Merge pull request #1655 from hut104/SoilNutrient

Soil nutrient

ApsimNG/ApsimNG.csproj

@@ -320,6 +320,9 @@
     <EmbeddedResource Include="Resources\PresenterPictures\RectangularZone.png" />
   </ItemGroup>
   <ItemGroup>
+    <EmbeddedResource Include="Resources\TreeViewImages\CFlow.png" />
+    <EmbeddedResource Include="Resources\TreeViewImages\NFlow.png" />
+    <EmbeddedResource Include="Resources\TreeViewImages\Solute.png" />
     <EmbeddedResource Include="Resources\TreeViewImages\LinearAfterThresholdFunction.png" />
     <EmbeddedResource Include="Resources\TreeViewImages\Evapotranspiration.png" />
     <EmbeddedResource Include="Resources\TreeViewImages\LayerStructure.png" />

Models/Agroforestry/TreeProxy.cs

@@ -628,8 +628,8 @@ public void SetNUptake(List<Soils.Arbitrator.ZoneWaterAndN> info)
                         ThisSoil = Apsim.Find(SearchZ, typeof(Soils.Soil)) as Soils.Soil;
                         double[] NewNO3 = new double[ZI.NO3N.Length];
                         for (int i = 0; i <= ZI.NO3N.Length - 1; i++)
-                            NewNO3[i] = ThisSoil.SoilNitrogen.NO3[i] - ZI.NO3N[i];
-                        ThisSoil.SoilNitrogen.NO3 = NewNO3;
+                            NewNO3[i] = ThisSoil.NO3N[i] - ZI.NO3N[i];
+                        ThisSoil.NO3N = NewNO3;
                     }
                 }
             }

Models/Interfaces/INutrient.cs

@@ -0,0 +1,24 @@
+// -----------------------------------------------------------------------
+// <copyright file="INutrient.cs" company="APSIM Initiative">
+//     Copyright (c) APSIM Initiative
+// </copyright>
+//-----------------------------------------------------------------------
+namespace Models.Interfaces
+{
+    using System.Collections.Generic;
+    using Models.Soils.Arbitrator;
+    using Models.Soils;
+
+    /// <summary>
+    /// This interface defines the communications between a soil arbitrator and
+    /// and crop.
+    /// </summary>
+    public interface INutrient
+    {
+
+        /// <summary>
+        /// Calculate actual decomposition
+        /// </summary>
+        SurfaceOrganicMatterDecompType CalculateActualSOMDecomp();
+    }
+}

Models/Models.csproj

@@ -174,6 +174,7 @@
     <Compile Include="Interfaces\ICanopy.cs" />
     <Compile Include="Interfaces\ISoilWater.cs" />
     <Compile Include="Interfaces\ISolute.cs" />
+    <Compile Include="Interfaces\INutrient.cs" />
     <Compile Include="Interfaces\IWeather.cs" />
     <Compile Include="Lifecycle\Cohort.cs" />
     <Compile Include="Lifecycle\Lifecycle.cs" />

Models/Soils/Nutrient/CFlow.cs

@@ -5,53 +5,55 @@ namespace Models.Soils.Nutrient
     using Models.PMF.Functions;
     using System;
     using APSIM.Shared.Utilities;
+    using System.Collections.Generic;
 
     /// <summary>
     /// Encapsulates a carbon flow between pools.
     /// </summary>
     [Serializable]
-    [ValidParent(ParentType = typeof(Nutrient))]
+    [ValidParent(ParentType = typeof(NutrientPool))]
     [PresenterName("UserInterface.Presenters.PropertyPresenter")]
     [ViewName("UserInterface.Views.GridView")]
     public class CarbonFlow : Model
     {
-        private NutrientPool source = null;
-        private NutrientPool destination = null;
+        private List<NutrientPool> destinations = new List<NutrientPool>();
 
-        [Link]
-        private IFunction rate = null;
+        [ChildLinkByName]
+        private IFunction Rate = null;
 
-        [Link]
+        [ChildLinkByName]
         private IFunction CO2Efficiency = null;
 
+        [Link]
+        private Clock Clock = null;
+
         [Link]
         private SoluteManager solutes = null;
 
