can't get sequential .exe execution to occur in matlab

Hi,

I'm trying to copy a reference file LEVEL_01.dir to a number of number of sub directories and then change the content of LEVEL_01.dir to hold the new dr

clear all;
clc;
%Solute transport parameters in row 47 of SELECTOR.IN file
SolTrans=[0.035 0 1 0.0479 0 0 0 0 273895 1 0 0 0 0]; %[Kd Nu Beta Henry SnkL1 SnkS1 SnkG1 SnkL1p SnkS1p SnkG1p SnkL10 SnkS10 SnkG10 Alfa] !! UPDATE NUMBERS IN BRACKETS !!

%~~~~~~
%ADD NOISE TO SOLUTE TRANSPORT PARAMETERS 
num_sim=100;    %100 Monte Carlo Simulations
Kd=SolTrans(1)+.02*rand(1,num_sim); %a vector with 100 values of Kd parameters. We assume that the error is normally distributed with a standard deviation of ##.
Nu=SolTrans(2)+.02*rand(1,num_sim);
Beta=SolTrans(3)+.02*rand(1,num_sim);      %!!! CHANGE .02 FOR ALL THESE TO APPROPRIATE STANDARD DEVIATIONSN !!!
Henry=SolTrans(4)+.02*rand(1,num_sim);
SnkL1=SolTrans(5); 
SnkS1=SolTrans(6);
SnkG1=SolTrans(7);
SnkL1p=SolTrans(8);
SnkS1p=SolTrans(9)+.02*rand(1,num_sim);      %!!! FOR AWI MODIFIED MODEL - KL - LANGMUIR EXPONENT FOR AWI FOR LANGMUIR SORPTION or 0 FOR FREUNDLICH SORPTION
SnkG1p=SolTrans(10);
SnkL10=SolTrans(11);
SnkS10=SolTrans(12);
SnkG10=SolTrans(13);
Alfa=SolTrans(14);



%~~~~~~
%INITIALIZE FILES AND DIRECTORIES

hydrus_exec='C:\Users\jessi\Desktop\Hydrus\Projects\ATSDR\AFFF1PFOS\H1D_CALC.exe';   %'C:\Program Files (x86)\PC-Progress\Hydrus-1D 4\H1D_calc.exe';   
hydrus_ref='C:\Users\jessi\Desktop\Hydrus\Projects\ATSDR\AFFF1PFOS';   
profileDAT='C:\Users\jessi\Desktop\Hydrus\Projects\ATSDR\AFFF1PFOS\PROFILE.DAT';    
options='C:\Users\jessi\Desktop\Hydrus\Projects\ATSDR\AFFF1PFOS\OPTIONS.IN';
atmosph='C:\Users\jessi\Desktop\Hydrus\Projects\ATSDR\AFFF1PFOS\ATMOSPH.IN';
selectorIN='C:\Users\jessi\Desktop\Hydrus\Projects\ATSDR\AFFF1PFOS\SELECTOR.IN';  
level='C:\Users\jessi\Desktop\Hydrus\Projects\ATSDR\AFFF1PFOS\LEVEL_01.dir';
work_dir='C:\Users\jessi\Desktop\Simulations\';
mkdir(work_dir);


%~~~~~~
%CREATE DIRECTORIES AND INPUT FILES - This block is doing the work. Creates the input files for all realizations. Copies the mandatory file Profile.dat to 
% the corresponding folder and creates the corresponding Selector
% .in. The Selector.in file is different for each realization since the solute transport parameters is 
% variable. The code reads the reference Selector.in, copies the first 46 lines to the new file, write the van Genuchten parameters to the 47th line, 
% and finally copies the last 10 lines from the reference Selector.in to the new file.

