//----------------------- Public methods -----------------------
/// <summary>Initialise this root instance (and tissues).</summary>
/// <param name="zone">The zone the roots belong to.</param>
/// <param name="minimumLiveWt">Minimum live DM biomass for this organ (kg/ha).</param>
public void Initialise(Zone zone, double minimumLiveWt)
{
// link to soil models parameters
soil = zone.FindInScope <Soil>();
if (soil == null)
{
throw new Exception($"Cannot find soil in zone {zone.Name}");
}
soilPhysical = soil.FindInScope <IPhysical>();
if (soilPhysical == null)
{
throw new Exception($"Cannot find soil physical in soil {soil.Name}");
}
waterBalance = soil.FindInScope <ISoilWater>();
if (waterBalance == null)
{
throw new Exception($"Cannot find a water balance model in soil {soil.Name}");
}
soilCropData = soil.FindDescendant <SoilCrop>(species.Name + "Soil");
if (soilCropData == null)
{
throw new Exception($"Cannot find a soil crop parameterisation called {species.Name + "Soil"}");
}
nutrient = zone.FindInScope <INutrient>();
if (nutrient == null)
{
throw new Exception($"Cannot find SoilNitrogen in zone {zone.Name}");
}
no3 = zone.FindInScope("NO3") as ISolute;
if (no3 == null)
{
throw new Exception($"Cannot find NO3 solute in zone {zone.Name}");
}
nh4 = zone.FindInScope("NH4") as ISolute;
if (nh4 == null)
{
throw new Exception($"Cannot find NH4 solute in zone {zone.Name}");
}
// initialise soil related variables
zoneName = soil.Parent.Name;
nLayers = soilPhysical.Thickness.Length;
mySoilNH4Available = new double[nLayers];
mySoilNO3Available = new double[nLayers];
mySoilWaterAvailable = new double[nLayers];
// save minimum DM and get target root distribution
MinimumLiveDM = minimumLiveWt;
TargetDistribution = RootDistributionTarget();
// initialise tissues
Live.Initialise();
Dead.Initialise();
}
/// <summary>Calculate the interception loss of water from the canopy</summary>
private void CalculateInterception(ZoneMicroClimate ZoneMC)
{
double sumLAI = 0.0;
double sumLAItot = 0.0;
for (int i = 0; i <= ZoneMC.numLayers - 1; i++)
{
for (int j = 0; j <= ZoneMC.Canopies.Count - 1; j++)
{
sumLAI += ZoneMC.Canopies[j].LAI[i];
sumLAItot += ZoneMC.Canopies[j].LAItot[i];
}
}
double totalInterception = a_interception * Math.Pow(weather.Rain, b_interception) + c_interception * sumLAItot + d_interception;
totalInterception = Math.Max(0.0, Math.Min(0.99 * weather.Rain, totalInterception));
for (int i = 0; i <= ZoneMC.numLayers - 1; i++)
{
for (int j = 0; j <= ZoneMC.Canopies.Count - 1; j++)
{
ZoneMC.Canopies[j].interception[i] = MathUtilities.Divide(ZoneMC.Canopies[j].LAI[i], sumLAI, 0.0) * totalInterception;
}
}
ISoilWater zonesoilwater = Apsim.Find(ZoneMC.zone, typeof(ISoilWater)) as ISoilWater;
if (zonesoilwater != null)
{
zonesoilwater.PotentialInfiltration = Math.Max(0, weather.Rain - totalInterception);
}
}
/// <summary>Calculate the amtospheric potential evaporation rate for each zone</summary>
private void CalculateEo(ZoneMicroClimate ZoneMC)
{
ISoilWater zoneSoilWater = Apsim.Find(ZoneMC.zone, typeof(ISoilWater)) as ISoilWater;
ISurfaceOrganicMatter zoneSurfaceOM = Apsim.Find(ZoneMC.zone, typeof(ISurfaceOrganicMatter)) as ISurfaceOrganicMatter;
double CoverGreen = 0;
for (int j = 0; j <= ZoneMC.Canopies.Count - 1; j++)
{
if (ZoneMC.Canopies[j].Canopy != null)
{
CoverGreen += (1 - CoverGreen) * ZoneMC.Canopies[j].Canopy.CoverGreen;
}
}
if (weather != null && zoneSoilWater != null && zoneSurfaceOM != null)
{
zoneSoilWater.Eo = AtmosphericPotentialEvaporationRate(weather.Radn,
weather.MaxT,
weather.MinT,
zoneSoilWater.Salb,
zoneSurfaceOM.Cover,
CoverGreen);
}
}
/// <summary>Constructor.</summary>
/// <param name="clockModel">The clock model.</param>
/// <param name="zoneModel">The zone model.</param>
/// <param name="minHeightDiffForNewLayer">Minimum canopy height diff for new layer.</param>
