/// <summary>
/// Document the model.
/// </summary>
public override IEnumerable <ITag> Document()
{
// Add heading and description.
foreach (ITag tag in base.Document())
{
yield return(tag);
}
// List the parameters, properties, and processes from this organ that need to be documented:
// Document DM demands.
yield return(new Section("Dry Matter Demand", DocumentDMDemand(dmDemands)));
// Document N demands.
yield return(new Section("Nitrogen Demand", DocumentNDemand(FindChild("nDemands"))));
// Document N concentration thresholds.
yield return(new Section("N Concentration Thresholds", DocumentNConcentrationThresholds()));
// todo: should this be in its own section?
IModel nDemandSwitch = FindChild("NitrogenDemandSwitch");
if (nDemandSwitch is Constant nDemandConst)
{
if (nDemandConst.Value() == 1)
{
// Don't bother documenting as it 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 senescence and detachment.
yield return(new Section("Senescence and Detachment", DocumentSenescence()));
if (biomassRemovalModel != null)
{
foreach (ITag tag in biomassRemovalModel.Document())
{
yield return(tag);
}
}
}
/// <summary>Writes documentation for this function by adding to the list of documentation tags.</summary>
/// <param name="tags">The list of tags to add to.</param>
/// <param name="headingLevel">The level (e.g. H2) of the headings.</param>
/// <param name="indent">The level of indentation 1, 2, 3 etc.</param>
public void Document(List <AutoDocumentation.ITag> tags, int headingLevel, int indent)
{
if (IncludeInDocumentation)
{
// add a heading, the name of this organ
tags.Add(new AutoDocumentation.Heading(Name, headingLevel));
// write the basic description of this class, given in the <summary>
AutoDocumentation.DocumentModelSummary(this, tags, headingLevel, indent, false);
// write the memos
foreach (IModel memo in Apsim.Children(this, typeof(Memo)))
{
AutoDocumentation.DocumentModel(memo, tags, headingLevel + 1, indent);
}
//// List the parameters, properties, and processes from this organ that need to be documented:
// document DM demands
tags.Add(new AutoDocumentation.Heading("Dry Matter Demand", headingLevel + 1));
tags.Add(new AutoDocumentation.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.", indent));
IModel DMDemand = Apsim.Child(this, "dmDemands");
AutoDocumentation.DocumentModel(DMDemand, tags, headingLevel + 2, indent);
// document N demands
tags.Add(new AutoDocumentation.Heading("Nitrogen Demand", headingLevel + 1));
tags.Add(new AutoDocumentation.Paragraph("The N demand is calculated as defined in NDemands, based on DM demand the N concentration of each biomass pool.", indent));
IModel NDemand = Apsim.Child(this, "nDemands");
AutoDocumentation.DocumentModel(NDemand, tags, headingLevel + 2, indent);
// document N concentration thresholds
IModel MinN = Apsim.Child(this, "MinimumNConc");
AutoDocumentation.DocumentModel(MinN, tags, headingLevel + 2, indent);
IModel CritN = Apsim.Child(this, "CriticalNConc");
AutoDocumentation.DocumentModel(CritN, tags, headingLevel + 2, indent);
IModel MaxN = Apsim.Child(this, "MaximumNConc");
AutoDocumentation.DocumentModel(MaxN, tags, headingLevel + 2, indent);
IModel NDemSwitch = Apsim.Child(this, "NitrogenDemandSwitch");
if (NDemSwitch is Constant)
{
if ((NDemSwitch as Constant).Value() == 1.0)
{
//Don't bother documenting as is does nothing
}
else
{
tags.Add(new AutoDocumentation.Paragraph("The demand for N is reduced by a factor of " + (NDemSwitch as Constant).Value() + " as specified by the NitrogenDemandSwitch", indent));
}
}
else
{
tags.Add(new AutoDocumentation.Paragraph("The demand for N is reduced by a factor specified by the NitrogenDemandSwitch.", indent));
AutoDocumentation.DocumentModel(NDemSwitch, tags, headingLevel + 2, indent);
}
// document DM supplies
tags.Add(new AutoDocumentation.Heading("Dry Matter Supply", headingLevel + 1));
IModel DMReallocFac = Apsim.Child(this, "DMReallocationFactor");
if (DMReallocFac is Constant)
{
if ((DMReallocFac as Constant).Value() == 0)
{
tags.Add(new AutoDocumentation.Paragraph(Name + " does not reallocate DM when senescence of the organ occurs.", indent));
}
else
{
tags.Add(new AutoDocumentation.Paragraph(Name + " will reallocate " + (DMReallocFac as Constant).Value() * 100 + "% of DM that senesces each day.", indent));
}
}
else
{
tags.Add(new AutoDocumentation.Paragraph("The proportion of senescing DM that is allocated each day is quantified by the DMReallocationFactor.", indent));