path=cell(1,num_sim);
for i=1:num_sim
    path{i}=strcat(work_dir,'run_',num2str(i)); %create folder for each run           
    mkdir(path{i});       
    copyfile(profileDAT,path{i}); %copy profileDAt from reference directory to the simulation directory 
    copyfile(options,path{i}); %copy options from reference directory to the simulation directory 
    copyfile(atmosph,path{i}); %copy atmosph from reference directory to the simulation director
    copyfile(level,path{i}); %copy options from reference directory to the simulation directory 
    copyfile(hydrus_exec,path{i}); %copy options from reference directory to the simulation directory 
   
    fileID_out=fopen(strcat(path{i},'\selector.in'),'wt'); %manipulate Selector.in for each run
                        % "wt"= permision for file axis type
                        % w=Open or create new file for writing. Discard existing contents, if any.
                       % To open files in text mode, attach the letter 't' to the permission argument,
    fileID_in=fopen(selectorIN);
    skip_lines=46;      %!!! THIS IS THE LINE THAT CHANGES IN SELECTOR.IN FILE , i.e. solute transport parameters!!!
    for k=1:(skip_lines)
        x=fgetl(fileID_in); %x = fgetl(fileID)= returns the next line of the specified file, removing the newline characters.
        fprintf(fileID_out,'%s\n',x);  % %s in the formatSpec input indicates that the values of the variables url and sitename, should be printed as text. 
                                       % '\n' as a newline indicator.   
                                       % "x" = prints the values from variable x
    end
    
    out_Sol=SolTrans; % Renaming...
    
    %Whatever the solute transport parameter is for that monte carlo run (i)
    out_Sol(1)=Kd(i);       % Solid phase sorption Kd
    out_Sol(2)=Nu(i);       % Van Genuchten parameter
    out_Sol(3)=Beta(i);     % Van Genuchten parameter
    out_Sol(4)=Henry(i);     % Kh = KL*Rmax
    out_Sol(9)=SnkS1p(i);    % KL - LANGMUIR EXPONENT FOR AWI FOR LANGMUIR SORPTION or 0 FOR FREUNDLICH SORPTION
  
    fprintf(fileID_out,'%f %f %f %f %f %f %f %f %f %f %f %f %f %f\n',out_Sol'); 
                             % %f = Fixed-point notation (Use a precision operator to specify the number of digits after the decimal point.)
                             % '\n' as a newline indicator. 
    fgetl(fileID_in);        % returns the next line of the specified file, removing the newline characters.
    skip_lines_end=5;       % CORRECT NUMBER???  DOUBLE CHECK
    for k=1:(skip_lines_end)
        x=fgetl(fileID_in);
        fprintf(fileID_out,'%s\n',x);
    end
    fclose('all');


end
path=cell(1,num_sim);

%For this section I want hydrus.exe to run in each path{1}...when I run the
%code as is, only the first of the 100 simulations is run. In other words,
%hydrus.exe is sucsessufully completed in path{1}, but then for path{2} and
%all the rest, the files are copied into these new directories, but the
%.exe doesn't run in any of the other sub files. I what think this has something
%to do with how the below segment is scripted but I don't know what to try
%next...

for i=1:num_sim
    exec_path=['"' hydrus_exec '" "' path{i} '"'];
    [x, y]= dos(exec_path);
    if x % unsuccessful
         error('exe failed'); % or take some other action besides throwing an error
    end
end

Answer 1

[Voss]

Try removing this line (between the for loops):

path=cell(1,num_sim);

That line has the effect of resetting path to a cell array of empty arrays, after path was already set up in the previous for loop but before path is used in exec_path in the next for loop.

[Wesser]

removed the line and still won't executethe .exe beyond the first path{1}. I'm realizing that the level_01 file that is copied to eacth path{i} is a reference driectory needed for the .exe to run. The level_01 content is literally just the file location of the current directory, so would need to rewrite the conent of level_01 in each path{i}. Any suggestions for this? The new content in each level_01 would change from:

C:\Users\jessi\Desktop\Hydrus\Projects\ATSDR\AFFF1PFOS

to

C:\Users\jessi\Desktop\Simulations\run_1 for path{1}

then

C:\Users\jessi\Desktop\Simulations\run_2 for path{2} etc.

If this is indeed my glitch I'm not sure why the .exe was executing in path{1} but worth a shot...

