Edit glass.py

src/glass.py

@@ -23,7 +23,19 @@ plt.rcParams.update({
     'axes.labelweight': 'bold'
 })
 
+######################################
+# Helper Function to Get Project Root
+######################################
+def get_project_root():
+    """
+    Returns the project root directory.
+    Assumes this file is in a container inside the project.
+    """
+    return os.path.abspath(os.path.join(os.path.dirname(os.path.abspath(__file__)), ".."))
+
+######################################
 # --- Utility Functions for GR Files ---
+######################################
 def read_gr_file(file_path):
     """
     Read a GR file and return:
@@ -54,7 +66,9 @@ def find_cutoff_distance(r, gr):
             return r[i]
     return 3.0
 
+######################################
 # --- Helper Function to Draw a Closed Cube ---
+######################################
 def draw_closed_cube(ax, x_min, x_max, y_min, y_max, z_min, z_max):
     """
     Draw a closed cube (with 12 edges) on the given 3D axis.
@@ -80,16 +94,19 @@ def draw_closed_cube(ax, x_min, x_max, y_min, y_max, z_min, z_max):
                 [p1[2], p2[2]],
                 color='black', linestyle='-', linewidth=2)
 
+######################################
 # --- Main Application Class ---
+######################################
 class SilicaNetworkAnalyzer(QMainWindow):
     def __init__(self):
         super().__init__()
         self.setWindowTitle("Silica Glass Network Analyzer")
         self.setGeometry(100, 100, 500, 800)  # reduced width since plot area is removed
         
-        # Directories for GR and XYZ files:
-        self.gr_directory = "Large_box/Large/Accumulation_dependence/"
-        self.xyz_directory = "Large_box/Large/Accumulation_dependence/DFT_box/"
+        # Directories for GR and XYZ files are now built relative to the project root.
+        root = get_project_root()
+        self.gr_directory = os.path.join(root, "Large_box", "Large", "Accumulation_dependence")
+        self.xyz_directory = os.path.join(root, "Large_box", "Large", "Accumulation_dependence", "DFT_box")
         
         # Data storage
         self.atoms = []         # List of tuples: (element, np.array([x,y,z]))
@@ -144,8 +161,6 @@ class SilicaNetworkAnalyzer(QMainWindow):
         self.ring_example_btn.clicked.connect(self.show_ring_example)
         control_layout.addWidget(self.ring_example_btn)
         
-        # Removed the "Save Current Plot" button since plots are external
-        
         # Input for maximum number of Si atoms to plot (to avoid overcrowding)
         control_layout.addWidget(QLabel("Max Si atoms to plot:"))
         self.max_atoms_input = QLineEdit("500")
@@ -613,5 +628,4 @@ if __name__ == "__main__":
     app = QApplication(sys.argv)
     window = SilicaNetworkAnalyzer()
     window.show()
-    sys.exit(app.exec_())
-
+    sys.exit(app.exec_())
\ No newline at end of file