//---------------------------------------------------------------------
protected override void InitializeSite(ActiveSite site,
ICommunity initialCommunity)
{
InitialBiomass initialBiomass = InitialBiomass.Compute(site, initialCommunity);
SiteVars.Cohorts[site] = InitialBiomass.Clone(initialBiomass.Cohorts);
//IEcoregion ecoregion = PlugIn.ModelCore.Ecoregion[site];
SiteVars.SurfaceDeadWood[site] = initialBiomass.SurfaceDeadWood.Clone();
SiteVars.SurfaceStructural[site] = initialBiomass.SurfaceStructural.Clone();
SiteVars.SurfaceMetabolic[site] = initialBiomass.SurfaceMetabolic.Clone();
SiteVars.SoilDeadWood[site] = initialBiomass.SoilDeadWood.Clone();
SiteVars.SoilStructural[site] = initialBiomass.SoilStructural.Clone();
SiteVars.SoilMetabolic[site] = initialBiomass.SoilMetabolic.Clone();
SiteVars.SOM1surface[site] = initialBiomass.SOM1surface.Clone();
SiteVars.SOM1soil[site] = initialBiomass.SOM1soil.Clone();
SiteVars.SOM2[site] = initialBiomass.SOM2.Clone();
SiteVars.SOM3[site] = initialBiomass.SOM3.Clone();
SiteVars.MineralN[site] = initialBiomass.MineralN;
SiteVars.CohortLeafC[site] = initialBiomass.CohortLeafC;
SiteVars.CohortFRootC[site] = initialBiomass.CohortFRootC;
SiteVars.CohortLeafN[site] = initialBiomass.CohortLeafN;
SiteVars.CohortFRootN[site] = initialBiomass.CohortFRootN;
SiteVars.CohortWoodC[site] = initialBiomass.CohortWoodC;
SiteVars.CohortCRootC[site] = initialBiomass.CohortCRootC;
SiteVars.CohortWoodN[site] = initialBiomass.CohortWoodN;
SiteVars.CohortCRootN[site] = initialBiomass.CohortCRootN;
}
//---------------------------------------------------------------------
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);
CohortBiomass.SpinupMortalityFraction = parameters.SpinupMortalityFraction;
//Initialize climate.
Climate.Initialize(parameters.ClimateConfigFile, false, modelCore);
FutureClimateBaseYear = Climate.Future_MonthlyData.Keys.Min();
EcoregionData.Initialize(parameters);
SpeciesData.Initialize(parameters);
EcoregionData.ChangeParameters(parameters);
OtherData.Initialize(parameters);
FunctionalType.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);
InitialBiomass.Initialize(Timestep);
Landis.Library.BiomassCohorts.Cohort.DeathEvent += CohortDied;
Landis.Library.LeafBiomassCohorts.Cohort.PartialDeathEvent += CohortPartialMortality;
AgeOnlyDisturbances.Module.Initialize(parameters.AgeOnlyDisturbanceParms);
Dynamic.Module.Initialize(parameters.DynamicUpdates);
FireEffects.Initialize(parameters);
InitializeSites(parameters.InitialCommunities, parameters.InitialCommunitiesMap, modelCore); //the spinup is heppend within this fucntion
if (parameters.CalibrateMode)
{
Outputs.CreateCalibrateLogFile();
}
Outputs.WritePrimaryLogFile(0);
Outputs.WriteShortPrimaryLogFile(0);
}
//---------------------------------------------------------------------
/// <summary>
/// Computes the initial biomass at a site.
/// </summary>
/// <param name="site">
/// The selected site.
/// </param>
/// <param name="initialCommunity">
/// The initial community of age cohorts at the site.
