//---------------------------------------------------------------------
protected override IInputParameters Parse()
{
ReadLandisDataVar();
int numLitterTypes = 4;
int numFunctionalTypes = 25;
InputParameters parameters = new InputParameters(speciesDataset, numLitterTypes, numFunctionalTypes);
InputVar <int> timestep = new InputVar <int>("Timestep");
ReadVar(timestep);
parameters.Timestep = timestep.Value;
InputVar <SeedingAlgorithms> seedAlg = new InputVar <SeedingAlgorithms>("SeedingAlgorithm");
ReadVar(seedAlg);
parameters.SeedAlgorithm = seedAlg.Value;
//---------------------------------------------------------------------------------
InputVar <string> initCommunities = new InputVar <string>("InitialCommunities");
ReadVar(initCommunities);
parameters.InitialCommunities = initCommunities.Value;
InputVar <string> communitiesMap = new InputVar <string>("InitialCommunitiesMap");
ReadVar(communitiesMap);
parameters.InitialCommunitiesMap = communitiesMap.Value;
InputVar <string> climateConfigFile = new InputVar <string>("ClimateConfigFile");
ReadVar(climateConfigFile);
parameters.ClimateConfigFile = climateConfigFile.Value;
InputVar <string> ageOnlyDisturbanceParms = new InputVar <string>("AgeOnlyDisturbances:BiomassParameters");
ReadVar(ageOnlyDisturbanceParms);
parameters.AgeOnlyDisturbanceParms = ageOnlyDisturbanceParms.Value;
InputVar <string> soilDepthMapName = new InputVar <string>("SoilDepthMapName");
ReadVar(soilDepthMapName);
parameters.SoilDepthMapName = soilDepthMapName.Value;
InputVar <string> soilDrainMapName = new InputVar <string>("SoilDrainMapName");
ReadVar(soilDrainMapName);
parameters.SoilDrainMapName = soilDrainMapName.Value;
InputVar <string> soilBaseFlowMapName = new InputVar <string>("SoilBaseFlowMapName");
ReadVar(soilBaseFlowMapName);
parameters.SoilBaseFlowMapName = soilBaseFlowMapName.Value;
InputVar <string> soilStormFlowMapName = new InputVar <string>("SoilStormFlowMapName");
ReadVar(soilStormFlowMapName);
parameters.SoilStormFlowMapName = soilStormFlowMapName.Value;
InputVar <string> soilFCMapName = new InputVar <string>("SoilFieldCapacityMapName");
ReadVar(soilFCMapName);
parameters.SoilFieldCapacityMapName = soilFCMapName.Value;
InputVar <string> soilWPMapName = new InputVar <string>("SoilWiltingPointMapName");
ReadVar(soilWPMapName);
parameters.SoilWiltingPointMapName = soilWPMapName.Value;
InputVar <string> soilSandMapName = new InputVar <string>("SoilPercentSandMapName");
ReadVar(soilSandMapName);
parameters.SoilPercentSandMapName = soilSandMapName.Value;
InputVar <string> soilClayMapName = new InputVar <string>("SoilPercentClayMapName");
ReadVar(soilClayMapName);
parameters.SoilPercentClayMapName = soilClayMapName.Value;
InputVar <string> som1CsurfMapName = new InputVar <string>("InitialSOM1CsurfMapName");
ReadVar(som1CsurfMapName);
parameters.InitialSOM1CSurfaceMapName = som1CsurfMapName.Value;
InputVar <string> som1NsurfMapName = new InputVar <string>("InitialSOM1NsurfMapName");
ReadVar(som1NsurfMapName);
parameters.InitialSOM1NSurfaceMapName = som1NsurfMapName.Value;
InputVar <string> som1CsoilMapName = new InputVar <string>("InitialSOM1CsoilMapName");
ReadVar(som1CsoilMapName);
