public static List <IEcoregionPnETVariables> GetData(IEcoregionPnET ecoregion, DateTime start, DateTime end)
{
// Monthly simulation data untill but not including end
List <IEcoregionPnETVariables> data = new List <IEcoregionPnETVariables>();
// Date: the last date in the collection of running data
DateTime date = new DateTime(start.Ticks);
while (end.Ticks > date.Ticks)
{
if (all_values[ecoregion].ContainsKey(date) == false)
{
IObservedClimate observedClimate = ObservedClimate.GetData(ecoregion, date);
List <ISpeciesPNET> species = PlugIn.SpeciesPnET.AllSpecies.ToList();
IEcoregionPnETVariables ecoregion_variables = new EcoregionPnETVariables(observedClimate, date, wythers, dtemp, species, ecoregion.Latitude);
all_values[ecoregion].Add(date, ecoregion_variables);
}
data.Add(all_values[ecoregion][date]);
date = date.AddMonths(1);
}
return(data);
}
public static List <IEcoregionPnETVariables> GetClimateRegionData(IEcoregionPnET ecoregion, DateTime start, DateTime end, Climate.Phase spinupOrfuture)
{
// Monthly simulation data untill but not including end
List <IEcoregionPnETVariables> data = new List <IEcoregionPnETVariables>();
// Date: the last date in the collection of running data
DateTime date = new DateTime(start.Ticks);
var oldYear = -1;
while (end.Ticks > date.Ticks)
{
if (!all_values[ecoregion].ContainsKey(date))
{
if (date.Year != oldYear)
{
//PlugIn.ModelCore.UI.WriteLine($"Retrieving Climate Library for year {date.Year}.");
if (spinupOrfuture == Climate.Phase.Future_Climate)
{
if (Climate.Future_MonthlyData.ContainsKey(date.Year))
{
ClimateRegionData.AnnualWeather[ecoregion] = Climate.Future_MonthlyData[date.Year][ecoregion.Index];
}
}
else
{
if (Climate.Spinup_MonthlyData.ContainsKey(date.Year))
{
ClimateRegionData.AnnualWeather[ecoregion] = Climate.Spinup_MonthlyData[date.Year][ecoregion.Index];
}
}
oldYear = date.Year;
}
var monthlyData = new MonthlyClimateRecord(ecoregion, date);
List <ISpeciesPNET> species = PlugIn.SpeciesPnET.AllSpecies.ToList();
IEcoregionPnETVariables ecoregion_variables = new ClimateRegionPnETVariables(monthlyData, date, wythers, dtemp, species, ecoregion.Latitude);
all_values[ecoregion].Add(date, ecoregion_variables);
}
data.Add(all_values[ecoregion][date]);
date = date.AddMonths(1);
}
return(data);
}
protected override void AgeCohorts(ActiveSite site,
ushort years,
int?successionTimestep
)
{
DateTime date = new DateTime(PlugIn.StartDate.Year + PlugIn.ModelCore.CurrentTime - Timestep, 1, 15);
DateTime EndDate = date.AddYears(years);
IEcoregionPnET ecoregion_pnet = EcoregionPnET.GetPnETEcoregion(PlugIn.ModelCore.Ecoregion[site]);
List <IEcoregionPnETVariables> climate_vars = UsingClimateLibrary ? EcoregionPnET.GetClimateRegionData(ecoregion_pnet, date, EndDate, Climate.Phase.Future_Climate) : EcoregionPnET.GetData(ecoregion_pnet, date, EndDate);
sitecohorts[site].Grow(climate_vars);
Date = EndDate;
}
public void Calculate_Establishment(IEcoregionPnETVariables pnetvars, IEcoregionPnET ecoregion, float PAR, IHydrology hydrology)
{
foreach (ISpeciesPNET spc in PlugIn.SpeciesPnET.AllSpecies)
{
if (pnetvars.Tmin > spc.PsnTMin)
{
float frad = (float)Math.Pow(Cohort.ComputeFrad(PAR, spc.HalfSat), spc.EstRad);
