private void OnDoPhenology(object sender, EventArgs e)
{
if (PlantIsAlive)
{
if (thermalTime.Value() < 0)
{
throw new Exception("Negative Thermal Time, check the set up of the ThermalTime Function in" + this);
}
// Calculate progression through current phase
double propOfDayToUse = 1;
bool incrementPhase = CurrentPhase.DoTimeStep(ref propOfDayToUse);
//sorghum resets the stage variable to 0 on the day the phase changes
//it will resume again normally the day after
double resetSorghumStage = SorghumFlag != null && incrementPhase ? 0.0 : 1.0;
while (incrementPhase)
{
if ((CurrentPhase is EmergingPhase) || (CurrentPhase.End == structure?.LeafInitialisationStage))
{
Emerged = true;
}
stagesPassedToday.Add(CurrentPhase.End);
if (currentPhaseIndex + 1 >= phases.Count)
{
throw new Exception("Cannot transition to the next phase. No more phases exist");
}
currentPhaseIndex = currentPhaseIndex + 1;
PhaseChangedType PhaseChangedData = new PhaseChangedType();
PhaseChangedData.StageName = CurrentPhase.Start;
PhaseChanged?.Invoke(plant, PhaseChangedData);
if (SorghumFlag != null && CurrentPhase is EmergingPhase)
{
propOfDayToUse = 0.0;
}
incrementPhase = CurrentPhase.DoTimeStep(ref propOfDayToUse);
}
AccumulatedTT += thermalTime.Value();
if (Emerged)
{
AccumulatedEmergedTT += thermalTime.Value();
}
Stage = (currentPhaseIndex + 1) + resetSorghumStage * CurrentPhase.FractionComplete;
if (plant != null)
{
if (plant.IsAlive && PostPhenology != null)
{
PostPhenology.Invoke(this, new EventArgs());
}
}
}
}
private void OnPhaseChanged(object sender, PhaseChangedType phaseChange)
{
if (phaseChange.StageName == SetEvent)
{
CropVernalised = true;
}
}
private void OnPhaseChanged(PhaseChangedType PhaseChange)
{
string message = Phenology.CurrentPhase.Start + "\r\n";
if (Leaf != null)
{
message += " LAI = " + Leaf.LAI.ToString("f2") + " (m^2/m^2)" + "\r\n";
message += " Above Ground Biomass = " + AboveGround.Wt.ToString("f2") + " (g/m^2)" + "\r\n";
}
Summary.WriteMessage(this, message);
}
private void OnPhaseChanged(object sender, PhaseChangedType phaseChange)
{
if (phaseChange.StageName == EndStage)
{
TodaysVernalisation = 0.0;
}
if (phaseChange.StageName == ResetStage)
{
DaysVernalised = 0.0;
DaysVernalising = 0.0;
}
}
private void OnPhaseChanged(object sender, PhaseChangedType phaseChange)
{
if (phaseChange.EventStageName == EndStage)
{
vernalisedToday = 0.0;
}
if (phaseChange.EventStageName == ResetStage)
{
permanentVernalisedDays = 0.0;
temporaryVernalisingDays = 0.0;
}
}
private void OnHarvesting(object sender, EventArgs e)
{
if (sender == Plant)
{
//Jump phenology to the end
string OldPhaseName = CurrentPhase.Name;
int EndPhase = Phases.Count;
PhaseChangedType PhaseChangedData = new PhaseChangedType();
PhaseChangedData.OldPhaseName = OldPhaseName;
PhaseChangedData.NewPhaseName = Phases[EndPhase - 1].Name;
PhaseChanged.Invoke(PhaseChangedData);
CurrentPhaseName = Phases[EndPhase - 1].Name;
}
}
private void OnDoPhenology(object sender, EventArgs e)
{
if (PlantIsAlive)
{
if (thermalTime.Value() < 0)
{
throw new Exception("Negative Thermal Time, check the set up of the ThermalTime Function in" + this);
}
// Calculate progression through current phase
double propOfDayToUse = 1;
bool incrementPhase = CurrentPhase.DoTimeStep(ref propOfDayToUse);
AccumulateTT(CurrentPhase.TTForTimeStep);
while (incrementPhase)
{
if ((CurrentPhase is EmergingPhase) || (CurrentPhase is BuddingPhase))
{
Emerged = true;
}
stagesPassedToday.Add(CurrentPhase.End);
if (currentPhaseIndex + 1 >= phases.Count)
{
throw new Exception("Cannot transition to the next phase. No more phases exist");
}
currentPhaseIndex = currentPhaseIndex + 1;
