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}, { "$type": "Models.Surface.SurfaceOrganicMatter, Models", "SurfOM": [], "Canopies": [], "InitialResidueName": "wheat_stubble", "InitialResidueType": "wheat", "InitialResidueMass": 500.0, "InitialStandingFraction": 0.0, "InitialCPR": 0.0, "InitialCNR": 100.0, "Name": "SurfaceOrganicMatter", "ResourceName": "SurfaceOrganicMatter", "Children": [], "Enabled": true, "ReadOnly": false }, { "$type": "Models.PMF.Plant, Models", "Name": "Wheat", "ResourceName": "Wheat", "Children": [], "Enabled": true, "ReadOnly": false }, { "$type": "Models.Manager, Models", "CodeArray": [ "using APSIM.Numerics;", "using Models.Climate;", "using System.Linq;", "using System;", "using Models.Core;", "using Models.PMF;", "using Models.Soils;", "using Models.Utilities;", "using APSIM.Shared.Utilities;", "using Models.Interfaces;", "", "namespace Models", "{", " [Serializable]", " public class Script : Model", " {", " [Link] private Clock Clock;", " [Link] private Fertiliser Fertiliser;", " [Link] private Summary Summary;", " [Link] private Soil Soil;", " private Accumulator accumulatedRain;", " [Link]", " private ISoilWater waterBalance;", " ", " [Description(\"Crop\")]", " public IPlant Crop { get; set; }", "", " [Description(\"Start of sowing window (d-mmm)\")]", " public string StartDate { get; set; }", "", " [Description(\"End of sowing window (d-mmm)\")]", " public string EndDate { get; set; }", "", " [Description(\"Minimum extractable soil water for sowing (mm)\")]", " public double MinESW { get; set; }", "", " [Description(\"Accumulated rainfall required for sowing (mm)\")]", " public double MinRain { get; set; }", "", " [Description(\"Duration of rainfall accumulation (d)\")]", " public int RainDays { get; set; }", "", " [Display(Type = DisplayType.CultivarName)]", " [Description(\"Cultivar to be sown\")]", " public string CultivarName { get; set; }", "", " [Description(\"Sowing depth (mm)\")]", " public double SowingDepth { get; set; }", "", " [Description(\"Row spacing (mm)\")]", " public double RowSpacing { get; set; }", "", " [Description(\"Plant population (/m2)\")]", " public double Population { get; set; }", " ", " ", " [EventSubscribe(\"StartOfSimulation\")]", " private void OnSimulationCommencing(object sender, EventArgs e)", " {", " accumulatedRain = new Accumulator(this, \"[Weather].Rain\", RainDays);", " }", "", " [EventSubscribe(\"DoManagement\")]", " private void OnDoManagement(object sender, EventArgs e)", " {", " accumulatedRain.Update();", " ", " if (DateUtilities.WithinDates(StartDate, Clock.Today, EndDate) &&", " !Crop.IsAlive &&", " MathUtilities.Sum(waterBalance.ESW) > MinESW &&", " accumulatedRain.Sum > MinRain)", " {", " Crop.Sow(population: Population, cultivar: CultivarName, depth: SowingDepth, rowSpacing: RowSpacing); ", " }", " }", " }", "}" ], "Parameters": [ { "Key": "Crop", "Value": "[Wheat]" }, { "Key": "StartDate", "Value": "1-may" }, { "Key": "EndDate", "Value": "10-jul" }, { "Key": "MinESW", "Value": "100" }, { "Key": "MinRain", "Value": "25" }, { "Key": "RainDays", "Value": "7" }, { "Key": "CultivarName", "Value": "Hartog" }, { "Key": "SowingDepth", "Value": "30" }, { "Key": "RowSpacing", "Value": "250" }, { "Key": "Population", "Value": "120" } ], "Name": "Sow using a variable rule", "ResourceName": null, "Children": [], "Enabled": true, "ReadOnly": false }, { "$type": "Models.Manager, Models", "CodeArray": [ "using Models.Soils;", "using System;", "using System.Linq;", "using Models.Core;", "using Models.PMF;", "namespace