//---------------------------------------------------------------------
/// <summary>
/// Adds frass for a species to the foliar LITTER pools at a site.
/// Assumes that some of the N has been resorbed.
/// </summary>
public static void AddFrassLitter(double inputFrassBiomass, ISpecies species, ActiveSite site)
{
double inputDecayValue = 1.0; // Decay value is calculated for surface/soil layers (leaf/fine root),
// therefore, this is just a dummy value.
if (inputFrassBiomass > 0)
{
//SiteVars.LitterfallC[site] += defoliatedLeafBiomass * 0.47;
//double frassBiomass = Math.Max(0.0, OtherData.frassdepk * defoliatedLeafBiomass);
// Frass C added is a function of defoliated leaf biomass, but adjusted for the CN of litter and frass
// Any C lost is due to insect metabolism
double inputFrassC = inputFrassBiomass * 0.47;
double inputFrassN = inputFrassC / (double) SpeciesData.LeafLitterCN[species];
double actualFrassC = inputFrassN * (double) OtherData.CNratiofrass; // the difference between input and actual is C lost to insect metabolism
double actualFrassBiomass = actualFrassC / 0.47;
//PlugIn.ModelCore.UI.WriteLine("AddFrass.Month={0:0}, inputfrassN={1:0.000}, inputfrassbiomass={2:0.00}, actualfrassbiomass={3:0.00} ", Century.Month, inputFrassN, inputFrassBiomass, actualFrassBiomass);
SiteVars.FrassC[site] += actualFrassC;
LitterLayer.PartitionResidue(
actualFrassBiomass,
inputDecayValue,
OtherData.CNratiofrass,
0.1,
OtherData.StructuralCN,
LayerName.Leaf,
LayerType.Surface,
site);
}
}
public void WriteHeader(ActiveSite site)
{
StreamWriter sw = new StreamWriter(OutputSiteFileName(site));
string s = "Year" + delim +
"Month" + delim +
"date" + delim +
"NrOfCohorts" + delim +
"Tday(C)" + delim +
"Precip(mm_mo)" + delim +
"RunOff(mm_mo)" + delim +
"Transpiration(mm_mo)" + delim +
"PrecipLoss(mm_mo)" + delim +
"water(mm)" + delim +
"SnowPack (mm)" + delim +
"LAI(m2)" + delim +
"VPD(kPa)" + delim +
"GrossPsn(gC_mo)" + delim +
"NetPsn(gC_mo)" + delim +
"AutoResp(gC_mo)" + delim +
"HeteroResp(gC_mo)" + delim +
"TotalBiomass (gDW)" + delim +
"TotalRoot (gDW)" + delim +
"TotalFol (gDW)" + delim +
"TotalNSC (gC)" + delim +
"Litter(gDW_m2)" + delim +
"CWD(gDW_m2)";
sw.WriteLine(s);
sw.Close();
}
//---------------------------------------------------------------------
/// <summary>
/// Computes the initial biomass for a cohort at a site.
/// </summary>
public static float[] InitialBiomass(ISpecies species, ISiteCohorts siteCohorts,
ActiveSite site)
{
IEcoregion ecoregion = PlugIn.ModelCore.Ecoregion[site];
double leafFrac = FunctionalType.Table[SpeciesData.FuncType[species]].FCFRACleaf;
double B_ACT = SiteVars.ActualSiteBiomass(site);
double B_MAX = SpeciesData.B_MAX_Spp[species][ecoregion];
// Initial biomass exponentially declines in response to
// competition.
