update: island custom nb

Author: VsevolodX

other/materials_designer/create_island_defect_custom.ipynb

@@ -70,14 +70,15 @@
    "id": "c360bd0ea9a5f262"
   },
   {
+   "metadata": {},
    "cell_type": "code",
    "source": [
     "import numpy as np\n",
     "from mat3ra.made.tools.utils.coordinate import CoordinateCondition\n",
     "\n",
     "# Custom Coordinate Condition for a torus shape\n",
     "class CustomCoordinateCondition(CoordinateCondition):\n",
-    "    center: List[float] = [0.5, 0.5, 0.5]\n",
+    "    center: List[float] = [0.5, 0.5, 0.0]\n",
     "    major_radius: float = 0.5\n",
     "    minor_radius: float = 0.1 \n",
     "\n",
@@ -89,10 +90,7 @@
     "        distance_to_torus = np.sqrt((xy_distance - self.major_radius) ** 2 + (coord[2] - self.center[2]) ** 2)\n",
     "        return distance_to_torus <= self.minor_radius\n"
    ],
-   "metadata": {
-    "collapsed": false
-   },
-   "id": "9d8b1890b34d850a",
+   "id": "55f4289a6545c504",
    "outputs": [],
    "execution_count": null
   },
@@ -107,17 +105,16 @@
    "id": "535bbac2c3f2832b"
   },
   {
+   "metadata": {},
    "cell_type": "code",
    "source": [
     "CENTER_POSITION = [0.5, 0.5, 0.5]  # Center of the torus in crystal coordinates\n",
     "MAJOR_RADIUS = 0.3  # Major radius of the torus\n",
     "MINOR_RADIUS = 0.1  # Minor radius of the torus\n",
+    "USE_CARTESIAN_COORDINATES = False # Use Cartesian coordinates for the condition\n",
     "\n",
     "NUMBER_OF_ADDED_LAYERS = 3  # Number of layers to add to the defect\n",
-    "USE_CARTESIAN_COORDINATES = False\n",
     "\n",
-    "AUTO_ADD_VACUUM = True  # Automatically add vacuum to the slab\n",
-    "VACUUM_THICKNESS = 5.0  # Thickness of the vacuum to add\n",
     "\n",
     "# Create slab with default parameters if imported material is not a slab\n",
     "DEFAULT_SLAB_PARAMETERS = {\n",
@@ -128,10 +125,7 @@
     "    \"xy_supercell_matrix\": [[10, 0], [0, 10]]\n",
     "}"
    ],
-   "metadata": {
-    "collapsed": false
-   },
-   "id": "79924b8b23c8850b",
+   "id": "4f6c437b81325730",
    "outputs": [],
    "execution_count": null
   },