//--------------------------------------------------------------------- /// <summary> /// Computes the initial biomass for a cohort at a site. /// </summary> public static float[] InitialBiomass(ISpecies species, ISiteCohorts siteCohorts, ActiveSite site) { IEcoregion ecoregion = PlugIn.ModelCore.Ecoregion[site]; double leafFrac = FunctionalType.Table[SpeciesData.FuncType[species]].FCFRACleaf; double B_ACT = SiteVars.ActualSiteBiomass(site); double B_MAX = SpeciesData.B_MAX_Spp[species][ecoregion]; // Initial biomass exponentially declines in response to // competition. double initialBiomass = 0.002 * B_MAX * Math.Exp(-1.6 * B_ACT / B_MAX); initialBiomass = Math.Max(initialBiomass, 5.0); double initialLeafB = initialBiomass * leafFrac; double initialWoodB = initialBiomass - initialLeafB; double[] initialB = new double[2] { initialWoodB, initialLeafB }; float[] initialWoodLeafBiomass = new float[2] { (float)initialB[0], (float)initialB[1] }; return(initialWoodLeafBiomass); }
//--------------------------------------------------------------------- public override void LoadParameters(string dataFile, ICore mCore) { modelCore = mCore; SiteVars.Initialize(); InputParametersParser parser = new InputParametersParser(); parameters = Landis.Data.Load <IInputParameters>(dataFile, parser); }
/// <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); }
//--------------------------------------------------------------------- public override void Run() { if (PlugIn.ModelCore.CurrentTime > 0) { SiteVars.InitializeDisturbances(); } // Update Pest only once. SpeciesData.EstablishProbability = Establishment.GenerateNewEstablishProbabilities(Timestep); EcoregionData.AnnualNDeposition = new Ecoregions.AuxParm <double>(PlugIn.ModelCore.Ecoregions); base.RunReproductionFirst(); if (ModelCore.CurrentTime % Timestep == 0) { // Write monthly log file: // Output must reflect the order of operation: 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 (int i = 0; i < 12; i++) { int month = months[i]; Outputs.WriteMonthlyLogFile(month); } Outputs.WritePrimaryLogFile(PlugIn.ModelCore.CurrentTime); Outputs.WriteShortPrimaryLogFile(PlugIn.ModelCore.CurrentTime); string pathH2O = MapNames.ReplaceTemplateVars(@"NECN_Hydro\Annual-water-budget-{timestep}.img", PlugIn.ModelCore.CurrentTime); using (IOutputRaster <IntPixel> outputRaster = PlugIn.ModelCore.CreateRaster <IntPixel>(pathH2O, PlugIn.ModelCore.Landscape.Dimensions)) { IntPixel pixel = outputRaster.BufferPixel; foreach (Site site in PlugIn.ModelCore.Landscape.AllSites) { if (site.IsActive) { pixel.MapCode.Value = (int)((SiteVars.AnnualPPT_AET[site])); } else { // Inactive site pixel.MapCode.Value = 0; } outputRaster.WriteBufferPixel(); } } if (SoilCarbonMapNames != null)// && (PlugIn.ModelCore.CurrentTime % SoilCarbonMapFrequency) == 0) { string path = MapNames.ReplaceTemplateVars(SoilCarbonMapNames, PlugIn.ModelCore.CurrentTime); using (IOutputRaster <IntPixel> outputRaster = modelCore.CreateRaster <IntPixel>(path, modelCore.Landscape.Dimensions)) { IntPixel pixel = outputRaster.BufferPixel; foreach (Site site in PlugIn.ModelCore.Landscape.AllSites) { if (site.IsActive) { pixel.MapCode.Value = (int)((SiteVars.SOM1surface[site].Carbon + SiteVars.SOM1soil[site].Carbon + SiteVars.SOM2[site].Carbon + SiteVars.SOM3[site].Carbon)); } else { // Inactive site pixel.MapCode.Value = 0; } outputRaster.WriteBufferPixel(); } } } if (SoilNitrogenMapNames != null)// && (PlugIn.ModelCore.CurrentTime % SoilNitrogenMapFrequency) == 0) { string path2 = MapNames.ReplaceTemplateVars(SoilNitrogenMapNames, PlugIn.ModelCore.CurrentTime); using (IOutputRaster <ShortPixel> outputRaster = modelCore.CreateRaster <ShortPixel>(path2, modelCore.Landscape.Dimensions)) { ShortPixel pixel = outputRaster.BufferPixel; foreach (Site site in PlugIn.ModelCore.Landscape.AllSites) { if (site.IsActive) { pixel.MapCode.Value = (short)(SiteVars.MineralN[site]); } else { // Inactive site pixel.MapCode.Value = 0; } outputRaster.WriteBufferPixel(); } } } if (ANPPMapNames != null)// && (PlugIn.ModelCore.CurrentTime % ANPPMapFrequency) == 0) { string path3 = MapNames.ReplaceTemplateVars(ANPPMapNames, PlugIn.ModelCore.CurrentTime); using (IOutputRaster <ShortPixel> outputRaster = modelCore.CreateRaster <ShortPixel>(path3, modelCore.Landscape.Dimensions)) { ShortPixel pixel = outputRaster.BufferPixel; foreach (Site site in PlugIn.ModelCore.Landscape.AllSites) { if (site.IsActive) { pixel.MapCode.Value = (short)SiteVars.AGNPPcarbon[site]; } else { // Inactive site pixel.MapCode.Value = 0; } outputRaster.WriteBufferPixel(); } } } if (ANEEMapNames != null)// && (PlugIn.ModelCore.CurrentTime % ANEEMapFrequency) == 0) { string path4 = MapNames.ReplaceTemplateVars(ANEEMapNames, PlugIn.ModelCore.CurrentTime); using (IOutputRaster <ShortPixel> outputRaster = modelCore.CreateRaster <ShortPixel>(path4, modelCore.Landscape.Dimensions)) { ShortPixel pixel = outputRaster.BufferPixel; foreach (Site site in PlugIn.ModelCore.Landscape.AllSites) { if (site.IsActive) { pixel.MapCode.Value = (short)(SiteVars.AnnualNEE[site] + 1000); } else { // Inactive site pixel.MapCode.Value = 0; } outputRaster.WriteBufferPixel(); } } } if (TotalCMapNames != null)// && (PlugIn.ModelCore.CurrentTime % TotalCMapFrequency) == 0) { string path5 = MapNames.ReplaceTemplateVars(TotalCMapNames, PlugIn.ModelCore.CurrentTime); using (IOutputRaster <IntPixel> outputRaster = modelCore.CreateRaster <IntPixel>(path5, modelCore.Landscape.Dimensions)) { IntPixel pixel = outputRaster.BufferPixel; foreach (Site site in PlugIn.ModelCore.Landscape.AllSites) { if (site.IsActive) { pixel.MapCode.Value = (int)(Outputs.GetOrganicCarbon(site) + SiteVars.CohortLeafC[site] + SiteVars.CohortFRootC[site] + SiteVars.CohortWoodC[site] + SiteVars.CohortCRootC[site] + SiteVars.SurfaceDeadWood[site].Carbon + SiteVars.SoilDeadWood[site].Carbon); } else { // Inactive site pixel.MapCode.Value = 0; } outputRaster.WriteBufferPixel(); } } } } }