//---------------------------------------------------------------------------------------------------------
public double calcLeafTemperature(PhotosynthesisModel PM, int layer, double _leafTemp)
{
EnvironmentModel EM = PM.envModel;
LeafCanopy canopy = PM.canopy;
double airTemp = EM.getTemp(PM.time);
s[layer] = (es[layer] - canopy.es_Ta) / (leafTemp[layer] - EM.maxT);
gs[layer] = gs_CO2[layer] / canopy.ra;
rs_H2O[layer] = (1 / gs[layer] - 1.3 * canopy.rb_H_LAIs[layer] - canopy.rts[layer]) / 1.6;
Sn[layer] = canopy.energyConvRatio * absorbedIrradiance[layer];
R_[layer] = canopy.Bz * Math.Pow((leafTemp[layer] + 273), 4) * canopy.fvap * canopy.fclear * LAIS[layer] / canopy.LAIs.Sum();
Rn[layer] = Sn[layer] - R_[layer];
lE[layer] = (s[layer] * Rn[layer] + canopy.airDensity * canopy.cp * VPD[layer] / (canopy.rb_H_LAIs[layer] + canopy.rts[layer])) /
(s[layer] + canopy.g * ((canopy.rb_H2O_LAIs[layer] + canopy.rts[layer] + rs_H2O[layer]) / (canopy.rb_H_LAIs[layer] + canopy.rts[layer])));
double calcLeafTemp = airTemp + (canopy.rb_H_LAIs[layer] + canopy.rts[layer]) * (Rn[layer] - lE[layer]) / (canopy.airDensity * canopy.cp);
//return Math.Pow(1 - _leafTemp / calcLeafTemp, 2);
return(Math.Pow(_leafTemp - calcLeafTemp, 2));
}
void CalcConductanceResistance(PhotosynthesisModel PM)
{
for (int i = 0; i < _nLayers; i++)
{
//Intercepted radiation
//Saturated vapour pressure
ES = PM.EnvModel.CalcSVP(PM.EnvModel.GetTemp(PM.Time));
ES1 = PM.EnvModel.CalcSVP(PM.EnvModel.GetTemp(PM.Time) + 1);
S = (ES1 - ES) / ((PM.EnvModel.GetTemp(PM.Time) + 1) - PM.EnvModel.GetTemp(PM.Time));
//Wind speed
//us[i] = u0 * Math.Exp(-ku * (i + 1));
Us[i] = U0;
Rair = PM.EnvModel.ATM * 100000 / (287 * (PM.EnvModel.GetTemp(PM.Time) + 273)) * 1000 / 28.966;
Gbh[i] = 0.01 * Math.Pow((Us[i] / LeafWidth), 0.5) *
(1 - Math.Exp(-0.5 * Ku * LAI)) / (0.5 * Ku);
//Boundary layer
//rb_Hs[i] = 100 * Math.Pow((leafWidths[i] / us[i]), 0.5);
//rb_H2Os[i] = 0.93 * rb_Hs[i];
//rb_CO2s[i] = 1.37 * rb_H2Os[i];
//rts[i] = 0.74 * Math.Pow(Math.Log(2 - 0.7 * Height) / (0.1 * Height), 2) / (0.16 * us[i]) / LAIs[i];
//rb_H_LAIs[i] = rb_Hs[i] / LAIs[i];
//rb_H2O_LAIs[i] = rb_H2Os[i] / LAIs[i];
}
}
//----------------------------------------------------------------------
public void CalcRdActivity25(LeafCanopy canopy, SunlitShadedCanopy sunlit, PhotosynthesisModel PM)
{
for (int i = 0; i < _nLayers; i++)
{
Rd25[i] = canopy.Rd25[i] - sunlit.Rd25[i];
}
}
//---------------------------------------------------------------------------------------------------------
public void CalcPRate25(LeafCanopy canopy, SunlitShadedCanopy sunlit, PhotosynthesisModel PM)
{
for (int i = 0; i < _nLayers; i++)
{
VpMax25[i] = canopy.VpMax25[i] - sunlit.VpMax25[i];
}
}
//---------------------------------------------------------------------------------------------------------
public virtual void run(int nlayers, PhotosynthesisModel PM, SunlitShadedCanopy counterpart)
{
_nLayers = nlayers;
initArrays(_nLayers);
calcIncidentRadiation(PM.envModel, PM.canopy, counterpart);
calcAbsorbedRadiation(PM.envModel, PM.canopy, counterpart);
calcMaxRates(PM.canopy, counterpart, PM);
}
//-----------------------------------------------------------------------