parameters.InitialSOM1CSoilMapName = som1CsoilMapName.Value;
InputVar <string> som1NsoilMapName = new InputVar <string>("InitialSOM1NsoilMapName");
ReadVar(som1NsoilMapName);
parameters.InitialSOM1NSoilMapName = som1NsoilMapName.Value;
InputVar <string> som2CMapName = new InputVar <string>("InitialSOM2CMapName");
ReadVar(som2CMapName);
parameters.InitialSOM2CMapName = som2CMapName.Value;
InputVar <string> som2NMapName = new InputVar <string>("InitialSOM2NMapName");
ReadVar(som2NMapName);
parameters.InitialSOM2NMapName = som2NMapName.Value;
InputVar <string> som3CMapName = new InputVar <string>("InitialSOM3CMapName");
ReadVar(som3CMapName);
parameters.InitialSOM3CMapName = som3CMapName.Value;
InputVar <string> som3NMapName = new InputVar <string>("InitialSOM3NMapName");
ReadVar(som3NMapName);
parameters.InitialSOM3NMapName = som3NMapName.Value;
InputVar <string> deadSurfMapName = new InputVar <string>("InitialDeadWoodSurfaceMapName");
ReadVar(deadSurfMapName);
parameters.InitialDeadSurfaceMapName = deadSurfMapName.Value;
InputVar <string> deadSoilMapName = new InputVar <string>("InitialDeadCoarseRootsMapName");
ReadVar(deadSoilMapName);
parameters.InitialDeadSoilMapName = deadSoilMapName.Value;
InputVar <bool> calimode = new InputVar <bool>("CalibrateMode");
if (ReadOptionalVar(calimode))
{
parameters.CalibrateMode = calimode.Value;
}
else
{
parameters.CalibrateMode = false;
}
InputVar <string> wt = new InputVar <string>("WaterDecayFunction");
ReadVar(wt);
parameters.WType = WParse(wt.Value);
InputVar <double> pea = new InputVar <double>("ProbabilityEstablishAdjust");
ReadVar(pea);
parameters.ProbEstablishAdjustment = pea.Value;
InputVar <double> iMN = new InputVar <double>("InitialMineralN");
ReadVar(iMN);
parameters.SetInitMineralN(iMN.Value);
InputVar <double> ans = new InputVar <double>("AtmosphericNSlope");
ReadVar(ans);
parameters.SetAtmosNslope(ans.Value);
InputVar <double> ani = new InputVar <double>("AtmosphericNIntercept");
ReadVar(ani);
parameters.SetAtmosNintercept(ani.Value);
InputVar <double> lat = new InputVar <double>("Latitude");
ReadVar(lat);
parameters.SetLatitude(lat.Value);
InputVar <double> denits = new InputVar <double>("DenitrificationRate");
ReadVar(denits);
parameters.SetDenitrif(denits.Value);
InputVar <double> drsoms = new InputVar <double>("DecayRateSurf");
ReadVar(drsoms);
parameters.SetDecayRateSurf(drsoms.Value);
InputVar <double> drsom1 = new InputVar <double>("DecayRateSOM1");
ReadVar(drsom1);
parameters.SetDecayRateSOM1(drsom1.Value);
InputVar <double> drsom2 = new InputVar <double>("DecayRateSOM2");
ReadVar(drsom2);
parameters.SetDecayRateSOM2(drsom2.Value);
InputVar <double> drsom3 = new InputVar <double>("DecayRateSOM3");
ReadVar(drsom3);
parameters.SetDecayRateSOM3(drsom3.Value);
InputVar <string> anppMaps = new InputVar <string>("ANPPMapNames");
if (ReadOptionalVar(anppMaps))
{
PlugIn.ANPPMapNames = anppMaps.Value;
InputVar <int> anppMapFreq = new InputVar <int>("ANPPMapFrequency");
ReadVar(anppMapFreq);
PlugIn.ANPPMapFrequency = anppMapFreq.Value;
}
InputVar <string> aneeMaps = new InputVar <string>("ANEEMapNames");
if (ReadOptionalVar(aneeMaps))
{
PlugIn.ANEEMapNames = aneeMaps.Value;
