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"); }