//---------------------------------------------------------------------
public static void WriteShortPrimaryLogFile(int CurrentTime)
{
double avgNEEc = 0.0;
double avgSOMtc = 0.0;
double avgAGB = 0.0;
double avgAGNPPtc = 0.0;
double avgMineralN = 0.0;
double avgDeadWoodC = 0.0;
foreach (ActiveSite site in PlugIn.ModelCore.Landscape)
{
avgNEEc += SiteVars.AnnualNEE[site] / PlugIn.ModelCore.Landscape.ActiveSiteCount;
avgSOMtc += GetOrganicCarbon(site) / PlugIn.ModelCore.Landscape.ActiveSiteCount;
avgAGB += Century.ComputeLivingBiomass(SiteVars.Cohorts[site]) / PlugIn.ModelCore.Landscape.ActiveSiteCount;
avgAGNPPtc += SiteVars.AGNPPcarbon[site] / PlugIn.ModelCore.Landscape.ActiveSiteCount;
avgMineralN += SiteVars.MineralN[site] / PlugIn.ModelCore.Landscape.ActiveSiteCount;
avgDeadWoodC += SiteVars.SurfaceDeadWood[site].Carbon / PlugIn.ModelCore.Landscape.ActiveSiteCount;
}
primaryLogShort.Clear();
PrimaryLogShort pl = new PrimaryLogShort();
pl.Time = CurrentTime;
pl.NEEC = avgNEEc;
pl.SOMTC = avgSOMtc;
pl.AGB = avgAGB;
pl.AG_NPPC = avgAGNPPtc;
pl.MineralN = avgMineralN;
pl.C_DeadWood = avgDeadWoodC;
primaryLogShort.AddObject(pl);
primaryLogShort.WriteToFile();
}
//---------------------------------------------------------------------
public static void WritePrimaryLogFile(int CurrentTime)
{
//PlugIn.SWHC_List.Sort();
//int soil_count = PlugIn.SWHC_List.Count;
//PlugIn.ModelCore.UI.WriteLine("soil count = {0}", soil_count);
double[] avgAnnualPPT = new double[PlugIn.ModelCore.Ecoregions.Count];
double[] avgJJAtemp = new double[PlugIn.ModelCore.Ecoregions.Count];
double[] avgNEEc = new double[PlugIn.ModelCore.Ecoregions.Count];
double[] avgSOMtc = new double[PlugIn.ModelCore.Ecoregions.Count];
double[] avgAGB = new double[PlugIn.ModelCore.Ecoregions.Count];
double[] avgAGNPPtc = new double[PlugIn.ModelCore.Ecoregions.Count];
double[] avgBGNPPtc = new double[PlugIn.ModelCore.Ecoregions.Count];
double[] avgLittertc = new double[PlugIn.ModelCore.Ecoregions.Count];
double[] avgWoodMortality = new double[PlugIn.ModelCore.Ecoregions.Count];
double[] avgMineralN = new double[PlugIn.ModelCore.Ecoregions.Count];
double[] avgGrossMin = new double[PlugIn.ModelCore.Ecoregions.Count];
double[] avgTotalN = new double[PlugIn.ModelCore.Ecoregions.Count];
double[] avgCohortLeafC = new double[PlugIn.ModelCore.Ecoregions.Count];
double[] avgCohortFRootC = new double[PlugIn.ModelCore.Ecoregions.Count];
double[] avgCohortWoodC = new double[PlugIn.ModelCore.Ecoregions.Count];
double[] avgWoodC = new double[PlugIn.ModelCore.Ecoregions.Count];
double[] avgCohortCRootC = new double[PlugIn.ModelCore.Ecoregions.Count];
double[] avgCRootC = new double[PlugIn.ModelCore.Ecoregions.Count];
double[] avgCohortLeafN = new double[PlugIn.ModelCore.Ecoregions.Count];
double[] avgCohortFRootN = new double[PlugIn.ModelCore.Ecoregions.Count];
