Merge pull request #3250 from hut104/SoilNutrientIncrementalMerge

First batch of files to merge for Soil Nutrient

APSIM.bib

@@ -16856,3 +16856,102 @@ @article{rubilar2018advances
   year={2018},
   publisher={Springer}
 }
+
+@article{Young2009_HudsonCarbon,
+Author = {Young, R. R. and Wilson, B. and Harden, S. and Bernardi, A.},
+Title = {{Accumulation of soil carbon under zero tillage cropping and perennial
+   vegetation on the Liverpool Plains, eastern Australia}},
+Journal = {{AUSTRALIAN JOURNAL OF SOIL RESEARCH}},
+Year = {{2009}},
+Volume = {{47}},
+Number = {{3}},
+Pages = {{273-285}},
+Publisher = {{CSIRO PUBLISHING}},
+Address = {{150 OXFORD ST, PO BOX 1139, COLLINGWOOD, VICTORIA 3066, AUSTRALIA}},
+Type = {{Article}},
+Language = {{English}},
+Affiliation = {{Young, RR (Reprint Author), Tamworth Agr Inst, NSW Dept Primary Ind, 4 Marsden Pk Rd, Calala, NSW 2340, Australia.
+   Young, R. R.; Harden, S.; Bernardi, A., Tamworth Agr Inst, NSW Dept Primary Ind, Calala, NSW 2340, Australia.
+   Wilson, B., Univ New England, NSW Dept Environm \& Climate Change, Armidale, NSW 2351, Australia.
+   Wilson, B., Univ New England, Sch Environm \& Rural Sci, Armidale, NSW 2351, Australia.}},
+DOI = {{10.1071/SR08104}},
+ISSN = {{0004-9573}},
+Keywords-Plus = {{NEW-SOUTH-WALES; ORGANIC-CARBON; NO-TILL; CONSERVATION TILLAGE;
+   SUBTROPICAL ACRISOL; STUBBLE MANAGEMENT; SEQUESTRATION; NITROGEN;
+   SYSTEMS; MATTER}},
+Research-Areas = {{Agriculture}},
+Web-of-Science-Categories  = {{Soil Science}},
+Author-Email = {{[email protected]}},
+ResearcherID-Numbers = {{Wilson, Brian/G-4996-2011
+   Management, Ecosystem/C-2259-2011
+   }},
+Journal-ISO = {{Aust. J. Soil Res.}},
+}
+
+@article{Rolston1984,
+   author = {Rolston, D.E.; Rao, P.S.C.; Davidson, J.M.; Jessup, R.E.},
+   title = {Simulation of denitrification losses of Nitrate fertiliser applied to uncropped, cropped, and manure-amended field plots},
+   journal = {Soil Science},
+   volume = {137},
+   number = {270-278},
+   year = {1984},
+   type = {Journal Article}
+}
+@article{Reddy1980,
+   author = {Reddy, K.R.; Khaleel, R.; Overcash, M.R.},
+   title = {Carbon transformations in land areas receiving organic wastes in relation to nonpoint source pollution: A conceptual model},
+   journal = {Journal of Environmental Quality},
+   volume = {9},
+   number = {434-442},
+   year = {1980},
+   type = {Journal Article}
+}
+
+@article{Schultz1995,
+   author = {Schultz, J.E.},
+   title = {Crop production in a rotation trial at Tarlee, South Australia},
+   journal = {Australian Journal of Experimental Agriculture},
+   volume = {35},
+   number = {865-876},
+   year = {1995},
+   type = {Journal Article}
+}
+
+@article{Skjemstad2004,
+   author = {Skjemstad, J.O., Spouncer, L.R., Cowie, B., Swift, R.S.},
+   title = {Calibration of the Rothamsted organic carbon turnover model (RothC ver.26.3), using measurable soil organic carbon pools},
+   journal = {Australian Journal of Soil Research},
+   volume = {42},
+   number = {79-88},
+   year = {2004},
+   type = {Journal Article}
+}
+
+@article{PARTON1998,
+title = "DAYCENT and its land surface submodel: description and testing",
+journal = "Global and Planetary Change",
+volume = "19",
+number = "1",
+pages = "35 - 48",
+year = "1998",
+issn = "0921-8181",
+doi = "https://doi.org/10.1016/S0921-8181(98)00040-X",
+url = "http://www.sciencedirect.com/science/article/pii/S092181819800040X",
+author = "William J. Parton and Melannie Hartman and Dennis Ojima and David Schimel",
+keywords = "soil water, ecological models, soil temperature, latent heat flux, DAYCENT, water flow, trace gas flux"
+}
+
+@article{THORBURN2010,
+title = "Using the APSIM model to estimate nitrous oxide emissions from diverse Australian sugarcane production systems",
+journal = "Agriculture, Ecosystems & Environment",
+volume = "136",
+number = "3",
+pages = "343 - 350",
+year = "2010",
+note = "Estimation of nitrous oxide emission from ecosystems and its mitigation technologies",
+issn = "0167-8809",
+doi = "https://doi.org/10.1016/j.agee.2009.12.014",
+url = "http://www.sciencedirect.com/science/article/pii/S0167880909003740",
+author = "P.J. Thorburn and J.S. Biggs and K. Collins and M.E. Probert",
+keywords = "Crop residues, Denitrification, Nitrification, Greenhouse gas, Nitrogen fertiliser, Irrigation"
+}