public MicroClimateZone(Clock clockModel, Zone zoneModel, double minHeightDiffForNewLayer)
{
clock = clockModel;
Zone = zoneModel;
MinimumHeightDiffForNewLayer = minHeightDiffForNewLayer;
canopyModels = Apsim.ChildrenRecursively(Zone, typeof(ICanopy)).Cast <ICanopy>();
modelsThatHaveCanopies = Apsim.ChildrenRecursively(Zone, typeof(IHaveCanopy)).Cast <IHaveCanopy>();
soilWater = Apsim.Find(Zone, typeof(ISoilWater)) as ISoilWater;
surfaceOM = Apsim.Find(Zone, typeof(ISurfaceOrganicMatter)) as ISurfaceOrganicMatter;
}
/// <summary>Constructor.</summary>
/// <param name="clockModel">The clock model.</param>
/// <param name="weatherModel">The weather model.</param>
/// <param name="zoneModel">The zone model.</param>
public MicroClimateZone(Clock clockModel, IWeather weatherModel, Zone zoneModel)
{
clock = clockModel;
weather = weatherModel;
Zone = zoneModel;
canopyModels = Apsim.ChildrenRecursively(Zone, typeof(ICanopy)).Cast <ICanopy>();
modelsThatHaveCanopies = Apsim.ChildrenRecursively(Zone, typeof(IHaveCanopy)).Cast <IHaveCanopy>();
soilWater = Apsim.Find(Zone, typeof(ISoilWater)) as ISoilWater;
surfaceOM = Apsim.Find(Zone, typeof(ISurfaceOrganicMatter)) as ISurfaceOrganicMatter;
}
/// <summary>Constructor.</summary>
/// <param name="clockModel">The clock model.</param>
/// <param name="zoneModel">The zone model.</param>
/// <param name="minHeightDiffForNewLayer">Minimum canopy height diff for new layer.</param>
public MicroClimateZone(Clock clockModel, Zone zoneModel, double minHeightDiffForNewLayer)
{
clock = clockModel;
Zone = zoneModel;
MinimumHeightDiffForNewLayer = minHeightDiffForNewLayer;
canopyModels = Zone.FindAllDescendants <ICanopy>().ToList();
modelsThatHaveCanopies = Zone.FindAllDescendants <IHaveCanopy>().ToList();
soilWater = Zone.FindInScope <ISoilWater>();
surfaceOM = Zone.FindInScope <ISurfaceOrganicMatter>();
}
private void OnSimulationCommencing(object sender, EventArgs e)
{
ZoneList = Parent.FindAllChildren <Zone>().ToList();
SetupTreeProperties();
//pre-fetch static information
forestryZones = Parent.FindAllDescendants <Zone>().ToList();
treeZone = ZoneList.FirstOrDefault();
treeZoneWater = treeZone.FindInScope <ISoilWater>();
TreeWaterUptake = new double[ZoneList.Count()];
}
/// <summary>
/// Constructor. Copy state from another instance.
/// </summary>
/// <param name="from">The instance to copy from.</param>
public ZoneWaterAndN(ZoneWaterAndN from)
{
NO3Solute = from.NO3Solute;
NH4Solute = from.NH4Solute;
soilInZone = from.soilInZone;
Zone = from.Zone;
WaterBalance = from.WaterBalance;
Water = from.Water;
NO3N = from.NO3N;
NH4N = from.NH4N;
}
private void OnSimulationCommencing(object sender, EventArgs e)
{
ZoneList = Apsim.Children(this.Parent, typeof(Zone));
SetupTreeProperties();
//pre-fetch static information
forestryZones = Apsim.ChildrenRecursively(Parent, typeof(Zone));
treeZone = ZoneList[0] as Zone;
treeZoneWater = Apsim.Find(treeZone, typeof(ISoilWater)) as ISoilWater;
TreeWaterUptake = new double[ZoneList.Count];
}
public void ImporterTests_SoilImports()
{
string oldXml = ReflectionUtilities.GetResourceAsString("UnitTests.ImporterTestsSoilImports.xml");
var importer = new Importer();
Simulations sims = importer.CreateSimulationsFromXml(oldXml);
Soil s = sims.Children[0].Children[0] as Soil;
Assert.AreEqual(s.Name, "Soil");
InitialWater initWater = s.Children[0] as InitialWater;
Assert.AreEqual(initWater.FractionFull, 0.5);
Assert.AreEqual(initWater.PercentMethod, InitialWater.PercentMethodEnum.FilledFromTop);
Physical w = s.Children[1] as Physical;
Assert.AreEqual(w.Thickness, new double[] { 150, 150, 300, 300 });
Assert.AreEqual(w.BD, new double[] { 1.02, 1.03, 1.02, 1.02 });
Assert.AreEqual(w.LL15, new double[] { 0.29, 0.29, 0.29, 0.29 });
ISoilWater sw = s.Children[2] as ISoilWater;
Assert.AreEqual(sw.Thickness, new double[] { 150, 150, 300, 300 });