double[] avgCohortWoodN = new double[PlugIn.ModelCore.Ecoregions.Count];
double[] avgCohortCRootN = new double[PlugIn.ModelCore.Ecoregions.Count];
double[] avgWoodN = new double[PlugIn.ModelCore.Ecoregions.Count];
double[] avgCRootN = new double[PlugIn.ModelCore.Ecoregions.Count];
double[] avgSurfStrucC = new double[PlugIn.ModelCore.Ecoregions.Count];
double[] avgSurfMetaC = new double[PlugIn.ModelCore.Ecoregions.Count];
double[] avgSoilStrucC = new double[PlugIn.ModelCore.Ecoregions.Count];
double[] avgSoilMetaC = new double[PlugIn.ModelCore.Ecoregions.Count];
double[] avgSurfStrucN = new double[PlugIn.ModelCore.Ecoregions.Count];
double[] avgSurfMetaN = new double[PlugIn.ModelCore.Ecoregions.Count];
double[] avgSoilStrucN = new double[PlugIn.ModelCore.Ecoregions.Count];
double[] avgSoilMetaN = new double[PlugIn.ModelCore.Ecoregions.Count];
double[] avgSurfStrucNetMin = new double[PlugIn.ModelCore.Ecoregions.Count];
double[] avgSurfMetaNetMin = new double[PlugIn.ModelCore.Ecoregions.Count];
double[] avgSoilStrucNetMin = new double[PlugIn.ModelCore.Ecoregions.Count];
double[] avgSoilMetaNetMin = new double[PlugIn.ModelCore.Ecoregions.Count];
double[] avgSOM1surfC = new double[PlugIn.ModelCore.Ecoregions.Count];
double[] avgSOM1soilC = new double[PlugIn.ModelCore.Ecoregions.Count];
double[] avgSOM2C = new double[PlugIn.ModelCore.Ecoregions.Count];
double[] avgSOM3C = new double[PlugIn.ModelCore.Ecoregions.Count];
double[] avgSOM1surfN = new double[PlugIn.ModelCore.Ecoregions.Count];
double[] avgSOM1soilN = new double[PlugIn.ModelCore.Ecoregions.Count];
double[] avgSOM2N = new double[PlugIn.ModelCore.Ecoregions.Count];
double[] avgSOM3N = new double[PlugIn.ModelCore.Ecoregions.Count];
double[] avgSOM1surfNetMin = new double[PlugIn.ModelCore.Ecoregions.Count];
double[] avgSOM1soilNetMin = new double[PlugIn.ModelCore.Ecoregions.Count];
double[] avgSOM2NetMin = new double[PlugIn.ModelCore.Ecoregions.Count];
double[] avgSOM3NetMin = new double[PlugIn.ModelCore.Ecoregions.Count];
//doubl[] avgNDeposition = new double[PlugIn.ModelCore.Ecoregions.Count];
double[] avgStreamC = new double[PlugIn.ModelCore.Ecoregions.Count];
double[] avgStreamN = new double[PlugIn.ModelCore.Ecoregions.Count];
double[] avgFireCEfflux = new double[PlugIn.ModelCore.Ecoregions.Count];
double[] avgFireNEfflux = new double[PlugIn.ModelCore.Ecoregions.Count];
double[] avgNvol = new double[PlugIn.ModelCore.Ecoregions.Count];
double[] avgNresorbed = new double[PlugIn.ModelCore.Ecoregions.Count];
double[] avgTotalSoilN = new double[PlugIn.ModelCore.Ecoregions.Count];
double[] avgNuptake = new double[PlugIn.ModelCore.Ecoregions.Count];
double[] avgfrassC = new double[PlugIn.ModelCore.Ecoregions.Count];
double[] avglai = new double[PlugIn.ModelCore.Ecoregions.Count];
