/// <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 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 void UpdateMesophyllCO2(AssimilationPathway pathway, TemperatureResponse leaf)
{
pathway.MesophyllCO2 = pathway.IntercellularCO2 - pathway.CO2Rate / leaf.GmT;
}
/// <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);
}
/// <summary> /// Retrieves a function describing assimilation along the Ac1 pathway /// </summary> protected abstract AssimilationFunction GetAc1Function(AssimilationPathway pathway, TemperatureResponse leaf);
/// <summary>
/// Updates the mesophyll CO2 parameter
/// </summary>
protected virtual void UpdateMesophyllCO2(AssimilationPathway pathway, TemperatureResponse leaf)
{ /*C4 & CCM overwrite this.*/
}
/// <summary>
///
/// </summary>
/// <param name="CP"></param>
/// <param name="PP"></param>
/// <param name="DOY"></param>
/// <param name="latitude"></param>
/// <param name="maxT"></param>
/// <param name="minT"></param>
/// <param name="radn"></param>
/// <param name="rpar"></param>
/// <returns></returns>
public static DCAPSTModel SetUpModel(
ICanopyParameters CP,
IPathwayParameters PP,
int DOY,
double latitude,
double maxT,
double minT,
double radn,
double rpar)
{
// Model the solar geometry
var SG = new SolarGeometry
{
Latitude = latitude.ToRadians(),
DayOfYear = DOY
};
// Model the solar radiation
var SR = new SolarRadiation(SG)
{
Daily = radn,
RPAR = rpar
};
// Model the environmental temperature
var TM = new Temperature(SG)
{
MaxTemperature = maxT,
MinTemperature = minT,
AtmosphericPressure = 1.01325
};
// Model the pathways
var SunlitAc1 = new AssimilationPathway(CP, PP);
var SunlitAc2 = new AssimilationPathway(CP, PP);
var SunlitAj = new AssimilationPathway(CP, PP);
var ShadedAc1 = new AssimilationPathway(CP, PP);
var ShadedAc2 = new AssimilationPathway(CP, PP);
var ShadedAj = new AssimilationPathway(CP, PP);
// Model the canopy
IAssimilation A;
if (CP.Type == CanopyType.C3)
{
A = new AssimilationC3(CP, PP);
}
else if (CP.Type == CanopyType.C4)
{
A = new AssimilationC4(CP, PP);
}
else
{
A = new AssimilationCCM(CP, PP);
}
var sunlit = new AssimilationArea(SunlitAc1, SunlitAc2, SunlitAj, A);
var shaded = new AssimilationArea(ShadedAc1, ShadedAc2, ShadedAj, A);
var CA = new CanopyAttributes(CP, PP, sunlit, shaded);
// Model the transpiration
var WI = new WaterInteraction(TM);
var TR = new TemperatureResponse(CP, PP);
var TS = new Transpiration(CP, PP, WI, TR);
// Model the photosynthesis
var DM = new DCAPSTModel(SG, SR, TM, PP, CA, TS)
{
B = 0.409
};
return(DM);
}
/// <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 GetAc2Function(AssimilationPathway pathway, TemperatureResponse leaf)
{
throw new Exception("The C3 model does not use the Ac2 pathway");
}
/// <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);
}
