Edit Hydrogen.py

src/Hydrogen.py

@@ -37,6 +37,16 @@ plt.rcParams.update({
     'axes.labelweight': 'bold'
 })
 
+######################################
+# Helper function: Project Root
+######################################
+def get_project_root():
+    """
+    Returns the project root directory.
+    Assumes this file is in a container (e.g., 'src') inside the project.
+    """
+    return os.path.abspath(os.path.join(os.path.dirname(os.path.abspath(__file__)), ".."))
+
 ######################################
 # Data Reading and Analysis Functions
 ######################################
@@ -292,7 +302,7 @@ def plot_ring_clusters_detail_3d(hbonds, molecules, selected_clusters=None, crop
                         legend_added[ring_size] = True
                     else:
                         ax.plot(x, y, z, color=color_map[ring_size], linewidth=3)
-                # NEW: Highlight the water molecules that form this ring.
+                # Highlight the water molecules that form this ring.
                 for i_node in ring:
                     ax.scatter(coords[i_node, 0], coords[i_node, 1], coords[i_node, 2],
                                color=color_map[ring_size], s=300, edgecolors='black', zorder=5)
@@ -602,9 +612,8 @@ class MainWindow(QMainWindow):
         cutoffGroup.setLayout(cutoffLayout)
         control_layout.addWidget(cutoffGroup)
 
-        # File paths (adjust if necessary)
-        self.xyz_directory = "Large_box/Large/Accumulation_dependence/DFT_box/"
-        # GR file directory removed since not used.
+        # Set xyz_directory using the absolute project root path.
+        self.xyz_directory = os.path.join(get_project_root(), "Large_box", "Large", "Accumulation_dependence", "DFT_box")
 
         # Plot style parameters
         self.plot_params = {
@@ -884,7 +893,7 @@ class MainWindow(QMainWindow):
                     f.write("Bar Plot Raw Data\n")
                     f.write("-----------------\n")
                     f.write(f"Plot type: {self.last_bar_plot_data.get('plot_type','')}\n")
-                    f.write("H-bond-per-molecules\percentage (%) \n")
+                    f.write("H-bond-per-molecules\tpercentage (%) \n")
                     for x, y in zip(self.last_bar_plot_data.get("x", []), self.last_bar_plot_data.get("y", [])):
                         f.write(f"{x}\t{y}\n")
                 QMessageBox.information(self, "Saved", f"Bar plot raw data saved as {fname}")