/// <summary>Test setup routine. Returns a soil properties that can be used for testing.</summary>
public static APSIM.Shared.Soils.Soil Setup()
{
APSIM.Shared.Soils.Soil soil = new APSIM.Shared.Soils.Soil();
soil.Water = new Water();
soil.Water.Thickness = new double[] { 100, 300, 300, 300, 300, 300 };
soil.Water.BD = new double[] { 1.36, 1.216, 1.24, 1.32, 1.372, 1.368 };
soil.Water.AirDry = new double[] { 0.135, 0.214, 0.261, 0.261, 0.261, 0.261 };
soil.Water.LL15 = new double[] { 0.27, 0.267, 0.261, 0.261, 0.261, 0.261 };
soil.Water.DUL = new double[] { 0.365, 0.461, 0.43, 0.412, 0.402, 0.404 };
soil.Water.SAT = new double[] { 0.400, 0.481, 0.45, 0.432, 0.422, 0.424 };
// Add a wheat crop.
SoilCrop crop = new SoilCrop();
crop.Thickness = soil.Water.Thickness;
crop.Name = "Wheat";
crop.KL = new double[] { 0.06, 0.060, 0.060, 0.060, 0.060, 0.060 };
crop.LL = new double[] { 0.27, 0.267, 0.261, 0.315, 0.402, 0.402 };
soil.Water.Crops = new List<SoilCrop>();
soil.Water.Crops.Add(crop);
// Add OC values into SoilOrganicMatter.
soil.SoilOrganicMatter = new SoilOrganicMatter();
soil.SoilOrganicMatter.Thickness = soil.Water.Thickness;
soil.SoilOrganicMatter.OC = new double[] { 2, 1, 0.5, 0.4, 0.3, 0.2 };
// Add in CL into analysis.
soil.Analysis = new Analysis();
soil.Analysis.Thickness = soil.Water.Thickness;
soil.Analysis.CL = new double[] { 38, double.NaN, 500, 490, 500, 500 };
// Add a sample.
Sample sample = new Sample();
sample.Thickness = new double[] { 100, 300, 300, 300 };
sample.SW = new double[] { 0.103, 0.238, 0.253, 0.247 };
sample.NO3 = new double[] { 23, 7, 2, 1 };
sample.OC = new double[] { 1.35, double.NaN, double.NaN, double.NaN };
sample.SWUnits = Sample.SWUnitsEnum.Gravimetric;
soil.Samples = new List<Sample>();
soil.Samples.Add(sample);
return soil;
}
/// <summary>Sets the sample thickness.</summary>
/// <param name="sample">The sample.</param>
/// <param name="thickness">The thickness to change the sample to.</param>
/// <param name="soil">The soil</param>
private static void SetSampleThickness(Sample sample, double[] thickness, Soil soil)
{
if (!MathUtilities.AreEqual(thickness, sample.Thickness))
{
sample.Name = sample.Name;
sample.Date = sample.Date;
if (sample.SW != null)
sample.SW = MapSW(sample.SW, sample.Thickness, thickness, soil);
if (sample.NH4 != null)
sample.NH4 = MapConcentration(sample.NH4, sample.Thickness, thickness, 0.01);
if (sample.NO3 != null)
sample.NO3 = MapConcentration(sample.NO3, sample.Thickness, thickness, 0.01);
// The elements below will be overlaid over other arrays of values so we want
// to have missing values (double.NaN) used at the bottom of the profile.
