update: use cartesian coords

Author: VsevolodX

other/materials_designer/specific_examples/defect_creation_point_substitution_graphene.ipynb

@@ -31,7 +31,8 @@
     "### 1.1. Set up defects parameters \n",
     "Defect Configuration parameters are described in [Defect Configuration](https://github.com/Exabyte-io/made/blob/main/src/py/mat3ra/made/tools/build/defect/configuration.py).\n",
     "\n",
-    "Note that we use approximate coordinates in crystal coordinates to define the defect positions. The approximate coordinates are used to find the closest site in the crystal to the given coordinates. The approximate coordinates are in the range of [0, 1] for each axis. Adjust the approximate coordinates to place the defect at the desired site in the crystal. Using the visuals provided in the notebook could help in determining the approximate coordinates."
+    "Note that we use approximate coordinates in crystal coordinates to define the defect positions. The approximate coordinates are used to find the closest site in the crystal to the given coordinates. The approximate coordinates are in the range of [0, 1] for each axis. Adjust the approximate coordinates to place the defect at the desired site in the crystal. Using the visuals provided in the notebook could help in determining the approximate coordinates.\n",
+    "(Coordinates found using 3D editor in Materials Designer)"
    ],
    "metadata": {
     "collapsed": false
@@ -46,26 +47,31 @@
     "CHEMICAL_ELEMENT = \"N\"\n",
     "\n",
     "SUPERCELL_MATRIX = [[4, 0, 0], [0, 4, 0], [0, 0, 1]]\n",
+    "USE_CARTESIAN_COORDINATES = True\n",
     "\n",
     "DEFECT_CONFIGS = [\n",
     "    {\n",
     "        \"defect_type\": \"substitution\",\n",
-    "        \"approximate_coordinate\": [0.65, 0.25, 0.5],\n",
+    "        \"approximate_coordinate\": [4.9, 2.85, 10],\n",
     "        \"chemical_element\": CHEMICAL_ELEMENT,\n",
+    "        \"use_cartesian_coordinates\": USE_CARTESIAN_COORDINATES\n",
     "    },\n",
     "      {\n",
     "        \"defect_type\": \"substitution\",\n",
-    "        \"approximate_coordinate\": [0.75, 0.55, 0.5],\n",
+    "        \"approximate_coordinate\": [3.7, 4.9, 10],\n",
     "        \"chemical_element\": CHEMICAL_ELEMENT,\n",
+    "        \"use_cartesian_coordinates\": USE_CARTESIAN_COORDINATES\n",
     "    },\n",
     "      {\n",
     "        \"defect_type\": \"substitution\",\n",
-    "        \"approximate_coordinate\": [0.45, 0.25, 0.5],\n",
+    "        \"approximate_coordinate\": [2.45, 2.85, 10],\n",
     "        \"chemical_element\": CHEMICAL_ELEMENT,\n",
+    "        \"use_cartesian_coordinates\": USE_CARTESIAN_COORDINATES\n",
     "    },\n",
     "      {\n",
     "        \"defect_type\": \"vacancy\",\n",
-    "        \"approximate_coordinate\": [0.55, 0.45, 0.5],\n",
+    "        \"approximate_coordinate\": [3.7, 3.55, 10],\n",
+    "        \"use_cartesian_coordinates\": USE_CARTESIAN_COORDINATES\n",
     "    },\n",
     "    \n",
     "]  "