//int swhc_cnt = 0;
foreach (IEcoregion ecoregion in PlugIn.ModelCore.Ecoregions)
{
//foreach (int swhc in PlugIn.SWHC_List)
//{
//int swhc_index = PlugIn.SWHC_List.BinarySearch(swhc);
//PlugIn.ModelCore.UI.WriteLine("SHWC Index = {0}", swhc_index);
//PlugIn.ModelCore.UI.WriteLine("SHWC = {0}", swhc);
// TO DO: ADD SWHC LOOP
avgAnnualPPT[ecoregion.Index] = 0.0;
avgJJAtemp[ecoregion.Index] = 0.0;
avgNEEc[ecoregion.Index] = 0.0;
avgSOMtc[ecoregion.Index] = 0.0;
avgAGB[ecoregion.Index] = 0.0;
avgAGNPPtc[ecoregion.Index] = 0.0;
avgBGNPPtc[ecoregion.Index] = 0.0;
avgLittertc[ecoregion.Index] = 0.0;
avgWoodMortality[ecoregion.Index] = 0.0;
avgMineralN[ecoregion.Index] = 0.0;
avgGrossMin[ecoregion.Index] = 0.0;
avgTotalN[ecoregion.Index] = 0.0;
avgCohortLeafC[ecoregion.Index] = 0.0;
avgCohortFRootC[ecoregion.Index] = 0.0;
avgCohortWoodC[ecoregion.Index] = 0.0;
avgCohortCRootC[ecoregion.Index] = 0.0;
avgWoodC[ecoregion.Index] = 0.0;
avgCRootC[ecoregion.Index] = 0.0;
avgSurfStrucC[ecoregion.Index] = 0.0;
avgSurfMetaC[ecoregion.Index] = 0.0;
avgSoilStrucC[ecoregion.Index] = 0.0;
avgSoilMetaC[ecoregion.Index] = 0.0;
avgCohortLeafN[ecoregion.Index] = 0.0;
avgCohortFRootN[ecoregion.Index] = 0.0;
avgCohortWoodN[ecoregion.Index] = 0.0;
avgCohortCRootN[ecoregion.Index] = 0.0;
avgWoodN[ecoregion.Index] = 0.0;
avgCRootN[ecoregion.Index] = 0.0;
avgSurfStrucN[ecoregion.Index] = 0.0;
avgSurfMetaN[ecoregion.Index] = 0.0;
avgSoilStrucN[ecoregion.Index] = 0.0;
avgSoilMetaN[ecoregion.Index] = 0.0;
avgSurfStrucNetMin[ecoregion.Index] = 0.0;
avgSurfMetaNetMin[ecoregion.Index] = 0.0;
avgSoilStrucNetMin[ecoregion.Index] = 0.0;
avgSoilMetaNetMin[ecoregion.Index] = 0.0;
avgSOM1surfC[ecoregion.Index] = 0.0;
avgSOM1soilC[ecoregion.Index] = 0.0;
avgSOM2C[ecoregion.Index] = 0.0;
avgSOM3C[ecoregion.Index] = 0.0;
avgSOM1surfN[ecoregion.Index] = 0.0;
avgSOM1soilN[ecoregion.Index] = 0.0;
avgSOM2N[ecoregion.Index] = 0.0;
avgSOM3N[ecoregion.Index] = 0.0;
avgSOM1surfNetMin[ecoregion.Index] = 0.0;
avgSOM1soilNetMin[ecoregion.Index] = 0.0;
avgSOM2NetMin[ecoregion.Index] = 0.0;
avgSOM3NetMin[ecoregion.Index] = 0.0;
//avgNDeposition[ecoregion.Index] = 0.0;
avgStreamC[ecoregion.Index] = 0.0;
avgStreamN[ecoregion.Index] = 0.0;
avgFireCEfflux[ecoregion.Index] = 0.0;
avgFireNEfflux[ecoregion.Index] = 0.0;
avgNuptake[ecoregion.Index] = 0.0;
avgNresorbed[ecoregion.Index] = 0.0;
avgTotalSoilN[ecoregion.Index] = 0.0;
avgNvol[ecoregion.Index] = 0.0;
avgfrassC[ecoregion.Index] = 0.0;
//swhc_cnt++;
//}
}
//int[,] Climate_SWHC_Count = new int[PlugIn.ModelCore.Ecoregions.Count, PlugIn.SWHC_List.Count];
foreach (ActiveSite site in PlugIn.ModelCore.Landscape)
{
IEcoregion ecoregion = PlugIn.ModelCore.Ecoregion[site];
//int swhc = (int)((SiteVars.SoilFieldCapacity[site] - SiteVars.SoilWiltingPoint[site]) * SiteVars.SoilDepth[site]);
