Allow DCaPST AmbientCO2 value to be read from weather component.

Models/DCaPST/DCaPSTModelNG.cs

@@ -1,3 +1,4 @@
+using Models.Climate;
 using Models.Core;
 using Models.DCAPST.Canopy;
 using Models.DCAPST.Environment;
@@ -169,98 +170,6 @@ public double ElectronTransportLimitedModifier
         /// </summary>
         public static ICropParameterGenerator ParameterGenerator { get; set; } = new CropParameterGenerator();
 
-        /// <summary>
-        /// Creates the DCAPST Model.
-        /// </summary>
-        /// <param name="canopyParameters"></param>
-        /// <param name="pathwayParameters"></param>
-        /// <param name="DOY"></param>
-        /// <param name="latitude"></param>
-        /// <param name="maxT"></param>
-        /// <param name="minT"></param>
-        /// <param name="radn"></param>
-        /// <param name="rpar"></param>
-        /// <param name="biolimit"></param>
-        /// <param name="reduction"></param>
-        /// <returns>The model</returns>
-        public static DCAPSTModel SetUpModel(
-            ICanopyParameters canopyParameters,
-            IPathwayParameters pathwayParameters,
-            int DOY,
-            double latitude,
-            double maxT,
-            double minT,
-            double radn,
-            double rpar,
-            double biolimit,
-            double reduction
-        )
-        {
-            // Model the solar geometry
-            var solarGeometry = new SolarGeometry
-            {
-                Latitude = latitude.ToRadians(),
-                DayOfYear = DOY
-            };
-
-            // Model the solar radiation
-            var solarRadiation = new SolarRadiation(solarGeometry)
-            {
-                Daily = radn,
-                RPAR = rpar
-            };
-
-            // Model the environmental temperature
-            var temperature = new Temperature(solarGeometry)
-            {
-                MaxTemperature = maxT,
-                MinTemperature = minT,
-                AtmosphericPressure = 1.01325
-            };
-
-            // Model the pathways
-            var sunlitAc1 = new AssimilationPathway(canopyParameters, pathwayParameters);
-            var sunlitAc2 = new AssimilationPathway(canopyParameters, pathwayParameters);
-            var sunlitAj = new AssimilationPathway(canopyParameters, pathwayParameters);
-
-            var shadedAc1 = new AssimilationPathway(canopyParameters, pathwayParameters);
-            var shadedAc2 = new AssimilationPathway(canopyParameters, pathwayParameters);
-            var shadedAj = new AssimilationPathway(canopyParameters, pathwayParameters);
-
-            IAssimilation assimilation = canopyParameters.Type switch
-            {
-                CanopyType.C3 => new AssimilationC3(canopyParameters, pathwayParameters),
-                CanopyType.C4 => new AssimilationC4(canopyParameters, pathwayParameters),
-                _ => new AssimilationCCM(canopyParameters, pathwayParameters)
-            };
-
-            var sunlit = new AssimilationArea(sunlitAc1, sunlitAc2, sunlitAj, assimilation);
-            var shaded = new AssimilationArea(shadedAc1, shadedAc2, shadedAj, assimilation);
-            var canopyAttributes = new CanopyAttributes(canopyParameters, pathwayParameters, sunlit, shaded);
-
-            // Model the transpiration
-            var waterInteraction = new WaterInteraction(temperature);
-            var temperatureResponse = new TemperatureResponse(canopyParameters, pathwayParameters);
-            var transpiration = new Transpiration(canopyParameters, pathwayParameters, waterInteraction, temperatureResponse);
-
-            // Model the photosynthesis
-            return new DCAPSTModel(
-                solarGeometry,
-                solarRadiation,
-                temperature,
-                pathwayParameters,
-                canopyAttributes,
-                transpiration
-            )
-            {
-                // From here, we can set additional options,
-                // such as verbosity, BioLimit, Reduction, etc.
-                PrintIntervalValues = false,
-                Biolimit = biolimit,
-                Reduction = reduction,
-            };
-        }
-
         /// <summary>
         /// Reset the default DCaPST parameters according to the type of crop.
         /// </summary>
@@ -278,13 +187,30 @@ public void Reset()
         /// <param name="args"></param>
         [EventSubscribe("StartOfSimulation")]
         private void OnStartOfSimulation(object sender, EventArgs args)
+        {
+            EnsureCropSelected();
+            EnsureAmbientCO2Available();
+        }
+
+        private void EnsureCropSelected()
         {
             if (string.IsNullOrEmpty(CropName))
             {
                 throw new ArgumentNullException(CropName, "No CropName was specified in DCaPST configuration");
             }
         }
 