InputVar <int> aneeMapFreq = new InputVar <int>("ANEEMapFrequency");
ReadVar(aneeMapFreq);
PlugIn.ANEEMapFrequency = aneeMapFreq.Value;
}
InputVar <string> soilCarbonMaps = new InputVar <string>("SoilCarbonMapNames");
if (ReadOptionalVar(soilCarbonMaps))
{
PlugIn.SoilCarbonMapNames = soilCarbonMaps.Value;
InputVar <int> soilCarbonMapFreq = new InputVar <int>("SoilCarbonMapFrequency");
ReadVar(soilCarbonMapFreq);
PlugIn.SoilCarbonMapFrequency = soilCarbonMapFreq.Value;
}
InputVar <string> soilNitrogenMaps = new InputVar <string>("SoilNitrogenMapNames");
if (ReadOptionalVar(soilNitrogenMaps))
{
PlugIn.SoilNitrogenMapNames = soilNitrogenMaps.Value;
InputVar <int> soilNitrogenMapFreq = new InputVar <int>("SoilNitrogenMapFrequency");
ReadVar(soilNitrogenMapFreq);
PlugIn.SoilNitrogenMapFrequency = soilNitrogenMapFreq.Value;
}
InputVar <string> totalCMaps = new InputVar <string>("TotalCMapNames");
if (ReadOptionalVar(totalCMaps))
{
PlugIn.TotalCMapNames = totalCMaps.Value;
InputVar <int> totalCMapFreq = new InputVar <int>("TotalCMapFrequency");
ReadVar(totalCMapFreq);
PlugIn.TotalCMapFrequency = totalCMapFreq.Value;
}
//--------------------------
// MinRelativeBiomass table
ReadName("MaximumLAI");
InputVar <byte> shadeClassVar = new InputVar <byte>("Shade Class");
InputVar <double> maxLAI = new InputVar <double>("Maximum LAI");
for (byte shadeClass = 1; shadeClass <= 5; shadeClass++)
{
if (AtEndOfInput)
{
throw NewParseException("Expected a line with available light class {0}", shadeClass);
}
StringReader currentLine = new StringReader(CurrentLine);
ReadValue(shadeClassVar, currentLine);
if (shadeClassVar.Value.Actual != shadeClass)
{
throw new InputValueException(shadeClassVar.Value.String,
"Expected the available light class {0}", shadeClass);
}
ReadValue(maxLAI, currentLine);
parameters.SetMaximumShadeLAI(shadeClass, maxLAI.Value);
CheckNoDataAfter("the " + maxLAI + " column", currentLine);
GetNextLine();
}
//----------------------------------------------------------
// Read table of sufficient light probabilities.
// Available light classes are in increasing order.
ReadName("LightEstablishmentTable");
InputVar <byte> sc = new InputVar <byte>("Available Light Class");
InputVar <double> pl0 = new InputVar <double>("Probability of Germination - Light Level 0");
InputVar <double> pl1 = new InputVar <double>("Probability of Germination - Light Level 1");
InputVar <double> pl2 = new InputVar <double>("Probability of Germination - Light Level 2");
InputVar <double> pl3 = new InputVar <double>("Probability of Germination - Light Level 3");
InputVar <double> pl4 = new InputVar <double>("Probability of Germination - Light Level 4");
InputVar <double> pl5 = new InputVar <double>("Probability of Germination - Light Level 5");
int previousNumber = 0;
while (!AtEndOfInput && CurrentName != Names.SpeciesParameters && previousNumber != 6)
{
StringReader currentLine = new StringReader(CurrentLine);
ISufficientLight suffLight = new SufficientLight();
ReadValue(sc, currentLine);
suffLight.ShadeClass = sc.Value;
// Check that the current shade class is 1 more than
// the previous number (numbers are must be in increasing order).