//int swhc_index = PlugIn.SWHC_List.BinarySearch(swhc);
//Climate_SWHC_Count[ecoregion.Index]++;
avgNEEc[ecoregion.Index] += SiteVars.AnnualNEE[site];
avgSOMtc[ecoregion.Index] += GetOrganicCarbon(site);
avgAGB[ecoregion.Index] += Century.ComputeLivingBiomass(SiteVars.Cohorts[site]);
avgAGNPPtc[ecoregion.Index] += SiteVars.AGNPPcarbon[site];
avgBGNPPtc[ecoregion.Index] += SiteVars.BGNPPcarbon[site];
avgLittertc[ecoregion.Index] += SiteVars.LitterfallC[site];
avgWoodMortality[ecoregion.Index] += SiteVars.WoodMortality[site] * 0.47;
avgMineralN[ecoregion.Index] += SiteVars.MineralN[site];
avgTotalN[ecoregion.Index] += GetTotalNitrogen(site);
avgGrossMin[ecoregion.Index] += SiteVars.GrossMineralization[site];
avgCohortLeafC[ecoregion.Index] += SiteVars.CohortLeafC[site];
avgCohortFRootC[ecoregion.Index] += SiteVars.CohortFRootC[site];
avgCohortWoodC[ecoregion.Index] += SiteVars.CohortWoodC[site];
avgCohortCRootC[ecoregion.Index] += SiteVars.CohortCRootC[site];
avgWoodC[ecoregion.Index] += SiteVars.SurfaceDeadWood[site].Carbon;
avgCRootC[ecoregion.Index] += SiteVars.SoilDeadWood[site].Carbon;
avgSurfStrucC[ecoregion.Index] += SiteVars.SurfaceStructural[site].Carbon;
avgSurfMetaC[ecoregion.Index] += SiteVars.SurfaceMetabolic[site].Carbon;
avgSoilStrucC[ecoregion.Index] += SiteVars.SoilStructural[site].Carbon;
avgSoilMetaC[ecoregion.Index] += SiteVars.SoilMetabolic[site].Carbon;
avgSOM1surfC[ecoregion.Index] += SiteVars.SOM1surface[site].Carbon;
avgSOM1soilC[ecoregion.Index] += SiteVars.SOM1soil[site].Carbon;
avgSOM2C[ecoregion.Index] += SiteVars.SOM2[site].Carbon;
avgSOM3C[ecoregion.Index] += SiteVars.SOM3[site].Carbon;
avgCohortLeafN[ecoregion.Index] += SiteVars.CohortLeafN[site];
avgCohortFRootN[ecoregion.Index] += SiteVars.CohortFRootN[site];
avgCohortWoodN[ecoregion.Index] += SiteVars.CohortWoodN[site];
avgCohortCRootN[ecoregion.Index] += SiteVars.CohortCRootN[site];
avgWoodN[ecoregion.Index] += SiteVars.SurfaceDeadWood[site].Nitrogen;
avgCRootN[ecoregion.Index] += SiteVars.SoilDeadWood[site].Nitrogen;
avgSurfStrucN[ecoregion.Index] += SiteVars.SurfaceStructural[site].Nitrogen;
avgSurfMetaN[ecoregion.Index] += SiteVars.SurfaceMetabolic[site].Nitrogen;
avgSoilStrucN[ecoregion.Index] += SiteVars.SoilStructural[site].Nitrogen;
avgSoilMetaN[ecoregion.Index] += SiteVars.SoilMetabolic[site].Nitrogen;
avgSOM1surfN[ecoregion.Index] += SiteVars.SOM1surface[site].Nitrogen;
avgSOM1soilN[ecoregion.Index] += SiteVars.SOM1soil[site].Nitrogen;
avgSOM2N[ecoregion.Index] += SiteVars.SOM2[site].Nitrogen;
avgSOM3N[ecoregion.Index] += SiteVars.SOM3[site].Nitrogen;
avgTotalSoilN[ecoregion.Index] += GetTotalSoilNitrogen(site);
avgSurfStrucNetMin[ecoregion.Index] += SiteVars.SurfaceStructural[site].NetMineralization;
avgSurfMetaNetMin[ecoregion.Index] += SiteVars.SurfaceMetabolic[site].NetMineralization;