public void run(PhotosynthesisModel PM, EnvironmentModel EM)
{
calcAbsorbedRadiation(EM);
calcLeafNitrogenDistribution(PM);
calcConductanceResistance();
calcLeafTemperature(PM, EM);
calcTotalLeafNitrogen(PM);
}
//-----------------------------------------------------------------------
void CalcLeafNitrogenDistribution(PhotosynthesisModel PM)
{
//-------------This is only when coupled with Apsim----------------------------------------
//-------------Otherwise use parameters----------------------------------------------------
if (PM.nitrogenModel == PhotosynthesisModel.NitrogenModel.APSIM)
{
SLNTop = PM.Canopy.CPath.SLNAv * PM.Canopy.CPath.SLNRatioTop;
LeafNTopCanopy = SLNTop * 1000 / 14;
NcAv = PM.Canopy.CPath.SLNAv * 1000 / 14;
NAllocationCoeff = -1 * Math.Log((NcAv - PM.Canopy.CPath.StructuralN) / (LeafNTopCanopy - PM.Canopy.CPath.StructuralN)) * 2;
}
//-------------This is only when coupled with Apsim----------------------------------------
else
{
SLNTop = LeafNTopCanopy / 1000 * 14;
NcAv = (LeafNTopCanopy - PM.Canopy.CPath.StructuralN) * Math.Exp(-0.5 * NAllocationCoeff) + PM.Canopy.CPath.StructuralN;
PM.Canopy.CPath.SLNAv = NcAv / 1000 * 14;
PM.Canopy.CPath.SLNRatioTop = SLNTop / PM.Canopy.CPath.SLNAv;
}
for (int i = 0; i < _nLayers; i++)
{
LeafNs[i] = CalcSLN(LAIAccums[i], PM.Canopy.CPath.StructuralN);
VcMax25[i] = LAI * CPath.PsiVc * (LeafNTopCanopy - PM.Canopy.CPath.StructuralN) * (
(i == 0 ? 1 : Math.Exp(-NAllocationCoeff * LAIAccums[i - 1] / LAI)) -
Math.Exp(-NAllocationCoeff * LAIAccums[i] / LAI)) / NAllocationCoeff;
//J2Max25[i] = LAI * CPath.PsiJ2 * (LeafNTopCanopy - PM.Canopy.CPath.StructuralN) * (
// (i == 0 ? 1 : Math.Exp(-NAllocationCoeff * LAIAccums[i - 1] / LAI)) -
// Math.Exp(-NAllocationCoeff * LAIAccums[i] / LAI)) / NAllocationCoeff;
JMax25[i] = LAI * CPath.PsiJ * (LeafNTopCanopy - PM.Canopy.CPath.StructuralN) * (
(i == 0 ? 1 : Math.Exp(-NAllocationCoeff * LAIAccums[i - 1] / LAI)) -
Math.Exp(-NAllocationCoeff * LAIAccums[i] / LAI)) / NAllocationCoeff;
Rd25[i] = LAI * CPath.PsiRd * (LeafNTopCanopy - PM.Canopy.CPath.StructuralN) * (
(i == 0 ? 1 : Math.Exp(-NAllocationCoeff * LAIAccums[i - 1] / LAI)) -
Math.Exp(-NAllocationCoeff * LAIAccums[i] / LAI)) / NAllocationCoeff;
VpMax25[i] = LAI * CPath.PsiVp * (LeafNTopCanopy - PM.Canopy.CPath.StructuralN) * (
(i == 0 ? 1 : Math.Exp(-NAllocationCoeff * LAIAccums[i - 1] / LAI)) -
Math.Exp(-NAllocationCoeff * LAIAccums[i] / LAI)) / NAllocationCoeff;
//Gm25[i] = CPath.PsiGm * (NcAv - PM.Canopy.CPath.StructuralN) + CPath.CGm;
Gm25[i] = LAI * CPath.PsiGm * (LeafNTopCanopy - PM.Canopy.CPath.StructuralN) * (
(i == 0 ? 1 : Math.Exp(-NAllocationCoeff * LAIAccums[i - 1] / LAI)) -
Math.Exp(-NAllocationCoeff * LAIAccums[i] / LAI)) / NAllocationCoeff;
}
}
//---------------------------------------------------------------------------------------------------------
public void calcPRate25(LeafCanopy canopy, SunlitShadedCanopy shaded, PhotosynthesisModel PM)
{
for (int i = 0; i < _nLayers; i++)
{
VpMax25[i] = canopy.LAI * canopy.CPath.psiVp * (canopy.leafNTopCanopy - canopy.CPath.structuralN) *
((i == 0 ? 1 : Math.Exp(-(canopy.beamExtCoeffs[i] + canopy.NAllocationCoeff / canopy.LAI) * canopy.LAIAccums[i - 1])) -
