Merge pull request #9 from EcoExtreML/refactor_drs

Remove relative paths and revise the readme

README.md

@@ -7,25 +7,28 @@ Integrated code of SCOPE and STEMMUS
     2. Find the 'Remote Desktop' in the Launcher and click it.
     3. Find the 'Applications'and click it, you will find the 'MATLAB' software in the 'Research'.
     4. Open the 'MATLAB' using your account.
-    5. The STEMMUS_SCOPE v1.0.0 was saved at the folder '/data/shared/EcoExtreML/STEMMUS_SCOPE v1.0.0/src/STEMMUS_SCOPE.m'
-    6. Open the 'STEMMUS_SCOPE.m' file and run it.
+    5. All the code can be found in the folder 'src' in this repository.
+    6. In a terminal, run:
+    ```bash
+    matlab -nodisplay -nosplash -nodesktop -r "run('STEMMUS_SCOPE.m');exit;"
+    ```
 
 (2) The dataflow of the STEMMUS_SCOPE v1.0.0:
 
-    1. The driving data provided by PLUMBER2 were saved at the folder named '../Plumber2 data'. 
-       The soil texture data and soil hydraulic parameters data were saved at the folder named '../SoilProperty'.
-       The results of the model will be saved at the folder named '../output'.
-       All the code can be find at the folder named '../src'.
+    1. The driving data provided by PLUMBER2 were saved at the folder named 'Plumber2_data'. 
+       The soil texture data and soil hydraulic parameters data were saved at the folder named 'SoilProperty'.
+       The results of the model will be saved at the folder named 'output'.
 
     2. The main program is 'STEMMUS_SCOPE.m'. Currently, the model can be run at the site scale. 
-    For example, if we put the 'AU-Tum_2002-2017_OzFlux_Met.nc' file in the 'input' folder. The model will be run at the AU-TUM site.
+    For example, if we put the 'FI-Hyy_1996-2014_FLUXNET2015_Met.nc' file in the 'input' folder. The model will be run at the FI-Hyy site.
 
     3. After the model was started, the workflow are as follows:
-       (1) The model will read the 'AU-Tum_2002-2017_OzFlux_Met.nc' file and transfer it into '.dat' files with 'filesread.m' (you can find the '.dat' files in the 'input' folder). In addition, the site information (including location and vegetation) were also read.
+       (1) The model will read the 'FI-Hyy_1996-2014_FLUXNET2015_Met.nc' file and transfer it into '.dat' files with 'filesread.m' (you can find the '.dat' files in the 'input' folder). In addition, the site information (including location and vegetation) were also read.
        (2) Then, the model will read the soil parameters with 'soilpropertyread.m'.
-       (3) Some constants will be load using 'constant.m'.
-       (4) The model will run step by step until the whole simulation period completed.
-       (5) The results were be saved as 'binary files' temporarily and the 'binary files' will be transfer to '.csv' files at the end.
-
+       (3) Some constants will be loaded using 'Constant.m'.
+       (4) The model will run step by step until the whole simulation period is completed.
+       (5) The results will be saved as 'binary files' temporarily and the 'binary files' will be transferred to '.csv' files at the end.
 
+(3) Run STEMMUS_SCOPE v1.0.0 on a different compute node:
 
+Open the file "filesread.m" and set all paths at the top of this file. The rest of the workflow is the same as explained above. 

src/+io/create_output_files.m

@@ -1,4 +1,4 @@
-function Output_dir = create_output_files(parameter_file, F, path_of_code, options, V, vmax, spectral)
+function Output_dir = create_output_files(parameter_file, F, path_of_code, input_path, output_path, options, V, vmax, spectral)
 %% Create DATA files
 % author J.timmermans
 % last modified      4 Aug 2008: Added the creation of log file (file with input parameters)
@@ -21,7 +21,7 @@
 string          = clock;
 
 Outdir_Name     = char(F(1).FileName);
-Output_dir      = sprintf(['../output/',Outdir_Name,'_%4.0f-%02.0f-%02.0f-%02.0f%02.0f/'],[string(1) string(2) string(3) string(4) string(5)]);
+Output_dir      = sprintf([output_path,Outdir_Name,'_%4.0f-%02.0f-%02.0f-%02.0f%02.0f/'],[string(1) string(2) string(3) string(4) string(5)]);
 warning('off','MATLAB:DELETE:FileNotFound')
 if any(~exist(Output_dir,'dir'))
     mkdir(Output_dir)
@@ -33,11 +33,11 @@
 