avgSoilStrucNetMin[ecoregion.Index] += SiteVars.SoilStructural[site].NetMineralization;
avgSoilMetaNetMin[ecoregion.Index] += SiteVars.SoilMetabolic[site].NetMineralization;
avgSOM1surfNetMin[ecoregion.Index] += SiteVars.SOM1surface[site].NetMineralization;
avgSOM1soilNetMin[ecoregion.Index] += SiteVars.SOM1soil[site].NetMineralization;
avgSOM2NetMin[ecoregion.Index] += SiteVars.SOM2[site].NetMineralization;
avgSOM3NetMin[ecoregion.Index] += SiteVars.SOM3[site].NetMineralization;
//avgNDeposition[ecoregion.Index] = ClimateRegionData.AnnualNDeposition[ecoregion];
avgStreamC[ecoregion.Index] += SiteVars.Stream[site].Carbon;
avgStreamN[ecoregion.Index] += SiteVars.Stream[site].Nitrogen; //+ SiteVars.NLoss[site];
avgFireCEfflux[ecoregion.Index] += SiteVars.FireCEfflux[site];
avgFireNEfflux[ecoregion.Index] += SiteVars.FireNEfflux[site];
avgNresorbed[ecoregion.Index] += SiteVars.ResorbedN[site];
avgNuptake[ecoregion.Index] += GetSoilNuptake(site);
avgNvol[ecoregion.Index] += SiteVars.Nvol[site];
avgfrassC[ecoregion.Index] += SiteVars.FrassC[site];
}
foreach (IEcoregion ecoregion in PlugIn.ModelCore.Ecoregions)
{
if (!ecoregion.Active || ClimateRegionData.ActiveSiteCount[ecoregion] < 1)
{
continue;
}
primaryLog.Clear();
PrimaryLog pl = new PrimaryLog();
pl.Time = CurrentTime;
pl.ClimateRegionName = ecoregion.Name;
pl.ClimateRegionIndex = ecoregion.Index;
//foreach (int swhc in PlugIn.SWHC_List)
//{
// int swhc_index = PlugIn.SWHC_List.BinarySearch(swhc);
//pl.SoilWaterHoldingCapacity = swhc;
pl.NumSites = ClimateRegionData.ActiveSiteCount[ecoregion]; //Climate_SWHC_Count[ecoregion.Index]; // ClimateRegionData.ActiveSiteCount[ecoregion];
pl.NEEC = (avgNEEc[ecoregion.Index] / (double)ClimateRegionData.ActiveSiteCount[ecoregion]);
pl.SOMTC = (avgSOMtc[ecoregion.Index] / (double)ClimateRegionData.ActiveSiteCount[ecoregion]);
pl.AGB = (avgAGB[ecoregion.Index] / (double)ClimateRegionData.ActiveSiteCount[ecoregion]);
pl.AG_NPPC = (avgAGNPPtc[ecoregion.Index] / (double)ClimateRegionData.ActiveSiteCount[ecoregion]);
pl.BG_NPPC = (avgBGNPPtc[ecoregion.Index] / (double)ClimateRegionData.ActiveSiteCount[ecoregion]);
pl.Litterfall = (avgLittertc[ecoregion.Index] / (double)ClimateRegionData.ActiveSiteCount[ecoregion]);
pl.AgeMortality = (avgWoodMortality[ecoregion.Index] / (double)ClimateRegionData.ActiveSiteCount[ecoregion]);
pl.MineralN = (avgMineralN[ecoregion.Index] / (double)ClimateRegionData.ActiveSiteCount[ecoregion]);
pl.TotalN = (avgTotalN[ecoregion.Index] / (double)ClimateRegionData.ActiveSiteCount[ecoregion]);
pl.GrossMineralization = (avgGrossMin[ecoregion.Index] / (double)ClimateRegionData.ActiveSiteCount[ecoregion]);
pl.TotalNdep = (ClimateRegionData.AnnualNDeposition[ecoregion] / (double)ClimateRegionData.ActiveSiteCount[ecoregion]);
