Bash scripts mostly for clean, modification, download, extraction

Dipolar-Gas-Simulator/+Scripts/run_locally.m

@@ -549,13 +549,13 @@ SaveDirectory = './Results/Data_3D/AnisotropicTrap/TiltedDipoles45';
 JobNumber     = 0;
 Plotter.visualizeGSWavefunction(SaveDirectory, JobNumber)
 %%
-SaveDirectory = './Results/Data_3D/GradientDescent/aS_079_theta_000_phi_000_N_50000';
+SaveDirectory = './Results/Data_3D/GradientDescent/Phi050/aS_089_theta_050_phi_000_N_100000';
 JobNumber     = 0;
 Plotter.visualizeGSWavefunction(SaveDirectory, JobNumber)
 %%
 % Parameters you can set before the loop
-N         = 60000;
-theta     = 0;
+N         = 105000;
+theta     = 50.0;
 phi       = 0;
 JobNumber = 0;
 
@@ -570,7 +570,7 @@ for aS = aS_values
     N_str     = sprintf('%d', N);  
 
     % Construct directory path
-    SaveDirectory = ['./Results/Data_3D/GradientDescent/aS_', aS_str, ...
+    SaveDirectory = ['./Results/Data_3D/GradientDescent/Phi',theta_str, '/aS_', aS_str, ...
                      '_theta_', theta_str, '_phi_', phi_str, '_N_', N_str];
 
     % Call the plotting function
@@ -586,12 +586,13 @@ for aS = aS_values
     pause(0.25)
 end
 
+
 %%
 SaveDirectory = './Results/Data_3D/GradientDescent/';
 JobNumber     = 1;
 Plotter.visualizeGSWavefunction(SaveDirectory, JobNumber)
 %% Visualize phase diagram
-load('phase_diagram_matrix_theta_0.mat')
+load('phase_diagram_matrix_theta_30.mat')
 PhaseDiagramMatrix   = M;
 ScatteringLengths    = SCATTERING_LENGTH_RANGE;
 NumberOfAtoms        = NUM_ATOMS_LIST * 1E-5;
@@ -604,13 +605,14 @@ set(gca,'FontSize',16,'Box','On','Linewidth',2);
 hImg = imagesc(M);
 set(gca, 'YDir', 'normal');
 colormap(parula);
-% colorbar;
+ax = gca;                % Get current axes
+ax.FontSize = 16;        % Set tick label font size (adjust as needed)
 axis equal tight;
 xticks(1:xlen);
 yticks(1:ylen);
 xticklabels(string(NumberOfAtoms));
 yticklabels(string(ScatteringLengths));
-xlabel('Number of Atoms (x 10^5)', FontSize=16);
+xlabel('Number of Atoms (x 10^5)', 'Interpreter', 'tex', FontSize=16);
 ylabel('Scattering Length (a0)', FontSize=16);
-title('Zero-temperature Phase Diagram for \theta = 0', 'Interpreter', 'tex', FontSize=16);
+% title('Zero-temperature Phase Diagram for \theta = 0', 'Interpreter', 'tex', FontSize=16);
 grid on;

Dipolar-Gas-Simulator/Results/Data_3D/GradientDescent/CleanUp.ps1

@@ -0,0 +1,27 @@
+$root = "C:\Users\Karthik\Documents\GitRepositories\Calculations\Dipolar-Gas-Simulator\Results\Data_3D\GradientDescent\Phi050"
+
+# Step 1: Delete all files except 'psi_gs.mat'
+Get-ChildItem -Path $root -Recurse -File -Force |
+Where-Object { $_.Name -ne "psi_gs.mat" } |
+ForEach-Object {
+    try {
+        Remove-Item -Path $_.FullName -Force -ErrorAction Stop
+        Write-Output "Deleted: $($_.FullName)"
+    } catch {
+        Write-Warning "Failed to delete: $($_.FullName)"
+    }
+}
+
+# Step 2: Delete all empty directories (deepest first)
+Get-ChildItem -Path $root -Recurse -Directory -Force |
+Sort-Object FullName -Descending |
+ForEach-Object {
+    if (-not (Get-ChildItem -Path $_.FullName -Force)) {
+        try {
+            Remove-Item -Path $_.FullName -Force -ErrorAction Stop
+            Write-Output "Deleted empty folder: $($_.FullName)"
+        } catch {
+            Write-Warning "Failed to delete folder: $($_.FullName)"
+        }
+    }
+}