Math.Exp(-(canopy.beamExtCoeffs[i] + canopy.NAllocationCoeff / canopy.LAI) * canopy.LAIAccums[i])) /
(canopy.NAllocationCoeff + canopy.beamExtCoeffs[i] * canopy.LAI);
}
}
public void Run(PhotosynthesisModel PM, EnvironmentModel EM)
{
//calcCanopyStructure(EM.sunAngle.rad);
CalcAbsorbedRadiation(EM);
CalcLeafNitrogenDistribution(PM);
CalcConductanceResistance(PM);
CalcLeafTemperature(PM, EM);
CalcTotalLeafNitrogen(PM);
}
//----------------------------------------------------------------------
public void CalcRdActivity25(LeafCanopy canopy, SunlitShadedCanopy shaded, PhotosynthesisModel PM)
{
for (int i = 0; i < _nLayers; i++)
{
Rd25[i] = canopy.LAI * canopy.CPath.PsiRd * (canopy.LeafNTopCanopy - canopy.CPath.StructuralN) *
((i == 0 ? 1 : Math.Exp(-(canopy.BeamExtCoeffs[i] + canopy.NAllocationCoeff / canopy.LAI) * canopy.LAIAccums[i - 1])) -
Math.Exp(-(canopy.BeamExtCoeffs[i] + canopy.NAllocationCoeff / canopy.LAI) * canopy.LAIAccums[i])) /
(canopy.NAllocationCoeff + canopy.BeamExtCoeffs[i] * canopy.LAI);
}
}
//---------------------------------------------------------------------------------------------------------
public override void CalcConductanceResistance(PhotosynthesisModel PM, LeafCanopy canopy)
{
for (int i = 0; i < canopy.NLayers; i++)
{
Gbh[i] = 0.01 * Math.Pow((canopy.Us[i] / canopy.LeafWidth), 0.5) *
(1 - Math.Exp(-1 * (0.5 * canopy.Ku + canopy.Kb) * canopy.LAI)) / (0.5 * canopy.Ku + canopy.Kb);
}
base.CalcConductanceResistance(PM, canopy);
}
//---------------------------------------------------------------------------------------------------------
public void calcPhotosynthesis(PhotosynthesisModel PM, int layer)
{
LeafCanopy canopy = PM.canopy;
leafTemp[layer] = PM.envModel.getTemp(PM.time);
double vpd = PM.envModel.getVPD(PM.time);
canopy.CPath.CiCaRatio = canopy.CPath.CiCaRatioSlope * vpd + canopy.CPath.CiCaRatioIntercept;
VcMaxT[layer] = TempFunctionExp.val(leafTemp[layer], VcMax25[layer], canopy.CPath.VcMax_c, canopy.CPath.VcMax_b);
RdT[layer] = TempFunctionExp.val(leafTemp[layer], Rd25[layer], canopy.CPath.Rd_c, canopy.CPath.Rd_b);
JMaxT[layer] = TempFunction.val(leafTemp[layer], JMax25[layer], canopy.CPath.JMax_TOpt, canopy.CPath.JMax_Omega);
VpMaxT[layer] = TempFunctionExp.val(leafTemp[layer], VpMax25[layer], canopy.CPath.VpMax_c, canopy.CPath.VpMax_b);
Vpr[layer] = canopy.Vpr_l * LAIS[layer];
//TODO: I2 = canopy.ja * absorbedIrradiance[layer]
canopy.ja = (1 - canopy.f) / 2;
J[layer] = (canopy.ja * absorbedIrradiance[layer] + JMaxT[layer] - Math.Pow(Math.Pow(canopy.ja * absorbedIrradiance[layer] + JMaxT[layer], 2) -
4 * canopy.θ * JMaxT[layer] * canopy.ja * absorbedIrradiance[layer], 0.5)) / (2 * canopy.θ);
Kc[layer] = TempFunctionExp.val(leafTemp[layer], canopy.CPath.Kc_P25, canopy.CPath.Kc_c, canopy.CPath.Kc_b);
Ko[layer] = TempFunctionExp.val(leafTemp[layer], canopy.CPath.Ko_P25, canopy.CPath.Ko_c, canopy.CPath.Ko_b);
VcVo[layer] = TempFunctionExp.val(leafTemp[layer], canopy.CPath.VcMax_VoMax_P25, canopy.CPath.VcMax_VoMax_c, canopy.CPath.VcMax_VoMax_b);
ScO[layer] = Ko[layer] / Kc[layer] * VcVo[layer];
g_[layer] = 0.5 / ScO[layer];
canopy.Sco = ScO[layer]; //For reporting ???
