chore: add crytal coord expalnation

Author: VsevolodX

other/materials_designer/specific_examples/defect_surface_adatom_graphene.ipynb

@@ -48,9 +48,11 @@
     "# Defect parameters\n",
     "DEFECT_TYPE = \"adatom\"\n",
     "PLACEMENT_METHOD = \"coordinate\"\n",
-    "HOLLOW_SITE_COORDINATE = [1/2, 1/2]\n",
-    "BRIDGE_SITE_COORDINATE = [3/8, 1/2]\n",
-    "TOP_SITE_COORDINATE = [7/12, 5/12]\n",
+    "# Using crystal coordinates for the defect placement\n",
+    "USE_CARTESIAN_COORDINATES = False \n",
+    "HOLLOW_SITE_COORDINATE = [1/2, 1/2] # in crystal coordinates\n",
+    "BRIDGE_SITE_COORDINATE = [3/8, 1/2] # in crystal coordinates\n",
+    "TOP_SITE_COORDINATE = [7/12, 5/12] # in crystal coordinates\n",
     "\n",
     "# Setting data according to Table 1 in the manuscript, distance_z is the `h` from the table.\n",
     "# Uncomment the lines to create the defect for the desired adatom.\n",
@@ -180,7 +182,8 @@
     "                                                     placement_method=PLACEMENT_METHOD,\n",
     "                                                     chemical_element=adatom_parameters[\"chemical_element\"],\n",
     "                                                     distance_z=adatom_parameters[\"distance_z\"],\n",
-    "                                                     position_on_surface=adatom_parameters[\"position_on_surface\"]\n",
+    "                                                     position_on_surface=adatom_parameters[\"position_on_surface\"],\n",
+    "                                                     use_cartesian_coordinates=USE_CARTESIAN_COORDINATES\n",
     "                                                     ) for adatom_parameters in ADATOM_PARAMETERS]\n",
     "\n",
     "defect_builder_parameters = PointDefectBuilderParameters()"