public static void SubtractTranspiration(CohortBiomass cohortbiomass)
{
if (cohortbiomass.NetPsn <= 0)
{
return;
}
waterconsumption = (float)Math.Min(Hydrology.Water[cohortbiomass.site], cohortbiomass.Transpiration);
Hydrology.Water[cohortbiomass.site] -= waterconsumption;
Hydrology.AnnualTranspiration[cohortbiomass.site] += waterconsumption;
}
public static void GrowTree(DateTime date, int canopylayer, CohortBiomass cohortbiomass, float AboveCanopyRadiation)
{
cohortbiomass = ComputePhotosynthesis(date, canopylayer, cohortbiomass, AboveCanopyRadiation);
CohortBiomass.Allocation(cohortbiomass);
CohortBiomass.MaintenanceRespiration(cohortbiomass);
ForestFloor.Litter[cohortbiomass.site].AddMass(FoliageSenescence(cohortbiomass), 0.1);
ForestFloor.WoodyDebris[cohortbiomass.site].AddMass(WoodSenescence(cohortbiomass), 0.1);
CohortOutput.WriteCohortData(date, cohortbiomass.site, cohortbiomass);
}
public static float WoodSenescence(CohortBiomass cohortbiomass)
{
rootsenescence = cohortbiomass.Cohort.Root * RootTurnover[cohortbiomass.spc] / 12;
cohortbiomass.Cohort.Root -= rootsenescence;
ForestFloor.WoodyDebris[cohortbiomass.site].AddMass(rootsenescence, 0);
woodsenescence = cohortbiomass.Cohort.Wood * WoodTurnover[cohortbiomass.spc] / 12;
cohortbiomass.Cohort.Wood -= woodsenescence;
ForestFloor.WoodyDebris[cohortbiomass.site].AddMass(woodsenescence, 0);
return(woodsenescence + rootsenescence);
}
public static void Shuffle(ref List <CohortBiomass> Cohorts)
{
Random rng = new Random();
int n = Cohorts.Count;
while (n > 1)
{
int k = rng.Next(n--);
CohortBiomass temp = Cohorts[n];
Cohorts[n] = Cohorts[k];
Cohorts[k] = temp;
}
}
public static void WriteCohortData(DateTime date, ActiveSite site, CohortBiomass cohortbiomass)
{
if (HasSiteOutput[cohortbiomass.Site] == false)
{
return;
}
FileName = "output/CohortData_" + site + "_" + cohortbiomass.Cohort.YearOfBirth + "_" + cohortbiomass.Cohort.Species.Name + Constants.ext;
string contents = date.Year + delim +
date.Month + delim +
date.ToString("yyyy/MM") + delim +
cohortbiomass.Cohort.CanopyLayer + delim +
cohortbiomass.AboveCanopyRadiation + delim +
cohortbiomass.Cohort.Leaf_On + delim +
cohortbiomass.LAI + delim +
Static.GDD[date][cohortbiomass.Cohort.Species] + delim +
cohortbiomass.GrossPsn + delim +
cohortbiomass.FolResp + delim +
cohortbiomass.MaintResp + delim +
cohortbiomass.NetPsn + delim +
cohortbiomass.ReleasedNSC + delim +
cohortbiomass.Folalloc + delim +
cohortbiomass.WoodAlloc + delim +
cohortbiomass.RootAlloc + delim +
Static.VPD[date] + delim +
cohortbiomass.WUE + delim +
Static.DelAmax[date][cohortbiomass.Cohort.Species] + delim +
cohortbiomass.Transpiration + delim +
cohortbiomass.Cohort.Fol + delim +
//cohortbiomass.Cohort.FolShed + delim +
cohortbiomass.Cohort.Root + delim +
cohortbiomass.Cohort.Wood + delim +
cohortbiomass.Cohort.NSC + delim +
Hydrology.Water[cohortbiomass.Site] + delim +
cohortbiomass.WFPS + delim +
cohortbiomass.DWater + delim +
Static.DTempPSN[date][cohortbiomass.Cohort.Species] + delim +
Static.DTempResp[date][cohortbiomass.Cohort.Species] + delim +
cohortbiomass.Fage + delim +
cohortbiomass.fRad;
System.IO.StreamWriter sw = System.IO.File.AppendText(FileName);
sw.WriteLine(contents);
sw.Close();
}
public static float FoliageSenescence(CohortBiomass cohortbiomass)
{
if (date.DayOfYear > SenescStart[cohortbiomass.spc] && cohortbiomass.Cohort.Leaf_On == true)//
{