if (sc.Value.Actual != (byte)previousNumber + 1)
{
throw new InputValueException(sc.Value.String,
"Expected the severity number {0}",
previousNumber + 1);
}
previousNumber = (int)sc.Value.Actual;
ReadValue(pl0, currentLine);
suffLight.ProbabilityLight0 = pl0.Value;
ReadValue(pl1, currentLine);
suffLight.ProbabilityLight1 = pl1.Value;
ReadValue(pl2, currentLine);
suffLight.ProbabilityLight2 = pl2.Value;
ReadValue(pl3, currentLine);
suffLight.ProbabilityLight3 = pl3.Value;
ReadValue(pl4, currentLine);
suffLight.ProbabilityLight4 = pl4.Value;
ReadValue(pl5, currentLine);
suffLight.ProbabilityLight5 = pl5.Value;
parameters.LightClassProbabilities.Add(suffLight);
CheckNoDataAfter("the " + pl5.Name + " column",
currentLine);
GetNextLine();
}
if (parameters.LightClassProbabilities.Count == 0)
{
throw NewParseException("No sufficient light probabilities defined.");
}
if (previousNumber != 5)
{
throw NewParseException("Expected shade class {0}", previousNumber + 1);
}
//-------------------------
// Species Parameters table
ReadName("SpeciesParameters");
speciesLineNums.Clear(); // If parser re-used (i.e., for testing purposes)
InputVar <int> ft = new InputVar <int>("Functional Type");
InputVar <bool> nt = new InputVar <bool>("Nitrogen Fixer");
InputVar <int> gddmn = new InputVar <int>("Growing Degree Day Minimum");
InputVar <int> gddmx = new InputVar <int>("Growing Degree Day Maximum");
InputVar <int> mjt = new InputVar <int>("Minimum January Temperature");
InputVar <double> maxd = new InputVar <double>("Maximum Allowable Drought");
InputVar <double> leafLongevity = new InputVar <double>("Leaf Longevity");
InputVar <bool> epicorm = new InputVar <bool>("Epicormic: Y/N");
InputVar <double> leafLignin = new InputVar <double>("Leaf Percent Lignin");
InputVar <double> wLignin = new InputVar <double>("Wood Percent Lignin");
InputVar <double> crLignin = new InputVar <double>("Coarse Root Percent Lignin");
InputVar <double> frLignin = new InputVar <double>("Fine Root Percent Lignin");
InputVar <double> leafCN = new InputVar <double>("Leaf CN Ratio");
InputVar <double> woodCN = new InputVar <double>("Wood CN Ratio");
InputVar <double> cRootCN = new InputVar <double>("Coarse Root CN Ratio");
InputVar <double> foliarCN = new InputVar <double>("Foliage CN Ratio");
InputVar <double> fRootCN = new InputVar <double>("Fine Root CN Ratio");
InputVar <int> maxANPP = new InputVar <int>("Maximum ANPP");
InputVar <int> maxBiomass = new InputVar <int>("Maximum Aboveground Biomass");
string lastColumn = "the " + maxBiomass.Name + " column";
while (!AtEndOfInput && CurrentName != Names.FunctionalGroupParameters)
{
StringReader currentLine = new StringReader(CurrentLine);
ISpecies species = ReadSpecies(currentLine);
ReadValue(ft, currentLine);
parameters.SetFunctionalType(species, ft.Value);
ReadValue(nt, currentLine);
parameters.NFixer[species] = nt.Value;
ReadValue(gddmn, currentLine);
parameters.SetGDDmin(species, gddmn.Value);
ReadValue(gddmx, currentLine);
parameters.SetGDDmax(species, gddmx.Value);
ReadValue(mjt, currentLine);
parameters.SetMinJanTemp(species, mjt.Value);
ReadValue(maxd, currentLine);
parameters.SetMaxDrought(species, maxd.Value);
ReadValue(leafLongevity, currentLine);
parameters.SetLeafLongevity(species, leafLongevity.Value);
ReadValue(epicorm, currentLine);
parameters.Epicormic[species] = epicorm.Value;
ReadValue(leafLignin, currentLine);
parameters.SetLeafLignin(species, leafLignin.Value);
ReadValue(frLignin, currentLine);
