Merge pull request #36 from EcoExtreML/add_timestep

Add variable DurationSize to config file

README.md

@@ -56,6 +56,9 @@ Integrated code of SCOPE and STEMMUS.
     the model runs at the site scale. For example, if we put the
     `FI-Hyy_1996-2014_FLUXNET2015_Met.nc` here, the model runs at the `FI-Hyy`
     site.
+    - DurationSize: total number of time steps in which model runs. It can be
+      `NA` or a number. Example `DurationSize=17520` runs the model for one year a
+      half-hour time step i.e. `365*24*2=17520`.
 
     To edit the config file, open the file with a text editor and change the
     paths. The variable names e.g. `SoilPropertyPath` should not be changed.
@@ -178,6 +181,9 @@ Dutch National supercomputer hosted at SURF.
     `FI-Hyy_1996-2014_FLUXNET2015_Met.nc` here, the model runs at the `FI-Hyy`
     site.
     - VegetationPropertyPath: path to required data except `Plumber2_data` and `SoilProperty`. 
+    - DurationSize: total number of time steps in which model runs. It can be
+      `NA` or a number. Example `DurationSize=17520` runs the model for one year a
+      half-hour time step i.e. `365*24*2=17520`.
 
     To edit the config file, open the file with a text editor and change the
     paths. The variable name e.g. `SoilPropertyPath` should not be changed.

config_file_crib.txt

@@ -2,4 +2,5 @@ SoilPropertyPath=/data/shared/EcoExtreML/STEMMUS_SCOPEv1.0.0/input/SoilProperty/
 InputPath=/home/jovyan/private/06_STEMMUS_SCOPE/GitEcoExtreML/data/
 OutputPath=/home/jovyan/private/06_STEMMUS_SCOPE/GitEcoExtreML/data/output/
 ForcingPath=/data/shared/EcoExtreML/STEMMUS_SCOPEv1.0.0/input/Plumber2_data/
-ForcingFileName=FI-Hyy_1996-2014_FLUXNET2015_Met.nc
+ForcingFileName=FI-Hyy_1996-2014_FLUXNET2015_Met.nc
+DurationSize=NA

config_file_snellius.txt

@@ -3,4 +3,5 @@ InputPath=/scratch-shared/ecoextreml/stemmus_scope/input/
 OutputPath=/scratch-shared/ecoextreml/stemmus_scope/output/
 ForcingPath=/projects/0/einf2480/forcing/plumber2_data/
 ForcingFileName=FI-Hyy_1996-2014_FLUXNET2015_Met.nc
-VegetationPropertyPath=/projects/0/einf2480/model_parameters/vegetation_property/
+VegetationPropertyPath=/projects/0/einf2480/model_parameters/vegetation_property/
+DurationSize=17520

src/+io/read_config.m

@@ -1,4 +1,4 @@
-function [SoilPropertyPath, InputPath, OutputPath, ForcingPath, ForcingFileName] = read_config(config_file)
+function [SoilPropertyPath, InputPath, OutputPath, ForcingPath, ForcingFileName, DurationSize] = read_config(config_file)
 
 file_id = fopen(config_file);
 config = textscan(file_id,'%s %s', 'HeaderLines',0, 'Delimiter', '=');
@@ -23,3 +23,7 @@
 
 indx = find(strcmp(config_vars, 'ForcingFileName'));
 ForcingFileName = config_paths{indx};
+
+% value of DurationSize is optional and can be NA
+indx = find(strcmp(config_vars, 'DurationSize'));
+DurationSize = str2double(config_paths{indx});

src/filesread.m

@@ -1,5 +1,5 @@
 %%%%%%% Set paths %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-global SoilPropertyPath InputPath OutputPath ForcingPath ForcingFileName
+global SoilPropertyPath InputPath OutputPath ForcingPath ForcingFileName DurationSize
 global CFG
 
 %% CFG is a path to a config file
@@ -9,7 +9,7 @@
 
 %% Read the CFG file. Due to using MATLAB compiler, we cannot use run(CFG)
 disp (['Reading config from ',CFG])
-[SoilPropertyPath, InputPath, OutputPath, ForcingPath, ForcingFileName] = io.read_config(CFG);
+[SoilPropertyPath, InputPath, OutputPath, ForcingPath, ForcingFileName, DurationSize] = io.read_config(CFG);
 
 %%%%%%% Prepare input files. %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 global DELT IGBP_veg_long latitude longitude reference_height canopy_height sitename
@@ -29,8 +29,22 @@
 time1=ncread(ForcingFilePath,'time');
 t1=datenum(startyear,1,1,0,0,0);
 DELT=time1(2);
+
+%get  time length of forcing file
+time_length=length(time1);
+
 %Set the end time of the main loop in STEMMUS_SCOPE.m
-Dur_tot=length(time1);
+%using config file or time length of forcing file
+if isnan(DurationSize)
+    Dur_tot=time_length;
+else
+    if (DurationSize>time_length)
+        Dur_tot=time_length;
+    else
+        Dur_tot=DurationSize;
+    end
+end
+
 dt=time1(2)/3600/24;
 t2=datenum(endyear,12,31,23,30,0);
 T=t1:dt:t2;