ApsimNG/Views/DirectedGraphView.cs

@@ -13,35 +13,70 @@ namespace UserInterface.Views
     using System.Collections.Generic;
     using System.Drawing;
     using System.IO;
+    using System.Linq;
 
     /// <summary>
     /// A view that contains a graph and click zones for the user to allow
     /// editing various parts of the graph.
     /// </summary>
     public class DirectedGraphView : ViewBase
     {
+        /// <summary>
+        /// The currently selected node/object.
+        /// </summary>
         private DGObject selectedObject;
+
+        /// <summary>
+        /// Keeps track of whether the mouse button is currently down.
+        /// </summary>
         private bool mouseDown = false;
+
+        /// <summary>
+        /// Drawing area upon which the graph is rendered.
+        /// </summary>
+        private DrawingArea drawable;
+
+        /// <summary>
+        /// Position of the last moved node.
+        /// </summary>
         private PointD lastPos;
-        private List<DGNode> Nodes = new List<DGNode>();
-        private List<DGArc> Arcs = new List<DGArc>();
+
+        /// <summary>
+        /// List of nodes. These are currently circles with text in them.
+        /// </summary>
+        private List<DGNode> nodes = new List<DGNode>();
+
+        /// <summary>
+        /// List of arcs which connect the nodes.
+        /// </summary>
+        private List<DGArc> arcs = new List<DGArc>();
 
         /// <summary>Initializes a new instance of the <see cref="DirectedGraphView" /> class.</summary>
         public DirectedGraphView(ViewBase owner = null) : base(owner)
         {
-            DrawingArea drawingArea = new DrawingArea();
-
-            drawingArea.AddEvents(
+            drawable = new DrawingArea();
+            
+            drawable.AddEvents(
             (int)Gdk.EventMask.PointerMotionMask
             | (int)Gdk.EventMask.ButtonPressMask
             | (int)Gdk.EventMask.ButtonReleaseMask);
 
-            drawingArea.ExposeEvent += OnDrawingAreaExpose;
-            drawingArea.ButtonPressEvent += OnMouseButtonPress;
-            drawingArea.ButtonReleaseEvent += OnMouseButtonRelease; ;
-            drawingArea.MotionNotifyEvent += OnMouseMove; ;
-            _mainWidget = drawingArea;
-            drawingArea.ModifyBg(StateType.Normal, new Gdk.Color(255, 255, 255));
+            drawable.ExposeEvent += OnDrawingAreaExpose;
+            drawable.ButtonPressEvent += OnMouseButtonPress;
+            drawable.ButtonReleaseEvent += OnMouseButtonRelease;
+            drawable.MotionNotifyEvent += OnMouseMove;
+
+            ScrolledWindow scroller = new ScrolledWindow(new Adjustment(0, 0, 100, 1, 1, 1), new Adjustment(0, 0, 100, 1, 1, 1))
+            {
+                HscrollbarPolicy = PolicyType.Always,
+                VscrollbarPolicy = PolicyType.Always
+            };
+
+            scroller.AddWithViewport(drawable);
+
+            _mainWidget = scroller;
+            drawable.ModifyBg(StateType.Normal, new Gdk.Color(255, 255, 255));
+            drawable.Realized += OnRealized;
         }
 
