public static void GrowCohorts(ActiveSite site,
DateTime Time,
DateTime ToTime,
bool issuccessionTimestep)
{
if (PlugIn.Cohorts[site] == null)
{
return;
}
while (Time.CompareTo(ToTime) < 0)
{
if (Time.Month == 1)
{
if (issuccessionTimestep && tstep > 1)//&& ClimateDependentData.Data[PlugIn.Date[site]] != null
{
PlugIn.Cohorts[site].CombineCohorts(site, tstep, Time.Year);
}
CanopyBiomass.SubCanopyPARmax[site] = float.MinValue;
Hydrology.AnnualTranspiration[site] = 0;
//CanopyBiomass.DefineAgeLayers(site);
CanopyBiomass.DefineBiomassLayers(site);
CanopyBiomass.CanopyLAI[site] = 0;
PlugIn.Cohorts[site].IncrementCohortsAge();
}
Hydrology.UpdateSiteHydrology(Time, site);
CanopyBiomass.SimulateCanopy(Time, site);
if (issuccessionTimestep)
{
EstablishmentProbability.Compute(Time, site);
}
ForestFloor.Decomposition(site);
SiteOutput.UpdateSiteData(Time, site);
CanopyBiomass.GrossPsn[site] = 0;
CanopyBiomass.NetPsn[site] = 0;
CanopyBiomass.AutotrophicRespiration[site] = 0;
ForestFloor.HeterotrophicRespiration[site] = 0;
Hydrology.Transpiration[site] = 0;
Time = Time.AddMonths(1);
}
CanopyBiomass.RemoveDeadCohorts(site);
PlugIn.Cohorts[site].UpdateMaturePresent();
SiteOutput.WriteSiteData(site);
DisturbanceDefoliation.Defoliate(site);
}
public SiteConditions(ActiveSite site, ICommunity initialCommunity)
{
cohorts = new SiteCohorts();
canopy = new Canopy();
if (PlugIn.HasSiteOutput[site] == true)
{
siteoutput = new SiteOutput(site);
estoutput = new EstablishmentOutput(site);
}
this.site = site;
foreach (ISpecies spc in PlugIn.modelCore.Species)
{
deadcohortages[spc] = new List <int>();
}
uint key = ComputeKey(initialCommunity.MapCode, PlugIn.ModelCore.Ecoregion[site].MapCode);
SiteConditions s = GetFromKey(key);
if (s != null)
{
return;
}
// If we don't have a sorted list of age cohorts for the initial
// community, make the list
List <Landis.Library.AgeOnlyCohorts.ICohort> sortedAgeCohorts;
if (!sortedCohorts.TryGetValue(initialCommunity.MapCode, out sortedAgeCohorts))
{
sortedAgeCohorts = PlugIn.RankCohortAgesOldToYoung(initialCommunity.Cohorts);
sortedCohorts[initialCommunity.MapCode] = sortedAgeCohorts;
}
hydrology = new Hydrology(PlugIn.modelCore.Ecoregion[site]);
forestfloor = new ForestFloor();
cohorts = new SiteCohorts();
establishment = new EstablishmentProbability(site);
if (sortedAgeCohorts.Count == 0)
{
return;
}
//PlugIn.ModelCore.UI.WriteLine("Making Biomass Cohorts "+ site);
BiomassSpinUp(sortedAgeCohorts, site);
initialSites[key] = this;
return;
}
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;
}
}
//---------------------------------------------------------------------
/// <summary>
/// Makes the set of biomass cohorts at a site based on the age cohorts
/// at the site, using a specified method for computing a cohort's
/// initial biomass.
/// </summary>
/// <param name="ageCohorts">
/// A sorted list of age cohorts, from oldest to youngest.
/// </param>
/// <param name="site">
/// Site where cohorts are located.
/// </param>
/// <param name="initialBiomassMethod">
/// The method for computing the initial biomass for a new cohort.
