//---------------------------------------------------------------------------------------------------------
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 double calcAj(LeafCanopy canopy, SunlitShadedCanopy s, int layer)
{
double x1 = (1 - canopy.CPath.x) * s.J[layer] / 3.0;
double x2 = 7.0 / 3.0 * s.g_[layer];
double x3 = 0;
double x4 = 0;
double x5 = canopy.CPath.x * s.J[layer] / 2.0;
double a, b, c, d;
double Ci = canopy.CPath.CiCaRatio * canopy.Ca;
double g_m = s.gm_CO2T[layer];
double g_bs = s.gbs[layer];
double α = canopy.alpha;
double R_d = s.RdT[layer];
double γ_ = s.g_[layer];
double O_m = s.Om[layer];
double R_m = s.Rm[layer];
a = -Ci * 0.047 * g_m * g_bs - Ci * 0.047 * g_m * x4 - α * g_m * R_d * x2 - α * g_m * γ_ * x1 - O_m * 0.047 * g_m * g_bs * x2 - 0.047 * g_m * g_bs * x3 +
0.047 * g_m * R_m + 0.047 * g_m * R_d - 0.047 * g_m * x1 - 0.047 * g_m * x5 + 0.047 * g_bs * R_d -
0.047 * g_bs * x1 + 0.047 * R_d * x4 - 0.047 * x1 * x4; // Eq (A56)
b = (-α * g_m * x2 + 0.047 * g_m + 0.047 * g_bs + 0.047 * x4) *
(-Ci * 0.047 * g_m * g_bs * R_d + Ci * 0.047 * g_m * g_bs * x1 - Ci * 0.047 * g_m * R_d * x4 + Ci * 0.047 * g_m * x1 * x4 -
O_m * 0.047 * g_m * g_bs * R_d * x2 - 0.047 * g_m * g_bs * R_d * x3 - O_m * 0.047 * g_m * g_bs * γ_ * x1 +
0.047 * g_m * R_m - 0.047 * g_m * R_m * x1 - 0.047 * g_m * R_d * x5 + 0.047 * g_m * x1 * x5); // Eq (A57)
c = Ci * 0.047 * g_m * g_bs + Ci * 0.047 * g_m * x4 + α * g_m * R_d * x2 + α * g_m * γ_ * x1 + O_m * 0.047 * g_m * g_bs * x2 +
0.047 * g_m * g_bs * x3 - 0.047 * g_m * R_m - 0.047 * g_m * R_d + 0.047 * g_m * x1 + 0.047 * g_m * x5 - 0.047 * g_bs * R_d +
0.047 * g_bs * x1 - 0.047 * R_d * x4 + 0.047 * x1 * x4; // Eq(A58)
d = -α * g_m * x2 + 0.047 * g_m + 0.047 * g_bs + 0.047 * x4; // Eq (A59)
return((-1 * Math.Pow((Math.Pow(a, 2) - 4 * b), 0.5) + c) / (2 * d)); //Eq (A55)
}
//---------------------------------------------------------------------------------------------------------
public void calcElectronTransportRate25(LeafCanopy canopy, SunlitShadedCanopy sunlit, PhotosynthesisModel PM)
{
for (int i = 0; i < _nLayers; 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);
}
//----------------------------------------------------------------------
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 calcRubiscoActivity25(LeafCanopy canopy, SunlitShadedCanopy sunlit, PhotosynthesisModel PM)
{
for (int i = 0; i < _nLayers; i++)
{
VcMax25[i] = canopy.VcMax25[i] - sunlit.VcMax25[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 double calcAc(LeafCanopy canopy, SunlitShadedCanopy s, int layer, double cm_, bool assimilation, bool AC1)
{
double x1 = s.VcMaxT[layer];
double x2 = s.Kc[layer] / s.Ko[layer];
double x3 = s.Kc[layer];
double x4, x5;
if (AC1)
{
x4 = s.VpMaxT[layer] / (cm_ + s.Kp[layer]); //Delta Eq (A56)
x5 = 0;
}
else
{
x4 = 0;
x5 = s.Vpr[layer];
}
double a, b, c, d;
double Ci = canopy.CPath.CiCaRatio * canopy.Ca;