         /// <summary>The description (nodes & arcs) of the directed graph.</summary>
@@ -50,14 +85,14 @@ public DirectedGraph DirectedGraph
             get
             {
                 DirectedGraph graph = new DirectedGraph();
-                Nodes.ForEach(node => graph.Nodes.Add(node.ToNode()));
-                Arcs.ForEach(arc => graph.Arcs.Add(arc.ToArc()));
+                nodes.ForEach(node => graph.Nodes.Add(node.ToNode()));
+                arcs.ForEach(arc => graph.Arcs.Add(arc.ToArc()));
                 return graph;
             }
             set
             {
-                value.Nodes.ForEach(node => Nodes.Add(new DGNode(node)));
-                value.Arcs.ForEach(arc => Arcs.Add(new DGArc(arc, Nodes)));
+                value.Nodes.ForEach(node => nodes.Add(new DGNode(node)));
+                value.Arcs.ForEach(arc => arcs.Add(new DGArc(arc, nodes)));
             }
         }
 
@@ -67,7 +102,7 @@ public System.Drawing.Image Export()
             int width;
             int height;
             MainWidget.GdkWindow.GetSize(out width, out height);
-            Gdk.Pixbuf screenshot = Gdk.Pixbuf.FromDrawable(MainWidget.GdkWindow, MainWidget.Colormap, 0, 0, 0, 0, width, height);
+            Gdk.Pixbuf screenshot = Gdk.Pixbuf.FromDrawable(drawable.GdkWindow, drawable.Colormap, 0, 0, 0, 0, width - 20, height - 20);
             byte[] buffer = screenshot.SaveToBuffer("png");
             MemoryStream stream = new MemoryStream(buffer);
             System.Drawing.Bitmap bitmap = new Bitmap(stream);
@@ -81,9 +116,9 @@ private void OnDrawingAreaExpose(object sender, ExposeEventArgs args)
 
             Cairo.Context context = Gdk.CairoHelper.Create(area.GdkWindow);
 
-            foreach (DGArc tmpArc in Arcs)
+            foreach (DGArc tmpArc in arcs)
                 tmpArc.Paint(context);
-            foreach (DGNode tmpNode in Nodes)
+            foreach (DGNode tmpNode in nodes)
                 tmpNode.Paint(context);
 
             ((IDisposable)context.Target).Dispose();
@@ -101,11 +136,11 @@ private void OnMouseButtonPress(object o, ButtonPressEventArgs args)
                 selectedObject.Selected = false;
 
             // Look through nodes for the click point
-            selectedObject = Nodes.FindLast(node => node.HitTest(clickPoint));
+            selectedObject = nodes.FindLast(node => node.HitTest(clickPoint));
 
             // If not found, look through arcs for the click point
             if (selectedObject == null)
-                selectedObject = Arcs.FindLast(arc => arc.HitTest(clickPoint));
+                selectedObject = arcs.FindLast(arc => arc.HitTest(clickPoint));
 
             // If found object, select it.
             if (selectedObject != null)
@@ -140,8 +175,35 @@ private void OnMouseMove(object o, MotionNotifyEventArgs args)
         private void OnMouseButtonRelease(object o, ButtonReleaseEventArgs args)
         {
             mouseDown = false;
+            CheckSizing();
         }
 
-
+        /// <summary>
+        /// Drawing area has been rendered - make sure it has enough space.
+        /// </summary>
+        /// <param name="sender">Sender object.</param>
+        /// <param name="args">Event arguments.</param>
+        private void OnRealized(object sender, EventArgs args)
+        {
+            CheckSizing();
+        }
+
+        /// <summary>
+        /// If the right-most node is out of the drawing area, doubles the width.
+        /// If the bottom-most node is out of the drawing area, doubles the height;
+        /// </summary>
+        private void CheckSizing()
+        {
+            if (nodes != null && nodes.Any())
+            {
+                DGNode rightMostNode = nodes.Aggregate((node1, node2) => node1.Location.X > node2.Location.X ? node1 : node2);
+                DGNode bottomMostNode = nodes.Aggregate((node1, node2) => node1.Location.Y > node2.Location.Y ? node1 : node2);
+                if (rightMostNode.Location.X + rightMostNode.Width >= drawable.Allocation.Width)
+                    drawable.WidthRequest = 2 * drawable.Allocation.Width;
+                // I Assume that the nodes are circles such that width = height.
+                if (bottomMostNode.Location.Y + bottomMostNode.Width >= drawable.Allocation.Height)
+                    drawable.HeightRequest = 2 * drawable.Allocation.Height;
+            }
+        }
     }
 }