Assert.IsTrue(s.Children[3] is SoilNitrogen);
Assert.IsTrue(s.Children[4] is CERESSoilTemperature);
Organic som = s.Children[5] as Organic;
Assert.AreEqual(som.Thickness, new double[] { 150, 150, 300, 300 });
Assert.AreEqual(som.Carbon, new double[] { 1.04, 0.89, 0.89, 0.89 });
Assert.AreEqual(som.FBiom, new double[] { 0.025, 0.02, 0.015, 0.01 });
Chemical a = s.Children[6] as Chemical;
Assert.AreEqual(a.Thickness, new double[] { 150, 150, 300, 300 });
Assert.AreEqual(a.NO3N, new double[] { 6.5, 2.1, 2.1, 1.0 });
Assert.AreEqual(a.NH4N, new double[] { 0.5, 0.1, 0.1, 0.2 });
Assert.AreEqual(a.EC, new double[] { 0.2, 0.25, 0.31, 0.40 });
Assert.AreEqual(a.PH, new double[] { 8.4, 8.8, 9.0, 9.2 });
Sample sam = s.Children[7] as Sample;
Assert.AreEqual(sam.Thickness, new double[] { 150, 150, 300 });
SoilCrop crop = s.Children[1].Children[0] as SoilCrop;
Assert.AreEqual(crop.LL, new double[] { 0.29, 0.29, 0.32, 0.38 });
Assert.AreEqual(crop.KL, new double[] { 0.1, 0.1, 0.08, 0.06 });
Assert.AreEqual(crop.XF, new double[] { 1, 1, 1, 1 });
}
/// <summary>Initialises this instance.</summary>
public void Initialise()
{
WaterBalance = soilInZone.FindInScope <ISoilWater>();
NO3Solute = soilInZone.FindInScope <ISolute>("NO3");
NH4Solute = soilInZone.FindInScope <ISolute>("NH4");
var PlantAvailableNO3Solute = soilInZone.FindInScope <ISolute>("PlantAvailableNO3");
if (PlantAvailableNO3Solute != null)
{
NO3Solute = PlantAvailableNO3Solute;
}
var PlantAvailableNH4Solute = soilInZone.FindInScope <ISolute>("PlantAvailableNH4");
if (PlantAvailableNH4Solute != null)
{
NH4Solute = PlantAvailableNH4Solute;
}
}
/// <summary>Constructor, initialise tissues for the roots.</summary>
/// <param name="zone">The zone the roots belong in.</param>
/// <param name="initialDM">Initial dry matter weight</param>
/// <param name="initialDepth">Initial root depth</param>
/// <param name="minLiveDM">The minimum biomass for this organ</param>
public void Initialise(Zone zone, double initialDM, double initialDepth,
double minLiveDM)
{
soil = zone.FindInScope <Soil>();
if (soil == null)
{
throw new Exception($"Cannot find soil in zone {zone.Name}");
}
soilPhysical = soil.FindInScope <IPhysical>();
if (soilPhysical == null)
{
throw new Exception($"Cannot find soil physical in soil {soil.Name}");
}
waterBalance = soil.FindInScope <ISoilWater>();
if (waterBalance == null)
{
throw new Exception($"Cannot find a water balance model in soil {soil.Name}");
}
soilCropData = soil.FindDescendant <SoilCrop>(species.Name + "Soil");
if (soilCropData == null)
{
throw new Exception($"Cannot find a soil crop parameterisation called {species.Name + "Soil"}");
}
nutrient = zone.FindInScope <INutrient>();
if (nutrient == null)
{
throw new Exception($"Cannot find SoilNitrogen in zone {zone.Name}");
}
no3 = zone.FindInScope("NO3") as ISolute;
if (no3 == null)
{
throw new Exception($"Cannot find NO3 solute in zone {zone.Name}");
}
nh4 = zone.FindInScope("NH4") as ISolute;
if (nh4 == null)
{
throw new Exception($"Cannot find NH4 solute in zone {zone.Name}");
}
// link to soil and initialise related variables
zoneName = soil.Parent.Name;
nLayers = soilPhysical.Thickness.Length;
dulMM = soilPhysical.DULmm;
ll15MM = soilPhysical.LL15mm;
mySoilNH4Available = new double[nLayers];
mySoilNO3Available = new double[nLayers];
// save minimum DM and get target root distribution
Depth = initialDepth;
minimumLiveDM = minLiveDM;
CalculateRootZoneBottomLayer();
TargetDistribution = RootDistributionTarget();
// initialise tissues
double[] initialDMByLayer = MathUtilities.Multiply_Value(CurrentRootDistributionTarget(), initialDM);
double[] initialNByLayer = MathUtilities.Multiply_Value(initialDMByLayer, NConcOptimum);
Live = tissue[0];
Dead = tissue[1];
Live.Initialise(initialDMByLayer, initialNByLayer);
Dead.Initialise(null, null);
}