Dipolar-Gas-Simulator/Results/Data_3D/GradientDescent/IdentifyMissingFiles.ps1

@@ -0,0 +1,41 @@
+$root = "C:\Users\Karthik\Documents\GitRepositories\Calculations\Dipolar-Gas-Simulator\Results\Data_3D\GradientDescent\Phi030"
+
+# Define parameter ranges
+$SCATTERING_LENGTH_RANGE = @(79.0..90.0)
+$POLAR_ANGLE_RANGE = @(30.0)
+$AZIMUTHAL_ANGLE_RANGE = @(0.0)
+$NUM_ATOMS_LIST = @(50000, 55000, 60000, 65000, 70000, 75000, 80000, 85000, 90000, 95000, 100000, 105000)
+
+# Utility function to format floating point values as zero-padded 3-digit integers
+function Format-Value($value) {
+    return "{0:D3}" -f [int]($value * 1)
+}
+
+# Generate all valid folder names
+$expectedFolders = @()
+foreach ($aS in $SCATTERING_LENGTH_RANGE) {
+    $aS_str = Format-Value $aS
+    foreach ($theta in $POLAR_ANGLE_RANGE) {
+        $theta_str = Format-Value $theta
+        foreach ($phi in $AZIMUTHAL_ANGLE_RANGE) {
+            $phi_str = Format-Value $phi
+            foreach ($N in $NUM_ATOMS_LIST) {
+                $folderName = "aS_${aS_str}_theta_${theta_str}_phi_${phi_str}_N_${N}"
+                $expectedFolders += $folderName
+            }
+        }
+    }
+}
+
+# Get actual folders in the root directory
+$actualFolders = Get-ChildItem -Path $root -Directory -Force | Select-Object -ExpandProperty Name
+
+# Compare and find missing folders
+$missingFolders = $expectedFolders | Where-Object { $_ -notin $actualFolders }
+
+# Output missing folders
+Write-Host "Missing folders:"
+$missingFolders | ForEach-Object { Write-Host $_ }
+
+# Optional: Save to a file
+$missingFolders | Out-File -FilePath "$root\missing_folders.txt" -Encoding UTF8

Dipolar-Gas-Simulator/create_tar_ball.slurm

@@ -0,0 +1,22 @@
+#!/bin/bash
+########### Begin SLURM header ###########
+#Partition
+#SBATCH --partition=cpu-single
+# Request number of nodes and CPU cores per node for job
+#SBATCH --nodes=1
+#SBATCH --ntasks-per-node=1
+#SBATCH --cpus-per-task=10
+#SBATCH --mem=2G  
+# Estimated wallclock time for job
+#SBATCH --time=01:00:00
+#SBATCH --job-name=tar
+#SBATCH --output=tar.out
+#SBATCH --error=tar.err
+
+SRC_DIR="/home/hd/hd_hd/hd_fz183/Dipolar-Gas-Simulator/Results/Data_3D/GradientDescent"
+TARBALL_NAME="gd_result_$(date +%Y%m%d_%H%M%S).tar.gz"
+
+# Create tarball
+echo "Creating tarball..."
+tar -czf "$TARBALL_NAME" -C "$SRC_DIR" .
+echo "Completed creation of tarball."

Dipolar-Gas-Simulator/generateRerunListsForBash.m

@@ -0,0 +1,40 @@
+% Read the lines from the text file
+filename = 'C:\Users\Karthik\Documents\GitRepositories\Calculations\Dipolar-Gas-Simulator\Results\Data_3D\GradientDescent\Phi050\missing_folders.txt'; % replace with your actual file name
+strs = readlines(filename);
+strs = strs(strs ~= ""); % remove empty lines if any
+
+% Initialize arrays
+aS = zeros(length(strs),1);
+theta = zeros(length(strs),1);
+phi = zeros(length(strs),1);
+N = zeros(length(strs),1);
+
+% Extract numbers using regular expressions
+for i = 1:length(strs)
+    tokens = regexp(strs(i), 'aS_(\d+)_theta_(\d+)_phi_(\d+)_N_(\d+)', 'tokens');
+    nums = str2double(tokens{1});
+    aS(i) = nums(1);
+    theta(i) = nums(2);
+    phi(i) = nums(3);
+    N(i) = nums(4);
+end
+
+% Convert to bash-style space-separated strings
+aS_str    = sprintf('%d ', unique(aS));
+theta_str = sprintf('%d ', unique(theta));
+phi_str   = sprintf('%d ', unique(phi));
+N_str     = sprintf('%d ', unique(N));
+
+% Trim trailing spaces
+aS_str    = strtrim(aS_str);
+theta_str = strtrim(theta_str);
+phi_str   = strtrim(phi_str);
+N_str     = strtrim(N_str);
+
+% Display Bash-compatible output
+fprintf('SCATTERING_LENGTH_RANGE=[%s]\n', aS_str);
+fprintf('POLAR_ANGLE_RANGE=[%s]\n', theta_str);
+fprintf('AZIMUTHAL_ANGLE_RANGE=[%s]\n', phi_str);
+fprintf('NUM_ATOMS_LIST=[%s]\n', N_str);
+
+%%