//---------------------------------------------------------------------
/// <summary>
/// Initializes the module.
/// </summary>
public static void Initialize()
{
leafBiomassCohorts = PlugIn.ModelCore.Landscape.NewSiteVar<Library.LeafBiomassCohorts.ISiteCohorts>();
biomassCohortsSiteVar = new BiomassCohortsSiteVar(leafBiomassCohorts);
baseCohortsSiteVar = new BaseCohortsSiteVar(leafBiomassCohorts);
timeOfLast = PlugIn.ModelCore.Landscape.NewSiteVar<int>();
// Dead biomass:
surfaceDeadWood = PlugIn.ModelCore.Landscape.NewSiteVar<Layer>();
soilDeadWood = PlugIn.ModelCore.Landscape.NewSiteVar<Layer>();
surfaceStructural = PlugIn.ModelCore.Landscape.NewSiteVar<Layer>();
surfaceMetabolic = PlugIn.ModelCore.Landscape.NewSiteVar<Layer>();
soilStructural = PlugIn.ModelCore.Landscape.NewSiteVar<Layer>();
soilMetabolic = PlugIn.ModelCore.Landscape.NewSiteVar<Layer>();
// Soil Layers
som1surface = PlugIn.ModelCore.Landscape.NewSiteVar<Layer>();
som1soil = PlugIn.ModelCore.Landscape.NewSiteVar<Layer>();
som2 = PlugIn.ModelCore.Landscape.NewSiteVar<Layer>();
som3 = PlugIn.ModelCore.Landscape.NewSiteVar<Layer>();
// Other Layers
stream = PlugIn.ModelCore.Landscape.NewSiteVar<Layer>();
sourceSink = PlugIn.ModelCore.Landscape.NewSiteVar<Layer>();
// Other variables
mineralN = PlugIn.ModelCore.Landscape.NewSiteVar<double>();
resorbedN = PlugIn.ModelCore.Landscape.NewSiteVar<double>();
waterMovement = PlugIn.ModelCore.Landscape.NewSiteVar<double>();
availableWater = PlugIn.ModelCore.Landscape.NewSiteVar<double>();
soilWaterContent = PlugIn.ModelCore.Landscape.NewSiteVar<double>();
decayFactor = PlugIn.ModelCore.Landscape.NewSiteVar<double>();
soilTemperature = PlugIn.ModelCore.Landscape.NewSiteVar<double>();
anaerobicEffect = PlugIn.ModelCore.Landscape.NewSiteVar<double>();
// Annual accumulators
grossMineralization = PlugIn.ModelCore.Landscape.NewSiteVar<double>();
ag_nppC = PlugIn.ModelCore.Landscape.NewSiteVar<double>();
bg_nppC = PlugIn.ModelCore.Landscape.NewSiteVar<double>();
litterfallC = PlugIn.ModelCore.Landscape.NewSiteVar<double>();
monthlyAGNPPC = PlugIn.ModelCore.Landscape.NewSiteVar<double[]>();
monthlyBGNPPC = PlugIn.ModelCore.Landscape.NewSiteVar<double[]>();
monthlyNEE = PlugIn.ModelCore.Landscape.NewSiteVar<double[]>();
AnnualNEE = PlugIn.ModelCore.Landscape.NewSiteVar<double>();
FireCEfflux = PlugIn.ModelCore.Landscape.NewSiteVar<double>();
FireNEfflux = PlugIn.ModelCore.Landscape.NewSiteVar<double>();
monthlyResp = PlugIn.ModelCore.Landscape.NewSiteVar<double[]>();
cohortLeafN = PlugIn.ModelCore.Landscape.NewSiteVar<double>();
