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 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 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 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()
{
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");
}
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);
}