Models", "{", " [Serializable]", " public class Script : Model", " {", " [Link] Clock Clock;", " [Link] Fertiliser Fertiliser;", " ", " [Description(\"Crop to be fertilised\")]", " public IPlant Crop { get; set; }", "", " [Description(\"Type of fertiliser to apply? \")] ", " [Display(Type = DisplayType.FertiliserType)]public string FertiliserType { get; set; }", " ", " [Description(\"Amount of fertiliser to be applied (kg/ha)\")]", " public double Amount { get; set; }", " ", " [EventSubscribe(\"Sowing\")]", " private void OnSowing(object sender, EventArgs e)", " {", " Model crop = sender as Model;", " if (Crop != null && crop.Name.ToLower() == (Crop as IModel).Name.ToLower())", " Fertiliser.Apply(amount: Amount, type: FertiliserType);", " }", " }", "}" ], "Parameters": [ { "Key": "Crop", "Value": "[Wheat]" }, { "Key": "FertiliserType", "Value": "UreaN" }, { "Key": "Amount", "Value": "120" } ], "Name": "Fertilise at sowing", "ResourceName": null, "Children": [], "Enabled": true, "ReadOnly": false }, { "$type": "Models.Manager, Models", "CodeArray": [ "using APSIM.Shared.Utilities;", "using Models.Utilities;", "using Models.Soils;", "using Models.PMF;", "using Models.Core;", "using System;", "using System.Linq;", "", "namespace Models", "{", " [Serializable] ", " public class Script : Model", " {", " [Description(\"Crop\")]", " public IPlant Crop { get; set; }", " ", " [EventSubscribe(\"DoManagement\")]", " private void OnDoManagement(object sender, EventArgs e)", " {", " if (Crop.IsReadyForHarvesting)", " {", " Crop.Harvest();", " Crop.EndCrop();", " }", " }", " }", "}", " " ], "Parameters": [ { "Key": "Crop", "Value": "[Wheat]" } ], "Name": "Harvest", "ResourceName": null, "Children": [], "Enabled": true, "ReadOnly": false }, { "$type": "Models.Manager, Models", "CodeArray": [ "// ============================================================================", "// WheatAmmoniaVolatilisation_v4.cs", "//", "// Two improvements over the previous version, based on what the last real", "// APSIM run revealed:", "//", "// 1. AMMONIUM POOL, NOT UREA POOL, FOR LOSS REMOVAL.", "// Real ammonia volatilisation occurs from the NH4<->NH3 equilibrium", "// AFTER urea hydrolysis, not from urea itself. Previously, our removal", "// logic was competing directly with APSIM's own built-in urea", "// hydrolysis for the same urea pool, which is why most of the applied", "// N \"disappeared\" (into NH4, via hydrolysis) before our script could", "// remove it as a loss. This version still WATCHES the urea pool to", "// detect when fertiliser has been applied (since that is how N", "// physically enters the system), but REMOVES the predicted", "// volatilisation loss from Nutrient.NH4.kgha[0] instead.", "//", "// 2. MULTIPLE INDEPENDENT SEASONAL EVENTS.", "// Previously, a single global loss-target ran for the entire", "// simulation, so a second fertiliser application (e.g. from another", "// Manager rule such as \"Fertilise at sowing\", in a later season) just", "// \"topped up\" the original event's leftover target instead of starting", "// its own fresh one. This version detects a NEW season whenever more", "// than SeasonGapDays have passed since urea was last added; a fresh", "// addition within that gap is treated as a new, independent episode", "// with its own full Model-2 season-total target. Additions that occur", "// close together (e.g. split applications within the same season) are", "// treated as topping up the SAME still-open episode.", "//", "// Output: Desktop\\NH3_Wheat_Output.csv (same file, extra \"Episode\" column).", "// ============================================================================", "", "using System;", "using System.IO;", "using Models.Core;", "using Models.Soils;", "using Models.Soils.Nutrients;", "", "namespace Models", "{", " [Serializable]", " public class Script : Model", " {", " [Link] private Clock Clock = null;", " [Link] private INutrient Nutrient = null;", "", " [Description(\"Tillage system: 0 = conservation, 1 = conventional\")]", " public int TillageSystem { get; set; } = 0;", "", " [Description(\"Basal-nitrogen-timing level, ordinal 1 (80% basal) to 4 (0% basal / fully sensor-guided)\")]", " public int TimingLevel { get; set; } = 1;", "", " [Description(\"Nitrogen source/placement index: 1-5 (S1..S5)\")]", " public int SourceIndex { get; set; } = 1;", "", " [Description(\"Minimum increase in surface urea pool (kg N/ha) to be treated as a fertiliser application\")]", " public double DetectionThreshold { get; set; } = 0.5;", "", " [Description(\"Days of no urea addition after which the NEXT addition is treated as a new season (not a top-up)\")]", " public double SeasonGapDays { get; set; } = 60.0;", "", " [Description(\"Daily loss rate constant, k (per day)\")]", " public double K { get; set; } = 0.20;", "", " private const double Intercept = 27.25;", " private const double bTillage = 0.20;", " private const double bTiming = -5.61;", " private static readonly double[] bSource = { 0.0, 2.59, 3.27, 4.45, 3.52 };", "", " private double previousUreaPool = -1;", " private double cumulativeLoss = 0.0;", " private double seasonTotal = 0.0;", " private DateTime episodeStartDate;", " private DateTime? lastAdditionDate = null;", " private int episodeNumber = 0;", " private bool tracking = false;", " private string outputPath;", "", " [EventSubscribe(\"StartOfSimulation\")]", " private void OnStartOfSimulation(object sender, EventArgs e)", " {", " outputPath = Path.Combine(", " Environment.GetFolderPath(Environment.SpecialFolder.Desktop),", " \"NH3_Wheat_Output.csv\");", "", " File.WriteAllText(outputPath,", " \"Date,UreaPool_kgha,NH4Pool_kgha,LossThisEvent_kgha,CumulativeLoss_kgha,SeasonTotalPrediction_kgha,Episode,NewUreaDetected\" + Environment.NewLine);", "", " previousUreaPool = -1;", " cumulativeLoss = 0.0;", " seasonTotal = 0.0;", " lastAdditionDate = null;", " episodeNumber = 0;", " tracking = false;", " }", "", " [EventSubscribe(\"DoManagement\")]", " private void OnDoManagement(object sender, EventArgs e)", " {", " double currentUrea = Nutrient.Urea.kgha[0];", " bool newUreaDetected = false;", "", " if (previousUreaPool < 0)", " {", " previousUreaPool = currentUrea;", " }", " else", " {", " double increase = currentUrea - previousUreaPool;", "", " if (increase > DetectionThreshold)", " {", " newUreaDetected = true;", "", " bool isNewSeason = (lastAdditionDate == null) ||", " (Clock.Today - lastAdditionDate.Value).TotalDays > SeasonGapDays;", "", " if (isNewSeason)", " {", " // Start a brand-new episode with its own fresh target.", " episodeNumber++;", " int sIdx = Math.Max(1, Math.Min(SourceIndex, 5)) - 1;", " seasonTotal = Intercept + bTillage * TillageSystem + bTiming * TimingLevel + bSource[sIdx];", " episodeStartDate = Clock.Today;", " cumulativeLoss = 0.0;", " tracking = true;", " }", " // else: this is a top-up within the same still-open episode;", " // seasonTotal, episodeStartDate and cumulativeLoss are left as-is.", "", " lastAdditionDate = Clock.Today;", " }", "", " previousUreaPool = currentUrea;", " }", "", " // Remove today's predicted increment of loss from the AMMONIUM pool.", " double