Molecule3D displays for some molecules but not all, bug where clicking on H2 breaks drop down

app.py

@@ -173,8 +173,8 @@ def create_interface():
                     choices=list(molecules.keys()),
                     value=list(molecules.keys())[0],
                     label="Select Molecule",
-                    allow_custom_value=False,  # Prevent text input
-                    type="value"  # Ensure it stays as a dropdown
+                    interactive=True,
+                    allow_custom_value=False  # Prevent text input
                 )
                 
                 # Get scale range from selected molecule
@@ -212,12 +212,10 @@ def create_interface():
                     label="VQE Convergence",
                     show_label=True
                 )
-            with gr.Column(scale=1):
-                # Create MolGallery3D component with more space
+            with gr.Column(scale=1, min_width=600):  # Set minimum width for the column
                 molecule_viz = MolGallery3D(
                     columns=1,
-                    height=600,  # Increased height
-                    width=600,   # Added explicit width
+                    height=600,  # Keep increased height
                     label="3D Molecule Viewer",
                     automatic_rotation=True
                 )

quantum_utils.py

@@ -218,7 +218,7 @@ def expand_geometry(geometry_template: List[List[Any]], scale_factor: float) ->
 # Edits in run_vqe_simulation to use the new approach
 # and a CUDA-Q optimizer
 # ----------------------------------------------------------
-@spaces.GPU(duration=20)
+@spaces.GPU(duration=30)
 def run_vqe_simulation(molecule_data: Dict[str, Any],
                       scale_factor: float) -> Dict[str, Any]:
     """
@@ -243,7 +243,9 @@ def run_vqe_simulation(molecule_data: Dict[str, Any],
         - 'message': (str) status or error message
     """
     logging.info(f"Starting VQE simulation for {molecule_data['name']} with scale factor {scale_factor}")
+    optimizer_max_iterations = 30
 
+    # Set up the CUDA-Q target
     # Ensure the correct GPU/CPU target is set
     setup_target()
 
@@ -266,7 +268,6 @@ def run_vqe_simulation(molecule_data: Dict[str, Any],
     # Create the UCCSD ansatz kernel
     qubit_count = 2 * molecule_data['spatial_orbitals']
     electron_count = molecule_data['electron_count']
-    optimizer_max_iterations = 10
 
     # Compute how many UCCSD parameters we need to optimize
     parameter_count = cudaq.kernels.uccsd_num_parameters(electron_count, qubit_count)

visualization.py

@@ -154,9 +154,11 @@ def create_molecule_viewer(molecule_id: str, scale_factor: float) -> MolGallery3
         
         molecule_data = molecules[molecule_id]
         
-        # Special handling for H2 and H2O
+        # Special handling for different molecules
         if molecule_id == "H2":
             mol = Chem.MolFromSmiles("[H][H]")
+            if mol is None:
+                mol = Chem.MolFromSmiles("[HH]")  # Alternative SMILES for H2
         elif molecule_id == "H2O":
             mol = Chem.MolFromSmiles("O")
             mol = Chem.AddHs(mol)
@@ -168,22 +170,30 @@ def create_molecule_viewer(molecule_id: str, scale_factor: float) -> MolGallery3
                 return None
             mol = Chem.AddHs(mol)
         
+        if mol is None:
+            logger.error(f"Failed to create molecule for {molecule_id}")
+            return None
+            
         # Generate 3D coordinates with distance matrix
-        AllChem.EmbedMolecule(mol, randomSeed=42)
-        
-        # Scale the molecule coordinates
-        conf = mol.GetConformer()
-        positions = conf.GetPositions()
-        centroid = np.mean(positions, axis=0)
-        
-        for i in range(mol.GetNumAtoms()):
-            pos = positions[i]
-            scaled_pos = centroid + (pos - centroid) * scale_factor
-            conf.SetAtomPosition(i, scaled_pos)
-        
-        # Create the MolGallery3D component
-        logger.info("Created MolGallery3D component")
-        return [mol]  # Return the molecule as a list as expected by MolGallery3D
+        try:
+            AllChem.EmbedMolecule(mol, randomSeed=42)
+            
+            # Scale the molecule coordinates
+            conf = mol.GetConformer()
+            positions = conf.GetPositions()
+            centroid = np.mean(positions, axis=0)
+            
+            for i in range(mol.GetNumAtoms()):
+                pos = positions[i]
+                scaled_pos = centroid + (pos - centroid) * scale_factor
+                conf.SetAtomPosition(i, scaled_pos)
+            
+            logger.info(f"Successfully created 3D coordinates for {molecule_id}")
+            return [mol]  # Return the molecule as a list as expected by MolGallery3D
+            
+        except Exception as e:
+            logger.error(f"Failed to generate 3D coordinates: {e}")
+            return None
         
     except Exception as e:
         logger.error(f"Failed to create molecule viewer: {e}")