double g_m = s.gm_CO2T[layer];
double g_bs = s.gbs[layer];
double α = canopy.alpha;
double R_d = s.RdT[layer];
double γ_ = s.g_[layer];
double O_m = s.Om[layer];
double R_m = s.Rm[layer];
double value;
a = -Ci * 0.047 * g_m * g_bs - Ci * 0.047 * g_m * x4 - α * g_m * R_d * x2 - α * g_m * γ_ * x1 - O_m * 0.047 * g_m * g_bs * x2 - 0.047 * g_m * g_bs * x3 +
0.047 * g_m * R_m + 0.047 * g_m * R_d - 0.047 * g_m * x1 - 0.047 * g_m * x5 + 0.047 * g_bs * R_d -
0.047 * g_bs * x1 + 0.047 * R_d * x4 - 0.047 * x1 * x4; // Eq (A56)
b = (-α * g_m * x2 + 0.047 * g_m + 0.047 * g_bs + 0.047 * x4) *
(-Ci * 0.047 * g_m * g_bs * R_d + Ci * 0.047 * g_m * g_bs * x1 - Ci * 0.047 * g_m * R_d * x4 + Ci * 0.047 * g_m * x1 * x4 -
O_m * 0.047 * g_m * g_bs * R_d * x2 - 0.047 * g_m * g_bs * R_d * x3 - O_m * 0.047 * g_m * g_bs * γ_ * x1 +
0.047 * g_m * R_m - 0.047 * g_m * R_m * x1 - 0.047 * g_m * R_d * x5 + 0.047 * g_m * x1 * x5); // Eq (A57)
c = Ci * 0.047 * g_m * g_bs + Ci * 0.047 * g_m * x4 + α * g_m * R_d * x2 + α * g_m * γ_ * x1 + O_m * 0.047 * g_m * g_bs * x2 +
0.047 * g_m * g_bs * x3 - 0.047 * g_m * R_m - 0.047 * g_m * R_d + 0.047 * g_m * x1 + 0.047 * g_m * x5 - 0.047 * g_bs * R_d +
0.047 * g_bs * x1 - 0.047 * R_d * x4 + 0.047 * x1 * x4; // Eq(A58)
d = -α * g_m * x2 + 0.047 * g_m + 0.047 * g_bs + 0.047 * x4; // Eq (A59)
double ass = (-1 * Math.Pow((Math.Pow(a, 2) - 4 * b), 0.5) + c) / (2 * d); //Eq (A55)
if (assimilation)
{
value = ass;
}
else
{
value = Ci - ass / g_m; //Eq 43
}
return(value);
}
//---------------------------------------------------------------------------------------------------------
public override void CalcLAI(LeafCanopy canopy, SunlitShadedCanopy sunlit)
{
LAIS = new double[canopy.NLayers];
for (int i = 0; i < canopy.NLayers; i++)
{
LAIS[i] = canopy.LAIs[i] - sunlit.LAIS[i];
}
}
//---------------------------------------------------------------------------------------------------------
public override void calcLAI(LeafCanopy canopy, SunlitShadedCanopy counterpart)
{
LAIS = new double[canopy.nLayers];
for (int i = 0; i < canopy.nLayers; i++)
{
LAIS[i] = ((i == 0 ? 1 : Math.Exp(-canopy.beamExtCoeffs[i] * canopy.LAIAccums[i - 1])) -
Math.Exp(-canopy.beamExtCoeffs[i] * canopy.LAIAccums[i])) * 1 / canopy.beamExtCoeffs[i];
}
}
//---------------------------------------------------------------------------------------------------------
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 override double calcAj(double Cc, LeafCanopy canopy, SunlitShadedCanopy s, int layer)
{
if (Cc == 0)
{
return(0);
}
return((1 - s.r_aj[layer] / Cc) * (1 - canopy.x) *
s.J[layer] / (3 * (1 + 7 * s.r_[layer] / (3 * Cc))) -
s.RdT[layer]);
}
//----------------------------------------------------------------------
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 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 double calcAj(LeafCanopy canopy, SunlitShadedCanopy s, int layer)
{
double x1 = s.J[layer] / 4;