pl.C_Leaf = (avgCohortLeafC[ecoregion.Index] / (double)ClimateRegionData.ActiveSiteCount[ecoregion]);
pl.C_FRoot = (avgCohortFRootC[ecoregion.Index] / (double)ClimateRegionData.ActiveSiteCount[ecoregion]);
pl.C_Wood = (avgCohortWoodC[ecoregion.Index] / (double)ClimateRegionData.ActiveSiteCount[ecoregion]);
pl.C_CRoot = (avgCohortCRootC[ecoregion.Index] / (double)ClimateRegionData.ActiveSiteCount[ecoregion]);
pl.C_DeadWood = (avgWoodC[ecoregion.Index] / (double)ClimateRegionData.ActiveSiteCount[ecoregion]);
pl.C_DeadCRoot = (avgCRootC[ecoregion.Index] / (double)ClimateRegionData.ActiveSiteCount[ecoregion]);
pl.C_DeadLeaf_Struc = (avgSurfStrucC[ecoregion.Index] / (double)ClimateRegionData.ActiveSiteCount[ecoregion]);
pl.C_DeadLeaf_Meta = (avgSurfMetaC[ecoregion.Index] / (double)ClimateRegionData.ActiveSiteCount[ecoregion]);
pl.C_DeadFRoot_Struc = (avgSoilStrucC[ecoregion.Index] / (double)ClimateRegionData.ActiveSiteCount[ecoregion]);
pl.C_DeadFRoot_Meta = (avgSoilMetaC[ecoregion.Index] / (double)ClimateRegionData.ActiveSiteCount[ecoregion]);
pl.C_SOM1surf = (avgSOM1surfC[ecoregion.Index] / (double)ClimateRegionData.ActiveSiteCount[ecoregion]);
pl.C_SOM1soil = (avgSOM1soilC[ecoregion.Index] / (double)ClimateRegionData.ActiveSiteCount[ecoregion]);
pl.C_SOM2 = (avgSOM2C[ecoregion.Index] / (double)ClimateRegionData.ActiveSiteCount[ecoregion]);
pl.C_SOM3 = (avgSOM3C[ecoregion.Index] / (double)ClimateRegionData.ActiveSiteCount[ecoregion]);
pl.N_Leaf = (avgCohortLeafN[ecoregion.Index] / (double)ClimateRegionData.ActiveSiteCount[ecoregion]);
pl.N_FRoot = (avgCohortFRootN[ecoregion.Index] / (double)ClimateRegionData.ActiveSiteCount[ecoregion]);
pl.N_Wood = (avgCohortWoodN[ecoregion.Index] / (double)ClimateRegionData.ActiveSiteCount[ecoregion]);
pl.N_CRoot = (avgCohortCRootN[ecoregion.Index] / (double)ClimateRegionData.ActiveSiteCount[ecoregion]);
pl.N_DeadWood = (avgWoodN[ecoregion.Index] / (double)ClimateRegionData.ActiveSiteCount[ecoregion]);
pl.N_DeadCRoot = (avgCRootN[ecoregion.Index] / (double)ClimateRegionData.ActiveSiteCount[ecoregion]);
pl.N_DeadLeaf_Struc = (avgSurfStrucN[ecoregion.Index] / (double)ClimateRegionData.ActiveSiteCount[ecoregion]);
pl.N_DeadLeaf_Meta = (avgSurfMetaN[ecoregion.Index] / (double)ClimateRegionData.ActiveSiteCount[ecoregion]);
pl.N_DeadFRoot_Struc = (avgSoilStrucN[ecoregion.Index] / (double)ClimateRegionData.ActiveSiteCount[ecoregion]);
pl.N_DeadFRoot_Meta = (avgSoilMetaN[ecoregion.Index] / (double)ClimateRegionData.ActiveSiteCount[ecoregion]);
pl.N_SOM1surf = (avgSOM1surfN[ecoregion.Index] / (double)ClimateRegionData.ActiveSiteCount[ecoregion]);
pl.N_SOM1soil = (avgSOM1soilN[ecoregion.Index] / (double)ClimateRegionData.ActiveSiteCount[ecoregion]);
pl.N_SOM2 = (avgSOM2N[ecoregion.Index] / (double)ClimateRegionData.ActiveSiteCount[ecoregion]);