/// </param>
public static ISiteCohorts MakeBiomassCohorts(List <Landis.Library.AgeOnlyCohorts.ICohort> ageCohorts, ActiveSite site)
{
PlugIn.Cohorts[site] = new Library.BiomassCohortsPnET.SiteCohorts();
Hydrology.Initialize(site);
Hydrology.AnnualTranspiration[site] = 0;
CanopyBiomass.CanopyLAI[site] = 0;
if (ageCohorts.Count == 0)
{
return(PlugIn.Cohorts[site]);
}
System.DateTime SpinUpDate = PlugIn.StartDate.AddYears(-(ageCohorts[0].Age) + ((successionTimestep == 1) ? -1 : 0));
while (SpinUpDate.CompareTo(PlugIn.StartDate) < 0)
{
CanopyBiomass.SubCanopyPAR[site] = Static.PAR0[SpinUpDate];
// Add those cohorts that were born at the current year
foreach (Library.AgeOnlyCohorts.ICohort ageonlycohort in ageCohorts)
{
if (PlugIn.StartDate.Year - SpinUpDate.Year == ageonlycohort.Age)
{
Cohort cohort = new Cohort(ageonlycohort.Species, 1, ConstantParameters.InitialFol, 0, 0, 0, 0, SpinUpDate.Year, true);
PlugIn.Cohorts[site].AddNewCohort(cohort);
CohortOutput.WriteHeader(site, cohort);
SiteOutput.WriteHeader(site);
}
}
PlugIn.GrowCohorts(site, SpinUpDate, SpinUpDate.AddYears(1), false);
SpinUpDate = SpinUpDate.AddYears(1);
}
return(PlugIn.Cohorts[site]);
}
public SiteConditions GetFromKey(uint key)
{
SiteConditions s = null;
if (initialSites.TryGetValue(key, out s) && siteoutput == null)
{
hydrology = s.hydrology;
establishment = s.Establishment;
cohorts = new SiteCohorts();
foreach (ISpeciesCohorts speciesCohorts in s.cohorts)
{
foreach (Cohort cohort in speciesCohorts)
{
Cohort newcohort = new Cohort(cohort);
cohorts.AddNewCohort(newcohort, PlugIn.TStep);
}
}
forestfloor = s.forestfloor;
canopylaimax = s.CanopyLAImax;
}
return(s);
}
//---------------------------------------------------------------------
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 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 void Grow(DateTime date, ActiveSite site, Hydrology hydrology, ForestFloor forestfloor, SiteCohorts Cohorts, SiteOutput siteoutput)
{
SetCanopyLayers(Cohorts, MaxAge, MaxBiom);
CalculateRadiationProfile(site, date);
CalculatePhotosynthesis(date, site, hydrology, forestfloor, siteoutput);
}
public SiteConditions GetFromKey(uint key)
{
SiteConditions s=null;
if (initialSites.TryGetValue(key, out s) && siteoutput == null)
{
hydrology = s.hydrology;
establishment = s.Establishment;
cohorts = new SiteCohorts();
foreach (ISpeciesCohorts speciesCohorts in s.cohorts)
{
foreach (Cohort cohort in speciesCohorts)
{
Cohort newcohort = new Cohort(cohort);
cohorts.AddNewCohort(newcohort, PlugIn.TStep);
}
}
forestfloor = s.forestfloor;
canopylaimax = s.CanopyLAImax;
}
return s;
}
public SiteConditions(ActiveSite site, ICommunity initialCommunity)
{
cohorts = new SiteCohorts();
canopy = new Canopy();
if (PlugIn.HasSiteOutput[site] == true)
{
siteoutput = new SiteOutput(site);
estoutput = new EstablishmentOutput(site);
}
this.site = site;
foreach (ISpecies spc in PlugIn.modelCore.Species)
{
deadcohortages[spc] = new List<int>();
}
uint key = ComputeKey(initialCommunity.MapCode, PlugIn.ModelCore.Ecoregion[site].MapCode);
SiteConditions s = GetFromKey(key);
if (s != null) return;
// If we don't have a sorted list of age cohorts for the initial