if (sample.CL != null)
sample.CL = MapConcentration(sample.CL, sample.Thickness, thickness, double.NaN, allowMissingValues:true);
if (sample.EC != null)
sample.EC = MapConcentration(sample.EC, sample.Thickness, thickness, double.NaN, allowMissingValues: true);
if (sample.ESP != null)
sample.ESP = MapConcentration(sample.ESP, sample.Thickness, thickness, double.NaN, allowMissingValues: true);
if (sample.OC != null)
sample.OC = MapConcentration(sample.OC, sample.Thickness, thickness, double.NaN, allowMissingValues: true);
if (sample.PH != null)
sample.PH = MapConcentration(sample.PH, sample.Thickness, thickness, double.NaN, allowMissingValues: true);
sample.Thickness = thickness;
}
}
/// <summary>Converts the paddock XML.</summary>
/// <param name="paddock">The paddock.</param>
/// <exception cref="System.Exception">Bad paddock name: + name</exception>
private static Paddock CreateSimulationSpec(XmlNode paddock, string baseFolder)
{
Paddock simulation = new Paddock();
string name = XmlUtilities.NameAttr(paddock);
string delimiter = "^";
int posCaret = name.IndexOf(delimiter);
if (posCaret == -1)
throw new Exception("Bad paddock name: " + name);
string remainder = StringUtilities.SplitOffAfterDelimiter(ref name, delimiter);
string growerName;
string paddockName = StringUtilities.SplitOffAfterDelimiter(ref remainder, delimiter);
if (paddockName == string.Empty)
{
growerName = name;
paddockName = remainder;
}
else
growerName = remainder;
simulation.StartSeasonDate = GetDate(paddock, "StartSeasonDateFull");
// Give the paddock a name.
string fullName = string.Format("{0}^{1}^{2}", simulation.StartSeasonDate.Year, growerName, paddockName);
simulation.Name = fullName;
// Set the report date.
simulation.NowDate = GetDate(paddock.ParentNode, "TodayDateFull");
if (simulation.NowDate == DateTime.MinValue)
simulation.NowDate = DateTime.Now;
// Store any rainfall data in the simulation.
simulation.RainfallSource = GetString(paddock, "RainfallSource");
if (simulation.RainfallSource != "Weather station")
{
string rainFileName = GetString(paddock, "RainfallFilename");
if (rainFileName != string.Empty)
{
string fullFileName = Path.Combine(baseFolder, rainFileName);
if (!File.Exists(fullFileName))
throw new Exception("Cannot find file: " + fullFileName);
simulation.ObservedData = ApsimTextFile.ToTable(fullFileName);
if (simulation.ObservedData.Rows.Count == 0)
simulation.ObservedData = null;
}
}
// Set the reset dates
simulation.SoilWaterSampleDate = GetDate(paddock, "ResetDateFull");
simulation.SoilNitrogenSampleDate = GetDate(paddock, "SoilNitrogenSampleDateFull");
simulation.StationNumber = GetInteger(paddock, "StationNumber");
simulation.StationName = GetString(paddock, "StationName");
// Create a sowing management
Sow sowing = new Sow();
simulation.Management.Add(sowing);
sowing.Date = GetDate(paddock, "SowDateFull");
sowing.EmergenceDate = GetDate(paddock, "EmergenceDateFull");
sowing.Crop = GetString(paddock, "Crop");
sowing.Cultivar = GetString(paddock, "Cultivar");
sowing.SkipRow = GetString(paddock, "SkipRow");
sowing.SowingDensity = GetInteger(paddock, "SowingDensity");
sowing.MaxRootDepth = GetInteger(paddock, "MaxRootDepth") * 10; // cm to mm
sowing.BedWidth = GetInteger(paddock, "BedWidth");
sowing.BedRowSpacing = GetDouble(paddock, "BedRowSpacing");
// Make sure we have a stubbletype
simulation.StubbleType = GetString(paddock, "StubbleType");
if (simulation.StubbleType == string.Empty || simulation.StubbleType == "None")
simulation.StubbleType = "Wheat";
simulation.StubbleMass = GetDouble(paddock, "StubbleMass");
simulation.Slope = GetDouble(paddock, "Slope");
simulation.SlopeLength = GetDouble(paddock, "SlopeLength");
simulation.UseEC = GetBoolean(paddock, "UseEC");
// Fertilise nodes.
List<XmlNode> fertiliserNodes = XmlUtilities.ChildNodes(paddock, "Fertilise");
for (int f = 0; f < fertiliserNodes.Count; f++)
{
Fertilise fertilise = new Fertilise();
simulation.Management.Add(fertilise);
fertilise.Date = GetDate(fertiliserNodes[f], "FertDateFull");
fertilise.Amount = GetDouble(fertiliserNodes[f], "FertAmount");
fertilise.Scenario = GetBoolean(fertiliserNodes[f], "Scenario");
}
// Irrigate nodes.