double initialBiomass = 0.002 * B_MAX * Math.Exp(-1.6 * B_ACT / B_MAX);
initialBiomass = Math.Max(initialBiomass, 5.0);
double initialLeafB = initialBiomass * leafFrac;
double initialWoodB = initialBiomass - initialLeafB;
double[] initialB = new double[2]{initialWoodB, initialLeafB};
float[] initialWoodLeafBiomass = new float[2] { (float)initialB[0], (float)initialB[1] };
//PlugIn.ModelCore.UI.WriteLine("Yr={0},Mo={1}, InitialB={2:0.0}, InitBleaf={3:0.00}, InitBwood={4:0.00}. LeafFrac={5:0.0}", PlugIn.ModelCore.CurrentTime, month, initialBiomass, initialB[1], initialB[0], leafFrac);
//PlugIn.ModelCore.UI.WriteLine("Yr={0},Mo={1}, B_MAX={2:0.0}, B_ACT={3:0.00}", PlugIn.ModelCore.CurrentTime, month, B_MAX, B_ACT);
return initialWoodLeafBiomass;
}
//---------------------------------------------------------------------
/// <summary>
/// Grows all cohorts at a site for a specified number of years. The
/// dead pools at the site also decompose for the given time period.
/// </summary>
public static void GrowCohorts(SiteCohorts cohorts,
ActiveSite site,
int years,
bool isSuccessionTimestep)
{
if (cohorts == null)
return;
//CurrentYearSiteMortality = 0.0;
for (int y = 1; y <= years; ++y)
{
SpeciesData.ChangeDynamicParameters(PlugIn.ModelCore.CurrentTime + y - 1);
SiteVars.ResetAnnualValues(site);
CohortBiomass.SubYear = y - 1;
CohortBiomass.CanopyLightExtinction = 0.0;
SiteVars.PercentShade[site] = 0.0;
SiteVars.LightTrans[site] = 1.0;
SiteVars.Cohorts[site].Grow(site, (y == years && isSuccessionTimestep));
SiteVars.WoodyDebris[site].Decompose();
SiteVars.Litter[site].Decompose();
}
//SiteVars.PreviousYearMortality[site] = CurrentYearSiteMortality;
}
/// <summary>
/// Adds some biomass for a species to the WOODY pools at a site.
/// </summary>
public static void AddWoody(double woodyBiomass,
ISpecies species,
ActiveSite site)
{
SiteVars.WoodyDebris[site].AddMass(woodyBiomass,
SpeciesData.WoodyDebrisDecay[species]);
}
//---------------------------------------------------------------------
/// <summary>
/// Computes the initial biomass for a cohort at a site.
/// </summary>
public static float[] InitialBiomass(ISpecies species, ISiteCohorts siteCohorts,
ActiveSite site)
{
IEcoregion ecoregion = PlugIn.ModelCore.Ecoregion[site];
double leafFrac = FunctionalType.Table[SpeciesData.FuncType[species]].FCFRACleaf;
double branchFraction = FunctionalType.Table[SpeciesData.FuncType[species]].FCFRACbranch;
//double Ndemand = 0.0;
double B_ACT = SiteVars.ActualSiteBiomass(site);
double B_MAX = SpeciesData.B_MAX_Spp[species][ecoregion];
// Initial biomass exponentially declines in response to
// competition.
double initialBiomass = 0.002 * B_MAX *
Math.Exp(-1.6 * B_ACT / B_MAX);
//Initial biomass is limited by nitrogen availability.
//initialBiomass *= SpeciesData.NLimits[species];
initialBiomass = Math.Max(initialBiomass, 5.0);
double initialLeafB = initialBiomass * leafFrac;
double initialBranchB = initialBiomass* branchFraction;
double initialWoodB = initialBiomass*(1 - leafFrac - branchFraction);
double[] initialB = new double[3] { initialWoodB, initialBranchB, initialLeafB };
//PlugIn.ModelCore.Log.WriteLine("Yr={0},Mo={1}, InitialB={2:0.0}, InitBleaf={3:0.00}, InitBwood={4:0.00}. LeafFrac={5:0.0}", PlugIn.ModelCore.CurrentTime, month, initialBiomass, initialB[1], initialB[0], leafFrac);
//PlugIn.ModelCore.Log.WriteLine("Yr={0},Mo={1}, B_MAX={2:0.0}, B_ACT={3:0.00}", PlugIn.ModelCore.CurrentTime, month, B_MAX, B_ACT);
float[] initialWoodLeafBiomass = new float[3] { (float)initialB[0], (float)initialB[1], (float)initialB[2] }; //wang?
return initialWoodLeafBiomass;
}
//---------------------------------------------------------------------
/// <summary>
/// Adds frass for a species to the foliar LITTER pools at a site.