Models/Core/Attributes/LinkAttribute.cs

@@ -57,6 +57,12 @@ public class LinkByPathAttribute : LinkAttribute
     {
         /// <summary>The path to use to find a link match.</summary>
         public string Path { get; set; }
+
+        /// <summary>Should the fields name be used when matching?</summary>
+        public override bool UseNameToMatch(IVariable field)
+        {
+            return false;
+        }
     }
 
     /// <summary>

Models/Functions/ExpressionFunction.cs

@@ -168,9 +168,18 @@ public void Document(List<AutoDocumentation.ITag> tags, int headingLevel, int in
             {
                 // add a heading.
                 tags.Add(new AutoDocumentation.Heading(Name, headingLevel));
+                // write memos.
+                foreach (IModel memo in Apsim.Children(this, typeof(Memo)))
+                    AutoDocumentation.DocumentModel(memo, tags, headingLevel + 1, indent);
+
+
                 string st = Expression.Replace(".Value()", "");
                 st = st.Replace("*", "x");
                 tags.Add(new AutoDocumentation.Paragraph(Name + " = " + st, indent));
+
+                foreach (IModel child in Apsim.Children(this, typeof(IFunction)))
+                    AutoDocumentation.DocumentModel(child, tags, headingLevel + 1, indent + 1);
+
             }
         }
 

Models/Functions/StringComparisonFunction.cs

@@ -0,0 +1,83 @@
+using System;
+using System.Collections.Generic;
+using Models.Core;
+
+
+namespace Models.Functions
+{
+    /// <summary>Value returned is determined according to given criteria</summary>
+    [Serializable]
+    [Description("Tests if value of a string property is equal to a given value and returns a value depending on the result.")]
+    [ViewName("UserInterface.Views.GridView")]
+    [PresenterName("UserInterface.Presenters.PropertyPresenter")]
+    public class StringComparisonFunction : Model, IFunction, ICustomDocumentation
+    {
+
+        /// <summary>The propertyname</summary>
+        [Description("Name of string property to compare")]
+        public string PropertyName { get; set; }
+
+        /// <summary>The string value</summary>
+        [Description("Text string for comparison to the property value")]
+        public string StringValue { get; set; }
+
+        /// <summary>The True Value</summary>
+        [Link]
+        IFunction TrueValue = null;
+
+        /// <summary>The False Value</summary>
+        [Link]
+        IFunction FalseValue = null;
+
+        [Link]
+        private ILocator locator = null;
+
+        /// <summary>Gets the value.</summary>
+        /// <value>The value.</value>
+        public double Value(int arrayIndex = -1)
+        {
+            object s = locator.Get(PropertyName);
+
+            string PropertyString;
+            if (s == null)
+                PropertyString = "";
+            else if (s is Array)
+                PropertyString = (string)(s as Array).GetValue(arrayIndex);
+            else if (s is IFunction)
+                PropertyString = (s as IFunction).Value(arrayIndex).ToString();
+            else
+                PropertyString = (string)s;
+
+            bool stringCompareTrue = PropertyString.Equals(StringValue, StringComparison.CurrentCultureIgnoreCase);
+
+            if (stringCompareTrue)
+                return TrueValue.Value(arrayIndex);
+            else
+                return FalseValue.Value(arrayIndex);
+        }
+
+        /// <summary>Writes documentation for this function by adding to the list of documentation tags.</summary>
+        /// <param name="tags">The list of tags to add to.</param>
+        /// <param name="headingLevel">The level (e.g. H2) of the headings.</param>
+        /// <param name="indent">The level of indentation 1, 2, 3 etc.</param>
+        public void Document(List<AutoDocumentation.ITag> tags, int headingLevel, int indent)
+        {
+            if (IncludeInDocumentation)
+            {
+
+                // add a heading.
+                tags.Add(new AutoDocumentation.Heading(Name, headingLevel));
+
+                // write memos.
+                foreach (IModel memo in Apsim.Children(this, typeof(Memo)))
+                    AutoDocumentation.DocumentModel(memo, tags, headingLevel + 1, indent);
+
+                tags.Add(new AutoDocumentation.Paragraph("If " + PropertyName + " = " + StringValue + " Then", indent));
+                AutoDocumentation.DocumentModel(TrueValue as IModel,tags, headingLevel+1, indent+1);
+
+                tags.Add(new AutoDocumentation.Paragraph("Else", indent));
+                AutoDocumentation.DocumentModel(FalseValue as IModel, tags, headingLevel+1, indent+1);
+            }
+        }
+    }
+}