//---------------------------------------------------------------------
/// <summary>
/// Grows the cohorts during spin-up
/// Makes the set of biomass cohorts at a site based on the age cohorts
/// at the site, using a specified method for computing a cohort's
/// initial biomass.
/// </summary>
/// <param name="ageCohorts">
/// A sorted list of age cohorts, from oldest to youngest.
/// </param>
/// <param name="site">
/// Site where cohorts are located.
/// </param>
/// <param name="initialBiomassMethod">
/// The method for computing the initial biomass for a new cohort.
/// </param>
public static ISiteCohorts MakeBiomassCohorts(List <Landis.Library.AgeOnlyCohorts.ICohort> ageCohorts,
ActiveSite site,
ComputeMethod initialBiomassMethod)
{
IEcoregion ecoregion = PlugIn.ModelCore.Ecoregion[site];
//if (Climate.Spinup_AllData.Count >= ageCohorts[0].Age)
//try
//{
//PlugIn.ModelCore.UI.WriteLine("Making Biomass Cohorts using spin-up climate data");
SiteVars.Cohorts[site] = new Library.LeafBiomassCohorts.SiteCohorts();
if (ageCohorts.Count == 0)
{
return(SiteVars.Cohorts[site]);
}
int indexNextAgeCohort = 0;
// The index in the list of sorted age cohorts of the next
// cohort to be considered
// Loop through time from -N to 0 where N is the oldest cohort.
// So we're going from the time when the oldest cohort was "born"
// to the present time (= 0). Because the age of any age cohort
// is a multiple of the succession timestep, we go from -N to 0
// by that timestep. NOTE: the case where timestep = 1 requires
// special treatment because if we start at time = -N with a
// cohort with age = 1, then at time = 0, its age will N+1 not N.
// Therefore, when timestep = 1, the ending time is -1.
//int endTime = (successionTimestep == 1) ? -1 : -1;
//PlugIn.ModelCore.UI.WriteLine(" Ageing initial cohorts. Oldest cohorts={0} yrs, succession timestep={1}, endTime={2}.", ageCohorts[0].Age, successionTimestep, endTime);
for (int time = -(ageCohorts[0].Age); time <= -1; time += successionTimestep)
{
//PlugIn.ModelCore.UI.WriteLine(" Ageing initial cohorts. Oldest cohorts={0} yrs, succession timestep={1}.", ageCohorts[0].Age, successionTimestep);
EcoregionData.SetSingleAnnualClimate(ecoregion, time + ageCohorts[0].Age, Climate.Phase.SpinUp_Climate); //the spinup climate array is sorted from oldest to newest years
// Add those cohorts that were born at the current year
while (indexNextAgeCohort < ageCohorts.Count && ageCohorts[indexNextAgeCohort].Age == -time)
{
ISpecies species = ageCohorts[indexNextAgeCohort].Species;
float[] initialBiomass = initialBiomassMethod(species, SiteVars.Cohorts[site], site);
SiteVars.Cohorts[site].AddNewCohort(ageCohorts[indexNextAgeCohort].Species, 1,
initialBiomass[0], initialBiomass[1]);
indexNextAgeCohort++;
}
Main.Run(site, successionTimestep, true);
}
return(SiteVars.Cohorts[site]);
}
//---------------------------------------------------------------------
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);
}