/// Assumes that some of the N has been resorbed.
/// </summary>
public static void AddFrassLitter(double defoliatedLeafBiomass, ISpecies species, ActiveSite site)
{
double inputDecayValue = 1.0; // Decay value is calculated for surface/soil layers (leaf/fine root),
// therefore, this is just a dummy value.
if (defoliatedLeafBiomass > 0)
{
SiteVars.LitterfallC[site] += defoliatedLeafBiomass * 0.47;
double frassBiomass = Math.Max(0.0, OtherData.frassdepk * defoliatedLeafBiomass);
double frassBiomassC = frassBiomass * 0.47;
SiteVars.FrassC[site] += frassBiomassC;
LitterLayer.PartitionResidue(
frassBiomass,
inputDecayValue,
OtherData.CNratiofrass,
1.0,
1.0,
//OtherData.CNratiofrass,
LayerName.Leaf,
LayerType.Surface,
site);
}
}
public CohortBiomass(ActiveSite Site, ICohort Cohort, int Index)
{
this.cohort = Cohort;
fRad = 0;
site = Site;
spc = Cohort.Species;
}
public static void UpdateSiteData(DateTime date, ActiveSite site)
{
if (SiteOutput.HasSiteOutput[site] ==false) return;
string s = date.Year.ToString() + delim +
date.Month + delim +
date.ToString("MM/yyyy") + delim +
CanopyBiomass.NumberOfCanopyLayers[site] + delim +
Static.Tday[date] + delim +
Static.Prec[date] + delim +
Hydrology.RunOff[site] + delim +
Hydrology.WaterLeakage[site] + delim +
Hydrology.Transpiration[site] + delim +
Hydrology.Evaporation[site] + delim +
Hydrology.Water[site] + delim +
CanopyBiomass.CanopyLAI[site] + delim +
Static.VPD[date] + delim +
CanopyBiomass.GrossPsn[site] + delim +
CanopyBiomass.NetPsn[site] + delim +
CanopyBiomass.AutotrophicRespiration[site] + delim +
ForestFloor.HeterotrophicRespiration[site] + delim +
CanopyBiomass.TotalBiomass[site] + delim +
CanopyBiomass.TotalRoot[site] + delim +
CanopyBiomass.TotalFoliage[site] + delim +
CanopyBiomass.TotalNSC[site] + delim +
ForestFloor.Litter[site].Mass + delim +
ForestFloor.WoodyDebris[site].Mass;
FileContent.Add(s);
}
public static void WriteHeader(ActiveSite site)
{
if (HasSiteOutput[site] == false) return;
string FileName = OutputSiteFileName(site);
StreamWriter sw = new StreamWriter(FileName);
string s = "Year" + delim +
"Month" + delim +
"date" + delim +
"CanopyLayers" + delim +
"Tday(C)" + delim +
"Precip(mm_mo)" + delim +
"RunOff(mm_mo)" + delim +
"WaterLeakage(mm_mo)" + delim +
"Transpiration(mm)" + delim +
"Evaporation(mm_mo)" + delim +
"water(mm)" + delim +
"LAI(m2)" + delim +
"VPD(kPa)" + delim +
"GrossPsn(gC_mo)" + delim +
"NetPsn(gC_mo)" + delim +
"AutoResp(gC_mo)" + delim +
"HeteroResp(gC_mo)" + delim +
"TotalBiomass (gDW)" + delim +
"TotalRoot (gDW)" + delim +
"TotalFol (gDW)" + delim +
"TotalNSC (gC)" + delim +
"Litter(gDW_m2)" + delim +
"CWD(gDW_m2)";
sw.WriteLine(s);
sw.Close();
}
//---------------------------------------------------------------------
/// <summary>
/// Cuts the cohorts at a site.