AutoDocumentation.DocumentModel(DMReallocFac, tags, headingLevel + 2, indent);
}
IModel DMRetransFac = Apsim.Child(this, "DMRetranslocationFactor");
if (DMRetransFac is Constant)
{
if ((DMRetransFac as Constant).Value() == 0)
{
tags.Add(new AutoDocumentation.Paragraph(Name + " does not retranslocate non-structural DM.", indent));
}
else
{
tags.Add(new AutoDocumentation.Paragraph(Name + " will retranslocate " + (DMRetransFac as Constant).Value() * 100 + "% of non-structural DM each day.", indent));
}
}
else
{
tags.Add(new AutoDocumentation.Paragraph("The proportion of non-structural DM that is allocated each day is quantified by the DMReallocationFactor.", indent));
AutoDocumentation.DocumentModel(DMRetransFac, tags, headingLevel + 2, indent);
}
// document N supplies
tags.Add(new AutoDocumentation.Heading("Nitrogen Supply", headingLevel + 1));
IModel NReallocFac = Apsim.Child(this, "NReallocationFactor");
if (NReallocFac is Constant)
{
if ((NReallocFac as Constant).Value() == 0)
{
tags.Add(new AutoDocumentation.Paragraph(Name + " does not reallocate N when senescence of the organ occurs.", indent));
}
else
{
tags.Add(new AutoDocumentation.Paragraph(Name + " will reallocate " + (NReallocFac as Constant).Value() * 100 + "% of N that senesces each day.", indent));
}
}
else
{
tags.Add(new AutoDocumentation.Paragraph("The proportion of senescing N that is allocated each day is quantified by the NReallocationFactor.", indent));
AutoDocumentation.DocumentModel(NReallocFac, tags, headingLevel + 2, indent);
}
IModel NRetransFac = Apsim.Child(this, "NRetranslocationFactor");
if (NRetransFac is Constant)
{
if ((NRetransFac as Constant).Value() == 0)
{
tags.Add(new AutoDocumentation.Paragraph(Name + " does not retranslocate non-structural N.", indent));
}
else
{
tags.Add(new AutoDocumentation.Paragraph(Name + " will retranslocate " + (NRetransFac as Constant).Value() * 100 + "% of non-structural N each day.", indent));
}
}
else
{
tags.Add(new AutoDocumentation.Paragraph("The proportion of non-structural N that is allocated each day is quantified by the NReallocationFactor.", indent));
AutoDocumentation.DocumentModel(NRetransFac, tags, headingLevel + 2, indent);
}
// document senescence and detachment
tags.Add(new AutoDocumentation.Heading("Senescence and Detachment", headingLevel + 1));
IModel SenRate = Apsim.Child(this, "SenescenceRate");
if (SenRate is Constant)
{
if ((SenRate as Constant).Value() == 0)
{
tags.Add(new AutoDocumentation.Paragraph(Name + " has senescence parameterised to zero so all biomass in this organ will remain alive.", indent));
}
else
{
tags.Add(new AutoDocumentation.Paragraph(Name + " senesces " + (SenRate as Constant).Value() * 100 + "% of its live biomass each day, moving the corresponding amount of biomass from the live to the dead biomass pool.", indent));
}
}
else
{
tags.Add(new AutoDocumentation.Paragraph("The proportion of live biomass that senesces and moves into the dead pool each day is quantified by the SenescenceRate.", indent));
AutoDocumentation.DocumentModel(SenRate, tags, headingLevel + 2, indent);
}
IModel DetRate = Apsim.Child(this, "DetachmentRateFunction");
if (DetRate is Constant)
{
if ((DetRate as Constant).Value() == 0)
{
tags.Add(new AutoDocumentation.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.", indent));
}
else
{
tags.Add(new AutoDocumentation.Paragraph(Name + " detaches " + (DetRate as Constant).Value() * 100 + "% of its live biomass each day, passing it to the surface organic matter model for decomposition.", indent));
}
}
else
{
tags.Add(new AutoDocumentation.Paragraph("The proportion of Biomass that detaches and is passed to the surface organic matter model for decomposition is quantified by the DetachmentRateFunction.", indent));
AutoDocumentation.DocumentModel(DetRate, tags, headingLevel + 2, indent);
}
if (biomassRemovalModel != null)
{
biomassRemovalModel.Document(tags, headingLevel + 1, indent);
}
}
}
/// <summary>Writes documentation for this function by adding to the list of documentation tags.</summary>
/// <param name="tags">The list of tags to add to.</param>
/// <param name="headingLevel">The level (e.g. H2) of the headings.</param>
/// <param name="indent">The level of indentation 1, 2, 3 etc.</param>
public override void Document(List <AutoDocumentation.ITag> tags, int headingLevel, int indent)
{
if (IncludeInDocumentation && StructuralFraction != null)
{
// add a heading.