lossThisEvent = 0.0;", " if (tracking)", " {", " double daysSince = (Clock.Today - episodeStartDate).TotalDays;", " if (daysSince >= 0)", " {", " double cumulativeTarget = seasonTotal * (1 - Math.Exp(-K * daysSince));", " double increment = Math.Max(0.0, cumulativeTarget - cumulativeLoss);", " double availableNH4 = Nutrient.NH4.kgha[0];", " double removed = Math.Min(increment, availableNH4);", "", " Nutrient.NH4.kgha[0] -= removed;", " cumulativeLoss += removed;", " lossThisEvent = removed;", " }", " }", "", " string line = string.Join(\",\",", " Clock.Today.ToString(\"yyyy-MM-dd\"),", " Nutrient.Urea.kgha[0].ToString(\"F3\"),", " Nutrient.NH4.kgha[0].ToString(\"F3\"),", " lossThisEvent.ToString(\"F3\"),", " cumulativeLoss.ToString(\"F3\"),", " seasonTotal.ToString(\"F3\"),", " episodeNumber.ToString(),", " newUreaDetected ? \"YES\" : \"\");", "", " File.AppendAllText(outputPath, line + Environment.NewLine);", " }", " }", "}", "" ], "Parameters": [ { "Key": "TillageSystem", "Value": "0" }, { "Key": "TimingLevel", "Value": "1" }, { "Key": "SourceIndex", "Value": "1" }, { "Key": "DetectionThreshold", "Value": "0.5" }, { "Key": "SeasonGapDays", "Value": "60" }, { "Key": "K", "Value": "0.2" } ], "Name": "Manager", "ResourceName": null, "Children": [], "Enabled": true, "ReadOnly": false }, { "$type": "Models.Manager, Models", "CodeArray": [ "// ============================================================================", "// RiceAmmoniaVolatilisation_v4.cs", "// APSIM Next Generation Manager script", "//", "// Implements Model 1 from the manuscript (Section 3.1):", "// NH3-N loss (kg/ha, season total) = 7.625 + 0.0483*N_rate + 0.603*T_level", "// (R2 = 0.943, RMSE = 0.69 kg/ha, n = 16)", "//", "// This version incorporates every fix discovered while debugging the wheat", "// (Model 2) coupling, applied from the start rather than iteratively:", "//", "// 1. Detects fertiliser application by watching the UREA pool for an", "// upward jump - NOT by subscribing to a \"FertiliserApplied\" event", "// (that event's argument-type name varies across APSIM versions and", "// caused repeated compile errors during the wheat testing).", "// 2. Removes the predicted volatilisation loss from the AMMONIUM pool", "// ([Nutrient].NH4.kgha[0]), not the urea pool - because our loss", "// logic would otherwise compete with APSIM's own built-in urea", "// hydrolysis for the same finite urea pool and under-count the loss", "// (this is exactly what happened on the first wheat test).", "// 3. Supports MULTIPLE independent fertiliser episodes within one run", "// (e.g. repeated applications across seasons), using a time-gap rule:", "// a new urea addition starts a fresh loss-target episode only if more", "// than SeasonGapDays have passed since urea was last added; additions", "// closer together than that are treated as topping up the same", "// still-open episode.", "// 4. Writes output directly to a CSV file on the Desktop using", "// System.IO, bypassing APSIM's Report component entirely - this", "// avoided an unresolved \"unknown model or property\" limitation that", "// affected custom Manager-script properties in Report on the tested", "// APSIM build.", "//", "// IMPORTANT CAVEAT (carried over from the manuscript, Section 6.2): the", "// TemperatureLevel input below is the ORDINAL 1-4 temperature-gradient-", "// tunnel category from the source thesis, not a continuous, real-world", "// temperature. Ideally, replace this with a re-fitted, continuous-", "// temperature version of Model 1 once you have simulated", "// [ISoilTemperature] (or