/// </summary>
public override void Cut(ActiveSite site,
CohortCounts cohortCounts)
{
if (isDebugEnabled)
{
log.DebugFormat(" {0} is cutting site {1}; cohorts are:",
GetType().Name,
site.Location);
Debug.WriteSiteCohorts(log, site);
}
// Use age-only cohort selectors to harvest whole cohorts
// Note: the base method sets the CurrentSite property, and resets
// the counts to 0 before cutting.
base.Cut(site, cohortCounts);
// Then do any partial harvesting with the partial cohort selectors.
this.cohortCounts = cohortCounts;
SiteVars.Cohorts[site].ReduceOrKillBiomassCohorts(this);
if (isDebugEnabled)
{
log.DebugFormat(" Cohorts after cutting site {0}:",
site.Location);
Debug.WriteSiteCohorts(log, site);
}
}
//---------------------------------------------------------------------
/// <summary>
/// Adds some biomass for a species to the foliar LITTER pools at a site.
/// </summary>
public static void AddFoliageLitter(double foliarBiomass,
ISpecies species,
ActiveSite site)
{
double inputDecayValue = 1.0; // Decay value is calculated for surface/soil layers (leaf/fine root),
// therefore, this is just a dummy value.
if(foliarBiomass > 0)
{
SiteVars.LitterfallC[site] += foliarBiomass * 0.47;
LitterLayer.PartitionResidue(
foliarBiomass,
inputDecayValue,
SpeciesData.LeafCN[species],
SpeciesData.LeafLignin[species],
OtherData.StructuralCN,
LayerName.Leaf,
LayerType.Surface,
site);
}
}
//---------------------------------------------------------------------
// Method for setting the available resorbed N for each cohort.
// Amount of resorbed N must be in units of g N m-2.
public static void SetResorbedNallocation(ICohort cohort, double resorbedNallocation, ActiveSite site)
{
int cohortAddYear = GetAddYear(cohort);
//PlugIn.ModelCore.UI.WriteLine("SETResorbedNallocation: year={0}, mo={1}, species={2}, cohortAge={3}, cohortAddYear={4}.", PlugIn.ModelCore.CurrentTime, Century.Month, cohort.Species.Name, cohort.Age, cohortAddYear);
Dictionary<int, double> cohortDict;
double oldResorbedNallocation;
// If the dictionary entry exists for the cohort, overwrite it:
if (SiteVars.CohortResorbedNallocation[site].TryGetValue(cohort.Species.Index, out cohortDict))
if (cohortDict.TryGetValue(cohortAddYear, out oldResorbedNallocation))
{
SiteVars.CohortResorbedNallocation[site][cohort.Species.Index][cohortAddYear] = resorbedNallocation;
return;
}
// If the dictionary does not exist for the cohort, create it:
Dictionary<int, double> newEntry = new Dictionary<int, double>();
newEntry.Add(cohortAddYear, resorbedNallocation);
if (SiteVars.CohortResorbedNallocation[site].ContainsKey(cohort.Species.Index))
{
SiteVars.CohortResorbedNallocation[site][cohort.Species.Index].Add(cohortAddYear, resorbedNallocation);
}
else
{
SiteVars.CohortResorbedNallocation[site].Add(cohort.Species.Index, newEntry);
}
//PlugIn.ModelCore.UI.WriteLine("SET ResorbedNallocation: ResorbedNallocation={0:0.00000}.", resorbedNallocation);
return;
}
//---------------------------------------------------------------------
// This method replaces the delegate method. It is called every year when
// ACT_ANPP is calculated, for each cohort. Therefore, this method is operating at
// an ANNUAL time step and separate from the normal extension time step.
