/// <summary>Document the model.</summary>
public override IEnumerable <ITag> Document()
{
// Write description of this class.
yield return(new Paragraph($"This phase goes from {Start.ToLower()} to {End.ToLower()} and simulates time to {End.ToLower()} as a function of sowing depth. The *ThermalTime Target* for ending this phase is given by:"));
yield return(new Paragraph($"*Target* = *SowingDepth* x *ShootRate* + *ShootLag*"));
yield return(new Paragraph($"Where:"));
yield return(new Paragraph($"*ShootRate* = {ShootRate} (deg day/mm),"));
yield return(new Paragraph($"*ShootLag* = {ShootLag} (deg day), "));
yield return(new Paragraph($"*SowingDepth* (mm) is sent from the manager with the sowing event."));
// Write memos.
foreach (var tag in DocumentChildren <Memo>())
{
yield return(tag);
}
IFunction thermalTime = FindChild <IFunction>("ThermalTime");
yield return(new Paragraph($"Progress toward emergence is driven by thermal time accumulation{(thermalTime == null ? "" : ", where thermal time is calculated as:")}"));
if (thermalTime != null)
{
foreach (var tag in thermalTime.Document())
{
yield return(tag);
}
}
}
/// <summary>
/// Document the model.
/// </summary>
public override IEnumerable <ITag> Document()
{
if (ChildFunctions == null)
{
ChildFunctions = FindAllChildren <IFunction>();
}
foreach (IFunction child in ChildFunctions)
{
if (child != Lower && child != Upper)
{
yield return(new Paragraph($"{Name} is the value of {child.Name} bound between a lower and upper bound where:"));
foreach (ITag tag in child.Document())
{
yield return(tag);
}
break;
}
}
if (Lower != null)
{
foreach (ITag tag in Lower.Document())
{
yield return(tag);
}
}
if (Upper != null)
{
foreach (ITag tag in Upper.Document())
{
yield return(tag);
}
}
}
/// <summary>Writes documentation for this function by adding to the list of documentation tags.</summary>
public override IEnumerable <ITag> Document()
{
// Write description of this class.
yield return(new Paragraph($"This phase goes from {Start.ToLower()} to {End.ToLower()}."));
// Write memos
foreach (var tag in DocumentChildren <Memo>())
{
yield return(tag);
}
yield return(new Paragraph($"The *Target* for completion is calculated as:"));
// Write target
foreach (var tag in target.Document())
{
yield return(tag);
}
yield return(new Paragraph($"*Progression* through phase is calculated daily and accumulated until the *Target* is reached."));
// Write progression
foreach (var tag in progression.Document())
{
yield return(tag);
}
}
/// <summary>
/// Document the model.
/// </summary>
/// <returns></returns>
public override IEnumerable <ITag> Document()
{
yield return(new Paragraph($"Each time {SetStage} occurs, bud number on each main-stem is set to:"));
yield return(new Paragraph($"*{FractionOfBudBurst.Name}* * *SowingData.BudNumber* (from manager at establishment)"));
yield return(new Section(FractionOfBudBurst.Name, FractionOfBudBurst.Document()));
}
private IEnumerable <ITag> DocumentNSupply()
{
if (nReallocationFactor is Constant nReallocConst)
{
if (nReallocConst.Value() == 0)
{
yield return(new Paragraph($"{Name} does not reallocate N when senescence of the organ occurs."));
}
else
{
yield return(new Paragraph($"{Name} will reallocate {nReallocConst.Value() * 100}% of N that senesces each day."));
}
}
else
{
yield return(new Paragraph("The proportion of senescing N that is allocated each day is quantified by the NReallocationFactor."));
foreach (ITag tag in nReallocationFactor.Document())
{
yield return(tag);
}
}
IModel nRetransFactor = FindChild("NRetranslocationFactor");
if (nRetransFactor != null)
{
if (nRetransFactor is Constant nRetransConst)
{
if (nRetransConst.Value() == 0)
{
yield return(new Paragraph($"{Name} does not retranslocate non-structural N."));
}
else
{
yield return(new Paragraph($"{Name} will retranslocate {nRetransConst.Value() * 100}% of non-structural N each day."));
}
}
else
{
yield return(new Paragraph("The proportion of non-structural N that is allocated each day is quantified by the NReallocationFactor."));
foreach (ITag tag in nRetransFactor.Document())
{
yield return(tag);
}
}
}
}
/// <summary>
/// Document the model.