K_[layer] = Kc[layer] * (1 + canopy.oxygenPartialPressure / Ko[layer]);
es[layer] = 5.637E-7 * Math.Pow(leafTemp[layer], 4) + 1.728E-5 * Math.Pow(leafTemp[layer], 3) + 1.534E-3 *
Math.Pow(leafTemp[layer], 2) + 4.424E-2 * leafTemp[layer] + 6.095E-1;
canopy.airDensity = 1.295 * Math.Exp(-3.6E-3 * PM.envModel.getTemp(PM.time));
canopy.ra = canopy.airDensity * 1000.0 / 28.966;
VPD[layer] = PM.envModel.getVPD(PM.time);
fVPD[layer] = canopy.a / (1 + VPD[layer] / canopy.Do);
gs[layer] = fVPD[layer];
gm_CO2T[layer] = LAIS[layer] * TempFunction.val(leafTemp[layer], canopy.CPath.gm_P25, canopy.CPath.gm_TOpt, canopy.CPath.gm_Omega);
gb_CO2[layer] = 1 / canopy.rb_CO2s[layer] * LAIS[layer] * canopy.ra;
}
public void CalcLeafTemperature(PhotosynthesisModel PM, EnvironmentModel EM)
{
//double airTemp = EM.getTemp(PM.time);
//fvap = 0.56 - 0.079 * Math.Pow(10 * Vair, 0.5);
//fclear = 0.1 + 0.9 * Math.Max(0, Math.Min(1, (EM.atmTransmissionRatio - 0.2) / 0.5));
//g = (cp * Math.Pow(10, -6)) * p / (l * mwRatio);
//es_Ta = 5.637E-7 * Math.Pow(airTemp, 4) + 1.728E-5 * Math.Pow(airTemp, 3) + 1.534E-3 *
// Math.Pow(airTemp, 2) + 4.424E-2 * airTemp + 6.095E-1;
//a2 = CPath.F2 * (1 - CPath.fcyc) / (CPath.F2 / CPath.F1 + (1 - CPath.fcyc));
}
public void CalcCanopyBiomassAccumulation(PhotosynthesisModel PM)
{
//for (int i = 0; i < nLayers; i++)
//{
// //TODO -- Rename / refactor variables to reflect units and time
// //TODO -- calculate biomass using B after daily A has ben summed (ie 1 calculation per day)
// //TODO -- check that we are only calculating between dawn and dusk
// //TODO -- use floor and cieling on dusk and dawn to calculate assimilation times
// Ac[i] = (PM.sunlit.A[i] + PM.shaded.A[i]) * 3600; // Rename (Acan, hour) (umolCo2/m2/s)
// // Acgross[i] = Ac[i] * Math.Pow(10, -6) * 44; // (gCo2/m2/s)
// biomassC[i] = Ac[i] * 44 * B * Math.Pow(10, -6); // Hourly Biomass
//}
//totalBiomassC = biomassC.Sum();
}
////---------------------------------------------------------------------------------------------------------
/// <summary>
///
/// </summary>
/// <param name="PM"></param>
/// <param name="canopy"></param>
public virtual void CalcConductanceResistance(PhotosynthesisModel PM, LeafCanopy canopy)
{
for (int i = 0; i < canopy.NLayers; i++)
{
//gbh[i] = 0.01 * Math.Pow((canopy.us[i] / canopy.leafWidth), 0.5) *
// (1 - Math.Exp(-1 * (0.5 * canopy.ku + canopy.kb) * canopy.LAI)) / (0.5 * canopy.ku + canopy.kb);
Gbw[i] = Gbh[i] / 0.92; //This 0.92 changed from 0.93 29/06
Rbh[i] = 1 / Gbh[i];
Rbw[i] = 1 / Gbw[i];
Gbw_m[i] = PM.EnvModel.ATM * PM.Canopy.Rair * Gbw[i];
GbCO2[i] = Gbw_m[i] / 1.37;
}
}
//--------------------------------------------------------------
public PhotoLayerSolverC3(PhotosynthesisModel PM, int layer) :
base(PM, layer)
{
}
//---------------------------------------------------------------------------------------------------------
public void CalcElectronTransportRate25(LeafCanopy canopy, SunlitShadedCanopy sunlit, PhotosynthesisModel PM)
{
for (int i = 0; i < _nLayers; i++)
{
//J2Max25[i] = canopy.J2Max25[i] - sunlit.J2Max25[i];
JMax25[i] = canopy.JMax25[i] - sunlit.JMax25[i];
}
}
//---------------------------------------------------------------------------------------------------------
