//---------------------------------------------------------------------
public ISpecies this[ISpeciesPNET species]
{
get
{
return(SpeciesCombinations.Where(spc => spc.Item2 == species).First().Item1);
}
}
public void RecordPest(int year, ISpeciesPNET spc, float annualPest, float annualfWater, float annualfRad, bool estab, int monthCount)
{
if (estab)
{
if (HasEstablished(spc) == false)
{
_hasEstablished.Add(spc);
}
}
if (establishment_siteoutput != null)
{
if (monthCount == 0)
{
establishment_siteoutput.Add(year.ToString() + "," + spc.Name + "," + annualPest + "," + 0 + "," + 0 + "," + 0 + "," + HasEstablished(spc));
}
else
{
establishment_siteoutput.Add(year.ToString() + "," + spc.Name + "," + annualPest + "," + annualfWater + "," + annualfRad + "," + monthCount + "," + HasEstablished(spc));
}
// TODO: win time by reducing calls to write
establishment_siteoutput.Write();
}
// Record annualPest to be accessed as Probability
_pest[spc] = annualPest;
}
public bool Establish(ISpecies species, ActiveSite site)
{
ISpeciesPNET spc = PlugIn.SpeciesPnET[species];
bool Establish = sitecohorts[site].EstablishmentProbability.HasEstablished(spc);
return(Establish);
}
public void AddNewCohort(ISpecies species, ActiveSite site, string reproductionType)
{
ISpeciesPNET spc = PlugIn.SpeciesPnET[species];
bool addCohort = true;
if (sitecohorts[site].cohorts.ContainsKey(species))
{
// This should deliver only one KeyValuePair
KeyValuePair <ISpecies, List <Cohort> > i = new List <KeyValuePair <ISpecies, List <Cohort> > >(sitecohorts[site].cohorts.Where(o => o.Key == species))[0];
List <Cohort> Cohorts = new List <Cohort>(i.Value.Where(o => o.Age < CohortBinSize));
if (Cohorts.Count() > 0)
{
addCohort = false;
}
}
bool addSiteOutput = false;
addSiteOutput = (SiteOutputNames.ContainsKey(site) && addCohort);
Cohort cohort = new Cohort(spc, (ushort)Date.Year, (addSiteOutput) ? SiteOutputNames[site] : null);
addCohort = sitecohorts[site].AddNewCohort(cohort);
if (addCohort)
{
if (reproductionType == "plant")
{
if (!sitecohorts[site].SpeciesEstablishedByPlant.Contains(species))
{
sitecohorts[site].SpeciesEstablishedByPlant.Add(species);
}
}
else if (reproductionType == "serotiny")
{
if (!sitecohorts[site].SpeciesEstablishedBySerotiny.Contains(species))
{
sitecohorts[site].SpeciesEstablishedBySerotiny.Add(species);
}
}
else if (reproductionType == "resprout")
{
if (!sitecohorts[site].SpeciesEstablishedByResprout.Contains(species))
{
sitecohorts[site].SpeciesEstablishedByResprout.Add(species);
}
}
else if (reproductionType == "seed")
{
if (!sitecohorts[site].SpeciesEstablishedBySeed.Contains(species))
{
sitecohorts[site].SpeciesEstablishedBySeed.Add(species);
}
}
}
}
// Constructor
public Cohort(ISpeciesPNET species, ushort year_of_birth, string SiteName)
{
this.species = species;
age = 0;
this.nsc = (ushort)species.InitialNSC;
// Initialize biomass assuming fixed concentration of NSC
this.biomass = (uint)(1F / species.DNSC * (ushort)species.InitialNSC);
biomassmax = biomass;
// Then overwrite them if you need stuff for outputs
if (SiteName != null)
{
InitializeOutput(SiteName, year_of_birth);
}
}
public Cohort(Cohort cohort)
{
this.species = cohort.species;
this.age = cohort.age;
this.nsc = cohort.nsc;
this.biomass = cohort.biomass;
biomassmax = cohort.biomassmax;
this.fol = cohort.fol;
}
//---------------------------------------------------------------------
private SpeciesPnETVariables GetSpeciesVariables(ref IObservedClimate climate_dataset, bool Wythers, bool DTemp, float daylength, float nightlength, ISpeciesPNET spc)
{
// Class that contains species specific PnET variables for a certain month
SpeciesPnETVariables speciespnetvars = new SpeciesPnETVariables();
// Gradient of effect of vapour pressure deficit on growth.