public static double ReduceCohortGrowth(ICohort cohort, ActiveSite site)//, int siteBiomass)
{
// PlugIn.ModelCore.UI.WriteLine(" Calculating cohort growth reduction due to insect defoliation...");
double summaryGrowthReduction = 0.0;
int sppIndex = cohort.Species.Index;
foreach(IInsect insect in PlugIn.ManyInsect)
{
if(!insect.ActiveOutbreak)
continue;
int suscIndex = insect.SppTable[sppIndex].Susceptibility - 1;
//if (suscIndex < 0) suscIndex = 0;
int yearBack = 0;
double annualDefoliation = 0.0;
if(insect.HostDefoliationByYear[site].ContainsKey(PlugIn.ModelCore.CurrentTime - yearBack))
{
// PlugIn.ModelCore.UI.WriteLine("Host Defoliation By Year: Time={0}, suscIndex={1}, spp={2}.", (PlugIn.ModelCore.CurrentTime - yearBack), suscIndex+1, cohort.Species.Name);
annualDefoliation += insect.HostDefoliationByYear[site][PlugIn.ModelCore.CurrentTime - yearBack][suscIndex];
}
double cumulativeDefoliation = annualDefoliation;
while(annualDefoliation > 0)
{
yearBack++;
annualDefoliation = 0.0;
if(insect.HostDefoliationByYear[site].ContainsKey(PlugIn.ModelCore.CurrentTime - yearBack))
{
// PlugIn.ModelCore.UI.WriteLine("Host Defoliation By Year: Time={0}, suscIndex={1}, spp={2}.", (PlugIn.ModelCore.CurrentTime - yearBack), suscIndex+1, cohort.Species.Name);
annualDefoliation = insect.HostDefoliationByYear[site][PlugIn.ModelCore.CurrentTime - yearBack][suscIndex];
cumulativeDefoliation += annualDefoliation;
}
}
double slope = insect.SppTable[sppIndex].GrowthReduceSlope;
double intercept = insect.SppTable[sppIndex].GrowthReduceIntercept;
double growthReduction = 1.0 - (cumulativeDefoliation * slope + intercept);
summaryGrowthReduction += growthReduction;
// PlugIn.ModelCore.UI.WriteLine("Time={0}, Spp={1}, SummaryGrowthReduction={2:0.00}.", PlugIn.ModelCore.CurrentTime,cohort.Species.Name, summaryGrowthReduction);
}
if (summaryGrowthReduction > 1.0) // Cannot exceed 100%
summaryGrowthReduction = 1.0;
if(summaryGrowthReduction > 1.0 || summaryGrowthReduction < 0)
{
PlugIn.ModelCore.UI.WriteLine("Cohort Total Growth Reduction = {0:0.00}. Site R/C={1}/{2}.", summaryGrowthReduction, site.Location.Row, site.Location.Column);
throw new ApplicationException("Error: Total Growth Reduction is not between 1.0 and 0.0");
}
return summaryGrowthReduction;
}
//---------------------------------------------------------------------
/// <summary>
/// Initializes a new instance.
/// </summary>
public DeathEventArgs(ICohort cohort,
ActiveSite site,
ExtensionType disturbanceType)
{
this.cohort = cohort;
this.site = site;
this.disturbanceType = disturbanceType;
}
public void RemoveCohort(Cohort cohort, Landis.SpatialModeling.ActiveSite site)
{
//ResetSpeciesCohorts();
//Speciescohorts = null;
cohorts.Remove(cohort);
Cohort.Died(this, cohort, site, null);
}
//ISiteCohorts cohorts)
//---------------------------------------------------------------------
public static double ComputeBiomass(ActiveSite site)
{
double total = 0.0;
if (SiteVars.Cohorts[site] != null)
foreach (ISpeciesCohorts speciesCohorts in SiteVars.Cohorts[site])
total += ComputeBiomass(speciesCohorts);
return total;
}
public static bool Algorithm(ISpecies species,
ActiveSite site)
{
return Reproduction.SufficientResources(species, site) &&
Reproduction.Establish(species, site) &&
Reproduction.MaturePresent(species, site);
//SiteVars.Cohorts[site].IsMaturePresent(species);
}
//---------------------------------------------------------------------
public void ApplyTo(ActiveSite site)
{
if (isDebugEnabled)
log.DebugFormat(" Applying LCC {0} to site {1}",
GetType().Name,
site.Location);
cohortHarvest.Cut(site);
}
/// <summary>
/// Default method for computing how much a cohort is defoliated at
/// a site.
/// </summary>
/// <returns>
/// 0%
/// </returns>
public static double Compute( ActiveSite site,
ISpecies species,
int cohortBiomass,
int siteBiomass)
{
return 0.0;
}
//---------------------------------------------------------------------
/// <summary>
/// Cut the trees at a site.
/// </summary>
public override void Cut(ActiveSite site)
{
// Use age-only cohort selectors to harvest whole cohorts
base.Cut(site);
// Then do any partial harvesting with the partial cohort selectors.