cohortbiomass.Cohort.Leaf_On = false;
//cohortbiomass.Cohort.FolShed += FolReten[cohortbiomass.spc] * FoliageTurnover[cohortbiomass.spc] * cohortbiomass.Cohort.Fol;
//cohortbiomass.Cohort.Fol -= FoliageTurnover[cohortbiomass.spc] * cohortbiomass.Cohort.Fol;
cohortbiomass.Cohort.FolShed = FolReten[cohortbiomass.spc] * FoliageTurnover[cohortbiomass.spc] * cohortbiomass.Cohort.Fol;
cohortbiomass.Cohort.Fol -= FoliageTurnover[cohortbiomass.spc] * cohortbiomass.Cohort.Fol;
return(FoliageTurnover[cohortbiomass.spc] * cohortbiomass.Cohort.Fol);// lost foliage
}
return(0);
}
public static void Allocation(CohortBiomass cohortbiomass)
{
folalloc = 0;
woodalloc = 0;
rootalloc = 0;
releasednsc = 0;
cohortbiomass.cohort.NSC += cohortbiomass.NetPsn;
if (cohortbiomass.cohort.NSC < 0)
{
cohortbiomass.cohort.NSC = 0;
}
if (Static.GDD[date][cohortbiomass.spc] > GDDFolStart[cohortbiomass.spc] &&
date.DayOfYear < SenescStart[cohortbiomass.spc])// &&
{
cohortbiomass.cohort.Leaf_On = true;
cohortbiomass.cohort.Fol += cohortbiomass.cohort.FolShed;
cohortbiomass.cohort.FolShed = 0;
releasednsc = DNSC[cohortbiomass.spc] * cohortbiomass.cohort.NSC;
cohortbiomass.cohort.NSC -= releasednsc;
if (Static.GDD[date][cohortbiomass.spc] < GDDFolEnd[cohortbiomass.spc])
{
//System.Console.WriteLine("FRESP = " + ClimateDependentData.FResp[PlugIn.Date[cohortbiomass.site]][cohortbiomass.spc]);
folalloc = frad * releasednsc;
}
cohortbiomass.cohort.Fol += folalloc / ConstantParameters.CFracBiomass;
RootPlusWoodAlloc = releasednsc - folalloc;
if (cohortbiomass.cohort.Root / cohortbiomass.cohort.Biomass < RootStemRatio[cohortbiomass.spc])
{
rootalloc = RootPlusWoodAlloc / ConstantParameters.CFracBiomass;
cohortbiomass.cohort.Root += rootalloc;
}
else
{
woodalloc = RootPlusWoodAlloc / ConstantParameters.CFracBiomass;
cohortbiomass.cohort.Wood += woodalloc;
}
}
}
public void SimulateCanopyLayers(DateTime date, int canopylayer, float radiation)
{
netpsn = 0;
grosspsn = 0;
lai = 0;
if (Cohorts.Count() == 0)
{
belowcanopyradiation = radiation;
}
else
{
belowcanopyradiation = 0;
}
Shuffle(ref Cohorts);
float SumLAI = 0;
foreach (CohortBiomass cohortbiomass in Cohorts)
{
CohortBiomass.GrowTree(date, canopylayer, cohortbiomass, radiation);
SumLAI += cohortbiomass.LAI;
belowcanopyradiation += cohortbiomass.BelowCanopyRadiation / Cohorts.Count();
netpsn += cohortbiomass.NetPsn;
grosspsn += cohortbiomass.GrossPsn;
folresp += cohortbiomass.FolResp;
Hydrology.SubstractTranspiration(date, cohortbiomass.Site, cohortbiomass.Transpiration);
}
if (Cohorts.Count() > 0)
{
lai = SumLAI / (float)Cohorts.Count();
}
else
{
lai = 0;
}
}
/*
* public static void DefineAgeLayers(ActiveSite site)
* {
* canopy.Clear();
*
* float SumFoliageBiomass = 0;
* foreach (ISpeciesCohorts speciesCohorts in PlugIn.Cohorts[site])
* {
* int index = 0;
* foreach (ICohort cohort in speciesCohorts)
* {
* SumFoliageBiomass += cohort.Fol;
*
* int CanopyLayer = (int)(cohort.Age / CanopyLayerAgeSpan);
*
* while (canopy.Count < CanopyLayer + 1)
* {
* canopy.Add(new CanopyLayerBiomass());
* }
*
* canopy[CanopyLayer].Add(new CohortBiomass(site, PlugIn.Cohorts[site][cohort.Species].Get(index), index));
* index++;
* }
* }
*
* for (int l = 0; l < canopy.Count; l++)
* {
* if (canopy[l].Count == 0)
* {
* canopy.Remove(canopy[l]);
* l--;
* }
* }
*
* NumberOfCanopyLayers[site] = canopy.Count;
*
* }
*/
public static void RemoveDeadCohorts(ActiveSite site)
{
