public void UpdateEstData(DateTime date, SiteConditions sc)
{
//System.Console.WriteLine("UpdateEstData");
string s = date.Year.ToString() + delim +
date.Month + delim +
date.ToString("MM/yyyy") + delim +
sc.hydrology.Water + delim +
sc.SubCanopyPAR + delim;
foreach (ISpecies spc in PlugIn.modelCore.Species)
{
s += sc.Establishment.Pest[spc] + delim ;
}
/*
foreach (ISpecies spc in PlugIn.modelCore.Species)
{
s += sc.Establishment.PotEstablishments[spc] + delim;
}
foreach (ISpecies spc in PlugIn.modelCore.Species)
{
s += sc.Establishment.Establishments[spc] + delim;
}
*/
FileContent.Add(s);
System.IO.File.WriteAllLines(OutputSiteFileName(site), FileContent.ToArray());
}
public void UpdateSiteData(DateTime date, SiteConditions sc)
{
IEcoregion ecoregion = PlugIn.modelCore.Ecoregion[sc.Site];
string s = date.Year.ToString() + delim +
date.Month + delim +
date.ToString("MM/yyyy") + delim +
sc.NrOfCohorts + delim +
StaticVariables.Tday[ecoregion, date] + delim +
StaticVariables.Prec[ecoregion, date] + delim +
sc.hydrology.RunOff + delim +
sc.hydrology.Transpiration + delim +
sc.hydrology.PrecipLoss + delim +
sc.hydrology.Water + delim +
sc.hydrology.SnowPack + delim +
sc.CanopyLAImax + delim +
StaticVariables.VPD[ecoregion, date] + delim +
sc.GrossPsn + delim +
sc.NetPsn + delim +
sc.AutotrophicRespiration + delim +
sc.forestfloor.HeterotrophicRespiration + delim +
sc.TotalBiomass + delim +
sc.TotalRoot + delim +
sc.TotalFoliage + delim +
sc.TotalNSC + delim +
sc.Litter.Mass + delim +
sc.WoodyDebris.Mass;
FileContent.Add(s);
}
public void UpdateSiteData(DateTime date, SiteConditions sc)
{
IEcoregion ecoregion = PlugIn.modelCore.Ecoregion[sc.Site];
string s = date.Year.ToString() + delim +
date.Month + delim +
date.ToString("MM/yyyy") + delim +
sc.NrOfCohorts + delim +
StaticVariables.Tday[ecoregion, date] + delim +
StaticVariables.Prec[ecoregion, date] + delim +
sc.hydrology.RunOff + delim +
sc.hydrology.Transpiration + delim +
sc.hydrology.PrecipLoss + delim +
sc.hydrology.Water + delim +
sc.hydrology.SnowPack + delim +
sc.CanopyLAImax + delim +
StaticVariables.VPD[ecoregion, date] + delim +
sc.GrossPsn + delim +
sc.NetPsn + delim +
sc.AutotrophicRespiration + delim +
sc.forestfloor.HeterotrophicRespiration + delim +
sc.TotalBiomass + delim +
sc.TotalRoot + delim +
sc.TotalFoliage + delim +
sc.TotalNSC + delim +
sc.Litter.Mass + delim +
sc.WoodyDebris.Mass;
FileContent.Add(s);
}
public void UpdateEstData(DateTime date, SiteConditions sc)
{
//System.Console.WriteLine("UpdateEstData");
string s = date.Year.ToString() + delim +
date.Month + delim +
date.ToString("MM/yyyy") + delim +
sc.hydrology.Water + delim +
sc.SubCanopyPAR + delim;
foreach (ISpecies spc in PlugIn.modelCore.Species)
{
s += sc.Establishment.Pest[spc] + delim;
}
/*
* foreach (ISpecies spc in PlugIn.modelCore.Species)
* {
* s += sc.Establishment.PotEstablishments[spc] + delim;
* }
* foreach (ISpecies spc in PlugIn.modelCore.Species)
* {
* s += sc.Establishment.Establishments[spc] + delim;
* }
*/
FileContent.Add(s);
System.IO.File.WriteAllLines(OutputSiteFileName(site), FileContent.ToArray());
}
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 ComputeEstablishment(DateTime date, SiteConditions sc)
{
double frad;
double fwater;
double w = sc.hydrology.Water / Porosity[PlugIn.modelCore.Ecoregion[site]];
// number of months that est is possible for stat purposes
foreach (ISpecies spc in PlugIn.modelCore.Species)
{
if (StaticVariables.PossibleEstmonth[PlugIn.modelCore.Ecoregion[sc.Site], spc, date] == false)
{
Pest[spc] = 0;
continue;
}
double v = Math.Min(1, sc.SubCanopyPAR / (2 * HalfSat[spc]));
if (v > 1 || v < 0)
{
throw new System.Exception("Error, subcanopy radiation cannot be " + sc.SubCanopyPAR);
}
if (w > 1 || w < 0)
{
throw new System.Exception("Error, bulk water cannot be " + sc.hydrology.Water);
}
frad = Math.Pow(v, EstRad[spc]);
fwater = Math.Pow(w, EstMoist[spc]);
Pest[spc] = 1 - (float)Math.Pow((1 - (float)Math.Min(1.0, frad * fwater)), (1 / (PlugIn.TStep * (float)PossibleEstmonthCount(date, spc, ecoregion))));
if (Pest[spc] > (float)R.NextDouble())
{
PotEstablishments[spc] = 1;
}
}
}
//---------------------------------------------------------------------
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");
}
//---------------------------------------------------------------------
protected override void InitializeSite(ActiveSite site,
ICommunity initialCommunity)
{
siteconditions[site] = new SiteConditions(site, initialCommunity);
}
//---------------------------------------------------------------------
protected override void InitializeSite(ActiveSite site,
ICommunity initialCommunity)
{
siteconditions[site] = new SiteConditions(site, initialCommunity);
}
public void ComputeEstablishment( DateTime date, SiteConditions sc)
{
double frad;
double fwater;
double w = sc.hydrology.Water / Porosity[PlugIn.modelCore.Ecoregion[site]];
// number of months that est is possible for stat purposes
foreach (ISpecies spc in PlugIn.modelCore.Species)
{
if (StaticVariables.PossibleEstmonth[PlugIn.modelCore.Ecoregion[sc.Site], spc, date] == false)
{
Pest[spc] = 0;
continue;
}
double v= Math.Min(1, sc.SubCanopyPAR / (2 * HalfSat[spc]));
if (v > 1 || v < 0) throw new System.Exception("Error, subcanopy radiation cannot be " + sc.SubCanopyPAR);
if (w > 1 || w < 0) throw new System.Exception("Error, bulk water cannot be " + sc.hydrology.Water);
frad = Math.Pow(v, EstRad[spc]);
fwater = Math.Pow(w, EstMoist[spc]);
Pest[spc] = 1 - (float)Math.Pow((1 - (float)Math.Min(1.0, frad * fwater)), (1 / (PlugIn.TStep * (float)PossibleEstmonthCount(date, spc, ecoregion))));
if (Pest[spc] > (float)R.NextDouble())
{
PotEstablishments[spc] = 1;
}
}
}