pl.N_SOM3 = (avgSOM3N[ecoregion.Index] / (double)ClimateRegionData.ActiveSiteCount[ecoregion]);
pl.SurfStrucNetMin = (avgSurfStrucNetMin[ecoregion.Index] / (double)ClimateRegionData.ActiveSiteCount[ecoregion]);
pl.SurfMetaNetMin = (avgSurfMetaNetMin[ecoregion.Index] / (double)ClimateRegionData.ActiveSiteCount[ecoregion]);
pl.SoilStrucNetMin = (avgSoilStrucNetMin[ecoregion.Index] / (double)ClimateRegionData.ActiveSiteCount[ecoregion]);
pl.SoilMetaNetMin = (avgSoilMetaNetMin[ecoregion.Index] / (double)ClimateRegionData.ActiveSiteCount[ecoregion]);
pl.SOM1surfNetMin = (avgSOM1surfNetMin[ecoregion.Index] / (double)ClimateRegionData.ActiveSiteCount[ecoregion]);
pl.SOM1soilNetMin = (avgSOM1soilNetMin[ecoregion.Index] / (double)ClimateRegionData.ActiveSiteCount[ecoregion]);
pl.SOM2NetMin = (avgSOM2NetMin[ecoregion.Index] / (double)ClimateRegionData.ActiveSiteCount[ecoregion]);
pl.SOM3NetMin = (avgSOM3NetMin[ecoregion.Index] / (double)ClimateRegionData.ActiveSiteCount[ecoregion]);
pl.StreamC = (avgStreamC[ecoregion.Index] / (double)ClimateRegionData.ActiveSiteCount[ecoregion]);
pl.StreamN = (avgStreamN[ecoregion.Index] / (double)ClimateRegionData.ActiveSiteCount[ecoregion]);
pl.FireCEfflux = (avgFireCEfflux[ecoregion.Index] / (double)ClimateRegionData.ActiveSiteCount[ecoregion]);
pl.FireNEfflux = (avgFireNEfflux[ecoregion.Index] / (double)ClimateRegionData.ActiveSiteCount[ecoregion]);
pl.Nuptake = (avgNuptake[ecoregion.Index] / (double)ClimateRegionData.ActiveSiteCount[ecoregion]);
pl.Nresorbed = (avgNresorbed[ecoregion.Index] / (double)ClimateRegionData.ActiveSiteCount[ecoregion]);
pl.TotalSoilN = (avgTotalSoilN[ecoregion.Index] / (double)ClimateRegionData.ActiveSiteCount[ecoregion]);
pl.Nvol = (avgNvol[ecoregion.Index] / (double)ClimateRegionData.ActiveSiteCount[ecoregion]);
pl.FrassC = (avgfrassC[ecoregion.Index] / (double)ClimateRegionData.ActiveSiteCount[ecoregion]);
primaryLog.AddObject(pl);
primaryLog.WriteToFile();
//}
}
//Reset back to zero:
//These are being reset here because fire effects are handled in the first year of the
//growth loop but the reporting doesn't happen until after all growth is finished.
SiteVars.FireCEfflux.ActiveSiteValues = 0.0;
SiteVars.FireNEfflux.ActiveSiteValues = 0.0;
}
/// <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);
}
//---------------------------------------------------------------------
/// <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);
}
//---------------------------------------------------------------------
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);
}
//---------------------------------------------------------------------
//Grows the cohorts for future climate
protected override void AgeCohorts(ActiveSite site,
ushort years,
int?successionTimestep)
{
Century.Run(site, years, successionTimestep.HasValue);
}
