//---------------------------------------------------------------------
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 void CompareWythersWithEarlier()
{
string ClimateFileName = @"C:\Users\debruijna\Desktop\PnET-Succession\EricCalibration\Oconto_weather_Temp0_Prec0_PAR0.txt";
IObservedClimate observed = new ObservedClimate(ClimateFileName);
//PnETSpeciesParameters FolN SLWmax SLWDel TOfol AmaxA AmaxB HalfSat H3 H4 PsnAgeRed PsnTMin PsnTOpt k
//tsugcana 1.2 190 0 0.3333 5.3 21.5 230 114 235 5 1 19 0.5
//PnETSpeciesParameters WUEcnst MaintResp DNSC FracBelowG EstMoist EstRad FracFol FrActWd
//tsugcana 6 0.0005 0.05 0.33 1 1 0.13 0.00005 <<tsugcan
/*
LandisData PnETGenericParameters
PnETGenericParameters Value
BFolResp 0.1
TOroot 0.02
TOwood 0.01
MaxCanopyLayers 2
IMAX 70
>>DNSC 0.05 <<target NSCfraction
>>MaintResp 0.0025
PreventEstablishment true
wythers true
*/
Landis.Core.PostFireRegeneration postfireregen = Landis.Core.PostFireRegeneration.Resprout;
float wuecnst = 6;
float dnsc =0.05F;
float cfracbiomass =0.45F;
float kwdlit = 0.1F;
float fracbelowg =0.33F;
float fracfol =0.13F;
float fractWd = 0.00005F;
float psnagered =5;
ushort h2 =0;
ushort h3 =114;
ushort h4 =235;
float slwdel =0;
float slwmax =190;
float tofol =0.3333F;
float toroot =0.02F;
float halfsat =230F;
float initialnsc =7;
float k =0.5F;
float towood =0.01F;
float estrad =1;
float estmoist =1;
float follignin =0.2F;
bool preventestablishment =false;
float psntopt =19F;
float q10 =2F;
float psntmin =1F;
float dvpd1 =0.05F;
float dvpd2 =2F;
float foln =1.2F;
float amaxa =5.3F;
float amaxb =21.5F;
float maintresp =0.0005F;
float bfolresp =0.1F;
int Index =0;
string name = "tsugcana";
int maxSproutAge =0;
int minSproutAge =0;
int maxSeedDist =100;
int effectiveSeedDist =30;
float vegReprodProb = 0;
byte fireTolerance =3;
byte shadeTolerance =5;
int maturity =60;
int longevity =450;
ISpeciesPNET species = new SpeciesPnET(Landis.Core.PostFireRegeneration.Resprout,
wuecnst,dnsc,cfracbiomass,kwdlit,fracbelowg,fracfol,fractWd,psnagered,h2,h3,h4,slwdel,slwmax,tofol
,toroot,halfsat,initialnsc,k,towood,estrad,estmoist,follignin,preventestablishment,psntopt,q10,psntmin,dvpd1
,dvpd2,foln,amaxa,amaxb,maintresp,bfolresp,Index,name,maxSproutAge,minSproutAge,maxSeedDist,effectiveSeedDist,vegReprodProb
,fireTolerance,shadeTolerance,maturity,longevity);
DateTime date = new DateTime(1910, 1,1);
string fn = @"C:\Users\debruijna\Desktop\FTempRespDayRefResp.txt";
System.IO.StreamWriter sw = new System.IO.StreamWriter(fn);
sw.WriteLine("date" + "\t" + "FTempRespDayRefRespWythers" + "\t" + "FTempRespDayRefRespNoWythers");
while (date < new DateTime(1950, 1, 1))
{
IObservedClimate climate = ObservedClimate.GetData(observed, date);
float FTempRespDayRefRespWythers = new EcoregionPnETVariables(climate, date, true, new System.Collections.Generic.List<ISpeciesPNET>() { species })[species.Name].FTempRespDayRefResp;
float FTempRespDayRefRespNoWythers = new EcoregionPnETVariables(climate, date, false, new System.Collections.Generic.List<ISpeciesPNET>() { species })[species.Name].FTempRespDayRefResp;
sw.WriteLine(date + "\t" + FTempRespDayRefRespWythers + "\t" + FTempRespDayRefRespNoWythers);
date = date.AddMonths(1);
}
sw.Close();
}
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 SpeciesPnET()
{
#region initialization of private static species variables
wuecnst = ((Landis.Library.Parameters.Species.AuxParm<float>)(Parameter<float>)PlugIn.GetParameter("WUEcnst"));
dnsc = ((Landis.Library.Parameters.Species.AuxParm<float>)(Parameter<float>)PlugIn.GetParameter("DNSC"));
cfracbiomass= ((Landis.Library.Parameters.Species.AuxParm<float>)(Parameter<float>)PlugIn.GetParameter("CFracBiomass"));