float PressureHead = hydrology.GetPressureHead(ecoregion);
float fwater = (float)Math.Pow(Cohort.ComputeFWater(spc.H2, spc.H3, spc.H4, PressureHead), spc.EstMoist);
float pest = 1 - (float)Math.Pow(1.0 - (frad * fwater), Timestep);
if (!spc.PreventEstablishment)
{
if (pest > _pest[spc])
{
_pest[spc] = pest;
_fwater[spc] = fwater;
_frad[spc] = frad;
if (pest > (float)PlugIn.ContinuousUniformRandom())
{
if (HasEstablished(spc) == false)
{
_hasEstablished.Add(spc);
}
}
}
}
if (establishment_siteoutput != null)
{
establishment_siteoutput.Add(((int)pnetvars.Year).ToString() + "," + spc.Name + "," + pest + "," + fwater + "," + frad + "," + HasEstablished(spc));
// TODO: win time by reducing calls to write
establishment_siteoutput.Write();
}
}
}
}
public static SortedList <float, float> CalculateMonthlySoilTemps(SortedList <float, float> depthTempDict, IEcoregionPnET Ecoregion, int daysOfWinter, float snowPack, IHydrology hydrology, float lastTempBelowSnow)
{
//SortedList<float, float> depthTempDict = new SortedList<float, float>(); //for permafrost
//float lambAir = 0.023f;
//float lambIce = 2.29f;
//float omega = (float)(2 * Math.PI / 12.0);
float[] snowResults = CalculateSnowDepth(daysOfWinter, snowPack);
float sno_dep = snowResults[0];
float Psno_kg_m3 = snowResults[1];
if (Ecoregion.Variables.Tave >= 0)
{
float fracAbove0 = Ecoregion.Variables.Tmax / (Ecoregion.Variables.Tmax - Ecoregion.Variables.Tmin);
sno_dep = sno_dep * fracAbove0;
}
// from CLM model - https://escomp.github.io/ctsm-docs/doc/build/html/tech_note/Soil_Snow_Temperatures/CLM50_Tech_Note_Soil_Snow_Temperatures.html#soil-and-snow-thermal-properties
// Eq. 85 - Jordan (1991)
//float lambda_Snow = (float)(lambAir + ((0.0000775 * Psno_kg_m3) + (0.000001105 * Math.Pow(Psno_kg_m3, 2))) * (lambIce - lambAir)) * 3.6F * 24F; //(kJ/m/d/K) includes unit conversion from W to kJ
//float damping = (float)Math.Sqrt(omega / (2.0F * lambda_Snow));
float damping = CalculateSnowDamping(Psno_kg_m3);
float DRz_snow = (float)Math.Exp(-1.0F * sno_dep * damping); // Damping ratio for snow - adapted from Kang et al. (2000) and Liang et al. (2014)
// Permafrost calculations - from "Soil thawing worksheet.xlsx"
//
//if (Ecoregion.Variables.Tave < minMonthlyAvgTemp)
// minMonthlyAvgTemp = Ecoregion.Variables.Tave;
float porosity = Ecoregion.Porosity / Ecoregion.RootingDepth; //m3/m3
float waterContent = hydrology.Water / Ecoregion.RootingDepth; //m3/m3
float ga = 0.035F + 0.298F * (waterContent / porosity);
float Fa = ((2.0F / 3.0F) / (1.0F + ga * ((Constants.lambda_a / Constants.lambda_w) - 1.0F))) + ((1.0F / 3.0F) / (1.0F + (1.0F - 2.0F * ga) * ((Constants.lambda_a / Constants.lambda_w) - 1.0F))); // ratio of air temp gradient
float Fs = PressureHeadSaxton_Rawls.GetFs(Ecoregion.SoilType);
float lambda_s = PressureHeadSaxton_Rawls.GetLambda_s(Ecoregion.SoilType);
float lambda_theta = (Fs * (1.0F - porosity) * lambda_s + Fa * (porosity - waterContent) * Constants.lambda_a + waterContent * Constants.lambda_w) / (Fs * (1.0F - porosity) + Fa * (porosity - waterContent) + waterContent); //soil thermal conductivity (kJ/m/d/K)
float D = lambda_theta / PressureHeadSaxton_Rawls.GetCTheta(Ecoregion.SoilType); //m2/day