tags.Add(new AutoDocumentation.Heading(Name, headingLevel));
// write description of this class.
AutoDocumentation.DocumentModel(this, tags, headingLevel, indent);
// Documment DM demands.
tags.Add(new AutoDocumentation.Heading("Dry Matter Demand", headingLevel + 1));
tags.Add(new AutoDocumentation.Paragraph("Total Dry matter demand is calculated by the DMDemandFunction", indent));
IModel DMDemand = Apsim.Child(this, "DMDemandFunction");
DMDemand.Document(tags, -1, indent);
IModel StrucFrac = Apsim.Child(this, "StructuralFraction");
if (StrucFrac.GetType() == typeof(Constant))
{
if (StructuralFraction.Value() == 1.0)
{
tags.Add(new AutoDocumentation.Paragraph("All demand is structural and this organ has no Non-structural demand", indent));
}
else
{
double StrucPercent = StructuralFraction.Value() * 100;
tags.Add(new AutoDocumentation.Paragraph("Of total biomass, " + StrucPercent + "% of this is structural and the remainder is non-structural demand", indent));
tags.Add(new AutoDocumentation.Paragraph("Any Non-structural Demand Capacity (StructuralWt/StructuralFraction) that is not currently occupied is also included in Non-structural DM Demand", indent));
}
}
else
{
tags.Add(new AutoDocumentation.Paragraph("The proportion of total biomass that is partitioned to structural is determined by the StructuralFraction", indent));
StrucFrac.Document(tags, -1, indent);
tags.Add(new AutoDocumentation.Paragraph("Any Non-structural Demand Capacity (StructuralWt/StructuralFraction) that is not currently occupied is also included in Non-structural DM Demand", indent));
}
// Document Nitrogen Demand
tags.Add(new AutoDocumentation.Heading("Nitrogen Demand", headingLevel + 1));
tags.Add(new AutoDocumentation.Paragraph("The daily structural N demand is the product of Total DM demand and a Minimum N concentration", indent));
IModel MinN = Apsim.Child(this, "MinimumNConc");
MinN.Document(tags, -1, indent);
tags.Add(new AutoDocumentation.Paragraph("The daily Storage N demand is the product of Total DM demand and a Maximum N concentration", indent));
IModel MaxN = Apsim.Child(this, "MaximumNConc");
MaxN.Document(tags, -1, indent);
IModel NDemSwitch = Apsim.Child(this, "NitrogenDemandSwitch");
if (NDemSwitch.GetType() == typeof(Constant))
{
if (NitrogenDemandSwitch.Value() == 1.0)
{
//Dont bother docummenting as is does nothing
}
else
{
tags.Add(new AutoDocumentation.Paragraph("The demand for N is reduced by a factor of " + NitrogenDemandSwitch.Value() + " as specified by the NitrogenDemandFactor", indent));
}
}
else
{
tags.Add(new AutoDocumentation.Paragraph("The demand for N is reduced by a factor specified by the NitrogenDemandFactor", indent));
NDemSwitch.Document(tags, -1, indent);
}
//Document DM supplies
tags.Add(new AutoDocumentation.Heading("Dry Matter Supply", headingLevel + 1));
IModel DMReallocFac = Apsim.Child(this, "DMReallocationFactor");
if (DMReallocFac.GetType() == typeof(Constant))
{
if (DMReallocationFactor.Value() == 0)
{
tags.Add(new AutoDocumentation.Paragraph(Name + " does not reallocate DM when senescence of the organ occurs", indent));
}
else
{
tags.Add(new AutoDocumentation.Paragraph(Name + " will reallocate " + DMReallocationFactor.Value() * 100 + "% of DM that senesces each day", indent));
}
}
else
{
tags.Add(new AutoDocumentation.Paragraph("The proportion of senescing DM tha is allocated each day is quantified by the DMReallocationFactor", indent));
DMReallocFac.Document(tags, -1, indent);
}
IModel DMRetransFac = Apsim.Child(this, "DMRetranslocationFactor");
if (DMRetransFac.GetType() == typeof(Constant))
{
if (DMRetranslocationFactor.Value() == 0)
{