/// </param>
public static InitialBiomass Compute(ActiveSite site,
ICommunity initialCommunity)
{
IEcoregion ecoregion = PlugIn.ModelCore.Ecoregion[site];
if (!ecoregion.Active)
{
string mesg = string.Format("Initial community {0} is located on a non-active ecoregion {1}", initialCommunity.MapCode, ecoregion.Name);
throw new System.ApplicationException(mesg);
}
uint key = ComputeKey(initialCommunity.MapCode, ecoregion.MapCode);
InitialBiomass initialBiomass;
if (initialSites.TryGetValue(key, out initialBiomass))
return initialBiomass;
// If we don't have a sorted list of age cohorts for the initial
// community, make the list
List<Landis.Library.AgeOnlyCohorts.ICohort> sortedAgeCohorts;
if (! sortedCohorts.TryGetValue(initialCommunity.MapCode, out sortedAgeCohorts)) {
sortedAgeCohorts = SortCohorts(initialCommunity.Cohorts);
sortedCohorts[initialCommunity.MapCode] = sortedAgeCohorts;
}
ISiteCohorts cohorts = MakeBiomassCohorts(sortedAgeCohorts, site);
initialBiomass = new InitialBiomass(
cohorts,
SiteVars.SurfaceDeadWood[site],
SiteVars.SurfaceStructural[site],
SiteVars.SurfaceMetabolic[site],
SiteVars.SoilDeadWood[site],
SiteVars.SoilStructural[site],
SiteVars.SoilMetabolic[site],
SiteVars.SOM1surface[site],
SiteVars.SOM1soil[site],
SiteVars.SOM2[site],
SiteVars.SOM3[site],
SiteVars.MineralN[site],
SiteVars.CohortLeafC[site],
SiteVars.CohortFRootC[site],
SiteVars.CohortLeafN[site],
SiteVars.CohortFRootN[site],
SiteVars.CohortWoodC[site],
SiteVars.CohortCRootC[site],
SiteVars.CohortWoodN[site],
SiteVars.CohortCRootN[site]
);
initialSites[key] = initialBiomass;
return initialBiomass;
}
//---------------------------------------------------------------------
/// <summary>
/// Computes the initial biomass at a site.
/// </summary>
/// <param name="site">
/// The selected site.
/// </param>
/// <param name="initialCommunity">
/// The initial community of age cohorts at the site.
/// </param>
public static InitialBiomass Compute(ActiveSite site,
ICommunity initialCommunity)
{
IEcoregion ecoregion = PlugIn.ModelCore.Ecoregion[site];
if (!ecoregion.Active)
{
string mesg = string.Format("Initial community {0} is located on a non-active ecoregion {1}", initialCommunity.MapCode, ecoregion.Name);
throw new System.ApplicationException(mesg);
}
uint key = ComputeKey(initialCommunity.MapCode, ecoregion.MapCode);
InitialBiomass initialBiomass;
if (initialSites.TryGetValue(key, out initialBiomass))
{
return(initialBiomass);
}
// If we don't have a sorted list of age cohorts for the initial
// community, make the list
List <Landis.Library.AgeOnlyCohorts.ICohort> sortedAgeCohorts;
if (!sortedCohorts.TryGetValue(initialCommunity.MapCode, out sortedAgeCohorts))
{
sortedAgeCohorts = SortCohorts(initialCommunity.Cohorts);
sortedCohorts[initialCommunity.MapCode] = sortedAgeCohorts;
}
ISiteCohorts cohorts = MakeBiomassCohorts(sortedAgeCohorts, site);
initialBiomass = new InitialBiomass(
cohorts,
SiteVars.SurfaceDeadWood[site],
SiteVars.SurfaceStructural[site],
SiteVars.SurfaceMetabolic[site],
SiteVars.SoilDeadWood[site],
SiteVars.SoilStructural[site],
SiteVars.SoilMetabolic[site],
SiteVars.SOM1surface[site],
SiteVars.SOM1soil[site],
SiteVars.SOM2[site],
SiteVars.SOM3[site],
SiteVars.MineralN[site],
SiteVars.CohortLeafC[site],
SiteVars.CohortFRootC[site],
SiteVars.CohortLeafN[site],
SiteVars.CohortFRootN[site],
SiteVars.CohortWoodC[site],
SiteVars.CohortCRootC[site],
SiteVars.CohortWoodN[site],
SiteVars.CohortCRootN[site]
);
initialSites[key] = initialBiomass;
return(initialBiomass);
}