+        private void EnsureAmbientCO2Available()
+        {
+            if (weather is null ||
+                weather is not Weather weatherModel ||
+                weatherModel.FindChild<CO2Value>() is null
+            )
+            {
+                throw new Exception($"Invalid DCaPST simulation. No {nameof(CO2Value)} model has been configured in {nameof(Weather)} model.");
+            }
+        }
+
         /// <summary>
         /// Called once per day when it's time for dcapst to run.
         /// </summary>
@@ -305,10 +231,7 @@ private void OnDoDCaPST(object sender, EventArgs args)
                 Parameters.Canopy,
                 Parameters.Pathway,
                 clock.Today.DayOfYear,
-                weather.Latitude,
-                weather.MaxT,
-                weather.MinT,
-                weather.Radn,
+                weather,
                 Parameters.Rpar,
                 Biolimit,
                 Reduction
@@ -333,6 +256,86 @@ private void OnDoDCaPST(object sender, EventArgs args)
             }
         }
 
+        /// <summary>
+        /// Creates the DCAPST Model.
+        /// </summary>
+        private static DCAPSTModel SetUpModel(
+            ICanopyParameters canopyParameters,
+            IPathwayParameters pathwayParameters,
+            int DOY,
+            IWeather weather,
+            double rpar,
+            double biolimit,
+            double reduction
+        )
+        {
+            // Model the solar geometry
+            var solarGeometry = new SolarGeometry
+            {
+                Latitude = weather.Latitude.ToRadians(),
+                DayOfYear = DOY
+            };
+
+            // Model the solar radiation
+            var solarRadiation = new SolarRadiation(solarGeometry)
+            {
+                Daily = weather.Radn,
+                RPAR = rpar
+            };
+
+            // Model the environmental temperature
+            var temperature = new Temperature(solarGeometry)
+            {
+                MaxTemperature = weather.MaxT,
+                MinTemperature = weather.MinT,
+                AtmosphericPressure = 1.01325
+            };
+
+            var ambientCO2 = weather.CO2;
+
+            // Model the pathways
+            var sunlitAc1 = new AssimilationPathway(canopyParameters, pathwayParameters, ambientCO2);
+            var sunlitAc2 = new AssimilationPathway(canopyParameters, pathwayParameters, ambientCO2);
+            var sunlitAj = new AssimilationPathway(canopyParameters, pathwayParameters, ambientCO2);
+
+            var shadedAc1 = new AssimilationPathway(canopyParameters, pathwayParameters, ambientCO2);
+            var shadedAc2 = new AssimilationPathway(canopyParameters, pathwayParameters, ambientCO2);
+            var shadedAj = new AssimilationPathway(canopyParameters, pathwayParameters, ambientCO2);
+
+            IAssimilation assimilation = canopyParameters.Type switch
+            {
+                CanopyType.C3 => new AssimilationC3(canopyParameters, pathwayParameters, ambientCO2),
+                CanopyType.C4 => new AssimilationC4(canopyParameters, pathwayParameters, ambientCO2),
+                _ => new AssimilationCCM(canopyParameters, pathwayParameters, ambientCO2)
+            };
+
+            var sunlit = new AssimilationArea(sunlitAc1, sunlitAc2, sunlitAj, assimilation);
+            var shaded = new AssimilationArea(shadedAc1, shadedAc2, shadedAj, assimilation);
+            var canopyAttributes = new CanopyAttributes(canopyParameters, pathwayParameters, sunlit, shaded);
+
+            // Model the transpiration
+            var waterInteraction = new WaterInteraction(temperature);
+            var temperatureResponse = new TemperatureResponse(canopyParameters, pathwayParameters);
+            var transpiration = new Transpiration(canopyParameters, pathwayParameters, waterInteraction, temperatureResponse, ambientCO2);
+
+            // Model the photosynthesis
+            return new DCAPSTModel(
+                solarGeometry,
+                solarRadiation,
+                temperature,
+                pathwayParameters,
+                canopyAttributes,
+                transpiration
+            )
+            {
+                // From here, we can set additional options,
+                // such as verbosity, BioLimit, Reduction, etc.
+                PrintIntervalValues = false,
+                Biolimit = biolimit,
+                Reduction = reduction,
+            };
+        }
+
         /// <summary>Event from sequencer telling us to do our potential growth.</summary>
         /// <param name="sender">The sender.</param>
         /// <param name="e">The <see cref="EventArgs"/> instance containing the event data.</param>
@@ -402,9 +405,9 @@ private void SetUpPlant()
         private ICanopy GetLeaf()
         {
             if (plant == null) return null;
-            ICanopy leafFind = plant.FindChild<ICanopy>("Leaf");
-            if (leafFind == null) throw new ArgumentNullException(nameof(leafFind), "Cannot find leaf configuration");
-            return leafFind;
+            ICanopy find = plant.FindChild<ICanopy>("Leaf");
+            if (find == null) throw new ArgumentNullException(nameof(find), "Cannot find leaf configuration");
+            return find;
         }
 
