Merge branch 'master' of https://github.com/LANDIS-II-Foundation/Exte…

…nsion-NECN-Succession
LANDIS-II-Foundation · Jan 26, 2022 · ee7fe37 · ee7fe37
2 parents 00a19df + 5cf0d8d
commit ee7fe37
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Showing 22 changed files with 391 additions and 34 deletions.
diff --git a/src/CohortBiomass.cs b/src/CohortBiomass.cs
@@ -372,13 +372,21 @@ private void UpdateDeadBiomass(ICohort cohort, ActiveSite site, double[] totalMo
             //  Add mortality to dead biomass pools.
             //  Coarse root mortality is assumed proportional to aboveground woody mortality
             //    mass is assumed 25% of aboveground wood (White et al. 2000, Niklas & Enquist 2002)
-            if(mortality_wood > 0.0)
+            if(mortality_wood > 0.0 && !SpeciesData.Grass[cohort.Species])
             {
                 ForestFloor.AddWoodLitter(mortality_wood, cohort.Species, site);
                 Roots.AddCoarseRootLitter(mortality_wood, cohort, cohort.Species, site);
             }
 
-            if(mortality_nonwood > 0.0)
+            //  Wood biomass of grass species is transfered to non wood litter. (W.Hotta 2021.12.16)
+            if (mortality_wood > 0.0 && SpeciesData.Grass[cohort.Species])
+            {
+                AvailableN.AddResorbedN(cohort, totalMortality[0], site); //ignoring input from scorching, which is rare, but not resorbed.             
+                ForestFloor.AddResorbedFoliageLitter(mortality_wood, cohort.Species, site);
+                Roots.AddFineRootLitter(mortality_wood, cohort, cohort.Species, site);
+            }
+
+            if (mortality_nonwood > 0.0)
             {
                 AvailableN.AddResorbedN(cohort, totalMortality[1], site); //ignoring input from scorching, which is rare, but not resorbed.             
                 ForestFloor.AddResorbedFoliageLitter(mortality_nonwood, cohort.Species, site);

diff --git a/src/ForestFloor.cs b/src/ForestFloor.cs
@@ -23,15 +23,15 @@ public static void AddWoodLitter(double woodBiomass,
                                     ISpecies   species,
                                     ActiveSite site)
         {
-
-            if(woodBiomass > 0)
-            WoodLayer.PartitionResidue(woodBiomass,  
-                            FunctionalType.Table[SpeciesData.FuncType[species]].WoodDecayRate,
-                            SpeciesData.WoodCN[species], 
-                            SpeciesData.WoodLignin[species], 
-                            LayerName.Wood,
-                            LayerType.Surface,
-                            site);
+            
+            if (woodBiomass > 0)
+                WoodLayer.PartitionResidue(woodBiomass,
+                                FunctionalType.Table[SpeciesData.FuncType[species]].WoodDecayRate,
+                                SpeciesData.WoodCN[species],
+                                SpeciesData.WoodLignin[species],
+                                LayerName.Wood,
+                                LayerType.Surface,
+                                site);
 
         }
 

diff --git a/src/HarvestEffects.cs b/src/HarvestEffects.cs
@@ -223,6 +223,12 @@ public static void ReduceLayers(string prescriptionName, Site site)
             SiteVars.SurfaceDeadWood[site].Nitrogen -= nitrogenLoss;
             SiteVars.SourceSink[site].Nitrogen        += nitrogenLoss;
 
+            // Reduce carbon from CWD
+            // Chihiro; 2020.01.20
+            SiteVars.OriginalDeadWoodC[site][PlugIn.ModelCore.CurrentTime - 1] -= carbonLoss;
+            SiteVars.CurrentDeadWoodC[site][PlugIn.ModelCore.CurrentTime - 1] -= carbonLoss;
+
+
             // Soil Organic Matter (Duff)
 
             carbonLoss = Math.Round(SiteVars.SOM1surface[site].Carbon * som_Multiplier, 2);

diff --git a/src/Layer.cs b/src/Layer.cs
@@ -10,7 +10,8 @@
 namespace Landis.Extension.Succession.NECN
 {
 
-    public enum LayerName {Leaf, FineRoot, Wood, CoarseRoot, Metabolic, Structural, SOM1, SOM2, SOM3, Other};
+    // Chihiro; add grass layer to track dead wood in grass species
+    public enum LayerName { Leaf, FineRoot, Wood, CoarseRoot, Metabolic, Structural, SOM1, SOM2, SOM3, Other };
     public enum LayerType {Surface, Soil, Other} 
 
     /// <summary>
@@ -36,7 +37,46 @@ public Layer(LayerName name, LayerType type)
             this.carbon = 0.0;
             this.nitrogen = 0.0;
 
-            this.decayValue = 0.0;
+            // Initial decay value of Wood is set to mean decay rate of all tree species.
+            // 
+            // 
+            // if this.name is LayerName.Wood:
+            //     double decayvalue = 0.0
+            //     double N_of_species = len(sppnames)
+            //     // Compute mean wood decay rate
+            //     for sppname in tree-sppnames:
+            //         decayrate += decayrate(sppname)
+            //     this.decayVlaue = decayvalue / N_of_species
+            //
+            // elif this.name is LayerName.Grass:
+            //     double decayvalue = 0.0
+            //     double N_of_species = len(sppnames)
+            //     // Compute mean wood decay rate
+            //     for sppname in grass-sppnames:
+            //         decayrate += decayrate(sppname)
+            //     this.decayVlaue = decayvalue / N_of_species
+            //
+            // else:
+            //     this.decayValue = 0.0
+            //
+            if (this.name == LayerName.Wood)
+            {
+                // Compute mean decay value
+                double decayvalue = 0.0;
+                double n_of_tree_species = 0.0;
+                foreach (ISpecies species in PlugIn.ModelCore.Species)
+                {
+                    if (!SpeciesData.Grass[species])
+                        decayvalue += FunctionalType.Table[SpeciesData.FuncType[species]].WoodDecayRate;
+                        n_of_tree_species += 1;
+                }
+                this.decayValue = decayvalue / n_of_tree_species;
+            }
+            else
+            {
+                this.decayValue = 0.0;
+            }
+            //this.decayValue = 0.0;
             this.fractionLignin = 0.0;
 
             this.netMineralization = 0.0;

diff --git a/src/Main.cs b/src/Main.cs
@@ -115,6 +115,11 @@ public static ISiteCohorts Run(ActiveSite site,
 
 
                     WoodLayer.Decompose(site);
+                    if (OtherData.CalibrateMode)
+                    {
+                        PlugIn.ModelCore.UI.WriteLine("currentDeadWoodC:{0},{1},{2}", PlugIn.ModelCore.CurrentTime, Month, string.Join(", ", SiteVars.CurrentDeadWoodC[site]));
+                        PlugIn.ModelCore.UI.WriteLine("SurfaceDeadWoodC: {0},{1},{2}", PlugIn.ModelCore.CurrentTime, Month, SiteVars.SurfaceDeadWood[site].Carbon);
+                    }
                     LitterLayer.Decompose(site);
                     SoilLayer.Decompose(site);