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 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 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()
{
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()
{
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 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");
}
