//---------------------------------------------------------------------
/// <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();
}
}
}
}
}