tags.Add(new AutoDocumentation.Paragraph(Name + " does not retranslocate non-structural DM", indent));
}
else
{
tags.Add(new AutoDocumentation.Paragraph(Name + " will retranslocate " + DMRetranslocationFactor.Value() * 100 + "% of non-structural DM each day", indent));
}
}
else
{
tags.Add(new AutoDocumentation.Paragraph("The proportion of non-structural DM tha is allocated each day is quantified by the DMReallocationFactor", indent));
DMRetransFac.Document(tags, -1, indent);
}
//Document N supplies
tags.Add(new AutoDocumentation.Heading("Nitrogen Supply", headingLevel + 1));
IModel NReallocFac = Apsim.Child(this, "NReallocationFactor");
if (NReallocFac.GetType() == typeof(Constant))
{
if (NReallocationFactor.Value() == 0)
{
tags.Add(new AutoDocumentation.Paragraph(Name + " does not reallocate N when senescence of the organ occurs", indent));
}
else
{
tags.Add(new AutoDocumentation.Paragraph(Name + " will reallocate " + NReallocationFactor.Value() * 100 + "% of N that senesces each day", indent));
}
}
else
{
tags.Add(new AutoDocumentation.Paragraph("The proportion of senescing N tha is allocated each day is quantified by the NReallocationFactor", indent));
NReallocFac.Document(tags, -1, indent);
}
IModel NRetransFac = Apsim.Child(this, "NRetranslocationFactor");
if (NRetransFac.GetType() == typeof(Constant))
{
if (NRetranslocationFactor.Value() == 0)
{
tags.Add(new AutoDocumentation.Paragraph(Name + " does not retranslocate non-structural N", indent));
}
else
{
tags.Add(new AutoDocumentation.Paragraph(Name + " will retranslocate " + NRetranslocationFactor.Value() * 100 + "% of non-structural N each day", indent));
}
}
else
{
tags.Add(new AutoDocumentation.Paragraph("The proportion of non-structural N that is allocated each day is quantified by the NReallocationFactor", indent));
NRetransFac.Document(tags, -1, indent);
}
//Document Biomass Senescence and Detachment
tags.Add(new AutoDocumentation.Heading("Senescence and Detachment", headingLevel + 1));
IModel Sen = Apsim.Child(this, "SenescenceRate");
if (Sen.GetType() == typeof(Constant))
{
if (SenescenceRate.Value() == 0)
{
tags.Add(new AutoDocumentation.Paragraph(Name + " has senescence parameterised to zero so all biomss in this organ will remain live", indent));
}
else
{
tags.Add(new AutoDocumentation.Paragraph(Name + " senesces " + SenescenceRate.Value() * 100 + "% of its live biomass each day, moving the corresponding amount of biomass from the live to the dead biomass pool", indent));
}
}
else
{
tags.Add(new AutoDocumentation.Paragraph("The proportion of live biomass that senesces and moves into the dead pool each day is quantified by the SenescenceFraction", indent));
Sen.Document(tags, -1, indent);
}
IModel Det = Apsim.Child(this, "DetachmentRateFunction");
if (Sen.GetType() == typeof(Constant))
{
if (DetachmentRateFunction.Value() == 0)
{
tags.Add(new AutoDocumentation.Paragraph(Name + " has detachment parameterised to zero so all biomss in this organ will remain with the plant until a defoliation or harvest event occurs", indent));
}
else
{
tags.Add(new AutoDocumentation.Paragraph(Name + " detaches " + DetachmentRateFunction.Value() * 100 + "% of its live biomass each day, passing it to the surface organic matter model for decomposition", indent));
}
}
else
{
tags.Add(new AutoDocumentation.Paragraph("The proportion of Biomass that detaches and is passed to the surface organic matter model for decomposition is quantified by the DetachmentRateFunction", indent));
Det.Document(tags, -1, indent);
}
if (biomassRemovalModel != null)
{
biomassRemovalModel.Document(tags, headingLevel + 1, indent);
}
}
}
/// <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);
}
}
}