Merge pull request #194 from Exabyte-io/feature/SOF-7528

Feature/SOF-7528 Pt adatoms island on MoS2 NB

Author: VsevolodX

other/materials_designer/create_adatom_defect.ipynb

@@ -50,18 +50,21 @@
    "cell_type": "code",
    "outputs": [],
    "source": [
-    "DEFECT_TYPE = \"adatom\"  \n",
-    "PLACEMENT_METHOD = \"equidistant\"  # Choose between \"equidistant\", \"crystal_site\", \"closest_site\",  and \"coordinate\"\n",
-    "CHEMICAL_ELEMENT = \"Si\"  # Element to be placed at the site \n",
-    "APPROXIMATE_POSITION_ON_SURFACE = [0.5, 0.5]  # Position of the defect in crystal coordinates\n",
-    "USE_CARTESIAN_COORDINATES = False  # If True, the position is in Cartesian coordinates\n",
-    "DISTANCE_Z = 2.0  # Distance of the defect from the surface in Angstrom\n",
-    "\n",
+    "DEFECT_CONFIGS = [\n",
+    "    {\n",
+    "        \"defect_type\": \"adatom\" ,\n",
+    "        \"placement_method\": \"equidistant\",\n",
+    "        \"chemical_element\": \"Si\",\n",
+    "        \"position_on_surface\": [0.5, 0.5],\n",
+    "        \"distance_z\": 2.0,\n",
+    "        \"use_cartesian_coordinates\": False\n",
+    "    },   \n",
+    "]\n",
     "# Slab parameters\n",
     "MILLER_INDICES = (1, 1, 1)  # Miller indices of the surface\n",
     "SLAB_THICKNESS = 3  # Thickness of the slab in unit cells\n",
     "VACUUM = 6  # Vacuum thickness in Angstrom\n",
-    "SUPERCELL_MATRIX = [[2, 0, 0], [0, 2, 0], [0, 0, 1]] "
+    "SUPERCELL_MATRIX = [[2, 0, 0], [0, 2, 0], [0, 0, 1]]  # Supercell matrix for the slab"
    ],
    "metadata": {
     "collapsed": false
@@ -101,8 +104,7 @@
   {
    "cell_type": "markdown",
    "source": [
-    "### 1.3. Get input material\n",
-    "Materials are loaded with `get_materials()`."
+    "### 1.3. Get input material"
    ],
    "metadata": {
     "collapsed": false
@@ -175,14 +177,17 @@
    "source": [
     "from mat3ra.made.tools.build.defect import AdatomSlabPointDefectConfiguration\n",
     "\n",
-    "adatom_config = AdatomSlabPointDefectConfiguration(crystal=slab, \n",
-    "                                              defect_type=DEFECT_TYPE, \n",
-    "                                              placement_method=PLACEMENT_METHOD,\n",
-    "                                              chemical_element=CHEMICAL_ELEMENT, \n",
-    "                                              position_on_surface=APPROXIMATE_POSITION_ON_SURFACE,\n",
-    "                                              distance_z=DISTANCE_Z, \n",
-    "                                              use_cartesian_coordinates=USE_CARTESIAN_COORDINATES\n",
-    ")"
+    "defect_configurations = [\n",
+    "    AdatomSlabPointDefectConfiguration(\n",
+    "        crystal=slab,\n",
+    "        defect_type=defect[\"defect_type\"],\n",
+    "        placement_method=defect[\"placement_method\"],\n",
+    "        chemical_element=defect[\"chemical_element\"],\n",
+    "        position_on_surface=defect[\"position_on_surface\"],\n",
+    "        distance_z=defect[\"distance_z\"],\n",
+    "        use_cartesian_coordinates=defect[\"use_cartesian_coordinates\"]\n",
+    "    ) for defect in DEFECT_CONFIGS\n",
+    "]"
    ],
    "metadata": {
     "collapsed": false
@@ -204,8 +209,8 @@
    "cell_type": "code",
    "outputs": [],
    "source": [
-    "from mat3ra.made.tools.build.defect import create_slab_defect\n",
-    "slab_with_adatom = create_slab_defect(adatom_config)"
+    "from mat3ra.made.tools.build.defect import create_defects\n",
+    "slab_with_adatom = create_defects(defect_configurations)"
    ],
    "metadata": {
     "collapsed": false
@@ -230,11 +235,11 @@
     "from utils.visualize import visualize_materials as visualize\n",
     "\n",
     "visualize([{\"material\": slab, \"title\": \"Original material\"},\n",
-    "           {\"material\": slab_with_adatom, \"title\": f\"Material with adatom defect at {PLACEMENT_METHOD} position\"}],\n",
+    "           {\"material\": slab_with_adatom, \"title\": f\"Material with adatom defects\"}],\n",
     "          rotation=\"-90x\"\n",
     "          )\n",
     "visualize([{\"material\": slab, \"title\": \"Original material\"},\n",
-    "           {\"material\": slab_with_adatom, \"title\": f\"Material with adatom defect at {PLACEMENT_METHOD} position\"}],\n",
+    "           {\"material\": slab_with_adatom, \"title\": f\"Material with adatom defects\"}],\n",
     ")"
    ],
    "metadata": {