public override void CalcMaxRates(LeafCanopy canopy, SunlitShadedCanopy counterpart, PhotosynthesisModel PM)
{
CalcRubiscoActivity25(canopy, counterpart, PM);
CalcElectronTransportRate25(canopy, counterpart, PM);
CalcRdActivity25(canopy, counterpart, PM);
CalcPRate25(canopy, counterpart, PM);
CalcGmRate25(canopy, counterpart, PM);
}
public abstract double calcPhotosynthesis(PhotosynthesisModel PM, SunlitShadedCanopy s, int layer, double _Cc);
//---------------------------------------------------------------------------------------------------------
/// <summary>
///
/// </summary>
/// <param name="PM"></param>
/// <param name="canopy"></param>
public virtual void DoWaterInteraction(PhotosynthesisModel PM, LeafCanopy canopy, TranspirationMode mode)
{
for (int i = 0; i < canopy.NLayers; i++)
{
Rn[i] = AbsorbedIrradiancePAR[i] + AbsorbedIrradianceNIR[i];
double BnUp = 8 * canopy.Sigma * Math.Pow((PM.EnvModel.GetTemp(PM.Time) + PM.EnvModel.AbsoluteTemperature), 3) * (LeafTemp__[i] - PM.EnvModel.GetTemp(PM.Time)); //This should be: HEnergyBalance - * (LeafTemp__[i]-PM.EnvModel.GetTemp(PM.Time));
double VPTLeaf = 0.61365 * Math.Exp(17.502 * LeafTemp__[i] / (240.97 + LeafTemp__[i]));
double VPTAir = 0.61365 * Math.Exp(17.502 * PM.EnvModel.GetTemp(PM.Time) / (240.97 + PM.EnvModel.GetTemp(PM.Time)));
double VPTAir_1 = 0.61365 * Math.Exp(17.502 * (PM.EnvModel.GetTemp(PM.Time) + 1) / (240.97 + (PM.EnvModel.GetTemp(PM.Time) + 1)));
double VPTMin = 0.61365 * Math.Exp(17.502 * PM.EnvModel.MinT / (240.97 + PM.EnvModel.MinT));
double s = VPTAir_1 - VPTAir;
VPD_la[i] = VPTLeaf - VPTMin;
double Wl = VPTLeaf / (PM.EnvModel.ATM * 100) * 1000;
double Wa = VPTMin / (PM.EnvModel.ATM * 100) * 1000;
if (mode == TranspirationMode.unlimited)
{
double a_var_gsCO2 = 1 / GbCO2[i];
double d_var_gsCO2 = (Wl - Wa) / (1000 - (Wl + Wa) / 2) * (canopy.Ca + Ci[i]) / 2;
double e_var_gsCO2 = A[i];
double f_var_gsCO2 = canopy.Ca - Ci[i];
double m_var_gsCO2 = 1.37; //Constant
double n_var_gsCO2 = 1.6; //Constant
double a_lump_gsCO2 = e_var_gsCO2 * a_var_gsCO2 * m_var_gsCO2 + e_var_gsCO2 * a_var_gsCO2 * n_var_gsCO2 + d_var_gsCO2 * m_var_gsCO2 * n_var_gsCO2 - f_var_gsCO2 * m_var_gsCO2;
double b_lump_gsCO2 = e_var_gsCO2 * m_var_gsCO2 * (e_var_gsCO2 * Math.Pow(a_var_gsCO2, 2) * n_var_gsCO2 + a_var_gsCO2 * d_var_gsCO2 * m_var_gsCO2 * n_var_gsCO2 - a_var_gsCO2 * f_var_gsCO2 * n_var_gsCO2);
double c_lump_gsCO2 = -a_lump_gsCO2;
double d_lump_gsCO2 = m_var_gsCO2 * A[i];
GsCO2[i] = 2 * d_lump_gsCO2 / (Math.Pow((Math.Pow(a_lump_gsCO2, 2) - 4 * b_lump_gsCO2), 0.5) - a_lump_gsCO2);
double Gtw = 1 / (1 / (1.37 * GbCO2[i]) + 1 / (1.6 * GsCO2[i])); //Are these the same constansts shown above
double GtCO2 = 1 / (1 / GbCO2[i] + 1 / GsCO2[i]);
//DO NOT DELETE - FILLED ARE OF SPREADSHEET
//double EMolsPerSecond = Gtw * (Wl - Wa) / (1000 - (Wl + Wa) / 2);
//double EMmPerHour = EMolsPerSecond * 18 / 1000 * 3600;
//double LambdaEEnergyBalance = 44100 * EMolsPerSecond; //44100 should be a parameter..discuss with AW
//double HEnergyBalance = 8 * canopy.Sigma * Math.Pow((PM.EnvModel.GetTemp(PM.Time) + PM.EnvModel.AbsoluteTemperature), 3);