float Dmonth = D * Ecoregion.Variables.DaySpan; // m2/month
float ks = Dmonth * 1000000F / (Ecoregion.Variables.DaySpan * (Constants.SecondsPerHour * 24)); // mm2/s
float d = (float)Math.Pow((Constants.omega / (2.0F * Dmonth)), (0.5));
float maxDepth = Ecoregion.RootingDepth + Ecoregion.LeakageFrostDepth;
float freezeDepth = maxDepth;
float testDepth = 0;
//if (lastTempBelowSnow == float.MaxValue)
//{
// //int mCount = Math.Min(12, data.Count());
// //float tSum = 0;
// //foreach (int z in Enumerable.Range(0, mCount))
// //{
// // tSum += data[z].Tave;
// //}
// //float annualTavg = tSum / mCount;
// float tempBelowSnow = Ecoregion.Variables.Tave;
// if (sno_dep > 0)
// {
// tempBelowSnow = annualTavg + (Ecoregion.Variables.Tave - annualTavg) * DRz_snow;
// }
// lastTempBelowSnow = tempBelowSnow;
// while (testDepth <= (maxDepth / 1000.0))
// {
// float DRz = (float)Math.Exp(-1.0F * testDepth * d); // adapted from Kang et al. (2000) and Liang et al. (2014)
// float zTemp = annualTavg + (tempBelowSnow - annualTavg) * DRz;
// depthTempDict[testDepth] = zTemp;
// if ((zTemp <= 0) && (testDepth < freezeDepth))
// freezeDepth = testDepth;
// testDepth += 0.25F;
// }
//}
//else
//{
float tempBelowSnow = Ecoregion.Variables.Tave;
if (sno_dep > 0)
{
tempBelowSnow = lastTempBelowSnow + (Ecoregion.Variables.Tave - lastTempBelowSnow) * DRz_snow;
}
lastTempBelowSnow = tempBelowSnow;
while (testDepth <= (maxDepth / 1000.0))
{
float DRz = (float)Math.Exp(-1.0F * testDepth * d); // adapted from Kang et al. (2000) and Liang et al. (2014)
float zTemp = depthTempDict[testDepth] + (tempBelowSnow - depthTempDict[testDepth]) * DRz;
depthTempDict[testDepth] = zTemp;
//if ((zTemp <= 0) && (testDepth < freezeDepth))
// freezeDepth = testDepth;
if (testDepth == 0f)
{
testDepth = 0.10f;
}
else if (testDepth == 0.10f)
{
testDepth = 0.25f;
}
else
{
testDepth += 0.25F;
}
}
//}
return(depthTempDict);
}
public float GetPressureHead(IEcoregionPnET ecoregion)
{
return pressureheadtable[ecoregion, (int)water];
}
// Makes sure that litters are allocated to the appropriate site
public static void SetSiteAccessFunctions(SiteCohorts sitecohorts)
{
Cohort.addlitter = sitecohorts.AddLitter;
Cohort.addwoodydebris = sitecohorts.AddWoodyDebris;
Cohort.ecoregion = sitecohorts.Ecoregion;
}
//---------------------------------------------------------------------
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 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 Dictionary<ISpeciesPNET, float> Calculate_Establishment_Month(IEcoregionPnETVariables pnetvars, IEcoregionPnET ecoregion, float PAR, IHydrology hydrology)
{
Dictionary<ISpeciesPNET, float> estabDict = new Dictionary<ISpeciesPNET, float>();
foreach (ISpeciesPNET spc in PlugIn.SpeciesPnET.AllSpecies)
{
if (pnetvars.Tmin > spc.PsnTMin)
{
float frad = (float)Math.Pow(Cohort.ComputeFrad(PAR, spc.HalfSat), spc.EstRad);
float PressureHead = hydrology.GetPressureHead(ecoregion);
float fwater = (float)Math.Pow(Cohort.ComputeFWater(spc.H2, spc.H3, spc.H4, PressureHead), spc.EstMoist);
float pest = 1 - (float)Math.Pow(1.0 - (frad * fwater), Timestep);
estabDict[spc] = pest;
if (fwater < _fwater[spc])
{
_fwater[spc] = fwater;
