//---------------------------------------------------------------------------------------------------------
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 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);
}