// community, make the list
List<Landis.Library.AgeOnlyCohorts.ICohort> sortedAgeCohorts;
if (!sortedCohorts.TryGetValue(initialCommunity.MapCode, out sortedAgeCohorts))
{
sortedAgeCohorts = PlugIn.RankCohortAgesOldToYoung(initialCommunity.Cohorts);
sortedCohorts[initialCommunity.MapCode] = sortedAgeCohorts;
}
hydrology = new Hydrology(PlugIn.modelCore.Ecoregion[site]);
forestfloor = new ForestFloor();
cohorts = new SiteCohorts();
establishment = new EstablishmentProbability(site);
if (sortedAgeCohorts.Count == 0) return;
//PlugIn.ModelCore.UI.WriteLine("Making Biomass Cohorts "+ site);
BiomassSpinUp(sortedAgeCohorts, site);
initialSites[key] = this;
return;
}
public override void Initialize()
{
PlugIn.ModelCore.UI.WriteLine("Initializing " + Names.ExtensionName + " version " + typeof(PlugIn).Assembly.GetName().Version);
Cohort.DeathEvent += DeathEvent;
Litter = PlugIn.ModelCore.Landscape.NewSiteVar <Landis.Library.Biomass.Pool>();
WoodyDebris = PlugIn.ModelCore.Landscape.NewSiteVar <Landis.Library.Biomass.Pool>();
sitecohorts = PlugIn.ModelCore.Landscape.NewSiteVar <SiteCohorts>();
FineFuels = ModelCore.Landscape.NewSiteVar <Double>();
PressureHead = ModelCore.Landscape.NewSiteVar <float>();
ExtremeMinTemp = ModelCore.Landscape.NewSiteVar <float>();
Landis.Utilities.Directory.EnsureExists("output");
Timestep = ((Parameter <int>)GetParameter(Names.Timestep)).Value;
Parameter <string> CohortBinSizeParm = null;
if (TryGetParameter(Names.CohortBinSize, out CohortBinSizeParm))
{
if (Int32.TryParse(CohortBinSizeParm.Value, out CohortBinSize))
{
if (CohortBinSize < Timestep)
{
throw new System.Exception("CohortBinSize cannot be smaller than Timestep.");
}
else
{
PlugIn.ModelCore.UI.WriteLine("Succession timestep = " + Timestep + "; CohortBinSize = " + CohortBinSize + ".");
}
}
else
{
throw new System.Exception("CohortBinSize is not an integer value.");
}
}
else
{
CohortBinSize = Timestep;
}
FTimeStep = 1.0F / Timestep;
//Latitude = ((Parameter<float>)PlugIn.GetParameter(Names.Latitude, 0, 90)).Value; // Now an ecoregion parameter
ObservedClimate.Initialize();
SpeciesPnET = new SpeciesPnET();
EcoregionPnET.Initialize();
Hydrology.Initialize();
SiteCohorts.Initialize();
// John McNabb: initialize climate library after EcoregionPnET has been initialized
InitializeClimateLibrary();
EstablishmentProbability.Initialize(Timestep);
IMAX = ((Parameter <ushort>)GetParameter(Names.IMAX)).Value;
//LeakageFrostDepth = ((Parameter<float>)GetParameter(Names.LeakageFrostDepth)).Value; //Now an ecoregion parameter
//PrecipEvents = ((Parameter<float>)GetParameter(Names.PrecipEvents)).Value;// Now an ecoregion parameter
// Initialize Reproduction routines:
Reproduction.SufficientResources = SufficientResources;
Reproduction.Establish = Establish;
Reproduction.AddNewCohort = AddNewCohort;
Reproduction.MaturePresent = MaturePresent;
Reproduction.PlantingEstablish = PlantingEstablish;
SeedingAlgorithms SeedAlgorithm = (SeedingAlgorithms)Enum.Parse(typeof(SeedingAlgorithms), parameters["SeedingAlgorithm"].Value);
base.Initialize(ModelCore, SeedAlgorithm);
StartDate = new DateTime(((Parameter <int>)GetParameter(Names.StartYear)).Value, 1, 15);