cohortLeafC = PlugIn.ModelCore.Landscape.NewSiteVar<double>();
cohortWoodN = PlugIn.ModelCore.Landscape.NewSiteVar<double>();
cohortWoodC = PlugIn.ModelCore.Landscape.NewSiteVar<double>();
TotalWoodBiomass = PlugIn.ModelCore.Landscape.NewSiteVar<double>();
AgeMortality = PlugIn.ModelCore.Landscape.NewSiteVar<double>();
Nvol = PlugIn.ModelCore.Landscape.NewSiteVar<double>();
PrevYearMortality = PlugIn.ModelCore.Landscape.NewSiteVar<int>();
totalNuptake = PlugIn.ModelCore.Landscape.NewSiteVar<double>();
monthlymineralN = PlugIn.ModelCore.Landscape.NewSiteVar<double[]>();
frassC = PlugIn.ModelCore.Landscape.NewSiteVar<double>();
lai = PlugIn.ModelCore.Landscape.NewSiteVar<double>();
HarvestPrescriptionName = PlugIn.ModelCore.GetSiteVar<string>("Harvest.PrescriptionName");
PlugIn.ModelCore.RegisterSiteVar(leafBiomassCohorts, "Succession.LeafBiomassCohorts");
PlugIn.ModelCore.RegisterSiteVar(biomassCohortsSiteVar, "Succession.BiomassCohorts");
PlugIn.ModelCore.RegisterSiteVar(baseCohortsSiteVar, "Succession.AgeCohorts");
foreach (ActiveSite site in PlugIn.ModelCore.Landscape)
{
// site cohorts are initialized by the PlugIn.InitializeSite method
//leafBiomassCohorts[site] = new SiteCohorts();
//Console.Write("-");
surfaceDeadWood[site] = new Layer(LayerName.Wood, LayerType.Surface);
soilDeadWood[site] = new Layer(LayerName.CoarseRoot, LayerType.Soil);
surfaceStructural[site] = new Layer(LayerName.Structural, LayerType.Surface);
surfaceMetabolic[site] = new Layer(LayerName.Metabolic, LayerType.Surface);
soilStructural[site] = new Layer(LayerName.Structural, LayerType.Soil);
soilMetabolic[site] = new Layer(LayerName.Metabolic, LayerType.Soil);
som1surface[site] = new Layer(LayerName.SOM1, LayerType.Surface);
som1soil[site] = new Layer(LayerName.SOM1, LayerType.Soil);
som2[site] = new Layer(LayerName.SOM2, LayerType.Soil);
som3[site] = new Layer(LayerName.SOM3, LayerType.Soil);
stream[site] = new Layer(LayerName.Other, LayerType.Other);
sourceSink[site] = new Layer(LayerName.Other, LayerType.Other);
monthlyAGNPPC[site] = new double[12];
monthlyBGNPPC[site] = new double[12];
monthlyNEE[site] = new double[12];
monthlyResp[site] = new double[12];
//monthlymineralN[site] = new double[12];
AvailableN.CohortResorbedNallocation = new Dictionary<int, Dictionary<int, double>>();
}
}
//---------------------------------------------------------------------
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");
}
//---------------------------------------------------------------------
/// <summary>
/// Initializes the module.