foreach (ISpeciesCohorts speciesCohorts in PlugIn.Cohorts[site])
{
for (int index = 0; index < speciesCohorts.Count; index++)
{
if (CohortBiomass.CohortIsDead(PlugIn.Cohorts[site][speciesCohorts.Species].Get(index)))
{
ForestFloor.WoodyDebris[site].AddMass(PlugIn.Cohorts[site][speciesCohorts.Species].Get(index).Biomass, 0.001);
DeadCohortAges[site][speciesCohorts.Species].Add(PlugIn.Cohorts[site][speciesCohorts.Species].Get(index).Age);
deadcohorts[site][speciesCohorts.Species]++;
PlugIn.Cohorts[site][speciesCohorts.Species].RemoveCohort(index, PlugIn.Cohorts[site][speciesCohorts.Species].Get(index), site, null);
}
}
}
}
public static void WriteCohortData(DateTime date, ActiveSite site, CohortBiomass cohortbiomass)
{
if (HasSiteOutput[cohortbiomass.Site] == false) return;
FileName = "output/CohortData_" + site + "_" + cohortbiomass.Cohort.YearOfBirth + "_" + cohortbiomass.Cohort.Species.Name + Constants.ext;
string contents = date.Year + delim +
date.Month + delim +
date.ToString("yyyy/MM") + delim +
cohortbiomass.Cohort.CanopyLayer + delim +
cohortbiomass.AboveCanopyRadiation + delim +
cohortbiomass.Cohort.Leaf_On + delim +
cohortbiomass.LAI + delim +
Static.GDD[date][cohortbiomass.Cohort.Species] + delim +
cohortbiomass.GrossPsn + delim +
cohortbiomass.FolResp + delim +
cohortbiomass.MaintResp + delim +
cohortbiomass.NetPsn + delim +
cohortbiomass.ReleasedNSC + delim +
cohortbiomass.Folalloc + delim +
cohortbiomass.WoodAlloc + delim +
cohortbiomass.RootAlloc + delim +
Static.VPD[date] + delim +
cohortbiomass.WUE + delim +
Static.DelAmax[date][cohortbiomass.Cohort.Species] + delim +
cohortbiomass.Transpiration + delim +
cohortbiomass.Cohort.Fol + delim +
//cohortbiomass.Cohort.FolShed + delim +
cohortbiomass.Cohort.Root + delim +
cohortbiomass.Cohort.Wood + delim +
cohortbiomass.Cohort.NSC + delim +
Hydrology.Water[cohortbiomass.Site] + delim +
cohortbiomass.WFPS + delim +
cohortbiomass.DWater + delim +
Static.DTempPSN[date][cohortbiomass.Cohort.Species] + delim +
Static.DTempResp[date][cohortbiomass.Cohort.Species] + delim +
cohortbiomass.Fage + delim +
cohortbiomass.fRad;
System.IO.StreamWriter sw = System.IO.File.AppendText(FileName);
sw.WriteLine(contents);
sw.Close();
}
public static void WriteCohortData(DateTime date, ActiveSite site, CohortBiomass cohortbiomass, float water)
{
string FileName = OutputCohortFileName(site, cohortbiomass.Cohort);
IEcoregion ecoregion = PlugIn.modelCore.Ecoregion[site];
string contents = date.Year + delim +
date.Month + delim +
date.ToString("yyyy/MM") + delim +
cohortbiomass.Cohort.Age + delim +
cohortbiomass.Cohort.CanopyLayer + delim +
cohortbiomass.AboveCanopyRadiation + delim +
//StaticVariables.Leaf_On[ecoregion, cohortbiomass.Cohort.Species, date] + delim +
cohortbiomass.SumLAI() + delim +
StaticVariables.GDD[ecoregion, cohortbiomass.Cohort.Species, date] + delim +
StaticVariables.HDD[ecoregion, cohortbiomass.Cohort.Species, date] + delim +
cohortbiomass.GrossPsn + delim +
cohortbiomass.FolResp + delim +
cohortbiomass.Autotrophicrespiration + delim +
cohortbiomass.NetPsn + delim +
cohortbiomass.ReleasedNSC + delim +
cohortbiomass.Folalloc + delim +
cohortbiomass.WoodAlloc + delim +
cohortbiomass.RootAlloc + delim +
StaticVariables.VPD[ecoregion, date] + delim +
cohortbiomass.WUE + delim +
cohortbiomass.Transpiration + delim +
cohortbiomass.Cohort.Fol + delim +
//cohortbiomass.Cohort.FolShed + delim +
cohortbiomass.Cohort.Root + delim +