/// </summary>
public override IEnumerable <ITag> Document()
{
yield return(new Paragraph($"If {PropertyName} = {StringValue} Then"));
foreach (ITag tag in TrueValue.Document())
{
yield return(tag);
}
yield return(new Paragraph("Else"));
foreach (ITag tag in FalseValue.Document())
{
yield return(tag);
}
}
/// <summary>Document this model.</summary>
public override IEnumerable <ITag> Document()
{
yield return(new Paragraph("The structure model simulates morphological development of the plant to inform the Leaf class when and how many leaves and branches appear and provides an estimate of height."));
yield return(new Section("Plant and Main-Stem Population", new Paragraph(
$"The *Plant.Population* is set at sowing with information sent from a manager script in the Sow method. " +
$"The *PrimaryBudNumber* is also sent with the Sow method. The main-stem population (*MainStemPopn*) for {Parent.Name} is calculated as:\n\n" +
$"*MainStemPopn* = *Plant.Population* x *PrimaryBudNumber*\n\n" +
$"Primary bud number is > 1 for crops like potato and grape vine where there are more than one main-stem per plant"
)));
var tags = new List <ITag>();
tags.Add(new Paragraph("Each day the number of main-stem leaf tips appeared (*LeafTipsAppeared*) is calculated as:"));
tags.Add(new Paragraph("*LeafTipsAppeared* += *DeltaTips*"));
tags.Add(new Paragraph("Where *DeltaTips* is calculated as:"));
tags.Add(new Paragraph("*DeltaTips* = *ThermalTime* / *Phyllochron*"));
tags.Add(new Paragraph("Where *Phyllochron* is the thermal time duration between the appearance of leaf tips given by:"));
tags.AddRange(phyllochron.Document());
tags.Add(new Paragraph("*ThermalTime* is given by"));
tags.AddRange(thermalTime.Document());
tags.Add(new Paragraph("*LeafTipsAppeared* continues to increase until *FinalLeafNumber* is reached where *FinalLeafNumber* is calculated as:"));
tags.AddRange(finalLeafNumber.Document());
yield return(new Section("Main-Stem leaf appearance", tags));
var branchingTags = new List <ITag>();
branchingTags.Add(new Paragraph("The total population of stems (*TotalStemPopn*) is calculated as:"));
branchingTags.Add(new Paragraph("*TotalStemPopn* = *MainStemPopn* + *NewBranches* - *NewlyDeadBranches*"));
branchingTags.Add(new Paragraph("Where:"));
branchingTags.Add(new Paragraph("*NewBranches* = *MainStemPopn* x *BranchingRate*"));
branchingTags.Add(new Paragraph("*BranchingRate* is given by:"));
branchingTags.AddRange(branchingRate.Document());
branchingTags.Add(new Paragraph("*NewlyDeadBranches* is calcualted as:"));
branchingTags.Add(new Paragraph("*NewlyDeadBranches* = (*TotalStemPopn* - *MainStemPopn*) x *BranchMortality*"));
branchingTags.Add(new Paragraph("where *BranchMortality* is given by:"));
branchingTags.AddRange(branchMortality.Document());
yield return(new Section("Branching and Branch Mortality", branchingTags));
var heightTags = new List <ITag>();
heightTags.Add(new Paragraph("The height of the crop is calculated by the *HeightModel*"));
heightTags.AddRange(heightModel.Document());
yield return(new Section("Height", heightTags));
}
/// <summary>
/// Document the model.
/// </summary>
/// <returns></returns>
public override IEnumerable <ITag> Document()
{
foreach (ITag tag in DocumentChildren <Memo>())
{
yield return(tag);
}
List <ITag> initialisationTags = new List <ITag>();
initialisationTags.Add(new Paragraph("The initialisation of Carbon and Nutrient contents of this pool is described as follows:"));
initialisationTags.AddRange(InitialCarbon.Document());
initialisationTags.AddRange(InitialNitrogen.Document());
// todo: include initial P in docs once soil P is released.