speciespnetvars.DVPD = Math.Max(0, 1.0f - spc.DVPD1 * (float)Math.Pow(VPD, spc.DVPD2));
// ** CO2 effect on growth **
// M. Kubiske method for wue calculation: Improved methods for calculating WUE and Transpiration in PnET.
float JH2O = (float)(0.239 * ((VPD / (8314.47 * (climate_dataset.Tmin + 273f)))));
speciespnetvars.JH2O = JH2O;
// GROSSPSN gross photosynthesis
// Modify AmaxB based on CO2 level
// Equations solved from 2 known points: (350, AmaxB) and (550, AmaxB * CO2AmaxBEff)
float AmaxB_slope = (float)(((spc.CO2AMaxBEff - 1.0) * spc.AmaxB) / 200.0); // Derived from m = [(AmaxB*CO2AMaxBEff) - AmaxB]/[550 - 350]
float AmaxB_int = (float)(-1.0 * (((spc.CO2AMaxBEff - 1.0) * 1.75) - 1.0) * spc.AmaxB); // Derived from b = AmaxB - (AmaxB_slope * 350)
float AmaxB_CO2 = AmaxB_slope * climate_dataset.CO2 + AmaxB_int;
speciespnetvars.AmaxB_CO2 = AmaxB_CO2;
//-------------------FTempPSN (public for output file)
if (DTemp)
{
speciespnetvars.FTempPSN = EcoregionPnETVariables.DTempResponse(Tday, spc.PsnTOpt, spc.PsnTMin, spc.PsnTMax);
}
else
{
//speciespnetvars.FTempPSN = EcoregionPnETVariables.LinearPsnTempResponse(Tday, spc.PsnTOpt, spc.PsnTMin); // Original PnET-Succession
speciespnetvars.FTempPSN = EcoregionPnETVariables.CurvelinearPsnTempResponse(Tday, spc.PsnTOpt, spc.PsnTMin, spc.PsnTMax); // Modified 051216(BRM)
}
// Dday maintenance respiration factor (scaling factor of actual vs potential respiration applied to daily temperature)
float fTempRespDay = CalcQ10Factor(spc.Q10, Tday, spc.PsnTOpt);
// Night maintenance respiration factor (scaling factor of actual vs potential respiration applied to night temperature)
float fTempRespNight = CalcQ10Factor(spc.Q10, Tmin, spc.PsnTOpt);
// Unitless respiration adjustment: public for output file only
float FTempRespWeightedDayAndNight = (float)Math.Min(1.0, (fTempRespDay * daylength + fTempRespNight * nightlength) / ((float)daylength + (float)nightlength));
speciespnetvars.FTempRespWeightedDayAndNight = FTempRespWeightedDayAndNight;
// Scaling factor of respiration given day and night temperature and day and night length
speciespnetvars.MaintRespFTempResp = spc.MaintResp * FTempRespWeightedDayAndNight;
// Respiration gC/timestep (RespTempResponses[0] = day respiration factor)
// Respiration acclimation subroutine From: Tjoelker, M.G., Oleksyn, J., Reich, P.B. 1999.
// Acclimation of respiration to temperature and C02 in seedlings of boreal tree species
// in relation to plant size and relative growth rate. Global Change Biology. 49:679-691,
// and Tjoelker, M.G., Oleksyn, J., Reich, P.B. 2001. Modeling respiration of vegetation:
// evidence for a general temperature-dependent Q10. Global Change Biology. 7:223-230.