PlugIn.ModelCore.UI.WriteLine("Spinning up biomass or reading from maps...");
string InitialCommunitiesTXTFile = GetParameter(Names.InitialCommunities).Value;
string InitialCommunitiesMapFile = GetParameter(Names.InitialCommunitiesMap).Value;
Parameter <string> LitterMapFile;
bool litterMapFile = TryGetParameter(Names.LitterMap, out LitterMapFile);
Parameter <string> WoodyDebrisMapFile;
bool woodyDebrisMapFile = TryGetParameter(Names.WoodyDebrisMap, out WoodyDebrisMapFile);
//Console.ReadLine();
InitializeSites(InitialCommunitiesTXTFile, InitialCommunitiesMapFile, ModelCore);
if (litterMapFile)
{
MapReader.ReadLitterFromMap(LitterMapFile.Value);
}
if (woodyDebrisMapFile)
{
MapReader.ReadWoodyDebrisFromMap(WoodyDebrisMapFile.Value);
}
// Convert PnET cohorts to biomasscohorts
ISiteVar <Landis.Library.BiomassCohorts.ISiteCohorts> biomassCohorts = PlugIn.ModelCore.Landscape.NewSiteVar <Landis.Library.BiomassCohorts.ISiteCohorts>();
foreach (ActiveSite site in PlugIn.ModelCore.Landscape)
{
biomassCohorts[site] = sitecohorts[site];
if (sitecohorts[site] != null && biomassCohorts[site] == null)
{
throw new System.Exception("Cannot convert PnET SiteCohorts to biomass site cohorts");
}
}
ModelCore.RegisterSiteVar(biomassCohorts, "Succession.BiomassCohorts");
ModelCore.RegisterSiteVar(WoodyDebris, "Succession.WoodyDebris");
ModelCore.RegisterSiteVar(Litter, "Succession.Litter");
ISiteVar <Landis.Library.AgeOnlyCohorts.ISiteCohorts> AgeCohortSiteVar = PlugIn.ModelCore.Landscape.NewSiteVar <Landis.Library.AgeOnlyCohorts.ISiteCohorts>();
ISiteVar <ISiteCohorts> PnETCohorts = PlugIn.ModelCore.Landscape.NewSiteVar <ISiteCohorts>();
foreach (ActiveSite site in PlugIn.ModelCore.Landscape)
{
AgeCohortSiteVar[site] = sitecohorts[site];
PnETCohorts[site] = sitecohorts[site];
FineFuels[site] = Litter[site].Mass;
IEcoregionPnET ecoregion = EcoregionPnET.GetPnETEcoregion(PlugIn.ModelCore.Ecoregion[site]);
IHydrology hydrology = new Hydrology(ecoregion.FieldCap);
PressureHead[site] = hydrology.GetPressureHead(ecoregion);
if (UsingClimateLibrary)
{
ExtremeMinTemp[site] = ((float)Enumerable.Min(Climate.Future_MonthlyData[Climate.Future_MonthlyData.Keys.Min()][ecoregion.Index].MonthlyTemp) - (float)(3.0 * ecoregion.WinterSTD));
}
else
{
ExtremeMinTemp[site] = 999;
}
}
ModelCore.RegisterSiteVar(AgeCohortSiteVar, "Succession.AgeCohorts");
ModelCore.RegisterSiteVar(PnETCohorts, "Succession.CohortsPnET");
ModelCore.RegisterSiteVar(FineFuels, "Succession.FineFuels");
ModelCore.RegisterSiteVar(PressureHead, "Succession.PressureHead");
ModelCore.RegisterSiteVar(ExtremeMinTemp, "Succession.ExtremeMinTemp");
}
//---------------------------------------------------------------------
public override void Initialize()
{
PlugIn.ModelCore.UI.WriteLine("Initializing " + Names.ExtensionName + " version " + typeof(PlugIn).Assembly.GetName().Version);
Cohort.DeathEvent += DeathEvent;
Globals.InitializeCore(ModelCore, ((Parameter <ushort>)Names.GetParameter(Names.IMAX)).Value);
EcoregionData.Initialize();
SiteVars.Initialize();
Landis.Utilities.Directory.EnsureExists("output");
Timestep = ((Parameter <int>)Names.GetParameter(Names.Timestep)).Value;
Parameter <string> CohortBinSizeParm = null;