         private IFunction GetRootShootRatioFunction()
@@ -490,4 +493,4 @@ private IEnumerable<string> GetPlantNames()
             return plants;
         }
     }
-}
+}

Models/DCaPST/Interfaces/Parameters/ICanopyParameters.cs

@@ -31,16 +31,6 @@ public interface ICanopyParameters
         /// </summary>
         CanopyType Type { get; set; }
 
-        ///// <summary>
-        ///// Parameters used in modelling an assimilation pathway
-        ///// </summary>
-        //IPathwayParameters Pathway { get; set; }
-
-        /// <summary>
-        /// Partial pressure of CO2 in air (microbar)
-        /// </summary>
-        double AirCO2 { get; set; }
-
         /// <summary>
         /// Partial pressure of O2 in air (microbar)
         /// </summary>

Models/DCaPST/Models/Assimilation/Assimilation.cs

@@ -21,14 +21,21 @@ public abstract class Assimilation : IAssimilation
         protected IPathwayParameters parameters;
 
         /// <summary>
-        /// 
+        /// The amount of CO2 in the air.
+        /// </summary>
+        protected double ambientCO2;
+
+        /// <summary>
+        /// Constructor.
         /// </summary>
         /// <param name="canopy"></param>
         /// <param name="parameters"></param>
-        public Assimilation(ICanopyParameters canopy, IPathwayParameters parameters)
+        /// <param name="ambientCO2"></param>
+        public Assimilation(ICanopyParameters canopy, IPathwayParameters parameters, double ambientCO2)
         {
             this.canopy = canopy;
             this.parameters = parameters;
+            this.ambientCO2 = ambientCO2;
         }       
 
         /// <summary>

Models/DCaPST/Models/Assimilation/AssimilationPathway.cs

@@ -93,15 +93,22 @@ public class AssimilationPathway
         /// </summary>
         public double Vpr { get; private set; }
 
+        /// <summary>
+        /// The amount of CO2 in the air.
+        /// </summary>
+        private readonly double ambientCO2;
+
         /// <summary>
         /// 
         /// </summary>
         /// <param name="canopy"></param>
         /// <param name="pathway"></param>
-        public AssimilationPathway(ICanopyParameters canopy, IPathwayParameters pathway)
+        /// <param name="ambientCO2"></param>
+        public AssimilationPathway(ICanopyParameters canopy, IPathwayParameters pathway, double ambientCO2)
         {
             Canopy = canopy;
             Pathway = pathway;
+            this.ambientCO2 = ambientCO2;
         }
 