// initialisationTags.AddRange(InitialPhosphorus.Document());
yield return(new Section("Initialisation", initialisationTags));
yield return(new Section("Organic Matter Flows", DocumentChildren <CarbonFlow>(true)));
}
private IEnumerable <ITag> DocumentDMSupply()
{
if (dmReallocationFactor is Constant dmReallocConst)
{
if (dmReallocConst.Value() == 0)
{
yield return(new Paragraph($"{Name} does not reallocate DM when senescence of the organ occurs."));
}
else
{
yield return(new Paragraph($"{Name} will reallocate {dmReallocConst.Value() * 100}% of DM that senesces each day."));
}
}
else
{
yield return(new Paragraph("The proportion of senescing DM that is allocated each day is quantified by the DMReallocationFactor."));
foreach (ITag tag in dmReallocationFactor.Document())
{
yield return(tag);
}
}
if (dmRetranslocationFactor is Constant dmRetransConst)
{
if (dmRetransConst.Value() == 0)
{
yield return(new Paragraph($"{Name} does not retranslocate non-structural DM."));
}
else
{
yield return(new Paragraph($"{Name} will retranslocate {dmRetransConst.Value() * 100}% of non-structural DM each day."));
}
}
else
{
yield return(new Paragraph("The proportion of non-structural DM that is allocated each day is quantified by the DMReallocationFactor."));
foreach (ITag tag in dmRetranslocationFactor.Document())
{
yield return(tag);
}
}
}
private IEnumerable <ITag> DocumentSenescenceRate()
{
if (senescenceRate is Constant senescenceConst)
{
if (senescenceConst.Value() == 0)
{
yield return(new Paragraph($"{Name} has senescence parameterised to zero so all biomass in this organ will remain alive."));
}
else
{
yield return(new Paragraph($"{Name} senesces {senescenceConst.Value() * 100}% of its live biomass each day, moving the corresponding amount of biomass from the live to the dead biomass pool."));
}
}
else
{
yield return(new Paragraph("The proportion of live biomass that senesces and moves into the dead pool each day is quantified by the SenescenceRate."));
foreach (ITag tag in senescenceRate.Document())
{
yield return(tag);
}
}
if (detachmentRateFunction is Constant detachmentConst)
{
if (detachmentConst.Value() == 0)
{
yield return(new Paragraph($"{Name} has detachment parameterised to zero so all biomass in this organ will remain with the plant until a defoliation or harvest event occurs."));
}
else
{
yield return(new Paragraph($"{Name} detaches {detachmentConst.Value() * 100}% of its live biomass each day, passing it to the surface organic matter model for decomposition."));
}
}
else
{
yield return(new Paragraph("The proportion of Biomass that detaches and is passed to the surface organic matter model for decomposition is quantified by the DetachmentRateFunction."));
foreach (ITag tag in detachmentRateFunction.Document())
{
yield return(tag);
}
}
}
/// <summary>
/// Document the model.
/// </summary>
public override IEnumerable <ITag> Document()
{
if (PreEventValue != null)
{
yield return(new Paragraph($"Before {SetEvent}"));
foreach (ITag tag in PreEventValue.Document())
{
yield return(tag);
}
}
if (PostEventValue != null)
{
yield return(new Paragraph($"On {SetEvent} the value is set to:"));
foreach (ITag tag in PostEventValue.Document())
{
yield return(tag);
}
}
}
/// <summary>
/// Document the model.
/// </summary>
public override IEnumerable <ITag> Document()
{
yield return(new Paragraph($"{Name} is calcualted using a sigmoid function of the form y = Ymax * 1 / 1 + e^-(Xvalue - Xo) / b^."));
// Document Ymax.
yield return(new Paragraph($"{nameof(Ymax)} is calculated as:"));
foreach (ITag tag in Ymax.Document())
{
yield return(tag);
}
// Document x0.
yield return(new Paragraph($"{nameof(Xo)} is calculated as:"));
foreach (ITag tag in Xo.Document())
{
yield return(tag);
}
// Document b.
yield return(new Paragraph($"{nameof(b)} is calculated as:"));
foreach (ITag tag in b.Document())
{
yield return(tag);
}
// Document x value.
yield return(new Paragraph($"{nameof(XValue)} is calculated as:"));
foreach (ITag tag in XValue.Document())
{
yield return(tag);
}
}
/// <summary>Writes documentation for this function by adding to the list of documentation tags.</summary>
public override IEnumerable <ITag> Document()
{
// Write description of this class from summary and remarks XML documentation.
foreach (var tag in GetModelDescription())
{
yield return(tag);
}
// Write memos.