cohortbiomass.Cohort.Wood + delim +
cohortbiomass.Cohort.NSC + delim +
cohortbiomass.FWater + delim +
StaticVariables.FTempPSN[ecoregion, cohortbiomass.Cohort.Species, date] + delim +
StaticVariables.FTempResp[ecoregion, cohortbiomass.Cohort.Species, date] + delim +
cohortbiomass.Fage + delim +
cohortbiomass.FRad + delim;
System.IO.StreamWriter sw = System.IO.File.AppendText(FileName);
sw.WriteLine(contents);
sw.Close();
}
public static void WriteCohortData(DateTime date, ActiveSite site, CohortBiomass cohortbiomass, float water)
{
string FileName = OutputCohortFileName(site, cohortbiomass.Cohort);
IEcoregion ecoregion = PlugIn.modelCore.Ecoregion[site];
string contents = date.Year + delim +
date.Month + delim +
date.ToString("yyyy/MM") + delim +
cohortbiomass.Cohort.Age + delim +
cohortbiomass.Cohort.CanopyLayer + delim +
cohortbiomass.AboveCanopyRadiation + delim +
//StaticVariables.Leaf_On[ecoregion, cohortbiomass.Cohort.Species, date] + delim +
cohortbiomass.SumLAI() + delim +
StaticVariables.GDD[ecoregion, cohortbiomass.Cohort.Species, date] + delim +
StaticVariables.HDD[ecoregion, cohortbiomass.Cohort.Species, date] + delim +
cohortbiomass.GrossPsn + delim +
cohortbiomass.FolResp + delim +
cohortbiomass.Autotrophicrespiration + delim +
cohortbiomass.NetPsn + delim +
cohortbiomass.ReleasedNSC + delim +
cohortbiomass.Folalloc + delim +
cohortbiomass.WoodAlloc + delim +
cohortbiomass.RootAlloc + delim +
StaticVariables.VPD[ecoregion, date] + delim +
cohortbiomass.WUE + delim +
cohortbiomass.Transpiration + delim +
cohortbiomass.Cohort.Fol + delim +
//cohortbiomass.Cohort.FolShed + delim +
cohortbiomass.Cohort.Root + delim +
cohortbiomass.Cohort.Wood + delim +
cohortbiomass.Cohort.NSC + delim +
cohortbiomass.FWater + delim +
StaticVariables.FTempPSN[ecoregion, cohortbiomass.Cohort.Species, date] + delim +
StaticVariables.FTempResp[ecoregion, cohortbiomass.Cohort.Species, date] + delim +
cohortbiomass.Fage + delim +
cohortbiomass.FRad + delim;
System.IO.StreamWriter sw = System.IO.File.AppendText(FileName);
sw.WriteLine(contents);
sw.Close();
}
public void Add(CohortBiomass c)
{
Cohorts.Add(c);
}
private static CohortBiomass ComputePhotosynthesis(DateTime Date, int canopylayer, CohortBiomass cohortbiomass, float AboveCanopyRadiation)
{
date = Date;
cohortbiomass.cohort.CanopyLayer = canopylayer;
abovecanopyradiation = AboveCanopyRadiation;
cohortbiomass.lai = 0;
grosspsn = 0;
folresp = 0;
netpsn = 0;
folresp = 0;
fage = 1 - cohortbiomass.cohort.Age / (cohortbiomass.cohort.Age + 1 / PsnAgeRed[cohortbiomass.spc]);
WiltingPoint_mm = WiltingPoint[cohortbiomass.spc] * Hydrology.WHC[PlugIn.modelCore.Ecoregion[cohortbiomass.site]];
wfps = (Hydrology.Water[cohortbiomass.site] - WiltingPoint_mm) / (Hydrology.WHC[PlugIn.ModelCore.Ecoregion[cohortbiomass.site]] - WiltingPoint_mm);
dWater = (float)Math.Pow(Math.Max(0, wfps), GrowthMoistureSensitivity[cohortbiomass.spc]);
frad = Get_frad(AboveCanopyRadiation, HalfSat[cohortbiomass.spc]);
if (cohortbiomass.cohort.Fol > 0)
{
//float PosCBalMass = cohortbiomass.cohort.Fol;
for (int ix = 1; ix <= IMAX; ix++)
{
slwlayer = SLWmax[cohortbiomass.spc] - (SLWDel[cohortbiomass.spc] * ix * (cohortbiomass.cohort.Fol / IMAX)); // SLW for this layer
cohortbiomass.lai += (cohortbiomass.cohort.Fol / IMAX) / slwlayer; // cumulative LAI for whole canopy to this depth