PhaseChangedType PhaseChangedData = new PhaseChangedType();
PhaseChangedData.StageName = CurrentPhase.Start;
PhaseChanged?.Invoke(plant, PhaseChangedData);
incrementPhase = CurrentPhase.DoTimeStep(ref propOfDayToUse);
AccumulateTT(CurrentPhase.TTForTimeStep);
}
Stage = (currentPhaseIndex + 1) + CurrentPhase.FractionComplete;
if (plant != null)
{
if (plant.IsAlive && PostPhenology != null)
{
PostPhenology.Invoke(this, new EventArgs());
}
}
}
}
private void OnPhaseChanged(object sender, PhaseChangedType phaseChange)
{
if (phaseChange.EventStageName == ResetStageName)
AccumulatedValue = 0.0;
}
private void OnPhaseChanged(object sender, PhaseChangedType phaseChange)
{
if (SWStress != null && NStress != null)
{
PhenologyEventToday = true;
AverageStressMessage += String.Format("{0,36}{1,13:F3}{2,13:F3}{3,13:F3}{4,13:F3}\r\n",
phaseChange.OldPhaseName,
1 - SWStress.PhotoAverage, 1 - SWStress.ExpansionAverage,
1 - NStress.PhotoAverage, 1 - NStress.GrainAverage);
SWStress.ResetAverage();
NStress.ResetAverage();
}
if (phaseChange.NewPhaseName.Contains("FloweringTo"))
FloweringDate = Clock.Today;
else if (phaseChange.NewPhaseName.Contains("MaturityTo"))
MaturityDate = Clock.Today;
}
/// <summary>Respond to a remove biomass event.</summary>
/// <param name="removeBiomPheno">The remove biom pheno.</param>
internal void OnRemoveBiomass(double removeBiomPheno)
{
string existingStage = CurrentStageName;
if (RewindDueToBiomassRemoved != null)
{
FractionBiomassRemoved = removeBiomPheno; // The RewindDueToBiomassRemoved function will use this.
double ttCritical = TTInAboveGroundPhase;
double removeFractPheno = RewindDueToBiomassRemoved.Value;
double removeTTPheno = ttCritical * removeFractPheno;
string msg;
msg = "Phenology change:-\r\n";
msg += " Fraction DM removed = " + removeBiomPheno.ToString() + "\r\n";
msg += " Fraction TT removed = " + removeFractPheno.ToString() + "\r\n";
msg += " Critical TT = " + ttCritical.ToString() + "\r\n";
msg += " Remove TT = " + removeTTPheno.ToString() + "\r\n";
double ttRemaining = removeTTPheno;
for (int i = Phases.Count - 1; i >= 0; i--)
{
Phase Phase = Phases[i];
if (Phase.TTinPhase > 0)
{
double ttCurrentPhase = Phase.TTinPhase;
if (ttRemaining > ttCurrentPhase)
{
Phase.ResetPhase();
ttRemaining -= ttCurrentPhase;
CurrentPhaseIndex -= 1;
if (CurrentPhaseIndex < 4) //FIXME - hack to stop onEmergence being fired which initialises biomass parts
{
CurrentPhaseIndex = 4;
break;
}
}
else
{
Phase.Add(-ttRemaining);
// Return fraction of thermal time we are through the current
// phenological phase (0-1)
//double frac = Phase.FractionComplete;
//if (frac > 0.0 && frac < 1.0) // Don't skip out of this stage - some have very low targets, eg 1.0 in "maturity"
// currentStage = frac + floor(currentStage);
break;
}
}
else
{ // phase is empty - not interested in it
}
}
Stage = (CurrentPhaseIndex + 1) + CurrentPhase.FractionComplete - PhaseIndexOffset;
if (existingStage != CurrentStageName)
{
PhaseChangedType PhaseChangedData = new PhaseChangedType();
PhaseChangedData.OldPhaseName = existingStage;
PhaseChangedData.NewPhaseName = CurrentPhase.Name;
PhaseChanged.Invoke(PhaseChangedData);
//Fixme MyPaddock.Publish(CurrentPhase.Start);
}
}
}
/// <summary>A function that resets phenology to a specified stage</summary>
public void SetToStage(double newStage)
{
int oldPhaseIndex = IndexFromPhaseName(CurrentPhase.Name);
stagesPassedToday.Clear();
if (newStage <= 0)
{
throw new Exception(this + "Must pass positive stage to set to");
}
if (newStage > phases.Count() + 1)
{
throw new Exception(this + " Trying to set to non-existant stage");
}
