/// <inheritdoc/>
public void UpdatePartialPressures(AssimilationPathway pathway, TemperatureResponse leaf, AssimilationFunction function)
{
var cm = pathway.MesophyllCO2;
var cc = pathway.ChloroplasticCO2;
var oc = pathway.ChloroplasticO2;
UpdateMesophyllCO2(pathway, leaf);
UpdateChloroplasticO2(pathway);
UpdateChloroplasticCO2(pathway, function);
pathway.MesophyllCO2 = (pathway.MesophyllCO2 + cm) / 2.0;
pathway.ChloroplasticCO2 = (pathway.ChloroplasticCO2 + cc) / 2.0;
pathway.ChloroplasticO2 = (pathway.ChloroplasticO2 + oc) / 2.0;
}
/// <summary>
/// Factory method for accessing the different possible terms for assimilation
/// </summary>
public AssimilationFunction GetFunction(AssimilationPathway pathway, TemperatureResponse leaf)
{
if (pathway.Type == PathwayType.Ac1)
{
return(GetAc1Function(pathway, leaf));
}
else if (pathway.Type == PathwayType.Ac2)
{
return(GetAc2Function(pathway, leaf));
}
else
{
return(GetAjFunction(pathway, leaf));
}
}
/// <inheritdoc/>
protected override AssimilationFunction GetAc2Function(AssimilationPathway pathway, TemperatureResponse leaf)
{
var x = new double[9];
x[0] = leaf.VcMaxT;
x[1] = leaf.Kc / leaf.Ko;
x[2] = leaf.Kc;
x[3] = 0.0;
x[4] = pathway.Vpr;
x[5] = 0.0;
x[6] = pathway.ChloroplasticCO2 * leaf.VcMaxT / (pathway.ChloroplasticCO2 + leaf.Kc * (1 + pathway.ChloroplasticO2 / leaf.Ko));
x[7] = 1.0;
x[8] = 1.0;
var func = new AssimilationFunction()
{
X = x,
MesophyllRespiration = leaf.GmRd,
HalfRubiscoSpecificityReciprocal = leaf.Gamma,
FractionOfDiffusivitySolubilityRatio = 0.1 / canopy.DiffusivitySolubilityRatio,
BundleSheathConductance = pathway.Gbs,
Oxygen = canopy.AirO2,
Respiration = leaf.RdT
};
return(func);
}
/// <inheritdoc/>
protected override void UpdateMesophyllCO2(AssimilationPathway pathway, TemperatureResponse leaf)
{
pathway.MesophyllCO2 = pathway.IntercellularCO2 - pathway.CO2Rate / leaf.GmT;
}
/// <inheritdoc/>
protected override AssimilationFunction GetAjFunction(AssimilationPathway pathway, TemperatureResponse leaf)
{
var x = new double[9];
x[0] = (1 - parameters.MesophyllElectronTransportFraction) * parameters.ATPProductionElectronTransportFactor * leaf.J / 3.0;
x[1] = 7.0 / 3.0 * leaf.Gamma;
x[2] = 0.0;
x[3] = 0.0;
x[4] = parameters.MesophyllElectronTransportFraction * parameters.ATPProductionElectronTransportFactor * leaf.J / parameters.ExtraATPCost;
x[5] = 0.0;
x[6] = pathway.ChloroplasticCO2 * (1 - parameters.MesophyllElectronTransportFraction) * parameters.ATPProductionElectronTransportFactor * leaf.J / (3 * pathway.ChloroplasticCO2 + 7 * leaf.Gamma * pathway.ChloroplasticO2);
x[7] = 1.0;
x[8] = 1.0;
var func = new AssimilationFunction()
{
X = x,
MesophyllRespiration = leaf.GmRd,
HalfRubiscoSpecificityReciprocal = leaf.Gamma,