double x2 = 2 * s.r_[layer];
double a, b, c, d;
a = -1 * canopy.CPath.CiCaRatio * canopy.Ca * s.gm_CO2T[layer] - s.gm_CO2T[layer] * x2 + s.RdT[layer] - x1; //Eq (A56)
b = -1 * canopy.CPath.CiCaRatio * canopy.Ca * s.gm_CO2T[layer] * s.RdT[layer] + canopy.CPath.CiCaRatio * canopy.Ca * s.gm_CO2T[layer] * x1 -
s.gm_CO2T[layer] * s.RdT[layer] * x2 - s.gm_CO2T[layer] * s.r_[layer] * x1; // Eq (A57)
c = canopy.CPath.CiCaRatio * canopy.Ca * s.gm_CO2T[layer] + s.gm_CO2T[layer] * x2 - s.RdT[layer] + x1; // Eq (A58)
d = 1;
return((-1 * Math.Pow((Math.Pow(a, 2) - 4 * b), 0.5) + c) / (2 * d)); //Eq (A55)
}
//---------------------------------------------------------------------------------------------------------
public double calcAc(LeafCanopy canopy, SunlitShadedCanopy s, int layer)
{
double x1 = s.VcMaxT[layer];
double x2 = s.Kc[layer] * (1 + canopy.oxygenPartialPressure / s.Ko[layer]);
double a, b, c, d;
a = -1 * canopy.CPath.CiCaRatio * canopy.Ca * s.gm_CO2T[layer] - s.gm_CO2T[layer] * x2 + s.RdT[layer] - x1; //Eq (A56)
b = -1 * canopy.CPath.CiCaRatio * canopy.Ca * s.gm_CO2T[layer] * s.RdT[layer] + canopy.CPath.CiCaRatio * canopy.Ca * s.gm_CO2T[layer] * x1 -
s.gm_CO2T[layer] * s.RdT[layer] * x2 - s.gm_CO2T[layer] * s.r_[layer] * x1; // Eq (A57)
c = canopy.CPath.CiCaRatio * canopy.Ca * s.gm_CO2T[layer] + s.gm_CO2T[layer] * x2 - s.RdT[layer] + x1; // Eq (A58)
d = 1;
return((-1 * Math.Pow((Math.Pow(a, 2) - 4 * b), 0.5) + c) / (2 * d)); //Eq (A55)
}
//--------------------------------------------------------------
public double calcAc(LeafCanopy canopy, SunlitShadedCanopy s, int layer)
{
int iteration = 1;
double cm_ = 160;
while (iteration <= 4)
{
cm_ = calcAc(canopy, s, layer, cm_, false, true);
iteration++;
}
s.Cm_ac[layer] = cm_;
double Ac1 = calcAc(canopy, s, layer, cm_, true, true);
double Ac2 = calcAc(canopy, s, layer, cm_, true, false);
return(Math.Min(Ac1, Ac2));
}
//----------------------------------------------------------------------
public override void CalcIncidentRadiation(EnvironmentModel EM, LeafCanopy canopy, SunlitShadedCanopy sunlit)
{
for (int i = 0; i < _nLayers; i++)
{
IncidentIrradiance[i] = EM.DiffuseRadiationPAR * canopy.PropnInterceptedRadns[i] / (sunlit.LAIS[i] + LAIS[i]) *
LAIS[i] + 0.15 * (sunlit.IncidentIrradiance[i] * sunlit.LAIS[i]) / (LAIS[i] + (i < (_nLayers - 1) ? LAIS[i + 1] : 0)) * LAIS[i]; //+ *((E70*E44)/(E45+F45)
}
}
//----------------------------------------------------------------------
public override void CalcAbsorbedRadiation(EnvironmentModel EM, LeafCanopy canopy, SunlitShadedCanopy sunlit)
{
for (int i = 0; i < _nLayers; i++)
{
AbsorbedIrradiance[i] = canopy.AbsorbedRadiation[i] - sunlit.AbsorbedIrradiance[i];
AbsorbedIrradianceNIR[i] = canopy.AbsorbedRadiationNIR[i] - sunlit.AbsorbedIrradianceNIR[i];
AbsorbedIrradiancePAR[i] = canopy.AbsorbedRadiationPAR[i] - sunlit.AbsorbedIrradiancePAR[i];
}
}
//--------------------------------------------------------------