currentPhaseIndex = Convert.ToInt32(Math.Floor(newStage), CultureInfo.InvariantCulture) - 1;
if (newStage < Stage)
{
//Make a list of phases to rewind
List <IPhase> phasesToRewind = new List <IPhase>();
foreach (IPhase phase in phases)
{
if ((IndexFromPhaseName(phase.Name) >= currentPhaseIndex) && (IndexFromPhaseName(phase.Name) <= oldPhaseIndex))
{
phasesToRewind.Add(phase);
}
}
foreach (IPhase phase in phasesToRewind)
{
if (!(phase is IPhaseWithTarget) && !(phase is GotoPhase) && !(phase is EndPhase) && !(phase is PhotoperiodPhase) && !(phase is LeafDeathPhase) && !(phase is DAWSPhase))
{
throw new Exception("Can not rewind over phase of type " + phase.GetType());
}
if (phase is IPhaseWithTarget)
{
IPhaseWithTarget rewindingPhase = phase as IPhaseWithTarget;
AccumulatedTT -= rewindingPhase.ProgressThroughPhase;
AccumulatedEmergedTT -= rewindingPhase.ProgressThroughPhase;
phase.ResetPhase();
}
else
{
phase.ResetPhase();
}
}
AccumulatedEmergedTT = Math.Max(0, AccumulatedEmergedTT);
}
else
{
//Make a list of phases to fast forward
List <IPhase> phasesToFastForward = new List <IPhase>();
foreach (IPhase phase in phases)
{
if (IndexFromPhaseName(phase.Name) >= oldPhaseIndex)
{
phasesToFastForward.Add(phase);
}
}
foreach (IPhase phase in phasesToFastForward)
{
if (phase is EndPhase)
{
stagesPassedToday.Add(phase.Start); //Fixme. This is a pretty ordinary bit of programming to get around the fact we use a phenological stage to match observed values. We should change this so plant has a harvest tag to match on.
}
stagesPassedToday.Add(phase.End);
PhaseChangedType PhaseChangedData = new PhaseChangedType();
PhaseChangedData.StageName = phase.End;
PhaseChanged?.Invoke(plant, PhaseChangedData);
}
}
if (phases[currentPhaseIndex] is IPhaseWithTarget)
{
IPhaseWithTarget currentPhase = (phases[currentPhaseIndex] as IPhaseWithTarget);
currentPhase.ProgressThroughPhase = currentPhase.Target * (newStage - currentPhaseIndex - 1);
if (currentPhase.ProgressThroughPhase == 0)
{
stagesPassedToday.Add(currentPhase.Start);
}
}
if ((phases[currentPhaseIndex] is PhotoperiodPhase) || (phases[currentPhaseIndex] is LeafDeathPhase))
{
stagesPassedToday.Add(phases[currentPhaseIndex].Start);
}
StageWasReset?.Invoke(this, new EventArgs());
}
private void OnPhaseChanged(PhaseChangedType PhenologyChange)
{
if (PhenologyChange.NewPhaseName == "GerminationToEmergence")
RootDepth = InitialRootDepth;
else if (PhenologyChange.NewPhaseName == "EmergenceToEndOfJuvenile")
{
Live.StructuralWt = InitialWt * Population.Density;
Live.StructuralN = InitialNConcentration * Live.StructuralWt;
// initial root length (mm/mm^2)
double initial_root_length = Live.Wt / Conversions.sm2smm * SpecificRootLength;
// initial root length density (mm/mm^3)
double rld = MathUtilities.Divide(initial_root_length, RootDepth, 0.0);
int deepest_layer = FindLayerNo(RootDepth);
for (int layer = 0; layer <= deepest_layer; layer++)
RootLength[layer] = rld * Soil.Thickness[layer] * RootProportion(layer, RootDepth);
Util.Debug("Root.InitGreen.StructuralWt=%f", Live.StructuralWt);
Util.Debug("Root.InitGreen.StructuralN=%f", Live.StructuralN);
Util.Debug("Root.InitRootLength=%f", MathUtilities.Sum(RootLength));
}
}
/// <summary>A function that resets phenology to a specified stage</summary>
public void SetToStage(double newStage)
{
string stageOnEvent = CurrentPhase.End;
double oldPhaseIndex = IndexFromPhaseName(CurrentPhase.Name);
stagesPassedToday.Clear();
if (newStage <= 0)
{
throw new Exception(this + "Must pass positive stage to set to");
}
if (newStage > phases.Count() + 1)
{
throw new Exception(this + " Trying to set to non-existant stage");
}
currentPhaseIndex = Convert.ToInt32(Math.Floor(newStage)) - 1;
