set gsMethod and phsOption via input_data.xlsx

EcoExtreML · Oct 4, 2024 · c477a40 · c477a40
1 parent d69c75a
commit c477a40
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Showing 2 changed files with 34 additions and 17 deletions.
diff --git a/src/STEMMUS_SCOPE.m b/src/STEMMUS_SCOPE.m
@@ -40,9 +40,6 @@
     % Read the configPath file. Due to using MATLAB compiler, we cannot use run(CFG)
     disp (['Reading config from ', CFG]);
     [InputPath, OutputPath, InitialConditionPath] = io.read_config(CFG);
-    gsOption = 'Medlyn'; % 1 for BallBerry's method; 2 for Medlyn's method
-    phsOption = 2; % 1 for CLM5, 2 for ED2, 3 for PHS
-
 
     % Prepare forcing and soil data
     [SiteProperties, SoilProperties, TimeProperties] = io.prepareInputData(InputPath);
@@ -88,12 +85,11 @@
     RWUs = [];
     RWUg = [];
 
-    %% Set senarios
-    [gsMethod, phwsfMethod] = setScenario(gsOption, phsOption);
+
 
     %% 1. define Constants
     Constants = io.define_constants();
-    ParaPlant = io.define_plant_constants(SiteProperties, phwsfMethod);
+
 
     RTB = 1000; % initial root total biomass (g m-2)
     if strcmp(SiteProperties.sitename, 'CH-HTC')
@@ -103,10 +99,6 @@
     % [Rl, Ztot] = Initial_root_biomass(RTB, ModelSettings.DeltZ_R, ModelSettings.rroot, ModelSettings.ML, SiteProperties.landcoverClass(1));
     numSoilLayer = ModelSettings.ML;
     soilThickness = ModelSettings.DeltZ_R';
-    [RootProperties,soilDepth] = calRootProperties(SiteProperties, ParaPlant, numSoilLayer, soilThickness, RTB);
-    Rl = RootProperties.lengthDensity;
-    Ztot = soilDepth;
-    soilDepthB2T = flipud(soilDepth);
 
 
     %% 2. simulation options
@@ -116,6 +108,20 @@
     parameter_file = {'input_data.xlsx'};
     options = io.readStructFromExcel([path_input char(parameter_file)], 'options', 2, 1);
 
+    % Set senarios
+    gsOption = options.gsOption;
+    phsOption = options.plantHydraulics;
+    [gsMethod, phwsfMethod] = setScenario(gsOption, phsOption);
+
+    % define parameters for plant hydraulics module
+    ParaPlant = io.define_plant_constants(SiteProperties, phwsfMethod);
+
+    % calculate root parameters
+    [RootProperties,soilDepth] = calRootProperties(SiteProperties, ParaPlant, numSoilLayer, soilThickness, RTB);
+    Rl = RootProperties.lengthDensity;
+    Ztot = soilDepth;
+    soilDepthB2T = flipud(soilDepth);
+
     if options.simulation > 2 || options.simulation < 0
         fprintf('\n simulation option should be between 0 and 2 \r');
         return

diff --git a/src/setScenario.m b/src/setScenario.m
@@ -4,11 +4,12 @@
     hydraulic pathway option.
 
     input:
-        gsOption: a string indicate which stomatal conductance will be used
+        gsOption: a number indicate the stomatal conductance approach: 
+                  1 for BallBerry, ref[1]
+                  2 for Medlyn, ref[2]
         phsOption: a number indicate whether use plant hydraulic pathway
 
     output:
-        biochemical: a string, indicate which function will be used
         gsMethod: a number indicate the stomatal conductance scheme:
                   1 for BallBerry
                   2 for Medlyn
@@ -17,15 +18,25 @@
                    2 for ED2,
                    3 for PHS
                    
+    references:
+        [1] Ball, J. T., et al. (1987). A Model Predicting Stomatal Conductance 
+            and its Contribution to the Control of Photosynthesis under 
+            Different Environmental Conditions, Springer, Dordrecht.
+
+        [2] Medlyn, B. E., et al. (2011). "Reconciling the optimal and empirical 
+            approaches to modelling stomatal conductance." 
+            Global Change Biology 17(6): 2134-2144.
+
 %}
 
     %% Set scenario
-    %biochemical = @biochemical;
-    if strcmp(gsOption, 'BallBerry')
-        gsMethod = 1;
-    elseif strcmp(gsOption, 'Medlyn')
-        gsMethod = 2;
+    switch gsOption
+        case 1
+            gsMethod = 1; % BallBerry stomatal conductance
+        case 2
+            gsMethod = 2; % Medlyn stomatal conductance
     end
+
     %% PHS setting
     if phsOption      % if phsOption is true, PHS open. Set plant water stress method.
         switch phsOption