}
if (frad < _frad[spc])
{
_frad[spc] = frad;
}
/*if (establishment_siteoutput != null)
{
establishment_siteoutput.Add(((int)pnetvars.Year).ToString() + "," + spc.Name + "," + pest + "," + fwater + "," + frad + "," + HasEstablished(spc));
// TODO: win time by reducing calls to write
establishment_siteoutput.Write();
}
* */
}
}
return estabDict;
}
//---------------------------------------------------------------------
// Get the pressurehead (mmH2O) for the current water content (converted from proportion to percent)
public float GetPressureHead(IEcoregionPnET ecoregion)
{
return(pressureheadtable[ecoregion, (int)Math.Round(water * 100.0)]);
}
/*public static void Initialize(int timestep)
* {
* Timestep = timestep;
*
*
* }*/
public Dictionary <ISpeciesPNET, float> Calculate_Establishment_Month(IEcoregionPnETVariables pnetvars, IEcoregionPnET ecoregion, float PAR, IHydrology hydrology, float minHalfSat, float maxHalfSat, bool invertPest)
{
Dictionary <ISpeciesPNET, float> estabDict = new Dictionary <ISpeciesPNET, float>();
float halfSatRange = maxHalfSat - minHalfSat;
foreach (ISpeciesPNET spc in PlugIn.SpeciesPnET.AllSpecies)
{
if (pnetvars.Tmin > spc.PsnTMin && pnetvars.Tmax < spc.PsnTMax)
{
// Adjust HalfSat for CO2 effect
float halfSatIntercept = spc.HalfSat - 350 * spc.CO2HalfSatEff;
float adjHalfSat = spc.CO2HalfSatEff * pnetvars.CO2 + halfSatIntercept;
float frad = (float)(Math.Min(1.0, (Math.Pow(Cohort.ComputeFrad(PAR, adjHalfSat), 2) * (1 / (Math.Pow(spc.EstRad, 2))))));
float adjFrad = frad;
// Optional adjustment to invert Pest based on relative halfSat
if (invertPest && halfSatRange > 0)
{
float frad_adj_int = (spc.HalfSat - minHalfSat) / halfSatRange;
float frad_slope = (frad_adj_int * 2) - 1;
adjFrad = 1 - frad_adj_int + frad * frad_slope;
}
float PressureHead = hydrology.GetPressureHead(ecoregion);
float fwater = (float)(Math.Min(1.0, (Math.Pow(Cohort.ComputeFWater(spc.H1, spc.H2, spc.H3, spc.H4, PressureHead), 2) * (1 / (Math.Pow(spc.EstMoist, 2))))));
float pest = (float)Math.Min(1.0, adjFrad * fwater);
estabDict[spc] = pest;
_fwater[spc] = fwater;
_frad[spc] = adjFrad;
}
}
return(estabDict);
}
/*public void Calculate_Establishment(IEcoregionPnETVariables pnetvars, IEcoregionPnET ecoregion, float PAR, IHydrology hydrology)
* {
* foreach (ISpeciesPNET spc in PlugIn.SpeciesPnET.AllSpecies)
* {
*
*
* if (pnetvars.Tmin > spc.PsnTMin)
* {
* // Adjust HalfSat for CO2 effect
* float halfSatIntercept = spc.HalfSat - 350 * spc.CO2HalfSatEff;
* float adjHalfSat = spc.CO2HalfSatEff * pnetvars.CO2 + halfSatIntercept;
* float frad = (float)Math.Pow(Cohort.ComputeFrad(PAR, adjHalfSat), spc.EstRad);
*
*
* float PressureHead = hydrology.GetPressureHead(ecoregion);
*
* float fwater = (float)Math.Pow(Cohort.ComputeFWater(spc.H1,spc.H2, spc.H3, spc.H4, PressureHead), spc.EstMoist);
*
* float pest = 1 - (float)Math.Pow(1.0 - (frad * fwater), Timestep);
* if (!spc.PreventEstablishment)
* {
* if (pest > _pest[spc])
* {
* _pest[spc] = pest;
* _fwater[spc] = fwater;
* _frad[spc] = frad;
*
* if (pest > (float)PlugIn.ContinuousUniformRandom())
* {
* if (HasEstablished(spc) == false)
* {
* _hasEstablished.Add(spc);
* }
*
* }
*
* }
* }