if (Names.TryGetParameter(Names.CohortBinSize, out CohortBinSizeParm))
{
if (Int32.TryParse(CohortBinSizeParm.Value, out CohortBinSize))
{
if (CohortBinSize < Timestep)
{
throw new System.Exception("CohortBinSize cannot be smaller than Timestep.");
}
else
{
PlugIn.ModelCore.UI.WriteLine("Succession timestep = " + Timestep + "; CohortBinSize = " + CohortBinSize + ".");
}
}
else
{
throw new System.Exception("CohortBinSize is not an integer value.");
}
}
else
{
CohortBinSize = Timestep;
}
string Parallel = ((Parameter <string>)Names.GetParameter(Names.Parallel)).Value;
if (Parallel == "false")
{
ParallelThreads = 1;
PlugIn.ModelCore.UI.WriteLine(" MaxParallelThreads = " + ParallelThreads.ToString() + ".");
}
else if (Parallel == "true")
{
ParallelThreads = -1;
PlugIn.ModelCore.UI.WriteLine(" MaxParallelThreads determined by system.");
}
else
{
if (Int32.TryParse(Parallel, out ParallelThreads))
{
if (ParallelThreads < 1)
{
throw new System.Exception("Parallel cannot be < 1.");
}
else
{
PlugIn.ModelCore.UI.WriteLine(" MaxParallelThreads = " + ParallelThreads.ToString() + ".");
}
}
else
{
throw new System.Exception("Parallel must be 'true', 'false' or an integer >= 1.");
}
}
this.ThreadCount = ParallelThreads;
FTimeStep = 1.0F / Timestep;
//Latitude = ((Parameter<float>)PlugIn.GetParameter(Names.Latitude, 0, 90)).Value; // Now an ecoregion parameter
ObservedClimate.Initialize();
SpeciesPnET = new SpeciesPnET();
Landis.Library.PnETCohorts.SpeciesParameters.LoadParameters(SpeciesPnET);
Hydrology.Initialize();
SiteCohorts.Initialize();
string PARunits = ((Parameter <string>)Names.GetParameter(Names.PARunits)).Value;
if (PARunits != "umol" && PARunits != "W/m2")
{
throw new System.Exception("PARunits are not 'umol' or 'W/m2'.");
}
InitializeClimateLibrary(); // John McNabb: initialize climate library after EcoregionPnET has been initialized
//EstablishmentProbability.Initialize(Timestep); // Not used
// Initialize Reproduction routines:
Reproduction.SufficientResources = SufficientResources;
Reproduction.Establish = Establish;
Reproduction.AddNewCohort = AddNewCohort;
Reproduction.MaturePresent = MaturePresent;
Reproduction.PlantingEstablish = PlantingEstablish;
SeedingAlgorithms SeedAlgorithm = (SeedingAlgorithms)Enum.Parse(typeof(SeedingAlgorithms), Names.parameters["SeedingAlgorithm"].Value);
base.Initialize(ModelCore, SeedAlgorithm);
StartDate = new DateTime(((Parameter <int>)Names.GetParameter(Names.StartYear)).Value, 1, 15);
PlugIn.ModelCore.UI.WriteLine("Spinning up biomass or reading from maps...");
string InitialCommunitiesTXTFile = Names.GetParameter(Names.InitialCommunities).Value;
string InitialCommunitiesMapFile = Names.GetParameter(Names.InitialCommunitiesMap).Value;
InitialCommunitiesSpinup = Names.GetParameter(Names.InitialCommunitiesSpinup).Value;
Parameter <string> LitterMapFile;
bool litterMapFile = Names.TryGetParameter(Names.LitterMap, out LitterMapFile);
Parameter <string> WoodyDebrisMapFile;
bool woodyDebrisMapFile = Names.TryGetParameter(Names.WoodyDebrisMap, out WoodyDebrisMapFile);
InitializeSites(InitialCommunitiesTXTFile, InitialCommunitiesMapFile, ModelCore);
if (litterMapFile)
{
MapReader.ReadLitterFromMap(LitterMapFile.Value);