//TDelta[i] = (Rn[i] - LambdaEEnergyBalance) / (HEnergyBalance + canopy.Rcp / Rbh[i]);
double rtw = canopy.Rair / Gtw * PM.EnvModel.ATM;
double a_lump_lambdaE = s * (Rn[i] - BnUp) + VPD_la[i] * canopy.Rcp / Rbh[i];
double b_lump_lambdaE = s + canopy.G * (rtw) / Rbh[i];
double lambdaE = a_lump_lambdaE / b_lump_lambdaE;
double EKgPerSecond = lambdaE / canopy.Lambda;
WaterUseMolsSecond[i] = EKgPerSecond / 18 * 1000;
WaterUse[i] = EKgPerSecond * 3600;
double a_lump_deltaT = canopy.G * (Rn[i] - BnUp) * rtw / canopy.Rcp - VPD_la[i];
double d_lump_deltaT = s + canopy.G * rtw / Rbh[i];
TDelta[i] = a_lump_deltaT / d_lump_deltaT;
VPD_la[i] = 0.61365 * Math.Exp(17.502 * LeafTemp__[i] / (240.97 + LeafTemp__[i])) - 0.61365 * Math.Exp(17.502 * PM.EnvModel.MinT / (240.97 + PM.EnvModel.MinT));
LeafTemp[i] = PM.EnvModel.GetTemp(PM.Time) + TDelta[i];
}
else
{
WaterUseMolsSecond[i] = WaterUse[i] / 18 * 1000 / 3600;
double EKgPerSecond = WaterUseMolsSecond[i] * 18 / 1000;
double rtw = (s * (Rn[i] - BnUp) + VPD_la[i] * canopy.Rcp / Rbh[i] - canopy.Lambda * EKgPerSecond * s) * Rbh[i] / (canopy.Lambda * EKgPerSecond * canopy.G);
Rsw[i] = rtw - Rbw[i];
GsCO2[i] = canopy.Rair * PM.EnvModel.ATM / Rsw[i] / 1.6;
double GtCO2 = 1 / (1 / GbCO2[i] + 1 / GsCO2[i]);
double a_lump_deltaT = canopy.G * (Rn[i] - BnUp) * rtw / canopy.Rcp - VPD_la[i];
double d_lump_deltaT = s + canopy.G * rtw / Rbh[i];
TDelta[i] = a_lump_deltaT / d_lump_deltaT;
//DO NOT DELETE - FILLED ARE OF SPREADSHEET
//double LambdaEEnergyBalance = 44100 * EMolsPerSecond; //44100 should be a parameter..discuss with AW
//double HEnergyBalance = 8 * canopy.Sigma * Math.Pow((PM.EnvModel.GetTemp(PM.Time) + PM.EnvModel.AbsoluteTemperature), 3);
//double Tdelta = (Rn[i] - LambdaEEnergyBalance) / (HEnergyBalance + canopy.Rcp / Rbh[i]); //This is not used anywhere
//double Gtw = EMolsPerSecond * (1000 - (Wl + Wa) / 2) / (Wl - Wa);
//GsCO2[i] = 1 / ((1 / Gtw - 1 / (1.37 * GbCO2[i])) * 1.6);
//GtCO2 = 1 / (1 / GbCO2[i] + 1 / GsCO2[i]);
LeafTemp[i] = PM.EnvModel.GetTemp(PM.Time) + TDelta[i];
}
}
}
//---------------------------------------------------------------------------------------------------------
public void CalcElectronTransportRate25(LeafCanopy canopy, SunlitShadedCanopy shaded, PhotosynthesisModel PM)
{
for (int i = 0; i < _nLayers; i++)
{
//J2Max25[i] = canopy.LAI * canopy.CPath.PsiJ2 * (canopy.LeafNTopCanopy - canopy.CPath.StructuralN) *
// ((i == 0 ? 1 : Math.Exp(-(canopy.BeamExtCoeffs[i] + canopy.NAllocationCoeff / canopy.LAI) * canopy.LAIAccums[i - 1])) -
// Math.Exp(-(canopy.BeamExtCoeffs[i] + canopy.NAllocationCoeff / canopy.LAI) * canopy.LAIAccums[i])) /
// (canopy.NAllocationCoeff + canopy.BeamExtCoeffs[i] * canopy.LAI);
JMax25[i] = canopy.LAI * canopy.CPath.PsiJ * (canopy.LeafNTopCanopy - canopy.CPath.StructuralN) *
((i == 0 ? 1 : Math.Exp(-(canopy.BeamExtCoeffs[i] + canopy.NAllocationCoeff / canopy.LAI) * canopy.LAIAccums[i - 1])) -
Math.Exp(-(canopy.BeamExtCoeffs[i] + canopy.NAllocationCoeff / canopy.LAI) * canopy.LAIAccums[i])) /
(canopy.NAllocationCoeff + canopy.BeamExtCoeffs[i] * canopy.LAI);
}
}
public void CalcTotalLeafNitrogen(PhotosynthesisModel PM)
{
