Fix Secondary Species Shell sampling.

documentation/tutorials/9-Secondary_Species_Shells.ipynb

@@ -260,6 +260,16 @@
     "structure = out3[list(out3.keys())[0]]['mol2string']"
    ]
   },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "0880c67d",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "structure"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": null,
@@ -274,6 +284,7 @@
     "      'parameters':{\n",
     "          'metal_ox':6, # Ox for only the initial molecule generated\n",
     "          'add_secondary_shell_species':True, # Add the docking routine\n",
+    "          'full_method':'UFF', # Make sure UFF is used as final method as well.\n",
     "          'species_grid_rad_skin':0.7, # Reduce to allow for closer molecules\n",
     "          'species_list':[structure]*4, # Specify how many local copies to add\n",
     "          'n_species_rotations':100, # Specify number of rotations to try.\n",
@@ -283,7 +294,7 @@
     "          \"species_intermediate_relax\":False, # Don't relax intermediate\n",
     "          \"species_intermediate_method\":'UFF', # Use UFF for speed\n",
     "          \"species_method\":'UFF', # Use UFF for speed\n",
-    "#           \"debug\":True, # Turn on if you want to see what it's doing in the background \n",
+    "          \"debug\":True, # Turn on if you want to see what it's doing in the background \n",
     "      }}\n",
     "out4 = build_complex(inp4)\n",
     "end = time.time()"
@@ -381,7 +392,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.10.8"
+   "version": "3.10.12"
   }
  },
  "nbformat": 4,