         /// <summary>
-        /// Name of source pool
+        /// Name of destination pool
         /// </summary>
-        [Description("Name of source pool")]
-        public string sourceName { get; set; }
-
+        [Description("Names of destination pools (CSV)")]
+        public string[] destinationNames { get; set; }
         /// <summary>
-        /// Name of destination pool
+        /// Fractions for each destination pool
         /// </summary>
-        [Description("Name of destination pool")]
-        public string destinationName { get; set; }
+        [Description("Fractions of flow to each pool (CSV)")]
+        public double[] destinationFraction { get; set; }
 
         /// <summary>Performs the initial checks and setup</summary>
         /// <param name="sender">The sender.</param>
         /// <param name="e">The <see cref="EventArgs"/> instance containing the event data.</param>
         [EventSubscribe("Commencing")]
         private void OnSimulationCommencing(object sender, EventArgs e)
         {
-            source = Apsim.Find(this, sourceName) as NutrientPool;
-            if (source == null)
-                throw new Exception("Cannot find source pool with name: " + sourceName);
-
-            destination = Apsim.Find(this, destinationName) as NutrientPool;
-            if (destination == null)
-                throw new Exception("Cannot find destination pool with name: " + destinationName);
+            foreach (string destinationName in destinationNames)
+            {
+                NutrientPool destination = Apsim.Find(this, destinationName) as NutrientPool;
+                if (destination == null)
+                    throw new Exception("Cannot find destination pool with name: " + destinationName);
+                destinations.Add(destination);
+            }
         }
 
         /// <summary>
@@ -62,21 +64,77 @@ private void OnSimulationCommencing(object sender, EventArgs e)
         [EventSubscribe("DoSoilOrganicMatter")]
         private void OnDoSoilOrganicMatter(object sender, EventArgs e)
         {
-            for (int i= 0; i < source.C.Length; i++)
+            if (DateUtilities.DatesEqual("01-Oct",Clock.Today))
+            { }
+
+            NutrientPool source = Parent as NutrientPool;
+            double[] NH4 = solutes.GetSolute("NH4");
+            double[] NO3 = solutes.GetSolute("NO3");
+
+            for (int i = 0; i < source.C.Length; i++)
             {
-                double carbonFlow = rate.Value(i) * source.C[i];
-                double nitrogenFlow = MathUtilities.Divide(carbonFlow, source.CNRatio[i],0);
-                double carbonFlowToDestination = carbonFlow * CO2Efficiency.Value(i);
-                double nitrogenFlowToDestination = carbonFlowToDestination / destination.CNRatio[i];
-                source.C[i] -= carbonFlow;
-                source.N[i] -= nitrogenFlow;
-                destination.C[i] += carbonFlowToDestination;
-                destination.N[i] += nitrogenFlowToDestination;
-                if (nitrogenFlowToDestination <= nitrogenFlow)
-                    solutes.AddToLayer(i, "NH4", nitrogenFlow - nitrogenFlowToDestination);
+                double carbonFlowFromSource = Rate.Value(i) * source.C[i];
+                double nitrogenFlowFromSource = MathUtilities.Divide(carbonFlowFromSource, source.CNRatio[i], 0);
+
+                double[] carbonFlowToDestination = new double[destinations.Count];
+                double[] nitrogenFlowToDestination = new double[destinations.Count];
+
+                for (int j = 0; j < destinations.Count; j++)
+                {
+                    carbonFlowToDestination[j] = carbonFlowFromSource * CO2Efficiency.Value(i) * destinationFraction[j];
+                    nitrogenFlowToDestination[j] = MathUtilities.Divide(carbonFlowToDestination[j],destinations[j].CNRatio[i],0.0);
+                }
+
+                double TotalNitrogenFlowToDestinations = MathUtilities.Sum(nitrogenFlowToDestination);
+                double NSupply = nitrogenFlowFromSource + NO3[i] + NH4[i];
+
+                if (MathUtilities.Sum(nitrogenFlowToDestination) > NSupply)
+                {
+                    double NSupplyFactor = MathUtilities.Bound(MathUtilities.Divide(NO3[i] + NH4[i], TotalNitrogenFlowToDestinations - nitrogenFlowFromSource, 1.0), 0.0, 1.0);
+
+                    for (int j = 0; j < destinations.Count; j++)
+                    {
+                        carbonFlowToDestination[j] *= NSupplyFactor;
+                        nitrogenFlowToDestination[j] *= NSupplyFactor;
+                        if (nitrogenFlowToDestination[j] > 0.5)
+                        { }
+                    }
+                    TotalNitrogenFlowToDestinations *= NSupplyFactor;
+
+                    carbonFlowFromSource *= NSupplyFactor;
+                    nitrogenFlowFromSource *= NSupplyFactor;
+
+                }
+
+                source.C[i] -= carbonFlowFromSource;
+                source.N[i] -= nitrogenFlowFromSource;
+                for (int j = 0; j < destinations.Count; j++)
+                {
+                    destinations[j].C[i] += carbonFlowToDestination[j];
+                    destinations[j].N[i] += nitrogenFlowToDestination[j];
+                }
+
+
+                if (TotalNitrogenFlowToDestinations <= nitrogenFlowFromSource)
+                    NH4[i] += nitrogenFlowFromSource - TotalNitrogenFlowToDestinations;
                 else
-                    throw new NotImplementedException();
+                {
+                    double NDeficit = TotalNitrogenFlowToDestinations - nitrogenFlowFromSource;
+                    double NH4Immobilisation = Math.Min(NH4[i], NDeficit);
+                    NH4[i] -= NH4Immobilisation;
+                    NDeficit -= NH4Immobilisation;
+
+                    double NO3Immobilisation = Math.Min(NO3[i], NDeficit);
+                    NO3[i] -= NO3Immobilisation;
+                    NDeficit -= NO3Immobilisation;
+
+                    if (MathUtilities.IsGreaterThan(NDeficit, 0.0))
+                        throw new Exception("Insufficient mineral N for immobilisation demand for C flow " + Name);
+                }
+
             }
+            solutes.SetSolute("NH4", NH4);
+            solutes.SetSolute("NO3", NO3);
         }
 