// This set of algorithms resets the veg parameter "BaseFolRespFrac" from
// the static vegetation parameter, then recalculates BaseFolResp based on the adjusted
// BaseFolRespFrac
// Base foliage respiration
float BaseFolRespFrac;
// Base parameter in Q10 temperature dependency calculation
float Q10base;
if (Wythers == true)
{
//Computed Base foliar respiration based on temp; this is species-level
BaseFolRespFrac = (0.138071F - 0.0024519F * Tave);
//Midpoint between Tave and Optimal Temp; this is also species-level
float Tmidpoint = (Tave + spc.PsnTOpt) / 2F;
// Base parameter in Q10 temperature dependency calculation in current temperature
Q10base = (3.22F - 0.046F * Tmidpoint);
}
else
{
// The default PnET setting
BaseFolRespFrac = spc.BFolResp;
Q10base = spc.Q10;
}
speciespnetvars.BaseFolRespFrac = BaseFolRespFrac;
// Respiration Q10 factor
speciespnetvars.Q10Factor = CalcQ10Factor(Q10base, Tave, spc.PsnTOpt);
return(speciespnetvars);
}
public void RecordPest(int year, ISpeciesPNET spc, float annualPest, bool estab)
{
if (estab)
{
if (HasEstablished(spc) == false)
{
_hasEstablished.Add(spc);
}
}
if (establishment_siteoutput != null)
{
establishment_siteoutput.Add(year.ToString() + "," + spc.Name + "," + annualPest + "," + _fwater[spc] + "," + _frad[spc] + "," + HasEstablished(spc));
// TODO: win time by reducing calls to write
establishment_siteoutput.Write();
}
}
public bool HasEstablished(ISpeciesPNET species)
{
return _hasEstablished.Contains(species);
}
public void EstablishmentTrue(ISpeciesPNET spc)
{
_hasEstablished.Add(spc);
}
private SpeciesPnETVariables GetSpeciesVariables(ref IObservedClimate climate_dataset, bool Wythers, bool DTemp, float daylength, float nightlength, ISpeciesPNET spc)
{
// Class that contains species specific PnET variables for a certain month
SpeciesPnETVariables speciespnetvars = new SpeciesPnETVariables();
// Gradient of effect of vapour pressure deficit on growth.
float DVPD = Math.Max(0, 1 - spc.DVPD1 * (float)Math.Pow(VPD, spc.DVPD2));
// Co2 ratio internal to the leave versus external
float cicaRatio = (-0.075f * spc.FolN) + 0.875f;
// Reference co2 ratio
float ci350 = 350 * cicaRatio;
// Elevated co2 effect
float Arel350 = 1.22f * ((ci350 - 68) / (ci350 + 136));
// Elevated leaf internal co2 concentration
float ciElev = climate_dataset.CO2 * cicaRatio;
float ArelElev = 1.22f * ((ciElev - 68) / (ciElev + 136));
// CO2 effect on growth
float delamax = 1 + ((ArelElev - Arel350) / Arel350);
speciespnetvars.DelAmax = delamax;
// CO2 effect on photosynthesis
// Calculate CO2 effect on conductance and set slope and intercept for A-gs relationship
//float Ci = climate_dataset.CO2 * (1 - cicaRatio);
//float Delgs = delamax / ((Ci / (350.0f - ci350))); // denominator -> CO2 conductance effect
float Delgs = delamax / ((climate_dataset.CO2 - climate_dataset.CO2 * cicaRatio) / (350.0f - ci350));
//_gsSlope = (float)((-1.1309 * delamax) + 1.9762); // used to determine ozone uptake
//_gsInt = (float)((0.4656 * delamax) - 0.9701);
//DWUE determined from CO2 effects on conductance
float wue = (spc.WUEcnst / VPD) * (1 + 1 - Delgs);
speciespnetvars.WUE = wue;
// water use efficiency in a co2 enriched atmosphere
//speciespnetvars.WUE_CO2_corr = wue / delamax;
//speciespnetvars.WUE_CO2_corr = (climate_dataset.CO2 - Ci) / 1.6f;
// NETPSN net photosynthesis
speciespnetvars.Amax = speciespnetvars.DelAmax * (spc.AmaxA + spc.AmaxB * spc.FolN);
//Reference net Psn (lab conditions) in gC/m2 leaf area/timestep
float RefNetPsn = _dayspan * (speciespnetvars.Amax * DVPD * daylength * Constants.MC) / Constants.billion;