[Voss]

In that case, don't copy LEVEL_01.dir to the different simulation directories. Instead, in each directory write a new LEVEL_01.dir that contains the correct path:

path=cell(1,num_sim);

for i=1:num_sim
    
    path{i}=strcat(work_dir,'run_',num2str(i)); %create folder for each run
    mkdir(path{i});
    
    copyfile(profileDAT,path{i}); %copy profileDAt from reference directory to the simulation directory 
    copyfile(options,path{i}); %copy options from reference directory to the simulation directory 
    copyfile(atmosph,path{i}); %copy atmosph from reference directory to the simulation director
    
    % don't copy LEVEL_01.dir:
%     copyfile(level,path{i}); %copy options from reference directory to the simulation directory 
    
    % instead, write it:
    fid_level = fopen(fullfile(path{i},'LEVEL_01.dir'),'w');
    fprintf(fid_level,'%s',path{i});
    fclose(fid_level);

    copyfile(hydrus_exec,path{i}); %copy options from reference directory to the simulation directory 
    
    % ...
    % rest of code
    % ...
    
end

And actually, it doesn't seem like you need to copy the exe itself to each directory, since you're always running the original exe located at C:\Users\jessi\Desktop\Hydrus\Projects\ATSDR\AFFF1PFOS\H1D_CALC.exe but with a different path{i} argument each time.

An alternative might be to copy the exe (like you are doing) and run the copies (which you are not doing), which might simplify the necessary setup, e.g., if the exe defaults to looking in its current working directory for the files it needs. Hard to say for sure without knowing what the exe expects.

[Wesser]

"An alternative might be to copy the exe (like you are doing) and run the copies (which you are not doing), which might simplify the necessary setup, e.g., if the exe defaults to looking in its current working directory for the files it needs. "

This is exaclty what the .exe does...it does not work well when trying to call files outside its working directory. How would I script this so that I am running the copies of the .exe in each path{i} ?

Also thank you SOOO much for your assistance with this!!!

Here is the current version of the code:

clear all;
clc;
%Solute transport parameters in row 47 of SELECTOR.IN file
SolTrans=[0.035 0 1 0.0479 0 0 0 0 273895 1 0 0 0 0]; %[Kd Nu Beta Henry SnkL1 SnkS1 SnkG1 SnkL1p SnkS1p SnkG1p SnkL10 SnkS10 SnkG10 Alfa] !! UPDATE NUMBERS IN BRACKETS !!

%~~~~~~
%ADD NOISE TO SOLUTE TRANSPORT PARAMETERS 
num_sim=100;    %100 Monte Carlo Simulations
Kd=SolTrans(1)+.02*rand(1,num_sim); %a vector with 100 values of Kd parameters. We assume that the error is normally distributed with a standard deviation of ##.
Nu=SolTrans(2)+.02*rand(1,num_sim);
Beta=SolTrans(3)+.02*rand(1,num_sim);      %!!! CHANGE .02 FOR ALL THESE TO APPROPRIATE STANDARD DEVIATIONSN !!!
Henry=SolTrans(4)+.02*rand(1,num_sim);
SnkL1=SolTrans(5); 
SnkS1=SolTrans(6);
SnkG1=SolTrans(7);
SnkL1p=SolTrans(8);
SnkS1p=SolTrans(9)+.02*rand(1,num_sim);      %!!! FOR AWI MODIFIED MODEL - KL - LANGMUIR EXPONENT FOR AWI FOR LANGMUIR SORPTION or 0 FOR FREUNDLICH SORPTION
SnkG1p=SolTrans(10);
SnkL10=SolTrans(11);
SnkS10=SolTrans(12);
SnkG10=SolTrans(13);
Alfa=SolTrans(14);



%~~~~~~
%INITIALIZE FILES AND DIRECTORIES

hydrus_exec='C:\Users\jessi\Desktop\Hydrus\Projects\ATSDR\AFFF1PFOS\H1D_CALC.exe';   %'C:\Program Files (x86)\PC-Progress\Hydrus-1D 4\H1D_calc.exe';   
hydrus_ref='C:\Users\jessi\Desktop\Hydrus\Projects\ATSDR\AFFF1PFOS';   
profileDAT='C:\Users\jessi\Desktop\Hydrus\Projects\ATSDR\AFFF1PFOS\PROFILE.DAT';    
options='C:\Users\jessi\Desktop\Hydrus\Projects\ATSDR\AFFF1PFOS\OPTIONS.IN';
atmosph='C:\Users\jessi\Desktop\Hydrus\Projects\ATSDR\AFFF1PFOS\ATMOSPH.IN';
selectorIN='C:\Users\jessi\Desktop\Hydrus\Projects\ATSDR\AFFF1PFOS\SELECTOR.IN';  
level='C:\Users\jessi\Desktop\Hydrus\Projects\ATSDR\AFFF1PFOS\LEVEL_01.dir';
work_dir='C:\Users\jessi\Desktop\Simulations\';
mkdir(work_dir);