if (!(phases[currentPhaseIndex] is IPhaseWithTarget))
{
throw new Exception("Can not set phenology to phase of type " + phases[currentPhaseIndex].GetType());
}
if (currentPhaseIndex <= oldPhaseIndex)
{
//Make a list of phases to rewind
List <IPhase> phasesToRewind = new List <IPhase>();
foreach (IPhase phase in phases)
{
if ((IndexFromPhaseName(phase.Name) >= currentPhaseIndex) && (IndexFromPhaseName(phase.Name) <= oldPhaseIndex))
{
phasesToRewind.Add(phase);
}
}
foreach (IPhase phase in phasesToRewind)
{
AccumulatedTT -= phase.TTinPhase;
AccumulatedEmergedTT -= phase.TTinPhase;
phase.ResetPhase();
}
AccumulatedEmergedTT = Math.Max(0, AccumulatedEmergedTT);
}
else
{
//Make a list of phases fast forward
List <IPhase> phasesToFastForward = new List <IPhase>();
foreach (IPhase phase in phases)
{
if (IndexFromPhaseName(phase.Name) >= oldPhaseIndex)
{
phasesToFastForward.Add(phase);
}
}
foreach (IPhase phase in phasesToFastForward)
{
stagesPassedToday.Add(phase.End);
if (PhaseChanged != null)
{
PhaseChangedType PhaseChangedData = new PhaseChangedType();
PhaseChangedData.StageName = phase.End;
PhaseChanged.Invoke(plant, PhaseChangedData);
}
}
}
IPhaseWithTarget currentPhase = (phases[currentPhaseIndex] as IPhaseWithTarget);
currentPhase.TTinPhase = currentPhase.Target * (newStage - currentPhaseIndex - 1);
if (currentPhase.TTinPhase == 0)
{
stagesPassedToday.Add(currentPhase.Start);
}
if (StageWasReset != null)
{
StageWasReset.Invoke(this, new EventArgs());
}
}
private void OnPhaseChanged(object sender, PhaseChangedType phaseChange)
{
if (phaseChange.EventStageName == SetEvent)
OnSetEvent();
if (phaseChange.EventStageName == ReSetEvent)
OnReSetEvent();
}
/// <summary>Respond to a remove biomass event.</summary>
/// <param name="removeBiomPheno">The remove biom pheno.</param>
internal void OnRemoveBiomass(double removeBiomPheno)
{
string existingStage = CurrentStageName;
if (RewindDueToBiomassRemoved != null)
{
FractionBiomassRemoved = removeBiomPheno; // The RewindDueToBiomassRemoved function will use this.
double ttCritical = TTInAboveGroundPhase;
double removeFractPheno = RewindDueToBiomassRemoved.Value();
double removeTTPheno = ttCritical * removeFractPheno;
string msg;
msg = "Phenology change:-\r\n";
msg += " Fraction DM removed = " + removeBiomPheno.ToString() + "\r\n";
msg += " Fraction TT removed = " + removeFractPheno.ToString() + "\r\n";
msg += " Critical TT = " + ttCritical.ToString() + "\r\n";
msg += " Remove TT = " + removeTTPheno.ToString() + "\r\n";
double ttRemaining = removeTTPheno;
for (int i = Phases.Count - 1; i >= 0; i--)
{
Phase Phase = Phases[i];
if (Phase.TTinPhase > 0)
{
double ttCurrentPhase = Phase.TTinPhase;
if (ttRemaining > ttCurrentPhase)
{
Phase.ResetPhase();
ttRemaining -= ttCurrentPhase;
CurrentPhaseIndex -= 1;
if (CurrentPhaseIndex < 4) //FIXME - hack to stop onEmergence being fired which initialises biomass parts
{
CurrentPhaseIndex = 4;
break;
}
}
else
{
Phase.Add(-ttRemaining);
// Return fraction of thermal time we are through the current
// phenological phase (0-1)
//double frac = Phase.FractionComplete;
//if (frac > 0.0 && frac < 1.0) // Don't skip out of this stage - some have very low targets, eg 1.0 in "maturity"
// currentStage = frac + floor(currentStage);
break;
}
}
else
{ // phase is empty - not interested in it
}
}
Stage = (CurrentPhaseIndex + 1) + CurrentPhase.FractionComplete - PhaseIndexOffset;
if (existingStage != CurrentStageName)
{
PhaseChangedType PhaseChangedData = new PhaseChangedType();
PhaseChangedData.OldPhaseName = existingStage;
PhaseChangedData.NewPhaseName = CurrentPhase.Name;