//-------------------FTempPSN (public for output file)
if (DTemp)
{
speciespnetvars.FTempPSN = EcoregionPnETVariables.DTempResponse(Tday, spc.PsnTOpt, spc.PsnTMin);
}
else
{
//speciespnetvars.FTempPSN = EcoregionPnETVariables.LinearPsnTempResponse(Tday, spc.PsnTOpt, spc.PsnTMin); // Original PnET-Succession
speciespnetvars.FTempPSN = EcoregionPnETVariables.CurvelinearPsnTempResponse(Tday, spc.PsnTOpt, spc.PsnTMin); // Modified 051216(BRM)
}
// PSN (gC/m2 leaf area/tstep) reference net psn in a given temperature
speciespnetvars.FTempPSNRefNetPsn = speciespnetvars.FTempPSN * RefNetPsn;
//EcoregionPnETVariables.RespTempResponse(spc, Tday, climate_dataset.Tmin, daylength, nightlength);
// Dday maintenance respiration factor (scaling factor of actual vs potential respiration applied to daily temperature)
float fTempRespDay = CalcQ10Factor(spc.Q10, Tday, spc.PsnTOpt);
// Night maintenance respiration factor (scaling factor of actual vs potential respiration applied to night temperature)
float fTempRespNight = CalcQ10Factor(spc.Q10, Tmin , spc.PsnTOpt);
// Unitless respiration adjustment: public for output file only
speciespnetvars.FTempRespWeightedDayAndNight = (float)Math.Min(1.0, (fTempRespDay * daylength + fTempRespNight * nightlength) / ((float)daylength + (float)nightlength)); ;
// Scaling factor of respiration given day and night temperature and day and night length
speciespnetvars.MaintRespFTempResp = spc.MaintResp * speciespnetvars.FTempRespWeightedDayAndNight;
// Respiration gC/timestep (RespTempResponses[0] = day respiration factor)
// Respiration acclimation subroutine From: Tjoelker, M.G., Oleksyn, J., Reich, P.B. 1999.
// Acclimation of respiration to temperature and C02 in seedlings of boreal tree species
// in relation to plant size and relative growth rate. Global Change Biology. 49:679-691,
// and Tjoelker, M.G., Oleksyn, J., Reich, P.B. 2001. Modeling respiration of vegetation:
// evidence for a general temperature-dependent Q10. Global Change Biology. 7:223-230.
// This set of algorithms resets the veg parameter "BaseFolRespFrac" from
// the static vegetation parameter, then recalculates BaseFolResp based on the adjusted
// BaseFolRespFrac
// Base foliage respiration
float BaseFolResp;
// Base parameter in Q10 temperature dependency calculation
float Q10base;
if (Wythers == true)
{
//Computed Base foliar respiration based on temp; this is species-level, so you can compute outside this IF block and use for all cohorts of a species
BaseFolResp = (0.138071F - 0.0024519F * Tave);
//Midpoint between Tave and Optimal Temp; this is also species-level
float Tmidpoint=(Tave+ spc.PsnTOpt)/2F;
// Base parameter in Q10 temperature dependency calculation in current temperature
Q10base = (3.22F - 0.046F * Tmidpoint);
}
else
{
// The default PnET setting is that these
BaseFolResp = spc.BFolResp;
Q10base = spc.Q10;
}
// Growth respiration factor
speciespnetvars.FTempRespDay = BaseFolResp * CalcQ10Factor(Q10base, Tave, spc.PsnTOpt);
return speciespnetvars;
}
public float Get_FRad(ISpeciesPNET species)
{
{
return(_frad[species]);
}
}
public float Get_FWater(ISpeciesPNET species)
{
{
return(_fwater[species]);
}
}
//private static int Timestep;
public bool HasEstablished(ISpeciesPNET species)
{
return(_hasEstablished.Contains(species));
}
public void EstablishmentTrue(ISpeciesPNET spc)
{
_hasEstablished.Add(spc);
}
public ISpecies this[ISpeciesPNET species]
{
get
{
return SpeciesCombinations.Where(spc => spc.Item2 == species).First().Item1;
}
}