TotalLeafNitrogen = LAI * ((LeafNTopCanopy - PM.Canopy.CPath.StructuralN) * (1 - Math.Exp(-NAllocationCoeff)) / NAllocationCoeff + PM.Canopy.CPath.StructuralN);
}
//---------------------------------------------------------------------------
public void runDaily()
{
if (!initialised)
{
return;
}
if (notifyStart != null)
{
notifyStart(true);
}
double modelTime = this.time;
instants = new List <double>();
ass = new List <double>();
Ios = new List <double>();
Idiffs = new List <double>();
Idirs = new List <double>();
SunlitACs = new List <double>();
SunlitAJs = new List <double>();
ShadedACs = new List <double>();
ShadedAJs = new List <double>();
dailyBiomass = 0;
interceptedRadn = 0;
AShadedMax = 0;
ASunlitMax = 0;
envModel.run();
for (double time = minTime; time <= maxTime; time += timeStep)
{
this.time = time;
instants.Add(canopy.Ac.Sum());
ass.Add(canopy.biomassC.Sum() * timeStep);
Idiffs.Add(envModel.diffuseRadiationPAR);
Idirs.Add(envModel.directRadiationPAR);
Ios.Add(envModel.diffuseRadiationPAR + envModel.directRadiationPAR);
dailyBiomass += canopy.totalBiomassC;
double propIntRadn = canopy.propnInterceptedRadns.Sum();
double interceptedRadnTimestep = envModel.totalIncidentRadiation * propIntRadn * timeStep * 3600;
interceptedRadn += interceptedRadnTimestep;
double RUEtimeStep = canopy.biomassC[0] / interceptedRadnTimestep;
PhotosynthesisModel PM = this;
if (ASunlitMax < sunlit.A.Max())
{
ASunlitMax = sunlit.A.Max();
}
if (AShadedMax < shaded.A.Max())
{
AShadedMax = shaded.A.Max();
}
}
dailyBiomassShoot = dailyBiomass * P_ag;
RUE = dailyBiomassShoot / interceptedRadn;
k = -Math.Log(1 - interceptedRadn / envModel.radn) / canopy.LAI;
A = instants.Sum() / 1000;
this.time = modelTime;
if (notifyFinish != null)
{
notifyFinish();
}
run(true);
if (notifyFinishDay != null)
{
notifyFinishDay();
}
}
//--------------------------------------------------------------
public PhotoLayerSolver(PhotosynthesisModel PM, int layer)
{
_PM = PM;
_layer = layer;
}
//--------------------------------------------------------------
public override double calcPhotosynthesis(PhotosynthesisModel PM, SunlitShadedCanopy s, int layer, double _A)
{
LeafCanopy canopy = PM.canopy;
s.calcPhotosynthesis(PM, layer);
s.Rm[layer] = s.RdT[layer] * 0.5;
canopy.z = (2 + canopy.fQ - canopy.CPath.fcyc) / (canopy.h * (1 - canopy.CPath.fcyc));
s.gbs[layer] = canopy.gbs_CO2 * s.LAIS[layer];
s.Oi[layer] = canopy.oxygenPartialPressure;
s.Om[layer] = canopy.oxygenPartialPressure;
s.gs_CO2[layer] = canopy.gs_CO2 * s.LAIS[layer];
s.Kp[layer] = TempFunctionExp.val(s.leafTemp[layer], canopy.CPath.Kp_P25, canopy.CPath.Kp_c, canopy.CPath.Kp_b);
//Caculate A's
s.Aj[layer] = calcAj(canopy, s, layer);
s.Ac[layer] = calcAc(canopy, s, layer);
if (s.Ac[layer] < 0 || double.IsNaN(s.Ac[layer]))
{
s.Ac[layer] = 0;
}
if (s.Aj[layer] < 0 || double.IsNaN(s.Aj[layer]))
{
s.Aj[layer] = 0;
}
s.A[layer] = Math.Max(0, Math.Min(s.Aj[layer], s.Ac[layer]));
if (PM.conductanceModel == PhotosynthesisModel.ConductanceModel.DETAILED)
{
s.Ci[layer] = canopy.Ca - s.A[layer] / s.gb_CO2[layer] - s.A[layer] / s.gs_CO2[layer];
}
else
{
s.Ci[layer] = canopy.CPath.CiCaRatio * canopy.Ca;
}
s.Cm_ac[layer] = s.Ci[layer] - s.Ac[layer] / s.gm_CO2T[layer];
s.Cm_aj[layer] = s.Ci[layer] - s.Aj[layer] / s.gm_CO2T[layer];