         /// <summary>
@@ -115,7 +122,7 @@ public void SetConditions(double temperature, double lai)
             Gbs = Pathway.BundleSheathConductance * lai;
             Vpr = Pathway.PEPRegeneration * lai;
 
-            MesophyllCO2 = Canopy.AirCO2 * Pathway.IntercellularToAirCO2Ratio;
+            MesophyllCO2 = ambientCO2 * Pathway.IntercellularToAirCO2Ratio;
             ChloroplasticCO2 = 1000;
             ChloroplasticO2 = 210000;
         }

Models/DCaPST/Models/Assimilation/CanopyTypes/AssimilationC3.cs

@@ -13,8 +13,9 @@ public class AssimilationC3 : Assimilation
         /// </summary>
         /// <param name="canopy"></param>
         /// <param name="parameters"></param>
+        /// <param name="ambientCO2"></param>
         /// <returns></returns>
-        public AssimilationC3(ICanopyParameters canopy, IPathwayParameters parameters) : base(canopy, parameters)
+        public AssimilationC3(ICanopyParameters canopy, IPathwayParameters parameters, double ambientCO2) : base(canopy, parameters, ambientCO2)
         { }
 
         /// <inheritdoc/>

Models/DCaPST/Models/Assimilation/CanopyTypes/AssimilationC4.cs

@@ -12,14 +12,15 @@ public class AssimilationC4 : Assimilation
         /// </summary>
         /// <param name="canopy"></param>
         /// <param name="parameters"></param>
+        /// <param name="ambientCO2"></param>
         /// <returns></returns>
-        public AssimilationC4(ICanopyParameters canopy, IPathwayParameters parameters) : base(canopy, parameters)
+        public AssimilationC4(ICanopyParameters canopy, IPathwayParameters parameters, double ambientCO2) : base(canopy, parameters, ambientCO2)
         { }
 
         /// <inheritdoc/>
         public override void UpdateIntercellularCO2(AssimilationPathway pathway, double gt, double waterUseMolsSecond)
         {
-            pathway.IntercellularCO2 = ((gt - waterUseMolsSecond / 2.0) * canopy.AirCO2 - pathway.CO2Rate) / (gt + waterUseMolsSecond / 2.0);
+            pathway.IntercellularCO2 = ((gt - waterUseMolsSecond / 2.0) * ambientCO2 - pathway.CO2Rate) / (gt + waterUseMolsSecond / 2.0);
         }
 
         /// <inheritdoc/>

Models/DCaPST/Models/Assimilation/CanopyTypes/AssimilationCCM.cs

@@ -17,14 +17,15 @@ public class AssimilationCCM : Assimilation
         /// </summary>
         /// <param name="canopy"></param>
         /// <param name="parameters"></param>
+        /// <param name="ambientCO2"></param>
         /// <returns></returns>
-        public AssimilationCCM(ICanopyParameters canopy, IPathwayParameters parameters) : base(canopy, parameters)
+        public AssimilationCCM(ICanopyParameters canopy, IPathwayParameters parameters, double ambientCO2) : base(canopy, parameters, ambientCO2)
         { }
 
         /// <inheritdoc/>
         public override void UpdateIntercellularCO2(AssimilationPathway pathway, double gt, double waterUseMolsSecond)
         {
-            pathway.IntercellularCO2 = ((gt - waterUseMolsSecond / 2.0) * canopy.AirCO2 - pathway.CO2Rate) / (gt + waterUseMolsSecond / 2.0);
+            pathway.IntercellularCO2 = ((gt - waterUseMolsSecond / 2.0) * ambientCO2 - pathway.CO2Rate) / (gt + waterUseMolsSecond / 2.0);
         }
 
         /// <inheritdoc/>