new matlab to plot transport from out_XX.txt files

matlab/read_flux_out_XX.m

+function [t_all, Pxi_all, Qxi_all] = read_flux_out_XX(folderPath,PLOT)
+    % Check if the prompt_string is provided as an argument
+    if nargin < 1
+        % If not provided, prompt the user for input
+        prompt_string = 'Enter the path to the simulation dir: ';
+        % Get the input from the user
+        folderPath = input(prompt_string, 's');   
+        PLOT = 1;
+    else if nargin == 1
+            PLOT = 0;
+    end
+
+    % Initialize empty arrays to store the values
+    t_all   = [];
+    Pxi_all = [];
+    Qxi_all = [];
+    Pxe_all = [];
+    Qxe_all = [];
+
+    % List all files in the folder with the pattern out_XX.txt
+    filePattern = fullfile(folderPath, 'out_*.txt');
+    files = dir(filePattern);
+
+    % Regular expression pattern to match numerical values
+    pattern = '[-+]?\d*\.?\d+(?:[eE][-+]?\d+)?';
+
+    % Loop through each file
+    for i = 1:length(files)
+        filename = fullfile(folderPath, files(i).name);
+        fid = fopen(filename, 'r');
+
+        if fid == -1
+            fprintf('Error opening file: %s\n', filename);
+            continue;
+        end
+
+        % Loop through each line of the file
+        while ~feof(fid)
+            line = fgetl(fid);
+
+            % Check if the line starts with "|t"
+            if startsWith(line, '|t')
+                % Check if the line contains numerical values
+                matches = regexp(line, pattern, 'match');
+
+                % Convert the matched strings to numerical values
+                values = str2double(matches);
+                % If matches are found, extract the numerical values and store them in the arrays
+                if ~isempty(matches)
+                    values = str2double(matches);
+                    if numel(values) == 4
+                        t_all   = [t_all, values(1)];
+                        Pxi_all = [Pxi_all, values(3)];
+                        Qxi_all = [Qxi_all, values(4)];
+                    elseif numel(values) == 3
+                        t_all   = [t_all, values(1)];
+                        Pxi_all = [Pxi_all, values(2)];
+                        Qxi_all = [Qxi_all, values(3)];
+                    elseif numel(values) == 5
+                        t_all   = [t_all,   values(1)];
+                        Pxi_all = [Pxi_all, values(2)];
+                        Qxi_all = [Qxi_all, values(3)];
+                        Pxe_all = [Pxe_all, values(4)];
+                        Qxe_all = [Qxe_all, values(5)];
+                    end
+                end
+            end
+        end
+
+        % Close the file
+        fclose(fid);
+    end
+
+    if PLOT
+    figure
+    subplot(211)
+    plot(t_all,Pxi_all,'r','DisplayName','$\Gamma_{xi}$'); hold on;
+    if(numel(t_all)==numel(Pxe_all))
+        plot(t_all,Pxe_all,'b','DisplayName','$\Gamma_{xe}$'); hold on;
+    end
+    title('Particle flux')
+    subplot(212)
+    plot(t_all,Qxi_all,'r','DisplayName','$Q_{xi}$'); hold on;
+    if(numel(t_all)==numel(Qxe_all))
+        plot(t_all,Qxe_all,'b','DisplayName','$Q_{xe}$'); hold on;
+    end
+    title('Heat flux')
+    end
+end