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 override double calcAj(double Cc, LeafCanopy canopy, SunlitShadedCanopy s, int layer)
{
return((Cc - s.r_[layer]) * s.J[layer] / (4 * (Cc + 2 * s.r_[layer])) - s.RdT[layer]);
}
public virtual void calcAbsorbedRadiation(EnvironmentModel EM, LeafCanopy canopy, SunlitShadedCanopy counterpart)
{
}
public virtual void calcMaxRates(LeafCanopy canopy, SunlitShadedCanopy counterpart, PhotosynthesisModel EM)
{
}
//---------------------------------------------------------------------------------------------------------
public virtual void calcLAI(LeafCanopy canopy, SunlitShadedCanopy counterpart)
{
}
//---------------------------------------------------------------------------------------------------------
public override void CalcAbsorbedRadiation(EnvironmentModel EM, LeafCanopy canopy, SunlitShadedCanopy shaded)
{
CalcAbsorbedRadiationDirect(EM, canopy);
CalcAbsorbedRadiationDiffuse(EM, canopy);
CalcAbsorbedRadiationScattered(EM, canopy);
for (int i = 0; i < _nLayers; i++)
{
AbsorbedIrradiance[i] = AbsorbedRadiationDirect[i] + AbsorbedRadiationDiffuse[i] + AbsorbedRadiationScattered[i];
AbsorbedIrradiancePAR[i] = AbsorbedRadiationDirectPAR[i] + AbsorbedRadiationDiffusePAR[i] + AbsorbedRadiationScatteredPAR[i];
AbsorbedIrradianceNIR[i] = AbsorbedRadiationDirectNIR[i] + AbsorbedRadiationDiffuseNIR[i] + AbsorbedRadiationScatteredNIR[i];
}
}
public abstract double calcPhotosynthesis(PhotosynthesisModel PM, SunlitShadedCanopy s, int layer, double _Cc);
//---------------------------------------------------------------------------------------------------------
public override void calcAbsorbedRadiation(EnvironmentModel EM, LeafCanopy canopy, SunlitShadedCanopy shaded)
{
calcAbsorbedRadiationDirect(EM, canopy);
calcAbsorbedRadiationDiffuse(EM, canopy);
calcAbsorbedRadiationScattered(EM, canopy);
for (int i = 0; i < _nLayers; i++)
{
absorbedIrradiance[i] = absorbedRadiationDirect[i] + absorbedRadiationDiffuse[i] + absorbedRadiationScattered[i];
}
}
//---------------------------------------------------------------------------------------------------------
public override void calcIncidentRadiation(EnvironmentModel EM, LeafCanopy canopy, SunlitShadedCanopy shaded)
{
for (int i = 0; i < _nLayers; i++)
{
incidentIrradiance[i] = EM.directRadiationPAR * canopy.propnInterceptedRadns[i] / LAIS[i] * LAIS[i] +
EM.diffuseRadiationPAR * canopy.propnInterceptedRadns[i] / (LAIS[i] + shaded.LAIS[i]) * LAIS[i];
}
}
//---------------------------------------------------------------------------------------------------------
public virtual void CalcIncidentRadiation(EnvironmentModel EM, LeafCanopy canopy, SunlitShadedCanopy counterpart)
{
}
//--------------------------------------------------------------------------------------------------------- public abstract double calcAj(double Cc, LeafCanopy canopy, SunlitShadedCanopy s, int layer);