belowcanopyradiation = AboveCanopyRadiation * (float)Math.Exp(-k[cohortbiomass.spc] * cohortbiomass.lai); // light intensity at this level
frad = Get_frad(belowcanopyradiation, HalfSat[cohortbiomass.spc]);
netpsn += dWater * frad * fage * Static.DTempPSN[date][cohortbiomass.spc] * Static.RefNetPsn[date][cohortbiomass.spc] * (cohortbiomass.cohort.Fol / IMAX);
folresp += dWater * Static.DTempRespDay[date][cohortbiomass.spc] * Static.RefResp[date][cohortbiomass.spc] * (cohortbiomass.cohort.Fol / IMAX);
} //for ix=1 to 50
} //if FolMass>0
grosspsn = netpsn + folresp;
//mm
// Constants.MCO2 / Constants.MC: gCO2/gC
transpiration = (grosspsn * (Constants.MCO2 / Constants.MC)) / Static.WUE_CO2_corr[date][cohortbiomass.spc];
// wue based on Net Photosynthesis
if (transpiration > 0)
{
cohortbiomass.wue = netpsn / transpiration;
}
else
{
cohortbiomass.wue = 0;
}
return(cohortbiomass);
}
public void Add(CohortBiomass c)
{
Cohorts.Add(c);
}
public void CalculatePhotosynthesis(DateTime date, ActiveSite site, Hydrology hydrology, ForestFloor forestfloor, SiteOutput siteoutput)
{
autotrophicrespiration = 0;
grosspsn = 0;
netpsn = 0;
totalnsc = 0;
totalroot = 0;
totalfoliage = 0;
totalbiomass = 0;
maxbiom = 0;
maxage = 0;
for (int canopylayer = canopy.Length - 1; canopylayer >= 0; canopylayer--)
{
for (int ix = 0; ix < IMAX; ix++)
{
if (canopy[canopylayer] == null)
{
continue;
}
for (int coh = canopy[canopylayer].Count - 1; coh >= 0; coh--)
{
CohortBiomass CB = canopy[canopylayer][coh];
if (ix == 0)
{
forestfloor.WoodyDebris.AddMass(CB.WoodSenescence(), KWdLit[CB.Cohort.Species]);
forestfloor.Litter.AddMass(CB.FoliageSenescence(date, PlugIn.modelCore.Ecoregion[site], CB.Cohort.Species), ForestFloor.KNwdLitter[PlugIn.modelCore.Ecoregion[site], CB.Cohort.Species]);
}
float transpiration_lyr = 0;
bool cohortisalive = CB.ComputePhotosynthesis(date, PlugIn.modelCore.Ecoregion[site], ix, (int)IMAX, hydrology, ref transpiration_lyr);
if (CB.Cohort.Age > MaxAge)
{
maxage = CB.Cohort.Age;
}
if (MaxBiom < CB.Cohort.Biomass)
{
maxbiom = CB.Cohort.Biomass;
}
autotrophicrespiration += CB.Autotrophicrespiration;
netpsn += CB.NetPsn;
grosspsn += CB.GrossPsn;
if (cohortisalive == false)
{
deadcohorts.Add(CB.Cohort);
forestfloor.WoodyDebris.AddMass(CB.Cohort.Biomass, KWdLit[CB.Cohort.Species]);
forestfloor.Litter.AddMass(CB.Cohort.Fol, ForestFloor.KNwdLitter[PlugIn.modelCore.Ecoregion[site], CB.Cohort.Species]);
}
transpiration += transpiration_lyr;
if (transpiration_lyr > hydrology.Water)
{
IncrementIMAX(site, date);
return;
}
else
{
hydrology.SubtractTranspiration(date, transpiration_lyr);
}
if (ix == 0)
{
totalbiomass += CB.Cohort.Biomass;
totalfoliage += CB.Cohort.Fol;
totalnsc += CB.Cohort.NSC;
totalroot += CB.Cohort.Root;
CB.MaintenanceRespiration(PlugIn.modelCore.Ecoregion[site], date);
if (siteoutput != null)
{
//System.Console.WriteLine("WriteCohortData\t" + site.ToString() + "\t" + date.ToString());
CohortOutput.WriteCohortData(date, site, canopy[canopylayer][coh], hydrology.Water);
}
}
}
}
}//IMAX
}
//---------------------------------------------------------------------
public override void Initialize()
{
cohorts = PlugIn.ModelCore.Landscape.NewSiteVar <ISiteCohorts>();
BiomassCohorts = new BiomassCohortsSiteVar(cohorts);
baseCohorts = new Landis.Library.Biomass.BaseCohortsSiteVar(BiomassCohorts);
// Counts added cohorts per site and per species
newcohorts = PlugIn.ModelCore.Landscape.NewSiteVar <Landis.Library.Biomass.Species.AuxParm <int> >();
