionData.AnnualWeather[ecoregion].MonthlyPrecip[Century.Month]; double monthlyNdeposition; if (PlugIn.AtmosNintercept != -1 && PlugIn.AtmosNslope != -1) { monthlyNdeposition = PlugIn.AtmosNintercept + (PlugIn.AtmosNslope * ppt); } else { monthlyNdeposition = ClimateRegionData.AnnualWeather[ecoregion].MonthlyNDeposition[Century.Month]; } ClimateRegionData.MonthlyNDeposition[ecoregion][Month] = monthlyNdeposition; ClimateRegionData.AnnualNDeposition[ecoregion] += monthlyNdeposition; SiteVars.MineralN[site] += monthlyNdeposition; double liveBiomass = (double)ComputeLivingBiomass(siteCohorts); double baseFlow, stormFlow, AET; SoilWater.Run(y, Month, liveBiomass, site, out baseFlow, out stormFlow, out AET); PlugIn.AnnualWaterBalance += ppt - AET; // 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] * PlugIn.DenitrificationRate); 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; SiteVars.FineFuels[site] = (SiteVars.SurfaceStructural[site].Carbon + SiteVars.SurfaceMetabolic[site].Carbon) * 2.0; } } ComputeTotalCohortCN(site, siteCohorts); return(siteCohorts); }
//--------------------------------------------------------------------- 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); //CohortBiomass.SpinupMortalityFraction = parameters.SpinupMortalityFraction; //Initialize climate. Climate.Initialize(parameters.ClimateConfigFile, false, modelCore); FutureClimateBaseYear = Climate.Future_MonthlyData.Keys.Min(); ClimateRegionData.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); AtmosNslope = parameters.AtmosNslope; AtmosNintercept = parameters.AtmosNintercept; Latitude = parameters.Latitude; DenitrificationRate = parameters.Denitrif; DecayRateSurf = parameters.DecayRateSurf; DecayRateSOM1 = parameters.DecayRateSOM1; DecayRateSOM2 = parameters.DecayRateSOM2; DecayRateSOM3 = parameters.DecayRateSOM3; ShadeLAI = parameters.MaximumShadeLAI; //.MinRelativeBiomass; OtherData.Initialize(parameters); FunctionalType.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); Landis.Library.LeafBiomassCohorts.Cohort.PartialDeathEvent += CohortPartialMortality; Landis.Library.BiomassCohorts.Cohort.DeathEvent += CohortDied; AgeOnlyDisturbances.Module.Initialize(parameters.AgeOnlyDisturbanceParms); //InitialBiomass.Initialize(Timestep); 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) { Century.ComputeTotalCohortCN(site, SiteVars.Cohorts[site]); } Outputs.WritePrimaryLogFile(0); Outputs.WriteShortPrimaryLogFile(0); }