 %% Log File
 for i = 1:length(parameter_file)  
-    copyfile(['../input/' parameter_file{i}],[Output_dir,'Parameters/', parameter_file{i}],'f')
+    copyfile([input_path parameter_file{i}],[Output_dir,'Parameters/', parameter_file{i}],'f')
 end
 fidpath          = fopen([Output_dir,'Parameters/SCOPEversion.txt'],'w');      % complete path of the SCOPE code
 fprintf(fidpath,'%s', path_of_code);
-%copyfile(['../' parameter_file],[Output_dir,'Parameters/', parameter_file ],'f')
+%copyfile([input_path parameter_file],[Output_dir,'Parameters/', parameter_file ],'f')
 
 %% Normal Output
 fidf            = fopen([Output_dir,'fluxes.dat'],'w');       %     fluxes
@@ -87,12 +87,12 @@
     end
 
 else
-    delete([Output_dir,'../output/leaftemp.dat'])
-    delete([Output_dir,'../output/layer_H.dat'])
-    delete([Output_dir,'../output/layer_lE.dat'])
-    delete([Output_dir,'../output/layer_A.dat'])
-    delete([Output_dir,'../output/layer_aPAR.dat'])
-    delete([Output_dir,'../output/layer_Rn.dat'])
+    delete([Output_dir,'leaftemp.dat'])
+    delete([Output_dir,'layer_H.dat'])
+    delete([Output_dir,'layer_lE.dat'])
+    delete([Output_dir,'layer_A.dat'])
+    delete([Output_dir,'layer_aPAR.dat'])
+    delete([Output_dir,'layer_Rn.dat'])
 end
 
 if options.calc_fluor

src/+io/create_output_files_binary.m

@@ -1,9 +1,9 @@
-function [Output_dir, f, fnames] = create_output_files_binary(parameter_file, sitename, path_of_code, input_path, spectral, options)
+function [Output_dir, f, fnames] = create_output_files_binary(parameter_file, sitename, path_of_code, input_path, output_path, spectral, options)
 %% Create Output dir
 string          = clock;
 simulation_name = char(sitename);
 outdir_name     = sprintf('%s_%4.0f-%02.0f-%02.0f-%02.0f%02.0f', simulation_name, string(1:5));
-Output_dir = [fullfile('../output/', outdir_name) filesep];
+Output_dir = [fullfile(output_path, outdir_name) filesep];
 
 warning('off','MATLAB:DELETE:FileNotFound')
 if any(~exist(Output_dir,'dir'))
@@ -70,12 +70,12 @@
     end
 
 else
-    delete([Output_dir,'../output/leaftemp.bin'])
-    delete([Output_dir,'../output/layer_H.bin'])
-    delete([Output_dir,'../output/layer_lE.bin'])
-    delete([Output_dir,'../output/layer_A.bin'])
-    delete([Output_dir,'../output/layer_aPAR.bin'])
-    delete([Output_dir,'../output/layer_Rn.bin'])
+    delete([Output_dir,'leaftemp.bin'])
+    delete([Output_dir,'layer_H.bin'])
+    delete([Output_dir,'layer_lE.bin'])
+    delete([Output_dir,'layer_A.bin'])
+    delete([Output_dir,'layer_aPAR.bin'])
+    delete([Output_dir,'layer_Rn.bin'])
 end
 
 if options.calc_fluor

src/Constants.m

@@ -29,7 +29,7 @@
 uERR=0.02;                  % Maximum desirable change of total water content;                                                                    
 Tot_Depth=500;           % Unit is cm. it should be usually bigger than 0.5m. Otherwise, 
                                  % the DeltZ would be reset in 50cm by hand;                                  
-R_depth=300; %¸ùÉî                                                                               
+R_depth=300; %����                                                                               
 Eqlspace=0;                 % Indicator for deciding is the space step equal or not;       
 NL=100;
 if ~Eqlspace                                                                     
@@ -434,7 +434,7 @@
 % Input for producing initial soil moisture and soil temperature profile
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 
-Mdata=textread('../input/Mdata.txt');
+Mdata=textread([InputPath, 'Mdata.txt']);
 Ta_msr=Mdata(:,2)';
 RH_msr=Mdata(:,3)';
 WS_msr=Mdata(:,4)';