foreach (ActiveSite site in PlugIn.ModelCore.Landscape)
{
newcohorts[site] = new Landis.Library.Biomass.Species.AuxParm <int>(PlugIn.ModelCore.Species);
}
PlugIn.ModelCore.RegisterSiteVar(NewCohorts, "Succession.NewCohorts");
PlugIn.ModelCore.RegisterSiteVar(cohorts, "Succession.BiomassCohortsPnET");
PlugIn.ModelCore.RegisterSiteVar(BiomassCohorts, "Succession.BiomassCohorts");
PlugIn.ModelCore.RegisterSiteVar(baseCohorts, "Succession.AgeCohorts");
Edu.Wisc.Forest.Flel.Util.Directory.EnsureExists("output");
CohortOutput.Initialize(parameters);
SiteOutput.Initialize(parameters);
CohortBiomass.Initialize(parameters);
EstablishmentProbability.Initialize(parameters);
CanopyBiomass.Initialize(parameters);
Static.Initialize(parameters);
Hydrology.Initialize(parameters);
Timestep = parameters.Timestep;
tstep = parameters.Timestep;
// Initialize Reproduction routines:
// Reproduction.SufficientResources = SufficientLight;
Reproduction.Establish = Establish;
Reproduction.AddNewCohort = AddNewCohort;
Reproduction.MaturePresent = MaturePresent;
Reproduction.PlantingEstablish = PlantingEstablish;
base.Initialize(modelCore, parameters.SeedAlgorithm);
InitialBiomass.Initialize(parameters);
Cohort.DeathEvent += CohortDied;
// TODO ARJAN !!
//Landis.Extension.Succession.Biomass.AgeOnlyDisturbances.Module.Initialize(parameters.AgeOnlyDisturbanceParms);
ForestFloor.Initialize(parameters);
SiteOutput.Initialize(parameters);
StartDate = new System.DateTime(parameters.StartYear, 1, 15);
year = StartDate.Year;
month = StartDate.Month;
InitializeSites(parameters.InitialCommunities, parameters.InitialCommunitiesMap, modelCore);
}
public static float WoodSenescence(CohortBiomass cohortbiomass)
{
rootsenescence = cohortbiomass.Cohort.Root * RootTurnover[cohortbiomass.spc] / 12;
cohortbiomass.Cohort.Root -= rootsenescence;
ForestFloor.WoodyDebris[cohortbiomass.site].AddMass(rootsenescence, 0);
woodsenescence = cohortbiomass.Cohort.Wood * WoodTurnover[cohortbiomass.spc] / 12;
cohortbiomass.Cohort.Wood -= woodsenescence;
ForestFloor.WoodyDebris[cohortbiomass.site].AddMass(woodsenescence, 0);
return woodsenescence + rootsenescence;
}
public static void SubtractTranspiration(CohortBiomass cohortbiomass)
{
if (cohortbiomass.NetPsn <= 0) return;
waterconsumption = (float)Math.Min(Hydrology.Water[cohortbiomass.site], cohortbiomass.Transpiration);
Hydrology.Water[cohortbiomass.site] -= waterconsumption;
Hydrology.AnnualTranspiration[cohortbiomass.site] += waterconsumption;
}
public static void MaintenanceRespiration(CohortBiomass cohortbiomass)
{
cohortbiomass.maintresp = Math.Min(cohortbiomass.cohort.NSC, Static.DTempResp[date][cohortbiomass.spc] * MaintRespFrac[cohortbiomass.spc] * cohortbiomass.Cohort.Biomass);
cohortbiomass.cohort.NSC -= cohortbiomass.MaintResp;
}
public static float FoliageSenescence(CohortBiomass cohortbiomass)
{
if (date.DayOfYear > SenescStart[cohortbiomass.spc] && cohortbiomass.Cohort.Leaf_On == true)//
{
cohortbiomass.Cohort.Leaf_On = false;
//cohortbiomass.Cohort.FolShed += FolReten[cohortbiomass.spc] * FoliageTurnover[cohortbiomass.spc] * cohortbiomass.Cohort.Fol;
//cohortbiomass.Cohort.Fol -= FoliageTurnover[cohortbiomass.spc] * cohortbiomass.Cohort.Fol;
cohortbiomass.Cohort.FolShed = FolReten[cohortbiomass.spc] * FoliageTurnover[cohortbiomass.spc] * cohortbiomass.Cohort.Fol;
cohortbiomass.Cohort.Fol -= FoliageTurnover[cohortbiomass.spc] * cohortbiomass.Cohort.Fol;