SiteVars.Cohorts[site].ReduceOrKillBiomassCohorts(this);
}
//---------------------------------------------------------------------
public static void WriteTotalsFor(ActiveSite site)
{
logFile.Write("{0},{1},{2}", Model.Core.CurrentTime, site.Location.Row, site.Location.Column);
foreach (ISpecies species in Model.Core.Species)
logFile.Write(",{0}", SiteBiomass.Harvested[species]);
logFile.WriteLine();
SiteBiomass.ResetHarvestTotals();
}
/// <summary>
/// Decomposes Structural Litter
/// </summary>
public static void Decompose(ActiveSite site)
{
SiteVars.SurfaceStructural[site].DecomposeStructural(site);
SiteVars.SurfaceMetabolic[site].DecomposeMetabolic(site);
SiteVars.SoilStructural[site].DecomposeStructural(site);
SiteVars.SoilMetabolic[site].DecomposeMetabolic(site);
}
//---------------------------------------------------------------------
// This method replaces the delegate method. It is called every year when
// ACT_ANPP is calculated, for each cohort. Therefore, this method is operating at
// an ANNUAL time step and separate from the normal extension time step.
public static double DefoliateCohort(ICohort cohort, ActiveSite site, int siteBiomass)
{
// This maintains backwards compatibility with succession versions that don't use Biomass Library
// but the functions must be sure to provide siteBiomass not cohortBiomass
double defoliation = Landis.Extension.Insects.Defoliate.DefoliateCohort(site, cohort.Species, cohort.Biomass, siteBiomass);
return defoliation;
}
//---------------------------------------------------------------------
/// <summary>
/// Raises a Cohort.DeathEvent.
/// </summary>
public static void Died(object sender,
ICohort cohort,
ActiveSite site,
ExtensionType disturbanceType)
{
if (DeathEvent != null)
DeathEvent(sender, new DeathEventArgs(cohort, site, disturbanceType));
}
//---------------------------------------------------------------------
/// <summary>
/// Reduces the biomass of cohorts that have been marked for partial
/// reduction.
/// </summary>
public static void ReduceCohortBiomass(ActiveSite site)
{
currentSite = site;
//PlugIn.ModelCore.Log.WriteLine("ReducingCohortBiomass NOW!");
SiteVars.Cohorts[site].ReduceOrKillBiomassCohorts(singleton);
}
//---------------------------------------------------------------------
public static double ComputeWoodBiomass(ActiveSite site)
{
double woodBiomass = 0;
if (SiteVars.Cohorts[site] != null)
foreach (ISpeciesCohorts speciesCohorts in SiteVars.Cohorts[site])
foreach (ICohort cohort in speciesCohorts)
woodBiomass += cohort.WoodBiomass;
return woodBiomass;
}
public static double ComputeBranchBiomass(ActiveSite site)
{
double branchBiomass = 0;
if (SiteVars.Cohorts[site] != null)
foreach (ISpeciesCohorts speciesCohorts in SiteVars.Cohorts[site])
foreach (ICohort cohort in speciesCohorts)
branchBiomass += cohort.BranchBiomass;
return branchBiomass;
}
//---------------------------------------------------------------------
void ICohortHarvest.Cut(ActiveSite site)
{
if (isDebugEnabled)
log.DebugFormat(" {0} is cutting site {1}:",
GetType().Name,
site.Location);
CurrentSite = site;
base.Cut(site);
}
private static string OutputSiteFileName(ActiveSite site)
{
string dir = Landis.Extension.Succession.BiomassPnET.InputParametersParser.Names.PNEToutputsites;
if (System.IO.Directory.Exists("output/" + dir) == false)
{
System.IO.Directory.CreateDirectory("output/" + dir);
}
return "output/" + dir + "/SiteEstData_" + site + Constants.ext;
}
//---------------------------------------------------------------------
public void ApplyTo(ActiveSite site)
{
if (isDebugEnabled)
log.DebugFormat(" Applying LCC {0} to site {1}",
GetType().Name,
site.Location);
CurrentSite = site;
Cut(site);
}