/// </summary>
public static void Initialize()
{
numberofcanopylayers = PlugIn.ModelCore.Landscape.NewSiteVar<int>();
cohorts = PlugIn.ModelCore.Landscape.NewSiteVar<ISiteCohorts>();
BiomassCohortsSiteVar = new BiomassCohortsSiteVar(cohorts);
baseCohortsSiteVar = new Landis.Extension.Succession.Biomass.BaseCohortsSiteVar(BiomassCohortsSiteVar);
woodyDebris = PlugIn.ModelCore.Landscape.NewSiteVar<Pool>();
litter = PlugIn.ModelCore.Landscape.NewSiteVar<Pool>();
HasSiteOutput = PlugIn.ModelCore.Landscape.NewSiteVar<bool>();
SnowPack = PlugIn.ModelCore.Landscape.NewSiteVar<float>();
Water = PlugIn.ModelCore.Landscape.NewSiteVar<float>();
Infiltration = PlugIn.ModelCore.Landscape.NewSiteVar<float>();
establishments = PlugIn.ModelCore.Landscape.NewSiteVar<Landis.Extension.Succession.Biomass.Species.AuxParm<bool>>();
pest = PlugIn.ModelCore.Landscape.NewSiteVar<Landis.Extension.Succession.Biomass.Species.AuxParm<float>>();
TotalBiomass = PlugIn.ModelCore.Landscape.NewSiteVar<int>();
AnnualTranspiration = PlugIn.ModelCore.Landscape.NewSiteVar<float>();
CanopyLAI = PlugIn.ModelCore.Landscape.NewSiteVar<float>();
GrossPsn = PlugIn.ModelCore.Landscape.NewSiteVar<float>();
NetPsn = PlugIn.ModelCore.Landscape.NewSiteVar<float>();
transpiration = PlugIn.ModelCore.Landscape.NewSiteVar<float>();
AutotrophicRespiration = PlugIn.ModelCore.Landscape.NewSiteVar<float>();
HeterotrophicRespiration = PlugIn.ModelCore.Landscape.NewSiteVar<float>();
WFPS = PlugIn.ModelCore.Landscape.NewSiteVar<float>();
CanopyLAImax = PlugIn.ModelCore.Landscape.NewSiteVar<float>();
SubCanopyPAR = PlugIn.ModelCore.Landscape.NewSiteVar<float>();
SubCanopyPARmax = PlugIn.ModelCore.Landscape.NewSiteVar<float>();
foreach (ActiveSite site in PlugIn.ModelCore.Landscape)
{
// site cohorts are initialized by the PlugIn.InitializeSite method
woodyDebris[site] = new Pool();
litter[site] = new Pool();
HasSiteOutput[site] = false;
SnowPack[site] = 0;
Water[site] = 0;
Infiltration[site] = 0;
TotalBiomass[site] = 0;
numberofcanopylayers[site] = 0;
GrossPsn[site] = 0;
NetPsn[site] = 0;
AutotrophicRespiration[site] = 0;
HeterotrophicRespiration[site] = 0;
transpiration[site] = 0;
WFPS[site] = 0;
establishments[site] = new Landis.Extension.Succession.Biomass.Species.AuxParm<bool>(PlugIn.ModelCore.Species);
pest[site] = new Landis.Extension.Succession.Biomass.Species.AuxParm<float>(PlugIn.ModelCore.Species);
AnnualTranspiration[site] = 0;
CanopyLAI[site] = 0;
SubCanopyPAR[site] = 0;
SubCanopyPARmax[site] = 0;
foreach (ISpecies spc in PlugIn.ModelCore.Species)
{
establishments[site][spc] = false;
pest[site][spc] = 0;
}
}
PlugIn.ModelCore.RegisterSiteVar(cohorts, "Succession.BiomassCohortsPnET");
PlugIn.ModelCore.RegisterSiteVar(BiomassCohortsSiteVar, "Succession.BiomassCohorts");
PlugIn.ModelCore.RegisterSiteVar(baseCohortsSiteVar, "Succession.AgeCohorts");
PlugIn.ModelCore.RegisterSiteVar(SiteVars.Establishments, "Succession.Establishments");
PlugIn.ModelCore.RegisterSiteVar(SiteVars.WoodyDebris, "Succession.WoodyDebris");
PlugIn.ModelCore.RegisterSiteVar(SiteVars.Litter, "Succession.Litter");
PlugIn.ModelCore.RegisterSiteVar(SiteVars.HasSiteOutput, "Succession.HasSiteOutput");
PlugIn.ModelCore.RegisterSiteVar(SiteVars.Water, "Succession.SoilWater");
PlugIn.ModelCore.RegisterSiteVar(SiteVars.AnnualTranspiration , "Succession.AnnualTranspiration");
PlugIn.ModelCore.RegisterSiteVar(SiteVars.SubCanopyPAR, "Succession.SubCanopyPARmax");
PlugIn.ModelCore.RegisterSiteVar(SiteVars.CanopyLAImax, "Succession.CanopyLAImax");
}
//---------------------------------------------------------------------
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);
}