foreach (var tag in DocumentChildren <Memo>())
{
yield return(tag);
}
// Document thermal time function.
yield return(new Section("ThermalTime", thermalTime.Document()));
// Write a table containing phase numers and start/end stages.
yield return(new Paragraph("**List of stages and phases used in the simulation of crop phenological development**"));
DataTable phaseTable = new DataTable();
phaseTable.Columns.Add("Phase Number", typeof(int));
phaseTable.Columns.Add("Phase Name", typeof(string));
phaseTable.Columns.Add("Initial Stage", typeof(string));
phaseTable.Columns.Add("Final Stage", typeof(string));
int n = 1;
foreach (IPhase child in FindAllChildren <IPhase>())
{
DataRow row = phaseTable.NewRow();
row[0] = n;
row[1] = child.Name;
row[2] = (child as IPhase).Start;
row[3] = (child as IPhase).End;
phaseTable.Rows.Add(row);
n++;
}
yield return(new Table(phaseTable));
// Document Phases
foreach (var phase in FindAllChildren <IPhase>())
{
yield return(new Section(phase.Name, phase.Document()));
}
// Document Constants
var constantTags = new List <ITag>();
foreach (var constant in FindAllChildren <Constant>())
{
foreach (var tag in constant.Document())
{
constantTags.Add(tag);
}
}
yield return(new Section("Constants", constantTags));
// Document everything else.
foreach (var phase in Children.Where(child => !(child is IPhase) &&
!(child is Memo) &&
!(child is Constant) &&
child != thermalTime))
{
yield return(new Section(phase.Name, phase.Document()));
}
}
/// <summary>Writes documentation for this function by adding to the list of documentation tags.</summary>
public override IEnumerable <ITag> Document()
{
foreach (var tag in GetModelDescription())
{
yield return(tag);
}
// Document memos.
foreach (var memo in FindAllChildren <Memo>())
{
foreach (var tag in memo.Document())
{
yield return(tag);
}
}
// List the parameters, properties, and processes from this organ that need to be documented:
yield return(new Section("Initial Dry Matter", initialWt.Document()));
// document DM demands
var dmDemandTags = new List <ITag>();
dmDemandTags.Add(new Paragraph("The dry matter demand for the organ is calculated as defined in DMDemands, based on the DMDemandFunction and partition fractions for each biomass pool."));
dmDemandTags.AddRange(dmDemands.Document());
yield return(new Section("Dry Matter Demand", dmDemandTags));
// document N demands
var nDemandTags = new List <ITag>();
nDemandTags.Add(new Paragraph("The N demand is calculated as defined in NDemands, based on DM demand the N concentration of each biomass pool."));
nDemandTags.AddRange(nDemands.Document());
yield return(new Section("Nitrogen Demand", nDemandTags));
// document N demands
var nConcTags = new List <ITag>();
nConcTags.AddRange(minimumNConc.Document());
nConcTags.AddRange(criticalNConc.Document());
nConcTags.AddRange(maximumNConc.Document());
yield return(new Section("Nitrogen Concentration Thresholds", nDemandTags));
// document DM supplies
var dmSupplyTags = new List <ITag>();
dmSupplyTags.AddRange(dmReallocationFactor.Document());
dmSupplyTags.AddRange(dmRetranslocationFactor.Document());
yield return(new Section("Dry Matter Supply", dmSupplyTags));
// document photosynthesis
yield return(new Section("Photosynthesis", photosynthesis.Document()));
// document N supplies
var nSupplyTags = new List <ITag>();
nSupplyTags.AddRange(nReallocationFactor.Document());
nSupplyTags.AddRange(nRetranslocationFactor.Document());
yield return(new Section("Nitrogen Supply", nSupplyTags));
// document canopy
var canopyTags = new List <ITag>();
if (area != null)
{
canopyTags.Add(new Paragraph(Name + " has been defined with a LAIFunction, cover is calculated using the Beer-Lambert equation."));
canopyTags.AddRange(area.Document());
}
if (cover != null)
{
canopyTags.Add(new Paragraph(Name + " has been defined with a CoverFunction. LAI is calculated using an inverted Beer-Lambert equation"));
canopyTags.AddRange(cover.Document());
}
canopyTags.AddRange(extinctionCoefficient.Document());
canopyTags.AddRange(tallness.Document());
yield return(new Section("Canopy Properties", canopyTags));