}
if (woodyDebrisMapFile)
{
MapReader.ReadWoodyDebrisFromMap(WoodyDebrisMapFile.Value);
}
// Convert PnET cohorts to biomasscohorts
ISiteVar <Landis.Library.BiomassCohorts.ISiteCohorts> biomassCohorts = PlugIn.ModelCore.Landscape.NewSiteVar <Landis.Library.BiomassCohorts.ISiteCohorts>();
foreach (ActiveSite site in PlugIn.ModelCore.Landscape)
{
biomassCohorts[site] = SiteVars.SiteCohorts[site];
if (SiteVars.SiteCohorts[site] != null && biomassCohorts[site] == null)
{
throw new System.Exception("Cannot convert PnET SiteCohorts to biomass site cohorts");
}
}
ModelCore.RegisterSiteVar(biomassCohorts, "Succession.BiomassCohorts");
ISiteVar <Landis.Library.AgeOnlyCohorts.ISiteCohorts> AgeCohortSiteVar = PlugIn.ModelCore.Landscape.NewSiteVar <Landis.Library.AgeOnlyCohorts.ISiteCohorts>();
ISiteVar <ISiteCohorts> PnETCohorts = PlugIn.ModelCore.Landscape.NewSiteVar <ISiteCohorts>();
foreach (ActiveSite site in PlugIn.ModelCore.Landscape)
{
AgeCohortSiteVar[site] = SiteVars.SiteCohorts[site];
PnETCohorts[site] = SiteVars.SiteCohorts[site];
SiteVars.FineFuels[site] = SiteVars.Litter[site].Mass;
IEcoregionPnET ecoregion = EcoregionData.GetPnETEcoregion(PlugIn.ModelCore.Ecoregion[site]);
IHydrology hydrology = new Hydrology(ecoregion.FieldCap);
SiteVars.PressureHead[site] = hydrology.GetPressureHead(ecoregion);
if (UsingClimateLibrary)
{
SiteVars.ExtremeMinTemp[site] = ((float)Enumerable.Min(Climate.Future_MonthlyData[Climate.Future_MonthlyData.Keys.Min()][ecoregion.Index].MonthlyTemp) - (float)(3.0 * ecoregion.WinterSTD));
}
else
{
SiteVars.ExtremeMinTemp[site] = 999;
}
}
ModelCore.RegisterSiteVar(AgeCohortSiteVar, "Succession.AgeCohorts");
ModelCore.RegisterSiteVar(PnETCohorts, "Succession.CohortsPnET");
}
public bool ComputePhotosynthesis(DateTime Date, IEcoregion ecoregion, int ix, int IMAX, Hydrology hydrology, ref float transpiration)
{
rootalloc = 0;
folalloc = 0;
woodalloc = 0;
releasednsc = 0;
netpsn = 0;
folresp = 0;
grosspsn = 0;
if (StaticVariables.Leaf_On[ecoregion, Cohort.Species, Date] == false)
{
return(true);
}
fWater = (float)Math.Pow(Math.Max(0, ((hydrology.Water - StaticVariables.WiltingPoint_mm[ecoregion, Cohort.Species]) / (Porosity[ecoregion] - StaticVariables.WiltingPoint_mm[ecoregion, Cohort.Species]))), GrMstSens[Cohort.Species]);
if (cohort.Fol > 0)
{
netpsn = fWater * frad[ix] * fage * StaticVariables.FTempPSN[ecoregion, Cohort.Species, Date] * StaticVariables.RefNetPsn[ecoregion, Cohort.Species, Date] * (cohort.Fol / IMAX);
folresp = fWater * StaticVariables.DTempRespDay[ecoregion, Cohort.Species, Date] * StaticVariables.RefResp[ecoregion, Cohort.Species, Date] * (cohort.Fol / IMAX);
grosspsn = netpsn + folresp;
}
//mm
// Constants.MCO2 / Constants.MC: gCO2/gC
transpiration = (grosspsn * (Constants.MCO2 / Constants.MC)) / StaticVariables.WUE_CO2_corr[ecoregion, Cohort.Species, Date];
if (transpiration > 0)
{
wue = netpsn / transpiration;
}
else
{
wue = 0;
}
cohort.NSC += netpsn;
if (cohort.NSC > (MaxNscFrac * cohort.Biomass))
{
releasednsc = cohort.NSC - (MaxNscFrac * cohort.Biomass);
}
else
{
releasednsc = Math.Min((DNSC[Cohort.Species] * (1 - frad[0])) / (float)IMAX * cohort.NSC, cohort.NSC);
}