* if (establishment_siteoutput != null)
* {
*
* establishment_siteoutput.Add(((int)pnetvars.Year).ToString() + "," + spc.Name + "," + pest + "," + fwater + "," + frad + "," + HasEstablished(spc));
*
* // TODO: win time by reducing calls to write
* establishment_siteoutput.Write();
* }
* }
* }
* }
*/
public Dictionary <ISpeciesPNET, float> Calculate_Establishment_Month(IEcoregionPnETVariables pnetvars, IEcoregionPnET ecoregion, float PAR, IHydrology hydrology, float minHalfSat, float maxHalfSat, bool invertPest)
{
Dictionary <ISpeciesPNET, float> estabDict = new Dictionary <ISpeciesPNET, float>();
//_fwater = new Dictionary<ISpeciesPNET, float>();
//_pest = new Dictionary<ISpeciesPNET, float>();
//_frad = new Dictionary<ISpeciesPNET, float>();
float halfSatRange = maxHalfSat - minHalfSat;
foreach (ISpeciesPNET spc in PlugIn.SpeciesPnET.AllSpecies)
{
if (pnetvars.Tmin > spc.PsnTMin && pnetvars.Tmax < spc.PsnTMax)
{
// Adjust HalfSat for CO2 effect
float halfSatIntercept = spc.HalfSat - 350 * spc.CO2HalfSatEff;
float adjHalfSat = spc.CO2HalfSatEff * pnetvars.CO2 + halfSatIntercept;
float frad = (float)(Math.Min(1.0, (Math.Pow(Cohort.ComputeFrad(PAR, adjHalfSat), 2) * (1 / (Math.Pow(spc.EstRad, 2))))));
float adjFrad = frad;
// Optional adjustment to invert Pest based on relative halfSat
if (invertPest && halfSatRange > 0)
{
float frad_adj_int = (spc.HalfSat - minHalfSat) / halfSatRange;
float frad_slope = (frad_adj_int * 2) - 1;
adjFrad = 1 - frad_adj_int + frad * frad_slope;
}
float PressureHead = hydrology.GetPressureHead(ecoregion);
float fwater = (float)(Math.Min(1.0, (Math.Pow(Cohort.ComputeFWater(spc.H1, spc.H2, spc.H3, spc.H4, PressureHead), 2) * (1 / (Math.Pow(spc.EstMoist, 2))))));
//float pest = 1 - (float)Math.Pow(1.0 - (frad * fwater * spc.MaxPest), Timestep);
float pest = (float)Math.Min(1.0, adjFrad * fwater);
estabDict[spc] = pest;
_pest[spc] = pest;
_fwater[spc] = fwater;
_frad[spc] = adjFrad;
/*if (fwater < _fwater[spc])
* {
* _fwater[spc] = fwater;
* }
* if (frad < _frad[spc])
* {
* _frad[spc] = frad;
* }
*/
/*if (establishment_siteoutput != null)
* {
*
* establishment_siteoutput.Add(((int)pnetvars.Year).ToString() + "," + spc.Name + "," + pest + "," + fwater + "," + frad + "," + HasEstablished(spc));
*
* // TODO: win time by reducing calls to write
* establishment_siteoutput.Write();
* }
* */
}
}
return(estabDict);
}
public static List<IEcoregionPnETVariables> GetData(IEcoregionPnET ecoregion, DateTime start, DateTime end)
{
// Monthly simulation data untill but not including end
List<IEcoregionPnETVariables> data = new List<IEcoregionPnETVariables>();
// Date: the last date in the collection of running data
DateTime date = new DateTime(start.Ticks);
while (end.Ticks > date.Ticks)
{
if (all_values[ecoregion].ContainsKey(date) == false)
{
IObservedClimate observedClimate = ObservedClimate.GetData(ecoregion, date);
List<ISpeciesPNET> species = PlugIn.SpeciesPnET.AllSpecies.ToList();
IEcoregionPnETVariables ecoregion_variables = new EcoregionPnETVariables(observedClimate, date, wythers, dtemp, species);
all_values[ecoregion].Add(date, ecoregion_variables);
}
data.Add(all_values[ecoregion][date]);
date = date.AddMonths(1);
}
return data;
}