parameters.SetFineRootLignin(species, frLignin.Value);
ReadValue(wLignin, currentLine);
parameters.SetWoodLignin(species, wLignin.Value);
ReadValue(crLignin, currentLine);
parameters.SetCoarseRootLignin(species, crLignin.Value);
ReadValue(leafCN, currentLine);
parameters.SetLeafCN(species, leafCN.Value);
ReadValue(fRootCN, currentLine);
parameters.SetFineRootCN(species, fRootCN.Value);
ReadValue(woodCN, currentLine);
parameters.SetWoodCN(species, woodCN.Value);
ReadValue(cRootCN, currentLine);
parameters.SetCoarseRootCN(species, cRootCN.Value);
ReadValue(foliarCN, currentLine);
parameters.SetFoliageLitterCN(species, foliarCN.Value);
ReadValue(maxANPP, currentLine);
parameters.SetMaxANPP(species, maxANPP.Value);
ReadValue(maxBiomass, currentLine);
parameters.SetMaxBiomass(species, maxBiomass.Value);
CheckNoDataAfter(lastColumn, currentLine);
GetNextLine();
}
//--------- Read In Functional Group Table -------------------------------
PlugIn.ModelCore.UI.WriteLine(" Begin parsing FUNCTIONAL GROUP table.");
ReadName("FunctionalGroupParameters");
InputVar <string> ftname = new InputVar <string>("Name");
InputVar <int> ftindex = new InputVar <int>("Index (< 25)");
InputVar <double> tempcurve1 = new InputVar <double>("TempCurve(1)");
InputVar <double> tempcurve2 = new InputVar <double>("TempCurve(2)");
InputVar <double> tempcurve3 = new InputVar <double>("TempCurve(3)");
InputVar <double> tempcurve4 = new InputVar <double>("TempCurve(4)");
InputVar <double> fcfleaf = new InputVar <double>("FCFRAC: Leaf");
InputVar <double> btolai = new InputVar <double>("BTOLAI");
InputVar <double> klai = new InputVar <double>("KLAI");
InputVar <double> maxlai = new InputVar <double>("MAXLAI");
InputVar <double> mwm = new InputVar <double>("Monthly Wood Mortality");
InputVar <double> wdr = new InputVar <double>("Wood Decay Rate");
InputVar <double> mortCurveShapeParm = new InputVar <double>("Mortality Curve Shape Parameter");
InputVar <int> leafNeedleDrop = new InputVar <int>("Leaf or Needle Drop Month");
InputVar <double> ppr2 = new InputVar <double>("MoistureCurve2");
InputVar <double> ppr3 = new InputVar <double>("MoistureCurve3");
InputVar <double> coarseRootFraction = new InputVar <double>("CRootFrac");
InputVar <double> fineRootFraction = new InputVar <double>("FRootFrac");
while (!AtEndOfInput && CurrentName != Names.FireReductionParameters)
{
StringReader currentLine = new StringReader(CurrentLine);
ReadValue(ftname, currentLine);
ReadValue(ftindex, currentLine);
int ln = ftindex.Value.Actual;
if (ln >= numFunctionalTypes)
{
throw new InputValueException(ftindex.Value.String,
"The index: {0} exceeds the allowable number of functional groups, {1}",
ftindex.Value.String, numFunctionalTypes - 1);
}
FunctionalType funcTParms = new FunctionalType();
parameters.FunctionalTypes[ln] = funcTParms;
ReadValue(tempcurve1, currentLine);
funcTParms.TempCurve1 = tempcurve1.Value;
ReadValue(tempcurve2, currentLine);
funcTParms.TempCurve2 = tempcurve2.Value;
ReadValue(tempcurve3, currentLine);
funcTParms.TempCurve3 = tempcurve3.Value;
ReadValue(tempcurve4, currentLine);
funcTParms.TempCurve4 = tempcurve4.Value;
ReadValue(fcfleaf, currentLine);
funcTParms.FCFRACleaf = fcfleaf.Value;
ReadValue(btolai, currentLine);
funcTParms.BTOLAI = btolai.Value;
ReadValue(klai, currentLine);
funcTParms.KLAI = klai.Value;
ReadValue(maxlai, currentLine);
funcTParms.MAXLAI = maxlai.Value;
ReadValue(ppr2, currentLine);
funcTParms.MoistureCurve2 = ppr2.Value;
