//---------------------------------------------------------------------
/// <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.Max_Biomass[species]; // 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);
}
//---------------------------------------------------------------------
public override void Run()
{
if (PlugIn.ModelCore.CurrentTime > 0)
{
SiteVars.InitializeDisturbances();
}
ClimateRegionData.AnnualNDeposition = new Landis.Library.Parameters.Ecoregions.AuxParm <double>(PlugIn.ModelCore.Ecoregions);
SpeciesByPlant = new int[ModelCore.Species.Count];
SpeciesByResprout = new int[ModelCore.Species.Count];
SpeciesBySerotiny = new int[ModelCore.Species.Count];
SpeciesBySeed = new int[ModelCore.Species.Count];
//base.RunReproductionFirst();
base.Run();
if (Timestep > 0)
{
ClimateRegionData.SetAllEcoregions_FutureAnnualClimate(ModelCore.CurrentTime);
}
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);
Outputs.WriteMaps();
Outputs.WriteReproductionLog(PlugIn.ModelCore.CurrentTime);
Establishment.LogEstablishment();
if (PlugIn.InputCommunityMapNames != null && ModelCore.CurrentTime % PlugIn.InputCommunityMapFrequency == 0)
{
Outputs.WriteCommunityMaps();
}
}
}
/// <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];
}
//PlugIn.ModelCore.UI.WriteLine("PlugIn_FutureClimateBaseYear={0}, y={1}, ModelCore_CurrentTime={2}, CenturyTimeStep = {3}, SimulatedYear = {4}.", PlugIn.FutureClimateBaseYear, y, PlugIn.ModelCore.CurrentTime, years, (PlugIn.FutureClimateBaseYear + y - years + PlugIn.ModelCore.CurrentTime));
SiteVars.ResetAnnualValues(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);
}
//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.MonthlyLAI[site][Month] = 0.0;
SiteVars.SourceSink[site].Carbon = 0.0;
SiteVars.TotalWoodBiomass[site] = Main.ComputeWoodBiomass((ActiveSite)site);
//SiteVars.LAI[site] = Century.ComputeLAI((ActiveSite)site);
double ppt = ClimateRegionData.AnnualWeather[ecoregion].MonthlyPrecip[Main.Month];
double monthlyNdeposition;
if (PlugIn.Parameters.AtmosNintercept != -1 && PlugIn.Parameters.AtmosNslope != -1)
{
monthlyNdeposition = PlugIn.Parameters.AtmosNintercept + (PlugIn.Parameters.AtmosNslope * ppt);
}
else
{
monthlyNdeposition = ClimateRegionData.AnnualWeather[ecoregion].MonthlyNDeposition[Main.Month];
}
if (monthlyNdeposition < 0)
{
throw new System.ApplicationException("Error: Nitrogen deposition less than zero.");
}
ClimateRegionData.MonthlyNDeposition[ecoregion][Month] = monthlyNdeposition;
ClimateRegionData.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, AET;
//if(OtherData.Henne_WaterMode)
// SoilWaterHenne.Run(y, Month, liveBiomass, site, out baseFlow, out stormFlow, out AET);
//else
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.Parameters.DenitrificationRate);
//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;
if (OtherData.Henne_WaterMode)
{
SoilWaterHenne.Leach(site, baseFlow, stormFlow);
}
else
{
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;
//SiteVars.FineFuels[site] = (System.Math.Min(1.0, (double) (PlugIn.ModelCore.CurrentTime - SiteVars.HarvestTime[site]) * 0.1));
}
}
ComputeTotalCohortCN(site, siteCohorts);
return(siteCohorts);
}