PhaseChanged.Invoke(Plant, PhaseChangedData);
//Fixme MyPaddock.Publish(CurrentPhase.Start);
}
}
}
private void OnPhaseChanged(PhaseChangedType PhenologyChange)
{
if (PhenologyChange.NewPhaseName == "EmergenceToEndOfJuvenile")
{
Live.StructuralWt = InitialWt * Population.Density;
Live.StructuralN = InitialNConcentration * Live.StructuralWt;
Util.Debug("Stem.InitGreen.StructuralWt=%f", Live.StructuralWt);
Util.Debug("Stem.InitGreen.StructuralN=%f", Live.StructuralN);
}
}
private void OnPhaseChanged(object sender, PhaseChangedType phaseChange)
{
if (phaseChange.EventStageName == EndStage)
vernalisedToday = 0.0;
if (phaseChange.EventStageName == ResetStage)
{
permanentVernalisedDays = 0.0;
temporaryVernalisingDays = 0.0;
}
}
private void OnPhaseChanged(object sender, PhaseChangedType phaseChange)
{
if (phaseChange.NewPhaseName == "EmergenceToEndOfJuvenile")
{
Live.StructuralWt = InitialWt * Population.Density;
Live.StructuralN = InitialNConcentration * Live.StructuralWt;
InitialiseAreas();
}
}
private void OnPhaseChanged(PhaseChangedType PhaseChange)
{
if (PhaseChange.EventStageName == SetEvent)
OnSetEvent();
if (PhaseChange.EventStageName == ReSetEvent)
OnReSetEvent();
}
private void OnHarvesting(object sender, EventArgs e)
{
if (sender == Plant)
{
//Jump phenology to the end
string OldPhaseName = CurrentPhase.Name;
int EndPhase = Phases.Count;
PhaseChangedType PhaseChangedData = new PhaseChangedType();
PhaseChangedData.OldPhaseName = OldPhaseName;
PhaseChangedData.NewPhaseName = Phases[EndPhase - 1].Name;
PhaseChanged.Invoke(PhaseChangedData);
CurrentPhaseName = Phases[EndPhase - 1].Name;
}
}
private void OnDoPhenology(object sender, EventArgs e)
{
if (PlantIsAlive)
{
if (thermalTime.Value() < 0)
{
throw new Exception("Negative Thermal Time, check the set up of the ThermalTime Function in" + this);
}
// Calculate progression through current phase
double propOfDayToUse = 1;
bool incrementPhase = CurrentPhase.DoTimeStep(ref propOfDayToUse);
//sorghum resets the stage variable to 0 on the day the phase changes
//it will resume again normally the day after
double resetSorghumStage = SorghumFlag != null && incrementPhase ? 0.0 : 1.0;
while (incrementPhase)
{
if ((CurrentPhase is EmergingPhase) || (CurrentPhase.End == structure?.LeafInitialisationStage) || (CurrentPhase is DAWSPhase))
{
Emerged = true;
}
stagesPassedToday.Add(CurrentPhase.End);
if (currentPhaseIndex + 1 >= phases.Count)
{
throw new Exception("Cannot transition to the next phase. No more phases exist");
}
currentPhaseIndex = currentPhaseIndex + 1;
PhaseChangedType PhaseChangedData = new PhaseChangedType();
PhaseChangedData.StageName = CurrentPhase.Start;
PhaseChanged?.Invoke(plant, PhaseChangedData);
if (SorghumFlag != null && CurrentPhase is EmergingPhase)
{
// void accumulate(...)
double dltPhase = 1.0 + Stage % 1.0;
double newStage = Math.Floor(Stage) + dltPhase;
double dltStage = newStage - Stage;
double pIndex = Stage;
double dltIndex = dltStage;
double indexDevel = pIndex - Math.Floor(pIndex) + dltIndex;
double portionInOld = 1 - APSIM.Shared.Utilities.MathUtilities.Divide(indexDevel - 1, dltIndex, 0);
propOfDayToUse = 1 - portionInOld;
}
incrementPhase = CurrentPhase.DoTimeStep(ref propOfDayToUse);
if (SorghumFlag != null && CurrentStageName == "Emergence")
{
AccumulatedEmergedTT -= (1 - propOfDayToUse) * thermalTime.Value();
}
}
AccumulatedTT += thermalTime.Value();
if (Emerged)
{
AccumulatedEmergedTT += thermalTime.Value();
}
Stage = (currentPhaseIndex + 1) + resetSorghumStage * CurrentPhase.FractionComplete;
if (plant != null && plant.IsAlive && PostPhenology != null)
{
PostPhenology.Invoke(this, new EventArgs());
}
}
}