ReadValue(ppr3, currentLine);
funcTParms.MoistureCurve3 = ppr3.Value;
ReadValue(wdr, currentLine);
funcTParms.WoodDecayRate = wdr.Value;
ReadValue(mwm, currentLine);
funcTParms.MonthlyWoodMortality = mwm.Value;
ReadValue(mortCurveShapeParm, currentLine);
funcTParms.MortCurveShape = mortCurveShapeParm.Value;
ReadValue(leafNeedleDrop, currentLine);
funcTParms.LeafNeedleDrop = leafNeedleDrop.Value;
ReadValue(coarseRootFraction, currentLine);
funcTParms.CoarseRootFraction = coarseRootFraction.Value;
ReadValue(fineRootFraction, currentLine);
funcTParms.FineRootFraction = fineRootFraction.Value;
CheckNoDataAfter("the " + fineRootFraction.Name + " column", currentLine);
GetNextLine();
}
//--------- Read In Fire Reductions Table ---------------------------
PlugIn.ModelCore.UI.WriteLine(" Begin reading FIRE REDUCTION parameters.");
ReadName(Names.FireReductionParameters);
InputVar <int> frindex = new InputVar <int>("Fire Severity Index MUST = 1-5");
InputVar <double> wred = new InputVar <double>("Wood Reduction");
InputVar <double> lred = new InputVar <double>("Litter Reduction");
while (!AtEndOfInput && CurrentName != Names.HarvestReductionParameters && CurrentName != Names.AgeOnlyDisturbanceParms)
{
StringReader currentLine = new StringReader(CurrentLine);
ReadValue(frindex, currentLine);
int ln = frindex.Value.Actual;
if (ln < 1 || ln > 5)
{
throw new InputValueException(ftindex.Value.String,
"The fire severity index: {0} must be 1-5,",
frindex.Value.String);
}
FireReductions inputFireReduction = new FireReductions(); // ignoring severity = zero
parameters.FireReductionsTable[ln] = inputFireReduction;
ReadValue(wred, currentLine);
inputFireReduction.WoodReduction = wred.Value;
ReadValue(lred, currentLine);
inputFireReduction.LitterReduction = lred.Value;
CheckNoDataAfter("the " + lred.Name + " column", currentLine);
GetNextLine();
}
//--------- Read In Harvest Reductions Table ---------------------------
ReadOptionalName(Names.HarvestReductionParameters);
{
PlugIn.ModelCore.UI.WriteLine(" Begin reading HARVEST REDUCTION parameters.");
InputVar <string> prescriptionName = new InputVar <string>("Prescription");
InputVar <double> wred_pr = new InputVar <double>("Wood Reduction");
InputVar <double> lred_pr = new InputVar <double>("Litter Reduction");
while (!AtEndOfInput && CurrentName != Names.AgeOnlyDisturbanceParms)
{
HarvestReductions harvReduction = new HarvestReductions();
parameters.HarvestReductionsTable.Add(harvReduction);
StringReader currentLine = new StringReader(CurrentLine);
ReadValue(prescriptionName, currentLine);
harvReduction.PrescriptionName = prescriptionName.Value;
ReadValue(wred_pr, currentLine);
harvReduction.WoodReduction = wred.Value;
ReadValue(lred_pr, currentLine);
harvReduction.LitterReduction = lred.Value;
GetNextLine();
}
}
return(parameters);
}
//---------------------------------------------------------------------
public override void Initialize()
{
PlugIn.ModelCore.UI.WriteLine("Initializing {0} ...", ExtensionName);
Timestep = parameters.Timestep;
SuccessionTimeStep = Timestep;
sufficientLight = parameters.LightClassProbabilities;
ProbEstablishAdjust = parameters.ProbEstablishAdjustment;
MetadataHandler.InitializeMetadata(Timestep, modelCore, SoilCarbonMapNames, SoilNitrogenMapNames, ANPPMapNames, ANEEMapNames, TotalCMapNames); //,LAIMapNames, ShadeClassMapNames);
//CohortBiomass.SpinupMortalityFraction = parameters.SpinupMortalityFraction;
//Initialize climate.
