public static void Initialize()
{
ClimateFileName = (Landis.Library.Parameters.Ecoregions.AuxParm <string>)PlugIn.GetParameter("climateFileName");
Dictionary <IEcoregion, IObservedClimate> dict = new Dictionary <IEcoregion, IObservedClimate>();
foreach (IEcoregion ecoregion in PlugIn.ModelCore.Ecoregions)
{
if (ecoregion.Active == false)
{
continue;
}
else
{
if (dict.ContainsKey(ecoregion))
{
ClimateData[ClimateFileName[ecoregion]] = dict[ecoregion];
}
else
{
ClimateData[ClimateFileName[ecoregion]] = new ObservedClimate(ClimateFileName[ecoregion]);
}
}
}
}
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 ObservedClimate(string filename)
{
List <string> ClimateFileContent = new List <string>(ReadClimateFile(filename));
ColumnNumbers columns = new ColumnNumbers(ClimateFileContent[0]);
ClimateFileContent.Remove(ClimateFileContent[0]);
foreach (string line in ClimateFileContent)
{
ObservedClimate climate = new ObservedClimate();
string[] terms = line.Split((char[])null, System.StringSplitOptions.RemoveEmptyEntries);
// Get one state of static information for the line in the climate file
climate.tmax = CheckInRange <float>(float.Parse(terms[columns.TMax]), -80, 80, "TMax");
climate.tmin = CheckInRange <float>(float.Parse(terms[columns.TMin]), -80, climate.tmax, "TMin");
climate.co2 = CheckInRange <float>(float.Parse(terms[columns.CO2]), 0, float.MaxValue, "CO2");
climate.par0 = (ushort)CheckInRange <float>(float.Parse(terms[columns.PAR0]), 0, float.MaxValue, "PAR0");
climate.prec = CheckInRange <float>(float.Parse(terms[columns.Prec]), 0, float.MaxValue, "PREC");
climate.o3 = columns.O3 > 0 ? CheckInRange <float>(float.Parse(terms[columns.O3]), 0, float.MaxValue, "O3") : 0;
climate.year = terms[columns.Year];
climate.month = terms[columns.Month];
data_lines.Add(climate);
}
}
//---------------------------------------------------------------------
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");
}