List<XmlNode> irrigateNodes = XmlUtilities.ChildNodes(paddock, "Irrigate");
for (int i = 0; i < irrigateNodes.Count; i++)
{
Irrigate irrigate = new Irrigate();
simulation.Management.Add(irrigate);
irrigate.Date = GetDate(irrigateNodes[i], "IrrigateDateFull");
irrigate.Amount = GetDouble(irrigateNodes[i], "IrrigateAmount");
irrigate.Efficiency = GetDouble(irrigateNodes[i], "IrrigateEfficiency");
irrigate.Scenario = GetBoolean(irrigateNodes[i], "Scenario");
}
// Tillage nodes.
foreach (XmlNode tillageNode in XmlUtilities.ChildNodes(paddock, "Tillage"))
{
Tillage tillage = new Tillage();
simulation.Management.Add(tillage);
tillage.Date = GetDate(tillageNode, "TillageDateFull");
string disturbance = GetString(tillageNode, "Disturbance");
if (disturbance == "Low")
tillage.Disturbance = Tillage.DisturbanceEnum.Low;
else if (disturbance == "Medium")
tillage.Disturbance = Tillage.DisturbanceEnum.Medium;
else
tillage.Disturbance = Tillage.DisturbanceEnum.High;
tillage.Scenario = GetBoolean(tillageNode, "Scenario");
}
// Stubble removed nodes.
foreach (XmlNode stubbleRemovedNode in XmlUtilities.ChildNodes(paddock, "StubbleRemoved"))
{
StubbleRemoved stubbleRemoved = new StubbleRemoved();
simulation.Management.Add(stubbleRemoved);
stubbleRemoved.Date = GetDate(stubbleRemovedNode, "StubbleRemovedDateFull");
stubbleRemoved.Percent = GetDouble(stubbleRemovedNode, "StubbleRemovedAmount");
}
// Look for a soil node.
XmlNode soilNode = XmlUtilities.FindByType(paddock, "Soil");
if (soilNode != null)
{
string testValue = XmlUtilities.Value(soilNode, "Water/Layer/Thickness");
if (testValue != string.Empty)
{
// old format.
soilNode = ConvertSoilNode.Upgrade(soilNode);
}
}
// Fix up soil sample variables.
Sample sample1 = new Sample();
sample1.Name = "Sample1";
sample1.Thickness = GetArray(paddock, "Sample1Thickness");
sample1.SW = GetArray(paddock, "SW");
if (sample1.SW == null)
{
// Really old way of doing samples - they are stored under soil.
List<XmlNode> sampleNodes = XmlUtilities.ChildNodes(soilNode, "Sample");
if (sampleNodes.Count > 0)
sample1 = XmlUtilities.Deserialise(sampleNodes[0], typeof(Sample)) as Sample;
}
else
{
sample1.NO3 = GetArray(paddock, "NO3");
sample1.NH4 = GetArray(paddock, "NH4");
}
Sample sample2 = null;
double[] sample2Thickness = GetArray(paddock, "Sample2Thickness");
if (sample2Thickness == null)
{
// Really old way of doing samples - they are stored under soil.
List<XmlNode> sampleNodes = XmlUtilities.ChildNodes(soilNode, "Sample");
if (sampleNodes.Count > 1)
sample2 = XmlUtilities.Deserialise(sampleNodes[1], typeof(Sample)) as Sample;
}
else
{
sample2 = sample1;
if (!MathUtilities.AreEqual(sample2Thickness, sample1.Thickness))
{
sample2 = new Sample();
sample2.Name = "Sample2";
}
sample2.OC = GetArray(paddock, "OC");
sample2.EC = GetArray(paddock, "EC");
sample2.PH = GetArray(paddock, "PH");
sample2.CL = GetArray(paddock, "CL");
sample2.OCUnits = SoilOrganicMatter.OCUnitsEnum.WalkleyBlack;
sample2.PHUnits = Analysis.PHUnitsEnum.CaCl2;
}
// Make sure we have NH4 values.
