Clean up of BMI code, add save/load run mode.

src/STEMMUS_SCOPE.m

@@ -283,21 +283,20 @@
     P_gg = InitialValues.P_gg;  % will be updated!
     P_g = InitialValues.P_g;  % will be updated!
 
-    disp('Finished initialization!');
-end
-
-% Save the workspace after initialization if running in the BMI-mode.
-if strcmp(runMode, 'initialize')
-    save([Output_dir, 'STEMMUS_SCOPE_state.mat'], "-v7.3", "-nocompression");
+    %% soil layer information
+    SoilLayer.thickness = ModelSettings.DeltZ_R;
+    SoilLayer.depth = Ztot';  % used in Initial_root_biomass
+
+    % NOTE: workspace will be saved, this code block is after the update step.
+    % (this is to not repeat the save-workspace code).
+    disp('Finished model initialization');
 end
 
+% If the runMode is update, retrieve the (possibly) updated state.
+% The state can be modified by the STEMMUS_SCOPE BMI. See PyStemmusScope.
 if strcmp(runMode, 'update')
-    [InputPath, OutputPath, InitialConditionPath] = io.read_config(CFG);
-    actualRunMode = runMode; % Will be overridden by load...
     load([OutputPath, 'STEMMUS_SCOPE_state.mat']); % Load the workspace to be able to (continue) running the model
-    runMode = actualRunMode;
-    clear actualRunMode % clear actual run mode so it won't be in the workspace on saving.
-    if KT >= TimeProperties.Dur_tot
+    if KT + 1 >= TimeProperties.Dur_tot
         runMode = 'finished';
         disp("Finished running the model. Updating won't do anything!");
     else
@@ -309,7 +308,7 @@
 end
 
 % Actually run the model
-if strcmp(runMode, 'update') | strcmp(runMode, 'full')
+if strcmp(runMode, 'update') || strcmp(runMode, 'full')
     % Will do one timestep in "update mode", and run until the end if in "full run" mode.
     while KT < endTime
         KT = KT + 1;  % Counting Number of timesteps
@@ -709,28 +708,26 @@
         n_col = io.output_data_binary(file_ids, k, xyt, rad, canopy, ScopeParameters, vi, vmax, options, fluxes, meteo, iter, thermal, spectral, gap, profiles, Sim_Theta_U, Sim_Temp, Trap, Evap);
         fclose("all");
     end
-    if strcmp(runMode, 'update')
-        save([Output_dir, 'STEMMUS_SCOPE_state.mat'], "-v7.3", "-nocompression");
-    end
 end
 
+if strcmp(runMode, 'initialize') || strcmp(runMode, 'update')
+    % Save the required variables to the model state file.
+    % NOTE: bmiVarNames are defined in STEMMUS_SCOPE_exe.m
+    save([Output_dir, 'STEMMUS_SCOPE_state.mat'], bmiVarNames{:}, "-v7.3", "-nocompression");
+end
+
+
 if strcmp(runMode, 'finalize')
-    [InputPath, OutputPath, InitialConditionPath] = io.read_config(CFG);
-    actualRunMode = runMode; % Will be overridden by load...
-    load([OutputPath, 'STEMMUS_SCOPE_state.mat']); % Load the workspace to be able to (continue) running the model
-    runMode = actualRunMode;
+    % Load the workspace to be able to finalize the model.
+    load([OutputPath, 'STEMMUS_SCOPE_state.mat']); 
 end
 
-if strcmp(runMode, 'finalize') | strcmp(runMode, 'full')
+if strcmp(runMode, 'finalize') || strcmp(runMode, 'full')
     disp('Finalizing STEMMUS_SCOPE');
     if options.verify
         io.output_verification(Output_dir);
     end
 
-    %% soil layer information
-    SoilLayer.thickness = ModelSettings.DeltZ_R;
-    SoilLayer.depth = Ztot';  % used in Initial_root_biomass
-
     io.bin_to_csv(fnames, n_col, k, options, SoilLayer);
     save([Output_dir, 'output.mat']);
 end

src/STEMMUS_SCOPE_exe.m

@@ -1,44 +1,63 @@
 %%%%%%% A function to run STEMMUS_SCOPE %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-function STEMMUS_SCOPE_exe(config_file, run_mode, debug)
+function STEMMUS_SCOPE_exe(config_file, run_mode)
     if ~exist('run_mode','var')
         runMode = "full";
     else
         runMode = run_mode;
     end
 
-    if exist('debug','var')
-        debugMode = true;
-    else
-        debugMode = false;
-    end
-
     % disable all warnings
     warning('off', 'all');
 
     % set the variable CFG
     CFG = config_file;
-    % set the variable runMode
 
+    % If the runMode is "full" or was not provided, the model will run as normal
+    if strcmp(runMode, "full")
+        run STEMMUS_SCOPE;
+
     % In interactive mode MATLAB stays open and waits for a new command...
-    if strcmp(runMode, "interactive")
+    elseif strcmp(runMode, "interactive")
+        % Define BMI required variable names:
+        bmiVarNames = {...
+            'ModelSettings', ... % Model settings struct
+            'TimeStep', ... % Time step size (in seconds)
+            'KT', ... % Index of current time step
+            'SiteProperties', ... % Site properties (e.g. lat, lon)
+            'fluxes', ... % Atmospheric fluxes
+            'TT', ... % Soil temperature over depth
+        }; %#ok
+
         % ...until finalize has been run, at which point it quits.
         while ~strcmp(runMode, "finalize")
             runMode = input("\nFinished command. Select run mode: ", "s");
-            if strcmp(runMode, "initialize") | strcmp(runMode, "update") | strcmp(runMode, "finalize")
-                if debugMode
-                    disp(["Running in mode: ", runMode]);
-                end
+
+            if strcmp(runMode, "initialize") || strcmp(runMode, "update") || strcmp(runMode, "finalize")
+                % The 'initialize', 'update' and 'finalize' run modes are dispatched to the model.
                 run STEMMUS_SCOPE;
-            else
-                if debugMode
-                    disp(["Run mode '", runMode, "' not recognised. Try again"]);
+
+            elseif strcmp(runMode, "save")
+                % Save entire model state to file. This can be retrieved with the
+                %  model run mode "load", where this file is opened again.
+                save([Output_dir, 'STEMMUS_SCOPE_full_state.mat'], "-v7.3", "-nocompression");
+
+            elseif strcmp(runMode, "load")
+                % Load the full workspace file
+                [~, OutputPath, ~] = io.read_config(CFG);
+                stateFile = [OutputPath, 'STEMMUS_SCOPE_full_state.mat'];
+                if isfile(stateFile)
+                    load(stateFile); %#ok
+                else
+                    disp(["No file found at ", stateFile, ". Could not load file."]);
                 end
+
+            else
+                % If the runMode is not one of the above, promt user again.
+                disp(["Run mode '", runMode, "' not recognised. Try again"]);
             end
         end
         disp("Finished clean up. Quitting...");
 
     else
-        % run STEMMUS_SCOPE main code, in the selected run mode, and then quit.
-        run STEMMUS_SCOPE;
+        disp(["Run mode '", runMode, "' not recognised. The only valid modes are 'full' or 'interactive'"]);
     end
-