canopy/air temperature) output from a real run,", "// by regressing the original 16 observed values against that continuous", "// variable instead of the ordinal category.", "//", "// HOW TO USE:", "// 1. Add a Manager node under your rice Zone/Field (right-click Zone ->", "// Add Model -> Manager).", "// 2. Paste this entire file (from \"using System;\" onward) into its", "// Script tab, replacing the default template.", "// 3. Set NRate and TemperatureLevel in the Properties panel to match the", "// scenario you want to simulate.", "// 4. No Report node changes are needed - this script does not rely on", "// Report at all. You can safely ignore or delete any Report node", "// variable list that references this Manager's properties.", "// 5. Run. Check Desktop\\NH3_Rice_Output.csv afterward.", "// ============================================================================", "", "using System;", "using System.IO;", "using Models.Core;", "using Models.Soils;", "using Models.Soils.Nutrients;", "", "namespace Models", "{", " [Serializable]", " public class Script : Model", " {", " [Link] private Clock Clock = null;", " [Link] private INutrient Nutrient = null;", "", " // ---------------- User-set scenario inputs ----------------", " [Description(\"Nitrogen rate applied (kg N/ha)\")]", " public double NRate { get; set; } = 120.0;", "", " [Description(\"Ordinal temperature level, 1 (ambient) to 4 (most elevated) - see header caveat\")]", " public int TemperatureLevel { get; set; } = 1;", "", " [Description(\"Minimum increase in surface urea pool (kg N/ha) to be treated as a new fertiliser application\")]", " public double DetectionThreshold { get; set; } = 0.5;", "", " [Description(\"Days of no urea addition after which the NEXT addition starts a new episode rather than topping up the current one\")]", " public double SeasonGapDays { get; set; } = 60.0;", "", " // ---------------- Internal state ----------------", " private double previousUreaPool = -1;", " private double cumulativeLoss = 0.0;", " private double seasonTotal = 0.0;", " private DateTime episodeStartDate;", " private DateTime? lastAdditionDate = null;", " private int episodeNumber = 0;", " private bool tracking = false;", " private string outputPath;", "", " [EventSubscribe(\"StartOfSimulation\")]", " private void OnStartOfSimulation(object sender, EventArgs e)", " {", " outputPath = Path.Combine(", " Environment.GetFolderPath(Environment.SpecialFolder.Desktop),", " \"NH3_Rice_Output.csv\");", "", " File.WriteAllText(outputPath,", " \"Date,UreaPool_kgha,NH4Pool_kgha,LossThisEvent_kgha,CumulativeLoss_kgha,SeasonTotalPrediction_kgha,Episode,NewUreaDetected\" + Environment.NewLine);", "", " previousUreaPool = -1;", " cumulativeLoss = 0.0;", " seasonTotal = 0.0;", " lastAdditionDate = null;", " episodeNumber = 0;", " tracking = false;", " }", "", " [EventSubscribe(\"DoManagement\")]", " private void OnDoManagement(object sender, EventArgs e)", " {", " double currentUrea = Nutrient.Urea.kgha[0];", " bool newUreaDetected = false;", "", " if (previousUreaPool < 0)", " {", " previousUreaPool = currentUrea;", " }", " else", " {", " double increase = currentUrea - previousUreaPool;", "", " if (increase > DetectionThreshold)", " {", " newUreaDetected = true;", "", " bool isNewSeason = (lastAdditionDate == null) ||", " (Clock.Today - lastAdditionDate.Value).TotalDays > SeasonGapDays;", "", " if (isNewSeason)", " {", " episodeNumber++;", " // Model 1: Lmax = 7.625 + 0.0483*N + 0.603*T (Section 3.1)", " seasonTotal = 7.625 + 0.0483 * NRate + 0.603 * TemperatureLevel;", " episodeStartDate = Clock.Today;", " cumulativeLoss = 0.0;", " tracking = true;", " }", " // else: top-up within the same still-open episode; seasonTotal,", " // episodeStartDate and cumulativeLoss are left unchanged.", "", " lastAdditionDate = Clock.Today;", " }", "", " previousUreaPool = currentUrea;", " }", "", " // Remove today's predicted increment of loss from the ammonium pool.", " double lossThisEvent = 0.0;", " if (tracking)", " {", " double daysSince = (Clock.Today - episodeStartDate).TotalDays;", " if (daysSince >= 0)", " {", " // Same exponential-rise-to-maximum shape as the wheat script,", " // with the rate constant scaled by temperature level exactly as", " // in the manuscript's Section 7 (rice) calibration:", " // k0 = 0.230/day at T1, k = k0*(1+alpha*(T-1)), alpha = 0.143", " double k0 = 0.230;", " double alpha = 0.143;", " double k = k0 * (1 + alpha * (TemperatureLevel - 1));", "", " double cumulativeTarget = seasonTotal * (1 - Math.Exp(-k * daysSince));", " double increment = Math.Max(0.0, cumulativeTarget - cumulativeLoss);", " double availableNH4 = Nutrient.NH4.kgha[0];", " double removed = Math.Min(increment, availableNH4);", "", " Nutrient.NH4.kgha[0] -= removed;", " cumulativeLoss += removed;", " lossThisEvent = removed;", " }", " }", "", " string line = string.Join(\",\",", " Clock.Today.ToString(\"yyyy-MM-dd\"),", " Nutrient.Urea.kgha[0].ToString(\"F3\"),", " Nutrient.NH4.kgha[0].ToString(\"F3\"),", " lossThisEvent.ToString(\"F3\"),", " cumulativeLoss.ToString(\"F3\"),", " seasonTotal.ToString(\"F3\"),", " episodeNumber.ToString(),", " newUreaDetected ? \"YES\" : \"\");", "", " File.AppendAllText(outputPath, line + Environment.NewLine);", " }", " }", "}" ], "Parameters": [ { "Key": "NRate", "Value": "120" }, { "Key": "TemperatureLevel", "Value": "1" }, { "Key": "DetectionThreshold", "Value": "0.5" }, { "Key": "SeasonGapDays", "Value": "60" } ], "Name": "Manager1", "ResourceName": null, "Children": [], "Enabled": true, "ReadOnly": false } ], "Enabled": true, "ReadOnly": false }, { "$type": "Models.Graph, Models", "Caption": null, "Axis": [ { "$type": "APSIM.Shared.Graphing.Axis, APSIM.Shared", "Title": "Date", "Position": 3, "Inverted": false, "CrossesAtZero": false, "LabelOnOneLine": false, "Minimum": null, "Maximum": null, "Interval": null }, { "$type": "APSIM.Shared.Graphing.Axis, APSIM.Shared", "Title": null, "Position": 0, "Inverted": false, "CrossesAtZero": false, "LabelOnOneLine": false, "Minimum": null, "Maximum": null, "Interval": null } ], "LegendPosition": 0, "LegendOrientation": 0, "AnnotationLocation": 0, "DisabledSeries": [], "LegendOutsideGraph": false, "Name": "Graph", "ResourceName": null, "Children": [ { "$type": "Models.Series, Models", "Type": 1, "XAxis": 3, "YAxis": 0, "ColourArgb": -16777216, "FactorToVaryColours": null, "FactorToVaryMarkers": null, "FactorToVaryLines": null, "Marker": 0, "MarkerSize": 0, "Line": 0, "LineThickness": 0, "TableName": "Report", "XFieldName": "Clock.Today", "YFieldName": "Wheat.Grain.Total.Wt", "X2FieldName": null, "Y2FieldName": null, "ShowInLegend": false, "IncludeSeriesNameInLegend": false, "Cumulative": false, "CumulativeX": false, "Filter": null, "Name": "Series", "ResourceName": null, "Children": [], "Enabled": true, "ReadOnly": false } ], "Enabled": true, "ReadOnly": false } ], "Enabled": true, "ReadOnly": false }, { "$type": "Models.Storage.DataStore, Models", "CustomFileName": null, "Name": "DataStore", "ResourceName": null, "Children": [], "Enabled": true, "ReadOnly": false } ], "Enabled": true, "ReadOnly": false }