if (sample1.NH4 == null && sample1.NO3 != null)
{
string[] defaultValues = StringUtilities.CreateStringArray("0.1", sample1.NO3.Length);
sample1.NH4 = MathUtilities.StringsToDoubles(defaultValues);
}
RemoveNullFieldsFromSample(sample1);
if (sample2 != null)
RemoveNullFieldsFromSample(sample2);
// Fix up <WaterFormat>
string waterFormatString = GetString(paddock, "WaterFormat");
if (waterFormatString.Contains("Gravimetric"))
sample1.SWUnits = Sample.SWUnitsEnum.Gravimetric;
else
sample1.SWUnits = Sample.SWUnitsEnum.Volumetric;
if (MathUtilities.ValuesInArray(sample1.Thickness))
simulation.Samples.Add(sample1);
if (sample2 != null && MathUtilities.ValuesInArray(sample2.Thickness) && sample2 != sample1)
simulation.Samples.Add(sample2);
// Check for InitTotalWater & InitTotalNitrogen
simulation.InitTotalWater = GetDouble(paddock, "InitTotalWater");
simulation.InitTotalNitrogen = GetDouble(paddock, "InitTotalNitrogen");
// Check to see if we need to convert the soil structure.
simulation.SoilPath = GetString(paddock, "SoilName");
if (soilNode != null)
{
// See if there is a 'SWUnits' value. If found then copy it into
// <WaterFormat>
string waterFormat = XmlUtilities.Value(paddock, "WaterFormat");
if (waterFormat == string.Empty)
{
int sampleNumber = 0;
foreach (XmlNode soilSample in XmlUtilities.ChildNodes(soilNode, "Sample"))
{
string swUnits = XmlUtilities.Value(soilSample, "SWUnits");
if (swUnits != string.Empty)
XmlUtilities.SetValue(paddock, "WaterFormat", swUnits);
// Also make sure we don't have 2 samples with the same name.
string sampleName = "Sample" + (sampleNumber + 1).ToString();
XmlUtilities.SetAttribute(soilSample, "name", sampleName);
sampleNumber++;
}
}
simulation.Soil = SoilUtilities.FromXML(soilNode.OuterXml);
if (simulation.Samples != null)
simulation.Soil.Samples = simulation.Samples;
}
return simulation;
}
private static void RemoveNullFieldsFromSample(Sample sample)
{
if (sample.CL == null) sample.CL = new double[0];
if (sample.EC == null) sample.EC = new double[0];
if (sample.ESP == null) sample.ESP = new double[0];
if (sample.NH4 == null) sample.NH4 = new double[0];
if (sample.NO3 == null) sample.NO3 = new double[0];
if (sample.OC == null) sample.OC = new double[0];
if (sample.PH == null) sample.PH = new double[0];
if (sample.SW == null) sample.SW = new double[0];
}
/// <summary>Checks the sample for missing values.</summary>
/// <param name="sample">The sample.</param>
/// <param name="soil">The soil.</param>
private static void CheckSampleForMissingValues(Sample sample, Soil soil)
{
if (!MathUtilities.ValuesInArray(sample.SW))
sample.SW = null;
if (!MathUtilities.ValuesInArray(sample.NO3))
sample.NO3 = null;
if (!MathUtilities.ValuesInArray(sample.CL))
sample.CL = null;
if (!MathUtilities.ValuesInArray(sample.EC))
sample.EC = null;
if (!MathUtilities.ValuesInArray(sample.ESP))
sample.ESP = null;
if (!MathUtilities.ValuesInArray(sample.PH))
sample.PH = null;
if (!MathUtilities.ValuesInArray(sample.OC))
sample.OC = null;
if (sample.SW != null)
sample.SW = MathUtilities.FixArrayLength(sample.SW, sample.Thickness.Length);
if (sample.NO3 != null)
sample.NO3 = MathUtilities.FixArrayLength(sample.NO3, sample.Thickness.Length);
