run hydrus 1D .exe multiple times with matlab

[waterislife]

I'm trying to do a monte carlo sensitivity analysis of hydraulic parameters using matlab. Per the template file on the hydrus page , I created the below matlab file that creates subdirectories for each monte carlo run, each with the .exe, level_01.dir, and all the other necessary input files. However, I can't get matlab to run the .exe in each subdirectory. My matlab file seems to be only calling the original reference .exe which hydrus doesn't like, as it wants to be in the same reference file as the input files. I have the same question into the matlab forum but I'm hoping someone on here can help as well.
Matlab code below:




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';
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

%created appropriate level_01.dir file in each path{i} that calls the path{i} working directory
fid_level = fopen(fullfile(path{i},'LEVEL_01.dir'),'w');
fprintf(fid_level,'%s',path{i});
fclose(fid_level);

%creates a new selector.in file for eacvh path{i} that has different
%solute transport parameters based on monte carlo
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

%SECTION THAT NEEDS WORK...I THINK CODE AS WRITTEN IS CALLING ORIGINAL
%.EXE, BUT i WOULD LIKE THE .EXE COPIES IN EACH PATH{i} TO EXECUTE AND CALL
%THEIR RESPECTIVE PATH{i} FILES. HOW SHOULD I CANGE THIS SECTION TO DO
%THAT?
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