return FoliageTurnover[cohortbiomass.spc] * cohortbiomass.Cohort.Fol;// lost foliage
}
return 0;
}
public static void Allocation(CohortBiomass cohortbiomass)
{
folalloc = 0;
woodalloc = 0;
rootalloc = 0;
releasednsc = 0;
cohortbiomass.cohort.NSC += cohortbiomass.NetPsn;
if (cohortbiomass.cohort.NSC < 0) cohortbiomass.cohort.NSC = 0;
if (Static.GDD[date][cohortbiomass.spc] > GDDFolStart[cohortbiomass.spc] &&
date.DayOfYear < SenescStart[cohortbiomass.spc])// &&
{
cohortbiomass.cohort.Leaf_On = true;
cohortbiomass.cohort.Fol += cohortbiomass.cohort.FolShed;
cohortbiomass.cohort.FolShed = 0;
releasednsc = DNSC[cohortbiomass.spc] * cohortbiomass.cohort.NSC;
cohortbiomass.cohort.NSC -= releasednsc;
if (Static.GDD[date][cohortbiomass.spc] < GDDFolEnd[cohortbiomass.spc])
{
//System.Console.WriteLine("FRESP = " + ClimateDependentData.FResp[PlugIn.Date[cohortbiomass.site]][cohortbiomass.spc]);
folalloc = frad * releasednsc;
}
cohortbiomass.cohort.Fol += folalloc / ConstantParameters.CFracBiomass;
RootPlusWoodAlloc = releasednsc - folalloc;
if (cohortbiomass.cohort.Root / cohortbiomass.cohort.Biomass < RootStemRatio[cohortbiomass.spc])
{
rootalloc = RootPlusWoodAlloc / ConstantParameters.CFracBiomass;
cohortbiomass.cohort.Root += rootalloc;
}
else
{
woodalloc = RootPlusWoodAlloc / ConstantParameters.CFracBiomass;
cohortbiomass.cohort.Wood += woodalloc;
}
}
}
public static void MaintenanceRespiration(CohortBiomass cohortbiomass)
{
cohortbiomass.maintresp = Math.Min(cohortbiomass.cohort.NSC, Static.DTempResp[date][cohortbiomass.spc] * MaintRespFrac[cohortbiomass.spc] * cohortbiomass.Cohort.Biomass);
cohortbiomass.cohort.NSC -= cohortbiomass.MaintResp;
}
private static CohortBiomass ComputePhotosynthesis(DateTime Date, int canopylayer, CohortBiomass cohortbiomass, float AboveCanopyRadiation)
{
date = Date;
cohortbiomass.cohort.CanopyLayer = canopylayer;
abovecanopyradiation = AboveCanopyRadiation;
cohortbiomass.lai = 0;
grosspsn = 0;
folresp = 0;
netpsn = 0;
folresp = 0;
fage = 1 - cohortbiomass.cohort.Age / (cohortbiomass.cohort.Age + 1 / PsnAgeRed[cohortbiomass.spc]);
WiltingPoint_mm = WiltingPoint[cohortbiomass.spc] * Hydrology.WHC[PlugIn.modelCore.Ecoregion[cohortbiomass.site]];
wfps = (Hydrology.Water[cohortbiomass.site] - WiltingPoint_mm) / (Hydrology.WHC[PlugIn.ModelCore.Ecoregion[cohortbiomass.site]] - WiltingPoint_mm);
dWater = (float)Math.Pow(Math.Max(0, wfps), GrowthMoistureSensitivity[cohortbiomass.spc]);
frad = Get_frad(AboveCanopyRadiation, HalfSat[cohortbiomass.spc]);
if (cohortbiomass.cohort.Fol > 0)
{
//float PosCBalMass = cohortbiomass.cohort.Fol;
for (int ix = 1; ix <= IMAX; ix++)
{
slwlayer = SLWmax[cohortbiomass.spc] - (SLWDel[cohortbiomass.spc] * ix * (cohortbiomass.cohort.Fol / IMAX)); // SLW for this layer
cohortbiomass.lai += (cohortbiomass.cohort.Fol / IMAX) / slwlayer; // cumulative LAI for whole canopy to this depth
belowcanopyradiation = AboveCanopyRadiation * (float)Math.Exp(-k[cohortbiomass.spc] * cohortbiomass.lai); // light intensity at this level
frad = Get_frad(belowcanopyradiation, HalfSat[cohortbiomass.spc]);
netpsn += dWater * frad * fage * Static.DTempPSN[date][cohortbiomass.spc] * Static.RefNetPsn[date][cohortbiomass.spc] * (cohortbiomass.cohort.Fol / IMAX);
folresp += dWater * Static.DTempRespDay[date][cohortbiomass.spc] * Static.RefResp[date][cohortbiomass.spc] * (cohortbiomass.cohort.Fol / IMAX);