FractionOfDiffusivitySolubilityRatio = 0.1 / canopy.DiffusivitySolubilityRatio,
BundleSheathConductance = pathway.Gbs,
Oxygen = canopy.AirO2,
Respiration = leaf.RdT
};
return(func);
}
/// <summary> /// Retrieves a function describing assimilation along the Ac2 pathway /// </summary> protected abstract AssimilationFunction GetAc2Function(AssimilationPathway pathway, TemperatureResponse leaf);
/// <summary>
/// Updates the mesophyll CO2 parameter
/// </summary>
protected virtual void UpdateMesophyllCO2(AssimilationPathway pathway, TemperatureResponse leaf)
{ /*C4 & CCM overwrite this.*/
}
/// <inheritdoc/>
protected override AssimilationFunction GetAc2Function(AssimilationPathway pathway, TemperatureResponse leaf)
{
throw new Exception("The C3 model does not use the Ac2 pathway");
}
/// <inheritdoc/>
protected override AssimilationFunction GetAjFunction(AssimilationPathway pathway, TemperatureResponse leaf)
{
var x = new double[9];
x[0] = leaf.J / 4.0;
x[1] = 2.0 * leaf.Gamma;
x[2] = 0.0;
x[3] = 0.0;
x[4] = 0.0;
x[5] = 0.0;
x[6] = 0.0;
x[7] = 0.0;
x[8] = 0.0;
var func = new AssimilationFunction()
{
X = x,
MesophyllRespiration = leaf.GmRd,
HalfRubiscoSpecificityReciprocal = leaf.Gamma,
FractionOfDiffusivitySolubilityRatio = 0.0,
BundleSheathConductance = 1.0,
Oxygen = canopy.AirO2,
Respiration = leaf.RdT
};
return(func);
}
/// <inheritdoc/>
protected override AssimilationFunction GetAjFunction(AssimilationPathway pathway, TemperatureResponse leaf)
{
var a = 0.1 / (canopy.DiffusivitySolubilityRatio * pathway.Gbs);
var y = parameters.MesophyllElectronTransportFraction;
var z = parameters.ATPProductionElectronTransportFactor;
var cc = pathway.ChloroplasticCO2;
var oc = pathway.ChloroplasticO2;
var x = new Terms()
{
_1 = (1 - y) * z * leaf.J / 3.0,
_2 = canopy.AirO2 * (7.0 / 3.0) * leaf.Gamma,
_3 = 0.0,
_4 = (y * z * leaf.J / parameters.ExtraATPCost) - cc * (1 - y) * z * leaf.J / (3 * cc + 7 * leaf.Gamma * oc),
_5 = 0.0,
_6 = 1.0,
_7 = a * leaf.Gamma,
_8 = leaf.Gamma * canopy.AirO2,
_9 = (7.0 / 3.0) * leaf.Gamma * a
};
var func = new AssimilationFunction()
{
x = x,
MesophyllRespiration = leaf.GmRd,
BundleSheathConductance = pathway.Gbs,
Respiration = leaf.RdT
};
return(func);
}
/// <inheritdoc/>
protected override AssimilationFunction GetAc2Function(AssimilationPathway pathway, TemperatureResponse leaf)
{
var a = 0.1 / (canopy.DiffusivitySolubilityRatio * pathway.Gbs);
var cc = pathway.ChloroplasticCO2;
var oc = pathway.ChloroplasticO2;
var x = new Terms()
{
_1 = leaf.VcMaxT,
_2 = leaf.Kc + canopy.AirO2 * (leaf.Kc / leaf.Ko),
_3 = 0.0,
_4 = pathway.Vpr - cc * leaf.VcMaxT / (cc + leaf.Kc * (1 + oc / leaf.Ko)),
_5 = 0.0,
_6 = 1.0,
_7 = a * leaf.Gamma,
_8 = leaf.Gamma * canopy.AirO2,