src/STEMMUS_SCOPE.m

@@ -23,7 +23,7 @@
 %%
 
 %% 0. globals
-run filesread %prepare input files
+run filesread %get paths and prepare input files
 run Constants %input soil parameters
 global i tS KT Delt_t TEND TIME MN NN NL ML ND hOLD TOLD h hh T TT P_gOLD P_g P_gg Delt_t0 g
 global KIT NIT TimeStep Processing
@@ -60,13 +60,14 @@
 [constants] = io.define_constants();
 [Rl] = Initial_root_biomass(RTB,DeltZ_R,rroot,ML);
 %% 2. simulation options
+path_input = InputPath;          % path of all inputs
 path_of_code                = cd;
 run set_parameter_filenames; 
 
 if length(parameter_file)>1, useXLSX = 0; else useXLSX = 1; end
 
 if ~useXLSX
-    run(['../' parameter_file{1}])
+    run([path_input parameter_file{1}])
 
     options.calc_ebal           = N(1);    % calculate the energy balance (default). If 0, then only SAIL is executed!
     options.calc_vert_profiles  = N(2);    % calculate vertical profiles of fluxes
@@ -90,16 +91,16 @@
     % 2: Lookup-Table (specify the values to be included)
     % 3: Lookup-Table with random input (specify the ranges of values)
 else
-    options = io.readStructFromExcel(['../input/' char(parameter_file)], 'options', 3, 1);
+    options = io.readStructFromExcel([path_input char(parameter_file)], 'options', 3, 1);
 end
 
 if options.simulation>2 || options.simulation<0, fprintf('\n simulation option should be between 0 and 2 \r'); return, end
 
 %% 3. file names
 if ~useXLSX
-    run(['../input/' parameter_file{2}])
+    run([path_input parameter_file{2}])
 else
-    [dummy,X]                       = xlsread(['../input/' char(parameter_file)],'filenames');
+    [dummy,X]                       = xlsread([path_input char(parameter_file)],'filenames');
     j = find(~strcmp(X(:,2),{''}));
     X = X(j,(1:end));
 end
@@ -118,10 +119,10 @@
 %% 4. input data
 
 if ~useXLSX
-    X                           = textread(['../input/' parameter_file{3}],'%s'); %#ok<DTXTRD>
+    X                           = textread([path_input parameter_file{3}],'%s'); %#ok<DTXTRD>
     N                           = str2double(X);
 else
-    [N,X]                       = xlsread(['../input/' char(parameter_file)],'inputdata', '');
+    [N,X]                       = xlsread([path_input char(parameter_file)],'inputdata', '');
     X                           = X(9:end,1);
 end
 V                           = io.assignvarnames();
@@ -260,7 +261,7 @@
     end
 end
 %% 5. Declare paths
-path_input      = '../input/';          % path of all inputs
+path_input      = InputPath;          % path of all inputs
 
 %% 6. Numerical parameters (iteration stops etc)
 iter.maxit           = 400;                          %                   maximum number of iterations
@@ -352,7 +353,7 @@
 atmo.M      = helpers.aggreg(atmfile,spectral.SCOPEspec);
 
 %% 13. create output files
-[Output_dir, f, fnames] = io.create_output_files_binary(parameter_file, sitename, path_of_code, path_input, spectral, options);
+[Output_dir, f, fnames] = io.create_output_files_binary(parameter_file, sitename, path_of_code, path_input, path_output, spectral, options);
 run StartInit;   % Initialize Temperature, Matric potential and soil air pressure.
 
 
@@ -782,7 +783,7 @@
     io.output_verification(Output_dir)
 end
 io.bin_to_csv(fnames, V, vmax, n_col, k, options,Ztot)
-if options.makeplots
-    plot.plots(Output_dir)
-end
+%if options.makeplots
+%    plot.plots(Output_dir)
+%end