var stomatalConductanceTags = new List <ITag>();
stomatalConductanceTags.Add(new Paragraph("Stomatal Conductance (gs) is calculated for use within the micromet model by adjusting a value provided for an atmospheric CO2 concentration of 350 ppm. The impact of other stresses (e.g. Temperature, N) are captured through the modifier, Frgr."));
stomatalConductanceTags.Add(new Paragraph(" gs = Gsmax350 x FRGR x stomatalConductanceCO2Modifier"));
stomatalConductanceTags.AddRange(stomatalConductanceCO2Modifier.Document());
yield return(new Section("StomatalConductance", stomatalConductanceTags));
// document senescence and detachment
var senescenceTags = new List <ITag>();
if (senescenceRate is Constant senescenceRateConstant)
{
if (senescenceRateConstant.Value() == 0)
{
senescenceTags.Add(new Paragraph(Name + " has senescence parameterised to zero so all biomass in this organ will remain alive."));
}
else
{
senescenceTags.Add(new Paragraph(Name + " senesces " + senescenceRateConstant.Value() * 100 + "% of its live biomass each day, moving the corresponding amount of biomass from the live to the dead biomass pool."));
}
}
else
{
senescenceTags.Add(new Paragraph("The proportion of live biomass that senesces and moves into the dead pool each day is quantified by the SenescenceRate."));
senescenceTags.AddRange(senescenceRate.Document());
}
if (detachmentRate is Constant detachmentRateConstant)
{
if (detachmentRateConstant.Value() == 0)
{
senescenceTags.Add(new Paragraph(Name + " has detachment parameterised to zero so all biomass in this organ will remain with the plant until a defoliation or harvest event occurs."));
}
else
{
senescenceTags.Add(new Paragraph(Name + " detaches " + detachmentRateConstant.Value() * 100 + "% of its dead biomass each day, passing it to the surface organic matter model for decomposition."));
}
}
else
{
senescenceTags.Add(new Paragraph("The proportion of Biomass that detaches and is passed to the surface organic matter model for decomposition is quantified by the DetachmentRateFunction."));
senescenceTags.AddRange(detachmentRate.Document());
}
yield return(new Section("Senescence and Detachment", senescenceTags));
if (biomassRemovalModel != null)
{
yield return(new Section("Biomass removal", biomassRemovalModel.Document()));
}
}
/// <summary>
/// Document the model.
/// </summary>
public override IEnumerable <ITag> Document()
{
foreach (ITag tag in GetModelDescription())
{
yield return(tag);
}
// Document DM demands.
yield return(new Section("Dry Matter Demand", DocumentDMDemands()));
// Document N demands.
yield return(new Section("Nitrogen Demand", DocumentNDemand()));
// Document N concentration thresholds.
// todo: Should these be in their own section?
foreach (ITag tag in minimumNConc.Document())
{
yield return(tag);
}
foreach (ITag tag in criticalNConc.Document())
{
yield return(tag);
}
foreach (ITag tag in maximumNConc.Document())
{
yield return(tag);
}
IModel nDemandSwitch = FindChild("NitrogenDemandSwitch");
if (nDemandSwitch != null)
{
if (nDemandSwitch is Constant nDemandConst)
{
if (nDemandConst.Value() == 1)
{
//Don't bother documenting as is does nothing
}
else
{
yield return(new Paragraph($"The demand for N is reduced by a factor of {nDemandConst.Value()} as specified by the NitrogenDemandSwitch"));
}
}
else
{
yield return(new Paragraph("The demand for N is reduced by a factor specified by the NitrogenDemandSwitch."));
foreach (ITag tag in nDemandSwitch.Document())
{
yield return(tag);
}
}
}
// document DM supplies
yield return(new Section("Dry Matter Supply", DocumentDMSupply()));
// Document N supplies.
yield return(new Section("Nitrogen Supply", DocumentNSupply()));
// Document N fixation.
IModel fixationRate = FindChild("FixationRate");
if (fixationRate != null)
{
foreach (ITag tag in fixationRate.Document())
{
yield return(tag);
}
}
// Document senescence and detachment.
yield return(new Section("Senescence and Detachment", DocumentSenescenceRate()));
if (biomassRemovalModel != null)
{
foreach (ITag tag in biomassRemovalModel.Document())
{
yield return(tag);
}
}
}