if (cohort.NSC < 0.01F * cohort.Wood)
{
hasdeadcohorts = true;
return(false);
}
cohort.NSC -= releasednsc;
folalloc = frad[frad.Length - 1] * releasednsc;
cohort.Fol += folalloc / ConstantParameters.CFracBiomass;
if ((cohort.Root / cohort.Wood) < RtStRatio[Cohort.Species])
{
rootalloc = (releasednsc - folalloc) / ConstantParameters.CFracBiomass;
cohort.Root += rootalloc;
}
else
{
woodalloc = (releasednsc - folalloc) / ConstantParameters.CFracBiomass;
//System.Console.WriteLine(cohort.Root / cohort.Wood +"\t" + cohort.Root + "\t" + cohort.Wood + "\t" + RtStRatio[spc] + "\twoodalloc " + woodalloc);
cohort.Wood += woodalloc;
}
return(true);
}
public bool ComputePhotosynthesis(DateTime Date, IEcoregion ecoregion, int ix, int IMAX, Hydrology hydrology, ref float transpiration)
{
rootalloc = 0;
folalloc = 0;
woodalloc = 0;
releasednsc = 0;
netpsn = 0;
folresp = 0;
grosspsn = 0;
if (StaticVariables.Leaf_On[ecoregion, Cohort.Species, Date] == false) return true;
fWater = (float)Math.Pow(Math.Max(0, ((hydrology.Water - StaticVariables.WiltingPoint_mm[ecoregion, Cohort.Species]) / (Porosity[ecoregion] - StaticVariables.WiltingPoint_mm[ecoregion, Cohort.Species]))), GrMstSens[Cohort.Species]);
if (cohort.Fol > 0)
{
netpsn = fWater * frad[ix] * fage * StaticVariables.FTempPSN[ecoregion, Cohort.Species, Date] * StaticVariables.RefNetPsn[ecoregion, Cohort.Species, Date] * (cohort.Fol / IMAX);
folresp = fWater * StaticVariables.DTempRespDay[ecoregion, Cohort.Species, Date] * StaticVariables.RefResp[ecoregion, Cohort.Species, Date] * (cohort.Fol / IMAX);
grosspsn = netpsn + folresp;
}
//mm
// Constants.MCO2 / Constants.MC: gCO2/gC
transpiration = (grosspsn * (Constants.MCO2 / Constants.MC)) / StaticVariables.WUE_CO2_corr[ecoregion, Cohort.Species, Date];
if (transpiration > 0) wue = netpsn / transpiration;
else wue = 0;
cohort.NSC += netpsn;
if (cohort.NSC > (MaxNscFrac * cohort.Biomass)) releasednsc = cohort.NSC - (MaxNscFrac * cohort.Biomass);
else releasednsc = Math.Min((DNSC[Cohort.Species] * (1 - frad[0])) / (float)IMAX * cohort.NSC, cohort.NSC);
if (cohort.NSC < 0.01F * cohort.Wood)
{
hasdeadcohorts = true;
return false;
}
cohort.NSC -= releasednsc;
folalloc = frad[frad.Length - 1] * releasednsc;
cohort.Fol += folalloc / ConstantParameters.CFracBiomass;
if ((cohort.Root / cohort.Wood) < RtStRatio[Cohort.Species])
{
rootalloc = (releasednsc - folalloc) / ConstantParameters.CFracBiomass;
cohort.Root += rootalloc;
}
else
{
woodalloc = (releasednsc - folalloc) / ConstantParameters.CFracBiomass;
//System.Console.WriteLine(cohort.Root / cohort.Wood +"\t" + cohort.Root + "\t" + cohort.Wood + "\t" + RtStRatio[spc] + "\twoodalloc " + woodalloc);
cohort.Wood += woodalloc;
}
return true;
}
//---------------------------------------------------------------------
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");
}
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 void Grow(DateTime date, ActiveSite site, Hydrology hydrology, ForestFloor forestfloor, SiteCohorts Cohorts, SiteOutput siteoutput)
{
SetCanopyLayers(Cohorts, MaxAge, MaxBiom);
CalculateRadiationProfile(site, date);
CalculatePhotosynthesis(date, site, hydrology, forestfloor, siteoutput);
}