_9 = (leaf.Kc / leaf.Ko) * a
};
var func = new AssimilationFunction()
{
x = x,
MesophyllRespiration = leaf.GmRd,
BundleSheathConductance = pathway.Gbs,
Respiration = leaf.RdT
};
return(func);
}
/// <inheritdoc/>
protected override AssimilationFunction GetAjFunction(AssimilationPathway pathway, TemperatureResponse leaf)
{
var x = new Terms()
{
_1 = leaf.J / 4.0,
_2 = 2.0 * leaf.Gamma * canopy.AirO2,
_3 = 0.0,
_4 = 0.0,
_5 = 0.0,
_6 = 0.0,
_7 = 0.0,
_8 = canopy.AirO2 * leaf.Gamma,
_9 = 0.0
};
var func = new AssimilationFunction()
{
x = x,
MesophyllRespiration = leaf.GmRd,
BundleSheathConductance = 1.0,
Respiration = leaf.RdT
};
return(func);
}
/// <inheritdoc/>
protected override AssimilationFunction GetAc1Function(AssimilationPathway pathway, TemperatureResponse leaf)
{
var x = new Terms()
{
_1 = leaf.VcMaxT,
_2 = leaf.Kc + canopy.AirO2 * leaf.Kc / leaf.Ko,
_3 = 0.0,
_4 = 0.0,
_5 = 0.0,
_6 = 0.0,
_7 = 0.0,
_8 = canopy.AirO2 * leaf.Gamma,
_9 = 0.0
};
var param = new AssimilationFunction()
{
x = x,
MesophyllRespiration = leaf.GmRd,
BundleSheathConductance = 1.0,
Respiration = leaf.RdT
};
return(param);
}
/// <inheritdoc/>
protected override AssimilationFunction GetAjFunction(AssimilationPathway pathway, TemperatureResponse leaf)
{
var alpha = 0.1 / (canopy.DiffusivitySolubilityRatio * pathway.Gbs);
var x = new Terms()
{
_1 = (1.0 - parameters.MesophyllElectronTransportFraction) * leaf.J / 3.0,
_2 = canopy.AirO2 * (7.0 / 3.0) * leaf.Gamma,
_3 = 0.0,
_4 = parameters.MesophyllElectronTransportFraction * leaf.J / parameters.ExtraATPCost,
_5 = 1.0,
_6 = 1.0,
_7 = alpha * leaf.Gamma,
_8 = leaf.Gamma * canopy.AirO2,
_9 = (7.0 / 3.0) * leaf.Gamma * alpha
};
var func = new AssimilationFunction()
{
x = x,
MesophyllRespiration = leaf.GmRd,
BundleSheathConductance = pathway.Gbs,
Respiration = leaf.RdT
};
return(func);
}
/// <inheritdoc/>
protected override AssimilationFunction GetAc1Function(AssimilationPathway pathway, TemperatureResponse leaf)
{
var alpha = 0.1 / (canopy.DiffusivitySolubilityRatio * pathway.Gbs);
var x = new Terms()
{
_1 = leaf.VcMaxT,
_2 = leaf.Kc + canopy.AirO2 * (leaf.Kc / leaf.Ko),
_3 = leaf.VpMaxT / (pathway.MesophyllCO2 + leaf.Kp),
_4 = 0.0,
_5 = 1.0,
_6 = 1.0,
_7 = alpha * leaf.Gamma,
_8 = leaf.Gamma * canopy.AirO2,
_9 = (leaf.Kc / leaf.Ko) * alpha
};
var func = new AssimilationFunction()
{
x = x,
MesophyllRespiration = leaf.GmRd,
BundleSheathConductance = pathway.Gbs,
Respiration = leaf.RdT
};
return(func);
}
/// <inheritdoc/>
public void UpdatePartialPressures(AssimilationPathway pathway, TemperatureResponse leaf, AssimilationFunction function)
{
UpdateMesophyllCO2(pathway, leaf);
UpdateChloroplasticO2(pathway);
UpdateChloroplasticCO2(pathway, function);
}