}//for ix=1 to 50
}//if FolMass>0
grosspsn = netpsn + folresp;
//mm
// Constants.MCO2 / Constants.MC: gCO2/gC
transpiration = (grosspsn * (Constants.MCO2 / Constants.MC)) / Static.WUE_CO2_corr[date][cohortbiomass.spc];
// wue based on Net Photosynthesis
if (transpiration > 0) cohortbiomass.wue = netpsn / transpiration;
else cohortbiomass.wue = 0;
return cohortbiomass;
}
public static void GrowTree(DateTime date, int canopylayer, CohortBiomass cohortbiomass, float AboveCanopyRadiation)
{
cohortbiomass = ComputePhotosynthesis(date, canopylayer, cohortbiomass, AboveCanopyRadiation);
CohortBiomass.Allocation(cohortbiomass);
CohortBiomass.MaintenanceRespiration(cohortbiomass);
ForestFloor.Litter[cohortbiomass.site].AddMass(FoliageSenescence(cohortbiomass), 0.1);
ForestFloor.WoodyDebris[cohortbiomass.site].AddMass(WoodSenescence(cohortbiomass), 0.1);
CohortOutput.WriteCohortData(date, cohortbiomass.site, cohortbiomass);
}
//---------------------------------------------------------------------
public override void Initialize()
{
PlugIn.ModelCore.UI.WriteLine("Initializing " + ExtensionName + " version " + typeof(PlugIn).Assembly.GetName().Version);
/*Testing
* Landis.Library.BiomassCohorts.Cohort C;
* Cohort D;
*
* C = (Landis.Library.BiomassCohorts.Cohort)D;
*/
hassiteoutput = parameters.HasSiteOutput;
siteconditions = PlugIn.ModelCore.Landscape.NewSiteVar <SiteConditions>();
Edu.Wisc.Forest.Flel.Util.Directory.EnsureExists("output");
//CohortOutput.Initialize(parameters);
Hydrology.Initialize(parameters);
StaticVariables.InitializeStatic(parameters);
ForestFloor.Initialize(parameters);
SiteConditions.Initialize(parameters);
CohortBiomass.Initialize(parameters);
Timestep = parameters.Timestep;
tstep = parameters.Timestep;
// Initialize Reproduction routines:
Reproduction.SufficientResources = SufficientResources;
Reproduction.Establish = Establish;
Reproduction.AddNewCohort = AddNewCohort;
Reproduction.MaturePresent = MaturePresent;
Reproduction.PlantingEstablish = PlantingEstablish;
base.Initialize(modelCore, parameters.SeedAlgorithm);
Cohort.DeathEvent += CohortDied;
StartDate = new System.DateTime(parameters.StartYear, 1, 15);
year = StartDate.Year;
month = StartDate.Month;
InitializeSites(parameters.InitialCommunities, parameters.InitialCommunitiesMap, modelCore);
EstablishmentProbability.Initialize(parameters);
ISiteVar <ISiteCohorts> cohorts = PlugIn.ModelCore.Landscape.NewSiteVar <ISiteCohorts>();
foreach (ActiveSite site in PlugIn.modelCore.Landscape)
{
cohorts[site] = siteconditions[site].Cohorts;
}
BiomassCohorts = new BiomassCohortsSiteVar(cohorts);
baseCohorts = new Landis.Library.Biomass.BaseCohortsSiteVar(BiomassCohorts);
PlugIn.ModelCore.RegisterSiteVar(BiomassCohorts, "Succession.BiomassCohorts");
PlugIn.ModelCore.RegisterSiteVar(siteconditions, "Succession.SiteConditionsPnET");
PlugIn.ModelCore.RegisterSiteVar(baseCohorts, "Succession.AgeCohorts");
ISiteVar <Pool> WoodyDebris = PlugIn.ModelCore.Landscape.NewSiteVar <Pool>();
foreach (ActiveSite site in PlugIn.modelCore.Landscape)
{
WoodyDebris[site] = siteconditions[site].WoodyDebris;
}
PlugIn.ModelCore.RegisterSiteVar(WoodyDebris, "Succession.WoodyDebris");
ISiteVar <Pool> Litter = PlugIn.ModelCore.Landscape.NewSiteVar <Pool>();
foreach (ActiveSite site in PlugIn.modelCore.Landscape)
{
Litter[site] = siteconditions[site].WoodyDebris;
}
PlugIn.ModelCore.RegisterSiteVar(Litter, "Succession.Litter");
}