double Vp_ac = Math.Min(s.Cm_ac[layer] * s.VpMaxT[layer] / (s.Cm_ac[layer] + s.Kp[layer]), s.Vpr[layer]);
double Vp_aj = canopy.CPath.x * s.J[layer] / 2;
s.Oc_ac[layer] = canopy.alpha * s.Ac[layer] / (0.047 * s.gbs[layer]) + s.Om[layer];
s.Oc_aj[layer] = canopy.alpha * s.Aj[layer] / (0.047 * s.gbs[layer]) + s.Om[layer];
s.r_ac[layer] = s.g_[layer] * s.Oc_ac[layer];
s.r_aj[layer] = s.g_[layer] * s.Oc_aj[layer];
s.Ccac[layer] = s.Cm_ac[layer] + (Vp_ac - s.Ac[layer] - s.Rm[layer]) / s.gbs[layer];
s.Ccaj[layer] = s.Cm_aj[layer] + (Vp_aj - s.Aj[layer] - s.Rm[layer]) / s.gbs[layer];
if (s.Ccac[layer] < 0 || double.IsNaN(s.Ccac[layer]))
{
s.Ccac[layer] = 0;
}
if (s.Ccaj[layer] < 0 || double.IsNaN(s.Ccaj[layer]))
{
s.Ccaj[layer] = 0;
}
double F_ac = s.gbs[layer] * (s.Ccac[layer] - s.Cm_ac[layer]) / Vp_ac;
double F_aj = s.gbs[layer] * (s.Ccaj[layer] - s.Cm_aj[layer]) / Vp_aj;
if (s.Ac[layer] < s.Aj[layer])
{
s.Vp[layer] = Vp_ac;
s.Cc[layer] = s.Ccac[layer];
s.Cm[layer] = s.Cm_ac[layer];
s.Oc[layer] = s.Oc_ac[layer];
s.r_[layer] = s.r_ac[layer];
s.F[layer] = F_ac;
}
else
{
s.Vp[layer] = Vp_aj;
s.Cc[layer] = s.Ccaj[layer];
s.Cm[layer] = s.Cm_aj[layer];
s.Oc[layer] = s.Oc_aj[layer];
s.r_[layer] = s.r_aj[layer];
s.F[layer] = F_aj;
}
s.CiCaRatio[layer] = s.Ci[layer] / canopy.Ca;
//return Math.Pow(s.A[layer] - _A, 2);
return(0);
}
//--------------------------------------------------------------
public override double calcPhotosynthesis(PhotosynthesisModel PM, SunlitShadedCanopy s, int layer, double _Cc)
{
LeafCanopy canopy = PM.canopy;
s.calcPhotosynthesis(PM, layer);
s.Oi[layer] = canopy.oxygenPartialPressure;
s.Oc[layer] = s.Oi[layer];
s.r_[layer] = s.g_[layer] * s.Oc[layer];
s.Ac[layer] = calcAc(canopy, s, layer);
s.Aj[layer] = calcAj(canopy, s, layer);
if (s.Ac[layer] < 0 || double.IsNaN(s.Ac[layer]))
{
s.Ac[layer] = 0;
}
if (s.Aj[layer] < 0 || double.IsNaN(s.Aj[layer]))
{
s.Aj[layer] = 0;
}
s.A[layer] = Math.Min(s.Aj[layer], s.Ac[layer]);
if (PM.conductanceModel == PhotosynthesisModel.ConductanceModel.DETAILED)
{
// s.Ci[layer] = canopy.Ca - s.A[layer] / s.gb_CO2[layer] - s.A[layer] / s.gs_CO2[layer];
}
else
{
s.Ci[layer] = canopy.CPath.CiCaRatio * canopy.Ca;
}
s.Ccac[layer] = s.Ci[layer] - s.Ac[layer] / s.gm_CO2T[layer];
s.Ccaj[layer] = s.Ci[layer] - s.Aj[layer] / s.gm_CO2T[layer];
if (s.Ccac[layer] < 0 || double.IsNaN(s.Ccac[layer]))
{
s.Ccac[layer] = 0;
}
if (s.Ccaj[layer] < 0 || double.IsNaN(s.Ccaj[layer]))
{
s.Ccaj[layer] = 0;
}
if (s.Ac[layer] < s.Aj[layer])
{
s.Cc[layer] = s.Ac[layer];
}
else
{
s.Cc[layer] = s.Aj[layer];
}
s.Cc[layer] = s.Ci[layer] - s.A[layer] / s.gm_CO2T[layer];
if (s.Cc[layer] < 0 || double.IsNaN(s.Cc[layer]))
{
s.Cc[layer] = 0;
}
s.CiCaRatio[layer] = s.Ci[layer] / canopy.Ca;
return(Math.Pow(s.Cc[layer] - _Cc, 2));
}
public virtual void calcMaxRates(LeafCanopy canopy, SunlitShadedCanopy counterpart, PhotosynthesisModel EM)
{
}
//----------------------------------------------------------------------
public void calcRubiscoActivity25(LeafCanopy canopy, SunlitShadedCanopy sunlit, PhotosynthesisModel PM)
{
for (int i = 0; i < _nLayers; i++)
{
VcMax25[i] = canopy.VcMax25[i] - sunlit.VcMax25[i];
}
}