if (sample.NH4 != null)
sample.NH4 = MathUtilities.FixArrayLength(sample.NH4, sample.Thickness.Length);
if (sample.CL != null)
sample.CL = MathUtilities.FixArrayLength(sample.CL, sample.Thickness.Length);
if (sample.EC != null)
sample.EC = MathUtilities.FixArrayLength(sample.EC, sample.Thickness.Length);
if (sample.ESP != null)
sample.ESP = MathUtilities.FixArrayLength(sample.ESP, sample.Thickness.Length);
if (sample.PH != null)
sample.PH = MathUtilities.FixArrayLength(sample.PH, sample.Thickness.Length);
if (sample.OC != null)
sample.OC = MathUtilities.FixArrayLength(sample.OC, sample.Thickness.Length);
double[] ll15 = LayerStructure.LL15Mapped(soil, sample.Thickness);
for (int i = 0; i < sample.Thickness.Length; i++)
{
if (sample.SW != null && double.IsNaN(sample.SW[i]))
sample.SW[i] = ll15[i];
if (sample.NO3 != null && double.IsNaN(sample.NO3[i]))
sample.NO3[i] = 1.0;
if (sample.NH4 != null && double.IsNaN(sample.NH4[i]))
sample.NH4[i] = 0.1;
if (sample.CL != null && double.IsNaN(sample.CL[i]))
sample.CL[i] = 0;
if (sample.EC != null && double.IsNaN(sample.EC[i]))
sample.EC[i] = 0;
if (sample.ESP != null && double.IsNaN(sample.ESP[i]))
sample.ESP[i] = 0;
if (sample.PH != null && (double.IsNaN(sample.PH[i]) || sample.PH[i] == 0.0))
sample.PH[i] = 7.0;
if (sample.OC != null && (double.IsNaN(sample.OC[i]) || sample.OC[i] == 0.0))
sample.OC[i] = 0.5;
}
}
/// <summary>Calculates volumetric soil water for the given sample.</summary>
/// <param name="sample">The sample.</param>
/// <param name="soil">The soil.</param>
/// <returns>Volumetric water (mm/mm)</returns>
private static double[] SWVolumetric(Sample sample, Soil soil)
{
if (sample.SWUnits == Sample.SWUnitsEnum.Volumetric || sample.SW == null)
return sample.SW;
else
{
// convert the numbers
if (sample.SWUnits == Sample.SWUnitsEnum.Gravimetric)
{
double[] bd = LayerStructure.BDMapped(soil, sample.Thickness);
return MathUtilities.Multiply(sample.SW, bd);
}
else
return MathUtilities.Divide(sample.SW, sample.Thickness); // from mm to mm/mm
}
}
/// <summary>Checks the soil sample.</summary>
/// <param name="parentSoil">The parent soil.</param>
/// <param name="sample">The sample.</param>
private static void CheckSample(Soil parentSoil, Sample sample)
{
// Do some checking of NO3 / NH4
CheckMissingValuesAreNaN(sample.NO3);
CheckMissingValuesAreNaN(sample.NH4);
CheckMissingValuesAreNaN(sample.OC);
CheckMissingValuesAreNaN(sample.EC);
CheckMissingValuesAreNaN(sample.PH);
if (sample.NO3 != null)
sample.NO3 = FixArrayLength(sample.NO3, sample.Thickness.Length);
if (sample.NH4 != null)
sample.NH4 = FixArrayLength(sample.NH4, sample.Thickness.Length);
// NH4 can be null so give default values if that is the case.
for (int i = 0; i < sample.NH4.Length; i++)
if (double.IsNaN(sample.NH4[i]))
sample.NH4[i] = 0.1;
sample.OCUnits = SoilOrganicMatter.OCUnitsEnum.WalkleyBlack;
if (sample.OC != null)
sample.OC = FixArrayLength(sample.OC, sample.Thickness.Length);
if (sample.EC != null)
sample.EC = FixArrayLength(sample.EC, sample.Thickness.Length);
if (sample.PH != null)
sample.PH = FixArrayLength(sample.PH, sample.Thickness.Length);
}