kwdlit = ((Landis.Library.Parameters.Species.AuxParm<float>)(Parameter<float>)PlugIn.GetParameter("kwdlit"));
fracbelowg = ((Landis.Library.Parameters.Species.AuxParm<float>)(Parameter<float>)PlugIn.GetParameter("fracbelowg"));
fracfol = ((Landis.Library.Parameters.Species.AuxParm<float>)(Parameter<float>)PlugIn.GetParameter("fracfol"));
fractWd = ((Landis.Library.Parameters.Species.AuxParm<float>)(Parameter<float>)PlugIn.GetParameter("fractWd"));
psnagered = ((Landis.Library.Parameters.Species.AuxParm<float>)(Parameter<float>)PlugIn.GetParameter("psnagered"));
h2 = ((Landis.Library.Parameters.Species.AuxParm<ushort>)(Parameter<ushort>)PlugIn.GetParameter("h2"));
h3 = ((Landis.Library.Parameters.Species.AuxParm<ushort>)(Parameter<ushort>)PlugIn.GetParameter("h3"));
h4 = ((Landis.Library.Parameters.Species.AuxParm<ushort>)(Parameter<ushort>)PlugIn.GetParameter("h4"));
slwdel = ((Landis.Library.Parameters.Species.AuxParm<float>)(Parameter<float>)PlugIn.GetParameter("slwdel"));
slwmax = ((Landis.Library.Parameters.Species.AuxParm<float>)(Parameter<float>)PlugIn.GetParameter("slwmax"));
tofol = ((Landis.Library.Parameters.Species.AuxParm<float>)(Parameter<float>)PlugIn.GetParameter("tofol"));
halfsat = ((Landis.Library.Parameters.Species.AuxParm<float>)(Parameter<float>)PlugIn.GetParameter("halfsat"));
toroot = ((Landis.Library.Parameters.Species.AuxParm<float>)(Parameter<float>)PlugIn.GetParameter("toroot"));
initialnsc = ((Landis.Library.Parameters.Species.AuxParm<float>)(Parameter<float>)PlugIn.GetParameter("initialnsc")); ;
k = ((Landis.Library.Parameters.Species.AuxParm<float>)(Parameter<float>)PlugIn.GetParameter("k")); ;
towood = ((Landis.Library.Parameters.Species.AuxParm<float>)(Parameter<float>)PlugIn.GetParameter("towood")); ;
estrad = ((Landis.Library.Parameters.Species.AuxParm<float>)(Parameter<float>)PlugIn.GetParameter("estrad")); ;
estmoist = ((Landis.Library.Parameters.Species.AuxParm<float>)(Parameter<float>)PlugIn.GetParameter("estmoist"));
follignin = ((Landis.Library.Parameters.Species.AuxParm<float>)(Parameter<float>)PlugIn.GetParameter("follignin"));
preventestablishment = ((Landis.Library.Parameters.Species.AuxParm<bool>)(Parameter<bool>)PlugIn.GetParameter("preventestablishment"));
psntopt = ((Landis.Library.Parameters.Species.AuxParm<float>)(Parameter<float>)PlugIn.GetParameter("psntopt"));
q10 = ((Landis.Library.Parameters.Species.AuxParm<float>)(Parameter<float>)PlugIn.GetParameter("q10"));
psntmin = ((Landis.Library.Parameters.Species.AuxParm<float>)(Parameter<float>)PlugIn.GetParameter("psntmin"));
dvpd1 = ((Landis.Library.Parameters.Species.AuxParm<float>)(Parameter<float>)PlugIn.GetParameter("dvpd1"));
dvpd2 = ((Landis.Library.Parameters.Species.AuxParm<float>)(Parameter<float>)PlugIn.GetParameter("dvpd2"));
foln = ((Landis.Library.Parameters.Species.AuxParm<float>)(Parameter<float>)PlugIn.GetParameter("foln"));
amaxa = ((Landis.Library.Parameters.Species.AuxParm<float>)(Parameter<float>)PlugIn.GetParameter("amaxa"));
amaxb = ((Landis.Library.Parameters.Species.AuxParm<float>)(Parameter<float>)PlugIn.GetParameter("amaxb"));
maintresp = ((Landis.Library.Parameters.Species.AuxParm<float>)(Parameter<float>)PlugIn.GetParameter("maintresp"));
bfolresp = ((Landis.Library.Parameters.Species.AuxParm<float>)(Parameter<float>)PlugIn.GetParameter("bfolresp"));
#endregion
SpeciesCombinations = new List<Tuple<ISpecies, ISpeciesPNET>>();
foreach (ISpecies spc in PlugIn.ModelCore.Species)
{
SpeciesPnET species = new SpeciesPnET(spc);
SpeciesCombinations.Add(new Tuple<ISpecies, ISpeciesPNET>(spc, species));
}
}