%~~~~~~
%CREATE DIRECTORIES AND INPUT FILES - This block is doing the work. Creates the input files for all realizations. Copies the mandatory file Profile.dat to 
% the corresponding folder and creates the corresponding Selector
% .in. The Selector.in file is different for each realization since the solute transport parameters is 
% variable. The code reads the reference Selector.in, copies the first 46 lines to the new file, write the van Genuchten parameters to the 47th line, 
% and finally copies the last 10 lines from the reference Selector.in to the new file.

path=cell(1,num_sim);
for i=1:num_sim
    path{i}=strcat(work_dir,'run_',num2str(i)); %create folder for each run           
    mkdir(path{i});    

    copyfile(profileDAT,path{i}); %copy profileDAt from reference directory to the simulation directory 
    copyfile(options,path{i}); %copy options from reference directory to the simulation directory 
    copyfile(atmosph,path{i}); %copy atmosph from reference directory to the simulation director
    copyfile(hydrus_exec,path{i}); %copy options from reference directory to the simulation directory 

    fid_level = fopen(fullfile(path{i},'LEVEL_01.dir'),'w');
    fprintf(fid_level,'%s',path{i});
    fclose(fid_level);

    fileID_out=fopen(strcat(path{i},'\selector.in'),'wt'); %manipulate Selector.in for each run
                        % "wt"= permision for file axis type
                        % w=Open or create new file for writing. Discard existing contents, if any.
                       % To open files in text mode, attach the letter 't' to the permission argument,
    fileID_in=fopen(selectorIN);
    skip_lines=46;      %!!! THIS IS THE LINE THAT CHANGES IN SELECTOR.IN FILE , i.e. solute transport parameters!!!
    for k=1:(skip_lines)
        x=fgetl(fileID_in); %x = fgetl(fileID)= returns the next line of the specified file, removing the newline characters.
        fprintf(fileID_out,'%s\n',x);  % %s in the formatSpec input indicates that the values of the variables url and sitename, should be printed as text. 
                                       % '\n' as a newline indicator.   
                                       % "x" = prints the values from variable x
    end
    
    out_Sol=SolTrans; % Renaming...
    
    %Whatever the solute transport parameter is for that monte carlo run (i)
    out_Sol(1)=Kd(i);       % Solid phase sorption Kd
    out_Sol(2)=Nu(i);       % Van Genuchten parameter
    out_Sol(3)=Beta(i);     % Van Genuchten parameter
    out_Sol(4)=Henry(i);     % Kh = KL*Rmax
    out_Sol(9)=SnkS1p(i);    % KL - LANGMUIR EXPONENT FOR AWI FOR LANGMUIR SORPTION or 0 FOR FREUNDLICH SORPTION
  
    fprintf(fileID_out,'%f %f %f %f %f %f %f %f %f %f %f %f %f %f\n',out_Sol'); 
                             % %f = Fixed-point notation (Use a precision operator to specify the number of digits after the decimal point.)
                             % '\n' as a newline indicator. 
    fgetl(fileID_in);        % returns the next line of the specified file, removing the newline characters.
    skip_lines_end=5;       % CORRECT NUMBER???  DOUBLE CHECK
    for k=1:(skip_lines_end)
        x=fgetl(fileID_in);
        fprintf(fileID_out,'%s\n',x);
    end
    fclose('all');
end


for i=1:num_sim
    exec_path=['"' hydrus_exec '" "' path{i} '"'];
    [x, y]= dos(exec_path);
    if x % unsuccessful
         error('exe failed'); % or take some other action besides throwing an error
    end
end