 

Models/Soils/Nutrient/NFlow.cs

@@ -10,7 +10,7 @@ namespace Models.Soils.Nutrient
     /// Encapsulates a nitrogen flow between mineral N pools.
     /// </summary>
     [Serializable]
-    [ValidParent(ParentType = typeof(Nutrient))]
+    [ValidParent(ParentType = typeof(Solute))]
     [PresenterName("UserInterface.Presenters.PropertyPresenter")]
     [ViewName("UserInterface.Views.GridView")]
     public class NFlow : Model
@@ -24,8 +24,14 @@ public class NFlow : Model
         [Link]
         private SoluteManager solutes = null;
 
-        [Link]
-        private Soil soil = null;
+        /// <summary>
+        /// Value of total N flow into destination
+        /// </summary>
+        public double[] Value { get; set; }
+        /// <summary>
+        /// Value of total loss
+        /// </summary>
+        public double[] Loss { get; set; }
 
         /// <summary>
         /// Name of source pool
@@ -46,22 +52,34 @@ public class NFlow : Model
         /// <param name="e">The <see cref="EventArgs"/> instance containing the event data.</param>
         [EventSubscribe("DoSoilOrganicMatter")]
         private void OnDoSoilOrganicMatter(object sender, EventArgs e)
-        {
-
-            double[] source = solutes.GetSolute(sourceName);
+        {            
+            double[] source = solutes.GetSolute(Parent.Name);
+            if (Value == null)
+                Value = new double[source.Length];
+            if (Loss == null)
+                Loss = new double[source.Length];
 
-            double[] destination = solutes.GetSolute(destinationName);
+            double[] destination = null;
+            if (destinationName !=null)
+                destination = solutes.GetSolute(destinationName);
 
-            for (int i= 0; i < soil.Thickness.Length; i++)
+            for (int i= 0; i < source.Length; i++)
             {
                 double nitrogenFlow = rate.Value(i) * source[i];
-                double nitrogenFlowToDestination = nitrogenFlow * (1-NLoss.Value(i));
+                Loss[i]= nitrogenFlow * NLoss.Value(i);  // keep value of loss for use in output
+                double nitrogenFlowToDestination = nitrogenFlow - Loss[i];
+
+                if (destination == null && NLoss.Value(i) != 1)
+                    throw new Exception("N loss fraction for N flow must be 1 if no destination is specified.");
 
                 source[i] -= nitrogenFlow;
-                destination[i] += nitrogenFlowToDestination;
+                Value[i] = nitrogenFlowToDestination;  // keep value of flow for use in output
+                if (destination != null)
+                    destination[i] += nitrogenFlowToDestination;
             }
             solutes.SetSolute(sourceName, source);
-            solutes.SetSolute(destinationName, destination);
+            if (destination != null)
+                solutes.SetSolute(destinationName, destination);
         }