Climate.Initialize(parameters.ClimateConfigFile, false, modelCore);
FutureClimateBaseYear = Climate.Future_MonthlyData.Keys.Min();
ClimateRegionData.Initialize(parameters);
SpeciesData.Initialize(parameters);
Util.ReadSoilDepthMap(parameters.SoilDepthMapName);
Util.ReadSoilDrainMap(parameters.SoilDrainMapName);
Util.ReadSoilBaseFlowMap(parameters.SoilBaseFlowMapName);
Util.ReadSoilStormFlowMap(parameters.SoilStormFlowMapName);
Util.ReadFieldCapacityMap(parameters.SoilFieldCapacityMapName);
Util.ReadWiltingPointMap(parameters.SoilWiltingPointMapName);
Util.ReadPercentSandMap(parameters.SoilPercentSandMapName);
Util.ReadPercentClayMap(parameters.SoilPercentClayMapName);
Util.ReadSoilCNMaps(parameters.InitialSOM1CSurfaceMapName,
parameters.InitialSOM1NSurfaceMapName,
parameters.InitialSOM1CSoilMapName,
parameters.InitialSOM1NSoilMapName,
parameters.InitialSOM2CMapName,
parameters.InitialSOM2NMapName,
parameters.InitialSOM3CMapName,
parameters.InitialSOM3NMapName);
Util.ReadDeadWoodMaps(parameters.InitialDeadSurfaceMapName, parameters.InitialDeadSoilMapName);
AtmosNslope = parameters.AtmosNslope;
AtmosNintercept = parameters.AtmosNintercept;
Latitude = parameters.Latitude;
DenitrificationRate = parameters.Denitrif;
DecayRateSurf = parameters.DecayRateSurf;
DecayRateSOM1 = parameters.DecayRateSOM1;
DecayRateSOM2 = parameters.DecayRateSOM2;
DecayRateSOM3 = parameters.DecayRateSOM3;
ShadeLAI = parameters.MaximumShadeLAI; //.MinRelativeBiomass;
OtherData.Initialize(parameters);
FunctionalType.Initialize(parameters);
FireEffects.Initialize(parameters);
// Cohorts must be created before the base class is initialized
// because the base class' reproduction module uses the core's
// SuccessionCohorts property in its Initialization method.
Library.LeafBiomassCohorts.Cohorts.Initialize(Timestep, new CohortBiomass());
// Initialize Reproduction routines:
Reproduction.SufficientResources = SufficientLight;
Reproduction.Establish = Establish;
Reproduction.AddNewCohort = AddNewCohort;
Reproduction.MaturePresent = MaturePresent;
base.Initialize(modelCore, parameters.SeedAlgorithm);
Landis.Library.LeafBiomassCohorts.Cohort.PartialDeathEvent += CohortPartialMortality;
Landis.Library.BiomassCohorts.Cohort.DeathEvent += CohortDied;
AgeOnlyDisturbances.Module.Initialize(parameters.AgeOnlyDisturbanceParms);
//InitialBiomass.Initialize(Timestep);
InitializeSites(parameters.InitialCommunities, parameters.InitialCommunitiesMap, modelCore);
if (parameters.CalibrateMode)
{
Outputs.CreateCalibrateLogFile();
}
Establishment.InitializeLogFile();
B_MAX = 0;
foreach (ISpecies species in ModelCore.Species)
{
if (SpeciesData.Max_Biomass[species] > B_MAX)
{
B_MAX = SpeciesData.Max_Biomass[species];
}
}
foreach (ActiveSite site in PlugIn.ModelCore.Landscape)
{
Century.ComputeTotalCohortCN(site, SiteVars.Cohorts[site]);
}
Outputs.WritePrimaryLogFile(0);
Outputs.WriteShortPrimaryLogFile(0);
}